Complete Genome Sequences of Paenibacillus Larvae Phages BN12, Dragolir, Kiel007, Leyra, Likha, Pagassa, PBL1c, and Tadhana

We present here the complete genomes of eight phages that infect Paenibacillus larvae, the causative agent of American foulbrood in honeybees. Phage PBL1c was originally isolated in 1984 from a P. larvae lysogen, while the remaining phages were isolated in 2014 from bee debris, honeycomb, and lysogens from three states in the USA

Measuring Forest Biodiversity Status and Changes Globally

The world's forests are crucially important for both biodiversity conservation and climate mitigation. New forest status and forest change spatial layers using remotely sensed data have revolutionised forest monitoring globally, and provide fine-scale deforestation alerts that can be actioned in near-real time. However, existing products are restricted to representing tree cover and do not reflect the considerable spatial variation in the biological importance of forests. Here we link modelled biodiversity values to remotely sensed data on tree cover to develop global maps of forest biodiversity significance (based on the rarity-weighted richness of forest mammal, bird, amphibian and conifer species) and forest biodiversity intactness (based on the modelled relationship between anthropogenic pressures and community intactness). The strengths and weaknesses of these products for policy and local decision-making are reviewed and we map out future improvements and developments that are needed to enhance their usefulness

Assessing the cost of global biodiversity and conservation knowledge

Knowledge products comprise assessments of authoritative information supported by stan-dards, governance, quality control, data, tools, and capacity building mechanisms. Considerable resources are dedicated to developing and maintaining knowledge productsfor biodiversity conservation, and they are widely used to inform policy and advise decisionmakers and practitioners. However, the financial cost of delivering this information is largelyundocumented. We evaluated the costs and funding sources for developing and maintain-ing four global biodiversity and conservation knowledge products: The IUCN Red List ofThreatened Species, the IUCN Red List of Ecosystems, Protected Planet, and the WorldDatabase of Key Biodiversity Areas. These are secondary data sets, built on primary datacollected by extensive networks of expert contributors worldwide. We estimate that US$160million (range: US$116–204 million), plus 293 person-years of volunteer time (range: 278–308 person-years) valued at US$14 million (range US$12–16 million), were invested inthese four knowledge products between 1979 and 2013. More than half of this financingwas provided through philanthropy, and nearly three-quarters was spent on personnelcosts. The estimated annual cost of maintaining data and platforms for three of these knowl-edge products (excluding the IUCN Red List of Ecosystems for which annual costs were notpossible to estimate for 2013) is US$6.5 million in total (range: US$6.2–6.7 million). We esti-mated that an additional US$114 million will be needed to reach pre-defined baselines ofdata coverage for all the four knowledge products, and that once achieved, annual mainte-nance costs will be approximately US$12 million. These costs are much lower than those tomaintain many other, similarly important, global knowledge products. Ensuring that biodi-versity and conservation knowledge products are sufficiently up to date, comprehensiveand accurate is fundamental to inform decision-making for biodiversity conservation andsustainable development. Thus, the development and implementation of plans for sustain-able long-term financing for them is critical

Innovations and advances in instrumentation at the W. M. Keck Observatory

Since the start of operations in 1993, the twin 10 meter W. M. Keck Observatory telescopes have continued to maximize their scientific impact and to produce transformative discoveries that keep the observing community on the frontiers of astronomical research. Upgraded capabilities and new instrumentation are provided though collaborative partnerships with Caltech and UC instrument development teams. The observatory adapts and responds to the observers’ evolving needs as defined in the observatory’s strategic plan, periodically refreshed in collaboration with the science community. This paper summarizes the performance of recently commissioned infrastructure projects, technology upgrades, and new additions to the suite of instrumentation at the observatory. We will also provide a status of projects currently in the design or development phase, and since we need to keep our eye on the future, we mention projects in exploratory phases that originate from our strategic plan. Recently commissioned projects include telescope control system upgrades, OSIRIS spectrometer and imager upgrades, and deployments of the Keck Cosmic Web Imager (KCWI), the Near-Infrared Echellette Spectrometer (NIRES), and the Keck I Deployable Tertiary Mirror (KIDM3). Under development are upgrades to the NIRSPEC instrument and adaptive optics (AO) system. Major instrumentation in design phases include the Keck Cosmic Reionization Mapper and the Keck Planet Finder. Future instrumentation studies and proposals underway include a Ground Layer Adaptive Optics system, NIRC2 upgrades, the energy sensitive instrument KRAKENS, an integral field spectrograph LIGER, and a laser tomography AO upgrade. Last, we briefly discuss recovering MOSFIRE and its return to science operations

Rapid helium isotopic variability in Mauna Kea shield lavas from the Hawaiian Scientific Drilling Project

Author Posting. © American Geophysical Union, 2004. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 5 (2004): Q04G14, doi:10.1029/2002GC000439.This paper presents new magmatic helium isotopic compositions in a suite of lavas from phase II of the Hawaiian Scientific Drilling Project (HSDP2) core, which sampled Mauna Kea volcano to a maximum depth of 3098 m below sea level. Most of the measurements were performed by in vacuo crushing of olivine phenocrysts, but include submarine pillow glasses from the 2200 to 2500 meter depth interval, and orthopyroxene phenocrysts from an intrusive at 1880 m. The magmatic 3He/4He ratios range from 6 to 24.7 times atmospheric (Ra), which significantly extends the range of values for Mauna Kea volcano. The 3He/4He ratios are lowest (i.e., close to MORB values of ∼8 Ra) near the top of the Mauna Kea section and rise slowly, to 10–12 Ra, at 1000 m below sea level, consistent with results from the HSDP1 core. At depths greater than 1000 m in the core, primarily in the submarine lavas, there are brief periods when the 3He/4He ratios are higher than 14.5 Ra, always returning to a baseline value. Twelve such excursions were identified in the core; all but one are in the submarine section, and most (7) are in the deepest section, at depths of 1950 to 3070 m. The baseline 3He/4He value rises from 10–12 Ra near 1000 m depth to 12–14 Ra at 3000 m. The helium spikes are found only in lavas that are older than 380 Ka in age, based on an age model derived from Ar-Ar data (W. D. Sharp et al., manuscript in preparation, 2003). Excluding the excursions defined by single lava flows (3) and intrusive units (3), the average spike duration is approximately 15 (±9) Ka (n = 6). The high 3He/4He spikes are interpreted as pulses of magma from the center of the actively upwelling Hawaiian hot spot. The short duration of the high 3He/4He excursions suggests that Mauna Kea was never directly over high the 3He/4He component of the plume (during the HSDP2 eruptive period), presumed to be the plume center. Assuming that the Mauna Kea helium spikes result from melting of heterogeneities within the plume, their short duration implies that the length scales of heterogeneities in the solid upwelling mantle are between 60 m and 12 km (for upwelling rates of 2 to 40 cm/yr). The high 3He/4He are associated with high 208Pb/204Pb, and relatively low 143Nd/144Nd, Zr/Nb, and SiO2. The correlations with major elements, trace elements and isotopes demonstrate that helium is coupled to the other geochemical variations, and that the Mauna Kea isotopic variability is caused by heterogeneities within the upwelling plume.This work was supported by EAR/NSF through the Continental Dynamics and Instrumentation and Facilities programs

A Novel Mouse Fgfr2 Mutant, Hobbyhorse (hob), Exhibits Complete XY Gonadal Sex Reversal

The secreted molecule fibroblast growth factor 9 (FGF9) plays a critical role in testis determination in the mouse. In embryonic gonadal somatic cells it is required for maintenance of SOX9 expression, a key determinant of Sertoli cell fate. Conditional gene targeting studies have identified FGFR2 as the main gonadal receptor for FGF9 during sex determination. However, such studies can be complicated by inefficient and variable deletion of floxed alleles, depending on the choice of Cre deleter strain. Here, we report a novel, constitutive allele of Fgfr2, hobbyhorse (hob), which was identified in an ENU-based forward genetic screen for novel testis-determining loci. Fgr2hob is caused by a C to T mutation in the invariant exon 7, resulting in a polypeptide with a mis-sense mutation at position 263 (Pro263Ser) in the third extracellular immunoglobulin-like domain of FGFR2. Mutant homozygous embryos show severe limb and lung defects and, when on the sensitised C57BL/6J (B6) genetic background, undergo complete XY gonadal sex reversal associated with failure to maintain expression of Sox9. Genetic crosses employing a null mutant of Fgfr2 suggest that Fgr2hob is a hypomorphic allele, affecting both the FGFR2b and FGFR2c splice isoforms of the receptor. We exploited the consistent phenotype of this constitutive mutant by analysing MAPK signalling at the sex-determining stage of gonad development, but no significant abnormalities in mutant embryos were detected

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe