Periodic force induced stabilization or destabilization of the denatured state of a protein

We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding time first increases with driving frequency and then decreases passing through a maximum. With further increase of the driving frequency the mean folding time starts increasing as the noise-induced hoping event (from the denatured state to the native state) begins to experience many oscillations over the mean barrier crossing time period. Thus unlike one-dimensional barrier crossing problems, the external oscillating force field induces both \emph{stabilization or destabilization of the denatured state} of a protein. We have also studied the parametric dependence of the folding dynamics on temperature, viscosity, non-Markovian character of bath in presence of the external field

Active habitat selection by Capitella sp. I larvae. II. Multiple-choice experiments in still water and flume flow

Experiments on larval settlement of the opportunistic polychaete, Capitella sp. I, using three natural sediment treatments from the Buzzards Bay area (organic-rich mud from Sippewissett Marsh, organic-rich mud from New Bedford Harbor and low-organic sand from off the Weepecket Islands), and a glass bead mixture similar in grain size distribution to the New Bedford Harbor mud, were carried out in still water and two flume flows (near-surface velocities of 5 cm s−1 and 15 cm s−1; boundary-shear velocities of 0.26 cm s−1 and 0.64 cm s−1). For all three flow conditions the larvae settled in significantly greater numbers in the two mud treatments than in the glass beads. In some experiments there was significant discrimination between one or both mud treatments and sand. There was significantly higher settlement in sand than in glass beads in two of three experiments in both slow and fast flow. There was no difference in the ability of larvae to discriminate between the sediment treatments in the slow and fast flow. Strong row and column effects in the settlement of larvae in flow experiments (row 1 at the leading edge and column 4 toward the inner wall of the flume having the highest settlement) lend support to a model of interaction between larval swimming behavior and near-bottom flow. Larvae that were not offered a settlement cue for 3–6 d showed no diminution in their subsequent settlement rate or capacity for habitat selection in fast flow. Capitella sp. I larvae are adapted to contribute to the large, local population increases that characterize the species by virtue of being competent to settle immediately after hatching. Once they are mixed up into the water column, however, their capacity for postponing metamorphosis and their habitat selectivity will promote dispersal and discriminate settlement in organic-rich patches

Large-area alginate/PEO-PPO-PEO hydrogels with thermoreversible rheology at physiological temperatures

Alginate hydrogels have shown great promise for applications in wound dressings, drug delivery, and tissue engineering. Here, we report the fabrication, rheological properties, and dynamics of a multicomponent hydrogel consisting of alginate and poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) (PEO-PPO-PEO) triblock copolymers, and the achievement of thick, castable gels with tunable, thermoreversible behavior at physiological temperatures (Figure 1). PEO-PPO-PEO triblock copolymers can form temperature-sensitive hydrogels that exist as liquids at low temperatures and soft solids at high temperatures. In this work, we have employed PEO-PPO-PEO triblock copolymers to impart thermoresponsive properties to alginate hydrogels in the form of a multicomponent hydrogel. These systems can transition between a weak gel and a stiff gel, with a corresponding increase in the viscoelastic moduli of approximately two orders of magnitude as temperature is increased. The temperatures corresponding to the upper and lower boundaries of the stiff gel region, as well as the storage modulus at physiological temperatures (e.g., 36 – 40 C), can be controlled through the PEO-PPO- PEO concentration. Additionally, we explore the properties of these materials under compression and large deformations, and describe how alginate and F127 concentration can be used to control the fracture stress and strain. Finally, we compare the results from bulk rheology to the structure and dynamics of the gels measured via small-angle X-ray scattering (SAXS) and X-ray photon correlation spectroscopy (XPCS) experiments. Please click Additional Files below to see the full abstract

Delineation of the Native Basin in Continuum Models of Proteins

We propose two approaches for determining the native basins in off-lattice models of proteins. The first of them is based on exploring the saddle points on selected trajectories emerging from the native state. In the second approach, the basin size can be determined by monitoring random distortions in the shape of the protein around the native state. Both techniques yield the similar results. As a byproduct, a simple method to determine the folding temperature is obtained.Comment: REVTeX, 6 pages, 5 EPS figure

Scoping study on natural resources and climate change in Southeast Asia with a focus on agriculture. Final report

Climate change / Natural resources / Environmental effects / Agroecology / Agricultural production / Crops / Cropping systems / Farming systems / Livestock / Fisheries / Food security / Water management / Economic aspects / Rural poverty / Policy / Nutrient management / South East Asia / Cambodia / Laos / Thailand / Vietnam / Myanmar / China / Greater Mekong Subregion / Tonle Sap / Yunnan

A guide to chemokines and their receptors

The chemokines (or chemotactic cytokines) are a large family of small, secreted proteins that signal through cell surface G‐protein coupled heptahelical chemokine receptors. They are best known for their ability to stimulate the migration of cells, most notably white blood cells (leukocytes). Consequently, chemokines play a central role in the development and homeostasis of the immune system, and are involved in all protective or destructive immune and inflammatory responses. Classically viewed as inducers of directed chemotactic migration, it is now clear that chemokines can stimulate a variety of other types of directed and undirected migratory behaviour, such as haptotaxis, chemokinesis, and haptokinesis, in addition to inducing cell arrest or adhesion. However, chemokine receptors on leukocytes can do more than just direct migration, and these molecules can also be expressed on, and regulate the biology of, many non‐leukocytic cell types. Chemokines are profoundly affected by post‐translational modification, by interaction with the extracellular matrix (ECM), and by binding to heptahelical ‘atypical’ chemokine receptors that regulate chemokine localisation and abundance. This guide gives a broad overview of the chemokine and chemokine receptor families; summarises the complex physical interactions that occur in the chemokine network; and, using specific examples, discusses general principles of chemokine function, focussing particularly on their ability to direct leukocyte migration

Laser tattoo removal comparison between 1064 and 532 NM of a Q-switched ND:YAG laser treatment

Invention of the Q-switch advanced laser method is the most effective methods of tattoo removal compared to other methods of i.e. chemical, mechanical and surgical. In this study, we are reporting black pigment tattoo removal by comparing two wavelengths 532 nm and 1064 nm of Q-switched Nd-YAG laser. Using a single-pulse laser at 1064 nm wavelength, the maximum laser fluence for skin damage is 3.04 J/cm2 with pulse energy 0.55 J. While, at 532 nm wavelength, maximum laser fluence is 0.5 J/cm2 with pulse energy 0.42 J at 8-10 ns for tattooed skins. Moreover, after 1064 nm and 532 nm laser irradiations, skin biopsy of black tattooed rat’s skin demonstrates the ink granules local redistribution. Microscopic study indicates that black ink particles become smaller and vanished from the skins after 1064 nm laser treatment. The findings of this study indicate that 1064 nm wavelengths of Q-switched Nd-YAG laser treatment with 0.55 J pulse energy, is one of the significant methods of black tattoo removal with remarkable differences

Assessment of Watershed Technologies

Dealing with various topics such as watershed classification, computer simulation and modeling and computer application in watershed research, this paper assembles and summarizes technologies that are currently being used or have potential for application in the Philippines. This is in the hope of helping watershed managers, planners and researchers.watershed

Can softer junctions lead to stiffer gels? Understanding the role of stereochemistry in associative polymer gels

The ability to create synthetic materials that mimic the structural and mechanical properties of soft biological tissues remains a significant challenge. In this presentation, we focus on creating stiff hydrogels and novel nanoscale and microscale structure by engineering crystalline domains into associative hydrogels of poly(lactic acid)-poly(ethylene oxide)-poly(lactic acid) (PLA-PEO-PLA) triblock copolymers. In aqueous media, these materials form associative gels of micelles with PLA cores that serve as network junctions. We extend previous studies from our group and others by varying the stereochemistry of the PLA block to create polymers with PLA blocks with ratios of L/D lactide units varying from 100/0 to 50/50. We had previously found that the 100/0 systems (triblocks with poly(L-lactide) blocks) formed gels with nanoscale crystalline domains, and these gels displayed a high value of the elastic modulus which was strongly dependent on PLA block length. Interestingly, our most recent results show that the storage modulus of these gels does not vary monotonically with L/D ratio. Rather, systems at intermediate L/D values are stiffer than the 100/0 systems, displaying higher storage moduli in spite of the fact that the PLA domains are expected to have a lower degree of crystallinity than in the 100/0 systems. Small-angle neutron scattering (SANS) results also indicate that the strongest interactions between micelles occurs for systems with intermediate L/D ratios, and ultra-small angle neutron scattering (USANS) shows evidence of larger structures in these gels, reminiscent of the hierarchical structures observed in biological gels. Collectively, our work shows that stereochemistry can be used in unexpected ways to access novel structures and properties in relatively simple synthetic polymers, giving insight into new routes for creating complex soft materials

Finite size effects on thermal denaturation of globular proteins

Finite size effects on the cooperative thermal denaturation of proteins are considered. A dimensionless measure of cooperativity, Omega, scales as N^zeta, where N is the number of amino acids. Surprisingly, we find that zeta is universal with zeta = 1 + gamma, where the exponent gamma characterizes the divergence of the susceptibility for a self-avoiding walk. Our lattice model simulations and experimental data are consistent with the theory. Our finding rationalizes the marginal stability of proteins and substantiates the earlier predictions that the efficient folding of two-state proteins requires the folding transition temperature to be close to the collapse temperature.Comment: 3 figures. Physical Review Letters (in press