A Cis-Regulatory Map of the Drosophila Genome

Systematic annotation of gene regulatory elements is a major challenge in genome science. Direct mapping of chromatin modification marks and transcriptional factor binding sites genome-wide1, 2 has successfully identified specific subtypes of regulatory elements3. In Drosophila several pioneering studies have provided genome-wide identification of Polycomb response elements4, chromatin states5, transcription factor binding sites6, 7, 8, 9, RNA polymerase II regulation8 and insulator elements10; however, comprehensive annotation of the regulatory genome remains a significant challenge. Here we describe results from the modENCODE cis-regulatory annotation project. We produced a map of the Drosophila melanogaster regulatory genome on the basis of more than 300 chromatin immunoprecipitation data sets for eight chromatin features, five histone deacetylases and thirty-eight site-specific transcription factors at different stages of development. Using these data we inferred more than 20,000 candidate regulatory elements and validated a subset of predictions for promoters, enhancers and insulators in vivo. We identified also nearly 2,000 genomic regions of dense transcription factor binding associated with chromatin activity and accessibility. We discovered hundreds of new transcription factor co-binding relationships and defined a transcription factor network with over 800 potential regulatory relationships

Uptake of Team Care Arrangements for adults newly diagnosed with cancer

Background. Medicare-subsidised Team Care Arrangements (TCAs) support Australian general practitioners to implement shared care between collaborating health professionals for patients with chronic medical conditions and complex needs. We assessed the prevalence of TCAs, factors associated with TCA uptake and visits to TCA-subsidised allied health practitioners, for adults newly diagnosed with cancer in New South Wales, Australia. Methods. We carried out a retrospective individual patient data linkage study with 13 951 45 and Up Study participants diagnosed with incident cancer during 2006–16. We used a proportional hazards model to estimate the factors associated with receipt of a TCA after cancer diagnosis. Results. In total, 6630 patients had a TCA plan initiated (47.5%). A TCA was more likely for patients aged ≥65 years, those with higher service utilisation 4–15 months prior to cancer diagnosis, a higher number of comorbidities, lower self-rated overall health status, living in areas of greater socio-economic disadvantage, lower educational attainment and those with no private health insurance. A total of 4084 (61.6%) patients with a TCA had at least one TCA-subsidised allied health visit within 24 months of the TCA. Conclusions. TCAs appear to be well targeted at cancer patients with chronic health conditions and lower socioeconomic status. Nevertheless, not all patients with a TCA subsequently attended a TCA-subsidised allied healthcare professional. This suggests either a misunderstanding of the plan, the receipt of allied health via other public schemes, a low prioritisation of the plan compared to other health care, or suboptimal availability of these service

Hydro-bio-geo-socio-chemical interactions and the sustainability of residential landscapes

Significance statement: The paper presents major new insights into the multidisciplinary controls of nitrogen export (a widespread environmental concern) from residential landscapes. We conducted biogeochemical and social survey studies to identify locations (hotspots) or times (hot moments) with a disproportionate influence on this export. Results showed high variation in the vulnerability/sensitivity of individual parcels to cause environmental damage and in the knowledge and practices of individual managers. To the extent that hotspots are the result of management choices by homeowners, there are straightforward approaches to improve outcomes, e.g. fertilizer restrictions. If, however, hotspots arise from the configuration and inherent characteristics of parcels and neighborhoods, efforts to improve outcomes may involve more intensive and complex interventions, such as conversion to alternative ecosystem type

Concert recording 2017-04-27

[Track 1]. Adoramus te, Christe / Giovanni Pierluigi da Palestrina -- [Track 2]. Ubi caritas / Maurice Duruflé -- [Track 3]. Three Hungarian folk songs. I. The handsome butcher II. Apple, apple III. The old woman / Matyas Seiber -- [Track 4]. He watching over Israel from Elijah / Felix Mendelssohn Bartholdy -- [Track 5]. Ain\u27t got time to die / Hall Johnson

Role of CYP27A in cholesterol and bile acid metabolism

The CYP27A gene encodes a mitochondrial cytochrome P450 enzyme, sterol 27-hydroxylase, that is expressed in many different tissues and plays an important role in cholesterol and bile acid metabolism. In humans, CYP27A deficiency leads to cerebrotendinous xanthomatosis. To gain insight into the roles of CYP27A in the regulation of cholesterol and bile acid metabolism, cyp27A gene knockout heterozygous, homozygous, and wild-type littermate mice were studied. In contrast to homozygotes, heterozygotes had increased body weight and were mildly hypercholesterolemic, with increased numbers of lipoprotein particles in the low density lipoprotein size range. Cyp7A expression was not increased in heterozygotes but was in homozygotes, suggesting that parts of the homozygous phenotype are secondary to increased cyp7A expression and activity. Homozygotes exhibited pronounced hepatomegaly and dysregulation in hepatic cholesterol, bile acid, and fatty acid metabolism. Hepatic cholesterol synthesis and synthesis of bile acid intermediates were increased; however, side chain cleavage was impaired, leading to decreased bile salt concentrations in gallbladder bile. Expression of Na-taurocholate cotransporting polypeptide, the major sinusoidal bile salt transporter, was increased, and that of bile salt export pump, the major canalicular bile salt transporter, was decreased. Gender played a modifying role in the homozygous response to cyp27A deficiency, with females being gen

SLC35A2â CDG: Functional characterization, expanded molecular, clinical, and biochemical phenotypes of 30 unreported Individuals

Pathogenic de novo variants in the Xâ linked gene SLC35A2 encoding the major Golgiâ localized UDPâ galactose transporter required for proper protein and lipid glycosylation cause a rare type of congenital disorder of glycosylation known as SLC35A2â congenital disorders of glycosylation (CDG; formerly CDGâ IIm). To date, 29 unique de novo variants from 32 unrelated individuals have been described in the literature. The majority of affected individuals are primarily characterized by varying degrees of neurological impairments with or without skeletal abnormalities. Surprisingly, most affected individuals do not show abnormalities in serum transferrin Nâ glycosylation, a common biomarker for most types of CDG. Here we present data characterizing 30 individuals and add 26 new variants, the single largest study involving SLC35A2â CDG. The great majority of these individuals had normal transferrin glycosylation. In addition, expanding the molecular and clinical spectrum of this rare disorder, we developed a robust and reliable biochemical assay to assess SLC35A2â dependent UDPâ galactose transport activity in primary fibroblasts. Finally, we show that transport activity is directly correlated to the ratio of wildâ type to mutant alleles in fibroblasts from affected individuals.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/150498/1/humu23731_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150498/2/humu23731-sup-0001-Supp_Mat__2019.2.10_.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/150498/3/humu23731.pd

Serum Biomarkers Correlated with Liver Stiffness Assessed in a Multicenter Study of Pediatric Cholestatic Liver Disease

BACKGROUND AND AIMS: Detailed investigation of the biological pathways leading to hepatic fibrosis and identification of liver fibrosis biomarkers may facilitate early interventions for pediatric cholestasis. APPROACH AND RESULTS: A targeted enzyme-linked immunosorbent assay-based panel of nine biomarkers (lysyl oxidase, tissue inhibitor matrix metalloproteinase (MMP) 1, connective tissue growth factor [CTGF], IL-8, endoglin, periostin, Mac-2-binding protein, MMP-3, and MMP-7) was examined in children with biliary atresia (BA; n = 187), alpha-1 antitrypsin deficiency (A1AT; n = 78), and Alagille syndrome (ALGS; n = 65) and correlated with liver stiffness (LSM) and biochemical measures of liver disease. Median age and LSM were 9 years and 9.5 kPa. After adjusting for covariates, there were positive correlations among LSM and endoglin ( p = 0.04) and IL-8 ( p \u3c 0.001) and MMP-7 ( p \u3c 0.001) in participants with BA. The best prediction model for LSM in BA using clinical and lab measurements had an R2 = 0.437; adding IL-8 and MMP-7 improved R2 to 0.523 and 0.526 (both p \u3c 0.0001). In participants with A1AT, CTGF and LSM were negatively correlated ( p = 0.004); adding CTGF to an LSM prediction model improved R2 from 0.524 to 0.577 ( p = 0.0033). Biomarkers did not correlate with LSM in ALGS. A significant number of biomarker/lab correlations were found in participants with BA but not those with A1AT or ALGS. CONCLUSIONS: Endoglin, IL-8, and MMP-7 significantly correlate with increased LSM in children with BA, whereas CTGF inversely correlates with LSM in participants with A1AT; these biomarkers appear to enhance prediction of LSM beyond clinical tests. Future disease-specific investigations of change in these biomarkers over time and as predictors of clinical outcomes will be important

Accuracy versus precision in boosted top tagging with the ATLAS detector

The identification of top quark decays where the top quark has a large momentum transverse to the beam axis, known as top tagging, is a crucial component in many measurements of Standard Model processes and searches for beyond the Standard Model physics at the Large Hadron Collider. Machine learning techniques have improved the performance of top tagging algorithms, but the size of the systematic uncertainties for all proposed algorithms has not been systematically studied. This paper presents the performance of several machine learning based top tagging algorithms on a dataset constructed from simulated proton-proton collision events measured with the ATLAS detector at √s = 13 TeV. The systematic uncertainties associated with these algorithms are estimated through an approximate procedure that is not meant to be used in a physics analysis, but is appropriate for the level of precision required for this study. The most performant algorithms are found to have the largest uncertainties, motivating the development of methods to reduce these uncertainties without compromising performance. To enable such efforts in the wider scientific community, the datasets used in this paper are made publicly available

Studies of the Energy Dependence of Diboson Polarization Fractions and the Radiation-Amplitude-Zero Effect in WZ Production with the ATLAS Detector

: This Letter presents the first study of the energy dependence of diboson polarization fractions in WZ→lνl^{'}l^{'}(l,l^{'}=e,μ) production. The dataset used corresponds to an integrated luminosity of 140 fb^{-1} of proton-proton collisions at a center-of-mass energy of 13 TeV recorded by the ATLAS detector. Two fiducial regions with an enhanced presence of events featuring two longitudinally polarized bosons are defined. A nonzero fraction of events with two longitudinally polarized bosons is measured with an observed significance of 5.3 standard deviations in the region with 100200 GeV, where p_{T}^{Z} is the transverse momentum of the Z boson. This Letter also reports the first study of the radiation-amplitude-zero effect. Events with two transversely polarized bosons are analyzed for the ΔY(l_{W}Z) and ΔY(WZ) distributions defined respectively as the rapidity difference between the lepton from the W boson decay and the Z boson and the rapidity difference between the W boson and the Z boson. Significant suppression of events near zero is observed in both distributions. Unfolded ΔY(l_{W}Z) and ΔY(WZ) distributions are also measured and compared to theoretical predictions