Positive selection results in frequent reversible amino acid replacements in the G protein gene of human respiratory syncytial virus

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a flipflop phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites.

Structural insights into selectivity and cofactor binding in snake venom l-amino acid oxidases

l-Amino acid oxidases (LAAOs) are flavoenzymes that catalytically deaminate l-amino acids to corresponding α-keto acids with the concomitant production of ammonia (NH 3) and hydrogen peroxide (H 2O 2). Particularly, snake venom LAAOs have been attracted much attention due to their diverse clinical and biological effects, interfering on human coagulation factors and being cytotoxic against some pathogenic bacteria and Leishmania ssp. In this work, a new LAAO from Bothrops jararacussu venom (BjsuLAAO) was purified, functionally characterized and its structure determined by X-ray crystallography at 3.1å resolution. BjsuLAAO showed high catalytic specificity for aromatic and aliphatic large side-chain amino acids. Comparative structural analysis with prokaryotic LAAOs, which exhibit low specificity, indicates the importance of the active-site volume in modulating enzyme selectivity. Surprisingly, the flavin adenine dinucleotide (FAD) cofactor was found in a different orientation canonically described for both prokaryotic and eukaryotic LAAOs. In this new conformational state, the adenosyl group is flipped towards the 62-71 loop, being stabilized by several hydrogen-bond interactions, which is equally stable to the classical binding mode. © 2012 Elsevier Inc.

Development of sustainable precision farming systems for swine: Estimating realtime individual amino acid requirements in growing-finishing pigs

The objective of this study was to develop and evaluate a mathematical model used to estimate the daily amino acid requirements of individual growing-finishing pigs. The model includes empirical and mechanistic model components. The empirical component estimates daily feed intake (DFI), BW, and daily gain (DG) based on individual pig information collected in real time. Based on DFI, BW, and DG estimates, the mechanistic component uses classic factorial equations to estimate the optimal concentration of amino acids that must be offered to each pig to meet its requirements. The model was evaluated with data from a study that investigated the effect of feeding pigs with a 3-phase or daily multiphase system. The DFI and BW values measured in this study were compared with those estimated by the empirical component of the model. The coherence of the values estimated by the mechanistic component was evaluated by analyzing if it followed a normal pattern of requirements. Lastly, the proposed model was evaluated by comparing its estimates with those generated by the existing growth model (InraPorc). The precision of the proposed model and InraPorc in estimating DFI and BW was evaluated through the mean absolute error. The empirical component results indicated that the DFI and BW trajectories of individual pigs fed ad libitum could be predicted 1 d (DFI) or 7 d (BW) ahead with the average mean absolute error of 12.45 and 1.85%, respectively. The average mean absolute error obtained with the InraPorc for the average individual of the population was 14.72% for DFI and 5.38% for BW. Major differences were observed when estimates from InraPorc were compared with individual observations. The proposed model, however, was effective in tracking the change in DFI and BW for each individual pig. The mechanistic model component estimated the optimal standardized ileal digestible Lys to NE ratio with reasonable between animal (average CV = 7%) and overtime (average CV = 14%) variation. Thus, the amino acid requirements estimated by model are animal- and time-dependent and follow, in real time, the individual DFI and BW growth patterns. The proposed model can follow the average feed intake and feed weight trajectory of each individual pig in real time with good accuracy. Based on these trajectories and using classical factorial equations, the model makes it possible to estimate dynamically the AA requirements of each animal, taking into account the intake and growth changes of the animal. © 2012 American Society of Animal Science. All rights reserved.

Advances in drug design based on the amino acid approach: Taurine analogues for the treatment of CNS diseases

Amino acids are well known to be an important class of compounds for the maintenance of body homeostasis and their deficit, even for the polar neuroactive aminoacids, can be controlled by supplementation. However, for the amino acid taurine (2-aminoethanesulfonic acid) this is not true. Due its special physicochemical properties, taurine is unable to cross the blood-brain barrier. In addition of injured taurine transport systems under pathological conditions, CNS supplementation of taurine is almost null. Taurine is a potent antioxidant and anti-inflammatory semi-essential amino acid extensively involved in neurological activities, acting as neurotrophic factor, binding to GABA A/glycine receptors and blocking the excitotoxicity glutamate-induced pathway leading to be a neuroprotective effect and neuromodulation. Taurine deficits have been implicated in several CNS diseases, such as Alzheimer's, Parkinson's, epilepsy and in the damage of retinal neurons. This review describes the CNS physiological functions of taurine and the development of new derivatives based on its structure useful in CNS disease treatment.&; 2012 by the authors; licensee MDPI, Basel, Switzerland.

A procedure to evaluate the efficiency of utilization of dietary amino acid for poultry

The aim of this study was to develop a procedure based on Gompertz function to determine the efficiency of utilization of amino acid. The procedure was applied to determine the efficiency of utilization of dietary lysine, methionine+cystine and threonine by growing pullets and based on the efficiencies were estimated the requirements for the growth phase of birds. The Gompertz function was fitted to the data of feed intake, body weight, feather-free body protein weight and feather protein weight of four strains of laying hens in the growth phase. The rates of consumption and daily protein deposition (PD) were calculated. The amino acid deposition was obtained by multiplying the PD by the amino acid concentration in feather protein and feather-free body protein. The results showed that the efficiency of utilization of amino acid decreased with maturity and, conversely, there was a proportional increase of the requirement per kg of weight gain. The procedure based on the Gompertz function to determine the efficiency of utilization of amino acid proved to be suitable to evaluate the efficiency of utilization of amino acid and can be a useful tool to diagnose the effectiveness of the nutritional management, aiding in decision-making on the nutritional management.

The use of stable isotopes to investigate the effects of supplemental lysine and methionine on protein turnover and amino acid utilization in pacu, Piaractus mesopotamicus, juveniles

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Crystallization and preliminary X-ray diffraction studies of an L-amino-acid oxidase from Lachesis muta venom

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

Cytoxicity and Apoptotic Mechanism of Ruthenium(II) Amino Acid Complexes in Sarcoma-180 Tumor Cells

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

Apparent protein and energy digestibility and amino acid availability of corn and co-products in extruded diets for nile tilapia, oreochromis niloticus

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Learning HMMs for nucleotide sequences from amino acid alignments

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

Site and extent of amino acid digestion in dairy cattle fed with corn and its byproducts

The study was conducted to evaluated the site and extent of dry matter (DM), crude protein (CP), methionine (Met), lysine (Lys), and threonine (Thr) digestion of corn and byproducts obtained from corn germ mixed with different amounts of extruded or non-extruded ether extract (EE) in dairy cattle. Treatments consisted in eight types of feed and two processing in a 4 x 2 factorial design. There were four feeds: corn grain cracked (Corn), corn germ meal with 1% EE (CG1), corn germ meal with 7% EE (CG7), and corn germ meal with 10% EE (CG10). The feeds were processed in one of two ways: extruded (Ex) and not extruded. In situ techniques were used to determine DM, CP, Met, Lys, and Thr partial and total tract digestion. A basic diet was compounded of corn germ meal, soybean meal and coastcross hay in a 70: 30 roughage to concentrate ratio. There was no interaction (P>0.05) between feeds and processing method. Extrusion improved (P<0.05) total tract digestibility of corn DM but not CP. Intestinal digestibility was similar (P>0.05) for corn and corn germ meal mixed with 7 and 10% EE, regardless of EE processing method. The CP total tract digestibility of corn germ meal with 1% non-extruded EE was 16.62% higher (P<0.05) than that of the extruded form. The best total CP digestibility was obtained for corn germ meal with 7% EE, independently of the processing method. The effects of EE processing method on partial and total digestibility differed between amino acid. Corn and corn byproduct extrusion may improve dry matter digestibility, but do not necessarily influence crude protein digestion. Ruminal and intestinal digestibility of Met, Lys, and Thr depends on both feed type and processing method. Therefore, amino acid availability should be considered individually.

Modeling amino acid requirements of poultry

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

Mycorrhization alters foliar soluble amino acid composition and influences tolerance to Pb in Calopogonium mucunoides

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Identities among actin-encoding cDNAs of the Nile tilapia (Oreochromis niloticus) and other eukaryote species revealed by nucleotide and amino acid sequence analyses

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

l-amino acid oxidase from Bothrops marajoensis causes nephrotoxicity in isolated perfused kidney and cytotoxicity in MDCK renal cells

Renal alterations caused by Bothrops venom and its compounds are studied to understand these effects and provide the best treatment. Previously, we studied the renal effect of the whole venom of Bothrops marajoensis and its phospholipase A2 (PLA2), but these effects could not to be attributed to PLA2. To continue the study, we report in this short communication the effects of l-amino acid oxidase from B. marajoensis venom (LAAOBm) on renal function parameter alterations observed in the same model of isolated perfused kidney, as well as the cytotoxic effect on renal cells. LAAOBm caused a decrease in PP, RVR, UF, GFR, %TNa(+) and %TCl(-), very similar to the effects of whole venom using the same model. We also demonstrated its cytotoxicity in MDCK cells with IC50 of 2.5 μg/mL and late apoptotic involvement demonstrated by flow cytometry assays. In conclusion, we suggested that LAAOBm is a nephrotoxic compound of B. marajoensis venom.