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]

 

 

Summer Seminars Start on the Sixth

Science is a year-round endeavor, so science seminars will continue over the seminar, though the venues and times may shift.

D-Day for summer seminars this year is June 6, when the Biochemistry & Biophysics Summer Pizza Talks series kicks off with Dr Markus Grütter of the University of Zurich. Grütter will give a special summer on his recent breakthrough-structure of the first heterodimeric ABC transporter. This structure is important because the ABC transporter is a homologue of the CFTR channel (disrupted in cystic fibrosis, one of the most common human genetic diseases). The talk will be in Gerstenzang 121 at Noon on Thursday, June 6.

The Life Sciences Summer Research Seminar Series will start on Monday, June 24, with a talk by distinguished alumna Leslie Meltzer ’03, who has returned to the Boston area as Associate Director of U.S. Medical Affairs at Biogen IDEC, having paid a visit to the other coast to get a Ph.D. in Neuroscience at Stanford in 2008, working with Karl Deisseroth. The Life Sciences Summer Research Seminar Series is organized by the Brandeis University Postdoctoral Association and will be held on Mondays at noon in Gerstenzang 121.

The Genetics Training Grant hosts a panel discussion and lunch focused on careers outside academia

This past Monday, April 29th, students and post-docs, eager to learn more about careers outside of academia, had the opportunity to hear from, and question, panelist who have successfully harnessed their PhD experience to excel in non-academic careers. The event, hosted by the Genetics Training Grant, brought together panelists from several different fields, including scientific publishing, pharmaceutical research, consulting, and intellectual property law. The panelists were Priya Budde, Reviews Editor, The Journal of Cell Biology; Sadanand Vodala, Research Scientist, ARIAD Pharmaceuticals; Derek Buhl, Principal Scientist, Pfizer Neuroscience; Peter Bak, Consultant, Back Bay Life Science Advisors; and John Garvey, Partner, K&L Gates LLP. Each panelist spoke about their background in academia, how they made the transition to their current position, and fielded numerous questions from the audience both during the panel and at the networking lunch that followed.

The panelists gave the audience a sense of what their specific careers entail, and how skills they had acquired during their PhDs were highly relevant to their current work. Some of the transferable skills mentioned included critical thinking and the ability to quickly synthesize information and distill what is most important and interesting about a given scientific finding. These skills enabled them to be highly effective in their jobs, whether efficiently evaluating scientific manuscripts as an editor, or determining the crux of a client’s research as a consultant or intellectual property lawyer.

Current jobs for recent Brandeis Life Science PhDs (graduates 2002 and beyond, n=200)

Current jobs for recent Brandeis Life Science PhDs (Neuro, Mol Cell Biol, Biochem, Biophys graduates, 2002 and beyond, n=200)

Having completed their transition from academia to the business world, panelists were able to highlight some of key cultural and practical differences associated with working in a profit-driven industry. While Derek described his lab at Pfizer as largely mimicking an academic environment (minus the need to perpetually write grants), he and other panelists noted that, unlike academia, business evaluations are based almost exclusively on having achieved specific pre-determined goals. On the upside, for those who exceed expectations in business, there are lots of opportunities to move up the ladder. Other differences that panelists encountered in their non-academic professions included firmer deadlines, higher dressing standards, and less flexible hours.

While the majority of the discussion was specific to the panelists’ career paths, much of the advice applied to career searches in general. The importance of good networking was emphasized. Job seekers were encouraged to make the most of their networks – and their network’s network as well. Each panelist explained how he or she had acquired their job through a combination of effective networking, being proactive, and in some cases, luck. Panelists were quick to point out, though, that time and effort invested were positively correlated with “luck.”

Panelists stressed that effective networking required quickly following through with contacts, and being prepared to impress key contacts with excellent questions that demonstrate your research on a given company. They encouraged the audience to be proactive, and if needed persistent, in reaching out to people whose work they find interesting. Several panelists also emphasized the benefits of acquiring job-related experience. They noted this was a good way to both boost your resume and get a better sense of whether a given profession is the right fit for you. For example, John Garvey recommended joining a consulting or biotech club, and/or taking a business class. Getting involved in job-related activities is also excellent ways to establish good contacts for networking.

Overall the panelist presented several attractive alternatives to a traditional academic career. By carefully analyzing his or her personality, strengths, and working style, each of them had found a rewarding career that effectively utilized their scientific background/training. Priya, the editor, described how she enjoyed being able to see where scientific fields are going and staying up to date with the latest scientific breakthroughs. Derek, the pharmaceutical researcher, explained how it was gratifying for him to be working directly to develop drugs that could benefit people. John, the lawyer, explained how his work solving business problems was important because it helped provide pharmaceutical companies with the financial resources to bring new life-saving drugs to market. The general take-home message from all of the panelists was that, using the right career strategies, one can effectively use one’s PhD as a launching point to successfully pursue many different avenues outside of academia. Those interested in getting a better sense of what career might be a good fit for them are encouraged to visit http://myidp.sciencecareers.org and fill out the survey.

What do Brandeis life science PhD students go on to do?

John Lowenstein (1926-2012)

Professor Gregory Petsko delivered the following tribute for John Lowenstein at Brandeis University Faculty Meeting late last year:

lowensteinJohn Lowenstein, who passed away from pancreatic cancer on November 3, 2012 at the age of 86, joined the Brandeis community in 1958 as a Senior Research Fellow, and became a member of the faculty two years later. From 1974-1995 he held the Helen Rubenstein Chair in Biochemistry; and he was also chair of the department in the 1990s.  John was not only a highly accomplished scientist; he was also an extraordinarily literate man, well versed in English, Russian and German literature, and a staunch devotee of opera, too. Even after his retirement in 2008, he continued to pursue his research interests and to work with students – he continued, in fact, to supervise an undergraduate until a few weeks before he died.

Those are the bare bones facts.  Let me tell you the story.  Many of you may know that John was one of the first members of the Biochemistry Department.  He came in the fall of 1958.  He’d been a Fellow at Oxford University, a position that allowed him a lot of independence, so when Mary Ellen Jones persuaded Nate Kaplan, the legendary founder of the department, to offer him a job, John already had the beginnings of a research program going.  He accepted the offer because America was, at that time, a better place for his wife, who was a clinician.  So he actually came here as an accompanying spouse (he once told me that he considered that a surprisingly liberated role for a man in the 1950s).  Before leaving England, he wrote to both the NIH and NSF to ask if it was OK for a foreigner to apply for a research grant; when they said it was, he wrote two different proposals, one to each of them.  He thought it was unethical to ask for salary on a grant, so he didn’t.  To his surprise, both grants were funded, so he ended up with full research support but no salary support.  Clearly, as we all know, Brandeis is a perfect choice for someone who wants to work without a salary!

Somebody then suggested he write a fellowship proposal, which he did, to the Helen Hay Whitney Foundation.  That was at the time, and still is, one of the most prestigious fellowships in the sciences.  Of course, he got that too, so when he finally showed up at Brandeis as, in essence, a postdoc, he had two grants and full salary support – more than most of the faculty!  Three weeks after he arrived, he started to lecture in Biochemistry on the 3rd floor of Kalman.  John once told me he was delighted that he was able to say that he had outlived that building!  Within 6 years of his arrivak, the Biochemistry Department was listed among the top 10 departments in the country, and it remained there until the mid-70s, when the practice of ranking departments stopped. 

After less than 2 years as a Whitney Fellow at Brandeis, John was already getting offers of faculty positions from other institutions for his work on nonenzymatic phosphate transfer by ATP, a very important process that he discovered.  Kaplan talked him out of considering most of them, but when one came from Tufts, Kaplan immediately promoted him to assistant professor.  By then, John had overcome his ethical objections to putting his salary on research grants…

purine nucleotide cycle

By the early 1970s, John had worked out the function of the important enzyme AMP-deaminase, the founding member of a family of enzymes that are very important in health and disease.  He then went on to do something only a handful of scientists have ever done: he discovered a metabolic pathway, the purine nucleotide cycle that AMP deaminase functions in.  This ought to be called the Lowenstein Cycle, but John once told me that if you discover something so important that you don’t have to name it after yourself, you’ve really done something special!

John always ran a small research lab but in many ways he ran the department for quite some time.  He had served on every possible departmental committee, popular and unpopular, sometimes all at the same time, or at least it seemed that way to him!  He was Chair of the Department in the early 1990s.  When I became chair of the department, a few years ago, I immediately sought out his advice.  He said, “Greg, my advice to you is to start drinking heavily.” 

He taught Biochem 101, the department’s signature graduate course, for many years, and then led the movement for the department to teach undergraduates.  Putting his money where his mouth was, he then taught the basic undergraduate course, Biochem 100 – sometimes two sections a day – until 2005. 

John had three sons; his middle son is a scientist at Johns Hopkins; the youngest is a professor of music, and his oldest is a businessman.  John was very, very proud of his family, but said to me on more than one occasion that the major place in his life, outside that family, was Brandeis.  It’s no accident that, for many years, John was the faculty member all the graduate students went to for advice.  He had a pilot’s license and used to fly sailplanes, but I think the students were quick to identify someone who was always good at keeping his feet on the ground. 

John once said that if he were independently wealthy he would still do what he does.  I was thrilled to hear that because it meant that, even after becoming emeritus, John would still be around a lot, and he was.  The best raconteur in the department, John had a warm, wise and often dryly funny story for every occasion.  It was part of the way he imparted his enormous common sense.  No one here meant more to me as a colleague, a friend, and a role model. He said to me that, when he retired, it meant the Biochemistry Department was going to gain in reputation, because he was going to have much more time for research… Few did it better, or with more style. 

On the occasion of his retirement, I asked John to sum up his years at Brandeis.  He just smiled and said, in his typical understated way, “I like to think I’ve been a cog in something worthwhile.”  We should all be such a cog!

Remembrances may be made to the American Jewish Joint Distribution Committee, www.jdc.org.

Lab flag competition

Brandeis Life Sciences groups combined graphic design, photoshop, latin composition, and punnery in a “lab flag” competition at the holiday party on December 15. Pick your favorite from the entrants below!

 

Pieter Wensink (1941-2012)

Professor Jim Haber presented the following memorial tribute at Faculty Meeting on Nov 8, 2012:

Professor Emeritus Pieter Croissant Wensink passed away on October 2, 2012 in Wellesley, MA. Pieter was born in Washington, DC, in 1941, and grew up in Bethesda and Chevy Chase, MD. He attended Lawrence College in Appleton, WI, but like many young people in the 60s, dropped out. He ended up working in a laboratory at Johns Hopkins, where he discovered a passion for science. He never got his BA, but by taking night courses Pieter got himself accepted as a graduate student at Johns Hopkins, where he received his PhD in Biology in 1971, working with Don Brown, a pioneer in studying the regulation of gene expression in frogs. Pieter then went to Stanford, where he did post-doctoral work with David Hogness. At Stanford, Pieter got in on the ground floor of the new recombinant DNA technology. He published, with Hogness, a landmark paper entitled “A system for mapping DNA sequences in the chromosomes of Drosophila melanogaster” – the fruit fly.

In 1975 Pieter came to Brandeis as an Assistant Professor in the Rosenstiel Center and in the Department of Biochemistry, bringing to Boston the then-rare and prized knowledge of how to clone genes. I remember clearly in 1976 when an MIT professor, David Botstein, and his postdoc, Tom Petes, camped out at Brandeis for several weeks learning from Pieter how to clone yeast genes. Their collaboration resulted in another major paper “Isolation and analysis of recombinant DNA molecules containing yeast DNA.” Soon thereafter Matthew Mesleson arrived from Harvard, to collaborate with Pieter on the “Sequence organization and transcription at two heat-shock loci in Drosophila.” All of these papers were pioneering works.

Pieter also taught these “dark arts” to the people in my lab and launched us and others at Brandeis on the way to understanding the mysteries of chromosome architecture and gene regulation. In 1981 Pieter also wrote a book in collaboration with his Biochemistry colleague Bob Schleif: Practical Methods in Molecular Biology.

Pieter’s own work, carried out with a series of superb graduate students, focused on genes that encode the proteins that make up the yolk of Drosophila eggs. The study of these genes revealed the complicated way that yolk protein genes are turned on only in females and only in their ovaries. Many of Pieter’s students are now Professors in their own right at major universities around the country.

In the early 1990s Pieter was diagnosed with a benign brain tumor – a meningioma – that required two surgeries to extirpate. Probably his tumor was the result of the now-impossible-to-believe treatment of a ringworm infection with X-rays when he was about 2 years old. The second operation left him unable to concentrate as he had, and Pieter, sadly, decided that he could no longer run his lab or give the clear lectures had had been offering. So he left Brandeis as an emeritus Professor with a medical disability. Pieter was remarkably calm and accepting about his situation. He decided to pursue a long-deferred passion to paint, and some years ago he earned his BFA with distinction in painting from the Massachuetts College of Art. Altogether, Pieter had 5 operations on the cancers that led to his death.

Pieter’s greatest joy in life was his family. He was married to Dorothy E. (Perry) for 43 years and was the devoted father of Tom, Alan and Joe (who recently earned his PhD in English from Brandeis).

Most of you never met Pieter, so I thought it would be good to see Pieter and some of his colleagues as we looked in the late1970s (Pieter, Michael Rosbash, Marion Nestle (now oft-interviewed nutritionist at NYU), myself, and David DeRosier). And to see two of his paintings. He was a fine man.

 

Deciding the fate of a stalled RNA polymerase

Ever wondered what happens when the transcription machinery runs into a DNA lesion or a protein roadblock? Alexandra M. Deaconescu, corresponding author and research associate in the Grigorieff laboratory together with HHMI Investigator and Biochemistry Professor Dr. Nikolaus Grigorieff and Dr. Irina Artsimovitch (Ohio State University) address this question in a new review “Interplay of DNA repair with transcription: from structures to mechanisms” featured in the latest issue of Trends in Biochemical Sciences. The review describes emerging mechanisms of transcription-coupled DNA repair with emphasis on the bacterial system.

Materials in Motion: Engineering Bio-Inspired Motile Matter

Life is on the move! Motion is ubiquitous in biology. From the gargantuan steps of an elephant to the tiniest single celled amoeba, movement in biology is a complex phenomenon that originates at the cellular level and involves the organization and regulation of thousands of proteins. These proteins do everything from mixing the cytoplasm to driving cell motility and cell division. Deciphering the origins of motion is no easy feat and scientists have been studying such complex behavior for quite some time. With biology as an inspiration, studying these complex behaviors provides insight into engineering principals which will allow researchers to develop an entirely new category of far-from-equilibrium materials that spontaneously move, flow or swim.

In a recent report in the journal Nature, a team of researchers from Brandeis University consisting of Tim Sanchez, Daniel T. N. Chen, Stephen J. DeCamp, Michael Heymann, and Zvonimir Dogic have constructed a minimal experimental system for studying far-from-equilibrium materials. This system demonstrates the assembly of a simple mixture of proteins that results in a hierarchy of phenomena. This hierarchy begins with extending bundles of bio-filaments, produces networks that mix themselves, and finally culminates in active liquid crystals that impart self-motility to large emulsion droplets.

Their system consists of three basic components: 1) microtubule filaments, 2) kinesin motor proteins which exert forces between microtubule filaments, and 3) a depletion agent which bundles microtubule filaments together. When put together under well-defined conditions, these components form bundled active networks (BANs) that exhibit large-scale spontaneous motion driven by internally generated active stresses. These motions, in turn, drive coherent fluid flows. These features bear a striking resemblance to a biological process called cytoplasmic streaming, in which the cellular cytoskeleton spontaneously mixes its content. Additionally, the system has great potential for testing active matter theories because the researchers can precisely tune the relevant system parameters, such as ATP and protein concentration.

 

The researchers also demonstrate the utility of this biologically-inspired synthetic system by studying materials science topics that have no direct biological analog. Under dense confinement to an oil-water interface, microtubule bundles undergo a spontaneous transition to an aligned state. Soft matter physics describes such materials as liquid crystals, which are the materials used to make liquid crystal displays (LCDs). These active liquid crystals show a rich variety of dynamical behavior that is totally inaccessible to their equilibrium analogs and opens an avenue for studying an entirely new class of materials with highly desirable properties.

Lastly, inspired by streaming flows that occur in cells, the researchers encapsulate the bundled active networks into spherical emulsion droplets. Within the droplet, microtubules again formed a self-organized nematic liquid crystal at the oil-water interface. When the droplets were partially squished between glass plates, the streaming flows generated by the dynamic liquid crystals lead to the emergence of spontaneous self-motility.

This research constitutes several important advances in the studies of the cytoskeleton, non-equilibrium statistical mechanics, soft-condensed matter, active matter, and the hydrodynamics of fluid mixing. The researchers have demonstrated the use of biological materials to produce biomimetic functions ranging from self-motility to spontaneous fluid flows using fundamentally new mechanisms. Additionally, the experimental system of bundled active microtubules is poised to be a model for exploring the physics of gels, liquid crystals, and emulsions under far-from-equilibrium conditions.

To see more videos from the Dogic lab at Brandeis University, check out their YouTube page.

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