BIOMEDICAL RESEARCH EXPERIENCES
FOR ENGINEERING MAJORS
2005
We would like to announce a new summer research program for Tufts undergraduates. It’s
called Biomedical Research Experiences for Engineering Majors, or BREEM. This NIHfunded program is designed for Tufts students who are majoring in engineering or computer
science and are interested in how these disciplines can be applied to biomedical research. Ten
students will work individually with faculty on a research project over the summer, for a
minimum of ten weeks. Accepted students will receive a stipend of $5,160 and up to $750 to
defray research costs.
Students must first identify and contact a faculty mentor. The attached list describes some
of the available research opportunities, but you are not limited to these faculty as mentors. The
application deadline is March 11, and should include the materials listed in the application
packet. Once accepted to the program, you will work with the faculty mentor during the spring
semester to develop a proposal for the summer project. This is due May 15. Depending on the
needs of the project, we will also pair you with a mentor from the School of Engineering. The
summer experience will include a seminar series given by Tufts investigators actively engaged
in research using biomedical engineering or analyzing complex biological systems with
computer modeling.
If you have questions, please contact the program directors listed below:
Prof. Claire Moore
Sackler School of Graduate Biomedical Research
Claire.moore@tufts.edu 617-636-6935
Prof. Peter Wong
School of Engineering
Peter.Wong@tufts.edu
617-627-2985
Research Opportunities, 2005
Alphabetically Listed by Research Mentor
Anselm Blumer (Engineering) and Alan Kopin (Sackler): The long range goal of this project
is to screen a collection of mutant fruit flies to find ones that show alterations in feeding behavior
or locomotion, and by this approach find genes that might be similar to ones responsible for
obesity in humans. The first task is to determine which flies in the collection of 25,000 that
contained mapped insertions have mutations at genomic positions likely to cause defects in
gene expression. The second task is to determine which subset of these show significant
homology to human genes. This should narrow the number of flies to be screened in
behavioral assays to a more manageable amount. For this purpose, we need help in
developing a computer program to automate searches of biological databases.
ablumer@cs.tufts.edu 617-627-3651 www.cs.tufts.edu/~ablumer/ and
www.neurosci.tufts.edu/kopin.html
Andrew Bohm: Protein crystallography, the primary technique employed by my laboratory, lies
at the interface between biochemistry and experimental physics. Data analysis is very
computer intensive, and we are interested in improving existing methods of collection of
diffraction data, molecular model building, and molecular dynamics refinement. We also want to
build small devices to facilitate sample handling, work out transformation matrices so that the
coordinate systems used by some of our hardware and software could be inter-converted, and
write drivers so that joysticks and other 3D interface devices could be productively used in
conjunction with our molecular modeling software. Andrew.bohm@tufts.edu. 617-636-2994
www.tufts.edu/med/biochemistry/faculty/bohm/bohm.html
Caroline Cao: Augmented reality simulators, not unlike many commercially available
videogames, are being used to train surgical skills. We are interested in exploring the use of
augmented reality for training dynamic surgical skills, and developing a multi-dimensional metric
to quantify the skill
performance. Caroline.Cao@tufts.edu 617-627-2484
ase.tufts.edu/faculty-guide/faculty.asp?id=ccao03&deptId=mecheng
Brent Cochran: The primary research focus of my laboratory is to understand how peptide
growth factors are able to regulate cell growth and differentiation. We have encountered several
problems that require computer science solutions. First, our research requires statistical
analysis of the large data sets generated using microarray technology to determine gene
expression. We need to use real and simulated datasets to compare the performance of several
methodologies for the analysis of this microarray data. In addition, we would like to use
computational linguistics to develop a text mining project tool which can construct biological
pathways. Another project involves the extension of our pattern matching algorithms to extract
phosphorylation site information and cellular localization information from Medline abstracts.
cochran@cochranlab.org 617-636-0442 www.cochranlab.org
James Dice: My research interest is in the lysosomal pathway of proteolysis that is activated
when cells are stressed. The activity of this protein degradation pathway, chaperone-mediated
autophagy, can be used as an indicator of cell stress to monitor cell response to different
bioengineered materials. In addition, I am interested in how cells take up and degrade
extracellular matrix materials such as collagens that are used as support matrices for artificial
organs. james.dice@tufts.edu 617-636-6707 www.tufts.edu/sackler/physiology/faculty/dice/
2
Kathy Dunlap: Research in our laboratory focuses on the molecular and biophysical
mechanisms underlying the modulation of voltage-dependent calcium channels and on
identifying the functional consequences of such modulation for synaptic transmission in the
nervous system. We use neurophysiological methods to understand how mutations in these
channels lead to neurological diseases. We are interested in someone who could help us
develop an efficient means of electrically stimulating cells in culture. kathleen.dunlap@tufts.edu
617-636-4942 www.neurosci.tufts.edu/dunlap.html
Eddie Goldberg: We work in Bio-Nanotechnology. We redesign genes to make bio-molecular
carpentry kits to develop a technology for massive parallel manufacture of new materials.
Biomimetic fabrication of functional protein nanostructures requires control of self-assembly.
The basic constructs are made of stiff, rugged protein rods of 10-100nm, to which molecular
moieties (nanocrystals to individual proteins) are attached at specific sites for function. Site
placement need not be monotonous and can form arrays on matrices, or open frameworks, in 1,
2 and 3 dimensions. Composite materials and devices are hierarchically assembled, from
nanometer to macroscopic level as porous, non-random, functional materials for various
biological and non-biological applications, from light structural reinforcement and boundaries, to
composite materials for separation, catalysis, tissue
engineering and diagnostics. Reference: Hyman, P., Valluzzi, R. and E. Goldberg. 2002.
Design of protein struts for self-assembling nanoconstructs. Proc. Natl. Acad. Sci. USA
99:8488-8493. eddie.Goldberg@tufts.edu 617-636-6754
www.tufts.edu/sackler/microbiology/faculty/goldberg/index.html
Ronald Hammer: Mesocorticolimbic circuits regulate sensorimotor gating in normal human
brains and dysfunction produces sensorimotor gating deficits in schizophrenia. The relevant
neural pathways involving various neurotransmitters have been studied, as have molecular
processes involved in signal transduction underlying sensorimotor gating. The interaction of
these circuits, signals and processes could be modeled in such a way as to predict behavioral
outcomes and develop testable hypotheses. The student will develop a model to represent this
process, and will test the model against experimental paradigms using acute and chronic
administration of various receptor agonists and antagonists that affect sensorimotor gating.
Ron.hammer@tufts.edu 617-636-8936 www.neurosci.tufts.edu/hammer.html
Daniel Jay: Our work on protein function in neurogenesis and cancer metastasis uses highthroughput functional screens that require knowledge of microfabrication and bioinformatics,
mathematical modeling of how cells and growing axons move and how force is integrated and
converted into cell movement, and biotechnology development using light to inactivate proteins
in living cells. Daniel.jay@tufts.edu 617-636-6714 www.tufts.edu/sackler/physiology/faculty/jay/
Alan Kopin (Sackler): Our research interests are focused in molecular endocrinology with an
emphasis on G protein-coupled receptors (GPCRs). Investigations are aimed at defining
structure-function relationships of GPCRs including the identification of ligand binding
determinants and the mechanisms of signal transduction (ligand and/or mutation induced).
Based on this expertise, the laboratory has developed molecular tools to expedite GPCR drug
discovery. We would like to conduct high throughput screening for drugs that affect GPCRs.
We are looking for a student who can adapt existing robotics for use with our assays. The
student would need to also find a suitable comentor in Engineering. akopin@Tufts-nemc.org
(617) 636-4834 www.neurosci.tufts.edu/kopin.html
3
Kyongbum Lee (Engineering): Our research is aimed at better understanding at a systems
level the metabolic regulation in cells and tissues in vivo and in vitro in order to optimize the
performance of tissue engineered therapeutic devices as well as elucidate mechanisms of
disease. Current projects include metabolic control of adipose tissue expansion, optimization of
stem cell differentiation on nano-crystalline ceramics, and development of novel biosensors for
real-time metabolite detection. Kyongbum.Lee@tufts.edu 617-627-4323
ase.tufts.edu/chemical/faculty-staff/faculty/lee.asp
Natesa Pandian: Our work focuses on 3D ultrasound imaging of the heart in health and
disease. Specific projects include determining volume:mass relations of the left ventricle (the
main pumping chamber) in heart failure patients.
NPandian@tufts-nemc.org 617-636-6151 www.tufts-nemc.org/medicine/card/CardImaging.htm
Susan Roberts: We study the dietary composition factors and eating behaviors that cause
overeating and weight gain at different stages of life. We are very interested in collaborating
with engineers to create inconspicuous ways of measuring or verifying dietary intake and
physical activity. Projects in our research group would involve the development and validation
of a remote data collection system for food intake and body weight, perhaps by creating a
radiowave communication network for data collection within subjects' houses.
Susan.Roberts@tufts.edu 617-556-3238 hnrc.tufts.edu/scientists/people/sroberts.php
Satyapriya Sarkar: Our research involves the structure and function of muscle proteins in the
Ca 2+ regulation of vertebrate striated muscle contraction. We use a multidisciplinary approach
to study how biological motion in striated muscle is regulated by “information transfer” through
multi protein complexes. We are also interested in how this process is correlated with the
structure and function of the genes encoding these proteins. Computer assisted analysis of
nucleotide and amino acid sequences is an important component of these studies. We also use
biophysical approaches such as fluorescence enhancement and/or decay of appropriately
labeled native and mutant proteins circular dichroism and isothermal calorimetry to study protein
– protein interactions involved in this biological system. The ongoing projects deal with the
mechanistic aspects of muscle biology and physiology. Participation in these projects should
expand the perspective of engineering students in biological systems.
Satyapriya.sarkar@tufts.edu 617-636-2931www.tufts.edu/sackler/facultyIntros/sarkarS.html
Barry Trimmer & David Kaplan: A project in our group would involve the design & fabrication
of biologically inspired, soft-bodied robots. Most of today’s crawling robots are constructed with
hard materials, motorized actuators and rigid “skeletons” that have a limited range of
movements. However, most crawling animals have soft-bodies that use combinations of fluid
(hydrostatic), and tissue pressure (muscular hydrostats), to provide stiffness against which
muscles can work. Such movements are particularly interesting from a neural control
perspective. With no easily defined joints, each muscle contraction has the potential to move the
body in any plane and to cause crumpling, rotation and complex bending; little is known about
how such behaviors are organized. None of the current multisegmental crawling robots
adequately mimic the remarkable abilities of soft-bodied animals, for example they do not climb
and do not have the static and dynamic stability of caterpillars. In this collaborative project we
will begin to design and fabricate soft bodied robots based on principles learned from our
kinematic and physiological studies of the tobacco hawkmoth (Manduca sexta) caterpillar.
These robots have potential applications in navigating pipelines and wiring conduits or in the
exploration of intricate biological structures such as guts, blood vessels and air tubes. Specific
topic areas include the design and fabrication of instruments to measure biomechanical
properties; measurement of mechanical performance by caterpillars; designing neurally inspired
4
control systems; testing novel actuators (such as artificial muscles), and modeling of motor
patterns or deformations by finite element analysis.
barry.trimmer@tufts.edu 617-627-392 Ase.tufts.edu/BIOLOGY/faculty/bios/trimmer/trimmer.html
Paula Watnick: My laboratory studies the genetic basis of adhesion of pathogenic bacteria to
surfaces. We are currently in the process of designing flow cells that we can use to study this
process microscopically. We wish to more closely simulate the natural forces that these
bacteria would encounter in the environment and upon colonizing tissues and analyze how gene
expression patterns change during this process. Paula.Watnick@tufts.edu 617-636-2545
www.tufts-nemc.org/infdisease/faculty_individuals/Paula_Watnick.html
5
TUFTS BIOMEDICAL RESEARCH EXPERIENCES
FOR ENGINEERING MAJORS
APPLICATION
Name:
____________________
Expected Graduation Year:
____________________
Major(s):
____________________
____________________
Minor(s):
____________________
____________________
Academic Advisor(s):
____________________
____________________
Mailing Address:
____________________
____________________
____________________
Telephone:
____________________
Email Address:
____________________
Mentor with whom you are applying:
____________________
Names of people submitting
letters of recommendation on your behalf:
____________________
____________________
Applicant’s signature affirming agreement to
program requirements
____________________
6
Applicant Requirements




You must have a GPA of 3.0 or greater.
You must be a Tufts sophomore, junior or senior during the 2005-2006 academic year
and a U.S. citizen or permanent resident.
You must submit your application following the instructions described below.
You and your mentor must agree to the expectations outlined below.
Application Procedure
Applicants must submit 2 copies of the application to Dr. Peter Wong, Anderson 109, or send it
in .pdf format via email to Peter.Wong@tufts.edu by 11AM on Friday, March 11.
The completed application contains the following:
1. Completed Application Form.
2. College transcript. An unofficial copy printed from SIS online is acceptable. Transfer
students should include their transcript from their former institution.
3. A description of your project (not more than 1000 words). Please include the following
components:
 A description of the question to be explored and how engineering or computer
science will be applied to this biological problem
 A brief statement as to why this question is important
 Project location
4. A personal statement (not more than 1000 words). This essay should address your
interest in exploring the connections between engineering and biomedical science and
your plans for the future. If you have had previous research experience, please describe
it.
5. A letter of collaboration written jointly by the student and mentor, signed by both.
The letter should include the following components:
 Explanation of how the student’s and mentor’s research interests are similar
 Proposed timeline of events
 Expectations for those involved with the project
Completed applications must be submitted by 11AM on Friday, March 11, 2005. Any
applications received after that date will be considered only if space is available.
Letters of Recommendation
Applicants must submit at least one and no more than two letters of recommendation. At least
one of these letters must be from a current Tufts faculty member.
These letters may be submitted with the application or sent separately to Dr. Peter Wong,
School of Engineering, Anderson 109, or by e-mail to Peter.Wong@tufts.edu. All letters must
be received by 11 AM on Friday, March 11.
7
Student Expectations
Employment
 Students may not be otherwise employed during the summer program without consent
from the Program Directors before the application is submitted.
 Enrollment in courses relevant to the research project is permitted, but only with the
express consent of the Program. Plans for Summer School should be mentioned in the
application; questions concerning Summer School should be addressed before
application is made.
Residency
 Students may work at any one of Tufts’ three Massachusetts campuses
(Medford/Somerville, Boston, Grafton) or at one of Tufts’ affiliated hospitals or clinics.
 Recipients must arrange their own housing.
 On-campus housing can be arranged if necessary.
Research Project
 Must be supervised by a Tufts faculty member.
 Must involve an application of engineering or computer science to biomedical research.
 The project will conclude with written and oral presentations.
o A written report on the results of the summer research to one’s mentor and to the
Program Directors (3-5 pages).
o You will be asked to participate in a poster session put on by the Program, and in
the Tufts Undergraduate Research and Scholarship Symposium in the Spring of
2006.
Mentor Expectations
A core component of the program is the joint commitment between faculty/clinical mentors and
students during the research process. Faculty mentors are expected to work with the students
to design a project that is sufficiently well-defined so that meaningful progress can be made
over the summer session. Development of a timetable and milestones is encouraged to ensure
that the project can be managed within the time frame of the program.
During the summer internship period, the mentor has the following responsibilities:
 Train the student in the necessary skills or assign a competent member of the laboratory
to this role
 Help the student understand how the project fits in the broader scope of the laboratory’s
research goals and how the research is addressing important questions in the mentor’s
field
 Supervise the student’s research project, and if necessary, assign a graduate student or
post-doctoral research associate for day-to-day interactions with the intern
 Assist in preparation of the written proposal, the final written report, and the poster
presentation
 Provide an evaluation of the student at the end of the summer.
 Actively participate in the poster session and in the Tufts Undergraduate Research and
Scholarship Symposium (see ase.tufts.edu/symposium).
8