LegumeGRN: A Gene Regulatory Network Prediction Server for Functional and Comparative Studies

Building accurate gene regulatory networks (GRNs) from high-throughput gene expression data is a long-standing challenge. However, with the emergence of new algorithms combined with the increase of transcriptomic data availability, it is now reachable. To help biologists to investigate gene regulatory relationships, we developed a web-based computational service to build, analyze and visualize GRNs that govern various biological processes. The web server is preloaded with all available Affymetrix GeneChip-based transcriptomic and annotation data from the three model legume species, i.e., Medicago truncatula, Lotus japonicus and Glycine max. Users can also upload their own transcriptomic and transcription factor datasets from any other species/organisms to analyze their in-house experiments. Users are able to select which experiments, genes and algorithms they will consider to perform their GRN analysis. To achieve this flexibility and improve prediction performance, we have implemented multiple mainstream GRN prediction algorithms including co-expression, Graphical Gaussian Models (GGMs), Context Likelihood of Relatedness (CLR), and parallelized versions of TIGRESS and GENIE3. Besides these existing algorithms, we also proposed a parallel Bayesian network learning algorithm, which can infer causal relationships (i.e., directionality of interaction) and scale up to several thousands of genes. Moreover, this web server also provides tools to allow integrative and comparative analysis between predicted GRNs obtained from different algorithms or experiments, as well as comparisons between legume species. The web site is available at http://legumegrn.noble.org

Commonalities and Differences in Carotid Body Dysfunction in Hypertension and Heart Failure

Carotid body pathophysiology is associated with many cardiovascular-respiratory-metabolic diseases. This pathophysiology reflects both hyper-sensitivity and hyper-tonicity. From both animal models and human patients, evidence indicates that amelioration of this pathophysiological signalling improves disease states such as a lowering of blood pressure in hypertension, a reduction of breathing disturbances with improved cardiac function in heart failure (HF) and a re-balancing of autonomic activity with lowered sympathetic discharge. Given this, we have reviewed the mechanisms of carotid body hyper-sensitivity and hyper-tonicity across disease models asking whether there is uniqueness related to specific disease states. Our analysis indicates some commonalities and some potential differences, although not all mechanisms have been fully explored across all disease models. One potential commonality is that of hypoperfusion of the carotid body across hypertension and HF, where the excessive sympathetic drive may reduce blood flow in both models and, in addition, lowered cardiac output in HF may potentiate the hypoperfusion state of the carotid body. Other mechanisms are explored that focus on neurotransmitter and signalling pathways intrinsic to the carotid body (e.g. ATP, carbon monoxide) as well as extrinsic molecules carried in the blood (e.g. leptin); there are also transcription factors found in the carotid body endothelium that modulate its activity (Krüppel-like factor 2). The evidence to date fully supports that a better understanding of the mechanisms of carotid body pathophysiology is a fruitful strategy for informing potential new treatment strategies for many cardiovascular, respiratory and metabolic diseases, and this is highly relevant clinically

LegumeGRN: a gene regulatory network prediction server for functional and comparative studies

Building accurate gene regulatory networks (GRNs) from high-throughput gene expression data is a long-standing challenge. However, with the emergence of new algorithms combined with the increase of transcriptomic data availability, it is now reachable. To help biologists to investigate gene regulatory relationships, we developed a web-based computational service to build, analyze and visualize GRNs that govern various biological processes. The web server is preloaded with all available Affymetrix GeneChip-based transcriptomic and annotation data from the three model legume species, i.e., Medicago truncatula, Lotus japonicus and Glycine max. Users can also upload their own transcriptomic and transcription factor datasets from any other species/organisms to analyze their in-house experiments. Users are able to select which experiments, genes and algorithms they will consider to perform their GRN analysis. To achieve this flexibility and improve prediction performance, we have implemented multiple mainstream GRN prediction algorithms including co-expression, Graphical Gaussian Models (GGMs), Context Likelihood of Relatedness (CLR), and parallelized versions of TIGRESS and GENIE3. Besides these existing algorithms, we also proposed a parallel Bayesian network learning algorithm, which can infer causal relationships (i.e., directionality of interaction) and scale up to several thousands of genes. Moreover, this web server also provides tools to allow integrative and comparative analysis between predicted GRNs obtained from different algorithms or experiments, as well as comparisons between legume species. The web site is available at http://legumegrn.noble.org.Oklahoma Center for The Advancement of Science and Technology: (OCAST Grant No. PSB11-031)

Influence of recirculation rate on the performance of a combined anaerobic-aerobic reactor applied to the removal of carbon and nitrogen from poultry slaughterhouse wastewater

The objective of this study was to evaluate a combined anaerobic-aerobic upflow fixed-bed reactor with liquid phase recirculation for the removal of nitrogen and organic matter from poultry slaughterhouse wastewater. The reactor performance was evaluated with a hydraulic retention time (HRT) of 11 h and three different recirculation rates (R=0.5; 1 and 2). The highest nitrogen removal efficiency value was obtained with an HRT of 11 h (6.8 h in the anaerobic zone and 4.2 h in the aerobic zone) and a recirculation rate of 2. In this condition, the total nitrogen removal efficiency was 69%,  with effluent concentrations of 6 mg NH4+ L-1 and 12 mg NO3- L-1. For all tested conditions, there was good chemical oxygen demand (COD) removal, with efficiency above 95%. The effect of dilution and the favoring of mass transfer caused by the increase in the recirculation rate positively influenced reactor performance.Key words: Anaerobic degradation, nitrification, denitrification, combined reactor

Beer industry in Brazil: Economic aspects, characteristics of the raw material and concerns

Barley is one of the most cultivated grains in the world with numbers rising every year due to market demand. In the past decade, Brazil has shown impressive numbers considering beer production. However, barley cultivation does not reach the necessary amount for the beer industry which raises the need to import barley or to use some alternatives, such as, adjuncts. The most common adjunct used is corn, which is considered a good source of carbohydrates, but also a very contaminated grain. Research and monitoring of all of the steps of the chain is being carried out to improve not only the malt quality but also the competitiveness in world market

Direct, stereodivergent, and catalytic Michael additions of thioimides to α,β-unsaturated aldehydes – Total synthesis of Tapentadol

Direct and stereodivergent Michael additions of N-acyl 1,3-thiazinane-2-thiones to α,β-unsaturated aldehydes catalyzed by chiral nickel(II) complexes are reported. The reactions proceed with a remarkable regio-, diastereo-, and enantioselectivity, so access to any of the four potential Michael stereoisomers is granted through the appropriate choice of the chiral ligand of the nickel(II) complex. Simple removal of the heterocyclic scaffold furnishes a wide array of either syn or anti enantiomerically pure derivatives, which can be exploited for the asymmetric synthesis of biologically active compounds, as demonstrated in a new approach to tapentadol. In turn, a mechanism, based on theoretical calculations, is proposed to account for the stereochemical outcome of these transformations

Morphophysiological and biochemical changes in Enterolobium contortisiliquum seedlings under abiotic stresses

Among the main problems that compromise the development of forest species are water and salt stresses, especially in the early stages of development, when seedlings are more sensitive. Thus, the objective of this study was to evaluate the morphophysiological and biochemical changes in Enterolobium contortisiliquum seedlings subjected to abiotic stresses. The experimental design was randomized complete blocks (RCB), composed of fi ve treatments, with four replicates, and the experimental plot consisted of twenty plants. From the 31st day after sowing, when the seedlings reached approximately 15 cm in height, they began to receive the treatments, which consisted of different levels of electrical conductivity of irrigation water (0.3; 2; 4; 6; 8 dS m-1) for salt stress and periods of water restriction (0; 4; 8; 12 and 16 days without irrigation) for water stress. The traits evaluated were: plant height, root length, stem diameter, number of leaves, leaf area, total dry matter, Dickson quality index, height/shoot dry matter ratio, total soluble sugars, starch, total amino acids and proline. An increase in the electrical conductivity of irrigation water and days without irrigation compromised the development of E. contortisiliquum seedlings, which was intensified from 2 dS m-1 and four days without irrigation for salt and water stresses, respectively. The mechanism of survival of E. contortisiliquum to abiotic stresses involves reduction in the growth and quality of seedlings, with activation of biochemical defense mechanisms of the species