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Songbird Neurogenomics
Headed by Prof. David Clayton working with the W. M. Keck
Center. Gene expression in the songbird zebra finch studied to
gain further insight into the molecular and cellular processes that
underlie normal brain development and function. The songbird is one of
the best models to study the functional significance and control of
adult neurogenesis. Up to 50,000 expressed sequence tags (ESTs) will be
sequenced from normalized and subtracted zebra finch brain cDNA
libraries derived from combination of adult and juvenile brains of both
sexes. The goal will be to create a "unigene" set of up to
20,000 genes which would represent a majority of the genes being
expressed in the songbird brain. Gene expression studies will then be
conducted using cDNA microarrays from this unigene library.
http://www.life.uiuc.edu/clayton/songgene.html
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Cattle
Functional Genomics
Headed by Prof. Harris Lewin. High-Throughput sequencing of
the 5' ends of 17,000 cattle spleen and placental cDNAs has provided
for the identification of novel genes as well as an economical
sampling of the rarer mRNAs present in placental tissue. This
project has produced and hybridized a 7,000 gene array produced with
cattle spleen and placenta sequences. Initial comparisons of
fetal and adult spleen samples with a 764 gene microarray have
demonstrated the utility of this technology for developmental assays
of the cattle immune system. Current projects with larger
microarrays are being used for studies on disease resistances, tissue
development and phenotype identification related to production traits
in cattle. An expressed sequence tag website with gene
ontologies has been created and is available at:
http://lewinlab.igb.uiuc.edu/index.html |
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Honeybee
Functional Genomics
Headed by Prof. Gene Robinson. This project focuses on the relation
of gene expression to animal behavior patterns using the honeybee as
model organism. The High-Throughput Unit has performed 5' end
sequencing of a normalized cDNA bee brain library with about 20,000
sequences completed. The group has produced a pilot gene array
consisting of 384 genes and has conducted initial hybridization
experiments. Emphasis is now being put on the development and testing
of protocols for hybridizations using minute amounts of RNA. EST data
is being processed with the aid of the Bioinformatics unit for
comparative annotation with Drosophila genes in order to
prepare a large set of clones for production of expanded microarrays.
An expressed sequence tag website with gene ontologies has been
created and is available at:
http://titan.biotec.uiuc.edu/bee/honeybee_project.htm
and
http://www.life.uiuc.edu/robinson/
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NIA 15K Mouse MicroArray
Headed by Mark Band. A set of two slides of the NIA 15K
clone set microarray is now available to researchers of the
Urbana-Champaign and Chicago campuses of the University of
Illinois. Each slide contains 7680 clones, mouse control spots
and plant genes as negative or spiking control (A spiking control kit
is available from Stratagene catalog #252011). All spots are
printed in duplicate in 32 subgrids in a 4 x 8 pattern. Each
grid contains 2 rows of the entire control set of genes.
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Soybean
Functional Genomics
Headed by Prof. Lila Vodkin. High-Throughput
sequencing of the 3' ends of 30,000 soybean cDNAs has
characterized the range of mRNA transcripts expressed in different
tissues and developmental stages of soybean plants. Miroarrays
have been designed and printed for over 9,000 genes; transcript
profiling of different soybean tissues and developmental stages is
underway. Transcription profiling by Prof. Vodkin's group has
been conducted for over 70 comparative hybridization.
http://soybeangenomics.cropsci.uiuc.edu
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Evolutionary Genomics: Investigating Male Fertility Variation
in Drosophila melanogaster
Headed by Kim Hughes. Goals: 1) To use the
Affymetrix system to investigate phenotypic variation in fertility and
longevity in Drosophila melanogaster; 2) To find candidate genes
that account for the high levels of within-population genetic variation
in traits related to male fertility in this species; 3) To combine these
gene expression results with the results of quantitative trait loci
study of the same traits.
http://www.life.uiuc.edu/kahughes/research.htm
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Genomic
Analysis of Salmonella Evolution
Headed by Prof. Stanley Maloy. Salmonella enterica are a
large group of Gram-negative bacteria that cause severe, often fatal,
disease in many farm animals. Salmonella enterica consist of
many serovars, but three in particular, Pullorum, Dublin, and
Choleraesuis are responsible for a high incidence of illness. S.
enterica Pullorum is primarily a chicken pathogen, S. enterica
Fubli is primarily a
cattle pathogen, and S. enterica Choleraesuis is primarily a swine pathogen.
Sequencing of these three genomes and comparison with the well
characterized Salmonella serovars Typhi, Tyhimurium and
Enteritidis
will enable us to identify the virulence factors which are responsible
for disease in Pullorum, Dublin, and Choleraesuis.
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Corn Rootworm
EST Project
Headed by Michael E. Gray, Susan Ratcliffe and others. In recent
years, crop rotation has been collapsing as a pest management tool for
western corn rootworm in East Central Illinois and Northern Indiana.
Rotation resistance is fundamentally a problem of movement: egg laying
females now disperse from cornfields to deposit their eggs in soybean
and other crops rotated with corn. The behavioral shift in the
egg-laying preference of the western corn rootworm variant has raised
questions regarding the evolution of a new strain within this species.
An RFLP-PCR (Restriction Fragment Length Polymorphism - Polymerase
Chain) diagnostic marker will be developed if variation within rRNA
genes is identified that will allow researchers to easily separate the
two behavioral types of western corn rootworm. In addition, microarray
profiling will allow us to evaluate gene expression variation between
the two populations and possibly identify the mechanisms controlling
these behaviors. This research will provide insight into how
gene expression is linked to environmentally induced behavior and
provide guidance for effective measures to control this pest. Sequencing from the normalized library is currently underway.
We
expect to identify about 8,000 unique sequences from sequencing of
12,000 clones.
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Coral Diseases
Headed by Bruce Fouke. Disease in tropical corals has emerged
as one of the primary causes of the accelerating global destruction of
coral reef ecosystems. In collaboration with Abigail Salyers,
Bruce Fouke is completing a pilot study funded by the Office of Naval
Research that has shown the greatest number of black band disease (BBD)
infections occur directly down-current from sewage effluents.
Polymerase chain reaction (PCR) amplification and sequencing of
bacterial DNA collected from coral surfaces has identified over 524
unique types of bacteria. These bacterial communities are distinctly
partitioned between seawater and healthy, BBD-infected and dead coral
surfaces. Several bacterial pathogens previously known to live only in
humans were found inhabiting the BBD ring. This suggests that human
sewage influences the development of BBD in reef corals. Transplantation
and inoculation experiments in the field and under controlled laboratory
conditions are now being completed to determine the process by which BBD
develops and the means of transmission of human-derived bacteria in
seawater. Sequencing of different microbial species
is underway at the Keck Center. Information about Dr. Fouke's
research is available at: http://www.geology.uiuc.edu/%7Efouke/CoralResearch.html |
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Functional Genomics of Ruminococcus flavefaciens FD-1
Headed by Bryan White. Application of functional genomics
techniques to the cellulolytic ruminal bacterium Ruminococcus
flavefaciens FD-1 to detect and identify candidate genes expressed
in response to different carbon sources. Prior to microarray
construction and analysis, a dataset of putative genes based on homology
with other genomic databases as well as ORF demarcations need to be
acquired. Using high-throughput sequencing, shotgun libraries are
being sequenced to provide low level coverage of the genome (1-3x
coverage of the 4.4 Mb genome; approximately 8,800-26,400 clones) to
then be followed by a directed effort to provide closure of the entire
genome. The power of this approach lies with the immunity of the
technique to organisms recalcitrant to classical bacterial genetic and
molecular techniques.
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High-Resolution
Physical Mapping of the Porcine Genome by BAC Fingerprinting
Headed by Prof. Jonathan Beever. The objective of this project is
to construct a genome-wide framework for a high-resolution physical
map of the swine genome by BAC fingerprinting. Approximately 100,000
fingerprints (5.5X genome coverage) from clones of the RPCI-44 porcine
BAC library and other publicly available resources will be generated.
Analysis of the fingerprints will be performed by assembling
overlapping clones into small contigs. The W.M. Keck Center is
performing DNA template isolations of approximately 70,000 BAC clones
on a Qiagen robot using the Millipore kit.
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Identification of
Genes Influencing Pork Quality
Headed by Prof. Jonathan Beever. A genome scanning approach will be
used to identify chromosomal regions that contain genes influencing
economically important traits in swine termed economic trait loci (ETL).
Trait data will be collected from a resource population composed of
breeds genetically divergent for meat quality and production traits.
Molecular genetic markers will be used to monitor the segregation of
ETL in an F2 generation of approximately 750 animals. Results of the
study can be used to implement marker-assisted selection programs
within the swine industry. The W.M. Keck Center is providing
genotyping for the approximately 90,000 genotypes using Applied
Biosystems Genescan on an automated 3700 ABI sequencer.
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Pig Genome Sequencing
The objective of this cooperative research project is to
participate in an international effort to develop a physical map
(BAC map) for cattle and pigs. The goal of the international
effort is to develop a 15X physical map for cattle and a 20X
physical map for pigs. This will include fingerprinting and
sequencing both ends of 300,000 pig BAC clones. The fingerprint
and sequence data will be analyzed to identify overlapping BAC
clones and place the ordered clones into 'contigs' that will
represent the majority of the genome. Physical BAC maps are
needed to facilitate the discovery of genes affecting economically
important traits. |
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Comparative Genomics of Dog and Horse Tissue
Headed by Douglas Antzak and Gustavo Aguirre. The James A.
Baker Institute for Animal Health, Cornell University. The Keck
Center is constructing 7 normalized cDNA libraries from dogs and
horses. Some of these libraries will be subtracted and partially
sequenced.
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Arabidopsis Functional
Genomics
Headed by Prof. Mary Schuler.
Microarray analysis of the 273-member cytochrome P450 monooxygenase
gene family in Arabidopsis is being initiated to define the
expression patterns of these transcripts with respect to plant
development as well as chemical and environmental stresses.
Isolation of full-length cDNAs and functional expression of their
encoded proteins in baculovirus and yeast systems will provide for
high-throughput analysis of the substrate reactivities of P450 enzymes
critical for biosynthetic and detoxicative pathways in plants.
Expression of P450 promotor: reporter gene fusions in transgenic Arabidopsis
will be used to visualize the responses of individual cells and
tissues to environmental stresses. For more information please visit:
http://arabidopsis-p450.biotec.uiuc.edu/
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Arabidopsis and Rice
Functional Genomics
Headed by Prof. Hans Bohnert. EST and
cDNA analysis of the transcripts expressed in Arabidopsis and
rice exposed to high salinity and drought conditions is defining the
range of mRNAs responding to these environmental stresses.
Comparative microarray analyses in these plant species as well as
corn, barley, ice plant, yeast and Synechocystis is providing
an indication of the general and species-specific responses to these
stresses and identifying those genes most essential for genetic
manipulation of drought and salt tolerance.
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Arabidopsis Functional
Genomics
Headed by Prof. Daniel Bush.
Microarray analysis of the large network of genes involved in nitrogen
uptake, metabolism and allocation in Arabidopsis is being pursued in order to better
understand how changes in nitrogen-status
control plant growth and development at the molecular level. Regulation of these genes have dramatic effects on seed set and yield
and, as a result, significant agronomic importance. The identity
of clusters of co-regulated genes and transcriptional regulatory
elements will be determined by using bioinformatics.
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The Use of DNA Microchip Arrays to Identify Changes in Gene
Expression
Headed by Romana Nowak. Economic losses to the pork industry
from outbreaks of infectious and non-infectious diseases are
enormous. One of the most troublesome is porcine reproductive and
respiratory syndrome (PRRS). The Keck Center will generate cDNA
libraries from both, porcine hypothalamus and uterus, sequence about
10,000 ESTs and generate a porcine cDNA microchip array containing both
hypothalamic and uterine genes for gene expression studies. RNA
samples from tissues of two different pork breeds will be hybridized to
the porcine cDNA microchip array. Objectives are to identify genes
whose expressions are changed during immune challenge to gilts and to
identify genes whose expressions are altered during the acute phase of
infection with PRRS.
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Mapping the Cattle Genome by BAC End Sequencing of 60,000 Clones
Headed by Harris Lewin. BAC end sequencing will be used to
produce a physical map of the cattle genome that will serve as the
scaffold for the genomic mapping and genome sequencing project.
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Projects in Bioinformatics
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"COMPASS
The COMPASS (Comparative Mapping by Annotation and Sequence
Similarity) is a powerful tool for comparative gene mapping in
silico. The concept is based upon the extensive
conservation of synteny and gene order among mammalian genomes.
For two species in which the comparative genome organization is known,
the chromosome location of any gene or DNA sequence can be predicted
if the sequence is conserved and the map location is known in one of
the two species. Our first generation informatics tool
demonstrated 95% accuracy of chromosome prediction in the cattle
genome (Band et al., Genome Research 10:1359,
2000). Our goal was to develop an enhanced tool that would
incorporate data from an ordered radiation hybrid map of the cattle
genome thus permitting the predication of location on a
chromosome. We have seamlessly integrated the multiple steps of
the COMPASS procedure into a web-based interfaced. These steps
are i) identification of putative orthologs by BLASTN search against
human UniGene, ii) retrieval of UniGene cluster identification,
accession numbers of best hits and other annotation, and iii)
prediction of cattle chromosome and bin identification based on a
look-up table containing coordinates on an RH-based comparative map of
the cattle and human genomes. The new COMPASS II tool provides a
significant advancement over the previous version of COMPASS in that
RH bin location on the cattle map can be accurately predicted.
Furthermore, the tool can be extended to any other species that has
adequate RH mapping information.
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for public use.
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ESTIMA
ESTIMA (EST Information Management and Annotation tools) is an
extensible resource that interfaces with EST databases and powerful
search tools for functional genomics, comparative gene mapping, and for
functional annotation. This interface provides access to the Cattle and
Honey Bee Brain EST databases with the potential for other model
organism EST databases to be included in the near future.
Every sequence is annotated with detailed information arising from CAP3
clustering and similarity search against the human UniGene for Cattle
and against the Flybase for the Honey Bee. The clusters may be
viewed using an in-house contig viewer. The resource allows the
users to BLAST their sequences against the EST, as well as, locally
available non-redundant GenBank databases; query by almost any
attribute of a sequence or cluster and keywords; and allows
sequence and chromatogram retrieval. The annotation centers around
a controlled vocabulary as defined by the Gene Ontology (GO)
Consortium. A static GO term tree for any term can be navigated
and annotated ESTs for that term retrieved. The linkages and
associations with GO and LocusLink provide an excellent resource to
explore orthologous relationships and to begin the process of defining
complex phenotypes at the molecular level.
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Microarray Database and Data Mining
Project focus is on integration of experimental
data from microarray with information such as metabolic pathways
and development of new tools to visualize the complex and multidimensional
expression profiling data in the context of genome, cellular processes,
and developmental stages. First step is to establish a
database system for microarray data management. Currently, we are
investigating freeware including Stanford Microarray Database
and GeneX. We have established collaboration with NCSA's Automated
Learning Group, Computer Science Department, and Statistics Department
to explore new data mining methods.
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NIH Skin Disease Research Core Center
The Bioinformatics Unit at the W. M. Keck Center for Comparative and
Functional Genomics will provide the following technical services as a
core facility in the Skin Disease Research Core Center at the University
of Texas Southwestern Medical Center:
- batch processing of BLAST search including blastn,
blastp, blastx, tblastn, tblastx. Search results will be inserted
into an Oracle database. A web interface will be provided for
users to retrieve the results. All public available databases
and customized database will be available for BLAST search.
- help users interpret the BLAST search results, explain
the parameters used, and provide advice on searching strategies.
- provide training workshops to teach users the basic
database search tools and various databases related to biomedical
research.
- make available a Bioinformatics Core
Facility website with links to various bioinformatics
resources.
- give users access to tools we are developing
such as Genome Project Management System and information
visualization tools for microarrays.
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Web Oligo
To support high throughput oligo synthesis, we developed a web based
submission system WebOligo. Customers can submit oligo orders
directly from the web. We are developing an oligo design module
for the system. Clients can input sequences then run Primer3
program to generate sequences which can be directly submitted for
synthesis.
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Core Sequencing Database System
We are developing a web-based data management system for core DNA
sequencing to replace the DNA server.
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NCSA High Performance Computing
We are working with NCSA scientific computing groups to develop a
scheme for large BLAST jobs to accommodate the demand for large
scale comparative genomics. Computation of large scale sequence
comparison is a daunting task for our current infrastructure.
Collaboration with NCSA will provide additional resources for the
campus.
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NSF 2010: Functional Genomics of Arabidopsis P450s
The focus of this project the integration of experimental data
from microarray hybridization experiments with other information about
metabolic pathways. The first issue is the analysis of expression
patterns using clustering techniques. The second issue is the
development of a database to organize and manage the experimental RNA
expressions data, metabolic pathways information, genome map positions,
transgenic promoter:reporter expression profiles, as well as, any P450
mutant phenotype data which becomes available through these and other
on-going projects. For more information:
http://arabidopsis-p450.biotec.uiuc.edu/
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