Defining the role of common variation in the genomic and biological architecture of adult human height.

Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated ∼2,000, ∼3,700 and ∼9,500 SNPs explained ∼21%, ∼24% and ∼29% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/β-catenin and chondroitin sulfate-related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.

Database resources for the tuberculosis community.

Access to online repositories for genomic and associated "-omics" datasets is now an essential part of everyday research activity. It is important therefore that the Tuberculosis community is aware of the databases and tools available to them online, as well as for the database hosts to know what the needs of the research community are. One of the goals of the Tuberculosis Annotation Jamboree, held in Washington DC on March 7th-8th 2012, was therefore to provide an overview of the current status of three key Tuberculosis resources, TubercuList (tuberculist.epfl.ch), TB Database (www.tbdb.org), and Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org). Here we summarize some key updates and upcoming features in TubercuList, and provide an overview of the PATRIC site and its online tools for pathogen RNA-Seq analysis.

Multispectral brain morphometry in Tourette syndrome persisting into adulthood.

Tourette syndrome is a childhood-onset neuropsychiatric disorder with a high prevalence of attention deficit hyperactivity and obsessive-compulsive disorder co-morbidities. Structural changes have been found in frontal cortex and striatum in children and adolescents. A limited number of morphometric studies in Tourette syndrome persisting into adulthood suggest ongoing structural alterations affecting frontostriatal circuits. Using cortical thickness estimation and voxel-based analysis of T1- and diffusion-weighted structural magnetic resonance images, we examined 40 adults with Tourette syndrome in comparison with 40 age- and gender-matched healthy controls. Patients with Tourette syndrome showed relative grey matter volume reduction in orbitofrontal, anterior cingulate and ventrolateral prefrontal cortices bilaterally. Cortical thinning extended into the limbic mesial temporal lobe. The grey matter changes were modulated additionally by the presence of co-morbidities and symptom severity. Prefrontal cortical thickness reduction correlated negatively with tic severity, while volume increase in primary somatosensory cortex depended on the intensity of premonitory sensations. Orbitofrontal cortex volume changes were further associated with abnormal water diffusivity within grey matter. White matter analysis revealed changes in fibre coherence in patients with Tourette syndrome within anterior parts of the corpus callosum. The severity of motor tics and premonitory urges had an impact on the integrity of tracts corresponding to cortico-cortical and cortico-subcortical connections. Our results provide empirical support for a patho-aetiological model of Tourette syndrome based on developmental abnormalities, with perturbation of compensatory systems marking persistence of symptoms into adulthood. We interpret the symptom severity related grey matter volume increase in distinct functional brain areas as evidence of ongoing structural plasticity. The convergence of evidence from volume and water diffusivity imaging strengthens the validity of our findings and attests to the value of a novel multimodal combination of volume and cortical thickness estimations that provides unique and complementary information by exploiting their differential sensitivity to structural change.

A genome-wide association search for type 2 diabetes genes in African Americans.

African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations.

Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection.

Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species' prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic. We identify four DRB codons, predicted to be involved in antigen binding, that are evolving under adaptive evolution. Our data suggest diversity at DRB may be maintained by balancing selection, consistent with the role of this locus as an antigen-binding region and the species' recent history of mass mortality during a series of bacterial epizootics. Phylogenetic analyses of DQB and DRB sequences from pinnipeds and other carnivores revealed significant allelic diversity, but little phylogenetic depth or structure among pinniped alleles; thus, we could neither confirm nor refute the possibility of trans-species polymorphism in this group. The phylogenetic pattern observed however, suggests some significant evolutionary constraint on these loci in the recent past, with the pattern consistent with that expected following an epizootic event. These data may help further elucidate some of the genetic factors underlying the unusually high susceptibility to bacterial infection of the threatened NZSL, and help us to better understand the extent and pattern of MHC diversity in pinnipeds.

Draft genome of the red harvester ant Pogonomyrmex barbatus.

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

New evidence for the social embeddedness of infants' early triangular capacities.

Infants appear to be active participants in complex interactional sequences with their parents far earlier than previously theorized. In this report, we document the capacity of 3-month-old infants to share attention with two partners (mothers and fathers) simultaneously, and trace links between this capacity and early family group-level dynamics. During comprehensive evaluations of the family's emergent coparenting alliance completed in 113 homes, we charted infants' eye gaze patterns during two different mother-father-infant assessment paradigms. Triangular capacities (operationalized as the frequency of rapid multishift gaze transitions between parents during interactions) were stable across interaction context. Infants exhibiting more advanced triangular capacities belonged to families showing evidence of better coparental adjustment. Theoretical and practice implications of these findings are discussed.

Disegni come documento e disegni come monumento : Giovanni Ciampini, Sebastiano Resta e la fortuna del Medioevo artistico nella Roma di Bellori

La tesi di Dottorato, condotta in accordo di colutela tra l'Università di Roma Tor Vergata e l'UNIL di Losanna, ha affrontato l'analisi di un gruppo di undici disegni custodia presso la National Gallery of Scotland di Edimburgo, copie di alcuni dei più significativi mosaici medioevali delle chiese di Roma, ricostruendone la genesi, quindi le vicende legate alla committenza, e il percorso collezionistico. I disegni scozzesi, oggetto di un importante articolo di Julian Gardner pubblicato sul Burlington Magatine nel 1973, furono commissionati intorno agli anni Settanta del XVII secolo dall'antiquario romano Giovanni Giustino Ciampini (1633-1698) in connessione alla stesura della sua opera di erudizione più avvertita e famosa: i Vetera Mommenta in' quibus praecipue Musiva Opera, sacrarum, profanan,mque, Aedìum structura, ac nonnulli antiqui ritus dissertationibus iconìbusque illustrantur. La composizione dei Vetera Mommenta - un'opera riccamente illustrata che nasce per rispondere alle esigenze della ideologia della Chiesa di Roma in un momento di rinnovata crisi del sistema - impone a Ciampini di porsi da un lato nella prospettiva della più alta tradizione antiquaria cinque e seicentesca, di cui recupera i metodi di lettura e di analisi applicati allo studio delle monete e dei monumenti antichi interpretati quali prove per la ricostruzione storica, e dall'altra, come è emerso dalle mie ricerche, lo pone immediatamente in contatto con gli avamposti del più moderno metodo di indagine storica e filologica applicato alle fonti e ai documenti della storia ecclesiastica, inaugurato dall'ambiente bollandista e inaurino. I monumenti paleocristiani e medioevali assumono in quest'ottica lo status di 'fatti incontestabili', le fonti primarie attraverso le quali Ciampini ricuce le tappe salienti della storia della Chiesa, da Costantino fino al XV secolo. Nel 1700 le copie di Edimburgo arrivano nelle mani del mercante e connoisseur milanese il padre oratoriano Sebastiano Resta (1635-1714), di stanza a Roma presso la Chiesa Nuova della Vallicella dal 1660, che decide di rilegarle tutte insieme in un volume da donare al suo maggiore acquirente e patrono, il vescovo di Arezzo Giovanni Matteo Marchetti. Come spiega Resta in alcune sue lettere, il presente avrebbe dovuto costituire insieme una curiosità ed offrire un confronto: infatti «le copie delli mosaici di Roma che erano di Monsignor Ciampini» - afferma Resta - avrebbero mostrato al Marchetti «le maniere di que' tempi gottici, barbari e divoti de cristiani e [fatto] spiccare i secoli seguenti». Questa indagine infatti ha fatto riemergere aspetti della precoce attenzione di Sebastiano Resta per l'arte dei "secoli bassi", mai debitamente affrontata dagli studi. E' infatti sulla scorta di una profonda conoscenza dei testi della letteratura artistica, e in connessione alla esplosione vivacissima della controversia Malvasia/Baldinucci sul primato del risorgere delle arti in Toscana, che Sebastiano a partire dagli anni Ottanta del Seicento comincia a meditare sul Medioevo artistico con il fine di spiegare l'evoluzione del linguaggio tecnico e formale che ha condotto alla perfezione dell'atte moderna. In questa prospettiva ι disegni del XIV e XV secolo che egli riuscì ad intercettare sul mercato valgono quali testimonianze delle maniere degli artefici più antichi e sono imbastiti nei molteplici album che Resta compone nel rispetto della successione cronologica dei presunti autori, e ordinati in base alle scuole pittoriche di pertinenza. La tesi permette perciò di descrivere nelle loro diverse specificità: da un lato il modo dei conoscitori come Resta, interessati nell'opera al dato stilistico, con immediate e sensibili ricadute sul mercato, e disposti anche con passione a ricercare i documenti relativi all'opera in quanto pressati dall'urgenza di collocarla nella sequenza cronologica dello sviluppo del linguaggio formale e tecnico; dall'altro gli antiquari come Ciampini e come Bianchini, per i quali le opere del passato valgono come prove irrefutabili della ricostruzione storica, e divengono quindi esse stesse, anche nel loro statuto di copia, documento della stona. Sono due approcci che si manifestano nel Seicento, e talvolta in una medesima persona, come mostra il caso anche per questo cruciale di Giovati Pietro Bellori, ma che hanno radici cinquecentesche, di cui i protagonisti di queste vicende sono ben consapevoli: e se dietro Resta c'è palesemente Vasari, dietro Ciampini e soprattutto Bianchini c'è la più alta tradizione antiquaria del XVI secolo, da Antonio Augustin a Fulvio Orsini.

Research recommendations for selected IARC-classified agents.

OBJECTIVES: There are some common occupational agents and exposure circumstances where evidence of carcinogenicity is substantial but not yet conclusive for humans. The objectives are to identify research gaps and needs for twenty agents prioritized for review based on evidence of widespread human exposures and potential carcinogenicity in animals or humans. DATA SOURCES: A systematic review was conducted of new data published since the most recent pertinent IARC monograph meeting. DATA EXTRACTION: Reviewers were charged with identifying data gaps and general and specific approaches to address them, focusing on research that would be important in resolving classification uncertainties. An expert meeting brought reviewers together to discuss each agent and the identified data gaps and approaches. DATA SYNTHESIS: Several overarching issues were identified that pertained to multiple agents; these included the importance of recognizing that carcinogenic agents can act through multiple toxicity pathways and mechanisms, including epigenetic mechanisms, oxidative stress and immuno- and hormonal modulation. CONCLUSIONS: Studies in occupational populations provide important opportunities to understand the mechanisms through which exogenous agents cause cancer and intervene to prevent human exposure and/or prevent or detect cancer among those already exposed. Scientific developments are likely to increase the challenges and complexities of carcinogen testing and evaluation in the future, and epidemiologic studies will be particularly critical to inform carcinogen classification and risk assessment processes.[Authors]

A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.

Recent genome-wide association studies have described many loci implicated in type 2 diabetes (T2D) pathophysiology and β-cell dysfunction but have contributed little to the understanding of the genetic basis of insulin resistance. We hypothesized that genes implicated in insulin resistance pathways might be uncovered by accounting for differences in body mass index (BMI) and potential interactions between BMI and genetic variants. We applied a joint meta-analysis approach to test associations with fasting insulin and glucose on a genome-wide scale. We present six previously unknown loci associated with fasting insulin at P < 5 × 10(-8) in combined discovery and follow-up analyses of 52 studies comprising up to 96,496 non-diabetic individuals. Risk variants were associated with higher triglyceride and lower high-density lipoprotein (HDL) cholesterol levels, suggesting a role for these loci in insulin resistance pathways. The discovery of these loci will aid further characterization of the role of insulin resistance in T2D pathophysiology.

Loss of phenotypic plasticity generates genotype-caste association in harvester ants.

Caste differentiation and reproductive division of labor are the hallmarks of insect societies. In ants and other social Hymenoptera, development of female larvae into queens or workers generally results from environmentally induced differences in gene expression. However, several cases in which certain gene combinations may determine reproductive status have been described in bees and ants. We investigated experimentally whether genotype directly influences caste determination in two populations of Pogonomyrmex harvester ants in which genotype-caste associations have been observed. Each population contains two genetic lineages. Queens are polyandrous and mate with males of both lineages , but in mature colonies, over 95% of daughter queens have a pure-lineage genome, whereas all workers are of F1 interlineage ancestry. We found that this pattern is maintained throughout the colony life cycle, even when only a single caste is being produced. Through controlled crosses, we demonstrate that pure-lineage eggs fail to develop into workers even when interlineage brood are not present. Thus, environmental caste determination in these individuals appears to have been lost in favor of a hardwired genetic mechanism. Our results reveal that genetic control of reproductive fate can persist without loss of the eusocial caste structure.