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An association study of a neurotrophic3 (NT-3) gene polymorphism with schizophrenia | Since abnormalities of brain development play a role in the aetiology of schizophrenia, growth factors, known to play a role in neurodevelopment, such as neurotrophin-3 (NT-3), are therefore candidate genes for this disorder. The A3/147 bp allele of a dinucleotide repeat polymorphism in the promoter region of the NT-3 gene has been reported as occurring more frequently in a sample of Japanese schizophrenics compared to controls. We have determined the frequency of alleles of this polymorphism in 175 Caucasian schizophrenic patients and 147 control subjects. The patient and control samples showed no significant deviation from Hardy-Weinberg equilibrium and, in a test of all alleles, the patients and controls did not differ significantly in allele frequencies. However, the male schizophrenics were more likely than male controls to have the A3/147 bp allele (P = 0.029). | Cross-linking a single polymer chain with itself leads to soft nanoparticles with well-defined properties. We study such single-chain nanoparticles (SCNP) obtained by cross-linking in good and in poor solvents using Monte Carlo simulations and theoretical models. We show that SCNP obtained by cross-linking in poor solvents preserve their shape during swelling in good solvents only if the precursor chain is very long. In this case the Flory–Rehner model describes the swelling of SCNP. Shorter chains and SCNPs cross-linked in good solvent generate noncompact structures. Here we obtain a good theoretical description of the simulated swelling properties using a mean-field model by taking into account the cross-linking topology using the connectivity matrix of the cross-linked chain. The crossover between the two regimes can consistently be described using a scaling argument. We further show that the distances between cross-links along the chain contour follows the distribution for Gaussian chains after cross-... | eng_Latn | 19,400 |
Immune Heterogeneity in Neuroinflammation: Dendritic Cells in the Brain | Dendritic cells (DC) are critical to an integrated immune response and serve as the key link between the innate and adaptive arms of the immune system. Under steady state conditions, brain DC’s act as sentinels, continually sampling their local environment. They share this function with macrophages derived from the same basic hemopoietic (bone marrow-derived) precursor and with parenchymal microglia that arise from a unique non-hemopoietic origin. While multiple cells may serve as antigen presenting cells (APCs), dendritic cells present both foreign and self-proteins to naive T cells that, in turn, carry out effector functions that serve to protect or destroy. The resulting activation of the adaptive response is a critical step to resolution of injury or infection and is key to survival. In this review we will explore the critical roles that DCs play in the brain’s response to neuroinflammatory disease with emphasis on how the brain’s microenvironment impacts these actions. | Simulated annealing of chemical potential located the highest affinity positions of eight organic probes and water on eight static structures of hen egg white lysozyme (HEWL) in various conformational states. In all HELW conformations, a diverse set of organic probes clustered in the known binding site (hot spot). Fragment clusters at other locations were excluded by tightly-bound waters so that only the hot-spot cluster remained in each case. The location of the hot spot was correctly predicted irrespective of the protein conformation and without accounting for protein flexibility during the simulations. Any one of the static structures could have been used to locate the hot spot. A site on a protein where a diversity of organic probes is calculated to cluster, but where water specifically does not bind, identifies a potential small-molecule binding site or protein–protein interaction hot spot. | eng_Latn | 19,401 |
Enzyme Active Site Loop Revealed as a Gatekeeper for Cofactor Flip by Targeted Molecular Dynamics Simulations and FRET-Based Kinetics | Structural motions are key events in enzyme catalysis, as exemplified by the conformational dynamics associated with the cofactor in the catalytic mechanism of hydrolytic NAD(P)-dependent aldehyde dehydrogenases. We previously showed that, after the oxidoreduction step, the reduced cofactor must adopt a flipped conformation, which positions the nicotinamide in a conserved cavity that might constitute the exit door for NAD(P)H. However, the molecular basis that make this movement possible is unknown. Based on the pre- and postflip X-ray structures, targeted molecular dynamic simulations enabled us to identify the E268LGG271 conserved loop that must shift to allow reduced nicotinamide conformational switch. To monitor cofactor movements within the active site, we used an intrinsic fluorescence resonance energy transfer signal between Trp177 and the reduced nicotinamide moiety to kinetically track the flip during the catalytic cycle of retinal dehydrogenase 2 (ALDH1A2). Decreasing loop flexibility by substit... | Regulation of enzymatic activity is essential for living organisms. Nowadays, with the emergence of synthetic biology, there is a rising interest in placing the activity of synthetic catalysts under the control of a cell. This short review aims at summarizing the regulation strategies developed to date, and at presenting the development of an artificial zymogen, which is upregulated by a natural protease. In our view, this constitutes a first step towards the cellular control of the activity of an artificial metalloenzyme. | eng_Latn | 19,402 |
Functional Roles of Pulsing in Genetic Circuits | A fundamental problem in biology is to understand how genetic circuits implement core cellular functions. Time-lapse microscopy techniques are beginning to provide a direct view of circuit dynamics in individual living cells. Unexpectedly, we are discovering that key transcription and regulatory factors pulse on and off repeatedly, and often stochastically, even when cells are maintained in constant conditions. This type of spontaneous dynamic behavior is pervasive, appearing in diverse cell types from microbes to mammalian cells. Here, we review recent work showing how pulsing is generated and controlled by underlying regulatory circuits and how it provides critical capabilities to cells in stress response, signaling, and development. A major theme is the ability of pulsing to enable time-based regulation analogous to strategies used in engineered systems. Thus, pulsatile dynamics is emerging as a central, and still largely unexplored, layer of temporal organization in the cell. | In this paper, simulations are conducted to investigate high speed uni-traveling-carrier photodiodes (UTC-PDs). The Gaussian doping profile, which can introduce potential gradient and electric field, is presented to be used in the absorption layer. Compared to constant doping and step-graded doping, bandwidth of UTC-PD with Gaussian doping is improved substantially. | eng_Latn | 19,403 |
Load Balancing for Flow-Based Parallel Processing Systems in CMP Architecture | Load balancing is critical to the performance of parallel processing systems. It is more difficult for network systems such as NIDS and Web Servers, because they must preserve flow order. But traditional flow-based load balancing schemes of network parallel processing systems, such as LLF, cost much resource and introduce lots of communication overhead. With the rapid popularization of multi-core system, it is a good choice to apply NIDS in CMP architecture to achieve higher performance. Some companies have taken the first step. Their scheduling algorithm operates at a custom NIC based on FPGA technology. LLF algorithm can't be used in such environment because it needs much more memory than NIC owns. ::: ::: In this paper, we propose a scheduling scheme that remaps the new arrival flows when the system is unbalanced. To make effective adjustments we design a new triggering policy based on waiting lengths and their difference. Compared with LLF, our algorithm costs about 5% memory to get the same performance. | Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FAMUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. | eng_Latn | 19,404 |
The Effect of Aging on Rat Striatal D1 Receptor mRNA-Containing Neurons | In situ hybridization of a digoxigenin-labeled oligonucleotide probe combined with computer assisted image assessment was used to directly visualize D1 dopamine receptor mRNA-containing neurons in rat striata, and quantify age-related changes in the sizes and relative mRNA content of these neurons. It was found that: 1) numbers of D1 mRNA-containing neurons appear to decrease in striata of aged rats; 2) relative amounts of D1 receptor mRNA in individual striatal neurons do not change during aging; and 3) neurons of all sizes appear to be lost, with the greatest absolute decrease in those larger than 150 μm2. These data confirm the age associated loss of D1 dopamine receptors reported for some other rat strains in that species, and further suggest that neuronal loss is responsible for the decrement. The latter finding contrasts with the aging associated loss of D2 dopamine receptors, which additionally involves decreased amounts of mRNA per cell. | Approximate expressions for the NMR spin relaxation rate constant in the rotating frame of reference R 1ρ are derived for two-site chemical exchange by consideration of the evolution of the average density operator using the stochastic Liouville equation. R 1ρ is obtained as a linearized approximation to the largest (least negative) eigenvalue of the matrix describing the evolution of the average density operator in the long-term limit. The expressions obtained are more accurate than existing expressions when exchange is not fast and the populations of the exchanging sites are close to equal. The new expressions for R 1ρ facilitate the interpretation of chemical exchange phenomena in proteins and other biological macromolecules. | eng_Latn | 19,405 |
Rings and threads as linkers in metal–organic frameworks and poly-rotaxanes | Coordination polymers and metal-organic rotaxane frameworks are reported where the organic linker is replaced by functionalised inorganic clusters that act as bridging ligands. | Nuclear organization can impact on all aspects of the genome life cycle. This organization is thoroughly investigated by advanced imaging and chromosome conformation capture techniques, providing considerable amount of datasets describing the spatial organization of chromosomes. In this review, we will focus on polymer models to describe chromosome statics and dynamics in the yeast Saccharomyces cerevisiae. We suggest that the equilibrium configuration of a polymer chain tethered at both ends and placed in a confined volume is consistent with the current literature, implying that local chromatin interactions play a secondary role in yeast nuclear organization. Future challenges are to reach an integrated multi-scale description of yeast chromosome organization, which is crucially needed to improve our understanding of the regulation of genomic transaction. | eng_Latn | 19,406 |
Unexpected Effects of Macromolecular Crowding on Protein Stability | Most theories about macromolecular crowding focus on two ideas: the macromolecular nature of the crowder and entropy. For proteins, the volume excluded by the crowder favors compact native states over expanded denatured states, enhancing protein stability by decreasing the entropy of unfolding. We tested these ideas with the widely used crowding agent Ficoll-70 and its monomer, sucrose. Contrary to expectations, Ficoll and sucrose have approximately the same stabilizing effect on chymotrypsin inhibitor 2. Furthermore, the stabilization is driven by enthalpy, not entropy. These results point to the need for carefully controlled studies and more sophisticated theories for understanding crowding effects. | The structure of GMA is introduced. Static displacement-force model and magnetism-machine coupling model for helping understand the magnetostriction and establishes simulation model are given. Simulation result shows that response time of machine part is slowness. It brings some disbennifit affection if minish damp. For example,exceed quantity and undulation will argument. It is important to ameliorate dynamic characteristic of the system to append a reasonable adjustor. | eng_Latn | 19,407 |
Metabolic effects of exogenous ketone supplementation – an alternative or adjuvant to the ketogenic diet as a cancer therapy? | Cancers exhibit an abnormal metabolism characterized by increased glucose consumption. Studies suggest that unlike healthy tissues, cancer cells are unable to efficiently utilize ketones for energy... | Enhanced sampling techniques are used to increase the frequency of "rare events" during computer simulations of complex molecules. Although methods exist that allow accurate thermodynamics to be recovered from enhanced simulations, recovering kinetics proves to be more challenging. Here we present an extrapolation approach that allows reliable kinetics to be recovered from potential-scaled MD simulations. The approach, based on Kramers' rate theory, is simple and computationally efficient, and allows kinetics to be recovered without defining reaction coordinates. To test our approach, we use it to determine the kinetics of barrier crossing between two metastable states on the 2D-Müller potential and the C7eq to αR transition in alanine dipeptide. The mean first passage time estimates obtained are in excellent agreement with reference values obtained from direct simulations on the unscaled potentials performed over times that are orders of magnitude longer. | eng_Latn | 19,408 |
Geochemical behavior and activity ratios of Fukushima-derived radionuclides in aerosols at the Geological Survey of Japan, Tsukuba, Japan | Aerosols from the Fukushima Dai-ichi Nuclear Power Plant accident were collected at the Geological Survey of Japan. The temporal patterns of the 134Cs/137Cs, 136Cs/137Cs, and 132Te/137Cs activity ratios were consistent with expectations based on their half-lives. Those for 131I and 129mTe decreased with some fluctuations. 110mAg/137Cs declined more rapidly than expected and 95Nb/137Cs increased with time. The results suggest that the temporal patterns depended not only on their half-lives but also on many factors such as chemical speciation, the diversity of sources, changes in the temperature and discharge rate from the reactors, and the processes of transport. | AbstractTo understand how cells respond to the nanoscale extracellular environment in vivo, cells from various sources have been cultured on nanoscale patterns fabricated using bottom-up and top-down techniques. Human fetal osteoblasts (hFOBs) and stem cells are some of them and they are known to be overtly responsive to nanoscale topographies – allowing us to investigate the hows and whys of the response in vitro. Information gathered from these in vitro studies could be used to control the cells, i.e. make the stem cells differentiate or retain their characteristics without the use of medium supplements. In this review, hFOB and stem cell responses to nanotopographies are summarized and discussed to shed some light on the influence of patterns on the reactions. Although both types of cells are responsive to nanoscale topographies, the responses are found to be unique to topographical dimension, shape, orientation and the types of cells used. This implies that cellular responses are influenced by multitu... | eng_Latn | 19,409 |
Muscimol differentially facilitates stereotypy but antagonizes motility induced by dopaminergic drugs: A complex GABA-dopamine interaction | Abstract Muscimol is the most potent and specific GABA agonist presently available. The influence of muscimol on two behavioral parameters, dependent on dopamine was studied: locomotor activity and stereotyped gnawing induced by apomorphine, cocaine or methylphenidate. In mice pretreated with a non-sedative subcutaneous dose of muscimol, a sedative effect was seen a few minutes after the injection of a stimulant dose of the dopaminergic drugs; the combination muscimol - apomorphine being most sedative. Contrastingly, muscimol strongly facilitates the development of stereotyped gnawing induced by higher doses of cocaine, methylphenidate or apomorphine. Pretreatment with α-methyltyrosine, an inhibitor of the catecholamine synthesis given before muscimol, did not antagonize the stereotyped gnawing after cocaine or methylphenidate. This finding suggests that the muscimol effect primarily depends on a direct GABA-ergic mechanism facilitating stereotyped gnawing. | Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FAMUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. | eng_Latn | 19,410 |
Oscillation and Nonoscillation of Neutral Differential Equations with Positive and Negative Coefficients | In this paper, oscillattion and nonoscillation criteria are established for neutral differential equations with positive and negative coefficients. Our criteria improve and extend many results known in the literature. | Structural motions are key events in enzyme catalysis, as exemplified by the conformational dynamics associated with the cofactor in the catalytic mechanism of hydrolytic NAD(P)-dependent aldehyde dehydrogenases. We previously showed that, after the oxidoreduction step, the reduced cofactor must adopt a flipped conformation, which positions the nicotinamide in a conserved cavity that might constitute the exit door for NAD(P)H. However, the molecular basis that make this movement possible is unknown. Based on the pre- and postflip X-ray structures, targeted molecular dynamic simulations enabled us to identify the E268LGG271 conserved loop that must shift to allow reduced nicotinamide conformational switch. To monitor cofactor movements within the active site, we used an intrinsic fluorescence resonance energy transfer signal between Trp177 and the reduced nicotinamide moiety to kinetically track the flip during the catalytic cycle of retinal dehydrogenase 2 (ALDH1A2). Decreasing loop flexibility by substit... | eng_Latn | 19,411 |
Platinated DNA oligonucleotides: new probes forming ultrastable conjugates with graphene oxide | University of Waterloo ::: Canadian 95 Foundation for Innovation ::: Natural Sciences and Engineering Research Council and the Early Researcher Award ::: Ministry of Research, Innovation and Science of Ontario | Background ::: In animals and fungi, dimerization is crucial for targeting GRIP domain proteins to the Golgi apparatus. Only one gene in the Arabidopsis genome, AtGRIP, codes for a GRIP domain protein. It remains unclear whether AtGRIP has properties similar to those of GRIP domain proteins. | eng_Latn | 19,412 |
The Structural and Functional Organization of Ribosomal Compartment in the Cell: A Mystery or a Reality? | Great progress has been made toward solving the atomic structure of the ribosome, which is the main biosynthetic machine in cells, but we still do not have a full picture of exactly how cellular ribosomes function. Based on the analysis of crystallographic and electron microscopy data, we propose a basic model of the structural organization of ribosomes into a compartment. This compartment is regularly formed by arrays of ribosomal tetramers made up of two dimers that are actually facing in opposite directions. The compartment functions as the main 'factory' for the production of cellular proteins. The model is consistent with the existing biochemical and genetic data. We also consider the functional connections of such a compartment with cellular transcription and ribosomal biogenesis. | Thank you for downloading religion and social organization in central polynesia. Maybe you have knowledge that, people have search hundreds times for their favorite readings like this religion and social organization in central polynesia, but end up in malicious downloads. Rather than reading a good book with a cup of tea in the afternoon, instead they cope with some harmful virus inside their laptop. | eng_Latn | 19,413 |
Directed self-avoiding walks and statistics of rigid-chain polymer molecules | The statistics of rigid-chain polymer conformations is described on the basis of a model of directed self-avoiding walks. The generating functions for the distribution function of a chain in one-, two-, and three-dimensional spaces are constructed. It is shown that the statistics of the conformational states of chains with finite interunit flexural stiffness can differ strongly from Gaussian statistics. If the chain length is comparable to the Kuhn segment length, then the molecule is strongly anisotropic (almost rectilinear), but as the chain length increases, the molecule starts to bend and ultimately coils up. However, since a coil contains extended, almost rectilinear, chain sections, the coil is not truly Gaussian, even though the squared average size of the coil is directly proportional to the chain length. It is shown that under certain conditions the existence of almost rectilinear chain sections results in the appearance of orientational order in the system. | Abstract A sort of the random flight theory is applied to the measurement of the fibre length with special reference to the length of a bipolymer DNA from its image contour in an electron micrograph. | eng_Latn | 19,414 |
Drivers of Spatial Structure in Social Microbial Communities | Microbes are social organisms, interacting primarily through secreted biomolecules. Many traits have evolved based solely on their effects upon other community members, yet even individually beneficial traits often create social side effects that are mediated by spatial population structure. Predicting the evolution of many microbial traits thus requires a comprehensive understanding of their social consequences. In this review, we examine the critical role of population spatial structure in microbial social evolution. We briefly review key mechanisms structuring microbial communities, focusing primarily on the universal roles of cellular death and reproduction. Finally, we explain how spatial assortment can be efficiently calculated in two-dimensional, surface-attached populations. | ABSTRACTThis paper concerns on the bearing-based leader–follower formation manoeuvre control problem for two- (2D) and three-dimensional (3D) multi-agent systems with nonholonomic constraint. The t... | eng_Latn | 19,415 |
A far-red fluorescent probe based on a phospha-fluorescein scaffold for cytosolic calcium imaging | The far-red emissive fluorescent probe CaPF-1 based on a phospha-fluorescein scaffold enables the detection of cytosolic calcium ions in living cells. The probe can be excited in the red region (λabs = 636 nm) and exhibits a sufficiently high fluorescence turn-on response in the far-red region (λem = 663 nm) upon complexation with calcium ions. The hydrophilic and anionic characteristics of this phospha-fluorescein fluorophore allowed the cytosolic localization of CaPF-1. Moreover, it was possible to visualize histamine-induced calcium oscillation in HeLa cells using CaPF-1. | AbstractTo understand how cells respond to the nanoscale extracellular environment in vivo, cells from various sources have been cultured on nanoscale patterns fabricated using bottom-up and top-down techniques. Human fetal osteoblasts (hFOBs) and stem cells are some of them and they are known to be overtly responsive to nanoscale topographies – allowing us to investigate the hows and whys of the response in vitro. Information gathered from these in vitro studies could be used to control the cells, i.e. make the stem cells differentiate or retain their characteristics without the use of medium supplements. In this review, hFOB and stem cell responses to nanotopographies are summarized and discussed to shed some light on the influence of patterns on the reactions. Although both types of cells are responsive to nanoscale topographies, the responses are found to be unique to topographical dimension, shape, orientation and the types of cells used. This implies that cellular responses are influenced by multitu... | eng_Latn | 19,416 |
Demonstration of Pulsed Electron Beam Applications (PEBA) for Fabricating Small Geometry Semiconductor Devices | Abstract : This is the final report of a program demonstrating the applicability of pulsed electron beam processing to the fabrication of small-geometry silicon semiconductor devices, with the concomitant elimination of the high-temperature thermal treatments that can degrade performance. The report documents the use of pulsed annealing techniques to fabricate diodes, ion-implanted resistors, and transistors with electrical characteristics comparable to devices fabricated by high temperature thermal processing. Pulsed liquid phase epitaxial regrowth of polysilicon films were demonstrated. Resolution with oxide masks to one micron has been shown to be feasible. | PEP is a database of Predictions for Entire Proteomes. The database contains summaries of analyses of protein sequences from a range of organisms representing all three major kingdoms of life: eukaryotes, prokaryotes and archaea. All proteins publicly available for organisms were aligned against SWISS-PROT, TrEMBL and PDB. Additionally, the following annotations are provided: secondary structure, transmembrane helices, coiled coils, regions of low complexity, signal peptides, PROSITE motifs, nuclear localization signals and classes of cellular function. Proteins that contain long regions without regular secondary structure are also identified. We have produced a related database of structural domain-like fragments derived from PEP and clusters based on homology between all fragments. The PEP database, fragments and clusters are distributed freely as a set of flat files and have been integrated into SRS. The PEP group of databases can be accessed from: http://cubic.bioc.columbia.edu/pep. | eng_Latn | 19,417 |
The response of a molecule to an external electric field: predicting structural and spectroscopic change | Abstract The accuracy of expanding the response of a molecule to an external electric field, E, as a power series in the field is investigated in the model hydrogen-bonded complex, ClH:NH3. Even at field strengths large enough to cause dramatic structural change in the complex, both the structure and vibrational frequencies are quantitatively predicted using only terms linear in E. These results suggest that knowledge of the zero-field molecular potential energy and dipole moment surfaces may be sufficient to accurately model the interactions of molecules in a wide range of external electric fields. | In this work, we show a mathematical model for the angiogenesis by endothelial cells. We present the model at the level of partial differential equations, describing the spatiotemporal evolution of the cell population, the extracellular matrix macromolecules, the proteases, the tumor angiogenic factors, and the possible presence of inhibitors. We mainly focus, however, on a complementary, more physiologically realistic, hybrid approach in which the cells are treated as individual particles. We examine the model numerically in two-dimensional settings, discussing its comparison with experimental results. | eng_Latn | 19,418 |
Breast cancer selective gene expression and therapy mediated by recombinant adenoviruses containing the DF3/MUC1 promoter. | Abstract ::: The high molecular weight mucin-like glycoprotein, DF3 (MUC1), is overexpressed in the majority of human breast cancers. Here we demonstrate that replication defective recombinant adenoviral vectors, containing the DF3 promoter (bp -725 to +31), can be used to express beta-galactosidase (Ad.DF3-betagal) and the herpes simplex virus thymidine kinase (HSV-tk) gene (Ad.Df3-tk) in DF3 positive breast carcinoma cell lines. In vivo experiments using breast tumor implants in nude mice injected with Ad.DF3-betagal demonstrated that expression of the beta-galactosidase gene is limited to DF3-positive breast cancer xenografts. Moreover, in an intraperitoneal breast cancer metastases model, we show that i.p. injection of Ad.DF3-tk followed by GCV treatment results in inhibition of tumor growth. These results demonstrate that utilization of the DF3 promoter in an adenoviral vector can confer selective expression of heterologous genes in breast cancer cells in vitro and in vivo. | In this work, we show a mathematical model for the angiogenesis by endothelial cells. We present the model at the level of partial differential equations, describing the spatiotemporal evolution of the cell population, the extracellular matrix macromolecules, the proteases, the tumor angiogenic factors, and the possible presence of inhibitors. We mainly focus, however, on a complementary, more physiologically realistic, hybrid approach in which the cells are treated as individual particles. We examine the model numerically in two-dimensional settings, discussing its comparison with experimental results. | eng_Latn | 19,419 |
Extended kinetic model of real-time polymerase chain reaction process | Real-time polymerase chain reaction (real-time PCR) is the main molecular genetic method used for qualitative and quantitative analysis of specific nucleic acid sequences in many areas of biomedical research. Theoretical study of pCr models allows to estimate the influence of various reaction components and parameters, and to determine the unknown parameter values by approximating the experimental real-time PCR curves. An extended kinetic model of real-time PCR is presented. The model takes into account the enzyme activity based on Michaelis-Menten kinetics, the hybridization of complementary DNA fragments, the presence of a fluorescent probe used for detection of the reaction products, and the temperature dependence of primers and probe hybridization. | © 2012 Fraschini et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Protein Phosphorylation is an Important Tool to Change the Fate of Key Players in the Control of Cell Cycle Progression in Saccharomyces cerevisiae | eng_Latn | 19,420 |
Stability diagram for 4D linear periodic systems with applications to homographic | We consider a family of 4-dimensional Hamiltonian time-periodic linear systems depending on three parameters, λ1, λ2 and e such that for e=0 the system becomes autonomous. Using normal form techniques we study stability and bifurcations for e>0 small enough. We pay special attention to the d'Alembert case. The results are applied to the study of the linear stability of homographic solutions of the planar three-body problem, for some homogeneous potential of degree −α, 0 | ConspectusThe axioms of stereoelectronic theory constitute an atlas to navigate the contours of molecular space. All too rarely lauded, the advent and development of stereoelectronic theory has been one of organic chemistry’s greatest triumphs. Inevitably, however, in the absence of a comprehensive treatise, many of the field’s pioneers do not receive the veneration that they merit. Rather their legacies are the stereoelectronic pillars that persist in teaching and research. This ubiquity continues to afford practitioners of organic chemistry with an abundance of opportunities for creative endeavor in reaction design, in conceiving novel activation modes, in preorganizing intermediates, or in stabilizing productive transition states and products. Antipodal to steric governance, which mitigates destabilizing nonbonding interactions, stereoelectronic control allows well-defined, often complementary, conformations to be populated. Indeed, the prevalence of stabilizing hyperconjugative interactions in biosynt... | eng_Latn | 19,421 |
Computational Modeling of Collective Cell Migration: Mechanical and Biochemical Aspects | Collective cell migration plays key roles in various physiological and pathological processes in multicellular organisms, including embryonic development, wound healing, and formation of cancer metastases. Such collective migration involves complex crosstalk among cells and their environment at both biochemical and mechanical levels. Here, we review various computational modeling strategies that have been helpful in decoding the dynamics of collective cell migration. Most of such attempts have focused either aspect – mechanical or biochemical regulation of collective cell migration, and have yielded complementary insights. Finally, we suggest some possible ways to integrate these models to gain a more comprehensive understanding of collective cell migration. | 1. First question ::: The definition of the CDC for molecular epidemiology is: “the various techniques derived from immunology, biochemistry, and genetics for typing or subtyping pathogens”. This definition is technology-based and does not make any reference to evolutionary genetic concepts. Do you think that this approach is misleading for medical and epidemiological applications, or do you think that molecular epidemiology can be performed based only on technology? | eng_Latn | 19,422 |
TCF-1 Flips the Switch on Eomes | The interaction between different transcriptional pathways in CD8+ T cell memory remains incompletely understood. In this issue, Zhou et al. (2010) demonstrate an important role for T cell factor 1 in regulating CD8+ T cell memory via control of a second transcription factor, Eomesodermin. | It is shown that under the influence of tunnel currents, superconductors may exhibit a ''first order transition'' to a state with two coexisting energy gaps. An energy and number conserving approximation for the collision operator is used to explicitly take into account in the theory the effect of nonequilibrium phonons. Quantitative predictions for experiments are presented. | eng_Latn | 19,423 |
Cell Migration: A Physically Integrated Molecular Process | The authors are grateful for financial support from the National Institutes of Health (grants GM23244 and GM53905), and to very helpful comments on the manuscript from Elliot Elson, Vlodya Gelfand, Paul Matsudaira, Julie Theriot, and Sally Zigmond. D. A. L. and A. F. H. would also like to thank Alan Wells, and Anna Huttenlocher and Rebecca Sandborg, respectively, for stimulating conversations on this subject, and Sean Palecek for Figure 2Figure 2. Finally, we extend our apologies to all our colleagues in the field whose work we were unable to cite formally because of imposed reference limitations. | The authors summarise semiclassical modelling methods, including drift-diffusion, kinetic transport equation and Monte Carlo simulation approaches, utilised in studies of spin dynamics and transport in semiconductor structures. As a review of the work by the authors' group, several examples of applications of these modelling techniques are presented. | eng_Latn | 19,424 |
Flash FPGA-Based Numerical Pulse-Width Modulator | A pulse-width modulator to drive three-phase AC motors is described. It performs a numerical modulation technique, also known as optimum or calculated modulation, but, in order to reduce hardware resources, a hybrid approach merging that calculated modulation with proportional modulation is proposed. The modulator is tested in a flash-based field programmable gate array (FPGA) implementation. | Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FAMUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. | eng_Latn | 19,425 |
Metabolic dynamics in the human red cell. Part I--A comprehensive kinetic model. | The experimental investigation of the red cell over the last three decades has accumulated extensive biochemical data on its enzymes and metabolites. The goal of this work is to provide a unified theoretical framework for the integration and consistent interpretation of these data by means of a comprehensive mathematical metabolic model of the red cell. This model is described in four parts. Here, we describe the general conception, scope and the biological assumptions of the model. The model is comprised of dynamic mass balances based on stoichiometry and enzyme kinetics with the imposed physico-chemical constraints of osmotic balance and electroneutrality. | Kinematics analysis and Kinematics errors considering structural erro rs calculating formula are deduced.The calculating software i s developed by means of Visual Basic 6.0.senior language The Kinematics analysis of plane linkage mechanism considering structural errors are r ealized by using this software. | eng_Latn | 19,426 |
Protein Phosphorylation is an Important Tool to Change the Fate of Key Players in the Control of Cell Cycle Progression in Saccharomyces cerevisiae | © 2012 Fraschini et al., licensee InTech. This is an open access chapter distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Protein Phosphorylation is an Important Tool to Change the Fate of Key Players in the Control of Cell Cycle Progression in Saccharomyces cerevisiae | Abstract A simple pseudopotential (PP) model developed by us earlier was used here to study lattice dynamics and lattice statics of copper. Comparison of the accuracy attainable in different model calculations of the off-symmetry phonon frequencies was made, and the PP model appeared to be at least as accurate as the embedded atom method (EAM). We suggest that calculation of further lattice properties is necessary to evaluate any microscopic model properly. As an example we give a brief review of the PP model application in the lattice dynamics of alloys including the calculation of frequency shifts in different palladium-based alloys. | eng_Latn | 19,427 |
New insights on the role of paired membrane structures in coronavirus replication | The replication of coronaviruses, as in other positive-strand RNA viruses, is closely tied to the formation of membrane-bound replicative organelles inside infected cells. The proteins responsible for rearranging cellular membranes to form the organelles are conserved not just among the Coronaviridae family members, but across the order Nidovirales. Taken together, these observations suggest that the coronavirus replicative organelle plays an important role in viral replication, perhaps facilitating the production or protection of viral RNA. However, the exact nature of this role, and the specific contexts under which it is important have not been fully elucidated. Here, we collect and interpret the recent experimental evidence about the role and importance of membrane-bound organelles in coronavirus replication. | The Monte Carlo simulation with CORSIKA is ran to simulate EAS events at the high altitude,make certain the selecting criterion to get EAS events with low first interaction height.The hadronic interaction in the forward region from TeV region can be studied by detecting the EAS core of low first interaction height events.It is confirmed that a perfect information of forward region can be gotten by researching the development of cosmic ray with high energy,the hadronic interaction models in the forward region from TeV region can be discussed effectively. | eng_Latn | 19,428 |
On the Impact of Data Scheduling to Reduce Latency for Telephony Signaling Traffic using CMT-SCTP | SCTP is a transport protocol targeted for telephony signaling traffic. Although SCTP from its inception supported multihoming, it has until now not supported concurrent mul- tipath transfer. Howeve ... | This work benchmarks density functional theory, with several different exchange-correlation functionals, for prediction of isotropic one-bond phosphorus-hydrogen NMR spin-spin coupling constants (SSCCs). Our test set consists of experimental SSCCs from 30 diverse molecules representing multiple phosphorus bonding environments. The results suggest the importance of a balance between the choice of correlation functional and the admixture of nonlocal exchange. Overall, standard DFT methods appear to suffice for usefully accurate predictions of (31)P-(1)H SSCCs. | eng_Latn | 19,429 |
Electronic to vibrational-rotational energy transfer in collisions of Na (3 2P) with simple molecules | Abstract Differential cross sections of the process Na* (3 2P) + M(ν = 0) Na(3S) + M(ν′) have been measured for several molecules: H2, D2, N2, O2, CO, CO2, N2O, C2H4. We observed two different types of energy spectra. One of them displays a typically non-resonant electronic to vibrational energy transfer accompanied by a distinct maximum, the other one a near resonant behaviour. | The engineering of ECM in vitro is a critical area of research in tissue engineering. Cells respond to mechanical stimuli and regulate the metabolic functions via mechanotransduction and synthesise ECM. This paper reviews key pathways. In vitro studies of mechanotransduction on macroscopic tissues in specialised automated bioreactors that are capable of mimicking the physiological environment by applying different loads will help us to examine how mechanical loads influence intracellular signalling, subsequent behaviour of cells and the synthesis of ECM components. | eng_Latn | 19,430 |
An Organometallic Compound which Exhibits a DNA Topology-Dependent One-Stranded Intercalation Mode | Understanding how small molecules interact with DNA is essential since it underlies a multitude of pathological conditions and therapeutic interventions. Many different intercalator compounds have been studied because of their activity as mutagens or drugs, but little is known regarding their interaction with nucleosomes, the protein-packaged form of DNA in cells. Here, using crystallographic methods and molecular dynamics simulations, we discovered that adducts formed by [(η(6) -THA)Ru(ethylenediamine)Cl][PF6 ] (THA=5,8,9,10-tetrahydroanthracene; RAED-THA-Cl[PF6 ]) in the nucleosome comprise a novel one-stranded intercalation and DNA distortion mode. Conversely, the THA group in fact remains solvent exposed and does not disrupt base stacking in RAED-THA adducts on B-form DNA. This newly observed DNA binding mode and topology dependence may actually be prevalent and should be considered when studying covalently binding intercalating compounds. | We investigate the spatial quantum properties of the light emitted by a perfectly spatially degenerate optical parametric oscillator (self-imaging OPO). We show that this device produces local squeezing for areas bigger than a coherence are that depends on the crystal length and pump width. Furthermore, it generates local EPR beams in the far field. We show, calculating the eigenmodes of the system, that it is highly multimode for realistic experimental parameters. | eng_Latn | 19,431 |
Nuclear-magnetic control over energy carrier synthesis in living organisms | Synthesis of molecular energy carriers in living organisms is performed by enzymes, molecular “engines.” All of them work only in the presence of magnesium ions. However, if natural magnesium in enzymes is substituted by its pure isotopic form 25Mg, the generation of energy carriers will increase two to three times. This outstanding discovery of the authors of this article underlies the development of new medicines for curing hypoxia and heart failure. | Using a density matrix approach, we study the simplest systems that display both gain and feedback: clusters of 2 to 5 atoms, one of which is pumped. The other atoms supply feedback through multiple scattering of light. We show that, if the atoms are in each other's near field, the system exhibits large gain narrowing and spectral mode redistribution. The observed phenomena are more pronounced if the feedback is enhanced. Our system is to our knowledge the simplest exactly solvable microscopic system which shows the approach to laser oscillation. | eng_Latn | 19,432 |
Compact right-handed (RH) and left-handed (LH) lattice-network unit cells implemented in monolayer printed circuits | The implementation of right-handed (RH) and left-handed (LH) X-type lattice network structures in monolayer printed circuits is investigated in this work. The resulting structures, based on semi-lumped planar elements, are compact, exhibit a broad bandwidth, and can be easily fabricated in conventional microwave substrates since only two metal layers (plus via holes) are required. This latter aspect is the main advantage of the proposed approach as compared to other existing lattice network structures. The circuit model of the structures, including parasitics, is proposed and compared to full wave electromagnetic simulations. Finally, a prototype device has been fabricated, where the baluns for measurement have been added to the input and output ports. Due to the broadband operation, these structures can be of interest for the design of compact enhanced bandwidth and multiband components with superior performance as compared to those based on conventional Π- or T-type artificial lines. | We have developed a common framework for topographic mapping and elastic net algorithms. The considered model is a net of stochastic neurons where steepest descent minimization of its free energy function results in a soft topographic mapping algorithm with elastic synaptic interactions. In a batch-mode, minimization of the free energy function results in an elastic net algorithm with lateral interactions. We show that elastic synaptic interactions can construct a topology in the system as well as the more usual lateral interactions. With no lateral and no synaptic interactions, lowering the temperature leads to a sequence of phase transitions from degenerate ordered to degenerate disordered configurations, and finally to complete disorder. The lateral and synaptic interactions can be viewed respectively as weak parametric and weak force perturbations stabilizing the topological order in the system. | eng_Latn | 19,433 |
Flash Mob Organization in Heterogeneous Wireless Sensor Networks | We present a synchronization algorithm that is able to let the nodes in a sensor network perform a certain task at a given point in time. In contrast to other time synchronization algorithms we do not provide a global time basis that is shared on all nodes. Instead, any node in the network can spontaneously initiate a process that allows the synchronous execution of arbitrary tasks. We show that our approach is advantageous in scenarios where a global time is not needed, because it requires little communication compared with other time synchronization algorithms. ::: ::: We also show that our algorithm works in heterogeneous systems where the hardware provides highly varying clock accuracies. Moreover, heterogeneity does not only affect the hardware, but also the communication channels. We deal with different connection types--from highly unreliable and fluctuative wireless channels to reliable and fast wired connections. | Bioorthogonally activated smart probes greatly facilitate the selective labeling of biomolecules in living system. Herein, we described a novel type of smart probes with tunable reaction rates, high fluorescence turn-on ratio, and easy access. The practicality of such probes was demonstrated by selective labeling of lipid and hCAII in Hela cells. | eng_Latn | 19,434 |
External, extrinsic and intrinsic noise in cellular systems: analogies and implications for protein synthesis | Multicellular systems, typically in bioreactors with one or more feed streams, are under the influences ::: of intrinsic (intra-cellular), extrinsic (inter-cellular) and external (environmental) noise. Of these, ::: intrinsic noise is relatively less important in determining protein synthesis and reactor behavior. ::: Although extrinsic noise and external noise have different origins and controls, they have similarities ::: and interactions. The interactions make it important to control both kinds of noise optimally to enhance ::: the gene expression of a desired protein, and the similarities enable this to be done. These aspects are ::: discussed to evolve a comprehensive noise filtering and control strategy for large bioreactors operated ::: in realistic (noisy) environments. | We argue that in the measured $p_T$ domain of RHIC, collisional rather than the radiative energy loss is the dominant mechanism for jet quenching. Accordingly we calculate nuclear suppression factor for light hadrons by taking only the elastic energy loss in sharp contrast with the previous calculations where only the radiative loss are considered. | eng_Latn | 19,435 |
Comparative Analysis of Free Optical Vibration of Lamination Composite Optical Beams Using the Boubaker Polynomials Expansion Scheme and the Differential Quadrature Method | The effects of stacking sequences of composite laminated optical beams on free vibration frequencies are investigated using two methods: the Boubaker Polynomials Expansion Scheme (pbes) and the Differential Quadrature Method (dqm). In the last decades, these two techniques have been separately performed for obtaining accurate numerical solutions to several initial boundary value problems (Vo et al. 2010, Li et al. 2008, Chen 2003, Hu et al. 2008, Karami et al. 2003, Malekzadeh et al. 2004, Khare et al. 2004, Della and Shu 2005, Ramtekkar et al. 2002, Adam 2003). Conjointly yielded results are compared and discussed. | The concept of molecular structure is fundamental to the practice and understanding of chemistry, but the meaning of this term has evolved and is still evolving. The Born–Oppenheimer separation of electronic and nuclear motions lies at the heart of most modern quantum chemical models of molecular structure. While this separation introduces a great computational and practical simplification, it is neither essential to the conceptual formulation of molecular structure nor universally valid. Going beyond the Born–Oppenheimer approximation introduces new paradigms, bringing fresh insight into the chemistry of fluxional molecules, proteins, superconductors and macroscopic dielectrics, thus opening up new avenues for exploration. But it requires that our ideas of molecular structure need to evolve beyond simple ball-and-stick-type models. | eng_Latn | 19,436 |
Effect of spark repetition rate on the ignition limits of a single tubular combustor | The effect of spark repitition rate on the altitude ignition limits of a single tubular (turbojet engine) combustor was investigated. An increase in sparking rate from 3 to 140 sparks per second reduced the ignition limiting combustor-inlet pressure about 2 to 4 inches of mercury for air-flow rates of 1.87 and 2.80 pounds per second per square foot.520::At 3.75 pounds pe At 3.75 pounds per second per square foot, the corresponding reduction was 4 to 12 inches of mercury. The trend was similar for both low-and high-volatility fuels and for two spark-energy levels. | A fundamental problem in biology is to understand how genetic circuits implement core cellular functions. Time-lapse microscopy techniques are beginning to provide a direct view of circuit dynamics in individual living cells. Unexpectedly, we are discovering that key transcription and regulatory factors pulse on and off repeatedly, and often stochastically, even when cells are maintained in constant conditions. This type of spontaneous dynamic behavior is pervasive, appearing in diverse cell types from microbes to mammalian cells. Here, we review recent work showing how pulsing is generated and controlled by underlying regulatory circuits and how it provides critical capabilities to cells in stress response, signaling, and development. A major theme is the ability of pulsing to enable time-based regulation analogous to strategies used in engineered systems. Thus, pulsatile dynamics is emerging as a central, and still largely unexplored, layer of temporal organization in the cell. | eng_Latn | 19,437 |
Chromatin domains and territories: flexibly rigid. | The nucleus is a highly organized solid-state system, rigid and flexible at the same time, where enzymes are organized in complex processing factories. This is achieved by the organization of nuclear DNA into territories and domains, which allow compartmentalization and compaction without sacrificing accessibility. The present review discusses the implications of the organization of chromosomal domains and territories in development and carcinogenesis. | We show that if a CR homeomorphism can be holomorphically extended to a neighborhood of a nonminimal point (in Tumanov's sense), then the extended map is proper, and, near a minimal point, the holomorphic extension is biholomorphic in a neighborhood of the point. | eng_Latn | 19,438 |
Heterotic string in background gauge fields | Abstract The higher order corrections to the two-dimensional nonlinear σ-model for the heterotic string are considered. The divergent parts of the effective action are calculated explicitly to two-loop order in the presence of arbitrary background gauge fields. It is shown that the full gauge Chern-Simons term appears in the divergent terms. We also discuss its relevance to the equations of motion for the massless modes of the heterotic string with emphasis on the local gauge invariance of the heterotic string theory. | Carbon-13 nuclear magnetic resonance studies were made on mouse hemoglobin specifically labeled at the C-2 histidine position. Measurement of the spin lattice relaxation times of the label before and after hemolysis of the erythrocytes provides information on the intracellular fluid viscosities. | eng_Latn | 19,439 |
Modeling of Ribosome Dynamics on a ds-mRNA under an External Load | Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to the recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using our model, we study the translation rate in different biological relevant situations in the presence of external force and the translation through the RNA double stranded region in the absence or presence of the external force. In the present study, we give a quantitative theory for translation rate and show that the ribosome behaves more like a Brownian Ratchet motor. Our findings could shed some light on understanding behaviors of the ribosome in biological conditions. | The aim of this thesis is to propose a new efficient numerical tool, based on the ::: kinematic theorem of limit analysis, for the study of masonry shell and 3D ::: structures with or without FRP reinforcement. ::: The approach consists of two steps. In step I unreinforced masonry strength ::: domains are obtained with a FE limit analysis procedure applied to a representative ::: element of volume constituted by a central brick interacting with its six neighbours ::: by means of rigid plastic interfaces (mortar joint). In step II, the unreinforced ::: strength domains are implemented in a novel upper bound FE limit analysis code ::: for the analysis at collapse of entire masonry curved and 3D structures. | eng_Latn | 19,440 |
Straightforward Synthesis of Cysteine-Reactive Telechelic Polystyrene | Synthesis of a thiol-reactive telechelic polystyrene and conjugation of cysteine is reported. A dimethylfulvene-protected maleimide-functionalized atom transfer radical polymerization (ATRP) initiator (3) was synthesized, and the thermostability was compared to the analogous furan-protected initiator (1) by thermogravometric analysis (TGA). The former protecting group was stable to a higher temperature than the latter in the bulk phase (143 °C vs 125 °C) and thus was investigated as an initiator for the ATRP of styrene. Kinetic studies of the polymerization of styrene mediated by copper(I)/N,N,N‘,N‘ ‘,N‘ ‘-pentamethyldiethylenetriamine (PMDETA) indicated that the reaction proceeded in a controlled manner with high initiator efficiency (92%). Polystyrene with a number-average molecular weight (Mn) of 2530 Da and a narrow polydispersity index (PDI) of 1.15 was then synthesized and subjected to atom transfer radical (ATR) coupling to form the bis-functionalized polymer. Gel permeation chromatography (GPC) an... | Nuclear organization can impact on all aspects of the genome life cycle. This organization is thoroughly investigated by advanced imaging and chromosome conformation capture techniques, providing considerable amount of datasets describing the spatial organization of chromosomes. In this review, we will focus on polymer models to describe chromosome statics and dynamics in the yeast Saccharomyces cerevisiae. We suggest that the equilibrium configuration of a polymer chain tethered at both ends and placed in a confined volume is consistent with the current literature, implying that local chromatin interactions play a secondary role in yeast nuclear organization. Future challenges are to reach an integrated multi-scale description of yeast chromosome organization, which is crucially needed to improve our understanding of the regulation of genomic transaction. | eng_Latn | 19,441 |
Synaptic transmission as a cooperative phenomenon in confined systems | In this review paper, the theory of synaptic transmission (ST) was developed and discussed. We used the hypothesis of isomorphism between: (a) the cooperative behavior of mediators --- acetylcholine molecules (ACh) and cholinoreceptors in a synaptic cleft with binding into mediator-receptor (AChR) complexes, (b) the critical phenomena in confined binary liquid mixtures. The systems of two (or three) nonlinear differential equations were proposed to find the change of concentrations of ACh, AChR complexes, and ferment acetylcholinesterase. The main findings of our study: the linear size of the activation zone was evaluated; the process of postsynaptic membrane activation was described as a cooperative process; different approximations of ACh synchronous release were examined; stationary states and types of singular points were studied for the proposed models of ST; the nonlinear kinetic model with three order parameters demonstrated a strange-attractor behavior. | We present a novel approach to the synchronization problem. It is a well-known fact that a problem of finding minimal (or: the shortest) synchronizing word (MSW) for a given synchronizing automaton is NP-complete. In this paper we present the genetic algorithm which tries, for a given automaton, to find possibly short word that synchronizes it. We use a modified version of a classical simple genetic algorithm (SGA). | eng_Latn | 19,442 |
In vitro construction of yeast tRNAAsp variants: nucleotide substitutions and additions in T-stem and T-loop. | A procedure for the construction of 3'-end labelled yeast tRNAAsp harboring substitutions or additions of any desired nucleotide in T-stem and T-loop (position 57 to 61) has been developed. This was done by in vitro enzymatic manipulations of the yeast tRNAAsp involving specific hydrolysis with RNases, phosphorylation and dephosphorylation with T4 polynucleotide kinase and ligation with T4 RNA ligase. Using this procedure we have replaced conserved or semi-conserved nucleotides located in position 57 to 61 of yeast tRNAAsp. We have also constructed different yeast tRNAAsp with eight bases instead of seven in T-loop. Further use of these tRNAAsp variants will be discussed with the help of the crystallographic three-dimensional structure. | Tailor-made additives are generally designed by optimizing the chemical compatibility between an adsorbing additive and a flat crystalline surface. Crystal growth, however, mainly takes place at step edges where growth units incorporate into the advancing step. In this paper, a new method is introduced that quantifies the importance of all possible growth site configurations from Monte Carlo crystal growth simulations, taking the crystalline surface, steps, and other configurations into account. This allows the identification of growth site configurations that are good candidates for a blocking strategy using tailor-made additives. Application to an anisotropic Kossel model shows that the importance of growth sites at step edges is equal to or higher than the importance of growth sites at a flat crystalline surface. As a “real-world” example, aspartame phase II-A, which has a needle-like morphology, is studied. When comparing the needle side faces with faces on top of the needle, it turns out that there a... | eng_Latn | 19,443 |
Histological structural abnormalities of superficial temporal arteries used for extracranial-intracranial anastomosis | ✓ Histological evaluation of the superficial temporal artery resected at the time of extracranial-intracranial anastomosis was performed in 64 consecutive patients. A neuropathologist who was not aware of the medical condition of these patients studied all specimens under light microscopy with hemotoxylin and eosin, Verhoff, and Mallory strains. Intimal proliferation was observed in 62 samples, intimal fibrosis in 56, fragmentation of the internal elastic lamina in 45, splitting of the internal elastic lamina in 41, fragmentation of the media in 38, and fragmentation of the minimal external elastic tissue in 17. Stenosis of the vessel was observed, and graded from 0% to 50%, with a mean of 20%. The development of intraluminal stenosis was considered to be secondary to the development of intimal fibrosis and hyperplasia. The changes observed were progressive and conformed with those previously described; there was no evidence of correlation with sex, diabetes, or hypertension. The implications for the deve... | In this work, we show a mathematical model for the angiogenesis by endothelial cells. We present the model at the level of partial differential equations, describing the spatiotemporal evolution of the cell population, the extracellular matrix macromolecules, the proteases, the tumor angiogenic factors, and the possible presence of inhibitors. We mainly focus, however, on a complementary, more physiologically realistic, hybrid approach in which the cells are treated as individual particles. We examine the model numerically in two-dimensional settings, discussing its comparison with experimental results. | eng_Latn | 19,444 |
Conformational Dynamics Simulations of Proteins | Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FAMUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. | Analytical procedure, utilizing matrix algebra, is developed for determining longitudinal stresses, transverse moments, and vertical deflections in folded plate structures; sequence of matrix operations can be readily programmed for digital computer having available matrix subroutines; sequence programmed for IBM 704 digital computer is described. | eng_Latn | 19,445 |
Magnetic field design for ‘dynamical’ neutron polarization | The method of ‘dynamical polarization’ allows in principle to polarize a beam of slow neutrons in a completely loss-free way just by interaction with magnetic fields of proper space and time-dependence. In this work we describe the mathematical approach to find out the optimal field configuration for such a novel kind of neutron polarizer. | We attempt quantitative implementation of a previous suggestion that asymmetric charge neutralization of DNA phosphate groups may provide part of the driving force for nucleosome folding. Polyelectrolyte theory can be used to estimate the effective compressive force acting along the length of one side of the DNA surface when a fraction of the phosphate groups are neutralized by histones bound to that side. A standard engineering formula then relates the force to the bending amplitude caused by it. Calculated bending amplitudes are consistent with the curvature of nucleosomal DNA and the overall extent of charge neutralization by the histones. The relation of the model to various aspects of nucleosome folding, including the detailed path of core-particle DNA, is discussed. Several other DNA-protein complexes are listed as examples of possible asymmetric charge-induced bending. | eng_Latn | 19,446 |
Evidence for a loop mechanism of protein transport by the thylakoid Delta pH pathway. | The thylakoid Delta pH pathway is a protein transport system with unprecedented characteristics. To investigate its mechanism, the topology of precursor insertion was determined. A fusion protein comprising a large polypeptide domain fused to the amino terminus of pOE17 (a Delta pH pathway precursor) was efficiently processed by thylakoid membranes. The amino terminus, including the targeting peptide, remained on the cis side of the membrane. Mature OE17 was transported to the lumen. These experiments demonstrate that Delta pH directed precursors enter the thylakoid membrane in a loop, implying that the Delta pH pathway has evolved from an export-type protein translocation system. | A delayed periodic Holling-type predator-prey model without instantaneous negative feedback is investigated. By using the continuation theorem of coincidence degree theory and by constructing suitable Lyapunov functionals, a set of easily verifiable sufficient conditions are derived for the existence, uniqueness and global stability of positive periodic solutions to the model. Numerical simulation is carried out to illustrate the feasibility of our main results. | eng_Latn | 19,447 |
Alignment of H(2p) in collisions of protons and antiprotons with hydrogen atoms with screened Coulomb interaction | The effects of screened Coulomb interaction on the alignment of H(2p ) state produced in collisions of hydrogen atoms with protons and antiprotons are investigated in the energy range 1–200 keV by using the two-center atomic orbital close-coupling (TC-AOCC) method. It is shown that the decrease of the binding energy of hydrogen nl -states and the reduction of the number of bound states with increasing the strength of the screening affect significantly the alignment degree and its energy dependence. In the case of antiproton-H collision the difference between the alignments with screened and unscreened Coulomb potential increases with increasing the strength of the screening in the entire energy range above 2 keV/u, while in the case of proton-H collision it does so only in the energy range 5–25 keV/u. | We attempt quantitative implementation of a previous suggestion that asymmetric charge neutralization of DNA phosphate groups may provide part of the driving force for nucleosome folding. Polyelectrolyte theory can be used to estimate the effective compressive force acting along the length of one side of the DNA surface when a fraction of the phosphate groups are neutralized by histones bound to that side. A standard engineering formula then relates the force to the bending amplitude caused by it. Calculated bending amplitudes are consistent with the curvature of nucleosomal DNA and the overall extent of charge neutralization by the histones. The relation of the model to various aspects of nucleosome folding, including the detailed path of core-particle DNA, is discussed. Several other DNA-protein complexes are listed as examples of possible asymmetric charge-induced bending. | eng_Latn | 19,448 |
Structural Insights into Ring Formation of Cohesin and Related Smc Complexes | Cohesin facilitates sister chromatid cohesion through the formation of a large ring structure that encircles DNA. Its function relies on two structural maintenance of chromosomes (Smc) proteins, which are found in almost all organisms tested, from bacteria to humans. In accordance with their ubiquity, Smc complexes, such as cohesin, condensin, Smc5-6, and the dosage compensation complex, affect almost all processes of DNA homeostasis. Although their precise molecular mechanism remains enigmatic, here we provide an overview of the architecture of eukaryotic Smc complexes with a particular focus on cohesin, which has seen the most progress recently. Given the evident conservation of many structural features between Smc complexes, it is expected that architecture and topology will have a significant role when deciphering their precise molecular mechanisms. | In this paper we consider certain prop- erties of an general access structure and its dual. In particular we prove that corer = corerL. We also es- tablish a new upper bound for the size of MSP, which computes connected access structure I?. We show that the size of a MSP is limited above by the sum of the number of minimal and the number of maximal sets minus one. This is the first upper bound on the size of MSPs to our knowledge. | eng_Latn | 19,449 |
Synthesis of Colloidal Graphene by Electrochemical Exfoliation of Graphite in Lithium Sulphate | Abstract We report the synthesis of colloidal graphene via electrochemical exfoliation of graphite in Li 2 SO 4 aqueous solution. In this electrochemical exfoliation method, high quality graphene was prepared within short time of 1.5 hr. This electrochemical exfoliation mechanism suggests that SO 4 2- and H 2 O are intercalated into graphite sheets and as a result single and few-layer graphene sheets are produced with SO 2 and O 2 gases. The electrochemically exfoliated colloidal graphene was stable in NMP solvent for more than 2 weeks. The colloidal graphene was used for preparing the conducting graphene electrodes by brush painting on A4 paper for flexible supercapacitor applications. Our method exhibits potential for large-scale synthesis of good-quality graphene and its applications in flexible energy storage devices such as supercapacitors. | Abstract ::: Unlike tailed bacteriophages, which use a preformed tail for transporting their genomes into a host bacterium, the ssDNA bacteriophage ΦX174 is tailless. Using cryo-electron microscopy and time-resolved small-angle X-ray scattering, we show that lipopolysaccharides (LPS) form bilayers that interact with ΦX174 at an icosahedral fivefold vertex and induce single-stranded (ss) DNA genome ejection. The structures of ΦX174 complexed with LPS have been determined for the pre- and post-ssDNA ejection states. The ejection is initiated by the loss of the G protein spike that encounters the LPS, followed by conformational changes of two polypeptide loops on the major capsid F proteins. One of these loops mediates viral attachment, and the other participates in making the fivefold channel at the vertex contacting the LPS. | eng_Latn | 19,450 |
18.1: Development of a permanent magnet focused Ka-band klystron | A 2 kW cw, 34.365 GHz, permanent magnet focused klystron with over 150 MHz of −1 dB instantaneous bandwidth has been developed for NASA's Juno mission. The design and test results are presented. | Nuclear organization can impact on all aspects of the genome life cycle. This organization is thoroughly investigated by advanced imaging and chromosome conformation capture techniques, providing considerable amount of datasets describing the spatial organization of chromosomes. In this review, we will focus on polymer models to describe chromosome statics and dynamics in the yeast Saccharomyces cerevisiae. We suggest that the equilibrium configuration of a polymer chain tethered at both ends and placed in a confined volume is consistent with the current literature, implying that local chromatin interactions play a secondary role in yeast nuclear organization. Future challenges are to reach an integrated multi-scale description of yeast chromosome organization, which is crucially needed to improve our understanding of the regulation of genomic transaction. | eng_Latn | 19,451 |
Vibrational energies of monodeuterated dimethyl ether based on high level ab initio potential energy surfaces | Abstract Torsion and COC bending vibrational energies for monodeuterated dimethyl ether are reported. A total number of 78 torsion-bending sublevels below 700 cm −1 have been obtained using a three dimensional Hamiltonian at a CCSD(T)/aug-cc-VTZ level of theory. Guided by the results obtained for other dimethyl ether isotopologues, the Hamiltonian parameters have been readjusted to obtain a spectrum that is expected to lie closer to future experimental results. In addition to this, a torsional-torsional two dimensional potential has been derived projecting the three dimensional potential energy surface and the torsional barrier height and level splitting magnitudes have also been reckoned. | Bioorthogonal metabolic DNA labeling with fluorochromes is a powerful strategy to visualize DNA molecules and their functions. Here, we report the development of a new DNA metabolic labeling strategy enabled by the catalyst-free bioorthogonal ligation using vinyl thioether modified thymidine and o-quinolinone quinone methide. With the newly designed vinyl thioether-modified thymidine (VTdT), we added labeling tags on cellular DNA, which could further be linked to fluorochromes in cells. Therefore, we successfully visualized the DNA localization within cells as well as single DNA molecules without other staining reagents. In addition, we further characterized this bioorthogonal DNA metabolic labeling using DNase I digestion, MS characterization of VTdT as well as VTdT-oQQF conjugate in cell nuclei or mitochondria. This technique provides a powerful strategy to study DNA in cells, which paves the way to achieve future spatiotemporal deciphering of DNA synthesis and functions. | eng_Latn | 19,452 |
Theory of Accretion Disks I: Angular Momentum Transport Processes | Accretion disk flow is a common phenomenon in astrophysics. It provides the nursery for planetary system formation and the channel for mass transfer in interacting binary stars. Such flows are also associated with the central engine for active galactic nuclei. Mass is redistributed in accretion disks as a consequence of angular momentum transfer. The identification of the dominant process involved is an important task in the development of accretion disk theory. Here, we review recent theoretical investigations on several important physical processes, including: 1. the removal of angular momentum from disks through hydromagnetic winds, 2. the amplification of local viscous stress through the onset of turbulence resulting from possible hydromagnetic, convective, or shear flow instabilities, 3. the transport of angular momentum carried by propagating waves, and 4. torque resulting from the presence of nonaxisymmetric unstable modes in self-gravitating and geometrically thick disks. Because of the technical ... | Fluorescence microscopic analysis of cytoskeletal organization and dynamics, Yu-li-Wang an ultrastructural approach to understanding the cytoskeleton, John H. Hartwig actin filament assembly and organization in vitro, John A. Cooper mapping structural and functional domains in actin-binding proteins, Paul Matsudaira the generation and isolation of mutant actins, R. Kimberley Cook and Peter A. Rubinstein association of cytoskeletal proteins with membranes, Carolie A. Carothers Carraway analysis of microtubule dynamics in vitro, Robley C. Williams, Jr methods for the purification and assay of microtubule-associated motility proteins, Roger D. Sloboda methods for studying the cytoskeleton in yeast, P. Solomon et al studying intermediate filaments, Alberto Domingo et al. | kor_Hang | 19,453 |
Driven flow with exclusion and transport in graphene-like structures | The totally asymmetric simple exclusion process (TASEP), a well-known model in its strictly one-dimensional (chain) version, is generalized to cylinder (nanotube) and ribbon (nanoribbon) geometries. A mean-field theoretical description is given for very narrow ribbons ("necklaces"), and nanotubes. For specific configurations of bond transmissivity rates, and for a variety of boundary conditions, theory predicts equivalent steady state behavior between (sublattices on) these structures and chains. This is verified by numerical simulations, to excellent accuracy, by evaluating steady-state currents. We also numerically treat ribbons of general width. We examine the adequacy of this model to the description of electronic transport in carbon nanotubes and nanoribbons, or specifically-designed quantum dot arrays. | 1. ::: ::: A complex type of intercellular contact, requiring cluster formation among three cells or more, is a prerequisite to growth control for a large number of established fibroblast lines. ::: ::: ::: ::: ::: 2. ::: ::: This form of contact occurs at lowest cell densities among cells that synthesize a specific protein that blocks intercellular WGA agglutination. ::: ::: ::: ::: ::: 3. ::: ::: High saturation density cells, lacking this protein, are rapidly agglutinated by WGA. ::: ::: ::: ::: ::: 4. ::: ::: Low saturation density cells, including a line containing SV40 T antigen and the SV40 genome, make this protein, and consequently are agglutinated poorly. ::: ::: ::: ::: ::: 5. ::: ::: The presence of the SV40 genome and SV40 T antigen are not sufficient to guarantee that a cell lines will have a high saturation density or that it will respond well to the WGA agglutinin. | eng_Latn | 19,454 |
Coherent synchrotron radiation of a bunch of particles | The dependence on the size and shape of a particle bunch is found for the region of the synchrotron radiation spectrum in the transition from coherent to incoherent radiation. | Nuclear organization can impact on all aspects of the genome life cycle. This organization is thoroughly investigated by advanced imaging and chromosome conformation capture techniques, providing considerable amount of datasets describing the spatial organization of chromosomes. In this review, we will focus on polymer models to describe chromosome statics and dynamics in the yeast Saccharomyces cerevisiae. We suggest that the equilibrium configuration of a polymer chain tethered at both ends and placed in a confined volume is consistent with the current literature, implying that local chromatin interactions play a secondary role in yeast nuclear organization. Future challenges are to reach an integrated multi-scale description of yeast chromosome organization, which is crucially needed to improve our understanding of the regulation of genomic transaction. | eng_Latn | 19,455 |
Narrow Escape: Theory and Applications to Cellular Microdomains | We consider a Brownian particle (molecule, protein) conflned to a bounded domain (a cell or a compartment) by a re∞ecting boundary, except for a small window through which it can escape. The narrow escape problem is to calculate the mean sojourn time before it escapes. This time diverges as the window shrinks, thus rendering the calculation of the mean escape time a singular perturbation problem. We summarize the various asymptotic formulas we obtained for several cases, including regular domains in two and three dimensions and some singular domains in two dimensions. The escape time is linked to many applications, because it corresponds to the mean time it takes for a molecule to hit a target binding site. We review applications in cellular biology. | The DNA sequence of one of the smallest eukaryotic genomes has recently been finished - that of the reduced nucleus, or nucleomorph, of an algal endosymbiont that resides within a cryptomonad host cell. Its sequence promises insights into chloroplast acquisition, the constraints on genome size and the basic workings of eukaryotic cells. | eng_Latn | 19,456 |
From cardiac cells to genetic regulatory networks | A fundamental question in the treatment of cardiac disorders, such as tachycardia and fibrillation, is under what circumstances does such a disorder arise? To answer to this question, we develop a multiaffine hybrid automaton (MHA) cardiac-cell model, and restate the original question as one of identification of the parameter ranges under which the MHA model accurately reproduces the disorder. The MHA model is obtained from the minimal cardiac model of one of the authors (Fenton) by first bringing it into the form of a canonical, genetic regulatory network, and then linearizing its sigmoidal switches, in an optimal way. By leveraging the Rovergene tool for genetic regulatory networks, we are then able to successfully identify the parameter ranges of interest. | In this article, we study a piecewise smooth dynamical system inspired by a previous reduced system modeling compartimentalized brain metabolism. The piecewise system allows the introduction of an autoregulation induced by a feedback of the extracellular or capillary Lactate concentrations on the Capillary Blood Flow. New dynamical phenomena are uncovered and we discuss existence and nature of two equilibrium points, attractive segment, boundary equilibrium and periodic orbits depending of the Capillary Blood Flow. | eng_Latn | 19,457 |
Development of the PID controller and real-time monitoring system for a low-temperature furnace | The PID controller and real-time monitoring system for a low-temperature furnace was developed. The system has two part, the PID controller, and the real-time monitoring part. An Arduino mega2560 microcontroller board was used for measuring and control the furnace temperature. A type-K thermocouple and a MAX31850 IC was applied for a furnace temperature measurement. The microcontroller board and a MAX31850 were connected via the One-wire bus for convert the temperature values and sent to a personal computer. The PID parameters can be varied by a user in the program, which developed by LabVIEW Software on a computer. The laboratory made furnace was established for testing the controller and monitoring system. The results have shown that the temperature with the range of 25-500 degree Celsius can be controlled. By the trial and error method with the PID parameters, kp was 250, Ti was 0.05 and Td was 0.20, the target temperature can be controlled with the maximum error of 1 degree Celsius. | A fundamental problem in biology is to understand how genetic circuits implement core cellular functions. Time-lapse microscopy techniques are beginning to provide a direct view of circuit dynamics in individual living cells. Unexpectedly, we are discovering that key transcription and regulatory factors pulse on and off repeatedly, and often stochastically, even when cells are maintained in constant conditions. This type of spontaneous dynamic behavior is pervasive, appearing in diverse cell types from microbes to mammalian cells. Here, we review recent work showing how pulsing is generated and controlled by underlying regulatory circuits and how it provides critical capabilities to cells in stress response, signaling, and development. A major theme is the ability of pulsing to enable time-based regulation analogous to strategies used in engineered systems. Thus, pulsatile dynamics is emerging as a central, and still largely unexplored, layer of temporal organization in the cell. | eng_Latn | 19,458 |
Structure of Group II Chaperonin in Open State | Thermosomes are group II chaperonins responsible for protein refolding in an ATP-dependent manner. Little is known regarding the conformational changes of thermosomes during their functional cycle due to lack of high-resolution structure in open state. Here we report the first complete crystal structure of thermosome (rATcpnβ) in open state from Acidianus tengchongensis. There is a ∼30° rotation of the apical and lid domains compared to the previous closed structure. Besides, the structure reveals a conspicuous hydrophobic patch in the lid domain and residues locating in this patch are conserved across species. Both the closed and open forms of rATcpnβ were also reconstructed by electron microscopy (EM). Structural fitting revealed the detailed conformational change from open to closed state. Further cryoEM studies revealed the balance between structural flexibility and stability of chaperonin assembly. | Abstract The spatial configuration of the polysaccharide chain of chitin is discussed. It is concluded that the only arrangement which is sterically satisfactory and fits X-ray diffraction data is that of a “bent” chain. | kor_Hang | 19,459 |
Spatio‐Temporal Parameters of Endosomal Signaling in Cancer: Implications for New Treatment Options | The endo/lysosomal system in cells provides membranous platforms to assemble specific signaling complexes and to terminate signal transduction, thus, is essential for physiological signaling. Endocytic organelles can significantly extend signaling of activated cell surface receptors, and may additionally provide distinct locations for the generation of specific signaling outputs. Failures of regulation at different levels of endocytosis, recycling, degradation as well as aberrations in specific endo/lysosomal signaling pathways, such as mTORC1, might lead to different diseases including cancer. Therefore, a better understanding of spatio-temporal compartmentalization of sub-cellular signaling might provide an opportunity to interfere with aberrant signal transduction in pathological processes by novel combinatorial therapeutic approaches. J. Cell. Biochem. 117: 836–843, 2016. © 2015 The Authors. Journal of Cellular Biochemistry Published by Wiley Periodicals Inc. | Abstract We present a convenient analytical parametrization, in both configuration and momentum spaces, of the deuteron wave-function calculated with the Paris potential. | eng_Latn | 19,460 |
Evolution of small guide RNA genes in hyperthermophilic archaea. | Profiling the RNA production in hyperthermophilic archaea revealed an abundance of small RNA-guided processes near the upper temperature limit of life. Archaea utilize the base-pairing ability of RNA guide sequences to target ribosomal RNAs, transfer RNAs, messenger RNAs, and viral genomes. Cellular processes that are guided by small RNAs include the modification of RNA molecules, trans-splicing, gene regulation, and RNA and DNA degradation. Here, a brief overview of our knowledge on small guide RNA genes in archaeal genomes is provided and examples of their putative roles in genome evolution are described. | AbstractTo understand how cells respond to the nanoscale extracellular environment in vivo, cells from various sources have been cultured on nanoscale patterns fabricated using bottom-up and top-down techniques. Human fetal osteoblasts (hFOBs) and stem cells are some of them and they are known to be overtly responsive to nanoscale topographies – allowing us to investigate the hows and whys of the response in vitro. Information gathered from these in vitro studies could be used to control the cells, i.e. make the stem cells differentiate or retain their characteristics without the use of medium supplements. In this review, hFOB and stem cell responses to nanotopographies are summarized and discussed to shed some light on the influence of patterns on the reactions. Although both types of cells are responsive to nanoscale topographies, the responses are found to be unique to topographical dimension, shape, orientation and the types of cells used. This implies that cellular responses are influenced by multitu... | eng_Latn | 19,461 |
Anisotropy of the transport properties of single-crystal Bi2 Te3 disordered by electron bombardment | Using single-crystal samples of Bi2Te3 bombarded by 5-MeV electrons at a temperature of 250 K, we study the electrical resistivity and the Hall effect in the temperature range 1.7–370 K and the Shubnikov-de Haas effect at T=4.2 K in magnetic fields up to 14 T. We find that electron bombardment of Bi2Te3 crystals results in a transition from the metallic p-type state to the metallic state with a Fermi surface. Annealing at 350 K eliminates the radiation defects and restores the p-type metallic conductance. | The Escherichia coli Ig-binding (Eib) proteins are trimeric autotransporter adhesins (TAAs) and receptors for IgG Fc. We present the structure of a large fragment of the passenger domain of EibD, the first TAA structure to have both a YadA-like head domain and the entire coiled-coil stalk. The stalk begins as a right-handed superhelix, but switches handedness halfway down. An unexpected β-minidomain joins the two and inserts a ∼120° rotation such that there is no net twist between the beginning and end of the stalk. This may be important in folding and autotransport. The surprisingly large cavities we found in EibD and other TAAs may explain how TAAs bend to bind their ligands. We identified how IgA and IgG bind and modeled the EibD-IgG Fc complex. We further show that EibD promotes autoagglutination and biofilm formation and forms a fibrillar layer covering the cell surface making zipper-like contacts between cells. | eng_Latn | 19,462 |
Electric field-enhanced activation of hematoporphyrin derivative: effects on a human tumour cell line. | In a recent report we described the effects of combined electroactivation and photoactivation of hematoporphyrin derivative (HPD) on human erythrocytes and established that activation-induced cell lysis was more pronounced when both modes of activation were sequentially applied to the system. Here we demonstrate that electric field-induced activation of HPD-treated HeLa cells results in cell death. This effect is shown to be dependant on both electric field strength and on HPD concentration. In addition, we demonstrate that exposure of HPD-treated cells to short and intense electric pulses prior to photoactivation, results in increased cell mortality. The results confirm our earlier suggestion that HPD may be activated in the presence of an applied electric field. The results further suggest that activation of photosensitizers using combined exposure to electric fields and light may play an important role in increasing the efficiency of photodynamic therapy (PDT) in the treatment of cancer. | We attempt quantitative implementation of a previous suggestion that asymmetric charge neutralization of DNA phosphate groups may provide part of the driving force for nucleosome folding. Polyelectrolyte theory can be used to estimate the effective compressive force acting along the length of one side of the DNA surface when a fraction of the phosphate groups are neutralized by histones bound to that side. A standard engineering formula then relates the force to the bending amplitude caused by it. Calculated bending amplitudes are consistent with the curvature of nucleosomal DNA and the overall extent of charge neutralization by the histones. The relation of the model to various aspects of nucleosome folding, including the detailed path of core-particle DNA, is discussed. Several other DNA-protein complexes are listed as examples of possible asymmetric charge-induced bending. | eng_Latn | 19,463 |
Analytical results for front pinning between an hexagonal pattern and a uniform state in pattern-formation systems | In pattern-forming systems, localized patterns are states of intermediate complexity between fully extended ordered patterns and completely irregular patterns. They are formed by stationary fronts enclosing an ordered pattern inside an homogeneous background. In two dimensions, the ordered pattern is most often hexagonal and the conditions for fronts to stabilize are still unknown. In this letter, we show how the locking of these fronts depends on their orientation relative to the pattern. The theory rests on general asymptotic arguments valid when the spatial scale of the front is slow compared to that of the hexagonal pattern. Our analytical results are confirmed by numerical simulations with the Swift-Hohenberg equation, relevant to hydrodynamical and buckling instabilities, and a nonlinear optical cavity model. | Linear and cyclic peptides containing the His 6 -Pro 7 -Phe 8 -His 9 sequence of renin's substrate (angiotensinogen) have been shown to be effective competitive inhibitors of the enzyme. Calculations and comparison of low energy structures for these peptides give support to the existence of a β-turn-like structure involving the His-Pro-Phe-His region of the renin substrate and of the competitive inhibitors containing that sequence. This structure may be regarded as a possible “inhibition conformation”, occurring in the process of binding to renin. | eng_Latn | 19,464 |
RNA Interference Therapy for Machado–Joseph Disease: Long-Term Safety Profile of Lentiviral Vectors Encoding Short Hairpin RNAs Targeting Mutant Ataxin-3 | Machado–Joseph disease (MJD) or spinocerebellar ataxia type 3 is a neurodegenerative disorder caused by an abnormal repetition of a CAG codon in the MJD1 gene. This expansion translates into a long... | In this work, we show a mathematical model for the angiogenesis by endothelial cells. We present the model at the level of partial differential equations, describing the spatiotemporal evolution of the cell population, the extracellular matrix macromolecules, the proteases, the tumor angiogenic factors, and the possible presence of inhibitors. We mainly focus, however, on a complementary, more physiologically realistic, hybrid approach in which the cells are treated as individual particles. We examine the model numerically in two-dimensional settings, discussing its comparison with experimental results. | eng_Latn | 19,465 |
Design, analysis and fabrication of a high-performance fractional-slot concentrated winding surface PM machine | A high-performance 55 kW (peak) fractional-slot concentrated winding (FSCW) surface permanent magnet (SPM) machine has been designed to meet demanding performance requirements based on the FreedomCar advanced traction motor requirements prepared by the US Department of Energy. This paper describes key steps in the design, analysis, fabrication, and testing of this machine. Design challenges arising from the high-speed, high-efficiency requirements are presented followed by a discussion of design features that have been introduced to address them. A prototype version of the machine has been fabricated using a segmented stator configuration and segmented neodymium-iron rotor magnets. Test results gathered to date demonstrate promising torque production and efficiency characteristics that are consistent with the machine performance predictions. | Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FAMUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. | eng_Latn | 19,466 |
Design of Hardware about 0-70 V Power Digital Pressure Regulator Based on Doubly Salient Electric Generator | Digital pressure regulator is the core of the power supply system, it decides that the generator system performance is good or bad, the structure of the digital pressure regulator is three pieces of function board and a female version, we make a design about the three pieces which are DSP control board, power board, the control power board from the digital pressure regulator function board at first, then we achieve to make a design of hardware about 0-70 V power digital pressure regulator. | A fundamental problem in biology is to understand how genetic circuits implement core cellular functions. Time-lapse microscopy techniques are beginning to provide a direct view of circuit dynamics in individual living cells. Unexpectedly, we are discovering that key transcription and regulatory factors pulse on and off repeatedly, and often stochastically, even when cells are maintained in constant conditions. This type of spontaneous dynamic behavior is pervasive, appearing in diverse cell types from microbes to mammalian cells. Here, we review recent work showing how pulsing is generated and controlled by underlying regulatory circuits and how it provides critical capabilities to cells in stress response, signaling, and development. A major theme is the ability of pulsing to enable time-based regulation analogous to strategies used in engineered systems. Thus, pulsatile dynamics is emerging as a central, and still largely unexplored, layer of temporal organization in the cell. | eng_Latn | 19,467 |
Stabilization of the activated αMβ2 integrin by a small molecule inhibits leukocyte migration and recruitment | Integrins are potential targets for the development of antiinflammatory agents. Here we develop a novel high-throughput assay by allowing a chemical library to compete with phage display peptide binding and identify a novel small-molecule ligand to the leukocyte-specific αMβ2 integrin. The identified thioxothiazolidine-containing compound, IMB-10, had an unexpected activity in that it stabilized binding of αMβ2 to its endogenous ligands proMMP-9 and fibrinogen. Single amino acid substitutions in the activity-regulating C-terminal helix and the underlying region in the ligand-binding I domain of the integrin suppressed the effect of IMB-10. A computational model indicated that IMB-10 occupies a distinct cavity present only in the activated form of the integrin I domain. IMB-10 inhibited αMβ2-dependent migration in vitro and inflammation-induced neutrophil emigration in vivo. Stabilization of integrin-mediated adhesion by a small molecule is a novel means to inhibit cell migration and may have a utility in ... | A fundamental problem in computational biophysics is to deduce the function of a protein from the structure. Many biological macromolecules such as enzymes, molecular motors or membrane transport proteins perform their function by cycling between multiple conformational states. Understanding such conformational transitions, which typically occur on the millisecond to second time scale, is central to understanding protein function. Molecular dynamics (MD) computer simulations have become an important tool to connect molecular structure to function, but equilibrium MD simulations are rarely able to sample on time scales longer than a few microseconds – orders of magnitudes shorter than the time scales of interest. A range of different simulation methods have been proposed to overcome this time-scale limitation. These include calculations of the free energy landscape and path sampling methods to directly sample transitions between known conformations. All these methods solve the problem to sample infrequentl... | eng_Latn | 19,468 |
Several studies have , however , been done to determine rate preferences for [ 1,5 ] alkyl shifts in cyclic systems : carbonyl and carboxyl > hydride > phenyl and vinyl '' alkyl . | Chemists have determined rate preferences for [ 1,5 ] alkyl shifts in cyclic systems : carbonyl and carboxyl > hydride > phenyl and vinyl '' alkyl . | Crick also used the term `` central dogma '' to summarize an idea that implies that genetic information flow between macromolecules would be essentially one-way : DNA → RNA → Protein In his thinking about the processes linking DNA genes to proteins , Crick made clear the distinction between the materials involved , the energy required , and the information flow . | eng_Latn | 19,469 |
What are some ways to make a maze-solving robot using an ATMega32 microcontroller? | What are the ways to make a maze solving robot? | How would you establish that the configuration of C3,c4 and c5 atoms of glucose and manose are same? | eng_Latn | 19,470 |
What if every cell in your body is slowly replaced by a nano machine equivalent, able to perform each and every function of those biological cells? | What would happen if every cell in your body is slowly replaced by a nano machine equivalent (functionally and structurally identical)? | What if Hillary Clinton hired Trump to sabotage the Republican Party but Trump now believes he can fly solo and become president? | eng_Latn | 19,471 |
Consequence of charging the Odyssey before visiting boss level? I got enough Power Moons to charge the Odyssey before getting to the Showdown on the Inverted Pyramid (Sand Kingdom). When I charged the Odyssey, Bowser flew away and I was asked to choose a fork in the road. It looks like I can still go beat the boss and get the multi-moon on the Inverted Pyramid, but Bowser’s airship is no longer there. Did I miss anything? (Power ups, power moons, etc.?) | If you finish a world without fighting the Broodal, can you still fight them later? I've just seen that in a speedrun: If you collect enough moons to move on to the next world, and cash them in at the ship, the broodal ship just leaves. Does that mean that the Broodal fight wont happen, so you missed the triple moon it gives? Or if you go to the arena, even without the ship you will have the fight happen? Clip where this happens : | why do chaperones bring protein into mitochondria? why would mitochondria need protein? Sounds trivial? Please help to sort out. I saw this picture while looking at dehydration reactions and cell revision. And proceeded to the Protein Folding and Processing in the ER: Various changes occur to proteins in the ER. Chaperones and Folding: Polypeptides must assume the correct folding pattern in order to function properly. The correct folding of a protein is mediated by chaperones (they also are proteins--chaperones are abundant in the ER lumen). A completed polypeptide will assume the correct folding pattern spontaneously, however before translation is complete, it could assume an incorrect formation or it could aggregate with other partially made polypeptides. To prevent this, chaperones in the ER (and cytosol) bind to the nascent polypeptide and keep it from interacting with anything until the polypeptide is completely synthesized. (Chaperones bind to polypeptides destined for mitochondria then release them as they pass through the mitochondrial membranes. Chaperones on the inside of mitochondria bind until these polypeptides have completely entered.) With regards to protein synthesis and folding, this kind of info is not in my textbook. Not in couple of the online open textbooks either. I even search for where do protein fold? to find out if there was a relationship. It doesn't say protein fold in mitochondria and turns out it's a question most scientist are looking for answers. For whatever protein synthesis I have learnt so far, there was no mentioning of protein strands going into mitochondria but mitochondria as a power houses. What's going on here? Why would a protein go into a mitochondria? How does it exit and where to? | eng_Latn | 19,472 |
Are intercellular junctions, synapses and light-capturing photosynthetic complexes mobile? | Domains in cell membrane | There are no interfaces on which a capture can be done | eng_Latn | 19,473 |
Protein change in function? | the bacterial flagella is a well studied model used to display the evolution of proteins. For example, there are great similarities between some of the flagellar proteins and those of prokaryotic thype III secretion systems. Proteins that change function over time are generally discovered by different people in different models and thus provided different names. | most definitely, and chemist wish to be smarter to become Physicists ;) | eng_Latn | 19,474 |
Design and characterization of a powered elbow prosthesis | A Multigrasp Hand Prosthesis for Providing Precision and Conformal Grasps | Intercellular mRNA trafficking via membrane nanotube-like extensions in mammalian cells | eng_Latn | 19,475 |
Biomolecular Computing Systems | Algorithmic Self-Assembly of DNA Sierpinski Triangles | Life After Ashby: Ultrastability and the Autopoietic Foundations of Biological Autonomy | kor_Hang | 19,476 |
gDLS: A Scalable Solution to the Generalized Pose and Scale Problem | Go-ICP: Solving 3D Registration Efficiently and Globally Optimally | A dual gold nanoparticle conjugate-based lateral flow assay (LFA) method for the analysis of troponin I. | eng_Latn | 19,477 |
Network models in neuroscience | Beyond the Connectome: The Dynome | Non-canonical amino acids in protein engineering. | eng_Latn | 19,478 |
VisiCon: a robot control interface for visualizing manipulation using a handheld projector | A self-correcting projector | Cardiolipin membrane domains in prokaryotes and eukaryotes. | eng_Latn | 19,479 |
feature - based vector simulation of water waves . | Curl-noise for procedural fluid flow | Rewiring yeast acetate metabolism through MPC1 loss of function leads to mitochondrial damage and decreases chronological lifespan | eng_Latn | 19,480 |
Efficient SIMD code generation for runtime alignment and length conversion | Automatic Intra-Register Vectorization for the Intel® Architecture | Detecting individual extracellular vesicles using a multicolor in situ proximity ligation assay with flow cytometric readout | eng_Latn | 19,481 |
On computing task-oriented grasps | On the implementation of an interior-point filter line-search algorithm for large-scale nonlinear programming | Osmotic Stress Signaling and Osmoadaptation in Yeasts | eng_Latn | 19,482 |
A simplified extension of the Area under the ROC to the multiclass domain | Basic principles of ROC analysis | A computational model of cell polarization and motility coupling mechanics and biochemistry | eng_Latn | 19,483 |
Graph rigidity and distributed formation stabilization of multi-vehicle systems | INFORMATION FLOW AND COOPERATIVE CONTROL OF VEHICLE FORMATIONS | THE CARBON MONOXIDE-BINDING PIGMENT OF LIVER MICROSOMES. I. EVIDENCE FOR ITS HEMOPROTEIN NATURE. | eng_Latn | 19,484 |
An Integrated Web-based Interactive Data Platform for Molecular Dynamics Simulations | GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit | health benefits of fruit and vegetables are from additive and synergistic combinations of phytochemicals . | kor_Hang | 19,485 |
Learning Algorithms from Data | Laplacian Eigenmaps and Spectral Techniques for Embedding and Clustering | A D53 repression motif induces oligomerization of TOPLESS corepressors and promotes assembly of a corepressor-nucleosome complex | kor_Hang | 19,486 |
Artificial Mitochondria Transfer: Current Challenges, Advances, and Future Applications | Cell Connections by Tunneling Nanotubes: Effects of Mitochondrial Trafficking on Target Cell Metabolism, Homeostasis, and Response to Therapy | the local binary pattern approach to texture analysis - extensions and applications . | kor_Hang | 19,487 |
TyTAN: tiny trust anchor for tiny devices | Innovative Instructions and Software Model for Isolated Execution | Biomolecular Simulation: A Computational Microscope for Molecular Biology | eng_Latn | 19,488 |
The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications | The large-scale organization of metabolic networks | deformation constraints in a mass - spring model to describe rigid cloth behavior . | eng_Latn | 19,489 |
Active shape models their training and application | Fitting Parameterized Three-Dimensional Models to Images | The interferon response to intracellular DNA:why so many receptors? | eng_Latn | 19,490 |
Engaging the ethics of data science in practice | Inherent Trade-Offs in the Fair Determination of Risk Scores | Determining Charge Transport Pathways through Single Porphyrin Molecules Using Scanning Tunneling Microscopy Break Junctions | eng_Latn | 19,491 |
We demonstrate single-molecule fluorescence imaging beyond the optical diffraction limit in 3 dimensions with a wide-field microscope that exhibits a double-helix point spread function (DH-PSF). The DH-PSF design features high and uniform Fisher information and has 2 dominant lobes in the image plane whose angular orientation rotates with the axial (z) position of the emitter. Single fluorescent molecules in a thick polymer sample are localized in single 500-ms acquisitions with 10- to 20-nm precision over a large depth of field (2 microm) by finding the center of the 2 DH-PSF lobes. By using a photoactivatable fluorophore, repeated imaging of sparse subsets with a DH-PSF microscope provides superresolution imaging of high concentrations of molecules in all 3 dimensions. The combination of optical PSF design and digital postprocessing with photoactivatable fluorophores opens up avenues for improving 3D imaging resolution beyond the Rayleigh diffraction limit.. Title: Attempted suicide in Europe: rates, trends and sociodemographic characteristics of suicide attempters during the period 1989-1992. Results of the WHO/EURO Multicentre Study on Parasuicide. | Recently, single-molecule imaging and photocontrol have enabled superresolution optical microscopy of cellular structures beyond Abbe's diffraction limit, extending the frontier of noninvasive imaging of structures within living cells. However, live-cell superresolution imaging has been challenged by the need to image three-dimensional (3D) structures relative to their biological context, such as the cellular membrane. We have developed a technique, termed superresolution by power-dependent active intermittency and points accumulation for imaging in nanoscale topography (SPRAIPAINT) that combines imaging of intracellular enhanced YFP (eYFP) fusions (SPRAI) with stochastic localization of the cell surface (PAINT) to image two different fluorophores sequentially with only one laser. Simple light-induced blinking of eYFP and collisional flux onto the cell surface by Nile red are used to achieve single-molecule localizations, without any antibody labeling, cell membrane permeabilization, or thiol-oxygen scavenger systems required. Here we demonstrate live-cell 3D superresolution imaging of Crescentin-eYFP, a cytoskeletal fluorescent protein fusion, colocalized with the surface of the bacterium Caulobacter crescentus using a double-helix point spread function microscope. Three-dimensional colocalization of intracellular protein structures and the cell surface with superresolution optical microscopy opens the door for the analysis of protein interactions in living cells with excellent precision (20-40 nm in 3D) over a large field of view (12 12 μm).. Title: A randomized trial of aspirin to prevent colorectal adenomas in patients with previous colorectal cancer. | Optical imaging of the dynamics of living specimens involves tradeoffs between spatial resolution, temporal resolution, and phototoxicity, made more difficult in three dimensions. Here, however, we report that rapid three-dimensional (3D) dynamics can be studied beyond the diffraction limit in thick or densely fluorescent living specimens over many time points by combining ultrathin planar illumination produced by scanned Bessel beams with super-resolution structured illumination microscopy. We demonstrate in vivo karyotyping of chromosomes during mitosis and identify different dynamics for the actin cytoskeleton at the dorsal and ventral surfaces of fibroblasts. Compared to spinning disk confocal microscopy, we demonstrate substantially reduced photodamage when imaging rapid morphological changes in D. discoideum cells, as well as improved contrast and resolution at depth within developing C. elegans embryos. Bessel beam structured plane illumination thus promises new insights into complex biological phenomena that require 4D subcellular spatiotemporal detail in either a single or multicellular context.. Title: Noninvasive Imaging beyond the Diffraction Limit of 3D Dynamics in Thickly Fluorescent Specimens | eng_Latn | 19,492 |
Oscillations in patterns of expression of a large fraction of yeast genes are associated with the "metabolic cycle," usually seen only in prestarved, continuous cultures of yeast. We used FISH of mRNA in individual cells to test the hypothesis that these oscillations happen in single cells drawn from unsynchronized cultures growing exponentially in chemostats. Gene-expression data from synchronized cultures were used to predict coincident appearance of mRNAs from pairs of genes in the unsynchronized cells. Quantitative analysis of the FISH results shows that individual unsynchronized cells growing slowly because of glucose limitation or phosphate limitation show the predicted oscillations. We conclude that the yeast metabolic cycle is an intrinsic property of yeast metabolism and does not depend on either synchronization or external limitation of growth by the carbon source.. Title: A clinical approach to circadian rhythm sleep disorders. | Daily synchronous rhythms of cell division at the tissue or organism level are observed in many species and suggest that the circadian clock and cell cycle oscillators are coupled. For mammals, despite known mechanistic interactions, the effect of such coupling on clock and cell cycle progression, and hence its biological relevance, is not understood. In particular, we do not know how the temporal organization of cell division at the single-cell level produces this daily rhythm at the tissue level. Here we use multispectral imaging of single live cells, computational methods, and mathematical modeling to address this question in proliferating mouse fibroblasts. We show that in unsynchronized cells the cell cycle and circadian clock robustly phase lock each other in a 1:1 fashion so that in an expanding cell population the two oscillators oscillate in a synchronized way with a common frequency. Dexamethasone-induced synchronization reveals additional clock states. As well as the low-period phase-locked state there are distinct coexisting states with a significantly higher period clock. Cells transition to these states after dexamethasone synchronization. The temporal coordination of cell division by phase locking to the clock at a single-cell level has significant implications because disordered circadian function is increasingly being linked to the pathogenesis of many diseases, including cancer.. Title: Children's estimates of food portion size: the development and evaluation of three portion size assessment tools for use with children. | Budding yeast grown under continuous, nutrient-limited conditions exhibit robust, highly periodic cycles in the form of respiratory bursts. Microarray studies reveal that over half of the yeast genome is expressed periodically during these metabolic cycles. Genes encoding proteins having a common function exhibit similar temporal expression patterns, and genes specifying functions associated with energy and metabolism tend to be expressed with exceptionally robust periodicity. Essential cellular and metabolic events occur in synchrony with the metabolic cycle, demonstrating that key processes in a simple eukaryotic cell are compartmentalized in time.. Title: Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. | eng_Latn | 19,493 |
Pattern formation of biological structures involves organizing different types of cells into a spatial configuration. In this study, we investigate the physical basis of biological patterning of the Drosophila retina in vivo. We demonstrate that E- and N-cadherins mediate apical adhesion between retina epithelial cells. Differential expression of N-cadherin within a sub-group of retinal cells (cone cells) causes them to form an overall shape that minimizes their surface contact with surrounding cells. The cells within this group, in both normal and experimentally manipulated conditions, pack together in the same way as soap bubbles do. The shaping of the cone cell group and packing of its components precisely imitate the physical tendency for surfaces to be minimized. Thus, simple patterned expression of N-cadherin results in a complex spatial pattern of cells owing to cellular surface mechanics.. Title: The Ran GTPase regulates mitotic spindle assembly | Subdividing proliferating tissues into compartments is an evolutionarily conserved strategy of animal development [1-6]. Signals across boundaries between compartments can result in local expression of secreted proteins organizing growth and patterning of tissues [1-6]. Sharp and straight interfaces between compartments are crucial for stabilizing the position of such organizers and therefore for precise implementation of body plans. Maintaining boundaries in proliferating tissues requires mechanisms to counteract cell rearrangements caused by cell division; however, the nature of such mechanisms remains unclear. Here we quantitatively analyzed cell morphology and the response to the laser ablation of cell bonds in the vicinity of the anteroposterior compartment boundary in developing Drosophila wings. We found that mechanical tension is approximately 2.5-fold increased on cell bonds along this compartment boundary as compared to the remaining tissue. Cell bond tension is decreased in the presence of Y-27632 [7], an inhibitor of Rho-kinase whose main effector is Myosin II [8]. Simulations using a vertex model [9] demonstrate that a 2.5-fold increase in local cell bond tension suffices to guide the rearrangement of cells after cell division to maintain compartment boundaries. Our results provide a physical mechanism in which the local increase in Myosin II-dependent cell bond tension directs cell sorting at compartment boundaries.. Title: Fluconazole prophylaxis: can we eliminate invasive Candida infections in the neonatal ICU? | During pupation, long-range order is imposed on the autonomously developing ommatidia which compose the Drosophila eye. To accomplish this, eight additional cell types arise: the primary, secondary, and tertiary pigment cells, and the four cells that form the bristle. These cells form an interweaving lattice between ommatidia. The lattice is refined when excess cells are removed to bring neighboring ommatidia into register. Recent evidence suggests that in larval development, local contacts direct cell fate. The same appears to be true during pupal development: the contacts a cell makes predict the cell type it will become. Cells which contact the anterior or posterior cone cells in an ommatidium invariably become primary pigment cells. Cells which contact primary pigment cells from different ommatidia become secondary and tertiary pigment cells. Bristle development is in several ways distinct from ommatidial development. The four cells of each bristle group appear to be immediate descendents of a single founder cell. During their early differentiation, they do not make stereotyped contacts with surrounding ommatidial cells, but do make particular contacts within the bristle group. And unlike the surrounding ommatidia, differentiation of the bristles radiates from the center of the eye to the edges. As cells are removed during two stages of programmed cell death, the bristles are brought into their final position. When all cells in the lattice have achieved their final position, a second stage of retinal development begins as structures specific to each cell type are produced. This paper follows these various stages of pupal development, and suggests how local cell-cell contacts may produce the cells needed for a functional retina.. Title: The emergence of order in the Drosophila pupal retina. | eng_Latn | 19,494 |
Cooperation among individuals is necessary for evolutionary transitions to higher levels of biological organization. In such transitions, groups of individuals at one level (such as single cells) cooperate to form selective units at a higher level (such as multicellular organisms). Though the evolution of cooperation is difficult to observe directly in higher eukaryotes, microorganisms do offer such an opportunity. Here we report the evolution of novel cooperative behaviour in experimental lineages of the bacterium Myxococcus xanthus. Wild-type strains of M. xanthus exhibit socially dependent swarming across soft surfaces by a mechanism known as ‘S-motility’ that requires the presence of extracellular type IV pili. In lineages of M. xanthus unable to make pili, a new mechanistic basis for cooperative swarming evolved. Evolved swarming is mediated, at least in part, by enhanced production of an extracellular fibril matrix that binds cells—and their evolutionary interests—together. Though costly to individuals, fibril production greatly enhanced population expansion in groups of interconnected cells. These results show that fundamental transitions to primitive cooperation can readily occur in bacteria.. Title: Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus | Repression of competition within groups joins kin selection as the second major force in the history of life shaping the evolution of cooperation. When opportunities for competition against neighbors are limited within groups, individuals can increase their own success only by enhancing the efficiency and productivity of their group. Thus, characters that repress competition within groups promote cooperation and enhance group success. Leigh first expressed this idea in the context of fair meiosis, in which each chromosome has an equal chance of transmission via gametes. Randomized success means that each part of the genome can increase its own success only by enhancing the total number of progeny and thus increasing the success of the group. Alexander used this insight about repression of competition in fair meiosis to develop his theories for the evolution of human sociality. Alexander argued that human social structures spread when they repress competition within groups and promote successful group-against-group competition. Buss introduced a new example with his suggestion that metazoan success depended on repression of competition between cellular lineages. Maynard Smith synthesized different lines of thought on repression of competition. In this paper, I develop simple mathematical models to illustrate the main processes by which repression of competition evolves. With the concepts made clear, I then explain the history of the idea. I finish by summarizing many new developments in this subject and the most promising lines for future study.. Title: Perspective: repression of competition and the evolution of cooperation. | The organization of cells, emerging from cell-cell interactions, can give rise to collective properties. These properties are adaptive when together cells can face environmental challenges that they separately cannot. One particular challenge that is important for microorganisms is migration. In this study, we show how flagellum-independent migration is driven by the division of labor of two cell types that appear during Bacillus subtilis sliding motility. Cell collectives organize themselves into bundles (called "van Gogh bundles") of tightly aligned cell chains that form filamentous loops at the colony edge. We show, by time-course microscopy, that these loops migrate by pushing themselves away from the colony. The formation of van Gogh bundles depends critically on the synergistic interaction of surfactin-producing and matrix-producing cells. We propose that surfactin-producing cells reduce the friction between cells and their substrate, thereby facilitating matrix-producing cells to form bundles. The folding properties of these bundles determine the rate of colony expansion. Our study illustrates how the simple organization of cells within a community can yield a strong ecological advantage. This is a key factor underlying the diverse origins of multicellularity.. Title: Microvascular and Macrovascular Complications of Diabetes | eng_Latn | 19,495 |
when properly aligned, the enzyme and substrate form an enzyme-substrate (es) | When an enzyme binds its substrate, it forms an enzyme-substrate complex. This complex lowers the activation energy of the reaction and promotes its rapid progression by providing certain ions or chemical groups that actually form covalent bonds with molecules as a necessary step of the reaction process. | INDUCED FIT MODEL. The enzyme s active site has a shape closely complementary to the substrate The substrate locks into the active site of the enzyme. The active site alters its shape holding the substrate more tightly and straining it. An enzyme-substrate complex is formed. | eng_Latn | 19,496 |
what correctly traces the path of a protein in the cell | Best Answer: The protein is synthesized in the rough E.R. A piece of the E.R. then creates something like a bubble around the protein, called a vesicle and travels to the golgi apparatus which is like the shipping center for the cell. The golgi makes modifications to the protein and ships it off to another part of the cell. Therefore the correct answer is A. | As already noted, all of the proteins that enter the secretory pathway contain an ER signal sequence, generally at the N-terminus (see Table 17-1). This sequence directs the ribosomes that are synthesizing these proteins to the rough ER. | eng_Latn | 19,497 |
yeast cells clumps | For yeast, having clumps of amyloid is not fatal. Researchers exposed amyloid-containing cells of bakerâs yeast to 104 F, a temperature that would be a high fever in a human. When exposed to that environment, the cells activated a stress response that changed the clumping proteins back to the no-clumping shape. | But in experiments on yeast, which has many structures similar to those in human cells, the Johns Hopkins scientists unexpectedly found that many of those protein clumps break down in the cell's energy-producing powerhouses, called mitochondria. They also found that too many misfolded proteins can clog up and damage this vital structure. | eng_Latn | 19,498 |
what happens at the active site of an enzyme | In biology, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of residues that form temporary bonds with the substrate (binding site) and residues that catalyse a reaction of that substrate (catalytic site). | Denaturing of enzymes. The important part of an enzyme is called the active site. This is where specific molecules bind to the enzyme and the reaction occurs. Anything that changes the shape of the active site stops the enzyme from working.This is similar to a key that opens a door lock.It does not matter what a key handle looks like, but if you change the shape of the âteethâ the key no longer works.nything that changes the shape of the active site stops the enzyme from working. This is similar to a key that opens a door lock. It does not matter what a key handle looks like, but if you change the shape of the âteethâ the key no longer works. | eng_Latn | 19,499 |
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