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)

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. 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. 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