Summer 2008

The Biotechnology Program offers the following short courses on various techniques used in biotechnology research. If you would like to receive training in any of the areas listed below, please register through UCD Conference and Event Services. Their link is provided below each of the courses and by selecting it, registration will be possible for that particular class.

FLOW CYTOMETRY COURSE

Co-Sponsored with FloCyte

Flow cytometry is a powerful tool in modern biology.  The applications are numerous, and have contributed to many fields including by virology, immunology, and molecular biology.  This course begins with introductory flow cytometry and progresses through development and design of multicolor panels.  Afternoon sessions will include hands-on training in applications and training on various instruments.   Students will be exposed to the Cytomation MoFlo cell sorter, Becton Dickinson FACScan flow cytometer, Coulter XL-MCL flow cytometers and Compucyte laser scanning cytometer, and others.

Enrollment is limited to 25 students (lecture/lab), 40 lecture only. Register through UCD Conference & Event Services at: http://www.cevs.ucdavis.edu/Flow

See schedule of course      Agenda

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ADVANCED PCR TECHNIQUES: QUANTITATIVE REAL-TIME PCR

Co-sponsored by the Lucy Whittier Molecular Core Facility

This very popular course covers sampling strategies to obtain high quality sample material, micro-dissection of frozen or paraffin embedded tissues using the new state-of –the art PALM Laser Catapult (Zeiss, PALM Microlaser Technologies), sample preparation and nucleic acid recovery from tissue, blood and paraffin samples, quality controls for sample preparation, and real-time TaqMan PCR and contamination control and monitoring. Students can work on their own samples, including micro-dissection of frozen or paraffin embedded tissues, RNA extraction, QC and gene profiling. 

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PROTEOMICS: FUNDAMENTALS & TECHNOLOGY PLATFORM

Co-Sponsored by the UCD Genome Center Proteomics Core

This introductory proteome analysis workshop is designed to expose participants to fundamental technology platforms and current information in the field of proteomics. The course will cover quantitative and non-quantitative liquid chromatography (LC) based proteomics and “multidimensional protein identification technology (Mudpit)” employing complex mixture of proteins.  Participants will also perform quantitative ITRAQ experiments, in-gel digestions, liquid isoelectric focusing, and database searching using X! Tandem and Mascot with MS/MS data generated during the course.  Lectures will cover: fundamentals of protein chemistry and mass spectrometry (MS), MS based protein identification, posttranslational modification of proteins, database search using MS data, and traditional tools of protein biochemistry.  Lab sessions will include hands on practical applications of the techniques, using state of the art instrumentation.

Dr. Phinney has taught similar Proteomic courses at Cold Spring Harbor in New York.

Guest Lecturers: Dawei Lin, PhD (UCD Bioinformatics Core), Alan Buckpitt, PhD (UCD Molecular Biosciences, Veterinary Medicine), Jon Gingrich (Simga-Aldrich Corp.), Kerry Nugent (Michrom Bioresources, Inc.), Chris Becker, PhD (PPD, Inc.), Chris Adams, PhD (Stanford University Mass Spectrometry), David Arnott, PhD (Genentech, Inc.), Amy Zumwalt (Thermo Fisher Scientific)

See course schedule here

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DNA MICROARRAYS: THEORY, TECHNIQUES AND ANALYSIS

Co-Sponsored by DNA Microarray Core Facility and Affymetrix, Inc.

This hands-on course is a must for any researcher who wants explore the global analysis of gene expression through DNA microarray analysis.  Lectures will be presented by industry scientists as well as academic researchers on the basics of chip technology, including analysis and quality control, and application of this technology in a wide range of research fields.  The laboratory sessions will include preparation of cDNA from RNA, DNA hybridization to and processing of the microchip.  Computer laboratory sessions will include data analysis with clustering as well as other bioinformatics tools.

Guest Lecturers: 

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Next Generation DNA Sequencing Data Analysis For Genome Wide Research

A Bioinformatics Intensive Short Course

Co-Sponsored by the UC Davis Bioinformatics Core and the Genome Center

Next generation sequencing technology is touted as the next wave of the genomics revolution.  The capability to generate tens of millions of sequence reads in a short time and at low cost is stimulating a large array of innovative ways to investigate genome-wide questions.  This course introduces the most popular next generation technologies, including Roche 454 sequencing and the Illumina Genome Analyzer, or Solexa sequencing.  It also provides hand-on training in data analysis pertinent to these two platforms.  Topics include understanding the basics of technology, associated Information Technology (IT) challenges, de novo sequence assembly, mapping to a reference genome, SNP discovery with or without a reference genome, ChIP-seq (Chromatin immunoprecipitation – sequencing) analysis, gene expression, gene predictions, functional annotation, data analysis using the UCSC genome browser, and cluster computing.

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