Project Description

Laurence (Larry) A. Moran

Dept. of Biochemistry

Medical Sciences Building

Rm. 5318 (until Feb. 24) Rm. 5253 (after Feb. 24)

There are many interesting problems in evolution that can best be studied by comparing the sequences of genes and proteins. An enormous amount of new data is available thanks to many recently completed genome projects. My main interest is in using highly conserved genes to explore the earliest steps in the evolution of living organisms. The most highly conserved genes in all of biology are the members of the dnaK/HSP70 gene family. BCH299Y students will assist in maintaining, annotatiing, and updating, the HSP70 Sequence Database. They will help sort out and identify the various members of the HSP70 multigene family in chimpanzee, Arabidopsis, dog, and other recently completed genomes.

Students will also address questions such as: the relationship between bacteria, archaebacteria, and eukaryotes; the origin of introns; rates of evolution in different genes; genome evolution; and the validity of various techniques for constructing phylogenetic trees.

The basic methodology involves retrieving homologous sequences from the major databases, such as GenBank, and using computer programs to align the sequences and construct phylogenetic trees. Here's an example of a phylogenetic tree using HSP70 genes ...

By the time you're finished this project you will have constructed an analyzed many trees like this one!

Description of Student Participation

Students will be expected to spend some time in the laboratory where they can learn how to interact with the server (Linux) and the database webpages. In addition, there will be regular meetings to discuss progress and share information and ideas. After the initial learning period, you will find that much of the work on this project can be done remotely on your own personal computer.

No advanced knowledge of computers or computer science is required for this project. You should be familiar with your own computer and know the basic techniques such as word processing and accessing the internet. You should know enough about your operating system to install programs and manipulate files. The minimum equipment requirements are a fast Pentium-based PC running Windows XP with high-speed internet access.

Each student will choose an interesting problem in molecular evolution and write up a proposal. In some cases, the research will address deep phylogenetic problems concerning events that took place hundreds of millions of years ago. Other research topics might include analysis of the HSP70 gene families in selected species. We will concentrate on using the HSP70 sequence database since the HSP70 genes are the most highly conserved genes known and there are hundreds of sequenced genes from many diverse species.

At the end of the year, students will write a research report describing their results and conclusions. The final grade will be based on marks for the research proposal, the research report, participation, and results.

Application

Send me an email message ["Larry Moran" lamoran@bioinfo.med utoronto.ca] confirming that you're still interested after you read these webpages. Make sure you fill out the application form and give to the Reseach Opportunity Program Office by Friday, March 17, 2006. I'd like to meet with you so you can find out more about me (and the project) and I can find out more about you. Here are some possible dates and times - let me know if you are available and we will set up a meeting. There will usually be several students at each meeting.

                     Monday, March 20, 2006 at 4 PM
                     Wednesday, March 22, 2006 at 2 PM
                     Wednesday, March 22, 2006 at 6 PM
                     Thursday, March 23, 2006 at 2 PM

Please write a brief letter of application and bring it to my office before the date of our meeting. The letter should list the courses you are taking and how well you expect to do in each course. (Grades are not an important determinant in the selection process.) You should also explain why you want to take BCH299Y and what you hope to achieve. What Program (POSt) are you applying to next month (e.g., Biochemistry, Molecular Genetics & Microbiology, Immunology, etc.)? What are your long-term goals? Do you want to be a scientist or enter medical school (or both ... or neither)? It would be helpful to include a resume (curriculum vitae) with your letter in order to tell me more about yourself. (Please do not email your letter and CV. I want to see a nice printed version that shows off your formatting and presention skills.)

More Information

There's a brief introduction of the project at [Introduction]. This is intended for students who are starting the BCH299Y project in September. If you want to learn more about this project, follow the links from that webpage. They contain descriptions of the HSP70 Sequence Database, the Aligned Sequence Database, programs that we will use, and a short lesson on how to make a phyogenetic tree.