Apprentissage mobile et acquisition de la compétence pluriculturelle

Directory of Open Access Journals (Sweden)

LI Yue

2016-11-01

Full Text Available À mesure de l’évolution accélérée des technologies modernes, de nouveaux moyens d’apprentissage sont apparus dans le domaine de l’éducation, ce qui nous amène à nous demander comment en profiter en vue de favoriser l’enseignement/apprentissage du FLE. Dans cet article, nous prêtons une attention particulière à l’application de l’apprentissage mobile dans l’acquisition de la compétence pluriculturelle. Après une analyse de la compétence pluriculturelle, de l’apprentissage mobile, et de sa potentialité de développement en Chine, nous présentons les applications potentielles de l’apprentissage mobile dans l’acquisition de la compétence pluriculturelle des apprenants chinois de français.

CompTIA A+ complete study guide exams 220-801 and 220-802

CERN Document Server

Docter, Quentin; Skandier, Toby

2012-01-01

CompTIA Authorized, fully updated Study Guide for the leading IT certification: CompTIA A+ CompTIA A+ is the de facto certification for IT technicians. Some vendors even require employees to achieve certification as part of their job training. This book prepares you for both required exams: 220-801 and 220-802. Totally updated to cover the 2012 exams, this popular prep guide covers all the exam objectives. Readers will also have access to additional study tools, including the Sybex Test Engine with bonus practice exams, electronic flashcards, and a glossary of important terms in searchable PD

MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics.

Science.gov (United States)

Zhai, Peng; Yang, Longshu; Guo, Xiao; Wang, Zhe; Guo, Jiangtao; Wang, Xiaoqi; Zhu, Huaiqiu

2017-10-02

During the past decade, the development of high throughput nucleic sequencing and mass spectrometry analysis techniques have enabled the characterization of microbial communities through metagenomics, metatranscriptomics, metaproteomics and metabolomics data. To reveal the diversity of microbial communities and interactions between living conditions and microbes, it is necessary to introduce comparative analysis based upon integration of all four types of data mentioned above. Comparative meta-omics, especially comparative metageomics, has been established as a routine process to highlight the significant differences in taxon composition and functional gene abundance among microbiota samples. Meanwhile, biologists are increasingly concerning about the correlations between meta-omics features and environmental factors, which may further decipher the adaptation strategy of a microbial community. We developed a graphical comprehensive analysis software named MetaComp comprising a series of statistical analysis approaches with visualized results for metagenomics and other meta-omics data comparison. This software is capable to read files generated by a variety of upstream programs. After data loading, analyses such as multivariate statistics, hypothesis testing of two-sample, multi-sample as well as two-group sample and a novel function-regression analysis of environmental factors are offered. Here, regression analysis regards meta-omic features as independent variable and environmental factors as dependent variables. Moreover, MetaComp is capable to automatically choose an appropriate two-group sample test based upon the traits of input abundance profiles. We further evaluate the performance of its choice, and exhibit applications for metagenomics, metaproteomics and metabolomics samples. MetaComp, an integrative software capable for applying to all meta-omics data, originally distills the influence of living environment on microbial community by regression analysis

Autosomal dominant precocious osteoarthropathy due to a mutation of the cartilage oligomeric matrix protein (COMP) gene: further expansion of the phenotypic variations of COMP defects

Energy Technology Data Exchange (ETDEWEB)

Kawaji, Hiroyuki [Department of Orthopaedic Surgery, Sanyudo Hospital, 6-1-219 Chuou, Yonezawa, Yamagata 992-0045 (Japan); Nishimura, Gen [Department of Radiology, Nasu Chuou Hospital, Tochigi (Japan); Watanabe, Sobei; Sasaki, Akira; Sano, Tokuhisa [Department of Orthopaedic Surgery, Tohoku Kohsei-Nenkin Hospital, Miyagi (Japan); Mabuchi, Akihiko; Ikeda, Toshiyuki; Ikegawa, Shiro [Laboratory for Bone and Joint Diseases, SNP Research Center, Tokyo (Japan); Ohashi, Hirofumi [Division of Medical Genetics, Saitama Children' s Medical Center, Saitama (Japan)

2002-12-01

We report on a Japanese family of four generations with an autosomal dominant precocious osteoarthropathy. The cardinal clinical manifestations of affected individuals were painful weight-bearing large joints, which started in late childhood or adolescence. The radiological hallmarks included coxa plana, mild epiphyseal dysplasia of the knee, and round talar domes with tibiotalar slant in childhood, which evolved into degenerative joint diseases in adulthood. The disease phenotype was cosegregated with a mutation of the cartilage oligomeric matrix protein (COMP) gene in the family members, who underwent molecular evaluation. COMP mutations have been reported in a mild form of multiple epiphyseal dysplasia (MED), Ribbing type, as well as allied disorders with more severe manifestations, such as MED Fairbank type and pseudoachondroplasia. Unlike previously reported cases with the Ribbing type, the present patients did not have short stature or brachydactyly. This report expands further the phenotypic variations of COMP defects. (orig.)

Compétences pour les PME de l'Amérique centrale dans l'économie ...

International Development Research Centre (IDRC) Digital Library (Canada)

... compétences nécessaires; b) des recherches pour comprendre les modèles sociaux ... Il existe un lien bien documenté entre les compétences nécessaires pour ... Bien que ces compétences ne soient pas nécessairement axées sur les TIC, ...

Les compétences évaluatives des formateurs d'enseignants

OpenAIRE

Jorro , Anne

2005-01-01

Dans cette communication, je présenterai une recherche exploratoire conduite auprès de formateurs d'enseignants dont les missions d'accompagnement des professeurs - stagiaires supposent des compétences évaluatives. Or, les formateurs d'enseignants entrevoient quasi naturellement la nécessité de gagner des compétences analytiques sur l'activité observée. Ces professionnels recourent plus volontiers à des moments d'analyse de pratiques et déclarent éprouver des difficultés à investir l'évaluati...

CompTIA Security+ Review Guide Exam SY0-301

CERN Document Server

Stewart, James M

2011-01-01

Reinforce your preparation for CompTIA's new Security+ exam with this focused review tool Before you take CompTIA's new Security+ exam SY0-301, reinforce your learning with a thorough review and lots of practice. The new edition of this concise guide helps you do just that. It covers all six domains of exam SY0-301, all exam objectives, and includes a helpful "Exam Essentials" section after each domain to help you zero in on what you need to know for the exam. A companion CD offers additional study tools, including two complete practice exams, over a hundred electronic flashcards, and more.Rev

A new Brief computerized cognitive screening battery (CompCogs for early diagnosis of Alzheimer's disease

Directory of Open Access Journals (Sweden)

Helenice Charchat Fichman

Full Text Available Abstract Screening tests for early diagnosis of dementia are of great clinical relevance. The ideal test set must be brief and reliable, and should probe cognitive components impaired in Alzheimer's disease (AD. Objectives: To develop a new Computerized Cognitive Screening test (CompCogs, and to investigate its validity for the early diagnosis of AD, and evaluate its heuristic value in understanding the processing of information in AD. Methods: The computerized neuropsychological performance battery, originally including six tests, was applied in forty seven patients with probable mild AD and 97 controls matched for age and education. This computerized neuropsychological test battery, developed with MEL Professional, allows control of timing and order of stimuli presentation, as well as recording of response type and latency. A brief-screening version, CompCogs, was selected using the most discriminative neuropsychological test variables derived from logistic regression analysis. Full battery administration lasted about 40 minutes, while the CompCogs took only 15 minutes. Results: CompCogs included the Face test (correct response and Word and Forms with Short term memory tests (reaction time. CompCogs presented 91.8% sensitivity and 93.6% specificity for the diagnosis of AD using ROC analyses of AD diagnosis probability derived by logistic regression. Conclusions: CompCogs showed high validity for AD early diagnosis and, therefore, may be a useful alternative screening instrument.

[Clinical features and COMP gene mutation in a family with a pseudoachondroplasia child].

Science.gov (United States)

Lu, Chun-Ting; Guo, Li; Zahng, Zhan-Hui; Lin, Wei-Xia; Song, Yuan-Zong; Feng, Lie

2013-11-01

This study aimed to report the clinical characteristics and COMP gene mutation of a family with pseudoachondroplasia (PSACH), a relatively rare spinal and epiphyseal dysplasia that is inherited as an autosomal dominant trait. Clinical information on a 5-year-2-month-old PSACH child and his parents was collected and analyzed. Diagnosis was confirmed by PCR amplification and direct sequencing of all the 19 exons and their flanking sequences of COMP gene, and the mutation was further ascertained by cloning analysis of exon 10. The child presented with short and stubby fingers, bow leg, short limb dwarfism and metaphysic broadening in long bone as well as lumbar lordosis. A mutation c.1048_1116del (p.Asn350_Asp372del) in exon 10, inherited from his father who did not demonstrate any phenotypic feature of PSACH, was detected in the child. PSACH was diagnosed definitively by means of COMP mutation analysis, on the basis of the child's clinical and imaging features. The non-penetrance phenomenon of COMP mutation was described for the first time in PSACH.

Cloud essentials CompTIA authorized courseware for exam CLO-001

CERN Document Server

Hausman, Kirk; Sampaio, Telmo

2013-01-01

CompTIA-Authorized courseware for the Cloud Essentials Exam (CLO-001) What better way to get up to speed on cloud computing than with this new book in the popular Sybex Essentials series? Cloud Essentials covers the basics of cloud computing and its place in the modern enterprise. Explore public and private clouds; contrast the ""as a service"" models for PaaS, SaaS, IaaS, or XaaS platforms; plan security; and more. In addition, the book covers the exam objectives for the both the CompTIA Cloud Essentials (Exam CLO-001) exam and the EXIN Cloud Computing Foundation (EX0-1

Immediate loading versus immediate provisionalization of maxillary single-tooth replacements: a prospective randomized study with BioComp implants

NARCIS (Netherlands)

Lindeboom, Jerome A.; Frenken, Joost W.; Dubois, Leander; Frank, Michael; Abbink, Ingmar; Kroon, Frans H.

2006-01-01

PURPOSE: The aim of this prospective randomized study was to evaluate the clinical outcome of immediately loaded solid plasma sprayed (TPS) BioComp (BioComp Industries BV, Vught, The Netherlands) implants versus immediate provisionalized but non-loaded BioComp implants in the anterior and premolar

Ingénierie des compétences et scénarisation pédagogique

Directory of Open Access Journals (Sweden)

Josianne Basque

2007-01-01

Full Text Available Cet article décrit un processus d’ingénierie éducative orienté compétences d’une activité d’autoévaluation et son intégration à un scénario pédagogique de cours à distance. Cette description est documentée par deux cas d’application dans un contexte de formation universitaire à distance. Le travail d’ingénierie utilise une approche en autogestion des compétences pour concevoir l’activité d’autoévaluation et l’instrumentaliser avec l’outil logiciel web d’autodiagnostic des compétences, appelé Compétences+. Cet acte d’ingénierie pédagogique porte l’attention de l’enseignant-concepteur sur une démarche centrée sur l’apprentissage dans une perspective d’autogestion des connaissances et de sa validation dans un usage en contexte isomorphe à une situation professionnelle réelle.

SlaVaComp Fonts Converter

Directory of Open Access Journals (Sweden)

Simon Skilevic

2013-12-01

Full Text Available This paper presents a fonts converter that was developed as a part of the Freiburg project on historical corpus linguistics. The tool named SlaVaComp-Konvertierer converts Church Slavonic texts digitized with non-Unicode fonts into the Unicode format without any loss of information contained in the original file and without damage to the original formatting. It is suitable for the conversion of all idiosyncratic fonts—not only Church Slavonic—and therefore can be used not only in Palaeoslavistic, but also in all historical and philological studies.

SyGuS-Comp 2016: Results and Analysis

Directory of Open Access Journals (Sweden)

Rajeev Alur

2016-11-01

Full Text Available Syntax-Guided Synthesis (SyGuS is the computational problem of finding an implementation f that meets both a semantic constraint given by a logical formula φ in a background theory T, and a syntactic constraint given by a grammar G, which specifies the allowed set of candidate implementations. Such a synthesis problem can be formally defined in SyGuS-IF, a language that is built on top of SMT-LIB. The Syntax-Guided Synthesis Competition (SyGuS-Comp is an effort to facilitate, bring together and accelerate research and development of efficient solvers for SyGuS by providing a platform for evaluating different synthesis techniques on a comprehensive set of benchmarks. In this year's competition we added a new track devoted to programming by examples. This track consisted of two categories, one using the theory of bit-vectors and one using the theory of strings. This paper presents and analyses the results of SyGuS-Comp'16.

Hydroxychloroquine induces inhibition of collagen type II and oligomeric matrix protein COMP expression in chondrocytes

Directory of Open Access Journals (Sweden)

Tao Li

2016-06-01

Full Text Available The aim of this study was to investigate the effect of hydroxychloroquine on the level of collagen type II and oligomeric matrix protein COMP expression in chondrocytes of knee osteoarthritis. The rate of growth in cartilage cells was analyzed using MTT assay whereas the Col-2 and COMP expression levels were detected by RT-PCR and Western blotting analyses. For the determination of MMP-13 expression, ELISA test was used. The results revealed no significant change in the rate of cartilage cell proliferation in hydroxychloroquine-treated compared to untreated cells. Hydroxychloro-quine treatment exhibited concentration- and time-dependent effect on the inhibition of collagen type II and COMP expression in chondrocytes. However, its treatment caused a significant enhancement in the expression levels of MMP-13 compared to the untreated cells. Therefore, hydroxychloro-quine promotes expression of MMP-13 and reduces collagen type II and COMP expression levels in chondrocytes without any significant change in the growth of cells.

Informatisation de la gestion des compétences : évaluation de la démarche dans une collectivité territoriale

OpenAIRE

Bachelet, Catherine; Galey, Béatrice

2013-01-01

Notion répandue mais difficile à cerner, la gestion des compétences peut être définie comme une instrumentation sur laquelle les acteurs professionnels de la GRH se fondent pour instruire leurs décisions de gestion (Gilbert, 2003). Constituée d'un « ensemble de pratiques visant à acquérir, stimuler et réguler les compétences des salariés » (Defélix et Retour, 2003), elle permet d'améliorer l'adéquation entre les compétences nécessaires et les compétences disponibles, pour optimiser la compéti...

Radar Precoder Design for Spectral Coexistence with Coordinated Multi-point (CoMP) System

OpenAIRE

Mahal, Jasmin A.; Khawar, Awais; Abdelhadi, Ahmed; Clancy, T. Charles

2015-01-01

This paper details the design of precoders for a MIMO radar spectrally coexistent with a MIMO cellular network. We focus on a coordinated multi-point (CoMP) system where a cluster of base stations (BSs) coordinate their transmissions to the intended user. The radar operates in two modes, interference-mitigation mode when it avoids interference with the CoMP system and cooperation mode when it exchanges information with it. Using either the conventional Switched Null Space Projection (SNSP) or...

Multi-particle phase space integration with arbitrary set of singularities in CompHEP

International Nuclear Information System (INIS)

Kovalenko, D.N.; Pukhov, A.E.

1997-01-01

We describe an algorithm of multi-particle phase space integration for collision and decay processes realized in CompHEP package version 3.2. In the framework of this algorithm it is possible to regularize an arbitrary set of singularities caused by virtual particle propagators. The algorithm is based on the method of the recursive representation of kinematics and on the multichannel Monte Carlo approach. CompHEP package is available by WWW: http://theory.npi.msu.su/pukhov/comphep. html (orig.)

COMP-angiopoietin-1 recovers molecular biomarkers of neuropathy and improves vascularisation in sciatic nerve of ob/ob mice.

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Joanna Kosacka

Full Text Available BACKGROUND: Leptin-deficient ob/ob mice are a model of type 2 diabetes induced peripheral neuropathy. Ob/ob mice exhibit obesity, insulin resistance, hyperglycaemia, and alterations of peripheral nerve fibres and endoneural microvessels. Here we test the hypothesis that cartilage oligomeric matrix protein (COMP-Ang-1, a soluble and stabile form of Ang-1 which promotes angiogenesis and nerve growth, improves regeneration of nerve fibres and endoneural microvessels in ob/ob mice. METHODS AND FINDINGS: COMP-Ang-1 (100 ng/ml or NaCl were intraperitoneally (i.p. injected into male (N = 184, 3-month old, ob/ob or ob/+ mice for 7 and 21 days. We measured expression of Nf68, GAP43, Cx32, Cx26, Cx43, and TNFα in sciatic nerves using Western blot analysis. To investigate the inflammation in sciatic nerves, numbers of macrophages and T-cells were counted after immunofluorescence staining. In ultrathin section, number of myelinated/non-mylinated nerve fibers, g-ratio, the thickness of Schwann cell basal lamina and microvessel endothelium were investigated. Endoneural microvessels were reconstructed with intracardial FITC injection. Treatment with COMP-Ang-1 over 21 days significantly reduced fasting blood glucose and plasma cholesterol concentrations compared to saline treated ob/ob mice. In addition, COMP-Ang-1 treatment: 1 up-regulated expression of Nf68 and GAP43; 2 improved expression of gap junction proteins including connexin 32 and 26; 3 suppressed the expression of TNFα and Cx43 and 4 led to decreased macrophage and T-cell infiltration in sciatic nerve of ob/ob mice. The significant changes of sciatic nerve ultrastructure were not observed after 21-day long COMP-Ang-1 treatment. COMP-Ang-1 treated ob/ob mice displayed regeneration of small-diameter endoneural microvessels. Effects of COMP-Ang-1 corresponded to increased phosphorylation of Akt and p38 MAPK upon Tie-2 receptor. CONCLUSIONS: COMP-Ang-1 recovers molecular biomarkers of neuropathy

Cartilage oligomeric matrix protein (COMP) in rheumatoid arthritis and its correlation with sonographic knee cartilage thickness and disease activity.

Science.gov (United States)

Sakthiswary, Rajalingham; Rajalingam, Shamala; Hussein, Heselynn; Sridharan, Radhika; Asrul, Abdul Wahab

2017-12-01

The aim of the study is to investigate the correlation of serum cartilage oligomeric matrix protein (COMP) levels with articular cartilage damage based on sonographic knee cartilage thickness (KCT) and disease activity in rheumatoid arthritis (RA). A total of 61 RA patients and 27 healthy controls were recruited in this study. Serum samples were obtained from all subjects to determine the serum COMP levels. All subjects had bilateral ultrasound scan of their knees. The KCT was based on the mean of measurements at three sites: the medial condyle, lateral condyle and intercondylar notch. Besides, the RA patients were assessed for their disease activity based on 28-joint-based Disease Activity Score (DAS 28). Serum COMP concentrations were significantly elevated in the RA patients compared to the controls (p = 0.001). The serum COMP levels had an inverse relationship with bilateral KCT in RA subjects and the healthy controls. COMP correlated significantly with disease activity based on DAS 28 (r = 0.299, p = 0.010), disease duration (r = 0.439, p = correlation between serum COMP and DAS 28 scores was comparable to the traditional markers of inflammation: erythrocyte sedimentation rate (ESR) (r = 0.372, p = 0.003) and C-reactive protein (CRP) (r = 0.305, p = 0.017). The serum COMP is a promising biomarker in RA which reflects disease activity and damage to the articular cartilage.

Modelagem de dispositivo Iosipescu para medição de propriedades de cisalhamento de materiais compósitos

OpenAIRE

Fabrício Nascimento Ribeiro

2013-01-01

Os projetos de novas aeronaves possuem suas estruturas primárias fabricados em materiais compósitos, o que resulta em diferentes tipos de cargas agindo em peças de compósitos. O comportamento de compósitos sujeitos a carga de cisalhamento é algo difícil de caracterizar especialmente porque os ensaios de cisalhamento possuem dificuldades em obter uma condição de cisalhamento puro e uniforme. O presente trabalho busca modelar o ensaio de cisalhamento Iosipescu com o método de elementos finitos,...

Développer des compétences interactionnelles en collaborant à distance

Directory of Open Access Journals (Sweden)

Charlotte Dejean-Thircuir

2010-01-01

Full Text Available Cet article vise à montrer de quelles façons des étudiants d’un Master2 professionnel de didactique des langues engagés dans la réalisation d’une tâche collaborative à distance sont amenés à mettre en œuvre et à développer des compétences interactionnelles et des compétences instrumentales en construisant des schèmes d’utilisation de l’outil de communication qu’est le chat, dans ce contexte particulier. Cette étude s’inscrit dans le champ de la communication pédagogique médiatisée par ordinateur; l’analyse des interactions verbales entre étudiants s’appuie sur des outils issus du champ de la pragmatique linguistique interactionniste.

Compósitos a partir de materiais de fontes renováveis como alternativa para o desenvolvimento de produtos

Directory of Open Access Journals (Sweden)

Eliana Paula Calegari

2016-04-01

Full Text Available A preocupação ambiental tem gerado interesse na pesquisa de novos materiais que estejam alinhados com os princípios da sustentabilidade. Entre esses materiais, atualmente, encontram-se os compósitos produzidos a partir de recursos de fontes renováveis. Este artigo apresenta os resultados de um estudo de caso acerca de produtos em que são empregados os referidos compósitos. Realizou-se uma pesquisa na rede mundial de computadores usando a ferramenta de buscas google sobre produtos fabricados com esses compósitos e comparou-se com produtos fabricados a partir de materiais usualmente utilizados na indústria, tais como polímeros, metais e cerâmicas. Constatou-se que os compósitos feitos a partir de fontes renováveis estão sendo, principalmente, aplicados em embalagens, na produção de ferramentas para jardinagem e vasos para plantas. Dessa forma, observou-se que os referidos compósitos podem substituir materiais comumente empregados na indústria atendendo aos requisitos funcionais e estéticos demandados na confecção desses produtos.

Compósitos de borracha natural com polianilina Composites of natural rubber with polyaniline

Directory of Open Access Journals (Sweden)

Patrini D. Galiani

2007-06-01

Full Text Available Compósitos de borracha natural (Hevea brasiliensis-BN/polianilina - PANI, com diferentes composições foram obtidos através da polimerização por emulsão do monômero anilina na presença da BN e do ácido dodecilbenzeno sulfônico (DBSA. Filmes finos e homogêneos foram obtidos por prensagem a quente. Os compósitos foram caracterizados por condutividade elétrica, FTIR, UV-vis-NIR, DSC e difração de raios X. Compósito com condutividade elétrica cerca de 14 ordens de grandeza maior que a BN foi obtido. Este alto valor de condutividade é atribuído à formação da PANI no estado dopado no compósito, que foi verificado através das técnicas de UV-vis-NIR e FTIR. Os resultados obtidos com a técnica de DSC e difratometria de raios X indicaram que os polímeros são imiscíveis e que a presença da borracha não altera significantemente a fase cristalina da PANI-DBSA no compósito.In this work composites with different compositions were obtained from natural rubber (Hevea brasiliensis (NR and polyaniline (PANI using the emulsion polymerization of aniline in the presence of NR and dodecylbenzenesulfonic acid (DBSA. The samples in film form were obtained by pressing the precipitate at 100 °C for 5 minutes. The composites were characterized by electrical conductivity, Fourier-transform infrared spectroscopy (FTIR, UV-vis-NIR spectroscopy, differential scanning calorimetry (DSC and X ray diffraction. Composites with electrical conductivity about 14 orders of magnitude higher than NR were obtained. The UV-vis-NIR and FTIR spectra showed that PANI-DBSA was formed in the composites, thus making it responsible for their high conductivity. The DSC thermograms indicated that the two polymers are immiscible and X ray diffraction evidenced that NB does not considerably affect PANI-DBSA crystalline phase in the composite.

Êtres capables et compétents : lecture anthropologique et pistes pragmatiques

OpenAIRE

Genard, Jean-Louis; Cantelli, Fabrizio

2008-01-01

Les termes « compétences » et « capacités » occupent depuis quelques années une place de plus en plus importante dans le vocabulaire de la sociologie, notamment de la sociologie pragmatique. On les retrouve toutefois aussi dans d’autres champs théoriques (le terme capabilities chez Amartya Sen) ou dans le vocabulaire des politiques publiques qui évoquent des politiques de « capacitation », ou des « seuils de compétences ». Face à ce constat, l’article développe l’hypothèse d’un véritable tour...

The semantics of Chemical Markup Language (CML for computational chemistry : CompChem

Directory of Open Access Journals (Sweden)

Phadungsukanan Weerapong

2012-08-01

Full Text Available Abstract This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.

On-line process analysis innovation: DiComp (tm) shunting dielectric sensor technology

Science.gov (United States)

Davis, Craig R.; Waldman, Frank A.

1993-01-01

The DiComp Shunting Dielectric Sensor (SDS) is a new patent-pending technology developed under the Small Business Innovation Research Program (SBIR) for NASA's Kennedy Space Center. The incorporation of a shunt electrode into a conventional fringing field dielectric sensor makes the SDS uniquely sensitive to changes in material dielectric properties in the KHz to MHz range which were previously detectable only at GHz measurement frequencies. The initial NASA application of the SDS for Nutrient Delivery Control has demonstrated SDS capabilities for thickness and concentration measurement of Hoagland nutrient solutions. The commercial introduction of DiComp SDS technology for concentration and percent solids measurements in dispersions, emulsions and solutions represents a new technology for process measurements for liquids in a variety of industries.

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem.

Science.gov (United States)

Phadungsukanan, Weerapong; Kraft, Markus; Townsend, Joe A; Murray-Rust, Peter

2012-08-07

: This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.

Estudo do comportamento da resina base na formulação de compósitos de politetrafluoretileno com bronze

OpenAIRE

Ronaldo Euzébio Bento

2011-01-01

Resumo: Esse trabalho concentra os estudos na investigação das propriedades de resistência a tração e alongamento do compósito de Politetrafluoretileno (PTFE) com 60% de bronze após a substituição do tipo de PTFE utilizado na formulação desse compósito. Atualmente esse compósito utiliza PTFE convencional na formulação e o objetivo é alterar para PTFE modificado. A motivação para essa alteração deveu-se ao fato que o PTFE convencional apresenta disponibilidade limitada dificultando o desenvolv...

CompTIA Linux+ study guide exam LX0-103 and exam LX0-104

CERN Document Server

Bresnahan, Christine

2015-01-01

CompTIA Authorized Linux+ prepCompTIA Linux+ Study Guide is your comprehensive study guide for the Linux+ Powered by LPI certification exams. With complete coverage of 100% of the objectives on both exam LX0-103 and exam LX0-104, this study guide provides clear, concise information on all aspects of Linux administration, with a focus on the latest version of the exam. You'll gain the insight of examples drawn from real-world scenarios, with detailed guidance and authoritative coverage of key topics, including GNU and Unix commands, system operation, system administration, system services, secu

CompTIA Linux+ Complete Study Guide (Exams LX0-101 and LX0-102)

CERN Document Server

Smith, Roderick W

2010-01-01

Prepare for CompTIA's Linux+ Exams. As the Linux server and desktop markets continue to grow, so does the need for qualified Linux administrators. CompTIA's Linux+ certification (Exams LX0-101 and LX0-102) includes the very latest enhancements to the popular open source operating system. This detailed guide not only covers all key exam topics—such as using Linux command-line tools, understanding the boot process and scripts, managing files and file systems, managing system security, and much more—it also builds your practical Linux skills with real-world examples. Inside, you'll find:. Full co

Emprego experimental da placa de compósito poli-hidroxibutirado/hidroxiapatita na fixação femoral em gatos

Directory of Open Access Journals (Sweden)

E.G.L. Alves

2010-10-01

Full Text Available Avaliou-se o compósito de poli-hidroxibutirado (PHB 70% e hidroxiapatita (HA 30% na forma de placas para fixação óssea em gatos. Foram usadas placas do compósito com 60mm de comprimento por 10mm de largura e espessura variando de 3mm no centro a 5mm nas extremidades, com seis orifícios. A placa do compósito foi empregada na fixação de osteotomia de fêmur em quatro gatos, totalizando seis intervenções. Verificou-se a ruptura de cinco placas (83,3% até o quarto dia e de uma placa (16,7% aos 21 dias, quando se observou um calo ósseo exuberante. O resultado da implantação da placa no gato mostrou que o compósito não possui resistência suficiente para ser empregado como placas de fixação de fêmur em gatos.

Teaching Competencies for the Online Environment | Enseigner les compétences pour l’environnement en ligne

Directory of Open Access Journals (Sweden)

Heather Marie Farmer

2016-08-01

Full Text Available The goals of this study are to identify key competency areas that lead to success in online instruction and to develop a framework that supports professional development and self-assessment. To identify the key competency areas, skills and behaviours presented within current literature were analyzed. Secondly, gaps were identified and levels of competence were determined within each key competency area. The resulting analysis produced the Online Teaching Competency (OTC Matrix including five competency areas: Community & Netiquette, Active Teaching/Facilitating, Instructional Design, Tools & Technology, and Leadership & Instruction. This leveled competency matrix can be used to inform professional development in the online teaching environment and is also a useful guide in the areas of self-assessment, portfolio design, and the development and evaluation of professional development opportunities. Cette étude a comme objectifs de cerner les principaux domaines de compétences qui mènent à la réussite de l’instruction en ligne et de développer un cadre qui soutient le développement professionnel et l’autoévaluation. Afin de cerner les principaux domaines de compétences, une analyse des aptitudes et comportements présentés dans les études actuelles a été réalisée. Deuxièmement, les écueils ont été cernés et les niveaux de compétence ont été déterminés au sein de chaque domaine de compétences. L’analyse qui en a résulté a généré la matrice des compétences de l’enseignement en ligne, comprenant cinq domaines de compétences : collectivité et nétiquette, enseignement actif/animation active, conception de l’instruction, outils et technologie, ainsi que leadership et instruction. Cette matrice graduée peut servir à façonner le développement professionnel dans un environnement d’enseignement en ligne. Elle sert aussi de guide pratique pour les domaines de l’auto-évaluation, de la conception de

Mild myopathy is associated with COMP but not MATN3 mutations in mouse models of genetic skeletal diseases.

Directory of Open Access Journals (Sweden)

Katarzyna A Piróg

Full Text Available Pseudoachondroplasia (PSACH and multiple epiphyseal dysplasia (MED are skeletal disorders resulting from mutations in COMP, matrilin-3 or collagen IX and are characterised by short-limbed dwarfism and premature osteoarthritis. Interestingly, recent reports suggest patients can also manifest with muscle weakness. Here we present a detailed analysis of two mouse models of the PSACH/MED disease spectrum; ΔD469 T3-COMP (PSACH and V194D matrilin-3 (MED. In grip test experiments T3-COMP mice were weaker than wild-type littermates, whereas V194D mice behaved as controls, confirming that short-limbed dwarfism alone does not contribute to PSACH/MED-related muscle weakness. Muscles from T3-COMP mice showed an increase in centronuclear fibers at the myotendinous junction. T3-COMP tendons became more lax in cyclic testing and showed thicker collagen fibers when compared with wild-type tissue; matrilin-3 mutant tissues were indistinguishable from controls. This comprehensive study of the myopathy associated with PSACH/MED mutations enables a better understanding of the disease progression, confirms that it is genotype specific and that the limb weakness originates from muscle and tendon pathology rather than short-limbed dwarfism itself. Since some patients are primarily diagnosed with neuromuscular symptoms, this study will facilitate better awareness of the differential diagnoses that might be associated with the PSACH/MED spectrum and subsequent care of PSACH/MED patients.

COMP-angiopoietin 1 increases proliferation, differentiation, and migration of stem-like cells through Tie-2-mediated activation of p38 MAPK and PI3K/Akt signal transduction pathways

Energy Technology Data Exchange (ETDEWEB)

Kook, Sung-Ho [Cluster for Craniofacial Development and Regeneration Research, Institute of Oral Biosciences and School of Dentistry, Chonbuk National University, Jeonju (Korea, Republic of); Lim, Shin-Saeng [School of Dentistry and Dental Research Institute, Seoul National University, Seoul (Korea, Republic of); Cho, Eui-Sic; Lee, Young-Hoon; Han, Seong-Kyu; Lee, Kyung-Yeol [Cluster for Craniofacial Development and Regeneration Research, Institute of Oral Biosciences and School of Dentistry, Chonbuk National University, Jeonju (Korea, Republic of); Kwon, Jungkee [College of Veterinary Medicine, Chonbuk National University, Jeonju (Korea, Republic of); Hwang, Jae-Won; Bae, Cheol-Hyeon [Cluster for Craniofacial Development and Regeneration Research, Institute of Oral Biosciences and School of Dentistry, Chonbuk National University, Jeonju (Korea, Republic of); Seo, Young-Kwon [Research Institute of Biotechnology, Dongguk University, Seoul (Korea, Republic of); Lee, Jeong-Chae, E-mail: leejc88@jbnu.ac.kr [Cluster for Craniofacial Development and Regeneration Research, Institute of Oral Biosciences and School of Dentistry, Chonbuk National University, Jeonju (Korea, Republic of)

2014-12-12

Highlights: • COMP-Ang1 induces Tie-2 activation in BMMSCs, but not in primary osteoblasts. • Tie-2 knockdown inhibits COMP-Ang1-stimulated proliferation and osteoblastogenesis. • Tie-2 knockdown prevents COMP-Ang1-induced activation of PI3K/Akt and p38 MAPK. • COMP-Ang1 induces migration of cells via activation of PI3K/Akt and CXCR4 pathways. • COMP-Ang1 stimulates in vivo migration of PDLSCs into a calvarial defect site of rats. - Abstract: Recombinant COMP-Ang1, a chimera of angiopoietin-1 (Ang1) and a short coiled-coil domain of cartilage oligomeric matrix protein (COMP), is under consideration as a therapeutic agent capable of inducing the homing of cells with increased angiogenesis. However, the potentials of COMP-Ang1 to stimulate migration of mesenchymal stem cells (MSCs) and the associated mechanisms are not completely understood. We examined the potential of COMP-Ang1 on bone marrow (BM)-MSCs, human periodontal ligament stem cells (PDLSCs), and calvarial osteoblasts. COMP-Ang1 augmented Tie-2 induction at protein and mRNA levels and increased proliferation and expression of runt-related transcription factor 2 (Runx2), osterix, and CXCR4 in BMMSCs, but not in osteoblasts. The COMP-Ang1-mediated increases were inhibited by Tie-2 knockdown and by treating inhibitors of phosphoinositide 3-kinase (PI3K), LY294002, or p38 mitogen-activated protein kinase (MAPK), SB203580. Phosphorylation of p38 MAPK and Akt was prevented by siRNA-mediated silencing of Tie-2. COMP-Ang1 also induced in vitro migration of BMMSCs and PDLSCs. The induced migration was suppressed by Tie-2 knockdown and by CXCR4-specific peptide antagonist or LY294002, but not by SB203580. Furthermore, COMP-Ang1 stimulated the migration of PDLSCs into calvarial defect site of rats. Collectively, our results demonstrate that COMP-Ang1-stimulated proliferation, differentiation, and migration of progenitor cells may involve the Tie-2-mediated activation of p38 MAPK and PI3K/Akt pathways.

COMP-angiopoietin 1 increases proliferation, differentiation, and migration of stem-like cells through Tie-2-mediated activation of p38 MAPK and PI3K/Akt signal transduction pathways

International Nuclear Information System (INIS)

Kook, Sung-Ho; Lim, Shin-Saeng; Cho, Eui-Sic; Lee, Young-Hoon; Han, Seong-Kyu; Lee, Kyung-Yeol; Kwon, Jungkee; Hwang, Jae-Won; Bae, Cheol-Hyeon; Seo, Young-Kwon; Lee, Jeong-Chae

2014-01-01

Highlights: • COMP-Ang1 induces Tie-2 activation in BMMSCs, but not in primary osteoblasts. • Tie-2 knockdown inhibits COMP-Ang1-stimulated proliferation and osteoblastogenesis. • Tie-2 knockdown prevents COMP-Ang1-induced activation of PI3K/Akt and p38 MAPK. • COMP-Ang1 induces migration of cells via activation of PI3K/Akt and CXCR4 pathways. • COMP-Ang1 stimulates in vivo migration of PDLSCs into a calvarial defect site of rats. - Abstract: Recombinant COMP-Ang1, a chimera of angiopoietin-1 (Ang1) and a short coiled-coil domain of cartilage oligomeric matrix protein (COMP), is under consideration as a therapeutic agent capable of inducing the homing of cells with increased angiogenesis. However, the potentials of COMP-Ang1 to stimulate migration of mesenchymal stem cells (MSCs) and the associated mechanisms are not completely understood. We examined the potential of COMP-Ang1 on bone marrow (BM)-MSCs, human periodontal ligament stem cells (PDLSCs), and calvarial osteoblasts. COMP-Ang1 augmented Tie-2 induction at protein and mRNA levels and increased proliferation and expression of runt-related transcription factor 2 (Runx2), osterix, and CXCR4 in BMMSCs, but not in osteoblasts. The COMP-Ang1-mediated increases were inhibited by Tie-2 knockdown and by treating inhibitors of phosphoinositide 3-kinase (PI3K), LY294002, or p38 mitogen-activated protein kinase (MAPK), SB203580. Phosphorylation of p38 MAPK and Akt was prevented by siRNA-mediated silencing of Tie-2. COMP-Ang1 also induced in vitro migration of BMMSCs and PDLSCs. The induced migration was suppressed by Tie-2 knockdown and by CXCR4-specific peptide antagonist or LY294002, but not by SB203580. Furthermore, COMP-Ang1 stimulated the migration of PDLSCs into calvarial defect site of rats. Collectively, our results demonstrate that COMP-Ang1-stimulated proliferation, differentiation, and migration of progenitor cells may involve the Tie-2-mediated activation of p38 MAPK and PI3K/Akt pathways

Resistência de união de compósitos do tipo Bulk Fill: análise in vitro

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Caroline de Farias CHARAMBA

2017-03-01

Full Text Available Resumo Introdução A classe dos compósitos Bulk-Fill tem obtido popularidade com a promessa de ser fotopolimerizado efetivamente em camadas de até quatro milímetros, fato que contrasta com os dois milímetros requisitados para os compósitos convencionais para manutenção da adesividade da restauração. Objetivo O objetivo deste estudo foi analisar a resistência de união à dentina de restaurações confeccionadas com compósitos do tipo Bulk-Fill. Material e método Foram utilizados 15 terceiros molares humanos, cuja superfície oclusal foi cortada e a dentina foi exposta. Esses elementos dentários foram divididos em três grupos conforme o material restaurador utilizado. O sistema adesivo usado foi o mesmo para todos os grupos. Posteriormente, os dentes restaurados foram cortados para originar palitos de aproximadamente 1 mm de largura, 1 mm de profundidade e 8 mm de altura, que foram fixados às garras do dispositivo de microtração. Foram utilizados dez palitos de cada dente, totalizando 50 palitos por grupo. Os dados de resistência de união à microtração foram expressos em megapascal (MPa. As fraturas foram analisadas em microscópio óptico. Os dados foram analisados através dos testes ANOVA e Tukey (p<0,05. Resultado Os três compósitos estudados diferiram estatisticamente entre si (p<0,000. Os compósitos Bulk-Fill apresentaram resistências de união semelhantes e superiores ao convencional (p<0,000. A fratura mais encontrada foi a mista, em todos os grupos. Conclusão Os compósitos Bulk-Fill apresentaram maiores valores de resistência de união com a técnica restauradora utilizada.

Modelos de percolação elétrica aplicados para compósitos poliméricos condutores

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Paulo Henrique da Silva Leite Coelho

Full Text Available Resumo O presente artigo apresenta a aplicação e adequação dos modelos de percolação elétrica em trabalhos experimentais e teóricos da literatura para compósitos poliméricos condutores. Foi realizado um levantamento das publicações referentes aos modelos estudados para os diferentes tipos de cargas condutoras mais aplicadas na preparação destes compósitos, tais como pós metálicos, grafite, negro de fumo, nanofibras e nanotubos de carbono. A discussão está apresentada quanto à adequação dos modelos ao comportamento dos compósitos na influência das cargas nas propriedades elétricas de matrizes poliméricas.

Equivalent flow rate concept used in near field transport model COMP23 - Proposed values for SR 97

International Nuclear Information System (INIS)

Moreno, L.

1998-11-01

SKB is using NUCTRAN to calculate transport of radionuclides from a possible defective canister into the far field. NUCTRAN is included in the Performance Assessment model chain that calculates the release from the canister into the biosphere. In the chain, NUCTRAN is denoted COMP23. In order to calculate the transport of radionuclides by diffusion into the flowing water in the rock, NUCTRAN uses the concept of equivalent flow rate, Q eq . To calculate the value of Q eq in the different paths, COMP23 needs information about the Darcy velocity, the geometry of the system, material properties and the flow porosity in the rock. At present, this information is supplied to COMP23 by means of three parameters. The aim of this note is to propose a method to calculate the flow equivalent within the SR 97 project. Estimated intervals of the factors to adopt HYDRASTAR results to COMP23 are presented. Since it is difficult to give general validity to the factors, solely proposed factor intervals are presented to obtain equivalent flow rate values for COMP23. To obtain accurate equivalent flow rate values, information about the hydraulic conditions at canister locations in the groundwater model should be available for the near field model or the Q eq values could be calculated directly in the groundwater flow model. One of the main tasks in the SR 97 project is to show the barrier performance of the rock using different alternative models for flow and transport. In addition, the Alternative Model Project (AMP) aims to show how robust the assessment model description is, in terms of relevant far field performance measures. In the AMP, three main approaches were used, namely, the Stochastic Continuum approach, the Channel Network model and the Discrete Feature Network model

Efeito do tratamento alcalino de fibras de Curauá sobre as propriedades de compósitos de matriz biodegradável

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Lílian Vanessa Rossa Beltrami

2014-06-01

Full Text Available Neste trabalho avaliou-se a influência do tratamento alcalino das fibras de curauá, nas concentrações de 1, 5 e 10%(m/v de NaOH, nas propriedades dos compósitos com matriz de PHBV e 20% m/m de fibras de curauá. Os compósitos foram moldados por extrusão e injeção e avaliadas suas as propriedades morfológicas, térmicas e mecânicas. Os resultados de FTIR mostraram que o tratamento alcalino promoveu modificações na estrutura das fibras de curauá, comprovadas pela remoção da hemicelulose e da lignina, evidenciadas pela ausência das bandas típicas destes compostos. Nos compósitos com fibras de curauá tratadas com solução de NaOH na concentração de 5% apresentaram um aumento de 30% na resistência à flexão e 12% na resistência ao impacto, quando comparados aos compósitos com fibras sem tratamento. Estes resultados indicam que o tratamento alcalino promoveu uma melhoria na adesão das fibras na matriz, o que melhorou significativamente as propriedades mecânicas dos compósitos.

Desenvolvimento e análise de compósitos cimentícios híbridos de alto desempenho

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V. J. Ferrari

Full Text Available Neste trabalho, estudou-se o efeito da hibridização em compósitos cimentícios numa tentativa de modificar o material em sua microestrutura e melhorar o processo de transferência de tensões da matriz cimentícia para as fibras de aço. Para tanto, fibras curtas e microfibras de aço foram adicionadas a uma matriz cimentícia de argamassa para confecção de corpos-de-prova prismáticos entalhados e com dimensões de 150 mm x 150 mm x 500 mm. Os corpos-de-prova foram submetidos a ensaios de flexão com carga no meio do vão sob o controle dos deslocamentos de abertura da entrada do entalhe (CMOD. O desempenho dos compósitos híbridos foi comparado ao dos compósitos produzidos somente com a adição da fibra curta de aço e também ao da matriz sem fibras. Os resultados foram analisados considerando-se os parâmetros de tenacidade flexional e tenacidade ao fraturamento do material. O processo de hibridização permitiu obter compósitos de alto desempenho.

Compósitos à base de gesso com resíduos de EVA e vermiculita

OpenAIRE

Oliveira,Marilia P. de; Barbosa,Normando P.; Torres,Sandro M.; Leal,Antonio F.; Silva,Cibelle G.

2012-01-01

O gesso é um dos materiais de construção mais antigos de que se tem conhecimento. Algumas de suas propriedades lhes conferem vantagens, tais como resistência ao fogo e isolamentos térmico e acústico. Objetivou-se, com este trabalho, avaliar as propriedades físico-mecânicas de compósitos à base de gesso com a incorporação de resíduos da indústria de calçados, o etileno acetato de vinila (EVA) e a vermiculita. O desenvolvimento desses compósitos tem como propósito a produção de elementos de rev...

Entre structure et action : la compétence communicative des TIC

Directory of Open Access Journals (Sweden)

Serge Agostinelli

2011-06-01

Full Text Available Cet article théorique explore comment les concepts de structure et d’action permettent une approche originale du concept de compétence dans le domaine des TIC. Cette approche relève d’une recherche de compatibilité entre des modèles issus des Technologies qui proposent les structures socio-techniques et ceux des Sciences Humaines qui organisent l’action des individus. Les modèles théoriques invoqués de domaines disciplinaires différents (sociologie, ethnométhodologie, psychologie sociale, linguistique, sciences de l’éducation et sciences de l’information-communication donnent au concept de compétence en TIC une nouvelle consistance, plus anthropocentrée et moins technico-pratique. Ils posent la question du rapport entre micro et macro, du rapport de l’individu au groupe, et posent aussi la question ontologique des structures. Les compétences ne se réduisent pas à la seule connaissance des aspects techniques, mais sont élargies à la maîtrise des conditions d’utilisation adéquate et des possibilités offertes par la technique. Utiliser les technologies, c’est construire de la relation grâce aux compétences communicatives des TIC.This theoretical article investigates how the concepts of structure and action allow an original approach of the concept of skill in the field of ICT. This approach concerns a search for compatibility between stemming models Technologies which propose the socio-technical structures and those of the Human Sciences who organize the action of the individuals. The theoretical models called by different disciplinary domains (sociology, ethnomethodology, social psychology, linguistic, education, communication and information science give to the concept of skill in ICT a new consistency, more anthropology centred and less technico-practical. They ask the question of the relationship between micro and macro, the relationship of the individual to the group, and also ask the ontological question

La transmission efficace des compétences via Internet : exemple pratique

NARCIS (Netherlands)

Caniëls, M.C.J.

2005-01-01

Les universités sont de plus en plus nombreuses à adopter des modèles pédagogiques novateurs, plutôt axés sur le développement des compétences que sur la reproduction des connaissances. Ces nouveaux modèles pédagogiques soulignent l’importance de la mise en application des connaissances et du

CompTIA A+ certification all-in-one for dummies

CERN Document Server

Clarke, Glen E

2012-01-01

Comprehensive coverage of everything you must know to pass CompTIA's A+ exam A+ is the gateway certification into many IT careers, and interest in certification is exploding. This bestselling A+ certification guide is updated to cover the new A+ exam. It includes the new Windows coverage and reflects the revised emphasis on objectives. Nine minibooks focus individually on specific hardware and OS characteristics including installation and configuration, diagnostics, preventive maintenance, motherboard and processors, printers, networking, and fundamentals. A companion website contains the popu

CompTIA network+ study guide exam N10-006

CERN Document Server

Lammle, Todd

2015-01-01

All-star N10-006 prep, fully updated for the new exam The CompTIA Network+ Study Guide is your one-stop comprehensive resource in preparing for exam N10-006 Bestselling author and networking Guru Todd Lammle guides you through 100% of all exam objectives detailing the fundamental concepts you will need to know to prepare for the exam. Coverage includes network technologies, installation and configuration, media and topologies, security, and much more, plus practical examples drawn from real-world situations. You also gain access to practice exams and electronic flashcards that facilitate info

Intelligence économique, compétitivité et cohésion sociale

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Luc Marie Quoniam

2005-12-01

Full Text Available Book review: Intelligence économique, compétitivité et cohésion sociale by Bernard Carayon (.pdf rapportPublished by: Ministère de l’Intérieur français Année d'édition : 2003 Réf. : 9782110054913, 176 pages, 21x29,7 cm ISBN : 2-11-005491-3

Análise da influência do traço nas propriedades do compósito cimento-madeira

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Alessandra Monique Weber

2017-08-01

Full Text Available Os compósitos de cimento com adição de madeira apresentam vantagens, quando comparados a outros materiais convencionais da construção civil, como resistência à água, ao fogo e aos agentes deterioradores. Um dos obstáculos para o uso desse compósito é a inibição causada pela madeira na cura do cimento, devido aos componentes da madeira afetarem as reações, tendo como consequência um compósito de baixa qualidade. Dessa forma, este trabalho teve por objetivo avaliar diferentes traços do compósito cimento-madeira, utilizando resíduos de Pinus spp., por meio de ensaios de laboratório. Foi utilizado o cimento Portland CP II Z 32, relação água/cimento igual a 0,4; o aditivo químico escolhido foi o cloreto de cálcio para acelerar a pega. Para a comparação de desempenho, foram delimitadas quatro dosagens diferentes, com teores de adição de madeira de 10%, 20%, 25% e 33% em relação à massa de cimento. Para a análise, foram feitos ensaios das propriedades físicas e mecânicas para todas as dosagens, sendo, posteriormente, submetidas à análise da variância e teste de Tukey. Os resultados dos ensaios das propriedades físicas e mecânicas dos compósitos demonstraram que, para as relações escolhidas, quanto menor for a adição de madeira melhores serão os resultados das propriedades, mas mesmo os traços com maiores teores de madeira apresentam resultados relevantes, atentando-se apenas para o fato da relação água/cimento ser baixa para os casos analisados, e, devido a isso, ter influenciado negativamente nos resultados.

Developing Consensus on the CompHP Professional Standards for Health Promotion in Europe

Science.gov (United States)

Speller, Viv; Parish, Richard; Davison, Heather; Zilnyk, Anna

2012-01-01

Building on the CompHP Core Competencies for health promotion the Professional Standards for Health Promotion have been developed and consulted on across Europe. The standards were formulated to fit within the complexity of professional, occupational and educational standards frameworks in Europe as learning outcome standards with performance…

CompTIA Network+ Review Guide (Exam N10-004)

CERN Document Server

Ferguson, Bill

2009-01-01

Serving as a concise, focused study aid to help you prepare for the leading non-vendor-specific networking certification exam, this book features more review questions and study review features than any other guide, with over 120 review questions, two bonus exams, and electronic Flashcard, as well as a searchable Glossary of Terms database on CD-ROM. Fully updated for the first revision of the CompTIA Network+ exam since 2005, the book is organized by exam objectives and broken into six parts corresponding to the six domain areas of the Network+ exam: technologies, media and topologies, device

La compétence interculturelle et la formation initiale : le point sur le CECR et l’IDI

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Karen Olivia Ragoonaden

2011-12-01

Full Text Available Abstract Ce projet pilote traite principalement de la compétence interculturelle des étudiants en formation initiale du français langue seconde. Douze étudiants ont répondu au questionnaire de l’IDI (inventaire de développement interculturel, un outil méthodologique qui mesure les orientations concernant la différence culturelle. Les profils interculturels, calculés d’après les résultats de l’IDI, servent de toile de fond pour proposer la mise en œuvre des interventions interculturelles selon les paramètres établis par les compétences générales du Cadre européen commun de référence pour les langues (CECR. Les travaux menés pourraient contribuer à l’élaboration des cours/ateliers en compétence interculturelle, à l’intégration des savoirs socioculturels et à la prise de conscience interculturelle identifiés dans les compétences générales du Cadre européen commun de référence pour les langues dans les cours de formation initiale. Resume This pilot study focuses on the intercultural competence of preservice French as a second language (FSL teachers. The Intercultural Development Index (IDI, a statistically valid tool used to measure intercultural competence, was administered to twelve preservice candidates. These results serve as a basis to discuss the integration of intercultural competencies along the parameters established in the general competencies of the CEFR. This study has the potential to contribute to a growing area of research in the field of intercultural competence in preservice teacher education and explores how sociocultural saviors and intercultural awareness, identified by the Common European Framework of Reference for Languages, can be integrated into Teacher Education.

Alors ? méthode de français fondée sur l'approche des compétences : niveau B1 : CD et DVD inclus

CERN Document Server

Di Giura, Marcella

2008-01-01

Une nouvelle méthode qui propose des stratégies spécifiques pour l'acquisition des compétences communicatives, linguistiques et culturelles. Alors ? respecte les échelles de compétences des niveaux A1, A2 et B1 du CECRL.

De la terre à la table : renforcer les compétences des agriculteurs ...

International Development Research Centre (IDRC) Digital Library (Canada)

De la terre à la table : renforcer les compétences des agriculteurs urbains en organisation et en mise en marché (Moyen-Orient et Afrique du Nord). Le réseau ... Stichting International Network of Resource Centres on Urban Agriculture and Food Security. Pays d' institution. Pays-Bas. Site internet. http://www.ruaf.org ...

CompTIA Network+ Certification Study Guide, Exam N10-004

CERN Document Server

Shimonski, Robert

2009-01-01

CompTIA's Network+ certification is a globally-recognized, vendor neutral exam that has helped over 235,000 IT professionals reach further and higher in their careers. The 2009 Network+ exam (N10-004) is a major update with more focus on security and wireless aspects of networking. Our new study guide has been updated accordingly with focus on network, systems, and WAN security and complete coverage of today's wireless networking standards. As always this companion covers the core Network+ material including basic design principles, management and operation of a network infrastructure, and tes

Compósitos polímero-madeira preparados por polimerização in situ de metil metacrilato usando aditivos bifuncionais

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Bruno Dufau Mattos

2015-12-01

Full Text Available Resumo O presente trabalho teve por objetivo a confecção de compósitos polímero-madeira por meio de polimerização in situ de metil metacrilato (MMA, utilizando ácido metacrílico (MAA e glicidil metacrilato (GMA como agentes de ligação e reticulação. Amostras de madeira de guapuruvu foram impregnadas em um sistema de vácuo e pressão e polimerizadas em estufa a 90°C por 10h, usando 1,5% de peroxido de benzoíla como catalisador. Os compósitos foram caracterizados por meio de testes de absorção de água e estabilidade dimensional, molhabilidade, ATR-IR, TGA, MEV e WPG. Os espectros de ATR-IR mostraram incrementos nas bandas a 1746, 1460, e 1145 cm–1, referentes as estruturas químicas dos polímeros dentro da madeira, confirmado posteriormente pelas imagens de MEV. A termogravimetria apontou reações químicas entre os copolímeros e a parede celular da madeira nos compósitos com GMA e MAA. Os compósitos preparados com MMA apresentaram incrementos acima de 50% nas propriedades higroscópicas e de estabilidade dimensional, entretanto a adição de GMA e MAA resultou em maiores incrementos nas mesmas propriedades, entre 66-90%.

Correlation of serum cartilage oligomeric matrix protein (COMP) and interleukin-16 (IL-16) levels with disease severity in primary knee osteoarthritis: A pilot study in a Malaysian population.

Science.gov (United States)

Das Gupta, Esha; Ng, Wei Ren; Wong, Shew Fung; Bhurhanudeen, Abdul Kareem; Yeap, Swan Sim

2017-01-01

The aim of this study was to investigate the correlations between serum cartilage oligomeric matrix protein (COMP), interleukin-16 (IL-16) and different grades of knee osteoarthritis (KOA) in Malaysian subjects. Ninety subjects were recruited comprising 30 with Kellgren-Lawrence (K-L) grade 2 KOA, 27 with K-L grade 3 KOA, 7 with grade 4 KOA, and 30 healthy controls. All subjects completed the Western Ontario and McMaster Universities Arthritis Index (WOMAC) questionnaire. Serum COMP and IL-16 levels were measured using ELISA and their values log transformed to ensure a normal distribution. There was no significant differences in levels of log serum COMP and IL-16 between healthy controls and KOA patients. There were no significant differences in the log serum COMP and IL-16 levels within the different K-L grades in the KOA patients. In KOA patients, log serum IL-16 levels significantly correlated with the WOMAC score (p = 0.001) and its subscales, pain (p = 0.005), stiffness (p = 0.019) and physical function (p<0.0001). Serum IL-16 levels were significantly higher in Malaysian Indians compared to Malays and Chinese (p = 0.024). In this multi-ethnic Malaysian population, there was no difference in serum COMP and IL-16 levels between healthy controls and patients with KOA, nor was there any difference in serum COMP or IL-16 levels across the various K-L grades of KOA. However, there were significant inter-racial differences in serum IL-16 levels.

Processamento de plásticos e materiais compósitos: comportamento mecânico de componentes em serviço

OpenAIRE

Capela, Carlos Alexandre Bento

2010-01-01

As vantagens dos materiais plásticos, tais como facilidade de processamento, baixo custo, alta produtividade e versatilidade, permite obter plásticos e materiais compósitos de matriz polimérica para um grande número de aplicações em engenharia. Os materiais compósitos são, actualmente, muito utilizados não só na indústria aeroespacial, mas, também, num crescente número de aplicações de Engenharia Mecânica, tais como componentes de máquinas, vasos de pressão, equipamentos industriais de proces...

Efeito do condicionamento ambiental nas propriedades de cisalhamento e viscoelásticas de compósitos híbridos metal-fibra

OpenAIRE

Damato, Cesar Augusto [UNESP

2010-01-01

O desenvolvimento da tecnologia dos compósitos híbridos, combinando laminados poliméricos reforçados com fibras longas e placas metálicas, normalmente ligas de alumínio, denominados de CHMF, tem como uma de suas finalidades formar um conjunto de materiais que combine elevados valores de resistência mecânica, resistência ao impacto, rigidez e baixa massa específica. Essa combinação de propriedades torna os CHMF particularmente atrativos como substituintes das ligas metálicas e dos compósitos t...

Avaliação dos modos de falha sob impacto de compósitos de matriz polimérica reforçados por fibras

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Marcelo M. M. Naglis

1998-03-01

Full Text Available RESUMO: Neste trabalho é feita uma avaliação dos modos de falha de compósitos de matriz polimérica reforçados por fibras de vidro, carbono ou aramida, submetidos a carregamento dinâmico. Os compósitos unidirecionais analisados foram fabricados por prensagem e cura à vácuo de lâminas de pré-impregnados. A energia total absorvida na fratura mostrou uma correlação inversamente proporcional ao módulo elástico das fibras usadas como reforço. Os compósitos com fibras de carbono falharam de um modo frágil. Para estes compósitos o comportamento ao impacto pode ser modelado usando-se uma análise puramente elástica. Para os compósitos com fibras de vidro a falha foi controlada por um mecanismo misto de cisalhamento ao longo da interface fibra-matriz e tensão normal trativa atuando perpendicularmente às fibras. O modelo elástico empregado para simular o comportamento ao impacto subestima a energia absorvida por estes compósitos, porém, a diferença entre os valores experimentais e os calculados não ultrapassou 20 %. A falha dos compósitos com fibras aramidas foi atribuída, principalmente, ao componente de tensão trativa atuando perpendicularmente às fibras. Nestes compósitos foi observado arrancamento superficial nas fibras aramidas e o comportamento ao impacto não obedece o modelo elástico empregado.ABSTRACT: In this work an evaluation of the fracture mode of fiber reinforced resin matrix composites submitted to three point bending dynamic impact testing was undertaken. The unidirectional glass, carbon and aramid fiber-epoxy matrix composites used were fabricated by vacuum bagging prepreg laminas. The energy absorbed to fracture the composites had an inverse correlation to the fibres' elastic modulus. The carbon fiber composites failed in a brittle mode. The analysis of the fracture surfaces showed that for the glass fiber composites, the failure is controlled by a coupled mechanism of shear along the fiber

Efeito de aditivos desaerantes nas características de compósitos de epóxi/fibras de vidro

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Alexsandro Oliveira

2014-01-01

Full Text Available A presença de vazios é um importante fator a afetar as propriedades de compósitos poliméricos. Existem várias causas para a formação de vazios, entre elas, o aprisionamento de gás (frequentemente gás úmido durante o processo de impregnação dos reforços fibrosos com resina e os voláteis gerados durante a formulação da resina. A quantidade de bolhas de ar aprisionadas pode ser, por vezes, reduzida se o sistema de resina é sujeito a um processo de desgaseificação por vácuo ou pelo uso de aditivos químicos especiais. O objetivo deste trabalho é investigar o efeito de um agente desaerante nas propriedades finais de compósitos de resina epóxi moldados pelo processo de RTM utilizando como reforço mantas e tecidos de fibras de vidro. Os compósitos produzidos foram avaliados quanto as suas propriedades de tração, flexão, dureza, short beam e análise dinâmico mecânica (DMA. Em geral, a utilização do aditivo desaerante não provocou alterações significativas nas propriedades mecânicas, tais como resistência e módulo de tração e flexão, as quais são determinadas principalmente pelo tipo e fração volumétrica de fibras. Contudo, os resultados de resistência ao cisalhamento e de dureza mostram um efeito positivo com a inclusão do agente desaerante, levando à melhora na qualidade dos compósitos.

Influência de Negro de Fumo Modificado com Polianilina na Estrutura de Compósitos com Poli(Fluoreto de Vinilideno

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Zucolotto Valtencir

2002-01-01

Full Text Available Compósitos condutores elétricos a base de poli(fluoreto de vinilideno (PVDF e negro de fumo modificado com polianilina (Eeonomer® foram preparados através do processamento por fusão. Resultados de reometria de torque indicaram que a presença de polianilina no negro de fumo é vantajosa ao processamento por fusão, reduzindo a viscosidade do fundido em comparação com a aditivação com negro de fumo puro. Compósitos contendo acima de 5% em peso de Eeonomer® apresentaram condutividade da ordem de 10-2 S/cm. Esse valor se manteve estável mesmo após tratamento térmico a 150degreesC por 170 h em atmosfera ambiente. Análises por calorimetria diferencial de varredura (DSC e difração de Raios-X mostraram que o tipo e a quantidade de Eeonomer®, assim como a taxa de resfriamento da amostra, podem afetar a temperatura de fusão, o grau de cristalinidade e a fase cristalina do PVDF presente no compósito.

Resistência ao Cisalhamento Interlaminar de Compósitos com Resina Epóxi com Diferentes Arranjos das Fibras na Presença de Vazios

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Costa Michelle L.

2001-01-01

Full Text Available A presença de vazios em compósitos estruturais pode ter efeitos significativos. Em geral, os vazios diminuem a resistência estática e a vida em fadiga de laminados. Essa influência é bastante pronunciada na resistência ao cisalhamento interlaminar, compressão, entre outras, onde as propriedades mecânicas da matriz exercem maior influência sobre o comportamento do compósito. O presente artigo descreve o estudo do efeito da porosidade na resistência ao cisalhamento interlaminar de sistemas de compósitos de tecido e tape (fitas unidirecionais de carbono aglutinados com matriz epóxi. Os laminados foram produzidos de maneira semelhante, bem como o processo de introdução de vazios (na faixa de 0a 12% de porosidade.Os compósitos foram avaliados por análises microscópicas e inspeção ultra-sônica e os valores de atenuação medidos foram convertidos em coeficientes de absorção para permitir uma normalização dos dados. O critério de fratura de Mar-Lin apresentou bom ajuste, mostrando-se adequado para o estudo de porosidade em compósitos. Por meio desse critério foi determinado que somente os laminados com porosidade acima de 0,9% para tecido de carbono/epóxi e acima de 0,75% para laminados de tape de carbono/epóxi é que apresentam redução de suas propriedades mecânicas

Influência do tratamento químico da fibra de bananeira em compósitos de poli(etileno-co-acetato de vinila com e sem agente de expansão

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Matheus V. G. Zimmermann

2014-01-01

Full Text Available Neste trabalho foi avaliada a influência do tratamento alcalino na fibra de bananeira (FB e seu uso como agente de reforço em compósitos expandidos de poli(etileno-co-acetato de vinila - EVA. O processo de mistura dos compósitos ocorreu em um misturador de rolos aberto e após conformados e expandidos em uma prensa aquecida com moldes de volumes variáveis. Os compósitos foram avaliados por suas propriedades mecânicas, térmicas e morfológicas. Os resultados indicam que o tratamento alcalino promove a extração de componentes menos estáveis na FB, tais como a lignina, hemicelulose, ceras e óleos de baixo peso molecular. O uso da FB nos compósitos proporciona um decréscimo das propriedades mecânicas de resistência à tração e rasgo em relação ao EVA puro devido a moderadas propriedades de interface polímero-fibra. Nos compósitos expandidos, as propriedades mecânicas decrescem com a diminuição da densidade em função da maior presença de espaços vazios no interior dos compósitos, porém as propriedades mecânicas específicas de resistência ao rasgo apresentaram melhores resultados com 10 pcr de FB em todos os moldes utilizados.

GEAR: A database of Genomic Elements Associated with drug Resistance

Science.gov (United States)

Wang, Yin-Ying; Chen, Wei-Hua; Xiao, Pei-Pei; Xie, Wen-Bin; Luo, Qibin; Bork, Peer; Zhao, Xing-Ming

2017-01-01

Drug resistance is becoming a serious problem that leads to the failure of standard treatments, which is generally developed because of genetic mutations of certain molecules. Here, we present GEAR (A database of Genomic Elements Associated with drug Resistance) that aims to provide comprehensive information about genomic elements (including genes, single-nucleotide polymorphisms and microRNAs) that are responsible for drug resistance. Right now, GEAR contains 1631 associations between 201 human drugs and 758 genes, 106 associations between 29 human drugs and 66 miRNAs, and 44 associations between 17 human drugs and 22 SNPs. These relationships are firstly extracted from primary literature with text mining and then manually curated. The drug resistome deposited in GEAR provides insights into the genetic factors underlying drug resistance. In addition, new indications and potential drug combinations can be identified based on the resistome. The GEAR database can be freely accessed through http://gear.comp-sysbio.org. PMID:28294141

Modèles et méthodologies d’analyse des compétences. Le double éclairage des pratiques et des recherches de Hajjar et Baubion-Broye

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Jacques Leplat

2005-11-01

Full Text Available Le thème des compétences est d’actualité et de nombreuses disciplines se sentent concernées par son étude, notamment différentes spécialités de la psychologie, de l’ergonomie et de la sociologie. Octares témoigne de cet intérêt puisqu’il a déjà édité deux ouvrages sur ce thème : Leplat, J. et de Montmollin, M. (eds. (2001. Les compétences en ergonomie. Recueil de textes. Dupray, A., Guitton, C. & Monchatre, S. (eds.. (2003. Réfléchir la compétence. Approches sociologiques, juridiques, éco...

Conservation of transcription factor binding events predicts gene expression across species

OpenAIRE

Hemberg, Martin; Kreiman, Gabriel

2011-01-01

Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to funct...

Avaliação das propriedades mecânicas e morfológicas de compósitos de PEAD com pó de Pinus taeda e alumina calcinada

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Karine Grison

2015-08-01

Full Text Available ResumoNeste estudo foram desenvolvidos compósitos utilizando PEAD, pó de madeira (Pinus taeda, alumina calcinada e dois diferentes tipos de agentes compatibilizantes para avaliação das propriedades morfológicas e mecânicas dos mesmos. Para aumentar a interação entre a matriz polimérica e o pó de madeira foram utilizados 2% de polietileno graftizado com anidrido maleico em todas as formulações. Para efeito comparativo foi desenvolvida uma formulação com viniltrietoxisilano como compatibilizante para a alumina calcinada. O teor de cargas variou de 4% a 33% para os compósitos de carga única e mantiveram o percentual de 28% para os compósitos com as duas cargas. A interação entre a matriz polimérica e as cargas, proporcionada pelo agente compatibilizante anidrido maleico, foi observada nas micrografias da interface da matriz/carga. A utilização do silano não proporcionou efeito adicional nas propriedades mecânicas dos compósitos. Os compósitos isentos de alumina apresentaram maior resistência à tração, porém na resistência à flexão a presença da alumina contribuiu para o aumento desta propriedade provavelmente devido à pequena interação existente entre a interface do seu grão e a matriz polimérica.

Structure Identification Using High Resolution Mass Spectrometry Data and the EPA’s CompTox Chemistry Dashboard (EAS)

Science.gov (United States)

The iCSS CompTox Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoC...

Chenu F. (2015). L’évaluation des compétences professionnelles. Une mise à l'épreuve des notions et présupposés théoriques sous-jacents

OpenAIRE

Wittorski, Richard

2016-01-01

Dans son ouvrage intitulé L’évaluation des compétences professionnelles, Florent Chenu s’intéresse à une question « chargée » tant sur le plan scientifique (définitions multiples du terme compétence, souvent aujourd’hui considéré comme un « mot valise ») que sur le plan social (des enjeux et débats sociaux vifs concernant les modalités d’évaluation des compétences et, au-delà, concernant la façon de les reconnaître dans les milieux du travail). Dans ce contexte particulier, proposer une publi...

Compósitos à base de gesso com resíduos de EVA e vermiculita Gypsum-based composites with EVA waste and vermiculite

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Marilia P. de Oliveira

2012-06-01

Full Text Available O gesso é um dos materiais de construção mais antigos de que se tem conhecimento. Algumas de suas propriedades lhes conferem vantagens, tais como resistência ao fogo e isolamentos térmico e acústico. Objetivou-se, com este trabalho, avaliar as propriedades físico-mecânicas de compósitos à base de gesso com a incorporação de resíduos da indústria de calçados, o etileno acetato de vinila (EVA e a vermiculita. O desenvolvimento desses compósitos tem como propósito a produção de elementos de revestimento para proteção térmica de alvenarias. Para determinar a influência dos teores de resíduo de EVA e vermiculita e da relação água/gesso nas propriedades massa específica aparente e nas resistências a flexão e a compressão, foram incorporados cinco diferentes percentuais desses materiais, combinados com três relações água/gesso. Os resultados foram analisados por meio da estatística multivariável e indicaram que a massa específica aparente de ambos os compósitos e a resistência à flexão do compósito com vermiculita, mostraram maior dependência da relação água/gesso; por sua vez, o percentual de agregado apresentou maior influência na resistência à flexão do compósito com EVA e na resistência a compressão de ambos os compósitos.Gypsum is one of the oldest known building materials. Some of its properties confer advantages such as fire resistance, thermal and acoustic insulation. This work aims to study the physical and mechanical properties of gypsum-based composite with the incorporation of residues from the footwear industry ethylene vinyl acetate (EVA and vermiculite. The aim to develop these composites is to produce components for thermal protection of masonry. To determine the influence of different residue levels of EVA and vermiculite, and the water/plaster ratio on the bulk density, flexural and compressive strength, five different percentages of these materials were incorporated combined with

Deployed Flight Test of the Iraqi Air Force Comp Air 7SLX (CA-7)

Science.gov (United States)

2014-02-28

been built with a castering nose wheel mounted to the engine mount, a simple yet effective design. The team purchased new engine mounts and castering ...nose wheels from Aero Comp Inc. to solve these problems on all the CA-7s they refurbished, which Fred Webster called “a pretty big modification .”22...from a Cessna 310. The UAE had made numerous other modifications .2 The United States Central Command Air Forces (CENTAF) was working with the

Effects of Dicto-Comp and Dictation on the Writing Skill of Female Adult Iranian EFL Learners

Science.gov (United States)

Adel, Rahil; Hashemian, Mahmood

2015-01-01

This study was an attempt to clarify and remind L2 learners/teachers of 2 kinds of writing: dicto-comp and dictation. We explored the effect of controlled writing on the accuracy of the writing of adult Iranian EFL learners. Prior to the study, the homogeneity of 30 adult EFL learners was checked through an OPT test. Thirty participants were…

Comparação do comportamento à flexão com restrições à deflexão de placas de compósitos de matriz polimérica epoxídica em função do tipo de fibra de reforço

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Morais Willy A. de

2003-01-01

Full Text Available Placas finas de compósitos de matriz polimérica epoxídica reforçada por fibras de vidro, carbono ou aramida, bem como placas de um compósito híbrido vidro-aramida, foram submetidas a ensaios de flexão. As condições de fixação dos corpos de prova foram tais que o ensaios foram realizados com deflexão restrita. Os resultados experimentais obtidos para a deflexão máxima dos compósitos puderam ser qualitativamente previstos usando-se o método de balanço de energia de Ritz. Os compósitos reforçados por fibras de carbono apresentaram os maiores valores de energia de iniciação e de força máxima, o que foi atribuído às altas propriedades intrínsecas das fibras. As propriedades específicas do compósito híbrido foram superiores às dos compósitos apenas com fibras de vidro ou fibras aramidas. Este efeito sinergístico indicou um projeto adequado na fabricação deste compósito. O modo de falha macroscópico de todos os compósitos foi semelhante. Na face frontal, a interação compósito - punção seguiu o comportamento previsto pela Lei de Hertz. Na face posterior, houve preferencialmente delaminação.

Effet sur la compétitivité des réglementations relatives à la gestion des effluents

DEFF Research Database (Denmark)

Andersen, Mikael Skou

2004-01-01

Grâce à un regard approfondi sur le secteur laitier dans les pays de l'OCDE, cette étude permet de mieux analyser l'impact des subventions à l'agriculture et des politiques de l'environnement sur l'environnement et sur la compétitivité internationale des produits laitiers. Ce chapitre étudie les ...

Non-Radial Oscillation Modes of Superfluid Neutron Stars Modeled with CompOSE

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Prashanth Jaikumar

2018-03-01

Full Text Available We compute the principal non-radial oscillation mode frequencies of Neutron Stars described with a Skyrme-like Equation of State (EoS, taking into account the possibility of neutron and proton superfluidity. Using the CompOSE database and interpolation routines to obtain the needed thermodynamic quantities, we solve the fluid oscillation equations numerically in the background of a fully relativistic star, and identify imprints of the superfluid state. Though these modes cannot be observed with current technology, increased sensitivity of future Gravitational-Wave Observatories could allow us to observe these oscillations and potentially constrain or refine models of dense matter relevant to the interior of neutron stars.

Do Deregulated Cas Proteins Induce Genomic Instability In Early Stage Ovarian Cancer?

Science.gov (United States)

2007-12-01

Tensional homeostasis and the malignant phenotype. Cancer Cell 2005;8:241–54. [PubMed: 16169468] 40. Zhang Z, Hernandez- Lagunas L, Horne WC, Baron R...disassembly. Nat Cell Biol 2004;6:154–61. [PubMed: 14743221] 58. Huang J, Hamasaki H, Nakamoto T, Honda H, Hirai H, Saito M, Takato T, Sakai R...Cell Struct Funct 2001;26:619–26. [PubMed: 11942617] 87. Yi J, Kloeker S, Jensen CC, Bockholt S, Honda H, Hirai H, Beckerle MC. Members of the zyxin

Usinabilidade de materiais compósitos poliméricos para aplicações automotivas

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Juan Carlos Horta Gutiérrez

2014-12-01

Full Text Available A cada dia o avanço tecnológico nos leva a encruzilhadas como a construção de veículos mais leves, com menor consumo de combustível e mais seguros. Neste sentido, materiais compósitos poliméricos são materiais usados atualmente em diferentes aplicações nas quais a leveza combinada com um alto módulo de elasticidade são características importantes. Poliamidas reforçadas com fibras de vidro se apresentam como materiais de grande futuro em aplicações automotivas. Desta forma, torna-se importante o estudo do comportamento deste tipo de material quando submetidos a processos de usinagem. Dentre os processos de usinagem o processo de furação é um dos mais utilizados nos componentes de material compósito. Neste trabalho será analisada a influência do avanço, da velocidade de corte e da geometria da ferramenta na força de avanço, pressão específica de corte e desvios dimensionais do furo realizado. Os testes foram realizados em poliamida sem reforço (PA6 e reforçada com 30% fibra de vidro (PA66-GF30 utilizando brocas de carbonetos sinterizados (K20 com ângulos de ponta diferente. Os resultados apontam claramente para a melhor usinabilidade do material reforçado em comparação ao sem reforço.

Dicósimo, Daniel y Simonassi, Silvia (comp., Trabajadores y empresarios en la Argentina del siglo XX: indagaciones desde la historia social

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Valeria Ianni

2013-01-01

Full Text Available Dicósimo, Daniel y Simonassi, Silvia (comp., Trabajadores y empresarios en la Argentina del siglo XX: indagaciones desde la historia social, Prohistoria ediciones, Rosario, 2011 (194 págs..

Security Administrator Street Smarts A Real World Guide to CompTIA Security+ Skills

CERN Document Server

Miller, David R

2011-01-01

A step-by-step guide to the tasks involved in security administration If you aspire to a career in security administration, one of your greatest challenges will be gaining hands-on experience. This book takes you through the most common security admin tasks step by step, showing you the way around many of the roadblocks you can expect on the job. It offers a variety of scenarios in each phase of the security administrator's job, giving you the confidence of first-hand experience. In addition, this is an ideal complement to the brand-new, bestselling CompTIA Security+ Study Guide, 5th Edition o

The US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for chemical sources of risk

Science.gov (United States)

Chemical risk assessment is both time-consuming and difficult because it requires the assembly of data for chemicals generally distributed across multiple sources. The US EPA CompTox Chemistry Dashboard is a publicly accessible web-based application providing access to various da...

Real-time prediction of Physicochemical and Toxicological Endpoints Using the Web-based CompTox Chemistry Dashboard (ACS Fall meeting) 10 of 12

Science.gov (United States)

The EPA CompTox Chemistry Dashboard developed by the National Center for Computational Toxicology (NCCT) provides access to data for ~750,000 chemical substances. The data include experimental and predicted data for physicochemical, environmental fate and transport and toxicologi...

Compósitos de Borracha Natural com Compostos Condutivos à Base de Negro de Fumo e Polímero Condutor Natural Rubber Composites with Conductive Compounds based on Carbon Black and Conducting Polymers

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Marinalva A. dos Santos

2001-09-01

Full Text Available Neste trabalho foram desenvolvidos compósitos condutores elétricos de borracha natural contendo negro de fumo e compostos condutivos baseados em polímeros condutores (Eenomer®. Os compósitos foram processados a quente num reômetro de torque HAAKE e moldados por prensagem. Foram obtidas placas homogêneas, flexíveis e com ótimo acabamento superficial. Os compósitos foram analisados pelas medidas de torque no processamento, medidas de condutividade elétrica, análise termogravimétrica (TGA, calorimetria diferencial de varredura (DSC e ensaios de tração. Estes compósitos apresentaram valores de condutividade elétrica entre 10-7 a 10-1 S/cm, dependendo do tipo de negro de fumo ou composto condutivo utilizado e da quantidade destes no compósito. A análise térmica demonstrou que os compósitos são termicamente estáveis até cerca de 300°C. Os compostos condutivos atuam como reforço para a borracha natural melhorando suas propriedades mecânicas sem perder significativamente sua flexibilidade.In this work, electrically conducting composites of natural rubber with carbon black and natural rubber with conductive compounds containing electrically conducting polymers (Eenomer® were developed. The composites were processed in a torque reometer HAAKE and then hot pressed. Homogeneous and flexible plates were obtained with excellent surface finish. The composites were analysed by the torque measurement during processing, electrical conductivity, thermogravimetric analysis (TGA, differential scanning calorimetric (DSC and mechanical analysis. Conductivity in the order of 10-7 to 10-1 S/cm were achieved, depending on the type of carbon black or conductive compound used and their content in the composite. Thermal analysis demonstrated that the compounds are thermally stable until 300°C. The conductive compounds act as reinforcements in the natural rubber matrix, improving its mechanical properties without significant loss on its

Mass-Spectrometry Based Structure Identification of "Known-Unknowns" Using the EPA's CompTox Dashboard (ACS Spring National Meeting) 4 of 7

Science.gov (United States)

The CompTox Dashboard is a publicly accessible database provided by the National Center for Computational Toxicology at the US-EPA. The dashboard provides access to a database containing ~720,000 chemicals and integrates a number of our public-facing projects (e.g. ToxCast and Ex...

Compósito de colágeno com silicato e hidroxiapatita como material para endodontia: preparação e caracterização = Collagen composite with silicate and hydroxyapatite as endodontic material: preparation and characterization

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E'Gues, Miguel Antônio Menezes

2008-01-01

Full Text Available Objetivo: Este trabalho teve por objetivo preparar e caracterizar um novo compósito de colágeno com silicato e hidroxiapatita que possa vir a ser utilizado como material endodôntico em capeamento pulpar direto e em pulpotomia. Metodologia: Os materiais utilizados como matéria-prima foram colágeno do tipo I na forma aniônica, silicato (cimento Portland Branco e hidroxiapatita sintetizada. Estes materiais foram misturados em proporções variadas de modo a obter um material compósito na forma de pasta. Os materiais obtidos foram caracterizados por técnicas de calorimetria exploratória diferencial, termogravimetria, microscopia eletrônica de varredura (MEV, espectrometria de dispersão de energia de Raios-X e espectroscopia na região do infravermelho. Resultados: A presença de colágeno no compósito foi demonstrada por transições térmicas típicas daquelas encontradas para o colágeno do tipo I (~48ºC, independentemente da proporção utilizada, e também por imagens de MEV, onde as fibras colagênicas também puderam ser observadas interligando as partículas de silicato. A composição química de todos compósitos de colágeno foi praticamente idêntica à do silicato utilizado. Conclusão: Os resultados mostraram que a estrutura da matriz de colágeno nos compósitos testados não foi alterada. Esta é uma característica importante para a utilização em endodontia do material compósito proposto, objetivando uma reparação tecidual de forma "mais natural"

Eugeniusz Misiło, comp. and ed., with an intro. Akcja “Wisła” 1947: Dokumenty i materiały.

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Jerzy Borzęcki

2016-02-01

Full Text Available Eugeniusz Misiło, comp. and ed., with an intro. Akcja “Wisła” 1947: Dokumenty i materiały. Warsaw: Archiwum Ukraińskie and Management Academy Group, 2012. 1246 pp. Illustrations. Maps. Documents section. Appendices section. Biographies sections. Miscellaneous lists. English-language summary. Indexes. Cloth.

Compósitos SiCf /SiC utilizados em sistemas de proteção térmica SiCf /SiC composites for thermal protection systems

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M. Florian

2005-09-01

Full Text Available Compósitos de carbeto de silício (SiC reforçado com fibras de carbeto de silício (SiCf são materiais candidatos em potencial para utilização em sistemas de proteção térmica em altas temperaturas devido principalmente à boa condutividade térmica na direção da fibra e muito baixa condutividade térmica na direção transversal à fibra, alta dureza, estabilidade térmica e à corrosão por oxidação. O compósito SiCf/SiC possui uma matriz de SiC reforçada com fibras contínuas policristalinas de SiC e é obtido por reações de conversão em altas temperaturas e atmosfera controlada, utilizando o compósito carbono/carbono como precursor. O processo de Reação Química em Vapor (CVR foi utilizado para a fabricação de compósitos SiCf/SiC com alta pureza na fase de SiC-beta. O compósito precursor de carbono/carbono foi fabricado com fibra de carbono não estabilizada e matriz carbonosa derivada da resina fenólica na forma de carbono isotrópico. O compósito convertido exibiu uma densidade de 1,75 g/cm³, com 40% de porosidade aberta e resistência à flexão de 80 MPa medida por ensaio flexão em 4 pontos. A área especifica medida pela técnica de BET é dependente da temperatura de conversão e das condições inicias do precursor de carbono, podendo chegar a 18 m²/g.Composites based on silicon carbide are potential candidate materials for thermal protection systems mainly due to its good thermal conductivity in fiber direction and very low transversal thermal conductivity, high hardness, corrosion and thermal resistance. SiCf/SiC composite presents a SiC matrix reinforced with SiC polycrystalline continuous fibers. The composite was obtained by conversion reactions at high temperature and controlled atmosphere from a carbon/carbon composite precursor. The CVR process was used to fabricate SiC /SiC composite with crystalline high-purity beta-SiC from a carbon-carbon precursor fabricated with non-stabilized carbon fiber and

Influência da relação estequiométrica resina/endurecedor em propriedades mecânicas de compósitos ternários hierárquicos resina - epóxi/tecido de fibra de carbono/nanotubos de carbono

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Kássio André Lacerda

2014-01-01

Full Text Available A produção de materiais que apresentem alto desempenho em suas aplicações exige avanços tecnológicos e científicos. Os elevados valores de resistência à tração e módulo de elasticidade, aliados à flexibilidade, baixa densidade e alta razão de aspecto, fazem dos nanotubos de carbono excepcionais candidatos para reforçar compósitos poliméricos. Preparamos por laminação sistemas compósitos ternários à base de resina epóxi/tecidos de fibra de carbono (para os binários, acrescendo nanotubos de carbono para os sistemas ternários. Os parâmetros estequiométricos do sistema epoxídico (valor de Phr e concentração de nanotubos de carbono empregado nos sistemas compósitos tiveram avaliadas suas morfologias (MEV, propriedades térmicas (TG e mecânicas (ASTM D790. Embora o sistema epoxídico com Phr 10,0 tenha apresentado uma maior estabilidade térmica, os compósitos ternários produzidos a partir do sistema com Phr 26,6 mostraram valores de tensão máxima e módulo de elasticidade até 8 vezes maiores que aqueles produzidos com o sistema Phr 10. A adição de nanotubos de carbono aos compósitos com Phr 26,6 resultou em ganhos adicionais de aproximadamente 38 e 15% na tensão máxima e no módulo de elasticidade, respectivamente. Esses resultados revelaram a limitação nos métodos de integralização de nanoestruturas a sistemas compósitos, onde as dispersões estão limitadas a uma série de fatores inerentes a interação química e/ou física durante a fabricação dos compósitos nanoestruturados.

Invention de soi et compétences à l’ère des réseaux sociaux

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Daniel Apollon

2011-06-01

Full Text Available Les réseaux sociaux en ligne encouragent de nouvelles approches de la compétence centrées sur la construction biographique de l’individu et l’invention de soi. Ce nouvel art de faire des « produsagers », répond au besoin d’inventer une réponse individuelle et collective au sentiment aliénant de vacuité des sociétés post-industrielles et post-traditionnelles. Combinant opposition et soumission aux éléments structurants et aliénants de cette modernité tardive, ces produsagers réactualisent diverses ruses, tactiques et schèmes immémoriaux déjà explorés par divers auteurs avant Internet. Sur cette toile de fond, l’auteur propose une réinterprétation plus large de la notion de compétence.Social media practices encourage new approaches and visions of competence focusing on the construction of individual biography and the "invention of oneself". The new "artful skills" of "produsers" address the need to invent individual and collective responses to the sense of alienating emptiness pervading postindustrial and posttraditional societies. Combining and submission and opposition to both structuring and alienating aspects of late modernity, these produsagers actualize various tricks, tactics and immemorial schemes already mapped by various authors before the Internet. On this backdrop the author proposes a broader reinterpretation of the concept of competence.

Les représentations des enseignants quant à leurs profils de compétences relatives à l’ordinateur : vers une théorie des TIC en éducation

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François Desjardins

2005-02-01

Full Text Available Depuis plusieurs années, dans la littérature, on peut sentir un besoin de préciser l’ensemble de connaissances et de compétences relatives aux ordinateurs nécessaires à l’enseignement et à l’apprentissage. Dans ce contexte, cette recherche vise à développer un modèle global qui permettrait de classer à la fois les outils, leurs usages, leurs incidences ainsi que les connaissances et compétences impliquées dans l’intégration des TIC en éducation de façon à pouvoir comprendre les diverses relations qui existent entre chacune de ces composantes. Une première opérationnalisation de ce modèle a donné lieu au développement d’un instrument permettant de recueillir les représentations des enseignants quant à leurs compétences. Cet article présente le modèle élaboré, le questionnaire qui en a découlé et les résultats des premières analyses statistiques des profils recueillis auprès de plus de 600 enseignants francophones de l’Ontario.

Evaluar la Coordinación Motriz Global en Educación Secundaria: El Test Motor SportComp. [Motor co-ordination assessment in Secondary Education: The SportComp Test].

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Luis Miguel Ruiz-Perez

2017-07-01

Full Text Available El objetivo de este estudio fue el desarrollo y evaluación métrica del Test Motor SportComp, instrumento diseñado para ayudar a los profesores de educación física en la evaluación de la coordinación motriz global de sus alumnos de Educación Secundaria. En la actualidad no existen tests que evalúen la coordinación motriz de forma válida y fiable y que puedan ser empleados por el profesorado de educación física en el contexto de sus clases de manera rápida y económica. El presente test se construyó a partir de una revisión de la literatura científica sobre medición motriz entre los 12 y 17 años. La validez de contenido de las pruebas empleadas fue evaluada por expertos y las pruebas seleccionadas fueron aplicadas a 5732 escolares de estas edades. Se analizaron los resultados mediante la técnica de componentes principales que permitió la extracción de un solo factor formado por 5 tareas motrices relacionadas con la coordinación motriz global. El Coeficiente de Correlación Intraclase (CCI permitió obtener una fiabilidad test-retest de (CCI=0,91. Asimismo, mostró una satisfactoria validez criterial con la batería MABC-2 uno de los más reconocidos para la detección de problemas de coordinación motriz. Las propiedades métricas del presente test son muy satisfactorias y ofrecen buenas posibilidades para ser empleado por los profesores de educación física en sus clases por su bajo coste económico, poco tiempo de aplicación reclamado y poseer normas ajustadas por edad y sexo. Asimismo, este test ofrece el potencial de poder servir para detectar a los alumnos con sospecha de poseer problemas de coordinación motriz y por lo tanto contribuir a la mejora de los programas de educación física que palíen esta condición. Abstract The purpose of this study was the development and metric evaluation of the SportComp Motor Test, an instrument designed to aid physical education teachers in the assessment of gross motor

Impregnação de filmes do compósito de policarbonato (PC e sílica-gel (Si com corante fotocrômico em fluido supercrítico - DOI: 10.4025/actascitechnol.v32i1.1999

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Fernanda de Almeida Fin de Lima

2009-12-01

Full Text Available O objetivo deste trabalho foi estudar a impregnação do corante fotocromático Reversacol Graphit® em filmes do compósito de policarbonato (PC e sílica-gel (Si, com a finalidade de obter aplicações em lentes fotocrômicas. Filmes de PC puros também foram impregnados nas mesmas condições, para verificar o efeito da adição de sílica-gel. Os filmes do compósito foram produzidos em proporções de Si:PC de 1:40 e 1:80 (m m-1, pelo método casting. Para a impregnação do corante Reversacol Graphit® nos filmes obtidos foi utilizado o processo supercrítico, pela sua eficiência e benefícios. A impregnação foi feita nos tempos de 15, 30, 45, 60, 90, 120, 150 e 180 min. A temperatura e a pressão adotadas foram de 60ºC e 120 bar. A quantidade de pigmento impregnado nos filmes de Si:PC – 1:40 e 1:80 (m m-1 foi de 29 e 23% de massa de corante por massa de compósito, respectivamente, e para o filme de PC puro foi de apenas 2,2% massa de corante por massa de compósito. Pelas análises térmicas, verificou-se que os filmes do compósito apresentaram maior estabilidade térmica. Pela técnica de microscopia eletrônica, observou-se que os filmes de PC puro e dos compósitos Si:PC – 1:40 e 1:80 (m m-1 apresentaram uma superfície lisa e homogênea.

Desenvolvimento de perfis extrudados de compósitos de polietileno de alta densidade com farinha de madeira

OpenAIRE

Cristiano Ribeiro de Santi

2009-01-01

A extrusão de perfis poliméricos apresenta algumas peculiaridades decorrentes do comportamento de fluxo destes materiais durante o processamento. Por outro lado, o projeto e construção de matrizes para perfis ainda tem sido mais resultado da experiência dos profissionais envolvidos do que um projeto de engenharia na sua essência. Neste trabalho, procurou-se aliar conceitos de engenharia auxiliada por computador ao comportamento reológico de compósitos termoplásticos reforçados com madeira no ...

Desenvolvimento e fabrico de compósitos de matriz polimérica com fibras naturais

OpenAIRE

Pereira, Júlio Miguel da Cruz Rodrigues

2017-01-01

Os compósitos de matriz polimérica com fibras curtas têm propriedades que se têm vindo a relevar como extremamente interessantes para uma ampla variedade de aplicações. Presentemente são fabricados, com recurso a diversas técnicas de processamento, desde componentes específicos para aplicação aeroespacial até artefactos de grande difusão. Estão na agenda mundial, os problemas com a poluição de materiais de origem plástica que fazem uso do petróleo como matéria-prima, a biodegradação destes...

Reforço em compósito de cimento portland através da adição nanotubos de carbono de paredes múltiplas

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Rogerio Daltro Knuth

2016-07-01

Full Text Available A pesquisa desenvolvida no presente trabalho esta embasada na aplicação da nanotecnologia a novos compósitos cimentícios, visando à melhoria das propriedades das argamassas. O objetivo do trabalho foi o de analisar o desempenho físico e mecânico e a ancoragem de uma argamassa de revestimento produzida com nanotubos de carbono de paredes múltiplas (NTCPM, adicionados na quantidade de 0,30% em relação à massa de cimento do compósito, comparativamente ao desempenho com uma argamassa industrializada. Para o presente estudo foi necessário funcionalizar e dispersar os NTCPM, utilizando-se os ácidos sulfúrico (H2SO4 e nítrico (HNO3, e a dispersão foi por ultrassom. Os NTCPM funcionalizados foram neutralizados com hidróxido de amônio (NH3. Foram realizados ensaios de caracterização física e mecânica no estado fresco e no estado endurecido nas argamassas de revestimento com NTCPM e industrializada e análise microestrutura. Os resultados obtidos indicam que a argamassa com NTCPM apresenta melhor desempenho que a argamassa industrializada, no tocante a densidade, consistência, viscosidade, resistência à tração e resistência a compressão axial. Palavras-chave: Argamassas de revestimento. Nanotubos de carbono. Compósitos. Propriedades físicas e mecânicas. Microestrutura.

SDN-controlled topology-reconfigurable optical mobile fronthaul architecture for bidirectional CoMP and low latency inter-cell D2D in the 5G mobile era.

Science.gov (United States)

Cvijetic, Neda; Tanaka, Akihiro; Kanonakis, Konstantinos; Wang, Ting

2014-08-25

We demonstrate the first SDN-controlled optical topology-reconfigurable mobile fronthaul (MFH) architecture for bidirectional coordinated multipoint (CoMP) and low latency inter-cell device-to-device (D2D) connectivity in the 5G mobile networking era. SDN-based OpenFlow control is used to dynamically instantiate the CoMP and inter-cell D2D features as match/action combinations in control plane flow tables of software-defined optical and electrical switching elements. Dynamic re-configurability is thereby introduced into the optical MFH topology, while maintaining back-compatibility with legacy fiber deployments. 10 Gb/s peak rates with <7 μs back-to-back transmission latency and 29.6 dB total power budget are experimentally demonstrated, confirming the attractiveness of the new approach for optical MFH of future 5G mobile systems.

Les compétences infirmières mobilisées dans un service d'oncologie pédiatrique pour répondre aux besoins de l'enfant et sa famille: travail de Bachelor

OpenAIRE

Alemanno, Gaëtan; Lorency, Vincent; Morf, Benjamin; Delajoux, Annie

2013-01-01

Dans ce travail de bachelor, nous nous intéressons aux compétences infirmières en onco-hématologie pédiatrique. En faisant cette recherche, nous mettons en évidences le vécu des parents dont l’enfant est malade, ainsi que leurs différents besoins ressentis, que ce soit de l’enfant ou des proches aidants. Nous identifions ces compétences en comparant, les actions et pratiques infirmières, avec le modèle de Calgary.

Estudo de propriedades dinâmico-mecânicas de um compósito aeronáutico de CFRP com fios de ligas com memória de forma embebidos

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Zoroastro Torres Vilar

2016-01-01

Full Text Available Resumo Este trabalho trata-se de um estudo experimental do comportamento de propriedades termomecânicas de um compósito ativo, obtido através da introdução de diferentes frações volumétricas de fios de uma liga NiTi com efeito de memoria de forma em uma matriz polimérica reforçada com fibras de carbono (CFRP. Para tal estudo, inicialmente fez-se uma análise do módulo elástico de um pré preg de CFRP aeronáutico com diferentes posições de ângulo de fibras de carbono, a fim de determinar a matriz mais adequada para a introdução de fios de NiTi para obter compósito ativo. Verificou-se que a matriz com fibras alinhadas a 15º apresenta-se como uma boa opção para a obtenção de compósitos ativos, sendo utilizada para a fabricação de amostras de CFRP/NiTi. As amostras tiveram seu potencial de ativação avaliado através da análise da variação do módulo de elasticidade com o aumento da temperatura usando a técnica de Análise Dinâmico-Mecânica (DMA. Através dos resultados obtidos, verificou-se a capacidade de ativação dos compósitos CFRP/NiTi, os quais apresentam variação positiva de módulo de elasticidade ao serem aquecidos acima da temperatura de transformação dos fios NiTi.

The EPA CompTox Dashboard and Underpinning Software Architecture – a platform for data integration for environmental chemistry data (ACS Fall Meeting 7 of 12)

Science.gov (United States)

The CompTox Dashboard was developed by the Environmental Protection Agency’s National Center for Computational Toxicology. This dashboard has been architected in a manner that allows for the deployment of multiple “applications”, both as publicly available databases, and for dep...

Influência da adição de uma carga nanoparticulada no desempenho de compósitos poliuretano/fibra de juta Influence of a nanoparticulate filler addition on the mechanical properties of polyurethane/jute fiber composites

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José R. A. Neto

2007-03-01

Full Text Available Neste trabalho as propriedades mecânicas de um compósito, formado a partir de uma matriz de poliuretano derivado do óleo de mamona e reforçada por um tecido tramado de juta, foram avaliadas. O efeito da adição de pequenos teores de bentonita cálcica e sódica sobre as propriedades mecânicas da matriz de poliuretano e de compósitos poliuretano/juta também foi investigado. Os resultados indicam que a incorporação de fibra de juta à matriz poliuretana promoveu melhora significativa nas propriedades sob tração dos compósitos. A adição de pequenos teores de argila à matriz alterou o desempenho mecânico dos compósitos, porém os resultados não foram os esperados. O compósito híbrido poliuretano/argila/fibra de juta, contudo, apresentou propriedades mecânicas superiores às dos compósitos reforçados unicamente com tecido de juta, o que indica uma atuação sinérgica dos reforços híbridos argila/juta.In this work the mechanical properties of polyurethane/jute fiber composites were evaluated as a function of fiber content and mineral filler addition. A polyurethane (PU derived from castor oil was used as the matrix and hessian cloth as reinforcement. The effect of the incorporation of small amounts of local clay (bentonite, in its calcium and sodium forms, on the mechanical properties of polyurethane/jute composites was also investigated. The results indicate that the tensile properties of the composites substantially increased with jute fiber addition and that although the mechanical properties of the matrix were affected by the addition of nanoparticulate clay, the improvement was not as expected. This was attributed to poor mixing and dispersion of the filler, which was confirmed by SEM. A synergistic effect was observed for the hybrid clay/jute fiber composites, with considerable improvement in the mechanical performance of the hybrid composites.

MED, COMP, multilayered and NEIN: an overview of multiple epiphyseal dysplasia

Energy Technology Data Exchange (ETDEWEB)

Lachman, Ralph S. [International Skeletal Dysplasia Registry, UCLA School of Medicine, Radiological Services, Department of Pediatrics, Los Angeles, CA (United States); International Skeletal Dysplasia Registry, Los Angeles, CA (United States); Krakow, Deborah; Cohn, Daniel H.; Rimoin, David L. [International Skeletal Dysplasia Registry, UCLA School of Medicine, Radiological Services, Department of Pediatrics, Los Angeles, CA (United States)

2005-02-01

This overview covers the group of disorders that presents radiographically as multiple epiphyseal dysplasia (MED). The disorders include ''classic MED'' (Ribbing and Fairbank types): MED that is caused by mutations in the cartilage oligomeric matrix protein (COMP), type IX collagen, and matrilin 3 genes (MATN3); and MED with multilayered patella, brachydactyly, and clubbed feet resultant from mutations in gene defect diastrophic dysplasia (DTDST). The recently identified gene/molecular abnormalities in these disorders have made more exact identification possible in many cases, although clinical testing is not always available. However, there are specific radiographic findings that allow the accurate diagnosis to be made, thus potentially guiding which molecular defect(s) should be investigated. The modes of inheritance of these distinct MED conditions are not identical. When a specific diagnosis is made, proper genetic counseling as well as prognostication, management issues and complications can be delineated to the patient and family. This review will include the mechanics of diagnostic and molecular triage for these disorders. (orig.)

Former aux TICE : entre compétences techniques et modèles pédagogiques

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Jacques Béziat

2012-01-01

Full Text Available Cette contribution discute des enjeux et des limites d’une formation aux compétences techniques attendues des futurs enseignants d’école primaire. Une formation est certainement nécessaire pour espérer voir des pratiques pédagogiques avec les TICE se développer en classe. Mais ce n’est qu’un des leviers pour leur intégration dans les pratiques scolaires. Une formation aux TICE suppose que l’on mette l’accent sur l’analyse de pratiques. Plus que de former « simplement » à l’usage pédagogique d’outils numériques, il est indispensable de former à la complexité de leurs enjeux intellectuels et pratiques.

Codon Bias Patterns of E. coli's Interacting Proteins.

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Maddalena Dilucca

Full Text Available Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, CompAI, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for E.coli, comparing CompAI with other widely used indices: tAI, CAI, and Nc. We show that CompAI and tAI capture similar information by being positively correlated with gene conservation, measured by the Evolutionary Retention Index (ERI, and essentiality, whereas, CAI and Nc appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of tAI and CompAI with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs. We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in E.coli. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by CompAI and tAI. Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, CompAI turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation. Notably, CompAI may potentially correlate with translation speed measurements, by accounting for the specific delay induced by wobble-pairing between codons and anticodons.

Estudos das propriedades mecânicas e térmicas do polímero biodegradável poli-3-hidroxibutirato (PHB) e de compósitos PHB/pó de madeira.

OpenAIRE

Miriam Lúcia Chiquetto Machado

2008-01-01

O objetivo deste trabalho foi o estudo das propriedades mecânicas e térmicas do PHB e de compósitos de PHB/pó de madeira processados, reprocessados e irradiados. Foram preparados compósitos com PHB e pó de madeira com concentrações de PHB/pó de madeira de 90/10, 80/20 e 70/30 (m/m). Foram realizados ensaios de propriedades mecânicas, HDT, ponto de amolecimento Vicat, TGA e DSC. A incorporação do pó de madeira aumentou o grau de cristalinidade e a temperatura de cristalização do polímero, e no...

GeoComp-n, an advanced system for the processing of coarse and medium resolution satellite data. Part 2: biophysical products for Northern ecosystems

Energy Technology Data Exchange (ETDEWEB)

Cihlar, J. [Canada Centre for Remote Sensing, Natural Resources Canada, Ottawa, Ontario (Canada); Chen, J. [Canada Centre for Remote Sensing, Natural Resources Canada, Ottawa, Ontario (Canada); Univ. of Toronto, Dept. of Geography, Toronto, Ontario (Canada); Li, Z. [Canada Centre for Remote Sensing, Natural Resources Canada, Ottawa, Ontario (Canada); Univ. of Maryland, Dept of Meteorology, College Park, MD (United States)] [and others

2002-02-01

Effective use of satellite data for environmental monitoring requires consistent, high-throughput processing of large volumes of data as it is transformed from raw measurements to useful higher level products. 'GeoComp-n', the next generation of the Geocoding and Compositing System developed at the Canada Centre for Remote Sensing, Natural Resources Canada, was developed as a software solution to this challenge, for use with satellites that provide daily data for the landmass of Canada or comparably large areas. In this paper, the authors discuss the characteristics of the algorithms and methods used in the generation of GeoComp-n products. The theoretical basis and assumptions in the algorithms are described, and the quality of the products is discussed based on validation studies. Examples of a suite of products for Canada during one 10-day period illustrate the diversity and quality of observations for the terrestrial biosphere that may be derived frequently and over large areas from satellites. Issues related to quality assessment in a production environment are also discussed. (author)

GeoComp-n, an advanced system for the processing of coarse and medium resolution satellite data. Part 2: biophysical products for Northern ecosystems

International Nuclear Information System (INIS)

Cihlar, J.; Chen, J.; Li, Z.

2002-01-01

Effective use of satellite data for environmental monitoring requires consistent, high-throughput processing of large volumes of data as it is transformed from raw measurements to useful higher level products. 'GeoComp-n', the next generation of the Geocoding and Compositing System developed at the Canada Centre for Remote Sensing, Natural Resources Canada, was developed as a software solution to this challenge, for use with satellites that provide daily data for the landmass of Canada or comparably large areas. In this paper, the authors discuss the characteristics of the algorithms and methods used in the generation of GeoComp-n products. The theoretical basis and assumptions in the algorithms are described, and the quality of the products is discussed based on validation studies. Examples of a suite of products for Canada during one 10-day period illustrate the diversity and quality of observations for the terrestrial biosphere that may be derived frequently and over large areas from satellites. Issues related to quality assessment in a production environment are also discussed. (author)

Les effets sur la compétitivité internationale des réglementations relatives à la gestion des effluents d'élevage

DEFF Research Database (Denmark)

Andersen, Mikael Skou

2003-01-01

différences sensibles de compétitivité de la production porcine et d’une concurrence internationale croissante sur le marché de la viande de porc explique que l’on se préoccupe de la charge financière imposée par les politiques de l’environnement aux éleveurs, notamment en ce qui concerne la gestion des...

COMP report: CPQR technical quality control guidelines for low-dose-rate permanent seed brachytherapy.

Science.gov (United States)

Beaulieu, Luc; Radford, Dee-Ann; Eduardo Villarreal-Barajas, J

2018-03-14

The Canadian Organization of Medical Physicists (COMP), in close partnership with the Canadian Partnership for Quality Radiotherapy (CPQR) has developed a series of Technical Quality Control (TQC) guidelines for radiation treatment equipment. These guidelines outline the performance objectives that equipment should meet in order to ensure an acceptable level of radiation treatment quality. The TQC guidelines have been rigorously reviewed and field tested in a variety of Canadian radiation treatment facilities. The development process enables rapid review and update to keep the guidelines current with changes in technology. This article contains detailed performance objectives and safety criteria for low-dose-rate (LDR) permanent seed brachytherapy. © 2018 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Les facteurs influançant les compétences des infirmiers et des infirmières en matière de soins spirituels dans un contexte de soins somatiques: une revue de littérature étoffée

OpenAIRE

Bédaton, Stéphanie; Hayoz, Marine; Schenevey Perroulaz, Eliane

2013-01-01

Les facteurs influençant les compétences des infirmiers et des infirmières en matière de soins spirituels dans un contexte de soins somatiques. Objectif : identifier la place de la spiritualité dans les soins et identifier les facteurs aidants et les obstacles qui influencent les compétences des infirmières dans le domaine de la spiritualité dans un contexte de soins somatiques.

B(H) B(H) ⊗ B(H)

Indian Academy of Sciences (India)

[8] Lance C, On nuclear C∗. -algebras. J. Funct. Anal. 12 (1973) 157–176. [9] Ozawa N, An application of expanders to B(l2)⊗B(l2), J. Funct. Anal. 198 (2003) 499–. 510. [10] Pisier G, Introduction to operator space theory, London Mathematical Society Lecture. Note Series 294, (Cambridge: Cambridge University Press) ...

Using semi-automated curation workflows to collect, organize, and curate the data and models necessary to support the EPA CompTox chemical dashboard (ACS Spring meeting)

Science.gov (United States)

With the increasing need to leverage data and models to perform cutting edge analyses within the environmental science community, collection and organization of that data into a readily accessible format for consumption is a pressing need. The EPA CompTox chemical dashboard is i...

Using the US EPA's CompTox Dashboard to support identification and screening of emerging organic contaminants in the environment (ACS Spring National meeting) 2 of 7

Science.gov (United States)

The US EPA’s iCSS CompTox Dashboard is a curated, publicly accessible resource provided by the National Center for Computational Toxicology (https://comptox.epa.gov). The Dashboard provides support for toxicology and risk assessment within and external to the EPA (including ToxC...

Classe de langue et compétence évaluative des enseignants : entre pratiques évaluatives et politique éducative

Directory of Open Access Journals (Sweden)

Mina Sadiqui

2014-12-01

Dans une dernière partie nous esquisserons, en nous basant sur une approche didactique, quelques repères qui permettraient à tout enseignant ou futur enseignant de repenser les éléments organisateurs d’un dispositif d’évaluation ,et donc de construire une compétence évaluative en classe de langue, si on veut vraiment mettre en place une nouvelle politique éducative relative à l’enseignement/apprentissage des langues ,en l’occurrence celle du FLE au lycée au Maroc.

The Influence of Neck Posture and Helmet Configuration on Neck Muscle Demands

Science.gov (United States)

2014-06-22

10/06/14 10:19 AM C:\\Users\\cdmckinn\\Docume...\\data_pad.m 1 of 1 function data_padded = data_pad(funct,indata,pad_size, datatype ... datatype == 1 %EMG data_padded = indata(pad_size+1:length(indata)-pad_size,:); elseif datatype == 2 %KINEMATICS (with differentiation...data_pad.m 1 of 1 function data_padded = data_pad(funct,indata,pad_size, datatype

Les pôles de compétitivité : le recours au modèle des clusters ?

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Jean Bouinot

2007-03-01

Full Text Available Introduction : définition d’un cluster En novembre 2004, le gouvernement a lancé un appel d’offre pour structurer des pôles de compétitivité que les praticiens français n’hésitent pas à qualifier de cluster, littéralement un rassemblement du type « bouquet de fleurs ». Pour une définition théorique on peut s’appuyer sur une comparaison avec le modèle du district industriel italien (MDII. Le district est spécialisé dans un produit donné (chaussures de sport à Montebelluna, le leader mondial e...

FoRSIC : De l'ingénierie des compétences à l'ingénierie des connaissances.

OpenAIRE

Ertzscheid , Olivier; Link-Pezet , Jo; Lacombe , Elisabeth

2002-01-01

FoRSIC [1] est un dispositif d'ingénierie des connaissances, qui s'ancre dans le champ de la formation à la recherche documentaire. Après avoir précisé le contexte théorique qui le sous-tend, nous décrirons ici les méthodologies qui nous ont permis de faire émerger des représenta-tions structurantes et partageables de ce domaine, à l'aide d'une ontologie des compétences docu-mentaires que nous relions au réseau sémantique du modèle de domaine.

Avaliação da Resistência Interlaminar do Compósito PEI/Fibras de Carbono Soldado pelo Método de Resistência Elétrica

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Jonas Frank Reis

Full Text Available Resumo: O presente trabalho tem como principal objetivo avaliar a efetividade do processo de soldagem por resistência elétrica em compósitos de matriz poli (éterimida reforçados com fibras contínuas de carbono, a partir do estudo das propriedades térmicas e mecânicas da junta soldada. Para a avaliação das propriedades térmicas, as amostras do material soldado foram submetidas às análises por termogravimetria e por análise termomecânica. Já com o intuito de se estudar a interface resultante da soldagem, estudos foram realizados a partir dos ensaios de cisalhamento ILSS e Iosipescu, assim como por End-Notched Flexure (ENF. Os resultados das análises térmicas em laminados de PEI/fibras de carbono não soldados mostram que o início da degradação para estes compósitos ocorre a 460 °C, e ainda é evidenciado que a temperatura de transição vítrea para amostras soldadas é aproximadamente 15% superior aos resultados provenientes de amostras não soldadas. Nos ensaios mecânicos mostram que houve um aumento de 32% e de 20%, respectivamente, nos resultados de cisalhamento interlaminar por ILSS e por Iosipescu nas amostras soldadas, quando estas são comparadas a amostras não soldadas. Os resultados do ensaio de ENF apresentam valores satisfatórios de tenacidade à fratura interlaminar nos compósitos soldados em relação aos valores encontrados em literatura.

SCIDAC Center for simulation of wave particle interactions CompX participation

Energy Technology Data Exchange (ETDEWEB)

Harvey, R.W. [CompX, Del Mar, CA (United States)

2017-11-14

beyond to achieve the needed physics, resolution, and/or statistics to address these issues. CompX provides computer codes and analysis for the calculation of the electron and ion distributions in velocity-space and plasma radius which are necessary for reliable calculations of power deposition and toroidal current drive due to combined radiofrequency and neutral beam at high injected powers. It has also contributed to ray tracing modeling of injected radiofrequency powers, and to coupling between full-wave radiofrequency wave models and the distribution function calculations. In the course of this research, the Fokker-Planck distribution function calculation was made substantially more realistic by inclusion of finite-width drift-orbit effects (FOW). FOW effects were also implemented in a calculation of the phase-space diffusion resulting from radiofrequency full-wave models. Average level of funding for CompX was approximately three man-months per year.

Compósitos Bioativos Obtidos a Partir da Inserção de Vidro Bioativo em Matriz de Poli(Metacrilato de Metila Bioactive Composites Obtained from Bioactive Glass Particles into Poly(Methyl Methacrylate

Directory of Open Access Journals (Sweden)

Paulo E. Silva Junior

2001-09-01

Full Text Available Várias biocerâmicas são capazes de se ligarem a tecidos vivos (bioatividade, no entanto apresentam propriedades mecânicas muito diferentes daquelas exibidas por tecidos naturais. Tal fato acaba por restringir o uso desses materiais em um mais extenso número de aplicações biomédicas. Compósitos de matriz polimérica reforçada com uma fase bioativa podem combinar o comportamento bioativo característico de algumas biocerâmicas com propriedades mecânicas próximas à de tecidos humanos. O presente trabalho tem como objetivo sintetizar e caracterizar compósitos de matriz polimérica reforçada por partículas de vidro bioativo. Os compósitos foram produzidos a partir da polimerização em massa de metacrilato de metila na presença de partículas de vidro bioativo (vidro de silicato de cálcio, fósforo e sódio. Partículas de vidro foram adicionadas ao monômero em diversas concentrações para permitir a variação das propriedades mecânicas e da bioatividade desses compósitos. A bioatividade dos materiais produzidos foi avaliada através de testes in vitro realizados a 37ºC em uma solução simuladora do fluido humano por períodos de tempo de 0 hora a 30 dias. Em seguida, os compósitos submetidos aos testes in vitro foram caracterizados por espectroscopia de infravermelho. O procedimento de síntese mostrou-se eficaz na produção de compósitos com diferentes frações volumétricas de partículas distribuídas homogeneamente pelo material. Os resultados dos testes in vitro revelaram a deposição de uma camada de hidroxiapatita carbonatada (HCA na superfície dos materiais, comprovando a bioatividade dos compósitos. Foi ainda observado que a cinética de deposição da camada de HCA pode ser controlada pela fração volumétrica da fase bioativa.Some bioceramics have the ability to bind to tissues but they show mechanical properties very different from the ones of natural tissues. This fact restricts the use of these

Apport de la théorie du sentiment d’autoefficacité pour le développement de la compétence technopédagogique des futurs enseignants

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Sonia Lefebvre

2015-01-01

Full Text Available Le texte s’intéresse à la formation technopédagogique des futurs enseignants, et plus précisément, aux pratiques à déployer en formation initiale pour accroître leur compétence professionnelle à intégrer les TIC. Les pratiques proposées prennent appui sur la théorie du sentiment d’autoefficacité d’Albert Bandura, ce sentiment pouvant influencer leur compétence à intégrer les TIC. Appuyé par des travaux empiriques, le texte aborde les sources susceptibles d’influencer l’autoefficacité à intégrer les TIC dans un cadre pédagogique et identifie des pistes d’action à envisager. Enfin, la réflexion amène à repenser les interventions des formateurs tant en formation initiale qu’en formation continue et à remettre en question, sur le plan empirique, les dispositifs de formation.

État des lieux de la Gestion prévisionnelle des Emplois et des Compétences dans le secteur de la métallurgie : cas de l'entreprise Duferco Coating de Beautor

OpenAIRE

Marie Amélie Cloez

2011-01-01

Ce mémoire traite de la gestion prévisionnelle des emplois et des compétences dans le secteur de la métallurgie, plus précisément au sein de l'entreprise Duferco Coating située à Beautor. Ce mémoire cible le secteur de la métallurgie parce qu'il fut l'un des premiers secteurs à mettre en place cette démarche. Depuis la loi de deux mille cinq, les entreprises de plus de trois cent salariés doivent mettre en place un accord GPEC qui leur permet de prévoir leurs besoins en termes de compétences ...

Diametral tensile strength of composite resins submitted to different activation techniques Resistência à tração diametral de compósitos resinosos submetidos a diferentes técnicas de ativação

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Denise Sá Maia Casselli

2006-09-01

Full Text Available The aim of this study was to evaluate the diametral tensile strength (DTS of composite resins submitted to different curing techniques. Four composite resins were tested in this study: Targis (Ivoclar, Solidex (Shofu, Charisma (Heraeus-Kulzer and Filtek Z250 (3M Espe. Sixty-four cylindrical specimens were prepared and divided into eight groups according to each polymerization technique (n = 8. The indirect composite resins (Targis and Solidex were polymerized with their respective curing systems (Targis Power and EDG-lux; Charisma and Filtek Z250 were light-cured with conventional polymerization (halogen light and additionally, with post-curing systems. Specimens were stored in artificial saliva at 37°C for one week. DTS tests were performed in a Universal Testing Machine (0.5 mm/min. The data were statistically analyzed by ANOVA and Duncan tests. The results were (MPa: Z250/EDG-lux: 69.04ª; Z250/Targis Power: 68.57ª; Z250/conventional polymerization: 60.75b; Charisma/Targis Power: 52.34c; Charisma/conventional polymerization: 49.17c; Charisma/EDG-lux: 47.98c; Solidex: 36.62d; Targis: 32.86d. The results reveal that the post-cured Z250 composite resin showed the highest DTS means. Charisma composite presented no significant differences when activation techniques were compared. Direct composite resins presented higher DTS values than indirect resins.O objetivo do trabalho foi avaliar a resistência à tração diametral (DTS de compósitos submetidos a diferentes técnicas de polimerização. Foram testados quatro compósitos neste estudo: Targis (Ivoclar, Solidex (Shofu, Charisma (Heraeus-Kulzer e Filtek Z250 (3M Espe. Foram confeccionados 64 corpos-de-prova cilíndricos, que foram divididos em 8 grupos de acordo com a técnica de polimerização (n = 8. Os compósitos indiretos (Targis e Solidex foram polimerizados com seus respectivos sistemas de ativação (Targis Power e EDG-lux; Charisma e Filtek Z250 foram fotoativados com polimeriza

Resposta tecidual ao compósito 50% hidroxiapatita: 50% poli-hidroxibutirato para substituição óssea em coelhos Tissue response to the composite 50% hydroxyapatite: 50% polyhydroxybutyrate for bone substitution in rabbits

Directory of Open Access Journals (Sweden)

E.C. Carlo

2009-08-01

Full Text Available Avaliaram-se a biocompatibilidade, a osseointegração, a osseocondução e a biodegradação de compósitos de 50% hidroxiapatita (HAP-91® e 50% poli-hidroxibutirato. O compósito foi implantado em defeitos ósseos em 12 coelhos (grupo experimental, sendo comparado a defeitos não preenchidos (grupo-controle, de igual número. Os parâmetros clínicos dor, claudicação, infecção, deiscência e edema foram avaliados nos primeiros oito dias após a cirurgia e aos 45 e 90 dias. Radiografias foram realizadas aos oito, 45 e 90 dias após a cirurgia em quatro animais por grupo que, em seguida, foram submetidos à eutanásia para coleta de amostras destinadas a análises histológica e histomorfométrica. Não ocorreram diferenças entre os grupos para todos os parâmetros clínicos. Radiografias demonstraram um compósito com radiopacidade semelhante à do osso vizinho e contato direto entre osso e compósito aos 45 e 90 dias. Diferença significativa foi observada entre a porcentagem dos tecidos ósseo e conjuntivo dentro do defeito nos dias oito, 45 e 90, assim como na interface aos 45 e 90 dias. Foram observadas projeções dos tecidos ósseo e conjuntivo no interior do compósito e sinais de biodegradação na ausência de infiltrado inflamatório. Pode-se concluir que o compósito é biocompatível, osseocondutor, biodegradável e se integra ao tecido ósseo.The biocompatibility, osseointegration, osseoconductivity, and biodegradation of a 50-50% hydroxyapatite (HAP-91®-polyhydroxybutyrate were evaluated. The composite was implanted in bone defects of 12 rabbits (experimental group, being compared to unfilled defects (control group, 12 animals. The clinical parameters of pain, lameness, infection, dehiscence, and edema were evaluated during the first eight days and on the 45th and 90th days after surgery. Radiographs were taken in four animals per group at 8, 45, and 90 days after surgery, when animals were euthanized to collect samples for

Propriedades mecânicas de tração de compósitos poliéster/tecidos híbridos sisal/vidro Properties of polyester/hibrid sisal-glass fabrics

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Laura H. de Carvalho

2006-03-01

Full Text Available O desempenho e o custo de compósitos podem ser alterados por hibridização e, neste sentido, é relativamente comum o uso combinado de fibras e reforços minerais no desenvolvimento destes materiais. No presente trabalho o desempenho mecânico de compósitos poliéster insaturado/ tecidos híbridos sisal-vidro foram investigados em função do teor de fibra e direção do teste. Foram confeccionados três tecidos híbridos (com 30, 40 e 50% em peso de vidro com fios de sisal no urdume e fibras de vidro na trama. Os compósitos foram moldados por compressão à temperatura ambiente com os tecidos alinhados. Os resultados indicam que houve um aumento nas propriedades mecânicas de tração de todos os compósitos com o aumento do teor de fibras. Para os compósitos reforçados por tecidos com baixo teor de fibra de vidro, as propriedades tenderam a ser mais elevadas quando os testes foram conduzidos na direção do sisal, enquanto que para os tecidos com elevado teor de vidro, o oposto foi observado. Estes comportamentos foram associados ao teor de fibra de vidro na direção do teste e ao diâmetro das fibras de sisal. Em baixos teores de fibra o sisal agiria como inclusão ou defeito, prejudicando as propriedades mecânicas; em elevados teores as propriedades do vidro suplantariam os defeitos provocados pelo sisal.Hybridization can alter both mechanical performance and cost of polymer composites, and novel composite materials can be obtained by the combination of both fibrous and mineral reinforcements. In the present work the mechanical performance of unsaturated polyester/hybrid sisal-glass fabrics was determined as a function of fibre content and test direction. Three different hybrid fabrics (30, 40 and 50% w/w glass content with sisal strings in the warp and glass roving in the weft were hand weaved. Aligned fabric compression moulded composites were obtained at room temperature. The results showed enhanced properties with fibre content

How should collective and distributed skills be considered in professional skills management? Quelle prise en compte des compétences collectives et distribuées dans la gestion des compétences professionnelles ? Cómo tomar en cuenta las competencias colectivas y distribuidas en la gestión de las competencias profesionales ?

Directory of Open Access Journals (Sweden)

Catherine Delgoulet

2008-05-01

Full Text Available The purpose of this paper is to discuss how collective and distributed skills are considered in a professional competence management system by associating sociological and ergonomic work approaches. Collective work in companies is currently paradoxical: on the one hand, its value is increased through various forms of cooperation, and on the other hand, it is restricted in its makeup and sustainability by new kinds of employment. However, the results of our study, carried out in a large industrial and retailing company in a high-risk sector, highlight that a “single” and individual professional competence management system is a partial system. Work contexts should take into account technical specialties, changes in populations, changes in technology, etc. An efficient skills management system therefore ought to combine both individual and collective approaches in order to anticipate organizations that promote the development of collective and/or distributed skills, and training situations that promote their construction and transmission.L’objectif de cet article est de discuter de la prise en compte des compétences collectives et distribuées dans un dispositif de gestion des compétences en associant des approches sociologiques et ergonomiques du travail. Le travail collectif dans l’entreprise est aujourd’hui paradoxal : valorisé dans l’organisation par des formes variées de coopérations et contraint et fragilisé dans sa constitution et pérennité face à de nouvelles formes d’emploi. Cependant, les résultats de cette étude, réalisée dans une grande entreprise industrielle et commerciale d’un secteur à risques, montrent qu’un dispositif de gestion de compétences ne peut être « unique ». Il doit se décliner selon des contextes, des spécialités, des évolutions de populations, des évolutions technologiques, etc. Une articulation des points de vue individuel et collectif est nécessaire pour une gestion des

Quelle prise en compte des compétences collectives et distribuées dans la gestion des compétences professionnelles ? How should collective and distributed skills be considered in professional skills management? Cómo tomar en cuenta las competencias colectivas y distribuidas en la gestión de las competencias profesionales ?

Directory of Open Access Journals (Sweden)

Catherine Delgoulet

2008-05-01

Full Text Available L’objectif de cet article est de discuter de la prise en compte des compétences collectives et distribuées dans un dispositif de gestion des compétences en associant des approches sociologiques et ergonomiques du travail. Le travail collectif dans l’entreprise est aujourd’hui paradoxal : valorisé dans l’organisation par des formes variées de coopérations et contraint et fragilisé dans sa constitution et pérennité face à de nouvelles formes d’emploi. Cependant, les résultats de cette étude, réalisée dans une grande entreprise industrielle et commerciale d’un secteur à risques, montrent qu’un dispositif de gestion de compétences ne peut être « unique ». Il doit se décliner selon des contextes, des spécialités, des évolutions de populations, des évolutions technologiques, etc. Une articulation des points de vue individuel et collectif est nécessaire pour une gestion des compétences qui permette de prévoir : des organisations propices au développement des compétences distribuées ou collectives, des situations de formation favorisant leur construction et leur transmission.The purpose of this paper is to discuss how collective and distributed skills are considered in a professional competence management system by associating sociological and ergonomic work approaches. Collective work in companies is currently paradoxical: on the one hand, its value is increased through various forms of cooperation, and on the other hand, it is restricted in its makeup and sustainability by new kinds of employment. However, the results of our study, carried out in a large industrial and retailing company in a high-risk sector, highlight that a “single” and individual professional competence management system is a partial system. Work contexts should take into account technical specialties, changes in populations, changes in technology, etc. An efficient skills management system therefore ought to combine both

PC Technician Street Smarts, Updated for the 2009 Exam A Real World Guide to CompTIA A+ Skills

CERN Document Server

Pyles, James

2009-01-01

An inside look into the life of a PC technician-from everyday tasks to the challenging roadblocks Gaining hands-on experience is considered the most difficult part of trying to break into the PC technician. Building on the standards set by CompTIA-and endorsed by the IT industry worldwide-this book takes you one step further than what you might simply learn in a classroom and shows you how to actually perform the various tasks you can expect to encounter on the job. The Street Smarts series is designed to help current or aspiring IT professionals put their certification to work for them. Full

Fabricação de compósitos com matriz de alumina reforçada com whiskers de mulita

OpenAIRE

Salles, Mário César Fernandez de

2008-01-01

Neste trabalho foram fabricados compósitos cerâmicos utilizando alumina como matriz e whiskers de mulita como reforço. As composições de whiskers foram 10, 20, 30 e 40% em peso. Os whiskers de mulita utilizados como matérias-primas foram obtidos através do tratamento térmico do mineral topázio incolor no Laboratório de Tratamento Térmico de Materiais do ICEB/UFOP. A alumina de elevada pureza foi fornecida pela empresa Alfa Apesar. As matérias primas, após serem pesadas, foram submetidas a um ...

Les compétences infirmières forensiques en milieu carcéral face aux patients atteints de troubles mentaux: une revue de littérature étoffée

OpenAIRE

Davet, Eloïse; Friedli, Karen; Machuret, Bastien; Reyff, Marie de

2015-01-01

Le but de cette revue de littérature étoffée est de mettre en évidence les compétences des infirmières forensiques travaillant, en milieu carcéral, avec des patients atteints de troubles mentaux.

Compósitos de borracha natural ou policloropreno e celulose II: influência do tamanho de partícula Natural rubber or chloroprene rubber and cellulose II composites: influence of particle size

Directory of Open Access Journals (Sweden)

Bruno de A. Napolitano

2004-01-01

Full Text Available O objetivo deste trabalho foi o desenvolvimento de compósitos claros com propriedades de interesse tecnológico utilizando elastômeros com diferentes polaridades. Para que este objetivo fosse atingido, celulose II em pó foi usada como carga, em borracha natural (NR ou policloropreno (CR. A celulose II foi obtida por coagulação da solução de xantato de celulose em meio ácido, sob agitação constante e à temperatura ambiente, constituindo uma nova forma de obtenção deste tipo de carga. Compósitos com 10 phr de celulose II com NR e CR, respectivamente, foram desenvolvidos tendo como variável o tamanho de partícula da carga. As propriedades mecânicas e os aspectos microscópicos dos diferentes compósitos foram avaliados e comparados com aqueles das formulações sem carga. Os resultados permitiram identificar o compósito como o de melhor resultado, influenciado pela polaridade da matriz elastomérica e pelo tamanho de partícula da carga, conseqüência das condições de moagem usadas.The aim of this work was to develop light composites with properties of technological interest by using elastomers of different polarities. This was achieved by employing cellulose II, in the powder form, as filler in natural rubber (NR and chloroprene (CR. Cellulose II was obtained by coagulation of cellulose xanthate solution, in acid medium, under stirring and at room temperature, which represents, to our knowledge, a new way of obtaining this type of filler. Composites with 10phr of cellulose II and NR or CR were prepared having the particle size as variable. The mechanical properties and the microscopic aspect of the different composites were evaluated and compared with compounds without filler. The results indicated best results for the CR composite, influenced by the polarity of the elastomeric matrix and by the particle size, as a consequence of the milling conditions of the filler used.

Compósitos biodegradáveis de polihidroxibutirato (PHB reforçado com farinha de madeira: propriedades e degradação

Directory of Open Access Journals (Sweden)

José Claudio Caraschi

2002-04-01

Full Text Available O objetivo deste trabalho foi preparar e avaliar compósitos poliméricos mais compatíveis com o ambiente, ou seja, a obtenção de materiais que sejam biodegradáveis e que apresentem uma maior velocidade de degradação no ambiente. Os compósitos foram preparados a partir do plástico biodegradável polihidroxibutirato (PHB com e sem reforço de farinha de madeira, um resíduo agroindustrial, nas proporções de 10% a 40% em massa, pelo processo de extrusão e moldagem por injeção. As amostras foram avaliadas quanto à estabilidade dimensional, à absorção de água, à resistência química e à degradação natural em cinco diferentes situações ambientais, por diversos períodos de tempo. Os resultados obtidos indicaram que todas as amostras sofreram degradações evidenciadas pela perda de massa e pela descoloração em todas as situações avaliadas, e que a utilização de farinha de madeira resultou em materiais com menor resistência química e maiores taxa de absorção de umidade e velocidade de degradação no ambiente.

Análise de ensaios in vitro do compósito de 50% HA-50% TiO2 fabricados pelo método da esponja polimérica

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A. G. S. Galdino

2014-12-01

Full Text Available À medida que há uma melhoria na tecnologia aplicada à saúde humana, a expectativa de vida vem aumentando, mas nem todas as partes do corpo podem manter suas funções com o processo de envelhecimento. A engenharia tecidual foi desenvolvida para substituir, reparar ou reconstruir tecidos ou órgãos perdidos ou danificados por acidentes ou doenças graves através da utilização e desenvolvimento de novos materiais, que sejam biocompatíveis, bioabsorvíveis, porosos, entre outras características. O objetivo deste trabalho é avaliar através dos ensaios in vitro o compósito poroso de hidroxiapatita - titânia (HA-TiO2, com composição de 50% HA - 50% TiO2 para obter arcabouços utilizados para engenharia tecidual óssea. Os corpos de prova foram produzidos pelo método da esponja polimérica, utilizando bicarbonato de sódio como ligante e floculante. A sinterização foi realizada em três temperaturas: a 1250 ºC; 1300 ºC e 1350 ºC. Linhagens imortalizadas de fibroblastos e osteoblastos foram utilizadas para avaliar o compósito frente à citotoxicidade, crescimento e adesão celular. Nesses ensaios foram utilizados três corpos de prova porosos em um intervalo de cinco dias. Os resultados obtidos mostraram-se satisfatórios, com adesão e crescimento das células de fibroblastos e osteoblastos, o que serve como indicador para que esse compósito seja submetido posteriormente a ensaios in vivo.

Ada Compiler Validation Summary Report: Certificate Number: 901112W1. 11116 Cray Research, Inc., Cray Ada Compiler, Release 2.0, Cray X-MP/EA (Host & Target)

Science.gov (United States)

1990-11-12

semaphores : 0.00 44858 Waiting on shared registers : 0.00 0 Waiting on A-registers/funct.units : 19.69 5551338711 Waiting on S-registers/funct.units...dependent bodies that implement the fundamental low-level primitives on which SR-3082 2.0 Cray Research, Inc. 73 Ada Program Runtime Model Cray Ada...operations provided by the runtime library are performed synchronously , with program execution suspended until the 1/O operation is complete. The

Predição do comportamento térmico de tubos compósitos através de redes neurais Prediction of thermal behavior of composite tubes using neural networks

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Sheila Contant

2004-12-01

Full Text Available Compósitos poliméricos (plásticos reforçados são materiais formados a partir de um reforço (fase descontínua, normalmente uma fibra e uma matriz polimérica. Esse tipo de material apresenta várias vantagens em relação aos materiais convencionais de engenharia. Entre os métodos de fabricação de compósitos poliméricos está o filament winding (filamento contínuo ou enrolamento filamentar, um processo empregado na fabricação de sólidos de revolução, como tubos e tanques. Neste trabalho, redes neurais artificiais, uma ferramenta computacional inspirada no funcionamento do cérebro humano, foram aplicadas ao processo de filament winding para predição do comportamento térmico de tubos compósitos durante a etapa de cura. Informações sobre o comportamento térmico das peças compósitas podem auxiliar na seleção do ciclo de cura, que é um dos desafios na obtenção de peças de qualidade e a um baixo custo. As redes neurais foram treinadas com dados obtidos através do modelo Lee-Springer. A metodologia foi validada com resultados experimentais da literatura.Polymeric composites or reinforced plastics are materials made with a polymer matrix and a reinforcement. These materials have many advantages when compared to conventional engineering materials. Among the manufacturing methods for composite parts from continuous fiber reinforcement is the filament winding, often used to fabricate closed-surface structures such as tubes and tanks. In this work artificial neural networks, a computational tool inspired in the human brain, were applied in the filament winding process to predict the thermal behavior of composite tubes during the curing step. Information about the thermal behavior of composite parts may help in the selection of the appropriate cure cycle, which is one of the challenges in obtaining quality parts at low cost. Networks were trained with data obtained with the Lee-Springer model. The methodology was validated

Influência da espessura nas propriedades mecânicas de compósitos híbridos interlaminares de curauá/vidro/poliéster

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Clarissa C. Angrizani

2014-01-01

Full Text Available O interesse do uso de fibras vegetais (ex. juta, sisal e curauá para aplicações mais nobres, como em reforço de materiais compósitos poliméricos, vem aumentando com o passar dos anos devido a aspectos diversos e, em especial, à legislação ambiental e à conscientização sobre o ciclo de vida dos produtos. Diante deste contexto, o objetivo deste trabalho é obter materiais compósitos híbridos interlaminares curauá/vidro/poliéster insaturado por moldagem por compressão à quente e analisar a dependência das suas propriedades mecânicas com a espessura. A resistência short beam da amostra mais espessa diminuiu devido ao seu maior teor de vazios. Além disso, a amostra mais delgada apresentou menor dureza, e resistência ao impacto, à tração e ao cisalhamento Iosipescu, atribuído em parte a sua menor fração volumétrica de fibras. De modo geral, o laminado considerado mais adequado foi aquele formado por oito camadas, sendo quatro de fibra de vidro e quatro de curauá, desde que esforços fletores não sejam críticos.

Feixes de fibras Lignocelulósicas refinadas mecanicamente em compósitos cimentícios para avaliação da resistência à tração

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Flávio Airton knuth

2017-07-01

Full Text Available As fibras vegetais têm características particulares em relação a outros tipos de fibras usadas em compósitos. Os estudos utilizam, em sua maioria, fibras cuja lignina fora previamente removida pelo processo de polpação. Segundo a literatura, a lignina prejudica a ancoragem fibra-matriz. No entanto, sem a lignina, é necessário que seja feito tratamento superficial no conjunto fibroso. Isso por que as fibras sofrem processo de inchamento e retração no interior da matriz devido a seu caráter hidrofílico, o que diminui sua vida útil. No entanto, a despeito das considerações literárias, esse trabalho se propõe a fazer uso da vantagem de proteção, estruturação e impermeabilização que a lignina exerce sobre as fibras vegetais. Isso implica na necessidade de suprir a redução da resistência do compósito, especialmente à tração, que a lignina causa pela sua atuação negativa na ancoragem fibra-matriz. Para tanto, fibras lignocelulósicas extraídas de talos de banana foram submetidas a processo de refinamento mecânico. Segundo a literatura, a fibra sofre modificações na sua parede externa quando submetida a esse refinamento. Ao final do processo, foram obtidas fibras com formato helicoidal e superfície corrugada o que resultou em maior aderência no conjunto fibra-matriz. As fibras submetidas ao maior grau de refinamento aumentaram a resistência do compósito à tração na compressão diametral em 40% em relação a corpo de prova de cimento puro.

Sinterização ultrarrápida por micro-ondas de compósitos particulados PZT/FCO preparados por mistura em ultrassom

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C. P. Fernandez

Full Text Available Resumo Pós de Pb(Zr0,53Ti0,47O3 (PZT e Fe2CoO4 (FCO, foram sintetizados separadamente pelo método Pechini e misturados em ultrassom, nas proporções molares 80/20 e 50/50 (PZT/FCO. Os compósitos preparados foram prensados e submetidos à sinterização em forno convencional e sinterização ultrarrápida assistida por micro-ondas. A caracterização estrutural e microestrutural das amostras foram realizadas por difração de raios X e microscopia eletrônica de varredura, respectivamente. Medidas de constante dielétrica em função da temperatura, resistividade elétrica e coeficiente de acoplamento magnetoelétrico foram também realizadas. Os resultados evidenciaram que o método de mistura do PZT com a FCO por ultrassom foi rápido e eficiente, gerando, após sinterização, compósitos particulados com conectividade global (0-3 e distribuição uniforme de grãos da fase ferromagnética (FCO na matriz ferroelétrica (PZT. Da análise estrutural, verificou-se que a sinterização por micro-ondas propiciou um arranjo diferenciado no esquema de conectividade local na amostra (1-3 e (2-3, relacionada com a intensificação dos processos de difusão que ocorrem nesse tipo de sinterização principalmente em sistemas nanométricos. Pelos altos valores de resistividade obtidos, comprovou-se que a integridade das fases foi conservada nos dois métodos de sinterização, sendo mais eficiente na sinterização por micro-ondas, característica que garantiu o comportamento magnetoelétrico em todos os compósitos estudados neste trabalho. Os valores do campo Hmax foram dependentes da concentração da fase ferrita e da sinterização; para a composição 80/20 de 1,4 e 1,9 kOe, e para 50/50 de 3,5 e 3,0 kOe nas amostras sinterizadas por micro-ondas e convencionalmente, compatíveis com a literatura e que confirmaram a integridade das fases constituintes PZT e FCO.

A3byComp: A Support tool for Basic Implementation of Competency Management Systems in Social Entities

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Daniel CLAVERO HERRERO

2015-12-01

Full Text Available The importance of managing processes related to people working in institutions within the scope of FEAPS evidenced by the increasing incorporation into the strategy of the organizations policies aimed at improving the working conditions of workers and in the development of competence management systems aimed at promoting professional development, which aims greater effectiveness and efficiency in providing support for improving the quality of life of people with disabilities and their families. At the same time, banks have highlighted the need for specific instruments and tools that facilitate the implementation of these systems. In Extremadura, it has been developed a software tool for the implementation of basic competence management systems called A3byComp that has been freely available to the entire network promoting industry collaboration aimed mutual learning.

L’usage des contes francophones pour le développement des compétences langagières

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Nataša Žugelj

2015-12-01

Full Text Available Les contes traditionnels sont un genre littéraire qui constitue un excellent support authentique pour le travail sur la langue dans une classe de FLE. S’ils sont accompagnés d’activités variées et ludiques, la découverte ou le perfectionnement d’une langue étrangère peut se faire d’une manière plaisante avec des apprenants de tous âges. En effet, ils se prêtent bien au développement des compétences langagières et sont un excellent terrain d’observations linguistiques, d’enrichissement lexical. De plus, par leur relative brièveté et par un contenu universellement connu, ils proposent un cadre rassurant pour l’exploitation pédagogique.    

Compósito para fabricação de implantes reabsorvíveis para osteossíntese: avaliação da biocompatibilidade em coelhos Composite for the fabrication of resorbable implants for osteosynthesis: biocompatibility evaluation in rabbits

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Emily Correna Carlo

2009-02-01

Full Text Available A biocompatibilidade, a osseointegração e a reabsorção de compósitos contendo 10% de hidroxiapatita (HAP-91® e 90% de polihidroxibutirato foram analisadas após implantação em defeitos ósseos em coelhos. Foram obtidos dados clínicos, radiográficos, histológicos e histomorfométricos aos oito, 45 e 90 dias após a realização da cirurgia, sendo os resultados comparados aos de defeitos não-preenchidos. Não foram observadas diferenças significativas entre os grupos para os parâmetros clínicos avaliados. Radiografias demonstraram o compósito em contato direto com osso aos 45 e 90 dias. Tecido ósseo se formou normalmente no defeito e na interface com o material, quando comparado ao controle. Não foi observado infiltrado inflamatório. Em todos os dias, a porcentagem de tecido ósseo foi maior que a de tecido conjuntivo (P=0,001 aos 8 e 45 dias e 0,022 aos 90 dias dentro dos defeitos. Foram observados tecidos ósseo e conjuntivo na interface com o compósito, sendo o último significativamente maior que o primeiro aos 90 dias (P=0,004. Foram observados sinais de reabsorção do compósito: células gigantes na superfície de fragmentos do compósito separados do bloco original. Portanto, pode-se concluir que o compósito é biocompatível em coelhos, reabsorvível e se integra ao tecido ósseo.Biocompatibility, osseointegration, and resorption of a 10% hydroxyapatite (HAP-91® - 90% polyhydroxybutyrate composite were analyzed after implantation in rabbits´ bone defects. Clinical, radiographic, histologic and histomorphometric data were collected on the 8th, 45th, and 90th days after surgery and the results were compared to those of unfilled defects. No significant differences between groups for the evaluated clinical parameters existed. Radiographs showed bone-composite direct contact. Bone tissue was formed normally in the defect and at the composite-tissue interface when compared to the control. No inflammatory infiltrated was

Consumer skills contribute to maintaining and diffusing heritage food products Les compétences des consommateurs contribuent au maintien et à la diffusion d’aliments patrimoniaux

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Didier Chabrol

2011-05-01

Full Text Available Our food heritage is not only limited to food products and production techniques, it also includes the consumption skills and technologies (CST used to obtain what the consumer requires from a food product. In a specific food culture, a given food product is linked to specific CSTs. In this paper, we examine this aspect of food heritage through the examples of raw ham in Italy, France and Spain, rice varieties and chocolate. We then discuss two types of conjunction / disjunction between food products and food CSTs: controlled diffusion and diffusion through education. We conclude that the sustainability of localized, “origin” or “terroir” products depends on the existence of skilled consumers. The transmission and diffusion of these skills and technologies are thus factors in the permanence and diffusion of the product itself.Le patrimoine alimentaire n’est pas constitué exclusivement de produits et de techniques de production, mais aussi de compétences et techniques de consommation (CTC utilisées par les consommateurs pour obtenir d’un produit alimentaire l’utilité ou le service qu’ils en attendent. Dans une culture alimentaire donnée, un produit alimentaire spécifique est lié à des CTC spécifiques. Cette dimension du patrimoine alimentaire est examinée à travers les exemples du jambon cru en Italie, en Espagne et en France, de différents riz, et du chocolat. Nous discutons ensuite deux types de cohérences / incohérences entre produits et CTC : contrôle par la source, diffusion par l’éducation. Nous concluons que la durabilité de produits locaux, d’origine ou de terroir dépend de l’existence de consommateurs compétents. La transmission et la diffusion des compétences et techniques de consommation sont donc des facteurs de la pérennité et de la diffusion du produit lui-même.

Un test de classement en ligne pour évaluer les niveaux de compétence et constituer des groupes classes

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Patricia Kohler

2012-01-01

Full Text Available L’Université de Fribourg a développé un test de classement en ligne avec la plateforme Moodle pour évaluer les compétences des étudiants en langues étrangères (compréhension orale, compréhension écrite et production écrite selon le Cadre européen commun de référence du Conseil de l’Europe. Une démarche qualité nous a aidé à réfléchir sur les modèles de tests de classement en ligne de sorte que nos résultats soient transférables à d’autres contextes que l’enseignement des langues étrangères. Nous avons évalué l’acceptabilité de notre test avec, d’une part, les données quantitatives produites par Moodle lorsque les étudiants passent le test. D’autre part, nous avons analysé les entretiens d’étudiants décrivant leur expérience avec le test. Certains résultats montrent la pertinence du modèle de test : la durée des sous-tests, l’utilité d’une auto-évaluation et la nécessité de sous-tests sur chaque compétence. D’autres résultats se dégagent sur la représentation qu’a l’usager d’un test en ligne qui remet en question des rapports fondamentaux de l’individu au temps, à l’espace, à l’identité et à ses sensibilités d’ordre culturel.

On implicit abstract neutral nonlinear differential equations

Energy Technology Data Exchange (ETDEWEB)

Hernández, Eduardo, E-mail: lalohm@ffclrp.usp.br [Universidade de São Paulo, Departamento de Computação e Matemática, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto (Brazil); O’Regan, Donal, E-mail: donal.oregan@nuigalway.ie [National University of Ireland, School of Mathematics, Statistics and Applied Mathematics (Ireland)

2016-04-15

In this paper we continue our developments in Hernández and O’Regan (J Funct Anal 261:3457–3481, 2011) on the existence of solutions for abstract neutral differential equations. In particular we extend the results in Hernández and O’Regan (J Funct Anal 261:3457–3481, 2011) for the case of implicit nonlinear neutral equations and we focus on applications to partial “nonlinear” neutral differential equations. Some applications involving partial neutral differential equations are presented.

Influência de estabilizantes na degradação foto-oxidativa de filmes de compósitos de SWy-1/poli(óxido de etileno

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Patrícia Coelho Lombardo

2015-02-01

Full Text Available Compósitos de poli(óxido de etileno (PEO com argila montmorilonita SWy-1 e estabilizantes (2-hidroxibenzofenona e tinuvin 770 foram preparados pelo método de intercalação em solução. Os filmes obtidos foram expostos a irradiação UV, e os produtos da fotodegradação foram monitorados por FTIR (Fourier Transform Infrared Spectroscopy, ou Espectroscopia no infravermelho por transformada de Fourier e SEC (Size Exclusion Chromatography, ou cromatografia de exclusão por tamanho. O PEO puro apresentou maior coeficiente de degradação, kd, comparado com as demais amostras. O sistema que apresentou o menor valor para o coeficiente de degradação (kd = 1,9×10–6 mol g–1 h-1 foi o compósito de PEO/5%SWy-1 com 0,25% de tinuvin 770. Nesse caso, a estabilização da matriz de PEO pode ser atribuída à argila juntamente com o tinuvin 770. A argila dispersa e absorve a irradiação UV, e o tinuvin age como estabilizante do tipo HALS (do inglês hindered amine light stabilizer, ou estabilizantes à luz tipo aminas impedidas.

Compósitos à base de cimento reforçados com polpa celulósica de bambu. Parte I: Determinação do teor de reforço ótimo Cement-based composite reinforced with bamboo pulp. Part I: Determination of optimum reinforcement percentage

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Marcos A. S. dos Anjos

2003-08-01

Full Text Available Este trabalho apresenta os resultados experimentais de um estudo em que se procurou desenvolver compósitos de matriz cimentícia reforçada com polpa de bambu. Foram usados dois tipos de polpa: refinada e sem refino. Fez-se variar o teor de fibras de 0 a 16% em massa de cimento e se desenvolveu um processo com sucção, moldagem e prensagem para fabricação dos compósitos. As relações constitutivas dos compósitos foram definidas através de ensaio a compressão e tração de corpos-de-prova cilíndricos de 5x10 cm e do ensaio de flexão em três pontos. A partir delas, foi obtida a capacidade de absorção de energia. Determinaram-se, também, algumas propriedades físicas, como absorção, porosidade aparente, densidade seca e úmida dos compósitos. Os resultados mostraram melhor performance dos compósitos com fibras refinadas em relação àquelas com fibras sem refino e também indicaram que o teor ótimo de fibras refinadas se situou em torno de 8%, quando promoveram notáveis melhoramentos das propriedades mecânicas dos compósitos em relação à matriz plena.This work presents the experimental results of a study which intended to develop a composite with cementations matrix reinforced with bamboo pulp. Two types of pulps were used: refined and unrefined pulps. The fibre content varied between 0 and 16% cement (weight basis. After the preparation of fresh composite mix the experimental specimens were prepared applying a specially developed process based on Hastshek method using suction then moulding and pressing. The compression, tension and the flexural behavior and their constitutive relations were established using 5 cm diameter by 10 cm high cylindrical specimens and three point bending tests at respectively. The energy absorbing capacity of the new composites was also established. Physical properties such as water absorption, apparent porosity, dry and humid density were also obtained. The results showed a better performance

Avaliação da biodegradação de compósitos de poli(ε-caprolactona/fibra de coco verde Evaluation of biodegradation poly(ε-caprolactone/green coconut fiber

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Marcia C. A. M. Leite

2010-01-01

Full Text Available Uma classe de plásticos com destaque crescente são os polímeros biodegradáveis, como a Poli(ε-caprolactona (PCL. Quando esses polímeros são utilizados para elaboração de compósitos com fibras naturais, novas propriedades são agregadas. Existem vários métodos de modificação química da fibra para melhorar a adesão dessas fibras em matrizes poliméricas. Neste trabalho foi estudada a biodegradabilidade em solo simulado de compósitos de PCL/fibra de coco (antes e após a modificação química da fibra por reação de acetilação com avaliação da perda de massa e da modificação da morfologia. A espectroscopia na região do infravermelho mostrou a eficiência da reação de acetilação nas fibras. Os compósitos enterrados em solo simulado apresentaram perda de massa e a degradação das amostras foi confirmada pela modificação da morfologia observada através de análises como as Microscopias Óptica e Eletrônica de Varredura. O comportamento térmico dos compósitos, analisado por Calorimetria Diferencial de Varredura mostrou diferença no teor de cristalinidade da matriz com a incorporação da fibra.Biodegradable polymers such as poly (ε-caprolactone (PCL have received increasing attention. New properties are achieved when these polymers are used in composites with natural fibers. Several methods exist for the chemical modification of the fiber to improve adhesion to the polymer matrices. This work deals with the biodegradation in simulated soil of PCL/coconut fiber composites (before and after fiber chemical modification by acetylation - reaction with the evaluation of mass loss and morphology. Infrared spectroscopy has shown the efficiency of fiber acetylation. The composites buried in simulated soil presented weight loss. The degradation of the samples was confirmed by the morphology modification observed by Scanning Electron Microscopy and Optical Microscopy analysis. The thermal properties analyzed with

Efeitos do tipo de poliestireno de alto impacto nas propriedades de compósitos termoplásticos com farinha de resíduo de madeira The effects of the high impact polystyrene morphology on the properties of wood-plastic composites

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Wladimir L. Vianna

2004-12-01

Full Text Available A tecnologia dos chamados Compósitos Termoplásticos com Madeira envolve conceitos de compatibilidade e processabilidade e apresenta grandes desafios tecnológicos para a formulação e estabilização da mistura. Devido à baixa estabilidade térmica da celulose, a grande maioria das resinas termoplásticas utilizadas na preparação desses compósitos está restrita às resinas poliolefinicas, estirênicas e ao poli(cloreto de vinila. O Poliestireno de Alto Impacto (HIPS é um termoplástico bifásico de grande versatilidade de propriedades decorrentes das variações de composição e morfologia das partículas de borracha dispersas na matriz estirênica. Além da sua temperatura relativamente baixa de processamento, estas características tornam o HIPS um termoplástico de grande interesse para aplicações em compósitos com farinha de resíduo de madeira, uma vez que a otimização do balanço de propriedades de rigidez e impacto pode ser alcançada através do controle da morfologia e da formulação do compósito. No presente estudo, "tipos" comerciais de HIPS com diferenças no índice de fluidez e na distribuição do tamanho de partículas foram utilizados na preparação de compósitos termoplásticos com farinha de resíduo de madeira. As propriedades mecânicas dos compósitos obtidos foram discutidas em termos das características morfológicas dos HIPS utilizados e da quantidade de farinha de resíduo de madeira no compósito. Pela simples aplicação da regra das misturas, mostrou-se que devido à baixa densidade do resíduo de madeira, o reforço celulósico poderia ser utilizado eficientemente na substituição de cargas minerais ou fibra de vidro em compósitos termoplásticos com um melhor desempenho em termos de resistência e rigidez específica. A microscopia eletrônica de varredura foi utilizada na análise de superfícies de fratura para ilustrar a dispersão da farinha de madeira na matriz estirênica, a

Efeito de impactos repetidos de baixa energia em compósitos pultrudados

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Morais Willy Ank de

2001-01-01

Full Text Available Danos internos podem ser gerados em compósitos de matriz polimérica submetidos a impactos de baixa energia. O efeito repetido de eventos desse tipo pode levar, eventualmente, à falha da estrutura. Neste trabalho dois tipos de perfis pultrudados foram submetidos a impactos por queda livre de peso de 0,5 m e 1,0 m de altura. Os resultados obtidos foram analisados em função da disposição das fibras nos perfis e mostram que a existência de uma camada rica em resina em um dos perfis, contribui para reduzir significativamente o desempenho deste perfil. Este comportamento foi associado à formação prematura de trincas na camada rica em resina. O número de eventos de impacto, o tempo de duração de cada choque e a forma da área danificada foram correlacionados com a presença, ou não, da região rica em resina. Os resultados obtidos indicam ainda que a diferença na microestrutura dos perfis analisados é mais significativa para os ensaios de menor energia (queda de 0,5 m. Para os ensaios de maior energia (queda de 1 m a configuração do material teve apenas uma importância secundária.

Caracterização mecânica e térmica de compósitos de poli (cloreto de vinila reforçados com fibras de sisal Mechanical and thermal characterization of the polyvinyl chloride-sisal fibers composites

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Gilson S. Martins

2004-12-01

Full Text Available Compósitos de PVC, plastificados com diferentes sistemas de plastificação e reforçados com fibras de sisal, foram processados em moinho de dois rolos. A influência do tipo e teor do plastificante, do comprimento e do teor das fibras nas propriedades dos compósitos obtidos foi estudada. Dois tipos de plastificantes foram usados, um líquido (do tipo poliéster e um sólido permanente (copolímero etileno/ acetato de vinila/ monóxido de carbono. As fibras usadas foram previamente lavadas com água a 80 °C por uma hora. Os compósitos, com fibras curtas aleatoriamente distribuídas, foram caracterizados através de ensaio mecânico de resistência à tração, microscopia eletrônica de varredura (MEV, e análises térmicas de calorimetria exploratória diferencial (DSC e análise por termogravimetria (TG. O comprimento ótimo de fibra obtido para os compósitos foi de 6 mm. O uso do plastificante sólido mostrou-se viável e promoveu uma maior molhabilidade da fibra pela matriz nos compósitos, principalmente para teores acima de 40 pcr. As análises térmicas mostraram que a substituição do plastificante líquido pelo plastificante sólido não afetou a estabilidade térmica das matrizes e dos compósitos.Composites consisting of flexible polyvinyl chloride (PVC, plasticized with two different types of plasticizers and reinforced with sisal fibers, were processed on a two-roll mixing mill. Two plasticizers were used, a liquid plasticizer (polyester and a permanent solid plasticizer (ethylene/ vinyl acetate/ carbon monoxide copolymer - Elvaloy® , to form two kinds of polymeric matrices. For each one of these matrices, the influence of plasticizers type, plasticizers content, size and quantity of sisal fibers in the composite properties has been studied. The fibers were washed with water at 80 °C during one hour. The composites with randomly distributed short fibers were characterized by mechanical analysis, scanning electron microscopy

Efeito da modificação de superfície de fibras nas propriedades mecânicas de compósitos a base de poli (tereftalato de butileno reforçado por fibras naturais inorgânicas

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Felipe Darabas Rzatki

2014-06-01

Full Text Available O presente trabalho visa investigar a viabilidade de utilização de fibras naturais de sílica amorfa (FNSA como agente de reforço em polímeros de engenharia, assim como avaliar o seu potencial como alternativa às fibras de vidro curtas em aplicações industriais. Diferentes modificações na química de superfície dessas fibras foram avaliadas buscando melhorar a adesão na interface entre fibras e matriz, e consequentemente, melhorar as propriedades mecânicas do compósito. As modificações superficiais das FNSA foram realizadas através de agentes de acoplamento do tipo silano, providos com funções orgânicas distintas. O PBT foi selecionado como matriz devido a sua conhecida facilidade de processamento, mesmo após a incorporação de grandes quantidades de aditivos. A modificação das FNSA foi avaliada a partir da análise termogravimétrica acoplada à espectroscopia no infravermelho com transformada de Fourier. A resistência mecânica e fratura dos compósitos foi investigada por ensaios de tração e microscopia eletrônica de varredura. Finalmente, obtiveram-se compósitos com fibras modificadas com resistência à tração 40% superior ao material base puro.

Comportamento da viscosidade de um compósito vidro-partícula de alumina Viscosity behaviour of a glass-alumina particle composite

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J. A. Rodrigues

2003-04-01

Full Text Available O aumento na produção de concretos refratários de alto desempenho tem demandado proporcional acréscimo no entendimento do comportamento reológico de suspensões concentradas de sólidos. Os concretos podem ser considerados como sistemas contendo agregados cujo diâmetro médio de partícula é superior a 100 mm e partículas finas que constituem a matriz. A reologia desse sistema é determinada, predominantemente, pela viscosidade da matriz, porém influenciada por parâmetros associados aos agregados. Este trabalho simula um sistema fluido-partícula, empregando um compósito vidro-partícula de alumina, caracterizando-o quanto à sua viscosidade em temperaturas em torno de 600 °C. Um viscosímetro de flexão foi empregado para medir as altas viscosidades do compósito. São mostrados resultados de viscosidade para diferentes teores de partículas de alumina. O sistema vidro-partícula apresentou um máximo na viscosidade para teores em torno de 50%-vol de partículas. Até aproximadamente 40%-vol de partículas, o compósito se comporta como um sistema newtoniano entre 560 ºC e 670 °C. Os resultados deste trabalho indicam a possibilidade de simulação da reologia na preparação de concretos refratários e da fluência do concreto operando em alta temperatura.Basic knowledge on rheological behaviour of highly concentrated suspensions is nowadays a very important issue in the refractory industry, regarding the production of high-performance castables. Refractory castables can be considered as a system containing aggregates and particles larger than 100 mm and finer ones constituting a matrix. In that system, the rheological behaviour is mainly determined by the viscosity of the matrix, although it is affected by parameters related to the aggregates. This work simulates a fluid-particle system through the use of a glass-alumina particle composite which viscosity was evaluated at temperatures close to 600 ºC. A beam-bending viscometer

Leader mode d'emploi 10 compétences essentielles pour communiquer, collaborer et innover

CERN Document Server

Paquet, René

2013-01-01

Communiquer efficacement, favoriser la collaboration, stimuler la créativité et résoudre les conflits dans un climat de coopération, voilà les aptitudes qui caractérisent le leader qui dirige avec brio. Que vous soyez à la barre d'une équipe de cinq ou de trente personnes, vous trouverez dans cet ouvrage tous les outils pour entretenir la motivation de vos employés, susciter les bonnes réactions, éviter les faux pas, maximiser votre productivité et ainsi devenir un meneur de premier ordre. Quelques conseils à appliquer : Prendre le temps de créer une relation avec chacun de mes collaborateurs. Apprendre les règles, les normes et les valeurs de l'organisation. Favoriser le développement des compétences et l'acquisition des connaissances. Établir des canaux de communication. Exprimer des attentes claires. Quelques erreurs à éviter Faire de la micro-gestion : tenter de tout contrôler. Travailler en vase clos. Remettre à plus tard les tâches moins agréables. Rester dans ma zone de confort ...

Estudo da flamabilidade e resistência à chama de compósito de poliéster insaturado e fibra da folha do abacaxizeiro (PALF)

OpenAIRE

Ribeiro, Luciene Mendes

2011-01-01

Na presente pesquisa foram desenvolvidos compósitos com fibras da folha do abacaxizeiro (PALF - Pineapple Leaf Fiber), utilizando resina de poliéster insaturado como matriz, incorporando retardante de chama em diferentes composições. As fibras da folha do abacaxizeiro foram obtidas na ramada 4 do município de Ielmo Marinho no Estado do Rio Grande do Norte. A resina de poliéster insaturado e o catalisador foram comprados no comércio. O retardante de chama de alumina trihidratada (hidróxido de ...

Effect of resin liners on the microleakage of class V dental composite restorations Efeito do uso de forradores resinosos sobre a microinfiltração de restaurações classe V em compósito odontológico

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Roberta Caroline Bruschi Alonso

2004-03-01

Full Text Available PURPOSE: The aim of this study was to evaluate the effect of an adhesive applied in layers of different thickness or in association with a filled adhesive or with a low viscosity composite liner on the microleakage of composite restorations. METHODS: Forty bovine incisors were prepared with round cavities (4mm diameter X 2mm depth on the cementoenamel junction. The teeth were assigned to four groups according to the liner used: 1 (control - application of 1 layer of the Scotchbond Multi Purpose adhesive system (SBMP; 2 - application of 3 layers of SBMP; 3 - application of 1 layer of SBMP followed by application of one layer of Optibond FL adhesive; 4 - application of one layer of SBMP followed by application of flowable composite Flow-it. All cavities were restored using composite resin Z100. The microleakage test was conducted according to ISO (TR11405. Data were analyzed by Kruskall-Wallis test (a=0.05. RESULTS: Group 4 showed less leakage than Group 1. Groups 2 and 3 showed intermediate values and there were no statistical differences when they were compared to the values of Groups 1 and 4 CONCLUSION: The use of resin liners with flowable composites can reduce the microleakage of composite restorations.OBJETIVO: O objetivo desse estudo foi avaliar os efeitos da aplicação de um adesivo em diferentes espessuras ou em associação com um adesivo com carga ou com compósito de baixa viscosidade na microinfiltração marginal de restaurações com compósito odontológico. MÉTODOS: Quarenta incisivos bovinos foram selecionados e cavidades circulares (4mm de diâmetro X 2mm de profundidade foram preparadas na região da junção cemento-esmalte. Os dentes foram então divididos em quatro grupos de acordo com o forramento utilizado: 1: (controle aplicação do sistema de união Scotchbond Multi Uso (SBMU - 1 camada de adesivo; 2: aplicação de 3 camadas do adesivo SBMU; 3: aplicação do SBMU, seguido pela aplicação de uma camada do adesivo

Compósitos de HDPE com resíduos de fibras têxteis. Parte I: caracterização mecânica HDPE composites with textile fibers waste. Part I: mechanical characterization

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Maira Finkler

2005-07-01

Full Text Available Neste trabalho são apresentados e discutidos os resultados das propriedades mecânicas de novos materiais compósitos preparados com resíduos de fibras têxteis poliméricas e de polímeros commodities. As fibras naturais oferecem vantagens sobre as sintéticas, em termos de propriedades mecânicas e térmicas. Os compósitos foram preparados a partir da mistura de polietileno de alta densidade (HDPE e resíduos de fibras têxteis (50% algodão /50% acrílico em teores crescentes de 10 a 40%, em um misturador de alta velocidade, utilizando Surlyn 2601, Polybond 3009 e Polybond 1009 como agentes compatibilizantes. Corpos-de-prova para ensaios de tração, flexão e impacto foram produzidos a partir de chapas obtidas em uma prensa hidráulica. Os compósitos que utilizaram agentes compatibilizantes apresentaram os melhores resultados de resistência à tração e à flexão, principalmente com 5% do agente Polybond 3009 e 20 a 40% de resíduos de fibras têxteis.In this work, results of mechanical properties of new composites based on textile fiber residues from clothing industry and commodity polymers are discussed. Natural fibers offer some advantages over synthetic ones, regarding mechanical and thermal properties. The composites were produced by mixing high density polyethylene with the textile fibers (50% cotton /50% acrylic in increasing contents, from 10 to 40% in a thermokinetic mixer, using Surlyn 2601, Polybond 3009 and Polybond 1009 as coupling agents. The tensile, flexural and impact samples were produced by cutting sheets obtained in a hydraulic press. The composites with coupling agents showed good results of tensile and flexural strength, mainly with 5% of Polybond 3009 and 20-40% of textile fiber residues.

Formation des formateurs en ligne : obstacles, rôles et compétences

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Louise Sauvé

2004-01-01

Full Text Available L’adoption d’une technologie de l’information et de la communication (TIC pour la formation ne peut se faire sans changement dans l’organisation. Ces changements touchent les formateurs, hommes et femmes, qui ont une histoire professionnelle, une mentalité, des pratiques qui se sont construites au cours des années et dans un contexte précis de travail. Or les changements technologiques peuvent déstabiliser la vie professionnelle des formateurs. Il est donc essentiel de gérer ce changement, car le succès des projets d’introduction des TIC dans la formation n’est plus fonction de la puissance des technologies, mais plutôt de la capacité des formateurs à exploiter leur potentiel afin de changer et d’améliorer l’efficience du processus d’apprentissage. C’est dans un contexte d’implantation d’une formation des formateurs en ligne que se situe cet article qui aborde les questions suivantes : quels sont les obstacles au changement par rapport à l’adoption des TIC dans le milieu de la formation? Quels sont les principaux rôles d’un formateur en ligne (ou e-formateur? Quelles sont les compétences générales que les formateurs doivent développer pour soutenir les apprenants dans un contexte de formation en ligne (synchrone et asynchrone?

Análise da durabilidade de compósitos cimentícios de elevada capacidade de deformação reforçados com fibras

OpenAIRE

Fernanda Bianchi Pereira da Costa

2015-01-01

Apesar do avanço tecnológico crescente na construção civil, a falta de durabilidade das estruturas de concreto, tanto em edificações como pavimentação, tem sido constatada com acentuada assiduidade e proporção. O compósito cimentício de elevada deformação, também conhecido como Engineered Cementitious Composites (ECC), foi difundido a partir do conceito de concretos de alto desempenho reforçado com fibras, visando suprir o comportamento frágil do concreto convencional e problemas relacionados...

Análise modal teórica via método dos elementos finitos de uma viga feita a base de materiais compósitos

OpenAIRE

Faria, Antônio; Silva, Vânia; Carvalho, Jonas; Tita, Volnei

2002-01-01

Com o desenvolvimento tecnológico houve um aumento nos requisitos de projeto que promoveram um conseqüente aumento na necessidade de novos materiais que combinassem propriedades de baixo peso e alta resistência que atendessem a esses requisitos. Dentre estes materiais, destacam-se os materiais compósitos por combinar baixo peso e alta rigidez. Assim procura-se neste artigo, através de análises numéricas, descrever a influência da seqüência de empilhamento das lâminas no comportame...

Osseointegração clínica-radiológica do compósito hidroxiapatita-lignina entre implante metálico e tecido ósseo em coelho Clinical-radiographic osseointegration of hydroxyapatite-lignin composite between metallic implant and bone tissue in rabbit

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M.M. Martinez

2009-08-01

Full Text Available Para avaliar o compósito hidroxiapatita-lignina na osseointegração entre implante metálico e o tecido ósseo, foram utilizados 20 coelhos adultos, nos quais foi realizada uma falha óssea na face lateral proximal de ambas as tíbias. Na tíbia esquerda, introduziu-se, no canal medular, um pino intramedular de Schanz revestido com o compósito em sua parte rosqueada, após o preenchimento daquele com 1000mg do compósito. A falha cortical foi preenchida com o compósito. O mesmo foi feito na tíbia direita, porém sem a utilização do compósito, servindo como controle. A avaliação clínica baseou-se na deiscência, claudicação, sensibilidade dolorosa e circunferência tibial. Foram realizadas radiografias imediatamente após a cirurgia e aos oito, 30, 60, 90 e 120 dias do pós-operatório. A maioria dos animais apresentou evolução clínica normal. Nas radiografias do grupo tratado, houve decréscimo da radiopacidade no defeito e no espaço medular até tornar-se semelhante à do osso circunvizinho, quadro inverso ao do grupo-controle. Conclui-se que o compósito hidroxiapatita-lignina não mostrou indícios clínicos de rejeição e que o tecido visualizado na altura da falha óssea e ao redor do pino intramedular tinha radiopacidade semelhante à do osso circunvizinho, o que sugere que o material promoveu a integração com o tecido ósseo.This study evaluated a sinthetic hydroxyapatite-lignin composite for osseoingration between metallic implant and bone tissue. Twenty New Zealand rabbits were used. A defect was made a the proximal region of lateral surfaces of both tibias. An intramedullary pin was inserted in the medullary cavity of the left tibia after filling the cavity with 1,000mg of the composite and covering the thread part of the pin with the composite. The same procedure was made in control tibias without the composite. Clinical evaluation was based on inflammatory reaction, dehiscence, lameness, pain, and tibial

Propriedades de compósitos híbridos de borracha nitrílica, fibras de sisal e carbonato de cálcio Properties of nitrile rubber, sisal fiber and calcium carbonate hybrid composites

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Marco A. Iozzi

2004-06-01

Full Text Available Neste trabalho, estudou-se a influência do teor de carbonato de cálcio nas propriedades mecânicas e térmicas da borracha nitrílica, e do comprimento das fibras de sisal nas propriedades mecânicas dos compósitos de borracha nitrílica/fibras de sisal, e borracha nitrílica/carbonato de cálcio/fibras de sisal. Os materiais foram caracterizados através de ensaios mecânicos de resistência à tração, microscopia eletrônica de varredura (MEV, e termogravimetria (TG. O melhor desempenho mecânico dos compósitos com as fibras curtas aleatoriamente distribuídas foi obtido para o comprimento das fibras de 6 mm, e teor de carbonato de 67 pcr. A análise térmica mostrou que os compósitos são estáveis até cerca de 300 °C. Os resultados mostraram que os materiais obtidos possuem uma boa relação custo/benefício tornando promissora sua utilização.In this work, nitrile rubber with sisal fibers composites and nitrile rubber with calcium carbonate and sisal fibers composites were developed. The influence from the calcium carbonate amount and size of sisal fibers on the composite properties was studied. The composites, with short fibers randomly distributed, were characterized by mechanical analysis, scanning electron microscopy (SEM, and thermogravimetric analysis (TGA. The optimal size of sisal fibers to reinforce the nitrile matrix was 6 mm. The ideal volume of calcium carbonate was 67 phr. TGA analysis demonstrated that the composites are stable up to 300 °C. The materials developed have a good cost/benefits relation, being therefore promising their utilization.

Preparação e caracterização de materiais compósitos SiC/caulim/Al via "squeeze-casting" Preparation and characterization of SiC/kaolin/Al composite materials by squeeze- casting

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M. Freitas

2009-09-01

Full Text Available Na busca de materiais com propriedades diferenciadas, vem aumentando nos últimos anos as pesquisas em materiais compósitos. Um dos importantes métodos de fabricação destes compósitos é o processo de infiltração sob pressão de metal fundido denominado "squeeze-casting". Este processo oferece algumas vantagens, tais como facilidade de produzir o compósito, baixo custo e capacidade de formação de estruturas em rede. Neste trabalho foram produzidos e caracterizados compósitos SiC-Al, com concentrações em caulim variando entre 10 e 50% em substituição a fase majoritária SiC. As pré-formas cerâmicas foram produzidas controlando-se a fração granulométrica do SiC/caulim para uma melhor infiltração. Estas pré-formas, após sinterização a 1100 ºC/1 h, resultaram altamente porosas, sendo a porosidade aumentada com o aumento do caulim em substituição ao SiC. Análises de DRX mostraram a existência de partículas de quartzo além da fase SiC como constituintes das pré-formas. Durante o processo de infiltração e tratamento térmico, o alumínio no estado líquido reagiu preferencialmente com o quartzo e outros aluminossilicatos da pré-forma reduzindo-os, precipitando alumina e silício na microestrutura, a qual apresentou também alumínio em excesso que não reagiu no processo. A sílica e os silicatos da pré-forma, ao reagirem preferencialmente com o alumínio, evitaram a reação do Al com o SiC, prevenindo a formação da fase Al4C3,, a qual é altamente higroscópica e causa a degradação do compósito. Dependendo da composição, os compósitos SiC-caulim-Al desenvolvidos neste trabalho, podem ser usados em aplicações que envolvam elevada resistência mecânica à flexão (240 a 300 MPa, baixa densidade e dureza superficial entre 180 e 380 kgf/mm².In search of materials with different properties, has been increasing the research on composite materials in recent years. One of the important methods of

Resíduos de sisal como reforço em compósitos de polipropileno virgem e reciclado Virgin and recycled polypropylene composites reinforced with sisal by-product

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Francisco Rosário

2011-01-01

Full Text Available Foram estudadas as propriedades térmicas e mecânicas de compósitos de polipropileno, virgem e reciclado, reforçados com 30% em massa de fibras residuais de sisal, assim como o perfil de processamento e a morfologia da matriz polimérica. Para tanto, foram determinadas a resistência à tração, o módulo de Young, alongamento na ruptura, e energia de impacto. As amostras também foram caracterizadas por MEV, DMTA e TG. Para ambos os compósitos de polipropileno, virgem e reciclado, com a adição das fibras, o alongamento na ruptura mostrou uma queda significativa, enquanto que a resistência à tração não sofreu grandes variações. Houve um aumento significativo nos valores de tração na ruptura e de energia de impacto com a adição das fibras de sisal na matriz de polipropileno. As análises térmicas mostraram ligações secundárias, como as ligações polares, entre as fibras e a matriz, concordando com o comportamento mecânico dos compósitos. Constatou-se que a temperatura de transição vítrea não variou após a adição da fibra.The mechanical and thermal properties of virgin and recycled polypropylene composites reinforced with 30% by mass of residual sisal fibers were studied, in addition to an analysis of the extrusion process and morphology of the polymeric matrix. Tensile strength, Young's modulus, elongation at break, and impact energy were determined. The samples were also characterized by SEM, DMTA and TG analyses. Elongation at break of the composites presented a significant decrease, while the tensile strength was not affected significantly by addition of sisal fibers. A significant increase was observed in the tension of rupture and in the impact energy of the composite reinforced with sisal fiber. The thermal analyses indicated secondary interactions, such as polar interactions, between the fibers and the matrix, consistent with the mechanical behavior of the composites. The glass transition temperature has not

Avaliação da remoção de cromo (III por materiais compósitos porosos adsorventes de PE-g-MA, fibra de coco e quitosana, usando planejamento experimental

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Dilma Alves Costa

2017-04-01

Full Text Available RESUMO Os processos de adsorção podem ser empregados no tratamento de efluentes líquidos contendo metais pesados visando a reduzir os danos ambientais. Porém, o alto custo dos materiais adsorventes justifica a aplicação de adsorventes alternativos, como a fibra de coco (FC e a quitosana (Q. Assim, este trabalho teve como objetivo desenvolver compósitos porosos adsorventes a partir da mistura de polietileno graftizado com anidrido maleico/FC/Q/NaCl, como agente porogênico (PE-g-MA/FC/Q/NaCl, e avaliar estatisticamente a capacidade de adsorção do cromo (III em solução, com auxílio do software Statistica 5.0®. Os resultados mostraram que a eficiência do processo sofreu influência das dimensões da FC, do teor de Q e do pH da solução contendo Cr (III. A capacidade máxima de remoção de Cr (III por unidade de massa do compósito foi de 42,28 mg.g-1.

L’ingénierie pédagogique à base d’objets et le référencement par les compétences

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Gilbert Paquette

2004-01-01

Full Text Available Nous situons l’ingénierie pédagogique au confluent du design pédagogique, du génie logiciel et de l’ingénierie cognitive. Puis, dans l’optique d’une ingénierie pédagogique à base d’objets, nous proposons une méthode permettant de représenter graphiquement les connaissances et les compétences, puis de les associer aux ressources d’apprentissage. Par la suite, nous montrons comment cette méthode peut contribuer à améliorer la qualité des environnements en ligne à chacune des phases de leur cycle de vie.

AMDLIBGZ, IBM 360 Subroutine Library for Data Processing, Graphics, Sorting

International Nuclear Information System (INIS)

Wang, Jesse Y.

1980-01-01

Description of problem or function: AMDLIBGZ is a subset of the IBM 360 Subroutine Library at the Applied Mathematics Division at Argonne National Laboratory. This subset includes library categories G-Z: Identification/Description: G552S F RANF: Random number generator; J952S F YOLYPLOT: CalComp plots; J955S P GRAF: Prints a graph of points on line printer; K250S A1: Core to core conversion; K251S A HEXINP: Hexadecimal input for PL/I programs; K252S A HEXOUT: Hexadecimal output conv. PL/I programs; M101S F SORT: Algebraic sort; M150S F CSORT: Algebraic sort; M151S P2 ANLKWIC: KWIC sort; M250S A SMALLIST: Squeezes assembler listing to 8 x 11; N251S A ABEND: Calls ABEND dump; Q052S A CLOCK: Time; Q053S A COPYAGO: Copy load module from tape to disk; Q054S A DATE: Current date in form MM/DD/YY; Q055S A TIME: Time (24 hour clock) in EBCDIC HH.MM.SS; Z013S F: Variable metric minimization; Z057S A LOCF: Locate machine addresses of variables; Z071S A ALLOC: Allocate LCS for FORTRAN programs; Z074S A ANLMNP: Exponent and mantissa manipulative functs.

An unusual form of spondyloepiphyseal dysplasia, with advanced carpal and spinal end-plate ossification mimicking COMP-mutation-like multiple epiphyseal dysplasia

Energy Technology Data Exchange (ETDEWEB)

Pazzaglia, Ugo E.; Zarattini, Guido [University of Brescia Medical School, Department of Orthopaedics and Traumatology, Brescia (Italy); Beluffi, Giampiero [Fondazione IRCCS Policlinico S. Matteo, Section of Paediatric Radiology, Department of Radiodiagnosis, Pavia (Italy)

2008-07-15

We present a child with irregular ossification of tubular bone epiphyses, short bones, and spine. The radiographic evolution of bones undergoing endochondral ossification was followed from the age of 1 year 9 months to 6 years. The unusual features demonstrated in this child made classification difficult: pseudoachondroplasia was excluded because no mutations of the COMP gene were found. Considering the evolution of the radiographic appearances, the most likely diagnosis would seem to be an unusual form of spondyloepiphyseal dysplasia, mimicking some aspects of multiple epiphyseal dysplasia. Endochondral ossification was diffusely altered with a mixture of epiphyseal ossification delay associated with acceleration and early fusion. This case was a unique presentation within the family, suggesting a mutation in the affected child. (orig.)

An unusual form of spondyloepiphyseal dysplasia, with advanced carpal and spinal end-plate ossification mimicking COMP-mutation-like multiple epiphyseal dysplasia

International Nuclear Information System (INIS)

Pazzaglia, Ugo E.; Zarattini, Guido; Beluffi, Giampiero

2008-01-01

We present a child with irregular ossification of tubular bone epiphyses, short bones, and spine. The radiographic evolution of bones undergoing endochondral ossification was followed from the age of 1 year 9 months to 6 years. The unusual features demonstrated in this child made classification difficult: pseudoachondroplasia was excluded because no mutations of the COMP gene were found. Considering the evolution of the radiographic appearances, the most likely diagnosis would seem to be an unusual form of spondyloepiphyseal dysplasia, mimicking some aspects of multiple epiphyseal dysplasia. Endochondral ossification was diffusely altered with a mixture of epiphyseal ossification delay associated with acceleration and early fusion. This case was a unique presentation within the family, suggesting a mutation in the affected child. (orig.)

Síntese e caracterização de compósito magnético nanoestruturado contendo óxido de manganês para remoção de íons Cd(II do meio aquoso

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A. P. Heitmann

2014-09-01

Full Text Available O tratamento de efluentes contendo cádmio é de grande interesse devido à persistência desse contaminante no meio ambiente e às graves doenças que pode causar ao homem. No presente trabalho, foi utilizado o compósito magnético Mn3O4/Fe3O4 como adsorvente do íon cádmio (II em meio aquoso. O material adsorvente foi sintetizado e caracterizado segundo as técnicas de difração de raios X (DRX, espectroscopia Raman, microscopia eletrônica de transmissão e sorção de N2 (BET. Ênfase foi dada à quantificação das fases do compósito pela análise de DRX combinada ao método Rietveld. O estudo de adsorção foi realizado variando o pH do meio e a concentração do íon cádmio em solução. A análise dos resultados possibilitou verificar que a remoção de Cd(II utilizando compósito magnético Mn3O4/Fe3O4 em meio aquoso é dependente do pH duplicando a medida que o pH varia de 3 para 7. O estudo de imobilização do íon contaminante em solução apresentou valores significativos de capacidade máxima de adsorção, de 12,3 mgCd/g no pH 6 e 13,6 mgCd/g no pH 7, indicando uma remoção de até 98% para concentrações baixas do íon, sugerindo que o adsorvente apresenta elevado potencial para remoção de Cd(II em meio aquoso.

Peregrinação e alegoria: uma leitura doCompêndio Narrativo do Peregrino da América

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Jean Luiz Neves Abreu

Full Text Available Resumo:A obra de Nuno Marques Pereira, Compêndio narrativo do peregrino da América, publicada em 1728, pertence ao vasto repertório da literatura de cunho moralizante produzida entre os séculos XVI e XVIII. Trata-se da narrativa de viagem que um suposto "peregrino" faz da Baía de Todos os Santos à Capitania das Minas, na qual discorre sobre os costumes religiosos no Brasil e aborda temas diversos, analisados à luz de uma teologia moral. Este artigo propõe analisar como Nuno Marques Pereira articula elementos discursivos disponíveis na tradição, como é o caso da alegoria e do diálogo, e o exame dos costumes e das práticas religiosas que observa na sociedade da América Portuguesa no século XVIII, que atuam como elementos decisivos na construção do texto.

Tutorat à distance et développement des compétences professionnelles des futurs enseignants d’anglais langue seconde

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Mariane Gazaille

2011-03-01

Full Text Available S’insérant au cœur du processus d’enseignement et définissant l’intervention éducative, l’enseignant joue un rôle crucial dans tout système d’éducation. La qualité de la formation des maîtres (FM prend ici toute son importance en ce qu’elle vise à former des enseignants professionnels compétents. Pourtant, malgré la révision des programmes de FM, avance-t-on encore aujourd’hui que davantage pourrait être fait pour rapprocher théorie et pratique en FM. La présente étude vise à documenter cette question en s’intéressant aux effets d’un projet expérimental de tutorat inter-ordre2 à distance comme outil de formation pour les futurs enseignants de langues secondes. Les apprentissages rapportés sont classifiés puis comparés aux 12 compétences professionnelles (CP qui orientent la FM au Québec (Canada. Les résultats suggèrent que le tutorat à distance permet le développement intégré de plusieurs composantes des CPs visées en FM et la conscientisation des futurs enseignants vis-à-vis de celles-ci.Shaping and defining the instruction process, teachers play a pivotal role in any education system. In this perspective, the quality of teacher education is an issue of high importance in that it aims at training professional and competent teachers. Yet, and in spite of the revisions teacher training programs have undergone, it seems that more could be done to bring theory and practice closer in the field of teacher education. The current study aimed at documenting the question by studying the impacts of an experimental cross-level distance tutoring project on second language student teachers’ learning. Learning reported is first grouped and then contrasted to the 12 core professional competencies that orientate teacher training programs in Québec (Canada. Results suggest that distance tutoring allows for the integrated development of a number of features from different professional competencies as well as

Reconnaître et valoriser les compétences "associatives" : les enjeux de la transmission dans l'accompagnement des parcours bénévoles

OpenAIRE

Tardif Bourgoin , Florence

2012-01-01

Atelier 22 : Travail social et bénévolat; Les exigences de professionnalisation dans le champ de l'action sociale préoccupent les associations dans un contexte de réduction des financements. Sont formulés des objectifs en vue de la qualification des bénévoles. Les dispositifs d'accompagnement qui se développent posent alors la question des transmissions mises en oeuvre : s'agit-il de transmettre une activité, des compétences, des valeurs ? Qu'en est-il du côté des Centres sociaux qui inscrive...

Ensembl Genomes 2016: more genomes, more complexity.

Science.gov (United States)

Kersey, Paul Julian; Allen, James E; Armean, Irina; Boddu, Sanjay; Bolt, Bruce J; Carvalho-Silva, Denise; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Aranganathan, Naveen K; Langridge, Nicholas; Lowy, Ernesto; McDowall, Mark D; Maheswari, Uma; Nuhn, Michael; Ong, Chuang Kee; Overduin, Bert; Paulini, Michael; Pedro, Helder; Perry, Emily; Spudich, Giulietta; Tapanari, Electra; Walts, Brandon; Williams, Gareth; Tello-Ruiz, Marcela; Stein, Joshua; Wei, Sharon; Ware, Doreen; Bolser, Daniel M; Howe, Kevin L; Kulesha, Eugene; Lawson, Daniel; Maslen, Gareth; Staines, Daniel M

2016-01-04

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper provides an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integration of archival data (genome sequence, but also associated RNA sequence data and variant calls) within the context of reference genomes and make it available through the Ensembl user interfaces. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

La professionnalisation de la formation universitaire d’enseignants de français : quelles compétences visées ?

Directory of Open Access Journals (Sweden)

PHAM Duy Thien

2016-12-01

Full Text Available Bien former à un métier est devenu une préoccupation de la société vietnamienne. Car la qualité de la formation professionnelle laisse toujours à désirer. L’université dispensant traditionnellement des formations dites académiques les repense dans une perspective de professionnalisation. La logique académique et la logique professionnelle peuvent-elles être compatibles l’une avec l’autre ? Si la formation universitaire se professionnalise, qu’est-ce qu’elle apportera aux étudiants pour que ceux-ci, une fois diplômés, soient reconnus comme étant compétents et aptes à travailler ? Notre article propose de répondre à ces questions. Les réflexions qui y sont présentées proviennent de notre travail de thèse, portant sur la professionnalisation des guides touristiques vietnamiens.

Efeito de diferentes fotopolimerizadores e meio de imersão na rugosidade e na cor de um compósito nanoparticulado

Directory of Open Access Journals (Sweden)

Suéllen Campos PLASTER

Full Text Available Resumo Introdução O consumo excessivo de refrigerantes parece alterar as propriedades dos compósitos e essa alteração pode estar relacionada à unidade fotopolimerizadora. Objetivo Avaliar a alteração da rugosidade superficial (ΔR e da cor (ΔE de um compósito polimerizado por diferentes fotopolimerizadores, imerso em água destilada ou Coca-Cola®. Metodologia Sessenta amostras da resina nanoparticulada (FiltekMR Z350 XT, 3M foram distribuídas de acordo com as diferentes unidades de fotopolimerização: a luz halógena de quartzo-tungstênio-halogênio (QTH; b Luz de Emissão Diodo - LED 1 com ponteira de polímero; c LED 2 com ponteira de fibra ótica. Metade de cada grupo (n=10 foi mantida em água destilada ou imersa em Coca-Cola® 2×/dia por 20 minutos, durante 14 dias. Os dados foram submetidos aos testes Mann-Whitney e Kruskal-Wallis (p≤0,05. Resultado A ΔR não foi significante entre os grupos: em água: QTH = 0,006; LED 1 = 0,019; LED 2 = 0,010 (p=0,33; em refrigerante: QTH = 0,021; LED 1= 0,011; LED 2 = 0,030 (p=0,86. A ΔE não foi significativa entre os fotopolimerizadores: em água: QTH = 1,40; LED 1 = 1,80; LED 2 = 1,60 (p=0,31; em refrigerante: QTH = 2,51; LED 1= 1,91; LED 2 = 2,61 (p=0,41, mas foi significante comparando os meios de imersão (p=0,01, exceto para LED 1 (p=0,54. Conclusão As unidades fotopolimerizadoras não interferiram na rugosidade superficial e na cor da resina composta nanoparticulada. Os mergulhos diários em refrigerante não alteraram a lisura, mas alteraram a cor de modo visualmente perceptível, mas clinicamente aceitável, conforme os parâmetros da literatura científica.

phiGENOME: an integrative navigation throughout bacteriophage genomes.

Science.gov (United States)

Stano, Matej; Klucar, Lubos

2011-11-01

phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and designed for graphical representation of gene regulations. Bringing 542 complete genome sequences accompanied with their rich annotations and references, makes phiGENOME a unique information resource in the field of phage genomics. Copyright © 2011 Elsevier Inc. All rights reserved.

CompNanoTox2015: novel perspectives from a European conference on computational nanotoxicology on predictive nanotoxicology

Energy Technology Data Exchange (ETDEWEB)

Bañares, Miguel A. [Instituto de Catalisis y Petroleoquimica, ICP, CSIC, Madrid, Spain,; Haase, Andrea [German Federal Institute for Risk Assessment (BfR), Department of Chemical and Product Safety, Berlin, Germany,; Tran, Lang [Statistics and Toxicology Section, Institute of Occupational Medicine, Edinburgh, UK,; Lobaskin, Vladimir [School of Physics, University College Dublin, Dublin, Ireland,; Oberdörster, Günter [Department of Environmental Medicine, University of Rochester, Rochester, NY, USA,; Rallo, Robert [Departament d’Enginyeria Informatica i Matematiques, Universitat Rovira i Virgili, Tarragona, Spain,; Advanced Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, WA, USA,; Leszczynski, Jerzy [Interdisciplinary Nanotoxicity Center, Jackson State University, Jackson, MS, USA,; Hoet, Peter [Public Health, Unit Lung Toxicology, K. U. Leuven, Leuven, Belgium,; Korenstein, Rafi [Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel,; Hardy, Barry [Technology Park Basel, Douglas Connect GmbH, Basel, Switzerland,; Puzyn, Tomasz [Laboratory of Environmental Chemometrics, Faculty of Chemistry, University of Gdansk, Gdansk, Poland

2017-08-09

A first European Conference on Computational Nanotoxicology, CompNanoTox, was held in November 2015 in Benahavís, Spain with the objectives to disseminate and integrate results from the European modeling and database projects (NanoPUZZLES, ModENPTox, PreNanoTox, MembraneNanoPart, MODERN, eNanoMapper and EU COST TD1204 MODENA) as well as to create synergies within the European NanoSafety Cluster. This conference was supported by the COST Action TD1204 MODENA on developing computational methods for toxicological risk assessment of engineered nanoparticles and provided a unique opportunity for crossfertilization among complementary disciplines. The efforts to develop and validate computational models crucially depend on high quality experimental data and relevant assays which will be the basis to identify relevant descriptors. The ambitious overarching goal of this conference was to promote predictive nanotoxicology, which can only be achieved by a close collaboration between the computational scientists (e.g. database experts, modeling experts for structure, (eco) toxicological effects, performance and interaction of nanomaterials) and experimentalists from different areas (in particular toxicologists, biologists, chemists and material scientists, among others). The main outcome and new perspectives of this conference are summarized here.

Genome Maps, a new generation genome browser.

Science.gov (United States)

Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

2013-07-01

Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

Influência do método de polimerização na microdureza de compósitos microhíbridos armazenados em água destilada = Influence of curing method on the micro hardness of microhybrid composites immersed in distilled water

Directory of Open Access Journals (Sweden)

Herbstrith Segundo, Regênio Mahfuz

2007-01-01

Full Text Available O objetivo do presente estudo é comparar e avaliar a microdureza Vickers de um compósito restaurador microhíbrido ativado por dois tipos de unidades polimerizadoras e armazenados em água destilada. Trinta espécimes foram feitos com resina Charisma B1, para cada um dos regimes de polimerização: fotopolimerização por luz halógena, fotopolimerização por LED e fotopolimerização mais ciclo adicional em autoclave. Foram feitas duas leituras de microdureza Vickers por corpo de prova em 1 dia, 7 dias e 14 dias de imersões. O ciclo adicional de polimerização mostrou uma tendência de aumentar os valores de microdureza dos compósitos restauradores, não mostrando diferenças estatisticamente significantes entre LED e Luz Halógena (p > 0,05

Genomics using the Assembly of the Mink Genome

DEFF Research Database (Denmark)

Guldbrandtsen, Bernt; Cai, Zexi; Sahana, Goutam

2018-01-01

The American Mink’s (Neovison vison) genome has recently been sequenced. This opens numerous avenues of research both for studying the basic genetics and physiology of the mink as well as genetic improvement in mink. Using genotyping-by-sequencing (GBS) generated marker data for 2,352 Danish farm...... mink runs of homozygosity (ROH) were detect in mink genomes. Detectable ROH made up on average 1.7% of the genome indicating the presence of at most a moderate level of genomic inbreeding. The fraction of genome regions found in ROH varied. Ten percent of the included regions were never found in ROH....... The ability to detect ROH in the mink genome also demonstrates the general reliability of the new mink genome assembly. Keywords: american mink, run of homozygosity, genome, selection, genomic inbreeding...

Visualization for genomics: the Microbial Genome Viewer.

NARCIS (Netherlands)

Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D; Siezen, R.J.

2004-01-01

SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a

Caracterização Mecânica de Compósitos de Poliamida/Fibra de Carbono Via Ensaios de Cisalhamento Interlaminar e de Mecânica da Fratura Mechanical Characterization of Polyamide/Carbon Fiber Composites by Using Interlaminar Shear Strength and Fracture Mechanical Tests

Directory of Open Access Journals (Sweden)

Edson C. Botelho

2002-01-01

Full Text Available Compósitos termoplásticos a partir de poliamidas 6 e 6,6 e tecido de fibras de carbono com 40, 50 e 60 % em volume de reforço foram processados via moldagem por compressão a quente e caracterizados por ensaios mecânicos destrutivos (cisalhamento interlaminar em três pontos (short-beam, cisalhamento interlaminar por compressão (CST e ensaios de mecânica da fratura e por inspeção não-destrutiva (ultra-som e microscopias óptica e eletrônica de varredura. Os resultados obtidos mostraram que os compósitos termoplásticos processados apresentaram uma distribuição homogênea do polímero no reforço. Entretanto, nos compósitos com maior quantidade de poliamida (40 % de reforço foram observadas regiões ricas em matriz entre as camadas de tecido. Os ensaios de mecânica da fratura (DCB e ENF e de cisalhamento interlaminar em três pontos não apresentaram falha interlaminar, não sendo observada a propagação de trincas de forma homogênea e retilínea no interior do material. Em função destes resultados foi utilizado o ensaio de cisalhamento por compressão, desenvolvido no Institute of Polymer Research Dresden da Alemanha, que permitiu uma caracterização mais precisa dos compósitos termoplásticos estudados. Foi observado também, a partir dos ensaios de CST, que os compósitos obtidos da poliamida 6,6 apresentaram um aumento no valor do cisalhamento interlaminar de até 20 % com o aumento do volume de fibras.Thermoplastics composites of polyamide 6 and 6.6 reinforced with carbon fiber fabric were obtained by compression molding and characterized by destructive (short-beam, compression shear (CST and fracture mechanics testing as well as by non-destructive inspection (ultrasound analysis, optical and scanning electron microscopy. The results show that, in general, the matrix was homogeneously distributed about the reinforcing fabric. However, for the composites with higher polyamide content (>50% matrix-rich regions were

Resistência mecânica de compósitos cimentícios leves utilizando resíduos industriais e fibras de sisal Mechanical resistence of lightweight cement composites utilizing industrial residues and fibers of sisal

Directory of Open Access Journals (Sweden)

Nivaldo T. de Arruda Filho

2012-08-01

Full Text Available A valorização de materiais alternativos incorporados com resíduos como opção ao convencional deve possibilitar a geração de um produto com qualidade, estética, produtividade e com potencial de reduzir impactos da poluição ambiental. Este trabalho foi realizado com o objetivo de desenvolver elementos construtivos para forro e divisórias, a partir de matrizes cimentícias com incorporação de resíduos industriais (resíduo cerâmico, etil vinil acetato - EVA e fibras de sisal. Desenvolveram-se técnicas de moldagem em matrizes cimentícias autoadensáveis e se avaliou a resistência mecânica dos novos compósitos. Uma placa com resíduos de EVA foi produzida e, através de trabalhos de reologia, encontrou-se a pasta matriz de revestimento desta placa, com teor adequado de adições pozolânicas e aditivo superplastificante. Avaliaram-se as resistências mecânicas das placas, da pasta matriz de revestimento encontrada, com e sem adição de fibras, e do novo compósito formado pela união desses dois elementos. Utilizou-se a técnica de alinhamento de fibras com o intuito de incrementar resistência ao novo compósito leve. A adição da matriz com fibras alinhadas melhorou a resistência a flexão do novo compósito.The appreciation of alternative materials incorporated in waste as an option to conventional material should enable to generate a product with quality, aesthetics, productivity and reduce the potential impacts of environmental pollution. This study aims to develop constructive elements for ceilings and walls from cementitious matrix incorporating industrial waste (ceramic waste, ethyl vinyl acetate - EVA and sisal fibers. Moulding techniques to produce self-compacting cementitious matrices were developed and the strength of the new composites were evaluated. A plate with EVA waste was produced and through rheology studies, a matrix plaster for coating of plate surface was found, with appropriate content of pozzolanic and

Impregnação de filmes do compósito de policarbonato (PC e sílicagel (Si com corante fotocrômico em fluido supercrítico = Impregnation of composite from polycarbonate (PC and silica gel (Si films with photochromic dye in supercritical fluid

Directory of Open Access Journals (Sweden)

Fernanda de Almeida Fin de Lima

2010-01-01

Full Text Available O objetivo deste trabalho foi estudar a impregnação do corante fotocromático Reversacol Graphit® em filmes do compósito de policarbonato (PC e sílica-gel (Si, com a finalidade de obter aplicações em lentes fotocrômicas. Filmes de PC puros também foramimpregnados nas mesmas condições, para verificar o efeito da adição de sílica-gel. Os filmes do compósito foram produzidos em proporções de Si:PC de 1:40 e 1:80 (m m-1, pelo método casting. Para a impregnação do corante Reversacol Graphit nos filmes obtidos foiutilizado o processo supercrítico, pela sua eficiência e benefícios. A impregnação foi feita nos tempos de 15, 30, 45, 60, 90, 120, 150 e 180 min. A temperatura e a pressão adotadas foram de 60ºC e 120 bar. A quantidade de pigmento impregnado nos filmes de Si:PC – 1:40e 1:80 (m m-1 foi de 29 e 23% de massa de corante por massa de compósito, respectivamente, e para o filme de PC puro foi de apenas 2,2% massa de corante por massa de compósito. Pelas análises térmicas, verificou-se que os filmes do compósito apresentarammaior estabilidade térmica. Pela técnica de microscopia eletrônica, observou-se que os filmes de PC puro e dos compósitos Si:PC – 1:40 e 1:80 (m m-1 apresentaram uma superfície lisa e homogênea.The aim of this work was to study the impregnation of the photochromic dye Reversacol Graphit® in composite films ofpolycarbonate (PC and silica gel, with the purpose of finding applications in photochromic lenses. Pure PC films were also impregnated in the same conditions, to verify the effect of the silica-gel addition. The composites films were produced in Si:PC ratios of 1:40 and 1:80 (m m-1, using the casting method . For the impregnation of the dye Reversacol Graphit in the obtained films, the supercritical process was used due to its efficiency and benefits. The impregnation was made in the times of 15, 30, 45, 60, 90, 120, 150 and 180 minutes. The adopted temperature and pressure

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

El programa “Regla y compás”. Una experiencia utilizando un software gratuito para generar ambientes de aprendizaje en matemática

Directory of Open Access Journals (Sweden)

Zuleyka Suárez Valdes-Ayala

2004-12-01

Full Text Available The program “Regla y Compás” (“Ruler and Compasses” is useful to support the teaching of Math processes in geometry by means of a computer. One of the advantages it offers is that it may be obtained gratuitously in the internet. The way in which this type of programs allows for corporative and interdisciplinary work will by analyzed. For this purpose, the experiences obtained during the research project “Teaching high school mathematics whit free online software: The Ruler and Compasses case” will be discussed. The latter enabled the elaboration of tree manuals: “User's manual”, “Student's manual” and Teacher`s manual”. The objective is to facilitate the teaching of geometry through 32 practice and learning sessions.

Family genome browser: visualizing genomes with pedigree information.

Science.gov (United States)

Juan, Liran; Liu, Yongzhuang; Wang, Yongtian; Teng, Mingxiang; Zang, Tianyi; Wang, Yadong

2015-07-15

Families with inherited diseases are widely used in Mendelian/complex disease studies. Owing to the advances in high-throughput sequencing technologies, family genome sequencing becomes more and more prevalent. Visualizing family genomes can greatly facilitate human genetics studies and personalized medicine. However, due to the complex genetic relationships and high similarities among genomes of consanguineous family members, family genomes are difficult to be visualized in traditional genome visualization framework. How to visualize the family genome variants and their functions with integrated pedigree information remains a critical challenge. We developed the Family Genome Browser (FGB) to provide comprehensive analysis and visualization for family genomes. The FGB can visualize family genomes in both individual level and variant level effectively, through integrating genome data with pedigree information. Family genome analysis, including determination of parental origin of the variants, detection of de novo mutations, identification of potential recombination events and identical-by-decent segments, etc., can be performed flexibly. Diverse annotations for the family genome variants, such as dbSNP memberships, linkage disequilibriums, genes, variant effects, potential phenotypes, etc., are illustrated as well. Moreover, the FGB can automatically search de novo mutations and compound heterozygous variants for a selected individual, and guide investigators to find high-risk genes with flexible navigation options. These features enable users to investigate and understand family genomes intuitively and systematically. The FGB is available at http://mlg.hit.edu.cn/FGB/. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Estudo da influência de tratamentos químicos da fibra de sisal nas propriedades de compósitos com borracha nitrílica Study of the influence from chemical treatments of sisal fibers on the properties of composites with nitrile rubber

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Marco A. Iozzi

2010-01-01

Full Text Available A influência de diferentes tratamentos das fibras de sisal nas propriedades dos compósitos de borracha nitrílica/fibras de sisal, e borracha nitrílica/carbonato de cálcio/fibras de sisal foi investigada. Os compósitos, com fibras curtas aleatoriamente distribuídas, foram processados em moinho de dois rolos e caracterizados através de ensaios mecânicos de resistência à tração, microscopia eletrônica de varredura (MEV, análise por termogravimetria (TG e calorimetria exploratória diferencial (DSC. O tratamento de mercerização das fibras levou a uma maior adesão na interface fibra/matriz. O uso combinado de 67 pcr de carbonato com 33 pcr de fibras de sisal mercerizadas produziu um compósito com aumento significativo no módulo de elasticidade e sem perda da resistência à tração de ruptura. Os resultados da análise térmica mostraram que os compósitos são termicamente estáveis até cerca de 300 °C. Os materiais obtidos possuem uma boa relação custo/benefício tornando promissora sua utilização.In this work, composites were produced with nitrile rubber and sisal fibers, and nitrile rubber with calcium carbonate and sisal fibers. The composites were processed on a two-roll mixing mill and their properties were investigated with regard to the influence of chemical treatments of the fibers. The composites, with short fibers randomly distributed, were characterized by mechanical analysis, scanning electron microscopy (SEM, thermogravimetric analysis (TGA and differential scanning calorimetry (DSC. Mercerization treatment of the fibers promoted increasing the adhesion between the fiber and the rubber matrix. The composites of nitrile rubber with 67 pcr of calcium carbonate and 33 pcr of mercerized sisal fibers showed the best mechanical properties. Thermal analysis demonstrated that the composites are thermally stable up to 300 °C. The materials developed have a good cost/benefit relationship making their utilization

eGenomics: Cataloguing Our Complete Genome Collection III

Directory of Open Access Journals (Sweden)

Dawn Field

2007-01-01

Full Text Available This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS, Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS specification (v1.1, consensus on a variety of features to be added to the Genome Catalogue (GCat, agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates and working towards a single, global list of all public genomes and metagenomes.

Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project

DEFF Research Database (Denmark)

Hayes, Benjamin J; MacLeod, Iona M; Daetwyler, Hans D

Advantages of using whole genome sequence data to predict genomic estimated breeding values (GEBV) include better persistence of accuracy of GEBV across generations and more accurate GEBV across breeds. The 1000 Bull Genomes Project provides a database of whole genome sequenced key ancestor bulls....... In a dairy data set, predictions using BayesRC and imputed sequence data from 1000 Bull Genomes were 2% more accurate than with 800k data. We could demonstrate the method identified causal mutations in some cases. Further improvements will come from more accurate imputation of sequence variant genotypes...

Materiais compósitos à base de gesso contendo eva (Etileno Acetato de Vinila) e vermiculita: otimização de misturas e propriedades termomecânicas

OpenAIRE

Oliveira, Marilia Pereira de

2009-01-01

O gesso é um dos materiais de construção mais antigos que se tem conhecimento. Algumas de suas propriedades lhe confere vantagens como, resistência ao fogo, isolamentos térmico e acústico. Em virtude de ser um ligante menos agressivo ao ambiente que o cimento Portland, seu uso deve ser incentivado e novas aplicações estudadas. Este trabalho teve como objetivo estudar as propriedades físico-mecânicas e térmicas de compósitos à base de gesso com a incorporação de vermiculita e de...

Síntese de um poli (ácido âmico para aplicação como interfase em compósitos termoplásticos de alto desempenho Synthesis of a poly (amic acid for appplication as interphase in high performance thermoplastic composites

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Liliana B. Nohara

2004-06-01

Full Text Available O objetivo do presente trabalho é apresentar a síntese de um poli (ácido âmico (PAA a ser utilizado como formador de interfase no processamento de compósitos termoplásticos de alto desempenho. Os materiais compósitos termoplásticos constituídos de um reforço rígido e de uma matriz dúctil têm as suas propriedades mecânicas fortemente dependentes do mecanismo de transferência de carga fibra/matriz. Por esse motivo, a região da interface/interfase nos materiais compósitos possui um papel fundamental nas propriedades finais do material. O PAA surge como uma alternativa para melhorar a adesão fibra/matriz na região interfacial em compósitos de alto desempenho, constituídos de matrizes termoplásticas, reforçadas com fibras de carbono ou vidro. O PAA é utilizado na forma de sal, na preparação de suspensões poliméricas de matrizes termoplásticas. O PAA estudado neste trabalho foi sintetizado utilizando-se os reagentes BTDA e DHPr. Em seguida, o PAA foi convertido em PI por imidização em solução. Análises por FTIR mostram o sucesso da síntese do PAA e da sua conversão em PI. As técnicas de DSC e TGA determinaram as temperaturas de transição vítrea (~213 °C e de decomposição (~310 °C, respectivamente. Estes resultados motivam a utilização do PAA/PI como formador de interfase na obtenção de compósitos termoplásticos com temperaturas de processamento abaixo de 310 °C.This work is aimed at presenting the synthesis of a poly (amic acid (PAA to be used as interphase precursor in the manufacturing of high performance thermoplastic composites. Thermoplastic composites comprising a rigid reinforcement and a ductile matrix have their mechanical properties strongly dependent on the load transfer mechanism between the reinforcement and matrix. For this reason, the interface/interphase region plays a fundamental hole in the final properties of the composite materials. PAA appeared as an alternative to improve the

Pharmacophore-based screening of differentially-expressed PGF, DDIT4, COMP and CHI3L1 from hMSC cell lines reveals five novel therapeutic compounds for primary osteoporosis

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Catherine Jessica Lai

2016-06-01

Full Text Available As many societies age, primary osteoporosis (PO is increasingly a major health problem. Current drug treatments such as alendronate and risedronate have known side effects. We took an agnostic empirical approach to find PO therapeutic compounds. We examined 13,548,960 probe data-points from mesenchymal stromal cell (hMSC lines and found that PGF, DDIT4, and COMP to be up-regulated, and CHI3L1, down-regulated. We then identified their druggable domains. For the up-regulated differentially-expressed genes, we used protein–protein interactions to find residue clusters as binding surfaces. We then employed pharmacophore models to screen 15,407,096 conformations of 22,723,923 compounds, which identified (6R,9R-6-(2-furyl-9-(1H-indol-3-yl-2-(trifluoromethyl-5,6,7, 9-tetrahydro-4H[1,2,4]triazolo[5,1],(2S-N1-[2-[2-(methylamino-2-oxo-ethyl]phenyl]-N2-phenylpyrrolidine-1,2-dicarboxamide, and 2-furyl-(1H-indol-3-yl-methyl-BLAHone as candidate compounds. For the down-regulated CH13L1, we relied on genome-wide disease signatures to identify (11alpha-9-fluoro-11,17,21-trihydroxypregn-4-ene-3,20-dione and Genistein as candidate compounds. Our approach differs from previous research as we did not confine our drug targets to hypothesized compounds in the existing literature. Instead, we allowed the full expression profile of PO cell lines to reveal the most desirable targets. Second, our differential gene analysis revealed both up- and down-regulated genes, in contrast to the literature, which has focused on inhibiting only up-regulated genes. Third, our virtual screening universe of 22,723,923 compounds was more than 100 times larger than those in the known literature.

De la compétence de service aux compétences de coordination et d’orchestration : Autour du conseiller funéraire From service competency to coordination and orchestration skills: the funeral director De la competencia de servicio a las competencias de coordinación y de orquestación : el consejero fúnebre

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Sandrine Caroly

2006-05-01

Full Text Available Partir à la découverte du « conseiller funéraire », personnage emblématique de la profession de pompes funèbres, nous donne accès aux principaux registres de compétence des opérateurs funéraires, tout au long d’une prestation de service qui conjugue traitement du corps, service public et ritualité funéraire. Maître d’œuvre des obsèques, le conseiller se découvre historiquement comme une figure à géométrie variable, évoluant d’une fonction de personnage public, au cœur des réseaux notables et religieux de la communauté locale, à celle de conseiller technico-commercial, cependant de plus en plus investi d’un rôle « d’officiant » dans la production des funérailles comme bien culturel et symbolique. Cet article s’intéresse à la manière dont les compétences du conseiller funéraire sont mises en œuvre à travers trois principaux registres de compétence : la gestion de l’interaction avec le client, la coordination interprofessionnelle et enfin « l’orchestration » de l’événement et du sacré dans le déroulement des opérations funéraires. L’analyse de l’activité funéraire révèle des propriétés essentielles des compétences de service.In describing the funeral director, who is the symbol of funeral services, we gain access to the main skill registries of funeral operators during the entire provision of services, which include: the handling of the deceased, the public service, and the funeral ritual. As the individual who manages the funeral, the funeral director historically is a person with variable geometry, evolving from a public persona within the local community’s important religious networks to that of a technical and commercial consultant, but increasingly invested with the role of "officiant" in the production of funerals as cultural and symbolic property. This article is interested in how the funeral director’s skills are applied through three main skill registries

La compétition interspécifique entre la truite commune (Salmo trutta L. et la truite arc-en-ciel (Oncorhynchus Mykiss Walbaum : influence sur les modèles d'habitat

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BARAN P.

1995-04-01

Full Text Available L'influence de la compétition interspécifique sur l'occupation de l'habitat physique du ruisseau d'Estibère a été étudiée sur deux populations de truite arc-en-ciel (Oncorhynchus mykiss, vivant respectivement en allopatrie et en sympatrie avec une population de truite commune (Salmo trutta L.. Le taux d'occupation de la Surface Pondérée Utile (SPU calculée par la méthode des microhabitats (BOVEE, 1982 est significativement supérieur (t de Student, p < 0.05 pour la population allopatrique de truite arc-en-ciel par rapport à la population sympatrique. La surface d'abris, la pente et le taux d'occupation de la SPU par les truites communes permettent d'expliquer 77 % de la variation d'occupation de l'habitat physique par les adultes de truites arc-en-ciel. Pour les truites communes, la surface d'abris explique à elle seule, 81 % de la variation du taux d'occupation de l'habitat par les adultes. Selon l'espèce et le stade de développement considéré, la compétition interspécifique peut être un élément déterminant dans l'occupation de l'habitat physique potentiel.

Genome U-Plot: a whole genome visualization.

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Gaitatzes, Athanasios; Johnson, Sarah H; Smadbeck, James B; Vasmatzis, George

2018-05-15

The ability to produce and analyze whole genome sequencing (WGS) data from samples with structural variations (SV) generated the need to visualize such abnormalities in simplified plots. Conventional two-dimensional representations of WGS data frequently use either circular or linear layouts. There are several diverse advantages regarding both these representations, but their major disadvantage is that they do not use the two-dimensional space very efficiently. We propose a layout, termed the Genome U-Plot, which spreads the chromosomes on a two-dimensional surface and essentially quadruples the spatial resolution. We present the Genome U-Plot for producing clear and intuitive graphs that allows researchers to generate novel insights and hypotheses by visualizing SVs such as deletions, amplifications, and chromoanagenesis events. The main features of the Genome U-Plot are its layered layout, its high spatial resolution and its improved aesthetic qualities. We compare conventional visualization schemas with the Genome U-Plot using visualization metrics such as number of line crossings and crossing angle resolution measures. Based on our metrics, we improve the readability of the resulting graph by at least 2-fold, making apparent important features and making it easy to identify important genomic changes. A whole genome visualization tool with high spatial resolution and improved aesthetic qualities. An implementation and documentation of the Genome U-Plot is publicly available at https://github.com/gaitat/GenomeUPlot. vasmatzis.george@mayo.edu. Supplementary data are available at Bioinformatics online.

A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

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Lack, Justin B; Lange, Jeremy D; Tang, Alison D; Corbett-Detig, Russell B; Pool, John E

2016-12-01

The Drosophila Genome Nexus is a population genomic resource that provides D. melanogaster genomes from multiple sources. To facilitate comparisons across data sets, genomes are aligned using a common reference alignment pipeline which involves two rounds of mapping. Regions of residual heterozygosity, identity-by-descent, and recent population admixture are annotated to enable data filtering based on the user's needs. Here, we present a significant expansion of the Drosophila Genome Nexus, which brings the current data object to a total of 1,121 wild-derived genomes. New additions include 305 previously unpublished genomes from inbred lines representing six population samples in Egypt, Ethiopia, France, and South Africa, along with another 193 genomes added from recently-published data sets. We also provide an aligned D. simulans genome to facilitate divergence comparisons. This improved resource will broaden the range of population genomic questions that can addressed from multi-population allele frequencies and haplotypes in this model species. The larger set of genomes will also enhance the discovery of functionally relevant natural variation that exists within and between populations. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Visualization for genomics: the Microbial Genome Viewer.

Science.gov (United States)

Kerkhoven, Robert; van Enckevort, Frank H J; Boekhorst, Jos; Molenaar, Douwe; Siezen, Roland J

2004-07-22

A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a MySQL database. The generated images are in scalable vector graphics (SVG) format, which is suitable for creating high-quality scalable images and dynamic Web representations. Gene-related data such as transcriptome and time-course microarray experiments can be superimposed on the maps for visual inspection. The Microbial Genome Viewer 1.0 is freely available at http://www.cmbi.kun.nl/MGV

Propriedades reométricas e mecânicas e morfologia de compósitos desenvolvidos com resíduos elastoméricos vulcanizados Cure characteristics, mechanical properties and morphology of composites developed with addition of elastomeric vulcanized ground scraps

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Aline Zanchet

2007-03-01

Full Text Available Uma alternativa para as empresas geradoras de resíduos elastoméricos é a incorporação dos mesmos em suas formulações. Esse trabalho tem como objetivo preparar compósitos a partir da incorporação de resíduos industriais de SBR (copolímero de butadieno-estireno e de EPDM (terpolímero de etileno-propileno-dieno, em formulação ASTM específica para cada tipo de elastômero. Foram avaliadas as propriedades reométricas, mecânicas e morfológicas dos compósitos desenvolvidos. A incorporação do resíduo permitiu a obtenção de produtos que vulcanizam em menores tempos quando comparados a composições sem resíduo. A quantidade de resíduo, para o melhor resultado de resistência à tração foi de 37 e de 196 phr para os compósitos com SBR e EPDM, respectivamente. As micrografias de MEV corroboraram os resultados mecânicos dessas composições, indicando melhor homogeneidade do resíduo na respectiva matriz elastomérica.One alternative for elastomeric scraps generation is its incorporation in conventional formulations in the industry itself. In this work, compositions with incorporation of SBR (styrene butadiene rubber and EPDM (ethylene propylene diene rubber industrial scraps, in specific ASTM formulation for each elastomer, were prepared. Rheometric characteristics, mechanical properties and the morphology of the compounds developed were evaluated. With the ground scraps incorporation the vulcanization time decreases, comparing with compounds without ground scraps. The amount of scraps for the best tensile strength properties was 37 and 196 phr for SBR and EPDM compositions, respectively. Micrographs corroborated the mechanical results, indicating the best homogeneity of the scraps in the elastomeric matrix for these compositions.

The Sequenced Angiosperm Genomes and Genome Databases.

Science.gov (United States)

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

Intercomparison of measurements of NO2 concentrations in the atmosphere simulation chamber SAPHIR during the NO3Comp campaign

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H. Fuchs

2010-01-01

Full Text Available NO2 concentrations were measured by various instruments during the NO3Comp campaign at the atmosphere simulation chamber SAPHIR at Forschungszentrum Jülich, Germany, in June 2007. Analytical methods included photolytic conversion with chemiluminescence (PC-CLD, broadband cavity ring-down spectroscopy (BBCRDS, pulsed cavity ring-down spectroscopy (CRDS, incoherent broadband cavity-enhanced absorption spectroscopy (IBB\\-CEAS, and laser-induced fluorescence (LIF. All broadband absorption spectrometers were optimized for the detection of the main target species of the campaign, NO3, but were also capable of detecting NO2 simultaneously with reduced sensitivity. NO2 mixing ratios in the chamber were within a range characteristic of polluted, urban conditions, with a maximum mixing ratio of approximately 75 ppbv. The overall agreement between measurements of all instruments was excellent. Linear fits of the combined data sets resulted in slopes that differ from unity only within the stated uncertainty of each instrument. Possible interferences from species such as water vapor and ozone were negligible under the experimental conditions.

L’exercice fédéré des compétences locales. À propos de la fonction de «chef de file» en droit des collectivités territoriales français

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Cédric Groulier

2009-06-01

Full Text Available La révision constitutionnelle du 28 mars 2003 a introduit dans le droit des collectivités territoriales un dispositif que l’on pourrait qualifier d’exercice fédéré des compétences locales. Selon l’article 72 alinéa 5 de la Constitution, lorsque l’exercice d’une compétence nécessite le concours de plusieurs collectivités territoriales, la loi peut autoriser l’une d’entre elles ou un de leurs groupements à organiser les modalités de leur action commune, autrement dit à exercer les fonctions de chef de file. À travers cette figure du chef de file, la Constitution semble admettre un principe de superposition entre collectivités territoriales, dérogeant à la règle de l’interdiction des tutelles entre collectivités, liée à leur liberté d’administration. Toutefois, la portée effective de ce nouveau dispositif repose sur sa mise en œuvre législative : or, le législateur fait montre d’une grande réserve, sans doute injustifiée, qui maintient l’idée de superposition entre collectivités à l’état de virtualité.

GenColors-based comparative genome databases for small eukaryotic genomes.

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Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2013-01-01

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

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Manolio, Teri A

2016-10-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. Published by Elsevier Ireland Ltd.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

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Machado, Henrique; Gram, Lone

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur , amino-acid usage, ANI), which allowed us to identify two misidentified strains. Genome analyses also revealed occurrence of higher and lower GC content clades, correlating with phylogenetic clusters. Pan- and core-genome analysis revealed the conservation of 25% of the genome throughout the genus, with a large and open pan-genome. The major source of genomic diversity could be traced to the smaller chromosome and plasmids. Several of the physiological traits studied in the genus did not correlate with phylogenetic data. Since horizontal gene transfer (HGT) is often suggested as a source of genetic diversity and a potential driver of genomic evolution in bacterial species, we looked into evidence of such in Photobacterium genomes. Genomic islands were the source of genomic differences between strains of the same species. Also, we found transposase genes and CRISPR arrays that suggest multiple encounters with foreign DNA. Presence of genomic exchange traits was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.

Rodent malaria parasites : genome organization & comparative genomics

NARCIS (Netherlands)

Kooij, Taco W.A.

2006-01-01

The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P.

Compósito cimentício reforçado com fibras de carbono para recuperação de monumentos históricos Cementicious composites made with steatite residue reinforced with carbon fiber

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T. H. Panzera

2010-12-01

Full Text Available O intemperismo, como fenômeno natural, atinge não somente materiais produzidos pelo homem, como também construções feitas de rochas naturais. No entanto, a evolução intempérica geralmente ocorre em ritmo muito lento em relação à duração dos empreendimentos humanos. Contudo, há situações em que este se acelera, afetando as obras de engenharia, sobretudo as obras de arte, monumentos históricos e fachadas de igrejas consideradas patrimônio da humanidade. O presente trabalho investigou o efeito da adição de fibra de carbono em compósitos cimentícios de resíduos de esteatito visando à recuperação de peças confeccionadas com este mineral, popularmente conhecido como "pedra-sabão". As propriedades físico-mecânicas tais como, densidade volumétrica e resistência mecânica à flexão foram investigadas neste experimento. Concluiu-se que a adição de fibra de carbono aumenta significativamente a resistência mecânica dos compósitos além da redução de seu peso específico, permitindo o reaproveitamento de um maior percentual de resíduos de esteatito no compósito final.Weathering is a natural phenomenon that affects both the engineering materials and natural rocks used for construction. The weathering evolution generally occurs at a slow pace when compared with the overall durability of the construction elements. However, in some cases the weathering may develop much quicker, affecting the engineering constructions and also historical buildings such as monuments and churches. This work investigated the effect of carbon fibre addition into cementitious composites made with residues of steatite, a mineral, also known as soapstone, for restoration of craftwork elements. The material's properties, such as bulk density and flexural strength were investigated. It is possible to conclude that the carbon fibre addition increases the flexural strength of the composites and reduces the specific weight, allowing for the use of a

Genome size analyses of Pucciniales reveal the largest fungal genomes.

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Tavares, Sílvia; Ramos, Ana Paula; Pires, Ana Sofia; Azinheira, Helena G; Caldeirinha, Patrícia; Link, Tobias; Abranches, Rita; Silva, Maria do Céu; Voegele, Ralf T; Loureiro, João; Talhinhas, Pedro

2014-01-01

Rust fungi (Basidiomycota, Pucciniales) are biotrophic plant pathogens which exhibit diverse complexities in their life cycles and host ranges. The completion of genome sequencing of a few rust fungi has revealed the occurrence of large genomes. Sequencing efforts for other rust fungi have been hampered by uncertainty concerning their genome sizes. Flow cytometry was recently applied to estimate the genome size of a few rust fungi, and confirmed the occurrence of large genomes in this order (averaging 225.3 Mbp, while the average for Basidiomycota was 49.9 Mbp and was 37.7 Mbp for all fungi). In this work, we have used an innovative and simple approach to simultaneously isolate nuclei from the rust and its host plant in order to estimate the genome size of 30 rust species by flow cytometry. Genome sizes varied over 10-fold, from 70 to 893 Mbp, with an average genome size value of 380.2 Mbp. Compared to the genome sizes of over 1800 fungi, Gymnosporangium confusum possesses the largest fungal genome ever reported (893.2 Mbp). Moreover, even the smallest rust genome determined in this study is larger than the vast majority of fungal genomes (94%). The average genome size of the Pucciniales is now of 305.5 Mbp, while the average Basidiomycota genome size has shifted to 70.4 Mbp and the average for all fungi reached 44.2 Mbp. Despite the fact that no correlation could be drawn between the genome sizes, the phylogenomics or the life cycle of rust fungi, it is interesting to note that rusts with Fabaceae hosts present genomes clearly larger than those with Poaceae hosts. Although this study comprises only a small fraction of the more than 7000 rust species described, it seems already evident that the Pucciniales represent a group where genome size expansion could be a common characteristic. This is in sharp contrast to sister taxa, placing this order in a relevant position in fungal genomics research.

Influência da adição e da modificação química de uma carga mineral nanoparticulada nas propriedades mecânicas e no envelhecimento térmico de compósitos poliuretano/sisal Influence of a nanoparticulate mineral filler addition and chemical modification of the mechanical properties and thermal aging of PU/Sisal composites

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Maria Roberta O. Pinto

2005-11-01

Full Text Available Este trabalho trata do efeito da hibridização do reforço, através da adição de uma carga mineral (bentonita nanoparticulada, no desempenho mecânico de compósitos poliuretano/sisal contendo 25% em massa de fibras de sisal e moldados por compressão. As propriedades mecânicas, de tração e impacto, dos sistemas compósitos estudados foram avaliadas em função do teor (0-10% em massa e de modificações químicas da carga mineral. Os efeitos do envelhecimento térmico nas propriedades tênseis (sigma, E, épsilon de compósitos selecionados também foram investigados. O reforço mineral (Bentonita sódica Brasgel-PA foi empregado em quatro formas, a saber: a como fornecido (sem tratamento, b tratado com ácido clorídrico (0,6N, c modificado com cloreto de dodecil dimetil benzil amônio (Dodigen e d modificado com brometo de cetil trimetil amônio (Cetremide. Os resultados indicam que a incorporação da bentonita eleva as propriedades mecânicas dos compósitos e que melhores propriedades foram obtidas quando a bentonita foi tratada com o ácido clorídrico. O envelhecimento térmico em tempos curtos (até 4 dias provocou elevação no módulo elástico e resistência na ruptura dos compósitos, o que foi atribuído à pós-cura da matriz. Em tempos longos (32 dias a exposição térmica causou decréscimo nas propriedades tênseis (sigma, E, épsilon dos compósitos investigados, o que foi atribuído à degradação oxidativa da matriz e dos reforços. O compósito mais resistente ao envelhecimento térmico foi o híbrido cuja carga mineral foi organofilizada com o sal Cetremide. Anáslies por DRX e MEV indicam que a estrutura dos compósitos híbridos é um misto de micro e nanocompósito.This work deals with filler hybridization effects, by the addition of a nanoparticulate mineral filler (bentonite, on the mechanical performance of compression molded Polyurethane/sisal composites with 25 wt % fiber content. Composite tensile and

Sequence Classification - TMBETA-GENOME | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ansmembrane helical proteins by applying statistical and machine learning methods to each amino acid sequenc.... Amino Acid Result of predicting β-barrel membrane protein with a statistical method using amino acid compo...sition. ( TMBETADISC-COMP ) Dipeptide Result of predicting β-barrel membrane protein with a statistic...ting β-barrel membrane protein with a statistical method using motifs. ( TMBETADISC-MOTIF ) SVM Result of pr

RPAN: rice pan-genome browser for ∼3000 rice genomes.

Science.gov (United States)

Sun, Chen; Hu, Zhiqiang; Zheng, Tianqing; Lu, Kuangchen; Zhao, Yue; Wang, Wensheng; Shi, Jianxin; Wang, Chunchao; Lu, Jinyuan; Zhang, Dabing; Li, Zhikang; Wei, Chaochun

2017-01-25

A pan-genome is the union of the gene sets of all the individuals of a clade or a species and it provides a new dimension of genome complexity with the presence/absence variations (PAVs) of genes among these genomes. With the progress of sequencing technologies, pan-genome study is becoming affordable for eukaryotes with large-sized genomes. The Asian cultivated rice, Oryza sativa L., is one of the major food sources for the world and a model organism in plant biology. Recently, the 3000 Rice Genome Project (3K RGP) sequenced more than 3000 rice genomes with a mean sequencing depth of 14.3×, which provided a tremendous resource for rice research. In this paper, we present a genome browser, Rice Pan-genome Browser (RPAN), as a tool to search and visualize the rice pan-genome derived from 3K RGP. RPAN contains a database of the basic information of 3010 rice accessions, including genomic sequences, gene annotations, PAV information and gene expression data of the rice pan-genome. At least 12 000 novel genes absent in the reference genome were included. RPAN also provides multiple search and visualization functions. RPAN can be a rich resource for rice biology and rice breeding. It is available at http://cgm.sjtu.edu.cn/3kricedb/ or http://www.rmbreeding.cn/pan3k. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

Science.gov (United States)

CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of human, animals, microorganisms, and plants. Success of such genome editing is highly dependent on the availability of suitable target sites in the genomes to be edited. Many specific t...

Genomics Portals: integrative web-platform for mining genomics data.

Science.gov (United States)

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Viabilidade de utilização de um compósito de matriz cerâmica com cargas recicláveis na fabricação de equipamentos solares

OpenAIRE

Mota, Maria Kalionara de Freitas

2012-01-01

Foi concebido e estudado um compósito de matriz cerâmica composto por gesso, cimento, EPS, pneu, PET e água para construir protótipos solares competitivos em eficiência com outros equipamentos de materiais convencionais já construídos e estudados e de menor custo de fabricação. Foram construídos dois fornos/fogões solares tipo caixa, uma caixa térmica para ser refrigerada por energia solar, um secador solar e um fogão solar a concentração. Foram determinadas as proporções dos materiais ...

i-Genome: A database to summarize oligonucleotide data in genomes

Directory of Open Access Journals (Sweden)

Chang Yu-Chung

2004-10-01

Full Text Available Abstract Background Information on the occurrence of sequence features in genomes is crucial to comparative genomics, evolutionary analysis, the analyses of regulatory sequences and the quantitative evaluation of sequences. Computing the frequencies and the occurrences of a pattern in complete genomes is time-consuming. Results The proposed database provides information about sequence features generated by exhaustively computing the sequences of the complete genome. The repetitive elements in the eukaryotic genomes, such as LINEs, SINEs, Alu and LTR, are obtained from Repbase. The database supports various complete genomes including human, yeast, worm, and 128 microbial genomes. Conclusions This investigation presents and implements an efficiently computational approach to accumulate the occurrences of the oligonucleotides or patterns in complete genomes. A database is established to maintain the information of the sequence features, including the distributions of oligonucleotide, the gene distribution, the distribution of repetitive elements in genomes and the occurrences of the oligonucleotides. The database can provide more effective and efficient way to access the repetitive features in genomes.

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics1[C][W

Science.gov (United States)

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F.X.; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-01-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species. PMID:23184232

Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute’s genomic medicine portfolio

Science.gov (United States)

Manolio, Teri A.

2016-01-01

Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual’s genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of “Genomic Medicine Meetings,” under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and diffficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI’s genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so. PMID:27612677

Comparing Mycobacterium tuberculosis genomes using genome topology networks.

Science.gov (United States)

Jiang, Jianping; Gu, Jianlei; Zhang, Liang; Zhang, Chenyi; Deng, Xiao; Dou, Tonghai; Zhao, Guoping; Zhou, Yan

2015-02-14

Over the last decade, emerging research methods, such as comparative genomic analysis and phylogenetic study, have yielded new insights into genotypes and phenotypes of closely related bacterial strains. Several findings have revealed that genomic structural variations (SVs), including gene gain/loss, gene duplication and genome rearrangement, can lead to different phenotypes among strains, and an investigation of genes affected by SVs may extend our knowledge of the relationships between SVs and phenotypes in microbes, especially in pathogenic bacteria. In this work, we introduce a 'Genome Topology Network' (GTN) method based on gene homology and gene locations to analyze genomic SVs and perform phylogenetic analysis. Furthermore, the concept of 'unfixed ortholog' has been proposed, whose members are affected by SVs in genome topology among close species. To improve the precision of 'unfixed ortholog' recognition, a strategy to detect annotation differences and complete gene annotation was applied. To assess the GTN method, a set of thirteen complete M. tuberculosis genomes was analyzed as a case study. GTNs with two different gene homology-assigning methods were built, the Clusters of Orthologous Groups (COG) method and the orthoMCL clustering method, and two phylogenetic trees were constructed accordingly, which may provide additional insights into whole genome-based phylogenetic analysis. We obtained 24 unfixable COG groups, of which most members were related to immunogenicity and drug resistance, such as PPE-repeat proteins (COG5651) and transcriptional regulator TetR gene family members (COG1309). The GTN method has been implemented in PERL and released on our website. The tool can be downloaded from http://homepage.fudan.edu.cn/zhouyan/gtn/ , and allows re-annotating the 'lost' genes among closely related genomes, analyzing genes affected by SVs, and performing phylogenetic analysis. With this tool, many immunogenic-related and drug resistance-related genes

A universal genomic coordinate translator for comparative genomics.

Science.gov (United States)

Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

2014-06-30

Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across

Genomics Portals: integrative web-platform for mining genomics data

Directory of Open Access Journals (Sweden)

Ghosh Krishnendu

2010-01-01

Full Text Available Abstract Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc, and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Genomic selection: genome-wide prediction in plant improvement.

Science.gov (United States)

Desta, Zeratsion Abera; Ortiz, Rodomiro

2014-09-01

Association analysis is used to measure relations between markers and quantitative trait loci (QTL). Their estimation ignores genes with small effects that trigger underpinning quantitative traits. By contrast, genome-wide selection estimates marker effects across the whole genome on the target population based on a prediction model developed in the training population (TP). Whole-genome prediction models estimate all marker effects in all loci and capture small QTL effects. Here, we review several genomic selection (GS) models with respect to both the prediction accuracy and genetic gain from selection. Phenotypic selection or marker-assisted breeding protocols can be replaced by selection, based on whole-genome predictions in which phenotyping updates the model to build up the prediction accuracy. Copyright © 2014 Elsevier Ltd. All rights reserved.

OryzaGenome: Genome Diversity Database of Wild Oryza Species

KAUST Repository

Ohyanagi, Hajime

2015-11-18

The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a textbased browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tabdelimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/ scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/.

Using Partial Genomic Fosmid Libraries for Sequencing CompleteOrganellar Genomes

Energy Technology Data Exchange (ETDEWEB)

McNeal, Joel R.; Leebens-Mack, James H.; Arumuganathan, K.; Kuehl, Jennifer V.; Boore, Jeffrey L.; dePamphilis, Claude W.

2005-08-26

Organellar genome sequences provide numerous phylogenetic markers and yield insight into organellar function and molecular evolution. These genomes are much smaller in size than their nuclear counterparts; thus, their complete sequencing is much less expensive than total nuclear genome sequencing, making broader phylogenetic sampling feasible. However, for some organisms it is challenging to isolate plastid DNA for sequencing using standard methods. To overcome these difficulties, we constructed partial genomic libraries from total DNA preparations of two heterotrophic and two autotrophic angiosperm species using fosmid vectors. We then used macroarray screening to isolate clones containing large fragments of plastid DNA. A minimum tiling path of clones comprising the entire genome sequence of each plastid was selected, and these clones were shotgun-sequenced and assembled into complete genomes. Although this method worked well for both heterotrophic and autotrophic plants, nuclear genome size had a dramatic effect on the proportion of screened clones containing plastid DNA and, consequently, the overall number of clones that must be screened to ensure full plastid genome coverage. This technique makes it possible to determine complete plastid genome sequences for organisms that defy other available organellar genome sequencing methods, especially those for which limited amounts of tissue are available.

Polimerização complementar em autoclave, microondas e estufa de um compósito restaurador direto = The effect of post-cure heating in autoclave, microwave oven and conventional oven on direct composite resin

Directory of Open Access Journals (Sweden)

Arossi, Guilherme Anziliero

2007-01-01

Full Text Available Com o objetivo de tornar o processo de confecção de restaurações indiretas mais acessível, reduzindo seus custos com a resina utilizada e os métodos de polimerização complementar, este estudo testou a possibilidade de se utilizar resinas diretas com métodos de polimerização complementar alternativos. Corpos de prova foram confeccionados com a resina Charisma e fotopolimerizados por 20 segundos. Em seguida as amostras foram submetidas à polimerização complementar em autoclave, microondas e estufa. Foram estabelecidos dois grupos controles: um controle negativo, que consistiu na utilização da resina Charisma fotopolimerizada convencionalmente (20s; e um grupo controle positivo, formado por amostras do compósito restaurador indireto Targis. O ensaio de microdureza Knoop foi realizado após uma semana de armazenagem e os resultados submetidos à análise estatística. Os três métodos de polimerização complementar propostos determinaram um aumento na microdureza do compósito restaurador direto quando comparado ao controle negativo (p 0,05. Conclui-se que, considerando o desenho experimental deste estudo, a polimerização complementar em autoclave, microondas ou estufa aumenta a microdureza da resina Charisma previamente fotopolimerizada

Grass genomes

OpenAIRE

Bennetzen, Jeffrey L.; SanMiguel, Phillip; Chen, Mingsheng; Tikhonov, Alexander; Francki, Michael; Avramova, Zoya

1998-01-01

For the most part, studies of grass genome structure have been limited to the generation of whole-genome genetic maps or the fine structure and sequence analysis of single genes or gene clusters. We have investigated large contiguous segments of the genomes of maize, sorghum, and rice, primarily focusing on intergenic spaces. Our data indicate that much (>50%) of the maize genome is composed of interspersed repetitive DNAs, primarily nested retrotransposons that in...

Fulltext PDF

Indian Academy of Sciences (India)

2016-09-28

Sep 28, 2016 ... acute toxicity of Triphala Mashi, an Ayurvedic formulation. J. Herb. Pharmacother. ... status in the liver and kidney of young and aged rats. Cell. Biochem. Funct. ... acetaminophen-induced hepatotoxicity in mice. J. Pharmacol.

Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

Science.gov (United States)

Smith, David Roy

2017-05-01

Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise. This increase is largely because some journals have created a new category of manuscript called genome reports, which are short, fast-tracked papers describing a chromosome sequence(s), its GenBank accession number and little else. In 2015, for example, more than 2000 genome reports were published, and 2016 is poised to bring even more. Here, I highlight the growing popularity of genome reports and discuss their merits, drawbacks and impact on science and the academic publication infrastructure. Genome reports can be excellent assets for the research community, but they are also being used as quick and easy routes to a publication, and in some instances they are not peer reviewed. One of the best arguments for genome reports is that they are a citable, user-generated genomic resource providing essential methodological and biological information, which may not be present in the sequence database. But they are expensive and time-consuming avenues for achieving such a goal. © The Author 2016. Published by Oxford University Press.

Estudo das propriedades de compósitos biodegradáveis de amido/glúten de milho/glicerol reforçados com fibras de sisal Study of properties of biodegradable composites of starch/gluten/glycerol reinforced with sisal fibers

Directory of Open Access Journals (Sweden)

Elisângela Corradini

2008-01-01

Full Text Available Neste estudo, fibras de sisal foram utilizadas como reforço para a matriz constituída de amido, glúten de milho e glicerol. O teor de fibra em relação a matriz variou de 5 a 30%. O processamento da matriz e dos compósitos foi realizado em um reômetro de torque Haake à 130 °C, 50 rpm por 10 minutos. As misturas obtidas foram moldadas por compressão à quente. As propriedades mecânicas; termodinâmico-mecânico (DMTA e de absorção de água foram investigadas em função do teor de fibras na matriz de amido/glúten de milho/glicerol. O aumento do conteúdo de fibra provocou uma melhoria nas propriedades mecânicas dos compósitos com relação à matriz. O compósito reforçado com 30% de fibra de sisal apresentou aumento no módulo de elasticidade e tensão na ruptura de aproximadamente de 560 e 162%, respectivamente e diminuição nos valores de elongação na ruptura de 81%. Os resultados obtidos por DMTA mostraram aumento progressivo do módulo de armazenamento (E' e diminuição do módulo de amortecimento (tan d com o aumento do teor de fibra, confirmando o efeito de reforço das fibras de sisal na matriz de amido/glúten de milho/glicerol. A incorporação das fibras na matriz também provocou diminuição da absorção de umidade e no coeficiente de difusão de água. A análise da morfologia dos compósitos mostrou boa dispersão das fibras na matriz.Biocomposites using starch/gluten/glycerol as matrix and sisal fibers were produced by melt-mixing in an intensive batch mixer connected to a torque rheometer at 130 °C. The samples were compression molded and than characterized by water absorption and mechanical test. In tensile test, the increasing in the Young's modulus and ultimate tensile strenght were respectively of aproximately 560 and 162% in relation to matrix, whereas elongation at break decreased. The storage modulus increased with increasing fiber content whereas tan d curves decreased, confirming the reinforcing

Genome update: the 1000th genome - a cautionary tale

DEFF Research Database (Denmark)

Lagesen, Karin; Ussery, David; Wassenaar, Gertrude Maria

2010-01-01

conclusions for example about the largest bacterial genome sequenced. Biological diversity is far greater than many have thought. For example, analysis of multiple Escherichia coli genomes has led to an estimate of around 45 000 gene families more genes than are recognized in the human genome. Moreover......There are now more than 1000 sequenced prokaryotic genomes deposited in public databases and available for analysis. Currently, although the sequence databases GenBank, DNA Database of Japan and EMBL are synchronized continually, there are slight differences in content at the genomes level...... for a variety of logistical reasons, including differences in format and loading errors, such as those caused by file transfer protocol interruptions. This means that the 1000th genome will be different in the various databases. Some of the data on the highly accessed web pages are inaccurate, leading to false...

Pre-genomic, genomic and post-genomic study of microbial communities involved in bioenergy.

Science.gov (United States)

Rittmann, Bruce E; Krajmalnik-Brown, Rosa; Halden, Rolf U

2008-08-01

Microorganisms can produce renewable energy in large quantities and without damaging the environment or disrupting food supply. The microbial communities must be robust and self-stabilizing, and their essential syntrophies must be managed. Pre-genomic, genomic and post-genomic tools can provide crucial information about the structure and function of these microbial communities. Applying these tools will help accelerate the rate at which microbial bioenergy processes move from intriguing science to real-world practice.

Effect of light curing tip distance and resin shade on microhardness of a hybrid resin composite Efeito da distância da ponta do aparelho de fotoativação e da cor na microdureza superficial de um compósito híbrido

Directory of Open Access Journals (Sweden)

Flávio Henrique Baggio Aguiar

2005-12-01

Full Text Available Resin composite shades and resin composite polymerization performed with a distanced light tip are factors that can affect polymerization effectiveness. Thisin vitro study aimed to evaluate the influence of curing tip distance and resin shade on the microhardness of a hybrid resin composite (Z250 - 3M ESPE. Forty-five resin composite specimens were randomly prepared and divided into nine experimental groups (n = 5: three curing tip distances (2 mm, 4 mm, and 8 mm and three resin shades (A1, A3.5, and C2. All samples were polymerized with a continuous output at 550 mW/cm². After 24 hours, Knoop microhardness measurements were obtained on the top and bottom surfaces of the sample, with a load of 25 grams for 10 seconds. Five indentations were performed on each surface of each sample. Results showed that bottom surface samples light-cured at 2 mm and 4 mm presented significantly higher hardness values than samples light-cured at 8 mm. The resin shade A1 presented higher hardness values and was statistically different from C2. The resin shade A3.5 did not present statistical differences from A1 and C2. For the top surface, there were no statistical differences among the curing tip distances. For all experimental conditions, the top surface showed higher hardness values than the bottom surface. It was concluded that light curing tip distance and resin shade are important factors to be considered for obtaining adequate polymerization.A cor do compósito e a polimerização realizada com a ponta do aparelho de fotoativação distante da superfície do compósito são fatores que podem afetar a efetividade de polimerização. Assim, o objetivo deste estudo in vitro foi avaliar a influência desses fatores na microdureza superficial de um compósito híbrido (Z250 - 3M ESPE. Quarenta e cinco espécimes de compósito foram aleatoriamente preparados de acordo com os nove grupos experimentais (n = 5: três distâncias de fotoativação (2 mm, 4 mm e 8 mm e

Genome Surfing As Driver of Microbial Genomic Diversity.

Science.gov (United States)

Choudoir, Mallory J; Panke-Buisse, Kevin; Andam, Cheryl P; Buckley, Daniel H

2017-08-01

Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

Estudo experimental do reforço à flexão em vigas de concreto armado com balanço utilizando compósitos com tecidos de fibras de carbono

OpenAIRE

Araújo, Ana; Sánchez, Emil; Velasco, Marta

2004-01-01

Esse trabalho apresenta um estudo sobre o comportamento e o desempenho de vigas de concreto armado reforçadas à flexão utilizando-se compósitos de fibra de carbono. O programa experimental constituído pelo ensaio de sete vigas biapoiadas com um vão em balanço, todas com a mesma seção transversal, armaduras de aço e vãos idênticos, sendo o momento positivo máximo igual ao do momento negativo máximo. O concreto utilizado foi projetado para fornecer uma resistência à compressão de 20 MPa e o aço...

Deep whole-genome sequencing of 90 Han Chinese genomes.

Science.gov (United States)

Lan, Tianming; Lin, Haoxiang; Zhu, Wenjuan; Laurent, Tellier Christian Asker Melchior; Yang, Mengcheng; Liu, Xin; Wang, Jun; Wang, Jian; Yang, Huanming; Xu, Xun; Guo, Xiaosen

2017-09-01

Next-generation sequencing provides a high-resolution insight into human genetic information. However, the focus of previous studies has primarily been on low-coverage data due to the high cost of sequencing. Although the 1000 Genomes Project and the Haplotype Reference Consortium have both provided powerful reference panels for imputation, low-frequency and novel variants remain difficult to discover and call with accuracy on the basis of low-coverage data. Deep sequencing provides an optimal solution for the problem of these low-frequency and novel variants. Although whole-exome sequencing is also a viable choice for exome regions, it cannot account for noncoding regions, sometimes resulting in the absence of important, causal variants. For Han Chinese populations, the majority of variants have been discovered based upon low-coverage data from the 1000 Genomes Project. However, high-coverage, whole-genome sequencing data are limited for any population, and a large amount of low-frequency, population-specific variants remain uncharacterized. We have performed whole-genome sequencing at a high depth (∼×80) of 90 unrelated individuals of Chinese ancestry, collected from the 1000 Genomes Project samples, including 45 Northern Han Chinese and 45 Southern Han Chinese samples. Eighty-three of these 90 have been sequenced by the 1000 Genomes Project. We have identified 12 568 804 single nucleotide polymorphisms, 2 074 210 short InDels, and 26 142 structural variations from these 90 samples. Compared to the Han Chinese data from the 1000 Genomes Project, we have found 7 000 629 novel variants with low frequency (defined as minor allele frequency genome. Compared to the 1000 Genomes Project, these Han Chinese deep sequencing data enhance the characterization of a large number of low-frequency, novel variants. This will be a valuable resource for promoting Chinese genetics research and medical development. Additionally, it will provide a valuable supplement to the 1000

Fungal Genomics Program

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor

2012-03-12

The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

Comparative Genome Analysis and Genome Evolution

NARCIS (Netherlands)

Snel, Berend

2002-01-01

This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies.

Genome projects and the functional-genomic era.

Science.gov (United States)

Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

2005-12-01

The problems we face today in public health as a result of the -- fortunately -- increasing age of people and the requirements of developing countries create an urgent need for new and innovative approaches in medicine and in agronomics. Genomic and functional genomic approaches have a great potential to at least partially solve these problems in the future. Important progress has been made by procedures to decode genomic information of humans, but also of other key organisms. The basic comprehension of genomic information (and its transfer) should now give us the possibility to pursue the next important step in life science eventually leading to a basic understanding of biological information flow; the elucidation of the function of all genes and correlative products encoded in the genome, as well as the discovery of their interactions in a molecular context and the response to environmental factors. As a result of the sequencing projects, we are now able to ask important questions about sequence variation and can start to comprehensively study the function of expressed genes on different levels such as RNA, protein or the cell in a systematic context including underlying networks. In this article we review and comment on current trends in large-scale systematic biological research. A particular emphasis is put on technology developments that can provide means to accomplish the tasks of future lines of functional genomics.

GAAP: Genome-organization-framework-Assisted Assembly Pipeline for prokaryotic genomes.

Science.gov (United States)

Yuan, Lina; Yu, Yang; Zhu, Yanmin; Li, Yulai; Li, Changqing; Li, Rujiao; Ma, Qin; Siu, Gilman Kit-Hang; Yu, Jun; Jiang, Taijiao; Xiao, Jingfa; Kang, Yu

2017-01-25

Next-generation sequencing (NGS) technologies have greatly promoted the genomic study of prokaryotes. However, highly fragmented assemblies due to short reads from NGS are still a limiting factor in gaining insights into the genome biology. Reference-assisted tools are promising in genome assembly, but tend to result in false assembly when the assigned reference has extensive rearrangements. Herein, we present GAAP, a genome assembly pipeline for scaffolding based on core-gene-defined Genome Organizational Framework (cGOF) described in our previous study. Instead of assigning references, we use the multiple-reference-derived cGOFs as indexes to assist in order and orientation of the scaffolds and build a skeleton structure, and then use read pairs to extend scaffolds, called local scaffolding, and distinguish between true and chimeric adjacencies in the scaffolds. In our performance tests using both empirical and simulated data of 15 genomes in six species with diverse genome size, complexity, and all three categories of cGOFs, GAAP outcompetes or achieves comparable results when compared to three other reference-assisted programs, AlignGraph, Ragout and MeDuSa. GAAP uses both cGOF and pair-end reads to create assemblies in genomic scale, and performs better than the currently available reference-assisted assembly tools as it recovers more assemblies and makes fewer false locations, especially for species with extensive rearranged genomes. Our method is a promising solution for reconstruction of genome sequence from short reads of NGS.

The Perennial Ryegrass GenomeZipper – Targeted Use of Genome Resources for Comparative Grass Genomics

DEFF Research Database (Denmark)

Pfeiffer, Matthias; Martis, Mihaela; Asp, Torben

2013-01-01

(Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold......Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass...... to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous...

Population Genomics of Infectious and Integrated Wolbachia pipientis Genomes in Drosophila ananassae

Science.gov (United States)

Choi, Jae Young; Bubnell, Jaclyn E.; Aquadro, Charles F.

2015-01-01

Coevolution between Drosophila and its endosymbiont Wolbachia pipientis has many intriguing aspects. For example, Drosophila ananassae hosts two forms of W. pipientis genomes: One being the infectious bacterial genome and the other integrated into the host nuclear genome. Here, we characterize the infectious and integrated genomes of W. pipientis infecting D. ananassae (wAna), by genome sequencing 15 strains of D. ananassae that have either the infectious or integrated wAna genomes. Results indicate evolutionarily stable maternal transmission for the infectious wAna genome suggesting a relatively long-term coevolution with its host. In contrast, the integrated wAna genome showed pseudogene-like characteristics accumulating many variants that are predicted to have deleterious effects if present in an infectious bacterial genome. Phylogenomic analysis of sequence variation together with genotyping by polymerase chain reaction of large structural variations indicated several wAna variants among the eight infectious wAna genomes. In contrast, only a single wAna variant was found among the seven integrated wAna genomes examined in lines from Africa, south Asia, and south Pacific islands suggesting that the integration occurred once from a single infectious wAna genome and then spread geographically. Further analysis revealed that for all D. ananassae we examined with the integrated wAna genomes, the majority of the integrated wAna genomic regions is represented in at least two copies suggesting a double integration or single integration followed by an integrated genome duplication. The possible evolutionary mechanism underlying the widespread geographical presence of the duplicate integration of the wAna genome is an intriguing question remaining to be answered. PMID:26254486

Dramatic improvement in genome assembly achieved using doubled-haploid genomes.

Science.gov (United States)

Zhang, Hong; Tan, Engkong; Suzuki, Yutaka; Hirose, Yusuke; Kinoshita, Shigeharu; Okano, Hideyuki; Kudoh, Jun; Shimizu, Atsushi; Saito, Kazuyoshi; Watabe, Shugo; Asakawa, Shuichi

2014-10-27

Improvement in de novo assembly of large genomes is still to be desired. Here, we improved draft genome sequence quality by employing doubled-haploid individuals. We sequenced wildtype and doubled-haploid Takifugu rubripes genomes, under the same conditions, using the Illumina platform and assembled contigs with SOAPdenovo2. We observed 5.4-fold and 2.6-fold improvement in the sizes of the N50 contig and scaffold of doubled-haploid individuals, respectively, compared to the wildtype, indicating that the use of a doubled-haploid genome aids in accurate genome analysis.

Cancer genomics

DEFF Research Database (Denmark)

Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

2007-01-01

Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

Personal genomics services: whose genomes?

Science.gov (United States)

Gurwitz, David; Bregman-Eschet, Yael

2009-07-01

New companies offering personal whole-genome information services over the internet are dynamic and highly visible players in the personal genomics field. For fees currently ranging from US$399 to US$2500 and a vial of saliva, individuals can now purchase online access to their individual genetic information regarding susceptibility to a range of chronic diseases and phenotypic traits based on a genome-wide SNP scan. Most of the companies offering such services are based in the United States, but their clients may come from nearly anywhere in the world. Although the scientific validity, clinical utility and potential future implications of such services are being hotly debated, several ethical and regulatory questions related to direct-to-consumer (DTC) marketing strategies of genetic tests have not yet received sufficient attention. For example, how can we minimize the risk of unauthorized third parties from submitting other people's DNA for testing? Another pressing question concerns the ownership of (genotypic and phenotypic) information, as well as the unclear legal status of customers regarding their own personal information. Current legislation in the US and Europe falls short of providing clear answers to these questions. Until the regulation of personal genomics services catches up with the technology, we call upon commercial providers to self-regulate and coordinate their activities to minimize potential risks to individual privacy. We also point out some specific steps, along the trustee model, that providers of DTC personal genomics services as well as regulators and policy makers could consider for addressing some of the concerns raised below.

Insights into structural variations and genome rearrangements in prokaryotic genomes.

Science.gov (United States)

Periwal, Vinita; Scaria, Vinod

2015-01-01

Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Parasite Genome Projects and the Trypanosoma cruzi Genome Initiative

Directory of Open Access Journals (Sweden)

Wim Degrave

1997-11-01

Full Text Available Since the start of the human genome project, a great number of genome projects on other "model" organism have been initiated, some of them already completed. Several initiatives have also been started on parasite genomes, mainly through support from WHO/TDR, involving North-South and South-South collaborations, and great hopes are vested in that these initiatives will lead to new tools for disease control and prevention, as well as to the establishment of genomic research technology in developing countries. The Trypanosoma cruzi genome project, using the clone CL-Brener as starting point, has made considerable progress through the concerted action of more than 20 laboratories, most of them in the South. A brief overview of the current state of the project is given

IGESS: a statistical approach to integrating individual-level genotype data and summary statistics in genome-wide association studies.

Science.gov (United States)

Dai, Mingwei; Ming, Jingsi; Cai, Mingxuan; Liu, Jin; Yang, Can; Wan, Xiang; Xu, Zongben

2017-09-15

Results from genome-wide association studies (GWAS) suggest that a complex phenotype is often affected by many variants with small effects, known as 'polygenicity'. Tens of thousands of samples are often required to ensure statistical power of identifying these variants with small effects. However, it is often the case that a research group can only get approval for the access to individual-level genotype data with a limited sample size (e.g. a few hundreds or thousands). Meanwhile, summary statistics generated using single-variant-based analysis are becoming publicly available. The sample sizes associated with the summary statistics datasets are usually quite large. How to make the most efficient use of existing abundant data resources largely remains an open question. In this study, we propose a statistical approach, IGESS, to increasing statistical power of identifying risk variants and improving accuracy of risk prediction by i ntegrating individual level ge notype data and s ummary s tatistics. An efficient algorithm based on variational inference is developed to handle the genome-wide analysis. Through comprehensive simulation studies, we demonstrated the advantages of IGESS over the methods which take either individual-level data or summary statistics data as input. We applied IGESS to perform integrative analysis of Crohns Disease from WTCCC and summary statistics from other studies. IGESS was able to significantly increase the statistical power of identifying risk variants and improve the risk prediction accuracy from 63.2% ( ±0.4% ) to 69.4% ( ±0.1% ) using about 240 000 variants. The IGESS software is available at https://github.com/daviddaigithub/IGESS . zbxu@xjtu.edu.cn or xwan@comp.hkbu.edu.hk or eeyang@hkbu.edu.hk. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Short and long-term genome stability analysis of prokaryotic genomes.

Science.gov (United States)

Brilli, Matteo; Liò, Pietro; Lacroix, Vincent; Sagot, Marie-France

2013-05-08

Gene organization dynamics is actively studied because it provides useful evolutionary information, makes functional annotation easier and often enables to characterize pathogens. There is therefore a strong interest in understanding the variability of this trait and the possible correlations with life-style. Two kinds of events affect genome organization: on one hand translocations and recombinations change the relative position of genes shared by two genomes (i.e. the backbone gene order); on the other, insertions and deletions leave the backbone gene order unchanged but they alter the gene neighborhoods by breaking the syntenic regions. A complete picture about genome organization evolution therefore requires to account for both kinds of events. We developed an approach where we model chromosomes as graphs on which we compute different stability estimators; we consider genome rearrangements as well as the effect of gene insertions and deletions. In a first part of the paper, we fit a measure of backbone gene order conservation (hereinafter called backbone stability) against phylogenetic distance for over 3000 genome comparisons, improving existing models for the divergence in time of backbone stability. Intra- and inter-specific comparisons were treated separately to focus on different time-scales. The use of multiple genomes of a same species allowed to identify genomes with diverging gene order with respect to their conspecific. The inter-species analysis indicates that pathogens are more often unstable with respect to non-pathogens. In a second part of the text, we show that in pathogens, gene content dynamics (insertions and deletions) have a much more dramatic effect on genome organization stability than backbone rearrangements. In this work, we studied genome organization divergence taking into account the contribution of both genome order rearrangements and genome content dynamics. By studying species with multiple sequenced genomes available, we were

Genomic Data Commons and Genomic Cloud Pilots - Google Hangout

Science.gov (United States)

Join us for a live, moderated discussion about two NCI efforts to expand access to cancer genomics data: the Genomic Data Commons and Genomic Cloud Pilots. NCI subject matters experts will include Louis M. Staudt, M.D., Ph.D., Director Center for Cancer Genomics, Warren Kibbe, Ph.D., Director, NCI Center for Biomedical Informatics and Information Technology, and moderated by Anthony Kerlavage, Ph.D., Chief, Cancer Informatics Branch, Center for Biomedical Informatics and Information Technology. We welcome your questions before and during the Hangout on Twitter using the hashtag #AskNCI.

The genomes and comparative genomics of Lactobacillus delbrueckii phages.

Science.gov (United States)

Riipinen, Katja-Anneli; Forsman, Päivi; Alatossava, Tapani

2011-07-01

Lactobacillus delbrueckii phages are a great source of genetic diversity. Here, the genome sequences of Lb. delbrueckii phages LL-Ku, c5 and JCL1032 were analyzed in detail, and the genetic diversity of Lb. delbrueckii phages belonging to different taxonomic groups was explored. The lytic isometric group b phages LL-Ku (31,080 bp) and c5 (31,841 bp) showed a minimum nucleotide sequence identity of 90% over about three-fourths of their genomes. The genomic locations of their lysis modules were unique, and the genomes featured several putative overlapping transcription units of genes. LL-Ku and c5 virions displayed peptidoglycan hydrolytic activity associated with a ~36-kDa protein similar in size to the endolysin. Unexpectedly, the 49,433-bp genome of the prolate phage JCL1032 (temperate, group c) revealed a conserved gene order within its structural genes. Lb. delbrueckii phages representing groups a (a phage LL-H), b and c possessed only limited protein sequence homology. Genomic comparison of LL-Ku and c5 suggested that diversification of Lb. delbrueckii phages is mainly due to insertions, deletions and recombination. For the first time, the complete genome sequences of group b and c Lb. delbrueckii phages are reported.

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry.

Science.gov (United States)

Williams, Antony J; Grulke, Christopher M; Edwards, Jeff; McEachran, Andrew D; Mansouri, Kamel; Baker, Nancy C; Patlewicz, Grace; Shah, Imran; Wambaugh, John F; Judson, Richard S; Richard, Ann M

2017-11-28

Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and computational toxicology communities. The U.S. Environmental Protection Agency's (EPA) web-based CompTox Chemistry Dashboard is addressing these needs by integrating diverse types of relevant domain data through a cheminformatics layer, built upon a database of curated substances linked to chemical structures. These data include physicochemical, environmental fate and transport, exposure, usage, in vivo toxicity, and in vitro bioassay data, surfaced through an integration hub with link-outs to additional EPA data and public domain online resources. Batch searching allows for direct chemical identifier (ID) mapping and downloading of multiple data streams in several different formats. This facilitates fast access to available structure, property, toxicity, and bioassay data for collections of chemicals (hundreds to thousands at a time). Advanced search capabilities are available to support, for example, non-targeted analysis and identification of chemicals using mass spectrometry. The contents of the chemistry database, presently containing ~ 760,000 substances, are available as public domain data for download. The chemistry content underpinning the Dashboard has been aggregated over the past 15 years by both manual and auto-curation techniques within EPA's DSSTox project. DSSTox chemical content is subject to strict quality controls to enforce consistency among chemical substance-structure identifiers, as well as list curation review to ensure accurate linkages of DSSTox substances to chemical lists and associated data. The Dashboard, publicly launched in April 2016, has expanded considerably in content and user traffic over the past year. It is continuously evolving with the growth of DSSTox into high-interest or data-rich domains of interest to EPA, such

Genome-wide characterization of centromeric satellites from multiple mammalian genomes.

Science.gov (United States)

Alkan, Can; Cardone, Maria Francesca; Catacchio, Claudia Rita; Antonacci, Francesca; O'Brien, Stephen J; Ryder, Oliver A; Purgato, Stefania; Zoli, Monica; Della Valle, Giuliano; Eichler, Evan E; Ventura, Mario

2011-01-01

Despite its importance in cell biology and evolution, the centromere has remained the final frontier in genome assembly and annotation due to its complex repeat structure. However, isolation and characterization of the centromeric repeats from newly sequenced species are necessary for a complete understanding of genome evolution and function. In recent years, various genomes have been sequenced, but the characterization of the corresponding centromeric DNA has lagged behind. Here, we present a computational method (RepeatNet) to systematically identify higher-order repeat structures from unassembled whole-genome shotgun sequence and test whether these sequence elements correspond to functional centromeric sequences. We analyzed genome datasets from six species of mammals representing the diversity of the mammalian lineage, namely, horse, dog, elephant, armadillo, opossum, and platypus. We define candidate monomer satellite repeats and demonstrate centromeric localization for five of the six genomes. Our analysis revealed the greatest diversity of centromeric sequences in horse and dog in contrast to elephant and armadillo, which showed high-centromeric sequence homogeneity. We could not isolate centromeric sequences within the platypus genome, suggesting that centromeres in platypus are not enriched in satellite DNA. Our method can be applied to the characterization of thousands of other vertebrate genomes anticipated for sequencing in the near future, providing an important tool for annotation of centromeres.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

DEFF Research Database (Denmark)

Machado, Henrique; Gram, Lone

2017-01-01

was widespread and abundant in the genus, suggesting a role in genomic evolution. The high genetic variability and indications of genetic exchange make it difficult to elucidate genome evolutionary paths and raise the awareness of the roles of foreign DNA in the genomic evolution of environmental organisms.......Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand...... the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationships using several analyses (16S rRNA, MLSA, fur, amino-acid usage, ANI), which allowed us to identify two...

SNUGB: a versatile genome browser supporting comparative and functional fungal genomics

Directory of Open Access Journals (Sweden)

Kim Seungill

2008-12-01

Full Text Available Abstract Background Since the full genome sequences of Saccharomyces cerevisiae were released in 1996, genome sequences of over 90 fungal species have become publicly available. The heterogeneous formats of genome sequences archived in different sequencing centers hampered the integration of the data for efficient and comprehensive comparative analyses. The Comparative Fungal Genomics Platform (CFGP was developed to archive these data via a single standardized format that can support multifaceted and integrated analyses of the data. To facilitate efficient data visualization and utilization within and across species based on the architecture of CFGP and associated databases, a new genome browser was needed. Results The Seoul National University Genome Browser (SNUGB integrates various types of genomic information derived from 98 fungal/oomycete (137 datasets and 34 plant and animal (38 datasets species, graphically presents germane features and properties of each genome, and supports comparison between genomes. The SNUGB provides three different forms of the data presentation interface, including diagram, table, and text, and six different display options to support visualization and utilization of the stored information. Information for individual species can be quickly accessed via a new tool named the taxonomy browser. In addition, SNUGB offers four useful data annotation/analysis functions, including 'BLAST annotation.' The modular design of SNUGB makes its adoption to support other comparative genomic platforms easy and facilitates continuous expansion. Conclusion The SNUGB serves as a powerful platform supporting comparative and functional genomics within the fungal kingdom and also across other kingdoms. All data and functions are available at the web site http://genomebrowser.snu.ac.kr/.

New treatment option for women with hormone-sensitive breast cancer

Science.gov (United States)

A drug used for treating breast cancer, known as exemestane, is more effective than a common breast cancer prevention drug, tamoxifen, in preventing breast cancer recurrence in young women who also receive post-surgical treatment to suppress ovarian funct

Propriedades mecânicas de materiais compósitos à base de cimento Portland e resina epoxi Mechanical properties of composite materials based on portland cement and epoxy resin

Directory of Open Access Journals (Sweden)

T. H. Panzera

2010-03-01

Full Text Available O estudo de materiais de alto desempenho e multifuncionais, como os compósitos poliméricos cimentícios, tem sido o foco de inúmeras pesquisas na indústria da construção civil. Este trabalho investiga o efeito da combinação de uma fase polimérica termorrígida, uma resina epóxi, com cimento Portland branco estrutural, seguido da avaliação da resistência à compressão e módulo de elasticidade. Este compósito, quando comparado individualmente com as suas matérias-prima originais, promove um aumento da resistência mecânica à compressão, redução da massa específica e, também uma mudança significativa do comportamento mecânico. As mudanças nas propriedades mecânicas estão associadas à hidratação da fase cimentícia na presença da resina, fato comprovado através da análise espectroscópica na região do infravermelho.The study of multi-functional materials of high performance, as the polymeric-cementitious composites, has been the focus of several researches in the industry of the civil engineering. This work investigates the effect of the combination of a thermorigid epoxy phase and the white Portland cement, followed by the evaluation of its compressive strength and modulus of elasticity. This composite, when the phases are individually compared, provides an increase of the compressive strength, a reduction of the density, and a significant change of the mechanical behaviour. The changes in mechanical behaviour are associated with the hydration of cement in the presence of resin, which was evident after infrared spectroscopy analysis.

Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

Energy Technology Data Exchange (ETDEWEB)

Kuo, Alan; Grigoriev, Igor

2009-04-17

Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria.

Science.gov (United States)

Zhao, Meicheng; Zhi, Hui; Doust, Andrew N; Li, Wei; Wang, Yongfang; Li, Haiquan; Jia, Guanqing; Wang, Yongqiang; Zhang, Ning; Diao, Xianmin

2013-04-11

The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC'C'. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The

Genome-derived vaccines.

Science.gov (United States)

De Groot, Anne S; Rappuoli, Rino

2004-02-01

Vaccine research entered a new era when the complete genome of a pathogenic bacterium was published in 1995. Since then, more than 97 bacterial pathogens have been sequenced and at least 110 additional projects are now in progress. Genome sequencing has also dramatically accelerated: high-throughput facilities can draft the sequence of an entire microbe (two to four megabases) in 1 to 2 days. Vaccine developers are using microarrays, immunoinformatics, proteomics and high-throughput immunology assays to reduce the truly unmanageable volume of information available in genome databases to a manageable size. Vaccines composed by novel antigens discovered from genome mining are already in clinical trials. Within 5 years we can expect to see a novel class of vaccines composed by genome-predicted, assembled and engineered T- and Bcell epitopes. This article addresses the convergence of three forces--microbial genome sequencing, computational immunology and new vaccine technologies--that are shifting genome mining for vaccines onto the forefront of immunology research.

JGI Fungal Genomics Program

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor V.

2011-03-14

Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

Genomic Encyclopedia of Fungi

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor

2012-08-10

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

The Genomic Code: Genome Evolution and Potential Applications

KAUST Repository

Bernardi, Giorgio

2016-01-25

The genome of metazoans is organized according to a genomic code which comprises three laws: 1) Compositional correlations hold between contiguous coding and non-coding sequences, as well as among the three codon positions of protein-coding genes; these correlations are the consequence of the fact that the genomes under consideration consist of fairly homogeneous, long (≥200Kb) sequences, the isochores; 2) Although isochores are defined on the basis of purely compositional properties, GC levels of isochores are correlated with all tested structural and functional properties of the genome; 3) GC levels of isochores are correlated with chromosome architecture from interphase to metaphase; in the case of interphase the correlation concerns isochores and the three-dimensional “topological associated domains” (TADs); in the case of mitotic chromosomes, the correlation concerns isochores and chromosomal bands. Finally, the genomic code is the fourth and last pillar of molecular biology, the first three pillars being 1) the double helix structure of DNA; 2) the regulation of gene expression in prokaryotes; and 3) the genetic code.

Non-deletion mutations in Egyptian patients with Duchenne ...

African Journals Online (AJOL)

Rabah M. Shawky

2014-04-19

Apr 19, 2014 ... The Egyptian Journal of Medical Human Genetics www.ejmhg.eg.net .... Serum CPK levels ranged between 2134IU/L and. 24,000 IU/L .... Previous studies reported a correlation for IQ values in affected .... Behav Brain Funct.

Cryopreservation of turkey semen: effect of breeding line and freezing method on post-thaw sperm quality, fertilization, and hatching

Science.gov (United States)

Cryopreservation methods for poultry semen are not reliable for germplasm preservation, especially for turkeys, where fertility rates from frozen/thawed semen are particularly low. The objective was to evaluate cryopreservation methods for effectiveness in promoting cryosurvival and post-thaw funct...

Neuroproteomics and Environmental Chemical-induced Adverse Effects

Science.gov (United States)

Technological advances in science have aided the field of neuroproteomics with refined tools for the study of the expression, interaction, and function of proteins in the nervous system. With the aid of bioinformatics, neuroproteomics can reveal the organization of dynamic, funct...

Understanding Chemical-induced Adverse Effects with Neuroproteins

Science.gov (United States)

Technological advances in science have aided the field of neuroproteomics with refined tools for the study of the expression, interaction, and function of proteins in the nervous system. With the aid of bioinformatics, neuroproteomics can reveal the organization of dynamic, funct...

PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

Directory of Open Access Journals (Sweden)

Wasnick Michael

2008-03-01

Full Text Available Abstract Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any

The whole genome sequences and experimentally phased haplotypes of over 100 personal genomes.

Science.gov (United States)

Mao, Qing; Ciotlos, Serban; Zhang, Rebecca Yu; Ball, Madeleine P; Chin, Robert; Carnevali, Paolo; Barua, Nina; Nguyen, Staci; Agarwal, Misha R; Clegg, Tom; Connelly, Abram; Vandewege, Ward; Zaranek, Alexander Wait; Estep, Preston W; Church, George M; Drmanac, Radoje; Peters, Brock A

2016-10-11

Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology. Here, we present the experimental whole genome haplotyping and sequencing of these samples to an average read coverage depth of 100X. This is approximately three-fold higher than the read coverage applied to most whole human genome assemblies and ensures the highest quality results. Currently, 114 genomes from this dataset are freely available in the GigaDB repository and are associated with rich phenotypic data; the remaining 70 should be added in the near future as they are approved through the PGP data release process. For reproducibility analyses, 20 genomes were sequenced at least twice using independent LFR barcoded libraries. Seven genomes were also sequenced using Complete Genomics' standard non-barcoded library process. In addition, we report 2.6 million high-quality, rare variants not previously identified in the Single Nucleotide Polymorphisms database or the 1000 Genomes Project Phase 3 data. These genomes represent a unique source of haplotype and phenotype data for the scientific community and should help to expand our understanding of human genome evolution and function.

Estudo das propriedades mecânicas e térmicas do polímero Poli-3-hidroxibutirato (PHB e de compósitos PHB/pó de madeira Study of mechanical and thermal properties of the polymer Poly-3-hydroxybutyrate (PHB and PHB/wood flour composites

Directory of Open Access Journals (Sweden)

Miriam L. C. Machado

2010-01-01

Full Text Available O PHB (Poli-3-hidroxibutirato é um termoplástico biodegradável sintetizado por fermentação submersa a partir de matérias-primas renováveis. A utilização de fibras naturais tem sido pesquisada visando melhorar as propriedades e reduzir o custo do PHB. O objetivo deste trabalho foi o estudo das propriedades mecânicas (resistência à tração, térmicas (Análise termogravimétrica,TGA, e Calorimetria Exploratória Diferencial, DSC e reológicas (torque em câmera de mistura e Índice de Fluidez do PHB e de compósitos de PHB/pó de madeira processados e irradiados. Foram preparados compósitos com concentrações de PHB/pó de madeira de 90/10, 80/20 e 70/30 (m/m. Os materiais foram processados através das seguintes etapas de processamento: calandragem, fragmentação, extrusão, granulação, secagem e moldagem por injeção para confecção dos corpos de prova. A incorporação do pó de madeira aumentou o grau de cristalinidade e a temperatura de cristalização do polímero, e nos compósitos PHB/pó de madeira 80/20 e 70/30 a rigidez do material aumentou. A irradiação após o processamento (dose de 30 kGy provocou aumento da rigidez do PHB puro e dos compósitos PHB/pó de madeira 90/10 e 80/20, embora outras propriedades tenham decrescido. O compósito PHB/pó de madeira 70/30 apresentou os melhores resultados em termos econômicos e de processamento.PHB (Polyhydroxybutyrate is a biodegradable thermoplastic synthesized by submerse fermentation of renewable raw materials. The use of natural fibers has been largely researched to improve PHB properties, as well as reducing its cost. The purpose of this work was the study of the mechanical, thermal properties and rheological analyses (torque in mixer camera and melt flow index of processed and irradiated PHB, as well as PHB/wood flour composites. PHB/wood flour composites were prepared with PHB/wood relation of 90/10, 80/20 and 70/30 (w/w. Both pure PHB and composites were

Brief Guide to Genomics: DNA, Genes and Genomes

Science.gov (United States)

... clinic. Most new drugs based on genome-based research are estimated to be at least 10 to 15 years away, though recent genome-driven efforts in lipid-lowering therapy have considerably shortened that interval. According ...

MIPS plant genome information resources.

Science.gov (United States)

Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

2007-01-01

The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

Étude de la technique d'échange ionique avec compétition. Cas du dépôt de platine sur support solide acide par échange cationique Research on the Ion Exchange Technique with Competition. Case of Platinum Deposit on a Solid Acid Support by Cation Exchange

Directory of Open Access Journals (Sweden)

Ribeiro F.

2006-11-01

Full Text Available Cet article présente une étude détaillée de la technique de dépôt de platine sur support acide par échange cationique avec compétition. Cette technique permet d'obtenir à la fois une dispersion quasi atomique et une répartition macroscopique homogène du métal sur la surface du solide. En l'absence de limitations diffusionnelles extra-granulaires, les résultats expérimentaux sont en bon accord avec les prévisions théoriques . This article is a detailed examination of the technique of depositing platinum on an acid support by cation exchange with compétition. This technique produces both a quasi-atomic dispersion and a homogeneous macroscopic distribution of the métal onthe surface of the solid. In the absence of extragranular diffusion limitations, experimental findings are in good agreement with theoretical predictions.

Ensembl Genomes 2013: scaling up access to genome-wide data.

Science.gov (United States)

Kersey, Paul Julian; Allen, James E; Christensen, Mikkel; Davis, Paul; Falin, Lee J; Grabmueller, Christoph; Hughes, Daniel Seth Toney; Humphrey, Jay; Kerhornou, Arnaud; Khobova, Julia; Langridge, Nicholas; McDowall, Mark D; Maheswari, Uma; Maslen, Gareth; Nuhn, Michael; Ong, Chuang Kee; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Tuli, Mary Ann; Walts, Brandon; Williams, Gareth; Wilson, Derek; Youens-Clark, Ken; Monaco, Marcela K; Stein, Joshua; Wei, Xuehong; Ware, Doreen; Bolser, Daniel M; Howe, Kevin Lee; Kulesha, Eugene; Lawson, Daniel; Staines, Daniel Michael

2014-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.

Toward genome-enabled mycology.

Science.gov (United States)

Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

2013-01-01

Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

Final Scientific/Technical Report, USDOE Award DE-FG-02ER54684, Recipient: CompX, Project Title: Fokker-Planck/Ray Tracing for Electron Bernstein and Fast Wave Modeling in Support of NSTX

International Nuclear Information System (INIS)

Harvey, R.W.

2009-01-01

This DOE grant supported fusion energy research, a potential long-term solution to the world's energy needs. Magnetic fusion, exemplified by confinement of very hot ionized gases, i.e., plasmas, in donut-shaped tokamak vessels is a leading approach for this energy source. Thus far, a mixture of hydrogen isotopes has produced 10's of megawatts of fusion power for seconds in a tokamak reactor at Princeton Plasma Physics Laboratory in New Jersey. The research grant under consideration, ER54684, uses computer models to aid in understanding and projecting efficacy of heating and current drive sources in the National Spherical Torus Experiment, a tokamak variant, at PPPL. The NSTX experiment explores the physics of very tight aspect ratio, almost spherical tokamaks, aiming at producing steady-state fusion plasmas. The current drive is an integral part of the steady-state concept, maintaining the magnetic geometry in the steady-state tokamak. CompX further developed and applied models for radiofrequency (rf) heating and current drive for applications to NSTX. These models build on a 30 year development of rf ray tracing (the all-frequencies GENRAY code) and higher dimensional Fokker-Planck rf-collisional modeling (the 3D collisional-quasilinear CQL3D code) at CompX. Two mainline current-drive rf modes are proposed for injection into NSTX: (1) electron Bernstein wave (EBW), and (2) high harmonic fast wave (HHFW) modes. Both these current drive systems provide a means for the rf to access the especially high density plasma--termed high beta plasma--compared to the strength of the required magnetic fields. The CompX studies entailed detailed modeling of the EBW to calculate the efficiency of the current drive system, and to determine its range of flexibility for driving current at spatial locations in the plasma cross-section. The ray tracing showed penetration into NSTX bulk plasma, relatively efficient current drive, but a limited ability to produce current over the whole

The effect of invasive hybrid taxa on the ecological succession of coastal marshes

Science.gov (United States)

Hybridization following colonization of invasive species in novel environments frequently results in offspring with improved biological and competitive functions referred to as heterosis or hybrid vigor. However, little is known about the effect of these invasive hybrids on the structuring and funct...

Constraint-Based Abstract Semantics for Temporal Logic

DEFF Research Database (Denmark)

Banda, Gourinath; Gallagher, John Patrick

2010-01-01

Abstract interpretation provides a practical approach to verifying properties of infinite-state systems. We apply the framework of abstract interpretation to derive an abstract semantic function for the modal mu-calculus, which is the basis for abstract model checking. The abstract semantic funct...

Plantagora: modeling whole genome sequencing and assembly of plant genomes.

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Roger Barthelson

Full Text Available BACKGROUND: Genomics studies are being revolutionized by the next generation sequencing technologies, which have made whole genome sequencing much more accessible to the average researcher. Whole genome sequencing with the new technologies is a developing art that, despite the large volumes of data that can be produced, may still fail to provide a clear and thorough map of a genome. The Plantagora project was conceived to address specifically the gap between having the technical tools for genome sequencing and knowing precisely the best way to use them. METHODOLOGY/PRINCIPAL FINDINGS: For Plantagora, a platform was created for generating simulated reads from several different plant genomes of different sizes. The resulting read files mimicked either 454 or Illumina reads, with varying paired end spacing. Thousands of datasets of reads were created, most derived from our primary model genome, rice chromosome one. All reads were assembled with different software assemblers, including Newbler, Abyss, and SOAPdenovo, and the resulting assemblies were evaluated by an extensive battery of metrics chosen for these studies. The metrics included both statistics of the assembly sequences and fidelity-related measures derived by alignment of the assemblies to the original genome source for the reads. The results were presented in a website, which includes a data graphing tool, all created to help the user compare rapidly the feasibility and effectiveness of different sequencing and assembly strategies prior to testing an approach in the lab. Some of our own conclusions regarding the different strategies were also recorded on the website. CONCLUSIONS/SIGNIFICANCE: Plantagora provides a substantial body of information for comparing different approaches to sequencing a plant genome, and some conclusions regarding some of the specific approaches. Plantagora also provides a platform of metrics and tools for studying the process of sequencing and assembly

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

Science.gov (United States)

Puigbò, Pere; Lobkovsky, Alexander E; Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

2014-08-21

Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes

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Michael Strong

2009-12-01

Full Text Available As the number of completely sequenced microbial genomes continues to rise at an impressive rate, it is important to prepare students with the skills necessary to investigate microorganisms at the genomic level. As a part of the core curriculum for first-year graduate students in the biological sciences, we have implemented a web-based tutorial to introduce students to the fields of comparative and functional genomics. The tutorial focuses on recent computational methods for identifying functionally linked genes and proteins on a genome-wide scale and was used to introduce students to the Rosetta Stone, Phylogenetic Profile, conserved Gene Neighbor, and Operon computational methods. Students learned to use a number of publicly available web servers and databases to identify functionally linked genes in the Escherichia coli genome, with emphasis on genome organization and operon structure. The overall effectiveness of the tutorial was assessed based on student evaluations and homework assignments. The tutorial is available to other educators at http://www.doe-mbi.ucla.edu/~strong/m253.php.

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

Science.gov (United States)

Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

2014-07-01

Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Between Two Fern Genomes

Science.gov (United States)

2014-01-01

Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves. PMID:25324969

Exploring Other Genomes: Bacteria.

Science.gov (United States)

Flannery, Maura C.

2001-01-01

Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

Comparative Pan-Genome Analysis of Piscirickettsia salmonis Reveals Genomic Divergences within Genogroups

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Guillermo Nourdin-Galindo

2017-10-01

Full Text Available Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these

A Genome-Wide Landscape of Retrocopies in Primate Genomes.

Science.gov (United States)

Navarro, Fábio C P; Galante, Pedro A F

2015-07-29

Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (∼7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (∼10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

Science.gov (United States)

Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2014-06-01

To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

Funding Opportunity: Genomic Data Centers

Science.gov (United States)

Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

MicroScope: a platform for microbial genome annotation and comparative genomics.

Science.gov (United States)

Vallenet, D; Engelen, S; Mornico, D; Cruveiller, S; Fleury, L; Lajus, A; Rouy, Z; Roche, D; Salvignol, G; Scarpelli, C; Médigue, C

2009-01-01

The initial outcome of genome sequencing is the creation of long text strings written in a four letter alphabet. The role of in silico sequence analysis is to assist biologists in the act of associating biological knowledge with these sequences, allowing investigators to make inferences and predictions that can be tested experimentally. A wide variety of software is available to the scientific community, and can be used to identify genomic objects, before predicting their biological functions. However, only a limited number of biologically interesting features can be revealed from an isolated sequence. Comparative genomics tools, on the other hand, by bringing together the information contained in numerous genomes simultaneously, allow annotators to make inferences based on the idea that evolution and natural selection are central to the definition of all biological processes. We have developed the MicroScope platform in order to offer a web-based framework for the systematic and efficient revision of microbial genome annotation and comparative analysis (http://www.genoscope.cns.fr/agc/microscope). Starting with the description of the flow chart of the annotation processes implemented in the MicroScope pipeline, and the development of traditional and novel microbial annotation and comparative analysis tools, this article emphasizes the essential role of expert annotation as a complement of automatic annotation. Several examples illustrate the use of implemented tools for the review and curation of annotations of both new and publicly available microbial genomes within MicroScope's rich integrated genome framework. The platform is used as a viewer in order to browse updated annotation information of available microbial genomes (more than 440 organisms to date), and in the context of new annotation projects (117 bacterial genomes). The human expertise gathered in the MicroScope database (about 280,000 independent annotations) contributes to improve the quality of

Ebolavirus comparative genomics

DEFF Research Database (Denmark)

Jun, Se-Ran; Leuze, Michael R.; Nookaew, Intawat

2015-01-01

The 2014 Ebola outbreak in West Africa is the largest documented for this virus. To examine the dynamics of this genome, we compare more than 100 currently available ebolavirus genomes to each other and to other viral genomes. Based on oligomer frequency analysis, the family Filoviridae forms...

SIGMA: A System for Integrative Genomic Microarray Analysis of Cancer Genomes

Directory of Open Access Journals (Sweden)

Davies Jonathan J

2006-12-01

Full Text Available Abstract Background The prevalence of high resolution profiling of genomes has created a need for the integrative analysis of information generated from multiple methodologies and platforms. Although the majority of data in the public domain are gene expression profiles, and expression analysis software are available, the increase of array CGH studies has enabled integration of high throughput genomic and gene expression datasets. However, tools for direct mining and analysis of array CGH data are limited. Hence, there is a great need for analytical and display software tailored to cross platform integrative analysis of cancer genomes. Results We have created a user-friendly java application to facilitate sophisticated visualization and analysis such as cross-tumor and cross-platform comparisons. To demonstrate the utility of this software, we assembled array CGH data representing Affymetrix SNP chip, Stanford cDNA arrays and whole genome tiling path array platforms for cross comparison. This cancer genome database contains 267 profiles from commonly used cancer cell lines representing 14 different tissue types. Conclusion In this study we have developed an application for the visualization and analysis of data from high resolution array CGH platforms that can be adapted for analysis of multiple types of high throughput genomic datasets. Furthermore, we invite researchers using array CGH technology to deposit both their raw and processed data, as this will be a continually expanding database of cancer genomes. This publicly available resource, the System for Integrative Genomic Microarray Analysis (SIGMA of cancer genomes, can be accessed at http://sigma.bccrc.ca.

Genomics With Cloud Computing

OpenAIRE

Sukhamrit Kaur; Sandeep Kaur

2015-01-01

Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computin...

Genomics technologies to study structural variations in the grapevine genome

Directory of Open Access Journals (Sweden)

Cardone Maria Francesca

2016-01-01

Full Text Available Grapevine is one of the most important crop plants in the world. Recently there was great expansion of genomics resources about grapevine genome, thus providing increasing efforts for molecular breeding. Current cultivars display a great level of inter-specific differentiation that needs to be investigated to reach a comprehensive understanding of the genetic basis of phenotypic differences, and to find responsible genes selected by cross breeding programs. While there have been significant advances in resolving the pattern and nature of single nucleotide polymorphisms (SNPs on plant genomes, few data are available on copy number variation (CNV. Furthermore association between structural variations and phenotypes has been described in only a few cases. We combined high throughput biotechnologies and bioinformatics tools, to reveal the first inter-varietal atlas of structural variation (SV for the grapevine genome. We sequenced and compared four table grape cultivars with the Pinot noir inbred line PN40024 genome as the reference. We detected roughly 8% of the grapevine genome affected by genomic variations. Taken into account phenotypic differences existing among the studied varieties we performed comparison of SVs among them and the reference and next we performed an in-depth analysis of gene content of polymorphic regions. This allowed us to identify genes showing differences in copy number as putative functional candidates for important traits in grapevine cultivation.

The genome portal of the Department of Energy Joint Genome Institute: 2014 updates

Energy Technology Data Exchange (ETDEWEB)

Nordberg, Henrik [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Cantor, Michael [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dusheyko, Serge [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hua, Susan [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Poliakov, Alexander [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Shabalov, Igor [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Smirnova, Tatyana [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Grigoriev, Igor V. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Dubchak, Inna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

2013-11-12

The U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a national user facility, serves the diverse scientific community by providing integrated high-throughput sequencing and computational analysis to enable system-based scientific approaches in support of DOE missions related to clean energy generation and environmental characterization. The JGI Genome Portal (http://genome.jgi.doe.gov) provides unified access to all JGI genomic databases and analytical tools. The JGI maintains extensive data management systems and specialized analytical capabilities to manage and interpret complex genomic data. A user can search, download and explore multiple data sets available for all DOE JGI sequencing projects including their status, assemblies and annotations of sequenced genomes. In this paper, we describe major updates of the Genome Portal in the past 2 years with a specific emphasis on efficient handling of the rapidly growing amount of diverse genomic data accumulated in JGI.

Herbarium genomics

DEFF Research Database (Denmark)

Bakker, Freek T.; Lei, Di; Yu, Jiaying

2016-01-01

Herbarium genomics is proving promising as next-generation sequencing approaches are well suited to deal with the usually fragmented nature of archival DNA. We show that routine assembly of partial plastome sequences from herbarium specimens is feasible, from total DNA extracts and with specimens...... up to 146 years old. We use genome skimming and an automated assembly pipeline, Iterative Organelle Genome Assembly, that assembles paired-end reads into a series of candidate assemblies, the best one of which is selected based on likelihood estimation. We used 93 specimens from 12 different...... correlation between plastome coverage and nuclear genome size (C value) in our samples, but the range of C values included is limited. Finally, we conclude that routine plastome sequencing from herbarium specimens is feasible and cost-effective (compared with Sanger sequencing or plastome...

Effects of sample treatments on genome recovery via single-cell genomics

Energy Technology Data Exchange (ETDEWEB)

Clingenpeel, Scott [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Schwientek, Patrick [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Hugenholtz, Philip [Univ. of Queensland, Brisbane (Australia); Woyke, Tanja [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

2014-06-13

It is known that single-cell genomics is a powerful tool for accessing genetic information from uncultivated microorganisms. Methods of handling samples before single-cell genomic amplification may affect the quality of the genomes obtained. Using three bacterial strains we demonstrate that, compared to cryopreservation, lower-quality single-cell genomes are recovered when the sample is preserved in ethanol or if the sample undergoes fluorescence in situ hybridization, while sample preservation in paraformaldehyde renders it completely unsuitable for sequencing.

Informational laws of genome structures

Science.gov (United States)

Bonnici, Vincenzo; Manca, Vincenzo

2016-06-01

In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

How genome complexity can explain the difficulty of aligning reads to genomes.

Science.gov (United States)

Phan, Vinhthuy; Gao, Shanshan; Tran, Quang; Vo, Nam S

2015-01-01

Although it is frequently observed that aligning short reads to genomes becomes harder if they contain complex repeat patterns, there has not been much effort to quantify the relationship between complexity of genomes and difficulty of short-read alignment. Existing measures of sequence complexity seem unsuitable for the understanding and quantification of this relationship. We investigated several measures of complexity and found that length-sensitive measures of complexity had the highest correlation to accuracy of alignment. In particular, the rate of distinct substrings of length k, where k is similar to the read length, correlated very highly to alignment performance in terms of precision and recall. We showed how to compute this measure efficiently in linear time, making it useful in practice to estimate quickly the difficulty of alignment for new genomes without having to align reads to them first. We showed how the length-sensitive measures could provide additional information for choosing aligners that would align consistently accurately on new genomes. We formally established a connection between genome complexity and the accuracy of short-read aligners. The relationship between genome complexity and alignment accuracy provides additional useful information for selecting suitable aligners for new genomes. Further, this work suggests that the complexity of genomes sometimes should be thought of in terms of specific computational problems, such as the alignment of short reads to genomes.

Phytozome Comparative Plant Genomics Portal

Energy Technology Data Exchange (ETDEWEB)

Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

2014-09-09

The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

A Taste of Algal Genomes from the Joint Genome Institute

Energy Technology Data Exchange (ETDEWEB)

Kuo, Alan; Grigoriev, Igor

2012-06-17

Algae play profound roles in aquatic food chains and the carbon cycle, can impose health and economic costs through toxic blooms, provide models for the study of symbiosis, photosynthesis, and eukaryotic evolution, and are candidate sources for bio-fuels; all of these research areas are part of the mission of DOE's Joint Genome Institute (JGI). To date JGI has sequenced, assembled, annotated, and released to the public the genomes of 18 species and strains of algae, sampling almost all of the major clades of photosynthetic eukaryotes. With more algal genomes currently undergoing analysis, JGI continues its commitment to driving forward basic and applied algal science. Among these ongoing projects are the pan-genome of the dominant coccolithophore Emiliania huxleyi, the interrelationships between the 4 genomes in the nucleomorph-containing Bigelowiella natans and Guillardia theta, and the search for symbiosis genes of lichens.

PGSB/MIPS Plant Genome Information Resources and Concepts for the Analysis of Complex Grass Genomes.

Science.gov (United States)

Spannagl, Manuel; Bader, Kai; Pfeifer, Matthias; Nussbaumer, Thomas; Mayer, Klaus F X

2016-01-01

PGSB (Plant Genome and Systems Biology; formerly MIPS-Munich Institute for Protein Sequences) has been involved in developing, implementing and maintaining plant genome databases for more than a decade. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable datasets for model plant genomes as a backbone against which experimental data, e.g., from high-throughput functional genomics, can be organized and analyzed. In addition, genomes from both model and crop plants form a scaffold for comparative genomics, assisted by specialized tools such as the CrowsNest viewer to explore conserved gene order (synteny) between related species on macro- and micro-levels.The genomes of many economically important Triticeae plants such as wheat, barley, and rye present a great challenge for sequence assembly and bioinformatic analysis due to their enormous complexity and large genome size. Novel concepts and strategies have been developed to deal with these difficulties and have been applied to the genomes of wheat, barley, rye, and other cereals. This includes the GenomeZipper concept, reference-guided exome assembly, and "chromosome genomics" based on flow cytometry sorted chromosomes.

Genomic treasure troves: complete genome sequencing of herbarium and insect museum specimens.

Science.gov (United States)

Staats, Martijn; Erkens, Roy H J; van de Vossenberg, Bart; Wieringa, Jan J; Kraaijeveld, Ken; Stielow, Benjamin; Geml, József; Richardson, James E; Bakker, Freek T

2013-01-01

Unlocking the vast genomic diversity stored in natural history collections would create unprecedented opportunities for genome-scale evolutionary, phylogenetic, domestication and population genomic studies. Many researchers have been discouraged from using historical specimens in molecular studies because of both generally limited success of DNA extraction and the challenges associated with PCR-amplifying highly degraded DNA. In today's next-generation sequencing (NGS) world, opportunities and prospects for historical DNA have changed dramatically, as most NGS methods are actually designed for taking short fragmented DNA molecules as templates. Here we show that using a standard multiplex and paired-end Illumina sequencing approach, genome-scale sequence data can be generated reliably from dry-preserved plant, fungal and insect specimens collected up to 115 years ago, and with minimal destructive sampling. Using a reference-based assembly approach, we were able to produce the entire nuclear genome of a 43-year-old Arabidopsis thaliana (Brassicaceae) herbarium specimen with high and uniform sequence coverage. Nuclear genome sequences of three fungal specimens of 22-82 years of age (Agaricus bisporus, Laccaria bicolor, Pleurotus ostreatus) were generated with 81.4-97.9% exome coverage. Complete organellar genome sequences were assembled for all specimens. Using de novo assembly we retrieved between 16.2-71.0% of coding sequence regions, and hence remain somewhat cautious about prospects for de novo genome assembly from historical specimens. Non-target sequence contaminations were observed in 2 of our insect museum specimens. We anticipate that future museum genomics projects will perhaps not generate entire genome sequences in all cases (our specimens contained relatively small and low-complexity genomes), but at least generating vital comparative genomic data for testing (phylo)genetic, demographic and genetic hypotheses, that become increasingly more horizontal

Next-Generation Genomics Facility at C-CAMP: Accelerating Genomic Research in India

Science.gov (United States)

S, Chandana; Russiachand, Heikham; H, Pradeep; S, Shilpa; M, Ashwini; S, Sahana; B, Jayanth; Atla, Goutham; Jain, Smita; Arunkumar, Nandini; Gowda, Malali

2014-01-01

Next-Generation Sequencing (NGS; http://www.genome.gov/12513162) is a recent life-sciences technological revolution that allows scientists to decode genomes or transcriptomes at a much faster rate with a lower cost. Genomic-based studies are in a relatively slow pace in India due to the non-availability of genomics experts, trained personnel and dedicated service providers. Using NGS there is a lot of potential to study India's national diversity (of all kinds). We at the Centre for Cellular and Molecular Platforms (C-CAMP) have launched the Next Generation Genomics Facility (NGGF) to provide genomics service to scientists, to train researchers and also work on national and international genomic projects. We have HiSeq1000 from Illumina and GS-FLX Plus from Roche454. The long reads from GS FLX Plus, and high sequence depth from HiSeq1000, are the best and ideal hybrid approaches for de novo and re-sequencing of genomes and transcriptomes. At our facility, we have sequenced around 70 different organisms comprising of more than 388 genomes and 615 transcriptomes – prokaryotes and eukaryotes (fungi, plants and animals). In addition we have optimized other unique applications such as small RNA (miRNA, siRNA etc), long Mate-pair sequencing (2 to 20 Kb), Coding sequences (Exome), Methylome (ChIP-Seq), Restriction Mapping (RAD-Seq), Human Leukocyte Antigen (HLA) typing, mixed genomes (metagenomes) and target amplicons, etc. Translating DNA sequence data from NGS sequencer into meaningful information is an important exercise. Under NGGF, we have bioinformatics experts and high-end computing resources to dissect NGS data such as genome assembly and annotation, gene expression, target enrichment, variant calling (SSR or SNP), comparative analysis etc. Our services (sequencing and bioinformatics) have been utilized by more than 45 organizations (academia and industry) both within India and outside, resulting several publications in peer-reviewed journals and several genomic

Frequency and Prognostic Significance of Abnormal Liver Function Tests in Patients With Cardiogenic Shock

DEFF Research Database (Denmark)

Jäntti, Toni; Tarvasmäki, Tuukka; Harjola, Veli Pekka

2017-01-01

Cardiogenic shock (CS) is a cardiac emergency often leading to multiple organ failure and death. Assessing organ dysfunction and appropriate risk stratification are central for the optimal management of these patients. The purpose of this study was to assess the prevalence of abnormal liver funct...

Starch-based Foam Composite Materials: processing and bioproducts

Science.gov (United States)

Starch is an abundant, biodegradable, renewable and low-cost commodity that has been explored as a replacement for petroleum-based plastics. By itself, starch is a poor replacement for plastics because of its moisture sensitivity and brittle properties. Efforts to improve starch properties and funct...

Extreme genomes

OpenAIRE

DeLong, Edward F

2000-01-01

The complete genome sequence of Thermoplasma acidophilum, an acid- and heat-loving archaeon, has recently been reported. Comparative genomic analysis of this 'extremophile' is providing new insights into the metabolic machinery, ecology and evolution of thermophilic archaea.

GenomePeek—an online tool for prokaryotic genome and metagenome analysis

Directory of Open Access Journals (Sweden)

Katelyn McNair

2015-06-01

Full Text Available As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.

GRAbB : Selective Assembly of Genomic Regions, a New Niche for Genomic Research

NARCIS (Netherlands)

Brankovics, Balázs; Zhang, Hao; van Diepeningen, Anne D; van der Lee, Theo A J; Waalwijk, Cees; de Hoog, G Sybren

GRAbB (Genomic Region Assembly by Baiting) is a new program that is dedicated to assemble specific genomic regions from NGS data. This approach is especially useful when dealing with multi copy regions, such as mitochondrial genome and the rDNA repeat region, parts of the genome that are often

Comparative Genome Viewer

International Nuclear Information System (INIS)

Molineris, I.; Sales, G.

2009-01-01

The amount of information about genomes, both in the form of complete sequences and annotations, has been exponentially increasing in the last few years. As a result there is the need for tools providing a graphical representation of such information that should be comprehensive and intuitive. Visual representation is especially important in the comparative genomics field since it should provide a combined view of data belonging to different genomes. We believe that existing tools are limited in this respect as they focus on a single genome at a time (conservation histograms) or compress alignment representation to a single dimension. We have therefore developed a web-based tool called Comparative Genome Viewer (Cgv): it integrates a bidimensional representation of alignments between two regions, both at small and big scales, with the richness of annotations present in other genome browsers. We give access to our system through a web-based interface that provides the user with an interactive representation that can be updated in real time using the mouse to move from region to region and to zoom in on interesting details.

Genomics With Cloud Computing

Directory of Open Access Journals (Sweden)

Sukhamrit Kaur

2015-04-01

Full Text Available Abstract Genomics is study of genome which provides large amount of data for which large storage and computation power is needed. These issues are solved by cloud computing that provides various cloud platforms for genomics. These platforms provides many services to user like easy access to data easy sharing and transfer providing storage in hundreds of terabytes more computational power. Some cloud platforms are Google genomics DNAnexus and Globus genomics. Various features of cloud computing to genomics are like easy access and sharing of data security of data less cost to pay for resources but still there are some demerits like large time needed to transfer data less network bandwidth.

IMA Genome-F 5G

OpenAIRE

Wingfield, Brenda D.; Barnes, Irene; Wilhelm de Beer, Z.; De Vos, Lieschen; Duong, Tuan A.; Kanzi, Aquillah M.; Naidoo, Kershney; Nguyen, Hai D.T.; Santana, Quentin C.; Sayari, Mohammad; Seifert, Keith A.; Steenkamp, Emma T.; Trollip, Conrad; van der Merwe, Nicolaas A.; van der Nest, Magriet A.

2015-01-01

The genomes of Ceratocystis eucalypticola, Chrysoporthe cubensis, Chrysoporthe deuterocubensis, Davidsoniella virescens, Fusarium temperatum, Graphilbum fragrans, Penicillium nordicum and Thielaviopsis musarum are presented in this genome announcement. These seven genomes are from plant pathogens and otherwise economically important fungal species. The genome sizes range from 28 Mb in the case of T. musarum to 45 Mb for Fusarium temperatum. These genomes include the first reports of genomes f...

Experimental Induction of Genome Chaos.

Science.gov (United States)

Ye, Christine J; Liu, Guo; Heng, Henry H

2018-01-01

Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.

Genome Sequences of Oryza Species

KAUST Repository

Kumagai, Masahiko

2018-02-14

This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

Genome Sequences of Oryza Species

KAUST Repository

Kumagai, Masahiko; Tanaka, Tsuyoshi; Ohyanagi, Hajime; Hsing, Yue-Ie C.; Itoh, Takeshi

2018-01-01

This chapter summarizes recent data obtained from genome sequencing, annotation projects, and studies on the genome diversity of Oryza sativa and related Oryza species. O. sativa, commonly known as Asian rice, is the first monocot species whose complete genome sequence was deciphered based on physical mapping by an international collaborative effort. This genome, along with its accurate and comprehensive annotation, has become an indispensable foundation for crop genomics and breeding. With the development of innovative sequencing technologies, genomic studies of O. sativa have dramatically increased; in particular, a large number of cultivars and wild accessions have been sequenced and compared with the reference rice genome. Since de novo genome sequencing has become cost-effective, the genome of African cultivated rice, O. glaberrima, has also been determined. Comparative genomic studies have highlighted the independent domestication processes of different rice species, but it also turned out that Asian and African rice share a common gene set that has experienced similar artificial selection. An international project aimed at constructing reference genomes and examining the genome diversity of wild Oryza species is currently underway, and the genomes of some species are publicly available. This project provides a platform for investigations such as the evolution, development, polyploidization, and improvement of crops. Studies on the genomic diversity of Oryza species, including wild species, should provide new insights to solve the problem of growing food demands in the face of rapid climatic changes.

Genome Variation Map: a data repository of genome variations in BIG Data Center

OpenAIRE

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2017-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research a...

Patient-controlled encrypted genomic data: an approach to advance clinical genomics

Directory of Open Access Journals (Sweden)

Trakadis Yannis J

2012-07-01

Full Text Available Abstract Background The revolution in DNA sequencing technologies over the past decade has made it feasible to sequence an individual’s whole genome at a relatively low cost. The potential value of the information generated by genomic technologies for medicine and society is enormous. However, in order for exome sequencing, and eventually whole genome sequencing, to be implemented clinically, a number of major challenges need to be overcome. For instance, obtaining meaningful informed-consent, managing incidental findings and the great volume of data generated (including multiple findings with uncertain clinical significance, re-interpreting the genomic data and providing additional counselling to patients as genetic knowledge evolves are issues that need to be addressed. It appears that medical genetics is shifting from the present “phenotype-first” medical model to a “data-first” model which leads to multiple complexities. Discussion This manuscript discusses the different challenges associated with integrating genomic technologies into clinical practice and describes a “phenotype-first” approach, namely, “Individualized Mutation-weighed Phenotype Search”, and its benefits. The proposed approach allows for a more efficient prioritization of the genes to be tested in a clinical lab based on both the patient’s phenotype and his/her entire genomic data. It simplifies “informed-consent” for clinical use of genomic technologies and helps to protect the patient’s autonomy and privacy. Overall, this approach could potentially render widespread use of genomic technologies, in the immediate future, practical, ethical and clinically useful. Summary The “Individualized Mutation-weighed Phenotype Search” approach allows for an incremental integration of genomic technologies into clinical practice. It ensures that we do not over-medicalize genomic data but, rather, continue our current medical model which is based on serving

EUPAN enables pan-genome studies of a large number of eukaryotic genomes.

Science.gov (United States)

Hu, Zhiqiang; Sun, Chen; Lu, Kuang-Chen; Chu, Xixia; Zhao, Yue; Lu, Jinyuan; Shi, Jianxin; Wei, Chaochun

2017-08-01

Pan-genome analyses are routinely carried out for bacteria to interpret the within-species gene presence/absence variations (PAVs). However, pan-genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan-genome analysis toolkit, enabling automatic large-scale eukaryotic pan-genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan-genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re-sequencing projects primarily focusing on single nucleotide polymorphisms. EUPAN is implemented in Perl, R and C ++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non-commercial use (CC BY-NC 4.0) at http://cgm.sjtu.edu.cn/eupan/index.html . ccwei@sjtu.edu.cn or jianxin.shi@sjtu.edu.cn. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Annual Targets, UAVs and Range Operations Symposium and Exhibition (49th) Held in Fort Walton Beach, Florida on October 25-27, 2011

Science.gov (United States)

2011-10-27

COMP Mountain Home COMP Shaw COMP Barksdale COMP Hill COMP Homestead ARB COMP Savannah CRTC COMP Gulfport CRTC COMP Alpena CRTC COMP Montana...Spangdahlem AB Aviano AB Kadena AB Programmed: 165 Baseline Pods purchase in FY12 (del FY13) Alpena CRTC Holloman AFB Eielson AFB Planned: 368...ARQ-52(V)2 ARQ-52B(V)2 ARDS (HDIS) ASQ- T35A P4NS (NACTS-RSI) KITS (Kadena) ASQ-T34 ASQ-T46 AKITS ( Alpena ) Israel No Datalink No Datalink P4R1 ASQ

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

Science.gov (United States)

Lack, Justin B; Cardeno, Charis M; Crepeau, Marc W; Taylor, William; Corbett-Detig, Russell B; Stevens, Kristian A; Langley, Charles H; Pool, John E

2015-04-01

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets. Copyright © 2015 by the Genetics Society of America.

GI-POP: a combinational annotation and genomic island prediction pipeline for ongoing microbial genome projects.

Science.gov (United States)

Lee, Chi-Ching; Chen, Yi-Ping Phoebe; Yao, Tzu-Jung; Ma, Cheng-Yu; Lo, Wei-Cheng; Lyu, Ping-Chiang; Tang, Chuan Yi

2013-04-10

Sequencing of microbial genomes is important because of microbial-carrying antibiotic and pathogenetic activities. However, even with the help of new assembling software, finishing a whole genome is a time-consuming task. In most bacteria, pathogenetic or antibiotic genes are carried in genomic islands. Therefore, a quick genomic island (GI) prediction method is useful for ongoing sequencing genomes. In this work, we built a Web server called GI-POP (http://gipop.life.nthu.edu.tw) which integrates a sequence assembling tool, a functional annotation pipeline, and a high-performance GI predicting module, in a support vector machine (SVM)-based method called genomic island genomic profile scanning (GI-GPS). The draft genomes of the ongoing genome projects in contigs or scaffolds can be submitted to our Web server, and it provides the functional annotation and highly probable GI-predicting results. GI-POP is a comprehensive annotation Web server designed for ongoing genome project analysis. Researchers can perform annotation and obtain pre-analytic information include possible GIs, coding/non-coding sequences and functional analysis from their draft genomes. This pre-analytic system can provide useful information for finishing a genome sequencing project. Copyright © 2012 Elsevier B.V. All rights reserved.

The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly

Directory of Open Access Journals (Sweden)

J. W. Clouse

2016-03-01

Full Text Available Amaranth ( L. is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32, and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and and their putative progenitor ( were resequenced. A single nucleotide polymorphism (SNP phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics’ Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L. and estimated, using analysis, the age of the most recent polyploidization event in amaranth.

Whole genome sequencing and bioinformatics analysis of two Egyptian genomes.

Science.gov (United States)

ElHefnawi, Mahmoud; Jeon, Sungwon; Bhak, Youngjune; ElFiky, Asmaa; Horaiz, Ahmed; Jun, JeHoon; Kim, Hyunho; Bhak, Jong

2018-05-15

We report two Egyptian male genomes (EGP1 and EGP2) sequenced at ~ 30× sequencing depths. EGP1 had 4.7 million variants, where 198,877 were novel variants while EGP2 had 209,109 novel variants out of 4.8 million variants. The mitochondrial haplogroup of the two individuals were identified to be H7b1 and L2a1c, respectively. We also identified the Y haplogroup of EGP1 (R1b) and EGP2 (J1a2a1a2 > P58 > FGC11). EGP1 had a mutation in the NADH gene of the mitochondrial genome ND4 (m.11778 G > A) that causes Leber's hereditary optic neuropathy. Some SNPs shared by the two genomes were associated with an increased level of cholesterol and triglycerides, probably related with Egyptians obesity. Comparison of these genomes with African and Western-Asian genomes can provide insights on Egyptian ancestry and genetic history. This resource can be used to further understand genomic diversity and functional classification of variants as well as human migration and evolution across Africa and Western-Asia. Copyright © 2017. Published by Elsevier B.V.

Genomic Testing

Science.gov (United States)

... this database. Top of Page Evaluation of Genomic Applications in Practice and Prevention (EGAPP™) In 2004, the Centers for Disease Control and Prevention launched the EGAPP initiative to establish and test a ... and other applications of genomic technology that are in transition from ...

St2-80: a new FISH marker for St genome and genome analysis in Triticeae.

Science.gov (United States)

Wang, Long; Shi, Qinghua; Su, Handong; Wang, Yi; Sha, Lina; Fan, Xing; Kang, Houyang; Zhang, Haiqin; Zhou, Yonghong

2017-07-01

The St genome is one of the most fundamental genomes in Triticeae. Repetitive sequences are widely used to distinguish different genomes or species. The primary objectives of this study were to (i) screen a new sequence that could easily distinguish the chromosome of the St genome from those of other genomes by fluorescence in situ hybridization (FISH) and (ii) investigate the genome constitution of some species that remain uncertain and controversial. We used degenerated oligonucleotide primer PCR (Dop-PCR), Dot-blot, and FISH to screen for a new marker of the St genome and to test the efficiency of this marker in the detection of the St chromosome at different ploidy levels. Signals produced by a new FISH marker (denoted St 2 -80) were present on the entire arm of chromosomes of the St genome, except in the centromeric region. On the contrary, St 2 -80 signals were present in the terminal region of chromosomes of the E, H, P, and Y genomes. No signal was detected in the A and B genomes, and only weak signals were detected in the terminal region of chromosomes of the D genome. St 2 -80 signals were obvious and stable in chromosomes of different genomes, whether diploid or polyploid. Therefore, St 2 -80 is a potential and useful FISH marker that can be used to distinguish the St genome from those of other genomes in Triticeae.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium

OpenAIRE

Henrique Machado; Henrique Machado; Lone Gram

2017-01-01

Vibrionaceae is a large marine bacterial family, which can constitute up to 50% of the prokaryotic population in marine waters. Photobacterium is the second largest genus in the family and we used comparative genomics on 35 strains representing 16 of the 28 species described so far, to understand the genomic diversity present in the Photobacterium genus. Such understanding is important for ecophysiology studies of the genus. We used whole genome sequences to evaluate phylogenetic relationship...

Generation of L cells in mouse and human small intestine organoids

DEFF Research Database (Denmark)

Petersen, Natalia; Reimann, Frank; Bartfeld, Sina

2014-01-01

Upon a nutrient challenge, L cells produce glucagon-like peptide 1 (GLP-1), a powerful stimulant of insulin release. Strategies to augment endogenous GLP-1 production include promoting L-cell differentiation and increasing L-cell number. Here we present a novel in vitro platform to generate funct...

Belousov Zhabotinsky Autonomic Hydrogel Composites: Regulating Waves via Asymmetry (Postprint)

Science.gov (United States)

2016-09-23

Zhabotinsky (BZ)‐gelatin composites by synchronicity. Adv. Funct. Mater. 23, 2835–2842 (2013). 6. R. Yoshida, T. Takahashi, T. Yamaguchi , H. Ichijo, Self...2014). 12. R. Yoshida, M. Tanaka, S. Onodera, T. Yamaguchi , E. Kokufuta, In-phase synchronization of chemical and mechanical oscillations in self

Memorization in Type-Directed Partial Evaluation

DEFF Research Database (Denmark)

Balat, Vincent; Danvy, Olivier

2002-01-01

We use a code generator—type-directed partial evaluation— to verify conversions between isomorphic types, or more precisely to verify that a composite function is the identity function at some complicated type. A typed functional language such as ML provides a natural support to express the funct...

Baculovirus Genomics

NARCIS (Netherlands)

Oers, van M.M.; Vlak, J.M.

2007-01-01

Baculovirus genomes are covalently closed circles of double stranded-DNA varying in size between 80 and 180 kilobase-pair. The genomes of more than fourty-one baculoviruses have been sequenced to date. The majority of these (37) are pathogenic to lepidopteran hosts; three infect sawflies

Molluscan Evolutionary Genomics

Energy Technology Data Exchange (ETDEWEB)

Simison, W. Brian; Boore, Jeffrey L.

2005-12-01

In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

Molecular cytogenetic and genomic analyses reveal new insights into the origin of the wheat B genome.

Science.gov (United States)

Zhang, Wei; Zhang, Mingyi; Zhu, Xianwen; Cao, Yaping; Sun, Qing; Ma, Guojia; Chao, Shiaoman; Yan, Changhui; Xu, Steven S; Cai, Xiwen

2018-02-01

This work pinpointed the goatgrass chromosomal segment in the wheat B genome using modern cytogenetic and genomic technologies, and provided novel insights into the origin of the wheat B genome. Wheat is a typical allopolyploid with three homoeologous subgenomes (A, B, and D). The donors of the subgenomes A and D had been identified, but not for the subgenome B. The goatgrass Aegilops speltoides (genome SS) has been controversially considered a possible candidate for the donor of the wheat B genome. However, the relationship of the Ae. speltoides S genome with the wheat B genome remains largely obscure. The present study assessed the homology of the B and S genomes using an integrative cytogenetic and genomic approach, and revealed the contribution of Ae. speltoides to the origin of the wheat B genome. We discovered noticeable homology between wheat chromosome 1B and Ae. speltoides chromosome 1S, but not between other chromosomes in the B and S genomes. An Ae. speltoides-originated segment spanning a genomic region of approximately 10.46 Mb was detected on the long arm of wheat chromosome 1B (1BL). The Ae. speltoides-originated segment on 1BL was found to co-evolve with the rest of the B genome. Evidently, Ae. speltoides had been involved in the origin of the wheat B genome, but should not be considered an exclusive donor of this genome. The wheat B genome might have a polyphyletic origin with multiple ancestors involved, including Ae. speltoides. These novel findings will facilitate genome studies in wheat and other polyploids.

RadGenomics project

Energy Technology Data Exchange (ETDEWEB)

Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu [National Inst. of Radiological Sciences, Chiba (Japan). Frontier Research Center] [and others

2002-06-01

Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

RadGenomics project

International Nuclear Information System (INIS)

Iwakawa, Mayumi; Imai, Takashi; Harada, Yoshinobu

2002-01-01

Human health is determined by a complex interplay of factors, predominantly between genetic susceptibility, environmental conditions and aging. The ultimate aim of the RadGenomics (Radiation Genomics) project is to understand the implications of heterogeneity in responses to ionizing radiation arising from genetic variation between individuals in the human population. The rapid progression of the human genome sequencing and the recent development of new technologies in molecular genetics are providing us with new opportunities to understand the genetic basis of individual differences in susceptibility to natural and/or artificial environmental factors, including radiation exposure. The RadGenomics project will inevitably lead to improved protocols for personalized radiotherapy and reductions in the potential side effects of such treatment. The project will contribute to future research into the molecular mechanisms of radiation sensitivity in humans and will stimulate the development of new high-throughput technologies for a broader application of biological and medical sciences. The staff members are specialists in a variety of fields, including genome science, radiation biology, medical science, molecular biology, and informatics, and have joined the RadGenomics project from various universities, companies, and research institutes. The project started in April 2001. (author)

Rumen microbial genomics

International Nuclear Information System (INIS)

Morrison, M.; Nelson, K.E.

2005-01-01

Improving microbial degradation of plant cell wall polysaccharides remains one of the highest priority goals for all livestock enterprises, including the cattle herds and draught animals of developing countries. The North American Consortium for Genomics of Fibrolytic Ruminal Bacteria was created to promote the sequencing and comparative analysis of rumen microbial genomes, offering the potential to fully assess the genetic potential in a functional and comparative fashion. It has been found that the Fibrobacter succinogenes genome encodes many more endoglucanases and cellodextrinases than previously isolated, and several new processive endoglucanases have been identified by genome and proteomic analysis of Ruminococcus albus, in addition to a variety of strategies for its adhesion to fibre. The ramifications of acquiring genome sequence data for rumen microorganisms are profound, including the potential to elucidate and overcome the biochemical, ecological or physiological processes that are rate limiting for ruminal fibre degradation. (author)

Análise do efeito higrotérmico no comportamento em fadiga de compósitos de PPS/fibras de carbono On the analysis of hygrothermal effect on fatigue behavior of PPS/carbon fiber composite

Directory of Open Access Journals (Sweden)

Maria C. M. de Faria

2012-01-01

Full Text Available O contínuo crescimento na utilização de compósitos termoplásticos em componentes estruturais na indústria aeroespacial deve-se, primordialmente, à flexibilidade de projeto, excelência de suas propriedades mecânicas e baixa massa específica, aliadas aos elevados valores de resistência mecânica e rigidez e baixa incidência de corrosão, atendendo aos severos requisitos de desempenho quando em serviço dessas estruturas. Componentes com exigências estruturais, quando expostos a ambientes agressivos como elevada temperatura e umidade, podem ter suas propriedades mecânicas sensibilizadas por esses fatores ambientais, e devem ser cuidadosamente avaliados antes de serem colocados em serviço. Em função do que foi exposto este trabalho tem como objetivo contribuir para a avaliação do efeito higrotérmico na resistência à fadiga do compósito termoplástico PPS/fibras de carbono. Os materiais estudados foram cedidos pela empresa holandesa TenCate, fornecedora de laminados da Airbus e EMBRAER. Os resultados obtidos neste trabalho mostram que compósitos de PPS/fibras de carbono apresentam um aumento nos valores de resistência à tração quando condicionados higrotermicamente, devido à plasticização desta matriz polimérica, aumentando, consecutivamente, sua tenacidade à fratura. Entretanto, a partir dos ensaios realizados, foi constatado que o condicionamento higrotérmico não alterou de forma significativa o comportamento de vida em fadiga dos laminados PPS-C.The continued growth in the use of polymer composites in structural components in the aerospace industry is due primarily to the design flexibility, excellent mechanical properties and low density, combined with the high values of mechanical strength and stiffness and low incidence of corrosion, with which these structures meet several performance requirements when in service. Components with structural requirements may have their mechanical properties affected when

Comparative genomics reveals insights into avian genome evolution and adaptation

Science.gov (United States)

Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

2015-01-01

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

Energy Technology Data Exchange (ETDEWEB)

Hu, Tina T.; Pattyn, Pedro; Bakker, Erica G.; Cao, Jun; Cheng, Jan-Fang; Clark, Richard M.; Fahlgren, Noah; Fawcett, Jeffrey A.; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hollister, Jesse D.; Ossowski, Stephan; Ottilar, Robert P.; Salamov, Asaf A.; Schneeberger, Korbinian; Spannagl, Manuel; Wang, Xi; Yang, Liang; Nasrallah, Mikhail E.; Bergelson, Joy; Carrington, James C.; Gaut, Brandon S.; Schmutz, Jeremy; Mayer, Klaus F. X.; Van de Peer, Yves; Grigoriev, Igor V.; Nordborg, Magnus; Weigel, Detlef; Guo, Ya-Long

2011-04-29

In our manuscript, we present a high-quality genome sequence of the Arabidopsis thaliana relative, Arabidopsis lyrata, produced by dideoxy sequencing. We have performed the usual types of genome analysis (gene annotation, dN/dS studies etc. etc.), but this is relegated to the Supporting Information. Instead, we focus on what was a major motivation for sequencing this genome, namely to understand how A. thaliana lost half its genome in a few million years and lived to tell the tale. The rather surprising conclusion is that there is not a single genomic feature that accounts for the reduced genome, but that every aspect centromeres, intergenic regions, transposable elements, gene family number is affected through hundreds of thousands of cuts. This strongly suggests that overall genome size in itself is what has been under selection, a suggestion that is strongly supported by our demonstration (using population genetics data from A. thaliana) that new deletions seem to be driven to fixation.

Genome Imprinting

Indian Academy of Sciences (India)

the cell nucleus (mitochondrial and chloroplast genomes), and. (3) traits governed ... tively good embryonic development but very poor development of membranes and ... Human homologies for the type of situation described above are naturally ..... imprint; (b) New modifications of the paternal genome in germ cells of each ...

Genomes to Proteomes

Energy Technology Data Exchange (ETDEWEB)

Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

2009-03-01

Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

Genome Improvement at JGI-HAGSC

Energy Technology Data Exchange (ETDEWEB)

Grimwood, Jane; Schmutz, Jeremy J.; Myers, Richard M.

2012-03-03

Since the completion of the sequencing of the human genome, the Joint Genome Institute (JGI) has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes.

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

Directory of Open Access Journals (Sweden)

Lincoln D Stein

2003-11-01

Full Text Available The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp and C. elegans (100.3 Mbp genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C

A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China.

Science.gov (United States)

Yu, Jun; Wong, Gane Ka-Shu; Liu, Siqi; Wang, Jian; Yang, Huanming

2007-06-29

In May 2000, the Beijing Institute of Genomics formally announced the launch of a comprehensive crop genome research project on rice genomics, the Chinese Superhybrid Rice Genome Project. SRGP is not simply a sequencing project targeted to a single rice (Oryza sativa L.) genome, but a full-swing research effort with an ultimate goal of providing inclusive basic genomic information and molecular tools not only to understand biology of the rice, both as an important crop species and a model organism of cereals, but also to focus on a popular superhybrid rice landrace, LYP9. We have completed the first phase of SRGP and provide the rice research community with a finished genome sequence of an indica variety, 93-11 (the paternal cultivar of LYP9), together with ample data on subspecific (between subspecies) polymorphisms, transcriptomes and proteomes, useful for within-species comparative studies. In the second phase, we have acquired the genome sequence of the maternal cultivar, PA64S, together with the detailed catalogues of genes uniquely expressed in the parental cultivars and the hybrid as well as allele-specific markers that distinguish parental alleles. Although SRGP in China is not an open-ended research programme, it has been designed to pave a way for future plant genomics research and application, such as to interrogate fundamentals of plant biology, including genome duplication, polyploidy and hybrid vigour, as well as to provide genetic tools for crop breeding and to carry along a social burden-leading a fight against the world's hunger. It began with genomics, the newly developed and industry-scale research field, and from the world's most populous country. In this review, we summarize our scientific goals and noteworthy discoveries that exploit new territories of systematic investigations on basic and applied biology of rice and other major cereal crops.

Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.

Directory of Open Access Journals (Sweden)

Tamara Smokvina

Full Text Available Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis

A Trichosporonales genome tree based on 27 haploid and three evolutionarily conserved 'natural' hybrid genomes.

Science.gov (United States)

Takashima, Masako; Sriswasdi, Sira; Manabe, Ri-Ichiroh; Ohkuma, Moriya; Sugita, Takashi; Iwasaki, Wataru

2018-01-01

To construct a backbone tree consisting of basidiomycetous yeasts, draft genome sequences from 25 species of Trichosporonales (Tremellomycetes, Basidiomycota) were generated. In addition to the hybrid genomes of Trichosporon coremiiforme and Trichosporon ovoides that we described previously, we identified an interspecies hybrid genome in Cutaneotrichosporon mucoides (formerly Trichosporon mucoides). This hybrid genome had a gene retention rate of ~55%, and its closest haploid relative was Cutaneotrichosporon dermatis. After constructing the C. mucoides subgenomes, we generated a phylogenetic tree using genome data from the 27 haploid species and the subgenome data from the three hybrid genome species. It was a high-quality tree with 100% bootstrap support for all of the branches. The genome-based tree provided superior resolution compared with previous multi-gene analyses. Although our backbone tree does not include all Trichosporonales genera (e.g. Cryptotrichosporon), it will be valuable for future analyses of genome data. Interest in interspecies hybrid fungal genomes has recently increased because they may provide a basis for new technologies. The three Trichosporonales hybrid genomes described in this study are different from well-characterized hybrid genomes (e.g. those of Saccharomyces pastorianus and Saccharomyces bayanus) because these hybridization events probably occurred in the distant evolutionary past. Hence, they will be useful for studying genome stability following hybridization and speciation events. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

Science.gov (United States)

Liu, Shengyi; Liu, Yumei; Yang, Xinhua; Tong, Chaobo; Edwards, David; Parkin, Isobel A. P.; Zhao, Meixia; Ma, Jianxin; Yu, Jingyin; Huang, Shunmou; Wang, Xiyin; Wang, Junyi; Lu, Kun; Fang, Zhiyuan; Bancroft, Ian; Yang, Tae-Jin; Hu, Qiong; Wang, Xinfa; Yue, Zhen; Li, Haojie; Yang, Linfeng; Wu, Jian; Zhou, Qing; Wang, Wanxin; King, Graham J; Pires, J. Chris; Lu, Changxin; Wu, Zhangyan; Sampath, Perumal; Wang, Zhuo; Guo, Hui; Pan, Shengkai; Yang, Limei; Min, Jiumeng; Zhang, Dong; Jin, Dianchuan; Li, Wanshun; Belcram, Harry; Tu, Jinxing; Guan, Mei; Qi, Cunkou; Du, Dezhi; Li, Jiana; Jiang, Liangcai; Batley, Jacqueline; Sharpe, Andrew G; Park, Beom-Seok; Ruperao, Pradeep; Cheng, Feng; Waminal, Nomar Espinosa; Huang, Yin; Dong, Caihua; Wang, Li; Li, Jingping; Hu, Zhiyong; Zhuang, Mu; Huang, Yi; Huang, Junyan; Shi, Jiaqin; Mei, Desheng; Liu, Jing; Lee, Tae-Ho; Wang, Jinpeng; Jin, Huizhe; Li, Zaiyun; Li, Xun; Zhang, Jiefu; Xiao, Lu; Zhou, Yongming; Liu, Zhongsong; Liu, Xuequn; Qin, Rui; Tang, Xu; Liu, Wenbin; Wang, Yupeng; Zhang, Yangyong; Lee, Jonghoon; Kim, Hyun Hee; Denoeud, France; Xu, Xun; Liang, Xinming; Hua, Wei; Wang, Xiaowu; Wang, Jun; Chalhoub, Boulos; Paterson, Andrew H

2014-01-01

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. PMID:24852848

Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology

Science.gov (United States)

Ping, Zheng; Siegal, Gene P.; Almeida, Jonas S.; Schnitt, Stuart J.; Shen, Dejun

2014-01-01

Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA) is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer. PMID:24672738

Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology

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Zheng Ping

2014-01-01

Full Text Available Background: Genetics and genomics have radically altered our understanding of breast cancer progression. However, the genomic basis of various histopathologic features of breast cancer is not yet well-defined. Materials and Methods: The Cancer Genome Atlas (TCGA is an international database containing a large collection of human cancer genome sequencing data. cBioPortal is a web tool developed for mining these sequencing data. We performed mining of TCGA sequencing data in an attempt to characterize the genomic features correlated with breast cancer histopathology. We first assessed the quality of the TCGA data using a group of genes with known alterations in various cancers. Both genome-wide gene mutation and copy number changes as well as a group of genes with a high frequency of genetic changes were then correlated with various histopathologic features of invasive breast cancer. Results: Validation of TCGA data using a group of genes with known alterations in breast cancer suggests that the TCGA has accurately documented the genomic abnormalities of multiple malignancies. Further analysis of TCGA breast cancer sequencing data shows that accumulation of specific genomic defects is associated with higher tumor grade, larger tumor size and receptor negativity. Distinct groups of genomic changes were found to be associated with the different grades of invasive ductal carcinoma. The mutator role of the TP53 gene was validated by genomic sequencing data of invasive breast cancer and TP53 mutation was found to play a critical role in defining high tumor grade. Conclusions: Data mining of the TCGA genome sequencing data is an innovative and reliable method to help characterize the genomic abnormalities associated with histopathologic features of invasive breast cancer.

Whole-genome sequence of the Tibetan frog Nanorana parkeri and the comparative evolution of tetrapod genomes.

Science.gov (United States)

Sun, Yan-Bo; Xiong, Zi-Jun; Xiang, Xue-Yan; Liu, Shi-Ping; Zhou, Wei-Wei; Tu, Xiao-Long; Zhong, Li; Wang, Lu; Wu, Dong-Dong; Zhang, Bao-Lin; Zhu, Chun-Ling; Yang, Min-Min; Chen, Hong-Man; Li, Fang; Zhou, Long; Feng, Shao-Hong; Huang, Chao; Zhang, Guo-Jie; Irwin, David; Hillis, David M; Murphy, Robert W; Yang, Huan-Ming; Che, Jing; Wang, Jun; Zhang, Ya-Ping

2015-03-17

The development of efficient sequencing techniques has resulted in large numbers of genomes being available for evolutionary studies. However, only one genome is available for all amphibians, that of Xenopus tropicalis, which is distantly related from the majority of frogs. More than 96% of frogs belong to the Neobatrachia, and no genome exists for this group. This dearth of amphibian genomes greatly restricts genomic studies of amphibians and, more generally, our understanding of tetrapod genome evolution. To fill this gap, we provide the de novo genome of a Tibetan Plateau frog, Nanorana parkeri, and compare it to that of X. tropicalis and other vertebrates. This genome encodes more than 20,000 protein-coding genes, a number similar to that of Xenopus. Although the genome size of Nanorana is considerably larger than that of Xenopus (2.3 vs. 1.5 Gb), most of the difference is due to the respective number of transposable elements in the two genomes. The two frogs exhibit considerable conserved whole-genome synteny despite having diverged approximately 266 Ma, indicating a slow rate of DNA structural evolution in anurans. Multigenome synteny blocks further show that amphibians have fewer interchromosomal rearrangements than mammals but have a comparable rate of intrachromosomal rearrangements. Our analysis also identifies 11 Mb of anuran-specific highly conserved elements that will be useful for comparative genomic analyses of frogs. The Nanorana genome offers an improved understanding of evolution of tetrapod genomes and also provides a genomic reference for other evolutionary studies.

Sur la reconnaissance de la compétence exclusive des groupements religieux afin d‘instaurer leur structure intrinsèque et les normes intérieures des relations en tant qu’une des garanties ...

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Philip Ryabykh

2012-11-01

SOMMAIRE: 1. Brève histoire de l’affaire – 2. Préambule – 3. Protection de la compétence exclusive des groupements religieux en vue d’instaurer leur structure intrinsèque et les normes intérieures des relations au point de vue de la législation de la Roumanie – 4. Application du principe de l’autonomie des groupements religieux et du principe de l’inadmissibilité d’intervenir pour l’État aux affaires intérieures des groupements religieux – 5. Non-contradiction de la Convention des exigences intérieures des groupements religieux sur la loyauté et la conformité des personnes se trouvant dans les relations de service avec le groupement religieux – 6. Absence des raisons fournies par les faits juridiques suffisantes et justifiant réellement l’assimilation (la mise au même niveau des groupements religieux avec n’importe quelles autres organisations-employeurs dans la sphère de la réglementation des relations de travail – 7. Légalité de l’instauration des restrictions à la création et les activités des syndicats dans les certaines sphères des relations publiques – 8. Compétence de la Roumanie de fixer dans la législation les restrictions à la liberté des syndicats conformément à la sphère des relations religieuses – 9. Signification des résultats du jugement de l’affaire «Syndicat “Le Bon Pasteur” c. Roumanie» (requête 2330/09 pour L’Église Orthodoxe Russe- 10. Conclusion.

The complete mitochondrial genome of Gossypium hirsutum and evolutionary analysis of higher plant mitochondrial genomes.

Science.gov (United States)

Liu, Guozheng; Cao, Dandan; Li, Shuangshuang; Su, Aiguo; Geng, Jianing; Grover, Corrinne E; Hu, Songnian; Hua, Jinping

2013-01-01

Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes. We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes. The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.

Microbial Genomes Multiply

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Doolittle, Russell F.

2002-01-01

The publication of the first complete sequence of a bacterial genome in 1995 was a signal event, underscored by the fact that the article has been cited more than 2,100 times during the intervening seven years. It was a marvelous technical achievement, made possible by automatic DNA-sequencing machines. The feat is the more impressive in that complete genome sequencing has now been adopted in many different laboratories around the world. Four years ago in these columns I examined the situation after a dozen microbial genomes had been completed. Now, with upwards of 60 microbial genome sequences determined and twice that many in progress, it seems reasonable to assess just what is being learned. Are new concepts emerging about how cells work? Have there been practical benefits in the fields of medicine and agriculture? Is it feasible to determine the genomic sequence of every bacterial species on Earth? The answers to these questions maybe Yes, Perhaps, and No, respectively.

Genomic research perspectives in Kazakhstan

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Ainur Akilzhanova

2014-01-01

Full Text Available Introduction: Technological advancements rapidly propel the field of genome research. Advances in genetics and genomics such as the sequence of the human genome, the human haplotype map, open access databases, cheaper genotyping and chemical genomics, have transformed basic and translational biomedical research. Several projects in the field of genomic and personalized medicine have been conducted at the Center for Life Sciences in Nazarbayev University. The prioritized areas of research include: genomics of multifactorial diseases, cancer genomics, bioinformatics, genetics of infectious diseases and population genomics. At present, DNA-based risk assessment for common complex diseases, application of molecular signatures for cancer diagnosis and prognosis, genome-guided therapy, and dose selection of therapeutic drugs are the important issues in personalized medicine. Results: To further develop genomic and biomedical projects at Center for Life Sciences, the development of bioinformatics research and infrastructure and the establishment of new collaborations in the field are essential. Widespread use of genetic tools will allow the identification of diseases before the onset of clinical symptoms, the individualization of drug treatment, and could induce individual behavioral changes on the basis of calculated disease risk. However, many challenges remain for the successful translation of genomic knowledge and technologies into health advances, such as medicines and diagnostics. It is important to integrate research and education in the fields of genomics, personalized medicine, and bioinformatics, which will be possible with opening of the new Medical Faculty at Nazarbayev University. People in practice and training need to be educated about the key concepts of genomics and engaged so they can effectively apply their knowledge in a matter that will bring the era of genomic medicine to patient care. This requires the development of well

Modificação de fibra de carbono com PBLH e sua utilização em compósitos com resina epoxídica Hydroxyl-terminated polybutadiene-grafted carbon fiber in epoxy resin-based composites

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Fábio L. Barcia

1999-06-01

Full Text Available Fibras de carbono contendo 1,4 e 2,1mmol/g de grupos carboxila e hidroxila fenólica, respectivamente, foram modificadas através de reação com TDI, resultando em fibras contendo 3,1 mmol/g de grupos isocianato. A introdução de grupos isocianato na superfície da fibra tornou possível a sua modificação com polibutadieno líquido hidroxilado. Fibras de carbono modificadas e não modificadas foram empregadas na preparação de compósitos com resina epoxídica, sendo observado um aumento considerável de resistência ao impacto em compósitos constituídos de fibras de carbono enxertadas com PBLH, devido, provavelmente, à natureza elastomérica da interface e à melhor adesão interfacial.Carbon fibers containing 1,4 e 2,1 mmol/g of carboxyl and phenolic hydroxyl groups, respectively, were modified through the reaction with TDI. The presence of isocyanate groups at the fiber surface made possible the fiber modification with hydroxyl terminated polybutadiene (HTPB. These modified and unmodified carbon fibers were employed in the preparation of epoxy resin-based composites. A substantial improvement in the impact properties was observed in the composites with HTPB-grafted carbon fibers when compared to unmodified carbon fibers. These results may be attributed to a higher interfacial adhesion promoted by reactions between the functional groups present at the modified carbon fiber surface and the epoxy matrix.

Efficient Breeding by Genomic Mating.

Science.gov (United States)

Akdemir, Deniz; Sánchez, Julio I

2016-01-01

Selection in breeding programs can be done by using phenotypes (phenotypic selection), pedigree relationship (breeding value selection) or molecular markers (marker assisted selection or genomic selection). All these methods are based on truncation selection, focusing on the best performance of parents before mating. In this article we proposed an approach to breeding, named genomic mating, which focuses on mating instead of truncation selection. Genomic mating uses information in a similar fashion to genomic selection but includes information on complementation of parents to be mated. Following the efficiency frontier surface, genomic mating uses concepts of estimated breeding values, risk (usefulness) and coefficient of ancestry to optimize mating between parents. We used a genetic algorithm to find solutions to this optimization problem and the results from our simulations comparing genomic selection, phenotypic selection and the mating approach indicate that current approach for breeding complex traits is more favorable than phenotypic and genomic selection. Genomic mating is similar to genomic selection in terms of estimating marker effects, but in genomic mating the genetic information and the estimated marker effects are used to decide which genotypes should be crossed to obtain the next breeding population.

The life cycle of a genome project: perspectives and guidelines inspired by insect genome projects.

Science.gov (United States)

Papanicolaou, Alexie

2016-01-01

Many research programs on non-model species biology have been empowered by genomics. In turn, genomics is underpinned by a reference sequence and ancillary information created by so-called "genome projects". The most reliable genome projects are the ones created as part of an active research program and designed to address specific questions but their life extends past publication. In this opinion paper I outline four key insights that have facilitated maintaining genomic communities: the key role of computational capability, the iterative process of building genomic resources, the value of community participation and the importance of manual curation. Taken together, these ideas can and do ensure the longevity of genome projects and the growing non-model species community can use them to focus a discussion with regards to its future genomic infrastructure.

Genomic prediction using subsampling

OpenAIRE

Xavier, Alencar; Xu, Shizhong; Muir, William; Rainey, Katy Martin

2017-01-01

Background Genome-wide assisted selection is a critical tool for the?genetic improvement of plants and animals. Whole-genome regression models in Bayesian framework represent the main family of prediction methods. Fitting such models with a large number of observations involves a prohibitive computational burden. We propose the use of subsampling bootstrap Markov chain in genomic prediction. Such method consists of fitting whole-genome regression models by subsampling observations in each rou...

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.

Science.gov (United States)

Jayakodi, Murukarthick; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Nam-Hoon; Park, Jee Young; Jang, Woojong; Lakshmanan, Meiyappan; Mohan, Shobhana V G; Lee, Dong-Yup; Yang, Tae-Jin

2018-04-12

The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page. This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

Genome Modeling System: A Knowledge Management Platform for Genomics.

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Malachi Griffith

2015-07-01

Full Text Available In this work, we present the Genome Modeling System (GMS, an analysis information management system capable of executing automated genome analysis pipelines at a massive scale. The GMS framework provides detailed tracking of samples and data coupled with reliable and repeatable analysis pipelines. The GMS also serves as a platform for bioinformatics development, allowing a large team to collaborate on data analysis, or an individual researcher to leverage the work of others effectively within its data management system. Rather than separating ad-hoc analysis from rigorous, reproducible pipelines, the GMS promotes systematic integration between the two. As a demonstration of the GMS, we performed an integrated analysis of whole genome, exome and transcriptome sequencing data from a breast cancer cell line (HCC1395 and matched lymphoblastoid line (HCC1395BL. These data are available for users to test the software, complete tutorials and develop novel GMS pipeline configurations. The GMS is available at https://github.com/genome/gms.

Ancient genomes

OpenAIRE

Hoelzel, A Rus

2005-01-01

Ever since its invention, the polymerase chain reaction has been the method of choice for work with ancient DNA. In an application of modern genomic methods to material from the Pleistocene, a recent study has instead undertaken to clone and sequence a portion of the ancient genome of the cave bear.

Governance in genomics: a conceptual challenge for public health genomics law

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Tobias Schulte in den Bäumen

2006-12-01

Full Text Available Increasing levels of genomic knowledge has led to awareness that new governance issues need to be taken into consideration. While some countries have created new statutory laws in the last 10 years, science supports the idea that genomic data should be treated like other medical data. In this article we discuss the three core models of governance in medical law on a conceptual level. The three models, the Medical, Public Health and Fundamental Rights Model stress different values, or in legal terms serve different principles. The Medical Model stands for expert knowledge and the standardisation of quality in healthcare. The Public Health Model fosters a social point of view as it advocates distribution justice in healthcare and an awareness of healthcare as a broader concept. The Fundamental Rights Model focuses on individual rights such as the right to privacy and autonomy. We argue that none of the models can be used in a purist fashion as governance in genomics should enable society and individuals to protect individual rights, to strive for a distribution justice and to ensure the quality of genomic services in one coherent process. Thus, genomic governance in genomics requires procedural law and a set of applicable principles. The principle which underlies all three models is the principle of medical beneficence. Therefore genomic governance should refer to it as a key principle when conflicting rights of individuals or communities need to be balanced.

Genetical Genomics for Evolutionary Studies

NARCIS (Netherlands)

Prins, J.C.P.; Smant, G.; Jansen, R.C.

2012-01-01

Genetical genomics combines acquired high-throughput genomic data with genetic analysis. In this chapter, we discuss the application of genetical genomics for evolutionary studies, where new high-throughput molecular technologies are combined with mapping quantitative trait loci (QTL) on the genome

Human social genomics.

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Steven W Cole

2014-08-01

Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

Reference-quality genome sequence of Aegilops tauschii, the source of wheat D genome, shows that recombination shapes genome structure and evolution

Science.gov (United States)

Aegilops tauschii is the diploid progenitor of the D genome of hexaploid wheat and an important genetic resource for wheat. A reference-quality sequence for the Ae. tauschii genome was produced with a combination of ordered-clone sequencing, whole-genome shotgun sequencing, and BioNano optical geno...

Genomic taxonomy of vibrios

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Iida Tetsuya

2009-10-01

Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

Comparative genome analysis of Bacillus cereus group genomes withBacillus subtilis

Energy Technology Data Exchange (ETDEWEB)

Anderson, Iain; Sorokin, Alexei; Kapatral, Vinayak; Reznik, Gary; Bhattacharya, Anamitra; Mikhailova, Natalia; Burd, Henry; Joukov, Victor; Kaznadzey, Denis; Walunas, Theresa; D' Souza, Mark; Larsen, Niels; Pusch,Gordon; Liolios, Konstantinos; Grechkin, Yuri; Lapidus, Alla; Goltsman,Eugene; Chu, Lien; Fonstein, Michael; Ehrlich, S. Dusko; Overbeek, Ross; Kyrpides, Nikos; Ivanova, Natalia

2005-09-14

Genome features of the Bacillus cereus group genomes (representative strains of Bacillus cereus, Bacillus anthracis and Bacillus thuringiensis sub spp israelensis) were analyzed and compared with the Bacillus subtilis genome. A core set of 1,381 protein families among the four Bacillus genomes, with an additional set of 933 families common to the B. cereus group, was identified. Differences in signal transduction pathways, membrane transporters, cell surface structures, cell wall, and S-layer proteins suggesting differences in their phenotype were identified. The B. cereus group has signal transduction systems including a tyrosine kinase related to two-component system histidine kinases from B. subtilis. A model for regulation of the stress responsive sigma factor sigmaB in the B. cereus group different from the well studied regulation in B. subtilis has been proposed. Despite a high degree of chromosomal synteny among these genomes, significant differences in cell wall and spore coat proteins that contribute to the survival and adaptation in specific hosts has been identified.

What does it mean to be genomically literate?: National Human Genome Research Institute Meeting Report.

Science.gov (United States)

Hurle, Belen; Citrin, Toby; Jenkins, Jean F; Kaphingst, Kimberly A; Lamb, Neil; Roseman, Jo Ellen; Bonham, Vence L

2013-08-01

Genomic discoveries will increasingly advance the science of medicine. Limited genomic literacy may adversely impact the public's understanding and use of the power of genetics and genomics in health care and public health. In November 2011, a meeting was held by the National Human Genome Research Institute to examine the challenge of achieving genomic literacy for the general public, from kindergarten to grade 12 to adult education. The role of the media in disseminating scientific messages and in perpetuating or reducing misconceptions was also discussed. Workshop participants agreed that genomic literacy will be achieved only through active engagement between genomics experts and the varied constituencies that comprise the public. This report summarizes the background, content, and outcomes from this meeting, including recommendations for a research agenda to inform decisions about how to advance genomic literacy in our society.

Ultrafast comparison of personal genomes

OpenAIRE

Mauldin, Denise; Hood, Leroy; Robinson, Max; Glusman, Gustavo

2017-01-01

We present an ultra-fast method for comparing personal genomes. We transform the standard genome representation (lists of variants relative to a reference) into 'genome fingerprints' that can be readily compared across sequencing technologies and reference versions. Because of their reduced size, computation on the genome fingerprints is fast and requires little memory. This enables scaling up a variety of important genome analyses, including quantifying relatedness, recognizing duplicative s...

Bioinformatics decoding the genome

CERN Multimedia

CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

2006-01-01

Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

DEFF Research Database (Denmark)

Gopalakrishnan, Shyam; Samaniego Castruita, Jose Alfredo; Sinding, Mikkel Holger Strander

2017-01-01

Background An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a......Background An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data...... that regardless of the reference genome choice, most evolutionary genomic analyses yield qualitatively similar results, including those exploring the structure between the wolves and dogs using admixture and principal component analysis. However, we do observe differences in the genomic coverage of re-mapped...

The Small Nuclear Genomes of Selaginella Are Associated with a Low Rate of Genome Size Evolution.

Science.gov (United States)

Baniaga, Anthony E; Arrigo, Nils; Barker, Michael S

2016-06-03

The haploid nuclear genome size (1C DNA) of vascular land plants varies over several orders of magnitude. Much of this observed diversity in genome size is due to the proliferation and deletion of transposable elements. To date, all vascular land plant lineages with extremely small nuclear genomes represent recently derived states, having ancestors with much larger genome sizes. The Selaginellaceae represent an ancient lineage with extremely small genomes. It is unclear how small nuclear genomes evolved in Selaginella We compared the rates of nuclear genome size evolution in Selaginella and major vascular plant clades in a comparative phylogenetic framework. For the analyses, we collected 29 new flow cytometry estimates of haploid genome size in Selaginella to augment publicly available data. Selaginella possess some of the smallest known haploid nuclear genome sizes, as well as the lowest rate of genome size evolution observed across all vascular land plants included in our analyses. Additionally, our analyses provide strong support for a history of haploid nuclear genome size stasis in Selaginella Our results indicate that Selaginella, similar to other early diverging lineages of vascular land plants, has relatively low rates of genome size evolution. Further, our analyses highlight that a rapid transition to a small genome size is only one route to an extremely small genome. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

1000 Bull Genomes - Toward genomic Selectionf from whole genome sequence Data in Dairy and Beef Cattle

NARCIS (Netherlands)

Hayes, B.; Daetwyler, H.D.; Fries, R.; Guldbrandtsen, B.; Mogens Sando Lund, M.; Didier A. Boichard, D.A.; Stothard, P.; Veerkamp, R.F.; Hulsegge, B.; Rocha, D.; Tassell, C.; Mullaart, E.; Gredler, B.; Druet, T.; Bagnato, A.; Goddard, M.E.; Chamberlain, H.L.

2013-01-01

Genomic prediction of breeding values is now used as the basis for selection of dairy cattle, and in some cases beef cattle, in a number of countries. When genomic prediction was introduced most of the information was to thought to be derived from linkage disequilibrium between markers and causative

Musa sebagai Model Genom

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RITA MEGIA

2005-12-01

Full Text Available During the meeting in Arlington, USA in 2001, the scientists grouped in PROMUSA agreed with the launching of the Global Musa Genomics Consortium. The Consortium aims to apply genomics technologies to the improvement of this important crop. These genome projects put banana as the third model species after Arabidopsis and rice that will be analyzed and sequenced. Comparing to Arabidopsis and rice, banana genome provides a unique and powerful insight into structural and in functional genomics that could not be found in those two species. This paper discussed these subjects-including the importance of banana as the fourth main food in the world, the evolution and biodiversity of this genetic resource and its parasite.

Human-specific HERV-K insertion causes genomic variations in the human genome.

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Wonseok Shin

Full Text Available Human endogenous retroviruses (HERV sequences account for about 8% of the human genome. Through comparative genomics and literature mining, we identified a total of 29 human-specific HERV-K insertions. We characterized them focusing on their structure and flanking sequence. The results showed that four of the human-specific HERV-K insertions deleted human genomic sequences via non-classical insertion mechanisms. Interestingly, two of the human-specific HERV-K insertion loci contained two HERV-K internals and three LTR elements, a pattern which could be explained by LTR-LTR ectopic recombination or template switching. In addition, we conducted a polymorphic test and observed that twelve out of the 29 elements are polymorphic in the human population. In conclusion, human-specific HERV-K elements have inserted into human genome since the divergence of human and chimpanzee, causing human genomic changes. Thus, we believe that human-specific HERV-K activity has contributed to the genomic divergence between humans and chimpanzees, as well as within the human population.

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

Science.gov (United States)

Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

2017-06-01

Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Genomic Resource and Genome Guided Comparison of Twenty Type Strains of the Genus Methylobacterium

Directory of Open Access Journals (Sweden)

Vasvi Chaudhry

2017-12-01

Full Text Available Bacteria of the genus Methylobacterium are widespread in diverse habitats ranging from soil, water and plant (phyllosphere, rhizosphere and endosphere. In the present study, we in house generated genomic data resource of six type strains along with fourteen database genomes of the Methylobacterium genus to carry out phylogenomic, taxonomic, comparative and ecological studies of this genus. Overall, the genus shows high diversity and genetic variation primarily due to its ability to acquire genetic material from diverse sources through horizontal gene transfer. As majority of species identified in this study are plant associated with their genomes equipped with methylotrophy and photosynthesis related gene along with genes for plant probiotic traits. Most of the species genomes are equipped with genes for adaptation and defense for UV radiation, oxidative stress and desiccation. The genus has an open pan-genome and we predicted the role of gain/loss of prophages and CRISPR elements in diversity and evolution. Our genomic resource with annotation and analysis provides a platform for interspecies genomic comparisons in the genus Methylobacterium, and to unravel their natural genome diversity and to study how natural selection shapes their genome with the adaptive mechanisms which allow them to acquire diverse habitat lifestyles. This type strains genomic data display power of Next Generation Sequencing in rapidly creating resource paving the way for studies on phylogeny and taxonomy as well as for basic and applied research for this important genus.

Genomic instability following irradiation

International Nuclear Information System (INIS)

Hacker-Klom, U.B.; Goehde, W.

2001-01-01

Ionising irradiation may induce genomic instability. The broad spectrum of stress reactions in eukaryontic cells to irradiation complicates the discovery of cellular targets and pathways inducing genomic instability. Irradiation may initiate genomic instability by deletion of genes controlling stability, by induction of genes stimulating instability and/or by activating endogeneous cellular viruses. Alternatively or additionally it is discussed that the initiation of genomic instability may be a consequence of radiation or other agents independently of DNA damage implying non nuclear targets, e.g. signal cascades. As a further mechanism possibly involved our own results may suggest radiation-induced changes in chromatin structure. Once initiated the process of genomic instability probably is perpetuated by endogeneous processes necessary for proliferation. Genomic instability may be a cause or a consequence of the neoplastic phenotype. As a conclusion from the data available up to now a new interpretation of low level radiation effects for radiation protection and in radiotherapy appears useful. The detection of the molecular mechanisms of genomic instability will be important in this context and may contribute to a better understanding of phenomenons occurring at low doses <10 cSv which are not well understood up to now. (orig.)

Evolution of small prokaryotic genomes

Directory of Open Access Journals (Sweden)

David José Martínez-Cano

2015-01-01

Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

Insights into Conifer Giga-Genomes1

Science.gov (United States)

De La Torre, Amanda R.; Birol, Inanc; Bousquet, Jean; Ingvarsson, Pär K.; Jansson, Stefan; Jones, Steven J.M.; Keeling, Christopher I.; MacKay, John; Nilsson, Ove; Ritland, Kermit; Street, Nathaniel; Yanchuk, Alvin; Zerbe, Philipp; Bohlmann, Jörg

2014-01-01

Insights from sequenced genomes of major land plant lineages have advanced research in almost every aspect of plant biology. Until recently, however, assembled genome sequences of gymnosperms have been missing from this picture. Conifers of the pine family (Pinaceae) are a group of gymnosperms that dominate large parts of the world’s forests. Despite their ecological and economic importance, conifers seemed long out of reach for complete genome sequencing, due in part to their enormous genome size (20–30 Gb) and the highly repetitive nature of their genomes. Technological advances in genome sequencing and assembly enabled the recent publication of three conifer genomes: white spruce (Picea glauca), Norway spruce (Picea abies), and loblolly pine (Pinus taeda). These genome sequences revealed distinctive features compared with other plant genomes and may represent a window into the past of seed plant genomes. This Update highlights recent advances, remaining challenges, and opportunities in light of the publication of the first conifer and gymnosperm genomes. PMID:25349325

Genome chaos: survival strategy during crisis.

Science.gov (United States)

Liu, Guo; Stevens, Joshua B; Horne, Steven D; Abdallah, Batoul Y; Ye, Karen J; Bremer, Steven W; Ye, Christine J; Chen, David J; Heng, Henry H

2014-01-01

Genome chaos, a process of complex, rapid genome re-organization, results in the formation of chaotic genomes, which is followed by the potential to establish stable genomes. It was initially detected through cytogenetic analyses, and recently confirmed by whole-genome sequencing efforts which identified multiple subtypes including "chromothripsis", "chromoplexy", "chromoanasynthesis", and "chromoanagenesis". Although genome chaos occurs commonly in tumors, both the mechanism and detailed aspects of the process are unknown due to the inability of observing its evolution over time in clinical samples. Here, an experimental system to monitor the evolutionary process of genome chaos was developed to elucidate its mechanisms. Genome chaos occurs following exposure to chemotherapeutics with different mechanisms, which act collectively as stressors. Characterization of the karyotype and its dynamic changes prior to, during, and after induction of genome chaos demonstrates that chromosome fragmentation (C-Frag) occurs just prior to chaotic genome formation. Chaotic genomes seem to form by random rejoining of chromosomal fragments, in part through non-homologous end joining (NHEJ). Stress induced genome chaos results in increased karyotypic heterogeneity. Such increased evolutionary potential is demonstrated by the identification of increased transcriptome dynamics associated with high levels of karyotypic variance. In contrast to impacting on a limited number of cancer genes, re-organized genomes lead to new system dynamics essential for cancer evolution. Genome chaos acts as a mechanism of rapid, adaptive, genome-based evolution that plays an essential role in promoting rapid macroevolution of new genome-defined systems during crisis, which may explain some unwanted consequences of cancer treatment.

Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria

Directory of Open Access Journals (Sweden)

Keeling Patrick J

2007-09-01

Full Text Available Abstract Background Dinoflagellates comprise an ecologically significant and diverse eukaryotic phylum that is sister to the phylum containing apicomplexan endoparasites. The mitochondrial genome of apicomplexans is uniquely reduced in gene content and size, encoding only three proteins and two ribosomal RNAs (rRNAs within a highly compacted 6 kb DNA. Dinoflagellate mitochondrial genomes have been comparatively poorly studied: limited available data suggest some similarities with apicomplexan mitochondrial genomes but an even more radical type of genomic organization. Here, we investigate structure, content and expression of dinoflagellate mitochondrial genomes. Results From two dinoflagellates, Crypthecodinium cohnii and Karlodinium micrum, we generated over 42 kb of mitochondrial genomic data that indicate a reduced gene content paralleling that of mitochondrial genomes in apicomplexans, i.e., only three protein-encoding genes and at least eight conserved components of the highly fragmented large and small subunit rRNAs. Unlike in apicomplexans, dinoflagellate mitochondrial genes occur in multiple copies, often as gene fragments, and in numerous genomic contexts. Analysis of cDNAs suggests several novel aspects of dinoflagellate mitochondrial gene expression. Polycistronic transcripts were found, standard start codons are absent, and oligoadenylation occurs upstream of stop codons, resulting in the absence of termination codons. Transcripts of at least one gene, cox3, are apparently trans-spliced to generate full-length mRNAs. RNA substitutional editing, a process previously identified for mRNAs in dinoflagellate mitochondria, is also implicated in rRNA expression. Conclusion The dinoflagellate mitochondrial genome shares the same gene complement and fragmentation of rRNA genes with its apicomplexan counterpart. However, it also exhibits several unique characteristics. Most notable are the expansion of gene copy numbers and their arrangements

Correction for Measurement Error from Genotyping-by-Sequencing in Genomic Variance and Genomic Prediction Models

DEFF Research Database (Denmark)

Ashraf, Bilal; Janss, Luc; Jensen, Just

sample). The GBSeq data can be used directly in genomic models in the form of individual SNP allele-frequency estimates (e.g., reference reads/total reads per polymorphic site per individual), but is subject to measurement error due to the low sequencing depth per individual. Due to technical reasons....... In the current work we show how the correction for measurement error in GBSeq can also be applied in whole genome genomic variance and genomic prediction models. Bayesian whole-genome random regression models are proposed to allow implementation of large-scale SNP-based models with a per-SNP correction...... for measurement error. We show correct retrieval of genomic explained variance, and improved genomic prediction when accounting for the measurement error in GBSeq data...

Genomic research in Eucalyptus.

Science.gov (United States)

Poke, Fiona S; Vaillancourt, René E; Potts, Brad M; Reid, James B

2005-09-01

Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.

Genome Sequences of Marine Shrimp Exopalaemon carinicauda Holthuis Provide Insights into Genome Size Evolution of Caridea.

Science.gov (United States)

Yuan, Jianbo; Gao, Yi; Zhang, Xiaojun; Wei, Jiankai; Liu, Chengzhang; Li, Fuhua; Xiang, Jianhai

2017-07-05

Crustacea, particularly Decapoda, contains many economically important species, such as shrimps and crabs. Crustaceans exhibit enormous (nearly 500-fold) variability in genome size. However, limited genome resources are available for investigating these species. Exopalaemon carinicauda Holthuis, an economical caridean shrimp, is a potential ideal experimental animal for research on crustaceans. In this study, we performed low-coverage sequencing and de novo assembly of the E. carinicauda genome. The assembly covers more than 95% of coding regions. E. carinicauda possesses a large complex genome (5.73 Gb), with size twice higher than those of many decapod shrimps. As such, comparative genomic analyses were implied to investigate factors affecting genome size evolution of decapods. However, clues associated with genome duplication were not identified, and few horizontally transferred sequences were detected. Ultimately, the burst of transposable elements, especially retrotransposons, was determined as the major factor influencing genome expansion. A total of 2 Gb repeats were identified, and RTE-BovB, Jockey, Gypsy, and DIRS were the four major retrotransposons that significantly expanded. Both recent (Jockey and Gypsy) and ancestral (DIRS) originated retrotransposons responsible for the genome evolution. The E. carinicauda genome also exhibited potential for the genomic and experimental research of shrimps.

Tolerance of Whole-Genome Doubling Propagates Chromosomal Instability and Accelerates Cancer Genome Evolution

DEFF Research Database (Denmark)

Dewhurst, Sally M.; McGranahan, Nicholas; Burrell, Rebecca A.

2014-01-01

The contribution of whole-genome doubling to chromosomal instability (CIN) and tumor evolution is unclear. We use long-term culture of isogenic tetraploid cells from a stable diploid colon cancer progenitor to investigate how a genome-doubling event affects genome stability over time. Rare cells...

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects.

Science.gov (United States)

Holt, Carson; Yandell, Mark

2011-12-22

Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies. We present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review. MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets.

Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

Science.gov (United States)

Abe, Takashi; Hamano, Yuta; Ikemura, Toshimichi

2014-01-01

A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.

Compétition pour l'azote inorganique entre le pelagos et le benthos dans un écosystème côtier oligotrophe. Effets sur la dynamique de l'écosystème.

OpenAIRE

Lepoint, Gilles

2001-01-01

Résumé de la thèse intitulée : Compétition pour l’azote inorganique entre le benthos et le pelagos d’un milieu côtier oligotrophe. Effets sur la dynamique de l’écosystème. Dissertation présentée le 9 mai 2001 par Gilles Lepoint en vue de l’obtention du grade de Docteur en Sciences de l’Université de Liège. Dans la Baie de la Revellata (Calvi, Corse, France), comme dans de nombreux sites côtiers méditerranéens, les biocénoses benthiques sont très développées et productives, malgré le c...

Rapid detection of structural variation in a human genome using nanochannel-based genome mapping technology

DEFF Research Database (Denmark)

Cao, Hongzhi; Hastie, Alex R.; Cao, Dandan

2014-01-01

mutations; however, none of the current detection methods are comprehensive, and currently available methodologies are incapable of providing sufficient resolution and unambiguous information across complex regions in the human genome. To address these challenges, we applied a high-throughput, cost......-effective genome mapping technology to comprehensively discover genome-wide SVs and characterize complex regions of the YH genome using long single molecules (>150 kb) in a global fashion. RESULTS: Utilizing nanochannel-based genome mapping technology, we obtained 708 insertions/deletions and 17 inversions larger...... fosmid data. Of the remaining 270 SVs, 260 are insertions and 213 overlap known SVs in the Database of Genomic Variants. Overall, 609 out of 666 (90%) variants were supported by experimental orthogonal methods or historical evidence in public databases. At the same time, genome mapping also provides...

A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

Science.gov (United States)

Swain, Martin T; Tsai, Isheng J; Assefa, Samual A; Newbold, Chris; Berriman, Matthew; Otto, Thomas D

2012-06-07

Genome projects now produce draft assemblies within weeks owing to advanced high-throughput sequencing technologies. For milestone projects such as Escherichia coli or Homo sapiens, teams of scientists were employed to manually curate and finish these genomes to a high standard. Nowadays, this is not feasible for most projects, and the quality of genomes is generally of a much lower standard. This protocol describes software (PAGIT) that is used to improve the quality of draft genomes. It offers flexible functionality to close gaps in scaffolds, correct base errors in the consensus sequence and exploit reference genomes (if available) in order to improve scaffolding and generating annotations. The protocol is most accessible for bacterial and small eukaryotic genomes (up to 300 Mb), such as pathogenic bacteria, malaria and parasitic worms. Applying PAGIT to an E. coli assembly takes ∼24 h: it doubles the average contig size and annotates over 4,300 gene models.

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species.

Science.gov (United States)

Kersey, Paul J; Staines, Daniel M; Lawson, Daniel; Kulesha, Eugene; Derwent, Paul; Humphrey, Jay C; Hughes, Daniel S T; Keenan, Stephan; Kerhornou, Arnaud; Koscielny, Gautier; Langridge, Nicholas; McDowall, Mark D; Megy, Karine; Maheswari, Uma; Nuhn, Michael; Paulini, Michael; Pedro, Helder; Toneva, Iliana; Wilson, Derek; Yates, Andrew; Birney, Ewan

2012-01-01

Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.

Exponential decay rate of the power spectrum for solutions of the Navier--Stokes equations

International Nuclear Information System (INIS)

Doering, C.R.; Titi, E.S.

1995-01-01

Using a method developed by Foias and Temam [J. Funct. Anal. 87, 359 (1989)], exponential decay of the spatial Fourier power spectrum for solutions of the incompressible Navier--Stokes equations is established and explicit rigorous lower bounds on a small length scale defined by the exponential decay rate are obtained

The Sturm-Liouville inverse spectral problem with boundary conditions depending on the spectral parameter

Directory of Open Access Journals (Sweden)

Cornelis van der Mee

2005-01-01

Full Text Available We present the complete version including proofs of the results announced in [van der Mee C., Pivovarchik V.: A Sturm-Liouville spectral problem with boundary conditions depending on the spectral parameter. Funct. Anal. Appl. 36 (2002, 315–317 [Funkts. Anal. Prilozh. 36 (2002, 74–77 (Russian

Strichartz Estimates for the Schrödinger Propagator for the Laguerre ...

Indian Academy of Sciences (India)

We obtain homogeneous Strichartz estimate for the Schrödinger propagator e − i t L for the Laguerre operator L on R + n . We follow regularization technique as introduced in J. Funct. Anal. 224(2) (2005) 371–385. We also establish inhomogeneous Strichartz estimates for different admissible pairs.

Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.

Science.gov (United States)

Jeong, Young-Min; Kim, Namshin; Ahn, Byung Ohg; Oh, Mijin; Chung, Won-Hyong; Chung, Hee; Jeong, Seongmun; Lim, Ki-Byung; Hwang, Yoon-Jung; Kim, Goon-Bo; Baek, Seunghoon; Choi, Sang-Bong; Hyung, Dae-Jin; Lee, Seung-Won; Sohn, Seong-Han; Kwon, Soo-Jin; Jin, Mina; Seol, Young-Joo; Chae, Won Byoung; Choi, Keun Jin; Park, Beom-Seok; Yu, Hee-Ju; Mun, Jeong-Hwan

2016-07-01

This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

Lophotrochozoan mitochondrial genomes

Energy Technology Data Exchange (ETDEWEB)

Valles, Yvonne; Boore, Jeffrey L.

2005-10-01

Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Science.gov (United States)

Thorvaldsdóttir, Helga; Robinson, James T; Mesirov, Jill P

2013-03-01

Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license.

Causes of genome instability

DEFF Research Database (Denmark)

Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel

2015-01-01

function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

Statistical analysis plan for the Pneumatic CompREssion for PreVENting Venous Thromboembolism (PREVENT) trial: a study protocol for a randomized controlled trial.

Science.gov (United States)

Arabi, Yaseen; Al-Hameed, Fahad; Burns, Karen E A; Mehta, Sangeeta; Alsolamy, Sami; Almaani, Mohammed; Mandourah, Yasser; Almekhlafi, Ghaleb A; Al Bshabshe, Ali; Finfer, Simon; Alshahrani, Mohammed; Khalid, Imran; Mehta, Yatin; Gaur, Atul; Hawa, Hassan; Buscher, Hergen; Arshad, Zia; Lababidi, Hani; Al Aithan, Abdulsalam; Jose, Jesna; Abdukahil, Sheryl Ann I; Afesh, Lara Y; Dbsawy, Maamoun; Al-Dawood, Abdulaziz

2018-03-15

The Pneumatic CompREssion for Preventing VENous Thromboembolism (PREVENT) trial evaluates the effect of adjunctive intermittent pneumatic compression (IPC) with pharmacologic thromboprophylaxis compared to pharmacologic thromboprophylaxis alone on venous thromboembolism (VTE) in critically ill adults. In this multicenter randomized trial, critically ill patients receiving pharmacologic thromboprophylaxis will be randomized to an IPC or a no IPC (control) group. The primary outcome is "incident" proximal lower-extremity deep vein thrombosis (DVT) within 28 days after randomization. Radiologists interpreting the lower-extremity ultrasonography will be blinded to intervention allocation, whereas the patients and treating team will be unblinded. The trial has 80% power to detect a 3% absolute risk reduction in the rate of proximal DVT from 7% to 4%. Consistent with international guidelines, we have developed a detailed plan to guide the analysis of the PREVENT trial. This plan specifies the statistical methods for the evaluation of primary and secondary outcomes, and defines covariates for adjusted analyses a priori. Application of this statistical analysis plan to the PREVENT trial will facilitate unbiased analyses of clinical data. ClinicalTrials.gov , ID: NCT02040103 . Registered on 3 November 2013; Current controlled trials, ID: ISRCTN44653506 . Registered on 30 October 2013.

The Banana Genome Hub

Science.gov (United States)

Droc, Gaëtan; Larivière, Delphine; Guignon, Valentin; Yahiaoui, Nabila; This, Dominique; Garsmeur, Olivier; Dereeper, Alexis; Hamelin, Chantal; Argout, Xavier; Dufayard, Jean-François; Lengelle, Juliette; Baurens, Franc-Christophe; Cenci, Alberto; Pitollat, Bertrand; D’Hont, Angélique; Ruiz, Manuel; Rouard, Mathieu; Bocs, Stéphanie

2013-01-01

Banana is one of the world’s favorite fruits and one of the most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given the taxonomic position of Musa, the completed genomic sequence has particular comparative value to provide fresh insights about the evolution of the monocotyledons. The study of the banana genome has been enhanced by a number of tools and resources that allows harnessing its sequence. First, we set up essential tools such as a Community Annotation System, phylogenomics resources and metabolic pathways. Then, to support post-genomic efforts, we improved banana existing systems (e.g. web front end, query builder), we integrated available Musa data into generic systems (e.g. markers and genetic maps, synteny blocks), we have made interoperable with the banana hub, other existing systems containing Musa data (e.g. transcriptomics, rice reference genome, workflow manager) and finally, we generated new results from sequence analyses (e.g. SNP and polymorphism analysis). Several uses cases illustrate how the Banana Genome Hub can be used to study gene families. Overall, with this collaborative effort, we discuss the importance of the interoperability toward data integration between existing information systems. Database URL: http://banana-genome.cirad.fr/ PMID:23707967

Comparative genomics reveals insights into avian genome evolution and adaptation

DEFF Research Database (Denmark)

Zhang, Guojie; Li, Cai; Li, Qiye

2014-01-01

Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, ...

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

Science.gov (United States)

Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

2016-01-04

The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Human genetics and genomics a decade after the release of the draft sequence of the human genome

Science.gov (United States)

2011-01-01

Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade. PMID:22155605

The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics

DEFF Research Database (Denmark)

Gopalakrishnan, Shyam; Samaniego Castruita, Jose Alfredo; Sinding, Mikkel Holger Strander

2017-01-01

Background An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data - that of a......Background An increasing number of studies are addressing the evolutionary genomics of dog domestication, principally through resequencing dog, wolf and related canid genomes. There is, however, only one de novo assembled canid genome currently available against which to map such data...

Cephalopod genomics

DEFF Research Database (Denmark)

Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

2012-01-01

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria......, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers...... active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described...

Organizational heterogeneity of vertebrate genomes.

Science.gov (United States)

Frenkel, Svetlana; Kirzhner, Valery; Korol, Abraham

2012-01-01

Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS) analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers) in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM) allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

Organizational heterogeneity of vertebrate genomes.

Directory of Open Access Journals (Sweden)

Svetlana Frenkel

Full Text Available Genomes of higher eukaryotes are mosaics of segments with various structural, functional, and evolutionary properties. The availability of whole-genome sequences allows the investigation of their structure as "texts" using different statistical and computational methods. One such method, referred to as Compositional Spectra (CS analysis, is based on scoring the occurrences of fixed-length oligonucleotides (k-mers in the target DNA sequence. CS analysis allows generating species- or region-specific characteristics of the genome, regardless of their length and the presence of coding DNA. In this study, we consider the heterogeneity of vertebrate genomes as a joint effect of regional variation in sequence organization superimposed on the differences in nucleotide composition. We estimated compositional and organizational heterogeneity of genome and chromosome sequences separately and found that both heterogeneity types vary widely among genomes as well as among chromosomes in all investigated taxonomic groups. The high correspondence of heterogeneity scores obtained on three genome fractions, coding, repetitive, and the remaining part of the noncoding DNA (the genome dark matter--GDM allows the assumption that CS-heterogeneity may have functional relevance to genome regulation. Of special interest for such interpretation is the fact that natural GDM sequences display the highest deviation from the corresponding reshuffled sequences.

Genomic signal processing

CERN Document Server

Shmulevich, Ilya

2007-01-01

Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score.

Science.gov (United States)

Lee, Hayan; Schatz, Michael C

2012-08-15

Genome resequencing and short read mapping are two of the primary tools of genomics and are used for many important applications. The current state-of-the-art in mapping uses the quality values and mapping quality scores to evaluate the reliability of the mapping. These attributes, however, are assigned to individual reads and do not directly measure the problematic repeats across the genome. Here, we present the Genome Mappability Score (GMS) as a novel measure of the complexity of resequencing a genome. The GMS is a weighted probability that any read could be unambiguously mapped to a given position and thus measures the overall composition of the genome itself. We have developed the Genome Mappability Analyzer to compute the GMS of every position in a genome. It leverages the parallelism of cloud computing to analyze large genomes, and enabled us to identify the 5-14% of the human, mouse, fly and yeast genomes that are difficult to analyze with short reads. We examined the accuracy of the widely used BWA/SAMtools polymorphism discovery pipeline in the context of the GMS, and found discovery errors are dominated by false negatives, especially in regions with poor GMS. These errors are fundamental to the mapping process and cannot be overcome by increasing coverage. As such, the GMS should be considered in every resequencing project to pinpoint the 'dark matter' of the genome, including of known clinically relevant variations in these regions. The source code and profiles of several model organisms are available at http://gma-bio.sourceforge.net

Dicty_cDB: Contig-U04426-1 [Dicty_cDB

Lifescience Database Archive (English)

Full Text Available MMBB... 32 2.9 5 ( AC174151 ) Homo sapiens chromosome 4 clone WI2-1953O14, comp... 42 2.9 2 ( CD147127 ) ML1...1-734E9, WORKI... 42 2.8 3 ( CC262481 ) CH261-167M9_Sp6.1 CH261 Gallus gallus gen...omic clo... 32 2.8 3 ( CD147117 ) ML1-0002T-M115-B10-U.G ML1-0002 Schistosoma manso... 38 2.8 2 ( BX842699 )

The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies.

Science.gov (United States)

Argout, X; Martin, G; Droc, G; Fouet, O; Labadie, K; Rivals, E; Aury, J M; Lanaud, C

2017-09-15

Theobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes. We used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome. We combined four Illumina large insert size mate paired libraries with 52x of Pacific Biosciences long reads to correct misassembled regions and reduced the number of scaffolds. We then used genotyping by sequencing (GBS) methods to increase the proportion of the assembly anchored to chromosomes. The scaffold number decreased from 4,792 in assembly V1 to 554 in V2 while the scaffold N50 size has increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence. Theobroma cacao Criollo genome version 2 will be a valuable resource for the investigation of complex traits at the genomic level and for future comparative genomics and genetics studies in cacao tree. New functional tools and annotations are available on the Cocoa Genome Hub ( http://cocoa-genome-hub.southgreen.fr ).

Sequencing of a new target genome: the Pediculus humanus humanus (Phthiraptera: Pediculidae) genome project.

Science.gov (United States)

Pittendrigh, B R; Clark, J M; Johnston, J S; Lee, S H; Romero-Severson, J; Dasch, G A

2006-11-01

The human body louse, Pediculus humanus humanus (L.), and the human head louse, Pediculus humanus capitis, belong to the hemimetabolous order Phthiraptera. The body louse is the primary vector that transmits the bacterial agents of louse-borne relapsing fever, trench fever, and epidemic typhus. The genomes of the bacterial causative agents of several of these aforementioned diseases have been sequenced. Thus, determining the body louse genome will enhance studies of host-vector-pathogen interactions. Although not important as a major disease vector, head lice are of major social concern. Resistance to traditional pesticides used to control head and body lice have developed. It is imperative that new molecular targets be discovered for the development of novel compounds to control these insects. No complete genome sequence exists for a hemimetabolous insect species primarily because hemimetabolous insects often have large (2000 Mb) to very large (up to 16,300 Mb) genomes. Fortuitously, we determined that the human body louse has one of the smallest genome sizes known in insects, suggesting it may be a suitable choice as a minimal hemimetabolous genome in which many genes have been eliminated during its adaptation to human parasitism. Because many louse species infest birds and mammals, the body louse genome-sequencing project will facilitate studies of their comparative genomics. A 6-8X coverage of the body louse genome, plus sequenced expressed sequence tags, should provide the entomological, evolutionary biology, medical, and public health communities with useful genetic information.

Theory of microbial genome evolution

Science.gov (United States)

Koonin, Eugene

Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

Applied Genomics of Foodborne Pathogens

DEFF Research Database (Denmark)

and customized source of information designed for and accessible to microbiologists interested in applying cutting-edge genomics in food safety and public health research. This book fills this void with a well-selected collection of topics, case studies, and bioinformatics tools contributed by experts......This book provides a timely and thorough snapshot into the emerging and fast evolving area of applied genomics of foodborne pathogens. Driven by the drastic advance of whole genome shot gun sequencing (WGS) technologies, genomics applications are becoming increasingly valuable and even essential...... at the forefront of foodborne pathogen genomics research....

Genome Variation Map: a data repository of genome variations in BIG Data Center.

Science.gov (United States)

Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang; Zhang, Zhang

2018-01-04

The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genome Variation Map: a data repository of genome variations in BIG Data Center

Science.gov (United States)

Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

2018-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

The bonobo genome compared with the chimpanzee and human genomes

Science.gov (United States)

Prüfer, Kay; Munch, Kasper; Hellmann, Ines; Akagi, Keiko; Miller, Jason R.; Walenz, Brian; Koren, Sergey; Sutton, Granger; Kodira, Chinnappa; Winer, Roger; Knight, James R.; Mullikin, James C.; Meader, Stephen J.; Ponting, Chris P.; Lunter, Gerton; Higashino, Saneyuki; Hobolth, Asger; Dutheil, Julien; Karakoç, Emre; Alkan, Can; Sajjadian, Saba; Catacchio, Claudia Rita; Ventura, Mario; Marques-Bonet, Tomas; Eichler, Evan E.; André, Claudine; Atencia, Rebeca; Mugisha, Lawrence; Junhold, Jörg; Patterson, Nick; Siebauer, Michael; Good, Jeffrey M.; Fischer, Anne; Ptak, Susan E.; Lachmann, Michael; Symer, David E.; Mailund, Thomas; Schierup, Mikkel H.; Andrés, Aida M.; Kelso, Janet; Pääbo, Svante

2012-01-01

Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours1–4, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other. PMID:22722832

Study of surface alterations of composite and ionomeric materials submitted to simulation of a high cariogenic challenge Estudo da erosão superficial de materiais compósitos e inoméricos submetidos à simulação de um alto desafio cariogênico

Directory of Open Access Journals (Sweden)

Alexandre Rezende VIEIRA

1999-12-01

Full Text Available We evaluated the surface of composite resins and glass-ionomer cements in a situation of high cariogenic challenge. Based on seventy-five standard test specimens of one glass-ionomer cement (Chelon Fil - ESPE, one resin-modified glass-ionomer (Vitremer - 3M, two polyacid-modified composite (VariGlass and Dyract - Dentsply and one composite resin (Heliomolar - Vivadent, submitted to fourteen days of demineralization and remineralization cycling to simulate a high cariogenic challenge, the erosive aspects of the surface of the materials were assessed. All of the samples were evaluated by scanning electronic microscope and compared with another five test specimens of each material, prepared in the same way and serving as control. All of the materials studied suffered erosive action by the media, with different characteristics due to the different compositions, after being submitted to in vitro simulation of a high cariogenic challenge.O objetivo deste trabalho foi avaliar a superfície de compósitos e cimentos de ionômero de vidro, frente a uma situação de alto desafio cariogênico. A partir de setenta e cinco corpos-de-prova padronizados de um cimento de ionômero de vidro (Chelon Fil - ESPE, um ionômero de vidro resina-modificado (Vitremer - 3M, dois compósitos poliácido-modificados (VariGlass e Dyract - Dentsply e um compósito (Heliomolar - Vivadent, e após serem submetidos a quatorze dias a ciclagens de desmineralização e remineralização, para simular um alto desafio cariogênico, foram avaliados os aspectos erosivos da superfície dos materiais. Todos os corpos-de-prova foram avaliados ao microscópio eletrônico de varredura e comparados com cinco outros corpos-de-prova de cada material, confeccionados da mesma forma e que serviram como controle. Todos os materiais estudados sofreram ação erosiva dos meios, com características distintas, devido às suas diferentes composições, após serem submetidos à simulação in vitro

Fungal Genomics for Energy and Environment

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor V.

2013-03-11

Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Sequencing Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 200 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome

NARCIS (Netherlands)

Sharp, Andrew J.; Hansen, Sierra; Selzer, Rebecca R.; Cheng, Ze; Regan, Regina; Hurst, Jane A.; Stewart, Helen; Price, Sue M.; Blair, Edward; Hennekam, Raoul C.; Fitzpatrick, Carrie A.; Segraves, Rick; Richmond, Todd A.; Guiver, Cheryl; Albertson, Donna G.; Pinkel, Daniel; Eis, Peggy S.; Schwartz, Stuart; Knight, Samantha J. L.; Eichler, Evan E.

2006-01-01

Genomic disorders are characterized by the presence of flanking segmental duplications that predispose these regions to recurrent rearrangement. Based on the duplication architecture of the genome, we investigated 130 regions that we hypothesized as candidates for previously undescribed genomic

The fishes of Genome 10K

KAUST Repository

Bernardi, Giacomo

2012-09-01

The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

The fishes of Genome 10K

KAUST Repository

Bernardi, Giacomo; Wiley, Edward O.; Mansour, Hicham; Miller, Michael R.; Ortí , Guillermo; Haussler, David H.; O'Brien, Stephen J O; Ryder, Oliver A.; Venkatesh, Byrappa

2012-01-01

The Genome 10K project aims to sequence the genomes of 10,000 vertebrates, representing approximately one genome for each vertebrate genus. Since fishes (cartilaginous fishes, ray-finned fishes and lobe-finned fishes) represent more than 50% of extant vertebrates, it is planned to target 4,000 fish genomes. At present, nearly 60 fish genomes are being sequenced at various public funded labs, and under a Genome 10K and BGI pilot project. An additional 100 fishes have been identified for sequencing in the next phase of Genome 10K project. © 2012 Elsevier B.V.

Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease

NARCIS (Netherlands)

Versteeg, Bart; Bruisten, Sylvia M.; Pannekoek, Yvonne; Jolley, Keith A.; Maiden, Martin C. J.; van der Ende, Arie; Harrison, Odile B.

2018-01-01

Background: Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated. Results: WGS data

Yeast genome sequencing:

DEFF Research Database (Denmark)

Piskur, Jure; Langkjær, Rikke Breinhold

2004-01-01

For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

Genome size variation affects song attractiveness in grasshoppers: evidence for sexual selection against large genomes.

Science.gov (United States)

Schielzeth, Holger; Streitner, Corinna; Lampe, Ulrike; Franzke, Alexandra; Reinhold, Klaus

2014-12-01

Genome size is largely uncorrelated to organismal complexity and adaptive scenarios. Genetic drift as well as intragenomic conflict have been put forward to explain this observation. We here study the impact of genome size on sexual attractiveness in the bow-winged grasshopper Chorthippus biguttulus. Grasshoppers show particularly large variation in genome size due to the high prevalence of supernumerary chromosomes that are considered (mildly) selfish, as evidenced by non-Mendelian inheritance and fitness costs if present in high numbers. We ranked male grasshoppers by song characteristics that are known to affect female preferences in this species and scored genome sizes of attractive and unattractive individuals from the extremes of this distribution. We find that attractive singers have significantly smaller genomes, demonstrating that genome size is reflected in male courtship songs and that females prefer songs of males with small genomes. Such a genome size dependent mate preference effectively selects against selfish genetic elements that tend to increase genome size. The data therefore provide a novel example of how sexual selection can reinforce natural selection and can act as an agent in an intragenomic arms race. Furthermore, our findings indicate an underappreciated route of how choosy females could gain indirect benefits. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

The tiger genome and comparative analysis with lion and snow leopard genomes.

Science.gov (United States)

Cho, Yun Sung; Hu, Li; Hou, Haolong; Lee, Hang; Xu, Jiaohui; Kwon, Soowhan; Oh, Sukhun; Kim, Hak-Min; Jho, Sungwoong; Kim, Sangsoo; Shin, Young-Ah; Kim, Byung Chul; Kim, Hyunmin; Kim, Chang-Uk; Luo, Shu-Jin; Johnson, Warren E; Koepfli, Klaus-Peter; Schmidt-Küntzel, Anne; Turner, Jason A; Marker, Laurie; Harper, Cindy; Miller, Susan M; Jacobs, Wilhelm; Bertola, Laura D; Kim, Tae Hyung; Lee, Sunghoon; Zhou, Qian; Jung, Hyun-Ju; Xu, Xiao; Gadhvi, Priyvrat; Xu, Pengwei; Xiong, Yingqi; Luo, Yadan; Pan, Shengkai; Gou, Caiyun; Chu, Xiuhui; Zhang, Jilin; Liu, Sanyang; He, Jing; Chen, Ying; Yang, Linfeng; Yang, Yulan; He, Jiaju; Liu, Sha; Wang, Junyi; Kim, Chul Hong; Kwak, Hwanjong; Kim, Jong-Soo; Hwang, Seungwoo; Ko, Junsu; Kim, Chang-Bae; Kim, Sangtae; Bayarlkhagva, Damdin; Paek, Woon Kee; Kim, Seong-Jin; O'Brien, Stephen J; Wang, Jun; Bhak, Jong

2013-01-01

Tigers and their close relatives (Panthera) are some of the world's most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats' hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species.

From Genomics to Gene Therapy: Induced Pluripotent Stem Cells Meet Genome Editing.

Science.gov (United States)

Hotta, Akitsu; Yamanaka, Shinya

2015-01-01

The advent of induced pluripotent stem (iPS) cells has opened up numerous avenues of opportunity for cell therapy, including the initiation in September 2014 of the first human clinical trial to treat dry age-related macular degeneration. In parallel, advances in genome-editing technologies by site-specific nucleases have dramatically improved our ability to edit endogenous genomic sequences at targeted sites of interest. In fact, clinical trials have already begun to implement this technology to control HIV infection. Genome editing in iPS cells is a powerful tool and enables researchers to investigate the intricacies of the human genome in a dish. In the near future, the groundwork laid by such an approach may expand the possibilities of gene therapy for treating congenital disorders. In this review, we summarize the exciting progress being made in the utilization of genomic editing technologies in pluripotent stem cells and discuss remaining challenges toward gene therapy applications.

The tiger genome and comparative analysis with lion and snow leopard genomes

Science.gov (United States)

Cho, Yun Sung; Hu, Li; Hou, Haolong; Lee, Hang; Xu, Jiaohui; Kwon, Soowhan; Oh, Sukhun; Kim, Hak-Min; Jho, Sungwoong; Kim, Sangsoo; Shin, Young-Ah; Kim, Byung Chul; Kim, Hyunmin; Kim, Chang-uk; Luo, Shu-Jin; Johnson, Warren E.; Koepfli, Klaus-Peter; Schmidt-Küntzel, Anne; Turner, Jason A.; Marker, Laurie; Harper, Cindy; Miller, Susan M.; Jacobs, Wilhelm; Bertola, Laura D.; Kim, Tae Hyung; Lee, Sunghoon; Zhou, Qian; Jung, Hyun-Ju; Xu, Xiao; Gadhvi, Priyvrat; Xu, Pengwei; Xiong, Yingqi; Luo, Yadan; Pan, Shengkai; Gou, Caiyun; Chu, Xiuhui; Zhang, Jilin; Liu, Sanyang; He, Jing; Chen, Ying; Yang, Linfeng; Yang, Yulan; He, Jiaju; Liu, Sha; Wang, Junyi; Kim, Chul Hong; Kwak, Hwanjong; Kim, Jong-Soo; Hwang, Seungwoo; Ko, Junsu; Kim, Chang-Bae; Kim, Sangtae; Bayarlkhagva, Damdin; Paek, Woon Kee; Kim, Seong-Jin; O’Brien, Stephen J.; Wang, Jun; Bhak, Jong

2013-01-01

Tigers and their close relatives (Panthera) are some of the world’s most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species. PMID:24045858

Estudo das propriedades elétricas e térmicas de compósitos nanoestruturados de poli(sulfeto de fenileno reforçados com nanotubos de carbono

Directory of Open Access Journals (Sweden)

Bruno Ribeiro

2015-02-01

Full Text Available Neste trabalho o comportamento de cristalização e a condutividade elétrica de compósitos nanoestruturados de poli(sulfeto de fenileno reforçado com nanotubos de carbono de paredes múltiplas obtidos através da técnica de mistura em fusão foram estudados. A incorporação do nanoreforço na matriz polimérica foi responsável por um aumento da cristalinidade devido ao fenômeno de nucleação heterogênea. A condutividade elétrica do PPS apresentou um aumento de 11 ordens de magnitude quando 2,0 m/m% de MWCNT foram adicionados a matriz polimérica. Além disso, o limite de percolação elétrica encontrado para este sistema foi de 1,4 m/m% de MWCNT, revelando a formação de uma rede condutiva tridimensional no interior da matriz polimérica.

Human Genome Project

Energy Technology Data Exchange (ETDEWEB)

Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

1998-01-04

The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

Human Genome Program

Energy Technology Data Exchange (ETDEWEB)

1993-01-01

The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

Genomic insight into the common carp (Cyprinus carpio genome by sequencing analysis of BAC-end sequences

Directory of Open Access Journals (Sweden)

Wang Jintu

2011-04-01

Full Text Available Abstract Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio, a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3

Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences

Science.gov (United States)

2011-01-01

Background Common carp is one of the most important aquaculture teleost fish in the world. Common carp and other closely related Cyprinidae species provide over 30% aquaculture production in the world. However, common carp genomic resources are still relatively underdeveloped. BAC end sequences (BES) are important resources for genome research on BAC-anchored genetic marker development, linkage map and physical map integration, and whole genome sequence assembling and scaffolding. Result To develop such valuable resources in common carp (Cyprinus carpio), a total of 40,224 BAC clones were sequenced on both ends, generating 65,720 clean BES with an average read length of 647 bp after sequence processing, representing 42,522,168 bp or 2.5% of common carp genome. The first survey of common carp genome was conducted with various bioinformatics tools. The common carp genome contains over 17.3% of repetitive elements with GC content of 36.8% and 518 transposon ORFs. To identify and develop BAC-anchored microsatellite markers, a total of 13,581 microsatellites were detected from 10,355 BES. The coding region of 7,127 genes were recognized from 9,443 BES on 7,453 BACs, with 1,990 BACs have genes on both ends. To evaluate the similarity to the genome of closely related zebrafish, BES of common carp were aligned against zebrafish genome. A total of 39,335 BES of common carp have conserved homologs on zebrafish genome which demonstrated the high similarity between zebrafish and common carp genomes, indicating the feasibility of comparative mapping between zebrafish and common carp once we have physical map of common carp. Conclusion BAC end sequences are great resources for the first genome wide survey of common carp. The repetitive DNA was estimated to be approximate 28% of common carp genome, indicating the higher complexity of the genome. Comparative analysis had mapped around 40,000 BES to zebrafish genome and established over 3,100 microsyntenies, covering over 50% of

A decade of human genome project conclusion: Scientific diffusion about our genome knowledge.

Science.gov (United States)

Moraes, Fernanda; Góes, Andréa

2016-05-06

The Human Genome Project (HGP) was initiated in 1990 and completed in 2003. It aimed to sequence the whole human genome. Although it represented an advance in understanding the human genome and its complexity, many questions remained unanswered. Other projects were launched in order to unravel the mysteries of our genome, including the ENCyclopedia of DNA Elements (ENCODE). This review aims to analyze the evolution of scientific knowledge related to both the HGP and ENCODE projects. Data were retrieved from scientific articles published in 1990-2014, a period comprising the development and the 10 years following the HGP completion. The fact that only 20,000 genes are protein and RNA-coding is one of the most striking HGP results. A new concept about the organization of genome arose. The ENCODE project was initiated in 2003 and targeted to map the functional elements of the human genome. This project revealed that the human genome is pervasively transcribed. Therefore, it was determined that a large part of the non-protein coding regions are functional. Finally, a more sophisticated view of chromatin structure emerged. The mechanistic functioning of the genome has been redrafted, revealing a much more complex picture. Besides, a gene-centric conception of the organism has to be reviewed. A number of criticisms have emerged against the ENCODE project approaches, raising the question of whether non-conserved but biochemically active regions are truly functional. Thus, HGP and ENCODE projects accomplished a great map of the human genome, but the data generated still requires further in depth analysis. © 2016 by The International Union of Biochemistry and Molecular Biology, 44:215-223, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

[Genome editing of industrial microorganism].

Science.gov (United States)

Zhu, Linjiang; Li, Qi

2015-03-01

Genome editing is defined as highly-effective and precise modification of cellular genome in a large scale. In recent years, such genome-editing methods have been rapidly developed in the field of industrial strain improvement. The quickly-updating methods thoroughly change the old mode of inefficient genetic modification, which is "one modification, one selection marker, and one target site". Highly-effective modification mode in genome editing have been developed including simultaneous modification of multiplex genes, highly-effective insertion, replacement, and deletion of target genes in the genome scale, cut-paste of a large DNA fragment. These new tools for microbial genome editing will certainly be applied widely, and increase the efficiency of industrial strain improvement, and promote the revolution of traditional fermentation industry and rapid development of novel industrial biotechnology like production of biofuel and biomaterial. The technological principle of these genome-editing methods and their applications were summarized in this review, which can benefit engineering and construction of industrial microorganism.

Cartilage oligomeric matrix protein specific antibodies are pathogenic

DEFF Research Database (Denmark)

Geng, Hui; Nandakumar, Kutty Selva; Pramhed, Anna

2012-01-01

-specific monoclonal antibodies (mAbs). METHODS: B cell immunodominant regions on the COMP molecule were measured with a novel enzyme-linked immunosorbent assay using mammalian expressed full-length mouse COMP as well as a panel of recombinant mouse COMP fragments. 18 mAbs specific to COMP were generated......ABSTRACT: INTRODUCTION: Cartilage oligomeric matrix protein (COMP) is a major non-collagenous component of cartilage. Earlier, we developed a new mouse model for rheumatoid arthritis using COMP. This study was undertaken to investigate the epitope specificity and immunopathogenicity of COMP...

Genome Update: alignment of bacterial chromosomes

DEFF Research Database (Denmark)

Ussery, David; Jensen, Mette; Poulsen, Tine Rugh

2004-01-01

There are four new microbial genomes listed in this month's Genome Update, three belonging to Gram-positive bacteria and one belonging to an archaeon that lives at pH 0; all of these genomes are listed in Table 1⇓. The method of genome comparison this month is that of genome alignment and, as an ...

Genome-wide analysis of wild-type Epstein-Barr virus genomes derived from healthy individuals of the 1,000 Genomes Project.

Science.gov (United States)

Santpere, Gabriel; Darre, Fleur; Blanco, Soledad; Alcami, Antonio; Villoslada, Pablo; Mar Albà, M; Navarro, Arcadi

2014-04-01

Most people in the world (∼90%) are infected by the Epstein-Barr virus (EBV), which establishes itself permanently in B cells. Infection by EBV is related to a number of diseases including infectious mononucleosis, multiple sclerosis, and different types of cancer. So far, only seven complete EBV strains have been described, all of them coming from donors presenting EBV-related diseases. To perform a detailed comparative genomic analysis of EBV including, for the first time, EBV strains derived from healthy individuals, we reconstructed EBV sequences infecting lymphoblastoid cell lines (LCLs) from the 1000 Genomes Project. As strain B95-8 was used to transform B cells to obtain LCLs, it is always present, but a specific deletion in its genome sets it apart from natural EBV strains. After studying hundreds of individuals, we determined the presence of natural EBV in at least 10 of them and obtained a set of variants specific to wild-type EBV. By mapping the natural EBV reads into the EBV reference genome (NC007605), we constructed nearly complete wild-type viral genomes from three individuals. Adding them to the five disease-derived EBV genomic sequences available in the literature, we performed an in-depth comparative genomic analysis. We found that latency genes harbor more nucleotide diversity than lytic genes and that six out of nine latency-related genes, as well as other genes involved in viral attachment and entry into host cells, packaging, and the capsid, present the molecular signature of accelerated protein evolution rates, suggesting rapid host-parasite coevolution.

Fueling the Future with Fungal Genomes

Energy Technology Data Exchange (ETDEWEB)

Grigoriev, Igor V.

2014-10-27

Genomes of fungi relevant to energy and environment are in focus of the JGI Fungal Genomic Program. One of its projects, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts and pathogens) and biorefinery processes (cellulose degradation and sugar fermentation) by means of genome sequencing and analysis. New chapters of the Encyclopedia can be opened with user proposals to the JGI Community Science Program (CSP). Another JGI project, the 1000 fungal genomes, explores fungal diversity on genome level at scale and is open for users to nominate new species for sequencing. Over 400 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics will lead to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such ‘parts’ suggested by comparative genomics and functional analysis in these areas are presented here.

Genomic individuality and its biological implications.

Science.gov (United States)

Zhao, J

1996-06-01

It is a widely accepted fundamental concept that all somatic genomes of a human individual are identical to each other. The theoretical basis of this concept is that all of these somatic genomes are the descendants of the genome of a single fertilized cell as well as the simple replicated products of asexual reproduction, thus not forming any new recombined genomes. The question here is whether such a concept might only represent one side of somatic genome biology and, even worse, whether it has perhaps already led to a very prevalent misconception that within the organism body, there exists no variability among individual somatic genomes. A hypothesis, called genomic individuality, is proposed, simply saying that every individual somatic genome, perhaps with rare exceptions, has its own unique or individual 'genetic identity' or 'fingerprint', which is characterized by its distinctive sequences or patterns of deoxyribonucleic acid molecules, or both. Thus, no two somatic genomes can be identical to each other in every or all aspects, and consequently, there must be a great deal of genomic variation present within the body of any multicellular organism. The concept or hypothesis of genomic individuality would not only provide a more complete understanding of genome biology, but also suggest a new insight into the studies of the biology of cells and organisms.

Comparative genomics of Lactobacillus and other LAB

DEFF Research Database (Denmark)

Wassenaar, Trudy M.; Lukjancenko, Oksana

2014-01-01

that of the others, with the two Streptococcus species having the shortest genomes. The widest distribution in genome content was observed for Lactobacillus. The number of tRNA and rRNA gene copies varied considerably, with exceptional high numbers observed for Lb. delbrueckii, while these numbers were relatively......The genomes of 66 LABs, belonging to five different genera, were compared for genome size and gene content. The analyzed genomes included 37 Lactobacillus genomes of 17 species, six Lactococcus lactis genomes, four Leuconostoc genomes of three species, six Streptococcus genomes of two species...

One bacterial cell, one complete genome.

Directory of Open Access Journals (Sweden)

Tanja Woyke

2010-04-01

Full Text Available While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200-900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA. Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs, indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.

One Bacterial Cell, One Complete Genome

Energy Technology Data Exchange (ETDEWEB)

Woyke, Tanja; Tighe, Damon; Mavrommatis, Konstantinos; Clum, Alicia; Copeland, Alex; Schackwitz, Wendy; Lapidus, Alla; Wu, Dongying; McCutcheon, John P.; McDonald, Bradon R.; Moran, Nancy A.; Bristow, James; Cheng, Jan-Fang

2010-04-26

While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete or even partial genomes from these environmental species. Single cell genomics is a novel culture-independent approach, which enables access to the genetic material of an individual cell. No single cell genome has to our knowledge been closed and finished to date. Here we report the completed genome from an uncultured single cell of Candidatus Sulcia muelleri DMIN. Digital PCR on single symbiont cells isolated from the bacteriome of the green sharpshooter Draeculacephala minerva bacteriome allowed us to assess that this bacteria is polyploid with genome copies ranging from approximately 200?900 per cell, making it a most suitable target for single cell finishing efforts. For single cell shotgun sequencing, an individual Sulcia cell was isolated and whole genome amplified by multiple displacement amplification (MDA). Sanger-based finishing methods allowed us to close the genome. To verify the correctness of our single cell genome and exclude MDA-derived artifacts, we independently shotgun sequenced and assembled the Sulcia genome from pooled bacteriomes using a metagenomic approach, yielding a nearly identical genome. Four variations we detected appear to be genuine biological differences between the two samples. Comparison of the single cell genome with bacteriome metagenomic sequence data detected two single nucleotide polymorphisms (SNPs), indicating extremely low genetic diversity within a Sulcia population. This study demonstrates the power of single cell genomics to generate a complete, high quality, non-composite reference genome within an environmental sample, which can be used for population genetic analyzes.