Spring 2014 Schedule

Date Speaker
1/17 NA
1/24 Zhenhai Li (Zhu lab)
1/31 Tung Le (Kim lab)
2/7 Ben McInroe (Goldman lab)
2/14 Henry Astley (Goldman & Hu Lab)
2/21 Patrick Chang (Curtis lab)
2/28 James Waters (Kim lab)
3/7 APS meeting, NA
3/14 Sridhar Ravi (Stacey Combes’s Lab)
3/21 Spring Break, NA
3/28 Jiyoun Jeong (Kim lab)
4/4 Andrea Welsh (Fenton lab)
4/11 Daria Monaenkova (Goldman lab)
4/18 Bo Broadwater (Kim lab)

Spring 2014 Abstracts


Bo Broadwater Kim’s Lab

Creating long, bespoke DNA with tandem repeats

Regulation of gene expression is an essential process for all forms of ife. The most common mode of gene regulation occurs at the level of transcription with the initiation of messenger RNA. Transcription factors (TFs) can specifically bind to the operator sequence thereby inhibiting or activating RNA polymerase. Despite a preference for binding to the operator sequence, experiments have shown the surprising result that TFs do not saturate a tandem array of binding sites. This suggest that there is a negative allosteric interaction between TFs through DNA. In this week’s PoLS meeting, I will talk about our plans to investigate the suspected contribution of the 3D configuration of DNA to the anti-cooperative allostery in TetR binding. I will also present a novel method for the creation of bespoke DNA with tandem repeats using rolling circle replication. Finally, I will present preliminary data evidencing early success in attempting this new method.


Daria Monaenkova

Goldman’s Lab


Many social insects construct underground nests composed of networks of tunnels and chambers. Such cooperative construction is a challenge: individuals must effectively manipulate soil in confined, crowded, dark conditions without interfering with the flow and functioning of the collective. To begin to discover principles by which colonies balance these competing demands, we studied excavation strategies employed by fire ants during nest construction in substrates composed of particles of different sizes and moisture content. Ants constructed tunnels through the repetitive excavation and transport of cohesive soil pellets. Individual ants used complex, coordinated motion of limbs, mandibles and antennae to create pellets. Mean pellet size was comparable to head width, differed slightly depending on soil moisture and particle size, and was significantly smaller than the maximum pellet size an ant could form. We hypothesize that these intermediate-sized pellets are actively shaped by ants and passively shaped by the tunnel to optimally balance individual carrying capacity against clogging, pellet disruption and locomotor hindrance, which could diminish the transport efficacy of the collective.


Andrea Welsh

Flavio Fenton’s Lab


Synchronization and de-synchronization are important phenomena that occur in many biological systems, including the heart and brain. Therefore, understanding how to better control and induce synchronization or de-synchronization may be vital in the area of cardiac and brain dynamics. For this project, we seek to study spatially extended synchronization through a mechanical-induced coupling of Mexican jumping beans. The frequency of their jumps, set by temperature gradients, display a bursting behavior with periods of jumping and periods of rest. We experimentally characterize their ability to synchronize after inducing nearest neighbor coupling through the attachment of string. We compare the resulting jumping behavior to simulations of oscillators undergoing a similar bursting pattern whose time evolution is governed by an adaptation of the Kuramoto model. We also use Arduino electronics for visual representations of these simulations for outreach and education.



Jiyoun Jeong (Kim lab)

Thermal fluctuations within double-stranded DNA (dsDNA) can lead to transient, local opening of base pairs known as bubbles. Bubble formation (or “melting”) of dsDNA plays an important role in gene regulation; for example, RNA polymerases require single-stranded DNA in the genome to initiate transcription. Despite numerous theoretical and computational studies on thermodynamics and kinetics of bubble formation, experimental demonstration of bubble formation well below the melting temperature remains elusive. Nevertheless, bubble formation has been invoked as a mechanism to enhance DNA flexibility. In this week’s PoLS meeting, I will talk about how we experimentally study the effect of melting on dsDNA flexibility. We calculate the probability of bubble formation along a given DNA sequence using statistical mechanical models and design short DNA molecules that are highly likely to form a bubble near their center. Bubble formation in such DNA would cause a dramatic increase in the looping probability, which we measure using single-molecule fluorescent resonance energy transfer (FRET). We are investigating how the looping rate increases as a function of temperature to test the prediction of the meltable worm-like chain model.



Sridhar Ravi (Stacey Combes Lab)

Insects and birds reside in the outdoor environment where the wind can be very unsteady and complex. Due to various factors, including terrain, meteorological conditions, etc. the wind profile within the Atmospheric Boundary Layer can be very turbulent, i.e. wind speed and direction changes rapidly, rendering very unfavorable conditions for flight. Insects and birds seem to be capable of flying even in such adverse conditions by utilizing various flight control strategies. In this talk, I will be presenting on some of these strategies, in particular, I will be presenting on the flight of bumblebees in von Karman streets, hummingbirds flying in discrete vortices and fully mixed turbulence.



James Waters (Kim Lab)

The looping of short segments of DNA plays an important role in gene regulation. The stability of the loop will be affected by the restoring force arising from bending elasticity of DNA. In thermal equilibrium, this force fluctuates in time, but the time-dependent force is only accessible from a dynamics simulation, which is computationally expensive. An alternative approach to obtain instantaneous forces is to generate an ensemble of looped chains and measure the force of constraint for each conformation using Lagrangian dynamics. In this talk, I will introduce a microscopic approach to explore the conformational phase space of an end-constrained polymer and calculate the force distribution about the mean that would be lacking from a purely thermodynamic approach. By applying this method to polymers attached to a surface at one end, we design a simple experiment that can measure the persistence length of a semiflexible chain.



Patrick Chang (Curtis Lab)

The pericellular matrix (PCM) is a polymer coat grafted on the membrane surface of many eukaryotic cells. The PCM is known to associate with different physiological processes of the cells, such as adhesion, migration and proliferation. After investigating the structure of the PCM through different biophysical assays we developed, it is found that the proteoglycan, protein with sugar chains, in the matrix plays an important role in determining the structure, more so then the polymer backbone the proteoglycan attached to. When the PCM is acting as a chemical reservoir, it is the proteoglycan that sequester the chemical and later release at specific condition to change the cells’ state. Before particles, such as drug, from the outside enter the cell, they have to go through the PCM, and it is the distribution of the proteoglycan that determines the opening of the matrix that let the particles through. In the process of cell migration, it is the proteoglycan’s conformation in the PCM that affects the adhesion and detachment of the cell. Although the key player has been identified, little is known on the mechanism of proteoglycan during different biophysical processes. In our research, we aim to start uncovering the role of proteoglycan in pericellular matrix and its interaction with the cells’ environment.



Henry Astley, Goldman and Hu Labs

Sidewinding is an unusual form of snake locomotion used to move rapidly on yielding substrates such as desert sands. Posteriorly propagating waves alternate between static contact with the substrate and elevated motion, resulting in a “stepping” motion of body segments. Unlike lateral undulation, the direction of travel is not collinear with the axis of the body wave, and posterior body segments do not follow the path of anterior segments. Field observations indicate that sidewinding snakes are highly maneuverable, but the mechanisms by which these snakes change direction during this complex movement are unknown. Motion capture data from four Colorado Desert sidewinder rattlesnakes (Crotalus cerastes laterorepens) shows a variety of turn magnitudes and behaviors. Shallow turns are achieved via “differential sidewinding”, in which the motion is altered such that the head moves further than the tail. Additionally, sidewinders are capable of “reversals” in which the snakes halts forward progress and begins locomotion in the opposite direction without rotation of the body. Because the head is re-oriented with respect to the body during these reversals, the snake is able to reverse direction without rotation yet continue moving in the new direction without impediment to perception or mechanics, a rare level of maneuverability in animals. We are able to reproduce these turning mechanics on a sidewinding robot snake, and have begun investigation into sidewinding in other snake species.



Ben McInroe, Goldman Lab

Throughout history, many organisms have used flipper-like limbs for both aquatic and terrestrial locomotion. Modern examples include mudskippers and sea turtles; extinct examples include walkers such as the early tetrapod\textit{ Ichthyostega}. In the transition from an aquatic to a terrestrial environment, early walkers had to adapt to the challenges of locomotion over flowable media like sand and mud. Previously, we discovered that a flipper with an elbow-like joint that could passively flex and extend toward and away from the body aided crawling on dry granular media [Mazouchova et. al. 2013], a result related to the jamming of material behind and beneath the flipper. To gain insight into how an additional degree of freedom of this joint affects flipper-based locomotors, we have built a robotic model with limb-joint morphology inspired by \textit{Ichthyostega}. We add to our previous limb design a passive degree of freedom that allows for supination/pronation of the flipper about a variable insertion angle. Springs at the joints restore the flippers to equilibrium positions after interaction with the media. We study the crutching locomotion of the robot performing a symmetric gait, varying flipper-joint degrees of freedom and limb cycle frequency.



Tung Le, Kim lab

Elevated temperature or sharp bending can induce disruptions in the double helix of DNA, which are known as kinks. Recent experiments using small circular and teardrop-shaped DNA loops demonstrate that DNA can experience local disruptions solely by strong bending. However, energetics and sequence-dependence of kink formation remains unexplored. In this preliminary study, we investigated kink distribution in small circular and teardrop-shaped DNA loops using Monte Carlo simulation. We found that both a circular and teardrop loops less than 70 bp readily develop kinks by thermal excitation. Kinks are delocalized in a circular loop, but in a teardrop loop, a single kink tends to be localized near the bottom and efficiently relaxes the bending stress of the loop. Our result suggests that stability of a teardrop loop is most sensitive to the sequence located near the bottom, which can be exploited to measure sequence-dependent kinkability in the sharp bending regime.



Zhenhai Li, Zhu lab

Many biomolecular interactions are regulated by mechanical force. Bell model indicates the mechanical force applied to the interactions accelerate the bond dissociation. However recent research shows some biomolecular interactions exhibit a mechanical strengthening under mechanical force, which is termed as catch bond. Using atomic force microscopy, we observed catch bond in integrin/FNIII7-10 interaction. Furthermore the strengthening effect became stronger after cyclic mechanical force applied to integrin/FNIII7-10 interaction, indicating the force history is memorized by the molecules. This phenomenon is termed as cyclic mechanical reinforcement (CMR). Comparing to the previous two-state two pathway model which explain the mechanism for catch bond, the molecules need an additional memory state and pathway to store and present the mechanical force history information. Herein we propose a three-state three-pathway model, in which loading and unloading regulate the molecular interactions switch among three states. Cyclic mechanical force trap more bonds in the memory state, and by assuming the memory states has low off-rate, the model provide a mechanism for the CMR.