Bioinformatics at the U.

Bioinformatics is the application of information technology to the field of molecular biology.

The USD Computer Science Department is committed to developing production quality software while giving students a valuable research experience. The department offers students opportunities for involvement in bioinformatics research at both the undergraduate and graduate levels. Students are involved in developing the infrastructure necessary to carry on bioinformatics research by creating software solutions that fit the needs of researchers.

 

Click on the TEAM MEMBERS tab to contact us. We will be glad to answer your questions.

Computer Science Dept. | University of South Dakota
Arts & Sciences #202 | 414 E Clark St
Vermillion, SD 57069-2307 | 605.677.5388
csci@usd.edu

 

 

Carol Lushbough, M.S. Bioinformatics Co-Director Assistant Professor USD Computer Science Dept. 605.677.6138 Click here for Carol's CV		Carol has been with The U since 1997. She received her master's degree in Computer Science from USD in 1991. Carol teaches bioinformatics, software engineering and systems analysis. Her main research interest is bioinformatics.
Joe Reynoldson, M.S. Research Computing Mgr. Instructor USD Computer Science Dept. 605.677.6131 Click here for Joe's CV		Joe is the Research Computing Manager/Instructor for the Computer Science Department; he has been at USD since 1994. He received his master's degree from USD in 1997. Joe teaches Topics in Perl, systems management and Web development.
Doug Jennewein, M.S. Research Analyst USD Computer Science Dept. 605.677.5388 Click here for Doug's CV		Doug is a computer science research analyst and has been at USD since 1998. He received his master's degree from USD in 2004. Doug recently taught Computer Science 150. His main research interest is high performance computing.
Brent Anderson, M.S. Research Analyst USD Computer Science Dept. 605.677.5388		Brent is a research analyst in Computer Science and has been with The U since 2004. He received his master's degree in from USD in 2007. Brent's interest are in software engineering and Web development.

 

 

We are working on a variety of projects in conjunction with the USD Sanford School of Medicine. This collaboration is intended to get computer science students involved in bioinformatics research at both the graduate and undergraduate levels. Students in our department are involved in developing the infrastructure necessary to carry on research in bioinformatics by creating software solutions to fit the needs of faculty involved in this field of research. These projects are funded through external grant sources.

 

 

 

 

The Brendl Group @ ISU

 

 

 

The SD BRIN Genomics Core Facility provides support to faculty members who wish to apply genomic technologies to their individual research projects. This support ranges from teaching novice molecular biologists how to extract RNA from tissue samples to running and analyzing DNA microarray experiments. The genomics core supports the DNA microarray technology, RNA extraction, real time RT-PCR, the Agilent Bioanalyzer and the Amaxa nucleofection system.

Kathleen M. Eyster, Ph.D., Director Professor, Sanford School of Medicine University of South Dakota Phone: 605.677.5159 E-mail

 

 

Services offered include:

• Experimental design in genomics
  
• RNA extraction
  
• RNA quantitation
  
• DNA microarray
  
• Analysis of differential gene expression
  
• Real-time RT-PCR
  
• Amaxa nucleofection
  
  

Please contact Dr. Kathy Eyster information about rates and services.

 

Instrumentation and technologies supported by the SD BRIN Genomics Core Facility

The SD BRIN Genomics Core Facility provides support to research investigators who wish to apply genomics technologies to their individual research projects. The focus of the facility is DNA microarray analysis of differential gene expression. The services offered by the genomics core support this focus, although all of the equipment and technologies of the core have stand-alone functions separate from DNA microarray as well.

Core personnel assist investigators with experimental design in genomics to ensure that the maximum amount and quality of data possible will be extracted from an experiment. The core will extract RNA from an investigator’s sample, or will teach investigators the techniques of RNA hygiene and RNA extraction. Expertise is available for extraction of RNA from cultured cells, tissues, and paraformaldehyde-fixed tissues.  Microfluidics chips are used to quantitate RNA using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, Calif.). The DNA microarrays of choice are the CodeLink Whole Human Genome Bioarrays, CodeLink Whole Rat Genome Bioarrays, and CodeLink Whole Mouse Genome Bioarrays from Applied Microarrays (Tempe, Ariz.). Other microarrays spotted on slides can also be scanned with the Axon GenePix 4000b scanner (left, MDS Analytical Technologies, Toronto, Canada) in the core. Several software packages are used for analysis of microarray data; these include CodeLink, Acuity, GeneSpring, and Ariadne Pathways software.

Microarray data are acquired and aligned with GenePix Pro software (MDS Analytical Technologies, Toronto, Canada). CodeLink software (Applied Microarrays, Tempe, Ariz.) is used to apply background correction and to associate individual spots with their gene identifiers. Acuity software (MDS, Inc., Toronto, Canada) is used to obtain fold expression values. GeneSpring software (Agilent, Santa Clara, Calif.) is used for statistical analysis of the microarray data and to normalize the expression of each gene to the median gene expression and each slide to the 50th percentile of gene expression. Ariadne Pathways (Ariadne Genomics, Rockville, Md.) is used to identify relationships among differentially expressed genes. Personnel in the genomics core perform the protocols for DNA microarray. Data are analyzed to the extent desired by investigators from raw data to refined analysis. The core also assists investigators in publishing genomics data in appropriate MIAME (minimum information about a microarray experiment) format.

Differential gene expression identified by DNA microarray needs to be confirmed by an independent technique. Real-time RT-PCR provides an ideal platform for such confirmation studies, and is used for a variety of other types of experiments as well. The SD BRIN Genomics Core recently up-graded its real-time PCR/RT-PCR capabilities with the purchase of an Applied Biosystems StepOne Plus real-time PCR machine (left).

When genes have been shown to be differentially expressed in a disease state or in response to a specific treatment, one of the next steps is to determine the function of that gene. To support the study of gene function by transfection of overexpression vectors or silencing RNA, for example, the genomics core supports the Amaxa Nucleofector II technology (Lonza, Cologne, Germany).

A logical extension of studies of gene expression is the regulation of gene expression by microRNA. The genomics core is currently in the process of establishing protocols for extraction and analysis of microRNA. Once established, these technologies will be made available to other investigators through the core.

Please contact Dr. Kathy Eyster for information about instrumentation.

 

 

Please contact Dr. Kathy Eyster for information about rates and services.

 

 

 

The SD BRIN Proteomics Core Facility provides state-of-the-art proteomics services to researchers from South Dakota and the region. Since 2002, the USD PCF has been providing proteomic analyses, as well as collaborating in the training of the use of common equipment such as the scanner, spot cutter, imaging software, technique and protocol issues, and sample preparation. Our goal is to provide all South Dakota researchers with the capability to rapidly analyze and identify protein expression patterns in their experimental systems.

OUR STAFF:

Dr. Michael S. Chaussee, Director Associate Professor, Infectious Disease Sanford School of Medicine University of South Dakota Phone: 605.677.6681 E-mail

Dr. Eduardo Callegari Research Staff Scientist Sanford School of Medicine University of South Dakota Phone: 605.677.5530 E-mail

Reach us at:
USD Proteomics Core Facility
Lee Medical Bldg #127
The University of South Dakota
414 E Clark St
Vermillion, SD 57069-2307
Fax: 605.677.6381

 

We offer the following services:

• Peptide mass fingerprinting (LC-MS analysis) or/and peptide fragment fingerprinting (LC-M/MS analysis) through in gel or in solution digestion. Typically, protein spots or bands excised from previously 1D or 2D gels are digested with trypsin and the peptides resolved using a NanoAcquity UPLC (Ultra Performance Liquid Chromatography). Specifically, tryptic peptides are desalted and concentrated using a reverse-phase trapping column and then resolved using a C18 reverse phase analytical column. The mass of peptides is determined using a nano-ESI Q-ToF (Quadrupole-Time of Flight) mass spectrometer in MS and MS/MS mode. The peptide masses are used to query various databases, using ProteinLynx global server v2.3 (Waters-Micromass) or Mascot server (www.matrixscience.com) to identify the most probable proteins in the sample.
• Intact protein analysis: This type of analysis determines the molecular weight of an intact protein and can be used to identify post-translational modifications (phosphorylation, acetylation, etc.) proteolytic modifications,  and to determine the number of proteins in a sample. A typical procedure involves injecting the sample into the mass spectrometer using a regular electrospray or nano-electrospray configuration. Multiple charged spectra are generated, and the spectra is deconvoluted using maximun entropy conversion software.
• Training and assistance in common equipment and tools located in the facility: Typhoon 9410 scanner, spot cutter, image software analysis, and basic excision tools for the cutter.
• Consultation and advice related to sample preparation, technique and protocol development or proteomics applications.

 

nanoAcquity UPLC (nano-HPLC) coupled to Waters Microass Q-Tof micro™/Waters		ProteomeWorks MassPREP Station Robotic Protein Handling System
Agilent Technologies 2100 Bioanalyzer	ÄKTA FPLC controlled by UNICORN™ software		Thermo Scientific SPD1010 SpeedVac Vaccuum Concentrator
ProteomeWorks Spot Cutter		Typhoon 9410 Variable Mode Imager

 

• Mascot Server and Mascot Daemon Toolbox (Matrix Science)
• Mascot Distiller (Matrix Science)
• ProteinLynx Global Server v2.3 (Micromass)
• PDQuest (BioRad)
• ImageQuant (Web site)
• MassLynx v4.1 (incl. Biolyns, Transformation, MAxEnt1 & 3) (Micromass)
  

 

 

Fee Schedule (as of March 24, 2008):

Faculty members from	will pay (per sample):
SD BRIN PUIs	No charge
S.D. (BBS)	$50
S.D. (non-BBS)	$150
other IDeA states	$150
non-IDeA states	$250
A fee committee has been established to consider requests for adjustments. Please contact Dr. Callegari with your request.

 

 

 

 

Mass Spectrometry Analysis Requisition Form
Mass Spectromotry Analysis Requisition Form