News and Events from and for the Division of Science, Brandeis University
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.
With increasing vaccination rates and declining positive Covid test rates, the Division of Science is looking forward to a vibrant, in-person summer undergraduate research program kicking off right after Memorial Day.
The Division of Science summer program pairs first-hand research, community building, and guidance from Brandeis graduate students and postdoctoral fellows to provide undergraduate students a high-quality research experience. Past summer undergraduates have gone on to make substantial contributions (even as first authors!) to peer-reviewed research publications in fields such as materials chemistry (Shi et al., “Sunlight-activated phase change materials for controlled heat storage and triggered release”), molecular biology (Lamper et al., “A phosphorylation-regulated eIF3d translation switch mediates cellular adaptation to metabolic stress”) and neuroscience (He et al., “Rapid adaptation to Elevated Extracellular Potassium in the Pyloric Circuit of the Crab, Cancer borealis”).
For Summer 2021, we are excited to announce that 58 Brandeis undergraduate researchers will be supported through the Division of Science programs and funding sources including NSF, NIH, and generous Brandeis alumni and foundation donors.
Additionally, the MRSEC Research Experience for Undergraduates (REU) program will support 6 undergraduate students from Hampton University for a 10-week, hands-on research program that runs in parallel with the MRSEC Summer Materials Undergraduate Research Fellowship. REU participants are mentored by MRSEC graduate students and postdoctoral fellows and contribute to materials science research efforts on Brandeis’s campus.
We will conclude the summer with SciFest, our annual summer poster session showcasing undergraduate research in the sciences, on August 5. Check the SciFest website for updates about the time and details for the session.
Congratulations to all fellowship recipients!
Seminars PubMed: Brandeis MCB seminarsBrandeis University | Blogs @ Brandeis | Write a Blog
Welcome Guest | Login (Brandeis Members Only)