Field evaluation of a simple fluorescence method for detection of viable Mycobacterium tuberculosis in sputum specimens during treatment follow-up.

Simple tuberculosis (TB) treatment monitoring tools are needed. We assessed the performance of fluorescein-diacetate (FDA) smear microscopy for detection of viable Mycobacterium tuberculosis in sputum specimens (n = 288) of TB cases under treatment compared to culture (17.4% culture positivity). FDA sensitivity was moderate (83.7% [95% confidence interval {CI}, 70.3 to 92.6]), and specificity was low (66.1% [59.5 to 72.2]). The good negative predictive value (94.8% [90.1 to 97.8]) and negative likelihood ratio (0.2) suggest using this method to rule out treatment failure in settings without access to culture

First Detection of Mycobacterium ulcerans DNA in Environmental Samples from South America

The occurrences of many environmentally-persistent and zoonotic infections are driven by ecosystem changes, which in turn are underpinned by land-use modifications that alter the governance of pathogen, biodiversity and human interactions. Our current understanding of these ecological changes on disease emergence however remains limited. Buruli ulcer is an emerging human skin disease caused by the mycobacterium, Mycobacterium ulcerans, for which the exact route of infection remains unclear. It can have a devastating impact on its human host, causing extensive necrosis of the skin and underlying tissue, often leading to permanent disability. The mycobacterium is associated with tropical aquatic environments and incidences of the disease are significantly higher on floodplains and where there is an increase of human aquatic activities. Although the disease has been previously diagnosed in South America, until now the presence of M. ulcerans DNA in the wild has only been identified in Australia where there have been significant outbreaks and in western and central regions of Africa where the disease is persistent. Here for the first time, we have identified the presence of the aetiological agent's DNA in environmental samples from South America. The DNA was positively identified using Real-time Polymerase Chain Reaction (PCR) on 163 environmental samples, taken from 23 freshwater bodies in French Guiana (Southern America), using primers for both IS2404 and for the ketoreductase-B domain of the M. ulcerans mycolactone polyketide synthase genes (KR). Five samples out of 163 were positive for both primers from three different water bodies. A further nine sites had low levels of IS2404 close to a standard CT of 35 and could potentially harbour M. ulcerans. The majority of our positive samples (8/14) came from filtered water. These results also reveal the Sinnamary River as a potential source of infection to humans. © 2014 Morris et al

Building development and roads: implications for the distribution of stone curlews across the Brecks

Background: Substantial new housing and infrastructure development planned within England has the potential to conflict with the nature conservation interests of protected sites. The Breckland area of eastern England (the Brecks) is designated as a Special Protection Area for a number of bird species, including the stone curlew (for which it holds more than 60% of the UK total population). We explore the effect of buildings and roads on the spatial distribution of stone curlew nests across the Brecks in order to inform strategic development plans to avoid adverse effects on such European protected sites. Methodology: Using data across all years (and subsets of years) over the period 1988 – 2006 but restricted to habitat areas of arable land with suitable soils, we assessed nest density in relation to the distances to nearest settlements and to major roads. Measures of the local density of nearby buildings, roads and traffic levels were assessed using normal kernel distance-weighting functions. Quasi-Poisson generalised linear mixed models allowing for spatial auto-correlation were fitted. Results: Significantly lower densities of stone curlew nests were found at distances up to 1500m from settlements, and distances up to 1000m or more from major (trunk) roads. The best fitting models involved optimally distance-weighted variables for the extent of nearby buildings and the trunk road traffic levels. Significance : The results and predictions from this study of past data suggests there is cause for concern that future housing development and associated road infrastructure within the Breckland area could have negative impacts on the nesting stone curlew population. Given the strict legal protection afforded to the SPA the planning and conservation bodies have subsequently agreed precautionary restrictions on building development within the distances identified and used the modelling predictions to agree mitigation measures for proposed trunk road developments

Evaluación de la contaminación con agentes citotóxicos en hospitales en Colombia.

Introducción: Las revisiones del 2007 a la farmacopea americana vigente en todo el hemisferio occidental (USP capítulo 797) incluyen una sección sobre el manejo de fármacos peligrosos como preparaciones magistrales estériles, donde se recomienda el muestreo ambiental para detectar trazas de fármacos peligrosos no contenidos, afirmando que esta medida de calidad debe llevarse a cabo de forma rutinaria. Objetivo: Determinar la tasa de contaminación con agentes citotóxicos en las áreas de trabajo de tres instituciones hospitalarias de Colombia. Material y métodos: Estudio descriptivo, prospectivo, transversal. Se recolectaron muestras de 18 áreas evaluando simultáneamente la presencia de tres fármacos que han sido históricamente usados como trazadores de contaminación química: Ciclofosfamida, 5-Fluorouracilo y Carboplatino. Se evalúan superficies de áreas de preparación (cabina de seguridad biológica-CSB o aislador de barrera-AB), alistamiento y administración de medicamentos oncológicos incluyendo áreas comunes a la central de mezclas y la sala de administración de medicamentos oncológicos. Resultados: En el departamento de enfermería y farmacia existe contaminación química debido a los medicamentos citostáticos. En enfermería la contaminación se dio más debido a Carboplatino mientras que en el área de central de mezclas, el fármaco que más detectado fue 5-fluoruracilo. La comparación entre ambos departamentos permite evidenciar que la mayor tasa de contaminación se ha encontrado en farmacia. El principio activo más detectado fue 5-fluoruracilo. Conclusión: Se recomienda que las instituciones revisen los estándares para la preparación y administración de fármacos peligrosos a la luz de la normatividad mundial (USP, ASHP, ISOPP) en aspectos como la política y el procedimiento actual, controles de ingeniería, procedimientos de limpieza, manipulación de los viales del fabricante, evaluación de la CSB o AB, capacitación y educación del personal tanto en las áreas de preparación y administración, uso de EPP adecuados, la incidencia de derrames recientes en el área de la farmacia o de preparación que podrían elevar los niveles de detección y la implementación de CSTD

Evaluación de la contaminación con agentes citotóxicos en hospitales en Colombia.

Introducción: Las revisiones del 2007 a la farmacopea americana vigente en todo el hemisferio occidental (USP capítulo 797) incluyen una sección sobre el manejo de fármacos peligrosos como preparaciones magistrales estériles, donde se recomienda el muestreo ambiental para detectar trazas de fármacos peligrosos no contenidos, afirmando que esta medida de calidad debe llevarse a cabo de forma rutinaria. Objetivo: Determinar la tasa de contaminación con agentes citotóxicos en las áreas de trabajo de tres instituciones hospitalarias de Colombia. Material y métodos: Estudio descriptivo, prospectivo, transversal. Se recolectaron muestras de 18 áreas evaluando simultáneamente la presencia de tres fármacos que han sido históricamente usados como trazadores de contaminación química: Ciclofosfamida, 5-Fluorouracilo y Carboplatino. Se evalúan superficies de áreas de preparación (cabina de seguridad biológica-CSB o aislador de barrera-AB), alistamiento y administración de medicamentos oncológicos incluyendo áreas comunes a la central de mezclas y la sala de administración de medicamentos oncológicos. Resultados: En el departamento de enfermería y farmacia existe contaminación química debido a los medicamentos citostáticos. En enfermería la contaminación se dio más debido a Carboplatino mientras que en el área de central de mezclas, el fármaco que más detectado fue 5-fluoruracilo. La comparación entre ambos departamentos permite evidenciar que la mayor tasa de contaminación se ha encontrado en farmacia. El principio activo más detectado fue 5-fluoruracilo. Conclusión: Se recomienda que las instituciones revisen los estándares para la preparación y administración de fármacos peligrosos a la luz de la normatividad mundial (USP, ASHP, ISOPP) en aspectos como la política y el procedimiento actual, controles de ingeniería, procedimientos de limpieza, manipulación de los viales del fabricante, evaluación de la CSB o AB, capacitación y educación del personal tanto en las áreas de preparación y administración, uso de EPP adecuados, la incidencia de derrames recientes en el área de la farmacia o de preparación que podrían elevar los niveles de detección y la implementación de CSTD

Genome-wide analysis of genetic susceptibility to language impairment in an isolated Chilean population

Specific language impairment (SLI) is an unexpected deficit in the acquisition of language skills and affects between 5 and 8% of pre-school children. Despite its prevalence and high heritability, our understanding of the aetiology of this disorder is only emerging. In this paper, we apply genome-wide techniques to investigate an isolated Chilean population who exhibit an increased frequency of SLI. Loss of heterozygosity (LOH) mapping and parametric and non-parametric linkage analyses indicate that complex genetic factors are likely to underlie susceptibility to SLI in this population. Across all analyses performed, the most consistently implicated locus was on chromosome 7q. This locus achieved highly significant linkage under all three non-parametric models (max NPL=6.73, P=4.0 × 10−11). In addition, it yielded a HLOD of 1.24 in the recessive parametric linkage analyses and contained a segment that was homozygous in two affected individuals. Further, investigation of this region identified a two-SNP haplotype that occurs at an increased frequency in language-impaired individuals (P=0.008). We hypothesise that the linkage regions identified here, in particular that on chromosome 7, may contain variants that underlie the high prevalence of SLI observed in this isolated population and may be of relevance to other populations affected by language impairments

Minimising Mortality in Endangered Raptors Due to Power Lines: The Importance of Spatial Aggregation to Optimize the Application of Mitigation Measures

Electrocution by power lines is one of the main causes of non-natural mortality in birds of prey. In an area in central Spain, we surveyed 6304 pylons from 333 power lines to determine electrocution rates, environmental and design factors that may influence electrocution and the efficacy of mitigation measures used to minimise electrocution cases. A total of 952 electrocuted raptors, representing 14 different species, were observed. Electrocuted raptors were concentrated in certain areas and the environmental factors associated with increased electrocution events were: greater numbers of prey animals; greater vegetation cover; and shorter distance to roads. The structural elements associated with electrocutions were shorter strings of insulators, one or more phases over the crossarm, cross-shaped design and pylon function. Of the 952 carcasses found, 148 were eagles, including golden eagle (Aquila chrysaetos), Spanish imperial eagle (Aquila adalberti) and Bonelli's eagle (Aquila fasciata). Electrocuted eagles were clustered in smaller areas than other electrocuted raptors. The factors associated with increased eagle electrocution events were: pylons function, shorter strings of insulators, higher slopes surrounding the pylon, and more numerous potential prey animals. Pylons with increased string of insulators had lower raptor electrocution rates than unimproved pylons, although this technique was unsuccessful for eagles. Pylons with cable insulation showed higher electrocution rates than unimproved pylons, both for raptors and eagles, despite this is the most widely used and recommended mitigation measure in several countries. To optimize the application of mitigation measures, our results recommend the substitution of pin-type insulators to suspended ones and elongating the strings of insulators

A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers

<p>Abstract</p> <p>Background</p> <p>Sweetpotato (<it>Ipomoea batatas </it>(L.) Lam.), a hexaploid outcrossing crop, is an important staple and food security crop in developing countries in Africa and Asia. The availability of genomic resources for sweetpotato is in striking contrast to its importance for human nutrition. Previously existing sequence data were restricted to around 22,000 expressed sequence tag (EST) sequences and ~ 1,500 GenBank sequences. We have used 454 pyrosequencing to augment the available gene sequence information to enhance functional genomics and marker design for this plant species.</p> <p>Results</p> <p>Two quarter 454 pyrosequencing runs used two normalized cDNA collections from stems and leaves from drought-stressed sweetpotato clone <it>Tanzania </it>and yielded 524,209 reads, which were assembled together with 22,094 publically available expressed sequence tags into 31,685 sets of overlapping DNA segments and 34,733 unassembled sequences. Blastx comparisons with the UniRef100 database allowed annotation of 23,957 contigs and 15,342 singletons resulting in 24,657 putatively unique genes. Further, 27,119 sequences had no match to protein sequences of UniRef100database. On the basis of this gene index, we have identified 1,661 gene-based microsatellite sequences, of which 223 were selected for testing and 195 were successfully amplified in a test panel of 6 hexaploid (<it>I. batatas</it>) and 2 diploid (<it>I. trifida</it>) accessions.</p> <p>Conclusions</p> <p>The sweetpotato gene index is a useful source for functionally annotated sweetpotato gene sequences that contains three times more gene sequence information for sweetpotato than previous EST assemblies. A searchable version of the gene index, including a blastn function, is available at <url>http://www.cipotato.org/sweetpotato_gene_index</url>.</p

Genotype at the P554L Variant of the Hexose-6 Phosphate Dehydrogenase Gene Is Associated with Carotid Intima-Medial Thickness

Objective: The combined thickness of the intima and media of the carotid artery (carotid intima-medial thickness, CIMT) is associated with cardiovascular disease and stroke. Previous studies indicate that carotid intima-medial thickness is a significantly heritable phenotype, but the responsible genes are largely unknown. Hexose-6 phosphate dehydrogenase (H6PDH) is a microsomal enzyme whose activity regulates corticosteroid metabolism in the liver and adipose tissue; variability in measures of corticosteroid metabolism within the normal range have been associated with risk factors for cardiovascular disease. We performed a genetic association study in 854 members of 224 families to assess the relationship between polymorphisms in the gene coding for hexose-6 phosphate dehydrogenase (H6PD) and carotid intima-medial thickness. Methods: Families were ascertained via a hypertensive proband. CIMT was measured using B-mode ultrasound. Single nucleotide polymorphisms (SNPs) tagging common variation in the H6PD gene were genotyped. Association was assessed following adjustment for significant covariates including "classical" cardiovascular risk factors. Functional studies to determine the effect of particular SNPs on H6PDH were performed. Results: There was evidence of association between the single nucleotide polymorphism rs17368528 in exon five of the H6PD gene, which encodes an amino-acid change from proline to leucine in the H6PDH protein, and mean carotid intima-medial thickness (p = 0.00065). Genotype was associated with a 5% (or 0.04 mm) higher mean carotid intima-medial thickness measurement per allele, and determined 2% of the population variability in the phenotype. Conclusions: Our results suggest a novel role for the H6PD gene in atherosclerosis susceptibility