Biology Department

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

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!

Non-muscle Myosin II (NMII) generated contractility is a fundamental cellular process that occurs during cell migration and division, however it is particularly important to morphogenesis, or the cell shape change that occurs during development. NMII forms bi-polar anti-parallel filaments upon activation, binding to actin filaments to generate force. While many of the kinetic and biophysical properties of NMII are well known, the molecular cues dictating when and where it is activated are far less well understood. What is also lacking is a complete list of the molecules involved in the regulation filament dynamics and contractility. This research aims to dissect the recruitment and activation of NMII through the analysis of a novel, NMII regulatory molecule RN-tre. With RN-tre as an example, we will identify additional regulators of NMII contractility during this critical morphogenic process, apical constriction, using complementary experimental and computational methodologies. Drosophila tissue culture cells have been used in multiple studies that have made significant contributions to our knowledge of the cytoskeleton. Their sensitivity to RNAi, allowing for effective depletion of one or more proteins, and their confined geometry make them ideal for high-resolution imaging techniques such as total internal reflection microscopy (TIRF). Furthermore, this we will take advantage of testing computationally-predicted NMII regulators using a cell-based assay of apical constriction which will allow important questions to be asked about this developmental process, while side-stepping the complications of imaging in an embryo.

Tobacco addiction affects millions throughout the world, and kills up to 50% of its users according to the World Health Organization. Nicotine is the primary compound in tobacco that has been associated with the addictive properties of this drug. Nicotine is known to adversely affect the offspring of mothers exposed to nicotine during gestation. Although the receptors for nicotine are known, the genetic, cellular and molecular mechanisms that mediate nicotine's effects on development are not well understood. Drosophila melanogaster is a great and proven model system to identify genes and novel mechanisms for drugs of abuse. My lab has developed a Drosophila model for the effects of developmental nicotine exposure. Developmental nicotine exposure has specific effects on Drosophila development and behavior that are similar to those reported in mammals, including humans. The conservation in receptors and neurotransmitters that mediate the effects of nicotine make this organism a suitable model system to elucidate novel mechanisms for nicotine’s effects.

Deep ocean environments are largely under studied and organisms that thrive in these ecosystems, under such extreme conditions, are not well understood. Research in environmental microbiology in recent years has resulted in a dramatic change in the way we view microbial diversity in these systems. New bacterial and archaeal groups have been identified and studied thanks to advances in molecular biology, sequencing and bioinformatic technologies. For this presentation we will focus on data associated with single cell genomes recovered from the Mariana Trench and metagenomic samples recovered from the Costa Rica margin. Single cell genomes from the Mariana Trench provide a deeper understanding of the candidate phyla Parcubacteria and their potential for expanded metabolic capacity in the deep ocean. Preliminary results on the Costa Rica margin suggest that sub-seafloor microbial communities are dynamic, as their composition and metabolic potential varies with depth. Within this environment, archaea from the newly described ASGAR super phylum are abundant, which provides a unique opportunity to better understand their metabolic potential. Ultimately the goal of this research is to speculate about the biogeography of the microbial community and their adaptive metabolic processes to low temperature, high-pressure, recalcitrant nutrient sources and energy requirements.

The prospect of replacing cells of the central nervous system by cell transplantation remains a focal point of vision repair science. Rods and cones, the cells of the retina that mediate light detection, can be enriched and transplanted into wildtype and retinal degeneration mouse models. We and others recently discovered that in contrast to the historical interpretation that transplanted cells migrate into recipient tissue, donor and host cells participate in fluorescent reporter and photoreceptor material exchange. The result of this material exchange is the appearance of donor cell-derived fluorescent reporter (I.e. GFP) in mature cells in the recipient retina. Identifying the mechanism(s) involved in donor/host material exchange will help us to understand the mechanistic underpinnings of cell-based vision rescue, address safety concerns raised by donor/host intercellular communication, and lead to more general insights into the regulation and function of intercellular material exchange.

Plants do not have a germline that is separate from their soma. Consequently, plants have the potential to generate large numbers of somatic mutations as they grow. However, rates of mutation accumulation in plants are generally similar to animals. We provide evidence that that selection occurring on clonal cell lineages filters mutations and results in an disproportionately high frequency of beneficial mutations being passed on to the next generation. These data are the first to indicate that somatic mutations accumulating during vegetative growth can have substantial phenotypic effects on the fitness of offspring. We develop a model that accounts for the moderate levels of mutation accumulation in plants and the observed phenotypic effects. We test predictions of the model by quantifying somatic variants using methods used to detect mutations in human cancer. The patterns we detect are consistent with the predictions of large numbers of low-frequency mutations, and with the occurrence of beneficial mutations that result in selective sweeps of meristem cell lineage populations.

Biodiversity change and ecological responses to climate change are topics of major concern, and we rely on ecological theory to guide how we relate observed or suspected changes to potential consequences for ecosystem functions and services. Our major theories of life emphasize either energy and materials (metabolic theories) or information (biodiversity, evolution). I aim for unification across these conceptual pillars. I will highlight recent advances in detecting biodiversity change across scales in coastal marine systems and potential implications for ecosystem functions and seafood derived nutritional benefits to humans. I will also present recent work that strengthens our understanding of how general temperature dependence of metabolism constrains population-level processes and fitness potential, providing a key link between temperature and ecological and evolutionary outcomes. I am deeply interested in unifying our ecological science across scales, and hope to start a discussion about how we can continue to take steps in that direction.

The traditional theory of cancer evolution posits that cancer genomes will acquire mutations over a long period of time as the result of an evolutionary process. However, in recent years it has been suggested that some cancer genomes may instead undergo a one-time catastrophic event, such as chromothripsis, where a large number of mutations instead occur simultaneously. A better understanding of how tumors development has important diagnostic and therapeutic implications. In this talk I will describe these different models of tumor evolution and introduce computational techniques for analyzing tumor DNA sequence data according to both of these models. In particular, I will describe a computational method that undergraduates in my lab developed to infer the evolutionary history of a tumor as a type of rooted tree given a set of plausible tumor histories. I will also describe a measure my group developed to help distinguish cancer genomes that acquired mutations simultaneously from those where mutations were acquired sequentially.

The Vizcarra group studies molecular mechanisms in the formin family of cytoskeletal regulators using reconstituted systems. The human genome has 15 formin genes, whose encoded proteins play specialized cellular roles. One of the first human genes to be linked to hereditary deafness encodes the formin DIAPH1, mutations in which are associated with autosomal dominant, non-syndromic progressive hearing loss called DFNA1. Like other formins, DIAPH1 interacts directly with the actin and microtubule cytoskeletons. Despite the great progress made in understanding the molecular basis of other forms of hereditary deafness, very little is known about the mechanisms underlying DFNA1, and more generally about the role of formins in the inner ear. We take a biochemical approach to testing various hypotheses about the etiology of hearing loss in DFNA1. Other projects in our lab include understanding the basis of small molecule inhibition of formins and studying how metalloproteins of the central nervous system control actin dynamics.

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

Reedies take many paths after they leave Reed. Come meet three alumni who now work in the fields of Science Journalism, BioTech Entrepreneurship, & Nature Photography/Nonprofit Citizen Science. Join us for Q&As and stories to hear about what they do, why they do it, and how they got to where they are.

Changes in wildfire locations, extents, severities, and frequencies will be a hallmark of this century. Will forests keep pace and recover? We take an admitted hydrologist’s approach to this ecological question, with the premise that forest recovery requires plant growth and plant growth requires water. Yet, it is a conundrum: post-fire soils are notoriously (a) hydrophobic or (b) exceptionally freely draining. (Or both? When? Where?) What happens to seedlings and soils when a site reburns after only a short time? There are many open questions about the effects of fire on soils, soil physics, and plant available water. Bookended by the wealth of top-down research on visible forest regrowth after wildfire and by studies of post-fire watershed-scale hydrological responses, this research dives below ground to seek to better understand soil-fire-water-vegetation interactions in the vadose zone during post-fire recovery periods. This talk will lay down challenges and discuss preliminary results seeking to connect heterogeneous pyrology, hydrology, and ecology responses through space and time from point to hillslope scales.

The Di Stilio lab broadly investigates the genetic basis of key transitions during land plant evolution. The flower, and the interactions with pollinators that it enhances, are amongst the key innovations that have allowed angiosperms to become the most species-rich lineage of land plants. Current research takes an evolution-of-development approach to investigate the genetic basis of flower diversification. Our focus is on modulators of floral development (ABC model genes and the flower meristem identity gene LEAFY) as candidate genes for angiosperm diversification, and on their functional fate after gene duplication. Early on, we capitalized on the diversity of breeding and pollination systems in the genus Thalictrum, an early-diverging eudicot with a strategic phylogenetic position between model systems. In an attempt to reconstruct ancestral function, we have recently begun to explore the role of flowering-related gene orthologs in non-flowering plant lineages, in particular LEAFY orthologs in the fern Ceratopteris richardii.

The oxygen in every fifth breath you take was produced by phytoplankton, the abundant photosynthetic microorganisms of the ocean. These abundant and tiny cells create “The Invisible Forest”, an ecosystem that contributes to global primary productivity on the same scale as forests and grasslands, only it is invisible to our eyes. To understand how the Earth System works, we must understand the ecology of phytoplankton. The phytoplankton Prochlorococcus is the most abundant photosynthetic cell on Earth. Prochlorococcus thrives in the vast warm and nutrient poor surface oceans far from land. Here, we present the results of oceanographic field expeditions and laboratory experiments that examine how genetic diversity and oceanographic factors control the contributions of Prochlorococcus to the ocean ecosystem.

Along a developmental cell lineage trajectory, transitions from one cell identity to another are key control points – yet it remains largely unclear how these transitions are regulated. To investigate fundamental principles that direct cell fate and identity, we utilize the multipotent stomatal lineage on the epidermal surface of developing leaves from the plant model system Arabidopsis thaliana. Stomata are specialized pores comprised of two cells that are essential for atmospheric gas and water exchange. Stomatal formation is initiated by and proceeds through three discrete lineage states sequentially driven by conserved basic helix-loop-helix transcriptional regulators. To uncover additional layers of functionally heterogeneous and adaptable cell states, we are integrating single-cell systems biology with whole-tissue developmental biology and molecular genetics. Our preliminary single-cell RNA sequencing analysis indicates that cell identity is surprisingly heterogenous within the lineage, especially during the early self-renewing stages, which extends our understanding of both evolutionary divergent and conserved pathways in stomatal development. Moving forward, we are interrogating molecular mechanisms that underlie lineage adaptability and allow for developmental flexibility in response to environmental cues.

Decades of research have provided ample evidence of the presence of numerous neurotransmitters in the inner ear, including dopamine and gamma-aminobutyric acid (GABA). However, the sources, targets, and functions of these neurotransmitters have remained unclear. We use the zebrafish lateral line sensory organ to study dopamine and GABA signaling in peripheral auditory and vestibular systems. I will present data that support a model in which these two neurotransmitters play distinct and opposing roles in sensory hair cell circuitry. Our data suggest that efferent neurons release dopamine onto peripheral hair cells, resulting in increased hair cell activity, while GABA is synthesized by hair cells and targets sensory afferents in order to dampen the transmission of sensory information to the brain. Together, these data contribute to our growing understanding of the remarkable complexity of sensory perception.

By comparing animals to their closest living relatives, the choanoflagellates, we can reconstruct the biology of animal ancestors to illuminate how cellular and genetic changes contributed to the origin of animal development. Importantly, choanoflagellates express genes that are otherwise only found in animals, suggesting that the cellular and genetic foundations of animal development were in place before the emergence of animals. Furthermore, choanoflagellates differentiate into distinct cell types and morphologies, including multicellular colonies that resemble early stages of animal embryogenesis. Previously, the absence of reverse genetic tools in choanoflagellates stunted functional comparisons between choanoflagellates and animals. With the first tools that I have developed for performing transgenics, genome editing, and functional genomics, I will explain how a choanoflagellate species, Salpingoeca rosetta, now serves a simple model for investigating the origin and evolution of animal multicellularity.