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O artigo trata da elaboração de um Plano Diretor de Digitalização (PDD) para uma nova fábrica de Bio-Manguinhos/Fiocruz que será destinada ao processamento final de vacinas e biofármacos, baseado nas ferramentas tecnológicas propostas pela Indústria 4.0 (I.4.0) e que considera os conceitos de Fábrica Inteligente (Smart Factory). O Complexo Industrial para Biotecnologia em Saúde (CIBS) aumentará significativamente a capacidade da instituição no atendimento ao Sistema Único de Saúde brasileiro e às emergências sanitárias globais. Para tanto, é fundamental que o CIBS esteja na fronteira tecnológica do setor biofarmacêutico mundial. Um projeto de digitalização bem-sucedido envolve fatores além da implantação das tecnologias em si, tais como cultura organizacional, gestão de mudança, profissionais capacitados, dentre outros. Assim sendo, a metodologia proposta considerou diversas etapas, tais como identificação de gaps a partir de uma detalhada análise de maturidade digital da organização, critérios para seleção e priorização dos programas a serem implantados, avaliação de viabilidade financeira deles e, por fim, a construção de um roadmap de digitalização (PDD) contemplando todos esses aspectos de forma holística. Este pode ser considerado um trabalho fundamental para que o CIBS tenha uma jornada de digitalização planejada, organizada e estruturada rumo à construção de uma fábrica moderna e inteligente.

A obesidade torna-se um fator de grande importância para o desenvolvimento de doenças metabólicas. Em termos estatísticos, observa-se aumento considerável da população com sobrepeso, obesa e obesidade grau III, a tornar-se um problema relevante de saúde pública. A Cirurgia Bariátrica se converte em possibilidade terapêutica para redução dos riscos à saúde do paciente obeso, com necessidade de avaliação, e interpretações Médicas para autorização dessa metodologia intervencionista. A construção do estudo busca descrever em quais requisitos se podem utilizar da Cirurgia Bariátrica como método de intervenção para diminuição dos riscos cardiovasculares em pacientes obesos. O estudo apresenta natureza descritiva com revisão bibliográfica da literatura com utilização de artigos com relevância científica que constam em base de dados confiáveis como PUBMED, MEDLINE, LILACS, Google Acadêmico e SCIELO, selecionados para utilização após crivo dos critérios de inclusão e exclusão pré-estabelecidos. Os ricos cardiovasculares em pacientes com sobrepeso e principalmente com algum grau de obesidade são altos, logo, a intervenção bariátrica após preenchimento dos critérios para realização cirúrgica, se torna fundamental para proporcionar um retorno a melhor qualidade de vida e redução dos acometimentos cardiovasculares.

Este estudo tem como objetivo aplicar a análise multicritério para estabelecer relação entre o desempenho financeiro e o desempenho técnico dos clubes que atuam na série A do campeonato Brasileiro, com a finalidade de avaliação de desempenho. Adota uma abordagem quantitativa utilizando-se da ferramenta Análise Relacional de Grey. Como achados identificou-se o Flamengo como o clube de melhor desempenho técnico e entre os melhores clubes também nos quesitos financeiros, estando ao lado de Cruzeiro e Atlético-MG. Identificou-se que clubes que ficaram mal colocados no Rankeamento de indicadores financeiros se sagraram campeões em diferentes torneios disputados ao longo do ano.

De que maneira a relação corpo e mundo nos ajudam a pensar o atual momento pandêmico e, além disso, quais seriam suas implicações existenciais, isto é, de que maneira a dada situação influencia em nosso sentido de vida? Essa é nossa pergunta norteadora. O presente artigo/ensaio é uma proposta de incitar reflexões outras ou um convite ao diálogo a respeito de dimensões nas quais atravessam no ser e sentido de ser-no-mundo. Casa, corpo, mundo e tempo são exemplos de dimensões que, há pelo menos 1 ano, vem exigindo um novo posicionamento referente aos nossos valores humanos. Dessa maneira, pretende-se trazer a reflexão a distinção entre “pandemias” e COVID-19, ao modo que a primeira é o todo dos problemas estruturais e simbólicos evidenciados pelo segundo.

Este artigo tem como objetivo revisitar as trajetórias da educação em e para os Direitos Humanos no Brasil e discutir uma possibilidade prática de formação de professores de história em e para os Direitos Humanos a partir da ferramenta de pesquisa-formação denominada ateliê (auto)biográfico. O ateliê é parte de uma pesquisa de doutorado em andamento e os atores da pesquisa são professores de História em formação e bolsistas do PIBID. Iniciamos refletindo sobre os caminhos que a educação em e para os Direitos Humanos tem trilhado nas últimas décadas no Brasil e como estas trajetórias implicam no ensino de história. Em seguida apresentamos e discutimos o ateliê para defender a ideia de que ele tem a capacidade de promover reflexões e práticas relacionadas aos Direitos Humanos e contribuir com a formação para a docência no ensino de história.

A Constituicao Federal de 1988 fundou a Republica Federativa do Brasil como Estado Democratico de Direito compromissado na promocao da dignidade da pessoa humana. Nesse sentido, a dignidade humana e vetor de toda a atividade estatal, inclusive em materia penal. Entretanto, no contexto de expansao do Direito Penal decorrente do aumento expressivo da criminalidade, exsurge o discurso do Direito Penal do inimigo, modernamente apresentado por Gunther Jakobs, segundo o qual e necessario negar a condicao pessoa a certos individuos que por seu comportamento demonstrem um afastamento permanente da ordem juridica. A esses individuos, rotulados como inimigos, dispensa-se um Direito Excepcional, com caracteristicas proprias de um direito de guerra cuja finalidade e eliminar um perigo do seio social. Nas recentes legislacoes antiterroristas pelo mundo, inclusive no Brasil atraves da Lei 13.260/2016, observa-se certa aproximacao com a teoria do Direito Penal do inimigo, tendo em vista a adocao de mecanismos excepcionais de atuacao estatal, a exemplo da ampla antecipacao da intervencao penal, bem como a cominacao de penas excessivamente elevadas aos que preparam ou praticam atos de terrorismo.

Apresentação

Background: Aberrant methylation is a frequent event in oral cancer. Methods: In order to better characterize these alterations, a search for genes downregulated by aberrant methylation in oral squamous cell carcinoma (OSCC) was conducted through the mining of ORESTES dataset. Findings were further validated in OSCC cell lines and patients? samples and confirmed using TCGA data. Differentially expressed genes were identified in ORESTES libraries and validated in vitro using RT-PCR in HNSCC cell-lines and OSCC tumor samples. Further confirmation of these results was performed using mRNA expression and methylation data from The Cancer Genome Atlas (TCGA) data. Results: From the set of genes selected for validation, CA3 and FHL1 were downregulated in 60% (12/20) and 75% (15/20) of OSCC samples, respectively, and in HNSCC cell lines. The treatment of cell lines JHU-13 and FaDu with the demethylating agent 5'-aza-dC was efficient in restoring CA3 and FHL1 expression. TCGA expression and methylation data on OSCC confirms the downregulation of these genes in OSCC samples and also suggests that expression of CA3 and FHL1 is probably regulated by methylation. The downregulation of CA3 and FHL1 observed in silico was validated in HNSCC cell lines and OSCC samples, showing the feasibility of integrating different datasets to select differentially expressed genes in silico. Conclusions: These results showed that the downregulation of CA3 and FHL1 data observed in the ORESTES libraries was validated in HNSCC cell lines and OSCC samples and in a large cohort of samples from the TCGA database. Moreover, it suggests that expression of CA3 and FHL1 could probably be regulated by methylation having an important role the oral carcinogenesis. Made available in DSpace on 2020-01-07T18:10:32Z (GMT). No. of bitstreams: 1 APInVitroFelipe.pdf: 1315888 bytes, checksum: ea33d6217f7d184bc536baa3eee21e68 (MD5) Previous issue date: 2018 Article number: 193.

Introducción: Las concentraciones plasmáticas (CPs) de voriconazol (VCZ) son erráticas y en el caso de encontrarse bajo rango terapéutico para el tratamiento de aspergilosis invasora (AI) se asocian a un aumento de mortalidad. Objetivo: Analizar las CPs de VCZ obtenidas en pacientes pediátricos para alcanzar valores que se estiman efectivos para profilaxis (≥ 0,5 mg/L) y tratamiento (≥ 1,0 y 2,0 mg/L) de AI y su relación con toxicidades. Pacientes y Métodos: Análisis retrospectivo de CPs de VCZ y toxicidades asociadas obtenidas en pacientes oncológicos pediátricos desde febrero de 2013 hasta noviembre 2014. Se analizó la dosis diaria y CPs de acuerdo a la vía de administración: intravenosa (iv) u oral (vo), tipo de terapia (profilaxis y tratamiento) y edad (< 12 y ≥ 12 años). Resultados: Se analizaron 112 CPs valle de 26 pacientes, con una edad promedio de 9,3 años. El 43,7% de las CPs correspondió a administración iv. Se obtuvieron más CPs ≥ 0,5 mg/L y ≥ 1,0 mg/L con la vía iv en relación a vo (p < 0,05). Pacientes bajo 12 años de edad recibieron mayor dosis en comparación a los ≥ 12 años (medianas 18,6 y 9,2 mg/kg/día, respectivamente, p < 0,05). La dosis vo más efectiva para alcanzar CPs ≥ 0,5 mg/L fue de 200 mg cada 12 h en todos los pacientes (80-100% de CPs ≥ 0,5 mg/L). En pacientes ≥ 12 años con dosis iv entre 14 y 20 mg/kg/día, 80% de las CPs fueron ≥ 1 mg/L y ≥ 2 mg/L. En pacientes bajo 12 años de edad, dosis entre 8-30 mg/ kg/día generaron similares resultados (50-63% para CPs ≥ 1 mg/L y 36-40% para CPs ≥ 2 mg/L). Ocho pacientes (30,8%), tuvieron alguna reacción adversa al fármaco, no encontrándose relación con la CP alcanzada. Conclusión: Una dosis estándar vo de 200 mg c/12 h de VCZ mostró los mejores resultados para profilaxis de AI en todos los pacientes. Pacientes bajo 12 años de edad requerirían dosis mayores a las utilizadas en este estudio para obtener CPs efectivas para tratamiento de AI. No se encontró relación entre CPs tóxicas y reacciones adversas.

Augmented e-books provide the reader with a better quality of experience (QoE) by enriching the e-books with multimedia content and interactive elements. In the multimedia field, an improve in QoE has been performed by the use of sensory effects, creating the so-called mulsemedia applications. In this paper, it is considered that e-books augmented with mulsemedia content influence the reader perception of the history environment, besides improving its QoE. It is presented a mulsemedia setup with light, wind and audio effects, which are synchronized with a written history. Among other discoveries, the collected data suggest that such elements have a more significant influence on the reader when the environment description tend to be vague, whereas in scenes whose details are precisely described this influence is rather minored.

Flowering in citrus plants grown from seeds occurs between four to ten years; therefore, the reduction of the juvenile period is a challenge for the genetic improvement of citrus. However, the Embrapa Mandioca e Fruticultura created a hybrid called Microcitrangemonia [Lemon Tree 'Rangpur' (LCR) X Citrus 'Yuma' (CTYM) – 005) X Microcitrus papuana (MCP) – 011] which presents a short juvenile period (one year) and flowering in all seasons of the year. It has a rare genotype for citrus cultivation. Other varieties with similar characteristics are only transgenic. This work describes the genes expressed in flowering-related pathways in the citrus hybrid Microcitrangemonia, which shows early and constant flowering and compares the gene function of each pathway with the existing Arabidopsis thaliana homologues. We performed RNA extraction, RNA-sequence library construction and sequencing from leaves, reproductive buds and stems of the H011 plant. We identified flowering-related transcripts and cladograms of similarity for the SOC1, AP1 and FLC proteins. Sequence annotation showed that most of the hits are similar to Citrus sinensis, 57%, and Citrus clementina, 38.9%. Different sequences similar to 29 proteins belonging to different flowering-related pathways have been identified, such as gibberellin, photoperiod, autonomous and vernalization. The analysis of similarity allowed inferring that H011 has greater evolutionary kinship with Citrus sinensis. The outcomes contribute to the understanding of the early and constant flowering of H011 as well as provide an important resource for breeding programs in citrus aimed at juvenile period reduction. Keywords: Citrus spp, precocious, molecular, reproduction

Many economically important crops have large and complex genomes that hamper their sequencing by standard methods such as whole genome shotgun (WGS). Large tracts of methylated repeats occur in plant genomes that are interspersed by hypomethylated gene-rich regions. Gene-enrichment strategies based on methylation profiles offer an alternative to sequencing repetitive genomes. Here, we have applied methyl filtration with McrBC endonuclease digestion to enrich for euchromatic regions in the sugarcane genome. To verify the efficiency of methylation filtration and the assembly quality of sequences submitted to gene-enrichment strategy, we have compared assemblies using methyl-filtered (MF) and unfiltered (UF) libraries. The use of methy filtration allowed a better assembly by filtering out 35% of the sugarcane genome and by producing 1.5× more scaffolds and 1.7× more assembled Mb in length compared with unfiltered dataset. The coverage of sorghum coding sequences (CDS) by MF scaffolds was at least 36% higher than by the use of UF scaffolds. Using MF technology, we increased by 134× the coverage of gene regions of the monoploid sugarcane genome. The MF reads assembled into scaffolds that covered all genes of the sugarcane bacterial artificial chromosomes (BACs), 97.2% of sugarcane expressed sequence tags (ESTs), 92.7% of sugarcane RNA-seq reads and 98.4% of sorghum protein sequences. Analysis of MF scaffolds from encoded enzymes of the sucrose/starch pathway discovered 291 single-nucleotide polymorphisms (SNPs) in the wild sugarcane species, S. spontaneum and S. officinarum. A large number of microRNA genes was also identified in the MF scaffolds. The information achieved by the MF dataset provides a valuable tool for genomic research in the genus Saccharum and for improvement of sugarcane as a biofuel crop.

Background Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome. Results We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. Conclusion These results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.

Background Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited. Results We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains. Conclusions InteractiVenn allows set unions in Venn diagrams to be explored thoroughly, by consequence extending the ability to analyze combinations of sets with additional observations, yielded by novel interactions between joined sets. InteractiVenn is freely available online at: www.interactivenn.net.

In this article, we selected some analyses developed from questions of the entitled research Curriculum policies of the History teaching: the time games and language games. This project has a profile that investigates the senses of subject and time in the curriculum policy of History of the municipal schools of a Santa Catarina city, built by teachers, in the context of National Curriculum Parameters of History orientations. In this specific part of the article, we analyzed the senses of time of that curriculum policy and took as empiricism the current curriculum, created in 2011, that is analyzed from the suggestions of “chains of equivalence”, “significant void” and disputes by “hegemonies” studied by Ernesto Laclau (2011). In the field of education and curriculum, we approached the research by Alice Casimiro Lopes (2012), Alice Casemiro Lopes and Danielle dos Santos Matheus (2011), as also the investigations by Elizabeth Macedo (2006, 2009) and the theories by Carmen Teresa Gabriel (2011, 2013). In the first section, we did a brief cartography of the discussions about time considering what matters to a short panorama of the established debates over the theme in multiple areas of knowledge. In sequence, we highlighted the discussions in the consolidated concept of time in the field of History, as well as the ones related to time and teaching of History. Based on those arguments, we socialized the analyses about the senses of time that are mobilized in this curriculum policy. Keywords: curriculum, public policies, History teaching, time.

Nitric oxide (NO) exerts pleiotropic effects on plant development; however, its involvement in cell wall modification during root hair formation (RHF) has not yet been addressed. Here, mutants of Arabidopsis thaliana with altered root hair phenotypes were used to assess the involvement of S-nitrosoglutathione (GSNO), the primary NO source, in cell wall dynamics and gene expression in roots induced to form hairs. GSNO and auxin restored the root hair phenotype of the hairless root hair defective 6 (rhd6) mutant. A positive correlation was observed between increased NO production and RHF induced by auxin in rhd6 and transparent testa glabra (ttg) mutants. Deposition of an epitope within rhamnogalacturonan-I recognized by the CCRC-M2 antibody was delayed in root hair cells (trichoblasts) compared with nonhair cells (atrichoblasts). GSNO, but not auxin, restored the wild-type root glycome and transcriptome profiles in rhd6, modulating the expression of a large number of genes related to cell wall composition and metabolism, as well as those encoding ribosomal proteins, DNA and histone-modifying enzymes and proteins involved in post-translational modification. Our results demonstrate that NO plays a key role in cell wall remodelling in trichoblasts and suggest that it also participates in chromatin modification in root cells of A. thaliana.

The presence of aluminum (Al) is one of the main factors limiting crop yield in Brazil and worldwide. Plant responses to Al are complex, and the use of techniques such as microarrays can facilitate their comprehension. In a previous work, we evaluated the transcriptome of two maize lines, Cat100-6 and S1587-17, after growing the plants for 1 or 3 days in acid soil (pH 4.1) or alkaline soil with Ca(OH)₂ (pH 5.5), and we identified genes that likely contribute to Al tolerance. The mapping of these genes to the chromosomes allowed the identification of the genes that are localized in maize QTLs previously reported in the literature as associated with the tolerant phenotype. We were able to map genes encoding proteins possibly involved with acid soil tolerance, such as the ones encoding an RNA binding protein, a protease inhibitor, replication factors, xyloglucan endotransglycosylase and cyclins, inside QTLs known to be important for the Al-tolerant phenotype.

The aim of this study was to investigate the molecular mechanisms underlying drought acclimation in coffee plants by the identification of candidate genes (CGs) using different approaches. The first approach used the data generated during the Brazilian Coffee expressed sequence tag (EST) project to select 13 CGs by an in silico analysis (electronic northern). The second approach was based on screening macroarrays spotted with plasmid DNA (coffee ESTs) with separate hybridizations using leaf cDNA probes from drought-tolerant and susceptible clones of Coffea canephora var. Conilon, grown under different water regimes. This allowed the isolation of seven additional CGs. The third approach used two-dimensional gel electrophoresis to identify proteins displaying differential accumulation in leaves of drought-tolerant and susceptible clones of C. canephora. Six of them were characterized by MALDI-TOF-MS/MS (matrix-assisted laser desorption-time of flight-tandem mass spectrometry) and the corresponding proteins were identified. Finally, additional CGs were selected from the literature, and quantitative real-time polymerase chain reaction (qPCR) was performed to analyse the expression of all identified CGs. Altogether, >40 genes presenting differential gene expression during drought acclimation were identified, some of them showing different expression profiles between drought-tolerant and susceptible clones. Based on the obtained results, it can be concluded that factors involved a complex network of responses probably involving the abscisic signalling pathway and nitric oxide are major molecular determinants that might explain the better efficiency in controlling stomata closure and transpiration displayed by drought-tolerant clones of C. canephora.

In apomixis, asexual mode of plant reproduction through seeds, an unreduced megagametophyte is formed due to circumvented or altered meiosis. The embryo develops autonomously from the unreduced egg cell, independently of fertilization. Brachiaria is a genus of tropical forage grasses that reproduces sexually or by apomixis. A limited number of studies have reported the sequencing of apomixis-related genes and a few Brachiaria sequences have been deposited at genebank databases. This work shows sequencing and expression analyses of expressed sequence-tags (ESTs) of Brachiaria genus and points to transcripts from ovaries with preferential expression at megasporogenesis in apomictic plants. From the 11 differentially expressed sequences from immature ovaries of sexual and apomictic Brachiaria brizantha obtained from macroarray analysis, 9 were preferentially detected in ovaries of apomicts, as confirmed by RT-qPCR. A putative involvement in early steps of Panicum-type embryo sac differentiation of four sequences from B. brizantha ovaries: BbrizHelic, BbrizRan, BbrizSec13 and BbrizSti1 is suggested. Two of these, BbrizSti1 and BbrizHelic, with similarity to a gene coding to stress induced protein and a helicase, respectively, are preferentially expressed in the early stages of apomictic ovaries development, especially in the nucellus, in a stage previous to the differentiation of aposporous initials, as verified by in situ hybridization.

Peanut (Arachis hypogaea) is amongst the most important legume crops in the world. One of its main yield constraints is the root-knot nematode Meloidogyne arenaria. A number of wild Arachis species, including A. stenosperma, are resistant to nematodes, and are a potential source of new resistance alleles for cultivated peanut. Using in silico subtraction of ESTs and macroarray analysis, we identified genes differentially expressed in A. stenosperma roots during its resistance response to M. arenaria. The three most differentially expressed genes [Auxin Repressed Protein (AsARP), Cytokinin Oxidase (AsCKX) and Metallothionein Type 2 (AsMET2)] were further analyzed using northern-blot and showed distinct expression profiles in the resistant A. stenosperma and susceptible A. hypogaea, both after, and sometimes even before, challenge with nematodes. Of the three most differentially expressed genes, AsARP and AsCKX are potentially involved in plant hormonal balance, and AsMET2 may be related to the reactive oxygen reaction triggered by the hypersensitive response (HR).

The transcriptome-wide endosperm-preferred expression of maize genes was addressed by analyzing a large database of expressed sequence tags (ESTs). We generated 30,531 high quality sequence-reads from the 5'-ends of cDNA libraries from maize endosperm harvested at 10, 15, and 20 days after pollination. A further 196,900 maize sequence-reads retrieved from public databases were added to this endosperm collection to generate MAIZEST, a database with tools for data storage and analysis. MAIZEST contains 227,431 ESTs, one third of which represents developing endosperm and the remaining two-thirds represent transcripts from 49 cDNA libraries constructed from different organs and tissues. Assembling the MAIZEST ESTs generated 29,206 putative transcripts, of which a set of 4032 assembled sequences was composed exclusively of sequences derived from endosperm cDNA libraries. After sequence analysis using overlapping parameters, a sub-set of 2403 assembled sequences was functionally annotated and revealed a wide variety of putative new genes involved in endosperm development and metabolism.

In view of the medical, sanitary and forensic importance of Chrysomya species, a knowledge of their nucleotide sequences would be useful for the molecular characterization of this genus, and would help in designing primers and in improving the molecular identification of Calliphoridae species. In this work, the mitochondrial genome of the blowfly Chrysomya chloropyga (Diptera: Calliphoridae) was completely sequenced. The entire mitochondrial DNA (mtDNA) molecule was 15,837 bp long and was sequenced using the shotgun approach. The overall nucleotide composition was heavily biased towards As and Ts, which accounted for 76.7% of the whole genome. The cox1 gene had a serine as the start codon, while incomplete termination codons mediated by tRNA signals were found for cox2 , nd4 and nd5 . The C. chloropyga genes were in the same order and orientation as the mitochondrial genome of other dipteran species, except for the occurrence of a 123 bp region that included a complete duplication of tRNA Ile and a partial duplication of tRNA Gln genes. C. chloropyga is the first species of Diptera with 23 tRNA genes instead of the usual 22 already described. A phylogenetic analysis showed a split of Brachycera into Calyptratae and Acalyptratae subdivisions. The complete sequence of C. chloropyga mtDNA described here will be a useful source of sequence information for general molecular and evolutionary studies in Diptera.

Over 40,000 sugarcane (Saccharum officinarum) consensus sequences assembled from 237,954 expressed sequence tags were compared with the protein and DNA sequences from other angiosperms, including the genomes of Arabidopsis and rice (Oryza sativa). Approximately two-thirds of the sugarcane transcriptome have similar sequences in Arabidopsis. These sequences may represent a core set of proteins or protein domains that are conserved among monocots and eudicots and probably encode for essential angiosperm functions. The remaining sequences represent putative monocot-specific genetic material, one-half of which were found only in sugarcane. These monocot-specific cDNAs represent either novelties or, in many cases, fast-evolving sequences that diverged substantially from their eudicot homologs. The wide comparative genome analysis presented here provides information on the evolutionary changes that underlie the divergence of monocots and eudicots. Our comparative analysis also led to the identification of several not yet annotated putative genes and possible gene loss events in Arabidopsis.

Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium) to generate ~80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae) and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade). Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily) were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i) anatomical differentiation of spinning glands and (ii) behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution. Made available in DSpace on 2013-04-02T23:33:43Z (GMT). No. of bitstreams: 1 spinningjournal.pone.0021634.pdf: 1140596 bytes, checksum: 76fd13b774c83ae57842557cf8eda437 (MD5) Previous issue date: 2011-10-04

Background Aluminum (Al) toxicity is one of the most important yield-limiting factors of many crops worldwide. The primary symptom of Al toxicity syndrome is the inhibition of root growth leading to poor water and nutrient absorption. Al tolerance has been extensively studied using hydroponic experiments. However, unlike soil conditions, this method does not address all of the components that are necessary for proper root growth and development. In the present study, we grew two maize genotypes with contrasting tolerance to Al in soil containing toxic levels of Al and then compared their transcriptomic responses. Results When grown in acid soil containing toxic levels of Al, the Al-sensitive genotype (S1587-17) showed greater root growth inhibition, more Al accumulation and more callose deposition in root tips than did the tolerant genotype (Cat100-6). Transcriptome profiling showed a higher number of genes differentially expressed in S1587-17 grown in acid soil, probably due to secondary effects of Al toxicity. Genes involved in the biosynthesis of organic acids, which are frequently associated with an Al tolerance response, were not differentially regulated in both genotypes after acid soil exposure. However, genes related to the biosynthesis of auxin, ethylene and lignin were up-regulated in the Al-sensitive genotype, indicating that these pathways might be associated with root growth inhibition. By comparing the two maize lines, we were able to discover genes up-regulated only in the Al-tolerant line that also presented higher absolute levels than those observed in the Al-sensitive line. These genes encoded a lipase hydrolase, a retinol dehydrogenase, a glycine-rich protein, a member of the WRKY transcriptional family and two unknown proteins. Conclusions This work provides the first characterization of the physiological and transcriptional responses of maize roots when grown in acid soil containing toxic levels of Al. The transcriptome profiles highlighted several pathways that are related to Al toxicity and tolerance during growth in acid soil. We found several genes that were not found in previous studies using hydroponic experiments, increasing our understanding of plant responses to acid soil. The use of two germplasms with markedly different Al tolerances allowed the identification of genes that are a valuable tool for assessing the mechanisms of Al tolerance in maize in acid soil.

Soil acidity limits crop yields worldwide and is a common result of aluminum (Al) phytotoxicity, which is known to inhibit root growth. Here, we compared the transcriptome of leaves from maize seedlings grown under control conditions (soil without free Al) and under acidic soil containing toxic levels of Al. This study reports, for the first time, the complex transcriptional changes that occur in the leaves of maize plants grown in acidic soil with phytotoxic levels of Al. Our data indicate that 668 genes were differentially expressed in the leaves of plants grown in acidic soil, which is significantly greater than that observed in our previous work with roots. Genes encoding TCA cycle enzymes were upregulated, although no specific transporter of organic acids was differentially expressed in leaves. We also provide evidence for positive roles for auxin and brassinosteroids in Al tolerance, whereas gibberellin and jasmonate may have negative roles. Our data indicate that plant responses to acidic soil with high Al content are not restricted to the root; tolerance mechanisms are also displayed in the aerial parts of the plant, thus indicating that the entire plant responds to stress.

Several Brazilian sugarcane varieties have the ability to grow with little addition of inorganic nitrogen fertilizers, showing high contributions of Biological Nitrogen Fixation (BNF). A particular type of nitrogen-fixing association has been described in this crop, where endophytic diazotrophs such as Gluconacetobacter diazotrophicus and Herbaspirillum spp. colonize plant tissues without causing disease symptoms. In order to gain insight into the role played by the sugarcane in the interaction between this plant and endophytic diazotrophs, we investigated gene expression profiles of sugarcane plants colonized by G. diazotrophicus and H. rubrisubalbicans by searching the sugarcane expressed sequence tag SUCEST Database (http://sucest.lad.ic.unicamp.br/en/). We produced an inventory of sugarcane genes, candidates for exclusive or preferential expression during the nitrogen-fixing association. This data suggests that the host plant might be actively involved in the establishment of the interaction with G. diazotrophicus and H. rubrisubalbicans.Diversos genótipos brasileiros de cana-de-açúcar são capazes de crescer com baixa adição de adubos nitrogenados, obtendo elevadas contribuições da Fixação Biológica de Nitrogênio (FBN). Um tipo especial de associação com bactérias fixadoras de nitrogênio foi descrito em cana-de-açúcar, onde as bactérias endofíticas, como Gluconacetobacter diazotrophicus e Herbaspirillum spp., colonizam o interior dos tecidos vegetais, sem causar sintomas de doença. Com o objetivo de tentar entender o papel da cana-de-açúcar nesse tipo de associação, nós investigamos os perfis de expressão gênica de plantas colonizadas pelos diazotróficos endofíticos, usando o banco de dados do SUCEST. Um catálogo com os genes de cana-de-açúcar que são candidatos a se expressar exclusivamente ou preferencialmente durante a associação foi gerado. Esses dados preliminares sugerem que a cana-de-açúcar deve ter uma participação ativa na interação, respondendo a diversos processos metabólicos durante a associação.

The Gram-negative bacterium Xylella fastidiosa was the first plant pathogen to be completely sequenced. This species causes several economically important plant diseases, including citrus variegated chlorosis (CVC). Analysis of the genomic sequence of X. fastidiosa revealed a 12 kb DNA fragment containing an operon closely related to the gum operon of Xanthomonas campestris. The presence of all genes involved in the synthesis of sugar precursors, existence of exopolysaccharide (EPS) production regulators in the genome, and the absence of three of the X. campestris gum genes suggested that X. fastidiosa is able to synthesize an EPS different from that of xanthan gum. This novel EPS probably consists of polymerized tetrasaccharide repeating units assembled by the sequential addition of glucose-1-phosphate, glucose, mannose and glucuronic acid on a polyprenol phosphate carrier.

A RT-PCR assay was developed for early and accurate detection of Papaya meleira virus (PMeV) in the latex from infected papayas. The meleira disease is characterized by an excessive exudation of more fluidic latex from fruits, leaves and stems. This latex oxidises and gives the fruit a ¿sticky¿ texture. In the field, disease symptoms are seen almost exclusively on fruit. However, infected plants can be a source of virus for dissemination by insects. Primers specific for PMeV were designed based on nucleotide sequences of the viral dsRNA obtained using a RT-RAPD approach. When tested for RT-PCR amplification, one of these primers (C05-3¿) amplified a 669-nucleotide fragment using dsRNA obtained from purified virus particles as a template. The translated sequence of this DNA fragment showed a certain degree of similarity to the amino acid sequence of RNA-dependent RNA polymerases from other dsRNA viruses. When used as the single primer in two RT-PCR kits available commercially, primer C05-3¿ also amplified the DNA fragment from papaya latex of infected, but not from healthy plants. The RT-PCR-based method developed in this study could simplify early plant disease diagnosis, assist in monitoring the dissemination of the pathogen within and between fields, and assist in guiding plant disease management.

Background Sugarcane breeding has significantly progressed in the last 30 years, but achieving additional yield gains has been difficult because of the constraints imposed by the complex ploidy of this crop. Sugarcane cultivars are interspecific hybrids between Saccharum officinarum and Saccharum spontaneum. S. officinarum is an octoploid with 2n = 80 chromosomes while S. spontaneum has 2n = 40 to 128 chromosomes and ploidy varying from 5 to 16. The hybrid genome is composed of 70-80% S. officinaram and 5-20% S. spontaneum chromosomes and a small proportion of recombinants. Sequencing the genome of this complex crop may help identify useful genes, either per se or through comparative genomics using closely related grasses. The construction and sequencing of a bacterial artificial chromosome (BAC) library of an elite commercial variety of sugarcane could help assembly the sugarcane genome. Results A BAC library designated SS_SBa was constructed with DNA isolated from the commercial sugarcane variety SP80-3280. The library contains 36,864 clones with an average insert size of 125 Kb, 88% of which has inserts larger than 90 Kb. Based on the estimated genome size of 760–930 Mb, the library exhibits 5–6 times coverage the monoploid sugarcane genome. Bidirectional BAC end sequencing (BESs) from a random sample of 192 BAC clones sampled genes and repetitive elements of the sugarcane genome. Forty-five per cent of the total BES nucleotides represents repetitive elements, 83% of which belonging to LTR retrotransposons. Alignment of BESs corresponding to 42 BACs to the genome sequence of the 10 sorghum chromosomes revealed regions of microsynteny, with expansions and contractions of sorghum genome regions relative to the sugarcane BAC clones. In general, the sampled sorghum genome regions presented an average 29% expansion in relation to the sugarcane syntenic BACs. Conclusion The SS_SBa BAC library represents a new resource for sugarcane genome sequencing. An analysis of insert size, genome coverage and orthologous alignment with the sorghum genome revealed that the library presents whole genome coverage. The comparison of syntenic regions of the sorghum genome to 42 SS_SBa BES pairs revealed that the sorghum genome is expanded in relation to the sugarcane genome.