Encounters between domestic dogs and free-ranging non-human primates

Records of responses of free-ranging primates to domestic dogs are summarized and evaluated. Although dogs are often considered as potential predators of primates, members of only 7 species of monkey are reported as actually having been killed by dogs. Most injurious or fatal attacks by dogs on primates occur near human settlements in Asia. It is suggested that neither domestic dogs nor wild canids are important predators of primates. Since dogs are often used by hunters, primates probably have a conditioned aversion to them, which is expressed through alarm responses, fleeing, and sometimes aggression.     

Quantitative Protein Localization Signatures Reveal an Association between Spatial and Functional Divergences of Proteins

Protein subcellular localization is a major determinant of protein function. However, this important protein feature is often described in terms of discrete and qualitative categories of subcellular compartments, and therefore it has limited applications in quantitative protein function analyses. Here, we present Protein Localization Analysis and Search Tools (PLAST), an automated analysis framework for constructing and comparing quantitative signatures of protein subcellular localization patterns based on microscopy images. PLAST produces human-interpretable protein localization maps that quantitatively describe the similarities in the localization patterns of proteins and major subcellular compartments, without requiring manual assignment or supervised learning of these compartments. Using the budding yeast Saccharomyces cerevisiae as a model system, we show that PLAST is more accurate than existing, qualitative protein localization annotations in identifying known co-localized proteins. Furthermore, we demonstrate that PLAST can reveal protein localization-function relationships that are not obvious from these annotations. First, we identified proteins that have similar localization patterns and participate in closely-related biological processes, but do not necessarily form stable complexes with each other or localize at the same organelles. Second, we found an association between spatial and functional divergences of proteins during evolution. Surprisingly, as proteins with common ancestors evolve, they tend to develop more diverged subcellular localization patterns, but still occupy similar numbers of compartments. This suggests that divergence of protein localization might be more frequently due to the development of more specific localization patterns over ancestral compartments than the occupation of new compartments. PLAST enables systematic and quantitative analyses of protein localization-function relationships, and will be useful to elucidate protein functions and how these functions were acquired in cells from different organisms or species. A public web interface of PLAST is available at http://plast.bii.a-star.edu.sg.     

Integrative Proteomics and Tissue Microarray Profiling Indicate the Association between Overexpressed Serum Proteins and Non-Small Cell Lung Cancer

Lung cancer is the leading cause of cancer deaths worldwide. Clinically, the treatment of non-small cell lung cancer (NSCLC) can be improved by the early detection and risk screening among population. To meet this need, here we describe the application of extensive peptide level fractionation coupled with label free quantitative proteomics for the discovery of potential serum biomarkers for lung cancer, and the usage of Tissue microarray analysis (TMA) and Multiple reaction monitoring (MRM) assays for the following up validations in the verification phase. Using these state-of-art, currently available clinical proteomic approaches, in the discovery phase we confidently identified 647 serum proteins, and 101 proteins showed a statistically significant association with NSCLC in our 18 discovery samples. This serum proteomic dataset allowed us to discern the differential patterns and abnormal biological processes in the lung cancer blood. Of these proteins, Alpha-1B-glycoprotein (A1BG) and Leucine-rich alpha-2-glycoprotein (LRG1), two plasma glycoproteins with previously unknown function were selected as examples for which TMA and MRM verification were performed in a large sample set consisting about 100 patients. We revealed that A1BG and LRG1 were overexpressed in both the blood level and tumor sections, which can be referred to separate lung cancer patients from healthy cases.     

Kinetics of the Chemiluminescence Associated to the Reaction Between Peroxyl Radicals and Proteins

Protein oxidation, mediated by peroxyl radicals derived from 2,2-azobis(2-amidinopropane) dihydrochloride is sided by a significant visible chemiluminescence (CL). The light emission shows a complex dependence with the protein concentration and with the incubation time that cannot be interpreted in terms of peroxyl radicals recombination (Russell's mechanism). In all the systems studied, the chemiluminescent behavior requires to consider the participation of several oxidation products as precursors of the excited states. These compounds lead to the formation of excited states by competing radical and nonradical mediated pathways. These intermediates (most probably hydroperoxide-like compounds) would arise from the oxidation of Trp and Tyr residues. This conclusion is based on the similarity of the time profile of the chemiluminescence observed in the oxidation of the free amino acids and the proteins, both in the presence of and absence of free-radical scavengers.     

Encounters between aphids and their predators: the relative frequencies of disturbance and consumption

Ecologists may wish to evaluate the potential for predators to suppress prey populations through the costs of induced defensive behaviors as well as through consumption. In this paper, we measure the ratio of non‐consumptive, defense‐inducing encounters relative to consumptive encounters (henceforth the ‘disturbed : consumed ratio’) for two species of aphids and propose that these disturbed : consumed ratios can help evaluate the potential for behaviorally mediated prey suppression. For the pea aphid, Acyrthosiphon pisum (Harris) (Homoptera: Aphididae), the ratio of induced disturbances to consumption events was high, 30 : 1. For the cotton aphid, Aphis gossypii (Glover) (Homoptera: Aphididae), the ratio of induced disturbances to consumption events was low, approximately 1 : 14. These results indicate that the potential for predators to suppress pea aphid populations through induction of defensive behaviors is high, whereas the potential for predators to suppress cotton aphid populations through induced behaviors is low. In measuring the disturbed : consumed ratios of two prey species, this paper makes two novel points: it highlights the variability of the disturbed : consumed ratio, and it offers a simple statistic to help ecologists draw connections between predator–prey behaviors and predator–prey population dynamics.     

The Church of Women: Gendered Encounters between Maasai and Missionaries

The Church of Women: Gendered Encounters between Maasai and Missionaries . Dorothy L. Hodgson. Bloomington: Indiana University Press, 2005.     

Crystallographic Snapshots along the Reaction Pathway of Nucleoside Triphosphate Diphosphohydrolases

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Controlled One-on-One Encounters between Immune Cells and Microbes Reveal Mechanisms of Phagocytosis

Among many challenges facing the battle against infectious disease, one quandary stands out. On the one hand, it is often unclear how well animal models and cell lines mimic human immune behavior. On the other hand, many core methods of cell and molecular biology cannot be applied to human subjects. For example, the profound susceptibility of neutropenic patients to infection marks neutrophils (the most abundant white blood cells in humans) as vital immune defenders. Yet because these cells cannot be cultured or genetically manipulated, there are gaps in our understanding of the behavior of human neutrophils. Here, we discuss an alternative, interdisciplinary strategy to dissect fundamental mechanisms of immune-cell interactions with bacteria and fungi. We show how biophysical analyses of single-live-cell/single-target encounters are revealing universal principles of immune-cell phagocytosis, while also dispelling misconceptions about the minimum required mechanistic determinants of this process.     

Application of the S-Pyridylethylation Reaction to the Elucidation of the Structures and Functions of Proteins

Cysteine (Cys) and cystine residues in proteins are unstable under conditions used for acid hydrolysis of peptide bonds. To overcome this problem, we proposed the use of the S-pyridylethylation reaction to stabilize Cys residues as pyridylethyl-cysteine (PEC) protein derivatives. This suggestion was based on our observation that two synthetic derivatives formed by pyridylethylation of the SH group of Cys with either 2-vinylpyridine (2-VP) or 4-vinylpyridine (4-VP), designated as S--(2-pyridylethyl)-L-cysteine (2-PEC) and S--(4-pyridylethyl)-L-cysteine (4-PEC), were stable under acid conditions used to hydrolyze proteins. This was also the case for protein-bound PEC groups. Since their discovery over 30 years ago, pyridylethylation reactions have been widely modified and automated for the analysis of many structurally different proteins at levels as low as 20 picomoles, to determine the primary structures of proteins and to define the influence of SH groups and disulfide bonds on the structures and functional, enzymatic, medical, nutritional, pharmacological, and toxic properties of proteins isolated from plant, microbial, marine, animal, and human sources. Pyridylethylation has been accepted as the best method for the modification of Cys residues in proteins for subsequent analysis and sequence determination. The reaction has also been proposed to measure D-Cys, homocysteine, glutathione, tryptophan, dehydroalanine, and furanthiol food flavors. This integrated overview of the diverse literature on these reactions emphasizes general concepts. It is intended to serve as a resource and guide for further progress based on the reported application of pyridylethylation reactions to more than 150 proteins.     

Association between income and the hippocampus

Facets of the post-natal environment including the type and complexity of environmental stimuli, the quality of parenting behaviors, and the amount and type of stress experienced by a child affects brain and behavioral functioning. Poverty is a type of pervasive experience that is likely to influence biobehavioral processes because children developing in such environments often encounter high levels of stress and reduced environmental stimulation. This study explores the association between socioeconomic status and the hippocampus, a brain region involved in learning and memory that is known to be affected by stress. We employ a voxel-based morphometry analytic framework with region of interest drawing for structural brain images acquired from participants across the socioeconomic spectrum (n = 317). Children from lower income backgrounds had lower hippocampal gray matter density, a measure of volume. This finding is discussed in terms of disparities in education and health that are observed across the socioeconomic spectrum.     

The Association of BAG6 with SGTA and Tail-Anchored Proteins

Background

The BAG6 protein is a subunit of a heterotrimeric complex that binds a range of membrane and secretory protein precursors localized to the cytosol, enforcing quality control and influencing their subsequent fate.

Methodology and Principal Findings

BAG6 has an N-terminal ubiquitin-like domain, and a C-terminal Bcl-2-associated athanogene domain, separated by a large central proline-rich region. We have used in vitro binding approaches to identify regions of BAG6 important for its interactions with: i) the small-glutamine rich tetratricopeptide repeat-containing protein alpha (SGTA) and ii) two model tail-anchored membrane proteins as a paradigm for its hydrophobic substrates. We show that the BAG6-UBL is essential for binding to SGTA, and find that the UBL of a second subunit of the BAG6-complex, ubiquitin-like protein 4A (UBL4A), competes for SGTA binding. Our data show that this binding is selective, and suggest that SGTA can bind either BAG6, or UBL4A, but not both at the same time. We adapted our in vitro binding assay to study the association of BAG6 with an immobilized tail-anchored protein, Sec61β, and find both the UBL and BAG domains are dispensable for binding this substrate. This conclusion was further supported using a heterologous subcellular localization assay in yeast, where the BAG6-dependent nuclear relocalization of a second tail-anchored protein, GFP-Sed5, also required neither the UBL, nor the BAG domain of BAG6.

Significance

On the basis of these findings, we propose a working model where the large central region of the BAG6 protein provides a binding site for a diverse group of substrates, many of which expose a hydrophobic stretch of polypeptide. This arrangement would enable the BAG6 complex to bring together its substrates with potential effectors including those recruited via its N-terminal UBL. Such effectors may include SGTA, and the resulting assemblies influence the subsequent fate of the hydrophobic BAG6 substrates.     

A Population Based Study of the Genetic Association between Catecholamine Gene Variants and Spontaneous Low-Frequency Fluctuations in Reaction Time

The catecholamines dopamine and noradrenaline have been implicated in spontaneous low-frequency fluctuations in reaction time, which are associated with attention deficit hyperactivity disorder (ADHD) and subclinical attentional problems. The molecular genetic substrates of these behavioral phenotypes, which reflect frequency ranges of intrinsic neuronal oscillations (Slow-4: 0.027-0.073 Hz; Slow-5: 0.010-0.027 Hz), have not yet been investigated. In this study, we performed regression analyses with an additive model to examine associations between low-frequency fluctuations in reaction time during a sustained attention task and genetic markers across 23 autosomal catecholamine genes in a large young adult population cohort (n = 964), which yielded greater than 80% power to detect a small effect size (f² = 0.02) and 100% power to detect a small/medium effect size (f² = 0.15). At significance levels corrected for multiple comparisons, none of the gene variants were associated with the magnitude of low-frequency fluctuations. Given the study’s strong statistical power and dense coverage of the catecholamine genes, this either indicates that associations between low-frequency fluctuation measures and catecholamine gene variants are absent or that they are of very small effect size. Nominally significant associations were observed between variations in the alpha-2A adrenergic receptor gene (ADRA2A) and the Slow-5 band. This is in line with previous reports of an association between ADRA2A gene variants and general reaction time variability during response selection tasks, but the specific association of these gene variants and low-frequency fluctuations requires further confirmation. Pharmacological challenge studies could in the future provide convergent evidence for the noradrenergic modulation of both general and time sensitive measures of intra-individual variability in reaction time.     

Staining Isolated Proteins and Polysaccharides on Slides; Phosphotungstic Acid-Hematoxylin versus the Rosindole Reaction

Investigations of hyaline deposits in arteriosclerotic lesions disclosed striking differences in the amount of fibrin demonstrated by these two stains. To test their specificity, model slides carrying dried 10% solutions or suspensions of polysaccharides, fractions of plasma and other proteins were used. Preparations stained with phosphotungstic acid-hema-toxylin (PTAH) were fixed in Zenker-formol, in formaldehyde vapor, and in Carnoy's (6:3:1) solution; those stained by the rosindole reaction, in Carnoy's only. No relation could be found between the chemical nature of the substances tested and their coloration by PTAH; furthermore, the staining reactions were strongly affected by the nature of the fixation. In contrast, only plasma proteins, elastase and gliadin yielded an intense rosindole reaction, thus showing that it is much more reliable for the demonstration of plasma proteins, including fibrin, than is PTAH. Apparently, PTAH gives information on molecular structure rather than on chemical composition.     

球形红假单胞菌反应中心中蛋白的量子化学研究

采用重叠二体近似方法和建立在从算水平上的扩展负本征值因数计算方法（extended negative factor counter method）研究了球形红假单胞菌（Rhodobacter sphaeroides(Van Niel)Imhoff,Truper et Pfennin）中兴合反应中心中蛋白链L及M的电子结构。结果表明：（1）对组成蛋白链L（M）的前线轨道有重要贡献的氨基酸残基分布在L链的自由螺旋区（M链的α螺旋区）。由于自由螺旋是有柔曲性的,它易于在电子转移的过程中改变其构象并降低体系的能量,而α螺旋结构却相对稳定,这种差别有可能是光合反庆中心中电子转移只沿L支进行的原因之一。（2）与特殊对分子及辅助叶绿素分子形成轴向配位的组氨酸残基对于特殊对P和辅助叶绿素分子的ELUMO有重要影响,但此组氨酸的相应分子轨道的贡献并没有出现在蛋白链的前线轨道组成中。这意味着色素分子与蛋白链之间的相互作用对蛋白链前线轨道的贡献没有影响,但却能影响相应色素分子的ELUMO能级。     

Quantum Chemical Studies on Proteins in the Reaction Center of Rhodobacter sphaeroides

The electronic structure of protein chains L and M in photosynthetic reaction center (PRC) of Rhodobacter sphaeroides (Van Niel) Imhoff, Truper et Pfennig) was studied by using the Overlapping Dimer Approximation method and the Extended Negative Factor Counter method at ab initio level. The result indicated that: (1) Amino acid residues, the molecular orbitals of which composed the main components of frontier orbitals of protein chain L (M ), are located at the random coil areas of chain L (α helix areas of chain M ). Since the random coil is flexible and more easy to change its conformation in the electron transfer process and to reduce the energy of the system, and the structure of the α helix is reletively stable, this difference might be one of the causes for the electron transfer in photosynthetic reaction center (PRC) only takes place along the L branch. (2) The His residues which axially coordinated to the “special pair” P and accessory chlorophyll molecules （ABChls） are essentially important for the ELUMO levels of P and ABChl. But, the corresponding molecular orbitals of these His residues do not appear in the composition of frontier orbitals of protein chains. It means that the interaction between pigment molecules and protein chains do not influence the contribution to the frontier orbitals of protein chains explicitly, but influences the corresponding ELUMO levels significantly.     

Induction of Pathogenesis-related Proteins in Barley during the Resistance Reaction to Mildew

Changes in the soluble protein pattern of leaves of eight lines of barley, carrying different resistance genes to mildew, were analysed by SDS-polyacrylamide gel electrophoresis and isoelectric focusing. Apparently new host proteins were induced by Erysiphe graminis f. sp. hordei in the incompatible reaction which were not present in the immune or susceptible response. These proteins are of low molecular weight, 13,500–27,500 d, and have either very low or very high isoelectric points. Thus, they resemble the pathogenesis-related proteins found in many dicotyledonous species.     

Excursions along the Interface between Disruptive and Stabilizing Selection

When a polygenic character is exposed to natural selection in which the curve giving fitness as a function of phenotype is a mixture of two Gaussian (normal) curves, the population may respond either by evolving to a specialized phenotype near one of the two optimum phenotypes, or by evolving to a generalized phenotype between them. Using approximate multivariate normal distribution methods, it is demonstrated that the condition for selection to result in a specialized phenotype is that the curve of fitness as a function of breeding value be bimodal. This implies that a specialized phenotype is more likely to result the higher is the heritability of the character. Numerical iterations of four-locus models and algebraic analysis of a symmetric two-locus model generally support the conclusions of the normal approximation.     

SNARE蛋白及其相关蛋白在精子顶体反应中的作用

精子顶体反应是指精子顶体外膜与精子质膜发生细胞内多点融合的反应,其过程属于特殊的胞吐过程。精子顶体反应是一个复杂严谨的生理过程,不仅需要诱导剂的诱导,还需要多种相关膜融合蛋白的参与。SNARE蛋白及其相关蛋白能够调控哺乳动物细胞内的融合,尤其在精子顶体反应过程中发挥着重要作用。其中SNARE蛋白是核心成分,与其相关蛋白相互作用,共同参与精子顶体反应过程。现主要对SNAREs、Rab、Munc-18、complexin、synaptotagmin和α-SNAP等蛋白质在精子顶体反应中的作用进行概述。