The Science Behind the Image Contest Winners: MinD, Spirals, and Turing Patterns

Each year the Biophysical Society hosts an image contest in conjunction with the Annual Meeting. And each year we are blown away by the beauty, the variety, and the scientific advancements encaptured by the submitted images.

Annual meeting attendees vote for their favorite images and the top three vote getters are recognized with prizes, as well as in the Society newsletter. To follow-up this year, we will be featuring the winners here on the BPS blog, so that readers can learn more about the images and the research behind them.  Today, we start off with the third place winner, Anthony G. Vecchiarelli, a research fellow in the laboratory of Kiyoshi Mizuuchi at the National Institutes of Health, where he uses microfluidics and single-molecule microscopy to reconstitute and visualize self-organizing systems involved in intracellular organization. Vecchiarelli notes that “Collectively, these studies have fundamentally changed our understanding of intracellular spatial organization and unveiled a new mode of transport that uses protein patterns on biological surfaces for the positioning of DNA, organelles, and the cell-division apparatus.”

Min-Spiral---3rd-place_2My submission to the 2015 BPS image contest shows one of the many stunning and dynamic patterns that this minimal system can achieve when reconstituted in our flowcell. At a wave front, MinD binds the membrane. Towards the rear of the wave, MinE accumulates up to a threshold density that results in the precipitous release of both proteins. Once MinE also releases the bilayer, MinD initiates another wave. As shown in our image, this interplay can form spirals, which are consistent with Turing patterns based on reaction-diffusion principles.

Similar spirals were first reconstituted on flat bilayers by Martin Loose while in the Schwille group (Loose et al., 2008). Together, the Schwille and Mizuuchi labs have used this technique to provide significant advances in understanding the patterning mechanism (Loose et al., 2008; Ivanov et al., 2010; Vecchiarelli et al., 2014). It is an exciting time to study this unique positioning mechanism as a growing diversity of intracellular cargos have been shown to use related systems for their subcellular organization (Vecchiarelli et al., 2012). We anticipate that surface-mediated bio-molecular patterning will become an emerging theme throughout all kingdoms of life.

I submitted this image to the BPS Image contest because I love how it emphasizes what can be achieved with proteins when released from the confines of the cell. In vivo, MinD and MinE form a pole-to-pole oscillator. But on an expansive flat bilayer, their biochemical potential for pattern formation is unleashed. MinD and MinE can form a variety of patterns including the spirals shown in my image. Dissecting how these patterns form outside of the cell is unraveling the oscillatory mechanism used inside the cell.

“What I cannot create, I do not understand.”  This quote by Richard Feynman is the essence of synthetic biology. To say that we fully understand a cell, we must first build one from the bottom up. We are approaching a time where it is feasible to experimentally challenge the concept of a protocell. The MinCDE system, and related positioning systems, will be key to such an endeavor because they are composed of a minimal number of components that self-organize to position essential cargos, such as the cell division apparatus. But first we must define the systems and develop a full biochemical understanding of the components, which can be achieved via cell-free reconstitution experiments presented in the image. I hope this image gets others just as excited and motivated as I am about studying this fascinating pattern-mediated positioning system, which may turn out to be the norm as opposed to the exception in all cells.

This image shown is a Turing pattern. Alan Turing was first to describe a mathematical model called “reaction-diffusion” that explains how the concentration of one or more substances distributed in space changes after a local reaction and subsequent diffusion. Alan is mainly known for conceiving of a machine that we now call a computer, and for breaking the German Enigma code, which played a pivotal role in ending WWII. But he always had a fascination with patterns in nature and his one and only Biology paper that describes reaction-diffusion is also his most cited. Turing was not applauded for these extraordinary efforts. Rather, because Alan Turing was gay at a time it was illegal, he was sentenced to chemical castration, labeled a security risk, and lost his job as perhaps one of the best code breakers that ever lived. The resultant depression led to suicide. I hope this image reminds viewers of Alan’s ongoing contributions to science.

Supporting Scientific Information

The intricate subcellular organization of a eukaryotic cell is mainly communicated by actin filaments, microtubules, and motor proteins that drive along these cables. Recent improvements in microscopy have recently shown that bacteria also display complex intracellular organization. The view of bacterial cells as simply sacks of enzymes is obsolete. But instead of using cables and motors for moving the ‘innards’ of a bacteria cell, dynamic protein patterns on biological surfaces, such as the inner membrane, are emerging as the critical driving forces for positioning a wide variety of cargos such as the bacterial chromosome, plasmids, organelles, and even the cell division apparatus.

In E. coli, the MinCDE system self-organizes into a cell-pole-to-cell-pole oscillator that positions the divisome at mid-cell so that daughter cells are equal in size. The MinD protein is an ATPase that binds the membrane in its ATP-bound form and recruits the cell division inhibitor MinC. MinE stimulates the ATP-hydrolysis activity of MinD, which releases MinD from the membrane. The perpetual chase of MinD by MinE creates the pole-to-pole oscillator, which maintains a low level of the division inhibitor at mid-cell where divisome assembly and cell division is allowed to take place. How Min proteins interact with the membrane surface to generate the in vivo oscillations is a subject of intense study.

The number of factors involved in subcellular organization makes it difficult to study individual systems under controlled conditions in vivo. We in Dr. Kiyoshi Mizuuchi’s group developed a cell-free technique to visualize and study spatial organization mechanisms.  The MinD protein was fused to Green Fluorescent Protein and the MinE protein was labeled with an Alexa dye. The two proteins were mixed in a buffer containing ATP and infused into a flowcell that had its surfaces coated with a flat lipid bilayer, which acts as a biomimetic of the inner membrane. The dynamics of MinD and MinE were then visualized by total internal reflection fluorescence microscopy (TIRFM), a technique that specifically resolves surface-associated processes.

References

Loose M, Fischer-Friedrich E, Ries J, Kruse K, Schwille P. 2008. Spatial Regulators for Bacterial Cell Division Self-Organize into Surface Waves in vitro. Science 320: 789
Ivanov V, Mizuuchi K. Multiple modes of interconverting dynamic pattern formation by bacterial cell division proteins. 2010. Proc Natl Acad Sci USA 107: 8071
Vecchiarelli AG, Li M, Mizuuchi M, Mizuuchi K. 2014. Differential affinities of MinD and MinE to anionic phospholipid influence Min patterning dynamics in vitro. Mol Microbiol 93: 453
Vecchiarelli AG, Mizuuchi K, Funnell BE. 2012. Surfing biological surfaces: exploiting the nucleoid for partition and transport in bacteria. Mol Microbiol 86:513

Biophysics and a Better Understanding of Osteoarthritis

With May being designated Arthritis Awareness Month by the Arthritis Foundation, BPS went searching for a member conducting research related to this debilitating condition.  We were fortunate to find Alan Grodzinsky, Director of the Center for Biomedical Engineering at MIT, whose research group studies problems motivated by diseases of the musculoskeletal system including arthritis, connective tissue pathologies and, more generally, the molecular biology and biophysics of the extracellular matrix.  Grodzinsky  offers us a glimpse of the exciting work going on in his lab related to osteoarthritis.

What is the connection between your research and Arthritis?
We work on biophysical, biological and biochemical aspects of osteoarthritis (OA), a disease that has been estimated to affect over 150 million individuals worldwide. OA is a complex disease caused by a combination of mechanical and biological factors. It is not a single disease, but rather constitutes a heterogeneous combination of subtypes associated with risk factors for initiation and progression that include age, gender, genetic factors, obesity, improper mechanical joint articulation and congenital deformities of joints. Importantly, it is now recognized that OA is not just a disease of old people; traumatic joint injury in young active individuals involving knee ligament and meniscal tears, for example, can lead to OA at a young age. These injuries are especially common in young women of high
school and college age and are known to progress to OA within 10‐15 years. Finally, OA is much more common than rheumatoid arthritis (RA), the latter involving autoimmune pathways distinct from the pathology of OA.

Why is your research important to those concerned about these diseases?
In our lab, we use in vitro models of joint injury involving living cartilage specimens from animal or human donor sources. Cartilage subjected to mechanical injury is co‐cultured with inflammatory cytokines known to be present in human joint synovial fluid during the weeks following a traumatic joint injury. We use these in vitro systems to try to quantify the cell biological/biochemical pathways of cartilage degradation that is a hallmark of progression to OA, pathways that are additionally initiated by mechanical damage to cartilage that can be imposed in a quantitative fashion using incubator‐housed
loading instruments. These instruments also enable us to measure the biophysical changes in cartilage material properties to can occur in vivo. Additionally, these in vitro systems provide invaluable means to study the efficacy of potential drugs that can halt cartilage degradation and progression to OA. We have an active program for the design of nanoparticles that can be functionalized with small molecule or biologic drugs; the nanoparticles are designed to home directly into cartilage (and other adjacent soft
tissues) for drug release inside cartilage after intra‐articular injection, thereby avoiding problematic systemic side effects that may be associated with sustained release of many otherwise suitable drug candidates. Finally, we also have a research program in our group aimed at the repair of cartilage defects which, if not otherwise treated, could rapidly lead to OA and joint failure. These studies involve the use of a functionalized self‐assembling peptide hydrogel scaffold that will soon be incorporated into animal studies in vivo.

How did you get into this area of research?
As an electrical engineer by training, I spent a year early on in my career on sabbatical at Children’s Hospital in Boston, working with Dr. Mel Glimcher, who was then Chief of Orthopaedic Surgery and a leading basic scientist in bone and cartilage research. Since cartilage is the mostly highly electrically charged tissue in the body (due to the presence of negatively charged proteoglycans (aggrecans) in the tissue matrix), I found that my deep interest in this subject could fit right into an academic career in research and tissue at the interface between engineering and biology. Continuous ongoing collaborations with cell biologists, extracellular matrix biochemists and clinicians have been extraordinarily helpful and exciting.

How long have you been working on it?
There is still no “cure” for OA, and there are currently no disease modifying drugs available (unlike the situation with RA, where new biologic drugs have emerged during the pasts 15 years that help ~65% of the individuals afflicted with RA). As a result, we and many other groups around the world are still working actively in many aspects of this field to try to achieve a better understanding of ways of halting disease progression, regenerating injured cartilage tissue and eventually identifying drugs that can halt
the progression of OA disease. My research group has been involved in various evolving aspects of this research since the late 1970s.

Do you receive federal funding for this work? 
Most of our funding related to cartilage biophysics, OA disease, and cartilage repair has comes from NIH.  We’ve also received important funding over the years from programs within NSF, especially targeted to  the discovery and use of biophysical tools for studies of cartilage and matrix molecular nanomechanics.

Have you had any surprise findings thus far?
Researchers in our group have recently discovered pathways and potential therapeutics that may help to preserve the collagen network of cartilage even after initial loss of other essential matrix components (such as aggrecan). However, delivery of such therapeutics to involved tissues, like cartilage, has not been solved. But students in our group have discovered that highly positively charged nanoparticles may provide an ideal means to home into cartilage with attached drug molecules in tow. So we’re pursuing those studies and also using the same potential therapeutics functionalized to hydrogel scaffolds for
cartilage repair. In addition, Atomic Force Microscopy‐based imaging of cartilage tissue molecules and nanomechanical properties of cells and matrix have opened a window to the study of cartilage repair that we did not anticipate at all.

What is particularly interesting about the work from the perspective of other researchers?
The interdisciplinary nature of this kind research has been one of the most important and exciting features that have been of great interest to a wide variety of researchers in the field.

What is particularly interesting about the work from the perspective of the public?
Of course the hope of this kind of research is that it may lead to advances in diagnostics and patient treatment for OA disease, which has been a major concern of the public for many decades. While OA is not necessarily life‐threatening, it is the major concern for our aging population in terms of quality of life and freedom from pain and disability that is so common as a result of OA.

Do you have a cool image you want to share with the blog post related to this research?

may blog
These are “aggrecan” macromolecules (tapping mode AFM imaging, Laurel Ng et al., J Structural Biology, 2003) which are critically important for the ability of cartilage in our joints to resist static and dynamic loading in our daily activities. These molecules are extremely densely packed inside cartilage and are the first molecules to be degraded and lost from cartilage at the very earliest stages of osteoarthritis. These molecules also regulate the transport of drugs to cells inside dense cartilage tissue, and they are currently the subject of nanomechanical and biophysical studies within our lab as a means to understand the progression of OA and attempts to stop OA.

IDPs: Coming to an Institution near You

Adult Ed - Homework HelpStudents and postdocs have asked for it–more career guidance.  The request has become more frequent as research funding stagnates and trainees are worried about their future job prospects. They want to make sure they have the skills they need to succeed, whether at the bench or by using their science knowledge in a different way. NIH has heard the call.

In July, the NIH took a step to encourage the use of Individual Development Plans for graduate students and postdocs across the US.  The Notice posted in the NIH Guide for Grants and Contracts encourages NIH grantees to develop an institutional policy requiring an Individual Development Plan (IDP) for every graduate student and postdoc supported by any NIH grant, whether it is a training grant or an R01 grant.  The notice also asks grantee institutions to explain how they are using IDPs when it submits a Research Performance Progress report (RPPR) for all projects reporting graduate student and/or postdoctoral researchers.   The move to encourage IDPs is based on recommendations of the Biomedical Workforce Working Group of the Advisory Committee to the Director, NIH, which was tasked with examining the state of the workforce and making suggestions on how to improve career prospects.

NIH is still developing instructions for reporting IDPs in the RPPR-they will be available October 18th of this year.  Recognizing that it takes time to implement policies like this, institutions will not be asked to submit information on IDPS until October 1, 2014.  With that said, NIH wants schools that already have IDP policies to start reporting as soon as the instructions are issued.  It is important to note that the reporting is not a requirement.

The goal of the IDPS is to focus both students/postdocs and their mentors on the career development of the trainees. The IDP can help monitor a student’s progress towards career goals and ensure they have the skills they need to achieve those goals.  It can also be helpful in just facilitating that conversation between trainees and mentors, which can often be hard to start or easy to put off in a busy lab.

NIGMS created a list of resources for developing IDPs, as part of the Institutes strategic planning for training two years ago. That strategic plan also recommended that NIGMS grantees be required to use IDPS with trainees.

Since the notice encourages rather than requires reporting on IDPs, it will be interesting to see what transpires in the coming year.

Biophysics at the NIGMS 50th Anniversary Symposium

Thomas Chew, University of California, San Diego
Photo courtesy of NIGMS

At the recent celebration of the 50th Anniversary of the National Institute of General Medical Sciences (NIGMS), Thomas Chew, an undergraduate student at the University of California, San Diego, presented his poster, “Structural Investigations of CLC-ec1, A Large Integral Membrane Protein, Using Solution-State NMR and Nanodisc Technology.” Chew had been selected for a travel award to present his poster at the NIGMS Symposium after a stellar presentation at the Biophysical Society’s 56th Annual Meeting, held earlier this year in San Francisco. He wrote the post below about his experiences at the NIGMS event.

The morning started with the poster winners from various NIGMS-sponsored societies meeting in the hotel lobby. There were people of all different
career stages from undergrads to new professors, who came from various
parts of the country. Coming from the San Diego the night before, the 8 am
meeting time was really early. We took the subway to the nearby NIH campus.
Once there, we had breakfast in the Natcher conference center, where all
the poster winners got together to meet and mingle with many of the NIGMS
staff. Then they led us to one of the conference rooms to tell us more
about what they did and formally introduce themselves. Along the way, there
was a wall of all the different Nobel laureates the NIGMS had supported
throughout the years. It was impressive to see all of their accomplishments.

We then split up into groups, based on what we had signed up for
previously. One group went on a tour of the Library of Medicine. I had
signed up to talk with some of the NIGMS staff, as I figured there weren’t
many opportunities to meet one-on-one with these types of people. Dr. Jean
Chin and I met and talked for about 30 minutes. She told me a little about her
work at the NIGMS, reading over grants, deciding what to fund, and making
sure everything runs smoothly. I also asked her for career advice and her views
on the current funding situation. One of the unique things I learned about the
NIGMS is that it’s the primary institute of the NIH for funding basic
science research. Despite the trend towards more translational
applications, I think it’s important to keep funding work in the basic
sciences because of the payoff that those sorts of discoveries can have in
the long run.

Lunch was next. I sat next to Cathy Lewis, who had judged my poster at the
Biophysical Society poster competition. We also got to talk with the
speakers – Carlos Bustamante, Kathy Giacomini, and Tim Mitchison. Then
there was some photo-taking, followed by the three research talks. I really
enjoyed the talks, because they were general enough that I could understand
most of what they were saying, yet still included enough details to follow
through each of the scientists’ though processes as they designed their
experiments. After the talks, there was a reception where all of the poster
winners presented our research to everyone else. People slowly trickled
out, and after the poster session was over, a group of us walked around to
explore the NIH campus. All in all, it was an incredible opportunity to see
some of the great research the NIGMS has funded, and to hear about research
and scientific funding from the NIH perspective.

– Thomas Chew

Attention Students: Science Funding Needs Your Help!

US Capitol BuildingAs a student, federal funding for science education and research has a profound impact on your professional future as a scientist. This funding is currently being threatened by the impending ‘fiscal cliff.’ If Congress cannot reach a budget agreement by January 2, 2013, immediate across–the–board budget cuts will slash all federal discretionary spending – including science accounts.

These cuts will impact undergraduate research opportunities, funding for graduate students to pursue research, as well as postdoc and industry jobs; not to mention the damage it will do to the largest single driver of economic growth: scientific and technological innovation.

The American Physical Society has drafted a letter to Congress on behalf of students to make sure our lawmakers know the importance of science funding. You can read the letter and add your signature on the APS website. Sign on by September 14, 2012 to make sure your voice is heard!

As a future leader in the scientific enterprise and technological innovation, your voice is important on Capitol Hill!

For further information about the potential cuts, please visit the Biophysical Society’s website or contact Ellen Weiss at eweiss@biophysics.org.

NIH Investigators Face Increased Scrutiny of Financial Conflicts of Interest

Last August, the US Department of Health and Human Services adopted new Financial Conflict of Interest (FCOI) regulations that apply to NIH-funded investigators.  The rules must be implemented by Institutions receiving public health service funds by August 24, 2012, which means many Institutions are rolling out new conflict of interest policies this summer.  While all Institutions have to meet the new requirements, they can implement stricter rules.  BPS members have reported a variety a range of ways in which their institutions are implementing the policy.

Here are the most relevant changes to the FCOI regulations to BPS members:

  •  Investigators must disclose to their universities all of their significant financial interests related to their institutional responsibilities.  This includes financial interested related to the research that could be affected by the research, or is an entity whose financial interest could be affected by the research.
  •  Investigators must report significant financial interests of their spouse and dependent children.
  • The threshold to be considered a “significant financial interest” requiring disclosure is being lowered from $10,000 to $5,000, and in some cases, eliminates the threshold all together.
  • Income from investment vehicles, such as mutual funds and retirement accounts, as long as the investigator does not directly control the investment decisions made in these vehicles, are excluded.
  •  Institutions must make information related to identified financial conflicts of interest publicly accessible via a website or by a written response.  This includes the investigator’s name, title, role with respect to the research project, name of the entity in which the significant financial interest is held, the nature of the significant financial interest, and the approximate dollar value of that interest.
  • Requires investigators to undergo FCOI training at least every four years
  • Investigators must disclose any reimbursed or sponsored travel.  That includes travel which is paid on behalf of the investigator and not reimbursed to the investigator, so that the exact monetary value may not be readily available.  There is no minimum for disclosure; all reimbursed or sponsored travel must be reported to the investigator’s institution, unless it was sponsored by a university, medical school, or government agency.

The NIH Office of Extramural Research has made materials related to the updated FCOI regulations available on their website, http://grants.nih.gov/grants/policy/coi/. The rules apply to all individuals receiving NIH funding through grants or cooperative agreements.  Additional rules apply to investigators receiving NIH funds for clinical trials.

Please share in the comments how your institution is implementing the new financial conflict of interest regulations.

Summer Course in Biophysics: Why Apply?

Hi, my name is Michael Jarstfer and I am the new director of the Biophysical Society’s NIH-sponsored Summer Course, hosted at the beautiful University of North Carolina campus in the southern part of heaven. If you are considering this course, you might have some questions. Like, what is biophysics? What would I do if I joined the Summer Course in Biophysics at UNC? Why not deliver pizza this summer?

To answer the first question, consider physics and biology. Physics is the fundamental science focused on the study of matter, its motions through space/time, and the forces that control and are controlled by these motions. Biology is the natural science focused on understanding life. Biophysics is the marriage of these two disciplines. By bringing principles of the physical sciences to the study of life, biophysicists have solved several important problems, for example: the structure of DNA, the structure of the ribosome, development of techniques to study high resolution structures of biomolecules in solution, and development of techniques to follow protein biogenesis within a cell. These limited examples, each of which was recognized by the Nobel committees in Chemistry or Medicine, highlight critical contributions of biophysics.

The students in the BPS Summer Course engage in a truly unique experience that captures the essence of a graduate school education in biophysics. The course offers lectures covering diverse topics including thermodynamics and its role in the energetics of life, membrane structure and function, DNA packaging and replication, and protein machines. In each case the focus is on the big questions in the fields and how biophysical approaches can address the issues. In addition to this lecture type portion, students are provided a series of hands-on lab instructions in the techniques of biophysics.  Students also join a laboratory on the UNC campus to conduct an independent research project. Often, the data students generate become part of a publication! To round things out, students are provided several professional development opportunities, including networking, resume production, interviewing for graduate school, poster presenting, and giving scientific talks.

Sounds like some work, but there is also some fun, including many planed social activities with faculty and students, and trips to the beach and to a Durham Bulls baseball game (the stadium used in the movie Bull Durham). Not only that, all costs are covered, and you get a stipend to cover your living expenses, too! So you don’t need to deliver pizza! At the end of the day, it is important to know if all of this work is worth it. The overwhelming majority of students that have completed the course have gone on to do exactly what they wanted after graduation, the majority are in biomedical/biophysical graduate programs throughout the USA, some are in medical school, and others are gainfully employed in the sciences. The success rate is remarkably high.

There are other intangible reasons to consider the course. UNC and Chapel Hill are beautiful places with great people. The atmosphere here is perfect for interdisciplinary research and the faculty are extremely excited to be working with the young, bright people that come through the BPS Summer Course. I hope you apply!