The Science Behind the Image Contest Winners: Fluorescent Muscles in Living C. elegans

The BPS Art of Science Image Contest took place again this year, during the 61st Annual Meeting in New Orleans. The image that won third place was submitted by Ryan Littlefield, assistant professor, Department of Biology, University of South Alabama. Littlefield took some time to provide information about the image and the science it represents.

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How did you compose this image?

Usually these C. elegans worms move around quite vigorously.  I added muscimol to prevent muscle contraction.  I picked three different types of worms that appear red only, green only, and red and green (which appear mostly yellow) and mixed them together on a thin pad of agarose.  The worms in the image all happened to clump together, resulting in a nice demonstration of the different color patterns.  I collected Z-stacks for each of the fields of view on an Andor spinning disk confocal microscope.  Using ImageJ software, I then made projections for the images that included the body wall muscle of the worms and pair-wise stitching of about six different projections.

What do you love about this image? 

The juxtaposition of all three types of transgenic worms being next to each other was very striking. The image includes all the different regions of the worms in various orientations, shows many of the different muscle types in these worms, and shows how the muscle cells fit together.

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

The striated myofibrils in these worms are beautifully organized along their lengths, and it naturally raises the question of how this organization is achieved. In addition, the different muscle types show the viewer that there is a lot of diversity along the length of these 1mm worms.

How does this image reflect your scientific research?

I am interested in how actin and myosin become organized into functional, contractile bundles. In particular, I am interested in how actin filament lengths are specified in striated muscle.  In these worms, I modified an isoform of muscle myosin and tropomodulin with fluorescent proteins (mCherry and GFP, respectively) to determine how thin filaments are organized within these muscles.

What are some real-world applications of your research?

Both the uniformity of and specific lengths of actin filaments are important components of muscle physiology. Misregulation of actin filament lengths may be important factor in diseases including cardio- and skeletal and myopathies.  In addition, muscle damage from extended spaceflight, sarcopenia from aging, and acute muscle injuries may be slowed or prevented by interventions that prevent actin filament lengths from changing.

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

Striated myofibrils are a dramatic example of a dynamic, self-organizing biological system that is attuned to a specific function (contraction).  Similar mechanisms for functional self-organization may also be used for other contractile actomyosin bundles, such as stress fibers and contractile fibers in smooth muscle, and for other dynamic cytoskeletal systems, such as flagella and microtubules in the mitotic spindle.

The Science Behind the Image Contest Winners: Group II Intron Ribozyme

The BPS Art of Science Image Contest took place again this year, during the 61st Annual Meeting in New Orleans. The winning image was submitted by Giulia Palermo, a postdoctoral fellow in the group of J. Andrew McCammon at the University of California, San Diego. A team of three scientists composed the image:  Giulia Palermo created the original design, Amelia Palermo (ETH, Zurich) made the handmade painting, and Lorenzo Casalino (SISSA, Trieste) performed digital manipulation on the picture. Giulia Palermo took some time to provide information about the image and the science it represents.

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With this picture we would like to send as the main message that Physics and Art try to interpret the beauty of Nature in different ways but there is a natural overlap between these disciplines, which could lead to wonderful discoveries and amazing beauty.

Group II intron ribozyme perform self-splicing reactions. In the picture, two scissors are used to represent this mechanism. What we like about this image is how a handmade painting could capture the fundamental aspects of the mechanistic action of the system. Besides the beauty of handmade painting, we enjoyed our teamwork and, fostered by the passion for this research, we have been motivated to submit this image to the Art of Science Image Contest.

This image has been inspired by the work we have done in the group of Prof. Alessandra Magistrato (SISSA, Trieste), in collaboration with Prof. Ursula Rothlisberger (EPFL), which resulted in the publication of our research in the Journal of American Chemical Society and in the Journal of Chemical Theory and Computation, while other equally exciting results are in preparation for publication. Below, we report details of our publications:

  1. Casalino, G. Palermo, U. Rothlisberger and A. Magistrato. Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns. J. Am. Chem. Soc. 2016, 138, 1034.
  1. Casalino, G. Palermo, N. Abdurakhmonova, U. Rothlisberger and A. Magistrato. Development of Site-specific Mg-RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations. J. Chem. Theory Comput. 2017, 13, 340–352.

My research exploits advanced computational methods – based on classical and quantum molecular dynamics (MD), novel cryo-electron microscopy (cryo-EM) refinement – and their integration with experiments to unravel the function and improve biological applications of key protein/nucleic acids complexes directly responsible for gene regulation, with important therapeutic applications for cancer treatment and genetic diseases. As a next-generation computational biophysicist, I aim at going beyond the current limits of time scale and system size of biomolecular simulations, unraveling the function of increasingly realistic biological systems of extreme biological importance, contributing in their applications for effective translational research.

The World Health Organization reported that ~8.2 million citizens die each year for cancer, while genetic diseases affect millions of people. As such, the clarification of the fundamental mechanisms responsible of gene expression and of their therapeutic implications is of key urgency to society.  By using advanced computational methods and by their integration with experiments, I seek to unravel the function and improve applications of biological systems of extreme importance. My current interest – as a post-doc in McCammon’s lab at UCSD – is in the clarification of the mechanistic function of the CRISPR-Cas9 system via computational methods. Additionally, I am interested in long non-coding RNA, which regulates gene expression, and in intriguing protein/DNA systems, whose mechanistic function is at the basis of genetic inheritance.

The Traveling Biophysicist

I struggle with good planning during conference meetings. We are only in a host city for a limited amount of time, and we are expected to not only engage in meaningful scientific discussion but also explore the surrounding community. This is my third time at a Biophysical Society Annual Meeting, and I do not yet have a solution.

As a simulationist, I of course find a good comparison between this problem and the one of the traveling salesperson. The traveling salesperson is the story of some unfortunate individual who, starting from home, is expected to go between a number of cities spaced out in a certain geometry and visit each city only once (hopefully making a sale) before returning home. This is directly relatable to our experience as conference attendees. Starting from the Ernest N. Morial Conference Center (or your hotel if you wish), you must not only work to your way to all posters, platform sessions, and symposia you’re interested in but also find your way to the most popular tourist destinations: Bourbon Street, Café du Monde, the Mercedes-Benz Superdome—how can you possibly manage this?

The problem presented by the traveling salesperson is one of note to computational scientists. It’s in the class of NP-complete problems, meaning that (in colloquial terms) this problem is very, very difficult and takes a lot of time to solve. Protein folding is another example of an NP-complete problem. To my students, I like to present a naïve (and classical) brute-force algorithm to fold proteins illustrating this point. You presume that you have a protein 100 amino acids in length, and you take the backbone phi and psi angles as the only interesting structural feature of this protein. Very ignorantly, you assume that each phi and psi angle can only adopt 3 possible conformations (a quite dramatic simplification). Excluding one phi and one psi angle from the termini, you can say that the protein therefore can adopt 3198 conformations. If your (somewhat old) computer takes 0.33×10-9 seconds to sample a single conformation, then you are expecting 2.8×1096 years of simulation time to go through all possible conformations. This is a very long time (much longer than the age of the current universe) and is therefore unthinkable to address computationally.

As biophysicists, we know that protein folding does not occur in a brute-force manner. Levinthal’s paradox, in a few words, stipulates that protein folding must be a directed and nonrandom process. In reality, proteins fold along a pathway driven by energetic and entropic demands. Likewise, there must be a way to direct our exploration of conformational space within the city of New Orleans—how can we minimize our travel along our trajectory through the city?

Despite the scientist in me wanting to construct an energetic function that considers my position and affinity to proximal points of interest, I know that I will not solve this problem during this year’s meeting. As the only alternative, I am more inclined to follow the fate of the randomly folding peptide, often at times making arbitrary choices out of sheer convenience. Yet, the desire within me remains to optimize my time and achieve true efficiency. Maybe next year.

Chris Lockhart

7 Things To Do In New Orleans Before You Leave: A Biophysicist’s Guide

We find ourselves immersed in New Orleans, Louisiana, an old city with an abundance of history. As our time remaining at the Biophysical Society Annual Meeting 2017 dwindles, it’s important to ask ourselves what local experiences we’ve missed. Maybe it’s just me, but as a tourist I have an eternal struggle to find authentic experiences. But according to the Atlantic, authentic experiences don’t exist. Among many reasons, they cite the “traveler quantum effect” in causing this: because we are tourists, the mere fact of our being results in inauthenticity. Once we accept this, we can shrug off any doubts about experiencing “true” New Orleans, and we can focus on simply having fun. Here’s a list of 7 arguably “fun” activities to do after a day at the convention center.

1. Walk Along the Mississippi River
The Ernest N. Morial Convention Center is situated right next to the Outlet Collection at Riverwalk. When you’re done with the day’s sessions, enter the mall and continue walking north until you exit the mall again. Continue north along the choppy waters of the Mississippi. Along the way, you’ll be pleasantly serenaded by street music and will eventually find the Steamboat Natchez (which offers a dinner jazz cruise). Once you see Jackson Square on your left, stop.

2. Beignets at Café du Monde
You’re at the river. Before crossing Decatur Street to get to Jackson Square, you’ll find Café du Monde. This locale is known for its beignets and café au lait. Sadly, I attempted to visit the café Sunday morning but was beset by an incredibly long line. If you brave the wait, when you receive your beignet, you can ponder about the ratio of sugar to bread. How much is enough? Hopefully the answer you’ll find is similar to the answer I arrived at during previous visits to New Orleans: there is never enough. If you’re besmitten by the beignets, you can even buy the mix for home use!

3. Pirate Alley
After crossing Decatur Street and making your way through Jackson Square, you should turn left at the cathedral and then immediately right into Pirate Alley. I won’t distract you with the historical details, but this quaint alley is also one of the most allegedly haunted in New Orleans. As you walk through the alley and contemplate the existence of ghosts, be sure to stop at Pirates Alley Café.

4. See the Dueling Pianists at Pat O’Brien’s
Once through Pirate Alley, turn left onto Royal Street and then right onto St. Peter Street. On the left you’ll find Pat O’Brien’s, known for their dueling pianos and hurricane cocktail. Sunday evening I found myself at Pat O’Brien’s and quickly lost myself in the music. As one of the pianists belted out the lyric to the Eagles’ song “Hotel California” that “you can check out any time you like, but you can never leave”, I checked my watch and realized that too much time had passed. Beware: Pat O’Brien’s resists the flow of time.

5. Preservation Hall Jazz Band
Once sufficiently sated by piano renditions of the golden oldies, you can walk just up St. Peter Street to the Preservation Hall. Every evening at 8pm, 9pm, and 10pm they put on a performance featuring the world-renowned Preservation Hall Jazz Band. Tickets cost $15 per person and are first-come first-served (you must wait in line before the performance). The music is boisterous jazz from another era that shouldn’t be missed. If you have time, I definitely recommend going.

6. Lafitte’s Blacksmith Shop Bar
Once you exit Preservation Hall, continue up St. Peters Street and then turn right on Bourbon Street. Walk 3 or 4 blocks and then you’ll find Lafitte’s Blacksmith Shop Bar on the left. This bar is quite old (built between 1722 and 1732) and is claimed to be the oldest bar in the United States. Interestingly, the bar is lit by candles, which give it a very mellow atmosphere.

7. Frenchman Street
After Lafitte’s, continue along Bourbon Street until it becomes Pauger Street and then take a right on Dauphine Street. You’ll walk two blocks and then be on Frenchman, which is acclaimed for its jazz and nightlife. I will leave you to explore on your own here. When you’re done, order an Uber back to your hotel rather than taking the long walk back. Why not?

You will notice that this route avoids the heart of Bourbon Street. If you want to subject yourself to Bourbon Street crowds (see my previous post), I recommend stopping by the Musical Legends Park with its jazz at night. There is also a cocktail bar called the 21st Amendment—my favorite bar in the city—just off Bourbon Street on Iberville Street that has good late night jazz. If you have some time in the morning, I recommend trying brunch at the Court of Two Sisters, which operates from 9am-3pm. Finally, if you wish to mobilize yourself, I recommend taking a ride on the streetcar through the Garden District and appreciating the gorgeous buildings you’ll see along the way.

Chris Lockhart

“Keep Going”: a take home inspiration from Graduate Student Breakfast

Eating breakfast and getting inspired? That’s the best possible start of the day for a graduate student. Two panelists at the Graduate Student Breakfast, Dr. Jeanne  Small from Quantum Northwest and Dr. Hugo Sanabria from Clemson University shared their inspiring life stories that many of us could relate to.

“Keep going, because science needs you” was one message resonated over and over again during the entire breakfast session and even later, on my head.

It was an excellent opportunity for the graduate students to share their questions and concerns with two senior scientists and seeking advice. Questions were about recovering from frustration, work- life balance, plans after graduation and many more. Both the panelists emphasized on finding passion in ones’ own research, it’s hard to make a real change otherwise. “If you don’t have passion for your research, you are not doing it right”, said Dr. Sanabria.

Dr. Small shared her experience of pursuing her graduate studies and academic career as a Professor against all the odds which was very motivational, specially for young female scientists. She also epitomized how she used   her parental skills to her class while teaching and later, on her career at her own company. Every skill set that you develop can be utilized in many ways -was her message towards us.

After the session, few of us had a chance to talk to Dr. Small and to me, that was the best part. An Iranian student shared her frustration in the changed situation for past few weeks. It was heart wrenching to all of us. Besides all the pressure of graduate research life and uncertainty about next career goal, this extra tension must be unbearable to those, who are going through it right now.

“No matter what, keep going, because science needs you, we need you” was Dr. Smalls’ compassionate response to her and to all of us. And that was the most inspiring conversion I was part of   in this BPS till now.

Later on, I went to a platform talk that I have been planning to attend since the beginning. But to everyone’s surprise, the presenter was someone else, the PI of the student who was originally planning to present. But she could not come because of her Iranian passport and traveling from outside USA.She canceled her flight during the executive order and did not feel welcomed to book it again. But that could not bar her excellent work to be presented at the BPS. It was another vibe of Dr. Smalls’ message ” No matter what, keep going, because science needs you” , to me.

This BPS has been very reassuring to me as an international student. I feel welcomed again after a while. I now know, I will keep going, no matter what.

 

Bourbon Street and Macromolecular Crowding

On Saturday evening a parade—the Krewe du Vieux—bore its way through the French Quarter, featuring a menagerie of individuals dressed in a wide array of colorful outfits. In particular, the Krewe du Vieux is known for its satirical element, taking on politics with a rather heavy dose of absurdity. Of course, as is to be expected for any sort of Mardi Gras event, the streets were lined with eager observers. But crowds are no stranger to the French Quarter: anyone who has walked down Bourbon Street at night can attest to the dense thicket that inevitably grounds movement to a halt in some places. To the layperson, these crowds represent something crossed between a delight and a nuisance. To a biophysicist, these crowds provide a particularly interesting case study—what can we learn about biophysics from observing the crowds of Bourbon Street?

With crowds comes disorder and ultimately, in New Orleans particularly, debauchery. It’s no secret that excessive macromolecular crowding has potentially deleterious effects on proteins, resulting in their misfolding and loss of native function. Here, at least in part, I’m talking about amyloidogenic diseases such as Alzheimer’s and Parkinson’s. Proteins (or peptides) such as Aβ, which are typically benign in isolation, can aggregate under high concentration conditions and form toxic plaques. This applies as well to many other proteins, which will aggregate and misfold beyond a certain critical macromolecular concentration.

The viscosity of the cellular milieu is noted in the Biophysical Journal Best of 2016 volume, which attendees of the Biophysical Society Annual Meeting 2017 received as part of their welcome materials bag. In the first article of this volume, Jennifer L. Ross wrote about the so-called “dark matter” of biology—components within the cell that are difficult to measure yet have potentially profound effects. Along this vein, we must remember that biomolecules do not exist in isolation. To some degree, crowding effects within the cell are tolerated and can even help a protein collapse into its native state. As Dr. Ross surmises, in some fashion cells may even be able to exert control over local crowding. Chaperones, for instance, allow some degree of control as misfolded proteins are able to be reconfigured back into their native conformations.

The topic of crowding is covered several times over the course of this year’s meeting. For instance, on Tuesday at 12:10 PM in room 206/207, Jeanne Stachowiak will be discussing the impact of membrane-protein crowding on spontaneous membrane fission events, and a poster by Niraja Kedia on Monday will present research into the effect of crowding agents on Aβ oligomer structure. If your interest is piqued, consult this year’s program, and you’ll be happy to find that there are many other platforms and posters relevant to this topic.

As a final word, I recommend that you embrace the opportunity to extract comparisons between the vibrant city around us and biophysics. Whether gazing upon the Mississippi River and dreaming of fluid dynamics (a bit on the nose?), channeling yourself from one side of the city to another across the transport machinery that is the New Orleans streetcar, or dreaming of a crowded cellular environment while amidst the throes of people stumbling down Bourbon Street, there exist parallels between macro- and microscopic life. Go out, explore, (be safe), and have fun.

Chris Lockhart

Cardinal Directions of New Orleans

Hello Everyone!

I thought I’d stat off blogging with a little lighthearted information about New Orleans.  I was fortunate enough to spend some time working in Bill Wimley’s lab at Tulane a few years ago and I got used to how to orient myself in NOLA.  For those people visiting for the first time please note that it’s a little funny to describe directions as: North, South, East, and West.  Local directions are as such:

Downtown (where you are likely currently)

Uptown (Where the beautiful Audobon Park is located among many other sights)

Lakeside (Towards Lake Pontchartrain and, in my opinion, very good seafood restaurants)

And

Riverside (Towards the Mississippi, scenic views, riverboat tours and outdoor places to relax)

Hopefully this provides you with a little bit of orientation and ability to interact with the residents of NOLA to determine where you want to go!

Cheers!

GRW