The Science Behind the Image Contest Winners: Light Trails of Receptor Tyrosine Kinase EphA2

The BPS Art of Science Image Contest took place again this year, during the 60th Annual Meeting in Los Angeles. The image that won second place was submitted by Thomas Newport, a PhD student at the University of Oxford. His image shows simulated dynamics of the ectodomain of the receptor tyrosine kinase EphA2 (shown as glowing lines) as well as different conformations that highlight the possible movement of this receptor relative to the membrane surface. Newport writes here about the image and the science it represents, as well as his experience as a first-time BPS Annual Meeting attendee.

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The Biophysical Society’s 2016 meeting was unlike any other conference I have attended in my admittedly fairly short academic career. Thousands of posters, talks, and exhibits clamour for attention over a packed six day schedule. Distinguished professors haggle over conclusions with terrified grad students, while suited salespeople draw in new customers with the promise of free bags, USB drives, and flat-pack microscopes.

Probably the highlight of this, my first Biophysical Society meeting, was winning second prize in the Art of Science image competition, or as my supervisor helpfully emailed me a few minutes later, “congratulations, you’ve won second prize in a beauty contest, collect $10.” The competition: ten gorgeous images, some computer generated, some from microscopes, telling a selection of stories from across the vast field of biophysics.

My image was developed in collaboration with Matthieu Chavent, and shows simulated motions of a key signalling protein as it interacts with the cell membrane. His paper explains more of the scientific background and is well worth a read. Matthieu had already visualised the protein using VMD, a popular open source visualisation tool for molecular dynamics simulations, and traced the paths followed by several atoms as the protein moved between two states. By this point my enthusiasm for digital art and 3D visualisation was fairly well known so we met up to discuss turning this data into art.

Blender3D has been my tool of choice for 3D digital art since I was in high school. It’s open source, has great developer and user communities, and can be used for anything from game development to movie production. Working on the data in Blender gave me complete control of the scene, letting me get the composition, lighting and materials just right. I drew inspiration from long-exposure “light painting” photography, where movement can be captured using trails of light. The light trails were probably the most difficult part to get right – transparent and glowing enough to look ethereal but clear enough to be easy to follow.

It seems to have been a hit – the image has been used as the cover of Structure journal and even appeared on the 2015 Biochemistry Department Christmas card (Matthieu even photoshopped some festive hats onto the proteins, although sadly they didn’t make it to the final card). I’ve run a couple of courses teaching Blender to structural biologists, and it definitely seems like a few people were put off by easily fixable data compatibility issues. Once I’ve got a moment free I’d really like to improve the way Blender handles structural biology data to take some of the data wrangling out of developing scientific art. If you’d like to help, you can find me on GitHub or Twitter (@tnewport).

Concepts in biophysics and structural biology are often most effectively communicated through images, from the iconic double helix of DNA to Jane Richardson’s now ubiquitous protein ribbon diagrams. New technologies are creating new ways for us to tell scientific stories in visual media, as still images, videos, and interactivities. This year’s BPS Art of Science competition showcased some amazing works of art that have come out of these advances, and I’m looking forward to an even tougher competition next year.

The Science Behind the Image Contest Winners: Bacterial Networking

The BPS Art of Science Image Contest took place again this year, during the 60th Annual Meeting in Los Angeles. The winning image was submitted by Zeinab Jahed, a PhD student at the University of California, Berkeley. Jahed took some time to provide information about the image and the science it represents.

BPS_image contest_HR

The image was taken using a field emission scanning electron microscope (SEM). It shows three colonies of Staphylococcus aureus bacterial cells (false-colored in purple) each with a diameter of ~500nm.  These colonies are “networking” and connected via nano-scale strings of bacterial cells embedded within a self-produced matrix of extracellular polymeric substance (EPS). The only visual effect we added was false-coloring the bacterial cells to make them stand out from the micropost in the background.

When my colleagues and I first observed these samples under the SEM, we were quite amazed, as we had seen nothing like it before. SEM images generally look appealing as they provide a familiar and interpretable 3D reconstruction of the sample surface morphology. However, we thought the organized and symmetric arrangement of these bacterial cells at such a small scale is what made this image particularly unique. We supposed the biophysical community might appreciate it as well, and I guess we were right!

When people view this image, we hope to draw their attention to the sophisticated but highly organized world of bacterial cells at the nano and submicron scale. Bacterial cells survive surprisingly harsh conditions through networking and cross talk.

Staphylococcus aureus cells are found all around us: they colonize our nasal cavities, attach to our skin, and adhere to organic and metallic surfaces around us. Although not always infectious, this bacterium can cause nosocomial infections, and is a common cause of food borne illnesses. Most of us have heard of staph infections; you’re more likely to get a staph infection if you come into contact with a surface that has staph attached to it. With the rise of antibiotic resistant strains of these bacteria, it is becoming more important to understand the mechanisms of attachment of these strains to surfaces. Having this knowledge, we can ultimately develop new “drug-free” methods for fighting infectious diseases by inhibiting the first step of infection – that is, bacterial attachment.

Our research program is aimed at understanding the mechanisms of cell-cell and cell-surface interactions at the nano and submicron scales. One derivative of this research is designing chemical-free antibacterial surfaces that inhibit or reduce bacterial adhesion. We study the interaction of cells with surfaces containing nano and micro-topographic features.  In previous studies we showed that bacterial attachment rates are sensitive to the nanotopographic features of metallic surfaces. In the work associated with this image, we are looking at the attachment characteristics of Staphylococcus aureus on hydrophobic poly-dimethyl-siloxane (PDMS) micro-posts. The research article associated with this image is in preparation and soon to be published.

This image resulted from a collaboration between the Molecular Cell Biomechanics Laboratory at the University of California, Berkeley, and the Nanomechanics Research Institute, the Laboratory of Biopolymers and Nanomedicine, and the Surface Science and Bio-nanomaterials Laboratory at the University of Waterloo in Canada.   Other than myself, the students involved were Hamed Shahsavan, Mohit Verma, Jacob Rogowski, and Brandon Seo. The PIs involved were Mohammad Mofrad, Frank Gu, Ting Tsui and Boxin Zhao.

The Science Behind the Image Contest Winners: Bovine Knees Are Beautiful

This year’s winning entry in the BPS Art of Sciences Image Contest was submitted by Chiara Peres, a postdoctoral student at the Istituto Italiano di Tecnologia in Genoa.  The image shows collagen fibers in a radial section of an ex vivo bovine knee meniscus, which based on the votes, was a crowd pleaser among the BPS Meeting attendees.  Peres took some time to provide some information about the image and the science it represents.

Peres-Chiara-1st-placeTo produce this image, I used a custom made microscope for Second Harmonic Generation (SHG) Microscopy, a label free technique that exploits a second order nonlinear coherent optical process to image macromolecules with non-centrosymmetric structure, like collagen fibers. The picture is a mosaic of false colored images given by the overlay of the Backward and Forward SHG signal from the not-stained collagen fibers. In particular the image shows the big long branches of radial “tie” collagen fibers which pack together circumferential fibers, perpendicularly aligned with respect to the plane of the image.

I submitted this image because I love the hierarchical structure of the collagen and the harmonious branched, natural organization of the collagen fibers in this section of the meniscus that makes it to look like a big tree in a forest. I love also the fact that this image is “natural” and staining independent, being an image taken with a label-free technique, just collecting and false coloring the endogenous Second Harmonic Generation signal and the Two-Photon autofluorescence of the collagen, without any modification of the sample.

I also like this image because it is a good example of my research activity: I am working to improve and develop new microscopy techniques for biological applications. In particular I am using SHG microscopy as an imaging tool for morphological characterization. This image gives us an easy and immediate means to visualize at a glance the hierarchical structure, organization and orientation of collagen fibers in different areas of the bovine meniscus, the final aim of this study.

When others look at the image, I hope that this image reminds them of an expressionist painting of a forest, as if they were looking at a “micro Van Gogh” being, at the same time, an important method of tissue imaging which connects structures at the micro-scale to macroscopic properties.

Supporting Scientific Information

The cartilage meniscus regeneration after an injury is rarely successful, because the soft scaffolds used lack the mechanical properties to withstand immediate loading. For this reason a strong effort is being done in tissue engineering area to design and to develop a new scaffold that mimics the original tissue, selecting an appropriate material and paying close attention at its mechanical and structural properties. We are studying ex vivo bovine meniscus to realize a proper model for a meniscus scaffold. Our work provides insights on the link between microscopic organization of collagen in different areas of meniscus and its biomechanical macroscopic functions. These results offer, for example, precious guidance for tissue engineers to evaluate the good outcome of the artificial tissues.

In addition to tissue engineering applications, our work can be useful for medical applications. In fact collagen is essential for the biomechanical integrity and the physical properties of various biological tissues and organs. In this context SHG microscopy can be used for ex-vivo imaging of different kinds of collagenous tissues that have a crucial structural and mechanical role in organism. Not only collagen, but also the myosin presents in muscle sarcomeres is another biological macromolecules which generates second harmonic. So SHG microscopy can be used to visualize the organization of these macromolecules in tissue, giving a powerful tool to monitor tissue development and pathology diagnosis.

To learn more about this research, visit my website or LinkedIn profile.

The Science Behind the Image Contest Winners: Influenza A Virus and Mammalian Plasma Membrane Models

We are starting off the week taking a look at the science and scientist behind the scenes of the influenza A virus model that won second place in the Society’s 2015 Image contest.  The image was created by Heidi Koldsø, a postdoctoral researcher in Mark Sansom’s group in the Department of Biochemistry at Oxford University. Koldsø moved to Oxford from Denmark three years ago on an independent fellowship from the Alfred Benzon foundation.  Her research is mainly focused on understanding in details how membrane proteins, which are the largest pharmaceutical target, interact with their surrounding environment. She notes that understanding of not only the membrane proteins but also the lipids surrounding them is of the utmost importance – for example understanding how antimicrobial peptides target bacterial membranes and not human ones. Also, as illustrated in this image, if it is possible to understand how a virus interacts with the cell membrane, scientists can hopefully come up with solutions for better antiviral pharmaceuticals.

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The images of the molecular models that captured the attention (and votes) of the 2015 BPS annual meeting attendees were constructed using the molecular visualization program Visual Molecular Dynamics (VMD). Ambient occlusion shading and rendering techniques were applied to the images within VMD. The image depicts an influenza A virus model in close proximity to a coarse grained mammalian plasma membrane model. Due to the large number of particles within these models we used a powerful workstation with lots of memory and a recent graphics card to create the image.

I chose this particular image to submit to the contest because it encapsulates both the achievements we have already made and those that are to come and it was a natural choice as an image that represents the science we study, the hard work we put into it and the potential real world applications it has. Both the project on the outer envelope of the influenza A virus and the large scale cell membranes are very ambitious and time consuming projects and are the result of a lot of hard work from a number of people. This image is the culmination of those two separate endeavours but also the beginning of the next.

When looking at the image, I hope it inspires the viewer to appreciate the current advances in computational modelling and how far we have come in our efforts to probe very real and relevant problems. The image is not only a pretty representation of a simulation as being able to visualize systems at these length scales provide us with unique insight to how these elements might look in vivo. The image does not only give a first glimpse of the molecular details of virus interactions with the membrane but also hopefully provides scientists and the general public with something that they can relate to and will hopefully promote intelligent discussion.

Supporting Scientific Information

The image is a product of the combined efforts of two large ongoing projects in the Sansom research lab at Department of Biochemistry, University of Oxford. The specific research from which the structures are taken involves performing coarse grained molecular dynamics simulations that we run on super-computing resources.

During the last couple of years I have been working on methods to construct complex asymmetric membrane models that allows us to move towards more ‘in vivo’ like systems. Our initial results on studies of complex membranes and the correlation between membrane nano-domains and curvature was published last year (Koldsø et al. PLoS Comput Biol (2014) 10(10): e1003911. doi:10.1371/journal.pcbi.1003911). We have recently started to move toward studying ‘in vivo’ like plasma membrane models at experimental length scales, meaning we are running simulations of systems >100 nm in dimensions and composed or millions of particles.

A complete model of the outer envelope of influenza A virus has recently been revealed, this project was initiated by a previous Postdoc in the Sansom lab,. Daniel Parton (currently working with John Chodera at MSKCC in New York) and has been continued by Tyler Reddy during the last 3 years in Oxford. This Influenza A virion model was recently published in Structure (Reddy et al. (2015) Structure, 23, 584-597).

The image is a result of combining these two projects on the influenza A virus and large scale mammalian cell membranes. We are exploiting the large deformations and curvatures that we observe in the mammalian plasma membrane model to accommodate the virus. This system is extremely complex and large (> 10 M particles) and Tyler and I are currently in the process of equilibrating and optimizing this model. Computational studies of the influenza A virus in close proximity to the cell membrane will potentially provide us with valuable information regarding how viruses enters the human cell during infection.

More information about my research and publications can be found on my website  and the website of my collaborator, Tyler Reddy.

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