Rheumatoid Arthritis and Biophysics

July has been designated Juvenile Arthritis Awareness Month by the Arthritis Foundation. NIAMS estimates that about 294,000 American children under age 18 have arthritis or other rheumatic conditions. The Biophysical Society is taking this opportunity to highlight how advances in basic research contribute to our understanding of this disease. We spoke with BPS member Christine Beeton, Baylor College of Medicine, about her research related to rheumatoid arthritis, the most common form of arthritis in children. Her work focuses on targeting potassium channels for the treatment of chronic diseases including multiple sclerosis, rheumatoid arthritis, and type 1 myotonic dystrophy, and using antioxidant nanomaterials for the treatment of T lymphocyte-mediated autoimmune diseases (multiple sclerosis and rheumatoid arthritis).

What is the connRA-FLS bright fieldection between your research and arthritis?

The term arthritis encompasses a number of diseases that affect joints; my focus is on rheumatoid arthritis (RA) that is characterized as a systemic inflammatory and chronic disease. In the last decades the role of resident joint cells, the fibroblast-like synoviocytes (FLS), has come to light in this disease. However, no therapeutic currently specifically targets these cells. We have identified KCa1.1 (BK, KCNMA1) as the major potassium channels at the plasma membrane of FLS isolated from patients with RA and have shown that blocking this channel inhibits pathogenic functions of FLS ex vivo and reduces the severity of two animal models of RA (Hu et al. J. Biol. Chem. 2012; Tanner et al. Arthritis Rheumatol. 2015). We are currently investigating the roles of these channels in the pathogenic functions of FLS and also as a potential target for therapy.

Why is your research important to those concerned about arthritis?

Current therapeutics for RA have significantly improve the wellbeing of the patients. However, most induce immunosuppression and therefore place the patients at risk for infections and tumor development. Our ability to target FLS has the potential of development effective treatments for RA that do not immunocompromised the patients. In addition, targeting both immune cells and FLS by combination therapy may offer the added benefit of using reduced amounts of drugs if the effect is synergistic.

How did you get into this area of research?

During my PhD in Immunology, I had the opportunity to study Kv1.3 channels in T lymphocytes, cells involved in autoimmune diseases. As a student my work focused on multiple sclerosis but as a postdoctoral fellow I extended this work to RA. When testing Kv1.3 blockers in animal models of RA and analyzing potassium channel expression in synovium biopsies from patients with RA I became interested in the potassium channel phenotype of other cells involved in RA. When I started my own laboratory I started a collaboration with Dr. Gulko, a rheumatologist now at Mount Sinai in New York, and focused my attention to FLS. This lead to the identification of KCa1.1 as the major potassium channel at the plasma membrane of these cells.

How long have you been working on it?

I started working on potassium channels in FLS from patients with RA in 2008, soon after starting my laboratory at Baylor College of Medicine.

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

This work is not funded by the NIH but we have received funding fromX-rays the Alkek Foundation for Medical Research and from Baylor College of Medicine.

Have you had any surprise findings thus far?

Many. The happiest was to find out that FLS from patients with RA express one major potassium channel at their plasma membrane and not a combination of many channels, which would have made the work of identifying them and defining their roles a lot more complicated. The most puzzling was the finding, repeated many times, that blocking KCa1.1 induces a calcium transient in these cells. This really intrigued us and started us into studying the cell signaling downstream of the channel.

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

Over the last few years, FLS have emerged as important players in the pathogenesis of RA. While many signaling molecules have been identified as regulators of various pathogenic functions of these cells, nothing was known about the expression and function of potassium channels. Our work therefore brings a new cell signaling regulator to light.

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

Getting a better understanding of the different cell types that play a role in rheumatoid arthritis will help design better drugs to combat this disease. In addition, understanding the roles of KCa1.1 channels in the function of FLS during RA may help understand the roles of these and other potassium channels in other tissues and diseases.

Do you have a cool image you want to share with the blog post related to this research?

I am showing two cool images; one of an FLS, isolated from the joint of a patient with RA who had to undergo therapeutic joint surgery due to disease severity. The other shows X-ray images of the hind paws of rats with a model of RA induced by the injection of pristane. In the top X-ray, joint damage (yellow arrows) is visible; In contrast, the joints are much healthier in the paw of the rat that was treated with a KCa1.1 blocker for 21 days, starting at onset of clinical signs.

Charting the Course: How the BPS Summer Program Prepares Students for Success

Stephani Page, currently a doctoral student at University of North Carolina at Chapel Hill in the Biochemistry & Biophysics Department, was one of the first students to complete the Biophysical Society Summer Research Program, in 2008. After this year’s reunion weekend, she reflected on her experiences in the program and how it helped lay the foundation for success in her PhD program.

ThougStephani-Page-headshoth it feels like yesterday, the swath of gray hairs growing from my temple tells me otherwise: the first day of the Biophysics Summer Course was over seven years ago.  Barry Lentz, the director at the time, laid out his expectations for the next two and half months.  In what I know now to be typical Barry fashion, he announced to my fellow classmates that I was accepted into the PhD program at UNC and that I would gain a lot from the summer program.  He was correct.

The summer program was an opportunity to transition into my PhD program, and I needed to make the most of it.  Looking back on the experience, I can think of many key benefits – but I narrowed it down to just two.  I built a network that would prove to be very important for my tenure as a graduate student; and as I gained knowledge in biophysical applications, I developed skills that would prove beneficial for my classes and research.

Graduate school is stressful, to say the least.  My favorite analogy calls a PhD program an endurance race.  I considered it paramount to build a network of people invested in my success.  The summer course gave me the opportunity to encounter different faculty so that I could begin to assess who would be a part of my system of advocates and advisors.  I met my graduate PI, my committee chair, and two of my committee members during the summer course.  One of those committee members was my summer course PI.  In a broad sense, through the summer course, I learned more about how to identify those individuals who are invested in my success and who care about my wellbeing as I strive to reach my goals.  I began to learn the difference between a mentor and an advisor, why each is important, and the ways that they can overlap.  I learned to identify my own needs as a budding scientist – a skill that I build on to this day.  Though not everyone who participates in the summer course chooses to attend UNC or get a PhD, the ability to identify what you need in order to thrive in any environment is invaluable.

I had a bachelor’s degree in Chemical Engineering and graduated from my master’s program in Biology during the summer course.  To that point, I hadn’t been in an environment where I could blend those two backgrounds, much less make sense of a broad, interdisciplinary field such as biophysics.  The summer course exposed me to biophysical techniques such as x-ray crystallography, NMR, mass spectrometry, and fluorescence spectroscopy.  We were exposed to molecular dynamics simulations and bioinformatics.  Statistical mechanics, partition functions, and Boltzmann – the physics of life took on meaning.  And I was able to apply what I was learning through my own research project.  By the time I was sitting in classes as a graduate student, I had experienced (and endured) these primers on topics that were complex and difficult.  I was able to approach my classes without being intimidated.  In moments of difficulty, I had relationships with faculty and more senior graduate students (who I had encountered during the summer course) and I was able to get help.  As a teaching assistant, I had examples to use in order to help other graduate students grasp concepts.  Overall, it was a crash course in critical analysis, collaboration, and interdisciplinary approaches applicable to any environment

As I mentioned earlier, the majority of my faculty support system during my PhD program were individuals I had encountered during the summer course.  I am thankful to say that I have built a support system of people who had completed the summer course with me, and in years after my class.  There is a common bond that we share as the select few who were able to encounter this experience.  As a graduate student on the cusp of completing my PhD, I look back on the experience with fondness.  The summer course is geared toward students from backgrounds that are underrepresented in biophysics and related areas or science.  Whether those individuals from underrepresented groups adopt the banner or not, as we navigate the various fields of science, we are trailblazers.  We will bring others along.  We will clear paths.  We will mentor, advise, and advocate.  The Biophysics Summer Course, to me, continues to represent an opportunity to learn more about oneself, to gain knowledge and skills applicable to any environment, and to build networks aimed at ensuring one’s own success.

Find out more about the Biophysical Society Summer Research Program in Biophysics.

Simulating Cell Packing to Understand Organ Growth

BPJ_109_2.c1.inddStem cells are fundamental building blocks for organ growth. They are cells that have not committed to doing a specific job and, therefore, can be directed by different signals to perform a wide range of tasks. The cover image shows the shapes of stem cells while they undergo the process of organ growth, in a computational model. The cells themselves are packed tightly, and so to reduce the amount of unused space in the organ they form a hexagonal arrangement. This isn’t unique to cells; if you pack oranges or balls on a shelf tightly you can see the same kind of packing. The type of packing reflects both the shape of the cells, and the amount of crowding in their environment.

Our simulations don’t generate these images automatically. When we want to analyse this type of system we take the raw data, typically in a text file, and use a specialized tool to view it as a 3D object. We did this using the tool VMD (http://www.ks.uiuc.edu/Research/vmd/) and rendering the cells as spheres. This is a very powerful way to show how the cells move and grow and is important for many types of analysis.

For this image we wanted to generate a different kind of visualization. We wanted an image that showed the cell packing unambiguously and more closely resembled the experimental microscopy data. To do this we performed a mathematical analysis—a Voronoi decomposition—to calculate the edges of the cells. For each cell we then rendered these faces as colored blue glass and drew in a small green sphere to show the center of the cell. This clearly shows how cells in the niche pack hexagonally, and the resulting image resembles the microscopy images much more closely. This makes direct comparison much simpler and can be used to validate the simulations.

Both the cover image and our article show what can be done using detailed computational models to understand organ growth. Although the work is focused on one specific system—the germline from the nematode C. elegans—both the model and the approach may have significant impacts beyond this system. The organ structure, a stem cell niche, is found commonly in many different systems, and just as tumors may grow in the C. elegans germline, mutations may cause human stem cell niches to develop into cancers. Similarly, our group at the MRC Cancer Unit, University of Cambridge, is looking to use the same methods and tools to model different pre-cancer and cancer systems. This includes studying detailed models of individual components and large biochemical networks in cells. The Fisher group at Microsoft Research and the Department of Biochemistry, Cambridge University, is using the same computational methods to model the molecular mechanisms underlying cancer (e.g., leukaemia, glioblastoma) as well as blood development.

For information on our research, visit  the  group’s website http://www.mrc-cu.cam.ac.uk/hall.html and blog http://drhallba.wordpress.com. For more information on some other work we have recently done on the structure of IKK-gamma, also visit the MRC Cancer Unit’s news section http://www.mrc-cu.cam.ac.uk/news.html. For information on the Fisher group, view http://research.microsoft.com/en-us/people/jfisher/ and recent press release related to their work on blood development http://research.microsoft.com/en-us/news/features/leukemia-drugs-computer-model.aspx.

– Benjamin A. Hall, Nir Piterman, Alex Hajnal, Jasmin Fisher

Dear Molly Cule: How do I staff my lab?

Professor Molly Cule is delighted to receive comments on her answers and (anonymized) questions at mollycule@biophysics.org, or visit her on the BPS Blog.molly_cule_blog1

I’m a new PI. How do I go about staffing my lab?

First, congratulations on becoming a principle investigator! Now how do you make your laboratory successful and productive?  Many resources exist to help get you started, one of which is a guide to scientific management called Making the Right Moves.  This guide was developed by the Burroughs Wellcome Fund and the Howard Hughes Medical Institute, and can be downloaded as a PDF from the HHMI website that provides resources to early career scientists: http://www.hhmi.org/programs/resources-early-career-scientist-development/making-right-moves. A full chapter of the guide focuses on staffing the laboratory, as well as managing a laboratory and developing a vision for your laboratory. Take advantage of this helpful resource.

An important step towards staffing the laboratory is considering what type of laboratory you want to run, which may be highly dependent upon your institution and startup package. As an example, there are big differences between the type of laboratory and laboratory personnel at a liberal arts college, a mid-sized research university, and a large medical school. This is where your vison for your laboratory comes in to play.  A helpful exercise to establish this vision is to look around your department and institution and observe the types of laboratories that are successful, but also to recognize that it takes time to build a successful laboratory. In generating the vision for your laboratory, you must weigh the costs and benefits of hiring a technician vs. recruiting a postdoc or recruiting undergraduate vs. graduate students to your laboratory. These costs and benefits do include monetary costs and benefit packages, but they also include differences in scientific acumen, capacity to work independently, and expected productivity. It is also important to recognize that technicians and postdocs are employees, but students are not. There are some subtle details that you will have to learn about related to these differences, but your departmental business manager or chair is usually a good resource for understanding these differences at your institution.

When I started my own laboratory, I thought the best place to start hiring was with a postdoc or lab technician. I wanted to hire a person with some knowledge of research, who would need minimal training, and ultimately be able to help get my lab up and running as quickly as possible. Next, I chose to proceed by acquiring students, who require more training. Do not be afraid to be picky about who joins your laboratory, it is okay to tell a student that he/she cannot join the lab. Although saying “no” can be difficult, it is necessary. Focus on quality, not quantity, in your hiring, particularly when you are just starting out.

Now that you’ve established where you want the laboratory to go and what types of people you want to have in the laboratory, you need to go out and get them.  You will need to create a job description that you can distribute on the human resources site at your institution, on the website for your laboratory, on  email list serves, and on job boards hosted by scientific societies to which you belong. It is very important to write a job description that attracts the specific skill set that you need regarding techniques that will be required, areas of research that you study, any minimum requirements that will be required for the level of the position, etc.

Once you have a set of applications, you will need to select candidates to interview  The interview is an important part of the hiring process, because you will want to determine the quality and ‘fit’ of an individual with your particular laboratory. Spend time generating a list of questions to ask during the interview. Think about why you are asking these questions, and be able to articulate (in your head or out loud) how and why the candidates’ answers to these  questions are important to the future success of your laboratory. Be aware of any red flags that suggest a person may not be a good fit for the position. For me, personality and ease of engagement between a perspective member of my laboratory and me are critical components of the interview process. You may have the most qualified candidate on earth, but if you and that person cannot easily communicate or get along, the working relationship will suffer. Remember, it is your laboratory and you need to assemble the best, most productive team possible to achieve the scientific vision that you’ve set out for your laboratory.

Once you’ve determined who would be the best person to hire, you will have to make an offer.  Many of the details related to these offers are less flexible that you may think, particularly when starting up a new laboratory. The pay scale may be dictated by the institution or tied to an offer letter related to your startup package. Hopefully these details won’t get in the way of you hiring the best person for the job, but you may want to investigate these details at the start of your hiring process, when you are drafting the job description

Good luck in staffing your laboratory,

Molly Cule

Biophysicists Share Their Science in the Czech Republic

Czech Republic Networking Event, which took place on June 12, was the first event BPS-supported event to take place in the area. Hosted at the Institute of Photonics and Electronics, The Czech Academy of Sciences, the conference had over 30 participants, including professionals, graduate students and undergrads from the local area. One of the organizers, Michal Cifra, wrapped it up for our blog readers below!

Czech Republic 1The one day event was primarily aimed to facilitate networking in the region of Czech Republic where several high quality molecular biophysics groups in different research institutions are based. These groups did not have much opportunity to interact locally to fully cross-fertilize ideas and further develop their potential beyond pure biophysics towards hot topics such as bioelectronic and biophotonic medicine and other bio-inspired technological applications in photonics and electronics. “Electrostatic, Electrodynamic and Electronic Properties of Biomolecular Systems” was the scientific subtitle of the event. Main specific topics covered were electrostatic, electrodynamic, vibrational and electronic properties of biomolecules and biomolecular nanostructures with the focus on proteins and DNA.

In the first part of the event, 9 speakers, experts in molecular biophysics, bioelectrochemistry and coherent processes in biology, presented the basic concepts of their individual fields as well as their current results. In the second part, the speakers were able to networking with the attendees and have in-depth discussions during the posters session. Finally, a brief tour to the laboratories of Bioelectrodynamics research team was provided.

Czech Republic 2The speakers we had were not only great researchers, but also great lecturers who can really attract and keep attention; so their talks were very enjoyable. We learned that this kind of event provides a great format for the exchange of scientific information as well as networking. The event was really a great way to meet new people. As an organizer, I personally met not only PIs and professors but also postdocs and PhD students.

We hope to organize similar event in the near future!

Were you at the Czech Republic Networking Event? Share your favorite part of the event in the comments below!

Doodling Science: Protein Folding Deconstructed

BPJ_109_1.c1.inddHow did you compose this image?

The image is intended to illustrate a complex scientific idea in a naive and somewhat fairytale-like manner in the form of a doodle. In the creative process of designing experiments, scientists often doodle their notes and ideas in similar simplistic form before taking their design to the next level.

The image was composed on-the-fly by a graphical artist (Hanne Grønne) and a 16 year old girl (Asta Andersen) while the work was orally described to them and it reflects their direct interpretations. Neither of them have any scientific background.

How does this image reflect your scientific research?

The image reflects the main experimental method and the background of the project, which focused on deciphering details of the folding mechanism of a protein called neuronal calcium sensor-1 (NCS-1). Our approach involves applying force to individual NCS-1 protein molecules. To do this, we attach DNA molecular handles to the protein, and the handles are subsequently attached to micrometer-sized beads that are trapped using optical laser tweezers. With this method we can pull a single protein molecule and unravel its three-dimensional structure, while monitoring in real-time its dimensions and the resulting tension. This allows us to determine important details regarding the folding mechanism of a protein molecule under various conditions. In this paper we study the effects of ions on the folding mechanism of NCS-1. The figure, therefore, shows DNA molecules attached to a protein (NCS-1) and stick-figures holding each DNA, representing the unique control we have over the fate of the individual protein molecule, where we essentially grab the protein by its ends and pull it apart. The protein is shown as a clover leaf with ions bound (shown as black circles) and there are references to a membrane (NCS-1 attaches to the membrane), forces (picoNewton and Kg), dimensions (nanometers shown on a ruler), a laser (used to both induce and measure forces), a neuron (NCS-1 is localized primarily in neurons), and ions (spheres throughout the image). The picture is also meant to convey the complexity of biology in simplistic terms.

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

Various ions act as messenger molecules in cells such as calcium, magnesium, zinc, and iron ions. Calcium-binding proteins are ubiquitous signaling proteins in cells and many, including NCS-1, also bind other ions, mostly magnesium. Therefore, at any given time in the cell, at least three states can be envisioned: The Ca2+-bound state, the Mg2+-bound state, and a free state (with no ions bound). For NCS-1 and its related family, not much is known about the effects of ions on their folding mechanism. Because conformational dynamics is a hallmark of signaling, understanding the folding energy landscape is important to rationalize the conformational response to different ions, which is the process  that relays signals throughout the cell.

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

Our work is highly relevant for a broad cross-section of bio-scientists working in the field of calcium- binding proteins, protein folding and dynamics, and neuroscience, and our methodology brings together physics, chemistry, and biology. Our results may be generally applicable to the vast superfamily of proteins that have EF-hand-motifs. In addition, experimentally derived folding energy landscapes are rare as they are difficult to determine with traditional methods and so our work may aid in understanding the general principles of protein folding.

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

The website of the Structural Biology and NMR Laboratory (Dr. Kragelund): http://www1.bio.ku.dk/english/research/bms/research/sbinlab/groups/bbk/

The website of the optical tweezers Laboratory (Dr. Cecconi): http://personale.unimore.it/rubrica/dettaglio/ccecconi

– Mohsin M. Naqvi, Pétur O. Heidarsson, Mariela R. Otazo, Alessandro Mossa, Birthe B. Kragelund, and Ciro Cecconi

Biophysical Society Summer Research Program: A Novel Internship for the Science-Addicted

My name is Manuel Castro, I am a rising senior at Arizona State University, and my major is Biochemistry with a focus in medicinal chemistry. From a relatively young age, I knew that my love of science was considerably broad. I enjoy the fields of chemistry, biology, and physics; through undergraduate lab reseCastro,Manuel headshotarch opportunities, I became more familiar with the interdisciplinary concept of biophysics, and subsequently, the breadth and depth associated with this area of study. When my lab mentor told me about the Biophysical Society Summer Research Program, I enthusiastically applied.

At Arizona State, I work in an NMR lab that focuses on characterizing the structure and function of membrane proteins. Under Dr. Wade Van Horn, my work in his lab has helped direct me towards achieving a career within the large realm of biophysics; namely, structural biology. Upon receiving my acceptance letter to the BPS Summer Program, I began looking into various professors at UNC Chapel Hill that complemented my interests. I quickly found Dr. Matt Redinbo, a professor whose lab also focuses in the structural and chemical biology of proteins involved in human disease, but with X-ray diffraction instead.

Coming from an NMR lab, I entered Dr. Redinbo’s crystallography lab with the intention of exploring the structural biology spectrum more broadly. I really wanted to learn X-ray crystallography first hand to help me decide this coming year where to focus my applications for graduate school programs. I expected my work in Dr. Redinbo’s lab would be very general, including making buffers, cleaning dishes, etc. To my pleasant surprise, the same day I met Dr. Redinbo in person, he already had me setting up crystal trays. Within a few more weeks into the BPS course, I was shadowing graduate students using the x-ray source, which I consider my favorite part of the summer course thus far. In addition to the research, I have learned a lot about scientific communication. We give presentations which help train us for graduate-level coursework by having us present on what their research is about and the direction it is headed.

The program also offers classes that introduce important topics of physical chemistry, biochemistry, molecular biology and biophysics. For those who have taken those classes, the course serves as a wonderful review; for those that have not, it is a fantastic introduction to central themes of biophysical studies. These are formal courses with important feedback such graded assignments and quizzes; however, the courses are not for credit. This promotes a comfortable learning environment for students of all levels of education and disciplines.

Overall, I think that this summer has been one of the best of my life so far. The BPS Summer Program allowed me to travel across the country and make new friends from various fields and interests. I would strongly suggest this internship to anyone who is passionate about science, and I have no regrets when I reflect upon my stay at UNC Chapel Hill.