MRSEC offers 2 one-week courses in Summer 2017

Brandeis’ MRSEC is offering two one-week courses in June 2017. “Introduction to Microfluidics Technology” and “Biomaterials: Kinesin Production for Beginners” are both hands-on laboratory courses with no prerequisites.

  • Introduction to Microfluidics Technology
    Date: June 19-23, 2017
    This course is intended for graduate students, post docs, faculty, and industrial scientists/engineers interested in utilizing microfluidic technology in their work, both in the physical and life sciences
  • Biomaterials: Kinesin Production for Beginners
    Date: June 26-30, 2017
    This course is intended for graduate students, postdocs, faculty, and industrial scientists/engineers interested in laboratory-scale expression and purification of kinesins, the biomolecular motors that power Brandeis MRSEC’s highly regarded active liquid crystals. The course is suitable for non-biologists who do not have access to any major specialized equipment at their home institution, since the goal of the course is to make protein production accessible to a wider variety of labs.

Register early (by March 1) for a $50 discount. Regular registration for both courses closes March 31, 2017.

Both courses are sponsored by the National Science Foundation’s Bioinspired Soft Materials Research Science and Engineering Center (MRSEC) at Brandeis.

The Benefits of Middle Age

Almost all our cells harbor a sensory organelle called the primary cilium, homologous to the better known flagella found in protists. Some of these cilia can beat and allow the cell to move (eg. in sperm), or move fluid (eg. cerebrospinal fluid) around them. However, other specialized cilia such as those found in photoreceptor cells and in our olfactory neurons function solely as sensory organelles, providing the primary site for signal reception and transduction. The vast majority of our somatic cells display a short and simple rod-like cilium that plays crucial roles during development and in adulthood. For instance, during development, they are essential for transducing critical secreted developmental signals such as Sonic hedgehog that is required for the elaboration of cell types in almost every tissue (eg. in brain, bones, muscles, skin). In adults, cilia are required for normal functioning of our kidneys, and primary cilia in hypothalamic neurons have been shown to regulate hunger and satiety.

Given their importance, it is not surprising that defects in cilia structure and function lead to a whole host of diseases ranging from severe developmental disorders and embryonic lethality to hydrocephalus (fluid accumulation in the brain), infertility, obesity, blindness, and polycystic kidney among others. Often these diseases manifest early in development resulting in prenatal death or severe disability, but milder ciliary dysfunction leads to disease phenotypes later in life.

Much is now known about how cilia are formed and how they function during development. However, surprisingly, how aging affects cilia, and possibly the severity of cilia-related diseases, is not well studied. A new study by postdocs Astrid Cornils and Ashish Maurya, and graduate student Lauren Tereshko from Piali Sengupta’s laboratory, and collaborators at University College Dublin and University of Iowa, begins to address this question using the microscopic roundworm C. elegans (pictured below). These worms display cilia on a set of sensory neurons; these cilia are built by mechanisms that are similar to those in other animals including in humans. Worms have a life span of about 2-3 weeks, thereby making the study of how aging affects cilia function quite feasible.


They find that cilia structure is somewhat altered in extreme old age in control animals. However, unexpectedly, when they looked at animals carrying mutations that lead to human ciliary diseases, the severely defective cilia seen in larvae and young adults displayed a partial but significant recovery during middle-age, a period associated with declining reproductive function. They went on to show that the heat-shock response and the ubiquitin-proteasome system, two major pathways required for alleviating protein misfolding stress in aging and neurodegenerative diseases, are essential for this age-dependent cilia recovery in mutant animals. This restoration of cilia function is transient; cilia structure becomes defective again in extreme old age. These results suggest that increased function of protein quality control mechanisms during middle age can transiently suppress the effects of some mutations in cilia genes, and raise the possibility that these findings may help guide the design of therapeutic strategies to target specific ciliary diseases. Some things can improve with aging!

How different metals stick together

Editor: Tamara Hanna JEM: Esther RTP: Bryan Nolte

Cover artwork from Inorganic Chemistry featuring paper from the Thomas group

Metal-metal interactions are at the heart of some of the most interesting metal-catalyzed transformations and are found everywhere from Nature (metalloenzymes) to industrially important heterogeneous catalysis (surfaces, nanomaterials).  While textbooks have been written about metal-metal multiple bonds, surprising gaps in knowledge remain, including bonding between first row transition metals and bonding between different metals.  The Thomas group in the Brandeis Chemistry Department seeks to fill these gaps in knowledge through the systematic synthesis of heterobimetallic complexes featuring a wide range of different transition metals and developing a thorough understanding of the electronic structure and bonding of these novel compounds.

The latest issue of Inorganic Chemistry features cover artwork highlighting the recent paper from the Thomas laboratory titled “Exploring Trends in Metal–Metal Bonding, Spectroscopic Properties, and Conformational Flexibility in a Series of Heterobimetallic Ti/M and V/M Complexes (M = Fe, Co, Ni, and Cu).” The paper describes an extensive study of a series of Ti/M and V/M heterobimetallic complexes, where M is systematically varied across the periodic table from left to right (Fe, Co, Ni, Cu).  These complexes are classified as “early/late” heterobimetallic complexes because they feature one metal from the left half of the periodic table (“early”) and one metal from the right half of the periodic table (“late”).  The inherent differences between the properties of the two metals makes their metal-metal bonding quite polar and sensitive to a variety of different factors, but also poises these compounds for interesting reactivity because of the two electronically different metal sites presented. This latest installation from the Thomas group uncovers trends in metal-metal bond distance determined using X-ray crystallography, and uses a variety of spectroscopic (EPR, NMR, Mossbauer) and computational tools to probe the electronic structure of these compounds.  Most interestingly, these compounds are shown to be conformationally flexible, with ligand rearrangements occurring rapidly in solution and this ligand hemilability, which is ideal for facilitating reactivity, can be correlated directly with the strength of metal-metal interactions.

This paper was highly collaborative and its preparation involved researchers from both Brandeis and Harvard University. The synthesis and characterization of the new compounds were largely carried out by Bing Wu, a graduate student in the Thomas group, along with Chris Thomas herself. Matt Wilding, a recent Ph.D. graduate student from the Betley laboratory at Harvard University, assisted with the collection and interpretation of Mossbauer data and designed the cover artwork. Recent Ph.D. graduate Mark Bezpalko, of the Thomas/Foxman groups, and Bruce Foxman carried out all of the structural work in the Brandeis X-ray Diffraction Facility, and all of the computational studies were carried out by Bing Wu and Chris Thomas using the Brandeis high performance cluster.

Irving Epstein has been named AAAS Fellow


In recognition of his contribution to the study of oscillating chemical reactions, Irving Epstein, the Henry F. Fischbach Professor of Chemistry, has been selected as a Fellow in the American Association for the Advancement of Science (AAAS).

Epstein, who in his 45 years at Brandeis has served as Provost and Dean of the Arts and Sciences, said he was honored to receive the award from the AAAS. “I’m delighted and grateful for the recognition,” he said. “It’s always nice to be appreciated by fellow scientists.”


Brandeis Receives Major Grant from the Mellon Foundation

Brandeis University has received a major grant to expand the LAPPS Grid Project that seamlessly connects open-source computer programs to quickly analyze huge amounts of language from diverse sources and genres.

James Pustejovsky

James Pustejovsky

Brandeis University has been awarded a two-year, $390,000 grant from the Andrew W. Mellon Foundation to lead an international collaboration to link the two major American and European infrastructures for the computational analysis of natural language. The resulting meta-framework has the potential to transform scholarship and development across multiple disciplines in the sciences, language and social sciences, and digital humanities by enabling scholars in Europe, the US, and Asia to work seamlessly across a massive range of software tools and data resources, developed separately by the American and European efforts. Led by James Pustejovsky, the TJX/ Feldberg Professor of Computer Science at Brandeis, the project team includes Nancy Ide (Vassar College), Erhard Hinrichs (University of Tübingen), and Jan Hajic (Charles University Prague).

The Language Applications (LAPPS) Grid Project—a collaborative, NSF-funded effort among Vassar, Brandeis, Carnegie Mellon University, and the Linguistic Data Consortium at the University of Pennsylvania—and the European Common Language Resources and Technology Infrastructure (CLARIN) are both frameworks (“grids”) that create and provide access to a broad range of computational resources for analyzing vast bodies of natural language data: digital language data collections, digital tools to work with them, and expertise for researchers to use them. Within each framework, members adhere to common standards and protocols, so that tools and data from different projects are “interoperable”: users can access, combine, and chain data from different repositories and tools from different sources to perform complex operations on a single platform with a single sign-on.

But the LAPPS Grid and CLARIN are not themselves interoperable. Researchers using data and tools in one framework cannot easily access or add data and tools from the other. LAPPS Grid users cannot access CLARIN’s multi-lingual services for digital humanities, social sciences, and language technology research and development, like Prague’s tools for search of oral history archives (developed to support their hosting the USC Shoah Archive), or Tübingen’s WebLicht services for data mining political and social science documents. CLARIN users don’t have access to the LAPPS Grid’s state-of-the-art tools for English and, through the LAPPS Grid’s federation with five Asian grids, to services providing a broad spectrum of capabilities for work in Asian languages. Scholars manually annotating a text corpus with CLARIN’s WebAnno (developed at TU-Darmstadt) would love to feed their work through iterative machine learning and evaluation facilities in the LAPPS Grid—but can’t.

The new Mellon Foundation funding will enable the project team to make the two grids interoperable on three levels:

  • Infrastructural: While the LAPPS Grid and CLARIN are both committed to open data and software, they do provide secure access to licensed resources, including the vast majority of the language data available over the web. The team will create a “trust network” between the two services, enabling single-authentication sign-on;
  • Technical: The LAPPS Grid and CLARIN have different underlying architectures and data exchange formats. The team will map these architectures and formats onto one another, enabling communication between the two frameworks over the web;
  • Semantic: To combine differently curated datasets, the data needs not only to share or be converted into a common format, but must also share a vocabulary for describing basic linguistic structures (a common language ontology) that tells computers how to combine the data into meaningful statements. The project team will extend the common exchange vocabulary developed by the LAPPS Grid to the web services of both frameworks and implement a set of conversion services.

The project will dramatically extend the power and reach of both the European and American frameworks and put their combined resources at the direct disposal of scholars from a broad range of fields in the humanities and social sciences, without requiring them to be computer programmers. “It will effectively create an ‘internet of language applications’ for the everyday computer user,” explained Dr. Pustejovsky. “We’re going to give every scholar access to a toolkit that’s now only available to the largest corporations.”


Division of Science Hosts the 2016 Undergraduate Science Symposium

Written by Jena Pitman-Leung.


The Division of Science Graduate Affairs group hosted the 2nd annual Brandeis University Undergraduate Science Symposium on Saturday 17th, 2016. More than 60 students representing institutions from Massachusetts, Rhode Island, and New Hampshire attended the event, which was held in the Shapiro Science Center. The morning session included research talks from faculty in the Life Sciences (Don Katz, Liz Hedstrom) and the Physical Sciences (Matt Headrick, Christine Thomas), followed by panel discussions with faculty in the Life Sciences (Liz Hedstrom, Bruce Goode, and Maria Miara) and Physical Sciences (Gabriella Sciolla, Isaac Krauss, Jordan Pollack) on how to apply to graduate school. The students then came together for a networking lunch with Brandeis students, postdocs, and faculty. Lunch was followed by a well attended poster session, where 38 students had the opportunity to present their independent research. The day ended by awarding prizes for the best posters in five disciplines. The winners were:

Biology: Rahim Hirani, Hampshire College, “The regulatory role of Beta-Arrestin 1 in prostate cancer cell proliferation”
Neuroscience: Paige Miranda, Wellesley College, “Metabolic Processes Driving Hippocampal Long Term Potentiatio”
Biochemistry: Myfanwy Adams, Wellesley College, “Expression of a Cardiac ATP-sensitive Potassium Channel in a Heterologous Cell Line”
Chemistry: Natsuko Yamagata, Brandeis University, “Exploring the Unexplored: Supramolecular Hydrogels of Retro-Inverso Peptides for 3D Cell Culture”
Physics: Jameson O’Reilly, Northeastern University, “A capillary-mimicking optical tissue phantom for diffuse correlation spectroscopy”

The Division of Science is committed to supporting local undergraduate research, and is excited about the possibility of these bright young scientist choosing Brandeis for their graduate study. We look forward to hosting similar events in the future!

68th New England Complex Fluids Workshop, September 23, 2016

The 68th New England Complex Fluids Workshop will be held 9:00 am – 4:00 pm Friday, September 23, 2016 at the Shapiro Campus Center on Brandeis University. NECFW68 will feature two research talks, two soundbite sessions and one panel of scientists who are thriving after leaving academia for industry.

Online registration for the meeting is required, but thanks to the NSF Brandeis MRSEC, it is free. However, please register by 8 am, September 20 so we can order enough food for you.

NECFW‘s goal is to encourage collaboration among researchers from industry and academe in the New England area studying Soft Condensed Matter. We hold one day workshops four times a year which offer the opportunity for discussion and exchange of ideas between students, post-docs, and professionals. An additional objective is to further the career development of students and post-docs by introducing them to the local academic and industrial research community.

Please register at the complex fluids website: If you would like to present a 4:00 minute soundbite, submit your talk title and abstract when you register for the meeting. Soundbites are restricted to the first 25 submissions. Additional information such as maps, directions, schedule and a list of registered attendees is available at the website as well.

This year will feature an Industrial Panel to tell tales of life after academia. Entrepreneurs and industrial scientists will describe their pathway to creating companies, discuss which qualities they seek in applicants and answer the following questions. What kind of training and education do industrial labs seek in job applicants? What scientific and other knowledge should applicants possess? experience? skills? creativity? business knowledge? What should the universities do to better prepare students for a career in industry? What do the panel members wish they did differently in college to better prepare themselves for industry? What should students / postdocs be doing now to prepare for an industrial career? How can students find an internship? How should students build a network of contacts to help them find a job? How does research done in industry compare to that done in universities? What (if any) is the relevancy of research being done at universities to entrepreneurs, industrial scientists and managers?

Recycling is good for your brain

If you were able to remember where you put your keys on your way out the door this morning, it’s because – somehow – synapses in your brain changed their properties to encode this information and store it until you needed it. This process, known as “synaptic plasticity”, is essential for the continuity of our memory and sense of self, and yet we are only beginning to grasp the molecular mechanisms that enable this amazing feat of constant information storage and retrieval. Now a collaborative paper from the Turrigiano and Nelson labs just published in Cell Reports sheds important new light into how experience interacts with the genome to allow synapses to change their strength to store information.

Synapses are the connections between neurons, and it has long been appreciated that information is stored in large part through changes in the strength of these connections. Changes in strength at many synapses are in turn determined by the number of neurotransmitter receptors that are clustered at synaptic sites – the more receptors synapses have, the easier it is for neurons to excite each other to transmit information. Synapses are highly complicated molecular machines that utilize at least 300 different proteins that interact to traffic these receptors to synapses and sequester them there, and exactly how a change in experience alters the function of this nano-machine to enhance the number of synaptic receptors is still a matter of puzzlement.

In this study the Brandeis team devised a way to screen for candidate proteins that are critical for a particular form of synaptic plasticity: “synaptic scaling”, thought to be especially important for maintaining brain stability during learning and development. They were able to induce synaptic scaling within specific labelled neurons in the intact mouse brain (layer 4 star pyramidal neurons), and then sort out those labelled neurons from the rest of the brain and probe for changes in gene expression that were correlated with (and potentially causally involved in) the induction of plasticity.  This approach produced a small number of candidate genes that were up- or down-regulated during plasticity, to produce more or less of a given protein.  The team then went on to show that – when upregulated – one of these candidates (known as µ3A) acts to prevent neurotransmitter receptors from going into the cellular garbage bin (the lysosomes, where proteins are degraded) and instead recycles them to the synapse. Thus increased µ3A flips a switch within cells to enhance receptor recycling, and this in turn increases synaptic strength.

µ3A plays a critical role in the recycling of AMPA-type neurotransmitter receptors

A screen for genes with altered expression during synaptic plasiticity in specific neurons revealed that µ3A plays a critical role in the recycling of AMPA-type neurotransmitter receptors at the synapse. When this protein is upregulated, it prevents receptors from being trafficked into lysosomes, and instead allows them to be recycled back to synapses, increasing synapse number and enhancing synaptic strength.

It turns out that many other forms of synaptic plasticity use the same receptor recycling machinery as synaptic scaling, so it is likely that this mechanism represents  an important and general way for neurons to alter synaptic strength. This study also raises the possibility that defects in this pathway might contribute to the genesis of neurological disorders in which the stability of brain circuits is disrupted, such as epilepsy and autism. So next time you complain about having to sort your garbage, consider that your neurons do it all the time –  and what’s good for the planet turns out to be good for your brain as well.

Steinmetz CC, Tatavarty V, Sugino K, Shima Y, Joseph A, Lin H, Rutlin M, Lambo M, Hempel CM, Okaty BW, Paradis S, Nelson SB, Turrigiano G. Upregulation of μ3A Drives Homeostatic Plasticity by Rerouting AMPAR into the Recycling Endosomal Pathway. Cell reports. 2016.

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