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.  https://doi.org/10.1016/j.jinorgbio.2018.08.006.

2019 Sprout Awards Competition Announced

SPROUT logoThe Office of Technology Licensing (OTL) is excited to announce this year’s SPROUT awards competition!  SPROUT was created to help you bring your scientific research and entrepreneurial ambitions to life by providing seed funding and training to make your innovation a reality.

“It’s not just about the funding. It’s about all the opportunities that arise from participating in SPROUT” – Michael Rosbash, 2018 SPROUT PI

OTL, with support from the Office of the Provost & the Hassenfeld Family Innovation Center, will award up to a total of $100,000 divided among the most promising proposals seeking funding for lab-based innovations that require bench research, lab space and/or lab equipment.   All members of the Brandeis science community, including faculty, staff and students, are invited to submit an abstract for the 2019 round of funding. The preliminary application for abstract submission is now online.  These pre-applications must be received prior to 11pm on March 8th, 2019

In the past, successful SPROUT applications have come from all departments in the sciences including Biology, Biochemistry, Physics, and Chemistry.  Past candidates have proposed projects ranging from early-stage research and development to patent-ready projects.  Many undergraduates, graduates, staff and faculty have all pitched various projects from Vaccines Targeting HIV Sugars (Krauss Lab) to an Assay Kit for RNA-binding Protein Target (Rosbash Lab).

Have questions?  OTL is offering 20 minute appointment slots the week of February 28 at our office in Bernstein-Marcus, room 140.  Sign up here.

How do batteries work?

How do batteries really work? A convincing simple yet quantitative answer to this question has remained elusive. Textbooks and on-line sources have provided only descriptions but not explanations of basic electrochemistry. All calculations in electrochemistry are based on measured voltages, not atomic or molecular properties. Made-up explanations of batteries in terms of different “electron affinities” of different metals are widely believed but easily disproved, e.g. by concentration cells using the same metal for both electrodes.

A paper in the Journal of Chemical Education by Klaus Schmidt-Rohr (Chemistry) explains how batteries store and release energy, in quite simple terms but based on quantitative data. In the classical Zn/Cu galvanic cell, it is the difference in the lattice cohesive energies of Zn and Cu metals, without and with d-electron bonding, respectively, that is released as electrical energy. Zinc is also the high-energy material in a 1.5-V alkaline household battery. In the lead–acid car battery, intriguingly the energy is stored in split water (two protons and an oxide ion). Atom transfer into or out of bulk metals or molecules plays as big a role as electron transfer in driving the processes in batteries.

How Batteries Store and Release Energy: Explaining Basic Electrochemistry, Klaus Schmidt-Rohr, Journal of Chemical Education, 2018, 95 (10), pp 1801–1810.

Computer Science, Biology & Chemistry have opened faculty searches

Brandeis has open searches for tenure-track faculty in three departments within the Division of Science for this fall.  We are looking forward to a busy season of intriguing seminars from candidates this winter.

  1. Assistant Professor of Computational Linguistics. Computer Science invites applications for a full-time, tenure-track assistant professor, beginning Fall 2019, in the area of Computational Linguistics including, but not limited to Statistical and Neural Machine Translation, Question Answering, Information Extraction, Text Summarization, Syntactic and Semantic Parsing, Dialogue Systems, etc.
  2. Assistant Professor(s) of Biology Biology invites applications for up to two full-time tenure-track positions at the level of Assistant Professor, beginning Fall 2019. Ideal candidates will be conducting innovative research in the broad area of cell biology using any organismal, cellular or in vitro system. Areas of emphasis include, but are not limited to, cell architecture, cell motility, cell division and morphogenesis, organelle function, intracellular trafficking, and compartmentalization.
  3. Assistant Professor of ChemistryChemistry is seeking a creative individual at the assistant professor level for a tenure-track faculty position in organic chemistry or chemical biology.  Exceptional senior candidates in all areas of chemistry will also be considered at the appropriate rank.

Brandeis University is an equal opportunity employer, committed to building a culturally diverse intellectual community, and strongly encourages applications from women and minorities.  Diversity in its student body, staff and faculty is important to Brandeis’ primary mission of providing a quality education.  The search committees are therefore particularly interested in candidates who, through their creative endeavors, teaching and/or service experiences, will increase Brandeis’ reputation for academic excellence and better prepare its students for a pluralistic society.

SciFest VIII will be on Thursday, Aug 2

Scifest VIII, our annual Poster Session featuring undergraduate researchers, will be held on Thursday, August 2. The poster session will be 1:00 to 3:00 pm in the Shapiro Science Center atrium.

SciFest features undergrads who have spent their summers working in both on-campus and off-campus labs doing scientific research, usually alongside grad students, postdocs and faculty members. It an opportunity for these dedicated students from across the Division of Science, including summer visitors and Brandeis students, to present their research for peers and the community.

As of today, 107 students have registered to present.

The public is invited to attend and to discuss research with the students. As always, refreshments will be served.

2018 Prizes and Awards Announced

Congratulations to all recipients of the 2018 prizes and awards for the Division of Science and the departments and programs within the Division.

Division of Science Prizes and Awards

  • Doris Brewer Cohen Award: Richard Haburcak (Math, Chemistry)
  • Rishon M. BIaler ’64 Memorial Prize: Abraham Cheloff (Biology, Neuroscience, Chemistry)
  • Schiff Memorial Award in Science: Meisui Liu (Biology) and Kathryn Shangraw (Biology)
  • Division of Science Prize for Outstanding Research Accomplishment: Heather Schiller (Biology, Neuroscience) and Jordan Saadon (Biology, Neuroscience)
  • Dr. Ralph Berenberg ’65 Prize (dentistry): Brandon Tran
  • Elihu A. Silver Prize (junior research): Julia Tartaglia (Biochemistry)
  • Steinberg Prize (Physical Science with interest in History): Mihir Khanna (Physics, Art History minor)

Biochemistry Prizes and Awards

  • Nathan O. Kaplan Prize in Biochemistry: Jessie Moore (Senior)
  • Professor Dagmar Ringe Biochemistry Award: Miriam Hood (Senior)
  • William P. Jencks Award in Biochemistry: Senmiao Sun (Senior)

Biology Prizes and Awards

  • Biology Department Award For Excellence in Research: Jason Xin
  • Chandler Fulton Prize for Undergraduate Research: Theresa Weis

Chemistry Prizes and Awards

  • Anatol Zhabotinsky Memorial Prize: Sumner Alperin-Lea
  • American Chemical Society Division of Physical Chemistry 2018 Undergraduate Award: Sumner Alperin-Lea
  • Chemistry Department Excellence Award: Samantha Shepherd
  • Melvin M. Snider Prize in Chemistry: Jamie Soohoo
  • American Chemical Society Division of Inorganic Chemistry 2018 Undergraduate Award: Elishua D. Litle
  • American Chemical Society Division of Organic Chemistry 2018 Undergraduate Award: Elishua D. Litle
  • Emily Dudek Undergraduate Teaching Assistant Award: Miriam Hood; Steven Wilhelm

Mathematics Prizes and Awards

  • Jerome Levine Thesis Prize (given annually to a graduate student in mathematics finishing with an outstanding PhD thesis): Yan Zhuang
  • Arnold Shapiro Prize in Mathematics (to a senior who has shown unusual talent and accomplishments in mathematical studies): Richard Haburcak

Neuroscience Prizes and Awards

  • Reis and Sowul Family Prize in Neuroscience: Amanda Shilton
  • John Lisman ’66 Memorial Award for Excellence in Neuroscience Research: Megan Leubner and Casey Lamar

Physics Prizes and Awards

  • Stephan Berko Memorial Prize (This endowed prize was established in 1991 by the family of the late Dr. Berko to annually recognize an outstanding student in Physics): Ali Aghvami (graduate); Carl Merrigan (graduate); Zachary Sustiel (undergraduate)
  • David L. Falkoff Prize (The Falkoff  Prize annually recognizes a graduate student in Physics who demonstrates excellence in teaching): Daichi Hayakawa
  • Physics Faculty Prize (Awarded to a graduating senior for excellence in Physics): Guillermo Narvaez Paliza; Liana Simpson

 

 

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