Avaliação espaço-temporal das armazenagens gravimétrica e volumétrica da água num Latossolo com citros

A estabilidade temporal é descrita como a persistência temporal de um padrão espacial e é avaliada pela análise de correlação de medidas em datas sucessivas. Neste trabalho, foi avaliada a armazenagem de água no solo em duas transeções de 76 m cada, contendo 20 pontos em cada uma. em um Latossolo Vermelho-Amarelo argissólico cultivado com citros com 11 anos em Piracicaba/SP. A umidade do solo para determinação da armazenagem, na camada de 0,00-1,10 m, ao longo do tempo, foi obtida com uma sonda de nêutrons, calibrada para o solo em estudo, realizando leituras semanais às profundidades de 0,20, 0,40, 0,60, 0,80, 1,0 e 1,10 m. A armazenagem de água no solo foi determinada utilizando-se o método de Simpson. Os dados da armazenagem média de água no solo nos três anos de estudo mostraram que sua distribuição, ao longo do tempo, apresentou comportamento semelhante e que os coeficientes de correlação linear e de posição de Spearman foram altos entre o ano 1 e o ano 2, o ano 2 e o ano 3 e o ano 1 e o ano 3, indicando existência de estabilidade temporal e persistência temporal significativa do padrão espacial observado. Foi verificada dependência espacial moderada de 17,10 m pelo semivariograma exponencial. Pela técnica da diferença relativa, os pontos que apresentaram comportamento estável no tempo foram o ponto 29, para os anos 1 e 2, e os pontos 16, 29 e 39, para o ano 3, que podem ser usados para estimar com segurança a armazenagem média de água no solo. O ponto 29 foi o que se apresentou estável para os três anos de estudo, sendo, portanto, o mais recomendável tanto para a armazenagem gravimétrica como para a volumétrica.

Establishment of the epithelial-specific transcriptome of normal and malignant human breast cells based on MPSS and array expression data.

INTRODUCTION: Diverse microarray and sequencing technologies have been widely used to characterise the molecular changes in malignant epithelial cells in breast cancers. Such gene expression studies to identify markers and targets in tumour cells are, however, compromised by the cellular heterogeneity of solid breast tumours and by the lack of appropriate counterparts representing normal breast epithelial cells. METHODS: Malignant neoplastic epithelial cells from primary breast cancers and luminal and myoepithelial cells isolated from normal human breast tissue were isolated by immunomagnetic separation methods. Pools of RNA from highly enriched preparations of these cell types were subjected to expression profiling using massively parallel signature sequencing (MPSS) and four different genome wide microarray platforms. Functional related transcripts of the differential tumour epithelial transcriptome were used for gene set enrichment analysis to identify enrichment of luminal and myoepithelial type genes. Clinical pathological validation of a small number of genes was performed on tissue microarrays. RESULTS: MPSS identified 6,553 differentially expressed genes between the pool of normal luminal cells and that of primary tumours substantially enriched for epithelial cells, of which 98% were represented and 60% were confirmed by microarray profiling. Significant expression level changes between these two samples detected only by microarray technology were shown by 4,149 transcripts, resulting in a combined differential tumour epithelial transcriptome of 8,051 genes. Microarray gene signatures identified a comprehensive list of 907 and 955 transcripts whose expression differed between luminal epithelial cells and myoepithelial cells, respectively. Functional annotation and gene set enrichment analysis highlighted a group of genes related to skeletal development that were associated with the myoepithelial/basal cells and upregulated in the tumour sample. One of the most highly overexpressed genes in this category, that encoding periostin, was analysed immunohistochemically on breast cancer tissue microarrays and its expression in neoplastic cells correlated with poor outcome in a cohort of poor prognosis estrogen receptor-positive tumours. CONCLUSION: Using highly enriched cell populations in combination with multiplatform gene expression profiling studies, a comprehensive analysis of molecular changes between the normal and malignant breast tissue was established. This study provides a basis for the identification of novel and potentially important targets for diagnosis, prognosis and therapy in breast cancer.

Macrofauna do solo influenciada pelo uso de fertilizantes químicos e dejetos de suínos no oeste do estado de Santa Catarina

Este estudo objetivou avaliar o efeito da adição de doses crescentes de dejetos de suínos, adubação organomineral e adubação mineral sobre a abundância e diversidade da macrofauna edáfica. O estudo foi realizado no município de Campos Novos, SC, em um Latossolo Vermelho distroférrico, cultivado anualmente com milho (Zea mays) e aveia (Avena sativa), em sucessão e semeadura direta. Os seis tratamentos utilizados foram: testemunha (TT); adubação mineral (AM); adubação organomineral (AOM); adubação orgânica na doses de 3 t ha-1 (AO3); 6 t ha-1 (AO6) e 12 t ha-1 (AO12) de dejeto de suínos em base seca. O fertilizante mineral foi aplicado em semeadura na linha do plantio e a adubação orgânica, após semeadura do milho. A macrofauna edáfica foi avaliada utilizando-se um amostrador cilíndrico com 17 cm de diâmetro, coletando-se amostras de solo na profundidade de 0-10 cm. As amostragens foram realizadas em três épocas: a primeira em 5/5/2005 (um mês após a colheita do milho), a segunda em 9/09/2005 (sob a cultura de aveia), e a terceira em 23/1/2006 (sob a cultura do milho). A diversidade de organismos foi avaliada por meio dos índices de Shannon, Simpson e Pielou, riqueza de grupos, abundância e análise de agrupamento. A freqüência relativa das ordens foi afetada pela adição do dejeto suíno, sendo os grupos mais freqüentes Hymenoptera e Oligochaeta, variando conforme o tratamento e a época de amostragem. A maior diversidade da macrofauna foi encontrada no tratamento AOM, demonstrando que a macrofauna edáfica foi influenciada pela adição consorciada das diferentes formas de adubação.

Rational design of indoleamine 2,3-dioxygenase inhibitors.

Indoleamine 2,3-dioxygenase (IDO) is an important therapeutic target for the treatment of diseases such as cancer that involve pathological immune escape. We have used the evolutionary docking algorithm EADock to design new inhibitors of this enzyme. First, we investigated the modes of binding of all known IDO inhibitors. On the basis of the observed docked conformations, we developed a pharmacophore model, which was then used to devise new compounds to be tested for IDO inhibition. We also used a fragment-based approach to design and to optimize small organic molecule inhibitors. Both approaches yielded several new low-molecular weight inhibitor scaffolds, the most active being of nanomolar potency in an enzymatic assay. Cellular assays confirmed the potential biological relevance of four different scaffolds.

Identification of CT46/HORMAD1, an immunogenic cancer/testis antigen encoding a putative meiosis-related protein.

Transcripts with ESTs derived exclusively or predominantly from testis, and not from other normal tissues, are likely to be products of genes with testis-restricted expression, and are thus potential cancer/testis (CT) antigen genes. A list of 371 genes with such characteristics was compiled by analyzing publicly available EST databases. RT-PCR analysis of normal and tumor tissues was performed to validate an initial selection of 20 of these genes. Several new CT and CT-like genes were identified. One of these, CT46/HORMAD1, is expressed strongly in testis and weakly in placenta; the highest level of expression in other tissues is <1% of testicular expression. The CT46/HORMAD1 gene was expressed in 31% (34/109) of the carcinomas examined, with 11% (12/109) showing expression levels >10% of the testicular level of expression. CT46/HORMAD1 is a single-copy gene on chromosome 1q21.3, encoding a putative protein of 394 aa. Conserved protein domain analysis identified a HORMA domain involved in chromatin binding. The CT46/HORMAD1 protein was found to be homologous to the prototype HORMA domain-containing protein, Hop1, a yeast meiosis-specific protein, as well as to asy1, a meiotic synaptic mutant protein in Arabidopsis thaliana.

Prognostic factors and role of adjuvant therapies in the management of parasagittal meningiomas

Background: The goal of the present study was to retrospectively analyze our series of parasagittal meningiomas, treated by either single or combined therapies (surgery and/or SRS and FSRT), in order to determine the factors that influence patient outcome. Methods: Between January 1999 and May 2007, 37 parasagittal meningiomas were treated in our center. We compared the outcome of the parasagittal meningiomas in relation to the treatment and adjuvant treatment given, their location along the SSS, their volume, their histological and resection grade as well as the patient's sex and age to understand which factors influenced their natural history. Findings: Median follow-up was 6.7 years (2.4-12 years). Tumor grades and Simpson resection grade were distributed evenly along the SSS. The actuarial overall tumor control rate was 65.9%. Regression analysis showed, that the tumor histological grade and the Simpson resection grade were two significant factors in determining the tumor control (p<0.002 and p<0.008). Location along the SSS showed a lower control rate in the posterior third (p<0.002). Sex, age and tumor volume, however, were not significant factors. Moreover, and unexpectedly, the In our series, the proportion of adjuvant treatment was much higher than in former described series (39% vs 7%) but with similar control rate and lower morbidity and mortality. Conclusions: In our series, histological grade and Simpson grade are independent factors for recurrence and tumor control. Interestingly, location in the posterior third of the SSS seems to be another independent factor for recurrence. In order to avoid major morbidities related to surgery we advocate earlier use of adjuvant therapies for higher histological grade tumors and for tumors located at the posterior portion of the SSS, but definitive conclusions might warrant a larger series.

Land-use systems affect Archaeal community structure and functional diversity in western Amazon soils

The study of the ecology of soil microbial communities at relevant spatial scales is primordial in the wide Amazon region due to the current land use changes. In this study, the diversity of the Archaea domain (community structure) and ammonia-oxidizing Archaea (richness and community composition) were investigated using molecular biology-based techniques in different land-use systems in western Amazonia, Brazil. Soil samples were collected in two periods with high precipitation (March 2008 and January 2009) from Inceptisols under primary tropical rainforest, secondary forest (5-20 year old), agricultural systems of indigenous people and cattle pasture. Denaturing gradient gel electrophoresis of polymerase chain reaction-amplified DNA (PCR-DGGE) using the 16S rRNA gene as a biomarker showed that archaeal community structures in crops and pasture soils are different from those in primary forest soil, which is more similar to the community structure in secondary forest soil. Sequence analysis of excised DGGE bands indicated the presence of crenarchaeal and euryarchaeal organisms. Based on clone library analysis of the gene coding the subunit of the enzyme ammonia monooxygenase (amoA) of Archaea (306 sequences), the Shannon-Wiener function and Simpson's index showed a greater ammonia-oxidizing archaeal diversity in primary forest soils (H' = 2.1486; D = 0.1366), followed by a lower diversity in soils under pasture (H' = 1.9629; D = 0.1715), crops (H' = 1.4613; D = 0.3309) and secondary forest (H' = 0.8633; D = 0.5405). All cloned inserts were similar to the Crenarchaeota amoA gene clones (identity > 95 %) previously found in soils and sediments and distributed primarily in three major phylogenetic clusters. The findings indicate that agricultural systems of indigenous people and cattle pasture affect the archaeal community structure and diversity of ammonia-oxidizing Archaea in western Amazon soils.

Comunidade de fungos micorrízicos arbusculares: diversidade, composição e glomalina em área revegetada com sesbânia

A composição de comunidades e diversidade de fungos micorrízicos arbusculares (FMAs) pode ser influenciada por diversos fatores como o clima, a biota do solo e as plantas hospedeiras. Este estudo objetivou avaliar a influência da revegetação de uma cava de extração de argila com Sesbania virgata (SV) em plantios puro e consorciado com Eucalyptus camaldulensis (EC) e Acacia mangium (AM), na composição e diversidade de fungos micorrízicos arbusculares (FMAs), bem como na quantidade da proteína do solo relacionada à glomalina (PSRG). O delineamento experimental utilizado foi em blocos casualizados com quatro tratamentos (plantio puro de SV - 100SV; consórcio de SV + EC - 50SV:50EC; consórcio de SV + AM - 50SV:50AM; e área degradada com vegetação espontânea - ADVE), com três repetições. A revegetação da cava de extração de argila com SV, em plantios puro ou consorciado, reduziu a abundância de esporos e a dominância de espécies (Índice de Simpson - IDS) e aumentou a riqueza de espécies de FMAs e o índice de diversidade de Shannon e Wiener. Além disso, aumentou a quantidade de proteína do solo relacionada à glomalina, quando comparada a área degradada com vegetação espontânea.

Tempo de Captura de Organismos da Mesofauna do Solo e seus Reflexos na Interpretação de Índices da Comunidade Edáfica

RESUMO A mesofauna edáfica compreende organismos de dimensões entre 100 μm e 2 mm, sendo importante avaliar os métodos utilizados para sua caracterização. Os objetivos deste trabalho foram definir o período de tempo de permanência do material de solo no extrator Berlese-Tüllgren para a captura dos organismos da mesofauna e determinar o tempo mínimo de extração para a correta utilização dos índices de Shannon, Simpson, Pielou e Margalef, empregados na avaliação da diversidade, dominância e equabilidade das comunidades da mesofauna. O estudo foi conduzido no Departamento de Solos do Instituto de Agronomia da Universidade Federal Rural do Rio de Janeiro, Seropédica, Rio de Janeiro, em terreno altamente antropizado. Foram instaladas parcelas experimentais com os seguintes tratamentos: feijão-de-porco (Canavalia ensiformis), mucuna-preta (Mucuna aterrima), feijão-bravo-do-Ceará (Canavalia brasiliensis), guandu (Cajanus cajan) e vegetação espontânea, em delineamento de quadrado latino. Em cada uma das unidades experimentais, foram coletadas amostras formadas por serapilheira e material de solo, nos primeiros 5 cm da camada superficial do solo realizada um dia antes do plantio das leguminosas (outubro) e, posteriormente, por ocasião do corte da parte aérea das plantas (março). As amostras foram submetidas a uma bateria de extratores do tipo Berlese-Tüllgren, por um período de 15 dias, realizando-se a contagem diária dos organismos. A partir da contagem e identificação em nível de grupo (Ordem/Família) dos organismos capturados, foram determinados os índices de Margalef, Simpson, Shannon e Pielou, bem como verificou-se a correlação por ordem de Kendall entre os valores obtidos dia a dia até o 8º dia de extração, usando-se o índice de Shannon como referência. Concluiu-se que é possível a redução do tempo de permanência das amostras de material de solo nos funis Berlese-Tüllgren, não sendo recomendável a adoção de período de tempo inferior a seis dias para se determinar a composição da mesofauna edáfica ou para se obterem dados mais consistentes e confiáveis para se avaliarem os índices de diversidade, quando se utiliza esse procedimento.

Temporal and spatial dynamics of benthic invertebrate communities in an alpine glacier-fed alluvial system

Summary The present thesis work focused on the ecology of benthic invertebrates in the proglacial floodplain of the Rhone in the Swiss Alps. The main glacial Rhone River and a smaller glacial tributary, the Mutt River, joined and entered a braiding multi-thread area. A first part concentrated on the disruption of the longitudinal patterns of environmental conditions and benthic invertebrate fauna in the Rhone by its tributary the Mutt. The Mutt had less harsh environmental conditions, higher taxonomic richness and more abundant zoobenthos compared to the Rhone upstream of the confluence. Although the habitat conditions in the main stream were little modified by the tributary, the fauna was richer and more diverse below the confluence. Colonisation from the Mutt induced the occurrence of faunal elements uncommon of glacial streams in the upper Rhone, where water temperature remains below 4°C. Although the glacial Rhone dominated the system with regard to hydrology and certain environmental conditions, the Mutt tributary has to be seen as the faunal driver of the system. The second part of the study concerned the spatio-temporal differentiation of the habitats and the benthic communities along and across the flood plain. No longitudinal differentiation was found. The spatial transversal differentiation of three habitat types with different environmental characteristics was successfully reflected in the spatial variability of benthic assemblages. This typology separated marginal sites of the flood plain, left bank sites under the influence of the Mutt, and the right bank sites under the influence of the Rh6ne. Faunistic spatial differences were emphasized by the quantitative structure of the fauna, richness, abundances and Simpson index of diversity. Seasonal environmental variability was positively related with Simpson index of diversity and the total richness per site. Low flow conditions were the most favourable season for the fauna and November was characterized by low spatial environmental heterogeneity, high spatial heterogeneity of faunal assemblage, maximum taxonomic richness, a particular taxonomic composition, highest abundances, as well as the highest primary food resources. The third part studied the egg development of three species of Ephemeroptera in the laboratory at 1.5 to 7°C and the ecological implications in the field. Species revealed very contrasting development strategies. Baetis alpinus has a synchronous and efficient egg development, which is faster in warmer habitats, enabling it to exploit short periods of favourable conditions in the floodplain. Ecdyonurus picteti has a very long development time slightly decreasing in warmer conditions. The high degree of individual variation suggests a genetic determination of the degree-days demand. Combined with the glacial local conditions, this strategy leads to an extreme delay of hatching and allows it to develop in very unpredictable habitats. Rhithrogena nivata is the second cold adapted species in Ephemeroptera. The incubation duration is long and success largely depends on the timing of hatching and the discharge conditions. This species is able to exploit extremely unstable and cold habitats where other species are limited by low water temperatures. The fourth part dealt with larval development in different habitats of the floodplain. Addition of data on egg development allowed the description of the life histories of the species from oviposition until emergence. Rhithrogena nivata and loyolaea generally have a two-year development, with the first winter passed as eggs and the second one as larvae. Development of Ecdyonurus picteti is difficult to document but appears to be efficient in a harsh and unpredictable environment. Baetis alpinus was studied separately in four habitats of the floodplain system with contrasting thermal regimes. Differences in success and duration of larval development and in growth rates are emphasised. Subvention mechanisms between habitats by migration of young or grown larvae were demonstrated. Development success and persistence of the populations in the system were thus increased. Emergence was synchronised to the detriment of the optimisation of the adult's size and fecundity. These very different development strategies induce a spatial and temporal distribution in the use of food resources and ecological niches. The last part of this work aimed at the synthesis of the characteristics and the ecological features of three distinct compartments of the system that are the upper Rhone, the Mutt and the floodplain. Their particular role as well as their inter-dependence concerning the structure and the dynamics of the benthic communities was emphasised. Résumé Ce travail de thèse est consacré à l'écologie des invertébrés benthiques dans la zone alluviale proglaciaire du Rhône dans les Alpes suisses. Le Rhône, torrent glaciaire principal, reçoit les eaux de la Mutt, affluent glaciaire secondaire, puis pénètre dans une zone de tressage formée de plusieurs bras. La première partie de l'étude se concentre sur la disruption par la Mutt des processus longitudinaux, tant environnementaux que faunistiques, existants dans le Rhône. Les conditions environnementales régnant dans la Mutt sont moins rudes, la richesse taxonomique plus élevée et le zoobenthos plus abondant que dans le Rhône en amont de la confluence. Bien que les conditions environnementales dans le torrent principal soient peu modifiées par l'affluent, la faune s'avère être plus riche et plus diversifiée en aval de la confluence. La colonisation depuis la Mutt permet l'occurrence de taxons inhabituels dans le Rhône en amont de la confluence, où la température de l'eau se maintient en dessous de 4°C. Bien que le Rhône, torrent glaciaire principal, domine le système du point de vu de l'hydrologie et de certains paramètres environnementaux, l'affluent Mutt doit être considéré comme l'élément structurant la faune dans le système. La deuxième partie concerne la différentiation spatiale et temporelle des habitats et des communautés benthiques à travers la plaine alluviale. Aucune différentiation longitudinale n'a été mise en évidence. La différentiation transversale de trois types d'habitats sur la base des caractéristiques environnementales a été confirmée par la variabilité spatiale de la faune. Cette typologie sépare les sites marginaux de la plaine alluviale, ceux sous l'influence de la Mutt (en rive gauche) et ceux sous l'influence du Rhône amont (en rive droite). Les différences spatiales de la faune sont mises en évidence par la structure quantitative de la faune, la richesse, les abondances et l'indice de diversité de Simpson. La variabilité saisonnière du milieu est positivement liée avec l'indice de diversité de Simpson et la richesse totale par site. L'étiage correspond à la période la plus favorable pour la faune et novembre réunit des conditions de faible hétérogénéité spatiale du milieu, de forte hétérogénéité spatiale de la faune, une richesse taxonomique maximale, une composition faunistique particulière, les abondances ainsi que les ressources primaires les plus élevées. La troisième partie est consacrée à l'étude du développement des oeufs de trois espèces d'Ephémères au laboratoire à des températures de 1.5 à 7°C, ainsi qu'aux implications écologiques sur le terrain. Ces espèces présentent des stratégies de développement très contrastées. Baetis alpinus a un développement synchrone et efficace, plus rapide en milieu plus chaud et lui permettant d'exploiter les courtes périodes de conditions favorables. Ecdyonurus picteti présente une durée de développement très longue, diminuant légèrement dans des conditions plus chaudes. L'importante variation interindividuelle suggère un déterminisme génétique de la durée de développement. Cette stratégie, associée aux conditions locales, conduit à un décalage extrême des éclosions et permet à l'espèce de se développer dans des habitats imprévisibles. Rhithrogena nivata est la seconde espèce d'Ephémères présentant une adaptation au froid. L'incubation des oeufs est longue et son succès dépend de la période des éclosions et des conditions hydrologiques. Cette espèce est capable d'exploiter des habitats extrêmement instables et froids, où la température est facteur limitant pour d'autres espèces. La quatrième partie traite du développement larvaire dans différents habitats de la plaine alluviale. Le développement complet est décrit pour les espèces étudiées de la ponte jusqu'à l'émergence. Rhithrogena nivata et loyolaea atteignent généralement le stade adulte en deux ans, le premier hiver étant passé sous forme d'oeuf et le second sous forme de larve. Le développement de Ecdyonurus picteti est difficile à documenter, mais s'avère cependant efficace dans un environnement rude et imprévisible. Baetis alpinus a été étudié séparément dans quatre habitats de la plaine ayant des régimes thermiques contrastés. La réussite et la durée du développement embryonnaire ainsi que les taux de croissance y sont variables. Des mécanismes de subvention entre habitats sont possibles par la migration de larves juvéniles ou plus développées, augmentant ainsi la réussite du développement et le maintien des populations dans le système. L'émergence devient synchrone, au détriment de l'optimisation de la taille et de la fécondité des adultes. Ces stratégies très différentes induisent une distribution spatiale et temporelle dans l'usage des ressources et des niches écologiques. La dernière partie synthétise les caractéristiques écologiques des trois compartiments du système que sont le Rhône amont, la Mutt et la zone alluviale. Leurs rôles particuliers et leurs interdépendances du point de vue de la structure et de la dynamique des communautés benthiques sont mis en avant.

High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites.

The ability to determine the location and relative strength of all transcription-factor binding sites in a genome is important both for a comprehensive understanding of gene regulation and for effective promoter engineering in biotechnological applications. Here we present a bioinformatically driven experimental method to accurately define the DNA-binding sequence specificity of transcription factors. A generalized profile was used as a predictive quantitative model for binding sites, and its parameters were estimated from in vitro-selected ligands using standard hidden Markov model training algorithms. Computer simulations showed that several thousand low- to medium-affinity sequences are required to generate a profile of desired accuracy. To produce data on this scale, we applied high-throughput genomics methods to the biochemical problem addressed here. A method combining systematic evolution of ligands by exponential enrichment (SELEX) and serial analysis of gene expression (SAGE) protocols was coupled to an automated quality-controlled sequence extraction procedure based on Phred quality scores. This allowed the sequencing of a database of more than 10,000 potential DNA ligands for the CTF/NFI transcription factor. The resulting binding-site model defines the sequence specificity of this protein with a high degree of accuracy not achieved earlier and thereby makes it possible to identify previously unknown regulatory sequences in genomic DNA. A covariance analysis of the selected sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism.