Multidimensional free energy surface of unfolding of HP-36: Microscopic origin of ruggedness

The protein folding funnel paradigm suggests that folding and unfolding proceed as directed diffusion in a multidimensional free energy surface where a multitude of pathways can be traversed during the protein's sojourn from initial to final state. However, finding even a single pathway, with the detail chronicling of intermediates, is an arduous task. In this work we explore the free energy surface of unfolding pathway through umbrella sampling, for a small globular a-helical protein chicken-villin headpiece (HP-36) when the melting of secondary structures is induced by adding DMSO in aqueous solution. We find that the unfolding proceeds through the initial separation or melting of aggregated hydrophobic core that comprises of three phenylalanine residues (Phe7, Phe11, and Phe18). This separation is accompanied by simultaneous melting of the second helix. Unfolding is found to be a multistage process involving crossing of three consecutive minima and two barriers at the initial stage. At a molecular level, Phe18 is observed to reorient itself towards other hydrophobic grooves to stabilize the intermediate states. We identify the configuration of the intermediates and correlate the intermediates with those obtained in our previous works. We also give an estimate of the barriers for different transition states and observe the softening of the barriers with increasing DMSO concentration. We show that higher concentration of DMSO tunes the unfolding pathway by destabilizing the third minimum and stabilizing the second one, indicating the development of a solvent modified, less rugged pathway. The prime outcome of this work is the demonstration that mixed solvents can profoundly transform the nature of the energy landscape and induce unfolding via a modified route. A successful application of Kramer's rate equation correlating the free energy simulation results shows faster rate of unfolding with increasing DMSO concentration. This work perhaps presents the first systematic theoretical study of the effect of a chemical denaturant on the microscopic free energy surface and rates of unfolding of HP-36. (C) 2014 AIP Publishing LLC.

Sensitivity of polarization fluctuations to the nature of protein-water interactions: Study of biological water in four different protein-water systems

Since the time of Kirkwood, observed deviations in magnitude of the dielectric constant of aqueous protein solution from that of neat water (similar to 80) and slower decay of polarization have been subjects of enormous interest, controversy, and debate. Most of the common proteins have large permanent dipole moments (often more than 100 D) that can influence structure and dynamics of even distant water molecules, thereby affecting collective polarization fluctuation of the solution, which in turn can significantly alter solution's dielectric constant. Therefore, distance dependence of polarization fluctuation can provide important insight into the nature of biological water. We explore these aspects by studying aqueous solutions of four different proteins of different characteristics and varying sizes, chicken villin headpiece subdomain (HP-36), immunoglobulin binding domain protein G (GB1), hen-egg white lysozyme (LYS), and Myoglobin (MYO). We simulate fairly large systems consisting of single protein molecule and 20000-30000 water molecules (varied according to the protein size), providing a concentration in the range of similar to 2-3 mM. We find that the calculated dielectric constant of the system shows a noticeable increment in all the cases compared to that of neat water. Total dipole moment auto time correlation function of water < dM(W) (0)delta M-W (t) > is found to be sensitive to the nature of the protein. Surprisingly, dipole moment of the protein and total dipole moment of the water molecules are found to be only weakly coupled. Shellwise decomposition of water molecules around protein reveals higher density of first layer compared to the succeeding ones. We also calculate heuristic effective dielectric constant of successive layers and find that the layer adjacent to protein has much lower value (similar to 50). However, progressive layers exhibit successive increment of dielectric constant, finally reaching a value close to that of bulk 4-5 layers away. We also calculate shellwise orientational correlation function and tetrahedral order parameter to understand the local dynamics and structural re-arrangement of water. Theoretical analysis providing simple method for calculation of shellwise local dielectric constant and implication of these findings are elaborately discussed in the present work. (C) 2014 AIP Publishing LLC.

A Gold Sensors Array for Imaging The Real Tissue Phantom in Electrical Impedance Tomography

Surface electrodes in Electrical Impedance Tomography (EIT) phantoms usually reduce the SNR of the boundary potential data due to their design and development errors. A novel gold sensors array with high geometric precision is developed for EIT phantoms to improve the resistivity image quality. Gold thin films are deposited on a flexible FR4 sheet using electro-deposition process to make a sixteen electrode array with electrodes of identical geometry. A real tissue gold electrode phantom is developed with chicken tissue paste and the fat cylinders as the inhomogeneity. Boundary data are collected using a USB based high speed data acquisition system in a LabVIEW platform for different inhomogeneity positions. Resistivity images are reconstructed using EIDORS and compared with identical stainless steel electrode systems. Image contrast parameters are calculated from the resistivity matrix and the reconstructed images are evaluated for both the phantoms. Image contrast and image resolution of resistivity images are improved with gold electrode array.

异硫氰酸荧光素-溶菌酶的制备及晶体生长预研究

迄今尚未有适用于光源为488 nm激光扫描共聚焦显微镜研究用的溶菌酶.为此,用异硫氰酸荧光素作为探针标记了溶菌酶,测定了溶菌酶标记物的紫外-可见吸收光谱和荧光光谱,摸索了其晶体的生长条件.实验结果表明,在标记过程中异硫氰酸荧光素没有影响溶菌酶的生化性质,标记后的溶菌酶可用于激光扫描共聚焦显微镜进行后续研究.

El juego anidado de la reforma constitucional argentina

Resumen: El presente trabajo aspira a explicar la dinámica vivida por el proceso que condujo a la reforma constitucional de 1994 en la Argentina, en especial a la sucesión de acontecimientos que culminaron en la celebración del Pacto de Olivos y la sanción de la ley de necesidad de la reforma en 1993. ¿Por qué la Unión Cívica Radical y el Partido Justicialista optaron por celebrar un pacto en el proceso reformista, que podría considerarse un resultado subóptimo, en lugar de conducir cada uno su estrategia dominante: resistir la reforma o promoverla a toda costa? Observado como un “juego anidado”, el proceso que llevó a la reforma, lejos de ser un resultado subóptimo, fue un juego que se desarrolló simultáneamente en tres arenas. Desde esta posición, el trabajo discute la extendida tesis de que el proceso de reforma fue un clásico “juego del gallina”.

气相扩散法生长溶菌酶晶体的动态光散射研究

首次采用动态光散射研究了气相扩散法生长溶菌酶晶体 .实验中采用了两种溶解溶菌酶的方法，所得实验结果是有区别的 .这种区别表明了 NaCl对溶菌酶分子间相互作用产生十分重要的影响 .实验结果表明，晶体生长过程中，溶液中溶菌酶始终保持单分子与两分子聚集体的状态，这种状态是生长晶体的基础 .

Investment potentials in shellfish culture in Nigeria

Shellfish are a major but cheap protein source for human consumption as well as source of income for coastal towns and villages of the Niger Delta in Rivers State, Cross River, and Lagos States. A research into the nutritive value of some of these marine shellfish viz: bivalves (oyster - Crassostrea gasar and cockle - Anadara senilis); gastropods (periwinkle - Tympanotonus fuscatus, obtuse periwinkle - Semifusus morio and the giant whelk - Thais callifera) and mangrove crabs (green crab - Goniopsis pelli, ghost crab - Cardisoma ormatum, and common blue crab - Callinectes latimanus) was carried out to compare their quality and cost with beef, chicken meat, pork and egg in order to identify those most suitable for commercial culture. Results show that all shellfish had at least 16% crude protein except blue crab (13.38%). All shellfish had higher protein content than egg (13.36%). Cockle with protein content 25.47% compared favourably with beef, (29.60%). Beef, chicken meat and pork cost 11.50, 9.00 and 8.00 per kilo respectively while oyster, periwinkle and the common blue crab cost 3.50, 3.00, and 1.50 per kilo respectively. Oysters and Cockles are recommended for commercial culture based on the findings of this research

International Climate Finance and its Influence on Fairness and Policy

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I. The crystal structure of trimesic acid. II. Topics in crystallographic calculations

I. Trimesic acid (1, 3, 5-benzenetricarboxylic acid) crystallizes with a monoclinic unit cell of dimensions a = 26.52 A, b = 16.42 A, c = 26.55 A, and β = 91.53° with 48 molecules /unit cell. Extinctions indicated a space group of Cc or C2/c; a satisfactory structure was obtained in the latter with 6 molecules/asymmetric unit - C₅₄O₃₆H₃₆ with a formula weight of 1261 g. Of approximately 12,000 independent reflections within the CuK_α sphere, intensities of 11,563 were recorded visually from equi-inclination Weissenberg photographs.

The structure was solved by packing considerations aided by molecular transforms and two- and three-dimensional Patterson functions. Hydrogen positions were found on difference maps. A total of 978 parameters were refined by least squares; these included hydrogen parameters and anisotropic temperature factors for the C and O atoms. The final R factor was 0.0675; the final "goodness of fit" was 1.49. All calculations were carried out on the Caltech IBM 7040-7094 computer using the CRYRM Crystallographic Computing System.

The six independent molecules fall into two groups of three nearly parallel molecules. All molecules are connected by carboxylto- carboxyl hydrogen bond pairs to form a continuous array of sixmolecule rings with a chicken-wire appearance. These arrays bend to assume two orientations, forming pleated sheets. Arrays in different orientations interpenetrate - three molecules in one orientation passing through the holes of three parallel arrays in the alternate orientation - to produce a completely interlocking network. One third of the carboxyl hydrogen atoms were found to be disordered.

II. Optical transforms as related to x-ray diffraction patterns are discussed with reference to the theory of Fraunhofer diffraction.

The use of a systems approach in crystallographic computing is discussed with special emphasis on the way in which this has been done at the California Institute of Technology.

An efficient manner of calculating Fourier and Patterson maps on a digital computer is presented. Expressions for the calculation of to-scale maps for standard sections and for general-plane sections are developed; space-group-specific expressions in a form suitable for computers are given for all space groups except the hexagonal ones.

Expressions for the calculation of settings for an Eulerian-cradle diffractometer are developed for both the general triclinic case and the orthogonal case.

Photographic materials on pp. 4, 6, 10, and 20 are essential and will not reproduce clearly on Xerox copies. Photographic copies should be ordered.

Part I. Synchronization of the cell division cycle of HeLa cells in suspension cultures. Part II. Studies on chromosomal proteins of HeLa cells during the cell division cycle

Part I

These studies investigate the potential of single and double treatments with either 5-fluorodeoxyuridine of excess thymidine to induce cell division synchrony in suspension cultures of HeLa cells. The patterns of nucleic acid synthesis and cell proliferation have been analyzed in cultures thus synchronized. Several changes in cell population during long incubation with 5-fluorodeoxyuridine or excess thymidine are also described. These results are subjected to detailed evaluation in terms of the degree and quality of synchrony finally achieved.

Part II

Histones and non-histone proteins associated with interphase and metaphase chromosomes of HeLa cells have been qualitatively and quantitatively analyzed. Histones were fractionated by chromatography on Amberlite CG-50 and further characterized by analytical disc electrophoresis and amino acid analysis of each chromatographic fraction. It is concluded that histones of HeLa cells are comprised of only a small number of major components and that these components are homologous to those of other higher organisms. Of all the histones, arginine-rich histone III alone contains cysteine and can polymerize through formation of intermolecular disulfide bridges between histone III monomers.

A detailed comparison by chromatography and disc electrophoresis established that interphase and metaphase histones are made up of similar components. However, certain quantitative differences in proportions of different histones of interphase and metaphase cells are reported. Indirect evidence indicates that a certain proportion of metaphase histone III is polymerized through intermolecular disulfide links, whereas interphase histone III occurs mainly in the monomeric form.

Metaphase chromosomes are associated with an additional acid-soluble protein fraction which is absent from interphase chromosomes. All of these additional acid-soluble proteins of metaphase chromosomes are shown to be non-histones and it is concluded that the histone/DNA ratio is identical in interphase and metaphase chromosomes. The bulk of acid-soluble non-histone proteins of metaphase chromosomes were found to be polymerized through disulfide bridges; corresponding interphase non-histone proteins displayed no evidence of similar polymerization.

The factors responsible for the condensed configuration and metabolic inactivity of metaphase chromosomes are discussed in light of these findings.

The relationship between histone and DNA synthesis in nondividing differentiated chicken erythrocyte cells and in rapidly dividing undifferentiated HeLa cells is also investigated. Of all the histones, only arginine-rich histones are synthesized in mature erythrocytes. Histone synthesis in HeLa cells was studied in both unsynchronized and synchronized cultures. In HeLa cells, only part of the synthesis of all histone fractions is dependent on concurrent DNA synthesis, whereas all histones are synthesized in varying degrees even in the absence of DNA synthesis.

Estudo fenotípico da região Aorta-Gônada-Mesonefros, de embriões de galinhas Gallus gallus domesticus, com ênfase na aorta dorsal

Acredita-se que os primeiros progenitores da hematopoese definitiva surjam da diferenciação do endotélio da aorta dorsal, na altura da região da Aorta-Gônada-Mesonefros (AGM). Com o intuito de estudar esta região e o fenótipo das células do endotélio da aorta dorsal nesta posição topográfica, ovos galados de Gallus gallus domesticus L. foram incubados em chocadeira, classificados em estádios de E16 a E25 e processados histotecnologicamente para obtenção de secções seriadas na altura da região AGM. Estas passaram por coloração por Hematoxilina-Eosina, histoquímica para PAS, PAS-diastase e Alcian Blue pH 1.0 e pH 2.5, histoquímica por lectinas fluoresceinadas e imunofluorescência para moléculas de superfície, citoesqueleto e matriz extracelular. Foi observada hipertrofia endotelial no assoalho da aorta nos estádios observados, o qual se apresentava positivo ao PAS, com ocorrência frequente de vacuolizações basais PAS negativas, e o surgimento ocasional de grupamentos celulares intravasculares. Nestes, as células que se destacavam da membrana basal do endotélio expressavam progressivamente mais material PAS positivo, o qual, no entanto, em nenhum momento pareceu se tratar de glicogênio. Em relação às glicosaminoglicanas, notamos a presença predominante de ácido hialurônico por todo o mesênquima da região e em outras estruturas como periferia da notocorda, tubo neural e mesoderma lateral. Ocorreu co-expressão de fibronectina e α-actina de músculo liso em células circunjacentes à aorta, na face ventral do vaso. GFAP e BMP-4 são expressas entre as células do tubo neural e em sua periferia, assim como na notocorda do embrião. As lectinas Abrus precatorius, Lens culinarise Ricinus communis mostraram-se positivas principalmente na região subedotelial do assoalho da aorta nos estádios observados neste trabalho. Bandeiraea simplicifolia exibiu pouca marcação na aorta dorsal e a Arachis hypogeae foi negativa. Outras estruturas da região AGM também expressaram resíduos de açúcares revelados por estas lectinas, tais como: notocorda, tubo neural, mesênquima, intestino primitivo e saco vitelínico. Estes resultados acrescentam elementos morfológicos e bioquímicos ao conhecimento sobre a região AGM de embriões de galinha e sobre o endotélio, possivelmente hemogênico, da aorta dorsal.

Changes in consumer tastes in the demand for fish and meat in Malaysia

In this article the demand for fish and its substitute was estimated using a very flexible demand function, the Almost Ideal Demand System (AIDS) developed by Deaton and Muelllbaeur (1980), incorporating the habit formation variable to measure the impact of the changes in tastes in comsumer demand for fish and meat products from 1960 to 1990 in Malaysia. Information on price and income elasticities for these meat groups was also obtained. To incorporate consumption habit variables, the dynamic translating procedure proposed by Pollak (1970) and Pollak and Wales (1981) has been adopted. The overall results of the maximum likelihood estimates of the dynamic AIDS model are quite good where 19 of 30 coefficients are significantly different from zero and the minimum budget shares, the constant, are between zero and one for each meat type. Consumers tend to purchase and consume fish, chicken, and pork almost daily. Beef and mutton are only consumed occassionally since they are relatively more expensive. This finding is consistent with the trend observed in the per capita consumption and budget share where fish, chicken, and pork tended to dominate over beef and mutton from 1960 to 1990.

Aquaculture technology transfer to smallholder farmers in Malawi, Southern Africa

Details are given of activities conducted in Zomba, Malawi, in order to demonstrate new aquaculture technologies and encourage their use by smallholder fish farmers. The following technologies were introduced: napier grass as a pond output; use of a reed fence for harvesting fish; developing a high-quality compost as a pond input; vegetable-pond integration; chicken-pond integration; smoking kiln; pond stirring; and rice-fish integration. The reactions of the farmers to these technologies and their testing by the farmers are outlined briefly.

Trade and Management: Exclusive Economic Zones and the Changing Japanese Surimi Market

The United States' increasing competitive advantage in international seafood trade in Alaska walleye pollock. Theragra chalcogramma, has contributed to higher prices for surimi-based goods and structural changes in seafood production and trade in Japan. The objectives of this analytical investigation include: 1) Evaluation of the role reversal of Japan and the United States in international seafood trade and 2) quantification of the impact of rising prices of frozen surimi on household consumption of surimi-based foods in Japan. This study documents Japan's regression from "seafood self-sufficiency" to increasing dependence on imported products and raw materials. In particular, Japan's growing dependence on American fishermen and seafood producers is described. Surimi production by the United States, and its emerging dominance over Japanese sources of supply, are especially significant. Results of the analysis suggest that Japanese consumer demand for surimi-based food stuffs correlates directly with "competitive" food prices, e.g., pork, chicken, and beef, and inversely with personal income. Also revealed is how rising household income and relative price shifts among competing animal protein sources in the Japanese diet have contributed to declining household consumption of surimi-based foods, specifically, and a shift away from seafoods in favor of beef, in general. The linkages between, for example. Japanese domestic seafood production and consumption, international trade in marine products, and resource management decisions in the U.S. EEZ present a picture of a changing global marketplace. Increasingly, actions in one arena will have perhaps profound implications in the others.

Motor coordination: when two have to act as one.

Trying to pass someone walking toward you in a narrow corridor is a familiar example of a two-person motor game that requires coordination. In this study, we investigate coordination in sensorimotor tasks that correspond to classic coordination games with multiple Nash equilibria, such as "choosing sides," "stag hunt," "chicken," and "battle of sexes". In these tasks, subjects made reaching movements reflecting their continuously evolving "decisions" while they received a continuous payoff in the form of a resistive force counteracting their movements. Successful coordination required two subjects to "choose" the same Nash equilibrium in this force-payoff landscape within a single reach. We found that on the majority of trials coordination was achieved. Compared to the proportion of trials in which miscoordination occurred, successful coordination was characterized by several distinct features: an increased mutual information between the players' movement endpoints, an increased joint entropy during the movements, and by differences in the timing of the players' responses. Moreover, we found that the probability of successful coordination depends on the players' initial distance from the Nash equilibria. Our results suggest that two-person coordination arises naturally in motor interactions and is facilitated by favorable initial positions, stereotypical motor pattern, and differences in response times.