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RESEARCH POSTER PRESENTATION DESIGN © 2012
www.PosterPresentations.com
The Genomics Education Partnership (GEP) combines
r...
RESEARCH POSTER PRESENTATION DESIGN © 2012
www.PosterPresentations.com
Introduction
The small “dot” chromosome (Muller F e...
RESEARCH POSTER PRESENTATION DESIGN © 2012
www.PosterPresentations.com
The Small World Initiative (SWI) 1,2, spear-
headed...
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Three posters presented at AAAS2015

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Three posters presented at AAAS 2015:
- Genomics Education Partnership general poster (Barral et al)
- GEP student poster (Arko and Chagani, National University)
- Small World Initiative student poster (Yeagley et al, National University)

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Three posters presented at AAAS2015

  1. 1. RESEARCH POSTER PRESENTATION DESIGN © 2012 www.PosterPresentations.com The Genomics Education Partnership (GEP) combines research in Drosophila genomics with undergraduate education. Based at Washington University in St. Louis, GEP comprises more than 100 colleges across the US, and allows students to both learn valuable bioinformatics skills and participate in cutting edge research. Success in GEP implementation is helped by a central support system and regular faculty workshops. The curriculum can be adapted to the specific needs of each class and institution type, including large universities, small undergraduate institutions, and community colleges. INTRODUCTION RESEARCH QUESTION Starting genome sequence is taken from the NCBI Trace Archive and the Sequence Read Archive. Students check the assembly and design additional sequencing reactions as needed to achieve a high quality finished project (1 error per 1000 bases), and then annotate an improved project. Each project is finished and annotated by at least two students working independently to provide quality control; checked projects are assembled at WU. Student work is incorporated into scientific publications (with authorship). WORKFLOW COURSES • Genetics • Genomics • Molecular Biology • Bioinformatics • Independent/Research courses GEP STUDENT LEARNING GAINS MATCH THOSE OF A SUMMER RESEARCH EXPERIENCE GEP STUDENTS DEMONSTRATE LEARNING GAINS 1. Shaffer CD, et al. A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time. CBE-Life Sci. Educ. (2014) 13: 111- 130. 2. Lopatto D, et al. A Central Support System Can Facilitate Implementation and Sustainability of a Classroom-Based Undergraduate Research Experience (CURE) in Genomics. CBE-Life Sci. Educ. (2014) 13: 711-23. 3. Leung W, et al. Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis. Genetics (2010) 185(4): 1519-34. 4. Lopatto D, et al. Undergraduate research. Genomics Education Partnership. Science. (2008) 322: 684-5. 5. Leung W, et al. Drosophila Muller F Elements Maintain a Distinct set of Genomic Properties over 40 Million Years of Evolution (Submitted). REFERENCES • Professional development via training and alumni meetings • TA training for students • Centralized project, with course materials and tools provided by Washington U • Flexible curriculum adapted to institutional needs by individual instructors Website: http://gep.wustl.edu Contact: Sarah C R Elgin selgin@biology.wustl.edu Supported by HHMI grant # 52005780 & NSF #1431407 to SCRE and by Washington University NO PREVIOUS BIOINFORMATICS EXPERIENCE REQUIRED! The fourth chromosome (Muller F element) of D. melanogaster has many heterochromatic features, including a high density of repeats, lack of meiotic recombination, late replication, and association with heterochromatic proteins. Nonetheless, this region contains ≈80 genes. A comparative genomic analysis of Muller F chromosomes of Drosophila is providing insights into the nature of heterochromatin formation and evolution. Our students have completed sequence improvement and analysis of the D. virilis, D. erecta, D. mojavensis and D. grimshawi dot chromosomes. We are working currently on the F element and a euchromatic reference region of D. ananassae and D. biarmipes. A.M. Barral1, A. Sreenivasan2, C.D. Shaffer3, W. Leung3, D. Lopatto4, and S.C.R. Elgin3. 1National University, CA; 2CSU Monterey Bay, CA; 3Washington University St. Louis, MO; 4Grinnell College, IA The Genomics Education Partnership (GEP) provides undergraduate research using bioinformatics FlyBase: http://flybase.org Reference Status Completed Annotation Sequence Improvement GEP IMPLEMENTATION AND ASSESSMENT MODE OF IMPLEMENTATION • Stand-alone course • Module within a broader course • Independent study Implementation can include engagement in both sequence improvement and annotation, or participation in annotation only. Sample of available evidence tracks to be analyzed by studentsSequence improvement and annotation workflow Characteristics of the GEP partner institutions ASSESSMENT • Pre- and post course knowledge quiz (cognitive domain) • Pre- and post CURE survey (emotional domain) 11. Reading/understanding primary science literature 2. Knowledge construction 1. Understanding the research process 3. Readiness for research 4. Tolerance for obstacles 5. Skill interpreting results 6. Clarifying career choices 7. Integrating theory/practice 8. Tackling real problems 9. Assertions need evidence 10. Ability to analyze data 12. Understanding science 13. Ethical conduct 14. Lab techniques 19. Learning community 15. Skill- oral presentation 16. Skill in scientific writing 17. Understanding how scientists think 18. Independence 20. Teaching potential 2345 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Means Q1 Q4 SURE But requires a significant investment of scheduled class time Comparison of student responses on the 20 learning gain items from the SURE survey. The data are separated into quartiles based on the number of hours devoted to the annotation project. The responses from the Q1 (1-10 hr; blue squares) and Q4 (more than 36 hr; red squares) students are shown here plotted against SURE results (green squares). Questions 1-20 from the SURE survey are described below. In an on-line quiz, GEP students demonstrated increased understanding of eukaryotic genes and genomes (20 point multiple-choice quiz, designed to cover the range of Bloom's taxonomy). Students at participating schools who had completed the prerequisites to the GEP-affiliated course but were not engaged in the GEP research-based curriculum were recruited as controls. CONCLUSIONS For an example of student work see Arko & Chagani at the Student Poster Competition 2/14 PM. • GEP provides students a research opportunity with learning gains comparable to summer research experiences, without the need for substantial laboratory resources1 • Students participating in GEP show higher learning gains in genomics than comparable non-GEP students 1 • Considerable (> 36 h) time investment in GEP is required for significant learning gains1 • The GEP provides a centralized project with logistical support and regular in-person training is critical for GEP success2 • GEP student work has contributed to the understanding of chromatin structure and its impact on gene expression, covering 40 million years of evolution3,5 CONTACT Year joined: 2006 2007 2008 2009 2010 2011 2012 2013 2014 GEP MEMBERS The Genomics Workflow Public “draft” genomes Divide into overlapping student projects(~40kb) Sequence and assembly improvement Collect projects, compare and verify final consensus sequence Evidence-based gene annotation Collect projects, compare and confirm annotations Reassemble into high quality annotated sequence Analyze and publish results Sequence Improvement (Finishing) Annotation Scale contig10: Level 1 Level 2 Level 3 Level 4 Level 5 Level 6 RepeatMasker Simple Repeats 10 kb Dere2 5,000 10,000 15,000 20,000 25,000 30,000 35,000 40,000 45,000 BLASTX Alignment to D. melanogaster Proteins Genscan Gene Predictions Geneid Gene Predictions Twinscan Gene Predictions SGP Gene Predictions Junctions predicted by TopHat using D. yakuba modENCODE RNA-Seq D. yakuba modENCODE RNA-Seq Coverage dm2 (dm2) Alignment Net Repeating Elements by RepeatMasker Simple Tandem Repeats by TRF CORL-PC CORL-PB CORL-PD CG32016-PH CG32016-PG CG32016-PB CG32016-PC CG32016-PF mGluRA-PB mGluRA-PA mGluRA-PC contig10.1 contig10.2 gid_contig10_1 gid_contig10_2 contig10.001.1 contig10.002.1 sgp_contig10_1 sgp_contig10_2 sgp_contig10_3 sgp_contig10_4 JUNC00000863 JUNC00000864 JUNC00000865 JUNC00000866 JUNC00000867 JUNC00000868 JUNC00000869 JUNC00000870 JUNC00000871 JUNC00000872 JUNC00000873 JUNC00000874 JUNC00000875 JUNC00000876 JUNC00000877 JUNC00000878 JUNC00000879 JUNC00000880 JUNC00000881 D. yakuba modENCODE RNA-Seq Coverage BLASTX alignments Gene predictions RNA-Seq Comparative genomics Repeats Genomic sequence Evidencetracks Q1 Q4 SURE
  2. 2. RESEARCH POSTER PRESENTATION DESIGN © 2012 www.PosterPresentations.com Introduction The small “dot” chromosome (Muller F element) of D. melanogaster exhibits unique properties, making it the focus of a comparative genomics study organized by the Genomics Education Partnership (GEP) at Washington University in St. Louis. This chromosome exhibits many heterochromatic features, including a high density of repeats, lack of meiotic recombination, late replication, and association with heterochromatic proteins. Nonetheless, it contains ~80 genes. A comparative genomic analysis of Muller F elements of Drosophila species should provide insights into the nature of heterochromatin formation and evolution. GEP students have completed sequence improvement and analysis of the D. virilis, D. erecta, D. mojavensis and D. grimshawi dot chromosomes, to look at the patterns over 40 million years of evolution. We are now working on the F element chromosome and a euchromatic reference region of D. biarmipes, a species closely related to D. melanogaster, which should facilitate identifying dot chromosome regulatory motifs. Materials and methods As part of a Molecular Biology Lab course (BIO407A) we annotated contig38 of the D. biarmipes Dot chromosome 2013 (Dbia3) assembly. Our goals were to determine:  The number of genes  Gene structure including exon-intron boundaries  Transcription starting sites (TSS) and core promoter motifs (preliminary) Tools employed included:  UCSC genome browser to study sequence homology between the two species, including a large number of gene predictor and RNA-Seq tracks, as well as splice site predictors such as TopHat  NCBI-Blast analyses  RepeatMasker to reveal repetitive sequences  Gene Model Checker  TSS prediction tracks, such as the 9-state model track (chromatin structure/histone modification), DNAse I sensitivity sites, and TSS predictor track Celniker (ModEncode) Conclusions • We annotated three genes found in contig 38 of the D. biarmipes Dot chromosome 2013 assembly. • The three genes were determined to be highly homologous to the D. mel genes Slip1, gw, and CG9935, as supported by multiple evidence, including blast analysis, gene prediction algorithms, and RNA-Seq data. • Only minor changes could be observed between the D.bia and D.mel orthologs: one missing untranslated exon in gw-RI, lack of stop codon in CG9935-RA. • We preliminarily assigned transcription starting sites to positions 32,213 of gw-RI, 33,284 for Slip1 (all isoforms), and 11,942 for CG9935 (all isoforms), based on blastn analysis, TSS predictions, and RNA-Seq data . Results (continued) Untranslated regions (UTRs) tend to be less conserved than translated exons, and therefore harder to annotate due to less homology. Moreover, 75% of D. melanogaster genes lack core promoter sequences. Therefore, for TSS annotation a combination of blast, RNA-Seq data, and splice-site predictors are used. Acknowledgments We want to thank Drs. Sarah C.R. Elgin, Wilson Leung, Christopher D. Shaffer and David Lopatto for organizing and sustaining the GEP initiative, and all the help and support. GEP is supported by HHMI grant # 52005780 & NSF #1431407 to SCRE and by Washington University. Please see the poster by Barral et al. for more Results }}}} } References 1. Leung W, et al. Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis. Genetics (2010) 185(4): 1519-34. 2. Slawson EE, et al. Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains. Genome Biology (2006) 7:R15. 3. Leung W, et al. Drosophila Muller F Elements Maintain a Distinct set of Genomic Properties over 40 Million Years of Evolution (Submitted to Genetics). Available evidence tracks Blastx alignment to D-mel proteins Gene prediction tracks RNA-Seq data Conservation tracks within 7 Drosophila species Repeat density Structures of the D. melanogaster genes in FlyBase are considered 1. Determination of genetic homology using different types of evidence (blastx, gene predictors, RNA-Seq) } } } 2. Annotation of D. biarmipes genes based on homology with D. melanogaster genes Identification of matching donor and acceptor splice sites, corresponding to the correct reading frame and phase CG9935 (3 isoforms) gw (gawky) (6 isoforms) Slip1 (3 isoforms) Blastx analysis of translated D-mel exons against the contig, to help define the exon boundaries 3. Evaluation of the proposed gene model using Gene Model checker Other available tools include splice site predictors, synteny analysis, and protein homology analysis. Gene model of D.biarmipes Dot chromosome (2013) contig 38, including UTRs Annotation of Transcription Starting Sites (TSS): Preliminary results Active chromatin state and DNAse I hypersensitivity regions are good predictors of transcriptional activity Other evidence tracks include Celniker TSS predictions, as well as the presence of core motifs such as the TATA Box and Inr. Tr an sc ri pt io na lly ac ti ve ch ro m at in D N As e I hy p er se ns iti vi ty sit es
  3. 3. RESEARCH POSTER PRESENTATION DESIGN © 2012 www.PosterPresentations.com The Small World Initiative (SWI) 1,2, spear- headed by Yale University, incorporates the search for soil microbes producing antibiotics in the undergraduate biology curriculum. At NU, SWI has been implemented in Introductory Microbiology Laboratory (BIO203A) courses3. The major rationale behind SWI is the current antibiotic crisis. The ESKAPE pathogens (see table below) are responsible for a substantial percentage of nosocomial infections in the modern hospital and represent the vast majority of antibiotic resistant isolates. Soil bacteria, particularly from the genera Bacillus and Pseudomonas, produce a large variety of secondary metabolites with antibiotic activity that not only protect them other microbes, but also play an important part in quorum sensing, biofilm formation, interactions with plants, and sporulation 4,5,6–8. We plated soil samples from diverse locations in Orange and San Diego counties. Colonies were tested for antibiotic production using spread/patch technique against safe surrogates of the “ESKAPE” organisms. Cultures exhibiting antibiotic production were further characterized using a combination of biochemical and genetic techniques. BACKGROUND MATERIALS AND METHODS ACKNOWLEDGMENTS NU contact: abarral@nu.edu @Bio_prof Tammy Yeagley, Caleb McNeal, Kassia Valverde (advisor: Dr. Ana Maria Barral) National University, Costa Mesa, CA Isolation and characterization of antibiotic producing soil Bacilli from Southern California RESULTS C1, C9, K1, and T were identified as Gram positive rods CONCLUSIONS AND RECOMMENDATIONS • We describe four Bacillus isolates with antibiotic activity against several ESKAPE surrogates. • To identify both microbe and compound, more advanced genetic (more targeted PCR, whole genome sequencing) and chemical methods are required. • Purification of supernatants by organic extraction and chromatography-mass spectrometry are currently underway. • Soil samples were serially diluted and plated on different media (TSA, PDA) at 22 or 35 oC. • Colonies were tested for antibiotic activity against ESKAPE surrogates using spread/patch technique. • Isolates with activity were further characterized by biochemical, morphological, and genetic (16S rRNA) tests. We describe four Bacillus soil isolates with antibiotic activity against ESKAPE surrogates, which were characterized by 16S rRNA sequencing and traditional methods. Antibiotic activity was more prominent against Gram positive bacteria. Due to high genetic similarity in the genus Bacillus, species identification was not possible. Preliminary chemical extractions point to multiple active compounds, present in both organic and aqueous fractions. ESKAPE PATHOGENS & THEIR SURROGATES Phylogenetic tree of the isolates, including Bacillus species and 2 other SWI Bacilli (CFU4 from Orange County & SWI2 from New Haven, CT Four isolates: C1, C9, K1, and T inhibited the growth of ESKAPE surrogates. Best activity was observed against Gram positives. DISCUSSION REFERENCES Thanks to all the BIO203A SWI students, as well as Lab Manager Jeremy Marion. The SWI initiative is generously supported by Yale University & the Helmsley Charitable Trust. 1. A. M. Barral, H. Makhluf, P. Soneral, B. Gasper, FASEB J. 28, 618.41 (2014). 2. http://smallworldinitiative.org/. 3. A. M. Barral, H. Makhluf, in ASMCUE Microbrew Abstracts (Danvers, MA, 2014). 4. H. Chen et al., Lett. Appl. Microbiol. 47, 180–186 (2008). 5. J. M. Raaijmakers, I. de Bruijn, O. Nybroe, M. Ongena, Natural functions of lipopeptides from Bacillus and Pseudomonas: More than surfactants and antibiotics. FEMS Microbiol. Rev. 34 (2010), pp. 1037–1062. 6. I. Mora, J. Cabrefiga, E. Montesinos, Int. Microbiol. 14, 213–23 (2011). 7. T. Stein, Mol. Microbiol. 56, 845–57 (2005). 8. J. Shoji, H. Hinoo, Y. Wakisaka, K. Koizumi, M. Mayama, J. Antibiot. (Tokyo). 29, 366–374 (1976). 9. S. a Cochrane, J. C. Vederas, Med. Res. Rev., 1–28 (2014). Summary of the characteristics of the 4 isolates and the Bacillus species most similar by 16S rRNA analysis (nd: not done, u: unknown) Based on endospore formation & 16S rRNA analysis, all 4 isolates were identified as Bacilli. Characteristic C1 C9 K1 T B. subtilis B. anthracis B. mojavensis B. megaterium B. tequilensis Pigmentation Creamy White Light yellow White Opaque Opaque Opaque Yellowish/ brown Yellowish Cell Morphology G+ pointed rods G+ short rods G+ rods G+ short rods G+ rods G+ long rods G+ rods G+ rods G+ rods Known to produce antibiotic + + + + + + + + u Anaerobic Growth nd nd − + − + − − − MR/VP nd +/− +/− +/− −/+ −/+ −/+ +/− −/+ Starch Hydrolysis (amylase) + + + + + + + + + Motility nd nd + − + − + + + Indole nd nd − − − − − + ESKAPE C1 C9 K1 T E.coli - - - - P.putida - + - - A.bayley - + - - E.aerogenes - - - +/- S.cohnii + + + + B. subtilis nd + +/- +/- E. raffinosus + + - - 16S rRNA sequences were amplified using primers 27F and 149R and puRE Taq Ready-To-Go PCR beads. Sequencing was done by Retrogen. Data were evaluated by Blast & MEGA. A B C D A: soil plate; B: pick/patch master plate; C: testing for antibiotic activity via spread/patch, D: isolates streaked ready for characterization C1 & C9 Shannon index 1.27 K1 Shannon index 1.04 T The July 2014 BIO203A class 1.4-1.5 kb PCR products Endospore staining

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