GeneMCL in microarray analysis

Accurately and reliably identifying the actual number of clusters present with a dataset of gene expression profiles, when no additional information on cluster structure is available, is a problem addressed by few algorithms. GeneMCL transforms microarray analysis data into a graph consisting of nodes connected by edges, where the nodes represent genes, and the edges represent the similarity in expression of those genes, as given by a proximity measurement. This measurement is taken to be the Pearson correlation coefficient combined with a local non-linear rescaling step. The resulting graph is input to the Markov Cluster (MCL) algorithm, which is an elegant, deterministic, non-specific and scalable method, which models stochastic flow through the graph. The algorithm is inherently affected by any cluster structure present, and rapidly decomposes a graph into cohesive clusters. The potential of the GeneMCL algorithm is demonstrated with a 5730 gene subset (IGS) of the Van't Veer breast cancer database, for which the clusterings are shown to reflect underlying biological mechanisms. (c) 2005 Elsevier Ltd. All rights reserved.

Palladium(II) and platinum(II) complexes with tridentate iminophosphine ligands; synthesis and structural studies

The previously synthesised Schiff-base ligands 2-(2-Ph2PC6H4N = CH) - R' - C6H3OH (R' = 3-OCH3, HL1; 5-OCH3, HL2; 5-Br, HL3; 5-Cl, HL4) were prepared by a faster, more efficient route involving a microwave assisted co-condensation of 2-(diphenylphosphino) aniline with the appropriate substituted salicylaldehyde. HL1-4 react directly with (MCl2)-Cl-II (M = Pd, Pt) or (PtI2)-I-II(cod) affording neutral square-planar complexes of general formula [(MCl)-Cl-II(eta(3)-L1-4)] (M = Pd, Pt, 1 - 8) and [(PtI)-I-II(eta(3)-L1-4)] (M = Pd, Pt, 9 - 12). Reaction of complexes 1 - 4 with the triarylphosphines PR3 (R = Ph, p-tolyl) gave the novel ionic complexes [Pd-II(PR3)(eta(3)- L1-4)] ClO4 (13 - 20). Substituted platinum complexes of the type [Pt-II(PR3)(eta(3)- L1-4)] ClO4 (R = P(CH2CH2CN)(3) 21 - 24) and [Pt-II( P(p-tolyl)(3))(eta(3)-L-3,L-4)] ClO4 ( 25 and 26) were synthesised from the appropriate [(PtCl)-Cl-II(eta(3)-L1-4)] complex (5 - 8) and PR3. The complexes are characterised by microanalytical and spectroscopic techniques. The crystal structures of 3, 6, 10, 15, 20 and 26 were determined and revealed the metal to be in a square-planar four-coordinate environment containing a planar tridentate ligand with an O, N, P donor set together with one further atom which is trans to the central nitrogen atom.

Draft genome sequence of pseudomonas corrugata, a phytopathogenic bacterium with potential industrial applications

Pseudomonas corrugata was first described as the causal agent of a tomato disease called 'pith necrosis' yet it is considered as a biological resource in various fields such as biocontrol of plant diseases and production of industrially promising microbial biopolymers (mcl-PHA). Here we report the first draft genome sequence of this species.

Draft genome sequence of Pseudomonas corrugata, a phytopathogenic bacterium with potential industrial applications

Pseudomonas corrugata was first described as the causal agent of a tomato disease called ‘pith necrosis’ yet it is considered as a biological resource in various fields such as biocontrol of plant diseases and production of industrially promising microbial biopolymers (mcl-PHA). Here we report the first draft genome sequence of this species.

Polyhydroxyalkanoates production by actinobacteria isolated from soil

Polyhydroxyalkanoates (PHAs) are biodegradable and renewable polymers produced by a wide range of bacterial groups. New microbial bioprospection approaches have become an important way to find new PHA producers and new synthesized polymers. Over the past years, bacteria belonging to actinomycetes group have become known as PHA producers, such as Nocardia and Rhodococcus species, Kineosphaera limosa Liu et a]. 2002, and, more recently, Streptomyces species. In this paper, we disclose that there are more actinobacteria PHA producers in addition to the genera cited. Some unusual genera, such as Streptoalloteichus, and some genera frequently present in soil, such as Streptacidiphilus, have been found. Thirty-four isolates were able to accumulate poly(3-hydroxybutyrate) and a number of these have traces of poly(3-hydroxyvalerate) when cultivated on glucose or glucose and casein as carbon source. Furthermore, some strains showed traces of medium chain length PHA. Transmission electron microscopy demonstrated that the PHA accumulation occurs in hyphae and spores.

Cassava wastewater as a substrate for the simultaneous production of rhamnolipids and polyhydroxyalkanoates by Pseudomonas aeruginosa

Glycerol, cassava wastewater (CW), waste cooking oil and CW with waste frying oils were evaluated as alternative low-cost carbon substrates for the production of rhamnolipids and polyhydroxyalkanoates (PHAs) by various Pseudomonas aeruginosa strains. The polymers and surfactants produced were characterized by gas chromatography-mass spectrophotometry (MS) and by high-performance liquid chromatography-MS, and their composition was found to vary with the carbon source and the strain used in the fermentation. The best overall production of rhamnolipids and PHAs was obtained with CW with frying oil as the carbon source, with PHA production corresponding to 39% of the cell dry weight and rhamnolipid production being 660 mg l(-1). Under these conditions, the surface tension of the culture decreased to 30 mN m(-1), and the critical micelle concentration was 26.5 mg l(-1). It would appear that CW with frying oil has the highest potential as an alternative substrate, and its use may contribute to a reduction in the overall environmental impact generated by discarding such residues.

Lesões de cárie em esmalte submetidas a diferentes tratamentos com flúor tópico in situ

O presente estudo teve por objetivo avaliar se a aplicação tópica de flúor fosfato acidulado (FFA) em alta concentração tem efeito adicional no controle de lesões de esmalte, comparado ao uso de dentifrício fluoretado (baixa concentração). A freqüência de FFA como auxiliar no tratamento de lesões de cárie e a deposição de flúor no esmalte após diferentes aplicações de flúor am alta e baixa concentração também foram avaliadas. Para tanto, 5 indivíduos utilizaram, por 42 dias, próteses parciais removíveis inferiores contendo blocos de esmalte bovino desmineralizados. Os espécimes de esmalte forma divididos em 5 grupos: (1) escovação 3 vezes ao dia com dentifrício fluoretado (DF) (1100 ppm F), (2) DF+1 aplicação tópica FFA (12300 ppm F), (3) DF+2 FFA, (4) DF+3 FFA, e 5) DF+4 FFA. O intervalo entre as aplicações foi de uma semana. Cinco blocos hígidos e 5 blocos desmineralizados foram utilizados como controle e não foram submetidos ao período intraoral. As alterações clínicas foram registradas com relação à textura, coloração e brilho superficiais. Análises de microdureza superficial (MS) e em cortes longitudinais (MCL), de rugosidade superficial (RS) e de conteúdo de flúor depositado no esmalte foram realizadas. Modificações clínicas semelhantes de coloração foram observadas em todos os grupos após formação da lesão in vitro, apesar da ausência de mudanças na textura e brilho superficiais. Após escovação e tratamento com flúor, todos os blocos desmineralizados (esbranquiçados), independentemente do tratamento, tornaram-se mais amarelados. Não foram detectadas mudanças na textura e brilho superficiais. Os valores de MS e de conteúdo de flúor aumentaram (p<0,05) em relação aos blocos demineralizados somente a partir de 2 FFA. Os valores de MCL não mostraram diferenças entre os blocos tratados e os desmineralizados em qualquer distância da superfície do esmalte. Os grupos DF+3 FFA e DF+ 4 FFA foram os únicos capazes de aumentar os valores de MS em relação aos blocos desmineralizados. Estes tratamentos levaram a um aumento significativo de flúor solúvel e insolúvel comparado aos espécimes hígidos e desmineralizados. Ainda que todas as lesões tenham sido controladas clinicamente e não mostrem diferenças de microdureza, parece que aquelas tratadas com maior número de FFA produziram um maior reservatório de flúor disponível para inibir novos processos de desmineralização.

Avaliação dos parâmetros hematológicos e imunofenotípicos de pacientes com doenças linfoproliferativas crônicas no Rio Grande do Norte

Chronic lymphoproliferative disorders (DLPC) are lymphoid system diseases characterized by the abnormal proliferation of mature lymphocytes that affect B cells, T lymphocytes and NK cells. The aim of the study was to demonstrate the relevance of immunophenotyping by flow cytometry in patients with prolonged lymphocytosis and / or cytomorphological changes compatible with lymphoproliferative diseases. In this study 460 patients (244 men and 216 women) with DLPC were evaluated. Were analyzed by flow cytometry with a panel of monoclonal antibodies consisting of CD3, CD4, CD5, CD8, CD10, CD19, CD22, CD23, CD25, CD38, CD45, CD16/CD56, and HLADR heavy and light chains of immunoglobulins. It also examines information regarding age, gender of patients and laboratory data as leucocytes, cytomorphological analysis, platelet count and hemoglobin determination. The results showed 398 cases of chronic lymphoproliferative disorders and 62 of DLPC B cell lymphoproliferative diseases T. B showed the following distribution : 253 cases of chronic lymphocytic leukemia (CLL), 42 cases of multiple myeloma ( MM ), 37 cases of lymphoma non - Hodgkin lymphoma in leukemic phase (NHL) , 17 cases of pro- B lymphocytic leukemia ( B -PLL), 15 cases of mantle cell lymphoma (MCL ), 12 cases of plasma cell leukemia ( PCL), 9 cases of lymphoma Burkitt (Linf B), 8 cases of leukemia villous cells ( LCV), 3 cases of splenic lymphoma with villous cells (LECV), a case of follicular lymphoma (LF) and a Waldenströn macroglobulinemia ( MW). The diseases source NK / T were 23 cases of peripheral T cell lymphoma (LCTP), 14 cases of T prolymphocytic leukemia (T -PLL), 10 cases of leukemia T of large granular lymphocytes (LGL -T) 9 cases of leukemia cells of adult T (LCTA), 5 cases of Sezary syndrome (SS) and a case of large granular NK leukemia (LGL -NK) lymphocytes. In conclusion, the combined use of the monoclonal antibody panel careful cytomorphological analysis was shown to be essential in immune diagnosis and classification of chronic lymphoproliferative disorders. This study was approved by the IRB - HUOL under number 356 / 09

Polyhydroxybutyrate in Rhizobium and Bradyrhizobium: quantification and phbC gene expression

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

Antibody-targeted horseradish peroxidase associated with indole-3-acetic acid induces apoptosis in vitro in hematological malignancies

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

Estudo dos principais fatores que influenciam na solubilização dos hpas em águas

Polycyclic aromatic hydrocarbons (PAHs) constitute a family of compounds characterized by having two or more condensed aromatic rings and for being a class of substances that are widely distributed in the environment as a complex mixture, being very persistent in the environment due to its low solubility in water. The application of chemometric methods to analytical chemistry has provided excellent results in studying the solubility of PAHs in aqueous media in order to understand the mechanisms involved in environmental contamination. The method consists in analyzing the solubilization of PAHs from diesel oil in water varying parameters such as stirring time, volume of oil added and pH, using a full factorial design of two levels and three factors. PAHs were extracted with n-hexane and analyzed by fluorescence spectroscopy because they have molecular characteristics fluorescent due to the large number of condensed rings and links, and gas chromatography coupled to a mass spectrometer (GC-MS). The results of fluorescence analysis showed that only the stirring time and pH influenced the solubility of PAHs in diesel fuel. How is a non-selective technique for the study of fluorescence was performed on form and semi-quantitative. And for the chromatographic analysis the results showed that the solubility of the different PAHs is influenced differently so that you can classify them into groups by the results of the effects

Microdissecção e captura a laser na investigação do gene TP53 em tecidos incluídos em parafina

INTRODUÇÃO: Microdissecção e captura a laser (MCL) é uma técnica de desenvolvimento recente que permite a coleta de células individuais ou pequeno conjunto de células para análise molecular. Atualmente, no Brasil, há raros microscópios para MCL, de modo que a divulgação dos procedimentos inerentes a essa técnica é oportuna para destacar seu amplo potencial para diagnóstico e investigação. OBJETIVO: Este trabalho descreve a padronização dos procedimentos de MCL e de extração de DNA de material fixado em formalina e incluído em parafina. MATERIAL E MÉTODOS: Foram estudados o éxon 8 do gene TP53 e o gene da ciclofilina em amostras de tecido normal e de neoplasias de fígado e rim provenientes de modelo de carcinogênese química induzida em rato. A extração do DNA foi comprovada por reação em cadeia da polimerase (nested-PCR). RESULTADOS: Foram padronizados os procedimentos de preparo dos cortes histológicos, de microdissecção e captura a laser e de obtenção de seqüências gênicas pela reação de nested-PCR para tecidos incluídos em parafina. Obtivemos amplificação de 48,3% das amostras para o éxon 8 do gene TP53 e 51,7% para o gene da ciclofilina. Considerando pelo menos um dos dois segmentos gênicos, foram amplificadas 79,3% das amostras. DISCUSSÃO E CONCLUSÃO: A extração de DNA de tecidos fixados em formalina e incluídos em parafina e a técnica de nested-PCR foram adequadamente padronizadas para produtos gênicos de interesse, obtidos de material coletado por MCL. Esses procedimentos podem ser úteis para a obtenção de seqüências de DNA de arquivos para análise molecular.

Efeito protetor da microbiota cecal congelada e liofilizada sobre a infecção experimental de frangos de corte por Salmonella enterica sorovar Enteritidis

Estudaram-se os efeitos do tratamento de frangos de corte com microbiota cecal anaeróbia liofilizada (MCL) e congelada (MCC) sobre a infecção do trato digestivo das aves por Salmonella enterica sorovar Enteritidis. Foi usada microbiota intestinal sem prévia identificação bacteriana. A infecção foi persistente, em ordem, no ceco, inglúvio e duodeno. A infecção também foi autolimitante nos grupos tratados e no controle. Não ocorreu diferença entre o grupo-controle positivo e os tratados com MCL ou MCC. Houve redução da colonização do ceco no período de 12 dias após o desafio nos grupos tratados com MCL e MCC, o que não ocorreu no grupo-controle positivo. Não houve variação entre os tratamentos com MCL e MCC quanto às características pesquisadas. A S. Enteritidis reduziu o ganho de peso médio nas aves inoculadas. Os tratamentos com MCL e MCC minimizaram a redução de peso nos grupos infectados.

Shear bond strength of metal-ceramic repair systems

Statement of problem. When clinical fractures of the ceramic veneer on metal-ceramic prostheses can be repaired, the need for remake may be eliminated or postponed. Many different ceramic repair materials are available, and bond strength data are necessary for predicting the success of a given repair system.Purpose. This study evaluated the shear bond strength of different repair systems for metal-ceramic restorations applied on metal and porcelain.Material and methods. Fifty cylindrical specimens (9 X 3 mm) were fabricated in a nickel-chromium alloy (Vera Bond 11) and 50 in feldspathic porcelain (Noritakc). Metal (M) and porcelain (P) specimens were embedded in a polyvinyl chloride (PVC) ring and received I of the following bonding and resin composite repair systems (n=10): Clearfil SE Bond/Clearfil AP-X (CL), Bistite II DC/Palfique (BT), Cojet Sand/Z100 (Q), Scotchbond Multipurpose Plus/Z100 (SB) (control group), or Cojet Sand plus Scotchbond Multipurpose Plus/Z100 (CJSB). The specimens were stored in distilled water for 24 hours at 37 degrees C, thermal cycled (1000 cycles at 5 degrees C to 55 degrees C), and stored at 37 degrees C for 8 days. Shear bond tests between the metal or ceramic specimens and repair systems were performed in a mechanical testing machine with a crosshead speed of 0.5 mm/min. Mean shear bond strength values (MPa) were submitted to 1-way ANOVA and Tukey honestly significant difference tests (alpha=.05). Each specimen was examined under a stereoscopic lens with X 30 magnification, and mode of failure was classified as adhesive, cohesive, or a combination.Results. on metal, the mean shear bond strength values for the groups were as follows: MCL, 18.40 +/- 2.88(b); MBT, 8.57 +/- 1.00(d); MCJ, 25.24 +/- 3.46(a); MSB, 16.26 +/- 3.09(bc); and MCJSB, 13.11 +/- 1.24(c). on porcelain, the mean shear bond strength values ofeach group were as follows: PCL, 16.91 +/- 2.22(b); PBT, 18.04 +/- 3.2(ab); PCJ, 19.54 +/- 3.77(ab); PSB, 21.05 +/- 3.22(a); and PCJSB, 16.18 +/- 1.71(b). Within each substrate, identical superscript letters denote no significant differences among groups.Conclusions. The bond strength for the metal substrate was significantly higher using the Q system. For porcelain, SB, Q, and BT systems showed the highest shear bond strength values, and only SB was significantly different compared to CL and CJSB (P <.05).

Peroxidase and phenylalanine ammonia-lyase activities, phenolic acid contents, and allelochemicals-inhibited root growth of soybean

The influence of the allelochemicals ferulic (FA) and vanillic (VA) acids on peroxidase (POD, EC 1.11.1.7) and phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) activities and their relationships with phenolic acid (PhAs) contents and root growth of soybean (Glycine max (L.) Merr.) were examined. Three-day-old seedlings were cultivated in nutrient solution containing FA or VA (0.1 to 1 mM) for 48 h. Both compounds (at 0.5 and 1 mM) decreased root length (RL), fresh weight (FW) and dry weight (DW) and increased PhAs contents. At 0.5 and 1 mM, FA increased soluble POD activity (18% and 47%, respectively) and cell wall (CW)-bound POD activity (61% and 34%), while VA increased soluble POD activity (33% and 17%) but did not affect CW-bound POD activity. At I mM, FA increased (82%) while VA reduced (32%) PAL activities. The results are discussed on the basis of the role of these compounds on phenylpropanoid metabolism and root growth and suggest that the effects caused on POD and PAL activities are some of the many mechanisms by which allelochemicals influence plant growth.