Sequencing of 16S rRNA Gene: A Rapid Tool for Identification of Bacillus anthracis

In a bioterrorism event, a tool is needed to rapidly differentiate Bacillus anthracis from other closely related spore-forming Bacillus species. During the recent outbreak of bioterrorism-associated anthrax, we sequenced the 16S rRNA generom these species to evaluate the potential of 16S rRNA gene sequencing as a diagnostic tool. We found eight distinct 16S types among all 107 16S rRNA gene seqs fuences that differed from each other at 1 to 8 positions (0.06% to 0.5%). All 86 B. anthracis had an identical 16S gene sequence, designated type 6; 16S type 10 was seen in all B. thuringiensis strains; six other 16S types were found among the 10 B. cereus strains. This report describes the first demonstration of an exclusive association of a distinct 16S sequence with B. anthracis. Consequently, we were able to rapidly identify suspected isolates and to detect the B. anthracis 16S rRNA gene directly from culture-negative clinical specimens from seven patients with laboratory-confirmed anthrax

Leptospirosis during Dengue Outbreak, Bangladesh

We collected acute-phase serum samples from febrile patients at 2 major hospitals in Dhaka, Bangladesh, during an outbreak of dengue fever in 2001. A total of 18% of dengue-negative patients tested positive for leptospirosis. The case-fatality rate among leptospirosis patients (5%) was higher than among dengue fever patients (1.2%)

Author Correction: A consensus-based transparency checklist.

An amendment to this paper has been published and can be accessed via a link at the top of the paper

Characterization of Burkholderia rhizoxinica and B. endofungorum Isolated from Clinical Specimens

Eight isolates submitted to CDC from 1989 to 2006 from clinical specimens were initially identified as members of the genus Burkholderia based on preliminary cellular fatty acid analysis and/or 16S rRNA gene sequencing. With the recent descriptions of the new species B. rhizoxinica and B. endofungorum, which are considered endosymbiotic bacteria in Rhizopus microsporus fungi, we now identify seven of these clinical isolates as B. rhizoxinica and one as B. endofungorum based on biochemical testing, 16s rRNA, and DNA-DNA hybridization results. We also further characterize these isolates by assessing toxin production and/or by multiple locus sequence typing

A consensus-based transparency checklist

We present a consensus-based checklist to improve and document the transparency of research reports in social and behavioural research. An accompanying online application allows users to complete the form and generate a report that they can submit with their manuscript or post to a public repository

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

Crop surface dynamics through remote sensing in Catalonia in the period 1987-2012

L’objectiu d’aquest treball és l’estudi dels canvis succeïts a Catalunya durant els 25 anys transcorreguts entre 1987 i 2012 amb relació a les superfícies dedicades a l’agricultura. Es basa en les dades de les sis edicions del Mapa d’usos i cobertes del sòl de Catalunya (MUCSC), obtinguts mitjançant la classificació automàtica d’imatges de satèl·lit del programa Landsat, que posa de relleu els avantatges d’aquest tipus d’informació per a l’estudi de grans extensions de terreny en llargues sèries temporals. Els resultats mostren que la superfície mitjana ocupada per conreus a Catalunya al llarg d’aquests anys se situa en el 32 %, amb predomini dels conreus de secà per sobre dels de regadiu (24 % i 8 %, respectivament) i dels herbacis per sobre dels llenyosos (20 % i 12 %, respectivament). La superfície ocupada per aquesta coberta ha anat disminuint durant el període d’estudi a una velocitat mitjana de gairebé 8.000 ha/any, tot i que l’acceleració mitjana (-47 ha/any2) sembla indicar que el procés de regressió s’està frenant, particularment els darrers anys. Aquesta pèrdua afecta principalment els conreus de secà, mentre que el regadiu es manté força estable, i es deu sobretot a l’abandonament de terres i la posterior renaturalització dels camps, així com a l’augment de les superfícies urbanitzades (en aquest cas, en especial a les comarques de la costa central). Malgrat les pèrdues, apareixen noves terres de conreu en comarques de les terres de Lleida, a Osona i a l’Empordà.Paraules clau: teledetecció, Landsat, MUCSC, conreus, canvis en les cobertes del sòl.El objetivo de este trabajo es el estudio de los cambios sucedidos en Cataluña durante los 25 años comprendidos entre 1987 y 2012 en relación con las superficies dedicadas a la agricultura. Este estudio se basa en los datos de las seis ediciones del Mapa de usos y cubiertas del suelo de Catalunya (MUCSC), obtenidos mediante clasificación automática de imágenes de satélite del programa Landsat, y pone de relieve las ventajas del uso de este tipo de información para el estudio de grandes extensiones de terreno en largas series temporales. Los resultados muestran que la superficie media ocupada por cultivos en Cataluña a lo largo de estos años se sitúa en el 32 %: predominan los cultivos de secano sobre los de regadío (24 % y 8 %, respectivamente) y los herbáceos sobre los leñosos (20 % y 12 %, respectivamente). La superficie ocupada por esta cubierta ha ido disminuyendo durante el periodo de estudio a una velocidad media de casi 8.000 ha/año, aunque la aceleración media (-47 ha/año2) parece indicar que el proceso de regresión se está ralentizando, particularmente en los últimos años. Este descenso afecta principalmente a los cultivos de secano, mientras que el regadío se mantiene bastante estable, y se debe sobre todo al abandono de tierras y la posterior renaturalización de los campos, así como al aumento de las superficies urbanizadas (en este caso, sobre todo en las comarcas de la costa central). A pesar de las pérdidas, aparecen nuevas tierras de cultivo en comarcas de las tierras de Lleida, en Osona o en el Empordà.Palabras clave: teledetección, Landsat, MUCSC, cultivos, cambios en las cubiertas del suelo.This paper presents a study of the changes that occurred in Catalonia during the 25 years between 1987 and 2012 in the areas devoted to agriculture. This study is based on data from the six editions of Land use and land cover map of Catalonia (MUCSC, from Catalan) obtained through automatic classification of Landsat satellite imagery, highlighting the advantages of this type of information for the study of large land extensions in long time series. The results show that the average area occupied by crops in Catalonia over these years is 32 %, with rainfed crops predominating over irrigated crops (24 % and 8 %, respectively) and herbaceous crops over woody crops (20 % and 12 %, respectively). The area occupied by this cover has been decreasing during the study period at an average rate of almost 8,000 ha/year, although the average acceleration (-47 ha/year2) seems to indicate that the regression process has been slowing down, particularly in recent years. This loss mainly affects rainfed crops, while irrigated crops remain fairly stable, and it is mainly due to the abandonment of croplands and the subsequent renaturation of fields, as well as to the increase in urbanized areas (in this case particularly in the central coast regions). Despite the losses, new cropland is appearing in the areas of Lleida and of the Osona and Empordà regions.Keywords: remote sensing, Landsat, MUCSC, crops, land cover changes

Incidence of Human Astrovirus in Central Australia (1995 to 1998) and Comparison of Deduced Serotypes Detected from 1981 to 1998

The incidence of astrovirus infection was determined among infants and young children admitted to Alice Springs Hospital (central Australia) with gastroenteritis from 1995 to 1998. Astrovirus was detected by reverse transcription-PCR in 33 of 495 stool samples, and this represented 4.3% of a total of 774 stool samples tested for astrovirus, rotavirus, and Norwalk-like viruses. Astrovirus incidence was substantially lower than that of rotavirus but higher than that of Norwalk-like viruses both overall and in each of the 4 years individually. Over the period from 1981 to 1998, including the period from 1981 to 1994 during which astrovirus was identified only by electron microscopy, astrovirus serotypes (deduced from genotypes) 1, 2, 3, and 4 were identified. Deduced serotypes 1, 3, and 4 all appeared regularly over this 18-year period. Also over this period, nucleotide variation (in some cases substantial) in a section of the capsid protein precursor region of the virus genome was evident among strains of all four of the deduced central Australian serotypes. Consequent amino acid changes were, however, only evident among deduced serotype 3 strains. Geographic variation at both the genome and the resultant amino acid levels was evident among strains of all four of the deduced central Australian serotypes and their respective prototypes isolated in the United Kingdom