Interactions between nucleoid associated proteins and DNA in the presence of mechanical and chemical forces

The way that DNA is organized within a cell controls its physiological behavior. DNA must be condensed in order to fit into the much smaller cell, but must also be accessible to proteins responsible for biological processes. Architectural proteins assist with this large-scale arrangement of DNA to achieve the correct balance between these two competing requirements. The structural proteins that interact with DNA in prokaryotes are known as nucleoid associated proteins (NAPs). These proteins play a vital role in shaping the DNA and assist in many cell processes, including gene expression, replication, and transcription. NAPs have been studied extensively in order to elucidate how their physical properties (such as binding kinetics or DNA manipulation) aid in regulating cell function. It has been shown in experiment and simulation that NAPs can adopt multiple binding states (i.e., the protein can be partially associated with its DNA substrate), which leads to complex binding and unbinding kinetics. For a simple binary system, where a protein can either be bound or unbound, the kinetics are relatively straightforward: there is a concentration dependent on-rate (kon) and a concentration independent off-rate (koff). When a protein-substrate complex has a non-binary set of bound states (including an intermediate "partially bound" state), other molecules in solution can impact the dissociation behavior. In fact, these competitors compete with the original protein for binding sites, which enhances the dissociation of the protein from its original substrate. This concentration-dependent dissociation is called "facilitated dissociation" (FD). We have developed a coarse-grained model of a typical NAP-DNA system that is built up from local interactions, such as the mutlivalent binding that leads to FD as well as physical deformations of DNA induced by protein binding. This methodical coarse-graining allows us to investigate the effect that these short-range interactions have on the mesoscale behavior of the system. We have investigated the cooperative and competing behavior of NAP-DNA interactions that result in concentration-, force-, and topology-dependent changes to both protein kinetics and physical DNA behavior. Our model qualitatively matches experimental observations, and provides a physical explanation for the observed behavior based on cooperative local interactions. We demonstrate how the competition for binding sites along a DNA strand is affected by the energy barriers between the three possible bound states in the system (bound, partially bound, and unbound). This is the driving force behind facilitated dissociation; thus, changing the level of binding competition changes the dissociation behavior. Our model allows us to manually manipulate the binding energy landscape that other methods are unable to achieve. We can independently change the energy barriers between the three bound states, which in turn changes a protein's preferred bound state. This leads to three different concentration-dependent FD kinetic regimes: a concentration-independent off-rate, a linear dependence on concentration, and a combination of the two. The multivalent binding also leads to multiple dissociation pathways: spontaneous and facilitated. The dissociation pathway a protein undergoes is dependent on a number of factors including force, the local geometric deformation, and protein concentration. We investigate how these factors impact the dissociation kinetics of a system that undergoes FD by expanding our model to account for the physical bends that NAPs induce in DNA upon binding in the DNA model, and also in the energy barrier landscape. At low forces, more proteins will be bound due to the more relaxed nature of the DNA strand that more easily allows local kinks caused by NAPs. As force is increased, there will be fewer bound proteins because of the more extended nature of the DNA strand, which is in a less preferential conformation. This force-enhanced unbinding and force-inhibited binding changes how a protein dissociates from DNA, either through FD at low force or spontaneously at high force. We observe two two classes of dissociation: a classical "slip bond," where a bond weakens with force, and a "catch bond," where a bond is strengthened with force. The physical deformation that NAPs cause affects not only the binding and unbinding kinetics; it also impacts the long-scale equilibrium and dynamic DNA elasticity. As more NAPs are bound to the DNA, there are more local kinks, decreasing the end-to-end distance of the single DNA strand. Because NAPs can adopt two possible binding states, DNA can undergo two different types of deformations. This leads to a non-monotonic effect of concentration on the force-extension behavior of the DNA strand. Our method allows us to study non-equilibrium elastic behaviors as well, such as DNA extending dynamically. The competition between the two characteristic time scales of the system (unbinding time and pulling time) leads to extension-rate dependent effects on both DNA elasticity and binding behavior. We are able to show that NAPs help stabilize DNA supercoils due to these same local, cooperative effects. DNA supercoiling occurs when DNA wraps around itself to relieve torsional stress. Both DNA supercoiling and NAPs are present in prokaryotic cells, but the role of NAPs in supercoiling activity is not fully understood. Our model demonstrates that NAPs are more likely to bind to supercoiled DNA, due to the protein's preference to bind to already-bent DNA, which in turn stabilizes the supercoil. This leads to a concentration-dependent change of the phase transition between extended and supercoiled DNA in the force-torque ensemble. We are able to use a combination of simulation data and theoretical predictions of the various energies of the system, such as the stretching, bending, and excluded volume energies, as a function of both force and concentration. This information can be used to develop a theory that provides a thorough understanding of how NAPs affect DNA supercoiling

Progress Report: Pasture Finishing of Beef Steers Using Contemporary Feedlot Protocols

Environmental regulations in Iowa can place animal population restrictions on a given site. This study explores the possibility of finishing cattle in a remote pasture location to handle an overflow of animals and yet remain in compliance with environmental mandates

Progress Report: Effects of Condensed Corn Distillers Solubles on Steer Performance and Carcass Composition

Condensed, corn, distillers solubles provides an effective energy supplement for finishing cattle across a number of finishing systems

Accelerated Projected Gradient Method for Linear Inverse Problems with Sparsity Constraints

Regularization of ill-posed linear inverse problems via $\ell_1$ penalization has been proposed for cases where the solution is known to be (almost) sparse. One way to obtain the minimizer of such an $\ell_1$ penalized functional is via an iterative soft-thresholding algorithm. We propose an alternative implementation to $\ell_1$-constraints, using a gradient method, with projection on $\ell_1$-balls. The corresponding algorithm uses again iterative soft-thresholding, now with a variable thresholding parameter. We also propose accelerated versions of this iterative method, using ingredients of the (linear) steepest descent method. We prove convergence in norm for one of these projected gradient methods, without and with acceleration.Comment: 24 pages, 5 figures. v2: added reference, some amendments, 27 page

Induced Crystallization of Polyelectrolyte-Surfactant Complexes at the Gas-Water Interface

Synchrotron-X-ray and surface tension studies of a strong polyelectrolyte (PE) in the semi-dilute regime (~ 0.1M monomer-charges) with varying surfactant concentrations show that minute surfactant concentrations induce the formation of a PE-surfactant complex at the gas/solution interface. X-ray reflectivity and grazing angle X-ray diffraction (GIXD) provide detailed information of the top most layer, where it is found that the surfactant forms a two-dimensional liquid-like monolayer, with a noticeable disruption of the structure of water at the interface. With the addition of salt (NaCl) columnar-crystals with distorted-hexagonal symmetry are formed.Comment: 4 pages, 5 eps figure

Effects of Condensed Corn Distillers Solubles on Steer Performance and Carcass Composition

Condensed corn distillers solubles (CCDS) have become a prevalent feed source in Iowa. In this study, we looked at the impact of CCDS in finishing steer rations and the influence CCDS had on steer performance as well as carcass composition. In the first year of the study, 112 steers were randomly sorted into four equal groups where each group contained four pens and 7 steers per pen. The second year of the study was a repeat of the first year however a fifth treatment was added in which 28 steers were placed on pasture and provided a finishing grain diet. The first of the four treatments consisted of the feedlot group (F), which was placed directly in to the feedlot and fed shelled corn, alfalfa hay, a protein, vitamin, and mineral supplement, and molasses. The second treatment was feedlot + CCDS (F+CCDS). This treatment group was placed directly into the feedlot and received shelled corn, alfalfa hay, a protein, vitamin and mineral supplement, and CCDS. The third treatment group was backgrounded on pasture for the duration of the summer (P), and then put into the feedlot where they received the same ration as the F group. The fourth treatment group was backgrounded on pasture for the duration of the summer, and while on pasture had access to free choice CCDS via a lick tank (P+CCDS). In the fall this group was placed into the feedlot and received the same ration as the F+CCDS group. In the second year, a fifth treatment was added, called the pasture finishing group (PF). The steers in this treatment received the same shelled corn, and protein, vitamin and mineral supplement, and CCDS as the cattle in the F+CCDS treatment, minus the alfalfa hay. Grass consumption for the PF cattle was estimated using the 2007 BRANDS program. Although the study is not yet completed, it appears as though CCDS can be implemented in feedlot rations successfully. The existing trends of the study would indicate that a feedlot ration containing CCDS will slightly increase steer ADG and improve F:G, without effecting QG

Progress Report: Effects of Condensed Corn Distillers Solubles on Steer Performance and Carcass Composition

This study looked at the use of condensed corn distillers solubles (CCDS) as a feed source for steers backgrounded on pasture as well as steers being fed in the feedlot. In addition, a treatment group was finished on pasture with CCDS as a part of their ration. The two feedlot rations were isocaloric and isonitrogenous. The pasture finishing steers were fed a ration based on the feedlot ration containing CCDS but were not fed any hay. The goal of this study was to establish the benefits, as well as the limitations, of feeding CCDS to feedlot and backgrounded steers

Enhancing Tc in field-doped Fullerenes by applying uniaxial stress

Capitalizing on the two-dimensional nature of superconductivity in field-effect doped C60, we show that it should be possible to increase the transition temperature Tc by applying uniaxial stress perpendicular to the gate electrode. This method not only holds the promise of substantially enhancing Tc (by about 30 K per GPa), but also provides a sensitive check of the current understanding of superconductivity in the doped Fullerenes.Comment: 3 pages RevTe