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:

Postbac Amy Platenkamp (Biology '16) is the first author on a paper in MBoC that investigates a novel regulator of nonmuscle myosin II....and the Applewhite's Lab photo was chosen for the cover of the issue!
The Drosophila melanogaster Rab GAP RN-tre cross-talks with the Rho1 signaling pathway to regulate nonmuscle myosin II localization and function
Platenkamp, Detmar, Sepulveda, Ritz, Rogers & Applewhite. Molecular Biology of the Cell. Sep 2020.

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.

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:

• 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.

(January 2021)

Neuroscience major Stephanie Gee ’20 wins a Watson Fellowship to explore effects of radiation. Read more at Reed Magazine.

(April 2020)

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.

(November 2020)

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:

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:

(June 2020)

The Biology Department reaffirms Reed College's statements on diversity and anti-racism, and pledges to combat racism in all its forms. Please see the college's statments here:

(June 2020)

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.

(January 2020)

Prof. Sam Fey [biology], a population and community ecologist and assistant professor in Biolgoy , won a $700,000 grant from the National Science Foundation (shared between his lab at Reed and collaborators at Yale University) to study phytoplankton. These minuscule aquatic plants are responsible for producing about half the world’s oxygen. Read more on the Reed Magazine website.

(October 2019)

Research into PET-plastic-degrading bacteria by Morgan Vauge and the Mellies Lab is continuing to generate wide interest.

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.

(June 2019)

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.

(April 2019)

The virus looks like a spaceship. Spindly tail fibers jut out from its neck like landing supports, while its icosahedral head adds to the otherworldly appearance. But this microscopic life form is not science fiction—it is a real entity, swimming in the petri dish I hold in my hand. Its name is PDX, and one day it could save thousands of lives from fatal foodborne illness. Read more at Reed magazine.

(August 2018)

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.

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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.

(May 2018)

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.

(October 2018)

The National Science Foundation has awarded $930,000 to support a Reed biology professor’s research into the way cells send signals—potentially leading to future discoveries about why cells go haywire in complex diseases such as cancer. Read more at Reed Magazine.

(April 2019)

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.

(February 2019)

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.

(April 2019)

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"
Don Asher
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)

(February 2019)

The faculty and students in Biology have been busy researching this year and they have been rewarded with grants, press, and publications!

Recent Grants

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”

Recent Press

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
Nature, 2018

Vocal neurons encode evolution of frog calls
EurkAlerts, 2018

Recent Publications

“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
Dalton, D.A.
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. 
Springer. 2018.

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
GENOME, (2018)

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

(August 2018)

Professor Erik's Zornik's research on the the neuroscience that helped two species of frogs to evolve distinct courting trills was recently featured in Nature.

(May 2018)

The biology department's work was featured by the Reed magazine in January. Congrats to everyone for their hard work and accomplishments! Read the piece here.

(January 2017)

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: A memorial service will take place at a later date.

(November 2016)

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.

(July 2015)

Wilson Horner (senior biology major) was awarded the best life sciences presentation prize at the Murdock College Science Research Conference. His talk, titled “How retinoic acid influences retinal growth and neurogenesis in the zebrafish retina”, focused on his summer research and thesis work in Kara Cerveny’s lab. Congratulations Wilson and Kara!

(November 2014)

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"

(August 2013)

The Biology Department mourns the passing of Professor Emerita Helen Stafford. Professor Stafford was a key figure in the establishment of the Department's national reputation. An extensive obituary may be found on The Oregonion.

(August 2011)

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.

(December 2009)

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.

(August 2009)

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.

(August 2008)

Reed College ranks fourth in preparing Ph.D.s in engineering and sciences, according to the latest study from the National Science Foundation.

(July 2008)

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.

(November 2008)

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.

(October 2008)

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).

(July 2008)

Reed's 2008 Commencement ceremony included an address by Biology Dept. alum and environmental writer Michelle Nijhuis (Reed '96).

(May 2008)

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.

(May 2008)

Reed College honored pioneering geneticist Stanley Fields with the Vollum Award for Distinguished Accomplishment in Science and Technology at its August convocation ceremony.

(August 2007)

Biology professor Janis Shampay has been awarded $344,000 from the NSF to study telomeric protein function in Xenopus spp.

(May 2006)

Biology professor Peter Russell has been awarded $150,000 from the NIH to study virus-host interactions.

(December 2006)

Reed College awarded five-year NSF S-STEM grant of $356,388 to support promising math and science students with financial need.

(October 2006)

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.

(September 2006)