Shinji Rho named 2020 Goldwater Scholar

Shinji Rho, Brandeis UndergraduateCongratulations 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.


Alumni and Student Researchers Wow Crowd at 2019 SciFest

With a new alumni symposium in the morning and a poster session filling three floors of the Science Center atrium in the afternoon, this year’s SciFest IX set a new standard for Brandeis Science’s annual celebration of undergraduate research.

Photos: Heratch Ekmekjian

Since 2011, a poster session featuring the results from ongoing projects belonging to undergraduates doing science research has been the high point of summer in the Division of Science at Brandeis. This year, for the first time, we invited Brandeis alumni scientists to speak in a morning symposium entitled “A Celebration of Brandeis’ Undergraduate Science Education”, including:

Students and faculty in the audience were treated to a history of Brandeis and reflections on many of the Brandeis professors and courses that set them on their career path and whose influence persists to the present in how they approach their science, and on lessons they learned that continue to guide their work.

After lunch in the campus center, the crowd climbed up to the Shapiro Science Center for the poster session. 123 students presented 117 posters on topics from high-energy physics to biomaterials and from quantum chemistry to fruit fly behavior. As President Ron Liebowitz noted in an email to the Science community after the event:

The energy in Shapiro during the poster session was electric.  The students’ confidence and excitement over sharing their research can only give us great optimism about the future: they are “all in” when it comes to doing basic research, but also seeing how such research can be applied in the name of helping others.

Many of the posters can be found in the hallway in Gerstenzang – look for them when classes start again in a few weeks!

SciFest IX by the numbers

  • 117 posters
  • 123 student presenters (out of approx. 210 summer student researchers)
    • 105 Brandeis students
      • 99 presenting research done on campus
      • 6 presenting work done over the summer off-campus
    • 18 visiting students
  • 45 Brandeis faculty advisors from 7 departments
    • Biochemistry (7)
    • Biology (18)
    • Chemistry (8)
    • Computer Science (1)
    • Physics (6)
    • Psychology (5)
    • Sociology (1)

Even Dankowicz is named 2019 Goldwater Scholar

Even Dankowicz, fly image

photo: Even Dankowicz

Even Dankowicz, a rising senior majoring in Biology, has been named a 2019 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.

He has always been particularly interested in animals (including insects), but it was a high school biology teacher that inspired Even to think more seriously about working with insects. “Insects and other arthropods seemed especially worth studying because they are disproportionately diverse and abundant, making up ~95% of the species I found in my yard. Up close, they are also often exceptionally beautiful.” The image above is one of his favorites – it is a wasp-like flower fly from his yard in Illinois.

After his freshman year at Brandeis, Even spent the summer at the Smithsonian revising the taxonomy of a tropical Asian Mydas-fly genus, discovering six new species. Last summer he worked at Harvard on a gene-sequence-based evolutionary tree of a tropical Asian butterfly genus. He has continued to be involved with both of these projects/research groups, and is currently back at the Smithsonian looking at the comparative morphology of fly pupae.

Along with Colleen Hitchcock, Assistant Professor of Ecology, Even worked on local biodiversity-focused citizen science, which has shown him the potential value of this data and motivated him to curate insect observations on iNaturalist and BugGuide, two citizen science websites. Even (with Chris Cohen from East Carolina University) recently contributed an article to Fly Times titled “Diptera and iNaturalist: A case study from Asiloidea”. The article provides a detailed description of iNaturalist. Dankowicz and Cohen used this platform extensively for their studies in Diptera.

In the future, Even says that he thinks he’d like to keep working with insects, “either to understand their evolution or another aspect of their biology.” This spring, Even took an class on evolutionary developmental biology (evo-devo) with Assistant Professor Maria de Boef Miara, which has been useful in his current project at the Smithsonian. Additionally, he is starting to work on applications for graduate school next year.

Student Research Results in Recent JIB Paper

Images from research paper from Pochapsky and Lovett labsBy Thomas Pochapsky, Professor of Chemistry & Biochemistry

We don’t usually consider PineSol, Vick’s VapoRub and Lemon Pledge as food, but it is a good thing that some bacteria can.  The active components of those products are terpenes, small organic molecules that are produced by evergreens to repel insects, promote wound healing and prevent infection.  The bacteria that can use terpenes as food are a critical part of the forest ecosystem:  Without them, the soil would rapidly become saturated with toxic terpenes.  Members of the Pochapsky and Lovett laboratories in Chemistry and Biology are curious about what enzymes are involved in terpene metabolism.  In particular, why would one bacterial strain feast on a particular terpene (camphor, for example) while ignoring others?

The first step in terpene breakdown by bacteria is often the addition of an oxygen atom at a particular place in the terpene molecule, providing a “handle” for subsequent enzymes in the breakdown pathway.  The enzymes that catalyze these oxygenation reactions are called cytochromes P450.  P450 enzymes perform important reactions in humans, including steroid hormone biosynthesis and drug metabolism and activation.  Human P450s are targets for cancer chemotherapy and treatment of fungal infections.  A specific inhibitor of P450 is a component of the AIDS “cocktail” treatment, slowing the breakdown of the other cocktail components so the drugs do not have to be taken as often.

Despite the importance and wide scope of the P450 enzyme family, we don’t know much about how a particular P450 goes about choosing a molecule to work on (the substrate) or where it will put the oxygen (the product).  This is what the Brandeis labs are interested in finding out.  What particular sequence of amino acids gives rise to the substrate/product combination of a given P450? Answers to this question will aid in drug design and bio-engineering projects.

The project employs multiple scientific techniques in order to get at the answers to these questions, including bacterial genome sequencing, messenger RNA transcription, enzyme isolation, activity assays, mass spectrometry and enzyme structure determination.  As complicated as it sounds, though, the project lends itself nicely to undergraduate research:  Three of the authors on this paper are undergraduates, Phillix Esquea ‘18, Hannah Lloyd ’20 and Yihao Zhuang ’18.  Phillix was a Brandeis Science Posse recruit, and is now working with a Wall Street investment bank in NYC.  Yihao is enrolled in graduate school at the University of Michigan School of Pharmacy, and Hannah Lloyd is still at Brandeis, continuing her work on the project.  Even high school students got in on the act:  Teddy Pochapsky and Jeffrey Matthews are both seniors at Malden Catholic High School, and collected soil samples used for isolation of terpene-eating bacterial strains.  (One of the newly isolated bacterial strains is named in their honor, Pseudomonas strain TPJM).

“A new approach to understanding structure-function relationships in cytochromes P450 by targeting terpene metabolism in the wild.” Nathan R.Wong, Xinyue Liu, Hannah Lloyd, Allison M. Colthart, Alexander E. Ferrazzoli, Deani L. Cooper, Yihao Zhuang, Phillix Esquea, Jeffrey Futcher, Theodore M. Pochapsky, Jeffrey M. Matthews, Thomas C. Pochapsky.  Journal of Inorganic Biochemistry. Volume 188, November 2018, Pages 96-101.

Encoding taste and place in the hippocampus

The ambience of a good meal can sometimes be as memorable as the taste of the food itself. A new study from Shantanu Jadhav and Donald Katz’s labs, published in the February 18 edition of The Journal of Neuroscience, may help explain why. This research identified a subset of neurons in the hippocampus of rats that respond to both places and tastes.

The hippocampus is a brain region that has long been implicated in learning and memory, especially in the spatial domain. Neurons in this area called “place cells” respond to specific locations as animals explore their environments. The hippocampus is also connected to the taste system and active during taste learning. However, little is known about taste processing in the hippocampus. Can place cells help demarcate the locations of food?

To test this hypothesis, Neuroscience PhD student Linnea Herzog, together with staff member Leila May Pascual and Brandeis undergraduates Seneca Scott and Elon Mathieson, recorded from neurons in the hippocampus of rats as the rats explored a chamber. At the same time, different tastes were delivered directly onto the rats’ tongues.

Analyzing how place cells responded to tastes delivered inside or outside of their place field

The researchers found that about 20% of hippocampal neurons responded to tastes, and could discriminate between tastes based on palatability. Of these taste-responsive neurons, place cells only responded to tastes that were consumed within that cell’s preferred location. These results suggest that taste responses are overlaid onto existing mental maps. These place- and taste-responsive cells form a cognitive “taste map” that may help animals remember the locations of food.

Read more:  So close, rats can almost taste it

Undergrad summer research funding, 2019

The Division of Science announces the opening of the Division of Science Summer Undergraduate Research Fellowship competition for Brandeis students who will be doing undergraduate research in Summer 2019.  These fellowships are funded by generous alumni donations and by grants. Winners will get $5000 stipends for the summer.

Some funding programs have changed since last year; please see the Div Sci website for details of the programs which fund students across all the sciences. We expect to fund about 30 students this summer.

The due date for applications  is February 27, 2019  at 6:00 PM EST.

Students who will be rising Brandeis sophomores, juniors, or seniors in Summer 2019 (classes of ’20, ’21 and ’22), who in addition are working in a lab in the Division of Science at the time of application, are eligible to apply. A commitment from a Brandeis faculty member to serve as your mentor in Summer 2019 is required.

The Division of Science Summer Program will run from June 3 – Aug 9, 2019. Recipients are expected to be available to do full time laboratory research during that period, and must commit to presenting a poster at the final poster session (SciFest IX) on Aug 8, 2019.

Interested students should apply online (Brandeis login required). Questions that are not answered in the online FAQs may be addressed to Steven Karel <divsci at>.

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