|Dr. Rob Jackson, Director
Center for Neuroscience Research
This newsletter marks the beginning of year 10 for the NINDS-funded Tufts Center for Neuroscience Research (CNR).
As always, the newsletter highlights new CNR initiatives, new core personnel and changes that have occurred in core facilities supported by the center.
A major new initiative in the coming year will be a significant expansion of the CNR Animal Behavior Core, funded in part by a G20 construction grant awarded to Dr. Phil Haydon. The core continues to be
managed by Dr. Jennifer Newman who has contributed significantly to plans for the Core expansion. The expansion will result in new behavioral testing space and animal holding facilities. The CNR Imaging
Core – managed by Dr. Alenka Lovy – is actively used by neuroscientists and other university investigators. During this grant cycle alone, more than 80 Tufts laboratories have utilized instruments and
facilities of the Imaging Core. Dr. Lax Iyer continues to serve as Senior Manager of the CNR Computational Genomics Core, providing computational genomics and bioinformatics services to Tufts investigators.
Dr. Iyer is now joined by Ms. Hannah Raines, who supervises use of core equipment and facilities and provides training to new core users. The CNR Electrophysiology Core, under the management of Dr. Chuang Du,
continues to offer single-cell and tissue slice recording facilities. With the help of Dr. Eric Frank, the core will begin to help Tufts investigators integrate sophisticated in vivo multi-electrode recording
techniques into their research programs.
The center continues its Pilot Award and Core Award programs, which provide funds to Tufts investigators to promote new research areas and increase the likelihood of additional extramural funding for the university.
Letters of intent for the next Pilot Award application deadline are due May 1, 2013. Core Award applications can be submitted at any time and are reviewed on an ad hoc basis.
We are a successful center primarily because of the dedicated efforts of participating CNR faculty and staff. The center owes a special thanks to Ms. Megan Morgove (right) who continues to supervise the CNR
Administrative Core and all CNR activities. Contact information for participating faculty and staff is included at the end of this newsletter.
I urge you to take advantage of CNR core facilities, which are available to all Tufts investigators. Our mission is to support research efforts of Tufts neuroscience faculty and other investigators.
Additional information about the center is available through our website or by contacting Ms. Morgove, the center administrator.
Rob Jackson, Director
Tufts Center for Neuroscience Research
|Megan W. Morgove, Administrator
Center for Neuroscience Research
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SPOTLIGHT: THE MANY HATS OF DR. LAX IYER - MAKING COMPUTATIONAL BIOLOGY ACCESSIBLE TO EVERYONE THROUGH THE CBI
Dr. Lakshmanan Iyer (Lax) came to Tufts in October of 2006. You may know this Research Assistant Professor as the Senior Manger and Bioinformaticist
of the CNR Genomics Core, but when it comes to passion for Computational Biology, Lax's cup runneth over - and he is working to make this growing field
easy and accessible to the entire Tufts community. Armed with a Tufts Collaborates! seed grant from the Office of the Provost, Dr. Iyer makes moves to
promote Computational Biology in a collaborative environment through the CBI: Computational Biology Initiative.
Q: You seem to wear many hats as the CNR Bioinformaticist - working on multiple projects with different needs. And now you have
taken on the task of starting the Computation Biology Initiatve (CBI) at Tufts- Where do you find the time?
Lakshmanan Iyer, PhD
Genomics Core Sr. Manager/Bioinformaticist
A: I very much enjoy doing this work. As the CNR Bioinformaticist, my focus is serving the genomics needs within the Neuroscience
community. The Genomics Core is an accessible resource for researchers in the Neuroscience Department, facilitating the use
of bioinformatics techniques that might not have been utilized otherwise. Its a great mission - and through the CBI the goal
is to extend this accessibility accross all Tufts campuses. As for time, they say, "Work expands to occupy all time available"!
It gets hectic but I have very understanding and accommodating colleagues, especially my bosses so it works out fine.
Q: That's quite a undertaking! Who else is involved in this initiative?
A: First, the funding support from the Office of the Provost is making this possible. The foundation of the CBI is collaboration.
There are multiple groups closely involved to serve the CBI mission. Within Tufts University: University Information Technology
(UIT), the Office of Information Technnology (OIT), the Tufts Human Nutrition Research Center on Aging (HNRCA), Tufts Libraries,
Tufts Clinical and Translational Sciences Institute (CTSI), and The Center for Neuroscience Research of course. Within Tufts
Medical Center: the
Molecular Cardiolody Research Institute (MCRI), the Mother and Infant Research Institute, and the
Translational Immunology Science Center.
Q: You mentioned the CBI mission. What is it exactly?
A: The mission of the CBI is to "Raise awareness, enhance infrastructure and promote computational biology in a collaborative environment among
a diverse group of biologists, clinicians, high throughout technologists, information technology professionals, statiticians,
bioinformaticists and computational biologists at Tufts Medical Center and Tufts University." This mission is stated on our website which
will be going live soon.
Q: What type of outreach will be involved, to raise awareness as mentioned in the CBI mission?
The newly-designed CBI logo
Stay tuned for the launch of the new CBI website!
A: The CBI aready co-hosted a symposium last month, "Next Generation Sequencing: Applications for Transcriptome Studies"
and will host many more short courses in bioinformatics and genomics in early 2013. These events are recorded and can
be watched on the CBI website as well. The website will also include a discussion board where CBI members can post
comments or questions and stay updated on CBI events and Computation Biology research news. And the good old meeting
in the corridors or the street and catching up also works!
Q: Do you have to be a member to access the website? How does one become a member?
A: The CBI website will be open to the
public. However, we encourage membership. Members will be
able to indicate their research interests so that they may be ideally matched to the right resources. Furthermore,
we plan to use Tufts exclusive resources such Trunk web portal to share and disseminate private data and information.
To join, you can simply send me an email including your affiliations.
Q: With the CBI in existance, will your focus on Neuroscience research change?
A: The change will hopefully be that I am even more available for Neuroscience projects! Once the CBI is well established and in
use, researchers across the Tufts Community will have a one-stop online resource for genomic education and for
establishing research collaborations. Tufts Neurscientists can utilize the CBI of course, but I look forward to continuing
to be the main bioinformatics contact for Neuroscience projects through the CNR Genomics Core.
Q: What other projects do you have going on?
A: Many scientific collaborations! I am also working with Lionel Zupan of University Information Technology to develop a
suite of applications for Next Generation Sequencing Anlysis, to be available school-wide. UIT is a driving partner in the
Computational Biology Initiative. Additionally, I have an industry-academia collaboration to develop a web based neuroscience
resource. My interest truly remains in the research work that I do, and I am enjoying my current collaborations within the
Neuroscience Deparment and MCRI.
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The CNR Genomics Core
Genomics Core Technician
INGENUITY PATHWAYS ANALYSIS (IPA)
The CNR continues to contribute to making Ingenutiy Pathways Analysis (IPA) an available tool for all.
With help from Dr. Lax Iyer, the previous CNR IPA license was transitioned to a University-wide resource
during the Summer of 2011. The CNR sponsors this license along side the Hirsh Health Sciences Library
(HHSL), the Tisch Library and the University Information Technology (UIT) departments.
Welcome Hannah Raines, the new CNR Genomics Core Technician!
Hannah has come to us from Oregon State University, where she earned her B.S. in both Bichemistry and Biophysics.
During her schooling she also worked in Dr. Maret Traber’s lab at the Linus Pauling Institute, studying the mechanism
of vitamin E interference of vitamin K activity in rats, and becoming very familiar with RT-QPCR techniques, among others.
Hannah has recently moved to Boston to enter the Biochemical and Molecular Nutrition Graduate Program at the Tufts Friedman
School of Nutrition. We are thrilled to have her here!
Hannah will be in the core 10-15 hours each week, supervising equipment use and maintenance, and making herself available
for training and questions. She will post her hours on the Genomics Core room door (ST207a), and can also be reached at her
email address firstname.lastname@example.org.
Along with Hannah's supervision, the CNR Genomics Core is managed by Dr. Lax Iyer. The mission of the core is
to provide investigators with tools and services for keeping up with the never-ending flow of biological data.
We are always happy to assist users with any of their computational needs.
Within the CNR Genomics Core, located in Stearns, Room 207A, is our Expression Array Facility. This facility is equipped with instruments
and expertise for conducting gene expression studies. It contains instruments for nucleic acid analysis (Nanodrop and Agilent Bioanalyzer),
and two Q-PCR machines (Stratagene real-time cyclers). Sign-up for these instruments is easy through our
online sign-up calendars.
- Gene Expression Analysis
Our continued collaboration with the Yale Center for Genome Analysis (W.M. Keck Foundation) gives our users
a simplified process for their microarray analysis needs.
Researchers can drop off their samples at our facility, and with our negotiated Tufts pricing, we will arrange
for experiments to be carried out at Yale, and provide analysis of your data.
- DNA Sequencing through the Tufts Core Facility
We encourage Tufts researchers to utilize the high-throughput sequencing services of the
Tufts Core Facility.
We are happy to consult with you to ensure both your sequencing and analysis needs are met.
- Coming Soon - Multidisciplinary Short Courses in Genomics Analysis
Are you wondering how you can keep pace with the genomic revolution? Representatives from the Computational Biology
Initiative (CBI), Tufts CTSI, and Tufts University are pleased to offer five one-week courses to provide practicing
researchers with the skills necessary to perform cutting-edge analyses of genomic data. Courses are offered at no
cost and will feature an expert multidisciplinary team and a problem-based curriculum. Researchers at all levels
(techs, students, post-docs and faculty) are welcome to attend. Sign up for all five courses, or pick the topics that
most apply to you. Please visit the Tufts CTSI website for more details,
or contact Dr. Lax Iyer.
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IMAGING AND CELL ANALYSIS CORE
|Alenka Lovy, PhD|
Imaging Core Manager
The CNR Imaging Core continues to provide a broad range of imaging services to the Tufts community, and is the only shared imaging facility within the Tufts Medical School and Tufts Medical Center.
The core is managed by Dr. Alenka Lovy, Research Assistant Professor in the Neuroscience Department. Alenka supervises the day-to-day operations of the core and provides training and her expertise
to Tufts neuroscientists. She has extensive experience with multiple types of imaging equipment and techniques - she is a valuable resource to our users!
- »While the Nikon confocal system is being widely used, most users have yet to discover how Total Internal Reflection Fluorescence Microscopy (TIRF) can benefit their research. And our Nikon system is fully equipped! Stay tuned for information
on a TIRF workshop this Spring that will include system demos by Dr. Alenka Lovy.
- »There are two computers available in the core, separate from the microscopes, that can be used for image analysis. The software programs available are: Imaris 7.2, MetaMorph, and NIS Elements. Please sign up to use a computer, and record any Imaris
use on the provided log sheets.
|Dr. Fanny Ng, Supervisor of the A309 CNR scopes, stands next to the newly restored Nkon TE300 inverted microscope|
The newest member of the Imaging Core is the Nikon A1R confocal microscope, the acquisition of which was made possible by an NINDS instrumentation grant awarded to Dr. Lovy. Housed in Stearns
room 207 adjacent to our Leica TCS SP2 confocal, this new system has quickly become one of the heaviest used instruments within the CNR. Over 20 labs within the Tufts community have used this confocal
in the last year, totalling 2,400 hours of use!
Restored and Upgraded Microscopes Available!
The CNR recently restored and upgraded two Nikon microscopes: a Nikon E800 upright and a Nikon TE300 inverted. Both instruments are
fully equipped with brightfield/epifluorescence capabilities, digital cameras, and the most recent version of NIS Elements software.
- Plan Apo 2x, 4x, 10x, 20x, 40x, 60x and 100x objectives are available.
- Reserve time on these instruments using the Neuroscience online calendars.
- If it is your first time using the microscope (even if you are a skilled microscopist!) contact Dr. Fanny Ng (right)
- Don't need image acquisition? Want to qualify your samples before reserving the confocal? Use the CNR Zeiss microscope in A309! No sign-up required!
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The Electrophysiology and Biophysics Core Facility (EBCF)
Electrophysiology Core Manager
WELCOME DR. ERIC FRANK - CO-DIRECTOR
Dr. Chang Du continues to manage the CNR Electrophysiology facilities, which include three setups: one
dissociated cell patch-clamp setup, and two single cell slice recording setups. All setups are equipped with
epifluorescence capability. Dr. Du is in the core Mondays, Wedesdays, and every other Friday to assist users with equipment questions and training.
|Dr. Eric Frank, Professor of Molcular Physiology & Pharmacology|
Electrophysiology Core Co-Director
Dr. Eric Frank has joined the EBCF team! Dr. Frank's experience with combining in vivo and in vitro recording methods with behavioral
measurements, immunohistochemistry, and chronic in vivo druge delivery adds a new perspective to the core.
The two EBCF co-Directors, Dr. Kathleen Dunlap and Dr. Eric Frank, are available for consult and to provide expertise
to non-electrophysiologists interested in using these methods to broaden their own research programs.
For more information about EBCF's current and future services, fee structure, etc., please visit the Electrophysiology core website or call Kathy Dunlap (6-4010) or Chuang Du (6-6988).
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The Animal Behavior Research Core (ABRC)
|Behavior Core Manger, Dr. Jennifer Newman, stands|
in the South Cove 374 acoustic chamber, which
houses our Metabolic Cages
WHATEVER HAPPEND TO...
The aim of the CNR Behavior Core is to train researchers and provide behavioral testing services to neuroscientists. Using instruments that can assess motor,
sensorimotor, cognitive and emotional functions, the Core provides behavioral models for neuropsychiatric disorders that include
anxiety, depression, drug and alcohol abuse, aggression, schizophrenia, and memory impairment. The Behavior Core is available to help in all steps of
a study, including consultation for selection of the most appropriate assays, experimental design, behavioral testing, data analysis and graphical display of results.
You may remember seeing this email a year ago!
Plans still exist to expand the Behavior Core to more than double its size. Due to a NINDS G20 grant
(Grant for Repair, Renovation, and Modernization of Existing Research Facilities) awarded to Dr. Phil
Haydon in 2011, this expansion is possible. Final drawings are being reviewed, and you will be
notified as soon as a start date has been set.
The ABRC is located within the Department of Laboratory Animal Medicine on the third floor of the South Cove building (SC379), and consists of a rat housing room,
a mouse housing room, a surgery room, and 3 testing rooms. Rooms and equipment can be reserved at
- Our video camera is on the move - A small change makes a big difference! Our video camera is now mounted on an adjustable rod, to accommodate experiments that need
to be recorded at closer ranges.
- EQUIPMENT UPGRADE! With the start of the new grant year (Dec 1st), we have made it a priority to upgrade heavily used equipment and software that is outdated.
Stay tuned for more info on new Open Field activity frames, Elevated Plus Maze, and more.
- ANIMAL HEALTH SERVICES WORKSHOPS - Under the supervision of experienced DLAM staff, these courses are designed to teach a variety of basic rodent techniques
and to provide valuable information to investigative staff. These training sessions can also serve as a refresher course for those who need to practice techniques
that they haven’t utilized recently. Registration is required, and you must be included on an approved IACUC protocol and have your Occupational Health Clearance.
Please see the informational email sent out earlier this month for
more details, including workshop descriptions.
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PILOT AWARDS 2012
We thank the Office of the Vice Provost and the Medical Dean's Office for their generous contributions that make the CNR Pilot Award Program possible.
For the past eight years, this program has provided funds to support collaborative projects amongst Tufts neuroscientists. The award recipients for 2012-2013 are:
|Dr. Gizem Donmez and Dr. Emmanuel Pothos
were awarded Pilot funds this year to support their project entitled
"The role of SIRT2 in Parkinson's Disease." The project will test the effect of
deletion of SIRT2 gene by using a knockout mouse on a chemical model (MPTP) of
Parkinson’s Disease. It is hypothesized that deletion of SIRT2 will result in a reduction
of neurodegeneration in MPTP model, which will be measured by immunohistochemistry
(tyrosine hydroxylase (TH), Nissl and Neu-N stainings), apoptosis and behavior assays
and biochemical techniques. The CNR Imaging Core (fluorescence imaging), Genomics Core (qPCR), and Behavior Core
(Open-field, Rotarod and grip-strength tests) will all be used in this project.
||Dr. Maribel Rios and Dr. Beverly Rubin
are collaborating on a project entitled, “The role of hypothalamic brain-derived neurotrophic
factor (BDNF) in BPA-induced obesity." They will test the hypothesis
that diminished BDNF activity in the hypothalamus contributes to mechanisms triggered by bisphenol
A (BPA) exposure and that lead to obesity. They will furthermore seek to ascertain whether BPA reduces estrogen
receptor-alpha (ER-a) activity with concomitant decreases in BDNF signaling in the ventromedial
hypothalamus (VMH), an energy balance-regulating center. This work will include use of the CNR Imaging Core
(laser cature microdissection), the Genomics Core (qPCR), and the Behavior Core (food intake and locomotor
Congratulations to the recipients of this year's Pilot awards! Interested in submitting an application for the next cycle of awards? 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 2012
The Core Award mechanism was introduced in 2007. Like the Pilot AWards,
Core Awards are 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.
So far in 2012, Dr. Yongjie Yang was given a core award to support
his research which investigates the molecular/morphological changes of in vivo astrocytes from cortex and hippocampus in various
stages of pilocarpine-induced epilepsy model by employing novel astrocyte transgenic mice BAC ALDH1L1 TRAP and EAAT2-tdtomato.
For more information on the core awards, please visit the
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Recent CNR Publications (selected list)
* please note that individuals outside of Tufts network may not be granted free access to the articles below.
Butovsky O, Siddiqui S, Gabriely G, Lanser AJ, Dake B, Murugaiyan G, Doykan CE, Wu PM, Gali RR, Iyer LK, Lawson R, Berry J, Krichevsky AM, Cudkowicz ME, Weiner HL (2012). Modulating inflammatory monocytes with a unique microRNA gene signature ameliorates murine ALS.
Journal of Clinical Investigation 122(9):3063-3087.
Graham CE, Vetter DE (2011). The mouse cochlea expresses a local hypothalamic-pituitary-adrenal equivalent signaling system and requires corticotropin-releasing factor receptor 1 to establish normal hair cell innervation and cochlear sensitivity.
Journal of Neuroscience 31(4):1267-78.
Kang EL, Biscaro B, Piazza F, Tesco G (2012). BACE1 protein endocytosis and trafficking are differentially regulated by ubiquitination at lysine 501 and the di-leucine motif in the carboxyl terminus.
Journal of Biological Chemistry 2012 Oct 29. [Epub ahead of print]
Kittelberger KA, Piazza F, Tesco G, Reijmers LG (2012).Natural alyloid-beta oligomers acutely impair the formation of a contextual fear memory in mice.
PLoS ONE 7(1) e29940.
Kowalski JR, Dahlberg CL, Juo P (2011).The deubiquitinating enzyme USP-46 negatively regulates the degradation of glutamate receptors to control their abundance in the ventral nerve cord of Caenorhabditis elegans.
Journal of Neuroscience 31(4):1341-54.
Ng FS, Tangredi MM, Jackson FR (2011).Glial cells physiologically modulate clock neurons and circadian behavior in a calcium-dependent manner.
Current Biology 21(8):625-34.
Odajima J, Wills ZP, Ndassa YM, Terunuma M, Kretschmannova K, Deeb TZ, Geng Y, Gawrzak A, Quadros IM, Newman J, Das M, Jecrois ME, Yu Q, Li N, Bienvenu F, Moss SJ, Greenberg ME, Marto JA, Sicinski P (2012).Cyclin E constrains Cdk5 activity to regulate aynaptic plasticity and memory formation.
Developmental Cell 21(4):655-668.
Saaverdra-Rodriguez L, Feig LA (2012).Chronic social instability induces anxiety and defective social interactions across generations.
Biological Psychiatry 2012 Aug 18 [epub ahead of print].
Sarkar J, Wakefield S, MacKenzie G, Moss SJ, Maguire J (2011).Neurosteroidogenesis is required for the physiological response to stress: role of neurosteroid-sensitive GABAa receptiors.
Journal of Neuroscience 31(50):18198-18210.
Walker KR, Kang EL, Whalen MJ, Shen Y, Tesco G (2012).Depletion of GGA1 mediates postinjury elevation of BACE1.
Journal of Neuroscience 32(30):10423-10437.
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