Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium.

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, , , zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium.

Bimetallic copper palladium nanorods: plasmonic properties and palladium content effects.

Cu is an inexpensive alternative plasmonic metal with optical behaviour comparable to Au but with much poorer environmental stability. Alloying with a more stable metal can improve stability and add functionality, with potential effects on the plasmonic properties. Here we investigate the plasmonic behaviour of Cu nanorods and Cu-CuPd nanorods containing up to 46 mass percent Pd.

Expression Atlas update: insights from sequencing data at both bulk and single cell level.

Expression Atlas (www.ebi.ac.

GA4GH Phenopackets: A Practical Introduction.

The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. A detailed example is presented that illustrates how to use the schema to represent the clinical course of a patient with retinoblastoma, including demographic information, the clinical diagnosis, phenotypic features and clinical measurements, an examination of the extirpated tumor, therapies, and the results of genomic analysis.

Solvent effects on the kinetics of 4-nitrophenol reduction by NaBH in the presence of Ag and Au nanoparticles.

The reduction of 4-nitrophenol (4-NiP) to 4-aminophenol (4-AP) with an excess of sodium borohydride is commonly used as a model reaction to assess the catalytic activity of metallic nanoparticles. This reaction is considered both a potentially important step in industrial water treatment and an attractive, commercially relevant synthetic pathway. Surprisingly, an important factor, the role of the reaction medium on the reduction performance, has so far been overlooked.

Potential of deep learning segmentation for the extraction of archaeological features from historical map series.

Historical maps present a unique depiction of past landscapes, providing evidence for a wide range of information such as settlement distribution, past land use, natural resources, transport networks, toponymy and other natural and cultural data within an explicitly spatial context. Maps produced before the expansion of large-scale mechanized agriculture reflect a landscape that is lost today. Of particular interest to us is the great quantity of archaeologically relevant information that these maps recorded, both deliberately and incidentally.

The major barriers to evidence-informed conservation policy and possible solutions.

Conservation policy decisions can suffer from a lack of evidence, hindering effective decision-making. In nature conservation, studies investigating why policy is often not evidence-informed have tended to focus on Western democracies, with relatively small samples. To understand global variation and challenges better, we established a global survey aimed at identifying top barriers and solutions to the use of conservation science in policy.

Anatomy of the Ediacaran rangeomorph .

The Ediacaran macrofossil Ford is perhaps the most iconic member of the Rangeomorpha: a group of seemingly sessile, frondose organisms that dominates late Ediacaran benthic, deep-marine fossil assemblages. Despite exhibiting broad palaeogeographical and stratigraphical ranges, there have been few morphological studies that consider the variation observed among populations of specimens derived from multiple global localities. We present an analysis of that evaluates specimens from the UK, Canada and Russia, representing the largest morphological study of this taxon to date.

Enhanced control of plasmonic properties of silver-gold hollow nanoparticles a reduction-assisted galvanic replacement approach.

Hollow noble metal nanoparticles are of growing interest due to their localized surface plasmon resonance (LSPR) tunability. A popular synthetic approach is galvanic replacement which can be coupled with a co-reducer. Here, we describe the control over morphology, and therefore over plasmonic properties including energy, bandwidth, extinction and scattering intensity, offered by co-reduction galvanic replacement.

The effects of catchment and riparian forest quality on stream environmental conditions across a tropical rainforest and oil palm landscape in Malaysian Borneo.

Freshwaters provide valuable habitat and important ecosystem services but are threatened worldwide by habitat loss and degradation. In Southeast Asia, rainforest streams are particularly threatened by logging and conversion to oil palm, but we lack information on the impacts of this on freshwater environmental conditions, and the relative importance of catchment versus riparian-scale disturbance. We studied 16 streams in Sabah, Borneo, including old-growth forest, logged forest, and oil palm sites.

The association between in vivo central noradrenaline transporter availability and trait impulsivity.

The brain noradrenaline (NA) system, particularly NA transporters (NAT), are thought to play an important role in modulating impulsive behavior. Impaired impulsivity is implicated in a variety of neuropsychiatric conditions; however, an in vivo link between central NAT availability and human impulsivity has not been shown. Using positron emission tomography (PET) and S,S-[C]O-methylreboxetine (MRB), we tested whether NAT availability is associated with this basic behavioral trait based on the Barratt Impulsiveness Scale (BIS-11) in twenty healthy individuals (12 females, 33.

No evidence for maintenance of a sympatric species barrier by chromosomal inversions.

Mechanisms that suppress recombination are known to help maintain species barriers by preventing the breakup of coadapted gene combinations. The sympatric butterfly species and are separated by many strong barriers, but the species still hybridize infrequently in the wild, and around 40% of the genome is influenced by introgression. We tested the hypothesis that genetic barriers between the species are maintained by inversions or other mechanisms that reduce between-species recombination rate.

Tree-centric mapping of forest carbon density from airborne laser scanning and hyperspectral data.

Forests are a major component of the global carbon cycle, and accurate estimation of forest carbon stocks and fluxes is important in the context of anthropogenic global change. Airborne laser scanning (ALS) data sets are increasingly recognized as outstanding data sources for high-fidelity mapping of carbon stocks at regional scales.We develop a tree-centric approach to carbon mapping, based on identifying individual tree crowns (ITCs) and species from airborne remote sensing data, from which individual tree carbon stocks are calculated.

Differentiation in putative male sex pheromone components across and within populations of the African butterfly Bicyclus anynana as a potential driver of reproductive isolation.

Sexual traits are often the most divergent characters among closely related species, suggesting an important role of sexual traits in speciation. However, to prove this, we need to show that sexual trait differences accumulate before or during the speciation process, rather than being a consequence of it. Here, we contrast patterns of divergence among putative male sex pheromone (pMSP) composition and the genetic structure inferred from variation in the mitochondrial cytochrome oxidase 1 and nuclear CAD loci in the African butterfly Bicyclus anynana (Butler, 1879) to determine whether the evolution of "pheromonal dialects" occurs before or after the differentiation process.

Drivers of aboveground wood production in a lowland tropical forest of West Africa: teasing apart the roles of tree density, tree diversity, soil phosphorus, and historical logging.

Tropical forests currently play a key role in regulating the terrestrial carbon cycle and abating climate change by storing carbon in wood. However, there remains considerable uncertainty as to whether tropical forests will continue to act as carbon sinks in the face of increased pressure from expanding human activities. Consequently, understanding what drives productivity in tropical forests is critical.

The effect of genetic structure on molecular dating and tests for temporal signal.

'Dated-tip' methods of molecular dating use DNA sequences sampled at different times, to estimate the age of their most recent common ancestor. Several tests of 'temporal signal' are available to determine whether data sets are suitable for such analysis. However, it remains unclear whether these tests are reliable.

A limit on the extent to which increased egg size can compensate for a poor postnatal environment revealed experimentally in the burying beetle, Nicrophorus vespilloides.

It is often assumed that there is a positive relationship between egg size and offspring fitness. However, recent studies have suggested that egg size has a greater effect on offspring fitness in low-quality environments than in high-quality environments. Such observations suggest that mothers may compensate for poor posthatching environments by increasing egg size.

Dominant male song performance reflects current immune state in a cooperatively breeding songbird.

Conspicuous displays are thought to have evolved as signals of individual "quality", though precisely what they encode remains a focus of debate. While high quality signals may be produced by high quality individuals due to "good genes" or favourable early-life conditions, whether current immune state also impacts signalling performance remains poorly understood, particularly in social species. Here, we experimentally demonstrate that male song performance is impaired by immune system activation in the cooperatively breeding white-browed sparrow weaver (Plocepasser mahali).

Molecular neuropathology of the synapse in sheep with CLN5 Batten disease.

Aims: Synapses represent a major pathological target across a broad range of neurodegenerative conditions. Recent studies addressing molecular mechanisms regulating synaptic vulnerability and degeneration have relied heavily on invertebrate and mouse models. Whether similar molecular neuropathological changes underpin synaptic breakdown in large animal models and in human patients with neurodegenerative disease remains unclear.

The sight of an adult brood parasite near the nest is an insufficient cue for a honeyguide host to reject foreign eggs.

Hosts of brood-parasitic birds typically evolve anti-parasitism defences, including mobbing of parasitic intruders at the nest and the ability to recognize and reject foreign eggs from their clutches. The Greater Honeyguide is a virulent brood parasite that punctures host eggs and kills host young, and accordingly, a common host, the Little Bee-eater frequently rejects entire clutches that have been parasitized. We predicted that given the high costs of accidentally rejecting an entire clutch, and that the experimental addition of a foreign egg is insufficient to induce this defence, Bee-eaters require the sight of an adult parasite near the nest as an additional cue for parasitism before they reject a clutch.

Retaining biodiversity in intensive farmland: epiphyte removal in oil palm plantations does not affect yield.

The expansion of agriculture into tropical forest frontiers is one of the primary drivers of the global extinction crisis, resulting in calls to intensify tropical agriculture to reduce demand for more forest land and thus spare land for nature. Intensification is likely to reduce habitat complexity, with profound consequences for biodiversity within agricultural landscapes. Understanding which features of habitat complexity are essential for maintaining biodiversity and associated ecosystem services within agricultural landscapes without compromising productivity is therefore key to limiting the environmental damage associated with producing food intensively.

Towards the identification of the loci of adaptive evolution.

Establishing the genetic and molecular basis underlying adaptive traits is one of the major goals of evolutionary geneticists in order to understand the connection between genotype and phenotype and elucidate the mechanisms of evolutionary change. Despite considerable effort to address this question, there remain relatively few systems in which the genes shaping adaptations have been identified. Here, we review the experimental tools that have been applied to document the molecular basis underlying evolution in several natural systems, in order to highlight their benefits, limitations and suitability.

Post-transcriptional regulation of early embryogenesis.

Gene expression is controlled by diverse mechanisms before, during, and after transcription. Chromatin modification factors as well as transcriptional repressors, silencers, and enhancers all feed into how eukaryotes transcribe RNA in the nucleus. However, there is increasing evidence that post-transcriptional regulation of gene expression is as widespread as transcriptional control if not more so.