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 literature2. 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

2

3

4

5

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

Me

an

s

Q1

Q4

SURE

But requires a significant investment of scheduled class timeComparison 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

Evid

ence tra

cks

Q1 Q4 SURE

RESEARCH POSTER PRESENTATION DESIGN © 2012

www.PosterPresentations.com

IntroductionThe small “dot” chromosome (Muller F element) ofD. melanogaster exhibits unique properties, makingit the focus of a comparative genomics studyorganized by the Genomics Education Partnership(GEP) at Washington University in St. Louis. Thischromosome exhibits many heterochromaticfeatures, including a high density of repeats, lack ofmeiotic recombination, late replication, andassociation with heterochromaticproteins. Nonetheless, it contains ~80 genes. Acomparative genomic analysis of Muller F elementsof Drosophila species should provide insights into thenature of heterochromatin formation andevolution. GEP students have completed sequenceimprovement and analysis of the D. virilis, D. erecta,D. mojavensis and D. grimshawi dot chromosomes, tolook at the patterns over 40 million years ofevolution. We are now working on the F elementchromosome and a euchromatic reference region ofD. biarmipes, a species closely related to D.melanogaster, which should facilitate identifying dotchromosome regulatory motifs.

Materials and methodsAs part of a Molecular Biology Lab course (BIO407A)we annotated contig38 of the D. biarmipes Dotchromosome 2013 (Dbia3) assembly. Our goals wereto 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 alarge number of gene predictor and RNA-Seqtracks, as well as splice site predictors such asTopHat

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 trackCelniker (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.

AcknowledgmentsWe want to thank Drs. Sarah C.R. Elgin,

Wilson Leung, Christopher D. Shaffer and David

Lopattofor 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 information on GEP. Email:

Results

}}}}}

References1. 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 Propertiesover 40 Million Years of Evolution (Submitted to Genetics).

Available evidence tracksBlastx alignment to D-melproteins

Gene prediction tracks

RNA-Seq dataConservation tracks within 7 Drosophila speciesRepeat density

Structures of the D. melanogaster genes in FlyBaseare 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-melexons 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.

Transcriptionally active chromatin

DNAse I hypersensitivity sites

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 & C9Shannon index 1.27

K1 Shannon index 1.04T

The July

2014

BIO203A

class

1.4-1.5 kb PCR products

Endospore staining