Genomes correction and assembling: present methods and tools

Science.gov (United States)

Wojcieszek, Michał; Pawełkowicz, Magdalena; Nowak, Robert; Przybecki, Zbigniew

2014-11-01

Recent rapid development of next generation sequencing (NGS) technologies provided significant impact into genomics field of study enabling implementation of many de novo sequencing projects of new species which was previously confined by technological costs. Along with advancement of NGS there was need for adjustment in assembly programs. New algorithms must cope with massive amounts of data computation in reasonable time limits and processing power and hardware is also an important factor. In this paper, we address the issue of assembly pipeline for de novo genome assembly provided by programs presently available for scientist both as commercial and as open - source software. The implementation of four different approaches - Greedy, Overlap - Layout - Consensus (OLC), De Bruijn and Integrated resulting in variation of performance is the main focus of our discussion with additional insight into issue of short and long reads correction.

Neutrino oscillations: present status and outlook

International Nuclear Information System (INIS)

Schwetz, T.

2005-01-01

In this talk the present status of neutrino oscillations is reviewed, based on a global analysis of world neutrino oscillation data from solar, atmospheric, reactor, and accelerator neutrino experiments. Furthermore, I discuss the expected improvements in the determination of neutrino parameters by future oscillation experiments within a timescale of 10 years. (author)

Present status and physics prospects of SSC

International Nuclear Information System (INIS)

Sugimoto, Shojiro

1990-01-01

Physics prospects of Superconducting Super Collider (SSC) are discussed, referring to other coming colliders. In addition, the present status of the SSC project and detector proposals for the experiments are described. (author)

Genetic link between family socioeconomic status and children's educational achievement estimated from genome-wide SNPs.

Science.gov (United States)

Krapohl, E; Plomin, R

2016-03-01

One of the best predictors of children's educational achievement is their family's socioeconomic status (SES), but the degree to which this association is genetically mediated remains unclear. For 3000 UK-representative unrelated children we found that genome-wide single-nucleotide polymorphisms could explain a third of the variance of scores on an age-16 UK national examination of educational achievement and half of the correlation between their scores and family SES. Moreover, genome-wide polygenic scores based on a previously published genome-wide association meta-analysis of total number of years in education accounted for ~3.0% variance in educational achievement and ~2.5% in family SES. This study provides the first molecular evidence for substantial genetic influence on differences in children's educational achievement and its association with family SES.

Present status of mirror stability theory

International Nuclear Information System (INIS)

Baldwin, D.E.; Berk, H.L.; Byers, J.A.

1976-01-01

A status report of microinstability as it applies to 2XIIB and MX theory for mirror machines is presented. It is shown that quasilinear computations reproduce many of the parameters observed in the 2XIIB experiment. In regard to large mirror machines, there are presented detailed calculations of the linear theory of the drift cyclotron loss-cone mode, with inhomogeneous geometry and nonlinear diffusive effects. Further, the stability of a mirror machine to the Alfven ion-cyclotron instability is assessed, and the Baldwin-Callen diffusion is estimated for a spatially varying plasma

Bupropion Overdose Presenting as Status Epilepticus in an Infant.

Science.gov (United States)

Rivas-Coppola, Marianna S; Patterson, Amy L; Morgan, Robin; Wheless, James W

2015-09-01

Bupropion is a monocyclic antidepressant in the aminoketone class, structurally related to amphetamines. The Food and Drug Administration withdrew this product from the market in 1986 after seizures were reported in bulimic patients. It was later reintroduced in 1989 when the incidence of seizures was shown to be dose-related in the immediate release preparation. Massive bupropion ingestion has been associated with status epilepticus and cardiogenic shock in adults. Seizures have been reported in children, but not status epilepticus. This report highlights a patient who presented with status epilepticus and developed cardiopulmonary arrest after bupropion ingestion. False-positive amphetamine diagnosis from urine drug screen on presentation was reported. We review the presentation, clinical course, diagnostic studies, and outcome of this patient. We then review the literature regarding bupropion overdose in children. Symptoms of bupropion toxicity and risk for seizures are dose-dependent and fatalities have been reported. Our patient developed status epilepticus and cardiopulmonary arrest and then progressed to have a hypoxic ischemic encephalopathy and refractory symptomatic partial seizures. Our report highlights the need to keep this medication away from children in order to prevent accidental overdose. Copyright © 2015 Elsevier Inc. All rights reserved.

ATLAS experimental equipment. November 1983 workshop and present status

International Nuclear Information System (INIS)

1984-01-01

The latest workshop was held in November 1983 with the purpose of presenting an overview of the experimental stations planned for ATLAS, describing the current status of each individual apparatus, soliciting final input on devices of the first phase (i.e. on those that will be ready when beams from ATLAS become available in late Spring of 1985), and discussing and collecting new ideas on equipment for the second phase. There were short presentations on the status of the various projects followed by informal discussions. The presentations mainly concentrated on new equipment for target area III, but included some descriptions of current apparatus in target area II that might also be of interest for experiments with the higher-energy beams available in area III. The meeting was well attended with approx. 50 scientists, approximately half of them from institutions outside Argonne. The present proceedings summarize the presentations and discussions of this one-day meeting. In addition we take the opportunity to include information about developments since this meeting and an update of the current status of the various experimental stations. We would like to emphasize again that outside-user input is extremely welcome

Primary Amoebic (Naegleria fowleri Meningoencephalitis Presenting as Status Epilepticus

Directory of Open Access Journals (Sweden)

A Sharma

2011-04-01

Full Text Available Primary amebic meningoencephalitis (PAM is a rare entity. Usual presenting features are fever, headache and seizures with meningeal signs and this disease carries high mortality rate. We present a case report of PAM presenting as status epilepticus.

Genome-wide association study for claw disorders and trimming status in dairy cattle.

Science.gov (United States)

van der Spek, D; van Arendonk, J A M; Bovenhuis, H

2015-02-01

Performing a genome-wide association study (GWAS) might add to a better understanding of the development of claw disorders and the need for trimming. Therefore, the aim of the current study was to perform a GWAS on claw disorders and trimming status and to validate the results for claw disorders based on an independent data set. Data consisted of 20,474 cows with phenotypes for claw disorders and 50,238 cows with phenotypes for trimming status. Recorded claw disorders used in the current study were double sole (DS), interdigital hyperplasia (IH), sole hemorrhage (SH), sole ulcer (SU), white line separation (WLS), a combination of infectious claw disorders consisting of (inter-)digital dermatitis and heel erosion, and a combination of laminitis-related claw disorders (DS, SH, SU, and WLS). Of the cows with phenotypes for claw disorders, 1,771 cows were genotyped and these cow data were used for the GWAS on claw disorders. A SNP was considered significant when the false discovery rate≤0.05 and suggestive when the false discovery rate≤0.20. An independent data set of 185 genotyped bulls having at least 5 daughters with phenotypes (6,824 daughters in total) for claw disorders was used to validate significant and suggestive SNP detected based on the cow data. To analyze the trait "trimming status" (i.e., the need for claw trimming), a data set with 327 genotyped bulls having at least 5 daughters with phenotypes (18,525 daughters in total) was used. Based on the cow data, in total 10 significant and 45 suggestive SNP were detected for claw disorders. The 10 significant SNP were associated with SU, and mainly located on BTA8. The suggestive SNP were associated with DS, IH, SU, and laminitis-related claw disorders. Three of the suggestive SNP were validated in the data set of 185 bulls, and were located on BTA13, BTA14, and BTA17. For infectious claw disorders, SH, and WLS, no significant or suggestive SNP associations were detected. For trimming status, 1 significant

The Genome 10K Project: a way forward.

Science.gov (United States)

Koepfli, Klaus-Peter; Paten, Benedict; O'Brien, Stephen J

2015-01-01

The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species.

On the present status of the ARAMAKO system

International Nuclear Information System (INIS)

Nikolaev, M.N.; Savos'kin, M.M.

1987-01-01

This paper reviews the present status of the ARAMAKO multigroup constant calculation system for solving neutron and gamma quantum transport equations and for calculations of linear and bilinear functionals of their fields. (author)

EMOTIONAL SELF-PRESENTATION ON WHATSAPP: ANALYSIS OF THE PROFILE STATUS

Directory of Open Access Journals (Sweden)

Кармен Маис-Аревало

2018-12-01

Full Text Available Self-presentation can be defined as “the process through which individuals communicate an image of themselves to others” (Yang and Brown, 2015: 404 and it is an essential part of human communication. Self-presentation has been widely studied both in face-to-face communication and online. Most online research, however, has focused on social networking sites, blogs, chatrooms, etc. while less attention has been paid to other online means of communication such as WhatsApp despite the growing im-portance of WhatsApp as a means of communication. The present paper aims to redress this imbalance by analysing self-presentation on WhatsApp; more specifically, by paying attention to emotional self-pre-sentation in profile status. To that purpose, a corpus of 206 WhatsApp statuses was gathered in Spanish. Results show the existence of recurrent patterns connected to variables such as sex1 or age, which play a crucial role in determining the emotions users choose to display in their profile status.

Present status and future prospect of research reactors

International Nuclear Information System (INIS)

Takemi, Hirokatsu

1996-01-01

The present status of research reactors more than MW class reactor in JAERI and the Kyoto University and the small reactors in the Musashi Institute of Technology, the Rikkyo University, the Tokyo University, the Kinki University and other countries are explained in the paper. The present status of researches are reported by the topics in each field. The future researches of the beam reactor and the irradiation reactor are reviewed. On various kinds of use of research reactor and demands of neutron field of a high order, new type research reactors under investigation are explained. Recently, the reactors are used in many fields such as the basic science: the basic physics, the material science, the nuclear physics, and the nuclear chemistry and the applied science; the earth and environmental science, the biology and the medical science. (S.Y.)

The Past, Present, and Future of Human Centromere Genomics

Directory of Open Access Journals (Sweden)

Megan E. Aldrup-MacDonald

2014-01-01

Full Text Available The centromere is the chromosomal locus essential for chromosome inheritance and genome stability. Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome. Contiguous alpha satellite DNA sequence is absent from the assembled reference genome, limiting current understanding of centromere organization and function. Here, we review the progress in centromere genomics spanning the discovery of the sequence to its molecular characterization and the work done during the Human Genome Project era to elucidate alpha satellite structure and sequence variation. We discuss exciting recent advances in alpha satellite sequence assembly that have provided important insight into the abundance and complex organization of this sequence on human chromosomes. In light of these new findings, we offer perspectives for future studies of human centromere assembly and function.

Celiac crisis presenting with status epilepticus and encephalopathy.

Science.gov (United States)

Hijaz, Nadia M; Bracken, Julia M; Chandratre, Sonal R

2014-12-01

Celiac crisis is a life-threatening presentation of celiac disease which is described in the context of classic gastrointestinal (GI) symptoms of diarrhea, leading to dehydration and electrolyte imbalance. Neurologic manifestations are atypical symptoms of celiac crisis. To the best of our knowledge, there is no published report on seizure or encephalopathy as the presenting manifestation of celiac crisis. We describe a 2-year-old boy presenting with acute status epilepticus and lethargy. Prior to presentation, he had mild abdominal distention and intermittent diarrhea. Laboratory analysis revealed hyponatremia, anemia, hypocalcemia, transaminitis, and hyperglycemia. Electroencephalography revealed severe diffuse encephalopathy, and complete infectious work-up was negative. Initial brain magnetic resonance imaging was normal; however, repeat imaging showed osmotic demyelination syndrome. Given the history of GI symptoms and hyperglycemia, celiac serology was obtained revealing elevated tissue transglutaminase, and a diagnosis was confirmed by Marsh 3c lesions in the duodenum. He significantly improved with steroid therapy in addition to adequate nutrition, fluids, and initiation of a gluten-free diet. We report herein on the first case of celiac crisis presenting with status epilepticus and encephalopathy in the absence of profound GI symptoms. Our case suggests that celiac crisis should be considered in the differential of seizures and encephalopathy in children.

Status epilepticus as the only presentation of the neonatal Bartter syndrome.

Science.gov (United States)

Patra, Soumya; Konar, Mithun C; Basu, Rajarshi; Khaowas, Ajoy K; Dutta, Soumyadeep; Sarkar, Debanjali

2012-03-01

Bartter syndrome is a rare hereditary (autosomal recessive) salt-losing tubulopathy characterized by hypokalemia, hypochloremia, metabolic alkalosis, and normal blood pressure with hyperreninemia, The underlying renal abnormality results in excessive urinary losses of sodium, chloride, and potassium. We report a case of a four-month-old infant with neonatal Bartter syndrome, who presented only with status epilepticus. To the best of our present knowledge, there is no reported case of Bartter syndrome who presented with status epilepticus.

Genomic Tools in Pea Breeding Programs: Status and Perspectives

Science.gov (United States)

Tayeh, Nadim; Aubert, Grégoire; Pilet-Nayel, Marie-Laure; Lejeune-Hénaut, Isabelle; Warkentin, Thomas D.; Burstin, Judith

2015-01-01

Pea (Pisum sativum L.) is an annual cool-season legume and one of the oldest domesticated crops. Dry pea seeds contain 22–25% protein, complex starch and fiber constituents, and a rich array of vitamins, minerals, and phytochemicals which make them a valuable source for human consumption and livestock feed. Dry pea ranks third to common bean and chickpea as the most widely grown pulse in the world with more than 11 million tons produced in 2013. Pea breeding has achieved great success since the time of Mendel's experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Taking advantage of the diversity present in the pea genepool, many mapping populations have been constructed in the last decades and efforts have been deployed to identify loci involved in the control of target traits and further introgress them into elite breeding materials. Pea now benefits from next-generation sequencing and high-throughput genotyping technologies that are paving the way for genome-wide association studies and genomic selection approaches. This review covers the significant development and deployment of genomic tools for pea breeding in recent years. Future prospects are discussed especially in light of current progress toward deciphering the pea genome. PMID:26640470

Genomic tools in pea breeding programs: status and perspectives

Directory of Open Access Journals (Sweden)

Nadim eTAYEH

2015-11-01

Full Text Available Pea (Pisum sativum L. is an annual cool-season legume and one of the oldest domesticated crops. Dry pea seeds contain 22-25 percent protein, complex starch and fibre constituents and a rich array of vitamins, minerals, and phytochemicals which make them a valuable source for human consumption and livestock feed. Dry pea ranks third to common bean and chickpea as the most widely grown pulse in the world with more than 11 million tonnes produced in 2013. Pea breeding has achieved great success since the time of Mendel’s experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Taking advantage of the diversity present in the pea genepool, many mapping populations have been constructed in the last decades and efforts have been deployed to identify loci involved in the control of target traits and further introgress them into elite breeding materials. Pea now benefits from next-generation sequencing and high-throughput genotyping technologies that are paving the way for genome-wide association studies and genomic selection approaches. This review covers the significant development and deployment of genomic tools for pea breeding in recent years. Future prospects are discussed especially in light of current progress towards deciphering the pea genome.

Computational pan-genomics: status, promises and challenges

NARCIS (Netherlands)

The Computational Pan-Genomics Consortium; T. Marschall (Tobias); M. Marz (Manja); T. Abeel (Thomas); L.J. Dijkstra (Louis); B.E. Dutilh (Bas); A. Ghaffaari (Ali); P. Kersey (Paul); W.P. Kloosterman (Wigard); V. Mäkinen (Veli); A.M. Novak (Adam); B. Paten (Benedict); D. Porubsky (David); E. Rivals (Eric); C. Alkan (Can); J.A. Baaijens (Jasmijn); P.I.W. de Bakker (Paul); V. Boeva (Valentina); R.J.P. Bonnal (Raoul); F. Chiaromonte (Francesca); R. Chikhi (Rayan); F.D. Ciccarelli (Francesca); C.P. Cijvat (Robin); E. Datema (Erwin); C.M. van Duijn (Cornelia); E.E. Eichler (Evan); C. Ernst (Corinna); E. Eskin (Eleazar); E. Garrison (Erik); M. El-Kebir (Mohammed); G.W. Klau (Gunnar); J.O. Korbel (Jan); E.-W. Lameijer (Eric-Wubbo); B. Langmead (Benjamin); M. Martin; P. Medvedev (Paul); J.C. Mu (John); P.B.T. Neerincx (Pieter); K. Ouwens (Klaasjan); P. Peterlongo (Pierre); N. Pisanti (Nadia); S. Rahmann (Sven); B.J. Raphael (Benjamin); K. Reinert (Knut); D. de Ridder (Dick); J. de Ridder (Jeroen); M. Schlesner (Matthias); O. Schulz-Trieglaff (Ole); A.D. Sanders (Ashley); S. Sheikhizadeh (Siavash); C. Shneider (Carl); S. Smit (Sandra); D. Valenzuela (Daniel); J. Wang (Jiayin); L.F.A. Wessels (Lodewyk); Y. Zhang (Ying); V. Guryev (Victor); F. Vandin (Fabio); K. Ye (Kai); A. Schönhuth (Alexander)

2018-01-01

textabstractMany disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. In case of Homo sapiens, the number of sequenced genomes will approach hundreds of thousands in the next few

Status epilepticus as the only presentation of the neonatal Bartter syndrome

Directory of Open Access Journals (Sweden)

Soumya Patra

2012-01-01

Full Text Available Bartter syndrome is a rare hereditary (autosomal recessive salt-losing tubulopathy characterized by hypokalemia, hypochloremia, metabolic alkalosis, and normal blood pressure with hyperreninemia, The underlying renal abnormality results in excessive urinary losses of sodium, chloride, and potassium. We report a case of a four-month-old infant with neonatal Bartter syndrome, who presented only with status epilepticus. To the best of our present knowledge, there is no reported case of Bartter syndrome who presented with status epilepticus.

Cosmic microwave background: present status and future prospects

International Nuclear Information System (INIS)

Muller, R.A.

1978-12-01

After a brief review of the origin of the radiation according to the standard model, the status of present measurements of the spectrum and the large-scale isotropy is discussed. Finally, it is indicated what are the prospects for improved measurements in the next decade. 17 references

The INCA project: present status and outlook

International Nuclear Information System (INIS)

Aleksandrov, K.V.; Ammosov, V.V.; Chechin, V.A.; Chubenko, A.P.; Erlykin, A.D.; Ladygin, E.A.; Merzon, G.I.; Mukhamedshin, R.A.; Murashov, V.N.; Pavlyuchenko, V.P.; Ryabov, V.A.; Ryazhskaya, O.G.; Saito, T.; Sobolevskii, N.M.; Shchepetov, A.L.; Starkov, N.I.; Trostin, I.S.; Tsarev, V.A.; Wolfendale, A.; Zatsepin, G.T.; Zhdanov, G.B.; Zhukov, A.P.

2002-01-01

Scientific objectives, foundations, status, and outlook of the INCA Project are presented. Fundamentally new technique based on the ionization-neutron calorimeter (INCA) and designed to study local nearby sources of high-energy cosmic rays by direct measuring the spectrum and composition of the nuclear component in the 'knee' region and the spectrum of primary electrons in the energy range 0.1-10 TeV with the proton-background suppression factor up to 10 7 is discussed. Experimental data on exposition of the INCA prototypes to electron, pion, and proton beams at various energies and corresponding simulation results are presented. Prospects are considered

Present status and perspectives of nuclear power in Latin America

International Nuclear Information System (INIS)

Mondino, M.A.

1995-01-01

The paper describes the present status of nuclear power in Latin America, giving an analysis of Argentina, Brazil, Cuba and Mexico - the countries that have committed themselves to nuclear power undertakings. The historical development of the energy sector is studied and analysed, comparing Latin America with developed countries and groups of countries. Projected data are also studied and analysed, defining the present status of nuclear power in Latin American and its future possibilities. The region's future needs are analyzed on the basis of various indicators and the most important conclusions are highlighted. (author). 10 refs, 9 figs, 21 tabs

Croatian repository construction project - present status and main obstacles

International Nuclear Information System (INIS)

Kucar Dragicevic, S.; Subasic, D.; Schaller, A.; Lokner, V.; Cerskov Klika, M.

1999-01-01

Croatia has been preparing backgrounds for the construction of the repository for low and intermediate radioactive waste on its territory, almost for a decade, now. In the name of Hrvtaska elektroprivreda, the co-owner of the NE Krsko, APO has been co-ordinating and organising numerous activities and projects during that time period. Siting process, safety assessment, disposal technology and repository design and public acceptance issues are the main fields of activities. The overall status of the project at the moment, including the overview of the present status of the main four aspects of activities, will be presented. Relatively, big and important progress made on the project work out during the last two years, as well as the main obstacles we were faced with during that time period, will be discussed.(author)

Present status of the TOHOKU 300 MeV linac

International Nuclear Information System (INIS)

Takahashi, Shigenobu; Oyamada, Masayuki; Urasawa, Shigekazu; Nakazato, Toshiharu; Kurihara, Akira; Mutoh, Masakatu; Shibasaki, Yoshinobu; Oonuma, Tadahiro

1993-01-01

The TOHOKU linac that was constructed about a quarter century before has been operated without serious trouble recently. This report describes as follows: main trouble, maintenance, present performance of the machine and status of operation. (author)

Present status of HTGR research and development

International Nuclear Information System (INIS)

1991-04-01

The HTTR is a test reactor with thermal output of 30MW and outlet coolant temperature of 950degC, employing the pin-in-block type fuel, and has the capability to demonstrate nuclear process heat utilization using an intermediate heat exchanger. The official construction of the HTTR facility is scheduled to start on March 15, 1991. This publication summarizes the present status of R and D of high temperature gas cooled reactors in JAERI. (J.P.N.)

Present status of TCA/BR Tokamak

International Nuclear Information System (INIS)

Nascimento, I.C.; Galvao, R.M.O.; Tuszel, A.G.

1997-01-01

The TCA tokamak is being partially reconstructed and reassembled in the Plasma Laboratory of The University of Sao Paulo, and afterwards it will be named TCA/BR. The first discharges are expected by June/July of next year. The main scientific objectives envisaged for the machine are: Alfven wave heating and current drive, confinement improvement, disruptions and turbulence. In this paper we also describe: (i) the present status of the project; (ii) the diagnostic system; (iii) the control and data acquisition system; (iv) the RF system for the excitation of Alfven waves, that are being developed, and also the results of predictive transport simulations of its performance. (author)

The present status of artificial intelligence for nuclear power plants

International Nuclear Information System (INIS)

Suda, Kazunori; Yonekawa, Tuyoshi; Yoshikawa, Shinji; Hasegawa, Makoto

1999-03-01

JNC researches the development of distributed intelligence systems at autonomous plants and intelligent support system at nuclear power plant. This report describes the present status of artificial intelligence (AI) technologies for this research. The following are represented in this report: present research study for AI, Implementation of AI system and application of AI technologies in the field of industries, requirement for AI by industries, problems of social acceptance for AI. A development of AI systems has to be motivated both by current status of AI and requirement for AI. Furthermore a problem of social acceptance for AI technologies has to be solved for using AI systems in society. (author)

Present status and perspectives for hydroelectric power in world

International Nuclear Information System (INIS)

Malquori, E.

1991-01-01

In the note a review of the present status and perspectives of hydroelectric power in the world is introduced. The present status regards, in chronological order, the last decade, as to say the works carried out in the 80ies whereas the perspectives regard the next twenty years as to say until 2010. The mentioned electric power potentiality refers to pure generation plants of great, middle and small size and to what could be achieved by already existing plants after changes and/or replacements and improvement of the machinery. Beside the figures regarding powers, great generation and pumping plants whose contribution has been and will be remarkable have been properly mentioned. The Italian contribution - civil works design, construction, and machinery supply - in the last hydroelectric development is briefly mentioned with particular reference to the developing countries

Recent results on polarizations and the present status of the Fermilab polarized beams

International Nuclear Information System (INIS)

Yokosawa, Akihiko.

1986-01-01

Experimental results are reviewed on polarization phenomena in nucleon-nucleon scattering at intermediate energies. The present status of S = 0 dibaryon resonances is presented. The status of the Fermilab polarized beam program is presented, including the construction of polarized beam, two polarimeters being installed in the experimental hall, and the experimental program

Differential DNA methylation patterns define status epilepticus and epileptic tolerance.

Science.gov (United States)

Miller-Delaney, Suzanne F C; Das, Sudipto; Sano, Takanori; Jimenez-Mateos, Eva M; Bryan, Kenneth; Buckley, Patrick G; Stallings, Raymond L; Henshall, David C

2012-02-01

Prolonged seizures (status epilepticus) produce pathophysiological changes in the hippocampus that are associated with large-scale, wide-ranging changes in gene expression. Epileptic tolerance is an endogenous program of cell protection that can be activated in the brain by previous exposure to a non-harmful seizure episode before status epilepticus. A major transcriptional feature of tolerance is gene downregulation. Here, through methylation analysis of 34,143 discrete loci representing all annotated CpG islands and promoter regions in the mouse genome, we report the genome-wide DNA methylation changes in the hippocampus after status epilepticus and epileptic tolerance in adult mice. A total of 321 genes showed altered DNA methylation after status epilepticus alone or status epilepticus that followed seizure preconditioning, with >90% of the promoters of these genes undergoing hypomethylation. These profiles included genes not previously associated with epilepsy, such as the polycomb gene Phc2. Differential methylation events generally occurred throughout the genome without bias for a particular chromosomal region, with the exception of a small region of chromosome 4, which was significantly overrepresented with genes hypomethylated after status epilepticus. Surprisingly, only few genes displayed differential hypermethylation in epileptic tolerance. Nevertheless, gene ontology analysis emphasized the majority of differential methylation events between the groups occurred in genes associated with nuclear functions, such as DNA binding and transcriptional regulation. The present study reports select, genome-wide DNA methylation changes after status epilepticus and in epileptic tolerance, which may contribute to regulating the gene expression environment of the seizure-damaged hippocampus.

Present status of the Penrose inequality

Energy Technology Data Exchange (ETDEWEB)

Mars, Marc [Facultad de Ciencias, Universidad de Salamanca, Plaza de la Merced s/n, 37008 Salamanca (Spain)

2009-10-07

The Penrose inequality gives a lower bound for the total mass of a spacetime in terms of the area of suitable surfaces that represent black holes. Its validity is supported by the cosmic censorship conjecture, and therefore its proof (or disproof) is an important problem in relation with gravitational collapse. The Penrose inequality is a very challenging problem in mathematical relativity and it has received continuous attention since its formulation by Penrose in the early seventies. Important breakthroughs have been made in the last decade or so, with the complete resolution of the so-called Riemannian Penrose inequality and a very interesting proposal to address the general case by Bray and Khuri. In this review, the most important results on this field will be discussed and the main ideas behind their proofs will be summarized, with the aim of presenting what is the status of our present knowledge in this topic. (topical review)

The present status of software engineering

CERN Document Server

Pressman, Roger S

1991-01-01

In this seminar, we will discuss the present status and future directions of software engeneering and CASE. Key topics to be discussed include: new paradigms for software engineering; software metrics; process assessment; the current state of analysis and design methods; reusability and re-engineering; formal methods. Among the questions to be answered are: How will software engineering change as the 1990s progress? What are the "technology drivers"? What will analysis, design, coding, testing, quality assurance and software management look like in the year 2000? How will CASE tools evolve in the 1990s and will they be as "integrated" as many people believe? How can you position your Organization to accommodate the coming changes?

Present status and expected progress in radiation processing dosimetry

DEFF Research Database (Denmark)

Kovács, A.; Miller, A.

2004-01-01

The paper describes the present status of radiation processing dosimetry including the methods used most widely in gamma- and electron processing as well as the new methods under development or introduction. The recent trends with respect to calibrationof routine dosimetry systems as well...

Safety analysis of the present status of the research reactor 'RA' at 'Vinca' Institute

International Nuclear Information System (INIS)

Jovic, V.; Jovic, L.; Zivotic, Z.; Milovanovic, Dj.

1995-01-01

Safety analysis of the nuclear facility which has been out of work for a long time and whose future is not defined at the present moment, can not be connected to the usual, normatively regulated system analysis procedure in both operational and accidental regimes. Therefore, the safety analysis of the present status of the present status of the reactor RA is related to system and components analysis which, in present conditions maintain their nuclear functions operational. In the first place, it refers to components and equipment in which radioactive radiation generation still exists and to installations and equipment maintaining radiation level below permitted limit. in the context of the analysis the following areas are being covered: present status characteristics, accidental events while operating period from 1959. to 1984., nuclear fuels and radioactive waste inventory, basic characteristics and status of safety-related systems and equipment, radiation protection, potential accident analysis at present status of the reactor RA, potential accidental situations due to natural events (earthquakes, water flood) or man-induced events and security. 8 refs

Human social genomics.

Directory of Open Access Journals (Sweden)

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.

Ancient human genomes suggest three ancestral populations for present-day Europeans

Science.gov (United States)

Lazaridis, Iosif; Patterson, Nick; Mittnik, Alissa; Renaud, Gabriel; Mallick, Swapan; Kirsanow, Karola; Sudmant, Peter H.; Schraiber, Joshua G.; Castellano, Sergi; Lipson, Mark; Berger, Bonnie; Economou, Christos; Bollongino, Ruth; Fu, Qiaomei; Bos, Kirsten I.; Nordenfelt, Susanne; Li, Heng; de Filippo, Cesare; Prüfer, Kay; Sawyer, Susanna; Posth, Cosimo; Haak, Wolfgang; Hallgren, Fredrik; Fornander, Elin; Rohland, Nadin; Delsate, Dominique; Francken, Michael; Guinet, Jean-Michel; Wahl, Joachim; Ayodo, George; Babiker, Hamza A.; Bailliet, Graciela; Balanovska, Elena; Balanovsky, Oleg; Barrantes, Ramiro; Bedoya, Gabriel; Ben-Ami, Haim; Bene, Judit; Berrada, Fouad; Bravi, Claudio M.; Brisighelli, Francesca; Busby, George B. J.; Cali, Francesco; Churnosov, Mikhail; Cole, David E. C.; Corach, Daniel; Damba, Larissa; van Driem, George; Dryomov, Stanislav; Dugoujon, Jean-Michel; Fedorova, Sardana A.; Romero, Irene Gallego; Gubina, Marina; Hammer, Michael; Henn, Brenna M.; Hervig, Tor; Hodoglugil, Ugur; Jha, Aashish R.; Karachanak-Yankova, Sena; Khusainova, Rita; Khusnutdinova, Elza; Kittles, Rick; Kivisild, Toomas; Klitz, William; Kučinskas, Vaidutis; Kushniarevich, Alena; Laredj, Leila; Litvinov, Sergey; Loukidis, Theologos; Mahley, Robert W.; Melegh, Béla; Metspalu, Ene; Molina, Julio; Mountain, Joanna; Näkkäläjärvi, Klemetti; Nesheva, Desislava; Nyambo, Thomas; Osipova, Ludmila; Parik, Jüri; Platonov, Fedor; Posukh, Olga; Romano, Valentino; Rothhammer, Francisco; Rudan, Igor; Ruizbakiev, Ruslan; Sahakyan, Hovhannes; Sajantila, Antti; Salas, Antonio; Starikovskaya, Elena B.; Tarekegn, Ayele; Toncheva, Draga; Turdikulova, Shahlo; Uktveryte, Ingrida; Utevska, Olga; Vasquez, René; Villena, Mercedes; Voevoda, Mikhail; Winkler, Cheryl; Yepiskoposyan, Levon; Zalloua, Pierre; Zemunik, Tatijana; Cooper, Alan; Capelli, Cristian; Thomas, Mark G.; Ruiz-Linares, Andres; Tishkoff, Sarah A.; Singh, Lalji; Thangaraj, Kumarasamy; Villems, Richard; Comas, David; Sukernik, Rem; Metspalu, Mait; Meyer, Matthias; Eichler, Evan E.; Burger, Joachim; Slatkin, Montgomery; Pääbo, Svante; Kelso, Janet; Reich, David; Krause, Johannes

2014-01-01

We sequenced the genomes of a ~7,000 year old farmer from Germany and eight ~8,000 year old hunter-gatherers from Luxembourg and Sweden. We analyzed these and other ancient genomes1–4 with 2,345 contemporary humans to show that most present Europeans derive from at least three highly differentiated populations: West European Hunter-Gatherers (WHG), who contributed ancestry to all Europeans but not to Near Easterners; Ancient North Eurasians (ANE) related to Upper Paleolithic Siberians3, who contributed to both Europeans and Near Easterners; and Early European Farmers (EEF), who were mainly of Near Eastern origin but also harbored WHG-related ancestry. We model these populations’ deep relationships and show that EEF had ~44% ancestry from a “Basal Eurasian” population that split prior to the diversification of other non-African lineages. PMID:25230663

Present status of the SRRC Project

International Nuclear Information System (INIS)

Chang, C.; Cheng, K.C.; Liu, Y.C.; Tseng, P.K.

1985-01-01

Upon the recommendation of the overseas Chinese scholars and the feasibility study group organized by the National Science Council, the government approved the establishment of the Synchrotron Radiation Research Center (SRRC) on July 9, 1983. The main goal of the SRRC project is to construct and operate an up-to-date 1 GeV synchrotron radiation source, with three beam lines for general experiments, in five to six years; to provide local scientists and returned scientists from abroad a facility to carry out frontier researches in both basic and applied science; and to elevate the technological capabilities of the related industries, universities, and research institutes through the construction of the machine. The background and present status of the project are discussed

Multimedia Presentations on the Human Genome: Implementation and Assessment of a Teaching Program for the Introduction to Genome Science Using a Poster and Animations

Science.gov (United States)

Kano, Kei; Yahata, Saiko; Muroi, Kaori; Kawakami, Masahiro; Tomoda, Mari; Miyaki, Koichi; Nakayama, Takeo; Kosugi, Shinji; Kato, Kazuto

2008-01-01

Genome science, including topics such as gene recombination, cloning, genetic tests, and gene therapy, is now an established part of our daily lives; thus we need to learn genome science to better equip ourselves for the present day. Learning from topics directly related to the human has been suggested to be more effective than learning from…

Present status of accelerator-based BNCT: Focus on developments in Argentina

International Nuclear Information System (INIS)

Cartelli, D.; Capoulat, M.E.; Bergueiro, J.; Gagetti, L.; Suárez Anzorena, M.; Grosso, M.F. del; Baldo, M.; Castell, W.; Padulo, J.; Suárez Sandín, J.C.; Igarzabal, M.; Erhardt, J.; Mercuri, D.

2015-01-01

In this work we provide some information on the present status of accelerator-based BNCT (AB-BNCT) worldwide and subsequently concentrate on the recent accelerator technology developments in Argentina. - Highlights: • The current status of projects and associated facilities for AB-BNCT worldwide is shown. • Only low (few MeV) energy accelerators are included. • The recent progress of the Argentine AB-BNCT program is described.

Integration of nuclear power in the Portuguese network. Present status

International Nuclear Information System (INIS)

Videira, F.M.

1977-01-01

The main characteristics of the Portuguese electric energy production system and their evolution in the past and near future are presented. Taking into consideration the Portuguese energy resources the alternatives to meet the additional long range electric energy needs are evaluated. Finally some comments are made about the present status of the nuclear option. (Auth.)

Transmutation of radioactive nuclear waste – present status and ...

Indian Academy of Sciences (India)

Transmutation of long-lived actinides and fission products becomes an important issue of the overall nuclear fuel cycle assessment, both for existing and future reactor systems. Reliable nuclear data are required for analysis of associated neutronics. The present paper gives a review of the status of nuclear data analysis ...

De-novo simple partial status epilepticus presenting as Wernicke's aphasia.

Science.gov (United States)

Patil, Bhimanagouda; Oware, Agyepong

2012-04-01

Language disturbances manifesting as brief periods of speech arrest occur with seizures originating in the frontal or temporal lobes. These language disturbances are usually present with other features of seizures or may occur in an episodic fashion suggesting their likely epileptic origin. Sustained but reversible aphasia as the sole manifestation of partial status epilepticus is rare, particularly without a history of prior seizures. A few cases have been described in the literature where Broca's or mixed aphasia seems to be more common than Wernicke's aphasia. Here we describe a patient who presented with Wernicke's aphasia secondary to simple partial status epilepticus but without any other features of seizures. The diagnosis was confirmed on EEG and the aphasia reversed after antiepileptic treatment. Copyright © 2011 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

A Genome-wide multidimensional RNAi screen reveals pathways controlling MHC class II antigen presentation

NARCIS (Netherlands)

Paul, Petra; van den Hoorn, Tineke; Jongsma, Marlieke L. M.; Bakker, Mark J.; Hengeveld, Rutger; Janssen, Lennert; Cresswell, Peter; Egan, David A.; van Ham, Marieke; ten Brinke, Anja; Ovaa, Huib; Beijersbergen, Roderick L.; Kuijl, Coenraad; Neefjes, Jacques

2011-01-01

MHC class II molecules (MHC-II) present peptides to T helper cells to facilitate immune responses and are strongly linked to autoimmune diseases. To unravel processes controlling MHC-II antigen presentation, we performed a genome-wide flow cytometry-based RNAi screen detecting MHC-II expression and

Superdeformation- present status and some new universal features

International Nuclear Information System (INIS)

Jain, A.K.; Jain, S.R.

1995-01-01

The present status of understanding of superdeformed (SD) bands has been presented. The puzzles raised by the experimental data have been highlighted. Besides the well known problems related to feeding and depopulation, moment of inertia and identical bands, we have also pointed out the existence of a weak oscillation in the I vs. E γ plots, the negative value for the net alignment in many SD bands and the general identical band pattern found in each mass region. Theoretical explanation for many of these features have been suggested individually but there is no single theoretical framework which would be able to explain all the features together. (author). 32 refs

Present status and prospects of radioisotopes and radiation utilization in Indonesia

International Nuclear Information System (INIS)

Baiquni, A.

1982-01-01

The present status and prospects of RI and radiation utilization in Indonesia, which developed under the Government's assistance and supervision since the opening of the research reactor in 1965, was reviewed. Utilization of short half-life RI in various fields was described. Utilization in medicine, sterilization of medical supplies, the industrial world and hydrology was detailed. Annual changes in these fields were shown and tables were presented. The status of various types of radiation and RI utilization in Indonesia, which included nuclear analytical techniques in industry and various laboratories in agriculture, industry and biology, was reported. Finally, the plan of construction of a third research reactor was referred to. (Chiba, N.)

A present status for dry storage of spent nuclear fuel

Energy Technology Data Exchange (ETDEWEB)

Bang, K. S.; Lee, J. C.; Park, H. Y.; Seo, K. S

2003-04-01

National policy for management of a spent nuclear fuel does not establish in Korea yet. A storage capacity of a storage pool that is to store the spent nuclear fuel will be exceeded an amount of accumulation from the first Woljin nuclear power plant in 2007. Therefore it is necessary that dry storage facility is secured to store safely the spent nuclear fuel on site of the nuclear power plant until national policy for a back-end spent nuclear fuel cycle is established. In order to store safely spent nuclear fuel, it is important that the present status and technology on dry storage of spent nuclear fuel is looked over. Therefore, the present status on dry storage of spent nuclear fuel was analyzed so as to develop dry storage system and choose a proper dry storage method domestic.

Aspergillus Niger Genomics: Past, Present and into the Future

Energy Technology Data Exchange (ETDEWEB)

Baker, Scott E.

2006-09-01

Aspergillus niger is a filamentous ascomycete fungus that is ubiquitous in the environment and has been implicated in opportunistic infections of humans. In addition to its role as an opportunistic human pathogen, A. niger is economically important as a fermentation organism used for the production of citric acid. Industrial citric acid production by A. niger represents one of the most efficient, highest yield bioprocesses in use currently by industry. The genome size of A. niger is estimated to be between 35.5 and 38.5 megabases (Mb) divided among eight chromosomes/linkage groups that vary in size from 3.5 - 6.6 Mb. Currently, there are three independent A. niger genome projects, an indication of the economic importance of this organism. The rich amount of data resulting from these multiple A. niger genome sequences will be used for basic and applied research programs applicable to fermentation process development, morphology and pathogenicity.

Nuclear power in the world: Its present status and development trends

International Nuclear Information System (INIS)

Bennett, L.L.

1994-01-01

Present status of nuclear power development in the world is presented showing data on power reactors in operation and under construction, on growth of nuclear electricity generation since 1970, the distribution of nuclear electricity generation during 1993. Development trends in the field are also outlined. 7 figs, 5 tabs

Present status and needs of research on severe core damage

International Nuclear Information System (INIS)

1982-05-01

The needs for research on severe core damage accident have been emphasized recently, in particular, since TMI-2 accident. The Severe Core Damage Research Task Force was established by the Divisions of Reactor Safety and Reactor Safety Evaluation to evaluate individual phenomenon, to survey the present status of research and to provide the recommended research subjects on severe accidents. This report describes the accident phenomena involving some analytical results, status of research and recommended research subjects on severe core damage accidents, divided into accident sequence, fuel damage, and molten material behavior, fission product behavior, hydrogen generation and combustion, steam explosion and containment integrity. (author)

Present status of fuel motion detection by radiation

International Nuclear Information System (INIS)

Sumita, Kenji; Mizuta, Hiroshi; Ishizuka, Makoto; Ara, Katsuyuki; Nakata, Hirokatsu.

1978-05-01

In reactor safety research, it is important to know transient fuel behavior under accidental conditions. Transient histories such as temperature and axial expansion of fuel and cladding and internal pressure of fuel rod are thus measured in experiments simulating accidents. If fuel motion could then be observed during and after fuel failure, this would greatly make for fuel behavior research. The present status is reviewed of fuel motion detections by radiations such as neutron, γ-ray and X-ray, including the principle and system. A neutron hodoscope among them is used already with practical results in in-reactor safety experiments of sodium-cooled fast breeder reactor. So, this is described in detail and its conceptual design as applied to the NSRR is presented. (auth.)

Present status of the radiative neutron capture mechanisms -nonstatistical effects

International Nuclear Information System (INIS)

Brzosko, J.S.

1976-01-01

The present status of our knowledge about neutron radiative capture mechanisms is described. In the first section there are given a review on mathematical description of the neutron capture cross section and possible sources of correlation effects. The point of lecture is the explanation of connections between the intermediate structures and correlation effects. In one of the sections the explanation of the bump in γ-ray spectra is discussed. The typical experimental results are presented. (author)

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.

VGKC antibodies in pediatric encephalitis presenting with status epilepticus.

Science.gov (United States)

Suleiman, J; Brenner, T; Gill, D; Brilot, F; Antony, J; Vincent, A; Lang, B; Dale, R C

2011-04-05

Voltage-gated potassium channel antibodies (VGKC Ab) are associated with limbic encephalitis and neuromyotonia in adults. There have been no systematic investigations in children to date. We looked for antibodies that are associated with CNS syndromes in adults including antibodies to VGKCs, NMDARs, glutamic acid decarboxylase (GAD), and glycine receptor (GlyR) in the stored acute serum from 10 children with unexplained encephalitis presenting with encephalopathy and status epilepticus. We also looked for antibodies to leucine-rich glioma-inactivated 1 (Lgi1) and contactin-associated protein-like 2 (Caspr2), which are now known to be tightly complexed with VGKCs in vivo. Sixty-nine pediatric controls were used for comparison. An elevated VGKC Ab (>100 pM) was detected in 4/10 patients with encephalitis compared to only 1/69 controls (p VGKC Ab-positive patients with encephalitis was variable including good recovery (n = 1), cognitive impairment (n = 3), temporal lobe epilepsy (n = 2), and mesial temporal sclerosis (n = 1). No other antibodies were detected, including those to Lgi1 and Caspr2. Encephalitis associated with VGKC Ab occurs in children and presents with status epilepticus and focal epilepsy. These antibodies are not directed against Lgi1 or Caspr2.

Genomics of lactic acid bacteria: Current status and potential applications.

Science.gov (United States)

Wu, Chongde; Huang, Jun; Zhou, Rongqing

2017-08-01

Lactic acid bacteria (LAB) are widely used for the production of a variety of foods and feed raw materials where they contribute to flavor and texture of the fermented products. In addition, specific LAB strains are considered as probiotic due to their health-promoting effects in consumers. Recently, the genome sequencing of LAB is booming and the increased amount of published genomics data brings unprecedented opportunity for us to reveal the important traits of LAB. This review describes the recent progress on LAB genomics and special emphasis is placed on understanding the industry-related physiological features based on genomics analysis. Moreover, strategies to engineer metabolic capacity and stress tolerance of LAB with improved industrial performance are also discussed.

Present status of the European Community's Fusion Materials Programme

International Nuclear Information System (INIS)

Nihoul, J.; Boutard, J.L.

1990-01-01

The Fusion Materials Programme of the European Communities is largely focused on the next step in the European strategy towards fusion energy development, i.e. on NET, the Next European Torus. The main objectives and operating conditions of NET are therefore first briefly presented. A review is then given of the present status of our knowledge regarding the main metallic structural materials envisaged for the first wall/blanket and for the divertor plates. Attention is paid to the need for longer term research and development towards low activation structural materials to be used in a post-NET Demonstration Reactor. Finally, a survey is presented of the current European Fusion Technology Programme devoted to the various candidate structural and protection materials for fusion devices. (author)

Whole-genome DNA methylation status associated with clinical PTSD measures of OIF/OEF veterans

Science.gov (United States)

Hammamieh, R; Chakraborty, N; Gautam, A; Muhie, S; Yang, R; Donohue, D; Kumar, R; Daigle, B J; Zhang, Y; Amara, D A; Miller, S-A; Srinivasan, S; Flory, J; Yehuda, R; Petzold, L; Wolkowitz, O M; Mellon, S H; Hood, L; Doyle, F J; Marmar, C; Jett, M

2017-01-01

Emerging knowledge suggests that post-traumatic stress disorder (PTSD) pathophysiology is linked to the patients’ epigenetic changes, but comprehensive studies examining genome-wide methylation have not been performed. In this study, we examined genome-wide DNA methylation in peripheral whole blood in combat veterans with and without PTSD to ascertain differentially methylated probes. Discovery was initially made in a training sample comprising 48 male Operation Enduring Freedom (OEF)/Operation Iraqi Freedom (OIF) veterans with PTSD and 51 age/ethnicity/gender-matched combat-exposed PTSD-negative controls. Agilent whole-genome array detected ~5600 differentially methylated CpG islands (CpGI) annotated to ~2800 differently methylated genes (DMGs). The majority (84.5%) of these CpGIs were hypermethylated in the PTSD cases. Functional analysis was performed using the DMGs encoding the promoter-bound CpGIs to identify networks related to PTSD. The identified networks were further validated by an independent test set comprising 31 PTSD+/29 PTSD− veterans. Targeted bisulfite sequencing was also used to confirm the methylation status of 20 DMGs shown to be highly perturbed in the training set. To improve the statistical power and mitigate the assay bias and batch effects, a union set combining both training and test set was assayed using a different platform from Illumina. The pathways curated from this analysis confirmed 65% of the pool of pathways mined from training and test sets. The results highlight the importance of assay methodology and use of independent samples for discovery and validation of differentially methylated genes mined from whole blood. Nonetheless, the current study demonstrates that several important epigenetically altered networks may distinguish combat-exposed veterans with and without PTSD. PMID:28696412

Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas

International Nuclear Information System (INIS)

Xiang, Shengyan; Liu, Zhaojun; Zhang, Baozhen; Zhou, Jing; Zhu, Bu-Dong; Ji, Jiafu; Deng, Dajun

2010-01-01

Alu methylation is correlated with the overall level of DNA methylation and recombination activity of the genome. However, the maintenance and methylation status of each CpG site within Alu elements (Alu) and its methylation status have not well characterized. This information is useful for understanding natural status of Alu in the genome and helpful for developing an optimal assay to quantify Alu hypomethylation. Bisulfite clone sequencing was carried out in 14 human gastric samples initially. A Cac8I COBRA-DHPLC assay was developed to detect methylated-Alu proportion in cell lines and 48 paired gastric carcinomas and 55 gastritis samples. DHPLC data were statistically interpreted using SPSS version 16.0. From the results of 427 Alu bisulfite clone sequences, we found that only 27.2% of CpG sites within Alu elements were preserved (4.6 of 17 analyzed CpGs, A ~ Q) and that 86.6% of remaining-CpGs were methylated. Deamination was the main reason for low preservation of methylation targets. A high correlation coefficient of methylation was observed between Alu clones and CpG site J (0.963), A (0.950), H (0.946), D (0.945). Comethylation of the sites H and J were used as an indicator of the proportion of methylated-Alu in a Cac8I COBRA-DHPLC assay. Validation studies showed that hypermethylation or hypomethylation of Alu elements in human cell lines could be detected sensitively by the assay after treatment with 5-aza-dC and M.SssI, respectively. The proportion of methylated-Alu copies in gastric carcinomas (3.01%) was significantly lower than that in the corresponding normal samples (3.19%) and gastritis biopsies (3.23%). Most Alu CpG sites are deaminated in the genome. 27% of Alu CpG sites represented in our amplification products. 87% of the remaining CpG sites are methylated. Alu hypomethylation in primary gastric carcinomas could be detected with the Cac8I COBRA-DHPLC assay quantitatively

Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

Science.gov (United States)

Pandey, Manish K.; Roorkiwal, Manish; Singh, Vikas K.; Ramalingam, Abirami; Kudapa, Himabindu; Thudi, Mahendar; Chitikineni, Anu; Rathore, Abhishek; Varshney, Rajeev K.

2016-01-01

Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gains is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last 5 years. The availability of the draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale genomic resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seems appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries. PMID:27199998

Radioisotopes and fungicide research- present status and future prospects

International Nuclear Information System (INIS)

Chatrath, M.S.

1996-01-01

The developments in pesticides and radioisotopes fields were so near to each other that at a very early stage in this history, both became linked together and their usefulness was recognised for faster development. The purpose of this communication is to illustrate the present status these techniques in fungicide research by drawing suitable examples and also to bring out the directions in which future research will be going with the aid of these tools. 72 refs

Radiation sterilization of medical supplies: conceptions, regulations, present status and further developments

International Nuclear Information System (INIS)

Peteu, Gh.

1994-01-01

A general view on the present stage and tendencies in the development of radiation sterilization of biomedical supplies is presented. Specific concepts in correlation with some regulations of the World Health Organization and of the National Public Health Authorities concerning the present state, the possibilities and criteria of development in our country, are discussed. Finally the present status of the design and execution of the project of two mobile and multipurpose irradiators is presented. (Author)

Refractory status epilepticus and glutamic acid decarboxylase antibodies in adults: presentation, treatment and outcomes.

Science.gov (United States)

Khawaja, Ayaz M; Vines, Brannon L; Miller, David W; Szaflarski, Jerzy P; Amara, Amy W

2016-03-01

Glutamic acid decarboxylase antibodies (GAD-Abs) have been implicated in refractory epilepsy. The association with refractory status epilepticus in adults has been rarely described. We discuss our experience in managing three adult patients who presented with refractory status epilepticus associated with GAD-Abs. Case series with retrospective chart and literature review. Three patients without pre-existing epilepsy who presented to our institution with generalized seizures between 2013 and 2014 were identified. Seizures proved refractory to first and second-line therapies and persisted beyond 24 hours. Patient 1 was a 22-year-old female who had elevated serum GAD-Ab titres at 0.49 mmol/l (normal: status epilepticus. Causation cannot be established since GAD-Abs may be elevated secondary to concurrent autoimmune diseases or formed de novo in response to GAD antigen exposure by neuronal injury. Based on this report and available literature, there may be a role for immuno- and chemotherapy in the management of refractory status epilepticus associated with GAD-Abs.

Recent advances of genomic testing in perinatal medicine.

Science.gov (United States)

Peters, David G; Yatsenko, Svetlana A; Surti, Urvashi; Rajkovic, Aleksandar

2015-02-01

Rapid progress in genomic medicine in recent years has made it possible to diagnose subtle genetic abnormalities in a clinical setting on routine basis. This has allowed for detailed genotype-phenotype correlations and the identification of the genetic basis of many congenital anomalies. In addition to the availability of chromosomal microarray analysis, exome and whole-genome sequencing on pre- and postnatal samples of cell-free DNA has revolutionized the field of prenatal diagnosis. Incorporation of these technologies in perinatal pathology is bound to play a major role in coming years. In this communication, we briefly present the current experience with use of classical chromosome analysis, fluorescence in situ hybridization, and microarray testing, development of whole-genome analysis by next-generation sequencing technology, offer a detailed review of the history and current status of non-invasive prenatal testing using cell-free DNA, and discuss the advents of these new genomic technologies in perinatal medicine. Copyright © 2014 Elsevier Inc. All rights reserved.

Present status of libraries processed from JENDL-3.2

International Nuclear Information System (INIS)

Yamano, Naoki

1996-01-01

Data libraries processed from JENDL-3.2 were produced by JAERI for use of typical applications in the area of nuclear reactor and shielding. These libraries had the distinction of being free of restrictions on distribution. The other data libraries for decay, activation, dosimetry, nuclide transmutation, burn-up, PKA, KERMA and DPA calculations are now being accumulated. The current status on the development of these libraries has been described. A discussion is presented about how to disseminate and share the products of JNDC activities. (author)

Present status and issues for accelerator driven transmutation system

International Nuclear Information System (INIS)

Mizumoto, Motoharu

2003-01-01

Proper treatment of high-level nuclear wastes (HLW) that are produced in operation of nuclear power plants is one of the most important problems for further utilization of nuclear energy. The purpose of the accelerator driven nuclear waste transmutation system (ADS) is to transmute these nuclei to stable or short-lived nuclei by various radiation-induced nuclear reactions. When ADS for HLW can be realized, burden to deep geological disposal can be considerably reduced. In the paper, present status and issues for ADS will be discussed. (author)

Present status of nuclear education and training in Japan

International Nuclear Information System (INIS)

Kiyose, R.; Sumita, K.; Moriya, F.

1994-01-01

In Japan, where about 30% of electricity is supplied by nuclear actives require a good number of able and ambitious young scientists and engineers especially in the future. On the other hand, almost all Japanese electric power companies, which operate nuclear power plants, are striving to keep expertise of reactor operators as high as possible. Present status in Japan of education at universities, research and training reactors, training courses at governmental institutions and nonprofit organizations, and operator training centers of electric power companies, are reviewed. 3 tabs

Present status of storage ring free electron laser experiment at ETL

International Nuclear Information System (INIS)

Yamazaki, T.; Nakamura, T.; Tomimasu, T.; Sugiyama, S.; Noguchi, T.

1988-01-01

Outline is described of the present status of the ETL storage-ring free electron laser project. The structure and the performance of the ETL-type transverse optical klystron are given. A modification of the dispersive section has decreased the degradation of the shape of the spontaneous-emission spectrum due to energy spread of the electron beam. Relevant parameters of the stored beam are presented. Measurement of the optical-cavity loss is under way. (author)

Present status and legal countermeasures of electromagnetic radiation pollution in China

International Nuclear Information System (INIS)

Qiu Qiu

2007-01-01

With the wide utilization of electronic technology, electromagnetic radiation has rapidly been one of the most serious pollution sources, causing corresponding disputes of pollution on the rise and the contradictions sharp increasingly because of the limited supply and research of law. The article analyses the characters and present status of electromagnetic radiation pollution, points out the inadequacy supply of relevant law and its reasons and presents legal countermeasures, that is: complying with present laws, establishing national standard systems, strengthening local legislation. The paper also presents the basic idea and principle of making 'Prevention Electromagnetic Radiation Pollution'. (authors)

Present status of transport code development based on Monte Carlo method

International Nuclear Information System (INIS)

Nakagawa, Masayuki

1985-01-01

The present status of development in Monte Carlo code is briefly reviewed. The main items are the followings; Application fields, Methods used in Monte Carlo code (geometry spectification, nuclear data, estimator and variance reduction technique) and unfinished works, Typical Monte Carlo codes and Merits of continuous energy Monte Carlo code. (author)

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.

Genomic rearrangements of PTEN in prostate cancer

Directory of Open Access Journals (Sweden)

Sopheap ePhin

2013-09-01

Full Text Available The phosphatase and tensin homolog gene on chromosome 10q23.3 (PTEN is a negative regulator of the PIK3/Akt survival pathway and is the most frequently deleted tumor suppressor gene in prostate cancer. Monoallelic loss of PTEN is present in up to 60% of localized prostate cancers and complete loss of PTEN in prostate cancer is linked to metastasis and androgen independent progression. Studies on the genomic status of PTEN in prostate cancer initially used a two-color fluorescence in-situ hybridization (FISH assay for PTEN copy number detection in formalin fixed paraffin embedded tissue preparations. More recently, a four-color FISH assay containing two additional control probes flanking the PTEN locus with a lower false-positive rate was reported. Combined with the detection of other critical genomic biomarkers for prostate cancer such as ERG, AR, and MYC, the evaluation of PTEN genomic status has proven to be invaluable for patient stratification and management. Although less frequent than allelic deletions, point mutations in the gene and epigenetic silencing are also known to contribute to loss of PTEN function, and ultimately to prostate cancer initiation. Overall, it is clear that PTEN is a powerful biomarker for prostate cancer. Used as a companion diagnostic for emerging therapeutic drugs, FISH analysis of PTEN is promisingly moving human prostate cancer closer to more effective cancer management and therapies.

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

The present status of artificial rain making

International Nuclear Information System (INIS)

Choudhury, A.M.

1987-11-01

In this paper a review has been made of the present status of artificial rainmaking. The history of artificial rainmaking goes back to 1946 when Vincent Schaefer of the USA discovered the general principles. During the last 40 years cloud seeding activities have stirred the imagination of scientists all over the world. If this could be carried out in an operational manner, mankind could have solved the problems of drought which threaten many parts of the globe with famine. However, though a lot of progress has been made in cloud physics, an operational rainmaking programme is yet far from reality. In some cases seeding increases the rainfall whereas in other cases a decrease in rainfall has been noticed. It would be necessary to approach the subject more thoroughly and systematically and while making experiments on rainmaking a proper experimental design should be carried out so that the results of such experiments could be evaluated scientifically. (author). 11 refs

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.

Present status of the JT-60 control system

International Nuclear Information System (INIS)

Kimura, T.

1992-01-01

The present status of the control system for a large fusion device of the JT-60 upgrade tokamak is reported including its original design concept, the progress of the system in the past five-year operation and modification for the upgrade. The control system has the features of hierarchical structure, computer control, adoption of CAMAC interfaces and protective interlock by both software and hard-wired systems. Plant monitoring and control are performed by an efficient data communication via CAMAC highways. Sequential discharge control of is executed by a combination of computers and a timing system. A plasma feedback control system with fast 32-bit microprocessors and a man/machine interface with modern workstations have been newly developed for the operation of the JT-60 upgrade. (author)

Present status of development of uranium resources in foreign countries

International Nuclear Information System (INIS)

1983-10-01

The book with the same title as this was published in 1981. Thereafter, the necessity to correct the contents arose, such as the remarkable change in uranium market condition and the change of uranium resource policy in Australia accompanying the change of regime, accordingly, the revision was carried out by adding more new information. As the main sources of the information collected in this book, 25 materials are shown. The confirmed resources of uranium in the free world as of the beginning of 1981 amounted to 2,293,000 t U, and the estimated additional resources were 2,720,000 t U. The political system and uranium policy, the present status of uranium export, the quantity of resources and the estimated amount of deposits, the uranium production and the status of uranium exploration and development of 25 foreign countries are reported. Japan has carried out uranium development activities in Australia, Canada, Niger, Gabon, Zambia and so on. (Kako, I.)

Overview of the present status and challenges of neutrino oscillation physics

Energy Technology Data Exchange (ETDEWEB)

Mocioiu, Irina [Pennsylvania State University, 104 Davey Lab, University Park, PA 16802 (United States)

2012-11-20

This is an overview of the current status of neutrino oscillation physics, including atmospheric, solar, reactor and accelerator neutrino experiments. After summarizing our present understanding of all data, I discuss the open questions and how they might be addressed in the future. I also discuss how neutrinos can be used to learn about new physics and astrophysics.

Present status on atomic and molecular data relevant to fusion plasma diagnostics and modeling

International Nuclear Information System (INIS)

Tawara, H.

1997-01-01

This issue is the collection of the paper presented status on atomic and molecular data relevant to fusion plasma diagnostics and modeling. The 10 of the presented papers are indexed individually. (J.P.N.)

The past, present, and future of Leishmania genomics and transcriptomics

Science.gov (United States)

Cantacessi, Cinzia; Dantas-Torres, Filipe; Nolan, Matthew J.; Otranto, Domenico

2015-01-01

It has been nearly 10 years since the completion of the first entire genome sequence of a Leishmania parasite. Genomic and transcriptomic analyses have advanced our understanding of the biology of Leishmania, and shed new light on the complex interactions occurring within the parasite–host–vector triangle. Here, we review these advances and examine potential avenues for translation of these discoveries into treatment and control programs. In addition, we argue for a strong need to explore how disease in dogs relates to that in humans, and how an improved understanding in line with the ‘One Health’ concept may open new avenues for the control of these devastating diseases. PMID:25638444

CMS: Present status, limitations, and upgrade plans

International Nuclear Information System (INIS)

Cheung, H.W.K.

2011-01-01

An overview of the CMS upgrade plans will be presented. A brief status of the CMS detector will be given, covering some of the issues we have so far experienced. This will be followed by an overview of the various CMS upgrades planned, covering the main motivations for them, and the various R and D efforts for the possibilities under study. The CMS detector has been working extremely well since the start of data-taking at the LHC as is evidenced by the numerous excellent results published by CMS and presented at this workshop and recent conferences. Less well documented are the various issues that have been encountered with the detector. In the spirit of this workshop I will cover some of these issues with particular emphasis on problems that motivate some of the upgrades to the CMS detector for this decade of data-taking. Though the CMS detector has been working extremely well and expectations are great for making the most of the LHC luminosity, there have been a number of issues encountered so far. Some of these have been described and while none currently presents a problem for physics performance, some of them are expected to become more problematic, especially at the highest Phase 1 luminosities for which the majority of the integrated luminosity will be collected. These motivate upgrades for various parts of the CMS detector so that the current excellent physics performance can be maintained or even surpassed in the realm of the highest Phase 1 luminosities.

Clinical Characteristics and Outcome of Patients with Neuroblastoma Presenting Genomic Amplification of Loci Other than MYCN

Science.gov (United States)

Guimier, Anne; Ferrand, Sandrine; Pierron, Gaëlle; Couturier, Jérôme; Janoueix-Lerosey, Isabelle; Combaret, Valérie; Mosseri, Véronique; Thebaud, Estelle; Gambart, Marion; Plantaz, Dominique; Marabelle, Aurélien; Coze, Carole; Rialland, Xavier; Fasola, Sylvie; Lapouble, Eve; Fréneaux, Paul; Peuchmaur, Michel; Michon, Jean; Delattre, Olivier; Schleiermacher, Gudrun

2014-01-01

Background Somatically acquired genomic alterations with MYCN amplification (MNA) are key features of neuroblastoma (NB), the most common extra-cranial malignant tumour of childhood. Little is known about the frequency, clinical characteristics and outcome of NBs harbouring genomic amplification(s) distinct from MYCN. Methods Genomic profiles of 1100 NBs from French centres studied by array-CGH were re-examined specifically to identify regional amplifications. Patients were included if amplifications distinct from the MYCN locus were seen. A subset of NBs treated at Institut Curie and harbouring MNA as determined by array-CGH without other amplification was also studied. Clinical and histology data were retrospectively collected. Results In total, 56 patients were included and categorised into 3 groups. Group 1 (n = 8) presented regional amplification(s) without MNA. Locus 12q13-14 was a recurrent amplified region (4/8 cases). This group was heterogeneous in terms of INSS stages, primary localisations and histology, with atypical clinical features. Group 2 (n = 26) had MNA as well as other regional amplifications. These patients shared clinical features of those of a group of NBs MYCN amplified (Group 3, n = 22). Overall survival for group 1 was better than that of groups 2 and 3 (5 year OS: 87.5%±11% vs 34.9%±7%, log-rank p<0.05). Conclusion NBs harbouring regional amplification(s) without MNA are rare and seem to show atypical features in clinical presentation and genomic profile. Further high resolution genetic explorations are justified in this heterogeneous group, especially when considering these alterations as predictive markers for targeted therapy. PMID:25013904

Clinical characteristics and outcome of patients with neuroblastoma presenting genomic amplification of loci other than MYCN.

Directory of Open Access Journals (Sweden)

Anne Guimier

Full Text Available Somatically acquired genomic alterations with MYCN amplification (MNA are key features of neuroblastoma (NB, the most common extra-cranial malignant tumour of childhood. Little is known about the frequency, clinical characteristics and outcome of NBs harbouring genomic amplification(s distinct from MYCN.Genomic profiles of 1100 NBs from French centres studied by array-CGH were re-examined specifically to identify regional amplifications. Patients were included if amplifications distinct from the MYCN locus were seen. A subset of NBs treated at Institut Curie and harbouring MNA as determined by array-CGH without other amplification was also studied. Clinical and histology data were retrospectively collected.In total, 56 patients were included and categorised into 3 groups. Group 1 (n = 8 presented regional amplification(s without MNA. Locus 12q13-14 was a recurrent amplified region (4/8 cases. This group was heterogeneous in terms of INSS stages, primary localisations and histology, with atypical clinical features. Group 2 (n = 26 had MNA as well as other regional amplifications. These patients shared clinical features of those of a group of NBs MYCN amplified (Group 3, n = 22. Overall survival for group 1 was better than that of groups 2 and 3 (5 year OS: 87.5%±11% vs 34.9%±7%, log-rank p<0.05.NBs harbouring regional amplification(s without MNA are rare and seem to show atypical features in clinical presentation and genomic profile. Further high resolution genetic explorations are justified in this heterogeneous group, especially when considering these alterations as predictive markers for targeted therapy.

The present status of the Telescope Array experiment

Energy Technology Data Exchange (ETDEWEB)

Nonaka, T. [Institute for Cosmic Ray Research University of Tokyo, 5-1-5 Kashiwanoha Kashiwa Chiba (Japan); Abu-Zayyad, T.; Allen, M. [University of Utah - High Energy Astrophysics Institute, 115 S 1400 E 201, Salt Lake City, UT 84112-0830 (United States); Azuma, R. [Tokyo Institute of Technology, 2-12-1 Ohokayama Meguro-ku, Tokyo 152-8550 (Japan); Belz, J.W. [University of Utah - High Energy Astrophysics Institute, 115 S 1400 E 201, Salt Lake City, UT 84112-0830 (United States); Bergman, D.R. [Rutgers University, 136 Frelinghuysen Road, Piscataway, NJ 08854 (United States); Blake, S.A.; Brusova, O.; Cady, R.; Cao, Z. [University of Utah - High Energy Astrophysics Institute, 115 S 1400 E 201, Salt Lake City, UT 84112-0830 (United States); Chiba, J. [Tokyo University of Science, 2641 Yamazaki Noda-shi, Chiba 278-8510 (Japan); Chikawa, M. [Kinki University, 3-4-1 Kowakae, Higashiosaka-shi, Osaka 577-8582 (Japan); Cho, I.S. [Yonsei University, 134 Sinchon-dong, Seodaemun-gu, Seoul (Korea, Republic of); Fujii, H. [KEK - Institute of Particle And Nuclear Studies, 1-1 Oho Tsukuba-shi, Ibaraki 305-0801 (Japan); Fujii, T. [Osaka City University, 3-3-138 Sugimoto-cho, Sumiyoshi-ku, Osaka 558-8585 (Japan); Fukuda, T. [Tokyo Institute of Technology, 2-12-1 Ohokayama Meguro-ku, Tokyo 152-8550 (Japan); Fukushima, M. [Institute for Cosmic Ray Research University of Tokyo, 5-1-5 Kashiwanoha Kashiwa Chiba (Japan); Hayashi, K. [Tokyo Institute of Technology, 2-12-1 Ohokayama Meguro-ku, Tokyo 152-8550 (Japan); Hayashida, N. [Institute for Cosmic Ray Research University of Tokyo, 5-1-5 Kashiwanoha Kashiwa Chiba (Japan); Hibino, K. [Kanagawa University, 3-27-1 Rokkakubashi Kanagawa-ku, Yokohama-shi, Kanagawa 221-8686 (Japan)

2009-05-15

The Telescope Array(TA) experiment located at western desert in Utah USA (N39.3,W112.9) is designed for observation of air shower from extreme high energy cosmic rays. The TA detector consists of 2 types of detector to enable a cross check on systematic difference from the two main methods of observation for the energy region. One is a Fluorescence detector (FD) for detecting fluorescence light from air shower and another is surface detector (SD) array for detecting air shower particles at ground level. Each SD consists of 2 layers of plastic scintillator with 3m{sup 2} of surface and more sensitive to electromagnetic component in air shower. The full operation using 3FD stations and full SD array has started. Here we present the updated status of Telescope Array experiment.

Clinical presentation and visual status of retinitis pigmentosa patients: a multicenter study in southwestern Nigeria.

Science.gov (United States)

Onakpoya, Oluwatoyin Helen; Adeoti, Caroline Olufunlayo; Oluleye, Tunji Sunday; Ajayi, Iyiade Adeseye; Majengbasan, Timothy; Olorundare, Olayemi Kolawole

2016-01-01

To review the visual status and clinical presentation of patients with retinitis pigmentosa (RP). Multicenter, retrospective, and analytical review was conducted of the visual status and clinical characteristics of patients with RP at first presentation from January 2007 to December 2011. Main outcome measure was the World Health Organization's visual status classification in relation to sex and age at presentation. Data analysis by SPSS (version 15) and statistical significance was assumed at Ppresent in their siblings 15 (71.4%), grandparents 11 (52.3%), and parents 4 (19.4%). Forty (41.7%) were blind at presentation and 23 (24%) were visually impaired. Blindness in six (15%) patients was secondary to glaucoma. Retinal vascular narrowing and retinal pigmentary changes of varying severity were present in all patients. Thirty-five (36.5%) had maculopathy, 36 (37.5%) refractive error, 19 (20%) lenticular opacities, and eleven (11.5%) had glaucoma. RP was typical in 85 patients (88.5%). Older patients had higher rates of blindness at presentation (P=0.005); blindness and visual impairment rate at presentation were higher in males than females (P=0.029). Clinical presentation with advanced diseases, higher blindness rate in older patients, sex-related difference in blindness/visual impairment rates, as well as high glaucoma blindness in RP patients requires urgent attention in southwestern Nigeria.

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms.

Directory of Open Access Journals (Sweden)

Kevin Anthony Meyer

Full Text Available Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M. wesenbergii LE013-01 and one from upstream Lake St. Clair (M. cf aeruginosa LSC13-02, and compared these data to the genomes of seventeen Microcystis spp. from across the globe as well as one metagenome and seven metatranscriptomes from a 2014 Lake Erie Microcystis bloom. For the publically available strains analyzed, the core genome is ~1900 genes, representing ~11% of total genes in the pan-genome and ~45% of each strain's genome. The flexible genome content was related to Microcystis subclades defined by phylogenetic analysis of both housekeeping genes and total core genes. To our knowledge this is the first evidence that the flexible genome is linked to the core genome of the Microcystis species complex. The majority of strain-specific genes were present and expressed in bloom communities in Lake Erie. Roughly 8% of these genes from the lower Great Lakes are involved in genome plasticity (rapid gain, loss, or rearrangement of genes and resistance to foreign genetic elements (such as CRISPR-Cas systems. Intriguingly, strain-specific genes from Microcystis cultured from around the world were also present and expressed in the Lake Erie blooms, suggesting that the Microcystis pangenome is truly global. The presence and expression of flexible genes, including strain-specific genes, suggests that strain-level genomic diversity may be important in maintaining Microcystis abundance during bloom events.

Beamlines on Indus-1 and Indus-2: present status

International Nuclear Information System (INIS)

Lodha, G.S.; Deb, S.K.

2010-01-01

Indus-1 (450 MeV) is an efficient synchrotron radiation (SR) source in the soft X-ray/vacuum ultra violet region of the electromagnetic spectrum. For Indus-1 the higher order energy contamination in soft X-ray region, heat load and radiation safety problems are also significantly low. At present five beamlines are operational. This SR source is a national science facility being used by various research group across the country. Strong efforts are underway to increase the user base of Indus-1. The talk presents some of the recent studies carried out using Indus-1. Indus-2 (2.5 GeV) synchrotron source is one of the most important accelerator based science facilities being setup in India. A few beamlines have been commissioned and are being used by researchers from different institutes. This talk gives present status of the various beamlines and experimental stations on Indus-2. It is envisaged that the atomic and molecular science community can actively participate in planning experiments on Indus-1 and Indus-2 and setup experimental stations on Indus-2. (author)

The Present Status of Nuclear Medicine in Korea

International Nuclear Information System (INIS)

Lee, Mun Ho

1968-01-01

It is my privilege to give you a brief history on the status of nuclear medicine in Korea. There is nothing much to mention, as the history of the peaceful use of atomic energy is rather short and the RI facilities are limited in the number. It is my sincere hope, however, that you may understand what steps nuclear medicine in the developing countries did take and how it has been developed, seeing the present status of nuclear medicine in Korea, as one of the models. In our country, the peaceful use of atomic energy was actualized since the Law of Atomic Energy had been enacted in March 1959, and the Office of Atomic Energy and the Atomic Energy Research Institute had been established. The Korea Society of Nuclear Medicine was organized in 1961, which i think is one of the older in the Far East area. The Society now held about 170 members and the annual meetings in addition to the quarterly meeting have been held. The 6th general scientific meeting for 1967 is scheduled to be held in 25 November. The society publishes the Korean Journal of Nuclear Medicine twice a year, and the second issue appeared Oct. 1967. The instruments used in nuclear medicine are mostly expensive, therefore, the hospitals equipped with such instruments are inevitably limited in number and the after-service or repair of such instruments are technically not easy. Some of these difficulties, i hope, shall be overcome in the near future.

Present status of laser technology for maintenance and repair

International Nuclear Information System (INIS)

Sano, Yuji

2001-01-01

A laser has superior spatial and timely controllability and has no repulsive force at its use, it is a tool suitable for remote operation. And, as a partial processing with low exotherm and deformation by its use becomes possible, it can have an advantage omissible for post processes such as heat treatment and so on. Therefore, on in-situ repair of present constructions, laser is thought to be an optimum tool. And, in nuclear energy plants, maintenance and management of their instruments are important, and then a number of technical developments activating its advantages have been carried out. Above all, repair engineering around a reactor has a number of places difficult to access them for its operators, so remote engineering using laser is desired for in special. Here was described on the present status of development and realization containing protect conservation and inspection repair technology using laser. (G.K.)

Present Status of Odour Management in Malaysia

International Nuclear Information System (INIS)

Mohd Nahar Othman

2014-01-01

The nuisance odour complaints received by the Department of Environment of Malaysia in 2006 are about 1082 cases. The trend shows that odor problems have become more and more acute every year. The sources of odor complaints come from many types of industries such as animal raring industry, chemical industries, rubber processing industries, municipal solid wastes (MSW), sewage treatment plants, palm oil industries, petroleum industries and etc. There are no specific odour control technology to solve the odour problem in the country. Some of the odour problems became more acute because the sources odour are located in places which are in the living area because lack of space. At the same time, there is no regulation concerning the specific odor parameter stated in the Environment Quality Acts 1974. The Department of Environment had drafted a regulation in order to monitor this problem, relating to the nuisance coming from these industries but until now the regulation still pending. The aim of this paper is to describe the present status of odour problem in Malaysia and the public exception of this problem. (author)

Present status of space nuclear reactor

International Nuclear Information System (INIS)

Kaneko, Yoshihiko

1996-01-01

USA and former USSR led space development, and had the experience of launching nuclear reactor satellites. In USA, the research and development of space nuclear reactor were advanced mainly by NASA, and in 1965, the nuclear reactor for power source ''SNAP-10A'' was launched and put on the orbit around the earth. Thereafter, the reactor was started up, and the verifying test at 500 We was successfully carried out. Also for developing the reactor for thermal propulsion, NERVA/ROVER project was done till 1973, and the technological basis was established. The space Exploration Initiative for sending mankind to other solar system planets than the earth is the essential point of the future projects. In former USSR, the ground experiment of the reactor for 800 We power source ''Romashka'', the development of the reactor for 10 kWe power source ''Topaz-1 and 2'', the flight of the artificial satellites, Cosmos 954 and Cosmos 1900, on which nuclear reactors were mounted, and the operation of 33 ocean-monitoring satellites ''RORSAT'' using small fast reactors were carried out. The mission of space development and the nuclear reactors as power source, the engineering of space nuclear reactors, the present status and the trend of space nuclear reactor development, and the investigation by the UN working group on the safety problem of space nuclear reactors are described. (K.I.)

Present status of FLNR (JINR) ECR ion sources

International Nuclear Information System (INIS)

Bogomolov, S.; Efremov, A.; Loginov, V.; Lebedev, A.; Yazvitsy, N.; Bekhterev, V.; Kostukhov, Y.; Gulbekian, G.; Gikal, B.; Drobin, V.; Seleznev, V.; Seleznev, V.

2012-01-01

Six ECR ion sources have been operated in the Flerov Laboratory of Nuclear Reactions (JINR). Two 14 GHz ECR ion sources (ECR4M and DECRIS-2) supply various ion species for the U400 and U400M cyclotrons correspondingly for experiments on the synthesis of heavy and exotic nuclei using ion beams of stable and radioactive isotopes. The 18 GHz DECRIS-SC ion source with superconducting magnet system produces ions from Ar up to W for solid state physics experiments and polymer membrane fabrication at the IC-100 cyclotron. The third 14 GHz ion source DECRIS-4 with 'flat' minimum of the axial magnetic field is used as a stand alone machine for test experiments and also for experiments on ion modification of materials. The other two compact ECR ion sources with all permanent magnet configuration have been developed for the production of single charged ions and are used at the DRIBs installation and at the MASHA mass-spectrometer. In this paper, present status of the ion sources, recent developments and plans for modernization are reported. The paper is followed by the slides of the presentation. (authors)

Genome analysis methods - PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods Genome analysis... methods Data detail Data name Genome analysis methods DOI 10.18908/lsdba.nbdc01194-01-005 De...scription of data contents The current status and related information of the genomic analysis about each org...anism (March, 2014). In the case of organisms carried out genomic analysis, the d...e File name: pgdbj_dna_marker_linkage_map_genome_analysis_methods_en.zip File URL: ftp://ftp.biosciencedbc.j

Analysis of The Cancer Genome Atlas sequencing data reveals novel properties of the human papillomavirus 16 genome in head and neck squamous cell carcinoma.

Science.gov (United States)

Nulton, Tara J; Olex, Amy L; Dozmorov, Mikhail; Morgan, Iain M; Windle, Brad

2017-03-14

Human papillomavirus (HPV) DNA is detected in up to 80% of oropharyngeal carcinomas (OPC) and this HPV positive disease has reached epidemic proportions. To increase our understanding of the disease, we investigated the status of the HPV16 genome in HPV-positive head and neck cancers (HNC). Raw RNA-Seq and Whole Genome Sequence data from The Cancer Genome Atlas HNC samples were analyzed to gain a full understanding of the HPV genome status for these tumors. Several remarkable and novel observations were made following this analysis. Firstly, there are three main HPV genome states in these tumors that are split relatively evenly: An episomal only state, an integrated state, and a state in which the viral genome exists as a hybrid episome with human DNA. Secondly, none of the tumors expressed high levels of E6; E6*I is the dominant variant expressed in all tumors. The most striking conclusion from this study is that around three quarters of HPV16 positive HNC contain episomal versions of the viral genome that are likely replicating in an E1-E2 dependent manner. The clinical and therapeutic implications of these observations are discussed.

Present status of the EPFL (Swiss) fusion-fission experiment 'LOTUS'

International Nuclear Information System (INIS)

Haldy, P.A.; Frueh, R.; Ligou, J.; Schneeberger, J.P.; Kumar, A.

1984-01-01

The present status of the LOTUS project - a fusion-fission hybrid research facility under construction at the Ecole Polytechnique Federale de Lausanne (EPFL) Switzerland - is presented. Emphasis is places on the description of the facility and on the design studies of an initial blanket of the ''fission-suppressed'' type. The LOTUS facility consists of a parallelepiped-shaped blanket, occupying roughly a volume of 1 m 3 , driven by a sealed 14 MeV (D,T) neutron generator with a rated source strength of 5x10 12 n/s. The experiment is housed in a massive concrete shielding of 220 cm thick walls, which leaves an experimental test chamber of 360 cm by 240 cm lateral dimensions and a height of 300 cm. (orig.) [de

Marital status and outcome of patients presenting with acute coronary syndrome: an observational report.

Science.gov (United States)

Hadi Khafaji, Hadi A R; Al Habib, Khalid; Asaad, Nidal; Singh, Rajvir; Hersi, Ahmad; Al Falaeh, Husam; Al Saif, Shukri; Al-Motarreb, Ahmed; Almahmeed, Wael; Sulaiman, Kadhim; Amin, Haitham; Al-Lawati, Jawad; Al-Sagheer, Norah Q; Alsheikh-Ali, Alawi A; Al Suwaidi, Jassim

2012-12-01

BACKGROUND & HYPOTHESIS: Data on the clinical characteristics and outcome of patients presenting with acute coronary syndrome (ACS) according to their marital status is not clear. A total of 5334 patients presenting with ACS in 65 hospitals in 6 Middle East countries in the 2nd Gulf Registry of Acute Coronary Events (Gulf RACE-2) were studied according to their marital status (5024 married, 100 single, and 210 widowed patients). When compared to married patients, widowed patients were older and more likely to be female. Widowed patients were more likely to have diabetes mellitus, hypertension, history of heart failure, and peripheral vascular disease and were less likely to be tobacco users when compared to the other groups. Widowed patients were also more likely to present with atypical symptoms and have advanced Killip class. Widowed patients were more likely to present with non-ST-elevation myocardial infarction (NSTEMI) when compared to the other 2 groups. Widowed patients were more likely to have heart failure (P = 0.001), cardiogenic shock (P = 0.001), and major bleeding (P = 0.002) when compared to the other groups. No statistically significant difference was observed in regard to duration of hospital stay, door to needle time in STEMI patients, or cardiac arrhythmias between the various groups. Widowed patients had higher in-hospital, 30-day, and 1-year mortality rates (P = 0.001). Marital status was an independent predictor for in-hospital mortality. Widowed marital status was associated with worse cardiovascular risk profile, and worse in-hospital and 1-year outcome. Future work should be focused on whether the provision of psychosocial support will result in improved outcomes among this high-risk group. © 2012 Wiley Periodicals, Inc.

Present status and problems of remote systems technology in nuclear industry

Energy Technology Data Exchange (ETDEWEB)

1989-02-01

This reports the activities of Special Committee on Remote Systems Technology, Atomic Energy Society of Japan, during the period from Oct. 1984 to Sep. 1988. The Committee studied and reviewed the present status and problems of remote operation and maintenance in various fields of nuclear industry. Reported items are; reactor operation, reprocessing, nuclear fusion and decommissioning. It also reviews robotics and remote systems tehcnology applied to space and marine development.

Present status and problems of remote systems technology in nuclear industry

International Nuclear Information System (INIS)

1989-01-01

This reports the activities of Special Committee on Remote Systems Technology, Atomic Energy Society of Japan, during the period from Oct. 1984 to Sep. 1988. The Committee studied and reviewed the present status and problems of remote operation and maintenance in various fields of nuclear industry. Reported items are; reactor operation, reprocessing, nuclear fusion and decommissioning. It also reviews robotics and remote systems tehcnology applied to space and marine development. (author)

Workshop summary of 'nuclear knowledge management: Present status and perspective'

International Nuclear Information System (INIS)

Yonezawa, Minoru

2007-03-01

The workshop on 'Nuclear Knowledge Management (NKM): Present Status and Perspective' was held at the Tokyo Institute of Technology (supported by the Japan Atomic Energy Agency), Tokyo, Japan on the 14th and 15th of December 2006. The purpose of the workshop is to introduce NKM activities inside and outside Japan so that concerned parties/professionals could share related information and enhance awareness of the issues on NKM. Participants from various sectors, such as authorities, industry, universities/research institutes, etc, made presentations. Issues on NKM are recognized and discussed. The workshop consisted of 18 oral lectures and a panel discussion. The 55 participants attended the workshop. Under permission of the Tokyo Institute of Technology which is the sponsor of the workshop, this report compiles these lecture's presentation materials which got permission of a lecturer and synopses which were submitted after the workshop. (author)

Present status and plans of JENDL FP data evaluation project

International Nuclear Information System (INIS)

Kawano, Toshihiko

2003-01-01

The Fission Product (FP) data evaluation is one of the key issues for the next revision of JENDL, since many data were carried over from JENDL-3.2 to 3.3. The new FP Working Group (FPWG) was organized in the Japanese Nuclear Data Committee (JNDC) to perform new evaluations of FP data for JENDL. In the present review of FP data evaluation, we show the history and current status of FP nuclear data, requirements of FP data, new measurements, the international cooperation, and the future plans toward the new JENDL. (author)

Overview of mycotoxin methods, present status and future needs.

Science.gov (United States)

Gilbert, J

1999-01-01

This article reviews current requirements for the analysis for mycotoxins in foods and identifies legislative as well as other factors that are driving development and validation of new methods. New regulatory limits for mycotoxins and analytical quality assurance requirements for laboratories to only use validated methods are seen as major factors driving developments. Three major classes of methods are identified which serve different purposes and can be categorized as screening, official and research. In each case the present status and future needs are assessed. In addition to an overview of trends in analytical methods, some other areas of analytical quality assurance such as participation in proficiency testing and reference materials are identified.

Historical review, present status and perspectives of nuclear sciences education at the Sofia University

International Nuclear Information System (INIS)

Djingova, R.; Kuleff, I.; Todorovsky, D.; Kovacheva, P.; Tsankov, L.; Staevski, K.; Tsenov, R.

2004-01-01

A brief review of the history of the education in nuclear sciences at the Faculty of Physics and Faculty of Chemistry of the Sofia University is made in the report. The present status of Bachelor, Master and PhD programmes in both Faculties is presented. (authors)

Present Status of Inclusive Rare $B$ Decays

CERN Document Server

Hurth, Tobias

2003-01-01

We give a status report on inclusive rare B decays, highlighting recent developments and open problems. We focus on the decay modes $B \\to X_{s,d} \\gamma$, $ B \\to X_s \\ell^+\\ell^-$ and $B \\to X_s \

Present status and prospect of the experimental study of QED in high Z ions

International Nuclear Information System (INIS)

Briand, J.P.

1993-01-01

I summarize in this paper the present status of our experimental knowledge on the Lamb shift of high Z hydrogenlike ions. Some tentative prospect on the future improvements with the new large accelerators and ion sources are discussed and compared with the present accuracy of QED corrections. (orig.)

a potential source of spurious associations in genome-wide ...

Indian Academy of Sciences (India)

2010-04-01

Apr 1, 2010 ... Genome-wide association studies (GWAS) examine the entire human genome with the goal of identifying genetic variants. (usually single nucleotide polymorphisms (SNPs)) that are associated with phenotypic traits such as disease status and drug response. The discordance of significantly associated ...

Present status of the NIRS-ECR ion source for the HIMAC

International Nuclear Information System (INIS)

Kitagawa, A.; Matsushita, H.; Shibuya, S.

1995-01-01

The present status of NIRS-ECR ion source for the Heavy Ion Medical Accelerator in Chiba (HIMAC) at National Institute of Radiological Sciences (NIRS) is reported. The beam intensity of the NIRS-ECR was increased by modifications on the magnetic field structure, chamber cooling system, vacuum conductance and the extraction configuration. The output current of Ar 6+ reached 365 eμA after improvements. The good stability, easy operation, and good reproducibility were realized. (author)

Present status and problems of marine reactor

International Nuclear Information System (INIS)

1987-01-01

The activities of the Research Committee on Marine Reactors are summarized, and the present status of marine reactors on the world is reviewed. The characteristics of marine reactors are discussed, and the prospect and problems of the research and development of an advanced marine reactor in Japan are reported. This Committee was established in fiscal year 1983, when the 'Mutsu' project was going to be on the right track, and the project of developing an advanced marine reactor was advanced. During four years since then, it has carried out the investigation and exchanged opinion about the activities and results of the research in foreign countries and Japan and the problems peculiar to marine reactors, that is, making small size and light weight reactors, the rolling and pitching, vibration and impact of ship hulls, the competitive power against conventional ships and so on. The idea of utilizing atomic energy for ship propulsion preceded that of electricity generation, and it was materialized in 1955 by the submarine 'Nautilus'. Now more than 300 nuclear war ships have been commissioned. Also nuclear merchant ships have been built, but the research and development were interrupted because of their economical efficiency. (Kako, I.)

Present status of fusion reactor materials, 4

International Nuclear Information System (INIS)

Nagasaki, Ryukichi; Shiraishi, Kensuke; Watanabe, Hitoshi; Murakami, Yoshio; Takamura, Saburo

1982-01-01

Recently, the design of fusion reactors such as Intor has been carried out, and various properties that fusion reactor materials should have been clarified. In the Japan Atomic Energy Research Institute, the research and development of materials aiming at a tokamak type experimental fusion reactor are in progress. In this paper, the problems, the present status of research and development and the future plan about the surface materials and structural materials for the first wall, blanket materials and magnet materials are explained. The construction of the critical plasma testing facility JT-60 developed by JAERI has progressed smoothly, and the operation is expected in 1985. The research changes from that of plasma physics to that of reactor technology. In tokamak type fusion reactors, high temperature D-T plasma is contained with strong magnetic field in vacuum vessels, and the neutrons produced by nuclear reaction, charged particles diffusing from plasma and neutral particles by charge exchange strike the first wall. The PCA by improving 316 stainless steel is used as the structural material, and TiC coating techniques are developed. As the blanket material, Li 2 O is studied, and superconducting magnets are developed. (Koko, I.)

Genomics and Evolution in Traditional Medicinal Plants: Road to a Healthier Life.

Science.gov (United States)

Hao, Da-Cheng; Xiao, Pei-Gen

2015-01-01

Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide. This review presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with the evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of the plant genotype and metabolic phenotype, interaction between medicinal plant genomes and their environment, the correlation between genomic diversity and metabolite diversity, and so on. Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.

CMS Tracker Upgrades: R\\&D Plans, Present Status and Perspectives

CERN Document Server

AUTHOR|(CDS)2091649

2015-01-01

The present CMS pixel detector designed for a luminosity of $10^{34}\\,\\mathrm{cm}^{-2}\\mathrm{s}^{-1}$ will have to be replaced at the end of 2016. The new upgraded detector will have higher tracking efficiency and lower mass with four barrel layers and three forward/backward disks to provide a hit coverage up to absolute pseudorapidities of $\\mid\\eta\\mid<2.5$. In a second stage, in order to maintain its physics reach during the high luminosity phase of the LHC (HL-LHC), when the machine is expected to deliver an instantaneous luminosity of $5\\times 10^{34}\\,\\mathrm{cm}^{-2} \\mathrm{s}^{-1}$ for a total of $3000\\,\\mathrm{fb}^{-1}$, CMS will build a new tracker, comprising a completely new pixel detector and outer tracker. The ongoing R\\&D activities on both pixel and strip sensors are presented. The present status of the Inner and Outer Tracker projects are illustrated, and the possible perspectives are discussed.

The past, present and future of mitochondrial genomics: have we sequenced enough mtDNAs?

Science.gov (United States)

Smith, David Roy

2016-01-01

The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank-an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission. © The Author 2015. Published by Oxford University Press.

Present status of radiation utilization in Thailand

International Nuclear Information System (INIS)

Chongkum, S.

1994-01-01

Present development of radiation utilization in Thailand covers two main areas, i.e. (1) production and utilization of radioisotopes and (2) radiation processing and technology. Radioisotope production from 2 megawatts Thai Research Reactor (TRR1/M1) is being studied, directed toward expanding the varieties of radioisotopes, improvement of quality, and technological development on quantity producing to meet the total national needs. However a large amount of radioisotopes is also imported mainly for industrial and medical applications. Radioisotopes and radiations are utilized in nuclear medicine for diagnosis and therapy from 30 hospitals and institutions. X-ray photographing, X-ray computer tomography and others are typical use for medical examination purposes, while Co-60 gamma rays and electron beam are in used for curing. Since 1972, Thailand has been participated to the IAEA/RCA Industrial Project, through the liaison of the Office of Atomic Energy for Peace (OAEP), and increases the awareness of industry to the economic benefits through the uses of nuclear technology. More than 60 companies are using radioisotopes for gauging, examination purposes and production controls, while these radioisotopes are mostly imported. Nuclear techniques in agriculture are addressed concerns with optimizing fertilizer application, determination soil-water-nitrogen fixation relationships, improving animal health and reproduction, measurement of toxic residues, appropriated food preservation techniques and breeding plant for better yield and disease resistance. The eradication of fruit flies by Sterile Insect Technique (SIT) with gamma rays has been successfully applied in northern and middle part of Thailand. The progress and present status of radiation utilization and processing in Thailand will be introduced. (author)

The present status of the blowdown code BRUCH

International Nuclear Information System (INIS)

Karwat, H.

1975-01-01

The present status and the important features of the blowdown code for a PWR, BRUCH-D version 04 which is presently in use, are described. The code is to investigate the depressurization process, fluid dynamic situation in the core, the fuel temperature and the core mass flow as influenced by important primary system components such as steam generators, pumps etc. The code is a multinode point model with a fixed node arrangement. It makes use of the basic fluid dynamic equations describing the mass, energy and volume conservation as well as the momentum equation and the equation of state with appropriate assumptions. The core heat generation and heat transfer to the fluid is simulated by a given number of average fuel rods with up to 20 axial segmentation independent of the axial subdivision of the core fluid region. In parallel up to 5 types of the fuel rods can be studied. The pump behaviour is specified by input. For the break flow, the code provides three models; Bernoulli, homogenous and moody. The implicit-explicit method IMEX is used for the integration of the differential equations. An example for application of BRUCH-S to an experiment which is for a BWR but has some basis of BRUCH-D is also shown in the paper

The CAREM project: Present status and development activities

International Nuclear Information System (INIS)

Boado Magan, H.J.; Ordonez, J.P.; Hey, A.

1997-01-01

The CAREM Project is a low power NPP of 25 Mwe, with an integrated self pressurized primary system. The cooling of the primary system is of the natural circulation type and several passive safety systems are included. The owner of the Project is Argentina's CNEA (Comision Nacional de Energia Atomica) and its associated company, INVAP, is the main contractor. The present status of the CAREM Project is presented. The possible evolution of the CAREM project is mentioned in relation with a new containment design. A short description of the Experimental Facilities, listed below, already in operation and under construction are also included: CAPCN High Pressure Loop. Natural convection loop to verify dynamic response and critical heat flux; RA-8. Critical Facility, designed and constructed for the CAREM Project (that may be used as a general uses facility); RPV lnternals. The whole assembly of absorbent rods, connecting rods and the rode guides are being constructed in a 1:1 scale. The aims of this experimental facility are vibration analysis and manufacturing parameters definitions. Control Drive Mechanisms. A series of verification and tests are being carried out on these within RPV Hydraulically driven mechanisms. Other development activities are mentioned in relation with the thermalhydraulics, Steam Generators and Control. (author)

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

Directory of Open Access Journals (Sweden)

Mark F Richardson

Full Text Available Wolbachia are maternally inherited symbiotic bacteria, commonly found in arthropods, which are able to manipulate the reproduction of their host in order to maximise their transmission. The evolutionary history of endosymbionts like Wolbachia can be revealed by integrating information on infection status in natural populations with patterns of sequence variation in Wolbachia and host mitochondrial genomes. Here we use whole-genome resequencing data from 290 lines of Drosophila melanogaster from North America, Europe, and Africa to predict Wolbachia infection status, estimate relative cytoplasmic genome copy number, and reconstruct Wolbachia and mitochondrial genome sequences. Overall, 63% of Drosophila strains were predicted to be infected with Wolbachia by our in silico analysis pipeline, which shows 99% concordance with infection status determined by diagnostic PCR. Complete Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with strict vertical transmission through the maternal cytoplasm and imperfect transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most recent common ancestor of all Wolbachia and mitochondrial genomes in D. melanogaster dates to around 8,000 years ago. We find evidence for a recent global replacement of ancestral Wolbachia and mtDNA lineages, but our data suggest that the derived wMel lineage arose several thousand years ago, not in the 20th century as previously proposed. Our data also provide evidence that this global replacement event is incomplete and is likely to be one of several similar incomplete replacement events that have occurred since the out-of-Africa migration that allowed D. melanogaster to colonize worldwide habitats. This study provides a complete genomic analysis of the evolutionary mode and temporal dynamics of the D. melanogaster-Wolbachia symbiosis, as well as important resources for further analyses of the impact of Wolbachia on host biology.

Present status of the ETL LINAC facility

International Nuclear Information System (INIS)

Suzuki, Ryoichi; Mikado, Tomohisa; Ohgaki, Hideaki

1993-01-01

The ETL LINAC has been operated for the beam injection to the storage rings NIJI-II, III, IV, and TERAS, and for the generation of an intense slow positron beam. The status of the ETL LINAC on the operations, the maintenances, and the improvements is described. (author)

Investigation of neutrino properties in experiments at nuclear reactors: Present status and prospects

International Nuclear Information System (INIS)

Mikaelyan, L.A.

2002-01-01

The present status of experiments that are being performed at nuclear reactors in order to seek the neutrino masses, mixing, and magnetic moments, whose discovery would be a signal of the existence of physics beyond the Standard Model, is considered, along with their future prospects

Radwaste management in the UK - present status and future plans

International Nuclear Information System (INIS)

Eyre, B.

1991-01-01

In 1976, the Royal Commission on Environmental Pollution, chaired by Lord Flowers, undertook a thorough review of the status of radioactive waste management in the United Kingdom (UK). Its report became the stimulus which launched a new programme of strategic and technical work to establish a total system plan for the processing, storage, transport and disposal of all radioactive wastes in the UK. This article, which describes the evolution of the programme, is the basis of the presentation to the Korean nuclear industry earlier this year by the Deputy Chairman and Chief Executive of AEA Technology. (author)

Present status of spallation target development. JAERI/KEK Joint Project

International Nuclear Information System (INIS)

Hino, R.; Kaminaga, M.; Haga, K.

2001-01-01

The Japan Atomic Energy Research Institute (JAERI) and the High Energy Accelerator Research Organization (KEK) are promoting a plan to construct a neutron scattering facility under the JAERI/KEK Joint Project. Design and R and D works are being carried out vigorously for realizing the mercury target system consisting of the mercury target, moderators and reflectors working as a spallation neutron source, as well as a remote handling system for exchanging such components which will be highly irradiated. This report introduces an outline of the present status of design and development activities on the spallation target system. (author)

Cytoscape: the network visualization tool for GenomeSpace workflows [v2; ref status: indexed, http://f1000r.es/47f

Directory of Open Access Journals (Sweden)

Barry Demchak

2014-08-01

Full Text Available Modern genomic analysis often requires workflows incorporating multiple best-of-breed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded over 850 times since the release of its first version in September, 2013.

Cytoscape: the network visualization tool for GenomeSpace workflows [v1; ref status: indexed, http://f1000r.es/3ph

Directory of Open Access Journals (Sweden)

Barry Demchak

2014-07-01

Full Text Available Modern genomic analysis often requires workflows incorporating multiple best-ofbreed tools. GenomeSpace is a web-based visual workbench that combines a selection of these tools with mechanisms that create data flows between them. One such tool is Cytoscape 3, a popular application that enables analysis and visualization of graph-oriented genomic networks. As Cytoscape runs on the desktop, and not in a web browser, integrating it into GenomeSpace required special care in creating a seamless user experience and enabling appropriate data flows. In this paper, we present the design and operation of the Cytoscape GenomeSpace app, which accomplishes this integration, thereby providing critical analysis and visualization functionality for GenomeSpace users. It has been downloaded it over 850 times since the release of its first version in September, 2013.

Present status of ESNIT (energy selective neutron irradiation test facility) program

International Nuclear Information System (INIS)

Noda, K.; Ohno, H.; Sugimoto, M.; Kato, Y.; Matsuo, H.; Watanabe, K.; Kikuchi, T.; Sawai, T.; Usui, T.; Oyama, Y.; Kondo, T.

1994-01-01

The present status of technical studies of a high energy neutron irradiation facility, ESNIT (energy selective neutron irradiation test facility), is summarized. Technological survey and feasibility studies of ESNIT have continued since 1988. The results of technical studies of the accelerator, the target and the experimental systems in ESNIT program were reviewed by an International Advisory Committee in February 1993. Recommendations for future R and D on ESNIT program are also summarized in this paper. ((orig.))

Genomic tools in pearl millet breeding for drought tolerance: Status and prospects

Directory of Open Access Journals (Sweden)

Desalegn Debelo Serba

2016-11-01

Full Text Available Pearl millet (Penisetum glaucum (L R. Br. is a hardy cereal crop grown in the arid and semiarid tropics where other cereals are likely to fail to produce economic yields due to drought and heat stresses. Adaptive evolution, a form of natural selection shaped the crop to grow and yield satisfactorily with limited moisture supply or under periodic water deficits in the soil. Drought tolerance is a complex polygenic trait that various morphological and physiological responses are controlled by hundreds of genes and significantly influenced by the environment. The development of genomic tools will have enormous potential to improve the efficiency and precision of conventional breeding. The apparent independent domestication events, highly outcrossing nature and traditional cultivation in stressful environments maintained tremendous amount of polymorphism in pearl millet. This high polymorphism of the crop has been revealed by genome mapping that in turn stimulated the mapping and tagging of genomic regions controlling important traits such as drought tolerance. Mapping of a major QTL for terminal drought tolerance in independent populations envisaged the prospect for the development of molecular breeding in pearl millet. To accelerate genetic gains for drought tolerance targeted novel approaches such as establishment of marker-trait associations, genomic selection tools, genome sequence and genotyping-by-sequencing are still limited. Development and application of high throughput genomic tools need to be intensified to improve the breeding efficiency of pearl millet to minimize the impact of climate change on its production.

The ACES mission: scientific objectives and present status

Science.gov (United States)

Cacciapuoti, L.; Dimarcq, N.; Salomon, C.

2017-11-01

"Atomic Clock Ensemble in Space" (ACES) is a mission in fundamental physics that will operate a new generation of atomic clocks in the microgravity environment of the International Space Station (ISS). The ACES clock signal will combine the medium term frequency stability of a space hydrogen maser (SHM) and the long term stability and accuracy of a frequency standard based on cold cesium atoms (PHARAO). Fractional frequency stability and accuracy of few parts in 1016 will be achieved. The on-board time base distributed on Earth via a microwave link (MWL) will be used to test fundamental laws of physics (Einstein's theories of Special and General Relativity, Standard Model Extension, string theories…) and to develop applications in time and frequency metrology, universal time scales, global positioning and navigation, geodesy and gravimetry. After a general overview on the mission concept and its scientific objectives, the present status of ACES instruments and sub-systems will be discussed.

Impact of SNPs on Protein Phosphorylation Status in Rice (Oryza sativa L.

Directory of Open Access Journals (Sweden)

Shoukai Lin

2016-11-01

Full Text Available Single nucleotide polymorphisms (SNPs are widely used in functional genomics and genetics research work. The high-quality sequence of rice genome has provided a genome-wide SNP and proteome resource. However, the impact of SNPs on protein phosphorylation status in rice is not fully understood. In this paper, we firstly updated rice SNP resource based on the new rice genome Ver. 7.0, then systematically analyzed the potential impact of Non-synonymous SNPs (nsSNPs on the protein phosphorylation status. There were 3,897,312 SNPs in Ver. 7.0 rice genome, among which 9.9% was nsSNPs. Whilst, a total 2,508,261 phosphorylated sites were predicted in rice proteome. Interestingly, we observed that 150,197 (39.1% nsSNPs could influence protein phosphorylation status, among which 52.2% might induce changes of protein kinase (PK types for adjacent phosphorylation sites. We constructed a database, SNP_rice, to deposit the updated rice SNP resource and phosSNPs information. It was freely available to academic researchers at http://bioinformatics.fafu.edu.cn. As a case study, we detected five nsSNPs that potentially influenced heterotrimeric G proteins phosphorylation status in rice, indicating that genetic polymorphisms showed impact on the signal transduction by influencing the phosphorylation status of heterotrimeric G proteins. The results in this work could be a useful resource for future experimental identification and provide interesting information for better rice breeding.

The interaction of iron and the genome: For better and for worse.

Science.gov (United States)

Troadec, Marie-Bérengère; Loréal, Olivier; Brissot, Pierre

2017-10-01

Iron, as an essential nutrient, and the DNA, as the carrier of genetic information which is physically compacted into chromosomes, are both needed for normal life and well-being. Therefore, it is not surprising that close interactions exist between iron and the genome. On the one hand, iron, especially when present in excess, may alter genome stability through oxidative stress, and may favor cell cycle abnormalities and the development of malignant diseases. The genome also receives a feedback signal from the systemic iron status, leading to promotion of expression of genes that regulate iron metabolism. Conversely, on the other hand, DNA mutations may cause genetic iron-related diseases such as hemochromatosis, archetype of iron-overload diseases, or refractory iron deficiency anemia (IRIDA). Copyright © 2017 Elsevier B.V. All rights reserved.

New Onset Refractory Status Epilepticus as an Unusual Presentation of a Suspected Organophosphate Poisoning

Directory of Open Access Journals (Sweden)

Shahan Waheed

2014-01-01

Full Text Available New onset refractory status epilepticus (NORSE is a new entity in medical literature. It has different infectious and noninfectious etiologies showing a devastating impact onto the clinical outcome of patients. Therapy with anaesthetic and antiepileptic agents often fails to improve the condition, unless the primary cause is rectified. Here is presented the case of a young female with a history of depression who after a recent bereavement came to the Emergency Department of Aga Khan University Hospital with complaints of drowsiness that lasted for few hours. Though she had no history of organophosphate poisoning, her physical examination and further investigations were suggestive of the diagnosis. During her hospital stay, she developed refractory status epilepticus. Her seizures did not respond to standard antiepileptic and intravenous anesthetic agents and subsided only after intravenous infusion of atropine for a few days. Organophosphate poisoning is a very common presentation in the developing world and the associated status epilepticus poses a devastating problem for emergency physicians. In patients with suspected organophosphate poisoning with favoring clinical exam findings, the continuation of atropine intravenous infusion can be a safe option to abate seizures.

The proactive historian: Methodological opportunities presented by the new archives documenting genomics.

Science.gov (United States)

García-Sancho, Miguel

2016-02-01

In this paper, I propose a strategy for navigating newly available archives in the study of late-twentieth century genomics. I demonstrate that the alleged 'explosion of data' characteristic of genomics-and of contemporary science in general-is not a new problem and that historians of earlier periods have dealt with information overload by relying on the 'perspective of time': the filtering effect the passage of time naturally exerts on both sources and memories. I argue that this reliance on the selective capacity of time results in inheriting archives curated by others and, consequently, poses the risk of reifying ahistorical scientific discourses. Through a preliminary examination of archives documenting early attempts at mapping and sequencing the human genome, I propose an alternative approach, in which historians proactively problematize and improve available sources. This approach provides historians with a voice in the socio-political management of scientific heritage and advances methodological innovations in the use of oral histories. It also provides a narrative framework in which to address big science initiatives by following second order administrators, rather than individual scientists. The new genomic archives thus represent an opportunity for historians to take an active role in current debates concerning 'big data' and critically embed the humanities in pressing global problems. Copyright © 2015 Elsevier Ltd. All rights reserved.

The research progress of genomic selection in livestock.

Science.gov (United States)

Li, Hong-wei; Wang, Rui-jun; Wang, Zhi-ying; Li, Xue-wu; Wang, Zhen-yu; Yanjun, Zhang; Rui, Su; Zhihong, Liu; Jinquan, Li

2017-05-20

With the development of gene chip and breeding technology, genomic selection in plants and animals has become research hotspots in recent years. Genomic selection has been extensively applied to all kinds of economic livestock, due to its high accuracy, short generation intervals and low breeding costs. In this review, we summarize genotyping technology and the methods for genomic breeding value estimation, the latter including the least square method, RR-BLUP, GBLUP, ssGBLUP, BayesA and BayesB. We also cover basic principles of genomic selection and compare their genetic marker ranges, genomic selection accuracy and operational speed. In addition, we list common indicators, methods and influencing factors that are related to genomic selection accuracy. Lastly, we discuss latest applications and the current problems of genomic selection at home and abroad. Importantly, we envision future status of genomic selection research, including multi-trait and multi-population genomic selection, as well as impact of whole genome sequencing and dominant effects on genomic selection. This review will provide some venues for other breeders to further understand genome selection.

Food preservation by ionizing radiation in Nigeria. Present and future status

International Nuclear Information System (INIS)

Olorunda, A.O.; Aboaba, F.O.

1978-01-01

Research into the use of ionizing radiation in food preservation in Nigeria is still in its very infancy and most of the work done to date is at the exploratory stage. Such work has, however, demonstrated the potential of ionizing radiation in prolonging the shelf-life of yams and, possibly, onions. The paper reviews the present status of the use of radiation food preservation in Nigeria. The present research programme of the Faculty of Technology, University of Ibadan, which includes a wider application of ionizing radiation to fruit and vegetable preservation and grain storage, is also highlighted. The primary objectives of this programme are to establish the wholesomeness of the irradiated foods and the economics of the process. (author)

Mitogenomes from The 1000 Genome Project reveal new Near Eastern features in present-day Tuscans.

Directory of Open Access Journals (Sweden)

Alberto Gómez-Carballa

Full Text Available Genetic analyses have recently been carried out on present-day Tuscans (Central Italy in order to investigate their presumable recent Near East ancestry in connection with the long-standing debate on the origins of the Etruscan civilization. We retrieved mitogenomes and genome-wide SNP data from 110 Tuscans analyzed within the context of The 1000 Genome Project. For phylogeographic and evolutionary analysis we made use of a large worldwide database of entire mitogenomes (>26,000 and partial control region sequences (>180,000.Different analyses reveal the presence of typical Near East haplotypes in Tuscans representing isolated members of various mtDNA phylogenetic branches. As a whole, the Near East component in Tuscan mitogenomes can be estimated at about 8%; a proportion that is comparable to previous estimates but significantly lower than admixture estimates obtained from autosomal SNP data (21%. Phylogeographic and evolutionary inter-population comparisons indicate that the main signal of Near Eastern Tuscan mitogenomes comes from Iran.Mitogenomes of recent Near East origin in present-day Tuscans do not show local or regional variation. This points to a demographic scenario that is compatible with a recent arrival of Near Easterners to this region in Italy with no founder events or bottlenecks.

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

Present status of inertial confinement fusion reactor design

International Nuclear Information System (INIS)

Mima, Kunioki; Ido, Shunji; Nakai, Sadao.

1986-01-01

Since inertial nuclear fusion reactors do not require high vacuum and high magnetic field, the structure of the reactor cavity becomes markedly simple as compared with tokamak type fusion reactors. In particular, since high vacuum is not necessary, liquid metals such as lithium and lead can be used for the first wall, and the damage of reactor structures by neutrons can be prevented. As for the core, the energy efficiency of lasers is not very high, accordingly it must be designed so that the pellet gain due to nuclear fusion becomes sufficiently high, and typically, the gain coefficient from 100 to 200 is necessary. In this paper, the perspective of pellet gain, the plan from the present status to the practical reactors, and the conceptual design of the practical reactors are discussed. The plan of fuel ignition, energy break-even and high gain by the implosion mode, of which the uncertain factor due to uneven irradiation and instability was limited to the minimum, was clarified. The scenario of the development of laser nuclear fusion reactors is presented, and the concept of the reactor system is shown. The various types of nuclear fusion-fission hybrid reactors are explained. As for the design of inertial fusion power reactors, the engineering characteristics of the core, the conceptual design, water fall type reactors and DD fuel reactors are discussed. (Kako, I.)

Present status of cryogenic system for e-linac at VECC

International Nuclear Information System (INIS)

Ahammed, Manir; Mondal, Manas; Pal, Sandip; Duttagupta, Anjan; Bandyopadhyay, Arup; Naik, Vaishali; Chakrabarti, Alok; Laxdal, Robert E.; Koveshnikov, Alexy

2015-01-01

VECC is constructing a 50 MeV, 100 kW, superconducting electron linear accelerator (e-Linac) for the upcoming ANURIB (Advanced National facility for Unstable and Rare Isotope Beams) project at the new campus. Presently a 10 MeV injector for the e-Linac is being developed in collaboration with TRIUMF laboratory in Canada.The Injector comprises a 300 kV electron gun, low energy beam transport (LEBT) line and an injector cryo-module (ICM) that houses one 9-cell beta=1, 1.3 GHz niobium elliptical cavity operated at 2K. Alternatively, a capture cryo-module (CCM) having two single cell beta=1, 1.3 GHz niobium cavities that will allow the electron gun to be operated at 100 kV is also being developed. The e-Linac has been jointly designed by VECC and TRIUMF. The ICM is being built by TRIUMF whereas front-end of the injector is being built indigenously at VECC. In this report the details and present status of the cryogenic system for the e-Linac will be presented

Applications of flow cytometry in plant pathology for genome size determination, detection and physiological status.

Science.gov (United States)

D'Hondt, Liesbet; Höfte, Monica; Van Bockstaele, Erik; Leus, Leen

2011-10-01

Flow cytometers are probably the most multipurpose laboratory devices available. They can analyse a vast and very diverse range of cell parameters. This technique has left its mark on cancer, human immunodeficiency virus and immunology research, and is indispensable in routine clinical diagnostics. Flow cytometry (FCM) is also a well-known tool for the detection and physiological status assessment of microorganisms in drinking water, marine environments, food and fermentation processes. However, flow cytometers are seldom used in plant pathology, despite FCM's major advantages as both a detection method and a research tool. Potential uses of FCM include the characterization of genome sizes of fungal and oomycete populations, multiplexed pathogen detection and the monitoring of the viability, culturability and gene expression of plant pathogens, and many others. This review provides an overview of the history, advantages and disadvantages of FCM, and focuses on the current applications and future possibilities of FCM in plant pathology. © 2011 THE AUTHORS. MOLECULAR PLANT PATHOLOGY © 2011 BSPP AND BLACKWELL PUBLISHING LTD.

Genome health nutrigenomics and nutrigenetics--diagnosis and nutritional treatment of genome damage on an individual basis.

Science.gov (United States)

Fenech, Michael

2008-04-01

The term nutrigenomics refers to the effect of diet on gene expression. The term nutrigenetics refers to the impact of inherited traits on the response to a specific dietary pattern, functional food or supplement on a specific health outcome. The specific fields of genome health nutrigenomics and genome health nutrigenetics are emerging as important new research areas because it is becoming increasingly evident that (a) risk for developmental and degenerative disease increases with DNA damage which in turn is dependent on nutritional status and (b) optimal concentration of micronutrients for prevention of genome damage is also dependent on genetic polymorphisms that alter function of genes involved directly or indirectly in uptake and metabolism of micronutrients required for DNA repair and DNA replication. Development of dietary patterns, functional foods and supplements that are designed to improve genome health maintenance in humans with specific genetic backgrounds may provide an important contribution to a new optimum health strategy based on the diagnosis and individualised nutritional treatment of genome instability i.e. Genome Health Clinics.

Comparative chloroplast genomics: Analyses including new sequencesfrom the angiosperms Nuphar advena and Ranunculus macranthus

Energy Technology Data Exchange (ETDEWEB)

Raubeso, Linda A.; Peery, Rhiannon; Chumley, Timothy W.; Dziubek,Chris; Fourcade, H. Matthew; Boore, Jeffrey L.; Jansen, Robert K.

2007-03-01

The number of completely sequenced plastid genomes available is growing rapidly. This new array of sequences presents new opportunities to perform comparative analyses. In comparative studies, it is most useful to compare across wide phylogenetic spans and, within angiosperms, to include representatives from basally diverging lineages such as the new genomes reported here: Nuphar advena (from a basal-most lineage) and Ranunculus macranthus (from the basal group of eudicots). We report these two new plastid genome sequences and make comparisons (within angiosperms, seed plants, or all photosynthetic lineages) to evaluate features such as the status of ycf15 and ycf68 as protein coding genes, the distribution of simple sequence repeats (SSRs) and longer dispersed repeats (SDR), and patterns of nucleotide composition.

Impact of genome assembly status on ChIP-Seq and ChIP-PET data mapping

Directory of Open Access Journals (Sweden)

Sachs Laurent

2009-12-01

Full Text Available Abstract Background ChIP-Seq and ChIP-PET can potentially be used with any genome for genome wide profiling of protein-DNA interaction sites. Unfortunately, it is probable that most genome assemblies will never reach the quality of the human genome assembly. Therefore, it remains to be determined whether ChIP-Seq and ChIP-PET are practicable with genome sequences other than a few (e.g. human and mouse. Findings Here, we used in silico simulations to assess the impact of completeness or fragmentation of genome assemblies on ChIP-Seq and ChIP-PET data mapping. Conclusions Most currently published genome assemblies are suitable for mapping the short sequence tags produced by ChIP-Seq or ChIP-PET.

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

Science.gov (United States)

Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos; Tavernarakis, Nektarios; Hugenholtz, Philip; Markowitz, Victor M.; Kyrpides, Nikos C.

2010-01-01

The Genomes On Line Database (GOLD) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2009, GOLD contains information for more than 5800 sequencing projects, of which 1100 have been completed and their sequence data deposited in a public repository. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about a (Meta)Genome Sequence (MIGS/MIMS) specification. GOLD is available at: http://www.genomesonline.org and has a mirror site at the Institute of Molecular Biology and Biotechnology, Crete, Greece, at: http://gold.imbb.forth.gr/ PMID:19914934

Present status of intermediate band solar cell research

International Nuclear Information System (INIS)

Cuadra, L.; Marti, A.; Luque, A.

2004-01-01

The intermediate band solar cell is a theoretical concept with the potential for exceeding the performance of conventional single-gap solar cells. This novel photovoltaic converter bases its superior theoretical efficiency over single-gap solar cells by enhancing its photogenerated current, via the two-step absorption of sub-band gap photons, without reducing its output voltage. This is achieved through a material with an electrically isolated and partially filled intermediate band located within a higher forbidden gap. This material is commonly named intermediate band material. This paper centres on summarising the present status of intermediate band solar cell research. A number of attempts, which aim to implement the intermediate band concept, are being followed: the direct engineering of the intermediate band material, its implementation by means of quantum dots and the highly porous material approach. Among other sub-band gap absorbing proposals, there is a renewed interest on the impurity photovoltaic effect, the quantum well solar cells and the particularly promising proposal for the use of up- and down-converters

Molecular genetic contributions to socioeconomic status and intelligence.

Science.gov (United States)

Marioni, Riccardo E; Davies, Gail; Hayward, Caroline; Liewald, Dave; Kerr, Shona M; Campbell, Archie; Luciano, Michelle; Smith, Blair H; Padmanabhan, Sandosh; Hocking, Lynne J; Hastie, Nicholas D; Wright, Alan F; Porteous, David J; Visscher, Peter M; Deary, Ian J

2014-05-01

Education, socioeconomic status, and intelligence are commonly used as predictors of health outcomes, social environment, and mortality. Education and socioeconomic status are typically viewed as environmental variables although both correlate with intelligence, which has a substantial genetic basis. Using data from 6815 unrelated subjects from the Generation Scotland study, we examined the genetic contributions to these variables and their genetic correlations. Subjects underwent genome-wide testing for common single nucleotide polymorphisms (SNPs). DNA-derived heritability estimates and genetic correlations were calculated using the 'Genome-wide Complex Trait Analyses' (GCTA) procedures. 21% of the variation in education, 18% of the variation in socioeconomic status, and 29% of the variation in general cognitive ability was explained by variation in common SNPs (SEs ~ 5%). The SNP-based genetic correlations of education and socioeconomic status with general intelligence were 0.95 (SE 0.13) and 0.26 (0.16), respectively. There are genetic contributions to intelligence and education with near-complete overlap between common additive SNP effects on these traits (genetic correlation ~ 1). Genetic influences on socioeconomic status are also associated with the genetic foundations of intelligence. The results are also compatible with substantial environmental contributions to socioeconomic status.

A case of nonconvulsive status epilepticus presenting as ...

African Journals Online (AJOL)

disorders has generated interest since ancient times. ... disorders and personality disorders. ... He was hospitalised for a diagnostic work-up. ... Nonconvulsive status epilepticus is characterised by changes in behaviour, memory, affect or level ...

The simulation for the ATLAS experiment Present status and outlook

CERN Document Server

Rimoldi, A; Gallas, M; Nairz, A; Boudreau, J; Tsulaia, V; Costanzo, D

2004-01-01

The simulation program for the ATLAS experiment is presently operational in a full OO environment. This important physics application has been successfully integrated into ATLAS's common analysis framework, ATHENA. In the last year, following a well stated strategy of transition from a GEANT3 to a GEANT4-based simulation, a careful validation programme confirmed the reliability, performance and robustness of this new tool, as well as its consistency with the results of previous simulation. Generation, simulation and digitization steps on different sets of full physics events we retested for performance. The same software used to simulate the full the ATLAS detector is also used with testbeam configurations. Comparisons to real data in the testbeam validate both the detector description and the physics processes within each subcomponent. In this paper we present the current status of ATLAS GEANT4 simulation, describe the functionality tests performed during its validation phase, and the experience with distrib...

Present status of reactor physics in the United States and Japan-II. 6. Present Status of GNF New Nodal Simulator

International Nuclear Information System (INIS)

Iwamoto, T.; Tamitani, M.; Moore, B.

2001-01-01

This paper presents core simulator consolidation work done at Global Nuclear Fuel (GNF). The unified simulator needs to supersede the capabilities of past simulator packages from the original GNF partners: GE (Ref. 1), Hitachi (Ref. 2), and Toshiba (Ref. 3). At the same time, an effort is being made to produce a simulation package that will be a state-of-the-art analysis tool when released, in terms of the physics solution methodology and functionality. The core simulator will be capable and qualified for (a) high-energy cycles in the U.S. markets, (b) mixed-oxide (MOX) introduction in Japan, and (c) high-power density plants in Europe, etc. The unification of the lattice physics code is also in progress based on a transport model with collision probability methods. The AETNA core simulator is built upon the PANAC11 software base. The goal is to essentially replace the 1.5-energy group model with a higher-order multigroup nonlinear nodal solution capable of the required modeling fidelity, while keeping highly automated library generation as well as functionality. All required interfaces to PANAC11 will be preserved, which minimizes the impact on users and process automation. Preliminary results show statistical accuracy improvement over the 1.5- group model. The status of the GNF new nodal simulator is presented. It is built on a highly automated software base by combining the best technologies of GE, Hitachi, and Toshiba and will provide a BWR core analysis tool with high functionality and fidelity. (authors)

Opencast coal mining in India: present status and future trends

Energy Technology Data Exchange (ETDEWEB)

Khare, B.P. [Kakatiya University, Warangal (India)

2007-07-01

This paper discussed the opencast coal mining in India, present status and future trends including technology trends. The opencast coal mines in the coming years will have to switch over more and more to semi continuous and continuous mining. Whatever be the system adopted it should be sustainable to meet the output levels commensurate with environmental protection, safety, health, conservation and economics. It could, therefore, be summed up that the search for new technologies should be based on: (1) use of continuous miners; (2) use of bucket wheel excavators, conveyors, and spreaders; (3) shovel-crusher and conveyor system; and (4) application of high angle conveyors, cross-pit conveyors, and OB bridges. 4 tabs.

Survey on present status and trend of parallel programming environments

International Nuclear Information System (INIS)

Takemiya, Hiroshi; Higuchi, Kenji; Honma, Ichiro; Ohta, Hirofumi; Kawasaki, Takuji; Imamura, Toshiyuki; Koide, Hiroshi; Akimoto, Masayuki.

1997-03-01

This report intends to provide useful information on software tools for parallel programming through the survey on parallel programming environments of the following six parallel computers, Fujitsu VPP300/500, NEC SX-4, Hitachi SR2201, Cray T94, IBM SP, and Intel Paragon, all of which are installed at Japan Atomic Energy Research Institute (JAERI), moreover, the present status of R and D's on parallel softwares of parallel languages, compilers, debuggers, performance evaluation tools, and integrated tools is reported. This survey has been made as a part of our project of developing a basic software for parallel programming environment, which is designed on the concept of STA (Seamless Thinking Aid to programmers). (author)

Thermal hydraulic codes for LWR safety analysis - present status and future perspective

Energy Technology Data Exchange (ETDEWEB)

Staedtke, H. [Commission of the European Union, Ispra (Italy)

1997-07-01

The aim of the present paper is to give a review on the current status and future perspective of present best-estimate Thermal Hydraulic codes. Reference is made to internationally well-established codes which have reached a certain state of maturity. The first part of the paper deals with the common basic code features with respect to the physical modelling and their numerical methods used to describe complex two-phase flow and heat transfer processes. The general predictive capabilities are summarized identifying some remaining code deficiencies and their underlying limitations. The second part discusses various areas including physical modelling, numerical techniques and informatic structure where the codes could be substantially improved.

Present status and future perspective of research and test reactors in JAERI

International Nuclear Information System (INIS)

Baba, Osamu; Kaieda, Keisuke

1999-01-01

Since 1957, Japan Atomic Energy Research Institute (JAERI) has constructed several research and test reactors to fulfil a major role in the study of nuclear energy and fundamental research. At present, four reactors, the Japan Research Reactor No. 3 and No. 4 (JRR-3M and JRR-4 respectively), the Japan Materials Testing Reactor (JMTR) and the Nuclear Safety Research Reactor (NSRR), are in operation, and a new High Temperature Engineering Test Reactor (HTTR) has reached first criticality and is waiting for the power-up test. This paper introduce these reactors and describe their present operational status. The recent tendency of utilization and future perspectives are also reported. (author)

Thermal hydraulic codes for LWR safety analysis - present status and future perspective

International Nuclear Information System (INIS)

Staedtke, H.

1997-01-01

The aim of the present paper is to give a review on the current status and future perspective of present best-estimate Thermal Hydraulic codes. Reference is made to internationally well-established codes which have reached a certain state of maturity. The first part of the paper deals with the common basic code features with respect to the physical modelling and their numerical methods used to describe complex two-phase flow and heat transfer processes. The general predictive capabilities are summarized identifying some remaining code deficiencies and their underlying limitations. The second part discusses various areas including physical modelling, numerical techniques and informatic structure where the codes could be substantially improved

Present status and future perspective of research and test reactors in JAERI

Energy Technology Data Exchange (ETDEWEB)

Baba, Osamu [Japan Atomic Energy Research Inst., Oarai, Ibaraki (Japan). Oarai Research Establishment; Kaieda, Keisuke

1999-08-01

Since 1957, Japan Atomic Energy Research Institute (JAERI) has constructed several research and test reactors to fulfil a major role in the study of nuclear energy and fundamental research. At present, four reactors, the Japan Research Reactor No. 3 and No. 4 (JRR-3M and JRR-4 respectively), the Japan Materials Testing Reactor (JMTR) and the Nuclear Safety Research Reactor (NSRR), are in operation, and a new High Temperature Engineering Test Reactor (HTTR) has reached first criticality and is waiting for the power-up test. This paper introduce these reactors and describe their present operational status. The recent tendency of utilization and future perspectives are also reported. (author)

Colliding beam experiments in the Siberian Institute for Nuclear Physics (Present status and prospects)

International Nuclear Information System (INIS)

Budker, G.I.

1982-01-01

Present status of construction of colliding (electron, positron, proton, antiproton and muon) beam facilities is described. Experiments conducted at the VEP-1 and VEPP-2 facilities in 1968-1970 are enumerated. The program of forthcoming investigations at the VAPP-NAP facility is described in brief

Evaluation of Genomic Instability in the Abnormal Prostate

National Research Council Canada - National Science Library

Haaland-Pullus, Christina; Griffith, Jeffrey K

2006-01-01

...: prognosis and diagnosis. Several tools are being used to investigate this effect, specifically the assessment of telomere length, allelic imbalance, and methylation status, all markers of genomic instability...

Evaluation of Genomic Instability in the Abnormal Prostate

National Research Council Canada - National Science Library

Haaland-Pullus, Christina; Griffth, Jeffrey K

2008-01-01

...: prognosis and diagnosis. Several tools are being used to investigate this effect, specifically the assessment of telomere length, allelic imbalance, and methylation status, all markers of genomic instability...

Present status of the Liquid Breeder Validation Module for IFMIF

International Nuclear Information System (INIS)

Casal, Natalia; Mas, Avelino; Mota, Fernando; García, Ángela; Rapisarda, David; Nomen, Oriol; Arroyo, Jose Manuel; Abal, Javier; Mollá, Joaquín; Ibarra, Ángel

2013-01-01

Highlights: • The LBVM will be used to perform irradiation experiments on functional materials for fusion reactors. • It houses 16 experimental rigs, each one containing a EUROFER capsule partially filled with lithium lead, at 300–550 °C. • A helium purge gas will sweep the tritium permeated through the capsule walls to a tritium measuring station. • A helium cooling system will keep tritium diffusion within safe margins and guarantee its mechanical integrity. • Thermal hydraulic and mechanical calculations, the module instrumentation and aspects as safety or RAMI are presented. -- Abstract: One of the objectives of IFMIF (International Fusion Materials Irradiation Facility), as stated in its specifications, is the validation of breeder blanket concepts for DEMO design. The so-called Liquid Breeder Validation Module (LBVM) will be used in IFMIF to perform experiments under irradiation on functional materials related to liquid breeder concepts for future fusion reactors. This module, not considered in previous IFMIF design phases, is currently under design by CIEMAT in the framework of the IFMIF/EVEDA project. In this paper, the present status of the design of the LBVM is presented

Present status of the Liquid Breeder Validation Module for IFMIF

Energy Technology Data Exchange (ETDEWEB)

Casal, Natalia, E-mail: natalia.casal@ciemat.es [Laboratorio Nacional de Fusión por Confinamiento Magnético – CIEMAT, 28040 Madrid (Spain); Mas, Avelino; Mota, Fernando; García, Ángela; Rapisarda, David [Laboratorio Nacional de Fusión por Confinamiento Magnético – CIEMAT, 28040 Madrid (Spain); Nomen, Oriol [Institut de Recerca en Energia de Catalunya (IREC), Barcelona (Spain); Centre de Disseny d’Equips Industrials (CDEI), Technical University of Catalonia (UPC), Barcelona (Spain); Arroyo, Jose Manuel [Laboratorio Nacional de Fusión por Confinamiento Magnético – CIEMAT, 28040 Madrid (Spain); Abal, Javier [Fusion Energy Engineering Laboratory (FEEL), Technical University of Catalonia (UPC) Barcelona-Tech, Barcelona (Spain); Mollá, Joaquín; Ibarra, Ángel [Laboratorio Nacional de Fusión por Confinamiento Magnético – CIEMAT, 28040 Madrid (Spain)

2013-10-15

Highlights: • The LBVM will be used to perform irradiation experiments on functional materials for fusion reactors. • It houses 16 experimental rigs, each one containing a EUROFER capsule partially filled with lithium lead, at 300–550 °C. • A helium purge gas will sweep the tritium permeated through the capsule walls to a tritium measuring station. • A helium cooling system will keep tritium diffusion within safe margins and guarantee its mechanical integrity. • Thermal hydraulic and mechanical calculations, the module instrumentation and aspects as safety or RAMI are presented. -- Abstract: One of the objectives of IFMIF (International Fusion Materials Irradiation Facility), as stated in its specifications, is the validation of breeder blanket concepts for DEMO design. The so-called Liquid Breeder Validation Module (LBVM) will be used in IFMIF to perform experiments under irradiation on functional materials related to liquid breeder concepts for future fusion reactors. This module, not considered in previous IFMIF design phases, is currently under design by CIEMAT in the framework of the IFMIF/EVEDA project. In this paper, the present status of the design of the LBVM is presented.

Present status of controversies regarding the thermal Casimir force

International Nuclear Information System (INIS)

Mostepanenko, V M; Bezerra, V B; Decca, R S; Geyer, B; Fischbach, E; Klimchitskaya, G L; Krause, D E; Lopez, D; Romero, C

2006-01-01

It is well known that, beginning in 2000, the behaviour of the thermal correction to the Casimir force between real metals has been hotly debated. As was shown by several research groups, the Lifshitz theory, which provides the theoretical foundation for the calculation of both the van der Waals and Casimir forces, leads to different results depending on the model of metal conductivity used. To resolve these controversies, theoretical considerations based on the principles of thermodynamics and new experimental tests were invoked. We analyse the present status of the problem (in particular, the advantages and disadvantages of the approaches based on the surface impedance and on the Drude model dielectric function) using rigorous analytical calculations of the entropy of a fluctuating field. We also discuss the results of a new precise experiment on the determination of the Casimir pressure between two parallel plates by means of a micromechanical torsional oscillator

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.

Present status of practical aspects of individual dosimetry. Pt. 1. EC Member States

International Nuclear Information System (INIS)

Goeksu, H.Y.; Regulla, D.; Drexler, G.

1995-01-01

The study reviews the present status of radiation protection practices of occupationally exposed persons in the Member States of the European Communities by taking account of the new legislative changes. A special emphasis is given to identify and describe the difference in procedures and methods of personnel monitoring, dose assessment, record keeping and collective dose assessment in each country. (orig./HP)

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.

Amplification of HER2 is a marker for global genomic instability

International Nuclear Information System (INIS)

Ellsworth, Rachel E; Ellsworth, Darrell L; Patney, Heather L; Deyarmin, Brenda; Love, Brad; Hooke, Jeffrey A; Shriver, Craig D

2008-01-01

Genomic alterations of the proto-oncogene c-erbB-2 (HER-2/neu) are associated with aggressive behavior and poor prognosis in patients with breast cancer. The variable clinical outcomes seen in patients with similar HER2 status, given similar treatments, suggests that the effects of amplification of HER2 can be influenced by other genetic changes. To assess the broader genomic implications of structural changes at the HER2 locus, we investigated relationships between genomic instability and HER2 status in patients with invasive breast cancer. HER2 status was determined using the PathVysion ® assay. DNA was extracted after laser microdissection from the 181 paraffin-embedded HER2 amplified (n = 39) or HER2 negative (n = 142) tumor specimens with sufficient tumor available to perform molecular analysis. Allelic imbalance (AI) was assessed using a panel of microsatellite markers representing 26 chromosomal regions commonly altered in breast cancer. Student t-tests and partial correlations were used to investigate relationships between genomic instability and HER2 status. The frequency of AI was significantly higher (P < 0.005) in HER2 amplified (27%) compared to HER2 negative tumors (19%). Samples with HER2 amplification showed significantly higher levels of AI (P < 0.05) at chromosomes 11q23, 16q22-q24 and 18q21. Partial correlations including ER status and tumor grade supported associations between HER2 status and alterations at 11q13.1, 16q22-q24 and 18q21. The poor prognosis associated with HER2 amplification may be attributed to global genomic instability as cells with high frequencies of chromosomal alterations have been associated with increased cellular proliferation and aggressive behavior. In addition, high levels of DNA damage may render tumor cells refractory to treatment. In addition, specific alterations at chromosomes 11q13, 16q22-q24, and 18q21, all of which have been associated with aggressive tumor behavior, may serve as genetic modifiers to HER2

Overview and present status of the IAEA/RADWASS programme

International Nuclear Information System (INIS)

Abe, Masayoshi

1998-01-01

Since 1991 the International Atomic Energy Agency (IAEA) has been developing a series of safety standards documents in the field of radioactive waste management, named 'the Radioactive Waste Safety Standards (RADWASS) Programme'. The RADWASS programme is intended to establish and promote, in a coherent and comprehensive manner, the basic safety philosophy for radioactive waste management and the step necessary to ensure its implementation. And has main purposes that RADWASS publication will; (a) reflect the existing international consensus in the approaches and methodologies for a safe radioactive waste management, including disposal, and provide mechanisms to establish consensus where it does not yet exist; and (b) provide Member States with a comprehensive series of internationally agreed documents to assist in the derivation of and to complement national criteria, standards and practices. In progress, the programme was changed in 1996 its structure and documents preparation process as well as properties of RADWASS documents, the former phase was supervised by the International Radioactive Waste Management Advisory Committee (INWAC), and present phase is by the Waste Safety Standards Advisory Committee (WASSAC). Six safety series documents were published in the former programme, and several safety standards documents in the present RADWASS programme are in progress of publishing, some of them are expected to be published within several months. The overview and present status of the RADWASS programme including outline of those documents' contents already published and under the preparation are described in this report. (author)

The present status of the n-TOF facility at CERN

International Nuclear Information System (INIS)

Igashira, Masayuki

2005-01-01

The main aim of the n - TOF facility at CERN is to provide precise neutron cross-section data relevant to the R and D of accelerator driven systems, nuclear astrophysics, etc. It is composed of a spallation neutron source, a 187.5-m flight path, a variety of detectors, a data acquisition system, etc. A 20 GeV proton synchrotron is employed together with a lead target for the spallation neutron source. The measurement of capture and fission cross sections started in 2002 and had been performed until the mid of November in 2004. The capture and fission measurements were performed for 28 and 7 isotopes, respectively. The brief history, present status, and future plan of the n - TOF facility are reported. (author)

[Umbilical blood-gas status at cesarean section for breech presentation: a comparison with vertex presentation].

Science.gov (United States)

Haruta, M; Saeki, N; Naka, Y; Funato, T; Ohtsuki, Y

1989-10-01

Umbilical blood-gas status at elective cesarean section with oxygen inhalation for breech presentation (25 cases) was compared with that for vertex presentation (25 cases), so as to confirm the security of full-term breech fetuses delivered by cesarean section under spinal anesthesia. Umbilical arterial oxygen levels were significantly lower in the breech group (Mean PO2:18.9 mmHg; SO2:37.3%; Oxygen content:7.6 ml/dl). The number of hypoxemic fetuses was significantly higher in the breech group (the breech: 7; the vertex; 0). The other umbilical blood-gas values revealed no significant differences between the breech and vertex groups, and were within normal limits in both groups. Oxygen extraction in the breech (Mean: 49.0%) was higher than that in the vertex (32.9%). Therefore decreased umbilical blood flow in the breech was suggested. The incidence of depression at 1 minute after delivery in the breech infants (24%) was significantly higher than that in the vertex infants (0%). It became obvious in the breech that as the interval between the uterine incision and delivery increased, umbilical arterial blood tended to acidosis and the 1 minute Apgar score decreased. Cesarean section for breech presentation requires sufficient and optimal incisions of the abdominal wall and uterus as well as a skillful manual delivery technique, because the fetus or neonate should be protected against asphyxia resulting from umbilical compression and prolonged delivery interval.

Dengue vector control: present status and future prospects.

Science.gov (United States)

Yap, H H; Chong, N L; Foo, A E; Lee, C Y

1994-12-01

Dengue Fever (DF) and Dengue Haemorrhagic Fever (DHF) have been the most common urban diseases in Southeast Asia since the 1950s. More recently, the diseases have spread to Central and South America and are now considered as worldwide diseases. Both Aedes aegypti and Aedes albopictus are involved in the transmission of DF/DHF in Southeast Asian region. The paper discusses the present status and future prospects of Aedes control with reference to the Malaysian experience. Vector control approaches which include source reduction and environmental management, larviciding with the use of chemicals (synthetic insecticides and insect growth regulators and microbial insecticide), and adulticiding which include personal protection measures (household insecticide products and repellents) for long-term control and space spray (both thermal fogging and ultra low volume sprays) as short-term epidemic measures are discussed. The potential incorporation of IGRs and Bacillus thuringiensis-14 (Bti) as larvicides in addition to insecticides (temephos) is discussed. The advantages of using water-based spray over the oil-based (diesel) spray and the use of spray formulation which provide both larvicidal and adulticidal effects that would consequently have greater impact on the overall vector and disease control in DF/DHF are highlighted.

The present status of medical physics education and training in Europe: an EFOMP survey

DEFF Research Database (Denmark)

Eudaldo, T.; Olsen, K.

2008-01-01

The aim of this work is to present the results of an EFOMP's survey on the status of Education and Training of Medical Physics in Europe. This survey has been undertaken by EFOMP in 2005, to update the document "Policy Statement No. 1", which represents the starting point of the EFOMP recommendat......The aim of this work is to present the results of an EFOMP's survey on the status of Education and Training of Medical Physics in Europe. This survey has been undertaken by EFOMP in 2005, to update the document "Policy Statement No. 1", which represents the starting point of the EFOMP...... recommendations on Education and Training in Medical Physics. Ultimate results have been collected at the end of 2006. To perform the survey, a questionnaire was sent to 34 National Member Organisations (NMOs) for Medical Physics, to collect information on the present state of education and training in each...... European country. Twenty-five countries participated in the enquiry and responded to it. The most outstanding results are as follows: In all countries, the basic requirement to enter the Medical Physics education is a university degree. The length of this university education ranges from 2 to 5 years...

Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses.

Science.gov (United States)

Bracho, Maria A; Saludes, Verónica; Martró, Elisa; Bargalló, Ana; González-Candelas, Fernando; Ausina, Vicent

2008-06-05

Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region) are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest. We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence. In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.

Amplification of HER2 is a marker for global genomic instability

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Love Brad

2008-10-01

Full Text Available Abstract Background Genomic alterations of the proto-oncogene c-erbB-2 (HER-2/neu are associated with aggressive behavior and poor prognosis in patients with breast cancer. The variable clinical outcomes seen in patients with similar HER2 status, given similar treatments, suggests that the effects of amplification of HER2 can be influenced by other genetic changes. To assess the broader genomic implications of structural changes at the HER2 locus, we investigated relationships between genomic instability and HER2 status in patients with invasive breast cancer. Methods HER2 status was determined using the PathVysion® assay. DNA was extracted after laser microdissection from the 181 paraffin-embedded HER2 amplified (n = 39 or HER2 negative (n = 142 tumor specimens with sufficient tumor available to perform molecular analysis. Allelic imbalance (AI was assessed using a panel of microsatellite markers representing 26 chromosomal regions commonly altered in breast cancer. Student t-tests and partial correlations were used to investigate relationships between genomic instability and HER2 status. Results The frequency of AI was significantly higher (P P Conclusion The poor prognosis associated with HER2 amplification may be attributed to global genomic instability as cells with high frequencies of chromosomal alterations have been associated with increased cellular proliferation and aggressive behavior. In addition, high levels of DNA damage may render tumor cells refractory to treatment. In addition, specific alterations at chromosomes 11q13, 16q22-q24, and 18q21, all of which have been associated with aggressive tumor behavior, may serve as genetic modifiers to HER2 amplification. These data not only improve our understanding of HER in breast pathogenesis but may allow more accurate risk profiles and better treatment options to be developed.

Genomic evolution of 11 type strains within family Planctomycetaceae.

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Min Guo

Full Text Available The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes orthology system. Subsequently, we identified genomic islands (GIs and structural variations (SVs among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.

Nonextensive statistical mechanics: a brief review of its present status

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CONSTANTINO TSALLIS

2002-09-01

Full Text Available We briefly review the present status of nonextensive statistical mechanics. We focus on (i the central equations of the formalism, (ii the most recent applications in physics and other sciences, (iii the a priori determination (from microscopic dynamics of the entropic index q for two important classes of physical systems, namely low-dimensional maps (both dissipative and conservative and long-range interacting many-body hamiltonian classical systems.Revisamos sumariamente o estado presente da mecânica estatística não-extensiva. Focalizamos em (i as equacões centrais do formalismo; (ii as aplicações mais recentes na física e em outras ciências, (iii a determinação a priori (da dinâmica microscópica do índice entrópico q para duas classes importantes de sistemas físicos, a saber, mapas de baixa dimensão (tanto dissipativos quanto conservativos e sistemas clássicos hamiltonianos de muitos corpos com interações de longo alcance.

Present status of high-temperature engineering test reactor (HTTR) program

International Nuclear Information System (INIS)

Tanaka, Toshiyuki; Baba, Osamu; Shiozawa, Shusaku; Okubo, Minoru; Tobioka, Toshiaki

1994-01-01

The 30MWt HTTR is a high-temperature gas-cooled reactor (HTGR), with a maximum helium coolant temperature of 950degC at the reactor outlet. The construction of the HTTR started in March 1991, with first criticality to be followed in 1998 after commissioning testing. At present the HTTR reactor building (underground part) and its containment vessel have been almost completed and its main components, such as a reactor pressure vessel (RPV), an intermediate heat exchanger, hot gas pipings and graphite core structures, are now manufacturing at their factories at the target of their installation starting in 1994. The project is intended to establish and upgrade the technology basis necessary for HTGR developments. Japan Atomic Energy Research Institute (JAERI) also plans to conduct material and fuel irradiation tests as an innovative basic research after attaining rated power and coolant temperature. Innovative basic researches are now in great request. The paper describes major features of HTTR, present status of its construction and research and test using HTTR. (author)

Present status of High-Temperature engineering Test Reactor (HTTR) program

International Nuclear Information System (INIS)

Tanaka, Toshiyuki; Baba, Osamu; Shiozawa, Shusaku; Okubo, Minoru; Tobioka, Toshiaki

1993-01-01

The 30MWt HTTR is a high-temperature gas-cooled reactor (HTGR), with a maximum helium coolant temperature of 950 deg C at the reactor outlet. The construction of the HTTR started in March 1991, with first criticality to be followed in 1998 after commissioning testing. At present the HTTR reactor building (underground part) and its containment vessel have been almost completed and its main components, such as a reactor pressure vessel (RPV), an intermediate heat exchanger, hot gas pipings and graphite core structures, are now manufacturing at their factories at the target of their installation starting in 1994. The project is intended to establish and upgrade the technology basis necessary for HTGR developments. Japan Atomic Energy Research Institute (JAERI) also plans to conduct material and fuel irradiation tests as an innovative basic research after attaining rated power and coolant temperature. Innovative basic researches are now in great request. The paper describes major features of HTTR, present status of its construction and research and test plan using HTTR. (author)

A Thousand Fly Genomes: An Expanded Drosophila Genome Nexus.

Science.gov (United States)

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.

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.

The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases.

Science.gov (United States)

Maldonado, Lucas L; Assis, Juliana; Araújo, Flávio M Gomes; Salim, Anna C M; Macchiaroli, Natalia; Cucher, Marcela; Camicia, Federico; Fox, Adolfo; Rosenzvit, Mara; Oliveira, Guilherme; Kamenetzky, Laura

2017-02-27

The parasite Echinococcus canadensis (G7) (phylum Platyhelminthes, class Cestoda) is one of the causative agents of echinococcosis. Echinococcosis is a worldwide chronic zoonosis affecting humans as well as domestic and wild mammals, which has been reported as a prioritized neglected disease by the World Health Organisation. No genomic data, comparative genomic analyses or efficient therapeutic and diagnostic tools are available for this severe disease. The information presented in this study will help to understand the peculiar biological characters and to design species-specific control tools. We sequenced, assembled and annotated the 115-Mb genome of E. canadensis (G7). Comparative genomic analyses using whole genome data of three Echinococcus species not only confirmed the status of E. canadensis (G7) as a separate species but also demonstrated a high nucleotide sequences divergence in relation to E. granulosus (G1). The E. canadensis (G7) genome contains 11,449 genes with a core set of 881 orthologs shared among five cestode species. Comparative genomics revealed that there are more single nucleotide polymorphisms (SNPs) between E. canadensis (G7) and E. granulosus (G1) than between E. canadensis (G7) and E. multilocularis. This result was unexpected since E. canadensis (G7) and E. granulosus (G1) were considered to belong to the species complex E. granulosus sensu lato. We described SNPs in known drug targets and metabolism genes in the E. canadensis (G7) genome. Regarding gene regulation, we analysed three particular features: CpG island distribution along the three Echinococcus genomes, DNA methylation system and small RNA pathway. The results suggest the occurrence of yet unknown gene regulation mechanisms in Echinococcus. This is the first work that addresses Echinococcus comparative genomics. The resources presented here will promote the study of mechanisms of parasite development as well as new tools for drug discovery. The availability of a high

Clinical array-based karyotyping of breast cancer with equivocal HER2 status resolves gene copy number and reveals chromosome 17 complexity

International Nuclear Information System (INIS)

Gunn, Shelly; Gorre, Mercedes; Mohammed, Mansoor; Yeh, I-Tien; Lytvak, Irina; Tirtorahardjo, Budi; Dzidic, Natasha; Zadeh, Soheila; Kim, Jaeweon; McCaskill, Chris; Lim, Lony

2010-01-01

HER2 gene copy status, and concomitant administration of trastuzumab (Herceptin), remains one of the best examples of targeted cancer therapy based on understanding the genomic etiology of disease. However, newly diagnosed breast cancer cases with equivocal HER2 results present a challenge for the oncologist who must make treatment decisions despite the patient's unresolved HER2 status. In some cases both immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are reported as equivocal, whereas in other cases IHC results and FISH are discordant for positive versus negative results. The recent validation of array-based, molecular karyotyping for clinical oncology testing provides an alternative method for determination of HER2 gene copy number status in cases remaining unresolved by traditional methods. In the current study, DNA extracted from 20 formalin fixed paraffin embedded (FFPE) tissue samples from newly diagnosed cases of invasive ductal carcinoma referred to our laboratory with unresolved HER2 status, were analyzed using a clinically validated genomic array containing 127 probes covering the HER2 amplicon, the pericentromeric regions, and both chromosome 17 arms. Array-based comparative genomic hybridization (array CGH) analysis of chromosome 17 resolved HER2 gene status in [20/20] (100%) of cases and revealed additional chromosome 17 copy number changes in [18/20] (90%) of cases. Array CGH analysis also revealed two false positives and one false negative by FISH due to 'ratio skewing' caused by chromosomal gains and losses in the centromeric region. All cases with complex rearrangements of chromosome 17 showed genome-wide chromosomal instability. These results illustrate the analytical power of array-based genomic analysis as a clinical laboratory technique for resolution of HER2 status in breast cancer cases with equivocal results. The frequency of complex chromosome 17 abnormalities in these cases suggests that the two

Present status of research activities conducted by research group for heavy elements microbiology in JAERI

International Nuclear Information System (INIS)

Ohnuki, Toshihiko; Ozaki, Takuo; Yoshida, Takahiro

2004-01-01

It has been recognized that microbial transformations of radionuclides and toxic metals could be significant in the environment, but there is a paucity of information on the mechanisms of biotransformation of radionuclides by the microorganisms. An understanding at the fundamental level the mechanisms of mobilization, immobilization and bioavailability of radioactive elements in particular the actinides is important from the standpoint of mobility of actinides in the environment, disposal of radioactive wastes in deep geological formation, remediation of contaminated soils and materials, and development of strategies for the long-term stewardship of the contaminated sites. The microbiology research group in Japan Atomic Energy Research Institute (JAERI) is conducting basic scientific research on microbial interactions with actinides. Fundamental research on microbial transformations of actinides include elucidation of the mechanisms of dissolution and precipitation of various chemical forms such as ionic, oxides, organic and inorganic complexes of actinides by aerobic or anaerobic microorganisms under relevant microbial process conditions. State-of-the-art analytical techniques are used to determine the interaction of actinides with microorganisms at the molecular level to understand the structure function relationship. These techniques include time-resolved laser fluorescence spectroscopy (TRLFS) to determine the coordination number, oxidation states and the nearest neighbor by X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) at the Synchrotron Light Source, identification of functional groups by nuclear magnetic resonance (NMR), determination of chemical forms by transmission electron microscopy (TEM), and genomic (DNA) manipulation by molecular techniques. We here report the present status of our research activities on accumulation of lanthanides(III) by microorganisms, application of micro-particle induced X

Present status of NMCC and sample preparation method for bio-samples

International Nuclear Information System (INIS)

Futatsugawa, S.; Hatakeyama, S.; Saitou, S.; Sera, K.

1993-01-01

In NMCC(Nishina Memorial Cyclotron Center) we are doing researches on PET of nuclear medicine (Positron Emission Computed Tomography) and PIXE analysis (Particle Induced X-ray Emission) using a small cyclotron of compactly designed. The NMCC facilities have been opened to researchers of other institutions since April 1993. The present status of NMCC is described. Bio-samples (medical samples, plants, animals and environmental samples) have mainly been analyzed by PIXE in NMCC. Small amounts of bio-samples for PIXE are decomposed quickly and easily in a sealed PTFE (polytetrafluoroethylene) vessel with a microwave oven. This sample preparation method of bio-samples also is described. (author)

The Majorana Double Beta Decay Experiment: Present Status

Energy Technology Data Exchange (ETDEWEB)

Aguayo, Estanislao; Avignone, Frank T.; Back, Henning O.; Barabash, Alexander S.; Beene, Jim; Bergevin, M.; Bertrand, F.; Boswell, M.; Brudanin, V.; Busch, Matthew; Chan, Yuen-Dat; Christofferson, C. D.; Collar, J. I.; Combs, Dustin C.; Cooper, R. J.; Detwiler, Jason A.; Doe, Peter J.; Efremenko, Yuri; Egorov, Viatcheslav; Ejiri, H.; Elliott, S. R.; Esterline, James H.; Fast, James E.; Fields, N.; Finnerty, P.; Fraenkle, Florian; Gehman, Victor M.; Giovanetti, G. K.; Green, M. P.; Guiseppe, V. E.; Gusey, K.; Hallin, A. L.; Hazama, R.; Henning, Reyco; Hime, Andrew; Hoppe, Eric W.; Horton, Mark; Howard, Stanley; Howe, M. A.; Johnson, R. A.; Keeter, K.; Keller, C.; Kidd, M. F.; Knecht, A.; Kochetov, Oleg; Konovalov, S.; Kouzes, Richard T.; Laferriere, Brian D.; LaRoque, B. H.; Leon, Jonathan D.; Leviner, L.; Loach, J. C.; MacMullin, S.; Marino, Michael G.; Martin, R. D.; Mei, Dong-Ming; Merriman, Jason H.; Miller, M. L.; Mizouni, Leila; Nomachi, Masaharu; Orrell, John L.; Overman, Nicole R.; Phillips II, D. G.; Poon, Alan; Perumpilly, Gopakumar; Prior, Gersende; Radford, D. C.; Rielage, Keith; Robertson, R. G. H.; Ronquest, M. C.; Schubert, Alexis G.; Shima, T.; Shirchenko, M.; Snavely, Kyle J.; Steele, David; Strain, J.; Thomas, K.; Timkin, V.; Tornow, W.; Vanyushin, I.; Varner, R. L.; Vetter, Kai; Vorren, Kris R.; Wilkerson, J. F.; Yakushev, E.; Young, A.; Yu, Chang-Hong; Yumatov, Vladimir; Zhang, C.

2013-06-01

The Majorana collaboration is actively pursuing research and development aimed at a tonne-scale 76Ge neutrinoless double-beta decay experiment, an R&D effort that will field approximately 40 kg of germanium detectors with mixed enrichment levels. This article provides a status update on the construction of the Demonstrator

New Markov Model Approaches to Deciphering Microbial Genome Function and Evolution: Comparative Genomics of Laterally Transferred Genes

Energy Technology Data Exchange (ETDEWEB)

Borodovsky, M.

2013-04-11

Algorithmic methods for gene prediction have been developed and successfully applied to many different prokaryotic genome sequences. As the set of genes in a particular genome is not homogeneous with respect to DNA sequence composition features, the GeneMark.hmm program utilizes two Markov models representing distinct classes of protein coding genes denoted "typical" and "atypical". Atypical genes are those whose DNA features deviate significantly from those classified as typical and they represent approximately 10% of any given genome. In addition to the inherent interest of more accurately predicting genes, the atypical status of these genes may also reflect their separate evolutionary ancestry from other genes in that genome. We hypothesize that atypical genes are largely comprised of those genes that have been relatively recently acquired through lateral gene transfer (LGT). If so, what fraction of atypical genes are such bona fide LGTs? We have made atypical gene predictions for all fully completed prokaryotic genomes; we have been able to compare these results to other "surrogate" methods of LGT prediction.

Application of Genomic In Situ Hybridization in Horticultural Science

Directory of Open Access Journals (Sweden)

Fahad Ramzan

2017-01-01

Full Text Available Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example, Diospyros hybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such as Clivia, Rhododendron, and Lycoris ornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH techniques in horticultural plants.

From undocumented to lawfully present: Do changes to legal status impact psychological wellbeing among latino immigrant young adults?

Science.gov (United States)

Patler, Caitlin; Laster Pirtle, Whitney

2018-02-01

Exclusionary immigration policies, as a form of structural racism, have led to a sizeable undocumented population that is largely barred from access to resources in the United States. Existing research suggests that undocumented immigration status detrimentally impacts mobility, yet few studies have tested the impacts of legal status on psychological wellbeing. Most importantly, we know little about how changes to legal status impact wellbeing. Announced in 2012, the Deferred Action for Childhood Arrivals (DACA) program allows eligible undocumented youth to apply for temporary lawful status. Drawing on cross-sectional survey data from 487 Latino immigrant young adults in California collected in 2014 and 2015, we analyze the predictors of three specialized outcomes related to immigrants' psychological wellbeing-distress, negative emotions, and deportation worry before and after a transition from undocumented to lawfully present status. Results show that retrospective reports of past psychological wellness, when all respondents were undocumented, are predicted primarily by socioeconomic status. However, reports of current psychological wellness are predicted by DACA status. Our results demonstrate, for the first time, the positive emotional consequences of transitioning out of undocumented status for immigrant young adults. Copyright © 2017 Elsevier Ltd. All rights reserved.

Progress and present status of ITER cryoline system

International Nuclear Information System (INIS)

Badgujar, S.; Bonneton, M.; Chalifour, M.; Forgeas, A.; Serio, L.; Sarkar, B.; Shah, N.

2014-01-01

The cryoline system at ITER forms a very complex network localized inside the Tokamak building, on a dedicated plant bridge and in cryoplant areas. The cooling power produced in the cryoplant is distributed via these lines with a total length of about 3.7 km and interconnecting all the cold boxes of the cryogenic system as well as the cold boxes of various clients (magnets, cryopumps and thermal shield). Distinct layouts and polygonal geometry, nuclear safety and confinement requirements, difficult installation and in-service inspection/repair demand very high reliability and availability for the cryolines. The finalization of the building-embedded plates for supporting the lines, before the detailed design, has made this project technologically more challenging. The conceptual design phase has been completed and procurement arrangements have been signed with India, responsible for providing the system of cryolines and warm lines to ITER, as in kind contribution. The prototype test for the design and performance validation has been planned on a representative cryoline section. After describing the basic features and general layout of the ITER cryolines, the paper presents key design requirements, conceptual design approach, progress and status of the cryolines project as well as challenges to build such a complex cryoline system

An overview of the present status of food irradiation and its prospect in Malaysia

International Nuclear Information System (INIS)

Muhammad bin Lebai Juri

1984-01-01

The paper seeks to review the present state of development in the food irradiation as a post harvest preservation technique. Brief discussion is focussed on the past and current status of the subject. The application of this method in Malaysia is explored due to its potential to be succesfully implemented. The prospect of its application is also highlighted. (author)

Present status and future plan of the research using HIMAC of NIRS

International Nuclear Information System (INIS)

Kawachi, Kiyomitsu

1996-01-01

The Heavy Ion Medical Accelerator in Chiba (HIMAC) was completed in 1993, and since June of 1994 heavy ion therapy has made a new start at this facility after closed-down of the BEVALAC accelerator at LBL in Berkeley, California in 1992. The HIMAC is also opened for the researchers of outside of NIRS as well as the clinical trial of the heavy ion therapy. In this report, I will describe on the present status of HIMAC facility, the beam characteristics and the future developments of HIMAC. (author)

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.

Unsupervised Analysis of Array Comparative Genomic Hybridization Data from Early-Onset Colorectal Cancer Reveals Equivalence with Molecular Classification and Phenotypes

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María Arriba

2017-01-01

Full Text Available AIM: To investigate whether chromosomal instability (CIN is associated with tumor phenotypes and/or with global genomic status based on MSI (microsatellite instability and CIMP (CpG island methylator phenotype in early-onset colorectal cancer (EOCRC. METHODS: Taking as a starting point our previous work in which tumors from 60 EOCRC cases (≤45 years at the time of diagnosis were analyzed by array comparative genomic hybridization (aCGH, in the present study we performed an unsupervised hierarchical clustering analysis of those aCGH data in order to unveil possible associations between the CIN profile and the clinical features of the tumors. In addition, we evaluated the MSI and the CIMP statuses of the samples with the aim of investigating a possible relationship between copy number alterations (CNAs and the MSI/CIMP condition in EOCRC. RESULTS: Based on the similarity of the CNAs detected, the unsupervised analysis stratified samples into two main clusters (A, B and four secondary clusters (A1, A2, B3, B4. The different subgroups showed a certain correspondence with the molecular classification of colorectal cancer (CRC, which enabled us to outline an algorithm to categorize tumors according to their CIMP status. Interestingly, each subcluster showed some distinctive clinicopathological features. But more interestingly, the CIN of each subcluster mainly affected particular chromosomes, allowing us to define chromosomal regions more specifically affected depending on the CIMP/MSI status of the samples. CONCLUSIONS: Our findings may provide a basis for a new form of classifying EOCRC according to the genomic status of the tumors.

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/.

Meeting Report: The Twelfth International Mouse Genome Conference

Energy Technology Data Exchange (ETDEWEB)

Manolakou, Katerina; Cross, Sally H.; Simpson, Eleanor H.; Jackson, Ian J.

1998-10-01

The annual International Mouse Genome Conference (IMGC) is where, scientifically speaking, classical mouse genetics meets the relative newcomer of genomics. The 12th meeting took place last October in the delightful Bavarian village of Garmisch-Partenkirchen, and we were greeted by the sight on the mountains of the first snowfall of the season. However the discussions left little time for exploration. Minds of participants in Garmisch were focused by a recent document produced by the NIH and by discussions within other funding agencies worldwide. If implemented, the proposals will further enhance the status of the mouse as the principal model for study of the function of the human genome.

Genome U-Plot: a whole genome visualization.

Science.gov (United States)

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.

Present status of dibaryons

International Nuclear Information System (INIS)

Locher, M.P.

1981-01-01

In the present notes the author tries to assess the situation regarding dibaryons in the various channels with baryon number two, emphasizing the problems and discussing in greater detail the most recent developments since the Versailles Conference. One of the motivations for the present search of B=2 states is the possibility of colored subclusters for systems with six quarks which cannot occur for ordinary baryons or mesons. (Auth.)

Correcting Inconsistencies and Errors in Bacterial Genome Metadata Using an Automated Curation Tool in Excel (AutoCurE).

Science.gov (United States)

Schmedes, Sarah E; King, Jonathan L; Budowle, Bruce

2015-01-01

Whole-genome data are invaluable for large-scale comparative genomic studies. Current sequencing technologies have made it feasible to sequence entire bacterial genomes with relative ease and time with a substantially reduced cost per nucleotide, hence cost per genome. More than 3,000 bacterial genomes have been sequenced and are available at the finished status. Publically available genomes can be readily downloaded; however, there are challenges to verify the specific supporting data contained within the download and to identify errors and inconsistencies that may be present within the organizational data content and metadata. AutoCurE, an automated tool for bacterial genome database curation in Excel, was developed to facilitate local database curation of supporting data that accompany downloaded genomes from the National Center for Biotechnology Information. AutoCurE provides an automated approach to curate local genomic databases by flagging inconsistencies or errors by comparing the downloaded supporting data to the genome reports to verify genome name, RefSeq accession numbers, the presence of archaea, BioProject/UIDs, and sequence file descriptions. Flags are generated for nine metadata fields if there are inconsistencies between the downloaded genomes and genomes reports and if erroneous or missing data are evident. AutoCurE is an easy-to-use tool for local database curation for large-scale genome data prior to downstream analyses.

Complete mitochondrial genome of the Indian peafowl (Pavo cristatus), with phylogenetic analysis in phasianidae.

Science.gov (United States)

Zhou, Tai-Cheng; Sha, Tao; Irwin, David M; Zhang, Ya-Ping

2015-01-01

Pavo cristatus, known as the Indian peafowl, is endemic to India and Sri Lanka and has been domesticated for its ornamental and food value. However, its phylogenetic status is still debated. Here, to clarify the phylogenetic status of P. cristatus within Phasianidae, we analyzed its mitochondrial genome (mtDNA). The complete mitochondrial DNA (mtDNA) genome was determined using 34 pairs of primers. Our data show that the mtDNA genome of P. cristatus is 16,686 bp in length. Molecular phylogenetic analyses of P. cristatus was performed along with 22 complete mtDNA genomes belonging to other species in Phasianidae using Bayesian and maximum likelihood methods, where Aythya americana and Anas platyrhynchos were used as outgroups. Our results show that P. critatus has its closest genetic affinity with Pavo muticus and belongs to clade that contains Gallus, Bambusicola and Francolinus.

Electricity in Europe. Present status and prospects for the 1990s

Energy Technology Data Exchange (ETDEWEB)

Holmes, A

1986-01-01

Europe's electricity industry is entering a period of extreme uncertainty. This report sets out the reasons for this and tabulates the current electricity capacity in Europe. Chapter 2 considers the Electricity trade in Europe. Chapter 3 concentrates on nuclear power. In this, nuclear energy consumption in 1974 -1984, estimates of total and nuclear electricity generation to 2000, the European nuclear reactor types and the performance of reactors are tabulated. Nuclear power stations under construction are listed. A forecast is made of European nuclear capacity to 2000. The status of nuclear power in 1986 in Europe is summarized country by country. The future of nuclear power in Europe, following the Chernobyl reactor accident is considered, taking the situation in each country separately. Chapter 4 considers Electricity and the Environment, Chapter 5 looks at the prices of electricity in Europe, Chapter 6 is a country by country profile which presents the present and predicted electricity power situation in that country.

Electricity in Europe. Present status and prospects for the 1990s

International Nuclear Information System (INIS)

Holmes, Andrew.

1986-01-01

Europe's electricity industry is entering a period of extreme uncertainty. This report sets out the reasons for this and tabulates the current electricity capacity in Europe. Chapter 2 considers the Electricity trade in Europe. Chapter 3 concentrates on nuclear power. In this, nuclear energy consumption in 1974 -1984, estimates of total and nuclear electricity generation to 2000, the European nuclear reactor types and the performance of reactors are tabulated. Nuclear power stations under construction are listed. A forecast is made of European nuclear capacity to 2000. The status of nuclear power in 1986 in Europe is summarized country by country. The future of nuclear power in Europe, following the Chernobyl reactor accident is considered, taking the situation in each country separately. Chapter 4 considers Electricity and the Environment, Chapter 5 looks at the prices of electricity in Europe, Chapter 6 is a country by country profile which presents the present and predicted electricity power situation in that country. (UK)

Present status of the ion ring compressor approach to fusion

International Nuclear Information System (INIS)

Fleischmann, H.H.

1975-01-01

A short review is given of the present research status with regard to the Ion Ring Compressor. A consideration of the reactor characteristics of this fusion scheme indicates the potential for a number of technologically and economically interesting features, in particular with respect to the high-confinement characteristics expected for such minimum-B configurations. Experimental results from the RECE-program at Cornell indicate generally good gross stability of strong electron rings, including purely collisional decay, stability against field perturbations and others. Most-recent experiments have extended the ring lifetime to more than 2 x 10 5 electron orbits. Strong electron rings have been shifted over an axial distance of up to 30 cm. Experiments with magnetic-field insulated diodes indicate ion pulses of up to 300 nsec, and field insulation of up to 800 nsec when metallic electrodes are used

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...

Creutzfeldt-Jakob Disease Presenting as Expressive Aphasia and Nonconvulsive Status Epilepticus

Directory of Open Access Journals (Sweden)

Hafiz B. Mahboob

2018-01-01

Full Text Available Creutzfeldt-Jakob disease (CJD, the most common form of human prion diseases, is a fatal condition with a mortality rate reaching 85% within one year of clinical presentation. CJD is characterized by rapidly progressive neurological deterioration in combination with typical electroencephalography (EEG and magnetic resonance imaging (MRI findings and positive cerebrospinal spinal fluid (CSF analysis for 14-3-3 proteins. Unfortunately, CJD can have atypical clinical and radiological presentation in approximately 10% of cases, thus making the diagnosis often challenging. We report a rare clinical presentation of sporadic CJD (sCJD with combination of both expressive aphasia and nonconvulsive status epilepticus. This patient presented with slurred speech, confusion, myoclonus, headaches, and vertigo and succumbed to his disease within ten weeks of initial onset of his symptoms. He had a normal initial diagnostic workup, but subsequent workup initiated due to persistent clinical deterioration revealed CJD with typical MRI, EEG, and CSF findings. Other causes of rapidly progressive dementia and encephalopathy were ruled out. Though a rare condition, we recommend consideration of CJD on patients with expressive aphasia, progressive unexplained neurocognitive decline, and refractory epileptiform activity seen on EEG. Frequent reimaging (MRI, video EEGs and CSF examination might help diagnose this fatal condition earlier.

Present status of unsealed radioisotope therapy in Japan based on the nation-wide questionnaire

International Nuclear Information System (INIS)

Oyamada, Hiyoshimaru

1999-01-01

In Japan, clinical application of unsealed radioisotopes is strictly regulated. Especially in the field of therapy, we are allowed to use only Na 131 I at present. Under such circumstances, the present status of therapeutic nuclear medicine in Japan was surveyed by means of a nation-wide questionnaire, conducted in 193 hospitals. Then, 113 hospitals replied to such questionnaire (recovery rate: 58.5%), and it was found that in 77 hospitals, radioisotope therapy is being performed for Graves' disease and/or thyroid cancer. The questionnaire covered the following points: for Graves' disease-the basic strategy of 131 I therapy, its indications, absorbed doses planned to be given, whether the therapy had been conducted on outpatient basis or in-patient basis, method of thyroid weight estimation, interval of administration in case of multiple doses, number of patients treated per year (1996) etc., and for thyroid cancer-strategy for thyroid remnant, the doses to be given, the maximum doses permitted by the authorities in each hospital both per day and per year, handling of highly contaminated urine in each hospital, interval of administration in case of multiple doses, number of patients treated per year (1996) etc. Also questioned were dissatisfaction with the present regulation by the authorities and/or requests for the better daily work, if any. Based on the above questionnaire, the present status of unsealed radioisotope therapy in Japan was investigated. (author)

Construction, characteristics and present status of high-fluence irradiation facility at University of Tokyo

International Nuclear Information System (INIS)

Tabata, Yoneho; Kobayashi, Hitoshi; Tagawa, Seiichi; Kouchi, Noriyuki.

1989-01-01

New ion accelerator facility (HIT Facility) was constructed at Research Center for Nuclear Science and Technology, University of Tokyo. This facility, which was equipped with some special apparatus, has been mainly dedicated to the study of radiation effects of ion beams on materials. In this report, the construction, the characteristics and the present status of this facility are described. (author)

Status of the present ATLAS RPC system and overview towards HL-LHC

CERN Document Server

Alberghi, Gian Luigi; The ATLAS collaboration

2018-01-01

The RPC system covers the barrel region of the ATLAS muon spectrometer in the pseudo-rapidity range of |eta|<1.05 with six independent detector layers, and solely provides the L1 trigger signal and the track coordinate in the non-bending plane of the muon candidates. The system has been designed to operate up to the nominal LHC luminosity (1e34cm-2s-1) which has been already exceeded thanks to the excellent performance of the collider. The experience in operating the present RPC system, up to the maximum instantaneous luminosity of 2.05 x 1e34 cm-2 s-1 reached in 2017, is reported. The performance of the system, in the severe background and pileup conditions of the last data taking period, is presented together with the improved tools implemented in order to have an effective monitoring of the detector status. The plans to successfully operate the present system during the HL-LHC phase are also introduced.

Mumps vaccine virus genome is present in throat swabs obtained from uncomplicated healthy recipients.

Science.gov (United States)

Nagai, T; Nakayama, T

2001-01-08

Seven children were followed for up to 42 days post-vaccination with live mumps vaccine and 37 throat swabs were obtained serially. Viral genomic RNA was detected by reverse transcription-polymerase chain reaction (RT-PCR) in the phosphoprotein (P) and hemagglutinin-neuraminidase (HN) regions. Virus isolation was also attempted. Genomic differentiation of detected mumps virus genome was performed by sequence analysis and/or restriction fragment length polymorphism (RFLP). No adverse reaction was observed in these children. Although mumps virus was not isolated from any of the samples, viral RNA was detected in four samples from three vaccine recipients, 18, 18 and 26, and 7 days after vaccination, respectively. Detected viral RNA was identified as the vaccine strain. Our data suggests that vaccine virus inoculated replicates in the parotid glands but the incidence of virus transmission from recipients to other susceptible subjects should be low.

QUALITY ASSURANCE IN SECONDARY EDUCATION PROGRAME OF BANGLADESH OPEN UNIVERSITY: Present Status and Challenges

Directory of Open Access Journals (Sweden)

Zobaida AKHTER

2008-04-01

Full Text Available In the present day in national and international perspectives, quality is the top of most agendas. Quality of education has significant impact and invaluable contribution to the area of development. Recently, the SSC & HSC program of BOU have earned recognition of equivalency with the formal education sector, which has naturally raised the question of quality assurance of these programs By applying the quantitative method, the study has assessed the present status of the quality of SSC & HSC program of BOU and also put some recommendations to meet the challenges for further development.

Neutrino Oscillations Present Status and Future Plans

CERN Document Server

Thomas, Jennifer

2008-01-01

This book reviews the status of a very exciting field - neutrino oscillations - at a very important time. The fact that neutrinos have mass has only been proved in the last few years and the acceptance of that fact has opened up a whole new area of study to understand the fundamental parameters of the mixing matrix. The book summarizes the results from all the experiments which have played a role in the measurement of neutrino oscillations and briefly describes the scope of some new planned experiments. Contributions include a theoretical introduction by Stephen Parke from FNAL, as well as art

Clinical presentation and visual status of retinitis pigmentosa patients: a multicenter study in southwestern Nigeria

Directory of Open Access Journals (Sweden)

Onakpoya OH

2016-08-01

Full Text Available Oluwatoyin Helen Onakpoya,1 Caroline Olufunlayo Adeoti,2 Tunji Sunday Oluleye,3 Iyiade Adeseye Ajayi,4 Timothy Majengbasan,4,5 Olayemi Kolawole Olorundare1 1Department of Ophthalmology, Obafemi Awolowo University Teaching Hospital, Ile-Ife, 2Department of Ophthalmology, Ladoke Akintola University of Technology Teaching Hospital, Osogbo, 3Department of Ophthalmology, University College Hospital, Ibadan, 4Department of Ophthalmology, University Teaching Hospital, Ado-Ekiti, 5Department of Ophthalmology, Federal Medical Centre, Ido-Ekiti, Nigeria Background: To review the visual status and clinical presentation of patients with retinitis pigmentosa (RP.Methodology: Multicenter, retrospective, and analytical review was conducted of the visual status and clinical characteristics of patients with RP at first presentation from January 2007 to December 2011. Main outcome measure was the World Health Organization’s visual status classification in relation to sex and age at presentation. Data analysis by SPSS (version 15 and statistical significance was assumed at P<0.05.Results: One hundred and ninety-two eyes of 96 patients with mean age of 39.08±18.5 years and mode of 25 years constituted the study population; 55 (57.3% were males and 41 (42.7% females. Loss of vision 67 (69.8% and night blindness 56 (58.3% were the leading symptoms. Twenty-one (21.9% patients had a positive family history, with RP present in their siblings 15 (71.4%, grandparents 11 (52.3%, and parents 4 (19.4%. Forty (41.7% were blind at presentation and 23 (24% were visually impaired. Blindness in six (15% patients was secondary to glaucoma. Retinal vascular narrowing and retinal pigmentary changes of varying severity were present in all patients. Thirty-five (36.5% had maculopathy, 36 (37.5% refractive error, 19 (20% lenticular opacities, and eleven (11.5% had glaucoma. RP was typical in 85 patients (88.5%. Older patients had higher rates of blindness at presentation (P=0

Comparative genomics of the Bifidobacterium breve taxon

NARCIS (Netherlands)

Bottacini, Francesca; O'Connell Motherway, Mary; Kuczynski, Justin; O'Connell, Kerry Joan; Serafini, Fausta; Duranti, Sabrina; Milani, Christian; Turroni, Francesca; Lugli, Gabriele Andrea; Zomer, Aldert|info:eu-repo/dai/nl/304642754; Zhurina, Daria; Riedel, Christian; Ventura, Marco; van Sinderen, Douwe

2014-01-01

BACKGROUND: Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium

Present status of doctors' awareness for radiation-induced carotid artery disease in Japan

International Nuclear Information System (INIS)

Taguchi, Yoshiharu; Takashima, Shutaro; Tanaka, Kortaro

2013-01-01

Radiation-induced carotid artery disease (RCAD) often develops in patients who have received neck radiotherapy for the treatment of various malignant tumors. However, the doctors who ordered or performed neck radiotherapy seem to pay little attention to RCAD which may subsequently occur, and the present status of the awareness in these doctors for RCAD is unclear in Japan. Therefore, we conducted a questionnaire survey of the present status of these doctors' awareness for RCAD. A questionnaire form regarding the recognition of RCAD was sent to 368 departments of otolaryngology, oral surgery, or radiology of university hospitals in Japan. Responses to the questionnaire were received from 213 of the 368 departments of otolaryngology, oral surgery or radiology of university hospitals (response collection rate: 57.9%). One hundred and sixty-one departments (75.9%) were aware of the existence of RCAD, but only 20 departments (9.4%) conducted regular examinations for RCAD after neck radiotherapy such as ultrasound neck echography and MR angiography. Only 6.3% departments took preventive measures for RCAD such as reduction in radiation dose or administration of antiplatelets. The present survey revealed that many patients who had undergone neck radiotherapy for the treatment of malignancy did not receive proper medical attention for RCAD in Japan. Healthcare providers should be given adequate education about RCAD including its risk factors, possible preventive measures, diagnostic modalities, and treatment. Furthermore, a systematic clinical network should be established in which stroke specialists conduct proper examinations for early diagnosis of RCAD. (author)

Present status of computational tools for maglev development

Energy Technology Data Exchange (ETDEWEB)

Wang, Z.; Chen, S.S.; Rote, D.M.

1991-10-01

High-speed vehicles that employ magnetic levitation (maglev) have received great attention worldwide as a means of relieving both highway and air-traffic congestion. At this time, Japan and Germany are leading the development of maglev. After fifteen years of inactivity that is attributed to technical policy decisions, the federal government of the United States has reconsidered the possibility of using maglev in the United States. The National Maglev Initiative (NMI) was established in May 1990 to assess the potential of maglev in the United States. One of the tasks of the NMI, which is also the objective of this report, is to determine the status of existing computer software that can be applied to maglev-related problems. The computational problems involved in maglev assessment, research, and development can be classified into two categories: electromagnetic and mechanical. Because most maglev problems are complicated and difficult to solve analytically, proper numerical methods are needed to find solutions. To determine the status of maglev-related software, developers and users of computer codes were surveyed. The results of the survey are described in this report. 25 refs.

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...

Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses

Directory of Open Access Journals (Sweden)

Bargalló Ana

2008-06-01

Full Text Available Abstract Background Hepatitis C virus isolates have been classified into six main genotypes and a variable number of subtypes within each genotype, mainly based on phylogenetic analysis. Analyses of the genetic relationship among genotypes and subtypes are more reliable when complete genome sequences (or at least the full coding region are used; however, so far 31 of 80 confirmed or proposed subtypes have at least one complete genome available. Of these, 20 correspond to confirmed subtypes of epidemic interest. Results We present and analyse the first complete genome sequence of a HCV subtype 1g isolate. Phylogenetic and genetic distance analyses reveal that HCV-1g is the most divergent subtype among the HCV-1 confirmed subtypes. Potential genomic recombination events between genotypes or subtype 1 genomes were ruled out. We demonstrate phylogenetic congruence of previously deposited partial sequences of HCV-1g with respect to our sequence. Conclusion In light of this, we propose changing the current status of its subtype-specific designation from provisional to confirmed.

Genomic context drives transcription of insertion sequences in the bacterial endosymbiont Wolbachia wVulC.

Science.gov (United States)

Cerveau, Nicolas; Gilbert, Clément; Liu, Chao; Garrett, Roger A; Grève, Pierre; Bouchon, Didier; Cordaux, Richard

2015-06-10

Transposable elements (TEs) are DNA pieces that are present in almost all the living world at variable genomic density. Due to their mobility and density, TEs are involved in a large array of genomic modifications. In eukaryotes, TE expression has been studied in detail in several species. In prokaryotes, studies of IS expression are generally linked to particular copies that induce a modification of neighboring gene expression. Here we investigated global patterns of IS transcription in the Alphaproteobacterial endosymbiont Wolbachia wVulC, using both RT-PCR and bioinformatic analyses. We detected several transcriptional promoters in all IS groups. Nevertheless, only one of the potentially functional IS groups possesses a promoter located upstream of the transposase gene, that could lead up to the production of a functional protein. We found that the majority of IS groups are expressed whatever their functional status. RT-PCR analyses indicate that the transcription of two IS groups lacking internal promoters upstream of the transposase start codon may be driven by the genomic environment. We confirmed this observation with the transcription analysis of individual copies of one IS group. These results suggest that the genomic environment is important for IS expression and it could explain, at least partly, copy number variability of the various IS groups present in the wVulC genome and, more generally, in bacterial genomes. Copyright © 2015 Elsevier B.V. All rights reserved.

The Majorana Double Beta Decay Experiment:. Present Status

Science.gov (United States)

Aguayo, E.; Avignone, F. T.; Back, H. O.; Barabash, A. S.; Beene, J. R.; Bergevin, M.; Bertrand, F. E.; Boswell, M.; Brudanin, V.; Busch, M.; Chan, Y.-D.; Christofferson, C. D.; Collar, J. I.; Combs, D. C.; Cooper, R. J.; Detwiler, J. A.; Doe, P. J.; Efremenko, Yu.; Egorov, V.; Ejiri, H.; Elliott, S. R.; Esterline, J.; Fast, J. E.; Fields, N.; Finnerty, P.; Fraenkle, F. M.; Gehman, V. M.; Giovanetti, G. K.; Green, M. P.; Guiseppe, V. E.; Gusey, K.; Hallin, A. L.; Hazama, R.; Henning, R.; Hime, A.; Hoppe, E. W.; Horton, M.; Howard, S.; Howe, M. A.; Johnson, R. A.; Keeter, K. J.; Keller, C.; Kidd, M. F.; Knecht, A.; Kochetov, O.; Konovalov, S. I.; Kouzes, R. T.; Laferriere, B. D.; Laroque, B. H.; Leon, J.; Leviner, L. E.; Loach, J. C.; Macmullin, S.; Marino, M. G.; Martin, R. D.; Mei, D.-M.; Merriman, J. H.; Miller, M. L.; Mizouni, L.; Nomachi, M.; Orrell, J. L.; Overman, N. R.; Phillips, D. G.; Poon, A. W. P.; Perumpilly, G.; Prior, G.; Radford, D. C.; Rielage, K.; Robertson, R. G. H.; Ronquest, M. C.; Schubert, A. G.; Shima, T.; Shirchenko, M.; Snavely, K. J.; Steele, D.; Strain, J.; Thomas, K.; Timkin, V.; Tornow, W.; Vanyushin, I.; Varner, R. L.; Vetter, K.; Vorren, K.; Wilkerson, J. F.; Yakushev, E.; Young, A. R.; Yu, C.-H.; Yumatov, V. I.; Zhang, C.

2013-11-01

The Majorana collaboration is actively pursuing research and development aimed at a tonne-scale 76Ge neutrinoless double-beta decay (0νββ) experiment. The current, primary focus is the construction of the Majorana Demonstrator experiment, an R&D effort that will field approximately 40 kg of germanium detectors with mixed enrichment levels. This article provides a status update on the construction of the Demonstrator.

Present status of uranium resource development in foreign countries, 1984

International Nuclear Information System (INIS)

1984-12-01

The book of the same title as this one was published in 1983. Since then, the situation requiring the correction of the contents, such as the correction of uranium resource policy in various countries accompanying the change of uranium market condition and the change of uranium policy in Australia due to the political situation, has occurred, consequently, the revision has been made adding these new information. The confirmed resources of uranium and the resources of uranium to be added by estimation in the free world are tabulated. About each country, the organization and policy, the policy of exporting uranium and the present status of the export, the quantity of uranium resources, the production of uranium, the state of exploration and development and so on are reported. Japan has taken part in the development of uranium resources in Australia, Canada, Gabon, Zambia, Morocco, Guinea, Mali and so on. (Kako, I.)

The prevalence of the HPV 16 genome, integrated viral status and p53 genotype in cervical cancer population of north-eastern Hungary, the correlation with the established markers of tumour progression.

Science.gov (United States)

Hernádi, Zoltán; Sápy, Tamás; Krasznai, Zoárd T

2004-03-15

To evaluate the prevalence of the HPV 16 integrated status and the p53 genotype in cervical cancer in north-eastern Hungary and their correlation with the established prognostic factors. Parallel with the routine histological examination, Southern blot hybridisation and multiplex PCRs were used to detect type/physical state of HPV DNA in primary tumours and in regional lymph nodes combined with p53 genotyping of 83 patients. 46.9% (39/83) prevalence rate of HPV 16 genome was found. The frequency of viral integration (76.9% in primary tumours and 95.2% in regional lymph nodes) and that of the p53Arg homozygous genotype (64.1%) proved to be higher than reported from other parts of the world. The HPV 16 integration and the p53 genotype, failed to correlate with the FIGO stage and lymphatic spread. The prevalence of the integrated status of the HPV 16 genome combined with homozygous p53Arg genotype is relatively high in Hungary. These factors however failed to show a strong correlation with the established markers of tumour progression.

Present status and future trend of radiation chemistry and its application

International Nuclear Information System (INIS)

Tabata, Yoneho

1977-01-01

The recent reports or reviews on the results of basic study of radiation chemistry were introduced. Especially, vapor-phase radiation chemistry, electron behavior in liquid glass and molecular crystal were reviewed. The basic study of radiation chemistry which has attracted much attention contains the short-life pico-second pulse radiolysis, the study on the effect of LET and the study by ESR in the various fields. The present status of these studies were explained as well as the chemistry of positron e + and positronium Ps. As the studies of radiation chemistry in the field of macromolecules, radiation polymerization, degradation of polymer and the graft-polymerization were reviewed to discuss the prospective development and problem for its industrial application. (Kobatake, H.)

Present status and future perspectives of research and test reactor in Japan

International Nuclear Information System (INIS)

Kaneko, Yoshihiko; Kaieda, Keisuke

2000-01-01

Since 1957, Japan Atomic Energy Research Institute (JAERI) has constructed several research and test reactors to fulfill a major role in the study of nuclear energy and fundamental research. At present four reactors, the Japan Research Reactor No. 3 and No. 4 (JRR-3M and JRR-4 respectively), the Japan Materials Testing Reactor (JMTR) and the Nuclear Safety Research Reactor (NSRR) are in operation, and a new High Temperature Engineering Test Reactor (HTTR) has recently reached first criticality and now in the power up test. In 1966, the Kyoto University built the Kyoto University Reactor (KUR) and started its operation for joint use program of the Japanese universities. This paper introduces these reactors and describes their present operational status and also efforts for aging management. The recent tendency of utilization and future perspectives is also reported. (author)

Present status and future perspectives of research and test reactor in Japan

Energy Technology Data Exchange (ETDEWEB)

Kaneko, Yoshihiko [Atomic Energy Research Laboratory, Musashi Institute of Technology, Kawasaki, Kanagawa (Japan); Kaieda, Keisuke [Department of Research Reactor, Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan)

2000-10-01

Since 1957, Japan Atomic Energy Research Institute (JAERI) has constructed several research and test reactors to fulfill a major role in the study of nuclear energy and fundamental research. At present four reactors, the Japan Research Reactor No. 3 and No. 4 (JRR-3M and JRR-4 respectively), the Japan Materials Testing Reactor (JMTR) and the Nuclear Safety Research Reactor (NSRR) are in operation, and a new High Temperature Engineering Test Reactor (HTTR) has recently reached first criticality and now in the power up test. In 1966, the Kyoto University built the Kyoto University Reactor (KUR) and started its operation for joint use program of the Japanese universities. This paper introduces these reactors and describes their present operational status and also efforts for aging management. The recent tendency of utilization and future perspectives is also reported. (author)

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.

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...

Type 2 diabetes genes – Present status and data from Norwegian studies

Directory of Open Access Journals (Sweden)

Jens K. Hertel Hertel

2013-06-01

Full Text Available The worldwide rise in prevalence of type 2 diabetes has led to an intense search for the genetic risk factors of this disease. In type 2 diabetes and other complex disorders, multiple genetic and environmental factors, as well as the interaction between these factors, determine the phenotype. In this review, we summarize present knowledge, generated by more than two decades of efforts to dissect the genetic architecture of type 2 diabetes. Initial studies were either based on a candidate gene approach or attempted to fine-map signals generated from linkage analysis. Despite the detection of multiple genomic regions proposed to be linked to type 2 diabetes, subsequent positional fine-mapping of candidates were mostly inconclusive. However, the introduction of genome-wide association studies (GWAS, applied on thousands of patients and controls, completely changed the field. To date, more than 50 susceptibility loci for type 2 diabetes have been detected through the establishment of large research consortia, the application of GWAS on intermediary diabetes phenotypes and the use of study samples of different ethnicities. Still, the common variants identified in the GWAS era only explain some of the heritability seen for type 2 diabetes. Thus, focus is now shifting towards searching also for rare variants using new high-throughput sequencing technologies. For genes involved in the genetic predisposition to type 2 diabetes the emerging picture is that there are hundreds of different gene variants working in a complex interplay influencing pancreatic beta cell function/mass and, only to a lesser extent, insulin action. Several Norwegian studies have contributed to the field, extending our understanding of genetic risk factors in type 2 diabetes and in diabetes-related phenotypes like obesity and cardiovascular disease.

Comparative Genomics Reveals High Genomic Diversity in the Genus Photobacterium.

Science.gov (United States)

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.

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...

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.

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

Present status of iodine research at IPSN

Energy Technology Data Exchange (ETDEWEB)

Bardelay, J [IPSN/DPEA/SEAC (France)

1996-12-01

Since several years, IPSN has conducted an effort in order to evaluate the release of radioactive iodine in case of hypothetical severe accident in a realistic manner. This source-term evaluation is performed with IODE code which is a module of the EXCADRE system of codes. This code is validated against: -analytical experiments: in these experiments, IPSN studies radiolytic effects and chemical processes in the sump, organic formation, mass transfer, effect of spray (CARAIDAS experiment), - the CAIMAN semi global experiment; this experiment will allow to study the phenomena linked to iodine behavior under representative containment geometry in the presence of painted surfaces and global irradiation, - the PHEBUS FP program. The paper consists to describe succinctly the current status of IODE and the various experiments for its validation. In case of hypothetical severe accident iodine can induce important perturbations of human organism. The effects are principally radiological, in particular on the thyroid. At short term, radioactive iodine is the most important contributor for the sanitary risk. It represents 55% of effective dose and 92% of thyroid dose at 10 km in case of controlled rejects with current assumptions. This is the reason why it must be actively studied. In France, the safety evaluations are performed with mechanistic codes or lumped parameter codes like EXCADRE which contains a module devoted to iodine studies: IODINE. The objective of the French experimental program on iodine is to understand and quantify important phenomena in order to put kinetic parameters in IODE module. The experiments can be classified in analytical experiments, the semi-global experiment CAIMAN which takes into account different phenomena studied in analytical experiments and the global experiment PHEBUS PF, not only devoted to iodine behavior study. In the following text we will present the needs of IODINE code and these different experiments. (author).

Present status of iodine research at IPSN

International Nuclear Information System (INIS)

Bardelay, J.

1996-01-01

Since several years, IPSN has conducted an effort in order to evaluate the release of radioactive iodine in case of hypothetical severe accident in a realistic manner. This source-term evaluation is performed with IODE code which is a module of the EXCADRE system of codes. This code is validated against: -analytical experiments: in these experiments, IPSN studies radiolytic effects and chemical processes in the sump, organic formation, mass transfer, effect of spray (CARAIDAS experiment), - the CAIMAN semi global experiment; this experiment will allow to study the phenomena linked to iodine behavior under representative containment geometry in the presence of painted surfaces and global irradiation, - the PHEBUS FP program. The paper consists to describe succinctly the current status of IODE and the various experiments for its validation. In case of hypothetical severe accident iodine can induce important perturbations of human organism. The effects are principally radiological, in particular on the thyroid. At short term, radioactive iodine is the most important contributor for the sanitary risk. It represents 55% of effective dose and 92% of thyroid dose at 10 km in case of controlled rejects with current assumptions. This is the reason why it must be actively studied. In France, the safety evaluations are performed with mechanistic codes or lumped parameter codes like EXCADRE which contains a module devoted to iodine studies: IODINE. The objective of the French experimental program on iodine is to understand and quantify important phenomena in order to put kinetic parameters in IODE module. The experiments can be classified in analytical experiments, the semi-global experiment CAIMAN which takes into account different phenomena studied in analytical experiments and the global experiment PHEBUS PF, not only devoted to iodine behavior study. In the following text we will present the needs of IODINE code and these different experiments. (author)

[Present status and sustainable development of Dendrobium officinale industry].

Science.gov (United States)

Wu, Yunqin; Si, Jinping

2010-08-01

To understand the present status and characteristics of Dendrobium officinale industry and to provide a rationale for the sustainable industrial development. Based on references and an on-site investigation of main Dendrobium officinale-producing enterprises and market, to analyze main existing problems and to propose suggestions for sustainable development. More than 10 provinces and regions are involved in the production around the center of Zhejiang and Yunnan provinces. These two provinces are different from each other in development pattern. Yunnan adopts a mode of companies minus farmer households but Zhejiang mainly employs a mode that a leading company establishes a production base with production, processing and marketing combined together. Zhejiang mode is characterized by high tech, high investment, high risk and high return. Existence of non-genuine species, stagnancy in development and application of varieties and techniques for quality control and a narrow channel for marketing are the key problems limiting sustainable development of the industry. The key to sustainable development of the industry is to establish a technological alliance to speed up development of common techniques and application of integrated innovations, to strengthen self-discipline and monitoring of production, and to expand sales market.

Present status and prospects of photovoltaic market in China

International Nuclear Information System (INIS)

Zhao Ruirui; Shi Guang; Chen Hongyu; Ren Anfu; Finlow, David

2011-01-01

In 2009, the photovoltaic (PV) industry expanded greatly in China. Developing PV technology is both necessary and urgent, as China is a large country, which consumes huge amounts of energy. In addition, because China has a natural advantage of excellent solar resources, its government has provided significant support in this field. In order to motivate the PV industry, the Ministries of Finance and Construction established coordinated policies to offer financial inducements. The government will implement the Jintaiyang project in the near future: 15 billion US dollars will be invested and 294 demonstration projects will be built. The developing Chinese PV market holds great promise. The aim of this paper is to analyze the present status of the Chinese PV market, discuss the opportunities available, and the potential challenges anticipated in the developing process including some engineering roadblocks encountered in the PV system, and to outline possible future scenarios in this field. - Research highlights: → In 2009, the photovoltaic (PV) industry expanded greatly in China. → The price of electricity generated by PV will be gradually reduced. → A photovoltaic industrial chain in China has already formed. → Research on PV systems will also promote the development of improved technologies.

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.

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.

Present status and future development of the European Community rapid information system

International Nuclear Information System (INIS)

Fraser, G.

1990-01-01

Following the Chernobyl reactor accident it was rapidly appreciated that, in addition to upgrading national radiological monitoring systems, action was required to facilitate international communication of the results obtained. The first such system was established by the Vienna Convention, drawn up under the auspices of the IAEA, which came into force in September, 1986. Subsequently the EC Council of Ministers decided in December, 1987, to set up a Community system which in many ways parallels that established by the Convention but differs significantly in certain aspects concerning its legal basis, initiation criteria, data provisions and communications requirements. The present paper describes the present status of the Community system and foreseeable future developments. It is a matter of policy that, to avoid unnecessary complications, this system should be, to the maximum extent practicable, fully compatible with that established by the Convention. Where appropriate, therefore, reference is also made to the latter system

A Case Of Primary Central Nervous System Vasculitis Who Presented With Status Epilepticus

Directory of Open Access Journals (Sweden)

Sırma Geyik

2014-12-01

Full Text Available Primary central nervous system vasculitis (PCNV is limited with central nervous system and rare vasculitis that mostly seen in middle-aged men. PCNV vasculitis is usually presented that headache, dementia, stroke and multifocal common neurological symptoms. PCNV especially involves small medium-sized leptomeningeal and cortical arteries. 43 years old male patient who have been progressive forgetfulness and headache for 3 years. He applied with recurrent that before starting right focal and than sprawling whole body which generalized tonic-clonic seizures to us. During management that he was transfered to the intensive care unit due to status epilepticus (SE. Later than we found right hemiparesis, motor aphasia and right babinski positivity in neurologic examination. Diffusion restriction was revealed in left MCA territory in diffusion magnetic resonance imaging(MRI. EEG showed two types abnormality that a slow background ritm and epileptiform activity. Biochemistry of blood, complete blood count, blood sedimentation rate, CRP and markers of vasculitis were found in the normal range. Cerebral anjiography revealed that irregularities in the distal vascular areas and fusiform aneurysm at the top of basilar artery. He was consulted with rheumatology and diagnosed central nervous system vasculitis with the existing findings. Biopsy couldn't be taken from the brain to verify the diagnosis. Finally, we applied treatment that pulse steroid and cyclophosphamide to patient. This case has been presented due to emphasize that PCNV rarely may play a role in the etiology of recurrent stroke and status epilepticus.

Design of the muon collider lattice: Present status

International Nuclear Information System (INIS)

Garren, A.; Courant, E.; Gallardo, J.

1996-05-01

The last component of a muon collider facility, as presently envisioned, is a colliding-beam storage ring. Design studies on various problems for this ring have been in progress over the past year. In this paper we discuss the current status of the design. The projected muon currents require very low beta values at the IP, β* = 3 mm, in order to achieve the design luminosity of L = 10 35 cm -2 s -1 . The beta values in the final-focus quadrupoles are roughly 400 km. To cancel the corresponding chromaticities, sextupole schemes for local correction have been included in the optics of the experimental insertion. The hour-glass effect constraints the bunch length to be comparable too. To obtain such short bunches with reasonable rf voltage requires a very small value of the momentum compaction a, which can be obtained by using flexible momentum compaction (FMC) modules in the arcs. A preliminary design of a complete collider ring has now been made; it uses an experimental insertion and arc modules as well as a utility insertion. The layout of this ring is shown schematically, and its parameters are summarized. Though some engineering features are unrealistic, and the beam performance needs some improvement, we believe that this study can serve as the basis for a workable collider design. The remaining sections of the paper will describe the lattice, show beam behaviour, and discuss future design studies

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.

Genome-enabled predictions for binomial traits in sugar beet populations.

Science.gov (United States)

Biscarini, Filippo; Stevanato, Piergiorgio; Broccanello, Chiara; Stella, Alessandra; Saccomani, Massimo

2014-07-22

Genomic information can be used to predict not only continuous but also categorical (e.g. binomial) traits. Several traits of interest in human medicine and agriculture present a discrete distribution of phenotypes (e.g. disease status). Root vigor in sugar beet (B. vulgaris) is an example of binomial trait of agronomic importance. In this paper, a panel of 192 SNPs (single nucleotide polymorphisms) was used to genotype 124 sugar beet individual plants from 18 lines, and to classify them as showing "high" or "low" root vigor. A threshold model was used to fit the relationship between binomial root vigor and SNP genotypes, through the matrix of genomic relationships between individuals in a genomic BLUP (G-BLUP) approach. From a 5-fold cross-validation scheme, 500 testing subsets were generated. The estimated average cross-validation error rate was 0.000731 (0.073%). Only 9 out of 12326 test observations (500 replicates for an average test set size of 24.65) were misclassified. The estimated prediction accuracy was quite high. Such accurate predictions may be related to the high estimated heritability for root vigor (0.783) and to the few genes with large effect underlying the trait. Despite the sparse SNP panel, there was sufficient within-scaffold LD where SNPs with large effect on root vigor were located to allow for genome-enabled predictions to work.

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.

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...

AMS using 14UD Pelletron at TIFR, Mumbai: present status and future prospects

International Nuclear Information System (INIS)

Surendran, P.; Gupta, A.K.; Nair, J.P.; Mahata, K.; Shrivastava, A.; Yadav, M.L.; Sparrow, H.; Thomas, R.G.; Bhagwat, P.V.; Kailas, S.; Kale, R.M.

2011-01-01

The AMS (Accelerator Mass Spectrometry) is a versatile tool employed in multidisciplinary programmes. The AMS programme at the BARC-TIFR 14UD Pelletron accelerator has been initiated with major emphasis on the determination of 36 Cl concentration in environment in general and water samples in particular. Preliminary measurements related to detection of 129 I have been carried out in recent past. The system used for AMS measurement is based on a 14 MV Tandem Accelerator. In this paper, the status and future prospects of AMS programme at BARC-TIFR Pelletron Accelerator Facility are presented

Present status of an integrated software system for HASP (Human Acts Simulation Program)

International Nuclear Information System (INIS)

Otani, Takayuki; Ebihara, Ken-ichi; Kambayashi, Shaw; Kume, Etsuo; Higuchi, Kenji; Fujii, Minoru; Akimoto, Masayuki

1994-01-01

In Human Acts Simulation Program (HASP), human acts to be realized by a human-shaped intelligent robot in a nuclear power plant are simulated by computers. The major purpose of HASP is to develop basic and underlying design technologies for intelligent and automatic power plant. The objectives of this paper is to show the present status of the HASP, with particular emphasis on activities targetted at the integration of developed subsystems to simulate the important capabilities of the intelligent robot such as planning, robot dynamics, and so on. (author)

Genome size analyses of Pucciniales reveal the largest fungal genomes.

Science.gov (United States)

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.

Genome-wide association study of pathological gambling.

Science.gov (United States)

Lang, M; Leménager, T; Streit, F; Fauth-Bühler, M; Frank, J; Juraeva, D; Witt, S H; Degenhardt, F; Hofmann, A; Heilmann-Heimbach, S; Kiefer, F; Brors, B; Grabe, H-J; John, U; Bischof, A; Bischof, G; Völker, U; Homuth, G; Beutel, M; Lind, P A; Medland, S E; Slutske, W S; Martin, N G; Völzke, H; Nöthen, M M; Meyer, C; Rumpf, H-J; Wurst, F M; Rietschel, M; Mann, K F

2016-08-01

Pathological gambling is a behavioural addiction with negative economic, social, and psychological consequences. Identification of contributing genes and pathways may improve understanding of aetiology and facilitate therapy and prevention. Here, we report the first genome-wide association study of pathological gambling. Our aims were to identify pathways involved in pathological gambling, and examine whether there is a genetic overlap between pathological gambling and alcohol dependence. Four hundred and forty-five individuals with a diagnosis of pathological gambling according to the Diagnostic and Statistical Manual of Mental Disorders were recruited in Germany, and 986 controls were drawn from a German general population sample. A genome-wide association study of pathological gambling comprising single marker, gene-based, and pathway analyses, was performed. Polygenic risk scores were generated using data from a German genome-wide association study of alcohol dependence. No genome-wide significant association with pathological gambling was found for single markers or genes. Pathways for Huntington's disease (P-value=6.63×10(-3)); 5'-adenosine monophosphate-activated protein kinase signalling (P-value=9.57×10(-3)); and apoptosis (P-value=1.75×10(-2)) were significant. Polygenic risk score analysis of the alcohol dependence dataset yielded a one-sided nominal significant P-value in subjects with pathological gambling, irrespective of comorbid alcohol dependence status. The present results accord with previous quantitative formal genetic studies which showed genetic overlap between non-substance- and substance-related addictions. Furthermore, pathway analysis suggests shared pathology between Huntington's disease and pathological gambling. This finding is consistent with previous imaging studies. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Present status and prospect of radiation and radioisotopes in China

International Nuclear Information System (INIS)

Zhou, Yong-Tian

1986-01-01

Production and application of radioisotopes in China started almost thirty years ago. At present there are 20 units producing more than 700 radioisotope products. This report outlines the present status and prospect of radiation and radioisotopes in some major areas. Remarkable achievements have been made in agriculture using nuclear technology. More than 70 new varieties or strains of cultivated plants have been bred by inducing mutation through irradiation. A new variety of silkworm bred by irradiation has unique characteristics such as high and stable yield. Application of radioisotopes in medical research and clinical practice began in 1956 and radionuclides have been progressively used in diagnosis and treatment of diseases. The most common radionuclide used in therapy is iodine-131 for hyperthyroidism. Isotope-tracer technique and activation analysis play an important role in the study of traditional Chinese medicine. Isotope methods in China have been used in many industrial branches, such as textile, plastic and printing, but not very widely now. The nation has produced more than 2,000 sets of nuclear radiation measuring instruments, which become important parts of industrial automation control. The radiation processing research started in the end of 1950's. Food irradiation research has been going on in a good cooperation of different branches. Now China is planning to set up some plants to produce gamma irradiated disposal syringes and other medical devices. (Nogami, K.)

Extreme-Scale De Novo Genome Assembly

Energy Technology Data Exchange (ETDEWEB)

Georganas, Evangelos [Intel Corporation, Santa Clara, CA (United States); Hofmeyr, Steven [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.; Egan, Rob [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division; Buluc, Aydin [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.; Oliker, Leonid [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.; Rokhsar, Daniel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Computational Research Division; Yelick, Katherine [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint Genome Inst.

2017-09-26

De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality end-to-end de novo assembler designed for extreme scale analysis, via efficient parallelization of the Meraculous code. Genome assembly software has many components, each of which stresses different components of a computer system. This chapter explains the computational challenges involved in each step of the HipMer pipeline, the key distributed data structures, and communication costs in detail. We present performance results of assembling the human genome and the large hexaploid wheat genome on large supercomputers up to tens of thousands of cores.

"Harnessing genomics to improve health in Africa" – an executive course to support genomics policy

Directory of Open Access Journals (Sweden)

Singer Peter A

2005-01-01

Full Text Available Abstract Background Africa in the twenty-first century is faced with a heavy burden of disease, combined with ill-equipped medical systems and underdeveloped technological capacity. A major challenge for the international community is to bring scientific and technological advances like genomics to bear on the health priorities of poorer countries. The New Partnership for Africa's Development has identified science and technology as a key platform for Africa's renewal. Recognizing the timeliness of this issue, the African Centre for Technology Studies and the University of Toronto Joint Centre for Bioethics co-organized a course on Genomics and Public Health Policy in Nairobi, Kenya, the first of a series of similar courses to take place in the developing world. This article presents the findings and recommendations that emerged from this process, recommendations which suggest that a regional approach to developing sound science and technology policies is the key to harnessing genome-related biotechnology to improve health and contribute to human development in Africa. Methods The objectives of the course were to familiarize participants with the current status and implications of genomics for health in Africa; to provide frameworks for analyzing and debating the policy and ethical questions; and to begin developing a network across different sectors by sharing perspectives and building relationships. To achieve these goals the course brought together a diverse group of stakeholders from academic research centres, the media, non-governmental, voluntary and legal organizations to stimulate multi-sectoral debate around issues of policy. Topics included scientific advances in genomics innovation systems and business models, international regulatory frameworks, as well as ethical and legal issues. Results Seven main recommendations emerged: establish a network for sustained dialogue among participants; identify champions among politicians; use the

The present status of a compact synchrotron radiation source LUNA of IHI

International Nuclear Information System (INIS)

Marushita, Motoharu; Oishi, Masaya; Takahashi, Mitsuyuki; Komatsu, Takahito; Mandai, Shinichi

1993-01-01

Synchrotron radiation is expected to apply to many fields of science and industry and we are specially interested in availability of SR for X-ray lithography. This paper presents the characteristics, the design parameters, the features and current status of LUNA. Ishikawajima-Harima Heavy Industries Co., Ltd. (IHI) has developed a compact synchrotron radiation source 'LUNA' for lithography and has successfully stored beam current at full energy. LUNA consists of a 45 MeV linear accelerator as an electron injector and an 800 MeV synchrotron as a storage ring. The construction of LUNA has been completed in April 1989 at IHI Tsuchiura facility near Tsukuba. Synchrotron Radiation was first observed at December 1989. The design goal, which is to store beam current of 50 mA with the beam lifetime of over 30 minutes, has been successfully achieved in March 1991. At present the stored beam current is 80 mA with the beam lifetime of over 5 hours. (author)

A subordinate status position increases the present value of financial resources for low 2D:4D men.

Science.gov (United States)

Millet, Kobe; Dewitte, Siegfried

2008-01-01

It has been suggested that the ratio of the length of the 2nd and 4th fingers (digit ratio or 2D:4D) is related to prenatal testosterone with lower ratios thought to be influenced by higher prenatal testosterone levels. Accordingly, low 2D:4D has been associated to a number of fitness-related factors, such as high status in competitive sports and in music. Recent evidence suggests that 2D:4D is also related to economic decision making. We combine both streams of research in the present paper. In two studies we manipulated status in two different ways. We found that a subordinate position raises discount rates, consistent with the reasoning that the present utility of money is higher for men in this position. Moreover, the effect was more pronounced for men with a low 2D:4D. There was a significant negative relationship between 2D:4D and level of discounting in a subordinate status position, but no significant relationship emerged in the dominant status position. Our studies add evidence to the recent line of research associating digit ratio and economic decision making. Moreover, our studies show that future 2D:4D research should focus on plausible interactions between 2D:4D and context cues rather than on linear relations. (c) 2007 Wiley-Liss, Inc.

Acute Promyelocytic Leukemia Presenting as Focal Neurologic Findings and Deteriorating Mental Status.

Science.gov (United States)

Dolan, Matthew; Ngaruiya, Christine

2017-01-01

Acute promyelocytic leukemia (APL) is a rare but particularly malignant form of acute leukemia that is characterized by a rapid progression to fatal hemorrhage. Survival rates of patients with APL have increased with the introduction of all-trans retinoic acid (ATRA), but early deaths caused by hemorrhage still persist. A man with undiagnosed APL presenting with focal neurologic findings and deteriorating altered mental status caused by an intracranial hemorrhage is discussed. WHY SHOULD AN EMERGENCY PHYSICIAN BE AWARE OF THIS?: It is important to consider APL when diagnosing etiologies for intracranial hemorrhage. In addition to standard care, early administration of ATRA is recommended upon clinical suspicion of the disease. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Radiation education in Poland. The present status and perspectives

International Nuclear Information System (INIS)

Goraczko, W.

1999-01-01

The necessity for the continued education about radiation (both in nuclear science and the technical application of radioisotopes) in the educational systems is obvious. For many years this subject has been part of a students education in physics as well as nonphysical areas of study, such as chemistry, biology, medicine, ecology and agriculture. Unfortunately in the wake of the disaster at Chernobyl, a number of negative factors have resulted that have undermined both educations in this crucial area and financial investment in Polish radiation institutes. Some sociologists have termed this behavior/viewpoint 'radio-phobia phenomena'. Might I be so bold as to recoin it as 'nuclear related paranoia' since it has caused a general breakdown in rational, 'cause and effect analysis' even within respectable scientific circles, including prominent radio biologists, who now accept radiation only as a destructive factor in biological and human life. The most important factor in this campaign will be the promotion and presentation of radiation in simple-understandable terms through the following outlets, (popular articles, TV programs, objective classroom presentation and so on), designed to be easily understandable to society as a whole. In this support is to be found in some governmental and independent organization, which do attempt to show radiation as bio-positive, human friendly and an economically indispensable factor for the future. However our fight with the so-called coal lobby' will continue to be difficult. Help by international organizations such as the I.A.E.A. will not suffice in this battle. In this article the author tries to describe the Polish education system and statistical data showing the present status of radiation science, radiation education and the quantity of students and experts in the field. As a nuclear physicist and specialist in radiation protection, lecturer and an Inspector of Radiation Protection, he provides insights from his own

Radiation education in Poland. The present status and perspectives

Energy Technology Data Exchange (ETDEWEB)

Goraczko, W. [Technical Univ. Poznan, Radio- and Photochemistry Dept., Poznan, Piotrowo (Poland)

1999-09-01

The necessity for the continued education about radiation (both in nuclear science and the technical application of radioisotopes) in the educational systems is obvious. For many years this subject has been part of a students education in physics as well as nonphysical areas of study, such as chemistry, biology, medicine, ecology and agriculture. Unfortunately in the wake of the disaster at Chernobyl, a number of negative factors have resulted that have undermined both educations in this crucial area and financial investment in Polish radiation institutes. Some sociologists have termed this behavior/viewpoint 'radio-phobia phenomena'. Might I be so bold as to recoin it as 'nuclear related paranoia' since it has caused a general breakdown in rational, 'cause and effect analysis' even within respectable scientific circles, including prominent radio biologists, who now accept radiation only as a destructive factor in biological and human life. The most important factor in this campaign will be the promotion and presentation of radiation in simple-understandable terms through the following outlets, (popular articles, TV programs, objective classroom presentation and so on), designed to be easily understandable to society as a whole. In this support is to be found in some governmental and independent organization, which do attempt to show radiation as bio-positive, human friendly and an economically indispensable factor for the future. However our fight with the so-called coal lobby' will continue to be difficult. Help by international organizations such as the I.A.E.A. will not suffice in this battle. In this article the author tries to describe the Polish education system and statistical data showing the present status of radiation science, radiation education and the quantity of students and experts in the field. As a nuclear physicist and specialist in radiation protection, lecturer and an Inspector of Radiation Protection, he

The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadata

Science.gov (United States)

Pagani, Ioanna; Liolios, Konstantinos; Jansson, Jakob; Chen, I-Min A.; Smirnova, Tatyana; Nosrat, Bahador; Markowitz, Victor M.; Kyrpides, Nikos C.

2012-01-01

The Genomes OnLine Database (GOLD, http://www.genomesonline.org/) is a comprehensive resource for centralized monitoring of genome and metagenome projects worldwide. Both complete and ongoing projects, along with their associated metadata, can be accessed in GOLD through precomputed tables and a search page. As of September 2011, GOLD, now on version 4.0, contains information for 11 472 sequencing projects, of which 2907 have been completed and their sequence data has been deposited in a public repository. Out of these complete projects, 1918 are finished and 989 are permanent drafts. Moreover, GOLD contains information for 340 metagenome studies associated with 1927 metagenome samples. GOLD continues to expand, moving toward the goal of providing the most comprehensive repository of metadata information related to the projects and their organisms/environments in accordance with the Minimum Information about any (x) Sequence specification and beyond. PMID:22135293

High-energy synchrotron radiation x-ray microscopy: Present status and future prospects

International Nuclear Information System (INIS)

Jones, K.W.; Gordon, B.M.; Spanne, P.; Rivers, M.L.; Sutton, S.R.

1991-01-01

High-energy radiation synchrotron x-ray microscopy is used to characterize materials of importance to the chemical and materials sciences and chemical engineering. The x-ray microscope (XRM) forms images of elemental distributions fluorescent x rays or images of mass distributions by measurement of the linear attenuation coefficient of the material. Distributions of sections through materials are obtained non-destructively using the technique of computed microtomography. The energy range of the x rays used for the XRM ranges from a few keV at the minimum value to more than 100 keV, which is sufficient to excite the K-edge of all naturally occurring elements. The work in progress at the Brookhaven NSLS X26 and X17 XRM is described in order to show the current status of the XRM. While there are many possible approaches to the XRM instrumentation, this instrument gives state-of-the-art performance in most respects and serves as a reasonable example of the present status of the instrumentation in terms of the spatial resolution and minimum detection limits obtainable. The examples of applications cited give an idea of the types of research fields that are currently under investigation. They can be used to illustrate how the field of x-ray microscopy will benefit from the use of bending magnets and insertion devices at the Advanced Photon Source. 8 refs., 5 figs

High-energy synchrotron radiation x-ray microscopy: Present status and future prospects

International Nuclear Information System (INIS)

Jones, K.W.; Gordon, B.M.; Spanne, P.; Rivers, M.L.; Sutton, S.R.

1991-01-01

High-energy radiation synchrotron x-ray microscopy is used to characterize materials of importance to the chemical and materials sciences and chemical engineering. The x-ray microscope (XRM) forms images of elemental distributions fluorescent x rays or images of mass distributions by measurement of the linear attenuation coefficient of the material. Distributions of sections through materials are obtained non-destructively using the technique of computed microtomography (CMT). The energy range of the x rays used for the XRM ranges from a few keV at the minimum value to more than 100 keV, which is sufficient to excite the K-edge of all naturally occurring elements. The work in progress at the Brookhaven NSLS X26 and X17 XRM is described in order to show the current status of the XRM. While there are many possible approaches to the XRM instrumentation, this instrument gives state-of-the-art performance in most respects and serves as a reasonable example of the present status of the instrumentation in terms of the spatial resolution and minimum detection limits (MDLs) obtainable. The examples of applications cited give an idea of the types of research fields that are currently under investigation. They can be used to illustrate how the field of x-ray microscopy will benefit from the use of bending magnets and insertion devices at the Advanced Photon Source (APS)

Moving through the stressed genome: Emerging regulatory roles for transposons in plant stress tolerance

Directory of Open Access Journals (Sweden)

Negi Pooja

2016-10-01

Full Text Available The recognition of a positive correlation between organism genome size with its transposable element (TE content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock’s original ’Controlling Element’ hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences which project TEs as distributed genomic control modules. According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution and function, and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.

Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response.

Science.gov (United States)

Negi, Pooja; Rai, Archana N; Suprasanna, Penna

2016-01-01

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.

Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response

Science.gov (United States)

Negi, Pooja; Rai, Archana N.; Suprasanna, Penna

2016-01-01

The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original ‘Controlling Element’ hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as “distributed genomic control modules.” According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement. PMID:27777577

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.

Illiteracy, Sex and Occupational Status in Present-Day China.

Science.gov (United States)

Lamontagne, Jacques

This study determined the magnitude of disparity between men and women in China in relation to illiteracy and occupational status. Region and ethnicity are used as control variables. The data collected are from a 10 percent sampling of the 1982 census; the total sample size includes a population of 100,380,000 nationwide. The census questionnaire…

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.

Present status and subjects of food irradiation in the world

International Nuclear Information System (INIS)

Hayashi, Toru

1995-01-01

Food irradiation is the technology of irradiating such radiations as gamma ray and electron beam to foods and farm products, and its objectives are the prevention of germination of potatoes and onions, the insecticide of cereals and fruits, the adjustment of the ripeness of fruits and vegetables, the sterilization of chickens and spices and so on. The food irradiation as the technology for preventing the loss of foods, the food irradiation as the substitute for the fumigation with chemicals and the food irradiation for improving food sanitation are discussed. The history of the soundness test of irradiated foods and the opinion of the international organizations are described. The safety evaluation in view of poisonous effect, nutrition and microorganisms is carried out, and the safety of the foods irradiated with the dose less than 10 kGy has been proved. The examples of utilizing food irradiation for sterilization, insecticide and germination prevention are shown. The present status of its practical use in America and Europe and the move of such international organizations as IAEA, FAO and WHO are reported. (K.I.)

Present status of radiation processing and its future development by using electron accelerator in Vietnam

International Nuclear Information System (INIS)

Tran Khac An; Tran Tich Canh; Doan Binh; Nguyen Quoc Hien

2003-01-01

In Vietnam, studies on Radiation Processing have been carried out since 1983. Some results are applicable in the field of agriculture, health and foodstuff, some researches were developed to commercial scale and others have high potential for development by using electron accelerator. The paper offers the present status of radiation processing and also give out the growing tendency of using electron accelerator in the future. (author)

Present status of radiation processing and its future development by using electron accelerator in Vietnam

Energy Technology Data Exchange (ETDEWEB)

Tran Khac An; Tran Tich Canh; Doan Binh [Research and Development Center for Radiation Technology (VINAGAMMA), Ho Chi Minh (Viet Nam); Nguyen Quoc Hien [Nuclear Research Institute (NRI), Dalat (Viet Nam)

2003-02-01

In Vietnam, studies on Radiation Processing have been carried out since 1983. Some results are applicable in the field of agriculture, health and foodstuff, some researches were developed to commercial scale and others have high potential for development by using electron accelerator. The paper offers the present status of radiation processing and also give out the growing tendency of using electron accelerator in the future. (author)

Using genomic information to conserve genetic diversity in livestock

NARCIS (Netherlands)

Eynard, Sonia E.

2018-01-01

Concern about the status of livestock breeds and their conservation has increased as selection and small population sizes caused loss of genetic diversity. Meanwhile, dense SNP chips and whole genome sequences (WGS) became available, providing opportunities to accurately quantify the impact of

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.

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

Science.gov (United States)

Reddy, T.B.K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

2015-01-01

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. PMID:25348402

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

Energy Technology Data Exchange (ETDEWEB)

Reddy, Tatiparthi B. K. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Thomas, Alex D. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Stamatis, Dimitri [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Bertsch, Jon [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Isbandi, Michelle [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Jansson, Jakob [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Mallajosyula, Jyothi [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Pagani, Ioanna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lobos, Elizabeth A. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Kyrpides, Nikos C. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)

2014-10-27

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Within this paper, we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. Lastly, GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.

MVisAGe Identifies Concordant and Discordant Genomic Alterations of Driver Genes in Squamous Tumors.

Science.gov (United States)

Walter, Vonn; Du, Ying; Danilova, Ludmila; Hayward, Michele C; Hayes, D Neil

2018-06-15

Integrated analyses of multiple genomic datatypes are now common in cancer profiling studies. Such data present opportunities for numerous computational experiments, yet analytic pipelines are limited. Tools such as the cBioPortal and Regulome Explorer, although useful, are not easy to access programmatically or to implement locally. Here, we introduce the MVisAGe R package, which allows users to quantify gene-level associations between two genomic datatypes to investigate the effect of genomic alterations (e.g., DNA copy number changes on gene expression). Visualizing Pearson/Spearman correlation coefficients according to the genomic positions of the underlying genes provides a powerful yet novel tool for conducting exploratory analyses. We demonstrate its utility by analyzing three publicly available cancer datasets. Our approach highlights canonical oncogenes in chr11q13 that displayed the strongest associations between expression and copy number, including CCND1 and CTTN , genes not identified by copy number analysis in the primary reports. We demonstrate highly concordant usage of shared oncogenes on chr3q, yet strikingly diverse oncogene usage on chr11q as a function of HPV infection status. Regions of chr19 that display remarkable associations between methylation and gene expression were identified, as were previously unreported miRNA-gene expression associations that may contribute to the epithelial-to-mesenchymal transition. Significance: This study presents an important bioinformatics tool that will enable integrated analyses of multiple genomic datatypes. Cancer Res; 78(12); 3375-85. ©2018 AACR . ©2018 American Association for Cancer Research.

Genome Investigations of Vector Competence in Aedes aegypti to Inform Novel Arbovirus Disease Control Approaches

Directory of Open Access Journals (Sweden)

David W. Severson

2016-10-01

Full Text Available Dengue (DENV, yellow fever, chikungunya, and Zika virus transmission to humans by a mosquito host is confounded by both intrinsic and extrinsic variables. Besides virulence factors of the individual arboviruses, likelihood of virus transmission is subject to variability in the genome of the primary mosquito vector, Aedes aegypti. The “vectorial capacity” of A. aegypti varies depending upon its density, biting rate, and survival rate, as well as its intrinsic ability to acquire, host and transmit a given arbovirus. This intrinsic ability is known as “vector competence”. Based on whole transcriptome analysis, several genes and pathways have been predicated to have an association with a susceptible or refractory response in A. aegypti to DENV infection. However, the functional genomics of vector competence of A. aegypti is not well understood, primarily due to lack of integrative approaches in genomic or transcriptomic studies. In this review, we focus on the present status of genomics studies of DENV vector competence in A. aegypti as limited information is available relative to the other arboviruses. We propose future areas of research needed to facilitate the integration of vector and virus genomics and environmental factors to work towards better understanding of vector competence and vectorial capacity in natural conditions.

Present status of medical treatment for patients of advanced lung cancer

Energy Technology Data Exchange (ETDEWEB)

Kira, Shiro; Kuratomi, Yushiro; Matsuoka, Rokuro; Ishihara, Teruo (Jichi Medical School, Minamikawachi, Tochigi (Japan))

1982-09-01

Management of patients with inoperable, advanced lung cancer is one of the most important problems for many chest physicians, because those patients with stage 3 and stage 4 are over 70% of total patients. Although surgical treatment is attempted even in the case of stage 3 patients, many factors such as age, performance status, pulmonary and circulatory disorders accompanied with them and sometimes patient's refusal for surgical treatment preclude it. Therefore, therapeutic approach for these patients is focused on relieving their pains and troubles in their daily life. Radiation therapy is only a local treatment, but it can often control variable clinical manifestations with a highly probable estimation. Many patients can be free of disease even for a limited period. From this view-point, even at present, radiation therapy is a preferable therapeutic modality to maintain individual patient's better quality of life.

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.

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

From plant genomes to phenotypes

OpenAIRE

Bolger, Marie; Gundlach, Heidrun; Scholz, Uwe; Mayer, Klaus; Usadel, Björn; Schwacke, Rainer; Schmutzer, Thomas; Chen, Jinbo; Arend, Daniel; Oppermann, Markus; Weise, Stephan; Lange, Matthias; Fiorani, Fabio; Spannagl, Manuel

2017-01-01

Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis.Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.

Present status and future prospects for a Higgs boson discovery at the Tevatron and LHC

International Nuclear Information System (INIS)

Haber, Howard E

2010-01-01

Discovering the Higgs boson is one of the primary goals of both the Tevatron and the Large Hadron Collider (LHC). The present status of the Higgs search is reviewed and future prospects for discovery at the Tevatron and LHC are considered. This talk focuses primarily on the Higgs boson of the Standard Model and its minimal supersymmetric extension. Theoretical expectations for the Higgs boson and its phenomenological consequences are reviewed.

No evidence for genome-wide interactions on plasma fibrinogen by smoking, alcohol consumption and body mass index: results from meta-analyses of 80,607 subjects.

Directory of Open Access Journals (Sweden)

Jens Baumert

Full Text Available Plasma fibrinogen is an acute phase protein playing an important role in the blood coagulation cascade having strong associations with smoking, alcohol consumption and body mass index (BMI. Genome-wide association studies (GWAS have identified a variety of gene regions associated with elevated plasma fibrinogen concentrations. However, little is yet known about how associations between environmental factors and fibrinogen might be modified by genetic variation. Therefore, we conducted large-scale meta-analyses of genome-wide interaction studies to identify possible interactions of genetic variants and smoking status, alcohol consumption or BMI on fibrinogen concentration. The present study included 80,607 subjects of European ancestry from 22 studies. Genome-wide interaction analyses were performed separately in each study for about 2.6 million single nucleotide polymorphisms (SNPs across the 22 autosomal chromosomes. For each SNP and risk factor, we performed a linear regression under an additive genetic model including an interaction term between SNP and risk factor. Interaction estimates were meta-analysed using a fixed-effects model. No genome-wide significant interaction with smoking status, alcohol consumption or BMI was observed in the meta-analyses. The most suggestive interaction was found for smoking and rs10519203, located in the LOC123688 region on chromosome 15, with a p value of 6.2 × 10(-8. This large genome-wide interaction study including 80,607 participants found no strong evidence of interaction between genetic variants and smoking status, alcohol consumption or BMI on fibrinogen concentrations. Further studies are needed to yield deeper insight in the interplay between environmental factors and gene variants on the regulation of fibrinogen concentrations.

Evolution and phylogeny of the mud shrimps (Crustacea: Decapoda) revealed from complete mitochondrial genomes.

Science.gov (United States)

Lin, Feng-Jiau; Liu, Yuan; Sha, Zhongli; Tsang, Ling Ming; Chu, Ka Hou; Chan, Tin-Yam; Liu, Ruiyu; Cui, Zhaoxia

2012-11-16

evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.

Complete genome sequence of Serratia sp. YD25 (KCTC 42987) presenting strong antagonistic activities to various pathogenic fungi and bacteria.

Science.gov (United States)

Su, Chun; Liu, Yibo; Sun, Yan; Li, Zhi

2017-03-10

Serratia sp. YD25 (KCTC 42987) was originally isolated from rhizosphere soil in a continuous cropping tobacco-planting farm. Here, we show that its metabolites efficiently suppress the growth of various important pathogenic fungi and bacteria, causing infection in both plants and humans. In addition, Serratia sp. YD25 has a special trait of simultaneous production of both serrawettin W2 and prodigiosin, two important bioactive secondary metabolites produced by Serratia strains. Such co-production has not been reported in other Serratia strains. The complete genome sequence of Serratia sp. YD25 is presented, which is valuable for further exploration of its biotechnological applications in agriculture and medicine. The genome sequence reported here is also useful for understanding the unique regulatory mechanisms underlying biosynthesis of active compounds. Copyright © 2017 Elsevier B.V. All rights reserved.

The Chlamydomonas genome project: a decade on

Science.gov (United States)

Blaby, Ian K.; Blaby-Haas, Crysten; Tourasse, Nicolas; Hom, Erik F. Y.; Lopez, David; Aksoy, Munevver; Grossman, Arthur; Umen, James; Dutcher, Susan; Porter, Mary; King, Stephen; Witman, George; Stanke, Mario; Harris, Elizabeth H.; Goodstein, David; Grimwood, Jane; Schmutz, Jeremy; Vallon, Olivier; Merchant, Sabeeha S.; Prochnik, Simon

2014-01-01

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis and micronutrient homeostasis. Ten years since its genome project was initiated, an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the “omics” era. Housed at Phytozome, the Joint Genome Institute’s (JGI) plant genomics portal, the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of RNA-Seq data. Here, we present the past, present and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes. PMID:24950814

Non-functional plastid ndh gene fragments are present in the nuclear genome of Norway spruce (Picea abies L. Karsch): insights from in silico analysis of nuclear and organellar genomes.

Science.gov (United States)

Ranade, Sonali Sachin; García-Gil, María Rosario; Rosselló, Josep A

2016-04-01

Many genes have been lost from the prokaryote plastidial genome during the early events of endosymbiosis in eukaryotes. Some of them were definitively lost, but others were relocated and functionally integrated to the host nuclear genomes through serial events of gene transfer during plant evolution. In gymnosperms, plastid genome sequencing has revealed the loss of ndh genes from several species of Gnetales and Pinaceae, including Norway spruce (Picea abies). This study aims to trace the ndh genes in the nuclear and organellar Norway spruce genomes. The plastid genomes of higher plants contain 11 ndh genes which are homologues of mitochondrial genes encoding subunits of the proton-pumping NADH-dehydrogenase (nicotinamide adenine dinucleotide dehydrogenase) or complex I (electron transport chain). Ndh genes encode 11 NDH polypeptides forming the Ndh complex (analogous to complex I) which seems to be primarily involved in chloro-respiration processes. We considered ndh genes from the plastidial genome of four gymnosperms (Cryptomeria japonica, Cycas revoluta, Ginkgo biloba, Podocarpus totara) and a single angiosperm species (Arabidopsis thaliana) to trace putative homologs in the nuclear and organellar Norway spruce genomes using tBLASTn to assess the evolutionary fate of ndh genes in Norway spruce and to address their genomic location(s), structure, integrity and functionality. The results obtained from tBLASTn were subsequently analyzed by performing homology search for finding ndh specific conserved domains using conserved domain search. We report the presence of non-functional plastid ndh gene fragments, excepting ndhE and ndhG genes, in the nuclear genome of Norway spruce. Regulatory transcriptional elements like promoters, TATA boxes and enhancers were detected in the upstream regions of some ndh fragments. We also found transposable elements in the flanking regions of few ndh fragments suggesting nuclear rearrangements in those regions. These evidences

[Preface for genome editing special issue].

Science.gov (United States)

Gu, Feng; Gao, Caixia

2017-10-25

Genome editing technology, as an innovative biotechnology, has been widely used for editing the genome from model organisms, animals, plants and microbes. CRISPR/Cas9-based genome editing technology shows its great value and potential in the dissection of functional genomics, improved breeding and genetic disease treatment. In the present special issue, the principle and application of genome editing techniques has been summarized. The advantages and disadvantages of the current genome editing technology and future prospects would also be highlighted.

Present energy status

Energy Technology Data Exchange (ETDEWEB)

Desprairies, P

1988-04-01

This paper reviews the past and present situation of the World Oil Market and assumes future trends and possible future evolution. Low oil prices between 1950 and 1973 have contributed to an exceptional growth of oil demand during more than 20 years which was more and more supplied by OPEC. The oil shocks of 1973 and 1979 have dramatically changed this situation. Some of the most important changes have been the emergence of non-OPEC new oil producers, the growth of substitute energies, especially natural gas and nuclear power, on the supply side; and substantial decrease of energy consumption in many industrialized countries which has greatly reduced oil demand to OPEC on the demand side. Today this situation seems somewhat stabilized (after the reversal of world oil prices in 1986) and OPEC is producing around 18 million b/day as against a producing capacity of about 30 million b/day. It is generally considered that in coming years oil prices will remain relatively low (or occasionally even become lower than today) due to excess oil production capacity and relative abundance of other types of energy. However, many experts think that these trends can be reversed when oil supply will more and more concentrate again in the Middle East; but it is hard to say if this will begin in 1995, 2000, 2010.

Integrating genomics into undergraduate nursing education.

Science.gov (United States)

Daack-Hirsch, Sandra; Dieter, Carla; Quinn Griffin, Mary T

2011-09-01

To prepare the next generation of nurses, faculty are now faced with the challenge of incorporating genomics into curricula. Here we discuss how to meet this challenge. Steps to initiate curricular changes to include genomics are presented along with a discussion on creating a genomic curriculum thread versus a standalone course. Ideas for use of print material and technology on genomic topics are also presented. Information is based on review of the literature and curriculum change efforts by the authors. In recognition of advances in genomics, the nursing profession is increasing an emphasis on the integration of genomics into professional practice and educational standards. Incorporating genomics into nurses' practices begins with changes in our undergraduate curricula. Information given in didactic courses should be reinforced in clinical practica, and Internet-based tools such as WebQuest, Second Life, and wikis offer attractive, up-to-date platforms to deliver this now crucial content. To provide information that may assist faculty to prepare the next generation of nurses to practice using genomics. © 2011 Sigma Theta Tau International.

Detection of genomic rearrangements in cucumber using genomecmp software

Science.gov (United States)

Kulawik, Maciej; Pawełkowicz, Magdalena Ewa; Wojcieszek, Michał; PlÄ der, Wojciech; Nowak, Robert M.

2017-08-01

Comparative genomic by increasing information about the genomes sequences available in the databases is a rapidly evolving science. A simple comparison of the general features of genomes such as genome size, number of genes, and chromosome number presents an entry point into comparative genomic analysis. Here we present the utility of the new tool genomecmp for finding rearrangements across the compared sequences and applications in plant comparative genomics.

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.

Operational present status and reliability analysis of the upgraded EAST cryogenic system

Science.gov (United States)

Zhou, Z. W.; Y Zhang, Q.; Lu, X. F.; Hu, L. B.; Zhu, P.

2017-12-01

Since the first commissioning in 2005, the cryogenic system for EAST (Experimental Advanced Superconducting Tokamak) has been cooled down and warmed up for thirteen experimental campaigns. In order to promote the refrigeration efficiencies and reliability, the EAST cryogenic system was upgraded gradually with new helium screw compressors and new dynamic gas bearing helium turbine expanders with eddy current brake to improve the original poor mechanical and operational performance from 2012 to 2015. Then the totally upgraded cryogenic system was put into operation in the eleventh cool-down experiment, and has been operated for the latest several experimental campaigns. The upgraded system has successfully coped with various normal operational modes during cool-down and 4.5 K steady-state operation under pulsed heat load from the tokamak as well as the abnormal fault modes including turbines protection stop. In this paper, the upgraded EAST cryogenic system including its functional analysis and new cryogenic control networks will be presented in detail. Also, its operational present status in the latest cool-down experiments will be presented and the system reliability will be analyzed, which shows a high reliability and low fault rate after upgrade. In the end, some future necessary work to meet the higher reliability requirement for future uninterrupted long-term experimental operation will also be proposed.

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.

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.

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

OpenAIRE

Pfeifer, Bastian; Wittelsbürger, Ulrich; Ramos-Onsins, Sebastian E.; Lercher, Martin J.

2014-01-01

Although many computer programs can perform population genetics calculations, they are typically limited in the analyses and data input formats they offer; few applications can process the large data sets produced by whole-genome resequencing projects. Furthermore, there is no coherent framework for the easy integration of new statistics into existing pipelines, hindering the development and application of new population genetics and genomics approaches. Here, we present PopGenome, a populati...

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.

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 and the human genome project: implications for psychiatry

OpenAIRE

Kelsoe, J R

2004-01-01

In the past decade the Human Genome Project has made extraordinary strides in understanding of fundamental human genetics. The complete human genetic sequence has been determined, and the chromosomal location of almost all human genes identified. Presently, a large international consortium, the HapMap Project, is working to identify a large portion of genetic variation in different human populations and the structure and relationship of these variants to each other. The Human Genome Project h...

Present status of nuclear containments in Korea

International Nuclear Information System (INIS)

Park, Jihong; Hong, Jaekeun; Lee, Byunghoon; Son, Youngho

2007-01-01

Since the first nuclear power plant in Korea, Kori unit no.1, was started in commercial service in 1978, 20 units including Kori unit no.1 have been operated and maintained until now in Korea. Recently several units were started to be constructed and also, additionally more than 4 units were planned to be constructed in the near future. The importance of nuclear containments has been always one of the hottest issues for the safety and protection of nuclear power plants until now. At the beginning of nuclear power plants construction in Korea, several typed nuclear containment systems were adopted. For those reasons, various codes, standards, and inspection technologies are applied to nuclear containment systems differently. In this study, the status of inservice inspection performed for the safety and maintenance of nuclear containments in Korea was researched. Overall nuclear containment systems and inspections performed up to recently in Korea including trends, inspection items, periods, and regulations were described briefly. (author)

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.

Analyses of charophyte chloroplast genomes help characterize the ancestral chloroplast genome of land plants.

Science.gov (United States)

Civaň, Peter; Foster, Peter G; Embley, Martin T; Séneca, Ana; Cox, Cymon J

2014-04-01

Despite the significance of the relationships between embryophytes and their charophyte algal ancestors in deciphering the origin and evolutionary success of land plants, few chloroplast genomes of the charophyte algae have been reconstructed to date. Here, we present new data for three chloroplast genomes of the freshwater charophytes Klebsormidium flaccidum (Klebsormidiophyceae), Mesotaenium endlicherianum (Zygnematophyceae), and Roya anglica (Zygnematophyceae). The chloroplast genome of Klebsormidium has a quadripartite organization with exceptionally large inverted repeat (IR) regions and, uniquely among streptophytes, has lost the rrn5 and rrn4.5 genes from the ribosomal RNA (rRNA) gene cluster operon. The chloroplast genome of Roya differs from other zygnematophycean chloroplasts, including the newly sequenced Mesotaenium, by having a quadripartite structure that is typical of other streptophytes. On the basis of the improbability of the novel gain of IR regions, we infer that the quadripartite structure has likely been lost independently in at least three zygnematophycean lineages, although the absence of the usual rRNA operonic synteny in the IR regions of Roya may indicate their de novo origin. Significantly, all zygnematophycean chloroplast genomes have undergone substantial genomic rearrangement, which may be the result of ancient retroelement activity evidenced by the presence of integrase-like and reverse transcriptase-like elements in the Roya chloroplast genome. Our results corroborate the close phylogenetic relationship between Zygnematophyceae and land plants and identify 89 protein-coding genes and 22 introns present in the chloroplast genome at the time of the evolutionary transition of plants to land, all of which can be found in the chloroplast genomes of extant charophytes.

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.

Genomic Tools in Cowpea Breeding Programs: Status and Perspectives

Science.gov (United States)

Boukar, Ousmane; Fatokun, Christian A.; Huynh, Bao-Lam; Roberts, Philip A.; Close, Timothy J.

2016-01-01

Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA). It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds, and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids, and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP) genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS)-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS), promises an increase in the number of improved

Genomic tools in cowpea breeding programs: status and perspectives

Directory of Open Access Journals (Sweden)

Ousmane eBoukar

2016-06-01

Full Text Available Cowpea is one of the most important grain legumes in sub-Saharan Africa (SSA. It provides strong support to the livelihood of small-scale farmers through its contributions to their nutritional security, income generation and soil fertility enhancement. Worldwide about 6.5 million metric tons of cowpea are produced annually on about 14.5 million hectares. The low productivity of cowpea is attributable to numerous abiotic and biotic constraints. The abiotic stress factors comprise drought, low soil fertility, and heat while biotic constraints include insects, diseases, parasitic weeds and nematodes. Cowpea farmers also have limited access to quality seeds of improved varieties for planting. Some progress has been made through conventional breeding at international and national research institutions in the last three decades. Cowpea improvement could also benefit from modern breeding methods based on molecular genetic tools. A number of advances in cowpea genetic linkage maps, and quantitative trait loci associated with some desirable traits such as resistance to Striga, Macrophomina, Fusarium wilt, bacterial blight, root-knot nematodes, aphids and foliar thrips have been reported. An improved consensus genetic linkage map has been developed and used to identify QTLs of additional traits. In order to take advantage of these developments single nucleotide polymorphism (SNP genotyping is being streamlined to establish an efficient workflow supported by genotyping support service (GSS-client interactions. About 1100 SNPs mapped on the cowpea genome were converted by LGC Genomics to KASP assays. Several cowpea breeding programs have been exploiting these resources to implement molecular breeding, especially for MARS and MABC, to accelerate cowpea variety improvement. The combination of conventional breeding and molecular breeding strategies, with workflow managed through the CGIAR breeding management system (BMS, promises an increase in the number of

Multiscale modeling of three-dimensional genome

Science.gov (United States)

Zhang, Bin; Wolynes, Peter

The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.

Sauropod dinosaurs evolved moderately sized genomes unrelated to body size.

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Organ, Chris L; Brusatte, Stephen L; Stein, Koen

2009-12-22

Sauropodomorph dinosaurs include the largest land animals to have ever lived, some reaching up to 10 times the mass of an African elephant. Despite their status defining the upper range for body size in land animals, it remains unknown whether sauropodomorphs evolved larger-sized genomes than non-avian theropods, their sister taxon, or whether a relationship exists between genome size and body size in dinosaurs, two questions critical for understanding broad patterns of genome evolution in dinosaurs. Here we report inferences of genome size for 10 sauropodomorph taxa. The estimates are derived from a Bayesian phylogenetic generalized least squares approach that generates posterior distributions of regression models relating genome size to osteocyte lacunae volume in extant tetrapods. We estimate that the average genome size of sauropodomorphs was 2.02 pg (range of species means: 1.77-2.21 pg), a value in the upper range of extant birds (mean = 1.42 pg, range: 0.97-2.16 pg) and near the average for extant non-avian reptiles (mean = 2.24 pg, range: 1.05-5.44 pg). The results suggest that the variation in size and architecture of genomes in extinct dinosaurs was lower than the variation found in mammals. A substantial difference in genome size separates the two major clades within dinosaurs, Ornithischia (large genomes) and Saurischia (moderate to small genomes). We find no relationship between body size and estimated genome size in extinct dinosaurs, which suggests that neutral forces did not dominate the evolution of genome size in this group.

Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.

Science.gov (United States)

Bergman, Casey M; Haddrill, Penelope R

2015-01-01

To contribute to our general understanding of the evolutionary forces that shape variation in genome sequences in nature, we have sequenced genomes from 50 isofemale lines and six pooled samples from populations of Drosophila melanogaster on three continents. Analysis of raw and reference-mapped reads indicates the quality of these genomic sequence data is very high. Comparison of the predicted and experimentally-determined Wolbachia infection status of these samples suggests that strain or sample swaps are unlikely to have occurred in the generation of these data. Genome sequences are freely available in the European Nucleotide Archive under accession ERP009059. Isofemale lines can be obtained from the Drosophila Species Stock Center.

Genetically contextual effects of smoking on genome wide DNA methylation.

Science.gov (United States)

Dogan, Meeshanthini V; Beach, Steven R H; Philibert, Robert A

2017-09-01

Smoking is the leading cause of death in the United States. It exerts its effects by increasing susceptibility to a variety of complex disorders among those who smoke, and if pregnant, to their unborn children. In prior efforts to understand the epigenetic mechanisms through which this increased vulnerability is conveyed, a number of investigators have conducted genome wide methylation analyses. Unfortunately, secondary to methodological limitations, these studies were unable to examine methylation in gene regions with significant amounts of genetic variation. Using genome wide genetic and epigenetic data from the Framingham Heart Study, we re-examined the relationship of smoking status to genome wide methylation status. When only methylation status is considered, smoking was significantly associated with differential methylation in 310 genes that map to a variety of biological process and cellular differentiation pathways. However, when SNP effects on the magnitude of smoking associated methylation changes are also considered, cis and trans-interaction effects were noted at a total of 266 and 4353 genes with no marked enrichment for any biological pathways. Furthermore, the SNP variation participating in the significant interaction effects is enriched for loci previously associated with complex medical illnesses. The enlarged scope of the methylome shown to be affected by smoking may better explicate the mediational pathways linking smoking with a myriad of smoking related complex syndromes. Additionally, these results strongly suggest that combined epigenetic and genetic data analyses may be critical for a more complete understanding of the relationship between environmental variables, such as smoking, and pathophysiological outcomes. © 2017 Wiley Periodicals, Inc.

Present construction status and future plan of JT-60

Energy Technology Data Exchange (ETDEWEB)

Iso, Yasuhiko; Yoshikawa, Masaji [Japan Atomic Energy Research Inst., Tokai, Ibaraki. Tokai Research Establishment

1982-04-01

As for the critical plasma test facility JT-60, its detailed design was initiated in 1975, and the manufacture of the main body components was started in April, 1978, through the trial manufacture and development of important components. The manufacture of all the system equipment in factories is in progress. Especially, the essential components of main body have been almost completed, and ready to be installed in the building. The building is under construction, and a part of the equipment was brought in and installed since the beginning of 1982 fiscal year. JT-60 is composed of heating system, toroidal magnetic field coil power supply, poloidal magnetic field coil power supply, total control system, associated system for main body and various measuring equipment as well as the main body which consists of vacuum vessel, toroidal and poloidal magnetic field coils, base, primary cooling system, movable limiter and evacuating system. In this report, first the significance of JT-60 development and the outline of JT-60 are described, and the present construction status is reported. The specifications of the essential equipment of the main body and heating system and the measuring system configuration are listed in tables. The aims in JT-60 design are to make plasma generating pulse width longer, to obtain higher beta value in circular cross-section plasma, to install the magnetic limiter, and to realize compound second stage heating.

Genomic copy number analysis of Chernobyl papillary thyroid carcinoma in the Ukrainian–American Cohort

Science.gov (United States)

Selmansberger, Martin; Braselmann, Herbert; Hess, Julia; Bogdanova, Tetiana; Abend, Michael; Tronko, Mykola; Brenner, Alina; Zitzelsberger, Horst; Unger, Kristian

2015-01-01

One of the major consequences of the 1986 Chernobyl reactor accident was a dramatic increase in papillary thyroid carcinoma (PTC) incidence, predominantly in patients exposed to the radioiodine fallout at young age. The present study is the first on genomic copy number alterations (CNAs) of PTCs of the Ukrainian–American cohort (UkrAm) generated by array comparative genomic hybridization (aCGH). Unsupervised hierarchical clustering of CNA profiles revealed a significant enrichment of a subgroup of patients with female gender, long latency (>17 years) and negative lymph node status. Further, we identified single CNAs that were significantly associated with latency, gender, radiation dose and BRAF V600E mutation status. Multivariate analysis revealed no interactions but additive effects of parameters gender, latency and dose on CNAs. The previously identified radiation-associated gain of the chromosomal bands 7q11.22-11.23 was present in 29% of cases. Moreover, comparison of our radiation-associated PTC data set with the TCGA data set on sporadic PTCs revealed altered copy numbers of the tumor driver genes NF2 and CHEK2. Further, we integrated the CNA data with transcriptomic data that were available on a subset of the herein analyzed cohort and did not find statistically significant associations between the two molecular layers. However, applying hierarchical clustering on a ‘BRAF-like/RAS-like’ transcriptome signature split the cases into four groups, one of which containing all BRAF-positive cases validating the signature in an independent data set. PMID:26320103

A trade secret model for genomic biobanking.

Science.gov (United States)

Conley, John M; Mitchell, Robert; Cadigan, R Jean; Davis, Arlene M; Dobson, Allison W; Gladden, Ryan Q

2012-01-01

Genomic biobanks present ethical challenges that are qualitatively unique and quantitatively unprecedented. Many critics have questioned whether the current system of informed consent can be meaningfully applied to genomic biobanking. Proposals for reform have come from many directions, but have tended to involve incremental change in current informed consent practice. This paper reports on our efforts to seek new ideas and approaches from those whom informed consent is designed to protect: research subjects. Our model emerged from semi-structured interviews with healthy volunteers who had been recruited to join either of two biobanks (some joined, some did not), and whom we encouraged to explain their concerns and how they understood the relationship between specimen contributors and biobanks. These subjects spoke about their DNA and the information it contains in ways that were strikingly evocative of the legal concept of the trade secret. They then described the terms and conditions under which they might let others study their DNA, and there was a compelling analogy to the commonplace practice of trade secret licensing. We propose a novel biobanking model based on this trade secret concept, and argue that it would be a practical, legal, and ethical improvement on the status quo. © 2012 American Society of Law, Medicine & Ethics, Inc.

Genome Modeling System: A Knowledge Management Platform for Genomics.

Directory of Open Access Journals (Sweden)

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.

Mitochondrial genome and epigenome: two sides of the same coin.

Science.gov (United States)

D'Aquila, Patrizia; Montesanto, Alberto; Guarasci, Francesco; Passarino, Giuseppe; Bellizzi, Dina

2017-01-01

The involvement of mitochondrial content, structure and function as well as of the mitochondrial genome (mtDNA) in cell biology, by participating in the main processes occurring in the cells, has been a topic of intense interest for many years. More specifically, the progressive accumulation of variations in mtDNA of post-mitotic tissues represents a major contributing factor to both physiological and pathological phenotypes. Recently, an epigenetic overlay on mtDNA genetics is emerging, as demonstrated by the implication of the mitochondrial genome in the regulation of the intracellular epigenetic landscape being itself object of epigenetic modifications. Indeed, in vitro and population studies strongly suggest that, similarly to nuclear DNA, also mtDNA is subject to methylation and hydroxymethylation. It follows that the mitochondrial-nucleus cross talk and mitochondrial retrograde signaling in cellular properties require a concerted functional cooperation between genetic and epigenetic changes. The present paper aims to review the current advances in mitochondrial epigenetics studies and the increasing indication of mtDNA methylation status as an attractive biomarker for peculiar pathological phenotypes and environmental exposure.

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.

Nuclear DNA-Content in Mesenchymal Lesions in Dogs: Its Value as Marker of Malignancy and Extent of Genomic Instability

International Nuclear Information System (INIS)

Boerkamp, Kim M.; Rutteman, Gerard R.; Kik, Marja J. L.; Kirpensteijn, Jolle; Schulze, Christoph; Grinwis, Guy C. M.

2012-01-01

DNA-aneuploidy may reflect the malignant nature of mesenchymal proliferations and herald gross genomic instability as a mechanistic factor in tumor genesis. DNA-ploidy and -index were determined by flow cytometry in canine inflammatory or neoplastic mesenchymal tissues and related to clinico-pathological features, biological behavior and p53 gene mutational status. Half of all sarcomas were aneuploid. Benign mesenchymal neoplasms were rarely aneuploid and inflammatory lesions not at all. The aneuploidy rate was comparable to that reported for human sarcomas with significant variation amongst subtypes. DNA-ploidy status in canines lacked a relation with histological grade of malignancy, in contrast to human sarcomas. While aneuploidy was related to the development of metastases in soft tissue sarcomas it was not in osteosarcomas. No relation amongst sarcomas was found between ploidy status and presence of P53 gene mutations. Heterogeneity of the DNA index between primary and metastatic sarcoma sites was present in half of the cases examined. Hypoploidy is more common in canine sarcomas and hyperploid cases have less deviation of the DNA index than human sarcomas. The variation in the presence and extent of aneuploidy amongst sarcoma subtypes indicates variation in genomic instability. This study strengthens the concept of interspecies variation in the evolution of gross chromosomal aberrations during cancer development

Nuclear DNA-Content in Mesenchymal Lesions in Dogs: Its Value as Marker of Malignancy and Extent of Genomic Instability

Science.gov (United States)

Boerkamp, Kim M.; Rutteman, Gerard R.; Kik, Marja J. L.; Kirpensteijn, Jolle; Schulze, Christoph; Grinwis, Guy C. M.

2012-01-01

DNA-aneuploidy may reflect the malignant nature of mesenchymal proliferations and herald gross genomic instability as a mechanistic factor in tumor genesis. DNA-ploidy and -index were determined by flow cytometry in canine inflammatory or neoplastic mesenchymal tissues and related to clinico-pathological features, biological behavior and p53 gene mutational status. Half of all sarcomas were aneuploid. Benign mesenchymal neoplasms were rarely aneuploid and inflammatory lesions not at all. The aneuploidy rate was comparable to that reported for human sarcomas with significant variation amongst subtypes. DNA-ploidy status in canines lacked a relation with histological grade of malignancy, in contrast to human sarcomas. While aneuploidy was related to the development of metastases in soft tissue sarcomas it was not in osteosarcomas. No relation amongst sarcomas was found between ploidy status and presence of P53 gene mutations. Heterogeneity of the DNA index between primary and metastatic sarcoma sites was present in half of the cases examined. Hypoploidy is more common in canine sarcomas and hyperploid cases have less deviation of the DNA index than human sarcomas. The variation in the presence and extent of aneuploidy amongst sarcoma subtypes indicates variation in genomic instability. This study strengthens the concept of interspecies variation in the evolution of gross chromosomal aberrations during cancer development. PMID:24213507

Nuclear DNA-Content in Mesenchymal Lesions in Dogs: Its Value as Marker of Malignancy and Extent of Genomic Instability

Energy Technology Data Exchange (ETDEWEB)

Boerkamp, Kim M., E-mail: K.M.Boerkamp@uu.nl; Rutteman, Gerard R. [Department of Clinical Science of Companion Animals, Faculty of Veterinary Medicine, UU, Yalelaan 104, 3584 CM, Utrecht (Netherlands); Kik, Marja J. L. [Department of Pathobiology, Faculty of Veterinary Medicine, UU, Yalelaan 1, 3508 TD, Utrecht (Netherlands); Kirpensteijn, Jolle [Department of Clinical Science of Companion Animals, Faculty of Veterinary Medicine, UU, Yalelaan 104, 3584 CM, Utrecht (Netherlands); Schulze, Christoph; Grinwis, Guy C. M. [Department of Pathobiology, Faculty of Veterinary Medicine, UU, Yalelaan 1, 3508 TD, Utrecht (Netherlands)

2012-12-03

DNA-aneuploidy may reflect the malignant nature of mesenchymal proliferations and herald gross genomic instability as a mechanistic factor in tumor genesis. DNA-ploidy and -index were determined by flow cytometry in canine inflammatory or neoplastic mesenchymal tissues and related to clinico-pathological features, biological behavior and p53 gene mutational status. Half of all sarcomas were aneuploid. Benign mesenchymal neoplasms were rarely aneuploid and inflammatory lesions not at all. The aneuploidy rate was comparable to that reported for human sarcomas with significant variation amongst subtypes. DNA-ploidy status in canines lacked a relation with histological grade of malignancy, in contrast to human sarcomas. While aneuploidy was related to the development of metastases in soft tissue sarcomas it was not in osteosarcomas. No relation amongst sarcomas was found between ploidy status and presence of P53 gene mutations. Heterogeneity of the DNA index between primary and metastatic sarcoma sites was present in half of the cases examined. Hypoploidy is more common in canine sarcomas and hyperploid cases have less deviation of the DNA index than human sarcomas. The variation in the presence and extent of aneuploidy amongst sarcoma subtypes indicates variation in genomic instability. This study strengthens the concept of interspecies variation in the evolution of gross chromosomal aberrations during cancer development.

Nuclear DNA-Content in Mesenchymal Lesions in Dogs: Its Value as Marker of Malignancy and Extent of Genomic Instability

Directory of Open Access Journals (Sweden)

Christoph Schulze

2012-12-01

Full Text Available DNA-aneuploidy may reflect the malignant nature of mesenchymal proliferations and herald gross genomic instability as a mechanistic factor in tumor genesis. DNA-ploidy and -index were determined by flow cytometry in canine inflammatory or neoplastic mesenchymal tissues and related to clinico-pathological features, biological behavior and p53 gene mutational status. Half of all sarcomas were aneuploid. Benign mesenchymal neoplasms were rarely aneuploid and inflammatory lesions not at all. The aneuploidy rate was comparable to that reported for human sarcomas with significant variation amongst subtypes. DNA-ploidy status in canines lacked a relation with histological grade of malignancy, in contrast to human sarcomas. While aneuploidy was related to the development of metastases in soft tissue sarcomas it was not in osteosarcomas. No relation amongst sarcomas was found between ploidy status and presence of P53 gene mutations. Heterogeneity of the DNA index between primary and metastatic sarcoma sites was present in half of the cases examined. Hypoploidy is more common in canine sarcomas and hyperploid cases have less deviation of the DNA index than human sarcomas. The variation in the presence and extent of aneuploidy amongst sarcoma subtypes indicates variation in genomic instability. This study strengthens the concept of interspecies variation in the evolution of gross chromosomal aberrations during cancer development.

The present status of medical treatment for patients of advanced lung cancer

International Nuclear Information System (INIS)

Kira, Shiro; Kuratomi, Yushiro; Matsuoka, Rokuro; Ishihara, Teruo

1982-01-01

Management of patients with inoperable, advanced lung cancer is one of the most important problems for many chest physicians, because those patients with stage 3 and stage 4 are over 70% of total patients. Although surgical treatment is attempted even in the case of stage 3 patients, many factors such as age, performance status, pulmonary and circulatory disorders accompanied with them and sometimes patient's refusal for surgical treatment preclude it. Therefore, therapeutic approach for these patients is focused on relieving their pains and troubles in their daily life. Radiation therapy is only a local treatment, but it can often control variable clinical manifestations with a highly probable estimation. Many patients can be free of disease even for a limited period. From this view-point, even at present, radiation therapy is a preferable therapeutic modality to maintain individual patient's better quality of life. (author)

International Fusion Materials Irradiation Facility conceptual design activity. Present status and perspective

International Nuclear Information System (INIS)

Kondo, Tatsuo; Noda, Kenji; Oyama, Yukio

1998-01-01

For developing the materials for nuclear fusion reactors, it is indispensable to study on the neutron irradiation behavior under fusion reactor conditions, but there is not any high energy neutron irradiation facility that can simulate fusion reactor conditions at present. Therefore, the investigation of the IFMIF was begun jointly by Japan, USA, Europe and Russia following the initiative of IEA. The conceptual design activities were completed in 1997. As to the background and the course, the present status of the research on heavy irradiation and the testing means for fusion materials, the requirement and the technical basis of high energy neutron irradiation, and the international joint design activities are reported. The materials for fusion reactors are exposed to the neutron irradiation with the energy spectra up to 14 MeV. The requirements from the users that the IFMIF should satisfy, the demand of the tests for the materials of prototype and demonstration fusion reactors and the evaluation of the neutron field characteristics of the IFMIF are discussed. As to the conceptual design of the IFMIF, the whole constitution, the operational mode, accelerator system and target system are described. (K.I.)

Genome-health nutrigenomics and nutrigenetics: nutritional requirements or 'nutriomes' for chromosomal stability and telomere maintenance at the individual level.

Science.gov (United States)

Bull, Caroline; Fenech, Michael

2008-05-01

It is becoming increasingly evident that (a) risk for developmental and degenerative disease increases with more DNA damage, which in turn is dependent on nutritional status, and (b) the optimal concentration of micronutrients for prevention of genome damage is also dependent on genetic polymorphisms that alter the function of genes involved directly or indirectly in the uptake and metabolism of micronutrients required for DNA repair and DNA replication. The development of dietary patterns, functional foods and supplements that are designed to improve genome-health maintenance in individuals with specific genetic backgrounds may provide an important contribution to an optimum health strategy based on the diagnosis and individualised nutritional prevention of genome damage, i.e. genome health clinics. The present review summarises some of the recent knowledge relating to micronutrients that are associated with chromosomal stability and provides some initial insights into the likely nutritional factors that may be expected to have an impact on the maintenance of telomeres. It is evident that developing effective strategies for defining nutrient doses and combinations or 'nutriomes' for genome-health maintenance at the individual level is essential for further progress in this research field.

Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes

Science.gov (United States)

Åvall-Jääskeläinen, Silja; Paulin, Lars; Blom, Jochen

2018-01-01

Non-aureus staphylococci (NAS) are most commonly isolated from subclinical mastitis. Different NAS species may, however, have diverse effects on the inflammatory response in the udder. We determined the genome sequences of 20 staphylococcal isolates from clinical or subclinical bovine mastitis, belonging to the NAS species Staphylococcus agnetis, S. chromogenes, and S. simulans, and focused on the putative virulence factor genes present in the genomes. For comparison we used our previously published genome sequences of four S. aureus isolates from bovine mastitis. The pan-genome and core genomes of the non-aureus isolates were characterized. After that, putative virulence factor orthologues were searched in silico. We compared the presence of putative virulence factors in the NAS species and S. aureus and evaluated the potential association between bacterial genotype and type of mastitis (clinical vs. subclinical). The NAS isolates had much less virulence gene orthologues than the S. aureus isolates. One third of the virulence genes were detected only in S. aureus. About 100 virulence genes were present in all S. aureus isolates, compared to about 40 to 50 in each NAS isolate. S. simulans differed the most. Several of the virulence genes detected among NAS were harbored only by S. simulans, but it also lacked a number of genes present both in S. agnetis and S. chromogenes. The type of mastitis was not associated with any specific virulence gene profile. It seems that the virulence gene profiles or cumulative number of different virulence genes are not directly associated with the type of mastitis (clinical or subclinical), indicating that host derived factors such as the immune status play a pivotal role in the manifestation of mastitis. PMID:29610707

Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes

Directory of Open Access Journals (Sweden)

Silja Åvall-Jääskeläinen

2018-03-01

Full Text Available Non-aureus staphylococci (NAS are most commonly isolated from subclinical mastitis. Different NAS species may, however, have diverse effects on the inflammatory response in the udder. We determined the genome sequences of 20 staphylococcal isolates from clinical or subclinical bovine mastitis, belonging to the NAS species Staphylococcus agnetis, S. chromogenes, and S. simulans, and focused on the putative virulence factor genes present in the genomes. For comparison we used our previously published genome sequences of four S. aureus isolates from bovine mastitis. The pan-genome and core genomes of the non-aureus isolates were characterized. After that, putative virulence factor orthologues were searched in silico. We compared the presence of putative virulence factors in the NAS species and S. aureus and evaluated the potential association between bacterial genotype and type of mastitis (clinical vs. subclinical. The NAS isolates had much less virulence gene orthologues than the S. aureus isolates. One third of the virulence genes were detected only in S. aureus. About 100 virulence genes were present in all S. aureus isolates, compared to about 40 to 50 in each NAS isolate. S. simulans differed the most. Several of the virulence genes detected among NAS were harbored only by S. simulans, but it also lacked a number of genes present both in S. agnetis and S. chromogenes. The type of mastitis was not associated with any specific virulence gene profile. It seems that the virulence gene profiles or cumulative number of different virulence genes are not directly associated with the type of mastitis (clinical or subclinical, indicating that host derived factors such as the immune status play a pivotal role in the manifestation of mastitis.

SigmaCalc recent development and present status of the evaluated cross-sections for IBA

Energy Technology Data Exchange (ETDEWEB)

Gurbich, A.F.

2016-03-15

A new version of the SigmaCalc Internet site ( (http://sigmacalc.iate.obninsk.ru)) intended to provide evaluated differential cross-sections for spectra simulation is presented. Results of the revision of previously evaluated cross-sections and new evaluations including data for PIGE were made available to the IBA community through a simple interface. New SigmaCalc features allow users to compare evaluated differential cross-sections with the available results of the cross-section measurements taken on-the-fly from the IBANDL database and to validate them against benchmarks. The current status of the evaluated cross-sections for IBA is discussed.

Overview on collision processes of highly charged ions with atoms present status and problems

International Nuclear Information System (INIS)

Janev, R.K.

1983-05-01

This paper provides a brief discussion on the present status of the collision physics of highly charged ions with atoms. The emphasis is on the main achievements in understanding and describing the most important collision processes, and as charge transfer, ionization and Auger-type processes, and even more on those open problems which, due either to their scientific or practical importance, represent challenges to current research in this field. The paper concentrates on general ideas and problems whose development and solutions have advanced or will advance our basic understanding of the collision dynamics of multiply charged ions with atoms

The infinite sites model of genome evolution.

Science.gov (United States)

Ma, Jian; Ratan, Aakrosh; Raney, Brian J; Suh, Bernard B; Miller, Webb; Haussler, David

2008-09-23

We formalize the problem of recovering the evolutionary history of a set of genomes that are related to an unseen common ancestor genome by operations of speciation, deletion, insertion, duplication, and rearrangement of segments of bases. The problem is examined in the limit as the number of bases in each genome goes to infinity. In this limit, the chromosomes are represented by continuous circles or line segments. For such an infinite-sites model, we present a polynomial-time algorithm to find the most parsimonious evolutionary history of any set of related present-day genomes.

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.

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.

Present Status of the JENDL Project (May, 2013). WPEC Meeting, Paris, France, 23-24 May, 2013

International Nuclear Information System (INIS)

Fukahori, Tokio; Iwamoto, Osamu; Ishikawa, Makoto

2013-01-01

This paper briefly presents the present status of the Japanese JENDL Project: organization of Japanese Nuclear Data Committee (JNDC), a research committee for JAEA research activities; Nuclear Data Evaluation (JENDL-4.0 Updated Files and JENDL-4.0 Plus, benchmarking for fission reactor applications (criticality for thermal systems, adjusted library for fast systems), new evaluations, covariances, evaluation tools, fission products decay data file); other activities such as the 2012 Symposium on Nuclear Data at Kyoto University Research Reactor Institute, the initiation of conversation on Covariance Data with users, the celebration of the Golden Jubilee (since 1963) of JNDC

A DNA-based pattern classifier with in vitro learning and associative recall for genomic characterization and biosensing without explicit sequence knowledge.

Science.gov (United States)

Lee, Ju Seok; Chen, Junghuei; Deaton, Russell; Kim, Jin-Woo

2014-01-01

Genetic material extracted from in situ microbial communities has high promise as an indicator of biological system status. However, the challenge is to access genomic information from all organisms at the population or community scale to monitor the biosystem's state. Hence, there is a need for a better diagnostic tool that provides a holistic view of a biosystem's genomic status. Here, we introduce an in vitro methodology for genomic pattern classification of biological samples that taps large amounts of genetic information from all genes present and uses that information to detect changes in genomic patterns and classify them. We developed a biosensing protocol, termed Biological Memory, that has in vitro computational capabilities to "learn" and "store" genomic sequence information directly from genomic samples without knowledge of their explicit sequences, and that discovers differences in vitro between previously unknown inputs and learned memory molecules. The Memory protocol was designed and optimized based upon (1) common in vitro recombinant DNA operations using 20-base random probes, including polymerization, nuclease digestion, and magnetic bead separation, to capture a snapshot of the genomic state of a biological sample as a DNA memory and (2) the thermal stability of DNA duplexes between new input and the memory to detect similarities and differences. For efficient read out, a microarray was used as an output method. When the microarray-based Memory protocol was implemented to test its capability and sensitivity using genomic DNA from two model bacterial strains, i.e., Escherichia coli K12 and Bacillus subtilis, results indicate that the Memory protocol can "learn" input DNA, "recall" similar DNA, differentiate between dissimilar DNA, and detect relatively small concentration differences in samples. This study demonstrated not only the in vitro information processing capabilities of DNA, but also its promise as a genomic pattern classifier that could

History and present status of field application of radiotracers, 3

International Nuclear Information System (INIS)

Kimura, Shigehiko; Sato, Otomaru.

1988-01-01

The history and present status of the utilization of RI tracers for hydrology are described by dividing into surface water and groundwater. By the birth of nuclear reactors, the availability of RIs became easy, and the utilization of tracers for hydrology has been attempted worldwide. The large scale development of water resources is required for increasing agricultural production, and the analysis of the actual condition of hydrological phenomena is indispensable for the purpose. The hydrology committee of IAEA aided the development of new techniques in the peaceful use of atomic energy, and let developing countries use the developed techniques together with researchers. The research on the field application of RI tracers in Japan began in agriculture, and the investigation of water leak in dams, the measurement of flow rate and flow velocity in rivers, the detection of the state of sand movement on sea bottom, the analysis of groundwater flow and so on have been carried out. Also the recent situation in foreign countries is reported about the measurement of flow rate, the measurement of flowing-down time and diffusion, the analysis of the behavior of lake water, the movement of mud and sediment, and the analysis of groundwater flow. (Kako, I.)

History and present status of field application of radiotracers, 3

Energy Technology Data Exchange (ETDEWEB)

Kimura, Shigehiko; Sato, Otomaru

1988-06-01

The history and present status of the utilization of RI tracers for hydrology are described by dividing into surface water and groundwater. By the birth of nuclear reactors, the availability of RIs became easy, and the utilization of tracers for hydrology has been attempted worldwide. The large scale development of water resources is required for increasing agricultural production, and the analysis of the actual condition of hydrological phenomena is indispensable for the purpose. The hydrology committee of IAEA aided the development of new techniques in the peaceful use of atomic energy, and let developing countries use the developed techniques together with researchers. The research on the field application of RI tracers in Japan began in agriculture, and the investigation of water leak in dams, the measurement of flow rate and flow velocity in rivers, the detection of the state of sand movement on sea bottom, the analysis of groundwater flow and so on have been carried out. Also the recent situation in foreign countries is reported about the measurement of flow rate, the measurement of flowing-down time and diffusion, the analysis of the behavior of lake water, the movement of mud and sediment, and the analysis of groundwater flow. (Kako, I.).

The Large Hadron Collider: Present Status and Prospects

CERN Document Server

Evans, Lyndon R

2000-01-01

The Large Hadron Collider (LHC), due to be commissioned in 2005, will provide particle physics with the first laboratory tool to access the energy frontier above 1 TeV. In order to achieve this , protons must be accelerated and stored at 7 TeV, colliding with an unprecedented luminosity of 1034 cm-2 s-1. The 8.3 Tesla guide field is obtained using conventional NbTi technology cooled to below the lambda point of helium. Considerable modification of the infrastructure around the existing LEP tunnel is needed to house the LHC machine and detectors. The project is advancing according to schedule with most of the major hardware systems including cryogenics and magnets under construction. A brief status report is given and future prospects are discussed.

The Large Hadron Collider Present Status and Prospects

CERN Document Server

Evans, Lyndon R

2001-01-01

The Large Hadron Collider (LHC), due to be commissioned in 2005, will provide particle physics with the first laboratory tool to access the energy frontier above 1 TeV. In order to achieve this , protons must be accelerated and stored at 7 TeV, colliding with an unprecedented luminosity of 1034 cm-2 s-1. The 8.3 Tesla guide field is obtained using conventional NbTi technology cooled to below the lambda point of helium. Considerable modification of the infrastructure around the existing LEP tunnel is needed to house the LHC machine and detectors. The project is advancing according to schedule with most of the major hardware systems including cryogenics and magnets under construction. A brief status report is given and future prospects are discussed.

Present status of the microscopic study of low-lying collective states in spherical and transitional nuclei

International Nuclear Information System (INIS)

Marumori, Toshio; Takada, Kenjiro; Sakata, Fumihiko.

1981-12-01

The history and the present status of the microscopic study of the low-lying collective excited states in spherical and transitional nuclei are discussed by putting emphasis on explaining the rather modern microscopic investigations of the concept of collective subspace. Importance of the dynamical interplay between the pairing and the quadrupole correlations is emphasized as a crucial element to mediate coupling between the collective and non-collective subspace. (author)

Present status of the NIJI-IV storage-ring free-electron lasers

Energy Technology Data Exchange (ETDEWEB)

Yamazaki, T.; Yamada, K.; Sei, N. [Electrotechnical Lab., Ibaraki (Japan)] [and others

1995-12-31

The tunable region of the free-electron-laser (FEL) wavelength with the NIJI-IV system is now 348{approximately}595 nm. After the lasing at 352 nm in 1994, the quality of the electron beam stored in the ring has been improved further, and the highest peak intensity of the laser obtained so far is more than 300 times as high as that of the resonated spontaneous emission. The macro-temporal structure of the lasing has been greatly improved. Recently, a single-bunch injection system was completed, and the system has been installed in the injector linac, which is expected to increase the peak stored-beam current. The commissioning and the test of the new system is under way. The beam transporting system from the linac to the ring is also being modified by increasing the number of quadrupole magnets. The experiments related to the FEL in the ultraviolet wavelength region will be begun in this coming May. The results and the status of the FEL experiments will be presented at the Conference.

Present status and future prospects for nonelectrical uses of geothermal resources

Energy Technology Data Exchange (ETDEWEB)

Howard, J.H. (ed.)

1975-10-03

This report, which is part of a study initiated by the NATO Committee on the Challenges of Modern Society (CCMS), describes the current status of nonelectrical uses of geothermal resources. Such resources are defined as geothermal fluids between the temperatures of 50 and 160/sup 0/C. Current and potential uses of these resources including residential and commercial, agricultural and industrial applications are described. Also discussed are exploration and drilling; extraction and distribution; environmental impact; and economic and regulatory problems. Applications in a number of countries are described. Among the report's conclusions are: (1) Geothermal resources are widely distributed throughout the world. (2) The extraction of these resources presents no serious technical problems. (3) A wide variety of economically viable applications for these resources currently exists. (4) Current nonelectrical applications have a favorable economic structure compared with those of other energy sources. (5) Disposal of spent fluids has a significant ecological impact. Reinjection appears to be the most likely alternative. (6) The legal and institutional framework surrounding these applications needs both clarification and simplification.

Draft Genome Sequence of Lactobacillus rhamnosus 2166.

OpenAIRE

Karlyshev, Andrey V.; Melnikov, Vyacheslav G.; Kosarev, Igor V.; Abramov, Vyacheslav M.

2014-01-01

In this report, we present a draft sequence of the genome of Lactobacillus rhamnosus strain 2166, a potential novel probiotic. Genome annotation and read mapping onto a reference genome of L. rhamnosus strain GG allowed for the identification of the differences and similarities in the genomic contents and gene arrangements of these strains.

Comparative Genomics in Homo sapiens.

Science.gov (United States)

Oti, Martin; Sammeth, Michael

2018-01-01

Genomes can be compared at different levels of divergence, either between species or within species. Within species genomes can be compared between different subpopulations, such as human subpopulations from different continents. Investigating the genomic differences between different human subpopulations is important when studying complex diseases that are affected by many genetic variants, as the variants involved can differ between populations. The 1000 Genomes Project collected genome-scale variation data for 2504 human individuals from 26 different populations, enabling a systematic comparison of variation between human subpopulations. In this chapter, we present step-by-step a basic protocol for the identification of population-specific variants employing the 1000 Genomes data. These variants are subsequently further investigated for those that affect the proteome or RNA splice sites, to investigate potentially biologically relevant differences between the populations.

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

Directory of Open Access Journals (Sweden)

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

Present Status of Intertidal Biodiversity in and around Mumbai (West Coast of India

Directory of Open Access Journals (Sweden)

Balasaheb Kulkarni

2017-03-01

Full Text Available During the present investigation, Girgaon, Marine Drive, Haji Ali and Gorai Creek in Mumbai were selected for biodiversity assessment following a protocol for natural geography in shore areas. Fifty nine macrobenthic molluscs, arthropods, coelenterates and echinoderms at these sites were recorded. The maximum density of gastropods and clams was observed at Marine Drive shore. At Gorai Creek, there were plentiful Telescopium telescopium, Potamidus cingulatis, mudskipper and fiddler crabs. Studies shows that the biodiversity status of the selected sites varies with respect to location, type of substratum and season. Pollution was observed to have a noticeable effect on clams at Girgaon coast, where many Paphia textile shells were observed to be filled with mud and coated with black colour.

The human homolog of S. cerevisiae CDC27, CDC27 Hs, is encoded by a highly conserved intronless gene present in multiple copies in the human genome

Energy Technology Data Exchange (ETDEWEB)

Devor, E.J.; Dill-Devor, R.M. [Univ. of Iowa College of Medicine, Iowa City (United States)

1994-09-01

We have obtained a number of unique sequences via PCR amplification of human genomic DNA using degenerate primers under low stringency (42{degrees}C). One of these, an 853 bp product, has been identified as a partial genomic sequence of the human homolog of the S. cerevisiae CDC27 gene, CDC27Hs (GenBank No. U00001). This gene, reported by Turgendreich et al. is also designated EST00556 from Adams et al. We have undertaken a more detailed examination of our sequence, MCP34N, and have found that: 1. the genomic sequence is nearly identical to CDC27Hs over its entire 853 bp length; 2. an MCP34N-specific PCR assay of several non-human primate species reveals amplification products in chimpanzee and gorilla genomes having greater than 90% sequence identity with CDC27Hs; and 3. an MCP34N-specific PCR assay of the BIOS hybrid cell line panel gives a discordancy pattern suggesting multiple loci. Based upon these data, we present the following initial characterization: 1. the complete MCP34N sequence identity with CDC27Hs indicates that the latter is encoded by an intronless gene; 2. CDC27Hs is highly conserved among higher primates; and 3. CDC27Hs is present in multiple copies in the human genome. These characteristics, taken together with those initially reported for CDC27Hs, suggest that this is an old gene that carries out an important but, as yet, unknown function in the human brain.

OI-57, a Genomic Island of Escherichia coli O157, Is Present in Other Seropathotypes of Shiga Toxin-Producing E. coli Associated with Severe Human Disease▿

Science.gov (United States)

Imamovic, Lejla; Tozzoli, Rosangela; Michelacci, Valeria; Minelli, Fabio; Marziano, Maria Luisa; Caprioli, Alfredo; Morabito, Stefano

2010-01-01

Strains of Shiga toxin-producing Escherichia coli (STEC) are a heterogeneous E. coli group that may cause severe disease in humans. STEC have been categorized into seropathotypes (SPTs) based on their phenotypic and molecular characteristics and the clinical features of the associated diseases. SPTs range from A to E, according to a decreasing rank of pathogenicity. To define the virulence gene asset (“virulome”) characterizing the highly pathogenic SPTs, we used microarray hybridization to compare the whole genomes of STEC belonging to SPTs B, C, and D with that of STEC O157 (SPT A). The presence of the open reading frames (ORFs) associated with SPTs A and B was subsequently investigated by PCR in a larger panel of STEC and in other E. coli strains. A genomic island termed OI-57 was present in SPTs A and B but not in the other SPTs. OI-57 harbors the putative virulence gene adfO, encoding a factor enhancing the adhesivity of STEC O157, and ckf, encoding a putative killing factor for the bacterial cell. PCR analyses showed that OI-57 was present in its entirety in the majority of the STEC genomes examined, indicating that it represents a stable acquisition of the positive clonal lineages. OI-57 was also present in a high proportion of the human enteropathogenic E. coli genomes assayed, suggesting that it could be involved in the attaching-and-effacing colonization of the intestinal mucosa. In conclusion, OI-57 appears to be part of the virulome of pathogenic STEC and further studies are needed to elucidate its role in the pathogenesis of STEC infections. PMID:20823207

The integrated microbial genome resource of analysis.

Science.gov (United States)

Checcucci, Alice; Mengoni, Alessio

2015-01-01

Integrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis.

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.

Ethical considerations of research policy for personal genome analysis: the approach of the Genome Science Project in Japan.

Science.gov (United States)

Minari, Jusaku; Shirai, Tetsuya; Kato, Kazuto

2014-12-01

As evidenced by high-throughput sequencers, genomic technologies have recently undergone radical advances. These technologies enable comprehensive sequencing of personal genomes considerably more efficiently and less expensively than heretofore. These developments present a challenge to the conventional framework of biomedical ethics; under these changing circumstances, each research project has to develop a pragmatic research policy. Based on the experience with a new large-scale project-the Genome Science Project-this article presents a novel approach to conducting a specific policy for personal genome research in the Japanese context. In creating an original informed-consent form template for the project, we present a two-tiered process: making the draft of the template following an analysis of national and international policies; refining the draft template in conjunction with genome project researchers for practical application. Through practical use of the template, we have gained valuable experience in addressing challenges in the ethical review process, such as the importance of sharing details of the latest developments in genomics with members of research ethics committees. We discuss certain limitations of the conventional concept of informed consent and its governance system and suggest the potential of an alternative process using information technology.

Status of Chandigarh variable energy cyclotron and present experimental programmes

International Nuclear Information System (INIS)

Govil, I.M.

2005-01-01

The paper describes the status report of the Chandigarh variable energy cyclotron and some of the recent modifications which has improved the stability and performance of the machine considerably. The machine is now used for Proton Induced X-Ray Emission (PIXE) for trace element analysis along with nuclear irradiation for material science research and Nuclear Spectroscopy using (p, n γ) reaction. (author)

Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences.

Science.gov (United States)

Haber, Marc; Doumet-Serhal, Claude; Scheib, Christiana; Xue, Yali; Danecek, Petr; Mezzavilla, Massimo; Youhanna, Sonia; Martiniano, Rui; Prado-Martinez, Javier; Szpak, Michał; Matisoo-Smith, Elizabeth; Schutkowski, Holger; Mikulski, Richard; Zalloua, Pierre; Kivisild, Toomas; Tyler-Smith, Chris

2017-08-03

The Canaanites inhabited the Levant region during the Bronze Age and established a culture that became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole genomes from ∼3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalog modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600-3,550 years ago, coinciding with recorded massive population movements in Mesopotamia during the mid-Holocene. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate that this Eurasian ancestry arrived in the Levant around 3,750-2,170 years ago during a period of successive conquests by distant populations. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Complete mitochondrial genome of threatened mahseer Tor tor (Hamilton 1822) and its phylogenetic relationship within Cyprinidae family.

Science.gov (United States)

Pavan-Kumar, A; Raman, Sudhanshu; Koringa, Prakash G; Patel, Namrata; Shah, Tejas; Singh, Rajeev K; Krishna, Gopal; Joshi, C G; Gireesh-Babu, P; Chaudhari, Aparna

2016-12-01

The mahseers (Tor, Neolissochilus and Naziritor) are an important group of fishes endemic to Asia with the conservation status of most species evaluated as threatened. Conservation plans to revive these declining wild populations are hindered by unstable taxonomy. Molecular phylogeny studies with mitochondrial genome have been successfully used to reconstruct the phylogenetic tree and to resolve taxonomic ambiguity. In the present study, complete mitochondrial genome of Tor tor has been sequenced using ion torrent next-generation sequencing platform with coverage of more than 1000 x. Comparative mitogenome analysis shows higher divergence value at ND1 gene than COI gene. Further, occurrence of a distinct genetic lineage of T. tor is revealed. The phylogenetic relationship among mahseer group has been defined as Neolissochilus hexagonolepis ((T. sinensis (T. putitora, T. tor), (T. khudree, T. tambroides)).

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.

Bioinformatics of genomic association mapping

NARCIS (Netherlands)

Vaez Barzani, Ahmad

2015-01-01

In this thesis we present an overview of bioinformatics-based approaches for genomic association mapping, with emphasis on human quantitative traits and their contribution to complex diseases. We aim to provide a comprehensive walk-through of the classic steps of genomic association mapping

Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

Directory of Open Access Journals (Sweden)

João Perdigão

2015-01-01

Full Text Available Multidrug- (MDR and extensively drug-resistant (XDR tuberculosis (TB present a challenge to disease control and elimination goals. Lisbon, Portugal, has a high TB incidencerate and unusual and successful XDR-TB strains that have been found in circulation foralmost two decades. For the last 20 years, a continued circulation of two phylogenetic clades, Lisboa3 and Q1, which are highly associated with MDR and XDR, have been observed. In recent years, these strains have been well characterized regarding the molecular basis of drug resistance and have been inclusively subjected to whole genome sequencing (WGS. Researchers have been studying the genomic diversity of strains circulating in Lisbon and its genomic determinants through cutting-edge next generation sequencing. An enormous amount of whole genome sequence data are now available for the most prevalent and clinically relevant strains circulating in Lisbon. It is the persistence, prevalence and rapid evolution towards drug resistance that has prompted researchers to investigate the properties of these strains at the genomic level and in the future at a global transcriptomic level. Seventy Mycobacterium tuberculosis (MTB isolates, mostly recovered in Lisbon, were genotyped by 24-loci Mycobacterial Interspersed Repetitive Unit – Variable Number of Tandem Repeats (MIRU-VNTR and the genomes sequenced using a next generation sequencing platform – Illumina HiSeq 2000. The genotyping data revealed three major clusters associated with MDR-TB (Lisboa3-A, Lisboa3-B and Q1, two of which are associated with XDR-TB (Lisboa3-B and Q1, whilst the genomic data contributed to elucidating the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of MTB clinical isolates, revealed two major clades responsible for MDR/XDR-TB in the region

Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

KAUST Repository

Perdigã o, Joã o; Silva, Hugo; Machado, Diana; Macedo, Rita; Maltez, Fernando; Silva, Carla; Jordao, Luisa; Couto, Isabel; Mallard, Kim; Coll, Francesc; Hill-Cawthorne, Grant A.; McNerney, Ruth; Pain, Arnab; Clark, Taane G.; Viveiros, Miguel; Portugal, Isabel

2015-01-01

Multidrug- (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) present a challenge to disease control and elimination goals. Lisbon, Portugal, has a high TB incidence rate and unusual and successful XDR-TB strains that have been found in circulation for almost two decades. For the last 20. years, a continued circulation of two phylogenetic clades, Lisboa3 and Q1, which are highly associated with MDR and XDR, have been observed. In recent years, these strains have been well characterized regarding the molecular basis of drug resistance and have been inclusively subjected to whole genome sequencing (WGS). Researchers have been studying the genomic diversity of strains circulating in Lisbon and its genomic determinants through cutting-edge next generation sequencing. An enormous amount of whole genome sequence data are now available for the most prevalent and clinically relevant strains circulating in Lisbon.It is the persistence, prevalence and rapid evolution towards drug resistance that has prompted researchers to investigate the properties of these strains at the genomic level and in the future at a global transcriptomic level. Seventy Mycobacterium tuberculosis (MTB) isolates, mostly recovered in Lisbon, were genotyped by 24-. loci Mycobacterial Interspersed Repetitive Unit - Variable Number of Tandem Repeats (MIRU-VNTR) and the genomes sequenced using a next generation sequencing platform - Illumina HiSeq 2000.The genotyping data revealed three major clusters associated with MDR-TB (Lisboa3-A, Lisboa3-B and Q1), two of which are associated with XDR-TB (Lisboa3-B and Q1), whilst the genomic data contributed to elucidating the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of MTB clinical isolates, revealed two major clades responsible for MDR/XDR-TB in the region: Lisboa3 and Q

Genomic diversity of drug-resistant Mycobacterium tuberculosis isolates in Lisbon Portugal: Towards tuberculosis genomic epidemiology

KAUST Repository

Perdigão, João

2015-03-01

Multidrug- (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) present a challenge to disease control and elimination goals. Lisbon, Portugal, has a high TB incidence rate and unusual and successful XDR-TB strains that have been found in circulation for almost two decades. For the last 20. years, a continued circulation of two phylogenetic clades, Lisboa3 and Q1, which are highly associated with MDR and XDR, have been observed. In recent years, these strains have been well characterized regarding the molecular basis of drug resistance and have been inclusively subjected to whole genome sequencing (WGS). Researchers have been studying the genomic diversity of strains circulating in Lisbon and its genomic determinants through cutting-edge next generation sequencing. An enormous amount of whole genome sequence data are now available for the most prevalent and clinically relevant strains circulating in Lisbon.It is the persistence, prevalence and rapid evolution towards drug resistance that has prompted researchers to investigate the properties of these strains at the genomic level and in the future at a global transcriptomic level. Seventy Mycobacterium tuberculosis (MTB) isolates, mostly recovered in Lisbon, were genotyped by 24-. loci Mycobacterial Interspersed Repetitive Unit - Variable Number of Tandem Repeats (MIRU-VNTR) and the genomes sequenced using a next generation sequencing platform - Illumina HiSeq 2000.The genotyping data revealed three major clusters associated with MDR-TB (Lisboa3-A, Lisboa3-B and Q1), two of which are associated with XDR-TB (Lisboa3-B and Q1), whilst the genomic data contributed to elucidating the phylogenetic positioning of circulating MDR-TB strains, showing a high predominance of a single SNP cluster group 5. Furthermore, a genome-wide phylogeny analysis from these strains, together with 19 publicly available genomes of MTB clinical isolates, revealed two major clades responsible for MDR/XDR-TB in the region: Lisboa3 and Q

Megabase replication domains along the human genome: relation to chromatin structure and genome organisation.

Science.gov (United States)

Audit, Benjamin; Zaghloul, Lamia; Baker, Antoine; Arneodo, Alain; Chen, Chun-Long; d'Aubenton-Carafa, Yves; Thermes, Claude

2013-01-01

In higher eukaryotes, the absence of specific sequence motifs, marking the origins of replication has been a serious hindrance to the understanding of (i) the mechanisms that regulate the spatio-temporal replication program, and (ii) the links between origins activation, chromatin structure and transcription. In this chapter, we review the partitioning of the human genome into megabased-size replication domains delineated as N-shaped motifs in the strand compositional asymmetry profiles. They collectively span 28.3% of the genome and are bordered by more than 1,000 putative replication origins. We recapitulate the comparison of this partition of the human genome with high-resolution experimental data that confirms that replication domain borders are likely to be preferential replication initiation zones in the germline. In addition, we highlight the specific distribution of experimental and numerical chromatin marks along replication domains. Domain borders correspond to particular open chromatin regions, possibly encoded in the DNA sequence, and around which replication and transcription are highly coordinated. These regions also present a high evolutionary breakpoint density, suggesting that susceptibility to breakage might be linked to local open chromatin fiber state. Altogether, this chapter presents a compartmentalization of the human genome into replication domains that are landmarks of the human genome organization and are likely to play a key role in genome dynamics during evolution and in pathological situations.

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

Directory of Open Access Journals (Sweden)

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

Present status and future directions of the Mayo/IBM PACS project

Science.gov (United States)

Morin, Richard L.; Forbes, Glenn S.; Gehring, Dale G.; Salutz, James R.; Pavlicek, William

1991-07-01

This joint project began in 1988 and was motivated by the need to develop an alternative to the archival process in place at that time (magnetic tape) for magnetic resonance imaging and neurological computed tomography. In addition, this project was felt to be an important step in gaining the necessary clinical experience for the future implementation of various aspects of electronic imaging. The initial phase of the project was conceived and developed to prove the concept, test the fundamental components, and produce performance measurements for future work. The key functions of this phase centered on attachment of imaging equipment (GE Signa) and archival processes using a non-dedicated (institutionally supplied) local area network (LAN). Attachment of imaging equipment to the LAN was performed using commercially available devices (Ethernet, PS/2, Token Ring). Image data were converted to ACR/NEMA format with retention of the vendor specific header information. Performance measurements were encouraging and led to the design of following projects. The second phase has recently been concluded. The major features of this phase have been to greatly expand the network, put the network into clinical use, establish an efficient and useful viewing station, include diagnostic reports in the archive data, provide wide area network (WAN) capability via ISDN, and establish two-way real-time video between remote sites. This phase has heightened both departmental and institutional thought regarding various issues raised by electronic imaging. Much discussion regarding both present as well as future archival processes has occurred. The use of institutional LAN resources has proven to be adequate for the archival function examined thus far. Experiments to date have shown that use of dedicated resources will be necessary for retrieval activities at even a basic level. This report presents an overview of the background present status and future directions of the project.

Epigenetics of obesity: beyond the genome sequence.

Science.gov (United States)

Cordero, Paul; Li, Jiawei; Oben, Jude A

2015-07-01

After the study of the gene code as a trigger for obesity, epigenetic code has appeared as a novel tool in the diagnosis, prognosis and treatment of obesity, and its related comorbidities. This review summarizes the status of the epigenetic field associated with obesity, and the current epigenetic-based approaches for obesity treatment. Thanks to technical advances, novel and key obesity-associated polymorphisms have been described by genome-wide association studies, but there are limitations with their predictive power. Epigenetics is also studied for disease association, which involves decoding of the genome information, transcriptional status and later phenotypes. Obesity could be induced during adult life by feeding and other environmental factors, and there is a strong association between obesity features and specific epigenetic patterns. These patterns could be established during early life stages, and programme the risk of obesity and its comorbidities during adult life. Furthermore, recent studies have shown that DNA methylation profile could be applied as biomarkers of diet-induced weight loss treatment. High-throughput technologies, recently implemented for commercial genetic test panels, could soon lead to the creation of epigenetic test panels for obesity. Nonetheless, epigenetics is a modifiable risk factor, and different dietary patterns or environmental insights during distinct stages of life could lead to rewriting of the epigenetic profile.

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.

Sequencing the CHO DXB11 genome reveals regional variations in genomic stability and haploidy

DEFF Research Database (Denmark)

Kaas, Christian Schrøder; Kristensen, Claus; Betenbaugh, Michael J.

2015-01-01

Background: The DHFR negative CHO DXB11 cell line (also known as DUX-B11 and DUKX) was historically the first CHO cell line to be used for large scale production of heterologous proteins and is still used for production of a number of complex proteins.  Results: Here we present the genomic sequence...... of the CHO DXB11 genome sequenced to a depth of 33x. Overall a significant genomic drift was seen favoring GC -> AT point mutations in line with the chemical mutagenesis strategy used for generation of the cell line. The sequencing depth for each gene in the genome revealed distinct peaks at sequencing...... in eight additional analyzed CHO genomes (15-20% haploidy) but not in the genome of the Chinese hamster. The dhfr gene is confirmed to be haploid in CHO DXB11; transcriptionally active and the remaining allele contains a G410C point mutation causing a Thr137Arg missense mutation. We find similar to 2...

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.

The effect of marital status on the presentation and outcomes of elderly male veterans hospitalized for pneumonia.

Science.gov (United States)

Metersky, Mark L; Fine, Michael J; Mortensen, Eric M

2012-10-01

Although marital status has been shown to affect the outcomes of many conditions, there are limited data on the relationships between marital status and the presentation and outcomes of pneumonia. We used Veterans Affairs administrative databases to identify a retrospective cohort of male veterans age ≥ 65 years hospitalized for pneumonia between 2002 and 2007. We assessed unadjusted and adjusted associations between marital status and mortality, hospital length of stay, and readmission to the hospital using generalized linear mixed-effect models with admitting hospital as a random effect and adjusted for baseline patient characteristics. There were 48,635 patients (26,558 married and 22,077 unmarried) in the study. Married men had a slightly higher Charlson comorbidity score (3.0 vs 2.8, P Married patients had significantly lower crude and adjusted in-hospital mortality (9.4% vs 10.6%; adjusted OR, 0.87; 95% CI, 0.81-0.93) and mortality during the 90 days after hospital discharge (14.7% vs 16.0%; adjusted OR, 0.92; 95% CI, 0.88-0.98). Their adjusted incidence rate ratio length of stay was also lower (0.92; 95% CI, 0.91-0.92). Unmarried elderly men admitted to the hospital with pneumonia have a higher risk of in-hospital and postdischarge mortality, despite having a lower degree of comorbidity. Although marital status may be a surrogate marker for other predictors, it is an easily identifiable one. These results should be considered by those responsible for care-transition decisions for patients hospitalized with pneumonia.

Present status of yellow fever: Memorandum from a PAHO Meeting

OpenAIRE

1986-01-01

An international seminar on the treatment and laboratory diagnosis of yellow fever, sponsored by the Pan American Health Organization (PAHO) and held in 1984, differed from previous meetings on yellow fever because of its emphasis on the care and management of patients and because the participants included specialists from several branches of medicine, such as hepatology, haematology, cardiology, infectious diseases, pathology and nephrology. The meeting reviewed the current status of yellow ...

Comparative genomics of the Bifidobacterium breve taxon.

Science.gov (United States)

Bottacini, Francesca; O'Connell Motherway, Mary; Kuczynski, Justin; O'Connell, Kerry Joan; Serafini, Fausta; Duranti, Sabrina; Milani, Christian; Turroni, Francesca; Lugli, Gabriele Andrea; Zomer, Aldert; Zhurina, Daria; Riedel, Christian; Ventura, Marco; van Sinderen, Douwe

2014-03-01

Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina. In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol. Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.

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.

Human Contamination in Public Genome Assemblies.

Science.gov (United States)

Kryukov, Kirill; Imanishi, Tadashi

2016-01-01

Contamination in genome assembly can lead to wrong or confusing results when using such genome as reference in sequence comparison. Although bacterial contamination is well known, the problem of human-originated contamination received little attention. In this study we surveyed 45,735 available genome assemblies for evidence of human contamination. We used lineage specificity to distinguish between contamination and conservation. We found that 154 genome assemblies contain fragments that with high confidence originate as contamination from human DNA. Majority of contaminating human sequences were present in the reference human genome assembly for over a decade. We recommend that existing contaminated genomes should be revised to remove contaminated sequence, and that new assemblies should be thoroughly checked for presence of human DNA before submitting them to public databases.

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

Directory of Open Access Journals (Sweden)

Stajich Jason E

2006-11-01

Full Text Available Abstract Background To date, most fungal phylogenies have been derived from single gene comparisons, or from concatenated alignments of a small number of genes. The increase in fungal genome sequencing presents an opportunity to reconstruct evolutionary events using entire genomes. As a tool for future comparative, phylogenomic and phylogenetic studies, we used both supertrees and concatenated alignments to infer relationships between 42 species of fungi for which complete genome sequences are available. Results A dataset of 345,829 genes was extracted from 42 publicly available fungal genomes. Supertree methods were employed to derive phylogenies from 4,805 single gene families. We found that the average consensus supertree method may suffer from long-branch attraction artifacts, while matrix representation with parsimony (MRP appears to be immune from these. A genome phylogeny was also reconstructed from a concatenated alignment of 153 universally distributed orthologs. Our MRP supertree and concatenated phylogeny are highly congruent. Within the Ascomycota, the sub-phyla Pezizomycotina and Saccharomycotina were resolved. Both phylogenies infer that the Leotiomycetes are the closest sister group to the Sordariomycetes. There is some ambiguity regarding the placement of Stagonospora nodurum, the sole member of the class Dothideomycetes present in the dataset. Within the Saccharomycotina, a monophyletic clade containing organisms that translate CTG as serine instead of leucine is evident. There is also strong support for two groups within the CTG clade, one containing the fully sexual species Candida lusitaniae, Candida guilliermondii and Debaryomyces hansenii, and the second group containing Candida albicans, Candida dubliniensis, Candida tropicalis, Candida parapsilosis and Lodderomyces elongisporus. The second major clade within the Saccharomycotina contains species whose genomes have undergone a whole genome duplication (WGD, and their close

Present status of Accelerator-Based BNCT.

Science.gov (United States)

Kreiner, Andres Juan; Bergueiro, Javier; Cartelli, Daniel; Baldo, Matias; Castell, Walter; Asoia, Javier Gomez; Padulo, Javier; Suárez Sandín, Juan Carlos; Igarzabal, Marcelo; Erhardt, Julian; Mercuri, Daniel; Valda, Alejandro A; Minsky, Daniel M; Debray, Mario E; Somacal, Hector R; Capoulat, María Eugenia; Herrera, María S; Del Grosso, Mariela F; Gagetti, Leonardo; Anzorena, Manuel Suarez; Canepa, Nicolas; Real, Nicolas; Gun, Marcelo; Tacca, Hernán

2016-01-01

This work aims at giving an updated report of the worldwide status of Accelerator-Based BNCT (AB-BNCT). There is a generalized perception that the availability of accelerators installed in hospitals, as neutron sources, may be crucial for the advancement of BNCT. Accordingly, in recent years a significant effort has started to develop such machines. A variety of possible charged-particle induced nuclear reactions and the characteristics of the resulting neutron spectra are discussed along with the worldwide activity in suitable accelerator development. Endothermic (7)Li(p,n)(7)Be and (9)Be(p,n)(9)B and exothermic (9)Be(d,n)(10)B are compared. In addition to having much better thermo-mechanical properties than Li, Be as a target leads to stable products. This is a significant advantage for a hospital-based facility. (9)Be(p,n)(9)B needs at least 4-5 MeV bombarding energy to have a sufficient yield, while (9)Be(d,n)(10)B can be utilized at about 1.4 MeV, implying the smallest possible accelerator. This reaction operating with a thin target can produce a sufficiently soft spectrum to be viable for AB-BNCT. The machines considered are electrostatic single ended or tandem accelerators or radiofrequency quadrupoles plus drift tube Linacs. (7)Li(p,n)(7)Be provides one of the best solutions for the production of epithermal neutron beams for deep-seated tumors. However, a Li-based target poses significant technological challenges. Hence, Be has been considered as an alternative target, both in combination with (p,n) and (d,n) reactions. (9)Be(d,n)(10)B at 1.4 MeV, with a thin target has been shown to be a realistic option for the treatment of deep-seated lesions.

Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes [v2; ref status: indexed, http://f1000r.es/2x3

Directory of Open Access Journals (Sweden)

Ted Kalbfleisch

2014-02-01

Full Text Available Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease.  High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals.  Comparisons between these species have provided unique insights into mammalian gene function.  However, the number of species with reference genomes is small compared to those needed for studying molecular evolutionary relationships in the tree of life.  For example, among the even-toed ungulates there are approximately 300 species whose phylogenetic relationships have been calculated in the 10k trees project.  Only six of these have reference genomes:  cattle, swine, sheep, goat, water buffalo, and bison.  Although reference sequences will eventually be developed for additional hoof stock, the resources in terms of time, money, infrastructure and expertise required to develop a quality reference genome may be unattainable for most species for at least another decade.  In this work we mapped 35 Gb of next generation sequence data of a Katahdin sheep to its own species’ reference genome (Ovis aries Oar3.1 and to that of a species that diverged 15 to 30 million years ago (Bos taurus UMD3.1.  In total, 56% of reads covered 76% of UMD3.1 to an average depth of 6.8 reads per site, 83 million variants were identified, of which 78 million were homozygous and likely represent interspecies nucleotide differences. Excluding repeat regions and sex chromosomes, nearly 3.7 million heterozygous sites were identified in this animal vs. bovine UMD3.1, representing polymorphisms occurring in sheep.  Of these, 41% could be readily mapped to orthologous positions in ovine Oar3.1 with 80% corroborated as heterozygous.  These variant sites, identified via interspecies mapping could be used for comparative genomics, disease association studies, and ultimately to understand

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

Energy Technology Data Exchange (ETDEWEB)

Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas; Harmon-Smith, Miranda; Doud, Devin; Reddy, T. B. K.; Schulz, Frederik; Jarett, Jessica; Rivers, Adam R.; Eloe-Fadrosh, Emiley A.; Tringe, Susannah G.; Ivanova, Natalia N.; Copeland, Alex; Clum, Alicia; Becraft, Eric D.; Malmstrom, Rex R.; Birren, Bruce; Podar, Mircea; Bork, Peer; Weinstock, George M.; Garrity, George M.; Dodsworth, Jeremy A.; Yooseph, Shibu; Sutton, Granger; Glöckner, Frank O.; Gilbert, Jack A.; Nelson, William C.; Hallam, Steven J.; Jungbluth, Sean P.; Ettema, Thijs J. G.; Tighe, Scott; Konstantinidis, Konstantinos T.; Liu, Wen-Tso; Baker, Brett J.; Rattei, Thomas; Eisen, Jonathan A.; Hedlund, Brian; McMahon, Katherine D.; Fierer, Noah; Knight, Rob; Finn, Rob; Cochrane, Guy; Karsch-Mizrachi, Ilene; Tyson, Gene W.; Rinke, Christian; Kyrpides, Nikos C.; Schriml, Lynn; Garrity, George M.; Hugenholtz, Philip; Sutton, Granger; Yilmaz, Pelin; Meyer, Folker; Glöckner, Frank O.; Gilbert, Jack A.; Knight, Rob; Finn, Rob; Cochrane, Guy; Karsch-Mizrachi, Ilene; Lapidus, Alla; Meyer, Folker; Yilmaz, Pelin; Parks, Donovan H.; Eren, A. M.; Schriml, Lynn; Banfield, Jillian F.; Hugenholtz, Philip; Woyke, Tanja

2017-08-08

We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

The present status and development of the state's system of safeguards in Japan

International Nuclear Information System (INIS)

Kurihara, H.; Haginoya, T.; Natsume, H.; Hirata, M.

1977-01-01

This paper summarizes developmental activities aiming at improving, the status of the Japan's System of safeguards. The integral tests are described which are now being implemented by the Japanese Government to check the effectiveness of the State's System, which must be maintained by the Government under the Safeguards Agreement between Japan and the IAEA under the Treaty on Non-Proliferation of Nuclear Weapons, ratified by Japan in June 1976. A joint experiment has been now implemented by the Nuclear Safety Bureau and the NMCC for knowing and improving the precision and accuracy of analytical measurements used at the bulk-facilities. JAERI, is conducting various R and D work on its own, and through cooperation with NMCC, NSB etc. The authors describe the results of non-destructive γ-spectrometry for the development of isotopic correlation techniques, as well as for the identification, and also refer briefly to measurement methods using the Fast Critical Assembly in JAERI. Measurement methods used in the Pu-fabrication facility of the PNC, and the problem of spent fuels application of safeguards for the reprocessing plant are discussed. The accounting reports coming from Japanese facilities are processed by the computer at the NMCC, and converted into (a) the State's material balance, and (b) the formats to be sent to IAEA. The authors discuss the experience of such data-processing as well as the developmental works for analysing MUF. As a part of the integral test, the experiences concerning planning and performance of inspection are discussed. The present status and future plans of the system of national analytical laboratories are described

The Mirror Fusion Test Facility cryogenic system: Performance, management approach, and present equipment status

International Nuclear Information System (INIS)

Slack, D.S.; Chronis, W.C.

1987-01-01

The cryogenic system for the Mirror Fusion Test Facility (MFTF) is a 14-kW, 4.35-K helium refrigeration system that proved to be highly successful and cost-effective. All operating objectives were met, while remaining within a few percent of initial cost and schedule plans. The management approach used in MFTF allowed decisions to be made quickly and effectively, and it helped keep costs down. Manpower levels, extent and type of industrial participation, key aspects of subcontractor specifications, and subcontractor interactions are reviewed, as well as highlights of the system tests, operation, and present equipment status. Organizations planning large, high-technology systems may benefit from this experience with the MFTF cryogenic system

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

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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.

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.

Evolution of small prokaryotic genomes

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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.

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

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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

Present status and prospects of nuclear power development in China

International Nuclear Information System (INIS)

Zhao Renkai

1994-01-01

The current status and the guiding principles of nuclear power in China are discussed. With the expansion of China's reform and opening to outside world policy, the national economy growth was increased very rapidly. For continuous, stable and fast development of national economy, the safe, clean and economic nuclear energy will play an even more important role. It is envisaged that by 2020 nuclear power will account for about 20%. 1 ref., 4 tabs

International regulatory landscape and integration of corrective genome editing into in vitro fertilization.

Science.gov (United States)

Araki, Motoko; Ishii, Tetsuya

2014-11-24

Genome editing technology, including zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas, has enabled far more efficient genetic engineering even in non-human primates. This biotechnology is more likely to develop into medicine for preventing a genetic disease if corrective genome editing is integrated into assisted reproductive technology, represented by in vitro fertilization. Although rapid advances in genome editing are expected to make germline gene correction feasible in a clinical setting, there are many issues that still need to be addressed before this could occur. We herein examine current status of genome editing in mammalian embryonic stem cells and zygotes and discuss potential issues in the international regulatory landscape regarding human germline gene modification. Moreover, we address some ethical and social issues that would be raised when each country considers whether genome editing-mediated germline gene correction for preventive medicine should be permitted.

The uranium industry in the former eastern block countries-present status and new challenges associated with remediation work

International Nuclear Information System (INIS)

Vels, B.Dr.; Ruhrmann, G.Dr.

1994-01-01

The main uranium producing countries and the individual production centres are briefly described, including their production status. In particular, an analysis of their present situation is given. The challenge of required remediation work lies in the successful handling of the complex transformation from the old to the new socio-economic environment within a tight financial framework

EFNS Task Force on Teaching of Neuroimaging in Neurology Curricula in Europe : present status and recommendations for the future

NARCIS (Netherlands)

Pantano, P; Chollet, F; Paulson, O; von Kummer, R; Laihinen, A; Leenders, K; Yancheva, S

A Task Force on 'Teaching of Neuroimaging in Neurology Curricula in Europe' was appointed in September 1998 by the education committee of the European Federation of Neurological Societies (EFNS) in order to: (1) examine the present status of teaching of neuroimaging in the training of neurology in

EFNS Task Force on Teaching of Neuroimaging in Neurology Curricula in Europe : present status and recommendations for the future

NARCIS (Netherlands)

Pantano, P; Chollet, F; Paulson, O; von Kummer, R; Laihinen, A; Leenders, K; Yancheva, S

2001-01-01

A Task Force on 'Teaching of Neuroimaging in Neurology Curricula in Europe' was appointed in September 1998 by the education committee of the European Federation of Neurological Societies (EFNS) in order to: (1) examine the present status of teaching of neuroimaging in the training of neurology in

Genome-wide comparative analysis of four Indian Drosophila species.

Science.gov (United States)

Mohanty, Sujata; Khanna, Radhika

2017-12-01

Comparative analysis of multiple genomes of closely or distantly related Drosophila species undoubtedly creates excitement among evolutionary biologists in exploring the genomic changes with an ecology and evolutionary perspective. We present herewith the de novo assembled whole genome sequences of four Drosophila species, D. bipectinata, D. takahashii, D. biarmipes and D. nasuta of Indian origin using Next Generation Sequencing technology on an Illumina platform along with their detailed assembly statistics. The comparative genomics analysis, e.g. gene predictions and annotations, functional and orthogroup analysis of coding sequences and genome wide SNP distribution were performed. The whole genome of Zaprionus indianus of Indian origin published earlier by us and the genome sequences of previously sequenced 12 Drosophila species available in the NCBI database were included in the analysis. The present work is a part of our ongoing genomics project of Indian Drosophila species.

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.

Genome-Based Identification of Active Prophage Regions by Next Generation Sequencing in Bacillus licheniformis DSM13

Science.gov (United States)

Hertel, Robert; Rodríguez, David Pintor; Hollensteiner, Jacqueline; Dietrich, Sascha; Leimbach, Andreas; Hoppert, Michael; Liesegang, Heiko; Volland, Sonja

2015-01-01

Prophages are viruses, which have integrated their genomes into the genome of a bacterial host. The status of the prophage genome can vary from fully intact with the potential to form infective particles to a remnant state where only a few phage genes persist. Prophages have impact on the properties of their host and are therefore of great interest for genomic research and strain design. Here we present a genome- and next generation sequencing (NGS)-based approach for identification and activity evaluation of prophage regions. Seven prophage or prophage-like regions were identified in the genome of Bacillus licheniformis DSM13. Six of these regions show similarity to members of the Siphoviridae phage family. The remaining region encodes the B. licheniformis orthologue of the PBSX prophage from Bacillus subtilis. Analysis of isolated phage particles (induced by mitomycin C) from the wild-type strain and prophage deletion mutant strains revealed activity of the prophage regions BLi_Pp2 (PBSX-like), BLi_Pp3 and BLi_Pp6. In contrast to BLi_Pp2 and BLi_Pp3, neither phage DNA nor phage particles of BLi_Pp6 could be visualized. However, the ability of prophage BLi_Pp6 to generate particles could be confirmed by sequencing of particle-protected DNA mapping to prophage locus BLi_Pp6. The introduced NGS-based approach allows the investigation of prophage regions and their ability to form particles. Our results show that this approach increases the sensitivity of prophage activity analysis and can complement more conventional approaches such as transmission electron microscopy (TEM). PMID:25811873

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.

Single-Cell (Meta-Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

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Beverly E. Flood

2016-05-01

Full Text Available The genus Thiomargarita includes the world’s largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria.Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence transposable elements and miniature inverted-repeat transposable elements (MITEs. In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsr

Genomic research perspectives in Kazakhstan

Directory of Open Access Journals (Sweden)

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

The international Genome sample resource (IGSR): A worldwide collection of genome variation incorporating the 1000 Genomes Project data.

Science.gov (United States)

Clarke, Laura; Fairley, Susan; Zheng-Bradley, Xiangqun; Streeter, Ian; Perry, Emily; Lowy, Ernesto; Tassé, Anne-Marie; Flicek, Paul

2017-01-04

The International Genome Sample Resource (IGSR; http://www.internationalgenome.org) expands in data type and population diversity the resources from the 1000 Genomes Project. IGSR represents the largest open collection of human variation data and provides easy access to these resources. IGSR was established in 2015 to maintain and extend the 1000 Genomes Project data, which has been widely used as a reference set of human variation and by researchers developing analysis methods. IGSR has mapped all of the 1000 Genomes sequence to the newest human reference (GRCh38), and will release updated variant calls to ensure maximal usefulness of the existing data. IGSR is collecting new structural variation data on the 1000 Genomes samples from long read sequencing and other technologies, and will collect relevant functional data into a single comprehensive resource. IGSR is extending coverage with new populations sequenced by collaborating groups. Here, we present the new data and analysis that IGSR has made available. We have also introduced a new data portal that increases discoverability of our data-previously only browseable through our FTP site-by focusing on particular samples, populations or data sets of interest. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Iodine status in the Nordic countries - past and present.

Science.gov (United States)

Nyström, Helena Filipsson; Brantsæter, Anne Lise; Erlund, Iris; Gunnarsdottir, Ingibjörg; Hulthén, Lena; Laurberg, Peter; Mattisson, Irene; Rasmussen, Lone Banke; Virtanen, Suvi; Meltzer, Helle Margrete

2016-01-01

Adequate iodine nutrition is dependent on ground water content, seafood, and, as many countries use iodized cow fodder, dairy products. In most countries, salt fortification programs are needed to assure adequate iodine intake. The objectives are threefold: 1) to describe the past and present iodine situation in the Nordic countries, 2) to identify important gaps of knowledge, and 3) to highlight differences among the Nordic countries' iodine biomonitoring and fortification policies. Historical data are compared with the current situation. The Nordic countries' strategies to achieve recommended intake and urine iodine levels and their respective success rates are evaluated. In the past, the iodine situation ranged from excellent in Iceland to widespread goiter and cretinism in large areas of Sweden. The situation was less severe in Norway and Finland. According to a 1960 World Health Organization (WHO) report, there were then no observations of iodine deficiency in Denmark. In Sweden and Finland, the fortification of table salt was introduced 50-75 years ago, and in Norway and Finland, the fortification of cow fodder starting in the 1950s helped improve the population's iodine status due to the high intake of milk. In Denmark, iodine has been added to household salt and salt in bread for the past 15 years. The Nordic countries differ with regard to regulations and degree of governmental involvement. There are indications that pregnant and lactating women, the two most vulnerable groups, are mildly deficient in iodine in several of the Nordic countries. The Nordic countries employ different strategies to attain adequate iodine nutrition. The situation is not optimal and is in need of re-evaluation. Iodine researchers, Nordic national food administrations, and Nordic governmental institutions would benefit from collaboration to attain a broader approach and guarantee good iodine health for all.

Interest in genomic SNP testing for prostate cancer risk: a pilot survey.

Science.gov (United States)

Hall, Michael J; Ruth, Karen J; Chen, David Yt; Gross, Laura M; Giri, Veda N

2015-01-01

Advancements in genomic testing have led to the identification of single nucleotide polymorphisms (SNPs) associated with prostate cancer. The clinical utility of SNP tests to evaluate prostate cancer risk is unclear. Studies have not examined predictors of interest in novel genomic SNP tests for prostate cancer risk in a diverse population. Consecutive participants in the Fox Chase Prostate Cancer Risk Assessment Program (PRAP) (n = 40) and unselected men from surgical urology clinics (n = 40) completed a one-time survey. Items examined interest in genomic SNP testing for prostate cancer risk, knowledge, impact of unsolicited findings, and psychosocial factors including health literacy. Knowledge of genomic SNP tests was low in both groups, but interest was higher among PRAP men (p testing in both groups. Multivariable modeling identified several predictors of higher interest in a genomic SNP test including higher perceived risk (p = 0.025), indicating zero reasons for not wanting testing (vs ≥1 reason) (p = 0.013), and higher health literacy (p = 0.016). Knowledge of genomic SNP testing was low in this sample, but higher among high-risk men. High-risk status may increase interest in novel genomic tests, while low literacy may lessen interest.

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.

Science.gov (United States)

Treangen, Todd J; Ondov, Brian D; Koren, Sergey; Phillippy, Adam M

2014-01-01

Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of multiple sequences simultaneously. Here we present the Harvest suite of core-genome alignment and visualization tools for the rapid and simultaneous analysis of thousands of intraspecific microbial strains. Harvest includes Parsnp, a fast core-genome multi-aligner, and Gingr, a dynamic visual platform. Together they provide interactive core-genome alignments, variant calls, recombination detection, and phylogenetic trees. Using simulated and real data we demonstrate that our approach exhibits unrivaled speed while maintaining the accuracy of existing methods. The Harvest suite is open-source and freely available from: http://github.com/marbl/harvest.

An evaluation of Comparative Genome Sequencing (CGS by comparing two previously-sequenced bacterial genomes

Directory of Open Access Journals (Sweden)

Herring Christopher D

2007-08-01

Full Text Available Abstract Background With the development of new technology, it has recently become practical to resequence the genome of a bacterium after experimental manipulation. It is critical though to know the accuracy of the technique used, and to establish confidence that all of the mutations were detected. Results In order to evaluate the accuracy of genome resequencing using the microarray-based Comparative Genome Sequencing service provided by Nimblegen Systems Inc., we resequenced the E. coli strain W3110 Kohara using MG1655 as a reference, both of which have been completely sequenced using traditional sequencing methods. CGS detected 7 of 8 small sequence differences, one large deletion, and 9 of 12 IS element insertions present in W3110, but did not detect a large chromosomal inversion. In addition, we confirmed that CGS also detected 2 SNPs, one deletion and 7 IS element insertions that are not present in the genome sequence, which we attribute to changes that occurred after the creation of the W3110 lambda clone library. The false positive rate for SNPs was one per 244 Kb of genome sequence. Conclusion CGS is an effective way to detect multiple mutations present in one bacterium relative to another, and while highly cost-effective, is prone to certain errors. Mutations occurring in repeated sequences or in sequences with a high degree of secondary structure may go undetected. It is also critical to follow up on regions of interest in which SNPs were not called because they often indicate deletions or IS element insertions.

REGEN: Ancestral Genome Reconstruction for Bacteria

OpenAIRE

Yang, Kuan; Heath, Lenwood S.; Setubal, João C.

2012-01-01

Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deleti...

Evolution of genes and genomes on the Drosophila phylogeny

DEFF Research Database (Denmark)

Clark, Andrew G; Eisen, Michael B; Smith, Douglas R

2007-01-01

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the ......Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here...... tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila...

Virtual Genome Walking across the 32 Gb Ambystoma mexicanum genome; assembling gene models and intronic sequence.

Science.gov (United States)

Evans, Teri; Johnson, Andrew D; Loose, Matthew

2018-01-12

Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence. These assemblies are then linked and refined to generate gene models including upstream and downstream genomic, and intronic, sequence. Our assemblies are validated by comparison with previously published axolotl bacterial artificial chromosome (BAC) sequences. Our analyses of axolotl intron length, intron-exon structure, repeat content and synteny provide novel insights into the genic structure of this model species. This resource will enable new experimental approaches in axolotl, such as ChIP-Seq and CRISPR and aid in future whole genome sequencing efforts. The assembled sequences and annotations presented here are freely available for download from https://tinyurl.com/y8gydc6n . The software pipeline is available from https://github.com/LooseLab/iterassemble .

Genomic characterization of large heterochromatic gaps in the human genome assembly.

Directory of Open Access Journals (Sweden)

Nicolas Altemose

2014-05-01

Full Text Available The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3. The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms, and as a result, the sequence composition and potential biological functions of these regions remain largely unexplored. Furthermore, existing genomic tools designed to predict consensus-based descriptions of repeat families cannot be readily applied to complex satellite repeats such as HSat2,3, which lack a consistent repeat unit reference sequence. Here we present an alignment-free method to characterize complex satellites using whole-genome shotgun read datasets. Utilizing this approach, we classify HSat2,3 sequences into fourteen subfamilies and predict their chromosomal distributions, resulting in a comprehensive satellite reference database to further enable genomic studies of heterochromatic regions. We also identify 1.3 Mb of non-repetitive sequence interspersed with HSat2,3 across 17 unmapped assembly scaffolds, including eight annotated gene predictions. Finally, we apply our satellite reference database to high-throughput sequence data from 396 males to estimate array size variation of the predominant HSat3 array on the Y chromosome, confirming that satellite array sizes can vary between individuals over an order of magnitude (7 to 98 Mb and further demonstrating that array sizes are distributed differently within distinct Y haplogroups. In summary, we present a novel framework for generating initial reference databases for unassembled genomic regions enriched with complex satellite DNA, and we further demonstrate the utility of these reference databases for studying patterns of sequence variation within human populations.

Genomic definition of species

Energy Technology Data Exchange (ETDEWEB)

Crkvenjakov, R.; Drmanac, R.

1991-07-01

The subject of this paper is the definition of species based on the assumption that genome is the fundamental level for the origin and maintenance of biological diversity. For this view to be logically consistent it is necessary to assume the existence and operation of the new law which we call genome law. For this reason the genome law is included in the explanation of species phenomenon presented here even if its precise formulation and elaboration are left for the future. The intellectual underpinnings of this definition can be traced to Goldschmidt. We wish to explore some philosophical aspects of the definition of species in terms of the genome. The point of proposing the definition on these grounds is that any real advance in evolutionary theory has to be correct in both its philosophy and its science.

Rapid whole genome sequencing and precision neonatology.

Science.gov (United States)

Petrikin, Joshua E; Willig, Laurel K; Smith, Laurie D; Kingsmore, Stephen F

2015-12-01

Traditionally, genetic testing has been too slow or perceived to be impractical to initial management of the critically ill neonate. Technological advances have led to the ability to sequence and interpret the entire genome of a neonate in as little as 26 h. As the cost and speed of testing decreases, the utility of whole genome sequencing (WGS) of neonates for acute and latent genetic illness increases. Analyzing the entire genome allows for concomitant evaluation of the currently identified 5588 single gene diseases. When applied to a select population of ill infants in a level IV neonatal intensive care unit, WGS yielded a diagnosis of a causative genetic disease in 57% of patients. These diagnoses may lead to clinical management changes ranging from transition to palliative care for uniformly lethal conditions for alteration or initiation of medical or surgical therapy to improve outcomes in others. Thus, institution of 2-day WGS at time of acute presentation opens the possibility of early implementation of precision medicine. This implementation may create opportunities for early interventional, frequently novel or off-label therapies that may alter disease trajectory in infants with what would otherwise be fatal disease. Widespread deployment of rapid WGS and precision medicine will raise ethical issues pertaining to interpretation of variants of unknown significance, discovery of incidental findings related to adult onset conditions and carrier status, and implementation of medical therapies for which little is known in terms of risks and benefits. Despite these challenges, precision neonatology has significant potential both to decrease infant mortality related to genetic diseases with onset in newborns and to facilitate parental decision making regarding transition to palliative care. Copyright © 2015 Elsevier Inc. All rights reserved.

Adopting genetics: motivations and outcomes of personal genomic testing in adult adoptees.

Science.gov (United States)

Baptista, Natalie M; Christensen, Kurt D; Carere, Deanna Alexis; Broadley, Simon A; Roberts, J Scott; Green, Robert C

2016-09-01

American adult adoptees may possess limited information about their biological families and turn to direct-to-consumer personal genomic testing (PGT) for genealogical and medical information. We investigated the motivations and outcomes of adoptees undergoing PGT using data from the Impact of Personal Genomics (PGen) Study. The PGen Study surveyed new 23andMe and Pathway Genomics customers before and 6 months after receiving PGT results. Exploratory analyses compared adoptees' and nonadoptees' PGT attitudes, expectations, and experiences. We evaluated the association of adoption status with motivations for testing and postdisclosure actions using logistic regression models. Of 1,607 participants, 80 (5%) were adopted. As compared with nonadoptees, adoptees were more likely to cite limited knowledge of family health history (OR = 10.1; 95% CI = 5.7-19.5) and the opportunity to learn genetic disease risks (OR = 2.7; 95% CI = 1.6-4.8) as strong motivations for PGT. Of 922 participants who completed 6-month follow-up, there was no significant association between adoption status and PGT-motivated health-care utilization or health-behavior change. PGT allows adoptees to gain otherwise inaccessible information about their genetic disease risks and ancestry, helping them to fill the void of an incomplete family health history.Genet Med 18 9, 924-932.

The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection.

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Leila do Nascimento Vieira

Full Text Available BACKGROUND: Podocarpus lambertii (Podocarpaceae is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. METHODOLOGY/PRINCIPAL FINDINGS: The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR. It contains 118 unique genes and one duplicated tRNA (trnN-GUU, which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi and Araucariaceae (Agathis dammara. Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. CONCLUSION: The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of

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

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.

GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome.

Science.gov (United States)

Lu, Bingxin; Leong, Hon Wai

2016-02-01

Genomic islands (GIs) are clusters of functionally related genes acquired by lateral genetic transfer (LGT), and they are present in many bacterial genomes. GIs are extremely important for bacterial research, because they not only promote genome evolution but also contain genes that enhance adaption and enable antibiotic resistance. Many methods have been proposed to predict GI. But most of them rely on either annotations or comparisons with other closely related genomes. Hence these methods cannot be easily applied to new genomes. As the number of newly sequenced bacterial genomes rapidly increases, there is a need for methods to detect GI based solely on sequences of a single genome. In this paper, we propose a novel method, GI-SVM, to predict GIs given only the unannotated genome sequence. GI-SVM is based on one-class support vector machine (SVM), utilizing composition bias in terms of k-mer content. From our evaluations on three real genomes, GI-SVM can achieve higher recall compared with current methods, without much loss of precision. Besides, GI-SVM allows flexible parameter tuning to get optimal results for each genome. In short, GI-SVM provides a more sensitive method for researchers interested in a first-pass detection of GI in newly sequenced genomes.

Research study on analysis/use technologies of genome information; Genome joho kaidoku riyo gijutsu no chosa kenkyu

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-03-01

For wide use of genome information in the industrial field, the required R and D was surveyed from the standpoints of biology and information science. To clarify the present state and issues of the international research on genome analysis, the genome map as well as sequence and function information are first surveyed. The current analysis/use technologies of genome information are analyzed, and the following are summarized: prediction and identification of gene regions in genome sequences, techniques for searching and selecting useful genes, and techniques for predicting the expression of gene functions and the gene-product structure and functions. It is recommended that R and D and data collection/interpretation necessary to clarify inter-gene interactions and information networks should be promoted by integrating Japanese advanced know-how and technologies. As examples of the impact of the research results on industry and society, the present state and future expected effect are summarized for medicines, diagnosis/analysis instruments, chemicals, foods, agriculture, fishery, animal husbandry, electronics, environment and information. 278 refs., 42 figs., 5 tabs.

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

Pipeline to upgrade the genome annotations

Directory of Open Access Journals (Sweden)

Lijin K. Gopi

2017-12-01

Full Text Available Current era of functional genomics is enriched with good quality draft genomes and annotations for many thousands of species and varieties with the support of the advancements in the next generation sequencing technologies (NGS. Around 25,250 genomes, of the organisms from various kingdoms, are submitted in the NCBI genome resource till date. Each of these genomes was annotated using various tools and knowledge-bases that were available during the period of the annotation. It is obvious that these annotations will be improved if the same genome is annotated using improved tools and knowledge-bases. Here we present a new genome annotation pipeline, strengthened with various tools and knowledge-bases that are capable of producing better quality annotations from the consensus of the predictions from different tools. This resource also perform various additional annotations, apart from the usual gene predictions and functional annotations, which involve SSRs, novel repeats, paralogs, proteins with transmembrane helices, signal peptides etc. This new annotation resource is trained to evaluate and integrate all the predictions together to resolve the overlaps and ambiguities of the boundaries. One of the important highlights of this resource is the capability of predicting the phylogenetic relations of the repeats using the evolutionary trace analysis and orthologous gene clusters. We also present a case study, of the pipeline, in which we upgrade the genome annotation of Nelumbo nucifera (sacred lotus. It is demonstrated that this resource is capable of producing an improved annotation for a better understanding of the biology of various organisms.

The mitochondrial genome of Grateloupia taiwanensis (Halymeniaceae, Rhodophyta) and comparative mitochondrial genomics of red algae.

Science.gov (United States)

DePriest, Michael S; Bhattacharya, Debashish; López-Bautista, Juan M

2014-10-01

Although red algae are economically highly valuable for their gelatinous cell wall compounds as well as being integral parts of marine benthic habitats, very little genome data are currently available. We present mitochondrial genome sequence data from the red alga Grateloupia taiwanensis S.-M. Lin & H.-Y. Liang. Comprising 28,906 nucleotide positions, the mitochondrial genome contig contains 25 protein-coding genes and 24 transfer RNA genes. It is highly similar to other red algal genomes in gene content as well as overall structure. An intron in the cox1 gene was found to be shared by G. taiwanensis and Grateloupia angusta (Okamura) S. Kawaguchi & H. W. Wang. We also used whole-genome alignments to compare G. taiwanensis to different groups of red algae, and these results are consistent with the currently accepted phylogeny of Rhodophyta. © 2014 Marine Biological Laboratory.

Whole genome shotgun sequencing of Indian strains of Streptococcus agalactiae

Directory of Open Access Journals (Sweden)

Balaji Veeraraghavan

2017-12-01

Full Text Available Group B streptococcus is known as a leading cause of neonatal infections in developing countries. The present study describes the whole genome shotgun sequences of four Group B Streptococcus (GBS isolates. Molecular data on clonality is lacking for GBS in India. The present genome report will add important information on the scarce genome data of GBS and will help in deriving comparative genome studies of GBS isolates at global level. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers NHPL00000000 – NHPO00000000.

Genomic resources in mungbean for future breeding programs

Directory of Open Access Journals (Sweden)

Sue K Kim

2015-08-01

Full Text Available Among the legume family, mungbean (Vigna radiata has become one of the important crops in Asia, showing a steady increase in global production. It provides a good source of protein and contains most notably folate and iron. Beyond the nutritional value of mungbean, certain features make it a well-suited model organism among legume plants because of its small genome size, short life-cycle, self-pollinating, and close genetic relationship to other legumes. In the past, there have been several efforts to develop molecular markers and linkage maps associated with agronomic traits for the genetic improvement of mungbean and, ultimately, breeding for cultivar development to increase the average yields of mungbean. The recent release of a reference genome of the cultivated mungbean (V. radiata var. radiata VC1973A and an additional de novo sequencing of a wild relative mungbean (V. radiata var. sublobata has provided a framework for mungbean genetic and genome research, that can further be used for genome-wide association and functional studies to identify genes related to specific agronomic traits. Moreover, the diverse gene pool of wild mungbean comprises valuable genetic resources of beneficial genes that may be helpful in widening the genetic diversity of cultivated mungbean. This review paper covers the research progress on molecular and genomics approaches and the current status of breeding programs that have developed to move toward the ultimate goal of mungbean improvement.

Present status of titanium removable dentures--a review of the literature.

Science.gov (United States)

Ohkubo, C; Hanatani, S; Hosoi, T

2008-09-01

Although porcelain and zirconium oxide might be used for fixed partial dental prostheses instead of conventional dental metals in the near future, removable partial denture (RPD) frameworks will probably continue to be cast with biocompatible metals. Commercially pure (CP) titanium has appropriate mechanical properties, it is lightweight (low density) compared with conventional dental alloys, and has outstanding biocompatibility that prevents metal allergic reactions. This literature review describes the laboratory conditions needed for fabricating titanium frameworks and the present status of titanium removable prostheses. The use of titanium for the production of cast RPD frameworks has gradually increased. There are no reports about metallic allergy apparently caused by CP titanium dentures. The laboratory drawbacks still remain, such as the lengthy burn-out, inferior castability and machinability, reaction layer formed on the cast surface, difficulty of polishing, and high initial costs. However, the clinical problems, such as discoloration of the titanium surfaces, unpleasant metal taste, decrease of clasp retention, tendency for plaque to adhere to the surface, detachment of the denture base resin, and severe wear of titanium teeth, have gradually been resolved. Titanium RPD frameworks have never been reported to fail catastrophically. Thus, titanium is recommended as protection against metal allergy, particularly for large-sized prostheses such as RPDs or complete dentures.

Present status and future plan on LMFBR steam generator safety study

International Nuclear Information System (INIS)

Tanabe, Hiromi; Kuroha, Mitsuo

1985-01-01

The results of the sodium-water reaction test which has been carried out for the safety evaluation of the water leak phenomena in the steam generators for the prototype FBR were summarized. This is related to the behavior of minute leak, the behavior of wear and damage propagation of neighboring tubes due to small and medium leaking jets, and the pressure/flow phenomena occurring at the time of large leak. Moreover, this is related to the development of analysis codes, the development of water leak-detecting system, and the development of the techniques for treating reaction products remaining in the system at the time of accidents. Also the research and development required hereafter for determining the basic specification of the steam generators for a demonstration FBR and future FBRs and reducing the cost were examined. The water leaks in the steam generators for FBRs have been reported in the Fermi reactor of USA, the PFR of Great Britain, the BN-350 of USSR, the Phenix reactor of France and so on. In Japan, the sodium-water reaction has been well understood, and the facilities for the countremeasures to it have been established. The sodium-water reaction phenomena, the present status of sodium-water reaction research and others are reported. (Kako, I.)

Vitamin D and the brain: Genomic and non-genomic actions.

Science.gov (United States)

Cui, Xiaoying; Gooch, Helen; Petty, Alice; McGrath, John J; Eyles, Darryl

2017-09-15

1,25(OH) 2 D 3 (vitamin D) is well-recognized as a neurosteroid that modulates multiple brain functions. A growing body of evidence indicates that vitamin D plays a pivotal role in brain development, neurotransmission, neuroprotection and immunomodulation. However, the precise molecular mechanisms by which vitamin D exerts these functions in the brain are still unclear. Vitamin D signalling occurs via the vitamin D receptor (VDR), a zinc-finger protein in the nuclear receptor superfamily. Like other nuclear steroids, vitamin D has both genomic and non-genomic actions. The transcriptional activity of vitamin D occurs via the nuclear VDR. Its faster, non-genomic actions can occur when the VDR is distributed outside the nucleus. The VDR is present in the developing and adult brain where it mediates the effects of vitamin D on brain development and function. The purpose of this review is to summarise the in vitro and in vivo work that has been conducted to characterise the genomic and non-genomic actions of vitamin D in the brain. Additionally we link these processes to functional neurochemical and behavioural outcomes. Elucidation of the precise molecular mechanisms underpinning vitamin D signalling in the brain may prove useful in understanding the role this steroid plays in brain ontogeny and function. Copyright © 2017 Elsevier B.V. All rights reserved.

CKM Phenomenology and B-mesons physics-present status and current issues

International Nuclear Information System (INIS)

Ali, A.

2004-01-01

We review the status of the Cabibbo-Kobayashi-Maskawa (CKM) matrix elements and the CP-violating phases in the CKM-unitarity triangle. The emphasis in these lecture notes is on B-meson physics, through we also review the current status and issues in the light quark sector of this matrix. Selected applications of theoretical methods in QCD used in the interpretation of data are given and some of the issues restricting the theoretical precision on the CKM matrix elements discussed. The overall consistency of the CKM theory with the available data in flavour physics is impressive and we quantify this consistency. Current data also show some anomalies which, however, are not yet statistically significant. They are discussed briefly. some benchmark measurements that remain to be done in experiments at the B-factories and hadron colliders are listed. Together with the already achieved results, they will provide unprecedented test of the CKM theory and by the same token may lead to the discovery of new physics. (Author) 284 refs

REGEN: Ancestral Genome Reconstruction for Bacteria.

Science.gov (United States)

Yang, Kuan; Heath, Lenwood S; Setubal, João C

2012-07-18

Ancestral genome reconstruction can be understood as a phylogenetic study with more details than a traditional phylogenetic tree reconstruction. We present a new computational system called REGEN for ancestral bacterial genome reconstruction at both the gene and replicon levels. REGEN reconstructs gene content, contiguous gene runs, and replicon structure for each ancestral genome. Along each branch of the phylogenetic tree, REGEN infers evolutionary events, including gene creation and deletion and replicon fission and fusion. The reconstruction can be performed by either a maximum parsimony or a maximum likelihood method. Gene content reconstruction is based on the concept of neighboring gene pairs. REGEN was designed to be used with any set of genomes that are sufficiently related, which will usually be the case for bacteria within the same taxonomic order. We evaluated REGEN using simulated genomes and genomes in the Rhizobiales order.

Fungal biology: compiling genomes and exploiting them

Energy Technology Data Exchange (ETDEWEB)

Labbe, Jessy L [ORNL; Uehling, Jessie K [ORNL; Payen, Thibaut [INRA; Plett, Jonathan [University of Western Sydney, Australia

2014-01-01

The last 10 years have seen the cost of sequencing complete genomes decrease at an incredible speed. This has led to an increase in the number of genomes sequenced in all the fungal tree of life as well as a wide variety of plant genomes. The increase in sequencing has permitted us to study the evolution of organisms on a genomic scale. A number of talks during the conference discussed the importance of transposable elements (TEs) that are present in almost all species of fungi. These TEs represent an especially large percentage of genomic space in fungi that interact with plants. Thierry Rouxel (INRA, Nancy, France) showed the link between speciation in the Leptosphaeria complex and the expansion of TE families. For example in the Leptosphaeria complex, one species associated with oilseed rape has experienced a recent and massive burst of movement by a few TE families. The alterations caused by these TEs took place in discrete regions of the genome leading to shuffling of the genomic landscape and the appearance of genes specific to the species, such as effectors useful for the interactions with a particular plant (Rouxel et al., 2011). Other presentations showed the importance of TEs in affecting genome organization. For example, in Amanita different species appear to have been invaded by different TE families (Veneault-Fourrey & Martin, 2011).

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

Impact of Socioeconomic Status and Ethnicity on Melanoma Presentation and Recurrence in Caucasian Patients.

Science.gov (United States)

Salvaggio, Christine; Han, Sung Won; Martires, Kathryn; Robinson, Eric; Madankumar, Reshmi; Gumaste, Priyanka; Polsky, David; Stein, Jennifer; Berman, Russell; Shapiro, Richard; Zhong, Judy; Osman, Iman

2016-01-01

The impact of ethnicity and the socioeconomic status (SES) among Caucasians is not well studied. Here, we examine the impact of income on melanoma presentation and prognosis within a Caucasian cohort, accounting for ethnicity, as some reports suggest increased melanoma incidence in Ashkenazi Jewish (AJ) BRCA mutation carriers. We studied prospectively enrolled primary melanoma patients at New York University. SES data were estimated using United States' Census Bureau data and patient zip codes. We evaluated associations between ethnicity, SES, and baseline characteristics using the χ² test and multivariate logistic regression. We compared survival distributions using Kaplan-Meier curves, log-rank tests, and Cox proportional hazard ratios. Of the 1,339 enrolled patients, AJ represented 32% (n = 423). Apart from AJ being older at presentation (p < 0.001), no significant differences were observed in baseline characteristics between ethnic groups. Patients with a median household income (MHI) lower than the median of the cohort were significantly more likely to present with advanced stages (p < 0.001) compared to patients with a higher MHI. Shorter overall (p = 0.016) and post-recurrence survival (p = 0.042) was also observed in patients from lower-income households. Data suggest that disparities in melanoma presentation in Caucasians stratify according to income independent of ethnic background. © 2016 S. Karger AG, Basel.

Report on the present status of scientific and engineering accelerators in Japan (I)

CERN Document Server

2003-01-01

For the purpose to know the present status of possible joint researches in use of accelerators in Japan, the Specialist Committee of Quantum Beam conducted a questionnaire to 69 organizations, of which 54 answered. The organizations have 97 accelerator facilities, which had 108 machines for research and educational purpose, and 7 for medical use. Of 97 facilities, 86 are found open for joint and cooperative researches. Based on the questionnaire results, following discussions are made: Definition and classification of quantum beam; Positioning of accelerators for research purpose among all machines in Japan (Increase of accelerator usage, economical scale and social contribution); Usage form of accelerators for research purpose (sort of accelerators, sort of secondary ions like neutron, synchrotron radiation, positron, radioisotope beam, muon and neutrino, high current accelerator for fusion, measurement and analyses, new elements, PET and gamma-ray); and The questionnaire results of the accelerators for rese...

Present status of brachytherapy using Co-RALS in the national hospital and sanatorium in Japan

International Nuclear Information System (INIS)

Uno, Takashi; Itami, Jun; Abe, Yoshihisa; Dokiya, Takushi; Yorozu, Atsunori; Nishio, Masamichi; Hata, Yoshihiro; Ogita, Mikio

1998-01-01

The present status of brachytherapy using Co-RALS machine in the national hospital and sanatorium were investigated, by a questionnaire method. Questionnaire concerned about the equipment, machine trouble, patient population, together with the stuff of each department. Most of the Co-RALS machines were introduced between 1982 and 1987. Quality of Co-RALS treatment is questionable in several hospitals which lacks radiation therapy personnel. Number of patients treated per year are too small to sustain the cost of Ir-HDR treatment. It is concluded that introduction of Ir-HDR machine should be considered for small number of hospitals where patients population and personnel scale are sufficient. (author)

Characterization of canine osteosarcoma by array comparative genomic hybridization and RT-qPCR: signatures of genomic imbalance in canine osteosarcoma parallel the human counterpart.

Science.gov (United States)

Angstadt, Andrea Y; Motsinger-Reif, Alison; Thomas, Rachael; Kisseberth, William C; Guillermo Couto, C; Duval, Dawn L; Nielsen, Dahlia M; Modiano, Jaime F; Breen, Matthew

2011-11-01

Osteosarcoma (OS) is the most commonly diagnosed malignant bone tumor in humans and dogs, characterized in both species by extremely complex karyotypes exhibiting high frequencies of genomic imbalance. Evaluation of genomic signatures in human OS using array comparative genomic hybridization (aCGH) has assisted in uncovering genetic mechanisms that result in disease phenotype. Previous low-resolution (10-20 Mb) aCGH analysis of canine OS identified a wide range of recurrent DNA copy number aberrations, indicating extensive genomic instability. In this study, we profiled 123 canine OS tumors by 1 Mb-resolution aCGH to generate a dataset for direct comparison with current data for human OS, concluding that several high frequency aberrations in canine and human OS are orthologous. To ensure complete coverage of gene annotation, we identified the human refseq genes that map to these orthologous aberrant dog regions and found several candidate genes warranting evaluation for OS involvement. Specifically, subsequenct FISH and qRT-PCR analysis of RUNX2, TUSC3, and PTEN indicated that expression levels correlated with genomic copy number status, showcasing RUNX2 as an OS associated gene and TUSC3 as a possible tumor suppressor candidate. Together these data demonstrate the ability of genomic comparative oncology to identify genetic abberations which may be important for OS progression. Large scale screening of genomic imbalance in canine OS further validates the use of the dog as a suitable model for human cancers, supporting the idea that dysregulation discovered in canine cancers will provide an avenue for complementary study in human counterparts. Copyright © 2011 Wiley-Liss, Inc.

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...

Genome editing: the road of CRISPR/Cas9 from bench to clinic

KAUST Repository

Eid, Ayman

2016-10-14

Molecular scissors engineered for site-specific modification of the genome hold great promise for effective functional analyses of genes, genomes and epigenomes and could improve our understanding of the molecular underpinnings of disease states and facilitate novel therapeutic applications. Several platforms for molecular scissors that enable targeted genome engineering have been developed, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and, most recently, clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated-9 (Cas9). The CRISPR/Cas9 system\\'s simplicity, facile engineering and amenability to multiplexing make it the system of choice for many applications. CRISPR/Cas9 has been used to generate disease models to study genetic diseases. Improvements are urgently needed for various aspects of the CRISPR/Cas9 system, including the system\\'s precision, delivery and control over the outcome of the repair process. Here, we discuss the current status of genome engineering and its implications for the future of biological research and gene therapy.

DEFINING THE CHEMICAL SPACE OF PUBLIC GENOMIC ...

Science.gov (United States)

The current project aims to chemically index the genomics content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information. By defining the chemical space of public genomic data, it is possible to identify classes of chemicals on which to develop methodologies for the integration of chemogenomic data into predictive toxicology. The chemical space of public genomic data will be presented as well as the methodologies and tools developed to identify this chemical space.

Approximation of reliability of direct genomic breeding values

Science.gov (United States)

Two methods to efficiently approximate theoretical genomic reliabilities are presented. The first method is based on the direct inverse of the left hand side (LHS) of mixed model equations. It uses the genomic relationship matrix for a small subset of individuals with the highest genomic relationshi...

Savant Genome Browser 2: visualization and analysis for population-scale genomics.

Science.gov (United States)

Fiume, Marc; Smith, Eric J M; Brook, Andrew; Strbenac, Dario; Turner, Brian; Mezlini, Aziz M; Robinson, Mark D; Wodak, Shoshana J; Brudno, Michael

2012-07-01

High-throughput sequencing (HTS) technologies are providing an unprecedented capacity for data generation, and there is a corresponding need for efficient data exploration and analysis capabilities. Although most existing tools for HTS data analysis are developed for either automated (e.g. genotyping) or visualization (e.g. genome browsing) purposes, such tools are most powerful when combined. For example, integration of visualization and computation allows users to iteratively refine their analyses by updating computational parameters within the visual framework in real-time. Here we introduce the second version of the Savant Genome Browser, a standalone program for visual and computational analysis of HTS data. Savant substantially improves upon its predecessor and existing tools by introducing innovative visualization modes and navigation interfaces for several genomic datatypes, and synergizing visual and automated analyses in a way that is powerful yet easy even for non-expert users. We also present a number of plugins that were developed by the Savant Community, which demonstrate the power of integrating visual and automated analyses using Savant. The Savant Genome Browser is freely available (open source) at www.savantbrowser.com.

Present Status And First Results of the Final Focus Beam Line at the KEK Accelerator Test Facility

International Nuclear Information System (INIS)

2010-01-01

ATF2 is a final-focus test beam line which aims to focus the low emittance beam from the ATF damping ring to a vertical size of about 37 nm and to demonstrate nanometer level beam stability. Several advanced beam diagnostics and feedback tools are used. In December 2008, construction and installation were completed and beam commissioning started, supported by an international team of Asian, European, and U.S. scientists. The present status and first results are described.

Present status and first results of the final focus beam line at the KEK Accelerator Test Facility