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91.
Jason N Woodhouse Lu Fan Mark V Brown Torsten Thomas Brett A Neilan 《The ISME journal》2013,7(9):1842-1851
The biosynthesis of non-ribosomal peptide and polyketide natural products is facilitated by multimodular enzymes that contain domains responsible for the sequential condensation of amino and carboxylic subunits. These conserved domains provide molecular targets for the discovery of natural products from microbial metagenomes. This study demonstrates the application of tag-encoded FLX amplicon pyrosequencing (TEFAP) targeting non-ribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) genes as a method for determining the identity and diversity of natural product biosynthesis genes. To validate this approach, we assessed the diversity of NRPS and PKS genes within the microbiomes of six Australian marine sponge species using both TEFAP and metagenomic whole-genome shotgun sequencing approaches. The TEFAP approach identified 100 novel ketosynthase (KS) domain sequences and 400 novel condensation domain sequences within the microbiomes of the six sponges. The diversity of KS domains within the microbiome of a single sponge species Scopalina sp. exceeded that of any previously surveyed marine sponge. Furthermore, this study represented the first to target the condensation domain from NRPS biosynthesis and resulted in the identification of a novel condensation domain lineage. This study highlights the untapped potential of Australian marine sponges for the isolation of novel bioactive natural products. Furthermore, this study demonstrates that TEFAP approaches can be applied to functional genes, involved in natural product biosynthesis, as a tool to aid natural product discovery. It is envisaged that this approach will be used across multiple environments, offering an insight into the biological processes that influence the production of secondary metabolites. 相似文献
92.
93.
Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding 总被引:4,自引:0,他引:4
Nathan T. Evans Brett P. Olds Mark A. Renshaw Cameron R. Turner Yiyuan Li Christopher L. Jerde Andrew R. Mahon Michael E. Pfrender Gary A. Lamberti David M. Lodge 《Molecular ecology resources》2016,16(1):29-41
Freshwater fauna are particularly sensitive to environmental change and disturbance. Management agencies frequently use fish and amphibian biodiversity as indicators of ecosystem health and a way to prioritize and assess management strategies. Traditional aquatic bioassessment that relies on capture of organisms via nets, traps and electrofishing gear typically has low detection probabilities for rare species and can injure individuals of protected species. Our objective was to determine whether environmental DNA (eDNA) sampling and metabarcoding analysis can be used to accurately measure species diversity in aquatic assemblages with differing structures. We manipulated the density and relative abundance of eight fish and one amphibian species in replicated 206‐L mesocosms. Environmental DNA was filtered from water samples, and six mitochondrial gene fragments were Illumina‐sequenced to measure species diversity in each mesocosm. Metabarcoding detected all nine species in all treatment replicates. Additionally, we found a modest, but positive relationship between species abundance and sequencing read abundance. Our results illustrate the potential for eDNA sampling and metabarcoding approaches to improve quantification of aquatic species diversity in natural environments and point the way towards using eDNA metabarcoding as an index of macrofaunal species abundance. 相似文献
94.
Rendy Ruvindy Richard Allen White III Brett Anthony Neilan Brendan Paul Burns 《The ISME journal》2016,10(1):183-196
Modern microbial mats are potential analogues of some of Earth''s earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic next-generation sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats. 相似文献
95.
96.
In Situ Measurement of Solid Electrolyte Interphase Evolution on Silicon Anodes Using Atomic Force Microscopy 下载免费PDF全文
Insun Yoon Daniel P. Abraham Brett L. Lucht Allan F. Bower Pradeep R. Guduru 《Liver Transplantation》2016,6(12)
In situ measurements of the growth of solid electrolyte interphase (SEI) layer on silicon and the lithiation‐induced volume changes in silicon in lithium ion half‐cells are reported. Thin film amorphous silicon electrodes are fabricated in a configuration that allows unambiguous separation of the total thickness change into contribution from SEI thickness and silicon volume change. Electrodes are assembled into a custom‐designed electrochemical cell, which is integrated with an atomic force microscope. The electrodes are subjected to constant potential lithiation/delithiation at a sequence of potential values and the thickness measurements are made at each potential after equilibrium is reached. Experiments are carried out with two electrolytes—1.2 m lithium hexafluoro‐phosphate (LiPF6) in ethylene carbonate (EC) and 1.2 m LiPF6 in propylene carbonate (PC)—to investigate the influence of electrolyte composition on SEI evolution. It is observed that SEI formation occurs predominantly during the first lithiation and the maximum SEI thickness is ≈17 and 10 nm respectively for EC and PC electrolytes. This study also presents the measured Si expansion ratio versus equilibrium potential and charge capacity versus equilibrium potential; both relationships display hysteresis, which is explained in terms of the stress–potential coupling in silicon. 相似文献
97.
Steven W. Paugh David R. Coss Ju Bao Lucas T. Laudermilk Christy R. Grace Antonio M. Ferreira M. Brett Waddell Granger Ridout Deanna Naeve Michael Leuze Philip F. LoCascio John C. Panetta Mark R. Wilkinson Ching-Hon Pui Clayton W. Naeve Edward C. Uberbacher Erik J. Bonten William E. Evans 《PLoS computational biology》2016,12(2)
98.
Stephanie T. Gumuchian Sandra Peláez Vanessa C. Delisle Marie-Eve Carrier Lisa R. Jewett Ghassan El-Baalbaki Catherine Fortune Marie Hudson Ann Impens Annett K?rner Jennifer Persmann Linda Kwakkenbos Susan J. Bartlett Brett D. Thombs 《PloS one》2016,11(3)
Background
Systemic sclerosis, or scleroderma, is a chronic and rare connective tissue disease with negative physical and psychological implications. Sources of emotional distress and the impact they have on the lives of people with scleroderma are not well understood.Objectives
To gain an in-depth understanding of the emotional experiences and sources of emotional distress for women and men living with scleroderma through focus group discussions.Methods
Three semi-structured focus group discussions were conducted (two in English, one in French) with a total of 22 people with scleroderma recruited through the Scleroderma Society of Ontario in Hamilton, Ontario and a scleroderma clinic in Montreal, Canada. Interviews were recorded, transcribed, and then coded for emerging themes using thematic inductive analysis.Results
Core themes representing sources of emotional distress were identified, including: (a) facing a new reality; (b) the daily struggle of living with scleroderma; (c) handling work, employment and general financial burden; (d) changing family roles; (e) social interactions; and (f) navigating the health care system. Collectively, these themes refer to the stressful journey of living with scleroderma including the obstacles faced and the emotional experiences beginning prior to receiving a diagnosis and continuing throughout the participants’ lives.Conclusion
Scleroderma was portrayed as being an unpredictable and overwhelming disease, resulting in many individuals experiencing multiple sources of emotional distress. Interventions and supportive resources need to be developed to help individuals with scleroderma and people close to them manage and cope with the emotional aspects of the disease. 相似文献99.
Protein kinase-mediated phosphorylation is among the most important post-translational modifications. However, few phosphorylation sites have been experimentally identified for most species, making it difficult to determine the degree to which phosphorylation sites are conserved. The goal of this study was to use computational methods to characterize the conservation of human phosphorylation sites in a wide variety of eukaryotes. Using experimentally-determined human sites as input, homologous phosphorylation sites were predicted in all 432 eukaryotes for which complete proteomes were available. For each pair of species, we calculated phosphorylation site conservation as the number of phosphorylation sites found in both species divided by the number found in at least one of the two species. A clustering of the species based on this conservation measure was concordant with phylogenies based on traditional genomic measures. For a subset of the 432 species, phosphorylation site conservation was compared to conservation of both protein kinases and proteins in general. Protein kinases exhibited the highest degree of conservation, while general proteins were less conserved and phosphorylation sites were least conserved. Although preliminary, these data tentatively suggest that variation in phosphorylation sites may play a larger role in explaining phenotypic differences among organisms than differences in the complements of protein kinases or general proteins. 相似文献
100.
Pascalis Vergidis Cornelius J. Clancy Ryan K. Shields Seo Young Park Brett N. Wildfeuer Richard L. Simmons M. Hong Nguyen 《PloS one》2016,11(4)
Intra-abdominal candidiasis (IAC) is poorly understood compared to candidemia. We described the clinical characteristics, microbiology, treatment and outcomes of IAC, and identified risk factors for mortality. We performed a retrospective study of adults diagnosed with IAC at our center in 2012–2013. Risk factors for mortality were evaluated using multivariable logistic regression. We identified 163 patients with IAC, compared to 161 with candidemia. Types of IAC were intra-abdominal abscesses (55%), secondary peritonitis (33%), primary peritonitis (5%), infected pancreatic necrosis (5%), and cholecystitis/cholangitis (3%). Eighty-three percent and 66% of secondary peritonitis and abscesses, respectively, stemmed from gastrointestinal (GI) tract sources. C. albicans (56%) and C. glabrata (24%) were the most common species. Bacterial co-infections and candidemia occurred in 67% and 6% of patients, respectively. Seventy-two percent of patients underwent an early source control intervention (within 5 days) and 72% received early antifungal treatment. 100-day mortality was 28%, and highest with primary (88%) or secondary (40%) peritonitis. Younger age, abscesses and early source control were independent predictors of survival. Younger age, abscesses and early antifungal treatment were independently associated with survival for IAC stemming from GI tract sources. Infectious diseases (ID) consultations were obtained in only 48% of patients. Consulted patients were significantly more likely to receive antifungal treatment. IAC is a common disease associated with heterogeneous manifestations, which result in poor outcomes. All patients should undergo source control interventions and receive antifungal treatment promptly. It is important for the ID community to become more engaged in treating IAC. 相似文献