Past Pilot Project Programs
Each year, CEHS solicites pilot project
applications
through support of the NIH-NIEHS Center Grant P30-ES002109. Below are the previous recipients:
HIGHLIGHTS From 2007
Sangeeta Bhatia
Assistant Professor
Harvard-MIT Division of Health Sciences & Technology and
Electrical Engineering & Computer Science
"Microscale Engineered Liver Tissues for Evaluating Chronic Toxicity of Environmental Toxicants"
Associate Professor
Department of Biological Engineering
"Development of a High-Throughput DNA Damage Sensor for Environmental Health Studies"
Jongyoon Han
Associate Professor
Departments of Electrical Engineering & Computer Science and
Biological Engineering
"Monitoring Low-Abundance Enzyme Activity by Preconcentration and Reaction in Micro/Nanofluidic Device"
Associate Professor
Departments of Electrical Engineering & Computer Science and
Biological Engineering
"Monitoring Low-Abundance Enzyme Activity by Preconcentration and Reaction in Micro/Nanofluidic Device"
Douglas Lauffenburger
Whitaker Professor Biological Engineering,
Chemical Engineering and Biology, and
Head, Dept. of Biological Engineering
"Systems Biology Analysis of Nuclear and Membrane-Initiated Signaling by Endocrine Disrupting Chemicals"
Lisiane Meira
Research Scientist
Center for Environmental Health Sciences
"A Clinical Study of a Base Excision-Repair Activity, Genetic Polymorphisms, and Chronic Inflammation"
HIGHLIGHTS From 2006
Patrick Doyle
Assistant Professor
Department of Chemical Engineering
"Technologies to Rapidly Scan Single Genomic DNA Molecules"
Prof. Doyle proposes to develop a microfluidic device that can rapidly map fluorescent moieties on single genomic DNA molecules. The specific aims of the project are to use finite elements and Brownian dynamics simulations to design a microfluidic genometry which will efficiently stretch single DNA molecules with electric field gradients, to fabricate microfluidic devices to quantify stretching of YOYO-labeled DNA, and to quantify mapping of YOYO-labeled DNA tagged with fluorescent nanoparticles conjugated to the restriction enzyme EcoRI. One of the ultimate goals of this technology will be to map the location of damage along single DNA molecules.
Associate Professor
Department of Chemistry
"Structural Studies of the AlkB Family of Proteins"
This research will focus on the
development of methods that will lead
to determining the crystal structure of the newly discovered AlkB class
of DNA repair enzymes that repair both alkylated and oxidatively
damaged DNA bases. A protein purification scheme for a human
homolog of the E. coli AlkB protein, hABH2, will be developed in order
to produce the quantity and quality of protein necessary for
crystallization experiments. Their goal is to begin
crystallization experiments, and to obtain data quality crystals of
AlkB and hABH2 and start the structure determination process.
Assistant Professor
Departments of Mechanical Engineering and
Biological Engineering
"Antisense gene regulation with nanparticle-DNA conjugates"
Prof. Hamad-Schifferli proposes to
develop a new nanoscale tool for
controlling antisense gene regulation remotely by an alternating
magnetic field. The PI will utilize nonparticles (NPs) that are
covalently attached to antisense DNA; such NPs can be heated by the
magnetic field and thus control translation in vitro. The
specific aims will be to construct NP-antisense DNA conjugates and
characterize their biophysical properties, to utilize NP-antisense DNA
conjugates to shut off translation, and to apply external fields to
control antisense gene regulation.
Chief, Comparative Pathology Laboratory
Division of Comparative Medicine
"Molecular determinants of liver tumorigensis following combined exposure to aflatoxin B1 and infectious hepatocarcinogens in a mouse model"
Dr. Rogers proposes to develop a
murine model system to investigate
synergy between environmental, infectious and host factors in liver
tumorigenesis. From the standpoint of the host they are focused
on two questions: what makes some mice prone to liver cancer while
others are resistant; why are males at greater risk than females. He
will characterize mutagenic, epigenetic, and metabolic perturbances
in a multiple risk model of murine hepatocarcinogenesis and identify
mechanisms of strain dependent and sexually dimorphic tumor
promotion.
Assistant Professor
Department of Materials Science and Engineering
"In vitro platforms to assess mechanically modulated environmental exposure"
The goals of this project are to
model, understand and modulate the
biological effects of environmental exposure to human health. It
is proposed to systematically explore the link between the mechanical
state of biological and engineered tissues with the genetic expression
profiles of adhered cells in vitro. The goals of this study will
be to develop and characterize the mechanical and interfacial chemical
characteristics of nanoscale polymeric films as a mechanically tunable
substrata for in vitro cell assays. Two cell types of interest to
the CEHS research cores will be used for this study; they will be tuned
to recapitulate the mechanical compliance of health stage-dependent
tissues, as well as comparably rigid surfaces used currently for
engineered tissues contracts. The genetic expression of key cell
surface receptors will be contrasted with the spatial distribution and
binding avidity of these receptors via functionalized force
imaging.
Director, Community Outreach & Education Program
Center for Environmental Health Sciences
"The Cell is a Molecular Machine"
The CEHS Community Outreach and
Education Program in collaboration with
the MIT Museum will develop an interactive exhibit entitled “The Cell
is a Molecular Machine”. The exhibit will include a large walk-in
section of a liver cell. Visitors will have he opportunity to
directly participate in the construction of a protein, building it
according to the instructions encoded in the cell’s DNA. They
will create LEGO proteins, produce channel proteins of the right
molecular shape and they will pace the newly folded structures into the
cell membrane, creating functional pores. The exhibit will
emphasize the molecular nature of life processes, and for many museum
goers it will radically change their idea about how a cell works.
HIGHLIGHTS From 2005
Martin Polz
Assistant Professor
Department of Civil and Environmental Engineering
"The Role of Exogenous Pathogens and Intestinal Microbiota in Colorectal Cancer"
Exposure to certain environmental
microbes, such as Helicobacter
pylori, is known to induce inflammation that leads to oxidative stress,
the formation of DNA adducts, and mutations, that ultimately result in
cancer. However, little is known about the role of endogenous
microbes, such as those that are normally found in our digestive tract,
in carcinogenesis. These microbes have been implicated in colon
carcinogenesis through their metabolism of secondary bile acids and
activation of pro-carcinogens, and touted as being protective against
carcinogenesis by the production of short-chain fatty acids and other
less well characterized anti-inflammatory mechanisms. To date, no
quantitative studies of microbial dynamics to investigate pro-carcinogenic and anti-carcinogenic populations in a relevant mouse
model of human colorectal cancer have been conducted. This pilot
project has, for the first time, utilized quantitative PCR and FISH to
characterize changes in endogenous intestinal microbial populations
after infection with environmental pathogens know to be tumor promoting
agents or carcinogenic agents in laboratory mice. These
preliminary findings will be confirmed and extended by monitoring
microbial populations during the progression of tumors through
carcinoma in situ and invasive adenocarcinoma. Intervention
studies will also be carried out by supplementing exogenous probiotic
species to ascertain if they provide anti-carcinogenic
properties. Ultimately, these studies are helping to clarify the
complex interactions of environmental agents, including pathogens and
chemicals, with endogenous microbes in the gut, that result in
oxidative stress, DNA damage, mutation, and increased cancer risk in
human populations.
Assistant Professor
Department of Mechanical Engineering
"Microfluidic Platform for High-Density Multiplexed Genetic Analysis"
Gene-environment interactions
underlie some of the most important
health issues related to the environment. To identify key genes
that modulate disease susceptibility, we need rapid and inexpensive
methods for high-throughput genotyping. This is especially
important in the context of large scale epidemiological studies, in
which scientific enquiry is often limited by the cost of genotype
analysis. Several platforms have emerged in the last decade to
probe the human genome (Affymetrix arrays, for example). Unfortunately,
current approaches have matured and the cost per sample
has stabilized, such that the cost of genotyping poses a significant
barrier to progress. The goal of this pilot proposal was to further
develop a combination of microtiter plate and microfluidics array
devices that performs genetic tests on a series of patient samples
simultaneously. This novel technology could potentially reduce the cost
of genotyping by three to five orders of magnitude (e.g., the cost per
target could be reduced from ~10 cents to ~0.0001 cents). Under
this pilot proposal, we developed elastomeric microfluidic devices that
can print high density DNA microarrays with dimensions as small as 10
µm. The devices, which hermetically seal to glass slides, pattern
hundreds of DNA probes in parallel as lines on the glass surface. DNA
samples are introduced into the sample entry ports and drawn along the
channels, where they are exposed to and bind to the slide. After
patterning, subsequent target-probe hybridization is simply achieved by
running fluorescently-labeled targets orthogonally over the probe
DNA-patterned glass slide using a second microfluidic chip. Using
devices that can be inexpensively and rapidly prototyped with 10 µm
wide microchannels, the hybridization spot density can be increased to
over 400,000 assays per cm2, equivalent to the number achieved by the
market leader, Affymetrix, through lithographic methods. Specific
milestones achieved follow:
○ 96 samples have been simultaneously tested against 96 probes in five minutes, resulting in 9,216 hybridization assays.
○ Sample volumes required for testing were reduced from 50 microliters needed by conventional hybridization platforms to 0.5 microliters for our microfluidic platform.
○ Microarrays were rapidly printed and hybridized without instrumentation or automation.
○ From 10 to 100 times lower target concentrations (picomolar) were detected vs. traditional microarrays.
Results from this project have
stimulated collaborations with several
investigators in the biological and clinical research communities, with
planned projects extending into the development of low cost-microarray
platforms for the genetic screening of pediatric samples and pathogen
screening in developing countries.
Forest White and Michael Yaffe
Assistant Professor (FW)
Biological Engineering Division
Associate Professor (MY)
Biology Department
"Phosphoproteomics of DNA Damage Repair"
Chromosomal DNA is constantly altered
by environmental and endogenous
agents, many of which induce DNA damage consisting of single-strand
breaks, double-strand breaks, and base-modifications. Our goal in
this project was to unravel the signaling pathways originating at
different types of DNA damage in human cells, focusing on the signaling
cascades associated with gamma irradiation, for which the ATM
(Ataxia-Telegiectasia Mutated) kinase appears to be critical. Since the
phosphorylation motif for ATM kinase has been
well-established, we chose to immunoprecipitate proteins or peptides
phosphorylated within this motif with an anti-phospho-S-Q-ATM.ATR
substrate antibody, following along our recently developed methodology
for tyrosine phosphorylation analysis. Preliminary studies
supported by this pilot project show that the proposed approach is
feasible pending improvements in the methodology for isolating ATM
kinase substrates (a subject of ongoing investigations by several
laboratories). This project represented a new line of research in
the White laboratory, away from global phosphorylation mapping and
towards studies of how environmental agents modulate serine/threonine
phosphorylation responses. Working on this project has exposed
the White laboratory to the importance of environmental health
sciences, which has in turn led to another new line of research focused
on investigating the effects of oxidative stress on kinase and
phosphatase activity in cellular signaling networks.
Bevin
EngelwardAssociate Professor
Biological Engineering Division
"Mechanisms of Chemotherapy-Induced Genetic Instability"
The goal of this pilot project was to
explore the long term effects of
exposure to DNA damage (persistent effects) and to explore the
possibility that communication between cells can affect genomic
stability (bystander effects). The potential impact of persistent
effects and bystander effects had not previously been studied in the
Engelward laboratory. Pilot project support for this work
resulted in the discovery that cells exposed to a DNA interstrand
cross-linking agent sustain an increased risk of de-novo sequence
rearrangements for more than 30 population doublings after
exposure. Furthermore, exposed cells can induce sequence
rearrangements in neighboring cells, which can in-turn induce similar
effects on a subsequent naïve population. These studies raise the
possibility that a significant portion of genetic change can be induced
indirectly, rather than via the direct effects, such as the ability of
DNA lesions to interfere with polymerase fidelity, for example.
Although for these particular studies the cross-linking agent was a
cancer chemotherapeutic, understanding the underlying pathways by which
exposures lead to mutations is fundamental in the context of
understanding the potential impact of environmental exposures on human
health. This work sparked a collaboration with Prof. J.
Greenberger of the University of Pittsburgh, where studies are ongoing
to investigate persistent and bystander effects in vivo. A grant
application in support of this work is currently pending. This
pilot project satisfied two of the goals for the Pilot Project Program:
it provided initial support for a new research area in this laboratory,
and it allowed for research studies that pose a significant departure
from ongoing research funded in this laboratory.
CONTACT INFORMATION
For information on the CEHS Pilot Project Program contact:Amanda Tat
Administrative Officer
MIT Center for Environmental Health Sciences
617-253-2848
atat@mit.edu
