Courses Offered


The credit courses listed below are offered to registered UF students only, with the exception of Summer B Lab that accepts other people. No previous knowledge of molecular techniques is required, but is helpful. A good deal of our students in our basic courses are not molecular biologists but want to learn more about it. For course registration, please contact the registration office of your department or college.

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Summer B Lab - Molecular Cloning and Protein Chemistry for Graduate Students (GMS 6004, ALS 5905, PHA 6522L, VME 6934, section 5261)

Registration
This is a two-credit, graduate-level laboratory course listed under various Colleges. Students who plan to take this course for credit must get approval from any of the colleges where the course is listed. Contact information is as follows: A limited number of spots are available for non-students (i.e., faculty, staff) who are interested in the material covered in this course. Those who are interested in taking the course not for credit must register through ICBR.
Date:
July 7-25, 2008
Time:
8:30AM - 5:00PM
Location:
ICBR Room 184-South Wing
Cancer and Genetics Research Complex
Gainesville, FL
Fees:
$600.00 for registered UF students, UF Faculty and UF Staff who are not taking the course for credit
$1200.00 for all others
Schedule & Topics:
Find out what we will cover or what we covered in previous sessions by viewing our past schedule(.pdf, size:2.47Mb).
Picture Gallery:
Description:
This is a extensive molecular techniques training course. It covers state-of-the-art technologies in current molecular biology field. There are three major components: protein chemistry, molecular cloning, and bioinformatics

Protein Chemistry:
Participants learn about the basic considerations in protein isolation and purification (i.e. choice of tissue, cellular fractionation, buffers, detergents, biological activity assays, choice of chromatographic method, etc.). They will gain practical experience by spending 75% of their time at the bench working with the recombinant human carbonic anhydrase. Techniques they will learn include the following:
  • Tris-glycine and tris-tricine SDS-PAGE gel electrophoresis
  • Isoelectric focusing (IEF) and two-dimensional gel electrophoresis
  • In-gel proteolytic digestion for peptide mapping and microsequencing
  • Protein concentration
  • Enzyme activity assays
  • Western Blotting
  • Matrix-assisted laser-desorption ionization time-of-flight (MALDI TOF) mass spectrometry
Lab lectures by UF faculty and ICBR personnel emphasize the practical applications of protein characterization technology and ground-breaking uses of advanced methods such as mass spectrometry, capillary electrophoresis, and nuclear magnetic resonance (NMR).
Molecular Cloning:
In this section of the course, participants will learn the most common methods of molecular cloning from a hands-on perspective. They will clone carbonic anhydrase and then verify their product. Techniques they will learn include:
  • RNA isolation
  • Reverse Transcription - Polymerase Chain Reaction (RT-PCR)
  • Genomic DNA isolation
  • Use of cloning vectors
  • Restriction endonucleases
  • Southern blotting and hybridization
  • Microarrays
Lab lectures by UF faculty and personnel will cover Northern blotting, Ribonuclease Protection Assay (RPA),basic and real time PCR theory, cDNA library synthesis, molecular cloning applications, ethical and public issues in biotechnology, etc.
Bioinformatics:
Course participants are introduced to the effective use of Biological databases and software packages designed to manipulate genetic data. Students will use the BioTools™suite of programs and will be required to complete assignments using GeneTool and PepTool (both part of BioTools™). Topics covered will consist of:
  • Where to find molecular information on the web
  • Assembling of DNA sequence fragments
  • How to conduct BLAST searches
  • Predicting secondary protein structures
  • Identification of antigenic sites
  • Design of PCR primers
  • Prediction of insert orientation from a cloning experiment
On the last day of the course, students will deliver a Power Point presentation in which they will present their findings from unknown DNA sequence fragments provided along with a series of questions designed to guide their work. Typically, students determine the identity of the gene that matches their assembled sequences (if any), its species of origin, the protein that it codes for, the protein's chemical and physical characteristics, strategies to clone the gene, and any polymorphisms that exist. All of this data will be determined using the tools that they learned during the bioinformatics sessions.
Course Material:
Here is the Lab Manual(.pdf, size: 2.47Mb).
Lecture Notes
  • Bioinformatics I: Introduction to Web-based Tools and Databases from William Farmerie, PhD
  • Bioinformatics II: Introduction to PepTools from Li Liu, MD
  • Bioinformatics III: Introduction to GeneTools from Li Liu, MD
  • Bioinformatics IV: Cloning in Silico from Li Liu, MD
  • Structural Analysis of Proteins: X-Ray Crystallography from Mavis Agbandje-McKenna, PhD
  • Immunocytochemical Detection of Antigens from Greg Erdos, PhD
  • Microarrays: The Basics and its Applications from ick Popp, PhD
  • Microarray Approaches to Environmental Studies from Patrick Larkin, PhD
  • ABI Prism 7700 Sequence Detection System (Taqman) from Nancy Denslow, PhD
  • Molecular Applications to Animal Sciences from Karen Moore, PhD
  • Ethical Issues in Biotechnology from Maria Gallo-Maegher
  • Immunocyto Chemistry from Greg W. Erdos, PhD
  • Tissue Array from Greg W. Erdos, PhD

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IDP Lab

Date:TBA

This course is under revision. It is going to be available soon.


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Medical Biochemistry Lab (BMS 5204)

Date: TBA by course coordinator

Time: TBA by course coordinator

Location:
ICBR Room 184-South Wing
Cancer and Genetics Research Complex
Gainesville, FL
Schedule & Topics:
Find out what we will cover or what we covered in previous sessions by viewing our past schedule(.pdf, size: 170Kb).
Picture Gallery:
Description:
The Education & Training Lab has taught this laboratory for fourteen consecutive years. It is part of the "Biotechnology and Molecular Biology of Disease" class (BMS 5204) that all medical students are required to take. Students use the Polymerase Chain Reaction (PCR) to amplify a DNA segment of the HIV genome as a potential method for the detection of the virus in the progeny of infected mothers. In a separate experiment, students utilize a DNA single-locus, polymorphic probe in a Southern transfer procedure simulating a situation where molecular DNA fingerprinting is used to determine relatedness.
Course Material:
Here is the Lab Manual(.pdf, size: 332Kb).

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