The Development of a Universal In Silico Predictor of Protein-Protein Interactions

Protein-protein interactions (PPIs) are essential for understanding the function of biological systems and have been characterized using a vast array of experimental techniques. These techniques detect only a small proportion of all PPIs and are labor intensive and time consuming. Therefore, the development of computational methods capable of predicting PPIs accelerates the pace of discovery of new interactions. This paper reports a machine learning-based prediction model, the Universal In Silico Predictor of Protein-Protein Interactions (UNISPPI), which is a decision tree model that can reliably predict PPIs for all species (including proteins from parasite-host associations) using only 20 combinations of amino acids frequencies from interacting and non-interacting proteins as learning features. UNISPPI was able to correctly classify 79.4% and 72.6% of experimentally supported interactions and non-interacting protein pairs, respectively, from an independent test set. Moreover, UNISPPI suggests that the frequencies of the amino acids asparagine, cysteine and isoleucine are important features for distinguishing between interacting and non-interacting protein pairs. We envisage that UNISPPI can be a useful tool for prioritizing interactions for experimental validation. © 2013 Valente et al.

Antifungal activity of flavonoids from Heteropterys byrsonimifolia and a commercial source against Aspergillus ochraceus: In silico interactions of these compounds with a protein kinase

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Transposable elements in Coffea (Gentianales : Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants

Transposable elements are major components of plant genomes and they influence their evolution, acting as recombination hot spots, acquiring specific cell functions or becoming part of protein-coding regions. The latter is the subject of the present analysis. This study is a report on the annotation of transposable elements (TEs) in expressed sequences of Coffea arabica, Coffea canephora and Coffea racemosa, showing the occurrence of 383 ESTs and 142 unigenes with TE fragments in these three Coffea species. Based on selected unigenes, it was possible to suggest 26 putative proteins with TE-cassette insertions, demonstrating a likely contribution to protein variability. The genes for two of those proteins, the fertility restorer (FR) and the pyrophosphate-dependent phosphofructokinase (PPi-PFKs) genes, were selected for evaluating the impact of TE-cassettes on host gene evolution of other plant genomes (Arabidopsis thaliana, Oryza sativa and populus trichocarpa). This survey allowed identifying a FR gene in O. sativa harboring multiple insertions of LTR retrotransposons that originated new exons, which however does not necessarily mean a case of molecular domestication. A possible transduction event of a fragment of the PPi-PFK beta-subunit gene mediated by Helitron ATREPX1 in Arabidopsis thaliana was also highlighted.

Molecular modeling databases: A new way in the search of protein targets for drug development

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic, pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. © 2007 Bentham Science Publishers Ltd.

Prediction of Hevea progeny performance in the presence of genotype-environment interaction

Twenty two open-pollinated Hevea progenies from different parental clones of the Asian origin were tested at five sites in the Northwestern São Paulo State Brazil to investigate the progeny girth growth, rubber yield, bark thickness and plant height. Except for the rubber yield, the analysis of variance indicated highly significant (p<0.01) genotype x environment interaction and heterogeneity of regressions among the progenies. However, the regression stability analysis identified only a few interacting progenies which had regression coefficients significantly different from the expected value of one. The linear regressions of the progeny mean performance at each test on an environmental index (mean of all the progenies in each test) showed the general stability and adaptability of most selected Hevea progenies over the test environments. The few progenies which were responsive and high yielding on different test sites could be used to maximize the rubber cultivars productivity and to obtain the best use of the genetically improved stock under different environmental conditions.

In silico evaluation of the Eucalyptus transcriptome

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

Identification of continuous interaction sites in PLA(2)-based protein complexes by peptide arrays

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

EFFECTS OF PROTEIN-DEFICIENCY AND NATURAL INTESTINAL INFECTION WITH GIARDIA-LAMBLIA ON JEJUNAL INTRAEPITHELIAL LYMPHOCYTES IN RATS OF DIFFERENT AGES

1. The interaction between experimental protein deprivation and natural intestinal infection by Giardia lamblia was studied in terms of its effects on the intraepithelial lymphocyte (IEL) population and morphology of the jejunal mucosa of rats of different ages.2. Young, adult and old male Wistar rats received a protein-deficient diet (2% casein) or a control diet (20% casein) for 42 days. Mucosal height and the number of lymphocytes located among 500 consecutive epithelial cells (EC) along the villi or crossing the basement membrane were determined in PAS-stained jejunal fragments.3. The number of IEL increased progressively with animal age, from 14 to 25 per 100 epithelial cells, with significant differences between age ranges. However, the number of IEL did not differ between control and protein-deficient rats in any of the age groups. The proportion of lymphocytes crossing the basement membrane was approximately two-fold greater in young (2.8/100 EC) and adult (5.8/100 EC) protein-deficient animals than in their respective controls (1.6 and 2.8/100 EC). The intensity of parasite colonization was moderate, from 3 to 5/100 EC and did not differ between groups. The pattern of morphologic changes of jejunal mucosa in protozoal infection did not differ between control and protein-deficient animals in any of the three age groups.4. We conclude that intestinal infection with Giardia lamblia probably stimulated the local immune response, masking the reduction of the IEL population induced by protein deficiency. The increase in lymphocyte numbers with age may be related to prolonged antigenic stimulation promoted by infection.

Effects of protein supplementation frequency on physiological responses associated with reproduction in beef cows

The objective of this experiment was to determine if frequency of protein supplementation impacts physiological responses associated with reproduction in beef cows. Fourteen nonpregnant, nonlactating beef cows were ranked by age and BW and allocated to 3 groups. Groups were assigned to a 3 x 3 Latin square design, containing 3 periods of 21 d and the following treatments: 1) soybean meal supplementation daily (D), 2) soybean meal supplementation 3 times/week (3WK), and 3) soybean meal supplementation once/week (1WK). Within each period, cows were assigned to an estrus synchronization protocol: 100 mu g of GnRH + controlled internal drug release device (CIDR) containing 1.38 g of progesterone (P-4) on d 1, 25 mg of PGF(2 alpha) on d 8, and CIDR removal + 100 mu g of GnRH on d 11. Grass-seed straw was offered for ad libitum consumption. Soybean meal was individually supplemented at a daily rate of 1 kg/cow (as-fed basis). Moreover, 3WK was supplemented on d 0, 2, 4, 7, 9, 11, 14, 16, and 18 whereas 1WK was supplemented on d 4, 11, and 18. Blood samples were collected from 0 (before) to 72 h after supplementation on d 11 and 18 and analyzed for plasma urea-N (PUN). Samples collected from 0 to 12 h were also analyzed for plasma glucose, insulin, and P-4 (d 18 only). Uterine flushing fluid was collected concurrently with blood sampling at 28 h for pH evaluation. Liver biopsies were performed concurrently with blood sampling at 0, 4, and 28 h and analyzed for mRNA expression of carbamoyl phosphate synthetase I (CPS-I; h 28) and CYP2C19 and CYP3A4 (h 0 and 4 on d 18). Plasma urea-N concentrations were greater (P < 0.01) for 1WK vs. 3WK from 20 to 72 h and greater (P < 0.01) for 1WK vs. D from 16 to 48 h and at 72 h after supplementation (treatment x hour interaction, P < 0.01). Moreover, PUN concentrations peaked at 28 h after supplementation for 3WK and 1WK (P < 0.01) and were greater (P < 0.01) at this time for 1WK vs. 3WK and D and for 3WK vs. D. Expression of CPS-I was greater (P < 0.01) for 1WK vs. D and 3WK. Uterine flushing pH tended (P <= 0.10) to be greater for 1WK vs. 3WK and D. No treatment effects were detected (P >= 0.15) on expression of CYP2C19 and CYP3A4, plasma glucose, and P-4 concentrations, whereas plasma insulin concentrations were greater (P <= 0.03) in D and 3WK vs. 1WK. Hence, decreasing frequency of protein supplementation did not reduce uterine flushing pH or plasma P-4 concentrations, which are known to impact reproduction in beef cows.

Alterations of protein expression in conditions of copper-deprivation for Paracoccidioides lutzii in the presence of extracellular matrix components

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

The effects of ovalbumin as a protein source during the in vitro production of bovine embryos

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

Isolation, solubility and in vitro hydrolysis of chickpea vicilin-like protein

The chickpea vicilin-like globulin was isolated and chromatographed on Sepharose CL-6B and Sephacryl S-300. The native globulin with a molecular weight of 140 kDa was resolved in Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) in seven polypeptide bands in the range of 12.4-67 kDa. The solubility profile of the protein in water and NaCl solutions was typical of a legume globulin. The purified vicilin-like globulin, native and heated, was hydrolyzed by pepsin, trypsin and chymotrypsin. The hydrolysis patterns indicated that the native vicilin-like protein was only partially degraded by the enzymes in comparison with casein. Heating increased its susceptibility to hydrolysis relative to the native form, for all the enzymes. However, the results obtained by the pH-drop method revealed that the in vitro digestibility of the vicilin-like protein was not altered by heating, while 11 S-like and total globulins suffered a small increase, indicating that the structural characteristics of storage globulins may be important factors limiting the protein digestion. (c) 2007 Swiss Society of Food Science and Technology. Published by Elsevier Ltd. All rights reserved.

Alterations in the intestinal wall due to protein malnutrition in rats. Evaluation of the rupture strength and the tissue's collagen

OBJETIVO: Avaliar o efeito da desnutrição protéica na parede intestinal do rato através da medida de força de ruptura e dosagem do colágeno tecidual no íleo e cólon distal. MÉTODOS: Foram utilizados 120 ratos, pesando em média 100g, que receberam durante 07 dias uma dieta padrão, contendo 20% de caseína para adaptação dos animais as condições do biotério. Após esse período os animais foram divididos em dois grupos de 60, o controle denominado grupo um que recebeu a dieta padrão, e o grupo teste denominado grupo dois, que recebeu dieta hipoprotéica contendo 2% de caseína. Os dois grupos receberam suas respectivas dietas por um período de 21 dias. Após esse período iniciou-se o sacrifício seqüencial dos animais em ambos os grupos, em número de 12 animais em cada momento, correspondendo ao dia Zero (MO), 4º dia (M1), 7º dia (M2), 14º dia (M3), e 21º dia (M4) sendo mantida a mesma dieta até o final do sacrifício. em cada momento foram avaliados o peso corpóreo, albumina sanguínea, hidroxiprolina tecidual, relação hidroxiprolina/proteína tecidual e a força de ruptura no segmento ileal e cólico dos animais. RESULTADOS: Observou-se que a força de ruptura do segmento ileal e do cólon distal foi menor nos animais desnutridos (Grupo 2). A perda da resistência mecânica foi maior no segmento do cólon distal do que no segmento ileal, provavelmente pela menor concentração do colágeno tecidual no cólon distal. CONCLUSÃO: A desnutrição protéica induz a diminuição da resistência mecânica no íleo e no cólon distal associado a diminuição do colágeno tecidual na parede intestinal.

Influence of protein intake and muscle mass on survival in chronic dialysis patients

Introduction: Some studies suggest that high body mass index (BMI) confers survival advantage in dialysis patients, but BMI does not differentiate muscle from fat mass, and the survival advantage conferred by its increase seems to be limited to patients with high muscle mass. Thus, discriminating body components when evaluating nutritional status and survival is highly important. This study evaluated the influence of nutritional parameters on survival in patients on chronic dialysis. Subjects and methods: Anthropometry, bioimpedance, biochemistry, and dietary recall were used to investigate the influence of nutritional parameters on survival in 79 prevalent patients on chronic dialysis. Results: Protein intake <1.2 g/kg/day and creatinine <9.7 mg/dL were independent predictors of mortality in all patients. Regarding dialysis method, protein intake <1.2 g/kg/ day was predictive of mortality among hemodialysis patients, and percent standard mid-arm muscle circumference <80% was identified as a risk factor among peritoneal dialysis patients. Conclusion: Higher muscle mass, possibly favored by a higher protein intake, conferred survival advantage in dialysis patients.