Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment

Since the recognition of prokaryotes as essential components of the oceanic food web, bacterioplankton have been acknowledged as catalysts of most major biogeochemical processes in the sea. Studying heterotrophic bacterioplankton has been challenging, however, as most major clades have never been cultured or have only been grown to low densities in sea water. Here we describe the genome sequence of Silicibacter pomeroyi, a member of the marine Roseobacter clade (Fig. 1), the relatives of which comprise approximately 10-20% of coastal and oceanic mixed-layer bacterioplankton. This first genome sequence from any major heterotrophic clade consists of a chromosome (4,109,442 base pairs) and megaplasmid (491,611 base pairs). Genome analysis indicates that this organism relies upon a lithoheterotrophic strategy that uses inorganic compounds (carbon monoxide and sulphide) to supplement heterotrophy. Silicibacter pomeroyi also has genes advantageous for associations with plankton and suspended particles, including genes for uptake of algal-derived compounds, use of metabolites from reducing microzones, rapid growth and cell-density-dependent regulation. This bacterium has a physiology distinct from that of marine oligotrophs, adding a new strategy to the recognized repertoire for coping with a nutrient-poor ocean.     

Fc receptor but not complement binding is important in antibody protection against HIV

Most successful vaccines elicit neutralizing antibodies and this property is a high priority when developing an HIV vaccine. Indeed, passively administered neutralizing antibodies have been shown to protect against HIV challenge in some of the best available animal models. For example, antibodies given intravenously can protect macaques against intravenous or mucosal SHIV (an HIV/SIV chimaera) challenge and topically applied antibodies can protect macaques against vaginal SHIV challenge. However, the mechanism(s) by which neutralizing antibodies afford protection against HIV is not understood and, in particular, the role of antibody Fc-mediated effector functions is unclear. Here we report that there is a dramatic decrease in the ability of a broadly neutralizing antibody to protect macaques against SHIV challenge when Fc receptor and complement-binding activities are engineered out of the antibody. No loss of antibody protective activity is associated with the elimination of complement binding alone. Our in vivo results are consistent with in vitro assays indicating that interaction of Fc-receptor-bearing effector cells with antibody-complexed infected cells is important in reducing virus yield from infected cells. Overall, the data suggest the potential importance of activity against both infected cells and free virus for effective protection against HIV.     

大熊猫电刺激采精及精液冷冻保存研究

对卧龙自然保护区大熊猫研究中心的９只５．５－１６．５岁的雄性大熊猫进行了１７次电刺激采精,其中３只是能进行自然交配并繁殖了后代的种公兽,比较研究了精液离心、不同稀释液和冷冻方法对大熊猫精液超低温冷冻保存后的活力、运动状态、精子和顶体形态的影响。细冷冻是１种较好的超低温冷冻精液的方法。     

Environmental site characteristics and incidence of chokecherry black knot in Utah

Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 st1\:*{behavior:url(#ieooui) } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;} Black knot disease of chokecherries, induced by Dibotryon morbosum (Schw.) Th. & Syd., is widely distributed in Utah. The incidence of black knot was measured by determining the ratio of total black knot gall length to total stem length of plants and then expressing that value as a percentage of diseased stems in the sample plot. The environmental site factors measured were elevation, exposure, slope, soil pH, soil depth, distance to surface water, plant moisture stress, and associated vegetation. Numerical values were determined for each of these variables at each of 18 randomly located plots. Correlation coefficients for plant moisture stress and soil temperature were –.439 (p = .065) and –.440 (p = .055). Multiple regression analyses using plant moisture stress and soil temperature gave a regression coefficient of –.641 (p = .05). As plant moisture stress and soil temperature decreased, incidence of black knot increased.        

Summer habitat use by Columbian Sharp-tailed Grouse in western Idaho

We studied summer habitat use by Columbian Sharp-tailed Grouse ( Tympanuchus phasianellus columbianus ) in western Idaho during 1983-85. Vegetative and topographic measurements were recorded at 716 locations of 15 radio-tagged grouse and at 180 random sites within the major vegetation/cover types in the study area. The mean size of summer home ranges was 1.87 ± 1.14 km 2 . Of eight cover types identified in the study area, individual grouse used the big sagebrush Artemisia tridentata ) cover type more than or in proportion to availability, the low sagebrush ( A. arbuscula ) in proportion to availability, and avoided the shrubby eriogonum ( Eriogonum spp.) type. Characteristics of the big sagebrush cover type that Sharp-tailed Grouse preferred include moderate vegetative cover, high plant species diversity, and high structural diversity. Grouse used areas of dense cover (i.e., mountain shrub and riparian cover types) primarily for escape cover. Compared with random sites, grouse selected areas with (1) greater horizontal and vertical cover, (2) greater canopy coverage of forbs typically decreased by livestock grazing, (3) greater density and canopy coverage of arrowleaf balsamroot ( Balsamorhiza sagittata ), and (4) greater canopy coverage of bluebunch wheatgrass ( Agropyron spicatum ) in the big sagebrush cover type in 1984 and the low sagebrush cover type in 1985. The importance of the native perennials arrowleaf balsamroot and bluebunch wheatgrass became apparent during a drought year when many exotic annuals dried up and provided no cover. Overall, grouse selected vegetative communities that were least modified by livestock grazing.     

Mutations in the gene encoding the 3'-5' DNA exonuclease TREX1 cause Aicardi-Goutières syndrome at the AGS1 locus

Aicardi-Goutières syndrome (AGS) presents as a severe neurological brain disease and is a genetic mimic of the sequelae of transplacentally acquired viral infection. Evidence exists for a perturbation of innate immunity as a primary pathogenic event in the disease phenotype. Here, we show that TREX1, encoding the major mammalian 3' --> 5' DNA exonuclease, is the AGS1 gene, and AGS-causing mutations result in abrogation of TREX1 enzyme activity. Similar loss of function in the Trex1(-/-) mouse leads to an inflammatory phenotype. Our findings suggest an unanticipated role for TREX1 in processing or clearing anomalous DNA structures, failure of which results in the triggering of an abnormal innate immune response.     

Mapping autism risk loci using genetic linkage and chromosomal rearrangements

Autism spectrum disorders (ASDs) are common, heritable neurodevelopmental conditions. The genetic architecture of ASDs is complex, requiring large samples to overcome heterogeneity. Here we broaden coverage and sample size relative to other studies of ASDs by using Affymetrix 10K SNP arrays and 1,181 [corrected] families with at least two affected individuals, performing the largest linkage scan to date while also analyzing copy number variation in these families. Linkage and copy number variation analyses implicate chromosome 11p12-p13 and neurexins, respectively, among other candidate loci. Neurexins team with previously implicated neuroligins for glutamatergic synaptogenesis, highlighting glutamate-related genes as promising candidates for contributing to ASDs.     

Complex Network Analysis of the Robustness of the Hanoi,Vietnam Bus Network

Many complex networks exist to facilitate the transport of material or information. In this capacity, the authors are often concerned with the continued flow of material or information when a fraction of the links in the complex network is disrupted. In other words, the authors are interested in the robustness of the complex network. In this paper, the authors survey measures of robustness like the average path length, the average clustering coefficient, the global efficiency, the size of largest cluster and use these to analyze the robustness of the bus network in Hanoi, Vietnam. The authors find that the bus network is robust against random failure but sensitive to targeted attack, in agreement with its scale-free character. By examining sharp drops in the average path length within the largest cluster of the Hanoi bus network under successive targeted attack, the authors identify five nodes whose loss lead to the fragmentation of the network into five or six disconnected clusters. These isolated clusters represent geographically the Central, Western, Southern, and Northwestern districts of Hanoi. Special considerations must therefore be given to these five nodes when planners wish to expand the bus network, or make it more robust.     

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

Fumarate hydratase (FH) is an enzyme of the tricarboxylic acid cycle (TCA cycle) that catalyses the hydration of fumarate into malate. Germline mutations of FH are responsible for hereditary leiomyomatosis and renal-cell cancer (HLRCC). It has previously been demonstrated that the absence of FH leads to the accumulation of fumarate, which activates hypoxia-inducible factors (HIFs) at normal oxygen tensions. However, so far no mechanism that explains the ability of cells to survive without a functional TCA cycle has been provided. Here we use newly characterized genetically modified kidney mouse cells in which Fh1 has been deleted, and apply a newly developed computer model of the metabolism of these cells to predict and experimentally validate a linear metabolic pathway beginning with glutamine uptake and ending with bilirubin excretion from Fh1-deficient cells. This pathway, which involves the biosynthesis and degradation of haem, enables Fh1-deficient cells to use the accumulated TCA cycle metabolites and permits partial mitochondrial NADH production. We predicted and confirmed that targeting this pathway would render Fh1-deficient cells non-viable, while sparing wild-type Fh1-containing cells. This work goes beyond identifying a metabolic pathway that is induced in Fh1-deficient cells to demonstrate that inhibition of haem oxygenation is synthetically lethal when combined with Fh1 deficiency, providing a new potential target for treating HLRCC patients.