DEPARTMENT OF MOLECULAR GENETICS, MICROBIOLOGY

DEPARTMENT OF MOLECULAR GENETICS, MICROBIOLOGY & IMMUNOLOGY ANNUAL REPORT JULY 1, 2005 - JUNE 30, 2006 SIDNEY PESTKA, M.D. PROFESSOR AND CHAIRMAN

Table of Contents Preface ............................................................................................................................................ 1 Introduction .................................................................................................................................... 2 Research Activities ........................................................................................................................ 5 Personnel........................................................................................................................................ 9 Departmental Activities ............................................................................................................... 13 Departmental Committees .......................................................................................................... 15 Activities of the Faculty Members.............................................................................................. 16 Gary Brewer, Ph.D. .................................................................................................... 17 Paul R. Copeland, Ph.D. ............................................................................................ 21 Joseph P. Dougherty, Ph.D........................................................................................ 26 Donald T. Dubin, M.D. ................................................................................................ 31 Terri Goss Kinzy, Ph.D. .............................................................................................. 32 Jerome Langer, Ph.D. ................................................................................................ 38 Michael J. Leibowitz, M.D., Ph.D................................................................................ 41 Honghua Li, Ph.D. ...................................................................................................... 46 Michael Newlon, Ph.D. ............................................................................................... 49 Stuart W. Peltz, Ph.D.................................................................................................. 50 Sidney Pestka, M.D., Chairman ................................................................................. 51 Arnold B. Rabson, M.D............................................................................................... 59 Yacov Ron, Ph.D. ....................................................................................................... 65 Aaron J. Shatkin, Ph.D. .............................................................................................. 67 Yufang Shi, D.V.M., Ph.D. .......................................................................................... 71 Victor Stollar, M.D., Vice Chairman............................................................................ 77 Nancy Woychik, Ph.D................................................................................................. 80 Research Activities of Joint and Adjunct Faculty .................................................................... 84 Sefik S. Alkan, Ph.D. .................................................................................................. 85 Eddy Arnold, Ph.D. ..................................................................................................... 87 David Beck, Ph.D. ...................................................................................................... 90 C. Thomas Caskey, M.D. ........................................................................................... 90 Chiann-Chyi Chen, Ph.D. ........................................................................................... 90 Graham Cleaves, Ph.D............................................................................................... 91 Ellen C. Ebert, Ph.D.. ................................................................................................. 92

Evelyn S. Erenrich ...................................................................................................... 93 Arthur M. Felix, Ph.D. ................................................................................................. 95 Janusz J. Godyn, M.D. ............................................................................................... 96 Suhayl Dhib-Jalbut, M.D........................................................................................... 100 Edmund C. Lattime, Ph.D......................................................................................... 102 Paola Leone, Ph.D. .................................................................................................. 106 Mei-Ling Li, Ph.D. ..................................................................................................... 108 Randall D. McKinnon, Ph.D...................................................................................... 109 M. Maral Mouradian, M.D. ........................................................................................ 111 Daniel Notterman, M.D. ............................................................................................ 114 Michael Reiss, M.D................................................................................................... 117 Hugh Rosen, Ph.D.................................................................................................... 119 Srijata Sarkar, Ph.D.................................................................................................. 120 Lee Ann Schein, Ph.D. ............................................................................................. 121 Leonard H. Sigal, M.D. ............................................................................................. 123 Michael Steinmetz, Ph.D. ......................................................................................... 124 George B. Weiss, Ph.D. ........................................................................................... 125 Lawrence P. Wennogle, Ph.D. ................................................................................. 125 Carol Wilusz, Ph.D. .................................................................................................. 125 Core Facilities............................................................................................................................. 128 Doctoral Program....................................................................................................................... 131 Courses .................................................................................................................................. 134 Microbiology for Physician Assistants ...................................................................... 135 Medical Genetics ...................................................................................................... 139 Medical Microbiology and Immunology .................................................................... 143 Holowczak Memorial Fund........................................................................................................ 148 Research Grant Support ........................................................................................................... 149 Gary Brewer ............................................................................................................. 150 Paul R. Copeland, Ph.D. .......................................................................................... 151 Joseph P. Dougherty, Ph.D...................................................................................... 152 Terri Goss Kinzy, Ph.D. ............................................................................................ 153 Jerome Langer, Ph.D. .............................................................................................. 155 Michael J. Leibowitz, M.D., Ph.D.............................................................................. 156

Honghua Li, Ph.D. .................................................................................................... 157 Mei-Ling Li ................................................................................................................ 158 Sidney Pestka, M.D., Chairman ............................................................................... 159 Arnold B. Rabson, M.D............................................................................................. 160 Yacov Ron, Ph.D. ..................................................................................................... 161 Yufang Shi, D.V.M., Ph.D. ........................................................................................ 162 Victor Stollar, M.D., Vice Chairman.......................................................................... 163 Nancy Woychik, Ph.D............................................................................................... 164 Summary of Outside Grant Support ......................................................................... 165 Seminars .................................................................................................................................. 166 Departmental Retreat................................................................................................................. 167 Departmental Organization Chart............................................................................................. 169

PREFACE During the past year, the faculty of the department has maintained its high level of performance in research, in teaching, and in service to the University community. Although the funding environment has been difficult, grant support in the department from national and non-governmental sources has continued at a good level. The total number of grants in the department was XXXXX. Many of the faculty are invited to lecture at other institutions, as well as at national and international symposia. Faculty also sit on review committees for the National Institutes of Health and for the Department of Defence. Publication in top level peer-reviewed journals also continues at a good level. Core facilities developed in the department have been made available to the broader University communities both at RWJMS and at Rutgers University. These include the DNA Synthesis and Sequencing Facility, and a Cell Imaging Facility. Both of these facilities are being continually upgraded. As well, in order to analyze specific protein-protein interactions in cells, equipment was constructed to carry out analysis of fluorescence energy transfer in single cells in real time. All of the faculty are active in teaching in either the medical school course for first year medical students, in graduate courses, or both. Graduate courses in virology and immunology directed by members of this faculty are the only such offerings in these fields on this campus. The medical school course is very well received by the medical students. One of the largest programs in the nation for the recruitment and training of under represented minority students is centered here at RWJMS and is under the direction of Drs. Michael Leibowitz, Jerome Langer, and Evelyn Erenrich, all of whom are members of this department. These programs are supported by two major grants from the National Institutes of Health. Many members of the department also serve on important committees of RWJMS or UMDNJ. Especially notable during the past year was the expansion of the MD/PhD program of which Dr. Terri Kinzi is director. These topics are all developed at greater length in the Annual Report.

INTRODUCTION By their activities in research, teaching, and service to the medical school the University, and the broader scientific community, the faculty of the department continue to make impressive contributions to the missions of RWJMS, and UMDNJ. The full time tenured or tenure-track faculty consists of 13 full professors, 3 associate professors, and 2 assistant professors. In addition there are 6 non-tenure track faculty including 6 adjunct assistant professors. Although the competition for research grants has, in the last few years, become quite difficult, the members of the department continue to do well in obtaining research support from federal agencies, from the State of New Jersey, as well as from non- governmental sources. Total funding for this academic year was ???????, and the total number of grants was XXXX . Forty-seven papers were published in peer-reviewed journals by the department faculty during the past year. The research interests of the faculty, as shown by the titles of the grants which have been awarded, are very broad and illustrate the wide range of their interests. These include protein synthesis, control of gene expression as manifest by the stability of mRNAs, the mode of action of interferons and other cytokines with emphasis on the signaling pathways which they activate, autoimmune diseases, apoptosis, virology, oncology, and bacterial toxins. Many in the department are involved in collaborative projects with other faculty in the department, or outside the department. All members of the department are involved in teaching either in the Microbiology and Immunology course taught to first year medical students or in a wide variety of graduate courses. The medical school course is well received by the medical students, and many compliments are paid to Dr. Michael Newlon, who is director of the course. Dr, Newlon continues to add web-based instruction, visual resources, and interactive quizzes to the course. Each year our medical students perform very well on the Microbiology section of the National Board exams, part I. Members of the department also play important administrative roles in RWJMS. Dr. Aaron Shatkin is Director of the Center for Advanced Biotechnology and Medicine (CABM). Dr. Arnold Rabson is Deputy Director of the Cancer Institute of New Jersey (CINJ), and also chairs the Appointments and Promotions Committee of RWJMS. Dr. Michael Leibowitz is Associate Dean of the Graduate School of Biomedical Science (GSBS) of UMDNJ at RWJMS. Dr. Terry Kinzy is director of the MD/PhD program which now encompasses not only RWJMS and Rutgers University, but also Princeton University. Dr. Joseph Dougherty is Director of the Graduate Program in Molecular Genetics, Microbiology, and Immunology, which includes faculty of both RWJMS and Rutgers University. Many members of the department also serve the broader scientific community by serving on the editorial board of journals, and on review panels at the National Institutes

of Health or other governmental agencies. The department has played a very important role in the training and recruitment of under-represented minority students. Dr. Leibowitz, in collaboration with Drs. Jerome Langer and Evelyn Erenrich is the Program Director of three NIH awards promoting training of minority graduate students on the Piscataway/New Brunswick campuses of RWJMS and Rutgers University. These include an Initiative to Maximize Student Diversity Award from NIH, which is now in its third four-year funding period, and provides $430,000 per year for support of the UMDNJ-Rutgers University Pipeline Program. This program supports Ph.D. and M.D.Ph.D. candidates as well as supervised individual research experiences for medical students. In addition to the Pipeline Program, the NIH-funded Bridge to the Doctoral Degree Program supports two articulated MS/PhD Programs on this campus. One, run jointly with the University of Puerto Rico, Mayagüez campus, is in its third funding period. An additional Bridge Program with Montclair State University is now in its second funding period. Dr. Erenrich, together with Dr. Langer, also directs the summer “Research in Science and Engineering (RISE) Program” at Rutgers/UMDNJ, which is currently funded by Rutgers University and by grants from corporate sponsors and the Federation of American Societies for Experimental Biology (FASEB). This is a nationally recognized outreach program, nearly half of whose alumni have gone on to Ph.D. and M.D./Ph.D. programs here and elsewhere, and which is a major source of recruitment of outstanding graduate students to this campus. UMDNJ and Rutgers University also participate in the Northeast Alliance for Graduate Education and the Professoriate, a consortium of research intensive universities in the Northeast and minority-serving undergraduate institutions, which is funded by the NSF. This consortium is a major support of recruitment and bridge programs on this campus, with Dr. Erenrich and Dr. Leibowitz serving as liaisons with Rutgers University and with the University of Massachusetts, to which the grant is awarded. Dr. Victor Stollar is Vice Chairman of the department. He assists the department chairman as is necessary, and is always available for advice and consultation on all matters which bear on the functioning of the department, both internal and those which relate to the role of the department in the medical school. Dr. Stollar often substitutes for the chairman at various functions, when the chair has scheduling conflicts. The annual department retreat was held on August 26, 2005, at the Hilton Garden Inn in Bridgewater, New Jersey. The goal of the retreats is to give graduate students and postdoctoral fellows an opportunity to present their work in a formal setting. In addition, the retreat serves to inform every one of the research activities of the other groups in the department. Not least, the retreats help promote good interactions and relationships within the department. Each research group gives one 12 minute presentation which is followed by a question and answer period. The program of the retreat is provided later in this report. In most years, the formal part of the retreat is followed by a buffet style lunch. The DNA Synthesis and Sequencing Core Facility of the Department of

Molecular Genetics, Microbiology and Immunology serves as a shared resource for faculty of Robert Wood Johnson Medical School and Rutgers. In addition this facility provides core resources for two joint institutes of RWJMS and Rutgers, the Cancer Institute of New Jersey (CINJ) and The National Institute of Environmental Health Sciences (NIEHS) Center at the Environmental and Occupational Health Sciences Institute (EOHSI). The overall purpose of this shared resource is to provide a centralized, high quality, cost-effective facility for DNA synthesis and sequencing for use by the entire scientific community at UMDNJ-RWJMS and Rutgers University. By providing synthetic oligonucleotides to all members of the University, many studies are greatly facilitated at significant cost discounts over what individual laboratories could obtain. Terri Goss Kinzy, Ph.D., Professor of Molecular Genetics, Microbiology and Immunology is Executive Director of this facility and Lee Ann Schein, Ph.D., is Director. This is one example where departmental resources have been used to develop a core facility that is essential for the scientific development of RWJMS. Mr. Rick Wernoski is the Business Manager of this facility. DNA Microarray Facilities were initiated from a shared instrumentation grant received by Dr. Pestka. A portion of the funds were used to establish the facilities at the CINJ in New Brunswick and in Piscataway to make it most accessible to investigators in both locations. The facility in Piscataway includes a Phosphorimager for analysis of the DNA microarrays. This is a shared facility open to investigators of RWJMS, Rutgers and all members of the UMDNJ community. We have also opened it up to outside academic and commercial institutions to facilitate collaborations and general research programs in New Jersey. This facility is used extensively. With the departure of Dr. Jeffry Cook, Dr. Gary Brewer is now the Director of the facility. This is a second example where departmental resources are used to support the scientific development of RWJMS, Rutgers and UMDNJ. Mr. Rick Wernoski is also the Business Manager of this facility. The department faculty are very ably assisted by an efficient office staff, who when called upon in special situations, give that extra effort which is often necessary and crucial. Rick Wernoski, MPA, Business Manager, was responsible for all day-to- day operations of the department including financial, administrative, staffing and facility needs until he left the department in May, 2006. Ellen Feibel, Senior Management Assistant, under the supervision of the department chairman, performs a wide variety of administrative and secretarial services. Jamie Carr, Administrative Analyst, was responsible for grant administration. Walter Barnes, Budget Analyst III, was responsible for maintaining, reviewing, and analyzing the departmental accounts. Andrea Finamore, Administrative Coordinator II, performed Human Resources services and assisted with the administrative activities of the department. Rosalie Reina, Program Assistant, served as the primary contact for undergraduate trainees involved in the UMDNJ- Rutgers University Pipeline Program and in coordinating the administrative functions related to the training grant “Virus-Host Interactions in Eukaryotic Cells”. Toni Thomas, Secretary IV, assisted departmental staff with administrative and secretarial services until her retirement in August of 2005.

In the department core facilities, Zofia Andes, Principal Laboratory Assistant, and May Tang, Laboratory Service Worker, were responsible for washing and sterilizing glassware. Octavia Gamble, Laboratory Assistant, prepared agar plates for growth of bacteria and yeast, as well as sterile tissue culture media, and various solutions used in different laboratories. In summary, by its activities in research, teaching, and administration, the department continued to make a strong contribution to the missions of RWJMS. Those activities dedicated to the training of scientists and physicians have always been considered especially important to the faculty.

.Research Activities The research activities in the department continue to open up new areas. Some highlights are given below; details are provided in a later section. Dr. Brewer’s laboratory published two seminal papers regarding regulation of genes involved in genotoxic stress responses and in breast cancer. These papers identify the RNA-binding protein AUF1, which we discovered in 1991, as a critical regulator of the GADD45α (genotoxic stress) and c-Yes (kinase involved in breast cancer) genes. Dr Copeland’s laboratory continues their investigation into the mechanism of selenocysteine incorporation as well into the larger questions that probe the balance between selenium efficacy and toxicity. Dr. Dougherty carried out a high throughput screen which has provided lead molecules that can be used to develop drugs to clear HIV-1 latent infection and that can be used as probes to study HIV-1 latency. He developed a very efficient and safe HIV-2 lentiviral vector system for gene transduction. He and his staff discovered that the recombination rate of disparate retroviruses is very high suggesting that all retroviruses including HIV are always subject to crossovers during each and every cycle of replication indicating that the basic model of retroviral reverse transcription should be modified. In Dr. Kinzy’s Laboratory their understanding of the role of the translation elongation factor 1A (eEF1A) has extended beyond its canonical role in delivery of aminoacyl-tRNA for elongation. They have published novel mutants that separate the actin and translation functions of eEF1A, providing a new example of a multifunctional protein and a link between the translational apparatus and regulation of the actin cytoskeleton. Additionally, the regulation of the levels of eEF2, the translocase, and the novel effect of dominant negative mutants on the cell were determined.. Dr. Langer found that alpha interferon appears to be inappropriately, perhaps continually, produced in people with systemic lupus erythematosus (“lupus”), and that this aberrant production of IFN likely contributes to the pathogenesis of this disease. To block the effects of IFN in lupus patients, He and his laboratory are designing and produceing modified IFNs that should act as competitive antagonists of endogenous IFN. They have investigated several parts of the IFN molecule for their importance in interactions with the 2 subunits of the IFN receptor. They demonstrated that a region of IFN previously reported to be important in one IFN subtype for receptor interactions does not make strong contributions to receptor interactions in the IFN subtype used in our lab. They have therefore proposed a novel model of IFN/receptor interactions, and are examining the effects of mutations in other parts of the IFN molecule.

Drug-carrying bioconjugates based on polyethylene glycol can be synthesized with attached ligands for cell surface receptors to target the conjugates to cells bearing those receptors, to which the drugs can then be delivered with great specificity. Dr. Leibowitz has shown that multiple copies of formyl-methionyl-leucyl-phenylalanine attached to the bioconjugates can greatly enhance their delivery to macrophages. This finding has great potential for developing drug delivery systems for these cells, which are the primary infected cell type in AIDS and tuberculosis. Dr. Li has made significant progress toward further extending the application of his high-throughput nucleic acid detection system. This system has been used for studying meiotic recombination in great detail and on a large scale. He has also used it for studying genetic variation in breast cancer tissues and cell lines, and in colon cancer. He has been very successful in using this marker system, for the first time, to detect meiotic recombination along entire chromosomes and to locate meiotic crossover points for understanding the mechanisms underlying meiotic recombination. He has also made significant progress in understanding the genetic structure of the human immunoglobulin VH region. This finding may have significant impact on understanding the contribution of the genetic structure of the VH region to the function of the immune system. In collaboration with other M-1 course directors and other interested faculty, Dr. Newlon planned and implemented a new course “M-1 Integrated Cases” designed to show how material from all first-year courses relates to specific medical cases. Each case began with a lecture-hall presentation which was followed by a small-group team- based learning exercise. This year seven cases were presented: Ethylene glycol poisoning, Duchenne muscular dystrophy, Marfan syndrome, alpha-1 antitrypsin deficiency, meningococcal meningitis, subacute bacterial endocarditis, and polycystic kidney disease. Dr. Newlon was chief author of two of the cases. Dr. Newlon was awarded an Educational Technology Advisory Committee to fund creation of visual resources for teaching medical bacteriology, which will become part of the MGMB 6000 Microbiology and Immunology course web site, and began developing these materials. Dr. Peltz has been on a leave of absence beginning November 2004 and continuing through December 2006. The work of his lab is now under the supervision of Dr. Joseph Dougherty. Dr. Pestka in this year discovered dscovered that the IL-10R2 binding hot spot on IL-22 is located on the N-terminal helix and is dependent on N-linked glycosylation. He and his laboratory staff discovered PRMT9, a new protein arginine methyltransferase that synthesizes symmetric dimethylarginine. They also discovered new Class 2 cytokines and receptors in many vertebrates and in humans, including new interferons as well as the discovery that IL-10 receptor chains are preassembled.

On May 3, 2006 at the Museum of Contemporary Art in Chicago Dr. Pestka received the Lemelson-MIT Lifetime Achievement Award for his seminal work on interferons. As stated by the Lemelson-MIT Program, “his work led to groundbreaking treatments for chronic hepatitis B and C, multiple sclerosis and cancers. The annual award, which recognizes a remarkable individual for his or her life-long commitment to improving society through invention.” “Dr. Pestka’s interferon discoveries and subsequent inventions have made a profound impact on medicine and health care,” said Merton Flemings, director of the Lemelson-MIT Program, which gives the annual award. “His work has opened doors to new treatments for millions of people who suffer from devastating diseases and it has fueled the multi-billion dollar biotherapeutics market.” On May 4, 2006 Dr. Pestka was honored with the Researcher Leader award by the New Jersey High Tech Hall of Fame. Dr. Rabson’s laboratory has further delineated a pathway for activation of latent HTLV-1 through T-cell receptor activation. This result provides a possible mechanism for the pathogenesis of HTLV-1-induced diseases, in particular, Adult T-cell leukemia (ATL) which is currently being explored in transgenic mice in order to develop a small animal model of this devastating leukemia. His laboratory has also identified genes that are critical for the development of a second human T-cell malignancy, cutaneous T-cell lymphoma, and is currently further characterizing these genes. Dr. Ron has used retroviral tagging to identify a myeloid precursor cell population in mouse spleen that can give rise to the whole myeloid system. This population is long-lived and will reconstitute the myeloid system for at least six months. Dr. Shatkin documented the essential role of mRNA capping in mammalian cells and the consequences of its disruption. Dr. Shi has made significant progress in several areas. He has made significant advancement in the understanding of the role of granzyme B in the regulation of AICD in different T cell populations. Mice deficient in granzyme B develop more severe allergic asthma. Importantly, they have found that CD4+ T cells are solely responsible for allergen-induced asthmatic reaction. Furthermore, through genetic modifications, Dr. Shi’s group found that MHC class Ib restricted CD8+ T cells are critical in the development of autoimmunity. They also made significant progress in the understanding of the mechanisms that regulate RANKL expression in T cells. Their new in vivo and in vitro system provided a unique opportunity to study how apoptotic cells regulate the immune response. The establishment of the mesenchymal stem cell project gives Dr. Shi’s group a unique niche to using their immunology expertise to investigate the mechanisms controlling mesenchymal stem cell-mediated immunosuppression; it is also hoped that their efforts in this direction will provide new information for proper clinical application of these cells. His project on stress and radiation has been focused on the development of new countermeasures in response to the directional changes in NASA research.

Dr. Stollar demonstrated that the size of the UTP and CTP pools in mosquito cells, as modified by PZF and uridine, determine not only the yield of the mutant, SVpzf, but also the ratio of SG/G RNA which is made in the SVpzf-infected cells. Thus the frequency of initiation at the SVpzf SG and G promoters may be influenced by the size of the UTP pool in the infected cells. He also is working on the development of cell-free systems for the synthesis of SV RNAs. Dr. Woychik has completed characterization of the function of one bacterial TA toxin, designed Doc. Doc leads to inhibition of bacterial cell growth by specifically binding to the bacterial 30S ribosome that leads to inhibition of translation elongation. We have also made considerable progress on understanding the structure and function of several other TA toxins. The structure of the antitoxin HigA has been completed and deposited into PDB (in collaboration with the Hunt laboratory, Columbia University).

PERSONNEL Faculty Gary Brewer, Ph.D., Professor Paul Copeland, Ph.D., Assistant Professor Joseph P. Dougherty, Ph.D., Professor Donald T. Dubin, M.D., Professor Terri Goss Kinzy, Ph.D., Professor Jerome A. Langer, Ph.D., Associate Professor Michael J. Leibowitz, M.D., Ph.D., Professor Honghua Li, Ph.D., Associate Professor Michael Newlon, Ph.D., Assistant Professor Stuart W. Peltz, Ph.D., Professor Sidney Peskta, M.D., Professor and Chairman Yacov Ron, Ph.D., Professor Yufang Shi, DVM, Ph.D., Professor Victor Stollar, M.D., Professor Nancy Woychik, Ph.D., Associate Professor Faculty Resident at CABM Arnold B. Rabson, M.D., Professor Aaron J. Shatkin, Ph.D., Professor Faculty (Coterminus) Philip Furmanski, Ph.D., Professor Emeritus Professors William A. Strohl, Ph.D., Emeritus Professor Joint Appointments Bruce C. Byrne, Ph.D., Adjunct Professor of Medicine and Molecular Genetics, Microbiology and Immunology Kiron M. Das, M.D., Ph.D., F.R.C.P., Professor of Medicine and Molecular Genetics, Microbiology and Immunology Ellen C. Ebert, M.D., Associate Professor of Medicine and Molecular Genetics, Microbiology and Immunology Janusz J. Godyn, Ph.D., Associate Professor of Pathology and Laboratory Medicine and Molecular Genetics, Microbiology and Immunology Suhayl Dhib-Jalbut, M.D., Professor of Neurology and Molecular Genetics, Microbiology and Immunology Edmund C. Lattime, Ph.D., Professor of Surgery and Molecular Genetics, Microbiology and Immunology Paola Leone, Ph.D., Associate Professor of Surgery and Molecular Genetics, Microbiology and Immunology

Joint Appointments, Cont'd Randall D. McKinnon, Ph.D., Associate Professor of Surgery and Molecular Genetics, Microbiology and Immunology M. Maral Mouradian, M.D., Professor of Neurology and Molecular Genetics, Microbiology and Immunology Daniel A. Notterman, M.D., Professor of Pediatrics and Molecular Genetics, Microbiology and Immunology Karel F. Raska, Jr., M.D., Ph.D., Clinical Professor of Pathology and Adjunct Professor of Molecular Genetics, Microbiology and Immunology Michael Reiss, M.D., Professor of Medicine and Molecular Genetics, Microbiology and Immunology Roger K. Strair, M.D., Ph.D., Associate Professor of Medicine and Adjunct Associate Professor of Molecular Genetics, Microbiology and Immunology Moti L. Tiku, M.D., MBBS, Associate Professor of Medicine and Adjunct Associate Professor of Molecular Genetics, Microbiology and Immunology Adjunct Faculty Chiann-Chyi Chen, Ph.D., Adjunct Assistant Professor Evelyn Erenrich, Ph.D., Adjunct Assistant Professor Stephane Gross, Ph.D., Adjunct Assistant Professor Mei-Ling Li, Ph.D., Adjunct Assistant Professor Srijata Sarkar, Ph.D., Adjunct Assistant Professor Lee Ann Schein, Ph.D., Adjunct Assistant Professor Volunteer Adjunct Faculty Sefik S.Alkan, Ph.D., Adjunct Professor Edward Arnold, Ph.D., Adjunct Professor David P. Beck, Ph.D., Adjunct Professor C. Thomas Caskey, M.D., Adjunct Professor Graham R. Cleaves, Ph.D., Adjunct Assistant Professor Dalia Cohen, Ph.D., Adjunct Associate Professor Jeffry Cook, Ph.D., Adjunct Assistant Professor Wendy D. Cornell, Ph.D., Adjunct Assistant Professor Lori R. Covey, Ph.D., Adjunct Associate Professor Gorbadhan Das, Ph.D., Adjunct Professor Jonathan D. Dinman, Ph.D., Adjunct Associate Professor Jürgen Drews, M.D., Adjunct Professor Arthur M. Felix, Ph.D., Adjunct Professor Robert C. Gallo, M.D., D.Sc., Adjunct Professor Gianni Garotta, Ph.D., Adjunct Professor Carlos I. Gonzalez, Ph.D., Adjunct Assistant Professor Alice B. Gottlieb, M.D., Ph.D., Adjunct Professor Christopher Janson, M.D., Adjunct Assistant Professor Florence C. Kimball, Ph.D., Adjunct Associate Professor King-Teh Lin, Ph. D., Adjunct Instructor George E. Mark III, Ph.D., Adjunct Professor

Volunteer Adjunct Faculty, cont'd Fred Mermelstein, Ph.D., Adjunct Assistant Professor Margaret Prescott, Ph.D., Adjunct Associate Professor Abbas Rashidbaigi, Ph.D., Adjunct Assistant Professor Karel Raska, M.D., Ph.D., Adjunct Professor Hugh Rosen, M.D., Ph.D., Adjunct Assistant Professor John J. Siekierka, Ph.D., Adjunct Assistant Professor Leonard H. Sigal, M.D., Adjunct Professor Michael Steinmetz, Ph.D., Adjunct Professor Peter Tolias, Ph.D., Adjunct Professor George B. Weiss, Ph.D., Adjunct Professor Lawrence P. Wennogle, Ph.D., Adjunct Assistant Professor Carol J. Wilusz, Ph.D., Adjunct Assistant Professor Junxia Xie, Ph.D., Adjunct Assistant Professor

Research Associates, Postdoctoral Appointees Full-time Laboratory Staff Xiangfeng Cui, Ph.D. Jyoti Das, M.S. Christopher Krause, Ph.D. Satish Devadas, Ph.D. Regina Felder-Gibbions Lara Izotova, Ph.D. Predoctoral Trainees Danny Tu Khounh Sandra Chesoni Scott Kinzy Jennifer Defren Xiangyang Li Lauren DeStefano Baisong Liao, Ph.D. Anthony Esposito Olga Mirochnitchenko, M.S. Frances Gratacos AnnMarie Pacchia, Ph.D Yvette Green Cheryl Rebsch Malavika Gupta Arthur Roberts Jennifer Hurley Barbara Schwartz, M.S. Patricia Irizarry-Barreto Xiao-Juan Xu Anna Knapinska Zengrong Yuan, Ph. D. Hui-Ling Rose Lee Liying Zhang, M.D.. Mohan Liu Sofiya Micheva-Viteva Sayandip Mukherjee Office Staff Sedide Ozturk Walter Barnes Bradley Phelan Jamie Carr Yvette Pittman Gabriel Dava Meredith Prysak Ellen Feibel Guangwen, Ren Andrea Finamore Rohini Roy Rosalie Reina Estelle Ruidiaz Shannon Smith Jared Sharp Antionette Thomas Kristina Sutphen Zhihong Yang Business Manager Yingyu Zhang Rick Wernoski, MPA Riza Ysla Part-time Laboratory Staff Octavia Gamble Yan Hu Xi Jiang, M.S. Sheila Mazar Beverly Novembre

DEPARTMENTAL ACTIVITIES Appointments Stephane Gross, Ph.D., Appointment as Adjunct Professor of Molecular Genetics, Microbiology and Immunology, effective 12/01/05 Students Receiving Ph.D. Degrees Pedro Ortiz, defended 1/20/2006 Departures/Transfers Antoniette Thomas, retired 8/31/2005 Rick Wernoski left, 6/1/2006

DEPARTMENTAL COMMITTEES Vice Chairman Victor Stollar Standing Advisory Committee Renovations Committee Jerome Langer Terri Goss Kinzy Michael Leibowitz Jerome Langer Victor Stollar Rick Wernoski Core Facility Committee MGMI Retreat Committee Terri Goss Kinzy Gary Brewer Lee Ann Schein Andrea Finamore Barbara Schwartz Victor Stollar Rick Wernoski Rick Wernoski Seminar Committee Equipment Committee Gary Brewer Donald Dubin Terri Goss Kinzy Terri Goss Kinzy Andrea Finamore Michael Leibowitz Rick Wernoski Barbara Schwartz Nancy Woychik Rick Wernoski Faculty Recruitment Committee Holowczak Memorial Committee Arnold Rabson Paul Copeland Yacov Ron Andrea Finamore Yufang Shi Victor Stollar Nancy Woychik Rick Wernoski

Activities of MGMI Faculty Members 2004-2005

Gary Brewer, Ph.D. Research Activities Dr. Brewer’s research involves the study of proto-oncogene and cytokine messenger RNA, specifically their stability and translation and their regulation. These mRNAs are controlled via A+U-rich elements (AREs) present in the 3’-untranslated regions of the mRNAs. AREs target the mRNAs for rapid degradation and/or translational repression. His main focus is on how the ARE-binding protein AUF1 recognizes its target RNA sequences and how its binding affects gene expression. He discovered previously that AUF1 exerts its actions via its association with other cytoplasmic proteins, including translation factors and heat shock proteins. Knockdown of AUF1 using RNA interference stabilizes the ARE-mRNAs examined, proving its role in ARE-mediated mRNA decay. Highlights of the Year He published two seminal papers regarding regulation of genes involved in genotoxic stress responses and in breast cancer. These papers identify the RNA-binding protein AUF1, which we discovered in 1991, as a critical regulator of the GADD45α (genotoxic stress) and c-Yes (kinase involved in breast cancer) genes. Publications Sommer, S., Cui, Y., Brewer, G., and S.A.W. Fuqua. 2005. The c-Yes 3’-UTR contains adenine/uridine-rich elements that bind AUF1 and HuR involved in mRNA decay in breast cancer cells. Steroid Biochem Mol Biol. 97:219-229. Lal, A., Abdelmohsen, K., Pullman, R., Kawai, T., Yang, X., Brewer, G., and Gorospe, M. 2006. Post-transcriptional derepression of GADD45α by genotoxic stress. Mol. Cell 22:117-128. Brewer, G. and Chesoni, S.A. 2006. hnRNP D. AfCS-Nature Molecule Pages, (doi:10.1038/mp.a003244.01). Knapinska, A.M., Irizarry-Barreto, P., Adusumalli, S., Androulakis, I., and Brewer, G. 2005. Molecular mechanisms regulating mRNA stability: Physiological and pathological significance. Curr. Genomics 6: 471-486. M. Gupta and Brewer, G. 2006. MicroRNAs: New players in an old game. Proc. Natl. Acad. Sci. USA 103: 3951-3952. Presentations “AUF1: Where nonsense-mediated meets ARE-mediated mRNA decay”. Delivered July 8, 2005 at the BBSRC USA-UK Workshop on Mechanism and Control of

Posttranscriptional Gene Expression, NY Academy of Sciences, New York, NY. “AUF1: Where nonsense-mediated meets ARE-mediated mRNA decay”. Delivered August 30, 2005 at the EMBO Workshop on Mechanisms of mRNA Decay, Arolla, Switzerland. “Posttranscriptional regulation within the transcriptome of human tissues”. Delivered May 10, 2006 at the DIMACS Workshop on Clustering Problems in Biological Networks, Rutgers University, Piscataway, NJ Teaching MGMB 6000, Microbiology & Immunology , 1 lecture hour MICR 9000, Research in Mol. Genetics, Virology, Cell Biol., Genetic Engineering Elective Contact Person 01:146:470+16:148:514, Advanced Cell Biology/Mol Biol of Cells , 6 lecture hours 01:146:470, Biointerfacial Characterizations, 1 laboratory hour MICMOLGEN 681:612, Lab Rotations, 60 laboratory hours Student mentor for three graduate rotation students BIOL 01:119:406, Research in Biology, 45 laboratory hours Mentor to four undergraduate students Honors Elsie Eggert/American Heart Association Research Fellow, 2003-2005. Graduate Student Committee Memberships Member, Preliminary Oral Examination for Rose Marie Caratozzolo (Gunderson), November 10, 2005 Member, Final Ph.D. Examination for Kristi Muldoon Jacobs (Dinman), May 1, 2006 Member, Preliminary Oral Examination for Kelvin Cuban (Copeland), June 14, 2006 Seminars Sponsored December 6, 2005; Philip Marsden, M.D.; University of Toronto, Dept of Medicine; "Post-transcriptional gene regulation in vascular endothelium: A tale of endothelin-1 and verotoxins (Shiga-like toxins)"

Laboratory Support Staff, Postdocs, Predocs, Visiting Scientists Rutgers Undergraduate Research in Biology/Genetics & Microbiology: Neha Das, Naznin Daginawala, Shannon Scabatto, Yoniara Rivera, Pamela Allahyari Douglass College Project SUPER students: Lauren Rose Maher, Breena Krieger, Aradia Herbst-Gervasoni, Jaquelyn Bradley Student Assistants: Swati Gupta, Alexandria Wierzbowski, Vickey Tsai, Yanan Zhou, Sri Adusumalli, Julianna Small RWJMS Summer Research Fellowship Program student: Tina Park Research Associate: Baisong Liao Graduate Students: Sandra Chesoni. Kristina Sutphen, Lili Banihashemi, Estelle Ruidiaz, Jennifer Defren, Anna Knapinska, Frances Gratacos, Malavika Gupta, Patricia Irizarry, Riza Ysla Graduate Rotation Students: Minnkyong Lee, Yanique Rattigan; Kaitlin Guzzi RISE summer students: Franchesca Fiorito, Chin-Ho Poon Administrative Committees Departmental

Member, Departmental Seminar Committee Member, Retreat Committee, Department of Molecular Genetics, Microbiology, & Immunology University Director, Tutoring Program for Graduate School of Biomedical Sciences (GSBS) Member, Student Affairs and Academic Standing Committee of Graduate Program in Molec. Genetics and Microbiology Federal/State Appointments Ad hoc reviewer: RITE Study Section for NIH, November 2, 2005; NIH Study Section on Genes, Genetics, Genomics (postdoc fellowships), March 2-3, 2006 and July 13- 14, 2006; BMCT Study Section for NIH, June 23, 2006;TRN-6 Study Section (predoc fellowships) for the DOD, June 28, 2006 Community Involvement on Behalf of University or Medical School Sponsor for Pamela Allahyari, Rutgers University, Research in Biology, Fall 2005 Sponsor for Neha Das, Rutgers University, Henry Rutgers Research in Biology, 2005- 2006 Sponsor for Naznin Daginawala, Rutgers University, Honors Research in Biology, 2005- 2006 Sponsor for Shannon Scabatto, Rutgers University, Research in Genetics, 2005-2006 Sponsor for Yonaira Rivera, Rutgers University, Honors Research in Biology, 2005- 2006 Sponsor for Franchesca Fiorito, University of Puerto Rico - Rio Piedras, RISE Program, Summer 2005 Sponsor for Chin-Ho Poon, University of Rochester, RISE Program, Summer 2006 Sponsor for Breena Krieger, Lauren Rose Maher, Aradia Herbst-Gervasoni, and Jaquelyn Bradley, Douglass College Project SUPER, Spring 2006

Paul R. Copeland, Ph.D. Research Activities Incorporation of selenocysteine Selenocysteine is a unique amino acid that is incorporated specifically into a select group of essential proteins. This process represents a modification of the standard protein synthetic machinery in that it requires the utilization of a novel translation elongation factor (eEFSec), a selenocysteine insertion sequence (SECIS) element in the 3' untranslated region (UTR) of selenoprotein mRNAs, and a novel SECIS binding protein termed SBP2. These factors act in concert to alter the coding potential of specific in-frame stop codons (UGA) by specifying the insertion of selenocysteine at that site. One of the goals of our work is to understand the interplay between SBP2 and the translation machinery. Since SBP2 is a limiting factor required for Sec incorporation, it is central to the regulation of synthesis of selenoprotein, many of which are known to play critical roles in cellular defense from oxidation. As a result, SBP2 will be a key target for methods designed to increase the beneficial properties of selenoproteins including the prevention of DNA damage in carcinogenesis and oxidation of pathogenic lipids involved in atherosclerosis. We seek to understand the detailed function of SBP2 by studying its specific interaction with ribosomes and its interaction with the machinery that would ordinarily dictate the termination of translation at selenocysteine (UGA) codons. Our preliminary studies indicate that SBP2 specifically interacts with ribosomal RNA from a variety of species, indicating that the SECIS element may have evolved from highly conserved rRNA structures. This study will focus on mammalian cells as well as the yeast S. cerevisiae in order to thoroughly explore this interaction while exploiting the unique benefits of each system. Specifically, we are using mammalian rRNA fragments to probe the binding characteristics of SBP2. This is being done in combination with an analysis of SBP2 binding to intact yeast ribosomes in vitro and in vivo. In addition, we will directly assess the role of SBP2 in preventing termination at selenocysteine codons by analyzing Sec incorporation from efficient and inefficient templates. The information we obtain about the function of SBP2 will be used to develop a detailed model for Sec incorporation that should shed light on the basic mechanism of translation termination as well as enable us to identify components of the system that can be manipulated in order to optimize selenoprotein synthesis. Selenium and Cancer In 1996, it was reported that dietary selenium supplementation resulted in a significant reduction in total cancer mortality and specifically reduced the incidence of lung, colorectal and prostate cancers (Clark et al., 1996). Increased dietary selenium is either acting through the increased production of selenoproteins or through the action of selenium-containing small molecules that have unknown function. Since many selenoproteins provide a protective barrier against oxidative damage to cellular components, including DNA, we believe that a significant part of the chemoprotective effect of selenium supplementation is the result of an increase in selenoprotein expression. If increased dietary selenium is primarily functioning through the

selenoprotein pathway, then prostate cancer cells are likely to have altered selenoprotein expression. Indeed, it has been observed that at least one selenoprotein is dramatically reduced in prostate cancer. It is therefore of great importance to determine whether selenoprotein synthesis is a central part of the protective action of selenium, and thus a study of the regulation of this process is a critical part of discovering the mechanism of selenium chemoprevention. Specifically, this study will assess the effects of both increased selenium and increased selenoprotein synthetic capacity on cadmium-induced carcinogenesis of normal prostate cells in culture. In addition, to address the regulation of selenoprotein synthesis during prostate oncogenesis, we will identify the point of regulation responsible for the dramatic down- regulation of selenoproteins in prostate cancer as well as determine the contribution of the selenocysteine incorporation machinery to this regulation. Within the context of selenoprotein synthesis, it is important to note that all of the required factors may not be known. One of the ultimate goals of this research is to identify means by which to modulate the efficiency of selenoprotein synthesis, ideally in a selenoprotein-specific manner. Toward this end we are studying the SBP2-like protein (SLP), which is preferentially expressed in human prostate. This protein has no known function, but is similar enough to SBP2 to strongly suggest that it is involved in selenocysteine incorporation. Our study will provide evidence for the contribution of SLP to selenocysteine incorporation in order to provide a foundation for future work that will dissect its apparently prostate-specific function. Highlights of the Year Kelvin Caban, a graduate student in the lab, has completed a saturation mutagenesis in the RNA binding domain of SBP2 and has obtained a number of very interesting mutants. We have mapped these mutations onto the structure of the conserved L7Ae RNA binding domain and found a clear indication that SBP2 makes at least two contacts with the ribosome (see image). The residues in white are required for SBP2 function and thus describe a new motif involved in Sec incorporation that is likely involved in ribosome modification. Publications Peer Reviewed Articles: Kinzy, S.A., Caban, K. and Copeland, P.R. (2005) Characterization of the SECIS binding protein 2 complex required for the co-translational insertion of

selenocysteine in mammals. Nucl Acid Res. 33:5172-5180. Caban, K. and Copeland, P.R. (2006) Size matters: a view of selenocysteine incorporation from the ribosome. Cell Mol. Life Sci. 63:73-81. Abstracts: Translational Control 2005. Heidelberg, Germany, “Characterization of the SBP2-dependent selenocysteine incorporation complex.” Caban, K., Kinzy, S.A., and Copeland, P.R. NJCCR Cancer Research Retreat, Piscataway, NJ May, 2006 Presentations FASEB Summer Conference on Trace Elements – invited speaker, Snomass, CO June, 2006 Urology Grand Rounds, RWJUH, New Brunswick, NJ January 2006 Teaching Biochemistry 501 Seminar Course Microbiology and Immunology MGMB-6000 – Antibiotics Lecture MICR 5684 RNA Protein Interactions Graduate Student Committee Memberships Pedro Ortiz (MGM doc) – thesis committee member Vasanti Subramanian (BIOC doc) – thesis committee member Kristina Sutphen (MGM doc) – thesis committee member Sandra Chesoni (MGM doc) – thesis committee member Lili Banihashemi (MGM doc) – thesis committee member Jennifer Hurley (MGM doc) – qual exam committee member Jennifer Defren (MGM doc) – qual exam committee member Yvette Green (MGM doc) - qual exam committee member Estelle Ruidiaz (MGM doc) – qual exam committee member Frances Gratacos (MGM doc) – qual exam committee member Malavika Gupta (MGM doc) – qual exam committee member Administrative Committees Elected member, Executive Council Member, Foundation Grant Review Committee Member, Graduate Initiatives Committee Departmental

Holowczak Memorial Committee Chairman, Department Website Committee RWJMS Research Day Committee Member, Molecular Biosciences Admissions Committee Member, Qualifying Exam Committee Laboratory Support Staff, Postdocs, Predocs, Visiting Scientists Kelvin Caban (MGMI Ph.D cand.) Ilyssa Bennet (Rutgers undergrad) Nicole Shea (MGMI Ph.D cand.) Shannon Smith (Rutgers undergrad) Jesse Donovan (MGMI Ph.D cand.) Scott Kinzy (RTS III) Neil Rodriguez (MGMI Ph.D cand.) Cheryl Rebsch (RTS V) Katie Wright (Rutgers undergrad) Ruchira Ranaweera (Rutgers undergrad) Editing/Consulting Reviewer for: NIH Special Emphasis Panel Study Section (Nutrition) – grant review Manuscript Review Genome Biology Mol. Cell Biol.

RNA Nucl. Acid. Res.

Joseph P. Dougherty, Ph.D. Research Activities Research in our laboratory focuses upon studying retroviral replication as well as the design and development of retroviral vectors for gene therapy and anti-HIV-1 drug discovery. A more detailed description of our most recent work follows. Forward Chemical Genomics to Query HIV-1 Latency and Replication. Latency. Highly active antiretroviral therapy (HAART) provides remarkable suppression of HIV-1 replication. However, HAART does not lead to complete viral clearance. A primary cause for the lack of viral eradication is a population of chronically infected cells not targeted by the antiretroviral therapy. Those cells form a latent reservoir perpetuating the viral infection. Small molecules with pharmacological properties that allow them to reach viral reservoirs and to activate latent HIV-1 proviruses could result in clearance of HIV-1 infection when supplemented with HAART. To initiate discovery of such molecules, a cell based system that models HIV-1 latency has been developed. It provides a safe, sensitive, and reliable assay that can be used for high throughput screening (HTS). We have applied the system to screen a chemical library containing 200,000 compounds aimed at discovery of novel scaffolds that antagonize HIV-1 latency. From a variety of hits three compounds were selected as leads for further mechanistic studies and chemical modifications. These compounds proved to reproducibly reactivate latent provirus from two different lymphocyte based clonal cell lines as monitored by the expression profile of the markers included in the latency model system, namely, secreted alkaline phosphatase (SEAP) and enhanced green fluorescence protein (eGFP). The consistent reactivation of viral genes as evidenced by the pattern of expression of the markers assayed correlated with an increase in the relative levels of total viral mRNA. All three compounds act in synergy with the histone deacetylase inhibitor valproic acid augmenting the levels of marker gene expression comparable with those achieved with TNF-α. Our preliminary data showed that the new chemical compounds reactivate the latent provirus through different mechanisms. Further studies have to be done in order to find the precise mechanisms of provirus activation, which may uncover unique mechanisms responsible for establishing and maintaining HIV-1 latency. This study is an example of efficient combination of HTS drug discovery with the forward chemical genomics. Replication. In response to attempts to quell its spread, HIV continues to evolve by generating new recombinant genotypes and developing drug resistance. The need for additional methods of control is highlighted by recent reports of strains resistant to entire classes of antiretroviral drugs which aggressively assault the body’s immune system, resulting in alarmingly rapid progression to AIDS. Our efforts have focused on a new form of high throughput assay, which unlike previous assays for antiviral compounds, reconstitutes as many aspects of the viral life cycle as possible. We sought to exploit the high incidence of recombination that occurs during reassociation of reverse transcriptase during synthesis of the provirus. To this end, we have engineered a marker which is conditionally null while in the viral producing cells, but activated after

being transduced into infected cells, resulting in a quantitative assay representing the entire viral life cycle in a single well. We have created the stable producer cell lines needed for the assay and now work on optimization of the assay in a 384-well format. This assay shows a high degree of reproducibility, is designed to be compatible with the robotics used in high throughput screening of chemical libraries, and has been tested for safety. Successful preliminary studies using known HAART drugs in a 384-well format demonstrate the potential for future discoveries. This assay holds promise not only for the potential discovery of new antiviral compounds, but should also expose previously unknown aspects of HIV-1 interaction with host proteins. Retroviral Recombination. The basic mechanism of retroviral reverse transcription has remained unchanged for more than twenty-five years. Every model depicts DNA synthesis as being continuous using a single RNA template. However, we have obtained data indicating that this is not the case. We propose that the leading strand switches from one RNA template to the other RNA template multiple times during each and every cycle of replication. To date, the most compelling evidence comes from our work examining HIV-1 recombination. The data suggest that proviral progeny of heterozygous virions produced by cells harboring two genetically distinct retroviruses are all recombinant. However, this was in sharp contrast to previously reported data from the gammaretrovirus murine leukemia virus (MLV). A significant difference in the recombination rates between HIV-1 and MLV was previously reported, with the former being 10 to 100 times more recombinogenic. It was possible that preferential copackaging of homodimers in the case of MLV led to underscoring of its rate of recombination. To reexamine the recombination rates for MLV, experiments were performed to control for non-random copackaging of viral RNA, and it was found that MLV and HIV-1 exhibit similar recombination rates. In addition, a similar experiment was carried out with HIV-2, and it was also found that crossovers occurred at asimilarly high rate. Our work suggests that the basic mechanism of retroviral reverse transcription should be modified to reflect that template switching occurs multiple times during minus-strand DNA synthesis. This also implies that retroviral genes are essentially unlinked, indicating that retroviral replication is genetically akin to orthomyxovirus reassortment with one difference being that the breakpoints are random for retroviruses while they are defined by the segmented genomes of orthomyxoviruses. If recombination always occurs during retrovirus replication, this would make the process of recombination a core component of the virus lifecycle. A Novel Regulated Gene Expression System Using HIV-2 Derived Vectors. During the examination of the crossover rate of HIV-2, it was found that the HIV-2 based vectors and packaging system yielded very effective levels of gene transduction. We decided to develop HIV-2 based self-inactivating (SIN) vectors. The idea behind SIN vectors is that by deleting a portion of U3 in the 3’LTR the promoter region is destroyed, therefore after reverse transcription the provirus produced will contain LTRs with inactivated promoters. This should ensure that vector mobilization or proto-oncogene

activation downstream of any proviral integration site does not occur. In order to prevent regeneration of fully intact LTR by recombination during transfection, we further developed the SIN vector by replacing the U3 of the 5’LTR with a heterologous cytomegalovirus (CMV) promoter. This not only guarantees the unlikelihood of regenerating an intact LTR, but also renders the SIN vector Tat-independent. The titers generated in different adherent and non-adherent cells by using the Tat-independent SIN vector was found to be comparable or better than when using the transducing vector containing intact LTRs. This shows great promise in using this system and vector for gene therapy purpose. Gene therapy is the delivery of the gene of interest into the host whereby the deficiency of certain protein leading to specific diseases will be alleviated or cured. A major concern of delivery of the gene has always been the safety of the delivery system. Therefore, a regulated system would be more desirable because certain proteins are toxic if expressed in excess. Aminoglycosides have long been used to combat prokaryotes by inhibiting translation of protein synthesis. However, at lower concentrations it has been found that some aminoglycosides can suppress premature stop codon thereby inducing readthrough to produce functional proteins in eukaryotes. Recently, other small molecules have been discovered which exhibit functions similar to these aminoglycosides but with decidedly less toxicity. One such molecule is in clinical phase II trails and has been shown to be very well tolerated by patients. We have decided to further develop the Tat-independent SIN vector by making it inducible. However, unlike all the other inducible systems regulating at the transcriptional level, we aim to use the mechanism of premature stop codon suppression to induce readthrough as the regulatory system at the translational level. We will first use genes such as firefly luciferase for quantitation and bioluminescence evaluation, and GFP for quick visual detection. Once this inducible system has been optimized then genes, like GDNF (glial cell derived neurotrophic factor), that has the ability to cure real diseases when delivered to specific tissues in the host will be used and delivered into animal models such as that of Parkinson’s Disease. This way the effectiveness of delivery and inducibility of the system to cure or alleviate diseases will be evaluated. Highlights of the Year Carried out a high throughput screen which has provided lead molecules that can be used to develop drugs to clear HIV-1 latent infection and that can be used as probes to study HIV-1 latency. Developed a very efficient and safe HIV-2 lentiviral vector system for gene transduction Discovered that the recombination rate of disparate retroviruses is very high suggesting

that all retroviruses including HIV are always subject to crossovers during each and every cycle of replication indicating that the basic model of retroviral reverse transcription should be modified Publications Micheva-Viteva, S., A.L. Pacchia, Y. Ron, S.W. Peltz, and J.P. Dougherty. Human immunodeficiency virus type 1 latency model for high-throughput screening. Antimicrobial Agents and Chemotherapy. 2005 Dec;49(12):5185-8. Duttagupta, R., B. Tian, C.J. Wilusz, D.T. Khounh, P. Soteropolous, M. Ouyang, J. P. Dougherty, and S.W. Peltz. Global analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Molecular & Cellular Biology. 2005 Jul;25(13):5499-513. Zhuang, J., S. Mukherjee, Y. Ron, and J.P. Dougherty. High rate of genetic recombination in murine leukemia virus: implications for influencing proviral ploidy. Journal of Virology. 2006, Manuscript in Press. Mukherjee, S., H.L. Lee, A.L. Pacchia, Y. Ron, and J.P. Dougherty. Self-inactivating HIV-2 vector for efficient gene transduction. Manuscript in preparation. A HIV-2-based self-inactivating vector for enhanced gene transduction. Manuscript Submitted. Teaching Microbiology & Immunology (Medical Students) - 01:680:544:545 Molecular Virology (Graduate Students) - 16:681:555 Graduate Student Committee Memberships Advisor for: Rose Lee Sofiya Micheva-Viteva Sayandip Mukherjee Bradley Phelan Jiangling Zhuang (received PhD) Committee member for: Natasha Telesford Laboratory Staff Md. Anwar Hossain Rose Lee

Florence LeRoy Sofiya Micheva-Viteva Sayandip Mukherjee Annmarie Pacchia Bradley Phelan Danny Tu Khounh Jiang Xi Jiangling Zhuang Administrative Committees Departmental Director of the Graduate program in Molecular Genetics, Microbiology & Immunology Director of HIV Culture Facility University Executive Committee for the Molecular Biosciences Program (UMDNJ/Rutgers Joint Graduate Program) Chair of Institutional Biosafety Committee Executive Committee for the Graduate School of Biological Sciences (UMDNJ) Editing/Consulting Reviewed manuscripts for the Journal of Virology, Virology, and the Journal of Virological Method

Donald T. Dubin, M.D. Research Activities Dr. Dubin has stopped active laboratory research. He continues to follow the current literature on molecular mechanisms of antibiotic resistance in staphylococci and pneumococci. Administrative Committees Departmental Core Facility Committee Student Affairs and Academic Standing Committee (Chairman). RWJMS Committee of Review.

Terri Goss Kinzy, Ph.D. Research Activities The goal of the work in the Kinzy laboratory is to understand the structural and functional basis of G-protein regulation and post-transcriptional mechanisms that regulate gene expression. The components of the Translation Elongation apparatus in yeast, from soluble protein factors to the ribosome, allow an integrated approach to these questions. These components are targets for antibiotics and antifungals, mutant forms and inappropriate expression of these proteins are found in several human carcinomas, one is a target for diphtheria and related toxins, and mutations in several components affect the accuracy and efficiency of protein synthesis and viral replication. We are applying complementary genetic, molecular, biochemical and structural techniques to dissect the mechanism of events occurring during protein synthesis, the physical and functional interaction of Elongations Factors (eEFs) with other factors that regulate gene expression, and the interaction between this G-protein and its GTPase activating factor (GAP), the ribosome. D aa eEF2 GTP OH aa-tRNA binding Translocation ATP A GTP C eEF3OH GTP aa OH E B GTP GDP E P A eEF1A GDP Peptidyl aa transfer Codon recognition GTP hydrolysis eEF1Bαγ Fig. 1: Translation elongation in S. cerevisiae, highlighting the role of eEF1A in aa-tRNA delivery (A), eEF2 in translocation (C), eEF3 in E-site function (A) and eEF1Bαγ in nucleotide exchange (E). The eEF1 protein complex is prototypical of all G-proteins, such as the oncogene Ras, and as such is regulated by a classic "GTPase" switch mechanism. The GTP- dependent activity of eEF1A is to deliver aminoacyl-tRNA to the ribosome and sense the accuracy of this process. The guanine nucleotide exchange factor (GEF) eEF1Balpha is essential in yeast and responsible for catalyzing the exchange of GDP for GTP to maintain the pool of active protein. Using a genetic system devoid of the eEF1Balpha protein allows us to manipulate eEF1A without its GEF to understand the regulation of G-protein activity and mutant forms of eEF1Balpha allow us to dissect the mechanism of guanine nucleotide exchange in vitro and the consequences of changes in this protein’s activity in vivo. Lastly, the eEF1Bgamma subunit affects the sensitivity of the cell to oxidative stress. Current work is addressing the implications of this finding in post-transcriptional control using a proteomics approach. The two other factors involved in elongation, eEF2 the translocase and eEF3, a fungal specific factor, are

integrated with above work to fully dissect the mechanisms of protein synthesis and to better understand their potential as drug targets. We have worked in collaboration with Dr. Gregers Andersen to perform X-ray crystallographic studies of the eEF1 subunits, eEF2 and eEF3. Highlights of the Year In the past year her understanding of the role of the translation elongation factor 1A (eEF1A) has extended beyond its canonical role in delivery of aminoacyl-tRNA for elongation. She have published novel mutants that separate the actin and translation functions of eEF1A, providing a new example of a multifunctional protein and a link between the translational apparatus and regulation of the actin cytoskeleton. Additionally, the regulation of the levels of eEF2, the translocase, and the novel effect of dominant negative mutants on the cell were determined. Publications Magazinnik, T., Anand, M., Sattlegger, E., Hinnebusch, A.G., and Kinzy, T.G (2005) Interplay between GCN2 and GCN4 expression, translation Elongation Factor 1 mutations, and translational fidelity in yeast. Nuc. Acids Res. 33: 4584-4592. Gross, S.R. and Kinzy, T.G. (2005) The translation elongation factor 1A plays essential regulatory functions in the organization of both the actin cytoskeleton and cell morphology Nature Struct. Mol. Bio. 12:772-778. COVER Ortiz, P.A. and Kinzy, T.G. (2005) Dominant Negative Mutant Phenotypes and the Regulation of Translation Elongation Factor 2 Levels in Yeast. Nuc. Acids Res 33:5740-5748. Chatterjee, I., Gross, S.R., Kinzy, T.G. and Chen, K.Y. (2006) Rapid depletion of mutant eukaryotic initiation factor 5A at restrictive temperature reveals connections to actin cytoskeleton and cell cycle progression. Mol. Gen. Genomics 275:264-276. Abstracts Nissen, P., Nilsson, J., Jørgensen, R., Andersen, C., Boesen, T., Andersen, G.R., Goldman, Y., Ortiz, P., Anand, M., Balar, B., Ulloque, R., Kinzy, T.G. , Structural and functional studies of the yeast ribosome and elongation factors, Human Frontier Science Program Meeting, Washington DC, 2005. (platform presentation) Kinzy, T.G., Pittman, Y.R., Ozturk, S., Patel, S., Jeppesen, M.G. and Andersen, G.R., Regulation of Translation Elongation via the Guanine Nucleotide Exchange Factor eEF1Bαγ, Mechanism and Control of Posttranscriptional Gene Expression: A UK-USA Workshop, New York, 2005. (platform presentation)

Pittman, Y., Valente, L., Jeppesen, M.G., Andersen, G.R., Patel, S. and Kinzy, T.G. Biochemical and Mutational Analysis of eukaryotic translation elongation guanine nucleotide exchange factor, eEF1B , Experimental Biology 2006. (platform presentation) Bockhorn, J., Balar, B., Copeland, P., Kinzy, T.G., Characterization of Selenium Metabolism in Saccharomyces cerevisiae: Implications in Anti-Oxidant Potential. The 2006 Annual Retreat on Cancer Research in New Jersey, Piscataway, NJ. Bockhorn, J., Balar, B., Copeland, P., Kinzy, T.G., Development of Selenomethionine Resistant Saccharomyces cerevisiae Strains for X-ray Crystallography. 2006 Aresty Undergraduate Research Symposium, Rutgers University, Piscataway, NJ. Presentation Johns Hopkins: Physical and functional interactions between the translational apparatus and the actin cytoskeleton in yeast. 5/9/2006 Teaching Medical Microbiology - UMDNJ RWJMS – 17 Laboratory Hours Intro. to Mol. Biol. and Biochemistry Research (RU 15:315) - Rutgers University – 1 Lecture Hour The Application of Fungal Systems to Mol. & Cell. Bio. MICR 5683 – UMDNJ-RWJMS/ GSBS – 2 Lecture Hours -- Co-Course director RNA protein interactions: Rutgers: 16:681:684RWJMS: MICR 5684 - UMDNJ RWJMS/ GSBS – 14 Lecture Hours -- Co-Course director Molecular Virology - UMDNJ RWJMS/GSBS – 15 Lecture Hours Summer clinical internship presentation “Use of fungal systems in drug target development” RISE presentation “The devil in the details: record-keeping and falsification of data” Honors R. Walter Schlesinger Basic Science Mentoring Award Recipient

Seminars Sponsored Christopher Hellen, SUNY Downstate, 2/14/06 Mechanisms of translation initiation by internal ribosomal entry Graduate Student Committee Memberships Thesis Committee Member: Sanaz Oghlidos (Rutgers CDB) Barbara Siminovich-Blok (RWJMS Biochem.) Radharani Duttagupta (RWJMS MGMI) Committee Member: Carmela Palmero (RWJMS Pharm) Mariela Reyes-Reyes (RWJMS Biochem) Tyra M. Hall-Pogar NJMS BMB) Sandra Chesoni (RWJMS MGMI) Barbara Siminovich-Blok (RWJMS Biochem.) Shin-Wu Liu (Rutgers CDB) Graduate Student Committee Memberships PhD Kristi L Muldoon Jacobs (RWJMS MGMI) Mariela Reyes-Reyes (RWJMS, Biochem) Carmela Palermo (RWJMS, Pharm) Bill Schneider (RWJMS, Biochem) Rutgers Undergraudates Jecssica Bockhorn Kathleen Wright PhD/MS committee member: Lizbeth Romero (RWJMS Biochem) Tyra M. Hall-Pogar (NJMS BMB) Shin-Wu Liu (Rutgers CDB) Kristina Sutphen (RWJMS MGMI) Jennifer Hurley (RWJMS MGMI) Johnny Ma (Rutgers MBB) Aníbal Soto (Rutgers MMG) Estelle M. Ruidiaz (RWJMS MGMI) Kelvin Caban (RWJMS MGMI) Danielle Macario (RWJMS BME)

Laboratory Support Staff, Postdocs, Predocs, Visiting Scientists Postdoctoral Appointees: Monika Anand Ph.D., Stephane Gross Ph.D. Doctoral Students: Pedro Ortiz, Yvette Green, Sedide Ozturk, Anthony Esposito Undergraduates: Jessica Bockhorn, Nidhi Sondhi, Natalie Colimon, Eden Seitomer, Peter Krueger Rotation Student: Connan Vasa Administrative Committees Department committees, task forces, projects MGMI Seminar Committee MGM Graduate Program Admissions Committee MGMI Core Facilities Committee MGMI Renovations Committee MGMI Equipment Committee Department of Medicine Grants Review School committees, task forces, projects UMDNJ RWJMS Director, UMDNJ RWJMS DNA Synthesis and Sequencing Laboratory Cancer Institute of New Jersey Scientific Council Research Committee Co-Chair, Core Facility Committee Co-organizer UMDNJ RWJMS/Rutgers Yeast Group NIEHS Center of Excellence Directors Internal Advisory Committee

RWJMS Master Educators Committee NIEHS Center of Excellence Pilot Grant Review Committee Foundation of UMDNJ RWJMS Grant Review Committee RWJMS Graduate initiatives committee RWJMS Year Long MD Student Research Fellowship Committee RWJMS HHMI Precollege Science Education Initiative for Biomedical Research Institutions Grant Committee University/Campus committees, task forces, projects UMDNJ Master Educator Guild UMDNJ Master Educator Guild Executive Committee Admissions activities RWJMS MD PhD Admissions Committee Recruitment activities RWJMS Reception for accepted medical students RWJMS Open House Community/state service Science outreach, Bridgewater-Raritan Middle School and Patrick McGowen School, Invited speaker Women in Science and Engineering Fashion Show for middle and high school girls. Executive Leadership in Academic Medicine (ELAM) Program for Women National Advisory Committee Executive Leadership in Academic Medicine (ELAM) Program for Women National Curriculum Committee Editing/Consulting Ad Hoc Reviewer: Nucleic Acids Research EMBO Journal EMBO Reports Journal of Biological Chemistry Genomics Genetics Molecular and Cellular Biology Biochemistry Protein Science European Journal of Biochemistry Molecular and General Genetics PLOS Cell Metabolism Service On Grant Review Panels, Study Sections, Committees: Reviewer, Wellcome Trust, U.K., International Science Foundation Member, N.I.H. Molecular Genetics C Study Section 2003-2007 National Science Foundation Biochemistry of Gene Expression Panel

Jerome Langer, Ph.D. Research Acitivities Dr. Langer continues work funded by the Alliance for Lupus Research directed at the design of inhibitors of Type I interferon that might be useful in the treatment of lupus (systemic lupus erythematosus). His laboratory is designing mutants of human interferon alpha that we hope will be competitive antagonists of natural interferon; i.e., they will bind to the receptor, will not trigger biological responses, and will block the activity of endogenous interferon. The project is a collaboration with Dr. Elizabeth Raveche (Dept. of Pathology and Laboratory Medicine, UMDNJ-New Jersey Medical School). We have used mutagenesis to examine in detail one area of the surface of alpha interferon which has been implicated in receptor binding. Surprisingly, in the interferon subtype that they are examining, this area may not play a major role in receptor binding, despite evidence that it plays an important role in another interferon subtype. They are shifting our attention to other parts of interferon. Highlights of the Year Alpha interferon appears to be inappropriately, perhaps continually, produced in people with systemic lupus erythematosus (“lupus”), and this aberrant production of IFN likely contributes to the pathogenesis of this disease. To block the effects of IFN in lupus patients, we are attempting to design and produce modified IFNs that act as competitive antagonists of endogenous IFN. Dr. Langer has investigated several parts of the IFN molecule for their importance in interactions with the 2 subunits of the IFN receptor. He demonstrated that a region of IFN previously reported to be important in one IFN subtype for receptor interactions does not make strong contributions to receptor interactions in the IFN subtype used in our lab. His laboratory therefore proposed a novel model of IFN/receptor interactions, and is examining the effects of mutations in other parts of the IFN molecule. Publications and Presentations May 24-24, 2006. “Type I Interferon Antagonists for Lupus and Autoimmunity”. Alliance for Lupus Research Collaborative Meeting, New York, NY. Nov. 14, 2005. “Graduate Education Opportunities in the Sciences on the New Brunswick/Piscataway Campuses of UMDNJ and Rutgers”. University of Maryland, Baltimore County (UMBC), Meyerhoff Program.

Teaching Microbiology & Immunology (RWJMS) (Spring 2006) Laboratory instructor. Molecular Virology, Lecturer (Spring 2006) Research/Technical Writing Seminar, “Research in Science & Engineering (“RISE”) at Rutgers/UMDNJ” summer undergraduate research program, Co-director and seminar leader (Summer 2005) Seminars Sponsored 5/9/06 Christine Biron, Brown University, "Regulation of Innate Cytokine Induction & Function During Viral Infection" Graduate Student Committee Memberships Eddie Perez. Ph.D. thesis committee. Dept. of Biochem (Ann Stock, advisor). Member. Xuelie (Julie) Song. Ph.D. thesis committee. Dept. of MGMI (Bill Moyle, advisor). Member. Thesis defense: 9/8/05. Jiaying (Joyce) Huang, Ph.D. thesis committee, Dept. of Biochem. & Molec. Biol., New Jersey Med. Sch. (Sergei Kotenko, advisor). Member. Sedide Ozturk, Ph.D. thesis committee Dept. of MGMI (Terri Kinzy, advisor). Member. Megha Gandhi, M.S. thesis committee. Dept of Food Science, Cook College, Rutgers. (Mikhail Tchikindas, advisor). Member. Thesis defense: 9/21/05. Stephanie Williams, M.S. Thesis committee. Dept. of Physiology & Biophysics, RWJMS. (Nicola Partridge, advisor). Member. Thesis defense: 10/21/05. Distinction in Research M.D. students (RWJMS): Matthew Wosnitzer, Jennifer Tan (Faculty liaison; final committee). . Administrative Committees Departmental MGMI Academic Standing Committee, Member MGMI Committee on Review, Member RWJMS and GSBS RWJMS Distinction in Research Committee: member RWJMS Committee on Research Integrity, member RWJMS Community Service Strategic Planning Committee, Member RWJMS Review of Foundation of UMDNJ Grant applications, Member Molecular Biosciences Graduate Programs, Student Academic Standing Committee,

Member. Molecular Biosciences Graduate Programs, Rotation advisory committee, Member Molecular Biosciences Graduate Programs, Minority Admissions Subcommittee, Member. AAUP RWJMS Chapter, Executive Committee University AAUP Council of Chapters (UMDNJ). Treasurer. Editing/Consulting Journal of Interferon & Cytokine Research, Editorial Board. Ad hoc reviewer: “Biochemistry”; “Proteins: Structure, Function and Bioinformatics”; “Journal of Molecular Biology”; “Journal of Interferon & Cytokine Research” Laboratory Staff Manjing Pan, Ph.D., Post-doctoral Fellow

Michael J. Leibowtiz, M.D., Ph.D. Research Activities Beta-sheet blockers as therapeutic agents In collaboration with Dr. Stanley Stein, Dr. Leibowitz has shown that peptidomimetic agents structurally related to the nucleation site of human A-beta(1-42) amyloid monomer peptide can specifically bind to the monomer and prevent the formation of amyloid in vitro. With Dr. William Welsh he plans to use these and other agents interacting with various amyloids to determine if they can develop bioinformatic approaches to predicting agents binding to proteins that are capable of forming amyloids, such agents might be useful to stain amyloids or to inhibit or reverse their formation. This would have potential application to the diagnosis and treatment of human amyloid diseases. Polymeric Bioconjugates for Drug Delivery In collaboration with Drs. Stanley Stein and Patrick Sinko (Rutgers University), the Leibowitz lab is studying the use of polymeric bioconjugate drug delivery methods to improve the bioefficacy of treatment of AIDS and cancer. The basis for much of this work is the use of conjugates in which various drugs are linked to polyethylene glycol (PEG), resulting in reduced hydrolysis and renal clearance of the drugs and increased half-life. In addition, PEG conjugates decorated with multimeric effector molecules including cell targeting agents, membrane penetration agents and drugs are being developed. Multiple ligands for one or multiple cell surface receptors are being tested as means to deliver these conjugates to specific cells. They have shown that multiple copies of the chemoattractant peptide fMLF result in targeting of macrophages; experiments are planned to determine if the macrophage-specific mannose ligand shows similar effects of multiple copies on a single conjugate, and whether the two ligands might show synergistic targeting effects. These methods are being pursued to develop new therapies for infectious agents which attack macrophages, such as HIV-1 and Mycobacterium tuberculosis. Highlights of the Year Drug-carrying bioconjugates based on polyethylene glycol can be synthesized with attached ligands for cell surface receptors to target the conjugates to cells bearing those receptors, to which the drugs can then be delivered with great specificity. The laboratory has shown that multiple copies of formyl-methionyl-leucyl-phenylalanine attached to the bioconjugates can greatly enhance their delivery to macrophages. This has great potential for developing drug delivery systems for these cells, which are the primary infected cell type in AIDS and tuberculosis. Publications

Wan, L., Zhang, X., Gunaseelan, S., Pooyan, S., Debrah, O., Leibowitz, M.J., Rabson, Arnold B., Stein, S., Sinko, P.J. Novel multi-component nanopharmaceuticals derived from poly(ethylene) glycol, retro-inverso-Tat nonapeptide and saquinavir demonstrate combined anti-HIV effects. AIDS Research & Therapy, 3:12. (2006). M. Palombo, L. Wan, S. Pooyan, X. Zhang, S. Stein, M. Leibowitz and P.J. Sinko, Increasing Avidity Improves Peg-fMLF (N-Formyl-Methionine-Leucine- Phenylalanine) Nanocarrier Uptake by Macrophages, PharmSci supplement, M1123, (2006). S. Pooyan, L. Wan, P. Hu, X. Zhang, S. Stein, M. Leibowitz and P.J. Sinko, Peritoneal Macrophage Uptake, Pharmacokinetics and Biodistribution of Macrophage- Targeted Peg-fMLF (N-Formyl-Methionyl-Leucyl-Phenylalanine) Nanocarriers, PharmSci supplement, (2006). Presentations September 15, 2005, invited presenter at New Student Orientation, Office for Diversity and Academic Success (ODASIS), Rutgers University. August 24, 2005, speaker, Molecular Biosciences Graduate Programs Orientation. September, 28, 2005, speaker, Neuroscience Graduate Program Orientation. November 1, 2005, recruitment talks at Morehouse College and Spelman College, Atlanta, GA. February 22, 2006, invited speaker at University of Puerto Rico, Medical Sciences Campus, San Juan, PR, “Multiplex Bioconjugates Mediating Drug Delivery to Macrophages.” March 10, 2006, invited speaker at Duke University, “[KIL-d]: A Transfectable Prion-Like Virus Control Element.” June 28, 2006, “Choosing and Applying to Graduate School,” RISE (Research in Science and Engineering) at Rutgers/UMDNJ summer undergraduate research program.

Meetings Attended November 2-5, 2005, represented UMDNJ–GSBS and RWJMS at the Annual Biomedical Research Conference for Minority Students (ABRCMS), Atlanta, GA. November 29, 2005, invited speaker on “The Graduate School of Biomedical Sciences,” New Faculty Orientation, UMDNJ-RWJMS. February 16, 2006, NEA (Northeast Alliance) Day, University of Puerto Rico, Mayagüez, PR, sponsored by the NSF. February 21, 2006, URGREAT-MBRS-RISE Project External Advisory Board Meeting, Universidad del Este, Carolina, PR February 22-24, invited consultant, SCORE project (NIH-supported), University of Puerto Rico, Medical Sciences Campus. Teaching Microbiology and Immunology for Medical and Graduate Students; 16:680:544 (MICR 6000). Biomedical Engineering; Senior Design II, 14:125:402, Rutgers University School of Engineering; Lecturer Spring 2004. Ethical Conduct of Research; GSBS/RU DST-5000/16:115:556. RISE (Research in Science and Engineering) Program and Summer Neuroscience Research Program, Lecturer. Student Advisor for Rutgers College course Biomedical Issues of AIDS ( 01:119:152), Fall 2005 Honors Dennis J. Thiele (former graduate student) was awarded 2006 Distinguished Alumnus Award by Graduate School-New Brunswick, Rutgers University Graduate Student Committee Memberships Li Wan (Pharmaceutical Sciences, Rutgers University), Proposal Examination October 17, 2005. Ramón Scharbaai Vazquez (University of Puerto Rico, Medical Science Campus, San Juan), Ph.D. Thesis Defense May 17, 2006. Research Staff: Xiangyang Li, Research Specialist Andrei Nesterov, Student Assistant Ralitza Varlakova, Student Assistant Odette Williams, Student Assistant Undergraduate Students Supervised:

Odette Williams, Livingston College. Ralitza Varlakova, Rutgers College. Andrei Nesterov, Rutgers College. Christina Hansen, Research in Science and Engineering (RISE) at Rutgers/UMDNJ summer undergraduate research program Administrative Committees Departmental - MGMI Equipment Committee Executive Committee Admissions Committee RWJMS Executive Council, non-voting member Chair, Graduate Education Committee (same as Executive Council, UMDNJ-GSBS) Ad hoc member, Graduate Initiatives Committee, UMDNJ-RWJMS University Associate Dean, UMDNJ-Graduate School of Biomedical Sciences, Piscataway Chair, Executive Council, GSBS/Piscataway Director, Core Curriculum in Molecular and Cell Biology, UMDNJ-Rutgers University Steering Committee, M.D./Ph.D. Program, UMDNJ-RWJMS Executive Committee, Rutgers University/UMDNJ Consolidated Programs in the Molecular Biosciences Director, UMDNJ-Rutgers University Pipeline Program, NIH Initiative for Maximizing Student Diversity Award Director, UMDNJ-University of Puerto Rico (Mayagüez Campus) Bridge to the Doctoral Degree Program (NIH funded) Director, UMDNJ Component, Montclair State University-UMDNJ Bridge to the Doctoral Degree Program (NIH funded) Director, Internal Bridge Program, Articulated M.S./Ph.D. Program Member, Cancer Institute of New Jersey and Scientific Advisory Council and Internal Advisory Council of CINJ Admissions Committee, Biotechnology Training Program (joint with Rutgers, NIH) Breast Cancer Research Program, CINJ Graduate Research And Education Training (GREAT) Group, AAMC, UMDNJ-RWJMS Representative Co-Director, Molecular BioSciences Graduate Programs, Rutgers University and UMDNJ-GSBS UMDNJ Representative, Northeast Alliance for Graduate Education and the Professoriate, (NSF funded) Member, Council of Graduate Schools Member, Society for the Advancement of Chicanos and Native Americans in Science

Member, Piscataway Campus Summer Program Directors Member, Advisory Committee for the UMDNJ Presidential Search. (July, 2004) Member, MBRS and Bridges Program Directors Organizations Member, Academic/Education Deans Working Group, UMDNJ Ad hoc member, Diversity Subcommittee, Admissions Committee, Molecular BioSciences Graduate Programs, Rutgers/UMDNJ Member, UMDNJ Intellectual Property Committee Editing/Consulting Consultant, SCORE Program (NIH-supported), Medical Sciences Campus, University of Puerto Rico, San Juan, PR External Advisory Board, URGREAT-MBRS-RISE Project (NIH-funded), Universidad del Este, Carolina, PR Consultant, HIKMA Pharmaceuticals Reviewer for: Biochemistry

Honghua Li, Ph.D. Research Activities Research Activities Our laboratory is interested in understanding the molecular mechanisms affecting human health in a comprehensive way. We have been continuously targeting at biological systems that may have a major and comprehensive impact on human health and have been looking at the life process from different angles. Extending the Application of Our High-throughput Genotyping System. Realizing that understanding the biological systems in a comprehensive way requires high- throughput approaches, we have devoted much effort to establish a high-throughput genotyping system for nucleic acid detection and have been very successful. With this system, >1000 SNPs can be analyzed in a single assay, with a sensitivity allowing the use of single haploid cells as starting material. We first applied this system to the analysis of Single Nucleotide Polymorphisms (SNPs) on a large scale. During the past two years, we have also used it for gene expression profiling with high sensitivity and specificity and have been also very successful. More importantly, we have shown that the high-throughput system can be used to study gene expression in a quantitative way. A number of bioinformatic tools have been developed for analyzing data from the high- throughput assays. Understanding the Genetic Structure of the Human Genome. Meiotic recombination in humans has received considerable attention recently because of its importantce for understanding the genetic structures of the human genome and human evolution. Meiotic recombination is also likely to be one of the primary mechanisms for the formation of haplotype blocks, which is important for mapping genes responsible for complex diseases. However, very little is known about the details of meiotic recombination and the underlying mechanisms. Recent advances in developing new techniques have allowed major progress in revealing the meiotic recombination process. However, study of this process still largely remains descriptive. Our success with developing the high-throughput multiplex genotyping system has enabled us to determine the genotypes of single sperm cells at a large number of genetic loci. This makes is possible to studyg a chromosomal region in a great detail and to reveal the sites of meiotic recombination along the length of chromosomes. Recent findings have allowed us to better understand the correlation between meiotic recombination and haplotype block formation and thus to understand the mechanisms underlying genetic recombination in a comprehensive way. We have shown a strong correlation between meiotic crossovers and haplotype structure in a 2.5-Mb region on the long arm of chromosome 21. To investigate the role of meiotic recombination on haplotype block formation, SNPs were selected at a high density from a 2.5-Mb region of human chromosome 21. Direct analysis of meiotic recombination by high-throughput multiplex genotyping of 662 single sperm identified 41

recombinants. The crossovers were nonrandomly distributed within 16 small areas. All, except one, of these crossovers fall in areas where the haplotype structure exhibits breakdown, displaying a strong statistically positive association between crossovers and haplotype block breaks. The data also indicate a particular clustered distribution of recombination hotspots within the region. This finding supports the hypothesis that meiotic recombination makes a primary contribution to haplotype block formation in the human genome. Understanding the Genetic Basis of Breast Cancer on a Genomic Scale. Breast cancer is present as a spectrum of neoplasm. Clinically, various forms of proliferative lesions and malignancy have been observed. Although extensive histological and cytological studies have been reported, the molecular mechanisms underlying the high degree of heterogeneity of breast cancer remain poorly understood. It is widely believed that breast cancer development is a multi-step process caused by genetic alterations in a number of tumor suppressor genes and protooncogenes. We hypothesize that the high degree of heterogeneity of breast cancer is a reflection of involvement of different molecular pathways. On the other hand, difference in morphology may reflect the activity of distinct molecular pathways and may be used for understanding the genetic basis of breast cancer. To test the above hypothesis, we take the advantage of the fact that loss of heterozygosity (LOH) is usually associated with cancer development and has been shown to be an indication of tumor suppressor inactivation or protooncogene amplification. In most cases, LOH affects relatively large chromosomal regions containing the affected genes. Therefore, LOH can be detected by using genetic markers in these regions, even though these markers may not be necessarily located within the affected genes many of which are unknown. By examining LOH, the correlation between the responsive genes and the corresponding proliferative lesions and malignancy may be studied even without knowing the genes and their protein products. Currently, we have showed that >1,000 SNPs in a single diploid cell can be detected robustly by a single assay and that a few hundred cells microdissected from breast tumor tissue sections can be used for LOH analysis. These kinds fo findings will allow us to understand the molecular pathways underlying breast cancer development in a comprehensive way. It is expected that genome-scale analysis of the breast cancer lesions and malignancy will generate a tremendous amount of information that has not been available before. Highlights of the Year During the academic year of 2004-2005, we have made significant progress toward accomplishing our research goals. We have further extended the application of our high-throughput nucleic acid detection system. This system has been used for studying meiotic recombination in much more detail and on a large scale. We have also used it for studying genetic variation in breast cancer tissues and cell lines, and in colon cancer. We have been very successful in using this marker system, for the first time, to detect sites of meiotic recombination along entire chromosomes and to locate meiotic crossover points which then will improve the understanding of the mechanisms

underlying meiotic recombination. We have also made significant progress in understanding the genetic structure of the human immunoglobulin VH region. These findings may have significant impact on understanding the contribution of the genetic structure of the VH region to the function of the immune system. Publications Chimge, N.O., Pramanik, S., Hu, G., Lin, Y., Gao, R., Shen, L., and Li, H. (2005). Determination of gene organization in the human IGHV region on single chromosomes. Genes Immun 6, 186-193. Wang, H.Y., Luo, M., Tereshchenko, I.V., Frikker, D.M., Cui, X., Li, J.Y., Hu, G., Chu, Y., Azaro, M.A., Lin, Y., Shen, L., Yang, Q., Kambouris, M.E., Gao, R., Shih, W., and Li, H. (2005). A genotyping system capable of simultaneously analyzing >1000 single nucleotide polymorphisms in a haploid genome. Genome Res 15, 276-283. Greenawalt, D.M., Cui, X., Wu, Y., Lin, Y., Wang, H.Y., Luo, M., Tereshchenko, I.V., Hu, G., Li, J.Y., Chu, Y., Azaro, M.A., Decoste, C.J., Chimge, N.O., Gao, R., Shen, L., Shih, W.J., Lange, K., and Li, H. (2006). Strong correlation between meiotic crossovers and haplotype structure in a 2.5-Mb region on the long arm of chromosome 21. Genome Res 16, 208-214. Li, H., Wang, H.Y., Cui, X., Luo, M., Hu, G., Greenawalt, D.M., Tereshchenko, I.V., Li, J.Y., Chu, Y., and Gao, R. (2006). High-throughput Genotyping of Single Nucleotide Polymorphisms with High Sensitivity. In Methods in Molecular Biology, Volume Comparative Genomics, N. Bergman, ed. (Totowa, New Jersey: Humana Press Inc.). Li, H., Cui, X., Greenawalt, D.M., Hu, G., Chimge, N.O., Pramanik, S., Luo, M., Wang, H.-Y., Tereshchenko, I.V., Azaro, M.A., Lin, Y., Yang, Q., Li, J.Y., Chu, Y., Lin, Z., Gao, R., Shen, L., Decoste, C.J., and Shih, W.J. (2006). Microarray Analysis of a Large Number of Single Nucleotide Polymorphisms in Individual Human Spermatozoa. In Genetics of Male Infertility, D.T. Carrell, ed. (Totowa, New Jersey: Humana Press Inc.), pp. 55-76. Teaching MGMB 6000 Microbiology and Immunology Laboratory Staff Xiangfeng Cui, Research Associate Editing/Consulting Study Section: Population Genetic Analysis Program: Immunity to Vaccines/Infections National Institute of Allergy and Infectious Disease

Michael Newlon, Ph.D. Highlights of the year In collaboration with other M-1 course directors and other interested faculty, Dr. Newlon planned and implemented a new course “M-1 Integrated Cases” designed to show how material from each of the first-year courses relates to specific medical cases. Each case began with a lecture-hall presentation which was followed by a small-group team-based learning exercise. This year seven cases were presented: Ethylene glycol poisoning, Duchenne muscular dystrophy, Marfan syndrome, alpha-1 antitrypsin deficiency, meningococcal meningitis, subacute bacterial endocarditis, polycystic kidney disease. Dr. Newlon was chief author of two cases. He was awarded an Educational Technology Advisory Committee to fund creation of visual resources for teaching medical bacteriology, to become part of the MGMB 6000 Microbiology and Immunology course web site, and began developing these materials. Teaching Dept of MGMI: MGMB 6000 Microbiology and Immunology Interdepartmental: MDC 6004 M-1 Integrated Cases MDC 6020 Cellular and Genetic Mechanisms SHRP: PHYA 1439 Cellular and Genetic Mechanisms Administrative Committees RWJMS: First-year course directors’ committee

Stuart W. Peltz, Ph.D. Dr. Peltz began a leave of absence from the University in November 2004. The work in his laboratory is covered under Dr. Joseph Dougherty’s section.

Sidney Pestka, M.D. Chairman Research Activities The study of interferons, their receptors and signal transduction has been a major focus of the laboratory for several decades. Our early research in this area has led to the isolation, purification and characterization of the interferons, and subsequently their cloning and expression in bacteria; and identification of their receptor complexes. Interferons developed in the laboratory are currently available as approved therapeutics in the United States and worldwide for the treatment of various malignancies, viral diseases and multiple sclerosis. During this academic year, members of the laboratory have continued our endeavors to understand the interferons and their mechanisms of action. These efforts have led to a number of new paths, discovery of new cytokines, and unexpected directions, that are described in this summary. This past year we discovered a series of new cytokines and cytokine receptors, including many novel interferons in many species. Of especial importance is the discovery of a new class of human interferon we named IFN-ν, and have begun to characterize this very unusual interferon. Evolution of the Class 2 Cytokines and Receptors, and Discovery of New Friends and Relatives. Recombinant interferon-alpha (IFN-α) was approved by regulatory agencies in many countries in 1986. As the first biotherapeutic approved, IFN-alpha paved the way for the development of many other cytokines and growth factors. Nevertheless, understanding the functions of the multitude of human IFNs and IFN-like cytokines has just touched the surface. Up to the current time the known IFNs and IFN-like cytokines are IFN-alpha, IFN-beta, IFN-epsilon, IFN-kappa, IFN-omega, IFN-delta, IFN-tau, IFN- gamma, limitin, interleukin-28A (IL-28A), IL-28B, and IL-29 as well as their receptors and signal transduction pathways. Analysis of the evolution of these molecules has provided some new insights into the development of these proteins as major elements of innate immunity. In the past year we analyze the evolution of the Class 2 ligands and their cognate receptors by analyzing Class 2 ligand and receptor chain gene sequences from a variety of DNA sequence databases (Krause and Pestka, Pharmacol Ther. 106, 299-346, 2005). In addition, the analyses enabled us to identify three new type I IFN families: IFN-αω, chicken IFN III and IFN-ν. IFN-αω proteins resemble evolutionary predecessors to IFN-α, IFN-ω and IFN-τ. Chicken IFN III is an avian type I IFN subtype that closely resembles mammalian type I IFNs. IFN-ν proteins appear to be obsolete IFN variants that have persisted as pseudogenes in primate lineages for about 40 million years. Since these IFN-ν pseudogenes have persisted virtually intact during this long period, they may have unique and novel functions to be discovered. This work was carried out by Christopher Krause.

Characterization of IFN-ν. This novel interferon was officially recognized as a new interferon molecule by the HUGO Gene Nomenclature Committee (HGNC), University College London, London NW1 2HE UK as a new class of human interferons as follows: approved symbol: IFNNP1 approved name: interferon, nu 1 (pseudogene) location: 9q21 PMID:15922016 Although we have not yet purified IFN-ν to homogeneity, we have begun to characterize this molecule a some extent. We have found it has very high anti-proliferative and antiviral activity. Because it is a pseudogene in human and primates, one might question why we are studying this protein. The major reason we have continued to study this molecule was the surprise that the same stop codon was present in primates at the same position for over 40 million years. Is it likely to have a unique molecule in primates for over 40 million years without any function? Because I believe this is unlikely, we decided to learn more about this interferon. Initial purification attempts demonstrated that IFN-ν is extremely difficult to purify. We did not purify IFN-ν during this past academic year, but we did determine that this molecule had very high activity, but true specific activity would take time to assess. During the next academic year, we expect that we will be able to find out if IFN-ν is a Type I interferon and whether IFN-ν uses the same signal transduction mechanism as Type I interferons. Continuing Discovery of New Protein Methyltransferases and Their Activities. In the past years we discovered the only three symmetrical protein arginine methytransferaces known: PRMT5, PRMT7and PRMT9. Our latest discovery of a new PRMT is PRMT9 (Cook, J.R., Lee, J-H., Yang, Z-H., Krause, C.D., Herth, N., Hoffmann, R., Pestka, S. (2006) “FBXO11/PRMT9, a New Protein Arginine Methyltransferase, Symmetrically Dimethylates Arginine Residues, ” Biochem Biophys Res Commun, 342, 472-481). We identified a protein, FLJ12673 or FBXO11, that contains domains characteristically present in protein arginine methyltransferases (PRMTs). Immuno- purified protein expressed from one of the four splice variants in HeLa cells and in Escherichia coli exhibited methyltransferase activity. Monomethylarginine, symmetric, and asymmetric dimethylarginine (SDMA, ADMA) were formed on arginine residues. Accordingly, we have designated the protein PRMT9. PRMT9 is the third member of the PRMT family that forms SDMA modifications in proteins. Structurally, this protein is distinct from all other known PRMTs implying that convergent evolution allowed this protein to develop the ability to methylate arginine residues and evolved elements conserved in PRMTs to accomplish this. The members of the laboratory performing this

work were Jeffry Cook, Jin-Hyung Lee, Zhihong Yang, Christopher Krauss, and foreign associates Nicole Herth and Ralf Hoffmann, University of Leipzig, Germany. Regulation of cytokine gene expression by mRNA turnover Cytokine expression by cells of the immune system plays a crucial role in the regulation of immune responses. Expression of many cytokines in response to external stimuli during an immune response is regulated by transcription as well as posttranscrptional events. A major post-transcriptional mechanism for regulating the level of gene expression of many cytokines, proto-oncogenes and growth factor mRNAs is through the control of mRNA turnover. The rapid turnover of mRNAs is determined in part by the A+U-rich elements in the 3'-untranslated region. The overall goal of this project is to understand the mechanisms of regulation of expression of cytokines involved in inflammation such as proinflammatory IFN-γ and anti-inflammatory IL-10. These cytokines have opposing effects and they antagonize each other’s production and functions. In the past year our work was focused on the regulation of expression of cytokines and their receptors. Since IL-10 plays a pivotal role in the regulation of inflammatory processes and the pathogenesis of various diseases, it is of critical significance to determine how the expression of IL-10 and IL-10 receptors is regulated. The laboratory used THP-1, a human promonocytic leukemia cell line, to examine how the expression of IL-10 and IL-10 receptors are modulated by inflammatory stimuli such as bacterial LPS and IFN-γ. We began to define protein factors involved in the regulation of IL-10 expression in THP-1 cells. It was demonstrated that AUF1, a mRNA destabilizing protein, interacts with the 3'-UTR of IL-10 mRNA. AUF1 has 4 isoforms (p37, p40, p42, and p45). Depletion of AUF1 by short-hairpin RNA (shRNA) that targets all 4 isoforms suppresses the LPS-mediated upregulation of IL-10 mRNA and protein in THP-1 cells. However, expression of AUF1 isotype p40 in AUF1 knockdown cells restored the LPS- mediated increase of IL-10 mRNA and protein definitively showing that AUF1 plays a critical role in the regulation of the anti-inflammatory cytokine IL-10 in response to LPS, likely through an indirect pathway that has not yet been defined. The specific role of IFN-γ in these functions is being evaluated. Srijata Sarkar, Randi Foster and Gary Brewer contributed to this project. Interactions Among the Components of the Interleukin-10 Receptor Complex We used fluorescence resonance energy transfer previously to show that the interferon-gamma (IFN-g) receptor complex is a preformed entity mediated by constitutive interactions between the IFN-γR2 and IFN-γR1 chains, and that this preassembled entity changes its structure after the treatment of cells with IFN-γ. We applied this technique to determine the structure of the interleukin-10 (IL-10) receptor complex and whether it undergoes a similar conformational change after treatment of cells with IL-10 and determined that, like the IFN-γ receptor complex, the IL-10 receptor complex is preassembled: constitutive but weaker interactions occur between the IL- 10R1 and IL-10R2 chains, and between two IL-10R2 chains. The IL-10 receptor

complex undergoes no major conformational changes when cells are treated with cellular or Epstein-Barr viral IL-10. Receptor complex preassembly appears to be an inherent feature of Class 2 cytokine receptor complexes. Similar analyses are being evaluated relative to the Type I interferon receptors, IFN-αR1 (IFNAR1) and IFN-αR2 (IFNAR2). This work was carried out by Chistopher Krause, Olga Mirochnitchenko, Natasha Lavnikova, Junxia Xie, Barbara Schwartz and outside associates at the University of Pennsylvania, Department of Chemistry (Erwin Mei, Robin Hochstrasser). Modulation of the Activation of Stat1 by the Interferon-gamma Receptor Complex The activation of Stat1 by the interferon-gamma (IFN-γ) receptor complex is responsible for the transcription of a significant portion of IFN-γ induced genes. Many of these genes are responsible for the induction of an apoptotic state in response to IFN-γ. In the absence of Stat1 activation, IFN-γ instead induces a proliferative response. Modifying Stat1 activation by IFN-γ may have pharmacological benefits. We found that the rate of activation of Stat1 can be altered in HeLa cells by overexpressing either the IFN-γR1 chain or the IFN-γR2 chain. These alterations occur in hematopoietic cell lines: Raji cells and monocytic cell lines, which have average and above-average IFN-γR2 surface expression, activate Stat1 similarly to HeLa cells and HeLa cells overexpressing IFN-γR2, respectively. The rapid Stat1 activation seen in HeLa cells can be inhibited by overexpressing a chimeric IFN-γR2 chain that does not bind Jak2 or (when high concentrations of IFN-γ are used) by overexpressing IFN-γR1. These data are consistent with a model in which the recruitment of additional Jak2 activity to a signaling complex accelerates the rate of Stat1 activation. We conclude that the rate of activation of Stat1 in cells by IFN-γ can be modified by regulating either receptor chain and speculate that pharmacological agents which modify receptor chain expression may alter IFN-gamma receptor signal transduction. This work was carried out by Chistopher Krause, Wen He and Sergei Kotenko. Ellen, Fig. 4 and the legend goes here. Preassembly and Ligand-Induced Restructuring of the Chains of the IFN-γ Receptor Complex: The Roles of Jak Kinases, Stat1 and the Receptor Chains We previously demonstrated using noninvasive technologies that the interferon- gamma (IFN-γ) receptor complex is preassembled. Expanding this work, we determined how the receptor complex is preassembled and how the ligand-mediated conformational changes occur. The interaction of Stat1 with the IFN-γR1 receptor chain results in a conformational change localized to IFN-γR1. Jak1 but not Jak2 is required for the two chains of the IFN-γ receptor complex (IFN-γR1 and IFN-γR2) to interact; however, the presence of both Jak1 and Jak2 is required to see any ligand-dependant conformational change. Two IFN-γR2 chains interact through species-specific determinants in their extracellular domains. Finally, these determinants also participate

in the interaction of IFN-γR2 with IFN-γR1. These results agree with a detailed model of the IFN-γ receptor that requires the receptor chains to be pre-associated constitutively for the receptor to be active. These investigators contributed to this work: Christopher Krause, Natasha Lavnikova, Junxia Xie, Olga Mirochnitchenko and outside associates at the University of Pennsylvania, Department of Chemistry (Yiwei Jia, Erwin Mei and Robin Hochstrasser). Prevention of Viral Diseases with Interferons We began a study to determine if new interferon molecules could prevent viral diseases. Human papillomaviruses (HPV) are nonenveloped, dsDNA viruses with about 8 kb circular genomes. HPV infect mucosal and cutaneous epithelium resulting in variety of clinically important conditions, most notably, cervical cancer. Because HPV replication and virion production are closely tied to epithelial cell differentiation, the studies of HPV replication, host interactions, and therapy development were constrained due to the difficulty of obtaining sufficient amounts of infectious virions. Initial experiments were begun to determine if new interferons can prevent HPV infection. Some of the new human interferons appeared to be able to block HPV infection. This study is continuing and should be completed in the next academic year. The following individuals contributed to this effort: Meiling Li, Barbara Schwartz and Kevin Anton. Lara Izotova, Zhi-hnog Yang, Sidney Pestka, Barbara Schwartz, Srijata Sarkar, Christopher Krause, Randi Foster

Publications Adler, V., Yongxia Qu, Y., Smith, S.J., Izotova, I., Pestka, S., Kung, H-F., Lin, M., Friedman, F.K., Chie, L., Chung, D., Boutjdir, M. and Pincus, M.R. (2005) “Functional Interactions of raf and MEK with jun-N-Terminal Kinase (JNK) Result in a Positive Feedback Loop on the Oncogenic ras Signaling Pathway” Biochemistry, 44 , 10784-10795. Qu, Y., Adler, V., Chu, T., Platica, O., Michl, J., Pestka, S., Izotova, L., Boutjdir, M. and Pincus, M.R.(2005) “Differences in Gene Expression in Xenopus Oocytes Induced to Mature with Oncogenic ras-p21 and with Insulin, which Requires Activation of Wild-Type ras-p21,” Frontiers in Bioscience, 11, 2420-2427. Krause, C.D., Mei, E. Mirochnitchenko, O.V., Lavnikova, N., Xie, J., Jia, Y., Hochstrasser, R.M., and Pestka, S. (2005) “Interactions Among the Components of the Interleukin-10 Receptor Complex,” Biochem Biophys Res Commun, 340, 377-385. Pestka, S. and Krause, K. (2006) “Interferon and Related Receptors,” Chapter 5 in The Interferons: Characterization and Application (A. Meager ed.), Wiley-VCH, 113- 140. Krause, C. D., Lavnikova. N., Xie, J., Mei, E., Mirochnitchenko, O.V., Jia, Y., Hochstrasser, R.M.and Pestka, S. (2006) “Preassembly and Ligand-Induced Restructuring of the Chains of the IFN-g Receptor Complex: The Roles of Jak Kinases, Stat1 and the Receptor Chains,” Cell Research, 16, 55-69. Krause, C.D., He, W.,Kotenko, S., and Pestka, S. (2006) “Modulation of the Activation of Stat1 by the Interferon-gamma Receptor Complex, ” Cell Research, 16, 113- 123. Desai, S.D, Haas, A.L., Wood, L.M., Tsai, Y.C, Pestka, S., Rubin, E.H., Saleem, A., Nur-E-Kamal A, Liu, L.F. (2006) “Elevated Expression of ISG15 in Tumor Cells Interferes with the Ubiquitin/26S Proteasome Pathway.,” Cancer Res. 66, 921- 928. Cook, J.R., Lee, J-H., Yang, Z-H., Krause, C.D., Herth, N., Hoffmann, R., Pestka, S. (2006) “FBXO11/PRMT9, a New Protein Arginine Methyltransferase, Symmetrically Dimethylates Arginine Residues, ” Biochem Biophys Res Commun, 342, 472-481. Teaching Molecular Biology & Pharmaceutical Biotechnology - RutgersUniversity - S. Chen, Ph.D. Course Coordinator - Development of Genetically Engineerd Pharmaceuticals: Interferon's discovery, Uses and Persepctives. Medical Microbiology and Immunology - RWJMS/Piscataway - M. Newlon, Ph.D. Course Coordinator. Current Concepts in Immunology, Robert Wood Johnson Medical School and Rutgers University – Yufang Shi, Ph.D., DVM, Course Coordinator.

Honors Lemelson-MIT Lifetime Achievement Award, May 3, 2006 Induction into the New Jersey High-Tech Hall of Fame, May 4, 2006 Graduate Student Committee Membership Zhihong Yang Laboratory Staff Srijata, Sarkar, Ph.D. Adjunct Assistant Professor Lara Izotova, Ph.D. Research Teaching Specialist II Barbara Schwartz, M.S. Research Teaching Specialist II Randi Foster Research Teaching Specialist III Olga Mirochnitchenko, M.S. Research Teaching Specialist IV Christopher Krause, Ph.D. Postdoctoral Appointee Zhihong Yang Graduate Student Administrative Committees and Programs University Director, Graduate Program, Molecular Genetics and Microbiology, Graduate School of Biomedical Sciences, UMDNJ-RWJMS Executive Council Clinical Research Center Advisory Board Scientific Council, Cancer Institute of New Jersey Executive Committee, Cancer Institute of New Jersey Internal Advisory Board, Cancer Institute of New Jersey Director, Cytokine, Growth Factors and Signal Transduction Program, Cancer Institute of NJ Executive Committee, Consolidated Program in the Biomedical Sciences, Rutgers University and Graduate School of Biomedical Sciences - UMDNJ at RWJMS Honorary Degree Award Committee Rutgers University Associate Director, Graduate Program in Microbiology and Molecular Genetics Community Involvement Member, North Caldwell Board of Health Member, Basic Pharmacology Advisory Committee of the Pharmaceutical Manufacturers Association Foundation, Inc.

Other Committe Memberships Secretary, International Society for Interferon and Cytokine Research Member, Columbia University Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University International Advisory Committee of the Institute of Chemical Biology, Institute of Molecular Biology and the Department of Chemistry, University of Hong Kong Editing/Consulting Editor, International Encyclopedia of Pharmacology and Therapeutics Editorial Board: Pharmacology and Therapeutics Journal of Interferon and Cytokine Research Anticancer Research Pharmaceutical Technology Cytokine and Growth Factor Reviews BioTechniques Associate Editor: Journal of Biological Regulators and Homeostatic Agents Oncology Research Molecular and Cellular Differentiation Editorial Academy The International Journal of Oncology

Arnold B. Rabson, M.D. Research Activities Dr. Rabson’s laboratory is continuing its research on the regulation of Human T-cell leukemia virus type 1 (HTLV-1) infection and on the roles of NF-κB and related proteins in human cancers. The laboratory is studying the mechanisms of latency and activation of integrated HTLV-1. The laboratory has identified the role of the T-cell activation pathway in activation of latent HTLV-1 This work suggests a model for activation of latent HTLV-1 in which T-cell receptor stimulation induces increased expression directed by the HTLV-1 long terminal repeat promoter, which in turn activates expression of the HTLV-1 Tax transactivation leading to a marked increase in HTLV-1 gene expression. Activation of the integrated HTLV-1 provirus may contribute to HTLV- 1 pathogenesis through induction of expression of the HTLV-1 Tax gene from latently infected cells in vivo, leading to increased lymphoid proliferation. In collaboration with Dr. Yufang Shi, the laboratory is also studying the effects of HTLV-1 Tax on T-cell function in HTLV-1 Tax transgenic mice and attempting to use these mice to model HTLV-1 latency and pathogenesis. These studies have shown that immune activation of T-cells carrying the HTLV-1 Tax oncogene leads to markedly enhanced T-cell proliferatrion and survival. This is associated with induction of cytokine secretion and characteristics of the T regulatory subset of T-cells. The laboratory also studies the functions of cellular and viral transcriptional regulators in regulating HTLV-1 gene expression in infection of target T-cells. Dr. Rabson’s laboratory has also characterized mutations and activation of the NF-κB pathways in human cancers. Previous studies had identified mutations in the NF-κΒ-2 gene in human cutaneous T-cell lymphomas which truncate the C-terminus of the p100 protein, an inhibitor of the alternative pathway of NF-κΒ activation, leading to constitutive activation of the alternative NF-κB pathway in these tumors. Recent studies have suggested that the truncated NF-κΒ-2 precursor proteins may also have biological roles in inducing gene expression that may contribute to T-cell lymphomas. On-going studies are dissecting the roles of NF-κΒ-2 mutation in lymphomagenesis and are using Affymetrix RNA expression arrays to identify genes activated by NF-κB mutations in lymphoma cells. In related studies, the Bcl-3 protein (related to the IκB regulators of NF-κB) is regulated by tyrosine kinases involved in T- and B-cell malignancies, and may mediate the oncogenic effects of these kinases. Dr. Rabson has continued to collaborate with Dr. Strair (CINJ) in the study of the possible therapeutic role of NF-κB inhibition in human leukemias. A therapeutic trial has been initiated to inhibit NF-κB using commonly employed anti-inflammatory compounds in conjunction with induction chemotherapy for acute myeloid leukemia. Dr. Rabson has continued to collaborate with Dr. Xiao of Rutgers to study the mechanisms by which HTLV-1 induces the NF-κB pathway as part of its oncogenic activity. Other collaborative studies with Drs. Leibowitz, Stein and Sinko continue to study the delivery of anti-HIV drugs through slow-release polymer delivery systems. Dr.

Rabson has also continued collaborations with Dr. A. Conney (Rutgers) on the possible effects of phorbol esters in cancer therapy. Highlights of the Year Dr. Rabson’s laboratory has further delineated a pathway for activation of latent HTLV-1 through T-cell receptor activation. This result provides a possible mechanism for the pathogenesis of HTLV-1-induced diseases, in particular, Adult T-cell leukemia (ATL) which is currently being explored in transgenic mice in order to develop a small animal model of this devastating leukemia. His laboratory has also identified genes that are critical for the development of a second human T-cell malignancy, cutaneous T-cell lymphoma, and is currently further characterizing these genes. Publications Rabson, A.B. and Weissman, D. From microarray to bedside: targeting NF-κB for therapy of lymphomas. Clinical Cancer Research, 2005; 11:2-5. Zhao, Y., Ramakrishnan, A., Kim, K.-E., and Rabson, A.B. Regulation of Bcl-3 through interaction with the Lck tyrosine kinase Biochemical and Biophysical Research Communications, 335:865-873, 2005. Hansson, A., Marin Y.E., Suh, J., Rabson, A.B., Chen, S., Huberman, E., Chang, R.L., Conney, A.H., Zheng, X., Enhancement of TPA-induced growth inhibition and apoptosis in myeloid leukemia cells by BAY11-7082, am NF-kappaB inhibitor. Int. J Oncol. 27L9410948, 2005. Medina, D.J., Sheay, W., Osman, M., Goodell, L., Rabson, A.B., and Strair, R.K. Adenovirus infection and cytotoxicity of primary mantle cell lymphoma cells. Experimental Hematology, 33:1337-1347, 2005. Wan. L, Zhang, X., Gunaseelan, S., Pooyan, S., Debrah, O., Leibowitz, M.J., Rabson, A.B., Stein, S., Sinko, P.J. Novel multi-component nanopharmaceuticals derived from poly(ethylene) glycol retro-inverso-Tat nonapeptide and saquinavir demonstrate combined anti-HIV effects. AIDS Res. Ther. 3: 12, 2006. Gu, X., Ke, S., Liu, D., Sheng, T., Thomas, P.E., Rabson, A.B., Gallo, M.A., Xie, W., Tian, Y. Role of NF-κB in regulation of PXR-mediated gene expression: a mechanism for the suppression of cytochrome p450 3A4 by proinflammatory agents. J. Biological Chemistry, 281: 17882-17889, 2006. Xiao, G., Rabson, A.B., Young, W., Qing, G., Qu, Z. Alternative pathways for NF-κB activation: a double-edged sword in health and disease. Cytokine and Growth Factor Reviews. 2006; 17:281-93.

Teaching UMDNJ-RWJMS Department of Microbiology and Molecular Genetics, Medical Microbiology and Immunology Course (First Year Medical Students), MGMB 6000 (Rutgers # 16:680:544). Lecture on HIV/AIDS (2 hours). UMDNJ-RWJMS Department of Pathology and Laboratory Medicine, Pathology and Laboratory Medicine Course (Second Year Medical Students), PATH 7000, Small Group Leader (Path Talk), (8 three hour sessions and 1 hour review lecture). UMDNJ-RWJMS Department of Family Practice, Alternative and Complementary Medicine Course, Seminar on Ayurveda, Indian traditional/herbal medicine for Medical School, (two hour seminar. Rutgers/UMDNJ Graduate Program in Molecular Genetics and Microbiology Course, Molecular Virology Course, HIV lecture (1.5 hours). UMDNJ "Topics in Molecular Medicine" seminar on molecular medicine (one hour) Rutgers University Molecular Biology and Biochemistry Senior Undergraduate Seminar, Session on Research Opportunities for Physician-Scientists CINJ Medical Oncology Fellows, Lectures in Molecular Oncology (2 lectures) UMDNJ-RWJMS Department of Pathology Resident Research Advisor, 4 meetings/yr. Honors Co-Chair, Workshop on HTLV Virology, 12th International Conference on Human Retrovirology Foundation of UMDNJ Award for Excellence in Teaching (Award for UMDNJ-Robert Wood Johnson Medical School Teaching for 2005) Seminars Sponsored July 2005, Dr. Gyan Bhanot, IBM and Institute for Advanced Studies, CINJ Division of Cancer Genomics and Molecular Oncology Seminar. October, 2005, Dr. Wendy Lo, M.D. Anderson Cancer Center, CINJ Division of Cancer Genomics and Molecular Oncology Seminar. October, 2005, Dr. Lizhao Wu, Ohio State University, CINJ Division of Cancer Genomics and Molecular Oncology Seminar. December, 2005, Dr. Ann Stock, UMDNJ-RWJMS and CABM, CINJ Distinguished Lecture Series. March, 2006, Dr. Iannis Aifantis, University of Chicago, CINJ Division of Cancer Genomics and Molecular Oncology Seminar. May, 2006, Dr. Gunaretnam Rajagopal, Bioinformatics Institute, Singapore, CINJ Division of Cancer Genomics and Molecular Oncology Seminar. June, 2006, Dr. Gabriele Alexe, IBM and Institute for Advanced Studies, CINJ Division of Cancer Genomics and Molecular Oncology Seminar.

Graduate Student Committee Memberships Xi Wang, UMDNJ-RWJMS Molecular Genetics, Microbiology, and Immunology Program, advisor, Dr. M. Shen, Defense 07/05. Jui Dutta, UMDNJ-RWJMS Biochemistry Program, advisor, Dr. C. Gélinas. Matthew Simmons, UMDNJ-RWJMS Biochemistry Program, advisor, Dr. C. Gélinas, Defense 12/05. Tin-Ting Tan, Rutgers University Molecular Biology and Biochemistry, advisor, Dr. E. White, Defense 11/05. Alison Tuske, UMDNJ-RWJMS Molecular Genetics, Microbiology, and Immunology Program, advisor, Dr. A. Rabson. Gayatri Subramanian, UMDNJ-RWJMS Molecular Genetics, Microbiology, and Immunology Program, advisor, Michael Reiss. Defense, 1/10/06. Rebecca Dryer-Minnerly, Rutgers University Cell and Developmental Biology Program, advisor: Lori Covey. Kristina Lu, Rutgers University Cell and Developmental Biology Program, advisor: Lori Covey, Defense, 4/25/06. Emmanuel Gabriel.UMDNJ-RWJMS Molecular Genetics, Microbiology, and Immunology Program, advisor: Dr. E. Lattime. Guoliang Qing, Rutgers University Cell and Developmental Biology Program, advisor: Gutian Xiao. Sandra Chesoni, UMDNJ-RWJMS Molecular Genetics, Microbiology, and Immunology Program, advisor: Dr. G. Brewer. Lili Banhashemi, UMDNJ-RWJMS Molecular Genetics, Microbiology, and Immunology Program, advisor: Dr. G. Brewer. Nupur Gupta, UMDNJ-RWJMS Biochemistry Program, advisor, Dr. C. Gélinas. Rajiv Rajendra, UMDNJ-RWJMS Toxicology Program, advisor, Dr. E. Rubin. M.S. Defense 7/05. Diana Anderson, Rutgers University Microbiology Program, advisor, Dr. E. White, M.S. Defense, 9/05. Laboratory Support Staff, Postdocs, Predocs, Visiting Scientists Hsin-Ching Lin, Ph.D., Research and Teaching Specialist Peter Simon, Ph.D., Postdoctoral Fellow Alison Tuske, Graduate Student Erin Macron, Undergraduate Student Lisa Stagmer, Undergraduate Student Amrita Aranake, Undergraduate Student

Administrative Committees UMDNJ-RWJMS Chair, Advisory Committee on Appointments and Promotions Core Facilities Subcommittee of the UMDNJ-RWJMS Research Committee UMDNJ-RWJMS GMP Laboratory Advisory COmmittee Departmental UMDNJ-RWJMS Child Health Institute Search Committee Rutgers Laboratory of Cancer Research, Search Committee Rutgers BIOMAPS, Member, Executive Committee, NIH Workforce Training Grant in Integrated Proteomics EOHSI Pilot Project Grant Review Committee Member, Executive Committee, NIH Workforce Training Grant in Integrated Proteomics. CINJ Deputy Director, The Cancer Institute of New Jersey (CINJ) Leader, Program in Transcriptional Regulation and Oncogenesis, CINJ Director, CINJ Cancer Genomics and Molecular Oncology Branch Co-Chairman, CINJ Collaborative Research Award Grant Review Committees Cancer Institute of New Jersey Scientific Council Cancer Institute of New Jersey Executive Committee Executive Committee, CINJ Training Program in Translational Cancer Research, Search Committee, CINJ Hematologic Malignancies Tumor Study Group Search Committee, CINJ Division of Medical Oncology Chairman, Search Committee, CINJ Division of Cancer Genomics and Molecular Oncology Search Committee, Director of Development Search Committee, Associate Director, Population Sciences Search Committee, Director, Information Sciences Member, Internal Advisory Board, Dean and Betty Gallo Prostate Cancer Center. Chair, Internal Advisory Board, Prostate Cancer SPORE Grant Initiative CINJ Strategic Planning Advisory Committee CINJ Cancer Center Support Grant and Research Subcommittee Co-Director and Member of the Executive Committee, CINJ Training Program in Translational Cancer Research, UMDNJ-RWJMS CINJ and Department of Radiation Therapy Basic Science Faculty Search Committee CINJ Space Management Committee

Federal/State Appointments Federal NIH Oncologic Sciences Cancer Molecular Pathobiology Study Section, ad hoc Editing/Consulting Senior Editor, Clinical Cancer Research Editorial Board, Journal of Biomedical Science Reviewer for: Blood Virology Journal of Clinical Investigation Molecular Cancer Therapeutics

Yacov Ron, Ph.D. Research Activities Prevention and treatment of EAE by the induction of clonal anergy to encephalitogenic determinants of myelin antigens. Retroviral-mediated gene transfer technology is employed to express synthetic genes encoding the whole myelin basic protein (MBP), proteolipid protein (PLP) or myelin oligodendrocyte glycoprotein (MOG) or minigenes encoding the encephalitogenic determinants of these proteins in normal antigen presenting B cells. These synthetic genes also encode lysosomal targeting sequences in order to facilitate association with MHC class II molecules. This approach is based on the findings that normal, resting B cells induce antigen-specific T cell unresponsiveness rather than activation. We have shown that B cells expressing a PLP-derived encephalitogenic determinant inhibit the ability to induce EAE in susceptible animals and completely block relapses in animals treated during the first remission period. We have also shown that treated animals were specifically tolerized (anergized) to the PLP determinant encoded by the synthetic gene. The same treatment was also efficacious in blocking spontaneous EAE induction as well as reversing ongoing disease in PLP-specific TCR transgenic animals ; these animals all develop terminal disease if not treated. Lymphoid and myelopoiesis and homeostasis. Using retroviral tagging, a myeloid precursor cell population that can give rise to the whole myeloid system was identified in the spleen. This cell population is non self- renewing, and will not reconstitute the BM of irradiated animals. It is, however, a very long-lived population and will reconstitute the myeloid system for at least 6 months. These findings contradict the common dogma according to which only pluripotential stem cells can replenish the entire hematopoietic system. Similarly, our studies on lymphopoiesis show that both B and T cells can develop independently from other hematopoietic lineages and that there is a lineage-specific homeostatic mechanism that engages the two lymphoid subpopulations. These studies are based on BM chimeras reconstituted with BM taken from mouse strains lacking one or more component of the lymphoid system ; the systems allows us to follow the appearance of host-derived lymphoid cells in the reconstituted mice. Etiology of antibody-mediated IgA deficiency. It has been suggested that food containing bovine IgA such as milk and meat could, in some individuals, induce a heteroclytic, anti-human IgA response resulting in the generation of a rheumatic IgG anti-IgA factor. The hypothesis is based on a case study where a patient had a high titer of anti-bovine IgA that cross reacted with human IgA which declined when IgA was removed from the food. This hypothesis will also be tested for the more common IgG anti-IgG rheumatic factor.

Publications Micheva-Viteva S, Pacchia AL, Ron Y, Peltz SW, and Dougherty JP. 2005. Human immunodeficiency virus type 1 latency model for high-throughput screening. Antimicrob Agents Chemother. 49:5185. Chen, C-C., and Y. Ron. 2006. New strategies for immune-mediated anti-viral drug and vaccine development. Current Pharmaceutical Design, 12:1391. Zhuang J., Mukherjee S, Ron Y, and Dougherty JP. High rate of genetic recombination in murine leukemia virus: implications for influencing proviral ploidy. J. Virol. 80:6706. Mukherjee S., Rose Lee H-L, Ron Y, and Dougherty JP. Proviral progeny of heterodimeric virions reveal a high crossover rate for human immunodeficiency virus type 2. 2006. J. Virol. In press. Mukherjee S., Rose Lee H-L, Paccia AL, Ron Y, and Dougherty JP. A HIV-2-based self inactivating vector for enhanced gene transduction. J. Biotechnology. 2006. In press Teaching Medical Microbiology & Immunology Molecular Biology and Pharmaceutical Biotechnology Molecular Biology of Cells (16-148-514) Laboratory Support Staff, Postdocs, Predocs, Visiting Scientists Chiann-Chyi Chen Nomi Ron Ayelet Avni Administrative Committees RWJMS: Safety Committee

Aaron J. Shatkin, Ph.D. Research Activities Characteristic of eukaryotic gene expression is the addition of a m7GpppN cap to nascent mRNA 5´ends. The cap structure marks transcription start sites and regulates mRNA stability, splicing, nuclear transport and translation initiation facilitated by cap binding proteins. Caps are synthesized in three enzymatic steps catalyzed sequentially by RNA triphosphatase (RT), guanylyltransferase (GT) and methyltransferase (MT). We have cloned, sequenced and characterized the human, mouse and worm capping enzymes. In contrast to separate enzymes in unicellular eukaryotes, metazoans contain a bifunctional capping enzyme (CE) consisting of N-terminal RT and C-terminal GT. We have separated the two domains by controlled proteolytic digestion of purified recombinant human CE and have obtained crystals of the enzymatically active CE domains for X-ray three-dimensional structural studies. CE selectively binds RNA polymerase II via interaction of the GT domain with the C- terminal heptad repeat sequences in the largest subunit of the polymerase. This association stimulated capping. CE binding also relieved repression by negative elongation factor in transcription complexes, suggesting that it plays a critical role in an elongation checkpoint control during promoter clearance. We are using a mass spectrometry approach to determine the number of CE molecules per Hela cell and the ratio of CE to RNA polymerase II under different culture conditions. Knockdown of CE in human cells by small interfering RNA (siRNA) resulted in apoptosis as measured by TUNEL assay and caspase-3 activation. The results demonstrate that as in yeast and worms, CE is essential for viability. Induction of apoptosis was independent of p53 function, and mouse embryo fibroblasts with deletions in the pro- apoptotic BAK and BAX genes failed to undergo programmed cell death. Instead they showed signs of autophagy, including relocalization and cleavage of LC3-1. siRNA knockdown of MT also induced apoptosis. Viability was restored by transfection of a truncated MT that retained a nuclear localization sequence (NLS) and was associated with transcription complexes in the nucleus. By contrast, a truncated MT that was missing a NLS and thus remaided localized in the cytoplasm, although catalytically active, failed to reverse the siRNA-induced apoptotic effects of MT knockdown. Thus mRNA capping appears to be a key component in the network of interacting pathways required for homeostasis in mammalian cells and likely in eukaryotes generally. We have also initiated two additional studies: (1) to define cis elements in the 3’ sequence of human and mouse bone morphogenetic protein 2 that determine distal vs. proximal polyadenylation site selection and (2) to elucidate the biological role of mRNA methylation at internal A-A-C and G-A-C sequences by siRNA. Highlights of the Year Documented the essential role of mRNA capping in mammalian cells and the

consequences of its disruption. Research Funding Source: NIHGMS 5 T32 GM 08339-17 2/5 Title: Rutgers-UMDNJ Training Grant in Biotechnology Period: 7/1/2005 – 6/30/2010 Amount: $223,349 (annual direct costs) Publications Shafer, B., Chu, C., and Shatkin, A.J. (2005) Human mRNA Cap Methyltransferase: Alternative Nuclear Localization Signal Motifs Ensure Nuclear Localization Required for Viability. Mol. Cell. Biol. 25:2644-49. Chu, C., Shafer, B. and Shatkin, A.J. (2005) Apoptosis Is Induced in Mammalian Cells by siRNA Knock-down of mRNA Capping Enzymes. Cold Spring Harbor Meeting on Eukaryotic mRNA Processing. Shatkin, A.J. (2005) Gene Regulation: mRNA Capping. Henry Stewart Talks, London (on line). Presentations Shatkin, A.J. (2005) mRNA Capping. Case Western Reserve University, Cleveland. Shatkin, A.J. (2005) Eukaryotic Gene Expression Mechanisms. Florida Gulf Coast University, Ft. Myers. Shatkin, A.J. (2005) CABM Research Programs. NJCST Meeting, Piscataway. Liu, D., Rogers, M.B. and Shatkin, A.J. (2006) Alternate Polyadenylation of BMP2 mRNA in Cancer Cells. The 2006 Annual Retreat on Cancer Research, New Jersey. Zheng, H., Chu, C. and Shatkin, A.J. (2006) A Mass Spectrometry-based Approach to Absolute Quantitation of mRNA Capping Enzyme in Mammalian Total Cell Lysate. ASM Annual Meeting, Orlando, Florida. Shatkin, A.J. (2006) Career Opportunities in Science and Technology. NSF Panel, University of Delaware. Teaching Honors Seminars Sponsored

10/18/05, 19th Annual CABM Symposium, “Stem Cells in Development and Organogenesis” 11/9/05, Dr. Mark Hochstrasser, Yale Medical School, “Ubiquitin-dependent Protein Degradation at the Nuclear Envelope” 11/16/05, Dr. Clifford J. Tabin, Harvard Medical School, “Patterning the Vertebrate Limb and Heart” 1/18/06, Dr. Dorothee Kern, Brandeis University, HHMI, “On the Move in the NMR Tube, the Crystal and the Computer: Protein Dynamics during Catalysis and Signaling” 2/8/06, Dr. Vincenzo Pirrotta, Rutgers University, “Polycomb Complexes and Epigenetic Chromatin Silencing Mechanisms” 3/22/06, Dr. Mario R. Capecchi, University of Utah, HHMI, “Gene Targeting into the 21st Century: Modeling Human Disease in the Mouse, from Cancer to Neuropsychiatric Disorders” 4/19/06, Dr. Daria Hazuda, Merck Research Laboratories, “HIV-1 Integrase Inhibitors: Basic Research to Clinical Development” 5/3/06, Dr. John Blenis, Harvard Medical School, “Regulations of Cell Growth through the Integration of Mitogenic and Nutrient Signaling Pathways” Graduate Student Committee Memberships Xi Wang, Biochemistry, Qualifying Exam Rushad Pavri, Biochemistry, Thesis Hudan Liu, Biochemistry, Thesis Xi Wang, Biochemistry, Thesis Laboratory Support Staff, Postdocs, Predocs, Visiting Scientists Mehreen Iqbal Undergraduate student

Sudipta Patel Undergraduate student Joseph Bauman Predoctoral student Chun Chu Predoctoral student Donglin Liu Postdoctoral student Administrative Committees Departmental: CABM Symposium CABM Lecture Series CABM Retreat NIH Biotechnology Training Program Retreat RWJMS Cancer Institute of New Jersey (CINJ) Internal Advisory Board and Scientific Council Child Health Institute of New Jersey (CHINJ) Advisory Board Chair, CHINJ Dedication Symposium CABM/Physiology Faculty Search Committee CABM/Biochemistry Faculty Search Committee Federal/State Appointments NIH Northeast Structural Genomics Consortium Scientific Advisory Board Spain Scientific Advisory Board Community Involvement on Behalf of University or Medical School: Howard Hughes Medical Institute Review Panel Panelist for review of NY State Center Grant Applications Rutgers Nutrition Department Chair Search Rutgers Research Advisory Board Waksman Institute Faculty A&P Committee Rutgers Proteomics Development and Building Committee Ivy Charitable Foundation Board of Directors Salzman Virology Award Selection Committee Organizing Committee-5th International Symposium on Virus Assembly Editing/Consulting Editor: Advances in Virus Research

Yufang Shi, D.V.M, Ph.D. Research Activities Mechanisms of Apoptosis in T Helper Subsets Investigating the molecular mechanisms that controls activation-induced cell death (AICD) in various T cell types has been one of the major focuses of Dr. Shi’s laboratory. Their recent efforts have been on elucidating the differences of the mechanisms that control AICD in Th1 and Th2 cells as well as Tc1 and Tc2 cells. They have shown that while Th1 cells die by the Fas-mediated caspase pathway, Th2 cells die through intracellular release of granzyme B. On the other hand, though TC1 cells, like Th1 cells, undergo AICD through Fas, AICD in Tc2 cells is mediated by TRAIL. They also found that prostaglandin E2 (PGE2) specifically protected Th2 cells from AICD by downregulating granzyme B. Thus, differences in the expression of, and susceptibility to, death effectors are a built-in mechanism that controls the Th1-Th2 as well as Tc1- Tc2 balance. One example is a more severe antigen induced asthma in granzyme B deficient mice. Identification of the function of MHC class Ib restricted CD8+ T cells. Unlike T cells restricted by major histocompatibility complex (MHC) class Ia or class II molecules, T cells restricted by MHC class Ib demonstrate properties of both innate and adaptive immunity and are therefore considered innate-like lymphocytes (ILLs). ILLs are believed to have immunoregulatory functions, but their roles in autoimmunity and defense against infections remain elusive. To study the properties of ILLs, Dr. Shi’s group generated mice expressing only MHC class Ib by crossing CIITA(-/-) with K(b-/- )D(b-/-) mice. Surprisingly, these mice developed a lymphoproliferative syndrome and autoimmunity, most notably inflammatory bowel disease (IBD) and insulitis. The CD8(+) ILLs in these mice exhibit a constitutively activated phenotype, and depletion of these cells abolished the autoimmune disorders. In addition, adoptive transfer of CD8(+) ILLs from K(b-/-)D(b-/-)CIITA(-/-) mice to Rag-1(-/-)pfn(-/-) mice also resulted in IBD and insulitis. These findings provide direct evidence that CD8(+) ILLs are sufficient to initiate and mediate autoimmune diseases. Regulation of RANKL expression in T cells The ligand for receptor-activator of NF- B (RANKL) plays a critical role in the homeostasis of bone metabolism, arthritis, immune regulation as well as cancer metastasis. They have shown that the expression of RANKL in T cells is mediated by TCR activation-induced Ca2+ mobilization. One major mechanism that regulates the expression of RANKL was found to involve the regulation of messenger RNA decay. They have demonstrated that a specific region in the 3’-end of the RANKL mRNA is critical in controlling the decay rate. They are currently investigating how TCR and PGE2 control RANKL mRNA stability in the context of autoimmune arthritis pathogenesis.

Regulation of Immunosuppression by Mesenchymal Stem Cells and Apoptotic Cells Druing this past year, Dr. Shi’s lab has been studying the mechanisms of bone marrow derived-mesenchymal stem cells in the regulation of immunosuppression. They have shown that mesenchymal stem cells have a dramatic effect on lymphocyte activation and proliferation. In vivo administration of mesenchymal stem cells was able to prevent the rejection of allogeneic skin grafts. Such an immunosuppressive effect was not innate to mesenchymal stem cells, rather it was induced by cytokines produced by lymphocytes. They are now investigating the cellular and molecular mechanisms that mediate such strong immunosuppressive effects by this specialized cell population and hope to develop new strategies for clinical applications. Dr. Shi’s group has shown that apoptotic cells can prevent heart transplant rejection. They have found that the interaction of apoptotic cell-educated dendritic cells with normal dendritic cells is crucial in mediating such a tolerigenic effect. They have recently established an in vivo system to investigate cell interactions during this tolerance induction process. In addition, they also studied the role of apoptotic cells in the immune response to tumors and with the goal of determining the effect of apoptotic cells in tolerance induction in the tumor microenvironment. Stress and the Immune System. Physical and psychological stressors have significant effects on the immune system. Their studies have shown that the reduction in lymphocyte numbers caused by chronic restraint in mice occurs through endogenous opioid-mediated Fas upregulation, which in turn mediates apoptosis. Dr. Shi’s group has recently found similar results with the mouse hindlimb unloading model, an experimental system simulating some of the deleterious effects of spaceflight. Hindlimb suspension was found to drastically deplete various cell populations in the spleen and thymus. Surprisingly, administration of opioid antagonists or interference with the Fas-FasL interaction was able to block the reduction in splenocytes, but not thymocytes. On the other hand, steroid receptor antagonists blocked lymphocyte losses in both spleen and thymus. Therefore, the effects of hindlimb suspension on the homeostasis of splenocytes and thymocytes must be exerted through distinct mechanisms. To elucidate which cells are responsible for the induction of apoptosis during hindlimb suspension, they depleted CD4+CD25+ cells and found that this treatment could protect splenocytes. In addition, mice depleted of CD4+CD25+ cells were protected from the immunosuppression caused by hindlimb suspension. Highlights of the Year In the past year, Dr. Shi has made significant progress in several areas. He has made significant advancement in the understanding of the role of granzyme B in the regulation of AICD in different T cell populations. Mice deficient in granzyme B develop more severe allergic asthma. Importantly, they have found that CD4+ T cells are solely responsible for allergen-induced asthmatic reaction. Furthermore, through genetic modifications, Dr. Shi’s group found that MHC class Ib restricted CD8+ T cells are

critical in the development of autoimmunity. They also made significant progress in the understanding of the mechanisms that regulate RANKL expression in T cells. Their new in vivo and in vitro system provided a unique opportunity to study how apoptotic cells regulate immune response. The establishment of the mesenchymal stem cell project gives Dr. Shi’s group a unique niche to using their immunology expertise to investigate the mechanisms controlling mesenchymal stem cell-mediated immunosuppression; it is also hoped that their efforts in this direction will provide new information for proper clinical application of these cells. His project on the stress response and radiation has been focused on the development of new countermeasures in response to the directional changes in NASA research. Publications Yuan, ZR, Wang, RX, Lou, XY, Zhang, LY and Shi, YF. 2005. Identification and Characterization of a Novel Cell Survival Gene Critical in Apoptosis and Tumorigenesis. Cancer Research, 65: 10716-24 Shi, YF. and Devadas A. 2006. Granulocyte Macrophage Colony Stimulating Factor (GM-CSF) and T-Cell Responses: What We Do and Don't Know. Cell Research, 16:126-33. Devadas, S. Das, J. Liu, C., Zhang, L., Roberts, A.I., Pan, Z., Moore, P., Das, G., and Shi, Y. 2006 Apoptosis Modulates the Th1/Th2 Balance: Distinct Roles for Caspases and Granzyme B. Immunity, 25:237-47 Presentations 2005, Oct. Major Symposium Presentation : Apoptosis in T helper cells. 2005 Annual Meeting of Interferon and Cytokine Research, Shanghai 2005, Oct. Plenary talk: T cell apoptosis and Immune regulation. Cytokine symposium, Taiwan Teaching Course Director, Micr 6005, Current Concepts in Immunology, Robert Wood Johnson Medical School and Rutgers University (course number: 16:681:543) Lecture on “Immunological Disorders” in the “Molecular Physiology” graduate course Lecture on “Flow cytometry” in the “Optical Microscopy and Cell Imaging” graduate course Seminars Sponsored Jim Xiang, Ph.D from the Department of Oncology and Immunology, University of Saskatchewan, Canada, Oct. 11, 2005 Doina Ganea, Ph.D., Department of Biological Sciences, Rutgers, The State University, Nov. Nov. 8, 2005 Beverly E. Barton, Ph.D, Department of Surgery/Division of Urology, UMDNJ-NJMS,

Jan. 10, 2006 Kodi Ravichandran, Ph.D., Beirne B. Carter Center for Immunology Research, University of Virginia, April 11, 2006. Graduate Student Committee Memberships Division of Life Sciences, Rutgers University, Ph.D. Committee, Kristina, Liu, 2002-2006 Division of Life Sciences, Rutgers University, Ph.D. Committee, Sabarna Kahn, 2003- 2005 Division of Life Sciences, Rutgers University, Ph.D. Committee, Hema Tirumalai, 2003- 2006 UMDNJ-RWJMS, Ph.D. Committee, Na Li, 2003-Present UMDNJ-RWJMS, Ph.D. Candidacy Lin Zheng, 2003-Present UMDNJ-RWJMS, Ph.D. Committee, Matt Simmons 2004-2004 UMDNJ-RWJMS, Ph.D. Committee, Anna Knapinska, 2004-present UMDNJ-RWJMS, Ph.D. Committee, Tanishia Williams 2003-2004 UMDNJ-RWJMS, Ph.D. Committee, Youyi Peng 2003-2005 UMDNJ-RWJMS, Ph.D. Committee, Amit Balakrishnan 2003-2006 UMDNJ-RWJMS, Ph.D. Committee, Xin Li, 2003-2006 UMDNJ-RWJMS, Ph.D. Committee, Ting Wen 2004-present Laboratory Support Staff, Postdocs, Predocs, Visiting Scientists Laboratory Support Staff Cathy Liu, M.Sc. Liying Zhang, M.D. Arthur Roberts, M.Sc. Postdocs Satish Devadas, Ph.D. Jyoti Das, Ph.D. Zeng-Rong Yuan, M.D., Ph.D. Guangwu Xu Predocs Guangwen Ren, Alison Tiske (co-supervisor) Arthur Roberts (part-time) Yingyu Zhang Kathryn Wang (co-supervisor) Jimin Zhang Summer Students Jonathan Gonzalez Rhea Chakraborty Moraima Castro

Junior Faculty Mentoring Robert Laumbach MD, MPH, CIH, Assistant Professor, Department of Environmental and Community Medicine, EOHSI Administrative Committees Departmental Director of the Flow Cytometry Facility Director of the Real-Time PCR Core RWJMS Medical Student Admission Comittee Award Nomination committee MD/Ph.D. Recruitment committee Federal/State Appointments Member, Team of Infection, Immunology and Hematology, National Space Biomedical Research Institute, NASA Community Involvement on Behalf of University or Medical School Grant review committees: Department of Defense, Molecular Genetics Peer Review Panel of the Congressionally Directed Medical Research Programs On Prostate Cancer Research Department of Defense, Molecular Biology Peer Review Panel of the Congressionally Directed Medical Research Programs On Breast Cancer Research External reviewer, Research Grant Council, Hong Kong Government Ad-hoc member, Experimental Immunology Study Section, National Institute of Health Ad-hoc member, Cellular and Molecular Immunology Study Section A, NIH Ad-hoc member, Cellular and Molecular Immunology Study Section B, NIH U.S. Civilian Research and Development Foundation, U.S. Department of State. Effect of Mesenchymal Stem Cells on Radiation Editing/Consulting Editors Editor: Cell Research Journal Editorial Boards

Member of Editorial Board: Cellular and Molecular Immunology Books Chapter 11: Chronic Stress Induces Death of Lymphocytes by E. Sun, L. Wei, A. Roberts, C. Liu and Y. Shi in Cytokines Stress and Immunity, edited by Nicholas Plotnikoff. Reviewer Journal of Immunology Proceedings of National Academy of Science Cancer Research Clinical Cancer Research Blood Brain Behavior and Immunity Cellular and Molecular Immunology Cell Death and Differentiation Brain Behavior and Immunity Experimental Hematology Cancer Gene Therapy Cell Research

Victor Stollar, M.D. Vice Chairman Research Activities The work in Dr. Stollar’s laboratory centers on Sindbis virus (Family Togaviridae, genus alphavirus), a mosquito transmitted virus. Sindbis virus(SV) encodes 4 nonstructura(ns) proteins, which together form a complex which is responsible for the replication and transcription of viral RNA. The central player in this complex is the nonstructural protein, nsP4 (610 amino acids), the viral RNA-dependent RNA polymerase (RDRP). In addition to the genomic (G) RNA, a second mRNA is made in infected cells; this is called the subgenomic (SG) RNA. Both of these viral RNAs are made off the negative-strand RNA template. In infections with wild-type (wt) virus, the SG RNA, which serves as the message for the viral structural proteins, is made in excess over the G RNA. In addition to being packaged into the progeny virions, the G RNA also serves as the message for the four ns proteins. A major interest in Dr. Stollar’s lab concerns the regulation of the synthesis of the SG RNA, and how the balance between the synthesis of G RNA and SG RNA is maintained. Some years ago, Dr. Stollar isolated a mutant of Sindbis virus, SVPZF, which is resistant to pyrazofurin (PZF) a nucleoside analog, which interferes with pyrimidine biosynthesis, and thus lowers the level of UTP and CTP in treated cells. This mutant, in contrast to the standard Sindbis virus (SVstd), is able to replicate in mosquito cells treated with PZF. Of some interest, he observed that the yield of SVPZF from these cells is increased from 20 to 50 fold in the presence of low levels of PZF, suggesting that this mutant actually replicates better in cells with low levels of UTP and CTP than in cells with normal levels of these rNTPs. This stimulatory effect of PZF on SVPZF is reversed by addition of uridine or cytidine to infected cells. Both of these nucleosides lead to an increase in the cellular levels of UTP and CTP. Thus, whereas PZF inhibits the replication of SVSTD, it stimulates the replication of SVPZF; and independent of whether PZF inhibits or stimulates the replication of virus, the effect of PZF is reversed by uridine. SVPZF has a second phenotype, i.e. it makes decreased amounts of the SG RNA, so that the ratio of SG/G RNA in infected cells is < 1. As noted above, in infections with wt virus, this ratio is >1. When PZF is added to SVpzf-infected mosquito cells, not only is the yield of virus increased, but the ratio of SG/G RNA, as measured by Northern analysis is changed from <1 to >1. Just as addition of uridine reversed the effect of PZF on the yield of SVpzf, it also reversed the effect of PZF on the SG/G RNA ratio. Thus both with respect to virus yield and the SG /G RNA ratio, SVpzf appears to “prefer” a cellular environment in which the concentrations of UTP and CTP are decreased. By titrating the effect of PZF on the yield of SVpzf, and on the SG/G RNA ratio, it should be possible to determine what is the ratio of SG/G RNA that correlates with the maximum production of virus.

To further facilitate the study of how the synthesis of SG RNA is regulated, Dr. Stollar recently established two cell-free RNA-synthesizing systems: the first makes a SG RNA, and the second makes both a G RNA and a SG RNA. These are the first such systems described for any alphavirus. The critical elements for these systems are (1) minus- strand SV RNAs which function as promoter-templates. These contain in one case only the SG promoter, and in the second case both the G and the SG promoters, and (2) A p15 fraction from cells infected with recombinant vaccinia viruses expressing the 4 Sindbis virus ns proteins. In addition to the Togaviruses, many other viruses, including many plant viruses, make subgenomic RNAs. Thus what is learned about the regulation of SG RNA synthesis in Sindbis virus-infected cells should have broad application to certain other virus families. All of this work was done together with Dr. Mei-Ling Li Highlights of the Year The demonstration that the size of the UTP and CTP pools in mosquito cells, as modified by PZF and uridine, determine not only the yield of the mutant, SVpzf, but also the ratio of SG/G RNA which is made in the SVpzf-infected cells. Thus the frequency of initiation at the SVpzf SG and G promoters may be influenced by the size of the UTP pool in the infected cells. The development of cell-free systems for the synthesis of SV RNAs. Publications Li, M-L., Lin,Y-H. and Stollar, V. (2005). A cell-free system for the synthesis of Sindbis virus subgenomic RNA: Importance of the concentration of the initiating NTP. Virology, 341: 24-33. Tsai, C.H., Lee, P.Y., Stollar, V., and Li, M.l. (2006) Antiviral therapy targeting viral polymerase. Current Pharm. Design, 12: 1339-55. Teaching Microbiology and Immunology: First year course for medical students – 3 lecture hours. Ethical Scientific Conduct, GSBS: IDST 5000 – 1 lecture hour Molecular Virology: a graduate course given in alternate years. It was given in the spring of 2006 – Co-direcgtor of the course – 3 lecture hours.

Laboratory Support Staff: Adjunct Ass’t Professor: Dr. Mei-Ling Li Administrative Committees Departmental Vice-Chairman Graduate Program in the Department of Molecular Genetics, Microbiology, and Immunology (several committees). RWJMS Chairman, New Brunswick/Piscataway Campus Committee on Research Integrity Member, Admission Committee for MD-PhD students Elected member to the RWJMS Nominations Committee UMDNJ Federal/State Appointments: None Editing/Consulting Journal Editorial Boards Member of Editorial Board, Journal of Virology, 1997-2009 Ad hoc reviewer for several other journals, including Virology

Nancy Woychik, Ph.D. Research Activities Free-living bacteria enlist a variety of mechanisms to facilitate stress survival. Toxin- antitoxin (TA) systems/modules, also referred to as suicide genes, represent one relatively new addition to the field of bacterial stress adaptation. The Escherichia coli genome appears to encode at least six chromosomal two-component TA systems that act inside the cell in a manner mechanistically distinct from the more familiar toxin proteins that are actually exotoxins exported from the cell (e.g. botulinum, anthrax or cholera toxins). However, as with the classic toxins, TA systems appear to impart a survival advantage. TA systems have recently been linked to other medically important processes such as biofilm formation, bacterial persistence after exposure to antibiotics and bacterial pathogenesis. TA systems comprise adjacent antitoxin and toxin genes within specialized operons. They encode proteins that form a stable protein complex, however, the antitoxin is labile relative to the toxin protein. Signals triggered by stress lead to a decrease in the amount of antitoxin, thus freeing up toxin to act on its intracellular target. Although the mechanisms of action for a few E. coli TA toxins have been uncovered, the intracellular targets of many other toxins have not been identified. In addition, many details regarding their physiological role during stress and how transcriptional and post- translational regulation maximizes their efficacy have yet to be elucidated. Dr. Woychik is continuing to characterize the function of families of TA modules in E. coli and Mycobacterium tuberculosis in collaboration with Masayori Inouye and his laboratory and Dr. Robert Husson at Children's Hospital/Harvard Medical School. Our laboratory is also beginning to study the role of TA toxins on bacterial pathogenesis, biofilm formation and bacterial persistence using E. coli or relevant pathogenic strains. We are also continuing to perform ectopic expression of individual bacterial TA toxins in Saccharomyces cerevisiae to both characterize their effects on yeast programmed cell death and exploit them as the foundation of novel yeast expression systems designed to express human proteins with virtually no background protein synthesis and no toxicity. Finally, the Woychik and Inouye labs are also members of the Northeast Structural Genomics Consortium (NESG) headed by Gaetano Montelione (Rutgers University) and the New York Consortium on Membrane Protein Structure (NYCOMPS) headed by Wayne Hendrickson (Columbia University). This work involves the design and optimization of novel protein expression systems in order to enhance success rates for NMR and X-ray crystal structures from selected prokaryotic and eukaryotic recombinant protein targets, including membrane proteins. Highlights of the Year Dr. Woychik’s lab has completed characterization of the function of one bacterial TA

toxin, designed Doc. Doc leads to inhibition of bacterial cell growth by specifically binding to the bacterial 30S ribosome which In turn leads to inhibition of translation elongation. We have also made considerable progress on understanding the structure and function of several other TA toxins. The crystal structure of the antitoxin HigA has been completed and deposited into the Protein Data Bank (Figure 1). The HigA structure suggests that it is a DNA binding protein, consistent with the autoregulatory role typically exhibited by antitoxins for their TA operon (in addition to their ability to bind to their cognate toxin protein). HigA structure was determined through the combined efforts of several individuals in NESG Consortium laboratories. Figure 1. Crystal structure of the antitoxin HigA homodimer (1.88 Å ; PDB accession codes 2ICP and 2ICT) Presentations Takara Bio Initiative for Innovative Biotechnology (TBIIB) Annual Retreat 4/24/06 Northeast Structural Genomics Consortium (NESG) Progress Report Meeting 3/13/06 Teaching Microbiology & Immunology for Medical and Graduate Students 16:680:544/5 (MICR 6000) Sponsored Seminars "Endothelial Cell Growth and Differentiation in Hemangioma- An Endothelial Tumor that Undergoes Spontaneous Regression" Dr. Joyce Bischoff, Harvard Medical School 3/8/05 Graduate Student Committee Memberships Megha Gandhi/Chikindas laboratory-Rutgers Food Science Program M.S. thesis defense committee member 9/21/05 Yvette Pittman/Kinzy laboratory-Ph.D. Oral Qualifier committee member 11/22/05

Amit Balakrishnan/Fan laboratory-Ph.D. Thesis Committee meeting 3/08/06 Angela Cook/Woychik laboratory-Rutgers Microbiology and Molecular Genetics M.S. thesis defense committee member 4/19/06 Lee Scozzare/ Woychik laboratory-Rutgers Cell and Developmental Biology Program M.S. thesis defense committee member 4/26/06 Ling Zhu/Inouye laboratory-Ph.D. Thesis Committee meeting 6/02/06 Laboratory Support Staff, Postdocs, Predocs, Visiting Scientists Nicholas Bauman - M.S. Student (Rutgers Microbiology and Molecular Genetics Program) Angela Cook - M.S. Student (Rutgers Microbiology and Molecular Genetics Program) Lauren DeStefano - Ph.D. Student Jennifer Hurley - Ph.D. Student Carl Kunda - Rutgers Undergraduate Student Mohan Liu - Ph.D. Student Christopher Mozdzierz - Ph.D. Student Christopher Pirozzi - Rutgers Undergraduate Student Meredith Prysak - Ph.D. Student Rohini Roy - Ph.D. Student Lee Scozzare, M.S. Student (Rutgers Cell and Developmental Biology Program)

Jared Sharp, Ph.D. Student Felicia Smith, NIH Postbaccalaureate Student Administrative Committees Departmental Co-organizer, Departmental Seminar Series Associate Director, Molecular Genetics, Microbiology & Immunology Graduate Program Faculty Recruitment Committee Website Committee Seminar Committee RWJMS Research Committee University Executive Council, UMDNJ-GSBS Recruitment Committee, Molecular Biosciences Graduate Program Curriculum Committee, Graduate Program in Molecular Genetics & Microbiology Community Involvement on Behalf of University Medical School Basic Research Advisory Group, New Jersey Commission on Cancer Research Editing/Consulting Editorial Board Molecular and Cellular Biology Ad hoc Reviewer Genes & Development Genetics Nature Structural Biology Nucleic Acids Research Editing/Consulting Editorial Board, Molecular and Cellular Biology Ad hoc Reviewer FEMS Microbiology Letters Journal of Cell Science Genes & Development Molecular Microbiology

Brief Research Interests Joint, Adjunct & Volunteer Faculty

Sefik S. Alkan, Ph.D. Research Activities This year we worked on the modulation Toll-like receptors (TLR) 7 and TLR 8 mediated responses by Oligodeoxynucleotides (ODNs). It is known that among the 11 human Toll-Like receptors (TLR) a subfamily TLR7, -8 and -9 display similarities in structure and endosomal localization. Natural agonists consisting of nucleic acids such as ssRNA or DNA with CpG motifs, activate the innate immune cells through these TLRs. Immune response modifiers (IRMs) of imidazoquinoline class compounds 3M-001, -2 and -3, have been shown to activate the innate immune system via TLR7, 8 and 7/8, respectively. In looking at the effect of the agonists of the TLR7, 8 and 9 on the activation of NFkB of transfected HEK cells, we discovered that some oligodeoxynucleotides (ODNs) could modulate imidazoquinoline effects in a negative or positive manner. We demonstrate that polyT ODNs can inhibit TLR7 and enhance TLR8 signaling events involving NFkB activation in HEK cells and cytokine production (IFN-a, TNF and IL-12) by human primary peripheral blood mononuclear cells. On the other hand, TLR3 agonist polyI:C did not affect imidazoquinoline-induced responses. The modulation of TLR7 and -8 responses was independent of CpG motifs or the nature of the ODN’s backbone structure. Furthermore, we showed that in order to be an effective modulator, the ODNs needed to be in the cell at the same time with either of the TLR7 or -8 agonist. We have also demonstrated that there is a physical interaction between IRMs and ODNs. We think that the cross talk between ODNs, IRMs and TLR7 and -8 uncovered by this study may have practical implications in the field of microbial infections, vaccination and tumor therapy. (Manuscripts describing the above work by Gorden et al. is now in press, J. Immunol.) Initiated Academic Collaborations (on Toll-like receptor and Immune response modifier-IRM): Minnesota Univ. IRM/Salmonella infection/Vaccination (Prof. M. Jenkins) Emory Univ. Vaccine center: IRM/HIV Vaccination (Prof. B. Pulendran) Vanderbilt Univ. IRM/HIV infection. (Prof. D. Unutmaz) Denver Univ. IRM-Antigen conjugates for vaccination (Prof. R. Kedl) UMDNJ (Univ.Med&Dent. of New Jersey): IRM/IFN subsets (Prof. S. Kotenko) Univ. Zurich, SIAF, Davos: IRM/Allergy (Prof. C. Akdis) NIH: IRM-HIV/antigen-conjugates/Tuberculosis vaccines (Prof. B. Seder) UT, MD Anderson: IRM-Ab conjugates for melanoma therapy (Prof. W. Overwijk) UT, MD Anderson: IRM-Ab conjugates for lymphoma therapy (Prof. L. Kwak)

Rockefeller Univ. IRM-mAb conjugates/malaria vaccines (Prof. M. Nussenzweig) Harvard Univ. Effects of IRMs T-reg cells in asthma (Prof. D. Umetsu) Publications Kevin S. Gorski, Emily L. Waller, Jacqueline Bjorton-Severson, Jeffrey S. Miller, John P. Vasilakos and Sefik S. Alkan. Distinct Indirect Pathways Govern Human NK-cell Activation by TLR-7 and TLR-8 Agonists. International. Immunol. 18(7): 1115- 26, 2006. Troy Querec, Soumaya Bennouna, Sefik Alkan, Yasmina Laouar, Keith Gorden, Richard Flavell, Shizuo Akira, Rafi Ahmed, Bali Pulendran. Yellow fever vaccine YF17D activates multiple dendritic cell subsets via TLR2, 7,8 and 9 to stimulate polyvalent immunity. J Exp Med. 203(2): 413-24, 2006. Cao, W, Chen Y, Alkan S, Subramaniam, A, Long F, Liu, H, Diao, R, Delohery, T, McCormic, J, Chen, R, Ni, D, Wright, P, Zhang, X, Busch, S, Zilberstein A.: Human T helper cell lineage commitment is not directly linked to the secretion of Th cells isolated by FACS based on IFN-g and IL-4 secretion. Eur. J. immunol. 35:2709-2717, 2005 Keith Gorden, Kevin S. Gorski, Sheila J. Gibson, Ross M. Kedl, William C. Kieper, Xiaohong Qiu, and Mark A. Tomai, Sefik S. Alkan, and John P. Vasilakos. Synthetic TLR Agonists Reveal Functional Differences Between Human TLR7 and TLR8, J. Immunol., 174:1259 – 1268, 2005. Presentation Abstract/posters presented: Gorski, K. Emily L. Waller, Jacqueline Bjorton-Severson, Jeffrey S. Miller, John P. Vasilakos and Sefik S. Alkan. Distinct Indirect Pathways Govern Human NK-cell Activation by TLR-7 and TLR-8 Agonists. Annual meeting of The American Association of Immunologists, Boston, May 12-16, 2006. Birmachu, W. J. Hanten, Alkan, SS et al. Gene/protein expression of highly purified human B cells in response to TLR7, TLR8 and TLR9 agonists. Annual meeting of The American Association of Immunologists, Boston, May 12-16, 2006. Alkan SS. et al. Oligodeoxynucleotides (ODNs) Modulate Activation of TLR7 and 8 by Imidazoquinolines, Annual meeting of The American Association of Immunologists, Boston, May 12-16, 2006.

Invited Speaker: Title: Immunity United: The Toll Bridges Between the Innate and Adaptive Immunities. Adnan Menderes Univ. 18. National Biology Congress, Kusadasi, Turkey, June 28, 2006. Title: Potential use of TLR7 and 8 agonists in vaccination and tumor therapy. MD Anderson cancer center, Univ. Texas, Houston, TX. June 13-15, 2006. Title: TLR7 and TLR8 Agonists: Their use in vaccination and tumor therapy. Rockefeller University, NY, April 21, 2006. Title: TLR7 and TLR8 Agonists: How do they work and how can we use them for vaccination and tumor therapy. UMDNJ, Newark, April 20, 2006. Title: Exploring the role of TLR7/8 agonists in connecting innate and adaptive immunities as a strategy for vaccination & tumor therapy, University of Minnesota, MN, Jan 23, 2006. Title: Utility of novel TLR7/8 and 9 agonists in connecting innate and adaptive immunities as a strategy for vaccination and tumor therapy. Aegean Conferences: Crossroads between Innate and Adaptive Immunity, Rhodes, Greece. Oct 9-14, 2005. Title: Utility of Immune Response Modifiers (TLR7/8) in Cancer Therapy, 7th Annual Sabin Colloquium on Cancer Vaccines and Immunotherapy, Cold Spring Harbor Laboratory Genome Center, Woodbury, Long Island, NY June 21-24, 2005. Honors Proposed and received a Genesis Grant on IRM-mAb targeting for tumor therapy (~$100,000.00). Eddy Arnold, Ph.D. Research Activities Drs. Eddy and Gail Ferstandig Arnold and their colleagues are working to develop and apply structure-based drug and vaccine designs for the treatment and prevention of serious human diseases. In pursuit of these goals, their laboratory takes advantage of cutting-edge research tools, including X-ray crystallography, molecular biology, virology, protein biochemistry, and macromolecular engineering. The approaches being developed in the Arnold laboratory are broadly applicable to a wide array of human health problems, ranging from infectious diseases to cancer and diseases caused by hereditary genetic defects. Much of the Arnold lab’s research effort to date has focused on the development of drugs and vaccines for the treatment of AIDS. Examples of the results of these studies include: 1) collaborative development of potential drugs for the treatment of AIDS, some of which may be more effective than

treatments in current use; and 2) production of AIDS vaccine candidates that have elicited protective immune responses against HIV. Dr. Arnold studies reverse transcriptase (RT), which is an essential component of the AIDS virus and the target of many of the most widely used anti-AIDS drugs. Using the techniques of X-ray crystallography, his team has solved the three-dimensional structures of HIV-1 RT in complex with antiviral drugs and pieces of the HIV genome. These studies have illuminated the working of an intricate and fascinating biological machine in atom-by-atom detail and have yielded numerous novel insights into polymerase structure-function relationships, detailed mechanisms of drug resistance, and structure-based design of RT inhibitors. Synthesis of the information being developed has led to the development of inhibitors that show great promise as potential treatments for AIDS. Another major project in his laboratory, co-directed by Dr. Gail Ferstandig Arnold, consists of engineering of a human common cold virus, rhinovirus, to display appropriate segments from more dangerous pathogens for the purpose of developing vaccines against these pathogens. This work involves generating large numbers of chimeric human rhinoviruses using a technique called random systematic mutagenesis. With this method, the foreign sequences are linked to the HRV sequences via adapters of randomized sequences and lengths, leading to a large array of presentations. Large sets of such viruses are generated and selected to optimize the isolation of vaccine candidates with the most effectively reconstructed foreign segments. Constructs have been made that elicit antibodies (in guinea pigs) capable of potently neutralizing the AIDS virus in cell culture. His team is also analyzing the structures of some of the engineered viruses using X-ray crystallography, with the long-term objectives of determining three-dimensional correlates of immunogenicity and developing a structural basis for design of more effective human vaccines. The Arnold group will continue to study medically important problems using basic scientific tools and approaches. In addition to potentially developing novel vaccines and chemotherapeutic agents, the laboratory aims to gain greater insights into the basic molecular processes of living systems. Teaching Chemistry 492, Spring 2005 Senior Seminar in Chemistry: “Scientific Communication”, 15 students Chemistry 491, Fall 2005 Senior Seminar in Chemistry: “Scientific Communication”, 15 students

Publications Tuske, S., S.G. Sarafianos, X. Wang, B. Hudson, E. Sineva, J. Mukhopadhyay, J. J. Birktoft, O. Leroy, S. Ismail, A.D. Clark, Jr., C. Dharia, A. Napoli, O. Laptenko, J. Lee, S. Borokhov, R. Ebright, and E.Arnold. 2005. Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell. 122:541-552. Oren, D.A., and E. Arnold. 2005. Viruses rock and roll with their receptors. Structure. 13:944-945. Himmel, D., K. Das, A.D. Clark, Jr., S.H. Hughes, A. Benjahad, S. Omoche, J. Guillemont, S. Coupa, A. Poncelet, I. Csoka, C. Meyer, K. Andries, C.H. Nguyen, D.S. Grierson, and E. Arnold. 2005. Crystal structures for HIV-1 reverse transcriptase in complexes with three pyridinone derivatives: A new class of non- nucleoside inhibitors effective against a broad range of drug-resistant strains. J. Med. Chem. 48:7582-7591. Honors Invited Speaker, 5th HIV Drug Resistance Program Symposium on Antiviral Drug Resistance, Chantilly, VA, 2004 Invited Faculty Member and Speaker, HIV DART 2004: Frontiers in Drug Development for Antiretroviral Therapies, Montego Bay, Jamaica, 2004 Primary Speaker, Johnson and Johnson 4th International Symposium on Drug Discovery, Antwerp, Belgium, 2005 Service Administrative Committees Member, Rutgers University Faculty of Arts and Sciences Structural Bioinformatics Council, 1998-present Co-organizer, “Protein Structure, Function, and Disease” at CABM, Piscataway, NJ, 2004 Member, Public Affairs Committee, Biophysical Society, 2002-2005 Member, The Cancer Institute of New Jersey, 1995-present Expert Witness, Promega Corporation, 1995-present Member of the MacCHESS Advisory Panel, 1992-present Reviewer of proposals to use radiation at the Cornell High Energy Synchrotron Source (CHESS), 1990-present Editing/Consulting Consultant, Wyeth Research Laboratories, 2002-present Consultant, Gilead Sciences, 1997-present

David Beck, Ph.D. Dr. David Beck is the principal of BioScience Consulting, Inc. In that capacity, he is active in private consulting to biotechnology investment managers, consulting in research administration, and lecturing to the public on stem cell biology. For part of the year, Dr. Beck served as a Commissioner on the New Jersey Commission on Science and Technology, a member of the Boards of Directors of the New Jersey Association of Biomedical Research, the New Jersey Technology Council, Chamber of Commerce of Southern New Jersey, and on the Advisory Committee of the Burlington County College Program in Biotechnology. For part of the year, her also served on the UMDNJ President’s Strategic Planning Committee. Dr. Beck has established a vineyard in the Willamette Valley of Oregon where he is applying his scientific background to the culture of winegrapes using sustainable farming practices. C. Thomas Caskey, M.D. Dr. Caskey is the founding director of Houston-based Cogene Biotech Ventures and Cogene Ventures, venture capital funds supporting early-stage biotechnology and life sciences companies. The Cogene Biotech Ventures fund, founded in March 2000, invests in companies that utilize genome technology to enable drug discovery in high growth therapeutic specialties such as cancer, neurology and the metabolic diseases of obesity and diabetes. He served as President of the Texas Academy of Medicine, Engineering, and Science until Jan of 05 and is a member of the Scientific Advisory Board of the Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases (IMM), part of The University of Texas Health Science Center at Houston. Dr. Caskey serves on Texas Governor Rick Perry’s Council on Science and Biotechnology, which makes funding recommendations for the $200 million Texas Emerging Technology Fund. Chiann-Chyi Chen, Ph.D. Research Activities Gene therapy based treatment of Experimental Autoimmune Encephalomyelitis (EAE). These studies are based on the induction of specific T cell tolerance to encephalitogenic determinants of various myelin proteins. This is achieved by

expressing a synthetic gene encoding for the encephalitogenic determinant in resting B cells. Gene transfer is mediated by retroviral vectors expressing a chimeric gene which also contains lysosomal targeting sequence to facilitate association with MHC class II presentation pathway. Protection from EAE induction and disease progression were shown in both experimental and spontaneous models of EAE. Hematopoiesis. These studies are focused on understanding the developmental pathway of the myeloid and lymphoid lineages. Contrary to the prevailing dogma, we have shown that long-lived, myeloid-committed stem cells exist in spleen and these cells can replenish the myeloid lineage for the life span of the mouse. Lymphopoiesis is studied in animals reconstituted with bone marrow cells lacking the ability to generate part or all of the lymphoid compartment. In these studies it was demonstrated that host stem cells can selectively reconstitute missing lymphoid lineages in irradiation bone marrow chimeras suggesting that contrary to the accepted dogma, a feedback between the mature lymphoid population and lymphoid-committed stem cells does exist and missing lymphoid lineages can dictate their own reconstitution. Publications Chen CC, Ron Y. Curr Pharm Des. 2006;12(11):1391-401. New strategies for immune- mediated anti-viral drug and vaccine development. Graham Cleaves, Ph.D. Workshops Conducted for teachers on how to teach AP Environmental Science. Service N.J. Junior Academy of Science – Coordinated the organization and publication of the Junior Academy Abstracts for the 2005 Annual Meeting N.J. Academy of Science – member of the Steering Committee Editing/Consulting Editor – Cell Research

Ellen C. Ebert, M.D. Research Activities Patients with ulcerative colitis develop antibodies against hTM5, a cytoskeletal protein found in all eukaryotic cells. We find that serum from patients with UC destroy the epithelial lining of autologous colon (obtained by biopsy during colonoscopy) and cause deposition of complement components. This effect is reduced by preincubating the sera with hTM5. We hypothesize that antibodies directed against hTM5 bind and destroy colonic epithelial cells in these patients through complement-mediated lysis. Teaching Undergraduate teaching activities: I organized the second-year medical student teaching. This involved scheduling attendings for lectures and small groups, mailing out chapters of Cecil to each attending, and reminding them of their responsibilities. I taught the second year medical student Pathophysiology lecture on the Stomach and Duodenum. Postgraduate Education: I gave the following lectures to the fellows: 1. Abnormal LFTs, 2. Esophageal motility disorders; 3. Hepatitis B; 4. GI complications of diabetes; 5. Diarrhea. I attended a CPC and several morning report sessions. I aided a resident in her lecture on lower GI bleeding. I organized the schedule for attendings to oversee lectures prepared by housestaff. Publications Abstracts: EC Ebert, X Geng, J Lin, KM Das. Sera from active ulcerative colitis contain IgG antibodies against human tropomyosin isoform 5 (hTM5) that kills normal colonic epithelial cells through antibody andd complement lysis. Presented at the AGA 2006. A. Panja, E.C. Ebert. Crosstalk between intraepithelial lymphocytes and epithelial cells increases IL-8 production through the CD2-CD58 interaction with regulation by interferon γ. Presented at the AGA 2006. E.C. Ebert. Human intestinal intraepithelial lymphocytes carry out fas ligand-mediated spontaneous cytotoxicity of epithelial cell tumors through NKG2D. Presented at the AGA 2006. Manuscripts

E. C. Ebert. IL-15 converts human intestinal intraepithelial lymphocytes to CD94+ producers of IFNγ and IL-10, the latter promoting fas ligand-mediated cytotoxicity. Immunology 115:118-126, 2005. E.C. Ebert, V Mehta, KM Das. Activation antigens on colonic T cells in inflammatory bowel disease: effects of IL-10. Clin Exp Immunol 140:157-165, 2005. E.C. Ebert. Endogenous inhibitory cytokines repress TNFα secretion. Cell Immunol 237:106-114, 2005. E.C. Ebert CD2 activation of human lamina propria lymphocytes reduces CD3 responsiveness. Immunol 117:71-77, 2005. E.C. Ebert. Gastrointestinal complications of diabetes. Disease-a-Month 51:620-663. E.C. Ebert. Esophageal disease in scleroderma. J Clin Gastroenterol (in press) E.C. Ebert. Hypoxic liver disease. Mayo Clinic Proceedings (in press) E. C. Ebert. Intraepithelial lymphocytes keep TNFα levels low by cell uptake and feedback inhibition of transcription. Cellular Immunology (in press). Presentations Three abstracts were presented at the national GI meeting (American Gastroenterological Association) in May 2006 Administrative Committees Departmental RWJMS: Charity care committee Editing/Consulting Reviewer for Gastroenterology, Immunology, Clinical Experimental Immunology. Evelyn S. Erenrich Grants and Awards 1. Awarded $100,000 from the Rutgers University Academic Excellence Fund (AEF) for her proposal, “Excellence and Diversity at the Graduate School – Expanding Our Reach.” The funds will be used to grow the RISE (Research In Science and Engineering) at Rutgers/UMDNJ summer program. RISE, co-directed by Dr. Erenrich and Dr. Jerome Langer, has been highly successful in preparing students for graduate studies and has become the single most productive source of successful diversity applicants to our Ph.D. programs. Dr. Erenrich will serve as the Lead Project Director for implementation of the AEF grant. 2. Awarded $29,786 from the Federation of American Societies for Experimental Biology (FASEB) for direct support of participants in RISE.

3. The Northeast Alliance for Graduate Education and the Professoriate (NEAGEP), a consortium award from the National Science Foundation - Our campus received $132,500 for the period March 1, 2006 – Feb. 28, 2007 under a subcontract. The Alliance supports students in the joint Rutgers-UMDNJ programs. Assistant Dean Evelyn S. Erenrich serves as Program Director for the subcontract. 4. Facilitated student travel awards to the Annual Biomedical Research Conference for Minority Students (ABRCMS), totaling $4000. 5. Facilitated travel awards for 2 graduate students to the Institute for Teaching and Mentoring, sponsored by the Compact for Faculty Diversity. Other Achievements/Activities 1. Implemented post-baccalaureate research model by recruiting college senior Felicia Smith from the University of Florida for a year of NIH-funded research on this campus. Ms. Smith worked in the laboratory of Dr. Nancy Woychik from August 2005 – June 2006, supported by a supplement to an NIH research grant. Ms. Smith was accepted to the Molecular Biosciences Graduate Program and enrolled in fall 2006. This lays the foundation for submission of a formal NIH- funded post-baccalaureate program (PREP) here. 2. Launched articulated MS/PhD program in physical sciences/engineering, appointing first Fellow from the joint UMDNJ-Rutgers Graduate Program in Biomedical Engineering. This new Bridge is funded through the grant from the NSF Northeast Alliance for Graduate Education & the Professoriate. The Bridge model was piloted successfully in Molecular Biosciences (through grants from NIH NIGMS, Michael Leibowitz, MD, PhD, PI). 3. Led planning for and interviews with visiting reporter from The Chronicle of Higher Education, who prominently featured our RISE summer research program in an article in the January 26,2006 on-line Chronicle of Higher Education, “As Colleges Open Race-Exclusive Programs to All, Some Minority Students May Be Left Out in the Cold.” 4. Served on the RWJMS Strategic Planning Committee, Promoting Diversity Subcommittee. 5. Chaired Molecular Biosciences Admissions Committee Diversity Subcommittee. 6. Led team of graduate students to the third annual Northeast Science Days at Pennsylvania State University (May 2006). 7. Recognized by Joint Molecular Biosciences Graduate Student Association for “dedication and commitment to the graduate students.” Presentations and Invited Talks: 1. Invited speaker and panelist at Morgan State University, "Applying to Graduate and Professional School,” September 2005. 2. Invited to 2nd annual "Biomedical Engineering Partnership Meeting," sponsored by the Medical Products Division of W. L. Gore in Flagstaff, Arizona. Dr. Erenrich

was joined by postdoctoral fellow Dr. Sharonda Meade and graduate student Charles Florek from the Rutgers/UMDNJ New Jersey Center for Biomaterials. 3. Presented overview of our campus to University of Puerto Rico top administration, showcasing key programmatic strengths, (Mayaguez, PR, February 2006). On-Campus Invited Talks 1. “Graduate School in the Sciences, Math, and Engineering,” presented to TRiO/Student Support Services Program, April 2006. 2. “Research Opportunities in the Sciences, Math, and Engineering), presented at annual Northeast Alliance and Partners meeting, Pennsylvania State University, May 2006. Recruitment 1. Conferences a. Annual Biomedical Research Conference for Minority Students (ABRCMS), November 2005 2. Campus Visits a. Morgan State Univ, September 2005 b. Puerto Rico – 8 colleges and universities, November 2005 Arthur M. Felix, Ph.D. Research Activities Synthesis of di- and tri-pegylating reagents to be used for conjugation to peptides and proteins Synthesis of novel pegylated derivatives of salicylic acid Teaching Courses taught (fall’05) Ramapo College of New Jersey SCHM 210.01 (Organic Chemistry I) SCHM 210.02 (Organic Chemistry I) SCHM 210.03 (Organic Chemistry 1) SCHM 425.01 (Biochemistry) Courses taught (spring’06) Ramapo College of New Jersey SCHM 212.01 (Organic Chemistry II) SCHM 212.02 (Organic Chemistry II) SCHM 426.01 (Experimental Biochemistry Laboratory) Presentations

B. Casey and A.M. Felix. “Synthesis of Novel di- and tri-Pegylating Reagents.” 54th Annual Undergraduate Research Symposium, St. John’s University; April, 2006(1,2). Sponsored by New York Section of American Chemical Society. A.A. Aggrey and A.M. Felix. “Site-Specific Pegylation of Acetylsalicylic acid and Derivatives.” 54th Annual Undergraduate Research Symposium, St. John’s University; April, 2006(1,2). Sponsored by New York Section of American Chemical Society. . Service – At Ramapo College Convener: Department of Chemistry (Ramapo College of NJ) Member: Research Honors Committee ((Ramapo College of NJ) Journal Referee: Biochemical Journal Organic Preparations and Procedures International Biochemistry Journal of Chemical Technology and Biotechnology Editing/Consulting Journal Editorial Boards Peptide Science Journal of Peptide Research Janusz J. Godyn, MD Research Activities To establish and maintain academic clinical services in community settings. Dr. Godyn has developed a remarkable program of academic pathology and laboratory medicine services at three community hospitals and several community laboratories. In these community hospitals, RWJ faculty members under Dr. Godyn’s mentorship provide leadership of Performance Improvement Committee and Tissue & Transfusion Committee, and significant input to Infection Control Committees, Cancer Committees, Bylaws Committee, Nominating Committee and Credentials Committees. Participation in Medical Executive Committees in all the three community hospitals has been a part of the community service process.

Teaching Continuing Medical Education, AMA Category A1 programs at RWJUH-Hamilton and Bayshore Community Hospital, has been highly rated by practicing physician participants from Mercer, Burlington, Monmouth and Ocean Counties: “Colitis with Bloody Diarrhea” RWJUHH 9/2005 Bayshore 9/2005 “TNM Staging” RWJUHH 11/2005 Bayshore 12/2005 “Anemia – The Diagnostic Differential” RWJUHH 2/2006 Bayshore 2/2006 “Infectious Diseases of the Esophagus & Stomach” RWJUHH 4/2006 Bayshore 5/2006 “Reactive Leukocytosis” RWJUHH 5/2006 Bayshore 6/2006 Microbiology Course for Sophomore Medical Students, Department of Molecular Genetics, Microbiology and Immunology, RWJMS, March 2006: “Anthrax, a review illustrated by clinical cases” Mentoring the faculty members as laboratory directors: three directorships of hospital laboratories, additional four directorships of free-standing laboratories, three directorships of blood bank & transfusion medicine, and five associate directorships. Medical Technology Program, Mercer County Community College, student rotations at RWJUH at Hamilton Medical Technology Program, UMDNJ, student rotations at Bayshore Community Hospital. Participation in Clinical-Pathologic conferences, Tumor Boards, and consultations on clinical/pathological issues for community physicians. Publications Godyn JJ, Hazra A, Gulli V. Subperitoneal placenta accreta succenturiate in a case of the successful near-term extrauterine abdominal pregnancy. Human Pathology 2005; 36:922-926. Godyn JJ. Laboratory Quality Pillars at Baldrige-winning Hospital. Leadership Outlook. Advance for Administrators of the Laboratory. 2005; 14:16. Siderits R, Dikon, A, 0uattara O, Godyn, JJ. Preparation and use of a Scabies skin scraping kit. Advances in Skin & Wound Care 2006; 19:22-25. Hazra A, Siderits R, Godyn JJ. Hypereosinophilic syndrome associated with cervical squamous cell carcinoma. The Female Patient 2006; 31:32-34.

Siderits RH, Godyn JJ, Tufankjian D, Ouattara O. T-cell lymphoproliferative disorder of hand-mirror cell morphology presenting in an eosinophilic loculated peritoneal effusion with omental caking. CytoJournal 2006; 3:13-16. Hazra A, Ricart C, Godyn JJ. Clinical significance of Helicobacter heilmanni colonizing human gastric antrum. Practical Gastroenterology 2006; XXX (2):47-50. Accepted for publication/presentation: Godyn JJ, Linder ES, Godyn JD, Siderits R. Failure of the CAP Category I-III Prognostic Factors for predicting an individual recurrence of prostate adenocarcinoma in a five-year follow-up of the post-prostatectomy patients in a community hospital. (abstract) accepted for publication Arch Pathol Lab Med 2006. Accepted for presentation at the annual meeting of the College of American Pathologists, September 2006 Siderits R., Hanna I., Baig Z., Godyn JJ. Localized ganglioneuromatosis of esophago- gastric junction in a patient with intestinal metaplasia and non-specific motility disorder. World Journal of Gastroenterology 2006. Godyn JJ, Siderits R, Stallone C. Constructive Analogy: An allegorical story for explaining the AJCC-TNM staging system to cancer patients. (abstract) accepted for publication Journal for Cancer Education 2006. Accepted for presentation at the annual meeting of American Association for Cancer Education, October 2006. Invited Presentations: Narutowicz City Specialty Hospital, Krakow, Poland, November 2005: “Fetal Pathology with Elevated Maternal Serum Alpha-Fetoprotein” Carolinas HealthCare System (bi-state multi-hospital group), Charlotte, North Carolina, December 2005: “Quality in Health Care” (presentation related to Malcom Baldrige National Quality Award received by RWJUH-Hamilton) The College of American Pathologists - Laboratory Accreditation Program Inspector Training Seminar for Mid-Atlantic Region, March 2006: “Laboratory General - Computers, Personnel, QI, Competency, Specimen Collection, Specimen Handling and Specimen Transport” “Laboratory General - in Reproductive Laboratory Accreditation Program” 6. Service: Chairman, Department of Pathology, Robert Wood Johnson University Hospital at Hamilton Chairman, Department of Pathology, Bayshore Community Hospital at Holmdel Chairman, Department of Pathology & Laboratory Medicine, Southern Ocean County Hospital at Manahwakin

Laboratory Director, Cancer Institute of New Jersey at Hamilton 7. Administrative Committees: Board of Directors, RWJ Health Network Physician Coordinating Council, RWJ Health Network Strategic Business Development and Planning Committee, UMG Professional Affairs Com., Board of Trustees, RWJ Hamilton Quality Oversight Com., Board of Trustees, RWJ Hamilton Medical Executive Com., RWJ Hamilton Performance Improvement Com., RWJ Hamilton, - Chairman Cancer Com, RWJ Hamilton Infection Control Com, RWJ Hamilton CME and Library Com, RWJ Hamilton, Medical Quality Council, RWJ Hamilton Peer Review Com (B), RWJ Hamilton Transfusion Com, RWJ Hamilton Institute for Excellence, RWJ Hamilton Bylaws Com. RWJ Hamilton Medical Executive Com, Bayshore Hospital. Credentials Com, Bayshore H. PI Com, Bayshore H. Cancer Com, Bayshore H. Infection Control Com, Bayshore H. Tissue & Transfusion Com, Bayshore H. Quality Oversight Com. Bayshore H. Nominating Com, Bayshore H. Medical Executive Com, Southern Ocean County Hospital Credentials Com, Southern Ocean County Hospital – Past Chairman Advisory Committee for Medical Technology Program, Mercer County Community College Inspector for the College of American Pathologists

Suhayl Dhib-Jalbut, MD Research Activities Therapeutic mechanisms of Interferon-ß and Copolymer-I in Multiple Sclerosis, Interferon-ß gene therapy in an animal model of multiple sclerosis Predictors of clinical response to Glatiramer acetate in MS. Laboratory Surrogate Markers of Clinical Response to Glatiramer Acetate (Copaxone) in Multiple Sclerosis Cooperative effects of IL-4 and Glatiramer Acetate on Th2 responses in MS. Teaching Neurology clerkship for 3rd year medical students Physical Diagnosis for medical students Bedside teaching of neurology residents Publications Dhib-Jalbut, S. Immunomodulation and the basis for multiple sclerosis therapy. International Journal of MS care. V7: No. 4:4-8, 2006. Dhib-Jalbut, S et al. Neuroprotective strategies in multiple sclerosis. J. Neuroimmunol. In press, 2006. Valenzuela R, Rus H, Ito K, Dhib-Jalbut S. Modulation of IL-18 and Caspase-1 expression correlates with the clinical response to Glatiramer Acetate in Multiple Sclerosis. Neurology 66 (Suppl 2), page A175, 2006. Edited a special issue on “B-cell immunity in MS” for the Journal of Neuroimmunology. Presentation Invited speaker: Symposium on The role of T-cells in pathological and clinical events in multiple sclerosis. Sponsored by Carolinas Health Care System. Sep. 9-11, 2005. Invited speaker. The 20th annual meeting of the European Committee for treatment and research in MS (ECTRIMS) and The 10th annual meeting of the Americas Committee for treatment and research in MS (ACTRIMS). Greece, Sep 28-Oct. 1, 2005. Invited speaker. Multiple Sclerosis: Advancement in management program. Sponsored by the University of Maryland office of Graduate and continuing medical

education. October 14-15, 2005. Invited speaker. Northern New England Neuroimmunology symposium. Sponsored by the University of Vermont and Dartmouth College. New Hampshire, Oct 22-23, 2005. Invited speaker and section moderator. Internal Medicine Update. Sponsored by UMDNJ-RWJMS. Atlantic City, NJ Oct 28-29. Neurology Grand Rounds speaker. University of Pittsburgh. November 9, 2005. Neurology Grand Rounds speaker. Stonybrook Medical Center, NY. Nov 1, 2005. Invited speaker. Johns Hopkins University Neuroimmunology Seminar Series. Nov 29, 2005. Neurology Visiting Professor and Grand Rounds speaker. University of Michigan. Nov 30, 2005. Keynote Speaker. Latin America 3rd Annual Symposium on Multiple Sclerosis (LATM). Cancun, Mexico, March 17, 2006. Session Chair, Multiple Sclerosis: Immunology. The 58th Annual Meeting of the American Academy of Neurology. San Diego, CA, April 6, 2006. Honors National Multiple Sclerosis Society, Mid-Jersey Chapter 2005 volunteer Award. Service 1997-current: NIH/NINDS Performance and Safety Monitoring Board, Regular member. Steering Committee: The Americas Committee for treatment and research in MS (ACTRIMS). Scientific Committee: The 20th annual meeting of the European Committee for treatment and research in MS (ECTRIMS) and The 10th annual meeting of the Americas Committee for treatment and research in MS (ACTRIMS). Greece, Sep 28-Oct. 1, 2005. National MS Society Mid-Jersey Chapter Board of Trustees Administrative Committees 2004-2006 Chair; University Medical Group (UMG) Finance Committee, Robert Wood Johnson Medical School (RWJMS) 2004-2006 University Medical Group-RWJ Strategic Planning Committee 2003-Current University Medical Group Board of Governors, RWJMS 2003-Current University Medical Group Operation Committee, RWJMS

2003-Current University Medical Group Executive Committee, RWJMS 2003-Current RWJUH Medical Board 2003-Current Board of Directors Professional Affairs Committee 2004-Current Task Force on Education Committee-RWJMS 2004-2006 Board Member, Neuroscience Product Line, Robert Wood Johnson Medical School 2005-2006 Chair, Search Committee for Chair of the Department of Family Medicine at RWJMS. 2006-current Member, Managed Care Coordination Committee. 2005-current Charity care committee Editing/Consulting Associate Editor for The Journal of Neuroimmunology; 2003-current Adhoc reviewer for several neurological and immunological journals Edmund C. Lattime, Ph.D. Research Activities Dr. Lattime¹s research focuses on the development of rationally designed immunotherapeutic strategies for the therapy of solid tumors. In particular, his laboratory focuses on modulating the tumor-host interface through the use of vaccines as well as local gene transfer with the goal of manipulating basic immune mechanisms towards the development of systemic cell-mediated antitumor immune responses. Through the use of murine models, Dr. Lattime’s lab in the last year has furthered his studies into major mechanisms of tumor escape from immune recognition (cytokine-mediated suppression of dendritic cell function) and developed a series of new gene based therapeutics for evaluation. Clinically, his laboratory has developed a protocol which was approved and funded by the NCI Cancer Therapeutics Evaluation Program (CTEP) involving the use of recombinant poxvirus given into the bladder in patients prior to cystectomy. In its first 6 mos., the trial accrued 6 pts and is continuing to accrue. This is an interdisciplinary project involving members of the Department of Surgery, the Department of Medicine, The Department of Pathology, and the School of Public Health. Teaching Phar-5581, Genomics in Cancer Therapeutics Lecture: Molecular Immunology, 2 contact hours UMDNJ-RWJMS Surgical Grand Rounds 9/2005 “Gene Therapy for Solid Tumors: Targeting Immune Escape Mechanisms”

UMDNJ-RWJMS Urology Grand Rounds 4/2006 “Gene Therapy for Solid Tumors: Targeting Immune Escape Mechanisms” Student research projects supervised: Emmanuel Gabriel, MD/PhD Student “ Regulation of Immunity to Tumors: Elucidating Tumor-Escape Mechanisms” Amal Mansour, M.D., Ph.D. Postdoctoral Fellow “Immunological effects of Intravesical Gene Therapy in Patients with Bladder Cancer” Presentations Eastern Cooperative Oncology Group: Organized and Chaired Symposium “Immunotherapy of Prostate Cancer” Dr. Lattime planned and chaired the Second Annual New Jersey Governor’s Conference on Effective Partnering in Cancer Research. The meeting was attended by national leaders in translational research from the NIH, NCI, FDA etc. and included a keynote address from Governor James McGreevey. Publications Peer Reviewed DiPaola, R., Plante, M., Kaufman, H., Petrylak, D., Israeli, R., Lattime, E., Manson, K., Schuetz, T. 2006, A Phase I trial of pox PSA vaccines (PROSTVAC(R)-VF) with B7-1, ICAM-1, and LFA-3 co-stimulatory molecules (TRICOMtrade mark) in patients with prostate cancer, J. Transl. Med. 4:1-5. Zhang, Z., Monken, C.E., Zhang, Y., Lenard, J., Mizushima, N., Lattime, E.C., Jin, S., 2006. Cellular autophagy machinery is not required for vaccinia virus replication and maturation, Autophagy 2:91-95. Ge, R., Rajeev, V. Ray, P., Lattime, E.C., Rittling, S., Medicherla, S., Protter, A., Murphy, A., Chakravarty, J., Dugar, S., Schreiner, G., Barnard, N., and Reiss, M. 2006. Inhibition of growth and metastasis of mouse mammary carcinoma by selective inhibitor of transforming growth factor-β type I receptor kinase in-vivo., Clinical Cancer Research (in press). Abstracts and posters Gabriel, E.M., Monken, C.E., and Lattime, E.C. Systemic depletion of CD4+CD25+ T regulatory cells (Tregs) enhances the therapeutic anti-tumor effects of a recombinant vaccinia virus vaccine encoding tumor-specific MHC Class I and

Class II dominant epitopes and the GM-CSF gene Proc. Am. Assn. Cancer Res.47: 334, 2006. Gabriel, E.M., Monken, C.E., and Lattime, E.C. Systemic depletion of CD4+CD25+ T regulatory cells (Tregs) enhances the therapeutic anti-tumor effects of a recombinant vaccinia virus vaccine encoding tumor-specific MHC Class I and Class II dominant epitopes and the GM-CSF gene. Proceedings of the XII Meeting of the Tumor Vaccine and Cell Therapy Working Group, 2006 Mansour, A.R., Weiss, R., Stein, M., Dipaola, R., Schuetz, T. Aisner, J., and Lattime, E.C. Effective tumor infection/transfection following intravesical therapy using recombinant fowlpox vectors encoding GM-CSF and TRICOM in patients with advanced bladder cancer Proc. Am. Assn. Cancer Res. 47: 677, 2006. Mansour, A.R., Weiss, R., Stein, M., Dipaola, R., Schuetz, T. Aisner, J., and Lattime, E.C. Effective tumor infection/transfection following intravesical therapy using recombinant fowlpox vectors encoding GM-CSF and TRICOM in patients with advanced bladder cancer Proceedings of the XII Meeting of the Tumor Vaccine and Cell Therapy Working Group, 2006 Strair, R., Gharibo, M., Taber, K., Kuriyan, M., Dipaola, R., Stein, M., Todd, M., Rubin, A., Lattime, E., Medina, D. Anti-tumor activity of partially HLA-matched irradiated blood mononuclear cells in patients with advanced malignancies. J. Clin. Oncol. 24: 18s, 2006. Review Articles Lattime, E.C. and Gerson, S.L. Introduction: gene therapy of cancer. Seminars in Oncology 2006; 32: 535-536. Awards and Honors University of Iowa Invited Professor 12/13/2005 – 12/15/2006 NCI Cancer Therapeutics Evaluation Program (CTEP), Invited speaker (9/12-13/2005) Service / Administrative Committees Academic Director, “Continuing Umbrella of Research Experiences (CURE) Minority and Undergraduate Training Program” P.I. and Program Director “Postdoctoral Training Program in Translational Research in Cancer” NCI T32-CA99946 Associate Director for Education and Training, The Cancer Institute of New Jersey

CoChair, Annual Retreat for Cancer Research in New Jersey, 2006. Department committees, task forces, projects Department of Surgery, A/P Committee School committees, task forces, projects Faculty Secretary, UMDNJ-RWJMS Voting Member, Committee on Nominations, UMDNJ-RWJMS Non-voting member, Dean’s Executive Council, UMDNJ-RWJMS Member, Dean’s Task Force on Conflicts of Interest UMDNJ-RWJMS UMDNJ-RWJMS Activities Member, M.D./Ph.D. Admissions Committee Steering Committee, Minority training program Community/state service Member, University Medical Center at Princeton, Cancer Committee Government and Agency Review Committees External Advisory Board, Fox Chase Cancer Center Ovarian SPORE, NCI Cancer Immunopathology and Immunotherapy (CII) Study Section, ad hoc member, 3/2-3/2006, 6/29-30/2006 NCI Special Emphasis Review Panel for Training Grants, ad hoc member, 2/13- 14/2006) Cooperative Group Involvement: (Eastern Cooperative Oncology Group, ECOG) 2003 – present Vice Chair, Pathology and Laboratory Sciences Committee 2003 – present Cochair, Developmental Therapeutics Committee Cancer Institute of New Jersey Associate Director for Education and Training Member, Scientific Council Co-Leader, Cytokines, Cytokine Signaling and Cancer Program Faculty Director, Laboratory Services CORE Cochair, Scientific Review Board Member, Executive Committee Member, Human Research Oversight Committee

Editing, Consulting Editor, Gene Therapy Issue, Seminars in Oncology 2005 Guest Editor: Gene Therapy of Cancer issue; Seminars in Oncology vol. 32 No. 6, December 2005 Editorial Boards and Activities: 1996 - present Associate Editor, Cancer Research 2005 Program Committee, Am Assn. Cancer Research 2005 – present Editorial Board, Journal Clinical Oncology Academic Advisory Panels 2001 – present: Cleveland Clinic, GU SPORE program, Scientific advisor 2001 – present: University of Iowa, VAMC REAP Program Scientific Advisor 2005 – present: Fox Chase Cancer Center Ovarian SPORE external advisory board Pharmaceutical Industry Relations Scientific Advisory Board, Jennerex Biologics Paola Leone, Ph.D. Research Activities Dr. Leone is currently the principal investigator of the first NINDS-sponsored clinical gene therapy Phase I study for Gene Therapy of Canavan Disease (CD) using AAV vectors. In addition to conducting a clinical research study on CD, Dr. Leone’s laboratory conducts basic research projects that directly study CD, a disorder that has been a focus of her research for nearly a decade. Dr. Leone is studying & characterizing the Canavan rat model for CD “tremor rat”. These studies run in parallel with the characterization of oligodendrocytes development in the human brain. Furthermore Dr. Leone’s laboratory is also studying the effect of common & novel CD genetic mutations on development & characterizing of altered genes and pathways in CD. She is also conducting a research project designed to generate pre-clinical data for a cell-based therapy for CD & other white matter disorders.

Teaching Member of the judging committee for the Resident's Research week and poster contest Publications Inoue, H., Osawa, I. , Murakami, T., Kimura, A., Hakamata Y., Sato, Y., Kaneko,T., Okada, T., Ozawa, K., Francis J., Leone, P., and Kobayashi, E. (2005) Development of Inbred Transgenic Strains of Rats with LacZ or GFP. Biochemical & Biophysical Research Communication. 329(1): 288-95. Assadi, M., Janson, C.G., Bilaniuk, L., Shera D., Leone, P. (2005) Case Report: Lithium Citrate for Canavan Disease. Pediatric Neurology. 33:235-243. Tavazzi, B., Lazzarino, G., Amorini, A.M., Bellia, F., Fazzina, G., Giardinia, B., Leone, P. (2005) Sensitive and reproducible high performance liquid chromatographic separation of N-Acetyl Aspartate, N-Acetyl Glutamate and N-Acetyl-Aspartyl Glutamate suitable for the biochemical evaluation of Canavan Disease patients. Clinical Biochemistry. 38(11):997-1008 Janson, C.G., Kolodny, E.H., Bilaniuk, L., Shera, D., Goldfarb, O., Zeng, B-J., Leone, P. (2006) Mild-onset presentation of Canavan disease associated with novel G212A point mutation in aspartoacylase gene. Annals of Neurology. 59(2):428-31 McPhee, S.W.J., Janson, C.G., Francis, J.S., Samulski, R.J., Freese, A., Shera, D., Leone, P. (2006) Immunological Profile of Patients Treated With AAV-2 Vectors. Journal of Gene Medicine. 8(5):577-88 Francis, J.S., McPhee, S.W.J., Olariu, A., Janson, C.G., Leone, P. (2006) A Role for Aspartoacylase in the Regulation of BDNF and the Timing of Postnatal Oligodendrogenesis. Journal of Neuroscience Research. In Press Janson CG, McPhee SWJ, Francis J, Shera D, Assadi M, Hurh P, Haselgrove J, Wang DJ, Bilaniuk L, Freese A, Leone P. (2006) Natural History of Canavan Disease Revealed by Serial MRI and Proton magnetic resonance spectroscopy (1H- MRS). Neuropediatrics. In press Zeng, B-J., Wang, Z-H; Torres, P.A., Pastores, G., Leone, P. Raghavan, S.S., Kolodny E.H. (2006) Rapid Detection of Three Large Novel Deletions of the Aspartoacylase Gene In Non-Jewish Patients With Canavan Disease. Molecular Genetics and Metabolism. In press Olariu, A., Francis, J.S., McPhee, S.W.J., Kobayashi, E, Leone, P. Neurosphere- Forming Cells Isolated From Green Fluorescent Protein-Transgenic Lewis Rats for Cell Replacement in White Matter Disease. Submitted

Presentation Leone., P. McPhee, S.W.J., Janson,C.G., Samulski J., Wang D.J., Bilaniuk L. (2005) Gene Therapy Case Study Report. National Tay Sachs & Allied Disorders, New Orleans, LA. Leone, P., McPhee, S.W.J., Janson,C.G., Samulski J., Goldfarb, O., Saslow, E., Goldman, H.W., Wang D.J., Bilaniuk L. (2005). Safety and Efficacy of AAV-mediated Gene Transfer for Canavan Disease. American Society of Gene Therapy. Symposium - Clinical Trials: Metabolic Disorders, St Louis, MI. Leone, P., McPhee, S.W.J., Janson,C.G., Samulski J., Goldfarb, O., Saslow, E., Goldman, H.W., Wang D.J., Bilaniuk L. (2005). Cell and Gene Based Experimental Therapies for White Matter Diseases. Pharmaness Symposium, Pula, Italy. . Honors Woman 2006 Lioness Club, Italy Editing/Consulting Books: Zeng, B-J., Pastores, G., Leone, P., Raghavan, S., Wang, Z-H., Ribeiro, L.A., Torres, P., Ong, E., Kolodny E. (2005) Mutation Analysis of the Aspartacylase Gene in Non- Jewish Patients with Canavan Disease. N-Acetylaspartate, Series: Advances in Experimental Medicine and Biology, Vol 576. Springer, 2006. Editor Janson CG, Leone P, Simeone F, Freese AM, Eds. Molecular Neurosurgery (Progress in Neurosurgery, Volume #17), Karger, Basel, 2005 Mei-Ling Li, Ph.D. Research Activities Development of an in vitro system for the synthesis of Sindbis virus (SV) SG RNA. Teaching Mentoring an undergraduate student to study the fidelity of SV polymerase.

Publications Li, M-L., Lin,Y-H. and Stollar, V. (2005). A cell-free system for the synthesis of Sindbis virus subgenomic RNA: Importance of the concentration of the initiating NTP. Virology, 341: 24-33. Randall D. McKinnon Ph.D. Research Funding Source: New Jersey Commission Spinal Cord Research Title: Netrin directed glial migration Dates: 06/15/05 -06/30/07 PI: R.D. McKinnon, 50% effort Direct/indirect/total Costs: $ 360,690 Source: New Jersey Commission on Stem Cell Research Title: "Gliogenic potential of human placental stem cells" Dates: 01/2006-12/2008 PI: R.D. McKinnon, 10% effort Direct/indirect/total Costs: $ 260,868; $ 39,132; $ 300,000 Source: Rutgers College Scholarship (Katherine Chen, Rutgers ‘09) Title: “Netrin directed glial migration in Drosophila embryogenesis” Source: RWJMS Neuroscience Summer Studentship (David Zagha, Yale U. ‘09) Title: “Netrin directed glial migration in rodent development” Teaching Molecular Biosciences Advanced Topics, Spring 2006 Fluorescent Cell Imaging 16:761:590, Spring 2006 Publications R.D. McKinnon, S. Waldron and M.E. Kiel (2005). PDGF -Receptor Signal Strength Controls an RTK Rheostat That Integrates Phosphoinositol 3'-Kinase and Phospholipase C Pathways during Oligodendrocyte Maturation. J. Neuroscience 25(14): 3499-3508. Labrador, J.P., D. O’Keefe, S .Yoshikawa, R.D. McKinnon, J.B. Thomas and G. Bashaw (2005). The homeobox transcription factor even-skipped regulates

Netrin-receptor expression to control dorsal motor-axon projections in Drosophila. Current Biol. 15(15):1413-1419. J.E. Reilly, A. Chang, A. Gordon, D. Zhao, K. Chen, M. Kiel, D.O’Keefe, S. Yoshikawa, J.B. Thomas and R.D. McKinnon. Asymmetric distribution of attractive (DCC/Unc40) and repulsive Unc5) netrin receptors on migrating glia (in preparation). C. Chen and R.D. McKinnon (2006). Stem Cells to Oligodendrocytes: Prospects for Brain Therapy. Mol. Neurobiology (in preparation). Abstracts and Posters (published/presented): Brandy L. Houser, M.E. Kiel and R.D. McKinnon (2005). The role of PDGF α-receptor in migration of glial progenitor cells. Cook Scholars Symposium New Brunswick NJ. James E. Reilly, Mary E. Kiel and R.D. McKinnon (2006). Asymmetric localization of Netrin receptors on migrating glial cells. RWJMS Research Day. R.D. McKinnon, A. Chang, Alan Gordon and Mirat Shah (2006). Control of glial position via the repulsive netrin receptor Unc5. RWJMS Research Day. M.E. Kiel and R.D. McKinnon (2006). PDGF signaling in glial development: matching pathways to responses RWJMS Research Day. James E. Reilly, Mary E. Kiel and R.D. McKinnon (2006). Asymmetric localization of Netrin receptors on migrating glial cells during neural development. Aresty Research Symposium, Rutgers University New Brunswick NJ. James E. Reilly, Mary E. Kiel and R.D. McKinnon (2006). Asymmetric localization of Netrin receptors on migrating glial cells during neural development. Rutgers University Honors Thesis Symposium, Piscataway. James E. Reilly, Katherine Chen, Mary Kiel and R.D. McKinnon (2006). Netrin-directed glial migration. Cold Spring Harbor, Glia in Health & Disease, CSH NY Presentation Celgene Cellular Therapeutics, Summit NJ, 18 April 2006. “From Stem Cells to Oligodendrocytes: Prospects for Brain Therapy” Cold Spring Harbor Symposia, Glia in Health and Disease, CSH NY, July 2006 “Netrin-directed glial migration” Administrative Committees Departmental Director, Neurosurgical Research Laboratory University Member, Grant Review Panel, UMDNJ Foundation Grants Academic Standing Committee, Grad Program in Physiology Integrative Biology Curriculum Committee, Graduate Program in Physiology Integrative Biology

Editing/Consulting Journal Editorial Boards J. Neuroscience, Mol. Cell. Neuroscience M. Maral Mouradian, M.D. Research Activities Dr. Mouradian’s research program focuses on the molecular pathogenesis of Parkinson’s disease and related neurodegenerative disorders. Among her discoveries during this academic year was the importance of the transcriptional activity of DJ-1, which is one of the genes that cause recessively inherited Parkinson’s disease, in regulating the expression of proteins that are key for the survival and maintenance of dopaminergic neurons in the brain. Additionally, a new grant from the NIH supports the laboratory’s efforts to study the in vivo implications of deleting both DJ-1 and apoptosis signal regulating kinase 1. Another new project initiated with a grant from the Michael J. Fox Foundation for Parkinson Research, was the epigenetic regulation of the alpha-synuclein gene as a biomarker of susceptibility to Parkinson’s disease. Dr. Mouradian’s laboratory is focusing on DNA methylation as a mechanism regulating alpha-synuclein gene expression. Increased alpha-synuclein protein levels are known to be deleterious to dopaminergic neurons and cause Parkinson’s disease. Teaching Physical Diagnosis course at RWJMS Publications Junn, E., Taniguchi. H., Jeong, B.S., Zhao, X., Ichijo, H., Mouradian, M.M.: Interaction of DJ-1 with Daxx inhibits ASK1 activity and cell death. Proc. Natl. Acad. Sci. USA, 102(27): 9691-9696, 2005. Bara-Jimenez W., Bibbiabi, F., Morris, M.J., Dimitrova, A., Sherzai, A., Mouradian, M.M., Chase, T.N.: Effects of serotonin 5HT1A agonist in advanced Parkinson’s disease. Mov. Disord., 20(8):932-936, 2005. Dhib-Jalbut, S., Arnold, D.L., Cleveland, D.W., Fisher, M., Friedlander, R.M., Mouradian, M.M., Przedborski, S., Trapp, B.D., Wyss-Coray, T., Yong, V.W.: Neurodegeneration and neuroprotection in multiple sclerosis and other neurodegenerative diseases. J. Neuroimmunol., In press, 2006. Mouradian, M.M., Tanaka, M., Lee, G., Junn, E.: The impact of inclusion formation on cell survival. In: The Proteasome in Neurodegeneration. Stefanis, L., Keller, J.N. (Eds). Springer, pp 57-67, 2006.

Mochizuki, H., Mouradian, M.M.: Progress in Gene Therapy. In: Parkinson’s Disease: Diagnosis and Clinical Management. Edition 2. S.A., Factor and W.J. Weiner (eds). In press. Jeong, B.S., Zhao, X., Mouradian, M.M., Junn, E.: The cellular effects of parkin / septin 4 interaction. Soc. Neurosci. Abstr., Washington, DC, Program No. 328.5, 2005. Junn, E., Zhao, X., Jeong, B.S., Mouradian, M.M.: DJ-1 protects cells by inhibiting the Daxx/ASK1 cell death pathway. Soc. Neurosci. Abstr., Washington, DC, Program No. 328.19, 2005. Presentations Delivered an invited lecture entitled “Scientific Rationale for Continuous Dopaminergic Stimulation in Parkinson’s Disease at the Fourth Nordic Meeting on Parkinson’s Disease, in Sigtuna, Sweden on April 25, 2006. Invited to chair a session on Gene Therapy at the International Congress of Parkinson´s Disease and Related Disorders, in Berlin, Germany. Gave two lectures about Epigenetic Regulation of the alpha-Synuclein Gene at the Michael J. Fox Foundation for Parkinson’s Research in New York, one on February 9, 2006 and one on June 20, 2006. Delivered a lecture about Molecular and Genetic Studies in Parkinson’s Disease at the Department of Molecular Genetics, Microbiology and Immunology at UMDNJ- RWJMS. Gave a presentation about epigenetic regulation of the alpha-synuclein gene in Parkinson’s disease at RWJMS. Service Wrote an article entitled: “Advances in Parkinson’s Disease Research” for the Winter 2005 issue of The Parkinson’s Bulletin, a newsletter published by the American Parkinson Disease Association’s New Jersey Chapter. Delivered a lecture entitled “What Causes Dopamine Neuron Loss in Parkinson’s Disease?” to the Parkinson’s Support Group of North Jersey held at Mountainside Hospital, Montclair, New Jersey, on Saturday, November 19, 2005. Delivered a lecture entitled “Overview of Parkinson’s Disease and its Treatment” to the American Parkinson Disease Association’s New Jersey Chapter for newly diagnosed patients with Parkinson’s disease, held at the Robert Wood Johnson University Hospital on November 28, 2005. Delivered two lectures to patient groups about “Research Advances in Parkinson’s Disease” for the New Jersey Chapter of the APDA held at the Robert Wood Johnson University Hospital on March 15 and 16, 2006. Represented the Scientific Advisory Board at the dedication ceremony of the American

Parkinson Disease Association’s new headquarters in Staten Island, New York, on Sunday, November 20, 2005. I was the featured speaker at the Parkinson’s Disease Awareness Day at the American Parkinson Disease Association in Staten Island, NY on April 11, 2006 (James Parkinson’s birthday). Title of lecture “Overview of Parkinson’s Disease and Research Advances.” Administrative Committees Departmental Appointment and Promotion Committee, Department of Neurology, RWJMS Website Designing for the Department of Neurology RWJMS Awards Nomination Committee member University UMDNJ Institutional Review Board Community Involvement on Behalf of University or Medical School Member, Scientific Advisory Board, American Parkinson Disease Association: This service involves reviewing applications for research grants and advanced centers of excellence. In addition, we meet annually to discuss these applications and to set the priorities and policies of the Board. Editing/Consulting Journal Editorial Boards Associate Editor, Pharmacology and Therapeutics: I cover the area of neurological diseases. Editorial Board Member, Neurology: this is the most widely circulated journal in the field of neurology. Ad hoc reviewer for Journal of Neuroscience, Journal of Neurochemistry, Journal of Biological Chemistry, Human Molecular Genetics, Human Mutation, Cell Death and Differentiation, and others. Reviewed grants for the Department of Defense, US army Medical Research and Materiel Command. Reviewed a grant for the Catalan Agency for Health Technology Assessment and Research. Reviewed a grant for the Czech Science Foundation.

Consulting Eisai Medical Research Solvay Pharmaceuticals Johnson and Johnson. Daniel Notterman, M.D. Research Activities Dr. Notterman continued to study the molecular genetics of colon cancer at the gene expression and biochemical level. He also operates the shared micro-array facility for CINJ. His laboratory studies molecular events that underlie the initiation and propagation of cancer. Most of the work of the lab is organized around the theme that cancer should be approached by correlating the global clinical, genetic, epigenetic and function (mRNA expression) characteristics of the patient and her malignancy. They use colon cancer as a model system, because of the availability of tissue of varying stages and because of its public health importance. To this end, his collaborators and he have developed a comprehensive molecular profile of almost 400 colon samples in about 280 patients. This data is now under analysis by several laboratories in the United States and Israel and a number of publications have resulted (see recent publications). Teaching RWJMS: Resident, Medical Student Preceptor Princeton University Molecular Biology 460: Diseases in Children Molecular Biology 532: Cancer Genetics Publications Journals Schaar D, Liu H, Sharma S, Ting Y, Martin J, Krier C, Ciardella M, Osman M,Goodell L, Notterman DA, Strair R. TPA-induced dual-specificity phosphatase expression and AML cell survival. Leukemia Research. 2005 Oct; 29(10):1171-9. Tsafrir D, Tsafrir I, Ein-Dor L, Zuk O, Notterman DA, and Domany E. Sorting points into neighborhoods (SPIN): Data analysis and visualization by ordering distance matrices. Bioinformatics. Feb; 21:2301-2308, 2005. Cheng Y, Shawber C, Notterman D, Paty P, and Barany F. Multiplexed profiling of candidate genes for CpG island methylation status using a flexible CR/LDR/Universal array assay. Genome Res 16(2):282-9 2006.

Tsafrir D, Bacolod M, Selvanayagam Z, Tsafrir I, Shia J, Zeng Z, Liu H, Krier C, Stengel RF, Barany F, Gerald WL, Paty PB, Domany E and Notterman D. Relationship of gene expression and chromosomal abnormalities in colorectal cancer. Cancer Research. 2006 Feb 15;66(4):2129-37. Wen Y, Hamming D, Greenman, J, Liu, H, Notterman DA, Cellular transformation by GRO_ may involve down-regulation of an ECM Protein, Fibulin-1. C Cancer Res. 2006 Oct 15;125951-9. Lee HJ, Liu H, Goodman C, Ji Y, Maehr H, Uskokovic M, Notterman DA, Reiss M, Suh N. Gene expression changes induced by a novel Gemini vitamin D derivative during the progression of breast cancer. Biochem Pharmaco, 2006 Jul 28;72(3):332-43.. Book Chapters Hanna N, Weinberger B, Notterman, D (2006). The Cell. In A. Slonim & M. Pollack (Eds.), Pediatric Critical Care Medicine. Philadelphia: Lippincott Williams & Wilkins, 2006. Notterman, D., Kelly, M., & Sturgill, M. (2005) Pharmacology of the cardiovascular system. In B. Fuhrman & J. Zimmerman (Eds.), Pediatric Critical Care, 3 Edition. St. Louis: Mosby, Inc, 2006. Malhotra, A., Choi, S., Notterman, D., (2006) The HIV patient: role of the pediatric intensive care unit. In Wheeler, Wong & Shanley (Eds.), Pediatric Critical Care Medicine. Springer-Verlag London, Limited. In press 2006. COMMENTARY AND INVITED ARTICLES Notterman, DA. Personalizing Medicine: The single nucleotide polymorphism and the treatment of status asthmaticus [Editorial] Pediatr Crit Care Med 7(1):87-9, 2006. Baden HP, Zimmerman JJ, Brilli RJ, Wong H, Wetzel RC, Burns JP, Nadkarni V, Checchia PA, Dalton HJ, Berger J, Pollack M, Notterman D, Green TP, Blumer J, Dean M. Intensivist-led team approach to critical care of children with heart disease. Pediatrics.2006 May;117(5):1854-6 Service Search Committee for Children’s Specialized Hospital CEO/President Children’s Specialized Hospital Board Member (2002 – present) RWJ Health Care Corporation RWJUH Board of Directors University Hospital Foundation RWJUH Board of Directors Health Network RWJUH Medical Board/Credentials Committee RWJUH Board of Trustees of the RWJ Fund for Health Care Excellence

RWJUH Joint Planning RWJUH Board of Directors - Pediatric Program Committee RWJUH Outcomes Steering Committee Administrative Committees Departmental RWJMS Chair, Search Committee for Anesthesia Chair Chair, Search Committee for Director, Child Health Institute of New Jersey Search Committee for OBGYN Chair Search Committee for Child Health Institute of New Jersey Cancer Institute of NJ Internal Advisory Board & Scientific Council Director, Core Expression Array Facility, Cancer Institute of New Jersey Cancer Institute of New Jersey Internal Advisory Board RWJMS Executive Council RWJMS Advisory Committee on Appointments and Promotions University University Medical Group - UMDNJ Board of Governors Chair, RWJUMG Finance Committee RWJUMG Executive Committee Federal/State Appointments NJ Department of Health Pediatric and Perinatal Task Force (2004 – present) American College of Critical Care Medicine Fellowship Services Committee (2005— present) Newborn Screening Annual Review Committee (2005 – present) Editing/Consulting Journal Editorial Boards – Critical Care Medicine, Cancer Research, JAMA, Bioinformatics, Oncogene

Michael Reiss, M.D. Research Activities Mechanisms of resistance of squamous cancer cells to inhibition of growth by Transforming Growth Factor-ß. Mechanisms of resistance of breast cancer cells to inhibition of growth by Transforming Growth Factor-ß. Development of selective TGFß receptor kinase antagonists as novel anti-cancer and anti-fibrotic agents Development of a Tissue Microarray Shared Resource of the Cancer Institute of New Jersey Teaching “Genomics in Cancer Therapeutics” Publications Manuscripts: Uemura M, Swenson ES, Gaca MD, Giordano FJ, Reiss M, Wells RG. Smad2 and Smad3 play different roles in rat hepatic stellate cell function and alpha-smooth muscle actin organization. Mol Biol Cell 2005;16(9):4214-24. Abu-Khalaf, M.M., Windsor, S., Ebisu, K., Salikooti, S., Ananthanarayanan, G., Chung, G.G., DiGiovanna, M.P., Haffty, B.G., Abrams, M., Farber, L.R., Hsu, A.D., Reiss, M., Zelterman, D., and Burtness, B.A. Five-Year Update of an Expanded Phase II Study of Dose-Dense and -Intense Doxorubicin, Paclitaxel and Cyclophosphamide (ATC) in High-Risk Breast Cancer. Oncology 2005;69(5):372- 83. Hong Jin Lee, Andrew Wislocki, Catherine Goodman, Yan Ji, Rongrong Ge, Hubert Maehr, Milan Uskokovic, Michael Reiss, and Nanjoo Suh.. A novel vitamin D derivative activates bone morphogenetic protein (BMP) signaling in MCF10 breast epithelial cells. Mol. Pharmacology. 2006. 69(6):1840-8 Lee HJ, Liu H, Goodman C, Ji, Y., Maehr, H., Uskokovic, M., Notterman, D., Reiss, M., Suh, N.. Gene expression profiling changes induced by a novel Gemini Vitamin D derivative during the progression of breast cancer. Biochem Pharmacol 2006. In press or submitted Xie, W. and Reiss, M. Immunohistochemistry of Smad Proteins in Carcinoma of the Breast and other Sites in “Immunohistochemistry and In Situ Hybridization of Human Carcinomas” Elsevier Academic Press. In Press, 2006. Ge, R., Rajeev, V., Ray, P., Lattime, E., Rittling, S., Medicherla, S., Protter, A., Murphy, A., Chakravarty, J., Dugar, S., Schreiner, G., Barnard, N. and Reiss, M. Inhibition

of growth and metastasis of mouse mammary carcinoma by selective inhibitor of Transforming Growth Factor-β type I receptor kinase in vivo. Clin. Cancer Res. In Press. Abstracts, letters Bharathy, S. and Reiss, M. Dual-function missense mutations of TGFβ type II receptor gene confer both loss of growth suppression and constitutive activation SMAD3 associated with an invasive phenotype. Proc Amer Assoc Cancer Res 2006; 47:2699 Hong Jin Lee, Hao Liu, Catherine Goodman, Yan Ji, Hubert Maehr, Milan Uskokovic, Daniel Notterman, Michael Reiss, Nanjoo Suh. Gene expression profile changes induced by a novel Gemini vitamin D3 analog during the progression of breast cancer. Proc Amer Assoc Cancer Res 2006; 47:4166 Presentations “Targeting the TGFβ pathway in man-How do we pick the winners?” Invited Speaker. 2nd Annual TGFβ Symposium; May 18-19, 2006; Eli Lilly and Company, Indianapolis, IN Service Attending Inpatient: November 2001-2005, May 2006 Outpatient Weekly CINJ Breast Center as of June 7, 2001 Consult service: November 2001-2005, May 2006 Affiliated hospital program: Date Time Institution Meeting 8/29/2005 12:30PM Mountainside Hospital Tumor Board 9/21/2005 8:00AM RWJ-Hamilton Cancer Committee 10/19/2005 8:00AM RWJ-Hamilton ACOS Survey 11/16/2005 8:00AM RWJ-Hamilton Cancer Committee 12/14/2005 8:00AM RWJ-Hamilton Cancer Committee 1/18/2006 8:00AM RWJ-Hamilton Cancer Committee 3/15/2006 8:00AM RWJ-Hamilton Cancer Committee 5/17/2006 8:00AM RWJ-Hamilton Cancer Committee 6/2/2006 7:30AM Jersey Shore University Medical Center Breast Cancer Conf. Director of CINJ Breast Cancer Research Program: I have organized and have been chairing a weekly monthly Breast Cancer Research Program meeting since 4/3/01. In addition, I have overseen the Breast Cancer Developmental Fund Awards at CINJ in 2001, 2002, 2003, 2004, 2005.

Administrative Committees Committees: National: Member, Pathobiology-1 Study Section, Department of Defense Breast Cancer Research Program Reviewer, Netherlands Cancer Foundation research grants. Member, Tumor Microenvironment Study Section, National Cancer Institute, National Institutes of Health University: Associate Director for Translational Research, The Cancer Institute of New Jersey Director, Breast Cancer Research Program, The Cancer Institute of New Jersey Editor: “Oncology Research-An International Journal” Associate Editor: “Cancer Research” and “Clinical Cancer Research” Associate Editor: “Cancer Research” and “Clinical Cancer Research” Reviewer: Cancer Research, Cell Growth & Differentiation; Oncology Research, Eur. J. Cancer Clin. Oncology, J. Cellular Physiology, Genomics, Lab. Investigation, J. Cellular Biochem., Clinical Clinical Cancer Research, J. Pathology, New England Journal of Medicine Hugh Rosen, Ph.D. Research Activities Studies on receptor regulation of lymphocyte egress and pulmonary barrier function. Chair, The Molecular Libraries Screening Center Network Steering Group of the NIH Roadmap. Publications Chun J, Rosen H. Lysophospholipid receptors as potential drug targets in tissue transplantation and autoimmune diseases. Curr Pharm Des. 2006;12(2):161-71 Alfonso C, McHeyzer-Williams MG, Rosen H. CD69 down-modulation and inhibition of thymic egress by short- and long-term selective chemical agonism of sphingosine 1-phosphate receptors. Eur J Immunol. 2006 Jan;36(1):149-59.

Rosen H. Chemical approaches to the lysophospholipid receptors. Prostaglandins Other Lipid Mediat. 2005 Sep;77(1-4):179-84. Martinez X, Kreuwel HT, Redmond WL, Trenney R, Hunter K, Rosen H, Sarvetnick N, Wicker LS, Sherman LA. CD8+ T cell tolerance in nonobese diabetic mice is restored by insulin-dependent diabetes resistance alleles. J Immunol. 2005 Aug 1;175(3):1677-85. Rosen H, Goetzl EJ. Sphingosine 1-phosphate and its receptors: an autocrine and paracrine network. Nat Rev Immunol. 2005 Jul;5(7):560-70. Srijata Sarkar, Ph.D. Research Activities Regulation of cytokine gene expression by mRNA turnover Cytokine expression by cells of the immune system plays a crucial role in the regulation of immune responses. Expression of many cytokines in response to external stimuli during an immune response is regulated by transcription as well as posttranscriptional events. A major posttranscriptional mechanism for regulating the level of gene expression of many cytokines, protooncogenes and growth factor mRNAs is through the control of mRNA turnover. The rapid turnover of mRNAs is determined in part by the A+U-rich elements in the 3'-untranslated region. The overall goal of this project is to understand the mechanisms of regulation of expression of cytokines involved in inflammation such as proinflammatory IFN-γ and anti-inflammatory IL-10. These cytokines have opposing effects and they antagonize each other’s production and functions. Our previous studies have indicated that the increased expression of IL-10 in human melanoma tumor cell MNT-1 as compared to its normal counterpart is in part due to the increased stability of the IL-10 mRNA. Examination of the 3'-untranslated region of IL-10 mRNA revealed the presence of multiple AU-rich elements (ARE) that might target the mRNA for rapid turnover. The cytoplasmic extract from MNT-1 cells has significantly lower ARE-binding activity compared to that of normal melanocytes. One of the major ARE-binding proteins in normal melanocytes was identified as AUF1, an mRNA destabilizing protein. In MNT-1 cells, AUF1 appears to be restricted to the nuclear fraction. A reduced cytoplasmic level of AUF1 in melanoma cells appears to be responsible for IL-10 overexpression with deleterious consequences for tumor surveillance and rejection. Nuclear sequestration of AUF1 appears to be a novel mechanism which can be used by tumor cells to alter the regulation of mRNA turnover. At present we are investigating the role of mRNA turnover in the regulation of IL- 10 and IL-10 receptor in response to inflammatory stimuli. IL-10 is expressed at a low

level in T- and B-lymphocytes, monocytes, macrophages, keratinocytes and many tumors. We have used THP-1, a human promonocytic leukemia cell line, as a model to examine whether the expression of IL-10 and IL-10 receptor chains is modulated in response to external stimuli such as bacterial LPS and IFN-γ. THP-1 cells, like primary monocytes are known to induce a host of inflammatory cytokines in response to appropriate stimuli. We have demonstrated that LPS stabilizes mRNAs encoding IL-10 and IL-10 receptor sub-unit 1 (IL-10R1). IFN-γ opposes LPS-mediated stabilization of IL-10 mRNA while it increases LPS-mediated stabilization of IL-10R1. The sequence analysis of the 3'-UTR of human IL-10 and IL-10R1 mRNA revealed the existence of multiple AUUUA pentamers. These ARE sequences destabilize IL-10 and IL-10R1 mRNA and contribute to the maintenance of a low level of IL-10 and IL-10R1 in unstimulated cells. We are investigating the role of the 3’-UTR in the regulation of stimulus-dependent (LPS and IFN-γ changes in IL-10 and IL-10R1 expression. In addition, we are examining the role of various mRNA binding proteins in the regulation of expression of IL-10 and IL-10R1 in THP-1 cells. Determining the mechanisms by which the expression of these cytokines is regulated will be useful in both understanding the complexity of the immune system and the interrelationships of these important cytokines. Furthermore, understanding the role of mRNA turnover in the regulation of the immune system will provide an opportunity to develop new therapeutics to control these processes and treat a variety of diseases such as rheumatoid arthritis and other immune disorders. Lee Ann Schein, Ph. D. Research Activities As the Director of the DNA Core Facility, Dr. Schein is responsible for overseeing, hiring, and training personnel; assisting in grant submissions; supervising billing; setting pricing policies; and aiding users in troubleshooting problems. Dr. Schein spends many hours a week interpreting sequencing data with users enabling them to optimize their sequencing results. In addition, she spends several hours a month helping users design oligo primers and labeled probes. She also spends much time designing experiments using the real-time PCR technology. Dr. Schein has been working with users to initiate applications utilizing the system. During this past year, the lab has spent a great deal of time optimizing conditions for several new applications. We have been working with end users in piloting experiments using STRP (Simple Tandem Repeat Polymorphisms) analysis. We have optimized the conditions for the studies on the ABI 3100 DNA Sequencer using fluorescent primers. This technique has been very successful in the genotyping of large numbers of samples effortlessly and rapidly.

In addition, the Core has a quantitative real-time PCR analysis system complete with robotics. Dr. Schein has been working with users to initiate applications utilizing the system including designing experiments, and primer and probe sets. The DNA Synthesis and Sequencing Core Facility has expanded, becoming increasingly more streamlined, and incorporating state-of-the-art technology. Oligonucleotide synthesis usage has also increased as well as becoming more efficient. Dr Schein continues to be active in The Cancer Institute of New Jersey, attending Scientific Council meetings and advising the CINJ Research Administration on billing and usage procedures for Core Facilities. She was asked to write a synopsis of the DNA Core Facility for the CINJ newsletter “caResearch Resources” (July/August 2005). In addition, Dr. Schein has been asked by the Cancer Institute of New Jersey to be part of a subcommittee on shRNA Libraries at RWJMS. She serves as the liaison between the vendor, Open Biosystems. and CINJ. Dr. Schein is responsible for the custodial care of the human Leniviral shRNA Library subscription purchased for RWJMS. In an effort to assist researchers in saving money, Dr. Schein initiated an Applied Biosystems Freezer Program at RWJMS. The DNA Core Facility is able to purchase ABI reagents and consumables at greatly reduced bulk prices. This savings gets passed on to the individual users who can obtain these items from the DNA Core. Laboratory Support Staff Regina Felders-Gibbions, Technician Sheila Mazar, Technician John Spychala, PhD, Technician Beverly Novembre, Accounts Clerk Nousheen Baig, Undergraduate Rori Hodges, Undergraduate Deonnae Lopez, Undergraduate Dhenu Solanki, Undergraduate Neal Mohandas, Undergraduate Navjot Kaur, Undergraduate Arti Dabholkar, Undergraduate Gustavo Churrango, Undergraduate Trishna Nath, Undergraduate Ronald Udasin, Undergraduate Jessica Akunna, Undergraduate Teaching Microbiology and Immunology MGMB 6000, Assistant to the Course Director

Microbiology and immunology UMDNJ-RWJMS (MGMB 6000) Cognitive skill reviews in microbiology UMDNJ-RWJMS Teaching of microbiology UMDNJ-RWJMS/GSBS (MICR 5011) Seminars Sponsored “Determination of Oligonucleotide Quality: Critical Factors to Consider for Successful Experiments”, Mitchell Gore, Ph.D., Integrated DNA Technologies, 9/29/05 “Improved Potency of 27mer Dicer-Substrate RNA Duplexes as Triggers of RNAi: exploiting the Biochemistry of Dicer”, Mitchell Gore, Ph.D., Integrated DNA Technologies, 11/2/05 “Genotyping Seminar Series – Effective Genotyping Project Management – Mapping to Execution”, Mary Baltazar, Ph.D., Applied Biosystems, and Scott Diehl, Ph.D., Director of Center for Pharmacogenomics and Complex Disease Research, 11/30/05 “Introduction to Real Time PCR: Quantitative PCR theory and Design”, Mary Baltazar, Ph.D., Applied Biosystems, 6/28/06 “Real Time PCR: Next Generation Assays”, Robert Genuario, Ph.D., Applied Biosystems, 6/28/06 Administrative Committees Departmental MGMI Core Facilities Committee RWJMS UMDNJ-RWJMS Summer Biomedical Careers Program RWJMS MD/PhD Curriculum Committee University Co - resource manager, Cancer Institute Of New Jersey Resource manager, National Institute Of Environmental Health Sciences Center Member of the Cancer Institute of New Jersey CINJ DNA Sequencing Shared Resource Advisory Committee CINJ Transcriptional Profiling Advisory committee CINJ sub-committee on shRNA Libraries Leonard H. Sigal, MD Research Activities Dr. Sigal is a Director in Immunology at the Pharmaceutical Research Institute of

Bristol-Myers Squibb. He is working with a compound known as abatacpet, marketed as Orencia. Abatacept is the first in a new class of drugs: costimulation modulators, that act on auto-immune disease by blocking the key co-stimulation signal (delivered by B7 interaction with CD28) needed to fully activate T cells. Orencia is approved for use in adult rheumatoid arthritis. I am currently Medical Monitor for studies using Orencia: two studies in systemic lupus erythematosus and one in juvenile idiopathic arthritis. I am also involved in developing future studies using Orencia in other auto-immune diseases. Publications Sigal LH. Basic science for the clinician 38: B cells, factories, and immunomodulators. J Clin Rheumatol. 2006 Jun;12(3):152-7. Sigal LH. Basic science for the clinician 37: Protecting against autoimmunity-tolerance: mechanisms of negative selection in the thymus. J Clin Rheumatol. 2006 Apr;12(2):99-101 Sigal LH. Basic science for the clinician 36: protecting against autoimmunity: tolerance and aire, the immunologic shadow, and other mechanisms of negative selection in the thymus. J Clin Rheumatol. 2006 Feb;12(1):44-6 Petersel DL, Sigal LH. Reactive arthritis. Infect Dis Clin North Am. 2005 Dec;19(4):863-83. Sigal LH, Hassett AL. Commentary: 'What's in a name? That which we call a rose by any other name would smell as sweet.' Shakespeare W. Romeo and Juliet, II, ii(47-48). Int J Epidemiol. 2005 Dec;34(6):1345-7. Sigal LH. Basic science for the clinician 35: CD1, invariant NKT (iNKT) Cells, and gammadelta T-cells. J Clin Rheumatol. 2005 Dec;11(6):336-9. Collins C, Wolfe J, Roessner K, Shi C, Sigal LH, Budd RC. Lyme arthritis synovial gammadelta T cells instruct dendritic cells via fas ligand. J Immunol. 2005 Nov 1;175(9):5656-65. Sigal LH. Basic science for the clinician 32: T-cells with regulatory function. J Clin Rheumatol. 2005 Oct;11(5):286-9 Sigal LH. Basic science for the clinician 30: The immunologic synapse. J Clin Rheumatol. 2005 Aug;11(4):234-9. Michael Steinmetz, Ph.D. Research Activities Michael Steinmetz, Ph.D. is Managing Director at Clarus Ventures, a venture capital firm with offices in Boston and San Francisco, focused on investments in biotechnology

and medical device companies in the USA and Europe. The firm is currently investing its first $500MM fund. More information can be found on their website: www.clarusventures.com George B. Weiss, Ph.D. Dr. Weiss has retired and moved full-time to Tucson Arizona and was not active in research or university activities this past year. Lawrence P. Wennogle, Ph.D. Research Activities Intra-Cellular Therapies, Inc. (ITI) is a pharmaceutical company located in Manhattan at the Columbia University Medical Complex in the Audubon Building. ITI was founded by Dr. Paul Greengard of Rockefeller University, Nobel Laureate for his pioneering work on signal transduction in the central nervous system (CNS). ITI is developing novel therapeutics for disorders of the CNS including schizophrenia, depression and neurodegenerative disorders such as Parkinson’s and Alzheimer’s Diseases. I lead a Drug Discovery effort including Medicinal Chemistry, Pharmacology and Assay Development Departments. Currently, ITI is involved in pre-clinical development of a pipeline of compounds. We plan our first human clinical trials in Q4-2006/Q1-2007. ITI has developed a platform technology to study the response of the central nervous system to drug administration at the level of protein phosphorylation changes of key phosphoproteins in the nervous systems. Using this technology, we have a large database to compare new development candidates to existing drugs, thereby leading to a superior understanding of drug mechanisms. The system is referred to as CNS- Profile. Teaching I continue to participate in teaching activities and have given several recent lectures to different Columbia University Medical Center graduate programs. Carol Wilusz, Ph.D. Research Activities The last year has been very productive. We have several projects ongoing in the lab, all focusing on various aspects of mRNA metabolism. Our work showing that Nucleophosmin associates with polyadenylated mRNAs was published in Nature

Structural & Molecular Biology in April 2006. We are now following up to discover the exact role of NPM as a marker of successful 3' end formation. We think this abundant protein may be influencing mRNA splicing or export. We published an article in RNA in May of 2006 describing the association of CUG-BP with the 3'UTR of TNFalpha mRNA. Intriguingly, CUG-BP appears to recruit a deadenylase to the transcript thus enhancing the rate of poly(A) shortening. As CUG- BP has been implicated in the pathogenesis of Myotonic Dystrophy we are very excited to follow this up and learn how changes in mRNA stability may be contributing to this debilitating disease. I have submitted two grant proposals to continue working on this project. A graduate student in the lab, Nicole Garneau, was a former undergraduate work study student in the Peltz lab. She has been studying the interactions between Sindbis Virus genomic RNA and the mRNA turnover machinery. She presented a talk at the American Society for Virology Meeting in Wisconsin this summer. I have received a small grant from the College Research Council to expand the Sindbis project. We were excited to get a review article entitled "The Highways & Byways of mRNA decay" recently accepted into Nature Reviews Molecular Cell Biology. This will be published in early 2007. In addition, we wrote a chapter for the third edition of the Cold Spring Harbor Translational Control book with Carlos Gonzalez, a former post-doc in the Peltz lab who is now at the University of Puerto Rico. Finally, I was very happy to be accepted as a member of the Cellular & Molecular Biology graduate program at CSU this fall. Publications Moraes KC, Wilusz CJ, Wilusz J. CUG-BP binds to RNA substrates and recruits PARN deadenylase. RNA. 2006 Jun;12(6):1084-91 Palaniswamy V, Moraes KC, Wilusz CJ, Wilusz J. Nucleophosmin is selectively deposited on mRNA during polyadenylation. Nat Struct Mol Biol. 2006 May;13(5):429-35. Opyrchal M, Anderson JR, Sokoloski KJ, Wilusz CJ, Wilusz J. A cell-free mRNA stability assay reveals conservation of the enzymes and mechanisms of mRNA decay between mosquito and mammalian cell lines. Insect Biochem Mol Biol. 2005 Dec;35(12):1321-34. Wilusz CJ, Wilusz J. Eukaryotic Lsm proteins: lessons from bacteria. Nat Struct Mol Biol. 2005 Dec;12(12):1031-6. Review. Duttagupta R, Tian B, Wilusz CJ, Khounh DT, Soteropoulos P, Ouyang M, Dougherty JP, Peltz SW. Global analysis of Pub1p targets reveals a coordinate control of

gene expression through modulation of binding and stability. Mol Cell Biol. 2005 Jul;25(13):5499-513. Service Outside of the laboratory, I taught one lecture on Innate Immunity in the Advanced Virology course here at CSU in the spring. In addition I am presently running the Departmental Seminar Series.

CORE FACILITIES CORE FACILITIES DNA Sequencing and Synthesis Core Facility The DNA Synthesis and Sequencing Core Facility of the Department of Molecular Genetics and Microbiology serves as a shared resource for the Cancer Institute of New Jersey (CINJ) and The National Institute of Environmental Health Sciences (NIEHS) Center at the Environmental and Occupational Health Sciences Institute (EOHSI) Center of Excellence. The overall purpose of this shared resource is to provide a centralized, high quality, cost-effective facility for DNA sequencing and synthesis for use by the entire scientific community at RWJMS and Rutgers University. Automated fluorescent sequencing provides much more data (generally 400 to 850 nucleotides) from a single loading than can be achieved by manual sequencing methods most researchers previously performed in their laboratories. The cost of such a system is prohibitively high, thus only a shared resource such as the DNA laboratory can maintain and operate this system efficiently. The facility runs two state of the art ABI 3100 capillary sequencers with a capacity of two 96 well plates per machine. For DNA Sequencing, CINJ and NIEHS members pay $8 per sequence with 400 bases of sequence guaranteed; this rate is 20% less than charged to other academic users ($10). User fees are designed to defray reagent costs and operating expenses, while ensuring members access to a state-of-the-art facility at low cost. The high throughput of the DNA sequencer and the use of three trained staff members for DNA sequencing now results in a typical turnaround time of 1 day for most sequencing. Thus, researchers are freed from performing these critical support experiments for their work, and can focus on the application of these technologies to addressing the important questions in their research programs. By providing synthetic oligonucleotides to all members of the University, many studies are greatly facilitated at significant cost discounts over what individual laboratories could obtain. The DNA Synthesis pricing policy reflects a significant discount on the list prices from IDT, the commercial provider of the service, based on the bulk orders placed by the facility. The DNA synthesis and sequencing facility serves our entire scientific community at RWJMS and Rutgers University. This is an example where our Departmental resources have been used to develop a core facility that is essential for the scientific development of RWJMS. Flow Cytometry and Cell Sorting Facility

The Flow Cytometry and Cell Sorting Core Facility is a departmental core comprised of a FacScan Analyzer and a FacSvantage SE with Diva and is located in the Staged Research Building with Dr. Yufang Shi as the Director. Flowcytometers can measure several parameters on many thousands of individual cells in a short time, by detecting their fluorescence and the way they scatter light. This facility provides services to many labs of our department for cell sorting, cloning, and analysis for cell surface markers, intracellular proteins, and cell cycle. Outside investigators may use this facility by paying a membership fee and providing their own reagents. Fluorescence Resonance Energy Transfer Facility This year sees the beginning of a new core facility for the Department. The Real-Time Fluorescence Resonance Energy Transfer Facility, directed by Christopher D. Krause, PhD., was established. The purpose of this facility is to observe interactions between proteins in intact cells using Fluorescence Resonance Energy Transfer (FRET). Equipment leasing funds were used to purchase the necessary instruments and build the machine. A confocal microscope (Olympus IX71FVSF confocal microscope) was coupled to a spectrophotometer (Acton SP-150 Spectrophotometer) so that fluorescent emission spectra as well as spatial imaging can be obtained from light emitted from a confocal scanning of a biological sample. Samples are illuminated either by transmitted light and visualized by light microscopy or differential image contrast microscopy (Nomarsky microscopy), by widefield epifluorescence using a mercury lamp as the excitation source, or by laser excitation from either of five continuous wave lasers: a solid-state helium-cadmium laser emitting 442 nm light, an argon laser emitting both 488 and 514 nm light, a 532 nm helium-neon laser, or a 633 nm helium-neon laser. This instrument is one of the first in the nation to rigorously measure Fluorescence Resonance Energy Transfer in real time in cells with the use of cyan and yellow fluorescence proteins by capturing the full spectra of the fluorescence transfer to precisely ascertain the quality of the interactions between proteins in live cells. (See Krause et al., Molecular and Cellular Proteomics, 1, 805-815, 2002 for further details.) Phosphorimager Facility Dr. Gary Brewer (PI) serves as the Director of this facility. The Imaging Facility consists of an Amersham Biosciences 9410 variable mode imager. The unit is housed in the Research Tower of the Piscataway, NJ campus. This instrument can detect and analyze fluorescent, chemiluminescent and radioactive signals. The phosphorimager requires the use of Molecular Dynamics cassettes for analysis of radioactive samples. The cassettes can be used with 3H, 14C, 35S, as well as 32 P and 33P. All members of the department use the instrument without charge for facility use. Other investigators pay an annual user fee of $400 to help cover the cost of the service contract. The Director trains users and any of their staff at periodic training sessions. Appropriate supplies are provided by the department to cover the costs of its use. Investigators who wish to use the facility will be trained by the Director

of the facility and/or his staff. Real-Time PCR Facility Real-time reverse transcription (RT) polymerase chain reaction (PCR) is the most sensitive and reliable method for the detection and quantitation of nucleic acids levels. A Stratagene Mx-4000 Multiplex Quantitative System provides an accurate method for real time determination of PCR products as they accumulate during PCR and thus enables accurate quantitation of the levels of specific DNA and RNA sequences in multiple tissue samples. This system is based on detection of fluorescent signals. The Real-Time PCR Core is located in the Staged Research Building. Dr. Yufang Shi is the Director of this facility and it is used by many labs in the department.

DOCTORAL PROGRAM IN MOLECULAR GENETICS, MICROBIOLOGY, and IMMUNOLOGY Program Description The Graduate Program in Molecular Genetics, Microbiology, and Immunology offers a comprehensive program leading to the Ph.D. for graduate students anticipating careers as investigators and teachers. An M.D./Ph.D. program is also available. Graduate studies include formal training in biochemistry, molecular and cell biology, immunology, virology and elective courses based on the student’s own interest, selected from among the offerings at UMDNJ-Robert Wood Johnson Medical School (RWJMS) and Rutgers, The State University of New Jersey. Course work is supplemented by seminars, journal clubs and laboratory rotations designed to provide students with a broad background in the theory and methodology of molecular and cell biology. The program offers research opportunities in the Department of Molecular Genetics, Microbiology, and Immunology of UMDNJ-Robert Wood Johnson Medical School and other departments of RWJMS, as well as Rutgers University, the New Jersey Center for Advanced Biotechnology and Medicine, the Cancer Institute of New Jersey, and the Environmental and Occupational Health Sciences Institute. Research training is provided in many aspects of molecular genetics, microbiology, and immunology, including cellular immunology, molecular genetics of eukaryotic and prokaryotic cells, the interaction of viruses with host cells, retrovirology, nucleic acid and protein structure, structure and action of interferon receptors, transmembrane signal transduction and many other areas. Program Consolidation and Coordination To improve recruitment of graduate students to this campus and to provide a comprehensive first year curriculum, the Graduate Program in Molecular Genetics, Microbiology, and Immunology merged its recruitment and admissions activities somel years ago with those of six other Coordinated Graduate Programs of Rutgers University and UMDNJ-Graduate School of Biomedical Sciences. This effort is designated the Consolidated Graduate Program in the Molecular Biosciences. These seven programs sponsor a shared first year Core Curriculum of graduate courses; these courses are taught by members of all participating programs.

Molecular Genetics and Microbiology Graduate Program ENTRY GRADUATE STUDENT PROGRAM MENTOR DATE BANIHASHEMI, Lili GSBS Micro Gary Brewer, PhD 9/1/04 CABAN-VEGA, Hector GSBS Paul Coplend, PhD 9/1/02 CABAN, Kelvin GSBS Micro Paul Copeland, PhD 9/1/03 CHESONI, Sandra GSBS Micro Gary Brewer, PhD 9/1/03 DEFREN, Jennifer GSBS Micro Gary Brewer, PhD 9/1/03 GRATACOS, Frances Joint Micro Gary Brewer, PhD 9/1/03 GREEN, Yvette GSBS Micro Terri Goss Kinzy, PhD 9/1/02 GUPTA, Malivika GSBS Micro Gary Brewer, PhD 7/1/04 LEE, Rose GSBS Micro Joseph Dougherty, PhD 9/0/04 *LIAO, Willey GSBS Micro S.Peltz, Ph.D. MGMI, 9/1/02 LIU, Mohan GSBS Micro Nancy Woychik, PhD 6/1/04 MICHEVA-VITEV, Sofiya GSBS Micro Joseph Dougherty, PhD 9/1/02 MUKHERJEE, Sayandip GSBS Micro Joseph Dougherty, PhD 9/1/01 ORTIZ, Pedro GSBS Micro Terri Goss Kinzy, PhD 9/1/00 OZTURK, Sedide GSBS Micro Terri Goss Kinzy, PhD 9/1/03 PHELAN, Bradley GSBS Micro Joseph Dougherty, PhD 9/1/03 PRYSAK, Meredith GSBS Micro Nancy Woychik, PhD 9/1/01 RUIDIAZ, Estelle GSBS Micro Gary Brewer, Ph.D. 9/1/02 SUTPHEN, Kristina GSBS Micro Gary Brewer, Ph.D. 9/1/02 SWAIMS, Alison GSBS Micro Arnold Rabson, M.D. 9/1/03 YANG, Zhihong GSBS Micro Sidney Pestka, MD 9/1/00 * Masters

Students Receiving Ph.D Degrees Date/Host Speaker Title 12/06/05 Pedro Ortiz “Analysis of the Regulation of Translation Elongation Dr. Kinzy Thesis Defense Factor 2 Levels and Posttraslational Modifications in Saccharomyces cervisiae” 05/01/06 Kristi Lynne Muldoon “CIS and Trans-Acting Factors Affecting Translational Dr. Dinman Thesis Defense Fidelity: Robosomal Protein L11 and the RAC Complex”

Courses

PA Microbiology 2005 – Schedule Lectures and examinations are held in the East Lecture Hall (ELH) Lab exercises are held in Rooms N-2 to N-6 & N-7 to N-11 on the second floor of the Teaching Laboratories Week 2: August 15-19 Tues 16 Aug 1:00 – 3:00 Lecture 1: Introduction to medical microbiology Lecture 2: What kinds of microbes cause disease? Wed 17 Aug 1:00 – 3:00 Lecture 3: Structure of bacterial cells Workshop: Serial dilutions (ELH) Thurs 18 Aug 1:00 – 3:00 Math & Chemistry Exam Fri 19 Aug 1:00 – 3:00 Lecture 4: Bacterial genomes Lecture 5: Bacterial genetics-1 Week 3: August 22-26 Tues 23 Aug 1:00 – 4:00 Lecture 6: Bacterial genetics-2 Lab 1: Normal flora; transmission of bacteria Wed 24 Aug 1:00 – 4:00 Lecture 7: Sterilization & disinfection; precautions against infection Review for Exam I Thurs 25 Aug 1:00 – 4:00 Lab 1: Results and Discussion Fri 26 Aug 1:00 – 4:00 Exam I: Lectures 1-7 Lab 1 Week 4: August 30 – September 2 Tues 30 Aug 1:00 – 4:00 Lab 2: Microscopy and culture of bacteria Wed 31 Aug 1:00 – 3:00 Lecture 8: Immunity Lecture 9: Antibodies -1 Thurs 1 Sept 1:00 – 3:00 Lab 2: Results and discussion Fri 2 Sept 1:00 – 3:00 Lecture 10: Antibodies -2 Lecture 11: Reaction between antigen & antibody - 1 Week 5: September 5-9 Tues 6 Sept 1:00 – 4:00 Lab 3: Nutritional requirements; urine culture Wed 7 Sept 1:00 – 3:00 Lecture 12: Reaction between antigen & antibody -2 Lecture 13: Complement Thurs 8 Sept 1:00 – 4:00 Lecture 14: Cells & tissues of the immune system -1 Lab 3: Results & discussion Fri 9 Sept 1:00 – 3:00 Lecture 15: Cells & tissues of the immune system -2 Lecture 16: Cells & tissues of the immune system -3

Week 6: September 12-16 Tues 13 Sept 1:00 – 4:00 Lab 4: Gram stain; Unknown 1 Thurs 15 Sept 1:00 – 3:00 Lecture 17: Cytokines Lecture 18: Transfusion immunology Fri 16 Sept 1:00 – 3:00 Lecture 19: The Major Histocompatibility Complex (MHC) Lecture 20: Transplantation Immunology Week 7: September 19-23 Tues 20 Sept 1:00 – 4:00 Lab 5a: Radial Immunodiffusion (RID) Lab 5b: Blood typing Wed 21 Sept 1:00 3:00 Lecture 21: Inflammation Lecture 22: Hypersensitivity Thurs 22 Sept 1:00 – 4:00 Lecture 23: Immunodeficiency Labs 5a/5b: Results and discussion Fri 23 Sept 1:00 – 4:00 Lecture 24: Antibiotics – 1 Lecture 25: Antibiotics – 2 Review for Exam II Week 8: September 26-30 Tues 27 Sept 1:00 – 3:00 Exam II: Lectures 8-23; Labs 2-5a/5b; Cumulative component Wed 28 Sept 1:00 – 3:00 Lecture 26: Bacteria and disease Lecture 27: Neisseria Thurs 29 Sept 1:00 - 3:00 Lecture 28: Streptococci Lecture 29: Staphylococci Fri 30 Sept 1:00 – 4:00 Lecture 30: Gram-negative rods-1 Lecture 31: Gram-negative rods-2 Cases 1: Pyogenic cocci Week 9: October 3-7 Tues 4 Oct 1:00 – 4:00 Lab 6: Neisseria Wed 5 Oct 1:00 – 3:00 Lecture 32: Gram-negative rods-3 Lecture 33: Gram-positive rods Thurs 6 Oct 1:00 – 4:00 Lecture 34: Gram-negative anaerobes Lab 6: Results & discussion

Fri 7 Oct 1:00 – 4:00 Lecture 35: Chlamydia, Rickettsia, Ehrlichia Lecture 36: Mycoplasma & Spirochetes Cases 2: Gram-negative rods Week 10: October 10-14 Tues 11 Oct 1:00 – 5:00 Lab 7: Gram-positive unknown Wed 12 Oct 1:00 – 4:00 Lab 7: Gram-positive unknown Thurs 13 Oct 1:00 – 4:00 Lecture 37: Fungi Lab 7: Gram-positive unknown Fri 14 Oct 1:00 – 3:00 Lecture 38: Mycobacteria Cases 3: Gram-positive rods, anaerobes, etc. Week 11: October 17-21 Tues 18 Oct 1:00 – 4:00 Lab 8: Gram-negative unknown Wed 19 Oct 1:00 – 5:00 Lecture 39: Mycoses Lab 8: Gram-negative unknown Thurs 20 Oct 1:00 – 5:00 Lecture 40: Protozoa – 1 Lab 8: Gram-negative unknown Fri 21 Oct 1:00 – 3:00 Lecture 41: Protozoa – 2 Cases 4: Mycobacteria, etc. Week 12: October 24-28 Tues 25 Oct 1:00 – 4:00 Lecture 42: Introduction to virology – 1 Lab 8: Gram-negative unknown Lab 9: Haemophilus, Clostridium, Mycobacterium Wed 26 Oct 1:00 – 3:00 Lab 8: Gram-negative unknown Lab 9: Haemophilus, Clostridium, Mycobacterium Thurs 27 Oct 1:00 – 4:15 Lab 10: Fungi Review for unknown IV (in lab) Fri 28 Oct 1:00 – 4:00 Lecture 43: Introduction to virology – 2 Cases 5: Fungi & Protozoa Review for Exam III Week 13: October 31-November 4 Tues 1 Nov 1:00 – 3:00 Exam III : Covers Lectures 24-41 ; Cases 1-5; Labs 6-10 ; Cumulative component Week 14: November 7-11 Mon 7 Nov 1:00 – 4:00 Lab 11: Unknown 4 Tues 8 Nov 1:00 – 4:00 Lab 11: Unknown 4 Wed 9 Nov 1:00 – 4:00 Lab 11: Unknown 4

Thurs 10 Nov 1:00 – 4:00 Lecture 44: (-) Strand ssRNA viruses -1 Review for Lab Practical Exam (in lecture hall) Lab 11: Unknown 4 Fri 11 Nov 3:00 – 4:00 Lab 11: Unknown 4 Week 15: November 14-18 Tues 15 Nov 1:00 – 5:00 Lab Practical Exam Wed 16 Nov 1:00 – 3:00 Lecture 45: (-)strand ssRNA viruses -2 Lecture 46: (+)strand ssRNA viruses - 1 Thurs 17 Nov 1:00 – 4:00 Lecture 47: (+)strand ssRNA viruses – 2 dsRNA viruses Lecture 48: Retroviruses Lecture 49: HIV Fri 18 Nov 3:00 – 4:00 Lecture 50: AIDS Week 16: November 21-25 Tues 22 Nov 1:00 – 3:00 Lecture 51: Introduction to DNA viruses; Herpesviruses-1 Lecture 52: Herpesviruses-2 Thurs 24 Nov 1:00 – 4:00 Optional laboratory exercise: Anatomical dissection of Meleagris gallopavo Week 17: November 28-December 2 Tues 29 Nov 1:00 – 3:00 Lecture 53: Papovaviruses and Adenoviruses Lecture 54: HBV; Poxviruses; Parvoviruses Thurs 1 Dec 1:00 – 3:00 Lecture 55: Prions Review: Exam IV Week 18: December 5-9 Tues 6 Dec 1:00 – 3:00 Exam IV: Lectures 42-55 ; Cumulative component Week 19: December 12-16 Fri 16 Dec 1:00 – 3:00 Microbiology Final Exam (Cumulative)

Cellular and Genetic Mechanisms 2005 – Schedule WEEK 8 Tue. Sep. 27 9:00 Course introduction Will Zehring, Ph.D. Cell membranes Frank Wilson, Ph.D. Mike Newlon, Ph.D. 9:50 Lecture: Overview of cell structure Frank Wilson, Ph.D. 10:35 Lab: Use of the Microscope & Cytology Frank Wilson, Ph.D. Thu. Sep. 29 10:00 Lecture: Receptors & cell signaling Patrizia Casaccia-Bonnefil, M.D., Ph.D. 11:00 Lecture: Apoptosis Geoff McAuliffe, Ph.D. Fri. Sep. 30 9:00 Lecture: Protein synthesis & cell secretion John Pintar, Ph.D. 10:00 Lecture: Endosome/lysosome pathway John Pintar, Ph.D. 10:45 Lab: Cytology WEEK 9 Tue. Oct. 4 9:00 Lecture: Cell adhesion molecules & cell junctions Frank Wilson, Ph.D. 10:00 Lecture: Introduction to epithelia Frank Wilson, Ph.D. 10:30 Lab: Epithelial tissue Thu. Oct. 6 10:00 Lab: Epithelial tissue 11:00 Lab: Epithelial tissue Fri. Oct. 7 9:00 Lecture: Extracellular matrix & ECM receptors John Pintar, Ph.D. 10:30 Lecture: Introduction to connective tissue Geoff McAuliffe, Ph.D. 11:00 Lab: Connective tissue WEEK 10 Tue. Oct. 11 9:00 Review Geoff McAuliffe, Ph.D. 10:00 Blood & myeloid tissue Frank Wilson, Ph.D. 10:30 Lab: Connective tissue Thu. Oct. 13 10:00 Structure and function of cartilage Geoff McAuliffe, Ph.D. 10:30 Introduction to cartilage & bone Frank Wilson, Ph.D. 10:45 Lab: Blood and cartilage Fri. Oct. 14 9:00 Bone: structure, function, development Sarah Hitchcock-DeGregori, Ph.D. 10:30 Lab: Cartilage and bone

Cellular and Genetic Mechanisms 2005 – Schedule x WEEK 11 Tue. Oct. 18 9:00 Cytoskeleton James Zheng, Ph.D. 10:00 Introduction to skeletal muscle Frank Wilson, Ph.D. 10:30 Lab: Skeletal muscle Thu. Oct. 20 10:00 Molecular Motors Sarah Hitchcock-DeGregori, Ph.D. 11:00 Muscle contraction Sarah Hitchcock-DeGregori, Ph.D. Fri. Oct. 21 9:00 Cardiac and smooth muscle Frank Wilson, Ph.D. 10:00 Lab: Skeletal, cardiac, & smooth muscle x WEEK 12 Tue. Oct. 25 9:00 Neurocytology – 1 Cheryl Dreyfus, Ph.D. 10:00 Neurocytology – 2 Cheryl Dreyfus, Ph.D. 10:30 Introduction to neural tissue Frank Wilson, Ph.D. 11:00 Lab: Neural tissue Thu. Oct. 27 10:00 Stem cells Geoff McAuliffe, Ph.D. 11:00 Neuroregeneration Cheryl Dreyfus, Ph.D. Fri. Oct. 28 9:00 Exam Review 10:00 Practice practical exam 11:00 Lab: Neural Tissue WEEK 13 Fri. Nov. 4 9:00 Exam I WEEK 14 Mon. Nov. 7 10:00 DNA structure, replication, repair, recombination Celine Gelinas, Ph.D. 11:00 DNA structure, replication, repair, recombination Celine Gelinas, Ph.D. Wed. Nov. 9 10:00 DNA structure, replication, repair, recombination Celine Gelinas, Ph.D. 11:00 DNA structure, replication, repair, recombination Celine Gelinas, Ph.D Thu. Nov. 10 10:00 RNA synthesis Michael Hampsey, Ph.D. 11:00 RNA synthesis Michael Hampsey, Ph.D. Fri. Nov. 11 1:00 RNA processing Michael Hampsey, Ph.D. 2:00 Review session

Cellular and Genetic Mechanisms 2005 – Schedule X WEEK 15 Mon. Nov. 14 10:00 Protein synthesis Marilyn Kozak, Ph.D. 11:00 Protein synthesis Marilyn Kozak, Ph.D. Wed. Nov. 16 10:00 Recombinant DNA Yuh-Hwa Wang, Ph.D. 11:00 Recombinant DNA Yuh-Hwa Wang, Ph.D. Thu. Nov. 17 10:00 Recombinant DNA Yuh-Hwa Wang, Ph.D. 11:00 Skills session: Restriction mapping & DNA sequence analysis Fri. Nov. 18 1:00 Mitosis and Chromosomes Mike Newlon, Ph.D. 2:00 Review WEEK 16 Mon. Nov. 21 10:00 Control of cell division - 1 James Millonig, Ph.D. 11:00 Control of cell division - 2 James Millonig, Ph.D. Wed. Nov. 23 10:00 Human genome & karyotype Mike Newlon, Ph.D. 11:00 Cancer - cell biology and genetics Mike Newlon, Ph.D. WEEK 17 Mon. Nov. 28 10:00 Meiosis and recombination Mike Newlon, Ph.D. 11:00 Sex chromosome anomalies & Lami Yeo, M.D. Autosomal trisomies Wed. Nov. 30 9:00 FISH Kiran Chada. D. Phil. 10:00 Clinical cytogenetics & Genetic imprinting Len Sciorra, Ph.D. 11:00 Pedigree analysis Mike Newlon, Ph.D. Thu. Dec. 1 10:00 Methods for prenatal diagnosis Lami Yeo, M.D. 11:00 Population genetics Mike Newlon, Ph.D. Fri. Dec. 2 1:00 Skills session: karyotypes, cytogenetics, FISH 2:00 Review session WEEK 18 Mon. Dec. 5 10:00 Genetic Counseling Elena Ashkinadze, M.S. 11:00. Triplet expansions Yuh-Hwa Wang, Ph.D. Wed. Dec. 7 9:00 DNA-based diagnostic tests Mike Newlon, Ph.D. 10:00 Microchip analysis of nucleic acids Kiran Chada. D. Phil. 11:00 Skills session: Risk analysis, DNA tests Thu. Dec. 8 10:00 Small-group case presentations 11:00 Small-group case presentations Fri. Dec. 9 1:00 Mutations and phenotypes Mike Newlon, Ph.D 2:00 Sexual differentiation disorders Cynthia Meyers-Seifer, Ph.D.

Cellular and Genetic Mechanisms 2005 – Schedule X WEEK 19 Mon. Dec. 12 10:00 Genetic basis of disease - single genes Mike Newlon, Ph.D. 11:00 Skills session: single-gene mapping Wed. Dec. 14 9:00 Complex disorders – 1 Linda Brzustowicz, M.D. 10:00 Complex disorders – 2 Linda Brzustowicz, M.D. 11:00 Skills session - Complex disorders Thu. Dec. 15 10:00 Skills session - Complex disorders 11:00 Exam Review WEEK 20 Wed. Dec. 21 9:00 Exam II

Medical Microbiology and Immunology–2006 T Lectures, Discussions, Case Presentations, and Exams are held in the Main Lecture Hall [MLH] unless otherwise specified. Laboratory Exercises meet in the Multi-discipline Labs S-212 and S-220, South Wing, second floor of the Teaching Laboratories. Patient-Oriented Problem-Solving [POPS] Exercises meet in the Small Group Rooms: C-1 through C-12, C-207, C-208. Unit I: Immunology & Basic Bacteriology Week 21: Cells and Tissues of the Immune System Weds 4 Jan 1:30-2:20 Overview of the Course [Drs. Pestka, Newlon] [ELH, overflow in WLH] 2:30-3:20 Lecture: Immunity and Inflammation [Dr. Newlon] [ELH/WLH] Thurs 5 Jan 10:30-11:20 Lecture: Cells & Organs of the Immune System [Dr. Newlon] [ELH/WLH] 11:30-12:20 Lecture: Identification of Immune-system Cells [ELH/WLH] Assigned reading: Cytokines, CD Antigens Fri 6 Jan 9:30-10:20 Discussion: Immune cells, CD antigens [ELH/WLH] Week 22: Antibodies Weds 11 Jan 11:30-12:20 Lecture: Antibodies [Dr. Li] Assigned reading: Immunization, Tumor Immunology Thurs 12 Jan 10:30-12:20 POPS Exercise I – Immunity to Tetanus Fri 13 Jan 9:30-10:20 Discussion: Antibody Structure Case presentation: Multiple Myeloma [MLH] Week 23: Immunochemistry Weds 18 Jan 10:30-11:20 Lecture: Immunochemistry [Dr. Kimball] Assigned reading: Serology: Diagnostic Use of Antibody-Antigen Reactions Assigned reading: Transfusion Immunology, Complement Thurs 19 Jan 10:30-12:20 POPS – Jaundiced Baby Fri 20 Jan 9:30-10:20 Discussion: Interpretation of Immunodiagnostic Tests; Blood Typing Week 24: The Major Histocompatibility Complex [MHC] and its Roles in the Immune System Weds 25 Jan 10:30-11:20 Lecture: The Major Histocompatibility Complex [Dr. Ron] Assigned reading in syllabus: Transplantation Immunology Thurs 26 Jan 10:30-12:20 POPS – MI Sick Fri 27 Jan 9:30-10:20 Discussion: MHC Week 25: Immunological Disease; Immunization

Weds 1 Feb 11:30-12:20 Lecture: Inflammation and Hypersensitivity [A. Kumar, M.D.] Assigned reading in syllabus: Immunodeficiency, Neuroimmunology Thurs 2 Feb 10:30-12:20 POPS – Immediate Hypersensitivity Fri 3 Feb 9:30-10:20 Discussion [MLH]: Diagnosis of Immunodeficiency Discussion [MLH]: Structure of Major Histocompatibility Antigens Discussion [MLH]: Pre-Transplantation Testing 1:00 Prep meeting for Lab 1 Week 26: Basic Bacteriology Tues 7 Feb 8:30- 9:20 Lecture: Structure of Bacteria [Dr. Newlon] Weds 8 Feb 10:30-11:20 Lecture: Genetics of Bacteria [Dr. Brewer] 11:30-12:20 Lab 1 – Microscopy and Culture of Bacteria Thurs 9 Feb 9:30-10:20 Q & A for Exam Review [MLH] [Optional] 10:30-12:20 Lab 1 – Concluded (Report due Thursday Feb 23) Week 27: Exam I [Covers Weeks 21 – 26] Fri 17 Feb 10:30-12:30 Exam I [in MLH] Unit II: Medical Bacteriology; Fungi & Parasitic Protozoa Week 28: Antimicrobial Agents Weds 22 Feb 10:30-11:20 Lecture: Antibiotics [Dr. Copeland] Assigned reading in Syllabus: Phagocytes Assigned reading in Syllabus: Introduction to Medical Microbiology [NB: read through this lightly now and seriously when reviewing for the exam.] Thurs 23 Feb 10:30-12:20 POPS – Antibiotics Fri 24 Feb 9:30-10:20 Discussion: Antibiotic Sensitivity Testing; determination of MIC & MBC 1:00 Prep meeting for Lab 2 Week 29: Pyogenic Cocci Weds 1 Mar 10:30-11:20 Lecture: Pyogenic Cocci [Lecturer TBA] Assigned reading in syllabus: Neisseria; Staphylococci; Streptococci ASM cases (on computers): 17, 26 (Skin and Soft Tissue infections, 3 (Respiratory tract infections), 2 (GU infections), 22 (CNS infections) 11:30-12:20 Lab 2: Gram-positive cocci unknown (Report due 3/8) Thurs 2 Mar 10:30-12:20 Lab 2 – Continued

Fri 3 Mar 8:30- 9:20 Discussion: Pyogenic Cocci; ASM CHx 2, 3, 17, 22, 26 9:30-10:20 Lab 2 – Concluded 1:00 Prep meeting for Lab 3 Week 30: Enterobacteriaceae and Related Bacteria Weds 8 Mar 10:30-11:20 Lecture: Enterobacteriaceae & Relatives: [Dr. Newlon] ASM cases (on computers): 1 (GU infections), 5 (Respiratory tract infections), 12 (GI Infections) 11:30-12:20 Lab 3 – Gram-negative rods unknown (Report due 3/15) Thurs 9 Mar 10:30-12:20 Lab 3 – Continued Fri 10 Mar 8:30- 9:20 Discussion: Enterobacteriaceae etc.; ASM CHx 1,5,12 9:30-10:20 Lab 3 – Concluded 1:00 Prep meeting for Lab 4 Week 31: Gram-Positive Rods Weds 15 Mar 10:30-11:20 Lecture: Anthrax [Dr. Godyn] Assigned Reading in Syllabus: Gram-Negative Rods – 2; Gram-Negative Anaerobes; Gram-positive rods ASM Cases (on computers): 11 (Respiratory Infections, 16 (GI Infections) 11:30-12:20 Lab 4 – CSF Unknown (Report due 3/22) Thurs 16 Mar 10:30-12:20 Lab 4 – Concluded Fri 17 Mar 9:30-10:20 Discussion: Gram-Positive Rods; Gram-Negative Rods; Anaerobes; ASM CHx 11, 16 Week 32: Mycoplasma, Spirochetes, Chlamydia, Rickettsia, Mycobacteria. Weds 22 Mar 10:30-12:20 Infectious Disease Case Presentations: Bruce Fisher, M.D. [MLH] Thurs 23 Mar 10:30-11:20 Lecture: Mycoplasma, Spirochetes, Chlamydia, Rickettsia. [Dr. Woychik] ASM Cases (on computers): 20 (Skin & Soft Tissue Infections), 33 (Emerging Infections) Assigned reading in syllabus: Mycobacteria ASM Cases (on computers): 4 (Respiratory Infections), 25 (CNS Infections), 28 (Systemic Infections) 11:30-12:20 Discussion: Q & A for Exam Review; Mycoplasma, etc. Week 33: Parasitic Protozoa & Fungi Weds 29 Mar 10:30-11:20 Lecture: Protozoa –1 [Dr. Leibowitz] 11:30-12:20 Lecture: Protozoa – 2 [Dr. Leibowitz] ASM Cases (on computers): 14 (GI Infections), 21 (Skin & Soft Tissue Infections), 30 (systemic Infections)

Thurs 30 Mar 10:30-11:20 Lecture: Fungi and Mycoses [Dr. Newlon] ASM Cases (on computers): 7-10 (Respiratory Tract), 23,24 (CNS Infections), 27, 29 (Systemic Infections) 11:30-12:20 Discussion: Protozoa; Fungi; ASM CHx 14, 21, 30; 7-10, 23-24; 27; 29 Week 34: Exam II Mon 3 Apr 10:30-12:30 Exam II [in MLH] Unit III: Viruses Week 35: Biology of Viruses Tues 11 Apr 2:30-3:20 Lecture: Introduction to Virology – 1 [Dr. Stollar] 3:30-4:20 Lecture: Introduction to Virology – 2 [Dr. Stollar] Weds 12Apr 10:30-12:20 Infectious Disease Case Presentations [Bruce Fisher, M.D.][MLH] Week 36: Influenza and Related Viruses Weds 19 Apr 10:30-11:20 Lecture: Influenza & Other Viruses with (-) ssRNA Genomes ASM Cases (on Computers): 2 (GI Infections), 6 (Respiratory Infections), 19 (Systemic Infections) Thurs 20 Apr 10:30-12:20 POPS: Serological Diagnosis of Influenza Fri 21 Apr 9:30-10:20 Discussion: (-) Strand ssRNA Viruses ASM Cases: 10, 11, 24, 35, 67 [in Book, not on computer] Week 37: Polio Virus, Hepatitis C Virus, and Their Relatives; Herpes and Other DNA Viruses Weds 26 Apr 10:30-12:20 Infectious Disease Case Presentations [Bruce Fisher, M.D.][MLH] Thurs 27 Apr 10:30-11:20 Lecture: Polio, HCV, & Related Viruses [Dr. Stollar] Assigned Reading: Polio, other (+)ssRNA viruses; ds RNA viruses ASM Cases: 6, 13, 19 11:30-12:20 Lecture: Herpesviruses [Dr. Schein] Fri 28 Apr 9:30-10:20 Discussion: (+)Strand ssRNA & DNA Viruses [MLH]; ASM CHx 2, 6, 19 Week 38: Retroviruses, HIV, and AIDS Weds 3 May 10:30-11:20 Lecture: Retroviruses [Dr. Dougherty] ASM Case (on Computers): 31 (Emerging Infections) Assigned reading in syllabus: Hepatitis B virus; ds RNA Viruses Thurs 4 May 10:30-11:20 Lecture: HIV [Dr. Rabson] 11:30-12:20 Lecture: AIDS [Dr. Rabson]

Fri 5 May 9:30-10:20 ASM Cases (on computers): 18 (Skin and Soft Tissue Infectons), 32 (Emerging Infections) Discussion: Retroviruses, HIV, AIDS; ASM CHx 31 Week 39: Antiviral Drugs; Interferons; Prions Weds 10 May 10:30-11:20 Discussion: Antiviral Drugs, Interferons, Prions ASM Case 34; Q & A for Exam Review 11:30-12:20 Lecture: Interferons [Dr. Pestka] Assigned Reading in Syllabus: Prions; Antiviral Drugs; ASM Case 34 [EM] Week 40: Exam III Fri 19 May 9:30-12:30 Exam III [in MLH]

HOLOWCZAK MEMORIAL FUND The Holowczak Memorial Fund was established in 1986 in memory of Professor John A. Holowczak. Dr. Holowczak was a member of the Department of Molecular Genetics, Microbiology and Immunology for 18 years before his untimely death in 1986. The fund was established for travel awards for graduate students and postdoctoral fellows in this department. The interest earned to date is $20,826.07. The current balance is $27,128.30. This year travel awards were made to the following students: $500 to Kelvin Caban, $500 to Pedro Ortiz, and $500 to Meredith Prysak. This fund has been extraordinarily useful for the department as it supports the travel of MGMI students and fellows to attend scientific meetings and to make presentations at national and international symposia. It provides these developing investigators with exposure to other colleagues in their area of research, which is a very important part of their experience and maturation as productive scientists. This fund serves to honor Dr. Holowczak who was an extraordinary professor who was cherished by students, fellows and other members of the faculty and school.

Research Grant Support

GARY BREWER, PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "Post transcriptional Regulation 09/01/99- 1,231,883 256,856 25% of Health of Oncogene Messenger RNA" 11/30/06 US Army "RNA-Binding Proteins as Novel 01/01/03- 300,000 100,000 20% Oncoproteins and Tumor Suppressors" 12/31/05 National Institutes "Regulated c-myc Destabilization 07/01/02- 1,149,766 259,936 20% of Health during Differentation" 06/30/07 National Institutes "Adherence Activated Monocyte 07/15/04- 971,382 184,454 20% of Health Genes" 06/30/09 National Institutes "Role of mRNA Deacy in the Immune 07/15/04- 69,610 13,445 20% of Health System" Imaging Core Facility 06/30/09 National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka Current Direct Costs 814,691 Current Indirect Costs 342487 TOTAL 1,157,178

PAUL R. COPELAND, PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "The translational control of 08/01/03- 1,020,206 214,568 25% of Health selenoprotein synthesis" 07/31/08 Dean and Betty Gallo "The role of dietary selenium 11/01/04- 43,000 13,000 10% Prostrate Cancer Center in prostrate chemoprevention" 04/30/06 NJCCR "The role of selenocysteine 06/01/05- 3,200 3,200 0% in chemoprevention" 08/31/05 Awardee: Ruchira Ranaweera National Institutes "Functional analysis of 01/06/06- 450,450 173,250 25% of Health SBP2" 12/31/09 National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka Current Direct Costs 404,018 Current Indirect Costs 215,979 TOTAL 619,997

JOSEPH P. DOUGHERTY, PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka National Institutes "Complex Involved in mRNA 05/01/99- 800,000 200,000 10% of Health Decay in Yeast" 08/31/07 National Institutes "Translational Regulation by 07/15/04- 948,155 179,096 10% of Health the TNF Alpha AU-rich Element" 06/30/09 Participating Faculty PI: Dr. S. Pestka National Institutes "High Throughput Screening to 06/01/06- 1,028,346 436,310 10% of Health Identify Antagonists of HIV-1 05/31/09 Latency" Current Direct Costs 815406 Current Indirect Costs 305,684 TOTAL 1,121,090

TERRI GOSS KINZY, PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "Regulators of Translation 08/01/98- 930,381 240,778 30% of Health Elongation Factor 1 Alpha" 07/31/07 National Science "CAREER: Molecular Interactions and 09/01/00- 276,830 10% Foundation Nucleotide Exchange Mechanism of 08/31/06 Translation Factor EF1B Alpha" National Science "Regulatory mechancisms in 12/01/05- 212,217 70,739 10% Foundation oxidative stress via the guanine 11/30/08 nucleotide exchange complex translation elongation factor eEF1Balphagamma" Core Facility "DNA Synthesis/Sequencing 07/01/05- 644,437 644,437 Laboratory" 06/30/06 National Institutes "Analysis of translation 09/15/04- 57,930 28,965 of Health elongation factor 2 in yeast" 09/16/06 Awardee: Pedro Ortiz Sponsor: Terri Goss Kinzy National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 2% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka National Institutes "Role of mRNA Decay in 7/15/2004 132,728 25,750 2% of Health the Immune System" 06/30/09 DNA Core Facilty

National Institutes "Cancer Center Support 03/01/00- 470,000 95,317 of Health Grant" 2/28/2009 National Institutes "Researach in Environmental 04/01/03- 380,000 74,150 of Health Health Sciences" 3/31/2008 Current Direct Costs 1,180,136 Current Indirect Costs 179,287 TOTAL 1,359,423

JEROME A. LANGER, PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS Alliance for Lupus "Type I Interferon Antagonists 03/01/05- 418,210 201,650 25% Research for Lupus and Autoimmunity" 02/28/07 National Institutes "UMDNJ-Rutgers University 09/01/96- 1,645,247 0 25% of Health Pipeline-Initiative for Minority 02/28/09 PI: Dr. M. Leibowitz Student Development" National Institutes "Bridge to the Doctoral Degree. 09/30/01- 354,814 0 10% of Health UPR to UMDNJ" 09/29/07 PI: Dr. M. Leibowitz National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka Current Direct Costs 201,650 Current Indirect Costs 16,132 TOTAL 217,782

MICHAEL J. LEIBOWITZ, M.D., PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "UMDNJ-Rutgers University 09/01/96- 4,882,628 400,179 10% of Health Pipeline-Initiative for Minority 02/28/09 Student Development" National Institutes "Bridge to the Doctoral Degree. 09/30/01- 710,220 174,785 10% of Health UPR to UMDNJ" 09/29/07 National Science "A Novel Epigenetic Regulator 09/01/02- 250,592 20% Foundation of Viral Gene Expression in Yeast" 08/31/06 National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka National Institutes "Biotechnology Training Grant" 07/01/88- 2,756,851 0 1% of Health 06/30/10 PI: Dr. H. Pederson National Instutes MSU-UMDNJ-GSBS 08/01/05- 675,000 76,298 5% of Health Bridges to the Doctorate 6/30/2006 National Institutes "Enhancing Intestinal & Brain 04/01/02- 1,375,457 0 10% of Health Uptake of Anti-AIDS Drugs" 03/31/06 Participating Faculty PI: Dr. P. Sinko Current Direct Costs 651,262 Current Indirect Costs 37,922 TOTAL 689,184

HONGHUA LI, PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka Current Direct Costs 0 Current Indirect Costs 0 TOTAL 0

MEI-LING LI, PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes Novel IRES-specific transacting 05/15/06- 100,000 50,000 50% of Health factors that modulate EV7-1 04/30/08 translation Current Direct Costs 50,000 Current Indirect Costs 27,750 TOTAL 77,750

SIDNEY PESTKA, M.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "Virus-Host Interactions in 09/30/91- 734,799 149,461 10% of Health Eukaryotic Cells" 08/31/08 National Institutes "Receptor-Signaling Protein 04/01/04- 900,000 225,000 5% of Health Interactions in Real Time" 03/31/08 National Institutes "Regulation of Cytokine Gene 07/15/04- 955,646 185,400 10% of Health Expression by mRNA Turnover" 06/30/09 National Institutes "Role of mRNA Decay in the 07/15/04- 250,591 48,616 2% of Health Immune System" 06/30/09 Administrative Core National Institutes "Role of mRNA Decay in the 07/15/04- 13,273 2,575 2% of Health Immune System" 06/30/09 Real-time FRET Core Healthcare Foundation Treatment & Prevention 08/01/05- 300,000 300,000 15% of Cervical Dysplasia & 7/31/2006 Cancer Current Direct Costs 911,052 Current Indirect Costs 265,796 TOTAL 1,176,848

ARNOLD RABSON, M.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "Activation of HTLV-1 Gene Expression 12/07/01- 890,000 173,817 25% of Health and Oncogensis" 11/30/06 National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka National Institutes "Effects of TPA on 07/01/03- 1,107,160 0 10% of Health Leukemia and Solid Tumors" 03/31/07 PI: Dr. A. Conney National Institutes "Training Program in 08/01/03- 985,621 0 5% of Health Translational Research in Cancer" 06/30/08 PI: Dr. E. Lattime Current Direct Costs 173,817 Current Indirect Costs 93,724 TOTAL 267,541

YACOV RON, PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "A Gene Therapy Approach 9/15/2004- 639,892 158,071 30% of Health for the treatment of EAE" 05/31/08 Quigley Corporation Effect of Quigley Pharm 09/01/05- 20,000 20,000 0% Compound QR440 product 06/29/06 on the induction and progression of EAE" Quigley Corporation "Assessment of anti-inflamatory 06/15/05- 12,000 12,000 0% properties of QR440" 06/14/06 Quigley Corporation "Assessment of protection 06/30/05- 25,000 25,000 0% from irradiation of QR336" 06/29/06 National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka Current Direct Costs 215,071 Current Indirect Costs 87,729 TOTAL 302,800

YUFANG SHI, PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "Opioid-Mediated Fas Expression 11/01/01- 1,109,973 225,000 20% of Health in Lymphocyte Apoptosis" 06/30/06 National Space Apoptosis and Immune 04/01/06- 855,342 285,114 15% Biomedical Research Homeostasis During 03/31/09 Institute Hindlimb Unloading NJ Commission of Science Immunobiology of Mesenchymal 01/01/06- 260,870 130,435 10% and Technology Stem Cells 12/31/07 National Institutes "Regulation of RANKL Expression 7/15/2004- 992,826 192,613 15% of Health in T-Lymphocytes" 06/30/09 National Institutes "Role of mRNA Decay in the 07/15/04- 78,766 15,281 1% of Health Immune System" 06/30/09 Flow Cytometry Core National Institutes "Role of mRNA Decay in the 07/15/04- 137,618 26,699 5% of Health Immune System" 06/30/09 Real-time PCR Core National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka Current Dircet Costs 875,142 Current Indirect Costs 426,217 TOTAL 1,301,359

VICTOR STOLLAR, M.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes Regulation of Sindbis Virus 05/15/06- 600,000 200,000 25% of Health Subgenomic RNA Synthesis 04/30/09 National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka Current Direct Costs 200,000 Current Indirect Costs 105,450 TOTAL 305,450

NANCY WOYCHIK, PH.D. SOURCE TITLE AWARD TOTAL CURRENT EFFORT PERIOD DIRECT DIRECT COSTS COSTS National Institutes "Virus-Host Interactions in 09/30/91- 734,799 0 5% of Health Eukaryotic Cells" 08/31/08 Participating Faculty PI: Dr. S. Pestka National Institutes "Structural Genomics of Eukaryotic 07/01/05- 555,500 91,447 0% of Health Domain Families" 06/30/10 PI: Dr. Inouye National Institutes "Structural Genomics of 07/01/05- 270,000 34,727 0 of Health Membrane Proteins" 6/30/2010 PI: Dr. Inouye Takara Bio, Inc., Japan "Takara Bio Initiative for 10/01/05- 250,000 50,000 0 PI: Dr. Inouye Innovative Biotechnology" 9/30/2010 Takara Bio, Inc. , Japan "Single Protein Production 06/01/04- 85,000 42,500 0 PI: Dr. Inouye in Yeast Cells" 5/30/2006 Current Direct Costs 218,674 Current Indirect Costs 0 TOTAL 218,674

Summary of Outside Grant Support Year 93-94 94-95 95-96 96-97 97-98 98-99 99-00 00-01 01-02 02-03 03-04 04-05 05-06 NIH SUPPORT Direct Costs 1,321,578 2,112,637 1,740,660 2,212,010 2,012,210 2,876,948 3,425,550 3,879,828 4,792,386 4,298,753 4,442,085 4269214 4,275,553 Indirect Costs 604,722 691,679 655,237 850,309 820,359 1,118,200 1,399,058 1,510,981 2,045,795 1,783,612 1,686,718 1733160 1,795,798 Total Costs 1,926,300 2,804,316 2,395,897 3,062,319 2,832,569 3,995,148 4,824,608 5,390,809 6,838,181 6,082,365 6,128,803 6,002,374 6,071,351 OTHER AGENCY SUPPORT Direct Costs 1,993,417 2,003,935 1,601,499 1,182,561 1,259,004 1,243,032 1,372,096 1,194,170 1,569,626 1,778,429 1,558,139 1290775 1,050,940 Indirect Costs 265,790 171,280 130,875 73,348 119,199 163,061 236,535 141,089 211,197 287,104 265,273 209,236 83,367 Total Costs 2,259,207 2,175,215 1,732,374 1,255,909 1,378,203 1,406,093 1,608,631 1,335,259 1,780,823 2,065,533 1,823,412 1,500,011 1,134,307 TOTAL Direct Costs 3,314,995 4,116,572 3,342,159 3,394,571 3,271,214 4,119,980 4,797,646 5,073,998 6,362,012 6,077,182 6,000,224 5,559,989 5,326,493 Indirect Costs 870,512 862,959 786,112 923,657 939,558 1,281,261 1,635,593 1,652,070 2,256,992 2,070,716 1,951,991 1,942,396 1,879,165 Total Costs 4,185,507 4,979,531 4,128,271 4,318,228 4,210,772 5,401,241 6,433,239 6,726,068 8,619,004 8,147,898 7,952,215 7,502,385 7,205,658

SEMINARS Date/Host Speaker Title 12/06/05 Pedro Ortiz “Analysis of the Regulation of Translation Dr. Kinzy Thesis Defense Elongation Factor 2 Levels and Posttraslational Modifications in Saccharomyces cervisiae” 12/05 Gianni Garotta “The Development of Monoclonal Antibodies for the Dr. Pestka Ribovax Treatment of Disease” Biothechnologies 2/06 “Gene Therapy for Immunologic Tolerance and Vice Dr. Pestka David Scott Versa” University of Maryland 3/06 “Is mda-7/IL-24 a ‘‘Magic Bullet’’ for Cancer?” Dr. Pestka Paul Fisher Columbia University 05/01/06 “CIS and Trans-Acting Factors Affecting Dr. Dinman Kristi Lynne Muldoon Translational Fidelity: Robosomal Protein L11 and Thesis Defense the RAC Complex”

DEPARTMENT OF MOLECULAR GENETICS, MICROBIOLOGY AND IMMUNOLOGY DEPARTMENTAL RETREAT The Hilton Garden Inn g Bridgewater, New Jersey Friday, August 26, 2005 Agenda 8:30 a.m. Continental Breakfast 9:00 a.m. Greetings - Dr. Sidney Pestka 9:10 a.m. Presentations - Estelle Ruidiaz, Moderator 9:15-9:30 Angela Cook (Dr. Nancy Woychik) Bacterial toxin-antitoxin systems 9:30-9:45 Annmarie Pacchia, PhD (Dr. Joseph Dougherty) Hide and seek: HIV-1 latency & eradication 9:45-10:00 George Xu (Dr. Yufang Shi) From RANTES to RANKL 10:00-10:15 Chris Krause, PhD (Dr. Sidney Pestka) Giving an interferon-nu life 10:15-10:30 Mei-Ling Li, PhD A cell-free system for the synthesis of Sindbis virus subgenomic RNA: Importance of the concentration of the initiating NTP 10:30-10:45 Florence LeRoy, PhD (Dr. Stuart Peltz) A newly discovered function for RNase L in regulating translation termination 10:45-11:00 Hsin-Ching Lin, PhD (Dr. Arnold Rabson) HTLV-1LTR luciferase reporter cells for study of Human T-Cell leukemia virus type 1 infection (Over)

11:00 - 11:25 BREAK 11:25 Presentations - Brad Phelan, Moderator 11:30-11:45 Lili Banihashemi (Dr. Gary Brewer) AUF1: Where Nonsense-mediated Meets ARE-mediated mRNA Decay 11:45-12:00 Yvette Pittman (Dr. Terri Goss Kinzy) Structural-based mutational analysis of the translation elongation guanine nucleotide exchange factor, eEF1Bá 12:00-12:15 Gobardham Das, PhD Immunobiology of MHC class Ib-restricted CD8+T cells 12:15-12:30 Kelvin Caban (Dr. Paul Copeland) The significance of SBP2/ribosome interactions for selenocysteine incorporation 12:30-12:45 Michael Leibowitz, MD, PhD [KIL-d]: A transfectable prion-like virus control element 12:45-1:00 Manjing Pan, PhD (Dr. Jerome Langer) Type 1 interferon antagonists against Lupus 1:00 LUNCH

Department of Molecular Genetics, Microbiology and Immunology Sidney Pestka Chairman & Professor R. Wernoski Joint Faculty Appt. Adjunct Faculty Business Mgr. (15) (35) W. Barnes J. Carr Budget Analyst III Admin. Analyst IV E. Feibel Sr. Mgmt. Asst. Core Facility: G. Dava. Tech. O. Gamble - Lab Assistant Supp. III Z. Andes - Princ. Lab Asst. A. Finamore Admin. Coord. II May Tang - Lab Svc. Wkr. R. Reina Program Asst. Student Assistant S. Peltz J. Dougherty D. Dubin T. Kinzy M. Leibowitz G. Brewer Y. Ron Y. Shi V. Stollar Professor Professor Professor Professor Professor Professor Professor Professor Professor / (leave of Vice Chair absence) P. Copeland J. Langer H. Li N. Woychik Asst. Professor Assoc. Professor Assoc. Professor Assoc. Professor L.A. Schein M. Li M. Newlon S. Sarkar C-C. Chen S. Gross Adj. Asst.. Prof. Adj. Asst. Prof Asst. Prof Adj. Asst. Prof Adj. Asst. Prof Adj. Asst. Prof GS (6) B.Liao/RTS GS (4) Y. Hu/RTS A.Pacchia/RTS GS (3) GS (1) Y Kobiyashi/RTS B. Balar/Sr Lab Tech GS (3) A.Roberts/RTS S. Devadas/RTS X. Cui /RA GS (1) J. Das/RTS GS (2) M. Pan/RTS PD (1) L.Zhang/RTS Peltz Lab Nomi Ron /RTS C. Rebesch/RTS O. Mirochnitchenko/RTS Z. Yuan/RTS GS (2) S. Kinzy/RTS L. Izotova/RTS G. Xu/RTS D. Khounh/RTS B. Schwartz/RTS L. Xu/Prin. Lab. Asst. X. Jiang/RTS

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