BICH 464

BICH464 Bacteriophage Genomics – 3 credit hours

BICH464, Bacteriophage Genomics, has actually been in operation for about a decade now.  Throughout its existence it has been supported by the National Science Foundation.  The general idea is to offer TAMU life science majors an opportunity to learn about modern genomics by a hands-on experience while doing a real research project in which they “annotate” a new phage genome. What does “annotate” mean?  Well, when you first get your genome, it will be just a long string of the four DNA bases (A, G, C, and T), probably 50,000 to 250,000 bases in length.

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When you are finished at the end of the semester, you will have mapped out all the phages’ genes and many of the gene control sequences.

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A student genome showing multiple tracks of annotation. Through bioinformatics, we can figure out the functionality of most proteins in the genome.

This annotation will then serve as a central element in a paper that will be submitted to a scientific journal in lieu of a final exam.  The journal is GenomeA, which is the main venue of the American Society for Microbiology for announcing completed genomes.

A published GenomeA paper from the 2015 class year.

The central concept for BICH464 is that if a student gets “ownership” of a novel genome, instead of a cookbook exercise, that sense of ownership will be a source of motivation and drive that will greatly enhance the learning process (as well as generate a scientific work-product!).  Bacteriophages, which are simply the viruses of bacteria, were chosen as the organisms of choice for the simple reason that they have relatively small genomes, typically on the order of 100,000 base pairs of DNA or ~100 genes.  That may sound like a lot, but it is an order of magnitude less than a typical bacterial genome, and 2-3 orders less than a typical eukaryotic genome, both of which would be just too large for a student to handle, especially in one semester.  Also, we know each phage genome has to have genes for things like the viral capsid, tail, DNA packaging and host lysis, which makes it a bit easier to assign gene function.  In any case, the system has worked well for a long time.

Course Content

So what actually happens in the course, and what would you be expected to do?  The course has three phases; lecture, lecture & computer lab, and finalising the genome. During the first phase, the classroom sessions are dedicated to an intensive survey of basic bacteriophage biology.  You will learn what phages are and how they work at the molecular level.  The second phase starts when you get assigned your new phage genome.   At that point, time is divided between lectures on phage biology continue and computer sessions devoted to genome annotation and learning bioinformatics methods and tools.  In the third phase, sessions are increasingly dedicated to the computer instruction and workshops focused on actual issues arising during the annotation of your particular genome, culminating in the completion of your annotation project and your GenomeA paper.

Gabby 130212 Barrett 120K

Throughout the semester, the laboratory component runs in parallel.  You will collect environmental samples and then learn how to isolate new bacteriophages from those samples.  During the semester, you will process these novel phages, purify them, and prepare electron micrograph images of the phage!  Some of these new phages will be the subject of annotation for the next year’s class.

In the early years of the course, we used to do the sequencing of the new phages ourselves.  However, in modern biology, whole genome sequencing is done commercially with “high-throughput” technologies, and the real scientific bottleneck is the annotation.  That’s where you come in…

Interested?

You are officially encouraged to drop us a line.  We have to limit the course to 20 students, and it is best if you have had some preparation for the microbiology and molecular biology concepts that are a central part of the course material.  Typically students are BICH or MICR or GENE majors who have had microbiology (e.g., MICR351) and/or basic molecular genetics (e.g., BICH/GENE 431), and/or bacterial genetics (MICR406).  However, we can be flexible, depending on your background and academic goals. The simplest approach is to email one of the course staff:

Position Name Contact
Dr. Ryland Young ryland@tamu.edu
Course Instructor Dr. Jason Gill jason.gill@tamu.edu
Secretary Mrs. Daisy Wilbert daisy@tamu.edu

You will need to supply a print-out of your grades and a short CV.  You can also come by room 308 in Bio/Bio and inquire directly to Daisy.  In either case, you will get a quick response!

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