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.

MGMT and MLH1 methylation in Helicobacter pylori-infected children and adults

AIM: To evaluate the association between Helicobacter pylori(H. pylori) infection and MLH1 and MGMT methylation and its relationship with microsatellite instability (MSI). METHODS: The methylation status of the MLH1 and MGMT promoter region was analysed by methylation specific methylation-polymerase chain reaction (MSPPCR) in gastric biopsy samples from uninfected or H. pylori -infected children (n = 50), from adults with chronic gastritis (n = 97) and from adults with gastric cancer (n = 92). MLH1 and MGMT mRNA expression were measured by real-time PCR and normalised to a constitutive gene (β actin). MSI analysis was performed by screening MSI markers at 4 loci (Bat-25, Bat-26, D17S250 and D2S123) with PCR; PCR products were analysed by single strand conformation polymorphism followed by silver staining. Statistical analyses were performed with either the χ 2 test with Yates continuity correction or Fisher's exact test, and statistical significance for expression analysis was assessed using an unpaired Student's t -test. RESULTS: Methylation was not detected in the promoter regions of MLH1 and MGMT in gastric biopsy samples from children, regardless of H. pylori infection status. The MGMT promoter was methylated in 51% of chronic gastritis adult patients and was associated with H. pylori infection (P < 0.05); this region was methylated in 66% of gastric cancer patients, and the difference in the percentage of methylated samples between these patients and those from H. pylori -infected chronic gastritis patients was statistically significant (P < 0.05). MLH1 methylation frequencies among H. pylori -infected and non-infected chronic gastritis adult patients were 13% and 7%, respectively. We observed methylation of the MLH1 promoter (39%) and increased MSI levels (68%) in samples from gastric cancer patients in comparison to samples from H. pylori -infected adult chronic gastritis patients (P < 0.001 and P < 0.01, respectively). The frequency of promoter methylation for both genes was higher in gastric cancer samples than in H. pylori -positive chronic gastritis samples (P < 0.05). The levels of MLH1 and MGMT mRNA were significantly reduced in chronic gastritis samples that were also hypermethylated (P < 0.01). MGMT promoter region was analysed by methylation specific methylation-polymerase chain reaction (MSPPCR) in gastric biopsy samples from uninfected or H. pylori -infected children (n = 50), from adults with chronic gastritis (n = 97) and from adults with gastric cancer (n = 92). MLH1 and MGMT mRNA expression were measured by real-time PCR and normalised to a constitutive gene (β actin). MSI analysis was performed by screening MSI markers at 4 loci (Bat-25, Bat-26, D17S250 and D2S123) with PCR; PCR products were analysed by single strand conformation polymorphism followed by silver staining. Statistical analyses were performed with either the χ 2 test with Yates continuity correction or Fisher's exact test, and statistical significance for expression analysis was assessed using an unpaired Student's t -test. RESULTS: Methylation was not detected in the promoter regions of MLH1 and MGMT in gastric biopsy samples from children, regardless of H. pylori infection status. The MGMT promoter was methylated in 51% of chronic gastritis adult patients and was associated with H. pylori infection (P < 0.05); this region was methylated in 66% of gastric cancer patients, and the difference in the percentage of methylated samples between these patients and those from H. pylori -infected chronic gastritis patients was statistically significant (P < 0.05). MLH1 methylation frequencies among H. pylori -infected and non-infected chronic gastritis adult patients were 13% and 7%, respectively. We observed methylation of the MLH1 promoter (39%) and increased MSI levels (68%) in samples from gastric cancer patients in comparison to samples from H. pylori -infected adult chronic gastritis patients (P < 0.001 and P < 0.01, respectively). The frequency of promoter methylation for both genes was higher in gastric cancer samples than in H. pylori -positive chronic gastritis samples (P < 0.05). The levels of MLH1 and MGMT mRNA were significantly reduced in chronic gastritis samples that were also hypermethylated (P < 0.01). CONCLUSION: In summary, MGMT and MLH1 methylation did not occur in earlier-stage H. pylori infections and thus might depend on the duration of infection. © 2013 Baishideng. All rights reserved.

Yeast proteins originated from the production of brazilian bioethanol quantification and content

The purpose of this work was to determine the levels of protein and the amino acid distribution in the cell mass of yeast strains (Saccharomyces sensu stricto) originated from Brazilian bioethanol industries. The protein was analyzed with the Kjeldahl method and the amino acids, by using high-performance liquid chromatography (HPLC). The percentages of the protein found ranged from 39 to 49%. The results show that in spite of some variation in numbers between the different yeast strains, all of them presented an amino acid profile similar to the one in the literature for S. cerevisae. The amino acids that have occurred in the largest amounts were: aspartic, glutamic acids and lysine, and those in the lowest amounts were: cysteine and methionine. Although the characteristics of the feedstock used and the process conditions are determinant of the protein values obtained in dry mass, this work elucidates that the intrinsic properties of the yeast strain influence these values.

Predictive formulas for food base excess and urine pH estimations of cats

Food base excess (BE, mEq/kg) can be calculated from the diet macroelements, together with either the sulfur amino acids methionine and cysteine (BEaa) or total sulfur (BEs) concentrations. The present study compared the use of sulfur or methionine and cysteine for calculating the food BE (experiment 1) and investigated the influence of food BE on blood gas analysis and the urine pH of cats, and proposes a prediction equation to estimate the urine pH of cats fed kibble diets based on the calculated food BE (experiments 2 and 3). In experiment 1, nine healthy, adult cats were used in a change-over design and fed with nine commercial dry cat foods. The cats were housed in metabolism cages over seven days for adaptation and three days for total urine collection. All of the urine produced over 24h was pooled by cat and diet. The cats' acid-base status was assessed through blood gas analysis after 10 days of diet consumption. A mean difference of -115mEq/kg between BEs and BEaa was observed, which could be explained by a greater concentration of sulfur in the whole diet than in methionine and cysteine. Urine pH presented a stronger correlation with food BEs (R2=0.95; P<0.001) than with food BEaa (R2=0.86; P<0.001). Experiment 2 included 30 kibble diets, and each diet was tested in six cats. The food BEs varied between -180 and +307mEq/kg, and the urine pH of the cats varied between 5.60 and 7.74. A significant correlation was found between the measured urine pH and the food BEs (urinary pH=6.269+[0.0036×BEs]+[0.000003×BEs2]; R2=0.91; P<0.001). In experiment 3, eight kibble diets were tested (food BEs between -187mEq/kg and +381mEq/kg) to validate the equation proposed in experiment 2 and to compare the obtained results with previously published formulae. The results of the proposed formula presented a high concordance correlation coefficient (0.942) and high accuracy (0.979) with the measured values, and the estimates of urine pH did not differ from the values obtained in cats (P>0.05). The cats' venous blood pH, bicarbonate, and blood BE were correlated with food BEs (P<0.001); the consumption of diets with low food BEs induced a reduction in these parameters. In conclusion, food macroelement composition has a strong influence on cats' acid-base equilibrium and food BEs calculation is a useful tool to formulate and balance kibble diets for felines. © 2013 Elsevier B.V.

Identification of duplicated and stress-inducible Aox2b gene co-expressed with Aox1 in species of the Medicago genus reveals a regulation linked to gene rearrangement in leguminous genomes

In flowering plants, alternative oxidase (Aox) is encoded by 3-5 genes distributed in 2 subfamilies (Aox1 and Aox2). In several species only Aox1 is reported as a stress-responsive gene, but in the leguminous Vigna unguiculata Aox2b is also induced by stress. In this work we investigated the Aox genes from two leguminous species of the Medicago genus (Medicago sativa and Medicago truncatula) which present one Aox1, one Aox2a and an Aox2b duplication (named here Aox2b1 and Aox2b2). Expression analyses by semi-quantitative RT-PCR in M. sativa revealed that Aox1, Aox2b1 and Aox2b2 transcripts increased during seed germination. Similar analyses in leaves and roots under different treatments (SA, PEG, H2O2 and cysteine) revealed that these genes are also induced by stress, but with peculiar spatio-temporal differences. Aox1 and Aox2b1 showed basal levels of expression under control conditions and were induced by stress in leaves and roots. Aox2b2 presented a dual behavior, i.e., it was expressed only under stress conditions in leaves, and showed basal expression levels in roots that were induced by stress. Moreover, Aox2a was expressed at higher levels in leaves and during seed germination than in roots and appeared to be not responsive to stress. The Aox expression profiles obtained from a M. truncatula microarray dataset also revealed a stress-induced co-expression of Aox1, Aox2b1 and Aox2b2 in leaves and roots. These results reinforce the stress-inducible co-expression of Aox1/Aox2b in some leguminous plants. Comparative genomic analysis indicates that this regulation is linked to Aox1/Aox2b proximity in the genome as a result of the gene rearrangement that occurred in some leguminous plants during evolution. The differential expression of Aox2b1/2b2 suggests that a second gene has been originated by recent gene duplication with neofunctionalization. © 2013 Elsevier GmbH. All rights reserved.

A new proposed rodent model of chemically induced prostate carcinogenesis: Distinct time-course prostate cancer progression in the dorsolateral and ventral lobes

Background. Characterization of novel rodent models for prostate cancer studies requires evaluation of either spontaneous and carcinogen-induced tumors as well as tumor incidence in different prostatic lobes. We propose a new short-term rodent model of chemically induced prostate carcinogenesis in which prostate cancer progression occurs differentially in the dorsolateral and ventral lobes. Methods. Adult gerbils were treated with MNU alone or associated with testosterone for 3 or 6 months of treatment. Tumor incidence, latency, localization, and immunohistochemistry (AR, PCNA, smooth muscle α-actin, p63, MGMT, and E-cadherin) were studied in both lobes. Results. Comparisons between both lobes revealed that lesions developed first in the DL while the VL presented longer tumor latency. However, after 6 months, there was a dramatic increase in tumor multiplicity in the VL, mainly in MNU-treated groups. Lesions clearly progressed from a premalignant to a malignant phenotype over time and tumor latency was decreased by MNU + testosterone administration. Three-dimensional reconstruction of the prostatic complex showed that the DL developed tumors exclusively in the periurethral area and showed intense AR, PCNA, and MGMT immunostaining. Moreover, VL lesions emerged throughout the entire lobe. MNU-induced lesions presented markers indicative of an aggressive phenotype: lack of basal cells, rupture of the smooth muscle cell layer, loss of E-cadherin, and high MGMT staining. Conclusions. There are distinct pathways involved in tumor progression in gerbil prostate lobes. This animal provides a good model for prostate cancer since it allows the investigation of advanced steps of carcinogenesis with shorter latency periods in both lobes. Copyright © 2013 Wiley Periodicals, Inc.

Glutathione and glutathione peroxidase expression in breast cancer: An immunohistochemical and molecular study

The use of prognostic markers for breast cancer allows therapeutic strategies to be defined more efficiently. The expression of glutathione (GSH) and glutathione peroxidase (GPX) in tumor cells has been evaluated as a predictor of prognosis and response to cytotoxic treatments. Its immunoexpression was assessed in 63 women diagnosed with invasive ductal carcinoma in a retrospective study. The results showed that high GSH expression was associated with tumors negative for the estrogen receptor (ER) (P<0.05), and GPX expression was associated with tumors negative for the progesterone receptor (PR) and patient mortality. Focusing on the 37 patients who received adjuvant chemotherapy/radiotherapy (Group I), high expression of GPX was associated with a high rate of patient mortality (P<0.05). The 19 patients who received only adjuvant chemotherapy (Group II) showed high expression of GSH in relation to metastasis (P<0.05). In addition, high levels of GPX expression were significantly associated with a shorter overall survival (P<0.05). To confirm this, the expression of precursor genes of GSH [glutamate cysteine ligase (GCLC) and glutathione synthetase (GSS)] and the GPX gene was analyzed using quantitative PCR in cultured neoplastic mammary cells treated with doxorubicin. Doxorubicin treatment was able to eliminate tumor cells without alterations in the gene expression of GSS, but led to underexpression of the GCLC and GPX genes. Our results suggest that high levels of GPX may be related to the development of resistance to chemotherapy in these tumors, response to treatment and the clinical course of the breast cancer patients.

In vitro and in vivo evaluation of the activity of pineapple (Ananas comosus) on Haemonchus contortus in Santa Inês sheep

The development of resistance to anthelmintics has prompted research into alternative methods of controlling intestinal nematodes in ruminants. This study aimed to assess the activity of Ananas comosus on Haemonchus contortus in Santa Inês sheep. The aqueous extract of pineapple skin (AEPS), bromelain from pineapple stems (B4882) and residue from pineapple processing was evaluated in in vitro and in vivo tests. The enzymatic activity of substances was analyzed by the azocasein method. The egg hatch test (EHT) and larval development test (LDT) were performed using the Embrapa2010 isolate of H. contortus. In the in vivo test, 36 sheep artificially infected with H. contortus were divided into six groups: G1: 2g/kg BW of the aqueous extract administered for three days; G2: 2g/kg BW of the industrial pineapple residue for 60 days; G3: 180mg/animal of bromelain in a single dose; G4: negative control I; G5: positive control (levamisole phosphate); and G6: negative control II. The eggs per gram (EPG) in the feces were counted till 28 days after treatment. LC50 and LC90 were obtained by the probit procedure, while the in vivo test results were analyzed by GLM. The aqueous extract in the in vitro and in vivo test, the bromelain and industrial residue presented 0.102, 0.157, 1.864 and 0.048 enzyme units/mL, respectively. In the egg hatch test, the LC50 and LC90 were respectively 31 and 81mg/mL for the aqueous extract and 0.50 and 2mg/mL for bromelain. In the larval development test, the LC50 and LC90 were respectively 1.7 and 7.3mg/mL for the aqueous extract and 0.019 and 0.086mg/mL for bromelain. In the in vivo test, the general efficacies of the treatments in relation to the negative control were 22.6%, 42.2%, 3.65% and 89% for the aqueous extract, industrial pineapple residue, bromelain and positive control respectively. The transformed EPG values were 3.19±0.59, 3.32±0.25, 2.85±0.66, 3.44±0.50, 2.28±0.93 and 2.75±0.94 for the aqueous extract, industrial residue, bromelain, negative control I, positive control and negative control II respectively. The results for all the treated groups differed significantly (p<0.05) from the positive control, and although the residue presented efficacy of 42.2%, there was no statistical difference (p>0.05) in relation to the negative control. Therefore, both the aqueous extract and bromelain were effective in vitro, but showed reduced anthelmintic efficacy in vivo. For the pineapple residue, the 42.2% in vivo efficacy in reducing the EPG and the possibility of reducing environmental contamination through reuse of industrial residue indicate it can also be useful for control of this parasite. © 2013 Elsevier B.V.

Structure-function relationships of the peptide Paulistine: A novel toxin from the venom of the social wasp Polybia paulista

Background: The peptide Paulistine was isolated from the venom of wasp Polybia paulista. This peptide exists under a natural equilibrium between the forms: oxidised - with an intra-molecular disulphide bridge; and reduced - in which the thiol groups of the cysteine residues do not form the disulphide bridge. The biological activities of both forms of the peptide are unknown up to now. Methods: Both forms of Paulistine were synthesised and the thiol groups of the reduced form were protected with the acetamidemethyl group [Acm-Paulistine] to prevent re-oxidation. The structure/activity relationships of the two forms were investigated, taking into account the importance of the disulphide bridge. Results: Paulistine has a more compact structure, while Acm-Paulistine has a more expanded conformation. Bioassays reported that Paulistine caused hyperalgesia by interacting with the receptors of lipid mediators involved in the cyclooxygenase type II pathway, while Acm-Paullistine also caused hyperalgesia, but mediated by receptors involved in the participation of prostanoids in the cyclooxygenase type II pathway. Conclusion: The acetamidemethylation of the thiol groups of cysteine residues caused small structural changes, which in turn may have affected some physicochemical properties of the Paulistine. Thus, the dissociation of the hyperalgesy from the edematogenic effect when the actions of Paulistine and Acm-Paulistine are compared to each other may be resulting from the influence of the introduction of Acm-group in the structure of Paulistine. General significance: The peptides Paulistine and Acm-Paulistine may be used as interesting tools to investigate the mechanisms of pain and inflammation in future studies. © 2013 Elsevier B.V.

Estado nutricional e níveis plasmáticos de trauma e seus precursores em pacientes portadores de neoplasias malignas de esôfago

Pós-graduação em Bases Gerais da Cirurgia - FMB

Determinação do grau de ionização de aminoácidos polares carregados

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

Efeito das plantas medicinais Curcuma zedoaria e Camellia sinensis no controle da halitose

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Peptídeos derivados da proteína bacteriana YacG : síntese e estudos de estrutura-função

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Contribuição ao estudo de polifenoloxidase e ascorbato oxidase de polpa de Passiflora edulis (maracujá-amarelo) visando o processamento industrial de suco

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Efeito da lisina na produção de compostos beta-lactâmicos produzidos por Sterptomuces clavuligerus

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)