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  • Open Access
    Authors: 
    Alanna C. Morrison; Joshua C. Bis; Shih-Jen Hwang; Georg Ehret; Thomas Lumley; Kenneth Rice; Donna M. Muzny; Richard A. Gibbs; Eric Boerwinkle; Bruce M. Psaty; +2 more
    Publisher: Public Library of Science (PLoS)
    Country: Switzerland
    Project: NIH | CHS-ULTRASOUND READING (N01HC045133-004), NIH | Building on GWAS for NHLB... (1RC2HL102419-01), NIH | CHS-Transition Phase -268... (N01HC055222-001), NIH | CORONARY HEART DISEASE &S... (N01HC085080-018), NIH | CHARGE consortium: gene d... (2R01HL105756-07), NIH | THE FRAMINGHAM HEART STUD... (N01HC025195-005), NIH | Hormonal trajectories in ... (5R01AG027058-04), NIH | CORONARY HEART DISEASE &S... (N01HC085081-016), NIH | Genomes and Genetics at t... (3U54HG003273-04S1), NIH | CORONARY HEART DISEASE &S... (N01HC085083-021),...

    Background Genome-wide association studies (GWAS) identified multiple loci for blood pressure (BP) and hypertension. Six genes – ATP2B1, CACNB2, CYP17A1, JAG1, PLEKHA7, and SH2B3 – were evaluated for sequence variation with large effects on systolic blood pressure (SBP), diastolic blood pressure (DBP), pulse pressure (PP), and mean arterial pressure (MAP). Methods and Results Targeted genomic sequence was determined in 4,178 European ancestry participants from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium. Common variants (≥50 minor allele copies) were evaluated individually and rare variants (minor allele frequency, MAF≤1%) were aggregated by locus. 464 common variants were identified across the 6 genes. An upstream CYP17A1 variant, rs11191416 (MAF = 0.09), was the most significant association for SBP (P = 0.0005); however the association was attenuated (P = 0.0469) after conditioning on the GWAS index single nucleotide polymorphism (SNP). A PLEKHA7 intronic variant was the strongest DBP association (rs12806040, MAF = 0.007, P = 0.0006) and was not in LD (r2 = 0.01) with the GWAS SNP. A CACNB2 intronic SNP, rs1571787, was the most significant association with PP (MAF = 0.27, P = 0.0003), but was not independent from the GWAS SNP (r2 = 0.34). Three variants (rs6163 and rs743572 in the CYP17A1 region and rs112467382 in PLEKHA7) were associated with BP traits (P<0.001). Rare variation, aggregately assessed in the 6 regions, was not significantly associated with BP measures. Conclusion Six targeted gene regions, previously identified by GWAS, did not harbor novel variation with large effects on BP in this sample.

  • Open Access English
    Authors: 
    Qing Chen; Jinwei Wang; Jun Tian; Xun Tang; Canqing Yu; Roger Marshall; Dafang Chen; Weihua Cao; Siyan Zhan; Jun Lv; +2 more
    Publisher: Public Library of Science

    Several studies have suggested an association between ambient air temperature and blood pressure. However, this has not been reliably confirmed by longitudinal studies. Also, whether the reaction to temperature stimulation is modified by other factors such as antihypertensive medication is rarely investigated. The present study explores the relationship between ambient temperature and blood pressure, without and with antihypertensive medication, in a study of 1,831 hypertensive patients followed up for three years, in two or four weekly check ups, accumulating 62,452 follow-up records. Both baseline and follow-up blood pressure showed an inverse association with ambient temperature, which explained 32.4% and 65.6% of variation of systolic blood pressure and diastolic blood pressure (P<0.05) respectively. The amplitude of individual blood pressure fluctuation with temperature throughout a year (a 29 degrees centigrade range) was 9.4/7.3 mmHg. Medication with angiotensin converting enzyme inhibitor benazepril attenuated the blood pressure fluctuation by 2.4/1.3 mmHg each year, though the inverse association of temperature and blood pressure remained. Gender, drinking behavior and body mass index were also found to modify the association between temperature and diastolic blood pressure. The results indicate that ambient temperature may negatively regulate blood pressure. Hypertensive patients should monitor and treat blood pressure more carefully in cold days, and it could be especially important for the males, thinner people and drinkers.

  • Open Access English
    Authors: 
    Judith Field; Sharon R. Browning; Laura J. Johnson; Patrick Danoy; Michael D. Varney; Brian D. Tait; Kaushal S. Gandhi; Jac Charlesworth; Robert Heard; Graeme J. Stewart; +10 more
    Publisher: Public Library of Science (PLoS)
    Project: WT | A national DNA control se... (068545), NHMRC | Identifying genes in the ... (509184), UKRI | Assessment of biomedical ... (G0000934)

    We conducted an association study across the human leukocyte antigen (HLA) complex to identify loci associated with multiple sclerosis (MS). Comparing 1927 SNPs in 1618 MS cases and 3413 controls of European ancestry, we identified seven SNPs that were independently associated with MS conditional on the others (each P ≤ 4 x 10(-6)). All associations were significant in an independent replication cohort of 2212 cases and 2251 controls (P ≤ 0.001) and were highly significant in the combined dataset (P ≤ 6 x 10(-8)). The associated SNPs included proxies for HLA-DRB1*15:01 and HLA-DRB1*03:01, and SNPs in moderate linkage disequilibrium (LD) with HLA-A*02:01, HLA-DRB1*04:01 and HLA-DRB1*13:03. We also found a strong association with rs9277535 in the class II gene HLA-DPB1 (discovery set P = 9 x 10(-9), replication set P = 7 x 10(-4), combined P = 2 x 10(-10)). HLA-DPB1 is located centromeric of the more commonly typed class II genes HLA-DRB1, -DQA1 and -DQB1. It is separated from these genes by a recombination hotspot, and the association is not affected by conditioning on genotypes at DRB1, DQA1 and DQB1. Hence rs9277535 represents an independent MS-susceptibility locus of genome-wide significance. It is correlated with the HLA-DPB1*03:01 allele, which has been implicated previously in MS in smaller studies. Further genotyping in large datasets is required to confirm and resolve this association.

  • Open Access English
    Authors: 
    Konstanze Gebauer; Katharine J. M. Dickinson; Peter A. Whigham; Philip J. Seddon;
    Publisher: Public Library of Science

    Modelling metapopulation dynamics is a potentially very powerful tool for conservation biologists. In recent years, scientists have broadened the range of variables incorporated into metapopulation modelling from using almost exclusively habitat patch size and isolation, to the inclusion of attributes of the matrix and habitat patch quality. We investigated the influence of habitat patch and matrix characteristics on the metapopulation parameters of a highly endangered lizard species, the New Zealand endemic grand skink (Oligosoma grande) taking into account incomplete detectability. The predictive ability of the developed zxmetapopulation model was assessed through cross-validation of the data and with an independent data-set. Grand skinks occur on scattered rock-outcrops surrounded by indigenous tussock (bunch) and pasture grasslands therefore implying a metapopulation structure. We found that the type of matrix surrounding the habitat patch was equally as important as the size of habitat patch for estimating occupancy, colonisation and extinction probabilities. Additionally, the type of matrix was more important than the physical distance between habitat patches for colonisation probabilities. Detection probability differed between habitat patches in the two matrix types and between habitat patches with different attributes such as habitat patch composition and abundance of vegetation on the outcrop. The developed metapopulation models can now be used for management decisions on area protection, monitoring, and the selection of translocation sites for the grand skink. Our study showed that it is important to incorporate not only habitat patch size and distance between habitat patches, but also those matrix type and habitat patch attributes which are vital in the ecology of the target species.

  • Open Access English
    Authors: 
    Nicola Anstice; Robert J. Jacobs; Samantha K Simkin; Melissa Thomson; Benjamin Thompson; Andrew V. Collins;
    Publisher: Public Library of Science

    Purpose Children may be tested with a variety of visual acuity (VA) charts during their ophthalmic care and differences between charts can complicate the interpretation of VA measurements. This study compared VA measurements across four pediatric charts with Sloan letters and identified chart design features that contributed to inter-chart differences in VA. Methods VA was determined for right eyes of 25 adults and 17 children (4–9 years of age) using Crowded Kay Pictures, Crowded linear Lea Symbols, Crowded Keeler logMAR, Crowded HOTV and Early Treatment of Diabetic Retinopathy Study (ETDRS) charts in focused and defocused (+1.00 DS optical blur) conditions. In a separate group of 25 adults, we compared the VA from individual Kay Picture optotypes with uncrowded Landolt C VA measurements. Results Crowded Kay Pictures generated significantly better VA measurements than all other charts in both adults and children (p < 0.001; 0.15 to 0.30 logMAR). No significant differences were found between other charts in adult participants; children achieved significantly poorer VA measurements on the ETDRS chart compared with pediatric acuity tests. All Kay Pictures optotypes produced better VA (p < 0.001), varying from -0.38 ± 0.13 logMAR (apple) to -0.57 ± 0.10 logMAR (duck), than the reference Landolt C task (mean VA -0.19 ± 0.08 logMAR). Conclusion Kay Pictures over-estimated VA in all participants. Variability between Kay Pictures optotypes suggests that shape cues aid in optotype determination. Other pediatric charts offer more comparable VA measures and should be used for children likely to progress to letter charts.

  • Open Access
    Authors: 
    Stewart G. Stevens; Chris M. Brown;
    Publisher: Public Library of Science (PLoS)

    Recently large scale transcriptome and proteome datasets for human cells have become available. A striking finding from these studies is that the level of an mRNA typically predicts no more than 40% of the abundance of protein. This correlation represents the overall figure for all genes. We present here a bioinformatic analysis of translation efficiency – the rate at which mRNA is translated into protein. We have analysed those human datasets that include genome wide mRNA and protein levels determined in the same study. The analysis comprises five distinct human cell lines that together provide comparable data for 8,170 genes. For each gene we have used levels of mRNA and protein combined with protein stability data from the HeLa cell line to estimate translation efficiency. This was possible for 3,990 genes in one or more cell lines and 1,807 genes in all five cell lines. Interestingly, our analysis and modelling shows that for many genes this estimated translation efficiency has considerable consistency between cell lines. Some deviations from this consistency likely result from the regulation of protein degradation. Others are likely due to known translational control mechanisms. These findings suggest it will be possible to build improved models for the interpretation of mRNA expression data. The results we present here provide a view of translation efficiency for many genes. We provide an online resource allowing the exploration of translation efficiency in genes of interest within different cell lines (http://bioanalysis.otago.ac.nz/TranslationEfficiency).

  • Open Access English
    Authors: 
    Hadriano M. Lacerda; Lorenzo Richiardi; Andreas Pettersson; Marine Corbin; Franco Merletti; Olof Akre;
    Publisher: Public Library of Science
    Country: Italy

    BackgroundUndescended testis, or cryptorchidism, occurs in 2-5% of boys born at term, and by 12 months of age about 1% of all boys have manifest cryptorchidism. Several hormonal substances control this process and disruption of the foetal sex-hormones balance is a potential cause of undescended testis, however, to a great extent the aetiology of cryptorchidism is unclear.MethodologyTo study risk factors involved in the aetiology of undescended testis, we assessed cancer risk in 15,885 mothers of men operated for undescended testis in Sweden. Women were followed-up for a median period of 23 years during which 811 first primary malignancies occurred. Their cancer incidence was compared with that in the general population estimating standardized incidence ratio (SIR) and corresponding 95% confidence interval (CI).Principal findingsThe overall cancer risk experienced by the mothers of cryptorchid men did not differ significantly from that of the general population (SIR = 0.94; 95% C.I. = 0.88-1.01). Specifically, there was a reduction in ovarian cancer risk (SIR = 0.72; 95% C.I. = 0.51-0.99), while the risk of lung (SIR = 1.38 95% C.I. 1.03-1.81) and biliary tract/liver cancer (SIR: 1.76, 95% CI: 1.03-2.82) were increased.ConclusionsAlthough we cannot rule out the role of chance, our data suggest a positive association between undescended testis and maternal lung cancer and a negative association with ovarian cancer, where the first may be partly attributable to smoking and the second to an altered hormonal milieu during pregnancy and thus both exposures may be risk factors for cryptorchidism.

  • Open Access
    Authors: 
    Jenny Saxton; Simone N. Rodda; Natalia Booth; Stephanie S Merkouris; Nicki A. Dowling;
    Publisher: Public Library of Science (PLoS)

    Personalized Normative Feedback (PNF) may help address addictive disorders. PNF highlights discrepancies between perceived and actual peer norms, juxtaposed against self-reported behavior. PNF can be self-directed and cost-efficient. Our study estimates the efficacy of PNF alone, and in combination with other self-directed interventions, to address frequency and symptom severity of hazardous alcohol use, problem gambling, illicit drug and tobacco use. We searched electronic databases, grey literature, and reference lists of included articles, for randomized controlled trials published in English (January 2000-August 2019). We assessed study quality using the Cochrane Risk of Bias tool. Thirty-four studies met inclusion criteria (k = 28 alcohol, k = 3 gambling, k = 3 cannabis, k = 0 tobacco). Thirty studies provided suitable data for meta-analyses. PNF alone, and with additional interventions, reduced short-term alcohol frequency and symptom severity. PNF with additional interventions reduced short-term gambling symptom severity. Effect sizes were small. PNF did not alter illicit drug use. Findings highlight the efficacy of PNF to address alcohol frequency and symptom severity. The limited number of studies suggest further research is needed to ascertain the efficacy of PNF for gambling and illicit drug use. Cost-effectiveness analyses are required to determine the scale of PNF needed to justify its use in various settings.

  • Open Access English
    Authors: 
    S. A. Michael; David T. S. Hayman; Rachael Gray; Ji Zhang; Lynn Rogers; Wendi D. Roe;
    Publisher: Public Library of Science

    New Zealand sea lions (Phocarctos hookeri) are an endemic and endangered species. Pup mortality at Enderby Island (50.5°S, 166.28°E) in the New Zealand sub-Antarctic has been well studied, with subsequent investigations yielding more intricate detail of the causes of mortality, as new diagnostic methods become available. Klebsiella pneumoniae was first reported in 2001-02 at this site, causing a pup mortality epizootic and is now known to be present at several colonies. This bacterium is a common mucosal commensal of humans and animals, however the agent found in pups at necropsy is a hypervirulent strain, readily recognised in microbial culture as being hypermucoviscous. Infection causes septicaemia with a common syndrome of subsequent meningitis and polyarthritis. This investigation uses histopathology and microbiology, with new modalities such as matrix assisted laser desorption/ionisation-time of flight mass spectrometry to show that Klebsiella septicaemia could have historically been, and continues to be, the most important cause of pup mortality, but has been previously underrepresented due to the often cryptic presentation and sometimes peracute course of disease. Hypermucoviscous K. pneumoniae should be considered a serious threat to pup survival in the species, causing on average 60.2% of pup deaths annually at Enderby Island between 2013 and 2018, with likely more continuing mortality following pup dispersal and the cessation of the summer monitoring season. Less common causes of death included starvation (14.8%), trauma/asphyxiation (9.9%) and other infections (7%). This study forms the basis for further evaluation of risk factors for pup mortality in the species, with a view to developing active mitigation.

  • Open Access English
    Authors: 
    Micha J. A. Rijkenberg; Rob Middag; Patrick Laan; Loes J. A. Gerringa; Hendrik M. van Aken; Véronique Schoemann; Jeroen de Jong; Hein J W de Baar;
    Publisher: Public Library of Science
    Countries: Belgium, Netherlands, Netherlands
    Project: NWO | Geotraces, Global Change ... (2300152311)

    Iron (Fe) is an essential trace element for marine life. Extremely low Fe concentrations limit primary production and nitrogen fixation in large parts of the oceans and consequently influence ocean ecosystem functioning. The importance of Fe for ocean ecosystems makes Fe one of the core chemical trace elements in the international GEOTRACES program. Despite the recognized importance of Fe, our present knowledge of its supply and biogeochemical cycle has been limited by mostly fragmentary datasets. Here, we present highly accurate dissolved Fe (DFe) values measured at an unprecedented high intensity (1407 samples) along the longest full ocean depth transect (17,500 kilometers) covering the entire western Atlantic Ocean. DFe measurements along this transect unveiled details about the supply and cycling of Fe. External sources of Fe identified included off-shelf and river supply, hydrothermal vents and aeolian dust. Nevertheless, vertical processes such as the recycling of Fe resulting from the remineralization of sinking organic matter and the removal of Fe by scavenging still dominated the distribution of DFe. In the northern West Atlantic Ocean, Fe recycling and lateral transport from the eastern tropical North Atlantic Oxygen Minimum Zone (OMZ) dominated the DFe-distribution. Finally, our measurements showed that the North Atlantic Deep Water (NADW), the major driver of the so-called ocean conveyor belt, contains excess DFe relative to phosphate after full biological utilization and is therefore an important source of Fe for biological production in the global ocean.

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