Laboratory

The research at Laboratory of Functional Genomics is involved in:

• Whole genome scanning and identification of QTL regions for the complex traits in mammals using DNA pooling techniques.
• Gene expression profiling and identification of anonymous expression sequence tags (ESTs) markers in mammalian genome using cDNA-AFLP technique.

The Laboratory of Functional Genomics at UMK is currently equipped with following gene function analysis systems used in Mammalian Genome research:

1. Li-COR DNA Genetic analyzer system:

A comprehensive system designed specifically for microsatellite (STR), AFLP® and cDNA-AFLP® techniques in Genomic research analysis.

2. Li-COR DNA sequencer system:

LI-COR sequencers can routinely provide 800-1100 nucleotide, one-pass reads with accuracy better than 99% on single and double-stranded DNA templates. The instruments produce long nucleotide reads through the use of a focusing microscope mounted on a scanning laser to detect near-infrared fluorescence labeled products from DNA sequencing reactions. The number of nucleotides determined from a set of four lanes is a function of the quality of DNA template and the length of the gel used to resolve the reaction products. The high accuracy levels are, in part, attributable to the use of the four-lane sequencing strategy. Since raw data are de-convoluted (fluorescent labeled reaction products for each of the dideoxy-nucleotide chain terminations are electrophoresed in separate lanes) spectral overlap leading to incorrect or ambiguous base calls does not occur. The four lane presentation format also permits the rapid review and editing of sequence reads; however, this format allows the analysis of fewer reactions on a single gel. The LI-COR system can detect primer labeled extension products of sequencing reactions at two different wavelengths. Coupled with the development of the dyes IRD700 and IRD800, two DNA sequence ladders can be simultaneously electrophoresed and analyzed on the LI-COR system in a single set of gel lanes. The two-dye system doubles the number of sequencing reactions that can be loaded.

3. THE ABI 341 GENEPURE NUCLEIC ACID PURIFICATION SYSTEM:

This system simplifies the process of DNA purification from all biological samples. The ABI's 341 Genepure enhances consistency and reliability for small sample extraction while reducing the chance of sample mix up or exposure to harmful contaminants. The 341 offers two automated chemistry options: standard and fast cycle. These cycles are optimal for small samples of DNA that are suitable for both PCR and Southern blot analysis.