Multiple conserved regulatory domains promote Fezf2 expression in the developing cerebral cortex.

BackgroundThe genetic programs required for development of the cerebral cortex are under intense investigation. However, non-coding DNA elements that control the expression of developmentally important genes remain poorly defined. Here we investigate the regulation of Fezf2, a transcription factor that is necessary for the generation of deep-layer cortical projection neurons.ResultsUsing a combination of chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) we mapped the binding of four deep-layer-enriched transcription factors previously shown to be important for cortical development. Building upon this we characterized the activity of three regulatory regions around the Fezf2 locus at multiple stages throughout corticogenesis. We identified a promoter that was sufficient for expression in the cerebral cortex, and enhancers that drove reporter gene expression in distinct forebrain domains, including progenitor cells and cortical projection neurons.ConclusionsThese results provide insight into the regulatory logic controlling Fezf2 expression and further the understanding of how multiple non-coding regulatory domains can collaborate to control gene expression in vivo

Kori Bustards (\u3ci\u3eArdeotis kori\u3c/i\u3e) respond to vegetation density and elevation in the Northern Tuli Game Reserve, Botswana L\u27abondance de l\u27Outarde kori (\u3ci\u3eArdeotis kori\u3c/i\u3e) varie selon la végétation et l\u27élévation dans la réserve de chasse de Northern Tuli, Botswana

Conservation planning and decision making for species of concern requires precise information on abundance and habitat associations. We conducted transect surveys throughout the Northern Tuli Game Reserve, Botswana during June–July 2014 and May– July 2015 to estimate the occupancy and abundance of Kori Bustards (Ardeotis kori). The probability of occupancy of Kori Bustards was greater in areas with tree canopy cover ≤ 50% (ψ2014 = 0.37, SE ± 0.09; ψ2015 = 0.39, SE ± 0.06) when compared with areas with tree canopy cover \u3e 50% (ψ2014 = 0.00, SE ± 0.00; ψ2015 = 0.00, SE ± 0.00). Densities of Kori Bustards ranged from 0.03–5.02 individuals/km² at our study sites. They showed annual variation, and densities were highest in areas where vegetation was classified as sparse or bare soil. Areas at low (≤ 540 m above sea level) and high (≥ 540 m above sea level) elevations at our study sites also exhibited differences in density of Kori Bustards but elevational differences varied among years. Areas categorized as both sparse vegetation and higher elevation had the highest estimated densities in 2014 with 5.02 individuals/km². Areas categorized as sparse vegetation and lower elevation had the highest densities in 2015 with 2.20 individuals/km². Our study demonstrates that areas of sparse vegetation and open canopy areas are important to Kori Bustards. However, open canopy areas outside of reserves may be at risk of conversion to row crop and other forms of agriculture as human populations and demands for food increase. Habitat-specific information will be useful for future studies to identify risks during landscape conservation planning within the range of the Kori Bustard. La planification de la conservation et la prise de décisions pour les espèces préoccupantes requièrent des données précises sur leur abondance et leurs associations avec l\u27habitat. Nous avons effectué des relevés par transects dans la réserve de chasse de Northern Tuli, au Botswana, en juin-juillet 2014 et mai-juillet 2015, afin de déterminer l\u27occurrence et la densité d\u27Outardes kori (Ardeotis kori). La probabilité d\u27occurrence des outardes était supérieure dans les endroits où la voûte forestière couvrait ≤ 50 % (ψ2014 = 0,37, écarttype ± 0,09; ψ2015 = 0,39, écart-type ± 0,06) comparativement aux endroits où la voûte couvrait \u3e 50 % (ψ2014 = 0,00, écart-type ± 0,00; ψ2015 = 0,00, écart-type ± 0,00). Les densités de cette outarde s\u27élevaient de 0,03 à 5,02 individus/km² dans nos sites d\u27étude. Les densités montraient des variations annuelles et étaient plus élevées dans les endroits où la végétation était classée comme « éparse » ou « sol nu ». Les densités ont aussi différé selon les endroits de basse (≤ 540 m au-dessus du niveau de la mer) ou de haute (≥ 540 m ASL) élévation dans nos sites d\u27étude, et ces différences ont varié entre les années. Les endroits classés à la fois comme de végétation éparse et de haute élévation ont hébergé les densités les plus élevées en 2014, soit 5,02 individus/km². Les endroits classés à la fois comme de végétation éparse et de basse élévation ont hébergé les densités les plus élevées en 2015, soit 2,20 individus/km². Notre étude indique que les endroits de végétation éparse et ceux où la voûte est ouverte sont importants pour les Outardes kori. Toutefois, les endroits où la voûte forestière est ouverte à l\u27extérieur des réserves risquent peut-être d\u27être affectés à la culture en rangs ou à d\u27autres formes d\u27agriculture considérant que la population humaine et la demande alimentaire augmentent. Les données relatives à l\u27habitat seront utiles pour les éventuelles recherches visant à identifier les risques au moment de la planification de la conservation du paysage dans l\u27aire de répartition de l\u27Outarde kori

Junior-elite football: time to re-position talent identification?

There remains limited understanding of the processes and factors which contribute to young footballers being identified as talented. Talent identification is imperative for the development of future elite performers, though most studies conflate talent identification and talent development. Moreover, within the literature there is a lack of operational or procedural distinction for talent identification, causing issues for those researching and working within applied contexts. This paper sought to clarify issues related to talent identification in junior-elite football, offering a review of the extant literature and proposing future directions for applied research. There are unanswered questions associated with how scouts, recruitment staff, and coaches decide what constitutes talent and the importance placed on particular attributes during that process. We suggest that further research into the ascribed processes, observations and perceptions of those involved in talent identification is needed to provide more sound understanding of the talent identification process in football

Ribosomal oxygenases are structurally conserved from prokaryotes to humans

2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components1,2 and in the hydroxylation of transcription factors3 and splicing factor proteins4. Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA5,6,7 and ribosomal proteins8 have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy9,10,11,12. The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans8 raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses arginine hydroxylation in the ribosomal protein L16; in humans, MYC-induced nuclear antigen (MINA53; also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone Nε-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases catalysing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate-oxidizing species reacts. This coordination flexibility has probably contributed to the evolution of the wide range of reactions catalysed by oxygenases

Non-equivalence of Wnt and R-spondin ligands during Lgr5+ intestinal stem-cell self-renewal

The canonical Wnt/β-catenin signaling pathway governs diverse developmental, homeostatic and pathologic processes. Palmitoylated Wnt ligands engage cell surface Frizzled (Fzd) receptors and Lrp5/6 co-receptors enabling β-catenin nuclear translocation and Tcf/Lef-dependent gene transactivation1–3. Mutations in Wnt downstream signaling components have revealed diverse functions presumptively attributed to Wnt ligands themselves, although direct attribution remains elusive, as complicated by redundancy between 19 mammalian Wnts and 10 Fzds1 and Wnt hydrophobicity2,3. For example, individual Wnt ligand mutations have not revealed homeostatic phenotypes in the intestinal epithelium4, an archetypal canonical Wnt pathway-dependent rapidly self-renewing tissue whose regeneration is fueled by proliferative crypt Lgr5+ intestinal stem cells (ISCs)5–9. R-spondin ligands (Rspo1–4) engage distinct Lgr4-6 and Rnf43/Znrf3 receptor classes10–13, markedly potentiate canonical Wnt/β-catenin signaling and induce intestinal organoid growth in vitro and Lgr5+ ISCs in vivo8,14–17. However, the interchangeability, functional cooperation and relative contributions of Wnt versus Rspo ligands to in vivo canonical Wnt signaling and ISC biology remain unknown. Here, we deconstructed functional roles of Wnt versus Rspo ligands in the intestinal crypt stem cell niche. We demonstrate that the default fate of Lgr5+ ISCs is lineage commitment, escape from which requires both Rspo and Wnt ligands. However, gain-of-function studies using Rspo versus a novel non-lipidated Wnt analog reveal qualitatively distinct, non-interchangeable roles for these ligands in ISCs. Wnts are insufficient to induce Lgr5+ ISC self-renewal, but rather confer a basal competency by maintaining Rspo receptor expression that enables Rspo to actively drive and specify the extent of stem cell expansion. This functionally non-equivalent yet cooperative interplay between Wnt and Rspo ligands establishes a molecular precedent for regulation of mammalian stem cells by distinct priming and self-renewal factors, with broad implications for precision control of tissue regeneration

Identification of Lysine 37 of Histone H2B as a Novel Site of Methylation

Recent technological advancements have allowed for highly-sophisticated mass spectrometry-based studies of the histone code, which predicts that combinations of post-translational modifications (PTMs) on histone proteins result in defined biological outcomes mediated by effector proteins that recognize such marks. While significant progress has been made in the identification and characterization of histone PTMs, a full appreciation of the complexity of the histone code will require a complete understanding of all the modifications that putatively contribute to it. Here, using the top-down mass spectrometry approach for identifying PTMs on full-length histones, we report that lysine 37 of histone H2B is dimethylated in the budding yeast Saccharomyces cerevisiae. By generating a modification-specific antibody and yeast strains that harbor mutations in the putative site of methylation, we provide evidence that this mark exist in vivo. Importantly, we show that this lysine residue is highly conserved through evolution, and provide evidence that this methylation event also occurs in higher eukaryotes. By identifying a novel site of histone methylation, this study adds to our overall understanding of the complex number of histone modifications that contribute to chromatin function

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

The combined application of next-generation sequencing platforms has provided an economical approach to unlocking the potential of the turkey genome

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction.

Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84-5.29) for men of European ancestry to 3.74 (95% CI, 3.36-4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14-2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71-0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction

The development and validation of a scoring tool to predict the operative duration of elective laparoscopic cholecystectomy

Background: The ability to accurately predict operative duration has the potential to optimise theatre efficiency and utilisation, thus reducing costs and increasing staff and patient satisfaction. With laparoscopic cholecystectomy being one of the most commonly performed procedures worldwide, a tool to predict operative duration could be extremely beneficial to healthcare organisations. Methods: Data collected from the CholeS study on patients undergoing cholecystectomy in UK and Irish hospitals between 04/2014 and 05/2014 were used to study operative duration. A multivariable binary logistic regression model was produced in order to identify significant independent predictors of long (> 90 min) operations. The resulting model was converted to a risk score, which was subsequently validated on second cohort of patients using ROC curves. Results: After exclusions, data were available for 7227 patients in the derivation (CholeS) cohort. The median operative duration was 60 min (interquartile range 45–85), with 17.7% of operations lasting longer than 90 min. Ten factors were found to be significant independent predictors of operative durations > 90 min, including ASA, age, previous surgical admissions, BMI, gallbladder wall thickness and CBD diameter. A risk score was then produced from these factors, and applied to a cohort of 2405 patients from a tertiary centre for external validation. This returned an area under the ROC curve of 0.708 (SE = 0.013, p  90 min increasing more than eightfold from 5.1 to 41.8% in the extremes of the score. Conclusion: The scoring tool produced in this study was found to be significantly predictive of long operative durations on validation in an external cohort. As such, the tool may have the potential to enable organisations to better organise theatre lists and deliver greater efficiencies in care