Analysis of a Brain Plasma Membrane

BPJ_113_10.c1.inddCellular plasma membranes (PM) contain hundreds of lipid species that are heterogeneously distributed in the membrane plane, forming local domains of altered composition. Cells tightly regulate their lipid composition because lipids influence membrane protein function both directly through lipid-protein interactions and indirectly through changes in bilayer properties. Yet larger differences in lipid composition can be observed between different cell types. By constructing a realistically complex lipid model of a neuronal PM, we can determine the membrane’s properties and compare to that of an average PM. Even though the neuronal lipid mixture is significantly different from the average mixture, the main changes in mixture are carefully counter balanced, resulting in a range of surprisingly similar membrane properties while domain behavior is unique.

The cover image for the November 21 issue of the Biophysical Journal illustrates the vast possibilities for analysis of a neuron’s realistically complex lipid membrane. A composition of many of our analysis features is shown stacked on top of a computer-rendered neuron-like cell. The features show a range of system characteristics from the distribution of the lipids and their tail types to analysis of membrane thickness and the lateral flow of the lipids to the fitted curvature surface of the membrane and distribution of cholesterol domains. The figure captures the depths of analyses that are required to properly characterize our simulations. The layers of analysis are complementary to each other, and all are required to fully appreciate and understand the sophistication and subtlety of complex, dynamic membranes.

The trajectory images of the membrane were rendered using Tachyon in VMD. The membrane thickness and lipid flows were calculated from the simulation and rendered with Python tools. The membrane curvature surface and the cholesterol domains were rendered using Paraview. The neuron-like cell was made and rendered using Blender 3D.

– Helgi Ingólfsson, Timothy Carpenter, Harsh Bhatia, Timo Bremer, Siewert Marrink, Felice Lightstone

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American Education Week

American Education Week (1)

November 13-17 is American Education Week, highlighting the importance of K-12 education. We asked Biophysical Society Education Committee members to tell us about teachers who made an impact on them.


stoked01-hero“In high school there was a fierce science teacher named Mr. Housek. I was unimpressed with the butterflies that my fellow students were collecting in Biology and, against all advice, took his Electronics class instead, where I learned to use a slide rule and to build circuits. Somehow, we got along and his Physics class provoked my curiosity in understanding how things worked. Little did I know how very complicated it was going to be to apply this understanding to biology.”

– David Stokes, New York University

 

“I had a remarkable science teacher, Mr. Griffith, at Wy’east High School, a small high downloadschool in rural Oregon – he was known for his pointed and sarcastic remarks, as well as his ability to teach science. He taught me Chemistry, Physics and Semi-Micro Quantitative Analysis, and oversaw my senior research project, which won a semi-finalist place in the Westinghouse Science Talent Search. He also graciously disposed of the batch of chemicals that I once mixed and realized after making it, that it might not be entirely safe. He taught science to many students, including a colleague at UNC Chapel Hill, Richard Cheney, who grew up in a small town up the road from my parents. Sadly, Mr. Griffith is no longer with us.”

– Sharyn Endow, Duke University

 

Me in Office“The biggest impact on me was not from any one teacher but from a family of teachers at St. Stephen’s Elementary School in Milwaukee.  They watched over me and my brother during difficult times in a turbulent family.  My debt to them is immeasurable.”

– Alex Small, Cal Poly Pomona

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“I would like to honor Mrs. Mader from Quarton Elementary School in Birmingham, MI. She taught us about self-esteem and confidence. She told me that you could go a long way in life if you believed in yourself, and she was right!”

-Ashley Carter, Amherst College

 

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“I did have a 9th grade math teacher who I have always remembered.  He recognized that I had some talent and let me work on my own in the back of the room during class.  I was a bit introverted at that time, and working on my own at my own pace really motivated me.”

-Allen Price, Emmanuel College

 

Linda Columbus Investigates Cell Membranes With Large New Grants

“Many teachers come to mind when asked about K-12 teachers that made an impact on me. I couldn’t read when I started first grade and my teacher took the time and effort to get me up to speed and performing well by the end of the year. I am confident without her attention to the way I learn and realizing it wasn’t for the lack of ability that I would not be a scientist. Another was my seventh grade science teacher that had very visual exams, which stimulated me. We were learning anatomy and doing dissections so on the day of the exam there were about 25 dissected animals or products from our labs that were tagged with numbers and we had to go around the classroom to identify or answer specific questions about the visual product. This was so aligned with my learning style and curiosity that I loved the exams. My third grade teacher let us self-pace in math if we wanted. So we could just keep going in the math book and several of us chose to do math instead of free time some days. Fourth grade was a shocker when we weren’t allowed to do that anymore. Another was a teacher in high school that I had for two classes, Calculus and Computing. She just got how I learned and most lessons were open ended or if we finished we were asked to help others in the class. Looking back, it seems the teachers that were inclusive of different learning styles and instruction were the ones I remember.”

– Linda Columbus, University of Virginia

 

 

Get to Know: Joanna Swain, BPS Council Member

We recently spoke to Biophysical Society council member Joanna Swain, Bristol-Myers Squibb, about her research, meeting her heroes, and what she loves about living in New England.


Joanna Swain_pictureWhat is your current position & area of research?

I am currently a Senior Principal Scientist in Molecular Discovery Technologies at Bristol-Myers Squibb, where I work to discover transformative medicines for patients whose medical needs are not being met by currently available treatments. My team uses in vitro selections to discover cyclic non-natural peptides that bind to pharmacologically important targets with high specificity, but that are small enough to hold the promise for intracellular delivery and oral bioavailability.

What drew you to a career as a biophysicist?

I was initially drawn to the field of structural biology by the idea of seeing the unseeable, with NMR as my first tool to illuminate protein structure and dynamics. I was captivated by the theoretical models of protein allostery, and wanted to understand allostery at a mechanistic level – how are protein structure & dynamics impacted by ligand binding, and how can information about binding site occupancy be transmitted to distal sites? It has been immensely rewarding to channel my interest in modulating protein activity toward drug discovery in an industry setting.

What do you find unique or special about BPS? What have you enjoyed about serving on Council?

In my early career, BPS was the meeting for finding other people who shared my interests and for learning about new technologies and applications that could be relevant to my own research. Since joining Council, I have been particularly impressed by the commitment of the Society to maintaining diversity at the podium in all of its meetings. Serving on Council has also given me the opportunity to meet many academic peers that I would not otherwise have gotten to know. I have to admit to being a little starstruck in a recent Council meeting sharing breakfast with my heroes Angela Gronenborn and Jane Dyson!

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Swain modeling her mother’s 1970s era ski gear. “It’s still going strong! Wooden waxless skis with real mohair strips, and leather boots with no insulation whatsoever! Perfect for New England winters,” she jokes.

Who do you admire and why?

I admire women like Margaret Oakley Dayhoff, who pushed their way past boundaries and first claimed access to male-dominated scientific fields, allowing me to follow my interests and gather opportunities that were never so easily offered to them. I admire local and global citizens, faith leaders, and activists, who build me up with messages of hope for a more just world, and give me both strength and mechanisms to help make it happen.

What do you like to do, aside from science?

Raising a family alongside an active career has not left much time for other pursuits, but now that my children have grown to teenagers, I look forward to a future that involves a whole lot more bicycling and travel, hopefully at the same time!

What is your favorite thing about living in New England?

I love the change of the seasons, and long cold snowy winters. It’s not everyone’s cup of tea.

What is something BPS members would be surprised to learn about you?

Sometimes the news on NPR’s Morning Edition becomes too much for me on my drive to work, so I start the day with Red Hot Chili Peppers or Ani DiFranco at volume 11 instead.  With enthusiastic tuneless singing.

Do you have a non-science-related recommendation you’d like to share?

This might be a better answer for the last question, but my guilty pleasure is the TV show “Shameless.” I think William H. Macy’s portrayal of deadbeat dad/addict Frank Gallagher is just brilliant. Again, it’s not everyone’s cup of tea.

Do leaf hairs swing to a caterpillar beat?

BPJ_113_9.c1.inddIn 2014, when Heidi Appel and Rex Cocroft demonstrated the ability of Arabidopsis leaves to respond to the sound of Pieris caterpillars feeding, people reacted with either disbelief or a sense of playfulness. For this cover image for the November 7 issue of Biophysical Journal, we have picked up the fanciful idea that plants can appreciate music.

The cover image conjures up the ghosts of science fairs past: playing music to plants, a favorite high school student project for well over half a century. Whether or not responses were measured, some responses should in theory occur if plant and parameters are selected appropriately. Many plants are extremely sensitive to small mechanical stimuli, and with a well-chosen plant it should be necessary to only include the right frequencies and a (perhaps unreasonably) high volume. Nevertheless, although plants have not evolved to appreciate Chopin and the Beatles, some certainly may have evolved to listen in on chompin’ and the beetles.

The cover illustrates the possibility that trichomes (hairs) of the weed called Arabidopsis thaliana are acoustic sensors. The trichomes are well known to have many other functions–for example protecting against the overly bright sunshine of the cover image, creating a layer of surface moisture to lessen dehydration, and greeting herbivores with a shield of distasteful toxins. But their evolution may have also been driven by the mechanical inputs shown. For example, they are the first cell type that insects touch when settling on an Arabidopsis leaf. And, as illustrated in the archetypal simulations on the cover, they have the form of miniature mechanical antennae.

The cover reflects how the percussion section contributes as well. Our recent study of trichome mechanoresponses showed that touching or brushing led to diverse complex patterns of acidification and cytosolic Ca2+ oscillations in the stalk, branches, and subsidiary cells (Zhou et al., Plant, Cell & Environment, 40:611-621. 2017).   Morphological observations suggest that information propagates to the leaf as a whole, where it was already shown that caterpillar feeding elicits rapid production of deterrent toxins.

The idyllic scene on the cover of Biophysical Journal highlights how the mechanoresponsive trichome is an idyllic system for studying plant signaling. The guard cells of the stomata that control gas exchange have been considered the premier system for such study, and it may be significant that the trichomes derive from the same kind of stem cells.  Evidences such as presented in our study play up the importance of the historical transition from the belief that walls are dead, to the concept that they play active and vital regulatory roles of mechanical, electrical, and biochemical character, especially when jamming out like the walls on the cover.

For more on our work in this area, please visit these websites: www.cemb.org, and http://bebc.xjtu.edu.cn/English/

– Shaobao Liu, Jiaojiao Jiao, Tianjian Lu, Feng Xu, Barbara Pickard, Guy Genin

On the State of Professional Opportunities for Women in Biophysics: Marina Ramirez-Alvarado

To investigate perceptions about the state of women in science, the BPS Committee for Professional Opportunities for Women is hosting a blog series where members can express their views on the subject by briefly answering these four questions: In your opinion,

  1. What is the current state of gender equality in science and biophysics?
  2. What is the value of having equality and true inclusiveness?
  3. What is one area that needs attention; and
  4. What is the one thing that can be done right away?

You are encouraged to read and comment on these blog posts, and to volunteer your own answers by emailing them to Laura Phelan at lphelan@biophysics.org.


Council- Marina_Ramirez_Alvarado

Marina Ramirez-Alvarado, Mayo Clinic

What is the current state of gender equality in science and specifically in biophysics?

MRA: Gender equality has definitely improved over the past 25 years since I finished college and embarked on a scientific career, but unfortunately, things are still not great for women in science and biophysics.  We are all struggling with implicit biases that diminish and discourage the work of female scientists and biophysicists. Also, most often, when couples are faced with the two-body problem, the man’s career takes precedence. Many measures of progress, such as for example, the percentage of women professors in STEM fields, show that the pipeline is still leaky, especially at the top of the ladder, for full professors and leadership positions. In my view, a current problem is patchy support: some institutions are supportive, while others are less so; some colleagues are sensitive, supportive, and inclusive, while others are not. Further, even within biophysics, some sub-fields include more female speakers than others, and some journals (including Biophysical Journal) have more female representation in their editorial board than others. The same colleague/interaction/experience may be positive for one female scientist and negative for another. It can be confusing!

What is the value of striving towards equality and true inclusiveness?

MRA: More and more data show that diverse teams are more productive, more creative, and more successful. Female CEOs and female leaders are more effective in making their companies/institutions financially solvent. Female leaders inspire more loyalty and create welcoming and productive atmosphere where everyone feels valued. These seem to me compelling advantages for inclusive environments.

What is one area that needs attention?

MRA: Effective mentoring and increased visibility of female role models can help, and we must concentrate on closing this existing gap. Female scientists need mentors who can guide and advise them along fulfilling roles in research and leadership; further, it will be important to help women scientists identify possible sponsors and develop with them supportive and durable relationships. Mentors must recognize and acknowledge the multiple identities and roles that their mentees have; must learn to empower them to overcome barriers whether in the form of implicit bias, administrative burdens, and the sometimes-dangerous political waters of scientific careers.

What is the one thing that can be done right away?

MRA: We (all scientists) have to get involved. To those of us who are aware of the still real problem of gender inequity in science, I ask that that you speak up, voice your concerns and propose solutions; we have to express our concerns anytime we see gender inequality. To my colleagues who think we solved the problem of gender equality in science, I invite you to listen more to female colleagues, friends, and even relatives; every one of them has a story where she had to work harder than a male peer had to, for the same recognition.

Scientific societies, such as BPS, can play an important role by programming sessions at their annual meeting dedicated to addressing this problem.

In addition to programming educational sessions at their annual meetings, scientific societies can encourage all members to fill out the implicit bias assessment https://implicit.harvard.edu/implicit/education.html

One last thing: while we have to do more to include women scientists, we must extend an unbiased and welcoming hand to all colleagues regardless of ethnicity, race, sexual orientation, disabilities, etc. We need a broader view about what a diverse and inclusive environment is and work diligently to achieve it.

 

 

Architecture of Bacterial Cell Division Protein FtsZ Polymers

BPJ_113_8.c1.inddFtsZ is a self-assembling protein that forms the contractile ring guiding the cell division machinery in most bacteria. FtsZ is structurally homologous to tubulin, the subunit of eukaryotic microtubules. FtsZ monomers associate head-to-tail forming  single-stranded filaments that hydrolyze GTP, in a partially understood process. However, how FtsZ filaments organize in the dynamic division ring is still a challenging problem. Rather than forming a well-defined structure, such as band or tubule, FtsZ filaments laterally associate among them in a relatively disordered fashion.  FtsZ filaments bind partner and regulatory proteins, including those tethering them to the inner face of the plasma membrane.

The cover image for the October 17 issue of Biophysical Journal is an artistic representation of the organization that we propose for FtsZ assemblies.  FtsZ filaments made of FtsZ monomers laterally associate through the disordered C-terminal tails, forming loose bundles. Small-angle X-ray solution scattering results (exemplified by the graph on the left) indicated a characteristic 7 nm center-to-center lateral spacing between FtsZ filaments. By modeling comprehensive building and scattering calculations we saw that multiple associated filaments of variable curvature and length were required to reproduce the X-ray scattering features. These calculations also showed a 2-nm gap was left between core filament structures. We hypothesized that the gap would be bridged by the FtsZ intrinsically disordered C-terminal linker region, as in the model bundle in the center of the image. Cryo-electron microscopy provided views of unstained individual assemblies in vitrified solutions (blue background in the bottom half). Analyzing polymers assembled from FtsZ protein constructs with diverse C-termini supported the model.

Combining several biophysical approaches has provided insight into the self-organizing properties of FtsZ that we think underlie the assembly of the bacterial division ring. It should be noted that bacterial division is still a clinically unexplored target for the discovery of new antibacterials needed to counter the spread of antibiotic resistant pathogens.

-Sonia Huecas, Erney Ramirez-Aportela, Albert Vergoñós, Rafael Nuñez-Ramirez, Oscar Llorca, David Juan-Rodriguez, María A. Oliva, Patricia Castellen, and José M. Andreu

Importance of Biophysics in Breast Cancer Progression

October is Breast Cancer Awareness Month in the US. We spoke with University of California, San Diego graduate student Pranjali Beri and her PI, BPS member Adam J. Engler, about their research on breast cancer and other epithelial-based cancers. 


What is the connection between your research and cancer?

Cancer is the second leading cause of death in the US, resulting in approximately 600,000 deaths in 2016. The negative prognosis associated with cancer is due in large part to metastasis of a primary tumor. Cancer metastasis is the process by which tumor cells leave the primary tumor, enter the blood stream (intravasation), exit the blood stream at a different site in the body (extravasation), and establish a secondary tumor. However, tumors are exceedingly heterogeneous and only a small fraction of cancer cells from the primary tumor are capable of establishing secondary tumors. The metastatic potential of identical solid tumor types also varies from patient-to-patient due to expression differences of critical markers, making it nearly impossible to identify a universal biomarker that can predict metastatic potential of all solid tumors.

fig 1 A

Cancer cell migration away from the primary tumor is driven, in part, by physical interactions between cells and the surrounding extracellular matrix. Protein clusters known as focal adhesions allow cells to attach to the matrix proteins, and stability and strength of these attachments plays a role in regulating cancer cell migration. Our research is attempting to understand the link between adhesion strength via focal adhesions and cancer cell dissemination. In our recently publication, we quantify population adhesion strength of various epithelial cancer cell lines by utilizing a spinning-disk shear assay (Figure 1a). The shear stress required to detach 75% of the cell population serves as a metric to describe the adhesion strength of that population. In the presence of conditions that mimic the tissue adjacent to tumors, e.g. low divalent cations, we found that heterogeneous adhesion strength for the most aggressive cells indicate that subpopulations within aggressive cell lines were capable of metastatic behavior. This is similar to the small fraction of the primary tumor previously thought to contain stem cell-like properties of self-renewal, differentiation, and migration.

fig 1 B

Currently, our research further seeks to sort, capture, and analyze cells with more labile focal adhesions in response to stromal cation concentrations. We have developed a parallel plate flow chamber assay to isolate weakly adherent cells (Figure 1b) and characterize their migratory propensity in relation to strongly adherent as well as unselected cell populations. By demonstrating that there is a link between adhesion strength and migratory propensity of the cancer cells, we can use it as a biophysical marker for metastatic potential.

Why is your research important to those concerned about cancer?

Epithelial tumors, or carcinomas, are the most common type of cancer. There is no universal biomarker that acts as an indicator for metastatic potential. However, most epithelial cancers undergo metastasis. Having a physical indicator of metastasis can be beneficial in identifying the aggressiveness of a tumor and its likelihood of forming secondary metastases, independent of the type of epithelial tumor that it is.

How did you get into this research?

Throughout my undergraduate career, I have been interested in microfluidic devices and their applications as diagnostic devices. In graduate school, I joined the Engler lab in order to apply my microfluidics background towards cancer metastasis research.

How long have you been working on it?

I began working with microfluidic devices during my undergraduate studies. However, it was in graduate school that I used it to study cancer cell dissemination.

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

I am currently funded by the National Science Foundation through their Graduate Research Fellowship Program. This research is also funded by the National Institute of Health and the Department of Defense Congressionally Directed Medical Research Program.

Have you had any surprising findings thus far?

Tissue adjacent to tumors has dramatically lower ion concentrations than in the tumor. In our previous publication, heterogeneity is most pronounced in highly metastatic cancer cell lines, but only when exposed to low ion conditions that mimic adjacent tissue; in the presence of high cation concentration, akin to the tumor microenvironment, metastatic cells are mechanically indistinguishable from their non-metastatic counterparts. This shift in adhesion strength was not present in non-metastatic cancer cell lines but was present in epithelial cancer cell lines from other tumors as well, including prostate and lung. While these previous studies could isolate the strongly adherent fraction remaining attached, recent experiments using flow chamber assays indicate that weakly adherent cells from the same cell lines display increased migration speed and are more processive in comparison to unsorted or strongly adherent populations. These results indicate that adhesion strength can potentially act as a biophysical marker of metastatic potential, and that the weakly adherent cells are likely to have the highest metastatic potential.

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

Our fluidic-based separation method could allow us to isolate cancer cells by their metastatic potential. The adhesion strength-based separation method can serve as a potential prognostic device that exposes patient biopsies to shear stress, correlates weakly adherent cell isolation with metastatic potential, and makes a prognostic determination about the likelihood to metastatic disease in the future.

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

By establishing the link between adhesion strength of the cells in the tumor and the metastatic potential of the tumor, we can ascertain the aggressiveness of patient tumors and tailor treatments accordingly.