Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems

Background: Sorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds of whole genome duplication events. Therefore, it has become possible to generate a high-quality genome sequence. Furthermore, cultivars exists that rival sugarcane in levels of stem sugar so that a genetic approach can be used to investigate which genes are differentially expressed to achieve high levels of stem sugar. Results: Here, we characterized the small RNA component of the transcriptome from grain and sweet sorghum stems, and from F2 plants derived from their cross that segregated for sugar content and flowering time. We found that variation in miR172 and miR395 expression correlated with flowering time whereas variation in miR169 expression correlated with sugar content in stems. Interestingly, genotypic differences in the ratio of miR395 to miR395* were identified, with miR395* species expressed as abundantly as miR395 in sweet sorghum but not in grain sorghum. Finally, we provided experimental evidence for previously annotated miRNAs detecting the expression of 25 miRNA families from the 27 known and discovered 9 new miRNAs candidates in the sorghum genome. Conclusions: Sequencing the small RNA component of sorghum stem tissue provides us with experimental evidence for previously predicted microRNAs in the sorghum genome and microRNAs with a potential role in stem sugar accumulation and flowering time

Analysis of epidermis- and mesophyll-specific transcript accumulation in powdery mildew-inoculated wheat leaves

Powdery mildew is an important disease of wheat caused by the obligate biotrophic fungus Blumeria graminis f. sp. tritici. This pathogen invades exclusively epidermal cells after penetrating directly through the cell wall. Because powdery mildew colonizes exclusively epidermal cells, it is of importance not only to identify genes which are activated, but also to monitor tissue specificity of gene activation. Acquired resistance of wheat to powdery mildew can be induced by a previous inoculation with the non-host pathogen B. graminis f. sp. hordei, the causal agent of barley powdery mildew. The establishment of the resistant state is accompanied by the activation of genes. Here we report the tissue-specific cDNA-AFLP analysis and cloning of transcripts accumulating 6 and 24 h after the resistance-inducing inoculation with B. graminis f. sp. hordei. A total of 25 000 fragments estimated to represent about 17 000 transcripts were displayed. Out of these, 141 transcripts, were found to accumulate after Bgh inoculation using microarray hybridization analysis. Forty-four accumulated predominantly in the epidermis whereas 76 transcripts accumulated mostly in mesophyll tissu

Transcriptional changes in powdery mildew infected wheat and Arabidopsis leaves undergoing syringolin-triggered hypersensitive cell death at infection sites

Blumeria graminis f.sp. tritici, the causal agent of powdery mildew in wheat, is an obligate biotrophic fungus that exclusively invades epidermal cells. As previously shown, spraying of a solution of syringolin A, a circular peptide derivative secreted by the phytopathogenic bacterium Pseudomonas syringae pv. syringae, triggers hypersensitive cell death at infection sites in powdery mildew infected wheat. Thus, the fungus is essentially eradicated. Here we show that syringolin A also triggers hypersensitive cell death in Arabidopsis infected with the powdery mildew fungus Erysiphe cichoracearum. To monitor transcriptional changes associated with this effect, we cloned 307 cDNA clones representing 158 unigenes from powdery mildew infected, syringolin A sprayed wheat leaves by a suppression subtractive hybridization cloning procedure. These cDNAs were microarrayed onto glass slides together with 1088 cDNA-AFLP clones from powdery mildew-infected wheat. Microarray hybridization experiments were performed with probes derived from leaves, epidermal tissue, and mesophyll preparations of mildewed or uninfected wheat plants after syringolin A or control treatment. Similar experiments were performed in Arabidopsis using the Affymetrix ATH1 whole genome GeneChip. The results indicate a conserved mode of action of syringolin A as similar gene groups are induced in both species. Prominent groups include genes associated with the proteasomal degradation pathway, mitochondrial and other heat shock genes, genes involved in mitochondrial alternative electron pathways, and genes encoding glycolytic and fermentative enzymes. Surprisingly, in both species the observed transcriptional response to syringolin A was considerably weaker in infected plants as compared to uninfected plants. The results lead to the working hypothesis that cell death observed at infection sites may result from a parasite-induced suppression of the transcriptional response and thus to insufficient production of protective proteins necessary for the recovery of these cells from whatever insult is imposed by syringolin

Clinical sequencing: is WGS the better WES?

Current clinical next-generation sequencing is done by using gene panels and exome analysis, both of which involve selective capturing of target regions. However, capturing has limitations in sufficiently covering coding exons, especially GC-rich regions. We compared whole exome sequencing (WES) with the most recent PCR-free whole genome sequencing (WGS), showing that only the latter is able to provide hitherto unprecedented complete coverage of the coding region of the genome. Thus, from a clinical/technical point of view, WGS is the better WES so that capturing is no longer necessary for the most comprehensive genomic testing of Mendelian disorders

OpenGenomeBrowser: a versatile, dataset-independent and scalable web platform for genome data management and comparative genomics.

BACKGROUND As the amount of genomic data continues to grow, there is an increasing need for systematic ways to organize, explore, compare, analyze and share this data. Despite this, there is a lack of suitable platforms to meet this need. RESULTS OpenGenomeBrowser is a self-hostable, open-source platform to manage access to genomic data and drastically simplifying comparative genomics analyses. It enables users to interactively generate phylogenetic trees, compare gene loci, browse biochemical pathways, perform gene trait matching, create dot plots, execute BLAST searches, and access the data. It features a flexible user management system, and its modular folder structure enables the organization of genomic data and metadata, and to automate analyses. We tested OpenGenomeBrowser with bacterial, archaeal and yeast genomes. We provide a docker container to make installation and hosting simple. The source code, documentation, tutorials for OpenGenomeBrowser are available at opengenomebrowser.github.io and a demo server is freely accessible at opengenomebrowser.bioinformatics.unibe.ch . CONCLUSIONS To our knowledge, OpenGenomeBrowser is the first self-hostable, database-independent comparative genome browser. It drastically simplifies commonly used bioinformatics workflows and enables convenient as well as fast data exploration

Mushroom body-specific profiling of gene expression identifies regulators of long-term memory in Drosophila

Memory formation is achieved by genetically tightly controlled molecular pathways that result in a change of synaptic strength and synapse organization. While for short- term memory traces rapidly acting biochemical pathways are in place, the formation of long-lasting memories requires changes in the transcriptional program of a cell. Although many genes involved in learning and memory formation have been identified, little is known about the genetic mechanisms required for changing the transcriptional program during different phases of long-term memory formation. With Drosophila melanogaster as a model system we profiled transcriptomic changes in the mushroom body, a memory center in the fly brain, at distinct time intervals during long- term memory formation using the targeted DamID technique. We describe the gene expression profiles during these phases and tested 33 selected candidate genes for deficits in long-term memory formation using RNAi knockdown. We identified 10 genes that enhance or decrease memory when knocked-down in the mushroom body. For vajk-1 and hacd1, the two strongest hits, we gained further support for their crucial role in learning and forgetting. These findings show that profiling gene expression changes in specific cell-types harboring memory traces provides a powerful entry point to identify new genes involved in learning and memory. The presented transcriptomic data may further be used as resource to study genes acting at different memory phases

Sistematização da assistência de enfermagem: construção de um saber coletivo para implantação em um hospital psiquiátrico

Dissertação (mestrado profissional) - Universidade Federal de Santa Catarina, Centro de Ciências da Saúde, Programa de Pós-Graduação em Gestão do Cuidado em Enfermagem, Florianópolis, 2015.Trata-se de uma pesquisa qualitativa na modalidade de Pesquisa-Ação, com o objetivo de construir um saber coletivo com os enfermeiros para implantação da Sistematização da Assistência de Enfermagem em um hospital psiquiátrico, tendo como referencial teórico Michel Foucault. O estudo foi desenvolvido em um hospital psiquiátrico de referência em Santa Catarina/Brasil, com a participação de dezoito enfermeiros. Para sua realização, foram atendidos todos os preceitos éticos assegurados pela Resolução 466/12 do Conselho Nacional de Saúde, que dispõe sobre as Diretrizes e Normas Regulamentadoras da Pesquisa Envolvendo Seres Humanos, sendo aprovado pelo Comitê de Ética em Pesquisa da Universidade Federal de Santa Catarina sob o parecer 538.888. A coleta de dados ocorreu de março a junho de 2014 e foi realizada por meio de um questionário semiestruturado e de quatro oficinas. Como resultado dos questionários emergiram os seguintes temas abordados nas oficinas: o saber dos enfermeiros acerca da Sistematização da Assistência da Enfermagem, o poder dos enfermeiros para construção de um saber coletivo e implantação da Sistematização da Assistência da Enfermagem e a verdade dos enfermeiros a respeito Sistematização da Assistência da Enfermagem. Para a análise dos dados foi utilizada a técnica de análise de conteúdo de Bardin, à luz da abordagem de Michel Foucault sobre saber/poder e verdade. Obteve-se como resultados a construção dos seguintes instrumentos: histórico, diagnósticos e prescrição de enfermagem. Para a fase de avaliação de enfermagem se definiu a organização dos dados em quatro elementos: Subjetivo, Objetivo, Avaliação e Plano. O suporte teórico para sustentar a Sistematização da Assistência de Enfermagem na instituição está apoiado na teoria da relação pessoa-pessoa de Joyce Travelbee e todas as fases do Processo de Enfermagem foram pautadas na Resolução 358/2009 do Conselho Federal de Enfermagem. Deste modo, concluiu-se que o saber científico dos enfermeiros aliado a sua prática assistencial na enfermagem psiquiátrica, resultou na construção coletiva de instrumentos que compõem as etapas do Processo de Enfermagem. Também é relevante destacar que a percepção dos enfermeiros sobre este método científico, bem como a integração das suas etapas em sua vivência assistencial vislumbram expressivamente a completude desta pesquisa.Abstract : This is a qualitative research on Research-Action mode, aimed to build a collective knowledge with nurses to implement the nursing care systematization in a psychiatric hospital, based on Michel Foucault previous works. This study was conducted in the most important psychiatric hospital in Santa Catarina / Brazil, with the collaboration of eighteen nurses. For its realization, all ethical precepts provided by Resolution 466/12 of the National Health Council were conducted, which governs the Regulatory Guidelines and Standards of Research Involving Humans, being approved by the Research Ethics Committee of the Federal University of Santa Catarina in the opinion 538.888. Data collection took place from March to June 2014 and was performed using a semi-structured questionnaire and four workshops. Because of the questionnaires covered in the workshops, emerged the following topics: the nurses? knowledge about the Systematization of Nursing Assistance, the nurses? power to build a collective knowledge and implementation of the Systematization of Nursing Assistance and the truth about systematization of nursing assistance for that group. For data analysis, we used the Bardin content analysis technique, based on Michel Foucault approach to knowledge, power and truth. As a result, it was obtained the construction of the following instruments: historical, nursing diagnosis and prescription. For the nursing assessment phase, it was defined the organization of data on four elements: Subjective, Objective, Assessment and Plan. The theoretical basis to support the systematization of nursing care in the institution is structured around Joyce Travelbee?s person-person relation theory and all phases of nursing processes were guided in Resolution 358/2009 of the Federal Nursing Council. Thus, it was concluded that the scientific knowledge of nurses combined with their care practice in psychiatric nursing result in a collective construction of instruments, comprising the steps of the nursing process. It is also worth pointing out that the perception of nurses on this scientific method, as well as the integration of its stages in their care experience significantly glimpse the completion of this research