Faculty Listings

We have compiled a list of faculty members who have indicated they are interested in working with Summer Scholars:

Wayne Chudyk, Civil and Environmental Engineering: Save Lives with Fiber Optic Sensors

Fiber optic sensors are used in medical and environmental settings to obtain real-time data supporting critical decisions. This project will investigate prototyping and use of fiber optic sensors for medical or environmental applications. Possible measurements include those essential for diagnosing trauma, evaluating necrosis, applying water quality and climate models, tracking contaminated drinking water, and remediating hazardous waste sites. Students with interest or expertise in engineering, mathematics, or the physical sciences have an opportunity to apply their skills. Combined literature survey and laboratory work is needed to determine the most practical approach for making desired measurements. In consultation with the advisor, a type of measurement will be selected with the aim of producing a prototype fiber optic sensor.  Previous work in this group has investigated fiber optic sensors detecting water contaminants, biological components such as chlorophyll, and redox potential as it applies to water or blood plasma. Past prototypes have used either laser or LED light sources, while signal processing has included modifications of Arduino packages.

Ioannis Evrigenis, Political Science/Classics: The Modern Concept of Sovereignty: Digitzing Jean Bodin's Six Bookes of a Commonwealth

Jean Bodin's Six livres de la republique, published in French in 1576 and reissued with important changes in Latin, in 1586, is widely considered the locus of the modern definition of sovereignty, having shaped such thinkers as Hobbes, Locke, and Rousseau. Knolles produced an English edition out of the French and Latin, in 1606. As a result, no full English translation of either version exists. Moreover, there is no critical edition in print, in any language, nor any parallel edition displaying the changes in the text. Bodin's excellent knowledge of Greek, Roman, and Hebrew sources, as well as of historical events and myths renders this work a difficult one for readers. This project will make the Six Books available in an electronic edition that will be fully-editable and will provide open access to this seminal work.

Larry Feig, Neuroscience, Tufts Medical: Epigenetic Mechanisms Underlying the Transgenerational Effects of Stress

My lab studies how the effects of stress can be transmitted across generations through the male lineage via epigenetic mechanisms. In particular, we have implicated specific miRNA changes in sperm as mediators in mice, and have performed a study in men that suggests a similar process works in humans. In the latter study, we have shown that early life trauma in men alters the expression of a set of sperm miRNAs in adults. Available projects include testing whether any of these miRNAs are also altered sperm of mice exposed to early life stress, which offers the ability to test how they may contribute to transmitting stress phenotypes across generations.

Maria Flytzani-Stephanopoulos, Chemical Engineering: Nano Catalysis and Energy Laboratory

A Summer Scholars’ project involving the synthesis of PtCu, NiAu, PdAu alloys at the nanoscale and the use of these as catalysts for selective oxidation and selective hydrogenation reactions is offered through the NanoCatalysis and Energy Laboratory this year. The reaction selectivity is studied as a function of the alloy composition. New catalysts for the production of “green” chemicals are targeted through this approach.

Catherine Freudenreich, Biology: The molecular basis of chromosome fragility

Maintaining genome stability is critical for every cell. Interestingly, some areas of chromosomes, called “fragile sites” are more prone to breakage than others. Some of these sites consist of expanded repeat sequences, which are difficult to replicate and repair. An example is expanded CAG or CGG repeats, which are the cause of several genetic diseases, such as Huntington’s disease and fragile X syndrome. There are other fragile sites whose molecular basis is not understood. Some of these are hotspots for cancer-causing chromosome rearrangements, such as deletions and translocations. In this project, the molecular basis of chromosome fragility will be explored. Students involved in this project will use genetic and molecular techniques and the yeast model system to address the research question.

Irene Georgakoudi, Biomedical Engineering: Design of enhanced imaging laparoscope to improve detection of micro metastases

This is a project pursued in close collaboration with Dr. Thomas Schnelldorfer from the Department of Surgery at the Lahey Clinic Medical Center. The ultimate goal is to enhance the design of laparoscopes that are currently used in the clinic to improve detection of micro metastases in the peritoneal cavity of patients with primary pancreatic, ovarian, or gastric cancers. Such improvements could impact significantly upon specific medical decisions regarding the treatment of these patients. The method we propose to develop relies on identification of unique endogenous fluorescence, absorption, and light scattering signatures of the cancerous tissues compared to the surrounding healthy tissue. The project involves spectroscopic imaging measurements of human tissue specimens with an advanced non-linear microscope, as well as instrument design and characterization.

Irene Georgakoudi, Biomedical Engineering: Development of new biomarkers to assess neuronal function

The brain is the most complicated organ in our bodies and many of the ways in which it functions in a healthy vs. a diseased state remain unknown. Our goal is to develop and optimize non-invasive methods that will enable us to understand better how different components of brain tissue function during normal development and in response to injury. This project is pursued in collaboration with Dr. Kaplan, who has recently developed a novel simple engineered brain tissue. The project will introduce the student to novel imaging and image analysis approaches, as well as skills associated with tissue engineering.

Irene Georgakouki, Biomedical Engineering: TB or not TB? Development of non-invasive imaging to asses the role of metabolic heterogeneity in TB development and response to treatment

Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis (Mtb), remains a devastating disease and continues to pose a dire threat to global public health. To control the spread of disease, we have an urgent need to develop rapid diagnostics and shorter, more effective treatment regimens that would cure more individuals, limit transmission, and diminish the spread of drug-resistant strains. Treatment requires a minimum of six months of a four-drug regimen, making compliance difficult and facilitating the emergence of multidrug-resistant strains. Use of traditional methods has failed to improve TB treatment for decades, in part, because they do not have the capacity to capture the biology and variability of single cells. We propose a direct approach to create single-cell assays of mycobacterial metabolic state. Using two-photon excited fluorescence (TPEF), we will characterize the spectra of mycobacteria under different environmental conditions. We will use this knowledge to create measurements of the concentrations of coenzymes to track the metabolic state of mycobacteria. We anticipate that we can use these non-destructive measurement tools to measure the metabolic states of mycobacteria, which has direct application in developing improved drug regimens and affordable, rapid diagnostics for TB. This project is pursued in collaboration with Dr. Aldridge.

Julia Gouvea, Education and Biology: Student learning in introductory biology

My research group explores a variety of questions related to student learning in introductory biology. We are currently investigating questions related to the cognitive basis of learning concepts in biology, how courses influence student attitudes and approaches to learning in biology, issues of persistence and retention in the biology major, and student learning outcomes associated with inquiry-oriented labs. Students working in our group will have the opportunity to learn methods of educational research including both quantitative and qualitative methods. We are particularly interested in students who are excited about reflecting on their own learning experiences here at Tufts and who would want to pose their own research questions about biology learning and teaching. Ultimately much of this research will be used to inform the design and re-design of biology learning environments both at Tufts and beyond.

Jeffrey Guasto, Mechanical Engineering: Microfluidic control of liquid crystal optical devices

 Liquid crystals (LCs) are fluids comprised of elongated molecules that interact with light in a host of interesting and useful ways. LCs are widely used in switches for optical communication networks and play a prominent role in display technologies (such as TVs and LCD computer displays), which is a multi-billion dollar industry. The optical properties of LCs can be modulated by controlling their molecular orientation, usually through an applied electric field. However, generating a flow of the LC can also change their alignment through hydrodynamic shear. This project aims to develop a microfluidic device to control the topological landscape of LC orientation through precisely-controlled fluid flow fields for the purpose of generating novel methods to manipulate light. Students will design and fabricate microfluidic devices for which they will develop a flow control scheme and characterize the generated fluid flows using high-speed video microscopy and quantitative image analysis (such as PIV). Subsequently, polarization microscopy will be used to determine the resulting LC orientation field. This project is well-suited for physics, mechanical engineering, and chemical engineering students with interests in fluid dynamics/transport processes, statistical mechanics, optics, materials science, or microfabrication.

Jeffrey Guasto, Mechanical Engineering: Swimming cell transport in porous media

Swimming cells are integral to numerous environmental, human health, and engineering processes including bacteria in biodegradation, sperm in reproduction, and microalgae in biofuel production. Their natural and man-made environments are typically characterized by complex fluid flows through heterogeneous media including human tissues, medical devices, and soil. This project aims to determine the physical mechanisms governing the transport of swimming cells (bacteria, microalgae) in porous media flows using engineered microfluidic devices to control both environment microstructure and fluid flow. Students will design and fabricate microfluidic devices to mimic porous environments. Subsequently, they will characterize the fluid flows in these devices and quantify how cells (1-10 microns in size) navigate these complex, dynamic environments using high-speed video microscopy and quantitative image analysis (such as PIV). This project is well-suited for physics, mechanical engineering, chemical engineering, environmental engineering, and bioengineering students with interests in biophysics, fluid dynamics/transport processes, or microfluidics. No biology experience is necessary.

Katya Heldwein, Microbiology, Tufts Medical: Structural biology of herpesviruses

The Heldwein lab studies herpesviruses – ancient, complex viruses that also cause several important human diseases ranging from cold sores to encephalitis. Our work intends to answer the following broad questions. How do herpesviruses enter cells to initiate infection? How do herpesviruses assemble and get out of the cells once they have replicated? These complex processes involve multiple proteins. To understand how these proteins work together to bring about viral entry or egress, we use a structural approach. Our main tool is x-ray crystallography, which allows us to determine 3D structures of the proteins of interest at the level of atoms. The structures provide important clues regarding the mechanism, which we further pursue using an amalgamation of structural, biochemical, biophysical, and cellular approaches. The summer student will express, purify, and crystallize one of important herpesvirus proteins and, potentially, work on determining its crystal structure.

Daniel Jay, Developmental, Molecular, and Chemical Biology, Sackler School of Graduate Biomedical Sciences: Understanding breast cancer invasion: Testing inhibitors of extracellular Hsp90

Metastasis is responsible for the vast majority of cancer deaths and we have no drugs that inhibit metastasis.  The Jay lab has identified new proteins that act in invasion, the first step of metastasis by a screen that utilized chromophore-assisted light inactivation (CALI), a technology developed by our lab.  One protein we found is the molecular chaperone, heat shock protein 90 (Hsp90), but interestingly we found a novel role for this protein outside of cancer cells. We and many others have shown that extracellular Hsp90 activates a number of extracellular proteins that thus make cancers more invasive.  We now understand how Hsp90 functions on the outside of cancer cells and how to implicate it in aggressive cancers from patients. We have a collaboration with Synta Pharmaceuticals to test an Hsp90 inhibitor that cannot cross the cell membrane and will test this inhibitor initially with cells but eventually in animal models for metastasis.

Xiaocheng Jiang, Engineering Extracellular Matrices of Exoelectrogenic Bacteria for Promoting Bioelectricity Harvest

Microbial fuel cells (MFCs) are capable of harvesting electrical power directly from waste and renewable biomass and thus represent a promising technology for sustainable energy production. Central to MFC technology is the unique capability of exoelectrogenic bacteria, such as Shewanella and Geobacter, to divert electrons from the oxidative metabolism of organic substrates to the fuel cell anode. This is a complex process that has been extensively investigated in several model systems, revealing a diversity of electron pathways. These evolutionarily developed strategies for extracellular electron transfer, however, have been found to be among the major limiting factors in the process of current production. The goal of this project is to design and develop engineering approaches to modulate the microenvironment of exoelectrogens and create artificial matrices that will overcome the intrinsic limits in mass and charge transport within natural biofilms for improved fuel cell performance. The project will introduce the students to microfluidic design/implementation, electrochemical characterization, as well as microscopic imaging and image analysis approaches.

Peter Juo, Tufts School of Medicine: Identification and characterization of novel genes involved in synapse development and function.

My laboratory investigates the genes and mechanisms involved in synapse development and function, and how those genes ultimately regulate behavior. Studies revealing the normal function of genes at synapses will provide the foundation for understanding the molecular basis of aberrant synapse development and synaptic transmission observed in various neurodevelopmental and neuropsychiatric diseases such Autism Spectrum Disorders, Alzheimer’s Disease and Schizophrenia. We use a combination of genetics, biochemistry, in vivo fluorescence imaging and behavior in the genetic model organism C. elegans to study synapse development and function. Glutamate is the major excitatory neurotransmitter in the brain. We are currently performing a large-scale RNAi screen for genes involved in glutamate synapse development and signaling. We have already identified several interesting novel genes in this screen waiting to be characterized. We are looking for a Summer Scholar to help with the ongoing screen and to perform in-depth molecular characterization of a few promising candidate genes. A potential Senior Honors Thesis project could easily develop from this research at the end of the summer to investigate the molecular mechanisms by which a novel gene or gene family regulates synapse development. Several techniques will be learned during this project including C. elegans genetics, DNA subcloning, PCR genotyping, microscopy of fluorescently-tagged synaptic proteins and behavioral analysis of mutants.

Hyunmin Li, Chemical and Biological Engineering: Hydrogel microsphere suspension arrays for biosensing

Reliable and rapid sensing of biological molecules is important for numerous applications including medical diagnostics, bioprocess monitoring and control, and biological threat detection. Despite this importance and advances in high throughput platforms such as DNA and protein microarrays, there still exist critical challenges in fabrication of robust platforms and assembly of biological probes toward reliable and rapid bioassays. We tackle these challenges by an integrated fabrication-conjugation approach combining simple soft-lithographic micromolding techniques, bioorthogonal conjugation reactions, and functional biomaterials. In this project, we will examine replica molding-based fabrication of shape-encoded and macroporous hydrogel microparticles consisting of synthetic polymer networks and functional biopolymeric conjugation handles. Rapid cyclization reactions between tetrazine-modified fluorescent proteins and the microparticles activated with trans-cyclooctene will be enlisted to study the 3D structure and biosensing performance. Through this interdisciplinary project, the student will be exposed to a variety of experimental techniques and presentation opportunities at local biopharmaceutical technology workshops. 

Peter John Love, Physics: Quantum Information Theory

Summer research projects in Quantum Information Theory. Projects involve a combination of theoretical and numerical work. Projects are available in the areas of simulation of quantum systems using future quantum computers, with applications to chemistry, and of computation of entanglement of quantum states. Students from Physics, Mathematics, Chemistry and Computer Science are particularly encouraged to apply.

Jamie Maguire, Neuroscience, Tufts Medical: Investigating a potential mechanism underlying the role of stress in alcohol abuse

The goal of this project is to understand the contribution of stress neurocircuitry in alcohol consumption. Stress is a particularly salient physiological response that often triggers relapse among alcoholics and converging evidence from both clinical and animal studies has highlighted its critical role in drug reinstatement. One of the major molecules released during stress is the neuropeptide corticotropin-releasing factor (CRF). Not only has CRF has been shown to bind to CRF-type-1(-2) receptors, but our lab has identified a population of CRF-positive neurons which innervate the ventral tegmental area (VTA). Given that the VTA plays a prominent role in circuitry related to addiction, we hypothesize that CRF-positive neurons innervating the VTA may play a role in the effects of stress on addiction, specifically in alcohol abuse. This project will employ transgenic mice that express a light-sensitive ion channel (channelrhodopsin, ChR), which can selectively activate the CRF inputs into the VTA, to investigate the role of CRH inputs into the VTA on voluntary alcohol consumption. The prospective student will learn techniques related to in vivo optogenetics, behavioral testing, pharmacology, immunohistochemistry, and confocal microscopy.

Jamie Maguire, Neuroscience, Tufts Medical: Investigating the mechanisms underlying seizure progression and the development of treatment-resistant status epilepticus

The project will focus on investigating mechanisms underlying seizure progression in the brain and identification of novel therapeutic targets for effective control of seizures. In particular, the project will address the role of altered ionic mechanisms and inhibition in the brain during seizure progression and how they may lead to the development of drug resistance. The proposed work will utilize genetic mouse models to investigate the role of specific neuronal populations in neuronal network activity during epilepsy. This project will utilize electrophysiology as well as employ both pharmacological and optogenetic tools. The proposed work will make use of electrophysiology techniques that enable recording electrical activity of neurons from brain slices. In addition, the student will have the opportunity to learn about the fundamental principles of how the brain works and gain experience in various laboratory methods including dissection of the brain.

Paul Muentener, Psychology: The development of casual reasoning in early childhood

In the cognitive development lab, our broad goal is to investigate how children learn about the world around them in the first few years of life. Current studies are focused on how children represent causal relations from infancy through toddlerhood. For example, do children have an early expectation that all events have a cause? How does learning a language impact children’s causal reasoning? Finally, how do early differences in children’s causal search patterns relate to other areas of early learning? Students will gain experience recruiting infants and young children to participate in our research, running studies at local museums and on-campus, and coding and analyzing data. Please visit our website to learn more about the lab. 

Wai-Leung Ng, Molecular Biology and Microbiology, Tufts Medical: A chemical biology platform to study microbial small RNAs

One of the most fundamental questions in microbiology is to understand how bacteria sense, respond, and adapt to different environments. The bacterium that causes the diarrheal disease cholera, Vibrio cholerae, is a highly adaptive pathogen. It forms biofilm to survive in the aquatic environment, produces virulence factors to colonize the human small intestine, develop natural competence to take up exogenous DNA, and employs Type VI secretion to compete with other bacterial species. Our lab uses a multidisciplinary approach to study the signal transduction pathways that control these essential processes during its life cycle. We hope to harness our findings to develop novel therapeutics to combat this devastating disease.

Amy Pickering, Civil and Environmental Engineering: Zoonotic pathogens on hands in India

We have an opportunity for a Summer Scholars student to work with Dr. Amy Pickering and PhD student Marlene Wolfe on a study investigating contamination on the hands of caregivers of young children this summer. Many people worldwide keep domestic animals in close proximity in their home, and these animals can carry zoonotic pathogens that can be transmitted to humans cause illness. We will be doing DNA extraction and PCR/quantitative PCR analysis to identify pathogens (Giardia and E. coli) and markers of animal feces in samples that were taken from the hands of caregivers of young children in India. This analysis will allow us to examine the relationship between animal keeping and presence of zoonotic pathogens on hands. This project will be based on campus, and will involve primarily laboratory work. 

Lisa M. Shin, Psychology: Brain imaging studies of posttraumatic stress disorder (PTSD)

We are conducting functional magnetic resonance imaging (fMRI) studies of posttraumatic stress disorder (PTSD). Our research asks the questions: Do brain abnormalities in posttraumatic stress disorder (PTSD) arise from the disorder itself or are they familial vulnerability factors that increase the risk of PTSD following exposure to trauma.  Furthermore, can brain abnormalities in PTSD predict response to treatment? 

Gavin Schnitzler, Molecular Cardiology, Tufts Medical: Novel mechanisms of vasculoprotection through estrogen receptor alpha

Premenopausal women have half the incidence of cardiovascular disease relative to men, and this appears to be because of circulating estrogen levels. In mouse models, we know that estrogen protects against cardiovascular disease by binding to the transcription factor estrogen receptor alpha (ERa). We are exploring novel mechanisms by which ERa regulates transcription in vascular cells and alters their physiology.

The summer project would employ primary and immortalized vascular endothelial and smooth muscle cell cultures to examine gene regulation, proliferation, migration, and inflammatory responses in cells with normal ERa, no ERa, or mutant ERa that is unable to activate cellular kinases in response to estrogen binding. Techniques would likely include mammalian cell culture, real time PCR, Western blotting, and cell proliferation and migration assays.

Shomon Shamsuddin, Urban and Environmental Policy: Searching for Affordable Housing

Affordable housing is a persistent challenge for policymakers, community organizations, and families, especially in light of stagnant wages and rising house prices. Despite government programs to build, maintain, and preserve affordable housing, millions of U.S. households struggle to meet their housing needs. Further, the term “affordable housing” is not well defined. The standard measure of housing affordability is the ratio of housing costs to income: households that spend more than 30% of their income on housing are considered cost burdened. While this measure is appealing in its simplicity, it has several weaknesses. In this research project, we will develop a more detailed picture of housing affordability and understand how it varies across cities and has changed over time.

Taylor, Allen. Relations between aging, age-related eye diseases, protein quality control, and nutrition

Research indicates that the accumulation of damaged proteins is causally associated with aging in many tissues. Damaged proteins accumulate due to stresses of life : oxidation, nutrition, metabolism, as well as due to impaired cellular machinery to edit out and remove damaged proteins. We elucidate how dietary or environmental stresses affect visual function and risk for age related eye disease such as age related macular degeneration, cataract, diabetic retinopathy, specifically how such stresses affect the protein editing machinery. We work on systems from human to molecules.

David Tesini, Pediatric Dentristy, Tufts Dental School: Ergonomic Design of pacifiers

Lorem ipsum dolor sit amet.Pacifiers are often used by parents as soothing devices for their infants. A world-wide survey found pacifier usage rates to vary from 12.5% to 77% in babies 3 months of age. Often, however, pacifier use continues beyond ages recommended by the American Academy of Pediatrics and other health organizations. It is well known that these oral habits can cause negative effects on the oral development of toddlers (anterior open bites and posterior crossbites). Baby product development companies often attempt to design pacifiers that will prevent alterations in myo-functional development. Development of a model to test distortion of pacifier bulbs within the oral environment during sucking remains a challenging research area. Students involved in this project will work with a faculty member pediatric dentist from the School of Dental Medicine and a biomedical engineer from the School of Engineering to address both the design and clinical aspects of pacifier use. Knowledge of finite element analysis (FEA) and other in vitro force models would be helpful. This interdisciplinary project is anticipated to involve students from both schools.

Amy Yee, Developmental, Molecular, and Chemical Biology, Sackler School of Graduate Biomedical Sciences: The role of HBP1 and its signaling network in determining breast cancer progression

One goal of my laboratory is to understand the role of HBP1 and its signaling network in determining breast cancer progression and to advance new diagnostic and therapeutic strategies at the pre-clinical level. We have previously shown that reductions or mutations of the HBP1 gene are associated with invasive breast cancer and with a decreased relapse-free survival. We focus upon the Wnt and EGFR signaling networks with a new emphasis on the role of metabolic signaling in determining properties known to be associated with breast cancer, namely the acquisition of invasiveness, proliferation, and of self-renewal. We have implemented and developed relevant cell and animal models to address how Wnt and EGFR signaling may influence an altered metabolism in breast cancer. To address the important problem of recurrence, we have used statistical and bioinformatics tools to interrogate databases and develop new hypotheses for investigation in our pre-clinical models. Our goal is to develop mechanism-based pre-clinical models that recapitulate aspects of human breast cancer. These models should be valuable for evaluating new compounds and new therapeutic strategies with established compounds in future clinical trials. We are investigating the green tea compound EGCG as a collaborative chemotherapeutic agent in a targeted pre-clinical study of triple negative disease, an aggressive breast cancer subtype. We are also using NMR and MRI based methods to better characterize breast cancers and their brain metastases. Despite advances in treatment, death from metastatic disease remains unchanged for the past 25 years. Furthermore, while there is better management of non-brain metastases, the consequences are a sharp increase in fatal brain metastases. This multidisciplinary approach provides an excellent opportunity to delineate the complex processes for breast cancers and to discover new therapeutic strategies for definitive breast cancer treatment.

Amy Yee, Developmental, Molecular, and Chemical Biology, Sackler School of Graduate Biomedical Sciences: The Basic Mechanisms Underlying Epiliptogenesis

A second area of my laboratory is to understand the basic mechanisms underlying epileptogenesis. Together with a neurologist Dr. Audrey S. Yee, we have investigated and discovered that Wnt signaling is activated in the kainate and pilocarpine models of temporal lobe epilepsy at the earliest stages of status epilepticus (SE) and epileptogenesis. We reason that blocking SE and/or the immediate sequelae could alter the course of epileptogenesis and improve patient prognosis. Our collaboration is an advantageous marriage of expertise in breast cancer biology and neurology in order to discover new therapeutic strategies for epilepsy, a disease of unmet need and one in which there remain few new drugs. For some years, I have been investigating the role of Wnt signaling and a novel suppressor (HBP1) in breast cancer, but have now developed a new direction on the role of Wnt/b-catenin signaling in epileptogenesis. In fact, we have been developing pre-clinical frameworks and testing therapeutic strategies to attenuate Wnt signaling in both diseases. Our approach has been to rigorously apply our knowledge of the intricate circuitry of Wnt signaling biochemistry and genetics to develop and test informative pre-clinical frameworks. For this grant, we aim to bring unique and multidisciplinary perspective to delineating the molecular circuitry of epilepsies and to discovering new therapeutic strategies.

Learn more about the lab.