This year’s Honors & Summer Research Info session will be on TBD (ZOOM link). At this info session, Biology Majors can learn about honors research opportunities and/or summer research directly from faculty who will be taking students. Note: the deadline to apply to the honors program is February 22nd. Applications can be found here: https://biology.williams.edu/research/honors-research-form/
Faculty accepting honors students for academic year 2021-2022: Sonya Auer, Lois Banta, Ron Bassar, Pei-Wen Chen, Derek Dean, Joan Edwards, Allison Gill, Cynthia Holland, Tim Lebestky, David Loehlin, Luana Maroja, Martha Marvin, Manuel Morales, Rob Savage, Claire Ting, Damian Turner, Vincent van der Vinne, Heather Williams
Faculty accepting off-cycle honors students for academic year 2021-2022: Sonya Auer, Ron Bassar, Derek Dean, Cynthia Holland, Tim Lebestky, Rob Savage, Heather Williams
Faculty accepting summer students for 2021: Sonya Auer, Lois Banta, Ron Bassar, Pei-Wen Chen, Joan Edwards, Allison Gill, Cynthia Holland, Tim Lebestky, David Loehlin, Luana Maroja, Martha Marvin, Manuel Morales, Claire Ting, Damian Turner, Vincent van der Vinne, Heather Williams
If you are interested in the following labs, please email the professor directly:
Sonya Auer, [email protected]
Professor Bassar, [email protected]
Professor Loehlin, [email protected]
Professor Maroja, [email protected]
Claire Ting, [email protected]
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Biology Major Requirements
BIOL 101 The Cell BIOL 102 The Organism BIOL 202 Genetics 2 – 300-Level courses, both with a lab component 1 – 400-Level course 3 – additional electives at any level |
Biology Major Requirements w/Honors
BIOL 101 The Cell BIOL 102 The Organism BIOL 202 Genetics BIOL 493/494 Senior Thesis 2 – 300-Level courses, both with a lab component 1 – 400-Level course 2 – additional electives at any level |
What faculty are working on…
Sonya Auer
TBL 019 (laboratory), TBL 201 (office), x2808, [email protected]
Many organisms face novel conditions in an increasingly human-altered world. How do they cope with challenges imposed by climate change, altered nutrient cycling, biological invasions, and increased urbanization? These are timely questions given the current rapid pace of environmental change occurring across the globe. Research in the Auer lab uses question-driven observational, experimental, and comparative studies in both the field and laboratory to understand the role that physiology and behavior play in mediating responses to environmental change at the individual, population, and community levels. Recently completed student projects that are published or in review have focused on: 1) The repeatability of upper thermal tolerance (Journal of Thermal Biology 2020), 2) Energetic mechanisms for coping with environmental change (Biology Letters, 2020), and 3) Effects of reproduction on vulnerability to temperature extremes (in review at Journal of Thermal Biology).
Upcoming projects will continue to focus on whether and how organisms cope with challenges associated with warming temperatures and reductions in food quality and availability:
- Are adjustments in energy metabolism an adaptive strategy to deal with fluctuations in food availability?
- Can behavioral responses to oxygen limitation increase the thermal tolerance of aquatic organisms?
- How does an increase in temperature impact the trade-off between digestion and locomotion?
- Does the increased metabolic demand associated with digestion impair an organism’s tolerance of high temperatures?
- How are upper thermal tolerance limits impacted by life stage and food availability?
- Does increased reproductive effort lead to a reduction in upper thermal tolerance?
If any (or all!) of these research questions interest you, check out our website, www.sonyakauer.com, stop by (TBL 201), or email Prof A ([email protected]) for more information.
Lois Banta
HSB 116 (laboratory); TBL 213 (office), x4330, [email protected]
In the Banta lab, we study the interactions between the soil bacterium Agrobacterium tumefaciens and its host plants. In particular, we are interested in the transport of a large fragment of DNA across the membrane system surrounding the bacterium, and in the plant defense responses elicited by the bacterium. Infection of susceptible plants by A. tumefaciens results in crown gall tumor formation. The disease mechanism involves the transfer and integration into the plant genome of a specific DNA molecule (T-DNA) from a bacterial tumor-inducing (Ti) plasmid. Sequences on the T-DNA encode enzymes responsible for the biosynthesis of plant growth hormones; expression of these genes in the host plant leads to uncontrolled hormone production and hence unregulated plant cell division (“plant cancer”). This naturally occurring process of DNA transfer to plants is widely used to introduce new genes into plants, but its utility is limited by the fact that some plants, including the agriculturally important grains rice, wheat, corn and barley, are poor hosts. Thus, advances in our understanding of the mechanism of DNA delivery, and in particular the contributions made by bacterial proteins that are required for infection of some but not all hosts, may further the work of those scientists engaged in efforts to increase global food productivity.
Source: Griffiths, et al., An Introduction to Genetic Analysis (7th ed.)
Many bacteria including A. tumefaciens form biofilms, complex aggregates of bacteria, held together by polysaccharides, that are resistant to antibiotics and immune attack. Dental plaque and slime on rocks or metal in water are examples of biofilms; in the lungs of cystic fibrosis patients, biofilms serve as a clinically significant reservoir of bacteria. We have been exploring how the Type VI Secretion System (T6SS), implicated in virulence in several other human pathogens, plays a key role in Agrobacterium’s ability to form biofilms. We will continue to investigate why bacteria deficient in the T6SS exhibit enhanced attachment to biotic and host plant surfaces.
We also discovered that this T6SS mutant is less able than its wild-type parent to infect host plants efficiently, and we believe this is because substrates secreted by the T6SS are needed to dampen host defenses. Additional data from our lab have led us to hypothesize further, however, that those same substrates can also trigger defense responses through a previously unknown mechanism. Future students will have the opportunity to continue the work of current students Rachel Cross ’21, Surabhi Iyer ’21, Sofia Neaher ’22 and Georgia McClain ‘22, who are comparing the defenses mounted by Arabidopsis plants against T6SS mutant versus wild-type bacteria. The goal of our research in the coming year is to further characterize this novel pathogen-recognition pathway, using protein biochemistry, plant genetics, and molecular and cell biology approaches.
Formation of bacterial biofilmsSource: biology.binghamton.edu/davies/research.htm
Ron Bassar
TBL 019 (laboratory); TBL 204 (office), x2119, [email protected]
Darwin thought that evolution by natural selection occurred very slowly, over hundreds if not thousands of years. Evolutionary biologists now know that evolutionary changes in species can happen very quickly, over a relatively few generations. The consequence of this rapid evolutionary change is that ecological and evolutionary processes interact on the same timescale, sometimes drastically altering the outcomes of each. Research in the Bassar lab focuses on developing theory and conducting empirical research aimed at understanding the causes and consequences of this interaction in the generation and maintenance of biological diversity. Past research has demonstrated the role of biotic interactions in life history evolution, how these biotic interactions and their evolutionary outcomes alter community and ecosystem structure, and how abiotic factors, such as climate change, alter these dynamics. Current research is building upon this theme by testing the influence of short-term evolutionary change on species coexistence in structured populations. All research involves an ongoing synergism between theory and data using Trinidadian stream communities. We develop theory and then test predictions from theory with experiments in natural populations, semi-natural mesocosms, and the laboratory. As such, there are opportunities to conduct research in using any of these approaches.
Pei-Wen Chen
HSB 110 (laboratory); HSB 130 (office), x3536, [email protected]
Concurrent remodeling of cellular membrane and actin cytoskeleton occurs in many biological processes such as cytokinesis, phagocytosis and cell migration. Broadly, my lab is interested in understanding the mechanisms underlying the coordinated change in various cellular membrane and actin structures as this coordination is fundamental for normal physiology and often disrupted in pathological conditions like cancer cell invasion and metastasis.
Specifically, we use focal adhesions (FAs) in mammalian cells as a model structure to investigate the role of Arf GTPase-activating proteins (Arf GAPs) in regulating dynamics of membrane and actomyosin networks (Fig 1). FAs are mechanosensing organelles that not only mediate cell adhesion to the extracellular matrix (ECM) but also sense and activate signaling crucial for cell survival, proliferation and differentiation. We use a combination of approaches including molecular cloning, biochemical and biophysical analyses, quantitative microscopy and cell biology techniques in our studies.
Figure 1 Components of focal adhesions
Figure 2 Conformations of Myosin II
I. Molecular basis for the formation of Myosin II-Arf GAPs complex
Initial work will focus on one Arf GAP called ASAP1 because of its clinical relevance to cancer. ASAP1 is amplified in many human malignancies and elevated expression of which is implicated in cancer invasion and associated with poor prognosis. However, the mechanism by which ASAP1 contributes to cancer progress remains elusive. Through proteomic screens and subsequent biochemical, microscopic and functional analyses, we have identified the actin-associated motor, Myosin II as a novel binding partner and effector for ASAP1. Direct association of ASAP1 with Myosin II is essential for ASAP1 function in controlling actin remodeling, FAs and cell migration. We will generate, produce and purify mutants of ASAP1 recombinant proteins to determine the structural components in ASAP1 responsible for Myosin II-binding. We will also test if the formation of Myosin II-ASAP1 complex is modulated by other known binding partners of ASAP1, phosphoinositide PI(4,5)P2 and Arfs. By the end of the study, we will have defined the interacting motif/residues and a role of lipid in regulating Myosin II, which will position us to determine the biological function of the complex and rationally design small molecules that perturb the complex to block migration or invasion.
II. Regulation of Myosin II structural changes and bipolar filament formation
Myosin II assumes three forms: a folded assembly-incompetent monomer, an extended assembly-competent state and self-assembled bipolar filaments (Fig 2). The transition among the three forms regulates Myosin II ability to bind ATP and actin, which confers actin cross-linking and motor activity of Myosin II to generate contractility and cytoskeletal patterning in cells. Currently, there are no tools to detect Myosin II filament formation in live cells. Regulation of Myosin II filament formation in non-muscle cells has been centered on the phosphorylation of the regulatory light chain. Based on our result showing that siRNA-mediated knockdown of ASAP1 disrupted Myosin II structures in cells, we hypothesize that ASAP1 and perhaps a subset of Arf GAPs bind and control assembly of Myosin II filaments in specific time and space in cells. We will develop Föster resonance energy transfer (FRET) -based spectroscopy and microscopy assays to measure Myosin II filament formation and structural changes. We will first use purified Myosin II under conditions known to affect filament formation and computational modeling to establish the assay. We will then expand the study to live cells to test our hypothesis of Arf GAPs as a new class of Myosin II regulators.
III. Regulation of membrane and actin dynamics by Arf GAPs in cancer invasion and metastasis
There are multiple ways that ASAP1 may contribute to cancer invasion and metastasis. We will examine alternative hypotheses that can explain the effects of ASAP1 on cell movements and invasion. Given the known role of Arfs in membrane traffic, ASAP1 may control the secretion of collagen I and/or metalloproteases or delivery of integrin receptors to modulate cancer cell invasion. It is also possible that ASAP1 may regulate or under the regulation of signaling pathways such as RhoA and ROCK to affect actin dynamics and cell migration. Several cell-based assays, immunoblotting and immunofluorescence staining will be used in these projects.
Joan Edwards
HSB 202 (laboratory); TBL 217 (office); x2472; [email protected]
My research covers the areas described below:
Evolution of the biomechanics and adaptive behavior of ultra-rapid movements in plants. Examples of study plants include:
a. Splash-cup dispersal by raindrops in Marchantia,
b. Use of plant “poppers” to propel seeds in wood sorrel (Oxalis),
c. walking, jumping and gliding spores of horsetails (Equisetum),
d. catapulting pollen in gaywings (Polygala paucifolia), stinging nettle (Urtica spp.) and bunchberry (Cornus canadensis), which has the fastest blooming flower (opens in <0.05ms!),
e. fruit explosion in touch-me-not (Impatiens),
f. sphagnum moss (Sphagnum), which has a spore-filled capsule that explodes open propelling the spores over 15cm into the air using a vortex ring.
We use high-speed cameras (filming at up to 100,000fps), microscopy (including SEM and EM), and field studies that focus on understanding the biomechanics and adaptive significance of these rapid movements.
Conservation of flowers and their pollinators. Pollinators and their flowers are part of the 6th extinction and in a worldwide decline primarily due to habitat loss. In New England, forests are increasing whereas field habitats where many of our most spectacular asters and goldenrods grow, have decreased. Using permanent plots in Hopkins Memorial Forest, we are testing how different mowing patterns affect the abundance and diversity of flowers. Changes in the floral resources, in turn, can affect pollinator populations. We are testing to determine the best management plan for fields to maximize resources for flowers and their pollinators.
Pollination Networks. Plant-pollinator systems have classically been defined by tight co-evolutionary links between flowers and their pollinators. Our current understanding of pollination systems has been based on sampling for brief periods (e.g., direct observation or net captures). We have developed a long-term time-lapse system that allows recording near-complete records of visitors to flowers as well as recording simultaneously at several different locations. These complete records are changing the way we think of pollinators and their flowers. The diversity of insect visitors is much higher that we thought based on the shorter observations. The taxa of insect visitors also differed among sites with important implications for gene flow.
Evolution and behavior of the sawfly, Empria obscurata. These remarkable larvae turn the color of whatever they eat so that they remain cryptically colored even when eating very different colored foods. So far, our studies have shown that larvae that eat both flowers (yellow) and leaves (green) have higher survivorship, achieve a larger adult size and develop more quickly that larvae fed on either flowers or leaves alone. We have also demonstrated that they can complete their entire life cycle on alternate host plants—thus opening up the possibility of speciation by host-shift.
Long-term plant population studies of a) the invasive plant, Alliaria petiolata (Garlic mustard) in different successional stands in Hopkins forest—now in its 16th year— and b) the growth, survivorship and reproduction of arctic plants growing at the southern edge of their range on Isle Royale National Park, Lake Superior.
Phylogeography of arctic plants
This project is in collaboration with Professor Luana Maroja. Please see the description in her section.
Allison Gill
HSB 201 (laboratory); TBL 219 (office); x2811; [email protected]
My lab investigates how plant-microbe interactions influence the biological and biophysical processes that cycle carbon (C) and nutrients throughout terrestrial ecosystems. These processes critically govern how ecosystems will respond to ongoing global changes such as increasing atmospheric CO2 concentrations, warming temperatures, and anthropogenic nitrogen deposition. Soils in particular represent the largest terrestrial C store, and much of our work centers on understanding how biological activity and responses to global change inform the size and stability of the soil C pool. Approaches in my research group integrate long-term field studies, laboratory experiments, and data synthesis activities. Some ongoing projects are described below. Please get in contact if you are interested in learning more and getting involved!
Interactions between substrate chemistry and nitrogen enrichment on saprotrophic fungal metabolic activity, using a model Arabidopsis system. Fungi are important decomposers in terrestrial ecosystems and produce enzymes that break down soil organic compounds to access C and N resources for growth, but fungi vary in their resource acquisition strategies and enzymatic capabilities. This variation may influence their specific responses and competitive interactions following N addition. To understand the fungal metabolic response to changes in nutrient environments across variable substrates, we use laboratory decomposition experiments in which pure fungal cultures are grown on senescent Arabidopsis thaliana
tissue engineered to express varying lignin and carbohydrate chemistry. This approach allows us to target specific decomposer mechanisms and connect the detailed understanding enabled by laboratory experiments to broader patterns identified in the field.
Role of mycorrhizal fungi in mediating soil carbon pool responses to nitrogen fertilization, Cedar Creek, Minnesota. Mycorrhizal fungi, or fungi that maintain a mutualistic association with plants, play a critical role in the process of soil C accumulation or loss, as well as the nature of soil C responses to N fertilization. We previously conducted a field experiment evaluating the influence of competitive interactions between free-living saprotrophic and mycorrhizal fungal communities on soil C decomposition in a long-term N fertilization experiment across seven forests and grasslands in central Minnesota. The sites vary in plant species composition, soil C chemistry, and dominant mycorrhizal association. We are currently characterizing rates of microbially-produced enzyme activity, which break down structural compounds and carbohydrates and release nutrients in soils, as well as the degree of physical protection of soil C fractions to develop mechanistic understanding of the role of C chemistry, fungal decomposer activity, and fungal community interaction sin mediating the soil C response to N fertilization.
Mechanisms of soil carbon stabilization and ecosystem responses to nitrogen fertilization at Hopkins Forest. While the activity of plants and decomposer microbes largely define the a
mount of C substrates ‘added’ to soils, as well as the rate of C consumption through the process of decomposition, soil physical structure strongly influences soil C accessibility, and thus the likelihood of microbial attack and release to the atmosphere. This summer, our group is initiating a new N fertilization and C substrate addition experiment at Hopkins Forest, replicated in two areas of the forest with varying soil minerology. Current research students are characterizing pre-treatment microbial community composition using 16S and ITS amplicon sequencing, as well as the decomposer activity of the community using extracellular enzyme assays. This summer, we will characterize plant communities across experimental plots and measure rates of litterfall production and whole soil respiration prior to the initiation of experimental treatments in the fall. The experiment is globally unique and provides a wide range of opportunities to ask questions about plant, microbial, and biogeochemical responses to N fertilization.
Cynthia Holland
HSB 114 (laboratory); HSB 132 (office), [email protected]
About half of all modern pharmaceuticals are derived from or inspired by compounds found in nature, yet the biosynthetic pathways for many natural products remain unknown. These pathways generally use basic metabolic building blocks, like amino acids, as starting materials, which have also been largely under-investigated. Research questions in the Holland laboratory focus on the evolution of enzyme function and regulation in amino acid metabolism and natural product biosynthesis in plants.
Cardenolide biosynthesis in wallflower
Cardenolides are a chemically diverse group of natural products that act as allosteric inhibitors of Na+,K+-ATPase, an essential membrane ion transporter that is found in almost all animal cells. The pharmaceutical cardenolide digoxin is used to treat heart arrhythmias and is on the World Health Organization’s list of essential medicines, but the cardenolide biosynthetic pathway has yet to be investigated. Using a recently published genome for a cardenolide-producing species of wallflower (Erysimum cheiranthoides), our current efforts are focused on identifying and characterizing candidate genes using genomics, protein biochemistry, and analytical chemistry techniques (Fig. 1).
Tryptophan metabolism
Tryptophan-derived natural products and intermediates in tryptophan biosynthesis are used as flavoring agents (like the flavor of grape and bitter flavors in horseradish and mustard), fragrances, herbivore repellants, dyes, and cancer drugs, but very little is known about the substrate specificity and regulation of tryptophan biosynthesis in plants. While humans and animals must obtain tryptophan from their diet, plants and bacteria synthesize tryptophan using a 5-step, 7-enzyme pathway. Using a combination of plant genetics, biochemistry, and structural biology, our goal is to characterize the enzymes involved in tryptophan metabolism in Arabidopsis, maize, and fruits like strawberry and grape.
Tim Lebestky
HSB 203 (laboratory); HSB 226 (office), x4508, [email protected]
In the Lebestky lab, we utilize the genetic model system of Drosophila melanogaster for the study of behavioral genetics and molecular neurobiology techniques to understand arousal and sensory integration. Animals use their senses to learn about their 
immediate environment, parse the relevant information, and react in a meaningful way. If the sensory inputs are not interpreted correctly, this can cause inappropriate reactions, such as exaggerated behavioral responses to innocuous non-threatening stimuli, or by not reacting strongly enough to real threats. These concepts also translate into human biology, as imbalances in arousal and sensory gating are linked to pathologies, such as insomnia, attentional disorders, autism, and anxiety.
1. Behavioral Gating Mechanisms and Dopaminergic Circuitry in Arousal
My lab has used the mechanical startle assay to identify the Dopamine Receptor (DopR) as an important component of the gating mechanism for “stress-based” arousal in the Central Complex region of the brain (blue circle) and we will extend the analysis to more deeply investigate the role of Dopaminergic circuits as well as try to identify and characterize additional molecular components. Mammalian studies of the basal ganglia suggest that DA oppositely regulates locomotion based on separate subclasses of post-synaptic neurons, also implicating the complex relationships between D1 and D2 family DA receptors. However, nothing is known of the interplay between these type I and II receptor families in Drosophila, and our behavioral assays allow for precise functional characterization and analyses 
currently unavailable in mammalian systems. To investigate these interactions in Drosophila, we will use multiple molecular, genetic, and behavioral techniques to separate and compare different forms of dopaminergic signaling in the brain. By coupling functional circuit manipulations with traditional immunohistochemical imaging techniques, we will try to unlock the many functions of multiple brain regions and evaluate our insights for relevant comparative studies of higher vertebrates.
2. Sensory Integration of Vision and Arousal State
There are very few examples of well-defined circuitries and molecular mechanisms in any model system, for the integration of arousal state and output behaviors. Therefore, in order to understand how arousal states translate into modulation of a simple
se
nsory-based behavior, we use “the fly stampede” that measures visual responses to motion by tracking walking behavior. The arena of LED arrays create a pattern of moving light bars that elicit rapid reflexive walking behaviors in a freely moving population of flies. Furthermore, visual stimuli can be modulated to drive locomotor responses towards either the middle, or the ends of the arena. It was anecdotally noted in preliminary experiments that the fidelity and magnitude of the locomotor response is largely dependent on the animals’ arousal state, since animals that receive no mechanical startle prior to the visual stimuli perform poorly in responding to motion. Also, given my earlier analysis of arousal phenotypes of DopR mutants, we have tested their performance in the visual arena, and these mutant animals are indeed compromised in their ability to perform visual tasks. The visual system in Drosophila is well characterized and the extensive control of both stimuli parameters and genetic manipulation of specific cell types allows exact precise separability of potential hypotheses. We will functionally dissect the circuit requirements for DopR in vision and arousal by utilizing Gal4 lines as performed previously for separating sleep/wake and startle-based arousal (Figure in section I). These studies, coupled with new genetic screens, may provide new candidates and methods for understanding the molecular nature of disorders involving regulation of impulsive motor behaviors due to altered attentional or arousal states.
3. The Role of Serotonin in OCD and Autism
The primary molecular target for pharmacological treatment of depression and anxiety disorders is the human Serotonin Transporter (hSERT/SLC6A4). However, the mechanisms as to how blockade of hSERT results in therapeutic changes are not known. Human genetic studies have identified risk alleles that can provide critical clues about the molecular pathways responsible for disease. Moreover, the replication of these alleles in model organisms allows the experimental study of their activity in vivo, and testing of therapeutic strategies to mitigate their pathophysiological effects. Several highly conserved residues in SERT have been shown to be critical for its subcellular localization, and mutation of these sites may contribute to both obsessive-compulsive disorder (OCD) and autism. dSERT transgenes containing identical SERT mutations of interest can be used to test their ability to rescue the phenotype of a dSERT null mutant allele. Additionally, genetic model organisms such as Drosophila are highly amenable to directed genetic interaction studies and large-scale genetic screens. Such strategies may identify compensatory mutations that reduce the pathophysiological effects of the risk alleles, and help determine the cellular pathways required for the normal function of hSERT.
David Loehlin
HSB 220 (laboratory); HSB 206 (office), x2244, [email protected]
The Loehlin lab studies the structure, function, and evolution of tandem duplicated genes. These are both core elements of genomes and known causes of disease and individual variation, yet scientists have not yet mechanistically studied the “rules of the genome” that govern the level of gene expression from tandem genes. A simple prediction is that doubling the number of copies of a gene will double gene expression, but we and others have observed that this is often not the case. The lab is trying to figure out when and why deviations from two-fold expression occur.
We previously observed that tandem genes we were studying in Drosophila flies produced more than twice the level of matched single copy genes (Loehlin and Carroll 2016). Our basic hypothesis is that the excess expression from tandem duplicate genes is caused by identifiable genetic factors. To identify these factors, the lab uses modern genetic tools to build and modify genes at the DNA level, then we test their function by injecting them into flies and measuring RNA levels or the amount of enzyme they produce. The lab is looking at a couple of different features that we think might influence expression of a gene pair.
Is expression of tandem genes mediated by insulators?
Certain proteins bind to specific DNA sequences called “insulators”, which are thought to organize the genome into loops or “territories” within the nucleus and block regulatory interactions between the stuff on either side of the insulator. The lab is determining if tandem overexpression is caused by insulators or is independent from them. In one project, we are comparing the expression of single and tandem transgenes in the presence/absence of flanking and intervening insulators. One planned experiment is to determine the effects of removing insulator-mediating proteins on tandem gene expression. We are also using computational tools to predict native insulator sequences, then mutating the insulator sequence to see if that influences single vs tandem expression.
Is excess expression of tandem duplicates distance-dependent?
If tandem duplicates show excess expression, how important is it that they are close to one another? The lab developed a new technique, using recombination, to duplicate a native gene in the genome at varying gene-gene distances. The plan is to make a set of duplicates at varying distances and then measure the expression levels of the new tandem pairs. Does the expression level show some kind of distance-dependent curve, suggesting cooperative transcription? Is it a stair-step, suggesting a role for specific regulatory elements? What will happen when the two genes come within 6’ of one another?
How do naturally occurring tandem duplicates express themselves?
Naturally occurring tandem duplicated genes experience not only the structural influences described above, but also have had their expression level shaped by mutations and natural selection. New high-quality genome sequences from Drosophila populations and species make it possible to identify evolutionary changes in copy number of tandem duplicate genes, characterize their expression levels, and then unpack how the two neighbor genes influence one another through targeted deletions using the CRISPR technique.
Martha Marvin
MSL 126 (laboratory); MSL 128 (office); x3546, [email protected]
Our chief research interests are in cardiovascular development in zebrafish and the molecular mechanisms underlying variations in stress reactivity in embryos and adults.
Adult levels of stress reactivity are in part governed by early life experience of stress. We are investigating the genes that are modulated by early life exposure to stress, with a particular focus on genes that may undergo permanent epigenetic changes in expression levels from embryonic exposure through adulthood. These candidates could be key genes in setting the stress “thermostat” throughout life. We created mutations in fkbp5, a stress-modulating gene, using CRISPR/Cas9 mutagenesis. We study their motion and biochemical responses following stimuli to observe how the presence or absence of fkbp5 affects their stress response.
Zebrafish are an excellent model in which to study the developing heart, the most common organ to suffer birth defects in humans. The zebrafish heart begins beating at 24 hours, but is not required for survival for the first week, permitting the study of serious defects.
Zebrafish exposed to exogenous estrogen or estrogen-like compounds causes defects in heart valves. We are investigating the roles of signals such as Notch and prostaglandins, and their interaction with two estrogen receptors—the canonical nuclear receptor (ER) as well as the G-protein coupled estrogen receptor (GPER)—to clarify the developmental risks posed by exogenous endocrine disruptors.
Manuel Morales
TBL 011 (laboratory); TBL 215 (office), x2983, [email protected]
The overarching goal of my research program has been to understand the ecological and evolutionary dynamics of mutualism. My research addresses this goal using a variety of study systems, but focusing on the interaction between ants and the treehopper Publilia concava.
In this mutualism, treehoppers feed on the phloem (sap) of the host-plant Tall Goldenrod (Solidago altissima) which is nitrogen poor and carbohydrate rich. Treehoppers filter large quantities of sap to meet their nutritional needs, and the carbohydrate-rich excrement (honeydew) is collected by ants as a food resource. In return, ants protect treehoppers from predators, and the act of removing honeydew facilitates feeding by treehoppers. Below, I highlight two projects that illustrate the current direction of my research program.
Tri-trophic population dynamics of mutualism
The main project that I am involved with is an NSF-funded study to understand the consequences of mutualism in a community context. I have addressed this question using both modeling and empirical approaches. For example, a simple model of mutualism involving ants, treehoppers, treehopper predators, and host-plants shows that by reducing the impact of predators on treehoppers, protection by ants can allow treehoppers to overexploit their host plants. Thus, while ant protection can provide short term benefits, it can generate population cycles over the long term. I have begun to test these model predictions in the field. Early results suggest that treehoppers do have strong negative effects on host-plant quality between years but that treehopper mothers avoid these plants when deciding where to oviposit.
The European Fire Ant
A third project that I am involved in is a collaboration with colleagues at Skidmore College and the University of Connecticut to assess the role of mutualism in the spread of invasive species. In the spring of 2003, I discovered the invasive European Fire Ant (Myrmica rubra) in Williamstown MA, previously recorded outside of its native range almost exclusively along the coast of northern New England. Research in my lab found that this population of M. rubra appears to be concentrated along the Hoosic River watershed from North Adams, MA to Hoosic Falls, NY.
Interestingly, the presence of this ant species is correlated with the abundance of a second invasive species, the plant Japanese knotweed. Japanese knotweed has extrafloral nectaries that attract ants who defend these plants against their natural enemies. While there are few herbivores of Japanese knotweed in its introduced range, a third invasive species, Japanese beetles, can inflict high levels of herbivory. In these cases, ants effectively defend plants from beetle herbivory. Ongoing research is aimed at identifying how mutualistic interactions can affect the population dynamics of participants in these invaded communities.
Robert Savage
TBL 302 (Laboratory); TBL 203(Office), x3314, [email protected]
A hallmark feature that is observed in development is the gradual restriction of cell fates as a multicellular organism is constructed and patterned. Early in development, cells are totipotent; that is, they have the potential to give rise to every cell type in the body. However, as development proceeds, the available options in cell fate become restricted, presumably due to local cellular interactions and differential gene expression. At some point a cell is terminally differentiated and remains locked into one cell fate such as a neuronal or intestinal cell.
In all animals, stem cells do not follow this developmental paradigm. They remain undifferentiated and their progeny adopt a number of distinct cell fates. The current goal of my lab is to identify and to characterize stem cell factors that regulate the developmental potential of stem cell lineages. Surprisingly, this is an entirely open question in the field.
Stem Cell Biology The biochemical pathways in which stem cells operate are likely to be similar among animals given the high conservation in function. Therefore, experimentally tractable systems offer distinct advantages over mammalian or tissue culture systems. Annelid embryos are large and the stem cells are accessible to functional experimentation that targets gene function. In addition, the two annelids I work with in lab have had their genomes sequenced by the Department of Energy Joint Genome Institute (JGI). As a result, there are over thousands of cDNA fragments of known identity that can be characterized, many of which encode transcription regulators and signaling proteins. Once a probe (riboprobe) is synthesized, you can use it to label mRNA via in situ hybridization. Since we have the ESTs (cDNA fragments) in lab, we can instantly generate expression data needed to formulate a workable hypothesis that will guide your study.
In annelids, the entire trunk of the animal is generated from ten large and accessible stem cells. This is a unique property to annelids and therefore highlights the advantages of this system with respect to the model systems.
Your project involves an in situ expression screen of candidate regulatory gene products that may be expressed differentially in the distinct stem cell lineages. The goal is identify the stem cell factors and to determine how they restrict a stem cell fate in one particular lineage over another (i.e. what are the molecular factors that distinguish the neural from the muscle stem cell).
Each project involves a combination of molecular, cellular and comparative techniques that include PCR, basic cloning, in vitro transcription, in situ hybridization, antisense morpholinos, sequence comparison, molecular phylogeny, fate map, immunocytochemistry and intracellular injection.
Claire Ting
TBL 023 (laboratory); TBL 214 (office), x4053, [email protected]
Photosynthesis is a fundamental biological process upon which the majority of Earth’s life depends. How do differences at the genome level between closely related photosynthetic organisms translate into selective physiological advantages in photosynthetic capacity and in tolerance to abiotic stress? What is the significance of existing molecular/physiological diversity for the ecology of photosynthetic organisms and the evolution of niche differentiation?
In order to address these questions my laboratory is focusing on the ecologically successful marine cyanobacterium, Prochlorococcus. This microbe is thought to be the most abundant photosynthetic organism on our planet. In certain regions of the oceans, more than 10,000 cells can be found in a single drop of sea water. Prochlorococcus plays a key role in primary production and in global energy cycles, and is an excellent model for plant photosynthesis. The projects in my lab are interdisciplinary and integrate tools and concepts from fields including genomics, biochemistry, cell biology, ecology, and evolution.
Photosynthetic Physiology and Environmental Stress Response Mechanisms
Through comparative studies of closely related isolates, we are investigating the photosynthetic physiology and environmental stress response mechanisms of Prochlorococcus. The availability of 12 complete Prochlorococcus genome sequences has enabled us to formulate specific hypotheses regarding how isolates and ecotypes will respond to key environmental factors, such as light and temperature. These studies will contribute to our understanding of the survival and distribution of Prochlorococcus populations in the open ocean water column and how this important marine microbe will respond to global environmental change.
Comparative Genomics, Metagenomics, Metatranscriptomics
Our most recent grant from the National Science Foundation has funded our field work in the Sargasso Sea, an open ocean region where Prochlorococcus often dominates the bacterioplankton population. We are conducting metagenomic (characterization of genes/genomes isolated from environments) and metatranscriptomic (characterization of gene expression in natural communities) analyses in order to understand how key environmental factors impact community composition and biological activity in open ocean waters.
Structural Characterization of Photosynthetic Microorganisms
Because Prochlorococcus cells are tiny (approximately 100 cells can be lined up side by side across the width of a human hair!), we are using state-of-the-art microscopy techniques to characterize the cellular structure and organization of Prochlorococcus. We have discovered that closely related isolates exhibit significant differences at the ultrastructural level, including in the number and organization of their internal membranes, where proteins involved in photosynthesis are localized.
Damian Turner
TBL 012 (laboratory); TBL 216 (office), x2065, [email protected]
Resident memory T cells and the pathogenesis of asthma
Asthma is a chronic inflammatory disease of the lung which results in narrowing of the airways, breathing difficulties which can lead to death. According to CDC estimates, approximately 1 in 12 people (25 million) have asthma and asthma was responsible for 1.8 million emergency room visits in 2010. Current treatment strategies for asthma include inhaled corticosteroids that can control airway inflammation but do not cure chronic allergic asthma. Understanding the mechanisms leading to the development and chronicity of asthma is therefore critical to designing more effective therapies and to cure this disease.
Memory CD4 T cells play important roles in the initiation and regulation of asthma and have been shown to coordinate disease pathology through the recruitment and activation of effector cells like eosinophils and mast cells. Allergic asthma is driven by inhaled allergens that, over time, create populations of allergen-specific memory T cells. We have identified a new subset of tissue resident memory CD4 T cell (CD4 TRM) within the lung which are maintained independently of circulating populations and which exhibit peribronchiolar localization that ensure early exposure to inhaled matter. We have further found that CD4 TRM are generated in the lung of mice following long-term exposure to the common household allergen, house dust mite (HDM) allergen. We have found that allergen-specific TRM in the lung are rapidly activated and migrate into the airways upon re-exposure to the allergen. Lung TRM may therefore represent critical targets in new approaches to prevent chronic and recurrent asthma symptoms. I wish to investigate the role of lung TRM in the pathophysiology of allergic asthma. Furthermore I will use antigen specific immunotherapy to target the TRM population and assess the effect on disease severity and chronicity.
Vincent van der Vinne
HSB 216 (laboratory); HSB 222 (office), x2687, [email protected]
Understanding the mechanisms responsible for the adverse health effects of circadian disruption
Circadian clocks control rhythms in nearly all aspects of mammalian physiology and behavior. The mammalian circadian system consists of transcription-translation feedback loop oscillators in (nearly) every cell of the body that together form a hierarchical system with a master clock in the brain (SCN) and peripheral clocks in all organs of the body. The circadian clock system has evolved to enable organisms to cope with the predictable daily changes between day and night. Internal clocks are synchronized to rhythms in the environment through timing cues such as the timing of light and food, but living in our modern 24/7 society is associated with light exposure and food intake at all hours of the day. The resulting disturbance of circadian homeostasis is linked to a host of adverse health outcomes such as increased risk of cancer and metabolic syndrome in human shift workers.
Although the causal link between circadian disruption and adverse health outcomes is well established, the identification of the mechanisms responsible for these outcomes has been hindered by the complexity of the mammalian circadian system. Research in my lab aims to describe the response of clocks in different parts of the body during circadian disruption using different behavioral, physiological, molecular and computational approaches. The health consequences of specific aspects of circadian disruption can subsequently be assessed through the use of genetic models of disruption and exposure to artificial lighting and feeding schedules. Using these approaches, we hope to identify the mechanisms critical for linking circadian disruption to its adverse consequences and to be able to formulate effective strategies to remedy the circadian disruption inherent to living in our modern 24/7 society.
Heather Williams
TBL 015 (laboratory); TBL 205 (office), x3315, [email protected]
Research in the Williams lab focuses on how birds learn and use their songs, how variation in songs arises, and what that variation means.
Cultural evolution of song
Socially learned behaviors, such as bird songs, are transmitted and changed in ways analogous to and yet different from genes. Males may learn from their fathers, older neighbors, or even from males of the same age, and females may prefer certain song characteristics and so influence male learning. We seek to understand how, in a wild population of Savannah sparrows, these factors combine to cause some parts of the song to be stable for decades, others to vary rapidly and randomly, and still other song segments to vary systematically over time. To address these questions, we use observation (tracking changes in song and relating them to characteristics of the singers), comparisons (contrasting the songs of different populations), experiments (such as exposing young birds to a variety of songs to determine which novel sounds are incorporated into the population or playing carefully designed stimulus songs to adults and observing their responses), as well as mathematical modeling (collaborating with mathematicians to assess which processes best match the data).
Sexual selection and song complexity
House finches’ songs consist of a fixed number of syllables that can be sung in different arrangements. The syllable sequence can “branch” and take different paths at specific points in the song, with two or more options for the next syllable. House finches often 
sing many songs in succession, and they tend to vary the syllable sequence from song to song. They also frequently “countersing”: two males face each other and alternate songs. There are also specific syllables sung only when courting females. We study these variations in syllable order, an analog of syntax, and ask whether the variations have specific patterns, whether these patterns change when a male courts a female or countersings with another male, and how song patterns relate to other signals of male quality. The answers to these questions will inform our understanding of how signaling systems are organized and used. In addition, females sometimes sing, and we are interested in recording these songs and comparing their syllables and syntax to those of males’ songs.
Song organization
Like human speech, bird song can be divided into phonology and syntax. Birds learn phonological units (notes or syllables) from conspecific singers, and then assemble these subunits to form a song. The songs of different species appear to
follow different syntactical rules; winter wrens’ songs, though elaborate and complex in their phonology, have an invariant syntax, house finches have rules that define a variety of paths through their large syllable repertoires, and zebra finches have both a small syllable repertoire and a relatively simple linear syntax. We investigate how syntax arises through 1) comparative studies of related species and 2) tracking the responses of males and females to artificially constructed songs with either fixed or variable syntax.
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