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.

Dynamics of bone healing after osteotomy with piezosurgery or conventional drilling - histomorphometrical, immunohistochemical, and molecular analysis

Background: Piezosurgery is an osteotomy system used in medical and dental surgery. Many studies have proven clinical advantages of piezosurgery in terms of quality of cut, maneuverability, ease of use, and safety. However, few investigations have tested its superiority over the traditional osteotomy systems in terms of dynamics of bone healing. Therefore, the aim of this study was to evaluate the dynamics of bone healing after osteotomies with piezosurgery and to compare them with those associated to traditional bone drilling.Methods: One hundred and ten rats were divided into two groups with 55 animals each. The animals were anesthetized and the tibiae were surgically exposed to create defects 2 mm in diameter by using piezosurgery (Piezo group) and conventional drilling (Drill group). Animals were sacrificed at 3, 7, 14, 30 and 60 days post-surgery. Bone samples were collected and processed for histological, histomorphometrical, immunohistochemical, and molecular analysis. The histological analysis was performed at all time points (n = 8) whereas the histomorphometrical analysis was performed at 7, 14, 30 and 60 days post-surgery (n = 8). The immunolabeling was performed to detect Vascular Endothelial Growth Factor (VEGF), Caspase-3 (CAS-3), Osteoprotegerin (OPG), Receptor Activator of Nuclear Factor kappa-B Ligand (RANKL), and Osteocalcin (OC) at 3, 7, and 14 days (n = 3). For the molecular analysis, animals were sacrificed at 3, 7 and 14 days, total RNA was collected, and quantification of the expression of 21 genes related to BMP signaling, Wnt signaling, inflammation, osteogenenic and apoptotic pathways was performed by qRT-PCR (n = 5).Results: Histologically and histomorphometrically, bone healing was similar in both groups with the exception of a slightly higher amount of newly formed bone observed at 30 days after piezosurgery (p < 0.05). Immunohistochemical and qRT-PCR analyses didn't detect significant differences in expression of all the proteins and most of the genes tested.Conclusions: Based on the results of our study we conclude that in a rat tibial bone defect model the bone healing dynamics after piezosurgery are comparable to those observed with conventional drilling. © 2013 Esteves et al.; licensee BioMed Central Ltd.

Cost-effective composite electrode for the fast voltammetric screening and determination of riboflavin (B2) and pyridoxine (B6) in pharmaceuticals

Different solid composites made by mechanical dispersions of graphite particles into heated paraffin (from 65 to 80% graphite, in mass) were prepared and assessed in order to optimize their use in electrochemical and electroanalytical procedures for bioanalysis. Besides these, composites were also evaluated by thermoanalytical techniques aiming to study their conservation and long-term stability (over eight months without special care), among others. Best results were found at 80% m/m graphite in paraffin. Such electrode combines low-cost, stability, sensitivity, ease of maintenance and clearance, besides the possibilities of manufacture in many different forms and shapes (with or without modifications) and applicability in a wide range of pH. Electrochemical studies by different voltammetric techniques involving vitamins from complex B (riboflavin and pyridoxine) leaded to a better understanding about their electrooxidative processes onto carbon-composite electrodes, specially regarding reversibility and pH-dependence. Data were also acquired and optimized with analytical purposes, being square-wave voltammetry in pH 4.2 chosen by its many advantages. Good linearity between peak responses as function of concentration were reached from 5 to 43 μmol L-1 for riboflavin (peak at -0.257 V) and up to 8.5 × 10-4 mol L -1 for pyridoxine (peak at +1.04 V), best studied conditions; limits of detection (at an S/N of 3) for both analites showed to be circa 1.0 mol L-1. Different commercial samples were analyzed for riboflavin (EMS® complex B syrup) and pyridoxine (Citoneurin 5000 Merck® ampoules) providing 96.6% and 98.7% recoveries, respectively.

Effect of s/g ratio on kraft pulping and ecf bleaching of some poplars and eucalyptus

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

From west to east: Environmental influences on the rate and pathways of Polynesian colonization

The prime movers behind the prehistoric colonization of Remote Oceania, and in particular the large c. 2000-year temporal gap (i.e. long pause') seen between West and East Polynesia, has long been major point of interest in the Pacific. To address these events and the processes that may have led to the known chronological disparity of these diasporas, we present results from two different, but equally powerful, analytical tools which are used to examine Polynesian seafaring capabilities and trajectories. The first is a statistical model known as Seascape, which simulates voyages, while the second uses ease of eastward travel estimates based on land distribution and wind pattern analysis. These analyses were done with the goal of determining the potential role of environmental factors in the colonization process, particularly as they relate to the long pause. We show that the eastern boundary of West Polynesia, the limit of the initial colonization pulse, is marked by a discontinuity in land distribution, where the distances travelers would have to cross in order to reach islands further to the east become significantly larger. At the same time, in West Polynesia, the frequency and intensity of winds favorable to eastward displacement decrease continuously from west to east. As far as winds are concerned, eastward travel in West Polynesia is favored in the northern and southern areas and much more difficult across the central portion. Favorable winds have a clear seasonality, and eastward displacement along the northern area is much easier under El Nino conditions. Voyaging simulations show that intentional eastward voyages departing from Tonga and Samoa, when undertaken with vessels capable of sailing efficiently against the wind, afford a viable route toward several island groups in East Polynesia, with trips starting in Samoa having a higher probability of success.

Performance evaluation of multi-stage filtration with use of granular activated carbon and synthetic non-woven fabrics

The multi stage filtration (MSF) is an alternative that permits to enlarge the spectrum of application of the slow sand filtration as for the effluent quality and run duration. In this research the use of MSF technology associated to a granular activated carbon (GAC) column as polishing mechanism of the final effluent was evaluated; in the slow sand filters GAC was used as an intermediate layer and non-woven synthetic fabrics were utilized as a first layer of the filter media. Five different tests were conducted, where the systems subjected to the treatment were: water from the Ipe Lake (Ilha Solteira, Sao Paulo, Brazil); water from the lake with water from a recreational fish pond; water from the lake with a phytoplankton and cyanobacteria overload simulation, with and without the use of the pre-filters as a stage of the treatment. The synthetic fabrics and GAC use resulted in the best turbidity removal and an efficient apparent and true color removal; in spite that the polishing columns reported similar results for those parameters. The utilization of GAC as an intermediate layer contributed to a better organic matter removal and the fabrics improved chlorophyll-a removal. The pre-filtration columns made an efficient algae and cyanobacteria removal, a function that was completed by the filters and reached >98% efficiency. The synthetic non-woven fabrics and GAC inclusion in MSF operation improved performance of this technology with ease of application and operation.

Perspectives on the use of lakes and ponds as model systems for macroecological research

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Vertical distribution by demographic groups of ghost crab Ocypode quadrata (Crustacea: Brachyura)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Antitubercular activity of Ru (II) isoniazid complexes

Despite the resistance developed by the Mycobacterium tuberculosis (MTb) strains, isoniazid (INK) has been recognized as one of the best drug for treatment of Tuberculosis (Tb). The coordination of INH to ruthenium metal centers was investigated as a strategy to enhance the activity of this drug against the sensitive and resistant strains of MTb. The complexes trans-[Ru(NH3)(4)(L)(INH)](2+) (L = SO2 or NH3) were isolated and their chemical and antituberculosis properties studied. The minimal inhibitory concentration (MIC) data show that [Ru(NH3)(5)(INH)](2+) was active in both resistant and sensitive strains, whereas free INK (non-coordinated) showed to be active only against the sensitive strain. The coordination of INH to the metal center in both [Ru(NH3)(5)(INH)](2+) and trans-[Ru(NH3)(4)(SO2)(INH)](2+) complexes led to a shift in the INH oxidation potential to less positive values compared to free INH. Despite, the ease of oxidation of INH did not lead to an increase in the in vitro INH activity against MTb, it might have provided sensitivity toward resistant strains. Furthermore, ruthenium complexes with chemical structures analogous to those described above were synthesized using the oxidation products of INK as ligands (namely, isonicotinic acid and isonicotinamide). These last compounds were not active against any strains of MTb. Moreover, according to DFT calculations the formation of the acyl radical, a proposed intermediate in the INH oxidation, is favored in the [Ru(NH3)(5)(INH)](2+) complex by 50.7 kcal mol(-1) with respect to the free INH. This result suggests that the stabilization of the acyl radical promoted by the metal center would be a more important feature than the oxidation potential of the INH for the antituberculosis activity against resistant strains. (C) 2015 Elsevier B.V. All rights reserved.

Consumption Diagnosis of Sweet Cassava in three Municipalities in Cuba

Cassava is an important staple food for human and animal feeding in Cuba. Despite its importance, there is little or nonexistent information to diagnose preferences and frequency of consumption of cassava in that country. In this sense, the present article characterizes the preferences and frequency of consumption of cassava in the municipalities of Plaza de la Revolución-La Habana province, El Salvador–Guantanamo province and San José de Las Lajas–Mayabeque province in Cuba. A survey was conducted through a questionnaire containing twelve closed and two open questions. The sample was determined based on the number of total population of each municipality considering 95% as confidence interval and 5% as error margin. The results were statistically analyzed by calculating the absolute and the relative frequencies of each question. It was observed that the acquisition of cassava in the municipalities of Plaza de la Revolución, El Salvador and San José de las Lajas in Cuba is done by purchase small quantities of fresh cassava for home consumption within one week, due to the extreme perishability of cassava, which limits consumers' ability to store fresh roots at home. The choice of cassava is made based on both skin colour (light brown) and pulp (white) and empirical knowledge about its ease of cooking, and that cassava is mostly consumed in boiled and fried forms up to four times a week in times where there is root market supply with the desirable culinary characteristics (cooking facility), that is, from September to December.

Eficácia da imunoterapia no tratamento de pitiose facial em equino

Background: Pythiosis in horses is a proliferative and ulcerative disease that primarily affects the skin and subcutaneous tissue of limbs, thoracic-abdominal region and head. This disease sometimes can also affect limb bones or cause tumoral masses in abdomen. Usually, the cutaneous cases are confused with habronemiasis. The disease is more common in marshy areas, places with formation of slow drainage ponds and aquatic vegetation under high temperatures. The aim of this study was to describe the development of facial lesions in a horse caused by pythiosis in Cuiaba, Mato Grosso, and, additionally to discuss relevant issues regarding the diagnosis, clinical course and response to immunotherapy treatment.Case: One five years old mare of unknown breed, created in property located in the Cerrado region, had a wound on its face difficult to be healed and non-responsive to several treatments based on ivermectin and organophosphate administrated by either topical or systemic via. The animal was assisted on the farm of origin by the veterinary team of the Clinical Medicine sector, of the Veterinary Hospital, Universidade Federal de Mato Grosso (HOVET-UFMT). on the occasion of the visit, which occurred 60 days after onset of signs, the animal showed a circular single large lesion, ulcerative with serous discharge on the right part of its face, between the eyes and nostrils. There were some necrotic foci with sinus, from which kunkers were extracted; a condition compatible with pythiosis. The diagnosis was confirmed by histology, ELISA and PCR.Discussion: Assuming pythiosis from data obtained from the survey and profile of the lesion (secretory aspect, emaciation and presence of sinus and kunkers), immunotherapy treatment was immediately applied. The advanced clinical aspects and the fact that early diagnosis and treatment are essentials to satisfactory therapeutic response were also taken into consideration for starting the treatment. The remission of signs was achieved after five subcutaneous applications with 14 days between each application. From the second application, it was observed clinical improvement and after 60 days of treatment there was almost complete remission of signs. The signs for a satisfactory response in the injury site followed the order of decreasing secretory aspect, decreasing borders, decrease the itching and bringing the edges together with the formation of a thin layer of crust on the surface. Pythiosis cases with lesions on the face and lower abdomen are commonly confused with habronemiasis by macroscopic and widespread similarity between technicians and attendants, and essential support to the diagnosis through laboratory tests, which in turn are still underutilized. In this case, the authors demonstrated the therapeutic efficacy of immunotherapy as an advantage, considering the possibility of applying it in cases of lesions in areas of difficult surgical access, treatment conditions in the field, with low cost and ease of application. Further studies approaching this alternative therapy are necessary, since side effects have been observed in some cases.

Triticale, milheto e adubação fosfatada para formação de palhada em semeadura direta

As fontes de P mais utilizadas são os fosfatos solúveis em água, pela maior facilidade de liberação de P no solo. Entretanto, devido às características dos solos tropicais, grande parte desse P acaba adsorvida às partículas do solo, tornando-se indisponível. Os fosfatos reativos podem, inicialmente, liberar o P de maneira mais lenta; entretanto, a partir dos cultivos, este elemento poderá ser liberado de forma contínua, podendo haver menor fixação. O objetivo deste trabalho foi estudar a resposta à aplicação de duas fontes de P na cultura do triticale e o efeito residual dessa adubação no milheto, cultivados em semeadura direta, avaliando-se: fertilidade do solo; produção de matéria seca; teor e quantidade de P nas plantas e palha de cobertura; densidade de plantas; teor e quantidade de P nos grãos; e produtividade do triticale. O experimento foi conduzido em Latossolo Vermelho distroférrico. No mês de abril foram aplicados, a lanço, em superfície, três tratamentos: sem aplicação de P2O5; aplicação de 80 kg ha-1 de P2O5 de superfosfato triplo; e aplicação de 80 kg ha-1 de P2O5 de fosfato natural Arad. em seguida, semeou-se o triticale (X Triticosecale Wittmack), que foi conduzido até a colheita. em setembro, após a colheita do triticale, semeou-se o milheto (Pennisetum glaucum (L.) R. Brown), com o objetivo de elevar a cobertura de palha do solo, sendo ele dessecado no florescimento no mês de novembro. A aplicação de fosfato solúvel em superfície proporcionou lixiviação do P até a camada de 5-10 cm de profundidade do solo e melhor nutrição fosfatada do triticale cultivado em seguida, assim como maior produção de grãos. Apesar do aumento no teor de P disponível no solo, proporcionado pelo fosfato solúvel, a aplicação de P no triticale não redundou em elevação da produção de matéria seca, do teor e da quantidade de P na parte aérea do milheto cultivado em sequência.

Human breast tumor slices as an alternative approach to cell lines to individualize research for each patient

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

Extração de DNA de materiais de arquivo e fontes escassas para utilização em reação de polimerização em cadeia (PCR)

Este trabalho visou a comparação de cinco métodos diferentes de extração de DNA de materiais de arquivo (tecidos incluídos em parafina, esfregaços de sangue periférico - corados e não corados com Leishman, lâminas com mielogramas, gotas de sangue em Guthrie Card) e de fontes escassas (células bucais, um e três bulbos capilares e 2 mL de urina), para que fossem avaliadas a facilidade de aplicação e a facilidade de amplificação deste DNA pela técnica da reação de polimerização em cadeia (PCR). Os métodos incluíram digestão por proteinase K, seguida ou não por purificação com fenol/clorofórmio; Chelex 100® (BioRad); Insta Gene® (BioRad) e fervura em água estéril. O DNA obtido foi testado para amplificação de três fragmentos gênicos: Brain-derived neutrophic factor (764 pb), Factor V Leiden (220 pb) e Abelson (106 pb). de acordo com o comprimento do fragmento gênico estudado, da fonte potencial de DNA e do método de extração utilizado, os resultados caracterizaram o melhor caminho para padronização de procedimentos técnicos a serem incluídos no manual de Procedimentos Operacionais Padrão do Laboratório de Biologia Molecular do Hemocentro - HC - Unesp - Botucatu.

Caenorhabditis elegans as a model to screen plant extracts and compounds as natural anthelmintics for veterinary use

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)