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Presents an analysis of regional trends between 1980 and 1995 in indicators of acidification for 205 lakes and streams in eight regions of North America and Europe, to test whether emission regulations have led to recovery in surface-water acidification. Decrease in the rate of acid deposition from atmosphere (acid rain); Regional details; Implications.

Presents experiments which seek to identify a gene, lov-1 (for location of vulva) that is required for two male sensory behaviors seen in Caenorhabditis elegans. The four substeps involved in the mating behavior of the species; Discovery of a polycystic kidney-disease gene homologue.

Presents experimental findings which show that polycystin-L is a calcium-modulated nonselective cation channel that is permeable to sodium, potassium, and calcium ions. Increase of channel activity through the raising of extracellular and intracellular calcium-ion concentration.

Shows that a DNA polymerase, from HeLa cells, is a human homologue of the yeast Rad30 protein, also known as DNA polymerase eta. Members of a family of damage-bypass replication proteins; Discovery that all xeroderma pigmentosum variant (XP-V) cells examined carry mutations in their DNA polymerase eta gene; Effect of recombinant human DNA polymerase eta on XP-V cells; Indications.

Provides biochemical and pharmacological evidence for the heterodimerization of two fully opioid receptors, kappa and delta. Creation of a new receptor that exhibits ligand binding and functional properties that are distinct from those of either receptor; Binding of highly selective agonists and potentiates signal transduction; Suggestion that heterodimerization of these G-protein-coupled receptors (GPCRs) represents a novel mechanism that modulates their function.

Investigates the possibility that typhoid fever could be a disease where homozygous mutations in the fibrosis transmembrane conductance regulator (CFTR) occurs. How in the heterozygous state, increased resistance to infectious diseases may maintain mutmant CFTR alleles at high levels in selected population; Evidence indicating that Salmonella typhi uses CFTR for entry into epithelial cells; The conclusion of the research.

Reports on research which shows that spontaneous nicotine withdrawal in rats resulted in a significant decrease in brain reward function, as measured by elevations in brain reward thresholds. Effects of nictonic-receptor antagonist injections; How this research relates to physical symptoms associated with drug addiction withdrawal.

The article discusses the uncertainty surrounding the abundance of natural gas to power U.S. economic resurgence. Topics include studies conducted on the supply of gas from shale formations and how much they will last including studies conducted by a team of scientists from the University of Texas, forecasts on gas production from the U.S. Energy Information Administration (EIA) and graphs showing information on shale gas production levels from regions throughout the U.S.

Emerging infectious diseases (EIDs) pose a risk to human welfare, both directly and indirectly, by affecting managed livestock and wildlife that provide valuable resources and ecosystem services, such as the pollination of crops. Honeybees (Apis mellifera), the prevailing managed insect crop pollinator, suffer from a range of emerging and exotic high-impact pathogens, and population maintenance requires active management by beekeepers to control them. Wild pollinators such as bumblebees (Bombus spp.) are in global decline, one cause of which may be pathogen spillover from managed pollinators like honeybees or commercial colonies of bumblebees. Here we use a combination of infection experiments and landscape-scale field data to show that honeybee EIDs are indeed widespread infectious agents within the pollinator assemblage. The prevalence of deformed wing virus (DWV) and the exotic parasite Nosema ceranae in honeybees and bumblebees is linked; as honeybees have higher DWV prevalence, and sympatric bumblebees and honeybees are infected by the same DWV strains, Apis is the likely source of at least one major EID in wild pollinators. Lessons learned from vertebrates highlight the need for increased pathogen control in managed bee species to maintain wild pollinators, as declines in native pollinators may be caused by interspecies pathogen transmission originating from managed pollinators. [ABSTRACT FROM AUTHOR]

A type Ia supernova is thought to begin with the explosion of a white dwarf star. The explosion could be triggered by the merger of two white dwarfs (a 'double-degenerate' origin), or by mass transfer from a companion star (the 'single-degenerate' path). The identity of the progenitor is still controversial; for example, a recent argument against the single-degenerate origin has been widely rejected. One way to distinguish between the double- and single-degenerate progenitors is to look at the centre of a known type Ia supernova remnant to see whether any former companion star is present. A likely ex-companion star for the progenitor of the supernova observed by Tycho Brahe has been identified, but that claim is still controversial. Here we report that the central region of the supernova remnant SNR 0509?67.5 (the site of a type Ia supernova 400?±?50 years ago, based on its light echo) in the Large Magellanic Cloud contains no ex-companion star to a visual magnitude limit of 26.9 (an absolute magnitude of MV = +8.4) within a region of radius 1.43 arcseconds. (This corresponds to the 3? maximum distance to which a companion could have been 'kicked' by the explosion.) This lack of any ex-companion star to deep limits rules out all published single-degenerate models for this supernova. The only remaining possibility is that the progenitor of this particular type Ia supernova was a double-degenerate system. [ABSTRACT FROM AUTHOR]

The authors discuss aspects on how to stop plagiarism. According to John Loadsman, authors may write using their native language and a professional translator, in which the authors of the translated text will be running it through online plagiarism detection tools to check that it does not match anything. Moreover, it mentions that Ian Mcintosh and Yuehong Zhang have proposed an international database that will blacklist frequent offenders.

The article focuses on the laboratory studies which assess the impact of Deepwater Horizon oil spill on the ecosystems in the Gulf of Mexico. It states that Harriet Perry of Gulf Coast Research Laboratory had collected, identified, and measured the larvae and juveniles of various species to assess the damage brought by the oil spill. Meanwhile, it mentions that the greatest concerns of the scientists is the compound called polycyclic aromatic hydrocarbons (PAHs) that is present in oil.

On Jupiter’s moon Io, volcanic plumes and evaporating lava flows provide hot gases to form an atmosphere that is subsequently ionized. Some of Io’s plasma is captured by the planet’s strong magnetic field to form a co-rotating torus at Io’s distance; the remaining ions and electrons form Io’s ionosphere. The torus and ionosphere are also depleted by three time-variable processes that produce a banana-shaped cloud orbiting with Io, a giant nebula extending out to about 500 Jupiter radii, and a jet close to Io. No spatial constraints exist for the sources of the first two; they have been inferred only from modelling the patterns seen in the trace gas sodium observed far from Io. Here we report observations that reveal a spatially confined stream that ejects sodium only from the wake of the Io–torus interaction, together with a visually distinct, spherically symmetrical outflow region arising from atmospheric sputtering. The spatial extent of the ionospheric wake that feeds the stream is more than twice that observed by the Galileo spacecraft and modelled successfully. This implies considerable variability, and therefore the need for additional modelling of volcanically-driven, episodic states of the great jovian nebula. [ABSTRACT FROM AUTHOR]

Explores the predation-related benefits and costs for aposematic aggregated prey with the great tit as the prey. Benefits of gregariousness over just faster avoidance learning; Effects of group size and signal strength on the risk of prey detection; Favorability of grouping over a solitary lifestyle with respect to mortality risk per individual.

Discusses papers concerning genetic changes that make humans so different from chimpanzee. Identification of evolutionary changes that are specific to Homo sapiens; Signatures of positive natural selection in the sequences of the chimpanzee and human genomes; Other comparative analyses; Publication of the draft of the chimpanzee genome; Insertions/deletions and recent duplications of DNA segments; Evolutionary relationships among the higher primates; Human genetic variation.

The crab Xenograpsus testudinatus lives at enormously high densities around the sulphur-rich hydrothermal vents found in shallow waters off Taiwan, even though this acidic environment is low in nutrients. Here we show that these crabs swarm out of their crevices at slack water and feed on the vast numbers of zooplankton that are killed by the vents' sulphurous plumes, and that rain down like marine‘snow’. This opportunistic feeding behaviour explains how the crabs are able to survive in the adverse toxic environment of these shallow hydrothermal vents. [ABSTRACT FROM AUTHOR]

Examines the size separation of granular particles. Separation of bi-disperse granular mixtures according to particle size; Effects of particle density differences on size separation in mixtures of granular particles; Explanations of the 'Brazil-nut effect.'

Author(s): Job Dekker (corresponding author) [1]; Andrew S. Belmont [2]; Mitchell Guttman [3]; Victor O. Leshyk [4]; John T. Lis [5]; Stavros Lomvardas [6]; Leonid A. Mirny [7]; Clodagh C. [...], The 4D Nucleome Network aims to develop and apply approaches to map the structure and dynamics of the human and mouse genomes in space and time with the goal of gaining deeper mechanistic insights into how the nucleus is organized and functions. The project will develop and benchmark experimental and computational approaches for measuring genome conformation and nuclear organization, and investigate how these contribute to gene regulation and other genome functions. Validated experimental technologies will be combined with biophysical approaches to generate quantitative models of spatial genome organization in different biological states, both in cell populations and in single cells.

The primate brain develops through a series of stereotyped processes that are conserved across mammals (1), including the specification, migration, and maturation of diverse cell types and the formation and [...], The transcriptional underpinnings of brain development remain poorly understood, particularly in humans and closely related non-human primates. We describe a high-resolution transcriptional atlas of rhesus monkey (Macaca mulatta) brain development that combines dense temporal sampling of prenatal and postnatal periods with fine anatomical division of cortical and subcortical regions associated with human neuropsychiatric disease. Gene expression changes more rapidly before birth, both in progenitor cells and maturing neurons. Cortical layers and areas acquire adult-like molecular profiles surprisingly late in postnatal development. Disparate cell populations exhibit distinct developmental timing of gene expression, but also unexpected synchrony of processes underlying neural circuit construction including cell projection and adhesion. Candidate risk genes for neurodevelopmental disorders including primary microcephaly, autism spectrum disorder, intellectual disability, and schizophrenia show disease-specific spatiotemporal enrichment within developing neocortex. Human developmental expression trajectories are more similar to monkey than rodent, although approximately 9 % of genes show human-specific regulation with evidence for prolonged maturation or neoteny compared to monkey.

Transcription regulatory factors guide the development and cellular activities of all organisms through highly cooperative and dynamic control of gene expression programs. Regulatory factor coding genes are often conserved across [...], Despite the large evolutionary distances between metazoan species, they can show remarkable commonalities in their biology, and this has helped to establish fly and worm as model organisms for human biology (1,2). Although studies of individual elements and factors have explored similarities in gene regulation, a large-scale comparative analysis of basic principles of transcriptional regulatory features is lacking. Here we map the genome-wide binding locations of 165 human, 93 worm and 52 fly transcription regulatory factors, generating a total of 1,019 data sets from diverse cell types, developmental stages, or conditions in the three species, of which 498 (48.9%) are presented here for the first time. We find that structural properties of regulatory networks are remarkably conserved and that orthologous regulatory factor families recognize similar binding motifs in vivo and show some similar co-associations. Our results suggest that gene-regulatory properties previously observed for individual factors are general principles of metazoan regulation that are remarkably well-preserved despite extensive functional divergence of individual network connections. The comparative maps of regulatory circuitry provided here will drive an improved understanding of the regulatory underpinnings of model organism biology and how these relate to human biology, development and disease.

Humans share many elements of their anatomy and physiology with both gorillas and chimpanzees, and our similarity to these species was emphasized by Darwin and Huxley in the first evolutionary [...], Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

Of the four billion species estimated to have evolved on the Earth over the last 3.5 billion years, some 99% are gone (1). That shows how very common extinction is, [...], Palaeontologists characterize mass extinctions as times when the Earth loses more than three-quarters of its species in a geologically short interval, as has happened only five times in the past 540 million years or so. Biologists now suggest that a sixth mass extinction may be under way, given the known species losses over the past few centuries and millennia. Here we review how differences between fossil and modern data and the addition of recently available palaeontological information influence our understanding of the current extinction crisis. Our results confirm that current extinction rates are higher than would be expected from the fossil record, highlighting the need for effective conservation measures.

M cells are atypical epithelial cells that actively phagocytose macromolecules and microbes. Unlike dendritic cells (DCs) and macrophages, which target antigens to lysosomes for degradation, M cells mainly transcytose the [...], The mucosal immune system forms the largest part of the entire immune system, containing about three-quarters of all lymphocytes and producing grams of secretory IgA daily to protect the mucosal surface from pathogens (1-3). To evoke the mucosal immune response, antigens on the mucosal surface must be transported across the epithelial barrier into organized lymphoid structures such as Peyer's patches (4). This function, called antigen transcytotis, is mediated by specialized epithelial M cell (5,6). The molecular mechanisms promoting this antigen uptake, however, are largely unknown. Here we report that glycoprotein 2 (GP2), specifically expressed on the apical plasma membrane of M cells among enterocytes, serves as a transcytotic receptor for mucosal antigens. Recombinant GP2 protein selectively bound a subset of commensal and pathogenic enterobacteria, including Escherichia toll and Salmonella enterita serovar Typhimurium (S. Typhimurium), by recognizing FimH, a component of type I pill on the bacterial outer membrane. Consistently, these bacteria were colocalized with endogenous GP2 on the apical plasma membrane as well as in cytoplasmic vesicles in M cells. Moreover, deficiency of bacterial FimH or host GP2 led to defects in transcytotis of type-I-piliated bacteria through M cells, resulting in an attenuation of antigen-specific immune responses in Peyer's patches. GP2 is therefore a previously unrecognized transcytotic receptor on M cells for type-I-piliated bacteria and is a prerequisite for the mucosal immune response to these bacteria. Given that M cells are considered a promising target for oral vaccination against various infectious diseases (7,8), the GP2-dependent transcytotic pathway could provide a new target for the development of M-cell-targeted mucosal vaccines.

Mitochondria have important roles in cellular processes, for example, production of cellular energy in the form of ATP and programmed cell death (apoptosis). Each mitochondrion contains between two and ten [...], Mitochondria are found in all eukaryotic cells and contain their own genome (mitochondrial DNA or mtDNA). Unlike the nuclear genome, which is derived from both the egg and sperm at fertilization, the mtDNA in the embryo is derived almost exclusively from the egg; that is, it is of maternal origin. Mutations in mtDNA contribute to a diverse range of currently incurable human diseases and disorders. To establish preclinical models for new therapeutic approaches, we demonstrate here that the mitochondrial genome can be efficiently replaced in mature non-human primate oocytes (Macaca mulatto) by spindle-chromosomal complex transfer from one egg to an enucleated, mitochondrial-replete egg. The reconstructed oocytes with the mitochondrial replacement were capable of supporting normal fertilization, embryo development and produced healthy offspring. Genetic analysis confirmed that nuclear DNA in the three infants born so far originated from the spindle donors whereas mtDNA came from the cytoplast donors. No contribution of spindle donor mtDNA was detected in offspring. Spindle replacement is shown here as an efficient protocol replacing the full complement of mitochondria in newly generated embryonic stem cell lines. This approach may offer a reproductive option to prevent mtDNA disease transmission in affected families.

ASDs encompass a range of clinically defined conditions, including autism and pervasive developmental disorder not otherwise specified, which are more common and severe, as well as Asperger's syndrome, which appears [...], Autism spectrum disorders (ASDs) represent a group of childhood neurodevelopmental and neuropsychiatric disorders characterized by deficits in verbal communication, impairment of social interaction, and restricted and repetitive patterns of interests and behaviour. To identify common genetic risk factors underlying ASDs, here we present the results of genome-wide association studies on a cohort of 780 families (3,101 subjects) with affected children, and a second cohort of 1,204 affected subjects and 6,491 control subjects, all of whom were of European ancestry. Six single nucleotide polymorphisms between cadherin 10 (CDH10) and cadherin 9 (CDH9)-two genes encoding neuronal cell-adhesion molecules-revealed strong association signals, with the most significant SNP being rs4307059 (P = 3.4 X [10.sup.-8], odds ratio =1.19). These signals were replicated in two independent cohorts, with combined Pvalues ranging from 7.4 X [10.sup.-8] to 2.1 X [10.sup.-10]. Our results implicate neuronal cell-adhesion molecules in the pathogenesis of ASDs, and represent, to our knowledge, the first demonstration of genome-wide significant association of common variants with susceptibility to ASDs.

The baker's yeast S. cerevisiae has had a long association with human activity', leading to the idea that its use in fermentation lead to its domestication. Two domestication events have [...], Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions (3,4), population structure (5-8) and sexual versus asexual reproduction (9,10). Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.

Author(s): Christian Biémont [1]; Cristina Vieira [1] [illus. 1] Transposable elements (TEs) -- commonly called 'jumping genes' -- are stretches of DNA that move around the genome of a cell, [...]

Author(s): Donna M. Muzny [1]; Steven E. Scherer (corresponding author) [1]; Rajinder Kaul [2]; Jing Wang [3]; Jun Yu [3]; Ralf Sudbrak [4, 5]; Christian J. Buhay [1]; Rui Chen [...]

Author(s): L. Eichinger [1, 23]; J. A. Pachebat [1, 2, 23]; G. Glöckner [3, 23]; M.-A. Rajandream [4, 23]; R. Sucgang [5, 23]; M. Berriman [4]; J. Song [5]; R. [...]

Author(s): Silvia G. Acinas [1, 4]; Vanja Klepac-Ceraj [1, 4]; Dana E. Hunt [1]; Chanathip Pharino [1]; Ivica Ceraj [2]; Daniel L. Distel [3]; Martin F. Polz (corresponding author) [1] [...]

The United States is banking on decades of abundant natural gas to power its economic resurgence. That may be wishful thinking. When US President Barack Obama talks about the future, [...]

Author(s): Mouse Genome Sequencing Consortium ; Genome Sequencing Center: ; Asif T. Chinwalla [1, 47]; Lisa L. Cook [1]; Kimberly D. Delehaunty [1]; Ginger A. Fewell [1]; Lucinda A. Fulton [...]

Author(s): Laurence Florens [1]; Michael P. Washburn [2]; J. Dale Raine [3]; Robert M. Anthony [4]; Munira Grainger [5]; J. David Haynes [4, 6]; J. Kathleen Moch [4]; Nemone Muster [...]

Author(s): Arie J. van Noordwijk (corresponding author) Birds of the cuckoo family show a fascinating variety in parental care. There are 53 species, called brood parasites, that lay their eggs [...]

Author(s): Seong-Hee Bhoo [1, 2]; Seth J. Davis [1, 2, 3]; Joseph Walker [1]; Baruch Karniol [1]; Richard D. Vierstra (corresponding author) [1] Phytochromes comprise a principal family of red/far-red [...]

Author(s): Nisar P. Malek [1, 2, 3]; Holly Sundberg [2, 3]; Seth McGrew [1, 2]; Keiko Nakayama [4]; Themis R. Kyriakidis [5]; James M. Roberts (corresponding author) [1, 2, 5] [...]

Author(s): International Human Genome Sequencing Consortium; Whitehead Institute for Biomedical Research, Center for Genome Research:; Eric S. Lander [1]; Lauren M. Linton [1]; Bruce Birren [1]; Chad Nusbaum [1]; Michael [...]

Author(s): John Aach [1, 2]; Martha L. Bulyk [3]; George M. Church (corresponding author) [2]; Jason Comander [4]; Adnan Derti [2, 5]; Jay Shendure [1, 2] The two draft sequences [...]

Author(s): Chen Dong [1, 2, 6]; Amy E. Juedes [3, 4]; Ulla-Angela Temann [1, 4, 6]; Sujan Shresta [5]; James P. Allison [5]; Nancy H. Ruddle [3]; Richard A. Flavell [...]

Author(s): Andy Purvis [1]; Andy Hector [2] To proceed very far with the study of biodiversity, we need to pin the concept down. We cannot even begin to look at [...]

Author(s): Greta C. Dargie (corresponding author) [1, 2]; Simon L. Lewis [1, 2]; Ian T. Lawson [3]; Edward T. A. Mitchard [4]; Susan E. Page [5]; Yannick E. Bocko [6]; [...]

Duplication is easily detected by software, yet it remains a problem. Ten experts explain how to stamp it out. HAROLD GARNER Flag plagiarized studies Founder of HelioText, and creator of [...]

Author(s): Emmanuel A. Asante [1]; Michelle Smidak [1]; Andrew Grimshaw [1]; Richard Houghton [1]; Andrew Tomlinson [1]; Asif Jeelani [1]; Tatiana Jakubcova [1]; Shyma Hamdan [1]; Angela Richard-Londt [1]; Jacqueline [...]

Author(s): Armin Rest [1]; Nicholas B. Suntzeff (corresponding author) [1]; Knut Olsen [1]; Jose Luis Prieto [2]; R. Chris Smith [1]; Douglas L. Welch [3]; Andrew Becker [4]; Marcel Bergmann [...]

Author(s): Jonathan Flint (corresponding author) [1]; Marcus Munafo [2] A paper [1] published this week in Nature marks the culmination of a long debate about the genetic basis of a [...]