JBS Offers “Bio-Inspired Design” Course

Maria de Boef Miara, Lecturer in Biology at Brandeis University, will be leading a course titled Bio-Inspired Design this summer (June 1 thru August 7, 2015). Bio-Inspired Design is part of the Justice Brandeis Semester (JBS). JBS combines courses and experiential learning to provide complete, immersive experiences so students can deeply examine a specific area of study.

Bio-Inspired Design is designed for students from a wide spectrum of disciplines, but may be particularly appealing to students in Biology, Biological Physics, Environmental Studies or HSSP areas. This is a 10-week course providing 12 credits.

Students in Bio-Inspired Design will spend the summer working with biologists, engineers and artists in a variety of settings. They will explore intriguing life forms and develop the quantitative tools needed to work at the intersection of form and function.

Another way that flies sense temperature

If you remember your (bio-)physical chemistry, you’ll remember that most proteins are temperature sensitive. But which ones acts as the sensors that drive behavior in higher organisms? The Garrity Lab at Brandeis has been working on thermosensation in Drosophila, and previous work has implicated the channel protein TRPA1 as a key mediator of temperature preference and thermotaxis,  In a new paper in Nature, members of the Garrity lab working in collaboration with the Griffith and Theobald have have identified another protein, GR28B(D), a member of the family of gustatory receptor proteins, as another behaviorally important temperature sensor, involved in rapid avoidance of high temperatures. Authors on the paper include postdocs Lina Ni (lead author) and Peter Bronk, grad students April Lowell (Mol. Cell Biology) and Vincent Panzano (PhD ’13, Neuroscience), undergraduate Juliette Flam ’12, and technician Elaine Chang ’08.

  • Ni L, Bronk P, Chang EC, Lowell AM, Flam JO, Panzano VC, Theobald DL, Griffith LC, Garrity PA. A gustatory receptor paralogue controls rapid warmth avoidance in Drosophila. Nature. 2013.
  • story at BrandeisNOW


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/

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.

Two more NSF GRFP fellowship winners

Brandeis had 1 current undergraduate, 7 undergraduate alunmi, and 1 incoming graduate student win NSF graduate research fellowships this year. In addition to those cited below, Richard Stefan Isaac ’10 and Orly Wapinski ’09 were also selected. Isaac graduated magna cum laude with a BS/MS degree with high honors in Biochemistry. His thesis work “Functional Characterization of Regulators of Bacterial Pathogenicity and
” was done in the Petsko/Ringe lab. His work teaching in the Biology laboratory also resulted in a paper  in CBE Life Science Education. Isaac is currently a graduate student at Univ. of California, San Francisco. Wapinsky received a BS degree with Highest Honors in Biology, doing in her thesis work “Characterization of Interferon Regulatory Factor-4 mutants” with Professor Ruibao Ren. Wapinski is currently studying at Stanford.

Detecting Mutations the Easy Way

Recent Brandeis Ph.D graduate, Tracey Seier (Molecular and Cell Biology Program), Professor Sue Lovett, Research Assistant Vincent Sutera, together with former Brandeis undergraduates Noor Toha, Dana Padgett and Gal Zilberberg have developed a set of bacterial strains that can be used as “mutational reporters”.  Students in the Fall 2009 BIOL155a, Project Laboratory in Genetics and Genomics, course also assisted in the development of this resource. This work has recently been published in the journal Genetics.

These Escherichia coli strains carry mutations in the lacZ (β-galactosidase) gene that regain the ability to metabolize lactose by one, and only one, specific type of mutation. This set allows environmental compounds to be screened for effects on a broad set of potential mutations, establishing mutagen status and the mutational specificity in one easy step.

This strain set is improved over previous ones in the inclusion of reporters that are specific for certain types of mutations associated with mutational hotspots in gene. Mutations at these sites occur much more frequently than average and involve DNA strand misalignments at repeated DNA sequences rather than DNA polymerase errors. Such mutations are associated with human diseases, including cancer progression, and have been under-investigated because of the lack of specific assays. Using this strain set, Seier et al. also identified a mutagen, hydroxyurea, used in the treatment of leukemia and sickle cell disease, which affects only the “hotspot” class of mutations. This strain set, which will be deposited in the E. coli Genetic Stock Center,  will facilitate the screening of potential mutagens, environmental conditions or genetic loci for effects on a wide spectrum of mutational events.



Left: E. coli colonies showing lacZ mutant revertants (blue pimples) arising on a white colony on growth medium containing the beta-galactosidase indicator dye,  X-gal


Biology research experiences at Brandeis (Summer 2011)

Thanks to new funding from the National Science Foundation, starting in Summer 2011 Brandeis will offer a new research experiences for undergraduates (REU) program in Cell and Molecular Visualization. This new grant, organized by principal investigator Susan Lovett, will provide funding for 10 undergraduates to spend 10 weeks at Brandeis in the summer doing independent research projects in close collaboration with faculty mentors. NSF REU programs place special emphasis on providing research opportunities for under-represented groups in science, and for students whose colleges cannot provide cutting-edge research facilities.

The new program will join Brandeis’s  existing MRSEC REU and other summer research activities in providing a lively atmosphere for young researchers. This competitive program will provide stipends of $5000 each plus housing and meal allowances. Participants must be US citizens or permanent residents, and should have completed their sophomore or junior year of study and be enrolled in an accredited undergraduate college or university. Further information including an application form is available on the Biology website.

Being given the opportunity to do research as an undergrad was amazing, fun, intellectual, and extremely useful; I’ve done it for two summers now.   At the beginning of my college career I was pre-med, but it only took a summer of research to help me realize that I actually want to do science over the course of my career [...]

(see more quotes from undergraduates about summer research)

Alex’s life as a fly barista

Alex Dainis ’11 writes about her experiences in the Garrity lab studying the genetics of nociception in fruit flies in her story “My life as a fly barista” on the Life@Deis blog.

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