Hunting Novel Viruses in a Lab Course

Last Fall the Biology department mounted a new course (BIOL 152B),  the Virus Hunter Lab. This course combines practical experience in the lab with computer based approaches in bioinformatics. Students in the class isolated a type of virus that infects bacteria called a bacteriophage. In the wet lab, they learned basic microbiology techniques for isolating the viruses and basic molecular biology techniques for extracting the DNA of the viral genomes. With the biological material in hand the class prepared next generation sequencing libraries. The students assembled and annotated the complete genome of two previously unknown bacteriophage using next generation sequencing data from the samples they prepared. To find out more about it you can read their paper. Grad students Meghan Harris (MCB), their TA, and Tereasa Ho (Biotechnology) along with the inaugural group of undergraduate students are all authors on a paper recently published in the journal Microbiology Resource Announcements (MRA).

Harris MT, Ho TC, Fruchtman H, Garin ME, Kubatin V, Lu T, Xue L, Marr MT. Complete Genome Sequences of Two Vibrio natriegens Bacteriophages. Microbiology Resource Announcements. 2020;9(45).

Electron microscope image of the novel bacteriophage (VH2), photo by Jesse Cochrane

Griffith lab finds that time-keeping brain protein influences memory

Figure from Griffith lab paperIn the Journal of Neuroscience, members of the Griffith Lab found that memory impairments can result from disruptions in the release of the peptide Pigment-dispersing factor (PDF). PDF aligns the brain’s time-keeping mechanism to the correct time of day.

Upsetting the brain’s timekeeping can cause cognitive impairments, like when jetlag makes you feel foggy and forgetful. These impairments may stem from disrupting a protein that aligns the brain’s time-keeping mechanism to the correct time of day, according to new research in fruit flies published in JNeurosci.

The brain contains ‘clock’ neurons that collectively mold circadian behaviors and link them to cues from the environment, like light and seasonal changes. In fruit flies, the peptide Pigment-dispersing factor (PDF) is released from the clock to both synchronize the activity of the clock neurons and to drive time-based behaviors like mating and sleep. PDF may also underlie memory formation, explaining the cognitive dysfunction that occurs when the clock is desynchronized from the environment.

Flyer-Adams et al. tested how well fruit flies with a functioning core clock, but lacking the PDF output signal, could learn. They found that without PDF signaling, flies had severely impaired memory. Interestingly, memory regulation by PDF likely occurs without direct signaling to the main memory structure of flies. Their results suggest that PDF from the clock may promote normal memory throughout the day by acting as a timestamp to learning. The VIP pathway in humans may play a similar role.

Publication:

Regulation of olfactory associative memory by the circadian clock output signal Pigment-dispersing factor (PDF). Johanna G. Flyer-AdamsEmmanuel J. Rivera-RodriguezJunwei YuJacob D. MardovinMartha L. Reed and Leslie C. Griffith. 

Bruce Foxman Elected American Crystallographic Association Fellow

Bruce FoxmanThe American Crystallographic Association (ACA) has elected Bruce Foxman, Professor of Chemistry Emeritus, as a member of the 2020 class of ACA Fellows. The ACA recognized his leadership of the solid-state chemistry research community and his research in topotactic relationships, solid-state dimerization and polymerization, and polymorphism. Foxman has also contributed extensively to the development of new methods for X-ray crystal structure determination. Bruce joined the Brandeis faculty in 1972 and is still research-active and also collaborating with many colleagues at Brandeis and elsewhere. He is a superb teacher (2009 Brandeis Prize for Excellence in Teaching) and has developed widely-used downloadable tutorials on Symmetry and Space Groups and An Introduction to X-ray Structure Determination for High School Students.

Hedstrom Receives NIH Director’s Transformative Research Award

Liz HedstromBrandeis University chemical biologist Lizbeth Hedstrom received one of nine Director’s Transformative Research Awards this year from the National Institutes of Health under its High-Risk, High-Reward Research Program.  The 5-year, $3.5 mil grant will support the development of new methods for drug design relying on targeted protein degradation.  This emerging strategy has several potential therapeutic advantages over traditional approaches, including the development of more potent, longer acting, drugs.

The rational design of ‘degraders’ has focused almost exclusively on degradation induced when the target protein is modified with ubiquitin.  In contrast, Hedstrom will be developing ubiquitin-independent strategies.

Former Marder Student Receives Prestigious Award

Vatsala Thirumalai

Photo: NCBS

A former graduate student from Eve Marder’s lab has received the prestigious Shanti Swarup Bhatnagar Prize for 2020.  Vatsala Thirumalai was a graduate student in the Marder lab from 1996 to 2002. She received her PhD in Neuroscience from Brandeis University in 2002.

Thirumalai was one of twelve researchers to receive India’s highest science award. She is a faculty member in the Biochemistry, Biophysics and Bioinformatics department at the National Centre for Biological Sciences in Bangalore, India. Her lab is focused on neural circuits that control movement during development and adulthood in animals.

The Shanti Swarup Bhatnagar Prize is awarded by the Council of Scientific and Industrial Research (CSIR) to Indian scientists below the age of 45 for outstanding research in seven fields—Biology, Chemistry, Environment Science, Engineering, Mathematics, Medicine and Physics.

After receiving her degree from Brandeis, Vatsala did post-doctoral fellowships in Neuroscience at the Cold Spring Harbor Laboratory, Cold Spring Harbor, NY and the National Institutes of Health, Bethesda, MD.

More info: CSIR Announces Awardees of Shanti Swarup Bhatnagar Prize for 2020Shanti Swarup Bhatnagar Prize 2020: 12 researchers receive India’s highest science award.

Hagan and Fraden Elected APS Fellows

Seth Fraden

Seth Fraden

Michael Hagan

Michael Hagan

Michael F. Hagan, Professor of Physics and of Quantitative Biology and Seth Fraden, Professor of Physics have been elected Fellows of the American Physical Society (APS)

Hagan received his honor “For theoretical and computational advances in active matter, and in self-assembly of viruses and colloids.” Fraden received his honor “For leadership in experimental soft matter physics, notably entropy-driven order in phase behavior, structure, and dynamics.”

The fellowship is a distinct honor signifying recognition by one’s professional peers for outstanding contributions to physics. Each year, no more than one half of one percent of the Society’s membership is recognized by this honor. The 2020 Fellows will be added to the APS Fellow Archive and formally recognized at the annual meeting of the unit through which they were elected.

 

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