|01/26/17||Anthony Hazel||Gumbart Lab|
|02/02/17||Wenbin Wei||Curtis Lab|
|02/09/17||Gable Wadsworth||Kim Lab|
|02/16/17||Alexis Noel||Hu Lab|
|02/23/17||Marguerite Matherne||Hu Lab|
|03/02/17||Steven Chandler and Megan Matthews||Sponberg Lab|
|03/09/17||David Yanni||Yunker Lab|
|03/30/17||Curtis Balusek||Gumbart Lab|
|04/06/17||Joey Leung||Weitz Lab|
|04/13/17||Shane Jacobeen||Yunker Lab|
|04/20/17||Andrea Welsh||Fenton Lab|
Spring 2017 Abstracts
Examining the Folding Pathway of a Simple β-Hairpin Using Molecular Dynamics Simulations
β-Sheets are some of the most common secondary structure motifs in proteins, and are important for mediating protein-protein interactions through their association. This association can also lead to the aggregation of misfolded proteins into β-pleated-sheets in neurodegenerative disorders like Alzheimer’s disease. Fixed charge, all-atom molecular dynamics simulations have adequately reproduced the folding free energy landscape of a small β-hairpin, the GB1 domain of protein G, which is a prototype for a larger β-pleated-sheet. Polarizable force fields should, in theory, be able to more accurately reproduce experimental results as they are a more realistic model of the molecular system. The CHARMM Drude model is a relatively efficient polarizable force field that has been shown to perform as well or better than traditional non-polarizable force fields in reproducing helical content and folding mechanisms of model α-helical peptides. To assess the model’s accuracy for β-sheets, we examined the stability of the GB1 β-hairpin using the CHARMM Drude polarizable force field and two non-polarizable force fields, CHARMM36 and CHARMM22*. Two-dimensional replica exchange umbrella sampling (REUS) simulations show that the β-hairpin is unstable in the Drude system, whereas it is either stable or quasistable in CHARMM36 and CHARMM22*, respectively. The instability in Drude appears to be driven mostly by interactions between the peptide backbone and the surrounding water molecules. By tuning these interactions, we have shifted the stability back towards the β-hairpin state.
Dynamic Polymer Brush Interfaces Generated by Hyaluronan Synthase
Hyaluronan (HA) is a large polysaccharide that is naturally present in the human body. It has many applications such as in cosmetics and treatment of joint disorders and skin burn. HA synthase, an enzyme that produces HA, is a transmembrane protein embedded in cell membranes. During the synthesis, HA synthase binds one end of an HA chain where monomers are processively added for elongation. Under high surface coverage of HA synthase, the attached HA chains are stretched due to volume exclusion and form a structure called polymer brush. In Curtis Lab, we are interested in how external forces cause the release of HA from HA synthase which terminates the synthesis and defines the length of HA. A byproduct of our research is the thickness HA brush ever created. This brush is also much thicker than brushes made of another molecule. This gigantic thickness allows for new methods to study polymer brush. This thick brush also has a great potential to enhance the biomaterial and biomedical functionality of polymer brush because thickness makes the difference between a polymer brush and a thin layer of small molecules. Moreover, our HA brush can be synthesized on demand and recover from damage. In this talk, I will briefly introduce the fundamental physics of polymer brush, characterize our HA brush and discuss its potential application.
Single fluorophore in situ hybridization (FISH) in budding yeast
Quantitative determination of the copy number of RNA transcripts in single cells is crucial to understand the genotype-phenotype connection. Current single-molecule Fluorescence In Situ Hybridization (FISH) protocols commonly used for this purpose require a large number of fluorophores per target RNA for single RNA detection, thus limiting the length range of RNA that can be probed. We have developed a FISH protocol for budding yeast, which can detect RNA molecules with a singly labeled 24-nucleotide DNA probe. Our single-probe protocol features highly inclined illumination and methanol fixation. We demonstrated high signal-to-noise and specificity of our protocol when tested against both constitutive and inducible genes in budding yeast. Furthermore, we determine the hybridization efficiency of probes via two separate methods and demonstrate Fluorescence Resonance Energy Transfer (FRET) in yeast. The technique presented offers a cost effective and efficient means of quantifying short RNA transcripts at the single cell level.
The physics of cat tongues: gripping and grooming with soft tissue
A cat’s tongue is covered in an array of spines called papillae. These spines are thought to be used in grooming and rasping meat from bones of prey, although no mechanism has been given. Using high-speed video to film a cat grooming, we show that the spines on the tongue act as Velcro for deeply embedded particles. The tongue itself is highly elastic, while the spines are rigid. As the cat presses its tongue against a surface, the tongue flattens and the spines separate, allowing the sharp spines to penetrate fur mats and reach the skin. We model this grooming process using x-ray videography and a 3D printed cat tongue mimic. We also find that the cat tongue spines do not scale with feline mass, suggesting that size and shape of papillae is mechanically significant.
Marguerite E. Matherne
Mammal tails deter mosquitoes by wind generation
Insects such as mosquitoes can cause substantial blood loss, up to 0.5 L of blood loss per day in a horse. One way to combat these insects is through tail swinging. In this combined experimental and theoretical study, we elucidate how swishing tails fend off insects. We film horses, zebras, elephants, and giraffes at the Atlanta Zoo. We observe the tail swings at triple the frequency of a gravity-driven pendulum. This motion creates a breeze of 1 m/s which deters mosquitoes from landing. This is the same strategy used by the product Shoo-A-Way which has sold millions of items, and whose range of effectiveness we show here. Once a mosquito lands, it can be swatted by the tail at accelerations of 7 times gravity. We determine the torques required to generate swats of a two-link pendulum. This study may help us determine new kinds of mosquito repelling strategies for both humans and animals.
Free flight tracking in unsteady flow: probing hawkmoth maneuverability in an artificial flower wake
Birds, insects, and many other animals have developed mechanisms to maintain hovering flight to feed from flowers across varied biological length scales and environments. Although recent studies have examined flight performance in unsteady wind, few examine these flight mechanisms during a prescribed task. Understanding how flying insects feed from flowers in nature requires coupled analysis of the effects of unsteady flows in the wake of an object and flight maneuverability. We investigate the dynamics of insect maneuverability in an unsteady wake by having Manduca sexta, known to hover while feeding, track a 3D-printed robotic flower in a wind tunnel and compare to results from previous experiments in a still air flight chamber. In the unsteady tracking task, moths perform worse at natural flower oscillation frequencies (0-1 Hz) and consistently overshoot the flower at mid-range frequencies (2-5 Hz) before failure. Smoke visualization of the flower wake shows vortex shedding at approximately 2-5 Hz with a localized region of unsteady flow dominating the hovering location of the moths. Aerodynamic interactions between the moth and the flower wake may require the animal to make more small corrections to maintain a stable feeding position, thus leading to more overshoot at these frequencies than during tracking in still air. Despite the large effect on flight dynamics, smoke visualization of the hovering moth showed that the leading-edge vortex bound remains bound to the wing and thorax throughout the wingstroke, reflecting the need for better understanding of how flight dynamics and aerodynamics relate to each other. In general, flying in unsteady wind seems to decrease maneuverability, but may have little effect on the aerodynamic mechanisms necessary for hovering; the hawkmoths shift their dynamics and track effectively in a smaller frequency range, but are able to use similar lift mechanisms in both steady and unsteady environments.
Flight Control Compensation to Changing Body Mass in Feeding Hawkmoths
Motor control of animals has been shown to be quite robust to mechanical and environmental variation. In studying motor control, tracking behaviors have revealed important insights into sensory processing and motor performance due to their well-defined tasks. However, much of the work studying these behaviors has focused on manipulating the sensory side of animals’ sensorimotor feedback loops and less on examining the robustness of animals to behaviorally-relevant and quantifiable changes in their mechanics.
The hawkmoth, Manduca sexta, forages nectar from flowers while hovering and will feed enough to significantly increase its body mass. Using a robotic flower following a prescribed 2D sum-of-sines trajectory, we measured the dynamic response of continually feeding, freely-flying moths for a 60 second period leading to a mean increase in mass of 29% (5% SD). We used a control theoretic feedback model with three models of body mechanics of increasing complexity to compare the observed change in response to a predicted, uncompensated response given the measured increase in body mass. These mechanical models were also used to calculate a ‘controller’, the combined convolution of the moths’ sensory system, nervous system, and muscles, for both the low and high mass conditions.
The moths’ performance following the increase in mass did not match that of a constant controller. This suggests compensatory neural control that helps maintain the neuromechanical performance of the system. Increased wing beat frequency and a shift in the moths’ body conformation are notable compensatory mechanisms, but they may not completely account for the moths’ adjustments to increased body mass. These models and method support the idea of a high-pass sensory controller leading to an overall low-pass locomotor response as has been found in other animals. Furthermore, the method suggests how the moth may be adjusting to provide robust maneuverability in the face of an ecologically relevant change in inertia.
Ring of Death
Most bacteria live in biofilms, which are implicated in 60-80% of microbial infections in the body. The spatial structure of a biofilm confers advantages to its member-cells, such as antibiotic resistance, and is strongly affected by competition between strains and even taxa. However, a coherent picture of how competition affects the self-organized structure of these complex, far-from-equilibrium systems, is yet to fully emerge. To that end, we investigate phase separation dynamics driven by T6SS-facilitated bacterial warfare in a system composed of two strains of mutually antagonistic V. Cholerae T6SS is a widespread contact mediated killing mechanism present in [;25\%;] of all gram negative bacteria and has been shown by recent work to play a major role in the spatial assortment of biofilms. T6SS events induce lysis, causing variations in local mechanical pressure, and acting as thermalizing events.
We study the behavior of cells immobilized in biofilms at the air-solid interface, so our experimental system represents a different type active matter, wherein activity is due to cell death and reproduction, not mobility. Here, we discuss how that activity, along with underlying physical processes, shapes the architecture of a biofilm and gives rise to spatial patterning observed in the lab.
Constructing an in silico model of the Gram-negative Cell Envelope.
All living organisms regulate intracellular pressure by restricting the flow of solutes into and out of the cell, which occurs at the cell boundary, or envelope. The difference in intra- and extracellular pressure, known as the turgor pressure, can fluctuate drastically in unicellular organisms. Prokaryotes, or bacteria, have cell walls that bear the stress of turgor pressure, e.g. due to osmotic shock. It has been shown experimentally that bacteria will lyse under cell wall deletion or modification. Gram-negative bacteria are an interesting sub-population of prokaryotes because of their characteristic outer membrane surrounding the cell wall. In order to understand how the turgor pressure is translated from the cytoplasm to the cell wall in Gram-negative bacteria, an all-atom model of the Gram-negative cell envelope is constructed. Special attention is given to the proteomics of the tripartite, Gram-negative cell envelope.
Immunophage synergy as a mechanism of phage therapy in acute respiratory infections
The rise of antibiotic resistance in pathogenic bacteria has led to renewed interest in the use of phage as a treatment for bacterial infections . However, there is a lack of understanding of the mechanism(s) that make phage effective as therapeutic agents. For example, mathematical models show that combining phage and bacteria often leads to coexistence of phage and bacteria. Therefore, a potential resolution to the tension between the clinical aims of phage therapy and models of phage-bacteria interactions is the hypothesis that phage works synergistically with host immunity to eliminate pathogenic bacteria. We have developed a phage therapy model that considers the nonlinear dynamics arising from interactions between bacteria, phage and the immune system . The model builds upon earlier efforts  by incorporating a maximum capacity of the immune response and density-dependent immune evasion by bacteria. We have identified a synergistic regime in which phage and the immune response jointly contribute to the elimination of the target bacteria. To study the immune component responsible for the synergy, we adapted the model  to in vivo experiments of acute respiratory infection by Pseudomonas aeruginosa in immunomodulated mice. We find that phage adsorption rate measured in vitro grossly overestimates the phage killing rate in vivo, likely a result of spatial heterogeneity of the lungs or saturation of phage infection at high densities. We show that these effects can be modeled by phage killing rates that depend nonlinearly on phage densities. Our models predict that deficiency in innate immune activation is detrimental to the efficacy of phage therapy. In addition, phage-neutrophil alliance is predicted to be essential for therapeutic success. Both predictions are in accordance with observed phage therapy efficacies in experiments. We show that phage-immune synergy is caused by the phage reducing bacterial densities to levels manageable by host immunity, as well as host immunity preventing the outgrowth of phage-resistant bacteria. We discuss how the synergistic effect may guide use of phage therapy in clinically relevant applications.
 R. Young and J. J. Gill, Science 350, 1163 (2015).
 C. Y. J. Leung and J. S. Weitz, bioRxiv doi: 10.1101/057927 (2016).
 B. R. Levin and J. J. Bull, Nature Rev. Microbiol. 2, 166 (2004).
Optimization, entropy, and the evolution of nascent multicellularity
The evolution of multicellularity transformed life on earth—both by providing its bearers with immediate fitness advantages, and by setting the stage for profound increases in organismal complexity. However, these advances came at a price: even before the development of regulatory networks, bodies composed of multiple cells must contend with previously irrelevant forces capable of breaking intercellular bonds. Using the snowflake yeast model system, I examine the physical underpinnings of early evolution in nascent multicellular clusters. Snowflake yeast reproduce when internal stress from growth causes the cluster to fracture into independently viable propagules. Under daily selection for large size, snowflake yeast evolve improved fitness by increasing their mean size at fracture. This is achieved by increasing cellular aspect ratio, which improves packing efficiency within the cluster and thus delays fracture by decreasing the rate of internal stress accumulation. Geometric simulations confirm that the observed increase in cellular aspect ratio substantially increases the number of growth configurations – cell placements that won’t cause fracture – accessible to a cluster. Additionally, we offer a physical interpretation for information entropy in the context of evolving snowflake yeast.
Pattern Formation of Brine Shrimp Aggregation
Self-propelled systems are physically rich systems that describe many different biological systems such as microorganisms, schools of fish, flocks of birds, and even human crowds. This talk will cover the preliminary experimental work of the collective motion of Artemia franscicana otherwise known as brine shrimp. Large collections of these shrimp will aggregate in such a way that they will form spatial patterns, which depend on environmental properties that play into the driving and dissipation of the system. Also, the natural phototaxis of shrimp, especially 1st instar stage shrimp, effect pattern selection. We look a bit at the individual properties such as shrimp speed and how that changes when the shrimp is now part of a swarm.