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

Перевірка суб’єктів господарювання державного сектора економіки: ревізія чи аудит?

The house sparrow (Passer domesticus) is an important model species in ecology and evolution. However, until recently, genomic resources for molecular ecological projects have been lacking in this species. Here, we present transcriptome sequencing data (RNA-Seq) from three different house sparrow tissues (spleen, blood and bursa). These tissues were specifically chosen to obtain a diverse representation of expressed genes and to maximize the yield of immune-related gene functions. After de novo assembly, 15250 contigs were identified, representing sequence data from a total of 8756 known avian genes (as inferred from the closely related zebra finch). The transcriptome assembly contain sequence data from nine manually annotated MHC genes, including an almost complete MHC class I coding sequence. There were 407, 303 and 68 genes overexpressed in spleen, blood and bursa, respectively. Gene ontology terms related to ribosomal function were associated with overexpression in spleen and oxygen transport functions with overexpression in blood. In addition to the transcript sequences, we provide 327 gene-linked microsatellites (SSRs) with sufficient flanking sequences for primer design, and 3177 single-nucleotide polymorphisms (SNPs) within genes, that can be used in follow-up molecular ecology studies of this ecological well-studied species

Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies

Next-generation sequencing of transcriptomes (RNA-Seq) is being used increasingly in studies of nonmodel organisms. Here, we evaluate the effectiveness of normalising cDNA libraries prior to sequencing in a small-scale study of the zebra finch. We find that assemblies produced from normalised libraries had a larger number of contigs but used fewer reads compared to unnormalised libraries. Considerably more genes were also detected using the contigs produced from normalised cDNA, and microsatellite discovery was up to 73% more efficient in these. There was a positive correlation between the detected expression level of genes in normalised and unnormalised cDNA, and there was no difference in the number of genes identified as being differentially expressed between blood and spleen for the normalised and unnormalised libraries. We conclude that normalised cDNA libraries are preferable for many applications of RNA-Seq and that these can also be used in quantitative gene expression studies

Detecting prolonged sitting bouts with the ActiGraph GT3X

The ActiGraph has a high ability to measure physical activity; however, it lacks an accurate posture classification to measure sedentary behavior. The aim of the present study was to develop an ActiGraph (waist-worn, 30 Hz) posture classification to detect prolonged sitting bouts, and to compare the classification to proprietary ActiGraph data. The activPAL, a highly valid posture classification device, served as reference criterion. Both sensors were worn by 38 office workers over a median duration of 9 days. An automated feature selection extracted the relevant signal information for a minute-based posture classification. The machine learning algorithm with optimal feature number to predict the time in prolonged sitting bouts (>= 5 and >= 10 minutes) was searched and compared to the activPAL using Bland-Altman statistics. The comparison included optimized and frequently used cut-points (100 and 150 counts per minute (cpm), with and without low-frequency-extension (LFE) filtering). The new algorithm predicted the time in prolonged sitting bouts most accurate (bias <= 7 minutes/d). Of all proprietary ActiGraph methods, only 150 cpm without LFE predicted the time in prolonged sitting bouts non-significantly different from the activPAL (bias <= 18 minutes/d). However, the frequently used 100 cpm with LFE accurately predicted total sitting time (bias <= 7 minutes/d). To study the health effects of ActiGraph measured prolonged sitting, we recommend using the new algorithm. In case a cut-point is used, we recommend 150 cpm without LFE to measure prolonged sitting and 100 cpm with LFE to measure total sitting time. However, both cpm cut-points are not recommended for a detailed bout analysis.NoneAccepte

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

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

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

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

Domestic burglary drop and the security hypothesis

This study examines the role of household security devices in producing the domestic burglary falls in England and Wales. It extends the study of the security hypothesis as an explanation for the 'crime drop'. Crime Survey for England and Wales data are analysed from 1992 to 2011/12 via a series of data signatures indicating the nature of, and change in, the relationship between security devices and burglary. The causal role of improved security is strongly indicated by a set of interlocking data signatures: rapid increases in the prevalence of security, particularly in the availability of combinations of the most effective devices (door and window locks plus security lighting); a steep decline in the pro-portion of households without security accompanied by disproportionate rises in their burglary risk; and the decline being solely in forced rather than unforced entries to households. The study concludes that there is strong evidence that security caused the decline in burglary in England and Wales in the 1990s. Testing the security hypothesis across a wider range of crime types, countries and forms of security than examined to date, is required both to understand the crime drop and to derive lessons for future crime prevention practice and policy