9,784 research outputs found

    Molecular epidemiology of endemic Clostridium difficile infection

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    This is the first study to provide a comprehensive insight into the molecular epidemiology of endemic Clostridium difficile and particularly that associated with a recently recognized epidemic strain. We DNA fingerprinted all C. difficile isolates from the stools of patients with symptomatic antibiotic-associated diarrhoea and from repeated samples of the inanimate ward environment on two elderly medicine hospital wards over a 22-month period. Notably, C. difficile was not recoverable from either ward immediately before opening, but was found on both wards within 1–3 weeks of opening, and the level of environmental contamination rose markedly during the first 6 months of the study period. C. difficile infection (CDI) incidence data correlated significantly with the prevalence of environmental C. difficile on ward B (r = 0·76, P 0·05). We found that RAPD and RS–PCR typing had similar discriminatory power, although, despite fingerprinting over 200 C. difficile isolates, we identified only six distinct types. Only two distinct C. difficile strains were identified as causing both patient infection and ward contamination. Attempts to determine whether infected patients or contaminated environments are the prime source for cross-infection by C. difficile had limited success, as over 90% of C. difficile isolates were the UK epidemic clone. However, a non-epidemic strain caused a cluster of six cases of CDI, but was only isolated from the environment after the sixth patient became symptomatic. The initial absence of this strain from the environment implies patient-to-patient and/or staff-to-patient spread. In general, routine cleaning with detergent was unsuccessful at removing C. difficile from the environment. Understanding the epidemiology and virulence of prevalent strains is important if CDI is to be successfully controlled

    Report on identifying a protocol to elicit flowering in Brachiaria humidicola with photoperiod management

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    Two Genotypes of Brachiaria humidicola (A and B) were planted on the grounds of CIAT headquarters in Palmira during 2018 – 2019, 10 lamps were placed in the lot to evaluate 6 different photoperiods (1 - 6) with Light in 2 different wavelength range (W.R.) α and β, for this, 17 samples were carried out on the variables height, vigor, chlorophyll content and number of inflorescences; a total of 93 field work were carried out to support the trial, finding that the photoperiod 5 in the W.R. β and 3 photoperiod in the W.R. α for the B genotype show significant differences (p <0.05, Tukey) with respect to the other treatments for height and number of inflorescences, performing the statistical analysis in the SAS software. As to the seed production, it was found that any light stimulus generates greater seed production, despite the conditions under which the crops were made and the method of harvest used. I order to refine the protocol and validate the results in bigger genotype sample another trial with the 2 most efficient treatments was proposed for 2020, focusing on number of inflorescences and seed production

    Gene expression in large pedigrees: analytic approaches.

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    BackgroundWe currently have the ability to quantify transcript abundance of messenger RNA (mRNA), genome-wide, using microarray technologies. Analyzing genotype, phenotype and expression data from 20 pedigrees, the members of our Genetic Analysis Workshop (GAW) 19 gene expression group published 9 papers, tackling some timely and important problems and questions. To study the complexity and interrelationships of genetics and gene expression, we used established statistical tools, developed newer statistical tools, and developed and applied extensions to these tools.MethodsTo study gene expression correlations in the pedigree members (without incorporating genotype or trait data into the analysis), 2 papers used principal components analysis, weighted gene coexpression network analysis, meta-analyses, gene enrichment analyses, and linear mixed models. To explore the relationship between genetics and gene expression, 2 papers studied expression quantitative trait locus allelic heterogeneity through conditional association analyses, and epistasis through interaction analyses. A third paper assessed the feasibility of applying allele-specific binding to filter potential regulatory single-nucleotide polymorphisms (SNPs). Analytic approaches included linear mixed models based on measured genotypes in pedigrees, permutation tests, and covariance kernels. To incorporate both genotype and phenotype data with gene expression, 4 groups employed linear mixed models, nonparametric weighted U statistics, structural equation modeling, Bayesian unified frameworks, and multiple regression.Results and discussionRegarding the analysis of pedigree data, we found that gene expression is familial, indicating that at least 1 factor for pedigree membership or multiple factors for the degree of relationship should be included in analyses, and we developed a method to adjust for familiality prior to conducting weighted co-expression gene network analysis. For SNP association and conditional analyses, we found FaST-LMM (Factored Spectrally Transformed Linear Mixed Model) and SOLAR-MGA (Sequential Oligogenic Linkage Analysis Routines -Major Gene Analysis) have similar type 1 and type 2 errors and can be used almost interchangeably. To improve the power and precision of association tests, prior knowledge of DNase-I hypersensitivity sites or other relevant biological annotations can be incorporated into the analyses. On a biological level, eQTL (expression quantitative trait loci) are genetically complex, exhibiting both allelic heterogeneity and epistasis. Including both genotype and phenotype data together with measurements of gene expression was found to be generally advantageous in terms of generating improved levels of significance and in providing more interpretable biological models.ConclusionsPedigrees can be used to conduct analyses of and enhance gene expression studies

    A bird’s-eye view of chronic unilateral conjunctivitis : remember about Chlamydia psittaci

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    Chlamydia psittaci causes psittacosis in humans, mainly in people in contact with birds in either the setting of occupational or companion bird exposure. Infection is associated with a range of clinical manifestations from asymptomatic infection to severe atypical pneumonia and systemic disease. C. psittaci has also been associated with ocular adnexal lymphoma in human patients. The current paper describes successful doxycycline treatment of a male patient suffering from C. psittaci chronic unilateral conjunctivitis, most probably linked to the visit of a South African wildlife reserve. Increased awareness among general and occupational physicians, ophthalmologists, clinicians, and the public on the potential of C. psittaci to cause ocular infection is needed

    Multi-elemental speciation analysis of barley genotypes diering in tolerance to cadmium toxicity using SEC-ICP-MS and ESI-TOF-MS

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    Plants respond to Cd exposure by synthesizing heavy-metal-binding oligopeptides, called phytochelatins (PCs). These peptides reduce the activity of Cd2+ ions in the plant tissues by forming Cd chelates. The main objective of the present work was to develop an analytical technique, which allowed identication of the most prominent Cd species in plant tissue by SEC-ICP-MS and ESI-TOF-MS. An integrated part of the method development was to test the hypothesis that dierential Cd tolerance between two barley genotypes was linked to dierences in Cd speciation. Only one fraction of Cd species, ranging from 7001800 Da, was detected in the shoots of both genotypes. In the roots, two additional fractions ranging from 29004600 and 670015 000 Da were found. The Cd-rich SEC fractions were heart-cut, de-salted and demetallized using reversed-phase chromatography (RPC), followed by ESI-MS-TOF to identify the ligands. Three dierent families of PCs, viz. (gGlu-Cys)n-Gly (PCn), (gGlu-Cys)n-Ser (iso-PCn) and Cys-(gGlu-Cys)n-Gly (des-gGlu-PCn), the last lacking the N-terminal amino acid, were identied. The PCs induced by Cd toxicity also bound several essential trace elements in plants, including Zn, Cu, and Ni, whereas no Mn species were detected. Zn, Cu and Ni-species were distributed between the 7001800 Da and 670015 000 Da fractions, whereas only Cd species were found in the 29004600 Da fraction dominated by PC3 ligands. Although the total tissue concentration of Cd was similar for the two species, the tolerant barley genotype synthesized signicantly more CdPC3 species with a high Cd specicity than the intolerant genotype, clearly indicating a correlation between Cd tolerance and the CdPC speciation

    Evolution of oil droplets in a chemorobotic platform

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    Evolution, once the preserve of biology, has been widely emulated in software, while physically embodied systems that can evolve have been limited to electronic and robotic devices and have never been artificially implemented in populations of physically interacting chemical entities. Herein we present a liquid-handling robot built with the aim of investigating the properties of oil droplets as a function of composition via an automated evolutionary process. The robot makes the droplets by mixing four different compounds in different ratios and placing them in a Petri dish after which they are recorded using a camera and the behaviour of the droplets analysed using image recognition software to give a fitness value. In separate experiments, the fitness function discriminates based on movement, division and vibration over 21 cycles, giving successive fitness increases. Analysis and theoretical modelling of the data yields fitness landscapes analogous to the genotype–phenotype correlations found in biological evolution. , Trevor Hinkley, James Ward Taylor Kliment Yane

    VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees

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    Pedigree genotype datasets are used for analysing genetic inheritance and to map genetic markers and traits. Such datasets consist of hundreds of related animals genotyped for thousands of genetic markers and invariably contain multiple errors in both the pedigree structure and in the associated individual genotype data. These errors manifest as apparent inheritance inconsistencies in the pedigree, and invalidate analyses of marker inheritance patterns across the dataset. Cleaning raw datasets of bad data points (incorrect pedigree relationships, unreliable marker assays, suspect samples, bad genotype results etc.) requires expert exploration of the patterns of exposed inconsistencies in the context of the inheritance pedigree. In order to assist this process we are developing VIPER (Visual Pedigree Explorer), a software tool that integrates an inheritance-checking algorithm with a novel space-efficient pedigree visualisation, so that reported inheritance inconsistencies are overlaid on an interactive, navigable representation of the pedigree structure

    The pathogenesis of Acanthamoeba infections: current status and future implications

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    Acanthamoeba are opportunistic protozoan parasites that can cause painful, visionthreatening keratitis. However the pathogenesis and pathophysiology of Acanthamoeba keratitis remain incompletely understood. Most cases of Acanthamoeba keratitis develop as a result of poor hygiene in contact lens care but it is unclear how amoebae transmigrate from the environment into the cornea leading to inflammation, photophobia and blindness. Acanthamoeba keratitis has become increasingly important in the past few decades due to increasing populations of contact lens users. The mechanisms associated with the pathogenesis of Acanthamoeba are highly complex, depending on the virulence properties of the parasite, host susceptibility and the environmental conditions. Complete understanding of Acanthamoeba pathogenesis and its associated risks factors should allow us to design strategies for disease prevention and for the rational development of therapeutic interventions against these devastating infections. Acanthamoeba keratitis has become a significant problem in recent years, especially in contact lens wearers exposed to contaminated water
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