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

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

Targeted metatranscriptomics of compost derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity

Background: Using globally abundant crop residues as a carbon source for energy generation and renewable chemicals production stands out as a promising solution to reduce current dependency on fossil fuels. In nature, such as in compost habitats, microbial communities efficiently degrade the available plant biomass using a diverse set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and the inefficiency of the enzyme systems available, making the economic production of lignocellulosic biofuels difficult. Metatranscriptomic studies of microbial communities can unveil the metabolic functions employed by lignocellulolytic consortia and identify new biocatalysts that could improve industrial lignocellulose conversion. Results: In this study, a microbial community from compost was grown in minimal medium with sugarcane bagasse sugarcane bagasse as the sole carbon source. Solid-state nuclear magnetic resonance was used to monitor lignocellulose degradation; analysis of metatranscriptomic data led to the selection and functional characterization of several target genes, revealing the first glycoside hydrolase from Carbohydrate Active Enzyme family 11 with exo-1,4-β-xylanase activity. The xylanase crystal structure was resolved at 1.76 Å revealing the structural basis of exo-xylanase activity. Supplementation of a commercial cellulolytic enzyme cocktail with the xylanase showed improvement in Avicel hydrolysis in the presence of inhibitory xylooligomers. Conclusions: This study demonstrated that composting microbiomes continue to be an excellent source of biotechnologically important enzymes by unveiling the diversity of enzymes involved in in situ lignocellulose degradation

Increased Serum and Musculotendinous Fibrogenic Proteins following Persistent Low-Grade Inflammation in a Rat Model of Long-Term Upper Extremity Overuse.

We examined the relationship between grip strength declines and muscle-tendon responses induced by long-term performance of a high-repetition, low-force (HRLF) reaching task in rats. We hypothesized that grip strength declines would correlate with inflammation, fibrosis and degradation in flexor digitorum muscles and tendons. Grip strength declined after training, and further in weeks 18 and 24, in reach limbs of HRLF rats. Flexor digitorum tissues of reach limbs showed low-grade increases in inflammatory cytokines: IL-1β after training and in week 18, IL-1α in week 18, TNF-α and IL-6 after training and in week 24, and IL-10 in week 24, with greater increases in tendons than muscles. Similar cytokine increases were detected in serum with HRLF: IL-1α and IL-10 in week 18, and TNF-α and IL-6 in week 24. Grip strength correlated inversely with IL-6 in muscles, tendons and serum, and TNF-α in muscles and serum. Four fibrogenic proteins, TGFB1, CTGF, PDGFab and PDGFbb, and hydroxyproline, a marker of collagen synthesis, increased in serum in HRLF weeks 18 or 24, concomitant with epitendon thickening, increased muscle and tendon TGFB1 and CTGF. A collagenolytic gelatinase, MMP2, increased by week 18 in serum, tendons and muscles of HRLF rats. Grip strength correlated inversely with TGFB1 in muscles, tendons and serum; with CTGF-immunoreactive fibroblasts in tendons; and with MMP2 in tendons and serum. Thus, motor declines correlated with low-grade systemic and musculotendinous inflammation throughout task performance, and increased fibrogenic and degradative proteins with prolonged task performance. Serum TNF-α, IL-6, TGFB1, CTGF and MMP2 may serve as serum biomarkers of work-related musculoskeletal disorders, although further studies in humans are needed

Impact of Safety-Related Dose Reductions or Discontinuations on Sustained Virologic Response in HCV-Infected Patients: Results from the GUARD-C Cohort.

BACKGROUND: Despite the introduction of direct-acting antiviral agents for chronic hepatitis C virus (HCV) infection, peginterferon alfa/ribavirin remains relevant in many resource-constrained settings. The non-randomized GUARD-C cohort investigated baseline predictors of safety-related dose reductions or discontinuations (sr-RD) and their impact on sustained virologic response (SVR) in patients receiving peginterferon alfa/ribavirin in routine practice. METHODS: A total of 3181 HCV-mono-infected treatment-naive patients were assigned to 24 or 48 weeks of peginterferon alfa/ribavirin by their physician. Patients were categorized by time-to-first sr-RD (Week 4/12). Detailed analyses of the impact of sr-RD on SVR24 (HCV RNA <50 IU/mL) were conducted in 951 Caucasian, noncirrhotic genotype (G)1 patients assigned to peginterferon alfa-2a/ribavirin for 48 weeks. The probability of SVR24 was identified by a baseline scoring system (range: 0-9 points) on which scores of 5 to 9 and <5 represent high and low probability of SVR24, respectively. RESULTS: SVR24 rates were 46.1% (754/1634), 77.1% (279/362), 68.0% (514/756), and 51.3% (203/396), respectively, in G1, 2, 3, and 4 patients. Overall, 16.9% and 21.8% patients experienced ≥1 sr-RD for peginterferon alfa and ribavirin, respectively. Among Caucasian noncirrhotic G1 patients: female sex, lower body mass index, pre-existing cardiovascular/pulmonary disease, and low hematological indices were prognostic factors of sr-RD; SVR24 was lower in patients with ≥1 vs. no sr-RD by Week 4 (37.9% vs. 54.4%; P = 0.0046) and Week 12 (41.7% vs. 55.3%; P = 0.0016); sr-RD by Week 4/12 significantly reduced SVR24 in patients with scores <5 but not ≥5. CONCLUSIONS: In conclusion, sr-RD to peginterferon alfa-2a/ribavirin significantly impacts on SVR24 rates in treatment-naive G1 noncirrhotic Caucasian patients. Baseline characteristics can help select patients with a high probability of SVR24 and a low probability of sr-RD with peginterferon alfa-2a/ribavirin.This study was sponsored by F. Hoffmann-La Roche Ltd, Basel, Switzerland. Support for third-party writing assistance for this manuscript, furnished by Blair Jarvis MSc, ELS, of Health Interactions, was provided by F. Hoffmann-La Roche Ltd, Basel, Switzerland

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

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

Neuronal damage and memory deficits after seizures are reversed by ascorbic acid?

The objective of the present study was to evaluate the neuroprotective effects of ascorbic acid (AA) in rats, against the neuronal damage and memory deficit caused by seizures. Wistar rats were treated with 0.9% saline (i.p., control group), ascorbic acid (500 mg/kg, i.p., AA group), pilocarpine (400 mg/kg, i.p., pilocarpine group), and the association of ascorbic acid (500 mg/kg, i.p.) plus pilocarpine (400 mg/kg, i.p.), 30 min before of administration of ascorbic acid (AA plus pilocarpine group). After the treatments all groups were observed for 24 h. Pilocarpine group presented seizures which progressed to status epilepticus in 75% of the animals. Pretreatment with AA led to a reduction of 50% of this rate. Results showed that pretreatment with AA did not alter reference memory when compared to a control group. In the working memory task, we observed a significant day's effect with important differences between control, pilocarpine and AA plus pilocarpine groups. Pilocarpine and AA plus pilocarpine groups had 81 and 16% of animals with brain injury, respectively. In the hippocampus of pilocarpine animals, it was detected an injury of 60%. As for the animals tested with AA plus pilocarpine, the hippocampal region of the group had a reduction of 43% in hippocampal lesion. Our findings suggest that seizures caused cognitive dysfunction and neuronal damage that might be related, at least in part, to the neurological problems presented by epileptic patients. AA can reverse cognitive dysfunction observed in rats with seizures as well as decrease neuronal injury in rat hippocampus.O objetivo do presente estudo foi avaliar o efeito neuroprotetor do ácido ascórbico (AA), contra o dano neuronal e o déficit de memória em ratos causados pelas convulsões. Ratos Wistar foram tratados com solução salina a 0,9% (i.p., grupo controle), ácido ascórbico (500 mg/kg, i.p., grupo AA), pilocarpina (400 mg/kg, i.p., grupo pilocarpina), e a associação de ácido ascórbico (500 mg/kg, i.p.) com pilocarpina (400 mg/kg, i.p.), 30 min após a administração de ácido ascórbico (AA + pilocarpina grupo). Após os tratamentos todos os grupos foram observados durante 24 h. O grupo pilocarpina apresentou crises convulsivas que evoluíram para o estado de mal epiléptico em 75% dos animais. O pré-tratamento com AA produz uma redução de 50% nesta taxa. Os resultados mostraram que o pré-tratamento com AA não alterou a memória em relação ao controle. No teste de memória, observou-se um efeito significativo nos dias avaliados entre os grupos controle, pilocarpina e AA + pilocarpina. 81 e 16% dos animais dos grupos AA + pilocarpina e pilocarpina apresentaram danos cerebrais, respectivamente. No hipocampo dos animais do grupo pilocarpina, que foi detectada uma lesão de hipocampal de 60%. Quanto aos animais do grupo AA + pilocarpina, a região do hipocampo apresentou uma redução de 43% na extensão da lesão no hippocampo. Nosso resultados sugerem que as convulsões produzem disfunção cognitiva e dano neuronal que podem estar relacionados, pelo menos em parte, aos problemas neurológicos apresentados pelos pacientes epilépticos. O ácido ascórbico pode reverter essa disfunção cognitiva observado em ratos convulsivos, bem como reduz o desenvolvimento da lesão neuronal no hipocampo de ratos

Study of Microbial Interaction Formed by "Candida krusei" and "Candida glabrata": "In Vitro" and "In Vivo" Studies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Processo FAPESP: #2012/02184-9Processo FAPESP: #2013/25181-8Recently, the non-albicans Candida species have become recognized as an important source of infection and oral colonization by association of different species in a large number of immunosuppressed patients. The objective of this study was to evaluate the interactions between C. krusei and C. glabrata in biofilms formed in vitro and their ability to colonize the oral cavity of mouse model. Monospecies and mixed biofilms were developed of each strain, on 96-well microtiter plates for 48 h. These biofilms were analyzed by counting colony-forming units (CFU/mL) and by determining cell viability, using the XTT hydroxide colorimetric assay. For the in vivo study, twenty-four mice received topical applications of monospecie or mixed suspensions of each strain. After 48 h, yeasts were recovered from the mice and quantified by CFU/mL count. In the biofilm assays, the results for the CFU/mL count and the XTT assay showed that the two species studied were capable of forming high levels of in vitro monospecie biofilm. In mixed biofilm, the CFU of C. krusei increased (p=0.0001) and C. glabrata decreased (p=0.0001). The metabolic activity observed in XTT assay of mixed biofilm was significantly reduced compared with a single C. glabrata biofilm (p=0.0001). Agreeing with CFU in vitro count, C. glabrata CFU/mL values recovered from oral cavity of mice were statistically higher in the group with single infection (p=0.0001) than the group with mixed infection. We concluded that C. krusei inhibits C. glabrata and takes advantage to colonize the oral cavity and to form biofilms