|Dr. Rob Jackson, Director
Center for Neuroscience Research
Welcome to the first electronic newsletter of the Tufts Center for Neuroscience Research.
It is hard to believe that our center has been here at Tufts for almost 4 years. The CNR
was established in October 2003 coincident with the award of a center grant from the National
Institute of Neurological Disorders & Stroke (NINDS) to Tufts University School of Medicine (TUSM).
Since its inception, the mission of our center has been to augment the research capabilities
of NINDS and other neuroscience investigators at TUSM and its affiliated hospitals through
the provision of shared research core services. Our center now supports 5 different TUSM
shared research cores that provide services to facilitate advanced microscopy (fluorescence,
confocal & electron microscopy), electrophysiology, rodent behavioral studies and gene
expression profiling/computational genomics. All cores are supervised by Ph.D.-level
managers who provide training and help with experimental design and data analysis.
A full-time administrator supervises all center activities.
In addition to the research cores, the center has initiated two different small grant award
mechanisms (a collaborative research pilot grant award and a core award) that stimulate
collaborative neuroscience research efforts at TUSM and its affiliates. These programs are
possible thanks to generous contributions by the Tufts Medical School Dean and the Tufts Vice
Provost's office. For additional information about grant opportunities or other center activities,
please see the CNR website.
In my opinion, the most valuable resources of our center are the faculty and staff who have
dedicated - and continue to dedicate - time and effort to creating a successful TUSM enterprise.
We have been remarkably fortunate in attracting talented, motivated scientists and administrators
to the center. As the center enters its fifth year of operation, we are lucky to have such a
talented pool of individuals associated with it. You can read about some of these individuals
in the sections that follow.
I invite you to make use of our shared research facilities. If you have questions about the
CNR and its activities, please contact me or any other member of the center. We look forward
to continuing to serve the research programs of the neuroscience community at Tufts University
and its affiliated hospitals.
Rob Jackson, Director
Tufts Center for Neuroscience Research
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Spotlight: Alenka Lovy-Wheeler | Imaging Core Manager
The Imaging facility's latest appointment, Dr.Alenka Lovy-Wheeler, who started working
for the CNR last December, has become an outstanding success both for her technical
expertise as well as her sunny personality. Alenka comes to us from University of
Massachusetts (Amherst), where she did her Ph.D. in Plant Cell Biology under the
guidance of Dr. Peter Hepler. She has extensive experience in live cell imaging,
training of users on the confocal microscope and a keen interest in pursuing a career
in research. Having accepted the position of Imaging Facility Manager at the CNR, Alenka
relocated to Boston and finds it "invigorating to be in such a dynamic environment".
Q: How do you like working at the CNR?
Dr. Alenka Lovy-Wheeler,
Imaging Facility Core Manager
A: I love it! I enjoy being exposed to such a variety of research
projects. The opportunity to assist in these projects never fails to stimulate me.
Also, I have met some wonderful people her at Tufts and I'm very grateful to find myself
in such a collaborative and collegial atmosphere.
Q: Speaking of collaborations, care to share your research interests?
A: In grad school, I worked on cell polarity, specifically the
contribution of the cytoskeletal protein, actin, to the growth of pollen tubes. Using
confocal and electron microscopy, I studied the structural features of actin and also
followed pH microdomains in growing cells. Since coming to Tufts, I have been interested
in pursuing research in actin or other cytoskeletal protein dynamics and their role in
Q: And was it your research that helped develop your versatility with imaging techniques?
A: Yes, just looking at actin in the apex of pollen tubes, I used
differential interference (DIC), wide-field fluorescence, confocal and electron
microscopy. I've also used ratiometric dyes, wide-field fluorescence and time-lapse
microscopy in my work monitoring pH changes in growing pollen tubes.
Q: Does the CNR's Imaging Facility support these techniques?
A: Not only does the Imaging core have instruments (confocal, 2-photon
and 3-D imaging software) to support the techniques I mentioned, we also have a Laser Capture
Microdissection system (LCM) with which researchers can isolate single cells or groups of
cells to analyze RNA/DNA content. Users of the CNR are also welcome to avail of the Zeiss
Axiovert, run by Dr. Kathleen Yee in Anatomy, which is great for phase-contrast, time-lapse,
wide-field fluorescence and ratiometric imaging.
Q: The Imaging facility was recently relocated - what's your take on the new location?
A: Our recent move to Stearns 207 has had a very positive impact on the
facility - the space is much bigger, we have better airflow and temperature control, and
more bench space to prepare samples. There is a fume hood for LCM preparations, which is
now housed in a separate room that eases dehumidification. All round, the move also has
a more aesthetic and functional appeal, and my plants seem to enjoy, as I do, the sunlight
and the space :-)
Q: Any up-coming events/changes you'd like to share with us?
A: It's very exciting that Dr. Stephen Bunnell has made the Perkin-Elmer
Spinning Disk Confocal microscope available to researchers for live cell work. This confocal
can acquire optical sections of fluorescently labeled cells much faster than the Leica
confocal, making it the instrument of choice when examining fast dynamic processes.
I will be happy to help Dr. Bunnell train researchers on the use of the spinning disk
confocal. The instrument is run by Metamorph software, which I would like to purchase
for the Imaging Facility to aid with image analysis. This software is present at the
Zeiss Axiovert run by Dr. Yee, and used by other professors across departments, opening
up the possibility of sharing image analysis protocols. I've attended a helpful training
workshop on the use of Metamorph this summer as part of product evaluation, and am interested
to hear from people about their image analysis needs. I will become more informed on this
topic when I attend the "Optical Microscopy and Imaging in Biomedical Sciences Course" at
the Marine Biological Laboratory in Woods Hole this October 9-17, which I am REALLY looking
forward to. Please let me know if you have any microscopy techniques/image analysis
questions as I will be in contact with many microscopists and can gather lots of useful
Q: Is there any specific information you would like existing/future CNR users to be aware of?
A: Users of the imaging facility are asked to stay current on Imaging
Facility Updates by reading the blog (see link below). This is where the status of the equipment
will be reported, such as problems the instrument is having, whether the configuration of the
microscope is upright or inverted, and the date that data will be erased from the hard drive
(every two weeks).
The inverted microscope can perform all functions of the upright microscope. However, when using water
lenses and samples without coverslips, the upright is favorable. To change between these microscopes, the scanhead,
(or heart of the confocal) needs to be moved—risking possible damage and multiphoton laser misalignment.
Because the upright microscope cannot accept light from the multiphoton laser, the confocal will be in the
inverted position most of the time. Mondays, Tuesdays, and some weekends can be dedicated for the upright
configuration if people request it. When technical assistance is required, please email me
prior to signing up for time on the microscope.
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Genomics @ the CNR
The CNR Genomics Core is directed by Dr. Alan Kopin, and managed by Dr. Lakshmanan (Lax) Iyer and Chris Parkin, MS.
Lax joined the Tufts community last May from the Bauer Center for Genomics Research (now, FAS Center for
Systems Biology) at Harvard. Chris comes to Tufts from the Rochester Institute of Technology, where
he recently completed his Masters degree in Bioinformatics.
|Lakshmanan Iyer, PhD|
Genomics Core Manager
Among the challenges faced by computational biologists is how exactly to address the
needs of other investigators. The mission of the core is to provide investigators with
tools and services for keeping up with the never-ending flow of biological data. With the help of Yue Shao and her lab expertise, we also have
the ability to run complete gene expression experiments and analysis on our recently acquired Affymetrix GeneChip
To make the analysis a more interactive experience for investigators, we are currently
working to implement an online interface known as CARMAweb,
which is expected to go live within the next two months. We also plan to provide a
gene set enrichment analysis on gene expression data with neuroscience-specific gene sets. Further,
efforts are underway to provide the ability to link directly to the Allen Brain Atlas, which contains detailed
images of mapped gene expression in the mouse brain (see FOCUS section to the right).
While gene expression experiments tend to be the most widely used service offered by the Genomics
Core, we are always happy to assist users with any of their computational needs. Whether it's querying
online resources, sequence analysis, statistical analysis, data mining, or just to discuss new project ideas,
don't hesitate to contact us.
We also have a number of software licenses including GeneSpring GX, Imagene,
Ingenuity Pathway Analysis, SAS, TRANSFAC, and various other online databases.
|Chris Parkin, MS|
Bioinformaticist - Genomics Core
Periodically check the Genomics core website
for updates as new tools are developed.
For further questions, please contact Lax or Chris at Lax.Iyer@tufts.edu or
ALLEN BRAIN ATLAS
The Allen Institute for Brain Science
has created a created a detailed, high resolution, genome-wide map of gene expression
in the mouse brain. For more information on this project, please visit their home page
Genomics Core Expansion
The CNR and TEAC facilities have always worked very closely together, and this year we are happy to
formalize this collaboration by incorporating the TEAC facility under the umbrella of the CNR Genomics Core. The Expression Array facility has also moved into new space and is located in Stearns, Room 208C, adjacent to the CNR Imaging facility.
While the facility has two microarray platforms (1-color and 2-color), usage indicates that the
Affymetrix system is gradually becoming more popular amongst researchers here at Tufts. Yue Shao,
who continues to serve as the manager of this facility, has superlative knowledge of the Affymetrix
system and enjoys assisting researchers in running Q-PCR experiments.
Yue Shao, MS, stands next to the recently-acquired
Affymetrix 3000 hybridization platform.
Although the TEAC facility is happy to provide reagents/supplies for a limited number of assays,
we encourage users to purchase their own supplies/reagents/chips if they intend to use the facility
for large-scale experiments. Please note that all users are requested to fill out a profile form
BEFORE using the facility as this information will be entered into the CNR usage database.
For billing information, you may contact either Yue Shao or the CNR administrator, Tabitha
For detailed information on instruments, services and rates, please check the CNR Genomics Core Page.
Please contact Lax Iyer regarding planning and design of
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The Electrophysiology and Biophysics Core Facility (EBCF)
What can we do for you? The CNR's EBCF, under the able day-to-day management of Dr. Chuang Du
continues to expand its offerings and usage continues to rise. The facility, located in the Dunlap
lab on Tupper 11, provides equipment, expertise, and training to non-electrophysiologists interested
in using these methods to broaden their own research programs. Three setups are presently fully
functional and in use: a dissociated cell recording setup, a tissue slice field recording setup,
and a single cell slice recording setup. The latter was completed most recently, and its
capabilities have attracted new users to the EBCF. In particular, Shabrine Daftary, a postdoctoral
fellow in Dr. Maribel Rios' lab has been this setup's most active user. This setup is allowing
Shabrine to explore the role of brain derived neurotrophic factor in serotonin receptor signaling
in the brain, comparing the physiology of amygdala slices from wild-type and BDNF-knockout mice.
Electrophysiology Core Manager
What else is new? A recent and generous equipment donation from Baraba Talamo and John Kauer has made it possible to begin construction of a fourth setup in the EBCF. This new setup will allow rapid, simultaneous electrophysiological and fluorescence measurements on single dissociated cells. Stay tuned—we will let you know when this state-of-the-art recording station is ready for use.
For more information about EBCFs current and future services, fee structure, etc., please visit the electrophysiology core website or call Kathy Dunlap (64942) or Chuang Du (64938).
Behavior Core Update
The CNR Behavior Core has added to its existing experimental protocols to test for
cognitive impairment, which include the active and passive conditioned avoidance tasks
In addition to the shuttlebox apparatus (LM100 Learning & Memory System; Hamilton/Kinder) which is
used for conditioning avoidance response, the core recently purchased a contextual fear conditioning
apparatus which allows the user to administer a variety of stimuli including shock, tone and cue
lights. During the training day, a set of simple commands pairs the shock with the cues and invokes
a freezing behavior from the subject. On the following day the subject is tested without the foot
shock to see if the subject has "remembered" the pairing. The system comes with our new 7 x 15 beam
High Density Cage Rack System which has been designed especially for mice.
|Fear Conditioning Apparatus|
Since this summer, we have several PIs that are using the facility on almost a daily basis; indeed,
Dr. Jeanne Fahey, who manages the core, is acquiring a new laptop for the facility in order to
better serve the increasing number of users. Researchers are requested to ensure that they check
with Dr. Fahey about available time slots, before going to the core, as it serves to ensure the
smooth running of the different projects within the facility. Consultations with Dr. Fahey can also
be arranged by emailing her at Jeanne.Fahey@tufts.edu.
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PILOT AWARDS 2007
The CNR Pilot Award has been in place for three years now, and is awarded to support
collaborative projects amongst Tufts neuroscientists, particularly with a view to gathering
preliminary data that might eventually contribute to an NIH grant submission. As always, we
would like to thank the Office of the Vice Provost and the Medical Dean's Office for their
generous funding that makes this effort to foster collaborative research a possibility. The
2007 recipients are as follows:
|Dr. Karina Meiri and Dr. Kathleen Yee were awarded Pilot funds this year
to support their project, entitled "Molecular Regulation of Sensory Mapping". Drs. Meiri
and Yee are interested in gathering data that will allow them to directly compare effects
of GAP-43 on the primary auditory and visual pathways with the barrel system. The project
involves the complementary expertise of Dr Karina Meiri, who generated the GAP-43 (-/-)
mouse, and who established the initial data on the somatosensory system, and Dr Kathleen
Yee, an expert in developmental anatomy of the CNS to investigate the extent and location
of the visual and auditory deficits in GAP-43 (-/-) mouse. The CNR Genomics, Imaging and
Behavior cores were used in this project.
||Dr. Mercio Perrin and Dr. Arthur Tischler collaborated on a project to study
the characterization of a novel GDNF family ligand, P-GFL (parasite-derived GFL) in
Trypanosoma cruzi, the parasite responsible for Chagas' disease. Their aim was to collect
enough data over the course of the year about the structure and function of P-GFL to submit
an NIH grant application to study the role of this ligand in Chagas' disease. CNR funds were
mainly used towards purchase of necessary supplies and mass spectrometry charges at the
Tufts Molecular Core.
||A third award was given this year to Drs. Henry Querfurth, Jon DeGnore and Jin Xu
for their collaborative work on the role of Parkin (an E3 ubiquitin-protein ligase) The
team are testing the hypothesis that parkin has cross-disease function to target degradation
of misfolded proteins by the proteasome in Alzheimer's disease for ubiquitin (Ubq)-dependent
clearance by showing covalent Ubq linkage using mass spectrometry. The demonstration that
β-amyloid undergoes direct ubiquitination or sumoylation has large implication for
pharmacological efforts designed to improve neuronal viability and synaptic function by
increasing its removal.
Congratulations to the recipients of this year's Pilot awards! Application deadlines for
the forthcoming cycle of awards will be announced shortly - please check the CNR website
for dates and more detailed information. All questions concerning the awards can
be directed to the Center Administrator.
Core Awards 2007
In addition to the Pilot Awards, this year the CNR started a new award mechanism -
the Core Award - which is also meant to support neuroscientists in their efforts to
obtain sufficient evidence to prepare data for a grant submission. The major
differences between the Core and Pilot Awards are as follows:
- » The Core Awards can ONLY be used to pay for core services at the CNR and/or at the Tufts Molecular Facility (mass spectrometry).
- » The Core Awards are smaller and limited to $3,000 per recipient
- » The Core Awards have a rolling deadline, i.e. researchers may apply any time during the year.
In 2007, Dr. Douglas Vetter was given a core award to support his research on the
role of the olivocochlear system in normal synaptic development. Dr. Vetter used the
Genomics core (Affymetrix) to examine gene expression in the inner ears of normal
mice at distinct postnatal ages along with two transgenic mouse lines, the α-9 and the
SK2 nulls, that possess altered olivocochlear innervation to cochlear hair cells,
albeit in opposite directions - α-9 inducing a hypetrophic and SK2 a
hypotrophic/degenerative response by the synaptic terminal.
For more information on the core awards, please visit the
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What's new in the CNR?
- Facility has moved to Stearns second floor (ST207D)
- Spinning Disk Confocal available to users through Dr. Stephen Bunnell's lab.
Please refer to the web site for more information and rates.
- TEAC has been relocated to Stearns as well (ST208C)
- TEAC rates have been decreased this summer - please refer to the
CNR website or contact Yue Shao for the most current rates.
- Gene Set Enrichment Analysis (GSEA) of expression data using neuroscience-related gene sets
as well as gene sets available from the Broad Institute.
** We welcome your comments, suggestions and questions regarding our newsletter!
Please direct them to the Center Administrator.
Recent CNR Publications (selected list)
* please note that individuals outside of Tufts network may not be granted free access to the articles below.
Byrnes, E. M., Bridges, R. S., Scanlan, V. F., Babb, J. A., and Byrnes, J. J. (2007). Sensorimotor gating and dopamine function in postpartum rats. Neuropsychopharmacology 32: 1021-1031.
Chan, J. P., Unger, T. J., Byrnesa, J., and Rios, M. (9-29-2006). Examination of behavioral deficits triggered by targeting Bdnf in fetal or postnatal brains of mice.
Neuroscience 142: 49-58.
Draper, I., Kurshan, P. T., McBride, E., Jackson, F. R., and Kopin, A. S. (2-15-2007). Locomotor activity is regulated lay D2-like receptors in Drosophila: An anatomic and functional analysis.
Developmental Neurobiology 67: 378-393.
Li, S. M., Tian, X. J., Hartley, D. M., and Feig, L. A. (12-5-2006). The environment versus genetics in controlling the contribution of MAP kinases to synaptic plasticity.
Current Biology 16: 2303-2313.
Li, S. M., Tian, X. J., Hartley, D. M., and Feig, L. A. (2-8-2006). Distinct roles for Ras-guanine nucleotide-releasing factor 1 (Ras-GRF1) and Ras-GRF2 in the induction of long-term potentiation and long-term depression.
Journal of Neuroscience 26: 1721-1729.
Liu, W., Zscheppang, K., Murray, S., Nielsen, H.C., Dammann, C.E. (Jul 2007). The ErbB4 receptor in fetal rat lung fibroblasts and epithelial type II cells. Biochim Biophys Acta. 1772(7):737-47.
Olsen, D. P., Dunlap, K., and Jacob, M. H. (2007). Kainate receptors and RNA editing in cholinergic neurons.
Journal of Neurochemistry 101: 327-341.
Suh, J. and Jackson, F.R. (8-2-2007). Drosophila Ebony activity is required in glia for the circadian regulation of locomotor activity.
Neuron 55 (3): 435-447.
Zscheppang K., Liu, W., Volpe, M.V., Nielsen, H.C., and Dammann, C.E. (Aug 2007). ErbB4 regulates fetal surfactant phospholipid synthesis in primary fetal rat type II cells. Am J Physiol Lung Cell Mol Physiol. 293(2):L429-35.
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