Lunch & Learn

Lunch & Learn student led discussion and presentations are held on Thursdays from 12-1:30 in Howey. These sessions are an informal gathering of PoLS students and faculty in which one student presentation will be given followed by a discussion. If you would like to sign up to give a talk this semester please fill in your name in the spreadsheet below.

Fall 2012 Schedule

Date	Speaker	PPT
10/11	Tung Le (Kim Lab)	-
10/18	Nick Gravish (Goldman lab)	-
10/25	Louis McLane (Curtis Lab)	-
11/1	Gabriel Mitchel (Weitz Lab)	-
11/8	James Waters (Kim Lab)	-
11/15	Hamid Marvi (Hu Lab)	-
11/29	Dan Kovari (Curtis Lab)	-
12/6	César Flores (Weitz Lab)	-

Link to editable google doc here.

Fall 2012 Abstracts

 
Lunch & Learn 11/01/2012

THE BIOPHYSICS OF ENZYMATIC LYSIS: DETERMINING A CRITICAL HOLE SIZE
Gabriel Mitchell (Weitz Lab)

Gram-positive bacteria transport molecules necessary for their survival through holes in their cell wall. The holes in cell walls need to be large enough to let critical nutrients pass through. However, the cell wall must also function to prevent the bacteria's membrane from protruding through a large hole into the environment and lysing the cell. As such, we hypothesize that there exists a range of cell wall hole sizes that allow for molecule transport but prevent membrane protrusion. Here we (Gabriel Mitchell, Kurt Kurt Wiesenfeld, Joshua Wetiz) develop and analyze a biophysical theory of the response of a Gram-positive cell's membrane to the formation of a hole in the cell wall. We determine a critical hole size beyond which lysis occurs. Our prediction is corroborated by experiments (conducted by our collaborator Daniel Nelson) in that provide lower bounds on cell wall hole sizes that result in lysis. Together, the theory and experiments provide a means to quantify the mechanisms of death of Gram-positive cells via enzymatically mediated lysis and provides insight into the range of cell wall hole sizes compatible with bacterial homeostasis.

 
Lunch & Learn 10/25/2012

OPTICAL FORCE PROBE STUDIES OF THE PERICELLULAR COAT
Louis McLane (Curtis Lab)

A voluminous polymer coat adorns the surface of many eukaryotic cells. Although the pericellular matrix (PCM) often extends several microns from the cell surface, its macromolecular structure remains elusive. This massive cellular organelle negotiates the cell’s interaction with surrounding tissue, influencing important processes including cell adhesion, mitosis, locomotion, molecular sequestration, and mechanotransduction.  Investigations of the PCM’s architecture and function have been hampered by the difficulty of visualizing this invisible hydrated structure without disrupting its integrity. In this work, we establish several assays to non-invasively measure the ultrastructure of the PCM. Optical force probe assays show that the PCM of chondrocytes (RCJ-P) is not crosslinked and that it easily reconfigures around microparticles. We report distinct changes in forces measured from PCMs treated with exogenous aggrecan, illustrating the assay’s potential to probe proteoglycan distribution. Measurements detect an exponentially-increasing osmotic force in the PCM arising from an inherent concentration gradient. With this result, we estimate the variation of the PCM’s mesh size (correlation length) to range from approximately 100 nm at the surface to 500 nm at its periphery. Quantitative particle exclusion assays confirm this prediction, and show that the PCM acts like a sieve. These assays provide a much needed tool to study PCM ultrastructure and its poorly defined but important role in fundamental cellular processes.

 
10/18/2012

STABILIZING FALLS IN CONFINED ENVIRONMENTS
Nick Gravish (Goldman lab)

Subterranean animals must rapidly navigate unpredictable and perilous underground environments. Nests of the fire ant \em{Solenopsis invicta} (average body length 0.35  \pm 0.05 cm) consist of a subterranean network of large chambers and tunnels which can reach 2 meters into the earth and house up to 250,000 workers. Laboratory investigations of fire ants reveal that digging workers typically climb up and down tunnels slightly wider than the largest ant hundreds of times per hour. However the principles of locomotion within confined environments such as tubes have been largely unexplored. We hypothesize that the ability to engineer underground habitats provides opportunities to facilitate movement. We conducted laboratory experiments to monitor upward and downward tube climbing of isolated fire ant workers. Fire ants were challenged to climb in 9.4 cm long glass tunnels (diameter D = 0.1 – 0.9 cm) that separated a nest from an open arena with food and water. During ascending and descending climbs we induced falls by a rapid, short, translation of the tunnels downward. We monitored induced falls over 24 hours in groups from five separate colonies. The tunnel diameter has a significant affect on the ability of ants to rapidly recover from perturbations. Falls in smaller diameter tunnels were arrested through the use of rapid jamming of limbs, body and antennae against the tunnel walls, arresting in as low 30 ms. Falls in larger diameter tunnels were not arrested. We find that the transition to stable fall arrest occurs in tunnels equal to 1.4 BL. This tunnel size is  comparable to the natural tunnel diameter found near nest entrances. Our data indicates that fire ants moving through natural tunnels can employ antennae, limbs, and body to rapidly stabilize falls.

 
10/11/2012

MEASURING LOOPING KINETICS OF SHORT DOUBLE-STRANDED DNA
Tung Le (Kim Lab)

Bending of double-stranded DNA (dsDNA) is associated with fundamental biological processes such as genome packaging and gene regulation, and
therefore studying sequence-dependent dsDNA bending is a key to understanding biological impact of DNA sequence beyond the genetic code. Average mechanical behavior of long dsDNA is well described by the wormlike chain model, but the behavior of dsDNA at length scales
around or below the persistence length remains controversial. Here we used single-molecule FRET (Förster Resonance Energy Transfer) to measure spontaneous looping kinetics of 100~200 bp dsDNA in the absence of proteins. We showed that in this length regime, the apparent looping rate increased as dsDNA became more curved and longer, suggesting that the energy component dominates the free energy of looping. We also calculated the predicted dependence of looping rate as a function of deflection angle and length based on a dinucleotide wormlike chain model, and showed that the observed length and curvature dependence is much weaker than predicted. Our results suggest that dynamics of dsDNA deviates from the wormlike chain behavior below 200 bp.