Matthew Wawersik - College of William & Mary
BIO404/504-13: Genomics & Functional Proteomics Lab
Instructor: Dr. Matthew Wawersik (Va-Ver-Zick)
Credits: 1 credit laboratory course (unlinked)
Pre-requisites: Molecular Genetics (Bio 432)
Time: Wednesdays 1:00-3:50 pm
What is genomics? This field, broadly defined as the study of genes and their function, strives to characterize the complete genetic makeup of a wide array of organisms, and has applications in fields ranging from basic cell and molecular biology, to evolutionary biology, structural biology, pharmacology, human genetics and even forensics. This course is designed to help you gain a better understanding of this broad field and it’s applications. To do this, you will gain hands-on experience with DNA manipulation techniques used during the process of genome sequencing, basic bioinformatics tools used to analyze genes and genomes, as well as a current method for analyzing protein function (Fly-Trap anslysis) that is enabled by completion of the Drosophila melanogaster genome.
This course is also intended to provide direct exposure to primary research. The middle section of this lab (genome annotation) is part of a nation-wide effort to complete the genomes of all Drosophila species, while the final portion (FlyTrap analysis) is part of an effort in my lab to elucidate genes involved in the processes of germ cell sex determination and germline stem cell maintenance.
Note: You will need a computer of the genome annotation portion of this lab. Any laptop will suffice if it has wireless connectivity. If you do not have a laptop with reliable wireless access, please let me know me so we can get one for you.
Course structure & syllabus:
This course is divided into three sections (detailed syllabus below). The first section focuses on understanding the process of genome sequencing and uses of sequence analysis resources, the second concentrates on the annotation of the 4th/dot chromosome of D. erecta, and the final section will be centered around expression analysis of FlyTrap lines in ovaries and testes from D. melanogaster. Grades will be determined through performance on your laboratory notebook, course exercises and through oral and written reports of research findings (see below). Students who successfully submit annotated sequences from a ‘claimed’ fosmid (see below) will be eligible for authorship on a peer-reviewed scientific article.
Section #1 - Genome Sequencing & Intro to sequence Analysis (groups of 2):
1/28: Lab overview & course surveys
Lab #1: Lab safety & protocols
2/4: Lab #2: Yeast genomic DNA extraction & digestion
Prep for Lab Section #3: Intro to GFP-Trap data mining
2/11: Lab #3: Cloning and transformation of a genomic DNA fragment for sequencing
Prep for Lab #4: Intro to DNA sequencing technology
2/18: Lab #4: Plasmid purification for restriction digest & DNA sequencing
Lab demonstration: DNA sequencing
2/25: Lab #5: Sequence analysis: Basic BLAST & cloning confirmation
Prep for Lab Section #3: Selection of GFP-Trap lines (groups of 3)
Section #2 - Finishing & Annotating a Sequenced Genome (groups of 2):
3/4: Intro to sequence finishing & annotation
Lab #6: A simple introduction to BLAST
3/18: Lab #7: Detecting and Interpreting Genetic Homology
Claiming your fosmids from Washington University/GEP
3/25: Lab #8: Annotating your own fosmid
4/1: Lab #9: Annotating your own fosmid cont’d
4/8: Lab #10: Annotating your own fosmid & submission to Washington University/GEP (required for authorship!)
Section #3 - FlyTrap gene expression analysis (groups of 3):
4/15: Lab #10: Dissection, fixation & immunostaining of Drosophila testes from FlyTrap lines
4/22 Lab #11: Continuance of testes immunostains; intro to microscopy & live imaging of Drosophila ovaries
4/29: Lab #12: Completion and analysis of testes immunostains
Lab Notebook – 30%
Class Exercises – 30%
Final research reports: 30%
Class participation/attendance – 10%
Lab Notebook: You are expected to keep a daily lab notebook (a) summarizing the goal of each day’s project, (b) a ‘protocol notes’ section stating any details regarding specific experiments, and (c) a final summary section that provides a brief summary and conclusions of each day’s observations. As many of the protocols you will use are written up in detail already, you need not write every step of the protocol in this notebook. However, you should reference each protocol used in the ‘protocol notes’ section. In this same section, you should also discuss any steps where you might have accidentally diverged from the protocol and/or list any other observations you might have found strange or interesting. As a researcher, such notes are critical. If all goes well, a you may never look at this section again. But, when things don’t go well, these notes become critical for trouble shooting. Lab notebooks will count for 30% of the grade, and will be collected for grading over spring break and at the end of the semester (May 11th).
Class exercises: Throughout the course, we will have there will be a number of Pre-Lab hand-outs and Lab Exercises or Summaries. These exercises will count for 25% of your grade with each pre-lab valued at 5 points and Lab Excercises/Summaries valued at 15 points each.
Final Research Reports:
You are each expected to submit written reports summarizing research findings of your ‘Fosmid Annotation’ and ‘FlyTrap’ analyses. Each report should (a) summarize the question being asked, (b) briefly describe any methods used (with references to protocols), (c) fully describe any observations made, and (d) clearly summarize your research results and conclusions. For your annotation report should also provide an overview of your fosmid clone including all predicted genes, describe the gene structure for these genes, and provide information regarding functional orthologs, presence, function and location of any repetitive DNA elements, as well as any information regarding synteny (conservation of gene order) for at least one of these genes. These written reports will be due on Monday May 11th.
Recommended Text: A Primer of Genome Science, 3rd ed.; Gibson & Muse