Feb 5th

STUDENT MINI-PRESENTATIONS ON GENOMIC TECHNIQUES

Given rapid advances in genomic techniques we are now able to assay, at the whole genome level, gene expression level, genomic content and epigenetic state for a broad range of organisms not previously amenable to genetic/genomic techniques.

Student groups will present (in 5- 10 minutes) the basic methods for various genomic techniques that are likely to surface throughout the semester. When possible, students should discuss they type of inference that can be drawn from data generated by each technique. These presentations are not intended to give a comprehensive explanation, simply a rough understanding so that students are sufficiently prepared to select research papers for further discussion. Each week, the methods used for that specific research paper will be presented in more detail by the student discussion leaders.

Neenah >> Microarray (gene expression) = A miroarray is a collection of microscopic DNA spot, often representing known genes, attached to a solid surface. By hybridizing a cDNA sample (reverse transcribed from isolated mRNA)to the array it is possible to quantify the level of expression for each gene on the array.

Suzy >> CGH(structural variation) = Comparative Genomic Hybridization uses a microarray but the labeled sample is genomic DNA. Therefore, the hybridization intensity reflects the copy number for genomic elements.

Sara >> RNA-seq = Transciptome description by sequencing of reverse transcribed RNA. This technique can be used to identify transcripts or to compare expression level.

Leah >> GWAS = genome-wide association study is an method by which to examine the common genetic variants (using molecular markers, most often SNP's) in different individuals to see if any variant is statisitcally associated with a trait.

Audrey >> ChIP-seq is used to analyze protein interactions (such as transcription factor binding) with DNA. ChIP-seq combines chromatin immunoprecipitation (ChIP) with DNA sequencing to identify the binding sites of DNA-associated with particular proteins.

Bailey >> DNA-methylation(sequencing) (a.k.a. bisulfite sequencing) = When DNA is treated with bisulfite any C that is methylated is converted to a T. Therefore, comparison of sequence for treated and untreated DNA will reveal the methylation state.

Conrad >> QTL = Quantitative Trait Locus analysis is a statistical method that links two types of information—phenotypic data (trait measurements) and genotypic data ( molecular markers such as SNP's or AFLP's)—in an attempt to explain the genetic basis of variation in complex traits


 

STUDENT MINI-PRESENTATIONS ON Zuk & Balenger

All Students will read Zuk & Balenger 2014 and come ready to discuss the extent to which genomics is showing us new kinds of questions and previously unknowable answers. Each student will be responsible for presenting (potentially with the use of the white board) one subsection of the paper (listed below) and how these subsections contribute to the overall take home message of the paper.

Zuk, M., and Balenger S.L. (2014) Behavioral ecology and genomics: new directions, or just a more detailed map? Behavioral Ecology 25:1277-1282.

Mellisa >> LOST IN THE MAP

Hannah >> GENOMICS IN BHEAVIORAL ECOLOGY RECENT EXAMPLE

Robin >> THE SOCIOGENOMICS REVOLUTION: CONFINED TO HYMENOPTERA

Christina >> GENOMICS AND ALTERNATIVE MATING TACTICS

Maia >> GENOMICS AND SEXUAL CONFLICT

Jason >> NEW MODEL SYSTEMS

Liz >> MECHANISMS, GENES AND PLASTICITY