bac genomic library: Topics by WorldWideScience.org

A piggyBac transposon-based genome-wide library of insertionally mutated Blm-deficient murine ES cells

Lepidoptera, butterflies and moths, is the second largest animal order and includes numerous agricultural pests. To facilitate comparative genomics in Lepidoptera, we isolated BAC clones containing...Full Text Available

2011-01-01

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Construction of a genome-wide human BAC-Unigene resource. Final progress report, 1989--1996

Cultured mouse or human embryonic stem (ES) cells provide access to all of the genes required to elaborate the fundamental components and physiological systems of a mammalian cell. Chemical or insertional...Full Text Available

2009-04-01

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The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

Currently, over 30,000 mapped STSs and 27,000 mapped Unigenes (non-redundant, unigene sets of cDNA representing EST clusters) are available for human alone. A total of 44,000 Unigene cDNA clones have been supplied by Research Genetics. Unigenes, or cDNAs are excellent resource for map building for two reasons. Firstly, they exist in two alternative forms -- as both sequence information for PCR primer pairs, and cDNA clones -- thus making library screening by colony hybridization as well as pooled library PCR possible. The authors have developed an efficient and robust procedure to screen genomic libraries with large number of DNA probes. Secondly, the linkage and order of expressed sequences, or genes are highly conserved among human, mouse and other mammalian species. Therefore, mapping with cDNA markers rather than random anonymous STSs will greatly facilitate comparative, evolutionary studies as well ...

1996-12-31

4

A Marker-Dense Physical Map of the Bradyrhizobium japonicum Genome

BackgroundFood supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist...Full Text Available

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Human cDNA mapping using fluorescence in situ hybridization. Final progress report, April 1, 1994--July 31, 1997

Bacterial artificial chromosome (BAC) clones are effective mapping and sequencing reagents for use with a wide variety of small and large genomes. This report describes the development of a physical...Full Text Available

2001-08-01

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piggyBac is a flexible and highly active transposon as compared to Sleeping Beauty, Tol2, and Mos1 in mammalian cells

The ultimate goal of this research is to generate and apply novel technologies to speed completion and integration of the human genome map and sequence with biomedical problems. To do this, techniques were developed and genome-wide resources generated. This includes a genome-wide Mapped and Integrated BAC/PAC Resource that has been used for gene finding, map completion and anchoring, breakpoint definition and sequencing. In the last period of the grant, the Human Mapped BAC/PAC Resource was also applied to determine regions of human variation and to develop a novel paradigm of primate evolution through to humans. Further, in order to more rapidly evaluate animal models of human disease, a BAC Map of the mouse was generated in collaboration with the MTI Genome Center, Dr. Bruce Birren.

1997-12-31

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Reconstruction of the complete human cytomegalovirus genome in a BAC reveals RL13 to be a potent inhibitor of replication

A nonviral vector for highly efficient site-specific integration would be desirable for many applications in transgenesis, including gene therapy. In this study we directly compared the genomic integration...Full Text Available

2006-10-10

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Generation of a BAC-based physical map of the melon genome

Human cytomegalovirus (HCMV) in clinical material cannot replicate efficiently in vitro until it has adapted by mutation. Consequently, wild-type HCMV differ fundamentally from the passaged strains...Full Text Available

2010-09-01

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BackgroundCucumis melo (melon) belongs to the Cucurbitaceae family, whose economic importance among horticulture crops is second only to Solanaceae. Melon has high...Full Text Available

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Digital Libraries

Integrase-directed recovery of functional genes from genomic libraries

Digital Libraries

2008-01-01

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Genomic Expression Libraries for the Identification of Cross-Reactive Orthopoxvirus Antigens

Large population sizes, rapid growth and 3.8 billion years of evolution firmly establish microorganisms as a major source of the planet's biological and genetic diversity. However, up to 99% of the...Full Text Available

2009-09-01

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A genomic library-based amplification approach (GL-PCR) for the mapping of multiple IS6110 insertion sites and strain differentiation of Mycobacterium tuberculosis

Increasing numbers of human cowpox virus infections that are being observed and that particularly affect young non-vaccinated persons have renewed interest in this zoonotic disease. Usually causing...Full Text Available

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British Library Electronic Table of Contents (United Kingdom)

Evidence suggests that insertion of the IS6110 element is not without consequence to the biology of Mycobacterium tuberculosis complex strains. Thus, mapping of multiple IS6110 insertion sites in the genome of biomedically relevant clinical isolates would result in a better understanding of the role of this mobile element, particularly with regard to transmission, adaptability and virulence. In the present paper, we describe a versatile strategy, referred to as GL-PCR, that amplifies IS6110-flanking sequences based on the construction of a genomic library. M. tuberculosis chromosomal DNA is fully digested with HincII and then ligated into a plasmid vector between T7 and T3 promoter sequences. The ligation reaction product is transformed into Escherichia coli and selective PCR amplification...

2006-01-01

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The digital library toolkit

Construction of a human MluI YAC library

The digital library toolkit

2000-01-01

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Bacterial Artificial Chromosome Mutagenesis Using Recombineering

The authors describe a cloning strategy for the construction of a human genomic library in yeast artificial chromosomes (YACs) based on complete digestion of high-molecular-weight DNA with the infrequently cutting restriction enzyme MluI. Cloning of MluI fragments in the vector pYAC-RC and one subsequent size fractionation by preparative pulsed-field gel electrophoresis yielded a library with average insert sizes of 600 kb. Ninety-seven percent of the colonies were recombinant. An additional size fractionation of MluI fragments prior to ligation had no significant influence on the size of the YACs. The library currently consists of 5000 clones, which is the equivalent of one human genome. Nineteen percent of the YACs were larger than 1.2 Mb. Since smaller MluI fragments are lost during sizing, they also performed cloning without size fractionation. Only 20% of the colonies were ...

1994-05-01

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Genomic sequence for human prointerleukin 1 beta: possible evolution from a reverse transcribed prointerleukin 1 alpha gene.

Gene expression from bacterial artificial chromosome (BAC) clones has been demonstrated to facilitate physiologically relevant levels compared to viral and nonviral cDNA vectors. BACs are large enough...Full Text Available

2011-01-01

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Fiscal 1998 industrial science and technology R and D project. Research report on R and D of genome informatics technology (Development of stable oil supply measures using complex biosystem); 1998 nendo genome informatics gijutsu kenkyu kaihtsu seika hokokusho. Fukugo seibutsukei riyo sekiyu antei kyokyu taisaku kaihatsu

We have isolated the human prointerleukin 1 (proIL-1) beta gene from leukocyte and fetal liver libraries. The nucleotide sequence and its gene organization reveals that the proIL-1 beta gene is composed...Full Text Available

1986-10-24

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Yeast artificial chromosome libraries containing large inserts from mouse and human DNA

This report describes the fiscal 1998 result on development of genome informatics technology. As comparative analysis technique of genes, the combination of electrophoresis and PCR was used. For improvement of the throughput and reproducibility of the technique, module- shuffling primers were used, and the multi(96)-arrayed capillary fragment analyzer was devised. The system detecting SNPs rapidly was also developed successfully. As analysis technology of DNA sequence by use of triple- stranded DNA formation, study was made on construction of long cDNA libraries, selective subtraction of specific sequences from libraries, and the basic technology of homologous cloning. Study was also made on each reaction step of IGCR technique for fast analysis, and specifications of a fluorescence transfer monitor. As modeling technique of genetic sequence information, the simulation model was developed for gene expression regulatory ...

1999-03-01

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How to build a digital library

Yeast artificial chromosome (YAC) libraries have been difficult to construct with average insert sizes >400 kilobase pairs when DNA is size-fractionated in low-melting-point agarose. By using yeast chromosomes in mock cloning experiments, the authors found that polyamines should be present whenever agarose containing high molecular weight DNA is melted to protect DNA from degradation. By incorporating polyamines during the cloning procedure, they constructed YAC libraries from mouse and human DNA with average insert sizes of 700 and 620 kilobase pairs, respectively. Several genome equivalents of these YAC libraries were replicated onto the surface of many duplicate agar plates using a 40,000 multipin transfer device. High-density filter replicas were screened by hybridization, and 70 mouse YAC clones from 31 loci and 132 human YAC clones from 49 loci were isolated.

1991-05-15

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Digital libraries philosophies, technical design considerations, and example scenarios

How to build a digital library

2010-01-01

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Digital Library Technology Trends

Digital libraries

1999-01-01

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Digital Libraries Principles and Practice in a Global Environment

Digital Library Technology Trends

2002-01-01

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ACM Digital Library [Online database

Digital Libraries

2004-01-01

24

Molecular cloning of the human homeobox gene goosecoid (GSC) and mapping of the gene to human chromosome 14q32. 1

ACM Digital Library [Online database

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RFLP for a DNA clone which maps to 19q13. 2-19qter (D19S63)

Goosecoid is a homeobox gene first isolated from a Xenopus dorsal lip cDNA library. Homologous genes have been isolated from mouse, zebrafish, and chick. In all species examined, the gene is expressed and plays an important role during the process of gastrulation in early embryonic development. The authors report here the cloning of the human goosecoid (GSC) from a genomic library and the sequence of its encoded protein. The genomic organization and protein sequence of the human gene are highly conserved with respect to those of its Xenopus and mouse counterparts: all three genes consist of three exons, with conserved exon-intron boundaries. The sequence of the homeo-domain is 100% conserved in most vertebrates. Using somatic cell hybrid and chromosomal in situ hybridization, the gene was mapped to chromosome 14q32.1. 30 refs., 3 figs., 2 tabs.

1994-05-15

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Characterization of eight microsatellite markers in the white sea bream, Diplodus sargus (Teleostei, Sparidae)

pD10 is a 0.85 kb fragment with BamHI ends cloned in pSP64. It was sub-cloned from {lambda}D10 which was isolated from a genomic library constructed in {lambda}EMBL3 from a rodent human somatic cell hybrid. The probe was localized to 19q13.2-19qter on a panel of rodent human somatic cell hybrids. Co-dominant segregation was shown in 32 families of 280 individuals.

1990-02-25

27

British Library Electronic Table of Contents (United Kingdom)

Abstract The white sea bream, Diplodus sargus (Teleostei, Sparidae), is a species with a high commercial importance in Mediterranean aquaculture. There is currently little information available about the genetic characteristics of cultured populations. In this survey, we have developed eight polymorphic microsatellites for the white sea bream using an enriched genome library protocol. All of them were polymorphic in the 67 individuals tested, 32 of which were wild specimens, and 35 were individuals from a captive F1 broodstock. These markers can potentially be useful tools for use in population genetic studies.

2008-01-01

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Anode wire ageing in proportional detectors at the BAC calorimeter of the ZEUS experiment

DIGITAL LIBRARIES: IMPACT ON SCIENCE ... - MUSPIN - NASA

Experimental results of ageing effects in proportional counters are presented. The measurements were carried out for 158 ZEUS-BAC gas system monitoring counters. Deterioration of the pulse height distribution in azimuth and along the anode wire are presented. The influence of water admixture on counting gas is also described. (orig.).

1997-06-21

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Cloning and sequencing of cDNA encoding human DNA topoisomerase II and localization of the gene to chromosome region 17q21-22

digital libraries, which was identified as a national challenge in the Information ... The linkages between the many digital libraries and information services are ...

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Isolation and characterization of microsatellite markers in Acca sellowiana (Berg) Burret.

Two overlapping cDNA clones encoding human DNA topoisomerase II were identified by two independent methods. In one, a human cDNA library in phage {lambda} was screened by hybridization with a mixed oligonucleotide probe encoding a stretch of seven amino acids found in yeast and Drosophila DNA topoisomerase II; in the other, a different human cDNA library in a {lambda}gt11 expression vector was screened for the expression of antigenic determinants that are recognized by rabbit antibodies specific to human DNA topoisomerase II. The entire coding sequences of the human DNA topoisomerase II gene were determined from these and several additional clones, identified through the use of the cloned human TOP2 gene sequences as probes. Hybridization between the cloned sequences and mRNA and genomic DNA indicates that the human enzyme is encoded by a single-copy gene. The location of the gene was mapped to chromosome 17q21-22 by in ...

1988-10-01

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Involvement of the Tpl-2/cot oncogene in MMTV tumorigenesis.

Acca sellowiana has commercial potential because of the quality and the unique flavor of its fruit. Conservation of natural populations and management of breeding programmes would benefit from the availability of molecular markers that could be used to characterize levels and distribution of genetic variability. Thus, 13 microsatellite markers were developed from an enriched genomic library of A. sellowiana. They were characterized using 40 samples. The expected and observed heterozygosities ranged from 0.513 to 0.913 and from 0.200 to 0.889, respectively. These are the first microsatellite loci characterized from A. sellowiana that will contribute to improve researches on the genetic conservation, characterization and breeding. PMID:21586063

2008-07-08

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Human type I pituitary adenylate cyclase activating polypeptide receptor (ADCYAP1R): Localization to chromosome band 7p14 and integration into the cytogenetic, physical, and genetic map of chromosome 7

We report for the first time a relationship between the Tpl-2/cot oncogene and Mouse Mammary Tumor Virus (MMTV) associated transformation of mammary gland cells. A sub-genomic library generated from a primary mammary gland tumor yielded a novel MMTV integration site which disrupted the Tpl-2/cot proto-oncogene between exons 7 and 8. Comparison of a cell line derived from normal mammary gland (comma-D) and a cell line established from an MMTV induced mammary tumor (GR) demonstrated similar rearrangements within Tpl-2/cot for the GR cells but not in the comma-D cells. These rearrangements in the cell line were accompanied by an increase in the level of Tpl-2/cot specific mRNA. This data suggests that Tpl-2/cot expression may be important in epithelial cell transformation or tumor progression. PMID:8934549

1996-11-01

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The Design of an Interactive Online Help Desk in the Alexandria Digital Library

The gene encoding the human type I pituitary adenylate cyclase activating polypeptide receptor (ADCYAP1R1) was mapped to chromosome 7 by PCR analysis of genomic DNA from a human/rodent somatic cell hybrid mapping panel. This assignment was confirmed and the gene localized to chromosome band 7p14 by fluorescence in situ hybridization. A yeast artificial chromosome containing ADCYAP1R1 was identified in the CEPH {open_quotes}B{close_quotes} Mega-YAC library. This YAC includes two highly polymorphic dinucleotide repeat sequences that will facilitate genetic studies of the contribution of ADCYAP1R1 in disease states of the central nervous and neuroendocrine systems. 13 refs., 1 fig.

1994-10-01

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Networked Digital Library of Theses and Dissertations Federated Search

The Design of an Interactive Online Help Desk in the Alexandria Digital Library

1999-01-01

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Emerging technologies for academic libraries in the digital age

Networked Digital Library of Theses and Dissertations

1995-01-01

36

Digital Inclusion, Teens, and Your Library Exploring the Issues and Acting on Them

Emerging technologies for academic libraries in the digital age

2009-01-01

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Artificial intelligence in digital libraries moving from chaos to (more) order

Digital Inclusion, Teens, and Your Library

2005-01-01

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piggyBac Transposon-mediated Long-term Gene Expression in Mice

Artificial intelligence in digital libraries

1998-01-01

39

New library buildings. Part VII. The Health Sciences Library of the University of Virginia.

Transposons are promising systems for somatic gene integration because they can not only integrate exogenous genes efficiently, but also be delivered to a variety of organs using a range of transfection...Full Text Available

2010-04-01

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Intelligent Analyst Digital Video Library Prototype

This article describes the new Health Sciences Library at the University of Virginia Medical Center in Charlottesville, Virginia. The library was under construction for about two years and opened in...Full Text Available

1976-07-01

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Structural and operational complexity of the Geobacter sulfurreducens genome

... type. Sonic's digital libraries will provide a cross mapping between the narrative (speech and text) and imagery domains. ...

2002-10-01

42

Intrapopulation Genome Size Dynamics in Festuca pallens

Prokaryotic genomes can be annotated based on their structural, operational, and functional properties. These annotations provide the pivotal scaffold for understanding cellular functions on a genome-scale,...Full Text Available

2010-09-01

43

Cluster approach to quantum-chemical calculations of chemisorption and heterogeneous catalytic systems

Background and AimsIt is well known that genome size differs among species. However, information on the variation and dynamics of genome size in wild populations and on the early...Full Text Available

2008-10-01

44

Usability Studies and User-Centered Design in Digital Libraries

The increasing use of quantum-chemical methods in catalysis has underscored the importance of developing and improving semiempirical approximations oriented toward calculations of the total energy and geometry, offering a means for examining intermolecular interactions. In this article a general approach is proposed, using weighting factors for certain regions of distances, i.e., introducing different parametrization into the various regions. A scheme designated MINDO/3-HB is presented as an extension of the MINDO/3 scheme to the region of hydrogen bonds and ..pi..-complexes of olefins with Broensted acid centers (BACs). Examples of cluster calculations are given for the adsorption of ammonia, pyridine, ethylene, and ethanol on the BACs of zeolites. In the example of the process of zeolite synthesis, the possibilities of the cluster approach are discussed for calculations related to the formation of catalysts.

1987-07-01

45

FENDL multigroup libraries

Digital libraries continue to flourish. At the same time, the principles of user-centered design and the practice of usability testing have been growing in popularity, spreading their influence into the library sphere. This article explores the confluence of these two trends by surveying the current literature on usability studies of digital libraries. This article focuses on the methodology of studies of multimedia digital libraries. (Contains 1 table and 45 notes.)

2007-12-01

46

Advances in Library Administration and Organization

Selected neutron reaction nuclear data libraries and photon-atomic interaction cross section libraries for elements of interest to the IAEA's program on Fusion Evaluated Nuclear Data Library (FENDL) have been processed into MATXSR format using the NJOY system on the VAX4000 computer of the IAEA. This document lists the resulting multigroup data libraries. All the multigroup data generated are available cost-free upon request from the IAEA Nuclear Data Section. (author). 9 refs.

47

Whole-genome shotgun assembly and comparison of human genome assemblies

The Advances in Library Administration and Organization Series provides a body of research literature that contributes to the base of organizational theory upon which library administrators rely. Its mix of contributions to the literature of library administration and organization is both diverse and eclectic. This volume of the series covers a variety of topics relating to the management of academic, public and school libraries

2010-01-01

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The complete mitochondrial genome of the stomatopod crustacean Squilla mantis.

We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs...Full Text Available

2004-02-17

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The complete mitochondrial genome of the stomatopod crustacean Squilla mantis

PMID:16091132

2005-08-09

50

Molecular Imaging in the Age of Genomic Medicine

BackgroundAnimal mitochondrial genomes are physically separate from the much larger nuclear genomes and have proven useful both for phylogenetic studies and for understanding genome...Full Text Available

51

KoreaScience (Korea)

Full Text Available

2007-06-01

52

Genomics - from Neanderthals to high-throughput sequencing

The Use of Quality Benchmarking in Assessing Web Resources for the Dermatology Virtual Branch Library of the National electronic Library for Health (NeLH)

A report on 'The Biology of Genomes' meeting, Cold Spring Harbor, USA, 10-14 May 2006.

2006-01-01

53

Self-Study Digital Library Courseware

BackgroundIn 1998, the U.K. National Health Service Information for Health Strategy proposed the implementation of a National electronic Library for Health...Full Text Available

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Innovation and survival: a case study in planning medical library services.

Tutorial on digital libraries. Site also contains links to other reference materials on digital libraries as well as links to courses on the subject. Keywords: Information Systems - Information Systems Applications, Information Storage and Retrieval, Database Management, multimedia

2001-12-01

55

Clinical Digital Libraries Project: design approach and exploratory assessment of timely use in clinical environments*

In the information age, information utilities like libraries are as sensitive to the stresses of change as any other organization. This article is a case study of a small, specialized medical library...Full Text Available

1998-10-01

56

U.S. Department of the Interior Library - Reference Sources on...

Objective: The paper describes and evaluates the use of Clinical Digital Libraries Project (CDLP) digital library collections in terms of their facilitation of timely clinical information...Full Text Available

2006-04-01

57

Return on Investment: Libraries and Student Retention

and Vendors on the Web Bartleby.com "Great books online." Electronic Texts & Digital Libraries Links to the full text of books and other texts on the Web. Law and Politics...

2011-05-06

58

British Library Electronic Table of Contents (United Kingdom)

Using data on libraries collected by the Association of Research Libraries (ARL) and the Association of College and Research Libraries (ACRL), as well as fall-to-fall retention rates obtained from the Integrated Postsecondary Education Data System (IPEDS) of the National Center for Education Statistics (NCES), this study employs statistical measures of association to analyze the relationship of both library expenditures and number of professional library staff to student persistence. The strongest relationships found were those between student retention and total library expenditures, total library materials costs, and serial costs for institutions categorized as baccalaureate colleges within the Carnegie Classification System. The most significant relationship between persistence and numb...

2007-01-01

59

Real-time digital libraries based on widely distributed, high performance management of large-data-objects

FAQs for IIS Solicitation NSF-05551

Real-time digital libraries based on widely distributed, high performance management of large-data-objects

1997-01-01

60

METHOD FOR SYNTHESIZING DERIVATIVE, COMPOUND LIBRARY AND METHOD FOR PREPARING THE SAME AND METHOD FOR SCREENING

... Science, Computer Vision, Digital Government, Digital Libraries, Digital Society and Technologies ... for Robust Intelligence, Digital Government, and Digital Libraries and Archives. In subsequent years ...

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J-STORE (Japan)

Full Text Available

2006-04-28

62

Java Image I/O for VICAR, PDS, and ISIS

Digital Libraries from Concept to Practice

This library, written in Java, supports input and output of images and metadata (labels) in the

2011-01-01

63

The paper represents the result of research in the field of digital libraries functionalities in the context of new Grid infrastructure support. It is defined a new vector of knowledge society, informational vector - content vector. It presents a Grid European project which includes Romanian partners, and it defines on this base a digital library model which can be applied for the libraries in Romania.

2007-01-01

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Conservation Library

Complementary thoughts on the future of internet science: Can digital libraries avoid scientific tunnel-vision and lead to innovation?

... is Jin Ho Ocean Enterprise Co., Ltd., a Taiwanese business incorporated in 1985. Under the U.S. Oil ... ...

65

A novel application of the multi-group method: Coupled neutron-gamma-electron cross-section library

PMID:19147296

2009-01-14

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A novel application of the multi-group method: Coupled neutron-gamma-electron cross-section library

A multi-group neutron-gamma cross-section library in DTF-IV format is supplemented with electron production matrix to generate a coupled neutron-gamma-electron library. This is realized by estimating the contributions from Compton scattering, pair production and photoelectric effect to the electron production cross-sections. A novel application of this new library, which involves transport of neutrons, gammas and electrons, for estimating the Compton current due to a pulse of radiation in air is discussed.

2006-02-15

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Iranlib (Improved Range of ANISN/PC Library): P-3 coupled neutron-gamma cross-section libraries in ISOTXS format to be used by ANISN/PC (CCC-0514/02)

A multi-group neutron-gamma cross-section library in DTF-IV format is supplemented with electron production matrix to generate a coupled neutron-gamma-electron library. This is realized by estimating the contributions from Compton scattering, pair production and photoelectric effect to the electron production cross-sections. A novel application of this new library, which involves transport of neutrons, gammas and electrons, for estimating the Compton current due to a pulse of radiation in air is discussed.

2006-02-01

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IRAN. LIB (Improved Range of ANISN/PC LIBrary): a P-3 coupled neutron-gamma cross-section library in ISOTXS format to be used by ANISN/PC (CCC-0514/02)

IRAN.LIB is a Coupled Neutron-Gamma library which was developed to be used by the ANISN/PC (ccc-0514/02). The library was developed mainly for shielding calculations and it contains 33 elements mostly used as shielding materials, such as concrete. IRAN.LIB is a set of six libraries, each having the same elements but different number of energy groups. In order to use IRAN.LIB by ANISN/PC, this code must be modified. (author).

1991-09-17

69

The mode and tempo of genome size evolution in eukaryotes

IRAN.LIB is a coupled neutron-gamma cross section library which was developed to be used in the ANISN/PC (CCC-0514/02) code for transport calculations. The library was developed mainly for shielding calculations and it contains these 33 elements most used in shielding materials, such as concrete. IRAN.LIB is a set of six libraries, each having the same elements but a different number of energy groups. In order to use IRAN.LIB in ANISN/PC, this code must be modified. (author).

1991-01-01

70

Sequence space coverage, entropy of genomes and the potential to detect non-human DNA in human samples

Eukaryotic genome size varies over five orders of magnitude; however, the distribution is strongly skewed toward small values. Genome size is highly correlated to a number of phenotypic traits, suggesting...Full Text Available

2007-05-01

71

Massive turnover of functional sequence in human and other mammalian genomes

BackgroundGenomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties...Full Text Available

72

Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies

Despite the availability of dozens of animal genome sequences, two key questions remain unanswered: First, what fraction of any species' genome confers biological function, and second, are apparent...Full Text Available

2010-10-01

73

Genome Sequence and Comparative Analysis of the Solvent-Producing Bacterium Clostridium acetobutylicum

The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble...Full Text Available

2003-10-01

74

Full genome gene expression analysis of the heat stress response in Drosophila melanogaster

The genome sequence of the solvent-producing bacterium Clostridium acetobutylicum ATCC 824 has been determined by the shotgun approach. The genome consists of a 3.94-Mb chromosome and...Full Text Available

2001-08-01

75

Extensive synteny conservation of holocentric chromosomes in Lepidoptera despite high rates of local genome rearrangements

The availability of full genome sequences has allowed the construction of microarrays, with which screening of the full genome for changes in gene expression is possible. This method can provide a wealth...Full Text Available

2005-10-01

76

A DNA transposon-based approach to validate oncogenic mutations in the mouse

The recent assembly of the silkworm Bombyx mori genome with 432 Mb on 28 holocentric chromosomes has become a reference in the genomic analysis of the very diverse Order of Lepidoptera....Full Text Available

2010-04-27

77

A Computational Framework Discovers New Copy Number Variants with Functional Importance

Large-scale cancer genome projects will soon be able to sequence many cancer genomes to comprehensively identify genetic changes in human cancer. Genome-wide association studies have also identified...Full Text Available

2008-12-16

78

Reduction of dioxin emission by a multi-layer reactor with bead-shaped activated carbon in simulated gas stream and real flue gas of a sinter plant

Structural variants which cause changes in copy numbers constitute an important component of genomic variability. They account for 0.7% of genomic differences in two individual genomes, of which...Full Text Available

79

British Library Electronic Table of Contents (United Kingdom)

A laboratory-scale multi-layer system was developed for the adsorption of PCDD/Fs from gas streams at various operating conditions, including gas flow rate, operating temperature and water vapor content. Excellent PCDD/F removal efficiency (>99.99%) was achieved with the multi-layer design with bead-shaped activated carbons (BACs). The PCDD/F removal efficiency achieved with the first layer adsorption bed decreased as the gas flow rate was increased due to the decrease of the gas retention time. The PCDD/F concentrations measured at the outlet of the third layer adsorption bed were all lower than 0.1ng I-TEQNm-3. The PCDD/Fs desorbed from BAC were mainly lowly chlorinated congeners and the PCDD/F outlet concentrations increased as the operating temperature was increased. In addition, the r...

2011-01-01

80

A study of aging effects in gas proportional detectors at the BAC calorimeter of the ZEUS experiment

Cloning of the cDNA for the human. beta. /sub 1/-adrenergic receptor

The multicell proportional chambers at the backing calorimeter of the ZEUS experiment at the storage ring HERA are supplied with a gas mixture of Ar/CO[sub 2] by an open gas system. Flow proportional counters with the build-up [sup 55]Fe sources are used as gas system monitoring detectors. The ZEUS experiment is planned to collect data for about 10 years. Therefore, the lifetime of the Ar/CO[sub 2] mixture should be known. In this paper, the results of laboratory tests and preliminary measurements of the aging effects for monitoring counters are presented. ((orig.))

1994-09-01

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Cloning of Drosophila transcription factor Adf-1 reveals homology to Myb oncoproteins.

Screening of a human placenta lambdagt11 library has led to the isolation of the cDNA for the human ..beta../sub 1/-adrenergic receptor (..beta../sub 1/AR). Used as the probe was the human genomic clone termed G-21. This clone, which contains an intronless gene for a putative receptor, was previously isolated by virtue of its cross hybridization with the human ..beta../sub 2/-adrenergic receptor (..beta../sub 2/AR). The 2.4-kilobase cDNA for the human ..beta../sub 1/AR encodes a protein of 477 amino acid residues that is 69% homologous with the avian ..beta..AR but only 54% homologous with the human ..beta../sub 2/AR. This suggests that the avian gene encoding ..beta..AR and the human gene encoding ..beta../sub 1/AR evolved from a common ancestral gene. RNA blot analysis indicates a message of 2.5 kilobases in rat tissues, with a pattern of tissue distribution consistent with ..beta../sub 1/AR binding. This pattern is quite distinct from the ...

1987-11-01

82

Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum

The Drosophila sequence-specific DNA binding protein, Adf-1, is capable of activating transcription of the alcohol dehydrogenase gene, Adh, and is implicated in the transcriptional control of other developmentally regulated genes. We have cloned the cDNA encoding Adf-1 by generating specific DNA probes deduced from partial amino acid sequence of the protein. Several cDNA clones encoding an extended open reading frame were isolated from a phage lambda library. The complete amino acid sequence of Adf-1 deduced from the longest cDNA reveals structural similarities to the putative helix-turn-helix DNA binding motif of Myb and Myb-related proteins. DNA sequence analysis of genomic clones and Northern blot analysis of mRNA suggest that Adf-1 is a single-copy gene encoding a 1.9-kb transcript. Purified recombinant Adf-1 expressed in Escherichia coli binds specifically to Adf-1 recognition sites and activates transcription of a synthetic Adh promoter ...

1992-01-15

83

Time-dependent ARMA modeling of genomic sequences

BackgroundDuplications of stretches of the genome are an important source of individual genetic variation, but their unrecognized presence in laboratory organisms would be a confounding...Full Text Available

2008-01-01

84

Methods in DNA methylation profiling

BackgroundOver the past decade, many investigators have used sophisticated time series tools for the analysis of genomic sequences. Specifically, the correlation of the nucleotide...Full Text Available

85

Genomics of human longevity

Metastable and somatically heritable patterns of DNA methylation provide an important level of genomic regulation. In this article, we review methods for analyzing these genome-wide epigenetic...Full Text Available

2009-12-01

86

Genomic view of the evolution of the complement system

In animal models, single-gene mutations in genes involved in insulin/IGF and target of rapamycin signalling pathways extend lifespan to a considerable extent. The genetic, genomic and epigenetic influences...Full Text Available

2011-01-12

87

Genomic imprinting and the social brain

The recent accumulation of genomic information of many representative animals has made it possible to trace the evolution of the complement system based on the presence or absence of each complement...Full Text Available

2006-09-01

88

Genetics, Genomics, and Molecular Biology

Genomic imprinting refers to the parent-of-origin-specific epigenetic marking of a number of genes. This epigenetic mark leads to a bias in expression between maternally and paternally inherited imprinted...Full Text Available

2006-12-29

89

Enzymatic engineering of the porcine genome with transposons and recombinases

Genetics, Genomics, and Molecular Biology USGS scientists develop and integrate new genetic and molecular techniques into systematic analyses to describe individuals and populations of fish .....

90

Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera)

BackgroundSwine is an important agricultural commodity and biomedical model. Manipulation of the pig genome provides opportunity to improve production efficiency, enhance disease...Full Text Available

91

Cancer gene discovery in mouse and man

BackgroundNucleotide sequences and the gene arrangements of mitochondrial genomes are effective tools for resolving phylogenetic problems. Hemipteroid insects are known to possess...Full Text Available

92

Perceptions of Library Staff Regarding Challenges of Developing Digital Libraries: The Case of an Iranian University

AbstractThe elucidation of the human and mouse genome sequence and developments in high-throughput genome analysis, and in computational tools, have made it possible to profile entire...Full Text Available

2009-12-01

93

Return on investment (ROI) in German libraries: The Berlin School of Library and Information Science and the University Library at the Humboldt University, Berlin - a case study

Purpose: The present research aims to identify the difficulties and obstacles for developing digital libraries in the seven regional branches of Islamic Azad University (IAU), Iran, and to study the status of librarians' skills and education programmes at these institutions. Design/methodology/approach: The 40 individuals working in the regional branch libraries of IAU were surveyed by a questionnaire consisting of 34 questions, and the collected data were analysed using SPSS software (version 16). Findings: It was found that the most important difficulties are the lack of suitable equipment and untrained personnel (i.e. a lack of sufficient training programmes). Research limitations/implications: Because of the small number of participants, it is suggested that a larger scale study is carried out. It is also proposed that the suggestions made by the participants will be considered and implemented, based on the digital ...

2010-12-01

94

British Library Electronic Table of Contents (United Kingdom)

Purpose - The purpose of this paper is to verify the proposition by the University of Illinois, Urbana-Champaign (UIUC), that their return on investment (ROI) formula developed for academic libraries and based on hard facts is broad enough to be used throughout the world for ROI studies in academic institutions/libraries. It further aims to verify that UIUC's methodology is adaptable enough to work in other academic environments as well. Design/methodology/approach - The methodology developed by UIUC (an ROI formula developed for academic libraries based on grant proposal applications and citations) has been "copied" and thereby adapted to enable it to be used in an academic environment in Europe/Germany. Findings - The methodology developed by UIUC was adaptable enough to be used in a Ger...

2010-01-01

95

Expression and Characterization of a New Esterase Cloned Directly from Agrobacterium tumefaciens Genome

KoreaScience (Korea)

Full Text Available

2006-01-01

96

The Medical Library Association: promoting new roles for health information professionals

Programma PLOT per l'esecuzione ed il confronto di grafici con l'RGL-library del VAX-11/780 Digital

As the Medical Library Association (MLA) enters its second century, its role in providing leadership and focus for the education of health information professionals in a changing environment will be...Full Text Available

2002-01-01

97

Looking backward, 1984-1959: twenty-five years of library automation--a personal view.

Programma PLOT per l'esecuzione ed il confronto di grafici con l'RGL-library del VAX-11/780 Digital

1985-01-01

98

GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries

A brief profile of Janet Doe is given. Twenty-five years of library automation are reviewed from the author's point of view. Major projects such as the SUNY Biomedical Communication Network and the...Full Text Available

1984-10-01

99

Citation analysis of Minnesota Department of Health official publications and journal articles: a needs assessment for the RN Barr Library*

There are many methods for introducing random mutations into nucleic acid sequences. Previously, we described a suite of programmes for estimating the completeness and diversity of randomized DNA libraries...Full Text Available

2008-07-01

100

Biotin binders selected from a random peptide library expressed on phage.

Objective: The paper describes the information needs of a state public health agency, compares needs to its library's collection, and evaluates collection development policy accordingly.Methods:...Full Text Available

2007-07-01

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

101

BUBL LINK: Library organisations

Recombinant biotin-binding phages were affinity-selected from a random peptide library expressed on the surface of filamentous phage. Phage binding to biotinylated proteins was half-maximally inhibited...Full Text Available

1993-08-01

102

...6 Resource type: documents MmIT: Multimedia Information and Technology Group Group aiming to facilitate communication between CILIP members interested in multimedia developments in the library and information science field. Visits to places of interest like museums and archives are frequently organised, and an email discussion list ...

103

The EMSL Collaboratory

Technology in Coalition Training

sharing data and computational resources, and accessing information in digital libraries." Bill Wulf (1989) In a Collaboratory, the presentation/meeting concept embodied...

2011-10-07

104

... program incorporates the proven concepts of advanced distributed learning, modeling and simulation, and electronic digital libraries (Figure 1) to ...

2004-06-01

105

Sheet1

ProteoChip-based Library Screening of Integrin ${\\alpha}5{\\beta}1$ Antagonists from Korean Medicinal Plant Extracts

... 15, 14, Robert Constable, Cornell University, NY, Building Interactive Digital Libraries of Formal Algorithmic Knowledge, Navy. ...

106

KoreaScience (Korea)

Full Text Available

2007-12-01

107

National Agricultural Library:

Featured Collections Featured collections are information sources that use federated search or are known for presenting exceptional, authoritative information for...

2011-08-19

108

27 - NASA

Justice and the Human Genome Project

02.10.10 - NASA and Texas Instruments are using the theme of human space exploration to develop digital libraries of math and science problems for high ...

109

Interpreting Mammalian Evolution using Fugu Genome Comparisons

Most of the essays gathered in this volume were first presented at a conference, Justice and the Human Genome, in Chicago in early November, 1991. The goal of the, conference was to consider questions of justice as they are and will be raised by the Human Genome Project. To achieve its goal of identifying and elucidating the challenges of justice inherent in genomic research and its social applications the conference drew together in one forum members from academia, medicine, and industry with interests divergent as rate-setting for insurance, the care of newborns, and the history of ethics. The essays in this volume address a number of theoretical and practical concerns relative to the meaning of genomic research.

1992-01-01

110

Sandia equation of state data base: seslan File

Comparative sequence analysis of the human and the pufferfish Fugu rubripes (fugu) genomes has revealed several novel functional coding and noncoding regions in the human genome. In particular, the fugu genome has been extremely valuable for identifying transcriptional regulatory elements in human loci harboring unusually high levels of evolutionary conservation to rodent genomes. In such regions, the large evolutionary distance between human and fishes provides an additional filter through which functional noncoding elements can be detected with high efficiency.

2004-04-02

111

MCNPX analysis of 68 MeV neutron transmission on iron

Sandia National Laboratories maintains several libraries of equation of state tables, in a modified Sesame format, for use in hydrocode calculations and other applications. This report discusses one of those libraries, the seslan file, which contains 78 tables from the Los Alamos equation of state library. Minor changes have been made to these tables, making them more convenient for code users and reducing numerical difficulties that occasionally arise in hydrocode calculations.

1993-06-24

112

Strategies and computational tools for improving randomized protein libraries.

A 68 MeV neutron transmission experiment on iron has been analyzed with MCNPX using the Los Alamos LA150 neutron data library, the ECN/BRC 150 MeV neutron data library and with the intranuclear cascade code LAHET. The clear improvement of using the data libraries is confirmed. Also, other materials present in LA150 have been checked using the same MCNPX set-up. 10 refs.

1999-02-01

113

Libraries and return on investment (ROI): a meta-analysis

In the last decade, directed evolution has become a routine approach for engineering proteins with novel or altered properties. Concurrently, a trend away from purely 'blind' randomization strategies and towards more 'semi-rational' approaches has also become apparent. In this review, we discuss ways in which structural information and predictive computational tools are playing an increasingly important role in guiding the design of randomized libraries: web servers such as ConSurf-HSSP and SCHEMA allow the prediction of sites to target for producing functional variants, while algorithms such as GLUE, PEDEL and DRIVeR are useful for estimating library completeness and diversity. In addition, we review recent methodological developments that facilitate the construction of unbiased libraries, which are inherently more diverse than biased libraries and therefore more likely to yield improved variants. ...

2005-10-01

114

British Library Electronic Table of Contents (United Kingdom)

Purpose - The purpose of this paper is to show that the need to communicate the value of libraries is growing, and especially now during the global financial crisis. As a response library valuation research is expanding and there is now a need for a status report. Design/methodology/approach - The library valuation field is developing towards generating a critical mass of empirical studies. The focus of the meta-analytical review is on the subgroup that reports a return on investment (ROI) or a cost-benefit ratio. Meta-analysis is a quantitative analysis of findings of previous studies, conducted to infer general findings and lessons from prior empirical research. The dataset is 38 library valuation studies reporting a return on investment figure or cost-benefit ratio. Findings - Of the 38...

2009-01-01

115

Digitization of past question papers, dissertations and theses: A case study of 30 Nigerian university libraries

British Library Electronic Table of Contents (United Kingdom)

SummaryThis paper evaluates the status of digitization in 30 Nigerian university libraries with a view to identifying the status, progress, prospects and challenges to digitize library materials and form the basis of providing a roadmap to successful execution of digitization projects. The study assessed the status of digitization of past question papers, theses and dissertations in Nigerian university libraries from May to September 2006 through a self-administered questionnaire, site visits and interviews. It was found that, though there are automation services in those universities, there is no digitization of these materials mentioned in the surveyed institutions. The major obstacles militating against digitizing in the university libraries include lack of funds, lack of appropriate fa...

2007-01-01

116

Computer and Network Security in Small Libraries: A Guide for Planning.

An old tool with potential new uses: return on investment

This manual is intended to provide a free resource on essential network security concepts for non-technical managers of small libraries. Managers of other small nonprofit or community organizations will also benefit from it. An introduction defines network security; outlines three goals of network security; discusses why a library should be concerned with network security; and describes limits of this work. The manual is divided into three main parts. Part One features the management issues related to network security: analyzing risk, developing a security plan and policy, the funding requirements libraries can expect in operating their networks, and implementing adequate security. Part Two describes the areas of computer networks that need to be secured, and provides a description of many of the security measures necessary for adequate security. Part Three presents sample documents that may be help in the ...

2000-12-01

117

British Library Electronic Table of Contents (United Kingdom)

Purpose - The purpose of this paper is to examine potential new uses of return on investment (ROI) in alternative methods for library assessment and valuation. Design/methodology/approach - Uses examples of recent uses of ROI by libraries to identify potential new applications of ROI in library assessment and valuation. Findings - ROI investment has historically been used by libraries for the assessment of past performance of library organizations in a reactive/defensive nature or for assessing the value of customer services. ROI has not been widely used as a proactive assessment tool, to introspectively assess administrative or other internal services, or as an offensive assessment and valuation tool, especially for intangible performance assessment and valuation. Originality/value - New ...

2007-01-01

118

A digitization and multimedia project at Quinnipiac University, Hamden, Connecticut, USA

British Library Electronic Table of Contents (United Kingdom)

Purpose - The purpose of this paper is to encourage other libraries to provide access to their own original content via the web. By way of case study, the process of identifying materials, scanning them and creating web access to original content will be explored. Design/methodology/approach - To implement a book digitization project, three major things need to be present. The library must own material that was published prior to 1923, making them safely out of copyright in the USA; the library needs access to server space on the web and the library needs to own scanning equipment. Findings - This project demonstrated that a library does not necessarily need to obtain grant funding to begin an effective and successful digitization program. It also revealed a few things that would improve t...

2007-01-01

119

Automated Categorization Scheme for Digital Libraries in Distance Learning: A Pattern Recognition Approach

ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes

Digital libraries play a crucial role in distance learning. Nowadays, they are one of the fundamental information sources for the students enrolled in this learning system. These libraries contain huge amount of instructional data (text, audio and video) offered by the distance learning program. Organization of the digital libraries is therefore very important for easy and fast access to the desired information. Improper categorization of data may mislead the students searching the library. Since manual categorization of huge amount of data might be challenging, an automatic and reliable method is needed. In this sense, this paper proposes an automated categorization scheme for digital libraries in distance learning. The categorization scheme is designed and developed by a pattern recognition approach. Effectiveness of the proposed scheme is evaluated on widely used Reuters ...

2008-10-01

120

Chromatographic evaluation of microbial activity in biological activated carbon bed; Kuromatoho ni yoru seibutsu kasseitanso ni okeru biseibutsu kassei no hyoka

Evolutionary conservation of DNA sequences provides a tool for the identification of functional elements in genomes. We have created a database of evolutionary conserved regions (ECRs) in vertebrate genomes entitled ECRbase that is constructed from a collection of pairwise vertebrate genome alignments produced by the ECR Browser database. ECRbase features a database of syntenic blocks that recapitulate the evolution of rearrangements in vertebrates and a collection of promoters in all vertebrate genomes presented in the database. The database also contains a collection of annotated transcription factor binding sites (TFBS) in all ECRs and promoter elements. ECRbase currently includes human, rhesus macaque, dog, opossum, rat, mouse, chicken, frog, zebrafish, and two pufferfish genomes. It is freely accessible at http://ECRbase.dcode.org.

2006-08-08

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

121

Whole-genome cancer analysis as an approach to deeper understanding of tumour biology

The moment analysis of pulse responses was applied to a biological activated carbon (BAC) bed to evaluate the microbial activity. Glucose and activated carbon fiber (ACF) were employed in experiments as a model tracer and an activated carbon respectively. No significant difference in biodegradation rates of glucose by microorganisms attached on different solid supports such as activated carbon inactivated carbon and glass fibers was observed. However, higher microbial activity was obtained from microorganisms supported on the ACF in terms of the apparent degradation of total organic including metabolic byproducts by microorganisms, since part of the metabolic byproducts was irreversibly deposited onto the ACF. 11 refs., 6 figs.

1996-07-10

122

Using Regulatory and Epistatic Networks to Extend the Findings of a Genome Scan: Identifying the Gene Drivers of Pigmentation in Merino Sheep

Recent advances in DNA sequencing technology are providing unprecedented opportunities for comprehensive analysis of cancer genomes, exomes, transcriptomes, as well as epigenomic components. The integration...Full Text Available

2010-01-19

123

Transcriptional mapping of the 3' end of the bovine syncytial virus genome.

Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino...Full Text Available

124

Targeted plasmid integration into the human genome by an engineered zinc-finger recombinase

The bovine syncytial virus, a member of the retroviral subfamily Spumavirinae, causes a persistent, asymptomatic infection in cattle. Nucleotide sequence analysis of the viral genome revealed two overlapping...Full Text Available

1994-02-01

125

Synthesis and degradation of dinoflagellate plastid-encoded psbA proteins are light-regulated, not circadian-regulated

The development of new methods for gene addition to mammalian genomes is necessary to overcome the limitations of conventional genetic engineering strategies. Although a variety of DNA-modifying enzymes...Full Text Available

2011-09-01

126

Replication Stress Induces Genome-wide Copy Number Changes in Human Cells that Resemble Polymorphic and Pathogenic Variants

In many dinoflagellate species, the plastid genome has been proposed to exist as a limited number of single-gene minicircles, and many genes normally found in the plastid genome are nuclear-encoded....Full Text Available

2005-02-22

127

Reciprocal Silencing, Transcriptional Bias and Functional Divergence of Homeologs in Polyploid Cotton (Gossypium)

Copy number variants (CNVs) are an important component of genomic variation in humans and other mammals. Similar de novo deletions and duplications, or copy number changes (CNCs), are now known to be...Full Text Available

2009-03-13

128

Rai1 duplication causes physical and behavioral phenotypes in a mouse model of dup(17)(p11.2p11.2)

Polyploidy is an important force in the evolution of flowering plants. Genomic merger and doubling induce an extensive array of genomic effects, including immediate and long-term alterations in the...Full Text Available

2009-06-01

129

Rab protein evolution and the history of the eukaryotic endomembrane system

Genomic disorders are conditions that result from DNA rearrangements, such as deletions or duplications. The identification of the dosage-sensitive gene(s) within the rearranged genomic interval is...Full Text Available

2006-11-01

130

Presence of two independent chromosomes in the Brucella melitensis 16M genome.

Spectacular increases in the quantity of sequence data genome have facilitated major advances in eukaryotic comparative genomics. By exploiting homology with classical model organisms, this makes possible...Full Text Available

2010-10-01

131

Parallel Loss of Plastid Introns and Their Maturase in the Genus Cuscuta

Mapping the restriction fragments of the Brucella melitensis 16M genome with a new restriction endonuclease, PacI, which cut the DNA into only eight fragments, indicated that this species contains two...Full Text Available

1993-02-01

132

Nucleocapsid and Matrix Protein Contributions to Selective Human Immunodeficiency Virus Type 1 Genomic RNA Packaging

Plastid genome content and arrangement are highly conserved across most land plants and their closest relatives, streptophyte algae, with nearly all plastid introns having invaded the genome in their...Full Text Available

133

Natural mutagenesis of human genomes by endogenous retrotransposons

The nucleocapsid protein (NC) of retroviruses plays a major role in genomic RNA packaging, and some evidence has implicated the matrix protein (MA) of certain retroviruses in viral RNA binding. To further...Full Text Available

1998-03-01

134

Molecular characterization of a Chinese variant of the Flury-LEP strain

SUMMARYTwo abundant classes of mobile elements, namely Alu and L1 elements, continue to generate new retrotransposon insertions in human genomes. Estimates suggest that these...Full Text Available

2010-06-25

135

Mobilizing diversity: transposable element insertions in genetic variation and disease

The entire genome of rabies virus vaccine strain Flury-LEP-C, a Chinese variant of the rabies virus vaccine strain Flury-LEP, was sequenced. The overall length of the genome of Flury-LEP-C strain was...Full Text Available

136

Large-scale cross-species oncogenomics identifies candidate oncogenes and tumor suppressor genes

Transposable elements (TEs) comprise a large fraction of mammalian genomes. A number of these elements are actively jumping in our genomes today. As a consequence, these insertions provide a source...Full Text Available

137

Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

While genomic alterations identified in human tumors using techniques such as comparative genomic hybridisation (CGH) may be recurrent, they frequently encompass large regions, in some cases...Full Text Available

2010-02-01

138

Insights into Genome Plasticity and Pathogenicity of the Plant Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria Revealed by the Complete Genome Sequence

BackgroundGenome-scale metabolic reconstructions have been recognised as a valuable tool for a variety of applications ranging from metabolic engineering to evolutionary studies....Full Text Available

139

Impact of genetic changes to the CRPV genome and their application to the study of pathogenesis in vivo

The gram-negative plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically...Full Text Available

2005-11-01

140

The cottontail rabbit papillomavirus (CRPV)/rabbit model has been used to study oncogenicity and immunogenicity of different antigens from the papillomavirus genome and has therefore served...Full Text Available

2007-02-20

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

141

Genomic cloning and characterization of a ricin gene from Ricinus communis.

BackgroundA large fraction of the human genome is attributable to L1 retrotransposon sequences. Not only do L1s themselves make up a significant portion of the genome, but L1-encoded...Full Text Available

2003-01-01

142

Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"

A genomic clone that specifies a single polypeptide precursor for ricin, a toxic lectin of Ricinus communis (castor bean), was isolated, sequenced and Sl mapped. The gene encodes a 64 kDa precursor...Full Text Available

1985-11-25

143

Genome-wide detection and characterization of positive selection in human populations

BackgroundThe genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a given...Full Text Available

144

Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms...Full Text Available

2007-10-18

145

Genome-Wide Identification and Evolutionary Analysis of the Animal Specific ETS Transcription Factor Family

BackgroundCucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular...Full Text Available

146

Genome size and wing parameters in passerine birds

The ETS proteins are a family of transcription factors (TFs) that regulate a variety of biological processes. We made genome-wide analyses to explore the classification of the ETS gene family. We identified...Full Text Available

147

Genetic susceptibility to systemic lupus erythematosus in the genomic era

Despite their status as the most speciose group of terrestrial vertebrates, birds exhibit the smallest and least variable genome sizes among tetrapods. It has been suggested that this is because powered...Full Text Available

2009-01-07

148

Estimating Missing Heritability for Disease from Genome-wide Association Studies

Our understanding of the genetic basis of systemic lupus erythematosus (SLE) has been rapidly advanced using large-scale, case–control, candidate gene studies as well as genome-wide...Full Text Available

2010-12-01

149

Epitope tagging of endogenous proteins for genome wide Chromatin immunoprecipitation analysis

Genome-wide association studies are designed to discover SNPs that are associated with a complex trait. Employing strict significance thresholds when testing individual SNPs avoids false positives at...Full Text Available

2011-03-11

150

Dynamic Rearrangements Determine Genome Organization and Useful Traits in Soybean1[C][W

The development of chromatin immunoprecipitation methods coupled with DNA microarray (ChIP-chip) technology has enabled genome-wide identification of cis-DNA regulatory elements to which transcription...Full Text Available

2009-01-01

151

Completely phased genome sequencing through chromosome sorting

Soybean (Glycine max) is a paleopolyploid whose genome has gone through at least two rounds of polyploidy and subsequent diploidization events. Several studies have investigated the...Full Text Available

2009-11-01

152

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta

The two haploid genome sequences that a person inherits from the two parents represent the most fundamentally useful type of genetic information for the study of heritable diseases and the development...Full Text Available

2011-01-04

153

Comparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss

BackgroundPlastid genome content and protein sequence are highly conserved across land plants and their closest algal relatives. Parasitic plants, which obtain some or all of their...Full Text Available

154

Bunyamwera virus can repair both insertions and deletions during RNA replication

BackgroundThe bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii,...Full Text Available

155

Biophysical characterization of recombinant proteins: A key to higher structural genomics success

The genomic termini of RNA viruses contain essential cis-acting signals for such diverse functions as packaging, genome translation, mRNA transcription, and RNA replication, and thus...Full Text Available

2010-06-01

156

Behavioral genomics of honeybee foraging and nest defense

Hundreds of genomes have been successfully sequenced to date, and the data are publicly available. At the same time, the advances in large-scale expression and purification of recombinant proteins have...Full Text Available

2010-10-01

157

Avian Nephritis Virus (ANV) as a New Member of the Family Astroviridae and Construction of Infectious ANV cDNA

The honeybee has been the most important insect species for study of social behavior. The recently released draft genomic sequence for the bee will accelerate honeybee behavioral genetics. Although...Full Text Available

2007-04-01

158

Analysis of illegitimate genomic integration mediated by zinc-finger nucleases: implications for specificity of targeted gene correction

The complete RNA genome of the avian nephritis virus (ANV) associated with acute nephritis in chickens has been molecularly cloned and sequenced. Excluding the poly(A) tail, the genome comprises 6,927...Full Text Available

2000-09-01

159

A proposal to sequence the genome of a garter snake (Thamnophis sirtalis)

BackgroundFormation of site specific genomic double strand breaks (DSBs), induced by the expression of a pair of engineered zinc-finger nucleases (ZFNs), dramatically increases the...Full Text Available

160

A haplotype map of the human genome

Here we develop an argument in support of sequencing a garter snake (Thamnophis sirtalis) genome, and outline a plan to accomplish this. This snake is a common, widespread, nonvenomous...Full Text Available

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161

A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish

Inherited genetic variation has a critical but as yet largely uncharacterized role in human disease. Here we report a public database of common variation in the human genome: more than one million...Full Text Available

2005-10-27

162

Genomic Careers: Interactive Videos

BackgroundThe genomic organisation of the Major Histocompatibility Complex (MHC) varies greatly between different vertebrates. In mammals, the classical MHC consists of a large number...Full Text Available

163

Medline Plus

... the nature of DNA testing. 07:56 - President / CEO of a Biotechnology / Pharmaceutical Company - Sherri Bale President ...

164

Exons, Introns and Talking Genes: The Sience Behind the Human Genome Project

Genome-Wide Association Study SNPs in the Human Genome Diversity Project Populations: Does Selection Affect Unlinked SNPs with Shared Trait Associations?

This book presents in simple terms the basis of molecular genetics and how it is used to obtain an understanding of the human genome. The author's central focus is the transistion of genetics from statistics to experimental manipulations, and he offers analogies that help readers visualize the genome, thereby avoiding conventional scientific presentations. He illustrates how genetics is used in scientific laboratories, in courtrooms, and in hospitals. Little is presented about the complex social and ethical issues raised by the Human Genome project.

1993-01-01

165

Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC₁population between gossypium hirsutum and G. barbadense

Genome-wide association studies (GWAS) have identified more than 2,000 trait-SNP associations, and the number continues to increase. GWAS have focused on traits with potential consequences for human...Full Text Available

2011-01-01

166

User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries.

BackgroundCotton, with a large genome, is an important crop throughout the world. A high-density genetic linkage map is the prerequisite for cotton genetics and breeding. A genetic...Full Text Available

167

Optical Discs for Storage and Access in ARL Libraries. SPEC KIT 133.

Directed evolution of proteins depends on the production of molecular diversity by random mutagenesis. While a number of methods have been developed for introducing this diversity, the best ways to sample it are not always clear. Here we used simple statistics to analyse completeness and diversity in randomized libraries generated by oligonucleotide-directed mutagenesis, error-prone polymerase chain reaction (epPCR) and in vitro recombination of highly homologous sequences. For oligonucleotide-directed mutagenesis, we derive equations to estimate how complete a given library is expected to be and also to predict the size of library required to give a fixed probability of being 100% complete. We describe the statistical bases for computer programs which estimate the number of distinct variants represented in epPCR and shuffled libraries, dubbed PEDEL and DRIVeR, respectively. These programs allow the ...

2003-06-01

168

Giving voice to the past: digitizing oral history

This SPEC (Systems and Procedures Exchange Center) kit provides a sample of excerpts from technical and planning documents contributed by 40 Association of Research Libraries (ARL) member libraries that are planning to install or have already implemented optical disc technology. Selected to represent a variety of media and applications, the excerpts address general as well as technical issues. Comments received in telephone interviews with contributors, as well as with other ARL members whose endeavors are not represented in this kit, are incorporated in a concise summary which discusses the overlapping and interrelated concerns of technical considerations, management issues, and impact on user services. In addition, the following original documents are included: (1) a descriptive list of optical disc technology terms from the National Library of Canada; (2) planning documents from the libraries of the ...

1987-04-01

169

British Library Electronic Table of Contents (United Kingdom)

Purpose - The purpose of this paper is to describe the processes and procedures utilized by Jacksonville State University's Houston Cole Library to digitize an oral history collection and provide access to it through the Library's catalog, web presence, and the state-wide digital repository initiative, Alabama Mosaic (see www.alabamamosaic.org). Design/methodology/approach - The paper is based on the Library's experiences in acquiring, digitizing, creating metadata for and making accessible a collection of oral histories. Findings - The paper describes the obstacles overcome, issues encountered, procedures established, and ramifications of the project. Practical implications - Many institutions are currently digitizing unique collections as part of repository initiatives, both institutiona...

2009-01-01

170

The Goddard Library - Goddard Projects Directory - NASA

Teaching medical information retrieval and application courses in Chinese universities: a case study

Oct 2, 2007 ... Other payloads included the Orbiter Experiments Autonomous Supporting Instrumentation System-1 (OASIS-1), a cooling system designed for ...

171

British Library Electronic Table of Contents (United Kingdom)

Abstract An important aspect of Chinese academic health science libraries is their involvement in teaching medical information retrieval courses as part of the medical curriculum. Health science librarians in China have a more formal teaching role than is generally found in Western countries, including many full time teaching positions. This article provides a case study of Kunming Medical University Library, where courses are provided as credit units at both undergraduate and postgraduate levels. The teaching practices of Chinese health science libraries are compared with teaching experiences reported in Western countries. It is noted that Chinese government s educational policy is similar to that of the United States in promoting the role of the library in teaching subjects as part of th...

2010-01-01

172

Rare Book and Special Collections Reading Room (Library of Congress...

Photo Tours: Gulf of Mexico Integrated Science

any locality that is now in the United States. The English fleet lies at anchor, the infantry troops having disembarked and are attacking the Spanish settlement on May 28 and 29,...

2011-06-02

173

Inventory Project home page Reports, Posters, Presentations Internet Tools - Digital Libraries, IMS's Maps, Aerial Photographs Meetings & Conferences Photo Tours - all...

2011-10-08

174

NOAA Photo Library

NASA Procedural Requirements - + NODIS Library - NASA

Meat supply hung up for protection against blowflies, bears, dogs, etc. Triangulation work for military on Alcan Highway in Yukon Territory, Canada.

175

Library value (return on investment, ROI) and the challenge of placing a value on public services

Market based pricing only applies to the extent it is consistent with these other requirements. For example: .... work, market based pricing does not apply. ...

176

British Library Electronic Table of Contents (United Kingdom)

Purpose - The purpose of this paper is to interview Paula Kaufman, Dean of Libraries, to help better understand return on investment (ROI) and the increasing importance of demonstrating our value, as libraries, as librarians, indeed, as public service librarians. Design/methodology/approach - During 2007, a small project team was assembled to develop a model that would calculate a return on investment to an institution for its library. The team consisted of Chrysanne Lowe and Kira Cooper from Elsevier, Paula Kaufman from UIUC, Judy Luther of Informed Strategies, and Dr Carol Tenopir from the Center for Information and Communication Studies at the University of Tennessee, Knoxville. Findings - The results of this groundbreaking study were reported early this year in a white paper entitled, ...

2008-01-01

177

Internet and Electronic Information Management

Directory of Scientists: Gulf of Mexico Estuaries Integrated...

... 6(2): 36-45. Hedstrom, M. (1998). Digital preservation: a time bomb for digital libraries. [Online]. Available: http://www.uky ...

2004-12-01

178

Digitizing Dissertations for an Institutional Repository: A Process and Cost Analysis*

Inventory Project home page Reports, Posters, Presentations Internet Tools - Digital Libraries, IMS's Maps, Aerial Photographs Meetings & Conferences Photo Tours - all...

2011-10-08

179

Demonstrating RoI in the library: the Holy Grail search continues

Objective:This paper describes the Lamar Soutter Library's process and costs associated with digitizing 300 doctoral dissertations for a newly implemented institutional repository...Full Text Available

2008-07-01

180

British Library Electronic Table of Contents (United Kingdom)

Purpose - This article aims to examine approaches by academic libraries in demonstrating return on investment (RoI). Design/methodology/approach - As a participant in a recent international RoI study, the author reviews the various difficulties in developing a suitable methodology. Findings - Using grant income as the basis for demonstrating RoI, it was found that wide differences in results may be attributable to a number of factors related to the parent organisation, the availability of grant funding and the country of the study. Research limitations/implications - Further work is necessary to arrive at a suitable methodology for a diverse range of academic libraries. Practical implications - Library managers are alerted to issues and problems surrounding the development of return on inv...

2010-01-01

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181

Conference on Information Technology (2nd)/Special Session ...

Center for Intelligent Information Retrieval

... Topics includes: Formal methods in information engineering, Electronic documents and digital libraries Autonomous robots in embeded systems ...

2004-08-23

182

Browse Conditions - Genetics Home Reference

evaluation, novelty detection, resource discovery, interfaces and visualization, digital libraries, computational social science, and cross-lingual information retrieval. The CIIR...

2011-08-31

183

Baldwin, Tony Marcel - Goddard Library Repository

Home A service of the U.S. National Library of Medicine® Home Conditions Genes Chromosomes Handbook Glossary Resources Genetic Conditions > Browse Conditions 1-9 | A | B | C...

2011-09-24

184

BAMONA's blog | Butterflies and Moths of North America

Schmidlin F, Morrison B, Baldwin T, Moore P, Northam E. NASA AFRICAN MONSOON MULTIDISCIPLINARY ANALYSES MISSION: BALLOON-BORNE RADIOSONDE RESULTS FROM CAPE ...

185

A High Throughput Combinatorial Library Technique for Identifying Formalin-Sensitive Epitopes

site for reference information. Other recipients include Google's Translator, WikiLeaks, The ICUN Red List of Threatened Species, and the Public Library of Science (PLOS)....

2011-09-17

186

A CONCEPT FOR NATIONAL NUCLEAR FORENSIC LIBRARIES

We present a technique for identifying the amino acids responsible for a loss of immunoreactivity in response to treating an antigen with a chemical modifier. This is of particular interest...Full Text Available

2006-12-20

187

8 - NASA Technical Report Server (NTRS)

The interpretation of data from the nuclear forensic analysis of illicit nuclear material of unknown origin requires comparative data from samples of known origin. One way to provide such comparative data is to create a system of national nuclear forensics libraries, in which each participating country stores information about nuclear or other radioactive material that either resides in or was manufactured by that country. Such national libraries could provide an authoritative record of the material located in or produced by a particular country, and thus forms an essential prerequisite for a government to investigate illicit uses of nuclear or other radioactive material within its borders. We describe the concept of the national nuclear forensic library, recommendations for content and structure, and suggested querying methods for utilizing the information for addressing nuclear smuggling.

2010-07-11

188

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

feature similar to the face detection in Intel's OpenCV library, implement it in Matlab code, and test the performance of the new ROI detector against the ...

189

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 ...

2011-01-01

190

Proceedings of the 1st ACM international conference on digital libraries

An important goal for digital libraries is to enable researchers to more easily explore related work. While citation data is often used as an indicator of relatedness, in this paper we demonstrate that digital access records (e.g. http-server logs) can be used as indicators as well. In particular, we show that measures based on co-access provide better coverage than co-citation, that they are available much sooner, and that they are more accurate for recent papers.

2007-01-01

191

Impact of the ENDF/B-VI Cross Section on the RPV Fluence Determination

This document contains papers which were presented at the First ACM International Conference on Digital Libraries. Topics processed for this document included information retrieval and index structures for structured documents. Individual papers have been processed separately for the United States Department of Energy databases.

1996-12-31

192

GLUE-IT and PEDEL-AA: new programmes for analyzing protein diversity in randomized libraries.

The calculations with the broad-group cross-section library Bugle-96, and atom displacement (dpa) cross sections for iron, both derived from ENDF/B-VI data, result in higher calculated fast neutron fluxes, better agreement of calculations with radiometric dosimeter measurements, and significantly slower dpa rate attenuation through pressure vessel walls relative to the results with their predecessors: the Sailor library and ASTM iron dpa cross sections.

1999-09-12

193

Automatically Generating Interfaces for Personalized Interaction with Digital Libraries

There are many methods for introducing random mutations into nucleic acid sequences. Previously, we described a suite of programmes for estimating the completeness and diversity of randomized DNA libraries generated by a number of these protocols. Our programmes suggested some empirical guidelines for library design; however, no information was provided regarding library diversity at the protein (rather than DNA) level. We have now updated our web server, enabling analysis of translated libraries constructed by site-saturation mutagenesis and error-prone PCR (epPCR). We introduce GLUE-Including Translation (GLUE-IT), which finds the expected amino acid completeness of libraries in which up to six codons have been independently varied (according to any user-specified randomization scheme). We provide two tools for assisting with experimental design: CodonCalculator, for assessing ...

2008-04-28

194

Co-Authorship Networks in the Digital Library Research Community

We present an approach to automatically generate interfaces supporting personalized interaction with digital libraries; these interfaces augment the user-DL dialog by empowering the user to (optionally) supply out-of-turn information during an interaction, flatten or restructure the dialog, and enquire about dialog options. Interfaces generated using this approach for CITIDEL are described.

2004-01-01

195

Engineering Relative Compression of Genomes

The field of digital libraries (DLs) coalesced in 1994: the first digital library conferences were held that year, awareness of the World Wide Web was accelerating, and the National Science Foundation awarded $24 Million (U.S.) for the Digital Library Initiative (DLI). In this paper we examine the state of the DL domain after a decade of activity by applying social network analysis to the co-authorship network of the past ACM, IEEE, and joint ACM/IEEE digital library conferences. We base our analysis on a common binary undirectional network model to represent the co-authorship network, and from it we extract several established network measures. We also introduce a weighted directional network model to represent the co-authorship network, for which we define $AuthorRank$ as an indicator of the impact of an individual author in the network. The results are validated against conference program committee ...

2005-01-01

196

Ultraconserved Elements: Analyses of Dosage Sensitivity, Motifs and Boundaries

Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an LZ77-style compression scheme for relative compression of multiple genomes of the same species. While the solution bears similarity to known algorithms, it offers significantly higher compression ratios at compression speed over a order of magnitude greater. One of the new successful ideas is augmenting the reference sequence with phrases from the other sequences, making more LZ-matches available.

2011-01-01

197

The Importance of Mitochondrial DNA in Aging and Cancer

Ultraconserved elements (UCEs) are sequences that are identical between reference genomes of distantly related species. As they are under negative selection and enriched near or in specific classes...Full Text Available

2008-12-01

198

The COG database: an updated version includes eukaryotes

Mitochondrial dysfunction has been implicated in premature aging, age-related diseases, and tumor initiation and progression. Alterations of the mitochondrial genome accumulate both in aging tissue...Full Text Available

199

Systems medicine: the future of medical genomics and healthcare

BackgroundThe availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an...Full Text Available

200

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

High-throughput technologies for DNA sequencing and for analyses of transcriptomes, proteomes and metabolomes have provided the foundations for deciphering the structure, variation and function of the...Full Text Available

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201

Polymer Genomics: An Insight into Pharmacology and Toxicology of Nanomedicines 1

BackgroundOrthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood...Full Text Available

202

Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin

Synthetic polymers and nanomaterials display selective phenotypic effects in cells and in the body that affect signal transduction mechanisms involved in inflammation, differentiation, proliferation,...Full Text Available

2006-12-30

203

Open-source software accelerates bioinformatics

Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in...Full Text Available

2011-02-01

204

Nucleomorph Ribosomal DNA and Telomere Dynamics in Chlorarachniophyte Algae

A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003.

2003-01-01

205

British Library Electronic Table of Contents (United Kingdom)

ABSTRACT. Chlorarachniophytes are enigmatic marine unicellular algae that acquired photosynthesis by secondary endosymbiosis. Chlorarachniophytes are unusual in that the nucleus of the engulfed algal cell (a green alga) persists in a miniaturized form, termed a nucleomorph. The nucleomorph genome of the model chlorarachniophyte, Bigelowiella natans CCMP621, is 373 kilobase pairs (kbp) in size, the smallest nuclear genome characterized to date. The B. natans nucleomorph genome is composed of three chromosomes, each with canonical eukaryotic telomeres and sub telomeric ribosomal DNA (rDNA) operons transcribed away from the chromosome end. Here we present the complete rDNA operon and telomeric region from the nucleomorph genome of Lotharella oceanica CCMP622, a newly characterized chlorarachn...

2010-01-01

206

Manipulating the Xenopus genome with transposable elements

Identification of pork derivatives in food products by species-specific polymerase chain reaction (PCR) for halal verification

The study of amphibian embryogenesis has provided important insight into the mechanisms of vertebrate development. The frog Xenopus laevis has been an important model of vertebrate...Full Text Available

2007-01-01

207

British Library Electronic Table of Contents (United Kingdom)

Pork identification in four types of food products, which are sausages and the casings, bread and biscuits, using species-specific polymerase chain reaction (PCR) detection of a conserved region in the mitochondrial (mt) 12S ribosomal RNA (rRNA) gene was developed. Genomic DNA of the food products were successfully extracted except for the casing samples, where no genomic DNA was detected. The extracted genomic DNA was then subjected to PCR amplification targeting the specific regions of the 12S rRNA gene. The genomic DNA from the food products were found to be of good quality and produced clear PCR products on the amplification of 12S rRNA gene of 387 base pairs (bp) from pork species. The species-specific PCR identification yielded excellent results for identification of pork derivatives...

2007-01-01

208

Human endogenous retroviruses: transposable elements with potential ?

Genome analysis with inter-nucleotide distances

Human endogenous retroviruses (HERVs) are a significant component of a wider family of retroelements that constitute part of the human genome. These viruses, perhaps representative of previous exogenous...Full Text Available

2004-10-01

209

Extracellular Signaling through the Microenvironment: A Hypothesis Relating Carcinogenesis, Bystander Effects, and ...

Motivation: DNA sequences can be represented by sequences of four symbols, but it is often useful to convert the symbols into real or complex numbers for further analysis. Several mapping...Full Text Available

2009-12-01

210

Evaluating Phylogenetic Congruence in the Post-Genomic Era

... Extracellular Signaling through the Microenvironment: A Hypothesis Relating Carcinogenesis, Bystander Effects, and Genomic InstabilityMary Helen Barcellos-Hoff1a ... ...

211

Developmentally programmed endoreduplication in animals

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...Full Text Available

2011-01-01

212

Computational biology for ageing

Development of a fertilized egg into an adult human requires trillions of cell divisions, the vast majority of which duplicate their genome once and only once. Nevertheless, trophoblast giant...Full Text Available

2009-05-15

213

Comparing Genomes within the Species Mycobacterium tuberculosis

High-throughput genomic and proteomic technologies have generated a wealth of publicly available data on ageing. Easy access to these data, and their computational analysis, is of great importance in...Full Text Available

2011-01-12

214

Comparative genomics of insect juvenile hormone biosynthesis?

The study of genetic variability within natural populations of pathogens may provide insight into their evolution and pathogenesis. We used a Mycobacterium tuberculosis high-density...Full Text Available

2001-04-01

215

Ancestral Genomes, Sex, and the Population Structure of Trypanosoma cruzi

The biosynthesis of insect juvenile hormone (JH) and its neuroendocrine control are attractive targets for chemical control of insect pests and vectors of disease. To facilitate the molecular...Full Text Available

2006-04-01

216

A framework for evolutionary systems biology

Acquisition of detailed knowledge of the structure and evolution of Trypanosoma cruzi populations is essential for control of Chagas disease....Full Text Available

2006-03-01

217

Metadata aggregation and "automated digital libraries": A retrospective on the NSDL experience

BackgroundMany difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often...Full Text Available

218

Measuring e-CRM service quality in the library context: a preliminary study

Over three years ago, the Core Integration team of the National Science Digital Library (NSDL) implemented a digital library based on metadata aggregation using Dublin Core and OAI-PMH. The initial expectation was that such low-barrier technologies would be relatively easy to automate and administer. While this architectural choice permitted rapid deployment of a production NSDL, our three years of experience have contradicted our original expectations of easy automation and low people cost. We have learned that alleged "low-barrier" standards are often harder to deploy than expected. In this paper we report on this experience and comment on the general cost, the functionality, and the ultimate effectiveness of this architecture.

2006-01-01

219

British Library Electronic Table of Contents (United Kingdom)

Purpose - Customer relationship management (CRM) indicates a comprehensive strategy and an interactive process intended to achieve an optimum balance between corporate investment and the satisfaction of customer needs to generate the maximum profit. E-CRM refers to CRM using internet technology plus a database, OLAP, data warehouse, data mining, etc. In order to gain an understanding of the efficiency of implementing an e-CRM system within the library context, to develop theoretically and empirically an evaluation process for the e-CRM system and survey its impact on service quality, a pilot scheme was initiated in 2004. The pilot scheme was to design and implement an e-CRM prototype system for a particular academic library in Taiwan and to survey the system's performances. This paper aims...

2008-01-01

220

Improvements on burnup chain model and group cross section library in the SRAC system

Creating Virtual Collections in Digital Libraries: Benefits and Implementation Issues.

Data and functions of the cell burnup calculation of the SRAC system were revised to improve mainly the accuracy of the burnup calculation of high conversion light water reactors (HCLWRs). New burnup chain models were developed in order to treat fission products (FPs) and actinide nuclides in detail. Group cross section library, SRACLIB-JENDL2, was generated based on JENDL-2 nuclear data file. In generating this library, emphasis was placed on FPs and actinides. Also revised were the data such as the average energy release per fission for various actinides. These improved data were verified by performing the burnup analysis of PWR spent fuels. Some new functions were added to the SRAC system for the convenience to yield macroscopic cross sections used in the core burnup process. (author).

1992-01-01

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221

Comparison of the BUGLE-80 and SAILOR libraries for coupled neutron-gamma transport applications

Explicitly defining virtual collections in a digital library can benefit both users and contributors. This paper outlines the costs and benefits for defining virtual collections and describes an implementation of collection-level metadata in two digital libraries. Our work suggests that component repositories of NSDL would profit by describing their collection, and sub-collections, using a schema such as the one we implemented. This would enable NSDL to provide a rich, cross-linked hierarchy of virtual collections. By sharing collection-level, rather than item-level, metadata, collections would provide detailed resource information, presumably keeping most of their viewership, while NSDL would provide a broad description of resources.

2003-03-18

222

Calculation of neutron and gamma-ray emission spectra produced by p +2''2'Al reactions

The coupled neutron-gamma cross section libraries BUGLE-80 and SAILOR are compared, with focus on gamma production and transport and its sensitivity to the thermal component of the neutron flux. In addition, the importance of the prompt versus delayed components of the gamma source is addressed. Although BUGLE-80 shows some discrepancies in the core region, the two libraries demonstrate similar capability in the vicinity of the pressure vessel and beyond. The delayed fission product gammas from the core have little impact on the local gamma fluxes beyond the pressure vessel. Although thermal neutron capture is the dominant component of the gamma source, there is little sensitivity of the gamma source to uncertainties in the thermal neutron cross sections, due to compensating effects which tend to keep the thermal neutron capture rate relatively constant.

223

Targeted Capture and Next-Generation Sequencing Identifies C9orf75, Encoding Taperin, as the Mutated Gene in Nonsyndromic Deafness DFNB79

As a contribution to the US/Japan cooperative program in fusion neutronics, we have prepared a library of multigroup neutron cross sections, scattering matrices, and covariances (uncertainties and their correlations). This 74-group library, called COVFILS-2, is being used at Los Alamos and at the University of California at Los Angeles in the sensitivity and uncertainty analysis of the Li_2O integral experiment recently performed at the Fast Neutron Source (FNS) in Japan. Another intended use of this library is in the estimation of the uncertainty in key performance parameters (such as breeding ratio) of conceptual fusion reactors. The 14 materials included in the first version of COVFILS-2 are H, "6Li, "7Li, Be, C, N, O, Na, Al, Si, Cr, Fe, Ni, and Pb.

1985-01-01

224

Genome-wide association studies of gastric adenocarcinoma and esophageal squamous cell carcinoma identify a shared susceptibility locus in PLCE1 at 10q23

Targeted genome capture combined with next-generation sequencing was used to analyze 2.9 Mb of the DFNB79 interval on chromosome 9q34.3, which includes 108 candidate genes. Genomic...Full Text Available

2010-03-12

225

Draft Genome Sequence of Shewanella sp. Strain HN-41, Which Produces Arsenic-Sulfide Nanotubes.

We conducted a genome-wide association study of gastric cancer (GC) and esophageal squamous cell carcinoma (ESCC) in ethnic Chinese subjects in which we genotyped 551,152 single nucleotide polymorphisms...Full Text Available

2010-09-01

226

A unique horizontal gene transfer event has provided the octocoral mitochondrial genome with an active mismatch repair gene that has potential for an unusual self-contained function

The dissimilatory metal reducing bacterium Shewanella sp. strain HN-41 was first reported to produce novel photoactive As-S nanotubes via reduction of As(V) and S(2)O(3)(2-) under anaerobic conditions. Here we report the draft genome sequence and annotation of strain HN-41. PMID:21868804

2011-09-01

227

A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4

BackgroundThe mitochondrial genome of the Octocorallia has several characteristics atypical for metazoans, including a novel gene suggested to function in DNA repair. This mtMutS...Full Text Available

228

The viroid and viroid-like RNA database.

Case-parent trios were used in a genome wide association study of cleft lip with/without cleft palate (CL/P). SNPs near two genes not previously associated with CL/P [MAFB:...Full Text Available

2010-06-01

229

The Goddard Library - Goddard Projects Directory - NASA

The viroid and viroid-like RNA database is a compilation of all natural sequences published in journals or available from the GenBank and EMBL nucleotide sequence libraries. Several information regarding...Full Text Available

1998-01-01

230

Selecting Folded Proteins from a Library of Secondary Structural Elements

Oct 2, 2007 ... The Payload combines some of the most sensitive particle sensors .... provide state-of-the-art measurements of incoming x-ray, ultraviolet, .... It will be launched into a low-Earth orbit on a Delta 7320 rocket in September 2004. ...

231

Professions Australia - A national organisation of professional associations

A protein evolution strategy is described by which double-stranded DNA fragments encoding defined E. coli protein secondary structural elements (α-helices, β-strands...Full Text Available

2008-01-09

232

Negative Subtraction Hybridization: An efficient method to isolate large numbers of condition-specific cDNAs

...to have a representative on the YPRT 2004 Integrated approaches to sustainability among the professions For ICT to innovate it must have collaboration with other Information and Technology related groups such as ACM, Australian Library and Information Association, Records Management Association, Archivists Association of Australia, ...

233

NASA Procedural Requirements - + NODIS Library - NASA

BackgroundThe construction of cDNA libraries is a useful tool to understand gene expression in organisms under different conditions, but random sequencing of unbiased cDNA collections...Full Text Available

234

McMaster PLUS: A Cluster Randomized Clinical Trial of an Intervention to Accelerate Clinical Use of Evidence-based Information from Digital Libraries

and sick leave, and list of awardees. DESTROY WHEN 1. YEAR OLD. [GRS 1-12b] ...... FOR CSRS/FERS. RELATED. RECORDS,. DESTROY UPON. RECEIPT OF. OFFICIAL OPM ...

235

Integrated Advanced Information Management Systems: a twenty-year history at the University of Cincinnati*

BackgroundPhysicians have difficulty keeping up with new evidence from medical research.MethodsWe developed the McMaster Premium...Full Text Available

2006-11-01

236

IAIMS at Columbia-Presbyterian Medical Center: accomplishments and challenges.

The University of Cincinnati (UC) has been active in the National Library of Medicine's Integrated Advanced Information Management Systems (IAIMS) program since IAIMS' inception in 1984. UC received...Full Text Available

2004-04-01

237

High-Throughput Screen for Poly-3-Hydroxybutyrate in Escherichia coli and Synechocystis sp. Strain PCC6803

The concept of "one-stop information shopping" is becoming a reality at Columbia-Presbyterian Medical Center. Our goal is to provide access from a single workstation to clinical, research, and library...Full Text Available

1992-07-01

238

Generating Stimuli for Neuroscience Using PsychoPy

A novel, quantitative method for detecting poly-3-hydroxybutyrate (PHB) amounts in viable cells was developed to allow for high-throughput screening of mutant libraries. The staining technique was demonstrated...Full Text Available

2006-05-01

239

FEMA Media Library: Fire Safety

PsychoPy is a software library written in Python, using OpenGL to generate very precise visual stimuli on standard personal computers. It is designed to allow the construction of as wide a variety of...Full Text Available

240

ENDF-102 DATA FORMATS AND PROCEDURES FOR THE EVALUATION NUCLEAR DATA FILE ENDF-6.

Install. Inspect. Protect. Smoke Alarm Campaign Video 10/28/2009 | 04:09 Cooking_4 Cooking Fire Safety: Watch What You Heat 10/26/2007 | 01:40 Cooking_3 Cooking Fire...

2011-08-20

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241

Digital Talking Books: Planning for the Future.

The Evaluated Nuclear Data File (ENDF) formats and libraries are decided by the Cross Section Evaluation Working Group (CSEWG), a cooperative effort of national laboratories, industry, and universities in the U.S. and Canada, and are maintained by the National Nuclear Data Center (NNDC). Earlier versions of the ENDF format provided representations for neutron cross sections and distributions, photon production from neutron reactions, a limited amount of charged-particle production from neutron reactions, photo-atomic interaction data, thermal neutron scattering data, and radionuclide production and decay data (including fission products). Version 6 (ENDF-6) allows higher incident energies, adds more complete descriptions of the distributions of emitted particles, and provides for incident charged particles and photonuclear data by partitioning the ENDF library into sub-libraries. Decay data, fission product yield data, ...

2001-05-15

242

Cost analysis of a project to digitize classic articles in neurosurgery*

Ever-changing audio technology requires that National Library Service NLS always be aware of developments and prepare carefully for any systematic changes that may be desired or required. Usefulness, cost effectiveness, thoughtful stewardship, and educate...

1998-01-01

243

Comorbidities of hidradenitis suppurativa (acne inversa)

In summer 2000, the Cushing/Whitney Medical Library at Yale University began a demonstration project to digitize classic articles in neurosurgery from the late 1800s and early 1900s. The objective of...Full Text Available

2002-04-01

244

Characterization of the functional gene and several processed pseudogenes in the human triosephosphate isomerase gene family.

Comorbidities of hidradenitis suppurativa (acne inversa) were reviewed by extracting original and review publications included in MEDLINE, EMBASE and COCHRANE libraries using the terms “hidradenitis,”...Full Text Available

2010-01-01

245

Characterization of the H(+)-pumping F1F0 ATPase of Vibrio alginolyticus.

The functional gene and three intronless pseudogenes for human triosephosphate isomerase were isolated from a recombinant DNA library and characterized in detail. The functional gene spans 3.5 kilobase...Full Text Available

1985-07-01

246

The F1F0 ATPase of Vibrio alginolyticus was cloned from a chromosomal lambda library. The unc operon, which contains the structural genes for the ATPase, was sequenced and shown to have a gene organization...Full Text Available

1990-12-01

247

BOOKMARKS:

A cytochrome P450 terpenoid hydroxylase linked to the suppression of insect juvenile hormone synthesis

Heidelberg: Springer-Verlag. ABRAHART, R.J., SEE, L.& DAWSON, C. ...Water Science and Technology Library: Springer. AL-AHMADI, K., HEPPENSTALL, A.J., ...Springer. BIRKIN, M.H., TURNER, A., WU, B.

248

Complete genome sequence of Actinosynnema mirum type strain (101T)

A cDNA encoding a cytochrome P450 enzyme was isolated from a cDNA library of the corpora allata (CA) from reproductively active Diploptera punctata cockroaches. This P450 from the endocrine...Full Text Available

1998-10-27

249

Bisulfite genomic sequencing of DNA from dried blood spot microvolume samples.

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome ...

2009-05-20

250

DNA methylation is an important event in epigenetic changes in cells, and a fundamental regulator of gene transcription. Bisulfite genomic sequencing is a powerful technique used in studies of DNA methylation. However, the established procedures often require relatively large amounts of DNA. In everyday practice, samples submitted for analysis might contain very small amounts of poor quality material, as is often the case with forensic stain samples. In this study, we assess a modified, more efficient method of bisulfite genomic sequencing. Genomic DNA extracted from 3-mm dried blood spots using QIAamp micro kit was treated with sodium bisulfite (using EpiTect kit). Subsequent methylation-specific PCR (MSP) followed by DNA sequencing displayed the differentially methylated region of imprinted gene SNRPN. Our results show that this new combination of efficient DNA extraction and bisulfite treatment provides high quality ...

2011-07-01

251

NewProductsAndServices

Information Manpower Forecasting. Papers Presented at the FID/ET Seminar (Espoo, Finland, August 24-27, 1988).

... John Cannaday and Ken Weddle present the framework for a Product Design Engineering project (http://engineering.dartmouth.edu/~teps/images/ProductDesign.pdf) for high school students which may have relevance at a more advanced level. David Price has created a Mechanical Engineering Design (http://www.soton.ac.uk/~cds/) site containing engineering design notes. The Virtual Reality Engineering Library Home Page at the University of Bristol (http://www.dig.bris.ac.uk/virtual_lib/) is a library ...

252

IQARIS : a tool for the intelligent querying, analysis, and retrieval from information systems.

This collection contains 20 papers written by educators, administrators and information scientists who had conducted manpower surveys in the library and information fields: (1) "Background and Evolution of Educational Planning and Forecasting for Information Manpower" (Yves Courrier); (2) "Indicators for the Emerging Information Market" (Nick Moore); (3) "Information Scientists in the English-Speaking Caribbean: Challenges and Responses in the Development Process" (Gloria Greene, Reive Robb); (4) "National Survey on Manpower in Libraries, Information Centres and Archives in Thailand" (Suwakhon Phadungath); (5) "Predicting the Future: Manpower Forecasting for the Library and Information Professions in Southern Africa" (J. R. Neill, D. M. Mbaakanyi); (6) "Problems in Forecasting Manpower Needs" (Monique Jucquois-Delpierre); (7) "Electronic Measures for Human Resource Research" (Anthony Debons, Mariano Maura-Sardo, Anne ...

1990-12-01

253

IAEA Coordinated Research Project: Updated decay data library for actinides

Information glut is one of the primary characteristics of the electronic age. Managing such large volumes of information (e.g., keeping track of the types, where they are, their relationships, who controls them, etc.) can be done efficiently with an intelligent, user-oriented information management system. The purpose of this paper is to describe a concept for managing information resources based on an intelligent information technology system developed by the Argonne National Laboratory for managing digital libraries. The Argonne system, Intelligent Query (IQ), enables users to query digital libraries and view the holdings that match the query from different perspectives.

2002-04-26

254

Developing with Ext GWT Enterprise RIA Development

Recommended nuclear decay data for specific actinides are important in fuel-cycle studies for thermal and fast reactors and inventory studies for safeguards. Therefore, a programme of work was initiated in 2005 to improve the actinide decay data library of the International Atomic Energy Agency through the efforts of a Coordinated Research Project (CRP). The proposed contents of the new database are described, including the agreement to include additional actinides and a significant number of natural decay chain radionuclides. This work is on-going, and is estimated for completion in 2009/10.

2008-06-15

255

ALOHA: Automatic Libraries Of Helicity Amplitudes for Feynman diagram computations

Developing in Ext GWT is a fast--paced, practical guide to quickly learning the tasks necessary in building enterprise--class Rich Internet Applications. Based around the exciting new UI library from Ajax leaders Ext JS and the latest GWT release, this book takes the reader through setup, the available widgets, and advanced custom widgets and templates, and concludes with a functional sample client--server application in less than 150 pages. Not your typical beginner's guide to programming, this book provides a rapid approach to becoming effective with leading commercial RIA tools and librarie

2009-01-01

256

Trans-generational radiation-induced chromosomal instability in the female enhances the action of chemical mutagens

We present an application that automatically writes the Helas library corresponding to the Feynman rules of any Lagrangian, renormalizable or not, in quantum field theory. The code, written in Python, takes the Universal FeynRules Output as an input and produces the complete set of routines (wave-functions and amplitudes) that are needed for the computation of Feynman diagrams at leading as well as at higher orders. The representation is language independent and outputs in Fortran, C++, Python are currently available. A few key sample applications implemented in the MadGraph5 framework are presented.

2011-01-01

257

Exploiting rice-sorghum synteny for targeted development of EST-SSRs to enrich the sorghum genetic linkage map.

Genomic instability can be produced by ionising radiation, so-called radiation-induced genomic instability, and chemical mutagens. Radiation-induced genomic instability occurs in both germinal and somatic cells and also in the offspring of irradiated individuals, and it is characterised by genetic changes including chromosomal rearrangements. The majority of studies of trans-generational, radiation-induced genomic instability have been described in the male germ line, whereas the authors who have chosen the female as a model are scarce. The aim of this work is to find out the radiation-induced effects in the foetal offspring of X-ray-treated female rats and, at the same time, the possible impact of this radiation-induced genomic instability on the action of a chemical mutagen. In order to achieve both goals, the quantity and quality of chromosomal damage were analysed. In order to ...

2008-04-02

258

SEPT9_i1 and genomic instability: Mechanistic insights and relevance to tumorigenesis

The sequencing and detailed comparative functional analysis of genomes of a number of select botanical models open new doors into comparative genomics among the angiosperms, with potential benefits for improvement of many orphan crops that feed large populations. In this study, a set of simple sequence repeat (SSR) markers was developed by mining the expressed sequence tag (EST) database of sorghum. Among the SSR-containing sequences, only those sharing considerable homology with rice genomic sequences across the lengths of the 12 rice chromosomes were selected. Thus, 600 SSR-containing sorghum EST sequences (50 homologous sequences on each of the 12 rice chromosomes) were selected, with the intention of providing coverage for corresponding homologous regions of the sorghum genome. Primer pairs were designed and polymorphism detection ability was assessed using parental pairs of two existing sorghum ...

2009-08-08

259

British Library Electronic Table of Contents (United Kingdom)

Abstract Septins are highly conserved cytoskeletal GTP-binding proteins implicated in numerous cellular processes from apoptosis to vesicle trafficking. Septins have been associated with leukemia and solid tumor malignancies, including breast, ovarian, and prostate. We previously reported that high SEPT9_i1 expression in human mammary epithelial cell lines (HMECs) led to malignant cellular phenotypes such as increased cell proliferation, invasiveness, motility, and genomic instability. Our goal here was to better understand how SEPT9_i1 expression might contribute to genomic instability and malignant progression. First, we confirmed that even transient expression of SEPT9_i1 was sufficient to increase aneuploidy in HMECs. We then analyzed SEPT9_i1 by immunoprecipitation and immunofluoresce...

2011-01-01

260

Federal technology transfer and the human genome project. Background paper

Microbial dynamics in upflow anaerobic sludge blanket (UASB) bioreactor granules in response to short-term changes in substrate feed

As with other areas of biomedical research, the expectation is that the results of genome research will yield commercially valuable products of benefits to human health. The report, analyzes universities`, companies`, and researchers` experiences and perspectives since enactment of federal laws to enhance technology transfer--especially as it pertains to research funded by the National Institutes of Health and the Department of Energy, the agencies funding U.S. efforts in the Human Genome Project. OTA prepared this background paper with the assistance of a panel of advisors and reviewers selected for their expertise and diverse points of view. Additionally, hundreds of individuals cooperated with OTA staff through interviews or by providing written material. These authorities were drawn from government, academia, industry, and professional societies worldwide.

1995-09-01

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261

solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

The complexity and diversity of the microbial communities in biogranules from an upflow anaerobic sludge blanket (UASB) bioreactor were determined in response to short-term changes in substrate feeds. The reactor was fed simulated brewery wastewater (SBWW) (70% ethanol, 15% acetate, 15% propionate) for 1.5 months (phase 1), acetate / sulfate for 2 months (phase 2), acetate-alone for 3 months (phase 3), and then a return to SBWW for 2 months (phase 4). Performance of the reactor remained relatively stable throughout the experiment as shown by COD removal and gas production. 16S rDNA, methanogen-associated mcrA and sulfate reducer-associated dsrAB genes were PCR amplified, then cloned and sequenced. Sequence analysis of 16S clone libraries showed a relatively simple community composed mainly of the methanogenic Archaea (Methanobacterium and Methanosaeta), members of the Green Non-Sulfur (Chloroflexi) group of Bacteria, followed by fewer numbers of Syntrophobacter, ...

2010-08-01

262

chipD: a web tool to design oligonucleotide probes for high-density tiling arrays

BackgroundA common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL). Fine mapping QTLs requires...Full Text Available

263

Visual Genome-Wide RNAi Screening to Identify Human Host Factors Required for Trypanosoma cruzi Infection

chipD is a web server that facilitates design of DNA oligonucleotide probes for high-density tiling arrays, which can be used in a number of genomic applications such as ChIP-chip or gene-expression...Full Text Available

2010-07-01

264

Viruses with More Than 1,000 Genes: Mamavirus, a New Acanthamoeba polyphaga mimivirus Strain, and Reannotation of Mimivirus Genes

The protozoan parasite Trypanosoma cruzi is the etiologic agent of Chagas disease, a neglected tropical infection that affects millions of people in the Americas. Current chemotherapy...Full Text Available

265

Ubiquitin over-expression phenotypes and ubiquitin gene molecular misreading during aging in Drosophila melanogaster

The genome sequence of the Mamavirus, a new Acanthamoeba polyphaga mimivirus strain, is reported. With 1,191,693 nt in length and 1,023 predicted protein-coding genes, the Mamavirus...Full Text Available

2011-01-01

266

Two separate domains within vesicular stomatitis virus phosphoprotein support transcription when added in trans.

Molecular Misreading (MM) is the inaccurate conversion of genomic information into aberrant proteins. For example, when RNA polymerase II transcribes a GAGAG motif it synthesizes at low frequency RNA...Full Text Available

267

Tumour suppressor ING1b maintains genomic stability upon replication stress

The structural phosphoprotein NS of vesicular stomatitis virus, in association with the virion-associated RNA polymerase L protein, transcribes the genome ribonucleoprotein template in vitro. It contains...Full Text Available

1987-12-01

268

Tumor-Endothelial Interaction Links the CD44⁺/CD24^- Phenotype with Poor Prognosis in Early-Stage Breast Cancer1

The lesion bypass pathway, which is regulated by monoubiquitination of proliferating cell nuclear antigen (PCNA), is essential for resolving replication stalling due to DNA lesions. This process is...Full Text Available

2011-05-01

269

Transposons as tools for enhancer trap screens in vertebrates

Materials and MethodsThe genomic effects of tumor-endothelial interactions in cancer are not yet well characterized. To study this interaction in breast...Full Text Available

2009-10-01

270

Transposon-based screens for cancer gene discovery in mouse models

DNA transposons are efficient tools in transgenesis and have therefore become popular in the analysis of the regulatory genome in vertebrates via enhancer trap screens. Here, I discuss recent progress...Full Text Available

2007-01-01

271

Transposable elements in fish functional genomics: technical challenges and perspectives

Significant emphasis has recently been placed on the characterization of the human cancer genome. This effort has been assisted by the development of new DNA sequencing technologies that allow...Full Text Available

2010-08-01

272

Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes

The recent introduction of several transposable elements in zebrafish opens new frontiers for genetic manipulation in this important vertebrate model. This review discusses transposable elements as...Full Text Available

2007-01-01

273

Transcriptional Organization of the Avian Adenovirus CELO

BackgroundTransposons, i.e. transposable elements (TEs), are the major internal spontaneous mutation agents for the variability of eukaryotic genomes. To address the general issue...Full Text Available

274

Tissue Effect on Genetic Control of Transcript Isoform Variation

A detailed map of the transcriptional organization of the CELO virus genome was produced. Recent computer analysis of CELO virus has indicated the presence of 38 putative open reading frames (ORFs)....Full Text Available

1998-11-01

275

The struggle for life of the genome's selfish architects

Current genome-wide association studies (GWAS) are moving towards the use of large cohorts of primary cell lines to study a disease of interest and to assign biological relevance to the genetic signals...Full Text Available

2009-08-01

276

The polymorphism architecture of mouse genetic resources elucidated using genome-wide resequencing data: implications for QTL discovery and systems genetics

Transposable elements (TEs) were first discovered more than 50 years ago, but were totally ignored for a long time. Over the last few decades they have gradually attracted increasing interest from research...Full Text Available

277

The missing graphical user interface for genomics

Mouse genetic resources include inbred strains, recombinant inbred lines, chromosome substitution strains, heterogeneous stocks, and the Collaborative Cross (CC). These resources were generated through...Full Text Available

2007-07-01

278

The complete mitochondrial genome of Atelura formicaria (Hexapoda: Zygentoma) and the phylogenetic relationships of basal insects.

AbstractThe Galaxy package empowers regular users to perform rich DNA sequence analysis through a much-needed and user-friendly graphical web interface.See research article...Full Text Available

2010-01-01

279

The chromosomal association/dissociation of the chromatin insulator protein Cp190 of Drosophila melanogaster is mediated by the BTB/POZ domain and two acidic regions

In this study, the complete sequence of the mitochondrial DNA (mtDNA) of Atelura formicaria (Hexapoda: Zygentoma) is described. The molecule is 15.205 bp in length and it is the third complete mt genome sequenced from the Zygentoma. The genome organization conforms with the putative ancestral insect gene arrangement. All protein coding genes use standard initiation codons (methionine and isoleucine). The exception is nad4 that starts with GTG, a codon used for this purpose in other insect species. A peculiar strand skew bias is observed, given that the PCGs encoded on the J-strand contain more thymines than adenines and more cytosines than guanines. This trend in nucleotide composition has been observed also in the "firebrat" Thermobia domestica (Zygentoma, Lepismatidae), but differs from that of the majority of hexapod species, including Tricholepidion gertschi (Zygentoma, Lepidotrichidae), where adenines and cytosines outnumber thymines and ...

2009-03-11

280

The Pseudomonas aeruginosa PA01 Gene Collection

BackgroundChromatin insulators or boundary elements are a class of functional elements in the eukaryotic genome. They regulate gene transcription by interfering with promoter-enhancer...Full Text Available

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281

The Human Ageing Genomic Resources: online databases and tools for biogerontologists

Pseudomonas aeruginosa, a common inhabitant of soil and water, is an opportunistic pathogen of growing clinical relevance. Its genome, one of the largest among bacteria [5570 open reading...Full Text Available

2004-10-01

282

The Exceptionally Large Genome of Hendra Virus: Support for Creation of a New Genus within the Family Paramyxoviridae

SummaryAgeing is a complex, challenging phenomenon that will require multiple, interdisciplinary approaches to unravel its puzzles. To assist basic research on ageing, we developed...Full Text Available

2009-02-01

283

The Anopheles gambiae glutathione transferase supergene family: annotation, phylogeny and expression profiles

An outbreak of acute respiratory disease in Hendra, a suburb of Brisbane, Australia, in September 1994 resulted in the deaths of 14 racing horses and a horse trainer. The causative agent was a new member...Full Text Available

2000-11-01

284

Ternary Complex Formation on the Adenovirus Packaging Sequence by the IVa2 and L4 22-Kilodalton Proteins?

BackgroundTwenty-eight genes putatively encoding cytosolic glutathione transferases have been identified in the Anopheles gambiae genome. We manually annotated these...Full Text Available

285

Studying bacterial transcriptomes using RNA-seq

Assembly of infectious adenovirus particles requires seven functionally redundant elements at the left end of the genome, termed A repeats, that direct packaging of the DNA. Previous studies revealed...Full Text Available

2007-11-01

286

Structural analysis of a hepatitis B virus genome integrated into chromosome 17p of a human hepatocellular carcinoma.

Genome-wide studies of bacterial gene expression are shifting from microarray technology to second generation sequencing platforms. RNA-seq has a number of advantages over hybridization-based techniques,...Full Text Available

2010-10-01

287

Structural Basis for Acetylated Histone H4 Recognition by the Human BRD2 Bromodomain*

Hepatitis B virus (HBV) is clearly a factor in the development of hepatocellular carcinoma, but its mechanism of action remains obscure. One possibility is that the HBV integration event alters the...Full Text Available

1988-11-01

288

Statistical properties of nucleotide clusters in DNA sequences*

Recognition of acetylated chromatin by the bromodomains and extra-terminal domain (BET) family proteins is a hallmark for transcriptional activation and anchoring viral genomes to mitotic chromosomes...Full Text Available

2010-03-05

289

Short RNA half-lives in the slow-growing marine cyanobacterium Prochlorococcus

Using the complete genome of Plasmodium falciparum 3D7 which has 14 chromosomes as an example, we have examined the distribution functions for the amount of C or G and A or T consecutively...Full Text Available

2005-05-01

290

Severe teratozoospermia and its influence on pronuclear morphology, embryonic cleavage and compaction

BackgroundRNA turnover plays an important role in the gene regulation of microorganisms and influences their speed of acclimation to environmental changes. We investigated whole-genome...Full Text Available

2010-01-01

291

Restriction endonuclease analysis of porcine Pasteurella multocida isolates from Quebec.

BackgroundFertilization, cell division and embryo development depend on genomic contributions from male and female gametes. We hypothesize that teratozoospermic sperm influences...Full Text Available

292

Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays

We have used restriction endonuclease analysis (REA) of genomic DNA to classify porcine Pasteurella multocida isolates with similar capsular and somatic serotypes, and to monitor the distribution of...Full Text Available

1990-10-01

293

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data

We use high-density single nucleotide polymorphism (SNP) genotyping microarrays to demonstrate the ability to accurately and robustly determine whether individuals are in a complex genomic DNA mixture....Full Text Available

2008-08-01

294

Remobilization of Tol2 transposons in Xenopus tropicalis

BackgroundEukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously....Full Text Available

295

Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups

BackgroundThe Class II DNA transposons are mobile genetic elements that move DNA sequence from one position in the genome to another. We have previously demonstrated that the naturally...Full Text Available

296

Polymorphic Regions Affecting Human Height Also Control Stature in Cattle

The evolution of the human mitochondrial genome is characterized by the emergence of ethnically distinct lineages or haplogroups. Nine European, seven Asian (including Native American), and three African...Full Text Available

2002-05-01

297

Palindromic Sequence Plays a Critical Role in Human Foamy Virus Dimerization

Orthologous positions of 55 genes associated with height in four human populations were located on the bovine genome. Single nucleotide polymorphisms close to eight of these genes were significantly...Full Text Available

2011-03-01

298

Onset of Quiescence Following p53 Mediated Down-Regulation of H2AX in Normal Cells

The retroviral RNA genome is dimeric, consisting of two identical strands of RNA linked near their 5′ ends by a dimer linkage structure. Previously it was shown that human foamy virus (HFV)...Full Text Available

2001-04-01

299

New common variants affecting susceptibility to basal cell carcinoma

Normal cells, both in vivo and in vitro, become quiescent after serial cell proliferation. During this process, cells can develop immortality with genomic instability,...Full Text Available

300

New Pathogenicity Marker Found in the Plasticity Region of the Helicobacter pylori Genome

In a follow-up to our previously reported genome-wide association study of cutaneous basal cell carcinoma (BCC)1, we describe here several new susceptibility...Full Text Available

2009-08-01

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301

Mutations in TPRN Cause a Progressive Form of Autosomal-Recessive Nonsyndromic Hearing Loss

Comparison of gastric carcinoma and gastritis isolates showed the presence of genes, probably carcinoma associated (JHP947 and JHP940), that are situated in a Helicobacter...Full Text Available

2003-04-01

302

Mutational Analysis of cis-Acting RNA Signals in Segment 7 of Influenza A Virus?

We performed genome-wide homozygosity mapping in a large consanguineous family from Morocco and mapped the autosomal-recessive nonsyndromic hearing loss (ARNSHL) in this family to the DFNB79...Full Text Available

2010-03-12

303

Multiplexed, rapid detection of H5N1 using a PCR-free nanoparticle-based genomic microarray assay

The genomic viral RNA (vRNA) segments of influenza A virus contain specific packaging signals at their termini that overlap the coding regions. To further characterize cis-acting signals...Full Text Available

2008-12-01

304

Mapping cis-Regulatory Domains in the Human Genome UsingMulti-Species Conservation of Synteny

BackgroundFor more than a decade there has been increasing interest in the use of nanotechnology and microarray platforms for diagnostic applications. In this report, we describe...Full Text Available

305

Longitudinal assessment of lung cancer progression in the mouse using in vivo micro-CT imaging

Our inability to associate distant regulatory elements with the genes that they regulate has largely precluded their examination for sequence alterations contributing to human disease. One major obstacle is the large genomic space surrounding targeted genes in which such elements could potentially reside. In order to delineate gene regulatory boundaries we used whole-genome human-mouse-chicken (HMC) and human-mouse-frog (HMF) multiple alignments to compile conserved blocks of synteny (CBS), under the hypothesis that these blocks have been kept intact throughout evolution at least in part by the requirement of regulatory elements to stay linked to the genes that they regulate. A total of 2,116 and 1,942 CBS>200 kb were assembled for HMC and HMF respectively, encompassing 1.53 and 0.86 Gb of human sequence. To support the existence of complex long-range regulatory domains within these CBS we analyzed the prevalence and distribution of ...

2005-06-13

306

Lin28a transgenic mice manifest size and puberty phenotypes identified in human genetic association studies

Purpose: Small animal micro-CT imaging is being used increasingly in preclinical biomedical research to provide phenotypic descriptions of genomic models. Most of this imaging is coincident...Full Text Available

2010-09-01

307

Kinetic Complexity of the Global Response to Glucocorticoid Receptor Action

Recently, genome-wide association studies (GWAS) have linked the human LIN28B locus to height and timing of menarche [1-Full Text Available

2010-07-01

308

Involvement of the Matrix and Nucleocapsid Domains of the Bovine Leukemia Virus Gag Polyprotein Precursor in Viral RNA Packaging

We have characterized the kinetic response of gene targets throughout the murine genome to transcriptional modulation by the glucocorticoid receptor (GR). In contrast to a model in which multiple genes...Full Text Available

2009-04-01

309

Interpopulation hybridization results in widespread viability selection across the genome in Tigriopus californicus

The RNA packaging process for retroviruses involves a recognition event of the genome-length viral RNA by the viral Gag polyprotein precursor (PrGag), an important step in particle morphogenesis. The...Full Text Available

2003-09-01

310

Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments

BackgroundGenetic interactions within hybrids influence their overall fitness. Understanding the details of these interactions can improve our understanding of speciation. One experimental...Full Text Available

311

Inferring transcription factor complexes from ChIP-seq data

Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which...Full Text Available

2007-09-01

312

In vitro dimerization of human immunodeficiency virus type 1 (HIV-1) spliced RNAs

Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) allows researchers to determine the genome-wide binding locations of individual transcription factors (TFs) at high resolution....Full Text Available

2011-08-01

313

Impaired replication dynamics at the FRA3B common fragile site

The human immunodeficiency virus type 1 (HIV-1) packages its genomic RNA as a dimer of homologous RNA molecules that has to be selected among a multitude of cellular and viral RNAs. Interestingly, spliced...Full Text Available

2007-12-01

314

Identification of plasmid and Bacillus subtilis chromosomal recombination sites used for pE194 integration.

Chromosomal common fragile sites (CFSs) are genetically unstable regions of the genome that are induced by conditions that impair DNA replication. In this report, we show that treatment with the DNA...Full Text Available

2010-01-01

315

Identification of genomic differences between Campylobacter jejuni subsp. jejuni and C. jejuni subsp. doylei at the nap locus leads to the development of a C. jejuni subspeciation multiplex PCR method

The plasmid pE194 (3.7 kilobases) is capable of integrating into the genome of the bacterial host Bacillus subtilis in the absence of the major homology-dependent RecE recombination system. Multiple...Full Text Available

1989-05-01

316

Identification of copy number variations and common deletion polymorphisms in cattle

BackgroundThe human bacterial pathogen Campylobacter jejuni contains two subspecies: C. jejuni subsp. jejuni (Cjj)...Full Text Available

317

Identification of a Central DNA Flap in Feline Immunodeficiency Virus

BackgroundRecently, the discovery of copy number variation (CNV) led researchers to think that there are more variations of genomic DNA than initially believed. Moreover, a certain...Full Text Available

318

Identification of Genes Affecting the Toxicity of Anti-Cancer Drug Bortezomib by Genome-Wide Screening in S. pombe

A duplication of the polypurine tract (PPT) at the center of the human immunodeficiency virus type 1 (HIV-1) genome (the cPPT) has been shown to prime a separate plus-strand initiation and to result...Full Text Available

2001-10-01

319

Identification and In Vivo Characterization of NvFP-7R, a Developmentally Regulated Red Fluorescent Protein of Nematostella vectensis

Bortezomib/PS-341/Velcade, a proteasome inhibitor, is widely used to treat multiple myeloma. While several mechanisms of the cytotoxicity of the drug were proposed, the actual mechanism remains elusive....Full Text Available

320

Human Immunodeficiency Virus type-1 reverse transcriptase exists as post-translationally modified forms in virions and cells

BackgroundIn recent years, the sea anemone Nematostella vectensis has emerged as a critical model organism for comparative genomics and developmental biology. Although...Full Text Available

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321

Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis

BackgroundHIV-1 reverse transcriptase (RT) is a heterodimer composed of p66 and p51 subunits and is responsible for reverse transcription of the viral RNA genome into DNA. RT can...Full Text Available

322

Genomic but Not Antigenomic Hepatitis Delta Virus RNA Is Preferentially Exported from the Nucleus Immediately after Synthesis and Processing

BackgroundThe Gram-negative bacterium Burkholderia pseudomallei (Bp) is the causative agent of the human disease melioidosis. To understand the evolutionary mechanisms...Full Text Available

323

Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent

Hepatitis delta virus (HDV) contains a viroid-like circular RNA that replicates via a double rolling circle replication mechanism. It is generally assumed that HDV RNA is synthesized and remains exclusively...Full Text Available

2002-04-01

324

Genomic Evidence for the Evolution of Streptococcus equi: Host Restriction, Increased Virulence, and Genetic Exchange with Human Pathogens

Harmful algal blooms, caused by rapid growth and accumulation of certain microalgae in the ocean, pose considerable impacts on marine environments, aquatic industries and even public health. Here, we...Full Text Available

2005-01-01

325

Genomic Diversity and Evolution of Mycobacterium ulcerans Revealed by Next-Generation Sequencing

The continued evolution of bacterial pathogens has major implications for both human and animal disease, but the exchange of genetic material between host-restricted pathogens is rarely considered....Full Text Available

2009-03-01

326

Genomic Content of Bordetella pertussis Clinical Isolates Circulating in Areas of Intensive Children Vaccination

Mycobacterium ulcerans is the causative agent of Buruli ulcer, the third most common mycobacterial disease after tuberculosis and leprosy. It is an emerging infectious disease that...Full Text Available

2009-09-01

327

Genome-wide profiling of forum domains in Drosophila melanogaster

BackgroundThe objective of the study was to analyse the evolution of Bordetella pertussis population and the influence of herd immunity in different areas of the...Full Text Available

328

Genome-wide linkage scan for contraction velocity characteristics of knee musculature in the Leuven Genes for Muscular Strength Study

Forum domains are stretches of chromosomal DNA that are excised from eukaryotic chromosomes during their spontaneous non-random fragmentation. Most forum domains are 50–200 kb in length....Full Text Available

2011-05-01

329

Genome-wide expression profiling reveals distinct clusters of transcriptional regulation during bovine preimplantation development in vivo

The torque-velocity relationship is known to be affected by ageing, decreasing its protective role in the prevention of falls. Interindividual variability in this torque-velocity relationship is partly...Full Text Available

2008-09-01

330

Genome-Wide Transcriptome Profiling of Region-Specific Vulnerability to Oxidative Stress in the Hippocampus

Bovine embryos can be generated by in vitro fertilization or somatic nuclear transfer; however, these differ from their in vivo counterparts in many aspects and exhibit a higher proportion of developmental...Full Text Available

2008-12-16

331

Genome-Wide Transcriptional Response of Chemostat-Cultured Escherichia coli to Zinc

Neurons in the hippocampal CA1 region are particularly sensitive to oxidative stress (OS), whereas those in CA3 are resistant. To uncover mechanisms for selective CA1 vulnerability to OS, we...Full Text Available

2007-08-01

332

Genome-Wide Analysis Reveals a Major Role in Cell Fate Maintenance and an Unexpected Role in Endoreduplication for the Drosophila FoxA Gene Fork Head

Zinc is an essential trace metal ion for growth, but an excess of Zn is toxic and microorganisms express diverse resistance mechanisms. To understand global bacterial responses to excess Zn, we conducted...Full Text Available

2005-02-01

333

Genome Sequence of Campylobacter jejuni strain 327, a strain isolated from a turkey slaughterhouse

Transcription factors drive organogenesis, from the initiation of cell fate decisions to the maintenance and implementation of these decisions. The Drosophila embryonic salivary gland...Full Text Available

334

Genetic screening: The vista of genomic medicine

Campylobacter is one of the leading causes of food-borne gastroenteritis and has a high prevalence in poultry. Campylobacter jejuni subsp. jejuni 327 is a subspecies...Full Text Available

335

Genetic aspects of birth defects: new understandings of old problems

The accelerating development of biochemical and DNA-based diagnostic tests for human genetic conditions in the last decade has engendered a revolution in genetic diagnosis. Both genetic testing and...Full Text Available

2011-01-01

336

Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes

Over the past two decades, combined advances in genetics, developmental biology and biochemistry have transformed the study of human birth defects. This review describes the importance of genome architecture,...Full Text Available

2007-07-01

337

Gene-gene and gene-environment interactions: new insights into the prevention, detection and management of coronary artery disease

BackgroundDeveloping lepidopteran microsatellite DNA markers can be problematical, as markers often exhibit multiple banding patterns and high frequencies of non-amplifying "null"...Full Text Available

338

Gene expression patterns in four brain areas associate with quantitative measure of estrous behavior in dairy cows

Despite the recent success of genome-wide association studies (GWASs) in identifying loci consistently associated with coronary artery disease (CAD), a large proportion of the genetic components of...Full Text Available

339

Functional interaction between the Werner Syndrome protein and DNA polymerase ?

BackgroundThe decline noticed in several fertility traits of dairy cattle over the past few decades is of major concern. Understanding of the genomic factors underlying fertility,...Full Text Available

340

Exploring nervous system transcriptomes during embryogenesis and metamorphosis in Xenopus tropicalis using EST analysis

Werner Syndrome (WS) is an inherited disease characterized by premature onset of aging, increased cancer incidence, and genomic instability. The WS gene encodes a 1,432-amino acid polypeptide (WRN)...Full Text Available

2000-04-25

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341

Evidence That Two Major Replicons Comprise the Genome of Staphylococcus Aureus.

BackgroundThe western African clawed frog Xenopus tropicalis is an anuran amphibian species now used as model in vertebrate comparative genomics. It provides the...Full Text Available

342

Distinct signatures of diversifying selection revealed by genome analysis of respiratory tract and invasive bacterial populations

In Staphylococcus aureus, a pronounced shift in position of the acriflavin resistance locus was observed when gene order was determined by marker frequency analysis of cells of various ages. In young cells (2-hour culture), acriflavin resistance was mappe...

1967-01-01

343

Differentiation of trophoblast stem cells into giant cells is triggered by p57/Kip2 inhibition of CDK1 activity

Many pathogens colonize different anatomical sites, but the selective pressures contributing to survival in the diverse niches are poorly understood. Group A Streptococcus (GAS) is...Full Text Available

2011-03-22

344

Dietary factors related to body weight in adult Vietnamese in the rural area of Haiphong, Vietnam: the Korean Genome and Epidemiology Study (KoGES)

Genome endoreduplication during mammalian development is a rare event for which the mechanism is unknown. It first appears when fibroblast growth factor 4 (FGF4) deprivation induces differentiation...Full Text Available

2008-11-01

345

Detection of Streptococcus mutans Genomic DNA in Human DNA Samples Extracted from Saliva and Blood

The objectives of this study were to examine the association between dietary factors and underweight and overweight adult Vietnamese living in the rural areas of Vietnam. A cross-sectional study of...Full Text Available

2010-06-01

346

DNA Damage during G2 Phase Does Not Affect Cell Cycle Progression of the Green Alga Scenedesmus quadricauda

Caries is a multifactorial disease, and studies aiming to unravel the factors modulating its etiology must consider all known predisposing factors. One major factor is bacterial colonization,...Full Text Available

2011-01-01

347

Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, ...

DNA damage is a threat to genomic integrity in all living organisms. Plants and green algae are particularly susceptible to DNA damage especially that caused by UV light, due to their light dependency...Full Text Available

348

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae

Cyteogenetic maps of sorghum chromosomes 3-7, 9, and 10 were constructed on the basis of the fluorescence in situ hybridization (FISH) of ~ ... regions of heterchromatin were delimited for all 10 sorghum chrom...

349

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA

BackgroundOncidium spp. produce commercially important orchid cut flowers. However, they are amenable to intergeneric and inter-specific crossing making phylogenetic...Full Text Available

350

Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes

RNAs transcribed from the mitochondrial genome of Physarum polycephalum are heavily edited. The most prevalent editing event is the insertion of single Cs, with Us and dinucleotides...Full Text Available

2011-08-01

351

Comparative Transcriptional and Genomic Analysis of Plasmodium falciparum Field Isolates

BackgroundStructured noncoding RNAs perform many functions that are essential for protein synthesis, RNA processing, and gene regulation. Structured RNAs can be detected by comparative...Full Text Available

2010-01-01

352

Common genetic variation and susceptibility to partial epilepsies: a genome-wide association study

Mechanisms for differential regulation of gene expression may underlie much of the phenotypic variation and adaptability of malaria parasites. Here we describe transcriptional variation among culture-adapted...Full Text Available

2009-10-01

353

Common Familial Colorectal Cancer Linked to Chromosome 7q31: a genome-wide analysis

Partial epilepsies have a substantial heritability. However, the actual genetic causes are largely unknown. In contrast to many other common diseases for which genetic association-studies have successfully...Full Text Available

2010-07-01

354

Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler

Present investigations suggest that approximately 30% of colorectal cancer (CRC) cases arise on the basis of inherited factors. We hypothesize that the majority of inherited factors are moderately...Full Text Available

2008-11-01

355

Capture of genomic DNA on glass microscope slides

BackgroundThe rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many...Full Text Available

356

Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing

It is well known that DNA strands bind to silica surfaces in the presence of high concentrations of chaotropic salts. We developed simple methods to evaluate binding and recovery of DNA on flat...Full Text Available

2007-06-15

357

Blood leukocyte DNA hypomethylation and gastric cancer risk in a high-risk Polish population

BackgroundMimivirus, a giant dsDNA virus infecting Acanthamoeba, is the prototype of the mimiviridae family, the latest addition to the family of the nucleocytoplasmic...Full Text Available

358

Analysis of the genome-wide variations among multiple strains of the plant pathogenic bacterium Xylella fastidiosa

Global hypomethylation has been shown to increase genome instability potentially leading to increased cancer risk. We determined whether global methylation in blood leukocyte DNA was associated...Full Text Available

2010-10-15

359

Analysis of genomic differences among Clostridium botulinum type A1 strains

BackgroundThe Gram-negative, xylem-limited phytopathogenic bacterium Xylella fastidiosa is responsible for causing economically important diseases in grapevine,...Full Text Available

360

Analysis of European mtDNAs for Recombination

BackgroundType A1 Clostridium botulinum strains are a group of Gram-positive, spore-forming anaerobic bacteria that produce a genetically, biochemically, and biophysically...Full Text Available

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

361

An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer

The standard paradigm postulates that the human mitochondrial genome (mtDNA) is strictly maternally inherited and that, consequently, mtDNA lineages are clonal. As a result of mtDNA clonality, phylogenetic...Full Text Available

2001-01-01

362

An initial comparative map of copy number variations in the goat (Capra hircus) genome

BackgroundGenomics has substantially changed our approach to cancer research. Gene expression profiling, for example, has been utilized to delineate subtypes of cancer, and facilitated...Full Text Available

363

An excess of rare genetic variation in ABCE1 among Yorubans and African-American individuals with HIV-1

BackgroundThe goat (Capra hircus) represents one of the most important farm animal species. It is reared in all continents with an estimated world population of...Full Text Available

364

An Integrated Genomics Approach to Define Niche Establishment by Rhodococcus fascians1[C][W][OA

Signatures of natural selection occur throughout the human genome and can be detected at the sequence level. We have re-sequenced ABCE1, a host candidate gene essential for...Full Text Available

2009-12-01

365

Altering the ribosomal subunit ratio in yeast maximizes recombinant protein yield

Rhodococcus fascians is a Gram-positive phytopathogen that induces shooty hyperplasia on its hosts through the secretion of cytokinins. Global transcriptomics using microarrays combined...Full Text Available

2009-03-01

366

Actin-like sequences are present on human X and Y chromosomes.

BackgroundThe production of high yields of recombinant proteins is an enduring bottleneck in the post-genomic sciences that has yet to be addressed in a truly rational manner. Typically...Full Text Available

367

A supervised approach for predicting patient survival with gene expression data

The human genome contains greater than 20 actin-related sequences, six of which at least are expressed as protein. We have shown by blot hybridization the presence of actin-like sequences on both the...Full Text Available

1984-08-01

368

A novel role of the aryl hydrocarbon receptor (AhR) in centrosome amplification - implications for chemoprevention

Rapid development in genomics in recent years has allowed the simultaneous measurement of the expression levels of thousands of genes using DNA microarrays. This has offered tremendous potential...Full Text Available

2010-01-01

369

A novel custom high density-comparative genomic hybridization array detects common rearrangements as well as deep intronic mutations in dystrophinopathies

BackgroundCentrosome aberrations can cause genomic instability and correlate with malignant progression in common human malignancies such as breast and prostate cancer. Deregulation...Full Text Available

370

A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification?

BackgroundThe commonest pathogenic DMD changes are intragenic deletions/duplications which make up to 78% of all cases and point mutations (roughly 20%) detectable...Full Text Available

371

A new evolutionary scenario for the Mycobacterium tuberculosis complex

BackgroundThe order Tetraodontiformes consists of approximately 429 species of fishes in nine families. Members of the order exhibit striking morphological diversity and radiated...Full Text Available

372

A microarray analysis of the rice transcriptome and its comparison to Arabidopsis

The distribution of 20 variable regions resulting from insertion-deletion events in the genomes of the tubercle bacilli has been evaluated in a total of 100 strains of Mycobacterium tuberculosis,...Full Text Available

2002-03-19

373

A genomic and proteomic investigation of the impact of preimplantation factor on human decidual cells

Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently...Full Text Available

2005-09-01

374

A genome-wide study of PDZ-domain interactions in C. elegans reveals a high frequency of non-canonical binding

OBJECTIVEPreimplantation factor (PIF) is a novel, 15 amino acid peptide, secreted by viable embryos. This study aims to elucidate PIF’s effects in human endometrial...Full Text Available

2010-05-01

375

A Response Regulator That Represses Transcription of Several Virulence Operons in the Group A Streptococcus

BackgroundProteins may evolve through the recruitment and modification of discrete domains, and in many cases, protein action can be dissected at the domain level. PDZ domains are...Full Text Available

376

A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale

A search for homologs of the Bacillus subtilis PhoP response regulator in the group A streptococcus (GAS) genome revealed three good candidates. Inactivation of one of these, recently...Full Text Available

1999-06-01

377

A Coxiella burnetti repeated DNA element resembling a bacterial insertion sequence.

In this era of complete genomes, our knowledge of neuroanatomical circuitry remains surprisingly sparse. Such knowledge is critical, however, for both basic and clinical research into brain function....Full Text Available

2009-03-01

378

Search for a Methanopyrus-proximal last universal common ancestor based on comparative-genomic analysis

A DNA fragment located on the 3' side of the Coxiella burnetii htpAB operon was determined by Southern blotting to exist in approximately 19 copies in the Nine Mile I genome. The DNA sequences of this...Full Text Available

1992-09-01

379

British Library Electronic Table of Contents (United Kingdom)

The origin of life is a long-standing mystery puzzling many people. This mystery possesses not only philosophical but also important biological significance. To unveil this mystery, the searches for the root of life, or the last universal common ancestor (LUCA), based on comparative-genomic analysis have been intensively performed on rRNAs, tRNAs and proteins sequences. The current search pointed to a Methanopyrus-proximal LUCA, which opens up the reconstruction of Lucan biology and helps to delineate the evolutionary pathways.

2011-01-01

380

Genome Sequence of a Lancefield Group C Streptococcus zooepidemicus Strain Causing Epidemic Nephritis: New Information about an Old Disease

The integral experiment on beryllium with D-T neutrons for verification of tritium breeding

Outbreaks of disease attributable to human error or natural causes can provide unique opportunities to gain new information about host-pathogen interactions and new leads for pathogenesis research. Poststreptococcal glomerulonephritis (PSGN), a sequela of infection with pathogenic streptococci, is a common cause of preventable kidney disease worldwide. Although PSGN usually occurs after infection with group A streptococci, organisms of Lancefield group C and G also can be responsible. Despite decades of study, the molecular pathogenesis of PSGN is poorly understood. As a first step toward gaining new information about PSGN pathogenesis, we sequenced the genome of Streptococcus equi subsp. zooepidemicus strain MGCS10565, a group C organism that caused a very large and unusually severe epidemic of nephritis in Brazil. The genome is a circular chromosome of 2,024,171 bp. The genome shares extensive gene content, including many ...

2008-08-21

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

381

Plutonium build-up credits for a material test research reactor and influence of cross-section differences on actinide production

A clean benchmark experiment on beryllium was performed with D-T neutrons at the FNS facility of the Japan Atomic Energy Agency. The main objective was to verify the integral data related to the tritium production on lithium isotopes. Tritium production rates, as well as activation reaction rates were measured inside the beryllium assembly that was shaped as a pseudo-cylindrical slab with an area-equivalent diameter of 628 mm and a thickness of 355 mm. Experimental results were analyzed with a three-dimensional Monte Carlo transport code MCNP-4C and FENDL/MC-2.0, JENDL-3.2/3.3 neutron transport libraries. Evaluation of reaction rates was based on the cross section data taken from the JENDL Dosimetry File and ENDF B-VI data libraries. Analysis shows that all calculation combinations (transport and activation cross section libraries) used for evaluation of reaction rates give data that is agreeable with measured values within ...

2007-01-15

382

Dependence of fast reactor fuel burnup characteristics on nuclear data libraries

Burnup calculations with SARC system were carried out to analyse the effects of plutonium build-up on criticality of MTR type research reactor PARR-1 using several WIMSD libraries based on evaluated nuclear data files ENDFB-VI.8, JEF-2.2, JEFF-3.1 and JENDL-3.2. For equilibrium core of the reactor, it was found that a net reactivity of more than 3.5 mk is induced due to build-up of plutonium isotopes during depletion. The plutonium credit amounts to 3% of the length of equilibrium cycle. From the analysis of actinide production in the core during burnup, it was observed that in most of the cases, the amounts of actinides obtained using various cross section libraries agree fairly with each other, however, significant differences were observed for {sup 238}Pu, {sup 241}Pu, {sup 242m}Am, {sup 243}Am, {sup 242}Cm and {sup 244}Cm for some libraries. The actinide chain analysis was conducted to investigate the reasons for the ...

2006-12-15

383

Current Research in Library & Information Science. Volume 3, Numbers 1-4.

In the framework of the development of burnup calculation method for commercial fast reactors, a sensitivity analysis was carried out to clarify the dependence of fuel burnup characteristics on nuclear data libraries (NDLs). The following NDLs were compared: JEF-2.2, ENDF/B-VI Release 5, JENDL-3.2 and JENDL-3.3. The NDL-dependence of material balance for main heavy metal nuclides ("2"3"5U, "2"3"8U, "2"3"9Pu, "2"4"0Pu and "2"4"1Pu) was small, since the number densities at the end of one-cycle burnup did not change over 1 or 2% among the above-mentioned libraries. Relatively large differences were found for minor actinide nuclides, especially for "2"3"6U, "2"3"7Np, "2"4"2"mAm, "2"4"3Am and curium isotopes. The number densities for these nuclides after burning up showed remarkable NDL-dependence over 5% through 50%. A burnup sensitivity analysis system based on the generalized perturbation theory enabled us to find out quantitatively the causative ...

2005-04-01

384

COVFILS-2: neutron data and covariances for sensitivity and uncertainty analysis

Designed to provide international coverage of current research in library and information science, this quarterly journal indexes investigations, studies, surveys, and evaluated innovations. Doctoral, post-doctoral, and research staff-level work, and in-house or action research from practicing librarians, information workers, archivists, and documentalists are included in the main section, "Current Research, Development, and Investigation." Each standard entry provides information on personnel, expected duration of the work, funding, references, contacts, aims, and a full history of the project. Entries in the main section are arranged according to the Classification Research Group's "A Classification of Library and Information Science" (1971), and each project is assigned a serial number. Cross-references to main section entries are provided in the Alphabetical Subject Index and the Name Index. Sub-doctoral theses and dissertations are listed ...

1984-12-01

385

COVFILS-2: neutron data and covariances for sensitivity and uncertainty analysis

The author have prepared a new, fusion-oriented library of multigroup neutron cross sections, scattering matrices, and covariances (uncertainties and correlations). The 74-group library, called COVFILS-2, has been used, or will be used, by neutronics groups at Los Alamos National Lab. (LANL) at the University of California at Los Angeles, and at the Swiss Federal Institute for Reactor Research in the sensitivity and uncertainty analysis of fusion-relevant integral experiments such as the Li/sub 2/O experiment performed at the Fast Neutron Source Facility in Japan and the Lithium breeding module experiment planned at the LOTUS facility in Lausanne, Switzerland. Another intended use of this library is in the estimation of the uncertainty in key performance parameters (such as the breeding ratio) of conceptual fusion reactors. The 14 materials included in the first version of COVFILS-2 are hydrogen, /sup 6/Li, /sup 7/Li, ...

1986-01-01

386

ZZ GEFF-2-MATXS, Coupled Neutron-Gamma Fusion Neutronics Library in MATXS Format

The author have prepared a new, fusion-oriented library of multigroup neutron cross sections, scattering matrices, and covariances (uncertainties and correlations). The 74-group library, called COVFILS-2, has been used, or will be used, by neutronics groups at Los Alamos National Lab. (LANL) at the University of California at Los Angeles, and at the Swiss Federal Institute for Reactor Research in the sensitivity and uncertainty analysis of fusion-relevant integral experiments such as the Li_2O experiment performed at the Fast Neutron Source Facility in Japan and the Lithium breeding module experiment planned at the LOTUS facility in Lausanne, Switzerland. Another intended use of this library is in the estimation of the uncertainty in key performance parameters (such as the breeding ratio) of conceptual fusion reactors. The 14 materials included in the first version of COVFILS-2 are hydrogen, "6Li, "7Li, beryllium, carbon, ...

1986-06-15

387

Report on Challenges and Resolutions for the Purple Development Environment

1 - Description of program or function: This library for fusion neutronics calculations, to be used in conjunction with the TRANSX code, is the MATXS format version of ZZ-GEFF-2-GENDF from which it has been derived by means of the MATXSR NJOY module. It has a 175 neutron, 42 photon VITAMIN-J group structure with the standard weighting function: Maxwellian (at the temperature to which the material is referenced) + 1/E + fission spectrum + 1/E + fusion peak + 1/E. It includes 93 materials from 1-H-1 to Bi-209 - almost all from EFF-2 basic data; but Ag-107, Ag-109, natural Cd, the 6 Hf isotopes and the 4 W isotopes have been taken from JEF-2.2 - at 3 temperatures and 6 dilution cross section values; 10 thermal groups are provided below 3 eV. Neutron cross sections and diffusion matrices, photon and gas production, kerma and DPA are given. The library includes H in H2O, metallic Be and Graphite for which an accurate treatment with S(alpha, beta) ...

1997-04-01

388

The use of combinatorial topographical libraries for the screening of enhanced osteogenic expression and mineralization

Previous AIX development environment experience with ASC White and Early Delivery systems UV and UM was leveraged to provide a smooth and robust transition to the Purple development environment. Still, there were three major changes that initially caused serious problems for Purple users. The first was making 64-bit builds of executables the default instead of 32-bit. The second was requiring all executables to use large page memory. The third was the phase-out of the popular, but now defunct, third-party C++ compiler KCC, which required the migration of many codes to IBM's xlC C++ compiler. On Purple, the default build environment changed from 32-bit builds to 64-bit builds in order to enable executables to use the 4GB per processor (32GB per node) memory available, and in order for the MPI library to do collective optimizations that required the larger 64-bit address space. The 64-bit build environment was made default by setting the IBM environment ...

2006-12-12

389

British Library Electronic Table of Contents (United Kingdom)

Nano- and microstructured surfaces are known to impact on the binding and differentiation of cells, but the detailed basic understanding of the underlying regulatory mechanisms is still scarce, which impedes the rational design of smart biomaterials. Towards a comprehensive analysis of the interplay between topographical parameters such as feature design and lateral and vertical dimensions we here report on a combinatorial screening approach, BioSurface Structure Array (BSSA) of test squares each with a distinct topography. Using such BSSA libraries of 504 topographically distinct surface structures, we have identified combinations of size, gap and height of structures which enhance mineralization as well as the expression of osteogenic markers of a preosteoblastic murine cell line. This g...

2009-01-01

390

Searching for immunomodulatory sequences in sea bass (Dicentrarchus labrax L.): Transcripts analysis from thymus

British Library Electronic Table of Contents (United Kingdom)

The thymus is a key organ of the immune system in most vertebrates and, for this reason, it has been used in this paper for the generation of a normalized cDNA library from sea bass (Dicentrarchus labrax), one of the most extensively cultured species in South Mediterranean aquaculture. A total of 1632 ESTs from this library were initially analysed for sequence quality and vector sequences and, after this control, 1264 (77% of total clones sequenced) high-quality ESTs were further processed. The total collection of D. labrax thymus ESTs has been deposited in the EBI-GenBank-DBJ database (GenBank accession numbers from FN565576 to FN566839). The functional classification of ESTs was performed by Gene Ontology and KEGG annotation and, successively, the sequences were analysed using the Immuno...

2010-01-01

391

Nuclear data interface retrospective

LDL (Landscape Digital Library) a Digital Photographic Database of a Case Study Area in the River Po Valley, Northern Italy

The Nuclear Data Interface (NDI) code library and data formats are the standards for multigroup nuclear data at Los Alamos National Laboratory. NDI's analysis, design, implementation, testing, integration, and maintenance required a ten person-year and ongoing effort by the Nuclear Data Team. Their efforts provide a unique, contemporary experience in producing a standard component library. In reflection upon that experience at NDI's decennial, we have identified several factors critical to NDI's success: it addressed real problems with appropriate simplicity, it fully supported all users, it added extra value through the code to the raw nuclear data, and its team went the distance from analysis through maintenance. In this report we review these critical success factors and discuss their implications for future standardization projects.

2008-01-01

392

Isolation of full-length putative rat lysophospholipase cDNA using improved methods for mRNA isolation and cDNA cloning

Landscapes are both a synthesis and an expression of national, regional and local cultural heritages. It is therefore very important to develop techniques aimed at cataloguing and archiving their forms. This paper discusses the LDL (Landscape Digital Library) project, a Web accessible database that can present the landscapes of a territory with documentary evidence in a new format and from a new perspective. The method was tested in a case study area of the river Po valley (Northern Italy). The LDL is based on a collection of photographs taken following a systematic grid of survey points identified through topographic cartography; the camera level is that of the human eye. This methodology leads to an innovative landscape archive that differs from surveys carried out through aerial photographs or campaigns aimed at selecting "relevant" points of interest. Further developments and possible uses of the LDL are also discussed.

2001-01-01

393

Flexible Session Management in a Distributed Environment

The authors have cloned a full-length putative rat pancreatic lysophospholipase cDNA by an improved mRNA isolation method and cDNA cloning strategy using (/sup 32/P)-labelled nucleotides. These new methods allow the construction of a cDNA library from the adult rat pancreas in which the majority of recombinant clones contained complete sequences for the corresponding mRNAs. A previously recognized but unidentified long and relatively rare cDNA clone containing the entire sequence from the cap site at the 5' end to the poly(A) tail at the 3' end of the mRNA was isolated by single-step screening of the library. The size, amino acid composition, and the activity of the protein expressed in heterologous cells strongly suggest this mRNA codes for lysophospholipase.

1987-03-24

394

Digital Libraries: From Process Modelling to Grid-based Service Oriented Architecture

Many secure communication libraries used by distributed systems, such as SSL, TLS, and Kerberos, fail to make a clear distinction between the authentication, session, and communication layers. In this paper we introduce CEDAR, the secure communication library used by the Condor High Throughput Computing software, and present the advantages to a distributed computing system resulting from CEDAR's separation of these layers. Regardless of the authentication method used, CEDAR establishes a secure session key, which has the flexibility to be used for multiple capabilities. We demonstrate how a layered approach to security sessions can avoid round-trips and latency inherent in network authentication. The creation of a distinct session management layer allows for optimizations to improve scalability by way of delegating sessions to other components in the system. This session delegation creates a chain of trust that reduces the overhead of ...

2010-01-01

395

Cross-section libraries and analysis of fast reactor benchmarks

Graphical Business Process Modelling Languages (BPML) like Role Activity Diagrams (RAD) provide ease and flexibility for modelling business behaviour. However, these languages show limited applicability in terms of enactment over distributed systems paradigms like Service Oriented Architecture (SOA) based grid computing. This paper investigates RAD modelling of a Scientific Publishing Process (SPP) for Digital Libraries (DL) and tries to determine the suitability of Pi-Calculus based formal approaches to enact SOA based grid computing. In order to achieve this purpose, the Pi-Calculus based formal transformation from a RAD model of SPP for DL draws attention towards a number of challenging issues including issues that require particular design considerations for appropriate enactment in a SOA based grid system.

2006-01-01

396

Consensus sequence L/PKSSLL mimics crucial epitope on Loop III of Taiwan cobra cardiotoxin

Using indigenously developed computer program, coupled neutron gamma multi-group libraries have been generated from MA TXS-NJOY files. The MATXS format contains all the details for each reaction. Temperature and dilution factor dependent cross-sections have been generated and used in discrete ordinates method for benchmark studies of fast critical experiments. We have analyzed criticality benchmarks, which includes CSEWG fast critical benchmarks, "2"3"3U and Pu spheres and enriched uranium spheres using 30-group neutron cross-sections. Neutron and gamma spectra for spheres with point neutron source at the center, are also calculated with 42-group coupled neutron gamma cross-sections. (author)

2005-11-01

397

British Library Electronic Table of Contents (United Kingdom)

Phage display is effective in screening peptides that mimic venom's neutralizing epitopes. A phage display cyclized heptapeptide library (C7C library) was panned with purified divalent antivenin IgG, which neutralizes Naja naja atra venom (NAV) and Bungarus multicinctus venom (BMV). The selected heptapeptide sequences were aligned with known protein sequences of NAV and BMV in GenBank. One of the four consensus sequences, L/PKSSLL, mimicked the crucial epitope on Loop III of Taiwan cobra cardiotoxin that is associated with the venom's lethal potency. In dot blot analysis, several clones showed varying reactivities for NAV monovalent antivenin and lesser cross-reactions with BMV monovalent antivenin. The KSSLLRN-carrying phage occurred four times in selected clones and showed the strongest ...

2009-01-01

398

A Logic Programming Framework for Combinational Circuit Synthesis

Three-Dimensional Dispaly Of Document Set

Logic Programming languages and combinational circuit synthesis tools share a common "combinatorial search over logic formulae" background. This paper attempts to reconnect the two fields with a fresh look at Prolog encodings for the combinatorial objects involved in circuit synthesis. While benefiting from Prolog's fast unification algorithm and built-in backtracking mechanism, efficiency of our search algorithm is ensured by using parallel bitstring operations together with logic variable equality propagation, as a mapping mechanism from primary inputs to the leaves of candidate Leaf-DAGs implementing a combinational circuit specification. After an exhaustive expressiveness comparison of various minimal libraries, a surprising first-runner, Strict Boolean Inequality "<" together with constant function "1" also turns out to have small transistor-count implementations, competitive to NAND-only or NOR-only libraries. As a practical outcome, a ...

2008-01-01

399

The Iron- and Temperature-Regulated cjrBC Genes of Shigella and Enteroinvasive Escherichia coli Strains Code for Colicin Js Uptake

A method for spatializing text content for enhanced visual browsing and analysis. The invention is applied to large text document corpora such as digital libraries, regulations and procedures, archived reports, and the like. The text content from these sources may be transformed to a spatial representation that preserves informational characteristics from the documents. The three-dimensional representation may then be visually browsed and analyzed in ways that avoid language processing and that reduce the analysts' effort.

2003-06-24

400

Scalable digital libraries of event data and the NSCP meta-cluster

A cosmid library of DNA from colicin Js-sensitive enteroinvasive Escherichia coli (EIEC) strain O164 was made in colicin Js-resistant strain E. coli VCS257, and colicin...Full Text Available

2001-07-01

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25

401

In this paper we present the design, implementation, and experimental results of a system to mine and visualize event data using cluster computingbuilt upon an ATM network. Our approach is to build a system using light weight, modular software tools for data management, resource management, data analysis and visualization developed for local, campus and wide area clusters of workstations. (author)

1996-07-01

402

Research - Keyword Index

Regulation of the mRNA for monocyte-derived neutrophil-activating peptide in differentiating HL60 promyelocytes.

...understanding sweden publication publication market publications publications inco publications library public-private partnerships publishing publishing platform pufafeed puglia pulmonary diseases pulp puma pumped hydro storage pumped storage plants purity purpose purpose-grown energy crops purposes pv pv added value pv cells pv crystalline cells pv organic and polymer cells pv research pv ...

403

PRESTO-PREP: a data preprocessor for the PRESTO-II code

A cDNA library was constructed from HL60 human promyelocyte poly(A)+ RNA harvested 3 h after induction of macrophage differentiation with 12-O-tetradecanoyl phorbol-13-acetate in the presence of cycloheximide....Full Text Available

1989-05-01

404

PRESTO-II is a computer code developed to evaluate possible health effects from shallow land disposal of low level radioactive wastes. PRESTO-PREP is a data preprocessor that has been developed to expedite the formation of input data sets for PRESTO-II. PRESTO-PREP utilizes a library of nuclide and risk-specific data. Given an initial waste inventory, the code creates the radionuclide portion of the associated input data set for PRESTO-II. 2 references.

1984-07-01

405

NAME=\\

Isolation and characterization of cDNA clones for human skeletal muscle alpha actin.

... News In Practice UK work Key facts & information Mass Balance Projects Resources & Library Technical Area Contacts Site Map Benchmarking solvent waste in the UK furniture manufacturing industry OrganisationBritish Furniture Manufacturers Ltd Project ReportSolvent Waste in Furniture Manufacturing Website: www.bfmenvironment.co.uk Return to list � RSWT | Website Design Quiet Storm Solutions Ltd Please consider upgrading your browser! If you can see this ...

406

Integrated system for production of neutronics and photonics calculational constants. Volume 15, Part D. The LLL Evaluated Nuclear Data Library (ENDL): descriptions of individual evaluations for Z = 90 to 98

Two cDNA libraries corresponding to polyA+ RNA from human adult skeletal muscle have been constructed by cloning in the PstI site of pBR322. Skeletal alpha actin cDNA clones have been isolated and characterized....Full Text Available

1983-06-11

407

Efficient higher-order derivatives of the hypergeometric function.

Evaluation procedures used to produce sets of evaluated data for the 33 heavy isotopes that fall in the range Z = 90 to Z = 98 are described. At the beginning of the discussion for each individual isotope, a computer-generated listing is given which summarizes the main properties of the data sets that are contained in the evaluation. (RWR)

1977-06-17

408

Creating Open Digital Library Using XML Implementation of OAi-PMH Protocol at CERN

Various physics applications involve the computation of the standard hypergeometric function {sub 2}F{sub 1} and its derivatives. Because it is not an intrinsic in the common programming languages, automatic differentiation tools will either differentiate through the code that computes {sub 2}F{sub 1} if that code is available or require the user to provide a hand-written derivative code. We present options for the derivative computation in the context of an ionization problem and compare the approach implemented in the Diamant library to standard methods.

2008-01-01

409

Cloning, sequence analysis and over-expression of the gene for the class II fructose 1,6-bisphosphate aldolase of Escherichia coli.

This article describes the implementation of the OAi-PMH protocol within the CERN Document Server (CDS). In terms of the protocol, CERN acts both as a data provider and service provider and the two core applications are described. The application of XML Schema and XSLT technology is emphasized.

2002-01-01

410

Amarillo National Resource Center for Plutonium quarterly technical progress report, August 1, 1997--October 31, 1997

Nucleotide sequence analysis of the Escherichia coli chromosomal DNA inserted in the plasmid pLC33-5 of the Clarke and Carbon library [Clarke & Carbon (1976) Cell 9, 91-99] revealed the existence...Full Text Available

1989-01-15

411

Accessibility and Metadata in Digital Libraries

This report summarizes activities of the Amarillo National Resource Center for Plutonium during the quarter. The report describes the Electronic Resource Library; DOE support activities; current and future environmental health and safety programs; pollution prevention and pollution avoidance; communication, education, training, and community involvement programs; and nuclear and other material studies, including plutonium storage and disposition studies.

1997-12-31

412

The enhanced genomic instability was induced by alpha particle and low-energy ion irradiation in somatic cells of Arabidopsis thaliana

Metadata can be used to support accessibility in connection with improved discovery. ...certain metadata elements provide information about what capabilities are needed--either perceptual-motor, cognitive, socio-economic or geographic--to make use of a resource. This cam improve the ability of users who are disadvantaged in these ways to find resources that meet their needs--and avoid ones [resources] that do not.

2003-03-18

413

Genomic analysis of the symbiotic marine crenarchaeon, Cenarchaeumsymbiosum

Although low-energy ion radiation has been proven to have a wide range of biological effects and led to fruitful achievements as a new mutagenic source for genetic modification, there still exist some disputes about its mutagenic mechanisms because of its short-penetrating property. In present research, Arabidopsis thaliana transgenic for GUS recombination substrate was used to evaluate the genomic instability induced by irradiations of alpha particle (3.3MeV) and Low-energy-Argon ion (30 KeV). A pronounced effects of alpha particle irradiation to Arabidopsis thaliana seedlings and Argon ion irradiation to seeds on the somatic homologous recombination frequency (sHRF) were reported. The sHRFs increased 1.88-fold and 2.42-fold, respectively, which indicated that the short-penetrating radiation could effectively induce the plant genomic instability in either dry seeds or seedlings with active metabolism. The local alpha particle irradiation of ...

2008-08-12

414

The mouse formin (Fmn) gene: Genomic structure, novel exons, and genetic mapping

Crenarchaea are ubiquitous and abundant microbial constituents of soils, sediments, lakes and ocean waters, yet relatively little is known about their fundamental evolutionary, ecological, and physiological properties. To better describe the ubiquitous nonthermophilic Crenarchaea, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont, Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although synthetic, overlapping a- and b-type ribotypes harbored significant genetic variability. A single tiling path comprising the dominant a-type genotype was assembled, and used to explore the biological properties of C. symbiosum and its planktonic relatives. Out of a total of 2,066 predicted open reading frames, 36% were more highly conserved with other Archaea. The remainder partitioned between bacteria ...

2006-06-24

415

Genetic effects of introgression genomic components from Sea Island cotton (Gossypium barbadense L.) on fiber related traits in upland cotton (G. hirsutum L.)

Mutations in the mouse formin (Fmn) gene, formerly known as the limb deformity (ld) gene, give rise to recessively inherited limb deformities and renal malformations or aplasia. The Fmn gene encodes many differentially processed transcripts that are expressed in both adult and embryonic tissues. To study the genomic organization of the Fmn locus, we have used Fmn probes to isolate and characterize genomic clones spanning 500 kb. Our analysis of these clones shows that the Fmn gene is composed of at least 24 exons and spans 400 kb. We have identified two novel exons that are expressed in the developing embryonic limb bud as well as adult tissues such as brain and kidney. We have also used a microsatellite polymorphism from within the Fmn gene to map it genetically to a 2.2-cM interval between D2Mit58 and D2Mit103. 36 refs., 6 figs., 1 tab.

1997-02-01

416

British Library Electronic Table of Contents (United Kingdom)

The germplasm with exotic genomic components especially from Sea Island cotton (Gossypium barbadense L. Gb) is the dominant genetic resources to enhance fiber quality of upland cotton (G. hirsutum L., Gh). Due to low efficiency of phenotypic evaluation and selection on fiber quality, genetic dissection of favorable alleles using molecular markers is essential. Genetic dissection on putative Gb introgressions related to fiber traits were conducted by SSR markers with mapping populations derived from a cross between Luyuan343 (LY343), a superior fiber quality introgression line (IL) with genomic components from Gb, and an elite Upland cotton cv. Lumianyan#22 (LMY22). Among 82 polymorphic loci screened out from 4050 SSRs, 42 were identified as putative introgression alleles. A total of 29 fib...

2011-01-01

417

Gene discovery in the Acanthamoeba castellanii genome

Evolutionary dynamics of Newcastle disease virus

Acanthamoeba castellanii is a free-living amoeba found in soil, freshwater, and marine environments and an important predator of bacteria. Acanthamoeba castellanii is also an opportunistic pathogen of clinical interest, responsible for several distinct diseases in humans. In order to provide a genomic platform for the study of this ubiquitous and important protist, we generated a sequence survey of approximately 0.5 x coverage of the genome. The data predict that A. castellanii exhibits a greater biosynthetic capacity than the free-living Dictyostelium discoideum and the parasite Entamoeba histolytica, providing an explanation for the ability of A. castellanii to inhabit adversity of environments. Alginate lyase may provide access to bacteria within biofilms by breaking down the biofilm matrix, and polyhydroxybutyrate depolymerase may facilitate utilization of the bacterial storage compound polyhydroxybutyrate as a food source. Enzymes for the ...

2005-08-01

418

Complete genome sequence of Conexibacter woesei type strain (ID131577T)

A comprehensive dataset of NDV genome sequences was evaluated using bioinformatics to characterize the evolutionary forces affecting NDV genomes. Despite evidence of recombination in most genes, only one event in the fusion gene of genotype V viruses produced evolutionarily viable progenies. The codon-associated rate of change for the six NDV proteins revealed that the highest rate of change occurred at the fusion protein. All proteins were under strong purifying (negative) selection; the fusion protein displayed the highest number of amino acids under positive selection. Regardless of the phylogenetic grouping or the level of virulence, the cleavage site motif was highly conserved implying that mutations at this site that result in changes of virulence may not be favored. The coding sequence of the fusion gene and the genomes of viruses from wild birds displayed higher yearly rates of change in virulent viruses than in ...

2009-08-15

419

The genetic basis of salinity tolerance in Arctic charr (Salvelinus alpinus).

The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of des-cent within the class Actinobacteria. Strain ID131577T was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous fla-gella. They may form aggregates after a longer period of growth and, then as a typical charac-teristic, an undulate structure is formed by self-aggregation of flagella with entangled bacteri-al cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.

2010-01-01

420

ABSTRACT: BACKGROUND: The capacity to maintain internal ion homeostasis amidst changing conditions is particularly important for teleost fishes whose reproductive cycle is dependent upon movement from freshwater to seawater. Although the physiology of seawater osmoregulation in mitochondria-rich cells of fish gill epithelium is well understood, less is known about the underlying causes of inter- and intraspecific variation in salinity tolerance. We used a genome-scan approach in Arctic charr (Salvelinus alpinus) to map quantitative trait loci (QTL) correlated with variation in four salinity tolerance performance traits and six body size traits. Comparative genomics approaches allowed us to infer whether allelic variation at candidate gene loci (e.g., ATP1alpha1b, NKCC1, CFTR, and cldn10e) could have underlain observed variation. RESULTS: Combined parental analyses yielded genome-wide significant QTL on linkage groups 8, 14 ...

2011-09-21

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421

Universal Similarity

Summary of the OA biomarkers workshop 2010 - genetics and genomics: new targets in OA

We survey a new area of parameter-free similarity distance measures useful in data-mining, pattern recognition, learning and automatic semantics extraction. Given a family of distances on a set of objects, a distance is universal up to a certain precision for that family if it minorizes every distance in the family between every two objects in the set, up to the stated precision (we do not require the universal distance to be an element of the family). We consider similarity distances for two types of objects: literal objects that as such contain all of their meaning, like genomes or books, and names for objects. meaning, like genomes or books, and names for objects. The latter may have literal embodyments like the first type, but may also be abstract like ``red'' or ``christianity.'' For the first type we consider a family of computable distance measures corresponding to parameters expressing similarity according to particular features between ...

2005-01-01

422

British Library Electronic Table of Contents (United Kingdom)

On November fourth and fifth 2010 a group of more than 100 international investigators gathered in Atlanta for the second Osteoarthritis (OA) Biomarkers Global Initiative workshop titled ''Genetics and Genomics: New Targets in OA''. The first workshop took place in April 2009 and focused on in vitro (soluble) biomarkers whilst the third and final workshop will take place in 2012 and will focus on imaging biomarkers. The OA Research Society International (OARSI) has organized the workshops. In addition to OARSI, the National Institute of Arthritis, Musculoskeletal and Skin Diseases, the Arthritis Foundation, Amgen, Genzyme, the American Orthopaedic Society for Sports Medicine and Pfizer sponsored the second meeting. It was clear from this meeting that experiments in the genetics, epigenetic...

2011-01-01

423

Selective changes of retroelement expression in human prostate cancer

British Library Electronic Table of Contents (United Kingdom)

Retroelements constitute a large part of the human genome. These sequences are mostly silenced in normal cells, but genome-wide DNA hypomethylation in cancers might lead to their re-expression. Whether this re-expression really occurs in human cancers is largely unkown. We therefore investigated expression and DNA methylation of several classes of retroelements in human prostate cancer tissues and cell lines by quantitative reverse transcription-polymerase chain reaction and pyrosequencing, respectively. The most striking finding was strong and generalized increased expression of the HERV-K_22q11.23 provirus in cancers, including de novo expression of a spliced accessory Np9 transcript in some tumors. In parallel, DNA methylation in the long terminal repeat (LTR) decreased. Conversely, HER...

2011-01-01

424

Introduction to the Special Issue: Human Linkage Studies for Behavioral Traits

British Library Electronic Table of Contents (United Kingdom)

In the post Genome era, the aim of behavior genetics has shifted from estimating the relative contributions of genes and environmental factors to (co-)variation in human complex traits, to localization of genes and identification of functional genetic variants. This special issue reflects this transition and presents fifteen papers that report on genome-wide linkage scans for complex traits in humans and on methodological tools and innovations. Six papers focus on cognition and report overlapping linkage peaks on chromosomes 6p and 14p. Papers on addictive behavior, i.e. smoking and alcohol dependence and its endophenotypes, find moderate LOD scores on chromosomes 6p, 5q, 4p and 7q, respectively. Three papers concentrate on emotionality, depression and loneliness and examine chromosomes 2q...

2006-01-01

425

Genomic architecture of aggression: Rare copy number variants in intermittent explosive disorder

British Library Electronic Table of Contents (United Kingdom)

Abstract Copy number variants (CNVs) are known to be associated with complex neuropsychiatric disorders (e.g., schizophrenia and autism) but have not been explored in the isolated features of aggressive behaviors such as intermittent explosive disorder (IED). IED is characterized by recurrent episodes of aggression in which individuals act impulsively and grossly out of proportion from the involved stressors. Previous studies have identified genetic variants in the serotonergic pathway that play a role in susceptibility to this behavior, but additional contributors have not been identified. Therefore, to further delineate possible genetic influences, we investigated CNVs in individuals diagnosed with IED and/or personality disorder (PD). We carried out array comparative genomic hybridizati...

2011-01-01

426

Genome-wide association study identifies variants in the CFH region associated with host susceptibility to meningococcal disease

British Library Electronic Table of Contents (United Kingdom)

Meningococcal disease is an infection caused by Neisseria meningitidis. Genetic factors contribute to host susceptibility and progression to disease, but the genes responsible for disease development are largely unknown. We report here a genome-wide association study for host susceptibility to meningococcal disease using 475 individuals with meningococcal disease (cases) and 4,703 population controls from the UK. We performed, in Western European and South European cohorts (consisting of 968 cases and 1,376 controls), two replication studies for the most significant SNPs. A cluster of complement factor SNPs replicated independently in both cohorts, including SNPs within complement factor H (CFH) (rs1065489 (p.936D

2010-01-01

427

Complete genome sequences of Brucella melitensis strains M28 and M5-90, with different virulence backgrounds.

An integrated genome research network for studying the genetics of alcohol addiction

Brucella melitensis is a Gram-negative coccobacillus bacteria belonging to the Alphaproteobacteria subclass. It is an important zoonotic pathogen that causes brucellosis, a disease affecting sheep, cattle, and sometimes humans. The B. melitensis strain M5-90, a live attenuated vaccine cultured from the B. melitensis virulent strain M28, has been an effective tool to control brucellosis in goats and sheep in China. Here we report the complete genome sequences of B. melitensis M28 and M5-90, strains with different virulence backgrounds, which will serve as a valuable reference for future studies. PMID:21478357

2011-04-08

428

British Library Electronic Table of Contents (United Kingdom)

Abstract Alcohol drinking is highly prevalent in many cultures and contributes to the global burden of disease. In fact, it was shown that alcohol constitutes 3.2% of all worldwide deaths in the year 2006 and is linked to more than 60 diseases, including cancers, cardiovascular diseases, liver cirrhosis, neuropsychiatric disorders, injuries and foetal alcohol syndrome. Alcoholism, which has been proven to have a high genetic load, is one potentially fatal consequence of chronic heavy alcohol consumption, and may be regarded as one of the most prevalent neuropsychiatric diseases afflicting our society today. The aim of the integrated genome research network -Genetics of Alcohol Addiction--which is a German inter-/trans-disciplinary life science consortium consisting of molecular biologists,...

2010-01-01

429

The normal developmental regulation of a cloned sgs3 'glue' gene chromosomally integrated in Drosophila melanogaster by P element transformation.

The Complete Genome Sequence of Yersinia pseudotuberculosis IP31758, the Causative Agent of Far East Scarlet-Like Fever

A 7-kb genomic segment containing the coding sequence for the Drosophila melanogaster Formosa variant of salivary gland secretion protein 3 (sgs3) has been inserted into the snw y, bw, st strain of...Full Text Available

1983-01-01

430

The Acidic Domain of Hepatitis C Virus NS4A Contributes to RNA Replication and Virus Particle Assembly?

The first reported Far East scarlet-like fever (FESLF) epidemic swept the Pacific coastal region of Russia in the late 1950s. Symptoms of the severe infection included erythematous skin rash and desquamation,...Full Text Available

2007-08-01

431

Structural Chemistry of Human SET Domain Protein Methyltransferases

Hepatitis C virus NS3-4A is a membrane-bound enzyme complex that exhibits serine protease, RNA helicase, and RNA-stimulated ATPase activities. This enzyme complex is essential for viral genome replication...Full Text Available

2011-02-01

432

Sequencing and Comparative Genomic Analysis of pK29, a 269-Kilobase Conjugative Plasmid Encoding CMY-8 and CTX-M-3 ?-Lactamases in Klebsiella pneumoniae?

There are about fifty SET domain protein methyltransferases (PMTs) in the human genome, that transfer a methyl group from S-adenosyl-L-methionine (SAM) to substrate lysines on histone tails or other peptides. A number of structures in complex with cofactor, substrate, or inhibitors revealed the mechanisms of substrate recognition, methylation state specificity, and chemical inhibition. Based on these structures, we review the structural chemistry of SET domain PMTs, and propose general concepts towards the development of selective inhibitors.

2011-08-22

433

Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo)

A 269-kilobase conjugative plasmid, pK29, from a Klebsiella pneumoniae strain was sequenced. The plasmid harbors multiple antimicrobial resistance genes, including those encoding CMY-8...Full Text Available

2007-08-01

434

Production of Infectious Genotype 1b Virus Particles in Cell Culture and Impairment by Replication Enhancing Mutations

BackgroundLand plant genomes contain multiple members of a eukaryote-specific gene family encoding proteins with pentatricopeptide repeat (PPR) motifs. Some PPR proteins were shown...Full Text Available

435

Environmental Research Database

With the advent of subgenomic hepatitis C virus (HCV) replicons, studies of the intracellular steps of the viral replication cycle became possible. These RNAs are capable of self-amplification in cultured human hepatoma cells, but save for the genotype 2a isolate JFH-1, efficient replication of these HCV RNAs requires replication enhancing mutations (REMs), previously also called cell culture adaptive mutations. These mutations cluster primarily in the central region of non-structural protein 5A (NS5A), but may also reside in the NS3 helicase domain or at a distinct position in NS4B. Most efficient replication has been achieved by combining REMs residing in NS3 with distinct REMs located in NS4B or NS5A. However, in spite of efficient replication of HCV genomes containing such mutations, they do not support production of infectious virus particles. By using the genotype 1b isolate Con1, in this study we show that REMs interfere with HCV assembly. Strongest ...

2009-06-12

436

Plant Sulphur Nutrition

DescriptionThe recent sequencing of the complete genomes of several streptomycete species revealed the presence of a large number of cryptic' secondary metabolic gene clusters, and led to the realisation that these organisms have the ability to produce many more natural products than had previously been recognised. One of the aims of our work is to identify the physiological signals and regulatory mechanisms responsible for the activation of these 'cryptic' pathways, thus unleashing the full biosynthetic p [continued...

2010-01-31

437

Ordered Cloned DNA Map of the Genome of Vibrio cholerae 569B and Localization of Genetic Markers

Meta-Analysis for Genome-Wide Association Study Identifies Multiple Variants at the BIN1 Locus Associated with Late-Onset Alzheimer's Disease

By using a low-resolution macrorestriction map as the foundation (R. Majumder et al., J. Bacteriol. 176:1105–1112, 1996), an ordered cloned DNA map of the 3.2-Mb chromosome of the hypertoxinogenic...Full Text Available

1998-02-01

438

Isolation, sequence, and expression in Escherichia coli of an unusual thioredoxin gene from the cyanobacterium Anabaena sp. strain PCC 7120.

Recent GWAS studies focused on uncovering novel genetic loci related to AD have revealed associations with variants near CLU, CR1, PICALM and BIN1....Full Text Available

439

Investigation of genomic instability by assay of DNA fingerprint from the offspring of male mice exposed to chronic low-level #gamma#-radiation

Two sequences with homology to a thioredoxin oligonucleotide probe were detected by Southern blot analysis of Anabaena sp. strain PCC 7120 genomic DNA. One of the sequences was shown to code for a protein...Full Text Available

1989-01-01

440

Intragenic rearrangements of a mycoreovirus induced by the multifunctional protein p29 encoded by the prototypic hypovirus CHV1-EP713

By polymerase chain reaction with arbitrary primer (AP-PCR), the possibility of transmission of genome instability to somatic cells of the offspring (F_1 generation) from male parents of mice exposed to chronic low-dose #gamma#-radiation was studied. Male mice 15 days after exposure to 10-50 cGy were mated with unirradiated females. Biopsies were taken from tale tips of two month-old mice progeny for DNA separation. Primer in the AP-PCR was 20-mer oligonucleotide flanking the micro-satellite locus Atplb2 on chromosome 11 of the mouse. Comparative analysis of individual fingerprints of AP-PCR products on DNA-templates from the offspring of irradiated and unirradiated male mice revealed an increased variability of micro-satellite-associated sequences in the genome of the offspring of males exposed to 25 and 50 cGy. DNA-fingerprints of the offspring of male mice exposed to chronic irradiation doses 10 and 25 cGy. 15 days before fertilization (at ...

2000-11-20

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441

Human thrombomodulin gene is intron depleted: nucleic acid sequences of the cDNA and gene predict protein structure and suggest sites of regulatory control.

Mycoreovirus 1 (MyRV1), a member of the Reoviridae family possessing a genome consisting of 11 dsRNA segments (S1–S11), and the prototype hypovirus (CHV1-EP713)...Full Text Available

2008-12-01

442

Haplotyping and copy number estimation of the highly polymorphic human beta-defensin locus on 8p23 by 454 amplicon sequencing

We have isolated a human thrombomodulin cDNA, and a human genomic clone containing the putative promoter domain, as well as the translated and untranslated regions of the endothelial cell receptor....Full Text Available

1987-09-01

443

Global analysis of estrogen receptor beta binding to breast cancer cell genome reveals an extensive interplay with estrogen receptor alpha for target gene regulation

BackgroundThe beta-defensin gene cluster (DEFB) at chromosome 8p23.1 is one of the most copy number (CN) variable regions of the human genome. Whereas individual DEFB CNs have been...Full Text Available

444

Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)

BackgroundEstrogen receptors alpha (ERα) and beta (ERβ) are transcription factors (TFs) that mediate estrogen signaling and define the hormone-responsive phenotype...Full Text Available

445

Genome-wide analysis of N¹-methyl-adenosine modification in human tRNAs

BackgroundCotton fiber development undergoes rapid and dynamic changes in a single cell type, from fiber initiation, elongation, primary and secondary wall biosynthesis, to fiber...Full Text Available

2009-01-01

446

Genome analysis of F. nucleatum sub spp vincentii and its comparison with the genome of F. nucleatum ATCC 25586.

The N¹-methyl-Adenosine (m¹A58) modification at the conserved nucleotide 58 in the TΨC loop is present in most eukaryotic tRNAs. In yeast, m¹A58 modification...Full Text Available

2010-07-01

447

Genome Sequence of a Lancefield Group C Streptococcus zooepidemicus Strain Causing Epidemic Nephritis: New Information about an Old Disease

We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp. vincentii (FNV), and compare that genome with F. nucleatum ATCC 25586 (FN). A total of 441 FNV open reading frames (ORFs) with no orthologs in FN have been identified. Of these, 118 ORFs have no known function and are unique to FNV, whereas 323 ORFs have functional orthologs in other organisms. In addition to the excretion of butyrate, H2S and ammonia-like FN, FNV has the additional capability to excrete lactate and aminobutyrate. Unlike FN, FNV is likely to incorporate galactopyranose, galacturonate, and sialic acid into its O-antigen. It appears to transport ferrous iron by an anaerobic ferrous transporter. Genes for eukaryotic type serine/threonine kinase and phosphatase, transpeptidase E-transglycosylase Pbp1A are found in FNV but not in FN. Unique ABC transporters, cryptic phages, and three types of restriction-modification systems have been ...

2003-06-01

448

Explore - The Lab - Australian Broadcasting Corporation's Gateway to Science

Outbreaks of disease attributable to human error or natural causes can provide unique opportunities to gain new information about host-pathogen interactions and new leads for pathogenesis research....Full Text Available

449

Evolution of a cluster of innate immune genes (?-defensins) along the ancestral lines of chicken and zebra finch

...Explore - The Lab - Australian Broadcasting Corporation's Gateway to Science Radio TV Shop News Sport Local Children Science Environment more Topics help Science Home News in Science Features Explore TV & Radio Dr Karl Play Podcasts DNA - The discovery of the double helix structure of DNA completely changed biology and opened up the new field of genetics. The 'backbone of life' has given us the human genome, stem cell research, ...

450

Environmentally-Induced Malignancies: An In Vivo Model to Evaluate the Health Impact of Chemicals in Mixed Waste

BackgroundAvian β-defensins (AvBDs) represent a group of innate immune genes with broad antimicrobial activity. Within the chicken genome, previous work identified 14 AvBDs...Full Text Available

451

Dramatic Effects of 2-Bromo-5,6-Dichloro-1-?-d-Ribofuranosyl Benzimidazole Riboside on the Genome Structure, Packaging, and Egress of Guinea Pig Cytomegalovirus

Occupational and environmental exposure to organic ligands, solvents, fuel hydrocarbons, and polychlorinated biphenyls are linked with increased risk of hematologic malignancies. DOE facilities and waste sites in the U.S. are contaminated with mixtures of potentially hazardous chemicals such as metals, organic ligands, solvents, fuel hydrocarbons, polychlorinated biphenyls and radioactive isotopes. A major goal of this project was to establish linkage between chemical/radiation exposure and induction of genomic damage in target populations with the capability to undergo transformation.

2001-05-04

452

Differential decay of parent-of-origin-specific genomic sharing in cystic fibrosis-affected sib pairs maps a paternally imprinted locus to 7q34

The halogenated benzimidazoles BDCRB (2-bromo-5,6-dichloro-1-β-d-riborfuranosyl benzimidazole riboside) and TCRB (2,5,6-trichloro-1-β-d-riborfuranosyl benzimidazole...Full Text Available

2004-02-01

453

Deep short-read sequencing of chromosome 17 from the mouse strains A/J and CAST/Ei identifies significant germline variation and candidate genes that regulate liver triglyceride levels

Cystic fibrosis (CF) is a monogenic disease characterized by a high variability of disease severity and outcome that points to the role of environmental factors and modulating genes that shape the course...Full Text Available

2010-05-01

454

DNA rearrangements from #gamma#-irradiated normal human fibroblasts preferentially occur in transcribed regions of the genome

Genome sequences are essential tools for comparative and mutational analyses. Here we present the short read sequence of mouse chromosome 17 from the Mus musculus domesticus derived...Full Text Available

2009-01-01

455

Computational identification of developmental enhancers:conservation and function of transcription factor binding-site clustersin drosophila melanogaster and drosophila psedoobscura

Full text: DNA rearrangement events leading to chromosomal aberrations are central to ionizing radiation-induced cell death. Although DNA double-strand breaks are probably the lesion that initiates formation of chromosomal aberrations, little is understood about the molecular mechanisms that generate and modulate DNA rearrangement. Examination of the sequences that flank sites of DNA rearrangement may provide information regarding the processes and enzymes involved in rearrangement events. Accordingly, we developed a method using inverse PCR that allows the detection and sequencing of putative radiation-induced DNA rearrangements in defined regions of the human genome. The method can detect single copies of a rearrangement event that has occurred in a particular region of the genome and, therefore, DNA rearrangement detection does not require survival and continued multiplication of the affected cell. Ionizing radiation-induced DNA ...

2003-08-17

456

Comparative transcriptional pathway bioinformatic analysis of dietary restriction, Sir2, p53 and resveratrol life span extension in Drosophila

Background The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. Results We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the ...

2004-08-06

457

A multiple comparison approach using whole genome transcriptional arrays was used to identify genes and pathways involved in calorie restriction/dietary restriction (DR) life span extension in Drosophila....Full Text Available

2011-03-15

458

Biochemical and Structural Characterization of the Secreted Chorismate Mutase (Rv1885c) from Mycobacterium tuberculosis H₃₇R_v: an *AroQ Enzyme Not Regulated by the Aromatic Amino Acids

The state of chromatin during the cell cycle was examined using synchronized cultures of CHO hamster cells. Results support Mazia's dynamic chromosome cycle model and indicate that DNA-interactive chemotherapeutic agents elicit different types of kinetic responses in treated cells, suggesting a degree of specificity of interaction between various alkylating and intercalating agents and the genome. Effects of sarkosyl crystals, heparin, and chemotherapeutic agents, neocarzinostatin and adriamycin, on chromation are discussed. (HLW)

1976-01-01

459

Analysis of the transcript encoding the latent Epstein-Barr virus nuclear antigen I: a potentially polycistronic message generated by long-range splicing of several exons.

The gene Rv1885c from the genome of Mycobacterium tuberculosis H₃₇R_v encodes a monofunctional and secreted chorismate mutase (*MtCM) with a 33-amino-acid...Full Text Available

2006-12-01

460

Analysis of the 10q11 Cancer Risk Locus Implicates MSMB and NCOA4 in Human Prostate Tumorigenesis

The Epstein-Barr virus nuclear antigen (EBNA I) present in latently infected cells is encoded in a 2-kilobase exon contained in the BamHI K viral genomic fragment. This exon is, however, found within...Full Text Available

1985-12-01

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461

A Nonparametric Mean-Variance Smoothing Method to Assess Arabidopsis Cold Stress Transcriptional Regulator CBF2 Overexpression Microarray Data

Genome-wide association studies (GWAS) have established a variant, rs10993994, on chromosome 10q11 as being associated with prostate cancer risk. Since the variant is located outside of a protein-coding...Full Text Available

2010-11-01

462

Tridimensional analysis of the accelerator transmutation waste system

Microarray is a powerful tool for genome-wide gene expression analysis. In microarray expression data, often mean and variance have certain relationships. We present a non-parametric mean-variance smoothing...Full Text Available

463

Small heat shock protein LimHSP16.45 protects pollen mother cells and tapetal cells against extreme temperatures during late zygotene to pachytene stages of meiotic prophase I in David Lily

The Accelerator Transmutation Waste System is under development at the Los Alamos National Laboratory. The goal is to perform an independent verification of the feasibility of actinide and long-lived fission product burning in this system. The authors' work is divided into five tasks: (a) production of an actinide and long-lived fission product cross section library from JEF 2.2; (b) simulation using MCNP and KENO IV Monte Carlo codes, of the Accelerator Transmutation Waste System configurations existing in literature; (c) validation of HETC Monte Carlo code (production of spallation source); (d) validation of the cross sections by comparison of Keff and reaction rate results, calculated with MNCP and KENO IV, with experimental benchmarks and intercomparison between the authors' calculations of a PWR unit cell and the computations carried out with various codes and cross section libraries (NEACRP critically group data); and (e) simulation of ...

464

British Library Electronic Table of Contents (United Kingdom)

Plant meiotic prophase I is a complicated process involving the late zygotene and pachytene stages, both crucial for completing synapsis and recombination. Using David Lily (Lilium davidii var. Willmottiae) as our research material, we performed suppression subtractive hybridization to construct EST library of anthers at various stages of development by the pollen mother cells. From this library, we identified small heat shock protein LimHSP16.45 was highly expressed during the late zygotene to pachytene stages. Our results also showed that LimHSP16.45 was almost specifically expressed in the anther compared with the root, stem, or leaf, and in situ expression of LimHSP16.45 mRNAs showed strong signals in the pollen mother cells and tapetal cells. LimHSP16.45 could be induced by heat and c...

2011-01-01

465

Ranking Scientific Publications Based on Their Citation Graph

Physical mapping of human chromosome 16. Annual progress report

CDS Invenio is the web-based integrated digital library system developed at CERN. It is a suite of applications which provides the framework and tools for building and managing an autonomous digital library server. Within this framework, the goal of this project is to implement new ranking methods based on the bibliographic citation graph extracted from the CDS Invenio database. As a first step, we implemented the Citation Count as a baseline ranking method. The major disadvantage of this method is that all citations are treated equally, disregarding their importance and their publication date. To overcome this drawback, we consider two different approaches: a link-based approach which extends the PageRank model to the bibliographic citation graph and a time-dependent approach which takes into account time in the citation counts. In addition, we also combined these two approaches in a hybrid model based on a time-dependent PageRank. In the ...

2009-01-01

466

High Throughput Screening for the Discovery of More Efficient Catalysts for Emissions Control

We aim to isolate cDNAs mapping to human chromosome 16 and localise such cDNAs on the high resolution physical map. In collaboration with LANL, PCR primers will be synthesised from cDNA sequences mapped to chromosome 16 and used as ESTs in the generation of mega-YAC contigs for this chromosome. Probing of high density cosmid grids will enable integration of the ESTs into cosmid contigs and location of the cosmid contigs on the YAC contig. A hn-cDNA library has been constructed from the hybrid CY18 which contains chromosome 16 as the only human chromosome. A modified screening protocol has been successfully developed and 15 hn-cDNA clones have been sequenced and localised on the hybrid map. Sequence analysis of four of these revealed that they were known cDNAs, which are now mapped to chromosome 16. Development of techniques to allow the isolation of longer cDNAs from the identified exons is in progress. This will depend on PCR amplification of cDNAs from a total ...

1993-08-01

467

Advanced nuclear data for radiation-damage calculations

High-throughput synthesis and screening methods have been developed for the discovery of highly active catalysts for the control of emissions from stationary and mobile sources. Low temperature CO oxidation, CO methanation, NOx abatement and the destruction of Volatile Organic Compounds (VOCs) will be discussed. The discovery libraries for primary screening consisted of both 11x11 and 16x16 catalyst arrays on 3 inch and 4 inch quartz wafers, respectively. Catalysts were prepared by robotic liquid dispensing techniques and screened for catalytic activity in Symyx's Scanning Mass Spectrometer. The screening protocols encompassed mixed metal oxides, perovskites and supported base and noble metals. Active hits were further optimized in focus libraries using shallower compositional gradients. The ScanMS is a fast serial screening tool that uses flat wafer catalyst surfaces, local laser heating, a scanning/sniffing nozzle and a quadrupolar ...

2004-03-31

468

PARALLEL 3-D SPACE CHARGE CALCULATIONS IN THE UNIFIED ACCELERATOR LIBRARY.

Accurate calculations of atomic displacement damage in materials exposed to neutrons require detailed spectra for primary recoil nuclei. Such data are not available from direct experimental measurements. Moreover, they cannot always be computed accurately starting from evaluated nuclear data libraries such as ENDF/B-V that were developed primarily for neutron transport applications, because these libraries lack detailed energy-and-angle distributions for outgoing charged particles. Fortunately, a new generation of nuclear model codes is now available that can be used to fill in the missing spectra. One example is the preequilibrium statistical-model code GNASH. For heating and damage applications, a supplementary code called RECOIL has been developed. RECOIL uses detailed reaction data from GNASH, together with angular distributions based on Kalbach-Mann systematics to compute the energy and angle distributions of recoil nuclei. The ...

1983-01-01

469

Nuclear data activity at Atomic Energy Research Establishment, Savar, Dhaka

The paper presents the integration of the SIMBAD space charge module in the UAL framework. SIMBAD is a Particle-in-Cell (PIC) code. Its 3-D Parallel approach features an optimized load balancing scheme based on a genetic algorithm. The UAL framework enhances the SIMBAD standalone version with the interactive ROOT-based analysis environment and an open catalog of accelerator algorithms. The composite package addresses complex high intensity beam dynamics and has been developed as part of the FAIR SIS 100 project.

2006-06-26

470

Nastran nonlinear dynamic transient accident analysis for FFTF reactor component

The nuclear data activity at AERE, Savar is briefly presented in this paper. Major thrust is on the customization of cross section libraries for general purpose reactor and shielding calculations. The processing codes that are available are NJOY91.91, some AMPX-Modules and the modules in SCALE-PC. Recent measurements on cross section data over the energy range 13-15 MeV at the Institute of Nuclear science and Technology have been reviewed. Measurements and calculations are based on the determination of excitation functions of neutron induced reactions on the elements and isotopes of FRT-relevant structural materials. (author).

1995-03-01

471

A nonlinear dynamic transient analysis merging hand calculations and the NASTRAN structural analysis computer code was conducted for a Fast Flux Test Facility in-reactor test assembly during an extremely unlikely design basis accidental event which is considered a Hypothetical Core Disruptive Accident (HCDA). The finite element modeling of the problem took advantage of NASTRAN's versatility to create loads and nonlinear elements not previously found in NASTRAN's library. The structural criteria for the test assembly to withstand an HCDA stipulates that the test assembly and its spoolpiece shall remain integral with the reactor head such that missiles are not generated.

1976-11-15

472

MARS code developments

Implementation of a Federated Search System: Resource Accessibility Issues

Recent developments in the physical model of 1 MeV to 100 TeV hadron and lepton interactions with nuclei and atoms are described. These include a new nuclear cross section library, a model for soft pion production, the cascade-exciton model, the dual parton model, deuteron-nucleus and neutrino-nucleus interaction models, detailed description of mu, pi and anti p absorption and a unified treatment of muon and charged hadron electromagnetic interactions with matter. New algorithms are implemented into the MARS13(98) Monte Carlo code and benchmarked against experimental data. The code capabilities to simulate cascades and generate a variety of results in complex media have been also enhanced.

1998-12-01

473

British Library Electronic Table of Contents (United Kingdom)

During 2009, the Hilton M. Briggs Library, South Dakota State University, went live with MetaLib, a federated search engine from Ex Libris. This paper presents the implementation process, addresses resource accessibility issues, and suggests a number of resources that can be consulted about these issues. Readers can apply similar strategies to projects involving federated search systems, as many implementation projects involve the same basic considerations presented here. The author did not find any studies specifically focused on configurations of MetaLib resources, so this content should be singularly useful.

2009-01-01

474

Geothermal heat pump applications: Industrial/commercial

Fission yield measurements by inductively coupled plasma mass-spectrometry

The fastest rate of growth in the space conditioning market has been attributed to the application of geothermal heat pumps to the industrial and commercial markets. The author reviews and provides examples of the three most popular components of a large geothermal heat pump system: geothermal earth coupling, heat pumps and heat exchangers, and building side terminals. These components are applied to three example geothermal installations: a library, an office building, and a school. Examples of energy use before and after the installation of a geothermal space conditioning system are summarized. General design and cost guidelines and comments on the use of geothermal heat pump in these and similar applications are discussed.

1999-07-01

475

Fission yield measurements by inductively coupled plasma mass-spectrometry

Correct prediction of the fission products inventory in irradiated nuclear fuels is essential for accurate estimation of fuel burnup, establishing proper requirements for spent fuel transportation and storage, materials accountability and nuclear forensics. Such prediction is impossible without accurate knowledge of neutron induced fission yields. The uncertainty of the fission yields reported in the ENDF/B-VII.0 library is not uniform across all of the data and much of the improvement is desired for certain fissioning isotopes and fission products. We discuss our measurements of cumulative fission yields in nuclear fuels irradiated in thermal and fast reactor spectra using Inductively Coupled Plasma Mass Spectrometry. (author)

2009-11-01

476

British Library Electronic Table of Contents (United Kingdom)

Correct prediction of the fission products inventory in irradiated nuclear fuels is essential for accurate estimation of fuel burnup, establishing proper requirements for spent fuel transportation and storage, materials accountability and nuclear forensics. Such prediction is impossible without accurate knowledge of neutron induced fission yields. The uncertainty of the fission yields reported in the ENDF/B-VII.0 library is not uniform across all of the data and much of the improvement is desired for certain fissioning isotopes and fission products. We discuss our measurements of cumulative fission yields in nuclear fuels irradiated in thermal and fast reactor spectra using Inductively Coupled Plasma Mass Spectrometry.

2009-01-01

477

Evaluation of prompt neutron spectra for americium isotopes by multimodal Madland-Nix model

Connectivity in the Astronomy Digital Library

The prompt neutron spectra of {sup 241}Am, {sup 242m}Am, and {sup 243}Am were evaluated for the next version of Japanese Evaluated Nuclear Data Library, using the methodology developed by the authors. The method is based on the Madland-Nix theory with some improvements to consider the multimodal nature of the fission process, and shell effects on the level density parameters and the neutron multiplicity from light and heavy fragments. The results were compared with previous evaluations. (authors)

2008-07-01

478

BUBL LINK Catalogue of Internet Resources

The Astrophysics Data System (ADS) provides an extensive system of links between the literature and other on-line information. Recently, the journals of the American Astronomical Society (AAS) and a group of NASA data centers have collaborated to provide more links between on-line data obtained by space missions and the on-line journals. Authors can now specify which data sets they have used in their article. This information is used by the participants to provide the links between the literature and the data. The ADS is available at: http://ads.harvard.edu

2006-01-01

479

AONE Launches New Executive Coaching Resource for Members

...O | P | Q | R | S | T | U | V | W | X | Y | Z 230 Christianity: general resources ...com: Christianity: General Anno Domini: Jesus Through the Centuries Bible and Homosexuality Christian Theological Research Fellowship Papers Christianity Links and Resources Directory ...Good Digital Collections Lambert's Web Links MUNDUS New Testament Gateway Omnilist of Christian Starting Points Quartz Hill School of Theology Web Library Theology Online ...com: Christianity: General Offers original articles and features about Christianity in general plus annotated links to selected relevant Internet resources, compiled by ...

480

British Library Electronic Table of Contents (United Kingdom)

The American Organization of Nurse Executives (AONE) and The Leadership Studio have collaborated to create a one-of-a-kind Executive Coaching Resource Center for nurse leaders and their teams. This resource-designed specifically for AONE members-is a one-stop web-based library developed to assist nurse leaders who want to learn more about utilizing executive coaching services. It focuses on the overall benefits of coaching for nurse leaders-both tangible and intangible-and provides return on investment information for executive coaching based on the most current research.

2009-01-01

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481

A compilation of reports of the Advisory Committee on reactor safeguards. 1996 Annual report

Local chromatin structure of heterochromatin regulates repeatedDNA stability, nucleolus structure, and genome integrity

This compilation contains 47 ACRS reports submitted to the Commission, or to the Executive Director for Operations, during calendar year 1996. It also includes a report to the Congress on the NRC Safety Research Program. All reports have been made available to the public through the NRC Public Document Room, the U.S. Library of Congress, and the Internet at http://www.nrc.gov/ACRSACNW. The reports are divided into two groups: Part 1 contains ACRS reports by project name and by chronological order within project name. Part 2 categorizes the reports by the most appropriate generic subject area and by chronological order within subject area.

1997-04-01

482

Supercritical fluid extraction from dried banana peel (Musa spp., genomic group AAB): Extraction yield, mathematical modeling, economical analysis and phase equilibria

Heterochromatin constitutes a significant portion of the genome in higher eukaryotes; approximately 30% in Drosophila and human. Heterochromatin contains a high repeat DNA content and a low density of protein-encoding genes. In contrast, euchromatin is composed mostly of unique sequences and contains the majority of single-copy genes. Genetic and cytological studies demonstrated that heterochromatin exhibits regulatory roles in chromosome organization, centromere function and telomere protection. As an epigenetically regulated structure, heterochromatin formation is not defined by any DNA sequence consensus. Heterochromatin is characterized by its association with nucleosomes containing methylated-lysine 9 of histone H3 (H3K9me), heterochromatin protein 1 (HP1) that binds H3K9me, and Su(var)3-9, which methylates H3K9 and binds HP1. Heterochromatin formation and functions are influenced by HP1, Su(var)3-9, and the RNA interference (RNAi) pathway. My thesis project ...

2007-05-05

483

British Library Electronic Table of Contents (United Kingdom)

Supercritical fluid extraction from dried banana peel (Musa spp., subgroup Prata, genomic group AAB, popularly known in Brazil as Enxerto) was studied. The aspects investigated were: overall extraction curve (OEC), mass transfer modeling of the yield curves, economical analysis of the process and phase equilibrium data for the pseudo-ternary system of banana peel extract, carbon dioxide and ethanol. The extraction operating conditions evaluated were: pressure ranging from 100bar to 300bar, temperature from 40 to 50^oC and constant solvent flow rate of 5.0gCO2/min. Experimental extraction data were correlated using three kinetic models based on mass transfer equations (logistic, diffusion and Esquivel models). Phase equilibrium measurements were performed using pressure from 64.9bar to 239....

2010-01-01

484

Molecular cloning, genomic organization, and chromosomal localization of the human pancreatitis-associated protein (PAP) gene

Identification of three related human GRO genes encoding cytokine functions

Pancreatitis-associated protein (PAP) is a secretory pancreatic protein present in small amounts in normal pancreas and overexpressed during the acute phase of pancreatitis. In this paper, the authors describe the cloning, characterization, and chromosomal mapping of the human PAP gene. The gene spans 2748 bp and contains six exons interrupted by five introns. The gene has a typical promoter containing the sequences TATAAA and CCAAT 28 and 52 bp upstream of the cap site, respectively. They found striking similarities in genomic organization as well as in the promoter sequences between the human and rat PAP genes. The human PAP gene was mapped to chromosome 2p12 using rodent-human hybrid cells and in situ chromosomal hybridization. This localization coincides with that of the reg/lithostathine gene, which encodes a pancreatic secretory protein structurally related to PAP, suggesting that both genes derived from the same ancestral gene by duplication. 35 refs., 4 ...

1994-01-01

485

Human tissue factor pathway inhibitor (TFPI) gene: Complete genomic structure and localization on the genetic map of chromosome 2q

The product of the human GRO gene is a cytokine with inflammatory and growth-regulatory properties; GRO is also called MGSA for melanoma growth-stimulatory activity. The authors have identified two additional genes, GRO#beta# and GRO#gamma#, that share 90% and 86% identity at the deduced amino acid level with the original GRO#alpha# isolate. One amino acid substitution of proline in GRO#alpha# by leucine in GRO#beta# and GRO#gamma# leads to a large predicted change in protein conformation. Significant differences also exist in the 3' untranslated region, including different numbers of ATTTA repeats associated with mRNA instability. A 122-base-pair region in the 3' region is conserved among the three GRO genes, and a part of it is also conserved in the Chinese hamster genome, suggesting a role in regulation. DNA hybridization with oligonucleotide probes and partial sequence analysis of the genomic clones confirm that the three forms are derived ...

486

Genomic cloning and chromosomal localization of HRY, the human homolog to the Drosophila segmentation gene, hairy

Tissue factor pathway inhibitor (TFPI), a protease inhibitor that circulates in association with plasma lipoproteins (VLDL, LDL and HDL), helps to regulate the extrinsic blood coagulation cascade. The authors have cloned a 125-kb genomic region containing the entire human TFPI gene on six overlapping cosmids and prepared a restriction map of this contig to clarify gene structure. More than half (45 kb) of the 85-kb gene is occupied with 5[prime] noncoding elements: coding begins at exon 3. A HindIII RFLP identified with one cosmid was genotyped in the CEPH panel of 559 reference families. Linkage analysis using markers on human chromosome 2 located the TFPI gene on 2q, 36 cM proximal to D2S43(pYNZ15) and 13 cM distal to the crystalline [gamma]-polypeptide locus CRYGP1(p5G1). 31 refs., 3 figs., 3 tabs.

1993-08-01

487

Genome lability in radiation-induced transformants of C3H 10T1/2 mouse fibroblasts

The Drosophila hairy gene encodes a basic helix- loop-helix protein that functions in at least two steps during Drosophila development: (1) during embryogenesis, when it partakes in the establishment of segments, and (2) during the larval stage, when it functions negatively in determining the pattern of sensory bristles on the adult fly. In the rat, a structurally homologous gene (RHL) behaves as an immediate-early gene in its response to growth factors and can, like that in Drosophila, suppress neuronal differentiation events. Here, the authors report the genomic cloning of the human hairy gene homolog (HRY). The coding region of the gene is contained within four exons. The predicted amino acid sequence reveals only four amino acid differences between the human and rat genes. Analysis of the DNA sequence 5[prime] to the coding region reveals a putatitve untranslated exon. To increase the value of the HRY gene as a genetic marker and to assess its potential ...

1994-03-01

488

A multi-marker model for detecting chromosomal segments displaying QTL activity

We have been investigating radiation-induced neoplastic transformants of C3H 10T1/2 mouse fibroblasts for evidence of heritable changes. C3H 10T1/2 cells were treated with 8 Gy X rays. After approximately 8 weeks of culture, type II/III foci were isolated from the monolayer using cloning rings. Cell lines developed from these foci, and clones established from these cell lines, were examined for DNA content. The isolated focus-derived populations and derived clones often display aneuploidy and/or polyploidization. In one instance a clone (derived from a single cell) displayed multiple polyploidies. During passage the ploidy of many of the anomalous populations gradually reverted to the ploidy of the non-neoplastically transformed state. The morphological features associated with the neoplastic transformation event were nevertheless retained. The results demonstrate that exposure to radiation can induce, in association with morphological neoplastic transformation, a heritable, ...

1994-04-01

489

The nucleotide sequence and organization of nuclear 5S rRNA genes in yellow lupine

A statistical method is presented for detecting quantitative trait loci (QTLs), based on the linear model. Unlike methods able to detect a few well separated QTLs and to estimate their effects and positions, this method considers the genome as a whole and enables the detection of chromosomal segments involved in the differences between two homozygous lines, and their backcross, doubled haploid, or F[sub 2] progenies, for a quantitative trait. Genetic markers must be codominant, but missing markers are accepted, provided they are missing independently from the experiment. Asymptotic properties, which are of practical use, are developed. This method does not rely on strong genetic hypotheses, and thus does not permit any precise genetic analysis of the trait under study, but it does assess which regions of the genome are involved, whatever the complexity of the genetic determinism (number, effects and interactions among QTLs). Simultaneous use of ...

1993-08-01

490

The effect of mitochondrial dysfunction on cytosolic nucleotide metabolism

We have isolated a genomic clone containing 'Lupinus luteus' 5S ribosomal RNA genes by screening with 5S rDNA probe clones that were hybridized previously with the initiator methionine tRNA preparation (contaminated) with traces of rRNA or its degradation products). The clone isolated contains ten repeat units of 342 bp with 119 bp fragment showing 100% homology to the 5S rRNA from yellow lupine. Sequence analysis indicates only point heterogeneities among the flanking regions of the genes. (author). 6 refs, 3 figs.

1993-01-01

491

DEFF Research Database (Denmark)

Several enzymes of the metabolic pathways responsible for metabolism of cytosolic ribonucleotides and deoxyribonucleotides are located in mitochondria. Studies described in this paper suggest dysfunction of the mitochondria to affect these metabolic pathways and limit the available levels of cytosolic ribonucleotides and deoxyribonucleotides, which in turn can result in aberrant RNA and DNA synthesis. Mitochondrial dysfunction has been linked to genomic instability, and it is possible that the limiting effect of mitochondrial dysfunction on the levels of nucleotides and resulting aberrant RNA and DNA synthesis in part can be responsible for this link. This paper summarizes the parts of the metabolic pathways responsible for nucleotide metabolism that can be affected by mitochondrial dysfunction.

2010-01-01

492

Personality disorders and biosocial trait theories: The argument for radical legal reform.

Mitochondrial DNA variants in Drosophila melanogaster are expressed at the level of the organismal phenotype.

This article reviews antisocial personality disorder, psychopathy, and violence and develops a three factor model of personality traits. Then a discussion of related personality disorders precedes the development of a categorical two factor model of impulsive versus remorseless violence. A paradigm of proactive, medical, and school based early intervention and prevention is advocated as a useful addition to the reactive detention of criminal justice. Integration of psychological tests, neuroimaging, and genomic data in early childhood and school based intervention strategies to prevent the development of conduct disorder and attenuate criminal propensity inform this approach. PMID:20422651

493

Automated purification of Borrelia burgdorferi s.l. PCR products with KingFisher"T"M magnetic particle processor prior to genome sequencing

A plethora of experimental studies use mtDNA as a marker of demographic processes without questioning the possibility that selection may bias their interpretations. We studied four lines of Drosophila melanogaster that have a standardized nuclear DNA but variable mtDNA. We completed the sequencing of the mitochondrial genomes (excluding the A+T rich region) and compiled the differences. We then assayed male influence on oviposition, starvation resistance, lipid proportion and physical activity. We discuss these results in terms of the known differences between the lines and conclude that naturally occurring mtDNA variants in D. melanogaster are expressed at the level of the organismal phenotype. PMID:21757031

2011-07-05

494

An improved colony PCR procedure for genetic screening of Chlorella and related microalgae.

Borrelia burgdorferi sensu lato genospecies were differentiated by PCR-based sequencing of the borrelial flagellin gene. To evaluate the usefulness of KingFisher"T"M magnetic particle processor in PCR product purification, borrelia PCR products were purified with KingFisher"T"M magnetic particle processor prior to cycle sequencing and the quality of the sequence data received was analyzed. KingFisher was found to offer a rapid and reliable alternative for borrelial PCR product purification.

495

Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments.

A colony PCR technique was applied for both genomic and chloroplast DNA in the green microalgae Chlorella. Of five different lysis buffers, Chelex-100 was superior for DNA extraction, PCR and DNA storage. It also was insensitive to variations in cell density. The conditions established for an improved PCR formulation are applicable for screening of genetically-engineered transformants as well as bioprospecting of natural microalgal isolates. Besides multiple Chlorella species, we also demonstrate the efficacy of Chelex-100 for colony PCR with a number of other microalgal strains, including Chlamydomonas reinhardtii, Dunaliella salina, Nannochloropsis sp., Coccomyxa sp., and Thalassiosira pseudonana. PMID:21431847

2011-03-24

496

Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: Pathway description and gene discovery for production of next-generation biofuels

The emergence of bacterial antibiotic resistance is a growing problem, yet the variables that influence the rate of emergence of resistance are not well understood. In a microfluidic device designed to mimic naturally occurring bacterial niches, resistance of Escherichia coli to the antibiotic ciprofloxacin developed within 10 hours. Resistance emerged with as few as 100 bacteria in the initial inoculation. Whole-genome sequencing of the resistant organisms revealed that four functional single-nucleotide polymorphisms attained fixation. Knowledge about the rapid emergence of antibiotic resistance in the heterogeneous conditions within the mammalian body may be helpful in understanding the emergence of drug resistance during cancer chemotherapy. PMID:21940899

2011-09-23

497

Transcriptional regulation in Drosophila: the post-genome challenge.

BackgroundBiodiesel or ethanol derived from lipids or starch produced by microalgae may overcome many of the sustainability challenges previously ascribed to petroleum-based fuels and first generation plant-based biofuels. The paucity of microalgae genome sequences, however, limits gene-based biofuel feedstock optimization studies. Here we describe the sequencing and de novo transcriptome assembly for the non-model microalgae species, Dunaliella tertiolecta, and identify pathways and genes of importance related to biofuel production.ResultsNext generation DNA pyrosequencing technology applied to D. tertiolecta transcripts produced 1,363,336 high quality reads with an average length of 400 bases. Following quality and size trimming, ~ 45% of the high quality reads were assembled into 33,307 isotigs with a 31-fold coverage and 376,482 singletons. Assembled sequences and singletons were subjected to BLAST similarity searches and annotated with Gene Ontology (GO) and ...

2011-03-14

498

Molecular characterization of the Spirometra mansonoides genome: renaturation kinetics, methylation, and hybridization to human cDNA probes.

Drosophila melanogaster has long been at the forefront of studies of transcriptional regulation in animals. Many fundamental ideas--such as cis control elements that act over long distances, the regulation of development by hierarchical cascades of transcription factors, dosage compensation, and position effect variegation--originated from studies of the fruit fly. The recent completion of the euchromatic DNA sequence of Drosophila is another breakthrough. The sequence data highlight important unanswered questions. For example, only one-fifth of the 124 Mb of Drosophila euchromatic DNA codes for protein. The function of the remaining 100 Mb of mostly unique DNA is largely unknown. Some proportion of this non-reading frame DNA must encode the functional recognition sites targeted by the approximately 700 sequence-specific DNA binding proteins that regulate transcription in Drosophila, but what proportion? Most or very little? Promoter sequences by definition contain all of the cis ...

2001-03-01

499