REU Students Arrive for 2016 Summer Research


Amber Jones and Susan Okrah

Alongside the more than 100 Brandeis science undergrads doing research this summer, there are 19 students who are participating in our Research Experiences for Undergraduates (REU) programs. Some students are from Brandeis, but most call universities in Kansas, Virginia, Pennsylvania, New Jersey their academic homes. Eight students are from Hampton University as part of the Partnership for Research and Education in Materials (PREM) initiative between Hampton and Brandeis. The two universities are focused on fostering interest in research science in under-represented groups of undergraduates.

The two independent REU programs were each created 6 years ago with funding from the National Science Foundation (NSF) with a goal of providing a 10-week period of intensive lab research experience to rising sophomores and juniors interested in scientific careers. Professor Susan Lovett is the director of the Cell and Molecular Visualization REU and Dr. Anique Olivier-Mason is the director of the Material Research Science and Engineering Center (MRSEC) REU.

The online application process required each student to submit a transcript, two letters of recommendation and write two essays describing their research experience (if any) and their academic and research goals. This year, 8 students are participating in the MRSEC site; 11 students are working in the Biology-based Cell and Molecular Visualization REU.

Amber Jones, who is going to be a junior at Hampton University this fall, is working in the Avi Rodal lab where she is researching how proteins can be taken on and off of cell membranes. From here, she is hoping to target specific proteins that will ultimately aid in disease research.

Amber has worked in a lab before, but believes nothing could have prepared her for her experience at Brandeis. Her REU lab work has been very involved, but she wasn’t expecting the ups and downs that are a part of lab research. The graduate students and other lab members have been supportive. She has been told “it’s okay; it’s science!”

Returning REU student, Alex Cuadros is working in the Liz Hedstrom lab, says he can go to Cell and Molecular Visualization REU coordinators Cara Pina and Laura Laranjo for assistance. They “have more experience in the lab and they tell me that things don’t always work for them. They say that ‘it’s just part of the science’.”

Nicholas Martinez, who is working in Timothy Street’s lab said, “The biggest challenge I have encountered this summer with my research is being able to do cope with disappointment. Since I am working on a defined timetable and my time here at Brandeis is limited, I want to make as much progress as possible with my research.”

Susan Okrah is working in the Seth Fraden lab this summer. She believes this experience is different from a Chemistry class at Hampton University where you are given an experiment and the results are known. In the REU program, students are given a project that is a subset of their lab’s research. Unlike school, the outcome of their research is unknown. Susan said, “We are given a direction and told to see if it works.”

Alex said that in class he has learned how to do experiments, but at Brandeis he is “doing something that has not been done before so there’s no right method.” It’s also helpful to be able to ask advice about how to approach his research and “Then you go back and you figure out how to do it. You are forced to think independently.”

During the academic year, Alex works in a Biochemistry lab at UMass Amherst. He landed the job last fall as a direct result of his 2015 REU research. How did he get the job in a very competitive environment on the large UMass campus? He presented the poster that he prepared for SciFest 2015.

The most valuable lesson learned this summer? “Resilience” said Amber. Learning to cope with the changing tides of research is important. As Susan said, “people don’t really understand what goes into research until they’re here.”

Part of the REU program involves attending journal clubs and lab meetings, but the most valuable experience of this program is simply being in a lab. Both Amber and Susan agree that anyone thinking about a career in research should go through an intensive research experience such as this. Jones noted, “I wasn’t really expecting to get this type of understanding. I really appreciate that now that I’m here.”

Both Nicholas and Alex ultimately would like to attend graduate school. For Nicholas, “being able to participate in the Cell and Molecular Visualization REU program at Brandeis has been a great opportunity for me to diversify my knowledge and skill set in scientific research prior to applying for graduate school next year. This It has been a great way for me to gain experience in a new area of research that I am interested in and to become part of a different scientific community.”

The REU students are hard at work wrapping up their research and preparing their posters for the SciFest 2016 poster session that is scheduled for Thursday, August 4.

Sprout Award Winners Announced

The recipients of the 6th annual Sprout Awards have been announced. There will be eight teams from labs in the Biology, Biochemistry, and Chemistry departments sharing the $100,000 in funding in FY 2017. The Sprout program’s grant pool was doubled this year in order to expand the support for the promising innovation and research that is happening here at Brandeis University.  The Sprout program, created 6 years with the intent to encourage entrepreneurial activity, is sponsored by the Office of the Provost and the Hassenfeld Family Innovation Center. It is administered by the university’s Office of Technology Licensing

(read more at Brandeis Now).


DUB inhibitors _or_ why you should you eat your broccoli

Eat your broccoli!

We’re constantly bombarded by advice on which foods to eat or not eat, but skeptics among us often find compelling evidence for a convincing mechanism of how the foods promote health hard to come by – food has many components, and there are many different cells and metabolic pathways in those cells with which those components interact.

phenethyl isothiocyanate (a component of cruciferous vegetables)

phenethyl isothiocyanate (PEITC, a component of cruciferous vegetables)

Consider broccoli. It is well established that cruciferous vegetables have wide-ranging health benefits, apparently reducing cancer risks and lowering inflammation.  One set of phytochemicals responsible for the potent anti-cancer and anti-inflammatory properties are called isothiocyanates or ‘ITCs’.  It is now four decades since the discovery of ITCs, yet a molecular understanding of what ITCs do in a cell has proven elusive.

In a paper published this month in Cancer Research, Brandeis research scientist Ann Lawson, working in Liz Hedstrom’s laboratory, together with graduate students Marcus Long (Biochem) and Rory Coffey (Mol Cell Biol) and scientists from UbiQ and from Boston College, has shown that ITCs block the action of deubiquitinating enzymes (DUBs),  including the tumorigenesis-associated enzymes USP9x and UCH37, at physiologically relevant concentrations and time scales.

DUB inhibition provides a simple, unifying explanation that can account for many of the diverse health effects of ITCs. Understanding of how ITCs work at the molecular level may, one day, lead to new drug therapies for illnesses such as cancer, chronic inflammation, and neurodegenerative diseases.

Are you ready for your broccoli now? Me, I think I’ll have some kale sprouts.

Lawson AP, Long MJ, Coffey RT, Qian Y, Weerapana E, El Oualid F, Hedstrom L. Naturally occurring isothiocyanates exert anticancer effects by inhibiting deubiquitinating enzymes. Cancer Res. 2015

Sprout Grant Winners Announced

Winners of the 2013 Sprout Grant competition held by the Brandeis Office of Technology and Licensing have been announced. Sprout grants support research that is “novel, patentable and [has] commercial potential“, and encourage students to think about new and different ways to apply their basic science for practical good. Each team applying for a grant must be led by a Brandeis student or postdoc (noted in asterisks below), who were responsible for presenting their proposals to the review panel.

Teams that received funding.

  • Marcus Long (*), Ann Lawson, Lior Rozhansky ’15, and Liz Hedstrom: $20,000 to develop novel inhibitors of deubiquitinating enzymes;
  • Michael Heymann (*), Achini Opathalage, Dongshin Kim, and Seth Fraden: $5,500 for its development of CrystalChip;
  • Michael Spellberg (*), Calla Olson, Marissa Donovan, and Mike Marr: $10,000 to develop a tool to purify Calmodulin-tagged recombinant proteins;
  • Julian Eskin (*) and Bruce Goode: $2,000 for work on a rapid and efficient kit to purify actin;
  • Eugene Goncharov ’13 (*), Yuval Galor ’15,  and Alex Bardasu ’15: $2,500 towards development of their iPhone app LineSaver, which collects data on local hotspots and gives users an estimated wait-time for restaurants, clubs and tourist attractions.

You can read more at BrandeisNOW

Mushroom tyrosinase and the HA tag: a new method for protein labeling

In a new paper in ChemBioChem, researchers from the Hedstrom lab describe a novel method for protein labeling that is versatile and selective.  The method involves the modification of HA tags (a short amino acid sequence commonly used as an epitope tag that contains several tyrosines) selectively in a variety of ways using mushroom tyrosinase. This cheap and versatile chemical biological tool can effect HA tag cleavage, aggregation, or functionalization by changing conditions. The method for dye-labeling HA-tagged proteins has been applied in both E coli and mammalian cell lysates.

Long MJ, Hedstrom L. Mushroom Tyrosinase Oxidizes Tyrosine-Rich Sequences to Allow Selective Protein Functionalization. Chembiochem : a European journal of chemical biology. 2012. (DOI: 10.1002/cbic.201100792)

Greasy tags in Nature

A recent News & Views piece from Nature entitled “Chemical biology: Greasy tags for protein removal” talks about the significance of Long, Gollapalli & Hedstrom’s paper on “Inhibitor Mediated Protein Degradation” (Chem Biol. 2012 May 25;19(5):629-37.) in opening new avenues for drug design

Sprout Grants Awarded to Seven Groups

Another Brandeis NOW story covers the results of the 2012 Sprout Grant competition. Of 20 applications received, half were software related, half life sciences and physical science-related, so the groups were judged separately. Thirteen groups were asked to return for a second round of interviews, coaching and presentations to outside panels of industry judges.  Seven groups were awarded grants:

2012 Sprout Grant winners, life and physical sciences:

Radiation detector, Wellenstein, PI $20,000
  • Tuberculosis treatment, therapeutic, Hedstrom, PI $17,000
  • Cold Stage for Light Microscopy, microscope tools, Turrigiano, PI $16,000
  • Conditional gene silencing, research tool, Lau PI, $6,000

2012 Sprout Grant winners, software:

  • Innermost Labs, social network. Sahar Massachi and Adam Hughes, $7,500
  • Digital Learning Analytics, learning analytics, Larusson PI  $6,000
  • Campus Bash, social network, Y. Sebag, and M. Jafferji $6,500

For more information about the projects and the judging process, read the story at Brandeis NOW.

Who is Selma?

A new paper in Angewandte Chemie International Edition from a Brandeis group led by postdoc Iain MacPherson, Professor of Biology Liz Hedstrom and Assistant Professor of Chemistry Isaac Krauss introduces a new technique they dub SELMA, short for “selection with modified aptamers”. Currently available selection methods can identify the few oligonucleotides in a library of 107 random DNAs or RNAs that bind specifically to a target protein (these specific binders are termed aptamers). However, nucleic acids have a very limited repertoire of chemical functionality — SELMA expands this functionality by introducing an alkyne-modified nucleotide that can be coupled to virtually any azide-containing compound using a copper catalyzed azide-alkyne cycloaddition reaction (“click chemistry“).

The Brandeis group used SELMA to create a library of sugar-modified oligonucleotides and selected for glycoclusters that mimic the epitope of 2G12, an antibody that protects against HIV infection by binding to a cluster of high-mannose glycans on the HIV envelope protein gp120. This is the first example of the application of directed evolution to protein-carbohydrate interactions, a particularly difficult class of interactions to mimic with traditional synthetic methods. Protein carbohydrate interactions are involved in wide array of biological processes, including cell-cell signaling, cell migration and developmental programming as well as immune recognition, so this method should prove very useful.

MacPherson, I. S., Temme, J. S., Habeshian, S., Felczak, K., Pankiewicz, K., Hedstrom, L. and Krauss, I. J. (2011), Multivalent Glycocluster Design through Directed Evolution. Angewandte Chemie International Edition, 50: 11238–11242. doi: 10.1002/anie.201105555


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