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61.
Alfons R. Weig Derek Peršoh Sebastian Werner Amelie Betzlbacher Gerhard Rambold 《Mycological Progress》2013,12(4):719-725
Biodiversity research rapidly progresses due to the continuous improvement of high-throughput analysis platforms, which facilitate detailed analyses of the composition and architecture of microbial communities in various environmental niches. In the fields of applied forestry and agriculture, microbial communities are also increasingly considered, because they are involved in various kinds of biotic interactions with plants and therefore have high diagnostic value for assessing the health status of plants and soils. While in-depth identification of microbial species in environmental samples is currently achieved by next generation sequencing or microarray techniques, profiling of whole microbial communities can be accomplished via less labor-intensive approaches. We modified the protocol for automated ribosomal intergenic spacer analysis (ARISA) by targeting length polymorphism of the fungal ITS1 rRNA gene for a rapid diagnostic assessment of fungal community composition and surveyed its application spectrum. The approach allowed for spatial and temporal differentiation among fungal assemblages in soil samples and different plant species, and is therefore particularly useful for environmental screening and monitoring projects. Standardized experimental conditions permit the cumulative gathering of data, for instance during long-term projects. 相似文献
62.
A Elsäβer A Victor G Hommel 《Statistical applications in genetics and molecular biology》2011,10(1):Article 51
In candidate gene association studies, usually several elementary hypotheses are tested simultaneously using one particular set of data. The data normally consist of partly correlated SNP information. Every SNP can be tested for association with the disease, e.g., using the Cochran-Armitage test for trend. To account for the multiplicity of the test situation, different types of multiple testing procedures have been proposed. The question arises whether procedures taking into account the discreteness of the situation show a benefit especially in case of correlated data. We empirically evaluate several different multiple testing procedures via simulation studies using simulated correlated SNP data. We analyze FDR and FWER controlling procedures, special procedures for discrete situations, and the minP-resampling-based procedure. Within the simulation study, we examine a broad range of different gene data scenarios. We show that the main difference in the varying performance of the procedures is due to sample size. In small sample size scenarios,the minP-resampling procedure though controlling the stricter FWER even had more power than the classical FDR controlling procedures. In contrast, FDR controlling procedures led to more rejections in higher sample size scenarios. 相似文献
63.
McKay JD Truong T Gaborieau V Chabrier A Chuang SC Byrnes G Zaridze D Shangina O Szeszenia-Dabrowska N Lissowska J Rudnai P Fabianova E Bucur A Bencko V Holcatova I Janout V Foretova L Lagiou P Trichopoulos D Benhamou S Bouchardy C Ahrens W Merletti F Richiardi L Talamini R Barzan L Kjaerheim K Macfarlane GJ Macfarlane TV Simonato L Canova C Agudo A Castellsagué X Lowry R Conway DI McKinney PA Healy CM Toner ME Znaor A Curado MP Koifman S Menezes A Wünsch-Filho V Neto JE Garrote LF Boccia S 《PLoS genetics》2011,7(3):e1001333
Genome-wide association studies (GWAS) have been successful in identifying common genetic variation involved in susceptibility to etiologically complex disease. We conducted a GWAS to identify common genetic variation involved in susceptibility to upper aero-digestive tract (UADT) cancers. Genome-wide genotyping was carried out using the Illumina HumanHap300 beadchips in 2,091 UADT cancer cases and 3,513 controls from two large European multi-centre UADT cancer studies, as well as 4,821 generic controls. The 19 top-ranked variants were investigated further in an additional 6,514 UADT cancer cases and 7,892 controls of European descent from an additional 13 UADT cancer studies participating in the INHANCE consortium. Five common variants presented evidence for significant association in the combined analysis (p≤5×10−7). Two novel variants were identified, a 4q21 variant (rs1494961, p = 1×10−8) located near DNA repair related genes HEL308 and FAM175A (or Abraxas) and a 12q24 variant (rs4767364, p = 2×10−8) located in an extended linkage disequilibrium region that contains multiple genes including the aldehyde dehydrogenase 2 (ALDH2) gene. Three remaining variants are located in the ADH gene cluster and were identified previously in a candidate gene study involving some of these samples. The association between these three variants and UADT cancers was independently replicated in 5,092 UADT cancer cases and 6,794 controls non-overlapping samples presented here (rs1573496-ADH7, p = 5×10−8; rs1229984-ADH1B, p = 7×10−9; and rs698-ADH1C, p = 0.02). These results implicate two variants at 4q21 and 12q24 and further highlight three ADH variants in UADT cancer susceptibility. 相似文献
64.
Photosystem I is the light-driven plastocyanin-ferredoxin oxidoreductase in the photosynthetic electron transfer of cyanobacteria and plants. Two histidyl residues in the symmetric transmembrane helices A-j and B-j provide ligands for the P700 chlorophyll molecules of the reaction center of photosystem I. To determine the role of conserved aromatic residues adjacent to the histidyl molecule in the helix of B-j, we generated six site-directed mutants of the psaB gene in Synechocystis sp. PCC 6803. Three mutant strains with W645C, W643C/A644I and S641C/V642I substitutions could grow photoautotrophically and showed no obvious reduction in the photosystem I activity. Kinetics of P700 re-reduction by plastocyanin remained unaltered in these mutants. In contrast, the strains with H651C/L652M, F649C/G650I and F647C substitutions could not grow under photoautotrophic conditions because those mutants had low photosystem I activity, possibly due to low levels of proteins. A procedure to select spontaneous revertants from the mutants that are incapable to photoautotrophic growth resulted in three revertants that were used in this study. The molecular analysis of the spontaneous revertants suggested that an aromatic residue at F647 and a small residue at G650 may be necessary for maintaining the structural integrity of photosystem I. The (P700+ - P700) steady-state absorption difference spectrum of the revertant F647Y has a ∼5 nm narrower peak than the recovered wild-type, suggesting that additional hydroxyl group of this revertant may participate in the interaction with the special pair while the photosystem I complexes of the F649C/G650T and H651Q mutants closely resemble the wild-type spectrum. The results presented here demonstrate that the highly conserved residues W645, W643 and F649 are not critical for maintaining the integrity and in mediating electron transport from plastocyanin to photosystem I. Our data suggest that an aromatic residue is required at position of 647 for structural integrity and/or function of photosystem I. 相似文献
65.
66.
Jonatan Axelsson Lars Rylander Anna Rignell-Hydbom Karl ?gren Silfver Amelie Stenqvist Aleksander Giwercman 《PloS one》2013,8(6)
Background
Maternal smoking during pregnancy has been reported to negatively impact sperm counts of the sons. Sufficient data on the effect of paternal smoking is lacking.Objectives
We wished to elucidate the impact of maternal and paternal smoking during pregnancy and current own smoking on reproductive function of the male offspring.Methods
Semen parameters including sperm DNA integrity were analyzed in 295 adolescents from the general population close to Malmö, Sweden, recruited for the study during 2008–2010. Information on maternal smoking was obtained from the Swedish Medical Birth Register, and regarding own and paternal smoking from questionnaires. The impacts of maternal, paternal and own smoking were evaluated in a multivariate regression model and by use of models including interaction terms. Totally, three exposures and five outcomes were evaluated.Results
In maternally unexposed men, paternal smoking was associated with 46% lower total sperm count (95%CI: 21%, 64%) in maternally unexposed men. Both paternal and maternal smoking were associated with a lower sperm concentration (mean differences: 35%; 95%CI: 8.1%, 55% and 36%; 95%CI: 3.9%, 57%, respectively) if the other parent was a non-smoker. No statistically significant impact of own smoking on semen parameters was seen.Conclusions
Prenatal both maternal and paternal smoking were separately associated with some decrease in sperm count in men of whom the other parent was not reported to smoke. 相似文献67.
The study of protein binding mechanisms is a major topic of research in structural biology. Here, we implement a combination of metrics to systematically assess the cost of backbone conformational changes that protein domains undergo upon association. Through the analyses of 2090 unique unbound → bound transitions, from over 12,000 structures, we show that two-thirds of these proteins do not suffer significant structural changes upon binding, and could thus fit the lock-and-key model well. Among the remaining proteins, one-third explores the bound conformation in the unbound state (conformational selection model) and, while most transitions are possible from an energetic perspective, a few do require external help to break the thermodynamic barrier (induced fit model). We also analyze the relationship between conformational transitions and protein connectivity, finding that, in general, domains interacting with many partners undergo smaller changes upon association, and are less likely to freely explore larger conformational changes. 相似文献
68.
Shiryaev SA Remacle AG Ratnikov BI Nelson NA Savinov AY Wei G Bottini M Rega MF Parent A Desjardins R Fugere M Day R Sabet M Pellecchia M Liddington RC Smith JW Mustelin T Guiney DG Lebl M Strongin AY 《The Journal of biological chemistry》2007,282(29):20847-20853
Pathogens or their toxins, including influenza virus, Pseudomonas, and anthrax toxins, require processing by host proprotein convertases (PCs) to enter host cells and to cause disease. Conversely, inhibiting PCs is likely to protect host cells from multiple furin-dependent, but otherwise unrelated, pathogens. To determine if this concept is correct, we designed specific nanomolar inhibitors of PCs modeled from the extended cleavage motif TPQRERRRKKR downward arrowGL of the avian influenza H5N1 hemagglutinin. We then confirmed the efficacy of the inhibitory peptides in vitro against the fluorescent peptide, anthrax protective antigen (PA83), and influenza hemagglutinin substrates and also in mice in vivo against two unrelated toxins, anthrax and Pseudomonas exotoxin. Peptides with Phe/Tyr at P1' were more selective for furin. Peptides with P1' Thr were potent against multiple PCs. Our strategy of basing the peptide sequence on a furin cleavage motif known for an avian flu virus shows the power of starting inhibitor design with a known substrate. Our results confirm that inhibiting furin-like PCs protects the host from the distinct furin-dependent infections and lay a foundation for novel, host cell-focused therapies against acute diseases. 相似文献
69.
Anneli Ekblom Barbara Eichhorn Paul Sinclair Shaw Badenhorst Amelie Berger 《Vegetation History and Archaeobotany》2014,23(1):15-32
This paper discusses changing patterns of resource utilisation over time in the locality of Chibuene, Vilankulos, situated on the coastal plain of southern Mozambique. The macroscopic charcoal, bone and shell assemblages from archaeological excavations are presented and discussed against the off-site palaeoecological records from pollen, fungal spores and microscopic charcoal. The Chibuene landscape has experienced four phases of land use and resource utilisation that have interacted with changes in the environment. Phase 1 (a.d. 400–900), forest savanna mosaic, low intensity cattle herding and cultivation, trade of resources for domestic use. Phase 2 (a.d. 900–1400), forest savanna mosaic, high intensity/extensive cultivation and cattle herding. Phase 3 (a.d. 1400–1800), savanna woodland and progressive decrease in forests owing to droughts. Decline of agricultural activities and higher reliance on marine resources. Possible trade of resources with the interior. Phase 4 (a.d. 1800–1900), open savanna with few forest patches. Warfare and social unrest. Collapse of trade with the interior. Decline in marine resources and wildlife. Loss of cattle herds. Expansion of agriculture locally and introduction of New World crops and clearing of Brachystegia trees. The study shows the importance of combining different environmental resources for elucidating how land use and natural variability have changed over time. 相似文献
70.
Peter Recknagel Falk A. Gonnert Martin Westermann Sandro Lambeck Amelie Lupp Alain Rudiger Alex Dyson Jane E. Carré Andreas Kortgen Christoph Krafft Jürgen Popp Christoph Sponholz Valentin Fuhrmann Ingrid Hilger Ralf A. Claus Niels C. Riedemann Reinhard Wetzker Mervyn Singer Michael Trauner Michael Bauer 《PLoS medicine》2012,9(11)