acs boston update 2: wednesday

August 22, 2007 at 8:13 pm | | conferences, science community, seminars

Today started with the T Red Line turning around back toward Cambridge* two stops from my station. Then there were delays. All because of some switching problems. Or something. Well, I took a cab (slightly more expensive than the ones in San Francisco, but not bad). In the end, I actually made it to the seminar room before the first talk.


Also, I saw some wicked awesome graffiti on my walk to the convention center. I guess someone really like 2-methylpentane! And there was more than that. I saw a methylacetylene somewhere, too! And whatever this is:


Here are some highlights from the talks on Wednesday:

  • Sunney Xie talked about “old stuff” (SM Michaelis-Menton kinetics and reaction theory using data from beta-gal—see the Nat. Chem. Biol. paper here) and new in vivo work looking at fluorescently labeled lac repressor binding to DNA.
    • For the first part, Sunney mentioned a new SM enzyme kinetics theory he developed (with Haw Yang and others) based on Marcus theory of electron transfer; they’ve submitted a paper to J. Phys. Chem. B (first author is Min).
    • The second “half” of his talk was so fast it was hard to follow. But he discussed using very fast imaging (5-ms frames and excitation pulses) to differentiate proteins (lac repressor) specifically bound to DNA and those that are nonspecific or diffusing (because only bound proteins are imagable as a bright spot, while diffusing spots blur out). They can also do kinetics studies of protein binding or unbinding to DNA: by finding how long it takes for spots to appear or disappear, respectively. This is reported in his recent Science paper.
  • Peter Sims is a grad student in Sunney’s lab at Harvard. He talked about some molecular motor experiments in live cells. Using dark-field microscopy, he imaged the scattering of gold nanoparticles (endocytosized into vescicles, then transported by kinesin or dynein) onto a quandrant photodiode. Using this fast detector and many photons scattered by the GNPs, he was able to get 1.5-nm spatial precsion with very fast temporal resolution. In order to track the cargos throughout the cell, they used a piezo translation stage to keep the signal on the QPD. The results: “kinesin” (those dots moving consistently toward membrane) took 8-nm steps; “dynein” (dots moving toward nucleus) took steps of 8, 12, 20, 24, 32 nm and other factors of 4; and dynein also showed smaller steps when load was added. I suspect they’ll write a paper soon.
  • Paul Alivisados spoke during Daniel Chiu‘s slot; I don’t know why. The must have swapped slots, but I don’t know because I missed the previous slot. Paul talked about plasmon coupling of his nanoparticle pairs and different colors of scattering from transverse vs. lateral coupling modes of the pairs (and triples and different groupings). He also talked about his nanorods in which atoms sort into dots or bands, depending on the doping. He gave a similar talk at Stanford a few weeks ago.
  • Antoine van Oijen did his postdoc with Sunney I think; now he’s at Harvard Medical School. Anyway, he talked about replisomes and other replication machinery, trying to understand how lagging-strand synthesis works while the polymerases move in the other direction. He used flow cells to pull strands of DNA (attached on one end to the surface and on the other end to a bead), and watched the workings of the proteins. He used the fact that ssDNA is much shorter than dsDNA at the same flow rate (i.e. force) to convert the extension of the chain to percentage that is single-stranded. He could see replication loops being formed and move down the chain; he also saw pauses in the leading strand while primers were being synthesized, presumably allowing the lagging strand to catch up the leading strand. He also did some work on a Xenopus cell-free system to determine the distance between origins and pre-replication complexes on single DNA strands.
  • Both Stephen Kowalczykowski and Chirlmin Joo (a TJ Ha student) spoke about SM imaging of RecA filaments on DNA.
    • Steve uses laminar-flow channels and optical tweezers to move DNA from a region with proteins and ATP (or other sets of components). He watched fluorescently labeled RecA nucleate and grow on stretched DNA chains. He talked not only about RecA, but also other DNA-associated proteins: RecBCD, Rad54, and Tid1 (see new paper here). He watched stretched DNA strands to learn about speed and direction of DNA motor proteins (using a fluorescent bead attached to the protein).
    • The Ha lab uses SM FRET fluctuations to learn information about nucleation and dynamics of RecA fibers. They also noted faster FRET dynamics of systems locked in lipid vesicles, concluding that fully formed filament nuclei bind and unbind to the DNA (because the filament can find the DNA again in the vesicle, and one-at-a-time monomer addition shouldn’t change the FRET signal in the vesicle). Chirlmin also mentioned that they use a hidden Markov model in finding transitions in FRET levels.
  • Richard Ebright discussed careful FRET measurements of RNA polymerase movements and mechanisms. Some rigorous evidence for certain mechanisms or RNAP (and strong evidence against mechanisms). He also mentioned that he used non-natural amino acids (like Peter Schultz) to add azides to proteins and specifically label with fluorophores using the Staudinger reaction (see Bertozzi’s reviews here and here).

Tonight is the PHYS poster session, so I’ll probably write a post later about the coolest papers I saw. Stay tuned!


* I’m staying with a friend in Cambridge (thanks Stephen!). It’s really convenient and free. In fact, he’s treating me like a king. Which is the appropriate treatment.


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  1. […] the polymerases and chain length (using a similar technique to what Antoine van Oijen did—I summarized his stuff before). His conclusion was that DNAP moves past the position of RNAP (either over it or pushes it along […]

    Pingback by Everyday Scientist » acs boston update 2.5: posters — August 23, 2007 #

  2. Thanks for summarizing all these talks. Peter’s setup sounds very interesting and I wonder if it works the same way a typical AFM measures tip displacement.

    I also hadn’t realized SM-Michaelis-Menten had been done before Pat Collier’s recent work.

    Comment by joel — August 24, 2007 #

  3. that’s 2-methylbutane, dumbass.

    Comment by Matt — February 2, 2010 #

  4. ha! how come no one called me on that? i debated between “isopentane” and “2-methylbutane” … then chose neither.

    Comment by sam — February 3, 2010 #

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