My Experience at the Rally for Medical Research Capitol Hill Day

rally photo VA1

BPS public affairs committee member Seth Weinberg, far left, with other biomedical research advocates and U.S. Representative Robert Hurt (R-VA), far right.

On September 17, I joined members of over 300 national organizations to participate in the Rally for Medical Research Capitol Hill Day. Many rally participants were fellow scientists from all across the country, attending to urge Congress to provide robust, sustainable, and predictable funding for NIH in 2016 and beyond. However, most rally participants were patients and loved ones, attending to advocate and show support for biomedical research, as those directly affected by disease and those anticipating with hope new biomedical breakthroughs.

Rally participants were organized into groups based on their home state. My group from Virginia met with four House offices and the two Virginia Senate offices.  At these office meetings, I described my experience as an early career scientist, having seen my peers leave biomedical research or the country for more reliable career opportunities, a direct result of decade-low NIH funding levels. I conveyed that basic science research is critical for advances in patient treatment, but that the clinical implementation of basic science research may take decades, making the need for sustainable and predictability funding that much more crucial. In my group, my fellow rally participants expressed their own personal, and often heartbreaking, stories of how disease had directly touched their lives, and each voiced how imperative supporting NIH and biomedical research is to themselves and those similarly affected.

The House and Senate offices that we met with all agreed that NIH funding is important and optimistically stated that NIH support seems to be one issue that Congress members on both sides of the aisle can agree upon.

Seth H. Weinberg,Research Assistant Professor, Old Dominion University

Glucose Uptake and Consumption

bpj_109_7_3cWithin the cytosol of the cell, glucose is converted into pyruvate that is used as a fuel for mitochondria. The latter supply the cell with energy in the form of ATP (adenosine triphosphate) and also play an important role in many other cellular functions like calcium homeostasis. Glucose-to-pyruvate conversion is mediated by the glycolysis pathway, which also generates ATP. Interestingly, the balance between glycolytic and mitochondrial ATP production differs between cell types and metabolic conditions. Moreover, this balance is often altered during pathological conditions. We studied the effect of acute (30 min) mitochondrial dysfunction, induced by mitochondrial inhibitors, on the balance between glycolytic and mitochondrial ATP production. To this end we developed a strategy to analyze the uptake and consumption rate of glucose in single living muscle cells (C2C12 cells). Cytosolic glucose concentration was measured using the FRET-based glucose nanosensor FLII (FLII12Pglu-700μδ6), which was developed by the Frommer group (Takanaga et al., Biochim. Biophys. Acta 1778:1091-1099, 2008). This sensor consists of a glucose binding domain sandwiched between two fluorescent proteins (CFP and Citrine).

As exemplified by the cover illustration, glucose binding to FLII triggers a conformational change that increases the energy transfer from CFP to Citrine. This is reflected by an increase in Citrine fluorescence intensity (CitrineFRET; upper panel), paralleled by a decrease in CFP fluorescence intensity (middle panel). As a consequence, the ratio between these signals (CitrineFRET/CFP; lower panel) increases and can be used as a readout of free cytosolic glucose concentration. Calibration of the ratio signal and the use of specific inhibitors of glucose uptake/consumption allowed construction of a quantitative mathematical model to predict the steady-state glucose flux (in mM/min). We demonstrated that this flux was rapidly increased upon mitochondrial inhibition, and that this increase fully compensated for the loss in mitochondrial ATP production. The latter suggests that cells can alter the balance between glycolytic and mitochondrial ATP production on demand, to prevent energy crisis and maintain their viability. Our strategy can also be applied to study glucose uptake and consumption in other pathophysiological models such as cancer cells. Since individual cells are analyzed, it is possible to perform inter-cell variability analysis and correlative studies with other readouts. We are currently applying FLII to investigate glucose uptake and consumption in cells with inherited metabolic dysfunction. More information about our research is provided here.

A Young Scientist’s Guide to the Annual Meeting

The 60th Annual Meeting of the Biophysical Society is coming up this February, and I’m planning on being there. It will be my 10th scientific conference as a graduate student, and my 3rd time attending the BPS annual meeting. I’ve been to several different conferences and even organized a couple, but the BPS meeting is undoubtedly my favorite. The diversity and volume of sessions, the career guidance and networking events, and the various extracurricular events have all contributed to the tremendously positive experiences that I’ve had at the annual meetings. It’s also a great place to reconnect with former colleagues and foster new friendships and professional contacts. Of course, everyone has his or her “first time” attending the annual meeting, and it can seem daunting to a young researcher. Don’t panic! I once felt the same way, too. Remember that you are there just like everyone else is: not just an attendee, but a participant in a five-day smorgasbord of biophysics, and what you have to share is important, too.

20131002-Satchal_Erramilli-001At past meetings, I’ve presented my work both in the platform and poster formats, and found both experiences to be extremely enriching. The poster sessions are well organized by topics, and you’ll find yourself surrounded by other researchers who share your interests. This provides an excellent opportunity to get feedback from – and network with – other people who are in the trenches with you. I spent my assigned time at my poster, and used the additional time that day to wander around and converse with the others presenting in that area. One bit of advice that I’ve received – and I’m sure it’s ubiquitously doled out – is to have different versions of your research talk prepared, in 30 second, 2 minute, 15 minute, and 45 minute formats. The “elevator speech” is particularly useful to have down cold before getting to the meeting. Even if you’re not presenting your work, preparing for a meeting is important, and this is a big part of that preparation. No doubt someone at some point during those five days will ask, “So what do you do?” Be ready with a good answer!

In addition to the elevator speech, planning ahead is critical! There are concurrent sessions and tons of interesting things going on all day long, every single day. The schedule is released months in advance, giving you ample time to plan your days. I’ve found the mobile phone app (“BPS 360”) to be helpful, especially since I’m not fond of carrying things around with me. I would also say that it’s totally OK to move between rooms during concurrent sessions to catch talks that you’re interested in. I always felt guilty doing this and tried to skulk out of rooms unnoticed, but I realized it’s a totally normal thing to do. Just plan ahead! One other bit of advice that I’ll pass along to grad students: email someone whose talk you’re interested ahead of the meeting, or ask a question or approach them after a session. This is an easy way to network. Remember, you go to meetings definitely to learn new and exciting things, but also to meet people and have new people meet you. The BPS annual meeting is a great venue for that.

Staying current on social media is another great way to follow the meeting and network with fellow-participants. The Biophysical Society Blog ( is an excellent resource for proceedings from the meeting, in case you missed out on a talk or workshop. Twitter is also a great venue for discussion – be sure to set up an account! This can be a rewarding extension to your professional self, if used properly. In addition to following the society’s official Twitter account (@BiophysicalSoc), simply following the hashtag for the meeting (#BPS16) will yield hundreds of Tweets from participants. The updates are often entertaining and frequently useful, and it’s another great avenue to network with those who share your interests. At the least, you’ll get to find out where (and where not) to go for dinner!

–Satchal K. Erramilli, PhD Candidate, Structural Biology and Biophysics Stauffacher Research Group Department of Biological Sciences Purdue University

Is CPOW Still Relevant?

Gabriela Popescu, University of Buffalo and chair of the Biophysical Society’s Committee for Professional Opportunities for Women, shares her thoughts about the Committee’s place in a changing world, more than forty years after its inception.

As the incoming chair of the Committee for Professional Opportunities for Women (CPOW), I face an important question: More than 40 years since its inception, is CPOW still relevant to the needs of the Biophysical Society membership? To answer, one must determine whether the charge of the committee, its mission, has been accomplished and whether the membership still values this charge.Biophysical_0241(2-8-15)_1

CPOW was charged by BPS to promote a culture of excellence, fairness, inclusion, and diversity; to highlight contributions by women biophysicists; to educate girls and women; and to assist the advancement and retention of women biophysicists. Indeed, since 1972, much has changed in how women biophysicists participate in the Society. For example, women now have strong representation in BPS leadership, among officers as well as within Council and committees; with very few exceptions all symposia and panels include women speakers; and it is much easier for parents of young children, whether women or men, to attend and participate in the Annual Meeting. Still, much change must be brought about to achieve the standards of fairness and inclusion stated in the CPOW charge.

Experts tell us that among chairs of biophysics departments across the US, very few are women; many more men are nominated for BPS awards and fellowships each year than women; and while overt bias is promptly sanctioned, as Tim HuntIMG_8190_2 will tell you, implicit bias still prevents women from contributing at their full potential. That meaningful work remains to be done is also reflected in the energy and commitment with which members engage with the CPOW mission.

On the most recent conference call, in which CPOW-sponsored events for the incoming Annual Meeting in Los Angeles were being discussed, 17 Committee members called in from six countries, and from many time zones! And the consensus was that in addition to the now-traditional events organized by CPOW, more can be done to fulfill the charge of excellence, fairness, inclusion, and diversity that BPS wants to extend to its women members.

Clearly CPOW will continue to be instrumental in helping the BPS achieve these endeavors. Our work is supported by other BPS officers, Council, and committees, with the Early Careers, Inclusion and Diversity, and Membership committees playing key roles. Most importantly, we will welcome input and participation by all BPS members, women as well as men, to make CPOW obsolete in the nearest future.

Rally for Medical Research: September 17

Rally for Medical Research

Federal funding for medical research is in jeopardy, threatening the US biomedical research enterprise, the future health of our citizens, and the US economy.  On September 17th, the Biophysical Society will be joining with over 300 national organizations to bring together researchers, patients, and medical professionals to meet with House and Senate offices on Capitol Hill in Washington, D.C. to educate Congress on the important role federal funding plays in biomedical research.  Specfically, we will:

  • Urge Congress to make funding for the the NIH a national priority.
  • Raise awareness about the connection between today’s discoveries and tomorrow’s cures.
  • Explain why the federal government has a critical role to play in funding research.

While the Society will have four members of the public affairs committee participating in the Hill visits on Thursday, September 17, the Society leadership hopes that many more members will participate by picking up the phone, sending an email, or tweeting in support of the Rally. It’s easy to get started on the Biophysical Society’s website.

The Biophysical Society is proud to be a Bronze Level Supporter of the Rally for Medical Research.  

Dynamics and Allostery in Ferritin

bpj_109_6_3cWe all know it is important to get the proper amount of iron in our diet. If the protein that processes iron isn’t properly functioning, this aphorism is just that.  The protein responsible for this is called Ferritin, a 24 subunit protein whose functions is the oxidation and storage of iron. Disruption of ferritin can lead to a whole host of ailments from cataracts to Alzheimer’s disease.

The cover image is a ribbon diagram of human ferritin (PDBID 3AJO) colored by its dynamic flexibility index (DFI) profile, a measure of each residue’s contribution to a protein’s dynamics, where blue is the lowest (most rigid) and red is the highest (most flexible). Traditionally, proteins were thought to obey the sequence-structure-function paradigm—the function of a protein is embedded in its structure. The new paradigm is the sequence-structure encoded-dynamics-functions paradigm—a protein’s structure encodes its dynamics, which encodes its function, leading to a deeper understanding of protein function. We have found that disruption of dynamic allosteric residue coupling of residues in ferritin leads to impaired protein function. There are certain rigid parts of the protein that function as hinges, transmitting motion. If a mutation, which is further away from the hinge site, allosterically loosens the hinge, then the protein cannot properly transmit motion, breaking the dynamics, thus breaking the function. This is similar to the hinge of a door. If the hinge gets loosened, motion will not be properly transmitted and the door cannot function properly.

The DFI metric has led to advancements in understanding the fluorescence of GFP, finding new functions through protein evolution in betalactamase, and computational prediction of functional impact of non-synonymous single nucleotide polymorphisms observed in human populations. Using DFI analysis, we have investigated how the function diverged for a given protein family, while maintaining the same exact fold/ structure.  Comparing the DFI profiles of different members of the same protein family shows that mutations leading to shifts in hinge sites alter the dynamics, thus the function (1,2).  Our proteome-wide conformational dynamics analysis using DFI indicates that certain sites play a critical role in functionally related dynamics (i.e., those with low dfi values), therefore, mutations at those sites are more likely to be associated with disease (3,4)

– Avishek Kumar, Tyler Glembo, Sefika Ozkan


  • Zou T, Risso VA, Gavira JA, Sanchez-Ruiz JM, Ozkan SB “Evolution of Conformational Dynamics Determines the Conversion of a Promiscuous Generalist into a Specialist Enzyme”. (2015) Mol Biol. Evol. 32:132-143.
  • Kim H, Zou T, Modi C, Dorner K, Grunkmeyer TJ, Chen L, Fromme R, Matz MV, Ozkan SB, Wachter RM, “A hinge migration mechanism unlocks the evolution of green-to-red photoconversion in GFP-like proteins”. (2015) Structure , 23:34-43
  • Butler MA, Gerek ZN, Kumar S and Ozkan SB “Dynamically critical sites at protein interface are more prone to disease” (2015) Proteins, 83:428-435
  • Gerek ZN, Kumar S and Ozkan SB* Structural dynamics flexibility informs function and evolution at a proteome scale” (2013) Evol Appl. 6:4223-4332. doi: 10.1111/eva.12052

It’s Time to Raise the Caps on Capitol Hill

Capitol_hillThey say an ounce of prevention is worth a pound of cure, but some in Congress haven’t gotten the message. On October 1st, if Congress doesn’t take action, the disastrous budget cuts to our nation’s most critical programs—including research funding, national labs, and education– will go back into effect, causing pain to millions of Americans across the country.

How did we get here? In 2011, Congress passed a law that cut federal spending by nearly $1 trillion and said that if lawmakers couldn’t agree on a plan to reduce our deficit by $4 trillion, another $1 trillion in automatic, arbitrary and across the board budget cuts would start to take effect in 2013. Though the “Murray-Ryan” deal temporarily stopped these cuts from taking place, that deal expires in fiscal year 2016. That’s why the Biophysical Society is joining more than 2,500 other national, state and local organizations are calling on Congress to avoid the impending fiscal disaster and end sequestration. These organizations have come together to say, Raise the Spending Caps. Enough is enough.

The impending cuts will be bad, really bad. If Congress does not work together to stop sequestration, the resulting budget could:

  • Result in further cuts for the National Institutes of Health, which under sequestration would be reduced to 2002 spending levels–a major disinvestment in exactly the areas where investment is needed to support growth.
  • Sequestration relief would also cause the gross domestic product to grow by as much as 0.6 percent in 2016 and as much as 0.4 percent in 2017. Easing those ceilings would lead to increased government spending, which in turn would lead to an increase in economic output and higher employment, according to CBO.
  • Shortchange Veterans’ Administration medical care by $690 million, meaning 70,000 fewer veterans receiving medical care, fewer staff critical to improving quality of care, and delays in medical research;

Experts across the political spectrum agree these programs aren’t a driving factor behind our nation’s mid- and long-term fiscal challenges. In fact, reversing sequestration could actually create as many as 1.4 million jobs over the next two years, the nonpartisan Congressional Budget Office (CBO) reports.

So Congress can act to end a failed policy now and prevent another fiscal crisis, or deal with finding a cure for its aftermath. There is bipartisan agreement that sequestration is bad policy and ultimately hurts our nation. Let’s choose prevention over cure and Raise the Spending Caps.

ON THURSDAY SEPTEMBER 10, every Congressman and Senator will receive a “Raise the Caps” baseball cap along with a letter signed by over 2500 organizations asking them to fix the budget once and for all.  The Biophysical Society is proud to be a sponsor of this effort.