APS Practice 2013

We will be rehearsing talks for the 2013 APS "March Meeting" on March 14th, 2013. Following the APS format, presentation will be 10 minutes with 5 minutes of questions. The list of presenters and their abstracts can be found in the table below.

APS 2013 Practice Schedule

Time	Speaker
12:00	Patrick Chang (Curtis Lab)
12:15	Daria Monaenkova (Goldman Lab)
12:30	Gabriel Mitchell (Weitz Group)
12:45	Louis MchLane (Curtis Lab)
1:00	Cesar Flores (Weitz Group)
1:15	Daniel Kovari (Curtis Lab)

Abstracts

Patrick Chang (Curtis Lab) APS Abstract: N45.00006

Session N45: Focus Session: Cell Mechanics I
12:39 PM – 12:51 PM, Wednesday, March 20, 2013
Hilton Baltimore Room: Holiday Ballroom 4

Quantitative particle exclusion assays of the pericellular coat reveal changing mesh size

We present a quantitative assay of the pericellular coat, a tethered polymer matrix that decorates the surface of numerous cell types.  In these assays, we look at how passivated microspheres of varying diameter penetrate the cell coat. Distinct spatial distributions correspond to different particle sizes.  These measurements confirm that the cell coat (on the chondrocyte RCJ-P cell line) has a spatially varying mesh size, in agreement with our independent assays performed with optical force probe microscopy. The data indicate that particles with diameters of 500 nm or greater do not penetrate the inner layer of the matrix, while particles smaller than 500 nm reach different regions, with the smallest reaching the cell surface. In an ongoing effort, we are developing a model for the observed statistical distribution of the beads.  These experiments show that accessibility of the cell surface is strongly mediated by the presence of the cell coat, and they have important implications regarding the transport of molecules to the cell surface, protection from bacterial infection, drug delivery, as well as the way the cell interacts and adheres to the surrounding extracellular matrix.

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Daniel Kovari (Curtis Lab) APS Abstract: M45.00002

Session M45: Focus Session: Physics of the Cytoskeleton I
8:12 AM–8:24 AM, Wednesday, March 20, 2013
Hilton Baltimore Room: Holiday Ballroom 4

Measuring actin dynamics during phagocytosis using photo-switchable fluorescence

Phagocytosis has traditionally been investigated in terms of the relevant biochemical signaling pathways. However, a growing number of studies investigating the physical aspects of phagocytosis have demonstrated that several distinct forces are exerted throughout particle ingestion. We use variations on FRAP (Fluorescence Recovery After Photobleaching) in combination with photo-switchable fluorescent protein to investigate actin dynamics as a phagocyte attempts to engulf its prey. The goal of our actin studies are to determine the recruitment and polymerization rate of actin in the forming phagosome and whether an organized \textit{contractile actin ring} is present and responsible for phagosome closure, as proposed in the literature. These experiments are ongoing and contribute to our long term effort of developing a physics based model of phagocytosis.

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Louis McLane (Curtis Lab) APS Abstract: N45.00005

Session N45: Focus Session: Cell Mechanics I
12:27 PM–12:39 PM, Wednesday, March 20, 2013
Hilton Baltimore Room: Holiday Ballroom 4

Modifications of the structure of the pericellular matrix measured via optical force probe microscopy

The pericellular matrix is a large protein and polysaccharide rich polymer layer attached to the surface of many cells, and which often extends several microns out from the cell surface into the surrounding extracellular space. Here we study the intrinsic nature and modifications of the structure of the pericellular coat on rat chondrocytes with the use of optical force probe microscopy. Optical force probe studies allow us to make both dynamic force measurements as well as equilibrium force measurements throughout the coat. These force measurements are used to observe the structural change in the coat with the addition of exogenous aggrecan. Not only does addition of exogenous aggrecan dramatically swell our coat to well over twice in size, our analysis indicates that the addition of exogenous aggrecan decreases the mesh size throughout the coat. We speculate that the added aggrecan binds to available binding sites along the hyaluronan chain, both enlarging the coat's size as well as tightening up the opening within the coat. We further suggest that the available binding sites for the exogenous aggrecan are abundant in the outer edges of the coat, as both the dynamic and equilibrium forces in this region are changed. Here, both force measurements show that forces closest to the cell membrane remain relatively unchanged, while the forces in the outer region of the coat are increased. These results are consistent with those obtained with complementary measurements using quantitative particle exclusion assays.

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Nick Gravish (Goldman Lab) APS Abstract: W44.00009

Session W44: Focus Session: The Physics of Behavior
4:54 PM–5:06 PM, Thursday, March 21, 2013
Hilton Baltimore Room: Holiday Ballroom 1

Environmental engineering simplifies subterranean locomotion control

We hypothesize that ants engineer habitats which reduce locomotion control requirements. We studied tunnel construction, and locomotion, in fire ants ({\em Solenopsis invicta}, body length $L = 0.35 \pm 0.05$). In their daily life, ants forage for food above ground and return resources to the nest. This steady-state tunnel traffic enables high-throughput biomechanics studies of tunnel climbing. In a laboratory experiment we challenged fire ants to climb through 8 cm long glass tunnels (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 motion-activated rapid, short, downward translation of the tunnels. Normalized tunnel diameter ($D/L$) determined the ability of ants to rapidly recover from perturbations. Fall arrest probability was unity for small $D/L$, and zero for large $D/L$. The transition from successful to unsuccessful arrest occurred at $D/L = 1.4 \pm 0.3$. Through X-Ray computed tomography study we show that the diameter of ant-excavated tunnels is independent of soil-moisture content (studied from 1-20\%) and particle size (50-595 $\mu m$ diameter), and has a mean value of $D/L = 1.06 \pm 0.23$. Thus fire ants construct tunnels of diameter near the onset of fall instability.

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Daria Monaenkova (Goldman Lab) APS Abstract: M29.00011

Session M29: Focus Session: Wet Granular Material: Capillary Aggregation to Shaping of Landscapes
10:24 AM–10:36 AM, Wednesday, March 20, 2013
Room: 337

Effect of moisture content on nest construction activity of fire ants

Large underground nests protect ants from severe weather and predators. Field observations have revealed that the soil wetness affects the nest building activity. In this work we use x-ray computed tomography to study the growth of fire ants nests as a function of soil moisture content. Because capillary cohesion in wet soils leads to the competition between tunnel stability and the labor-intensity of the excavation, we expect to find an optimal soil wetness, which allows the most effective nest construction. We prepared digging containers (3.8 cm diameter by 14.5 cm deep aluminum tubes) with 2 types of simulated soil (50 and 210 um glass particles). The prepared moisture content W varied from 0.01 to 0.18 by mass. Hundred ants were allowed to dig in the containers for 20 hours. Although, the ants were able to construct tunnels in all moisture levels, the maximum tunnel depth, H, was significantly affected by W. At moderate moisture content (W$=$0.1) H was at least twice greater than at the lowest moisture content (W$=$0.01) for all tested colonies (n$=$9) for both particle sizes. The increase in H mirrors the dependence of the soil cohesion on W and we therefore conclude that the tunnel stability is a key factor influencing the digging strategy of fire ants.

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Gabriel Mitchell (Weitz Lab) APS Abstract: N31.00010

Session N31: Membrane and Membrane Protein Interactions
1:27 PM–1:39 PM, Wednesday, March 20, 2013
Room: 339

Critical cell wall hole size for lysis in Gram-positive bacteria

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 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 predict a critical hole size in the range 15-24nm beyond which lysis occurs. To test our theory, we measured hole sizes in \textit{Streptococcus pyogenes} cells undergoing enzymatic lysis via transmission electron microscopy. The measured hole sizes are in strong agreement with our theoretical prediction. 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.

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Cesar Flores (Weitz Lab) APS Abstract: J44.00011

Session J44: Biological Networks
4:30 PM-4:42 PM Tuesday, March 19, 2013
Room: Holiday Ballroom 1

Phage-bacteria infection networks: From nestedness to modularity

Bacteriophages (viruses that infect bacteria) are the most abundant biological life-forms on Earth. However, very little is known regarding the structure of phage-bacteria infections. In a recent study we re-evaluated 38 prior studies and demonstrated that phage-bacteria infection networks tend to be statistically nested in small scale communities (Flores et al 2011). Nestedness is consistent with a hierarchy of infection and resistance within phages and bacteria, respectively. However, we predicted that at large scales, phage-bacteria infection networks should be typified by a modular structure. We evaluate and confirm this hypothesis using the most extensive study of phage-bacteria infections (Moebus and Nattkemper 1981). In this study, cross-infections were evaluated between 215 marine phages and 286 marine bacteria. We develop a novel multi-scale network analysis and find that the Moebus and Nattkemper (1981) study, is highly modular (at the whole network scale), yet also exhibits nestedness and modularity at the within-module scale. We examine the role of geography in driving these modular patterns and find evidence that phage-bacteria interactions can exhibit strong similarity despite large distances between sites.