Amy Hark, Muhlenberg College

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Amy T. Hark, Ph.D.
Associate Professor of Biology
Co-director of Biochemistry
Director, Faculty Center for Teaching
Muhlenberg College
updated 6.14.13


I have had research/independent study students working on annotation projects for the past four years, typically beginning with D. erecta or D. biarmipes fosmids and moving on to more divergent D. grimshawi, D. mojavensis, or D. ananassae contigs.  Students generally spend the first 4 weeks of the fifteen-week semester doing background reading and practice exercises with BLAST and annotation, which seems to prepare them well for working on their own fosmids/contigs.  Specifically I use the following GEP curriculuar materials:

- An Introduction to NCBI BLAST is given to students initially as a reference/review.

- I use the Powerpoint Introduction to ab initio and evidence based gene finding to introduce both background on the dot chromosome and methods of gene annotation.

- Students tackle A Simple Annotation Problem before claiming a project of their own.

- Students are given the Annotation Instruction Sheet among other references when they are working on their annotations.


We are currently using electronic lab notebooks (Lab Archives platform), which I find works particularly well for this type of research.  I wanted to preserve the integrity of the record (all changes are saved and time-date stamped) but allow students to easily capture their work in a digital form.  This platform has the additional advantage of allowing me and research students to see each other's notebooks (if desired) from anywhere with internet access.


I am happy to share ideas with interested colleagues so feel free to contact me at hark@muhlenberg.edu.  Several of my students have continued their work into a second semester and some move on to other wet-lab projects in my lab.


One of our initial implementations of the GEP materials at Muhlenberg College (in Fall 2009) was in our third semester introductory course in molecular and cell biology (BIO 152 Principles of Biology III: Molecules and Cells). This effort was spearheaded by Kelsey Parry '11, a biochemistry major who attended the TA workshop and is now in her second year in Teach for America. The text that follows was drafted by Kelsey as part of her end-of-semester report; I hope it may give those of you who are interested an insight into how we carried out this small-scale implementation.


The BIO 152 differs in several fundamental ways from the course offered at Washington University and other undergraduate institutions in which this curriculum is typically implemented. This course is not offered as an elective but rather as a part of the core curriculum required for all biology, neuroscience, and biochemistry majors. While this is a general biology course, it is designed for students who have at least completed a full year of biology dealing with populations, organisms and cells. These students are more prepared for upper level work than the typically general biology student, as our Principles of Biology series spans over three semesters, the third of which served as the pilot for implementation of gene annotation and comparative genomics into the curriculum at Muhlenberg. Throughout the course, students are introduced to a variety of online bioinformatics tools such as OMIM, PubMed, NCBI Books, BLAST, and NCBI Structure. This is achieved via short independent assignments developed by Dr. Hark to allow students the opportunity to explore these databases in a structured format and become familiar with important functions of these tools. Through discussion we had determined, however, that it was often frustrating for students to use these tools for the first time. Unfortunately, more often than not, students tend to meet this frustration with a disinterest in what the databases have to offer. In an order to combat this frustration and exemplify the circumstances in which these tools may have a research application, we chose to take this opportunity to provide a lecture and hands on exercise for the students on NCBI BLAST and its importance to gene annotation.

It was my responsibility, having been trained as a TA for this type of curriculum, to prepare and lead a presentation and hands on exercise on the annotation of a D. erecta fosmid and the use of BLAST in my work.  It was our hope that hearing the material from a fellow student would heighten the validity of bioinformatics having practical application. By talking about my research specifically and how important BLAST and other bioinformatics tools are to my work, we hoped that students would be more enlightened regarding how invaluable these tools are. Additionally, it had not been long since I had been the student struggling to understand how to use BLAST and why it was important that I learn to do so. This perspective on the frustration of these tools put me in a position to better understand and address questions and concerns regarding the use of BLAST. On a more complex level, the format of this presentation was different from that of most lectures these students had experienced in the past – as courses at Muhlenberg are very rarely taught by a student. This change in format – though brief – was intended to serve many beneficial functions. Firstly, hearing the information from a fellow student was intended to make the message more relateable, less intimidating and more attainable. Additionally, we hoped to heighten student interest in pursuing undergraduate research as a part of their experience at Muhlenberg.

This presentation centered on the effective use of NCBI BLAST and served as an opportunity to express the importance of bioinformatics tools. The goals of my presentation were broad and varied. On a curriculum level, the presentation was intended to educate students regarding the various types of BLAST and the process of gene annotation and to engage students in a meaningful discussion regarding scores, e-values and percent identity and the significance of each. While the students had been previously introduced to the basics of BLAST, the material presented in my lecture and exercise expanded their knowledge beyond the basic function of this bioinformatics tool.  The lecture portion of this presentation began with a review of BLAST basics – the purpose of the tool, the ways in which it works, and the information it can provide. This introduction was followed by a discussion on the work that I perform in the lab and Muhlenberg’s connection to Washington University in St. Louis via the Genomics Education Partnership. What I feel was particularly valuable, however, was the opportunity that students were given to perform some hands on exercises to see the connections themselves. I developed an exercise to walk students through the process of finding the position of a D. melanogaster ortholog on both a D. erecta fosmid and a D. mojavensis contig. This exercise involved the application of various skills and knowledge of BLAST for successful completion. First, students needed to think about the various types of BLAST and determine which would be most useful for comparing their two sequences, this was also the first time the students had used BLAST2 to compare two known sequences rather than searching a database. Next the students reviewed phylogeny to compare the expected relatedness between the Drosophila species being examined and were asked to think about score, e-value and identity and what results they would expect. Additionally, once results had be obtained, the students were able to participate in a meaningful discussion regarding scores, e-values and percent identity and how the meaning of these values can differ under various search conditions. My presentation to the class was provided in three recitation sections to smaller groups of students in an attempt to facilitate hands on work with BLAST. The small groups afforded Dr. Hark and me the opportunity to engage in the learning process with the students and help work through their struggles.

While all of this information could have certainly been presented without the context of my work with the GEP and gene annotation, I truly believe that the undergraduate research angle of this presentation helped facilitate a better understanding of bioinformatic tools and their value to all scientists. Generally speaking I feel that my work on this presentation and the eventual incorporation of gene annotation and comparative genomics into the curriculum at Muhlenberg has been incredibly well spent and valuable for all involved. I have benefitted enormously from the opportunity to prepare and teach a lesson plan on the work that I do in the lab and I am under the impression that students in the class gained a considerable amount from my presentation as well. The presentation was evaluated by students with a simple assessment of how much they felt they learned regarding certain topics, whether they felt the presentation was beneficial to their learning, and whether or not the presentation increased their interest in participation in undergraduate research. On average, students agreed that several of our specific goals had been met, including reinforcement of the usage and importanceof BLAST and interpretation of e values, scores, and percent identity.