posted August 16, 2012

“Next-Generation” Genomic Sequencer Will Enhance Program

From tracking the ancestry of maple trees worldwide, to studying contamination in the Lake Macatawa Watershed, to a first-year class’s research into a mycobacteriophage, a new bench-top “next-generation” genomic sequencing platform coming to Hope College this fall will find many applications.

The college has received funding for the instrument through a $171,877 grant from the National Science Foundation (NSF).  The new instrument is scheduled for use in both research and teaching, generally at the same time since the college makes a point of linking the two, according to the two faculty coordinators of the grant project, Dr. Aaron Best and Dr. Jianhua Li, each of the biology faculty.

“We want to do research, and we want to apply this research to lectures and get students involved in the research process,” said Li, who is an associate professor of biology.  “We can get students involved in the whole process of getting data and analyzing data.”

Best, who holds the college’s Harrison C. and Mary L. Visscher Endowed Professorship in Genetics, noted that advances in genetic-research technology are so significant and continuous that the instrument has thousands of times the power of a sequencing instrument that the college acquired just 3.5 years ago, and makes available capability previously limited to major research laboratories with much larger and more expensive equipment.  In the time that the machine currently used at Hope could analyze four single genes, the new instrument will be able to analyze several complete microbial genomes, each comprised of up to a few thousand individual genes.

“I’m excited from the technology standpoint and from the standpoint of having students have access to that technology,” Best said.

“This is leading-edge technology,” he said.  “It will allow us to do a lot of different types of experiments that were unavailable to us before on campus.”

Li’s research projects include developing an understanding of how the world’s approximately 200 species of maples are related to one another by comparing their genomes and using the information to help determine where on the planet maples originated.  He is also examining the relationship between a parasitic plant found in Southeast Asia, Balanophora, and its host, testing the possibility that the host plant may transfer genes to the parasite.

Best’s research projects involving the new instrument will include his on-going investigation of how an intestinal parasite called Giardia lamblia turns its genes on and off, a process called transcription.  He will also analyze microbial sources of contamination such as E. coli in the Lake Macatawa Watershed, the better to identify the origins of the contamination, part of an on-going study of the watershed involving multiple researchers at the college.

The instrument will be an important resource in the freshman-level “phage genomics” course that the college has offered since the fall of 2008 and which Best co-teaches with faculty member Dr. Joseph Stukey.  Through the course, students isolate and characterize previously unknown bacteriophages, viruses that infect bacteria.  Each year, 20 students enroll in the course and study their own bacteriophage, with one or two samples chosen during each of the past four years to be sent to an external laboratory for sequencing and ultimately for inclusion in a national database.  With the new instrument, Best said, Hope will be able to sequence all 20 itself, and for only a fraction of the cost of sending just one for external analysis.

Hope students will work collaboratively during the school year and summer with both Best and Li on their research projects, and the instrument will also provide opportunities for students in other courses at the college.  For example, Best noted that students in upper-level laboratory-based courses will be able to conduct more advanced work focused on the bacteriophages, and students in the Plant Systematics and Evolutionary Biology courses that Li teaches will become involved in the maple research.