Even though the past year looked a lot different than a normal year, the Biology department managed to continue to have a productive year of teaching, learning and research. A few of the exciting accomplishments this year include:
The Fey lab and Ramirez lab collaborated with Meredith Theus (Biology '21) to publish a paper on their field-based pedagogy.
Fey, SB, Theus, ME, Ramirez, AR. Course‐based undergraduate research experiences in a remote setting: Two case studies documenting implementation and student perceptions. Ecol Evol. 2020; 10: 12528– 12541. https://doi.org/10.1002/ece3.6916
Postbac Amy Rose Lazarte (Bio '19) published a conference paper at a workshop for computer science education:
Lowering the barrier to learn about computational research through a course-based conference experience.
Lazarte & Ritz. 5th International Conference on Research in Equity and Sustained Participation in Engineering, Computing, and Technology (RESPECT). Mar 2020.
Postbac Tobias Rubel (Philosophy Fall '19) published a conference paper at a virtual Association for Computing Machinery (ACM) computational biology conference:
Augmenting signaling pathway reconstructions
Rubel & Ritz. Proceedings of the ACM Conference on Bioinformatics and Computational Biology (ACM-BCB). Sep 2020.
Grad Student Ananthan Nambiar (Computer Science '19) and a team of undergraduates at UIUC published a conference paper at ACM-BCB, mentored by Anna Ritz and Mark Hopkins in CS:
Transforming the language of life; transformer neural networks for protein prediction tasks.
Nambiar, Heflin, Liu, Maslov, Hopkins, and Ritz. Proceedings of the ACM Conference on Bioinformatics and Computational Biology (ACM-BCB). Sep 2020.
Also, these current & former students presented posters at ACM-BCB. You can see the posters here: https://www.reed.edu/biology/ritz/posters.html
• Gabe Preising (Biology '20): Preising, Faber-Hammond, Renn, & Ritz. A protein-protein interactome for an African cichlid.
• Frank Zhuang (Biology '22): Zhuang, Cerveny, & Ritz. Prefix/Suffix variation in retinoic acid response elements.
• Larry Zeng (CS '23): Zeng & Ritz. Graphery: a biological network algorithm tutorial webservice.
Neuroscience major Stephanie Gee ’20 wins a Watson Fellowship to explore effects of radiation. Read more at Reed Magazine.
Associate Professor of Biology Anna Ritz was recognized with the prestigious Lynwood W. Swanson Promise for Scientific Research Award from the M.J. Murdock Charitable Trust. The award honors junior faculty members who demonstrate exceptional potential to establish exemplary, productive, and sustainable research programs. Reed more at the Reed Magazine.
Prof. Derek Applewhite has written a response to the George Floyd demonstrations on behalf of The American Society for Cell Biology's LGBTQA+ Task Force: https://www.ascb.org/society-news/a-response-to-the-george-floyd-demonstrations/
From the piece:
"Why can’t we just stick to science? In principle, science is free from emotion and judgment. It is facts grounded in evidence and should be apolitical and neutral. But science is done by people and so, unfortunately, science is a product of our society—a society built on long-standing inequalities, a society that has actively suppressed the voices of minoritized individuals. If society is racist, so is science...Minoritized voices cannot just be heard; they must be amplified."
"We cannot and should not disentangle our identities from our science. Our diversity is one of our greatest strengths but we are far from utilizing it. We must recognize our contributions to the disenfranchisement Black and minoritized scientist experience and take serious, concrete measures to reverse the inequities that are built into the system. Black lives do matter and we cannot just show up for them, we must take action."
If you’re looking for resources or for ways to support others in solidarity against racial injustice, Reed's Office of Institutional Diversity has compiled a list of resources: https://reedienews.tumblr.com/post/619920094766710784/today-we-want-to-amplify-a-few-organizations-in
The Schaack Lab was awarded a $407,535 NIH grant titled Tissue, Time, and Genotype: Investigating the Effects of Cellular Environment, Age, and Germline Mutation Rate on the Genome-Wide Rate and Spectrum of Somatic Mutation
Sarah Schaack explain what the lab will investigate using the grant monies:
Somatic mutations are the changes that occur in the DNA of multicellular organisms when cells replicate during growth and development, but which are not inherited. Our lab studies mutation rates, and for the last (almost) 10 years has studied the rates and spectra of germline (heritable) mutations. The goal of our new project is to investigate three major factors influencing somatic mutation rates: tissue type, developmental stage, and germline mutation rate (which we have previously shown differs greatly among genotypes, populations, and species). We hope to determine if somatic mutation rates a) vary among tissue types based on their rates of celldivision or production of DNA damaging particles, b) differ between young and old individuals, and if so to what degree, and c) correlate positively with germline (heritable) mutation rates, suggesting the two rates are governed by common or linked mechanisms. We use the Daphnia model system to perform our research. Estimates of somatic mutation rates are important, as they are the cause of many cancers and age-related disorders.
Professor Jay Mellies was recently awarded a $684,000 NSF grant to further investigate the potential of soil bacteria in the degration of PET Plastic Waste.
This project, which grew out of summer and thesis research conducted by Morgan Vauge's '18 has garnered significant local and national attention:
Morgan recently gave a a TED Talk about the research, and the work was features in Microbiology Resource of the Month: Genomes of 5 PET-Plastic-Degrading Bacterial Isolates.
Ashland Forest Resiliency partners are working closely with Reed College students and professors on research projects in the Ashland Watershed.
Mechanical thinning and controlled burns are an important tool in the Ashland Forest Resiliency Project. Monitoring the health and growth of large, old legacy trees is an important part of evaluating the efficacy of this type of management. Reed students are helping with this monitoring effort by collect and analyzing data on Legacy tree survival and growth. Read more at the Ashland Resiliency Project.
Prof. Erik Zornik [biology 2012–] has won a $670,000 grant from the National Science Foundation to explore the ways in which patterns of behavior—phenomena such as breathing, walking, and vocalizing—are written into the neural circuits of the brain. Read more at Reed Magazine.
Bio major Morgan Vague ’18 has isolated and bred three strains of bacteria that consume and degrade polyethylene terephthalate (PET)—the ubiquitous plastic used in textiles, packaging, and soft-drink containers—opening up the tantalizing possibility of using microbes to fight pollution. Read more at Reed magazine.
Reed students working with Prof. Jay Mellies have developed a virus that attacks deadly strains of E. coli bacteria responsible for millions of cases of foodborne illness every year. With antibiotic resistance becoming increasingly widespread, the discovery of the virus—known as PDX—points the way towards a new therapeutic strategy in which the pathogen’s game plan of attacking a host from within is effectively turned against it. Read more at Reed Magazine.
Why do some individuals refuse to eat even when they’re starving? This puzzling question lies at the heart of a three-year study by Prof. Suzy Renn [biology], who recently won a $421,374 grant from the National Institutes of Health to seek clues to the biological basis of anorexia and cachexia, a syndrome that afflicts many cancer patients. Read more at Reed Magazine.
Prof. Anna Ritz has won the Undergraduate Research Mentoring Award from the National Center for Women and Information Technology for providing “outstanding mentorship” to Reed students in the field of computation. The award also recognizes her work in providing research opportunities, recruiting women and minority students, and generally encouraging students in computing. Read more at Reed Magazine.
If you are thinking about applying to graduate school or med school in your future. The special presentation this Thursday is very relevant for you...
"Bound for Graduate School"
Thursday February 7th 6:00 PM Vollum Lecture hall
** There will be advice on how to select school, how to apply to schools, how to get letters of recommendation etc. Much of this information is also relevant to landing a summer fellowship.
** There will be a STEM specific Q&A immediately after the talk in Vollum110 with Reed faculty to answer your questions (PIZZA PROVIDED)
The faculty and students in Biology have been busy researching this year and they have been rewarded with grants, press, and publications!
Cerveny Lab’s NIH grant was renewed entitled
“From susceptibility to signals: How cues from the retinal microenvironment influence stem and progenitor cell behavior”
Coate Lab: awarded a cloud computing allocation from XSEDE valued at $126,076.61 to use for a new Biology bioinformatics course this fall.
Renn Lab: Awarded NIH-15 grant for $419,497 entitled
"Mouth-brooding: a teleost adaptation as a tractable model of metabolic disorder"
NSF supplement "Research Assistantships for High School Students supplement to the active NIS-IOS grant for $5600 entitled
“RUI: Collaborative Research: Maternal Transitions in a Mouth-Brooding Cichlid.”
This has brought a Madison High School senior to the lab to assist in robotics and programming.
Ritz Lab: Awarded a NSF CAREER award of $938,147"CAREER: Network-Based Signaling Pathway Analysis: Methods and Tools for Turning Theory into Practice"
Zornik Lab: Awarded an NSF grant of $670,000.00 entitled “RUI: Identifying the Neural Mechanisms of Vocal Evolution”
Local news station KGW covered the thesis work of recent graduate Morgan Vauge:
“Reed student breeds plastic-eating bacteria”
The brain waves that make frogs pitch perfect
“Vocal neurons encode evolution of frog calls”
“Ploidy and size at multiple scales in the Arabidopsis sepal.”
Dana O. Robinson, Jeremy E. Coate, Abhyudai Singh, Lilan Hong, Max Bush, Jeff Doyle, Adrienne H.K. Roeder.
Plant Cell, 2018, (in press)
“Polyploidy, the nucleotype, and novelty: The impact of genome doubling on the biology of the cell.”
Jeff J. Doyle, Jeremy E. Coate
International Journal of Plant Sciences, 2019, (in press)
Essentiality of Nickel for Plants.
In: Nickel in Soils and Plants, Ed. C. Tsadilas, CRC Press. 2018.
Ascorbate metabolism and biological nitrogen fixation.
Matamoros, M.A., Dalton, D. A. and Becana, M.
In: Ascorbic Acid in Plant Growth, Development and Stress Tolerance.
Environment Controls LEE Regulation in Enteropathogenic Escherichia coli.
Platenkamp A and Mellies JL
(2018) Front. Microbiol. 9:1694. doi: 10.3389/fmicb.2018.01694
Gene Expression Signatures of Mating System Evolution.
Renn, SCP, Machado, HE, Duftner, N, Sessa*, AK, Harris, RM, Hofmann, HA
A Cell-based Assay to Investigate Non-muscle Myosin II Contractility via the Folded-gastrulation Signaling Pathway in Drosophila S2R+ Cells
Kimberly A. Peters, Elizabeth Detmar, Liz Sepulveda, Corrina Del Valle, Ruth Valsquier, Anna Ritz, Stephen L. Rogers, and Derek A. Applewhite
JOVE, 2018, (in press)
“Network-Based Prediction of Polygenic Disease Genes Involved in Cell Motility”
Miriam Bern, Alexander King, Derek A. Applewhite, and Anna Ritz.
To be presented at the Fifth International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC 2018) in Washington, D.C.
"Premotor Neuron Divergence Reflects Vocal Evolution"
Barkan CL, Kelley DB, and Zornik E.
J Neurosci. 2018 Jun 6;38(23):5325-5337
Update, Feb 16, 2017: Professor Gwilliam's memorial service has been scheduled for Saturday, March 11, 2017, at 10:30 a.m. in the Reed College Chapel.
Update, Dec 6, 2016: Obituary from the Oregonian
Bio mourns the passing of invertebrate neurobiologist G. Frank Gwilliam (biology 1957–96). The Reed Magazine has collected some of the community's reflections on our esteemed colleague and mentor here. If further information becomes available it will be posted here.
Gwilliam, G. Frank 91 Aug. 28, 1925 Nov. 27, 2016 Frank Gwilliam, born in Park City, Utah, lived in Salt Lake City until joining the Navy at 17. He served as a hospital corpsman in the Pacific during WWII and then graduated from UC Berkeley. After serving in Japan during the Korean war, he received his Ph.D. in zoology from Berkeley. He came to Reed College in 1957 and was a professor of biology there until his retirement in 1996. From 1979 to 1982, he was provost of Reed. After retiring, he volunteered as an Elder Ombudsman. He is survived by his beloved wife of 66 years, Marjorie; his son, Jeff (Amy); daughter, Tassie (Frank Stringfellow); and his grandchildren, David, Jessica, and Adam Gwilliam; Nicholas Stringfellow; and Anna and Nora Seidman. Frank's fascination with "critters" started in childhood, and his encounter with a coral reef off a Pacific island ignited a lifelong passion for marine invertebrates. Frank wholeheartedly enjoyed his work as a neuroscientist, a teacher, and a mentor of Reed students. With everyone in his life, he was loving, supportive, and funny. Contributions may be made to the G. Frank Gwilliam Memorial Scholarship at Reed College: http://www.reed.edu/givingtore
Prof. Suzy Renn won a $618,000 grant from the National Science Foundation to investigate a striking example of maternal behavior—voluntary starvation among African cichlid fish. Her research could shed light on the evolution of maternal instincts and deepen our understanding of metabolic and feeding disorders.
Prof. Erik Zornik won a $444,000 grant from the National Institutes of Health to research mechanisms in the brain that generate rhythmic behavior, with the goal of finding new treatments for neurological disorders.
Prof. Todd Schlenke won a $373,000 grant from the National Institute of Allergy and Infectious Diseases, a division of the National Institutes of Health, to study one of nature’s most unforgiving arms races—the struggle between fruit flies and venomous parasitic wasps. (May the contest be long and bloody.)
Prof. Jay Mellies won a $362,769 grant from the National Institutes of Health investigate a key regulatory protein that enables a sinister pathogen to sicken children.
Congratulations to the following biology faculty on recent grant awards:
Kara Cerveny, Assistant Professor of Biology
M.J. Murdock Charitable Trust-Murdock College Research Program for Life Sciences, 2013-2015
"How the vertebrate eye grows: Understanding the origin and maintenance of neural stem cells in the Zebrafish retina" ($52,000)
National Eye Institute/National Institutes of Health R15, 2013-2016
"From susceptibility to signals: How extrinsic cues alter progenitor cell behaviors in the retina" ($TBD)
M.J. Murdock Charitable Trust-Murdock Scientific Research Matching Funds
"Seeing is Believing: Bringing High-Resolution Time-Resolved Laser Scanning Confocal Microscopy to Reed College" ($150,000)
Jay Mellies, Professor of Biology
M.J. Murdock Charitable Trust-Murdock College Research Program for Life Sciences, 2013-2015
"A Virulence Regulator Stimulates Central Metabolism in Enteropathogenic Escherichia coli."
National Institutes of Health, R01 Award, 2010-2013
"Effect of Zinc in Attaching and Effacing E. coli Infection."
Sub-contract with John Crane, MD, Ph.D., State University of New York at Buffalo
Sarah Schaack, Assistant Professor of Biology
NSF CAREER Award, 2012-2017 ($993,344)
Upon Which Selection Can Act… Quantifying How Mutation and Environment Generate Genotypic & Phenotypic Variation in an Emerging Ecological & Evolutionary Genomic Model
M.J. Murdock Charitable Trust College Research Award, 2012-2014 ($51,223)
Study of the Effects of Spontaneous Mutation on Gene Expression in Daphnia
Fulbright Scholarship, 2013-14
Bioinformatics and Genomics in East Africa
EU Mois Invité, University of Lyon, 2013
Todd Schlenke, Visiting Assistant Professor of Biology
National Science Foundation IOS 1257469, 8/13-7/16
"Evolution Of Behavioral Immune Responses In Fruitflies: Tradeoffs, Mechanisms, And Genetics"
PI: Todd Schlenke; Co-PI: Jacobus de Roode
Total direct cost: $384,616; Total cost: $600,000
National Institutes of Health R01 AI081879, 7/09-6/14
"A Model System for Host-Pathogen Interactions: Drosophila and Its Parasitic Wasps"
PI: Todd Schlenke
Total direct cost: $917,000; Total cost: $1,420,000
Erik Zornik, Assistant Professor of Biology
Murdock Charitable Trust: Research Program for Life Sciences, 2013-2015
"Maintenance of vocal circuit function by circulating hormones"
Reed professor of biology Janis Shampay has authored a firsthand account of the telomere research that led to the 2009 Nobel Prize in Physiology or Medicine. The essay is freely available from the Trends in Biochemical Sciences website.
Reed professor of biology Peter Russell has received a 12 month supplement to his NIH AREA grant under the American Recovery and Reinvestment Act (ARRA) of 2009, providing $98,503 towards his research identifying and characterizing host genes involved in gene expression of a plant pathogenic virus, Barley yellow dwarf virus, using yeast as the model host.
Reed professor of biology Jay Mellies has received a three year Academic Research Enhancement Award grant of $235,634 from the National Institutes of Health to study the structure and function of the novel regulatory protein Ler of enteropathogenic Escherichia coli.
Reed College ranks fourth in preparing Ph.D.s in engineering and sciences, according to the latest study from the National Science Foundation.
The Medical Research Foundation honored professor Steve Arch with the 2008 Mentor Award and Reed alumna Dr. Rosalie Sears (Reed '86) with its 2008 New Investigator award.
Biology asst. professor Suzy Renn has received a four year grant of $350,000 from the National Science Foundation for the project "Molecular Modules of Aggression: Maternal Behavior in the African Cichlid Astatotilapia burtoni.", with Math professor Albyn Jones as co-PI on the project.
Emeritus Biology Professor Helen Stafford was named a Phytochemistry Pioneer at the 2008 meeting of the Phytochemical Society of North America. An article describing her scientific contributions appeared in the December, 2008 issue of Phytochemistry (download the pdf; this is the publisher's website, so a subscription is required from computers not on the campus network).
Reed's 2008 Commencement ceremony included an address by Biology Dept. alum and environmental writer Michelle Nijhuis (Reed '96).
Biology asst. professor Suzy Renn has been awarded $42,000 from the MJ Murdock Charitable Trust for her investigation of rapidly evolving genes in the East African Cichlid species flock.
Reed College honored pioneering geneticist Stanley Fields with the Vollum Award for Distinguished Accomplishment in Science and Technology at its August convocation ceremony.
Biology professor Janis Shampay has been awarded $344,000 from the NSF to study telomeric protein function in Xenopus spp.
Biology professor Peter Russell has been awarded $150,000 from the NIH to study virus-host interactions.
Reed College awarded five-year NSF S-STEM grant of $356,388 to support promising math and science students with financial need.
Biology stockroom manager Kristine Gunter and her dog, Rugby, were featured in a Tonight Show segment when Tom Greene visited the Biology Building basement to watch Riley skateboarding.