Transcript and metabolite profiling for the evaluation of tobacco tree and poplar as feedstock for the bio-based industry

The global demand for food, feed, energy and water poses extraordinary challenges for future generations. It is evident that robust platforms for the exploration of renewable resources are necessary to overcome these challenges. Within the multinational framework MultiBioPro we are developing biorefinery pipelines to maximize the use of plant biomass. More specifically, we use poplar and tobacco tree (Nicotiana glauca) as target crop species for improving saccharification, isoprenoid, long chain hydrocarbon contents, fiber quality, and suberin and lignin contents. The methods used to obtain these outputs include GC-MS, LC-MS and RNA sequencing platforms. The metabolite pipelines are well established tools to generate these types of data, but also have the limitations in that only well characterized metabolites can be used. The deep sequencing will allow us to include all transcripts present during the developmental stages of the tobacco tree leaf, but has to be mapped back to the sequence of Nicotiana tabacum. With these set-ups, we aim at a basic understanding for underlying processes and at establishing an industrial framework to exploit the outcomes. In a more long term perspective, we believe that data generated here will provide means for a sustainable biorefinery process using poplar and tobacco tree as raw material. To date the basal level of metabolites in the samples have been analyzed and the protocols utilized are provided in this article.

The reach and rationale for community health fairs

Latinos living in the USA account for one third of the uninsured population and face numerous cultural, linguistic, and financial barriers to accessing healthcare services. Community health fairs have developed to address the unmet need for no- and low-cost services that target prevention and education among underserved communities. The current research describes an ongoing effort in a community in Southern California and examines the barriers to health care among participants registering to receive free breast health screenings, one of the major services offered at a 2010 health fair. A total of 186 adult Latina women completed a brief questionnaire assessing their healthcare utilization and self-reported barriers to engaging in preventive and screening services. Approximately two thirds of the participants reported never receiving or having more than 2 years passing since receiving a preventive health check-up. Participants identified cost (64.5 %) and knowledge of locations for services (52.3 %) as the primary barriers to engaging in routine healthcare services. Engaging with health professionals represents a leading way in which adults obtain health information; health fairs offering cancer health screenings represent a culturally appropriate venue for increased cancer health equity. Implications of the current research for future health fairs and their role in community cancer education are discussed.

Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways

To newly identify loci for age at natural menopause, we carried out a meta-analysis of 22 genome-wide association studies (GWAS) in 38,968 women of European descent, with replication in up to 14,435 women. In addition to four known loci, we identified 13 loci newly associated with age at natural menopause (at P < 5 x 10(-8)). Candidate genes located at these newly associated loci include genes implicated in DNA repair (EXO1, HELQ, UIMC1, FAM175A, FANCI, TLK1, POLG and PRIM1) and immune function (IL11, NLRP11 and PRRC2A (also known as BAT2)). Gene-set enrichment pathway analyses using the full GWAS data set identified exoDNase, NF-kappaB signaling and mitochondrial dysfunction as biological processes related to timing of menopause.

Combinations of plant-derived compounds against Campylobacter in vitro

Campylobacter occur in fresh retail poultry products as a result of their colonization of the gastro-intestinal tract of chickens during growth. Feed additives could be used for suppression of Campylobacter levels in the chickens prior to slaughter. To address this opportunity, feed manufacturers are targeting natural antimicrobials from plant material as new forms of consumer-accepted feed additives. However, to be practical, these natural antimicrobials must be effective at low concentrations. The current study has validated an improved laboratory method to study minimal inhibitory concentrations of plant compounds and their combinations against Campylobacter. The assay was shown to be valid for testing lipid-soluble and water-soluble plant extracts and byproducts from the food industry. The study screened 29 extracts or plant-derived compounds and their mixtures for anti-Campylobacter activity using a laboratory assay. Combinations of oregano, lactic acid, and sorghum byproduct showed effective synergy in anti-Campylobacter activity. The synergies allowed a large reduction in the concentration of the individual compounds needed to kill the bacteria with an 80% reduction in concentration being achieved for oregano essential oil. The assay gives rise to further opportunities for the testing of a greater range of combinations of plant-derived compounds and other natural antimicrobials. The method is robust, simple, and easily automated, and it could be used to adjust the cost of feed formulations by reducing costs associated with antimicrobial feed additives.

Directional dominance on stature and cognition in diverse human populations

Homozygosity has long been associated with rare, often devastating, Mendelian disorders1, and Darwin was one of the first to recognize that inbreeding reduces evolutionary fitness2. However, the effect of the more distant parental relatedness that is common in modern human populations is less well understood. Genomic data now allow us to investigate the effects of homozygosity on traits of public health importance by observing contiguous homozygous segments (runs of homozygosity), which are inferred to be homozygous along their complete length. Given the low levels of genome-wide homozygosity prevalent in most human populations, information is required on very large numbers of people to provide sufficient power3, 4. Here we use runs of homozygosity to study 16 health-related quantitative traits in 354,224 individuals from 102 cohorts, and find statistically significant associations between summed runs of homozygosity and four complex traits: height, forced expiratory lung volume in one second, general cognitive ability and educational attainment (P < 1 × 10−300, 2.1 × 10−6, 2.5 × 10−10 and 1.8 × 10−10, respectively). In each case, increased homozygosity was associated with decreased trait value, equivalent to the offspring of first cousins being 1.2 cm shorter and having 10 months’ less education. Similar effect sizes were found across four continental groups and populations with different degrees of genome-wide homozygosity, providing evidence that homozygosity, rather than confounding, directly contributes to phenotypic variance. Contrary to earlier reports in substantially smaller samples5, 6, no evidence was seen of an influence of genome-wide homozygosity on blood pressure and low density lipoprotein cholesterol, or ten other cardio-metabolic traits. Since directional dominance is predicted for traits under directional evolutionary selection7, this study provides evidence that increased stature and cognitive function have been positively selected in human evolution, whereas many important risk factors for late-onset complex diseases may not have been.

Fast in-memory XPath search using compressed indexes

A large fraction of an XML document typically consists of text data. The XPath query language allows text search via the equal, contains, and starts-with predicates. Such predicates can be efficiently implemented using a compressed self-index of the document's text nodes. Most queries, however, contain some parts querying the text of the document, plus some parts querying the tree structure. It is therefore a challenge to choose an appropriate evaluation order for a given query, which optimally leverages the execution speeds of the text and tree indexes. Here the SXSI system is introduced. It stores the tree structure of an XML document using a bit array of opening and closing brackets plus a sequence of labels, and stores the text nodes of the document using a global compressed self-index. On top of these indexes sits an XPath query engine that is based on tree automata. The engine uses fast counting queries of the text index in order to dynamically determine whether to evaluate top-down or bottom-up with respect to the tree structure. The resulting system has several advantages over existing systems: (1) on pure tree queries (without text search) such as the XPathMark queries, the SXSI system performs on par or better than the fastest known systems MonetDB and Qizx, (2) on queries that use text search, SXSI outperforms the existing systems by 1-3 orders of magnitude (depending on the size of the result set), and (3) with respect to memory consumption, SXSI outperforms all other systems for counting-only queries.

Storage and retrieval of individual genomes

A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. Flexible and efficient data analysis on a such typically huge collection is plausible using suffix trees. However, suffix tree occupies O(N log N) bits, which very soon inhibits in-memory analyses. Recent advances in full-text self-indexing reduce the space of suffix tree to O(N log σ) bits, where σ is the alphabet size. In practice, the space reduction is more than 10-fold, for example on suffix tree of Human Genome. However, this reduction factor remains constant when more sequences are added to the collection. We develop a new family of self-indexes suited for the repetitive sequence collection setting. Their expected space requirement depends only on the length n of the base sequence and the number s of variations in its repeated copies. That is, the space reduction factor is no longer constant, but depends on N / n. We believe the structures developed in this work will provide a fundamental basis for storage and retrieval of individual genomes as they become available due to rapid progress in the sequencing technologies.

Expected Performance of the ATLAS Experiment - Detector, Trigger and Physics

A detailed study is presented of the expected performance of the ATLAS detector. The reconstruction of tracks, leptons, photons, missing energy and jets is investigated, together with the performance of b-tagging and the trigger. The physics potential for a variety of interesting physics processes, within the Standard Model and beyond, is examined. The study comprises a series of notes based on simulations of the detector and physics processes, with particular emphasis given to the data expected from the first years of operation of the LHC at CERN.

Influencia de cobertura muerta y fertilización sobre el comportamiento de las malezas y el crecimiento y rendimiento del frijol común (Phaseolus vulgaris L.)

En el Centro Experimental La Compañía ubicado en el municipio de San Marcos, departamento de Carazo, Nicaragua, se realizó un experimento para evaluar el efecto de cobertura muerta y fertilización sobre el comportamiento de las malezas y el crecimiento y rendimiento del frijol común (Phaseolus vulgaris L.). El diseño experimental utilizado fue bloques completos al azar en arreglo bifactorial. Se evaluó cobertura muerta de maíz (Zea mays L.) 4 532.33 kg/ha, cobertura muerta de sorgo (Sorghum bicolor L.) 8 202.5 kg/ha y control mecánico (periodo crítico 14 y 21 días después de la siembra). Los niveles de fertilización evaluados: fertilización normal 15.5 kg N/ha, 38.76 kg p2O5 y 12.92 kg K20/ha, fertilización media 7.75 kg N/ha, 19.38 kg P2O5 y 6.45 kg K2O/ha y sin fertilización. Las variables evaluadas de malezas fueron abundancia, dominancia y diversidad. Las variables evaluadas del cultivo fueron altura de plantas, numero de ramas por planta, biomasa, número de plantas por parcela útil, numero de vainas por planta, numero de granos por vaina, peso de cien granos y rendimiento del grano. Los datos se analizaron por medio del análisis de varianza, excepto las variables diversidad y grado de cobertura de malezas. Para realizar las separaciones de medias se utilizó la prueba de rangos múltiples de Tukey. El análisis económico se hizo a través de la metodología del presupuesto parcial y análisis marginal de beneficios netos. Las coberturas de maíz y sorgo, y el control mecánico tuvieron un efecto similar sobre la abundancia total de malezas en los distintos muestreos realizados. La fertilización no influyo sobre la abundancia ni sobre la acumulación de biomasa de malezas. El control mecánico permitió menor grado de cobertura y menor acumulación de biomasa a las malezas. Las variables del cultivo que presentaron diferencias significativas para el factor cobertura fueron altura de plantas, número de vainas por planta y peso de cien granos. Mientras el factor fertilización presento diferencias significativas para las variables altura de plantas, biomasa, número de plantas y rendimiento del grano. Ninguna de las variables evaluadas tanto de las malezas como del cultivo presentó diferencias significativas para la interacción de los factores en estudio. Los mejores resultados económicos los presentaron la cobertura de maíz y la fertilización normal que presento la mejor tasa de retorno marginal.

Evaluación preliminar de insecticidas químicos, botánicos y biológicos en el control de la mosquita del sorgo (Contarinia sorguicola Coq) y los rendimientos de granos en la variedad pinolero - 1

Con el propósito de determinar el producto más eficaz en el control de la mosquita del sorgo (Contarinia sorghicola Coq). Se realizó un experimento en el periodo comprendido entre los meses de septiembre a diciembre de 1996, en el Centro Nacional de Investigación Agropecuaria (CNIA/INTA), cuyos suelos pertenecen a la serie Sabana Grande con drenaje moderadamente rápido y textura que varia de franco a franco arenoso. El disefto utilizado fue un bloque completo al azar con cuatro repeticiones y seis tratamientos. Los tratamientos estudiados fueron insecticidas a base de (deltametrina) Decis 2.5 EC, (metamidophos) MTD 60 SL, (azadiractina) Nim 20%,(azadhiractina) Nim 80%, EM-5 (microorganismos efectivos) y un testigo absoluto (sin aplicación). La variedad utilizada fue Pinolero-1. Los resultados demuestran que no se presentaron diferencias significativas para ninguna de las variables evaluadas por lo que no hubo efecto de los tratamientos evaluados. Sin embargo el análisis económico de los tratamientos refleja que el testigo absoluto (sin aplicación) presentó la mayor tasa de rentabilidad.

Anuario Argentino de Derecho Canónico, 2006, Vol. XIII (número completo)

Contenido: Los requisitos psicológicos en el penitente y en el confesor para la eficacia del Sacramento de la Reconciliación / C. Baccioli – La belleza de la verdad sobre el matrimonio : comentario al discurso del Santo Padre a la Rota Romana el 27 de enero de 2007 / J. Bonet Alcón – Servidores de la verdad : la función pastoral de los patronos en los juicios de nulidad matrimonial / A. W. Bunge – Los derechos y las obligaciones del clérigo en la sociedad civil a la luz del Código de Derecho Canónico / A. D. Busso – El celibato : don, propuesta y tarea. (La necesaria madurez humana y el Derecho) / J. Fronza – Iglesias, medios de comunicación y libertad religiosa en la República Argentina / J. G. Navarro Floria – El régimen canónico de los bienes de propiedad de las personas jurídicas privadas / H. A. von Ustinov – Notas – Sentencias – Actualidad – Recensiones

Efecto del mal seco (Pythium myriotylum Drechs) en campo y sombreadero sobre la agromorfología de quince accesiones de quequisque (Xanthosoma spp) desarrollo de síntomas y detección microbiológica

El quequisque ( Xanthosoma spp.), familia Aráceae, es importante para el consumo interno y la exportación en Nicaragua, tiene como problema principal al mal seco ( Pythium myriotylum Drechs ) , que causa la pérdida total del rendimiento. Se establecieron cuatro ensayos para evaluar el efecto del mal seco sobre agromorfología de 15 accesiones de quequisque en suelos con (scams) y sin antecedentes de mal seco (ssams). Ensayo I: se evaluó el efecto del mal seco sobre la agromorfología de 15 accesiones en scams en Nueva Guinea. Se empleó el diseño BCA con tres bloques. Ensayo II: se estableció en DCA, se evaluó el comportamiento de 7 de las accesiones en ssams y se comparó con el rendimiento obtenido en scams. Ensayo III: se cultivó raíces de plantas infectadas en los medios de cultivo AN, V-8 y PARC y dilución en serie del scams para verificar la presencia de P myriotylum . Ensayo IV: se evaluó el desarrollo de síntomas de la enfermedad en las raíces, se establecieron 14 accesiones en scams en bolsas de polietileno (15 plantas por accesión) en sombreadero. Todas las accesiones desarrollaron mal seco, produjeron plantas débiles de 30-40 cm de altura, con tres hojas máximo y ningún rendimiento. Las accesiones en ssams reportaron 3-12 t ha -1 de rendimientos promedios. Las plantas en scams registrar on 91-100 % de pérdidas en el rendimiento. La infección en las raíces ocurre a partir de los 21 días después de la siembra, la planta genera nuevas raíces que también se infectan y muere por agotamiento de las reservas. La dilución en serie no resultó en el aislamiento del patógeno. Sembrar raíces recién infectadas resultó en la presencia de micelios del hongo en los medios V-8 y PARC.

Zeballos, la parábola de la narración : un estudio de "La rejión del trigo" como libro de viaje

Número monográfico: El viaje y sus discursos