The impact of post-genomics approaches in neurodegenerative demyelinating diseases: the case of Guillain-Barré syndrome.

Science.gov (United States)

Villar, Margarita; Mateos-Hernandez, Lourdes; de la Fuente, Jose

2018-03-14

Why an autoimmune disease that is the main cause of the acute neuromuscular paralysis worldwide has not yet a well-characterized cause or an effective treatment? The existence of different clinical variants for the Guillain-Barré syndrome (GBS) coupled with the fact that a high number of pathogens can cause an infection that sometimes, but not always, precedes the development of the syndrome, confers a high degree of uncertainty for both prognosis and treatment. In the post-genomic era, the development of omics technologies for the high-throughput analysis of biological molecules is allowing the characterization of biological systems in a degree of depth unimaginable before. In this context, this work summarize the application of post-genomics technologies to the study of GBS. We performed a structured search of bibliographic databases for peer-reviewed research literature to outline the state of the art with regard the application of post-genomics technologies to the study of GBS. The quality of retrieved papers was assessed using standard tools and thirty-four were included in the review. To date, transcriptomics and proteomics have been the unique post-genomics approaches applied to GBS study. Most of these studies have been performed on cerebrospinal fluid samples and only few studies have been conducted with other samples such as serum, Schwann cells and human peripheral nerve. In the post-genomics era, transcriptomics and proteomics have shown the possibilities that omics technologies can offer for a better understanding of the immunological and pathological mechanisms involved in GBS and the identification of potential biomarkers, but these results have only shown the tip of the iceberg and there is still a long way to exploit the full potential that post-genomics approaches could offer to the study of the GBS. The integration of different omics datasets through a systems biology approach could allow network-based analyses to describe the complexity and

Fungal biology in the post-genomic era.

Science.gov (United States)

Scazzocchio, Claudio

2014-01-01

In this review I give a personal perspective of how fungal biology has changed since I started my Ph. D. in 1963. At that time we were working in the shadow of the birth of molecular biology as an autonomous and reductionistic discipline, embodied in Crick's central dogma. This first period was methodologically characterised by the fact that we knew what genes were, but we could not access them directly. This radically changed in the 70s-80s when gene cloning, reverse genetics and DNA sequencing become possible. The "next generation" sequencing techniques have produced a further qualitative revolutionary change. The ready access to genomes and transcriptomes of any microbial organism allows old questions to be asked in a radically different way and new questions to be approached. I provide examples chosen somewhat arbitrarily to illustrate some of these changes, from applied aspects to fundamental problems such as the origin of fungal specific genes, the evolutionary history of genes clusters and the realisation of the pervasiveness of horizontal transmission. Finally, I address how the ready availability of genomes and transcriptomes could change the status of model organisms.

Personalized Medicine in a New Genomic Era: Ethical and Legal Aspects.

Science.gov (United States)

Shoaib, Maria; Rameez, Mansoor Ali Merchant; Hussain, Syed Ather; Madadin, Mohammed; Menezes, Ritesh G

2017-08-01

The genome of two completely unrelated individuals is quite similar apart from minor variations called single nucleotide polymorphisms which contribute to the uniqueness of each and every person. These single nucleotide polymorphisms are of great interest clinically as they are useful in figuring out the susceptibility of certain individuals to particular diseases and for recognizing varied responses to pharmacological interventions. This gives rise to the idea of 'personalized medicine' as an exciting new therapeutic science in this genomic era. Personalized medicine suggests a unique treatment strategy based on an individual's genetic make-up. Its key principles revolve around applied pharmaco-genomics, pharmaco-kinetics and pharmaco-proteomics. Herein, the ethical and legal aspects of personalized medicine in a new genomic era are briefly addressed. The ultimate goal is to comprehensively recognize all relevant forms of genetic variation in each individual and be able to interpret this information in a clinically meaningful manner within the ambit of ethical and legal considerations. The authors of this article firmly believe that personalized medicine has the potential to revolutionize the current landscape of medicine as it makes its way into clinical practice.

Bremsstrahlung: an experimentalists personal perspective on the post modern era

International Nuclear Information System (INIS)

Quarles, C.A.

2000-01-01

In this brief review I will discuss the recent experimental work on the doubly differential cross section, i.e. the photon energy and angular distribution, for electron Bremsstrahlung from thin solid film and gas targets. Since the beginning of the modern era in the study of Bremsstrahlung with the publication of the 1971 paper by Ts eng and Pratt, Professor Pratt has been the dominant influence in Bremsstrahlung research. Most, if not all, experimental research during the modern era has been motivated by the interest in comparing data with the theory of Pratt and his coworkers. As Bremsstrahlung research has moved into its post modern era, new experiments with increasing precision are concentrating on determining under what conditions ordinary Bremsstrahlung theory needs to be supplemented by a contribution from polarization Bremsstrahlung. Efforts to improve the comparison of thin-target experiment with theory have also led to new experimental and modeling work on Bremsstrahlung from thick solid targets. Thick-target Bremsstrahlung is interesting in its own right, but we also want to understand it better since it is the ever-present background in the thin-target experiments and the limiting factor in the effort to distinguish the polarization contribution to the total Bremsstrahlung spectrum. Professor Pratt ushered in the modern era in Bremsstrahlung research and has recently guided the transition into the post modern era. It can be expected that he will continue to have a formative influence on the developments of Bremsstrahlung research into the foreseeable future.

VAGINAL ECONOMY: Cinema and Globalization in the Post-Marcos Post-Brocka Era

Directory of Open Access Journals (Sweden)

Rolando B. Tolentino

2010-12-01

Full Text Available This essay explores the trope of the vaginal economy that is proliferated in the political economy and nature of Philippine migration. The vaginal economy is both receptacle and symptom of Philippine development. It represents the discourse through cinema, and historicizes the primal debate in the Marcos and Brocka contestation for image-building of the nation. Primarily through the sex-oriented (bomba films and their permutations in the various political life of the contemporary nation, the vaginal economy is historicized even in the after-life of the post-Marcos and post-Brocka era.

GPM Ground Validation: Pre to Post-Launch Era

Science.gov (United States)

Petersen, Walt; Skofronick-Jackson, Gail; Huffman, George

2015-04-01

NASA GPM Ground Validation (GV) activities have transitioned from the pre to post-launch era. Prior to launch direct validation networks and associated partner institutions were identified world-wide, covering a plethora of precipitation regimes. In the U.S. direct GV efforts focused on use of new operational products such as the NOAA Multi-Radar Multi-Sensor suite (MRMS) for TRMM validation and GPM radiometer algorithm database development. In the post-launch, MRMS products including precipitation rate, accumulation, types and data quality are being routinely generated to facilitate statistical GV of instantaneous (e.g., Level II orbit) and merged (e.g., IMERG) GPM products. Toward assessing precipitation column impacts on product uncertainties, range-gate to pixel-level validation of both Dual-Frequency Precipitation Radar (DPR) and GPM microwave imager data are performed using GPM Validation Network (VN) ground radar and satellite data processing software. VN software ingests quality-controlled volumetric radar datasets and geo-matches those data to coincident DPR and radiometer level-II data. When combined MRMS and VN datasets enable more comprehensive interpretation of both ground and satellite-based estimation uncertainties. To support physical validation efforts eight (one) field campaigns have been conducted in the pre (post) launch era. The campaigns span regimes from northern latitude cold-season snow to warm tropical rain. Most recently the Integrated Precipitation and Hydrology Experiment (IPHEx) took place in the mountains of North Carolina and involved combined airborne and ground-based measurements of orographic precipitation and hydrologic processes underneath the GPM Core satellite. One more U.S. GV field campaign (OLYMPEX) is planned for late 2015 and will address cold-season precipitation estimation, process and hydrology in the orographic and oceanic domains of western Washington State. Finally, continuous direct and physical validation

Bordetella pertussis evolution in the (functional) genomics era

Science.gov (United States)

Belcher, Thomas; Preston, Andrew

2015-01-01

The incidence of whooping cough caused by Bordetella pertussis in many developed countries has risen dramatically in recent years. This has been linked to the use of an acellular pertussis vaccine. In addition, it is thought that B. pertussis is adapting under acellular vaccine mediated immune selection pressure, towards vaccine escape. Genomics-based approaches have revolutionized the ability to resolve the fine structure of the global B. pertussis population and its evolution during the era of vaccination. Here, we discuss the current picture of B. pertussis evolution and diversity in the light of the current resurgence, highlight import questions raised by recent studies in this area and discuss the role that functional genomics can play in addressing current knowledge gaps. PMID:26297914

SYNESTHETIC ARTISTIC PERCEPTION IN THE ERA OF POST LITERACY

OpenAIRE

Margarita, Gudova; Irina, Lisovetc

2017-01-01

In the era of post-literacy, the development ofinformation technology and the technological basis of art as well as the mechanismsof not only artistic creativity, but also its perception, change. Thetransformation peculiarities of artistic perception of the new polymorphic andmultimedia art require their scientific and theoretical comprehension in theconditions of post-literacy that have developed in the last 50 years.In this case, we are interested in the nuancescharacterizing the changes in...

Simple sequence repeats in mycobacterial genomes

Indian Academy of Sciences (India)

2006-12-18

Dec 18, 2006 ... Although prokaryotic genomes derive some plasticity due to microsatellite mutations they have in-built mechanisms to arrest undue expansions of microsatellites and one such mechanism is constituted by post-replicative DNA repair enzymes MutL, MutH and MutS. The mycobacterial genomes lack these ...

Evaluating Phylogenetic Congruence in the Post-Genomic Era

Science.gov (United States)

Leigh, Jessica W.; Lapointe, François-Joseph; Lopez, Philippe; Bapteste, Eric

2011-01-01

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures. PMID:21712432

INVESTIGATIONS INTO MOLECULAR PATHWAYS IN THE POST GENOME ERA: CROSS SPECIES COMPARATIVE GENOMICS APPROACH

Science.gov (United States)

Genome sequencing efforts in the past decade were aimed at generating draft sequences of many prokaryotic and eukaryotic model organisms. Successful completion of unicellular eukaryotes, worm, fly and human genome have opened up the new field of molecular biology and function...

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

Energy Technology Data Exchange (ETDEWEB)

Thompson, Cristiane C. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Amaral, Gilda R. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Campeão, Mariana [Univ. of Rio de Janeiro (UFRJ) (Brazil); Edwards, Robert A. [Univ. of Rio de Janeiro (UFRJ) (Brazil); San Diego State Univ., CA (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Polz, Martin F. [Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States); Dutilh, Bas E. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Radbould Univ., Nijmegen (Netherlands); Ussery, David W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sawabe, Tomoo [Hokkaido Univ., Hakodate (Japan); Swings, Jean [Univ. of Rio de Janeiro (UFRJ) (Brazil); Ghent Univ. (Belgium); Thompson, Fabiano L. [Univ. of Rio de Janeiro (UFRJ) (Brazil); Advanced Systems Laboratory Production Management COPPE / UFRJ, Rio de Janeiro (Brazil)

2014-12-23

Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. We re-evaluated the prokaryote species twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. We will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

Freedom of Contract in the Post-Crisis Era: Quo Vadis?

NARCIS (Netherlands)

Cherednychenko, O.O.

2014-01-01

This article explores to what extent the future development of European financial services contract law will be determined by the information paradigm in the post-crisis era. By using the examples from the field of investment services and consumer credit, it shows that the regulatory measures

Perspectives in the control of infectious diseases by transgenic mosquitoes in the post-genomic era: a review

Directory of Open Access Journals (Sweden)

Márcia Aparecida Sperança

2007-06-01

Full Text Available Arthropod-borne diseases caused by a variety of microorganisms such as dengue virus and malaria parasites afflict billions of people worldwide imposing major economic and social burdens. Despite many efforts, vaccines against diseases transmitted by mosquitoes, with the exception of yellow fever, are not available. Control of such infectious pathogens is mainly performed by vector management and treatment of affected individuals with drugs. However, the numbers of insecticide-resistant insects and drug-resistant parasites are increasing. Therefore, inspired in recent years by a lot of new data produced by genomics and post-genomics research, several scientific groups have been working on different strategies to control infectious arthropod-borne diseases. This review focuses on recent advances and perspectives towards construction of transgenic mosquitoes refractory to malaria parasites and dengue virus transmission.

Perspectives in the control of infectious diseases by transgenic mosquitoes in the post-genomic era--a review.

Science.gov (United States)

Sperança, Márcia Aparecida; Capurro, Margareth Lara

2007-06-01

Arthropod-borne diseases caused by a variety of microorganisms such as dengue virus and malaria parasites afflict billions of people worldwide imposing major economic and social burdens. Despite many efforts, vaccines against diseases transmitted by mosquitoes, with the exception of yellow fever, are not available. Control of such infectious pathogens is mainly performed by vector management and treatment of affected individuals with drugs. However, the numbers of insecticide-resistant insects and drug-resistant parasites are increasing. Therefore, inspired in recent years by a lot of new data produced by genomics and post-genomics research, several scientific groups have been working on different strategies to control infectious arthropod-borne diseases. This review focuses on recent advances and perspectives towards construction of transgenic mosquitoes refractory to malaria parasites and dengue virus transmission.

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

Science.gov (United States)

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

2008-08-01

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

Macromolecular structure determination in the post-genome era

CERN Document Server

Kuhn, P

2001-01-01

Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system...

Curriculum Evolution at Air Command and Staff College in the Post-Cold War Era

Science.gov (United States)

Donovan, William Robert, II.

2010-01-01

This qualitative study used a historical research method to eliminate the gap in the historical knowledge of Air Command and Staff College (ACSC) curriculum evolution in the post-Cold War era. This study is the only known analysis of the forces that influenced the ACSC curriculum and the rationale behind curricular change at ACSC in the post-Cold…

Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement

Directory of Open Access Journals (Sweden)

Arun Prabhu Dhanapal

2015-01-01

Full Text Available The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.

Macromolecular structure determination in the post-genome era

International Nuclear Information System (INIS)

Kuhn, P.; Soltis, S.M.

2001-01-01

Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system for the structure determination steps of this process, starting with the initial characterization of the frozen sample, followed by data collection, data reduction, phase determination, and model building. This paper focuses on the data collection elements of this high-throughput system

[A review of the genomic and gene cloning studies in trees].

Science.gov (United States)

Yin, Tong-Ming

2010-07-01

Supported by the Department of Energy (DOE) of U.S., the first tree genome, black cottonwood (Populus trichocarpa), has been completely sequenced and publicly release. This is the milestone that indicates the beginning of post-genome era for forest trees. Identification and cloning genes underlying important traits are one of the main tasks for the post-genome-era tree genomic studies. Recently, great achievements have been made in cloning genes coordinating important domestication traits in some crops, such as rice, tomato, maize and so on. Molecular breeding has been applied in the practical breeding programs for many crops. By contrast, molecular studies in trees are lagging behind. Trees possess some characteristics that make them as difficult organisms for studying on locating and cloning of genes. With the advances in techniques, given also the fast growth of tree genomic resources, great achievements are desirable in cloning unknown genes from trees, which will facilitate tree improvement programs by means of molecular breeding. In this paper, the author reviewed the progress in tree genomic and gene cloning studies, and prospected the future achievements in order to provide a useful reference for researchers working in this area.

Nuclear Issues in the Post-September 11 era

International Nuclear Information System (INIS)

Dunn, Lewis; Wheeler, Michael; May, Michael; Pikayev, Alexander; Wolfstahl, Jon; Roberts, Brad; Tertrais, Bruno; Umbach, Frank

2003-03-01

In the fall of 2002, the Foundation for Strategic Research convened a small group of high-level experts on nuclear policy issues to discuss the consequences of September 11 and of the 'war on terrorism' for nuclear debates. Participants met in Paris on September 26-27, 2002, and later provided papers which are reproduced here. This project was sponsored by the French Commissariat a l'Energie Atomique (CEA). Contents: 1 - Nuclear Issues in the Post-September 11 era: emerging Trends (Bruno Tertrais); 2 - Nuclear energy Issues: Global Dimensions and Security Challenges (Frank Umbach); 3 - Proliferation and Non-Proliferation: What's Changed-What Hasn't? (Jon B. Wolfstahl); 4 - Non-Proliferation: Possible New Trends after September 11 (Alexander A. Pikayev); 5 - Nuclear Deterrence Issues in the Post-September 11 World: An American Perspective (Michael O. Wheeler); 6 - The Nuclear Balance of Terror and September 11 (Brad Roberts); 7 - Nuclear Weapons after September 11 (Lewis A. Dunn); 8 - September 11 and the Need for International Nuclear Agreements (Michael May)

Economic outcome for intensive care of infants of birthweight 500-999 g born in Victoria in the post surfactant era. The Victorian Infant Collaborative Study Group.

Science.gov (United States)

1997-06-01

To determine the incremental cost of improving the outcome for extremely low birthweight (ELBW, birthweight 500-999 g) infants born in Victoria after the introduction of exogenous surfactant (the post surfactant era). This was a geographically determined cohort study of ELBW children in Victoria, Australia of consecutive livebirths born in three distinct eras: (i) 1979-80 (n = 351); (ii) 1985-87 (n = 560); and (iii) 1991-92 (n = 429). Exogenous surfactant was first used in Victoria in March, 1991. The consumption of nursery resources per livebirth, and the survival and sensorineural disability rates at 2 years of age for each era were investigated. Utilities were assigned as follows: 0 for dead, 0.4 for severe disability, 0.6 for moderate disability, 0.8 for mild disability, and 1 for no disability. Utilities were multiplied for more than one disability. Dollar costs were assumed to be $1470 ($A 1992) per day of assisted ventilation, and one dose of exogenous surfactant was assumed to be equivalent to one third of a day of assisted ventilation. Cost-effectiveness (additional costs per additional survivor or life-year gained) and cost-utility (additional costs per additional quality-adjusted survivor or life-year gained) ratios were calculated for the pre-surfactant era (1985-87 vs 1979-80), and for the post surfactant era (1991-92 vs 1985-87). Considering only the costs incurred during the primary hospitalization, cost-effectiveness and cost-utility ratios were lower (i.e. economically better) in the post surfactant era than in the pre-surfactant era (pre-surfactant vs post surfactant; $7040 vs $4040 per life year gained; $6700 vs $5360 per quality-adjusted life year gained). Both ratios fell with increasing birthweight. In contrast with the pre-surfactant era, cost-utility ratios were less favourable than cost-effectiveness ratios in the post surfactant era. With costs for long-term care of severely disabled children added, both cost ratios were higher in the post

Use of genome-scale microbial models for metabolic engineering

DEFF Research Database (Denmark)

Patil, Kiran Raosaheb; Åkesson, M.; Nielsen, Jens

2004-01-01

Metabolic engineering serves as an integrated approach to design new cell factories by providing rational design procedures and valuable mathematical and experimental tools. Mathematical models have an important role for phenotypic analysis, but can also be used for the design of optimal metaboli...... network structures. The major challenge for metabolic engineering in the post-genomic era is to broaden its design methodologies to incorporate genome-scale biological data. Genome-scale stoichiometric models of microorganisms represent a first step in this direction....

Pea (Pisum sativum L. in the Genomic Era

Directory of Open Access Journals (Sweden)

Robert J. Redden

2012-04-01

Full Text Available Pea (Pisum sativum L. was the original model organism used in Mendel’s discovery (1866 of the laws of inheritance, making it the foundation of modern plant genetics. However, subsequent progress in pea genomics has lagged behind many other plant species. Although the size and repetitive nature of the pea genome has so far restricted its sequencing, comprehensive genomic and post genomic resources already exist. These include BAC libraries, several types of molecular marker sets, both transcriptome and proteome datasets and mutant populations for reverse genetics. The availability of the full genome sequences of three legume species has offered significant opportunities for genome wide comparison revealing synteny and co-linearity to pea. A combination of a candidate gene and colinearity approach has successfully led to the identification of genes underlying agronomically important traits including virus resistances and plant architecture. Some of this knowledge has already been applied to marker assisted selection (MAS programs, increasing precision and shortening the breeding cycle. Yet, complete translation of marker discovery to pea breeding is still to be achieved. Molecular analysis of pea collections has shown that although substantial variation is present within the cultivated genepool, wild material offers the possibility to incorporate novel traits that may have been inadvertently eliminated. Association mapping analysis of diverse pea germplasm promises to identify genetic variation related to desirable agronomic traits, which are historically difficult to breed for in a traditional manner. The availability of high throughput ‘omics’ methodologies offers great promise for the development of novel, highly accurate selective breeding tools for improved pea genotypes that are sustainable under current and future climates and farming systems.

Each cell counts: Hematopoiesis and immunity research in the era of single cell genomics.

Science.gov (United States)

Jaitin, Diego Adhemar; Keren-Shaul, Hadas; Elefant, Naama; Amit, Ido

2015-02-01

Hematopoiesis and immunity are mediated through complex interactions between multiple cell types and states. This complexity is currently addressed following a reductionist approach of characterizing cell types by a small number of cell surface molecular features and gross functions. While the introduction of global transcriptional profiling technologies enabled a more comprehensive view, heterogeneity within sampled populations remained unaddressed, obscuring the true picture of hematopoiesis and immune system function. A critical mass of technological advances in molecular biology and genomics has enabled genome-wide measurements of single cells - the fundamental unit of immunity. These new advances are expected to boost detection of less frequent cell types and fuzzy intermediate cell states, greatly expanding the resolution of current available classifications. This new era of single-cell genomics in immunology research holds great promise for further understanding of the mechanisms and circuits regulating hematopoiesis and immunity in both health and disease. In the near future, the accuracy of single-cell genomics will ultimately enable precise diagnostics and treatment of multiple hematopoietic and immune related diseases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Genome engineering for microbial natural product discovery.

Science.gov (United States)

Choi, Si-Sun; Katsuyama, Yohei; Bai, Linquan; Deng, Zixin; Ohnishi, Yasuo; Kim, Eung-Soo

2018-03-03

The discovery and development of microbial natural products (MNPs) have played pivotal roles in the fields of human medicine and its related biotechnology sectors over the past several decades. The post-genomic era has witnessed the development of microbial genome mining approaches to isolate previously unsuspected MNP biosynthetic gene clusters (BGCs) hidden in the genome, followed by various BGC awakening techniques to visualize compound production. Additional microbial genome engineering techniques have allowed higher MNP production titers, which could complement a traditional culture-based MNP chasing approach. Here, we describe recent developments in the MNP research paradigm, including microbial genome mining, NP BGC activation, and NP overproducing cell factory design. Copyright © 2018 Elsevier Ltd. All rights reserved.

Political Evolution at NATO Level in Post Cold War Era

Directory of Open Access Journals (Sweden)

Tomescu Cătălin Tomiţă

2015-06-01

Full Text Available The beginning of the post Cold era sounds like that: „The world has changed dramatically. The Alliance has made an essential contribution. The peoples of North America and the whole of Europe can now join in a community of shared values based on freedom, democracy, human rights and the rule of law. As an agent of change, a source of stability and the indispensable guarantor of its members' security, our Alliance will continue to play a key role in building a new, lasting order of peace in Europe: a Europe of cooperation and prosperity”[1].

Germplasm Management in the Post-genomics Era-a case study with lettuce

Science.gov (United States)

High-throughput genotyping platforms and next-generation sequencing technologies revolutionized our ways in germplasm characterization. In collaboration with UC Davis Genome Center, we completed a project of genotyping the entire cultivated lettuce (Lactuca sativa L.) collection of 1,066 accessions ...

Not Yet the Post-TV Era: Network and MVPD Adaptation to Emergent Distribution Technologies

Directory of Open Access Journals (Sweden)

Mike Van Esler

2016-07-01

Full Text Available Television as a medium is in transition. From DVRs, to Netflix, to HBO Now, consumers have never before had such control over how they consume televisual content. The rapid changes to the medium have led to rhetoric heralding the impending “post-TV era.” Looking at the ways that legacy television companies have adapted to new technologies and cultural practices suggests that rather than traditional television going the way of radio, television as a medium is actually not terribly different, at least not enough to conclude that we have entered a new era. Press releases, discursive practices by the news media, corporate structures and investments, and audience research all point to the rhetoric of post-TV as being overblown. By thinking about contemporary television as being in transition, greater emphasis and attention can be placed on the role that major media conglomerates play in developing, funding, and legitimizing new forms of television distribution, in addition to co-opting disruptive technologies and business models while hindering others.

Growing up at the intersection of the genomic era and the information age.

Science.gov (United States)

Driessnack, Martha

2009-06-01

Children actively seek to make sense of their worlds based on the information they receive and their experience. For children growing up at the intersection of genomic era and information age, the array of information and experience continues to expand. This article highlights the importance of exploring these early contexts for learning, including the children's exposure to books and mass media, and the impact of early learning on later health literacy and behaviors. This article presents a case study discussing the inheritance of cystic fibrosis using the Harry Potter book series.

Genome projects and the functional-genomic era.

Science.gov (United States)

Sauer, Sascha; Konthur, Zoltán; Lehrach, Hans

2005-12-01

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

Lifting All Boats? Finance Litigation, Education Resources, and Student Needs in the Post-"Rose" Era

Science.gov (United States)

Sims, David P.

2011-01-01

"Rose v. Council for Better Education" (1989) is often considered a transition point in education finance litigation, heralding an era of increasing concern for measurable adequacy of education across a broad spectrum of student needs. Prior research suggests that post-Rose lawsuits had less effect on the distribution of school spending…

Privacy in the Genomic Era

Science.gov (United States)

NAVEED, MUHAMMAD; AYDAY, ERMAN; CLAYTON, ELLEN W.; FELLAY, JACQUES; GUNTER, CARL A.; HUBAUX, JEAN-PIERRE; MALIN, BRADLEY A.; WANG, XIAOFENG

2015-01-01

Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward. PMID:26640318

Privacy in the Genomic Era.

Science.gov (United States)

Naveed, Muhammad; Ayday, Erman; Clayton, Ellen W; Fellay, Jacques; Gunter, Carl A; Hubaux, Jean-Pierre; Malin, Bradley A; Wang, Xiaofeng

2015-09-01

Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.

Description of Hymenolepis microstoma (Nottingham strain: a classical tapeworm model for research in the genomic era

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Olson Peter D

2010-12-01

Full Text Available Abstract Background Hymenolepis microstoma (Dujardin, 1845 Blanchard, 1891, the mouse bile duct tapeworm, is a rodent/beetle-hosted laboratory model that has been used in research and teaching since its domestication in the 1950s. Recent characterization of its genome has prompted us to describe the specific strain that underpins these data, anchoring its identity and bringing the 150+ year-old original description up-to-date. Results Morphometric and ultrastructural analyses were carried out on laboratory-reared specimens of the 'Nottingham' strain of Hymenolepis microstoma used for genome characterization. A contemporary description of the species is provided including detailed illustration of adult anatomy and elucidation of its taxonomy and the history of the specific laboratory isolate. Conclusions Our work acts to anchor the specific strain from which the H. microstoma genome has been characterized and provides an anatomical reference for researchers needing to employ a model tapeworm system that enables easy access to all stages of the life cycle. We review its classification, life history and development, and briefly discuss the genome and other model systems being employed at the beginning of a genomic era in cestodology.

BLAST Ring Image Generator (BRIG: simple prokaryote genome comparisons

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Beatson Scott A

2011-08-01

automatically. Conclusions There is a clear need for a user-friendly program that can produce genome comparisons for a large number of prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. Here we present BRIG, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. BRIG is freely available for all operating systems at http://sourceforge.net/projects/brig/.

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.

Science.gov (United States)

Alikhan, Nabil-Fareed; Petty, Nicola K; Ben Zakour, Nouri L; Beatson, Scott A

2011-08-08

-friendly program that can produce genome comparisons for a large number of prokaryote genomes with an emphasis on rapidly utilising unfinished or unassembled genome data. Here we present BRIG, a cross-platform application that enables the interactive generation of comparative genomic images via a simple graphical-user interface. BRIG is freely available for all operating systems at http://sourceforge.net/projects/brig/.

The Vietnamese Garment Industry in the Post MFA Era: Upgrading, Relocating, or Moving Out?

OpenAIRE

GOTO, Kenta

2008-01-01

This paper investigates how key export oriented garment suppliers of Vietnam are coping with emerging challenges in the post MFA era. The garment industry is Vietnam’s largest manufacturing based export sector, and is registering significant growth despite increased international competitiveness. The performance of those garment suppliers, however, is not even. While some were able to increase productivity and expand operations, others legged behind in upgrading and stagnated in terms of comp...

PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

Science.gov (United States)

Kumar, Pankaj; Chaitanya, Pasumarthy S; Nagarajaram, Hampapathalu A

2011-01-01

PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in some bacteria. Although SSR-mediated phase variation and antigenic variations have been well-studied in some bacteria there seems a lot of other species of prokaryotes yet to be investigated for SSR mediated adaptive and other evolutionary advantages. As a part of our on-going studies on SSR polymorphism in prokaryotes we compared the genome sequences of various strains and isolates available for 85 different species of prokaryotes and extracted a number of SSRs showing length variations and created a relational database called PSSRdb. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc. The information provided in this database is very useful for further research and analysis of SSRs in prokaryotes.

Identity and Othering in Past and Present: Representations of the Soviet Era in Estonian Post-Soviet Textbooks

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Katrin Kello

2018-02-01

Full Text Available This paper analyses representations of the ‘core Soviet era’ (1945-1985 in Estonian post-Soviet history textbooks (1989-2016. Attitudes towards the Soviet system have been a rich resource for identity building, and hence a powerful political tool across the whole of the post-Soviet block. Based on an analysis of sections about the Soviet era in Estonia in 21 textbooks, the paper takes a look at how textbooks reflect broader processes of social meaning making, identity building and othering after a profound social and political turn. In 1989 and during the early 1990s, perspectives and narratives in Estonian history textbooks were closely related to social memory and national politics, enacting a specific social representation of the Soviet era that dominated the Estonian-speaking public space during the 1990s. The Soviet era, Russia and local Russians became the main Others for Estonia and Estonians. Over time, public discourse has diversified. The national curriculum and textbooks, however, still maintain the canon that formed in 1990s and thus reflect earlier sentiments. Apart from the increasing salience of Soviet-era daily life in more recent textbooks, the thematic choices and emphases have changed little since the 1990s. Therefore, even if the style of writing has ‘cooled down’, issues of identity preservation, resistance and accommodation, together with a saliently negative representation of wrongdoings by the Soviet system, still prevail. On the one hand, this testifies to the resilience of an established tradition in the textbook genre in general. On the other hand, it reflects the dominance of an ethnocentric tradition in Estonian history textbook writing. The paper discusses the implications of these findings for interethnic relations in Estonia.

Visualizing information across multidimensional post-genomic structured and textual databases.

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Tao, Ying; Friedman, Carol; Lussier, Yves A

2005-04-15

Visualizing relationships among biological information to facilitate understanding is crucial to biological research during the post-genomic era. Although different systems have been developed to view gene-phenotype relationships for specific databases, very few have been designed specifically as a general flexible tool for visualizing multidimensional genotypic and phenotypic information together. Our goal is to develop a method for visualizing multidimensional genotypic and phenotypic information and a model that unifies different biological databases in order to present the integrated knowledge using a uniform interface. We developed a novel, flexible and generalizable visualization tool, called PhenoGenesviewer (PGviewer), which in this paper was used to display gene-phenotype relationships from a human-curated database (OMIM) and from an automatic method using a Natural Language Processing tool called BioMedLEE. Data obtained from multiple databases were first integrated into a uniform structure and then organized by PGviewer. PGviewer provides a flexible query interface that allows dynamic selection and ordering of any desired dimension in the databases. Based on users' queries, results can be visualized using hierarchical expandable trees that present views specified by users according to their research interests. We believe that this method, which allows users to dynamically organize and visualize multiple dimensions, is a potentially powerful and promising tool that should substantially facilitate biological research. PhenogenesViewer as well as its support and tutorial are available at http://www.dbmi.columbia.edu/pgviewer/ Lussier@dbmi.columbia.edu.

Kidney function and mortality post-liver transplant in the Model for End-Stage Liver Disease era

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Sethi A

2011-11-01

Full Text Available Aastha Sethi1, Michelle M Estrella1, Richard Ugarte2, Mohamed G Atta1 1Johns Hopkins University School of Medicine, Department of Medicine, Baltimore, MD, USA; 2University of Maryland Medical Center, Department of Medicine, Baltimore, MD, USA Abstract: The Model for End-Stage Liver Disease (MELD score incorporates serum creatinine and was introduced to facilitate allocation of orthotopic liver transplantation (LT. The objective is to determine the impact of MELD and kidney function on all-cause mortality. Among LTs performed in a tertiary referral hospital between 1995 and 2009, 419 cases were studied. Cox proportional hazards models were constructed to estimate the hazard ratios (HR and 95% confidence intervals (CI for death. Over mean follow-ups of 8.4 and 3.1 years during the pre-MELD and MELD era, 57 and 63 deaths were observed, respectively. Those transplanted during the MELD era had a higher likelihood of hepatorenal syndrome (8% vs 2%, P < 0.01, lower kidney function (median estimated glomerular filtration rate [eGFR] 77.8 vs 92.6 mL/min/1.73 m2, P < 0.01, and more pretransplantation renal replacement therapy (RRT (5% vs 1%; P < 0.01. All-cause mortality risk was similar in the MELD vs the pre-MELD era (HR: 0.98, 95% CI: 0.58–1.65. The risk of death, however, was nearly 3-fold greater (95% CI: 1.14–6.60 among those requiring pre-transplant RRT. Similarly, eGFR < 60 mL/min/1.73 m2 post-transplant was associated with a 2.5-fold higher mortality (95% CI: 1.48–4.11. The study suggests that MELD implementation had no impact on all-cause mortality post-LT. However, the need for pre-transplant RRT and post-transplant kidney dysfunction was associated with a more than 2-fold greater risk of subsequent death. Keywords: eGFR, mortality, MELD, liver transplant

The future of radiation therapy in the post-genomic era

International Nuclear Information System (INIS)

McBride, W. H.; Iwamoto, K. S.

2003-01-01

The cloning of the human genome has generated a tremendous resource of information that will improve treatment of cancer, and other diseases. Allied to these discoveries are powerful new investigative tools that have been, and are being, developed. These are being used to give a comprehensive biological profile of individuals and their cancer that will allow better classification, as well as identification of pathways that might be targeted with therapeutic benefit. The hope is that these approaches will allow intervention that is tailored to the needs of the individual patient and that the targeted cancer therapies will be associated with less toxicity than those currently used. This raises questions as to how best to use the new biotechnologies to predict responses to conventional therapies and indeed will conventional therapies, like radiation therapy, have a role in cancer treatment as specific biologically targeted drugs become commonplace. Here, it is argued that even the molecular staging of cancer that is currently being performed, if exploited correctly, will greatly aid patient selection for radiation therapy and that this should be the starting point for further studies aimed at developing predictive profiles for improving treatment outcome. It is also argued that because the biological anti-cancer agents target molecular pathways that overlap with those responsible for radiosensitivity, and because on their own they have little cytotoxic power, radiation therapists should incorporate biological agents into combined modality regimens and that this is likely to be a standard form of treatment in the next decade. (author)

From ‘Gads’ to ‘Apps’: the key challenges of post-web internet era

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Alan César Belo Angeluci

2013-12-01

Full Text Available This paper aims to discuss the main changes that device’s applications have faced along the past decades in order to show how internet connection has deeply influenced the way people communicate and interact with this media. From the Internet of Things (IoT perspective, the Hannibal serie and its second screen app case is briefly presented for supporting the key challenges of this post-web internet era: (1 protection of sensitive and private user data in a ubiquitous environment, (2 interoperability, (3 communication and (4 proper language.

Pedagogy in the Era of the Post-Non-Classical Science

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V. L. Benin

2015-02-01

Full Text Available The paper considers over again the problem of the low quality of the scientific pedagogic research of the recent time. The author analyses numerous publications concerning the above problem and presents his opinion on the actual reasons for stagnation in the modern national pedagogy. Its crisis is primarily caused by ignoring the complications of the world perception, changing world outlook, as well as by long ago developed but rejected necessity for devising new methodological principles and value- and objective-oriented educational attitudes. The exact forms and methods of professional activity of pedagogic process participants are derived from the definite historically developed complex lying in their foundation. The educational system structure depends on the logic of cultural structure of the related era both from the methodological and organizational viewpoint. However, our pedagogy retains the position of the New Time classical methodology not complying with the non-classical paradigm, all the more so with the post-non-classical science. The demonstrative appeal to synergetics – the attempt of pedagogy to position itself in terms of post-non-classical science – still remains doubtful.Not persisting on the absolute correctness of his position, the author invites teaches and specialists from educational sphere to the scientific discussion to facilitate, even partially, the existing problem solving. 

Simple Genome Editing of Rodent Intact Embryos by Electroporation.

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Takehito Kaneko

Full Text Available The clustered regularly interspaced short palindromic repeat (CRISPR/CRISPR-associated (Cas system is a powerful tool for genome editing in animals. Recently, new technology has been developed to genetically modify animals without using highly skilled techniques, such as pronuclear microinjection of endonucleases. Technique for animal knockout system by electroporation (TAKE method is a simple and effective technology that produces knockout rats by introducing endonuclease mRNAs into intact embryos using electroporation. Using TAKE method and CRISPR/Cas system, the present study successfully produced knockout and knock-in mice and rats. The mice and rats derived from embryos electroporated with Cas9 mRNA, gRNA and single-stranded oligodeoxynucleotide (ssODN comprised the edited targeted gene as a knockout (67% of mice and 88% of rats or knock-in (both 33%. The TAKE method could be widely used as a powerful tool to produce genetically modified animals by genome editing.

Population genomics of fungal and oomycete pathogens

Science.gov (United States)

We are entering a new era in plant pathology where whole-genome sequences of many individuals of a pathogen species are becoming readily available. This era of pathogen population genomics will provide new opportunities and challenges, requiring new computational and analytical tools. Population gen...

SUSTAINABLE DEVELOPMENT – HUMAN DEVELOPMENT CONNECTIONS IN THE POST-TRUTH ERA

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ANDREEA CONSTANTINESCU

2017-08-01

Full Text Available Following the distancing of current policy from economic rigors and ethical demands aimed at redistribution of wealth, modern societies are parasitized by post-truth of actual facts. It distorts the shape and content of general interest data, for example political distortion of scientific evidence proving anthropogenic climate change. Under these circumstances, the question "to what extent economist’s truth stating what you cannot measure you cannot manage is sustained?" becomes absolutely legitimate. Regarding sustainable development management, monitoring the degree of achievement of Sustainable Development Goals is no longer sufficient to track progress in this area. Therefore, experts propose to introduce as much as possible qualitative data which, combined with quantitative data, will enhance their relevance and make them harder to be diverted for political purposes. This paper follows this direction, trying to prove that protection of data’s real meaning can be achieved by systemic analysis of all data originating from monitoring certain processes, which can be aggregated, with applicability in sustainable development. Thus, analyzing together data on sustainable development and those that indicates the state of human development emphasizes on one hand, the intrinsic link between these concepts and, on the other, maintain the sense of sustainability even in the post-truth era.

Re-Form: FPGA-Powered True Codesign Flow for High-Performance Computing In The Post-Moore Era

Energy Technology Data Exchange (ETDEWEB)

Cappello, Franck; Yoshii, Kazutomo; Finkel, Hal; Cong, Jason

2016-11-14

Multicore scaling will end soon because of practical power limits. Dark silicon is becoming a major issue even more than the end of Moore’s law. In the post-Moore era, the energy efficiency of computing will be a major concern. FPGAs could be a key to maximizing the energy efficiency. In this paper we address severe challenges in the adoption of FPGA in HPC and describe “Re-form,” an FPGA-powered codesign flow.

Post-genomic approaches to understanding interactions between fungi and their environment.

Science.gov (United States)

de Vries, Ronald P; Benoit, Isabelle; Doehlemann, Gunther; Kobayashi, Tetsuo; Magnuson, Jon K; Panisko, Ellen A; Baker, Scott E; Lebrun, Marc-Henri

2011-06-01

Fungi inhabit every natural and anthropogenic environment on Earth. They have highly varied life-styles including saprobes (using only dead biomass as a nutrient source), pathogens (feeding on living biomass), and symbionts (co-existing with other organisms). These distinctions are not absolute as many species employ several life styles (e.g. saprobe and opportunistic pathogen, saprobe and mycorrhiza). To efficiently survive in these different and often changing environments, fungi need to be able to modify their physiology and in some cases will even modify their local environment. Understanding the interaction between fungi and their environments has been a topic of study for many decades. However, recently these studies have reached a new dimension. The availability of fungal genomes and development of post-genomic technologies for fungi, such as transcriptomics, proteomics and metabolomics, have enabled more detailed studies into this topic resulting in new insights. Based on a Special Interest Group session held during IMC9, this paper provides examples of the recent advances in using (post-)genomic approaches to better understand fungal interactions with their environments.

Diabetic foot infections: Current treatment and delaying the 'post-antibiotic era'.

Science.gov (United States)

Lipsky, Benjamin A

2016-01-01

Treatment for diabetic foot infections requires properly diagnosing infection, obtaining an appropriate specimen for culture, assessing for any needed surgical procedures and selecting an empiric antibiotic regimen. Therapy will often need to be modified based on results of culture and sensitivity testing. Because of excessive and inappropriate use of antibiotics for treating diabetic foot infections, resistance to the usually employed bacteria has been increasing to alarming levels. This article reviews recommendations from evidence-based guidelines, informed by results of systematic reviews, on treating diabetic foot infections. Data from the pre-antibiotic era reported rates of mortality of about 9% and of high-level leg amputations of about 70%. Outcomes have greatly improved with appropriate antibiotic therapy. While there are now many oral and parenteral antibiotic agents that have demonstrated efficacy in treating diabetic foot infections, the rate of infection with multidrug-resistant pathogens is growing. This problem requires a multi-focal approach, including providing education to both clinicians and patients, developing robust antimicrobial stewardship programmes and using new diagnostic and therapeutic technologies. Recently, new methods have been developed to find novel antibiotic agents and to resurrect old treatments, like bacteriophages, for treating these difficult infections. Medical and political leaders have recognized the serious global threat posed by the growing problem of antibiotic resistance. By a multipronged approach that includes exerting administrative pressure on clinicians to do the right thing, investing in new technologies and encouraging the profitable development of new antimicrobials, we may be able to stave off the coming 'post-antibiotic era'. Copyright © 2016 John Wiley & Sons, Ltd.

A primer on high-throughput computing for genomic selection.

Science.gov (United States)

Wu, Xiao-Lin; Beissinger, Timothy M; Bauck, Stewart; Woodward, Brent; Rosa, Guilherme J M; Weigel, Kent A; Gatti, Natalia de Leon; Gianola, Daniel

2011-01-01

genetic gain). Eventually, HTC may change our view of data analysis as well as decision-making in the post-genomic era of selection programs in animals and plants, or in the study of complex diseases in humans.

Field protocols for the genomic era

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N Bulatova

2009-08-01

Full Text Available For many decades karyotype was the only source of overall genomic information obtained from species of mammal. However, approaches have been developed in recent years to obtain molecular and ultimately genomic information directly from the extracted DNA of an organism. Molecular data have accumulated hugely for mammalian taxa. The growing volume of studies should motivate field researchers to collect suitable samples for molecular analysis from various species across all their ranges. This is the reason why we here include a molecular sampling procedure within a field work protocol, which also includes more traditional (including cytogenetic techniques. In this way we hope to foster the development of molecular and genomic studies in non-standard wild mammals.

Mathematics education practice in Nigeria: Its impact in a post-colonial era

Science.gov (United States)

Enime, Noble O. J.

This qualitative research method of study examined the impacts of the Nigerian pre-independence era Mathematics Education Practice on the Post-Colonial era Mathematics Education Practice. The study was designed to gather qualitative information related to Pre-independence and Postcolonial era data related to Mathematics Education Practice in Nigeria (Western, Eastern and the Middle Belt) using interview questions. Data was collected through face to face interviews. Over ten themes emerged from these qualitative interview questions when data was analyzed. Some of the themes emerging from the sub questions were as follows. "Mentally mature to understand the mathematics" and "Not mentally mature to understand the mathematics", "mentally mature to understand the mathematics, with the help of others" and "Not Sure". Others were "Contented with Age of Enrollment" and "Not contented with Age of Enrollment". From the questions of type of school attended and liking of mathematics the following themes emerged: "Attended UPE (Universal Primary Education) and understood Mathematics", and "Attended Standard Education System and did not like Mathematics". Connections between the liking of mathematics and the respondents' eventual careers were seen through the following themes that emerged. "Biological Sciences based career and enjoyed High School Mathematics Experience", "Economics and Business Education based career and enjoyed High School Mathematics Experience" and five more themes. The themes, "Very helpful" and "Unhelpful" emerged from the question concerning parents and students' homework. Some of the themes emerging from the interviews were as follows: "Awesome because of method of Instruction of Mathematics", "Awesome because Mathematics was easy", "Awesome because I had a Good Teacher or Teachers" and four other themes, "Like and dislike of Mathematics", "Heavy work load", "Subject matter content" and "Rigor of instruction". More emerging themes are presented in this

New criteria for supplementation of selected micronutrients in the era of nutrigenetics and nutrigenomics.

Science.gov (United States)

Schwartz, Betty

2014-08-01

Advances in molecular biology, emergence of novel techniques and huge amount of information generated in the post-Human Genome Project era have fostered the emergence of new disciplines in the field of nutritional research: Nutrigenomics deals with the effect of diet on gene expression whereas nutrigenetics refers to the impact of inherited traits on the response to a specific dietary pattern, functional food or supplement. Understanding the role of micronutrient supplementation with specific genetic backgrounds may provide an important contribution to a new optimum health strategy based on individualized nutritional treatment and may provide the strategies for the development of safer and more effective dietary interventions. This overview of the various aspects of supplementation of micronutrients in the era of nutrigenetics and nutrigenomics may provide a better understanding of novel nutritional research approach and provide an additional insight that can be applied to the daily dietary practice.

Insect Immunity: The Post-Genomic Era

OpenAIRE

Bangham, Jenny; Jiggins, Frank; Lemaitre, Bruno

2006-01-01

Insects have a complex and effective immune system, many components of which are conserved in mammals. But only in the last decade have the molecular mechanisms that regulate the insect immune response--and their relevance to general biology and human immunology--become fully appreciated. A meeting supported by the Centre National de la Récherche Scientifique (France) was held to bring together the whole spectrum of researchers working on insect immunity. The meeting addressed diverse aspects...

Islamism and Democratization in Indonesia Post-Reformation Era:

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SYAHRIR KARIM

2014-12-01

Full Text Available In general, this paper will explore features and patterns of Islamism in Indonesia after the downfall of Suharto’s regime in which people called it as reformation era. In Indonesian context, the Islamism at least have four characteristics; (i promoting Islam as a sole basis in transforming society, (ii acknowledging Islam as an ideology, (iii among at the establishment of Islamic state, (iv which is characterised by implementing Shari`ah laws in daily lives. These four attributes may be used in capturing the growth of Muslim’s perception on state and democracy in the era of Islamic revival. The above views spread in the various streams or any schools existed in Indonesia, both Islamic movements and other form that is very influential in the process of democracy in Indonesia.

A simple and effective method for construction of Escherichia coli strains proficient for genome engineering.

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Young Shin Ryu

Full Text Available Multiplex genome engineering is a standalone recombineering tool for large-scale programming and accelerated evolution of cells. However, this advanced genome engineering technique has been limited to use in selected bacterial strains. We developed a simple and effective strain-independent method for effective genome engineering in Escherichia coli. The method involves introducing a suicide plasmid carrying the λ Red recombination system into the mutS gene. The suicide plasmid can be excised from the chromosome via selection in the absence of antibiotics, thus allowing transient inactivation of the mismatch repair system during genome engineering. In addition, we developed another suicide plasmid that enables integration of large DNA fragments into the lacZ genomic locus. These features enable this system to be applied in the exploitation of the benefits of genome engineering in synthetic biology, as well as the metabolic engineering of different strains of E. coli.

A Simple Decision Rule for Recognition of Poly(A) Tail Signal Motifs in Human Genome

KAUST Repository

AbouEisha, Hassan M.

2015-05-12

Background is the numerous attempts were made to predict motifs in genomic sequences that correspond to poly (A) tail signals. Vast portion of this effort has been directed to a plethora of nonlinear classification methods. Even when such approaches yield good discriminant results, identifying dominant features of regulatory mechanisms nevertheless remains a challenge. In this work, we look at decision rules that may help identifying such features. Findings are we present a simple decision rule for classification of candidate poly (A) tail signal motifs in human genomic sequence obtained by evaluating features during the construction of gradient boosted trees. We found that values of a single feature based on the frequency of adenine in the genomic sequence surrounding candidate signal and the number of consecutive adenine molecules in a well-defined region immediately following the motif displays good discriminative potential in classification of poly (A) tail motifs for samples covered by the rule. Conclusions is the resulting simple rule can be used as an efficient filter in construction of more complex poly(A) tail motifs classification algorithms.

Genome-Wide Analysis of Simple Sequence Repeats in Bitter Gourd (Momordica charantia

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Junjie Cui

2017-06-01

Full Text Available Bitter gourd (Momordica charantia is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus, watermelon (Citrullus lanatus, and melon (Cucumis melo genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published. Here, we identified a total of 188,091 and 167,160 SSR motifs in the genomes of the bitter gourd lines ‘Dali-11’ and ‘OHB3-1,’ respectively. Subsequently, the SSR content, motif lengths, and classified motif types were characterized for the bitter gourd genomes and compared among all the cucurbit genomes. Lastly, a large set of 138,727 unique in silico SSR primer pairs were designed for bitter gourd. Among these, 71 primers were selected, all of which successfully amplified SSRs from the two bitter gourd lines ‘Dali-11’ and ‘K44’. To further examine the utilization of unique SSR primers, 21 SSR markers were used to genotype a collection of 211 bitter gourd lines from all over the world. A model-based clustering method and phylogenetic analysis indicated a clear separation among the geographic groups. The genomic SSR markers developed in this study have considerable potential value in advancing bitter gourd research.

Functional genomics approaches in parasitic helminths.

Science.gov (United States)

Hagen, J; Lee, E F; Fairlie, W D; Kalinna, B H

2012-01-01

As research on parasitic helminths is moving into the post-genomic era, an enormous effort is directed towards deciphering gene function and to achieve gene annotation. The sequences that are available in public databases undoubtedly hold information that can be utilized for new interventions and control but the exploitation of these resources has until recently remained difficult. Only now, with the emergence of methods to genetically manipulate and transform parasitic worms will it be possible to gain a comprehensive understanding of the molecular mechanisms involved in nutrition, metabolism, developmental switches/maturation and interaction with the host immune system. This review focuses on functional genomics approaches in parasitic helminths that are currently used, to highlight potential applications of these technologies in the areas of cell biology, systems biology and immunobiology of parasitic helminths. © 2011 Blackwell Publishing Ltd.

Persea americana (avocado): bringing ancient flowers to fruit in the genomics era.

Science.gov (United States)

Chanderbali, André S; Albert, Victor A; Ashworth, Vanessa E T M; Clegg, Michael T; Litz, Richard E; Soltis, Douglas E; Soltis, Pamela S

2008-04-01

The avocado (Persea americana) is a major crop commodity worldwide. Moreover, avocado, a paleopolyploid, is an evolutionary "outpost" among flowering plants, representing a basal lineage (the magnoliid clade) near the origin of the flowering plants themselves. Following centuries of selective breeding, avocado germplasm has been characterized at the level of microsatellite and RFLP markers. Nonetheless, little is known beyond these general diversity estimates, and much work remains to be done to develop avocado as a major subtropical-zone crop. Among the goals of avocado improvement are to develop varieties with fruit that will "store" better on the tree, show uniform ripening and have better post-harvest storage. Avocado transcriptome sequencing, genome mapping and partial genomic sequencing will represent a major step toward the goal of sequencing the entire avocado genome, which is expected to aid in improving avocado varieties and production, as well as understanding the evolution of flowers from non-flowering seed plants (gymnosperms). Additionally, continued evolutionary and other comparative studies of flower and fruit development in different avocado strains can be accomplished at the gene expression level, including in comparison with avocado relatives, and these should provide important insights into the genetic regulation of fruit development in basal angiosperms.

Risk of melanoma in people with HIV/AIDS in the pre- and post-HAART eras: a systematic review and meta-analysis of cohort studies.

Science.gov (United States)

Olsen, Catherine M; Knight, Lani L; Green, Adèle C

2014-01-01

Following the introduction of highly active antiretroviral therapy (HAART) the risk of AIDS-defining cancers decreased but incidence of many non-AIDS-defining cancers has reportedly increased in those with HIV/AIDS. Whether melanoma risk has also changed in HIV/AIDS patients post-HAART is unknown and therefore we evaluated this in comparison with the risk before HAART. Systematic review and meta-analysis. We searched Medline, Embase and ISI science citation index databases to April 2013. All cohort studies of patients diagnosed with HIV/AIDS that permitted quantitative assessment of the association with melanoma were eligible. Detailed quality assessment of eligible studies was conducted, focussing particularly on adjustment for ethnicity, a priori considered essential for an unbiased assessment of melanoma risk. Data were pooled using a random effects model. From 288 articles, we identified 21 that met the inclusion criteria, 13 presenting data for the post-HAART era and 8 for the pre-HAART era. Post-HAART the pooled relative risk (pRR) for the association between HIV/AIDS and melanoma was 1.26 (95% CI, 0.97-1.64) and 1.50 (95% CI 1.12-2.01) among studies that accounted for ethnicity, with evidence of significant heterogeneity (P = 0.004, I2 = 55.5). Pre-HAART pRRs were 1.26 (95% CI 1.11-1.43; P het = 0.82) and 1.28 (95% CI 1.10-1.49) among studies adjusted for ethnicity. People with HIV/AIDS remain at a significantly increased risk of developing melanoma in the post-HAART era. White skinned people with HIV/AIDS should be screened regularly and counselled against excessive sun exposure.

Plant molecular biology and biotechnology research in the post-recombinant DNA era.

Science.gov (United States)

Tyagi, Akhilesh K; Khurana, Jitendra P

2003-01-01

After the beginning of the recombinant DNA era in the mid-1970s, researchers in India started to make use of the new technology to understand the structure of plant genes and regulation of their expression. The outcome started to appear in print in early the 1980s and genes for histones, tubulin, photosynthetic membrane proteins, phototransduction components, organelles and those regulated differentially by developmental and extrinsic signals were sequenced and characterized. Some genes of biotechnological importance like those encoding an interesting seed protein and the enzyme glyoxalase were also isolated. While work on the characterization of genome structure and organization was started quite early, it remained largely focused on the identification of DNA markers and genetic variability. In this context, the work on mustard, rice and wheat is worth mentioning. In the year 2000, India became a member of the international consortium to sequence entire rice genome. Several laboratories have also given attention to regulated expression of plastid and nuclear genes as well as to isolate target-specific promoters or design promoters with improved potential. Simultaneously, transgenic systems for crops like mustard, rice, wheat, cotton, legumes and several vegetables have been established. More recently, genes of agronomic importance like those for insect resistance, abiotic stress tolerance, nutritional improvement and male sterility, isolated in India or abroad, have been utilized for raising transgenics for crop improvement. Some of these transgenics have already shown their potential in containment facility or limited field trials conducted under the stipulated guidelines. Plant molecular biology and biotechnology are thus clearly poised to make an impact on research in basic biology and agriculture in the near future.

[Progress of genome engineering technology via clustered regularly interspaced short palindromic repeats--a review].

Science.gov (United States)

Li, Hao; Qiu, Shaofu; Song, Hongbin

2013-10-04

In survival competition with phage, bacteria and archaea gradually evolved the acquired immune system--Clustered regularly interspaced short palindromic repeats (CRISPR), presenting the trait of transcribing the crRNA and the CRISPR-associated protein (Cas) to silence or cleaving the foreign double-stranded DNA specifically. In recent years, strong interest arises in prokaryotes primitive immune system and many in-depth researches are going on. Recently, researchers successfully repurposed CRISPR as an RNA-guided platform for sequence-specific gene expression, which provides a simple approach for selectively perturbing gene expression on a genome-wide scale. It will undoubtedly bring genome engineering into a more convenient and accurate new era.

‘There and back again’: revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era

Science.gov (United States)

Magiorkinis, Gkikas; Belshaw, Robert; Katzourakis, Aris

2013-01-01

Almost 8% of the human genome comprises endogenous retroviruses (ERVs). While they have been shown to cause specific pathologies in animals, such as cancer, their association with disease in humans remains controversial. The limited evidence is partly due to the physical and bioethical restrictions surrounding the study of transposons in humans, coupled with the major experimental and bioinformatics challenges surrounding the association of ERVs with disease in general. Two biotechnological landmarks of the past decade provide us with unprecedented research artillery: (i) the ultra-fine sequencing of the human genome and (ii) the emergence of high-throughput sequencing technologies. Here, we critically assemble research about potential pathologies of ERVs in humans. We argue that the time is right to revisit the long-standing questions of human ERV pathogenesis within a robust and carefully structured framework that makes full use of genomic sequence data. We also pose two thought-provoking research questions on potential pathophysiological roles of ERVs with respect to immune escape and regulation. PMID:23938753

Sino­Pakistan Relations and the Challenges of Post-­Cold War Era

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Mutahir Ahmed

2015-04-01

Full Text Available China has emerged as the world’s second largest economy, and the largest exporter of goods with 9.6 per cent of the global share. Moreover, the last two decades have seen China emerging as an international and regional power of the 21st century. Thus, in order to continue with the economic benefits, China wants peace and stability as well as to play an active role on international and regional fronts. On the other hand, Pakistan, the world’s sixth most populous country, is a major power of South Asia. While having a developed infrastructure and vibrant political and security institutions, Pakistan is nevertheless currently facing many challenges on the economic front, including political instability and religious extremism. This paper is an attempt to analyze the challenges faced by both China and Pakistan in the post-Cold War era.

Results of ERAS protocol in patients with colorectal cancer

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A. O. Rasulov

2016-01-01

Full Text Available Objective: explore the use of enhanced recovery after surgery (ERAS in the treatment of patients with colorectal cancer, evaluate its efficacy and safety.Materials and methods. Prospective, single-site, randomized study for the implementation of enhanced recovery after surgery in patients with colorectal cancer has been conducted from October 2014 till the present time. All patients after laparoscopic surgeries undergo treatment according to ERAS protocol, patients after open surgeries are randomized (1:1 in groups of the standard treatment or treatment according to ERAS protocol. The study included patients with localized and locally disseminated colorectal cancer aged from 18 to 75 years, ECOG score ≤ 2. The primary evaluated parameters were the following: the number of postoperative complications (according to Clavien– Dindo classification, postoperative hospital days, incidence of complications and mortality in the 30-day period, timing of activation.Results. Up to date, the study includes 105 patients: laparoscopic group – 51 patients, open-surgery group of patients treated by ERAS protocol – 27 patients, open-surgery group of patients with the standard post-op treatment – 26 patients. Complications requiring emergency surgery for anastomotic leak (p = 0.159 developed in 3.7 % of patients with the standard post-op treatment and in 3.9 % of patients after laparoscopic surgery, while 1 patient required repeat hospitalization. The total number of complications was significantly lower in opensurgery group of patients treated by ERAS protocol compared with the standard post-op treatment (p = 0.021. However, there were no differences between laparoscopic and open-surgery group with the standard post-op treatment (p = 0.159. An average hospitalization stay in patients with the standard post-op treatment was equal to 10 days compared to 7 days in patients treated by ERAS protocol (p = 0.067 and 6 days after laparoscopic

Feministische Philosophie in Zeiten des Post-Feminismus Feminist Philosophy in an Era of Post-Feminism

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Sidonia Blättler

2001-11-01

Full Text Available Herta Nagl-Docekal versucht im Durchgang durch verschiedene Teildisziplinen der Philosophie eine Zwischenbilanz: Wie hat feministisch motivierte Forschung das Fach verändert, und welche Fragen stehen heute zur Klärung an? Wie überzeugend ist die weit verbreitete These, wonach wir uns gegenwärtig in einer „postfeministischen“ Ära befinden und feministische Forschung obsolet geworden ist? Die von Herta Nagl-Docekal und Cornelia Klinger zusammengestellte Aufsatzsammlung enthält repräsentative Texte von deutschsprachigen Philosophinnen und soll ein englischsprachiges Publikum über hiesige Theorieentwicklungen innerhalb der feministischen Philosophie informieren.In her discussion of various sub-areas of philosophy Nagl-Docekal attempts a provisional survey of the state of the field: In what ways has feminist-motivated research changed the discipline of philosophy and what issues need to be addressed today? How relevant is the wide-spread idea that we are living in a “post-feminist” era and that feminist research has become obsolete? The other book is a reader, edited by Nagl-Docekal and Klinger, contains a number of representative essays of women philosophers from German-speaking countries. The editors intend to provide an English-speaking community about current developments in feminist theory in German-speaking countries.

Cardiovascular Precision Medicine in the Genomics Era

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Alexandra M. Dainis, BS

2018-04-01

Full Text Available Summary: Precision medicine strives to delineate disease using multiple data sources—from genomics to digital health metrics—in order to be more precise and accurate in our diagnoses, definitions, and treatments of disease subtypes. By defining disease at a deeper level, we can treat patients based on an understanding of the molecular underpinnings of their presentations, rather than grouping patients into broad categories with one-size-fits-all treatments. In this review, the authors examine how precision medicine, specifically that surrounding genetic testing and genetic therapeutics, has begun to make strides in both common and rare cardiovascular diseases in the clinic and the laboratory, and how these advances are beginning to enable us to more effectively define risk, diagnose disease, and deliver therapeutics for each individual patient. Key Words: genome sequencing, genomics, precision medicine, targeted therapeutics

A simple and inexpensive method for genomic restriction mapping analysis

International Nuclear Information System (INIS)

Huang, C.H.; Lam, V.M.S.; Tam, J.W.O.

1988-01-01

The Southern blotting procedure for the transfer of DNA fragments from agarose gels to nitrocellulose membranes has revolutionized nucleic acid detection methods, and it forms the cornerstone of research in molecular biology. Basically, the method involves the denaturation of DNA fragments that have been separated on an agarose gel, the immobilization of the fragments by transfer to a nitrocellulose membrane, and the identification of the fragments of interest through hybridization to /sup 32/P-labeled probes and autoradiography. While the method is sensitive and applicable to both genomic and cloned DNA, it suffers from the disadvantages of being time consuming and expensive, and fragments of greater than 15 kb are difficult to transfer. Moreover, although theoretically the nitrocellulose membrane can be washed and hybridized repeatedly using different probes, in practice, the membrane becomes brittle and difficult to handle after a few cycles. A direct hybridization method for pure DNA clones was developed in 1975 but has not been widely exploited. The authors report here a modification of their procedure as applied to genomic DNA. The method is simple, rapid, and inexpensive, and it does not involve transfer to nitrocellulose membranes

A novel rat genomic simple repeat DNA with RNA-homology shows triplex (H-DNA)-like structure and tissue-specific RNA expression

International Nuclear Information System (INIS)

Dey, Indranil; Rath, Pramod C.

2005-01-01

Mammalian genome contains a wide variety of repetitive DNA sequences of relatively unknown function. We report a novel 227 bp simple repeat DNA (3.3 DNA) with a d {(GA) 7 A (AG) 7 } dinucleotide mirror repeat from the rat (Rattus norvegicus) genome. 3.3 DNA showed 75-85% homology with several eukaryotic mRNAs due to (GA/CU) n dinucleotide repeats by nBlast search and a dispersed distribution in the rat genome by Southern blot hybridization with [ 32 P]3.3 DNA. The d {(GA) 7 A (AG) 7 } mirror repeat formed a triplex (H-DNA)-like structure in vitro. Two large RNAs of 9.1 and 7.5 kb were detected by [ 32 P]3.3 DNA in rat brain by Northern blot hybridization indicating expression of such simple sequence repeats at RNA level in vivo. Further, several cDNAs were isolated from a rat cDNA library by [ 32 P]3.3 DNA probe. Three such cDNAs showed tissue-specific RNA expression in rat. pRT 4.1 cDNA showed strong expression of a 2.39 kb RNA in brain and spleen, pRT 5.5 cDNA showed strong expression of a 2.8 kb RNA in brain and a 3.9 kb RNA in lungs, and pRT 11.4 cDNA showed weak expression of a 2.4 kb RNA in lungs. Thus, genomic simple sequence repeats containing d (GA/CT) n dinucleotides are transcriptionally expressed and regulated in rat tissues. Such d (GA/CT) n dinucleotide repeats may form structural elements (e.g., triplex) which may be sites for functional regulation of genomic coding sequences as well as RNAs. This may be a general function of such transcriptionally active simple sequence repeats widely dispersed in mammalian genome

ASPECTOS BIOÉTICOS DEL CONSEJO GENÉTICO EN LA ERA DEL PROYECTO DEL GENOMA HUMANO ASPECTOS BIOÉTICOS DO CONSELHO GENÉTICO NA ERA DO PROJETO DO GENOMA HUMANO THE GENETIC COUNCIL’S BIOETHIC ASPECTS IN THE HUMAN GENOME PROJECT’S ERA

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Manuel J Santos Alcántara

2004-01-01

Full Text Available El conocimiento obtenido a la fecha acerca del Genoma Humano a través del Proyecto Genoma Humano (PGH, ha impactado profundamente en la medicina. La medicina en la era genómica se va tornando cada vez más preventiva que curativa. El conocimiento obtenido por el PGH ha permitido desarrollar tests de diagnóstico genético que pueden aplicarse a personas ya enfermas o a aquellas que todavía no han desarrollado una particular afección genética (diagnóstico presintomático. También estos tests pueden aplicarse para el diagnóstico antenatal y embrionario preimplantacional de enfermedades genéticas. En la aplicación de estos tests el Consejo Genético, en su calidad de acto médico, tiene un rol esencial. En este artículo se presentará el Proyecto del Genoma Humano, el proceso del Consejo Genético y sus implicancias bioéticas desde una perspectiva principialista y personalistaO conhecimento obtido até hoje acerca do Genoma Humano através do Projeto Genoma Humano (PGH, impactou profundamente na Medicina. A Medicina na era genómica vai se tornando cada vez mais curativa. O conhecimento obtido através do PGH permitiu desenvolver testes de diagnóstico genético, que podem aplicar-se a pessoas já enfermas ou a aquelas que todavia não desenvolveram uma afecção genética particular (diagnóstico pré-sintomático. Estes testes também podem ser aplicados para o diagnóstico pré-natal e embrionário de doenças genéticas. Na aplicação destes testes, o Conselho Genético, na sua qualidade de ato médico, tem um papel essencial. Neste artigo será apresentado o Projeto do Genoma Humano, o Processo do Conselho Genético e suas implicações bioéticas de uma perspectiva principialista e personalistaThe Human Genome Project has had a significant impact in Medicine. Genomic Medicine is becoming more preventive than curative. The knowledge obtained by the Human Genome Project has allowed the development of genetic diagnostic tests for

‘Resource Wars’ in the Post-Cold War Era: The Persian Gulf Oil, US, and the Iraq War

OpenAIRE

S Naji

2012-01-01

This study focuses on the strategic region of the Persian Gulf and its oil resources, the US energy policy, and the Iraq War as a case in point. It refers to the importance of the Persian Gulf oil in the US policies and the US geopolitical practices to launch conflicts and wars in the post-Cold War era that scholars have categorized as “resource wars.” Reviewing relevant studies has revealed that amongst the natural resources oil as the most vital commodity has always played a major role in ...

The spectrum of genomic signatures: from dinucleotides to chaos game representation.

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Wang, Yingwei; Hill, Kathleen; Singh, Shiva; Kari, Lila

2005-02-14

In the post genomic era, access to complete genome sequence data for numerous diverse species has opened multiple avenues for examining and comparing primary DNA sequence organization of entire genomes. Previously, the concept of a genomic signature was introduced with the observation of species-type specific Dinucleotide Relative Abundance Profiles (DRAPs); dinucleotides were identified as the subsequences with the greatest bias in representation in a majority of genomes. Herein, we demonstrate that DRAP is one particular genomic signature contained within a broader spectrum of signatures. Within this spectrum, an alternative genomic signature, Chaos Game Representation (CGR), provides a unique visualization of patterns in sequence organization. A genomic signature is associated with a particular integer order or subsequence length that represents a measure of the resolution or granularity in the analysis of primary DNA sequence organization. We quantitatively explore the organizational information provided by genomic signatures of different orders through different distance measures, including a novel Image Distance. The Image Distance and other existing distance measures are evaluated by comparing the phylogenetic trees they generate for 26 complete mitochondrial genomes from a diversity of species. The phylogenetic tree generated by the Image Distance is compatible with the known relatedness of species. Quantitative evaluation of the spectrum of genomic signatures may be used to ultimately gain insight into the determinants and biological relevance of the genome signatures.

Biomarkers in molecular epidemiology study of oral squamous cell carcinoma in the era of precision medicine

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Qing-Hao Zhu

2017-01-01

Full Text Available Oral cancer, which occurs in the mouth, lips, and tongue, is a multifactorial disease whose etiology involves environment, genetic, and epigenetic factors. Tobacco use and alcohol consumption are regarded as the primary risk factors for oral squamous cell carcinoma (OSCC, and betel use, other chemicals, radiation, environmental, and genetics are reported as relevant risk factors for oral carcinogenesis. The human papillomavirus infection is an independent risk factor. Traditional epidemiology studies have revealed that environmental carcinogens are risk factors for OSCC. Molecular epidemiology studies have revealed that the susceptibility to OSCC is influenced by both environmental and genetic risk factors. However, the details and mechanisms of risk factors involved in OSCC are unclear. Advanced methods and techniques used in human genome studies provide great opportunities for researchers to explore and identify (a the details of such risk factors and (b genetic susceptibility involved in OSCC. Human genome epidemiology is a new branch of epidemiology, which leads the epidemiology study from the molecular epidemiology era into the era of genome-wide association study. In the era of precision medicine, molecular epidemiology studies should focus on biomarkers for cancer genomics and their potential utility in clinical practice. Here, we briefly reviewed several molecular epidemiology studies of OSCC, focusing on biomarkers as valuable utility in risk assessment, clinical screening, diagnosis, and prognosis prediction of OSCC in the era of precision medicine.

Scientific Education in the Post-Corporate University Era

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Bekhor, S. H.

2008-12-01

The emergence of electronic journals, online databases and online educational tools has provided our civilization with a plethora of opportunities to expand the impact of our educational system. Nonetheless, structures that were borne out of the post-World War II era remain firmly entrenched and, though they have undergone some transformation, continue to underperform the potential that is now attainable via a full- fledged incorporation of information technology into pedagogy even in the earliest stages of learning. The induction of talented, self-motivated individuals, irrespective of their financial background, should be at the forefront of any new approach to pedagogy as many of our talented youth with the potential for success have underappreciated capacities for independent learning. A more liberal system, which we call the "Open University," may encourage many such individuals to pursue a scientific career, save them the often prohibitive cost of attending prestigious universities, reduce the costs of operating universities and pave a fast-track to intellectual development for the most talented high-school students. This system may be implemented in tandem without detriment to our current system provided that educators take it upon themselves to reach out and collaborate with high-school teachers, and university bureaucracies begin to allow degree certification on the basis of standardized competency examinations and panel reviews of published work as opposed to the completion of a rigid set of cost-bearing requirements. In addition to the history and concepts outlined above, this work presents a model for a School for Rapid Intellectual Development (SFRID) which may be implemented at a minimal cost in developing countries and, thereby, can maximize the scope and extent of the Open University approach. Hopefully, this model will be tested in practice in the near future and, if successful, can be cloned both overseas and in North America.

Power Laws, Scale-Free Networks and Genome Biology

CERN Document Server

Koonin, Eugene V; Karev, Georgy P

2006-01-01

Power Laws, Scale-free Networks and Genome Biology deals with crucial aspects of the theoretical foundations of systems biology, namely power law distributions and scale-free networks which have emerged as the hallmarks of biological organization in the post-genomic era. The chapters in the book not only describe the interesting mathematical properties of biological networks but moves beyond phenomenology, toward models of evolution capable of explaining the emergence of these features. The collection of chapters, contributed by both physicists and biologists, strives to address the problems in this field in a rigorous but not excessively mathematical manner and to represent different viewpoints, which is crucial in this emerging discipline. Each chapter includes, in addition to technical descriptions of properties of biological networks and evolutionary models, a more general and accessible introduction to the respective problems. Most chapters emphasize the potential of theoretical systems biology for disco...

EchoBASE: an integrated post-genomic database for Escherichia coli.

Science.gov (United States)

Misra, Raju V; Horler, Richard S P; Reindl, Wolfgang; Goryanin, Igor I; Thomas, Gavin H

2005-01-01

EchoBASE (http://www.ecoli-york.org) is a relational database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. Its aim is to collate information from a wide range of sources to provide clues to the functions of the approximately 1500 gene products that have no confirmed cellular function. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. Experiments that can be held within EchoBASE include proteomics studies, microarray data, protein-protein interaction data, structural data and bioinformatics studies. EchoBASE also contains annotated information on 'orphan' enzyme activities from this microbe to aid characterization of the proteins that catalyse these elusive biochemical reactions.

Protein annotation in the era of personal genomics

DEFF Research Database (Denmark)

Holberg Blicher, Thomas; Gupta, Ramneek; Wesolowska, Agata

2010-01-01

the differences between many individuals of the same species-humans in particular-the focus needs be on the functional impact of individual residue variation. To fulfil the promises of personal genomics, we need to start asking not only what is in a genome but also how millions of small differences between......Protein annotation provides a condensed and systematic view on the function of individual proteins. It has traditionally dealt with sorting proteins into functional categories, which for example has proven to be successful for the comparison of different species. However, if we are to understand...... individual genomes affect protein function and in turn human health. Copyright © 2010 Elsevier Ltd. All rights reserved....

Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era

Science.gov (United States)

Tebani, Abdellah; Abily-Donval, Lenaig; Afonso, Carlos; Marret, Stéphane; Bekri, Soumeya

2016-01-01

Inborn errors of metabolism (IEM) represent a group of about 500 rare genetic diseases with an overall estimated incidence of 1/2500. The diversity of metabolic pathways involved explains the difficulties in establishing their diagnosis. However, early diagnosis is usually mandatory for successful treatment. Given the considerable clinical overlap between some inborn errors, biochemical and molecular tests are crucial in making a diagnosis. Conventional biological diagnosis procedures are based on a time-consuming series of sequential and segmented biochemical tests. The rise of “omic” technologies offers holistic views of the basic molecules that build a biological system at different levels. Metabolomics is the most recent “omic” technology based on biochemical characterization of metabolites and their changes related to genetic and environmental factors. This review addresses the principles underlying metabolomics technologies that allow them to comprehensively assess an individual biochemical profile and their reported applications for IEM investigations in the precision medicine era. PMID:27447622

Exploring the post-genomic world: differing explanatory and manipulatory functions of post-genomic sciences.

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Holmes, Christina; Carlson, Siobhan M; McDonald, Fiona; Jones, Mavis; Graham, Janice

2016-01-02

Richard Lewontin proposed that the ability of a scientific field to create a narrative for public understanding garners it social relevance. This article applies Lewontin's conceptual framework of the functions of science (manipulatory and explanatory) to compare and explain the current differences in perceived societal relevance of genetics/genomics and proteomics. We provide three examples to illustrate the social relevance and strong cultural narrative of genetics/genomics for which no counterpart exists for proteomics. We argue that the major difference between genetics/genomics and proteomics is that genomics has a strong explanatory function, due to the strong cultural narrative of heredity. Based on qualitative interviews and observations of proteomics conferences, we suggest that the nature of proteins, lack of public understanding, and theoretical complexity exacerbates this difference for proteomics. Lewontin's framework suggests that social scientists may find that omics sciences affect social relations in different ways than past analyses of genetics.

Harvesting Legume Genomes: Plant Genetic Resources

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Genomics and high through-put phenotyping are ushering in a new era of accessing genetic diversity held in plant genetic resources, the cornerstone of both traditional and genomics-assisted breeding efforts of food legume crops. Acknowledged or not, yield plateaus must be broken given the daunting ...

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop.

Science.gov (United States)

Brister, James Rodney; Bao, Yiming; Kuiken, Carla; Lefkowitz, Elliot J; Le Mercier, Philippe; Leplae, Raphael; Madupu, Ramana; Scheuermann, Richard H; Schobel, Seth; Seto, Donald; Shrivastava, Susmita; Sterk, Peter; Zeng, Qiandong; Klimke, William; Tatusova, Tatiana

2010-10-01

Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world's biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.

Towards Viral Genome Annotation Standards, Report from the 2010 NCBI Annotation Workshop

Directory of Open Access Journals (Sweden)

Qiandong Zeng

2010-10-01

Full Text Available Improvements in DNA sequencing technologies portend a new era in virology and could possibly lead to a giant leap in our understanding of viral evolution and ecology. Yet, as viral genome sequences begin to fill the world’s biological databases, it is critically important to recognize that the scientific promise of this era is dependent on consistent and comprehensive genome annotation. With this in mind, the NCBI Genome Annotation Workshop recently hosted a study group tasked with developing sequence, function, and metadata annotation standards for viral genomes. This report describes the issues involved in viral genome annotation and reviews policy recommendations presented at the NCBI Annotation Workshop.

Endogenous Retroviruses in the Genomics Era.

Science.gov (United States)

Johnson, Welkin E

2015-11-01

Endogenous retroviruses comprise millions of discrete genetic loci distributed within the genomes of extant vertebrates. These sequences, which are clearly related to exogenous retroviruses, represent retroviral infections of the deep past, and their abundance suggests that retroviruses were a near-constant presence throughout the evolutionary history of modern vertebrates. Endogenous retroviruses contribute in myriad ways to the evolution of host genomes, as mutagens and as sources of genetic novelty (both coding and regulatory) to be acted upon by the twin engines of random genetic drift and natural selection. Importantly, the richness and complexity of endogenous retrovirus data can be used to understand how viruses spread and adapt on evolutionary timescales by combining population genetics and evolutionary theory with a detailed understanding of retrovirus biology (gleaned from the study of extant retroviruses). In addition to revealing the impact of viruses on organismal evolution, such studies can help us better understand, by looking back in time, how life-history traits, as well as ecological and geological events, influence the movement of viruses within and between populations.

Inter-simple sequence repeat (ISSR) loci mapping in the genome of perennial ryegrass

DEFF Research Database (Denmark)

Pivorienė, O; Pašakinskienė, I; Brazauskas, G

2008-01-01

The aim of this study was to identify and characterize new ISSR markers and their loci in the genome of perennial ryegrass. A subsample of the VrnA F2 mapping family of perennial ryegrass comprising 92 individuals was used to develop a linkage map including inter-simple sequence repeat markers...... demonstrated a 70% similarity to the Hordeum vulgare germin gene GerA. Inter-SSR mapping will provide useful information for gene targeting, quantitative trait loci mapping and marker-assisted selection in perennial ryegrass....

Challenges to collective action in the post-Snowden era: visions from Latin America

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Paola Ricaurte Quijano

2015-12-01

Full Text Available This article aims to introduce the contributions to the monograph "The challenges of collective action in the post-Snowden era: readings from Latin America" ​​and is intended to promote further discussion in our social and cultural context. Techno-surveillance is located in the center of a regulatory system of relationships, interactions, and behaviours in contemporary societies. We argue that state institutions, Internet Service Providers, industries of personal data and surveillance, and the media are acting as articulated forces. Technological, financial, narrative, and legal devices are created to legitimate surveillance. The implications are reflected in the production of laws, artifacts, events, discourses, imaginaries, cultural practices, bodies and places for surveillance. Surveillance questions our understanding of privacy, freedom of expression, security, social relations, and the exercise of citizenship. Targeted and mass surveillance shape both public and private spheres. This fact demands a reflection on the possibilities of collective action and resistance. Analytical frameworks are needed to identify the mechanisms and implications of the surveillance society.

Post-Slavery? Post-Segregation? Post-Racial? A History of the Impact of Slavery, Segregation, and Racism on the Education of African Americans

Science.gov (United States)

Span, Christopher M.

2015-01-01

This chapter details how slavery, segregation, and racism impacted the educational experiences of African Americans from the colonial era to the present. It argues that America has yet to be a truly post-slavery and post-segregation society, let alone a post-racial society.

La era de la información

OpenAIRE

Florez Calderón, Mauro

2011-01-01

La revolución de la información basada en la información tiene como límite las fronteras del conocimiento. La información a diferencia de un bien material es inalienable, acumulativa y no produce los tipos de deterioro ambiental creados por la industria; por lo anterior, algunos especialistas, a la era de la información la denominan era Post-industrial. Si es necio pretender entender los procesos producidos por la revolución industrial, con una mentalidad pastoril, mucho más necio será tratar...

Genomic growth curves of an outbred pig population

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Fabyano Fonseca e Silva

2013-01-01

Full Text Available In the current post-genomic era, the genetic basis of pig growth can be understood by assessing SNP marker effects and genomic breeding values (GEBV based on estimates of these growth curve parameters as phenotypes. Although various statistical methods, such as random regression (RR-BLUP and Bayesian LASSO (BL, have been applied to genomic selection (GS, none of these has yet been used in a growth curve approach. In this work, we compared the accuracies of RR-BLUP and BL using empirical weight-age data from an outbred F2 (Brazilian Piau X commercial population. The phenotypes were determined by parameter estimates using a nonlinear logistic regression model and the halothane gene was considered as a marker for evaluating the assumptions of the GS methods in relation to the genetic variation explained by each locus. BL yielded more accurate values for all of the phenotypes evaluated and was used to estimate SNP effects and GEBV vectors. The latter allowed the construction of genomic growth curves, which showed substantial genetic discrimination among animals in the final growth phase. The SNP effect estimates allowed identification of the most relevant markers for each phenotype, the positions of which were coincident with reported QTL regions for growth traits.

BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes.

Directory of Open Access Journals (Sweden)

Laura J Marinelli

Full Text Available Advances in DNA sequencing technology have facilitated the determination of hundreds of complete genome sequences both for bacteria and their bacteriophages. Some of these bacteria have well-developed and facile genetic systems for constructing mutants to determine gene function, and recombineering is a particularly effective tool. However, generally applicable methods for constructing defined mutants of bacteriophages are poorly developed, in part because of the inability to use selectable markers such as drug resistance genes during viral lytic growth. Here we describe a method for simple and effective directed mutagenesis of bacteriophage genomes using Bacteriophage Recombineering of Electroporated DNA (BRED, in which a highly efficient recombineering system is utilized directly on electroporated phage DNA; no selection is required and mutants can be readily detected by PCR. We describe the use of BRED to construct unmarked gene deletions, in-frame internal deletions, base substitutions, precise gene replacements, and the addition of gene tags.

Assessing the origin of species in the genomic era

OpenAIRE

Moyle, Leonie C

2005-01-01

Advances in genomics have rapidly accelerated research into the genetics of species differences, reproductive isolating barriers, and hybrid incompatibility. Recent genomic analyses in Drosophila species suggest that modified olfactory cues are involved in discrimination that is reinforced by natural selection.

Integrated, multi-scale, spatial-temporal cell biology--A next step in the post genomic era.

Science.gov (United States)

Horwitz, Rick

2016-03-01

New microscopic approaches, high-throughput imaging, and gene editing promise major new insights into cellular behaviors. When coupled with genomic and other 'omic information and "mined" for correlations and associations, a new breed of powerful and useful cellular models should emerge. These top down, coarse-grained, and statistical models, in turn, can be used to form hypotheses merging with fine-grained, bottom up mechanistic studies and models that are the back bone of cell biology. The goal of the Allen Institute for Cell Science is to develop the top down approach by developing a high throughput microscopy pipeline that is integrated with modeling, using gene edited hiPS cell lines in various physiological and pathological contexts. The output of these experiments and models will be an "animated" cell, capable of integrating and analyzing image data generated from experiments and models. Copyright © 2015 Elsevier Inc. All rights reserved.

Perspectives of Integrative Cancer Genomics in Next Generation Sequencing Era

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So Mee Kwon

2012-06-01

Full Text Available The explosive development of genomics technologies including microarrays and next generation sequencing (NGS has provided comprehensive maps of cancer genomes, including the expression of mRNAs and microRNAs, DNA copy numbers, sequence variations, and epigenetic changes. These genome-wide profiles of the genetic aberrations could reveal the candidates for diagnostic and/or prognostic biomarkers as well as mechanistic insights into tumor development and progression. Recent efforts to establish the huge cancer genome compendium and integrative omics analyses, so-called "integromics", have extended our understanding on the cancer genome, showing its daunting complexity and heterogeneity. However, the challenges of the structured integration, sharing, and interpretation of the big omics data still remain to be resolved. Here, we review several issues raised in cancer omics data analysis, including NGS, focusing particularly on the study design and analysis strategies. This might be helpful to understand the current trends and strategies of the rapidly evolving cancer genomics research.

Simple genomes, complex interactions: Epistasis in RNA virus

Science.gov (United States)

Elena, Santiago F.; Solé, Ricard V.; Sardanyés, Josep

2010-06-01

Owed to their reduced size and low number of proteins encoded, RNA viruses and other subviral pathogens are often considered as being genetically too simple. However, this structural simplicity also creates the necessity for viral RNA sequences to encode for more than one protein and for proteins to carry out multiple functions, all together resulting in complex patterns of genetic interactions. In this work we will first review the experimental studies revealing that the architecture of viral genomes is dominated by antagonistic interactions among loci. Second, we will also review mathematical models and provide a description of computational tools for the study of RNA virus dynamics and evolution. As an application of these tools, we will finish this review article by analyzing a stochastic bit-string model of in silico virus replication. This model analyzes the interplay between epistasis and the mode of replication on determining the population load of deleterious mutations. The model suggests that, for a given mutation rate, the deleterious mutational load is always larger when epistasis is predominantly antagonistic than when synergism is the rule. However, the magnitude of this effect is larger if replication occurs geometrically than if it proceeds linearly.

Proteomic strategy for the identification of critical actors in reorganization of the post-meiotic male genome.

Science.gov (United States)

Govin, Jerome; Gaucher, Jonathan; Ferro, Myriam; Debernardi, Alexandra; Garin, Jerome; Khochbin, Saadi; Rousseaux, Sophie

2012-01-01

After meiosis, during the final stages of spermatogenesis, the haploid male genome undergoes major structural changes, resulting in a shift from a nucleosome-based genome organization to the sperm-specific, highly compacted nucleoprotamine structure. Recent data support the idea that region-specific programming of the haploid male genome is of high importance for the post-fertilization events and for successful embryo development. Although these events constitute a unique and essential step in reproduction, the mechanisms by which they occur have remained completely obscure and the factors involved have mostly remained uncharacterized. Here, we sought a strategy to significantly increase our understanding of proteins controlling the haploid male genome reprogramming, based on the identification of proteins in two specific pools: those with the potential to bind nucleic acids (basic proteins) and proteins capable of binding basic proteins (acidic proteins). For the identification of acidic proteins, we developed an approach involving a transition-protein (TP)-based chromatography, which has the advantage of retaining not only acidic proteins due to the charge interactions, but also potential TP-interacting factors. A second strategy, based on an in-depth bioinformatic analysis of the identified proteins, was then applied to pinpoint within the lists obtained, male germ cells expressed factors relevant to the post-meiotic genome organization. This approach reveals a functional network of DNA-packaging proteins and their putative chaperones and sheds a new light on the way the critical transitions in genome organizations could take place. This work also points to a new area of research in male infertility and sperm quality assessments.

Genome-wide identification and validation of simple sequence repeats (SSRs) from Asparagus officinalis.

Science.gov (United States)

Li, Shufen; Zhang, Guojun; Li, Xu; Wang, Lianjun; Yuan, Jinhong; Deng, Chuanliang; Gao, Wujun

2016-06-01

Garden asparagus (Asparagus officinalis), an important vegetable cultivated worldwide, can also serve as a model dioecious plant species in the study of sex determination and sex chromosome evolution. However, limited DNA marker resources have been developed and used for this species. To expand these resources, we examined the DNA sequences for simple sequence repeats (SSRs) in 163,406 scaffolds representing approximately 400 Mbp of the A. officinalis genome. A total of 87,576 SSRs were identified in 59,565 scaffolds. The most abundant SSR repeats were trinucleotide and tetranucleotide, accounting for 29.2 and 29.1% of the total SSRs, respectively, followed by di-, penta-, hexa-, hepta-, and octanucleotides. The AG motif was most common among dinucleotides and was also the most frequent motif in the entire A. officinalis genome, representing 14.7% of all SSRs. A total of 41,917 SSR primers pairs were designed to amplify SSRs. Twenty-two genomic SSR markers were tested in 39 asparagus accessions belonging to ten cultivars and one accession of Asparagus setaceus for determination of genetic diversity. The intra-species polymorphism information content (PIC) values of the 22 genomic SSR markers were intermediate, with an average of 0.41. The genetic diversity between the ten A. officinalis cultivars was low, and the UPGMA dendrogram was largely unrelated to cultivars. It is here suggested that the sex of individuals is an important factor influencing the clustering results. The information reported here provides new information about the organization of the microsatellites in A. officinalis genome and lays a foundation for further genetic studies and breeding applications of A. officinalis and related species. Copyright © 2016 Elsevier Ltd. All rights reserved.

Tracing Monotreme Venom Evolution in the Genomics Era

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Camilla M. Whittington

2014-04-01

Full Text Available The monotremes (platypuses and echidnas represent one of only four extant venomous mammalian lineages. Until recently, monotreme venom was poorly understood. However, the availability of the platypus genome and increasingly sophisticated genomic tools has allowed us to characterize platypus toxins, and provides a means of reconstructing the evolutionary history of monotreme venom. Here we review the physiology of platypus and echidna crural (venom systems as well as pharmacological and genomic studies of monotreme toxins. Further, we synthesize current ideas about the evolution of the venom system, which in the platypus is likely to have been retained from a venomous ancestor, whilst being lost in the echidnas. We also outline several research directions and outstanding questions that would be productive to address in future research. An improved characterization of mammalian venoms will not only yield new toxins with potential therapeutic uses, but will also aid in our understanding of the way that this unusual trait evolves.

Tracing monotreme venom evolution in the genomics era.

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Whittington, Camilla M; Belov, Katherine

2014-04-02

The monotremes (platypuses and echidnas) represent one of only four extant venomous mammalian lineages. Until recently, monotreme venom was poorly understood. However, the availability of the platypus genome and increasingly sophisticated genomic tools has allowed us to characterize platypus toxins, and provides a means of reconstructing the evolutionary history of monotreme venom. Here we review the physiology of platypus and echidna crural (venom) systems as well as pharmacological and genomic studies of monotreme toxins. Further, we synthesize current ideas about the evolution of the venom system, which in the platypus is likely to have been retained from a venomous ancestor, whilst being lost in the echidnas. We also outline several research directions and outstanding questions that would be productive to address in future research. An improved characterization of mammalian venoms will not only yield new toxins with potential therapeutic uses, but will also aid in our understanding of the way that this unusual trait evolves.

The Functional Genomics Initiative at Oak Ridge National Laboratory

Energy Technology Data Exchange (ETDEWEB)

Johnson, Dabney; Justice, Monica; Beattle, Ken; Buchanan, Michelle; Ramsey, Michael; Ramsey, Rose; Paulus, Michael; Ericson, Nance; Allison, David; Kress, Reid; Mural, Richard; Uberbacher, Ed; Mann, Reinhold

1997-12-31

The Functional Genomics Initiative at the Oak Ridge National Laboratory integrates outstanding capabilities in mouse genetics, bioinformatics, and instrumentation. The 50 year investment by the DOE in mouse genetics/mutagenesis has created a one-of-a-kind resource for generating mutations and understanding their biological consequences. It is generally accepted that, through the mouse as a surrogate for human biology, we will come to understand the function of human genes. In addition to this world class program in mammalian genetics, ORNL has also been a world leader in developing bioinformatics tools for the analysis, management and visualization of genomic data. Combining this expertise with new instrumentation technologies will provide a unique capability to understand the consequences of mutations in the mouse at both the organism and molecular levels. The goal of the Functional Genomics Initiative is to develop the technology and methodology necessary to understand gene function on a genomic scale and apply these technologies to megabase regions of the human genome. The effort is scoped so as to create an effective and powerful resource for functional genomics. ORNL is partnering with the Joint Genome Institute and other large scale sequencing centers to sequence several multimegabase regions of both human and mouse genomic DNA, to identify all the genes in these regions, and to conduct fundamental surveys to examine gene function at the molecular and organism level. The Initiative is designed to be a pilot for larger scale deployment in the post-genome era. Technologies will be applied to the examination of gene expression and regulation, metabolism, gene networks, physiology and development.

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

Science.gov (United States)

Leonard, Guy; Stevens, Jamie R.; Richards, Thomas A.

2009-01-01

The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment file, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree files (with a user-defined combination of species name and/or database accession number). Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file) and generation of species and accession number lists for use in supplementary materials or figure legends. PMID:19812722

EU Law and Mass Internet Metadata Surveillance in the Post-Snowden Era

Directory of Open Access Journals (Sweden)

Nora Ni Loideain

2015-09-01

Full Text Available Legal frameworks exist within democracies to prevent the misuse and abuse of personal data that law enforcement authorities obtain from private communication service providers. The fundamental rights to respect for private life and the protection of personal data underpin this framework within the European Union. Accordingly, the protection of the principles and safeguards required by these rights is key to ensuring that the oversight of State surveillance powers is robust and transparent. Furthermore, without the robust scrutiny of independent judicial review, the principles and safeguards guaranteed by these rights may become more illusory than real. Following the Edward Snowden revelations, major concerns have been raised worldwide regarding the legality, necessity and proportionality standards governing these laws. In 2014, the highest court in the EU struck down the legal framework that imposed a mandatory duty on communication service providers to undertake the mass retention of metadata for secret intelligence and law enforcement authorities across the EU. This article considers the influence of the Snowden revelations on this landmark judgment. Subsequently, the analysis explores the significance of this ruling for the future reform of EU law governing metadata surveillance and its contribution to the worldwide debate on indiscriminate and covert monitoring in the post-Snowden era.

Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers

Energy Technology Data Exchange (ETDEWEB)

Labbe, Jessy L [ORNL; Murat, Claude [INRA, Nancy, France; Morin, Emmanuelle [INRA, Nancy, France; Le Tacon, F [UMR, France; Martin, Francis [INRA, Nancy, France

2011-01-01

It is becoming clear that simple sequence repeats (SSRs) play a significant role in fungal genome organization, and they are a large source of genetic markers for population genetics and meiotic maps. We identified SSRs in the Laccaria bicolor genome by in silico survey and analyzed their distribution in the different genomic regions. We also compared the abundance and distribution of SSRs in L. bicolor with those of the following fungal genomes: Phanerochaete chrysosporium, Coprinopsis cinerea, Ustilago maydis, Cryptococcus neoformans, Aspergillus nidulans, Magnaporthe grisea, Neurospora crassa and Saccharomyces cerevisiae. Using the MISA computer program, we detected 277,062 SSRs in the L. bicolor genome representing 8% of the assembled genomic sequence. Among the analyzed basidiomycetes, L. bicolor exhibited the highest SSR density although no correlation between relative abundance and the genome sizes was observed. In most genomes the short motifs (mono- to trinucleotides) were more abundant than the longer repeated SSRs. Generally, in each organism, the occurrence, relative abundance, and relative density of SSRs decreased as the repeat unit increased. Furthermore, each organism had its own common and longest SSRs. In the L. bicolor genome, most of the SSRs were located in intergenic regions (73.3%) and the highest SSR density was observed in transposable elements (TEs; 6,706 SSRs/Mb). However, 81% of the protein-coding genes contained SSRs in their exons, suggesting that SSR polymorphism may alter gene phenotypes. Within a L. bicolor offspring, sequence polymorphism of 78 SSRs was mainly detected in non-TE intergenic regions. Unlike previously developed microsatellite markers, these new ones are spread throughout the genome; these markers could have immediate applications in population genetics.

La era de la información

Directory of Open Access Journals (Sweden)

Mauro Florez Calderón

1991-01-01

Full Text Available La revolución de la información basada en la información tiene como límite las fronteras del conocimiento. La información a diferencia de un bien material es inalienable, acumulativa y no produce los tipos de deterioro ambiental creados por la industria; por lo anterior, algunos especialistas, a la era de la información la denominan era Post-industrial. Si es necio pretender entender los procesos producidos por la revolución industrial, con una mentalidad pastoril, mucho más necio será tratar de comprender la era informacional con una concepción industrial. La nueva era implica formas y estructuras del pensamiento radicalmente diferentes, pues las profundas transformaciones sociales, técnicas, políticas, económicas que conlleva, no conducirán necesariamente por si mismos a un mayor bienestar para la humanidad. En el presente artículo pretendo dar una visión general sobre este apasionante y delicado tema.

Genome-derived vaccines.

Science.gov (United States)

De Groot, Anne S; Rappuoli, Rino

2004-02-01

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

Whole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.

Science.gov (United States)

Rusconi, Brigida; Sanjar, Fatemeh; Koenig, Sara S K; Mammel, Mark K; Tarr, Phillip I; Eppinger, Mark

2016-01-01

Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and

Simple sequence proteins in prokaryotic proteomes

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Ramachandran Srinivasan

2006-06-01

Full Text Available Abstract Background The structural and functional features associated with Simple Sequence Proteins (SSPs are non-globularity, disease states, signaling and post-translational modification. SSPs are also an important source of genetic and possibly phenotypic variation. Analysis of 249 prokaryotic proteomes offers a new opportunity to examine the genomic properties of SSPs. Results SSPs are a minority but they grow with proteome size. This relationship is exhibited across species varying in genomic GC, mutational bias, life style, and pathogenicity. Their proportion in each proteome is strongly influenced by genomic base compositional bias. In most species simple duplications is favoured, but in a few cases such as Mycobacteria, large families of duplications occur. Amino acid preference in SSPs exhibits a trend towards low cost of biosynthesis. In SSPs and in non-SSPs, Alanine, Glycine, Leucine, and Valine are abundant in species widely varying in genomic GC whereas Isoleucine and Lysine are rich only in organisms with low genomic GC. Arginine is abundant in SSPs of two species and in the non-SSPs of Xanthomonas oryzae. Asparagine is abundant only in SSPs of low GC species. Aspartic acid is abundant only in the non-SSPs of Halobacterium sp NRC1. The abundance of Serine in SSPs of 62 species extends over a broader range compared to that of non-SSPs. Threonine(T is abundant only in SSPs of a couple of species. SSPs exhibit preferential association with Cell surface, Cell membrane and Transport functions and a negative association with Metabolism. Mesophiles and Thermophiles display similar ranges in the content of SSPs. Conclusion Although SSPs are a minority, the genomic forces of base compositional bias and duplications influence their growth and pattern in each species. The preferences and abundance of amino acids are governed by low biosynthetic cost, evolutionary age and base composition of codons. Abundance of charged amino acids Arginine

Leptospira species molecular epidemiology in the genomic era.

Science.gov (United States)

Caimi, K; Repetto, S A; Varni, V; Ruybal, P

2017-10-01

Leptospirosis is a zoonotic disease which global burden is increasing often related to climatic change. Hundreds of whole genome sequences from worldwide isolates of Leptospira spp. are available nowadays, together with online tools that permit to assign MLST sequence types (STs) directly from raw sequence data. In this work we have applied R7L-MLST to near 500 genomes and strains collection globally distributed. All 10 pathogenic species as well as intermediate were typed using this MLST scheme. The correlation observed between STs and serogroups in our previous work, is still satisfied with this higher dataset sustaining the implementation of MLST to assist serological classification as a complementary approach. Bayesian phylogenetic analysis of concatenated sequences from R7-MLST loci allowed us to resolve taxonomic inconsistencies but also showed that events such as recombination, gene conversion or lateral gene transfer played an important role in the evolution of Leptospira genus. Whole genome sequencing allows us to contribute with suitable epidemiologic information useful to apply in the design of control strategies and also in diagnostic methods for this illness. Copyright © 2017 Elsevier B.V. All rights reserved.

Systems Biology Knowledgebase for a New Era in Biology A Genomics:GTL Report from the May 2008 Workshop

Energy Technology Data Exchange (ETDEWEB)

Gregurick, S.; Fredrickson, J. K.; Stevens, R.

2009-03-01

Biology has entered a systems-science era with the goal to establish a predictive understanding of the mechanisms of cellular function and the interactions of biological systems with their environment and with each other. Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies. Effectively exploiting these data requires developing a new generation of capabilities for analyzing and managing the information. By revealing the core principles and processes conserved in collective genomes across all biology and by enabling insights into the interplay between an organism's genotype and its environment, systems biology will allow scientific breakthroughs in our ability to project behaviors of natural systems and to manipulate and engineer managed systems. These breakthroughs will benefit Department of Energy (DOE) missions in energy security, climate protection, and environmental remediation.

REFGEN and TREENAMER: Automated Sequence Data Handling for Phylogenetic Analysis in the Genomic Era

Directory of Open Access Journals (Sweden)

Guy Leonard

2009-01-01

Full Text Available The phylogenetic analysis of nucleotide sequences and increasingly that of amino acid sequences is used to address a number of biological questions. Access to extensive datasets, including numerous genome projects, means that standard phylogenetic analyses can include many hundreds of sequences. Unfortunately, most phylogenetic analysis programs do not tolerate the sequence naming conventions of genome databases. Managing large numbers of sequences and standardizing sequence labels for use in phylogenetic analysis programs can be a time consuming and laborious task. Here we report the availability of an online resource for the management of gene sequences recovered from public access genome databases such as GenBank. These web utilities include the facility for renaming every sequence in a FASTA alignment fi le, with each sequence label derived from a user-defined combination of the species name and/or database accession number. This facility enables the user to keep track of the branching order of the sequences/taxa during multiple tree calculations and re-optimisations. Post phylogenetic analysis, these webpages can then be used to rename every label in the subsequent tree fi les (with a user-defined combination of species name and/or database accession number. Together these programs drastically reduce the time required for managing sequence alignments and labelling phylogenetic figures. Additional features of our platform include the automatic removal of identical accession numbers (recorded in the report file and generation of species and accession number lists for use in supplementary materials or figure legends.

Analysis of the international environment for the national nuclear technology development in the post-coldwar era

International Nuclear Information System (INIS)

Yang, Maeng Ho; Kim, Hwa Sup; Kim, Ji Whan; Lee, Dong Jin; Kim, Jong Sook; Kim, Hyun Joon; Yoon, Young Woo; Ham, Chul Hoon; Cho, Suck Hong

1992-12-01

The main objective of this study is to suggest future policy directions of national nuclear technology development and to define the role of nuclear power in the post-coldwar era. This study first reviews how the collapse of USSR have exerted subsequent effects on the international nuclear industry and analyses the efforts of the multinational nuclear enterprises to obtain technological, competitiveness and to expand the share in the international nuclear market in order to compete the economical and technological superiority. Finally, this study analyses scenarios for the global environmental regulations which may be imposed over internationally in the near future. This study suggests; firstly, increasing investment on science and technology, secondly, diversifying international cooperation, thirdly, rearranging and strengthening a national system for information collecting and analysis, fourthly, making up infrastructure to expand the role of nuclear power, fifthly, expanding the applications of nuclear energy including district heating, etc. (Author)

Kernel-based whole-genome prediction of complex traits: a review.

Science.gov (United States)

Morota, Gota; Gianola, Daniel

2014-01-01

Prediction of genetic values has been a focus of applied quantitative genetics since the beginning of the 20th century, with renewed interest following the advent of the era of whole genome-enabled prediction. Opportunities offered by the emergence of high-dimensional genomic data fueled by post-Sanger sequencing technologies, especially molecular markers, have driven researchers to extend Ronald Fisher and Sewall Wright's models to confront new challenges. In particular, kernel methods are gaining consideration as a regression method of choice for genome-enabled prediction. Complex traits are presumably influenced by many genomic regions working in concert with others (clearly so when considering pathways), thus generating interactions. Motivated by this view, a growing number of statistical approaches based on kernels attempt to capture non-additive effects, either parametrically or non-parametrically. This review centers on whole-genome regression using kernel methods applied to a wide range of quantitative traits of agricultural importance in animals and plants. We discuss various kernel-based approaches tailored to capturing total genetic variation, with the aim of arriving at an enhanced predictive performance in the light of available genome annotation information. Connections between prediction machines born in animal breeding, statistics, and machine learning are revisited, and their empirical prediction performance is discussed. Overall, while some encouraging results have been obtained with non-parametric kernels, recovering non-additive genetic variation in a validation dataset remains a challenge in quantitative genetics.

Kernel-based whole-genome prediction of complex traits: a review

Directory of Open Access Journals (Sweden)

Gota eMorota

2014-10-01

Full Text Available Prediction of genetic values has been a focus of applied quantitative genetics since the beginning of the 20th century, with renewed interest following the advent of the era of whole genome-enabled prediction. Opportunities offered by the emergence of high-dimensional genomic data fueled by post-Sanger sequencing technologies, especially molecular markers, have driven researchers to extend Ronald Fisher and Sewall Wright's models to confront new challenges. In particular, kernel methods are gaining consideration as a regression method of choice for genome-enabled prediction. Complex traits are presumably influenced by many genomic regions working in concert with others (clearly so when considering pathways, thus generating interactions. Motivated by this view, a growing number of statistical approaches based on kernels attempt to capture non-additive effects, either parametrically or non-parametrically. This review centers on whole-genome regression using kernel methods applied to a wide range of quantitative traits of agricultural importance in animals and plants. We discuss various kernel-based approaches tailored to capturing total genetic variation, with the aim of arriving at an enhanced predictive performance in the light of available genome annotation information. Connections between prediction machines born in animal breeding, statistics, and machine learning are revisited, and their empirical prediction performance is discussed. Overall, while some encouraging results have been obtained with non-parametric kernels, recovering non-additive genetic variation in a validation dataset remains a challenge in quantitative genetics.

Future Translational Applications From the Contemporary Genomics Era

Science.gov (United States)

Fox, Caroline S.; Hall, Jennifer L.; Arnett, Donna K.; Ashley, Euan A.; Delles, Christian; Engler, Mary B.; Freeman, Mason W.; Johnson, Julie A.; Lanfear, David E.; Liggett, Stephen B.; Lusis, Aldons J.; Loscalzo, Joseph; MacRae, Calum A.; Musunuru, Kiran; Newby, L. Kristin; O’Donnell, Christopher J.; Rich, Stephen S.; Terzic, Andre

2016-01-01

The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardiovascular clinical care. In brief, this scientific statement assesses the current timeline for effective translation of basic discoveries to clinical advances, highlighting past successes. Current discoveries in the area of genetics and genomics are covered next, followed by future expectations, tools, and competencies for achieving the goal of improving clinical care. PMID:25882488

Genome sequences of Phytophthora enable translational plant disease management and accelerate research

Science.gov (United States)

Niklaus J. Grünwald

2012-01-01

Whole and partial genome sequences are becoming available at an ever-increasing pace. For many plant pathogen systems, we are moving into the era of genome resequencing. The first Phytophthora genomes, P. ramorum and P. sojae, became available in 2004, followed shortly by P. infestans...

Ecology and genomics of Bacillus subtilis.

Science.gov (United States)

Earl, Ashlee M; Losick, Richard; Kolter, Roberto

2008-06-01

Bacillus subtilis is a remarkably diverse bacterial species that is capable of growth within many environments. Recent microarray-based comparative genomic analyses have revealed that members of this species also exhibit considerable genomic diversity. The identification of strain-specific genes might explain how B. subtilis has become so broadly adapted. The goal of identifying ecologically adaptive genes could soon be realized with the imminent release of several new B. subtilis genome sequences. As we embark upon this exciting new era of B. subtilis comparative genomics we review what is currently known about the ecology and evolution of this species.

Lampreys as Diverse Model Organisms in the Genomics Era.

Science.gov (United States)

McCauley, David W; Docker, Margaret F; Whyard, Steve; Li, Weiming

2015-11-01

Lampreys, one of the two surviving groups of ancient vertebrates, have become important models for study in diverse fields of biology. Lampreys (of which there are approximately 40 species) are being studied, for example, (a) to control pest sea lamprey in the North American Great Lakes and to restore declining populations of native species elsewhere; (b) in biomedical research, focusing particularly on the regenerative capability of lampreys; and (c) by developmental biologists studying the evolution of key vertebrate characters. Although a lack of genetic resources has hindered research on the mechanisms regulating many aspects of lamprey life history and development, formerly intractable questions are now amenable to investigation following the recent publication of the sea lamprey genome. Here, we provide an overview of the ways in which genomic tools are currently being deployed to tackle diverse research questions and suggest several areas that may benefit from the availability of the sea lamprey genome.

Risk and Outbreak Communication: Lessons from Taiwan's Experiences in the Post-SARS Era.

Science.gov (United States)

Hsu, Yu-Chen; Chen, Yu-Ling; Wei, Han-Ning; Yang, Yu-Wen; Chen, Ying-Hwei

In addition to the impact of a disease itself, public reaction could be considered another outbreak to be controlled during an epidemic. Taiwan's experience with SARS in 2003 highlighted the critical role played by the media during crisis communication. After the SARS outbreak, Taiwan's Centers for Disease Control (Taiwan CDC) followed the WHO outbreak communication guidelines on trust, early announcements, transparency, informing the public, and planning, in order to reform its risk communication systems. This article describes the risk communication framework in Taiwan, which has been used to respond to the 2009-2016 influenza epidemics, Ebola in West Africa (2014-16), and MERS-CoV in South Korea (2015) during the post-SARS era. Many communication strategies, ranging from traditional media to social and new media, have been implemented to improve transparency in public communication and promote civic engagement. Taiwan CDC will continue to maintain the strengths of its risk communication systems and resolve challenges as they emerge through active evaluation and monitoring of public opinion to advance Taiwan's capacity in outbreak communication and control. Moreover, Taiwan CDC will continue to implement the IHR (2005) and to promote a global community working together to fight shared risks and to reach the goal of "One World, One Health."

Rework of the ERA software system: ERA-8

Science.gov (United States)

Pavlov, D.; Skripnichenko, V.

2015-08-01

The software system that has been powering many products of the IAA during decades has undergone a major rework. ERA has capabilities for: processing tables of observations of different kinds, fitting parameters to observations, integrating equations of motion of the Solar system bodies. ERA comprises a domain-specific language called SLON, tailored for astronomical tasks. SLON provides a convenient syntax for reductions of observations, choosing of IAU standards to use, applying rules for filtering observations or selecting parameters for fitting. Also, ERA includes a table editor and a graph plotter. ERA-8 has a number of improvements over previous versions such as: integration of the Solar system and TT xA1 TDB with arbitrary number of asteroids; option to use different ephemeris (including DE and INPOP); integrator with 80-bit floating point. The code of ERA-8 has been completely rewritten from Pascal to C (for numerical computations) and Racket (for running SLON programs and managing data). ERA-8 is portable across major operating systems. The format of tables in ERA-8 is based on SQLite. The SPICE format has been chosen as the main format for ephemeris in ERA-8.

A simple method of genomic DNA extraction suitable for analysis of bulk fungal strains.

Science.gov (United States)

Zhang, Y J; Zhang, S; Liu, X Z; Wen, H A; Wang, M

2010-07-01

A simple and rapid method (designated thermolysis) for extracting genomic DNA from bulk fungal strains was described. In the thermolysis method, a few mycelia or yeast cells were first rinsed with pure water to remove potential PCR inhibitors and then incubated in a lysis buffer at 85 degrees C to break down cell walls and membranes. This method was used to extract genomic DNA from large numbers of fungal strains (more than 92 species, 35 genera of three phyla) isolated from different sections of natural Ophiocordyceps sinensis specimens. Regions of interest from high as well as single-copy number genes were successfully amplified from the extracted DNA samples. The DNA samples obtained by this method can be stored at -20 degrees C for over 1 year. The method was effective, easy and fast and allowed batch DNA extraction from multiple fungal isolates. Use of the thermolysis method will allow researchers to obtain DNA from fungi quickly for use in molecular assays. This method requires only minute quantities of starting material and is suitable for diverse fungal species.

A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.

Science.gov (United States)

Cheng, Jiaowen; Zhao, Zicheng; Li, Bo; Qin, Cheng; Wu, Zhiming; Trejo-Saavedra, Diana L; Luo, Xirong; Cui, Junjie; Rivera-Bustamante, Rafael F; Li, Shuaicheng; Hu, Kailin

2016-01-07

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum.

THE UNECIC: INTERNATIONAL TRADE IN THE DIGITAL ERA

African Journals Online (AJOL)

Dr Tanya du Plessis

THE UNECIC: INTERNATIONAL TRADE IN THE DIGITAL ERA. S Eiselen. *. 1. Introduction. The use of electronic means of communication such as e-mail, SMS and the internet in the last decade has outstripped and replaced other more traditional forms of communications such as post, telex and telegram. The only other ...

Advancing Crop Transformation in the Era of Genome Editing[OPEN

Science.gov (United States)

Blechl, Ann E.; Brutnell, Thomas P.; Conrad, Liza J.; Gelvin, Stanton B.; Jackson, David P.; Kausch, Albert P.; Lemaux, Peggy G.; Medford, June I.; Orozco-Cárdenas, Martha L.; Tricoli, David M.; Van Eck, Joyce; Voytas, Daniel F.

2016-01-01

Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized. PMID:27335450

An investigation into the nutritional status of patients receiving an Enhanced Recovery After Surgery (ERAS) protocol versus standard care following Oesophagectomy.

Science.gov (United States)

Benton, Katie; Thomson, Iain; Isenring, Elisabeth; Mark Smithers, B; Agarwal, Ekta

2018-06-01

Enhanced Recovery After Surgery (ERAS) protocols have been effectively expanded to various surgical specialities including oesophagectomy. Despite nutrition being a key component, actual nutrition outcomes and specific guidelines are lacking. This cohort comparison study aims to compare nutritional status and adherence during implementation of a standardised post-operative nutritional support protocol, as part of ERAS, compared to those who received usual care. Two groups of patients undergoing resection of oesophageal cancer were studied. Group 1 (n = 17) underwent oesophagectomy between Oct 2014 and Nov 2016 during implementation of an ERAS protocol. Patients in group 2 (n = 16) underwent oesophagectomy between Jan 2011 and Dec 2012 prior to the implementation of ERAS. Demographic, nutritional status, dietary intake and adherence data were collected. Ordinal data was analysed using independent t tests, and categorical data using chi-square tests. There was no significant difference in nutrition status, dietary intake or length of stay following implementation of an ERAS protocol. Malnutrition remained prevalent in both groups at day 42 post surgery (n = 10, 83% usual care; and n = 9, 60% ERAS). A significant difference was demonstrated in adherence with earlier initiation of oral free fluids (p nutrition protocol, within an ERAS framework, results in earlier transition to oral intake; however, malnutrition remains prevalent post surgery. Further large-scale studies are warranted to examine individualised decision-making regarding nutrition support within an ERAS protocol.

New Software for the Fast Estimation of Population Recombination Rates (FastEPRR in the Genomic Era

Directory of Open Access Journals (Sweden)

Feng Gao

2016-06-01

Full Text Available Genetic recombination is a very important evolutionary mechanism that mixes parental haplotypes and produces new raw material for organismal evolution. As a result, information on recombination rates is critical for biological research. In this paper, we introduce a new extremely fast open-source software package (FastEPRR that uses machine learning to estimate recombination rate ρ (=4Ner from intraspecific DNA polymorphism data. When ρ>10 and the number of sampled diploid individuals is large enough (≥50, the variance of ρFastEPRR remains slightly smaller than that of ρLDhat. The new estimate ρcomb (calculated by averaging ρFastEPRR and ρLDhat has the smallest variance of all cases. When estimating ρFastEPRR, the finite-site model was employed to analyze cases with a high rate of recurrent mutations, and an additional method is proposed to consider the effect of variable recombination rates within windows. Simulations encompassing a wide range of parameters demonstrate that different evolutionary factors, such as demography and selection, may not increase the false positive rate of recombination hotspots. Overall, accuracy of FastEPRR is similar to the well-known method, LDhat, but requires far less computation time. Genetic maps for each human population (YRI, CEU, and CHB extracted from the 1000 Genomes OMNI data set were obtained in less than 3 d using just a single CPU core. The Pearson Pairwise correlation coefficient between the ρFastEPRR and ρLDhat maps is very high, ranging between 0.929 and 0.987 at a 5-Mb scale. Considering that sample sizes for these kinds of data are increasing dramatically with advances in next-generation sequencing technologies, FastEPRR (freely available at http://www.picb.ac.cn/evolgen/ is expected to become a widely used tool for establishing genetic maps and studying recombination hotspots in the population genomic era.

The effect of FDI and foreign trade on wages in the Central and Eastern European Countries in the post-transition era: A sectoral analysis

OpenAIRE

Onaran, Özlem; Stockhammer, Engelbert

2006-01-01

The aim of this paper is to estimate the effect of FDI and trade openness on wages in the CEECs in the post-transition era. We utilize a cross-country sector-specific eceonometric analysis based on one-digit level panel data for manufacturing industry in the Czech Republic, Hungary, Poland, Slovakia, Slovenia, for the period of 2000-2004. The results suggest that the increases in productivity are reflected in wages only to a modest extent, even in the long-term, leading to a steady decline in...

The post-Human Genome Project mindset: race, reliability, and health care.

Science.gov (United States)

Kimmelman, J

2006-11-01

The following essay reports on the first session of a 2-day workshop on genetic diversity and science communication, organized by the Institute of Genetics. I argue that the four talks in this session reflected two different facets of a 'post-Human Genome Project (HGP)' view of human genetics. The first is characterized by an increasing interest in genetic differences. Two speakers - Troy Duster and Jasber Singh - expressed skepticism about one aspect of this trend: an emphasis on race in medicine and genetics. The other two speakers - Kenneth Weiss and Gustavo Turecki - spoke to a second facet of the post-HGP view: a recognition of the difficulty in translating genetic discovery into medical or public health applications. Though both sets of talks were highly critical of current trends in genetic research, they pulled in opposite directions: one warned about the role of genetics in stabilizing racial categories, while the other lamented the failure of any genetic claims or categories to stabilize at all. I argue that the use of racial categories in medicine seems likely to encounter scientific, medical, and social challenges.

Simple sequence repeats and compositional bias in the bipartite Ralstonia solanacearum GMI1000 genome

Directory of Open Access Journals (Sweden)

Vandamme Peter

2003-03-01

Full Text Available Abstract Background Ralstonia solanacearum is an important plant pathogen. The genome of R. solananearum GMI1000 is organised into two replicons (a 3.7-Mb chromosome and a 2.1-Mb megaplasmid and this bipartite genome structure is characteristic for most R. solanacearum strains. To determine whether the megaplasmid was acquired via recent horizontal gene transfer or is part of an ancestral single chromosome, we compared the abundance, distribution and compositon of simple sequence repeats (SSRs between both replicons and also compared the respective compositional biases. Results Our data show that both replicons are very similar in respect to distribution and composition of SSRs and presence of compositional biases. Minor variations in SSR and compositional biases observed may be attributable to minor differences in gene expression and regulation of gene expression or can be attributed to the small sample numbers observed. Conclusions The observed similarities indicate that both replicons have shared a similar evolutionary history and thus suggest that the megaplasmid was not recently acquired from other organisms by lateral gene transfer but is a part of an ancestral R. solanacearum chromosome.

A Multi-Faceted View of GPM GV in the Post-Launch Era

Science.gov (United States)

Petersen, W. A.

2015-12-01

NASA GPM Ground Validation (GV) activities in the early post-launch era have focused on: a) intercomparison of early version satellite products to GV data originating from NOAA Q3, WSR-88D, and Tier-1 research ground radar (GR) and instrument networks; b) continued physical validation of GPM algorithms using recent field campaign and site-specific datasets (warm and cold season); and c) development and use of rainfall products for hydrologic validation and bridging-validation of Level II and Level III satellite products (IMERG). Intercomparisons of GPM products with Q3 rainfall and WSR-88D ground-radar (GR) data over CONUS exhibit reasonable agreement. For example, DPR radar reflectivities geo-matched to reflectivity profiles from ~60 GRs generally differ by 2 dB or less. Occasional low-biases do appear in the rainwater portion of DPR Ku-Band convective reflectivity profiles. In stratiform precipitation, DPR-diagnosed reflectivity and rain drop size distributions are frequently very similar to those retrieved from GR products. DPR and Combined algorithm rainrate products compare reasonably well to each other and to Q3 at CONUS scales. GPROF2014 radiometer-based rain rates compare well to Q3 in a spatial sense (correlations of ~0.6); but, GMI estimates appear to be slightly low-biased relative to Q3 and to DPR and Combined algorithm products. The last NASA GPM GV-led field effort, OLYMPEX, will occur in Nov 2015 to Jan 2016. OLYMPEX is designed to study cold-season precipitation processes and hydrology in the orographic and oceanic domains of western Washington State. In addition to occasional field campaigns like OLYMPEX, continuous field measurements using multi-parameter radar and instrument networks targeted to direct validation and specific problems in physical validation (e.g., path-integrated attenuation and the impacts of drop size distribution, non-uniform beam filling and multiple scattering) are also being collected under coincident GPM core overpasses at

The Persistence of Informality: Small-Scale Water Providers in Manila’s Post-Privatisation Era

Directory of Open Access Journals (Sweden)

Deborah Cheng

2014-02-01

Full Text Available This article troubles the notion of a formal-informal dichotomy in urban water provision. Whereas expansion of a water utility typically involves the replacement of informal providers, the experience in Manila demonstrates that the rapid connection of low-income areas actually hinges, in part, on the selective inclusion and exclusion of these smaller actors. In this sense, privatisation has not eliminated small-scale water provision, but has led to the reconfiguration of its usage, blurring the boundaries between formal and informal. By examining the spatial and temporal evolution of small-scale water provision in Manila’s post-privatisation era, I show how certain spaces are seen as less serviceable than others. Critically, small providers working in partnership with the utilities are sanctioned because they supplement the utilities’ operations. The areas in which they work are considered served, factoring into aggregate coverage statistics, even though their terms of service are often less desirable than those of households directly connected to the utilities. In contrast, small providers that operate outside of the utilities’ zones of coverage are considered inferior, to be replaced. The result is a differentiation in informality – one in which the private utilities largely determine modes of access and thus the spatialisation of informal water provision.

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

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

Science.gov (United States)

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

2012-06-07

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

ERA`s Ranger uranium mine

Energy Technology Data Exchange (ETDEWEB)

Davies, W. [Energy Resources of Australia Ltd., Sydney, NSW (Australia)

1997-12-31

Energy Resource of Australia (ERA) is a public company with 68% of its shares owned by the Australian company North Limited. It is currently operating one major production centre - Ranger Mine which is 260 kilometres east of Darwin, extracting and selling uranium from the Ranger Mine in the Northern Territory to nuclear electricity utilities in Japan, South Korea, Europe and North America. The first drum of uranium oxide from Ranger was drummed in August 1981 and operations have continued since that time. ERA is also in the process of working towards obtaining approvals for the development of a second mine - Jabiluka which is located 20 kilometres north of Ranger. The leases of Ranger and Jabiluka adjoin. The Minister for the Environment has advised the Minister for Resources and Energy that there does not appear to be any environmental issue which would prevent the preferred Jabiluka proposal from proceeding. Consent for the development of ERA`s preferred option for the development of Jabiluka is being sought from the Aboriginal Traditional Owners. Ranger is currently the third largest producing uranium mine in the world producing 4,237 tonnes of U{sub 3}O{sub 8} in the year to June 1997.

Annotation-Based Whole Genomic Prediction and Selection

DEFF Research Database (Denmark)

Kadarmideen, Haja; Do, Duy Ngoc; Janss, Luc

Genomic selection is widely used in both animal and plant species, however, it is performed with no input from known genomic or biological role of genetic variants and therefore is a black box approach in a genomic era. This study investigated the role of different genomic regions and detected QTLs...... in their contribution to estimated genomic variances and in prediction of genomic breeding values by applying SNP annotation approaches to feed efficiency. Ensembl Variant Predictor (EVP) and Pig QTL database were used as the source of genomic annotation for 60K chip. Genomic prediction was performed using the Bayes...... classes. Predictive accuracy was 0.531, 0.532, 0.302, and 0.344 for DFI, RFI, ADG and BF, respectively. The contribution per SNP to total genomic variance was similar among annotated classes across different traits. Predictive performance of SNP classes did not significantly differ from randomized SNP...

Designing a post-genomics knowledge ecosystem to translate pharmacogenomics into public health action.

Science.gov (United States)

Dove, Edward S; Faraj, Samer A; Kolker, Eugene; Ozdemir, Vural

2012-01-01

Translation of pharmacogenomics to public health action is at the epicenter of the life sciences agenda. Post-genomics knowledge is simultaneously co-produced at multiple scales and locales by scientists, crowd-sourcing and biological citizens. The latter are entrepreneurial citizens who are autonomous, self-governing and increasingly conceptualizing themselves in biological terms, ostensibly taking responsibility for their own health, and engaging in patient advocacy and health activism. By studying these heterogeneous 'scientific cultures', we can locate innovative parameters of collective action to move pharmacogenomics to practice (personalized therapeutics). To this end, we reconceptualize knowledge-based innovation as a complex ecosystem comprising 'actors' and 'narrators'. For robust knowledge translation, we require a nested post-genomics technology governance system composed of first-order narrators (for example, social scientists, philosophers, bioethicists) situated at arm's length from innovation actors (for example, pharmacogenomics scientists). Yet, second-order narrators (for example, an independent and possibly crowd-funded think-tank of citizen scholars, marginalized groups and knowledge end-users) are crucial to prevent first-order narrators from gaining excessive power that can be misused in the course of steering innovations. To operate such 'self-calibrating' and nested innovation ecosystems, we introduce the concept of 'wiki-governance' to enable mutual and iterative learning among innovation actors and first- and second-order narrators. '[A] scientific expert is someone who knows more and more about less and less, until finally knowing (almost) everything about (almost) nothing.' [1] 'Ubuntu: I am because you are.' [2].

Dissecting DNA repair in adult high grade gliomas for patient stratification in the post-genomic era

Science.gov (United States)

Perry, Christina; Agarwal, Devika; Abdel-Fatah, Tarek M.A.; Lourdusamy, Anbarasu; Grundy, Richard; Auer, Dorothee T.; Walker, David; Lakhani, Ravi; Scott, Ian S.; Chan, Stephen; Ball, Graham; Madhusudan, Srinivasan

2014-01-01

Deregulation of multiple DNA repair pathways may contribute to aggressive biology and therapy resistance in gliomas. We evaluated transcript levels of 157 genes involved in DNA repair in an adult glioblastoma Test set (n=191) and validated in ‘The Cancer Genome Atlas’ (TCGA) cohort (n=508). A DNA repair prognostic index model was generated. Artificial neural network analysis (ANN) was conducted to investigate global gene interactions. Protein expression by immunohistochemistry was conducted in 61 tumours. A fourteen DNA repair gene expression panel was associated with poor survival in Test and TCGA cohorts. A Cox multivariate model revealed APE1, NBN, PMS2, MGMT and PTEN as independently associated with poor prognosis. A DNA repair prognostic index incorporating APE1, NBN, PMS2, MGMT and PTEN stratified patients in to three prognostic sub-groups with worsening survival. APE1, NBN, PMS2, MGMT and PTEN also have predictive significance in patients who received chemotherapy and/or radiotherapy. ANN analysis of APE1, NBN, PMS2, MGMT and PTEN revealed interactions with genes involved in transcription, hypoxia and metabolic regulation. At the protein level, low APE1 and low PTEN remain associated with poor prognosis. In conclusion, multiple DNA repair pathways operate to influence biology and clinical outcomes in adult high grade gliomas. PMID:25026297

Biobanks in Oral Health: Promises and Implications of Post-Neoliberal Science and Innovation

Science.gov (United States)

Dove, Edward S.; Chiappetta, Margaret; Gürsoy, Ulvi K.

2016-01-01

Abstract While biobanks are established explicitly as scientific infrastructures, they are de facto political-economic ones too. Many biobanks, particularly population-based biobanks, are framed under the rubric of the bio-economy as national political-economic assets that benefit domestic business, while national populations are framed as a natural resource whose genomics, proteomics, and related biological material and national health data can be exploited. We outline how many biobanks epitomize this ‘neoliberal’ form of science and innovation in which research is driven by market priorities (e.g., profit, shareholder value) underpinned by state or government policies. As both scientific and political-economic infrastructures, biobanks end up entangled in an array of problems associated with market-driven science and innovation. These include: profit trumping other considerations; rentiership trumping entrepreneurship; and applied research trumping basic research. As a result, there has been a push behind new forms of ‘post-neoliberal’ science and innovation strategies based on principles of openness and collaboration, especially in relation to biobanks. The proliferation of biobanks and the putative transition in both scientific practice and political economy from neoliberalism to post-neoliberalism demands fresh social scientific analyses, particularly as biobanks become further established in fields such as oral health and personalized dentistry. To the best of our knowledge, this is the first analysis of biobanks with a view to what we can anticipate from biobanks and distributed post-genomics global science in the current era of oral health biomarkers. PMID:26584410

Biobanks in Oral Health: Promises and Implications of Post-Neoliberal Science and Innovation.

Science.gov (United States)

Birch, Kean; Dove, Edward S; Chiappetta, Margaret; Gürsoy, Ulvi K

2016-01-01

While biobanks are established explicitly as scientific infrastructures, they are de facto political-economic ones too. Many biobanks, particularly population-based biobanks, are framed under the rubric of the bio-economy as national political-economic assets that benefit domestic business, while national populations are framed as a natural resource whose genomics, proteomics, and related biological material and national health data can be exploited. We outline how many biobanks epitomize this 'neoliberal' form of science and innovation in which research is driven by market priorities (e.g., profit, shareholder value) underpinned by state or government policies. As both scientific and political-economic infrastructures, biobanks end up entangled in an array of problems associated with market-driven science and innovation. These include: profit trumping other considerations; rentiership trumping entrepreneurship; and applied research trumping basic research. As a result, there has been a push behind new forms of 'post-neoliberal' science and innovation strategies based on principles of openness and collaboration, especially in relation to biobanks. The proliferation of biobanks and the putative transition in both scientific practice and political economy from neoliberalism to post-neoliberalism demands fresh social scientific analyses, particularly as biobanks become further established in fields such as oral health and personalized dentistry. To the best of our knowledge, this is the first analysis of biobanks with a view to what we can anticipate from biobanks and distributed post-genomics global science in the current era of oral health biomarkers.

Black out - The post-petroleum era has started

International Nuclear Information System (INIS)

Enderlin, S.

2009-01-01

The predictable shortage of petroleum resources raises up some worrying questions: how can we get rid of petroleum? What will be our life without petroleum? Will we have enough energy tomorrow to keep the same way of life as today? With what new energy sources tomorrow's world will turn? The author has travelled the world from the Americas to Asia and from Europe to the Persian Gulf to find the leads of the after-petroleum era. From the Chinese coal to the US ethanol, from the nuclear comeback to the Scandinavian innovations, this inquiry makes the world tour of projects, ideas and solutions. First world energy consumer and squanderer, the US hold a prominent place in the energy revolution that Barack Obama election will speed up. In Europe, Germany, Spain and Denmark have taken a serious lead in the green energies race, while China has become recently the first world power of greenhouse gas emissions. (J.S.)

Introduction to the Post-Human Genome Project era, a target for interactions between polygenic and/or multiphenotypical components in cancer control in South America Introducción a la post era del Proyeto Genoma Humano: la interrelación entre componentes multi-genéticos y multi-fenotípicos en el control del cáncer en América Latina como una meta

Directory of Open Access Journals (Sweden)

José Iscovich

1998-01-01

Full Text Available Epidemiological studies have suggested that the propensity to develop malignancy involves a complex mix of genetic and environmental determinants, however both older and innovative techniques display unresolved questions regarding etiology. Current barriers to achieving the potential benefit from this understanding are: 1 incomplete background on the various environmental and genetic factors involved in the carcinogenesis mechanism; 2 difficulties in accurately differentiating specific molecular subtypes and measuring the effective cellular exposure dose; and 3 difficulties in determining the multifactorial interaction between genetic and environmental factors. To extrapolate Human Genome Project research findings to the Post-Human Genome Project era, South America provides a large population and large-pedigree families, thus including genetically heterogeneous and less heterogeneous groups. An initial strategy might be to trace high risk populations and the respective exposures to which they are susceptible, such as: 1 migration, identifying rural migrant populations; 2 inherent susceptibility, studying "long term homogeneous populations" or large families living in similar rural environments; and 3 dissection of gene-environmental interaction.Estudios epidemiológicos han demonstrado que la susceptibilidad de la población a las enfermedades malignas está basada en interrelaciones genéticas hereditarias y no hereditarias. Las técnicas epidemiológicas tradicionales no han resuelto los problemas básicos de los mecanismos etiológicos. Las barreras existentes son: 1 el conocimiento incompleto de las etapas del mecanismo de la carcinogénesis accionada por factores genéticos y ambientales; 2 la dificultad en delimitar subtipos específicos de neoplasmas basados en mecanismos moleculares definidos, y las dosis efectivas de exposición celular; y 3 la capacidad en determinar la interrelación en el mecanismo genético-ambiental. Anticipandose

Challenges to the Japan-U.S. Security Alliance in the Post-Post Cold War Era

National Research Council Canada - National Science Library

Nodomi, Mistsuru

2005-01-01

The Japan-U.S. security alliance experienced the Cold War and post Cold War during the twentieth century, and is now facing a post-post Cold War environment triggered by the September 11 terrorist attacks...

Understanding patient and provider perceptions and expectations of genomic medicine.

Science.gov (United States)

Hall, Michael J; Forman, Andrea D; Montgomery, Susan V; Rainey, Kim L; Daly, Mary B

2015-01-01

Advances in genome sequencing technology have fostered a new era of clinical genomic medicine. Genetic counselors, who have begun to support patients undergoing multi-gene panel testing for hereditary cancer risk, will review brief clinical vignettes, and discuss early experiences with clinical genomic testing. Their experiences will frame a discussion about how current testing may challenge patient understanding and expectations toward the evaluation of cancer risk and downstream preventive behaviors. © 2014 Wiley Periodicals, Inc.

Morphology modification of perovskite film by a simple post-treatment process in perovskite solar cell

Energy Technology Data Exchange (ETDEWEB)

Song, J.; Yang, Y.; Zhao, Y.L., E-mail: sdyulong@cumt.edu.cn; Che, M.; Zhu, L.; Gu, X.Q.; Qiang, Y.H., E-mail: yhqiang@cumt.edu.cn

2017-03-15

Highlights: • Perovskite films were post-treated by DMF/CBZ, DMSO/CBZ, or GBL/CBZ blend solvents. • This process could repair pinholes and enhance coverage in perovskite film. • This technique could modify charge transfer process at TiO{sub 2}/perovskite interface. - Abstract: A homogenous perovskite thin film with high coverage is a determining factor for high performance perovskite solar cells. Unlike previous pre-treatments aiming at perovskite precursor, we proposed a simple method to modify the morphology of perovskite films by post-treatment process using mixed solvents of N,N-dimethylformamide (DMF), dimethyl sulfoxide (DMSO), or 1,4-butyrolactone (GBL) with chlorobenzene (CBZ) in this paper. As good solvent of perovskite, DMF, DMSO, and GBL could dissolve the formed perovskite film. Meanwhile, CBZ, anti-solvent of perovskite film, could decrease the dissolving capacity of these good solvents. Therefore, the perovskite film coverage might be improved by the partial dissolution and recrystallization after solvent post-treatment process. Electrochemical impedance spectrometry (EIS) and time-resolved photoluminescence (TRPL) indicated that this post-treatment process could enhance charge transfer at TiO{sub 2}/perovskite interface. Finally, the conversion efficiency increased from 10.10% to 11.82%, 11.68%, and 10.66% using perovskite films post-treated by DMF/CBZ, DMSO/CBZ, and GBL/CBZ blend solvents, respectively.

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

Science.gov (United States)

Chen, Wei-Hua; van Noort, Vera; Lluch-Senar, Maria; Hennrich, Marco L.; H. Wodke, Judith A.; Yus, Eva; Alibés, Andreu; Roma, Guglielmo; Mende, Daniel R.; Pesavento, Christina; Typas, Athanasios; Gavin, Anne-Claude; Serrano, Luis; Bork, Peer

2016-01-01

We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated ‘-omics’ data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size. Thus, the evolutionary forces constraining genome size and GC-content modify the relative contributions of the different regulatory layers to proteome homeostasis, and impact more genomic and genetic features than previously appreciated. Indeed, these scaling principles will enable us to develop more informed approaches when engineering minimal synthetic genomes. PMID:26773059

[Two simple questions to diagnose post-stroke depression].

Science.gov (United States)

Nolte, C H; Müller-Nordhorn, J; Jungehülsing, G J; Rossnagel, K; Reich, A; Roll, S; Laumeier, I; Beerfelde, D; Willich, S N; Villringer, A

2006-05-01

Many patients develop a depression after having suffered a stroke. Such a Post-Stroke Depression (PSD) impairs rehabilitation and quality of life. PSD is underdiagnosed in spite of available treatment. Several questionnaires have been created to diagnose a PSD. But questionnaires have been considered cumbersome and time-consuming. The aim of this study was to find out whether two simple, standardised questions will identify those stroke patients, who have developed a PSD. The two case-finding questions and the Beck Depression Inventory (BDI) were sent to patients of the Berlin Acute Stroke Study (BASS) four years after their stroke. Incomplete questionnaires were complemented via mail or telephone. Severity of depression was assessed by means of BDI. Out of 211 patients, 199 responded to the questionnaire (94 %). 193 questionnaires were complete (97 %). Forty-two patients affirmed both case-finding questions (22 %). Compared to patients, who did not affirm both questions, these patients had a higher BDI score (19 +/- 8 vs. 7 +/- 5; p two questions were 89 % and 90 %, respectively. The positive and negative predictive value were 60 % and 98 % respectively. The number of confirmed questions (0, 1, 2) correlated well with the BDI score (r (2) = 0.67, p Two standardized questions can identify patients with PSD for further diagnostic evaluation and therapy. Diagnosis of PSD might be facilitated by using them as screening instrument.

The first genetic map of a synthesized allohexaploid Brassica with A, B and C genomes based on simple sequence repeat markers.

Science.gov (United States)

Yang, S; Chen, S; Geng, X X; Yan, G; Li, Z Y; Meng, J L; Cowling, W A; Zhou, W J

2016-04-01

We present the first genetic map of an allohexaploid Brassica species, based on segregating microsatellite markers in a doubled haploid mapping population generated from a hybrid between two hexaploid parents. This study reports the first genetic map of trigenomic Brassica. A doubled haploid mapping population consisting of 189 lines was obtained via microspore culture from a hybrid H16-1 derived from a cross between two allohexaploid Brassica lines (7H170-1 and Y54-2). Simple sequence repeat primer pairs specific to the A genome (107), B genome (44) and C genome (109) were used to construct a genetic linkage map of the population. Twenty-seven linkage groups were resolved from 274 polymorphic loci on the A genome (109), B genome (49) and C genome (116) covering a total genetic distance of 3178.8 cM with an average distance between markers of 11.60 cM. This is the first genetic framework map for the artificially synthesized Brassica allohexaploids. The linkage groups represent the expected complement of chromosomes in the A, B and C genomes from the original diploid and tetraploid parents. This framework linkage map will be valuable for QTL analysis and future genetic improvement of a new allohexaploid Brassica species, and in improving our understanding of the genetic control of meiosis in new polyploids.

Newborn Screening in the Era of Precision Medicine.

Science.gov (United States)

Yang, Lan; Chen, Jiajia; Shen, Bairong

2017-01-01

As newborn screening success stories gained general confirmation during the past 50 years, scientists quickly discovered diagnostic tests for a host of genetic disorders that could be treated at birth. Outstanding progress in sequencing technologies over the last two decades has made it possible to comprehensively profile newborn screening (NBS) and identify clinically relevant genomic alterations. With the rapid developments in whole-genome sequencing (WGS) and whole-exome sequencing (WES) recently, we can detect newborns at the genomic level and be able to direct the appropriate diagnosis to the different individuals at the appropriate time, which is also encompassed in the concept of precision medicine. Besides, we can develop novel interventions directed at the molecular characteristics of genetic diseases in newborns. The implementation of genomics in NBS programs would provide an effective premise for the identification of the majority of genetic aberrations and primarily help in accurate guidance in treatment and better prediction. However, there are some debate correlated with the widespread application of genome sequencing in NBS due to some major concerns such as clinical analysis, result interpretation, storage of sequencing data, and communication of clinically relevant mutations to pediatricians and parents, along with the ethical, legal, and social implications (so-called ELSI). This review is focused on these critical issues and concerns about the expanding role of genomics in NBS for precision medicine. If WGS or WES is to be incorporated into NBS practice, considerations about these challenges should be carefully regarded and tackled properly to adapt the requirement of genome sequencing in the era of precision medicine.

ERA: Efficient serial and parallel suffix tree construction for very long strings

KAUST Repository

Mansour, Essam

2011-09-01

The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix tree are too large to fit into the main memory, most existing construction algorithms become very inefficient. This paper presents a disk-based suffix tree construction method, called Elastic Range (ERa), which works efficiently with very long strings that are much larger than the available memory. ERa partitions the tree construction process horizontally and vertically and minimizes I/Os by dynamically adjusting the horizontal partitions independently for each vertical partition, based on the evolving shape of the tree and the available memory. Where appropriate, ERa also groups vertical partitions together to amortize the I/O cost. We developed a serial version; a parallel version for shared-memory and shared-disk multi-core systems; and a parallel version for shared-nothing architectures. ERa indexes the entire human genome in 19 minutes on an ordinary desktop computer. For comparison, the fastest existing method needs 15 minutes using 1024 CPUs on an IBM BlueGene supercomputer.

Characterization of ERAS, a putative novel human oncogene, in skin and breast

Energy Technology Data Exchange (ETDEWEB)

Peña Avalos, B.L. de la

2014-07-01

Most human tumors have mutations in genes of the RAS small GTPase protein family. RAS works as a molecular switch for signaling pathways that modulate many aspects of cell behavior, including proliferation, differentiation, motility and death. Oncogenic mutations in RAS prevent GTP hydrolysis, locking RAS in a permanently active state, being the most common mutations in HRAS, KRAS and NRAS. The human RAS family consists of at least 36 different genes, many of which have been scarcely studied. One of these relatively unknown genes is ERAS (ES cell-expressed RAS), which is a constitutively active RAS protein, localized in chromosome X and expressed only in embryonic cells, being undetectable in adult tissues. New high throughput technologies have made it possible to screen complete cancer genomes for identification of mutations associated to cancer. Using the Sleeping Beauty (SB) transposon system, ERAS was identified as a putative novel oncogene in non-melanoma skin and breast cancers. The major aim of this project is to determine the general characteristics of ERAS as a putative novel human oncogene in skin and breast cells. Forced expression of ERAS results in drastic changes in cell shape, proliferation and motility. When ERAS is overexpressed in skin and breast human cells it is mainly localized in the cytoplasmic membrane. ERAS activates the phosphatidylinositol-3-OH kinase (PI3K) pathway but not the mitogen-activated protein kinase (MAPK) pathway. ERAS-expressing cells suffer spontaneous morphologic and phenotypic EMT-like changes, including cytoskeleton reorganization, vimentin and N-cadherin up-regulation and down-regulation of E-cadherin, which can be associated with increased malignancy, and invasive and metastatic potential. Our results suggest that inappropriate expression of ERAS lead to transformation of human cells. (Author)

Parenting and Military Children’s Behavior: Preliminary Finding in Military Family of New Order Era and Reformation

Directory of Open Access Journals (Sweden)

Ruri Dindasari Fatimah

2018-03-01

Full Text Available Abstrak Pola asuh keluarga militer berimplikasi terhadap pola perilaku anak sebagaimana ditunjukkan oleh beberapa kajian. Kajian-kajian tersebut lebih banyak membahas mengenai pola asuh tanpa melihat adanya hubungan dengan perubahan struktur organisasi yang bersifat fundamental pada tubuh militer Indonesia pasca Reformasi. Karena itu, kajian ini kemudian membahas tentang perbedaan pola asuh yang diterapkan pada keluarga militer di era Orde Baru dan pasca Reformasi serta implikasinya terhadap pola perilaku anak. Hal ini didasarkan pada argumentasi bahwa, sejalan dengan perubahan nilai-nilai di dalam tubuh militer Indonesia di masa Orde Baru dan pasca reformasi, terjadi juga perubahan pola asuh dalam keluarga anggota militer. Penelitian ini menggunakan kasus pada keluarga militer yang orang tuanya bergabung dengan militer pada era Orde Baru dan pasca Reformasi. Penelitian dilakukan dengan menggunakan metode kualitatif di mana data dikumpulkan dengan wawancara mendalam padakeluarga militer era Orde Baru dan pasca Reformasiyang masing-masing keluarga terdiri dari ayah, ibu, dan anak yang tinggal di Kota Depok. Hasil penelitian menunjukkan bahwa pola asuh pada keluarga militer Orde Baru dan pasca Reformasi berada pada ruang antara yang sifatnya demokratis dan otoriter. Pola asuh pada gilirannya juga berpengaruh pada pola perilaku anak-anak dalam keluarga militer. Penelitian ini juga mengemukakan faktor-faktor lain di luar pola asuh yang berkontribusi terhadap pola perilaku anak di dalam keluarga militer. Abstract The parenting patterns of military family has had a implication towards their children’s behavior as stated by several studies. Those studies discussed on the parenting patterns but few has associated it with the fundamental change of Indonesian military organization post Reformation era. Therefore, this study poladiscuss the difference of parenting pattern applied in the military family before (new order and post Reformation and how the

La motivación del alumnado como eje vertebrador en la era Post-MOOC

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María Dolores Guzmán Franco

2017-06-01

Full Text Available La evolución de MOOC en la última década ha significado una revolución en la formación abierta del alumnado en el contexto universitario. Diversidad de temáticas, experiencias y multitud de equipos multidisciplinares e interuniversitarios trabajan en la planificación, integración y mejora de este recurso con fin formativo en la educación superior. La producción científica sobre esta línea de investigación en el plano de la tecnología y la educación también ha sido muy fructífera en este intervalo temporal de expansión y consolidación, aunque consideramos que queda mucho por avanzar en aportaciones críticas que proyecten y permitan avanzar en la era post-MOOC. El eje central que nos propusimos en este estudio fue conocer las motivaciones que incitan al alumnado a la hora de participar en estas propuestas formativas, su grado de satisfacción y su intención de continuar avanzando en esta línea. Nuestros resultados evidencian que esta modalidad de aprendizaje posee ventajas valoradas muy positivamente por las personas que acceden a ellos y es considerada una experiencia atractiva y amena, que influye en la decisión de volver a cursarlos.

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

Science.gov (United States)

2011-01-01

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

Genomics, transcriptomics and proteomics: enabling insights into social evolution and disease challenges for managed and wild bees.

Science.gov (United States)

Trapp, Judith; McAfee, Alison; Foster, Leonard J

2017-02-01

Globally, there are over 20 000 bee species (Hymenoptera: Apoidea: Anthophila) with a host of biologically fascinating characteristics. Although they have long been studied as models for social evolution, recent challenges to bee health (mainly diseases and pesticides) have gathered the attention of both public and research communities. Genome sequences of twelve bee species are now complete or under progress, facilitating the application of additional 'omic technologies. Here, we review recent developments in honey bee and native bee research in the genomic era. We discuss the progress in genome sequencing and functional annotation, followed by the enabled comparative genomics, proteomics and transcriptomics applications regarding social evolution and health. Finally, we end with comments on future challenges in the postgenomic era. © 2016 John Wiley & Sons Ltd.

Agricultural genomics and sustainable development: perspectives ...

African Journals Online (AJOL)

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era is to establish how genes and proteins function to bring about changes in phenotype. Some of ... within the context of sustainable development of African economies. The greatest .... these strategies, the genomes of many organisms have now been ... gene structure and order, e.g. between rice, wheat, corn, millets and ...

METHODS IN THE POST-METHODS ERA. REPORT ON AN INTERNATIONAL SURVEY ON LANGUAGE TEACHING METHODS'

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Jun Liu

2004-06-01

Full Text Available Do methods still have a place in 21" century language teaching? To answer this question, an international survey was conducted in the surnmer of 1999. A sample of 800 language teachers world-wide randomly drawn from 17,800 TESOLers were each given a 2-page survey. The return rate was 58.5% with the actual usable data set of448, which was analyzed by using both descriptive and inferential statistics. Among the ten commonly recognized teaching methods surveyed, both the Communicative Language Teaching Approach and an eclectic method seem to have the highest rate in familiarity, preference, and use. But when multiple factors, such as teaching contexts, instructional settings, learners' proficiency levels, class size, teaching experience and educational backgrounds of the teachers, and the status of being a native or nonnative English speaking professional were taken into consideration, various patterns and themes emerged. One interesting finding is that Grammar Translation is still used in EFL contexts, in larger classes, and with learners at low proficiency levels, though the ratio between the actual use of this method and teachers' preference does not match. Based on the results of the survey, a new theoretical framework is proposed to conceptualize language teaching methods in the post-methods era.

The Effects of Pre- Versus Post-Presentation Input Flooding via Reading on the Young Iranian EFL Learners' Acquisition of Simple Past Tense

Science.gov (United States)

Rikhtegar, Omid; Gholami, Javad

2015-01-01

The purpose of this study was to find out the possible effects of pre-versus post-presentation input flooding via reading on simple past tense acquisition among young Iranian EFL learners. Sixty one elementary EFL learners were divided into two experimental and one control group. The experimental groups were exposed to pre and post presentation…

Meeting Report. Assessing Human Germ-Cell Mutagenesis in thePost-Genome Era: A Celebration of the Legacy of William Lawson (Bill)Russell

Energy Technology Data Exchange (ETDEWEB)

Wyrobek, Andrew J.; Mulvihill, John J.; Wassom, John S.; Malling,Heinrich V.; Shelby, Michael D.; Lewis, Susan E.; Witt, Kristine L.; Preston, R. Julian; Perreault-Darney, Sally; Allen, James W.; DeMarini,David M.; Woychik, Richard P.; Bishop Jack B; Workshop Presenters

2006-04-18

Although numerous germ-cell mutagens have been identified inanimal model systems, to date, no human germ-cell mutagens have beenconfirmed. Because the genomic integrity of our germ cells is essentialfor the continuation of the human species, a resolution of this enduringconundrum is needed. To facilitate such a resolution, we organized aworkshop at The Jackson Laboratory in Bar Harbor, Maine on September28-30, 2004. This interactive workshop brought together scientists from awide range of disciplines to assess the applicability of emergingmolecular methods for genomic analysis to the field of human germ-cellmutagenesis. Participants recommended that focused, coordinated humangerm-cell mutation studies be conducted in relation to important societalexposures. Because cancer survivors represent a unique cohort withwell-defined exposures, there was a consensus that studies should bedesigned to assess the mutational impact on children born to parents whohad received certain types of mutagenic cancer chemotherapy prior toconceiving their children. Within this high-risk cohort, parents andchildren could be evaluated for inherited changes in (a) gene sequencesand chromosomal structure, (b) repeat sequences and minisatelliteregions, and (c) global gene expression and chromatin. Participants alsorecommended studies to examine trans-generational effects in humansinvolving mechanisms such as changes in imprinting and methylationpatterns, expansion of nucleotide repeats, or induction of mitochondrialDNA mutations. Workshop participants advocated establishment of abio-bank of human tissue samples that could be used to conduct amultiple-endpoint, comprehensive, and collaborative effort to detectexposure-induced heritable alterations in the human genome. Appropriateanimal models of human germ-cell mutagenes is should be used in parallelwith human studies to provide insights into the mechanisms of mammaliangerm-cell mutagenesis. Finally, participants recommended that

Comparación de la cicatrización clínica alveolar post exodoncia simple con y sin sutura

OpenAIRE

Huamaní Muñoz, Balbín Wilder

2008-01-01

The purpose of the present research was to compare the characteristics the process of alveolar clinical healing post simple exodontia with and without suture. The research was a simple randomized clinico test and was made in the Hospital of Support I Albrecht — Trujillo of EsSalud, during the months of January to April of the 2008, with a sample of study of thirty insured patients between twenty to fifty years old of bot h sexes. The characteristics of the alveolar healing of hemostasia, ...

Manual stapedotomy still holds good in the era of laser.

Science.gov (United States)

Ganesan, Sivaraman; Anuprasad, S; Patra, Sisir Kumar; Parida, Pradipta Kumar; Gopalakrishnan, Suria; Verma, Nishikanta

2010-03-01

In the present era of stapedotomy, there is an inevitable role for laser. But the conventional technique with manual burr still has its own merits in various settings such as usage in resource poor setting in developing countries and avoidance of laser hazards. To evaluate the audiometric outcomes after manual stapedotomy. The present study was retrospective record-based study. Patients who have been diagnosed otosclerosis and those who were not willing for surgery with laser, but gave consent for manual stapedotomy were included for the study. Preoperatively, and at each subsequent post-operative follow-up visits, patients were required to undergo a pure-tone audiogram. The air-bone gaps at the end of 6 months were used for final analysis. Data was analyzed with using Statistical Package for Social Sciences (SPSS) version 12 (Chicago, IL, USA). Descriptive frequency distributions, mean, standard deviation of audiometric data were calculated. The paired t test was done to see the improvement in the air bone gap post-operatively. The mean age of presentation is 32.2 years. Overall, the male:female ratio was found to be 1:1.2. Post-operative air bone closure to 15 decibels was obtained in 80% of patients. There was no significant correlation between the pre-operative hearing loss and post-operative gain, age, and gender of distribution of focus. The post-operative hearing after stapedotomy has been remarkable in all the patients even with manual burr. There were no major vestibular complications in any of these patients. The study has shown that the significant post-operative hearing results can be still achieved with meticulous surgery by an experienced surgeon with manual burr in the present laser era.

Early onset of industrial-era warming across the oceans and continents.

Science.gov (United States)

Abram, Nerilie J; McGregor, Helen V; Tierney, Jessica E; Evans, Michael N; McKay, Nicholas P; Kaufman, Darrell S

2016-08-25

The evolution of industrial-era warming across the continents and oceans provides a context for future climate change and is important for determining climate sensitivity and the processes that control regional warming. Here we use post-ad 1500 palaeoclimate records to show that sustained industrial-era warming of the tropical oceans first developed during the mid-nineteenth century and was nearly synchronous with Northern Hemisphere continental warming. The early onset of sustained, significant warming in palaeoclimate records and model simulations suggests that greenhouse forcing of industrial-era warming commenced as early as the mid-nineteenth century and included an enhanced equatorial ocean response mechanism. The development of Southern Hemisphere warming is delayed in reconstructions, but this apparent delay is not reproduced in climate simulations. Our findings imply that instrumental records are too short to comprehensively assess anthropogenic climate change and that, in some regions, about 180 years of industrial-era warming has already caused surface temperatures to emerge above pre-industrial values, even when taking natural variability into account.

MEETING REPORT ASSESSING HUMAN GERM-CELL MUTAGENESIS IN THE POST-GENOME ERA: A CELEBRATION OF THE LEGACY OF WILLIAM LAWSON (BILL) RUSSELL

Science.gov (United States)

Although numerous germ-cell mutagens have been identified in animal model systems, to date, no human germ-cell mutagens have been confirmed. Because the genomic integrity of our germ cells is essential for the continuation of the human species, a resolution of this enduring conu...

Genomes, Phylogeny, and Evolutionary Systems Biology

Energy Technology Data Exchange (ETDEWEB)

Medina, Monica

2005-03-25

With the completion of the human genome and the growing number of diverse genomes being sequenced, a new age of evolutionary research is currently taking shape. The myriad of technological breakthroughs in biology that are leading to the unification of broad scientific fields such as molecular biology, biochemistry, physics, mathematics and computer science are now known as systems biology. Here I present an overview, with an emphasis on eukaryotes, of how the postgenomics era is adopting comparative approaches that go beyond comparisons among model organisms to shape the nascent field of evolutionary systems biology.

FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform

Directory of Open Access Journals (Sweden)

Pontarotti Pierre

2005-08-01

Full Text Available Abstract Background Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as well as of other features of genomes. Structural and functional annotation both require the complex chaining of numerous different software, algorithms and methods under the supervision of a biologist. The automation of these pipelines is necessary to manage huge amounts of data released by sequencing projects. Several pipelines already automate some of these complex chaining but still necessitate an important contribution of biologists for supervising and controlling the results at various steps. Results Here we propose an innovative automated platform, FIGENIX, which includes an expert system capable to substitute to human expertise at several key steps. FIGENIX currently automates complex pipelines of structural and functional annotation under the supervision of the expert system (which allows for example to make key decisions, check intermediate results or refine the dataset. The quality of the results produced by FIGENIX is comparable to those obtained by expert biologists with a drastic gain in terms of time costs and avoidance of errors due to the human manipulation of data. Conclusion The core engine and expert system of the FIGENIX platform currently handle complex annotation processes of broad interest for the genomic community. They could be easily adapted to new, or more specialized pipelines, such as for example the annotation of miRNAs, the classification of complex multigenic families, annotation of regulatory elements and other genomic features of interest.

The Ever-Evolving Concept of the Gene: The Use of RNA/Protein Experimental Techniques to Understand Genome Functions

Directory of Open Access Journals (Sweden)

Andrea Cipriano

2018-03-01

Full Text Available The completion of the human genome sequence together with advances in sequencing technologies have shifted the paradigm of the genome, as composed of discrete and hereditable coding entities, and have shown the abundance of functional noncoding DNA. This part of the genome, previously dismissed as “junk” DNA, increases proportionally with organismal complexity and contributes to gene regulation beyond the boundaries of known protein-coding genes. Different classes of functionally relevant nonprotein-coding RNAs are transcribed from noncoding DNA sequences. Among them are the long noncoding RNAs (lncRNAs, which are thought to participate in the basal regulation of protein-coding genes at both transcriptional and post-transcriptional levels. Although knowledge of this field is still limited, the ability of lncRNAs to localize in different cellular compartments, to fold into specific secondary structures and to interact with different molecules (RNA or proteins endows them with multiple regulatory mechanisms. It is becoming evident that lncRNAs may play a crucial role in most biological processes such as the control of development, differentiation and cell growth. This review places the evolution of the concept of the gene in its historical context, from Darwin's hypothetical mechanism of heredity to the post-genomic era. We discuss how the original idea of protein-coding genes as unique determinants of phenotypic traits has been reconsidered in light of the existence of noncoding RNAs. We summarize the technological developments which have been made in the genome-wide identification and study of lncRNAs and emphasize the methodologies that have aided our understanding of the complexity of lncRNA-protein interactions in recent years.

GenomeVx: simple web-based creation of editable circular chromosome maps.

Science.gov (United States)

Conant, Gavin C; Wolfe, Kenneth H

2008-03-15

We describe GenomeVx, a web-based tool for making editable, publication-quality, maps of mitochondrial and chloroplast genomes and of large plasmids. These maps show the location of genes and chromosomal features as well as a position scale. The program takes as input either raw feature positions or GenBank records. In the latter case, features are automatically extracted and colored, an example of which is given. Output is in the Adobe Portable Document Format (PDF) and can be edited by programs such as Adobe Illustrator. GenomeVx is available at http://wolfe.gen.tcd.ie/GenomeVx

NMD Microarray Analysis for Rapid Genome-Wide Screen of Mutated Genes in Cancer

Directory of Open Access Journals (Sweden)

Maija Wolf

2005-01-01

Full Text Available Gene mutations play a critical role in cancer development and progression, and their identification offers possibilities for accurate diagnostics and therapeutic targeting. Finding genes undergoing mutations is challenging and slow, even in the post-genomic era. A new approach was recently developed by Noensie and Dietz to prioritize and focus the search, making use of nonsense-mediated mRNA decay (NMD inhibition and microarray analysis (NMD microarrays in the identification of transcripts containing nonsense mutations. We combined NMD microarrays with array-based CGH (comparative genomic hybridization in order to identify inactivation of tumor suppressor genes in cancer. Such a “mutatomics” screening of prostate cancer cell lines led to the identification of inactivating mutations in the EPHB2 gene. Up to 8% of metastatic uncultured prostate cancers also showed mutations of this gene whose loss of function may confer loss of tissue architecture. NMD microarray analysis could turn out to be a powerful research method to identify novel mutated genes in cancer cell lines, providing targets that could then be further investigated for their clinical relevance and therapeutic potential.

The Obama Era: A Post-Racial Society?

Science.gov (United States)

Lum, Lydia

2009-01-01

With Barack Obama ensconced as the nation's first Black president, plenty of voices in the national conversation are trumpeting America as a post-racial society--that race matters much less than it used to, that the boundaries of race have been overcome, that racism is no longer a big problem. In this article, longtime scholars whose life's work…

The simple fool's guide to population genomics via RNA-Seq: An introduction to high-throughput sequencing data analysis

DEFF Research Database (Denmark)

De Wit, P.; Pespeni, M.H.; Ladner, J.T.

2012-01-01

to Population Genomics via RNA-seq' (SFG), a document intended to serve as an easy-to-follow protocol, walking a user through one example of high-throughput sequencing data analysis of nonmodel organisms. It is by no means an exhaustive protocol, but rather serves as an introduction to the bioinformatic methods...... used in population genomics, enabling a user to gain familiarity with basic analysis steps. The SFG consists of two parts. This document summarizes the steps needed and lays out the basic themes for each and a simple approach to follow. The second document is the full SFG, publicly available at http://sfg.......stanford.edu, that includes detailed protocols for data processing and analysis, along with a repository of custom-made scripts and sample files. Steps included in the SFG range from tissue collection to de novo assembly, blast annotation, alignment, gene expression, functional enrichment, SNP detection, principal components...

Survival of Er(a+) red cells in a patient with allo-anti-Era

International Nuclear Information System (INIS)

Thompson, H.W.; Skradski, K.J.; Thoreson, J.R.; Polesky, H.F.

1985-01-01

51 Chromium-labeled Er(a+) red cells survived nearly normally (T1/2 of 21 days) in a patient with allo-anti-Era. Transfusion of Er(a+) blood was without significant reaction and did not affect the anti-Era titer

Value-based genomics.

Science.gov (United States)

Gong, Jun; Pan, Kathy; Fakih, Marwan; Pal, Sumanta; Salgia, Ravi

2018-03-20

Advancements in next-generation sequencing have greatly enhanced the development of biomarker-driven cancer therapies. The affordability and availability of next-generation sequencers have allowed for the commercialization of next-generation sequencing platforms that have found widespread use for clinical-decision making and research purposes. Despite the greater availability of tumor molecular profiling by next-generation sequencing at our doorsteps, the achievement of value-based care, or improving patient outcomes while reducing overall costs or risks, in the era of precision oncology remains a looming challenge. In this review, we highlight available data through a pre-established and conceptualized framework for evaluating value-based medicine to assess the cost (efficiency), clinical benefit (effectiveness), and toxicity (safety) of genomic profiling in cancer care. We also provide perspectives on future directions of next-generation sequencing from targeted panels to whole-exome or whole-genome sequencing and describe potential strategies needed to attain value-based genomics.

Clinical research of traditional Chinese medicine in big data era.

Science.gov (United States)

Zhang, Junhua; Zhang, Boli

2014-09-01

With the advent of big data era, our thinking, technology and methodology are being transformed. Data-intensive scientific discovery based on big data, named "The Fourth Paradigm," has become a new paradigm of scientific research. Along with the development and application of the Internet information technology in the field of healthcare, individual health records, clinical data of diagnosis and treatment, and genomic data have been accumulated dramatically, which generates big data in medical field for clinical research and assessment. With the support of big data, the defects and weakness may be overcome in the methodology of the conventional clinical evaluation based on sampling. Our research target shifts from the "causality inference" to "correlativity analysis." This not only facilitates the evaluation of individualized treatment, disease prediction, prevention and prognosis, but also is suitable for the practice of preventive healthcare and symptom pattern differentiation for treatment in terms of traditional Chinese medicine (TCM), and for the post-marketing evaluation of Chinese patent medicines. To conduct clinical studies involved in big data in TCM domain, top level design is needed and should be performed orderly. The fundamental construction and innovation studies should be strengthened in the sections of data platform creation, data analysis technology and big-data professionals fostering and training.

The Anthropocene era. The Earth, the history and us

International Nuclear Information System (INIS)

Bonneuil, Christophe; Fressoz, Jean-Baptiste

2013-01-01

As some scientists state that the Earth entered the Anthropocene era which is an anthropogenic geological revolution: the traces of our urban, consumption, chemical and nuclear era will remain in the planet geological archives for thousands and even millions of years, and will result in huge difficulties for human societies. Between science and history, the authors give an overview of a development model which has become unsustainable: studies which highlighted the impossibility of an indefinite growth in the 1970's have been ignored, and instead of taking the three dimensions involved in sustainable development (economy, social, environment), into account, environment tends to become only a new item in firm accounting (markets of eco-systemic services, the biosphere, hydrosphere and atmosphere about to become simple subsystems of the financial and merchandising sphere)

A simple and efficient total genomic DNA extraction method for individual zooplankton.

Science.gov (United States)

Fazhan, Hanafiah; Waiho, Khor; Shahreza, Md Sheriff

2016-01-01

Molecular approaches are widely applied in species identification and taxonomic studies of minute zooplankton. One of the most focused zooplankton nowadays is from Subclass Copepoda. Accurate species identification of all life stages of the generally small sized copepods through molecular analysis is important, especially in taxonomic and systematic assessment of harpacticoid copepod populations and to understand their dynamics within the marine community. However, total genomic DNA (TGDNA) extraction from individual harpacticoid copepods can be problematic due to their small size and epibenthic behavior. In this research, six TGDNA extraction methods done on individual harpacticoid copepods were compared. The first new simple, feasible, efficient and consistent TGDNA extraction method was designed and compared with the commercial kit and modified available TGDNA extraction methods. The newly described TGDNA extraction method, "Incubation in PCR buffer" method, yielded good and consistent results based on the high success rate of PCR amplification (82%) compared to other methods. Coupled with its relatively consistent and economical method the "Incubation in PCR buffer" method is highly recommended in the TGDNA extraction of other minute zooplankton species.

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

NARCIS (Netherlands)

Noort, V. van; Snel, B.; Huynen, M.A.

2007-01-01

BACKGROUND: In the post-genomic era various functional genomics, proteomics and computational techniques have been developed to elucidate the protein interaction network. While some of these techniques are specific for a certain type of interaction, most predict a mixture of interactions.

Merging genomic and phenomic data for research and clinical impact.

Science.gov (United States)

Shublaq, Nour W; Coveney, Peter V

2012-01-01

Driven primarily by advances in genomics, pharmacogenomics and systems biology technologies, large amounts of genomic and phenomic data are today being collected on individuals worldwide. Integrative analysis, mining, and computer modeling of these data, facilitated by information technology, have led to the development of predictive, preventive, and personalized medicine. This transformative approach holds the potential inter alia to enable future general practitioners and physicians to prescribe the right drug to the right patient at the right dosage. For such patient-specific medicine to be adopted as standard clinical practice, publicly accumulated knowledge of genes, proteins, molecular functional annotations, and interactions need to be unified and with electronic health records including phenotypic information, most of which still reside as paper-based records in hospitals. We review the state-of-the-art in terms of electronic data capture and medical data standards. Some of these activities are drawn from research projects currently being performed within the European Virtual Physiological Human (VPH) initiative; all are being monitored by the VPH INBIOMEDvision Consortium. Various ethical, legal and societal issues linked with privacy will increasingly arise in the post-genomic era. This will require a closer interaction between the bioinformatics/systems biology and medical informatics/healthcare communities. Planning for how individuals will own their personal health records is urgently needed, as the cost of sequencing a whole human genome will soon be less than U.S. $100. We discuss some of the issues that will need to be addressed by society as a result of this revolution in healthcare.

Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

Science.gov (United States)

Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

2015-01-01

Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization. PMID:26000739

Post-placement temperature reduction techniques

DEFF Research Database (Denmark)

Liu, Wei; Nannarelli, Alberto

2010-01-01

With technology scaled to deep submicron era, temperature and temperature gradient have emerged as important design criteria. We propose two post-placement techniques to reduce peak temperature by intelligently allocating whitespace in the hotspots. Both methods are fully compliant with commercial...

Post What? Disarticulating Post-Discourses in Toni Morrison’s God Help the Child

Directory of Open Access Journals (Sweden)

Delphine Gras

2016-09-01

Full Text Available In the midst of the proliferation of post-discourses, this essay investigates how Toni Morrison’s God Help the Child (2015 offers a timely exploration of the hurting Black female body that calls into question, if not outright refutes, whether Americans have entered a post-racial, post-Black, and post-feminist era. This essay opens with a critical context section that situates God Help the Child within and against post-discourses, before examining how resemblances with Morrison’s prior works like Beloved (1987 and The Bluest Eye (1970 confirm that the legacy of slavery still dictates the way Black female bodies are seen and treated in twenty-first-century America. Ultimately, what this study intends is to speak the unspeakable: race still matters despite the silencing effects of post-discourses.

Post-Genomics and Vaccine Improvement for Leishmania

Science.gov (United States)

Seyed, Negar; Taheri, Tahereh; Rafati, Sima

2016-01-01

Leishmaniasis is a parasitic disease that primarily affects Asia, Africa, South America, and the Mediterranean basin. Despite extensive efforts to develop an effective prophylactic vaccine, no promising vaccine is available yet. However, recent advancements in computational vaccinology on the one hand and genome sequencing approaches on the other have generated new hopes in vaccine development. Computational genome mining for new vaccine candidates is known as reverse vaccinology and is believed to further extend the current list of Leishmania vaccine candidates. Reverse vaccinology can also reduce the intrinsic risks associated with live attenuated vaccines. Individual epitopes arranged in tandem as polytopes are also a possible outcome of reverse genome mining. Here, we will briefly compare reverse vaccinology with conventional vaccinology in respect to Leishmania vaccine, and we will discuss how it influences the aforementioned topics. We will also introduce new in vivo models that will bridge the gap between human and laboratory animal models in future studies. PMID:27092123

Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions

NARCIS (Netherlands)

Noort, V. van; Snel, B.; Huynen, M.A.

2007-01-01

ABSTRACT: BACKGROUND: In the post-genomic era various functional genomics, proteomics and computational techniques have been developed to elucidate the protein interaction network. While some of these techniques are specific for a certain type of interaction, most predict a mixture of interactions.

Lessons from a phenotyping center revealed by the genome-guided mapping of powdery mildew resistance loci

Science.gov (United States)

The genomics era brought unprecedented tools for genetic analysis of host resistance, but careful attention is needed on obtaining accurate and reproducible phenotypes so that genomic results appropriately reflect biology. Phenotyping host resistance by natural infection in the field can produce var...

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

Science.gov (United States)

Robins-Browne, Roy M.; Holt, Kathryn E.; Ingle, Danielle J.; Hocking, Dianna M.; Yang, Ji; Tauschek, Marija

2016-01-01

The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype E.coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of E. coli. Whole genome sequencing can be used to accurately determine E. coli subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of E. coli, which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for E. coli based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of E. coli spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods. PMID:27917373

Physicians' experiences of caring for late-stage HIV patients in the post-HAART era: challenges and adaptations.

Science.gov (United States)

Karasz, Alison; Dyche, Larry; Selwyn, Peter

2003-11-01

As medical treatment for AIDS has become more complex, the need for good palliative and end-of-life care has also increased for patients with advanced disease. Such care is often inadequate, especially among low-income, ethnic minority patients. The current study investigated physicians' experiences with caring for dying HIV patients in an underserved, inner city community in the Bronx, NY. The goals of the study included: (1) to investigate the barriers to effective end-of-life care for HIV patients; and (2) to examine physicians' experiences of role hindrance and frustration in caring for dying patients in the era of HAART. Qualitative, open-ended interviews were conducted with 16 physicians. Physicians identified two core, prescriptive myths shaping their care for patients with HIV. The 'Good Doctor Myth' equates good medical care with the delivery of efficacious biomedical care. The role of the physician is defined as technical curer, while the patient's role is limited to consultation and compliance. The 'Good Death Myth' envisions an ideal death which is acknowledged, organized, and pain free: the role of the physician is defined as that of comforter and supporter in the dying process. Role expectations associated with these myths were often disappointed. First, late-stage patients refused to adhere to treatment and were thus dying "unnecessarily." Second, patients often refused to acknowledge, accept, or plan for the end of life and as a result died painful, chaotic deaths. These realities presented intense psychological and practical challenges for providers. Adaptive coping included both behavioral and cognitive strategies. Successful adaptation resulted in "positive engagement," experienced by participants as a continuing sense of fascination, gratification, and joy. Less successful adaptation could result in detachment or anger. Participants believed that engagement had a powerful impact on patient care. Working with dying HIV patients in the post

Human Genome Sequencing in Health and Disease

Science.gov (United States)

Gonzaga-Jauregui, Claudia; Lupski, James R.; Gibbs, Richard A.

2013-01-01

Following the “finished,” euchromatic, haploid human reference genome sequence, the rapid development of novel, faster, and cheaper sequencing technologies is making possible the era of personalized human genomics. Personal diploid human genome sequences have been generated, and each has contributed to our better understanding of variation in the human genome. We have consequently begun to appreciate the vastness of individual genetic variation from single nucleotide to structural variants. Translation of genome-scale variation into medically useful information is, however, in its infancy. This review summarizes the initial steps undertaken in clinical implementation of personal genome information, and describes the application of whole-genome and exome sequencing to identify the cause of genetic diseases and to suggest adjuvant therapies. Better analysis tools and a deeper understanding of the biology of our genome are necessary in order to decipher, interpret, and optimize clinical utility of what the variation in the human genome can teach us. Personal genome sequencing may eventually become an instrument of common medical practice, providing information that assists in the formulation of a differential diagnosis. We outline herein some of the remaining challenges. PMID:22248320

A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification.

Directory of Open Access Journals (Sweden)

Saharnaz Bigdeli

Full Text Available Microdroplets are an effective platform for segregating individual cells and amplifying DNA. However, a key challenge is to recover the contents of individual droplets for downstream analysis. This paper offers a method for embedding cells in alginate microspheres and performing multiple serial operations on the isolated cells. Rhodobacter sphaeroides cells were diluted in alginate polymer and sprayed into microdroplets using a fingertip aerosol sprayer. The encapsulated cells were lysed and subjected either to conventional PCR, or whole genome amplification using either multiple displacement amplification (MDA or a two-step PCR protocol. Microscopic examination after PCR showed that the lumen of the occupied microspheres contained fluorescently stained DNA product, but multiple displacement amplification with phi29 produced only a small number of polymerase colonies. The 2-step WGA protocol was successful in generating fluorescent material, and quantitative PCR from DNA extracted from aliquots of microspheres suggested that the copy number inside the microspheres was amplified up to 3 orders of magnitude. Microspheres containing fluorescent material were sorted by a dilution series and screened with a fluorescent plate reader to identify single microspheres. The DNA was extracted from individual isolates, re-amplified with full-length sequencing adapters, and then a single isolate was sequenced using the Illumina MiSeq platform. After filtering the reads, the only sequences that collectively matched a genome in the NCBI nucleotide database belonged to R. sphaeroides. This demonstrated that sequencing-ready DNA could be generated from the contents of a single microsphere without culturing. However, the 2-step WGA strategy showed limitations in terms of low genome coverage and an uneven frequency distribution of reads across the genome. This paper offers a simple method for embedding cells in alginate microspheres and performing PCR on isolated

Energy security in the post-Cold War era: Identifying future courses for crises

Energy Technology Data Exchange (ETDEWEB)

Freund, M.T.; Wise, J.A.; Ulibarri, C.A.; Shaw, B.R.; Seely, H.E.; Roop, J.M.

1994-11-01

This paper addresses US energy security in the post-Cold War era for a conference on energy security jointly sponsored by the Department of Energy and the National Defense University. It examines the evolving nature of energy security based on analysis of past crisis-inducing events and-discusses potentially important geopolitical, environmental, regulatory, and economic developments during the next twenty-five years. The paper steps beyond the traditional economic focus of energy security issues to examine the interplay between fundamental economic and technical drivers on the one hand, and political, environmental, and perceptual phenomena, on the other hand, that can combine to create crises where none were expected. The paper expands on the premise that the recent demise of the Soviet Union and other changing world conditions have created a new set of energy dynamics, and that it is imperative that the United States revise its energy security perspective accordingly. It proceeds by reviewing key factors that comprise the concepts of ``energy security`` and ``energy crisis`` and how they may fit into the new world energy security equation. The study also presents a series of crisis scenarios that could develop during the next twenty-five years, paying particular attention to mechanisms and linked crisis causes and responses. It concludes with a discussion of factors that may serve to warn analysts and decision makers of impending future crises conditions. The crisis scenarios contained in this report should be viewed only as a representative sample of the types of situations that could occur. They serve to illustrate the variety of factors that can coalesce to produce a ``crisis.``

Functional genomics for food microbiology: Molecular mechanisms of weak organic acid preservative adaptation in yeast

NARCIS (Netherlands)

Brul, S.; Kallemeijn, W.; Smits, G.

2008-01-01

The recent era of genomics has offered tremendous possibilities to biology. This concise review describes the possibilities of applying (functional) genomics studies to the field of microbial food stability. In doing so, the studies on weak-organic-acid stress response in yeast are discussed by way

Genome network medicine: innovation to overcome huge challenges in cancer therapy.

Science.gov (United States)

Roukos, Dimitrios H

2014-01-01

The post-ENCODE era shapes now a new biomedical research direction for understanding transcriptional and signaling networks driving gene expression and core cellular processes such as cell fate, survival, and apoptosis. Over the past half century, the Francis Crick 'central dogma' of single n gene/protein-phenotype (trait/disease) has defined biology, human physiology, disease, diagnostics, and drugs discovery. However, the ENCODE project and several other genomic studies using high-throughput sequencing technologies, computational strategies, and imaging techniques to visualize regulatory networks, provide evidence that transcriptional process and gene expression are regulated by highly complex dynamic molecular and signaling networks. This Focus article describes the linear experimentation-based limitations of diagnostics and therapeutics to cure advanced cancer and the need to move on from reductionist to network-based approaches. With evident a wide genomic heterogeneity, the power and challenges of next-generation sequencing (NGS) technologies to identify a patient's personal mutational landscape for tailoring the best target drugs in the individual patient are discussed. However, the available drugs are not capable of targeting aberrant signaling networks and research on functional transcriptional heterogeneity and functional genome organization is poorly understood. Therefore, the future clinical genome network medicine aiming at overcoming multiple problems in the new fields of regulatory DNA mapping, noncoding RNA, enhancer RNAs, and dynamic complexity of transcriptional circuitry are also discussed expecting in new innovation technology and strong appreciation of clinical data and evidence-based medicine. The problematic and potential solutions in the discovery of next-generation, molecular, and signaling circuitry-based biomarkers and drugs are explored. © 2013 Wiley Periodicals, Inc.

Studying stress responses in the post-genomic era: its ecological ...

Indian Academy of Sciences (India)

Madhu Sudhan

2007-03-26

Mar 26, 2007 ... stress is regarded as an “environmental factor causing a change in a biological ... and evolutionary perspective and to investigate the role of stress ... and here more specifically, which genes affect acclimation and adaptation ...

FLP recombinase-mediated site-specific recombination in silkworm, Bombyx mori

Science.gov (United States)

A comprehensive understanding of gene function and the production of site-specific genetically modified mutants are two major goals of genetic engineering in the post-genomic era. Although site-specific recombination systems have been powerful tools for genome manipulation of many organisms, they h...

Current state and trends of access to sanitation in Ethiopia and the need to revise indicators to monitor progress in the Post-2015 era.

Science.gov (United States)

Beyene, Abebe; Hailu, Tamene; Faris, Kebede; Kloos, Helmut

2015-05-02

Investigating the current level and trends of access and identifying the underlying challenges to sanitation system development will be useful in determining directions developing countries are heading as they plan to promote sustainable development goals (post 2015 agenda). This research investigates the status and trends of access to improved sanitation coverage (ISC) in relation to the MDG target in Ethiopia with the aim of identifying prevailing constraints and suggesting the way forward in the post-MDG era. We examined data from a nationwide inventory conducted in accordance with the sanitation ladder at the national level and from a household survey in randomly selected urban slums in Addis Ababa. The inventory data were analyzed and interpreted using the conceptual model of the sanitation ladder. We used administrative reports and survey results to plot the time trend of the ISC. The data from the nationwide inventory of sanitation facilities, which are presented along the sanitation ladder reveal that more than half of the Ethiopian population (52.1%) still used unimproved sanitation facilities in 2014. The majority (35.6%) practiced open defecation, implying that the country is far from the MDG target for access to improved sanitation (56%). Most people in urban slums (88.6%) used unimproved sanitation facilities, indicating that the urban poor did not receive adequate sanitation services. Trend analysis shows that access to ISC has increased, but Central Statistical Authority (CSA) data reveal a decline. This discrepancy is due to differences in data collection methods and tools. Dry pit latrines are the most widely used toilet facilities in Ethiopia, accounting for about 97.5% of the ISC. The sanitation coverage is far from the MDG target and the majority of the population, mainly the urban poor, are living in a polluted environment, exposed to water and sanitation-related diseases. The sanitation coverage estimates might be even lower if proper

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.

Genes, race, and psychology in the genome era: an introduction.

Science.gov (United States)

Anderson, Norman B; Nickerson, Kim J

2005-01-01

The mapping of the human genome has reawakened interest in the topic of race and genetics, especially the use of genetic technology to examine racial differences in complex outcomes such as health and intelligence. Advances in genomic research challenge psychology to address the myriad conceptual, methodological, and analytical issues associated with research on genetics and race. In addition, the field needs to understand the numerous social, ethical, legal, clinical, and policy implications of research in this arena. Addressing these issues should not only benefit psychology but could also serve to guide such thought in other fields, including molecular biology. The purpose of this special issue is to begin a discussion of this issue of race and genetics within the field of psychology. Several scholars who work in the fields of genetics, race, or related areas were invited to write (or had previously submitted) articles sharing their perspectives. (c) 2005 APA

Large inserts for big data: artificial chromosomes in the genomic era.

Science.gov (United States)

Tocchetti, Arianna; Donadio, Stefano; Sosio, Margherita

2018-05-01

The exponential increase in available microbial genome sequences coupled with predictive bioinformatic tools is underscoring the genetic capacity of bacteria to produce an unexpected large number of specialized bioactive compounds. Since most of the biosynthetic gene clusters (BGCs) present in microbial genomes are cryptic, i.e. not expressed under laboratory conditions, a variety of cloning systems and vectors have been devised to harbor DNA fragments large enough to carry entire BGCs and to allow their transfer in suitable heterologous hosts. This minireview provides an overview of the vectors and approaches that have been developed for cloning large BGCs, and successful examples of heterologous expression.

Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases

Science.gov (United States)

Amos, Christopher I.; Bafna, Vineet; Hauser, Elizabeth R.; Hernandez, Ryan D.; Li, Chun; Liberles, David A.; McAllister, Kimberly; Moore, Jason H.; Paltoo, Dina N.; Papanicolaou, George J.; Peng, Bo; Ritchie, Marylyn D.; Rosenfeld, Gabriel; Witte, John S.

2014-01-01

Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled “Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases” at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to: (i) identify opportunities, challenges and resource needs for the development and application of genetic simulation models; (ii) improve the integration of tools for modeling and analysis of simulated data; and (iii) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation. PMID:25371374

A simple, rapid and efficient method for the extraction of genomic ...

African Journals Online (AJOL)

The isolation of intact, high-molecular-mass genomic DNA is essential for many molecular biology applications including long range PCR, endonuclease restriction digestion, southern blot analysis, and genomic library construction. Many protocols are available for the extraction of DNA from plant material, but obtain it is ...

A comprehensive and quantitative exploration of thousands of viral genomes

Science.gov (United States)

Mahmoudabadi, Gita

2018-01-01

The complete assembly of viral genomes from metagenomic datasets (short genomic sequences gathered from environmental samples) has proven to be challenging, so there are significant blind spots when we view viral genomes through the lens of metagenomics. One approach to overcoming this problem is to leverage the thousands of complete viral genomes that are publicly available. Here we describe our efforts to assemble a comprehensive resource that provides a quantitative snapshot of viral genomic trends – such as gene density, noncoding percentage, and abundances of functional gene categories – across thousands of viral genomes. We have also developed a coarse-grained method for visualizing viral genome organization for hundreds of genomes at once, and have explored the extent of the overlap between bacterial and bacteriophage gene pools. Existing viral classification systems were developed prior to the sequencing era, so we present our analysis in a way that allows us to assess the utility of the different classification systems for capturing genomic trends. PMID:29624169

Commemorating the future in post-war Chernivtsi.

Science.gov (United States)

Frunchak, Svetlana

2010-01-01

Throughout the Second World War and the post-war period, the city of Chernivtsi was transformed from a multiethnic and borderland urban microcosm into a culturally uniform Soviet socialist city. As the Soviets finally took power in this onetime capital of a Hapsburg province in 1944, they not only sponsored further large-scale population transfers but also "repopulated" its history, creating a new urban myth of cultural uniformity. This article examines the connection between war commemoration in Chernivtsi in the era of post-war, state-sponsored anti-Semitism and the formation of collective memory and identities of the city's post-war population. The images of homogeneously Ukrainian Chernivtsi and Bukovina were created through the art of monumental propaganda, promoting public remembrance of certain events and personalities while making sure that others were doomed to oblivion. Selective commemoration of the wartime events was an important tool of drawing the borders of Ukrainian national identity, making it exclusivist and ethnic-based. Through an investigation of the origins of the post-war collective memory in the region, this article addresses the problem of perceived discontinuity between all things Soviet and post-Soviet in Ukraine. It demonstrates that it is, on the contrary, the continuity between Soviet and post-Soviet eras that defines today's dominant culture and state ideology in Ukraine and particularly in its borderlands.

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

OpenAIRE

Karczewski, Konrad J.; Fernald, Guy Haskin; Martin, Alicia R.; Snyder, Michael; Tatonetti, Nicholas P.; Dudley, Joel T.

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technic...

Analysis of simple sequence repeats in the Gaeumannomyces graminis var. tritici genome and the development of microsatellite markers.

Science.gov (United States)

Li, Wei; Feng, Yanxia; Sun, Haiyan; Deng, Yuanyu; Yu, Hanshou; Chen, Huaigu

2014-11-01

Understanding the genetic structure of Gaeumannomyces graminis var. tritici is essential for the establishment of efficient disease control strategies. It is becoming clear that microsatellites, or simple sequence repeats (SSRs), play an important role in genome organization and phenotypic diversity, and are a large source of genetic markers for population genetics and meiotic maps. In this study, we examined the G. graminis var. tritici genome (1) to analyze its pattern of SSRs, (2) to compare it with other plant pathogenic filamentous fungi, such as Magnaporthe oryzae and M. poae, and (3) to identify new polymorphic SSR markers for genetic diversity. The G. graminis var. tritici genome was rich in SSRs; a total 13,650 SSRs have been identified with mononucleotides being the most common motifs. In coding regions, the densities of tri- and hexanucleotides were significantly higher than in noncoding regions. The di-, tri-, tetra, penta, and hexanucleotide repeats in the G. graminis var. tritici genome were more abundant than the same repeats in M. oryzae and M. poae. From 115 devised primers, 39 SSRs are polymorphic with G. graminis var. tritici isolates, and 8 primers were randomly selected to analyze 116 isolates from China. The number of alleles varied from 2 to 7 and the expected heterozygosity (He) from 0.499 to 0.837. In conclusion, SSRs developed in this study were highly polymorphic, and our analysis indicated that G. graminis var. tritici is a species with high genetic diversity. The results provide a pioneering report for several applications, such as the assessment of population structure and genetic diversity of G. graminis var. tritici.

Selective whole genome amplification for resequencing target microbial species from complex natural samples.

Science.gov (United States)

Leichty, Aaron R; Brisson, Dustin

2014-10-01

Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratory-prepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in >10(5)-fold amplification of the target genomes with genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs. Copyright © 2014 by the Genetics Society of America.

Advances in Miniaturized Instruments for Genomics

Directory of Open Access Journals (Sweden)

Cihun-Siyong Alex Gong

2014-01-01

Full Text Available In recent years, a lot of demonstrations of the miniaturized instruments were reported for genomic applications. They provided the advantages of miniaturization, automation, sensitivity, and specificity for the development of point-of-care diagnostics. The aim of this paper is to report on recent developments on miniaturized instruments for genomic applications. Based on the mature development of microfabrication, microfluidic systems have been demonstrated for various genomic detections. Since one of the objectives of miniaturized instruments is for the development of point-of-care device, impedimetric detection is found to be a promising technique for this purpose. An in-depth discussion of the impedimetric circuits and systems will be included to provide total consideration of the miniaturized instruments and their potential application towards real-time portable imaging in the “-omics” era. The current excellent demonstrations suggest a solid foundation for the development of practical and widespread point-of-care genomic diagnostic devices.

CENTRAL BANKING IN THE NEW ERA

Directory of Open Access Journals (Sweden)

Bilal Bagis

2017-12-01

Full Text Available This paper analyzes the evolution of central banking, and in particular the American experience of central banking. It provides projections for the future of central banking in the new era of post 2008. The paper initially demonstrates recent improvements in the financial and banking sectors, regulations and different measures of monetary and financial rules both in the USA and the rest of the advanced economies. Then, it claims institutions, such as central banks, will gain new objectives and more significance in this new era and thus will be given new roles, over time and along with the improvements and deepening in the financial system. The paper argues centuries long central bank evolution is not complete yet and that more objectives should be expected to come forward. In that line, there is need for a shift in the conventional policy measures. New trends in central banking such as the helicopter money, popular nominal GDP targeting regime and the retro developmental central banking are all critically analyzed. The paper provides a breakdown of financial development and central banking activities in a historical context and provides a rationale and a new basis for possible future innovations.

The renaissance of continuous culture in the post-genomics age.

Science.gov (United States)

Bull, Alan T

2010-10-01

The development of continuous culture techniques 60 years ago and the subsequent formulation of theory and the diversification of experimental systems revolutionised microbiology and heralded a unique period of innovative research. Then, progressively, molecular biology and thence genomics and related high-information-density omics technologies took centre stage and microbial growth physiology in general faded from educational programmes and research funding priorities alike. However, there has been a gathering appreciation over the past decade that if the claims of systems biology are going to be realised, they will have to be based on rigorously controlled and reproducible microbial and cell growth platforms. This revival of continuous culture will be long lasting because its recognition as the growth system of choice is firmly established. The purpose of this review, therefore, is to remind microbiologists, particularly those new to continuous culture approaches, of the legacy of what I call the first age of continuous culture, and to explore a selection of researches that are using these techniques in this post-genomics age. The review looks at the impact of continuous culture across a comprehensive range of microbiological research and development. The ability to establish (quasi-) steady state conditions is a frequently stated advantage of continuous cultures thereby allowing environmental parameters to be manipulated without causing concomitant changes in the specific growth rate. However, the use of continuous cultures also enables the critical study of specified transition states and chemical, physical or biological perturbations. Such dynamic analyses enhance our understanding of microbial ecology and microbial pathology for example, and offer a wider scope for innovative drug discovery; they also can inform the optimization of batch and fed-batch operations that are characterized by sequential transitions states.

Use of γ-ray-induced mutations in the genome era in rice

International Nuclear Information System (INIS)

Kusaba, Makoto

2007-01-01

Ionizing radiation has been used for inducing mutations and improving crops since the discovery by STADLER (1928) that X-rays could induce mutations in barley. At the end of 2004, the whole genome sequence of rice was determined (INTERNATIONAL RICE GENOME SEQUENCING PROJECT, 2005). What can γ-ray-induced mutations contribute now that this has been achieved? One answer could be the elucidation of the functions of the numerous genes revealed by the complete sequence of the rice genome. This includes identification of mutants through reverse genetics and the isolation of genes containing mutations through forward genetics using molecular markers and sequence information. Another answer could be mutation breeding using reverse genetics. But first we must know what kind of DNA lesions are caused by γ-rays. In this article, I describe the production of DNA lesions, and then discuss how γ-ray-induced mutations can contribute to the elucidation of gene function and to mutation breeding. (author)

Multitrait, Random Regression, or Simple Repeatability Model in High-Throughput Phenotyping Data Improve Genomic Prediction for Wheat Grain Yield.

Science.gov (United States)

Sun, Jin; Rutkoski, Jessica E; Poland, Jesse A; Crossa, José; Jannink, Jean-Luc; Sorrells, Mark E

2017-07-01

High-throughput phenotyping (HTP) platforms can be used to measure traits that are genetically correlated with wheat ( L.) grain yield across time. Incorporating such secondary traits in the multivariate pedigree and genomic prediction models would be desirable to improve indirect selection for grain yield. In this study, we evaluated three statistical models, simple repeatability (SR), multitrait (MT), and random regression (RR), for the longitudinal data of secondary traits and compared the impact of the proposed models for secondary traits on their predictive abilities for grain yield. Grain yield and secondary traits, canopy temperature (CT) and normalized difference vegetation index (NDVI), were collected in five diverse environments for 557 wheat lines with available pedigree and genomic information. A two-stage analysis was applied for pedigree and genomic selection (GS). First, secondary traits were fitted by SR, MT, or RR models, separately, within each environment. Then, best linear unbiased predictions (BLUPs) of secondary traits from the above models were used in the multivariate prediction models to compare predictive abilities for grain yield. Predictive ability was substantially improved by 70%, on average, from multivariate pedigree and genomic models when including secondary traits in both training and test populations. Additionally, (i) predictive abilities slightly varied for MT, RR, or SR models in this data set, (ii) results indicated that including BLUPs of secondary traits from the MT model was the best in severe drought, and (iii) the RR model was slightly better than SR and MT models under drought environment. Copyright © 2017 Crop Science Society of America.

A Simple Predictive Enhancer Syntax for Hindbrain Patterning Is Conserved in Vertebrate Genomes.

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Joseph Grice

Full Text Available Determining the function of regulatory elements is fundamental for our understanding of development, disease and evolution. However, the sequence features that mediate these functions are often unclear and the prediction of tissue-specific expression patterns from sequence alone is non-trivial. Previous functional studies have demonstrated a link between PBX-HOX and MEIS/PREP binding interactions and hindbrain enhancer activity, but the defining grammar of these sites, if any exists, has remained elusive.Here, we identify a shared sequence signature (syntax within a heterogeneous set of conserved vertebrate hindbrain enhancers composed of spatially co-occurring PBX-HOX and MEIS/PREP transcription factor binding motifs. We use this syntax to accurately predict hindbrain enhancers in 89% of cases (67/75 predicted elements from a set of conserved non-coding elements (CNEs. Furthermore, mutagenesis of the sites abolishes activity or generates ectopic expression, demonstrating their requirement for segmentally restricted enhancer activity in the hindbrain. We refine and use our syntax to predict over 3,000 hindbrain enhancers across the human genome. These sequences tend to be located near developmental transcription factors and are enriched in known hindbrain activating elements, demonstrating the predictive power of this simple model.Our findings support the theory that hundreds of CNEs, and perhaps thousands of regions across the human genome, function to coordinate gene expression in the developing hindbrain. We speculate that deeply conserved sequences of this kind contributed to the co-option of new genes into the hindbrain gene regulatory network during early vertebrate evolution by linking patterns of hox expression to downstream genes involved in segmentation and patterning, and evolutionarily newer instances may have continued to contribute to lineage-specific elaboration of the hindbrain.

Robust post-stall perching with a simple fixed-wing glider using LQR-Trees

International Nuclear Information System (INIS)

Moore, Joseph; Cory, Rick; Tedrake, Russ

2014-01-01

Birds routinely execute post-stall maneuvers with a speed and precision far beyond the capabilities of our best aircraft control systems. One remarkable example is a bird exploiting post-stall pressure drag in order to rapidly decelerate to land on a perch. Stall is typically associated with a loss of control authority, and it is tempting to attribute this agility of birds to the intricate morphology of the wings and tail, to their precision sensing apparatus, or their ability to perform thrust vectoring. Here we ask whether an extremely simple fixed-wing glider (no propeller) with only a single actuator in the tail is capable of landing precisely on a perch from a large range of initial conditions. To answer this question, we focus on the design of the flight control system; building upon previous work which used linear feedback control design based on quadratic regulators (LQR), we develop nonlinear feedback control based on nonlinear model-predictive control and ‘LQR-Trees’. Through simulation using a flat-plate model of the glider, we find that both nonlinear methods are capable of achieving an accurate bird-like perching maneuver from a large range of initial conditions; the ‘LQR-Trees’ algorithm is particularly useful due to its low computational burden at runtime and its inherent performance guarantees. With this in mind, we then implement the ‘LQR-Trees’ algorithm on real hardware and demonstrate a 95 percent perching success rate over 147 flights for a wide range of initial speeds. These results suggest that, at least in the absence of significant disturbances like wind gusts, complex wing morphology and sensing are not strictly required to achieve accurate and robust perching even in the post-stall flow regime. (papers)

The Environmental Acinetobacter baumannii Isolate DSM30011 Reveals Clues into the Preantibiotic Era Genome Diversity, Virulence Potential, and Niche Range of a Predominant Nosocomial Pathogen

Science.gov (United States)

Viale, Alejandro M.; Borges, Vítor; Cameranesi, María M.; Taib, Najwa; Espariz, Martín; Brochier-Armanet, Céline; Gomes, João Paulo; Salcedo, Suzana P.

2017-01-01

Abstract Acinetobacter baumannii represents nowadays an important nosocomial opportunistic pathogen whose reservoirs outside the clinical setting are obscure. Here, we traced the origins of the collection strain A. baumannii DSM30011 to an isolate first reported in 1944, obtained from the enriched microbiota responsible of the aerobic decomposition of the resinous desert shrub guayule. Whole-genome sequencing and phylogenetic analysis based on core genes confirmed DSM30011 affiliation to A. baumannii. Comparative studies with 32 complete A. baumannii genomes revealed the presence of 12 unique accessory chromosomal regions in DSM30011 including five encompassing phage-related genes, five containing toxin genes of the type-6 secretion system, and one with an atypical CRISPRs/cas cluster. No antimicrobial resistance islands were identified in DSM30011 agreeing with a general antimicrobial susceptibility phenotype including folate synthesis inhibitors. The marginal ampicillin resistance of DSM30011 most likely derived from chromosomal ADC-type ampC and blaOXA-51-type genes. Searching for catabolic pathways genes revealed several clusters involved in the degradation of plant defenses including woody tissues and a previously unreported atu locus responsible of aliphatic terpenes degradation, thus suggesting that resinous plants may provide an effective niche for this organism. DSM30011 also harbored most genes and regulatory mechanisms linked to persistence and virulence in pathogenic Acinetobacter species. This strain thus revealed important clues into the genomic diversity, virulence potential, and niche ranges of the preantibiotic era A. baumannii population, and may provide an useful tool for our understanding of the processes that led to the recent evolution of this species toward an opportunistic pathogen of humans. PMID:28934377

Recent Reanalysis Activities at ECMWF: Results from ERA-20C and Plans for ERA5

Science.gov (United States)

Dragani, R.; Hersbach, H.; Poli, P.; Pebeuy, C.; Hirahara, S.; Simmons, A.; Dee, D.

2015-12-01

This presentation will provide an overview of the most recent reanalysis activities performed at the European Centre for Medium-Range Weather Forecasts (ECMWF). A pilot reanalysis of the 20th-century (ERA-20C) has recently been completed. Funded through the European FP7 collaborative project ERA-CLIM, ERA-20C is part of a suite of experiments that also includes a model-only integration (ERA-20CM) and a land-surface reanalysis (ERA-20CL). Its data assimilation system is constrained by only surface observations obtained from ISPD (3.2.6) and ICOADS (2.5.1). Surface boundary conditions are provided by the Hadley Centre (HadISST2.1.0.0) and radiative forcing follows CMIP5 recommended data sets. First-guess uncertainty estimates are based on a 10-member ensemble of Data Assimilations, ERA-20C ensemble, run prior to ERA-20C using ten SST and sea-ice realizations from the Hadley Centre. In November 2014, the European Commission entrusted ECMWF to run on its behalf the Copernicus Climate Change Service (C3S) aiming at producing quality-assured information about the past, current and future states of the climate at both European and global scales. Reanalysis will be one of the main components of the C3S portfolio and the first one to be produced is a global modern era reanalysis (ERA5) covering the period from 1979 onwards. Based on a recent version of the ECMWF data assimilation system, ERA5 will replace the widely used ERA-Interim dataset. This new production will benefit from a much improved model, and better characterized and exploited observations compared to its predecessor. The first part of the presentation will focus on the ERA-20C production, provide an overview of its main characteristics and discuss some of the key results from its assessment. The second part of the talk will give an overview of ERA5, and briefly discuss some of its challenges.

Modified enhanced recovery after surgery (ERAS) protocols for patients with obstructive colorectal cancer.

Science.gov (United States)

Shida, Dai; Tagawa, Kyoko; Inada, Kentaro; Nasu, Keiichi; Seyama, Yasuji; Maeshiro, Tsuyoshi; Miyamoto, Sachio; Inoue, Satoru; Umekita, Nobutaka

2017-02-16

Enhanced recovery after surgery (ERAS) protocols are now well-known to be useful for elective colorectal surgery, as they result in shorter hospital stays without adversely affecting morbidity. However, the efficacy and safety of ERAS protocols for patients with obstructive colorectal cancer have yet to be clarified. We evaluated 122 consecutive resections for obstructive colorectal cancer performed between July 2008 and November 2012 at Tokyo Metropolitan Bokutoh Hospital. Patients with rupture or impending rupture and those who received simple colostomy were excluded. The first set of 42 patients was treated based on traditional protocols, and the latter 80 according to modified ERAS protocols. The main endpoints were length of postoperative hospital stay, postoperative short-term morbidity, rate of readmission within 30 days, and mortality. Differences in modified ERAS protocols relative to traditional care include intensive preoperative counseling (by both surgeons and anesthesiologists), perioperative fluid management (avoidance of sodium/fluid overload), shortening of postoperative fasting period and early provision of oral nutrition, intraoperative warm air body heating, enforced postoperative mobilization, stimulation of gut motility, early removal of urinary catheter, and a multidisciplinary team approach to care. Median (interquartile range) postoperative hospital stay was 10 (10-14.25) days in the traditional group, and seven (7-8.75) days in the ERAS group, showing a 3-day reduction in hospital stay (p < 0.01). According to the Clavien-Dindo classification, overall incidences of grade 2 or higher postoperative complications for the traditional and ERAS groups were 15 and 10% (p = 0.48), and 30-day readmission rates were 0 and 1.3% (p = 1.00), respectively. As for mortality, one patient in the traditional group died and none in the ERAS group (p = 0.34). Modified ERAS protocols for obstructive colorectal cancer reduced hospital stay

Nanobody®-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites

Science.gov (United States)

Nguyen-Duc, Trong; Peeters, Eveline; Muyldermans, Serge; Charlier, Daniel; Hassanzadeh-Ghassabeh, Gholamreza

2013-01-01

Nanobodies® are single-domain antibody fragments derived from camelid heavy-chain antibodies. Because of their small size, straightforward production in Escherichia coli, easy tailoring, high affinity, specificity, stability and solubility, nanobodies® have been exploited in various biotechnological applications. A major challenge in the post-genomics and post-proteomics era is the identification of regulatory networks involving nucleic acid–protein and protein–protein interactions. Here, we apply a nanobody® in chromatin immunoprecipitation followed by DNA microarray hybridization (ChIP-chip) for genome-wide identification of DNA–protein interactions. The Lrp-like regulator Ss-LrpB, arguably one of the best-studied specific transcription factors of the hyperthermophilic archaeon Sulfolobus solfataricus, was chosen for this proof-of-principle nanobody®-assisted ChIP. Three distinct Ss-LrpB-specific nanobodies®, each interacting with a different epitope, were generated for ChIP. Genome-wide ChIP-chip with one of these nanobodies® identified the well-established Ss-LrpB binding sites and revealed several unknown target sequences. Furthermore, these ChIP-chip profiles revealed auxiliary operator sites in the open reading frame of Ss-lrpB. Our work introduces nanobodies® as a novel class of affinity reagents for ChIP. Taking into account the unique characteristics of nanobodies®, in particular, their short generation time, nanobody®-based ChIP is expected to further streamline ChIP-chip and ChIP-Seq experiments, especially in organisms with no (or limited) possibility of genetic manipulation. PMID:23275538

Post-hypothermia fever is associated with increased mortality after out-of-hospital cardiac arres

DEFF Research Database (Denmark)

Bro-Jeppesen, John; Hassager, Christian; Wanscher, Michael

2013-01-01

Post-cardiac arrest fever has been associated with adverse outcome before implementation of therapeutic hypothermia (TH), however the prognostic implications of post-hypothermia fever (PHF) in the era of modern post-resuscitation care including TH has not been thoroughly investigated. The aim...

Analysis of the a genome genetic diversity among brassica napus, b. rapa and b. juncea accessions using specific simple sequence repeat markers

International Nuclear Information System (INIS)

Tian, H.; Yan, J.; Zhang, R.; Guo, Y.; Hu, S.; Channa, S.A.

2017-01-01

This investigation was aimed at evaluating the genetic diversity of 127 accessions among Brassica napus, B. rapa, and B. juncea by using 15 pairs of the A genome specific simple sequence repeat primers. These 127 accessions could be clearly separated into three groups by cluster analysis, principal component analysis, and population structure analysis separately, and the results analyzed by the three methods were very similar. Group I comprised of mainly B. napus accessions and the most of B. juncea accessions formed Group II, Group III included nearly all of the B. rapa accessions. The result showed that 36.86% of the variance was due to significant differences among populations of species, indicated that abundance genetic diversity existed among the A genome of B. napus, B. rapa, and B. juncea accessions. B. napus, B. rapa, and B. juncea have the abundant genetic diversity in the A genome, and some elite genes can be used to broaden the genetic base of them, especially for B. napus, in future rapeseed breeding program. (author)

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

Interpretation of Genomic Data Questions and Answers

Science.gov (United States)

Simon, Richard

2008-01-01

Using a question and answer format we describe important aspects of using genomic technologies in cancer research. The main challenges are not managing the mass of data, but rather the design, analysis and accurate reporting of studies that result in increased biological knowledge and medical utility. Many analysis issues address the use of expression microarrays but are also applicable to other whole genome assays. Microarray based clinical investigations have generated both unrealistic hyperbole and excessive skepticism. Genomic technologies are tremendously powerful and will play instrumental roles in elucidating the mechanisms of oncogenesis and in devlopingan era of predictive medicine in which treatments are tailored to individual tumors. Achieving these goals involves challenges in re-thinking many paradigms for the conduct of basic and clinical cancer research and for the organization of interdisciplinary collaboration. PMID:18582627

Challenges and Opportunities in Genome-Wide Environmental Interaction (GWEI) studies

Science.gov (United States)

Aschard, Hugues; Lutz, Sharon; Maus, Bärbel; Duell, Eric J.; Fingerlin, Tasha; Chatterjee, Nilanjan; Kraft, Peter; Van Steen, Kristel

2012-01-01

The interest in performing gene-environment interaction studies has seen a significant increase with the increase of advanced molecular genetics techniques. Practically, it became possible to investigate the role of environmental factors in disease risk and hence to investigate their role as genetic effect modifiers. The understanding that genetics is important in the uptake and metabolism of toxic substances is an example of how genetic profiles can modify important environmental risk factors to disease. Several rationales exist to set up gene-environment interaction studies and the technical challenges related to these studies – when the number of environmental or genetic risk factors is relatively small – has been described before. In the post-genomic era, it is now possible to study thousands of genes and their interaction with the environment. This brings along a whole range of new challenges and opportunities. Despite a continuing effort in developing efficient methods and optimal bioinformatics infrastructures to deal with the available wealth of data, the challenge remains how to best present and analyze Genome-Wide Environmental Interaction (GWEI) studies involving multiple genetic and environmental factors. Since GWEIs are performed at the intersection of statistical genetics, bioinformatics and epidemiology, usually similar problems need to be dealt with as for Genome-Wide Association gene-gene Interaction (GWAI) studies. However, additional complexities need to be considered which are typical for large-scale epidemiological studies, but are also related to “joining” two heterogeneous types of data in explaining complex disease trait variation or for prediction purposes. PMID:22760307

From simple to supercomplex: mitochondrial genomes of euglenozoan protists

Czech Academy of Sciences Publication Activity Database

Faktorová, Drahomíra; Dobáková, Eva; Peña-Diaz, Priscila; Lukeš, Julius

2016-01-01

Roč. 5, 15 NOV (2016), č. článku 392. ISSN 2046-1402 R&D Projects: GA ČR GA15-21974S Institutional support: RVO:60077344 Keywords : euglenozoa * mitochondria * mitochondrial genome Subject RIV: EB - Genetics ; Molecular Biology

Disease management in the genomics era - Summaries of focus issue papers

Science.gov (United States)

The genomics revolution has contributed enormously to research and disease management applications in plant pathology. This development has rapidly increased our understanding of the molecular mechanisms underpinning pathogenesis and resistance, contributed novel markers for rapid pathogen detectio...

Post Thawing Sperm Quality and Ca+2 Intensity Characters of Local Goat Sperm After Freezing by Simple Method Using Deep Freezing

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Gatot Ciptadi

2018-02-01

Full Text Available The objective of this research was to determine the effect of the simple modified freezing method, 1°C/minute freezing rate with different diluter ration on a post-thawing quality of local goat sperm namely Peranakan Etawah (PE. This work is aimed to study the quality of post-thawing sperm and to characterize the calcium intensity profile of both fresh and post thawing goat sperm. The method used is the experimental design of a laboratory. Freezing semen was performed in 2 main temperatures of -45°C then -196°C respectively using Mr. Frosty (® System. Early Sperm characters of Ca+2 intensity was performed by Confocal Laser Scanning Microscope (CLSM through Fluo-3 staining and Ca++ intensity was analysis descriptively. The result showed that post-thawing qualities are considered as good as standard qualities, at least, more than 40% based on Indonesian National Standard (SNI, 2014. The different level diluents commercial of Andromeda used were influenced highly significant (P<0.01. The best diluents ration is 1:4 (v/v for final sperms stocked at -196°C. However freezing sperm conserved in -196°C is better than in -45°C. Meanwhile, the sperm characters of two condition showed the important variation of Ca+2 intensity, with the length of region measurement of 39.06±4.595 and 32.696±9.011 µm each.  It was concluded that the calcium intensity pattern was varied more and higher in fresh sperm than in freezing sperms. This simple modified method of a freezing system was considered as a feasible alternative method for goat semen in a reason for both for sperm post-thawing quality and practical purposes.

Politics of a Different Kind: Chinese in Immigration Litigation in the Post White Australia Era

Directory of Open Access Journals (Sweden)

Jia Gao

2011-04-01

Full Text Available The first mass Chinese immigration to Australia occurred in the 19th century, with approximately 100,000 Chinese arriving between the 1840s and 1901 (Fitzgerald 2007; Ho 2007, during which questions were raised both in relation to the Chinese rights of migration and settlement in Australia, and the validity of the government's actions against the Chinese. The latter question was in fact considered in the colonial courts (Cronin 1993; Lake and Reynolds 2008. Since then, the Chinese in Australia have never shied away from taking various legal actions, although they are normally seen as people who keep to themselves. Australia abandoned its 'White Australia' policy in 1974, and lately Australia has placed more emphasis on skilled and business migration. As a result, many believe that Chinese migrants have come to Australia under its normal skilled, business or family migration programs, which ignores the fact that a high proportion of them have obtained their chance to stay in Australia directly or indirectly through a series of legal battles. This paper contributes to the discussion of the Chinese in Australian political life by looking at how the Chinese have fought in the Courts in the post-White Australia era in past decades, and the key features of their unique experiences. This is a different type of political activism, characterising the lives of many Australian Chinese, their engagement with the Australian political system, and becoming part of the background of their identity, transnationality, socio-political attitudes and behaviour and many other traits.

Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast

Directory of Open Access Journals (Sweden)

Simon M. Dittami

2017-11-01

Full Text Available Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast.

Using systematized tacit knowledge to prioritize implementation challenges in existing maternal health programs: implications for the post MDG era.

Science.gov (United States)

Becerril-Montekio, Victor; Alcalde-Rabanal, Jacqueline; Darney, Blair G; Orozco-Nuñez, Emanuel

2016-10-01

Strategic priority setting and implementation of strategies to reduce maternal mortality are key to the post Millennium Development Goal (MDG) 2015 agenda. This article highlights the feasibility and the advantages of using a systematized tacit knowledge approach, using data from maternal health program personnel, to identify local challenges to implementing policies and programs to inform the post MDG era. Communities of practice, conceived as groups of people sharing professional interests, experiences and knowledge, were formed with diverse health personnel implementing maternal health programs in Mexico and Nicaragua. Participants attended several workshops and developed different online activities aiming to strengthen their capacities to acquire, analyze, adapt and apply research results and to systematize their experience and knowledge of the actual implementation of these programs. Concept mapping, a general method designed to organize and depict the ideas of a group on a particular topic, was used to manage, discuss and systematize their tacit knowledge about implementation problems of the programs they work in. Using a special online concept mapping platform, participants prioritized implementation problems by sorting them in conceptual clusters and rating their importance and feasibility of solution. Two hundred and thirty-one participants from three communities of practice in each country registered on the online concept mapping platform and 200 people satisfactorily completed the sorting and rating activities. Participants further discussed these results to prioritize the implementation problems of maternal health programs. Our main finding was a great similarity between the Mexican and the Nicaraguan general results highlighting the importance and the feasibility of solution of implementation problems related to the quality of healthcare. The use of rigorously organized tacit knowledge of health personnel proved to be a feasible and useful tool for

Pengaruh Tipografi pada Era Massimo Vignelli terhadap Tipografi Michael Bierut

Directory of Open Access Journals (Sweden)

Irwan Harnoko

2011-10-01

Full Text Available Massimo Vignelli is a senior graphic designer lived in New York, as a vocal modernism against post-modernism. His statement firmly opposing post-modernism in several occasions: interview in Helvetica the movie, typeradio, talkshow, and some articles in Looking Closer or AIGA Journal. Graphic design works of Massimo Vignelli reflected his characteristic, which is firmly choosing typeface. Typefaces of Vignelly are around 5 typefaces: Bodoni, Helvetica, Times Roman, Century, and Futura. The article uses formal analysis method. The writers collected materials about Michael Bierut, Massimo VIgnelli and Tibor Kalman from books and websites. The writers compare the typeface opinion of Massimo Vignelli (modernism designer, Michael Bierut designer (transition era designer from modernism to post-modernism, and Tibor Kalman (a designer in A Century of Graphic Design, as the influencer of Bierut’s betrayal over Vignelli. 

Journal of Chemical Sciences | Indian Academy of Sciences

Indian Academy of Sciences (India)

In the post-genomic era, as more and more genome sequences are becoming known and hectic efforts are underway to decode the information content in them, it is becoming increasingly evident that flexibility in proteins plays a crucial role in many of the biological functions. Many proteins have intrinsic disorder either ...

Chromosomal Speciation in the Genomics Era: Disentangling Phylogenetic Evolution of Rock-wallabies.

Science.gov (United States)

Potter, Sally; Bragg, Jason G; Blom, Mozes P K; Deakin, Janine E; Kirkpatrick, Mark; Eldridge, Mark D B; Moritz, Craig

2017-01-01

The association of chromosome rearrangements (CRs) with speciation is well established, and there is a long history of theory and evidence relating to "chromosomal speciation." Genomic sequencing has the potential to provide new insights into how reorganization of genome structure promotes divergence, and in model systems has demonstrated reduced gene flow in rearranged segments. However, there are limits to what we can understand from a small number of model systems, which each only tell us about one episode of chromosomal speciation. Progressing from patterns of association between chromosome (and genic) change, to understanding processes of speciation requires both comparative studies across diverse systems and integration of genome-scale sequence comparisons with other lines of evidence. Here, we showcase a promising example of chromosomal speciation in a non-model organism, the endemic Australian marsupial genus Petrogale . We present initial phylogenetic results from exon-capture that resolve a history of divergence associated with extensive and repeated CRs. Yet it remains challenging to disentangle gene tree heterogeneity caused by recent divergence and gene flow in this and other such recent radiations. We outline a way forward for better integration of comparative genomic sequence data with evidence from molecular cytogenetics, and analyses of shifts in the recombination landscape and potential disruption of meiotic segregation and epigenetic programming. In all likelihood, CRs impact multiple cellular processes and these effects need to be considered together, along with effects of genic divergence. Understanding the effects of CRs together with genic divergence will require development of more integrative theory and inference methods. Together, new data and analysis tools will combine to shed light on long standing questions of how chromosome and genic divergence promote speciation.

Impact of genomics on the field of probiotic research: historical perspectives to modern paradigms.

Science.gov (United States)

Johnson, Brant R; Klaenhammer, Todd R

2014-07-01

For thousands of years, humans have safely consumed microorganisms through fermented foods. Many of these bacteria are considered probiotics, which act through diverse mechanisms to confer a health benefit to the host. However, it was not until the availability of whole-genome sequencing and the era of genomics that mechanisms of probiotic efficacy could be discovered. In this review, we explore the history of the probiotic concept and the current standard of integrated genomic techniques to discern the complex, beneficial relationships between probiotic microbes and their hosts.

Molecular target discovery for neural repair in the functional genomics era

NARCIS (Netherlands)

Verhaagen, J.; van Kesteren, R.E.; Bossers, K.A.; Mac Gillavry, H.D.; Mason, M.R.; Smit, A.B.

2012-01-01

A comprehensive understanding of the molecular pathways activated by traumatic neural injury is of major importance for the development of treatments for spinal cord injury (SCI). High-throughput gene expression profiling is a powerful approach to reveal genome-wide changes in gene expression during

Genome wide characterization of simple sequence repeats in watermelon genome and their application in comparative mapping and genetic diversity analysis.

Science.gov (United States)

Zhu, Huayu; Song, Pengyao; Koo, Dal-Hoe; Guo, Luqin; Li, Yanman; Sun, Shouru; Weng, Yiqun; Yang, Luming

2016-08-05

Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. A total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis

in silico Whole Genome Sequencer & Analyzer (iWGS): a computational pipeline to guide the design and analysis of de novo genome sequencing studies

Science.gov (United States)

The availability of genomes across the tree of life is highly biased toward vertebrates, pathogens, human disease models, and organisms with relatively small and simple genomes. Recent progress in genomics has enabled the de novo decoding of the genome of virtually any organism, greatly expanding it...

[Werner Leibbrand, Annemarie Wettley and controversies on "euthanasia" the background of medico-historical and ethical debates in the Post World War II era].

Science.gov (United States)

Wiesinger, Christine; Frewer, Andreas

2014-01-01

Psychiatrists and medical historians Werner Leibbrand (1896 - 1974) and Annemarie Wettley (1913 - 1996) are amongst the most striking figures in the field of history of medicine. Leibbrand was appointed director of the "Heil- und Pflegeanstalt" in Erlangen shortly after the war. Fuelled by his own experiences of suppression and persecution during the Nazi era he promised to unearth the crimes and atrocities which had happened under watch of the Nazi regime. He was joined by Annemarie Wettley, who worked as a physician at the hospital and had developed an increasing interest in the history of medicine. In 1946 they published "Um die Menschenrechte der Geisteskranken" ("Human Rights of the Mentally Ill") about the "euthanasia" campaign of the Nazi regime. Although a number of substantial works followed, Leibbrand and Wettley failed to inform in more depth on crimes and atrocities, for instance killings of patients and forced malnutrition. Doubts and charges against Wettley regarding her role in dietary programmes at the Erlangen hospital and against Leibbrand regarding special expert's reports--both had a short-term arrest warrant--might have contributed to stagnation in their efforts. In 1953 Leibbrand accepted the offer of a chair at the University in Munich, Wettley followed and habilitated in history of medicine; in the year 1962 they married. Contacts and exchange amongst medico-historical experts shed light on developments during the post-war era; still, a critical and fundamental review of the crimes within the medical system of the Nazi regime did not take place during this time.

Bacterial genome engineering and synthetic biology: combating pathogens.

Science.gov (United States)

Krishnamurthy, Malathy; Moore, Richard T; Rajamani, Sathish; Panchal, Rekha G

2016-11-04

The emergence and prevalence of multidrug resistant (MDR) pathogenic bacteria poses a serious threat to human and animal health globally. Nosocomial infections and common ailments such as pneumonia, wound, urinary tract, and bloodstream infections are becoming more challenging to treat due to the rapid spread of MDR pathogenic bacteria. According to recent reports by the World Health Organization (WHO) and Centers for Disease Control and Prevention (CDC), there is an unprecedented increase in the occurrence of MDR infections worldwide. The rise in these infections has generated an economic strain worldwide, prompting the WHO to endorse a global action plan to improve awareness and understanding of antimicrobial resistance. This health crisis necessitates an immediate action to target the underlying mechanisms of drug resistance in bacteria. The advent of new bacterial genome engineering and synthetic biology (SB) tools is providing promising diagnostic and treatment plans to monitor and treat widespread recalcitrant bacterial infections. Key advances in genetic engineering approaches can successfully aid in targeting and editing pathogenic bacterial genomes for understanding and mitigating drug resistance mechanisms. In this review, we discuss the application of specific genome engineering and SB methods such as recombineering, clustered regularly interspaced short palindromic repeats (CRISPR), and bacterial cell-cell signaling mechanisms for pathogen targeting. The utility of these tools in developing antibacterial strategies such as novel antibiotic production, phage therapy, diagnostics and vaccine production to name a few, are also highlighted. The prevalent use of antibiotics and the spread of MDR bacteria raise the prospect of a post-antibiotic era, which underscores the need for developing novel therapeutics to target MDR pathogens. The development of enabling SB technologies offers promising solutions to deliver safe and effective antibacterial therapies.

Genomics-based plant germplasm research (GPGR)

Institute of Scientific and Technical Information of China (English)

Jizeng Jia; Hongjie Li; Xueyong Zhang; Zichao Li; Lijuan Qiu

2017-01-01

Plant germplasm underpins much of crop genetic improvement. Millions of germplasm accessions have been collected and conserved ex situ and/or in situ, and the major challenge is now how to exploit and utilize this abundant resource. Genomics-based plant germplasm research (GPGR) or "Genoplasmics" is a novel cross-disciplinary research field that seeks to apply the principles and techniques of genomics to germplasm research. We describe in this paper the concept, strategy, and approach behind GPGR, and summarize current progress in the areas of the definition and construction of core collections, enhancement of germplasm with core collections, and gene discovery from core collections. GPGR is opening a new era in germplasm research. The contribution, progress and achievements of GPGR in the future are predicted.

Post-Structuralism and Ethical Practical Action: Issues of Identity and Power

Science.gov (United States)

Walshaw, Margaret

2013-01-01

In an era when familiar categories of identity are breaking down, an argument is made for using post-structuralist vocabulary to talk about ethical practical action in mathematics education. Using aspects of Foucault's post-structuralism, an explanation is offered of how mathematical identifications are tied to the social organization of power. An…

Genetic gatekeepers: regulating direct-to-consumer genomic services in an era of participatory medicine.

Science.gov (United States)

Palmer, Jessica Elizabeth

2012-01-01

Should consumers be able to obtain information about their own bodies, even if it has no proven medical value? Direct-to-consumer ("DTC") genomic companies offer consumers two services: generation of the consumer's personal genetic sequence, and interpretation of that sequence in light of current research. Concerned that consumers will misunderstand genomic information and make ill-advised health decisions, regulators, legislators and scholars have advocated restricted access to DTC genomic services. The Food and Drug Administration, which has historically refrained from regulating most genetic tests, has announced its intent to treat DTC genomic services as medical devices because they make "medical claims." This Article argues that FDA regulation of genomic services as medical devices would be counterproductive. Clinical laboratories conducting genetic tests are already overseen by a federal regime administered by the Centers for Medicare and Medicaid Services. While consumers and clinicians would benefit from clearer communication of test results and their health implications, FDA's gatekeeping framework is ill-suited to weigh the safety and efficacy of genomic information that is not medically actionable in traditional ways. Playing gatekeeper would burden FDA's resources, conflict with the patient-empowering policies promoted by personalized medicine initiatives, impair individuals' access to information in which they have powerful autonomy interests, weaken novel participatory research infrastructures, and set a poor precedent for the future regulation of medical information. Rather than applying its risk-based regulatory framework to genetic information, FDA should ameliorate regulatory uncertainty by working with the Federal Trade Commission and Centers for Medicare and Medicaid Services to ensure that DTC genomic services deliver analytically valid data, market and implement their services in a truthful manner, and fully disclose the limitations of their

Practical cryptographic strategies in the post-quantum era

Science.gov (United States)

Kabanov, I. S.; Yunusov, R. R.; Kurochkin, Y. V.; Fedorov, A. K.

2018-02-01

Quantum key distribution technologies promise information-theoretic security and are currently being deployed in com-mercial applications. We review new frontiers in information security technologies in communications and distributed storage applications with the use of classical, quantum, hybrid classical-quantum, and post-quantum cryptography. We analyze the cur-rent state-of-the-art, critical characteristics, development trends, and limitations of these techniques for application in enterprise information protection systems. An approach concerning the selection of practical encryption technologies for enterprises with branched communication networks is discussed.

Databases and web tools for cancer genomics study.

Science.gov (United States)

Yang, Yadong; Dong, Xunong; Xie, Bingbing; Ding, Nan; Chen, Juan; Li, Yongjun; Zhang, Qian; Qu, Hongzhu; Fang, Xiangdong

2015-02-01

Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience. The resources reviewed include data repository and analysis tools; and we hope such introduction will promote the awareness and facilitate the usage of these resources in the cancer research community. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Pengembangan Media Destinasi Pariwisata: Memanfaatkan Potensi dan Sumber Daya Lokal di Era Otonomi dan Pemekaran Daerah

Directory of Open Access Journals (Sweden)

Yosafati Hulu

2012-06-01

Full Text Available Concerning about: (1 an increase in regional demand (government and community in developing tourism destinations in the era of autonomy and separation, (2 the needs of tourists to choose the right attraction in accordance with their respective criteria, and (3 the needs of employers to offer sights of interest in accordance with the needs of potential tourists, a media is needed to be developed that can facilitate those needs. It is a web-based software system that can store and show tourist destinations of Indonesia in a comprehensive, systematic, and structured way. Besides, it can classify the various attractions based on attributes, such as: location (name of the island, province, district, tourism type/product, how to go to those objects, cost, and also another variety of informal information, such as: the ins and outs of the attraction area posted by the local community or travel experiences posted by tourists. The first phase will focus on a database system that enables local governments and local communities retain information attractions and products systematically and structurally so that potential tourists can find them easily through a simple search method. The database system is then a basis og other information that will be built on further research needs such as: Data Warehouse System, Decision Support System, and Expert System for Indonesia's tourism industry.

Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae.

Science.gov (United States)

Boo, Ga Hun; Hughey, Jeffery R; Miller, Kathy Ann; Boo, Sung Min

2016-10-14

DNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43-44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution.

Agrobacterium-mediated transformation as a tool for functional genomics in fungi

NARCIS (Netherlands)

Michielse, C.B.; Hooykaas, P.J.J.; Hondel, C.A.M.J.J. van den; Ram, A.F.J.

2005-01-01

In the era of functional genomics, the need for tools to perform large-scale targeted and random mutagenesis is increasing. A potential tool is Agrobacterium-mediated fungal transformation. A. tumefaciens is able to transfer a part of its DNA (transferred DNA; T-DNA) to a wide variety of fungi and

O desafio da malária: o caso brasileiro e o que se pode esperar dos progressos da era genômica The malaria challenge: the Brazilian case and what can be expected from progress in genomics

Directory of Open Access Journals (Sweden)

Luiz Hildebrando Pereira da Silva

2002-01-01

Full Text Available A área endêmica de malária no Brasil se estende atualmente à totalidade da região amazônica, com cerca de 500 mil casos anuais, em geral com situações de baixa e média endemicidade mas ainda apresentando focos de alto risco. Fatores demográficos e socioeconômicos são dominantes nos desafios que enfrentam os Serviços de Saúde Pública no controle da malária. No presente artigo são discutidos fatores determinantes da instabilidade da situação endêmica bem como a necessidade de ações permanentes de vigilância e de intervenção dos Serviços de Saúde para que se evitem surtos epidêmicos e alastramento das áreas endêmicas. No artigo, em seguida, apresenta-se uma síntese de progressos recentes nos estudos da era genômica e pós-genômica sobre o parasita, o vetor e o hospedeiro humano que podem favorecer, no futuro, o desenvolvimento e a melhoria dos métodos de controle da malária.Malaria endemic areas in Brazil are restricted to the Amazon Region, with an average of 500 thousand new cases every year. The situation can be defined as unstable hipoendemic with, however, foci of high endemicity. Demographic and socio economic factors are main determinants in the malaria challenge for the Public Health System. In the present paper, biological and social factors responsible for the unstable endemic situation are discussed. The need for a permanent surveillance and intervention of Public Health Services are stressed to avoid the occurrence of local epidemics and spreading of endemic areas. In the paper, are also summarised recent lines of research developed in the post genomic era in the studies of parasite, vector and human molecular genetics that would favour the development, in the future, of new tools and procedures for malaria control

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.

A Roadmap for Tick-Borne Flavivirus Research in the “Omics” Era

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Jeffrey M. Grabowski

2017-12-01

Full Text Available Tick-borne flaviviruses (TBFs affect human health globally. Human vaccines provide protection against some TBFs, and antivirals are available, yet TBF-specific control strategies are limited. Advances in genomics offer hope to understand the viral complement transmitted by ticks, and to develop disruptive, data-driven technologies for virus detection, treatment, and control. The genome assemblies of Ixodes scapularis, the North American tick vector of the TBF, Powassan virus, and other tick vectors, are providing insights into tick biology and pathogen transmission and serve as nucleation points for expanded genomic research. Systems biology has yielded insights to the response of tick cells to viral infection at the transcript and protein level, and new protein targets for vaccines to limit virus transmission. Reverse vaccinology approaches have moved candidate tick antigenic epitopes into vaccine development pipelines. Traditional drug and in silico screening have identified candidate antivirals, and target-based approaches have been developed to identify novel acaricides. Yet, additional genomic resources are required to expand TBF research. Priorities include genome assemblies for tick vectors, “omic” studies involving high consequence pathogens and vectors, and emphasizing viral metagenomics, tick-virus metabolomics, and structural genomics of TBF and tick proteins. Also required are resources for forward genetics, including the development of tick strains with quantifiable traits, genetic markers and linkage maps. Here we review the current state of genomic research on ticks and tick-borne viruses with an emphasis on TBFs. We outline an ambitious 10-year roadmap for research in the “omics era,” and explore key milestones needed to accomplish the goal of delivering three new vaccines, antivirals and acaricides for TBF control by 2030.

Using Genome Sequence to Enable the Design of Medicines and Chemical Probes.

Science.gov (United States)

Angelbello, Alicia J; Chen, Jonathan L; Childs-Disney, Jessica L; Zhang, Peiyuan; Wang, Zi-Fu; Disney, Matthew D

2018-02-28

Rapid progress in genome sequencing technology has put us firmly into a postgenomic era. A key challenge in biomedical research is harnessing genome sequence to fulfill the promise of personalized medicine. This Review describes how genome sequencing has enabled the identification of disease-causing biomolecules and how these data have been converted into chemical probes of function, preclinical lead modalities, and ultimately U.S. Food and Drug Administration (FDA)-approved drugs. In particular, we focus on the use of oligonucleotide-based modalities to target disease-causing RNAs; small molecules that target DNA, RNA, or protein; the rational repurposing of known therapeutic modalities; and the advantages of pharmacogenetics. Lastly, we discuss the remaining challenges and opportunities in the direct utilization of genome sequence to enable design of medicines.

Romanian spa tourism: a communist paradigm in a post communist era

Directory of Open Access Journals (Sweden)

George Erdeli

2011-11-01

Full Text Available Spa tourism is one of the oldest forms of tourism which continuously evolved in time as the leisure industry paradigm and the consumers’ behavior changed. Similar to other countries in Central and Eastern Europe, spa tourism is an old phenomenon in Romania which expanded to the dimensions of a well defined tourism industry during the mass tourism period which also corresponded to the communism epoch. Although severely affected by the major political and socio-economic changes which occurred after the Revolution in 1989, this industry coexists with new emergent forms of tourism orienting, itself towards new dimensions embraced by the contemporary leisure consumerism (e.g. medical tourism, cosmetic treatments. Lying on considerable balneal and climate resources and displaying an important communist heritage both in physical terms (large and massive tourism structures and in virtual and psychological terms (social supportive ticket granting system, Romanian spa tourism faces various challenges in the attempt to adapt in a new tourism era.

Public Health Genomics education in post-graduate schools of hygiene and preventive medicine: a cross-sectional survey.

Science.gov (United States)

Ianuale, Carolina; Leoncini, Emanuele; Mazzucco, Walter; Marzuillo, Carolina; Villari, Paolo; Ricciardi, Walter; Boccia, Stefania

2014-10-10

The relevance of Public Health Genomics (PHG) education among public health specialists has been recently acknowledged by the Association of Schools of Public Health in the European Region. The aim of this cross-sectional survey was to assess the prevalence of post-graduate public health schools for medical doctors which offer PHG training in Italy. The directors of the 33 Italian public health schools were interviewed for the presence of a PHG course in place. We stratified by geographical area (North, Centre and South) of the schools. We performed comparisons of categorical data using the chi-squared test. The response rate was 73% (24/33 schools). Among respondents, 15 schools (63%) reported to have at least one dedicated course in place, while nine (38%) did not, with a significant geographic difference. Results showed a good implementation of courses in PHG discipline in Italian post-graduate public health schools. However further harmonization of the training programs of schools in public health at EU level is needed.

The forthcoming era of precision medicine.

Science.gov (United States)

Gamulin, Stjepan

2016-11-01

The aim of this essay is to present the definition and principles of personalized or precision medicine, the perspective and barriers to its development and clinical application. The implementation of precision medicine in health care requires the coordinated efforts of all health care stakeholders (the biomedical community, government, regulatory bodies, patients' groups). Particularly, translational research with the integration of genomic and comprehensive data from all levels of the organism ("big data"), development of bioinformatics platforms enabling network analysis of disease etiopathogenesis, development of a legislative framework for handling personal data, and new paradigms of medical education are necessary for successful application of the concept of precision medicine in health care. In the present and future era of precision medicine, the collaboration of all participants in health care is necessary for its realization, resulting in improvement of diagnosis, prevention and therapy, based on a holistic, individually tailored approach. Copyright © 2016 by Academy of Sciences and Arts of Bosnia and Herzegovina.

The forthcoming era of precision medicine

Directory of Open Access Journals (Sweden)

Stjepan Gamulin

2016-11-01

Full Text Available Abstract. The aim of this essay is to present the definition and principles of personalized or precision medicine, the perspective and barriers to its development and clinical application. The implementation of precision medicine in health care requires the coordinated efforts of all health care stakeholders (the biomedical community, government, regulatory bodies, patients’ groups. Particularly, translational research with the integration of genomic and comprehensive data from all levels of the organism (“big data”, development of bioinformatics platforms enabling network analysis of disease etiopathogenesis, development of a legislative framework for handling personal data, and new paradigms of medical education are necessary for successful application of the concept of precision medicine in health care. Conclusion. In the present and future era of precision medicine, the collaboration of all participants in health care is necessary for its realization, resulting in improvement of diagnosis, prevention and therapy, based on a holistic, individually tailored approach.

A model for C-14 tracer evaporative rate analysis (ERA)

International Nuclear Information System (INIS)

Gardner, R.P.; Verghese, K.

1993-01-01

A simple model has been derived and tested for the C-14 tracer evaporative rate analysis (ERA) method. It allows the accurate determination of the evaporative rate coefficient of the C-14 tracer detector in the presence of variable evaporation rates of the detector solvent and variable background counting rates. The evaporation rate coefficient should be the most fundamental parameter available in this analysis method and, therefore, its measurements with the proposed model should allow the most direct correlations to be made with the system properties of interest such as surface cleanliness. (author)

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.

Ethnobotany genomics - discovery and innovation in a new era of exploratory research

Directory of Open Access Journals (Sweden)

Ragupathy Subramanyam

2010-01-01

Full Text Available Abstract We present here the first use of DNA barcoding in a new approach to ethnobotany we coined "ethnobotany genomics". This new approach is founded on the concept of 'assemblage' of biodiversity knowledge, which includes a coming together of different ways of knowing and valorizing species variation in a novel approach seeking to add value to both traditional knowledge (TK and scientific knowledge (SK. We employed contemporary genomic technology, DNA barcoding, as an important tool for identifying cryptic species, which were already recognized ethnotaxa using the TK classification systems of local cultures in the Velliangiri Hills of India. This research is based on several case studies in our lab, which define an approach to that is poised to evolve quickly with the advent of new ideas and technology. Our results show that DNA barcoding validated several new cryptic plant species to science that were previously recognized by TK classifications of the Irulas and Malasars, and were lumped using SK classification. The contribution of the local aboriginal knowledge concerning plant diversity and utility in India is considerable; our study presents new ethnomedicine to science. Ethnobotany genomics can also be used to determine the distribution of rare species and their ecological requirements, including traditional ecological knowledge so that conservation strategies can be implemented. This is aligned with the Convention on Biological Diversity that was signed by over 150 nations, and thus the world's complex array of human-natural-technological relationships has effectively been re-organized.

Ethnobotany genomics - discovery and innovation in a new era of exploratory research.

Science.gov (United States)

Newmaster, Steven G; Ragupathy, Subramanyam

2010-01-26

We present here the first use of DNA barcoding in a new approach to ethnobotany we coined "ethnobotany genomics". This new approach is founded on the concept of 'assemblage' of biodiversity knowledge, which includes a coming together of different ways of knowing and valorizing species variation in a novel approach seeking to add value to both traditional knowledge (TK) and scientific knowledge (SK). We employed contemporary genomic technology, DNA barcoding, as an important tool for identifying cryptic species, which were already recognized ethnotaxa using the TK classification systems of local cultures in the Velliangiri Hills of India. This research is based on several case studies in our lab, which define an approach to that is poised to evolve quickly with the advent of new ideas and technology. Our results show that DNA barcoding validated several new cryptic plant species to science that were previously recognized by TK classifications of the Irulas and Malasars, and were lumped using SK classification. The contribution of the local aboriginal knowledge concerning plant diversity and utility in India is considerable; our study presents new ethnomedicine to science. Ethnobotany genomics can also be used to determine the distribution of rare species and their ecological requirements, including traditional ecological knowledge so that conservation strategies can be implemented. This is aligned with the Convention on Biological Diversity that was signed by over 150 nations, and thus the world's complex array of human-natural-technological relationships has effectively been re-organized.

Clinical pharmacogenomics testing in the era of next generation sequencing: challenges and opportunities for precision medicine.

Science.gov (United States)

Ji, Yuan; Si, Yue; McMillin, Gwendolyn A; Lyon, Elaine

2018-04-23

The rapid development and dramatic decrease in cost of sequencing techniques have ushered the implementation of genomic testing in patient care. Next generation DNA sequencing (NGS) techniques have been used increasingly in clinical laboratories to scan the whole or part of the human genome in order to facilitate diagnosis and/or prognostics of genetic disease. Despite many hurdles and debates, pharmacogenomics (PGx) is believed to be an area of genomic medicine where precision medicine could have immediate impact in the near future. Areas covered: This review focuses on lessons learned through early attempts of clinically implementing PGx testing; the challenges and opportunities that PGx testing brings to precision medicine in the era of NGS. Expert commentary: Replacing targeted analysis approach with NGS for PGx testing is neither technically feasible nor necessary currently due to several technical limitations and uncertainty involved in interpreting variants of uncertain significance for PGx variants. However, reporting PGx variants out of clinical whole exome or whole genome sequencing (WES/WGS) might represent additional benefits for patients who are tested by WES/WGS.

A simple method for the parallel deep sequencing of full influenza A genomes

DEFF Research Database (Denmark)

Kampmann, Marie-Louise; Fordyce, Sarah Louise; Avila Arcos, Maria del Carmen

2011-01-01

Given the major threat of influenza A to human and animal health, and its ability to evolve rapidly through mutation and reassortment, tools that enable its timely characterization are necessary to help monitor its evolution and spread. For this purpose, deep sequencing can be a very valuable tool....... This study reports a comprehensive method that enables deep sequencing of the complete genomes of influenza A subtypes using the Illumina Genome Analyzer IIx (GAIIx). By using this method, the complete genomes of nine viruses were sequenced in parallel, representing the 2009 pandemic H1N1 virus, H5N1 virus...

The human Genome project and the future of oncology

International Nuclear Information System (INIS)

Collins, Francis S.

1996-01-01

The Human Genome Project is an ambitious 15-year effort to devise maps and sequence of the 3-billion base pair human genome, including all 100,000 genes. The project is running ahead of schedule and under budget. Already the effects on progress in disease gene discovery have been dramatic, especially for cancer. The most appropriate uses of susceptibility testing for breast, ovarian, and colon cancer are being investigated in research protocols, and the need to prevent genetic discrimination in employment and health insurance is becoming more urgent. In the longer term, these gene discoveries are likely to usher in a new era of therapeutic molecular medicine

Functional genomics unique to week 20 post wounding in the deep cone/fat dome of the Duroc/Yorkshire porcine model of fibroproliferative scarring.

Science.gov (United States)

Engrav, Loren H; Tuggle, Christopher K; Kerr, Kathleen F; Zhu, Kathy Q; Numhom, Surawej; Couture, Oliver P; Beyer, Richard P; Hocking, Anne M; Carrougher, Gretchen J; Ramos, Maria Luiza C; Klein, Matthew B; Gibran, Nicole S

2011-04-20

Hypertrophic scar was first described over 100 years ago; PubMed has more than 1,000 references on the topic. Nevertheless prevention and treatment remains poor, because 1) there has been no validated animal model; 2) human scar tissue, which is impossible to obtain in a controlled manner, has been the only source for study; 3) tissues typically have been homogenized, mixing cell populations; and 4) gene-by-gene studies are incomplete. We have assembled a system that overcomes these barriers and permits the study of genome-wide gene expression in microanatomical locations, in shallow and deep partial-thickness wounds, and pigmented and non-pigmented skin, using the Duroc(pigmented fibroproliferative)/Yorkshire(non-pigmented non-fibroproliferative) porcine model. We used this system to obtain the differential transcriptome at 1, 2, 3, 12 and 20 weeks post wounding. It is not clear when fibroproliferation begins, but it is fully developed in humans and the Duroc breed at 20 weeks. Therefore we obtained the derivative functional genomics unique to 20 weeks post wounding. We also obtained long-term, forty-six week follow-up with the model. 1) The scars are still thick at forty-six weeks post wounding further validating the model. 2) The differential transcriptome provides new insights into the fibroproliferative process as several genes thought fundamental to fibroproliferation are absent and others differentially expressed are newly implicated. 3) The findings in the derivative functional genomics support old concepts, which further validates the model, and suggests new avenues for reductionist exploration. In the future, these findings will be searched for directed networks likely involved in cutaneous fibroproliferation. These clues may lead to a better understanding of the systems biology of cutaneous fibroproliferation, and ultimately prevention and treatment of hypertrophic scarring.

Functional genomics unique to week 20 post wounding in the deep cone/fat dome of the Duroc/Yorkshire porcine model of fibroproliferative scarring.

Directory of Open Access Journals (Sweden)

Loren H Engrav

Full Text Available BACKGROUND: Hypertrophic scar was first described over 100 years ago; PubMed has more than 1,000 references on the topic. Nevertheless prevention and treatment remains poor, because 1 there has been no validated animal model; 2 human scar tissue, which is impossible to obtain in a controlled manner, has been the only source for study; 3 tissues typically have been homogenized, mixing cell populations; and 4 gene-by-gene studies are incomplete. METHODOLOGY/PRINCIPAL FINDINGS: We have assembled a system that overcomes these barriers and permits the study of genome-wide gene expression in microanatomical locations, in shallow and deep partial-thickness wounds, and pigmented and non-pigmented skin, using the Duroc(pigmented fibroproliferative/Yorkshire(non-pigmented non-fibroproliferative porcine model. We used this system to obtain the differential transcriptome at 1, 2, 3, 12 and 20 weeks post wounding. It is not clear when fibroproliferation begins, but it is fully developed in humans and the Duroc breed at 20 weeks. Therefore we obtained the derivative functional genomics unique to 20 weeks post wounding. We also obtained long-term, forty-six week follow-up with the model. CONCLUSIONS/SIGNIFICANCE: 1 The scars are still thick at forty-six weeks post wounding further validating the model. 2 The differential transcriptome provides new insights into the fibroproliferative process as several genes thought fundamental to fibroproliferation are absent and others differentially expressed are newly implicated. 3 The findings in the derivative functional genomics support old concepts, which further validates the model, and suggests new avenues for reductionist exploration. In the future, these findings will be searched for directed networks likely involved in cutaneous fibroproliferation. These clues may lead to a better understanding of the systems biology of cutaneous fibroproliferation, and ultimately prevention and treatment of hypertrophic scarring.

Genome sequence analysis with MonetDB - A case study on Ebola virus diversity

NARCIS (Netherlands)

Cijvat, R.; Manegold, S.; Kersten, M.; Klau, G.W.; Schönhuth, A.; Marschall, T.; Zhang, Y.

2015-01-01

Next-generation sequencing (NGS) technology has led the life sciences into the big data era. Today, sequencing genomes takes little time and cost, but yields terabytes of data to be stored and analyzed. Biologists are often exposed to excessively time consuming and error-prone data management and

Childhood Acute Lymphoblastic Leukemia: Integrating Genomics into Therapy

Science.gov (United States)

Tasian, Sarah K; Loh, Mignon L; Hunger, Stephen P

2015-01-01

Acute lymphoblastic leukemia (ALL), the most common malignancy of childhood, is a genetically complex entity that remains a major cause of childhood cancer-related mortality. Major advances in genomic and epigenomic profiling during the past decade have appreciably enhanced knowledge of the biology of de novo and relapsed ALL and have facilitated more precise risk stratification of patients. These achievements have also provided critical insights regarding potentially targetable lesions for development of new therapeutic approaches in the era of precision medicine. This review delineates the current genetic landscape of childhood ALL with emphasis upon patient outcomes with contemporary treatment regimens, as well as therapeutic implications of newly identified genomic alterations in specific subsets of ALL. PMID:26194091

Evolutionary constraint and disease associations of post-translational modification sites in human genomes.

Directory of Open Access Journals (Sweden)

Jüri Reimand

2015-01-01

Full Text Available Interpreting the impact of human genome variation on phenotype is challenging. The functional effect of protein-coding variants is often predicted using sequence conservation and population frequency data, however other factors are likely relevant. We hypothesized that variants in protein post-translational modification (PTM sites contribute to phenotype variation and disease. We analyzed fraction of rare variants and non-synonymous to synonymous variant ratio (Ka/Ks in 7,500 human genomes and found a significant negative selection signal in PTM regions independent of six factors, including conservation, codon usage, and GC-content, that is widely distributed across tissue-specific genes and function classes. PTM regions are also enriched in known disease mutations, suggesting that PTM variation is more likely deleterious. PTM constraint also affects flanking sequence around modified residues and increases around clustered sites, indicating presence of functionally important short linear motifs. Using target site motifs of 124 kinases, we predict that at least ∼180,000 motif-breaker amino acid residues that disrupt PTM sites when substituted, and highlight kinase motifs that show specific negative selection and enrichment of disease mutations. We provide this dataset with corresponding hypothesized mechanisms as a community resource. As an example of our integrative approach, we propose that PTPN11 variants in Noonan syndrome aberrantly activate the protein by disrupting an uncharacterized cluster of phosphorylation sites. Further, as PTMs are molecular switches that are modulated by drugs, we study mutated binding sites of PTM enzymes in disease genes and define a drug-disease network containing 413 novel predicted disease-gene links.

Use of the Operon Structure of the C. elegans Genome as a Tool to Identify Functionally Related Proteins

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Silvia Dossena

2013-12-01

Full Text Available One of the most pressing challenges in the post genomic era is the identification and characterization of protein-protein interactions (PPIs, as these are essential in understanding the cellular physiology of health and disease. Experimental techniques suitable for characterizing PPIs (X-ray crystallography or nuclear magnetic resonance spectroscopy, among others are usually laborious, time-consuming and often difficult to apply to membrane proteins, and therefore require accurate prediction of the candidate interacting partners. High-throughput experimental methods (yeast two-hybrid and affinity purification succumb to the same shortcomings, and can also lead to high rates of false positive and negative results. Therefore, reliable tools for predicting PPIs are needed. The use of the operon structure in the eukaryote Caenorhabditis elegans genome is a valuable, though underserved, tool for identifying physically or functionally interacting proteins. Based on the concept that genes organized in the same operon may encode physically or functionally related proteins, this algorithm is easy to be applied and, importantly, gives a limited number of candidate partners of a given protein, allowing for focused experimental verification. Moreover, this approach can be successfully used to predict PPIs in the human system, including those of membrane proteins.

CRISPR/Cas9-mediated genome engineering of CHO cell factories: application and perspectives

DEFF Research Database (Denmark)

Lee, Jae Seong; Grav, Lise Marie; Lewis, Nathan E.

2015-01-01

repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system enables rapid,easy and efficient engineering of mammalian genomes. It has a wide range of applications frommodification of individual genes to genome-wide screening or regulation of genes. Facile genomeediting using CRISPR/Cas9 empowers...... researchers in the CHO community to elucidate the mechanisticbasis behind high level production of proteins and product quality attributes of interest. Inthis review, we describe the basis of CRISPR/Cas9-mediated genome editing and its applicationfor development of next generation CHO cell factories while...... highlighting both future perspectivesand challenges. As one of the main drivers for the CHO systems biology era, genome engineeringwith CRISPR/Cas9 will pave the way for rational design of CHO cell factories....

Towards a Post-Antropocene Perspective on the Welfare City

DEFF Research Database (Denmark)

Braae, Ellen Marie; Bøggild, Signe Sophie

2015-01-01

The welfare city with its humanistic, anthropocentric and progressive design ideals of the good life and egalitarianism usually signifies the post-war welfare state’s tabula rasa suburbs with evergreen public landscapes as common ground for public happiness. Inspired by the recent discourse of th...... green heritage’; an umbrella term bridging the gap between perspectives of the anthropocentric, the anthropocene and a possible post-anthropocene era, both challenged and driven by climate change and urbanisation....

Archaeology of the western Saurashtra Coast: Post-urban Harappan era

Digital Repository Service at National Institute of Oceanography (India)

Gaur, A.S.; Sundaresh

The present essay deals with the post-Indus Valley Civilization phase in the context of the settlements along the western Saurashtra Coast, particularly the three sites: Bet Dwarka, Bokhira and Kindar Kheda that were excavated by the National...

Geography, Islands and Migration in an Era of Global Mobility

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Russell King

2009-05-01

Full Text Available This paper examines the changing role of islands in the age of globalization and in an era of enhanced and diversified mobility. There are many types of islands, many metaphors of insularity, and many types of migration, so the interactions are far from simple. The ‘mobilities turn’ in migration studies recognizes the diversification in motivations and time-space regimes of human migration. After brief reviews of island studies and of migration studies, and the power of geography to capture and distil the interdisciplinarity and relationality of these two study domains, the paper explores various facets of the generally intense engagement that islands have with migration. Two particular scenarios are identified for islands and migration in the global era: the heuristic role of islands as ‘spatial laboratories’ for the study of diverse migration processes in microcosm; and the way in which, especially in the Mediterranean and near-Atlantic regions, islands have become critical locations in the geopolitics of irregular migration routes. The case of Malta is taken to illustrate some of these new insular migration dynamics.

Staying alive: rethinking deterritorialization in a post-feminist era.

Science.gov (United States)

Lundberg, Anna

2015-07-01

In recent years, the concept 'post-feminism' and its links to neoliberal economic structures and to the extreme reinforcement of individualization as raison d'etre of Western civilization have been discussed at length by numerous distinguished scholars in feminist cultural studies and feminist philosophy. This article takes its point of departure in this discussion. Drawing on Wendy Brown, Elizabeth Grosz, Angela McRobbie, Wendy Larner, and others, the text is examining the discourse of post-feminism and neoliberalism, and its effects on overarching political scenarios, as well as on everyday life: What happens to feminist politics when the collective, both as figuration and as virtual political platform, is deemed to be something situated in the discursive outskirts? By drawing on examples form the contemporary cultural imaginaries, from popular culture, economic structures, and public debate, and by pointing out the links between the micro-perspective of our everyday living and overarching political structures, this article aims at bringing to the fore and critically discuss these issues, and the ways in which they intersect with contemporary Western feminism. The article ends with a discussion of possible points of exit or paths to follow in order to find alternatives. © 2015 John Wiley & Sons Ltd.

Genomic signals of migration and continuity in Britain before the Anglo-Saxons.

Science.gov (United States)

Martiniano, Rui; Caffell, Anwen; Holst, Malin; Hunter-Mann, Kurt; Montgomery, Janet; Müldner, Gundula; McLaughlin, Russell L; Teasdale, Matthew D; van Rheenen, Wouter; Veldink, Jan H; van den Berg, Leonard H; Hardiman, Orla; Carroll, Maureen; Roskams, Steve; Oxley, John; Morgan, Colleen; Thomas, Mark G; Barnes, Ian; McDonnell, Christine; Collins, Matthew J; Bradley, Daniel G

2016-01-19

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (∼ 1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

Evidence that personal genome testing enhances student learning in a course on genomics and personalized medicine.

Directory of Open Access Journals (Sweden)

Keyan Salari

Full Text Available An emerging debate in academic medical centers is not about the need for providing trainees with fundamental education on genomics, but rather the most effective educational models that should be deployed. At Stanford School of Medicine, a novel hands-on genomics course was developed in 2010 that provided students the option to undergo personal genome testing as part of the course curriculum. We hypothesized that use of personal genome testing in the classroom would enhance the learning experience of students. No data currently exist on how such methods impact student learning; thus, we surveyed students before and after the course to determine its impact. We analyzed responses using paired statistics from the 31 medical and graduate students who completed both pre-course and post-course surveys. Participants were stratified by those who did (N = 23 or did not (N = 8 undergo personal genome testing. In reflecting on the experience, 83% of students who underwent testing stated that they were pleased with their decision compared to 12.5% of students who decided against testing (P = 0.00058. Seventy percent of those who underwent personal genome testing self-reported a better understanding of human genetics on the basis of having undergone testing. Further, students who underwent personal genome testing demonstrated an average 31% increase in pre- to post-course scores on knowledge questions (P = 3.5×10(-6; this was significantly higher (P = 0.003 than students who did not undergo testing, who showed a non-significant improvement. Undergoing personal genome testing and using personal genotype data in the classroom enhanced students' self-reported and assessed knowledge of genomics, and did not appear to cause significant anxiety. At least for self-selected students, the incorporation of personal genome testing can be an effective educational tool to teach important concepts of clinical genomic testing.

The use of enhanced recovery after surgery (ERAS) principles in Scottish orthopaedic units--an implementation and follow-up at 1 year, 2010-2011: a report from the Musculoskeletal Audit, Scotland.

Science.gov (United States)

Scott, Nicholas B; McDonald, David; Campbell, Jane; Smith, Richard D; Carey, A Kate; Johnston, Ian G; James, Kate R; Breusch, Steffen J

2013-01-01

To establish whether a nationally guided programme can lead to more widespread implementation of enhanced recovery after surgery (ERAS), a well-established optimised care pathway for lower limb arthroplasty. In 2010, National Services Scotland's Musculoskeletal Audit was asked to perform a 'snapshot' audit of the current peri-operative management of patients undergoing total hip and knee arthroplasty in all 22 Scottish orthopaedic units with an identical follow-up audit in 2011 after input and support from the national steering group. Audit 1 and audit 2 involved 1,345 and 1,278 patients, respectively. The number of Scottish units that developed an ERAS programme increased from 8 (36 %) to 15 (68 %). Units that included more ERAS patients had earlier mobilisation rates (146/474, 36 % ERAS patients mobilised same day vs. 34/873, 4 % non-ERAS; n = 22 units, r = 0.55, p = 0.008) and shorter post-operative length of stay (median 4 days vs. ERAS, 5 days non-ERAS, n = 22 units, r = -0.64, p = 0.001). ERAS knee arthroplasty patients had lower blood transfusion rates (5/205, 2 % vs. 51/399, 13 %, n = 22 units, r = -0.62, p = 0.002). Units that restricted the use of IV fluids post-operatively had higher early mobilisation rates (n = 22 units, r = 0.48, p = 0.03) and shorter post-operative length of stay (n = 22 units, r = -0.56, p = 0.007). Reduced use of patient-controlled analgesia was also associated with earlier mobilisation (n = 22 units, r = 0.49, p = 0.02) and shorter length of stay (n = 22 units, r = -0.39, p = 0.07). Urinary catheterisation rates also dropped from 468/1,345 (35 %) in 2010 to 337/1,278 (26 %) in 2011 (n = 22 units, z = 2.19, p = 0.03). A clinically guided and nationally supported process has proven highly successful in achieving a further uptake of enhanced recovery principles after lower limb arthroplasty in Scotland, which has resulted in clinical benefits to patients and reduced length of hospital stay.

Toward genome-scale models of the Chinese hamster ovary cells: incentives, status and perspectives

DEFF Research Database (Denmark)

Kaas, Christian Schrøder; Fan, Yuzhou; Weilguny, Dietmar

2014-01-01

Bioprocessing of the important Chinese hamster ovary (CHO) cell lines used for the production of biopharmaceuticals stands at the brink of several redefining events. In 2011, the field entered the genomics era, which has accelerated omics-based phenotyping of the cell lines. In this review we...

Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach

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Claudia Bartoli

2017-05-01

Full Text Available The emergence and re-emergence of plant pathogenic microorganisms are processes that imply perturbations in both host and pathogen ecological niches. Global change is largely assumed to drive the emergence of new etiological agents by altering the equilibrium of the ecological habitats which in turn places hosts more in contact with pathogen reservoirs. In this context, the number of epidemics is expected to increase dramatically in the next coming decades both in wild and crop plants. Under these considerations, the identification of the genetic variants underlying natural variation of resistance is a pre-requisite to estimate the adaptive potential of wild plant populations and to develop new breeding resistant cultivars. On the other hand, the prediction of pathogen's genetic determinants underlying disease emergence can help to identify plant resistance alleles. In the genomic era, whole genome sequencing combined with the development of statistical methods led to the emergence of Genome Wide Association (GWA mapping, a powerful tool for detecting genomic regions associated with natural variation of disease resistance in both wild and cultivated plants. However, GWA mapping has been less employed for the detection of genetic variants associated with pathogenicity in microbes. Here, we reviewed GWA studies performed either in plants or in pathogenic microorganisms (bacteria, fungi and oomycetes. In addition, we highlighted the benefits and caveats of the emerging joint GWA mapping approach that allows for the simultaneous identification of genes interacting between genomes of both partners. Finally, based on co-evolutionary processes in wild populations, we highlighted a phenotyping-free joint GWA mapping approach as a promising tool for describing the molecular landscape underlying plant - microbe interactions.

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.

Albanian Foreign Policy in the Post-Comunist Era

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Abdurrahim F. Aydin

2011-05-01

Full Text Available Estando bajo un régimen totalitario durante el periodo comunista, la política exterior albanesa sacrificó sus objetivos políticos y sus intereses nacionales. Con el colapso del Comunismo, el liderazgo albanés tiene la encomiable tarea de relacionar correctamente los objetivos reales y los intereses genuinos de los albaneses en Albania, Serbia, Kosovo, KYROM, Montenegro y Grecia. Los propósitos de este artículo sn enfatizar la política exterior albanesa actual (post-comunista y mostrar qué falta en la política exterior de Albania para encajar sus intereses nacionales en sus continuos esfuerzos para establecer una exitosa europeización y democratización de su cultura.

Genomics and fish adaptation

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Agostinho Antunes

2015-12-01

Full Text Available The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied fish species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Group A rotavirus gastroenteritis: post-vaccine era, genotypes and zoonotic transmission

Science.gov (United States)

Luchs, Adriana; Timenetsky, Maria do Carmo Sampaio Tavares

2016-01-01

ABSTRACT This article provides a review of immunity, diagnosis, and clinical aspects of rotavirus disease. It also informs about the changes in epidemiology of diarrheal disease and genetic diversity of circulating group A rotavirus strains following the introduction of vaccines. Group A rotavirus is the major pathogen causing gastroenteritis in animals. Its segmented RNA genome can lead to the emergence of new or unusual strains in human populations via interspecies transmission and/or reassortment events. PMID:27462899

Simple visual review of pre- to post-operative renal ultrasound images predicts pyeloplasty success equally as well as geometric measurements: A blinded comparison with a gold standard.

Science.gov (United States)

Kern, Adam J M; Schlomer, Bruce J; Timberlake, Matthew D; Peters, Craig A; Hammer, Matthew R; Jacobs, Micah A

2017-08-01

MAG3 diuretic renal scan remains the gold standard for determination of improvement in renal drainage following pyeloplasty for ureteropelvic junction obstruction. We hypothesized that (i) a change in geometric measurements between pre-operative and post-operative renal ultrasound (RUS) images and (ii) blinded simple visual review of images both would predict pyeloplasty success. To determine if simple visual review and/or novel geometric measurement of renal ultrasounds can detect pyeloplasty failure. This study was a retrospective, blinded comparison with a gold standard. Included were children aged ≤18 years undergoing pyeloplasty at our institution from 2009 to 2015. For each kidney, representative pre-operative and post-operative RUS images were chosen. Our standard for pyeloplasty success was improved drainage curve on MAG3 and lack of additional surgery. Measurements for collecting system circularity, roundness, and renal parenchymal to collecting system area ratio (RPCSR) were obtained by three raters (Figure), who were blinded to the outcome of the pyeloplasty. Changes in geometric measurements were analyzed as a diagnostic test for MAG3-defined pyeloplasty success using ROC curve analysis. In addition, six reviewers blinded to pyeloplasty success reviewed pre-operative and post-operative images visually for improved hydronephrosis and categorized pyeloplasty as success or failure based on simple visual review of RUS. Fifty-three repaired renal units were identified (50 children). There were five pyeloplasty failures, four of which underwent revision or nephrectomy. While all geometric measurements could discriminate pyeloplasty failure and success, the geometric measurements that discriminated best between pyeloplasty failure and success were change in collecting system roundness and change in RPCSR. Consensus opinion among six blinded reviewers using simple visual review had a sensitivity of 94% and PPV of 100% with respect to identifying pyeloplasty

In Silico Genome Comparison and Distribution Analysis of Simple Sequences Repeats in Cassava

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Andrea Vásquez

2014-01-01

Full Text Available We conducted a SSRs density analysis in different cassava genomic regions. The information obtained was useful to establish comparisons between cassava’s SSRs genomic distribution and those of poplar, flax, and Jatropha. In general, cassava has a low SSR density (~50 SSRs/Mbp and has a high proportion of pentanucleotides, (24,2 SSRs/Mbp. It was found that coding sequences have 15,5 SSRs/Mbp, introns have 82,3 SSRs/Mbp, 5′ UTRs have 196,1 SSRs/Mbp, and 3′ UTRs have 50,5 SSRs/Mbp. Through motif analysis of cassava’s genome SSRs, the most abundant motif was AT/AT while in intron sequences and UTRs regions it was AG/CT. In addition, in coding sequences the motif AAG/CTT was also found to occur most frequently; in fact, it is the third most used codon in cassava. Sequences containing SSRs were classified according to their functional annotation of Gene Ontology categories. The identified SSRs here may be a valuable addition for genetic mapping and future studies in phylogenetic analyses and genomic evolution.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies.

Science.gov (United States)

Card, Daren C; Schield, Drew R; Reyes-Velasco, Jacobo; Fujita, Matthew K; Andrew, Audra L; Oyler-McCance, Sara J; Fike, Jennifer A; Tomback, Diana F; Ruggiero, Robert P; Castoe, Todd A

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (∼3.5-5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Two low coverage bird genomes and a comparison of reference-guided versus de novo genome assemblies

Science.gov (United States)

Card, Daren C.; Schield, Drew R.; Reyes-Velasco, Jacobo; Fujita, Matthre K.; Andrew, Audra L.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Tomback, Diana F.; Ruggiero, Robert P.; Castoe, Todd A.

2014-01-01

As a greater number and diversity of high-quality vertebrate reference genomes become available, it is increasingly feasible to use these references to guide new draft assemblies for related species. Reference-guided assembly approaches may substantially increase the contiguity and completeness of a new genome using only low levels of genome coverage that might otherwise be insufficient for de novo genome assembly. We used low-coverage (~3.5–5.5x) Illumina paired-end sequencing to assemble draft genomes of two bird species (the Gunnison Sage-Grouse, Centrocercus minimus, and the Clark's Nutcracker, Nucifraga columbiana). We used these data to estimate de novo genome assemblies and reference-guided assemblies, and compared the information content and completeness of these assemblies by comparing CEGMA gene set representation, repeat element content, simple sequence repeat content, and GC isochore structure among assemblies. Our results demonstrate that even lower-coverage genome sequencing projects are capable of producing informative and useful genomic resources, particularly through the use of reference-guided assemblies.

Improving recombinant protein purification yield

Science.gov (United States)

Production of adequate amounts of recombinant proteins is essential for antibody production, biochemical activity study, and structural determination during the post-genomic era. It’s technologically challenging and a limiting factor for tung oil research because analytical reagents such as high qua...

Nutrition-gene interactions (post-genomics). Changes in gene expression through nutritional manipulations

International Nuclear Information System (INIS)

Harper, G.S.; Lehnert, S.A.; Greenwood, P.L.

2005-01-01

This paper discusses the effects of severe nutritional restriction, both pre- and post-weaning, on development of skeletal muscle in food animals. Given recent predictions about growth in demand for muscle-foods in developing countries, the global community will need to face the food-feed dilemma, and balance efficiency of production against the quality-of-life aspects of local livestock husbandry. It is likely that production animals will be grown in successively more marginal environments and at higher stocking rates on unimproved pastures. Understanding the nutritional limits to animal growth at the level of muscle gene networks will help us find optima for nutrition, growth rate and meat yield. Genomic approaches give us unprecedented capacity to map the networks of control under nutritionally restricted conditions, though the challenges remain of identifying steps that regulate substrate flux. The paper describes some approaches currently being taken to understanding muscle development, and concludes that the genes contributing to two ruminant phenotypes should be mapped and characterized. These are: the capacity to depress metabolic rate in response to nutritional restriction; and the capacity to exhibit compensatory growth after restriction is relieved. (author)

GPSR: A Resource for Genomics Proteomics and Systems Biology

Indian Academy of Sciences (India)

GPSR: A Resource for Genomics Proteomics and Systems Biology · Simple Calculation Programs for Biology Immunological Methods · Simple Calculation Programs for Biology Methods in Molecular Biology · Simple Calculation Programs for Biology Other Methods · PowerPoint Presentation · Slide 6 · Slide 7 · Prediction of ...

Risk Assessment: Democratic Republic of Congo Post-Laurent ...

African Journals Online (AJOL)

political system as opposed to the view that it was merely a power struggle between Kabila on the .... Local actors and international mining companies built alliances exploiting Congo's minerals to gain a ... They are preparing a contingency plan for their activities in the post-Laurent Kabila era, for ... small arms in the DRC.33.

Training future physicians in the era of genomic medicine: trends in undergraduate medical genetics education.

Science.gov (United States)

Plunkett-Rondeau, Jevon; Hyland, Katherine; Dasgupta, Shoumita

2015-11-01

Advances in genomic technologies are transforming medical practice, necessitating the expertise of genomically-literate physicians. This study examined 2013-2014 trends in genetics curricula in US and Canadian medical schools to ascertain whether and how curricula are keeping pace with this rapid evolution. Medical genetics course directors received a 60-item electronic questionnaire covering curriculum design, assessment, remediation of failing grades, and inclusion of specific topics. The response rate was 74%. Most schools teach the majority of genetics during the first 2 years, with an increase in the number of integrated curricula. Only 26% reported formal genetics teaching during years 3 and 4, and most respondents felt the amount of time spent on genetics was insufficient preparation for clinical practice. Most participants are using the Association of Professors of Human and Medical Genetics Core Curriculum(1) as a guide. Topics recently added include personalized medicine (21%) and direct-to-consumer testing (18%), whereas eugenics (17%), linkage analysis (16%), and evolutionary genetics (15%) have been recently eliminated. Remediation strategies were heterogeneous across institutions. These findings provide an important update on how genetics and genomics is taught at US and Canadian medical schools. Continuous improvement of educational initiatives will aid in producing genomically-literate physicians.

Three eras of climate change

Energy Technology Data Exchange (ETDEWEB)

Huq, Saleemul; Toulmin, Camilla

2006-10-15

Climate change as a global challenge has evolved through a series of stages in the last few decades. We are now on the brink of a new era which will see the terms of the debate shift once again. The different eras are characterised by the scientific evidence, public perceptions, responses and engagement of different groups to address the problem. In the first era, from the late 1980s to 2000, climate change was seen as an “environmental” problem to do with prevention of future impacts on the planet's climate systems over the next fifty to hundred years, through reductions in emissions of greenhouse gases, known as “mitigation”. The second era can be said to have started around the turn of the millennium, with the recognition that there will be some unavoidable impacts from climate change in the near term (over the next decade or two). These impacts must be coped with through “adaptation”, as well as mitigation, to prevent much more severe and possibly catastrophic impacts in the longer term. It has become clear that many of the impacts of climate change in the near term are likely to fall on the poorest countries and communities. The third era, which we are just about to enter, will see the issue change from tackling an environmental or development problem to a question of “global justice”. It will engage with a much wider array of citizens from around the world than previous eras.

Genome sequence diversity and clues to the evolution of variola (smallpox) virus.

Science.gov (United States)

Esposito, Joseph J; Sammons, Scott A; Frace, A Michael; Osborne, John D; Olsen-Rasmussen, Melissa; Zhang, Ming; Govil, Dhwani; Damon, Inger K; Kline, Richard; Laker, Miriam; Li, Yu; Smith, Geoffrey L; Meyer, Hermann; Leduc, James W; Wohlhueter, Robert M

2006-08-11

Comparative genomics of 45 epidemiologically varied variola virus isolates from the past 30 years of the smallpox era indicate low sequence diversity, suggesting that there is probably little difference in the isolates' functional gene content. Phylogenetic clustering inferred three clades coincident with their geographical origin and case-fatality rate; the latter implicated putative proteins that mediate viral virulence differences. Analysis of the viral linear DNA genome suggests that its evolution involved direct descent and DNA end-region recombination events. Knowing the sequences will help understand the viral proteome and improve diagnostic test precision, therapeutics, and systems for their assessment.

Ecological recovery in ERA

DEFF Research Database (Denmark)

EFSA Scientific Committee (Scientific Committee); Topping, Christopher John

2016-01-01

knowledge and data retrieved from the literature. Finally, the information presented in this opinion was reviewed by experts from the relevant EFSA Panels, European risk assessment bodies and through an open consultation requesting input from stakeholders. A conceptual framework was developed to address...... recognises the importance of more integrated ERAs considering both the local and landscape scales, as well as the possible co-occurrence of multiple potential stressors that fall under the remit of EFSA, which are important when addressing ecological recovery. In this scientific opinion, the Scientific...... Committee gathered scientific knowledge on the potential for the recovery of non-target organisms for the further development of ERA. Current EFSA guidance documents and opinions were reviewed on how ecological recovery is addressed in ERA schemes. In addition, this scientific opinion is based on expert...

MEMAKNAI SUMPAH PEMUDA DI ERA REFORMASI

Directory of Open Access Journals (Sweden)

Sutejo K. Widodo

2013-03-01

Full Text Available The moment of Sumpah Pemuda (Young Man Oath took place 84 years ago, reflecting the spirit of nationalism that is still very important in this Reformation era. This paper endeavors to dig deeper meaning of Sumpah Pemuda in its pre-independence era and applying it to our contemporary situation. The method used here is historical research using literature resources, such as articles, books, and other readings in internet. It is then concluded that the spirit of Sumpah Pemuda should be our contemplative materials and valuable Iesson so that Reformation era may succeed in achieving national goals stated in the Constitution, a society that is fair, prosperous, and democratic. Keywords: Sumpah Pemuda, Reformation era, nationalism.

A tailing genome walking method suitable for genomes with high local GC content.

Science.gov (United States)

Liu, Taian; Fang, Yongxiang; Yao, Wenjuan; Guan, Qisai; Bai, Gang; Jing, Zhizhong

2013-10-15

The tailing genome walking strategies are simple and efficient. However, they sometimes can be restricted due to the low stringency of homo-oligomeric primers. Here we modified their conventional tailing step by adding polythymidine and polyguanine to the target single-stranded DNA (ssDNA). The tailed ssDNA was then amplified exponentially with a specific primer in the known region and a primer comprising 5' polycytosine and 3' polyadenosine. The successful application of this novel method for identifying integration sites mediated by φC31 integrase in goat genome indicates that the method is more suitable for genomes with high complexity and local GC content. Copyright © 2013 Elsevier Inc. All rights reserved.

Post-buckling analysis of composite beams: A simple intuitive ...

Indian Academy of Sciences (India)

and lateral displacement functions at any discrete location of the beam. ..... shells under combined axial compression and radial pressure. ... Razakamiadana A and Zidi M 1999 Buckling and post-buckling of concentric cylindrical tubes under.

Technical Education in Pre and Post Independent India

Science.gov (United States)

Janardhana, G.; Rajasekhar, M.

2012-01-01

This paper deals with technical education growth, policies in pre and post independent India. The world is moving forward rapidly and positively, into an era where societies and economies are incrementally based on knowledge. The importance of nations in the 21st Century shall be judged not by their economic strength alone, but also by their power…

Exploiting Genomic Knowledge in Optimising Molecular Breeding Programmes: Algorithms from Evolutionary Computing

Science.gov (United States)

O'Hagan, Steve; Knowles, Joshua; Kell, Douglas B.

2012-01-01

Comparatively few studies have addressed directly the question of quantifying the benefits to be had from using molecular genetic markers in experimental breeding programmes (e.g. for improved crops and livestock), nor the question of which organisms should be mated with each other to best effect. We argue that this requires in silico modelling, an approach for which there is a large literature in the field of evolutionary computation (EC), but which has not really been applied in this way to experimental breeding programmes. EC seeks to optimise measurable outcomes (phenotypic fitnesses) by optimising in silico the mutation, recombination and selection regimes that are used. We review some of the approaches from EC, and compare experimentally, using a biologically relevant in silico landscape, some algorithms that have knowledge of where they are in the (genotypic) search space (G-algorithms) with some (albeit well-tuned ones) that do not (F-algorithms). For the present kinds of landscapes, F- and G-algorithms were broadly comparable in quality and effectiveness, although we recognise that the G-algorithms were not equipped with any ‘prior knowledge’ of epistatic pathway interactions. This use of algorithms based on machine learning has important implications for the optimisation of experimental breeding programmes in the post-genomic era when we shall potentially have access to the full genome sequence of every organism in a breeding population. The non-proprietary code that we have used is made freely available (via Supplementary information). PMID:23185279

Genomic Selection in the Era of Next Generation Sequencing for Complex Traits in Plant Breeding.

Science.gov (United States)

Bhat, Javaid A; Ali, Sajad; Salgotra, Romesh K; Mir, Zahoor A; Dutta, Sutapa; Jadon, Vasudha; Tyagi, Anshika; Mushtaq, Muntazir; Jain, Neelu; Singh, Pradeep K; Singh, Gyanendra P; Prabhu, K V

2016-01-01

Genomic selection (GS) is a promising approach exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. In plant breeding, it provides opportunities to increase genetic gain of complex traits per unit time and cost. The cost-benefit balance was an important consideration for GS to work in crop plants. Availability of genome-wide high-throughput, cost-effective and flexible markers, having low ascertainment bias, suitable for large population size as well for both model and non-model crop species with or without the reference genome sequence was the most important factor for its successful and effective implementation in crop species. These factors were the major limitations to earlier marker systems viz., SSR and array-based, and was unimaginable before the availability of next-generation sequencing (NGS) technologies which have provided novel SNP genotyping platforms especially the genotyping by sequencing. These marker technologies have changed the entire scenario of marker applications and made the use of GS a routine work for crop improvement in both model and non-model crop species. The NGS-based genotyping have increased genomic-estimated breeding value prediction accuracies over other established marker platform in cereals and other crop species, and made the dream of GS true in crop breeding. But to harness the true benefits from GS, these marker technologies will be combined with high-throughput phenotyping for achieving the valuable genetic gain from complex traits. Moreover, the continuous decline in sequencing cost will make the WGS feasible and cost effective for GS in near future. Till that time matures the targeted sequencing seems to be more cost-effective option for large scale marker discovery and GS, particularly in case of large and un-decoded genomes.

Meiotic homoeologous recombination-based alien gene introgression in the genomics era of wheat

Science.gov (United States)

Wheat (Triticum spp.) has a narrow genetic basis due to its allopolyploid origin. However, wheat has numerous wild relatives usable for expanding genetic variability of its genome through meiotic homoeologous recombination. Traditionally, laborious cytological analyses have been employed to detect h...

Genome-wide association study of handedness excludes simple genetic models

Science.gov (United States)

Armour, J AL; Davison, A; McManus, I C

2014-01-01

Handedness is a human behavioural phenotype that appears to be congenital, and is often assumed to be inherited, but for which the developmental origin and underlying causation(s) have been elusive. Models of the genetic basis of variation in handedness have been proposed that fit different features of the observed resemblance between relatives, but none has been decisively tested or a corresponding causative locus identified. In this study, we applied data from well-characterised individuals studied at the London Twin Research Unit. Analysis of genome-wide SNP data from 3940 twins failed to identify any locus associated with handedness at a genome-wide level of significance. The most straightforward interpretation of our analyses is that they exclude the simplest formulations of the ‘right-shift' model of Annett and the ‘dextral/chance' model of McManus, although more complex modifications of those models are still compatible with our observations. For polygenic effects, our study is inadequately powered to reliably detect alleles with effect sizes corresponding to an odds ratio of 1.2, but should have good power to detect effects at an odds ratio of 2 or more. PMID:24065183

Convergence of advances in genomics, team science, and repositories as drivers of progress in psychiatric genomics.

Science.gov (United States)

Lehner, Thomas; Senthil, Geetha; Addington, Anjené M

2015-01-01

After many years of unfilled promise, psychiatric genetics has seen an unprecedented number of successes in recent years. We hypothesize that the field has reached an inflection point through a confluence of four key developments: advances in genomics; the orientation of the scientific community around large collaborative team science projects; the development of sample and data repositories; and a policy framework for sharing and accessing these resources. We discuss these domains and their effect on scientific progress and provide a perspective on why we think this is only the beginning of a new era in scientific discovery. Published by Elsevier Inc.

Genomic footprinting in mammalian cells with ultraviolet light

International Nuclear Information System (INIS)

Becker, M.M.; Wang, Z.; Grossmann, G.; Becherer, K.A.

1989-01-01

A simple and accurate genomic primer extension method has been developed to detect ultraviolet footprinting patterns of regulatory protein-DNA interactions in mammalian genomic DNA. The technique can also detect footprinting or sequencing patterns introduced into genomic DNA by other methods. Purified genomic DNA, containing either damaged bases or strand breaks introduced by footprinting or sequencing reactions, is first cut with a convenient restriction enzyme to reduce its molecular weight. A highly radioactive single-stranded DNA primer that is complementary to a region of genomic DNA whose sequence or footprint one wishes to examine is then mixed with 50 micrograms of restriction enzyme-cut genomic DNA. The primer is approximately 100 bases long and contains 85 radioactive phosphates, each of specific activity 3000 Ci/mmol (1 Ci = 37 GBq). A simple and fast method for preparing such primers is described. Following brief heat denaturation at 100 degrees C, the solution of genomic DNA and primer is cooled to 74 degrees C and a second solution containing Taq polymerase (Thermus aquaticus DNA polymerase) and the four deoxynucleotide triphosphates is added to initiate primer extension of genomic DNA. Taq polymerase extends genomic hybridized primer until its polymerization reaction is terminated either by a damaged base or strand break in genomic DNA or by the addition of dideoxynucleotide triphosphates in the polymerization reaction. The concurrent primer hybridization-extension reaction is terminated after 5 hr and unhybridized primer is digested away by mung bean nuclease. Primer-extended genomic DNA is then denatured and electrophoresed on a polyacrylamide sequencing gel, and radioactive primer extension products are revealed by autoradiography

Genetic counselors: translating genomic science into clinical practice

OpenAIRE

Bennett, Robin L.; Hampel, Heather L.; Mandell, Jessica B.; Marks, Joan H.

2003-01-01

In a time of emerging genetic tests and technologies, genetic counselors are faced with the challenge of translating complex genomic data into information that will aid their client’s ability to learn about, understand, make, and cope with decisions relating to genetic diagnoses. The first of two companion articles in this issue examines the role of the genetic counselor, particularly in counseling individuals at risk for or diagnosed with breast cancer, in an era of high-tech health care and...

The GPM Ground Validation Program: Pre to Post-Launch

Science.gov (United States)

Petersen, W. A.

2014-12-01

NASA GPM Ground Validation (GV) activities have transitioned from the pre to post-launch era. Prior to launch direct validation networks and associated partner institutions were identified world-wide, covering a plethora of precipitation regimes. In the U.S. direct GV efforts focused on use of new operational products such as the NOAA Multi-Radar Multi-Sensor suite (MRMS) for TRMM validation and GPM radiometer algorithm database development. In the post-launch, MRMS products including precipitation rate, types and data quality are being routinely generated to facilitate statistical GV of instantaneous and merged GPM products. To assess precipitation column impacts on product uncertainties, range-gate to pixel-level validation of both Dual-Frequency Precipitation Radar (DPR) and GPM microwave imager data are performed using GPM Validation Network (VN) ground radar and satellite data processing software. VN software ingests quality-controlled volumetric radar datasets and geo-matches those data to coincident DPR and radiometer level-II data. When combined MRMS and VN datasets enable more comprehensive interpretation of ground-satellite estimation uncertainties. To support physical validation efforts eight (one) field campaigns have been conducted in the pre (post) launch era. The campaigns span regimes from northern latitude cold-season snow to warm tropical rain. Most recently the Integrated Precipitation and Hydrology Experiment (IPHEx) took place in the mountains of North Carolina and involved combined airborne and ground-based measurements of orographic precipitation and hydrologic processes underneath the GPM Core satellite. One more U.S. GV field campaign (OLYMPEX) is planned for late 2015 and will address cold-season precipitation estimation, process and hydrology in the orographic and oceanic domains of western Washington State. Finally, continuous direct and physical validation measurements are also being conducted at the NASA Wallops Flight Facility multi

A Note on the Post-Revolution Iranian Economy and the Banking Sector

OpenAIRE

Dehghan Nejad, Omid

2010-01-01

This note provides an analysis of Iranian economy in its post-revolution era with special emphasis on the country’s banking sector and discusses the reasons for Iran’s failure in reaching sustained economic growth and financial development.

Monitoring vaccine and non-vaccine HPV type prevalence in the post-vaccination era in women living in the Basilicata region, Italy.

Science.gov (United States)

Carozzi, Francesca; Puliti, Donella; Ocello, Cristina; Anastasio, Pasquale Silvio; Moliterni, Espedito Antonio; Perinetti, Emilia; Serradell, Laurence; Burroni, Elena; Confortini, Massimo; Mantellini, Paola; Zappa, Marco; Dominiak-Felden, Géraldine

2018-01-15

A large free-of-charge quadrivalent HPV (qHPV) vaccination program, covering four cohorts annually (women 11, 14, 17 and 24 years), has been implemented in Basilicata since 2007. This study evaluated vaccine and non-vaccine HPV prevalence 5-7 years post-vaccination program implementation in vaccinated and unvaccinated women. This population-based, cross-sectional study was conducted in the public screening centers of the Local Health Unit in Matera between 2012 and 2014. Cervical samples were obtained for Pap and HPV testing (HC2, LiPA Extra® assay) and participants completed a sociodemographic and behavioral questionnaire. Detailed HPV vaccination status was retrieved from the official HPV vaccine registry. HPV prevalence was described overall, by type and vaccination status. The association between HPV type-detection and risk/protective factors was studied. Direct vaccine protection (qHPV vaccine effectiveness [VE]), cross-protection, and type-replacement were evaluated in cohorts eligible for vaccination, by analyzing HPV prevalence of vaccine and non-vaccine types according to vaccination status. Overall, 2793 women (18-50 years) were included, 1314 of them having been in birth cohorts eligible for the HPV vaccination program (18- to 30-year-old women at enrolment). Among the latter, qHPV vaccine uptake was 59% (at least one dose), with 94% completing the schedule; standardized qHPV type prevalence was 0.6% in vaccinated versus 5.5% in unvaccinated women (P HPV, high-risk non-vaccine HPV, or any single non-vaccine type prevalence was observed between vaccinated and unvaccinated women. These results, conducted in a post-vaccine era, suggest a high qHPV VE and that a well-implemented catch-up vaccination program may be efficient in reducing vaccine-type infections in a real-world setting. No cross-protective effect or evidence of type-replacement was observed a few years after HPV vaccine introduction.

Transcriptional and chromatin regulation during fasting – The genomic era

Science.gov (United States)

Goldstein, Ido; Hager, Gordon L.

2015-01-01

An elaborate metabolic response to fasting is orchestrated by the liver and is heavily reliant upon transcriptional regulation. In response to hormones (glucagon, glucocorticoids) many transcription factors (TFs) are activated and regulate various genes involved in metabolic pathways aimed at restoring homeostasis: gluconeogenesis, fatty acid oxidation, ketogenesis and amino acid shuttling. We summarize the recent discoveries regarding fasting-related TFs with an emphasis on genome-wide binding patterns. Collectively, the summarized findings reveal a large degree of co-operation between TFs during fasting which occurs at motif-rich DNA sites bound by a combination of TFs. These new findings implicate transcriptional and chromatin regulation as major determinants of the response to fasting and unravels the complex, multi-TF nature of this response. PMID:26520657

Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.

Science.gov (United States)

Fazal, Mohammed-Abbas; Alexander, Sarah; Burnett, Edward; Deheer-Graham, Ana; Oliver, Karen; Holroyd, Nancy; Parkhill, Julian; Russell, Julie E

2016-11-03

Salmonellae are a significant cause of morbidity and mortality globally. Here, we report the first complete genome sequence for Salmonella enterica subsp. enterica serovar Java strain NCTC5706. This strain is of historical significance, having been isolated in the pre-antibiotic era and was deposited into the National Collection of Type Cultures in 1939. © Crown copyright 2016.

Understanding the physiology and adaptation of staphylococci: a post-genomic approach.

Science.gov (United States)

Becker, Karsten; Bierbaum, Gabriele; von Eiff, Christof; Engelmann, Susanne; Götz, Friedrich; Hacker, Jörg; Hecker, Michael; Peters, Georg; Rosenstein, Ralf; Ziebuhr, Wilma

2007-11-01

Staphylococcus aureus as well as coagulase-negative staphylococci are medically highly important pathogens characterized by an increasing resistance rate toward many antibiotics. Although normally being skin and mucosa commensals, some staphylococcal species and strains have the capacity to cause a wide range of infectious diseases. Many of these infections affect immunocompromised patients in hospitals. However, community-acquired staphylococcal infections due to resistant strains are also currently on the rise. In the light of this development, there is an urgent need for novel anti-staphylococcal therapeutic and prevention strategies for which a better understanding of the physiology of these bacteria is an essential prerequisite. Within the past years, staphylococci have been in the focus of genomic research, resulting in the determination and publication of a range of full-genome sequences of different staphylococcal species and strains which provided the basis for the design and application of DNA microarrays and other genomic tools. Here we summarize the results of the project group 'Staphylococci' within the research network 'Pathogenomics' giving new insights into the genome structure, molecular epidemiology, physiology, and genetic adaptation of both S. aureus and coagulase-negative staphylococci.

Leadership in Crisis: Service Chiefs in the Post-Vietnam World

Science.gov (United States)

2012-06-01

stamina to continue the Cold War against the Soviet Union.144 Although Kissinger’s autobiography does not mention this exchange, other sources do...planning cell , are still used by the USAF today. Finally, Jones set the standard for civil-military relations in the post-Vietnam era. After the

El lenguaje en la era digital

Directory of Open Access Journals (Sweden)

Juan Carlos Vergara Silva

1998-02-01

Con base en la interrelación entre lenguaje y pensamiento se plantea el papel fundamental que el lenguaje ocupa en el modelo económico, educativo y cultural generado por la aparición de la era digital o era del conocimiento. en este artículo se evidencian los retos que genera una era marcada por un esquema digital en el desarrollo y uso de habilidades comunicativas tanto en la docencia superior como en el ejercicio profesional eficiente.

The diploid genome sequence of an individual human.

Directory of Open Access Journals (Sweden)

Samuel Levy

2007-09-01

Full Text Available Presented here is a genome sequence of an individual human. It was produced from approximately 32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome and the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel included 3,213,401 single nucleotide polymorphisms (SNPs, 53,823 block substitutions (2-206 bp, 292,102 heterozygous insertion/deletion events (indels(1-571 bp, 559,473 homozygous indels (1-82,711 bp, 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments >200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information.

EVERYDAY QUR’AN DI ERA POST-KONSUMERISME MUSLIM

Directory of Open Access Journals (Sweden)

M. Endy Saputro

2016-09-01

Full Text Available This paper aims to give a preliminary draft to formulate an innovative concept in the Qur’anic studies world in the age of post-consumerism Muslim. Recent studies on tug of war between globalization and religion have been identifying salient social transformation in some parts of Muslim world, such as the rise of new (media religious authority, religious commodification trends, varieties of Islamic consumption, the emergence of public Islam and so forth. Apart from these recent scholarships, which successfully grasp the globalization’s influence toward religion (Islam, this paper offers the concept of everyday Qur’an as an alternative basic approach of understanding the cultures of Qur’an in this changing (Muslim world and at the same time, seeking to briefly explain its emerging issues. Some exemplary issues then have analytically discussed to reflect how the proposed theory applied. Thus, everyday Qur’an can contribute the discourse of cultures based technology in the context of Qur’anic Studies. 

Can Genetics and Genomics Nursing Competencies Be Successfully Taught in a Prenursing Microbiology Course?

Science.gov (United States)

Shuster, Michele

2011-01-01

In recognition of the entry into the era of personalized medicine, a new set of genetics and genomics competencies for nurses was introduced in 2006. Since then, there have been a number of reports about the critical importance of these competencies for nursing practices and about the challenges of addressing these competencies in the preservice…

Dakwah di Era Digital

OpenAIRE

Budiantoro, Wahyu

2018-01-01

These days dakwah is not only interpreted as transformation of a pure religious value, but also transformation of a more relevant value including many aspects in digital era. Digital era is when society succumbed into the flow of information causing cultural shock and difficulties on synthesizing meaning from those scattered information. Dakwah on Digital age must accommodate societal needs which tend to move into a mass society. It results in strategy and more humane and innovative dakwah me...

Re-Ranking Sequencing Variants in the Post-GWAS Era for Accurate Causal Variant Identification

Science.gov (United States)

Faye, Laura L.; Machiela, Mitchell J.; Kraft, Peter; Bull, Shelley B.; Sun, Lei

2013-01-01

Next generation sequencing has dramatically increased our ability to localize disease-causing variants by providing base-pair level information at costs increasingly feasible for the large sample sizes required to detect complex-trait associations. Yet, identification of causal variants within an established region of association remains a challenge. Counter-intuitively, certain factors that increase power to detect an associated region can decrease power to localize the causal variant. First, combining GWAS with imputation or low coverage sequencing to achieve the large sample sizes required for high power can have the unintended effect of producing differential genotyping error among SNPs. This tends to bias the relative evidence for association toward better genotyped SNPs. Second, re-use of GWAS data for fine-mapping exploits previous findings to ensure genome-wide significance in GWAS-associated regions. However, using GWAS findings to inform fine-mapping analysis can bias evidence away from the causal SNP toward the tag SNP and SNPs in high LD with the tag. Together these factors can reduce power to localize the causal SNP by more than half. Other strategies commonly employed to increase power to detect association, namely increasing sample size and using higher density genotyping arrays, can, in certain common scenarios, actually exacerbate these effects and further decrease power to localize causal variants. We develop a re-ranking procedure that accounts for these adverse effects and substantially improves the accuracy of causal SNP identification, often doubling the probability that the causal SNP is top-ranked. Application to the NCI BPC3 aggressive prostate cancer GWAS with imputation meta-analysis identified a new top SNP at 2 of 3 associated loci and several additional possible causal SNPs at these loci that may have otherwise been overlooked. This method is simple to implement using R scripts provided on the author's website. PMID:23950724

ERA-40

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — ERA-40 project was to produce and promote the use of a comprehensive set of global analysis describing the state of the atmosphere and land and ocean-wave conditions...

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

Science.gov (United States)

Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Nutrigenomics and its Applications in Animal Science

Directory of Open Access Journals (Sweden)

Ankur Khare

2011-09-01

Full Text Available AbstractNutrigenomics applies genomic technologies to study how nutrients affect expression of genes. With the advent of the post genomic era and with the use of functional genomic tools, the new strategies for evaluating the effects of nutrition on production efficiency and nutrient utilization are becoming available. Nutrigenomics plays an efficient role in various fields of animal health like nutrition, production, reproduction, disease process etc. Nutrigenomic approaches will enhance researchers‟ abilities to maintain animal health, optimize animal performance and improve milk and meat quality.

Synergetic Paradigm of Geopolitical Confrontation in the Postmodern Era

Directory of Open Access Journals (Sweden)

Sergey N. Teplyakov

2014-01-01

Full Text Available The article analyzes current state and mechanisms of geopolitical struggle in postmodern information age that has come. The author judges from assumption that entirely new postmodern society appeared with expansion of information technology, accompanied by cardinal changes in mechanisms of political power. Information technologies have become one of the most important factors contributing to the transformation of modern society from industrial to informational (post-industrial. In modern conditions, ensuring national and global security is a comprehensive process that includes not only measures to ensure information and economic security individually, but also such an integrated component as providing both information and economic security. The author suggests that modem geopolitical confrontation is carried out based on the synergetic paradigm. The main tool is information and energy influence on enemy system weaknesses using information space control, organizing negative information campaigns and applying economic sanctions. If the main focus of geopolitical struggle in modern era was forced expansion of the territory, in information postmodern age control over economic and information space has become priority among forms of geopolitical struggle. Military expansion of modern era becomes substituted by information and economic expansionism of postmodern using synergetic paradigm of geopolitical confrontation in order to control and capture the opponent's political space.

Genomics of elite sporting performance: what little we know and necessary advances.

Science.gov (United States)

Pitsiladis, Yannis; Wang, Guan; Wolfarth, Bernd; Scott, Robert; Fuku, Noriyuki; Mikami, Eri; He, Zihong; Fiuza-Luces, Carmen; Eynon, Nir; Lucia, Alejandro

2013-06-01

Numerous reports of genetic associations with performance-related phenotypes have been published over the past three decades but there has been limited progress in discovering and characterising the genetic contribution to elite/world-class performance, mainly owing to few coordinated research efforts involving major funding initiatives/consortia and the use primarily of the candidate gene analysis approach. It is timely that exercise genomics research has moved into a new era utilising well-phenotyped, large cohorts and genome-wide technologies--approaches that have begun to elucidate the genetic basis of other complex traits/diseases. This review summarises the most recent and significant findings from sports genetics and explores future trends and possibilities.

The Global Genome Biodiversity Network (GGBN) Data Standard specification

Science.gov (United States)

Droege, G.; Barker, K.; Seberg, O.; Coddington, J.; Benson, E.; Berendsohn, W. G.; Bunk, B.; Butler, C.; Cawsey, E. M.; Deck, J.; Döring, M.; Flemons, P.; Gemeinholzer, B.; Güntsch, A.; Hollowell, T.; Kelbert, P.; Kostadinov, I.; Kottmann, R.; Lawlor, R. T.; Lyal, C.; Mackenzie-Dodds, J.; Meyer, C.; Mulcahy, D.; Nussbeck, S. Y.; O'Tuama, É.; Orrell, T.; Petersen, G.; Robertson, T.; Söhngen, C.; Whitacre, J.; Wieczorek, J.; Yilmaz, P.; Zetzsche, H.; Zhang, Y.; Zhou, X.

2016-01-01

Genomic samples of non-model organisms are becoming increasingly important in a broad range of studies from developmental biology, biodiversity analyses, to conservation. Genomic sample definition, description, quality, voucher information and metadata all need to be digitized and disseminated across scientific communities. This information needs to be concise and consistent in today’s ever-increasing bioinformatic era, for complementary data aggregators to easily map databases to one another. In order to facilitate exchange of information on genomic samples and their derived data, the Global Genome Biodiversity Network (GGBN) Data Standard is intended to provide a platform based on a documented agreement to promote the efficient sharing and usage of genomic sample material and associated specimen information in a consistent way. The new data standard presented here build upon existing standards commonly used within the community extending them with the capability to exchange data on tissue, environmental and DNA sample as well as sequences. The GGBN Data Standard will reveal and democratize the hidden contents of biodiversity biobanks, for the convenience of everyone in the wider biobanking community. Technical tools exist for data providers to easily map their databases to the standard. Database URL: http://terms.tdwg.org/wiki/GGBN_Data_Standard PMID:27694206

[Genomics and transcriptomics of the Chinese liver fluke Clonorchis sinensis (Opisthorchiidae, Trematoda)].

Science.gov (United States)

Chelomina, G N

2017-01-01

The review summarizes the results of first genomic and transcriptomic investigations of the liver fluke Clonorchis sinensis (Opisthorchiidae, Trematoda). The studies mark the dawn of the genomic era for opisthorchiids, which cause severe hepatobiliary diseases in humans and animals. Their results aided in understanding the molecular mechanisms of adaptation to parasitism, parasite survival in mammalian biliary tracts, and genome dynamics in the individual development and the development of parasite-host relationships. Special attention is paid to the achievements in studying the codon usage bias and the roles of mobile genetic elements (MGEs) and small interfering RNAs (siRNAs). Interspecific comparisons at the genomic and transcriptomic levels revealed molecular differences, which may contribute to understanding the specialized niches and physiological needs of the respective species. The studies in C. sinensis provide a basis for further basic and applied research in liver flukes and, in particular, the development of efficient means to prevent, diagnose, and treat clonorchiasis.

Cancer Genomics: Diversity and Disparity Across Ethnicity and Geography.

Science.gov (United States)

Tan, Daniel S W; Mok, Tony S K; Rebbeck, Timothy R

2016-01-01

Ethnic and geographic differences in cancer incidence, prognosis, and treatment outcomes can be attributed to diversity in the inherited (germline) and somatic genome. Although international large-scale sequencing efforts are beginning to unravel the genomic underpinnings of cancer traits, much remains to be known about the underlying mechanisms and determinants of genomic diversity. Carcinogenesis is a dynamic, complex phenomenon representing the interplay between genetic and environmental factors that results in divergent phenotypes across ethnicities and geography. For example, compared with whites, there is a higher incidence of prostate cancer among Africans and African Americans, and the disease is generally more aggressive and fatal. Genome-wide association studies have identified germline susceptibility loci that may account for differences between the African and non-African patients, but the lack of availability of appropriate cohorts for replication studies and the incomplete understanding of genomic architecture across populations pose major limitations. We further discuss the transformative potential of routine diagnostic evaluation for actionable somatic alterations, using lung cancer as an example, highlighting implications of population disparities, current hurdles in implementation, and the far-reaching potential of clinical genomics in enhancing cancer prevention, diagnosis, and treatment. As we enter the era of precision cancer medicine, a concerted multinational effort is key to addressing population and genomic diversity as well as overcoming barriers and geographical disparities in research and health care delivery. © 2015 by American Society of Clinical Oncology.

Simple model for post seismic ionospheric disturbances above an earthquake epicentre and along connecting magnetic field lines

Directory of Open Access Journals (Sweden)

R. Marchand

2008-12-01

Full Text Available The detection of ionospheric disturbances associated with seismic activity is one of the main objectives of the DEMETER micro-satellite. Its scientific payload provides a comprehensive set of electron and ion measurements. The present work describes a simple model of post-seismic disturbances in the ionosphere above the epicentre. Following a major seism, the neutral atmosphere is assumed to be subject to an acoustic pulse propagating upward, to high altitudes. By coupling this perturbation to the two-dimensional ionospheric model SAMI2 it is then possible to calculate the variations in a number of plasma parameters in the plume region and along connecting magnetic field lines, for an event of representative magnitude. The feasibility of identifying the signature of seismic events from satellite observations is then assessed in view of representative DEMETER measurements and of their natural variability.

Genetic analysis of wild apple resources in Shandong province ...

African Journals Online (AJOL)

Jane

2011-08-22

Aug 22, 2011 ... Apple (malus domestica Borkh.), which is a widely cultivated, important and economic fruit crop with nutritive and medicinal importance, has emerged as a model horticultural crop in this post-genomic era. Wild apple resources are important and they develop gradually in apple industry and genetic diversity.

Epigenetics in mammary gland biology and cancer

Science.gov (United States)

In the post genome era, the focus has shifted to understanding the mechanisms that regulate the interpretation of the genetic code. "Epigenetics" as a research field is taking center stage. Epigenetics is a term which is now being used throughout the scientific community in different contexts from p...

Are there laws of genome evolution?

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Eugene V Koonin

2011-08-01

Full Text Available Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks; the negative correlation between a gene's sequence evolution rate and expression level; and differential scaling of functional classes of genes with genome size. The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model. These models do not explicitly incorporate selection; therefore, the observed universal regularities do not appear to be shaped by selection but rather are emergent properties of gene ensembles. Although a complete physical theory of evolutionary biology is inconceivable, the universals of genome evolution might qualify as "laws of evolutionary genomics" in the same sense "law" is understood in modern physics.

Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes

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Putnam Nicholas H

2011-10-01

Full Text Available Abstract Background Many metazoan genomes conserve chromosome-scale gene linkage relationships (“macro-synteny” from the common ancestor of multicellular animal life 1234, but the biological explanation for this conservation is still unknown. Double cut and join (DCJ is a simple, well-studied model of neutral genome evolution amenable to both simulation and mathematical analysis 5, but as we show here, it is not sufficent to explain long-term macro-synteny conservation. Results We examine a family of simple (one-parameter extensions of DCJ to identify models and choices of parameters consistent with the levels of macro- and micro-synteny conservation observed among animal genomes. Our software implements a flexible strategy for incorporating genomic context into the DCJ model to incorporate various types of genomic context (“DCJ-[C]”, and is available as open source software from http://github.com/putnamlab/dcj-c. Conclusions A simple model of genome evolution, in which DCJ moves are allowed only if they maintain chromosomal linkage among a set of constrained genes, can simultaneously account for the level of macro-synteny conservation and for correlated conservation among multiple pairs of species. Simulations under this model indicate that a constraint on approximately 7% of metazoan genes is sufficient to constrain genome rearrangement to an average rate of 25 inversions and 1.7 translocations per million years.

Military westernization and state repression in the post-Cold War era.

Science.gov (United States)

Swed, Ori; Weinreb, Alexander

2015-09-01

The waves of unrest that have shaken the Arab world since December 2010 have highlighted significant differences in the readiness of the military to intervene in political unrest by forcefully suppressing dissent. We suggest that in the post-Cold War period, this readiness is inversely associated with the level of military westernization, which is a product of the acquisition of arms from western countries. We identify two mechanisms linking the acquisition of arms from western countries to less repressive responses: dependence and conditionality; and a longer-term diffusion of ideologies regarding the proper form of civil-military relations. Empirical support for our hypothesis is found in an analysis of 2523 cases of government response to political unrest in 138 countries in the 1996-2005 period. We find that military westernization mitigates state repression in general, with more pronounced effects in the poorest countries. However, we also identify substantial differences between the pre- and post-9/11 periods. Copyright © 2015 Elsevier Inc. All rights reserved.

The Banana Genome Hub

Science.gov (United States)

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

2013-01-01

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

Nuclear energy and the new era

International Nuclear Information System (INIS)

Sefidvash, F.

1992-01-01

The problem of the utilization of nuclear energy is not only technical but also has important social, economic, political and ethical ramifications. Therefore, to discuss nuclear energy for the future, a vision of the new era needs to be identified. A model for the new era, as a natural consequence of growing interdependence among nations and the process of human evolution is described. The problems of inherent and passive safety, waste disposal, ecology, proliferation, economy and regulatory institutions in the new era are discussed. The particular role of small nuclear power reactors and their potential advantages are described. (author). 12 refs

Risk factors for impaired health status differ in women and men treated with percutaneous coronary intervention in the drug-eluting stent era

DEFF Research Database (Denmark)

Pedersen, Susanne S.; Ong, Andrew T L; Lemos, Pedro A

2006-01-01

In patients treated with percutaneous coronary intervention (PCI) in the drug-eluting stent era, we compared women's and men's health status 6 and 12 months post-PCI and investigated whether predictors of poor health status at 12 months are similar for women and men....

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

Directory of Open Access Journals (Sweden)

Konrad J Karczewski

Full Text Available The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping, a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

God and religion in post-modern philosophers

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José J. Queiroz

2016-12-01

Full Text Available This paper is an essay on the positions of some post-modern philosophers on religion, with the debate about post-modernity as a background. Its preliminary objective is to situate post-modernity taking a position between plain acceptance and categorical refusal in contemporary society. In this polemical field, the paper focuses on three important post-modern philosophers by pointing their contributions for a new thinking about religion today. The procedure consists in the reading of the authors´ texts looking for an interpretation of their discourses on God, religion and the sacred. The conclusion is that post-modernity is not as new era overcoming modernity, but that it is comprised of new themes  that are on the fringes  or even  in opposite directions of modernity´s parameters . One can find these themes in many fields of human knowledge including theology and science of religion. On Derrida´s position, who is the most focused philosopher, the text is still embryonic as it comes from ongoing research.  

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.

METODE MUHADDITSIN DI ERA MODERN

Directory of Open Access Journals (Sweden)

Adriansyah Adriansyah

2016-05-01

Full Text Available After the era of tadwin, almost all disciplines of knowledge in the Islamic world, including the study of hadith, was considered “running on the spot.” Yet, attention and maintenance of the hadith was still favored by intellectuals. Similarly, in the modern era, the hadith remains the object of criticism by not only Muslim intellectuals but also outsiders, such as the West. Western imperialism against the Islamic world in the past was now the beginning of the history of how Muslims are only able to “survive” rather than “attack.” The emergence of defensive and reactive works against trends of the West in criticizing and blasphemed the hadith, then, such works became trends and supporting methodologies among Muslim observers of the hadith in today’s modern era

The Holocaust as Reflected in Communist and Post-Communist Romanian Textbooks

Science.gov (United States)

Barbulescu, Ana; Degeratu, Laura; Gusu, Cosmina

2013-01-01

Romanian history textbooks were mostly silent about the Holocaust during the Communist era. The authors reconstructed the different models of remembering the Holocaust that are present in post-Communist Romanian textbooks. The analysis revealed the existence of six different models of recollecting this history. The six models of representing the…

Genetic analysis of wild apple resources in Shandong province ...

African Journals Online (AJOL)

Apple (malus domestica Borkh.), which is a widely cultivated, important and economic fruit crop with nutritive and medicinal importance, has emerged as a model horticultural crop in this post-genomic era. Wild apple resources are important and they develop gradually in apple industry and genetic diversity. In this study, two ...

Functional annotation of rare gene aberration drivers of pancreatic cancer | Office of Cancer Genomics

Science.gov (United States)

As we enter the era of precision medicine, characterization of cancer genomes will directly influence therapeutic decisions in the clinic. Here we describe a platform enabling functionalization of rare gene mutations through their high-throughput construction, molecular barcoding and delivery to cancer models for in vivo tumour driver screens. We apply these technologies to identify oncogenic drivers of pancreatic ductal adenocarcinoma (PDAC).

Recommended Capacities for Educational Leadership: Pre-Reform Era Scholars versus Reform-Era Scholars versus National Standards

Science.gov (United States)

Gordon, Stephen P.; Taylor-Backor, Karen; Croteau, Susan

2017-01-01

We reviewed the scholarship on capacities for educational leadership for the past decade of the pre-reform era (1976-1985), as well as a recent decade of the reform era (2005-2015), and compared scholarship from both decades with the current Professional Standards for Educational Leaders. We found that scholars in the past decade of the pre-reform…

Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species.

Science.gov (United States)

Khan, Suliman; Nabi, Ghulam; Ullah, Muhammad Wajid; Yousaf, Muhammad; Manan, Sehrish; Siddique, Rabeea; Hou, Hongwei

2016-01-01

In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a "sixth" mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.

Design and development of modular DNA assembly tools for Multigene Engineering and Synthetic Biology in Plants

OpenAIRE

Sarrión Perdigones, Manuel Alejandro

2014-01-01

The post-genomics era has put at the disposal of modern plant breeders an endless list of genetic building blocks for the design of new biotechnological crops. After a first wave of single-gene transgenic with controversial public acceptance, genomic information and technology is paving the way for increasingly complex designs based in multiple gene engineering. Those designs aiming at the production of inexpensive health-promoting compounds are most likely to be welcomed by consumers. In thi...

Statistical methods to detect novel genetic variants using publicly available GWAS summary data.

Science.gov (United States)

Guo, Bin; Wu, Baolin

2018-03-01

We propose statistical methods to detect novel genetic variants using only genome-wide association studies (GWAS) summary data without access to raw genotype and phenotype data. With more and more summary data being posted for public access in the post GWAS era, the proposed methods are practically very useful to identify additional interesting genetic variants and shed lights on the underlying disease mechanism. We illustrate the utility of our proposed methods with application to GWAS meta-analysis results of fasting glucose from the international MAGIC consortium. We found several novel genome-wide significant loci that are worth further study. Copyright © 2018 Elsevier Ltd. All rights reserved.

Emerging interdisciplinary fields in the coming intelligence/convergence era

Science.gov (United States)

Noor, Ahmed K.

2012-09-01

Dramatic advances are in the horizon resulting from rapid pace of development of several technologies, including, computing, communication, mobile, robotic, and interactive technologies. These advances, along with the trend towards convergence of traditional engineering disciplines with physical, life and other science disciplines will result in the development of new interdisciplinary fields, as well as in new paradigms for engineering practice in the coming intelligence/convergence era (post-information age). The interdisciplinary fields include Cyber Engineering, Living Systems Engineering, Biomechatronics/Robotics Engineering, Knowledge Engineering, Emergent/Complexity Engineering, and Multiscale Systems engineering. The paper identifies some of the characteristics of the intelligence/convergence era, gives broad definition of convergence, describes some of the emerging interdisciplinary fields, and lists some of the academic and other organizations working in these disciplines. The need is described for establishing a Hierarchical Cyber-Physical Ecosystem for facilitating interdisciplinary collaborations, and accelerating development of skilled workforce in the new fields. The major components of the ecosystem are listed. The new interdisciplinary fields will yield critical advances in engineering practice, and help in addressing future challenges in broad array of sectors, from manufacturing to energy, transportation, climate, and healthcare. They will also enable building large future complex adaptive systems-of-systems, such as intelligent multimodal transportation systems, optimized multi-energy systems, intelligent disaster prevention systems, and smart cities.

Storm-Tracks in ERA-40 and ERA-Interim Reanalyses

Science.gov (United States)

Liberato, M. L. R.; Trigo, I. F.; Trigo, R. M.

2009-04-01

Extratropical cyclones, their dominant paths, frequency and intensity have long been the object of climatological studies. The analysis of cyclone characteristics for the Euro-Atlantic sector (85°W-70°E; 20°N-75°N) presented here is based on the cyclone detecting and tracking algorithm first developed for the Mediterranean region (Trigo et al., 1999, 2002) and recently extended to a larger Euro-Atlantic region (Trigo, 2006). The objective methodology, which identifies and follows individual lows (Trigo et al. 1999), is applied to 6-hourly geopotential data at 1000-hPa from two reanalyses datasets provided by the European Centre for Medium-Range Weather Forecasts (ECMWF): ERA-40 and ERA-Interim reanalyses. Two storm-track databases are built over the Northern Atlantic European area, spanning the common available extended winter seasons from October 1989 to March 2002. Although relatively short, this common period allows a comparison of systems represented in reanalyses datasets with distinct horizontal resolutions (T106 and T255, respectively). This exercise is mostly focused on the key areas of cyclone formation and dissipation and main cyclone characteristics for the Euro-Atlantic sector. Trigo, I. F., T. D. Davies, and G. R. Bigg, 1999: Objective climatology of cyclones in the Mediterranean region. J. Climate, 12, 1685-1696. Trigo I. F., G. R. Bigg and T. D. Davies, 2002: Climatology of Cyclogenesis Mechanisms in the Mediterranean. Mon. Weather Rev. 130, 549-569. Trigo, I. F. 2006: Climatology and Interannual Variability of Storm-Tracks in the Euro-Atlantic sector: a comparison between ERA-40 and NCEP/NCAR Reanalyses. Clim. Dyn. DOI 10.1007/s00382-005-0065-9.

Ireland – a test case of Post-colonialism / Post colonialism

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Brenda Murray

2006-05-01

Full Text Available Contextualisation This review attempts to set the stage for post-colonial theorising, in the light of alternative representations of ‘whiteness’, on issues of gender, race and language within the discourse of equality. In this paper Ireland and the Irish provide a backdrop against which the nature and impact of colonialism on the colonised and the coloniser are explored. Many challenging questions emerge about the ideological basis of post colonial theory, not least when traditional paradigms of racism, as conveyed by the black / white dichotomy, are examined: Ireland presents a context, it is argued, where subjugation is of white on white. Linked to this is the language of the coloniser, a powerful hegemonic force which, in some situations, has been nurtured by the colonised and later developed into a text which is unique, producing a new literature which, it is asserted, truly invokes the ‘post colonial’. Abstract: Post-colonialism – essentially a critique of colonialism, is characterised by a process of disengagement from the colonial epoch and has taken many forms. In this article a set of phenomena are examined that have become inscribed in the cultures of the colonised with a view to identifying alternative cultural origins and dispositions recovered in this post-colonial era. Ireland and the Irish provide the background context of this exploration into perspectives generated by the peripheral or post-colonial nations. Globalisation, too, has had a role to play in the increasing de-territorialisation of communities as a result of cross-frontier mobility, increased intra-community mobility and new communication technologies. A critical reflection on the process of disengagement leads the author to conclude that we must come to recognise new cultural forms which are accepting of a heterogeneous and inclusive society: one which is not characterised by difference.

12 CFR 360.7 - Post-insolvency interest.

Science.gov (United States)

2010-01-01

... becomes proven. (4) Post-insolvency interest shall be determined using a simple interest method of... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Post-insolvency interest. 360.7 Section 360.7... RESOLUTION AND RECEIVERSHIP RULES § 360.7 Post-insolvency interest. (a) Purpose and scope. This section...

Public attitudes to the promotion of genomic crop studies in Japan: correlations between genomic literacy, trust, and favourable attitude.

Science.gov (United States)

Ishiyama, Izumi; Tanzawa, Tetsuro; Watanabe, Maiko; Maeda, Tadahiko; Muto, Kaori; Tamakoshi, Akiko; Nagai, Akiko; Yamagata, Zentaro

2012-05-01

This study aimed to assess public attitudes in Japan to the promotion of genomic selection in crop studies and to examine associated factors. We analysed data from a nationwide opinion survey. A total of 4,000 people were selected from the Japanese general population by a stratified two-phase sampling method, and 2,171 people participated by post; this survey asked about the pros and cons of crop-related genomic studies promotion, examined people's scientific literacy in genomics, and investigated factors thought to be related to genomic literacy and attitude. The relationships were examined using logistic regression models stratified by gender. Survey results showed that 50.0% of respondents approved of the promotion of crop-related genomic studies, while 6.7% disapproved. No correlation was found between literacy and attitude towards promotion. Trust in experts, belief in science, an interest in genomic studies and willingness to purchase new products correlated with a positive attitude towards crop-related genomic studies.

Swabs to genomes: a comprehensive workflow

Directory of Open Access Journals (Sweden)

Madison I. Dunitz

2015-05-01

Full Text Available The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become much easier for research labs with access to standard molecular biology and computational tools. However, there are a confusing variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children.

Science.gov (United States)

Zhang, Chenhong; Yin, Aihua; Li, Hongde; Wang, Ruirui; Wu, Guojun; Shen, Jian; Zhang, Menghui; Wang, Linghua; Hou, Yaping; Ouyang, Haimei; Zhang, Yan; Zheng, Yinan; Wang, Jicheng; Lv, Xiaofei; Wang, Yulan; Zhang, Feng; Zeng, Benhua; Li, Wenxia; Yan, Feiyan; Zhao, Yufeng; Pang, Xiaoyan; Zhang, Xiaojun; Fu, Huaqing; Chen, Feng; Zhao, Naisi; Hamaker, Bruce R; Bridgewater, Laura C; Weinkove, David; Clement, Karine; Dore, Joel; Holmes, Elaine; Xiao, Huasheng; Zhao, Guoping; Yang, Shengli; Bork, Peer; Nicholson, Jeremy K; Wei, Hong; Tang, Huiru; Zhang, Xiaozhuang; Zhao, Liping

2015-08-01

Gut microbiota has been implicated as a pivotal contributing factor in diet-related obesity; however, its role in development of disease phenotypes in human genetic obesity such as Prader-Willi syndrome (PWS) remains elusive. In this hospitalized intervention trial with PWS (n = 17) and simple obesity (n = 21) children, a diet rich in non-digestible carbohydrates induced significant weight loss and concomitant structural changes of the gut microbiota together with reduction of serum antigen load and alleviation of inflammation. Co-abundance network analysis of 161 prevalent bacterial draft genomes assembled directly from metagenomic datasets showed relative increase of functional genome groups for acetate production from carbohydrates fermentation. NMR-based metabolomic profiling of urine showed diet-induced overall changes of host metabotypes and identified significantly reduced trimethylamine N-oxide and indoxyl sulfate, host-bacteria co-metabolites known to induce metabolic deteriorations. Specific bacterial genomes that were correlated with urine levels of these detrimental co-metabolites were found to encode enzyme genes for production of their precursors by fermentation of choline or tryptophan in the gut. When transplanted into germ-free mice, the pre-intervention gut microbiota induced higher inflammation and larger adipocytes compared with the post-intervention microbiota from the same volunteer. Our multi-omics-based systems analysis indicates a significant etiological contribution of dysbiotic gut microbiota to both genetic and simple obesity in children, implicating a potentially effective target for alleviation. Poorly managed diet and genetic mutations are the two primary driving forces behind the devastating epidemic of obesity-related diseases. Lack of understanding of the molecular chain of causation between the driving forces and the disease endpoints retards progress in prevention and treatment of the diseases. We found that children

Post-traumatic Perineal Pubic Rami Protrusion: A Simple Surgical Management

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Voon Victor

2014-06-01

Full Text Available Although pubic ramus fractures are common, they usually heal without surgical intervention and result in little long-term disability. We herein present two cases of symptomatic malunion of pubic rami fracture, which was successfully treated with a simple and safe surgical technique. The patients' local symptoms resolved afterwards.

Microsatellite Primer Development for Post Oak, Quercus stellata (Fagaceae

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Warren B. Chatwin

2014-10-01

Full Text Available Premise of the study: The American Cross Timbers forest ecosystem runs from southeastern Kansas to Central Texas and is primarily composed of post oak (Quercus stellata. This old-growth forest currently occupies only about 2% of its ancestral range. To facilitate genetic research on this species, we developed microsatellite primers specific to post oak from reduced genomic libraries. Methods and Results: Two Q. stellata individuals, sampled from the northern and southern range of the post oak forest, were subject to genomic reduction and 454 pyrosequencing. Bioinformatic analysis identified putative microsatellites from which 12 polymorphic primer sets were screened on three populations. The number of alleles observed ranged from five to 20 across all populations, while observed and expected heterozygosity values ranged from 0.05 to 0.833 and 0.236 to 0.893, respectively, within individual populations. Conclusions: We report the development of microsatellite markers, specific to post oak, to aid the study of genetic diversity and population structure of extant forest remnants.

Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

Directory of Open Access Journals (Sweden)

Huaiyong Luo

Full Text Available The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus.

Science.gov (United States)

Luo, Huaiyong; Wang, Xiaojie; Zhan, Gangming; Wei, Guorong; Zhou, Xinli; Zhao, Jing; Huang, Lili; Kang, Zhensheng

2015-01-01

The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.

Genome sequence of the Fleming strain of Micrococcus luteus, a simple free- living actinobacterium

Energy Technology Data Exchange (ETDEWEB)

Young, Michael; Artsatbanov, Vladislav; Beller, Harry R.; Chandra, Govind; Chater, Keith F.; Dover, Lynn G.; Goh, Ee-Been; Kahan, Tamar; Kaprelyants, Arseny S.; Kyrpides, Nikos; Lapidus, Alla; Lowry, Stephen R.; Lykidis, Athanasios; Mahillon, Jacques; Markowitz, Viktor; Mavrommatis, Konstantinos; Mukamolova, Galina V.; Oren, Aharon; Rokem, J. Stefan; Smith, Margaret C. M.; Young, Danielle I.; Greenblatt, Charles L.

2009-11-01

Micrococcus luteus (NCTC2665, Fleming strain) has one of the smallest genomes of free living actinobacteria sequenced to date, comprising a single circular chromosome of 2,501,097 bp (G+C content 73%) predicted to encode 2403 proteins. The genome shows extensive synteny with that of the closely related organism, Kocuria rhizophila, from which it was taxonomically separated relatively recently. Despite its small size, the genome harbors 73 IS elements, almost all of which are closely related to elements found in other actinobacteria. An IS element is inserted into the rrs gene of one of only two rrn operons found in M. luteus. The genome encodes only four sigma factors and fourteen response regulators, indicative of adaptation to a rather strict ecological niche (mammalian skin). The high sensitivity of M. luteus to {Beta}-lactam antibiotics may result from the presence of a reduced set of penicillin binding proteins and the absence of a wblC gene, which plays an important role in antibiotic resistance in other actinobacteria. Consistent with the restricted range of compounds it can use as a sole source of carbon for energy and growth, M. luteus has a minimal complement of genes concerned with carbohydrate transport and metabolism and its inability to utilize glucose as a sole carbon source may be due to the apparent absence of a gene encoding glucokinase. Uniquely among characterized bacteria, M. luteus appears to be able to metabolize glycogen only via trehalose, and to make trehalose only via glycogen. It has very few genes associated with secondary metabolism. In contrast to other actinobacteria, M. luteus encodes only one resuscitation-promoting factor (Rpf) required for emergence from dormancy and its complement of other dormancy-related proteins is also much reduced. M. luteus is capable of long-chain alkene biosynthesis, which is of interest for advanced biofuel production; a three gene cluster essential for this metabolism has been identified in the genome.

ERA's Ranger uranium mine

International Nuclear Information System (INIS)

Davies, W.

1997-01-01

Energy Resource of Australia (ERA) is a public company with 68% of its shares owned by the Australian company North Limited. It is currently operating one major production centre - Ranger Mine which is 260 kilometres east of Darwin, extracting and selling uranium from the Ranger Mine in the Northern Territory to nuclear electricity utilities in Japan, South Korea, Europe and North America. The first drum of uranium oxide from Ranger was drummed in August 1981 and operations have continued since that time. ERA is also in the process of working towards obtaining approvals for the development of a second mine - Jabiluka which is located 20 kilometres north of Ranger. The leases of Ranger and Jabiluka adjoin. The Minister for the Environment has advised the Minister for Resources and Energy that there does not appear to be any environmental issue which would prevent the preferred Jabiluka proposal from proceeding. Consent for the development of ERA's preferred option for the development of Jabiluka is being sought from the Aboriginal Traditional Owners. Ranger is currently the third largest producing uranium mine in the world producing 4,237 tonnes of U 3 O 8 in the year to June 1997

Complete genome sequence of the myxobacterium Sorangium cellulosum

DEFF Research Database (Denmark)

Schneiker, S; Perlova, O; Kaiser, O

2007-01-01

The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum Soce56, which produces several natural products and has...... morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between...... these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism...

Long-memory exchange rate dynamics in the euro era

International Nuclear Information System (INIS)

Barkoulas, John T.; Barilla, Anthony G.; Wells, William

2016-01-01

We investigate the long-run dynamics of a system of eight major exchange rates in the euro era using both integer and fractional cointegration methodologies. Contrary to the fragile evidence in the pre-euro era, robust evidence of linear cointegratedness is obtained in the foreign exchange market during the euro era. Upon closer examination, deviations from the cointegrating relationship exhibit nonstationary, long-memory dynamic behavior (Joseph effect). We find the long-memory evidence to be temporally stable in the most recent era. Finally, the foreign exchange system dynamics appears to be characterized by less persistence (smaller fractional exponent) in the euro era (as compared to pre-euro time periods), potentially indicating increased policy coordination by central banks in the recent period.

Theory of microbial genome evolution

Science.gov (United States)

Koonin, Eugene

Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

Communicating mathematics in the digital era

CERN Document Server

Borwein, Jonathan; Rodrigues, Jose Francisco

2008-01-01

The digital era has dramatically changed the ways that researchers search, produce, publish, and disseminate their scientific work. These processes are still rapidly evolving due to improvements in information science, new achievements in computer science technologies, and initiatives such as DML and open access journals, digitization projects, scientific reference catalogs, and digital repositories. These changes have prompted many mathematicians to play an active part in the developments of the digital era, and have led mathematicians to promote and discuss new ideas with colleagues from other fields, such as technology developers and publishers. This book is a collection of contributions by key leaders in the field, offering the paradigms and mechanisms for producing, searching, and exploiting scientific and technical scholarship in mathematics in the digital era.

Post-silking Factor Consequences for N Efficiency Changes Over 38 Years of Commercial Maize Hybrids

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Keru Chen

2017-10-01

Full Text Available Hybrid selection in maize (Zea mays L. over the decades has increased post-silking dry matter (PostDM and nitrogen (PostN accumulation, often with an accompanying increase in one or more N use efficiency (NUE metrics such as partial factor productivity (PFP, N conversion efficiency (NCE, and N internal efficiency (NIE. More certainty on the underlying mechanisms of how PostDM and PostN changes over time have contributed to NUE gains or losses in modern-era hybrids can only be realized by directly comparing hybrids of different eras in the context of production-system-relevant management systems. A two-year and two-location field study was conducted in Indiana with two N rates (55 and 220 kg N ha−1, three plant densities (54,000, 79,000, and 104,000 plants ha−1 and eight commercial hybrids that were released by a single seed company from 1967 to 2005. The main treatment effects of N rate, density, and hybrid dominated the PostDM and PostN responses, and there were no significant two-way or three-way interactions. Total dry matter at maturity gains averaged 80 kg ha−1 year−1 of hybrid release when averaged over locations, plant densities and N rates. Total N contents at maturity increased 0.68 kg ha−1 year−1, primarily due to annual increases in grain N content (0.8 kg ha−1 year−1. Post-silking N uptake rate increased 0.44 kg ha−1 year−1 for these era hybrids in more favorable production site-years. Slopes of grain N concentration increases per unit PostN gain were similar for all hybrids. Gains in average PFP over time were considerably higher at the low N rate (0.9 kg ha−1 year−1 than at the high N rate (0.3 kg kg−1 year−1. Hybrid gains in NIE were evident from 1967 to 1994, but not thereafter. The low N rate and higher plant densities also increased relative NIE and NCE values, but without hybrid interactions. There was no consistent trend of NIE or NCE gains in these hybrids primarily because grain and whole-plant N

Investigating the gene expression profiles of metastasising sarcoma cells

Czech Academy of Sciences Publication Activity Database

Cavanna, T.; Pokorná, Eva; Veselý, Pavel; Zicha, D.

2005-01-01

Roč. 40, č. 1 (2005), s. 37 ISSN 0035-9017. [Cytokinematics 2004. International Symposium on Microscopy of Live Cells in the Post Genomics Era /8./. 05.09.2004-07.09.2004, Hradec Králové] Institutional research plan: CEZ:AV0Z5052915 Keywords : sarcoma * metastasis Subject RIV: EB - Genetics ; Molecular Biology

Simplified extraction of good quality genomic DNA from a variety of ...

African Journals Online (AJOL)

Depending on the nature and complexity of plant material, proper method needs to be employed for extraction of genomic DNA, along with its performance evaluation by different molecular techniques. Here, we optimized and employed a simple genomic DNA isolation protocol suitable for a variety of plant materials ...

D-GENIES: dot plot large genomes in an interactive, efficient and simple way.

Science.gov (United States)

Cabanettes, Floréal; Klopp, Christophe

2018-01-01

Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots, but they are often limited in the input sequence size. D-GENIES is a standalone and web application performing large genome alignments using minimap2 software package and generating interactive dot plots. It enables users to sort query sequences along the reference, zoom in the plot and download several image, alignment or sequence files. D-GENIES is an easy-to-install, open-source software package (GPL) developed in Python and JavaScript. The source code is available at https://github.com/genotoul-bioinfo/dgenies and it can be tested at http://dgenies.toulouse.inra.fr/.

Lateral gene exchanges shape the genomes of amoeba-resisting microorganisms

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Claire eBertelli

2012-08-01

Full Text Available Based on Darwin’s concept of the tree of life, vertical inheritance was thought to be dominant, and mutations, deletions and duplication were streaming the genomes of living organisms. In the current genomic era, increasing data indicated that both vertical and lateral gene inheritance interact in space and time to trigger genome evolution, particularly among microorganisms sharing a given ecological niche. As a paradigm to their diversity and their survival in a variety of cell types, intracellular microorganisms, and notably intracellular bacteria, were considered as less prone to lateral genetic exchanges. Such specialized microorganisms generally have a smaller gene repertoire because they do rely on their host’s factors for some basic regulatory and metabolic functions. Here we review events of lateral gene transfer (LGT that illustrate the genetic exchanges among intra-amoebal microorganisms or between the microorganism and its amoebal host. We tentatively investigate the functions of laterally transferred genes in the light of the interaction with their host as they should confer a selective advantage and success to the amoeba-resisting microorganisms.

Implementation of the Spanish ERAS program in bariatric surgery.

Science.gov (United States)

Ruiz-Tovar, Jaime; Muñoz, José Luis; Royo, Pablo; Duran, Manuel; Redondo, Elisabeth; Ramirez, Jose Manuel

2018-03-08

The essence of Enhanced Recovery After Surgery (ERAS) programs is the multimodal approach, and many authors have demonstrated safety and feasibility in fast track bariatric surgery. According to this concept, a multidisciplinary ERAS program for bariatric surgery has been developed by the Spanish Fast Track Group (ERAS Spain). The aim of this study was to analyze the initial implementation of this Spanish National ERAS protocol in bariatric surgery, comparing it with a historical cohort receiving standard care. A multi-centric prospective study was performed, including 233 consecutive patients undergoing bariatric surgery during 2015 and following ERAS protocol. It was compared with a historical cohort of 286 patients, who underwent bariatric surgery at the same institutions between 2013 and 2014 and following standard care. Compliance with the protocol, morbidity, mortality, hospital stay and readmission were evaluated. Bariatric techniques performed were Roux-en-Y gastric bypass and sleeve gastrectomy. There were no significant differences in complications, mortality and readmission. Postoperative pain and hospital stay were significantly lower in the ERAS group. The total compliance to protocol was 80%. The Spanish National ERAS protocol is a safe issue, obtaining similar results to standard care in terms of complications, reoperations, mortality and readmissions. It is associated with less postoperative pain and earlier hospital discharge.

Advances in genome editing for improved animal breeding: A review

Directory of Open Access Journals (Sweden)

Shakil Ahmad Bhat

2017-11-01

Full Text Available Since centuries, the traits for production and disease resistance are being targeted while improving the genetic merit of domestic animals, using conventional breeding programs such as inbreeding, outbreeding, or introduction of marker-assisted selection. The arrival of new scientific concepts, such as cloning and genome engineering, has added a new and promising research dimension to the existing animal breeding programs. Development of genome editing technologies such as transcription activator-like effector nuclease, zinc finger nuclease, and clustered regularly interspaced short palindromic repeats systems begun a fresh era of genome editing, through which any change in the genome, including specific DNA sequence or indels, can be made with unprecedented precision and specificity. Furthermore, it offers an opportunity of intensification in the frequency of desirable alleles in an animal population through gene-edited individuals more rapidly than conventional breeding. The specific research is evolving swiftly with a focus on improvement of economically important animal species or their traits all of which form an important subject of this review. It also discusses the hurdles to commercialization of these techniques despite several patent applications owing to the ambiguous legal status of genome-editing methods on account of their disputed classification. Nonetheless, barring ethical concerns gene-editing entailing economically important genes offers a tremendous potential for breeding animals with desirable traits.

Organogenesis in deep time: A problem in genomics, development, and paleontology.

Science.gov (United States)

Pieretti, Joyce; Gehrke, Andrew R; Schneider, Igor; Adachi, Noritaka; Nakamura, Tetsuya; Shubin, Neil H

2015-04-21

The fossil record is a unique repository of information on major morphological transitions. Increasingly, developmental, embryological, and functional genomic approaches have also conspired to reveal evolutionary trajectory of phenotypic shifts. Here, we use the vertebrate appendage to demonstrate how these disciplines can mutually reinforce each other to facilitate the generation and testing of hypotheses of morphological evolution. We discuss classical theories on the origins of paired fins, recent data on regulatory modulations of fish fins and tetrapod limbs, and case studies exploring the mechanisms of digit loss in tetrapods. We envision an era of research in which the deep history of morphological evolution can be revealed by integrating fossils of transitional forms with direct experimentation in the laboratory via genome manipulation, thereby shedding light on the relationship between genes, developmental processes, and the evolving phenotype.

Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species

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Suliman Khan

2016-01-01

Full Text Available In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a “sixth” mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.

Genome-Wide Transcriptome Analysis Reveals Extensive Alternative Splicing Events in the Protoscoleces of Echinococcus granulosus and Echinococcus multilocularis

Science.gov (United States)

Liu, Shuai; Zhou, Xiaosu; Hao, Lili; Piao, Xianyu; Hou, Nan; Chen, Qijun

2017-01-01

Alternative splicing (AS), as one of the most important topics in the post-genomic era, has been extensively studied in numerous organisms. However, little is known about the prevalence and characteristics of AS in Echinococcus species, which can cause significant health problems to humans and domestic animals. Based on high-throughput RNA-sequencing data, we performed a genome-wide survey of AS in two major pathogens of echinococcosis-Echinococcus granulosus and Echinococcus multilocularis. Our study revealed that the prevalence and characteristics of AS in protoscoleces of the two parasites were generally consistent with each other. A total of 6,826 AS events from 3,774 E. granulosus genes and 6,644 AS events from 3,611 E. multilocularis genes were identified in protoscolex transcriptomes, indicating that 33–36% of genes were subject to AS in the two parasites. Strikingly, intron retention instead of exon skipping was the predominant type of AS in Echinococcus species. Moreover, analysis of the Kyoto Encyclopedia of Genes and Genomes pathway indicated that genes that underwent AS events were significantly enriched in multiple pathways mainly related to metabolism (e.g., purine, fatty acid, galactose, and glycerolipid metabolism), signal transduction (e.g., Jak-STAT, VEGF, Notch, and GnRH signaling pathways), and genetic information processing (e.g., RNA transport and mRNA surveillance pathways). The landscape of AS obtained in this study will not only facilitate future investigations on transcriptome complexity and AS regulation during the life cycle of Echinococcus species, but also provide an invaluable resource for future functional and evolutionary studies of AS in platyhelminth parasites. PMID:28588571

Development of a Post-Graduate Year 2 Pharmacy Residency in Clinical Pharmacogenetics

Science.gov (United States)

Hoffman, James M.; Gammal, Roseann S.; Relling, Mary V.; Crews, Kristine R.

2017-01-01

Purpose The structure and development of an innovative clinical pharmacogenetics post-graduate year 2 (PGY2) ASHP-accredited residency program is described. Summary The advent of the era of genomics has left practitioners wondering how to interpret the data obtained from sequencing and genotyping patients. In order to train the next leaders in the area of implementing pharmacogenetics, St. Jude Children’s Research Hospital established the first accredited residency program in clinical pharmacogenetics. The 12-month long PGY2 residency was created in accordance with the ASHP standards for advanced practice residencies. The resident learns to optimize patient outcomes through the expert provision of evidence-based, patient-centered precision medicine as an integral part of an interdisciplinary team. The resident gains hands-on experience in a dynamic environment regarding all aspects of running a clinical pharmacogenetics service. Since the first resident graduated in 2012, the program has graduated one resident each year. Conclusion To fill a need for pharmacists trained in pharmacogenetics, an innovative PGY2 residency in clinical pharmacogenetics was successfully developed. Upon completion of the program, residents are equipped with the clinical skills and necessary experience to drive precision medicine forward and lead the implementation of pharmacogenetics in various healthcare settings. PMID:28274984

Genome Editing in Sugarcane: Challenges ahead

Directory of Open Access Journals (Sweden)

Chakravarthi Mohan

2016-10-01

Full Text Available Genome editing opens new and unique opportunities for researchers to enhance crop production. Until 2013, the zinc finger nucleases (ZFNs and transcription activator-like effector nucleases (TALENs were the key tools used for genome editing applications. The advent of RNA-guided engineered nucleases - the type II clustered regularly interspaced short palindromic repeat (CRISPR/Cas9 (CRISPR-associated system from Streptococcus pyogenes holds great potential since it is simple, effective and more versatile than ZFNs and TALENs. CRISPR/Cas9 system has already been successfully employed in several crop plants. Use of these techniques is in its infant stage in sugarcane. Jung and Altpeter (2016 have reported TALEN mediated approach for the first time to reduce lignin content in sugarcane to make it amenable for biofuel production. This is so far the only report describing genome editing in sugarcane. Large genome size, polyploidy, low transformation efficiency, transgene silencing and lack of high throughput screening techniques are certainly great challenges for genome editing in sugarcane which would be discussed in detail in this review.

Foreword

Indian Academy of Sciences (India)

While the article on epigenetics would reveal how the basic paradigm of gene regulation is fast changing in the post-genome era, the article on a detailed study on one type of protein throws light on the amazing diversity in functions and thereby the physiology of organisms that evolution can throw up by varying the structure ...

In vitro dynamics of supra-posomal structures in RSK4 rat sarcoma cells

Czech Academy of Sciences Publication Activity Database

Veselý, Pavel; Blase, C.; Matoušková, Eva; Sukhorukov, V.; Bereiter-Hahn, J.

2005-01-01

Roč. 40, č. 1 (2005), s. 36 ISSN 0035-9017. [Cytokinematics 2004. International Symposium on Microscopy of Live Cells in the Post Genomics Era /8./. 05.09.2004-07.09.2004, Hradec Králové] Institutional research plan: CEZ:AV0Z5052915 Keywords : RSK4 rat sarcoma cells * podosomes Subject RIV: EB - Genetics ; Molecular Biology

Searching for genomic constraints

Energy Technology Data Exchange (ETDEWEB)

Lio` , P [Cambridge, Univ. (United Kingdom). Genetics Dept.; Ruffo, S [Florence, Univ. (Italy). Fac. di Ingegneria. Dipt. di Energetica ` S. Stecco`

1998-01-01

The authors have analyzed general properties of very long DNA sequences belonging to simple and complex organisms, by using different correlation methods. They have distinguished those base compositional rules that concern the entire genome which they call `genomic constraints` from the rules that depend on the `external natural selection` acting on single genes, i. e. protein-centered constraints. They show that G + C content, purine / pyrimidine distributions and biological complexity of the organism are the most important factors which determine base compositional rules and genome complexity. Three main facts are here reported: bacteria with high G + C content have more restrictions on base composition than those with low G + C content; at constant G + C content more complex organisms, ranging from prokaryotes to higher eukaryotes (e.g. human) display an increase of repeats 10-20 nucleotides long, which are also partly responsible for long-range correlations; work selection of length 3 to 10 is stronger in human and in bacteria for two distinct reasons. With respect to previous studies, they have also compared the genomic sequence of the archeon Methanococcus jannaschii with those of bacteria and eukaryotes: it shows sometimes an intermediate statistical behaviour.

Searching for genomic constraints

International Nuclear Information System (INIS)

Lio', P.; Ruffo, S.

1998-01-01

The authors have analyzed general properties of very long DNA sequences belonging to simple and complex organisms, by using different correlation methods. They have distinguished those base compositional rules that concern the entire genome which they call 'genomic constraints' from the rules that depend on the 'external natural selection' acting on single genes, i. e. protein-centered constraints. They show that G + C content, purine / pyrimidine distributions and biological complexity of the organism are the most important factors which determine base compositional rules and genome complexity. Three main facts are here reported: bacteria with high G + C content have more restrictions on base composition than those with low G + C content; at constant G + C content more complex organisms, ranging from prokaryotes to higher eukaryotes (e.g. human) display an increase of repeats 10-20 nucleotides long, which are also partly responsible for long-range correlations; work selection of length 3 to 10 is stronger in human and in bacteria for two distinct reasons. With respect to previous studies, they have also compared the genomic sequence of the archeon Methanococcus jannaschii with those of bacteria and eukaryotes: it shows sometimes an intermediate statistical behaviour

A strategy to compute plastic post-buckling of structures

International Nuclear Information System (INIS)

Combescure, A.

1983-08-01

The paper gives a general framework to the different strategies used to compute the post-buckling of structures. Two particular strategies are studied in more details and it is shown how they can be applied in the plastic regime. All the methods suppose that the loads F are proportional to a simple parameter lambda; more precisely: eq (1) F = lambda F 0 . The paper shows how these methods can be implemented in a very simple way. In the elastic case we show the application of the method to the calculation of post buckling response of a clamped arch. The method is also applied to a very simple case of two bars which can be calculated analytically. In the plastic range, the method is applied to the post-buckling of an imperfect ring which can be calculated analytically. Another example is the comparison of the comparison of the computed post-buckling of a thin cylinder under axial compression, and of the experimental behavior on the same cylinder. The limitation of these types of strategies are also mentionned and the physical signifiance of calculations in the post-buckling regime are discussed

Outcome of surgery in post-cytomegalovirus retinal detachment: Experience before and in the era of highly active anti-retroviral therapy in Indian eyes

Directory of Open Access Journals (Sweden)

Ramandeep Singh

2013-01-01

Full Text Available Purpose: To evaluate the outcome of surgery for cytomegalovirus associated retinal detachment (CMVRD in human immunodeficiency virus (HIV-infected patients in pre-highly active antiretroviral therapy (HAART and HAART era in Indian eyes. Materials and Methods: Retrospective, we reviewed medical records of all consecutive HIV patients, who underwent surgical repair for CMVRD from July 1998 to June 2011. We divided patients into two groups, i.e. group 1, pre HAART era and group 2, HAART era. We compared two groups for various parameters like visual outcome, surgical success, additional procedures, follow-up, etc., Results: Twenty-eight eyes of 26 patients were included; 12 eyes of the 11 patients in group 1 and 16 eyes of the 15 patients in group 2. Significant visual acuity improvement was seen in both groups. Complete anatomic success was seen in 11 eyes in group 1 and 15 eyes in group 2. One additional procedure in group 1 and 29 additional procedures were done in group 2. A mean follow-up was 16 months in group 1 and 41 months in group 2. Conclusion: There was no difference in outcome in pre-HAART and HAART group, except for longer follow-up and additional surgical procedures in HAART group.

Coastal Change Analysis Program (C-CAP) zone 66 1995-era and 2000-era land cover change analysis (NODC Accession 0042136)

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains the 1995-era and 2000-era classifications of US Coast zone 66 and can be used to analyze change. This imagery was collected as part of the...

Integrating population genetics and conservation biology in the era of genomics.

Science.gov (United States)

Ouborg, N Joop

2010-02-23

As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled 'Integrating Population Genetics and Conservation Biology' was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.

The Michelson Era in American Science, 1870--1930

International Nuclear Information System (INIS)

Goldberg, S.; Stuewer, R.H.

1988-01-01

The articles in this volume relate, in one way or another, to a single experiment: the Michelson-Morley ether-drift experiment of 1887. About one-half of the articles in the collection are based on papers delivered at a two-day symposium ''The Michelson Era in American Science: 1870--1930,'' held a Case Western Reserve University in Cleveland, Ohio, 28--29 October 1987, commemorating the centennial of the experiment. The Michelson-Morley experiment was designed to detect the motion of the earth through the luminiferous ether. At the time, physicists did not question the existence of the ether. The experiment, like many physical probes of nature, was simple in conception, yet uncompromisingly demanding of the art of contemporary craftsmanship. The state of the mechanical arts and its relationship to the pursuit of physical science in late nineteenth- century America is well documented in Section I, which also addresses the more general question of the link between state-of-the-art shop practice and engineering theory

The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima

NARCIS (Netherlands)

Chipman, Ariel D; Ferrier, David E K; Brena, Carlo; Qu, Jiaxin; Hughes, Daniel S T; Schröder, Reinhard; Torres-Oliva, Montserrat; Znassi, Nadia; Jiang, Huaiyang; Almeida, Francisca C; Alonso, Claudio R; Apostolou, Zivkos; Aqrawi, Peshtewani; Arthur, Wallace; Barna, Jennifer C J; Blankenburg, Kerstin P; Brites, Daniela; Capella-Gutiérrez, Salvador; Coyle, Marcus; Dearden, Peter K; Du Pasquier, Louis; Duncan, Elizabeth J; Ebert, Dieter; Eibner, Cornelius; Erikson, Galina; Evans, Peter D; Extavour, Cassandra G; Francisco, Liezl; Gabaldón, Toni; Gillis, William J; Goodwin-Horn, Elizabeth A; Green, Jack E; Griffiths-Jones, Sam; Grimmelikhuijzen, Cornelis J P; Gubbala, Sai; Guigó, Roderic; Han, Yi; Hauser, Frank; Havlak, Paul; Hayden, Luke; Helbing, Sophie; Holder, Michael; Hui, Jerome H L; Hunn, Julia P; Hunnekuhl, Vera S; Jackson, LaRonda; Javaid, Mehwish; Jhangiani, Shalini N; Jiggins, Francis M; Jones, Tamsin E; Kaiser, Tobias S; Kalra, Divya; Kenny, Nathan J; Korchina, Viktoriya; Kovar, Christie L; Kraus, F Bernhard; Lapraz, François; Lee, Sandra L; Lv, Jie; Mandapat, Christigale; Manning, Gerard; Mariotti, Marco; Mata, Robert; Mathew, Tittu; Neumann, Tobias; Newsham, Irene; Ngo, Dinh N; Ninova, Maria; Okwuonu, Geoffrey; Ongeri, Fiona; Palmer, William J; Patil, Shobha; Patraquim, Pedro; Pham, Christopher; Pu, Ling-Ling; Putman, Nicholas H; Rabouille, Catherine; Ramos, Olivia Mendivil; Rhodes, Adelaide C; Robertson, Helen E; Robertson, Hugh M; Ronshaugen, Matthew; Rozas, Julio; Saada, Nehad; Sánchez-Gracia, Alejandro; Scherer, Steven E; Schurko, Andrew M; Siggens, Kenneth W; Simmons, DeNard; Stief, Anna; Stolle, Eckart; Telford, Maximilian J; Tessmar-Raible, Kristin; Thornton, Rebecca; van der Zee, Maurijn; von Haeseler, Arndt; Williams, James M; Willis, Judith H; Wu, Yuanqing; Zou, Xiaoyan; Lawson, Daniel; Muzny, Donna M; Worley, Kim C; Gibbs, Richard A; Akam, Michael; Richards, Stephen

2014-01-01

Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present

The Whole Genome Assembly and Comparative Genomic Research of Thellungiella parvula (Extremophile Crucifer Mitochondrion

Directory of Open Access Journals (Sweden)

Xuelin Wang

2016-01-01

Full Text Available The complete nucleotide sequences of the mitochondrial (mt genome of an extremophile species Thellungiella parvula (T. parvula have been determined with the lengths of 255,773 bp. T. parvula mt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome of T. parvula, including 24 direct repeats, 28 tandem repeats (TRs, and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1% through simple sequence repeat (SSR analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes’ evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species, T. parvula is related to Arabidopsis thaliana whose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.

Adrenocortical carcinoma: the dawn of a new era of genomic and molecular biology analysis.

Science.gov (United States)

Armignacco, R; Cantini, G; Canu, L; Poli, G; Ercolino, T; Mannelli, M; Luconi, M

2018-05-01

Over the last decade, the development of novel and high penetrance genomic approaches to analyze biological samples has provided very new insights in the comprehension of the molecular biology and genetics of tumors. The use of these techniques, consisting of exome sequencing, transcriptome, miRNome, chromosome alteration, genome, and epigenome analysis, has also been successfully applied to adrenocortical carcinoma (ACC). In fact, the analysis of large cohorts of patients allowed the stratification of ACC with different patterns of molecular alterations, associated with different outcomes, thus providing a novel molecular classification of the malignancy to be associated with the classical pathological analysis. Improving our knowledge about ACC molecular features will result not only in a better diagnostic and prognostic accuracy, but also in the identification of more specific therapeutic targets for the development of more effective pharmacological anti-cancer approaches. In particular, the specific molecular alteration profiles identified in ACC may represent targetable events by the use of already developed or newly designed drugs enabling a better and more efficacious management of the ACC patient in the context of new frontiers of personalized precision medicine.

Epigenetics in the Vascular Endothelium: Looking From a Different Perspective in the Epigenomics Era.

Science.gov (United States)

Yan, Matthew S; Marsden, Philip A

2015-11-01

Cardiovascular diseases are commonly thought to be complex, non-Mendelian diseases that are influenced by genetic and environmental factors. A growing body of evidence suggests that epigenetic pathways play a key role in vascular biology and might be involved in defining and transducing cardiovascular disease inheritability. In this review, we argue the importance of epigenetics in vascular biology, especially from the perspective of endothelial cell phenotype. We highlight and discuss the role of epigenetic modifications across the transcriptional unit of protein-coding genes, especially the role of intragenic chromatin modifications, which are underappreciated and not well characterized in the current era of genome-wide studies. Importantly, we describe the practical application of epigenetics in cardiovascular disease therapeutics. © 2015 American Heart Association, Inc.

Cardiovascular genomics, personalized medicine, and the National Heart, Lung, and Blood Institute: part I: the beginning of an era.

Science.gov (United States)

O'Donnell, Christopher J; Nabel, Elizabeth G

2008-10-01

The inaugural issue of Circulation: Cardiovascular Genetics arrives at a remarkable time in the history of genetic research and cardiovascular medicine. Despite tremendous progress in knowledge gained, cardiovascular disease(CVD) remains the leading cause of death in the United States,1 and it has overcome infectious diseases as the leading cause of death worldwide.2 In addition, rates of CVD remain higher in black and Hispanic populations in the United States.1 The recent Strategic Plan of the National Heart, Lung,and Blood Institute (NHLBI) emphasizes research areas to fill the significant knowledge gaps needed to improve the diagnosis,treatment, and control of known risk factors and clinically apparent disease. Simultaneously, the NHLBI Strategic Plan recognizes a tremendous opportunity that is available for use of genetic and genomic research to generate new knowledge that might reduce the morbidity and mortality from CVD in US populations.3 Public availability of vast amounts of detailed sequence information about the human genome, completed sequence data on dozens of other animal genomes, and private sector development of high-throughput genetic technologies has transformed in a few short years the conduct of cardiovascular genetics and genomics research from a primary focus on mendelian disorders to a current emphasis on genome-wide association studies (GWAS; Figure1). In this review, we describe the rationale for the current emphasis on large-scale genomic studies, summarize the evolving approaches and progress to date, and identify immediate-term research needs. The National Institutes of Health (NIH) and the NHLBI are supporting a portfolio of large-scale genetic and genomic programs in diverse US populations with the longer-term objective of translating knowledge into the prediction, prevention, and preemption of CVD, as well as lung, sleep, and blood disorders. Underlying this portfolio is a strong commitment to make available participant-level data and

Future translational applications from the contemporary genomics era: a scientific statement from the American Heart Association.

Science.gov (United States)

Fox, Caroline S; Hall, Jennifer L; Arnett, Donna K; Ashley, Euan A; Delles, Christian; Engler, Mary B; Freeman, Mason W; Johnson, Julie A; Lanfear, David E; Liggett, Stephen B; Lusis, Aldons J; Loscalzo, Joseph; MacRae, Calum A; Musunuru, Kiran; Newby, L Kristin; O'Donnell, Christopher J; Rich, Stephen S; Terzic, Andre

2015-05-12

The field of genetics and genomics has advanced considerably with the achievement of recent milestones encompassing the identification of many loci for cardiovascular disease and variable drug responses. Despite this achievement, a gap exists in the understanding and advancement to meaningful translation that directly affects disease prevention and clinical care. The purpose of this scientific statement is to address the gap between genetic discoveries and their practical application to cardiovascular clinical care. In brief, this scientific statement assesses the current timeline for effective translation of basic discoveries to clinical advances, highlighting past successes. Current discoveries in the area of genetics and genomics are covered next, followed by future expectations, tools, and competencies for achieving the goal of improving clinical care. © 2015 American Heart Association, Inc.

A Genome-Wide Survey of the Microsatellite Content of the Globe Artichoke Genome and the Development of a Web-Based Database

Science.gov (United States)

Portis, Ezio; Portis, Flavio; Valente, Luisa; Moglia, Andrea; Barchi, Lorenzo; Lanteri, Sergio; Acquadro, Alberto

2016-01-01

The recently acquired genome sequence of globe artichoke (Cynara cardunculus var. scolymus) has been used to catalog the genome’s content of simple sequence repeat (SSR) markers. More than 177,000 perfect SSRs were revealed, equivalent to an overall density across the genome of 244.5 SSRs/Mbp, but some 224,000 imperfect SSRs were also identified. About 21% of these SSRs were complex (two stretches of repeats separated by artichoke accessions, as templates. PMID:27648830

Optimisation of post-weld heat treatment – A simple, practical method

Indian Academy of Sciences (India)

M. Senthilkumar (Newgen Imaging) 1461 1996 Oct 15 13:05:22

the post-necking regime during tensile deformation is dominated by microvoid ... Dissimilar metal weld (DMW) joints between austenitic stainless steels (SS) and .... The most well-known model for the macroscopic response of an isotropic.

Data mining and the human genome

Energy Technology Data Exchange (ETDEWEB)

Abarbanel, Henry [The MITRE Corporation, McLean, VA (US). JASON Program Office; Callan, Curtis [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, William [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, Freeman [The MITRE Corporation, McLean, VA (US). JASON Program Office; Hwa, Terence [The MITRE Corporation, McLean, VA (US). JASON Program Office; Koonin, Steven [The MITRE Corporation, McLean, VA (US). JASON Program Office; Levine, Herbert [The MITRE Corporation, McLean, VA (US). JASON Program Office; Rothaus, Oscar [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, Roy [The MITRE Corporation, McLean, VA (US). JASON Program Office; Stubbs, Christopher [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, Peter [The MITRE Corporation, McLean, VA (US). JASON Program Office

2000-01-07

As genomics research moves from an era of data acquisition to one of both acquisition and interpretation, new methods are required for organizing and prioritizing the data. These methods would allow an initial level of data analysis to be carried out before committing resources to a particular genetic locus. This JASON study sought to delineate the main problems that must be faced in bioinformatics and to identify information technologies that can help to overcome those problems. While the current influx of data greatly exceeds what biologists have experienced in the past, other scientific disciplines and the commercial sector have been handling much larger datasets for many years. Powerful datamining techniques have been developed in other fields that, with appropriate modification, could be applied to the biological sciences.

Anticipation of Personal Genomics Data Enhances Interest and Learning Environment in Genomics and Molecular Biology Undergraduate Courses.

Science.gov (United States)

Weber, K Scott; Jensen, Jamie L; Johnson, Steven M

2015-01-01

An important discussion at colleges is centered on determining more effective models for teaching undergraduates. As personalized genomics has become more common, we hypothesized it could be a valuable tool to make science education more hands on, personal, and engaging for college undergraduates. We hypothesized that providing students with personal genome testing kits would enhance the learning experience of students in two undergraduate courses at Brigham Young University: Advanced Molecular Biology and Genomics. These courses have an emphasis on personal genomics the last two weeks of the semester. Students taking these courses were given the option to receive personal genomics kits in 2014, whereas in 2015 they were not. Students sent their personal genomics samples in on their own and received the data after the course ended. We surveyed students in these courses before and after the two-week emphasis on personal genomics to collect data on whether anticipation of obtaining their own personal genomic data impacted undergraduate student learning. We also tested to see if specific personal genomic assignments improved the learning experience by analyzing the data from the undergraduate students who completed both the pre- and post-course surveys. Anticipation of personal genomic data significantly enhanced student interest and the learning environment based on the time students spent researching personal genomic material and their self-reported attitudes compared to those who did not anticipate getting their own data. Personal genomics homework assignments significantly enhanced the undergraduate student interest and learning based on the same criteria and a personal genomics quiz. We found that for the undergraduate students in both molecular biology and genomics courses, incorporation of personal genomic testing can be an effective educational tool in undergraduate science education.

ERA: Adverse Consequences

Science.gov (United States)

Martin, Brian

2011-01-01

Excellence in Research for Australia has a number of limitations: inputs are counted as outputs, time is wasted, disciplinary research is favoured and public engagement is discouraged. Most importantly, by focusing on measurement and emphasising competition, ERA may actually undermine the cooperation and intrinsic motivation that underpin research…

Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals

DEFF Research Database (Denmark)

Hellmann, Ines; Mang, Yuan; Gu, Zhiping

2008-01-01

We introduce a simple, broadly applicable method for obtaining estimates of nucleotide diversity from genomic shotgun sequencing data. The method takes into account the special nature of these data: random sampling of genomic segments from one or more individuals and a relatively high error rate...... for individual reads. Applying this method to data from the Celera human genome sequencing and SNP discovery project, we obtain estimates of nucleotide diversity in windows spanning the human genome and show that the diversity to divergence ratio is reduced in regions of low recombination. Furthermore, we show...

Be-Breeder - an application for analysis of genomic data in plant breeding

OpenAIRE

Matias,Filipe Inácio; Granato,Italo Stefanine Correa; Dequigiovanni,Gabriel; Fritsche-Neto,Roberto

2017-01-01

Abstract Be-Breeder is an application directed toward genetic breeding of plants, developed through the Shiny package of the R software, which allows different phenotype and molecular (marker) analysis to be undertaken. The section for analysis of molecular data of the Be-Breeder application makes it possible to achieve quality control of genotyping data, to obtain genomic kinship matrices, and to analyze genome selection, genome association, and genetic diversity in a simple manner on line. ...

Evaluation of ERA-Interim precipitation data in complex terrain

Science.gov (United States)

Gao, Lu; Bernhardt, Matthias; Schulz, Karsten

2013-04-01

Precipitation controls a large variety of environmental processes, which is an essential input parameter for land surface models e.g. in hydrology, ecology and climatology. However, rain gauge networks provides the necessary information, are commonly sparse in complex terrains, especially in high mountainous regions. Reanalysis products (e.g. ERA-40 and NCEP-NCAR) as surrogate data are increasing applied in the past years. Although they are improving forward, previous studies showed that these products should be objectively evaluated due to their various uncertainties. In this study, we evaluated the precipitation data from ERA-Interim, which is a latest reanalysis product developed by ECMWF. ERA-Interim daily total precipitation are compared with high resolution gridded observation dataset (E-OBS) at 0.25°×0.25° grids for the period 1979-2010 over central Alps (45.5-48°N, 6.25-11.5°E). Wet or dry day is defined using different threshold values (0.5mm, 1mm, 5mm, 10mm and 20mm). The correspondence ratio (CR) is applied for frequency comparison, which is the ratio of days when precipitation occurs in both ERA-Interim and E-OBS dataset. The result shows that ERA-Interim captures precipitation occurrence very well with a range of CR from 0.80 to 0.97 for 0.5mm to 20mm thresholds. However, the bias of intensity increases with rising thresholds. Mean absolute error (MAE) varies between 4.5 mm day-1 and 9.5 mm day-1 in wet days for whole area. In term of mean annual cycle, ERA-Interim almost has the same standard deviation of the interannual variability of daily precipitation with E-OBS, 1.0 mm day-1. Significant wet biases happened in ERA-Interim throughout warm season (May to August) and dry biases in cold season (November to February). The spatial distribution of mean annual daily precipitation shows that ERA-Interim significant underestimates precipitation intensity in high mountains and northern flank of Alpine chain from November to March while pronounced

Avian genomics lends insights into endocrine function in birds.

Science.gov (United States)

Mello, C V; Lovell, P V

2018-01-15

The genomics era has brought along the completed sequencing of a large number of bird genomes that cover a broad range of the avian phylogenetic tree (>30 orders), leading to major novel insights into avian biology and evolution. Among recent findings, the discovery that birds lack a large number of protein coding genes that are organized in highly conserved syntenic clusters in other vertebrates is very intriguing, given the physiological importance of many of these genes. A considerable number of them play prominent endocrine roles, suggesting that birds evolved compensatory genetic or physiological mechanisms that allowed them to survive and thrive in spite of these losses. While further studies are needed to establish the exact extent of avian gene losses, these findings point to birds as potentially highly relevant model organisms for exploring the genetic basis and possible therapeutic approaches for a wide range of endocrine functions and disorders. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification of novel type 1 diabetes candidate genes by integrating genome-wide association data, protein-protein interactions, and human pancreatic islet gene expression

DEFF Research Database (Denmark)

Bergholdt, Regine; Brorsson, Caroline; Palleja, Albert

2012-01-01

Genome-wide association studies (GWAS) have heralded a new era in susceptibility locus discovery in complex diseases. For type 1 diabetes, >40 susceptibility loci have been discovered. However, GWAS do not inevitably lead to identification of the gene or genes in a given locus associated with dis......-cells. Our results provide novel insight to the mechanisms behind type 1 diabetes pathogenesis and, thus, may provide the basis for the design of novel treatment strategies.......Genome-wide association studies (GWAS) have heralded a new era in susceptibility locus discovery in complex diseases. For type 1 diabetes, >40 susceptibility loci have been discovered. However, GWAS do not inevitably lead to identification of the gene or genes in a given locus associated...... with disease, and they do not typically inform the broader context in which the disease genes operate. Here, we integrated type 1 diabetes GWAS data with protein-protein interactions to construct biological networks of relevance for disease. A total of 17 networks were identified. To prioritize...

Behavior of restriction–modification systems as selfish mobile elements and their impact on genome evolution

Science.gov (United States)

Kobayashi, Ichizo

2001-01-01

Restriction–modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and

Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution.

Science.gov (United States)

Kobayashi, I

2001-09-15

Restriction-modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and

Post-streptococcal glomerulonephritis

Directory of Open Access Journals (Sweden)

Odalovic A.

2014-01-01

Full Text Available Post-streptococcal glomerulonephritis (PSGN is a frequent cause of acute nephritis in children. This case study was done with the aim to point out that the infections caused by Group A streptococci, in spite of antibiotic era, are still present in the population. An 8-year old boy was admitted in our hospital with a two-day history of fewer, tonsillopharyngitis. After hospital admission, patient was treated with penicillin during the period of 10 days, antihypertensive medications (captopril, furosemide, including restricted diet of salt. After the treatment, patient became better. On demission it was found proteinuria and microhematuria PSGN is very serious disease, which leaves severe complications if the valid therapy with penicillin is not used in propriety time, during the recommended period of 10 days.

MSDB: A Comprehensive Database of Simple Sequence Repeats.

Science.gov (United States)

Avvaru, Akshay Kumar; Saxena, Saketh; Sowpati, Divya Tej; Mishra, Rakesh Kumar

2017-06-01

Microsatellites, also known as Simple Sequence Repeats (SSRs), are short tandem repeats of 1-6 nt motifs present in all genomes, particularly eukaryotes. Besides their usefulness as genome markers, SSRs have been shown to perform important regulatory functions, and variations in their length at coding regions are linked to several disorders in humans. Microsatellites show a taxon-specific enrichment in eukaryotic genomes, and some may be functional. MSDB (Microsatellite Database) is a collection of >650 million SSRs from 6,893 species including Bacteria, Archaea, Fungi, Plants, and Animals. This database is by far the most exhaustive resource to access and analyze SSR data of multiple species. In addition to exploring data in a customizable tabular format, users can view and compare the data of multiple species simultaneously using our interactive plotting system. MSDB is developed using the Django framework and MySQL. It is freely available at http://tdb.ccmb.res.in/msdb. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Opening plenary speaker: Human genomics, precision medicine, and advancing human health.

Science.gov (United States)

Green, Eric D

2016-08-01

Starting with the launch of the Human Genome Project in 1990, the past quarter-century has brought spectacular achievements in genomics that dramatically empower the study of human biology and disease. The human genomics enterprise is now in the midst of an important transition, as the growing foundation of genomic knowledge is being used by researchers and clinicians to tackle increasingly complex problems in biomedicine. Of particular prominence is the use of revolutionary new DNA sequencing technologies for generating prodigious amounts of DNA sequence data to elucidate the complexities of genome structure, function, and evolution, as well as to unravel the genomic bases of rare and common diseases. Together, these developments are ushering in the era of genomic medicine. Augmenting the advances in human genomics have been innovations in technologies for measuring environmental and lifestyle information, electronic health records, and data science; together, these provide opportunities of unprecedented scale and scope for investigating the underpinnings of health and disease. To capitalize on these opportunities, U.S. President Barack Obama recently announced a major new research endeavor - the U.S. Precision Medicine Initiative. This bold effort will be framed around several key aims, which include accelerating the use of genomically informed approaches to cancer care, making important policy and regulatory changes, and establishing a large research cohort of >1 million volunteers to facilitate precision medicine research. The latter will include making the partnership with all participants a centerpiece feature in the cohort's design and development. The Precision Medicine Initiative represents a broad-based research program that will allow new approaches for individualized medical care to be rigorously tested, so as to establish a new evidence base for advancing clinical practice and, eventually, human health.

Setaria viridis floral-dip: A simple and rapid Agrobacterium-medicated transformation method

Science.gov (United States)

Setaria viridis was recently described as a new monocotyledonous model species for C4 photosynthesis research and genetic transformation. It has biological attributes (rapid life cycle, small genome, diploid, short stature and simple growth requirements) that make it suitable for use as a model plan...

Genomic Approaches in Marine Biodiversity and Aquaculture

Directory of Open Access Journals (Sweden)

Jorge A Huete-Pérez

2013-01-01

Full Text Available Recent advances in genomic and post-genomic technologies have now established the new standard in medical and biotechnological research. The introduction of next-generation sequencing, NGS,has resulted in the generation of thousands of genomes from all domains of life, including the genomes of complex uncultured microbial communities revealed through metagenomics. Although the application of genomics to marine biodiversity remains poorly developed overall, some noteworthy progress has been made in recent years. The genomes of various model marine organisms have been published and a few more are underway. In addition, the recent large-scale analysis of marine microbes, along with transcriptomic and proteomic approaches to the study of teleost fishes, mollusks and crustaceans, to mention a few, has provided a better understanding of phenotypic variability and functional genomics. The past few years have also seen advances in applications relevant to marine aquaculture and fisheries. In this review we introduce several examples of recent discoveries and progress made towards engendering genomic resources aimed at enhancing our understanding of marine biodiversity and promoting the development of aquaculture. Finally, we discuss the need for auspicious science policies to address challenges confronting smaller nations in the appropriate oversight of this growing domain as they strive to guarantee food security and conservation of their natural resources.

Brassica ASTRA: an integrated database for Brassica genomic research.

Science.gov (United States)

Love, Christopher G; Robinson, Andrew J; Lim, Geraldine A C; Hopkins, Clare J; Batley, Jacqueline; Barker, Gary; Spangenberg, German C; Edwards, David

2005-01-01

Brassica ASTRA is a public database for genomic information on Brassica species. The database incorporates expressed sequences with Swiss-Prot and GenBank comparative sequence annotation as well as secondary Gene Ontology (GO) annotation derived from the comparison with Arabidopsis TAIR GO annotations. Simple sequence repeat molecular markers are identified within resident sequences and mapped onto the closely related Arabidopsis genome sequence. Bacterial artificial chromosome (BAC) end sequences derived from the Multinational Brassica Genome Project are also mapped onto the Arabidopsis genome sequence enabling users to identify candidate Brassica BACs corresponding to syntenic regions of Arabidopsis. This information is maintained in a MySQL database with a web interface providing the primary means of interrogation. The database is accessible at http://hornbill.cspp.latrobe.edu.au.

PERANAN PEREMPUAN DALAM MASYARAKAT ISLAM DI ERA POST MODERNIASASI PENDEKATAN TAFSIR TEMATIK

Directory of Open Access Journals (Sweden)

Masturin Masturin

2015-12-01

Full Text Available Abstract: The role of women  seems still  to be a discourse that becomes a debate among the  feminist theoreticians. Something that becomes the crucial problem is how to position the role of women in contemporary Islamic societies. Through a thematic interpretation approach, this paper tried to describe the role of women in Islamic societies in the post-modern era. Discourse and gender movement had a great influence on Muslim society. The demands on the role of women were not only related to the role of freedom of their activities in the domestic realm but also related to the public domain. The Qur'an was present not in the empty time and but rather to respond to a variety of community activities in place in which it was revealed. He - the Qu’ran - had an idealistic normative values that should be believed, held and executed. The text data of the Qu’ran could be illustrated by a triadic system depicting the role of women and their relationships with the Lord, the roles and relationships of women in the family; and the roles and relationships in the community, including the Islamic community. Islam, as a religion, on the one hand was not only as a pure idea that was absolute and universal, but on the other hand, it was also as a product of the ideas that are not only relative but also limited. However, with its relativity and limitation as the product of the thought, it was still able to show the distinction of its egalitarian with the concept built by modern-secular feminism movement through the principle of parity.الملخص :أصبحت المرأة موضوع نقاش بين مفكّرات النسوية إلى الآن. القضية المهمّة هي كيف يكون دور المرأة في المجتمع المسلم المعاصر. حاولت هذه الدراسة – بمدخل التفسير الموضوعي – تصوير دور المرأة في المجتمع المسلم في العصر بعد الحداثة. الحركة �

Enhanced recovery after surgery (ERAS) in penetrating abdominal ...

African Journals Online (AJOL)

Background: Enhanced recovery after surgery (ERAS) programmes employed in elective surgery have provided strong evidence for decreased lengths of hospital stay without increase in postoperative complications. The aim of this study was to explore the role and benefits of ERAS implemented in patients undergoing ...

The First Complete Chloroplast Genome Sequences in Actinidiaceae: Genome Structure and Comparative Analysis.

Science.gov (United States)

Yao, Xiaohong; Tang, Ping; Li, Zuozhou; Li, Dawei; Liu, Yifei; Huang, Hongwen

2015-01-01

Actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. Availability of a complete Actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. We report here the complete nucleotide sequences of the chloroplast genomes for Actinidia chinensis and A. chinensis var deliciosa obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing. The total genome size ranges from 155,446 to 157,557 bp, with an inverted repeat (IR) of 24,013 to 24,391 bp, a large single copy region (LSC) of 87,984 to 88,337 bp and a small single copy region (SSC) of 20,332 to 20,336 bp. The genome encodes 113 different genes, including 79 unique protein-coding genes, 30 tRNA genes and 4 ribosomal RNA genes, with 16 duplicated in the inverted repeats, and a tRNA gene (trnfM-CAU) duplicated once in the LSC region. Comparisons of IR boundaries among four asterid species showed that IR/LSC borders were extended into the 5' portion of the psbA gene and IR contraction occurred in Actinidia. The clap gene has been lost from the chloroplast genome in Actinidia, and may have been transferred to the nucleus during chloroplast evolution. Twenty-seven polymorphic simple sequence repeat (SSR) loci were identified in the Actinidia chloroplast genome. Maximum parsimony analyses of a 72-gene, 16 taxa angiosperm dataset strongly support the placement of Actinidiaceae in Ericales within the basal asterids.

Starting Anew: Exploring the Links between Radio and Journalism Education in Post-Revolutionary Romania.

Science.gov (United States)

Hochheimer, John L.; Hochheimer, Joanne Dvorak

This paper examines the evolution of Romanian radio, as well as some of the inherent problems of journalism education in Romania in the post-revolutionary era. The paper discusses the legacy of repression during the Ceausescu dictatorship, which limited radio services throughout the country and left only one journalism school, a school that…

Genome Sequencing of Streptomyces atratus SCSIOZH16 and Activation Production of Nocardamine via Metabolic Engineering

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Yan Li

2018-06-01

Full Text Available The Actinomycetes are metabolically flexible microorganisms capable of producing a wide range of interesting compounds, including but by no means limited to, siderophores which have high affinity for ferric iron. In this study, we report the complete genome sequence of marine-derived Streptomyces atratus ZH16 and the activation of an embedded siderophore gene cluster via the application of metabolic engineering methods. The S. atratus ZH16 genome reveals that this strain has the potential to produce 26 categories of natural products (NPs barring the ilamycins. Our activation studies revealed S. atratus SCSIO ZH16 to be a promising source of the production of nocardamine-type (desferrioxamine compounds which are important in treating acute iron intoxication and performing ecological remediation. We conclude that metabolic engineering provides a highly effective strategy by which to discover drug-like compounds and new NPs in the genomic era.

Bionanoscience landscape in South Africa and its implications in the development of a post-graduate curriculum - Presentation

CSIR Research Space (South Africa)

Sparrow, R

2009-11-01

Full Text Available Africa and its Implications in the Development of a Post-Graduate Curriculum Presented at UWC – Nano-biotechnology Seminar. Dr. Raymond Sparrow Manager of the SynBioTIC Programme. CSIR – Synthetic Biology ERA. 20th November 2009 Nanoscience...

Genomics and the making of yeast biodiversity.

Science.gov (United States)

Hittinger, Chris Todd; Rokas, Antonis; Bai, Feng-Yan; Boekhout, Teun; Gonçalves, Paula; Jeffries, Thomas W; Kominek, Jacek; Lachance, Marc-André; Libkind, Diego; Rosa, Carlos A; Sampaio, José Paulo; Kurtzman, Cletus P

2015-12-01

Yeasts are unicellular fungi that do not form fruiting bodies. Although the yeast lifestyle has evolved multiple times, most known species belong to the subphylum Saccharomycotina (syn. Hemiascomycota, hereafter yeasts). This diverse group includes the premier eukaryotic model system, Saccharomyces cerevisiae; the common human commensal and opportunistic pathogen, Candida albicans; and over 1000 other known species (with more continuing to be discovered). Yeasts are found in every biome and continent and are more genetically diverse than angiosperms or chordates. Ease of culture, simple life cycles, and small genomes (∼10-20Mbp) have made yeasts exceptional models for molecular genetics, biotechnology, and evolutionary genomics. Here we discuss recent developments in understanding the genomic underpinnings of the making of yeast biodiversity, comparing and contrasting natural and human-associated evolutionary processes. Only a tiny fraction of yeast biodiversity and metabolic capabilities has been tapped by industry and science. Expanding the taxonomic breadth of deep genomic investigations will further illuminate how genome function evolves to encode their diverse metabolisms and ecologies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microsatellite DNA in genomic survey sequences and UniGenes of loblolly pine

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Craig S Echt; Surya Saha; Dennis L Deemer; C Dana Nelson

2011-01-01

Genomic DNA sequence databases are a potential and growing resource for simple sequence repeat (SSR) marker development in loblolly pine (Pinus taeda L.). Loblolly pine also has many expressed sequence tags (ESTs) available for microsatellite (SSR) marker development. We compared loblolly pine SSR densities in genome survey sequences (GSSs) to those in non-redundant...

Postkolonialismi pealetung post -sovetoloogias: kas paradigmamuutuse künnisel? The Rise of Post-Colonialism in Post-Soviet Studies: Witnessing the Paradigm Change

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Epp Annus

2012-04-01

Full Text Available This article analyses the current state of research in studies of Soviet colonialism and considers inner tensions within this emerging field. By now, dozens of monographs and hundreds of articles touch upon the various aspects of Soviet postcolonialism, yet the field is fragmented and full of inner contradictions and unanswered questions: What is the relationship of research in Soviet colonialism to postcolonial studies in general? What is its relationship to traditional Sovietology? Areas of tension are found through historical and geographical perspectives, in the Russian neglect of its own Soviet imperialism, and in the long-distance scholarship dominant in the area. This paper argues that what we are witnessing now is the pains of a paradigm change, further aggravated by special complexities within the field. The article offers a historical overview of the development of studies of Soviet colonialism and shows that a decisive turn took place in the first decade of the twenty-first century. In 1990s, postcolonial perspectives were more widely employed in analyses of Tsarist-era Russian history. In the 2000s, several important monographs about the Soviet Union were published, yet, interestingly, their main focus was the inter-war period, before the Baltic states were annexed to the Soviet Union. Thus, for research into Baltic Soviet history, these collections and monographs can only provide background information. As for the post-WWII era, most important work from the perspective of Baltic studies – that is, general arguments about the developments in Soviet Union – remain on the level of single articles, the best known of these being David Chioni Moore’s „Is the Post- in Postcolonial the Post- in Post-Soviet? Toward a Global Postcolonial Critique“ (2001. The article makes a distinction between the general term „empire-studies“ and the more restricted notion of „studies of colonialism“; it further distuinguishes post colonial

Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children☆

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Zhang, Chenhong; Yin, Aihua; Li, Hongde; Wang, Ruirui; Wu, Guojun; Shen, Jian; Zhang, Menghui; Wang, Linghua; Hou, Yaping; Ouyang, Haimei; Zhang, Yan; Zheng, Yinan; Wang, Jicheng; Lv, Xiaofei; Wang, Yulan; Zhang, Feng; Zeng, Benhua; Li, Wenxia; Yan, Feiyan; Zhao, Yufeng; Pang, Xiaoyan; Zhang, Xiaojun; Fu, Huaqing; Chen, Feng; Zhao, Naisi; Hamaker, Bruce R.; Bridgewater, Laura C.; Weinkove, David; Clement, Karine; Dore, Joel; Holmes, Elaine; Xiao, Huasheng; Zhao, Guoping; Yang, Shengli; Bork, Peer; Nicholson, Jeremy K.; Wei, Hong; Tang, Huiru; Zhang, Xiaozhuang; Zhao, Liping

2015-01-01

Gut microbiota has been implicated as a pivotal contributing factor in diet-related obesity; however, its role in development of disease phenotypes in human genetic obesity such as Prader–Willi syndrome (PWS) remains elusive. In this hospitalized intervention trial with PWS (n = 17) and simple obesity (n = 21) children, a diet rich in non-digestible carbohydrates induced significant weight loss and concomitant structural changes of the gut microbiota together with reduction of serum antigen load and alleviation of inflammation. Co-abundance network analysis of 161 prevalent bacterial draft genomes assembled directly from metagenomic datasets showed relative increase of functional genome groups for acetate production from carbohydrates fermentation. NMR-based metabolomic profiling of urine showed diet-induced overall changes of host metabotypes and identified significantly reduced trimethylamine N-oxide and indoxyl sulfate, host-bacteria co-metabolites known to induce metabolic deteriorations. Specific bacterial genomes that were correlated with urine levels of these detrimental co-metabolites were found to encode enzyme genes for production of their precursors by fermentation of choline or tryptophan in the gut. When transplanted into germ-free mice, the pre-intervention gut microbiota induced higher inflammation and larger adipocytes compared with the post-intervention microbiota from the same volunteer. Our multi-omics-based systems analysis indicates a significant etiological contribution of dysbiotic gut microbiota to both genetic and simple obesity in children, implicating a potentially effective target for alleviation. Research in context Poorly managed diet and genetic mutations are the two primary driving forces behind the devastating epidemic of obesity-related diseases. Lack of understanding of the molecular chain of causation between the driving forces and the disease endpoints retards progress in prevention and treatment of the diseases. We found

Gynecologic Malignancies Post-LeFort Colpocleisis

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Rayan Elkattah

2014-01-01

Full Text Available Introduction. LeFort colpocleisis (LFC is a safe and effective obliterative surgical option for older women with advanced pelvic organ prolapse who no longer desire coital activity. A major disadvantage is the limited ability to evaluate for post-LFC gynecologic malignancies. Methods. We present the first case of endometrioid ovarian cancer diagnosed after LFC and review all reported gynecologic malignancies post-LFC in the English medical literature. Results. This is the second reported ovarian cancer post-LFC and the first of the endometrioid subtype. A total of nine other gynecologic malignancies post-LFC have been reported in the English medical literature. Conclusions. Gynecologic malignancies post-LFC are rare. We propose a simple 3-step strategy in evaluating post-LFC malignancies.

A novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12.

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Miki, Takeyoshi; Yamamoto, Yoshihiro; Matsuda, Hideo

2008-01-01

We developed a novel, simple, high-throughput method for isolation of genome-wide transposon insertion mutants of Escherichia coli K-12. The basic idea of the method is to randomly disrupt the genes on the DNA fragments cloned on the Kohara library by inserting a mini-transposon first, and then transfer the disrupted genes from the lambda vector to the E. coli chromosome by homologous recombination. Using this method, we constructed a set of 8402 Km(r) cis-diploid mutants harboring a mini-Tn10 insertion mutation and the corresponding wild-type gene on a chromosome, as well as a set of 6954 haploid mutants derived from the cis-diploid mutants. The major advantage of the strategy used is that the indispensable genes or sites for growth can be identified. Preliminary results suggest that 415 open reading frames are indispensable for growth in E. coli cells. A total of 6404 haploid mutants were deposited to Genetic Strains Research Center, National Institute of Genetics, Japan (Chapter 26) and are available for public distribution upon request (http://shigen.lab.nig.ac.jp/ecoli/strain/nbrp/resource.jsp).

PCR-based approach to SINE isolation: simple and complex SINEs.

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Borodulina, Olga R; Kramerov, Dmitri A

2005-04-11

Highly repeated copies of short interspersed elements (SINEs) occur in eukaryotic genomes. The distribution of each SINE family is usually restricted to some genera, families, or orders. SINEs have an RNA polymerase III internal promoter, which is composed of boxes A and B. Here we propose a method for isolation of novel SINE families based on genomic DNA PCR with oligonucleotide identical to box A as a primer. Cloning of the size-heterogeneous PCR-products and sequencing of their terminal regions allow determination of SINE structure. Using this approach, two novel SINE families, Rhin-1 and Das-1, from the genomes of great horseshoe bat (Rhinolophus ferrumequinum) and nine-banded armadillo (Dasypus novemcinctus), respectively, were isolated and studied. The distribution of Rhin-1 is restricted to two of six bat families tested. Copies of this SINE are characterized by frequent internal insertions and significant length (200-270 bp). Das-1 being only 90 bp in length is one of the shortest SINEs known. Most of Das-1 nucleotide sequences demonstrate significant similarity to alanine tRNA which appears to be an evolutionary progenitor of this SINE. Together with three other known SINEs (ID, Vic-1, and CYN), Das-1 constitutes a group of simple SINEs. Interestingly, three SINE families of this group are alanine tRNA-derived. Most probably, this tRNA gave rise to short and simple but successful SINEs several times during mammalian evolution.

Scientific Advances with Aspergillus Species that Are Used for Food and Biotech Applications.

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Biesebeke, Rob Te; Record, Erik

2008-01-01

Yeast and filamentous fungi have been used for centuries in diverse biotechnological processes. Fungal fermentation technology is traditionally used in relation to food production, such as for bread, beer, cheese, sake and soy sauce. Last century, the industrial application of yeast and filamentous fungi expanded rapidly, with excellent examples such as purified enzymes and secondary metabolites (e.g. antibiotics), which are used in a wide range of food as well as non-food industries. Research on protein and/or metabolite secretion by fungal species has focused on identifying bottlenecks in (post-) transcriptional regulation of protein production, metabolic rerouting, morphology and the transit of proteins through the secretion pathway. In past years, genome sequencing of some fungi (e.g. Aspergillus oryzae, Aspergillus niger) has been completed. The available genome sequences have enabled identification of genes and functionally important regions of the genome. This has directed research to focus on a post-genomics era in which transcriptomics, proteomics and metabolomics methodologies will help to explore the scientific relevance and industrial application of fungal genome sequences.

Effects of informed consent for individual genome sequencing on relevant knowledge.

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Kaphingst, K A; Facio, F M; Cheng, M-R; Brooks, S; Eidem, H; Linn, A; Biesecker, B B; Biesecker, L G

2012-11-01

Increasing availability of individual genomic information suggests that patients will need knowledge about genome sequencing to make informed decisions, but prior research is limited. In this study, we examined genome sequencing knowledge before and after informed consent among 311 participants enrolled in the ClinSeq™ sequencing study. An exploratory factor analysis of knowledge items yielded two factors (sequencing limitations knowledge; sequencing benefits knowledge). In multivariable analysis, high pre-consent sequencing limitations knowledge scores were significantly related to education [odds ratio (OR): 8.7, 95% confidence interval (CI): 2.45-31.10 for post-graduate education, and OR: 3.9; 95% CI: 1.05, 14.61 for college degree compared with less than college degree] and race/ethnicity (OR: 2.4, 95% CI: 1.09, 5.38 for non-Hispanic Whites compared with other racial/ethnic groups). Mean values increased significantly between pre- and post-consent for the sequencing limitations knowledge subscale (6.9-7.7, p benefits knowledge subscale (7.0-7.5, p < 0.0001); increase in knowledge did not differ by sociodemographic characteristics. This study highlights gaps in genome sequencing knowledge and underscores the need to target educational efforts toward participants with less education or from minority racial/ethnic groups. The informed consent process improved genome sequencing knowledge. Future studies could examine how genome sequencing knowledge influences informed decision making. © 2012 John Wiley & Sons A/S.

Cultural complexity, post-colonialism and educational change: Challenges for comparative educators

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Hickling-Hudson, Anne

2007-01-01

This study explores various elements in the struggle for a post-colonial refashioning of cultural identity through education. Drawing on experiences in Australia and the Caribbean, the author illustrates how educational systems undergoing decolonisation reflect socio-cultural tensions of race and power. The author discusses the complexities for comparative educators in engaging with suppressed knowledge, recognising the yearnings of the marginalised, challenging the conditions that lead to poverty, and refashioning education for social justice in an era when the achievement of justice seems increasingly difficult. She argues that comparative educators can benefit from using post-colonial thinking to understand cultural complexity and promote lifeaffirming practices in educational change.

A New Era for Research Education in Australia?

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Marsh, Helene; Smith, Bradley; King, Max; Evans, Terry

2012-01-01

Use of the Australian research assessment exercise, Excellence in Research for Australia (ERA) to influence the policy and practice of research education in Australia will undoubtedly have many consequences, some of them unintended and potentially deleterious. ERA is a retrospective measure of research quality; research education is prospective.…

Universal pacemaker of genome evolution.

Science.gov (United States)

Snir, Sagi; Wolf, Yuri I; Koonin, Eugene V

2012-01-01

A fundamental observation of comparative genomics is that the distribution of evolution rates across the complete sets of orthologous genes in pairs of related genomes remains virtually unchanged throughout the evolution of life, from bacteria to mammals. The most straightforward explanation for the conservation of this distribution appears to be that the relative evolution rates of all genes remain nearly constant, or in other words, that evolutionary rates of different genes are strongly correlated within each evolving genome. This correlation could be explained by a model that we denoted Universal PaceMaker (UPM) of genome evolution. The UPM model posits that the rate of evolution changes synchronously across genome-wide sets of genes in all evolving lineages. Alternatively, however, the correlation between the evolutionary rates of genes could be a simple consequence of molecular clock (MC). We sought to differentiate between the MC and UPM models by fitting thousands of phylogenetic trees for bacterial and archaeal genes to supertrees that reflect the dominant trend of vertical descent in the evolution of archaea and bacteria and that were constrained according to the two models. The goodness of fit for the UPM model was better than the fit for the MC model, with overwhelming statistical significance, although similarly to the MC, the UPM is strongly overdispersed. Thus, the results of this analysis reveal a universal, genome-wide pacemaker of evolution that could have been in operation throughout the history of life.

Animal genomics and infectious disease resistance in poultry.

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Smith, J; Gheyas, A; Burt, D W

2016-04-01

Avian pathogens are responsible for major costs to society, both in terms of huge economic losses to the poultry industry and their implications for human health. The health and welfare of millions of birds is under continued threat from many infectious diseases, some of which are increasing in virulence and thus becoming harder to control, such as Marek's disease virus and avian influenza viruses. The current era in animal genomics has seen huge developments in both technologies and resources, which means that researchers have never been in a better position to investigate the genetics of disease resistance and determine the underlying genes/mutations which make birds susceptible or resistant to infection. Avian genomics has reached a point where the biological mechanisms of infectious diseases can be investigated and understood in poultry and other avian species. Knowledge of genes conferring disease resistance can be used in selective breeding programmes or to develop vaccines which help to control the effects of these pathogens, which have such a major impact on birds and humans alike.

Genome mining of the genetic diversity in the Aspergillus genus - from a collection of more than 30 Aspergillus species

DEFF Research Database (Denmark)

Rasmussen, Jane Lind Nybo; Vesth, Tammi Camilla; Theobald, Sebastian

In the era of high-throughput sequencing, comparative genomics can be applied for evaluating species diversity. In this project we aim to compare the genomes of 300 species of filamentous fungi from the Aspergillus genus, a complex task. To be able to define species, clade, and core features......, this project uses BLAST on the amino acid level to discover orthologs. With a potential of 300 Aspergillus species each having ~12,000 annotated genes, traditional clustering will demand supercomputing. Instead, our approach reduces the search space by identifying isoenzymes within each genome creating...... intragenomic protein families (iPFs), and then connecting iPFs across all genomes. The initial findings in a set of 31 species show that ~48% of the annotated genes are core genes (genes shared between all species) and 2-24% of the genes are defining the individual species. The methods presented here...

Molecular Tumor Boards: Ethical Issues in the New Era of Data Medicine.

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Stoeklé, Henri-Corto; Mamzer-Bruneel, Marie-France; Frouart, Charles-Henry; Le Tourneau, Christophe; Laurent-Puig, Pierre; Vogt, Guillaume; Hervé, Christian

2018-02-01

The practice and development of modern medicine requires large amounts of data, particularly in the domain of cancer. The future of personalized medicine lies neither with "genomic medicine" nor with "precision medicine", but with "data medicine" (DM) (big data, data mining). The establishment of this DM has required far-reaching changes, to establish four essential elements connecting patients and doctors: biobanks, databases, bioinformatic platforms and genomic platforms. The "transformation" of scientific research areas, such as genetics, bioinformatics and biostatistics, into clinical specialties has generated a new vision of care. Molecular tumor boards (MTB) are one response to these changes and are now providing better access to next-generation sequencing (NGS) and new cancer treatments to patients with inoperable or metastatic cancers, and those for whom the usual treatment has failed. However, MTB face a crucial ethical challenge: maintaining and improving the trust of patients, clinicians, researchers and industry in academic medical centers supported by private or public funding rather than providing genetic data directly to private companies. We believe that, in this era of DM, appropriate modern digital communication networks will be required to maintain this trust and to improve the organization and effectiveness of the system. There is, therefore, a need to reconsider the form and content of informed consent (IC) documents at all academic medical centers and to introduce dynamic and electronic informed consent (e-IC).

Distance learning training in genetics and genomics testing for Italian health professionals: results of a pre and post-test evaluation

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Maria Benedetta Michelazzo

2015-09-01

Full Text Available BackgroundProgressive advances in technologies for DNA sequencing and decreasing costs are allowing an easier diffusion of genetic and genomic tests. Physicians’ knowledge and confidence on the topic is often low and not suitable for manage this challenge. Tailored educational programs are required to reach a more and more appropriate use of genetic technologies.MethodsA distance learning course has been created by experts from different Italian medical associations with the support of the Italian Ministry of Health. The course was directed to professional figures involved in prescription and interpretation of genetic tests. A pretest-post-test study design was used to assess knowledge improvement. We analyzed the proportion of correct answers for each question pre and post-test, as well as the mean score difference stratified by gender, age, professional status and medical specialty.ResultsWe reported an improvement in the proportion of correct answers for 12 over 15 questions of the test. The overall mean score to the questions significantly increased in the post-test, from 9.44 to 12.49 (p-value < 0.0001. In the stratified analysis we reported an improvement in the knowledge of all the groups except for geneticists; the pre-course mean score of this group was already very high and did not improve significantly.ConclusionDistance learning is effective in improving the level of genetic knowledge. In the future, it will be useful to analyze which specialists have more advantage from genetic education, in order to plan more tailored education for medical professionals.

A lower degree of PBMC L1 methylation in women with lower folate status may explain the MTHFR C677T polymorphism associated higher risk of CIN in the US post folic acid fortification era.

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Suguna Badiga

Full Text Available Studies in populations unexposed to folic acid (FA fortification have demonstrated that MTHFR C677T polymorphism is associated with increased risk of higher grades of cervical intraepithelial neoplasia (CIN 2+. However, it is unknown whether exposure to higher folate as a result of the FA fortification program has altered the association between MTHFR C677T and risk of CIN, or the mechanisms involved with such alterations. The current study investigated the following in a FA fortified population: 1 The association between MTHFR C677T polymorphism and risk of CIN 2+; 2 The modifying effects of plasma folate concentrations on this association; and 3 The modifying effects of plasma folate on the association between the polymorphism and degree of methylation of long interspersed nucleotide elements (L1s, in peripheral blood mononuclear cell (PBMC DNA, a documented biomarker of CIN risk.The study included 457 US women diagnosed with either CIN 2+ (cases or ≤ CIN 1 (non-cases. Unconditional logistic regression models were used to test the associations after adjusting for relevant risk factors for CIN.The 677CT/TT MTHFR genotypes were not associated with the risk of CIN 2+. Women with CT/TT genotype with lower folate, however, were more likely to be diagnosed with CIN 2+ compared to women with CT/TT genotype with higher folate (OR = 2.41, P = 0.030. Women with CT/TT genotype with lower folate were less likely to have a higher degree of PBMC L1 methylation compared to women with CT/TT genotype with higher folate (OR = 0.28, P = 0.017.This study provides the first evidence that the MTHFR 677CT/TT genotype-associated lower degree of PBMC L1 methylation increases the risk of CIN 2+ in women in the US post-FA fortification era. Thus, even in the post-FA fortification era, not all women have adequate folate status to overcome MTHFR 677CT/TT genotype-associated lower degree of L1 methylation.

A Simple Test of Class-Level Genetic Association Can Reveal Novel Cardiometabolic Trait Loci.

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Jing Qian

Full Text Available Characterizing the genetic determinants of complex diseases can be further augmented by incorporating knowledge of underlying structure or classifications of the genome, such as newly developed mappings of protein-coding genes, epigenetic marks, enhancer elements and non-coding RNAs.We apply a simple class-level testing framework, termed Genetic Class Association Testing (GenCAT, to identify protein-coding gene association with 14 cardiometabolic (CMD related traits across 6 publicly available genome wide association (GWA meta-analysis data resources. GenCAT uses SNP-level meta-analysis test statistics across all SNPs within a class of elements, as well as the size of the class and its unique correlation structure, to determine if the class is statistically meaningful. The novelty of findings is evaluated through investigation of regional signals. A subset of findings are validated using recently updated, larger meta-analysis resources. A simulation study is presented to characterize overall performance with respect to power, control of family-wise error and computational efficiency. All analysis is performed using the GenCAT package, R version 3.2.1.We demonstrate that class-level testing complements the common first stage minP approach that involves individual SNP-level testing followed by post-hoc ascribing of statistically significant SNPs to genes and loci. GenCAT suggests 54 protein-coding genes at 41 distinct loci for the 13 CMD traits investigated in the discovery analysis, that are beyond the discoveries of minP alone. An additional application to biological pathways demonstrates flexibility in defining genetic classes.We conclude that it would be prudent to include class-level testing as standard practice in GWA analysis. GenCAT, for example, can be used as a simple, complementary and efficient strategy for class-level testing that leverages existing data resources, requires only summary level data in the form of test statistics, and

Chinese librarianship in the digital era

CERN Document Server

Fang, Conghui

2013-01-01

The library in China has been transformed by rapid socioeconomic development, and the proliferation of the Internet. The issues faced by Chinese libraries andlibrarians are those faced by library practitioners more globally, however, China also has its own unique set of issues in the digital era, including developmental imbalance between East and West, urban and rural areas, and availability of skilled practitioners. Chinese Librarianship in the Digital Era is the first book on Chinese libraries responding to these issues, and more.The first part of the book places discussion in historical con

A Perfect Match Genomic Landscape Provides a Unified Framework for the Precise Detection of Variation in Natural and Synthetic Haploid Genomes.

Science.gov (United States)

Palacios-Flores, Kim; García-Sotelo, Jair; Castillo, Alejandra; Uribe, Carina; Aguilar, Luis; Morales, Lucía; Gómez-Romero, Laura; Reyes, José; Garciarubio, Alejandro; Boege, Margareta; Dávila, Guillermo

2018-04-01

We present a conceptually simple, sensitive, precise, and essentially nonstatistical solution for the analysis of genome variation in haploid organisms. The generation of a Perfect Match Genomic Landscape (PMGL), which computes intergenome identity with single nucleotide resolution, reveals signatures of variation wherever a query genome differs from a reference genome. Such signatures encode the precise location of different types of variants, including single nucleotide variants, deletions, insertions, and amplifications, effectively introducing the concept of a general signature of variation. The precise nature of variants is then resolved through the generation of targeted alignments between specific sets of sequence reads and known regions of the reference genome. Thus, the perfect match logic decouples the identification of the location of variants from the characterization of their nature, providing a unified framework for the detection of genome variation. We assessed the performance of the PMGL strategy via simulation experiments. We determined the variation profiles of natural genomes and of a synthetic chromosome, both in the context of haploid yeast strains. Our approach uncovered variants that have previously escaped detection. Moreover, our strategy is ideally suited for further refining high-quality reference genomes. The source codes for the automated PMGL pipeline have been deposited in a public repository. Copyright © 2018 by the Genetics Society of America.

Research Guidelines in the Era of Large-scale Collaborations: An Analysis of Genome-wide Association Study Consortia

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Austin, Melissa A.; Hair, Marilyn S.; Fullerton, Stephanie M.

2012-01-01

Scientific research has shifted from studies conducted by single investigators to the creation of large consortia. Genetic epidemiologists, for example, now collaborate extensively for genome-wide association studies (GWAS). The effect has been a stream of confirmed disease-gene associations. However, effects on human subjects oversight, data-sharing, publication and authorship practices, research organization and productivity, and intellectual property remain to be examined. The aim of this analysis was to identify all research consortia that had published the results of a GWAS analysis since 2005, characterize them, determine which have publicly accessible guidelines for research practices, and summarize the policies in these guidelines. A review of the National Human Genome Research Institute’s Catalog of Published Genome-Wide Association Studies identified 55 GWAS consortia as of April 1, 2011. These consortia were comprised of individual investigators, research centers, studies, or other consortia and studied 48 different diseases or traits. Only 14 (25%) were found to have publicly accessible research guidelines on consortia websites. The available guidelines provide information on organization, governance, and research protocols; half address institutional review board approval. Details of publication, authorship, data-sharing, and intellectual property vary considerably. Wider access to consortia guidelines is needed to establish appropriate research standards with broad applicability to emerging forms of large-scale collaboration. PMID:22491085

ERA Panga pankrotiprotsess on lõppenud / Väinu Rozental

Index Scriptorium Estoniae

Rozental, Väinu, 1957-

2005-01-01

Viis ja pool aastat kestnud ERA Panga pankrotimenetlus on lõppenud ning mõlemad pankrotihaldurid said 3,53 miljonit krooni. Vt. samas: Järgmisena saab joone alla EVEA Panga pankrot. Lisa: ERA Panga pankrotil joon all

War in the Era of Declining U.S. Global Hegemony

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Francis Shor

2010-01-01

Full Text Available While Clausewitz’s perspective that ‘war is the continuation of politics by other means’ is widely quoted, the full implications of that perspective are rarely explored. What I propose to highlight in this essay is how the imperial political projects of the UnitedStates in the post-Vietnam era unleashed direct and indirect regional war strategies from Latin America to the Middle East. The essay will highlight, in particular, the wide variety of such strategies from covert intervention in Chile to proxy wars in Central America to military intervention in Iraq and Afghanistan. Attempting to re-assert its global hegemony after Vietnam, the U.S. became more committed to perpetrating war as an instrument of its global posture. Of course, relying on war strategies, whether through direct or indirect interventions, complicates, if not confounds, the imposition of global hegemony.

Variability of Iberian upwelling implied by ERA-40 and ERA-Interim reanalyses

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José M. R. Alves

2013-05-01

Full Text Available The Regional Ocean Modeling System ocean model is used to simulate the decadal evolution of the regional waters in offshore Iberia in response to atmospheric fields given by ECMWF ERA-40 (1961–2001 and ERA-Interim (1989–2008 reanalyses. The simulated sea surface temperature (SST fields are verified against satellite AVHRR SST, and they are analysed to characterise the variability and trends of coastal upwelling in the region. Opposing trends in upwelling frequency are found at the northern limit, where upwelling has been decreasing in recent decades, and at its southern edge, where there is some evidence of increased upwelling. These results confirm previous observational studies and, more importantly, indicate that observed SST trends are not only due to changes in radiative or atmospheric heat fluxes alone but also due to changes in upwelling dynamics, suggesting that such a process may be relevant in climate change scenarios.

Progressive-Era Resources on the World Wide Web.

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Howenstein, Amanda

1999-01-01

Provides a list of Progressive-era websites with the address and a detailed description of each of the websites. Includes topics such as the womens suffrage movement, the Triangle Shirtwaist Factory fire, the Prohibition, labor-management conflicts, the Hull House, the Chicago fire, Emma Goldman, Progressive-era entertainment, and the Worlds Fair.…

Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple

Science.gov (United States)

2012-01-01

Background Apple is an economically important fruit crop worldwide. Developing a genetic linkage map is a critical step towards mapping and cloning of genes responsible for important horticultural traits in apple. To facilitate linkage map construction, we surveyed and characterized the distribution and frequency of perfect microsatellites in assembled contig sequences of the apple genome. Results A total of 28,538 SSRs have been identified in the apple genome, with an overall density of 40.8 SSRs per Mb. Di-nucleotide repeats are the most frequent microsatellites in the apple genome, accounting for 71.9% of all microsatellites. AT/TA repeats are the most frequent in genomic regions, accounting for 38.3% of all the G-SSRs, while AG/GA dimers prevail in transcribed sequences, and account for 59.4% of all EST-SSRs. A total set of 310 SSRs is selected to amplify eight apple genotypes. Of these, 245 (79.0%) are found to be polymorphic among cultivars and wild species tested. AG/GA motifs in genomic regions have detected more alleles and higher PIC values than AT/TA or AC/CA motifs. Moreover, AG/GA repeats are more variable than any other dimers in apple, and should be preferentially selected for studies, such as genetic diversity and linkage map construction. A total of 54 newly developed apple SSRs have been genetically mapped. Interestingly, clustering of markers with distorted segregation is observed on linkage groups 1, 2, 10, 15, and 16. A QTL responsible for malic acid content of apple fruits is detected on linkage group 8, and accounts for ~13.5% of the observed phenotypic variation. Conclusions This study demonstrates that di-nucleotide repeats are prevalent in the apple genome and that AT/TA and AG/GA repeats are the most frequent in genomic and transcribed sequences of apple, respectively. All SSR motifs identified in this study as well as those newly mapped SSRs will serve as valuable resources for pursuing apple genetic studies, aiding the apple breeding

The ERA-EDTA today and tomorrow: a progress document by the ERA-EDTA Council.

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Zoccali, Carmine; Arici, Mustafa; Blankestijn, Peter J; Bruchfeld, Annette; Capasso, Giovambattista; Fliser, Danilo; Fouque, Denis; Goumenos, Dimitrios; Ketteler, Markus; Malyszko, Jolanta; Massy, Ziad; Rychlík, Ivan; Spasovski, Goce

2018-05-23

Scientific societies are increasingly seen as central to the advancement of information sharing and collaboration among scientists and clinical investigators for the progress of medical research and the promotion of education, professional competence, integrity and quality studies. To more effectively serve the practicing nephrologists and investigators dedicated to renal science, the Council of the European Renal Association and European Dialysis and Transplantation Association (ERA-EDTA) reorganized and integrated the various activities of the society into two branches, the Clinical Nephrology Governance branch and the Renal Science branch. New affordable initiatives to promote research, education and professional development and to advocate for the recognition of chronic kidney disease as a major public health issue at the European level will be put in place and/or potentiated in the new organizational frame. Educational initiatives will be espoused to Continuous Professional Development and, starting from 2019, 14 Education & Continuous Professional Development courses will be held covering the full range of knowledge areas of modern nephrology. Consolidation and development is the short- and medium-term mantra of the ERA-EDTA. The society has a rich portfolio of successful activities and brilliant, creative scientists among its members. Integrating the various activities of the ERA-EDTA and treasuring the expertise and wisdom of its most accomplished members will facilitate collaborative research, education and its public impact at large.

The complete chloroplast genome sequences of Lychnis wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes.

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Kang, Jong-Soo; Lee, Byoung Yoon; Kwak, Myounghai

2017-01-01

The complete chloroplast genomes of Lychnis wilfordii and Silene capitata were determined and compared with ten previously reported Caryophyllaceae chloroplast genomes. The chloroplast genome sequences of L. wilfordii and S. capitata contain 152,320 bp and 150,224 bp, respectively. The gene contents and orders among 12 Caryophyllaceae species are consistent, but several microstructural changes have occurred. Expansion of the inverted repeat (IR) regions at the large single copy (LSC)/IRb and small single copy (SSC)/IR boundaries led to partial or entire gene duplications. Additionally, rearrangements of the LSC region were caused by gene inversions and/or transpositions. The 18 kb inversions, which occurred three times in different lineages of tribe Sileneae, were thought to be facilitated by the intermolecular duplicated sequences. Sequence analyses of the L. wilfordii and S. capitata genomes revealed 39 and 43 repeats, respectively, including forward, palindromic, and reverse repeats. In addition, a total of 67 and 56 simple sequence repeats were discovered in the L. wilfordii and S. capitata chloroplast genomes, respectively. Finally, we constructed phylogenetic trees of the 12 Caryophyllaceae species and two Amaranthaceae species based on 73 protein-coding genes using both maximum parsimony and likelihood methods.

PREVALENCE AND AT EARLY AGE ONSET OF HYPO AND HYPERTHYROIDISM IN POST-IODIZATION ERA: A HOSPITAL BASED STUDY FROM SOUTH INDIA

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Fathima Nusrath, Baderuzzaman, Anees Syyeda , Siraj M, N Parveen , Ishaq M

2015-07-01

Full Text Available Background: Thyroid dysfunction has been considered as one of the most common endocrine disorder in clinical practice throughout the world. Its increasing prevalence had led to the screening of general population in different parts of the world in order to investigate causes for rising incidence. A nationwide survey on epidemiology of thyroid dysfunction in selected cities of India suggested the need for further studies in order to have a more comprehensive analysis of epidemiological aspect for better awareness and control of this endocrine disorder. Aim: The major objective of the present study was to identify the prevalence and early age at onset of hypo and hyperthyroidism in post-iodization era based on a hospital based study. Materials and Methods: A total of 516 subjects visiting department of Medicine, Princess ESRA Hospital, Hyderabad, in age group of 10 to 75 years were included in the study from June 2013 to January 2014. Serum TSH, T3, and T4 assays were assessed by chemiluminescence method. Based on thyroid dysfunction test results, subjects were classified into Hypothyroidism, Subclinical Hypothyroidism and Hyperthyroidism. Results: The prevalence of hypothyroidism was highest in the females 33.52 % (n=173 as compared to males 2.32% (n=12 and hyperthyroidism in females 4.06% (n=21 and 0.19% (n=1 in males. Subclinical hypothyroidism in females was 7.55% (n=39. Conclusions: An inordinately high increase in the prevalence rate in women was observed particularly in the age group 21-30years. Monitoring of thyroid profile is necessary to prevent adverse outcome at clinical and subclinical levels related to infertility, pregnancies and other complications.

Predicting human height by Victorian and genomic methods.

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Aulchenko, Yurii S; Struchalin, Maksim V; Belonogova, Nadezhda M; Axenovich, Tatiana I; Weedon, Michael N; Hofman, Albert; Uitterlinden, Andre G; Kayser, Manfred; Oostra, Ben A; van Duijn, Cornelia M; Janssens, A Cecile J W; Borodin, Pavel M

2009-08-01

In the Victorian era, Sir Francis Galton showed that 'when dealing with the transmission of stature from parents to children, the average height of the two parents, ... is all we need care to know about them' (1886). One hundred and twenty-two years after Galton's work was published, 54 loci showing strong statistical evidence for association to human height were described, providing us with potential genomic means of human height prediction. In a population-based study of 5748 people, we find that a 54-loci genomic profile explained 4-6% of the sex- and age-adjusted height variance, and had limited ability to discriminate tall/short people, as characterized by the area under the receiver-operating characteristic curve (AUC). In a family-based study of 550 people, with both parents having height measurements, we find that the Galtonian mid-parental prediction method explained 40% of the sex- and age-adjusted height variance, and showed high discriminative accuracy. We have also explored how much variance a genomic profile should explain to reach certain AUC values. For highly heritable traits such as height, we conclude that in applications in which parental phenotypic information is available (eg, medicine), the Victorian Galton's method will long stay unsurpassed, in terms of both discriminative accuracy and costs. For less heritable traits, and in situations in which parental information is not available (eg, forensics), genomic methods may provide an alternative, given that the variants determining an essential proportion of the trait's variation can be identified.

Enhanced post wash retention of combed DNA molecules by varying multiple combing parameters.

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Yadav, Hemendra; Sharma, Pulkit

2017-11-01

Recent advances in genomics have created a need for efficient techniques for deciphering information hidden in various genomes. Single molecule analysis is one such technique to understand molecular processes at single molecule level. Fiber- FISH performed with the help of DNA combing can help us in understanding genetic rearrangements and changes in genome at single DNA molecule level. For performing Fiber-FISH we need high retention of combed DNA molecules post wash as Fiber-FISH requires profuse washing. We optimized combing process involving combing solution, method of DNA mounting on glass slides and coating of glass slides to enhance post-wash retention of DNA molecules. It was found that average number of DNA molecules observed post-wash per field of view was maximum with our optimized combing solution. APTES coated glass slides showed lesser retention than PEI surface but fluorescent intensity was higher in case of APTES coated surface. Capillary method used to mount DNA on glass slides also showed lesser retention but straight DNA molecules were observed as compared to force flow method. Copyright © 2017 Elsevier Inc. All rights reserved.

A TaqMan real-time PCR-based assay for the identification of Fasciola spp.

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Alasaad, Samer; Soriguer, Ramón C; Abu-Madi, Marawan; El Behairy, Ahmed; Jowers, Michael J; Baños, Pablo Díez; Píriz, Ana; Fickel, Joerns; Zhu, Xing-Quan

2011-06-30

Real time quantitative PCR (qPCR) is one of the key technologies of the post-genome era, with clear advantages compared to normal end-point PCR. In this paper, we report the first qPCR-based assay for the identification of Fasciola spp. Based on sequences of the second internal transcribed spacers (ITS-2) of the ribosomal rRNA gene, we used a set of genus-specific primers for Fasciola ITS-2 amplification, and we designed species-specific internal TaqMan probes to identify F. hepatica and F. gigantica, as well as the hybrid 'intermediate'Fasciola. These primers and probes were used for the highly specific, sensitive, and simple identification of Fasciola species collected from different animal host from China, Spain, Niger and Egypt. The novel qPCR-based technique for the identification of Fasciola spp. may provide a useful tool for the epidemiological investigation of Fasciola infection, including their intermediate snail hosts. Copyright © 2011 Elsevier B.V. All rights reserved.

Group A rotavirus gastroenteritis: post-vaccine era, genotypes and zoonotic transmission.

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Luchs, Adriana; Timenetsky, Maria do Carmo Sampaio Tavares

2016-01-01

ABSTRACTThis article provides a review of immunity, diagnosis, and clinical aspects of rotavirus disease. It also informs about the changes in epidemiology of diarrheal disease and genetic diversity of circulating group A rotavirus strains following the introduction of vaccines. Group A rotavirus is the major pathogen causing gastroenteritis in animals. Its segmented RNA genome can lead to the emergence of new or unusual strains in human populations via interspecies transmission and/or reassortment events.RESUMOEste artigo fornece uma revisão sobre imunidade, diagnóstico e aspectos clínicos da doença causada por rotavírus. Também aponta as principais mudanças no perfil epidemiológico da doença diarreica e na diversidade genética das cepas circulantes de rotavírus do grupo A, após a introdução vacinal. O rotavírus do grupo A é o principal patógeno associado à gastroenterite em animais. Seu genoma RNA segmentado pode levar ao surgimento de cepas novas ou incomuns na população humana, por meio de transmissão entre espécies e eventos de rearranjo.

Integration of Structural Dynamics and Molecular Evolution via Protein Interaction Networks: A New Era in Genomic Medicine

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Kumar, Avishek; Butler, Brandon M.; Kumar, Sudhir; Ozkan, S. Banu

2016-01-01

Summary Sequencing technologies are revealing many new non-synonymous single nucleotide variants (nsSNVs) in each personal exome. To assess their functional impacts, comparative genomics is frequently employed to predict if they are benign or not. However, evolutionary analysis alone is insufficient, because it misdiagnoses many disease-associated nsSNVs, such as those at positions involved in protein interfaces, and because evolutionary predictions do not provide mechanistic insights into functional change or loss. Structural analyses can aid in overcoming both of these problems by incorporating conformational dynamics and allostery in nSNV diagnosis. Finally, protein-protein interaction networks using systems-level methodologies shed light onto disease etiology and pathogenesis. Bridging these network approaches with structurally resolved protein interactions and dynamics will advance genomic medicine. PMID:26684487

Origin and evolution of SINEs in eukaryotic genomes.

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Kramerov, D A; Vassetzky, N S

2011-12-01

Short interspersed elements (SINEs) are one of the two most prolific mobile genomic elements in most of the higher eukaryotes. Although their biology is still not thoroughly understood, unusual life cycle of these simple elements amplified as genomic parasites makes their evolution unique in many ways. In contrast to most genetic elements including other transposons, SINEs emerged de novo many times in evolution from available molecules (for example, tRNA). The involvement of reverse transcription in their amplification cycle, huge number of genomic copies and modular structure allow variation mechanisms in SINEs uncommon or rare in other genetic elements (module exchange between SINE families, dimerization, and so on.). Overall, SINE evolution includes their emergence, progressive optimization and counteraction to the cell's defense against mobile genetic elements.

Post-Affirmative Action: A Phenomenological Study of Admission Initiatives by Chief Diversity Officers to Support Diversity

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Gichuru, Margaret

2010-01-01

The purpose of this phenomenological study was to explore the experiences of chief diversity officers (CDOs) and how they enhanced admission of minority students in the post-affirmative action era. Six chief diversity officers, who played a pivotal leadership role in diversity of their respective campuses, described their experiences. Using…

Analgesic effectiveness of prophylactic therapy and continued therapy with naproxen sodium post simple extraction.

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Angel Asmat-Abanto

2015-02-01

Full Text Available To compare the analgesic effectiveness of the prophylactic therapy and continued therapy with naproxen sodium after a simple dental extraction. Material and methods: This prospective randomized, parallel, single-blind clinical trial was developed in the Dental Clinic of the Universidad Alas Peruanas in Trujillo (Peru. The patients, who required simple extraction due to dental caries, were randomly distributed into three groups: 30 of them took 550mg naproxen sodium in the preoperative period and then every 12 hours, other 30 took 550mg naproxen sodium in the postoperative period and then every 12 hours, and 30(control group, received 400mg ibuprofen in the postoperative period and then every 8 hours, depending on the established criteria. The procedure was standardized, analgesic effectiveness was assessed by visual analog scale and the presence of adverse drug reactions was evaluated as well. Data were analyzed using ANOVA and Duncan’s test using IBM SPSS 22 with a significance level of 5%. Results: Continued therapy with naproxen sodium showed greater analgesic effectiveness after a simple extraction at 1, 8 and 24 hours (p<0.005. Conclusion: Continued therapy with naproxen sodium presented greater effectiveness than prophylactic therapy with naproxen sodium after a simple extraction.

EuMicroSatdb: A database for microsatellites in the sequenced genomes of eukaryotes

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Grover Atul

2007-07-01

Full Text Available Abstract Background Microsatellites have immense utility as molecular markers in different fields like genome characterization and mapping, phylogeny and evolutionary biology. Existing microsatellite databases are of limited utility for experimental and computational biologists with regard to their content and information output. EuMicroSatdb (Eukaryotic MicroSatellite database http://ipu.ac.in/usbt/EuMicroSatdb.htm is a web based relational database for easy and efficient positional mining of microsatellites from sequenced eukaryotic genomes. Description A user friendly web interface has been developed for microsatellite data retrieval using Active Server Pages (ASP. The backend database codes for data extraction and assembly have been written using Perl based scripts and C++. Precise need based microsatellites data retrieval is possible using different input parameters like microsatellite type (simple perfect or compound perfect, repeat unit length (mono- to hexa-nucleotide, repeat number, microsatellite length and chromosomal location in the genome. Furthermore, information about clustering of different microsatellites in the genome can also be retrieved. Finally, to facilitate primer designing for PCR amplification of any desired microsatellite locus, 200 bp upstream and downstream sequences are provided. Conclusion The database allows easy systematic retrieval of comprehensive information about simple and compound microsatellites, microsatellite clusters and their locus coordinates in 31 sequenced eukaryotic genomes. The information content of the database is useful in different areas of research like gene tagging, genome mapping, population genetics, germplasm characterization and in understanding microsatellite dynamics in eukaryotic genomes.

Academic Freedom in the Post-9/11 Era. Education, Politics and Public Life

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Carvalho, Edward J., Ed.; Downing, David B.

2011-01-01

Academic freedom has been a principle that undergirds the university since 1915. Beyond this, it also protects a spirit of free inquiry essential to a democratic society. But in the post-9/11 present, the basic principles of academic freedom have been deeply challenged. There have been many startling instances where the rhetoric of national…

Electra en Piñera

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Elina Miranda Cancela

1991-12-01

Full Text Available Este artigo e uma análise da Electra Garrigó de Virgilio Piñera, teatrólogo cubano, e das suas vinculações com o teatro trágico grego, sobretudo com a Electra de Sófocles, acrescida ainda de aproximações com autores modernos que trataram do mesmo tema. Apesar da inspiração grega, Piñera permanece um típico teatrólogo nacional, marcado pelos momentos de grande tensão social da sua época (a tragédia em apreço data de 1941. O conflito produzido pela excessiva autoridade dos pais sobre os filhos, latente neste mito, interessa-o por seu significado dentro da família cubana.

Inflation with a smooth constant-roll to constant-roll era transition

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Odintsov, S. D.; Oikonomou, V. K.

2017-07-01

In this paper, we study canonical scalar field models, with a varying second slow-roll parameter, that allow transitions between constant-roll eras. In the models with two constant-roll eras, it is possible to avoid fine-tunings in the initial conditions of the scalar field. We mainly focus on the stability of the resulting solutions, and we also investigate if these solutions are attractors of the cosmological system. We shall calculate the resulting scalar potential and, by using a numerical approach, we examine the stability and attractor properties of the solutions. As we show, the first constant-roll era is dynamically unstable towards linear perturbations, and the cosmological system is driven by the attractor solution to the final constant-roll era. As we demonstrate, it is possible to have a nearly scale-invariant power spectrum of primordial curvature perturbations in some cases; however, this is strongly model dependent and depends on the rate of the final constant-roll era. Finally, we present, in brief, the essential features of a model that allows oscillations between constant-roll eras.

Second Nuclear Era

International Nuclear Information System (INIS)

Weinberg, A.M.; Spiewak, I.; Barkenbus, J.N.; Livingston, R.S.; Phung, D.L.

1984-03-01

The Institute for Energy Analysis with support from The Andrew W. Mellon Foundation has studied the decline of the present nuclear era in the United States and the characteristics of a Second Nuclear Era which might be instrumental in restoring nuclear power to an appropriate place in the energy options of our country. The study has determined that reactors operating today are much safer than they were at the time of the TMI accident. A number of concepts for a supersafe reactor were reviewed and at least two were found that show considerable promise, the PIUS, a Swedish pressurized water design, and a gas-cooled modular design of German and US origin. Although new, safer, incrementally improved, conventional reactors are under study by the nuclear industry, the complete lack of new orders in the United States will slow their introduction and they are likely to be more expensive than present designs. The study recommends that supersafe reactors be taken seriously and that federal and private funds both be used to design and, if feasible, to build a prototype reactor of substantial size. 146 references, 8 figures, 2 tables

Simple Math is Enough: Two Examples of Inferring Functional Associations from Genomic Data

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Liang, Shoudan

2003-01-01

Non-random features in the genomic data are usually biologically meaningful. The key is to choose the feature well. Having a p-value based score prioritizes the findings. If two proteins share a unusually large number of common interaction partners, they tend to be involved in the same biological process. We used this finding to predict the functions of 81 un-annotated proteins in yeast.

Tetrahedral gray code for visualization of genome information.

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Natsuhiro Ichinose

Full Text Available We propose a tetrahedral Gray code that facilitates visualization of genome information on the surfaces of a tetrahedron, where the relative abundance of each [Formula: see text]-mer in the genomic sequence is represented by a color of the corresponding cell of a triangular lattice. For biological significance, the code is designed such that the [Formula: see text]-mers corresponding to any adjacent pair of cells differ from each other by only one nucleotide. We present a simple procedure to draw such a pattern on the development surfaces of a tetrahedron. The thus constructed tetrahedral Gray code can demonstrate evolutionary conservation and variation of the genome information of many organisms at a glance. We also apply the tetrahedral Gray code to the honey bee (Apis mellifera genome to analyze its methylation structure. The results indicate that the honey bee genome exhibits CpG overrepresentation in spite of its methylation ability and that two conserved motifs, CTCGAG and CGCGCG, in the unmethylated regions are responsible for the overrepresentation of CpG.

Development of Chloroplast Genomic Resources in Chinese Yam (Dioscorea polystachya

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Junling Cao

2018-01-01

Full Text Available Chinese yam has been used both as a food and in traditional herbal medicine. Developing more effective genetic markers in this species is necessary to assess its genetic diversity and perform cultivar identification. In this study, new chloroplast genomic resources were developed using whole chloroplast genomes from six genotypes originating from different geographical locations. The Dioscorea polystachya chloroplast genome is a circular molecule consisting of two single-copy regions separated by a pair of inverted repeats. Comparative analyses of six D. polystachya chloroplast genomes revealed 141 single nucleotide polymorphisms (SNPs. Seventy simple sequence repeats (SSRs were found in the six genotypes, including 24 polymorphic SSRs. Forty-three common indels and five small inversions were detected. Phylogenetic analysis based on the complete chloroplast genome provided the best resolution among the genotypes. Our evaluation of chloroplast genome resources among these genotypes led us to consider the complete chloroplast genome sequence of D. polystachya as a source of reliable and valuable molecular markers for revealing biogeographical structure and the extent of genetic variation in wild populations and for identifying different cultivars.

Fukushima's lessons from the blue butterfly: A risk assessment of the human living environment in the post-Fukushima era.

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Otaki, Joji M

2016-10-01

A series of studies on the pale grass blue butterfly that were carried out to assess the biological effects of the Fukushima nuclear accident teach 3 important lessons. First, it is necessary to have an environmental indicator species, such as the pale grass blue butterfly in Japan, that is common (not endangered), shares a living environment (air, water, and soil) with humans, and is amenable to laboratory experiments. The monitoring of such indicator species before and immediately after a nuclear accident likely reflects acute impacts caused by initial exposure. To assess transgenerational and chronic effects, continuous monitoring over time is encouraged. Second, it is important to understand the actual health status of a polluted region and comprehend the whole picture of the pollution impacts, rather than focusing on the selected effects of radiation alone. In our butterfly experiments, plant leaves from Fukushima were fed to larval butterflies to access whole-body effects, focusing on survival rate and morphological abnormalities (rather than focusing on a specific disease or biochemical marker). Our results revealed that ionizing radiation is unlikely to be the exclusive source of environmental disturbances. Airborne particulate matter from a nuclear reactor, regardless of its radioactivity, is likely equally important. Finally, our butterfly experiments demonstrate that there is considerable variation in sensitivities to nuclear pollution within a single species or even within a local population. Based on these results, it is speculated that high pollution sensitivity in humans may be caused not only by low levels of functional DNA repair enzymes but also by immunological responses to particulate matter in the respiratory tract. These lessons from the pale grass blue butterfly should be integrated in studying future nuclear pollution events and decision making on nuclear and environmental policies at the local and international levels in the post

Integration of structural dynamics and molecular evolution via protein interaction networks: a new era in genomic medicine.