A model of striate response properties based on geniculate anisotropies

The orientation biases seen in the responses of cells in the retina and dLGN are dependent on the spatial frequency of the stimulus, being appreciable only at higher spatial frequencies. An inhibitory mechanism that suppresses the responses to low spatial frequencies would leave a striate cell receiving a biased geniculate input with an orientation sensitivity at the higher spatial frequencies. Such an inhibition could in fact come from one or a small group of LGN cells (through cortical interneurones), since their response extends to spatial frequencies much lower than for cortical cells at the same eccentricity. According to this scheme, a number of other striate response characteristics, e.g., their length and spatial frequency response functions, can also be explained.     

Cytochemical properties of mitochondria in the gastric parietal cell.

The matrix of some mitochondria in gastric parietal cells of rat and guinea pig evidenced affinity for the high iron diamine method which localizes sulfated complex carbohydrates selectively by light and electron microscopy. Such staining has not been observed elsewhere in the stomach. The high iron diamine reactive mitochondria about equaled in number those which were unreactive, and the two groups were indistinguishable morphologically. The distinction was not apparent either when mitochondria were stained by other cytochemical procedures including dialyzed iron for acidic complex carbohydrates, 3-3' diaminobenzidine-H2O2 at pH 6.0 for cytochrome oxidase, and Kominick's pyroantimonate osmium tetroxide for antimonate precipitable cations. The dialyzed iron method stained acid glycoconjugates in the outer intermembrane space in parietal cell mitochondria. These mitochondria stained more strongly with dialyzed iron than have any others examined heretofore with this method and comprised the only reactive mitochondria in the stomach. Parietal cell mitochondria also stained strongly for cytochrome oxidase but those of other gastric cells failed to evidence this reactivity.     

A new view of the spindle checkpoint

Previous studies of the spindle checkpoint suggested that its ability to prevent entry into anaphase was mediated by the inhibition of the anaphase-promoting complex (APC) ubiquitin ligase by Mad2. Two new studies challenge that view by demonstrating that another checkpoint protein, BubR1, is a far more potent inhibitor of APC function.     

A new view on dam lines in Polish Arabian horses based on mtDNA analysis

Polish Arabian horses are one of the oldest and the most important Arab populations in the world. The Polish Arabian Stud Book and the Genealogical Charts by Skorkowski are the main sources of information on the ancestors of Polish Arabs. Both publications were viewed as credible sources of information until the 1990s when the data regarding one of the dam lines was questioned. The aim of the current study was to check the accuracy of the pedigree data of Polish dam lines using mtDNA analysis. The analyses of a 458 bp mtDNA D-loop fragment from representatives of 15 Polish Arabian dam lines revealed 14 distinct haplotypes. The results were inconsistent with pedigree data in the case of two lines. A detailed analysis of the historical sources was performed to explain these discrepancies. Our study revealed that representatives of different lines shared the same haplotypes. We also noted a genetic identity between some lines founded by Polish mares of unknown origin and lines established by desert-bred mares.     

A new view of water dynamics in immobilized proteins.

The inflection frequency of the deuteron magnetic relaxation dispersion from water in rotationally immobilized protein samples has recently been found to be essentially independent of temperature and protein structure. This remarkable invariance has been interpreted in terms of a universal residence time of 1 microseconds for protein-associated water molecules. We demonstrate here that this interpretation is an artifact of the conventional perturbation theory of spin relaxation, which is not valid for rotationally immobile proteins. Using a newly developed non-perturbative, stochastic theory of spin relaxation, we identify the apparent correlation time of 1 microseconds with the inverse of the nuclear quadrupole frequency, thus explaining its invariance. The observed dispersion profiles are consistent with a broad distribution of residence times, spanning the microseconds range. Furthermore, we argue that the deuteron dispersion is due to buried water molecules rather than to the traditional surface hydration previously invoked, and that the contribution from rapidly exchanging protein hydrogens cannot be neglected. The conclusions of the present work are also relevant to proton relaxation in immobilized protein samples and to magnetic resonance imaging of soft tissue.     

A new view of the bacterial cytosol environment

The cytosol is the major environment in all bacterial cells. The true physical and dynamical nature of the cytosol solution is not fully understood and here a modeling approach is applied. Using recent and detailed data on metabolite concentrations, we have created a molecular mechanical model of the prokaryotic cytosol environment of Escherichia coli, containing proteins, metabolites and monatomic ions. We use 200 ns molecular dynamics simulations to compute diffusion rates, the extent of contact between molecules and dielectric constants. Large metabolites spend ～80% of their time in contact with other molecules while small metabolites vary with some only spending 20% of time in contact. Large non-covalently interacting metabolite structures mediated by hydrogen-bonds, ionic and π stacking interactions are common and often associate with proteins. Mg(2+) ions were prominent in NIMS and almost absent free in solution. Κ(+) is generally not involved in NIMSs and populates the solvent fairly uniformly, hence its important role as an osmolyte. In simulations containing ubiquitin, to represent a protein component, metabolite diffusion was reduced owing to long lasting protein-metabolite interactions. Hence, it is likely that with larger proteins metabolites would diffuse even more slowly. The dielectric constant of these simulations was found to differ from that of pure water only through a large contribution from ubiquitin as metabolite and monatomic ion effects cancel. These findings suggest regions of influence specific to particular proteins affecting metabolite diffusion and electrostatics. Also some proteins may have a higher propensity for associations with metabolites owing to their larger electrostatic fields. We hope that future studies may be able to accurately predict how binding interactions differ in the cytosol relative to dilute aqueous solution.     

Palaeomicrocodium: A new view on its origin

Remains of Palaeomicrocodium from the Silurian and Devonian carbonate and clay deposits from the Timan-Northern Ural region, Salair, and Western Siberia are studied using various lithological and geochemical techniques. Characters suggesting their paleoecological and geochemical specialization are discussed. It is suggested that Palaeomicrocodium structures belong to ancient lichens or actinolichens. This hypothesis is based on a number of features of Palaeomicrocodium, including the presence of typical biologically fixed microelements of soil, such as Co, Cu, Zn, Ni, and Cd, sourced from the atmosphere; presence of kerogen carbonaceous matter in prismatic calcite monocrystals of Palaeomicrocodium; identification in their structure of probable hypha-like and rhizoid-like structures; morphological similarity to extant encrusting lichens. Like lichens, Palaeomicrocodium significantly contributed to chemical weathering of rocks by excreting various organic acids, which could effectively dissolve minerals and chelate metallic cations. As a result of the weathering induced by vital function of Palaeomicrocodium, rock-forming minerals exhibit surface corrosion.     

A new protein-protein docking scoring function based on interface residue properties

MOTIVATION: Protein-protein complexes are known to play key roles in many cellular processes. However, they are often not accessible to experimental study because of their low stability and difficulty to produce the proteins and assemble them in native conformation. Thus, docking algorithms have been developed to provide an in silico approach of the problem. A protein-protein docking procedure traditionally consists of two successive tasks: a search algorithm generates a large number of candidate solutions, and then a scoring function is used to rank them. RESULTS: To address the second step, we developed a scoring function based on a Vorono? tessellation of the protein three-dimensional structure. We showed that the Vorono? representation may be used to describe in a simplified but useful manner, the geometric and physico-chemical complementarities of two molecular surfaces. We measured a set of parameters on native protein-protein complexes and on decoys, and used them as attributes in several statistical learning procedures: a logistic function, Support Vector Machines (SVM), and a genetic algorithm. For the later, we used ROGER, a genetic algorithm designed to optimize the area under the receiver operating characteristics curve. To further test the scores derived with ROGER, we ranked models generated by two different docking algorithms on targets of a blind prediction experiment, improving in almost all cases the rank of native-like solutions. AVAILABILITY: http://genomics.eu.org/spip/-Bioinformatics-tools-     

A new view of an old pore

Despite reports suggesting a potential role in membrane fusion, the V(0) subunit of the (+)H/ATPase has remained an unlikely candidate for the fusion pore. In this issue of Cell, Hiesinger and coworkers (Hiesinger et al., 2005) present a forward genetic screen that reveals it to be necessary for synaptic vesicle fusion, independent of its role in vesicle acidification.     

Physical and social diversity among nocturnal primates: A new view based on long term research

Social complexity is not restricted to day-living primates. Nocturnal primates provide a remarkably diverse, and largely overlooked, array of species for comparison with the better known monkeys, apes, and diurnal lemurs. Nocturnal and diurnal species differ markedly in terms of their sensory and perceptual abilities, but they share a high relative brain size in association with long periods of gestation, development of the young, and lifespan. Both groups also show within- and between-species diversity in their systems of feeding, defence, and reproduction, mediated by remarkably complex channels of communication, and varying locally in relation to habitat, demography, and social tradition. This paper provides a broad overview of the physical and social diversity of nocturnal primates, leading to new perspectives on their speciation, social behaviour and conservation status.     

The injury response of the neurones of Periplaneta Americana

Bilateral pairs of specific neurones in the metathoracic ganglion of the cockroach were used to study the ultrastructural changes which follow axon injury. The appearance of these matched pairs of cells was compared three days after the axons on one side of the ganglion only had been severed. The control or uninjured cell body appeared normal, but changes were observed in the neurones whose axon had been cut. These changes included a general increase in the number of ribosomes throughout the cytoplasm, dilatation of the cisternae of the endoplasmic reticulum and a reduction in size of the Golgi bodies. No ultrastructural features were seen which could correspond to the perinuclear ring of RNA observed histochemically with the light microscope. The possible nature of this RNA is discussed.     

A new point of view on the taxonomy ofPottia starckeana agg. (Musci,Pottiaceae)

A new taxonomic treatment is proposed for thePottia starckeana species complex. The peristome development is not considered to be a useful feature to separate the taxa. On the basis of spore morphology only two species are accepted:P. starckeana, with spores wavy in outline, andP. davalliana, with variously-shaped and developed processes on the spores.Pottia starckeana var.brachyoda is reduced to synonymy withP. starckeana; P. conica andP. commutata are treated as synonyms ofP. davalliana. The speciesP. mutica, P. affinis, P. salina, P. microphylla, P. texana, andP. arizonica (included var.mucronulata) are considered taxa of doubtful affinity, as they have spore features intermediate between the two spore types established for the group. The identity ofP. appertii andP. recurvifolia has not been elucidated because the type material has been destroyed.     

胡焕庸线存在性的大数据分析——中国人口分布特征的生态学及新经济地理学认识

基于大数据分析思路和数据挖掘工具,在县级尺度上,利用2010年第六次人口普查数据,计算各县的平均人口密度,以及合成海拔(地带性因素)、环境脆弱性、人生气候指数、农业生产潜力、适宜水资源偏离度、交通便捷性、区位指数等,克鲁格曼Krugman所谓的区域地理本性特征,对胡焕庸线的存在的地理基础和生态学基础进行了分析。研究结果表明:(1)中国人口密度与合成海拔、环境脆弱性、人生气候指数、适宜水资源偏离度、农业生产潜力等生态学因素密切相关,与交通便捷性、GDP和区位指数等显著相关。(2)对大多数省的人口密度的影响的贡献率排在强烈的是合成海拔、农业生产潜力和和水资源适应度,其次是交通便捷性和区位指数;它们是克鲁格曼Krugman新经济地理学认识的第一次区域本性和第二次地理本性因素。(3)新疆、山东、宁夏、内蒙古、黑龙江、江苏、北京和天津的人口分布比较独特,还需引入新的因子来解释其人口分布的影响因素;(4)胡焕庸线沿线是一个生态脆弱地带。研究基本展现了中国人口的空间分布的胡焕庸线的地理学与生态基础。