March 30, 2018

Gender equality accreditation programs: a solution to gender inequality in academia?

To perform world-class research and education, universities must strive towards gender balance among employees, from students to professors. Scientific data supports the idea that diverse teams perform better, but progress is extremely slow. However, in the United Kingdom, a pioneering gender certification program is successfully increasing female faculty retention and promotion, awareness of unconscious gender bias, and a more unbiased work environment. Is this the magic bullet?

pws

Pernilla Wittung-Stafshede, Chalmers University of Technology, writes about the program and its potential. 

Looking at the statistics, it is clear that there is a gender problem in academia. Even in a liberal country such as Sweden, where there is paid parental leave often shared by both parents, there is a shortage of female professors and women in other top positions. The average percentage of women among professors at Swedish universities is 25% and this number is increasing by 1%, or less, per year. This is true despite that the Swedish government, for many years now, has set goals for each university to reach higher percentages of women professors. However, because there is no incentive for following such directives or penalty for not doing so, little progress has been made. There are many reasons for gender imbalance at universities; explanations to ‘leaky pipelines’ and ‘glass ceilings’ include unconscious bias, systemic and cultural forces that favor men. Instead of discussing why this problem exists, I will here describe a solution that seems to work.

The Athena SWAN Charter evolved from work between the Athena Project and the Scientific Women’s Academic Network (SWAN), to advance the representation of women in science, technology, engineering, medicine, and mathematics. With the support of Equality Challenge Unit (ECU) and the UK Research Council, the Charter was officially launched in 2005. At the start, the program included a modest 10 allied institutions. Athena SWAN is an evaluation and accreditation program that is based on data gathering, analysis, and scientific evidence. Today, the Athena SWAN program has expanded dramatically and evaluations show it has promoted tremendous success in enhancing gender equity at universities and institutions in the UK.

Athena SWAN is governed by 10 principles that encourage institutions to ensure that women from diverse backgrounds become positioned to reach their full potential. Through bronze, silver, and gold awards that institutions apply for, the Charter recognizes excellence in employment practices that advance and promote the careers of women and gender minorities. After receiving a bronze award, institutions can work towards a silver award by demonstrating a record of activities and achievements towards improving gender equity (often over several years) and at the same time, individual departments are allowed to apply for department-level awards. The key point is that the awards need to be renewed every four years. Thus one has to follow up on action plans made; if not, the award is lost. Currently, in the UK; 97 institutions hold an Athena SWAN award (2 are gold), and 587 departments have obtained awards (of which ten are gold awards). Among similar award schemes in Europe, Athena SWAN is by far the largest and has undergone the most robust evaluation. Impact has been demonstrated through women’s perception of improvement in their career development, achieving top-level support, positive change in the work environment and cultural change.

Data gathering and analysis, through a lens of gender, are used as the basis for making concrete action plans for structural and cultural changes at each institution. Examples of Athena SWAN activities include improved mentoring and training in career planning for young female researchers, and active work to encourage females to apply for promotion. Greater openness in promotion and recruitment processes is encouraged, as is the measurement of quality, rather than quantity, in research output. There is also strong emphasis on family friendly practices, and on developing inclusive working practices and culture. Reports indicate that those departments that are most successful concentrate on activities and policies that benefit all, not just women. For higher level awards (silver and gold), planned actions must be not only measurable, but also innovative and aspirational.

The Chemistry Department at York University, UK, is one of the pioneers of the Athena SWAN accreditation and the department was the first to receive a gold award. The department has gone from 0% to 40% female faculty over 20 years. Professor Paul Walton, faculty in this department, was one of initiators of gender equity efforts and acting chair when the gold award was achieved. He argues that the Athena SWAN program is successful because it focuses on scientific evidence. He also points out that because of his department’s gender work, it is now both highly ranked and very attractive to top researchers.  However, he adds, there is no quick fix – establishing gender equality takes time.

The world is starting to open its eyes to Athena SWAN and it nowadays has pilots ongoing in Ireland and Australia. In the United States, NSF and AAAS are joining forces to start an initiative, and pilot efforts are also discussed in Japan and India. Athena SWAN received a major boost in 2011, when it was announced that the UK’s National Institute for Health Research would only shortlist medical schools for Biomedical Research Centre (BRC) and Unit (BRU) funding if the associate academic school holds a Silver Athena SWAN award. This was followed by similar requirements for other funding schemes. Clearly, such moves by funding agencies act as a strong incentive to universities (and their scientists) to participate and be successful with Athena SWAN accreditation.

Taken together, this may not be a magic bullet, but definitely a step in the right direction. One does not even need to develop something new, one can simply follow (with modifications) how they already do it in the UK. However, there is a caveat, which I noticed during my efforts along these lines: the country’s government must make a formal agreement with the Athena SWAN Charter in the UK to get going, and this costs money and requires commitment at the highest level. Thus, a first step is to lobby for this program’s potential with our leaders.

 

References

Athena SWAN Charter

https://www.ecu.ac.uk/equality-charters/athena-swan/

Athena SWAN 10 principles

https://www.ecu.ac.uk/equality-charters/athena-swan/about-athena-swan/

Statistics Athena SWAN 2017

https://www.ecu.ac.uk/equality-charters/athena-swan/2017-statistics/

Impact of Athena SWAN

https://www.ecu.ac.uk/equality-charters/charter-marks-explained/impact-equality-charters/

https://www.timeshighereducation.com/news/athena-swan-success-brings-new-challenges

March 27, 2018

Idling Melanoma Cells

BPJ_114_6.c1.inddTumor recurrence is an inevitable problem in cancer biology as it varies unpredictably among patients. Surprisingly, our knowledge of tumor recurrence still comes from analyses of post-resistant tumors or single time-point measurements. Critical events during early response that precede resistance and the actual dynamics of drug response in cancer cells is still largely unexplored. The differential sensitivity of melanoma cells has remained puzzling. For instance, why would melanoma cells with the same oncogenic driver (i.e., BRAF-mutations) respond differently to targeted therapies?

In our paper, we coupled experimentation and mathematical modeling to describe diverse dynamics of drug response of multiple melanoma cell lines.  We observed that melanoma cell lines under continued MAPK pathway inhibition, regardless of an initial drug response, transitioned into a previously unrecognized non-quiescent state of balanced death and division. We termed this state idling population state. The initial drug responses and time to reach idling population state varied among cell lines. To mathematically formalize these observations, we proposed that cells exist in three distinct states or subpopulations, characterized by their macroscopic proliferation behaviors. These behaviors are E (expanding), S (stationary), and R (regressing), the proportions of which are set the genetic background of the cell. The central assumption of the model is that drug-treatment alters the quasi-potential landscape of cells, and the cells re-equilibrate over the new drug-induced landscape. Therefore, “idling” state is not a property of individual cell types, but rather an emergent property of a drug-treated population as a whole. As such, the idling populations cannot be eradicated by targeting one particular subpopulation (i.e., a basin), but rather the landscape itself must be altered to favor basins for regressing states.

The cover image for the March 27 issue of the Biophysical Journal is an artistic depiction of the distinct epigenetic landscapes that an idling population can exist in to maintain their population size. Here, the four scales represent the balance between distinct phenotypic states and their relative stability. The depth of each basin denotes their stability in a drug-modified epigenetic landscape of melanoma cells. Each state can experience cell death and cell division. The image reflects that with red circles representing dividing cells and dark circles indicating apoptotic cells. This fine balance between cell division and cell death maintains a critical tumor mass, and may effectively model the “residual disease” observed in clinic.

This cover by Rachel Chandler, Biomedical Illustrator at Vanderbilt University, was inspired by the painting The Hallucinogenic Toreador by Salvador Dali. On a macroscopic level, the behaviors of different scales look the same, the state of zero-proliferation. By depicting different configurations for surviving cancer populations, the cover illustrates the complexity of residual disease — often simplified merely as quiescent or senescent cells.

-B. Bishal Paudel, Leonard A Harris, Keisha N. Hardeman, Arwa A. Abugable, Corey E. Hayford, Darren R. Tyson, Vito Quaranta

March 15, 2018

The Science Behind the Image Contest Winners: Reshaping Vesicles via Deflation

The BPS Art of Science Image Contest took place again this year, during the 62nd Annual Meeting in San Francisco. The image that won third place was submitted by Ziliang Zhao, a postdoc in Rumiana Dimova’s group at Max Planck Institute of Colloids and Interfaces. Zhao took some time to provide information about the image and the science it represents.

Zhao Ziliang-68-94066

How did you compose this image?

This final image actually consists of six individual images, each of them represents the various remarkable shape transformations of giant unilamellar vesicles (GUVs). These are cell-sized lipid vesicles in which the membrane can be directly observed under the microscope and tell you how it reacts to various substances and perturbations. The GUVs here encapsulate aqueous two-phase system (ATPS) of dextran and PEG solution (see e.g. http://dx.doi.org/10.1002/admi.201600451), which mimics the crowded environment in the cytosol. In practice, GUVs encapsulating ATPS represent an oversimplified version of the cell. Mimicking certain cell functionalities as is the case here, is one of the targets of the MaxSynBio consortium (https://www.maxsynbio.mpg.de/), which funds my work. When deflated, these ATPS-GUVs deform into all sorts of curious shapes. Some produce nanotubes protruding into the vesicle interior and accumulating at the ATPS interface. Others offer fascinating images like “the crying face” and “the jelly fish”, and this is what I call the beauty of science: sometimes doing nothing is better than doing something. This series of images was captured using confocal and STED (super resolution) microscopy, and assembled into a mini story: “The little fella is worried that his friends (snail and jellyfish) are being sucked into ‘the green hole.’”

What do you love about this image? Or, what about this image made you submit it for the contest?

I love the final combination of the image which enables storytelling. From the individual images, I like “the crying face” in particular. The moment I saw it during the experiment, two things flashed into my mind, Doraemon and the famous painting called “The Scream” by Edvard Munch. This image actually represents the beauty created by nature in my experiment; it cannot be controlled or replicated. When I first saw it, I already had the thought of combining it with other interesting images from my work into some funny picture. The good thing about doing microscopy work is that you get expected and unexpected results, and the images from both can astonish, even surprise and amaze you. The best time of the day is when I get some very expressive and interesting images from the experiment and share them with my girlfriend and my family ASAP. They are often amazed by how the micro-world in some way resembles the real-world. Fortunately, the Biophysical Society has this image contest at the Annual Meeting which provided me with the opportunity to show my work and also a little bit of this artistic image to the whole community.

What do you want viewers to see/think when they view this image?

I want to use my image to remind the viewers that beautiful things are everywhere. Please, always try to keep your mind open and see things from different perspectives. Even the “garbage” data for your experiments can be pretty and expressive in other ways. So, enjoy doing your work and it might surprise you in some other ways! Like winning an image contest 🙂

How does this image reflect your scientific research? 

Internal structures in GUVs can respond to deflation in quite a curious way. The jellyfish structure in the image is presumably a smaller deflated pancake-like vesicle with protrusions swimming along the interface of the ATPS, which is a curved quasi two-dimensional surface. Such structures would be normally viewed as data to discard as the structure is difficult to resolve and we cannot conclude much about the membrane response. However, the image is curious and pleasing to the eye. Vesicles without initial internal structures are the most suitable for the project that I have been working on. Upon deflation, the excess membrane area of the GUV is stored in the form of membrane nanotubes protruding into the vesicle interior, and based on the composition of the lipid membrane, the shape of the nanotubes can be either necklace-like or cylindrical. The thickness can be below or above the optical resolution. My research focuses on investigating nanotubes like those in “the green hole” image. Their thickness is below the optical resolution, which is why I employ super resolution microscopy (STED) to resolve them. The diameter of these nanotubes reflects changes in the spontaneous (preferred) curvature of the membrane. The related article is in preparation and soon to be published, so stay tuned!

Can you please provide a few real-world examples of your research?

The nanotube formation occurs in GUVs exhibiting phase separation (i.e. droplet formation) in their interior crowded by macromolecules. In real life, phase separation in the lens cell can cause cataract which is a disease affecting countless number of people. Phase separation or droplet formation in cells is an emerging topic, which was also covered in a symposium within this annual meeting. Our studies with GUVs aim at answering the mechanism of cellular events and diseases associated with the contact and interaction of the droplets with the membrane. Our vesicles are loaded with high concentration of macromolecules. This solution can dynamically phase separate above a certain concertation into two droplets within the GUV. Thus, this system can certainly act as a more robust mimetic cell to interpret the much more complex cellular phenomena. So, studying how biomembranes restructure themselves in the environment of macromolecules can certainly promote our understanding on certain diseases in the human body and might even provide a future in fighting against them.

How does your research apply to those who are not working in your specific field? 

Membrane nanotubes are ubiquitous and stand for the highly curved membrane structures and organelles in cells such as the endoplasmic reticulum and Golgi apparatus, as well as membrane vesicles generated for transport in and between the cells. They play a vital role in cellular events to regulate our life activities, and many of the mechanisms are still beyond our knowledge. Studying the generation and stabilization of their large curvature should be of immense importance to researchers in different fields.

 Do you have a website where our readers can view your recent research?

More work on the nanotube formation in the ATPS GUVs can be found via these links, https://www.dimova.de/, and https://www.researchgate.net/profile/Ziliang_Zhao3.

I would like to acknowledge two people who helped me with the final version of this image. My girlfriend Yubing Guo (currently master student at Ruhr-University, Bochum) provided the idea of the snail and combined the snail image (top left corner) for me; my supervisor Dr. Rumiana Dimova removed the exterior signal of “the green hole” (bottom right corner) to make it “real,” provided the image with a beautiful name (Reshaping Vesicles via Deflation) and revised the wording in the description for me. I also acknowledge MaxSynBio and the head of our department, Prof. Lipowsky, for the funding and support.

March 14, 2018

Biophysics Week Webinar — Liquid-Liquid Phase Separation: Interactions, Function, and Disease

Picture a cell.

You can probably see in your mind’s eye how different parts are compartmentalized by membranes. After all, that has been our understanding of major biological activities for many years. However, a recently emerging field of research shows that cells can compartmentalize without membranes. Instead, they use a process called liquid-liquid phase separation. To mark Biophysics Week 2018, we will explore this topic in our upcoming free Cell Press and Biophysical Society Webinar on March 15 at 1:00 p.m. ET.

Why does this matter for your research?
The implications of this liquid-liquid phase separation are far reaching and of interest not only to cell biologists but also to biochemists and biophysicists. “From the physical perspective, the idea that molecules can phase separate under physiologic conditions is causing many scientists to consider phase separation as a potential behavior that could have functional consequences,” says Michael K. Rosen, a webinar speaker from UT Southwestern.

What does it mean for our understanding of cells?
Those functional consequences are causing researchers to further question how exactly a cell works. “Understanding the biophysical process underlying compartmentalization without membranes enables us to ask mechanical questions,” says webinar moderator Tanja Mittag from St. Jude’s Children’s Research Hospital. How does a cell benefit from using liquid-liquid phase separation? When phase separation goes wrong, how does that cause diseases?

How can understanding this help solve larger issues?
One of the experts on liquid-liquid phase separation and diseases is Brown University’s Nicolas Fawzi, another webinar speaker. He says, “These insights are essential for understanding why unstructured regions of phase-separating proteins play critical roles in some cancer or neurodegenerative diseases and how to stop them.”

Register today to learn more about this rapidly advancing field. Hear three leading researchers from top-tier institutions discuss how this process is revolutionizing the way we think about cells. Please join us for engaging discussion and Q&A on the latest developments in liquid-liquid phase separation.

March 14, 2018

A computational insight into skin formation

BPJ_114_5.c1.inddWhen discussing biological lipid structures, the most commonly associated organizations are lamellar bilayers, liposomes, or micelles. Another organization is the bicontinuous cubic structure, where a lipid bilayer separates two water bodies tightly folded in three dimensions. A continuous unfolding between lamellar and apparent cubic-like organizations has been observed in the endoplasmatic reticulum of metazoan cells as well as the thylacoid membrane of chloroplasts. This behavior, along with their bicontinuous structure, has also made these structures an interesting target for drug delivery studies. Furthermore, continuous unfolding of cubic-like lipid structures has been proposed as a mechanism involved in the formation of the human skin barrier, which is situated in the top-most layer of the human skin, the stratum corneum. Utilizing coarse-grained molecular dynamics simulations, we set out to test the hypothesis that a deglycosylation of glycosylceramide headgroups, combined with dehydration of the lipid structure, could be important for the transformation of a cubic-like lipid structure into a lamellar bilayer structure.

The cover image for the March 13 issue of the Biophysical Journal displays a sliced section of a bicontinuous cubic structure containing a coarse-grained representation of skin ceramides and water. The three-dimensionally folded nature of the structure can be seen from the closest water channel (water depicted as blue hollow spheres) which curves into the plane of the image and disappears. The coarse-grained representation of the ceramides shows the hydrophilic headgroup region in white, and the hydrophobic carbon chains in pink.

This image was created from one of the starting structures in our coarse-grained molecular dynamics simulations and highlights the size and complex nature of these structures. Historically, these structures have been a prohibiting factor for in silico studies. With recent, and future advances in hardware and software, we hope that computational tools together with experimental studies will enable us to fully understand the mechanisms involved in the formation of cubic structures.

– Christian Wennberg, Ali Narangifard, Magnus Lundborg, Lars Norlén, Erik Lindahl

March 13, 2018

π is everywhere! The importance of π in mathematics and mathematical biology

By Robin Thompson

Junior Research Fellow, Christ Church, University of Oxford

π= 3.14…≈ 22/7 (almost!)

14th March and 22nd July are closely linked.  These are Pi Day, and Pi Approximation Day, based on the representations of the numbers above in the month/day and day/month formats.  Every Pi Day, mathematicians are commissioned to write articles like this one, some people recite the digits of π, and others use the day as an excuse to eat as much pie as possible. But why does π matter to mathematicians and mathematical biologists?

π is the ratio of any circle’s circumference to its diameter. This is what we are taught at school, and we learn a number of formulae and facts involving π, such as that the area of a circle is πr2, and that the trigonometric functions sine and cosine oscillate with period 2π.  If we go on to study mathematics at university, we learn about Euler’s identity: e^iπ+1=0, and there are a large number of other expressions that involve π .

π  just keeps appearing in mathematics, again and again! But this does not explain why  π is particularly important for mathematical biologists. As explained by Professor Santiago Schnell two years ago, π is related to the formation of patterns. π  is encoded in a zebra’s stripes, and in the spots on a leopard.

The number π is of great practical importance too. I study the mathematics of infectious disease epidemics, and use epidemiological models for forecasting how outbreaks are likely to progress. Models of the spread of many pathogens have involved π.  As described above, the sine and cosine functions oscillate with period 2π. So, if we want to describe oscillating features of epidemics, such as changes in influenza infection rates within each year, then a natural simple assumption might be to use an expression involving π :

Infection rate, β(t) = β(1+σcos(2πt)),

 where σ sets the amplitude of the seasonal variations in transmission.

pi day 3-14

But infection rates are not the only epidemiological quantities that oscillate seasonally. Following infection, hosts do not cause new infections immediately. Instead there is a latent period, during which an individual is infected but not yet causing new infections. Outbreaks of pathogens with short latent periods might be expected to progress more quickly than outbreaks of pathogens with long latent periods.  Latent periods are a feature of infections with pathogens of humans, but also pathogens of animals and plants. An important plant disease – citrus greening – is devastating citrus groves in Florida and is responsible for drastic recent increases in the price of orange juice.  A recent model representing the spread of citrus greening included a latent period that varied within each season.  And, of course, π appeared again in the formula describing seasonal variations in the length of the latent period.

So, as you enjoy π day – maybe you too will be involved in a competition to recite π, or you will eat as much pie as possible – I will be reflecting about the huge practical importance of π. This number appears everywhere throughout mathematics and throughout mathematical biology.

Robin— Robin Thompson is a Junior Research Fellow at Christ Church, one of the constituent  colleges of the University of Oxford. His research involves using mathematical models for forecasting during outbreaks of infectious disease in human, animal and plant populations. For more information about Dr Thompson or his most recent publications, or to collaborate with him on a project, see www.robin-thompson.co.uk/publications or email robin.thompson@chch.ox.ac.uk.

March 12, 2018

Biophysics of the Brain

Anna KosterIn honor of Biophysics Week and Brain Awareness Week, we asked Biophysical Society member Anna Koster, PhD student in the labs of Merritt Maduke and Justin Du Bois at Stanford University to write about her biophysics research related to brain functioning. 

What is the connection between your research and brain functioning?

All of the electrical signals that are transmitted in the human body are mediated by a class of proteins called ion channels that sit within cell membranes and allow a variety of electrolytes (primarily sodium, potassium, calcium, and chloride ions) to selectivity pass in and out of the cell. Specialized collections of ion channels present in different tissues and organs regulate everything from your heartbeat and muscle contraction to the signals sent from your brain. Essentially, you can think of “excitable” cells as miniature electrical circuits—the cell membrane acts as a capacitor that stores charge in the form of ions on either side of the cell membrane. The difference in amount of charge on either side of this membrane capacitor, together with the chemical concentration gradient of the ions, establishes the driving force for the transmission of electrical signals in the body.

Scientists understand how these processes work at a basic level, but they involve an incredibly complex system of interactions, and there is a lot we still have to learn. My particular research project focuses on an understudied piece of this puzzle, a class of ion channels called CLC chloride channels. There are nine different subtypes of this protein in the human body, and generally speaking, they allow the passage of negative charge (in the form of chloride ions) across cell membranes. One of these, CLC-2, is highly expressed in both neurons and glia in the brain, but its function remains poorly understood. My research seeks to develop new molecular tools that will facilitate study of this ion channel both in the healthy brain and in disease states.

Why is your research important to the public?

The CLC-2 chloride channel is present in both neurons and glia in the brain. Neurons, which compose about 20% of the cells in the brain, are the electrically excitable cells that are responsible for the firing of action potentials. Glia, which are non-excitable cells, make up about 80% of your brain. People once thought these cells had only a passive structural function, but we now know that glia play a number of mechanistic roles in overall brain function and health. While we know that CLC-2 is present in the brain, much of the insight into CLC-2 function in this organ has come from selective gene knockout studies in mice. Mice lacking the CLC-2 gene exhibit severe white matter degeneration (leukoencephalopathy) over time, which suggests a critical role for CLC-2 in glial cells. In neurons, a variety of suggestions have been made regarding the role of CLC-2 in cellular excitability and ion homeostasis.

While mouse genetic studies provide clear evidence that CLC-2 has an important function in the brain, such studies are a rather crude approach to studying its specific function and behavior, particularly since genetic knockouts can cause compensatory changes in protein expression. To avoid such complications, an alternative approach is to use small-molecule tools that can rapidly and reversibly modulate CLC-2 function. For many ion channels, nature has provided such tools in the form of molecular toxins that organisms produce as a defense mechanism. One common example is tetrodotoxin (TTX), a potent neurotoxin that is found in pufferfish, ocean sunfish, and rough-skinned newts. The poison works by acting as a molecular cork in voltage-gated sodium channels, blocking the passage of sodium ions, which results in paralysis and stopping the heart of any potential predator. Chemists have isolated these naturally occurring toxins, determined their structures, and figured out how to synthesize these same molecules in the lab. In doing so, chemists are able to take advantage of the exquisite ability of these molecules to recognize and bind with high affinity to a single ion channel out of the thousands of types of proteins in the human body. In the lab, small-molecule tools like TTX allow scientists to study ion channels in a variety of ways. Such molecules can be used as structural probes of sodium channels expressed in cultured cells, or they can be used to evaluate how inhibition of sodium channels in brain tissue affects action potential firing and overall signal propagation. These molecular tools have been invaluable for studying how ion channels work at the biophysical and physiological levels.

In contrast to sodium channels, the number of small molecules that specifically recognize and bind to members of the CLC chloride channel family is extremely limited. Of the molecules that are known to bind and inhibit the flow of chloride current, most require high concentrations to have an effect and will non-specifically stick to a variety of other proteins in the body besides CLC channels. The challenge set before us as chemists was to design a novel molecular tool that would selectively and potently bind to CLC-2, in order to study its function in the brain. By employing a combination of structural biology, electrophysiology, modern computational methods, and chemical synthesis, we are developing new CLC-2 specific small-molecule leads for elucidating the role of CLC-2 in healthy brain tissue, as well as in disease states like epilepsy and leukoencephalopathy. This knowledge can provide the basis for understanding and treating a variety of neurological disorders.

BPS Brain Blog Graphic, Koster

How did you get into this area of research?

I came to graduate school at Stanford with a background in organic chemistry but with a strong interest in learning to apply these skills to tackle molecular problems in the biological sphere. With the School of Medicine directly across the street from the Department of Chemistry, it was easy to establish a collaboration between the Maduke and Du Bois labs to combine their expertise in electrophysiology and CLC ion channel physiology with chemical synthesis. This collaboration, together with fellowship and grant support from a number of interdisciplinary institutes at Stanford (Bio-X, the Center for Molecular Analysis and Design (CMAD), and the center for Chemistry, Engineering, and Medicine for Human Health (ChEM-H)), enabled us to take on this challenging project at the interface of chemistry and biology. We were particularly drawn to CLC-2 because of its fascinating yet poorly understood physiology in the brain and the lack of tools available to study it.

How long have you been working on it?

We have been working on this project for approximately 4 years.

Have you had any surprise findings thus far?

CLCs have traditionally been very challenging targets, and we had very few leads to follow when we began this project. At the outset, we were working with molecules with potency towards CLC-2 in the ~1 mM range and with little to no selectivity among the human CLC homologs (and even other classes of ion channels). Employing a relatively small automated patch-clamp electrophysiology screen, we identified a first lead compound with potency in the low-micromolar range. With further structural modification and rounds of structure-activity relationship studies, we improved the potency to mid-nanomolar levels. These newly developed molecules are the most potent small-molecule CLC inhibitors discovered to-date—it was a very exciting day in lab when we first found those results! We are currently working to understand the basis for molecular recognition between these small-molecules and the CLC protein with the goal of being able to rationally design better small-molecule tools that can act as tunable modulators (either activators or inhibitors) of CLC-2 function.

What is particularly interesting about the work from the perspective of other researchers?

We believe that our research will be particularly impactful for other researchers in the field of neuroscience. We have developed the most potent small-molecule CLC-2 inhibitor known to-date. This molecule can be used as a pharmacological tool to establish the physiological function of CLC-2 in the brain. In addition, we are working to modify the molecular scaffold of our CLC-2 inhibitor to provide tools with a variety of purposes. For example, by attaching biotin and fluorescent dyes, we aim to provide a tool for imaging and visualizing under a microscope exactly where these ion channels are located and how they are trafficked within neuronal and glial cells. Altogether, the molecular tools we are developing will be vital for studying the function of CLC-2 ion channels in tissue, cells, and at the atomic level.

What is particularly interesting about the work from the perspective of the public?

Given the significant advances in science and technology, it is remarkable how little we still know about the workings of the human brain. Most of the work involving electrical signaling in the brain has focused on sodium, potassium, calcium, and protons as carriers of charge, however it is clear that chloride transport plays a critical, yet understudied, role as well. In the 26 years since the discovery of the CLC-2 chloride channel, some progress has been made in understanding its role in the brain, but many questions remain, arguably due to the absence of selective tools for reversibly modulating CLC channel function in live cells.  It is our hope that the molecular tools we are developing will enable research to give us an enhanced understanding of CLC-2 in the brain and allow us to begin studying the possible role of CLC-2 in epilepsy and normal brain development. This work also has potential therapeutic impact in that the small molecules we are developing can offer prospective leads for drug development in the treatment of neurological disorders.

February 27, 2018

Hydrodynamic Models

BPJ_114_4.c1.inddDoes the quaternary structure implied by crystal packing of a macromolecule exist in solution? Which one(s) of the variable loop positions suggested by NMR data exist? What conformations constitute the ensemble of structures in a solution of intrinsically disordered proteins or flexible nucleic acids? To answer these questions one requires a hydrodynamic model that connects the solution behavior to the structural coordinates.

The cover image for the February 27 issue of the Biophysical Journal shows a progression of such models used over the last century to interpret solution studies of proteins and nucleic acids. On the left is a familiar atomic sphere representation of a protein crystal structure. The earliest hydrodynamic models were ellipsoids of revolution, as shown in the image to the right of the atomic model. From these simple geometric objects, the famous Perrin shape parameter equations were derived. The next revolution was modeling macromolecules as a collection of beads, which developed into mini-bead, shell models. An example is depicted in the third image. This and other bead models capture the shape of a protein and provide a theoretically rigorous path to calculation of hydrodynamic molecular properties. The final image on the right is a convex hull model, a mathematical construct that is the smallest convex envelope to contain a set of points. Representing proteins and nucleic acids and their complexes as their convex hulls permits surprisingly accurate calculations of molecular hydrodynamic properties. The convex hull captures not only the shape and volume of the molecule itself, but also the volume of cavity-entrained solvent influencing molecular diffusion. The advantage of the convex hull hydrodynamic method is speed of calculation: it may be used to quickly predict properties of large ensembles of molecular structures or to encode real-time target restraints during molecular simulations.

The code is freely available, and the convex hull method of hydrodynamic property prediction has also been implemented as a web service. A link can be found at hullrad.wordpress.com.

– Patrick Fleming, Karen Fleming

February 22, 2018

Confidence is key

Monday, I went to the “How to present your best self” workshop led by Karen Fleming (John Hopkins) and Linda Columbus (UVA). The main message of the session was Confidence is key to success! And in general, Women don’t own their own confidence. During the session, they showed us multiple pieces of data from surveys from college freshman to mba scholars to show us what we already know. As women, we understatement our abilities when asked and we contribute our success to others or luck. This lack of confidence can lead to less promotions, less salaries, and overall less success. While gender stereotypes can play a role in killing our confidence, the only way to break through these stereotypes is to be strong, confidence women! First step to working on one’s confidence is identity your confidence killers. Some confidence killers are failure, fixed mindset, and the most aggressive at least for me, Imposter syndrome. Imposter syndrome is one thing many of us feel in science at times. The feeling that you are a fake or aren’t smart enough is one that haunts many graduates students, especially early on, and it really hurts your confidence. So to build confidence it’s important to surround yourself with confidence creators aka people who support your endeavors especially when you have failures. For me, my graduate advisor has been a major confidence creator for me during the rocky road that is graduate school. Mindset is also key to confidence. So always remember:

1)Set high goals but aim for good enough, not perfection.
2)Believe in yourself!
3)Remove negative people from your life
4)Failure is temporary! Setbacks are part of reaching success!
5)Don’t be scared to ask for help
6)Take risks. If you don’t even shoot, you will never score!

This BPS meeting was filled with great science but the workshops and career development session were a real highlight for me! Working on our personal growth is critical to becoming successful scientists in the future and I’m grateful that BPS is providing these opportunities! See you next year, fellow BPS goers.

February 22, 2018

Using Biophysics to Understand Heart Disease

February is American Heart Month. Heart disease is the leading cause of death for men and women in the United States, causing 1 in 4 deaths each year. We spoke with Biophysical Society members Daniel Beard, University of Michigan, and Andrew McCulloch, University of California, San Diego, about each of their labs’ research related to heart disease.

MIP_Dan_Beard_0Daniel Beard
University of Michigan

What is the connection between your research and heart disease? Why is your research important to those concerned about heart disease?

A major focus of our research is on the link between cardiac function and myocardial metabolism. In physical exercise, as the rate of work done by the heart increases compared to rest, the rate of cardiac ATP hydrolysis increases commensurately. By building computer models to represent kinetic control of oxidative (mitochondrial) ATP synthesis, we have been able to build a robust framework for simulating ATP supply/demand matching in vivo [1, 2]. Once we had a working understanding of physiological regulation of ATP synthesis in the heart, we used that working knowledge as a starting place to explore how the physiological system becomes dysfunction in heart disease. In particular, it has long been recognized that in heart failure—a condition in which the mechanical pumping ability of the heart is compromised—concentrations of adenosine triphosphate (ATP), its hydrolysis products, and related metabolites are depleted compared to normal. Neither the causes nor the consequences of these changes are well understood. We think that one consequence of impaired energy metabolism is that it directly contributes to impaired mechanical function. Our current research is squarely focused on determining these causes and consequences of mechano-energetic dysfunction, and on finding new ways to repair/restore myocardial metabolism to improve mechanical function in heart failure.

How did you get into this area of research?

My interest in this area goes back to work that was part of my PhD thesis, working in Jim Bassingthwaighte’s lab on simulating physiological transport of oxygen, and other solutes. I became increasingly interested in oxygen transport, and questions of how oxygen delivery is matched to oxygen demand in the myocardium. In this context I started to look in some depth at the physiological regulation of oxidative phosphorylation, not for its own sake, but because I was interested in how it contributed to governing oxygen transport. In other words, at first mitochondrial metabolism was on the periphery of what I was initially interested in. That peripheral interest gradually grew into a major research thrust.

Do you receive public funding for this work? If so, from what agency?

Yes, we have been fortunate to be supported for this work, primarily from the National Institutes of Health National Heart Lung and Blood Institute.

Have you had any surprise findings thus far? 

Our first big surprise followed from my lab’s first NIH funding award, for which we proposed to investigate a conundrum in the field cardiac energy metabolism: How is ATP synthesis supply matched to changing demand levels in light of apparently constant concentrations of ADP and inorganic phosphate (Pi) in the heart? Our answer to this question is that, in fact, the ATP supply is not matched to demand while maintaining constant levels of ADP and Pi. Specifically, our model-based analysis of the in vivo data on phosphate metabolite levels in the heart predicts that changing [Pi] provides a critical feedback signal to stimulate increasing ATP synthesis with increasing rates of ATP hydrolysis. This simple idea fundamentally challenges established ideas in the field. In fact, our hypothesized role of Pi as a primary feedback signal for oxidative ATP synthesis in the heart is still at least a little bit controversial and it would be incorrect to say that it is universally accepted. Regardless, the hypothesis has survived all of our attempts to disprove it!

Beard Image

The next big surprise came when we applied our models of cardiac energy metabolism to analyze data from animal models of heart failure. We found that hallmarks of myocardial energetics in heart failure—diminished ATP and ATP hydrolysis potential—could be effectively captured by simulations in which mitochondrial function is normal. At first blush that finding seems contradictory: Since 95% of ATP in the heart is produced by mitochondria, how can diseased hearts with diminished ATP have normally functioning mitochondria? The explanation pointed to by our analysis is that reduction in cytoplasmic metabolic pools is a critical driver of energetic/metabolic dysfunction in the failing heart. Those predictions were later put to the test when, in collaboration with Igor Efimov’s lab, we were able to measure mitochondrial function in samples from failing  human hearts, revealing no significant dysfunction compared to healthy controls [3]. This is not to say that mitochondrial function is normal in the heart in heart failure, but rather that we believe dysfunction in mitochondrial energy metabolism is not necessarily intrinsic to the mitochondria themselves, but rather driven by the local environment they find themselves in.

What is particularly interesting about the work from the perspective of the public?

Patients with heart failure wind up seeing a cardiologist, not with complaints of impaired cardiac energetics, but with health problems—shortness of breath, exercise intolerance—directly related to impaired heart pumping. Yet we think that metabolic/energetic dysfunction can contribute directly to mechanical dysfunction in heart failure. Our current research in this area is on the link between mechanics and energetics. We are using computer models that integrate metabolic and mechanical function to better understand the physiological connection between chemical and mechanical function in the heart, to determine ways in which this connection breaks down in heart disease, and identify new strategies to improve mechanical pump function by restoring the metabolic state.

  1. Wu, F., et al., Phosphate metabolite concentrations and ATP hydrolysis potential in normal and ischaemic hearts. J Physiol, 2008. 586(17): p. 4193-208.
  2. Bazil, J.N., D.A. Beard, and K.C. Vinnakota, Catalytic Coupling of Oxidative Phosphorylation, ATP Demand, and Reactive Oxygen Species Generation. Biophys J, 2016. 110(4): p. 962-71.
  3. Holzem, K.M., et al., Mitochondrial structure and function are not different between nonfailing donor and end-stage failing human hearts. FASEB J, 2016.

Andrew3Andrew McCulloch
University of California, San Diego

What is the connection between your research and heart disease?

We use in-vitro and in-vivo experiments primarily using mouse models of heart failure and arrhythmias together with multi-scale computational models to discover cellular and molecular mechanisms of electrical and mechanical dysfunction at the tissue and organ scales.

Why is your research important to those concerned about heart disease?

Our research is becoming of particular interest to cardiologists and patients with heart diseases because we have started to discover ways to apply the computational modeling tools we validated in the lab to analyze and predict therapeutic outcomes in patients, including heart failure patients with electrical dyssynchrony who are indicated for cardiac resynchronization therapy, patients with atrial fibrillation or at risk of ventricular fibrillation who can benefit from radiofrequency ablation therapy, and children and adults with congenital heart diseases who are at risk of developing heart failure or arrhythmias later in life.

How did you get into this area of research?

It started as a MS thesis project in Engineering Science when I was 19, that turned into a PhD in Physiology and Engineering and then a faculty career.

How long have you been working on it?

Over 35 years.

Do you receive public funding for this work? If so, from what agency?

Yes, we rely almost exclusively from NIH funding via the NHLBI, NIBIB and NIGMS though we have also received valuable support in the past from the NSF, NASA, DARPA, AHA and Heart Rhythm Society.

image1.001

Have you had any surprise findings thus far?

Yes, we have found with and novel mouse and computational models that phosphorylation of specific serine residues on cardiac myosin regulatory light chain not only affect crossbridge dynamics, but also give rise to a feedback that affects the calcium-dependent active of the thin filament. We have also found that patient-specific models have the unexpected potential to predict and optimize the outcomes of device therapies for heart failure.

What is particularly interesting about the work from the perspective of other researchers?

The power of modern multi-scale and systems biology modeling to help understand genotype-phenotype relations in animal models of heart diseases.

What is particularly interesting about the work from the perspective of the public?

The potential for computer models to improve the early diagnosis and clinical management of heart diseases in adults and children.