Ben Rogers Receives Smith Family Award for Excellence in Biomedical Research

Ben Rogers

photo: Mike Lovett

Assistant Professor of Physics, Ben Rogers, was chosen to receive the Smith Family Award for Excellence in Biomedical Research. This award, which is designed to launch the careers of newly independent biomedical researchers, is one of six given this year by the Smith Family Foundation. It will provide the Rogers Lab with $300,000 over three years to initiate a new direction in RNA structure and interactions.

RNA molecules are vital regulators of cell biology and their three-dimensional structures are essential to how they work. Thus having the ability to intentionally interfere with the structure of RNAs could hold immense potential for the study of their function, as well as the development of molecular medicine and other biotechnological applications. One way to do this is to bind short sequences of synthetic nucleic acids, called oligonucleotides, to specific sites on the RNA molecule. But designing oligonucleotides that bind rapidly and with high affinity to a RNA target remains a challenge. The Rogers Lab will use a combination of in vitro experiments and statistical mechanics to understand and design synthetic oligonucleotides that bind to RNA molecules in a prescriptive fashion. This work will complement existing research within the Rogers Lab, which explores the use of RNA’s chemical cousin, DNA, as a tool to study and build new kinds of materials.

Ben joined the Martin A. Fisher School of Physics at Brandeis University as an Assistant Professor in January 2016. Before coming to Brandeis, Ben was a postdoctoral fellow in the Manoharan Lab within the Department of Physics at Harvard University, where he studied assembly and optical properties of colloidal suspensions. He received his Ph.D. in Chemical and Biomolecular Engineering from the University of Pennsylvania in 2012. At Penn, Ben used optical tweezers to study single-molecule binding. His research program combines expertise in biomolecular engineering, applied optics, and condensed matter physics to study interactions and self-organization at the molecular and mesoscales.

Sebastian Kadener Returns to Brandeis as Associate Professor

Sebastian Kadener

From 2002 to 2008, Sebastian Kadener was a postdoc working in the Michael Rosbash laboratory. He is returning to Brandeis as an Associate Professor of Biology. Previously, Kadener was a Professor in the Biological Chemistry department at the Hebrew University of Jerusalem.

The Kadener laboratory studies how molecular processes in the brain determines behavior with a special emphasis on RNA metabolism. Additionally, they study the role of circular RNAs (circRNAs) at the molecular and neural levels as well as the mechanisms underlying circadian clocks.

Kadener’s paper, “Translation of CircRNAs”, appeared in Molecular Cell in April 2017. It was reviewed in Nature Reviews Genetics and Science Daily.

Brandeis University and NCBI to host Genomics Hackathon in April

Brandeis University is partnering with NCBI to host a Boston-area genomics hackathon April 25-27, 2016. Two previous hackathons held at NCBI successfully integrated scientists from across the country with different skill sets to tackle challenges in RNA-seq and genomics.

The August 2015 NCBI hackathon identified gaps in usability of current RNA-seq analysis tools and in just three days created software that greatly improved ease-of-use.

The August 2015 NCBI hackathon identified gaps in usability of current RNA-seq analysis tools and in just three days created software that greatly improved ease-of-use.

NCBI hackathons identify gaps in the current state-of-the-art analysis pipelines and outline feasible solutions to bring users, especially novices, closer to understanding genomic data and analysis. This hackathon will be highly cooperative: teams of 5-6 individuals will work on non-overlapping projects and share their expertise in a collaborative way. Projects planned for this session include:

  • Network Analysis of Variants
  • Structural Variation
  • RNA-Seq
  • Streaming Data and Metadata
  • Neuroscience/Immunity
  • Command-line user-interface design

The hackathon is an exciting opportunity to meet researchers in similar fields at different institutions, learn new ways of applying your work, and work with a team to contribute original work to the genomics field. Participants are also provided with the opportunity to publish their work in a newly-created F1000 hackathon channel.

Brandeis University and NCBI invite all genomics researchers to apply and visit the NCBI announcement for more information. Participants will need to bring their own laptops to the event and have some knowledge of a scripting language (Python, PERL, Shell, etc).

Please apply by 5:00 PM March 22, 2016.

Riboswitches and fluoride

Ronald Breaker (Yale and HHMI) gave an inspiring talk today to kick off this year’s Biochemistry-Biophysics Friday Lunchtime Pizza Talks series, discussing his lab’s work on Riboswitches: Biology’s Ancient Regulators. If you missed the talk, here’s a review that might help you catch up.

Breaker ended the talk by discussing the fluoride-sensing riboswitch, and pointing to the new avenues for research to which this called attention. Coincidentally(?), a new paper in PNAS is out today from Chris Miller‘s lab here at Brandeis on exactly that — take a look at Stockbridge et al., Fluoride resistance and transport by riboswitch-controlled CLC antiporters.


Bacteria have RNAs that sense fluoride, and channels that tranport it

Fluoride: unless you’re a synthetic chemist or a dentist, you probably don’t worry about this ion very often.  But, according to a new paper published in Science, bacteria do, and have done for a very long time.

The work, spearheaded by Ron Breaker’s group at Yale University, identified a novel RNA motif that selectively binds fluoride ion.  In response to Fbinding, this motif, called a riboswitch, undergoes a structural change that leads to increased transcription of downstream genes.  These genes encode crucial metabolic enzymes that are strongly inhibited by fluoride ion, like enolase and pyrophosphatase, as well as members of a family of chloride transport proteins, the CLC’s.  The CLC’s that are associated with F riboswitches are clustered together in a phylogenetic clade distant from well-characterized CLC’s.  Could these “chloride” channel proteins actually assist with fluoride export?  Randy Stockbridge, a Brandeis postdoc working in Chris Miller’s lab, contributed to the findings by showing that this subset of riboswitch-associated CLC’s do, in fact, transport F, whereas “conventional” CLC’s strictly exclude F.   The F riboswitches, and the F CLC’s, are found among a huge variety of bacteria and archaea, from plant and human pathogens to benign soil and seawater-dwelling bugs, leading to the inference that F toxicity has been a consistent evolutionary pressure.

You’re probably wondering just how much fluoride there is in the environment.  Fluoridated municipal drinking water contains about 80 micromolar F, and natural F- concentrations in the environment can be  higher and lower than that number.   In acidic environments especially, F might accumulate to much higher levels in bacteria.  With a pKa of 3.4, a small amount of F is present as HF at low pH, and the uncharged HF can diffuse cross the cell membrane into the cell.  Once in the cytoplasm, where the pH is around 7, HF dissociates, and F can’t diffuse across the membrane back into the environment.  Unless, of course, evolution has provided that bacterium a system to transport F out of the cell…

see also

New course on RNA

Professors Michael Rosbash and Nelson Lau will teach a new version of BIOL 176b RiboNucleicAcids (RNA) in Spring Semester, 2012. The course is now scheduled for Block S8   W 9:00 AM–11:50 AM.

RNA is a central molecule of all living organisms.  RNA is extremely versatile and can function as an information storage and transfer device, an enzyme, a regulator of gene expression, or a cellular scaffold.   As biologists discover new types of RNAs and new functions for these different types, students must become aware of this progress to gain a complete view of the integral nature of RNA in all branches of the life sciences.

This seminar course will be a weekly discussion of primary literature that broadly covers key breakthroughs in this important subfield of molecular biology. We will examine the versatility and biological functions of RiboNucleicAcides (RNA) in an upper-level seminar and primary-literature based course.Topics include splicing and the spliceosome, the ribosome, ribozymes and the RNA World Hypothesis, RNA editing, RNA interference, and long non-coding RNAs.

This course intends to educate students to become experts on the diverse biological function of RNA.  This course is designed for fulfilling the science requirement for Biology majors. Students will learn how to read the primary literature on classic and recent discoveries concerning RNA.

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