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1

Design of 240,000 orthogonal 25mer DNA barcode probes  

UK PubMed Central (United Kingdom)

DNA barcodes linked to genetic features greatly facilitate screening these features in pooled formats using microarray hybridization, and new tools are needed to design large sets of barcodes to allow...Full Text Available

2009-02-17

2

Choosing and Using a Plant DNA Barcode  

UK PubMed Central (United Kingdom)

The main aim of DNA barcoding is to establish a shared community resource of DNA sequences that can be used for organismal identification and taxonomic clarification. This approach was successfully...Full Text Available

3

Development of barcode system for internal dose monitoring  

International Nuclear Information System (INIS)

In Tarapur Atomic Power Station unit-3 and 4, which is 540 MWe pressurized heavy water reactor, tritium is produced in primary heat transport system and moderator system. Tritium is a major contributor to the internal dose. Internal dose contributes about 30% of the collective dose. Internal dose monitoring and its control are important to control the collective dose. Estimation of internal dose is done by analysis of bioassay samples of radiation workers. In a month, about 7000 bioassay samples are analysed for the internal dose assessment during normal operation, and about 12000 during the biennial shut down of the reactor. To enhance the sample preparation and counting performance, minimize the entry errors and reduce the processing time, barcode based label generation system was developed for the internal dose monitoring. This paper discusses about the use of barcode system in the internal dose monitoring at TAPS 3 and 4. (author)

2008-11-19

4

A post-labeling method for multiplexed and multicolored genotyping analysis of SSR, indel and SNP markers in single tube with bar-coded split tag (BStag)  

UK PubMed Central (United Kingdom)

BackgroundGenotyping analysis using capillary DNA sequencing with fluorescently labeled primer pairs obtained by polymerase chain reaction (PCR) is widely used, but is expensive....Full Text Available

5

Ovine reference materials and assays for prion genetic testing  

UK PubMed Central (United Kingdom)

BackgroundGenetic predisposition to scrapie in sheep is associated with several variations in the peptide sequence of the prion protein gene (PRNP). DNA-based tests...Full Text Available

6

Feeding ecology of Xenoturbella bocki (phylum Xenoturbellida) revealed by genetic barcoding  

British Library Electronic Table of Contents (United Kingdom)

Abstract The benthic marine worm Xenoturbella is frequently contaminated with molluscan DNA, which had earlier caused confusion resulting in a suggested bivalve relationship. In order to find the source of the contaminant, we have used molluscan sequences derived from Xenoturbella and compared them to barcodes obtained from several individuals of the nonmicroscopic molluscs sharing the same environment as Xenoturbella. Using cytochrome oxidase 1, we found the contaminating sequences to be 98% similar to the bivalve Ennucula tenuis. Using the highly variable D1-D2 region of the large ribosomal subunit in Xenoturbella, we found three distinct species of contaminating molluscs, one of which is 99% similar to the bivalve Abra nitida, one of the most abundant bivalves in the Gullmarsfjord where...

2008-01-01

7

Gene silencing induced by oxidative DNA base damage: association with local decrease of histone H4 acetylation in the promoter region  

UK PubMed Central (United Kingdom)

Oxidized DNA bases, particularly 7,8-dihydro-8-oxoguanine (8-oxoG), are endogenously generated in cells, being a cause of carcinogenic mutations and possibly interfering with gene expression. We found...Full Text Available

2010-07-01

8

Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils  

UK PubMed Central (United Kingdom)

The astonishingly efficient location and excision of damaged DNA bases by DNA repair glycosylases is an especially intriguing problem in biology. One example is the enzyme uracil DNA glycosylase (UNG),...Full Text Available

2008-08-05

9

Genetic screening: The vista of genomic medicine  

UK PubMed Central (United Kingdom)

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

10

DNA base mismatch detection with bulky rhodium intercalators: synthesis and applications  

UK PubMed Central (United Kingdom)

The syntheses and applications of two metallointercalators, Rh(bpy)2(chrysi)3+ and Rh(bpy)2(phzi)3+, that target single base mismatches in DNA are...Full Text Available

2007-01-01

11

Applications and Experience with PCR-Based Assays to Predict Blood Group Antigens  

UK PubMed Central (United Kingdom)

SummaryDNA-based tests are increasingly being used to predict a blood group phenotype. This is possible because genes encoding 29 of the 30 blood group systems have been cloned and sequenced,...Full Text Available

2009-01-01

12

Identification of mutations leading to the Lesch-Nyhan syndrome by automated direct DNA sequencing of in vitro amplified cDNA  

Energy Technology Data Exchange (ETDEWEB)

The Lesch-Nyhan (LN) syndrome is a severe X chromosome-linked disease that results from a deficiency of the purine salvage enzyme hypoxanthine phosphoribosyltransferase (HPRT). The mutations leading to the disease are heterogeneous and frequently arise as de novo events. The authors have identified nucleotide alterations in 15 independently arising HPRT-deficiency cases by direct DNA sequencing of in vitro amplified HPRT cDNA. They also demonstrate that the direct DNA sequence analysis can be automated, further simplifying the detection of new mutations at this locus. The mutations include DNA base substitutions, small DNA deletions, a single DNA base insertion, and errors in RNA splicing. The application of these procedures allows DNA diagnosis and carrier identification by the direct detection of the mutant alleles within individual families affected by LN.

1989-03-01

13

A quantum theoretical study of reactions of methyldiazonium ion with DNA base pairs  

British Library Electronic Table of Contents (United Kingdom)

Methylation of the DNA bases in the Watson-Crick GC and AT base pairs by the methyldiazonium ion was investigated employing density functional and second order Moller-Plesset (MP2) perturbation theories. Methylation at the N3, N7 and O6 sites of guanine, N1, N3 and N7 sites of adenine, O2 and N3 sites of cytosine and the O2 and O4 sites of thymine were considered. The computed reactivities for methylation follow the order N7(guanine)>N3(adenine)>O6(guanine) which is in agreement with experiment. The base pairing in DNA is found to play a significant role with regard to reactivities of the different sites.

2011-01-01

14

DNA barcoding as a tool for species identification in three forensic wildlife cases in South Africa  

British Library Electronic Table of Contents (United Kingdom)

Poaching of wildlife animals for subsistence and commercial purposes has lead to population declines in Africa. In forensic cases, a need exists to identify the species of origin of carcasses, meat or blood. In the study presented here, the mitochondrial COI gene was sequenced to determine the species of unknown samples in three suspect South African forensic wildlife cases. In two cases the unknown samples were identified as originating from domestic cattle (Bos taurus) and in the third case the sample was identified as common reedbuck (Redunca arundinum). This is the first report of the COI sequence of common reedbuck. The study highlights the need for accurate wildlife reference material from each country in order to convict wildlife cases.

2011-01-01

15

The poly dA helix: a new structural motif for high performance DNA-based molecular switches  

UK PubMed Central (United Kingdom)

We report a pH-dependent conformational transition in short, defined homopolymeric deoxyadenosines (dA15) from a single helical structure with stacked nucleobases at neutral pH to a double-helical,...Full Text Available

2009-05-01

16

Percent G+C Profiling Accurately Reveals Diet-Related Differences in the Gastrointestinal Microbial Community of Broiler Chickens  

UK PubMed Central (United Kingdom)

Broiler chickens from eight commercial farms in Southern Finland were analyzed for the structure of their gastrointestinal microbial community by a nonselective DNA-based method, percent G+C-based...Full Text Available

2001-12-01

17

Dual Functions of ASCIZ in the DNA Base Damage Response and Pulmonary Organogenesis  

UK PubMed Central (United Kingdom)

Zn2+-finger proteins comprise one of the largest protein superfamilies with diverse biological functions. The ATM substrate Chk2-interacting Zn2+-finger protein...Full Text Available

2010-10-01

18

An immunochemical approach to the study of DNA damage and repair  

Energy Technology Data Exchange (ETDEWEB)

The overall objective of this project is to produce antibodies to unique modified DNA bases and develop immunochemical assays to quantitate these lesions in damaged DNA. During this past year we have developed an antibody and chemical test to quantitate a basic sites in DNA and produced antibodies to the 8-oxopurines. This report discusses the detection of a basic sites in DNA and the preparation of antibodies to 8-hydroxyadenine and 8-hydroxyguanine.

1990-11-14

19

Report of activity, 1995 - 1996; Rapport d`activite, 1995 - 1996  

Energy Technology Data Exchange (ETDEWEB)

This Report of activity displays the work developed at Centre d`Etude Nucleaires de Bordeaux-Gradignan (CENBG) in the period 1995-1996. A number of 68 short progress notes are presented in the fields of Cosmic particles (3), Nuclear Astrophysics (4), High Spins-Large Deformations (8), Basic Interactions (9), Exotic Nuclei (10), Hybrid Systems (4), Theoretical Physics (28), Cellular Microanalysis by means of Nuclear Probes (3) and Technical Development (3). The main problems attacked at CENBG, established as orientations by scientific board of IN2P3 (CENBG is a UMR of Bordeaux-1 Univ. and CNRS-IN2P3) are the following: the research of Majorana/Dirac nature of neutrino (in the framework of NEMO Experiment) in relation with the problem of origin of mass in the Universe and the cosmological puzzle of dark matter, the investigation of the origin of high energy (20 to 200 GeV) cosmic radiation (in the framework of CELESTE Experiment), the study of extreme issues in ...

1997-06-01

20

Synthesis of histidine-stabilized cadmium sulfide quantum dots: Study of their fluorescence behaviour in the presence of adenine and guanine  

British Library Electronic Table of Contents (United Kingdom)

Cadmium sulfide particles have been synthesized in the aqueous medium using the amino acid histidine as a stabilizing agent. These particles demonstrate the phenomenon of size quantization effect. The fluorescence of histidine-stabilized CdS was found to be enhanced and quenched by the addition of DNA bases adenine and guanine, respectively. The fluorescence enhancement of CdS in the presence of adenine has been explained on the basis of interaction between the quantum dot stabilizer and the amino group of adenine. Quenching of CdS fluorescence by guanine occurs due to interaction of the substrate with the quantum dot surface.

2010-01-01

 
 
 
 
21

Development and pilot demonstration program of a waste minimization plan at Argonne National Laboratory  

Energy Technology Data Exchange (ETDEWEB)

In response to US Department of Energy directives, Argonne National Laboratory (ANL) has developed a waste minimization plan aimed at reducing the amount of wastes at this national research and development laboratory. Activities at ANL are primarily research- oriented and as such affect the amount and type of source reduction that can be achieved at this facility. The objective of ANL's waste minimization program is to cost-effectively reduce all types of wastes, including hazardous, mixed, radioactive, and nonhazardous wastes. The ANL Waste Minimization Plan uses a waste minimization audit as a systematic procedure to determine opportunities to reduce or eliminate waste. To facilitate these audits, a computerized bar-coding procedure is being implemented at ANL to track hazardous wastes from where they are generated to their ultimate disposal. This paper describes the development of the ANL Waste Minimization Plan and a pilot demonstration of the how the ...

1991-01-01

22

Quantum simulation of molecular interaction and dynamics at surfaces  

British Library Electronic Table of Contents (United Kingdom)

The interaction between molecules and solid surfaces plays important roles in various applications, including catalysis, sensors, nanoelectronics, and solar cells. Surprisingly, a full understanding of molecule-surface interaction at the quantum mechanical level has not been achieved even for very simple molecules, such as water. In this mini-review, we report recent progresses and current status of studies on interaction between representative molecules and surfaces. Taking water/metal, DNA bases/carbon nanotube, and organic dye molecule/oxide as examples, we focus on the understanding on the microstructure, electronic property, and electron-ion dynamics involved in these systems obtained from first-principles quantum mechanical calculations. We find that a quantum mechanical description ...

2011-01-01

23

Hsp90 gene, an additional target for discrimination between the potato cyst nematodes, Globodera rostochiensis and G. pallida, and the related species, G. tabacum tabacum  

British Library Electronic Table of Contents (United Kingdom)

The heat-shock gene, Hsp90, was targeted as a new variable genomic region to supplement other DNA-based tests for identification and discrimination of Globodera pallida, G. rostochiensis and G. tabacum tabacum. Populations of the potato cyst nematodes, G. pallida and G. rostochiensis (PCN), originating from Canada, France, Belgium and USA, together with two populations of G. tabacum tabacum from the USA and France were used for the amplification of a fragment of the Hsp90 gene. General and specific primers and probes for each species were derived from the consensus and non-consensus regions of the aligned sequences, respectively. A triplex conventional PCR assay, using a general forward and reverse or three specific reverse primers, as well as a real-time PCR using general primers and spec...

2011-01-01

24

Nuclear Forensics and Attribution for Improved Energy Security: The Use of Taggants in Nuclear Fuel  

International Nuclear Information System (INIS)

The Global Nuclear Energy Partnership (GNEP), recently announced by DOE Secretary Bodman, poses significant new challenges with regard to securing, safeguarding, monitoring and tracking nuclear materials. In order to reduce the risk of nuclear proliferation, new technologies must be developed to reduce the risk that nuclear material can be diverted from its intended use. Regardless of the specific nature of the fuel cycle, nuclear forensics and attribution will play key roles to ensure the effectiveness of nonproliferation controls and to deter the likelihood of illicit activities. As the leader of the DHS nuclear and radiological pre-detonation attribution program, LLNL is uniquely positioned to play a national leadership role in this effort. Ensuring that individuals or organizations engaged in illicit trafficking are rapidly identified and apprehended following theft or diversion of nuclear material provides a strong deterrent against unlawful activities. Key to establishing this ...

25

Atomic force microscopy and surface-enhanced Raman scattering detection of DNA based on DNA-nanoparticle complexes  

Energy Technology Data Exchange (ETDEWEB)

We report a simple method for the label-free detection of double-stranded DNA using surface-enhanced Raman scattering (SERS). We prepared cetyltrimethylammonium bromide (CTAB)-capped silver nanoparticles and a DNA-nanoparticle complex by adding silver nanoparticles to {lambda}-DNA solutions. In the present study, the utilization of CTAB-capped silver nanoparticles facilitates the electrostatic interaction between DNA molecules and silver nanoparticles; at the same time, the introduction of DNA avoids adding aggregating agent for the formation of nanoparticle aggregates to obtain large enhancement of DNA, because the DNA acts as both the probe molecules and aggregating agent of Ag nanoparticles. Atomic force microscopy (AFM) studies show that the morphology of DNA-Ag nanoparticle complexes seems to be determined by the concentrations of the DNA and the nanoparticles. Surface-enhanced Raman scattering (SERS) studies show that the morphology of the complexes plays a significant role in ...

2009-03-25

26

An immunochemical approach to the study of DNA damage and repair. Technical progress report, May 1, 1989--April 30, 1992  

Energy Technology Data Exchange (ETDEWEB)

The overall objective of this project has been to develop immunochemical methods to quantitate unique DNA base damages in order to facilitate studies on radiation-induced damage production and repair. Specifically, we have been using antibodies raised to damaged bases to quantitate unique lesions in model systems in order to evaluate their potential biological consequences. Our approach has been to synthesize modified nucleotides or nucleosides, conjugate them to protein carriers, and use the conjugates as immunogens in rabbits or to prepare monoclonal antibodies. We have been studying damages that are stable radiolysis products found in X-irradiated DNA and thus of potential biological consequence. Our aim is to build an in vitro and in vivo data base on the interactions between model DNA lesions and such cellular enzymes as DNA polymerases and repair endonucleases. Initial studies have focused on pyrimidine ring saturation products (thymine ...

1992-05-01

27

An immunochemical approach to the study of DNA damage and repair  

Energy Technology Data Exchange (ETDEWEB)

The overall objective of this project has been to develop immunochemical methods to quantitate unique DNA base damages in order to facilitate studies on radiation-induced damage production and repair. Specifically, we have been using antibodies raised to damaged bases to quantitate unique lesions in model systems in order to evaluate their potential biological consequences. Our approach has been to synthesize modified nucleotides or nucleosides, conjugate them to protein carriers, and use the conjugates as immunogens in rabbits or to prepare monoclonal antibodies. We have been studying damages that are stable radiolysis products found in X-irradiated DNA and thus of potential biological consequence. Our aim is to build an in vitro and in vivo data base on the interactions between model DNA lesions and such cellular enzymes as DNA polymerases and repair endonucleases. Initial studies have focused on pyrimidine ring saturation products (thymine ...

1992-05-01

28

Fossil avian eggshell preserves ancient DNA  

DEFF Research Database (Denmark)

Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for ...

2010-01-01

29

Biomimetic helical rosette nanotubes and nanocrystalline hydroxyapatite coatings on titanium for improving orthopedic implants  

Science.gov (United States)

Natural bone consists of hard nanostructured hydroxyapatite (HA) in a nanostructured protein-based soft hydrogel template (ie, mostly collagen). For this reason, nanostructured HA has been an intriguing coating material on traditionally used titanium for improving orthopedic applications. In addition, helical rosette nanotubes (HRNs), newly developed materials which form through the self-assembly process of DNA base pair building blocks in body solutions, are soft nanotubes with a helical architecture that mimics natural collagen. Thus, the objective of this in vitro study was for the first time to combine the promising attributes of HRNs and nanocrystalline HA on titanium and assess osteoblast (bone-forming cell) functions. Different sizes of nanocrystalline HA were synthesized in this study through a wet chemical precipitation process following either hydrothermal treatment or sintering. Transmission electron microscopy images showed that ...

2008-01-01