Summer course on building a microscope from simple components

This past June the MRSEC Center offered a condensed summer course based on the popular graduate course QB120: Quantitative Biology Instrumentation Laboratory.

Professor Dogic

The course was taught by Zvonimir Dogic of the Physics Department (pictured).   Prof. Dogic has extensive experience with several forms of microscopy and his Lab features several home-built or heavily modified optical setups.

The course is designed to offer students hands on experience with building their own optical setups from basic components as well as learning how to optimally acquire imaging data from commercial microscopes.  The focus was on understanding the physics behind microscope function and leveraging that knowledge towards improving data acquisition in the lab.

Initially, students used basic lenses, apertures, an objective, a camera and a light source to build the simplest possible light microscope.  This initial setup was quickly extended to include Köhler illumination, a core principle in microscopy which allows even illumination of the sample as well as access to the conjugate image plane for image filtering.

The next project required students to build a fluorescence microscope, a highly relevant and ubiquitous technique in biological imaging.  To image a slide with fluorescently labeled beads students used a dichroic mirror to separate excitation light at one wavelength from emission light at another wavelength.  A schematic diagram, a photo of this setup with the light path superimposed and actual data acquired with one of these microscopes can be seen in the video below.

Next, a more advanced technique in microscopy, total internal reflection microscopy (TIRF), was introduced and an imaging setup using this technique was built.  TIRF microscopes excel at imaging small molecules that are immobilized in a small area.  A laser beam was pointed to shine through a prism at an angle sufficient to cause total internal reflection and the resulting evanescent wave caused fluorescent excitation of the sample.  The video below shows a schematic and imaging data of a TIRF microscope built by students.

Finally, students used commercial microscopes to understand the principles behind phase contrast and difference interference contrast microscopy, both techniques well suited for imaging samples that are nearly transparent.

Overall the Course provided an excellent introduction to the physical principles behind microscope function.  I highly recommend it to anyone interested in using microscopes in their research!

Life science grads and postdocs pack room for Career Panel

On Monday, Brandeis University hosted a Career Panel specifically devoted to discussing job opportunities and career paths for individuals with life science PhDs.  The event, sponsored by the Genetics Training Grant, was organized and hosted by Prof. Bruce Goode (Biology) and was very successful in drawing a crowd, with an audience estimated at 90 students and postdocs,

The professional credentials of the assembled panelists reflected the purpose of the seminar itself: a broad sweep of career paths each making use of post-secondary education in the life sciences.  Beyond professional success, the panel was further notable because it was composed largely of women, most of whom managed families along with their careers.

First, representing the academic research career path, was the likable Prof. Avital Rodal of the Brandeis Biology Department.  As a recent hire, Prof. Rodal was extensively queried about the process of applying and successfully being offered a tenure track academic position.  Prof. Rodal cited receiving her own grant funding as well as a strong record of publication as reasons for her success.  Michelle Hoffmann (Back Bay Life Sciences Advisors) has built a career in business and management consulting and discussed which skills from her academic training prepared her for her success in the consulting industry.  Shoumita Dasgupta is an eight year veteran of the teaching faculty at Boston University and advised the audience on how to obtain relevant teaching experience during graduate training and also described how her own career as an educator has begun to include higher positions (she is now an assistant dean) in the admissions department at the medical school.  Meredith LeMasurier works as an editor for the journal Neuron and provided insight into the process of academic publishing.  Her role in the organization involves assessing the merit of submitted articles in the context of the literature and coordinating the efforts of reviewers and authors.  Finally, Jake Harrison (Joule Unlimited) works as an experimental scientist for a small biotechnology sector company.  Jake noted that, like academia, the small company environment allows him to pursue a rigorous scientific agenda combined with the professionalism of a corporate workplace.

After brief introductory statements from each of the panelists, the floor was open for questions, and audience members were interested to learn about job availability and job security.  Jake advised trainees to invest time in building comprehensive profiles on employment focused social networking sites such as LinkedIn.  Shoumita urged students to build their professional network by talking about their career aspirations often with peers and mentors as opportunities can often arise through existing connections.  Michelle emphasized the importance of putting together a sharp professional resume (different than an academic CV) and doing ample homework before contacting a company.

After the event, attendees expressed great interest in having panels on a regular basis, with panelists from additional areas of the job market. A particular interest was in individuals employed by the government or working in a public health or in health policy related fields.

An over arching theme of the discussion was that jobs in any of the career paths are highly competitive but, nevertheless, many exciting options exist for individuals with PhDs in the life sciences.  Overall, given the highly pertinent career information and the opportunities to network directly with individuals in a variety of career paths, all trainees would be well advised to attend future versions of this career panel.

Physics students present research at 20th Annual Berko Symposium on May 16

On Monday, May 16, the Physics Department will hold the Twentieth Annual Student Research Symposium in Memory of Professor Stephan Berko in Abelson 131. The symposium will end with talks by the two Berko Prize winning students, undergraduate Netta Engelhardt and graduate student Tim Sanchez. The whole department then gathers for a lunch of cold cuts, cookies and conversation. “It’s a great way to close out the academic year,” said Professor of Astrophysics and Department Chair John Wardle. “We come together to celebrate our students’ research and hear what the different research groups are doing.”

The undergraduate speakers will describe their senior thesis honors research. This is the final step in gaining an honors degree in physics, and most of them will also be co-authors on a paper published in a mainline science journal. The graduate student speakers are in the middle of their PhD research, and will disucss their progress and their goals.

The prize winners are nominated and chosen by the faculty for making particularly noteworthy progress in their research. Graduate student winner Sanchez’ talk is titled “Reconstructing cilia beating from the ground up.” He works in Professor Zvonimir Dogic’s lab studying soft condensed matter. Undergraduate winner Engelhardt’s talk is titled “A New Approach to Solving the Hermitian Yang-Mills Equations”. She works with Professors Matt Headrick and Bong Lian (Math) on problems in theoretical physics and string theory. The schedule for Monday morning and abstracts of all the talks can be found on the Physics Department website.

Sanchez’ research very much represents the growing interdisciplinary nature of science at Brandeis. Here, a physicist’s approach is used to study a biological organism. Professor Zvonimir Dogic says of his work “He has made a whole series of important discoveries that are going to have a measurable impact on a number of diverse fields ranging from cell biology, biophysics, soft matter physics and non-equilibrium statistical mechanics.  His discoveries have fundamentally transformed the direction of my laboratory and probably of many other laboratories as well.”

Engelhardt’s research is much more abstract and mathematical, and concerns fundamental problems in string theory, not usually an area tackled by undergraduates. Professor Headrick says “Netta really, really wants to be a theoretical physicist, preferably a string theorist. She has a passion for mathematics, physics, and the connections between them.” He adds that she is utterly fearless in tackling hard problems. Netta has been awarded an NSF Graduate Research Fellowship based on her undergraduate work here.  Next year she will enter graduate school at UC Santa Barbara and will likely work with eminent string theorist Gary Horowitz, who has already supervised the PhD research of two other Brandeis physics alumni, Matthew Roberts ’05, and Benson Way ’08.

This Student Research Symposium is now in its 20th year. The “First Annual…..” (two words which are always unwise to put next to each other) was initiated in 1992 by Wardle to honor Professor Stephan Berko, who had died suddenly the previous year. Family, friends and colleagues contributed to a fund to support and celebrate student research in his memory. This provides the prize money which Netta and Tim will share.

Stephan Berko was a brilliant and volatile experimental physicist who was one of the founding members of the physics department. He was born in Romania in 1924 and was a survivor of both the Auschwitz and Dachau concentration camps. He came to the United States under a Hillel Foundation scholarship and obtained his PhD at the University of Virginia. He came to Brandeis in 1961 to establish a program in experimental physics and worked tirelessly to build up the department. Together with Professors Karl Canter (dec. 2006) and Alan Mills (now at UC Riverside) he established Brandeis as a world center for research into positrons (the anti-matter mirror image of ordinary electrons). In a series of brilliant experiments they achieved many “firsts,” culminating in election to the National Academy of Sciences for Steve, and, it has been rumored, in a Nobel Prize nomination for the three of them. Steve was as passionate about teaching as he was about research, and when he died, it seemed most appropriate to honor his memory by celebrating the research of our graduate and undergraduate students. During the coffee break on Monday, we will show a movie of Steve lecturing on “cold fusion,” a headline-grabbing but phony claim for producing cheap energy from 1989.

Susan Lindquist talks about prions on Apr 8

Susan Lindquist of the Whitehead Institute will speak about at Brandeis on April 8 at 11;30 am in Gerstenzang 121 in the Biochemistry/Biophysics Friday Pizza Talks series, by special invitation of the Biochemistry graduate students. Lindquist’s talk is entitled “25 New Prions: surprising biology, surprising biochemistry“. The Lindquist lab has made remarkable progress in understanding the role of protein folding, elucidating the role of heat shock proteins (molecular chaperones) and most recently in discovering new prions (proteins that can change into a self-perpetuating form) and suggesting new roles for prions in processes such as memory. Lindquist has received numerous awards, including the National Medal of Science, Max Delbrück Medal, the Mendel Medal, and the Otto Warburg Prize.



Brandeis is one of the co-organizers of the third annual New England Undergraduate Computing Symposium which will be held on Saturday April 9th at Tufts University. This symposium is designed to build community among undergraduate Computer Science majors in New England and also to increase the diversity of our undergraduate majors by actively reaching out to under-represented groups and encouraging them to participate. Students register online at by completing a simple form describing the project they plan to demo or present as a poster. We expect to have 60-80 students projects and around 150 students and faculty attending the symposium. If you are an undergrad that has written an interesting mobile app, or completed a creative project in one of your classes, or are working in a research lab on an exciting problem involving computation, please visit the site and register to present your project and/or demo your code.


(EL)2 2011

(EL)2 2011. the Experiential Learning, Engaged Learners Symposium held each Spring at Brandeis, will take place on the afternoon of Thursday, March 24th, in the Levin Ballroom and International Lounge. Brandeis President Frederick M. Lawrence will be the keynote speaker. Student presenters include undergraduates from Biology, Chemistry, Mathematics, Neuroscience, Physics, Psychology, as well as a wide range of other disciplines across the university, will present results from research, internships, and other learning experiences.

For more information, see the symposium website or download the symposium program (PDF).

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