Detection and diversity of copper containing nitrite reductase genes (nirK) in prokaryotic and fungal communities of agricultural soils

Microorganisms are capable of producing N-2 and N2O gases as the end products of denitrification. Copper-containing nitrite reductase (NirK), a key enzyme in the microbial N-cycle, has been found in bacteria, archaea and fungi. This study seeks to assess the diversity of nirK genes in the prokaryotic and fungal communities of agricultural soils in the United States. New primers targeting the nirK genes in fungi were developed, while nirK genes in archaea and bacteria were detected using previously published methods. The new primers were able to detect fungal nirK genes as well as bacterial nirK genes from a group that could not be observed with previously published primers. Based on the sequence analyses from three different primer sets, five clades of nirK genes were identified, which were associated with soil archaea, ammonium-oxidizing bacteria, denitrifying bacteria and fungi. The diversity of nirK genes in the two denitrifying bacteria clades was higher than the diversity found in other clades. Using a newly designed primer set, this study showed the detection of fungal nirK genes from environmental samples. The newly designed PCR primers in this study enhance the ability to detect the diversity of nirK-encoding microorganisms in soils

Low temperature scattering with the R-matrix method: the Morse potential

Experiments are starting to probe collisions and chemical reactions between atoms and molecules at ultra-low temperatures. We have developed a new theoretical procedure for studying these collisions using the R-matrix method. Here this method is tested for the atom -- atom collisions described by a Morse potential. Analytic solutions for continuum states of the Morse potential are derived and compared with numerical results computed using an R-matrix method where the inner region wavefunctions are obtained using a standard nuclear motion algorithm. Results are given for eigenphases and scattering lengths. Excellent agreement is obtained in all cases. Progress in developing a general procedure for treating ultra-low energy reactive and non-reactive collisions is discussed.Comment: 18 pages, 6 figures, 3 tables, conferenc

La adhesión de las enfermeras al Método Canguro: subvención para la administración del cuidado de enfermería

;;OBJETIVO:;; construir um modelo teórico explicativo acerca da adesão das enfermeiras ao Método Canguru na Unidade de Terapia Intensiva Neonatal, a partir dos significados e interações para a gerência do cuidado.;;;;MÉTODO:;; pesquisa qualitativa, guiada pelo referencial da Grounded Theory. Foram entrevistadas oito enfermeiras de uma Unidade de Terapia Intensiva Neonatal da cidade do Rio de Janeiro. A análise comparativa dos dados percorreu as etapas de codificação aberta, axial e seletiva, sendo construído um modelo teórico do tipo condicional-causal.;;;;RESULTADOS:;; emergiram quatro categorias principais que compuseram o paradigma de análise: Vestindo a camisa do Método Canguru; Trabalhando com a complexidade do Método Canguru; Encontrando (des)motivação para aplicar o Método Canguru; e Deparando-se com os desafios para a adesão e aplicação do Método Canguru.;;;;CONCLUSÕES:;; o fenômeno central revelou que cada enfermeira e profissional da equipe possui um papel de multiplicador de valores e práticas que podem ou não ser construtivas, influenciando potencialmente na (des)continuidade do Método Canguru na Unidade de Terapia Intensiva Neonatal. Os achados podem ser utilizados para o delineamento de estratégias gerenciais que ultrapassem os cursos e treinamentos e garantam o fortalecimento do modelo assistencial.;;;;OBJECTIVE:;; construct an explanatory theoretical model about nurses' adherence to the Kangaroo Care Method at the Neonatal Intensive Care Unit, based on the meanings and interactions for care management.;;;;METHOD:;; qualitative research, based on the reference framework of the Grounded Theory. Eight nurses were interviewed at a Neonatal Intensive Care Unit in the city of Rio de Janeiro. The comparative analysis of the data comprised the phases of open, axial and selective coding. A theoretical conditional-causal model was constructed.;;;;RESULTS:;; four main categories emerged that composed the analytic paradigm: Giving one's best to the Kangaroo Method; Working with the complexity of the Kangaroo Method; Finding (de)motivation to apply the Kangaroo Method; and Facing the challenges for the adherence to and application of the Kangaroo Method.;;;;CONCLUSIONS:;; the central phenomenon revealed that each nurse and team professional has a role of multiplying values and practices that may or may not be constructive, potentially influencing the (dis)continuity of the Kangaroo Method at the Neonatal Intensive Care Unit. The findings can be used to outline management strategies that go beyond the courses and training and guarantee the strengthening of the care model.;;;;OBJETIVO:;; construir un modelo teórico explicativo acerca de la adhesión de las enfermeras al Método Canguro en la Unidad de Terapia Intensiva Neonatal, a partir de los significados e interacciones para la administración del cuidado.;;;;MÉTODO:;; investigación cualitativa, guiada por el referencial de la Grounded Theory. Fueron entrevistadas ocho enfermeras de una Unidad de Terapia Intensiva Neonatal de la ciudad de Rio de Janeiro. El análisis comparativo de los datos recorrió las etapas de codificación abierta, axial y selectiva, siendo construido un modelo teórico del tipo condicional-causal.;;;;RESULTADOS:;; surgieron cuatro categorías principales que compusieron los paradigmas del análisis: Vistiendo la camisa del Método Canguro; Trabajando con la complejidad del Método Canguro; Encontrando (des)motivación para aplicar el Método Canguro; y Encontrando los desafíos para la adhesión y aplicación del Método Canguro.;;;;CONCLUSIONES:;; el fenómeno central reveló que cada enfermera y profesional del equipo posee un papel de multiplicador de valores y prácticas que pueden o no ser constructivas, influenciando potencialmente en la (des)continuidad del Método Canguro en la Unidad de Terapia Intensiva Neonatal. Los hallazgos pueden ser utilizados para el delineamiento de estrategias de administración que sobrepasen los cursos y entrenamientos y garanticen el fortalecimiento del modelo asistencial.;

Maximising response to postal questionnaires – A systematic review of randomised trials in health research

Background Postal self-completion questionnaires offer one of the least expensive modes of collecting patient based outcomes in health care research. The purpose of this review is to assess the efficacy of methods of increasing response to postal questionnaires in health care studies on patient populations. Methods The following databases were searched: Medline, Embase, CENTRAL, CDSR, PsycINFO, NRR and ZETOC. Reference lists of relevant reviews and relevant journals were hand searched. Inclusion criteria were randomised trials of strategies to improve questionnaire response in health care research on patient populations. Response rate was defined as the percentage of questionnaires returned after all follow-up efforts. Study quality was assessed by two independent reviewers. The Mantel-Haenszel method was used to calculate the pooled odds ratios. Results Thirteen studies reporting fifteen trials were included. Implementation of reminder letters and telephone contact had the most significant effect on response rates (odds ratio 3.7, 95% confidence interval 2.30 to 5.97 p = <0.00001). Shorter questionnaires also improved response rates to a lesser degree (odds ratio 1.4, 95% confidence interval 1.19 to 1.54). No evidence was found that incentives, re-ordering of questions or including an information brochure with the questionnaire confer any additional advantage. Conclusion Implementing repeat mailing strategies and/or telephone reminders may improve response to postal questionnaires in health care research. Making the questionnaire shorter may also improve response rates. There is a lack of evidence to suggest that incentives are useful. In the context of health care research all strategies to improve response to postal questionnaires require further evaluation

Expression of CXCL10 is associated with response to radiotherapy and overall survival in squamous cell carcinoma of the tongue

Five-year survival for patients with oral cancer has been disappointingly stable during the last decades, creating a demand for new biomarkers and treatment targets. Lately, much focus has been set on immunomodulation as a possible treatment or an adjuvant increasing sensitivity to conventional treatments. The objective of this study was to evaluate the prognostic importance of response to radiotherapy in tongue carcinoma patients as well as the expression of the CXC-chemokines in correlation to radiation response in the same group of tumours. Thirty-eight patients with tongue carcinoma that had received radiotherapy followed by surgery were included. The prognostic impact of pathological response to radiotherapy, N-status, T-stage, age and gender was evaluated using Cox's regression models, Kaplan-Meier survival curves and chi-square test. The expression of 23 CXC-chemokine ligands and their receptors were evaluated in all patients using microarray and qPCR and correlated with response to treatment using logistic regression. Pathological response to radiotherapy was independently associated to overall survival with a 2-year survival probability of 81 % for patients showing a complete pathological response, while patients with a non-complete response only had a probability of 42 % to survive for 2 years (p = 0.016). The expression of one CXC-chemokine, CXCL10, was significantly associated with response to radiotherapy and the group of patients with the highest CXCL10 expression responded, especially poorly (p = 0.01). CXCL10 is a potential marker for response to radiotherapy and overall survival in patients with squamous cell carcinoma of the tongue

Species-level functional profiling of metagenomes and metatranscriptomes.

Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types

The influence of textile materials on flame resistance ratings of professional uniforms

This study compares the flame speed of different textile materials employed in professional uniforms. Five different garments of aeronauts’ uniforms were analyzed (totaling 200 specimens submitted to flammability tests). Plain weaves and twill weaves composed by 100% CO; 100% PES; 67% PES/33% CO; 50% PES/50% WO; and 55% PES/45%WO were analyzed in the warp and filling directions. The flame speed of each material was determined, and differences in the flame propagation of the fabrics were identified. The lowest flame speed occurred for the material 50% PES/50% WO plain weave and weft direction (0.742 ± 0.140 m/s). The highest flame speed was 3.698 ± 1.806 cm/s for the material 67%PES/33%CO, plain weave and filling direction. Future experiments for reducing the fabric flammability of the uniforms could be related to more closed fabric constructions; mixtures with synthetic fibers to add functionality; changing the direction of the fabric; and changing the weight and torsion of its constituent yarns.São Paulo Research Foundation—FAPESP (“Fundação de Amparo à Pesquisa do Estado de São Paulo”) Grant Number 2016/01331-

Benznidazole biotransformation and multiple targets in <i>Trypanosoma</i> cruzi revealed by metabolomics

&lt;b&gt;Background&lt;/b&gt;&lt;p&gt;&lt;/p&gt; The first line treatment for Chagas disease, a neglected tropical disease caused by the protozoan parasite Trypanosoma cruzi, involves administration of benznidazole (Bzn). Bzn is a 2-nitroimidazole pro-drug which requires nitroreduction to become active, although its mode of action is not fully understood. In the present work we used a non-targeted MS-based metabolomics approach to study the metabolic response of T. cruzi to Bzn.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Methodology/Principal findings&lt;/b&gt;&lt;p&gt;&lt;/p&gt; Parasites treated with Bzn were minimally altered compared to untreated trypanosomes, although the redox active thiols trypanothione, homotrypanothione and cysteine were significantly diminished in abundance post-treatment. In addition, multiple Bzn-derived metabolites were detected after treatment. These metabolites included reduction products, fragments and covalent adducts of reduced Bzn linked to each of the major low molecular weight thiols: trypanothione, glutathione, γ-glutamylcysteine, glutathionylspermidine, cysteine and ovothiol A. Bzn products known to be generated in vitro by the unusual trypanosomal nitroreductase, TcNTRI, were found within the parasites, but low molecular weight adducts of glyoxal, a proposed toxic end-product of NTRI Bzn metabolism, were not detected.&lt;p&gt;&lt;/p&gt; &lt;b&gt;Conclusions/significance&lt;/b&gt;&lt;p&gt;&lt;/p&gt; Our data is indicative of a major role of the thiol binding capacity of Bzn reduction products in the mechanism of Bzn toxicity against T. cruzi

SNP assay to detect the ‘Hyuuga’ red-brown lesion resistance gene for Asian soybean rust

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi Syd., has the potential to become a serious threat to soybean, Glycine max L. Merr., production in the USA. A novel rust resistance gene, Rpp?(Hyuuga), from the Japanese soybean cultivar Hyuuga has been identified and mapped to soybean chromosome 6 (Gm06). Our objectives were to fine-map the Rpp?(Hyuuga) gene and develop a high-throughput single nucleotide polymorphism (SNP) assay to detect this ASR resistance gene. The integration of recombination events from two different soybean populations and the ASR reaction data indicates that the Rpp?(Hyuuga) locus is located in a region of approximately 371 kb between STS70887 and STS70923 on chromosome Gm06. A set of 32 ancestral genotypes which is predicted to contain 95% of the alleles present in current elite North American breeding populations and the sources of the previously reported ASR resistance genes (Rpp1, Rpp2, Rpp3, Rpp4, Rpp5, and rpp5) were genotyped with five SNP markers. We developed a SimpleProbe assay based on melting curve analysis for SNP06-44058 which is tighly linked to the Rpp?(Hyuuga) gene. This SNP assay can differentiate plants/lines that are homozygous/homogeneous or heterozygous/heterogeneous for the resistant and susceptible alleles at the Rpp?(Hyuuga) locus