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The HUGO Gene Nomenclature Committee (HGNC) assigns unique symbols and names to human genes. The HGNC database (www.genenames.org) currently contains over 43 000 approved gene symbols, over 19 200 of which are assigned to protein-coding genes, 14 000 to pseudogenes and nearly 9000 to non-coding RNA genes. The public website, www.genenames.org, displays all approved nomenclature within Symbol Reports that contain data curated by HGNC nomenclature advisors and links to related genomic, clinical, and proteomic information. Here, we describe updates to our resource, including improvements to our search facility and new download features.

The HUGO Gene Nomenclature Committee (HGNC) has been providing standardized symbols and names for human genes since the late 1970s. As funding agencies change their priorities, finding financial support for critical biomedical resources such as the HGNC becomes ever more challenging. In this article, we outline the key roles the HGNC currently plays in aiding communication and the need for these activities to be maintained.

Summary The use of approved nomenclature in publications is vital to enable effective scientific communication and is particularly crucial when discussing genes of clinical relevance. Here, we discuss several examples of cases where the failure of researchers to use a HUGO Gene Nomenclature Committee (HGNC)-approved symbol in publications has led to confusion between unrelated human genes in the literature. We also inform authors of the steps they can take to ensure that they use approved nomenclature in their manuscripts and discuss how referencing HGNC IDs can remove ambiguity when referring to genes that have previously been published with confusing alias symbols.

Standardized gene nomenclature supports unambiguous communication and identification of the scientific literature associated with genes. To support the increasing number of annotated genomes that are now available for comparative studies, gene nomenclature authorities coordinate the assignment of approved gene names that can be readily propagated across species without losing their sense of meaning. Theofanopoulou et al (Theofanopoulou et al. 2021) propose nomenclature changes to the genes encoding oxytocin and arginine vasopressin and their receptors which would hinder comparative studies and literature identification. Instead, we propose minor updates to the current approved nomenclature of these vertebrate genes to better reflect their evolutionary history, without confusing the literature that already exists around these well-studied genes. We encourage authors to work with nomenclature committees to ensure any novel gene names fit current guidelines so that their publications can be readily indexed and made accessible. Moreover, we call on journal editors and reviewers to help support communication and indexing of gene-related publications by ensuring that standardized gene nomenclature is routinely used.

Background Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~ 1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights. Results Here, we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5. Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~ 50% in dog and cow and to ~ 30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature. Conclusions We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.

The HUGO Gene Nomenclature Committee (HGNC) based at EMBL’s European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problematic symbols, we are working towards stabilizing symbols where possible; over 2000 symbols for disease associated genes are now marked as stable in our symbol reports. All of our data is available at the HGNC website https://www.genenames.org. The Vertebrate Gene Nomenclature Committee (VGNC) was established to assign standardized nomenclature in line with human for vertebrate species lacking their own nomenclature committee. In addition to the previous VGNC core species of chimpanzee, cow, horse and dog, we now name genes in cat, macaque and pig. Gene groups have been added to VGNC and currently include two complex families: olfactory receptors (ORs) and cytochrome P450s (CYPs). In collaboration with specialists we have also named CYPs in species beyond our core set. All VGNC data is available at https://vertebrate.genenames.org/. This article provides an overview of our online data and resources, focusing on updates over the last two years.

The North Carolina Wildlife Resources Commission has used coded wire tags to mark fish. We evaluated coded wire tags placed at three different anatomical locations (left cheek, right cheek and snout) in brown trout (Salmo trutta) fingerlings (range of mean annual total lengths = 81.31 – 101.89 mm) prior to stockings (10,000 fish per tagging location). We determined the probability of tag retention at zero, 87 and 176 days posttagging across mean fish lengths. Anatomical tagging location influenced the probability of a fish being tagged. At all evaluation periods and for all mean sizes, brown trout fingerlings tagged in the left cheek had higher probabilities of being tagged than other positions of tags, with snout tags performing the worst. Intra-location comparisons revealed a decline in tag retention across temporal scales. Days posttagging had a negative effect on probability of tag retention, while length had a positive effect on the probability of tag retention. Our results indicated that the likelihood of a tag being present at 176 days was influenced by position of tag and initial tagging success more so than length or days posttagging. Although tag retention was generally high across all tag positions, differences in retention revealed the need to refine the tagging procedure. In addition, the underperformance of coded wire tags placed in the snout suggested that alternative marking locations should be explored.

The deutocerebral (second) head segment is putatively homologous across Arthropoda, in spite of remarkable disparity of form and function of deutocerebral appendages. In Mandibulata this segment bears a pair of sensory antennae, whereas in Chelicerata the same segment bears a pair of feeding appendages called chelicerae. Part of the evidence for the homology of deutocerebral appendages is the conserved function of homothorax (hth), which has been shown to specify antennal or cheliceral fate in the absence of Hox signaling, in both mandibulate and chelicerate exemplars. However, the genetic basis for the morphological disparity of antenna and chelicera is not understood. To test whether downstream targets of hth have diverged in a lineage-specific manner, we examined the evolution of the function and expression of spineless (ss), which in two holometabolous insects is known to act as a hth target and distal antennal determinant. Toward expanding phylogenetic representation of gene expression data, here we show that strong expression of ss is observed in developing antennae of a hemimetabolous insect, a centipede, and an amphipod crustacean. By contrast, ss orthologs are not expressed throughout the cheliceral limb buds of spiders or harvestmen during developmental stages when appendage fate is specified. RNA interference-mediated knockdown of ss in Oncopeltus fasciatus, which bears a simple plesiomorphic antenna, resulted in homeotic distal antenna-to-leg transformation, comparable to data from holometabolous insect counterparts. Knockdown of hth in Oncopeltus fasciatus abrogated ss expression, suggesting conservation of upstream regulation. These data suggest that ss may be a flagellar (distal antennal) determinant more broadly, and that this function was acquired at the base of Mandibulata.

Background: The Hemiptera (aphids, cicadas, and true bugs) are a key insect order, with high diversity for feeding ecology and excellent experimental tractability for molecular genetics. Building upon recent sequencing of hemipteran pests such as phloem-feeding aphids and blood-feeding bed bugs, we present the genome sequence and comparative analyses centered on the milkweed bug Oncopeltus fasciatus, a seed feeder of the family Lygaeidae. Results: The 926-Mb Oncopeltus genome is well represented by the current assembly and official gene set. We use our genomic and RNA-seq data not only to characterize the protein-coding gene repertoire and perform isoform-specific RNAi, but also to elucidate patterns of molecular evolution and physiology. We find ongoing, lineage-specific expansion and diversification of repressive C2H2 zinc finger proteins. The discovery of intron gain and turnover specific to the Hemiptera also prompted the evaluation of lineage and genome size as predictors of gene structure evolution. Furthermore, we identify enzymatic gains and losses that correlate with feeding biology, particularly for reductions associated with derived, fluid nutrition feeding. Conclusions: With the milkweed bug, we now have a critical mass of sequenced species for a hemimetabolous insect order and close outgroup to the Holometabola, substantially improving the diversity of insect genomics. We thereby define commonalities among the Hemiptera and delve into how hemipteran genomes reflect distinct feeding ecologies. Given Oncopeltus’s strength as an experimental model, these new sequence resources bolster the foundation for molecular research and highlight technical considerations for the analysis of medium-sized invertebrate genomes., La lista completa de autores puede verse en el archivo asociado., Facultad de Ciencias Exactas, Centro Regional de Estudios Genómicos

New cellular functions and developmental processes can evolve by modifying the functions or regulation of preexisting genes, but the creation of new genes and their contributions to novel processes is less well understood. New genes can arise not only from mutations or rearrangements of existing sequences, but also via acquisition of foreign DNA, also called horizontal gene transfer (HGT). Here we present evidence that HGT contributed to the creation of a novel gene indispensable for reproduction in some insects. The oskar gene evolved to fulfil a crucial role in insect germ cell formation, but was long considered a novel gene with unknown evolutionary origins. Our analysis of over 100 Oskar sequences suggests that Oskar arose through a novel gene formation history involving fusion of eukaryotic and prokaryotic sequences. One of its two conserved domains (LOTUS), was likely present in the genome of a last common insect ancestor, while the second (OSK) domain appears to have been acquired through horizontal transfer of a bacterial GDSL-like lipase domain. Our evidence suggests that the bacterial contributor of the OSK domain may have been a germ line endosymbiont. This shows that gene origin processes often considered highly unusual, including HGT and de novo coding region evolution, can give rise to novel genes that can both participate in pre-existing gene regulatory networks, and also facilitate the evolution of novel developmental mechanisms.

The HUGO Gene Nomenclature Committee (HGNC) based at EMBL’s European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 40 000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 to assign standardized nomenclature in line with human for vertebrate species that lack their own nomenclature committees. The VGNC initially assigned nomenclature for over 15000 protein-coding genes in chimpanzee. We have extended this process to other vertebrate species, naming over 14000 protein-coding genes in cow and dog and over 13 000 in horse to date. Our HGNC website https://www.genenames.org has undergone a major design update, simplifying the homepage to provide easy access to our search tools and making the site more mobile friendly. Our gene families pages are now known as ‘gene groups’ and have increased in number to over 1200, with nearly half of all named genes currently assigned to at least one gene group. This article provides an overview of our online data and resources, focusing on our work over the last two years.

The vertebrate limb is one of the most intensively studied organs in the field of developmental biology. Limb development in tetrapod vertebrates is highly conserved and dependent on the interaction of several important molecular pathways. The bone morphogenetic protein (BMP) signaling cascade is one of these pathways and has been shown to be crucial for several aspects of limb development. Here, we have used a Xenopus laevis transgenic line, in which expression of the inhibitor Noggin is under the control of the heat-shock promoter hsp70 to examine the effects of attenuation of BMP signaling at different stages of limb development. Remarkably different phenotypes were produced at different stages, illustrating the varied roles of BMP in development of the limb. Very early limb buds appeared to be refractory to the effects of BMP attenuation, developing normally in most cases. Ectopic limbs were produced by overexpression of Noggin corresponding to a brief window of limb development at about stage 49/50, as recently described by Christen et al. (2012). Attenuation of BMP signaling in stage 51 or 52 tadpoles lead to a reduction in the number of digits formed, resulting in hypodactyly or ectrodactyly, as well as occasional defects in the more proximal tibia-fibula. Finally, inhibition at stage 54 (paddle stage) led to the formation of dramatically shortened digits resulting from loss of distal phalanges. Transcriptome analysis has revealed the possibility that more Noggin-sensitive members of the BMP family could be involved in limb development than previously suspected. Our analysis demonstrates the usefulness of heat-shock-driven gene expression as an effective method for inhibiting a developmental pathway at different times during limb development.

Summary Primordial germ cell (PGC) formation in holometabolous insects like Drosophila melanogaster relies on maternally synthesised germ cell determinants that are asymmetrically localised to the oocyte posterior cortex. Embryonic nuclei that inherit this “germ plasm” acquire PGC fate. In contrast, historical studies of basally branching insects (Hemimetabola) suggest that a maternal requirement for germ line genes in PGC specification may be a derived character confined principally to Holometabola. However, there have been remarkably few investigations of germ line gene expression and function in hemimetabolous insects. Here we characterise PGC formation in the milkweed bug Oncopeltus fasciatus, a member of the sister group to Holometabola, thus providing an important evolutionary comparison to members of this clade. We examine the transcript distribution of orthologues of 19 Drosophila germ cell and/or germ plasm marker genes, and show that none of them localise asymmetrically within Oncopeltus oocytes or early embryos. Using multiple molecular and cytological criteria, we provide evidence that PGCs form after cellularisation at the site of gastrulation. Functional studies of vasa and tudor reveal that these genes are not required for germ cell formation, but that vasa is required in adult males for spermatogenesis. Taken together, our results provide evidence that Oncopeltus germ cells may form in the absence of germ plasm, consistent with the hypothesis that germ plasm is a derived strategy of germ cell specification in insects.

European regulations for the control of bovine spongiform encephalopathy (BSE) decree destruction of the intestines from slaughtered cattle, therefore producers have been obliged to import beef casings from countries with a negligible BSE risk. This study applies immunohistochemical and biochemical approaches to investigate the occurrence and distribution of disease-associated prion protein (PrP(Sc)) in the duodenum, jejunum and ileum of cattle orally exposed to a 1 g or 100 g dose of a titrated BSE brainstem homogenate. Samples were derived from animals at various times post exposure. Lymphoid follicles were counted and the frequency of affected follicles recorded. No PrP(Sc) was detected in the duodenum or jejunum of animals exposed to a 1 g dose or in the duodenum of animals receiving a 100 g dose. PrP(Sc) was detected in the lymphoid tissue of the ileum of 1/98 (1.0%) animals receiving the 1 g dose and in the jejunum and ileum of 8/58 (13.8%) and 45/99 (45.5%), respectively, of animals receiving the 100 g dose. The frequency of PrP(Sc)- positive follicles was less than 1.5% per case and biochemical tests appeared less sensitive than immunohistochemistry. The probability of detecting lymphoid follicles in the ileum declined with age and for the 100 g exposure the proportion of positive follicles increased, while the proportion of positive animals decreased with age. Detection of PrP(Sc) in intestinal neural tissue was rare. The results suggest that the jejunum and duodenum of BSE-infected cattle contain considerably less BSE infectivity than the ileum, irrespective of exposure dose. In animals receiving the low exposure dose, as in most natural cases of BSE, the rarity of PrP(Sc) detection compared with high-dose exposure, suggests a very low BSE risk from food products containing the jejunum and duodenum of cattle slaughtered for human consumption.

Elements are produced in stars through a variety of processes; some are well known, others are still the object of active research. The elements zirconium (Zr) and yttrium (Y) reside in the mass range where there is uncertainty about the production mechanism at early time. The rapid n-capture process (r-process) was believed to be responsible for the production, but no study has been able to successfully use the r-process to reproduce the abundance signature for elements in this mass range for metal-poor halo stars. It has been suggested that there may be an undiscovered component to the r-process. We have performed new abundance calculations for the elements Y and Zr in six metal-poor halo giants, using high-quality spectra, and in the case of Zr, new atomic data. Our results are consistent with previous authors' analysis of these stars, but with reduced values for the uncertainty, due to new laboratory data and better quality observational data. Comparison of the lighter n-capture elements' abundances to those of the heavier s-process element barium (Ba) show that there is no correlation between the production of the light elements to the heavy elements. This indicates that there seem to be a multiplicity of processes operating early in the history of the Galaxy. Our results suggest that the main r-process is responsible for production of the elements from Ba onward in atomic number, while some as yet unknown process (or processes) is responsible for the production of the lighter n-capture elements.

This article evaluates Jean-Luc Marion's retrieval of Dionysius against the backdrop of the debate in recent continental philosophy over the identity and meaning of “negative theology”. Marion's interpretation and use of Dionysius draws heavily on that of Hans Urs von Balthasar, both in his manner of approaching Dionysius and with the central elements of the Corpus Dionysiacum upon which he focuses. Through this comparison, it is clear that different polemical and apologetic interests shape their similar but distinct retrievals. Marion, like Balthasar before him, is translating Dionysius for a new audience. With this translation, I argue that Marion provides a richer and more complex confrontation with Dionysius than has previously been offered within the contemporary discussions of “negative theology”.

Background: A prospective audit of specialist registrars' (SRs') training in tympanomastoid surgery for chronic otitis media within the Anglia Regional Training Scheme is described. This audit recorded the surgical activity of the trainees and their contribution to operative procedures, and assessed the results of the procedures. This type of systematic approach to the audit of surgical training is important in light of the current shortened training programmes and increased accountability of trainers.Objectives: The study aimed to establish the levels of exposure to, supervision of and outcome of ear operations for chronic otitis media performed by ENT trainees in the East Anglia region.Method: A prospective, region-wide, minimum otology dataset-based proforma audit was undertaken, with compulsory SR participation. Proformas were completed at the time of operation (form one) and at a minimum interval of nine months post-operatively (form two). Data on form one included hospital, supervising consultant, name and training year of SR, contribution of SR (based on England Royal College of Surgeons guidelines interpreted by the SR), pre-operative audiology average (air conduction/bone conduction over 0.5, 1, 2 and 4 kHz), the pathology and the state of the ear at the time of surgery, and a breakdown of the procedure(s) undertaken. Form two recorded data relevant to form one as well as information regarding patient satisfaction and the operative result obtained, graded as ‘gold’ (no disease, dry ear and hearing average Results: Completed copies of 409 form ones and 156 form twos were analysed. With advancing years, SRs' contributions to procedures increased without significant effect on the graded outcome, which appeared to be independent of SR year of training. Different regional hospitals were compared. Data collected also provided an otology training portfolio for SRs, forming part of their registrar in-training assessment (RITA).Conclusion: The East Anglia SR audit of SRs' training in tympanomastoid surgery for chronic otitis media was a powerful training tool. It demonstrated the safe progression of SR training in supervised ear surgery, with SRs' results being comparable to those for consultant-performed procedures.

Observations along the southwest Atlantic WOCE A17 line made during the Dutch GEOTRACES-NL program (2010–2011) were compared with historical data from 1994 to quantify the changes in the anthropogenic component of the total pool of dissolved inorganic carbon (ΔCant). Application of the extended Multi Linear Regression (eMLR) method shows that the ΔCant from 1994 to 2011 has largely remained confined to the upper 1000 dbar. The greatest changes occur in the upper 200 dbar in the SubAntarctic Zone (SAZ), where a maximum increase of 37 μmol kg−1 is found. South Atlantic Central Water (SACW) experienced the highest rate of increase in Cant, at 0.99 ± 0.14 μmol kg−1 yr−1, resulting in a rate of decrease in pH of −0.0016 yr−1. The highest rates of acidification relative to ΔCant, however, were found in SubAntarctic Mode Water (SAMW) and Antarctic Intermediate Water (AAIW). The low buffering capacity of SAMW and AAIW combined with their relatively high rates of Cant increase of 0.53 ± 0.11 μmol kg−1 yr−1 and 0.36 ± 0.06 μmol kg−1 yr−1, respectively, will lead to rapid acidification in the SAZ and simultaneously reduce the chemical buffering capacity of this significant CO2 sink.

We report the case of a professional scuba diver who was unable to dive because he began experiencing severe frontal pain on descent. Following endoscopic surgery to open the frontal recess, the man was able to resume diving unrestricted by pain. We discuss the causes and treatment of this complaint, and we suggest that this might be considered a new indication for surgery in a limited number of cases.

The upregulation of a limited number of growth factors in our interferon-gamma transgenic model for regeneration within the pancreas lead us to propose that these factors are important during pancreatic regeneration. In this study, we have assessed the influence of two growth factors within the pancreas, epidermal growth factor (EGF) and keratinocyte growth factor (KGF), by ectopically expressing these proteins under the control of the human insulin promoter in transgenic mice. This beta-cell-targeted expression of either EGF or KGF resulted in significant morphological changes, including cellular proliferation and disorganized islet growth. Intercrossing the individual Ins-EGF and Ins-KGF transgenic mice resulted in more profound changes in pancreatic morphology including proliferation of pancreatic cells and extensive intra-islet fibrosis. Insulin-producing beta-cells were found in some of the ducts of older Ins-EGF and Ins-EGFxKGF transgenic mice, and amylase-producing cells were observed within the islet structures of the double transgenic mice. These data suggest that both EGF and KGF are capable of affecting pancreatic differentiation and growth, and that co-expression of these molecules in islets has a more substantial impact on the pancreas than does expression of either growth factor alone.

Keratinocyte growth factor, (KGF), a member of the fibroblast growth factor (FGF) family, is involved in wound healing. It also promotes the differentiation of many epithelial tissues and proliferation of epithelial cells as well as pancreatic duct cells. Additionally, many members of the highly homologous FGF family (including KGF), influence both growth and cellular morphology in the developing embryo. We have previously observed elevated levels of KGF in our interferon-gamma transgenic mouse model of pancreatic regeneration. To understand the role of KGF in pancreatic differentiation, we generated insulin promoter-regulated KGF transgenic mice. Remarkably, we have found that ectopic KGF expression resulted in the emergence of hepatocytes within the islets of Langerhans in the pancreas. Additionally, significant intra-islet duct cell proliferation in the pancreata of transgenic KGF mice was observed. The unexpected appearance of hepatocytes and proliferation of intra-islet duct cells in the pancreata of these mice evidently stemmed directly from local exposure to KGF.

SUMMARYThe objective of this study was to estimate the sensitivity and specificity of a culture method and a polymerase chain reaction (PCR) method for detection of two Campylobacter species: C. jejuni and C. coli. Data were collected during a 3-year survey of UK broiler flocks, and consisted of parallel sampling of caeca from 436 batches of birds by both PCR and culture. Batches were stratified by season (summer/non-summer) and whether they were the first depopulation of the flock, resulting in four sub-populations. A Bayesian approach in the absence of a gold standard was adopted, and the sensitivity and specificity of the PCR and culture for each Campylobacter subtype was estimated, along with the true C. jejuni and C. coli prevalence in each sub-population. Results indicated that the sensitivity of the culture method was higher than that of PCR in detecting both species when the samples were derived from populations infected with at most one species of Campylobacter. However, from a mixed population, the sensitivity of culture for detecting both C. jejuni or C. coli is reduced while PCR is potentially able to detect both species, although the total probability of correctly identifying at least one species by PCR is similar to that of the culture method.

All major JET systems have been fully commissioned for D-T and the DTE1 series of experiments has started with the D-T fuel mixture and operating conditions foreseen for ITER. In the area of ITER physics, significant results have been produced in both D-D and D-T. In D-D, the LH threshold power database has been extended, the bounds on edge-electron temperature and density in ELMy H-modes have been defined and the advantages of Types I and III ELMy discharges have been compared. In D-T plasmas, the isotope effect on H-mode threshold power and transport has been determined so that a more accurate assessment can be made of the ignition margin and heating requirements for ITER. Trace tritium experiments have provided first particle transport measurements and an assessment of the ITER reference ion-cyclotron resonance-frequency heating scenarios has been started, In the area of fusion performance, record D-D neutron yields have been obtained by controlling the plasma and current profiles in hot ion ELM-free H-modes and optimized shear modes. In D-T, internal transport barriers have been readily established in optimized shear discharges and Alfven eigenmodes have been observed.

Four models are presented investigating risks present on Great Britain (GB) turkey farms in breeding and fattening flocks for ciprofloxacin and cephalosporin resistance. Risk factors for ciprofloxacin resistance in fattening flocks were sourcing of feed from national compounders, antimicrobial use in the flock and evidence of mice. Disinfection of floors and walls at depopulation, older flocks and division of the flock with partitions reduced the risk. In breeding farms holding over 10,000 birds, administration of fluoroquinolones within the last year and horses on the neighbouring farm all increased the risk, whereas replenishing foot dips more than once a week reduced the risk. For cephalosporin-resistant Escherichia coli on fattening farms, being an independent farm, having a watercourse near the poultry houses, dividing the flock with partitions and providing staff with gloves reduced the risk. Factors that increased the risk included if staff worked with other livestock and if there were pigs on neighbouring farms. This work suggests that good hygiene and biosecurity, rodent control and responsible use of antimicrobials on turkey farms might help minimise the prevalence of fluoroquinolone and cephalosporin resistance in E coli, and restrict the spread of resistance genes to other organisms.

The Surface Ocean CO2 Atlas (SOCAT) is an effort by the international marine carbon research community. It aims to improve access to carbon dioxide measurements in the surface oceans by regular releases of quality controlled and fully documented synthesis and gridded fCO2 (fugacity of carbon dioxide) products. SOCAT version 2 presented here extends the data set for the global oceans and coastal seas by four years and has 10.1 million surface water fCO2 values from 2660 cruises between 1968 and 2011. The procedures for creating version 2 have been comparable to those for version 1. The SOCAT website (http://www.socat.info/) provides access to the individual cruise data files, as well as to the synthesis and gridded data products. Interactive online tools allow visitors to explore the richness of the data. Scientific users can also retrieve the data as downloadable files or via Ocean Data View. Version 2 enables carbon specialists to expand their studies until 2011. Applications of SOCAT include process studies, quantification of the ocean carbon sink and its spatial, seasonal, year-to-year and longer-term variation, as well as initialisation or validation of ocean carbon models and coupled-climate carbon models.

Water column dissolved inorganic carbon and total alkalinity were measured during five hydrographic sections in the Atlantic Ocean and Drake Passage. The work was funded through the Strategic Funding Initiative of the UK's Oceans2025 programme, which ran from 2007 to 2012. The aims of this programme were to establish the regional budgets of natural and anthropogenic carbon in the North Atlantic, the South Atlantic, and the Atlantic sector of the Southern Ocean, as well as the rates of change of these budgets. This paper describes in detail the dissolved inorganic carbon and total alkalinity data collected along east–west sections at 47° N to 60° N, 24.5° N, and 24° S in the Atlantic and across two Drake Passage sections. Other hydrographic and biogeochemical parameters were measured during these sections, and relevant standard operating procedures are mentioned here. Over 95% of dissolved inorganic carbon and total alkalinity samples taken during the 24.5° N, 24° S, and the Drake Passage sections were analysed onboard and subjected to a first-level quality control addressing technical and analytical issues. Samples taken along 47° N to 60° N were analysed and subjected to quality control back in the laboratory. Complete post-cruise second-level quality control was performed using cross-over analysis with historical data in the vicinity of measurements, and data were submitted to the CLIVAR and Carbon Hydrographic Data Office (CCHDO), the Carbon Dioxide Information Analysis Center (CDIAC) and and will be included in the Global Ocean Data Analyses Project, version 2 (GLODAP 2), the upcoming update of Key et al. (2004).

The JET neutral beam injection system has proved to be both effective and reliable as a plasma heating device. The ion heating and plasma fuelling characteristics of the system are ideally suited to the production of high fusion performance plasmas while the flexibility in the choice of beam species (H, D, T, 3 He or 4 He) and the ability to inject into almost any JET plasma configuration allows a wide variety of related physics experiments to be carried out. The capability to inject (for the first time) tritium beams was essential to the successful execution of the first tritium experiments in which 1.7 MW of power from DT fusion reactions was generated.

The influence of the island mass effect of South Georgia on the seasonal marine carbon cycle was investigated during austral summer (January-February) 2008. South Georgia (54-55 degrees S 36-38 degrees W) lies on the North Scotia Ridge, strongly influencing the passage of the Southern Antarctic Circumpolar Current Front to the south. Surface waters upstream of the island, in the central Scotia Sea, were characterised by relative high-nutrient low-chlorophyll (HNLC) conditions from winter (September) 2007 to summer, as indicated by satellite and shipboard observations. The fugacity of carbon dioxide (fCO(2)) was slightly supersaturated and the HNLC waters represented a summertime CO2 source of 2.6 +/- 1.5 mmol m(-2) day(-1). Extensive phytoplankton blooms developed in the Georgia Basin, downstream of South Georgia, in October 2007 and persisted until March 2008. The seasonal depletion in dissolved inorganic carbon (DIC) was 94 +/- 1 mu mol kg(-1) and the Delta fCO(2)(sea-air) was -92 +/- 21 mu atm in the core of the bloom by early February. These conditions created a strong sink for atmospheric CO2 of -12.9 +/- 11.7 mmol m(-2) day(-1). In contrast, wintertime mixing into DIC-rich sub-surface waters created a strong CO2 source of 22.0 +/- 14.4 mmol m(-2) day(-1). These processes drive substantial seasonal changes in DIC of up to -0.7 mu mol kg(-1) day(-1) from winter to summer. Similarly to the blooms of Kerguelen and Crozet, the South Georgia bloom is likely to be fuelled by natural iron fertilisation. A DIC deficit of 2.2 +/- 0.3 mol m(-2) upstream of South Georgia suggested that the relative HNLC waters were more productive than indicated by satellites. The DIC deficit more than doubled downstream of South Georgia (4.6 +/- 0.8 mol m(-2)) to create the strongest seasonal carbon uptake in ice-free waters of the Southern Ocean to date.

The carbonate chemistry of the surface ocean is rapidly changing with ocean acidification, a result of human activities(1). In the upper layers of the Southern Ocean, aragonite-a metastable form of calcium carbonate with rapid dissolution kinetics-may become undersaturated by 2050 (ref. 2). Aragonite undersaturation is likely to affect aragonite-shelled organisms, which can dominate surface water communities in polar regions(3). Here we present analyses of specimens of the pteropod Limacina helicina antarctica that were extracted live from the Southern Ocean early in 2008. We sampled from the top 200 m of the water column, where aragonite saturation levels were around 1, as upwelled deep water is mixed with surface water containing anthropogenic CO2. Comparing the shell structure with samples from aragonite-supersaturated regions elsewhere under a scanning electron microscope, we found severe levels of shell dissolution in the undersaturated region alone. According to laboratory incubations of intact samples with a range of aragonite saturation levels, eight days of incubation in aragonite saturation levels of 0.94-1.12 produces equivalent levels of dissolution. As deep-water upwelling and CO2 absorption by surface waters is likely to increase as a result of human activities(2,4), we conclude that upper ocean regions where aragonite-shelled organisms are affected by dissolution are likely to expand.

An account is given of the high performance plasmas established by development of the H-mode regime in JET in the experimental campaigns up to 1992. High performance in this case is measured in terms of the confinement enhancement achieved over the L-mode scaling as measured using the plasma diamagnetism. Three JET H-mode regimes have achieved enhancement factors (H G DIA ) over Goldston L-mode scaling of 2.5 < H G DIA < 4.0. These are the Pellet Enhanced Performance (PEP) H-MODE, the high bootstrap fraction (high β POL ) H-mode and the Hot Ion (HI) H-mode. The phenomenology of these three regimes is reviewed and contrasts and common threads are elucidated

Mendelian randomisation is a form of instrumental variable analysis that estimates the causal effect of an intermediate phenotype or exposure on an outcome or disease in the presence of unobserved confounding, using a genetic variant as the instrument. A Bayesian approach allows current knowledge to be incorporated into the analysis in the form of informative prior distributions, and the unobserved confounder can be modelled explicitly. We consider Bayesian methods for Mendelian randomisation in the case where all relationships are linear and there are no interactions. A 'full' model in which the unobserved confounder is included explicitly is not completely identifiable, although the causal parameter can be estimated. We compare inferences from this general but non-identified model with a reduced parameter model that is identifiable. We show that, theoretically, additional information about the causal parameter can be obtained by using the non-identifiable full model, rather than the identifiable reduced model, but that this is advantageous only when realistically informative priors are used and when the instrument is weak or the sample size is small. Furthermore, we consider the impact of using 'vague' versus 'informative' priors.

The gelsolin related actin binding protein, Flii, is able to regulate wound healing; mice with decreased Flii expression show improved wound healing whereas mice with elevated Flii expression exhibit impaired wound healing. In both mice and humans Flii expression increases with age and amelioration of FLII activity represents a possible therapeutic strategy for improved wound healing in humans. Despite analysis of Flii function in a variety of organisms we know little of the molecular mechanisms underlying Flii action. Two new murine alleles of Flii have been produced to drive constitutive or tissue-specific expression of Flii. Each strain is able to rescue the embryonic lethality associated with a Flii null allele and to impair wound healing. These strains provide valuable resources for ongoing investigation of Flii function in a variety of biological processes. genesis 49:681–688, 2011. © 2011 Wiley-Liss, Inc.