Jessica Oya, our High School Science Teacher, Returns!!

This summer we had the fortune of having Jessica Oya, the high school teacher from the Life Academy of Health and Biosciences in Oakland, come work in our lab again as part of the IISME program.  This year, Jessica worked with Jack on a project involving zebrafish development and learned how to fix and stain zebrafish embroys for various proteins.  In addition, she set up a curriculum for her chemistry class, incorporating some of the techniques she learned in our lab to pass on to her students.  She now has extensive experience teaching biology, physics, and chemistry at the high school level, with several demonstrations and experiments that she learned while working in our lab.

From my limited experience teaching (having just TA’ed 1 class so far), I learned both the difficulties and rewards of teaching.  And after visiting Jessica at her school and seeing her in action, I realized the expertise she has developed over the last several years.  I have often thought how awesome it would be to go back to high school (preferably my old high school) and teach chemistry.  My AP chemistry teacher in high school was an excellent teacher, so good that he was also our high school wrestling coach.  After the AP exams, he had the class participate in a competition to determine who was the best wrestler…  But from him, I learned the importance of having a teacher who spends the effort making sure every student understands difficult concepts.  Jessica also shares this quality.  It was truly a pleasure having her in our lab, and we wish her the best as she prepares to start the school year.

August 15, 2012 at 3:27 am Leave a comment

Excellent paper about stress fibers and focal adhesions from the lab of Margaret Gardel

Just a week ago, I presented a paper at our weekly literature review (journal club) which I found very interesting.  Many biophysics researchers are studying these complexes called focal adhesions.  Focal adhesions are complexes made of several different proteins that serve as the link between a cell’s actin cytoskeleton and the surrounding extracellular matrix (ECM).  It is thought that these complexes generate the tension necessary to pull a cell forward during migration.  Deficiencies in mechanotransduction of these complexes are implicated in numerous diseases, such as cardiomyopathies and cancer.

This paper, titled “Tension is required but not sufficient for focal adhesion maturation without a stress fiber template” is from the lab of Margaret Gardel at the University of Chicago.  The authors show that cellular tension and traction forces are still present even after disruption of the stress fiber template at adhesion sites.  The impaired stress fiber assembly also impeded focal adhesion compositional maturation and ECM remodeling.  Finally they showed that focal adhesion maturation can still proceed even when disrupting myosin II-dependent cellular tension up to 80%.  This study therefore argues against the current hypothesis that stress fibers induce focal adhesion maturation primarily by exerting myosin II-dependent tension at cell-ECM contacts.  Instead, they claim that the structure of the actin cytoskeleton serves to recruit multiple other proteins that are important to focal adhesion maturation.

What I found interesting about this study is that the authors were able to alter the structural framework of the actin cytoskeleton by disrupting only the radial stress fibers (perpendicular to the cell edge), while leaving the transverse arcs (parallel to the cell edge) unperturbed.

Here’s part of figure 1, which explains this.  Note the radial stress fibers in the wild type (WT) cells (indicated by the yellow arrows) and the transverse arcs (indicated by the red arrows), and then note the disappearance of the radial stress fibers in the subsequent images, all of which are ways to disrupt the radial stress fibers.  Also from the paxillin staining, we can see that the focal adhesions are unchanged (paxillin is a focal adhesion protein).

I find it very clever to change the architecture of the actin cytoskeleton, and then observe the changes in tension generation and focal adhesion maturation.  To be able to come up with this idea is a testament to a very creative group of researchers.

August 15, 2012 at 1:43 am Leave a comment

What do Green Fluorescent Protein, Black Pepper/Soap, and Magnetic Tweezers have in common?

A few months ago several members of the Dunn lab (Diego, Jack, and Armen) traveled to the Life Academy of Health and Biosciences in Oakland, CA to introduce high school students to the field of biophysics.  We thought it would be most useful to incorporate hands-on demonstrations and use visuals as a stepping stone to understand some of the more complicated concepts.  This event was organized with the help of Jessica Oya, who has worked in our lab over the past 2 summers as part of the IISME (Industry Initiatives for Science and Math Education) program at Stanford, and who invited us to teach her students about some things that we spend our days thinking of.

We set up 3 stations in her classroom.  1.) GFP- Green fluorescent protein.  In this station, Diego explained the concepts of fluorescence and protein structure, and used a vial of GFP under a black light to show how excitation/emission works.  He asked the students to come up with ideas how fluorescent proteins can be useful in biology to track motions of molecules, and was impressed with their creativity. 2.) Magnetic tweezers. In this station, Armen used magnetic beads and a microscope to explain concepts of magnetism and single-molecule biophysics.  By using an external magnet, the students were able to move the magnetic beads and align them in the direction of the magnetic field.  3.) Black pepper + soap in a dish.  In this station, Jack explained concepts of surface tension and hydrophobic vs. hydrophilic surfaces by placing black pepper in a dish of water, and then dropping some soap into the dish.  The visual effect is quite beautiful and serves as a wonderful way of teaching students about surface tension.

We truly enjoyed this experience, and hope that other schools in the greater Bay Area also partake in these programs.  Our plan is to scale up this event for the coming school year, and teach all the classrooms at this school.

August 10, 2012 at 9:16 pm Leave a comment

Dunn Lab in San Diego for Biophysical Society Annual Meeting

Recently, a majority of the group took a brief trip to San Diego for the Biophysical Society (BPS) annual meeting.  The conference was a great way to learn about all the current events in the field and meet the people whose papers we read and frequently discuss in literature reviews or just in colloquial fashion.  The single-molecule force spectroscopy studies were particularly interesting and complementary to our work involving force-dependent collagen proteolysis.   I personally found San Diego to be a beautiful city and considered myself fortunate to be in the presence of such great scientists.  At a certain point though, I felt like Dorothy from the Wizard of Oz while walking through the forest, “Myosins, kinesins, and dyneins! Oh My!”

The national lecture was given by Steve Block on his adventures with optical trapping.  I thought the highlight of his talk and probably the next generation biophysics research was the development of energy diagrams from optical trap data.  By generating data for energy versus extension as the reaction coordinate instead of hypothetical energy diagrams, one makes the concept of energy barriers very concrete and understandable.  This also limits the speculation when studying systems with complex energy diagrams.

March 12, 2012 at 7:26 am Leave a comment

Functional Simplicity from Physical Complexity

Biology can be pretty daunting sometimes.  So many different molecules that carry out different functions, all with very similar names and subnames (actin/actinin, alpha-catenin/beta-catenin/cadherin, fibrin/fibrinogen/fibronectin/fibroblast, Myosin-1/…Myosin-infinity).  Literature reviews can easily turn into an exercise in correct pronunciation, where we all mimic 5-year olds trying to say “hippopotamus”.  Thank goodness we don’t have to constantly talk about 1-52-6-7-cyclo-dodecyl-11-triphospho-pentahydroxide, at least….

In all seriousness though, biology is extremely exquisite.  Something I heard from Drew Endy (Stanford BioE) was that biology can be described as functional simplicity from physical complexity.  This struck me as interesting, because I’ve often heard people refer to their favorite molecule in the following way: “If we humans didn’t have this or if this didn’t work properly, we would be a big blob of goop….” Hmm, now is that so?  Or is biology more complicated than that.  Probably.  But we don’t know details, so we adopt this mickey-mouse apocalyptic scenario if our favorite molecule didn’t exist.  When I lift my arm while working out (yeah, ok, I never said I had to tell the truth on these things), it’s that simple right?  There aren’t hundreds of little myosin motors generating force for muscle contraction; there isn’t constant remodeling of the muscle tissues?  Well there are, and we as scientists know it.  But we know through experiments where we mix 2 invisible liquids together and observe bands move up or down on a gel.  And with this information, we create in our heads animations of what we believe is occurring on the molecular scale.  Now what do our animations look like?

Here are some Ted Talks (Drew Berry, David Bolinsky), where molecular animators describe biological processes using scientifically accurate (and entertaining!) animations to help researchers (and their grandmothers) see unseeable processes within our own cells.  The Drew Berry talk has the animation of DNA replication I linked in my first article and also chromosome separation in mitosis with all the motors zipping around.  The David Bolinsky’s 3-minute animation (near the end) is like watching the final battle scene in (pick your favorite epic movie).  I’ve linked the full animation titled “The Inner Life of the Cell” below.

Enjoy everyone!

February 8, 2012 at 8:11 am 1 comment

The Dunn Lab’s Newest Paper!!

I’m excited to announce that our lab’s newest paper, “Strain Tunes Proteolytic Degradation and Diffusive Transport in Fibrin Networks,” has been accepted by the ACS journal Biomacromolecules.  We’re quite pleased with this study, because we believe it highlights the biophysical mechanisms that govern fibrin degradation.  Here’s the LINK!! Look for the final version in the next journal issue.

Fibrin clots are proteinaceous gels that polymerize in the blood at sites of vascular injury.  They provide the structural scaffolding for cells to remodel and repair the tissue at wound sites, and therefore must be resistant to degradation.  However, improper or incomplete degradation of fibrin could lead to the formation of thrombi that block blood vessels, leading to myocardial infarction (heart attack) and other cardiovascular diseases.

In this study, we found that strain on fibrin clots due to platelet contraction, fluid shear, or mechanical stress causes up to a 10-fold reduction in the rate of fibrin degradation.  The most likely cause for this is the hindered diffusion of the fibrinolytic enzyme into the clot as strain is applied.  To this end, we also revealed that anisotropic diffusion of dextran molecules accompanies the application of strain, possibly due to fiber alignment.


January 6, 2012 at 8:17 am Leave a comment

(Cell) Death Most Beautiful

Now here’s quite an interesting Cell Picture Show.  The highlight of this one is “cell death.”

There are various forms of cell death.

Apoptosis refers to programmed cell death; the inability of cells to undergo apoptosis leads to numerous diseases, such as various cancers, autoimmune diseases, inflammatory diseases, and viral infections.  One common example of misprogrammed cell death is cancer, which is characterized by excessive cellular proliferation.  Necrosis on the other hand refers to the premature death of cells.  This can be caused by factors that are not programmed in the cells lifecycle and can be detrimental to the survival of an organism.  Because cells that die by necrosis do not send the same chemical signals as those that die by apoptosis, they are left unnoticed and can build up as dead tissue.

The picture (or actually movie) that is most interesting to me is the one titled “Mitochondria Let Loose.”  This is fascinating, because one can visualize (with colors) the activation of the caspase protease that aids in the apoptosis of the cell.  Using a FRET reporter is quite clever in this case, but I am wondering how they’ve arranged the donor and acceptor to report activation.  If anyone knows the details of this and wants to enlighten me, feel free to email at

I also quite like the one titled “Cytoskeleton Gives up the Ghost.”  It’s curious that the actin cytoskeleton is the first casualty in the necroptotic process.  One might naively suspect that there are some geometrical constraints in the way the cytoskeleton collapses, but considering this is not programmed by the cell, it could be a stochastic destruction of the structural components.  Feel free to email me regarding this as well.

Death Most Beautiful

By Thomas Deerinck and Mark Ellisman, NCMIR, UCSD

Programmed cell death ensures that our bodies contain just the right number of cells. This tightly regulated process removes damaged cells, shapes our organs and digits, and refines our immune systems. Here, multiphoton fluorescence imaging reveals an apoptotic HeLa cell (middle) amongst non-dying neighbors.

Image: HeLa cells expressing GFP targeted to the Golgi apparatus (yellow) are stained to reveal the distribution of microtubules (red) and cell nuclei (blue).

[from the Cell Press Website]

January 6, 2012 at 7:21 am Leave a comment

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