Molecular Diagnostics

1. V. Shyamala
1
Accomplishments (Selected) Venkatakrishna Shyamala, PhD
•Consultant: Research Diagnostics, Inc.
•Consultant: Novartis Dx-Scientific Affairs
•CLSI Document writer -Molecular Diagnostics
•Innovative Biosensors, Inc.
•Senior VP, Research and Development
•Digene Corporation
•Director, Research and Development
•Chiron Corporation
•Associate Director, Research
•Univ of California, Berkeley
•Visiting Scientist

2. V. Shyamala
2
Accomplishments (Selected) Venkatakrishna Shyamala, PhD
•Consultant: Research Diagnostics, Inc.
•Consultant: Novartis Dx-Scientific Affairs
•CLSI Document writer -Molecular Diagnostics
•Innovative Biosensors, Inc.
•Senior VP, Research and Development
•Digene Corporation
•Director, Research and Development
•Chiron Corporation
•Associate Director, Research
•Univ of California, Berkeley
•Visiting Scientist

3. V. Shyamala
3
Accomplishments (Selected) VenkatakrishnaShyamala, PhD
•Research Diagnostics, Inc. Bengaluru, IndiaV. Shyamala(2014) Nucleic acid technology (NAT) testing for blood screening: Impact of Individual donation and minipoolNAT testing on Analytical sensitivity, Screening sensitivity and Clinical sensitivity. ISBT Science Series. In press. V. Shyamala(2014) Transfusion transmitted infections in Thalassemics: Need for reappraisal of blood screening strategy in India. Transfusion Medicine.2,79-88. V. Shyamala(2014) Factors in Enhancing blood safety by Nucleic Acid Technology Testing for Human Immunodeficiency virus, Hepatitis C virus and Hepatitis B virus. Asian J. Trans. Sci. 8, 13-18. V. Shyamala,T. Sandisonand J. A. Holmberg (2014) Individual Donation Nucleic Acid Technology testing to minimize Human Immunodeficiency virus-1, Hepatitis C virus and Hepatitis B virus Transfusion Transmitted Infections. Asian J. Trans. Sci. 8, 68.
•

4. V. Shyamala
4
Nucleic acid technology (NAT) testing for blood screening: Impact of Individual donation and minipool NAT testing on Analytical sensitivity, Screening sensitivity and Clinical sensitivity
V. Shyamala
ISBT Science Series, in press (2014)
•Blood screening requires the most sensitive assays
•Globally the donated blood is screend for HIV, HCV and HBV
•The impact of NAT testing formats and its effect on limit of detection (LOD) is elaborated
•In individual donation NAT testing, the Analytical sensitivity is equivalent to LOD
•The LOD in pooled testing decreases depending on the pool size, and is called the detection limit is called as Screening sensitivity
•The pool size dependent increase in risk days, demonstrated experimentally, and projected by calculation is presented
•Reported cases of minimum infectious units for causing infection and the compromise with pooled testing is discussed
•The results of regional variations in serology prevalence in India, the NAT detected units, the NAT testing formats are analyzed

5. V. Shyamala
5
Transfusion transmitted infections in Thalassemics: Need for reappraisal of blood screening strategy in India.
V. Shyamala
Transfusion Medicine. 2,79-88 (2014)
•The donated blood in India is tested by serology assays for human immunodeficiency viruses (HIV)1/2, Hepatitis C virus (HCV), and Hepatitis B virus (HBV).
•The markers are anti-HIV-1/2, anti-HCV and HBsAg, and a prevalence of 0.3%, 0.4% and 1.2% in the Indian donors is reported.
•The development of these markers in an infected donor requires time. In the interim the unit though infectious is negative by the serology assays and released for use
•Using repeat recipient thalassemics as the model a prevalence of up to 26% of HCV, 6% of HBV, and 4% of HIV is reported
•Individual donation blood screening in India by nucleic acid technology assays shows serology marker negative NAT yields in the range of 1/350-1/2200.
•Though NAT testing is not mandated because of cost, the enormity of transfusion transmitted infections requires a reappraisal

6. V. Shyamala
6
Factors in Enhancing blood safety by Nucleic Acid Technology Testing for Human Immunodeficiency virus, Hepatitis C virus and Hepatitis B virus
V. Shyamala
Asian J Transfusion Science 8,13-18 (2014)
•Nucleic acid technology (NAT) testing is being increasingly adopted to detect HIV-1/2, HCV and HBV in the donated blood.
•The testing can be done either in the individual donation (ID) format or in the pooled format
•The pooled format compromises sensitivity of detection
•Globally with pooled testing several cases of transfusion transmitted infections (TTI) of HIV-1, HCV and HBV have been reported.
•Since very low copies of the viruses can be infectious there have been two cases of TTI by ID format testing also
•In nearly all of the cases infectious units are realized through a repeat donor turning positive.
In the absence of repeat donor base ID-NAT testing offers safer blood versus pooled NAT testing.

7. V. Shyamala
7
Accomplishments (Selected) Venkatakrishna Shyamala, PhD
•Consultant: Scientific Affairs Novartis Vaccines & Diagnostics
•Monitoring Blood screening by Procleix®Nucleic acid technology (NAT) assays at blood banks in India
•Assist in product trials, monitoring trials, data analysis
•Provide support with NAT awareness Seminars, Workshops, Conference Presentations and Publications

8. V. Shyamala
8Accomplishments (Selected) VenkatakrishnaShyamala, PhD
•Document writer -Molecular DiagnosticsClinical & Laboratory Standards InstituteReviewer , Consensus Committee on Molecular MethodsContributor: MM06: Quantitative Molecular Methods for Infectious DiseasesMM19: Establishing Molecular Testing in Clinical Laboratories MM01-A3: Diagnostic Molecular Methods for Genetic DiseasesMM09: Nucleic acid sequencing methods in Diagnostic Laboratory MedicineMM22: Microarrays for Diagnosis and Monitoring of Infectious DiseasesPOCT14: Point-of-Care Testing for Infectious Diseases

9. V. Shyamala
9
Molecular Methods and Platforms for Infectious Diseases TestingA review of FDA Approved and Cleared Assays*
R. Emmadi, J. B. Boonyaratanakornkit, R. Selvarangan, V. Shyamala, B. L. Zimmer, L. Williams, B. Bryant, T. Schutzbank, M. M. Schoonmaker, J. A. AmosWilson, L. Hall, P. Pancholi and K. Bernard
J. Mol. Diagnostics 13, 583-604 (2011)
•The performance of various assays as described in public forums, Product Inserts and publications are reviewed
•The challenges, limitations, testing and indications related to implementation of various assays in a clinical laboratory setting is summarized
•The categories of diseases include Sexually Transmitted Diseases - HPV, CT-GC, HIV-1, and HSV; Hospital Acquired Infections -MRSA, VRE, C. difficile, Respiratory tract and CNS infections, MTB, and CNS viral infections, other infections such as HCV, HBV, GBS, Culture tests for fungal and bacterial identification.
*A by-product of CLSI MM19 document

10. V. Shyamala
10
Accomplishments (Selected) Venkatakrishna Shyamala, PhD
•Consultant: Research Diagnostics, Inc.
•Consultant: Novartis Dx-Scientific Affairs
•CLSI Document writer -Molecular Diagnostics
•Innovative Biosensors, Inc.
•Senior VP, Research and Development
•Digene Corporation
•Director, Research and Development
•Chiron Corporation
•Associate Director, Research
•Univ of California, Berkeley
•Visiting Scientist

11. V. Shyamala11
Innovative Biosensors, Inc., http://www.innovativebiosensors.com/VP%20R&D_July2007.pdf
Management Team
IBI's management has extensive experience in the commercialization of innovative technologies in the pharmaceutical, research and diagnostic markets.
V. Shyamala, Ph.D. —Senior Vice President of Research and DevelopmentDr. Venkatakrishna Shyamala has extensive experience in commercializing NAT technologies, primer/probe designs and assay development, cDNA library screening, molecular cloning, sequencing and expression. She has also participated in IND and BLA preparations and submissions with broad project and people management experience. Dr. Shyamala has been cited as inventor on a dozen patents and published nearly fifty peer reviewed articles in leading industry journals. She has a PhD in Biochemistry and Molecular Biology.

12. V. Shyamala
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V. ShyamalaSenior Vice President Research and DevelopmentAccomplishmentshttp://www.innovativebiosensors. com/pressreleases_pathogen_detection.html
•Innovative Biosensors Inc. Expands Scientific Advisory Board — August 5, 2008
•Innovative Biosensors Inc. Raises $11.5 Million —Series B Financing Combines Equity and Debt Capital —May 19, 2008
•Innovative Biosensors Inc. and ATCC® Partnerto Develop High- speed Test for Avian Flu —April 9, 2008
•Innovative Biosensors, Inc. and the University of Maryland Receive Funding for Handheld Biosensor Development— February 25, 2008

13. V. Shyamala
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V. ShyamalaSenior Vice President Research and DevelopmentAccomplishments
•NSF Grant Reviewer –Ohio State Interdisciplinary Grant — October 2007
•AACC Oakridge Conference poster —A Rapid, Sensitive, Specific Assay for the Detection of Chlamydia trachomatisBy F. Benahmed, J. Simpson, N. Chakraborty, I. Mielzynska, K. Modarress, T. Hazel and V. Shyamala —April 2008
•Completion of MRSA CANARYTMAssay Feasibility —Feb 2008
•Pre-IDE Presentation —April 2008
•Alpha Clinical trials —Univ MD Shock Trauma Center; Indiana University —July 2008
•Three Provisional Patents —Feb -April 2008

14. V. Shyamala
14
Accomplishments (Selected) Venkatakrishna Shyamala, PhD
•Consultant: Research Diagnostics, Inc.
•Consultant: Novartis Dx-Scientific Affairs
•CLSI Document writer -Molecular Diagnostics
•Innovative Biosensors, Inc.
•Senior VP, Research and Development
•Digene Corporation
•Director, Research and Development
•Chiron Corporation
•Associate Director, Research
•Univ of California, Berkeley
•Visiting Scientist

15. V. Shyamala
15
V. ShyamalaDirector, Research and DevelopmentAccomplishments
•Evaluate comparator assays for Chlamydia trachomatis of Roche Amplicor, Gen-Probe Aptima, Abbott m2000, with in-house HC2, helicase-isothermal, whole genome amplification and real-time PCR technologies
•Optimize nucleic acid extraction with silica from large sample volume for increased Diagnostic Sensitivity
•Five Invention Disclosures —Dec 2007 -July 2008

16. V. Shyamala
16Accomplishments (Selected) Venkatakrishna Shyamala, PhD
•Consultant: Research Diagnostics, Inc.
•Consultant: Novartis Dx-Scientific Affairs
•CLSI Document writer -Molecular Diagnostics
•Innovative Biosensors, Inc.
•Senior VP, Research and Development
•Digene Corporation
•Director, Research and Development
•Chiron Corporation
•Associate Director, Research
•Univ of California, Berkeley
•Visiting Scientist

17. V. Shyamala
17
Alternative NAT HCV assay-Development, Validation , ImplementationScreen for Procleix®HIV-HCV Clinical positives
S. Nguyen, P. Arcangel, D. Madriaga, David Chien, V. Shyamala, B. Phelps, BSRI members
Chiron Corporation, Blood Systems Research Institute
•Development of an Alternative HCV Assay. June 2000
•Alternate Technology: Target amplification by PCR
•Nucleic acid isolation: Organon-Teknika NucliSens reagent
•Amp-Det: Roche COBAS Amplicor
•ValidationJuly-2000
•BSRI-reference lab Aug-Sep 2000
•Timeline BLA filing Oct 2000
•FDA ApprovalFeb 2002

18. V. Shyamala
18
Conference presentations: Hepatitis C virus RNA assay
VIIthEuropean congress of the ISBT meeting, 2001,15th-18thJuly, Paris, France
1.V. Shyamala, D. Chien, S. Nguyen, N. Lagwinski, D. Madriaga, P. Carmichael, B. Phelps. J. Heitman, D. Hirschkorn, L. Tobler, and M. Busch. Development and Evaluation of Alternative NAT assay: a highly sensitive RT-PCR based diagnostic assay for HCV RNA.
54thAnnual AABB meeting, 2001, 13th-17thOct. San Antonio, TX.
2. L. H. Tobler, J. M. Vargo, K. M. Smith, D. Hirschkorn, J. Heitman, C. Degula, V. Shyamala, D. Chien, B. Phelps, L. Mimms, M.P.Busch. Sensitivity and Specificity of an HCV supplemental NAT assay. Transfusion, 41, 83.
AACC meeting, 2000, 16th-18thNov, Anaheim, CA.
3. Shyamala, D. Madriaga, D. Chien and B. Phelps. A highly sensitive, Transcription mediated amplification (TMA) and Polymerase chain reaction (PCR) dual amplification assay for the detection of Hepatitis C viral RNA molecules.

19. V. Shyamala19
Alternative NAT WNV assay-Development, Validation , ImplementationScreen for Procleix®WNV Clinical positives
D. Madriaga, J. Cottrell, P. Arcangel, David Chien, V. Shyamala, B. Phelps, BRTL members
Chiron Corporation, Bayer Research and Testing Labs
•Development of an Alternative WNV Assay Nov 2002 –Feb 2003
•Alternate Technology: Target amplification by PCR
•Nucleic acid isolation: Specific target capture technology
•Amp-Det: PCR-TaqMan technology
•ValidationMarch 2003
•BRTL-Implement April 2003
•Timeline IND filing May 2003
•Blood Screening 2003-2004 WNV season

20. V. Shyamala
20
Analytical and Clinical sensitivity of West Nile virus RNA screening and Confirmatory assays
M Busch, L Tobler, J Saldahna, S Caglioti, V Shyamala, J Linnen, J Gallarda, B Phelps, R Smith, S Kleinman
BSRI , the Canadian blood Services, Blood Systems Laboratory, Chiron Corporation, Gen-Probe, Inc., Roche Molecular Systems, the National Genetics Institute, the National Microbiology Lab-Canada, Univ of BC
Transfusion 45, 492 -499 (2005)
•Coded samples, the First generation Chiron WNV assay implemented at Bayer Reference and Testing Labs had a 95% LoD of 33 Cps/mL and the improved Chiron assay had a 95% LoD of 6.4 Cps/mL
LoD Copies/mL Neat
Minipools
Assay
Study Code
G-P
A
Roche
B
NGI
C
Bayer (Chiron)
D
G-P
E
Chiron
F
G-P
1:4
G
G-P
1:16
H
Roche
1:6
I
95% LoD
15
125
26
33
6.4
6.4
55
184
1336
50% LoD
3.4
29
6.1
7.7
1.5
1.5
13
43
309

21. V. Shyamala
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Detection of West Nile Virus RNA and antibody in frozen plasma components from a voluntary market withdrawal during the 2002 peak epidemic
L Tobler, C Bianco, S A Glynn, G B Schriber, B J Dille, H E Prince, R S Lanciotti, J M Linnen, J Gallarda, V Shyamala, D Smith, S H Kleinman, and M P Busch for the REDS study Group
BSRI, America’s Blood Centers, Westat, Abbott Laboratories, Focus Technologies, The CDC and Prevention, Blood, Gen-Probe, Inc., Roche Molecular Systems, Chiron Corporation, UCSF
Transfusion 45, 480 -486 (2005) F
o
•During the year 2002 in the WNV peak epidemic regions 60,000 plasma units were voluntarily withdrawn from the market
•Of this 1468 were retrospectively screened by immunoassays (Focus Technologies, Abbott Labs) and RNA detection assays (Gen-Probe Inc., and Roche Molecular Systems)
•RNA screening yielded one positive sample that was negative by the immunoassays
•RNA quantitation by Target-capture RT PCR (Chiron Corporation) suggested 440 cps/mL in the positive unit

22. V. Shyamala
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Screening the Blood supply for West Nile virus RNA by Nucleic Acid Amplification testing
M Busch, S Caglioti, G Robertson, J McAuley, L Tobler, H Kamel, J Linnen, V Shyamala, P Tomasulo, S Kleinman
Blood Systems Research Institute, Dept. Of Laboratory Medicine, Blood Systems Laboratory, Blood Systems, Gen-Probe, Inc., Chiron Corporation, Univ of British Columbia
New Eng J Med 353, 460-467 (2005)
ms Foundation
•For the early part of 2003 WNV RNA screening assay was performed by minipool (16 samples) testing
•For the regions with highest reactivity in minipool screening, retrospective individual screening was performed
•Individual unit testing yielded additional positives that was IgM- negative
•Recommend Staged Minipool to Individual testing during the year

23. V. Shyamala
23
Conference presentations: West Nile virus RNA assay
58thAnnual AABB meeting, 2005, Seattle, WA
1. J. Cline, C. Deza, R. Cory, A. Garcia, M. Lewis, A. Broulik, M. Deras, V. Shyamala,S. Pichuantes, C. Giachetti, J. M. Linnen. Stability of WNV Viral RNA from tissue culture and blood donor samples in stored blood. Transfusion 45, 149.
2. L. H. Tobler, V. Shyamala,J. Saldhana, C. Cameron, R. Lanciotti, R. Smith, I. Walsh, B. Munneke, B. H. Phelps, D. Chien, M. P. Busch. West Nile virus (WNV) viral load comparison study. Transfusion 45, 151.
3. S. Nguyen, V. Shyamala, H. Huang, D. Madriaga, M. Badgett, J. Hedges, C. WalkerPeach, D. Chien, B. Phelps, S. Pichuantes. Cloning of West Nile virus internal control and nucleotide fragments spanning the full-length viral genome for production of stable RNA standards. Transfusion 45, 151.
2005 National conference on West Nile Virus, San Jose, CA
4. . S. Cagliotti, G. F. Robertson, J. McAuley, S. H. Kleinman, L. H. Tobler, H. Kamel, J. M. Linnen, V. Shyamala,P. A. Tomasulo, M. P. Busch. Screening the blood supply for West Nile Virus RNA by nucleic acid amplification testing.
57thAnnual AABB meeting, 2004, Baltimore, MD
5. V. Shyamala, D. Madriaga, S. Pichuantes, B. Jaitner, D. Chien and B. Phelps. Performance characteristics of the Validated and Improved qualitative and quantitative Target-Capture PCR WNV NAT assays. Transfusion 44, 140.
6. M. Busch, L. Tobler, J. McAuley, J. Linnen, V. Shyamala, G. Robertson, D. Wright, S. Kleinman, S. Cagliotti. West Nile Virus RNA dynamics and antibody evolution based on follow-up of viremic blood donors. Transfusion 44, 2.
7. J. Cline, M. Lewis, W. Wu, S. Miller, A. Broulik, J. Savage, V. Shyamala, M. Cass, C. Giachetti, J.M. Linnen. Gen-Probe Alternative WNV assay: A TMA-based confirmatory assay for West Nile Virus. Transfusion 44, 138.

24. V. Shyamala24Conference presentations: West Nile virus RNA assay (Cont.)
28thcongress of the ISBT meeting, 2004, Edinburgh, UK.
8.V. Shyamala, S. Pichunates, B. Jaitner, D. Madriaga, P. Arcangel, J. Cottrell, S. Nguyen, H. Huang, A. Medina-Selby, D. Coit, D. Chien B. Phelps. Performance characteristics of the qualitative and quantitative Target-Capture PCR WNV NAT assay. Vox Sanguinis, 87, 26.
9. L. H. Tobler, H. Prince, G. Hafner, B. Dille, R. A. Gutierrez, W. Andrews, C. Harrington,V. Shyamala, J. McAuley, V. Winkelman, S. Cagliotti, M. P. Busch. Relative performance of four West Nile Virus antibody assays in viremic blood donor specimens. Vox Sanguinis, 87, 65.
56thAnnual AABB meeting, 2003, San Diego, CA
10. V. Shyamala, S. Pichuantes, B. Jaitner, D. Madriaga, P. Arcangel, J. Cottrell, S. Nguyen, H. Huang, A. Medina-Selby, D. Coit, C. McCoin, D. Chien, B. Phelps. Detection and Quantitation of West Nile Virus RNA by the Alternative NAT WNV Assay. Transfusion. 43, 128.
11. B. Jaitner, V. Shyamala, S. Nguyen, H. Huang, Y-L Fong, D. Chien, B. Phelps, S. Pichuantes. Propagation, quantitation, and inactivation of West Nile Virus to support nucleic acid and IgM assay development. Transfusion. 43, 128.
12. V. Shyamala, P. Arcangel, D. Madriaga, J. Cottrell, J. Linnen, D. Chien, B. Phelps. Compatibility of ProcleixR-West Nile Virus (WNV) assay in various anticoagulants. Transfusion. 43, 129.
10thEPFA/NIBSC workshop & SOGAT meeting, 2003, Langen, Germany
13.V. Shyamala, S. Pichuantes, B. Jaitner, D. Madriaga, P. Arcangel, J. Cottrell, S. Nguyen, H. Huang, A. Medina-Selby, D. Coit, C. McCoin, D. Chien, B. Phelps. Use of quantitative NAT assay to correlate West Nile Virus titration bioassay (pfu/ml) with genomic copy numbers (geq/mL).

25. V. Shyamala25Alternative NAT HBV assay-Development, Validation , ImplementationScreen for Procleix® Ultrio Clinical positives
J. Cottrell, P. Arcangel, D. Madriaga, David Chien, V. Shyamala, B. Phelps, BRTL members
Chiron Corporation, Bayer Research and Testing Labs
Development of Target-Capture PCR HBV DNA Alternative
Assay for ProcleixRUltrio Clinical Trials 2001
Technology: Target-Capture PCR
Nucleic acid isolation: Specific Target-Capture
Amplification-Detection: TaqMan assay
Agreement with BRTL as the Reference lab Aug-Sep 2002
BLA filing Oct 2004
FDA Approval2006-2008
Used to Support TUV submission for Ultrio, Tigris-Ultrio,
RAS, FEP

26. V. Shyamala
26Assessment of the Target-Capture PCR Hepatitis B Virus (HBV) DNA Quantitative Assay and Comparison with Commercial HBV DNA Quantitative Assays
V. Shyamala,P. Arcangel, J. Cottrell, D. Coit, A. Medina-Selby, C. McCoin, D. Madriaga, D. Chien and B. Phelps
Chiron Corporation
J. Clin. Microbiol. 42, 5199 -5204 (2004)
•The performance of the Target-Capture HBV assay was demonstrated with Reference panels and Standards
•The range of Quantitation was 10-50 IU/mL
•The accuracy of quantitation of several concentrations of serially diluted WHO standard was between 100-142% and of the QCMD 2003 six member panel was in the 74-140% range
•The comparative commercial assays included Roche Amplicor, National Genetics Institute SuperQuant, Bayer Quantiplex version 2.0, and Digene Hybrid Capture assay
•The Target-Capture HBV assay was more sensitive, accurate, high- throughput, rapid, and reproducible.

27. ProcleixTM Ultrio Registration and Market Trials
V. Shyamala

28. V. Shyamala28External quality assessment for the detection of blood-borne viruses in plasma by nucleic acid amplification technology: the first human immunodeficiency virus and hepatitis B virus studies (HIV EQA/1 and HBV EQA/1) and the fifth hepatitis C virus study (HCV EQA/5).
G. Pisani, K. Cristiano, J. Saldanha, M. Wirz, G. M. Bisso, C. Mele, G. Gentili and the EQA Participants.
Department of Infectious, parasitic and immune-mediated Diseases, Rome, Italy, Canadian Blood services, Ottawa, Canada
Vox Sanguinis 87, 91-95 (2004)
•Sixteen laboratories received HBV EQA/1 coded panel of two HBV concentrations
•All qualitative assays detected both members
•The Chiron Target-Capture PCR assay (Lab 46) assigned a mean titer of 1506 IU/mL and 104 IU/mL to the 1000 IU/mL and 100 IU/mL samples respectively.

29. V. Shyamala
29The risk of hepatitis B virus infection by transfusion in Kumasi, Ghana
J.-P. Allain, D. Candotti, K. Soldan, F. Sarkodie, B. Phelps, C. Giachetti, V. Shyamala,F. Yeboah, M. Anokwa, S. Owusu-Ofori, and O. Opare-Sem
Division of Transfusion Medicine, Cambridge, UK, Departments of Medicine and Biochemistry, Komfo Anokye Teaching Hospital, Kumasi, Ghana, Chiron Corporation, Gen-Probe, Inc.
Blood 101, 2419-2425 (2003)
•In Africa more than 50% of blood donors and recipients are HBV positive through natural exposure
•There are currently no HBV screening programs
•Relative merits of various antigen screening methods such as Particle agglutination, dipstick, and EIA assays were compared
•The risk of HBV transmission was predicted by screening HBsAg negative donors and a group of potential blood recipients for HBV DNA (0.05% DNA positivity)
•The risk of transmission for <10 years old ranged between 1:11 and 1:326 for unscreened vs.EIA screened. This risk decreased four fold in adults due to natural exposure to HBV.

30. V. Shyamala
30
Conference presentations: Hepatitis B virus DNA assay
59thAnnual AABB meeting, 2006, Miami Beach, FL
1. Y.-L. Fong, D. Madriaga, V. Shyamala, J. Cottrell, R. Lewis, L. Eudey, G. Crutcher, N. Lelie, A. Heaton, B. Phelps, D. Chien. Evaluation of Analytical Sensitivity of Chiron Target Capture HBV DNA Assay for HBV Detection, and Comparison with NGI SuperQuantTMHBV DNA Assay. Transfusion 46, 96.
57thAnnual AABB meeting, 2004, Baltimore, MD
2.V. Shyamala, P. Arcangel, J. Cottrell, D. Coit, A. Medina-Selby, C. McCoin, D. Chien, B.Phelps. Performance characteristics of the qualitative and quantitative Target-Capture PCR HBV NAT assay. Transfusion 44, 85.
56thAnnual AABB meeting, 2003, San Diego, CA
3.V. Shyamala,J.Cottrell, P. Archangel, D. Coit, A. Medina-Selby, C. McCoin, J. Turczyn, D. Chien and B. Phelps. Validation Of Alternative NAT HBV Assay: A Highly Sensitive PCR Based Assay For HBV DNA. Transfusion. 43, 125.
27thcongress of the ISBT meeting, 2002, Vancouver, Canada.
4.V. Shyamala, P. Arcangel, J. Cottrell, J. Linnen, C. Giachetti, D. Chien, B. Phelps. Performance characteristics of hepatitis B virus DNA confirmatory assay for ProcleixRtriplex assay. Vox Sanguinis, 83, 183.
5. J. Linnen, A. Umali, A. Broulik, D. Kolk, J. Dockter, S. McDonough, V. Shyamala, J. Cottrell, P. Arcangel, L. Mimms and C. Giachetti. Effect of donor mini-pool size on closure of the HBV detection window: A comparison of Triplex TMA to surface antigen detection. Vox Sanguinis, 83, 42.
54thAnnual AABB meeting, 2001, San Antonio, TX.
6. J. Linnen, M. Ho-Sing-Lloy, M. Miyano, D. Kolk, A. Menez, A. Vaughn, E. Peterson, V.Shyamala, P. Arcangel, D. Chien, B. Phelps. Performance of the TMA Triplex Assay which simultaneously detects HIV-1, HCV and HBV nucleic acid. Transfusion, 41, 82.

31. V. Shyamala31Prevalence and quantitation of Parvovirus B19 DNA levels in blood donors using a sensitive PCR screening assay
S. Kleinman, S. Glynn, T.-H. Lee, L. Tobler, L. Montalvo, D. Todd, J. Kiss, V. Shyamala,M. Busch
Westat, Blood Systems Research Institute, The Institute for Transfusion Medicine, Chiron Corporation; National Heart, Lung, and Blood Institute Retrovirus Epidemiology Donor Study (REDS-II)
Transfusion 47, 1756-1764 (2007)
•A retrospective study was conducted with 5020 plasma samples for Parvo B19 DNA detection by Target Capture-PCR assay
•The Assay performance was 50% LoD at 1.6 IU/mL and 95% LoD at 16.5 IU/mL
•B19 DNA prevalence was 0.88 percent with 40 positives
•IgM positivity was associated with high DNA levels (median concn 105 IU/mL) indicating acute resolving infection
•IgG but not IgM positivity is indicative of chronic and persistent phase of B19 infection

32. V. Shyamala32
Characterization of the terminal regions of hepatitis C viral RNA: Identification of conserved sequences in the 5' untranslated region and poly(A) tails at the 3' end
J. H. Han, V. Shyamala, K. H. Richman, M. J. Brauer, B. Irvine, M. S. Urdea, P. Tekamp-Olson, G. Kuo, Q.-L. Choo, and M. Houghton
Chiron Corporation
Proc. Natl. Acad. Sci. USA 88, 1711-1715 (1991)
•The nucleotide sequence at the 5' and 3' termini of the hepatitis C virus (HCV) genome has been determined, with the sequence in the 5' untranslated region highly conserved among geographical isolates
•There are several features indicating relatedness of HCV to pestivirus but not to other flavi viruses such as, (a) blocks of 5’ nucleotide sequence and position of short open reading frames, (b) poly(A) tails present on 3' subgenomic RNAs, (c) RNAs truncated at the 5’ and 3’ end.
•However, HCV also appears to be substantially different from pesti virus with assignment to a separate viral genus.

33. V. Shyamala33Receptor recognition and specificity of interleukin-8 is determined by residues that cluster near a surface-accessible hydrophobic pocket
M. E. Wernette-Hammond, V. Shyamala, M. A. Siani, C. A. Gallegos,, P. H. Feucht, J. Abbott, G. Reza-Lapointe, M. Moghadam, H. Khoja, J. Zakel, and P. Tekamp-Olson
Chiron Corporation
J. Biol. Chem. 271, 8228-8235 (1996)
•Chemokine IL8 (C-C) binds both R1 and R2 receptors and gro gamma (CXC) binds only R2 receptor. Chimeric C-C and CXC ligands were used to determine the specificity and affinity of binding to recombinant R1 and R2 cell lines
•Substitution into C-C of CXC aa at the 1stbeta sheet reduced binding to both R1 and R2, and of 3rdbeta sheet reduced binding to R1 but not R2. Substitution into CXC of C-C aa at the second beta sheet conferred high affinity binding to both R1 and R2.
•Individual aa substitutions were made and the results explained through a homology model suggests that a hydrophobic pocket is essential for both R1 and R2 binding, while surrounding residues play an additional role for R1 binding.

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Interleukin-8 receptors R1 and R2 activate mitogen-activated protein kinases and induce c-fos, independent of Ras and Raf-1 in Chinese hamster ovary cells
V. Shyamala, and H. Khoja
Chiron Corporation
Biochemistry 37, 15918-15924 (1998)
•Biological effects of interleukin-8 (IL-8) are realized by binding to the two seven-transmembrane receptors IL-8 R1 and IL-8 R2.
•IL-8 R1 and R2 have been shown to interact with Galphai2 and Galpha16, with activation of several mitogen-activated protein kinases
•In CHO cells stably expressing either IL-8 R1 or R2 receptors results demonstrate that: (a) IL-8 activates ERK and ERK kinases (MEK) through R1. Both IL-8 and GROalpha activate ERK and MEK through R2, whereas MIP-1alpha, a beta chemokine, does not activate these kinases through either of these receptors. (b) ERK activation is inhibited by pertussis toxin and MEK1 inhibitor. (c) ERK activation is independent of the upstream mediators Ras and Raf-1. (d) The downstream effects of ERK activation result in increase of c-fos mRNA through both R1 and R2 receptors.

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High-throughput screening for ligand-induced c-fos mRNA expression by branched DNA assay in chinese hamster ovary cells
V. Shyamala, H. Khoja, M. L. Anderson, J.-X. Wang, H. Cen, and W. M. Kavanaugh
Chiron Corporation
Anal. Biochem. 266, 140-147 (1999)
•Cell based High-throughput screening requires use of standardized cell lines for universal signal read-outs for use with a variety of targets.
•The screening assay for receptor agonists and antagonists is in Chinese Hamster Ovary (CHO) cells overexpressing the relevant receptors.
•A universal signal readout is of endogenous c-fos mRNA which responds to a wide spectrum of stimuli.
•The signal readout was amplified with branched chain DNA (bDNA) assay which is highly sensitive, quantifiable, amenable to high- throughput analysis, and easy to execute.
•The combined benefit of the above three features was proven with CHO cells overexpressing insulin receptor to compare conventional signaling assays with the high-throughput c-fos branched DNA assay.

36. V. Shyamala36Tumor Necrosis factor alpha induced activation of c-jun N-terminal kinase is mediated by TRAF2
C. Reinhard, B. Shamoon, V. Shyamala, and L. T. Williams
Chiron Corporation
EMBO J. 16,1080-1092 (1997)
•Tumor necrosis factor alpha (TNF alpha) a pro-inflammatory cytokine is an endogenous mediator of septic shock, inflammation, anti-viral responses and apoptotic cell death through 55 kDa (TNF-RI) and 75 kDa (TNF-RII) receptors.
•TNF-RII specific signaling was examined by chimeric receptor with extracellular domain mouse CD4 antigen and intracellular domain TNF- RII, and activated it through anti-CD4 antibodies
•Results show that: (i) TNF-RII activates ERK and JNK; (ii) Overexpression of TRAF2, a molecule that binds TNF-RII activates JNK ; (iii) dominant-negative TRAF2 blocks JNK activation ; (iv) TRAF2 signals activation of JNK and NF-kappaB through different pathways.
•TNF alpha-mediated JNK activation in fibroblasts is independent of the cell death pathway.
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37. V. Shyamala
37Cloning of CCRL1, an orphan seven transmembrane receptor related to chemokine receptors, expressed abundantly in the heart
H. Khoja, G. Wang, C. T. Ng, J.Tucker, T. Brown, V. Shyamala
Chiron Corporation
Gene 246, 229-238 (2000)B
Involved in stroke
•To identify novel chemokine receptor genes, cDNA expressed sequence tags (EST) were analyzed for a significant homology with mammalian chemokine receptors.
•One EST clones sequence was used to generate a full-length cDNA encoding a putative seven transmembrane receptor, CCRL1-CC chemokine receptor like 1, encoding a polypeptide of 350 amino acids with 35% homology to the chemokine receptors CCR6 and CCR7. Coupled transcription-translation of CCRL1 cDNA yielded a glycosylated polypeptide of about 45kDa.
•Northern blot analysis indicates predominant expression of about 5.0, 2.0 and 1.3kb mRNA forms in human heart tissue. In-situ hybridization confirmed the presence of CCRL1 mRNA in cardiac muscle cells.
•CCRL1 maps to chromosome 6 and has one intron in the 5' untranslated region.

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Semirational design of a potent, artificial agonist of fibroblast growth factor receptors
M.D. Ballinger, V. Shyamala, L. D. Forrest, M. Deuter-Reinhard, L. V. Doyle, J. X.Wang, L. Panganiban-Lustan, J. R. Stratton, G. Apell, J. A. Winter, M. V. Doyle, S. Rosenberg, W.M. Kavanaugh
Chiron Corporation
Nature Biotechnology 17, 1199 -1204 (1999)B
Involved in stroke
•A 26 amino acid polypepetide with FGF receptor binding activity unrelated to any known FGF was identified through phage display.
•A heparin binding, and dimerizaion enabling domain of c-jun leucine zipper was tailored onto this peptide
•Such a synthetic polypeptide reproduced the intracellular kinase cascade, and mitogenic and morphogenic properties of bFGF with similar potency
•The synthetic peptide also reproduced corneal vascularization properties of FGF
•Artificial FGFR peptide and non-peptide agonists may be useful alternatives to FGF in the treatment of ischemic vascular disease.

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Accomplishments (Selected) Venkatakrishna Shyamala, PhD
•Consultant: Research Diagnostics, Inc.
•Consultant: Novartis Dx-Scientific Affairs
•CLSI Document writer -Molecular Diagnostics
•Innovative Biosensors, Inc.
•Senior VP, Research and Development
•Digene Corporation
•Director, Research and Development
•Chiron Corporation
•Associate Director, Research
•Univ of California, Berkeley
•Visiting Scientist

40. V. Shyamala40
Amplification of bacterial genomic DNA by the polymerase chain reaction and direct sequencing after asymmetric amplification: application to the study of periplasmic permeases
V. Shyamala, and G. F.-L. Ames
Dept. of Biochemistry, UC Berkeley, CA
J. Bacteriol. 171, 1602-1608, (1989)
•The polymerase chain reaction (PCR) was used to amplify bacterial genomic DNA and PCR amplicons of 4,400 base pairs obtained
•We discuss problems inherent in the direct sequencing of the amplified product, and solved the problems by developing an "asymmetric amplification" method in which one of the oligonucleotide primers is used in limiting amounts, thus allowing the accumulation of single-stranded copies of only one of the DNA strands.
•As an illustration of the use of PCR in bacteria, we have amplified, sequenced, and subcloned several DNA fragments carrying mutations in genes of the histidine permease operon. These mutations are part of a preliminary approach to studying protein-protein interactions in transport, and their nature is discussed.

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Genome walking by single-specific-primer polymerase chain reaction: SSP-PCR
V. Shyamala, and G. F. L. Ames
Division of Biochemistry and Molecular Biology, UC Berkeley, CA
Gene 84, 1-8, (1989)
•We have extended the use of the polymerase chain reaction (PCR) to amplify double-stranded DNA when sequence information is available only at one extremity sufficient to design a gene-specific primer.
•The unknown end is ligated to a vector and the gene-specific primer is used in combination with a second generic vector primer.
•Restriction, ligation, amplification and sequencing of the products can be achieved within three days.
•This method eliminates the laborious steps of shotgun cloning, colony screening and culturing of cells.
•We demonstrate the usefulness of this technique for chromosome walking in the absence of any restriction data.

42. V. Shyamala42
Tandem chromosomal duplications: role of REP sequences in the recombination event at the join-point
V. Shyamala, E. Schneider and G. F. L. Ames
Division of Biochemistry and Molecular Biology, UC Berkeley, CA
EMBO J. 9, 939-946 (1990)
•A family of prokaryotic repetitive sequences, called REP (repetitive extragenic palindromic) is involved in the formation of chromosomal rearrangements such as duplications.
•Here through SSP-PCR we have characterized the join-points of seven RecA+ tandem duplications in Salmonella typhimurium, that fuse the hisD gene to distant foreign promoters
•Such a recombination takes place even in a RecA-background. Thus, REPs can recombine with each other by a RecA(-)-independent mechanism
•Some RecA-duplications occurred outside of REP sequences by recombination within a 7 bp homology.
•Possible roles for the known interaction between DNA gyrase and REP in chromosomal rearrangements are discussed.
Blood

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Genome walking by Single-Specific Primer Polymerase Chain Reaction
V. Shyamala, and G. F.-L. Ames
Division of Biochemistry and Molecular Biology, UC Berkeley, CA
Methods in Enzymology 217, Part H, 436 –446 (1993) Ed. R. Wu B
ood

44. V. Shyamala
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Use of exonuclease for rapid polymerase-chain-reaction-based in vitro mutagenesis
V. Shyamala, and G. F.-L. Ames
Division of Biochemistry and Molecular Biology, UC Berkeley, CA
Gene 97, 1-6, (1991)
•In a previous publication we proposed Asymmetric Amplification as a method to preferentially amplify one of the two PCR strands to facilitate direct sequencing
•Here the extended application of Asymmetric amplification for in vitro mutagenesis has been demonstrated
•We also demonstrate a second method for in vitro mutagenesis following treatment of PCR fragments with lambda exonuclease. This requires kinasing one of the primers.
•The entire procedure of kinasing the primer, amplification by PCR, Exo lambda digestion and second step of PCR can be performed in less than 6 h. to generate a number of mutations in the S. typhimurium hisP gene of the histidine transport operon.

45. V. Shyamala
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Antimalarial activity of optical isomers of quinacrine dihydrochloride against chloroquine-sensitive and -resistant plasmodium falciparumin vitro
R. V. Webster, J. C. Craig, V. Shyamala, G. C. Kirby, and D. C. Warhurst
Dept. of Pharmacology, UCSF, Pacific Presbyterian Hospital
Biochem. Pharmacol. 42, S225-S227, (1991)
•Both enantiomers of quinacrine and the racemic form of the drug showed equal activity in vitro against chloroquine-sensitive and - resistant strains of Plasmodium falciparum, without detectable stereoselectivity.
•This contrasts with observations on chloroquine, where a similar lack of stereoselectivity in vitro is accompanied by a 10-fold loss of activity against the resistant strain.
•The reported in vivo differences for the enantiomers of chloroquine and the observations on the optically active metabolites of chloroquine and quinacrine may be ascribed to a difference in the pharmacokinetics of their enantiomers.