2 New Faculty Members Join Biochemistry

Tijana Ivanovic and Maria-Eirini Pantelia have joined the Biochemistry department. Both of the new faculty members will begin at Brandeis in January 2016.


tijana_photoTijana Ivanovic, is currently a postdoc at Harvard Medical School.  Stephen C. Harrison is her advisor. She received her PhD in Virology from HMS and her BS in Microbiology and Molecular Genetics from UCLA.

Her research focuses on uncovering fundamental molecular mechanisms of virus translocation across biological membranes, in the distinct contexts of enveloped-virus membrane fusion and nonenveloped-virus membrane penetration.  She applies and develops advanced biophysical and biochemical approaches and combines them with those of virology, molecular biology and cell biology.

Dr. Ivanovic received a grant from the L’Oréal USA For Women in Science fellowship program in 2011.


pandeliaMaria-Eirini Pandelia‘s ‘scientific journey’ started from Greece, where she received her undergraduate degree in Physics from the University of Patras and master of sciences degree in applied Mathematics and Physics from the National Technical University of Athens. She carried out her graduate studies in Germany at the Max-Planck Institute (MPI) of Chemical Energy Conversion (formerly known as MPI for Bioinorganic Chemistry) and received her doctoral degree from the Technical University of Berlin. This was followed by 3 years as a postdoc at PennState University in the Bollinger/Krebs laboratory.

Her research lies in the interface of Chemistry, Biology and Physics with particular focus on the study of metalloenzymes. Her work encompasses the combination of spectroscopic and biophysical techniques together with structural biology and phylogenetics to address the modus operandi of metalloproteins and bioinorganic complexes. Her main expertise is in Mössbauer and EPR spectroscopies coupled to time-resolved kinetics (optical, FTIR) and redox potentiometry. She is interested in understanding how diverse enzymes carry out their bio-transformations and how reaction selectivity in homologous proteins is achieved.

Maria-Eirini’s work at Brandeis will be centered on delineating the mechanisms according to which metalloproteins involved in processes essential for life perform the activation of small (or larger) molecules, how the specific identity of the metals in the active sites allows their chemical diversion and selectivity and what the functional role of iron-sulfur clusters in proteins involved in DNA synthesis and repair is.

 

 

 

 

 

Phi Beta Kappa Elects 51 Division of Science Students

Phi_Beta_Kappa_KeyThe Brandeis chapter of Phi Beta Kappa recently elected 97 new members. Of the 97, at least 51 undergraduate students are majors in the Division of Science (Biochemistry, Biological Physics, Biology, Chemistry, Computer Science, Mathematics, Neuroscience, Physics and Psychology).

Congratulations to the following new Phi Beta Kappa members from the Division of Science:

Biochemistry

Malia Barbra McAvoy
Yehonatan Otzar Meschede-Krasa
Juhee Park
Lior Rozhansky
Hanchen Zhao (double major with Chemistry)

Biological Physics

Abigail Rose Knecht

Biology

Ignatius Ang
Zachary Ian Fried
Jenna Leah Kahane
Ariel Jennifer Katz
Yang Li
Yixuan Liao
Alice Yuan Meng
Khang Vi Nguyen (double major with Chemistry)
Danielle Marie Quintin
Sarah Shin

Chemistry

Khang Vi Nguyen (double major with Biology)
Soobyung Park
Noam Isaac Saper
Hanchen Zhao (double major with Biochemistry)

Computer Science

Kenneth William Foner
Huy Quang Mai
Grady Berry Ward (double major in Mathematics)

Mathematics

Cameron Zhang Fen
Trevor Weiss Kafka
Linda Li
Huy Quang Mai
Stefan Stanojevic
Zhengyang Zhou
Daniel Jackson Kutner (double major in Physics)
Murielle Claire Tugendhaft
Grady Berry Ward (double major in Computer Science)

Neuroscience

Jessica Allison Haley (double major with Psychology)
Kiera Gillian Sarill (double major with Psychology)

 

Physics

Wei Zhong Goh
Stefan Stanojevic
Daniel Jackson Kutner

Psychology

Kyra Jordana Borenstein
Hannah Dvorah Caldwell
Nicole Danielle Cardona
Avi David Cohen
Annie Cui
Jason Michael Desimone
Emily Rose Friedman
Jonathan David Gilman
Clara Emily Gray
Cecilie Gromada
Sarah Jessica Hack-Chabot
Jessica Allison Haley (double major with Neuroscience)
Jessica Lynn Lieberman
Danielle Mizrachi
Emily April Mostow
Linda Sue Nakagawa
Talia Michelle Portal
Jenna Louise Rice
Kiera Gillian Sarill (double major with Neuroscience)
Aliza Naomi Shapiro

See full story on BrandeisNow.

Undergraduate Lab Tours Begin

Are you an undergraduate interested in gaining research experience by working in a lab at Brandeis? Not sure how to find a lab to work in?

The Biology Undergraduate Department Representative (UDRs) have created the Lab Tour Program. The first tour was held on Monday, April 13th. Lead by Biology junior, Sarita Biswas ’16, undergraduates toured the Dorothee Kern, Daniel Oprian and Chris Miller labs. Although a Biology major, Sarita has worked in Kern’s Biochemistry lab for nearly a year. During the tour, students were shown lab equipment and specialized research rooms (cold room, autoclave room) in the Volen Center. Throughout the tour, Sarita discussed the research that is being done in the labs.

Following the tour, Rashieda Pugh ’16 (UDR) and Sarita sat down with the students. Sarita discussed the kind of projects that she has worked on in the past year. Both Sarita and Rashieda shared their experiences in finding a suitable lab to work in, how they find a project to work on once in the lab, and the time commitment during the summer and academic year.

Some of the many questions asked:

  • Will there be a someone there to guide me? There is always a graduate student or postdoc mentoring you.
  • How do you find a lab to work in? Review the faculty webpages, find research that interests you and then email the professors. Do not write all the professors a generic email about opportunities in their lab. It’s unlikely to work. Take the time to find out what kind of research goes on in each lab. Target labs in which you have a genuine interest. Be prepared to show up in person and talk intelligently about research projects with the faculty member. Be prepared to emphasize what you have to offer – skills acquired in courses or other jobs, your dedication and willingness to apply yourself, your reliability and punctuality, your ability to communicate clearly and concisely, etc.
  • Is lab research considered an internship? Yes, it is very much like an internship.

Their advice is that there are a lot of labs here at Brandeis and a lot of ways to find rewarding research experience in a lab!

The Lab Tour continues on April 16th.

John Wardle Named Division of Science Head

John Wardle, Division of ScienceSusan Birren, Dean of Arts and Sciences, has announced that John Wardle, Professor of Physics, will be the new Head of the Division of Science.

The following is Susan’s email:

“I am pleased to announce that John Wardle will be the new Head of the Division of Science.  John is an astrophysicist and Professor of Physics and is a former chair of the Physics department.  In his new role he will oversee science-wide programs and initiatives, including the summer undergraduate research program and will work with Division of Science faculty and staff to identify new directions for the division.  I am delighted that he has agreed to take on this role and I hope that you will join with me in welcoming him.

We all owe a debt of gratitude to Eve Marder who, as the first Head of the Division, created and steered many of the priorities of the Division.  During her time as Head, Eve ably represented the Sciences at Brandeis and beyond, worked to make the Summer Undergraduate Science Program a flourishing success, changed the way we trained students and postdocs in the ethical conduct of research, and worked tirelessly to secure funding and recognition for the Sciences.  Thank you Eve!”

Tenure-track faculty position in Biochemistry

The Department of Biochemistry at Brandeis University invites applications for a tenure-track faculty position, to begin Fall 2014. We are searching for a creative scientist who will establish an independent research program and who in addition will maintain a strong interest in teaching Biochemistry at the undergraduate and graduate levels. The research program should address fundamental questions of biological, biochemical, or biophysical mechanism. Brandeis University offers the rare combination of a vigorous research institution in a liberal-arts college setting. The suburban campus is located 20 minutes from Boston and Cambridge and is part of the vibrant community of academic and biotechnology centers in the Boston area. The application should include a cover letter, curriculum vitae, statement of research accomplishments and future plans, copies of relevant publications, and three letters of reference. Applications will be accepted only through AcademicJobsOnline at https://academicjobsonline.org/ajo/jobs/3366. Additional inquiries may be directed to Dan Oprian, Professor of Biochemistry (oprian@brandeis.edu). First consideration will be given to applications received by December 1, 2013.

Brandeis University is an Equal Opportunity Employer, committed to building a culturally diverse intellectual community. We particularly welcome applications from women and minority candidates.

How bacteria resist fluoride

Fluoride anion is everywhere.  Released into water through the natural weathering of rocks, it’s present to the tune of 5 mM in toothpaste, 30 μM in Cape Cod bay, and 17 μM in Massell pond at Brandeis.

Fluoride levels in our environment (graph).001

Fluoride in the environment, measurements by Ashley Brammer (Miller lab)

Since F is ancient, ubiquitous and toxic to microbes, it’s not surprising that bacteria have evolved defenses to expel it from their cytoplasm.   In an article published in eLife on August 27, 2013, Randy Stockbridge, Janice Robertson, and Luci Partensky from Chris Miller’s lab describe one of these microbial defenses, a fluoride channel called Fluc.  The channel provides a pathway for F to exit the cell across the membrane at a rate of 107 ions per second, while rigorously excluding Cl in order to avoid catastrophic membrane depolarization. The world-record 10,000-fold selectivity isn’t the only remarkable aspect of Fluc, however. The Fluc channel is built on an antiparallel dimer scaffold, with one of the subunits facing the exterior of the cell, and the other facing the interior. Only one other modern-day membrane protein is known to dimerize like this, but the arrangement recalls the inverted structural repeats that are a common, important motif for membrane transporters. Inverted repeats are the product of an antiparallel dimer, like Fluc, that duplicated and fused eons ago.  The sequences drifted over time until the duplication was undetectable by sequence similarity, and the plethora of membrane transport proteins built on this plan was only discovered when the 3-D structures were solved. The Fluc family provides the opportunity to study microorganism resistance to an ancient xenobiotic, as well as membrane protein architecture from an evolutionary origin.

For more, you should read the paper:

Stockbridge RB, Robertson JL, Kolmakova-Partensky L, Miller C. A family of fluoride-specific ion channels with dual-topology architecture. eLife. 2013;2(0):e01084. PMCID: 3755343.

PS: If you’re wondering about the tea on the bar graph, tea plants accumulate F in their leaves.  Cheap teas, made from older tea leaves, actually carry a lot of F, and if you drink a couple quarts of lousy tea a day, you can give yourself skeletal fluorosis.

A facilitated diffusion confusion dissolution

To udirectbindfd1tilize the information contained within a cell’s genes, the enzyme RNA polymerase must find the beginning of each gene (the promoter).  Finding the beginning is a prodigious task:  RNAP must start at a particular base pair of DNA, but the cell contains millions of base pairs to choose from.  It has been proposed that gene-finding challenge is aided by a process termed ‘facilitated diffusion (FD).  In FD, RNA polymerase first binds to a random position on DNA and then slides along the DNA like a bead on a string until it encounters the target DNA sequence.

single-mol-testIn a recently published study in PNAS (1), biophysicists Larry Friedman and Jeffrey Mumm worked with Prof. Jeff Gelles in the Brandeis Biochemistry department to test key predictions of the FD model.  They used a novel light microscope that Friedman and colleagues invented and built at Brandeis, a microscope that can directly observe the binding of an individual RNA polymerase to a single DNA.  The scientists studied the σ54 RNA polymerase holoenzyme, an RNA polymerase found in most species of bacteria.  Surprisingly, none of the three predictions of the FD model that the experiments tested were found to be valid, demonstrating that target finding by the polymerase is not accelerated by sliding along DNA.  Friedman and colleagues instead propose that RNA polymerases are present in such large numbers that they can diffuse through the cell and efficiently bind to their target sites directly.  The absence of FD may explain how other proteins can bind to positions on the DNA that flank gene start sites and yet not interfere with RNA polymerase finding the gene.

Is this the end of the story? Not likely, given previous publications suggesting FD plays a role for some other DNA binding proteins. Using single-molecule techniques like those developed in the Gelles lab, scientists in next few years should give us a better idea if FD is very rare or very common. [editor: as a chemical engineer, I’m sad to see FD not have a role — it seemed like such a nice theory…]

Friedman LJ, Mumm JP, Gelles J. RNA polymerase approaches its promoter without long-range sliding along DNA.  Proc Natl Acad Sci U S A. 2013 May 29. [Epub ahead of print]

 

 

Dogic Lab Wins Andor Insight Award

The ‘Insight Awards‘  is a video contest showcasing research imagery from the physical and life sciences which utilize Andor technology to capture data.  This year, the Dogic Lab submitted a research video to the competition and garnered first prize in the Physical Sciences division for their video of Oscillating Microtubule Bundles.

From the competition notes:

Microtubules are a bio-polymer composed of the protein tubulin and are used extensively in the cell for cellular division, cell motility, and transportation of cargo within the cell. Here, we investigate the material properties of mixtures of microtubules, a depletion agent, and the molecular motor Kinesin. The microtubules, driven by Kinesin motors, spontaneously organize into bundles of microtubules that oscillate in a manner reminiscent of flagella and cilia found in biology. This engineered system will allow us to studying systems of self-propelled and self-organized matter that exist far from equilibrium in the field known as Active Matter.

We use standard fluorescent microscopy to image labeled microtubules in a thin, flow cell microscope chamber. An Andor Clara camera was used in conjunction with a Nikon Ti Eclipse microscope to capture this video.

Video and Entry by Stephen DeCamp.

For this, and more videos from the Dogic Lab, visit their YouTube page or their website at Brandeis University.

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