The University of Oklahoma Health Sciences Center
Laboratory for Genomics and Bioinformatics
http://microgen.ouhsc.edu
Vol. 3, No. 3 September 2005
University of Oklahoma Health Sciences Center/405-271-2337
New people, new home!
In this issue
• New people, new home! 1
OK INBRE
• INBRE News
2
• INBRE Summer
Undergraduate Research
Program
4
OUHSC COBRE
• COBRE
Investigator Focus
• COBRE News
2
3
Other core facilities
• OSU Core Facility
3
Bioinformatics
• OKBIOS 2005
4
Services and rates
6
We’ve had lots of changes over the
summer! As we mentioned in our last
newsletter, Chris Robinson, our primary
DNA sequencing technician, left us to begin
as a GPiBS student this fall. He’s been
replaced by Nicole Benton, who joined our
group from a similar position in the DNA
sequencing facility at Iowa State, so she is
already quite capable. With her additional
expertise, we will be able to expand our
genotyping offerings, which we will be
discussing in a later newsletter. Matt Carson
also
is
gone,
having
joined
the
Bioinformatics graduate program at the
University of Illinois at Chicago, where he
will pursue a doctorate. We’ve brought on
board Tim Schmidt, previously at Wayne
State University in Detroit, as a replacement
for his bioinformatics expertise. While we
are sad that Chris and Matt are gone, we wish
them well and are confident in their success
as graduate students.
The most exciting change has been our
move into the core facility lab in the new
west wing of the Stanton L. Young
Biomedical Research Center. This beautiful
new lab, which we’ll be sharing with Ken
Jackson’s Molecular Biology and Proteomics
Core, is on the first floor (Room 1102) with
adjacent offices in Room 1106, and our
bioinformatics group occupying space in
BRC1217 on the second floor (see below).
When you bring your samples to us for DNA
sequencing, you need only stop by Room
1106, where a freezer is available for your
samples and a box for your SUR. All of our
other contact information remains the same,
so you should easily be able to get in touch
with us to serve your needs. We appreciate
your patience while we were shut down
during the move, and hope to see you again
as a customer as we’ve reopened for
business. Thanks for your continued support!
-Dave Dyer & Allison Gillaspy
BRC1102, facing south
Acknowledgements
The OUHSC Laboratory for
Genomics and Bioinformatics
is partially supported by
USPHS grants 5P20-RR-15564
(COBRE)
and
5P20-RR016478 (INBRE), from the
National Center for Research
Resources of the National
Institutes of Health.
BRC1102, facing north
BRC1217 Bioinformatics suite
OUHSC Laboratory for Genomics and Bioinformatics
Page 2
INBRE News by Edgar Scott, M.S.
The National Center for Biotechnology
Information (NCBI) is a division of the
National Library of Medicine and the
National Institutes of Health, established by
Congress on November 4th 1988.
The
purpose of NCBI is to “develop new
information technologies to aid in the
understanding of fundamental molecular and
genetic processes that control health and
disease.”(http://www.ncbi.nlm.nih.gov/About
/glance/ourmission.html). To help the
scientific community better understand how
to use their resources, NCBI provides a free
training course, “A Field Guide to GenBank
and NCBI Molecular Biology Resources".
NCBI sends speakers to any university to
deliver a lecture and hands-on computer
sessions to expose people to their resources.
In September, Ursula Ellis (OUHSC
Reference Librarian) and I (OK INBRE)
sponsored NCBI’s Steve Pechous and Andrei
Gabrielian to deliver this workshop in the
Bird Library at OUHSC. The two-day
http://okinbre.org/
workshop began with a three-hour overview
of several of the databases and tools currently
maintained at NCBI.
This lecture was
followed by hands-on sessions to give
attendees an opportunity to explore the tools
on the NCBI web site. The lecturers touched
such issues as using Entrez, the NCBI
integrated text-based search and retrieval
system, and how to effectively utilize the
NCBI integrated databases to retrieve related
information stored in other databases.
Practical issues also were covered, such as
how one can optimize a Blast search by
modifying the blast parameters.
The attendance was quite good, with 90
registrants. Faculty, staff and students from
several institutions attended, including
OUHSC, NSU, UCO, OBU, Cameron Univ.,
OKCCC, OU, OSU, The Samuel Roberts
Noble Foundation, and KANresearch. For
those who would like additional information
about this workshop, please go to
http://www.ncbi.nlm.nih.gov/Class/FieldGui
de/.
COBRE Investigator Focus: Michael Sakalian, Ph.D.
Genomic and Proteomic Analysis of Betaretrovirus Pathogenesis
(–)
dexamethasone
(+)
dexamethasone
Stimulation of MMTV antigen
expression in cells by hormone
treatment.
Retroviruses cause several human diseases
including leukemia (HTLV) and AIDS
(HIV). Mouse mammary tumor virus
(MMTV) has long been suspected to play a
role in human breast cancer, due partly to its
ability to induce cancer in mice and the
presence of related sequences in many
human breast tumors. MMTV has now been
linked to another human disease, Primary
Biliary Cirrhosis (PBC), and has been termed
the Human betaretrovirus (HBRV).
PBC is a chronic liver disease where the
intrahepatic bile ducts are destroyed, leading
to bile acid accumulation and liver failure.
Biliary epithelial cells (BEC) from PBC
patients display a characteristic plasma
membrane expression of mitochondrial
antigens. This may explain the presence of
anti-mitochondrial antibodies in PBC
patients and the resulting inflammatory
response that destroys the bile ducts. Surface
expression of the mitochondrial antigen
pyruvate dehydrogenase-E2 can be induced
in cultured normal BEC when inoculated
with patient-sample conditioned medium or
with mouse-derived MMTV, suggesting that
this may be an in vitro model for PBC. This
opens the door to a molecular investigation
of the pathogenesis of PBC.
We will use genomic and proteomic
techniques to identify the cellular changes
associated with PBC pathology, since it may
be more feasible to control the consequences
of infection than to eliminate the retrovirus.
Using human DNA microarrays, the
transcriptome of uninfected and MMTV
infected cultured BEC will be compared to
identify genes that are specifically regulated
by viral infection. Uninfected and infected
cell fractions likewise will be processed to
identify proteins with altered expression,
posttranslational modification, or cellular
localization. Knowledge gained from this
project will then allow us to characterize the
cellular pathways involved in PBC and lend
insight into how to reverse or prevent their
induction.
For more information, please contact:
Michael Sakalian, Ph.D.
Dept. of Microbiology & Immunology
OU Health Sciences Center
940 S. L. Young Blvd., BMSB 1021
Oklahoma City, OK 73104-5020
E-mail: mike-sakalian@ouhsc.edu
OUHSC Laboratory for Genomics and Bioinformatics
Page 3
New Leadership at the OSU Core Facilities
The new leader of OSU’s INBREsupported core facilities is Dr. Peter R. Hoyt,
Research Associate Professor in OSU's
Department of Biochemistry and Molecular
Biology. Dr. Hoyt assumes the mantle of
leadership of OSU's multi-user Microarray
Core Facility and BioinfOSU, previously
worn by Dr. Patricia Ayoubi. Dr. Ayoubi
has become an Assistant Professor in the
Department with primary responsibility for
teaching and advising.
in the birth of the microarray field,
developing tools for automated RNA
isolation,
high-throughput
probe
production, array printing, and the
acquisition
and
interpretation
of
microarray data. In the process, Dr. Hoyt
trained an army of postdoctoral fellows,
technicians and students working in other
research areas to utilize diverse tools for
the manipulation and study of gene
expression.
Dr. Hoyt holds B.S. and M.S. degrees from
the University of Houston (Biology and
Microbiology, respectively). He earned a
doctoral degree in Human Genetics/Cell
Biology from the University of Texas
Medical Branch in Galveston. As a
postdoctoral fellow at the Oak Ridge
National Laboratory (ORNL), he guided the
development of transgenic mouse facilities,
including a pathogen-free barrier facility, and
a gene-targeting facility. He also guided the
implementation of numerous technologies for
the
genotypic
and
phenotypic
characterizations of these novel resources.
Dr. Hoyt's work at ORNL eventually shifted
toward characterization of DNA and gene
expression using atomic force microscopy
and microarray technologies. He participated
In Oklahoma, Dr. Hoyt will continue the
tradition of microarray training in the form
of workshops, and collaborate with others
on functional genomics projects.
His
independent research program investigates
cellular responses to low doses of ionizing
radiation. Using a battery of modern tools,
his broad base of expertise will be applied
to complex system responses and to
identifying biomarkers. To assist others
pursuing similar endeavors, he invites his
new colleagues in Oklahoma to visit with
him. Please welcome Dr. Hoyt to the
Oklahoma
biomedical
research
community. He can be reached at 405744-6209 or pHoyt@biochem.okstate.edu.
Peter R. Hoyt, Ph.D.
Research Associate Professor
Department of Biochemistry and
Molecular Biology
Oklahoma State University
Contributed by Steve Hartson and Ulrich
Melcher
COBRE News by John Iandolo, Ph.D.
The “Functional Genomics and
Proteomic Analysis of Pathogen-Host
Interactions” Center Of Biological Research
Excellence (COBRE) grant was renewed for
an additional five-year period. Among the
changes instituted in the administration of
the grant was the addition of Dr. David
Dyer as co-director. Further, the focus of
this award period will shift slightly to place
more emphasis on proteomics. We also
have consolidated the core laboratory
facilities onto the OUHSC campus.
Comprehensive services and consultation in
genomics, bioinformatics and proteomics
now will be available to COBRE and other
state scientists at one location. The External
Advisory Committee, which consists of Dr.
Michael Apicella, Dept. of Microbiology,
University of Iowa School of Medicine, Dr.
Sherwood Casjens, Dept of Oncological
Sciences, University of Utah School of
Medicine and Dr. Robert Munson, Dept. of
Microbiology and Immunology, Children’s
Research Institute, Ohio State University,
have graciously agreed to continue their
association with our COBRE. Budget
restructuring at the national level delayed
the start date until Sept. 1, but we are now
up and running again, which is great news.
The grant is essential to continued growth of
infectious disease research and Oklahoma
genomic sciences because it allows us to
continue to provide research funds to help
faculty develop their research careers. The
program is designed to support four junior
investigators and two pilot projects. At
present, we support 2 junior investigators
and efforts are under way to increase
support to the project limit. At the end of
July, a Request for Proposals was issued to
attract new investigators. The submission
deadline is Oct. 1. The proposals submitted
will then be sent out for external review to
assist in making funding decisions. New
investigators will be selected by the Director
and co-Director with the advice and consent
of the External Advisory Committee.
OUHSC
Center of Biomedical Research
Excellence
Page 4
OUHSC Laboratory for Genomics and Bioinformatics
OKBIOS 2005
OKBIOS
The second annual symposium of the
Oklahoma
Bioinformatics
Society
(OKBIOS) will be held Friday, Oct. 28th at
the Cox Convention Center in Oklahoma
City. Registration is free, courtesy of the OK
INBRE, but is limited to the first 150
registrants. This year’s symposium will be
hosted by the OU Health Sciences Center
and will expand the scope of the symposium
toward biomedical and clinical research.
OKBIOS 2005 will highlight the role of
bioinformatics as a means of advancing our
understanding both in the basic life sciences
and in clinical research. This symposium
will bring together Oklahoma researchers,
commercial developers, educators and
students to share their work, research and
experiences in bioinformatics, computational
and systems biology, biomedical data
integration,
clinical
informatics
and
biomedical
imaging.
The
daylong
symposium will feature plenary talks,
technical presentations, posters, panel
discussions, and oral presentations of original
research. The agenda can be accessed at:
http://register.perfectorder.com/okbios/2005/
agenda.php. Students participating in the
student poster competition may compete for
an award ($150/1st place, $100/2nd place,
$50/3rd place). The Oklahoma State
Chamber sponsors these student poster
awards. Postdoctoral fellows also are
encouraged to present their work, and all
accepted abstracts will be published in the
OKBIOS conference proceedings.
We also are seeking volunteers for the
Conference Program Committee to review
submissions, judge student posters and help
with registration at the conference. Please
contact
Dr.
Jonathan
Wren
(Jonathan.Wren@OU.edu) or Dr. Yuriy
Gusev (Yuriy-Gusev@ouhsc.edu) to be
included. If you have a vendor you would
like to see invited, please feel free to suggest
them. Refreshments, handouts and souvenirs
will be limited by available funds and are on
a first-registered, first-serve basis. An online
registration form, as well as conference and
travel information can be found at
http://register.perfectorder.com/okbios/2005/.
Regular updates to the symposium agenda
and details will appear on this web site.
Contributed by Jonathan Wren
INBRE Summer Undergraduate Research Program
One of the main goals of the OK INBRE
grant is to expose undergraduate students to
biomedical research and encourage them to
pursue careers in science and technology.
The INBRE Summer Research Program has
been one of the most successful avenues for
recruiting students into science.
The
program began in the summer of 2001 with
12 students from three undergraduate
institutions, growing this year to 25 students
from eight undergraduate institutions. The
students were selected by an independent
panel, and each student was paired with a
mentor conducting research in a shared area
of interest. One of the exciting additions to
the program this year was the participation of
six community college students.
Since
community college students may have
limited laboratory training, the students
attended a two-week long “boot camp” prior
to the beginning of the program. During the
“boot camp,” the students were placed in a
hands-on environment where they learned
necessary laboratory skills to prepare them
for the summer. Another new element of the
program was the pairing of some community
college students with mentors from
Oklahoma biotech companies, where the
students not only conducted research but saw
first-hand the marketable applications of
their work. The INBRE Summer Research
Program
concluded
with
a
poster
presentation and luncheon at OUHSC. All
students prepared an abstract and poster
based on their summer research, providing
the students an opportunity to discuss their
research in a public setting, and allowing the
public to see the research being conducted in
campuses all over Oklahoma (see page 5 for
a list of INBRE students and their research
projects). Applications will be solicited for
the 2006 summer program in the fall of 2005.
To learn more about the INBRE Summer
Research Program or OK INBRE, please
visit
the
INBRE
web
site
at
www.OKINBRE.org.
Contributed by Sasha Smith
OUHSC Laboratory for Genomics and Bioinformatics
Page 5
INBRE
Mentor
Host
Project
Student
Institution
Students from Northeastern Oklahoma State University
Dustin Beck
Christopher
NSU
Identification of Mycobacterium marinum Virulence Genes Using Signature-Tagged Mutagenesis
Pritchett
The Role of STAT3 in Regulating Inflammation in First Trimester Trophoblast-like Jeg-3
Christopher
Dr. James
OUHSC
Cells
McDaniels
Jarvis
Students from Southeastern Oklahoma State University
Cloning, Expression, and Isolation of Bacillus anthracis Serine Kinase (BaSK)
Sarah Boatner Dr. Jimmy
OUHSC
Ballard
Production of Isoflavonoid Beta-Glucosidase in E. coli
Ashly
Dr. Nancy
SOSU
Gammon
Paiva
Students from Oklahoma City Community College
Antibacterial Activity of Chitosan Matrices on Oral Pathogens
Phoebe Brown Dr.
OSU
Sundararajan
Madihally
Cytovance
Development of a Conventional Chromatography Purification Scheme of High Yield and
Patricia
Dr. Brad
Biologics,
Purity for Anti-CD40 Monoclonal Antibody
Parrish
Johnson
Inc.
Alteration of Hyaluronan Product Size by Expression of Synthases with Multiple Mutations
Zuzana
Dr. Philip
Hyalose,
Novakova
Pummill
LLC
Pathologic Role of IL-23 in Rheumatoid Arthritis
Clayton
Mr.
SOSU
Sandel
Choudary
Jagarlamudi
Students from Langston University
Prenatal Diagnosis of Chromosomal Anomalies: a Five-Year Experience
Ashley
Dr. John
OUHSC
Burdex
Mulvihill
Global Gene Expression Analysis to Define the High Light Response in the Photosynthetic
Christal
Dr. Robert
OSU
Model Cyanobacterium, Synechocystis sp. PCC6803
Carpenter
Burnap
Investigation of Target Epitopes of Protective Antigen and Lethal Factor in Bacillu s
Macole
Dr. Joel
OMRF
anthracis
Mayweather
Guthridge
Students from Redlands Community College
Detection of Anti-HLA Antibodies Using Single Specificity Human Leukocyte Antigen
Darcy Cox
Dr. William
Pure
Target Molecules
Hildebrand
Protein,
LLC
The Molecular Identification of Plant Vacuolar Ion Channels
Randy Knecht Dr. Gerald
OSU
Schoenknecht
Students from Cameron University
Study of Nitric Oxide Level in Ozone Sensitive and Ozone Resistant Arabidopsis after
Enock Faustin Dr.
OSU
Ozone Treatment
Ramamurthy
Mahalingam
Expression of Potential Glycanases Genes in Aspergillus nidulans Utilizing Different
Stancy Joseph Dr. Rolf
OSU
Carbohydrate Sources
Prade
MMS19’s Putative Role in Post Replication Repair (PRR)
Lora Repp
Dr. Lurdes
OUHSC
Queimado
A Hidden Markov Model for Autoantibody Development in Systemic Lupus Erythematosus
John Riddles
Dr. John
OMRF
Harley
Angiopoietin Protein Turnover by Vascular Smooth Muscle Cells (VSMC)
Kristi Thacker Dr. Eric
OUHSC
Howard
Students from Southwestern Oklahoma State University
Role of PhoP in Osmoadaptation of Pseudomonas aeruginosa
Donovan
Dr. Arden
SWOSU
Fuller
Aspedon
Prediction of 4-Helix Bundles in Filamentous Flexous and Nucleocapsid Virion Coat
Sebastian
Dr. Ulrich
OSU
Proteins and the Location of Aromatic Amino Acids
Harris
Melcher
Molecular Cloning of Dictyostelium 5’-Nucleotidase Promoter Upstream of a βAdarsha
Dr.
SWOSU
Koirala
Muatasem
Galactosidase Reporter Gene
Ubeidat
The Role of Vn50 Clip Domain in the Regulation of Prophenoloxidase Activation Pathway
Kathryn Walls Haobo Jiang
OSU
Purification and Kinetic Assessment of F755W: Mapping Allostery in E. coli Carbamoyl
David Webber Dr. Jason
SWOSU
Phosphate Synthetase
Johnson
Students from the University of Central Oklahoma
The Effect of Immortalizing Dupuytren’s (DP) Nodule Fibroblast on Phenotype
Armstrong
Dr. Melville
UCO
Isiaho
Vaughan
Sero-Prevalence of West Nile Virus in Small Mammals at Lake Arcadia
James Vaughn Dr. William
UCO
Caire
Rate structure
The University of
Oklahoma
Health Sciences
Center
Laboratory for
Genomics and
Bioinformatics
Stanton L. Young
Biomedical Research
Center, Room 1106
Phone:
405-271-2337
Fax:
405-271-1204
E-Mail:
For general information:
David-dyer@ouhsc.edu
Allisongillaspy@ouhsc.edu
For inquiries regarding DNA
sequencing:
(partial listing; please check our web page for details)
DNA sequencing (<96 samples)
$5/reaction Library construction
contact us
DNA sequencing (>96 samples)
$3/reaction Human genotyping
$500/sample
DNA Fragment analysis
HLA DNA sequencing
$3/sample Membrane array fabrication
$400 / locus
DNA normalization, 96 samples
$10.60
$11/array
Microarray scanning
$20/slide
Bioinformatics support
$45/hour
Bioinformatics Support
We offer bioinformatics support through our Informatics Core, directed by Jeremy Zaitshik.
The rate for support is $45/hour with a one-hour minimum charge. Please note: we do not
provide Tier 1 IT support. For inquiries or work requests contact:
Jeremy Zaitshik (Jeremy-zaitshik@ouhsc.edu)
Perl programming (for sequence analysis,
manipulation, etc.)
UNIX/Linux system administration
Security issues
Sequence analysis software questions
Data acquisition/automation
Database design (MySQL/PostgreSQL)
Web design (HTML/CGI)
Tim Schmidt (Tim-schmidt@ouhsc.edu)
Phylogenetic analysis (PAUP, PHYLIP,
MEGA, PAML, etc.)
Comparative genomics (Alignment, promoter
analysis, etc.)
Perl programming (Data manipulation, data
mining, etc.)
Proteomic analysis (Localization, structure,
display with spdv, Rasmol, etc.)
Web design/HTML
Nicole-benton@ouhsc.edu
Jenny-gipson@ouhsc.edu
INBRE Multicampus Bioinformatics Specialist
For inquiries about microarray
fabrication and hybridization:
The INBRE MBE Specialist is responsible for fostering the development of bioinformatics
education on 14 undergraduate campuses in the state of Oklahoma, and coordinating INBRErelated bioinformatics activities with the INBRE Bioinformatics Core. For inquiries and
INBRE information, please contact:
Mandy-gipson@ouhsc.edu
For bioinformatics support:
Jeremyzaitshik@ouhsc.edu
Tim-schmidt@ouhsc.edu
For billing information:
Paula-gladden@ouhsc.edu
For inquires regarding OK
INBRE activities:
Edgar-scott@ouhsc.edu
We’re on the Web!
See us at:
microgen.ouhsc.edu
Edgar Scott, M.S.
(edgar-scott@ouhsc.edu)
Bioinformatics education
Computational biology education
Sequence analysis software questions
Data acquisition/automation
Web design
INBRE activity scheduling
About Us…
The OUHSC Laboratory for Genomics and Bioinformatics is a full-service genomics facility
offering DNA sequencing (small- and large-scale projects), microarray design and
hybridization and other services. The Director of the Laboratory for Genomics and
Bioinformatics is Dr. David Dyer, Ph.D., a Professor in the Department of Microbiology and
Immunology at the University of Oklahoma Health Sciences Center. Dr. Allison Gillaspy,
Ph.D., is the Associate Director of the Laboratory for Genomics and Bioinformatics and a
Research Assistant Professor in the Department of Microbiology and Immunology. The
University of Oklahoma is an equal opportunity institution. This publication, printed by OU
Printing services, is issued by the University of Oklahoma. 150 copies have been prepared
and distributed at no cost to the taxpayers of the State of Oklahoma.