Graduate Research Labs

My lab works broadly in the emerging field of synthetic biology. Synthetic biology seeks to apply engineering design principles to the understanding and creation of biological systems. I use synthetic biology to design biosensors and bioremediation strategies for various environmental contaminants that impact human health, including lead, arsenic, and other toxic substances. We apply the tools of synthetic biology to address global challenges related to water, soil, and human health. Our water and soil applications focus around understanding how we can use genetically engineered microbes (GEMs) to detect and remediate contaminants in the environment. We use laboratory models of water and soil environments to measure, predict, and control GEM performance in a target environment.

My research interests lie at the intersection of RNA biology and reproductive biology, focusing on the contributions of RNA to oocyte quality and embryonic viability. Transcriptomic changes are associated with compromised oocyte quality. In turn, oocyte quality is intrinsically linked to fertility outcomes. Yet, little is known of the mechanisms by which these transcriptomic changes arise and how they contribute to cellular and metabolic health of oocytes. Transcriptomic changes are particularly important when transcription is undetectable during the oocyte-to-embryo transition. RNA modifications are central regulators of RNA stability and translation. Tailing is the addition of nucleotides to the 3' end of RNA molecules in an untemplated manner.  

My lab investigates signaling mechanisms of neuronal development. We are particularly interested in studying the role of the primary cilium in this context. Primary cilia are specialized filamentous structures that protrude from the surface of most human cells including neurons and mediate transduction of all major signaling pathways. Due to their central role in signaling, primary cilia are required for development and tissue homeostasis in vertebrates, and cilia defects are causal to a large spectrum of genetic disorders called ciliopathies. One research direction in the lab is centered around identification of novel signaling pathways required for ciliogenesis using two powerful genetic model systems (C. elegans and D. melanogaster) and mammalian cells. A second direction is focused on deciphering how cilia interact with other cellular compartments (e.g. synapses) to shape neuronal properties. To address these questions, we use a combination of experimental approaches that include genetics, bioinformatics, molecular biology, and high-resolution imaging.

I have a passion for understanding how living systems work, as well as for sharing my love of biology and research with the next generation of scientists and informed citizens. The central goal of my lab is to understand the regulatory mechanisms that underlie mycobacterial stress tolerance. We combine genetics, genomics, transcriptomics and biochemistry to understand how mycobacteria respond to, and ultimately survive, stressful conditions.  Our guiding principles are curiosity, respect, and scientific rigor. Together we strive to push the boundaries of knowledge and advance our field by addressing basic research questions that hold the keys to advancements in human health and understanding of the natural world.

My research aims at understanding the molecular and cellular mechanisms underlying plant cell organization and growth, with the long-term goal of increasing plant productivity. I am particularly interested in understanding the participation of the cytoskeleton in plant cell organization and growth. The cytoskeleton is one of the most conserved cellular systems between plants, fungi, and animals. This conservation is indicative of shared essential processes, such as the capacity for self-organization. Because these are complex problems, it is important to investigate them using a multidisciplinary approach and in a simple model organism. I was fortunate to identify the moss Physcomitrella patens as a simple plant with powerful molecular genetics. I was also fortunate to establish a fruitful collaboration with the Department of Physics at WPI.

Prof. Weathers is an internationally recognized expert on Artemisia annua and artemisinin, having worked with the plant and its phytochemicals including the antimalarial drug, artemisinin, for >25 years. She is a Fellow of AAAS and SIVB, won many awards, given many national and international presentations, reviews manuscripts for many journals and proposals for many national and international funding agencies. She is an Associate Editor for multiple journals. Her lab was the first to genetically transform A. annua. Of her > 130 peer-reviewed papers, about a third focus on bioreactors and another third on artemisinin or A. annua and now also including A. afra. She also has 3 patents (2 more pending). As of January 2022, her Google H index was 46 with nearly 6,500 citations and an i10 index of 96. She spearheaded the edible A. annua concept for treating malaria and other diseases and has led research to date on the project to establish proof-of-concept. She has supervised >20 MS and 16 PhD students and more than 80 undergraduate projects with about half of all theses and projects related to artemisinin/Artemisia. For >30 yrs she has managed a multidisciplinary research lab that may consist of a mix of visiting scientists, postdocs, graduate and undergraduate students in engineering, biology, and biochemistry. She has hosted Fulbright Fellows and visiting international students in her lab. Besides teaching 2-4 courses a year, she has obtained significant funding from NIH, NSF, NASA, USDA, and the private sector for her research and students. She has also consulted to the Biotechnology Industry since the mid-1980s. 

A member of the WPI faculty since 2004 and chair of the Department of Biology and Biotechnology since 2022, Professor Reeta Rao is a leader in the field of molecular genetics and genomics and has affiliate appointments at the Broad Institute of MIT and Harvard (Cambridge) as well as the Institute of Drug Resistance at the Univ. of Mass Chan Medical School (Worcester). Her primary research activities are focused on emerging infectious diseases, specifically understanding, and managing fungal diseases. Students and research associates in her laboratory are trained to use a variety of high biochemical, molecular-genetic, and genomic tools to study host-microbe interactions to explore fungal virulence strategies and identify novel therapeutics in a high throughput fashion.

Work in my lab is focused on defining the cellular mechanisms that maintain genome stability in normal cells and understanding how these pathways are corrupted in cancer cells. Genomic instability is a feature common in cancer that leads to aneuploidy and intra-tumor heterogeneity.  Whole chromosome instability (CIN) results from underlying defects in mitotic chromosome segregation and leads to gains and losses of entire whole chromosomes.  The ability of CIN cancer cells to ‘shuffle’ their genomic content can lead to gains of oncogenes, loss of tumor suppressors, and promotes tumor cell evolution.

Shane McInally is an assistant professor in the Department of Biology and Biotechnology. His research focuses on understanding the molecular and physical mechanisms that cells use to control and scale the size of their internal structures with distinct aspects of their geometry. He received a BS from the University of California, Riverside, an MPH from the University of California, Berkeley, and a PhD from the University of California, Davis. Most recently he was a postdoctoral fellow in the Biology and Physics Departments at Brandeis University.

My current research at WPI is highly inter-disciplinary and encompasses areas such as neurobiology, molecular genetics and chemical biology. I will be teaching courses at both the undergraduate and graduate levels. My philosophy for the courses I will teach at WPI will be to emphasize the importance of hypothesis-driven research and the need to carefully design biological experiments to test them. I feel this approach will allow students to develop their curiosity for a scientific problem and strongly encourage critical and independent thinking. It also represents an opportunity for students to bring in fresh ideas on topics that are not directly related with their research and curriculum. I have experienced that it is quite easy to excite a young student about a scientific problem but very difficult to maintain their enthusiasm. Therefore, I believe in a ‘hands on’ approach to teaching as being ‘hands on’ allows me to constantly keep track of my students’ progress. It also provides an environment for discussing problems and pitfalls of an experiment/concept. I have applied this approach very productively, as one of my undergraduate students, Omer Durak, has co-authored a paper with me in a peer-reviewed journal BMC Biology (See publication list). Many of the undergraduates that I have mentored have gone on to pursue graduate programs in several universities around the world. These success stories give me the confidence that as a teacher at WPI, I can reach shape the ideas and thoughts of many younger, keen minds.

Defining signaling pathways that program cellular diversity is one of the foremost problems in biology and is central to my research interests.  In the lab we use molecular, genetic, and biochemical approaches to characterize the function of these pathways and to gain insight into their role in disease.  To date, the lab has focused on the Epidermal Growth Factor Receptor network, a principal therapeutic target for a variety of human cancers.  This work involved the characterization of Kekkon1 (Kek1), an archetypal LIG molecule, as a novel feedback inhibitor of the EGFR network.  More recently, our work has branched out to neurobiology, adhesion/barrier biology, and lipid metabolism. 

At the undergraduate level, I enjoy relating the growing impact of biology in our world through teaching Intro to Biotech, Genetics, and mentoring students in the lab.  At the graduate level, I enjoy working with doctoral and master’s students in the lab and teaching classes on signal transduction, model experimental systems, and grant writing.  Outside of the lab, I enjoy snowshoeing, hiking, photography, and trying to keep up with graduate students on the soccer field.

I have a long-standing interest in applying computer science and mathematics to solve biological problems. I am currently the Associate Director of WPI’s Program in Bioinformatics and Computational Biology, and I am always looking for students with interests in this exciting interdisciplinary area. One of my goals in teaching biology is to help students to think more quantitatively about biological questions. A few years ago, my colleague Dr. Brian White of UMass Boston and I were awarded a grant from the NSF to develop a course, “Simulation in Biology”. In this class, students use an approach called agent-based modeling to simulate a biological system of their choice. The ‘agents’ can be molecules, cells, or organisms, and students program them to follow ‘rules’ that are drawn from what is known or hypothesized about how the agents actually behave. In constructing their simulation, students in the class develop a deeper understanding of both their biological system of interest, and of computer science.

I became so interested in this approach that I now focus my research in this area as well. I am currently collaborating with Dr. Rob Gegear, an ecologist who studies pollinator decline. Drastic declines in many pollinators have been observed in recent years, for reasons that are not well understood. Pollinators are important both for agricultural production, and also for maintenance of ecological food webs, as they are keystone species. Our students have developed “SimBee”, a model of virtual bumblebees in a floral environment, using the Netlogo platform. By incorporating what is known about bumblebee behavior and ecology into the model, we can ask many questions using the model that are difficult to address using field studies. We are also involved in funded research in collaboration with Dr. Alex Wyglinski (Electrical and Computer Engineering). In this research, we apply our knowledge of bumblebee foraging strategies to the problem of autonomous vehicle communication. It turns out that a bumblebee searching to find the best floral resources in a changing environment has many similarities to a vehicle searching for the best available communication channel. We also plan to use mathematical models derived from engineering concepts to experiment with various ways of representing memory in our SimBee model.

Dr. Gegear recently initiated ‘The Beecology Project’, a citizen science project which aims to gather critically needed ecological information on bumblebee pollinators and the flowers they pollinate. We have joined forces with two additional WPI colleagues, Dr. Carolina Ruiz (Computer Science) and Ms. Shari Weaver (STEM Education Center); the team recently received a $1.2M NSF Award to utilize The Beecology Project to motivate the integration of computer science and biology curriculum for high school students. Our team of students and faculty has developed smartphone and web apps, a database, simulations, and visualization tools to allow collection and analysis of ecological data that will help to determine the cause of wild pollinator decline. The curriculum we are developing in collaboration with high school teachers and students will allow students not only to use these data and tools, but to learn how to design and create their own digital tools to solve complex biological problems.

Research in my laboratory addresses questions in the field of evolutionary ecology and environmental biology, and typically combines field work and laboratory studies. Current projects focus on two disciplines.

One of the major goals of my laboratory is to understand the geographic and evolutionary processes that affect and generate biological diversity, particularly in aquatic habitats. In North America, freshwater faunas are particularly vulnerable to ecological changes because of heavy manipulation of habitats by human activity. In addition, North America harbors a substantial majority of the world’s biodiversity in freshwater crayfish, many of which are considered to be species of conservation concern. Furthermore, biodiversity in this group is poorly understood, and species may be declining or even disappearing even before they have been fully documented. We are working to understand the ecological and evolutionary interactions among native and invasive species of crayfish in the northeastern United States, with the ultimate goal of predicting how these interactions will change future distributions and diversity in this group.

Another research goal is to understand how ecological and phylogenetic factors contribute to social evolution. In crayfish, females bear most of the costs of reproduction, and males compete with one another for status in a dominance hierarchy, but the role of sexual selection on the social evolution of these animals is not well understood. We use both field data and laboratory experiments, including genetic analysis of family relationships, to test hypotheses about social behavior in this taxon.