Transcriptome of a mouse kidney cortical collecting duct cell line: effects of aldosterone and vasopressin.

Aldosterone and vasopressin are responsible for the final adjustment of sodium and water reabsorption in the kidney. In principal cells of the kidney cortical collecting duct (CCD), the integral response to aldosterone and the long-term functional effects of vasopressin depend on transcription. In this study, we analyzed the transcriptome of a highly differentiated mouse clonal CCD principal cell line (mpkCCD(cl4)) and the changes in the transcriptome induced by aldosterone and vasopressin. Serial analysis of gene expression (SAGE) was performed on untreated cells and on cells treated with either aldosterone or vasopressin for 4 h. The transcriptomes in these three experimental conditions were determined by sequencing 169,721 transcript tags from the corresponding SAGE libraries. Limiting the analysis to tags that occurred twice or more in the data set, 14,654 different transcripts were identified, 3,642 of which do not match known mouse sequences. Statistical comparison (at P < 0.05 level) of the three SAGE libraries revealed 34 AITs (aldosterone-induced transcripts), 29 ARTs (aldosterone-repressed transcripts), 48 VITs (vasopressin-induced transcripts) and 11 VRTs (vasopressin-repressed transcripts). A selection of the differentially-expressed, hormone-specific transcripts (5 VITs, 2 AITs and 1 ART) has been validated in the mpkCCD(cl4) cell line either by Northern blot hybridization or reverse transcription-PCR. The hepatocyte nuclear transcription factor HNF-3-alpha (VIT39), the receptor activity modifying protein RAMP3 (VIT48), and the glucocorticoid-induced leucine zipper protein (GILZ) (AIT28) are candidate proteins playing a role in physiological responses of this cell line to vasopressin and aldosterone.

Seleção de progênies de eucalipto pelo índice Z por MQM e Blup

O objetivo deste trabalho foi avaliar a eficiência do índice Z (índice somatório das variáveis padronizadas) na seleção de progênies de irmãos completos entre Eucalyptus grandis e Eucalyptus urophylla via método dos quadrados mínimos (MQM) e da melhor predição linear não viesada (Blup). Os experimentos foram realizados em dois tipos de solo e de ambiente, em blocos ao acaso com cinco repetições, oito plantas por parcela e espaçamento de 3x2 m. Aos três anos de idade, as plantas foram avaliadas quanto ao incremento médio anual de madeira, à densidade básica, ao rendimento de celulose e ao álcali efetivo. Para a comparação da eficiência da seleção das melhores progênies, pelos procedimentos MQM e Blup, foi obtido o índice Z para cada indivíduo. Posteriormente, foram obtidas as médias preditas das progênies para o índice Z, ranqueadas em sentido favorável ao melhoramento. O índice clássico também foi utilizado. A coincidência entre as melhores progênies selecionadas pelos índices clássico e Z foi boa. No entanto, o índice Z permite visualização gráfica, o que possibilita verificar em quais caracteres uma determinada progênie apresenta alguma deficiência. Não há diferença entre as melhores progênies selecionadas pelo índice Z via MQM e Blup.

Análise conjunta de atributos físicos e biológicos do solo sob sistema de integração lavoura-pecuária

O objetivo deste trabalho foi avaliar os efeitos do sistema integração lavoura-pecuária (ILP) sobre os atributos morfológicos, físicos e biológicos do solo. O experimento foi realizado em Dourados, MS, em Latossolo Vermelho distroférrico típico. Foram avaliados os seguintes sistemas: monocultura com sistema convencional de preparo do solo, ILP com sistema plantio direto, pastagem contínua de Urochloa decumbens (Syn. Brachiaria decumbens) e vegetação nativa. Em cada sistema, foi aberta uma trincheira com o intuito de detectar as modificações morfológicas provocadas pelos diferentes manejos com uso do método do perfil cultural. Os macroinvertebrados do solo foram avaliados conforme o método "Tropical Soil Biology and Fertility". Utilizaram-se, ainda, amostras de solo indeformadas para avaliação dos atributos físicos do solo (densidade do solo, porosidade total, macro e microporosidade). Entre os sistemas produtivos, a melhor estrutura do solo foi verificada no sistema ILP, nas camadas de 0-0,1 e 0,1-0,2 m. Os sistemas sob ILP e em pastagem cultivada continuamente favoreceram um ambiente edáfico biologicamente mais ativo em comparação aos outros sistemas cultivados. A visualização conjunta dos atributos do solo mostrou que a integração lavoura-pecuária é uma estratégia para desenvolver sistemas de produção sustentáveis e que o período de dois anos de manejo é adequado para a rotação lavoura-pecuária.

Prevalence, prenatal diagnosis and clinical features of oculo-auriculo-vertebral spectrum: a registry-based study in Europe.

Oculo-auriculo-vertebral spectrum is a complex developmental disorder characterised mainly by anomalies of the ear, hemifacial microsomia, epibulbar dermoids and vertebral anomalies. The aetiology is largely unknown, and the epidemiological data are limited and inconsistent. We present the largest population-based epidemiological study to date, using data provided by the large network of congenital anomalies registries in Europe. The study population included infants diagnosed with oculo-auriculo-vertebral spectrum during the 1990-2009 period from 34 registries active in 16 European countries. Of the 355 infants diagnosed with oculo-auriculo-vertebral spectrum, there were 95.8% (340/355) live born, 0.8% (3/355) fetal deaths, 3.4% (12/355) terminations of pregnancy for fetal anomaly and 1.5% (5/340) neonatal deaths. In 18.9%, there was prenatal detection of anomaly/anomalies associated with oculo-auriculo-vertebral spectrum, 69.7% were diagnosed at birth, 3.9% in the first week of life and 6.1% within 1 year of life. Microtia (88.8%), hemifacial microsomia (49.0%) and ear tags (44.4%) were the most frequent anomalies, followed by atresia/stenosis of external auditory canal (25.1%), diverse vertebral (24.3%) and eye (24.3%) anomalies. There was a high rate (69.5%) of associated anomalies of other organs/systems. The most common were congenital heart defects present in 27.8% of patients. The prevalence of oculo-auriculo-vertebral spectrum, defined as microtia/ear anomalies and at least one major characteristic anomaly, was 3.8 per 100,000 births. Twinning, assisted reproductive techniques and maternal pre-pregnancy diabetes were confirmed as risk factors. The high rate of different associated anomalies points to the need of performing an early ultrasound screening in all infants born with this disorder.

Developmental constraints on vertebrate genome evolution.

Constraints in embryonic development are thought to bias the direction of evolution by making some changes less likely, and others more likely, depending on their consequences on ontogeny. Here, we characterize the constraints acting on genome evolution in vertebrates. We used gene expression data from two vertebrates: zebrafish, using a microarray experiment spanning 14 stages of development, and mouse, using EST counts for 26 stages of development. We show that, in both species, genes expressed early in development (1) have a more dramatic effect of knock-out or mutation and (2) are more likely to revert to single copy after whole genome duplication, relative to genes expressed late. This supports high constraints on early stages of vertebrate development, making them less open to innovations (gene gain or gene loss). Results are robust to different sources of data -- gene expression from microarrays, ESTs, or in situ hybridizations; and mutants from directed KO, transgenic insertions, point mutations, or morpholinos. We determine the pattern of these constraints, which differs from the model used to describe vertebrate morphological conservation ("hourglass" model). While morphological constraints reach a maximum at mid-development (the "phylotypic" stage), genomic constraints appear to decrease in a monotonous manner over developmental time.

Identification of cancer/testis-antigen genes by massively parallel signature sequencing.

Massively parallel signature sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a single RNA preparation. Most MPSS tags can be unambiguously assigned to genes, thereby generating a comprehensive expression profile of the tissue of origin. From the comparison of MPSS data from 32 normal human tissues, we identified 1,056 genes that are predominantly expressed in the testis. Further evaluation by using MPSS tags from cancer cell lines and EST data from a wide variety of tumors identified 202 of these genes as candidates for encoding cancer/testis (CT) antigens. Of these genes, the expression in normal tissues was assessed by RT-PCR in a subset of 166 intron-containing genes, and those with confirmed testis-predominant expression were further evaluated for their expression in 21 cancer cell lines. Thus, 20 CT or CT-like genes were identified, with several exhibiting expression in five or more of the cancer cell lines examined. One of these genes is a member of a CT gene family that we designated as CT45. The CT45 family comprises six highly similar (>98% cDNA identity) genes that are clustered in tandem within a 125-kb region on Xq26.3. CT45 was found to be frequently expressed in both cancer cell lines and lung cancer specimens. Thus, MPSS analysis has resulted in a significant extension of our knowledge of CT antigens, leading to the discovery of a distinctive X-linked CT-antigen gene family.

From institutional repositories to personal collections of learning resources

Institutional digital repositories are a basic piece to provide preservation and reutilization of learning resources. However, their creation and maintenance is usually performed following a top-down approach, causing limitations in the search and reutilization of learning resources. In order to avoid this problem we propose to use web 2.0 functionalities. In this paper we present how tagging can be used to enhance the search and reusability functionalities of institutional learning repositories as well as promoting their usage. The paper also describes the evaluation process that was performed in a pilot experience involving open educational resources.

Analyzing hidden semantics in social bookmarking of open educational resources

Web 2.0 services such as social bookmarking allow users to manage and share the links they find interesting, adding their own tags for describingthem. This is especially interesting in the field of open educational resources, asdelicious is a simple way to bridge the institutional point of view (i.e. learningobject repositories) with the individual one (i.e. personal collections), thuspromoting the discovering and sharing of such resources by other users. In this paper we propose a methodology for analyzing such tags in order to discover hidden semantics (i.e. taxonomies and vocabularies) that can be used toimprove descriptions of learning objects and make learning object repositories more visible and discoverable. We propose the use of a simple statistical analysis tool such as principal component analysis to discover which tags createclusters that can be semantically interpreted. We will compare the obtained results with a collection of resources related to open educational resources, in order to better understand the real needs of people searching for open educational resources.

Repurposing Social Tagging Data for Extraction of Domain-level Concepts

The World Wide Web, the world¿s largest resource for information, has evolved from organizing information using controlled, top-down taxonomies to a bottom up approach that emphasizes assigning meaning to data via mechanisms such as the Social Web (Web 2.0). Tagging adds meta-data, (weak semantics) to the content available on the web. This research investigates the potential for repurposing this layer of meta-data. We propose a multi-phase approach that exploits user-defined tags to identify and extract domain-level concepts. We operationalize this approach and assess its feasibility by application to a publicly available tag repository. The paper describes insights gained from implementing and applying the heuristics contained in the approach, as well as challenges and implications of repurposing tags for extraction of domain-level concepts.

RDM1, a novel RNA recognition motif (RRM)-containing protein involved in the cell response to cisplatin in vertebrates.

A variety of cellular proteins has the ability to recognize DNA lesions induced by the anti-cancer drug cisplatin, with diverse consequences on their repair and on the therapeutic effectiveness of this drug. We report a novel gene involved in the cell response to cisplatin in vertebrates. The RDM1 gene (for RAD52 Motif 1) was identified while searching databases for sequences showing similarities to RAD52, a protein involved in homologous recombination and DNA double-strand break repair. Ablation of RDM1 in the chicken B cell line DT40 led to a more than 3-fold increase in sensitivity to cisplatin. However, RDM1-/- cells were not hypersensitive to DNA damages caused by ionizing radiation, UV irradiation, or the alkylating agent methylmethane sulfonate. The RDM1 protein displays a nucleic acid binding domain of the RNA recognition motif (RRM) type. By using gel-shift assays and electron microscopy, we show that purified, recombinant chicken RDM1 protein interacts with single-stranded DNA as well as double-stranded DNA, on which it assembles filament-like structures. Notably, RDM1 recognizes DNA distortions induced by cisplatin-DNA adducts in vitro. Finally, human RDM1 transcripts are abundant in the testis, suggesting a possible role during spermatogenesis.

GENCODE: producing a reference annotation for ENCODE.

BACKGROUND: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual annotation by the HAVANA team, experimental validation by the GENCODE consortium and a refinement of the annotation based on these experimental results. RESULTS: The GENCODE gene features are divided into eight different categories of which only the first two (known and novel coding sequence) are confidently predicted to be protein-coding genes. 5' rapid amplification of cDNA ends (RACE) and RT-PCR were used to experimentally verify the initial annotation. Of the 420 coding loci tested, 229 RACE products have been sequenced. They supported 5' extensions of 30 loci and new splice variants in 50 loci. In addition, 46 loci without evidence for a coding sequence were validated, consisting of 31 novel and 15 putative transcripts. We assessed the comprehensiveness of the GENCODE annotation by attempting to validate all the predicted exon boundaries outside the GENCODE annotation. Out of 1,215 tested in a subset of the ENCODE regions, 14 novel exon pairs were validated, only two of them in intergenic regions. CONCLUSION: In total, 487 loci, of which 434 are coding, have been annotated as part of the GENCODE reference set available from the UCSC browser. Comparison of GENCODE annotation with RefSeq and ENSEMBL show only 40% of GENCODE exons are contained within the two sets, which is a reflection of the high number of alternative splice forms with unique exons annotated. Over 50% of coding loci have been experimentally verified by 5' RACE for EGASP and the GENCODE collaboration is continuing to refine its annotation of 1% human genome with the aid of experimental validation.

RFID-tekniikan käyttö betonielementtien tunnistamiseen

RFID on 2000-luvulla yleisesti saatavilla tullut tekniikka erilaisten kohteiden tunnistamiseen. RFID-tekniikassa tunnistamiseen käytetään pienikokoisia tunnisteita, joiden tietosisältö pystytään lukemaan langattomasti ilman näköyhteyttä tarkoitukseen soveltuvalla lukulaitteella. Tunnisteet ovat halpoja ja yksinkertaisia. Yleensä ne eivät sisällä omaa virtalähdettä, vaan ne toimivat ainoastaan lukulaitteen luoman kentän voimalla. Tässä työssä tutkitaan RFID-tekniikan soveltuvuutta betonista valmistettujen rakennuselementtien tunnistamiseen. Ympäristön vaikutukset tekniikan käyttöön tutkitaan ja selvitetään, mitkä ovat parhaat toimintatavat elementtien tunnistamiseen nämä vaikutukset huomioon ottaen. Työssä esitellään ensin RFID-tekniikan toimintaperiaatteet sekä tunnisteiden ja lukulaitteiden rakenne. Tunnisteiden jaottelu erilaisten ominasisuuksien perusteella käydään läpi ja sovellusalan kannalta tärkeimmät standardit esitellään. Käytännön osuudessa esitellään RFID-tekniikan soveltamista betonista valmistettujen rakennuselementtien tunnistamiseen. Työssä esitellään saavutetut mittaustulokset sekä betonielementtien tunnistamiseen ja tietojen hallintaan toteutetun järjestelmän rakenne.

Metodologia para observação da camada de cera em maçãs, utilizando microscopia eletrônica de varredura

A estrutura mais superficial da epiderme dos frutos é constituída por fina camada de cera, responsável por mecanismos de proteção, principalmente relacionados à evapotranspiração e ao ataque de patógenos. A visualização de cera por microscopia eletrônica de varredura apresenta dificuldades no processamento da amostra, pois os métodos rotineiramente utilizados ocasionam sérios danos a esta camada ou, simplesmente, provocam sua eliminação devido ao processo de solubilização causado pelos reagentes utilizados. Alguns autores têm utilizado temperaturas baixas (-90ºC) para o processamento de amostras. No Brasil, tentativas de observação de cera em maçãs, utilizando a microscopia eletrônica de varredura, têm sido realizadas; entretanto, os resultados não foram satisfatórios. No Laboratório de Microscopia Eletrônica da Embrapa Clima Temperado, foi adaptado um método simples e que tem apresentado bons resultados. Para este experimento, foram retiradas pequenas porções da casca de maçãs da região equatorial dos frutos. As amostras foram fixadas em lâminas histológicas, utilizando fita adesiva nas extremidades. Posteriormente, foram colocadas em dessecador contendo sílica gel, para que ocorresse a desidratação. Após 72 horas, foram retirados fragmentos para fixação em stubs e metalização com ouro. Foi usado um microscópio eletrônico ZEISS (DSM-940A), regulado à distância de trabalho de 15mm, voltagem de aceleração de 10 kV e ampliação de 3.000 X. As imagens obtidas permitiram avaliar a interferência dos fatores ambientais utilizados no processo de frigoconservação de maçãs.

Sistema automàtic d'aprenentatge de preferències personals sobre notícies classificades en seccions i definides per paraules clau

Entrar a una pàgina web de continguts i trobar a l'instant allò que et ve de gust llegir, escoltar o veure en aquell precís instant és un dels somnis de molts internautes. Aquest projecte ha tingut com a objectiu dissenyar un prototip de sistema d'aprenentatge automàtic que va en aquesta línia, dins les possibilitats d'un projecte de final de carrera d'Enginyeria en Informàtica. El programa desenvolupat treballa sobre una mostra de documents classificats en una secció principal i definits per paraules clau. Està pensat per ser vàlid per a qualsevol repositori de dades però s'ha aplicat a un cas concret, l'aprenentatge de gustos sobre notícies del diari britànic 'The Guardian'. L'algoritme té un perfil ideal que modela el cervell d'un lector i un perfil evolutiu, que comença de zero i va aprenent a mesura que l'usuari va consumint notícies. L'aprenentatge s'ha aconseguit fent una simulació d'aquestes tries en dos corpus de notícies d'uns 6.000 articles cadascun. En cada iteració, l'algorisme té en compte un petit grup notícies, a les quals s'assignen dues valoracions, una d'acord amb el perfil ideal i una altra segons el perfil evolutiu. La diferència entre les dues seleccions és la que ens dóna informació per a l'aprenentatge, que s'ha abordat amb dues estratègies. L'aprenentatge online fa una petita variació al perfil evolutiu després de cada tria, mentre que l'offline s'espera a tenir més dades per trobar patrons de conducta i poder fer modificacions més de més magnitud. Després de diverses proves, s'ha comprovat que s'aconsegueix reduir la distància entre valoracions de les seccions principals i tags, comparant el perfil ideal i l'evolutiu abans i després de l'execució de l'algorisme d'aprenentatge.

Viabilidade do pólen e desenvolvimento do tubo polínico em macieira (Malus spp.)

No presente trabalho, estudaram-se características associadas à germinação in vitro e ao desenvolvimento in vivo do tubo polínico em seis variedades-copa e de porta-enxertos de macieira como subsídios para o estabelecimento de programas de melhoramento genético. Utilizou-se de pólen de seis cultivares de macieira inoculado em meio de cultura com ágar (10 g.L-1) em água destilada, combinados com concentrações de sacarose (0; 10; 20; 30; 40 e 50%) e ácido bórico (0 e 40 mg.L-1). Para o estudo do desenvolvimento do tubo polínico, realizou-se coleta das flores em quatro períodos (6; 12; 24 e 48 horas após as polinizações) em M9 x Marubakaido e a autofecundação em M9, sendo os tubos polínicos analisados em coloração de azul de anilina acidificada/carmim acético e em fluorescência. A sacarose, em concentrações entre 15% a 25%, pode ser empregada com sucesso para a germinação in vitro de grãos de pólen da macieira. O ácido bórico não teve efeito positivo para esta característica. Na ausência do ácido bórico e na presença de 15% de sacarose, observaram-se os maiores percentuais de germinação: Fuji (51,1%), Imperatriz (31,7%), M.9 (20,8%), Catarina (19,2%), Gala (13,7%) e Marubakaido (6,1%). Quanto ao desenvolvimento do tubo polínico, com 12 horas da polinização, iniciou-se a germinação no pólen, no estigma, no cruzamento M.9 x Marubakaido, e após 24 horas da polinização observou-se 83% de germinação. As técnicas de coloração com azul de anilina acidificada com carmim acético e de visualização em fluorescência foram eficientes na visualização e coloração dos grãos de pólen e do desenvolvimento dos tubos polínicos.