Array2BIO: A Comprehensive Suite of Utilities for the Analysis of Microarray Data

We have developed an integrative and automated toolkit for the analysis of Affymetrix microarray data, named Array2BIO. It identifies groups of coexpressed genes using two complementary approaches--comparative analysis of signal versus control microarrays and clustering analysis of gene expression across different conditions. The identified genes are assigned to functional categories based on the Gene Ontology classification, and a detection of corresponding KEGG protein interaction pathways. Array2BIO reliably handles low-expressor genes and provides a set of statistical methods to quantify the odds of observations, including the Benjamini-Hochberg and Bonferroni multiple testing corrections. Automated interface with the ECR Browser provides evolutionary conservation analysis of identified gene loci while the interconnection with Creme allows high-throughput analysis of human promoter regions and prediction of gene regulatory elements that underlie the observed expression patterns. Array2BIO is publicly available at http://array2bio.dcode.org

Polynucleobacter necessarius, a model for genome reduction in both free-living and symbiotic bacteria

We present the complete genomic sequence of the essential symbiont Polynucleobacter necessarius (Betaproteobacteria), which is a valuable case study for several reasons. First, it is hosted by a ciliated protist, Euplotes; bacterial symbionts of ciliates are still poorly known because of a lack of extensive molecular data. Second, the single species P. necessarius contains both symbiotic and free-living strains, allowing for a comparison between closely related organisms with different ecologies. Third, free-living P. necessarius strains are exceptional by themselves because of their small genome size, reduced metabolic flexibility, and high worldwide abundance in freshwater systems. We provide a comparative analysis of P. necessarius metabolism and explore the peculiar features of a genome reduction that occurred on an already streamlined genome. We compare this unusual system with current hypotheses for genome erosion in symbionts and free-living bacteria, propose modifications to the presently accepted model, and discuss the potential consequences of translesion DNA polymerase loss

Naive B cell output in HIV-infected and HIV-uninfected children.

In this study, we aimed to quantify KREC (kappa-deleting recombination excision circle) levels and naive B cell output in healthy HIV-uninfected children, compared with HIV-infected South African children, before and after starting ART (antiretroviral therapy). Samples were acquired from a Child Wellness Clinic (n = 288 HIV-uninfected South African children, 2 weeks-12 years) and the Children with HIV Early Antiretroviral Therapy (CHER) trial (n = 153 HIV-infected South African children, 7 weeks-8 years). Naive B cell output was estimated using a mathematical model combining KREC levels to reflect B cell emigration into the circulation, flow cytometry measures of naive unswitched B cells to quantify total body naive B cells, and their rates of proliferation using the intracellular marker Ki67. Naive B cell output increases from birth to 1 year, followed by a decline and plateau into late childhood. HIV-infected children on or off ART had higher naive B cell outputs than their uninfected counterparts (p = .01 and p = .04). This is the first study to present reference ranges for measurements of KRECs and naive B cell output in healthy and HIV-infected children. Comparison between HIV-uninfected healthy children and HIV-infected children suggests that HIV may increase naive B cell output. Further work is required to fully understand the mechanisms involved and clinical value of measuring naive B cell output in children

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage

OP9 is a yet-uncultivated bacterial lineage found in geothermal systems, petroleum reservoirs, anaerobic digesters and wastewater treatment facilities. Here we use single-cell and metagenome sequencing to obtain two distinct, nearly complete OP9 genomes, one constructed from single cells sorted from hot spring sediments and the other derived from binned metagenomic contigs from an in situ-enriched cellulolytic, thermophilic community. Phylogenomic analyses support the designation of OP9 as a candidate phylum for which we propose the name ‘Atribacteria’. Although a plurality of predicted proteins is most similar to those from Firmicutes, the presence of key genes suggests a diderm cell envelope. Metabolic reconstruction from the core genome suggests an anaerobic lifestyle based on sugar fermentation by Embden–Meyerhof glycolysis with production of hydrogen, acetate and ethanol. Putative glycohydrolases and an endoglucanase may enable catabolism of (hemi)cellulose in thermal environments. This study lays a foundation for understanding the physiology and ecological role of the ‘Atribacteria’.United States. National Aeronautics and Space Administration (Exobiology Grant EXO-NNX11AR78G)National Science Foundation (U.S.) (Grant MCB 0546865)National Science Foundation (U.S.) (Grant OISE 0968421)United States. Dept. of Energy (Grant DE-EE-0000716)Nevada Renewable Energy ConsortiumUnited States. Dept. of Energy. Office of Science. Joint Genome Institute (Contract DE-AC02-05CH11231

Valence band excitations in V_2O_5

We present a joint theoretical and experimental investigation of the electronic and optical properties of vanadium pentoxide. Electron energy-loss spectroscopy in transmission was employed to measure the momentum-dependent loss function. This in turn was used to derive the optical conductivity, which is compared to the results of band structure calculations. A good qualitative and quantitative agreement between the theoretical and the experimental optical conductivity was observed. The experimentally observed anisotropy of the optical properties of V_2O_5 could be understood in the light of an analysis of the theoretical data involving the decomposition of the calculated optical conductivity into contributions from transitions into selected energy regions of the conduction band. In addition, based upon a tight binding fit to the band structure, values are given for the effective V3d_xy-O2p hopping terms and are compared to the corresponding values for alpha'-NaV_2O_5.Comment: 6 pages (revtex),6 figures (jpg

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

MM received funding from the Max Planck innovation funds for this project. PGDF was supported by a Marie Curie European Reintegration Grant (proposal nr 270891). CE was supported by German Science Foundation grants (DFG, EI 841/4-1 and EI 841/6-1)

SIEGE: Sistema de información estrategica para la gestión escolar

[EN] The indicators on students are generated by the data associated with the record of the schooling. When we talk about complex populations, the handling of millions of related data is required, for this reason, this data constitutes scarcely used source. To support decision taking, planning and the balance statements, within the Universidad Veracruzana has been developed Integral System which gathers the data together in an easy and reliable way, systematize them into indicators and information that has been defined as outstanding. It is focused on how to make the data running and analysis easier, but above all, to generate the conditions that facilitate the look up of the results for the users to direct their decisions. The indicators gather based on the user´s needs, it is possible to look up any indicator from the perspective of the whole population or specific units: Knowledge sphere, Region, At faculty or even as a student. The information refers to School population (volume and distribution); School retention, Performance (passing, flunking, or school average) School progress (connection between required time and credit progress) and School path the relationship between performance and progress and puts up types of students.[ES] Los indicadores sobre estudiantes se generan de los datos asociados al registro y seguimiento de la escolaridad. Cuando se trata poblaciones grandes, complejas y diversas, requiere del manejo de millones de datos relacionados, por ello estos datos suelen constituir una fuente de información escasamente utilizada. Para apoyar la toma decisiones, la planeación, los procesos de acreditación y la rendición de cuentas, en la Universidad Veracruzana se desarrolló el Sistema Integral de Gestión Escolar SIEGE el cual recopila de manera fácil y fiable los datos, los sistematiza en indicadores e información que se ha definido como relevante. Está orientado a facilitar la explotación y análisis de los datos, pero sobre sobre todo a generar condiciones que faciliten la consulta de los resultados para que los usuarios orienten sus decisiones. Los indicadores se agrupan según las necesidades del usuario, es posible consultar cualquier indicador desde la perspectiva de la totalidad de la población o unidades específicas: Área de conocimiento, Región, o un área en una región; a nivel de Escuela o Facultad y hasta estudiante. La información se refiere a la Población escolar (volumen y distribución de la demanda, el primer ingreso y la población total por sexo y edad); la Permanencia (por periodo escolar y eficiencia terminal, avance en número de créditos) Desempeño (aprobación, reprobación y promedio escolar) y Avance escolar (relación tiempo de permanencia y avance crediticio) y Trayectoria escolar que indica la relación entre desempeño y avance y construye tipos de estudiantes. A lo anterior se agregan indicadores relativos a Horarios (número días, cursos y horas de asistencia a la semana, horas interclase no ocupadas). Así mismo, permite la consulta de indicadores de egreso, titulación y resultados de exámenes de egreso. Contiene además una Consulta Gerencial de Cursos e Inscripción que sistematiza la información de cursos (volumen y distribución ofertados por periodo), profesores (por tipo de contratación y número de horas que imparte) los indicadores de ocupación de las aulas y las horas. El sistema intenta en un nivel más cercano a los usuarios directos, que los indicadores ofrezcan información certera, confiable, oportuna y fácil de consultar. Pretende brindar conocimiento sobre la complejidad que caracteriza a la universidad, fomentar la transparencia y la rendición de cuentas.Chain R., R.; García T., C.; Rodríguez C., P.; Rodríguez P., MP.; Ortega G., JC. (2014). SIEGE: Sistema de información estrategica para la gestión escolar. En CONFERENCIA INTERNACIONAL INFOACES. UN SISTEMA DE INFORMACIÓN PARA LAS UNIVERSIDADES LATINOAMERICANAS. LIBRO DE ACTAS. Editorial Universitat Politècnica de València. 151-155. http://hdl.handle.net/10251/91474OCS15115

A cardinal role for cathepsin D in co-ordinating the host-mediated apoptosis of macrophages and killing of pneumococci

The bactericidal function of macrophages against pneumococci is enhanced by their apoptotic demise, which is controlled by the anti-apoptotic protein Mcl-1. Here, we show that lysosomal membrane permeabilization (LMP) and cytosolic translocation of activated cathepsin D occur prior to activation of a mitochondrial pathway of macrophage apoptosis. Pharmacological inhibition or knockout of cathepsin D during pneumococcal infection blocked macrophage apoptosis. As a result of cathepsin D activation, Mcl-1 interacted with its ubiquitin ligase Mule and expression declined. Inhibition of cathepsin D had no effect on early bacterial killing but inhibited the late phase of apoptosis-associated killing of pneumococci in vitro. Mice bearing a cathepsin D-/- hematopoietic system demonstrated reduced macrophage apoptosis in vivo, with decreased clearance of pneumococci and enhanced recruitment of neutrophils to control pulmonary infection. These findings establish an unexpected role for a cathepsin D-mediated lysosomal pathway of apoptosis in pulmonary host defense and underscore the importance of apoptosis-associated microbial killing to macrophage function

Single-Species Microarrays and Comparative Transcriptomics

BACKGROUND: Prefabricated expression microarrays are currently available for only a few species but methods have been proposed to extend their application to comparisons between divergent genomes. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that the hybridization intensity of genomic DNA is a poor basis on which to select unbiased probes on Affymetrix expression arrays for studies of comparative transcriptomics, and that doing so produces spurious results. We used the Affymetrix Xenopus laevis microarray to evaluate expression divergence between X. laevis, X. borealis, and their F1 hybrids. When data are analyzed with probes that interrogate only sequences with confirmed identity in both species, we recover results that differ substantially analyses that use genomic DNA hybridizations to select probes. CONCLUSIONS/SIGNIFICANCE: Our findings have implications for the experimental design of comparative expression studies that use single-species microarrays, and for our understanding of divergent expression in hybrid clawed frogs. These findings also highlight important limitations of single-species microarrays for studies of comparative transcriptomics of polyploid species