Cooperative RNA Polymerase Molecules Behavior on a Stochastic Sequence-Dependent Model for Transcription Elongation

The transcription process is crucial to life and the enzyme RNA polymerase (RNAP) is the major component of the transcription machinery. The development of single-molecule techniques, such as magnetic and optical tweezers, atomic-force microscopy and single-molecule fluorescence, increased our understanding of the transcription process and complements traditional biochemical studies. Based on these studies, theoretical models have been proposed to explain and predict the kinetics of the RNAP during the polymerization, highlighting the results achieved by models based on the thermodynamic stability of the transcription elongation complex. However, experiments showed that if more than one RNAP initiates from the same promoter, the transcription behavior slightly changes and new phenomenona are observed. We proposed and implemented a theoretical model that considers collisions between RNAPs and predicts their cooperative behavior during multi-round transcription generalizing the Bai et al. stochastic sequence-dependent model. In our approach, collisions between elongating enzymes modify their transcription rate values. We performed the simulations in Mathematica® and compared the results of the single and the multiple-molecule transcription with experimental results and other theoretical models. Our multi-round approach can recover several expected behaviors, showing that the transcription process for the studied sequences can be accelerated up to 48% when collisions are allowed: the dwell times on pause sites are reduced as well as the distance that the RNAPs backtracked from backtracking sites. © 2013 Costa et al.

Spatial distribution of Yellow Sigatoka Leaf Spot correlated with soil fertility and plant nutrition

This study analyzed the spatial distribution of Yellow Sigatoka Leaf Spot relative to soil fertility and plant nutritional status using geostatistics. The experimental area comprised 1.2 ha, where 27 points were georeferenced and spaced on a regular grid 18 × 18 m. The severity of Yellow Sigatoka, soil fertility and plant nutritional status were evaluated at each point. The spherical model was adjusted for all variables using restricted maximum likelihood. Kriging maps showed the highest infection rate of Sigatoka occurred in high areas of the field which had the highest concentration of sand, while the lowest disease was found in lower areas with lower silt, organic matter, total exchangeable bases, effective cation exchange capacity, base saturation, Ca and Mg in soil, and foliar sulfur (S). These results may help farmers manage Yellow Sigatoka disease more effectively, with balanced fertilization and reduced fungicide application. This practice minimizes the environmental impact and cost of production while contributing to production sustainability.

Características morfogênicas, estruturais e composição química de cultivares de Brachiaria submetidas a níveis de oferta de forragem sob pastejo rotativo

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Leaf-litter decomposition of the mangrove species Avicennia schaueriana, Laguncularia racemosa and Rhizophora mangle

This study evaluated the decomposition process of leaf litter from the main Brazilian mangrove species Avicennia schaueriana, Laguncularia racemosa and Rhizophora mangle. Senescent leaves were collected, dried and placed in nylon bags with different mesh sizes (fine: 2x2mm and coarse: 8x8mm). The bags were distributed over the sediment, and replicates of each species and mesh size were collected periodically over 4months. In the laboratory, the dry weight of the samples was measured, and the decomposition coefficient (k) for each species and mesh size was obtained over time. All species showed a rapid decomposition rate at the beginning of the experiment, followed by a slower but steady rate of decomposition over time. The rate of leaf litter decomposition was highest in A. schaueriana, intermediate in L. racemosa and lowest in R. mangle. The difference was mainly linked to the activity and abundance of detritivores, together with the different litter quality of the species, which determined their palatability and probably influenced the decomposition process.

Effects of leaf extracts of Myrcia guianensis (Aubl.) DC. on growth and gene expression during root development of Sorghum bicolor (L.) Moench

The allelopathic potential of leaf extracts from the medicinal plant Myrcia guianensis (Aubl.) DC. was studied in Petri dish bioassays on sorghum and determined the seed germination, germination rate index (GRI), root growth, secondary root number, the genes involved in root development (SHR, PHB, PHV and REV) and microRNA 166 that regulates these genes. The hydroalcoholic extract was more inhibitory than methanol extract (moderate inhibition) and aqueous extract at 25 and 100% concentration were least inhibitory. Application of higher dose of hydroalcoholic M. guianenesis leaf extracts on sorghum seeds, inhibited the root development and changed the expression of SHR and PHB genes and microRNA 166. This suggested that the expression of these genes could be indicator of allelopathic potential for inhibition of root development in sorghum.

Leaf gas exchange and yield of three upland rice cultivars

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Seed quality, chlorophyll content index and leaf nitrogen levels in maize inoculated with Azospirillum brasilense

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Maize leaf phytotoxicity and grain yield are affected by nitrogen source and application method

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Cotton leaf gas exchange responses to irradiance and leaf aging

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Wood and leaf anatomy of Copaifera langsdorffii dwarf trees

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Chloroacetamid Spray Drift and Leaf Tatters in Hackberry

During the last decade, leaf tatters has been reported in white oak and hackberry across several Midwestern states. Herbicide spray drift studies have shown that chloroacetamides can induce leaf tatters. The objectives of this research were to: 1) identify vulnerable bud developmental stages in hackberry and 2) determine if different commercial chloroacetamides affect severity of leaf tatters. In 2008, a preliminary spray drift experiment was conducted on mature trees from a former hackberry provenance test stand. Acetochlor (Harness), S-metolachlor (Dual II Magnum), and dimethenamid (Outlook) were applied at concentrations approximating 27%, 54%, 81%, or 108% of the recommended field rate. Three developmental stages before bud burst were present on the selected trees. Leaf tatters did not develop on the selected hackberry trees. However, symptoms were observed on neighboring, non-target hackberry trees, which had been in the leaf unfolding and expanding stages at the time of spraying. In 2009, three year old hackberry seedlings were treated with 1%, 10%, and 100% of the recommended field rate of acetochlor (Harness), S-metolachlor (Dual II Magnum), and dimethenamid (Outlook). Folded buds and two unfolding leaf developmental stages were present on seedlings. Another spray study was conducted on 32 mature hackberry trees from the provenance stand. A solution of 5608 mg a.i./L dimethenamid (Outlook) was applied to trees in the unfolding and/or expanding leaf stage. Treated trees represented four provenances. Image analysis was used to calculate seedling and mature tree leaf areas and estimate the seedling percentage of leaf tissue loss. Foliar damage was not significantly different between seedlings treated with water, 1%, or 10% of the field rate. Foliar damage was significantly different between seedlings treated with 1% or 100% of the field rate, and between seedlings treated with 10% or 100% of the field rate. Foliar damage in seedlings was not significantly different between the developmental stages. Additionally, symptoms of leaf tatters were observed on the treated mature hackberry. Future studies should focus on chloroacetamide concentrations above 10% of the recommended field rate.

A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide election

The enzymatically catalyzed template-directed extension of ssDNA/primer complex is an impor-tant reaction of extraordinary complexity. The DNA polymerase does not merely facilitate the insertion of dNMP, but it also performs rapid screening of substrates to ensure a high degree of fidelity. Several kinetic studies have determined rate constants and equilibrium constants for the elementary steps that make up the overall pathway. The information is used to develop a macro-scopic kinetic model, using an approach described by Ninio [Ninio J., 1987. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabili-ties. Proc. Natl. Acad. Sci. U.S.A. 84, 663–667]. The principle idea of the Ninio approach is to track a single template/primer complex over time and to identify the expected behavior. The average time to insert a single nucleotide is a weighted sum of several terms, in-cluding the actual time to insert a nucleotide plus delays due to polymerase detachment from ei-ther the ternary (template-primer-polymerase) or quaternary (+nucleotide) complexes and time delays associated with the identification and ultimate rejection of an incorrect nucleotide from the binding site. The passage times of all events and their probability of occurrence are ex-pressed in terms of the rate constants of the elementary steps of the reaction pathway. The model accounts for variations in the average insertion time with different nucleotides as well as the in-fluence of G+C content of the sequence in the vicinity of the insertion site. Furthermore the model provides estimates of error frequencies. If nucleotide extension is recognized as a compe-tition between successful insertions and time delaying events, it can be described as a binomial process with a probability distribution. The distribution gives the probability to extend a primer/template complex with a certain number of base pairs and in general it maps annealed complexes into extension products.

Characterization and properties of blended cement matrices containing activated bamboo leaf wastes

The worldwide production of bamboo generates large volumes of leaf wastes, which are deposited in landfills or burned in an uncontrolled manner, with negative effects in the environment. The ash obtained by calcining of the bamboo leaf waste, shows good qualities as supplementary cementing material for the production of blended cements. The current paper shows a detailed scientific study of a Brazilian bamboo leaf ash (BLA) calcined at 600 degrees C in small scale condition, by using different techniques (XRF, XRD, SEM/EDX, FT-IR, TG/DTG) and technical study in order. to analyse the behaviour of this ash in blended cements elaborated with 10% and 20% by mass of BLA. The results stated that this ash shows a very high pozzolanic activity, with a reaction rate constant K of the order of 10(-1)/h and type I CSH gel was the main hydrated phase obtained from pozzolanic reaction. The BLA blended cements (10% and 20%) complied with the physical and mechanical requirements of the existing European standards. (c) 2012 Elsevier Ltd. All rights reserved.

The importance of mesofauna and decomposition environment on leaf decomposition in three forests in southeastern Brazil

We examined the effects of soil mesofauna and the litter decomposition environment (above and belowground) on leaf decomposition rates in three forest types in southeastern Brazil. To estimate decomposition experimentally, we used litterbags with a standard substrate in a full-factorial experimental design. We used model selection to compare three decomposition models and also to infer the importance of forest type, decomposition environment, mesofauna, and their interactions on the decomposition process. Rather than the frequently used simple and double-exponential models, the best model to describe our dataset was the exponential deceleration model, which assumed a single organic compartment with an exponential decrease of the decomposition rate. Decomposition was higher in the wet than in the seasonal forest, and the differences between forest types were stronger aboveground. Regarding litter decomposition environment, decomposition was predominantly higher below than aboveground, but the magnitude of this effect was higher in the seasonal than in wet forests. Mesofauna exclusion treatments had slower decomposition, except aboveground into the Semi-deciduous Forest, where the mesofauna presence did not affect decomposition. Furthermore, the effect of mesofauna was stronger in the wet forests and belowground. Overall, our results suggest that, in a regional scale, both decomposers activity and the positive effect of soil mesofauna in decomposition are constrained by abiotic factors, such as moisture conditions.

Slow Strain Rate Testing and Stress Corrosion Cracking of Ultra-Fine Grained and Conventional Al-Mg Alloy

Stress corrosion cracking susceptibility was investigated for an ultra-fine grained (UFG) AI-7.5Mg alloy and a conventional 5083 H111 alloy in natural seawater using slow strain rate testing (SSRT) at very slow strain rates between 1E(-5) s(-1), 1E(-6) s(-1) and 1E(-7) s(-1). The UFG Al-7.5Mg alloy was produced by cryomilling, while the 5083 H111 alloy is considered as a wrought manufactured product. The response of tensile properties to strain rate was analyzed and compared. Negative strain rate sensitivity was observed for both materials in terms of the elongation to failure. However, the UFG alloy displayed strain rate sensitivity in relation to strength while the conventional alloy was relatively strain rate insensitive. The mechanical behavior of the conventional 5083 alloy was attributed to dynamic strain aging (DSA) and delayed pit propagation while the performance of the UFG alloy was related to a diffusion-mediated stress relaxation mechanism that successfully delayed crack initiation events, counteracted by exfoliation and pitting which enhanced crack initiation. (C) 2014 Elsevier B.V. All rights reserved.