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.

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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.

FluVirion_Koldsoe_2nd-place

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.

Bye bye Baltimore

For the first time in days, I woke up in the hotel room with sunlight sifting through the curtain. What a nice day with fresh air and ample daylight! Even for the last day, the schedules are packed with multiple platform talks and poster showing.

I want to feature the Cryo-EM structure talk in the afternoon, as it did cover a great variety of research topics and new progresses. All four speakers are working with very challenging protein systems and getting enough particles for comprehensive structural details is only the last thing on their to-do list. Due to highly dynamic nature of the protein system movements, the inherent heterogeneity of the particle conformations is probably the biggest challenge. To solve the problem involves locking the system in a particular state with different substrates, finding the right conditions for the protein preparation, and also collect particles with different orientations on the surface. I really appreciate that several speakers took the time to explain to the audience the technical difficulties they encounter during the structural solving processes. In a way, the story not only tells about a sophisticated structure, but also shows us countless trial-and-error progress from highly driven scientists.

I really do enjoy the BPS experience, even when I felt rather clueless at some moment.

Bye bye Baltimore, and hopefully see you’all soon in Los Angelos.

t-loop formation at single molecule level.

The average lifespan of a cell is approximately 50 cycles after which the cells go into senescence, inability to replicate. Early published work clearly suggests that the growing cells have an inherent knowledge of the number of cycles they have divided and this attribute of the cells is very much dependent on the structures on the end of the chromosomes known as the telomeres. These structures at the end of the chromosomes are known to shorten after every cell cycle. Once the telomere reserve has run out, cells stop dividing. Telomeres play important roles in maintaining the stability of linear chromosomes. The telomeric structure allows a cell to distinguish between natural chromosome ends and double-stranded DNA breaks. Telomere dysfunction and associated chromosomal abnormalities have been strongly associated with age-associated degenerative diseases and cancer. Telomere maintenance involves dynamic actions of multiple proteins on a long complex DNA structure. Given the heterogeneity and complexity of telomeres, single-molecule approaches are essential to fully understand the structure-function relationships that govern telomere maintenance. These telomeres form little loops at the end of the chromosomes, which are called the t-loops. These are formed by inserting the ends of the chromosome, which is usually 3’ overhang back into the DNA of the chromosome. Thus, very short telomeres, which is the scenario in old aging cells or sometimes cancer cells, can no longer form t-loops. The exposure of these chromosome ends, 3’ overhangs which cannot be inserted back into the DNA of the chromosome, would alert the cells and thus stop cells from dividing. If we can elucidate the mechanism of this t-loop formation, we can introduce methods to stop shortening of these telomeres and make drugs to stop these processes.
There were two talks this year focusing on the t-loop formation at the single molecule level. While Xi Long talk in the DNA structure session used Magnetic tweezers to understand this, Hong Wang’s talk in the Nanoscale Biophysics session on Saturday talked about these structures , using new technique developed in their lab , DREEM ( Dual Resonance Enhanced Electrostatic force Microscopy). Xi long et al was able to show the melting of telomeric DNA substrates on applying torque and the binding of these substrates with the single stranded oligos but the major drawback in her work being the absence of TRF2 protein from the shelterin complex, which has been shown to be required for the formation of t-loops. Hong et al was able to predict a possible mechanism of the t-loop formation based on the interaction of the telomeric DNA with the shelterin protein, very cool work and technique , actually showing the DNA inside the protein DNA complexes. How cool to be able to see what happens inside the protein DNA complex!!!
Would be looking forward to BPS 2016 for their work to better understand this mechanism…

Wrap Up & Some Thoughts On Students

With the #BPS15 nearly complete, I would like to share my observations about the meeting, and the students particularly.
As someone who has put on some modestly sized events myself, I have quite a bit of respect for executing one of this scale and quality. There are always bumps and glitches to be found at any event if one looks hard enough, but I can truly say that this event was one of the smoothest I’ve attended in quite some time. We were able to set up and break down our exhibits in record time and the staff was very helpful as well. I wish they all went this smoothly.
What about our exhibition time? One of the things I have noticed as a repeat exhibitor, is the number of academic and student attendees. Some previous exhibit “neighbors” adjoining our booth space had even expressed mild concern at this (?). I believe this is a strength of this meeting!
Our company, founded with academic roots by a university professor over three decades ago, had always strongly embodied those values. Yet I believe that interacting with potential future customers is not only good business, but imperative from an educational, strategic, and demographic standpoint.
That said, it was heartening to hear discussions and explanations of peptide science to these academic.s That, along with the many leads our company gathered during the course of the meeting, combined with the nice interactions with new and old friends, made for a highly successful visit to #bps15! Thanks for reading and see you next time – Bob

Ceci n’est pas une chaise: a story of the chair experience.

Arguably the most important thing I had to do this week was co-chair a platform. Not that blogging isn’t super important (and you know the people at my own talk, I’m sure were blown away) but in my and my co-chair’s hands was the success of 8 scientists talks and the audience experience that surrounds them.

I had never given a talk at BPS until yesterday, and felt woefully under-qualified to help others do this thing I had never done before myself. To top that off I kept hearing people say, ‘You’re not making any friends by going over time, either as a speaker or a chair.’ The errors just pile up. Rumors fly (‘Did you hear session XYZ has completely phase shifted?’). Everyone is angry. No one gets to ask questions. What if this happens to me?

Fortunately, after only previously knowing one other person to chair a BPS session, this time a handful of my friends were also chairing sessions! I think this is maybe related to the fact that the ‘theme’ of this year’s BPS is basically what I do, and therefore also up-regulated in my friendship circle.

Anyway, I was able to get some friendly advice from people who had chaired the day before me, which was comforting. I learned there would be an IT guy who would take care of both setting up computers and setting up the timer, which was a huge relief. There’s this green light that turns yellow at the twelve minute mark, as a warning for the red light of doom that’ll come at 15 minutes. It was also suggested I get a pad of paper to take notes and jot down question ideas, because it is the chairs responsibility to not only keep the session on time, but also pay attention to the science and have a question handy.

This quickly became the most terrifying aspect of chairing. Especially as I noticed in other sessions how often this extra chair-induced question lubricant was necessary. Furthermore, I am not usually that great at thinking of questions in talks, generally getting my brilliant ideas a few hours after they’re actually useful.

So when the time came, I was a bit riled up, but luckily my co-chair turned out to be a relatively senior guy who seemed to know what he was doing, and I relaxed quickly. According to a grad student witness, the best part of the whole session happened before it even started: my co-chair’s phone alarm accidentally went off with a jazzy little tune, and I instinctively did a little dance, apparently visible to the audience because they laughed.

The first few talks went pretty smoothly: things were pretty much on time, and I was able to think of good questions! Then somehow we started slipping minute by minute later off schedule. Maybe because the talks were pretty cool ( phosphorylation near drug binding sites, green and black tea polyphenol’s effect on amyloid-beta formation in alzheimers, finding ligands that increase the probability of a particular protein-protein interaction, etc.), and I was concentrating on question duties. I think by the time we hit the fourth speaker and I was introducing the speakers instead of my co-chair (as part of our splitting-of-duties agreement), we were starting a full 7 minutes late. Then we had some technical difficulties. One of the speakers had to reboot their computer so it would be able to connect to the projector! Utter disaster.

What do we do? Do we stop letting people ask questions? Should I be making wild hand gestures in conjunction with the lights? But all the speakers are being really great about being on time, it’s just me with the questions and transitions that has been a little off. The little green light is surprisingly misleading, as it only relates to the speaker’s internal timing, not to the overall fact that we had already started seven minutes late!

Luckily it didn’t really matter that much. We’re here to do science. The talks were good. The questions were good. We started encouraging people to keep their questions quick, and overlapped questions with next speaker setup a little bit more, and I think ultimately we ended on time, with my talk at the end. At the end of it all, I think it all wrapped up well. I even had someone come up to me and say ‘Nice job chairing,’ then I must have made a surprised face or something, cause they followed up with, ‘Oh yeah, and nice job on the talk, too!’

The best seat in the house for watching HIV entry

One of my major reasons for attending BPS this year was to expand my knowledge in a field that isn’t very important at all for the work that I do in my day to day.  My work involves designing molecules that can alter protein function and hopefully “drug” an interaction or protein conformation that is useful therapeutically.  The readouts for whether we are successful are pragmatic ones — we look at cell viability, downstream effects, preservation or desolation of certain cellular pathways as needed.  What we generally don’t concern ourself with is confirming with mechanistic insight how exactly the molecules we make do what they do.  So I decided to go learn more about biophysical techniques for looking at protein dynamics and allostery — the best place to do that was BPS.

Well I’ve learned a lot, and have a lot more to learn from all the papers and techniques that others have suggested I look into.  One of the most fascinating examples of a study hoping to shed light on protein dynamics of therapeutic importance was presented yesterday by James Munro.  Professor Munro used single molecule FRET to monitor conformational changes in the HIV envelope protein gp120 as it interacted with receptors on the host cell surface.  Only one envelope protein on each HIV virion was dually labeled, with a FRET donor at one relatively “fixed” location, and an acceptor at one of three locations on nearby loops of gp120.  FRET is a very powerful technique, and smFRET is even better since it gives conformational trajectories that can give valuable information about the kinetics being observed. However with two labels, the FRET readout is one dimensional — only one coordinate is generated, with points along a line of FRET efficiency indicating the distance between two points on a protein surface.  Can something as complex as HIV envelope binding and entry be observed usefully along a single coordinate?

The answer, as published in Science last year, is yes.  With the choice of a coordinate indicating the distance between the V1/V1 loop region and the V5 loop in the outer domain, Munro and his coworkers were able to observe three distinct conformations accessed by the envelope protein: a highly occupied low-FRET “ground” state indicating prefusion envelope protein, a high-FRET state indicating the envelope protein bound to its receptor CD4, and an intermediate-FRET state indicating binding to both CD4 and the HIV coreceptor.  Many experiments with both laboratory and clinically-derived HIV strains with a variety of ligands confirmed this result.  The smFRET kinetics also supported this view, as fitting the traces to a three-state Markov model showed many transitions from unbound to CD4-bound, and transitions from CD4-bound to CD4+Coreceptor-bound, but very rarely transitions from unbound directly to the doubly-bound conformation.

This choice of coordinate was not a lucky guess, it was guided by existing low-resolution structures of the envelope protein during membrane fusion, and even so, likely was the result of many grad student/postdoc-years of trial and error.  What this study does show is that even complicated and dynamic processes like HIV membrane fusion can often be monitored and deep information gleaned from a very clever choice of one coordinate.

I’ve often spend time choosing a coordinate to succinctly show the transitions in a molecular dynamics system of interest, and seeing someone not only choose the right coordinate, but get a working smFRET experiment working along it for such a cool system was a lot of fun.