Lunch & Learn

Lunch & Learn student led discussion and presentations are held on Thursdays from 12-1:30 in the Howey Physics Building. 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 2013 Schedule

Date	Speaker
8/29	Tung Le (Kim Lab)
9/5	--
9/12	--
9/19	--
9/26	--
10/3	--
10/10	--
10/17	Fall Break
10/24	--
10/31	--
11/7	--
11/14	--
11/21	--
11/28	Thanksgiving Break
12/5	--

Link to editable google doc here.

Fall 2013 Abstracts

Lunch & Learn 8/29/2013

Tung Le, Kim Lab

Measuring energetics of sharp DNA bending from breakage kinetics of small DNA loops

The bending energetics of double stranded DNA (dsDNA) at short length scales remains controversial. Notably, recent single-molecule experiments on DNA looping in the absence of proteins suggest that the wormlike chain (WLC) model fails to predict the looping probability of dsDNA shorter than its persistence length. However, measurement of the looping probability of short dsDNA is subject to significant statistical error because looping events are extremely rare in physiological salt conditions, and comparison to the WLC model is ambiguous because of the unknown geometry requirement for loop stabilization. In this work, we used a novel unlooping assay to investigate energetics of small DNA loops in physiological salt conditions. Based on the measured loop breakage rate vs. loop length, we find that the free energy stored in DNA loops can be well described by the WLC model down to 60 bp. We also observe strong signs of structural transitions below 60 bp, reminiscent of kink formation.

== Spring 2013 Abstracts ==
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Lunch & Learn 4/18/2013

EFFECT OF SOIL WETNESS ON NEST ARCHITECTURE BY FIRE ANTS
Daria Monaenkova (Goldman's Lab)

Large underground nests are crucial for fire ants survival, providing protection from severe weather and predators. Although, the fire ants nests are found in all soil types in both North America and South
America, the areas with excessive soil moisture as well as the dry areas seems to be less favorable for a colony foundation. In this work we use x-ray computed tomography to study the effect of soil moisture
content on the growth and architecture of fire ants nests.  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 3 types of simulated soil (50, 210 and
595 um glass particles). The prepared moisture content W varied from 0.01 to 0.2 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, and tunnels volume, V,  were significantly affected by W. At moderate moisture content (W=0.1) H and V were at least twice greater than at the lowest moisture content (W=0.01) for all tested colonies (n=9) for all 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.  In this presentation we will also discuss the influence of moisture content and particle size on nest geometry, excavation techniques employed by fire ants, and show in-progress work on social aspects of nest construction.

Lunch & Learn 4/11/2013

DEGRADATION OF LAMP1 and LAMP2 DECREASES LYSOSOME MOBILITY THROUGH ENLARGEMENT OF LYSOSOMES AND CELLULAR CROWDING
Austin Cyphersmith
Payne Laboratory, Chemistry and Biochemistry

The lysosome associated membrane proteins (LAMP1 and LAMP2) are the major lysosomal membrane proteins. Although the majority of the protein is contained within the lumen of the lysosome, the knockout or degradation of LAMPs significantly decreases lysosome mobility. Our goal was to degrade LAMP1 and LAMP2 in BS-C-1 cells and characterize lysosome transport to determine the underlying cause of decreased mobility. LAMP1 and LAMP2 were degraded using endoglycosidase H (endo H). Endo H cleaves oligosaccharides from LAMP1 and LAMP2 resulting in their degradation by lysosomal enzymes. Fluorescently labeled lysosomes were tracked during intracellular transport using live cell imaging and single particle tracking. Endo H treatment results in two populations of lysosomes; normal, punctate lysosomes and lysosomes with an increased diameter. The punctate lysosomes undergo standard long-range, microtubule-dependent transport throughout the cell. The enlarged lysosomes show highly localized motion and little long-range transport. To determine if this change in mobility was biochemical, due to LAMP degradation, or physical, due to the greater diameter of the lysosomes, single particle tracking experiments were carried out with sucrose-swollen lysosomes. These experiments show that the increased diameter of the lysosomes, and associated cellular crowding, results in the decreased mobility of the enlarged lysosomes.

Lunch & Learn 4/04/2013

MICROENVIRONMENT MATTERS: HOW FORCE AFFECTS MACROMOLECULE ASSEMBLIES AND THEIR FUNCTION IN LIVING CELLS
Jan Scrimgeour (Curtis Lab)

The behavior of macromolecules in living cells and their extracellular matrix can be dramatically modified by their local physical and chemical environment.  The formation, or breakdown, of macromolecular assemblies in response to the microenvironment can be interrogated using fluorescence microscopy, where techniques such as fluorescence recovery after photobleaching (FRAP) allow the measurement of molecular mobilities.  In combination with lab-on-a-chip devices, which allow precise control or measurement of environmental conditions, FRAP is a powerful experimental tool for studying macromolecule behavior.  Specifically, I will discuss the internal mechanics of cellular adhesion, probing how force can alter the function of proteins inside the adhesive complexes of living cells.  Through the use of force sensitive substrates, the protein vinculin was shown to exhibit anomalous behavior in response to applied force, suggesting it may play a mechanosensitive role during cell adhesion.

Lunch & Learn 3/28/2013

A TERRADYNAMICS OF LEGGED LOCOMOTION ON GRANULAR MEDIA[1]
Tingnan Zhang (Goldman Lab)

The theories of aero- and hydrodynamics form the bases for prediction of animal movement and device design in flowing air and water. For example, they allow computation of lift, thrust, and drag on wings and fins of a diversity of shapes and kinematics in a variety of flying and swimming animals. In contrast, we know little about how limb morphology and kinematics affect legged locomotion on natural substrates like sand and gravel which also flow in response to
movement. This is largely because predictive models for such flowing ground have been unavailable. Our recently developed “terradynamics” (Li et al, in review)—predictive force laws for legged locomotion on granular media (sand)—allow us to begin to investigate the role of limb morphology in locomotor performance on granular media. Using terradynamics, we develop a multi-body dynamic simulation of a small six-legged robot (13 cm, 150 g) moving on granular media, and predict the speed of the robot for c-shaped legs of a range of curvatures (1/R < 1/r < 1/R, where 2R = 4.1 cm is maximal leg length) and a range of stride frequencies (0 < f < 5 Hz). Our simulation reveals that the robot moves faster using positive curvature legs than negative curvature legs, because the former’s leg elements can access larger stresses and penetrate less deeply but generate larger thrust given the same average lift (robot weight). Further, our model
predicts that using an optimal c-shaped leg of curvature 1/r = 0.86/R, the robot can achieve maximal speed of ~70 cm/s (~5 BL/s) at 5 Hz. Our study demonstrates the power of terradynamics in the design of bio-inspired devices and promises to aid understanding of the functional morphology of sand-dwelling organisms.

Lunch & Learn 3/07/2013

CREATING CONTROLLED STATES OF WET GRANULAR MEDIA
Robyn Kuckuk (Goldman Lab)

Wet granular media, such as soil and beach sand, is abundant in nature.Numerous animals live on and within these soils and must cope with resistive forces which vary depending on wetness and compaction. Though
many studies have investigated animal kinematics in dry media, little work has been done that quantifies the effects of water content on animal locomotion. This study focused on the development of a method for the preparation of homogenous wet granular media states that are similar to naturally wet sand. In order to be biologically relevant in studying the mechanics of animals, water was used as the wetting medium. The independent variable was wetness content of the medium.   The compaction of the medium was also controllable. This method provides a technique for researchers in the field of biomechanics and robotics to create homogenous wet granular media systems with controlled compaction for use in other experiments. Next, we characterized the compaction of the system after initial shaking as well as prolonged shaking. A robot arm was used to drag an intruder of comparative size and shape to the animal to characterize how the resistive force changes with compaction and wetness content. We have successfully
used this technique in our studies of sandfish locomotion in dry granular media. We varied parameters such as speed of movement through the media and depth of movement, which helped us to further understand the characteristics of wet granular media. Additionally, we studied the Ocellated skink (figure 1) as a model animal to test how ground water affects locomotion strategy.  Building on our previous work studying sandfish lizard locomotion, we used x-ray imaging to visualize subsurface locomotion in the wet granular media so that we could track kinematics.

Lunch & Learn 2/28/2013

MODELING VIRUSES OF VIRUSES
Bradford Taylor (Weitz Lab)

IIn 2008 it was discovered that large viruses (size and genome comparable to bacteria) can have their own viruses called virophages.  While the large virus can reproduce within a eukaryotic host, the virophage requires coinfecting the host with the virus.  Two different modes for coinfection have been postulated.  As more and more examples of virophages are being discovered the importance of understanding the interactions between host, virus, and virophage is increasing.  Here we model the two different modes of coinfection in order to address how virophages control host and virus populations and to explore what dynamics are possible.

Lunch & Learn 2/21/2013

DNA EJECTION FROM BACTERIPHAGES TO BACTERIAL CELLS: A COMPUTATIONAL STUDY
Anton Petrov (Harvey Lab)

In the current presentation, we report on simulations of double-stranded DNA (dsDNA) ejection from bacteriophage φ29 into a bacterial cell. The ejection was studied with a coarse-grained model, in which viral dsDNA was represented by beads on a torsionless string. Our simplest simulations (involving constant viscosity and no external biasing forces) produced results compatible with the push-pull model of DNA ejection, with an ejection rate significantly higher in the first part of ejection than in the latter parts. Additionally, we performed more complicated simulations, in which we included additional factors such as external forces, osmotic pressure, condensing agents, and ejection-dependent viscosity. We found that, in general, the dependency of ejection forces and ejection rates on the amount of DNA ejected becomes more complex if the ejection is modeled with a broader, more realistic set of parameters and influences (such as variation in the solvent’s viscosity and the application of an external force). However, certain combinations of factors and numerical parameters led to the opposition of some ejection-driving and ejection-inhibiting influences, ultimately causing an apparent simplification of the ejection profiles.

Lunch & Learn 2/14/2013

BIOARTIFICIAL MATRICES TO MODULATE EPITHELIAL MORPHOGENESIS
Nduka Enemchukwu (Garcia Lab, Mech. Eng.)

We have developed synthetic polymer-based hydrogels with well-defined mechanical and cell-signaling properties to study the impact of the physical and chemical microenvironment on epithelial morphogenesis. In three-dimensional (3D) cell cultures of kidney epithelial cells, we found that hydrogel stiffness and cell adhesion peptide concentration control cell proliferation and cluster formation. Furthermore, we discovered a hydrogel stiffness that promotes assembly of spherical, hollow cyst structures that display physiological apical-basal polarity and laminin basement membrane assembly. Together, these findings establish a synthetic bioactive hydrogel platform for investigating epithelial morphogenesis.

Lunch & Learn 2/7/2013

WHAT IS HOLDING MY MAGNETIC MORTAR TOGETHER?
Carlos Orellana (Guest)

Magnetorheological (MR) fluids are colloidal suspensions of magnetizable particles that show an increment the yield stress and in the apparent viscosity in the presence of a magnetic field. It has been shown previously that MR fluids can be used for field-controlled static adhesion to non-magnetic surfaces [Phys. Fluids 23, 073104(2011)]. Here we demonstrate the important role the surface tension and viscosity play in this adhesion effect and that the adhesive property is not related to the shear resistance of the field-dependent yield stress suspension.

Lunch & Learn 1/31/2013

 
REAL-TIME OBSERVATIONS OF INTEGRIN CONFORMATIONAL CHANGES ON LIVING CELLS
Wei (Jack) Chen (Zhu Lab)

As adhesion molecules, integrins connect a cell to its environment and transduce signals across the membrane. Their different functional states correspond to distinct conformations. Using a biomembrane force probe, we observed real-time reversible switches between bent and extended conformations of a single integrin, aLb2, on the surface of a living cell by measuring its nanometer-scale headpiece displacements, bending and unbending frequencies, and molecular stiffness changes. We determined the stabilities of these conformations, their dynamic equilibrium, speeds and rates of conformational changes, and the impact of divalent cations and tensile forces. We quantified how initial and subsequent conformations of aLb2 regulate the force-dependent kinetics of dissociation from intercellular adhesion molecule-1 (ICAM-1). Our findings provide new insights into how integrins function as nano-machines to precisely control cell adhesion and signaling.

Lunch & Learn 1/24/2013

ANT TOWER
Nathan Mlot (Hu Lab)

Fire ants are capable of linking together to form bivouacs that serve as temporary shelter when alternatives cannot be found.  While the presence of army ant bivouacs has long been known, little to no studies have been carried out on the fire ant bivouac.  Much remains to be learned about the factors that limit the shape and speed of construction.  In this combined experimental and theoretical study, we use time-lapse video to investigate the construction of fire ant bivouacs that are built against a supporting Teflon rod.  We hypothesize that fire ants construct towers to uniformly distribute stress throughout the tower.  We test this hypothesis by designing an experiment to control tower building, gather data on tower shape and construction rate, and compare our findings to our uniform stress tower model.  We find that ants build towers into a shape that uniformly distributes stress with each ant supporting on average the weight of 3 neighbors.  We also test the effects of increasing gravity on the ant strength.  Finally we compare our model to self-assembled human towers to find the strength humans support within the towers.  Our future work involves developing an agent-based simulation for bivouac disassembly.

Lunch & Learn 1/17/2013

 
NEUROMECHANICS OF SAND-SWIMMING
Sarah Sharpe (Goldman Lab)

Animals like the sandfish lizard (Scincus scincus) that live in desert sand locomote on and within a granular medium whose resistance to intrusion is dominated by frictional forces. Recent kinematic studies reveal that the sandfish utilizes a wave of body undulation during swimming. Models predict that a particular combination of wave amplitude and wavelength yield maximum speed for a given frequency, and experiments have suggested that the sandfish targets this kinematic waveform. To investigate the neuromechanical strategy of the sandfish during sand-swimming, we used high speed x-ray and visible light imaging with synchronized electromyogram (EMG) recordings of epaxial muscle activity. During subsurface sand-swimming, EMG revealed an anterior-to-posterior traveling wave of muscle activation that travels faster than the wave of curvature. Muscle activation intensity increased as the animal swam deeper into the material but was insensitive to undulation frequency. These findings were in accord with empirical force measurements, which showed that resistance force increased with depth but was independent of speed. The change in EMG intensity with depth indicates that the sandfish targets a kinematic waveform (a template) which models predict maximizes swimming speed and minimizes mechanical cost of transport as it descends into granular media. In addition, we use a simple model of undulatory sand-swimming to explain the timing differences between muscle activation and curvature along the body. The differences in the EMG pattern as compared to undulatory swimmers in fluids can be attributed to the friction-dominated intrusion forces of granular media.

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)	-

Fall 2012 Abstracts

Lunch & Learn 12/06/2012

 
PHAGE-BACTERIA INFECTION NETWORKS: FROM NESTEDNESS TO MODULARITY
César Flores (Weitz lab)

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.

 
Lunch & Learn 11/29/2012


INVESTIGATION OF PHAGOCYTOSIS WITH PHYSICAL TOOLS
Daniel Kovari (Curtis Lab)

Phagocytosis has traditionally been investigated in terms of the relevant biochemical signaling pathways.  However, a growing number of studies have investigated how the physical attributes of cells affect phagocytosis.  In this talk I provide an overview of phagocytosis, highlighting how physical reasoning has been used to explain some of the hallmark behaviors of phagocytes.  I go on to describe some of the novel, physic-inspired, tools we (the Curtis group) have been developing to investigate phagocytosis.  These tools include: micro-pipette manipulators, traction force-microscopy, and the development of a photo-switchable fluorescent actin protein for use in molecular dynamics studies.   The work I present is ongoing and contributes to our long term effort of developing a physics based model of phagocytosis.

 
Lunch & Learn 11/15/2012

THE MECHANICS OF SNAKE LOCOMOTION
Hamid Marvi (Hu Lab)

Snakes are one of the worlds most versatile locomotors, at ease slithering through rubble or ratcheting up vertical tree trunks. In our experimental study, we measured the frictional properties of several species of snakes as well as the kinematics of their locomotion. We conducted experiments to show that snakes’ scales can dig into the underlying surface to prevent sliding. We used this novel paradigm, the active control of scales to modify frictional properties, to build Scalybot 1 and 2, two snake-like robots with individually controlled sets of belly scales. In our supporting theoretical study, we developed a dynamic model of snakes’ locomotion to predict its speed and the forces it applies to its environment. We focus on common modes of a snake’s motion such as concertina, rectilinear, and sidewinding.

 
Lunch & Learn 11/08/2012

TRANSCRIPTIONAL BURST GENERATION VIA CLUSTERING
James Waters (Kim Lab)

Certain gene transcription events occur in interesting temporal patterns, inadequately described by first-order kinetics, while still being governed by inherently stochastic processes. For instance, the production of messenger RNA in yeast cells is characterized by large bursts as opposed to individual uncorrelated events. We are investigating the co-localization or clustering of active sites as a mechanism to control this effect and we attempt to reproduce these bursts through numerical simulation of transcription factors diffusing in a model yeast nucleus. We present a detailed introduction to the development of our computational model, as well as preliminary results describing the effect of clustering sites on transcriptional bursting.

 
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.