Modeling recursive RNA interference.

An important application of the RNA interference (RNAi) pathway is its use as a small RNA-based regulatory system commonly exploited to suppress expression of target genes to test their function in vivo. In several published experiments, RNAi has been used to inactivate components of the RNAi pathway itself, a procedure termed recursive RNAi in this report. The theoretical basis of recursive RNAi is unclear since the procedure could potentially be self-defeating, and in practice the effectiveness of recursive RNAi in published experiments is highly variable. A mathematical model for recursive RNAi was developed and used to investigate the range of conditions under which the procedure should be effective. The model predicts that the effectiveness of recursive RNAi is strongly dependent on the efficacy of RNAi at knocking down target gene expression. This efficacy is known to vary highly between different cell types, and comparison of the model predictions to published experimental data suggests that variation in RNAi efficacy may be the main cause of discrepancies between published recursive RNAi experiments in different organisms. The model suggests potential ways to optimize the effectiveness of recursive RNAi both for screening of RNAi components as well as for improved temporal control of gene expression in switch off-switch on experiments

SPATIAL ANALYSE OF LITTERFALL IN A GALLERY FOREST

Matas de galeria possuem grande diversidade gen\ue9tica e desempenham importantes fun\ue7\uf5es ecol\uf3gicas, como a prote\ue7\ue3o das nascentes, controle da eros\ue3o e funcionam como filtros retendo poluentes. A serapilheira, que pode ser usada como um indicativo de produtividade ecol\uf3gica \ue9 amplamente coletada por meio de coletores que s\ue3o distribu\ueddos aleatoriamente em um ecossistema florestal. No entanto, a distribui\ue7\ue3o da vegeta\ue7\ue3o pode apresentar depend\ueancia espacial, logo, a produtividade da serapilheira pode ser mapeada utilizando t\ue9cnicas geoestat\uedsticas o que permite a delimita\ue7\ue3o de zonas de manejo. Portanto, o objetivo deste estudo foi avaliar a efici\ueancia de m\ue9todos geoestat\uedsticos na delimita\ue7\ue3o de zonas de manejo da produtividade de serapilheira em uma \ue1rea de mata de galeria. O estudo foi realizado na mata de galeria do c\uf3rrego Lava-p\ue9s (3 ha) em Ipameri - GO, utilizando-se 60 coletores (cada um com 0,33 m\ub2 de \ue1rea e suspensos a 0,65 m do solo) instalados em uma malha regular georreferenciada de 32 x 32 m. A serapilheira foi coletada mensalmente de dezembro de 2011 a novembro de 2012. Todas as amostras foram separadas manualmente nas fra\ue7\uf5es: folhas (FF), ramos (FR - galhos e cascas), e estruturas reprodutivas (FER - flores, frutos e sementes) e foram expressas em kg ha-1. Realizou-se a an\ue1lise estat\uedstica descritiva e geoestat\uedstica dos dados. A produtividade de serapilheira para a FF e o total apresentou forte depend\ueancia espacial. A FR e a FER apresentaram efeito pepita puro. O mapa dos valores de serapilheira total obtido pelo m\ue9todo de interpola\ue7\ue3o Krigagem indicaram \ue1reas de produtividade variando de 900 a 10.900 Kg ha-1ano, evidenciando alta variabilidade na \ue1rea. Foi poss\uedvel por meio da t\ue9cnica de interpola\ue7\ue3o krigagem delimitar zonas de manejo da produtividade de serapilheira na mata de galeria estudada, o que permitiu o manejo florestal espec\uedfico da serapilheira.The gallery forests have great genetic diversity and important ecological functions, such as protecting the headwaters, controlling erosion, and functioning as buffer zones and filtering chemicals. Litterfall, which can be used as an indicator of ecological productivity, is widely collected using litter traps that are randomly distributed in a forest plot. However, vegetation distribution may present spatial dependence, thus the yield of the litterfall can be mapped using geostatistical techniques allowing the delineation of management zones. Therefore, the objective of this study was to evaluate the efficiency of geostatistical methods using the zoning management productivity of litterfall on a gallery forest in central Brazil. The study was conducted on the gallery forest along the \u2018Lava-p\ue9s\u2019 stream in Goi\ue1s State, Brazil where the experimental site (3 ha) was structured in a grid of 60 litterfall traps, each of 0.33 m2 held 0.65 m above the ground, georeferenced, spaced at 32 x 32 m intervals. Litterfall was monthly collected from December 2011 to November 2012. All litterfall samples were manually separated into three fractions: leaves (LE), branch bark (BB), and reproductive parts (RP) and they were expressed in kg ha-1. Statistical analyses consisted of data description and geostatistics. The litterfall of for LE and total showed strong spatial dependence. The BB and RP showed pure nugget effect. The total litterfall maps obtained by the Kriging interpolation method indicated zones in the map ranging from 900 to 10,900 kg ha-1 per yr. The kriging interpolation technique delineate management zones of productivity in the gallery forest litterfall studied, which allowed the specific forest management of litterfall

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal

Biochemical characterization and low-resolution SAXS shape of a novel GH11 exo-1,4-β-xylanase identified in a microbial consortium

Biotechnologies that aim to produce renewable fuels, chemicals, and bioproducts from residual ligno(hemi)cellulosic biomass mostly rely on enzymatic depolymerization of plant cell walls (PCW). This process requires an arsenal of diverse enzymes, including xylanases, which synergistically act on the hemicellulose, reducing the long and complex xylan chains to oligomers and simple sugars. Thus, xylanases play a crucial role in PCW depolymerization. Until recently, the largest xylanase family, glycoside hydrolase family 11 (GH11) has been exclusively represented by endo-catalytic β-1,4- and β-1,3-xylanases. Analysis of a metatranscriptome library from a microbial lignocellulose community resulted in the identification of an unusual exo-acting GH11 β-1,4-xylanase (MetXyn11). Detailed characterization has been performed on recombinant MetXyn11 including determination of its low-resolution small angle Xray scattering (SAXS) molecular envelope in solution. Our results reveal that MetXyn11 is a monomeric globular enzyme that liberates xylobiose from heteroxylans as the only product. MetXyn11 has an optimal activity in a pH range from 6 to 9 and an optimal temperature of 50 oC. The enzyme maintained above 65% of its original activity in the pH range 5 to 6 after being incubated for 72 h at 50 oC. Addition of the enzyme to a commercial enzymatic cocktail (CelicCtec3) promoted a significant increase of enzymatic hydrolysis yields of hydrothermally pretreated sugarcane bagasse (16% after 24 h of hydrolysis)

Direct susceptibility testing for multi drug resistant tuberculosis: A meta-analysis

<p>Abstract</p> <p>Background</p> <p>One of the challenges facing the tuberculosis (TB) control programmes in resource-limited settings is lack of rapid techniques for detection of drug resistant TB, particularly multi drug resistant tuberculosis (MDR TB). Results obtained with the conventional indirect susceptibility testing methods come too late to influence a timely decision on patient management. More rapid tests directly applied on sputum samples are needed. This study compared the sensitivity, specificity and time to results of four direct drug susceptibility testing tests with the conventional indirect testing for detection of resistance to rifampicin and isoniazid in <it>M. tuberculosis</it>. The four direct tests included two in-house phenotypic assays – Nitrate Reductase Assay (NRA) and Microscopic Observation Drug Susceptibility (MODS), and two commercially available tests – Genotype^®MTBDR and Genotype^®MTBDR<it>plus </it>(Hain Life Sciences, Nehren, Germany).</p> <p>Methods</p> <p>A literature review and meta-analysis of study reports was performed. The Meta-Disc software was used to analyse the reports and tests for sensitivity, specificity, and area under the summary receiver operating characteristic (sROC) curves. Heterogeneity in accuracy estimates was tested with the Spearman correlation coefficient and Chi-square.</p> <p>Results</p> <p>Eighteen direct DST reports were analysed: NRA – 4, MODS- 6, Genotype MTBDR^®– 3 and Genotype^®MTBDR<it>plus </it>– 5. The pooled sensitivity and specificity for detection of resistance to rifampicin were 99% and 100% with NRA, 96% and 96% with MODS, 99% and 98% with Genotype^®MTBDR, and 99% and 99% with the new Genotype^®MTBDR<it>plus</it>, respectively. For isoniazid it was 94% and 100% for NRA, 92% and 96% for MODS, 71% and 100% for Genotype^®MTBDR, and 96% and 100% with the Genotype^®MTBDR<it>plus</it>, respectively. The area under the summary receiver operating characteristic (sROC) curves was in ranges of 0.98 to 1.00 for all the four tests. Molecular tests were completed in 1 – 2 days and also the phenotypic assays were much more rapid than conventional testing.</p> <p>Conclusion</p> <p>Direct testing of rifampicin and isoniazid resistance in <it>M. tuberculosis </it>was found to be highly sensitive and specific, and allows prompt detection of MDR TB.</p