You want to work in a lab, do you?

The Biology and Neuroscience Research Workshop on Nov 29 was very successful. Organizers estimated that between 60 and 80 eager undergraduates attended, most looking for advice on finding a research lab.  For those who could not attend, the powerpoint presentation, now available on the web, entitled “You want to work in a lab, do you?” has a lot of very practical advice on the process of finding a lab that is equally applicable to students in other disciplines.

see also: http://blogs.brandeis.edu/science/2011/12/20/funding-for-undergraduate-research/

Brandeis Undergrads Gain Awards at SACNAS

On October 29th, 2011, Brandeis undergrads Lamia Harper (’12), Charity Frempomaa (’12), Sadrach Pierre (’13) and Carlos Pérez (’13) from our local SACNAS chapter represented Brandeis at the Annual Conference of the Society for Advancing Chicanos and Native Americans in Science (SACNAS) in San José, California.  Lamia and Sadrach both received awards for their research poster presentations. Lamia, who works in the Paradis lab, won an award in the Cellular and Molecular Biology category for her poster: Gene Discovery: Protein Kinases that Affect Synapse Development in the Mammalian CNS. Sadrach, who works in the Thomas lab in Chemistry, was awarded under the Biochemistry category for his poster: Sulfoamide Boronic Acids as Inhibitors of Beta-Lactamase.

Biology and Neuroscience Research Workshop on Nov 29

Hey current and future science majors!

Are you interested in research, but don’t know where to begin or what your options are?

If so, join the Neuroscience and Biology UDRs at the first ever Biology and Neuroscience Research Workshop! Come and learn about the many options available, and find out how you can get involved in research.

The workshop will be held in the Shapiro Campus Center Multipurpose Room on Tuesday November 29th at 8:00pm, and food will be provided! If you’re considering doing research during your undergraduate career, then this is an event you don’t want to miss!

- Your Neuroscience and Biology UDRs

Sid Narayanan Monisha Rajinikanth Brian Slepian Roger Yang

Dynamics of double-strand break repair


In a new paper in the journal Genetics, former Brandeis postdoc Eric Coïc and undergrads Taehyun Ryu and Sue Yen Tay from Professor of Biology Jim Haber’s lab, along with grad student Joshua Martin and Professor of Physics Jané Kondev, tackle the problem of understanding the dynamics of homologous recombination after double strand breaks in yeast. According to Haber,

The accurate repair of chromosome breaks is an essential process that prevents cells from undergoing gross chromosomal rearrangements that are the hallmark of most cancer cells.  We know a lot about how such breaks are repaired.  The ends of the break are resected and provide a platform for the assembly of many copies of the key recombination protein, Rad51.  Somehow the Rad51 filament is then able to facilitate a search of the entire DNA of the nucleus to locate identical or nearly identical (homologous) sequences so that the broken end can pair up with this template and initiate local copying of this segment to patch up the chromosome break.  How this search takes place remains poorly understood.

The switching of budding yeast mating type genes has been a valuable model system in which to study the molecular events of broken chromosome repair, in real time.  It is possible to induce synchronously a site-specific double-strand break (DSB) on one chromosome, within the mating-type (MAT) locus.  At opposite ends of the same chromosome are two competing donor sequences with which the broken ends of the MAT sequence can pair up and copy new mating-type sequences into the MAT locus.

Normally one of these donors is used 9 times more often than the other.  We asked if this preference was irrevocable or if the bias could be changed by making the “wrong” donor more attractive – in this case by adding more sequences to that donor so that it shared more and more homology with the broken ends at MAT.  We found that the competition could indeed be changed and that adding more homologous sequences to the poorly-used donor increased its use.


In collaboration with Jané Kondev’s lab we devised both a “toy” model and a more rigorous thermodynamic model to explain these results.  They suggest that the Rad51 filament carrying the broken end of the MAT locus collides on average 4 times before with the preferred donor region before it actually succeeds in carrying out the next steps in the process that lead to repair and MAT switching.

Dynamics of homology searching during gene conversion in Saccharomyces cerevisiae revealed by donor competition Eric Coïc , Joshua Martin, Taehyun Ryu, Sue Yen Tay, Jané Kondev and James E. Haber. Genetics. 2011 Sep 27 2011 Sep 27

Cryo-electron tomography and the structure of doublet microtubules

In a new paper in PNAS entitled “Cryo-electron tomography reveals conserved features of doublet microtubules“, Assistant Professor of Biology Daniela Nicastro and coworkers describe in striking new detail the structure and organization of the doublet microtubules (DMTs), the most conserved feature of eukaryotic cilia and flagella.

Cilia and flagella are thin, hair-like appendages on the surface of most animal and lower plant cells, which use these organelles to move, and to sense the environment. Defects in cilia and flagella are known to cause disease and developmental disorders, including polycystic kidney disease, respiratory disease, and neurological disorders. An essential feature of these organelles is the presence of nine outer DMTs (hollow protein tubes) that form the cylindrical core of the structure known as the axoneme. The doublet microtubule is formed by tubulin protofilaments and other structural proteins, which provide a scaffold for the attachment of dynein motors (that drive ciliary and flagellar motility) and regulatory components in a highly specific and ordered manner.

To address long-standing questions and controversies about the assembly, stability, and detailed structure of DMTs , the Nicastro lab used a high-resolution imaging technique, cryo-electron microscope tomography (cryo-ET), to probe the structure of DMTs from Chlamydomonas (single-celled algae) and sea urchin sperm flagella. Cryo-ET involves:

  1. rapid freezing of the sample to cryo-immobilize the molecules without forming ice crystals,
  2. tilting the specimen in the electron microscope to collect ~70 different views from +65° to –65°,
  3. computational alignment of the views to calculate a tomogram (a three-dimensional reconstruction of the imaged sample), and
  4. computational averaging of repeating structures in the tomogram to reduce noise and increase resolution.

Cryo-ET provided the necessary resolution to show that the B-tubules of DMTs are composed of 10 protofilaments, not 11, and that the inner and outer junctions between the A- and B-tubules are fundamentally different (see figure). The outer junction, crucial for the initial formation of the DMT, appears to be formed by interactions between the tubulin subunits of three protofilaments with unusual tubulin interfaces, but one of these protofilaments does not fit with the conventionally accepted orientation for tubulin protofilaments. This outer junction is important physiologically, as shown by mutations affecting the usual pattern of posttranslational modifications of tubulin. In contrast, the inner junction is not formed by direct interactions between tubulin protofilaments. Instead, a ladder-like structure that is clearly thinner than tubulin connects protofilaments of the A- and B-tubules.

The level of detail also allowed the Nicastro lab to show that the recently discovered microtubule inner proteins (MIPs) located within the A- and B-tubules are more complex than previously thought. MIPs 1 and 2 are both composed of alternating small and large subunits recurring every 16 and/or 48 nm along the inner A-tubule wall. MIP 3 forms small protein arches connecting the two B-tubule protofilaments closest to the inner junction, but does not form the inner junction itself. MIP 4 is associated with the inner surface of the A-tubule along the partition protofilaments, i.e., the five protofilaments of the A-tubule bounded by the two junctions with the B-tubule.

The Nicastro lab plans to build on this foundation in future work on the molecular assembly and stability of the doublet microtubule and axoneme, and hope to use it to elucidate molecular mechanisms of ciliary and flagellar motility and signal transduction in normal and disease states.

Other authors on the paper include Brandeis postdocs Xiaofeng Fu and Thomas Heuser, Brandeis undergrad Alan Tso (’10), and collaborators Mary Porter and Richard Linck from the University of Minnesota.

New Computational Neuroscience Training Program

The National Institute on Drug Abuse has recently awarded Brandeis a pair of linked training grants to support student training in computational neuroscience. The program is unusual for NIH training grants in supporting both undergraduate and graduate student research. Funding for the program is approximately $1.8 million over the next five years.

Modeling a biconditional discrimination task, see Bourjaily & Miller, 2011

The program, directed by Professor Eve Marder, will support six Ph.D. students and six undergraduates (juniors or seniors) each year. Students must be working to fulfill an appropriate degree in the Division of Science at Brandeis, and must engaged in research in computational neuroscience. Said Marder,

We are extremely pleased to have received this grant, as it continues a long Brandeis tradition of integrating theory and experimental work in the neurosciences.  We are especially pleased to have the undergraduate component, as we know there are students who are interested in learning how to employ rigorous quantitative methods to study the brain.

Eligibility and program requirements to participate in the program will soon be available at the training grant website.

Some recent publications:

Bourjaily, M.A., and Miller, P. (2011). Synaptic plasticity and connectivity requirements to produce stimulus-pair specific responses in recurrent networks of spiking neurons. Plos Comput Biol 7, e1001091.

Piquado, T., Cousins, K.A., Wingfield, A., and Miller, P. (2010). Effects of degraded sensory input on memory for speech: Behavioral data and a test of biologically constrained computational models. Brain Res 1365, 48-65.

Berkes, P., Orban, G., Lengyel, M., and Fiser, J. (2011). Spontaneous cortical activity reveals hallmarks of an optimal internal model of the environment. Science 331, 83-87.

Grashow, R., Brookings, T., and Marder, E. (2010). Compensation for variable intrinsic neuronal excitability by circuit-synaptic interactions. J Neurosci 30, 9145-9156.

Postdoc with confessed aversion to genetics

“… now inspiring a new generation of neurophysiologists”

There’s a nice story on the ADInstruments website about Stefan Pulver (PhD ’09) and Nick Hornstein (’11) and the tools they developed in the Griffith lab for “Optogenetics in the Teaching Laboratory” using Drosophila and channelrhodopsin-2. Stefan is currently in Cambridge (England) doing a postdoc, and Nick is starting his MD/PhD at Columbia real soon now.

Brandeis Summer SciFest to be held on Aug 3

Brandeis Summer Scifest, an Undergraduate Research Poster Session, will be held on Wed, Aug 3 2011.   53 undergraduate students from across the Division of Science, including summer visitors and Brandeis students, will present posters on their work/research.  The poster session will run from 1-3 pm in the Shapiro Science Center atrium.

The public is cordially invited to attend and to discuss research with the students.

A listing of poster titles and abstracts is available at http://www.bio.brandeis.edu/UG/scifest-2011.pdf


Aug 4: The poster session went really well, we had a nice turnout and the students did a great job presenting.

Photo by Emma Griffith

Physics students present research at 20th Annual Berko Symposium on May 16

On Monday, May 16, the Physics Department will hold the Twentieth Annual Student Research Symposium in Memory of Professor Stephan Berko in Abelson 131. The symposium will end with talks by the two Berko Prize winning students, undergraduate Netta Engelhardt and graduate student Tim Sanchez. The whole department then gathers for a lunch of cold cuts, cookies and conversation. “It’s a great way to close out the academic year,” said Professor of Astrophysics and Department Chair John Wardle. “We come together to celebrate our students’ research and hear what the different research groups are doing.”

The undergraduate speakers will describe their senior thesis honors research. This is the final step in gaining an honors degree in physics, and most of them will also be co-authors on a paper published in a mainline science journal. The graduate student speakers are in the middle of their PhD research, and will disucss their progress and their goals.

The prize winners are nominated and chosen by the faculty for making particularly noteworthy progress in their research. Graduate student winner Sanchez’ talk is titled “Reconstructing cilia beating from the ground up.” He works in Professor Zvonimir Dogic’s lab studying soft condensed matter. Undergraduate winner Engelhardt’s talk is titled “A New Approach to Solving the Hermitian Yang-Mills Equations”. She works with Professors Matt Headrick and Bong Lian (Math) on problems in theoretical physics and string theory. The schedule for Monday morning and abstracts of all the talks can be found on the Physics Department website.

Sanchez’ research very much represents the growing interdisciplinary nature of science at Brandeis. Here, a physicist’s approach is used to study a biological organism. Professor Zvonimir Dogic says of his work “He has made a whole series of important discoveries that are going to have a measurable impact on a number of diverse fields ranging from cell biology, biophysics, soft matter physics and non-equilibrium statistical mechanics.  His discoveries have fundamentally transformed the direction of my laboratory and probably of many other laboratories as well.”

Engelhardt’s research is much more abstract and mathematical, and concerns fundamental problems in string theory, not usually an area tackled by undergraduates. Professor Headrick says “Netta really, really wants to be a theoretical physicist, preferably a string theorist. She has a passion for mathematics, physics, and the connections between them.” He adds that she is utterly fearless in tackling hard problems. Netta has been awarded an NSF Graduate Research Fellowship based on her undergraduate work here.  Next year she will enter graduate school at UC Santa Barbara and will likely work with eminent string theorist Gary Horowitz, who has already supervised the PhD research of two other Brandeis physics alumni, Matthew Roberts ’05, and Benson Way ’08.

This Student Research Symposium is now in its 20th year. The “First Annual…..” (two words which are always unwise to put next to each other) was initiated in 1992 by Wardle to honor Professor Stephan Berko, who had died suddenly the previous year. Family, friends and colleagues contributed to a fund to support and celebrate student research in his memory. This provides the prize money which Netta and Tim will share.

Stephan Berko was a brilliant and volatile experimental physicist who was one of the founding members of the physics department. He was born in Romania in 1924 and was a survivor of both the Auschwitz and Dachau concentration camps. He came to the United States under a Hillel Foundation scholarship and obtained his PhD at the University of Virginia. He came to Brandeis in 1961 to establish a program in experimental physics and worked tirelessly to build up the department. Together with Professors Karl Canter (dec. 2006) and Alan Mills (now at UC Riverside) he established Brandeis as a world center for research into positrons (the anti-matter mirror image of ordinary electrons). In a series of brilliant experiments they achieved many “firsts,” culminating in election to the National Academy of Sciences for Steve, and, it has been rumored, in a Nobel Prize nomination for the three of them. Steve was as passionate about teaching as he was about research, and when he died, it seemed most appropriate to honor his memory by celebrating the research of our graduate and undergraduate students. During the coffee break on Monday, we will show a movie of Steve lecturing on “cold fusion,” a headline-grabbing but phony claim for producing cheap energy from 1989.

Beckman Scholarships and URP Awards for Summer 2011

Beckman Scholars and Undergraduate Research Program Winners

Summer 2011

Beckman Scholars

The 2011 Beckman Scholars are:

Frank Scangarello (mentor: Suzanne Paradis, Biology)
Multivalent Metalloproteases Inhibitors to Increase Small Molecule Avidity and Selectivity to Study Semaphorin4D-Cleavage Mediated Synaptic Nerve Development

Zhequan Xu (mentor: Christine Thomas, Chemistry)
Novel Catalyst Design for Green Fuels

URP Recipients

(only students from the Division of Science are included in this list)

Heather Bernstein ’12 (Language & Linguistics; Neuroscience) with Prof. Stephen Van Hooser
Stimulus Therapy & its Implications for Rehabilitation: Using Channelrhodopsin-2 to determine spike time-dependent plasticity in neurons of the primary visual cortex in postnatal ferrets at eye opening

James En Wai Chin ’14 (Chemistry) with Prof. Lizbeth Hedstrom
IMP dehydrogenase nucleic acid association (How do IMPDH mutants affect IMPDH nucleic acid binding?)

Nimrod Deiss-Yehiely ’12 (Biology) with Prof. Sacha Nelson
A mouse model for Infantile Spasms involving TTX

Scott Finkelstein ’12 (Biology) with Prof. Paul Miller
Comparative Success of Strategies in a Continuous Iterated Prisoner’s Dilemma

Jessica Friedman ’13 (Biochemistry) with Prof. Tom Pochapsky
Insights into Substrate Recognition in Cytochrome P450cam

Julie Miller ’12 (Neuroscience) with Prof. Stephen Van Hooser
Roles of Inhibitory Neurons in Cortical Development

Anna Slavina ’12 (Psychology) with Prof. Art Wingfield
Selective syntactical attention among bilingual speakers

Sophie Travis ’13 (Biochemistry) with Prof. Dagmar Ringe
In vitro characterization of VPS35

Akash Vadalia ’12 (Biology; HSSP) with Prof. Angela Gutchess
Cross-Cultural Differences in the Specificity of Memory for Objects and Contexts

Alison White ’13 (Psychology) with Prof. Art Wingfield
Monitoring the Capacity of Short Term Memory

Abigail Zadina ’13 (Psychology) with Prof. Michael Rosbash
Huntington’s Disease: Insights into Mechanisms Involving Circadian Systems

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