Description of plant tRNA-derived RNA fragments (tRFs) associated with argonaute and identification of their putative targets

tRNA-derived RNA fragments (tRFs) are 19mer small RNAs that associate with Argonaute (AGO) proteins in humans. However, in plants, it is unknown if tRFs bind with AGO proteins. Here, using public deep sequencing libraries of immunoprecipitated Argonaute proteins (AGO-IP) and bioinformatics approaches, we identified the Arabidopsis thaliana AGO-IP tRFs. Moreover, using three degradome deep sequencing libraries, we identified four putative tRF targets. The expression pattern of tRFs, based on deep sequencing data, was also analyzed under abiotic and biotic stresses. The results obtained here represent a useful starting point for future studies on tRFs in plants. © 2013 Loss-Morais et al.; licensee BioMed Central Ltd.

TRFS: desenvolvimento de um protótipo para simulação microscópica de tráfego

Dissertação para obtenção do grau de Mestre em Engenharia Civil na Área de Especialização de Vias de Comunicação e Transportes

Análise da expressão gênica de pequenos RNAs derivados de tRNAs (tRFs) em plantas

Small non coding RNAs emerged as important characters in several biology aspects. Among then, the most studied are microRNAs (miRNAs) and short interfering RNAs (siRNAs), that regulate their target gene post-transcriptionally in plants, animals and RNAi pathway intermediates, respectively. Both of classes have similar biogenesis being processed by Dicer enzymes and subsequent association with Argonaute enzymes. In plants, miRNAs and siRNAs have important functions in development, genome integrity and biotic and abiotic stress responses. The advances in high-throughtput sequencing and in silico analisys provide the uncover of new small non coding RNAs classes, many of them with unknown functions and biogenesis. tRNA derived small RNAs (tRFs) are a small non coding RNA class, that have as precursor a tRNA molecule. These were uncovers in the last decade in many organisms and, recently, in plants. Recent works detected tRFs from different sizes, with different source portions of the mature tRNA molecule (5’ end; 3’ end, anti-codon loop) and some from the tRNA precursor (pre-tRNA), suggesting that may be a novel class of small RNA and not random degradation products. Works in humans showed that some tRFs are processed by the Dicer enzymes, have association with the Argonaute enzymes and cell differentiation, tumor appearance and gene silencing related functions. Works in Arabidopsis and pumpkin (Cucurbita maxima) showed, respectively, that the tRFs have nutritional stress response possible functions and long distance signaling function between source and drain tissues, and may affect the translation. The tRFs biogenesis in plants are, until now an unknown, absence information about it in the literature and its possible biological functions are few studied yet, making then interesting target for studies among the small non coding RNAs in plants

Microbial indicators related to yield and disease and changes in soil microbial community structure with ginger farm management practices

TRFLP (terminal restriction fragment length polymorphism) was used to assess whether management practices that improved disease suppression and/or yield in a 4-year ginger field trial were related to changes in soil microbial community structure. Bacterial and fungal community profiles were defined by presence and abundance of terminal restriction fragments (TRFs), where each TRF represents one or more species. Results indicated inclusion of an organic amendment and minimum tillage increased the relative diversity of dominant fungal populations in a system dependant way. Inclusion of an organic amendment increased bacterial species richness in the pasture treatment. Redundancy analysis showed shifts in microbial community structure associated with different management practices and treatments grouped according to TRF abundance in relation to yield and disease incidence. ANOVA also indicated the abundance of certain TRFs was significantly affected by farming system management practices, and a number of these TRFs were also correlated with yield or disease suppression. Further analyses are required to determine whether identified TRFs can be used as general or soil-type specific bio-indicators of productivity (increased and decreased) and Pythium myriotylum suppressiveness.

Effect of inclusion of lactulose and Lactobacillus plantarum on the intestinal environment and performance of piglets at weaning

The prebiotic lactulose, a probiotic strain of Lactobacillus plantarum (L. plantarum) and a synbiotic combination of these two agents were evaluated as growth promoters in 25–39-day old commercial weaning pigs. Ninety-six weaning pigs were allocated into 32 pens, taking initial weight into account, and distributed into four groups as follows: a control diet (CTR), the same diet supplemented daily with L. plantarum (109 CFU/mL sprayed on top; 20 mL/pig) (LPN); 10 g/kg lactulose (LAC) or a combination of both treatments (SYN). At day 14, eight piglets from each group were euthanized and proximal colon digesta was sampled for luminal pH, short-chain fatty acids (SCFA) and lactic acid concentrations. Deoxyribonucleic acid was extracted from colonic digesta and the microbial community was profiled by terminal restriction fragment length polymorphism analysis (T-RFLP) and qPCR. Blood urea nitrogen (BUN) and acute-phase proteins (Pig-MAP) were measured. Lactulose treatment (LAC) improved feed intake (P<0.05), average daily gain (P<0.01), feed:gain ratio (P<0.05) and reduced BUN (P<0.01). Both, LAC and LPN treatment, decreased the Enterobacteriaceae:Lactobacillus spp. ratio in the colonic luminal contents (P<0.05). Moreover LPN treatment promoted a decrease in the percentage of branched fatty acids (P<0.01) suggesting a reduction in proteolytic microbial activity. Microbial profiling of colonic luminal contents by T-RFLP revealed changes in some microbial species. Terminal restriction fragments (TRFs) compatible with Bifidobacterium thermoacidophilum were more frequently detected in experimental diets compared to CTR (P<0.05). Pigs receiving SYN diet demonstrated the combined positive effects of individual LAC and LPN treatment although we were not able to show a specific increase in the probiotic strain with the inclusion of lactulose. Collectively, these data suggest the combination of lactulose and L. plantarum acts as a complementary synbiotic, but not as a synergistic combination.

Modeling plant transpiration under limited soil water: comparison of different plant and soil hydraulic parameterizations and preliminary implications for their use in land surface models

Accurate estimates of how soil water stress affects plant transpiration are crucial for reliable land surface model (LSM) predictions. Current LSMs generally use a water stress factor, β, dependent on soil moisture content, θ, that ranges linearly between β = 1 for unstressed vegetation and β = 0 when wilting point is reached. This paper explores the feasibility of replacing the current approach with equations that use soil water potential as their independent variable, or with a set of equations that involve hydraulic and chemical signaling, thereby ensuring feedbacks between the entire soil–root–xylem–leaf system. A comparison with the original linear θ-based water stress parameterization, and with its improved curvi-linear version, was conducted. Assessment of model suitability was focused on their ability to simulate the correct (as derived from experimental data) curve shape of relative transpiration versus fraction of transpirable soil water. We used model sensitivity analyses under progressive soil drying conditions, employing two commonly used approaches to calculate water retention and hydraulic conductivity curves. Furthermore, for each of these hydraulic parameterizations we used two different parameter sets, for 3 soil texture types; a total of 12 soil hydraulic permutations. Results showed that the resulting transpiration reduction functions (TRFs) varied considerably among the models. The fact that soil hydraulic conductivity played a major role in the model that involved hydraulic and chemical signaling led to unrealistic values of β, and hence TRF, for many soil hydraulic parameter sets. However, this model is much better equipped to simulate the behavior of different plant species. Based on these findings, we only recommend implementation of this approach into LSMs if great care with choice of soil hydraulic parameters is taken

O princípio da precaução e a regulação sanitária no Brasil: defesa do interesse público ou mera arbitrariedade?

O presente trabalho tem como objetivo a análise da aplicação do princípio da precaução no setor de vigilância sanitária. Primeiramente, expõem-se diversas definições dadas ao instituto, de modo a compreendê-lo com mais clareza e precisão. Posteriormente, questionam-se eventuais excessos ou arbitrariedades na invocação desse princípio. Considera-se, em seguida, a competência normativa das agências reguladoras e a possibilidade da revisão de seus atos por parte do Poder Judiciário. Por fim, de modo a compreender como o princípio da precaução tem sido tratado pelo Poder Judiciário na seara da vigilância sanitária, realiza-se uma análise jurisprudencial nos Tribunais Regionais Federais (TRFs) do país, no Supremo Tribunal Federal (STF) e no Superior Tribunal de Justiça (STJ). Após uma minuciosa análise sustenta-se que o referido instituto não possui “densidade jurídica” para sua aplicação, visto que ainda se encontra extremamente indefinido e ilimitado.