Biophysical Society Network Meeting PA 2012

My colleague Ben Bratton and I just returned from an exciting day at Lehigh University about 50mi East of Princeton. This year’s Biophysical Society Network Meeting for Pennsylvania was an awesome opportunity to get in as much interesting science as fits in a single day. The list of speakers was pretty strong to begin with ranging from the innovative NMR research by Sharon Rozovsky to Phil Nelson, one of biophysics all-time heroes. In between, lucky me got a shot with a platform talk about our work on the gliding motors of M. xanthus, and I was thrilled about the positive feedback in the following discussions.

A good meeting always incorporates an outstanding poster session. In particular, I learnt a bunch from Moumita Das about the importance of crosslinkers in stabilizing the cytoskeleton.

Again, a great meeting with throughout awesome science, we need more of those regional network meetings.

DPG Frühjahrstagung 2012 ahead

Ever since I’d manifested that ‘biophysics rules my world’, I found the meetings of the Biological Physics Division at the DPG Frühjahrstagung (German Physical Society Meeting, section Condensed Matter) extremely inspiring and stimulating. This year’s meeting takes place in Berlin in the last week of March. In the course of a week, there are typically three parallel sessions of presentations on biophysics followed by poster sessions, plus the chance to join the sessions of other sections (e.g. Chemical and Polymer Physics Division).

The thrill caught me this year when we were informed that I’m allowed to present our most recent optical tweezers work:

Forces and Fast Dynamics of Gliding Motors in Myxococcus Xanthus
Wed, Mar 28 2012, 16:00-16:15, H 1028, Session: BP 16.3
The gram-negative bacterium Myxococcus xanthus is an important model organism for studies of multicellular grouping as well as biofilm formation. Individual cells use a combination of twitching and gliding motility to form large, multicellular structures. We identified a new class of molecular motors that power gliding motility. These mo- tors, made of the AglQRS proteins, assemble within focal adhesion sites that link the bacterial cytoskeleton to the extracellular surroundings.
Our goal is to understand control and cooperativity of these motor complexes within single cells. For this purpose, we combined optical tweezers, fluorescence microscopy, and real-time tracking of attached marker beads. This allows us to assess the step-like activity of motors embedded in the adhesion complexes at high temporal and spacial resolution. We found motor function correlated to the helical pitch of the bacterial cytoskeleton. We further measured motor stalling forces and the time delay between single motor responses to various cell-motility regulators. Measurements of the gliding force of whole cells will complement our results. Our experiments quantitatively explain how the AglRQS motors drive cell gliding and the formation of multicellular structures.

In December I had already learnt that I had been invited to the present in a symposium about the highlights of my PhD thesis:

Allan Variance Analysis and Fast Camera Detection Schemes for Optical Tweezers
Mon, Mar 26 2012, 12:00-12:20, EW 201, Session: SYSD 1.1
In soft-matter and biological physics, optical tweezers are among the most versatile force-microscopy techniques. Optical tweezers allow for non-invasive and localized sample control under physiological conditions. Within a tightly focused laser beam, an optical handle fluctuates. Its positions can be thought of as a thermal, stochastic sampling that is elegantly used to calibrate the trap. Previous protocols emphasize only the high-frequency spectrum (>400Hz), handling unavoidable low-frequency effects with unsatisfying arguments.
To rigorously quantify these low-frequency effects, we pioneered the usage of Allan variance analysis in addtion to existing calibration protocols. It measures an experimental accuracy map and is essentially assumption-free. It allows one to quantify the optimal calibration interval and determine the force sensitivity. It became one of the keystones to calibrate new tweezers setups. At the same time, Allan variance analysis was implemented for other biophysical techniques, including FRET, magnetic tweezers, and ionic currents through nanopores.
In a second project, we built a camera detection scheme to directly visualize fast biological processes. It acquired and stored optical tweezers data up to 40kHz. The scientific community and nanotech companies have been utilizing our hardware and open-source software solutions.

Most importantly though, the meeting is a great chance to exchange with friends about their latest research. I’ll be trying to resurrect an old habit (see blog during Biophysical Society Meeting 2010) and summarize some of the great work I’ll be running into in daily blog posts.

Poster Session Tuesday

This time finding the most relevant posters of the session was a simple task; they were all pretty much lined up in the poster session’s subgroup of “DNA, RNA Structure & Conformation II”. And I must say, there was not a single one that did not immediately caught my interest!
Jun Lin from UCSB has taken on the difficult task to shade light (in fact it’s done by YOYO-staining of torsionally constraint DNA) on the formation of plectonems in magnetic tweezers experiments. He was explaining his experiments to his former colleague Kipom Kim when I dropped by.

Especially interesting where Hergen Brutzer’s and Robert Schöpflin’s posters: Both next to each other dealing with the widely debated buckling transition of double-stranded DNA. Hergen did very careful and high resolution magnetic-tweezers measurements (doi: 10.1016/j.bpj.2009.12.4292) and Robert complemented those with Monte-Carlo simulations. Brilliantly aligned theoretical and experimental studies!

Platform DNA Replication

Monday evening had ended with a fairly nice reception after Roger Tsien’s National Lecture. But still, the single-molcule sessions on Tuesday morning were packed with people. Nanopores are a big issue and the talks mostly emphasized this trend whilst pointing out the difficulties and hurdles to deal with on the way. Pretty impressive once more, the direct force measurements on dsRNA in solid-state nanopores done by Michiel van den Hout in from the Dekker lab.

The Platform DNA Replication, Recombination, &Repair was packed with good presentations. Emory-based Ivan Rasnik did take a closer look at the Msh2-Msh3 regulatory system (actually the third talk on that I followed during the Meeting). The key to understanding the recognition of DNA hairpins and 3-way junctions might be the salt levels…

David Rueda did take a closer look at the dynamics of DNA polymerases and the exonuclease I klenow fragment. This shows a slow initiation phase which could be seen as an indicator for slow incorporation kinetics for the first three nucleotides. Might this correspond to a fidelity checking process? From David’s perspective, FRET reveals full time, but no reliable distance information, since e.g. the exact local refractive indices are not known.

The researches around John Marko at Northwestern University are investigating the proteins that are essential for the structural maintenance of chromosomes. Mingxuan Sun used magnetic tweezers to e.g. find SMC functioning in a step-wise manner surprisingly even in the absence of ATP. She also got hold on SMC with a mutated hinge domain and could draw interesting conclusions this way, e.g. it did not condensate the DNA!
I dropped by Elnaz Alipour-Assiabi‘s poster later this day. In the same lab, she developed a theoretical model fro dissociation and rebinding for type I restriction and condensin-like enzymes. Cool work!

Iwijn De Vlaminck‘s talk basically summed up his great work on the Torsional Regulation of hRPA-induced Unwinding of Double Stranded DNA. This pretty much put a nice line under a really, really good platform session.

Poster Session Monday

Whilst browsing the posters in today’s session I did find quite a few very interesting once (again, a personal very much non-representative selection purely driven by personal interest;-).
Holly Wolcott wants to attack critizism that often argues about the number of proteins specifically bound to quantum dots. In carefully conducted experiments, she found a nice binding efficiency curve for flag-tagged radio-labeled GFP.

My colleague Christine Selhuber-Unkel featured basically her experiments on the crowding inside the yeast S.pompe. By tracking naturally occuring fatty granuals Christine and the grad student Pernille Yde measured the diffusion coefficient during different stages of the cell cycle. In principle, this method is label free as the granuals are an intrinsic handle.Christine Selhuber-Unkel in front of her poster at the Biophysical Society Meeting 2010

Tobias Wolfram from the Spatz lab at Stuttgart showed experimental results with different cell lines on gold nanostructures. Those can be produced on a surface, or embedded in a hydrogel. The potential of these structures are enormous as emphasized by the number of the presented cell experiments.Tobias Wolfram explains his poster at the Biophysical Society Meeting 2010

Alycia Gailey explained me a very cool tool that is sampling a neurotransmitter signal from research animals. From the chip it is sent via bluetooth to a near by computer.
Understand the model for the chromosome movement during mitosis took me a while, but thanks to Blerta Shtylla who walked me through her model (doi:10.1016/j.jtbi.2009.12.023), I will remain a little less nescient.

Lunch close to Moscone Convention Center: Poll?

Almost tempted to start a poll on finishing the everlasting question of the best place for some (very) decent lunch during a meeting at the Moscone Convention Center, I’ve found my answer already: Check out the cafe at the Contemporary Jewish Museum, just 300yards from the backside of Moscone North (crossing Mission St). Healthy, fresh and kosher; definitely my recommendation.

Poster Session Sunday

Wow, what a poster session! Apparently, there was quite some interest in our work on the Allan variance which mostly covered our Optics Express and SPIE Proceeding, because even after the “regular stand-by time” people would not let me leave;-). Thanks to all of you that dropped by, I’ve learnt a lot and hope I could answer most of your questions sufficiently.

The downside was that I could not even remotely check as many interesting posters as anticipated. And there were quite a few.
Fernando Moreno presented some very, very nice AFM study on prevention of DNA reannealing by a certain helicase.
Jan Lipfert showed new data on the TopIB project (magnetic tweezers studies with drug-resistant topisomerase derivates) that I found especially interesting as his results basically confirm previous findings which we did in Nynke Dekker’s lab.
I also did like Ramsey Kamar‘s poster. Therein he described one part of his grad work on the oligomerization of the membrane protein prestin. Pretty cool stuff.

There were quite a few more really, really good posters. I think this first poster session confirms the trend of very strong contributions to this meeting from the entire field of biophysics.

Quite a few people made it to the workshops in the evening. They were rewarded with good presentations in particular I want to give two thumbs up to Adam Cohen‘s work that highlighted his group’s effort in developing neat biotech tools. [For the future: maybe grab’n’go sandwiches just before the evening sessions would help to keep the audience tight and together;-)]

Friends and the Meeting

This story could be told by anyone at the Biophysical Society Meeting. You run into friends that you haven’t spoken to for a few months and you are back on top of some nice discussion after just three sentences… There were quite a few of these instances for me, one just this morning. Manuel Neetz and I had done our diploma in Heidelberg, before he had joined the PhD school in Dresden. We both ran into each other just before his PI Iva Tolic-Norrelykke told the audience of the Cytoskeleton Symposium about Lessons from Fission Yeast. Though you will miss out on Iva’s very good way of giving a talk, she has published most of the talks bit in this paper: Self-Organization of Dynein Motors Generates Meiotic Nuclear Oscillations
“The number of friends that one runs into will increase even more during the next days’ poster sessions.” I go with Manuel’s bet.

If you are like Manuel and Iva interested in the function of the molecular motors kinesin and dynein there is among others one that you don’t want to miss:
Veikko Geyer: Direct Measurement of the Force-Velocity Relationship for Multiple Kinesin-1 Motors by Magnetic Tweezers, Feb 23, 4:30pm, room 305.

Session Biological Flourescence

Was there actually anybody willingly missing out on Steve Block’s talk? At least, none of the single-molecule people researchers, as the auditorium was filled! Steve’s 30min-firework on the experiments carried out by Nicholas Guydosh at Stanford had as a goal nothing less, but targeting the long lasting (and highly ranked) debate about how kinesin (another subfamily than the Kip3 Volker is looking at) walks on microtubuli. The idea is straight forward: instead of binding an handle bead in an optical tweezers assay to the tail, Steve and his coworkers simply bind the bead directly to one of the walking heads. They have achieved this by the use of a 23nm-DNA linker.

As the result: Kinesin walks with one head bound, ‘it’s so simple.’ The extraordinary setup also allowed a time shared trapping assay, that even showed a directed, slight overshooting that might be related to the ADP release (around an one-nanometer structural change in direction of load). The story was great and complete, the Nature paper came in 2009.

The excellent talk by Catherine Royer on the investigation of gene regulatory networks by means of flourescence techniques was interrupted by a power failure in the lecture hall. Regular confusion turned into some new coffee, though after six minutes Catherine was back on.
Very well handling this situation, she explained the heterodimer formation between cer-ER(alpha) and mcherry-ER(beta). This nucleus data was complemented by those about the CggR and CcpnR repressor network by fluctuations of flourescently labelled proteins in E. coli. But are there any models that take anything beyond simple diffusion (even inside the cells) into account?
This is according to Catherine a very complex, very difficult task. I definitely got really interested in the presented work, looking up this group’s papers etc. will happen back in Copenhagen.

Eric Greene entered the stage just before the break, reminding us about their cool DNA curtains they do at Columbia. He looked at two pairs of dimer-forming primers (Mlh1-Pms1, Msh2-Msh6). The bigger picture he has in mind though is the bypassing of those protein complexes on nucleosome-packed DNA. Funny thing: on his acknowledgement slide, we read

YOUR NAME HERE: ______

Was that meant as a job offer? And to whom? ;-)

After the coffee break, we were reminded of the Weber prize, find more details at lfd.uci.edu/weber/prize/.

I did like both of the students talks (I might drop my notes here later, when time permits). Richard Ludescher took us on the entire history lesson to finally arrive at the difference between flourescence and phosphorescence. Or would you know by heart which one goes through the triplett state ;-)?

At the end of the first day, 1.5 really good sessions, exposure to good new ideas”, own poster put up, and a few people gathered for a good dinner thing, don’t ask for much more.

Arriving at the Meeting, Subgroup Molecular Biophysics

Just one thing about arriving to the Biophysical Society Meeting 2010: Have this barcode thing printed, that was emailed to you before, and you will be done with registration quicker as reading this paragraph ;-)

Made it to the first scientific session and with a cup of coffee on may lap, three members of the Subgroup Molecular Biophysics did the kick-off. From an experimentalist point of view, James McKnight‘s talk was the most interesting one. He and his group are investigating the villin-type headpiece superfamily. Those proteins are involved in the deformation of red blood cells. In his talk James focused on the subspecies dematin that consists of a 315-residues core domain and a 68-residues long headpiece that is able to bind to actin filaments. Since the core domain can form trimers with others, dematin enables actin bundling. He convinced us with some electron micrographs of bundle/non-bundle forming dematin derivates. The phosphorylated dematin also formed bundles, though in a distinct fashion.

On the cellular level, dematin is most often associated with the junctional complex that stabilizes star-like spectrin patterns. It also links it to the membrane, thus might inhibit or at least alter the deformation red blood cells. What would now be the role of some post-translational regulation such as phosphorylation? In a nice and convincing combination of complementary techniques, such as CD spectra, gel electrophoresis after ultracentrifugation, and NMR structures a model was announced that focuses on the phosphorylated residue, just three residues away from the end of the head domain. It is located on a very flexible linker, which data suggests can fold back on itself. In this state it would still be able to bind F-actin, although in a spatially different fashion leading to more confined actin structures. To encounter for the variety of states actually found, James and his coworkers need the help of a steering argument.

Questions addressed again the role of dematin on the cellular level, the possible two F-actin bundling only (except three as working hypothesis through the entire talk) and the flexibility measures of the linker. Very nice and complete talk as a good start into the meeting. See what David Green has got to say about HIV after the coffee break.