A bacterial ratchet motor

Self-propelling bacteria are a dream of nano-technology. These unicellular organisms are not just capable of living and reproducing, but they can swim very efficiently, sense the environment and look for food, all packaged in a body measuring a few microns. Before such perfect machines could be artificially assembled, researchers are beginning to explore new ways to harness bacteria as propelling units for micro-devices. Proposed strategies require the careful task of aligning and binding bacterial cells on synthetic surfaces in order to have them work cooperatively. Here we show that asymmetric micro-gears can spontaneously rotate when immersed in an active bacterial bath. The propulsion mechanism is provided by the self assembly of motile Escherichia coli cells along the saw-toothed boundaries of a nano-fabricated rotor. Our results highlight the technological implications of active matter's ability to overcome the restrictions imposed by the second law of thermodynamics on equilibrium passive fluids.Comment: 4 pages, 3 figure

Oscillatory surface rheotaxis of swimming E. coli bacteria

Bacterial contamination of biological conducts, catheters or water resources is a major threat to public health and can be amplified by the ability of bacteria to swim upstream. The mechanisms of this rheotaxis, the reorientation with respect to flow gradients, often in complex and confined environments, are still poorly understood. Here, we follow individual E. coli bacteria swimming at surfaces under shear flow with two complementary experimental assays, based on 3D Lagrangian tracking and fluorescent flagellar labelling and we develop a theoretical model for their rheotactic motion. Three transitions are identified with increasing shear rate: Above a first critical shear rate, bacteria shift to swimming upstream. After a second threshold, we report the discovery of an oscillatory rheotaxis. Beyond a third transition, we further observe coexistence of rheotaxis along the positive and negative vorticity directions. A full theoretical analysis explains these regimes and predicts the corresponding critical shear rates. The predicted transitions as well as the oscillation dynamics are in good agreement with experimental observations. Our results shed new light on bacterial transport and reveal new strategies for contamination prevention.Comment: 12 pages, 5 figure

Possible origins of macroscopic left-right asymmetry in organisms

I consider the microscopic mechanisms by which a particular left-right (L/R) asymmetry is generated at the organism level from the microscopic handedness of cytoskeletal molecules. In light of a fundamental symmetry principle, the typical pattern-formation mechanisms of diffusion plus regulation cannot implement the "right-hand rule"; at the microscopic level, the cell's cytoskeleton of chiral filaments seems always to be involved, usually in collective states driven by polymerization forces or molecular motors. It seems particularly easy for handedness to emerge in a shear or rotation in the background of an effectively two-dimensional system, such as the cell membrane or a layer of cells, as this requires no pre-existing axis apart from the layer normal. I detail a scenario involving actin/myosin layers in snails and in C. elegans, and also one about the microtubule layer in plant cells. I also survey the other examples that I am aware of, such as the emergence of handedness such as the emergence of handedness in neurons, in eukaryote cell motility, and in non-flagellated bacteria.Comment: 42 pages, 6 figures, resubmitted to J. Stat. Phys. special issue. Major rewrite, rearranged sections/subsections, new Fig 3 + 6, new physics in Sec 2.4 and 3.4.1, added Sec 5 and subsections of Sec

Rhetoric and popular power in Cicero's early speeches

Thesis (Ph.D.)--Boston UniversityThis dissertation examines how Cicero characterizes the populus Romanus, its power, and its place in the Republic in speeches between 70 and 63 B.C. Cicero's rhetoric was inevitably a function ofhis persuasive aims and contemporary political ideology. Through close reading of relevant speeches and consideration of the circumstances surrounding their delivery, the present work aims to shed light on what Cicero and his Roman audience believed about the nature of the People's power and to show how an orator could manipulate those beliefs to achieve his rhetorical ends. For the period in question, Cicero consistently identifies the populus as the ultimate source of power and its interest as the end for which the res publica exists. The first chapter examines Cicero's first contional speech, pro Lege Manilia, in which the orator emphasizes the People's moral and political authority in an effort to persuade them to intervene in foreign affairs, a traditional purview of the Senate. The second chapter considers the first actio of the Verrines, specifically how Cicero puts pressure on the senatorial jury by appealing to the corona as "the People," thereby reminding the jurors that their conduct and, ultimately, their verdict are subject to public scrutiny. The third chapter treats the second actio of the Verrines and the fragmentary pro Cornelio, in which Cicero defends the legitimacy of collective violence in defense of the People's Iibertas. The fourth chapter looks at appeals to consensus in four consular speeches - the second de Lege Agraria, the pro Rabirio Perduellionis Reo, and the first and fourth Catilinarians. In each speech, Cicero points to reactions from various crowds as evidence of unanimous support for otherwise "unpopular" positions, including the abrogation of civil liberties under the senatus consultum ultimum. Though he never insisted that the senatus abdicate its leadership of the res publica, Cicero continued to appeal to the populus Romanus as a remedy for the nobility's failures even after his election as consul. The prevalence of this theme in his pre-consular and consular rhetoric suggests that Cicero saw it as a solution to the divide between optimates and populares

Integration of Water Resource Models with Fayetteville Shale Decision Support and Information System

Significant issues can arise with the timing, location, and volume of surface water withdrawals associated with hydraulic fracturing of gas shale reservoirs as impacted watersheds may be sensitive, especially in drought years, during low flow periods, or during periods of the year when activities such as irrigation place additional demands on the surface supply of water. Significant energy production and associated water withdrawals may have a cumulative impact to watersheds over the short-term. Hence, hydraulic fracturing based on water withdrawal could potentially create shifts in the timing and magnitude of low or high flow events or change the magnitude of river flow at daily, monthly, seasonal, or yearly time scales. These changes in flow regimes can result in dramatically altered river systems. Currently little is known about the impact of fracturing on stream flow behavior. Within this context the objective of this study is to assess the impact of the hydraulic fracturing on the water balance of the Fayetteville Shale play area and examine the potential impacts of hydraulic fracturing on river flow regime at subbasin scale. This project addressed that need with four unique but integrated research and development efforts: 1) Evaluate the predictive reliability of the Soil and Water Assessment Tool (SWAT) model based at a variety of scales (Task/Section 3.5). The Soil and Water Assessment Tool (SWAT) model was used to simulate the across-scale water balance and the respective impact of hydraulic fracturing. A second hypothetical scenario was designed to assess the current and future impacts of water withdrawals for hydraulic fracturing on the flow regime and on the environmental flow components (EFCs) of the river. The shifting of these components, which present critical elements to water supply and water quality, could influence the ecological dynamics of river systems. For this purpose, we combined the use of SWAT model and Richter et al.’s (1996) methodology to assess the shifting and alteration of the flow regime within the river and streams of the study area. 2) Evaluate the effect of measurable land use changes related to gas development (well-pad placement, access road completion, etc.) on surface water flow in the region (Task/Section 3.7). Results showed that since the upsurge in shale-gas related activities in the Fayetteville Shale Play (between 2006 and 2010), shale-gas related infrastructure in the region have increase by 78%. This change in land-cover in comparison with other land-cover classes such as forest, urban, pasture, agricultural and water indicates the highest rate of change in any land-cover category for the study period. A Soil and Water Assessment Tool (SWAT) flow model of the Little Red River watershed simulated from 2000 to 2009 showed a 10% increase in storm water runoff. A forecast scenario based on the assumption that 2010 land-cover does not see any significant change over the forecast period (2010 to 2020) also showed a 10% increase in storm water runoff. Further analyses showed that this change in the stream-flow regime for the forecast period is attributable to the increase in land-cover as introduced by the shale-gas infrastructure. 3) Upgrade the Fayetteville Shale Information System to include information on watershed status. (Tasks/Sections 2.1 and 2.2). This development occurred early in the project period, and technological improvements in web-map API’s have made it possible to further improve the map. The current sites (http://lingo.cast.uark.edu) is available but is currently being upgraded to a more modern interface and robust mapping engine using funds outside this project. 4) Incorporate the methodologies developed in Tasks/Sections 3.5 and 3.7 into a Spatial Decision Support System for use by regulatory agencies and producers in the play. The resulting system is available at http://fayshale.cast.uark.edu and is under review the Arkansas Natural Resources Commission

Extrinsic noise passing through a Michaelis-Menten reaction: A universal response of a genetic switch

The study of biochemical pathways usually focuses on a small section of a protein interactions network. Two distinct sources contribute to the noise in such a system: intrinsic noise, inherent in the studied reactions, and extrinsic noise generated in other parts of the network or in the environment. We study the effect of extrinsic noise entering the system through a nonlinear uptake reaction which acts as a nonlinear filter. Varying input noise intensity varies the mean of the noise after the passage through the filter, which changes the stability properties of the system. The steady-state displacement due to small noise is independent on the kinetics of the system but it only depends on the nonlinearity of the input function. For monotonically increasing and concave input functions such as the Michaelis-Menten uptake rate, we give a simple argument based on the small-noise expansion, which enables qualitative predictions of the steady-state displacement only by inspection of experimental data: when weak and rapid noise enters the system through a Michaelis-Menten reaction, then the graph of the system's steady states vs. the mean of the input signal always shifts to the right as noise intensity increases. We test the predictions on two models of lac operon, where TMG/lactose uptake is driven by a Michaelis-Menten enzymatic process. We show that as a consequence of the steady state displacement due to fluctuations in extracellular TMG/lactose concentration the lac switch responds in an asymmetric manner: as noise intensity increases, switching off lactose metabolism becomes easier and switching it on becomes more difficult.Comment: 25 pages, 9 figures, changed content, added figures, accepted for publication in Journal of Theoretical Biolog

Ascorbic acid and chronic alcohol consumption in the guinea pig

Protection against the toxic effects of chronic alcohol consumption was observed in male guinea pigs maintained on a high-ascorbic-acid diet (vitamin C-deficient chow plus 2.0 mg ascorbic acid/ml drinking water) as compared to animals on a low-ascorbic-acid diet (vitamin C-deficient chow and from 0.025 to 0.050 mg ascorbic acid/ml drinking water). Alcohol was orally administered to the guinea pigs at a dose of 2.5 g/kg for up to 14 weeks. Levels of serum aspartate aminotransferase and serum alanine aminotransferase were significantly elevated in animals on the low-ascorbic-acid diet that received alcohol, 120 and 250%, respectively. In contrast, in animals on the high-ascorbic-acid diet that received alcohol, levels of alanine aminotransferase were not significantly elevated and levels of aspartate aminotransferase were elevated 50%. In addition, some of the animals on the low-ascorbic-acid diet that received alcohol for 12 to 14 weeks developed hepatic steatosis and necrosis, whereas none of the animals on the high-ascorbic-acid diet that received alcohol for the same length of time manifested these changes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/26135/1/0000211.pd

Effect of body deformability on microswimming

In this work we consider the following question: given a mechanical microswimming mechanism, does increased deformability of the swimmer body hinder or promote the motility of the swimmer? To answer this we study a microswimmer model composed of deformable beads connected with springs. We determine the velocity of the swimmer analytically, starting from the forces driving the motion and assuming that the oscillations in the effective radii of the beads are known and are much smaller than the radii themselves. We find that to the lowest order, only the driving frequency mode of the surface oscillations contributes to the swimming velocity, and that this velocity may both rise and fall with the deformability of the beads depending on the spring constant. To test these results, we run immersed boundary lattice Boltzmann simulations of the swimmer, and show that they reproduce both the velocity-promoting and velocity-hindering effects of bead deformability correctly in the predicted parameter ranges. Our results mean that for a general swimmer, its elasticity determines whether passive deformations of the swimmer body, induced by the fluid flow, aid or oppose the motion