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.

Níveis plasmáticos de taurina e de seus precursores em pacientes com câncer de esôfago

RACIONAL: O câncer de esôfago tem impacto relevante no metabolismo protéico do hospedeiro, mas pouco se conhece sobre as implicações no metabolismo protéico sulfurado. Deste, destaca-se a taurina, composto participante de várias funções fisiológicas importantes como a manutenção do sistema de defesa celular e possível sobrevida do paciente. OBJETIVO: Estudar as variações plasmáticas da taurina e de seus precursores em pacientes com câncer de esôfago. MÉTODO: em estudo transversal foram triados 16 pacientes (43-73 anos) com câncer de esôfago e 20 voluntários (27-65 anos) controles sadios que preencheram os critérios clínicos e éticos da pesquisa. Para caracterização do estado geral de saúde efetuou-se avaliação antropométrica, hematimétrica (Hb, Ht, glóbulos brancos, linfócitos) e bioquímica (albumina, glicose, lipídios, aminotransferases). Adicionalmente, foram realizadas, no plasma, análises cromatográficas de taurina e seus precursores cisteína e homocisteína. Foi registrado o tempo de sobrevivência dos pacientes, a partir do diagnóstico histopatológico. RESULTADOS: Os pacientes com câncer de esôfago foram predominantemente do sexo masculino, raça branca, classe socioeconômica baixa, tipo carcinoma espinocelular de localização no terço superior, em estádio IV, sobrevida de 7,8 ± 5,5 anos, referindo perda de peso em 16,4% e apresentando hipoalbuminemia em 50%, com massa muscular e adiposa semelhante ao controle. Os pacientes apresentaram valores estatisticamente menores do que os controles para Hb, Ht, colesterol total, HDL-colesterol e cisteína e maiores de AST, ALT, taurina e homocisteína. Dentre os pacientes houve correlação positiva da taurina tanto com a contagem total de linfócitos, como com a sobrevida dos pacientes. CONCLUSÃO: Os níveis reduzidos de cisteína e elevados de homocisteína, taurina e as associações positivas da taurina com os indicadores da imunocompetência celular e da mortalidade sugerem participação efetiva da taurina na sobrevida dos pacientes e, portanto, os cuidados nutricionais específicos com a sua via geradora (cisteína, metionina e vitaminas do complexo B).

Efeitos da correção da acidose metabólica com bicarbonato de sódio sobre o catabolismo protéico na insuficiência renal crônica

A desnutrição protéico-energética constitui problema comum aos pacientes com insuficiência renal crônica, influenciando diretamente na sua morbi-mortalidade. A acidose metabólica tem papel no catabolismo protéico, ativando a via proteolítica proteasoma-ubiquitina, dependente de adenosina trifosfato, e conjuntamente com glicocorticóides induz uma maior atividade na desidrogenase que degrada os aminoácidos de cadeia ramificada. Esta revisão teve como objetivo descrever o mecanismo pelo qual a acidose metabólica nos pacientes com insuficiência renal crônica promove o catabolismo protéico, favorecendo assim a desnutrição, bem como avaliar os efeitos do uso de bicarbonato de sódio na correção da acidose e conseqüentemente redução do catabolismo protéico. Pesquisas mostram melhora da acidose pelo uso de bicarbonato de sódio e conseqüente redução do catabolismo protéico na insuficiência renal crônica, podendo ser esta uma conduta promissora na atenuação da desnutrição nestes pacientes.

The frequency of 844ins68 mutation in the cystathionine β-synthase gene is not increased in patients with venous thrombosis

Background and Objectives. A frequent mutation in the cystathionine β- synthase (CBS) gene (844ins68, a 68-bp insertion in the coding region of exon 8) was recently discovered. In the present study we investigated this mutation as a candidate risk factor for venous thrombosis. Design and Methods. The prevalence of the 844ins68 CBS mutation was determined in 101 patients with objectively diagnosed deep venous thrombosis and in 101 healthy controls matched for age, sex and race. PCR amplification of a DNA fragment containing exon 8 of the CBS gene was employed to determine the genotypes. Additionally, Bsrl restriction enzyme digestion of the PCR products was performed in all samples from carriers of the insertion, to test for concurrent presence of a second mutation (T833C) in the CBS gene. Results. The insertion was found in 21 out of 101 patients (20.8%; allele frequency 0.109) and in 20 out of 101 controls (19.8%; allele frequency 0.114), yielding a relative risk for venous thrombosis related to the 844ins68 CBS mutation close to 1.0. In addition, the T833C CBS mutation was detected in all alleles carrying the 844ins68 CBS insertion, confirming the co- inheritance of the two mutations. Interpretation and Conclusions. Our findings do not support the hypothesis that the 844ins68 mutation in the CBS gene is a genetic risk factor for venous thrombosis.

Expressão gênica diferencial em palmitos de cana-de-açúcar submetida a diferentes períodos de estresse hídrico

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Plasma levels of transthyretin and retinol-binding protein in child-a cirrhotic patients in relation to protein-calorie status and plasma amino acids, zinc, vitamin a and plasma thyroid hormones

Transthyretin and retinal-binding protein are sensitive markers of acute protein-calorie malnutrition both for early diagnosis and dietary evaluation. A preliminary study showed that retinal-binding protein is the most sensitive marker of protein-calorie malnutrition in cirrhotic patients, even those with the mild form of the disease (Child A). However, in addition to being affected by protein-calorie malnutrition, the levels of these short half-life-liver-produced proteins are also influenced by other factors of a nutritional (zinc, tryptophan, vitamin A, etc) and non-nutritional (sex, aging, hormones, renal and liver functions and inflammatory activity) nature. These interactions were investigated in 11 adult male patients (49.9 ± 9.2 years of age) with alcoholic cirrhosis (Child-Pugh grade A) and with normal renal function. Both transthyretin and retinol binding protein were reduced below normal levels in 55% of the patients, in close agreement with their plasma levels of retinal. In 67% of the patients (4/6), the reduced levels of transthyretin and retinal-binding protein were caused by altered liver function and in 50% (3/6) they were caused by protein-calorie malnutrition. Thus, the present data, taken as a whole, indicate that reduced transthyretin and retinal-binding protein levels in mild cirrhosis of the liver are mainly due to liver failure and/or vitamin A status rather than representing an isolated protein-calorie malnutrition indicator.

Nitrogen metabolism in coffee plants in response to nitrogen supply by fertigation

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Metabolomics method to comprehensively analyze amino acids in different domains

Amino acids play essential roles in both metabolism and the proteome. Many studies have profiled free amino acids (FAAs) or proteins; however, few have connected the measurement of FAA with individual amino acids in the proteome. In this study, we developed a metabolomics method to comprehensively analyze amino acids in different domains, using two examples of different sample types and disease models. We first examined the responses of FAAs and insoluble-proteome amino acids (IPAAs) to the Myc oncogene in Tet21N human neuroblastoma cells. The metabolic and proteomic amino acid profiles were quite different, even under the same Myc condition, and their combination provided a better understanding of the biological status. In addition, amino acids were measured in 3 domains (FAAs, free and soluble-proteome amino acids (FSPAAs), and IPAAs) to study changes in serum amino acid profiles related to colon cancer. A penalized logistic regression model based on the amino acids from the three domains had better sensitivity and specificity than that from each individual domain. To the best of our knowledge, this is the first study to perform a combined analysis of amino acids in different domains, and indicates the useful biological information available from a metabolomics analysis of the protein pellet. This study lays the foundation for further quantitative tracking of the distribution of amino acids in different domains, with opportunities for better diagnosis and mechanistic studies of various diseases.

Pool of Resistance Mechanisms to Glyphosate in Digitaria insularis

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Does low-protein diet improve broiler performance under heat stress conditions?

Nutrition for broilers under high temperatures is extremely important for brazilian broiler chicken industry because the amounts of consumed nutrients and environmental temperature have great effects on bird performance and carcass quality. Among diet nutrients, protein has the highest heat increment; thus, during many years, diets with low protein level were recommended in order to reduce heat production in broiler chickens under heat stress. However, reports have shown that low-protein diets have negative effects on broiler performance when environmental temperature is high, because during heat stress, low food intake associated to a low diet protein induce amino acid deficiencies. Other studies have shown that broilers fed low-protein diets increase their energy requirement for maintenance with higher heat production. Thus, with the growth of broiler industry in tropical areas more challenges need to be faced by the farmers. So, both the ambient and nutritional conditions ought to be well managed to avoid negative effects on poultry production once they can affect the metabolism (body heat production under low temperature and body heat dissipation under high temperature) with consequence on poultry performance (meat and eggs).