In Brief

Sugaring Time Again; Former President Writes Autobiography; Alum Signs with Baseball Team; News from the Nursing and Business Administration Departments and more.

Making Their Mark

Learn about how our community members engage in writing, presentations and exhibitions.

Past as Prologue

Explore Haystack, a portal to the history of Colby-Sawyer College.

Colby-Sawyer Courier

Keep up with campus news from students' perspectives through the Colby-Sawyer Courier.


This new literary magazine features creative writing in many genres by current students and alumni, faculty and staff, and a few friends and partners.


Find out what Colby-Sawyer alumni have been up to since graduation.

Currents: bioinformatics

Biology 106 Classes Conducts Genome Research

This semester Professor Kathryn Gogolin Reynolds' Biology 106 classes have "adopted" the Thermaerobacter marienesis genome. Genomes contain an organism's hereditary information, its genes and DNA, and by sequencing them, scientists discern how species of organisms function in their respective environments. This fall, Professor Reynolds has assigned groups of students in each class to research several genes involved in making the essential amino acids needed for this organism's survival.

Current technology doesn't yet allow scientists to sequence genomes in one long strand; each must be sequenced gene by gene. The genome can then be assembled virtually, piece by piece, within a database map that mirrors the genome's original state. Once it's virtually assembled, scientists can “annotate” the genome, the process of learning more by comparing the genome to better known organisms. Computer algorithms do an initial annotation, yet currently about 35 percent of these analyses are incorrect. People with strong critical thinking skills and background in biology can assist in finding, and reporting, these inconsistencies. Here's where Colby-Sawyer students in Biology 106, and the field of bioinformatics, come into the picture.

“Students are now studying their biosynthetic pathways by annotating the genes that are involved. One great aspect of sequence annotation is the ability to go through the scientific method in a virtual way," says Professor Reynolds. “Students can run a series of tests and gather data, and then come to a conclusion on whether they feel that this is the correct gene within our organism that functions in doing that particular job.

Emma Barre, a first-year student from Claremont, N.H., who plans to study nursing, has always enjoyed science and finds her recent research both challenging and rewarding. Unlike other labs, in which students use microscopes to view organisms, she and her classmates conduct their research through computer programs on their laptops.

“We're learning about metabolic pathways, and we're mapping things,” Barre says. “We're the first ones to look at Thermaerobacter marienesis. It's the first time we've ever done this; it's a challenge because there are a lot of steps to do it correctly.” If she or her clasmates find something incorrect, they can notify the Joint Genome Institute through its web site.

Like her classmate Emma, Rachel Robert of Richmond, Va., has been interested in and good at biology since middle school, and she too, hopes to enter the field of nursing one day. But while she took an Advanced Placement biology course in high school, the bioinformatic research she's now engaged in is completely new to her.

“It makes what we've been learning, and the importance of it, much more clear,” says Robert. “This is a study of bacteria and how the different pathways each have a different purpose. Ours is the histidine metabolic pathway, an essential amino acid important for all life, even humans. In fact, it has great importance in the proper growth and development of infants. This project shows me that anybody can really do it once you understand the basic processes.”

Kimberly Swick Slover

Colby-Sawyer College Hosts Workshop in Bioinformatics: the New Frontier that Combines Biology and Computer Science

Bioinformatics is an exciting new area of biology that uses computer science application tools to study DNA and protein sequence. The goal of this field is to learn more about biological processes in a variety of organisms with as little as some basic knowledge of biology and an internet connection. This new field has been accelerating ever since scientists sequenced the first full genome map of the bacterium Haemophilus influenza, which was published in 1995 and it's growing in popularity as the technology becomes more widely available and less expensive.

This month Colby-Sawyer College hosted a regional “IMG-ACT Bioinformatics Faculty Development Training Workshop” on Nov. 6 and 7, 2010. Fifteen faculty and staff members from five colleges, including Keene State College, Bennington College, Plymouth State College, New England College and Colby-Sawyer College, participated in the faculty workshop. The participants learned about the Integrated Microbial Genomes - Annotation Collaboration Toolkit (IMG-ACT), which provides training and teaching support for annotation of microbial genomes through a separate database just for instructors called IMG/EDU.

This event was sponsored by the Microbial Genome Annotation Network (MGAN), an organization funded by the National Science Foundation, as well as the National Center for Research Resources' IDeA Network of Biomedical Research Excellence (INBRE) grant, which is supported by the National Institutes of Health, in collaboration with the U.S. Department of Energy's Joint Genome Institute (JGI).

The Joint Genome Institute has currently sequenced more than 6,000 genomes from all three domains of life (Bacteria, Archaea, and Eukarya), as well as viruses and provided that information in a publicly accessible database called the Integrated Microbial Genomes (IMG). Approximately four years ago, the JGI reached out to colleges and universities to start a collaboration that would allow students to be involved in bioinformatics research (called sequence annotation) and help analyze the massive amount of sequence information that JGI was accumulating within the IMG database.

The workshop was organized and coordinated by Kathryn Reynolds, a new faculty member in the Department of Natural Sciences at Colby-Sawyer College. She has worked with Professor Goodner for the past three years at Hiram College in Ohio on integrating the IMG-ACT into laboratory courses and working with students on sequence annotation research.

“I have seen firsthand how much the students appreciate learning this valuable skill,” says Dr. Reynolds. “They really feel like they are making a worthwhile contribution to science and it's something to be proud of.” Currently this fall semester, Professor Reynolds is using the IMG-ACT platform in her Biology 106 (Chemical and Cellular Basis of Life) course and her students are helping annotate gene sequences from the organism Thermaerobacter marianensis, a thermophilic bacterium that lives in a deep ocean vent. “It's a great opportunity for the students to think about how an organism can survive in an environment very different from our own.”

Brad Goodner, professor of biology and director of the Center for Deciphering Life's Languages at Hiram College, has collaborated with JGI from the beginning. “This joint effort by the DOE and colleges around the world is a fantastic opportunity for students to make a contribution to the scientific community now rather than wait until they are in graduate school,” says Dr. Goodner, who was also the MGAN representative and workshop facilitator. “Several of my students have been authors on scientific publications as a result of their bioinformatics research and I hope that other faculty members can see the future benefit of such collaboration as well.”

With bioinformatics and the tools associated with the technology developing so rapidly, the workshop provided the perfect opportunity for faculty…to learn about all the developments in the field and quickly adapt teaching modules into their existing courses, according to one faculty participant. Another faculty member, Amie McClellan of Bennington College, also felt that the workshop was beneficial and is “...definitely inspired to incorporate genomics and bioinformatics into future course offerings and is confident that (she) will have the knowledge and support to successfully do so.”

Colby-Sawyer College, Keene State College, Plymouth State College, and New England College are part of the $14.5 million INBRE grant that was awarded to 10 colleges and universities in New Hampshire to form a network of biomedical research which is spearheaded and jointed operated by a partnership between Dartmouth Medical School (DMS) and the University of New Hampshire (UNH).

“The INBRE grant was happy to help sponsor this faculty training workshop because one of the goals of the grant is to help provide students with training in the state-of-the-art tools available in the field of bioinformatics,” says Steven Fiering, an associate professor of microbiology and immunology and of genetics at DMS and a member of Norris Cotton Cancer Center. “It fit with our mission perfectly, which is to provide support for research and research training at the partner colleges that are the heart of the NH-INBRE network.”

Kimberly Swick Slover