biochemistry – Science at Brandeis

Sprout pre-application deadline is 3/29

Funded by the Provost’s Office and the Office of Technology Licensing (OTL), Sprout is designed to encourage and support translational research activity within the Brandeis community for faculty, postdocs, and student researchers (graduate and undergraduate) in the Division of Science. The awards (up to $25,000) are intended to help advance early-stage technologies to industry adoption.

Pre-applications are due by March 29. Successful pre-applicants will be invited to submit a final application, followed by a final pitch to a panel of industry judges.

Meet the 2023-24 DEIS Scholars

2023-2024 Division of Science DEIS Scholars

GSAS recently published an article profiling the 2023-2024 DEIS Scholarship students. The profiles include a first-year PhD student from Biochemistry and Biophysics, a PhD student from Psychology and two Biotechnology master’s students. There is also a profile of a PhD English student and a PhD History student included in this article.

The DEIS Scholarship provides a full-tuition scholarship, a stipend and additional assistance to U.S. citizens and permanent residents from historically underrepresented backgrounds and first-generation college students. Students who have a history of activism in support of these communities are eligible as well. The scholarship is partially funded by the A. Philip Randolph Fellowship.

3MT Info Session to be held Jan. 24

The 3rd annual Brandeis 3MT (Three Minute Thesis) competition is fast approaching!

The 3MT is a spoken word competition designed to showcase graduate student research in three minutes using only one slide with the idea of appealing to a general audience. This competition is open to all graduate students who are working on a thesis/dissertation for the sciences, social sciences, and humanities/arts. Winners can win up to $1000! Learn more about the Brandeis 3MT competition.

The Preliminary 3MT competition will occur on Wednesday, March 27. The Finals are scheduled for Friday, April 5 from 4:00 to 5:30 PM. There is also a remote competition for Brandeis graduate students who live outside of Massachusetts on Tuesday, April 2.

You can learn more details about the competition during a virtual information session. Details about the info session are available here:

3MT Information Session
Wednesday, Jan 24, 2024, 12 -1 pm
Register to get Zoom link

In the past, Brandeis has had a very strong showing at the 3MT competitions. Liz Mahon, a PhD student in Psychology, received the top prize at the 2023 3MT Competition at Brandeis with her presentation “Armed Against Alzheimer’s: How Your Voice Could Save Your Mind”. She also won first place at the Northeastern Association of Graduate Schools (NAGS) Regional 3MT Competition and went on to compete nationally at the Council of Graduate Schools (CGS) 3MT Competition in Washington DC.

Updates to Microscopy Core Facilities

Electron Microscopy Core Facility update

The Brandeis Louise Mashal Gabbay Cellular Visualization electron microscopy core facility was awarded an NSF major research instrumentation grant for $1.77M for the purchase of a new Tundra Cryo-TEM. The Tundra is Thermo Fisher’s newest cryo TEM, dedicated to making high quality and high-resolution structural TEM accessible to novice users, as well as allowing for high throughput screening of cryo samples. It will be equipped with Thermo Fisher’s newest direct detector (the Falcon C), pushing its resolution capabilities and throughput even higher. We anticipate the instruments arrival in late spring/early summer of 2024.

Light Microscopy Core Facility Installs New Microscope

The newly renovated 3600 square foot Light Microscopy Core Facility in Bassine Science Building has just welcomed a “super-resolution” STED (stimulated emission depletion) microscope, funded by a $1.2M NIH shared equipment grant. This microscope uses a donut (or a “bagel” as we call it at Brandeis) shaped beam to visualize structures as small as 50 nanometers. (Brandeis Hoot)

STED image of *Drosophila* larval neuromuscular junction labeled for sites of synaptic vesicle release (green) and membrane remodeling (magenta). (DelSignore et al. 2022)

Eve Marder and Greg Petsko awarded the National Medal of Science

Eve Marder, the Victor and Gwendolyn Beinfield Professor of Neuroscience and a University Professor and Gregory Petsko, Professor Emeritus of Biochemistry, received the National Medal of Science from President Biden on October 24, 2023. The National Medal of Science is an honor bestowed by the President of the United States to individuals in science and engineering who have made important contributions to the advancement of knowledge in the fields of behavioral and social sciences, biology, chemistry, engineering, mathematics and physics.

Brandeis alum wins 2023 Nobel Prize in Physiology or Medicine

Drew Weissman ’81, GSAS MA’81, P’15, H’23 has won the 2023 Nobel Prize in Physiology or Medicine. While at Brandies, Weissman studied biochemistry and enzymology. Weissman and fellow collaborator and Nobel recipient, Katalin Karikó, H’23, received the Nobel for their research into messenger RNA. Their research led to the development of the COVID vaccinations.

In February 2021, Weissman and Karikó received the 50th Annual Lewis S. Rosenstiel Award in Basic Medical Research in February 2021.

Pre-Applications to Sprout Program Due 4/17

The Sprout Program is back!

Funded by the Provost’s Office and the Office of Technology Licensing (OTL), Sprout is designed to encourage and support translational research activity within the Brandeis community for faculty, postdocs, and student researchers (graduate and undergraduate) in the Division of Science. The awards (up to $25,000 – no overhead!) are intended to help to advance early-stage technologies to industry adoption thereby bringing your research and entrepreneurial ambitions to life.

Successful pre-applicants will be invited to submit a final application due in late May and to pitch to a panel of industry judges in early June. Pre-apply by April 17.

SciFest XI to be held on Thursday, 8/11/22

Save the Date for SciFest!

SciFest, the Division of Science’s annual celebration of undergraduate research, is a poster session featuring work done by undergraduates in Brandeis laboratories each summer. This is a capstone event for the undergraduate researchers where they can present the results of their research to peers, grad students, and faculty.

Join us for the SciFest XI which will be held on Thursday, August 11, 2022 in the Shapiro Science Center.

Ordabayev et al. developed an open-source analysis software for colocalization single-molecule fluorescence experiments

Yerdos Ordabayev et al. in the Department of Biochemistry use Bayesian probabilistic programming to implement computer software “Tapqir” for analysis of colocalization single-molecule spectroscopy (CoSMoS) image data. CoSMoS is a tool widely used in vitro to study the biochemical and physical mechanisms of the protein and nucleic acid macromolecular “machines” that perform essential biological functions. In this method, formation and/or dissociation of molecular complexes is observed by single-molecule fluorescence microscopy as the colocalization of binder and target macromolecules each labeled with a different color of fluorescent dye. Despite the use of the method for over twenty years, reliable analysis of CoSMoS data remains a significant challenge to the effective and more widespread use of the technique.

This work describes a holistic causal probabilistic model of CoSMoS image data formation. This model is physics-based and includes realistic shot noise in fluorescent spots, camera noise, the size and shape of spots, and the presence of both specific and nonspecific binder molecules in the images. Most importantly, instead of yielding a binary spot-/no-spot determination, the algorithm calculates the probability of a colocalization event. Unlike alternative approaches, Tapqir does not require subjective threshold settings of parameters so they can be used effectively and accurately by non-expert analysts. The program is implemented in the state-of-the-art Python-based probabilistic programming language Pyro (open-sourced by Uber AI Labs in 2017), which enables efficient use of graphics processing unit (GPU)-based hardware for rapid parallel processing of data and facilitates future modifications to the model. Tapqir is free, open-source software. We envision that Tapqir program is likely to be adopted by researchers who use single-molecule colocalization methods to study a wide range of different biological systems.

Reference:

Yerdos A Ordabayev, Larry J Friedman, Jeff Gelles, Douglas L Theobald. Bayesian machine learning analysis of single-molecule fluorescence colocalization images. eLife 2022;11:e73860.

Publication Date: March 23, 2022.

Drew Weissman ’81, MA ’81 Receives the Lasker Award

Katalin Karikó and Drew Weissman ’81, MA ’81 have received the Lasker-DeBakey Clinical Medical Research Award. Weissman is a professor of medicine at the Perelman School of Medicine at the University of Pennsylvania. Karikó is a senior vice president at BioNTech RNA Pharmaceuticals. The Lasker award is in recognition of their research into messenger RNA and the resulting therapeutic technology. It was their work that was so crucial in the rapid development of the COVID-19 vaccines. It should be noted that many winners of the Lasker award go on to receive the Nobel Prize.

Weissman and Kariko also received the Lewis S. Rosenstiel Award for Distinguished Work in Basic Medical Research award earlier this year.

The Washington Post profiled Weissman and his work in a recent article, “A scientific hunch. Then silence. Until the world needed a lifesaving vaccine.”

View Lasker acceptance remarks from Katalin Karikó and Drew Weissman.