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The successful isolation and characterization of an N-heterocyclic carbene in 1991 opened up a new class of organic compounds for investigation. From these beginnings as academic curiosities, N-heterocyclic carbenes today rank among the most powerful tools in organic chemistry, with numerous applications in commercially important processes. Here we provide a concise overview of N-heterocyclic carbenes in modern chemistry, summarizing their general properties and uses and highlighting how these features are being exploited in a selection of pioneering recent studies. [ABSTRACT FROM AUTHOR]

The physics of the superconducting state in two-dimensional (2D) electron systems is relevant to understanding the high-transition-temperature copper oxide superconductors and for the development of future superconductors based on interface electron systems. But it is not yet understood how fundamental superconducting parameters, such as the spectral density of states, change when these superconducting electron systems are depleted of charge carriers. Here we use tunnel spectroscopy with planar junctions to measure the behaviour of the electronic spectral density of states as a function of carrier density, clarifying this issue experimentally. We chose the conducting LaAlO3-SrTiO3 interface as the 2D superconductor, because this electron system can be tuned continuously with an electric gate field. We observed an energy gap of the order of 40 microelectronvolts in the density of states, whose shape is well described by the Bardeen-Cooper-Schrieffer superconducting gap function. In contrast to the dome-shaped dependence of the critical temperature, the gap increases with charge carrier depletion in both the underdoped region and the overdoped region. These results are analogous to the pseudogap behaviour of the high-transition-temperature copper oxide superconductors and imply that the smooth continuation of the superconducting gap into pseudogap-like behaviour could be a general property of 2D superconductivity. [ABSTRACT FROM AUTHOR]

The oxygen isotope ratio (δ18O) of cellulose is thought to provide a record of ambient temperature and relative humidity during periods of carbon assimilation. Here we introduce a method to resolve tree-canopy leaf temperature with the use of δ18O of cellulose in 39 tree species. We show a remarkably constant leaf temperature of 21.4 ± 2.2 °C across 50° of latitude, from subtropical to boreal biomes. This means that when carbon assimilation is maximal, the physiological and morphological properties of tree branches serve to raise leaf temperature above air temperature to a much greater extent in more northern latitudes. A main assumption underlying the use of δ18O to reconstruct climate history is that the temperature and relative humidity of an actively photosynthesizing leaf are the same as those of the surrounding air. Our data are contrary to that assumption and show that plant physiological ecology must be considered when reconstructing climate through isotope analysis. Furthermore, our results may explain why climate has only a modest effect on leaf economic traits in general. [ABSTRACT FROM AUTHOR]

Guanine-nucleotide exchange factors on ADP-ribosylation factor GTPases (ARF-GEFs) regulate vesicle formation in time and space by activating ARF substrates on distinct donor membranes. Mammalian GBF1 (ref. 2) and yeast Gea1/2 (ref. 3) ARF-GEFs act at Golgi membranes, regulating COPI-coated vesicle formation. In contrast, their Arabidopsis thaliana homologue GNOM (GN) is required for endosomal recycling, playing an important part in development. This difference indicates an evolutionary divergence of trafficking pathways between animals and plants, and raised the question of how endoplasmic reticulum–Golgi transport is regulated in plants. Here we demonstrate that the closest homologue of GNOM in Arabidopsis, GNOM-LIKE1 (GNL1; NM_123312; At5g39500), performs this ancestral function. GNL1 localizes to and acts primarily at Golgi stacks, regulating COPI-coated vesicle formation. Surprisingly, GNOM can functionally substitute for GNL1, but not vice versa. Our results suggest that large ARF-GEFs of the GBF1 class perform a conserved role in endoplasmic reticulum–Golgi trafficking and secretion, which is done by GNL1 and GNOM in Arabidopsis, whereas GNOM has evolved to perform an additional plant-specific function of recycling from endosomes to the plasma membrane. Duplication and diversification of ARF-GEFs in plants contrasts with the evolution of entirely new classes of ARF-GEFs for endosomal trafficking in animals, which illustrates the independent evolution of complex endosomal pathways in the two kingdoms. [ABSTRACT FROM AUTHOR]

The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human–chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human–chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently. [ABSTRACT FROM AUTHOR]

Emissions from fossil fuel combustion and biomass burning reduce local air quality and affect global tropospheric chemistry. Nitrogen oxides are emitted by all combustion processes and play a key part in the photochemically induced catalytic production of ozone, which results in summer smog and has increased levels of tropospheric ozone globally. Release of nitrogen oxide also results in nitric acid deposition, and—at least locally—increases radiative forcing effects due to the absorption of downward propagating visible light. Nitrogen oxide concentrations in many industrialized countries are expected to decrease, but rapid economic development has the potential to increase significantly the emissions of nitrogen oxides in parts of Asia. Here we present the tropospheric column amounts of nitrogen dioxide retrieved from two satellite instruments GOME and SCIAMACHY over the years 1996–2004. We find substantial reductions in nitrogen dioxide concentrations over some areas of Europe and the USA, but a highly significant increase of about 50 per cent—with an accelerating trend in annual growth rate—over the industrial areas of China, more than recent bottom-up inventories suggest. [ABSTRACT FROM AUTHOR]

Eukaryotic messenger RNAs contain a modified guanosine, termed a cap, at their 5'ends. Translation of mRNAs requires the binding of an initiation factor, eIF4E, to the cap structure. Here, we describe a family of proteins that through a shared sequence regulate cap-dependent translation. The biological importance of this translational regulation is immense, and affects such processes as cell growth, development, oncogenic transformation and perhaps even axon pathfinding and memory consolidation. [ABSTRACT FROM AUTHOR]

Presents endoscopic exploration of the Red Sea coral reefs revealing dense populations of cavity-dwelling sponges. Percentage of phytoplankton removed by coelobite community filtration; Source of nutrients; Effort of understanding the proliferation of rich ecosystem in nutrient-poor water.

Presents a forty-year study of carbon accumulation by pine ecosystems established on previously cultivated soils in South Carolina. Release of carbon to the atmosphere by clearing of forests; Tracking of newly accumulated carbon; Incorporation of bomb radiocarbon into the forest floor and the underlying mineral soil; Accounting for carbon accretion; Limits to carbon sequestration; Facilitation of decomposition.

Presents research which determined anomalies correlated for the heavy stable isotopes of tellurium in pre-solar diamond grains. Contents of pre-solar, carbon-rich carbonaceous meteorites; Importance of diamonds in meteorite grains; Isotope abundance ratios of Xe-H.

Examines the role of diffusive coupling in promoting convection in multicomponent silicate melt. Role of multicomponent convection in the convective evolution and differentiation of terrestrial magmas.

A letter to the editor is presented on the topic of electronic cigarettes, the dangers they pose to human health, and their increasing popularity among young people.

The age of Pleistocene Homo sapiens fossils and archaeological material from the Bouri Formation in the Middle Awash region of Ethiopia, discovered in 1997 by White and colleagues, has been constrained to between 160 ± 2 and 154 ± 7 kyr on the basis of isotopic dating and stratigraphic and geochemical evidence. However, our analysis of their stratigraphic and geochronological data indicate that, although the estimated maximum age (160 ± 2 kyr) is valid, the minimum age (154 ± 7 kyr) is doubtful. These important discoveries may therefore be distinctly younger than reported [ABSTRACT FROM AUTHOR]

Reports on the discovery of molecular hydrogen absorption in a high-velocity cloud (HVC) along the line of sight to the Large Magellanic Cloud. Evidence that gas in HVCs originated in the disk of the Milky Way; Use of a standard curve-of-growth technique for the quantitative analysis.

Arising from F. Huang, P. et al. 464, 396-400 (2010); Huang et al. replyIt was recently shown that relatively large (compared to analytical precision) steady state thermal isotope fractionations are produced in silicate melts whenever temperature differences are maintained for a sufficiently long time. Huang et al. reported new data on thermal isotopic fractionation of magnesium, calcium, and iron in silicate liquids, and claimed (1) that thermal isotopic fractionations in silicate liquids are independent of composition and temperature, and (2) that their 'results lead to a simple and robust framework for characterizing isotope fractionations by thermal diffusion in natural and synthetic systems'. Here I consider whether the data and arguments presented by Huang et al. support their claims. In summary, I caution against assuming (on the basis of the data presented by Huang et al.) that the thermal isotopic fractionations are independent of temperature and composition, or that a framework of the type claimed has been found. [ABSTRACT FROM AUTHOR]

In this article the author discusses the inaccuracy of information regarding the his controversial collection of pistols, the involvement with Congressman Dana Rohrabacher and the belief that scientists can provide their own projects.

Replying to: J. Wakeley 452, 10.1038/nature06805 (2008)In his communication, Wakeley does not find any flaw in our argument for complex speciation of humans and chimpanzees, nor has he identified a simple demographic model that can explain the notable differences in genetic divergence that we observe between humans and chimpanzees when comparing chromosome X and the autosomes. [ABSTRACT FROM AUTHOR]

A letter to the editor is presented in response to the previous article "Nobels in dubious causes."

Presents a letter to the editor about the site for the fusion project.

Somatic hypermutation introduces point mutations into immunoglobulin genes in germinal centre B cells during an immune response. The reaction is initiated by cytosine deamination by the activation-induced deaminase (AID) and completed by error-prone processing of the resulting uracils by mismatch and base excision repair factors. Somatic hypermutation represents a threat to genome integrity and it is not known how the B cell genome is protected from the mutagenic effects of somatic hypermutation nor how often these protective mechanisms fail. Here we show, by extensive sequencing of murine B cell genes, that the genome is protected by two distinct mechanisms: selective targeting of AID and gene-specific, high-fidelity repair of AID-generated uracils. Numerous genes linked to B cell tumorigenesis, including Myc, Pim1, Pax5, Ocab (also called Pou2af1), H2afx, Rhoh and Ebf1, are deaminated by AID but escape acquisition of most mutations through the combined action of mismatch and base excision repair. However, approximately 25% of expressed genes analysed were not fully protected by either mechanism and accumulated mutations in germinal centre B cells. Our results demonstrate that AID acts broadly on the genome, with the ultimate distribution of mutations determined by a balance between high-fidelity and error-prone DNA repair. [ABSTRACT FROM AUTHOR]

The field of organic synthesis has made phenomenal advances in the past fifty years, yet chemists still struggle to design synthetic routes that will enable them to obtain sufficient quantities of complex molecules for biological and medical studies. Total synthesis is therefore increasingly focused on preparing natural products in the most efficient manner possible. Here we describe the preparative-scale, enantioselective, total syntheses of members of the hapalindole, fischerindole, welwitindolinone and ambiguine families, each constructed without the need for protecting groups—the use of such groups adds considerably to the cost and complexity of syntheses. As a consequence, molecules that have previously required twenty or more steps to synthesize racemically in milligram amounts can now be obtained as single enantiomers in significant quantities in ten steps or less. Through the extension of the general principles demonstrated here, it should be possible to access other complex molecular architectures without using protecting groups. [ABSTRACT FROM AUTHOR]

Food webs are descriptions of who eats whom in an ecosystem. Although extremely complex and variable, their structure possesses basic regularities. A fascinating question is to find a simple model capturing the underlying processes behind these repeatable patterns. Until now, two models have been devised for the description of trophic interactions within a natural community. Both are essentially based on the concept of ecological niche, with the consumers organized along a single niche dimension; for example, prey size. Unfortunately, they fail to describe adequately recent and high-quality data. Here, we propose a new model built on the hypothesis that any species' diet is the consequence of phylogenetic constraints and adaptation. Simple rules incorporating both concepts yield food webs whose structure is very close to real data. Consumers are organized in groups forming a nested hierarchy, which better reflects the complexity and multidimensionality of most natural systems. [ABSTRACT FROM AUTHOR]

Mesenchymal stem cells occupy niches in stromal tissues where they provide sources of cells for specialized mesenchymal derivatives during growth and repair. The origins of mesenchymal stem cells have been the subject of considerable discussion, and current consensus holds that perivascular cells form mesenchymal stem cells in most tissues. The continuously growing mouse incisor tooth offers an excellent model to address the origin of mesenchymal stem cells. These stem cells dwell in a niche at the tooth apex where they produce a variety of differentiated derivatives. Cells constituting the tooth are mostly derived from two embryonic sources: neural crest ectomesenchyme and ectodermal epithelium. It has been thought for decades that the dental mesenchymal stem cells giving rise to pulp cells and odontoblasts derive from neural crest cells after their migration in the early head and formation of ectomesenchymal tissue. Here we show that a significant population of mesenchymal stem cells during development, self-renewal and repair of a tooth are derived from peripheral nerve-associated glia. Glial cells generate multipotent mesenchymal stem cells that produce pulp cells and odontoblasts. By combining a clonal colour-coding technique with tracing of peripheral glia, we provide new insights into the dynamics of tooth organogenesis and growth. [ABSTRACT FROM AUTHOR]

The ongoing regime shift of Arctic sea ice from perennial to seasonal ice is associated with more dynamic patterns of opening and closing sea-ice leads (large transient channels of open water in the ice), which may affect atmospheric and biogeochemical cycles in the Arctic. Mercury and ozone are rapidly removed from the atmospheric boundary layer during depletion events in the Arctic, caused by destruction of ozone along with oxidation of gaseous elemental mercury (Hg(0)) to oxidized mercury (Hg(ii)) in the atmosphere and its subsequent deposition to snow and ice. Ozone depletion events can change the oxidative capacity of the air by affecting atmospheric hydroxyl radical chemistry, whereas atmospheric mercury depletion events can increase the deposition of mercury to the Arctic, some of which can enter ecosystems during snowmelt. Here we present near-surface measurements of atmospheric mercury and ozone from two Arctic field campaigns near Barrow, Alaska. We find that coastal depletion events are directly linked to sea-ice dynamics. A consolidated ice cover facilitates the depletion of Hg(0) and ozone, but these immediately recover to near-background concentrations in the upwind presence of open sea-ice leads. We attribute the rapid recoveries of Hg(0) and ozone to lead-initiated shallow convection in the stable Arctic boundary layer, which mixes Hg(0) and ozone from undepleted air masses aloft. This convective forcing provides additional Hg(0) to the surface layer at a time of active depletion chemistry, where it is subject to renewed oxidation. Future work will need to establish the degree to which large-scale changes in sea-ice dynamics across the Arctic alter ozone chemistry and mercury deposition in fragile Arctic ecosystems. [ABSTRACT FROM AUTHOR]

Half of the microbial cells in the Earth's oceans are found in sediments. Many of these cells are members of the Archaea, single-celled prokaryotes in a domain of life separate from Bacteria and Eukaryota. However, most of these archaea lack cultured representatives, leaving their physiologies and placement on the tree of life uncertain. Here we show that the uncultured miscellaneous crenarchaeotal group (MCG) and marine benthic group-D (MBG-D) are among the most numerous archaea in the marine sub-sea floor. Single-cell genomic sequencing of one cell of MCG and three cells of MBG-D indicated that they form new branches basal to the archaeal phyla Thaumarchaeota and Aigarchaeota, for MCG, and the order Thermoplasmatales, for MBG-D. All four cells encoded extracellular protein-degrading enzymes such as gingipain and clostripain that are known to be effective in environments chemically similar to marine sediments. Furthermore, we found these two types of peptidase to be abundant and active in marine sediments, indicating that uncultured archaea may have a previously undiscovered role in protein remineralization in anoxic marine sediments. [ABSTRACT FROM AUTHOR]

Malnutrition affects up to one billion people in the world and is a major cause of mortality. In many cases, malnutrition is associated with diarrhoea and intestinal inflammation, further contributing to morbidity and death. The mechanisms by which unbalanced dietary nutrients affect intestinal homeostasis are largely unknown. Here we report that deficiency in murine angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 (Ace2), which encodes a key regulatory enzyme of the renin-angiotensin system (RAS), results in highly increased susceptibility to intestinal inflammation induced by epithelial damage. The RAS is known to be involved in acute lung failure, cardiovascular functions and SARS infections. Mechanistically, ACE2 has a RAS-independent function, regulating intestinal amino acid homeostasis, expression of antimicrobial peptides, and the ecology of the gut microbiome. Transplantation of the altered microbiota from Ace2 mutant mice into germ-free wild-type hosts was able to transmit the increased propensity to develop severe colitis. ACE2-dependent changes in epithelial immunity and the gut microbiota can be directly regulated by the dietary amino acid tryptophan. Our results identify ACE2 as a key regulator of dietary amino acid homeostasis, innate immunity, gut microbial ecology, and transmissible susceptibility to colitis. These results provide a molecular explanation for how amino acid malnutrition can cause intestinal inflammation and diarrhoea. [ABSTRACT FROM AUTHOR]

Cytoplasmic polyadenylation-induced translation controls germ cell development, neuronal synaptic plasticity and cellular senescence, a tumour-suppressor mechanism that limits the replicative lifespan of cells. The cytoplasmic polyadenylation element binding protein (CPEB) promotes polyadenylation by nucleating a group of factors including defective in germline development 2 (Gld2), a non-canonical poly(A) polymerase, on specific messenger RNA (mRNA) 3′ untranslated regions (UTRs). Because CPEB regulation of p53 mRNA polyadenylation/translation is necessary for cellular senescence in primary human diploid fibroblasts, we surmised that Gld2 would be the enzyme responsible for poly(A) addition. Here we show that depletion of Gld2 surprisingly promotes rather than inhibits p53 mRNA polyadenylation/translation, induces premature senescence and enhances the stability of CPEB mRNA. The CPEB 3′ UTR contains two miR-122 binding sites, which when deleted, elevate mRNA translation, as does an antagomir of miR-122. Although miR-122 is thought to be liver specific, it is present in primary fibroblasts and destabilized by Gld2 depletion. Gld4, a second non-canonical poly(A) polymerase, was found to regulate p53 mRNA polyadenylation/translation in a CPEB-dependent manner. Thus, translational regulation of p53 mRNA and cellular senescence is coordinated by Gld2/miR-122/CPEB/Gld4. [ABSTRACT FROM AUTHOR]

Cysteine is the most intrinsically nucleophilic amino acid in proteins, where its reactivity is tuned to perform diverse biochemical functions. The absence of a consensus sequence that defines functional cysteines in proteins has hindered their discovery and characterization. Here we describe a proteomics method to profile quantitatively the intrinsic reactivity of cysteine residues en masse directly in native biological systems. Hyper-reactivity was a rare feature among cysteines and it was found to specify a wide range of activities, including nucleophilic and reductive catalysis and sites of oxidative modification. Hyper-reactive cysteines were identified in several proteins of uncharacterized function, including a residue conserved across eukaryotic phylogeny that we show is required for yeast viability and is involved in iron-sulphur protein biogenesis. We also demonstrate that quantitative reactivity profiling can form the basis for screening and functional assignment of cysteines in computationally designed proteins, where it discriminated catalytically active from inactive cysteine hydrolase designs. [ABSTRACT FROM AUTHOR]

Past atmospheric methane concentrations show strong fluctuations in parallel to rapid glacial climate changes in the Northern Hemisphere superimposed on a glacial–interglacial doubling of methane concentrations. The processes driving the observed fluctuations remain uncertain but can be constrained using methane isotopic information from ice cores. Here we present an ice core record of carbon isotopic ratios in methane over the entire last glacial–interglacial transition. Our data show that the carbon in atmospheric methane was isotopically much heavier in cold climate periods. With the help of a box model constrained by the present data and previously published results, we are able to estimate the magnitude of past individual methane emission sources and the atmospheric lifetime of methane. We find that methane emissions due to biomass burning were about 45 Tg methane per year, and that these remained roughly constant throughout the glacial termination. The atmospheric lifetime of methane is reduced during cold climate periods. We also show that boreal wetlands are an important source of methane during warm events, but their methane emissions are essentially shut down during cold climate conditions. [ABSTRACT FROM AUTHOR]

p53, the tumour suppressor and transcriptional activator, is regulated by numerous post-translational modifications, including lysine methylation. Histone lysine methylation has recently been shown to be reversible; however, it is not known whether non-histone proteins are substrates for demethylation. Here we show that, in human cells, the histone lysine-specific demethylase LSD1 (refs 3, 4) interacts with p53 to repress p53-mediated transcriptional activation and to inhibit the role of p53 in promoting apoptosis. We find that, in vitro, LSD1 removes both monomethylation (K370me1) and dimethylation (K370me2) at K370, a previously identified Smyd2-dependent monomethylation site. However, in vivo, LSD1 shows a strong preference to reverse K370me2, which is performed by a distinct, but unknown, methyltransferase. Our results indicate that K370me2 has a different role in regulating p53 from that of K370me1: K370me1 represses p53 function, whereas K370me2 promotes association with the coactivator 53BP1 (p53-binding protein 1) through tandem Tudor domains in 53BP1. Further, LSD1 represses p53 function through the inhibition of interaction of p53 with 53BP1. These observations show that p53 is dynamically regulated by lysine methylation and demethylation and that the methylation status at a single lysine residue confers distinct regulatory output. Lysine methylation therefore provides similar regulatory complexity for non-histone proteins and for histones. [ABSTRACT FROM AUTHOR]

Although the first mouse embryonic stem (ES) cell lines were derived 25 years ago using feeder-layer-based blastocyst cultures, subsequent efforts to extend the approach to other mammals, including both laboratory and domestic species, have been relatively unsuccessful. The most notable exceptions were the derivation of non-human primate ES cell lines followed shortly thereafter by their derivation of human ES cells. Despite the apparent common origin and the similar pluripotency of mouse and human embryonic stem cells, recent studies have revealed that they use different signalling pathways to maintain their pluripotent status. Mouse ES cells depend on leukaemia inhibitory factor and bone morphogenetic protein, whereas their human counterparts rely on activin (INHBA)/nodal (NODAL) and fibroblast growth factor (FGF). Here we show that pluripotent stem cells can be derived from the late epiblast layer of post-implantation mouse and rat embryos using chemically defined, activin-containing culture medium that is sufficient for long-term maintenance of human embryonic stem cells. Our results demonstrate that activin/Nodal signalling has an evolutionarily conserved role in the derivation and the maintenance of pluripotency in these novel stem cells. Epiblast stem cells provide a valuable experimental system for determining whether distinctions between mouse and human embryonic stem cells reflect species differences or diverse temporal origins. [ABSTRACT FROM AUTHOR]

Angiotensin -converting enzyme 2 (ACE2) is a regulator of the renin angiotensin system involved in acute lung failure, cardiovascular functions and severe acute respiratory syndrome (SARS) infections in mammals. A gene encoding a homologue to ACE2, termed collectrin (Tmem27), has been identified in immediate proximity to the ace2 locus. The in vivo function of collectrin was unclear. Here we report that targeted disruption of collectrin in mice results in a severe defect in renal amino acid uptake owing to downregulation of apical amino acid transporters in the kidney. Collectrin associates with multiple apical transporters and defines a novel group of renal amino acid transporters. Expression of collectrin in Xenopus oocytes and Madin–Darby canine kidney (MDCK) cells enhances amino acid transport by the transporter B0AT1. These data identify collectrin as a key regulator of renal amino acid uptake. [ABSTRACT FROM AUTHOR]

Specific sites of lysine methylation on histones correlate with either activation or repression of transcription. The tumour suppressor p53 (refs 4–7) is one of only a few non-histone proteins known to be regulated by lysine methylation. Here we report a lysine methyltransferase, Smyd2, that methylates a previously unidentified site, Lys 370, in p53. This methylation site, in contrast to the known site Lys 372, is repressing to p53-mediated transcriptional regulation. Smyd2 helps to maintain low concentrations of promoter-associated p53. We show that reducing Smyd2 concentrations by short interfering RNA enhances p53-mediated apoptosis. We find that Set9-mediated methylation of Lys 372 inhibits Smyd2-mediated methylation of Lys 370, providing regulatory cross-talk between post-translational modifications. In addition, we show that the inhibitory effect of Lys 372 methylation on Lys 370 methylation is caused, in part, by blocking the interaction between p53 and Smyd2. Thus, similar to histones, p53 is subject to both activating and repressing lysine methylation. Our results also predict that Smyd2 may function as a putative oncogene by methylating p53 and repressing its tumour suppressive function. [ABSTRACT FROM AUTHOR]

Symbioses between bacteria and eukaryotes are ubiquitous, yet our understanding of the interactions driving these associations is hampered by our inability to cultivate most host-associated microbes. Here we use a metagenomic approach to describe four co-occurring symbionts from the marine oligochaete Olavius algarvensis, a worm lacking a mouth, gut and nephridia. Shotgun sequencing and metabolic pathway reconstruction revealed that the symbionts are sulphur-oxidizing and sulphate-reducing bacteria, all of which are capable of carbon fixation, thus providing the host with multiple sources of nutrition. Molecular evidence for the uptake and recycling of worm waste products by the symbionts suggests how the worm could eliminate its excretory system, an adaptation unique among annelid worms. We propose a model that describes how the versatile metabolism within this symbiotic consortium provides the host with an optimal energy supply as it shuttles between the upper oxic and lower anoxic coastal sediments that it inhabits. [ABSTRACT FROM AUTHOR]

Corneal avascularity—the absence of blood vessels in the cornea—is required for optical clarity and optimal vision, and has led to the cornea being widely used for validating pro- and anti-angiogenic therapeutic strategies for many disorders. But the molecular underpinnings of the avascular phenotype have until now remained obscure and are all the more remarkable given the presence in the cornea of vascular endothelial growth factor (VEGF)-A, a potent stimulator of angiogenesis, and the proximity of the cornea to vascularized tissues. Here we show that the cornea expresses soluble VEGF receptor-1 (sVEGFR-1; also known as sflt-1) and that suppression of this endogenous VEGF-A trap by neutralizing antibodies, RNA interference or Cre-lox-mediated gene disruption abolishes corneal avascularity in mice. The spontaneously vascularized corneas of corn1 and Pax6+/- mice and Pax6+/- patients with aniridia are deficient in sflt-1, and recombinant sflt-1 administration restores corneal avascularity in corn1 and Pax6+/- mice. Manatees, the only known creatures uniformly to have vascularized corneas, do not express sflt-1, whereas the avascular corneas of dugongs, also members of the order Sirenia, elephants, the closest extant terrestrial phylogenetic relatives of manatees, and other marine mammals (dolphins and whales) contain sflt-1, indicating that it has a crucial, evolutionarily conserved role. The recognition that sflt-1 is essential for preserving the avascular ambit of the cornea can rationally guide its use as a platform for angiogenic modulators, supports its use in treating neovascular diseases, and might provide insight into the immunological privilege of the cornea. [ABSTRACT FROM AUTHOR]

Many bacterial pathogens secrete proteins that activate host trypsinogen-like enzyme precursors, most notably the proenzymes of the blood coagulation and fibrinolysis systems. Staphylococcus aureus, an important human pathogen implicated in sepsis and endocarditis, secretes the cofactor staphylocoagulase, which activates prothrombin, without the usual proteolytic cleavages, to directly initiate blood clotting. Here we present the 2.2?Å crystal structures of human a-thrombin and prethrombin-2 bound to a fully active staphylocoagulase variant. The cofactor consists of two domains, each with three-helix bundles; this is a novel fold that is distinct from known serine proteinase activators, particularly the streptococcal plasminogen activator streptokinase. The staphylocoagulase fold is conserved in other bacterial plasma-protein-binding factors and extracellular-matrix-binding factors. Kinetic studies confirm the importance of isoleucine 1 and valine 2 at the amino terminus of staphylocoagulase for zymogen activation. In addition to making contacts with the 148 loop and (pro)exosite I of prethrombin-2, staphylocoagulase inserts its N-terminal peptide into the activation pocket of bound prethrombin-2, allosterically inducing functional catalytic machinery. These investigations demonstrate unambiguously the validity of the zymogen-activation mechanism known as ‘molecular sexuality’. [ABSTRACT FROM AUTHOR]

The ability to detect recent natural selection in the human population would have profound implications for the study of human history and for medicine. Here, we introduce a framework for detecting the genetic imprint of recent positive selection by analysing long-range haplotypes in human populations. We first identify haplotypes ata locus of interest (core haplotypes). We then assess the age of each core haplotype by the decay of its association to alleles at various distances from the locus, as measured by extended haplotype homozygosity (EHH). Core haplotypes that have unusually high EHH and a high population frequency indicate the presence of a mutation that rose to prominence in the human gene pool faster than expected under neutral evolution. We applied this approach to investigate selection at two genes carrying common variants implicated in resistance to malaria: G6PD[SUP 1] and CD40 ligand[SUP 2]. At both loci, the core haplotypes carrying the proposed protective mutation stand out and show significant evidence of selection. More generally, the method could be used to scan the entire genome for evidence of recent positive selection. [ABSTRACT FROM AUTHOR]

Provides information on an experiment which examined selected genomic regions in the United States to characterize linkage disequilibrium (LD). Use of single nucleotide polymorphisms (SNP) to characterize LD; Methodology of the study; Measurement of LD; Variability in the values of SNP; Nature of a population event that has created long-range LD.

Shows that infection by uropathogenic Escherichia coli induces a constant, low-frequency oscillatory calcium 2+ response in target primary rat renal epithelial cells induced by the secreted repeats-in-toxin (RTX) toxin alpha-haemolysin. Details of the response; Indication of a novel role for alpha-haemolysin in pyelonephritis as an inducer of an oscillating second messenger response in target cells

In this article the authors discusses the sustained agricultural methods to meet upto the food demand without harming the ecology. They are critical of the current farming systems and states that it should be analyzed to reduce the harmful effects of growing agricultural land. They emphasize on introducing a global network to keep a check on the impact of agricultural methods on environment.