What’s the Buzz? – Membrane Leaflet Crosstalk

BPJ_114_1.c1.indd

The cover image for the January 9 issue of Biophysical Journal is an artistic rendering of vesicles made up of lipids with shapes resembling either an inverted cone (cyan heads), or a right cylinder (yellow heads). In one type of vesicle, the cyan and yellow lipids populate the inner and outer leaflets, respectively, while in the other type of vesicle, they are reversed. A closer look reveals that the vesicle with an inner leaflet of cyan lipids has acyl chains that are “straight” in both leaflets, implying an ordered state or gel phase. However, when the yellow lipids are placed in the inner leaflet, their acyl chains go from being straight to being “wavy,” implying hydrocarbons in a disordered state or fluid phase. The difference between the two types of vesicles is related to interleaflet coupling. In other words, when the inverted cone (cyan) lipids are located in the inner leaflet, they are able to “communicate” information about their ordered state to the right cylinder with yellow lipids in the outer leaflet. Interestingly, when their places are inverted, this communication is lost.

We studied ~100 nm diameter asymmetric lipid vesicles composed of palmitoyl oleoyl phosphatidylethanolamine (POPE) and palmitoyl oleoyl phosphatidylcholine (POPC). Cyan lipids in the cover image represent POPE and yellow lipids represent POPC. Combining elastic X-ray/neutron scattering techniques with differential scanning calorimetry, dynamic light scattering, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy allowed us to compare leaflet- specific structural properties of vesicles with POPE-rich inner leaflets and POPC-rich outer leaflets, to vesicles with reversed lipid asymmetry. Our data reveal when the inner leaflet is predominantly made up of POPE, it is able to induce a gel phase in the POPC-enriched outer leaflet. When reversed, this communication between the leaflets is lost and the POPC-enriched inner leaflet remains fluid. This can be understood in terms of an energetic benefit of locating inverted cone-shaped lipids, such as POPE, in the inner monolayer, which is better able to match the overall vesicle curvature, compared to when it is located in the outer lipid monolayer.

Signal transduction and intercellular communication are essential for membranes, and are mostly due to integral proteins. However, physiological processes that require communication between, for example, receptors secreted to the exoplasm and components of signal transduction pathways in the cytoplasm, may rely on a bilayer leaflet coupling mechanism such as the one described  in our manuscript.

-Barbara Eicher, Drew Marquardt, Frederick Heberle, Ilse Letofsky-Papst, Gerald N. Rechberger, Marie-Sousai Appavou, John Katsaras, Georg Pabst

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Biophysics Week: An Opportunity for Public Outreach

Meenakshi Prabhune planned an affiliate event for Biophysics Week 2017; she reflects on that experience here.   

Biophysicists are encouraged to get involved an organize an event for Biophysics Week 2018, March 12-18.  Learn more on the Biophysics Week website.

Headshot_Meenakshi

You can take a biophysicist out of the lab, but you cannot take biophysics out of their mind. This realization dawned on me when I celebrated ‘Biophysics week’ on my blog last year. When I first came across the Biophysical Society (BPS) call for affiliate events, I wasn’t sure how I could help. It had been more than a year since I completed my PhD in biophysics from the University of Goettingen in Germany, and around 2 years since I last stepped in the lab. Yet, I felt compelled to contribute in some way to change the perception of this field among non-scientists.

The most common reaction of any non-scientist to “I work in biophysics” has been, “Wow, that sounds fancy”. More often than not, the conversation ended there. I don’t blame them. The vast amount of research that goes in laboratories all over the world involves a great investment of interdisciplinary topics. So, scientists have rightfully come up with legitimate interdisciplinary titles such as nanobiotechnologist, synthetic biologist, biophysicist, etc. The issue, however, is that the specifics of these fields remain confined within the lab or within a small inner circle of groups working on similar topics. Eventually, to the general public, they are all clubbed together under the ‘sounds fancy’ category.

Whenever I have these brief interactions with the general public, realizing that they were curious but intimidated by the field, I felt guilty for not informing more. Shouldn’t scientists be responsible for communicating their research to the public? After all, when we demand funding for science from the government, the taxpayers should know what exactly that ‘science’ is. Perhaps the right kind of explanation would help inform the utility of these fields beyond their fancy title.

Inspired by the mission of outreach, I chose to inform the public about biophysics via the medium of writing. I chose two representative topics for my blog. The first one was about nacre, which is the inner hard layer of mollusc shells, interesting in material sciences for its fracture resistance. This was the very project in my biophysics journey, wherein I investigated the role of one of the proteins involved in nacre biomineralization in its structural integrity. The second topic was unrelated to any of my own work topics, but more of general interest. Everyone has seen geckos defy gravity while running up a wall, but how do they achieve this feat? This topic beautifully captures the essence of biophysics; a perfect example of how a biological question can be answered using a quantitative physical approach.

In a way, participating in BPS ‘Biophysics Week’ was my way of giving back to the scientific community. I have learnt a lot from this field and loved its interdisciplinary aspect of balancing between diving into details as a biologist and generalizing to identify unified principles as a physicist. I believe that arousing public curiosity and interest regarding biophysics is the very least that I, or any of us, can do to increase its popularity beyond the lab.

Meenakshi is a researcher-turned-science writer, passionate about the dissemination of science. Check out her blog and portfolio for more articles.

Biophysical Society Creates Roadmap into the Future

Tamm, Lukas--15Biophysics as a discipline has experienced incredible growth in the last 15 years, which is reflected in the growth of the Biophysical Society membership and Annual Meeting.  With that growth, an increasing number of disciplines now use biophysical approaches to conduct their research, and elements of biophysics can be found in nearly every aspect of contemporary life sciences.

But biophysics as a field is still not well understood by those who do not identify themselves as biophysicists.  It is at this juncture that the Society Council undertook a year-long strategic planning effort to ensure that the Society’s activities, programs, and direction continue to best promote the field as a cohesive, unique discipline, and that the Society continues to provide a home and support network for the breadth of current and future biophysicists to showcase their research and the advancement of the field.

The Process

Council hired an outside facilitator to guide the strategic planning process, Marsha Rhea of Signaturei.  Her organization conducted an internal scan through member surveys and interviews, as well as an environmental scan of factors affecting the field and the researchers conducting biophysical research.  Armed with this wealth of data and information, Council and other Society members participated in a two-day retreat to draft the Society’s first ever strategic plan, then spent considerable additional time revising the draft, ultimately approving it at their fall meeting on October 28, 2017.

In the end, the new vision positions the Society to take full advantage of the interdisciplinary edge biophysics has as a unifying discipline with powerful quantitative methods that others need and that lead to significant new biological discoveries. The goals included in the plan affirm that the Society will work globally to enhance knowledge exchange, advocate for the value of biophysics, and support an increasingly diverse next generation of scientists.

In its deliberations, Council identified biophysics as a dynamic and evolving discipline within an increasingly interdisciplinary science landscape and determined that the term biophysics does not necessarily need a clear and coherent definition. The Society can exploit the strengths of this ambiguity as an advantage with biophysics seen as open to emerging fields of science and a discipline that continues to evolve and define quantitative biology.

Strategically Councilors agreed that it may be better to answer what biophysics is by describing its purpose and scope rather than defining its boundaries. The Society may also find this identity question can be an energizing and exciting discussion to continue when members gather. Councilors talked about how biophysicists are heroes of their own stories of scientific endeavor. Leaders of the field agree that biophysics and its quantitative methods are key to unlocking fundamental answers in the life sciences. Continuing to focus this identity conversation on what biophysics is doing rather than what it is may generate more opportunities for the Society to grow and thrive in the future.

The Outcome  

Vision

Biophysics is identified and recognized as the interdisciplinary scientific discipline that develops the quantitative methods and techniques needed by scientists as they seek fundamental understanding of the biological, chemical, and physical mechanisms of life and work to unlock answers essential to curing disease, solving biological problems, and discovering basic scientific insights.

Mission

The Biophysical Society convenes and connects a global community of scientists working at the interface of the physical and life sciences and creates, shares, and advocates for biophysical knowledge and methods through programs and communities that support biophysicists.

Values

  • Scientific excellence
  • Integrity and transparency
  • Diversity and inclusion
  • Community building

Goals and Objectives

Sharing Knowledge in and about Biophysics.  The Biophysical Society is the organization where one can find the whole breadth of research that is biophysics, and not just one small part.  While researchers can attend other meetings that have a biophysics track, or join societies that have a biophysics component, nowhere other than the Biophysical Society can they experience the diversity of what biophysics is and what biophysicists do around the world. The Biophysical Society’s meetings, publications, programs, and website will all work together to strengthen the identity of biophysics as a distinct and integrative discipline that underpins a quantitative understanding of biological processes. Together they will provide forums, resources, and opportunities for researchers to access biophysics-related research and information.

Fostering a Global Community. Biophysics bridges multiple scientific disciplines and does so around the world. The Biophysical Society is an international organization. Although headquartered in the United States, more than one third of its membership is working outside the United States and this international fraction is growing.  The collaborative and interdisciplinary nature of biophysics has allowed this growth to happen organically, but as a Society we pledge to do more to ensure that all members and prospective members feel more connected and that those members, particularly student and early career members who may not be able to travel to attend the Annual Meeting, can access all available resources and feel a part of the Society. To cater to its international membership, the Society organizes meetings in international locations around the globe. The Society will work to support biophysicists throughout the world at all career levels and foster collaborative efforts with national biophysics societies to strengthen the identity of biophysics.

Supporting the Next Generation. The future strength of biophysics and of the Society depends on the next generation.  It’s that simple.  We know that we have strong programs and services for our young members, but we also know that technology, job markets, and economies change, and we are committed to change with them to ensure that the next generation thrives. The Society will continuously improve the mechanisms to engage, support, and retain the next generation of biophysicists.

Advocating for Biophysics. Who better to be ambassadors for biophysics than biophysicists?  How many people know and understand what you as a biophysicist do?  As biophysicists, we all need to step up and make our science more accessible, understandable, and relatable to everyone’s lives.  The Biophysical Society will develop programs to help members communicate the value and importance of biophysics to lawmakers, funding bodies, and the public at large. While scientific organizations have learned that working together to advocate for science funding works and is crucial, we are the only global organization that can speak specifically and comprehensively for biophysics.  We will work to engage more members to participate in that effort.

We Are a Member Organization

To all of you who participated in the survey and interviews that led to this plan, a heartfelt thank you.  As part of our effort to respond to member needs, we have sent a separate survey asking for input on specific programs, and we encourage all of you to participate and help make the Biophysical Society even better.

One of the reasons for the Society’s growth and success is that it has always been a democratic, bottoms-up organization. That feedback came through in the surveys and interviews. Nearly every successful program the Society currently sponsors originated from a member suggestion.

Please help us continue that culture by participating and making your voice heard. As we develop programs that you ask for, tell us if and how they are meeting your needs or how they can be improved.

We are excited to march together and promote biophysics as a unified, yet constantly evolving field far into the future. We are also thrilled to accompany and support all scientists who identify as biophysicists – young and old and around the globe – throughout their careers for decades to come.

–Lukas Tamm, BPS President

 

New Year’s Resolutions for Researchers

As one year comes to a close and the next begins, conversation often turns to New Year’s resolutions. We spoke with three incoming Biophysical Society Council members about their goals for 2018.

Linda Columbus Investigates Cell Membranes With Large New Grants


Linda Columbus, University of Virginia

Less email and more science

As I sit here at the end of another year feeling overwhelmed with teaching, reviewing proposals, and trying to get several publications out the door, I have this strange need to clear my email inbox. What is in this inbox? There are some emails from students inquiring about there final grades, from the company that helps build my course content, TOCs from journals (including Biophysical Journal), several about travel to board meetings and study section, university paper work (effort reports, reconciliations, and pcards), department business, and the list goes on. There are only a few that are directly related to the scientific output of my laboratory.

Not all is awry; we recently moved most laboratory communications to Slack. As one of my colleagues who I introduced to Slack stated “I setup Slack for my group and I LOVE IT!  I just turn off email and do research for hours at a time… keep on top of experiments and don’t get distracted…”  So, Slack can keep me away from email, but it doesn’t decrease the amount of email that I need to handle. Each year in December, I unsubscribe from a ton of mailing lists (if it isn’t moving me towards a personal goal, bye-bye).

This year, I moved towards setting up twitter bots to help me (and anyone else interested in @memprot_biophys ) up-to-date with the literature.  Next year, I will pay the money to expand the posting beyond 10 a day.

Finally, I aim to reduce the number of emails I send by choosing not to respond to more email and by using the phone more often.


Pernilla Wittung-Stafshede, Chalmers University of Technology

Pernilla Wittung-Stafshede 350x500px

As my New Year’s resolutions, I have two things I have thought about:

First, I want to spend more time with my students. Since I started my position at Chalmers, now more than two years ago, I have become involved in many big-picture issues and committees on various levels. I love that and it is important, but the research and the students should not suffer. So my goal is to assure I spend more time with my students discussing data, projects and plans.

Having said that, my second resolution is to push hard for gender equality efforts to take off at my university and nationally in Sweden. We are looking into bringing in Athena Swan-like accreditation. I would love to see something like this begin at my university, as the first place in Sweden. I also will work towards facilitating a national initiative along these lines.


stoked01-heroDavid Stokes, New York University

In past years, I have made many lab-related new year’s resolutions: have regular group meetings, spend more time at the bench, organize the mass of data that has accumulated on lab computers, start using an electronic lab notebook. I find such resolutions generally productive and always feel good when I follow through.

For 2018, major changes are coming whether I like it or not. In December, two new electron microscopes arrived at our institution and the New Year will see me deeply involved in setting up a new cryo-EM core facility. Thus, my resolution is to use these powerful tools to change the way science is done at our institution. It never hurts to think big.

 

Let us know: What are your resolutions for 2018?

 

 

 

Scientific societies join forces to increase diversity in STEM

diversity-400x400With the support of the National Science Foundation, the Biophysical Society and the American Society for Cell Biology are leading an effort to create an Alliance of Scientific Societies for broad participation in STEM for the next generation of scientists. The founding partners are the American Society for Biochemistry and Molecular Biology, the American Society for Pharmacology and Experimental Therapeutics, the Endocrine Society, and the Scientific Career Research and Development Group at Northwestern University.  The ultimate goal is for other scientific societies to join the Alliance as these efforts move forward.

Building a diverse and inclusive STEM workforce is a goal shared by many institutions. However, the efforts to understand effective interventions leading to increased participation of underrepresented individuals in STEM remain isolated in their scientific disciplines. The Alliance aims to serve as a unified voice across disciplines to help community members establish effective ways to coordinate collective efforts to address the needs of minority scientists, thus improving the efficiency and dissemination of URM-serving programs.

The Alliance will achieve its goals by conducting a three-meeting conference series that will bring together the Committees for Diversity, Inclusion, and Minorities Affairs Committees (MACs) and society leadership from many professional/scientific societies and other stakeholders that advocate for the diversification of our STEM workforce.

If you would like to learn more about these efforts please contact Alliance leadership:

Marina Ramirez-Alvarado

ramirezalvarado.marina@mayo.edu

Veronica A. Segarra

vsegarra@highpoint.edu

A Second in the Life of Blood Cells

BPJ_113_12.c1.inddMicrovascular networks are highly complex structures comprised of the smallest blood vessels. Some of their major utilities include gas and nutrient exchange to surrounding tissues, and regulation of blood flow in individual organs. Blood cells squeeze and deform as they flow through the vessels that comprise them, an ability that is critical to the healthy functioning of the circulatory system. While much is known about the average behavior of blood cells flowing within these networks, little is known about the individual cellular-scale events giving rise to this average behavior. What is going on at the cellular-scale as the actual blood cells flow through such torturous geometries? To better understand this, we use a recently developed state-of-the-art simulation tool to model nearly one second in the life of red blood cells as they squeeze, twist, and tumble through physiologically realistic microvascular networks. The results are indeed surprising!

An image based on one such simulation is presented on the cover of the December 19 issue of the Biophysical Journal. Specifically shown is a snapshot of red blood cells flowing and deforming through a microvascular network. This network was designed following in vivo images and data, and was constructed by digitally rendering the geometry using a standard CAD software.  The 3D vascular surfaces were then imported into our simulation tool, and using this we captured the 3D flow field as well as the large deformation and dynamics of each individual blood cell. The blood cells shown are suspended in plasma, which conveys them through the network. The cells are modeled using the finite element method, with each cell surface discretized by about 5000 elements. During the nearly one second simulated, thousands of cellular-scale events occur. The statistics associated with the resulting hemodynamic quantities in vessels are utilized to better understand microvascular network blood flow.

The inspiration behind the simulation shown on the cover is our desire to mimic what actually occurs in physiology as closely as possible. That is, we wanted to capture the realistic features of the geometries through which cells flow without sacrificing the particulate nature of blood, and vice versa. In doing so, we uncover new and interesting features associated with the cellular-scale dynamics. Furthermore, we reveal some surprising counter-intuitive behavior that can only be captured by considering the time-dependent 3D deformation and dynamics of each individual cell.

– Peter Balogh, Prosenjit Bagchi

Ask A Biophysicist

Recently, the BPS Education Committee received an email from a high school student in Salt Lake City. The student was interested in a career in biophysics and had a few questions with the goal of learning more about what it is like to be a biophysicist. Committee member Patricia Soto Becerra, Creighton University, answered these questions. Read her responses below. 


CCAS_Soto_PatriciaHow much school did you have to go to in order to get the job you have now?
I did my BS in physics and MS in physics in my home country, PhD in computational biophysics in Europe and postdoctoral training in theoretical biophysics in the US.

Do you use all of the math you learned in school?
Yes, and I learn the extra math that I need by myself and discussing with research collaborators.

What kind of math do you use everyday?
In my research I do computer simulations. That is, I use numerical techniques on a regular basis (pieces of code that I use, not that I code myself). In addition, I use lots of statistical analysis tools. And, what I use the most: lots of quantitative reasoning.

What is your job title?
Associate professor of physics

What did you major in?
Physics

How many hours per day would you say you use math on average?
About three hours every day. I use the math skills I described on question 3 every time I do computer simulations set up and acquisition, and every time I do data analysis, interpretation and visualization. During the summer, I invest full time; and during the school year, I invest about three hours every week day.

What’s your favorite part of your job?
The intellectual joy of creating deep understanding of how proteins misshape and trigger a disease based on my interpretation of the output from high performance computer simulations. To me it is fascinating how we build a model using effective theories from physics and chemistry, code the model (that is, code equations corresponding to the model) so that a computer solves the equations numerically and then the output does make sense and has a valid meaning!

We compare the output from the simulations with experimental results, we help in further understanding the results of experiments, we go beyond and identify patterns that could not be seen in a wet lab experiment, and we provide knowledge on which others will build future knowledge. I feel excited and delightful!

What’s your least favorite part of your job?
When the day ends.

What does an average day look like for you?
The precise routine depends on my teaching schedule. This semester, for example, in the morning I invest my energy in my research projects and training my students. In the afternoon, I teach general physics to pre-health students (non-physics majors). Next semester, I will be teaching upper level physics courses to physics majors.

What are you working on right now?
We are studying prion proteins. Prion proteins are the hallmark of fatal neurodegenerative diseases such as mad cow disease in cattle, CWD in deer and Creutzfeld-Jakob disease in humans. Our goal is to elucidate the process by which the protein changes shape from the physiological to the pathological form. From wet lab experiments, researchers think that the protein changes shape all by itself and once the protein reaches the pathological form, the protein becomes infectious… but the misshaped protein is not a virus nor a bacterium, just a clump of misshaped proteins! This process is a complete new way of thinking in biology!! The outcome of our research will lay the ground work for the design of diagnostic tools and therapeutics to aid in the deadly prion diseases.

Do you enjoy your job?
110%

What would you tell someone who was interested in going to school to become a
biophysicist?

  • Get creative in articulating the fundamentals of physics, chemistry and biology in a variety of non-traditional contexts.
  • Appreciate, value and respect the contribution of the sciences in their strength and limitations.
  • Be fearless in exploring innovative techniques, whether wet lab or in silico.
  • Attend biophysics conferences… they are a lot of fun: fantastic people to meet, exciting new science and a dance party!

Did you get any other degrees in school?
No. I took a couple of courses in electrical engineering and philosophy, but my true passion at that stage in my life was physics.

What made you want to be a biophysicist?
I wanted to understand the brain, the most fascinating entity on Earth!

Were you good at math in high school?
Yes. Math was not my super favorite subject but I admit I enjoyed it. After I dedicated a bit of time to study, I would understand math fairly well.

Would you recommend this job to a high school student?
I would recommend this job to any student who wants to use her/his creativity to impact the humankind through science.

How should I prepare in high school if I wanted to be a biophysicist?
Become fluent in quantitative reasoning, digital literacy and lab skills. Develop strong written, verbal and non-verbal communication skills. Learn how to learn new skills.

If you could go back in time and choose to study something else, would you?
I do not think I would choose something else.

What is something you didn’t expect you would be doing in this job?
Administrative service.

How does your job help the world?
I see a chain reaction effect: At the personal level, my job fulfills my professional dream, which benefits my family and immediate community. On the next level, I train students that I expect in the future to be better scientists than me. Some former students of mine have gone into the knowledge-based industry, so my group has also the opportunity to have an impact outside of the sciences. And on the largest scale, the outcome of my research (which is in basic sciences) will help others to develop tools to diagnose, prevent and cure neurodegenerative diseases (not only prion diseases, but also Alzheimer’s and Parkinson’s among others).

 

Learn more about Becoming a Biophysicist.