Mutations That Hamper Dimerization of Foot-and-Mouth Disease Virus 3A Protein Are Detrimental for Infectivity

Foot-and-mouth disease virus (FMDV) nonstructural protein 3A plays important roles in virus replication, virulence, and host range. In other picornaviruses, homodimerization of 3A has been shown to be relevant for its biological activity. In this work, FMDV 3A homodimerization was evidenced by an in situ protein fluorescent ligation assay. A molecular model of the FMDV 3A protein, derived from the nuclear magnetic resonance (NMR) structure of the poliovirus 3A protein, predicted a hydrophobic interface spanning residues 25 to 44 as the main determinant for 3A dimerization. Replacements L38E and L41E, involving charge acquisition at residues predicted to contribute to the hydrophobic interface, reduced the dimerization signal in the protein ligation assay and prevented the detection of dimer/multimer species in both transiently expressed 3A proteins and in synthetic peptides reproducing the N terminus of 3A. These replacements also led to production of infective viruses that replaced the acidic residues introduced (E) by nonpolar amino acids, indicating that preservation of the hydrophobic interface is essential for virus replication. Replacements that favored (Q44R) or impaired (Q44D) the polar interactions predicted between residues Q44 and D32 did not abolish dimer formation of transiently expressed 3A, indicating that these interactions are not critical for 3A dimerization. Nevertheless, while Q44R led to recovery of viruses that maintained the mutation, Q44D resulted in selection of infective viruses with substitution D44E with acidic charge but with structural features similar to those of the parental virus, suggesting that Q44 is involved in functions other than 3A dimerization.     

The only exoribonuclease present in Haloferax volcanii has an unique response to temperature changes

Background

Little is known regarding mRNA degradation mechanisms in archaea. In some of these single-cell organisms the existence of a complex of exoribonucleases called the exosome has been demonstrated. However, in halophilic archaea the RNase R homologue is essential since it is the only enzyme described with exoribonucleolytic activity.

Methods

In this work we have characterized the mechanism of action of Haloferax volcanii RNase R and its implications for the RNA degradation process. We have determined the salt, pH and divalent ion preference, and set the best conditions for the activity assays. Furthermore, we have determined the activity of the protein at different temperatures using different substrates. The dissociation constants were also calculated by Surface Plasmon Resonance. Finally, we have built a model and compared it with the Escherichia coli counterparts.

Results

The results obtained showed that at 37 °C, in spite of being named RNase R, this protein behaves like an RNase II protein, halting when it reaches secondary structures, and releasing a 4 nt end-product. However, at 42 °C, the optimum temperature of growth, this protein is able to degrade secondary structures, acting like RNase R.

General significance

This discovery has a great impact for RNA degradation, since this is the first case reported where a single enzyme has two different exoribonucleolytic activities according to the temperature. Furthermore, the results obtained are very important to help to decipher the RNA degradation mechanisms in H. volcanii, since RNase R is the only exoribonuclease involved in this process.     

Simulium (Chirostilbia) brunnescens (Diptera: Simuliidae) - new species from the Brazilian cerrado, Manso Dam, state of Mato Grosso, Brazil

A new species of Simuliidae, Simulium (Chirostilbia) brunnescens, was discovered at Chapada dos Guimar?es, state of Mato Grosso, Brazil, and nearby municipalities (Paranatinga, Rosário do Oeste and Nobres). This species is described here based on the adults, pupae and larvae. This species is closely related to Simulium (C.) subpallidum Lutz, but could be differentiated in all stages: females, leg colour pattern and frontal dilatation size; males, gonostyle shape; pupae, number of gill filaments; larvae, body size and colour, postgenal cleft, ratio between antenna and stalk of labral fan.     

A Novel Vasoactive Proline-Rich Oligopeptide from the Skin Secretion of the Frog Brachycephalus ephippium

Proline-rich oligopeptides (PROs) are a large family which comprises the bradykinin-potentiating peptides (BPPs). They inhibit the activity of the angiotensin I-converting enzyme (ACE) and have a typical pyroglutamyl (Pyr)/proline-rich structure at the N- and C-terminus, respectively. Furthermore, PROs decrease blood pressure in animals. In the present study, the isolation and biological characterization of a novel vasoactive BPP isolated from the skin secretion of the frog Brachycephalus ephippium is described. This new PRO, termed BPP-Brachy, has the primary structure WPPPKVSP and the amidated form termed BPP-BrachyNH₂ inhibits efficiently ACE in rat serum. In silico molecular modeling and docking studies suggest that BPP-BrachyNH₂ is capable of forming a hydrogen bond network as well as multiple van der Waals interactions with the rat ACE, which blocks the access of the substrate to the C-domain active site. Moreover, in rat thoracic aorta BPP-BrachyNH₂ induces potent endothelium-dependent vasodilatation with similar magnitude as captopril. In DAF-FM DA-loaded aortic cross sections examined by confocal microscopy, BPP-BrachyNH₂ was found to increase the release of nitric oxide (NO). Moreover, BPP-BrachyNH₂ was devoid of toxicity in endothelial and smooth muscle cell cultures. In conclusion, the peptide BPP-BrachyNH₂ has a novel sequence being the first BPP isolated from the skin secretion of the Brachycephalidae family. This opens for exploring amphibians as a source of new biomolecules. The BPP-BrachyNH₂ is devoid of cytotoxicity and elicits endothelium-dependent vasodilatation mediated by NO. These findings open for the possibility of potential application of these peptides in the treatment of endothelial dysfunction and cardiovascular diseases.     

Morphological Analysis of Reticuloendothelial System in Capuchin Monkeys (Sapajus spp.) after Meso-2,3-Dimercaptosuccinic Acid (DMSA) Coated Magnetic Nanoparticles Administration

Magnetic nanoparticles can be used for numerous in vitro and in vivo applications. However, since uptake by the reticuloendothelial system represents an obstacle for the achievement of nanoparticle diagnostic and therapeutic goals, the aim of the present study was to evaluate the uptake of dimercaptosuccinic acid coated magnetic nanoparticles by reticuloendothelial system phagocytic cells present in lymph nodes, spleen, and liver tissue and how the presence of these particles could have an impact on the morphology of these organs in capuchin monkeys (Sapajus spp.). Animals were intravenously injected with dimercaptosuccinic acid coated magnetic nanoparticles and euthanized 12 hours and 90 days post-injection. Organs were processed by transmission electron microscopy and histological techniques. Samples of spleen and lymph nodes showed no morphological changes. Nevertheless, liver samples collected 90 days post-administration showed slight morphological alteration in space of Disse. Moreover, morphometrical analysis of hepatic mitochondria was performed, suggesting a clear positive correlation between mitochondrial area and dimercaptosuccinic acid coated magnetic nanoparticles administration time. The present results are directly relevant to current safety considerations in clinical diagnostic and therapeutic uses of magnetic nanoparticles.     

Prediction of the energy value of cattle diets based on the chemical composition of the feeds under tropical conditions

Determination of the energetic contribution of different chemical components of cattle diets based on the content of total digestible nutrients (TDN) has been suggested by several authors and was adopted by the NRC [National Research Council (NRC), 2001. Nutrient Requirements of Dairy Cattle, seventh ed. Academic Press, Washington]. The main objective of that proposal is to overcome the high costs and the extended time of traditional in vivo digestion assays. Although theoretically based, the summative system adopted by the NRC [National Research Council (NRC), 2001. Nutrient Requirements of Dairy Cattle, seventh ed. Academic Press, Washington] has been shown to be inaccurate in predicting the TDN content of individual feeds or diets under tropical conditions. Therefore, a new model, that also uses a summative approach, was developed but it was based on data obtained in the tropics. The new model consists of equations that predict the digestible fractions of ether extract (n = 108), crude protein (n = 93), non-fibrous carbohydrates (n = 84), and neutral detergent fibre (n = 164). Non-fibrous components were evaluated by the Lucas [Lucas, H.L., 1960. Relations Between Apparent Digestibility and the Composition of Feed and Feces. 1: A Quantitative Theory. North Caroline State College, Raleigh] test to obtain true digestibility coefficients, and by the factorial system to distinguish between truly digested and metabolic fractions. Fibre components were evaluated using an adaptation of the surface law to obtain the indigestible fraction and a meta-analysis approach to obtain digestibility coefficients of the potentially digestible fraction. The estimates obtained with the new model were validated and compared to those produced with the model adopted by the NRC [National Research Council (NRC), 2001. Nutrient Requirements of Dairy Cattle, seventh ed. Academic Press, Washington] for cattle managed under tropical conditions. Data from four trials, two with lactating cows (n = 63) and two with growing and finishing cattle (n = 44) were used. The estimates produced with the two models were compared based on the decomposition of the mean square prediction error. It can be concluded that the new model was more accurate in predicting TDN values than the NRC [National Research Council (NRC), 2001. Nutrient Requirements of Dairy Cattle, seventh ed. Academic Press, Washington] model under tropical conditions.     

Genomic models with genotype × environment interaction for predicting hybrid performance: an application in maize hybrids

Key message

A new genomic model that incorporates genotype?×?environment interaction gave increased prediction accuracy of untested hybrid response for traits such as percent starch content, percent dry matter content and silage yield of maize hybrids.

Abstract

The prediction of hybrid performance (HP) is very important in agricultural breeding programs. In plant breeding, multi-environment trials play an important role in the selection of important traits, such as stability across environments, grain yield and pest resistance. Environmental conditions modulate gene expression causing genotype?×?environment interaction (G?×?E), such that the estimated genetic correlations of the performance of individual lines across environments summarize the joint action of genes and environmental conditions. This article proposes a genomic statistical model that incorporates G?×?E for general and specific combining ability for predicting the performance of hybrids in environments. The proposed model can also be applied to any other hybrid species with distinct parental pools. In this study, we evaluated the predictive ability of two HP prediction models using a cross-validation approach applied in extensive maize hybrid data, comprising 2724 hybrids derived from 507 dent lines and 24 flint lines, which were evaluated for three traits in 58 environments over 12 years; analyses were performed for each year. On average, genomic models that include the interaction of general and specific combining ability with environments have greater predictive ability than genomic models without interaction with environments (ranging from 12 to 22%, depending on the trait). We concluded that including G?×?E in the prediction of untested maize hybrids increases the accuracy of genomic models.

     

Phototrophic growth of Rubrivivax gelatinosus in poultry slaughterhouse wastewater

Rubrivivax gelatinosus was grown in Pfennig's synthetic medium (PM) and in treated wastewater from poultry slaughterhouse (TW) to assess growth profiles for biomass production. Cultures inoculated at 1% (v/v) were grown under anaerobiosis at 30+/-2 degrees C and 1400+/-200 lux for 12 days. Regular absorbance curves for R. gelatinosus were found both on PM and TW. On PM, the highest dry weight of biomass, 0.39 gL(-1), was achieved in the 216-h culture and the highest specific growth rate of 0.2960 h(-1) occurred in the 24-h culture. On TW, the highest biomass of 0.57 gL(-1) was also obtained in the 216-h culture and the highest specific growth rate, 0.1970 h(-1), was achieved in the 48-h culture. For productivity and chemical oxygen demand investigations, the cultivation was accomplished in the TW under anaerobiosis at 32+/-2 degrees C and 4000+/-500 lux, for 10 days. Productivity was 0.085 g biomass (d.w.) L(-1) day(-1), with a COD decrease of 91%.     

Escherichia coli FtsZ polymers contain mostly GTP and have a high nucleotide turnover

The cell division protein FtsZ is a GTPase structurally related to tubulin and, like tubulin, it assembles in vitro into filaments, sheets and other structures. To study the roles that GTP binding and hydrolysis play in the dynamics of FtsZ polymerization, the nucleotide contents of FtsZ were measured under different polymerizing conditions using a nitrocellulose filter-binding assay, whereas polymerization of the protein was followed in parallel by light scattering. Unpolymerized FtsZ bound 1 mol of GTP mol(-1) protein monomer. At pH 7.5 and in the presence of Mg(2+) and K(+), there was a strong GTPase activity; most of the bound nucleotide was GTP during the first few minutes but, later, the amount of GTP decreased in parallel with depolymerization, whereas the total nucleotide contents remained invariant. These results show that the long FtsZ polymers formed in solution contain mostly GTP. Incorporation of nucleotides into the protein was very fast either when the label was introduced at the onset of the reaction or subsequently during polymerization. Molecular modelling of an FtsZ dimer showed the presence of a cleft between the two subunits maintaining the nucleotide binding site open to the medium. These results show that the FtsZ polymers are highly dynamic structures that quickly exchange the bound nucleotide, and this exchange can occur in all the subunits.