Automatic classification of enzyme family in protein annotation

Most of the tasks in genome annotation can be at least partially automated. Since this annotation is time-consuming, facilitating some parts of the process - thus freeing the specialist to carry out more valuable tasks - has been the motivation of many tools and annotation environments. In particular, annotation of protein function can benefit from knowledge about enzymatic processes. The use of sequence homology alone is not a good approach to derive this knowledge when there are only a few homologues of the sequence to be annotated. The alternative is to use motifs. This paper uses a symbolic machine learning approach to derive rules for the classification of enzymes according to the Enzyme Commission (EC). Our results show that, for the top class, the average global classification error is 3.13%. Our technique also produces a set of rules relating structural to functional information, which is important to understand the protein tridimensional structure and determine its biological function. © 2009 Springer Berlin Heidelberg.

Alternative measures of potential economic growth in Latin America

Includes bibliography

Can Latin America fly?: revising the engines of growth

Includes bibliography

Exercise training ameliorates the impairment of endothelial and nitrergic corpus cavernosum responses in diabetic rats

Aims: The effect of exercise training (ET) on vascular responsiveness in diabetes mellitus has been largely well studied. However, limited studies have investigated the effects of ET on functional responses of the corpus cavernosum (CC) in diabetic animals. Therefore, the aim of this study was to investigate whether prior ET prevents the impairment of erectile function in streptozotocin-induced diabetic rats. Main methods: Rats were exercised for four weeks prior to the induction of diabetes, and then again for another 4 weeks thereafter. Concentration-response curves to acetylcholine, sodium nitroprusside, Y-27632, BAY 412272 and phenylephrine (PE) were obtained in CC. The excitatory and inhibitory effects of electrical-field stimulation were also evaluated. Key findings: Plasma SOD levels were markedly decreased in the sedentary diabetic group (D-SD) as compared to control sedentary animals (C-SD), approximately 53% (P < 0.05) and this reduction was restored in trained diabetic animals. Physical training restored the impairment of endothelium-dependent and -independent relaxation responses seen in the D-SD group. The potency values for Y-27632 in the CC were significantly reduced in the D-SD group, which was reversed by physical training. The impairment of electrical-field stimulation (EFS)-induced relaxation seen in the D-SD group was restored by physical training. On the other hand, both EFS-induced contractions and concentration-response curves to PE in cavernosal strips were not modified by either diabetes or physical training. Significance: Practice of regular physical exercise may be an important approach in preventing erectile dysfunction associated with diabetes mellitus by re-establishment of the balance between NO production and its inactivation. © 2010 Elsevier Inc. All rights reserved.

Different prescribed doses of high-volume peritoneal dialysis and outcome of patients with acute kidney injury.

The optimal dialysis dose for the treatment of acute kidney injury (AKI) is controversial. No studies have directly examined the effects of peritoneal dialysis (PD) dose on outcomes in AKI. From January 2005 to January 2007, we randomly assigned critically ill patients with AKI to receive higher- or lower-intensity PD therapy (prescribed Kt/Vof 0.8 and 0.5 per session respectively). The main outcome measure was death within 30 days. Of the 61 enrolled patients, 30 were randomly assigned to higher-intensity therapy, and 31, to a lower-intensity PD dose. The two study groups had similar baseline characteristics and received treatment for 6.1 days and 5.7 days respectively (p = 0.42). At 30 days after randomization, 17 deaths had occurred in the higher-intensity group (55%), and 16 deaths, in the lower-intensity group (53%, p = 0.83). There was a significant difference between the groups in the PD dose prescribed compared with the dose delivered (higher-intensity group: 0.8 vs. 0.59, p = 0.04; lower-intensity group: 0.5 vs. 0.49, p = 0.89). The groups had similar metabolic control after 4 PD sessions (blood urea nitrogen: 69.3 +/- 14.4 mg/dL and 60.3 +/- 11.1 mg/dL respectively, p = 0. 71). In critically ill patients with AKI, an intensive PD dose did not lower the mortality or improve the recovery of kidney function or metabolic control. The PD dose is limited by dialysate flow and membrane permeability, and clearance per exchange can decrease if a shorter dwell time is applied.

The United Nations and ECLAC at the half-century mark of the Organization

Includes bibliography

The Deoxyhypusine Synthase Mutant dys1-1 Reveals the Association of eIF5A and Asc1 with Cell Wall Integrity

The putative eukaryotic translation initiation factor 5A (eIF5A) is a highly conserved protein among archaea and eukaryotes that has recently been implicated in the elongation step of translation. eIF5A undergoes an essential and conserved posttranslational modification at a specific lysine to generate the residue hypusine. The enzymes deoxyhypusine synthase (Dys1) and deoxyhypusine hydroxylase (Lia1) catalyze this two-step modification process. Although several Saccharomyces cerevisiae eIF5A mutants have importantly contributed to the study of eIF5A function, no conditional mutant of Dys1 has been described so far. In this study, we generated and characterized the dys1-1 mutant, which showed a strong depletion of mutated Dys1 protein, resulting in more than 2-fold decrease in hypusine levels relative to the wild type. The dys1-1 mutant demonstrated a defect in total protein synthesis, a defect in polysome profile indicative of a translation elongation defect and a reduced association of eIF5A with polysomes. The growth phenotype of dys1-1 mutant is severe, growing only in the presence of 1 M sorbitol, an osmotic stabilizer. Although this phenotype is characteristic of Pkc1 cell wall integrity mutants, the sorbitol requirement from dys1-1 is not associated with cell lysis. We observed that the dys1-1 genetically interacts with the sole yeast protein kinase C (Pkc1) and Asc1, a component of the 40S ribosomal subunit. The dys1-1 mutant was synthetically lethal in combination with asc1Δ and overexpression of TIF51A (eIF5A) or DYS1 is toxic for an asc1Δ strain. Moreover, eIF5A is more associated with translating ribosomes in the absence of Asc1 in the cell. Finally, analysis of the sensitivity to cell wall-perturbing compounds revealed a more similar behavior of the dys1-1 and asc1Δ mutants in comparison with the pkc1Δ mutant. These data suggest a correlated role for eIF5A and Asc1 in coordinating the translational control of a subset of mRNAs associated with cell integrity. © 2013 Galvão et al.

A randomized clinical trial of high volume peritoneal dialysis versus extended daily hemodialysis for acute kidney injury patients

Background: Acute kidney injury (AKI) requiring dialysis in critically ill patients is associated with an in-hospital mortality rate of 50-80 %. Extended daily hemodialysis (EHD) and high volume peritoneal dialysis (HVPD) have emerged as alternative modalities. Methods: A double-center, randomized, controlled trial was conducted comparing EHD versus HVPD for the treatment for AKI in the intensive care unit (ICU). Four hundred and seven patients were randomized and 143 patients were analyzed. Principal outcome measure was hospital mortality, and secondary end points were recovery of renal function and metabolic and fluid control. Results: There was no difference between the two groups in relation to median ICU stay [11 (5.7-20) vs. 9 (5.7-19)], recovery of kidney function (26.9 vs. 29.6 %, p = 0.11), need for chronic dialysis (9.7 vs. 6.5 %, p = 0.23), and hospital mortality (63.4 vs. 63.9 %, p = 0.94). The groups were different in metabolic and fluid control. Blood urea nitrogen (BUN), creatinine, and bicarbonate levels were stabilized faster in EHD group than in HVPD group. Delivered Kt/V and ultrafiltration were higher in EHD group. Despite randomization, there were significant differences between the groups in some covariates, including age, pre-dialysis BUN, and creatinine levels, biased in favor of the EHD. Using logistic regression to adjust for the imbalances in group assignment, the odds of death associated with HVPD was 1.4 (95 % CI 0.7-2.4, p = 0.19). A detailed investigation of the randomization process failed to explain the marked differences in patient assignment. Conclusions: Despite faster metabolic control and higher dialysis dose and ultrafiltration with EHD, this study provides no evidence of a survival benefit of EHD compared with HVPD. The limitations of this study were that the results were not presented according to the intention to treat and it did not control other supportive management strategies as nutrition support and timing of dialysis initiation that might influence outcomes in AKI. © 2012 Springer Science+Business Media Dordrecht.

Assessing the impact of menopause on salivary flow and xerostomia

Background: The aim of this study was to evaluate the symptoms of dry mouth and salivary flow in menarche and menopausal women. Methods: Objective and subjective assessment of salivary function were analysed by Xerostomia Inventory and Visual Analogue Scale questionnaire in menopausal and menarche women (control group). Salivary flow was evaluated by a chemical absorption stimulation test. Each subject provided three saliva samples: S1, non-stimulated saliva; S2, saliva initially stimulated with two drops of citric acid 2.5%; and S3, saliva super-stimulated with two drops of citric acid 2.5% every 30 seconds for two minutes. Results: No intergroup association was observed between Xerostomia Inventory and Visual Analogue Scale questionnaire. In both groups, the salivary flow was greatest at S3, followed by S2 and finally S1. Salivary flow was lower in the menopausal group compared to the control group only in S2 and S3. Conclusions: In the menopausal group, the salivary flow showed reduction but without clinical symptoms of dry mouth. It is important to normalize salivary flow to prevent oral abnormalities and maintain oral health. © 2013 Australian Dental Association.

The calcium wave model of the perception-action cycle: Evidence from semantic relevance in memory experiments

We present a general model of brain function (the calcium wave model), distinguishing three processing modes in the perception-action cycle. The model provides an interpretation of the data from experiments on semantic memory conducted by the authors. © 2013 Pereira Jr, Santos and Barros.

Expression, purification and molecular analysis of the human ZNF706 protein

Background: The ZNF706 gene encodes a protein that belongs to the zinc finger family of proteins and was found to be highly expressed in laryngeal cancer, making the structure and function of ZNF706 worthy of investigation. In this study, we expressed and purified recombinant human ZNF706 that was suitable for structural analysis in Escherichia coli BL21(DH3). Findings. ZNF706 mRNA was extracted from a larynx tissue sample, and cDNA was ligated into a cloning vector using the TOPO method. ZNF706 protein was expressed according to the E. coli expression system procedures and was purified using a nickel-affinity column. The structural qualities of recombinant ZNF706 and quantification alpha, beta sheet, and other structures were obtained by spectroscopy of circular dichroism. ZNF706's structural modeling showed that it is composed of α-helices (28.3%), β-strands (19.4%), and turns (20.9%), in agreement with the spectral data from the dichroism analysis. Conclusions: We used circular dichroism and molecular modeling to examine the structure of ZNF706. The results suggest that human recombinant ZNF706 keeps its secondary structures and is appropriate for functional and structural studies. The method of expressing ZNF706 protein used in this study can be used to direct various functional and structural studies that will contribute to the understanding of its function as well as its relationship with other biological molecules and its putative role in carcinogenesis. © 2013 Colombo et al.; licensee BioMed Central Ltd.

Time-course morphological and functional disorders of the kidney induced by long-term high-fat diet intake in female rats

BackgroundEvidence is emerging that highlights the far-reaching consequences of a high-fat diet (HFD) on kidney morphology and function disorders.MethodsThe present study was performed on 3-, 5-, 7- and 9-week-old HFD female rats compared with the appropriate gender and age-matched animals. We evaluated the kidney expression of angiotensin type II receptor and fibrotic and epithelial-to-mesenchymal transition (EMT) markers, by immunoblotting and immunohistochemical and histological techniques, in parallel with kidney function.ResultsIn the current study, the time-course HFD-treated group showed, by immunoblotting and immunohistochemical analysis, an early time-course increase in the expression of transforming growth factor β-1 (TGFβ-1) in the entire kidney of HFD-treated rats, compared with that observed in the control group. Simultaneously, the study shows a transient increase in the expression of ZEB2 in the HFD whole kidney accompanied by a fall in the E-cadherin expression and increased collagen and fibronectin deposition. A pronounced decrease in fractional urinary sodium excretion was also demonstrated in the long-term HFD-treated rats. The decreased FENa + was accompanied by a fall in FEPNa + and FEPP Na +, which occurred in association with significantly decreased CCr and, certainly on the sodium-filtered load. The reduction in the glomerular filtration rate (GFR) occurred in parallel to proteinuria and glomerular desmin overexpression.ConclusionsThe results of the current study suggest that podocyte injury in parallel with observed proteinuria and evidence of EMT transformation are associated with long-term loss of kidney function and renal sodium and water retention. © 2013 The Author. All rights reserved.

Uso de uma rede unidimensional harmônica com o potencial de Rosen-Morse on site para modelar o DNA

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A administração de GH atenua o desenvolvimento de fibrose miocádica em ratos com insuficiência cardíaca secundária a estenose aórtica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A genomic assisted breeding program for cassava to improve nutritional quality and industrial traits of storage root

A mandioca é cultivada como "mandioca mansa" para consumo in natura e "mandioca para indústria" como fonte de amidos e farinhas. Raças locais foram utilizadas para descoberta de "mutações espontâneas" e desenvolvimento de abordagem evolutiva e de melhoramento para estudos de função gênica. Recursos de Genômica e Proteômica foram obtidos. Análises de expressão gênica por blot de RNA e microarranjos foram desenvolvidos para identificação de expressão diferencial. "Mandioca açucarada" foi identificada, sendo relacionada com falta de expressão do gene da BEI e de uma mutação "nonsence" na sequência do gene GBSSI causando a formação do amido serose. "Mandioca avermelhada" apresentou falta de expressão do gene CasLYB, e a "amarela" uma regulação de repressão do gene CasHYb. Análise Proteômica do complexo carotenóide-proteína, juntamente com a análise de expressão de gene da CAP4, revelaram uma dupla fita de cDNA associada ao elevado acúmulo de carotenóide. Sequenciamento do gene da GBSSI identificou 22 haplótipos e grande diversidade de nucleotídios. Populações segregantes de cruzamentos de fenótipos bioquímicos diferenciados com cultivares elites dos Cerrados foram obtidas.