Digital gene expression analysis of the zebra finch genome

Background: In order to understand patterns of adaptation and molecular evolution it is important to quantify both variation in gene expression and nucleotide sequence divergence. Gene expression profiling in non-model organisms has recently been facilitated by the advent of massively parallel sequencing technology. Here we investigate tissue specific gene expression patterns in the zebra finch (Taeniopygia guttata) with special emphasis on the genes of the major histocompatibility complex (MHC). Results: Almost 2 million 454-sequencing reads from cDNA of six different tissues were assembled and analysed. A total of 11,793 zebra finch transcripts were represented in this EST data, indicating a transcriptome coverage of about 65%. There was a positive correlation between the tissue specificity of gene expression and non-synonymous to synonymous nucleotide substitution ratio of genes, suggesting that genes with a specialised function are evolving at a higher rate (or with less constraint) than genes with a more general function. In line with this, there was also a negative correlation between overall expression levels and expression specificity of contigs. We found evidence for expression of 10 different genes related to the MHC. MHC genes showed relatively tissue specific expression levels and were in general primarily expressed in spleen. Several MHC genes, including MHC class I also showed expression in brain. Furthermore, for all genes with highest levels of expression in spleen there was an overrepresentation of several gene ontology terms related to immune function. Conclusions: Our study highlights the usefulness of next-generation sequence data for quantifying gene expression in the genome as a whole as well as in specific candidate genes. Overall, the data show predicted patterns of gene expression profiles and molecular evolution in the zebra finch genome. Expression of MHC genes in particular, corresponds well with expression patterns in other vertebrates

Ensemble prediction using a new dataset of ECMWF initial states - OpenEnsemble 1.0

Ensemble prediction is an indispensable tool in modern numerical weather prediction (NWP). Due to its complex data flow, global medium-range ensemble prediction has almost exclusively been carried out by operational weather agencies to date. Thus, it has been very hard for academia to contribute to this important branch of NWP research using realistic weather models. In order to open ensemble prediction research up to the wider research community, we have recreated all 50 + 1 operational IFS ensemble initial states for OpenIFS CY43R3. The dataset (Open Ensemble 1.0) is available for use under a Creative Commons licence and is downloadable from an https server. The dataset covers 1 year (December 2016 to November 2017) twice daily. Downloads in three model resolutions (T(L)159, T(L)399, and T(L)639) are available to cover different research needs. An open-source workflow manager, called OpenEPS, is presented here and used to launch ensemble forecast experiments from the perturbed initial conditions. The deterministic and probabilistic forecast skill of OpenIFS (cycle 40R1) using this new set of initial states is comprehensively evaluated. In addition, we present a case study of Typhoon Damrey from year 2017 to illustrate the new potential of being able to run ensemble forecasts outside of major global weather forecasting centres.Peer reviewe

Genetic mapping of the major histocompatibility complex in the zebra finch (Taeniopygia guttata)

Genes of the major histocompatibility complex (MHC) have received much attention in immunology, genetics, and ecology because they are highly polymorphic and play important roles in parasite resistance and mate choice. Until recently, the MHC of passerine birds was not well-described. However, the genome sequencing of the zebra finch (Taeniopygia guttata) has partially redressed this gap in our knowledge of avian MHC genes. Here, we contribute further to the understanding of the zebra finch MHC organization by mapping SNPs within or close to known MHC genes in the zebra finch genome. MHC class I and IIB genes were both mapped to zebra finch chromosome 16, and there was no evidence that MHC class I genes are located on chromosome 22 (as suggested by the genome assembly). We confirm the location in the MHC region on chromosome 16 for several other genes (BRD2, FLOT1, TRIM7.2, GNB2L1, and CSNK2B). Two of these (CSNK2B and FLOT1) have not previously been mapped in any other bird species. In line with previous results, we also find that orthologs to the immune-related genes B-NK and CLEC2D, which are part of the MHC region in chicken, are situated on zebra finch chromosome Z and not among other MHC genes in the zebra finch

The changing pattern of domestic cannabis cultivation in the UK and its impact on the cannabis market

With improvements in both technology and information cannabis is being increasingly grown indoors for domestic use, rather than being imported. This study examines 50 cannabis farms detected by an English police force, and examines the characteristics of the 61 suspects associated with them. The study highlights a UK pattern in domestic cultivation, that is moving away from large scale commercial cultivation, at times co-ordinated by South East Asian organised crime groups, to increased cultivation within residential premises by British citizens. Offenders range from those who have no prior criminal history to those who are serious and persistent offenders. The ramifications for law enforcement agencies and policy formers are discussed

The effect of carbohydrate ingestion on the motor skill proficiency of soccer players

This study examined the effects of ingesting a glucose-polymer (GP) solution on the motor skill proficiencies of association football (soccer) players from two teams playing during two matches in a cool environment. Fifteen minutes before each match and at halftime, players from both teams ingested 5 ml/kg of either placebo or a 6.9% GP solution. GP ingestion did not improve tackling, heading, dribbling, or shooting ability. On the contrary, the mean of successful tackles was lower with GP ingestion than with placebo. The success rate for heading, dribbling, and shooting also tended to be lower in the GP than in the placebo condition. In contrast, success in passing and ball control was similar in the two conditions. Improvements in passing and ball control may have been related to a decrease in the intensity of play in the second half of the game. These data indicate that there are no measurable benefits of GP ingestion for the motor skill proficiencies of soccer players during games played in a cool environment.IS

Potential for increased connectivity between differentiated wolverine populations

Information on genetic population structure provides important knowledge for species conservation. Yet, few studies combine extensive genetic data to evaluate the structure and population dynamics of transboundary populations. Here we used single nucleotide polymorphisms (SNPs), microsatellites and mitochondrial haplotypes to analyze the genetic population structure of wolverines (Gulo gulo) across Fennoscandia using a long-term monitoring dataset of 1708 individuals. Clear population subdivision was detected between the Scandinavian and the eastern Finnish population with a steep cline in the contact zone. While the Scandinavian population showed isolation by distance, large swaths of this population were characterized by high connectivity. Areas with high resistance to gene flow are likely explained by a combination of factors, such as historical isolation and founder effects. From a conservation perspective, promoting gene flow from the population in eastern Finland to the northwest of Scandinavia could augment the less variable Scandinavian population, and increase the demographic resilience of all subpopulations. Overall, the large areas of low resistance to gene flow suggest that transboundary cooperation with aligned actions of harvest and conflict mitigation could improve genetic connectivity across Finland, Sweden, and Norway

Determination of consensus among professionals for community safety terms through a Delphi study

This is a post-peer-review, pre-copyedit version of an article published in Crime Prevention and Community Safety. The definitive publisher-authenticated version 2013, 15(4), pp. 258-277 is available online at: http://dx.doi.org/10.1057/cpcs.2013.9This article reports the findings from a study of Community Safety professionals (Academics, Policymakers and Practitioners), using the Delphi method to determine common definitions, if any, for Community Safety terms in current usage. The study investigated the differences in the way that the terms were used and understood by the members of the three groups. The study was predicated on the view that the groups of Community Safety professionals probably use the language of Community Safety in different ways. It is suggested that work in the field would benefit from a shared terminology, where the same term has the same meaning for different professional groups

Gene expression divergence and nucleotide differentiation between males of different color morphs and mating strategies in the ruff

By next generation transcriptome sequencing, it is possible to obtain data on both nucleotide sequence variation and gene expression. We have used this approach (RNA-Seq) to investigate the genetic basis for differences in plumage coloration and mating strategies in a non-model bird species, the ruff (Philomachus pugnax). Ruff males show enormous variation in the coloration of ornamental feathers, used for individual recognition. This polymorphism is linked to reproductive strategies, with dark males (Independents) defending territories on leks against other Independents, whereas white morphs (Satellites) co-occupy Independent's courts without agonistic interactions. Previous work found a strong genetic component for mating strategy, but the genes involved were not identified. We present feather transcriptome data of more than 6,000 de-novo sequenced ruff genes (although with limited coverage for many of them). None of the identified genes showed significant expression divergence between males, but many genetic markers showed nucleotide differentiation between different color morphs and mating strategies. These include several feather keratin genes, splicing factors, and the Xg blood-group gene. Many of the genes with significant genetic structure between mating strategies have not yet been annotated and their functions remain to be elucidated. We also conducted in-depth investigations of 28 pre-identified coloration candidate genes. Two of these (EDNRB and TYR) were specifically expressed in black- and rust-colored males, respectively. We have demonstrated the utility of next generation transcriptome sequencing for identifying and genotyping large number of genetic markers in a non-model species without previous genomic resources, and highlight the potential of this approach for addressing the genetic basis of ecologically important variation

Manipulating Permeability as a Process for Controlling Crime: Balancing Security and Sustainability in Local Contexts

In response to the sustainability agenda, planning policy in the UK, USA and Australia has shifted to promote compact, high-density, mixed-used residential developments in walkable and permeable street networks close to public transport (Commonwealth of Australia, 1995; DETR, 1998; American Planning Association, 2007). This is to encourage walking and the use of public transport and to reduce car-use, energy use, pollution, congestion and urban sprawl. However, although permeability is assumed to represent a positive built environment feature which reduces crime by promoting more "eyes on the street" (Jacobs, 1961), a significant body of research in the field of environmental criminology challenges this assumptions. This paper reviews the theories and evidence associated with permeability and crime.Pedestrian access ways (PAWs) are often associated with crime and this paper discusses research which was directed at providing practical guidance to local governments on how they could better manage existing PAWs in Western Australia (WA). A morphological analysis of existing PAWs was undertaken which analysed the purposes, roles, functionality, users and dynamics of PAWs in a variety of different settings. In addition to crime (which had commonly be used as an excuse to close PAWs), the research considered issues such as amenity, walkability, equity and sustainability. A suite of five tools for assessing and reducing crime risk were developed, which attempt to balance security and sustainability issues. Contrary to assumptions, most PAWs were not subject to high levels of crime and many were vital to the community. Intriguingly, findings indicated that neighbourhood permeability can potentially be manipulated (via the management, closure or construction of new PAWs) to achieve the desired outcomes of reducing crime and of enhancing walkability, liveability and ultimately, the sustainability and well-being of communities