El proyecto genómico del hongo Ophiostoma

The Canadian Ophiostoma Genome Project, which was initiated in 2001, is a collaborative effort between research teams in four different universities. Its general objective is to conduct a large-scale identification and analysis of genes controlling important aspects of the life cycle of Ophiostomatoid fungi. To this end, several expressed sequence tag (EST) libraries were obtained for the Dutch elm disease pathogen Ophiostoma novo-ulmi and the sapstainer O. piceae, following partial, single-pass automated sequencing of complementary DNA clones. The largest EST library, prepared from yeast like cells of O. novo-ulmi grown at 24 °C, contains over 3,400 readable sequences and serves as a general reference library for Ophiostomatoid fungi. Smaller, specific EST libraries were constructed from mycelia of O. novo-ulmi grown at suboptimal temperatures, from perithecia formed in laboratory crosses, as well as from O. piceae grown on different carbon sources. Ongoing bioinformatic searches in public databases have so far identified over 750 Ophiostoma unique ESTs which show significant homology with other fungal genes of known function, although a high proportion of Ophiostoma ESTs are either orphans (no match to any known gene) or show homology to genes of unknown function. In addition to EST analysis, differential expression of selected genes and structural genomics are also being studied.El programa canadiense sobre el genoma de Ophiostoma, iniciado en 2001, es una colaboración entre equipos de investigación de cuatro universidades diferentes. Su objetivo general es el desarrollo de la identificación y análisis a gran escala de los genes que controlan algunos aspectos importantes del ciclo vital de los hongos de Ophiostoma. Con este fin, se ha obtenido diversas bibliotecas de marcadores de secuencias expresadas (bibliotecas EST) para la el patógeno de la grafiosis Ophiostoma novo-ulmi y para el hongo de tinción vascular O. piceae, seguido de una secuenciación automática parcial de un único paso de clones complementarios de ADN. La mayor biblioteca EST, preparada a partir de conidios de O. novo-ulmi cultivadas a 24 ºC, contiene más de 3.400 secuencias legíbles, y sirve como biblioteca de referencia para los hongos de Ophiostoma. Se han desarrollado bibliotecas específicas menores a partir de micelios de O. novo-ulmi cultivados a temperaturas sub-óptimas, a partir de los peritecios formados en cruces realizados en laboratorio, así como a partir de O. piceae cultivado en distintas fuentes de carbón. Las búsquedas bioinformáticas en bases de datos públicas han permitido identificar hasta ahora más de 750 EST exclusivos de Ophiostoma, lo que muestra una significativa homología con otros genes fúngicos de función conocida, aunque una alta proporción de los EST de Ophiostoma son o bien huérfanos (no relacionados con ningún gen conocido), o bien muestran homología con genes cuya función es desconocida. Además del análisis EST, la expresión diferencial de genes seleccionados y la estructura genómica están siendo también estudiadas

The landscape of somatic copy-number alteration across human cancers

available in PMC 2010 August 18.A powerful way to discover key genes with causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here we present high-resolution analyses of somatic copy-number alterations (SCNAs) from 3,131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across several cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several gene families are enriched among these regions of focal SCNA, including the BCL2 family of apoptosis regulators and the NF-κΒ pathway. We show that cancer cells containing amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend on the expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in several cancer types.National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, P50CA90578)National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, R01CA109038))National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, R01CA109467)National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, P01CA085859)National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, P01CA 098101)National Institutes of Health (U.S.) (Dana-Farber/Harvard Cancer Center and Pacific Northwest Prostate Cancer SPOREs, K08CA122833

The landscape of somatic copy-number alteration across human cancers

A powerful way to discover key genes playing causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here, we report high-resolution analyses of somatic copy-number alterations (SCNAs) from 3131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across multiple cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several gene families are enriched among these regions of focal SCNA, including the BCL2 family of apoptosis regulators and the NF-κB pathway. We show that cancer cells harboring amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend upon expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in multiple cancer types

Vascular endothelial growth factor in gingival tissues and crevicular fluids of diabetic and healthy periodontal patients

WOS: 000189110800011PubMed ID: 15025220Background: Periodontal disease is one of the major oral problems encountered in patients with diabetes mellitus (DM). Vascular changes, neutrophil dysfunction, altered collagen synthesis, and genetic predisposition observed in DM may contribute to periodontitis; and the vascular alterations observed in such patients may depend on vascular endothelial growth factor (VEGF) actions. Few reports are available about the mechanism of neovascularization and the angiogenic factors that contribute to the periodontal pathology and the role of VEGF in periodontal diseases. The aim of this study is to compare VEGF expression in healthy and periodontally diseased tissues with gingival crevice fluid (GCF) of healthy persons and diabetic patients. Methods: Gingival tissue and GCF samples were collected from sites of periodontitis in 10 healthy subjects and in 10 type 2 diabetic patients, and from the sites of healthy gingiva within the same groups. Therefore, each patient became his/her own control. Additionally, 10 people without any systemic or periodontal diseases were enrolled, forming a negative control group. Thus, a total of 50 tissue and 50 GCF samples were provided. Results: No VEGF staining was observed in the negative control group or in the systemically healthy people's healthy tissue samples, whereas four samples of diabetic patients showed positive staining (P 0.05). In all test groups, GCF VEGF levels were higher in periodontal sites (P <0.05) than in healthy sites. Conclusion: The results of this study showed that VEGF is increased in all periodontal tissues of both groups and in the healthy sites of diabetic patients. Additionally, GCF VEGF values increased in periodontal sites of all test groups

Stress corrosion cracking of alpha-beta brass in distilled water and sodium sulfate solutions

Specimens of a Cu-42 wt pct Zn alpha-beta alloy have been tested to failure in uniaxial tension at constant extension rates in a variety of environments. Testing in distilled H25O and 1 N Na2SO4 solutions over a range of potential-pH conditions results in large ductility losses and an interfacial + transgranular cleavage-like fracture mode. The electrochemical potentials of the specimens have been monitored and/or controlled during testing, and a shift to significantly more active open circuit potentials on straining is observed in environments which cause large ductility losses. The appearance of the transgranular beta fracture surfaces and the effects of potentiostatic polarization on the observed SCC behavior are similar to those seen for alpha phase Cu-Zn, which suggests that SCC of alpha and beta phase Cu-Zn are mechanistically similar. It is concluded that the observed behavior is most consistent with an SCC mechanism based upon the adsorption of a damaging species from the environment. © 1985 The Metallurgical Society of American Institute of Mining