Teaching Enhancement Grant Application -- Biology
Title of Proposed Project: Development of a Case Study and Inquiry-Based Bioinformatics
Course
Abstract:
The field of Bioinformatics is a burgeoning field that has revolutionized how biologists do
science over the past 10 to 15 years. This past year I developed an upperdivision undergraduate
course (taught as a BIOL490 topics course) that centered on bioinformatics and the annotation of
the Pseudomonas putida F1 genome. The course was taught as part of the Department of Energy
and the Joint Genome Institute undergraduate bioinformatics education program. The project
proposed here is to re-develop the course with a change in pedagogy such that the course is a
student-led experience, with the goal of the course being taught solely through the use of case
studies and student led presentations. The changes to this course are intended to more fully
develop independent learning skills for the students, which is imperative for all courses, but most
importantly for an applied science course such as Bioinformatics.
NARRATIVE:
Project Narrative:
1. Rationale and need for the project:
The ultimate goal of this project is to expose and engage UST biology majors to the field
of Bioinformatics. Bioinformatics involves the use of computer programs and databases to
predict the molecular workings within an organism. This includes the ability to predict, based
upon known genetic DNA and protein sequences, the sum total of genes, proteins, and possibly
cellular activity of organisms. For example, one can use the genetic and protein information from
the (arguably) best-studied organism Escherichia coli to gain important information about
organisms that have not been as well studied (Galperin, 2004; Koonin and Galperin, 2002). Two
important caveats to the use of bioinformatic tools is that the information generated from these
types of very educated predictions is 1) only as good as the information that is entered into each
database and 2) that the predictions of gene function are merely predictions. Therefore, 1)
students and researchers must be properly educated in the strengths and limitations of
bioinformatics tools to correctly contribute to bioinformatics data bases and 2) experimental
evidence is required to definitively determine gene and protein function for an organism. In
addition, this knowledge of bioinformatics along with the advent of genome sequencing has
changed how scientists investigate problems; instead of looking at how one gene or protein is
affected by a particular problem, we now can look at how the entire genome (genomics) or the
entire organism (proteomics) responds. It is imperative to create new opportunities for our
students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics
on modern life sciences research (Saier, 2003; Konopka, 2004; Krilowicz et al., 2007).
The ways of science education have changed drastically over the past 10 to 15 years due
to the emergence of problem-based and inquiry-based learning techniques. It has always been my
teaching philosophy that the best way to teach science to students is though example- to educate
students about science by doing science. For the area of Bioinformatics, this concept is
imperative to demonstrate to the students so that they can take what they have learned about how
to annotate genes and apply that knowledge to a genome that has not yet been investigated. In the
Bioinformatics course I taught last fall, I designed the lecture portion of the course to involve my
disseminating information about each bioinformatic tool to the students through lecture. The
application of the information by the students came through by actively annotating, or assigning
putative gene functions, Pseudomonas putida F1 chemotaxis genes for one class period a week.
The information generated through student annotations was used in the laboratory portion of the
course, whereby they experimentally investigated their gene predictions, looking into the ability
of Pseudomonas putida F1 to respond chemotactically to the environmental pollutant toluene.
Making the connection between the gene predictions in class and the testing of those predictions
in the laboratory was the best part of this course as the students were actively engaged in asking
and answering a pertinent scientific question. Where the course desperately needs further
development is 1) in how each of the bioinformatics tools is presented to the students for their
understanding, 2) how these tools can be used for various applications besides the microbial
genome we focus on in the course, and 3) how this technology is changing how we ask and
answer questions in the broader scientific arena. Pure lecture on the annotation techniques in
courses cannot make these various important connections known.
My attention for course design thus far has been mostly focused on me personally earning
and understanding the basics of bioinformatics in the context of the Genomic Encyclopedia of
Bacteria and Archaea (GEBA) project developed by the Department of Energy’s Joint Genome
Institute (DOE-JGI). The goal of this project is to generate a basic understanding of microbial
diversity and will also require an unprecedented number of informed scientists in the area of
bioinformatics to make this wealth of information usable by the scientific community. Through
this GEBA program, the DOE-JGI has called upon undergraduate institutions in the United
States to collaborate in annotating the GEBA genomes and UST was chosen as a pilot school two
years ago for this new and exciting program based upon my application (see Other Supporting
Materials). I have been working with the program to pilot this bioinformatics course here at UST
using the web-interactive Integrative Microbial Genomes Annotation Concepts Tool (IMG-ACT)
designed by the DOE-JGI with input from pilot faculty. I have attended multiple workshops at
the DOE-JGI to introduce pilot schools and faculty to the program and to give feedback for my
initial implementations of the course (Krane and Raymer, 2003; Pevsner 2003; Zhou et al., 2004;
Higgs and Attwood, 2005).
In my proposal here, it is my goal to improve upon the bioinformatics course by no longer
focusing on the bioinformatics content of the course per se, but to now focus on how it is the
students are learning and applying this information. I plan to do this by having the students learn
about each bioinformatic tool in context by the use of case studies. I do have experience in using
and developing case studies, as I have been involved with the concept of inquiry-based learning
since I started teaching at UST in 2003. I have been involved in Bush-Grant sponsored casestudy workshops and have participated in Project Kaleidoscope meetings that are committed to
science education reform.
2. Goals and Objectives:
The broad project goal for this course is to incorporate active learning experiences into
the course curriculum that effectively describe the basis and purpose of various bioinformatic
tools and to broaden student understanding about the use of these tools, particularly when it
comes to systems outside of the bacteria, one important example is human health. In the previous
course, the only application of these tools was to bacterial systems, which is a very limited view.
Therefore, it is my goal to make this course more multi-disciplinary by using examples from a
number of model systems to reinforce the importance of this technology in our future and the
desperate need for scientists who know how to use it.
In terms of my professional development, the changes proposed for this course will allow
me to put into practice the concepts of inquiry-based learning that I have been actively involved
in since I started teaching at UST in 2003. The generation of cases that delve into the broader
implications of bioinformatics (human disease, biomedical technology) will all be new to me.
The genome annotation and laboratory experience that was developed for the first iteration of the
course will be maintained in future years. I have been actively involved in the field of aromatic
acid and aromatic hydrocarbon research since the mid-1990s (Ditty et al., 1998; Ditty and
Harwood, 1999; Parales et al., 2000; Ditty and Harwood, 2002; Parales and Ditty, 2005; Parales
et al., 2008). New findings generated by my student’s involvement in this research also enrich
my professional development. While this proposal will defiantly enhance my professional
development, the most important aspect of this project is how it will affect student learning.
What this course brings overall to our students is an important update to the curriculum, much
like the addition of “molecular biology” courses in the 1980s. It is imperative to create new
opportunities for our students to gain experiences reflecting the influence of genomics,
proteomics and bioinformatics on modern life sciences research (Saier, 2003; Konopka, 2004;
Campbell and Heyer, 2007; Krilowicz et al., 2007). Most current pedagogical studies have
indicated that using active learning techniques are more successful in facilitating student learning
because these varying types of techniques teach in the context of interesting questions and in an
independent manner.
Objective 1: Develop or utilize already published case-based modules that effectively describe
the purpose and use of the multitude of bioinformatics resources for gene calling (RAST,
Glimmer, Critica), protein calling (BLAST, Pfam, PDB), protein localization (TMHMM,
SignalP, PSORT) and organizing groups of proteins that function together for a cellular purpose
(COGS, KEGG).
Objective 2: Design the cases that introduce these bioinformatics tools using various types of
scientific questions which will specifically broaden student understanding and importance of
bioinformatics to model systems outside of the bacteria.
Objective 3: Design case studies that reflect how bioinformatic technology is changing how we
ask and answer scientific questions by focusing on the entire organism (genomics and
proteomics) and how this technology is changing how we understand the human condition
through investigating bioinformatic information on evolution, disease, and biomedical research.
3. Activities:
The activities that will be implemented in the lecture portion of the course are the use of
case studies that have been previously published or cases that I personally modify or develop
(Campbell and Heyer, 2007). For one example, a case will be utilized by the students that use the
human disease of muscular dystrophy (What’s Wrong with My Child; Campbell and Heyer,
2007) to introduce the key bioinformatic concepts of on-line databases of human genetic
information (National Center for Biotechnology Information [NCBI] and Online Mendelian
Inheritance in Man [OMIM] for example), identifying key differences in gene and protein
sequence from the patient’s protein to known, diseased proteins (BLAST database), and
subsequently determining if those differences are significant (statistical analysis through
Evalues).
All of the information generated by the students on each of these key concepts will be
accumulated by the students in a personal Bioinformatics Portfolio, which will be used as a
reference throughout the course for their own personal annotations. All of the data and
information used in the case studies is based upon scientific questions that have already been
answered. Therefore, a key to this course will still be for the students to then take what they have
learned from these cases, and apply that information to the annotation of unknown genes in
Pseudomonas putida F1, an organism that has not as of yet been fully investigated
bioinformatically.
4. Evaluation:
This project will be evaluated at multiple levels. At the student level, attitudinal surveys
of the course will be given at mid- and end of the semester. Student progress in scientific
experimental design and implementation will be evaluated by presentation of results at a
departmental seminar, either through a poster or oral presentation of data collected by this
project. Evaluations of the GEBA initiative will also be assessed by a survey of the students
conducted by the Oak Ridge Institute for Science and Education (ORISE) for the broader impact
of this program throughout all undergraduate institutions participating in the GEBA program.
5. Dissemination:
Dissemination of this project will be conducted at various levels. Here at UST, I have
been in contact with members of other programs (Biochemistry) to demonstrate the importance
and use of the GEBA annotation software across disciplines. An article for Synergia or the
Nucleus would also promote the importance of this project. The GEBA project is an initiative
that is attempting to change the face of science education and research at all undergraduate
institutions. The work of pilot institutions (again, one of which is UST) will be published in a
science education journal to promote this project nationally. In addition, the results of the
Pseudomonas putida F1 toluene chemotaxis research project that will be required of the students
will be publishable in a peer-reviewed scientific journal. It is overly optimistic to think that a
research publication will come from this one semester course; however the publication of the
cumulative work of our students over a few semesters of this course is achievable.