BICH 464: Bacteriophage Genomics – 3 credit hours
BICH 464: Bacteriophage Genomics has actually been in operation for almost 20 years 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.
When you are finished at the end of the semester, you will have identified all of the phage’s genes that code for proteins and functional RNA’s, and many accessory features as well. These features will be annotated on the phage DNA sequence, which makes the genome record useful to other researchers.
This annotated genome record will be deposited into GenBank at NCBI and serve as a central element in a final paper that will be submitted in lieu of a final exam. These phage genomes will also serve as the basis for future peer-reviewed publications, and students will be listed as co-authors papers that contain their genomes.
The central concept for BICH 464 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.
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 finalizing 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 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 final paper.
Throughout the semester, the “wet” 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…
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, MICR or GENE majors who have had microbiology (e.g., BIOL 351) and/or basic molecular genetics (e.g., BICH/GENE 431), and/or bacterial genetics (BIOL 406). However, we can be flexible, depending on your background and academic goals. We also accept graduate students in the course, and most programs will allow grad students to take a limited number of 400-level courses as part of their degree plans. The simplest approach is to email one of the course staff:
|Instructor||Dr. Ryland Youngemail@example.com|
|Instructor||Dr. Jason Gillfirstname.lastname@example.org|
|Secretary||Mrs. Daisy Wilbertemail@example.com|
You will need to submit an unofficial transcript (.pdf) to Daisy at firstname.lastname@example.org. You can also come by room 308 in Bio/Bio and inquire directly to Daisy. In either case, you will get a quick response!