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

Tapqir analysis

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

Drew WeissmanKatalin 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.

 

 

Brandeis Alumnus Receives Breakthrough Prize

Drew WeissmanBrandeis alumnus, Drew Weissman, ’81, MA ’81, P’15 along with Katalin Karikó have been awarded the Breakthrough Prize in Life Sciences.  Weissman and Karikó received the Lewis S. Rosenstiel Award for Distinguished Work in Basic Medical Research from Brandeis earlier this year.

While the Breakthrough Prize is considered the world’s largest science prize at $3 million, it is one of the many awards that Weissman and Kariko have been receiving as a result of their decades of research into mRNA therapies. It is this research that has led to the innovative COVID-19 vaccines developed by Pfizer/BioNTech and Moderna.

After earning his BA and MA degrees from Brandeis, Weissman went on to receive his PhD in Immunology from Boston University in 1987. He did a postdoctoral fellowship at the National Institutes of Health under Anthony Fauci. He is now a professor at University of Pennsylvania’s Perelman School of Medicine.

Additional information:

New Undergraduate Engineering Science Program Approved

Technology is central to our society. Universities play a key role as innovation hubs in new technology development, by linking knowledge creation, workforce development and commerce. After a multi-year planning process with Brandeis stakeholders and Engineering education experts, the Brandeis Faculty and Board of Trustees has approved the creation of a distinctively Brandeisian undergraduate Engineering Science program, designed for ABET accreditation. Unlike other models in which Engineers are siloed in their own department or school, this interdepartmental program is designed to  maximize horizontal integration across and beyond the Sciences.  All hands are now on deck to make this program a reality.  Institutional Advancement is working closely with faculty to raise the funds necessary to meet our ambitious goals.

Science Engineering LogoTo build up this program, we will  capitalize on the existing synergy between the life and physical sciences, while enhancing core research areas with an emphasis on translating basic research to technological applications.  Our goal is to integrate the engineering curriculum with the social justice mission that is integral to Brandeis. We envision providing opportunities for our students and faculty to deeply engage in science, design, and problem-solving while participating in a curriculum and culture that grapples with issues of social justice, business ethics and sustainability. The curriculum will be designed with these aspirations by engaging faculty from all of arts and sciences, IBS and Heller.  Ultimately, we hope that this new program will give our students the tools to intervene in the world and challenge them to build a better one.

We welcome input from our friends and alums as we begin to engage in the task of building up this exciting new program.

Tijana Ivanovic selected to speak at 2021 Future of Biophysics Burroughs Wellcome Fund Symposium

Tijana IvanovicTijana Ivanovic, Assistant Professor of Biochemistry, has been selected as one of four young scientists to speak at the 2021 Future of Biophysics Burroughs Wellcome Fund Symposium on February 23, 2021. This symposium is part of the 65th Annual Meeting of the Biophysical Society and due to COVID concerns, will be held virtually.

The purpose of this symposium is to highlight the work of young researchers who are currently conducting research at the intersection of the physical and life sciences. Research in the Ivanovic Laboratory uses biophysical methods to uncover fundamental molecular mechanisms of virus translocation across biological membranes.

The other speakers selected for the 2021 Symposium are Elisabeth Fischer-Friedrich, TU Dresden, Germany; Abhishek Singharoy, Arizona State University, USA; and Chen Song, Peking University, China.

Meet the Science UDRs at the Ultimate Science Navigation Event (9/23)

Ultimate Science Navigation posterAt The Ultimate Science Navigation event TOMORROW (9/23), students can collaborate with the science UDRs to learn about the different offerings in the sciences, how to navigate each major/minor, what each major/minor has to offer, all with an emphasis on exploring the intersections between different programs in the sciences. We will have UDRs representing biochemistry, biology, neuroscience, chemistry, physics, and biophysics!

Students can join in the morning on Zoom from 9:30-10AM, or for the rest of the day through the new Brandeis science community Slack workspace to discuss their questions related to the majors with the UDRs! Email Lance Babcock (lbabcock@brandeis.edu), Maggie Wang (maki@brandeis.edu) or the other science UDRs for the Zoom link and Slack workspace link.

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