Biology

Seminars

All Biology Department Seminars are free and open to the public. Seminars take place Fridays at 4:10 PM in B-19 in the basement of the Biology Building on the Reed College Campus (unless otherwise noted on the schedule). Seminars are immediately preceded by a service of coffee, tea, and other refreshments.

The Reed College campus is located in southeast Portland at 3203 SE Woodstock Blvd. (Online maps are available for getting to Reed and for the Campus).

2017-18 Schedule

Fall

4:10-5:00 in Biology B-19 (unless otherwise noted).
Directions to Reed.

Sept 1
Location: Kaul Lounge
Student Summer Research Fellows Poster Session

Join students from Biology, Chemistry, Math, Physics, and Psychology as they present the results of their summer research and projects.

Sept 8
Location: Performing Art Building 3rd Flr Atrium
How to Win at Being a Biology Major
Biology Resource Fair and Ice Cream Social

Join the Department in celebrating a new academic year with ice cream and prepare for a successful year. Reed College offers many resources to help students be successful both at Reed and beyond. Come meet some of the people from around campus who can help out and learn about what they can do for you!

Sept 14
Time: 7:30 PM Location: Vollum Lecture Hall
Mapping, modeling and Decoding the Human Brain
Jack Gallant, University of California, Berkely

One important goal of Psychology and Neuroscience is to understand the brain mechanisms mediating natural behavior. However, this is a challenging problem because natural behavior often involves many different perceptual, motor and cognitive systems distributed broadly across the brain. My laboratory has developed a new approach to functional brain mapping that recovers detailed information about the cortical maps mediating natural behavior. Our results show that even simple natural behaviors involve dozens or hundreds of distinct functional gradients and areas; that these are organized similarly in the brains of different individuals; and that top-down mechanisms such as attention can change these maps on a very short time scale. Our approach provides a powerful method for mapping the representation of many different perceptual and cognitive processes across the human brain and for decoding brain activity.

Sept 15
Location: Psych 105
Functional Mapping of the Human Brain: Promise, Problems and Prospects
Jack Gallant, University of California, Berkely

When functional MRI was developed it was hoped that this new tool could help validate and refine existing psychological models. However, linking psychological theories to maps produced by functional imaging has been a challenging problem, for several reasons. First, the experimental and data analysis paradigms developed for use in experimental psychology are not optimal for obtaining data in functional imaging experiments. Second, while psychological theories are usually pitched at the computational level, functional imaging produces data at the algorithmic level. Finally, both experimental psychology and functional imaging have been limited by various data quality and quantity issues that have caused a loss of confidence amongst scientists and the public. In this talk I will review some of the efforts undertaken in my lab to try to address these difficult problems. Our innovations include a naturalistic approach to experimental design, a voxel-wise modeling framework that provides quantitative predictions of brain activity in every individual subject; new tools for data visualization, and new methods for aggregating data across individuals while minimizing information loss. Although our approach provides detailed functional maps of the cerebral cortex, these maps do not provide a clear bridge to the computational models proposed in experimental psychology. Bridging this gap is a fundamental challenge for the cognitive neuroscience community.

Sept 22
Time: 10:00 AM Location: Gray Lounge & Gray Campus Center

PacNow Quantitative Biology Symposium

PacNow Qunatitative Biology Symposium talks and events throughout the day. See the symposium website for the schedule.

Sept 29Identification of Novel Regulators of Selective Autophagy in Tetrahymena thermophila.
Sabrice Guerrier, Millsaps College

Organellophagy is the selective degradation of organelles by autophagosomes. Alterations in organellophagy are associated with several disorders including neurodegeneration, heart disease, obesity, and cancer. Recent work has shown that, Nucleophagy, the selective degradation of the nucleus by autophagosomes, is up regulated in laminopathies and in response to oncogenic stress. However, it remains unclear exactly how nuclei are selected for degradation. Our primary goal is to understand the molecular mechanisms underlying how the nucleus is specifically degraded by autophagosomes. In order to uncover these mechanisms, we exploit nuclear degradation during mating in Tetrahymena thermophila. Tetrahymena selectively degrade their entire (macronucleus) nucleus in an autophagy-dependent manner as part of normal mating. Importantly, this process can be induced in the lab and occurs in predictable and identifiable stages making nucleophagy in Tetrahymena straightforward to monitor. Preliminary work in our lab has shown that nucleophagy in Tetrahymena may employ proteins involved in selective autophagy in other systems. Using both biochemical and bioinformatics approaches we plan to use this knowledge to identify novel regulators of nucleophagy in Tetrahymena with plans to test the role of such proteins in autophagy in mammalian systems.

Oct 6Community Ecology of Communication in Crickets and Katydids
Laurel Symes, Dartmouth College

Species occur in diverse communities, which affects both ecological interactions and their ability to send and receive signals. In communication, the signaler-receiver interaction can be confounded by eavesdropping predators, rival males, and signal interference from co-occurring species. In this talk, I consider the effects of community composition on the evolution of signals in temperate tree crickets and tropical katydids. I will discuss tree crickets communities that contain 1-4 species, examining how the similarity among co-occurring species corresponds to the shape of female preferences. I then address the metabolic cost of signaling and how this cost may constrain the divergence of mating traits during speciation. In the second part of the talk, I move to the neotropical rainforest, where over 100 katydid species co-occur with more than 70 species of bats, including gleaning bats that hunt katydids by the sounds that they make. Both bats and katydids can produce ultrasonic acoustic signals and can hear the signals of the other. I present evidence for suites of neural, behavioral, and ecological traits that represent different responses to predation.

Oct 13No Seminar Before Fall Break
Oct 20
Time: 12:00 AM
No Seminar, Fall Break
Oct 26
Time: 12:10 PM
Contingency and inevitability in biotic evolution
David E. Fastovsky, University of Rhode Island

The metaphysical idea of “purposefulness” in the existence of humans has historically led to the sense that biotic evolution must be inevitable. Evolution by natural selection as proposed by Darwin, however, suggested that the process was anything but inevitable, an idea that the late S.J. Gould termed “contingency.” Since these antithetical ideas have both found support, the question is, can contingency and inevitability coexist in biotic evolution? A broad reading of Darwin and the many evolutionary biologists who followed him leads to the conclusion that biotic evolution is contingent. Yet, shared ontogenetic pathways constrain developmental possibilities. And, as noted by S. Conway-Morris, while making an argument for inevitability in evolution, convergent features evolve repeatedly in disparate lineages. Beyond this, however, is Darwinian evolution inevitable? The answer is a qualified “yes,” when considered from a macroevolutionary or paleobiological perspective. Here, a consequence of Darwin’s (1859) “struggle for existence” is the repeated filling of the “hypothetical ecospace” niches first proposed by Bambach (1983). Ironically, it is mass extinctions that drive the process: after each mass extinction, the “hypothetical ecospace” niches are re-filled, commonly by new (replacement) organisms. This sometimes involves solving the challenges posed by the hypothetical ecospace in a manner convergent on pre-extinction antecedents, but sometimes it involves innovations. Innovation also drives hypothetical ecospace expansion, however, and this is ultimately the most inevitable aspect of biotic evolution. Perhaps in that sense inevitability is immanent to evolution by natural selection.

Oct 27Genomic evidence for a tropical hotspot of coevolution in a symbiotic marine invertebrate from Caribbean Panama
Post-doc Talk: Emily Bellis, Reed College

Rising ocean temperatures associated with global climate change induce breakdown of the symbiosis between corals and photosynthetic microalgae (genus Symbiodinium), threatening the persistence of coral reef ecosystems. Rapid evolutionary change in host specificity, or the range of symbiotic partners with which a host associates, is one mechanism that could contribute to coral resilience. In this talk, I will discuss recent work using genomic sequencing of natural populations from Caribbean Panama to explore evolution of host specificity in the sea anemone Aiptasia, a laboratory model system for studying the onset and breakdown of coral symbiosis.

Nov 3Topographic mapping by the vagus nerve: a matter of time.
Cecilia Moens, Fred Hutchinson Cancer Research Center

Many networks throughout the nervous system are organized into topographic maps, where the positions of neuron cell bodies in the projecting field correspond with the positions of their axons in the target field. How topographic maps form has fascinated developmental neurobiologists for decades, because they involve the point-to-point matching of developmental fields (the projecting and target fields) which were patterned independently far from one another in the embryo. Previous studies of topographic map development show evidence for spatial patterning mechanisms, in which molecular determinants expressed across the projecting and target fields are matched directly. I will present our discovery of a novel temporal mechanism of topographic map formation in zebrafish that depends on spatially regulated differences in the timing of axon outgrowth that correspond with the timing of target field development. I will focus on the vagus motor neurons, which innervate the muscles of the posterior pharyngeal arches, and which are topographically organized in both mammals and fish. I will describe the roles of independent spatial and temporal mechanisms that together serve to organize this musculotopic vagus map.

Nov 7
Time: 12:10 PM
Biosensors and Cell-based Screening to Identify Drugs Targeting Golgi-based O-glycosylation
Adam Linstedt ‘82, Carnegie Mellon University

Site-specific O-glycosylation taking place in the Golgi complex is a modification of proteins that controls their activities in crucial ways. Major diseases including chronic kidney disease and cancer involve misregulation of this process. Other diseases, viral outbreaks being an example, depend on this process to carryout their destruction. A family of closely related isozymes initiates site-specific O-glycosylation with individual isozymes acting on distinct sets of proteins. This avails a therapeutic opportunity in the sense that a single disease-relevant isozyme may be targeted leaving the others to carryout their myriad functions critical to normal health. But, crucially, there are no known drugs targeting these isozymes. To enable high-throughput screening for drug-like inhibitors, we are developing cell-based fluorescent sensors of O-glycosylation mediated by the ppGalNAc-T isozymes. Initial screening identified an inhibitor of ppGalNAc-T3 that opposed upregulation of the isozyme in driving metastatic-like behavior of cancer cells and it blocked ppGalNAc-T3-mediated glycan-masking of FGF23 thereby reducing secretion of intact FGF23, a possible treatment of chronic kidney disease. These findings commence a pharmacological approach for the ppGalNAc-transferase family and suggest that targeting specific GalNAc-transferases will yield new therapeutics.

Nov 10Perspectives on the prevalence, pattern, and process of plant polyploidy
Jeffrey Doyle, Cornell University

Polyploidy is a prevalent and ongoing genetic and evolutionary phenomenon in land plants. All flowering plants are derived from an ancestor that had undergone a whole genome duplication (WGD) event, and the genomes of extant flowering plant species bear evidence of multiple cycles of polyploidy. For example, several independent polyploidizations occurred in the legume family, making modern legumes such as soybean (Glycine max) highly polyploid, though showing diploid chromosome behavior. Elucidating the complex patterns of whole genome duplications in species complexes is illustrated by studies in Glycine, which in addition to soybean and its direct annual progenitor comprises over 30 “diploid” perennial species, several of which have hybridized in various combinations to form an extensive allopolyploid complex. These allopolyploids, like many plant polyploids, are successful colonizers: Whereas diploid perennial Glycine are confined to Australia and Papua New Guinea, several of the allopolyploids have colonized islands of the Pacific Ocean. Some of these allopolyploid species is superior to its diploid progenitors in photosynthesis and photoprotection; recent work in one allopolyploid species has shown that it has enhanced ability to form nodulation symbioses with rhizobial bacteria, and is more resistant to insect pests than its progenitors. Studies of natural Glycine allopolyploids have provided insights on many features of polyploid evolution, but they were formed by hybridization 300,000 years or more ago. To study the process of polyploidy not confounded by hybridity or adaptation, we, like others, are using synthetic autopolyploids produced in the laboratory from genetically characterized accessions of Arabidopsis thaliana to study the effect of polyploidy on the transcriptome and on development.

Nov 17Structural Variant Discovery: Integrating Multiple Lines of Evidence
Suzanne Sindi, University of California, Merced

Structural variants (SVs) – such as deletions, insertions, copy-number gains and inversions – are rearrangements of a region of DNA relative to a reference. Until relatively recently, SVs were thought to be rare in genomes of healthy individuals, especially mammals. However, advances in high-throughput DNA sequencing, combined with the availability of high-quality reference genomes, has demonstrated SVs to be common even in healthy individuals The dominant approach for SV prediction consists of paired-end (PE) sequencing of single target genome and mapping the resulting sequences to a reference genome. SVs are predicted through analysis of mapped read configuration. Early computational approaches to SV discovery focused on one of several PE signals consistent with an SV: discordant PEs, read depth and split read mappings. However, as we demonstrated with our computational approach GASV-Pro (Sindi; 2012) combining discordant PEs with read depth in a likelihood framework substantially reduces false positive predictions. Indeed, our likelihood approach allows for integration of data from multiple sequencing technologies (Ritz; 2014) Today, I will given an overview of computational methods for SV discovery and discuss two novel likelihood based approaches under development. The first employs a Hidden Markov Model (HMMs) for split-read alignment allowing for a likelihood model consisting of all three common signals for SV prediction in a single individual. The second addresses simultaneous prediction of SVs in populations including related individuals by framing SV prediction in populations as a constrained optimization problem. We solve this problem by using techniques from mathematical optimization where the constraints on the solution space come from relatedness between individuals.

Nov 24No Seminar, Thanksgiving Break
Dec 1No Seminar, Spring-Fall Thesis Parade

s

4:10-5:00 in Biology B-19 (unless otherwise noted).
Directions to Reed.

Jan 26Phylogenetic ecology and disease pressure
Ingrid Parker, University of California, Santa Cruz

Pathogens play an important part in shaping the structure and dynamics of natural communities, because species are not affected by them equally. A shared goal of ecology and epidemiology is to predict when a species is most vulnerable to disease. A leading hypothesis asserts that the impact of disease should increase with host abundance, producing a ‘rare-species advantage’. However, the impact of a pathogen may be decoupled from host abundance, because most pathogens infect more than one species, leading to pathogen spillover onto closely related species. We study how the phylogenetic and ecological structure of the surrounding community can be important predictors of disease pressure in a grassland plant community. We formulate predictive models of pathogen sharing using a global database, then use these models to predict disease pressure at the local scale. We find that we can both explain variation in disease across a community of hosts and predict disease pressure for experimentally introduced novel hosts. Our work has implications for the maintenance of biodiversity, biotic resistance against introduced weeds, and the success of managed plants in agriculture and forestry.

Feb 2Leakiness in the nitrogen cycle: nitrification under scrutiny.
Peter Bottomley, Oregon State University

Our research focuses upon the question of how the processes of NH3 oxidation and NO2- oxidation remain effectively coupled in soils where the relative contributions of ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB), and the overall rates of nitrification shift quickly in response to changes in NH4+ availability and temperature. In many Oregon soils, NH4+ dependent NO2- accumulation can represent between 10 to 100% of the total NO2- plus NO3- accumulation in 1-2d assays. Recoupling of nitrification occurs within a variable length of time, depending on the soil and incubation conditions. Soil NO2- oxidizing activity adapts to the accumulation of NO2- by increasing the Vmax of NO2- oxidizing activity in a protein synthesis dependent manner. As part of our efforts to understand how coupling is maintained in the nitrification process we have been studying the role of quorum sensing between ammonia oxidizing and nitrite oxidizing bacteria. We have utilized mass spectrometry to identify acyl homoserine lactones (AHLs) produced by the NH3 oxidizers and NO2- oxidizers. Through a quorum-quenching approach, combined with mRNA-Seq, we have shown that transcription of putative QS-controlled genes, including nitrite reductase (nirK) and nirK cluster genes (ncgABC), increase under QS-proficient conditions. This increase was accompanied by enhanced production and consumption of nitrogen oxides (NOx) under QS-proficient conditions.

Feb 9Summer Research, Internships & Other Opportunities

Learn about upcoming events in the department as well as opportunities for summer research, internships & fellowships.

Feb 16The Science of Resistance: Climate change refugia, landscape connectivity, and translational ecology
Toni Lyn Morelli, University of Massachusetts, Amherst; USGS

Toni Lyn Morelli will introduce the new sub-field of translational ecology and use it as a paradigm to explore work on climate change refugia. The concept of climate refugia has a long history in the field of paleontology, where areas of relatively stable climate have been seen as safe havens for species during past episodes of climate change. Recently, this concept has been updated to focus on its application to managing species and ecosystems in the face of anthropogenic climate change. As the effects of climate change expand nationally and globally, resistance strategies like managing climate change refugia—i.e., areas buffered from contemporary climate change that enable persistence of physical, ecological, and socio-cultural resources—are among the adaptation options that natural resource managers are turning to. Morelli's research has identified climate change refugia, and connectivity among them, in the Sierra Nevada, focusing on Belding's ground squirrel occupancy and genetic diversity to validate these locations. She will discuss how resistance strategies can increase conservation in the face of global change.

Feb 23Enhancing Symbiotic Nitrogen Fixation with Ascorbate (Vitamin C)
David Dalton, Reed College

Ascorbate (AsA, vitamin C) is a major antioxidant and redox buffer in plants that acts as a scavenger of reactive oxygen species (ROS), substrate of AsA peroxidase, and cofactor of key enzymes involved in cell wall expansion and hormone biosynthesis. Nitrogen-fixing legume root nodules contain high levels of AsA (1-2 mM), AsA peroxidase (0.9% of the total protein), and the other enzymes of the AsA-glutathione pathway. The AsA content and their associated enzyme activities are strongly correlated with nitrogen fixation, providing adequate protection of nodules against the ROS generated by, among other processes, the oxidation of nitrogenase and leghemoglobin. AsA can enhance nitrogen fixation four-five fold when supplied by stem infusion to soybean plants or when added, along with AsA peroxidase, to an in vitro reconstitution system. It is likely that GDP-L-galactose phosphorylase (GGP or Vtc2) catalyzes the rate limiting step in the biosynthesis of AsA. Consequently, studies are underway to produce transgenic nitrogen-fixing plants that overexpress GGP. Such plants should have higher amounts of AsA, fix more nitrogen, and better tolerate abiotic stress than the wild-type plants. Additionally, since AsA oxidation and decline are early symptoms of nodule aging, a high AsA content might delay nodule senescence, extend the period of nitrogen fixation, and increase plant yield.

Mar 2Cell Based Strategies for Wound Healing
Ronke Olabisi, Rutgers

Chronic wounds are skin injuries that recur or fail to heal by 6 weeks. These wounds affect 6.5 million patients in the US and this number is growing rapidly due to a drastic increase in the number of diabetics, the obese, and the elderly, all populations in which wound healing is impaired. Mesenchymal stem cells (commonly known as adult stem cells) and topically applied insulin have each shown promise in healing otherwise intractable wounds. Understanding how best to exploit their wound healing potential will improve our ability to accelerate wound healing. Mesenchymal stem cells assist wound healing by secreting a host of growth factors that promote actions critical to wound healing, such as new blood vessel formation, increases in the production of skin constituents, and recruitment of cells that clean wounds and form scar tissue. Insulin assists wound healing by activating the metabolic pathway that recruits mesenchymal stem cells and skin cells. Recently, we made the novel observation that diabetic excise wounds treated with both mesenchymal stem cells and insulin secreting cells together: 1) healed without intermediate scab or scar formation; 2) healed at faster rates than normal non-diabetic wounds; and 3) healed 3x faster than controls and 2x faster than wounds healed by either cell type alone. Although therapies using only mesenchymal stem cells have shown promise, the gains in healing have been too modest to justify widespread use beyond the most difficult wounds. Our discovery that the combination of these cells heal wounds faster than normal and without scar opens the door to potential widespread use of cell-based strategies to accelerate wound healing.

Mar 9
No seminar Friday before spring break
Mar 16
No seminar, Spring Break
Mar 23Reproduction in a Warming World
Kasey Fowler-Finn, Saint Louis University

Temperature affects a wide range of behaviors, including those associated with reproduction, with potentially important consequences for fitness fitness. I investigated how temperature affects sexual communication by studying how temperature affects reproductive activity levels as well as the signals that males produce to attract mates using Enchenopa binotata treehoppers (Hemiptera: Membracidae)—small plant feeding insects that communicate with plant-borne vibrations. I tested patterns of thermal sensitivity in males and females, and across multiple populations. I found similar levels of thermal sensitivity in all populations, with important implications for selection shaping responses to varying temperatures.

Mar 30Sex, Eggs and Plastics: Role of Bisphenols in Reproductive Neuroendocrine Regulation and Development
Siddharth Ramakrishnan, University of Pudget Sound

Bisphenols have become ubiquitous in our environment and animals including humans are exposed to chronic low doses from plastic usage. Using transgenic teleost model systems, this talk will tease apart effects of bispehnols on the development of the reproductive endocrine GnRH neural system. Further, cross-generational effects of parental bispehnol exposure will also be examined.

Apr 6Mi Casa es Su Casa: How an intracellular symbiont manipulates host biology
Irene Garcia Newton, Indiana University Bloomington

Wolbachia are obligate intracellular alpha-proteobacteria that infect nearly half of the insect species on the planet, making them the most prevalent intracellular infection on Earth. Wolbachia also manipulate the reproduction of their insect hosts in a myriad of ways, affecting insect evolution and geographic distributions. For that reason, they were long thought of as reproductive parasites. However, Wolbachia were recently discovered to protect insects from infection by certain pathogens, a phenomenon known as pathogen blocking. Because insects are vectors for disease, and Wolbachia alter the ability of these vectors to harbor important human pathogens, Wolbachia are being used to control the spread of diseases. Our lab seeks to understand, mechanistically, how these bacteria manipulate cell biology and protect their hosts. Although Wolbachia and many of their insect hosts cannot be genetically manipulated, Wolbachia naturally infect Drosophila melanogaster, which is amenable to genetic manipulation, and our lab uses this model to understand the basis of the symbiosis. I will present our lab's work on how Wolbachia manipulate their host, what genetic determinants are required for infection, and how Wolbachia protect the insect from RNA viruses.

Apr 13Tell Me, Too, About All These Things: An Odyssey into the Genome-Wide Dynamics of Mutations Across Animal Taxa
Sarah Schaack, Reed College

Mutation is the ultimate source of genetic variation for all traits upon which selection can act, yet our understanding of the rate, spectrum, and effects of spontaneous mutations remains extremely limited. In the Schaack lab, we endeavor to understand spontaneous mutations on short and long time-scales through a combination of laboratory experiments and collaborative whole genome sequencing projects. Although we specialize in the analysis of mutations caused by DNA that mobilizes and/or replicates in the genome (the "mobilome"), we are currently working on a suite of projects to understand how many different forms of mutation occur, accumulate, and shape the genome in flies, waterfleas, snakes, birds, and bats (to name a few!) In this talk, I'll discuss some of our recent work on these topics-- sharing insights gleaned from analyzing mutations rates and the mobilome in a diverse array of taxa (interspecific comparisons), as well as those gained from analyzing multiple lineages *within* a taxon (intraspecific comparisons). Ultimately, a better understanding of the evolution of the mutation rate, as a trait, and the adaptive potential of organisms in a changing world requires a deeper investigation of mutation dynamics across lineages.

Apr 20
STARS Talk

Hulali Alford
“Is it just me or is it getting a little hot in here?” The effects of rising temperatures on the survivability of C. Reinhardtii

Guananí Gomez-Van Cortright
Tales from the Rhizosphere: Effects of Polyploidy on Rhizobial Symbiosis

Elaine Kushkowski
Light, development, and zebrafish brains: The effects of light on neural development

Jethary Rader
The E. cology of enteropathogenic E. coli