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.
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.
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.
Brandeis 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:
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.
To 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, 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.
At 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.
Bulbul Chakraborty
Enid and Nate Ancell Professor of Physics
Division Head, Sciences, School of Arts and Sciences
This blog is addressed to my colleagues in the division of science.
As scientists, we pride ourselves on solving problems, often ones that lead to paradigm shifts. A challenge that we have all grappled with is how to cultivate and nurture a truly diverse community of scientists. How do we create an environment that is inclusive and accessible to all that seek to enter the sciences and experience the invigorating practice of science that we live and breathe? How do we open our doors and not be gatekeepers?
I am writing this blog because the many conversations that I have had over this summer has convinced me that this is the right time for a concerted effort to push towards our objectives. As scientists we know that half the battle is going to the core of a problem, and representing it in a way that tells us what actions to take. What I have become aware of is that the anecdotal evidence on who leaves the sciences is being made quantitative and rigorous. Words are being put to our experiences and structures are being offered that we can use to take actions. We have colleagues at Brandeis and in the broader community of science educators that have thought long and hard about how to bring about change in STEM education. We can all learn from them.
I am urging all of you to share resources that you are aware of that will help us create actionable goals and structural changes. Towards that, here is a link to an organization called “SEA CHANGE”, within the auspices of the American Association for the Advancement of Science: https://seachange.aaas.org/. In particular, they are hosting a series of Webinars under the banner “Talking about Leaving Revisited”: https://seachange.aaas.org/events that I have registered for and I encourage you to do so if you can.
I intend to make this a monthly blog that reflects my thoughts on diversity, equity and inclusion in the sciences at Brandeis.
Congratulations to Shinji Rho who has been named a 2020 Goldwater Scholar. The Goldwater Scholarship is a national scholarship designed to encourage outstanding students in their sophomore and junior year to pursue research careers in the fields of mathematics, the natural sciences, and engineering.
Shinji is currently a junior. Her project at Brandeis is on a transcriptional activator Gal4, which binds to upstream activating sequence (UAS) sites in the yeast genome to promote transcription. Previous studies have shown that dwell time of Gal4 on the UAS is significantly longer in purified systems than in cells. She is interested in finding the reason for this dwell time difference using single-molecule light microscopy. The findings of her project will provide a more realistic view of how transcription activation system behaves when nuclear proteins are present.
Shinji plans to obtain a PhD degree in cancer biology, ultimately conducting research on developing more accurate and easily accessible breast cancer diagnosis methods.
Her mentor is Jeff Gelles, Aron and Imre Tauber Professor of Biochemistry and Molecular Pharmacology.
The Brandeis Innovation SPROUT and I-Corps programs offer support for bench and non-bench research. Both programs offer funding in different amounts, mentorship, training and help in further exploring the commercial potential of inventions. SPROUT supports bench research, while I-Corps emphasizes training for both bench and non-bench researchers in developing the commercial potential of discoveries, with small grants and extensive training programs. You can apply to one or both programs.
SPROUT teams will get the chance to qualify for up to $30,000 in funding. The I-Corps program provides entrepreneurial training and covers the core of commercializing a technology or building a startup. It comes with an NSF $750 travel and training stipend and an NSF I-Corps certificate/digital badge.
Apply by February 25, 2020 at 11:59PM
Science at Brandeis 