Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci

It has been postulated that noncoding RNAs (ncRNAs) are involved in the posttranscriptional control of gene expression, and may have contributed to the emergence of the complex attributes observed in mammalians. We show here that the complement of ncRNAs expressed from intronic regions of the human and mouse genomes comprises at least 78,147 and 39,660 transcriptional units, respectively. To identify conserved intronic sequences expressed in both humans and mice, we used custom-designed human cDNA microarrays to separately interrogate RNA from mouse and human liver, kidney, and prostate tissues. An overlapping tissue expression signature was detected for both species, comprising 198 transcripts; among these, 22 RNAs map to intronic regions with evidence of evolutionary conservation in humans and mice. Transcription of selected human-mouse intronic ncRNAs was confirmed using strand-specific RT-PCR. Altogether, these results support an evolutionarily conserved role of intronic ncRNAs in human and mouse, which are likely to be involved in the fine tuning of gene expression regulation in different mammalian tissues. (C) 2008 Elsevier Inc. All rights reserved.

Ecologia da comunidade de diatomáceas epilíticas de um sistema de rio de baixa ordem da região hidrográfica do Guaíba : subsídios ao monitoramento ambiental de ecossistemas aquáticos sul brasileiros

Os sistemas de monitoramento utilizando diatomáceas foram desenvolvidos, em sua maioria, para monitorar os efeitos da poluição orgânica e da eutrofização, adotando como parâmetros de referência a demanda biológica de oxigênio após cinco dias e a concentração de fósforo total. Entretanto, vários fatores naturais têm sido apontados como causadores de variação na composição destas comunidades em rios. Por isso, grandes mudanças estruturais não provam necessariamente a hipótese de que tenha ocorrido algum evento poluidor. Neste contexto, a partir da relação entre a estrutura da comunidade de diatomáceas epilíticas da microbacia do arroio Schmidt, RS, Brasil, mudanças na qualidade da água e alterações físicas do meio, como fluxo, sombreamento ripário, largura e profundidade, objetivou-se colher subsídios para aplicação em programas de manejo e conservação de ecossistemas aquáticos. Durante os meses de janeiro e fevereiro de 2004, foram realizadas quatro excursões científicas a seis estações, totalizando 24 amostragens, para medição das seguintes variáveis: condutividade elétrica, oxigênio dissolvido em saturação, pH, turbidez, demanda biológica de oxigênio em cinco dias (DBO5), demanda química de oxigênio (DQO), fósforo total, nitrato, sólidos totais dissolvidos, sólidos suspensos, sílica, profundidade de submersão do substrato, velocidade da correnteza, diâmetro dos seixos, largura do rio e sombreamento em função da vegetação ripária. Para as análises qualitativas e quantitativas das diatomáceas epilíticas, uma área de 25 cm2 foi raspada de cinco replicatas O material foi oxidado com dicromato de potássio, ácido sulfúrico e clorídrico para confecção de lâminas permanentes. Padrões de distribuição e abundância das espécies foram explorados através da Análise de Espécies Indicadoras e os fatores ambientais responsáveis por esta distribuição foram evidenciados pela Análise de Correspondência Canônica. Os resultados confirmaram a preferência de Cymbella e Encyonema por águas lentas e elevada luminosidade, bem como a adaptabilidade de Cocconeis ao sombreamento. Nitzschia acicularis, Surirella tenera e Planothidium rupestoides revelaram-se indicadoras de ambientes meso-eutróficos. Encyonema perpusilum destacou-se no habitat oligo/β- mesossapróbico, e Sellaphora pupula no sítio de maior concentração de eletrólitos. Pelo cruzamento das respostas das espécies à saturação de oxigênio, DBO5, DQO, condutividade, fósforo total, sólidos totais dissolvidos e turbidez, foi possível estabelecer dois grupos sinalizadores de qualidade: Achnanthes sp. 3, Cocconeis fluviatilis, Navicula angusta, Nitzschia acicularis, Tryblionella victoriae, Pinnularia cf. obscura, Planothidium rupestoides, Sellaphora pupula, Stenopterobia sp. e Surirella tenera, relacionadas com maior impacto antropogênico, e Achnanthes sp. 2, Encyonema perpusilum, Geissleria aikenensis, Luticola goeppertiana, Navicula symmetrica e Nitzschia amphibia, referindo-se a ambientes mais oxigenados, pouco mineralizados e com reduzidos teores de compostos orgânicos. Estas informações também constituem subsídios para estudos paleolimnológicos envolvendo a reconstituição de paleoambientes (e.g. maior abundância de Cymbella indicando ambientes lênticos) e a concentração de paleonutrientes (e.g. Nitzschia acicularis designando períodos de maior eutrofização).

Transcriptoma diferencial entre células-tronco mesenquimais humanas jovens e senescentes

Human mesenchymal stem cells (MSC) are powerful sources for cell therapy in regenerative medicine. The long time cultivation can result in replicative senescence or can be related to the emergence of chromosomal alterations responsible for the acquisition of tumorigenesis features in vitro. In this study, for the first time, the expression profile of MSC with a paracentric chromosomal inversion (MSC/inv) was compared to normal karyotype (MSC/n) in early and late passages. Furthermore, we compared the transcriptome of each MSC in early passages with late passages. MSC used in this study were obtained from the umbilical vein of three donors, two MSC/n and one MSC/inv. After their cryopreservation, they have been expanded in vitro until reached senescence. Total RNA was extracted using the RNeasy mini kit (Qiagen) and marked with the GeneChip ® 3 IVT Express Kit (Affymetrix Inc.). Subsequently, the fragmented aRNA was hybridized on the microarranjo Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix Inc.). The statistical analysis of differential gene expression was performed between groups MSC by the Partek Genomic Suite software, version 6.4 (Partek Inc.). Was considered statistically significant differences in expression to p-value Bonferroni correction ˂.01. Only signals with fold change ˃ 3.0 were included in the list of differentially expressed. Differences in gene expression data obtained from microarrays were confirmed by Real Time RT-PCR. For the interpretation of biological expression data were used: IPA (Ingenuity Systems) for analysis enrichment functions, the STRING 9.0 for construction of network interactions; Cytoscape 2.8 to the network visualization and analysis bottlenecks with the aid of the GraphPad Prism 5.0 software. BiNGO Cytoscape pluggin was used to access overrepresentation of Gene Ontology categories in Biological Networks. The comparison between senescent and young at each group of MSC has shown that there is a difference in the expression parttern, being higher in the senescent MSC/inv group. The results also showed difference in expression profiles between the MSC/inv versus MSC/n, being greater when they are senescent. New networks were identified for genes related to the response of two of MSC over cultivation time. Were also identified genes that can coordinate functional categories over represented at networks, such as CXCL12, SFRP1, xvi EGF, SPP1, MMP1 e THBS1. The biological interpretation of these data suggests that the population of MSC/inv has different constitutional characteristics, related to their potential for differentiation, proliferation and response to stimuli, responsible for a distinct process of replicative senescence in MSC/inv compared to MSC/n. The genes identified in this study are candidates for biomarkers of cellular senescence in MSC, but their functional relevance in this process should be evaluated in additional in vitro and/or in vivo assays

Whole-genome expression profiling of Xylella fastidiosa in response to growth on glucose

Xylella fastidiosa is the etiologic agent of diseases in a wide range of economically important crops including citrus variegated chlorosis, a major threat to the Brazilian citrus industry. The genomes of several strains of this phytopathogen have been completely sequenced enabling large-scale functional studies. In this work we used whole-genome DNA microarrays to investigate the transcription profile of X. fastidiosa grown in defined media with different glucose concentrations. Our analysis revealed that while transcripts related to fastidian gum production were unaffected, colicin-V-like and fimbria precursors were induced in high glucose medium. Based on these results, we suggest a model for colicin-defense mechanism in X. fastidiosa.

Signal transduction-related responses to phytohormones and environmental challenges in sugarcane

Background: Sugarcane is an increasingly economically and environmentally important C4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. Sugarcane originated from crosses of Saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. Environmental stresses limit enormously sugarcane productivity worldwide. To investigate transcriptome changes in response to environmental inputs that alter yield we used cDNA microarrays to profile expression of 1,545 genes in plants submitted to drought, phosphate starvation, herbivory and N-2-fixing endophytic bacteria. We also investigated the response to phytohormones (abscisic acid and methyl jasmonate). The arrayed elements correspond mostly to genes involved in signal transduction, hormone biosynthesis, transcription factors, novel genes and genes corresponding to unknown proteins.Results: Adopting an outliers searching method 179 genes with strikingly different expression levels were identified as differentially expressed in at least one of the treatments analysed. Self Organizing Maps were used to cluster the expression profiles of 695 genes that showed a highly correlated expression pattern among replicates. The expression data for 22 genes was evaluated for 36 experimental data points by quantitative RT-PCR indicating a validation rate of 80.5% using three biological experimental replicates. The SUCAST Database was created that provides public access to the data described in this work, linked to tissue expression profiling and the SUCAST gene category and sequence analysis. The SUCAST database also includes a categorization of the sugarcane kinome based on a phylogenetic grouping that included 182 undefined kinases.Conclusion: An extensive study on the sugarcane transcriptome was performed. Sugarcane genes responsive to phytohormones and to challenges sugarcane commonly deals with in the field were identified. Additionally, the protein kinases were annotated based on a phylogenetic approach. The experimental design and statistical analysis applied proved robust to unravel genes associated with a diverse array of conditions attributing novel functions to previously unknown or undefined genes. The data consolidated in the SUCAST database resource can guide further studies and be useful for the development of improved sugarcane varieties.

Estudos sedimentológicos e o contexto estrutural da formação Serra do Martins, nos platôs de Portalegre, Martins e Santana/RN

This dissertation deals with sedimentological and structural framework of the siliciclastic rock of the Serra do Martins Formation (FSM) in the Portalegre, Martins and Santana plateau, located to the south of Potiguar Basin, in the southwest and central Rio Grande do Norte state. This formation, regarded as of Oligo-Miocene age based on intrusive relations of the Miocene Macau volcanics, has a still disputable age due to the lack of appropriate bio and/or chronostratigraphic markers. The FSSM deposits crop out along 650 to 750 m high plateau, as a remanescent sedimentary cover directly overlying topographically uplifted pre-cambrian crystalline rocks. During the last decades, these deposits were interpreted according to a Tertiary paleoclimatic evolutionary model, associated to pedogenetic processes. The sedimentological characterization of the FSM was done through a detailed study of its facies, petrography and diagenetic features. The facies study was based on description of field relations, textures and structures, the piling up of the strata and their lateral variations. The FSM was deposited by an anastomosing to coarse-meandering fluvial system, including deposits of lag, cannel-fill, ouver-bank and flood plain. The petrographic composition of the sediments, coupled to their facies and paleocurrent directions, suggest a rather distal sourcearea, to the south of the present plateau. The diagenetic study identified an incipient grain mechanical compaction, pronounced dissolution of the framework, matrix and/or cement components, intense precipitation of kaolinite, silic and, eventually, iron oxides, besides mechanical infiltration of the clays. Most of these events, regarded in the literature as associated to near-surface conditions (eo or telodiagenesis), indicate the FSM sediments were never deeply buried. Topographic relations along longitudinal and transversal sections reaching the Potiguar Basin to the north identified regional dips that allow to discuss stratigraphic correlations between the FSM and the basin formations. The sedimentological features of the different units and the intrusive relations of the Macau volcanics were also considered in these correlations,which support the Oligo-Miocene age previously accepted for the FSM. Concerning the tectonic framework of the FSM, this work investigated the pre-cambrian to cretaceous heritage and the cenozoic deformation, allowing the recognition of pre-, sin and post-FSM structures. The crystalline basement, belonging to the Seridó Belt, displays NE and WNW foliation trends related to the Brasiliano-age ductile shear zones. In this terrain, brittle-ductile and brittle NE- and NW-trending structures, associated with extensional joints filled with pegmatites and quartz veins, are related to an E-W compression by the end of Brasiliano Cycle. The E-W joints and NE-trending fractures were reactivated by N-S to N-S to NW extension during late Jurassic to Cretaceous times, controlling the emplacement of the Rio Ceará-Mirim basic dyke swarm and the opening of the Potiguar rift basin

Transcriptional Profile of Diuron-Induced Toxicity on the Urinary Bladder of Male Wistar Rats to Inform Mode of Action

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

Expression of genes related to apoptosis, cell cycle and signaling pathways are independent of TP53 status in urinary bladder cancer cells

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

A genômica funcional no âmbito da produção animal: estado da arte e perspectivas

Os últimos vinte anos caracterizaram-se pela proliferação de tecnologias que tornaram possível decifrar o genoma das espécies, localizar e identificar particularidades na sua seqüência, elucidar as suas funções dentro dos sistemas biológicos e, sobretudo, começar a entender os mecanismos que controlam as interações entre os genótipos e os estímulos ambientais, que são responsáveis pela diversidade fenotípica. Estes estudos sobre as bases moleculares da variabilidade fenotípica abriram uma nova abordagem científica, caracterizada pela multiplicidade das questões envolvidas, que resultou no surgimento de novas áreas de pesquisa, cujos conhecimentos estão sendo aplicados em diversos campos da biologia, inclusive na zootecnia. Tendo em vista o grande impacto que tais conhecimentos estão tendo sobre a compreensão dos fenômenos biológicos, parece ser oportuno fazer uma avaliação das potencialidades de aplicação das abordagens de Genômica Funcional em pesquisas de nutrição e alimentação de ruminantes. Nesse contexto, este artigo está focado na descrição das principais ferramentas genômicas disponíveis e na discussão sobre a viabilidade de se utilizar as informações por elas geradas em benefício da produção animal.

Chicken skeletal muscle-associated macroarray for gene discovery

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Loss of Expression and Function of SOCS3 Is an Early Event in HNSCC: Altered Subcellular Localization as a Possible Mechanism Involved in Proliferation, Migration and Invasion

Background: Suppressor of cytokine signaling 3 (SOCS3) is an inducible endogenous negative regulator of signal transduction and activator of transcription 3 (STAT3). Epigenetic silencing of SOCS3 has been shown in head and neck squamous cell carcinoma (HNSCC), which is associated with increased activation of STAT3. There is scarce information on the functional role of the reduction of SOCS3 expression and no information on altered subcellular localization of SOCS3 in HNSCC.Methodology/Principal Findings: We assessed endogenous SOCS3 expression in different HNSCC cell lines by RT-qPCR and western blot. Immunofluorescence and western blot were used to study the subcellular localization of endogenous SOCS3 induced by IL-6. Overexpression of SOCS3 by CMV-driven plasmids and siRNA-mediated inhibition of endogenous SOCS3 were used to verify the role of SOCS3 on tumor cell proliferation, viability, invasion and migration in vitro. In vivo relevance of SOCS3 expression in HNSCC was studied by quantitative immunohistochemistry of commercially-available tissue microarrays. Endogenous expression of SOCS3 was heterogeneous in four HNSCC cell lines and surprisingly preserved in most of these cell lines. Subcellular localization of endogenous SOCS3 in the HNSCC cell lines was predominantly nuclear as opposed to cytoplasmic in non-neoplasic epithelial cells. Overexpression of SOCS3 produced a relative increase of the protein in the cytoplasmic compartment and significantly inhibited proliferation, migration and invasion, whereas inhibition of endogenous nuclear SOCS3 did not affect these events. Analysis of tissue microarrays indicated that loss of SOCS3 is an early event in HNSCC and was correlated with tumor size and histological grade of dysplasia, but a considerable proportion of cases presented detectable expression of SOCS3.Conclusion: Our data support a role for SOCS3 as a tumor suppressor gene in HNSCC with relevance on proliferation and invasion processes and suggests that abnormal subcellular localization impairs SOCS3 function in HNSCC cells.

Aquatic macrophyte distribution in relation to water and sediment conditions in the Itaipu Reservoir, Brazil

Aquatic macrophyte community distribution along the eastern shoreline of the Itaipu Reservoir (one of the South America's largest impoundments) is described in relation to limnological and sedimentological factors. The central body of the reservoir is mesotrophic, while the arms (flooded influent river valleys) along the eastern shore may be oligo-mesotrophic to eutrophic, depending on time of year and sub-catchment characteristics. Macrophyte community composition and species cover were surveyed at 30 sites in four arms, in relation to sediment total P and organic matter; underwater light regime; and water total P and Kjeldahl N concentration, alkalinity, conductivity, depth and pH. Seventeen euhydrophyte and six emergent macrophyte species were recorded. Large stands of Egeria najas dominated the euhydrophyte vegetation, together with free-floating weed species (Pistia stratiotes Linn., Salvinia auriculata Aublet and Eichhornia crassipes (Mart.) Solms.). Canonical Correspondence Analysis of the data showed that two sets of variables were important predictors of aquatic macrophyte community structure. Floating macrophyte assemblage was closely related to concentration of nutrients in both water and sediment, while light penetration was the strongest predictor of submerged species occurrence. Although a large number of potential nuisance species were present, dense growths were restricted to shallower areas of the Itaipu Reservoir, causing localised problems. The possibility of increasing interference by these plants with fisheries, recreational use, transport and hydroelectricity generation suggests a need for continued monitoring of weed distribution and abundance, and investigation of appropriate management measures.

A degenerate primer allows amplification of part of the 3 '-terminus of three distinct carlavirus species

Sequences of the coat protein amino acids of definitive and tentative species of carlaviruses deposited in GenBank were aligned and a region of seven amino acids (GLGVPTE) was found to be conserved. The corresponding nucleotides were aligned, allowing the design of a degenerate primer that together with an oligo dT anti-sense primer, was effective for the detection of three distinct carlavirus species, two transmitted by aphids and one by whitefly. These primers have the advantage that about 940 nt from the 3'-terminus, comprising part of the CP gene (about 60%), the 11 K gene, and the terminal untranslated region can be amplified for sequencing. The fact that this amino acid sequence is conserved in almost all of the sequenced carlaviruses, allows the prediction that this primer pair will be useful as a diagnostic tool for carlavirus species. (C) 2007 Elsevier B.V. All rights reserved.

Production of DNA microarray and expression analysis of genes from Xylella fastidiosa in different culture media

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

Loss of RKIP expression during the carcinogenic evolution of endometrial cancer

Aims Endometrial cancer is one of the most common cancers in women worldwide, but there is a lack of diagnostic markers for early detection of these tumours. The raf kinase inhibitory protein (RKIP) negatively regulates the Raf/MEK/ERK pathway, and the downregulation of RKIP is associated with tumour progression and metastasis in several human neoplasms. The aim of this study was to assess the expression levels of RKIP in endometrial cancer and determine whether this expression correlates with clinical outcome in these patients.Methods Tissue microarrays constructed using tissue samples from 209 endometrial adenocarcinomas, 49 endometrial polyps and 48 endometrial hyperplasias were analysed for RKIP expression by immunohistochemistry.Results The authors found that RKIP expression decreases significantly during malignant progression of endometrial cancer; it is highly expressed in non-neoplastic tissues (polyps 79.6%; hyperplasias 87.5%) and expressed at very low levels in endometrioid adenocarcinomas (29.7%). No correlations were observed between RKIP expression, clinicopathological data and survival.Conclusion This study demonstrated for the first time that RKIP expression is lost during the carcinogenic evolution of endometrial tumours and that the loss of RKIP expression is associated with a malignant phenotype. Functional studies are needed to address the biological role of RKIP downregulation in endometrial cancer.