The draft genome of Ciona intestinalis: Insights into chordate and vertebrate origins

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains similar to16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.

Adoption and maintenance of contour bunds and hedgerows in a dynamic environment - Experience in the Philippine uplands

The widespread adoption of soil conservation technologies by farmers (notably contour hedgerows) observed in Guba, Cebu City, Philippines, is not often observed elsewhere In the country. Adoption of these technologies was because of the interaction of such phenomena as site-specific factors, appropriate extension systems, and technologies. However, lack of hedgerow maintenance, decreasing hedgerow quality, and disappearance of hedgerows raised concerns about sustainability. The dynamic nature of upland farming systems suggests the need for a location-specific farming system development framework, which provides farmers with ongoing extension for continual promotion of appropriate conservation practices.

pido, a non-long terminal repeat retrotransposon of the chicken repeat 1 family from the genome of the Oriental blood fluke, Schistosoma japonicum

A newly described non-long terminal repeat (non-LTR) retrotransposon element was isolated from the genome of the Oriental schistosome, Schistosoma japonicum. At least 1000 partial copies of the element, which was named pido, were dispersed throughout the genome of S. japonicum. As is usual with non-LTR retrotransposons, it is expected that many pido elements will be 5'-truncated. A consensus sequence of 3564 bp of the truncated pido element was assembled from several genomic fragments that contained pido-hybridizing sequences. The sequence encoded part of the first open reading frame (ORF), the entire second ORF and, at its 3'-terminus, a tandemly repetitive, A-rich (TA(6)TA(5)TA(8)) tail, The ORF1 of pido encoded a nucleic acid binding protein and ORF2 encoded a retroviral-like polyprotein that included apurinic/apyrimidinic endonuclease (EN) and reverse transcriptase (RT) domains, in that order. Based on its sequence and structure, and phylogenetic analyses of both the RT and EN domains, pido belongs to the chicken repeat 1 (CR1)-like lineage of elements known from the chicken, turtle, puffer fish, mosquitoes and other taxa. pido shared equal similarity with CRI from chicken, an uncharacterized retrotransposon from Caenorhabditis elegans and SR1 (a non-LTR retrotransposon) from the related blood fluke Schistosoma mansoni; the level of similarity between pido and SR1 indicated that these two schistosome retrotransposons were related but not orthologous. The findings indicate that schistosomes have been colonized by at least two discrete CRI-like elements. Whereas pido did not appear to have a tight target site specificity, at least one copy of pido has inserted into the 3'-untranslated region of a protein-encoding gene (GeriBank AW736757) of as yet unknown identity. mRNA encoding the RT of pido was detected by reverse transcription-polymerase chain reaction in the egg, miracidium. and adult developmental stages of S. japonicum, indicating that the RT domain was transcribed and suggesting that pido was replicating actively and mobile within the S. japonicum genome. (C) 2002 Elsevier Science B.V. All rights reserved.

Significance in replication of the terminal nucleotides of the Flavivirus genome

Point mutations that resulted in a substitution of the conserved 3'-penultimate cytidine in genomic RNA or the RNA negative strand of the self-amplifying replicon of the Flavivirus Kunjin virus completely blocked in vivo replication. Similarly, substitutions of the conserved 3'-terminal uridine in the RNA negative or positive strand completely blocked replication or caused much-reduced replication, respectively. The same preference for cytidine in the 3'-terminal dinucleotide was noted in reports of the in vitro activity of the RNA-dependent RNA polymerase (RdRp) for the other genera of Flaviviridae that also employ a double-stranded RNA (dsRNA) template to initiate asymmetric semiconservative RNA positive-strand synthesis. The Kunjin virus replicon results were interpreted in the context of a proposed model for initiation of RNA synthesis based on the solved crystal structure of the RdRp of phi6 bacteriophage, which also replicates efficiently using a dsRNA template with conserved 3'-penultimate cytidines and a 3'-terminal pyrimidine. A previously untested substitution of the conserved pentanucleotide at the top of the 3'-terminal stem-loop of all Flavivirus species also blocked detectable in vivo replication of the Kunjin virus replicon RNA.

The highly rearranged mitochondrial genome of the plague thrips, Thrips imaginis (Insecta : thysanoptera): Convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes

To help understand the mechanisms of gene rearrangement in the mitochondrial (mt) genomes of hemipteroid insects, we sequenced the mt genome of the plague thrips, Thrips imaginis (Thysanoptera). This genome is circular, 15,407 by long, and has many unusual features, including (1) rRNA genes inverted and distant from one another, (2) an extra gene for tRNA-Ser, (3) a tRNA-Val lacking a D-arm, (4) two pseudo-tRNA genes, (5) duplicate control regions, and (6) translocations and/or inversions of 24 of the 37 genes. The mechanism of rRNA gene transcription in T. imaginis may be different from that of other arthropods since the two rRNA genes have inverted and are distant from one another. Further, the rRNA genes are not adjacent or even close to either of the two control regions. Tandem duplication and deletion is a plausible model for the evolution of duplicate control regions and for the gene translocations, but intramitochondrial recombination may account for the gene inversions in T. imaginis. All the 18 genes between control regions #1 and #2 have translocated and/or inverted, whereas only six of the 20 genes outside this region have translocated and/or inverted. Moreover, the extra tRNA gene and the two pseudo-tRNA genes are either in this region or immediately adjacent to one of the control regions. These observations suggest that tandem duplication and deletion may be facilitated by the duplicate control regions and may have occurred a number of times in the lineage leading to T. imaginis. T. imaginis shares two novel gene boundaries with a lepidopsocid species from another order of hemipteroid insects, the Psocoptera. The evidence available suggests that these shared gene boundaries evolved by convergence and thus are not informative for the interordinal phylogeny of hemipteroid insects. We discuss the potential of hemipteroid insects as a model system for studies of the evolution of animal rut genomes and outline some fundamental questions that may be addressed with this system.

Histogram-based DNA analysis for the visualization of chromosome, genome and species information

We describe a novel approach to explore DNA nucleotide sequence data, aiming to produce high-level categorical and structural information about the underlying chromosomes, genomes and species. The article starts by analyzing chromosomal data through histograms using fixed length DNA sequences. After creating the DNA-related histograms, a correlation between pairs of histograms is computed, producing a global correlation matrix. These data are then used as input to several data processing methods for information extraction and tabular/graphical output generation. A set of 18 species is processed and the extensive results reveal that the proposed method is able to generate significant and diversified outputs, in good accordance with current scientific knowledge in domains such as genomics and phylogenetics.

Maintenance of fire sprinkler systems based on the dynamic assessment of its condition

Safety is one of the major concerns of process safety engineers in most industrial facilities all over the world. To this scope, some events play an important role once the effect of their consequences can be assumed as totally undesirable. One of these events refers to the occurrence of a fire. Such event can result in catastrophic consequences for life, equipment, and continuity of activities or even leading to environmental damage. A fire protection equipment with low reliability means that this equipment are often unavailable and thus the risk of a fire increases. Maintenance of fire protection equipment is very important because this kind of systems is mostly in a dormant mode, which gives uncertainty about their operability when demanded in a real situation of fire. This article outlines the importance of tests, inspection, and maintenance operations in the context of a fire sprinkler system and proposes a methodology based on international standards and supported by test/inspection reports to correct the frequency of these actions according to the level of degradation of the components and regarding safety purposes. © 2015 American Institute of Chemical Engineers.

The influence of the human genome on chronic viral hepatitis outcome

The mechanisms that determine viral clearance or viral persistence in chronic viral hepatitis have yet to be identified. Recent advances in molecular genetics have permitted the detection of variations in immune response, often associated with polymorphism in the human genome. Differences in host susceptibility to infectious disease and disease severity cannot be attributed solely to the virulence of microbial agents. Several recent advances concerning the influence of human genes in chronic viral hepatitis B and C are discussed in this article: a) the associations between human leukocyte antigen polymorphism and viral hepatic disease susceptibility or resistance; b) protective alleles influencing hepatitis B virus (HBV) and hepatitis C virus (HCV) evolution; c) prejudicial alleles influencing HBV and HCV; d) candidate genes associated with HBV and HCV evolution; d) other genetic factors that may contribute to chronic hepatitis C evolution (genes influencing hepatic stellate cells, TGF-beta1 and TNF-alpha production, hepatic iron deposits and angiotensin II production, among others). Recent discoveries regarding genetic associations with chronic viral hepatitis may provide clues to understanding the development of end-stage complications such as cirrhosis or hepatocellular carcinoma. In the near future, analysis of the human genome will allow the elucidation of both the natural course of viral hepatitis and its response to therapy.

Integration of the project team in the classic maintenance cycle

A manutenção é uma área extremamente importante, principalmente na indústria. Devidamente organizada, permitirá um fluxo produtivo devidamente planeado e executado, que permitirá a qualquer empresa manter o nível de facturação desejado e o prazo de entrega acordado com os clientes. De outra forma, poderá originar o caos. No entanto, os desafios de gestão da produção mais correntes, nomeadamente através do Lean Manufacturing, passam a exigir um pouco mais do que uma simples manutenção. Torna-se obrigatório fazer análises económicas que permitam averiguar quando cada equipamento passa a exigir custos de manutenção excessivos, os quais poderão obrigar a um recondicionamento mais acentuado do equipamento, o qual pode passar inclusivamente por uma melhoria da sua performance. Nestes casos, terá que existir uma “cumplicidade” entre a Direcção de Produção e a Manutenção, no sentido de averiguar o melhor momento para proceder a uma melhoria do equipamento, numa perspectiva de funcionamento global em linha de produção, adaptando-o à performance que será exigida ao conjunto. Neste domínio, o Projecto passa a prestar um serviço valiosíssimo à empresa, integrando-se no conjunto Produção + Manutenção, criando valor na intervenção, através do desenvolvimento de um trabalho que permite não só repor o estado natural da produção, mas sim promover uma melhoria sustentada da mesma. Este trabalho pretende reflectir e avaliar a relevância do Projecto neste tipo de operações, contribuindo de uma forma sistemática e sustentada para a melhoria contínua dos processos de fabrico. É apresentado um caso de estudo que pretende validar todo o desenvolvimento anteriormente realizado na matéria.

Aircraft Engines Maintenance Costs and Reliability: An Appraisal of the Decision Process to Remove an Engine for a Shop Visit Aiming at Minimum Maintenance Unit Cost

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação.

Identification of CNVs on the genome of Brazilian chicken lines.

2016

Deciphering the genome of Desulfovibrio gigas: the role of the hydrogenases

The work presented in this thesis describes the functional characterization of hydrogenases in the overall energy metabolism of the sulfate reducing bacterium Desulfovibrio gigas. With the complete annotation of the D. gigas genome, we were able to verify that only the two previously described hydrogenases are present in this organism, the periplasmic [NiFe] HynAB and the cytoplasmic membrane-bound [NiFe] Ech.(...)

Restriction enzyme analysis of the human cytomegalovirus genome in specimens collected from immunodeficient patients in Belém, State of Pará, Brazil

INTRODUCTION: Human cytomegalovirus is an opportunistic betaherpesvirus that causes persistent and serious infections in immunodeficient patients. Recurrent infections occur due to the presence of the virus in a latent state in some cell types. It is possible to examine the virus using molecular methods to aid in the immunological diagnosis and to generate a molecular viral profile in immunodeficient patients. The objective of this study was to characterize cytomegalovirus genotypes and to generate the epidemiological and molecular viral profile in immunodeficient patients. METHODS: A total of 105 samples were collected from immunodeficient patients from the City of Belém, including newborns, hemodialysis patients, transplant recipients and HIV+ patients. An IgG and IgM antibody study was completed using ELISA, and enzymatic analysis by restriction fragment length polymorphism (RFLP) was performed to characterize viral genotypes. RESULTS: It was observed that 100% of the patients had IgG antibodies, 87% of which were IgG+/IgM-, consistent with a prior infection profile, 13% were IgG+/IgM+, suggestive of recent infection. The newborn group had the highest frequency (27%) of the IgG+/IgM+ profile. By RFLP analysis, only one genotype was observed, gB2, which corresponded to the standard AD169 strain. CONCLUSIONS: The presence of IgM antibodies in new borns indicates that HCMV continues to be an important cause of congenital infection. The low observed genotypic diversity could be attributed to the small sample size because newborns were excluded from the RFLP analysis. This study will be continued including samples from newborns to extend the knowledge of the general and molecular epidemiology of HCMV in immunodeficient patients.

Basic sanitation, socioeconomic conditions, and degree of risk for the presence and maintenance of malaria in a low-transmission area in the Brazilian Amazon

ABSTRACTINTRODUCTION:This study aimed to evaluate basic sanitation and socioeconomic indicators, reported cases of malaria, and risk of contracting malaria in the Ananindeua municipality, State of Pará.METHODS:Data on basic sanitation and socioeconomic dimensions were taken from the Brazilian Institute of Geography and Statistics [ Instituto Brasileiro de Geografia e Estatística (IBGE)] 2010 census. Epidemiological malaria information was taken from the Epidemiological Malaria Surveillance Information System [ Sistema de Informação de Vigilância Epidemiológica de Malária (SIVEP/Malaria)], between 2003 and 2013 of the Ministry of Health and from the SIVEP/Malaria forms of the municipality's Endemic Diseases Unit for 2,013 cases.RESULTS:Our data do not confirm the correlation among indicators of basic sanitation, socioeconomic conditions, and water supply with malaria cases. Of the 1,557 cases evaluated, most were caused by Plasmodium vivax , with rare cases of Plasmodium falciparum and mixed infections. There were 756 notifications in 2003. The number of reported cases was sharply reduced between 2006 and 2012, but a 142-case outbreak occurred in 2013. Ananindeua municipality's Annual Parasite Index indicated low risk in 2003 and no risk in other years, and the 2,013 cases were predominantly male individuals aged ≥40 years.CONCLUSIONS:Our data confirm the non-endemicity of malaria in the Ananindeua municipality, as the Annual Parasite Indices described for the years 2004-2013 classify it as a risk-free area. However, the 2013 outbreak indicates the need to strengthen prevention, surveillance, and control activities to reduce the risk of new outbreaks and consequent economic and social impacts on the population.