t4 bacteriophage dna: Topics by WorldWideScience.org

Genetic Control of Capsid Length in Bacteriophage T4 I. Isolation and Preliminary Description of Four New Mutants

Amorphous silicates having small particles with a large surface area were found to have high nonspecific adsorption capacity. Investigations with Escherichia coli T4 bacteriophage have...Full Text Available

1980-01-01

3

Mutational analysis of bacteriophage lambda lysis gene S.

Four new mutants are described whose phenotypic expression affects the length of the head of bacteriophage T4D. All mutants produce some phenotypically normal phage particles. Mutant pt21-34...Full Text Available

1973-08-01

4

Characterization of T-Even Bacteriophage Substructures

A plasmid carrying the bacteriophage lambda lysis genes under lac control was subjected to hydroxylamine mutagenesis, and mutations eliminating the host lethality of the S gene were selected. DNA sequence...Full Text Available

1986-09-01

5

Isolation and sequence determination of 5'-terminal oligonucleotide fragments of RNA transcripts synthesized by bacteriophage T3-induced RNA polymerase from T3 DNA.

Tail plates obtained from T4D amber mutants were examined with respect to sedimentation behavior, subunit molecular weights, amino acid composition, isoelectric points, and morphology. Intact plates...Full Text Available

1970-10-01

6

Termination of transcription by bacteriophage T3 RNA polymerase: homogeneous 3'-terminal oligonucleotide sequence of in vitro T3 RNA polymerase transcripts.

The nucleotide sequence of the 5'-terminal oligonucleotides produced by pancreatic RNase digestion of bacteriophage T3 RNA polymerase (EC 2.7.7.6) transcripts of T3 DNA has been determined. The sequence...Full Text Available

1980-07-01

7

High-cell Density Shake-flask Expression and Rapid Purification of the Large Fragment of Thermus aquaticus DNA Polymerase I Using a New Chemically and Temperature Inducible Expression Plasmid in Escherichia coli*

RNA was synthesized in vitro from a T3 DNA template by T3 RNA polymerase and subsequently separated into seven discrete size classes (molecular weights ranging between 0.21 x 10(6) and 6.2 x 10(6))...Full Text Available

1979-10-01

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Simulation of DNA electrophoresis through microstructures

We have developed a new expression vector, pcI^ts ind⁺, based upon the powerful rightward promoter of bacteriophage lambda, which is controlled by a temperature-sensitive...Full Text Available

2009-02-01

9

British Library Electronic Table of Contents (United Kingdom)

The dependence of the mobility of DNA molecules through an hexagonal array of micropillars on their length and the applied electric field was investigated and it was found that mobility is a nonmonotonic function of their length. Results also revealed that the size dependence of the DNA mobility depends on the applied electric field and there is a crossover around E 25 V/cm for the mobility of l-DNA and T4-DNA. These observations are explained in terms of the diffusion process inside the structure affected by the solvent and are modeled using the Langevin and its corresponding Fokker-Planck equations. The phenomenon is generalized under three regimes in a phase diagram relating the electric field and the DNA lengths. The model and the associated phase diagram described here provide an expl...

2007-01-01

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DNA alterations photosensitized by tetracycline and some of its derivatives

In vitro and in vivo activities of T4 endonuclease V mutants altered in the C-terminal aromatic region

Bacteriophage M13 mp10 DNA were irradiated with near-UV light in the presence of tetracycline derivatives and primed with synthetic oligonucleotide to be used for DNA synthesis using Escherichia coli DNA polymerase. Chain terminations were observed by denaturing polyacrylamide gel electrophoresis and mapped precisely. All the synthesis stops occurred before or at the level of guanine residues, showing that the photoreaction mediated by tetracycline derivatives led to a preferential alteration of guanine residues. These lesions were demonstrated to be induced in DNA through a pathway involving singlet oxygen. Tetracycline derivatives also photoinduced the breakage of the DNA sugar-phosphate backbone monitored by the conversion of supercoiled phi X174 DNA to a relaxed form. This lesion was shown to be initiated by hydroxyl radicals. The ...

1986-06-01

11

Studies of inactivation, retardation and accumulation of viruses in porous media by a combination of dye labeled and native bacteriophage probes

Genes encoding mutants of the thymine photodimer repair enzyme from bacteriophage T4 (T4 endonuclease V) having an amino acid substitution (T127M, W128A, W128S, Y129A, K130L, Y131A, Y132A) were constructed by use of a previously obtained synthetic gene and expressed in Escherichia coli under the control of the E. coli tryptophan promoter. An in vitro assay of partially fractionated mutant proteins for glycosylase activity was performed with chemically synthesized substrates containing a thymine photodimer. T127M and K130L showed almost the same activity as the wild-type protein. Although W128S, Y131A, and Y132A were slightly active, W128A and Y129A lost activity. The results indicated that the aromatic amino acids around position 130 may be important for the glycosylase activity. Mutant T127M was purified, and the Km value was found to be of the same order as that of the wild type ...

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Analysis of forward mutations induced by N-methyl-N'-nitro-N-nitrosoguanidine in the bacteriophage P22 mnt repressor gene

Not Available

2011-06-01

13

Organization of Bacteriophage Tail-Like Particles in Cells of Chromobacterium violaceum

We describe the isolation and genetic characterization of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-induced mutations in the phage P22 mnt repressor gene cloned in plasmid pBR322. Mutations in the mnt repressor gene or its operator on this plasmid, pPY98, confer a tetracycline resistance phenotype, whereas the wild-type plasmid confers tetracycline sensitivity. Cells carrying pPY98 were briefly exposed to MNNG to give 20 to 40% survival and a 50- to 100-fold increase in tetracycline-resistant cells. DNA sequence analysis showed that 29 to 30 MNNG-induced mutations were GC-to-AT transitions and one was an AT-to-GC transition. About 80% of the mutations are in three hotspots. This mutation spectrum is consistent with the proposed mechanism of mutagenic action of MNNG, which involves mispairing of an alkylated base, O/sup 6/-methylguanine. The mnt gene may be a useful target for determining mutagenic specificity at the nucleotide level because (i) forward ...

1986-04-01

14

Comparative removal of pyrimidine dimers from human epidermal keratinocytes in vivo and in vitro

A strain of Chromobacterium violaceum has been isolated which produces bacteriophage tail-like particles in high numbers. The extracellular morphology and the intracellular arrangement...Full Text Available

1972-05-01

15

Comparative removal of pyrimidine dimers from human epidermal keratinocytes in vivo and in vitro

We have compared the kinetics for repair of UV-induced cyclobutane pyrimidine dimers in the DNA of keratinocytes in human skin and in cell culture. A small area of the buttocks of volunteers was exposed to UVB-irradiation and biopsies were taken at various time intervals. Epidermal keratinocytes in culture from the same subjects were exposed to UVC with doses chosen to elicit comparable yields of dimers in cellular DNA. The initial density of pyrimidine dimers and the kinetics of their removal were assessed utilizing the dimer-specific T4 endonuclease V and sedimentation of the unlabeled DNA through alkaline sucrose gradients. The position of DNA in the gradients was determined using a monoclonal antibody against random sequences of single-stranded DNA in a sensitive immunoassay. The initial dimer frequency was 3.9-6.7 per 10(8) daltons ...

1988-10-01

16

Practical experience in a direct method use for T4 free fraction measurement obtained by dialysis; Experiencia pratica no uso de um metodo direto para a medida da fracao livre do T4 (T4L) obtida por dialise

We have compared the kinetics for repair of UV-induced cyclobutane pyrimidine dimers in the DNA of keratinocytes in human skin and in cell culture. A small area of the buttocks of volunteers was exposed to UVB-irradiation and biopsies were taken at various time intervals. Epidermal keratinocytes in culture from the same subjects were exposed to UVC with doses chosen to elicit comparable yields of dimers in cellular DNA. The initial density of pyrimidine dimers and the kinetics of their removal were assessed utilizing the dimer-specific T4 endonuclease V and sedimentation of the unlabeled DNA through alkaline sucrose gradients. The position of DNA in the gradients was determined using a monoclonal antibody against random sequences of single-stranded DNA in a sensitive immunoassay. The initial dimer frequency was 3.9-6.7 per 10(8) daltons ...

1988-01-01

17

Sustained Benefit Lasting One Year from T4 Instead of T3-T4 Sympathectomy for Isolated Axillary Hyperhidrosis

Short communication.

1993-10-01

18

Structural aberrations in group A Staphylococcus bacteriophages.

INTRODUCTIONLevel T4 video-assisted thoracoscopic sympathectomy proved superior to T3-T4 treatment for controlling axillary hyperhidrosis at the initial and six-month follow-ups...Full Text Available

2008-12-01

19

Experimental Differential Light-Scattering Correction to the Circular Dichroism of Bacteriophage T2

Six related Staphylococcus phages spontaneously produced various abnormal head and tail structures: (i) giant capsids which were tailed and apparently contained nucleic acid; (ii) regular and irregular...Full Text Available

1976-05-01

20

Monovalent cation-induced structure of telomeric DNA: The G-quartet model

Experimental techniques are presented that can be used to assay and correct for differential light scattering effects in circular dichroism spectra of biological macrostructures. The assay is based...Full Text Available

1973-01-01

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CDC45 and DPB11 are required for processive DNA replication and resistance to DNA topoisomerase I-mediated DNA damage

We have investigated the structures formed by oligonucleotides composed of two or four repeats of the telomeric sequences from Oxytricha and Tetrahymena. The Oxytricha four-repeat molecule (d(T4G4)4 = Oxy-4) forms structures with increased electrophoretic mobility in nondenaturing gels containing Na+, K+, or Cs+, but not in gels containing Li+ or no added salt. Formation of the folded structure results in protection of a set of dG's from methylation by dimethyl sulfate. Efficient UV-induced cross-links are observed in Oxy-4 and the related sequence from Tetrahymena (d(T2G4)4 = Tet-4), and join thymidine residues in different repeats. Models proposed to account for these data involve G-quartets, hydrogen-bonded structures formed from four guanosine residues in a square-planar array. We propose that the G-quartet structure must be dealt with in vivo by the telomere replication machinery.

1989-12-01

22

Bacteriophage P22 capsid size determination: Roles for the coat protein telokin-like domain and the scaffolding protein amino-terminus

The antitumor agent camptothecin targets DNA topoisomerase I by reversibly stabilizing a covalent enzyme-DNA intermediate. The subsequent collision of DNA replication forks with these drug-enzyme-DNA...Full Text Available

1999-09-28

23

British Library Electronic Table of Contents (United Kingdom)

Assembly of icosahedral capsids of proper size and symmetry is not understood. Residue F170 in bacteriophage P22 coat protein is critical for conformational switching during assembly. Substitutions at this site cause assembly of tubes of hexamerically arranged coat protein. Intragenic suppressors of the ts phenotype of F170A and F170K coat protein mutants were isolated. Suppressors were repeatedly found in the coat protein telokin-like domain at position 285, which caused coat protein to assemble into petite procapsids and capsids. Petite capsid assembly strongly correlated to the side chain volume of the substituted amino acid. We hypothesize that larger side chains at position 285 torque the telokin-like domain, changing flexibility of the subunit and intercapsomer contacts. Thus, a sing...

2011-01-01

24

Photocleavage and photofootprinting of DNA by azidoacridines

DNA Extraction by Isotachophoresis in a Microfluidic Channel

Short item.

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Model system using coliphage phi X174 for testing virus removal by air filters.

Abstract not provided

2011-08-10

26

Is there a benefit to sentinel lymph node biopsy in patients with T4 melanoma?

Short-term (15-min-duration) and long-term (5- to 6-day-duration) test procedures have been developed for determining the efficiency of the removal of bacteriophage phi X174 by air-sterilizing filters....Full Text Available

1992-03-01

27

British Library Electronic Table of Contents (United Kingdom)

BACKGROUND: Controversy exists as to whether patients with thick (Breslow depth >4 mm), clinically lymph node-negative melanoma require sentinel lymph node (SLN) biopsy. The authors examined the impact of SLN biopsy on prognosis and outcome in this patient population. METHODS: A review of the authors institutional review board-approved melanoma database identified 293 patients with T4 melanoma who underwent surgical excision between 1998 and 2007. Patient demographics, histologic features, and outcome were recorded and analyzed. RESULTS: Of 227 T4 patients who had an SLN biopsy, 107 (47%) were positive. The strongest predictors of a positive SLN included angiolymphatic invasion, satellitosis, or ulceration of the primary tumor. Patients with a T4 melanoma and a negative SLN had a significa...

2009-01-01

28

Ultrasensitive fluorescence detection of DNA

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

Progress on Ultrasensitive fluorescence detection of DNA is briefly described. (CBS)

1991-01-01

29

DNA Display I. Sequence-Encoded Routing of DNA Populations

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

30

uv photobiology: postreplication repair. [Escherichia coli, synchrotron radiation

Recently reported technologies for DNA-directed organic synthesis and for DNA computing rely on routing DNA populations through complex networks. The reduction of these ideas to practice has been limited...Full Text Available

2004-07-01

31

DNA, Genes and Chromosomes

The following topics are discussed: insertion of incorrect bases in DNA; ability of DNA polymerase to copy uv-irradiated DNA; role of enzymes in repair of DNA; effects of uv radiation on molecular weight of DNA; photoreactivation; repair of DNA in Escherichia coli and xp cells following uv radiation; and synchrotron radiation studies on DNA repair. (HLW)

1978-01-01

32

Today you will learn about the parts of DNA and what DNA, genes and chromosomes are. Today you will learn what DNA, genes and chromosomes are and the parts of the DNA molecule. Look at all of the websites, take whatever notes you need to. At the end of the assignment, be able to describle DNA, the parts of DNA, genes and chromosomes. Covers Biology Core Curriculum, ...

2007-11-07

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STR Training Materials

Choosing and Using a Plant DNA Barcode

Typing Workshop": [Introductions] [Intro, DNA Basics, and Historical Perspective] [DNA Extraction] [Validation and QA/QC] [DNA Quantitation] [PCR Amplification] [STR Loci and Kits]...

2011-04-29

34

Phylogeny of Mitochondrial DNA Macrohaplogroup N in India, Based on Complete Sequencing: Implications for the Peopling of South Asia

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

35

Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology

To resolve the phylogeny of the autochthonous mitochondrial DNA (mtDNA) haplogroups of India and determine the relationship between the Indian and western Eurasian mtDNA pools more precisely, a diverse...Full Text Available

2004-12-01

36

Failure to detect circulating DNA--anti-DNA complexes by four radioimmunological methods in patients with systemic lupus erythematosus.

BackgroundDNA repair is the general term for the collection of critical mechanisms which repair many forms of DNA damage such as methylation or ionizing radiation. DNA repair has...Full Text Available

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Differential targeting of Tetrahymena ORC to ribosomal DNA and non-rDNA replication origins

The presence of DNA-anti-DNA complexes in sera from patients with systemic lupus erythematosus (SLE) was investigated by two new radioimmunoassays (RIA) developed for this purpose and by measuring the...Full Text Available

1977-12-01

38

DNA ENCODING MODIFIED SIGNAL PEPTIDE

The Tetrahymena thermophila origin recognition complex (ORC) contains an integral RNA subunit, 26T RNA, which confers specificity to the amplified ribosomal DNA (rDNA) origin by base...Full Text Available

2009-02-04

39

J-STORE (Japan)

Full Text Available

2005-01-11

40

DNA double strand breakage after UV irradiation of yeast cells; DNA-Doppelstrangbrueche nach UV-Bestrahlung in Hefezellen

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

No abstract prepared.

2000-07-01

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41

Type IVB Secretion Systems of Legionella and Other Gram-Negative Bacteria

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 ...

2009-03-25

42

Role of serum carrier proteins in the peripheral metabolism and tissue distribution of thyroid hormones in familial dysalbuminemic hyperthyroxinemia and congenital elevation of thyroxine-binding globulin.

Type IV secretion systems (T4SSs) play a central role in the pathogenicity of many important pathogens, including Agrobacterium tumefaciens, Helicobacter pylori, and...Full Text Available

43

Optimal bone strength and mineralization requires the type 2 iodothyronine deiodinase in osteoblasts

To investigate the role of thyroxine-binding globulin (TBG) and albumin in the availability of thyroid hormones to peripheral tissues, comprehensive kinetic studies of thyroxine (T4) and triiodothyronine...Full Text Available

1987-08-01

44

Does amiodarone affect heart rate by inhibiting the intracellular generation of triiodothyronine from thyroxine?

Hypothyroidism and thyrotoxicosis are each associated with an increased risk of fracture. Although thyroxine (T4) is the predominant circulating thyroid hormone, target cell responses are determined...Full Text Available

2010-04-20

45

Ultrafast fluorescence dynamics of Sybr Green I/DNA complexes

The hypothesis that the antiarrhythmic drug amiodarone slows down the heart rate by its inhibitory action on the intracellular conversion of thyroxine (T4) to 3,5,3' triiodothyronine (T3) was investigated....Full Text Available

1984-05-01

46

British Library Electronic Table of Contents (United Kingdom)

The ultrafast dynamics of the DNA fluorescent dye Sybr Green I (SG) has been studied in buffer, single-stranded (ssDNA), double-stranded (dsDNA) and triple-stranded DNA (tsDNA). The fluorescence quantum yield of SG increases dramatically when bound to DNA (including tsDNA). The fluorescence dynamics of the free SG has shown two decay components with 0.15-0.4ps and 1.3-2.1ps time constants, depending on the fluorescence wavelength. Upon binding to DNA, the dynamics becomes slower exhibiting four decay components. This is mainly due to the restriction of the internal motions of the dye caused by the relatively rigid environment of the dye complexed with DNA.

2010-01-01

47

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

An immunochemical approach to the study of DNA damage and repair

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 ...

1989-03-01

48

Uracil-DNA glycosylase: Structural, thermodynamic and kinetic aspects of lesion search and recognition

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

49

UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications

Uracil appears in DNA as a result of cytosine deamination and by incorporation from the dUTP pool. As potentially mutagenic and deleterious for cell regulation, uracil must be removed from DNA....Full Text Available

2010-03-01

50

Transitions between distinct compaction regimes in complexes of multivalent cationic lipids and DNA

Cytosine methylation in DNA is a major epigenetic signal, and plays a central role in propagating chromatin status during cell division. However the mechanistic links between DNA methylation...Full Text Available

2009-01-01

51

Transient Hoogsteen Base Pairs in Canonical Duplex DNA

We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\\Phi_{\\rm NL}$, the complexes show dramatic DNA compaction down to essentially close packed DNA arrays with a DNA interaxial spacing $d_{\\rm DNA}=25\\AA$. A gradual increase in $\\Phi_{\\rm NL}$ does not lead to a continuous increase in $d_{\\rm DNA}$ as observed for DNA complexes of monovalent cationic lipids (CLs). Instead, distinct spacing regimes exist, with sharp transitions between them. Three packing states have been identified: (i) close packed, (ii) condensed, but not close packed, with $d_{\\rm DNA}=27-28\\AA$, and (iii) an expanded state, where $d_{\\rm DNA}$ increases gradually with ...

2008-01-01

52

The role of Holliday junction resolvases in the repair of spontaneous and induced DNA damage

Sequence-directed variations in the canonical DNA double helix structure that retain Watson-Crick base-pairing play important roles in DNA recognition, topology, and nucleosome positioning....Full Text Available

2011-02-24

53

The first international standard for antibodies to double stranded DNA.

DNA double-strand breaks (DSBs) and other lesions occur frequently during cell growth and in meiosis. These are often repaired by homologous recombination (HR). HR may result in the formation of DNA...Full Text Available

2011-09-01

54

Rearrangement of a common cellular DNA domain on chromosome 4 in human primary liver tumors.

This paper announces the availability of the first international standard for anti-double-stranded DNA (anti-dsDNA). The material, coded Wo/80, was obtained after recalcification of plasma taken from...Full Text Available

1988-09-01

55

Rapid, sensitive detection of Mycoplasma pneumoniae in simulated clinical specimens by DNA amplification.

Hepatitis B virus (HBV) DNA integration has been shown to occur frequently in human hepatocellular carcinomas. We have investigated whether common cellular DNA domains might be rearranged, possibly...Full Text Available

1988-02-01

56

Rapid technique of DNA-DNA in situ hybridisation on formalin fixed tissue sections using microwave irradiation.

The polymerase chain reaction (PCR) was investigated as a means of diagnosing Mycoplasma pneumoniae infections. The target DNA sequence was a 375-bp segment of the P1 virulence protein. This DNA segment...Full Text Available

1992-12-01

57

Non-contiguous regions of Z-DNA in a DNA dodecamer.

The relative sensitivities of different protocols for detecting cytomegalovirus nucleic acid sequences in histological specimens, using a biotinylated cDNA probe, were assessed. Several commonly used...Full Text Available

1987-08-01

58

Molecular Variability of Pseudallescheria boydii, a Neurotropic Opportunist

The conformation of the self-complimentary DNA dodecamer d(br5CGbr5CGAATTbr5CGbr5CG) has been investigated in a variety of salt and solvent conditions by one and two-dimensional 1H NMR. In low salt...Full Text Available

1989-10-11

59

Mitochondrial transmission during mating in Saccharomyces cerevisiae is determined by mitochondrial fusion and fission and the intramitochondrial segregation of mitochondrial DNA.

The sequences of the internal transcribed spacer (ITS) ribosomal DNA (rDNA) domain data obtained by restriction fragment length polymorphism analysis with 18S rDNA and fingerprinting (M13) for clinical...Full Text Available

2000-09-01

60

Mitochondrial DNA repair and association with aging - an update

To gain insight into the process of mitochondrial transmission in yeast, we directly labeled mitochondrial proteins and mitochondrial DNA (mtDNA) and observed their fate after the fusion of two cells....Full Text Available

1997-07-01

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Mitochondrial DNA haplogroups in early-onset Alzheimer's disease and frontotemporal lobar degeneration

Mitochondrial DNA is constantly exposed to oxidative injury. Due to its location close to the main site of reactive oxygen species, the inner mitochondrial membrane, mtDNA is more susceptible...Full Text Available

2010-08-01

62

How DNA coiling enhances target localization by proteins

BackgroundMitochondrial dysfunction, oxidative damage and the accumulation of somatic mutations in mitochondrial DNA (mtDNA) have been associated with certain neurodegenerative disorders....Full Text Available

63

Flow microfluorometric and spectrophotofluorometric analysis of DNA staining in mammalian cells

Many genetic processes depend on proteins interacting with specific sequences on DNA. Despite the large excess of nonspecific DNA in the cell, proteins can locate their targets rapidly. After initial...Full Text Available

2008-10-14

64

Evidence for increased in vitro recombination with insertion of human hepatitis B virus DNA.

The effects of various fixative agents, pH, ionic strength, stain concentration, and magnesium concentration on DNA staining with the antibiotics olivomycin, chromomycin A3, and mithramycin were examined with DNA in solution and in mammalian cells.

1977-01-01

65

Escherichia coli DnaA Forms Helical Structures Along the Longitudinal Cell Axis Distinct From MreB Filaments

Chromosomal translocation, deletion, and inversion/duplication directly linked to hepatitis B virus (HBV) DNA integration occur frequently in host DNA of human hepatocellular carcinomas. To test the...Full Text Available

1991-10-15

66

DNA sequencing using biotinylated dideoxynucleotides and mass spectrometry

SummaryDnaA initiates chromosomal replication in E. coli at a well regulated time in the cell-cycle. To determine how the spatial distribution of DnaA is related...Full Text Available

2009-05-01

67

DNA replication in vertebrates requires a homolog of the Cdc7 protein kinase

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MS) has been explored widely for DNA sequencing. The major requirement for this method is that the DNA sequencing fragments...Full Text Available

2001-11-01

68

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

CDC7 is an essential gene required for DNA replication in Saccharomyces cerevisiae. Cdc7p homologs have recently been identified in vertebrates, but their role in DNA...Full Text Available

1999-03-16

69

Construction of DNA recognition sites active in Haemophilus transformation.

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

70

Capture of genomic DNA on glass microscope slides

Competent Haemophilus cells recognize and preferentially take up Haemophilus DNA during genetic transformation. This preferential uptake is correlated with the presence on incoming DNA of an 11-base-pair...Full Text Available

1982-04-01

71

Analysis of European mtDNAs for Recombination

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

72

A rapid and efficient method for region- and strand-specific mutagenesis of cloned DNA.

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

73

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

The single-stranded viral DNA of an M13 phage recombinant containing the early promoter region of SV40 was hybridized with linear, double-stranded replicative form DNA of a related M13 phage containing...Full Text Available

1982-01-01

74

The influence of tertiary structural restraints on conformational transitions in superhelical DNA.

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

75

Telomeres in cancer and ageing

This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The...Full Text Available

1987-12-10

76

Phylogeny of Steinernema Travassos, 1927 (Cephalobina: Steinernematidae) Inferred From Ribosomal DNA Sequences and ...

Telomeres protect the chromosome ends from unscheduled DNA repair and degradation. Telomeres are heterochromatic domains composed of repetitive DNA (TTAGGG repeats) bound to an array of specialized...Full Text Available

2011-01-12

77

Molecular cloning and analysis of lymphokines. Volume 13

... 0877:POSTCS]2.0.CO;2 Phylogeny of Steinernema Travassos, 1927 (Cephalobina: Steinernematidae) Inferred From Ribosomal DNA ... C...

78

Methods in DNA methylation profiling

These proceedings collect papers on the subject of lymphokines. Topics include: DNA-cloning of mouse and human lymphokine genes, inteferons, interleukins, gene expression, tumor necrosis factors, and recombinant DNA.

1987-01-01

79

Metallointercalators and Metalloinsertors

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

80

Gene repression by minimal lac loops in vivo

Since the elucidation of the structure of double helical DNA, the construction of small molecules that recognize and react at specific DNA sites has been an area of considerable interest. In...Full Text Available

2007-11-28

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81

Detection of genetic mutations in repetitive DNA sequences in somatic human cells after low-dose irradiation

The inflexibility of double-stranded DNA with respect to bending and twisting is well established in vitro. Understanding apparent DNA physical properties in vivo is...Full Text Available

2010-12-01

82

DNA synthesis inhibition in mammalian cells as a test for mutagenic carcinogens

... 3-89701-147-6 0949-2224 245 p. animal cells dna genetic radiation effects

1998-03-01

83

DNA Analysis of mtDNA COI Gene in the Sharp-toothed Eel (Muraenesox cinereus Forskal) from Yeosu, Jinhae, Jeju, Goseoung, Jangheung and Haenam Populations in Korea Using PCR-aided RFLP

Current models of DNA repair of biological damage are reviewed correlating the similarity between carcinogenesis and mutagenesis theories. (PCS)

1979-01-01

84

Compressing DNA sequence databases with coil

Full Text Available

85

A Critical Reassessment of the Role of Mitochondria in Tumorigenesis

BackgroundPublicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious...Full Text Available

86

Comparison of susceptibility to pitting corrosion of AA2024-T4, AA7075-T651 and AA7475-T761 aluminium alloys in neutral chloride solutions using electrochemical noise analysis

BackgroundMitochondrial DNA (mtDNA) is being analyzed by an increasing number of laboratories in order to investigate its potential role as an active marker of tumorigenesis...Full Text Available

2005-11-01

87

ATP-dependent partitioning of the DNA template into supercoiled domains by Escherichia coli UvrAB

The susceptibility to pitting corrosion of AA2024-T4, AA7075-T651 and AA7475-T761 aluminium alloys was investigated in aqueous neutral chloride solution for the purpose of comparison using electrochemical noise measurement. The experimentally measured electrochemical noises were analysed based upon the combined stochastic theory and shot-noise theory using the Weibull distribution function. From the occurrence of two linear regions on one Weibull probability plot, it was suggested that there existed two stochastic processes of uniform corrosion and pitting corrosion; pitting corrosion was distinguished from uniform corrosion in terms of the frequency of events in the stochastic analysis. Accordingly, the present analysis method allowed us to investigate pitting corrosion independently. The susceptibility to pitting corrosion was appropriately evaluated by determining pit embryo formation rate in the stochastic analysis. The susceptibility was ...

2008-01-15

88

Potentially pathogenic free-living amoebae isolated from hospital wards with immunodeficient patients in Tehran, Iran

The helicase action of the Escherichia coli UvrAB complex on a covalently closed circular DNA template was monitored using bacterial DNA topoisomerase I, which specifically removes negative supercoils. In the presence of E. coli DNA topoisomerase I and ATP, the UvrAB complex gradually introduced positive supercoils into the input relaxed plasmid DNA template. Positive supercoils were not produced when E. coli DNA topoisomerase I was replaced by eukaryotic DNA topoisomerase I or when both E. coli and eukaryotic DNA topoisomerases I were added simultaneously. These results suggest that like other DNA helix-tracking processes, the ATP-dependent action of the UvrAM complex on duplex DNA simultaneously generates both positive and negative supercoils, which are not constrained by protein binding but are ...

89

British Library Electronic Table of Contents (United Kingdom)

This study investigated the occurrence of free-living amoebae (FLA) in immunodeficiency wards of hospitals in Tehran, Iran. A total of 70 dust and biofilm samples from wards serving transplant, pediatric (malignancies), HIV, leukemia and oncology patients of five university hospitals were collected and examined for the presence of FLA using culturing and molecular approaches. Based on the morphology of the amoebae in plate cultures, primer sets were applied for molecular identification of Acanthamoeba, vahlkampfiid amoebae and Hartmannella. Out of 70 samples, 37 (52.9%) were positive for FLA. Acanthamoeba belonged to the T4 genotype was the most prevalent isolate. Presence of the T4 genotype on medical instruments, including an oxygen mask in an isolation room of an immunodeficiency pediat...

2011-01-01

90

No association between affective and behavioral dysregulation and parameters of thyroid function in youths

British Library Electronic Table of Contents (United Kingdom)

Objective: Evidence from adults suggests that changes in thyroid function are associated with the development of bipolar disorder (BD) and severe mood dysregulation. A dysregulation profile based on the Child Behavior Checklist (CBCL-DP) describes a phenotype with severe mood problems in youth. The present study investigated whether altered thyroid functioning in youths is associated with the severe mood dysregulation symptoms characterized by the CBCL-DP. Methods: We analyzed the thyroid function data from 262 children and adolescents (n=262 for serum TSH, n=148 for free triiodothyronine [fT3] and n=153 for free thyroxine [fT4]) with their CBCL-DP composite score. We created and compared high CBCL-DP and low CBCL-DP subgroups with regard to their serum TSH, fT3 and fT4 concentrations as w...

2011-01-01

91

The influence of copper(II) on radiation-induced damages to DNA

Removal of uv-induced pyrimidine dimers from the replicated and unreplicated DNA of human fibroblasts

Short communication. 5 refs., 2 figs.

1996-12-31

92

RecA protein acts at the initiation of stable DNA replication in rnh mutants of Escherichia coli K-12.

Excision repair in uv irradiated human fibroblasts has been examined in portions of DNA replicating after irradiation versus those remaining unreplicated. Two approaches, one using a uv-endonuclease to estimate pyrimidine dimers remaining in DNA, the other using density labeling to measure excision resynthesis, indicate that the extent of repair is the same for both replicated and unreplicated DNA.

1978-01-01

93

Introduction to proceedings of Molecular Quantum Mechanics 2010: from methylene to DNA and beyond

Escherichia coli rnh mutants lacking RNase H activity are capable of recA+-dependent DNA replication in the absence of concomitant protein synthesis (stable DNA replication). In rnh dnaA::Tn10 and rnh...Full Text Available

1985-08-01

94

British Library Electronic Table of Contents (United Kingdom)

[image omitted

2010-01-01

95

Fusion of GFP to the M.EcoKI DNA methyltransferase produces a new probe of Type I DNA restriction and modification enzymes

Expressional Characterization of Dehydroascorbate Reductase cDNA in Transgenic Potato Plants

AbstractWe describe the fusion of enhanced green fluorescent protein to the C-terminus of the HsdS DNA sequence-specificity subunit of the Type I DNA modification methyltransferase M.EcoKI....Full Text Available

2010-07-23

96

DNA adducts and cancer risk in prospective studies: a pooled analysis and a meta-analysis

Full Text Available

2008-01-01

97

Comparison between DNA damage investigated by the ''Comet'' assay and chromosomal damage induced in human lymphocytes by radiation and chemicals

Udgivelsesdato: 2008-May

2008-01-01

98

Comparing the caveolae mediated endocytosis of two DNA-chitosan polyplexes

Short communication.

1995-08-20

99

Norwegian Open Research Archives (NORA)

Full Text Available

100

A rapid DNA extraction method for PCR amplification from wetland soils.

A nonlinear model for DNA dynamics

PMID:21545471

2011-05-04

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101

A Genetic Screen for Ribosomal DNA Silencing Defects Identifies Multiple DNA Replication and Chromatin-Modulating Factors

In this paper the thermal equilibrium number of solitons in DNA as a function of absolute temperature and the number of base pairs is calculated. These calculations are effected by modeling DNA as a Toda lattice with parameters chosen to match experimentally measured properties of DNA. It is found that a significant number of solitons is generated at physiological temperature. 23 refs., 2 figs.

1989-07-01

102

Rearrangement of a common cellular DNA domain on chromosome 4 in human primary liver tumors

Transcriptional silencing in Saccharomyces cerevisiae occurs at several genetic loci, including the ribosomal DNA (rDNA). Silencing at telomeres (telomere position effect [TPE])...Full Text Available

1999-04-01

103

Rearrangement of a common cellular DNA domain on chromosome 4 in human primary liver tumors

Hepatitis B virus (HBV) DNA integration has been shown to occur frequently in human hepatocellular carcinomas. The authors have investigated whether common cellular DNA domains might be rearranged, possibly by HBV integration, in human primary liver tumors. Unique cellular DNA sequences adjacent to an HBV integration site were isolated from a patient with hepatitis B surface antigen-positive hepatocellular carcinoma. These probes detected rearrangement of this cellular region of chromosomal DNA in 3 of 50 additional primary liver tumors studied. Of these three tumor samples, two contained HBV DNA, without an apparent link between the viral DNA and the rearranged allele; HBV DNA sequences were not detected in the third tumor sample. By use of a panel of somatic cell hybrids, these unique cellular DNA sequences were shown ...

1988-02-01

104

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

Hepatitis B virus (HBV) DNA integration has been shown to occur frequently in human hepatocellular carcinomas. The authors have investigated whether common cellular DNA domains might be rearranged, possibly by HBV integration, in human primary liver tumors. Unique cellular DNA sequences adjacent to an HBV integration site were isolated from a patient with hepatitis B surface antigen-positive hepatocellular carcinoma. These probes detected rearrangement of this cellular region of chromosomal DNA in 3 of 50 additional primary liver tumors studied. Of these three tumor samples, two contained HBV DNA, without an apparent link between the viral DNA and the rearranged allele; HBV DNA sequences were not detected in the third tumor sample. By use of a panel of somatic cell hybrids, these unique cellular DNA sequences were shown ...

105

Affinity purification of sequence-specific DNA binding proteins.

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 ...

1988-10-01

106

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

We describe a method for affinity purification of sequence-specific DNA binding proteins that is fast and effective. Complementary chemically synthesized oligodeoxynucleotides that contain a recognition site for a sequence-specific DNA binding protein are annealed and ligated to give oligomers. This DNA is then covalently coupled to Sepharose CL-2B with cyanogen bromide to yield the affinity resin. A partially purified protein fraction is combined with competitor DNA and subsequently passed through the DNA-Sepharose resin. The desired sequence-specific DNA binding protein is purified because it preferentially binds to the recognition sites in the affinity resin rather than to the nonspecific competitor DNA in solution. For example, a protein fraction that is enriched for transcription factor Sp1 can be further purified 500- to 1000-fold by ...

1986-08-01

107

Design of intelligent nucleobases and DNA HOMO mapping.

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

108

Relative Rates of Transcapillary Movement of Free Thyroxine, Protein-Bound Thyroxine, Thyroxine-Binding Proteins, and Albumin

We have designed a new nucleobase, benzodeazaadenine (BDA) that has a stronger charge transport ability than guanine and is not destroyed during charge transport process. By incorporating this new nucleobase into DNA, we demonstrated a protocol for real DNA nano-wire that is far superior to natural DNA. We also demonstrated that the selectivity for the interaction of Mn(II) ion with guanine N7 in G runs is a HOMO-controlled process, and as a consequence, the selectivity for G-metal ion interactions obtained by 15N-NMR studies would directly reflect the HOMO distribution of G-containing sequences in B-DNA. PMID:12903077

2002-01-01

109

Targeted integration of baboon endogenous virus in the BEVI locus on human chromosome 6.

The rate of appearance of labeled thyroxine (T4) and albumin in lymph from various areas after simultaneous i.v. injection of the labeled substances in conscious ambulatory sheep has been used to estimate...Full Text Available

1974-07-01

110

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

The infection of cultured human cells with baboon endogenous virus (BEV) frequently leads to an association of viral DNA with a specific genetic locus (termed BEVI, for baboon endogenous virus infection) on chromosome 6. Restriction endonuclease digestion of DNA from BEV-infected human cells and their derived somatic cell clones frequently revealed a common cellular DNA sequence in the proximity of one of the junctions between cellular DNA and the integrated virus. We propose that a short cellular DNA sequence, repeated on chromosome 6 and separated by unique DNA sequences, presents a high-affinity target for the integration of BEV in human cells. PMID:6401843

1983-01-13

111

A PAC containing the human mitochondrial DNA polymerase gamma gene (POLG) maps to chromosome 15q25

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

112

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

The human mitochondrial DNA (mtDNA) is a closed circular, 16,569-bp double-stranded DNA, encoding 13 genes whose protein products are subunits of the oxidative phosphorylation system required for synthesis of most of the ATP consumed by eukaryotic cells. Point mutations of the mtDNA that cause multi-tissue, loss-of-energy syndromes, called mitochondrial encephalomyopathies (e.g., MERRF and MELAS), have been identified. In addition, large-scale deletions of the human mtDNA have been identified and are the molecular bases for the neonatal and adolescent onset loss-of-energy syndromes Pearson and Kearns-Sayer, respectively. 5 refs., 1 fig.

1997-03-01

113

Werner syndrome protein interacts functionally with translesion DNA polymerases

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) ...

2007-05-05

114

Use of synthetic oligonucleotide DNA probes for identification and direct detection of Bacteroides forsythus in plaque samples.

Werner syndrome (WS) is characterized by premature onset of age-associated disorders and predisposition to cancer. The WS protein, WRN, encodes 3′ → 5′ DNA helicase and 3′...Full Text Available

2007-06-19

115

UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications

Oligonucleotide DNA probes complementary to the hypervariable region of the 16S rRNA of Bacteroides forsythus were tested for their specificity and sensitivity against reference and clinical isolates...Full Text Available

1991-10-01

116

The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue.

Cytosine methylation in DNA is a major epigenetic signal, and plays a central role in propagating chromatin status during cell division. However the mechanistic links between DNA methylation and histone methylation are poorly understood. A multi-domain protein UHRF1 (ubiquitin-like, containing PHD and RING finger domains 1) is required for DNA CpG maintenance methylation at replication forks, and mouse UHRF1-null cells show enhanced susceptibility to DNA replication arrest and DNA damaging agents. Recent data demonstrated that the SET and RING associated (SRA) domain of UHRF1 binds hemimethylated CpG and flips 5-methylcytosine out of the DNA helix, whereas its tandom tudor domain and PHD domain bind the tail of histone H3 in a highly methylation sensitive manner. We hypothesize that UHRF1 brings the two components (histones and DNA) carrying ...

2009-01-01

117

The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals

DNA methylation of cytosine residues is a widespread phenomenon and has been implicated in a number of biological processes in both prokaryotes and eukaryotes. This methylation occurs at the 5-position...Full Text Available

1995-01-25

118

Testing the Efficacy of a Multi-Component DNA-Prime/DNA-Boost Vaccine against Trypanosoma cruzi Infection in Dogs

BackgroundDuring the last ten years, major advances have been made in characterizing and understanding the evolution of mitochondrial DNA, the most popular marker of molecular biodiversity....Full Text Available

119

Telomeric DNA in normal and leukemic blood cells.

BackgroundTrypanosoma cruzi, the etiologic agent of Chagas Disease, is a major vector borne health problem in Latin America and an emerging...Full Text Available

120

Structure of plant nuclear and ribosomal DNA containing chromatin.

We studied telomeric DNA in leukemic cells as well as in normal T cells, B cells, monocytes, polymorphonuclear leukocytes, and bone marrow hematopoietic progenitor cells. No marked differences were...Full Text Available

1995-03-01

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121

Stretched DNA Investigated Using Molecular-Dynamics and Quantum-Mechanical Calculations

Digestion of plant chromatin from Brassica pekinensis and Matthiola incana with staphylococcus nuclease leads to a DNA repeat of 175 plus or minus 8 and a core size of 140 base pairs. DNase I digestion...Full Text Available

1979-11-10

122

Secondary structure formation and DNA instability at fragile site FRA16B

AbstractWe combined atomistic molecular-dynamics simulations with quantum-mechanical calculations to investigate the sequence dependence of the stretching behavior of duplex DNA. Our...Full Text Available

2010-01-06

123

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

Human chromosomal fragile sites are specific loci that are especially susceptible to DNA breakage following conditions of partial replication stress. They often are found in genes involved in tumorigenesis...Full Text Available

2010-05-01

124

Remobilization of Tol2 transposons in Xenopus tropicalis

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

125

Rational design of DNA sequences for nanotechnology, microarrays and molecular computers using Eulerian graphs

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

126

Protein Coding Sequence Identification by Simultaneously Characterizing the Periodic and Random Features of DNA Sequences

Nucleic acids are molecules of choice for both established and emerging nanoscale technologies. These technologies benefit from large functional densities of ‘DNA processing elements’...Full Text Available

2004-01-01

127

Phylogenetic Network for European mtDNA

Most codon indices used today are based on highly biased nonrandom usage of codons in coding regions. The background of a coding or noncoding DNA sequence, however, is fairly random, and can be characterized...Full Text Available

2005-01-01

128

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

The sequence in the first hypervariable segment (HVS-I) of the control region has been used as a source of evolutionary information in most phylogenetic analyses of mtDNA. Population genetic inference...Full Text Available

2001-06-01

129

Multiple integration sites for Moloney murine leukemia virus in productively infected mouse fibroblasts.

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

130

Molecular dynamics of a ?B DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation

The integration sites for viral DNA in cells infected with Moloney murine leukemia virus (M-MuLV) were studied by restriction endonuclease cleavage of cellular DNA followed by electrophoresis in agarose...Full Text Available

1979-06-01

131

Molecular DNA Systematic Analyses of East Asian Mammals: Sequence Variation of Cytochrome b Gene and Control Region of Mitochondrial DNA of Common Otter, Lutra lutra lutra L. (Mammalia, Carnivora) from Korea

The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target...Full Text Available

2008-09-01

132

Mechanism of cell death resulting from DNA interstrand cross-linking in mammalian cells

Full Text Available

2004-09-01

133

Intracellular Copper Does Not Catalyze the Formation of Oxidative DNA Damage in Escherichia coli?

DNA interstrand cross-links (ICLs) are critical cytotoxic lesions produced by cancer chemotherapeutic agents such as the nitrogen mustards and platinum drugs; however, the exact mechanism of ICL-induced...Full Text Available

2011-08-01

134

Insertion of a Bulky Rhodium Complex into a DNA Cytosine-Cytosine Mismatch: An NMR Solution Study

Because copper catalyzes the conversion of H₂O₂ to hydroxyl radicals in vitro, it has been proposed that oxidative DNA damage may be an important component of copper toxicity....Full Text Available

2007-03-01

135

In Vivo Modulation of T-DNA Encoded Amidohydrolase Activity in Transformed Tobacco Cells ¹

The bulky octahedral complex, Rh(bpy)₂chrysi³⁺ (chrysi = 5, 6- chrysenequinone diimine), binds single base mismatches in a DNA duplex with micromolar binding affinities...Full Text Available

2007-10-10

136

Improved DNA Sequencing Accuracy and Detection of Heterozygous Alleles Using Manganese Citrate and Different Fluorescent Dye Terminators

Auxin autonomous growth of most crown gall tumor cells requires the expression of two auxin biosynthesizing genes (tms 1 and tms 2) from the T-DNA of Agrobacterium...Full Text Available

1991-04-01

137

Impaired replication dynamics at the FRA3B common fragile site

The use of dideoxynucleotide triphosphates labeled with different fluorescent dyes (dye terminators) is the most versatile method for automated DNA sequencing. However, variation in peak heights reduces...Full Text Available

1999-06-01

138

Identification and Functional Relevance of de novo DNA Methylation in Cancerous B-Cell Populations

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

139

Evidence for a lack of DNA double-strand break repair in human cells exposed to very low x-ray doses

Epigenetic remodeling is a hallmark of cancer, with the frequent acquisition of de novo DNA methylation in CpG islands. However, the functional relevance of de novo...Full Text Available

2010-03-01

140

Epitope tagging of endogenous proteins for genome wide Chromatin immunoprecipitation analysis

DNA double-strand breaks (DSBs) are generally accepted to be the most biologically significant lesion by which ionizing radiation causes cancer and hereditary disease. However, no information on the...Full Text Available

2003-04-29

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

Endogenous Fluctuations of DNA Topology in the Chloroplast of Chlamydomonas reinhardtii

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

142

Efficient preparation of internally modified single-molecule constructs using nicking enzymes

DNA supercoiling in the chloroplast of the unicellular green alga Chlamydomonas reinhardtii was found to change with a diurnal rhythm in cells growing in alternating 12-h dark–12-h...Full Text Available

1998-12-01

143

Effect of misonidazole pretreatment on nitrogen mustard-induced DNA cross-linking in mouse tissues in vivo.

Investigations of enzymes involved in DNA metabolism have strongly benefited from the establishment of single molecule techniques. These experiments frequently require elaborate DNA substrates, which...Full Text Available

2011-02-01

144

Developmental abnormalities and epimutations associated with DNA hypomethylation mutations.

In the present study we have used the alkaline elution technique to study the effect of misonidazole (MISO) on the initial amount of DNA cross-linking in various normal and neoplastic tissues of C3H...Full Text Available

1984-12-01

145

Detection of genetic mutations in repetitive DNA sequences in somatic human cells after low-dose irradiation; Nachweis genetischer Veraenderungen in repetitiven DNA-Sequenzen in somatischen menschlichen Zellen nach Bestrahlung im niedrigen Dosisbereich

A number of aberrant morphological phenotypes were noted during propagation of the Arabidopsis thaliana DNA hypomethylation mutant, ddm1, by repeated self-pollination. Onset of a spectrum of morphological...Full Text Available

1996-10-29

146

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

No abstract prepared

1998-03-01

147

Design of 240,000 orthogonal 25mer DNA barcode probes

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

148

DNA replication in Escherichia coli mutants that lack protein HU.

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

149

DNA ploidy, nuclear size, proliferation index and DNA-hypomethylation in ovarian cancer

DNA replication in Escherichia coli cells lacking protein HU was studied. HU has been suggested to be involved in the initiation of replication from in vitro studies. The isolated HU mutants, however,...Full Text Available

1989-10-01

150

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

ObjectiveThe present study was undertaken to analyze the impact of epigenetic alterations with a main focus on nuclear area, aneuploidy, hyperploidy, and proliferation...Full Text Available

2011-04-01

151

DNA alterations detected in the progeny of paternally irradiated Japanese medaka fish (Oryzias latipes).

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

152

Cation Involvement in Telomestatin Binding to G-Quadruplex DNA

A nonmammalian test system for germ-cell mutagenesis has been developed by using the Japanese medaka fish. We describe a system for detecting DNA alterations in F1 progeny descended from the gamma-irradiated...Full Text Available

1995-01-03

153

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

The binding mode of telomestatin to G-quadruplex DNA has been investigated using electrospray mass spectrometry, by detecting the intact complexes formed in ammonium acetate. The mass measurements show...Full Text Available

154

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

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

155

Biotin-labeled hairpin oligonucleotides: probes to detect double-strand breaks in DNA in apoptotic cells.

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 ...

2011-07-01

156

A second origin of DNA plus-strand synthesis is required for optimal human immunodeficiency virus replication.

Hairpin oligonucleotides were synthesized with stems ending in a double-stranded structure, which can be ligated to double-strand breaks in DNA, and with loops that contain nucleotides modified by the...Full Text Available

1998-04-01

157

A double antibody solid phase assay for DNA autoantibodies for clinical use.

We recently reported that human immunodeficiency virus type 1 (HIV-1) unintegrated linear DNA displays a discontinuity in its plus strand, precisely defined by a second copy of the polypurine tract...Full Text Available

1992-05-01

158

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

DNA antoantibodies in serum will bind to antigen-coated polystyrene tubes and can be detected by radiolabelled anti-immunoglobulin. The method is quantitative, gives information on the antibody class...Full Text Available

1976-08-01

159

A Novel Function of the DNA Repair Gene rhp6 in Mating-Type Silencing by Chromatin Remodeling in Fission Yeast

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

160

Primer for the Potato Specific Internal Control DNA and Screening Method for the Genetically Modified Potatoes by Competitive Duplex-PCR

Recent studies have indicated that the DNA replication machinery is coupled to silencing of mating-type loci in the budding yeast Saccharomyces cerevisiae, and a similar silencing mechanism...Full Text Available

1998-09-01

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

161

Genomic Careers: Interactive Videos

Full Text Available

2002-12-01

162

Medline Plus

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

163

Detection of Mitochondrial DNA Mutations in Mammary ...

Chromosomal localization and cDNA sequence of human BTEB, a GC box binding protein

... Loss of Heterozygosity in Normal Breast Epithelial Tissue and Benign Breast Lesions in BRCA1/2 Carriers with Breast Cancer. ...

2004-09-01

164

Primary organization of nucleosomal core particles is invariable in repressed and active nuclei from animal, plant and yeast cells.

Human BTEB cDNA clones have been isolated, sequenced, and the corresponding gene has been assigned to human chromosome 9, region q13, by fluorescent in situ hybridization and DNA blot analysis using DNAs from hybrid cell clones containing a single human chromosome. The cDNA clone encodes a polypeptide of 244 amino acids whose sequence shows a high sequence similarity with the rat BTEB (98% amino acid identity).

1993-09-01

165

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

A refined map for the linear arrangement of histones along DNA in nucleosomal core particles has been determined by DNA-protein crosslinking. On one strand of 145-bp core DNA, histones are aligned in...Full Text Available

1985-05-24

166

Induction of an abortive and futile DNA repair process in E. coli by the antitumor DNA bifunctional intercalator, ditercalinium: role in polA in death induction.

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

167

Ditercalinium, an antitumor bifunctional intercalator which forms a high affinity reversible complex with DNA, was found to be specifically cytotoxic for polA and lig7 E. coli strains. In the polA strain,...Full Text Available

1988-02-11

168

DNA repair genes

Cloning of rice DNA and identification of tRNA gene clones

Fission yeast S. pombe is assumed to be a good model for cloning of human DNA repair genes, because human gene is normally expressed in S. pombe and has a very similar protein sequence to yeast protein. We have tried to elucidate the DNA repair mechanisms of S. pombe as a model system for those of mammals. (J.P.N.)

1995-12-01

169

Cellular DNA region involved in induction of thymic lymphomas (Mlvi-2) maps to mouse chromosome 15.

DNA from 48 hr germinated rice embryos was cut with restriction endonuclease Bam H1 and cloned to the Bam H1 site on plasmid pBR 322. The clones containing recombinant DNA were selected by their sensitivity to tetracycline and resistance to ampicillin. Using /sup 32/P-labelled rice embryos tRNA as a probe two clones were identified to contain tRNA genes by colony hybridization.

1981-10-20

170

A rapid and simple DNA extraction procedure to detect Salmonella spp. and Listeria monocytogenes from fresh produce using real-time PCR

Two cellular DNA regions representing common domains for proviral DNA integration ( Mlvi -1 and Mlvi -2) have been identified in Moloney murine leukemia virus-induced rat thymic lymphomas. Cellular...Full Text Available

1984-05-01

171

A detailed comparison of the 5'-end of the ovalbumin gene cloned from chicken oviduct and erythrocyte DNA.

DNA isolation procedures significantly influence the outcome of PCR-based detection of human pathogens. Unlike clinical samples, DNA isolation from food samples such as fresh and fresh-cut produce has remained a formidable task and has hampered the sensitivity and accuracy of molecular methods. We...

172

Isothermal, total strain-controlled cyclic deformation of GGG-60 at temperatures of 20 C {<=}T {<=}500 C. Pt. 1; Isotherme totaldehnungskontrollierte Wechselverformung von GGG-60 im Temperaturbereich 20 C {<=}T {<=}500 C. T. 1

We have examined homologous fragments of DNA cloned from two different tissues for changes in the dNA sequence which might be related to tissue specific gene expression. The 5' end of the chicken ovalbumin...Full Text Available

1980-10-10

173

W_3-algebra constructed from the SU(3) parafermion

The paper examines the influence of various total strain amplitudes and mean strains on the cyclic deformation processes in GGG-60 at temperatures of 20 C, 350 C, and 500 C ,the total strain amplitudes being varied between 1.0 permille {<=}{epsilon}{sub a,t}{<=}3.8 permille , and the mean strains between -4.0 permille {<=}{epsilon}{sub m,t}{<=}4.0 permille . - [Deutsch] In der Arbeit wird der Einfluss unterschiedlicher Totaldehnungsamplituden und Mitteldehnungen auf das Wechselverformungsverhalten von GGG-60 bei Temperaturen von 20 C, 350 C und 500 C untersucht. Dabei werden die Totaldehnungsamplituden zwischen 1,0 permille {<=} {epsilon}{sub a,t} {<=} 3,8 permille und die Mitteldehnungen zwischen -4,0 permille {<=} {epsilon}{sub m,t} {<=} 4,0 permille variiert. (orig./MM)

1995-01-01

174

S-matrix elements and covariant tachyon action in type 0 theory

A construction of a W_3-algebra for the SU(3) parafermion is proposed. The details of the calculation are given, in which the Z-algebra technique is used instead of the popular free field realization. We find that the W_3-algebra is closed at level k=3, and the central charge of the underlying algebra is different from known series of Fateev-Lykyanov W-algebras; as a by-product we get a field T"("4")(z), whose conformal dimension is 4, and is null at k=3. ((orig.)).

8730-01-01

175

Solution state hybridization detection using time-resolved fluorescence anisotropy of quantum dot-DNA bioconjugates

We evaluate the sphere level S-matrix element of two tachyons and two massless NS states, the S-matrix element of four tachyons, and the S-matrix element of two tachyons and two Ramond-Ramond vertex operators, in type 0 theory. We then find an expansion for theses amplitudes that their leading order terms correspond to a covariant tachyon action. To the order considered, there are no T4, T2(-bar T)2, T2H2, nor T2R tachyon couplings, whereas, the tachyon couplings FF-bar T and T2F2 are non-zero.

2005-01-17

176

British Library Electronic Table of Contents (United Kingdom)

In this Letter, we demonstrate the application of time-resolved fluorescence anisotropy measurements to detect solution state hybridization of streptavidin conjugate (CdSe)ZnS quantum dots (QD). The study was performed on samples containing 10nM QD incubated with 800nM DNA. We show that the rotational correlation time of QD-DNA constructs increases significantly upon hybridization with values of 330ns (QD-ssDNA) and 1.3ms (QD-dsDNA), corresponding to a diameter of 14nm and 23nm respectively. The present study opens a new modality for hybridization detection using quantum dots.

2010-01-01

177

Mitochondrial DNA background modulates the assembly kinetics of OXPHOS complexes in a cellular model of mitochondrial disease

British Library Electronic Table of Contents (United Kingdom)

Lebers hereditary optic neuropathy (LHON), the most frequent mitochondrial disorder, is mostly due to three mitochondrial DNA (mtDNA) mutations in respiratory chain complex I subunit genes: 3460/ND1, 11778/ND4 and 14484/ND6. Despite considerable clinical evidences, a genetic modifying role of the mtDNA haplogroup background in the clinical expression of LHON remains experimentally unproven. We investigated the effect of mtDNA haplogroups on the assembly of oxidative phosphorylation (OXPHOS) complexes in transmitochondrial hybrids (cybrids) harboring the three common LHON mutations. The steady-state levels of respiratory chain complexes appeared normal in mutant cybrids. However, an accumulation of low molecular weight subcomplexes suggested a complex I assembly/stability defect, which was ...

2008-01-01

178

Metallointercalators and Metalloinsertors

Metallo-intercalators and metallo-insertors.

Since the elucidation of the structure of double helical DNA, the construction of small molecules that recognize and react at specific DNA sites has been an area of considerable interest. In particular, the study of transition metal complexes that bind DNA with specificity has been a burgeoning field. This growth has been due in large part to the useful properties of metal complexes, which possess a wide array of photophysical properties and allow for the modular assembly of an ensemble of recognition elements. Here we review recent experiments in our laboratory aimed at the design and study of octahedral metal complexes that bind DNA non-covalently and target reactions to specific sites. Emphasis is placed both on the variety of methods employed to confer site-specificity and upon the many applications for these complexes. Particular attention is given to the family of complexes recently designed that ...

2007-09-20

179

Investigation by physical methods of the possible role of telomeres in DNA in aging process

Since the elucidation of the structure of double helical DNA, the construction of small molecules that recognize and react at specific DNA sites has been an area of considerable interest. In particular, the study of transition metal complexes that bind DNA with specificity has been a burgeoning field. This growth has been due in large part to the useful properties of metal complexes, which possess a wide array of photophysical attributes and allow for the modular assembly of an ensemble of recognition elements. Here we review recent experiments in our laboratory aimed at the design and study of octahedral metal complexes that bind DNA non-covalently and target reactions to specific sites. Emphasis is placed both on the variety of methods employed to confer site-specificity and upon the many applications for these complexes. Particular attention is given to the family of complexes recently designed that ...

2007-09-20

180

Functional domain analysis of glass, a zinc-finger-containing transcription factor in Drosophila.

The interaction energies between the different types of bases of a single strand of DNA molecule have been calculated. Using these original values of energies the harmonic behavior of a number of base patterns of DNA has been studied. In view of the great interest aroused by the discovery of the role of the telomere segment of the DNA in the replication process and its possible link with the aging process, we have investigated, with simple models, the harmonic behavior of the telomeric pattern of bases as well as the thermodynamic response in the biological system. With these results a conclusion on the probable role of the telomeric pattern on aging has also been drawn. Here the calculated values of harmonic frequencies of the telomeric pattern of bases and of other possible patterns show that the telomeric pattern is associated with the highest vibrational frequency among all patterns of base combinations at the ...

2003-01-01

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181

DNA repair: As influenced by age, nutrition, and exposure to toxic substances

The glass gene is required for proper photo-receptor differentiation during development of the Drosophila eye glass codes for a DNA-binding protein containing five zinc fingers that we show is a transcriptional activator. A comparison of the sequences of the glass genes from two species of Drosophila and a detailed functional domain analysis of the Drosophila melanogaster glass gene reveal that both the DNA-binding domain and the transcriptional-activation domain are highly conserved between the two species. Analysis of the DNA-binding domain of glass indicates that the three carboxyl-terminal zinc fingers alone are necessary and sufficient for DNA binding. We also show that a deletion mutant of glass containing only the DNA-binding domain can behave in a dominant-negative manner both in vivo and in a cell culture assay that measures transcriptional activation. PMID:7604032

1995-07-01

182

Bioinformatic analysis of BBTV satellite DNA in Hainan

In evaluating the risk associated with low levels of exposure to toxicants, it is clear that DNA repair, one of the main defenses against agent damage, is not a constant. It can be modified by age, time of day, and physiological state. Nutrition, especially caloric restriction (CR), can modify almost every step in the process of protecting genomic integrity. And history of exposure can modify DNA repair. Thus, the conditions of exposure are almost as important to toxicity as the exposure itself, even at the level of DNA repair. Extrapolation from high to low dose, to be consistent with what is known, should be less a mathematical exercise than an exercise in toxicological judgement, which puts the exposure in proper perspective. This appears to be true at almost every level in the process including a response with a toxic stimulus, even those thought to be very basic, such as DNA repair.

183

British Library Electronic Table of Contents (United Kingdom)

Banana bunchy top virus (BBTV), family Nanaviridae, genus Babuvirus, is a single stranded DNA virus (ssDNA) that causes banana bunchy top disease (BBTD) in banana plants. It is the most common and most destructive of all viruses in these plants and is widespread throughout the Asia-Pacific region. In this study we isolated, cloned and sequenced a BBTV sample from Hainan Island, China. The results from sequencing and bioinformatics analysis indicate this isolate represents a satellite DNA component with 12 DNA sequences motifs. We also predicted the physical and chemical properties, structure, signal peptide, phosphorylation, secondary structure, tertiary structure and functional domains of its encoding protein, and compare them with the corresponding quantities in the replication initiatio...

2011-01-01

184

AFM Imaging of SWI/SNF action: mapping the nucleosome remodeling and sliding

Effects of perinatal exposure to low doses of cadmium or methylmercury on thyroid hormone metabolism in metallothionein-deficient mouse neonates

We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA complexed length distribution and nucleosome position in various contexts. First, we show that differences in the nucleo-proteic structure observed between conventional H2A and H2A.Bbd variant nucleosomes induce quantitative changes in the in the length distribution of DNA complexed with histones. Then, the sliding action of remodeling complex SWI/SNF is characterized through the evolution of the nucleosome position and wrapped DNA length mapping. Using a linear energetic model for the distribution of DNA complexed length, we extract the net wrapping energy of DNA onto the histone octamer, and compare it to previous studies.

2007-01-01

185

[Development of efficient DNA isolation procedures for Cryptosporidium and Trichinella PCR detection in fecal samples].

Perinatal exposure to cadmium (Cd) or methylmercury (MeHg) results in impaired neurodevelopment. Thyroid hormone is essential for normal brain development. However, the issue whether Cd or MeHg, especially at low doses, interrupts thyroid hormone action remains to be investigated. In the present study, effects of perinatal exposure to low levels of Cd or MeHg on thyroid hormone metabolism were examined using metallothionein I and II (MT-I/II) null or wild-type neonatal mice. Dams were exposed to 10 mg/L water of Cd or 5 mg/kg chow of MeHg from gestational day 0 to post-natal day 10 (PND 10). Sera, livers and brains were collected from neonates on PND 10. Iodothyronine deiodinase activities and serum thyroxine (T4) concentrations were measured. MeHg exposure failed to induce changes in serum T4 levels and liver type 1 deiodinase (D1) and brain type 2 deiodinase (D2) activities regardless of the MT ...

2006-11-10

186

Fossil avian eggshell preserves ancient DNA

PCR detection of genetic material of the parasites present in faeces may be an alternative for microscopic and serological tests routinely used for diagnosing parasitic enteral infections. However, small amount of target DNA combined with low efficiency of total DNA extraction, and presence of PCR inhibitors in the samples to be amplified, may cause false negative detection results. The aim of this work was to evaluate the impact of DNA isolation procedure used on the amplification of DNA fragments from the genomes of protozoan Cryptosporidium parvum and the nematode Trichinella spiralis. Two methods based on different principles of biological material lysis were evaluated; NucliSENS miniMAG employing simultaneously applied chemical lysis and mechanical disruption or mechanical disruption followed by enzymatic lysis in case of QIAamp DNA Stool Mini Kit. Both of the analyzed systems ...

2009-01-01

187

Use of the parmbsc0 force field and trajectory analysis to study the binding of netropsin to the DNA fragment (5'CCAATTGG)2 in the presence of excess NaCl salt in aqueous solution

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 ...

2010-01-01

188

British Library Electronic Table of Contents (United Kingdom)

The parmbsc0 force field was applied to study in detail the binding of netropsin, at a salt concentration of 0.28M Na^+, to the minor groove of an 8-mer (5'CCAATTGG)2 DNA duplex forming a netropsin.DNA complex which previously has been characterized by X-ray crystallography, albeit with the use of closely related DNA duplexes. The X-ray structure revealed that the terminal guanidinium and amidinium groups of netropsin interact with the extreme ends of the palindromic AATT sequence of the receptor DNA. The parmbsc0 parameters of B-DNA and AMBER v9 parameters of netropsin generated a stable 6ns molecular dynamics (MD) trajectory for a 1:1 class I binding motif of this complex. Trajectory analysis for the salt and hydration effects on the binding of netropsin to the 8-mer DNA duplex revealed ...

2011-01-01

189

The inhibition of mitochondrial DNA polymerase gamma from animal cells by intercalating drugs.

Radioadapted chicken embryo cells: challenge specificity and alterations in higher-order DNA structure

DNA polymerase gamma from purified nuclei of EMT-6 cells (mice) seems to be identical to the mitochondrial DNA polymerase from the same source following several criteria. These two enzyme activities are strongly inhibited by ethidium bromide and acriflavin, while proflavin, acridine orange, daunomycin and chloroquine inhibition is less pronounced. In the case of DNA polymerases alpha and beta very little inhibition by ethidium bromide was observed. Intercalation of this dye in a poly dA-dT 12-18 template-primer was studied spectrophotometrically under conditions similar to those in the in vitro DNA polymerase assay. The polymerase assay. The inhibition by this drug of the mitochondrial DNA polymerase gamma activity was shown to be competitive at varying concentrations of TTP while the inhibition was of the non-competitive type at different concentrations of poly dA-dT 12-18. We ...

1978-06-01

190

Organisms posses enzymes that function in the repair of DNA damaged by radiations, chemicals and metabolic events

Radioadapted chicken embryo cells (X-irradiation in ovo with 10 cGy at the 14th day of development with priming periods of 24 h) were treated in vitro by challenge doses of 14 different DNA- and/or chromatin-interactive agents, including X-rays. A decrease in the cellular damage, as measured by scheduled DNA synthesis, was only observed with X-irradiation. Sedimentation of nucleoids as well as viscosity of alkaline lysates from ethidium bromide (0.35-400 {mu}g/ml)-, vovobiocin (125-1800 {mu}g/ml)-, and hyperthermia (30 min at 43 and 45 )-treated cells suggest a higher tendency of radioadapted cells to undergo positive DNA supercoiling. When DNA from adapted and non-adapted chicken embryo cells was used as substrate, neither its digestion by DNase I nor the inhibition of DNase I activity by various DNA-interactive agents was changed in primed cells. From the previous investigations ...

1996-03-01

191

p73 protein regulates DNA damage repair.

This report briefly describes the studies on the mechanism of in vivo DNA repairing by the author in Research Reactor Institute, Kyoto Univ. for the past 30 years. First, the ability of UV radiation to induce transformation was investigated with viral DNA. The formation of thymine-thymine dimer was found harmful to organisms and such dimers were removable by UV-radiation at a low frequency. The mutability was determined in three different E.coli strains with mutator gene, mutT, mutS or mutL. The ability to excise 8-oxoguanin developed in primer DNA was deficient in mutT and miss-pairing left after DNA replication could not be recovered in mutL and mutS strains. Further, DNA repairing mechanism was investigated in other microorganisms; single-strand cleavage caused by exposure to BNCB radiation (boron-neutron-captured beam) could not be repaired in E. coli. Whereas for Deinococcus ...

1998-01-01

192

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

Although the p53 tumor suppressor is relatively well characterized, much less is known about the functions of other members of the p53 family, p73 and p63. Here, we present evidence that in specific pathological conditions caused by exposure of normal cells to bile acids in acidic conditions, p73 protein plays the predominant role in the DNA damage response. These pathological conditions frequently occur during gastric reflux in the human esophagus and are associated with progression to esophageal adenocarcinoma. We found that despite strong DNA damage induced by bile acid exposure, only p73 (but not p53 and p63) is selectively activated in a c-Abl kinase-dependent manner. The activated p73 protein induces DNA damage repair. Using a human DNA repair PCR array, we identified multiple DNA repair genes affected by p73. Two glycosylases involved in base excision repair, SMUG1 and MUTYH, ...

2011-09-01

193

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

High molecular weight DNA from pleroceroid larvae of the tapeworm Spirometra mansonoides was purified from isolated nuclei by conventional techniques. The DNA so isolated has a melting temperature (Tm) of 87 degrees C and a guanine plus cytosine (G/C) content of 44%. 5-Methyl cytosine could not be detected in plerocercoid DNA by HPLC analysis of DNA hydrolysates, by radiolabeling 5'-termini of MspI digests with polynucleotide kinase, or by comparing restriction patterns generated by MspI and HpaII. Renaturation kinetics demonstrated that the genome of S. mansonoides contains repetitive as well as single copy sequences and has a genome size estimated at approx. 1.6 X 10(9) bp. Hybridization was carried out between plerocercoid DNA and cDNAs for human beta-actin, alpha-tubulin and growth hormone (hGH). Rationale for this analysis was based on known homologies among actin and tubulin ...

1990-06-21

194

Photocatalytic probing of DNA sequence by using TiO{sub 2}/dopamine-DNA triads.

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 ...

2003-08-17

195

Molecular cloning, cDNA sequence, and chromosomal assignment of the human radixin gene and two dispersed pseudogenes

A method to control charge transfer reaction in DNA using hybrid nanometer-sized TiO{sub 2} nanoparticles was developed. In this system extended charge separation reflects the sequence of DNA and was measured using metallic silver deposition or by photocurrent response. Light-induced extended charge separation in these systems was found to be dependent on the DNA-bridge length and sequence. The yield of photocatalytic deposition of silver was studied in systems having GG accepting sites imbedded in AT runs at varying distances from the TiO{sub 2} nanoparticle surface. Weak distance dependence of charge separation indicative of a hole hopping through mediating adenine (A) sites was found. The quantum yield of silver deposition in the system having a GG accepting site placed 8.5 {angstrom} from the nanoparticle surface was found to be {Phi} = 0.70 (70%) and {Phi} = 0.56 (56%) for (A){sub n} and (AT){sub n/2} bridge, ...

2007-10-15

196

Electrochemical detection of DNA hybridization based on silver-enhanced gold nanoparticle label

Radixin is a cytoskeletal protein that may be important in linking actin to the plasma membrane. Recent cloning of the murine and porcine radixin cDNAs revealed a protein highly homologous to ezrin and moesin. The authors have cloned and sequenced the human radixin cDNA and found the predicted amino acid sequence for the human protein to be nearly identical to those predicted for radixin in the two other species. By Southern analyses of Chinese hamster x human somatic cell hybrid DNA and of PCR products derived from hybrids, the coding gene (RDX) was mapped to 11q. Fluorescence chromosomal in situ hybridization with a cDNA plasmid further localized this gene to band 11q23. However, PCR amplification with [open quotes]radixin-specific[close quotes] primers on the hybrid DNA panel yielded an additional, very similar DNA sequence that was further characterized by direct sequencing of ...

1993-04-01

197

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

An electrochemical detection method for analyzing sequence-specific DNA using gold nanoparticle DNA probes and subsequent signal amplification step by silver enhancement is described. The assay relies on the electrostatic adsorption of target oligonucleotides onto the sensing surface of the glassy carbon electrode (GCE) and its hybridization to the gold nanoparticle-labeled oligonucleotides DNA probe. After silver deposition onto gold nanoparticles, binding events between probe and target were monitored by the differential pulse voltammetry (DPV) signal of the large number of silver atoms anchored on the hybrids at the electrode surface. The signal intensity difference permits to distinguish between the match of two perfectly matched DNA strands and the near-perfect match where just one base pair was wrong. Coupled with this 'nanoparticle-promoted' reduction of silver signal ...

2002-10-03

198

An immunochemical approach to the study of DNA damage and repair

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 ...

1992-05-01

199

Topoisomerases of kinetoplastid parasites: why so fascinating?

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 ...

1992-05-01

200

British Library Electronic Table of Contents (United Kingdom)

Summary DNA topoisomerases are the key enzymes involved in carrying out high precision DNA transactions inside the cells. However, they are detrimental to the cell when a wide variety of topoisomerase-targeted drugs generate cytotoxic lesions by trapping the enzymes in covalent complexes on the DNA. The discovery of unusual heterodimeric topoisomerase I in kinetoplastid family added a new twist in topoisomerase research related to evolution, functional conservation and their preferential sensitivity to Camptothecin. On the other hand, structural and mechanistic studies on kinetoplastid topoisomerase II delineate some distinguishing features that differentiate the parasitic enzyme from its prokaryotic and eukaryotic counterparts. This review summarizes the recent advances in research in kin...

2006-01-01

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201

Preparation of NiZn-ferrite nanofibers by electrospinning for DNA separation

Plasmid-conferred tetracycline resistance confers collateral cadmium sensitivity to E. coli cells

We present the synthesis, magnetic and UV spectrometry of NiZn-ferrite nanofiber. The single phase of spinel ferrite was obtained at 600 {sup o}C. The NiZn-ferrite fibers fabricated by an electrospinning process were formed as a polygonal grain growth with firing temperature in fiber matrix. It appeared that the saturation magnetization (M{sub S}) of NiZn-ferrite nanofiber was dependent on Ni/Zn molar ratio which is similar to that of the inverse spinel ferrites. The NiZn-ferrite fibers showed good DNA adsorption efficiency that can be modified and utilized for DNA separation with magnetic nanofiber as a novel material in clinical applications.

2009-05-15

202

Gold and gold-silver core-shell nanoparticle constructs with defined size based on DNA hybridization

E. coli HB101 cells transformed to tetracycline resistance with the plasmids pMB9 or pBR322 display a 10/sup 5/-10/sup 6/-fold lower plating efficiency on agar containing 440 ..mu..M CdCl/sub 2/ than nontransformed cells. When DNA is inserted into the BamH1 site of the plasmid tet gene, or when DNA spanning the BamH1 site is deleted, tetracycline resistance and cadmium hypersensitivity are both lost. In contrast, insertion of DNA into the ampicillin resistance gene does not affect cadmium hypersensitivity.

1982-01-01

203

Biopsy examination during the course of radiotherapy. Progress report. [DNA content of tumor cells in biopsy samples determined by microfluorometric or multiangle light-scatter spectrometry

Nanoparticles represent versatile building blocks in material science and nanotechnology. Thereby, the defined assembly of nanostructures (13 and 56 nm in diameter, respectively) is of significant importance. Short DNA sequences can be bound to the nanoparticle surface thus enabling highly specific DNA hybridization-driven events that direct the formation of nanoparticle constructs.In this paper, examples for the defined formation of gold nanoparticle constructs are demonstrated. In addition, gold-silver core-shell nanoparticles are introduced as further building blocks for the hybridization-controlled formation of nanoparticle constructs.

2009-04-15

204

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

Studies begun during the first year of this project on biopsies from spontaneous tumors in dogs and from human patients undergoing radiotherapy treatment were continued. The results indicate that significant fractions of the spontaneous tumors in dogs and cervical carcinomas in patients undergoing radiotherapy have a DNA content higher than normal diploid cells. The higher DNA content in tumor cells permits distinguishing them from normal cells in the biopsy material with the aid of flow microfluorometric (FMF) instrumentation or multiangle light-scatter spectrometry.

1977-12-01

205

eDNA: A Bio-Inspired Reconfigurable Hardware Cell Architecture Supporting Self-organisation and Self-healing

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

206

Transformation by complementation of an adenine auxotroph of the lignin-degrading basidiomycete Phanerochaete chrysosporium

This paper presents the concept of a biological inspired reconfigurable hardware cell architecture which supports self-organisation and self-healing. Two fundamental processes in biology, namely fertilization-to-birth and cell self-healing have inspired the development of this cell architecture. In biology as well as in our hardware cell architecture it is the DNA which enables these processes. We propose a platform based on the electronic DNA (eDNA) and show through simulation, its capabilities as a new generation of robust reconfigurable hardware platforms. We have created a Java based simulator to simulate our self-organisation and self-healing algorithms and the results obtained from this looks promising.

2009-01-01

207

The Importance of Mitochondrial DNA in Aging and Cancer

Swollen basiodiospores of an adenine auxotroph of Phanerochaete chrysosporium were protoplasted with Novozyme 234 and transformed to prototrophy by using a plasmid containing the gene for an adenine biosynthetic enzyme from Schizophyllum commune. Transformation frequencies of 100 transformants per {mu}g of DNA were obtained. Southern blot analysis of DNA extracted from transformants demonstrated that plasmid DNA was integrated into the chromosomal DNA in multiple tandem copies. Analysis of conidia and basiodiospores from transformants demonstrated that the transforming character was mitotically and meiotically stable on both selective and nonselective media. Genetic crosses between double mutants transformed for adenine prototrophy and other auxotrophic strains yielded Ade{sup {minus}} progeny, which indicated that integration occurred at a site(s) other than the resident adenine biosynthetic gene.

1989-02-01

208

Targeting a Ruthenium Complex to the Nucleus with Short Peptides

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

209

Systems medicine: the future of medical genomics and healthcare

In an effort to develop octahedral metal complexes as chemotherapeutic and diagnostic agents targeted to DNA, it is critical to optimize the properties of their cellular uptake. Appending d-octaarginine...Full Text Available

2010-05-15

210

Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A

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

211

British Library Electronic Table of Contents (United Kingdom)

The penetrance of Lebers hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in different affected pedigrees. Here we describe two large Chinese families that show a striking difference in the penetrance of LHON, in which 53.3% and 15.0% of members were affected (Pin vivo mitochondrial oxidative metabolism as described in a previous study. Evolutionary analysis failed to indicate any putatively pathogenic mutation that cosegregated with G11778A in these two pedigrees. Our results suggest that the variable penetrance of LHON in the two Chinese families is independent of both their mtDNA haplotype background and a seconda...

2008-01-01

212

Site-Specific Methylation of the Promoter Alters Deoxyribonucleic Acid-Protein Interactions and Prevents ...

Regulation of Senescence in Cancer and Aging

... and R. L. Momparler. DNA methylation of retinoic acid receptor beta in breast cancer and possible therapeutic role of ... ...

213

Polycyclic Aromatic Hydrocarbon (PAH) Exposure and DNA Adduct Semi-Quantitation in Archived Human Tissues

Senescence is regarded as a physiological response of cells to stress, including telomere dysfunction, aberrant oncogenic activation, DNA damage, and oxidative stress. This stress response has an antagonistically...Full Text Available

214

Phylogenetic relationships in Cortinarius, section Calochroi, inferred from nuclear DNA sequences

Polycyclic aromatic hydrocarbons (PAHs) are combustion products of organic materials, mixtures of which contain multiple known and probable human carcinogens. PAHs occur in indoor and outdoor air, as well as in char-broiled meats and fish. Human exposure to PAHs occurs by inhalation, ingestion and topical absorption, and subsequently formed metabolites are either rendered hydrophilic and excreted, or bioactivated and bound to cellular macromolecules. The formation of PAH-DNA adducts (DNA binding products), considered a necessary step in PAH-initiated carcinogenesis, has been widely studied in experimental models and has been documented in human tissues. This review describes immunohistochemistry (IHC) studies, which reveal localization of PAH-DNA adducts in human tissues, and semi-quantify PAH-DNA adduct levels using the Automated Cellular Imaging System (ACIS). These studies have shown that ...

2011-07-29

215

Palladium polypyridyl complexes: synthesis, characterization, DNA interaction and biological activity on Leishmania (L.) mexicana

BackgroundSection Calochroi is one of the most species-rich lineages in the genus Cortinarius (Agaricales, Basidiomycota) and is widely distributed...Full Text Available

216

Ovine reference materials and assays for prion genetic testing

This paper describes the search for new potential chemotherapeutic agents based on transition metal complexes with planar ligands. In this study, palladium polypyridyl complexes were synthesized and characterized by elemental analysis, NMR, UV-VIS and IR spectroscopies. The interaction of the complexes with DNA was also investigated by spectroscopic methods. All metal-to-ligand charge transfer (MLCT) bands of the palladium polypyridyl complexes exhibited hypochromism and red shift in the presence of DNA. The binding constant and viscosity data suggested that the complexes [PdCl{sub 2}(phen)] and [PdCl{sub 2}(phendiamine)] interact with DNA by electrostatic forces. Additionally, these complexes induced an important leishmanistatic effect on L. (L.) mexicana promastigotes at the final concentration of 10 {mu}mol L{sup -1} in 48 h. (author)

2008-07-01

217

Nucleomorph Ribosomal DNA and Telomere Dynamics in Chlorarachniophyte Algae

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

218

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

219

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

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

220

Global Transcriptional Responses of Fission Yeast to Environmental Stress

Genome analysis with inter-nucleotide distances

We explored transcriptional responses of the fission yeast Schizosaccharomyces pombe to various environmental stresses. DNA microarrays were used to characterize changes in expression...Full Text Available

2003-01-01

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221

Effects of quantum vacuum fluctuations of the electric field on DNA condensation

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

222

British Library Electronic Table of Contents (United Kingdom)

By assuming that not only counter-ions but DNA molecules as well are thermally distributed according to a Boltzmann law, we propose a modified Poisson-Boltzmann equation, at the classical level, as a starting point to compute the effects of quantum fluctuations of the electric field on the interaction among DNA-cation complexes. The latter are modeled here as infinite one-dimensional wires (?-functions). Our goal is to single out such quantum-vacuum-driven interaction from the counterion-induced and water-related interactions. We obtain a universal, frustration-free Casimir-like (codimension 2) interaction that extensive numerical analysis show to be a good candidate to explain the formation and stability of DNA aggregates. Such Casimir energy is computed for a variety of configurations of...

2011-01-01

223

DNA methods for identification of Chinese medicinal materials

DNA Hypermethylation Patterns Detected in Serum as a Tool ...

As adulterated and substituted Chinese medicinal materials are common in the market, therapeutic effectiveness of such materials cannot be guaranteed. Identification at species-, strain- and locality-levels,...Full Text Available

224

Curcumin Binding to DNA and RNA

... Grant support: National Cancer Institute Center grant CA 16087 and National Cancer Institute grant CA091892, Department of Defense grant ...

2009-09-01

225

British Library Electronic Table of Contents (United Kingdom)

Curcumin, the yellow pigment from the rhizoma of Curcuma longa, is a widely studied phytochemical with a variety of biological activities. The ongoing research and clinical trials have proved that this natural phenolic compound has great and diverse pharmacological potencies. Beside its effective antioxidant, antiinflammatory, and antimicrobial/antiviral properties, curcumin is also considered as a cancer chemopreventive agent. While the antioxidant activity of curcumin is well documented, its interaction with DNA and RNA is not fully investigated. This study was designed to examine the interactions of curcumin with calf thymus DNA and yeast RNA in aqueous solution at physiological conditions, using constant DNA and RNA concentration (6.25?mM) and various curcumin/polynucleotide (phosphate...

2009-01-01

226

Changes in DNA content during rhizobial nodule development in Lupinus luteus L. 1

COBAS AMPLICOR CT/NG Test for Neisseia gonorrhoeae Package Insert

Cytophotometric measurements of DNA content after Feulgen's reaction and autoradiography after incubation with "3H-thymidine were performed to investigate the early stages of development of yellow lupin root nodule. The first response of the host plant to the contact with Rhizobium lupini was the enhancement of nuclear DNA endoreplication in root cortex cells. A conversion of the initially mixoploid nodule meristem into a diploid one during root nodule formation was found. Differentiation of bacteroid-containing tissue both from diploid and polyploid cells was observed. The highest content of nuclear DNA in the uninfected root cortex, nodule cortex and in bacteroid-containing tissue was 16 C. (author).

1989-01-01

227

Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase

... The thermostable Thermus aquaticus DNA polymerase, (Taq pol), in the presence of excess deoxynucleoside triphosphates (dNTPs), including deoxyadenosine ...

228

Accumulation, Activity and Localization of Cell Cycle Regulatory Proteins and the Chloroplast Division Protein FtsZ in the Alga Scenedesmus quadricauda under Inhibition of Nuclear DNA Replication

Adenine DNA glycosylase catalyzes the glycolytic removal of adenine from the promutagenic A {center_dot} oxoG base pair in DNA. The general features of DNA recognition by an adenine DNA glycosylase, Bacillus stearothermophilus MutY, have previously been revealed via the X-ray structure of a catalytically inactive mutant protein bound to an A:oxoG-containing DNA duplex. Although the structure revealed the substrate adenine to be, as expected, extruded from the DNA helix and inserted into an extrahelical active site pocket on the enzyme, the substrate adenine engaged in no direct contacts with active site residues. This feature was paradoxical, because other glycosylases have been observed to engage their substrates primarily through direct contacts. The lack of direct contacts in the case of MutY suggested that either MutY uses a distinctive logic for substrate ...

2010-01-14

229

British Library Electronic Table of Contents (United Kingdom)

Synchronized cultures of the green alga Scenedesmus quadricauda were grown in the absence (untreated cultures) or in the presence (FdUrd-treated cultures) of 5-fluorodeoxyuridine, the specific inhibitor of nuclear DNA replication. The attainment of commitment points, at which the cells become committed to nuclear DNA replication, mitosis and cellular division, and the course of committed processes themselves were determined for cell cycle characterization. FdUrd-treated cultures showed nearly unaffected growth and attainment of the commitment points, while DNA replication(s), nuclear division(s) and protoplast fission(s) were blocked. Interestingly, the FdUrd-treated cells possessed a very high mitotic histone H1 kinase activity in the absence of any nuclear division(s). Compared with the ...

2008-01-01

230

Abnormal chromosome repair and risk of developing cancer.

A PRELIMINARY PHYLOGENETIC ANALYSIS OF METAPENAEOPSIS (DECAPODA: PENAEIDAE) BASED ON MITOCHONDRIAL DNA SEQUENCES OF ...

Several scientists have proposed that DNA repair deficiencies and the induction of a mutator phenotype are responsible for the generation of multiple mutagenic alterations in cancer cells. I propose...Full Text Available

1993-10-01

231

A DNA recombinant database management system.

... each species studied are listed in Table 1. Penaeus monodon Fabricius, 1798 (family Penaeidae) and Solenocera koelbeli De Man, ... ...

232

Tachyons in gravitational field

A set of computer programs is described which constitutes a clone database management system. Maintenance of the database and the stocks of material is designed to be under the control of one person...Full Text Available

1983-07-11

233

Synthesis of N-(3-azido-4-chlorophenyl)-N'-["3H-methyl] thiourea, an efficient photoaffinity probe for the urea carrier

Behaviour of tachyons in gravitational field has been investigated by using imaginary as well as real superluminal Lorentz transformations. Using real superluminal transformations in four- and six-dimensional space-time, an expression for the gravitational force acting on a tachyon, moving along the tachyon corridor constructed to follow the tachyon geodesic, has been derived. The motion of a tachyon through a black hole has also been discussed and it is shown that the black hole acts like a gravitational tunnel for tachyons and the transition between the regions inside and outside the horizon can be understood as real superluminal transformations transforming a R"4=(r,t) world into a T"4=(t,r) world. 36 refs.. (author).

234

Nerve-Evoked Constriction of Rat Tail Veins Is Potentiated and Venous Diameter Is Reduced after Chronic Spinal Cord Transection

Starting from commercial 4-chloro-3-nitroaniline, through a 5 step synthesis, 3-azido-4-chlorophenylisothiocyanate was prepared and reacted with ["3H]-methylamine. The latter was obtained by three methods: (i) ["3H]-LiA1T_4 reduction of benzylcarbamate gave rise to ["3H]-methylamine (S.A.: > 70 Ci/mmol). (ii) Catalytic reduction of HCN with "3H_2 lead to ["3H]-CH_3NH_2 (S.A.: 0.7 Ci/mmol). (III) Schmidt rearrangement of ["3H]-sodium acetate gave ["3H]-CH_3NH_2 (S.A.: 29 Ci/mmol). (author).

235

British Library Electronic Table of Contents (United Kingdom)

Abstract Despite reduced sympathetic activity below the level of a spinal cord injury (SCI), venoconstriction during autonomic dysreflexia increases venous return to the heart. Here, contractions of isometrically mounted tail veins from rats with spinal transection at T4 performed 8???10 weeks earlier are compared with those from sham-operated rats. After SCI, lumen diameter was reduced by ?30% and the contractions evoked by electrical stimulation of the perivascular axons were larger than control. This augmentation of neurovascular transmission was not associated with enhanced sensitivity to ?-adrenoceptor agonists or to adenosine-5?-triphosphate (ATP) although contractions to depolarization with K+ were larger after SCI. The percentage reduction in nerve-evoked contraction after SCI prod...

2011-01-01

236

Identification and staging of bladder carcinoma

Effects of pork/beef levels and various casings on quality properties of semi-dried jerky

The purpose of the present study was to compare the effectiveness of MRI, CT and radioimmunoscintigraphy in the staging and detection of bladder cancers in 28 patients. We distinguish two groups: Group I included the tumour stages CIS-T_3_A and the second group the deep infiltrative tumours T_3_B-T_4. MRI was slightly superior to CT in respect of tumour staging (75% correct results as compared to 63%). No understaging occurred with MRI, whereas in 22% of the cases the stage of the tumour was underestimated using CT diagnostics. Overstaging occurred in 25% of the MRI and 15% of the CT-diagnostics, respectively. RIS cannot distinguish the tumour groups, and hence this method is useful only for the detection of the primary tumour and metastases. In 77% of cases the tumour was detected and in 15% the tumour could be safely excluded. (orig.).

237

British Library Electronic Table of Contents (United Kingdom)

The aim of this study was to investigate the effects of pork/beef levels and the casings on the quality properties of semi-dried jerky. The pork/beef levels in the four test formulations were as follows: T-1 (pork: beef=100:0), T-2 (95:5), T-3 (90:10), and T-4 (80:20). After tumbling for 30min with curing solution, the cured meats were stuffed into natural sheep casings, collagen casings, or cellulose casings, and then dried. The restructured jerky with cellulose casing had the lowest water content and the highest protein content, with no significant differences between various formulations. There were no significant differences among all formulations with regard to pH and total microbial counts, and jerky with cellulose casing had the lowest value of water activity. The processing yields ...

2008-01-01

238

cDNA sequence analysis of a 29-kDa cysteine-rich surface antigen of pathogenic Entamoeba histolytica

cDNA sequence analysis of a 29-kDa cysteine-rich surface antigen of pathogenic Entamoeba histolytica

A {lambda}gt11 cDNA library was constructed from poly(U)-Spharose-selected Entamoeba histolytica trophozoite RNA in order to clone and identify surface antigens. The library was screened with rabbit polyclonal anti-E. histolytica serum. A 700-base-pair cDNA insert was isolated and the nucleotide sequence was determined. The deduced amino acid sequence of the cDNA revealed a cysteine-rich protein. DNA hybridizations showed that the gene was specific to E. histolytica since the cDNA probe reacted with DNA from four axenic strains of E. histolytica but did not react with DNA from Entamoeba invadens, Acanthamoeba castellanii, or Trichomonas vaginalis. The insert was subcloned into the expression vector pGEX-1 and the protein was expressed as a fusion with the C terminus of glutathione S-transferase. Purified fusion protein was used to generate ...

1990-08-01

239

Wild-type p53 is not a negative regulator of simian virus 40 DNA replication in infected monkey cells.

A #lambda#gt11 cDNA library was constructed from poly(U)-Spharose-selected Entamoeba histolytica trophozoite RNA in order to clone and identify surface antigens. The library was screened with rabbit polyclonal anti-E. histolytica serum. A 700-base-pair cDNA insert was isolated and the nucleotide sequence was determined. The deduced amino acid sequence of the cDNA revealed a cysteine-rich protein. DNA hybridizations showed that the gene was specific to E. histolytica since the cDNA probe reacted with DNA from four axenic strains of E. histolytica but did not react with DNA from Entamoeba invadens, Acanthamoeba castellanii, or Trichomonas vaginalis. The insert was subcloned into the expression vector pGEX-1 and the protein was expressed as a fusion with the C terminus of glutathione S-transferase. Purified fusion protein was used to generate ...

240

Variations in Mre11/Rad50/Nbs1 status and DNA damage-induced S-phase arrest in the cell lines of the NCI60 panel

To analyze the proposed growth-inhibitory function of wild-type p53, we compared simian virus 40 (SV40) DNA replication in primary rhesus monkey kidney (PRK) cells, which express wild-type p53, and...Full Text Available

1993-02-01

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241

Transcription from the SV40 early-early and late-early overlapping promoters in the absence of DNA replication.

BackgroundThe Mre11/Rad50/Nbs1 (MRN) complex is a regulator of cell cycle checkpoints and DNA repair. Defects in MRN can lead to defective S-phase arrest when cells are damaged....Full Text Available

242

The role of the HCR system in the repair of lethal lesions of Bacillus subtilis phages and their transfecting DNA damaged by radiation and alkylating agents

Transcription for a hybrid SV40 promoter-beta globin coding sequence recombinant initiates from both early-early (EE) and late-early (LE) SV40 start sites (EES and LES) in the absence of DNA replication....Full Text Available

1983-01-01

243

The mutT Defect Does Not Elevate Chromosomal Fragmentation in Escherichia coli Because of the Surprisingly Low Levels of MutM/MutY-Recognized DNA Modifications?

The role of the HCR system in the repair of prelethal lesions induced by UV light, #gamma# radiation and alkylating agents was studied in the Bacillus subtilis SPP1 phage, its heat sensitive mutants (N3, N73 nad ts_1) and corresponding infectious DNA. The survival of phages and their transfecting DNA after treatment with UV light is substantially higher in hcr"+ cells than in hcr cells, the differences being more striking in intact phages than in their transfecting DNA's. Repair inhibitors reduce survival in hcr"+ cells: caffeine lowers the survival of UV-irradiated phage SPP1 in exponentially growing hcr"+ cells but has no effect on its survival in competent hcr"+ cells; acriflavin and ethidium bromide decrease the survival of the UV-irradiated SPP1 phage in both exponentially growing and competent hcr"+ cells to the level of survival observed in hcr cells; moreover, ethidium bromide lowers the number of infective centres ...

244

The human U1-70K snRNP protein: cDNA cloning, chromosomal localization, expression, alternative splicing and RNA-binding.

Nucleotide pool sanitizing enzymes Dut (dUTPase), RdgB (dITPase), and MutT (8-oxo-dGTPase) of Escherichia coli hydrolyze noncanonical DNA precursors to prevent incorporation of base...Full Text Available

2007-10-01

245

We have isolated and sequenced cDNA clones encoding the human U1-70K snRNP protein, and have mapped this locus (U1AP1) to human chromosome 19. The gene produces two size classes of RNA, a major 1.7-kb...Full Text Available

1987-12-23

246

The complete sequence of a full length cDNA for human liver glyceraldehyde-3-phosphate dehydrogenase: evidence for multiple mRNA species.

Previous studies using in vitro cell culture systems have shown the role of the dynamin-related GTPase Opa1 in apoptosis prevention and mitochondrial DNA (mtDNA) maintenance. However, it remains to...Full Text Available

2011-07-01

247

The DNA and RNA specificity of eilatin Ru(II) complexes as compared to eilatin and ethidium bromide

A recombinant M13 clone (O42) containing a 65 b.p. cDNA fragment from human fetal liver mRNA coding for glyceraldehyde-3-phosphate dehydrogenase has been identified and it has been used to isolate from...Full Text Available

1984-12-11

248

Simultaneous Detection of Multiplex-Amplified Human Immunodeficiency Virus Type 1 RNA, Hepatitis C Virus RNA, and Hepatitis B Virus DNA Using a Flow Cytometer Microsphere-Based Hybridization Assay

Eilatin-containing ruthenium complexes bind to a broad range of different nucleic acids including: calf thymus (CT) DNA, tRNA^Phe, polymeric RNAs and DNAs, and viral RNAs including the HIV-1...Full Text Available

2003-10-01

249

Sensitivity of Ru(bpy)₂dppz²⁺ Luminescence to DNA Defects

The feasibility of performing a multiplex assay for the detection of human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) RNAs and hepatitis B virus (HBV) DNA is demonstrated. This...Full Text Available

2000-03-01

250

SWI/SNF and Asf1 Independently Promote Derepression of the DNA Damage Response Genes under Conditions of Replication Stress

The luminescent characteristics of Ru(bpy)₂dppz²⁺ (dppz = dipyrido[3,2-a:2′,3′-c]phenazine), a DNA light switch, were...Full Text Available

2009-06-15

251

Radiation-induced damage to DNA; Les lesions radio-induites de l'ADN

The histone chaperone Asf1 and the chromatin remodeler SWI/SNF have been separately implicated in derepression of the DNA damage response (DDR) genes in yeast cells treated with genotoxins that cause...Full Text Available

252

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

This short survey focuses on the main radiation-induced base lesions that have been identified within cellular DNA. For this purpose, sensitive assays that are aimed at measuring a few modifications per 10{sup 7} normal bases were set-up. In that respect high performance liquid chromatography - tandem mass spectrometry (CLHP-MS/MS) was found to be able to single out the formation of 9 oxidized nucleosides and two modified nucleo-bases out of the 70 oxidative base lesions that have been identified in model systems. As a striking result, it was found that in the DNA of {gamma}-irradiated human monocytes, the formamide-pyrimidine derivative of guanine is produced in a higher yield than the ubiquitous 8-oxo-7,8-dihydro-guanine damage, both arising from the same radical precursor. However, relatively high doses of ionizing radiation (> 20 Gy) have to be applied in order to detect an increase in the level of the damage. This is due to the low ...

2002-03-01

253

Nucleotide sequence and genetic analysis of a 13.1-kilobase-pair Pseudomonas denitrificans DNA fragment containing five cob genes and identification of structural genes encoding Cob(I)alamin adenosyltransferase, cobyric acid synthase, and bifunctional cobinamide kinase-cobinamide phosphate guanylyltransferase.

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

254

Movable genetic elements: detection of changes in maize DNA at the Shrunken locus due to the intervention of Ds elements

A 13.1-kb DNA fragment carrying Pseudomonas denitrificans cob genes has been sequenced. The nucleotide sequence and genetic analysis revealed that this fragment contained five different cob genes named...Full Text Available

1991-10-01

255

Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator

This report describes our initial attempts at the molecular characterization of a maize controlling element. We have prepared a cDNA probe and used it to detect changes at a locus where Ds elements are found. Evidence of their presence are indicated by changes in the restriction patterns, but there is as yet no information on the physical nature of the controlling elements nor on the kinds of rearrangements they cause.

1980-05-28

256

Immunological detection and quantification of DNA components structurally modified by alkylating carcinogens, mutagens and chemotherapeutic agents

We report the 1.1-Å resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5′-(dCGGAAATTCCCG)₂-3′....Full Text Available

2007-01-09

257

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

The detection and quantification of defined reaction products of chemical mutagens and carcinogens (and of many cancer chemotherapeutic agents) with DNA require highly sensitive analytical techniques. The exceptional capability of immunoglobulins to recognize subtle alterations of molecular structure (especially when monoclonal antibodies are used to maximize specificity), outstanding sensitivity of immunoanalysis by high-affinity antibodies, and the fact that radioactively-labelled agents are not required suggest the utility of a radioimmunoassay to recognize and quantitate alkylated DNA products. We have recently developed a set of high-affinity monoclonal antibodies (secreted by mouse x mouse as well as by rat x rat hybridomas; antibody affinity constants, 10"9 to > 10"1"0 lmol) specifically directed against several DNA alkylation products with possible relevance in relation to both mutagenesis and malignant ...

1983-09-01

258

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

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

259

Features of two hepatitis B virus (HBV) DNA integrations suggest mechanisms of HBV integration.

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

260

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

Two integrated hepatitis B virus (HBV) DNA molecules were cloned from two primary hepatocellular carcinomas each containing only a single integration. One integration (C3) contained a single linear...Full Text Available

1989-06-01

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261

Wastenet

...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, ...

262

Equine infectious anemia virus and human immunodeficiency virus DNA synthesis in vitro: characterization of the endogenous reverse transcriptase reaction.

Elimination of L-A double-stranded RNA virus of Saccharomyces cerevisiae by expression of gag and gag-pol from an L-A cDNA clone.

The endogenous reverse transcriptase reaction of equine infectious anemia virus (EIAV) has been studied, and conditions allowing synthesis of full-length minus-strand DNA have been determined. In contrast...Full Text Available

1991-04-01

263

Deletion of Genes Implicated in Protecting the Integrity of Male Germ Cells Has Differential Effects on the Incidence of DNA Breaks and Germ Cell Loss

We report that expression of a nearly full-length cDNA clone of the L-A double-stranded RNA virus causes virus loss in a wild-type strain of Saccharomyces cerevisiae. We show that in this system exclusion...Full Text Available

1993-05-01

264

DNA-new combination: a practical application in the sugar industry

BackgroundInfertility affects ∼20% of couples in Europe and in 50% of cases the problem lies with the male partner. The impact of damaged DNA originating...Full Text Available

265

DNA damage intensity in fibroblasts in a 3-dimensional collagen matrix correlates with the Bragg curve energy distribution of a high LET particle

One of the first technical applications of gene technology is reported here. The DNA of E. coli cells was rearranged such that these cells produce large quantities of the enzyme ..cap alpha..-galactosidase. This enzyme is used to split the trisaccharide, raffinose, which is formed during the production of sugar from sugar beet. By this means sugar yields can be increased and the energy required for sugar crystallisation reduced.

1983-04-01

266

DNA adducts in peripheral blood lymphocytes from aluminum production plant workers determined by 32P-postlabeling and enzyme-linked immunosorbent assay.

The DNA double-strand break (DSB) damage response induced by high energy charged particles on lung fibroblast cells embedded in a 3-dimensional (3-D) collagen tissue equivalents was investigated using antibodies to the DNA damage response proteins gamma-histone 2AX (#gamma#-H2AX) and phosphorylated DNA-PKcs (p-DNA-PKcs). 3-D tissue equivalents were irradiated in positions across the linear distribution of the Bragg curve profiles of 307.7 MeV/nucleon, 556.9 MeV/nucleon, or 967.0 MeV/nucleon "5"6Fe ions at a dose of 0.30 Gy. Patterns of discrete DNA damage streaks across nuclei or saturated nuclear damage were observed, with saturated nuclear damage being more predominant as samples were positioned closer to the physical Bragg peak. Quantification of the DNA damage signal intensities at each distance for each of the examined energies revealed a biological Bragg ...

2010-03-01

267

Characterization of a novel plasmid-like element in Neurospora crassa derived mostly from the mitochondrial DNA.

32P-Postlabeling analysis and enzyme-linked immunosorbent assay (ELISA) have been used to detect DNA adducts in peripheral blood lymphocytes from primary aluminum production plant workers who were exposed...Full Text Available

1993-03-01

268

Binding the Mammalian High Mobility Group Protein AT-hook 2 to AT-Rich Deoxyoligonucleotides: Enthalpy-Entropy Compensation

We have identified a plasmid-like element within mitochondria of Neurospora crassa strain stp-B1. It is derived from the EcoRI-4 and EcoRI-6 regions of the mitochondrial DNA, and an additional 124 bp...Full Text Available

1990-10-11

269

Binding of Ru(bpy)₂(eilatin)²⁺ to Matched and Mismatched DNA

HMGA2 is a DNA minor-groove binding protein. We previously demonstrated that HMGA2 binds to AT-rich DNA with very high binding affinity where the binding of HMGA2 to poly(dA-dT)₂ is enthalpy-driven...Full Text Available

2009-05-20

270

Benzo[a]pyrene diol epoxide-DNA cis adduct formation through a trans?chlorohydrin?intermediate

The DNA-binding properties of Ru(bpy)₂(eilatin)²⁺ have been investigated to determine if the sterically expansive eilatin ligand confers specificity for destabilized single-base...Full Text Available

2008-07-21

271

A study of the interactions of some polypyridylruthenium (II) complexes with DNA using fluorescence spectroscopy, topoisomerisation and thermal denaturation.

Alkylation of DNA by 7r,8t-dihydroxy,9t,10t-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (anti-BPDE) forms mainly trans adducts (with respect to the C-9/10...Full Text Available

1997-03-04

272

A single-stranded gap in human immunodeficiency virus unintegrated linear DNA defined by a central copy of the polypurine tract.

The nature of binding of Ru(phen) 2+ (I), Ru(bipy) 2+ (II), Ru(terpy) 2+ (III) (phen = 1,10-phenanthroline, bipy 3 = 2,2'-bipyridyl, 3 terpy = 2,2'2," - 2 terpyridyl) to DNA, poly[d(G-C)] and poly[d(A-T)]...Full Text Available

1985-09-11

273

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

The structure of unintegrated human immunodeficiency virus type 1 (HIV-1) DNA from acutely infected human lymphoid cells was analyzed by nuclease S1 cleavage. We observed a unique, discrete single-stranded...Full Text Available

1991-05-01

274

Use of DNA probes to study tetracycline resistance determinants in gram-negative bacteria from swine

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

275

Isolation of fetal DNA from nucleated erythrocytes in maternal blood

Specific {sup 32}P-labeled DNA probes were prepared and used to evaluate the distribution of tetracycline resistance determinants carried by gram-negative enteric bacteria isolated from pigs in 3 swine herds with different histories of antibiotic exposure. Plasmid DNA, ranging in size from 2.1 to 186 Kb, was observed in over 84% of 114 isolates studied. Two of 78 tetracycline resistant strains did not harbor plasmids. The DNA probes were isolated from plasmids pSL18, pRT29/Tn10, pBR322 and pSL106, respectively, and they represented class A, B, C and D tetracycline resistance determinants. Hybridization conditions using 0.5X SSPE at 65{degrees}C minimize cross-hybridization between the different class of tetracycline resistance genes. Cross-hybridization between class A and class C determinants could be distinguished by simultaneous comparison of the intensity of their hybridization signals. Plasmids from over 44% of the ...

1989-01-01

276

Biophysical analysis of DNA modified by 1,2-diaminocyclohexane platinum(II) complexes

Fetal nucleated cells within maternal blood represent a potential source of fetal genes obtainable by venipuncture. The authors used monoclonal antibody against the transferrin receptor (TIR) to identify nucleated erythrocytes in the peripheral blood of pregnant women. Candidate fetal cells from 19 pregnancies were isolated by flow sorting at 12 1/2-17 weeks gestation. The DNA in these cells was amplified for a 222-base-pair (bp) sequence present on the short arm of the Y chromosome as proof that the cells were derived from the fetus. The amplified DNA was compared with standardized DNA concentrations. In the case of the female fetus, DNA prepared from samples at 32 weeks of gestation and cord blood at delivery also showed the presence of the Y chromosomal sequence, suggesting Y sequence mosaicism or translocation. In 10/12 cases where the 222-bp band was absent, the fetuses were female. Thus, they were ...

1990-05-01

277

On the cells of origin of radiogenic thyroid cancer: New studies based on an old idea

Modification of DNA and double-stranded deoxyoligonucleotides with antitumor 1,2-diamino-cyclohexanedinitroplatinum(II) (Pt-dach) complexes was investigated with the aid of physico-chemical methods and chemical probes of nucleic acid conformation. The three Pt-dach complexes were used which differed in isomeric forms of the dach non-leaving ligand-Pt(1R,2R-dach), Pt(1S,2S-dach) and Pt(1R,2S-dach) complexes. The latter complex has lower antitumor activity than the other two Pt-dach complexes. Pt(1R,2S-dach) complex exhibits the slowest kinetics of its binding to DNA and of the conversion of monofunctional binding to bifunctional lesions. The anomalously slow electrophoretic mobility of multimers of the platinated and ligated oligomers suggests that bifunctional binding of Pt-dach complexes to a d(GG) site within double-stranded oligonucleotides induces bending of the oligomer. It is proposed that different effects of the Pt-dach complexes on ...

1992-01-25

278

Molecular cloning of chicken metallothionein. Deduction of the complete amino acid sequence and analysis of expression using cloned cDNA

We have presented evidence that the functional thyroid follicles (follicular units, FU) which are formed in grafts of monodispersed rat thyroid cells, and hence the thyroid tumors which later develop in such grafts, are clonal in origin. Recent studies have been designed to investigate: whether cell number-dependent inhibition of promotion-progression is mediated by remote hormonal feed-back, local cell-cell interactions, or both; the cell population kinetics of the clonogen subpopulation during goitrogenesis and goiter involution; and the effect of prolonged exposure to high levels of TSH (thyrotropin) on the capacity of the clonogens to give rise to functional FU. The results indicate that local cell-cell interactions play an important role in the cell number-dependent suppression of neoplastic promotion-progression. They also show that if sufficient thyroid cells are grafted, the thyroid-pituitary axis can be reestablished in thyroidectomized rats fed normal diets. In such animals ...

1990-01-01

279

Detection of polychlorinated biphenyl degradation genes in polluted sediments by direct DNA extraction and polymerase chain reaction

A cDNA library was constructed using RNA isolated from the livers of chickens which had been treated with zinc. This library was screened with a RNA probe complementary to mouse metallothionein-I (MT), and eight chicken MT cDNA clones were obtained. All of the cDNA clones contained nucleotide sequences homologous to regions of the longest (375 bp) cDNA clone. The latter contained an open reading frame of 189 bp, and the deduced amino acid sequence indicates a protein of 63 amino acids of which 20 are cysteine residues. Amino acid composition and partial amino acid sequence analyses of purified chicken MT protein agreed with the amino acid composition and sequence deduced from the cloned cDNA. Amino acid sequence comparison establish that chicken MT shares extensive homology with mammalian MTs. Southern blot analysis of chicken DNA indicates that the chicken MT ...

1988-01-25

280

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

It was the aim of this study to specifically detect the DNA sequences for the bphC gene, the meta-cleavage enzyme of the aerobic catabolic pathway for biphenyl and polychlorinated biphenyl degradation, in aquatic sediments without prior cultivation of microorganisms by using extraction of total DNA, PCR amplification of bphC sequences, and detection with specific gene probes. The direct DNA extraction protocol used was modified to enhance lysis efficiency. Crude extracts of DNA were further purified by gel filtration, which yielded DNA that could be used for the PCR. PCR primers were designed for conserved regions of the bphC gene from a sequence alignment of five known sequences. The specificity of PCR amplification was verified by using digoxigenin-labeled DNA probes which were located internal to the amplified gene sequence. The detection limit for the bphC ...

1993-12-01

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281

Characterization of chicken octamer-binding proteins demonstrates that POU domain-containing homeobox transcription factors have been highly conserved during vertebrate evolution

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 ...

1992-01-15

282

mtDNA mutation C1494T, haplogroup A, and hearing loss in Chinese

The DNA sequence motif ATTTGCAT (octamer) or its inverse complement has been identified as an evolutionarily conserved element in the promoter region of immunoglobulin genes. Two major DNA-binding proteins that bind in a sequence-specific manner to the octamer DNA sequence have been identified in mammalian species--a ubiquitously expressed protein (Oct-1) and a lymphoid-specific protein (Oct-2). During characterization of the promoter region of the chicken immunoglobulin light chain gene, the authors identified two homologous octamer-binding proteins in chicken B cells. when the cloning of the human gene for Oct-2 revealed it to be a member of a distinct family of homeobox genes, they sought to determine if the human Oct-2 cDNA could be used to identify homologous chicken homeobox genes. Using a human Oct-2 homeobox-specific DNA probe, they were able to identify 6-10 ...

1990-02-01

283

British Library Electronic Table of Contents (United Kingdom)

Mutation C1494T in mitochondrial 12S rRNA gene was recently reported in two large Chinese families with aminoglycoside-induced and nonsyndromic hearing loss (AINHL) and was claimed to be pathogenic. This mutation, however, was first reported in a sample from central China in our previous study that was aimed to reconstruct East Asian mtDNA phylogeny. All these three mtDNAs formed a subclade defined by mutation C1494T in mtDNA haplogroup A. It thus seems that mutation C1494T is a haplogroup A-associated mutation and this matrilineal background may contribute a high risk for the penetrance of mutation C1494T in Chinese with AINHL. To test this hypothesis, we first genotyped mutation C1494T in 553 unrelated individuals from three regional Chinese populations and performed an extensive search ...

2006-01-01

284

Synthetic enantiopure aziridinomitosenes: preparation, reactivity, and DNA alkylation studies.

Selective changes of retroelement expression in human prostate cancer

An enantiocontrolled route to aziridinomitosenes had been developed from l-serine methyl ester hydrochloride. The tetracyclic target ring system was assembled by an internal azomethine ylide cycloaddition reaction based on silver ion-assisted intramolecular oxazole alkylation and cyanide-induced ylide generation via a labile oxazoline intermediate (62 to 66). Other key steps include reductive detritylation of 26, methylation of the N-H aziridine 56, oxidation of the sensitive cyclohexenedione 68 to quinone 70, and carbamoylation using Fmoc-NCO. Although the aziridinomitosene tetracycle is sensitive, a range of protecting group manipulations and redox chemistry can be performed if suitable precautions are taken. A study of DNA alkylation by the first C-6,C-7-unsubstituted aziridinomitosene 11a has been carried out, and evidence for DNA cross-link formation involving nucleophilic addition to the quinone subunit is described. PMID:14677970

2003-12-24

285

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

286

Programmed cell death during pigment gland formation in Gossypium hirsutum leaves

British Library Electronic Table of Contents (United Kingdom)

Abstract Ultrastructural studies have shown that the formation of pigment glands in Gossypium hirsutum L. leaves is a lysigenous process, originating from a cluster of cells in the ground meristem. Various techniques were used here to investigate whether programmed cell death (PCD) plays a critical role in this developmental process. Nuclei of internal cells in the pigment gland-forming tissue were TUNEL-positive and DAPI-negative, suggesting that DNA cleavage is an early event and complete DNA degradation is a late event. Smeared bands and a lack of laddering after gel electrophoresis indicate that DNA cleavage is random. Ultrastructurally, secretory cells in the pigment glands become distorted, nuclei are densely stained, and chromosomes become condensed until completely degraded at late...

2010-01-01

287

One-step RNA pathogen detection with reverse transcriptase activity of a mutated thermostable Thermus aquaticus DNA polymerase

British Library Electronic Table of Contents (United Kingdom)

We describe the cloning and characterization of a mutated thermostable DNA polymerase from Thermus aquaticus (Taq) that exhibits an increased reverse transcriptase activity and is therefore designated for one-step PCR pathogen detection using established real-time detection methods. We demonstrate that this Taq polymerase mutant (Taq M1) has similar PCR sensitivity and nuclease activity as the respective Taq wild-type DNA polymerase. In addition, and in marked contrast to the wild-type, Taq M1 exhibits a significantly increased reverse transcriptase activity especially at high temperatures (>60degreeC). RNA generally hosts highly stable secondary structure motifs, such as hairpins and G-quadruplexes, which complicate, or in the worst case obviate, reverse transcription (RT). Thus, RT at hi...

2010-01-01

288

Molecular characterization of Fasciola spp. from the endemic area of northern Iran based on nuclear ribosomal DNA sequences

British Library Electronic Table of Contents (United Kingdom)

Fasciolosis caused by Fasciola spp. (Platyhelminthes: Trematoda: Digenea) is considered as the most important helminth infection of ruminants in tropical countries, causing considerable socioeconomic problems. In the endemic regions of the North of Iran, Fasciola hepatica and Fasciola gigantica have been previously characterized on the basis of morphometric differences, but the use of molecular markers is necessary to distinguish exactly between species and intermediate forms. Samples from buffaloes and goats from different localities of northern Iran were identified morphologically and then genetically characterized by sequences of the first (ITS-1) and second (ITS-2) Internal Transcribed Spacers (ITS) of nuclear ribosomal DNA (rDNA). Comparison of the ITS of the northern Iranian samples ...

2011-01-01

289

Electron transport through asymmetric DNA molecules

British Library Electronic Table of Contents (United Kingdom)

We investigate quantum mechanical electron transport along the long axis of the DNA molecule using an effective tight-binding model. The overall contour plot of transmission, the current-voltage characteristics, and the differential conductance are examined for the variation of backbone onsite energy, the energy-dependent hopping strength, and the contact coupling between the leads and the DNA molecule. It is shown that as backbone asymmetry increases, the merging and collapse of the two mini-bands take place and an extra resonance peak in the transmission appears. In addition, we present the modulation of voltage threshold in the current-voltage curves and a double-peak structure in the differential conductance due to the disappearance of the merged mini-band. Finally, in the Coulomb bloc...

2010-01-01

290

Comparison of antioxidant abilities of magnolol and honokiol to scavenge radicals and to protect DNA

British Library Electronic Table of Contents (United Kingdom)

The antioxidant properties of magnolol and honokiol were evaluated in the experimental systems of reducing ONOO^- and ^1O"2, bleaching @b-carotene in linoleic acid (LH) emulsion, and trapping 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonate) cationic radical (ABTS^+?) and 2,2'-diphenyl-1-picrylhydrazyl radical (DPPH), and then were applied to inhibit the oxidation of DNA induced by Cu^2^+/glutathione (GSH) and 2,2'-azobis(2-amidinopropane hydrochloride) (AAPH). Magnolol and honokiol were active to reduce ONOO^- and ^1O"2. Honokiol showed a little higher activity to protect LH and to inhibit Cu^2^+/GSH-induced oxidation of DNA than magnolol. In addition, honokiol exhibited higher activities to trap ABTS^+? and DPPH than magnolol. In particular, honokiol trapped 2.5 radicals while magnolol o...

2011-01-01

291

Cloning of the cDNA and gene for a human D sub 2 dopamine receptor

Chromosomal rearrangement segregating with adrenoleukodystrophy: A molecular analysis

A clone encoding a human D{sub 2} dopamine receptor was isolated from a pituitary cDNA library and sequenced. The deduced protein sequence is 96% identical with that of the cloned rat receptor with one major difference: the human receptor contains an additional 29 amino acids in its putative third cytoplasmic loop. Southern blotting demonstrated the presence of only one human D{sub 2} receptor gene. Two overlapping phage containing the gene were isolated and characterized. DNA sequence analysis of these clones showed that the coding sequence is interrupted by six introns and that the additional amino acids present in the human pituitary receptor are encoded by a single exon of 87 base pairs. The involvement of this sequence in alternative splicing and its biological significance are discussed.

1989-12-01

292

Association of the polymorphism of the CAG repeat in the mitochondrial DNA polymerase gamma gene (POLG) with testicular germ-cell cancer

The relationship between X chromosome-linked adrenoleukodystrophy and the red/green color pigment gene cluster on Xq28 was investigated in a large kindred. The DNA in a hemizygous male showed altered restriction fragment sizes compatible with at least a deletion extending from the 5[prime] end of the color pigment genes. Segregation analysis using a DNA probe within the color pigment gene cluster showed significant linkage with adrenoleukodystrophy (logarithm of odds score of 3.19 at [theta] = 0.0). These data demonstrate linkage, rather than association, between a unique molecular rearrangement in the color pigment gene cluster and adrenoleukodystrophy. The DNA changes in this region are thus likely to be helpful for determining the location and identity of the responsible gene. 33 refs., 4 figs.

1993-10-15

293

British Library Electronic Table of Contents (United Kingdom)

Background: A possible association between the polymorphic CAG repeat in the DNA polymerase gamma (POLG) gene and the risk of testicular germ-cell tumours (TGCT) was investigated in this study. The hypothesis was prompted by an earlier preliminary study proposing an association of the absence of the common 10-CAG-long POLG allele with testicular cancer as well as previously reported in some European populations' association with male subfertility, which is a condition carrying an increased risk of TGCT. Patients and methods: The number of CAG repeats in both POLG alleles was established in 243 patients with TGCT and in 869 controls by the analysis of the genomic DNA fragment. Results: A significantly higher proportion of men homozygous allele of other than the common 10 CAG repeats was fou...

2008-01-01

294

Applications of CR-39 for the estimation of biological effects of heavy ion irradiation to DNA and living cells

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

We present two applications of CR-39 to estimate biological effects of heavy ion irradiation. The accurate measurement of fluence of ions using CR-39 is indispensable to calculate the action cross sections for biological effects. Ions with 6 MeV/n at the Medium Energy Beam Course, HIMAC (NIRS) were extracted to the air, and degraded with the air. DNA and living cells were irradiated by ions with various specific energies at several air columns along with the Bragg curve. DNA strand breaks and cell killing were measured and the results were converted to the action cross sections using the fluence measured with CR-39 at the irradiation positions. Another example of the application of CR-39 is to identify whether the ions with a specific energy pass through the cell or stop within the cell. (author)

2001-10-01

295

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

296

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

cDNA-AFLP analysis reveals differential gene expression in compatible interaction of wheat challenged with Puccinia striiformis f. sp. tritici

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

297

cDNA cloning, sequence analysis and organ distribution of horse preproendothelin-2.

BackgroundPuccinia striiformis f. sp. tritici is a fungal pathogen causing stripe rust, one of the most important wheat diseases worldwide. The...Full Text Available

298

c-Myc Mediates a Hypoxia-Induced Decrease in Acetylated Histone H4

We cloned and characterized horse preproendothelin-2 (PPET-2) cDNA from intestinal tissue. The cDNA encoded 178 amino acids of the PPET-2 polypeptide, in which a 21-amino-acid mature endothelin-2 peptide and a 16-amino acid endothelin-2-like peptide were found. For the open reading frame the correspondence of horse PPET-2 cDNA with those of the ferret, human, dog, mouse and rat was 85.1%, 84.9%, 82.1%, 77.8% and 77.2%, respectively. Analysis of the organ distribution of PPET-2 mRNA by reverse transcription-polymerase chain reaction demonstrated that the kidney, stomach and small intestine are major sites of expression of the PPET-2 gene. Surprisingly, the mRNA is not detected in the large intestine, where high expression is demonstrated in the mouse and rat. This difference may result from the underlying functional differences of the large intestine between a herbivore (horse) and an omnivore (mouse and rat). PMID:15838341

2004-11-01

299

X rays in molecular biophysics

Global acetylation of histone H4 is a mark of gene transcriptional activation. The c-Myc transcription factor binds to specific DNA sites in cellular chromatin and induces the acetylation of...Full Text Available

2009-10-01

300

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

An atom-by-atom understanding of life processes is emerging from a flurry of experiments fueled by synchrotron sources and DNA technology. {copyright} 1995 {ital American} {ital Institute} {ital of} {ital Physics}.

1995-11-01

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301

Weak Association between SEN Virus Viremia and Liver Disease

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

302

Use of DNA ladders for reproducible protein fractionation by SDS-PAGE for quantitative proteomics

Recently, a novel DNA virus designated SEN virus (SEN-V), which is thought to be related to posttransfusion hepatitis, was discovered. The aim of the present study was to clarify the relationship between...Full Text Available

2002-09-01

303

Tumour suppressor ING1b maintains genomic stability upon replication stress

In proteomics, one-dimensional (1D) SDS-PAGE is widely used for protein fractionation prior to mass spectrometric analysis to enhance dynamic range of analysis and to improve identification...Full Text Available

2008-02-01

304

Transposons as tools for enhancer trap screens in vertebrates

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

305

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

306

The role of DNA damage response pathways in chromosome fragility in Fragile X syndrome

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

307

The requirement of yeast replication origins for pre-replication complex proteins is modulated by transcription

FRAXA is one of a number of fragile sites in human chromosomes that are induced by agents like fluorodeoxyuridine (FdU) that affect intracellular thymidylate levels. FRAXA coincides with a >200...Full Text Available

2009-07-01

308

The region encompassing the procyclic acidic repetitive protein (PARP) gene promoter plays a role in plasmid DNA replication in Trypanosoma brucei.

The mini-chromosome maintenance proteins Mcm2–7 are essential for DNA replication. They are loaded onto replication origins during G1 phase of the cell cycle to form a pre-replication complex...Full Text Available

2005-01-01

309

The oncogenic transforming potential of the passage of single ? particles through mammalian cell nuclei

We have previously reported the construction and characterization of an autonomously replicating plasmid in Trypanosoma brucei. In this plasmid the procyclic acidic repetitive protein (PARP) gene promoter...Full Text Available

1994-10-11

310

The missing graphical user interface for genomics

Domestic, low-level exposure to radon gas is considered a major environmental lung-cancer hazard involving DNA damage to bronchial cells by α particles from radon progeny. At domestic exposure...Full Text Available

1999-01-05

311

The dimerization domain of SOX9 is required for transcription activation of a chondrocyte-specific chromatin DNA template

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

312

The Mitochondrial Isovaleryl-Coenzyme A Dehydrogenase of Arabidopsis Oxidizes Intermediates of Leucine and Valine Catabolism1

Mutations in SOX9, a gene essential for chondrocyte differentiation cause the human disease campomelic dysplasia (CD). To understand how SOX9 activates transcription, we characterized...Full Text Available

2010-10-01

313

The LW blood group glycoprotein is homologous to intercellular adhesion molecules.

We recently identified a cDNA encoding a putative isovaleryl-coenzyme A (CoA) dehydrogenase in Arabidopsis (AtIVD). In animals, this homotetrameric enzyme is located in mitochondria and catalyzes the...Full Text Available

2001-06-01

314

The Interaction between AID and CIB1 Is Nonessential for Antibody Gene Diversification by Gene Conversion or Class Switch Recombination

The LW blood group antigens reside on a 42-kDa erythrocyte membrane glycoprotein that was purified by immunoaffinity and partially sequenced. From this information, a specific PCR-amplified DNA fragment...Full Text Available

1994-06-07

315

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

Activation-induced deaminase (AID) initiates somatic hypermutation, gene conversion and class switch recombination by deaminating variable and switch region DNA cytidines to uridines. AID is predominantly...Full Text Available

316

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

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

317

Targeted gene transfection from microbubbles into vascular smooth muscle cells using focused, ultrasound-mediated delivery

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

318

Strand displacement synthesis capability of Moloney murine leukemia virus reverse transcriptase.

We investigate a method for gene delivery to vascular smooth muscle cells using ultrasound triggered delivery of plasmid DNA from electrostatically coupled cationic microbubbles. Microbubbles...Full Text Available

2010-09-01

319

Statistical properties of nucleotide clusters in DNA sequences*

The accepted model of retroviral reverse transcription includes a circular DNA intermediate which requires strand displacement synthesis for linearization and creation of an integration-competent, long...Full Text Available

1994-08-01

320

Stability of Trichomonas vaginalis DNA in Urine Specimens?

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

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321

Species-specific Fungal DNA in Airborne Dust as Surrogate for Occupational Mycotoxin Exposure?

Trichomonas vaginalis is an important pathogen in both men and women. Culture is considered the diagnostic gold standard, although studies have shown that PCR is more sensitive than...Full Text Available

2008-05-01

322

Simultaneous expression of different transgenes in neurons and glia by combining in utero electroporation with the Tol2 transposon-mediated gene transfer system

Possible health risks associated with occupational inhalation of mycotoxin-containing dust remain largely unknown, partly because methods for mycotoxin detection are not sensitive enough for the small...Full Text Available

323

Shielding of Sleeping Beauty DNA Transposon-delivered Transgene Cassettes by Heterologous Insulators in Early Embryonal Cells

In utero electroporation is widely used to study neuronal development and function by introducing plasmid DNA into neural progenitors during embryogenesis. This is an effective and...Full Text Available

2010-05-01

324

Sequential interim analyses of survival data in DNA microarray experiments

The Sleeping Beauty (SB) transposon system represents an important alternative to viral integrating vector systems but may, as its viral counterparts, be subject to transcriptional silencing. To investigate...Full Text Available

2009-01-01

325

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

BackgroundDiscovery of biomarkers that are correlated with therapy response and thus with survival is an important goal of medical research on severe diseases, e.g. cancer. Frequently,...Full Text Available

326

Separation of the bacterial species, Escherichia coli, from mixed-species microbial communities for transcriptome analysis

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

327

Selection and characterization of ricin toxin A-chain mutations in Saccharomyces cerevisiae.

BackgroundThe study of bacterial species interactions in a mixed-species community can be facilitated by transcriptome analysis of one species in the community using cDNA microarray...Full Text Available

328

Selecting Folded Proteins from a Library of Secondary Structural Elements

A DNA sequence encoding the A chain of ricin toxin (RTA) from the castor bean plant, Ricinus communis, was placed under GAL1 promoter control and transformed into Saccharomyces cerevisiae. Induction...Full Text Available

1989-02-01

329

Role of accelerator mass spectrometry in biological dosimetry

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

330

Role of Conserved Salt Bridges in Homeodomain Stability and DNA Binding*

Understanding risks from exposures to carcinogens and other chemicals depends upon measurement of their dose to target tissues and their reactivity with critical macromolecules. The authors have used AMS detection of radio-isotopes to assess doses and reactivities at low, environmentally relevant doses. Several biomedical investigations show the effectiveness of quantification of biologically important events at extremely high sensitivity with AMS. Specifically, they have measured the addition of environmental carcinogens such as 2-amino-3,8-dimethylimidazo[4,5-f]-quinoaxaline (MelQx), a chemical found in cooked food, to DNA at concentrations relevant to human exposure. Other low level detection problems in biology, such as immunoassay assessment of small environmental chemicals, is being developed with attomole sensitivity. AMS also aids the assessment of genotoxic risks from chemicals by quantifying the binding of labeled chemicals to DNA. ...

1992-04-05

331

Retinoic acid X receptor in the diploblast, Tripedalia cystophora

The sequence information available for homeodomains reveals that salt bridges connecting pairs 19/30, 31/42, and 17/52 are frequent, whereas aliphatic residues at these sites are rare and mainly restricted...Full Text Available

2009-08-28

332

Restriction endonuclease analysis of porcine Pasteurella multocida isolates from Quebec.

Nuclear hormone receptors comprise a characteristic family of transcription factors found in vertebrates, insects and nematodes. Here we show by cDNA and gene cloning that a Cnidarian, Tripedalia...Full Text Available

1998-11-10

333

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

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

334

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

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

335

Reduced PCR Sensitivity Due to Impaired DNA Recovery with the MagNA Pure LC Total Nucleic Acid Isolation Kit

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

336

Recovery of Pathogenic Measles Virus from Cloned cDNA

The increasing demand for molecular diagnostics in clinical microbiology laboratories necessitates automated sample processing. In the present study, we evaluated the performance of the MagNA Pure LC...Full Text Available

2005-09-01

337

Recent Applications of DNA Microarray Technology to Toxicology and Ecotoxicology

Reverse genetics technology so far established for measles virus (MeV) is based on the Edmonston strain, which was isolated several decades ago, has been passaged in nonlymphoid cell lines, and is no...Full Text Available

2000-07-01

338

Rapid Detection of Ophiostoma piceae and O. quercus in Stained Wood by PCR

Gene expression is a unique way of characterizing how cells and organisms adapt to changes in the external environment. The measurements of gene expression levels upon exposure to a chemical can be...Full Text Available

2006-01-01

339

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

A rapid, sensitive, and simple method was developed to detect the sapstain fungi Ophiostoma piceae and O. quercus in stained wood. By using microwave heating for DNA...Full Text Available

1999-01-01

340

Radioprotective Effect of American Ginseng on Human Lymphocytes at 90 Minutes Postirradiation: A Study of 40 Cases

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

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341

RNA:DNA Ratio and Other Nucleic Acid Derived Indices in Marine Ecology

AbstractBackgroundIonizing radiation (IR) initiates intracellular oxidative stress through enhanced formation of reactive oxygen species (ROS) that attack DNA leading...Full Text Available

2010-05-01

342

Protein Damage by Reactive Electrophiles: Targets and Consequences

Some of most used indicators in marine ecology are nucleic acid-derived indices. They can be divided by target levels in three groups: 1) at the organism level as ecophysiologic indicators, indicators...Full Text Available

343

Production of dissolved DNA, RNA, and protein by microbial populations in a Florida reservoir.

It has been sixty years since the Millers first described the covalent binding of carcinogens to tissue proteins. Protein covalent binding was gradually overshadowed by the emergence of DNA...Full Text Available

2008-01-01

344

Primary and secondary structure of the pore-forming peptide of pathogenic Entamoeba histolytica.

Production of dissolved macromolecules by ambient autotrophic and heterotrophic microbial populations was measured in a eutrophic Florida reservoir by in situ labeling with various radioactive substrates....Full Text Available

1990-10-01

345

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

A pore-forming peptide is implicated in the potent cytolytic activity of pathogenic Entamoeba histolytica. Using NH2-terminal sequence information of this peptide, the corresponding cDNA was isolated....Full Text Available

1992-10-01

346

Precise Detection and Tracing of Trichoderma hamatum 382 in Compost-Amended Potting Mixes by Using Molecular Markers

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

347

Phosphotriesters in rat liver deoxyribonucleic acid after the administration of the carcinogen NN-dimethylnitrosamine in vivo.

Randomly amplified polymorphic DNA (RAPD) analysis and the PCR assay were used in combination with dilution plating on a semiselective medium to detect and enumerate propagules of Trichoderma...Full Text Available

1999-12-01

348

Personalized Epigenomic Signatures That Are Stable Over Time and Covary with Body Mass Index

After treatment with NN-di[14C]methylnitrosamine, samples of DNA were isolated from rat livers by a conventional phenol procedure and examined for the presence of phosphotriesters. A method of capable...Full Text Available

1975-03-01

349

Parallel Arrays of Geometric Nanowells for Assembling Curtains of DNA with Controlled Lateral Dispersion

The epigenome consists of non–sequence-based modifications, such as DNA methylation, that are heritable during cell division and that may affect normal phenotypes and predisposition...Full Text Available

2010-09-15

350

Novel Human Erythrovirus Associated with Transient Aplastic Anemia

The analysis of individual molecules is evolving into an important tool for biological research, and presents conceptually new ways of approaching experimental design strategies. However, more...Full Text Available

2008-10-07

351

Nonnative Proteins Induce Expression of the Bacillus subtilis CIRCE Regulon

Erythrovirus (formerly parvovirus) B19 causes a wide range of diseases in humans, including anemia due to aplastic crisis. Diagnosis of B19 infection relies on serology and the detection of viral DNA...Full Text Available

1999-08-01

352

Natural variation in life history and aging phenotypes is associated with mitochondrial DNA deletion frequency in Caenorhabditis briggsae

The chaperone-encoding groESL and dnaK operons constitute the CIRCE regulon of Bacillus subtilis. Both operons are under negative control of the repressor...Full Text Available

1998-06-01

353

NF-kappaB mediates the survival of human bronchial epithelial cells exposed to cigarette smoke extract

BackgroundMutations that impair mitochondrial functioning are associated with a variety of metabolic and age-related disorders. A barrier to rigorous tests of the role of mitochondrial...Full Text Available

354

Most of the extant mtDNA boundaries in South and Southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans

BackgroundWe have previously reported that low concentrations of cigarette smoke extract induce DNA damage without leading to apoptosis or necrosis in human bronchial epithelial...Full Text Available

2008-01-01

355

Molecular basis of FIR-mediated c-myc transcriptional control

BackgroundRecent advances in the understanding of the maternal and paternal heritage of south and southwest Asian populations have highlighted their role in the colonization of Eurasia...Full Text Available

356

Molecular Evidence of Bartonella Infection in Domestic Dogs from Algeria, North Africa, by Polymerase Chain Reaction (PCR)

The Far UpStream Element (FUSE) regulatory system promotes a peak in the concentration of c-Myc during cell cycle. First, the FBP transcriptional activator binds to the FUSE DNA element upstream...Full Text Available

2010-09-01

357

Mitochondrial DNA Damage and Animal Longevity: Insights from Comparative Studies

Bartonella species are being recognized as important bacterial human and canine pathogens, and are associated with multiple arthropod vectors. Bartonella DNA extracted...Full Text Available

2010-08-05

358

Metabolic Engineering of Poly(3-Hydroxyalkanoates): From DNA to Plastic

Chemical reactions in living cells are under strict enzyme control and conform to a tightly regulated metabolic program. However, uncontrolled and potentially deleterious endogenous reactions occur,...Full Text Available

359

Mechanisms of chemotherapy-induced human ovarian aging: double strand DNA breaks and microvascular compromise

Poly(3-hydroxyalkanoates) (PHAs) are a class of microbially produced polyesters that have potential applications as conventional plastics, specifically thermoplastic elastomers. A wealth of biological...Full Text Available

1999-03-01

360

Los Alamos sequence analysis package for nucleic acids and proteins.

The mechanism of chemotherapy-induced acceleration of ovarian aging is not fully understood. We used doxorubicin, a widely used cancer chemotherapeutic, in a variety of in vivo xenograft,...Full Text Available

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361

Localized mutagenesis of the tetracycline promoter region in pBR322 by 4,5',8-trimethylpsoralen

An interactive system for computer analysis of nucleic acid and protein sequences has been developed for the Los Alamos DNA Sequence Database. It provides a convenient way to search or verify various...Full Text Available

1982-01-11

362

Lessons in Signaling and Tumorigenesis from Polyomavirus Middle T Antigen

In vitro mutagenesis of functional DNA gene fragments by covalently reactive agents permits one in principle to examine the consequent alterations in DNA sequence directly. I have carried out selective mutagenesis of the tetracycline resistance gene in the plasmid pBR322 using the long wavelength UV light activated reaction of 4,5',8-trimethylpsoralen (TMP). The mutagenized DNA sequence was the EcoR1-Hind III restriction fragment in the vicinity of the Tcsup(R) promoter. Two classes of mutants were obtained. One exhibited a high level of Tc resistance (40-60 ..mu..g/ml) but still lower than the wild-type. Interestingly, these showed no sequence alterations at all in the vicinity of the TMP-reacted fragment. The other class of mutants exhibited low levels of drug resistance (< 20 ..mu..g/ml) and two of those that were sequenced were found to contain a 15-base pair insertion to the right of the original Hind III ...

1982-04-01

363

Integrative Analysis of Epigenetic Modulation in Melanoma Cell Response to Decitabine: Clinical Implications

Summary: The small DNA tumor viruses have provided a very long-lived source of insights into many aspects of the life cycle of eukaryotic cells. In recent years, the emphasis has been on cancer-related...Full Text Available

2009-09-01

364

Identification of copy number variations and common deletion polymorphisms in cattle

Decitabine, an epigenetic modifier that reactivates genes otherwise suppressed by DNA promoter methylation, is effective for some, but not all cancer patients, especially those with solid tumors. It...Full Text Available

365

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

366

Identification and characterization of plasmids from the western aster yellows mycoplasmalike organism.

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

367

Human spumaretrovirus-related sequences in the DNA of leukocytes from patients with Graves disease.

Supercoiled double-stranded DNA molecules (plasmids) were isolated from plants infected with three laboratory strains of western aster yellows mycoplasma-like organism (AY-MLO) by using cesium chloride-ethidium...Full Text Available

1990-03-01

368

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

Viruses, and more particularly retroviruses, have been postulated to play a role in the pathogenesis of autoimmune diseases. In a search for spumaretrovirus infection markers, we screened a group of...Full Text Available

1992-11-01

369

Heterogeneous mutations in the human lipoprotein lipase gene in patients with familial lipoprotein lipase deficiency.

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

370

Gyrase B Inhibitor Impairs HIV-1 Replication by Targeting Hsp90 and the Capsid Protein*

The DNA sequences were determined for the lipoprotein lipase (LPL) gene from five unrelated Japanese patients with familial LPL deficiency. The results demonstrated that all five patients are homozygotes...Full Text Available

1991-12-01

371

Genome-wide profiling of forum domains in Drosophila melanogaster

Chemical genetics is an emerging approach to investigate the biology of host-pathogen interactions. We screened several inhibitors of ATP-dependent DNA motors and detected the gyrase B inhibitor coumermycin...Full Text Available

2010-12-10

372

Genital HPV infection not a local but a regional infection: experience from a female teenage group.

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

373

Genetic screening: The vista of genomic medicine

OBJECTIVES--To investigate the prevalence of human papillomavirus (HPV) infections in a group of female teenagers, and to analyse to what extent HPV DNA was also detectable, in urethra and cervix samples...Full Text Available

1993-02-01

374

Genetic heterogeneity in human T-cell leukemia/lymphoma virus type II.

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

375

Genetic Variation at the Mitochondrial DNA 9-bp Repeat Locus in the Sakha of Siberia

DNA from the peripheral blood mononuclear cells of 17 different individuals infected with human T-cell lymphoma/leukemia virus type II (HTLV-II) was successfully amplified by the polymerase chain reaction...Full Text Available

1993-03-01

376

Genetic Diversity Assessment of Rarely Cultivated Traditional Indica Rice (Oryza sativa L.) Varieties

... 16223, 16292, and 16295, which classify them as haplogroup W (Richards et al. 2000). The sample that was ... belonged to haplogroup B, 2 individuals belonged to haplogroup W, and 1 individual belonged to ...

377

Generation of microsatellite repeat families by RTE retrotransposons in lepidopteran genomes

Random amplified polymorphic DNA fingerprinting was performed to assess the genetic diversity among rarely cultivated traditional indica rice (Oryza sativa ...Full Text Available

378

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

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

379

Functional interaction between the Werner Syndrome protein and DNA polymerase ?

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

380

Formation, Repair, and Genotoxic Properties of Bulky DNA Adducts Formed from Tobacco-Specific Nitrosamines

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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381

Flowcytometry of {gamma}-ray irradiated mouse ovary

4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and N′-nitrosonornicotine (NNN) are tobacco-specific nitrosamines present in tobacco products and smoke. Both compounds...Full Text Available

382

Exercise alters SIRT1, SIRT6, NAD and NAMPT levels in skeletal muscle of aged rats

This study was carried out to evaluate the biochemical and morphological effects of ionizing radiation on ovary. Immature mice (ICR, 3 week-old) were irradiated at a dose of LD{sub 80(30)} at KAERI. The ovaries were collected after 6 hours, 12 hours, 1 day, and 2 days post irradiation. To analyze the morphological changes, histological staining with hematoxylin-eosin, immuno- histochemical preparation using in situ 3'-end labeling was performed. DNA fragmentation analysis and flowcytometric evaluation of DNA extracted from whole ovary were performed. As a result of DNA fragmentation analysis, DNA fragments with 185, 370, and 555 base pairs were clearly shown at 6 hours post irradiation. The percentage of A{sub 0} cell cycle was significantly increased in the irradiated group than control. In situ 3'-end labeled follicles were increased at 6 hours post irradiation. The radiation-induced ...

1998-10-01

383

Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex

Silent information regulators are potent NAD⁺-dependent protein deacetylases, which have been shown to regulate gene silencing, muscle differentiation and DNA damage repair. Here,...Full Text Available

2010-01-01

384

Evidence of perturbations of cell cycle and DNA repair pathways as a consequence of human and murine NF1-haploinsufficiency

BackgroundConcerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity....Full Text Available

385

Evidence for Sub-Haplogroup H5 of Mitochondrial DNA as a Risk Factor for Late Onset Alzheimer's Disease

BackgroundNeurofibromatosis type 1 (NF1) is a common monogenic tumor-predisposition disorder that arises secondary to mutations in the tumor suppressor gene NF1....Full Text Available

386

Epigallocatechin gallate inhibits HBV DNA synthesis in a viral replication - inducible cell line

BackgroundAlzheimer's Disease (AD) is the most common neurodegenerative disease and the leading cause of dementia among senile subjects. It has been proposed that AD can be caused...Full Text Available

387

Elk-1 a Transcription Factor with Multiple Facets in the Brain

AIM: To analyze the antiviral mechanism of Epigallocatechin gallate (EGCG) against hepatitis B virus (HBV) replication.METHODS: In this research, the HBV-replicating cell line HepG2.117 was used...Full Text Available

2011-03-21

388

Effect of butylated hydroxytoluene pretreatment on the excretion, tissue distribution and DNA binding of (/sup 14/C)aflatoxin B1 in the rat

The ternary complex factor (TCF) Elk-1 is a transcription factor that regulates immediate early gene (IEG) expression via the serum response element (SRE) DNA consensus site. Elk-1 is associated with...Full Text Available

389

Effect of 9-(2-Hydroxyethoxymethyl)guanine on Herpesvirus-Induced Keratitis and Iritis in Rabbits

The effect of butylated hydroxytoluene (BHT) pretreatment (0.5% in the diet for 10 days) on the excretion, tissue distribution and DNA binding of orally administered (/sup 14/C)aflatoxin B1 (AFB1) was determined in male Fischer F344 rats. The amount of radioactivity excreted in the urine and feces by 24 hr was higher in BHT-treated rats than in controls. Treatment with BHT enhanced the excretion of water-soluble metabolites in the urine and in the large intestines plus feces at the earlier sampling times. The amount of radioactivity bound to hepatic nuclear DNA was six times less in the BHT-pretreated rats than in controls 6 hr after administration of the isotope. The half-lives of (/sup 14/C)DNA in the rat liver were 30 and 46 hr for control and BHT-pretreated rats, respectively. These results indicate that BHT pretreatment may protect the animal from the carcinogenic effects of AFB1 by enhancing the detoxification and ...

1985-06-01

390

Early and late skin reactions to radiotherapy for breast cancer and their correlation with radiation-induced DNA damage in lymphocytes

Drugs used for the inhibition of DNA viruses, such as iododeoxyuridine, adenine arabinoside, or trifluorothymidine, are not biochemically selective in their action and also interfere with normal cellular...Full Text Available

1978-12-01

391

Does Damage to DNA and Other Macromolecules Play a Role in Aging? If So, How?

IntroductionRadiotherapy outcomes might be further improved by a greater understanding of the individual variations in normal tissue reactions that determine tolerance. Most published...Full Text Available

2005-01-01

392

Differential effects of procaine and phenethyl alcohol on excision repair of DNA in u. v. -irradiated Escherichia coli

One of the most pervasive ideas regarding the causes of aging is that longevity is constrained in large measure by damage to macromolecules. An increasing body of cellular and molecular data, generated...Full Text Available

2009-02-01

393

Detection of hepatitis B virus DNA among accepted blood donors in Nanjing, China

Experiments were performed to investigate the involvement of the cell membrane in the excision DNA repair process in Escherichia coli. Two membrane-binding drugs, procaine and phenethyl alcohol (PEA), inhibited liquid-holding recovery (LBR) in u.v.-irradiated E. coli wild-type and recA strains. In uvrB and polA strains where, after u.v.-irradiation, LHR was absent the two drugs had no effect. Both drugs markedly reduced the removal of u.v.-induced thymine dimers in the DNA of wild-type cells (H/r30). Analysis by alkaline sucrose gradients revealed that PEA inhibited the incision step in excision repair. In contrast, procaine had no effect on incision but apparently inhibited the late steps in excision repair. PEA dissociated DNA from the cell membrane, whereas procaine did not. The results suggest that the two drugs PEA and procaine inhibit LHR and the excision repair process operating on u.v.-induced damage in E. coli by ...

1986-12-01

394

Detection of TP53 mutation, loss of heterozygosity and DNA content in fine-needle aspirates of breast carcinoma.

BackgroundPosttransfusion hepatitis B virus (HBV) infection still occurs although its incidence has been substantially reduced since the introduction of screening of hepatitis B...Full Text Available

395

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development

Recent preclinical and clinical data suggest that TP53 status and TP53 mutations may be important in determining tumour aggressiveness and therapy response. In this study we investigate the feasibility...Full Text Available

1998-01-01

396

De Novo Induction of Genetically Engineered Brain Tumors In Mice Using Plasmid DNA

BackgroundMicroorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential...Full Text Available

397

DNA methylation and gene expression differences in children conceived in vitro or in vivo

Spontaneous mouse models of cancer show promise to more accurately recapitulate human disease and predict clinical efficacy. Transgenic mice or viral vectors have been required to generate spontaneous...Full Text Available

2009-01-15

398

Computational approaches to discovering semantics in molecular biology

Epidemiological data indicate that children conceived in vitro have a greater relative risk of low birth-weight, major and minor birth defects, and rare disorders involving imprinted...Full Text Available

2009-10-15

399

Comparisons of three polyethyleneimine-derived nanoparticles as a gene therapy delivery system for renal cell carcinoma

One of the central questions of molecular biology is the discovery of the semantics of DNA. This discovery relies in a critical way on a variety of expensive computations. In order to solve these computations, both parallel computers and special-purpose hardware play a major role.

1989-07-01

400

Cloning and expression of recombinant, functional ricin B chain.

BackgroundPolyethyleneimine (PEI), which can interact with negatively charged DNA through electrostatic interaction to form nanocomplexes, has been widely attempted to use as a gene...Full Text Available

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401

Cloning and expression of a human kidney cDNA for an /alpha//sub 2/-adrenergic receptor subtype

The cDNA encoding the B chain of the plant toxin ricin has been cloned and expressed in monkey kidney COS-M6 cells. The recombinant B chain was detected by labeling the transfected cells with [35S]methionine...Full Text Available

1987-08-01

402

Cloning and Nucleotide Sequence Determination of the Entire mec DNA of Pre-Methicillin-Resistant Staphylococcus aureus N315

An /alpha//sub 2/-adrenergic receptor subtype has been cloned from a human kidney cDNA library using the gene for the human platelet /alpha//sub 2/-adrenergic receptor as a probe. The deduced amino acid sequence resembles the human platelet /alpha//sub 2/-adrenergic receptor and is consistent with the structure of other members of he family of guanine nucleotide-binding protein-coupled receptors. The cDNA was expressed in a mammalian cell line (COS-7), and the /alpha//sub 2/-adrenergic ligand (/sup 3/H)rauwolscine was bound. Competition curve analysis with a variety of adrenergic ligands suggests that this cDNA clone represents the /alpha//sub 2/B-adrenergic receptor. The gene for this receptor is on human chromosome 4, whereas the gene for the human platelet /alpha//sub 2/-adrenergic receptor (/alpha//sub 2/A) lies on chromosome 10. This ability to express the receptor in mammalian cells, free of other adrenergic receptor ...

1988-09-01

403

Chromosome location of Oryza sativa recombination linkage groups.

In methicillin-resistant Staphylococcus aureus, the methicillin resistance gene mecA is localized within a large chromosomal region which is absent in the methicillin-susceptible...Full Text Available

1999-06-01

404

Chromosomal sites for hepatitis B virus integration in human hepatocellular carcinoma.

In situ hybridization, a powerful tool for the molecular cytogeneticist, can be used to physically map repetitive, low-copy, and unique DNA sequences in plant chromosomes. With the availability of a...Full Text Available

1992-09-15

405

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

The discovery that hepatitis B virus (HBV) integrates into host chromosomes raises the question of whether such viral DNA integration correlates directly with the activation of specific oncogenes or...Full Text Available

1991-12-01

406

Characterization of Two Divergent Lineages of Macaque Rhadinoviruses Related to Kaposi's Sarcoma-Associated Herpesvirus

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

407

Calculations of physical and chemical reactions produced in irradiated water containing DNA

We have cloned and characterized the entire DNA polymerase gene and flanking regions from Kaposi's sarcoma-associated herpesvirus (KSHV) and two closely related macaque homologs of KSHV, retroperitoneal...Full Text Available

2000-05-01

408

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

Initial results obtained with a Monte Carlo computer program designed to link initial physical events in irradiated liquid water with subsequent chemical and biological events are presented. 10 refs., 4 figs., 3 tabs.

1985-01-01

409

Binding of PFOS to serum albumin and DNA: insight into the molecular toxicity of perfluorochemicals

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

410

Bacterial Artificial Chromosome Mutagenesis Using Recombineering

BackgroundHealth risk from exposure of perfluorochemicals (PFCs) to wildlife and human has been a subject of great interest for understanding their molecular mechanism of toxicity....Full Text Available

411

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

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

412

Attitudes toward abortion among parents of children with cystic fibrosis.

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

413

Assessing phytoremediation potentials of selected tropical plants for acrylamide

BACKGROUND: DNA prenatal diagnosis for cystic fibrosis (CF) has been available for parents of affected children since late 1985. METHODS: Using anonymous questionnaires, we surveyed 395 parents of children...Full Text Available

1991-08-01

414

Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State

In biotechnology, acrylamide is being used in DNA and RNA analysis using the polyacrylamide gel electrophoreses procedure. Polymerized acrylamide is degraded into acrylamide through time; it is converted into a hazardous contaminant that is carcinogenic and neurotoxic to animals and humans. Because ...

415

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

DNA replication programs have been studied extensively in yeast and animal systems, where they have been shown to correlate with gene expression and certain epigenetic modifications. Despite the conservation...Full Text Available

2010-06-01

416

Air pollution induces heritable DNA mutations

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

417

Adaptive response of the chicken embryo to low doses of x-irradiation

Hundreds of thousands of people worldwide live or work in close proximity to steel mills. Integrated steel production generates chemical pollution containing compounds that can induce genetic damage...Full Text Available

2002-12-10

418

Acetylation of Histones and Transcription-Related Factors

Chicken embryos were x-irradiated in ovo with 5-30 cGy (=priming dose) at the 13th-15th day of development. After 3-48 h, brain- and liver-cell suspensions were x-irradiated in vitro with (challenge) doses of 4-32 Gy. Significantly less radiation damage was observed when the radiation response was measured by scheduled DNA synthesis, nucleoid sedimentation and viscosity of alkaline cell lysates 12-36 h after the priming exposure. In vivo, pre-irradiation with 10 cGy enhanced regeneration as evidenced by the DNA content of chicken embryo brain and liver 24 h following a challenge dose of 4 Gy. From nucleoid sedimentation analyses in brain and liver cells immediately after irradiation with 16 Gy and after a 30-min repair period in the presence of aphidicolin, dideoxythymidine and 3-aminobenzamide or in the absence of these DNA repair inhibitors, it is concluded that a reduction of the initial radiation damage is the dominant ...

1995-08-01

419

ATM-Dependent Phosphorylation of ATF2 Is Required for the DNA Damage Response

The state of chromatin (the packaging of DNA in eukaryotes) has long been recognized to have major effects on levels of gene expression, and numerous chromatin-altering strategies—including...Full Text Available

2000-06-01

420

A supervised approach for predicting patient survival with gene expression data

SummaryActivating transcription factor 2 (ATF2) is regulated by JNK/p38 in response to stress. Here, we demonstrate that the protein kinase ATM phosphorylates ATF2 on serines...Full Text Available

2005-05-27

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421

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)

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

422

A polyacetylene compound from herbal medicine regulates genes associated with thrombosis in endothelial cells

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

423

A cytosine methyltransferase homologue is essential for repeat-induced point mutation in Neurospora crassa

From Toki-shakuyaku-san, an herbal formulation for “cleansing stagnated blood,” a key gene regulatory compound was purified and identified through a screening based on DNA microarray...Full Text Available

2007-12-15

424

A catalase from the freshwater mussel Cristaria plicata with cloning, identification and protein characterization

During sexual development, Neurospora crassa inactivates genes in duplicated DNA segments by a hypermutation process, repeat-induced point mutation (RIP). RIP introduces C:G to T:A...Full Text Available

2002-06-25

425

British Library Electronic Table of Contents (United Kingdom)

Catalase is an important antioxidant protein which can protect organisms against various oxidative stresses by eliminating hydrogen peroxide. The catalase cDNA of Cristaria plicata@?cpCAT@? was cloned from the haemocytes using degenerate primers by the method of 3' and 5' rapid amplification of cDNA ends PCR. The gene is 4863 bp long and has a total of two introns and three exons. The precise size and location of the introns and exons have been determined. In addition the full-length cDNA of cpCAT contained 2618 bp, The cDNA contained a 5' untranslated region (UTR) of 136 nucleotides, the 3' UTR of 979 bp with a canonical polyadenylation signal sequence AATAAA and a polyA tail, and an open reading frame (ORF) of 1503 bp, encoding 501 amino acid residues with 56.86 kDa predicted molecular w...

2011-01-01

426

A Software System for Data Analysis in Automated DNA?Sequencing

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

Software for gel image analysis and base-calling in fluorescence-based sequencing consisting of two primary programs, BaseFinder and GelImager, is described. BaseFinder is a framework for trace processing,...Full Text Available

1998-06-01

427

A Brassica rapa Linkage Map of EST-based SNP Markers for Identification of Candidate Genes Controlling Flowering Time and Leaf Morphological Traits

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

428

For identification of genes responsible for varietal differences in flowering time and leaf morphological traits, we constructed a linkage map of Brassica rapa DNA markers including...Full Text Available

2009-12-01

429

?H2AX and cancer

The role of lesions of DNA in senescence of seeds of Lupinus polyphyllus L. induced by chronic low-intensity irradiation

Histone H2AX phosphorylation on a serine four residues from the carboxyl terminus (producing γH2AX) is a sensitive marker for DNA double-strand breaks (DSBs). DSBs may lead to cancer...Full Text Available

2008-12-01

430

The effect of mitochondrial dysfunction on cytosolic nucleotide metabolism

A nonlinear relationship between the time of accelerated aging of Lupine seeds and the indices of its survival as well as the single-strand DNA amount in cells from these seeds is established. The character of this relationship is essentially altered in chronically irradiated lupine seeds from the Chernobyl NPP exclusion zone and seems more complicated. The possible role of repair systems in these effects is discussed. The fact that chronic irradiation in low doses can modify the course of senescence in lupine seeds reflects its high biological efficiency comparing with acute irradiation.

2000-08-01

431

Programmed Assembly of Quantum-Dot Arrays on DNA Templates: Hardware for Quantum Computing?

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

432

Mathematical analysis of DNA histograms from asynchronous and synchronous cell populations

This paper reports progress in the fabrication and characterization of an array of 1nm-scale colloidal particles (i.e., quantum-dot array) that can be operated to execute nontrivial and innovative computations, possibly including quantum logic. We discuss the actual fabrication of 2-nm metal clusters as an example of possible quantum dot implementation. Innovative and unconventional paradigms underlie the different stages of this work. For example, regular array geometry is achieved by directing appropriately derivatized metal clusters to preselected locations along a stretched strand of an engineered DNA sequence.

2001-03-23

433

Localization of highly repetitive, species-specific EcoRI elements from 'Lupinus luteus' L

A technique is presented for the analyss of DNA histograms which is an extension of earlier discrete Gaussian summing methods. It alleviates the problems encountered with previous methods by extending the S-phase portions of the distribution under the G/sub 1/ and G/sub 2/ + M peaks. The resuts obtained by this method for the fraction of cells in the G/sub 1/, S, and G/sub 2/ + M phases of the life cycle are compared with autoradiographic results. With one or two exceptions which are discussed, agreement between autoradiography and the analytical method is good.

1977-01-01

434

Genotoxic damage in polychaetes: A study of species and cell-type sensitivities

Using Southern, dot-blot and 'in situ' hybridization, molecular and cytological localization of repetitive 'Lupinus lueteus' DNA sequence was shown. Under CsCl gradient centrifugation conditions CG-rich satellite fraction appeared. Dot-blot hybridization clearly indicated that 1070bp repetitive element being a member of previously described EcoRI fragments family appeared only in the main band. The use of that DNA fragment as an 'in situ' hybridization signal in the euchromatin area. (author). 26 refs, 3 figs.

435

British Library Electronic Table of Contents (United Kingdom)

The marine environment is becoming increasingly contaminated by environmental pollutants with the potential to damage DNA, with marine sediments acting as a sink for many of these contaminants. Understanding genotoxic responses in sediment-dwelling marine organisms, such as polychaetes, is therefore of increasing importance. This study is an exploration of species-specific and cell-specific differences in cell sensitivities to DNA-damaging agents in polychaete worms, aimed at increasing fundamental knowledge of their responses to genotoxic damage. The sensitivities of coelomocytes from three polychaetes species of high ecological relevance, i.e. the lugworm Arenicola marina, the harbour ragworm Nereis diversicolor and the king ragworm Nereis virens to genotoxic damage are compared, and dif...

2008-01-01

436

Dipyrone-induced changes in DNA repair and other cell membrane associated processes in Escherichia coli

Dipyrone-induced changes in DNA repair and other cell membrane associated processes in Escherichia coli

The analgesic, dipyrone (1,phenyl-2,3-dimethyl-5-pyrazolone-4-methylamino methane sulphonate sodium), at 20 mM concentration, inhibited the rejoining of single-strand scissions in DNA of Escherichia coli B/r cells induced by 20 krad gamma-radiation. The chemical altered the cell membrane structure as evidenced from the uptake of acriflavin, the efflux of potassium ions from the bacterial cells and the inhibition of alkaline phosphatase-a cell membrane associated enzyme. (author). 18 refs., 6 figures.

1982-09-01

437

DNA cleavage on photoexposure at the d-d band in ternary copper(II) complexes using red-light laser.

The analgesic, dipyrone (1,phenyl-2,3-dimethyl-5-pyrazolone-4-methylamino methane sulphonate sodium), at 20 mM concentration, inhibited the rejoining of single-strand scissions in DNA of Escherichia coli B/r cells induced by 20 krad gamma-radiation. The chemical altered the cell membrane structure as evidenced from the uptake of acriflavin, the efflux of potassium ions from the bacterial cells and the inhibition of alkaline phosphatase-a cell membrane associated enzyme. (author).

438

Analysis of the tet repressor-operator interactions using the uracil-DNA glycosylase footprinting system

Ternary copper(II) complexes [Cu(L1)B](ClO4) (1, 2) and [Cu(L2)B](ClO4) (3, 4), where HL1 and HL2 are tridentate NSO- and ONO-donor Schiff bases and B is a heterocyclic base, viz. dipyrido[3,2-d:2',3'-f]quinoxaline (dpq, 1 and 3) or dipyrido[3,2-a:2',3'-c]phenazine (dppz, 2 and 4), were prepared and their DNA binding and photoinduced DNA cleavage activity studied. Complex 1, structurally characterized by single-crystal X-ray crystallography, shows an axially elongated square-pyramidal (4 + 1) coordination geometry in which the monoanionic L1 binds at the equatorial plane. The NN-donor dpq ligand exhibits an axial-equatorial binding mode. The complexes display good binding propensity to calf thymus DNA, giving a relative order 2 (NSO-dppz) > 4 (ONO-dppz) > 1 (NSO-dpq) > 3 (ONO-dpq). They cleave supercoiled pUC19 DNA to its nicked circular form when treated with 3-mercaptopropionic acid (MPA) by ...

2006-12-25

439

Transcriptional regulation in Drosophila: the post-genome challenge.

The tet repressor regulated expression of the Tn-10-encoded tetracycline resistance determinant in a tetracycline-dependent manner. In the absence of tetracycline, the tet repressor binds as a dimer to the 19-base-pair palindromic tet operator sequence. Amino acid homologies and genetic studies with trans-dominant mutants suggest that sequence-specific recognition of the tet operator involves the extensively studied helix-turn-helix motif. We have used the uracil-DNA glycosylase (UDG) footprinting systems to identify thymine contacts in the tet operator that are essential for the formation of tet repressor-operator complexes.

1994-12-31

440

Functions of mammalian Cdc7 kinase in initiation/monitoring of DNA replication and development

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 ...

2001-03-01

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

441

Differential effects of chronic ingestion of tritiated water on prenatal brain development

Cdc7 kinase plays an essential role in firing of replication origins by phosphorylating components of the replication complexes. Cdc7 kinase has also been implicated in S phase checkpoint signaling downstream of the ATR and Chk1 kinases. Inactivation of Cdc7 in yeast results in arrest of cell growth with 1C DNA content after completion of the ongoing DNA replication. In contrast, conditional inactivation of Cdc7 in undifferentiated mouse embryonic stem (ES) cells leads to growth arrest with rapid cessation of DNA synthesis, suggesting requirement of Cdc7 functions for continuation of ongoing DNA synthesis. Furthermore, loss of Cdc7 function induces recombinational repair (nuclear Rad51 foci) and G2/M checkpoint responses (inhibition of Cdc2 kinase). Eventually, p53 becomes highly activated and the cells undergo massive p53-dependent apoptosis. Thus, defective origin activation in mammalian cells can ...

2003-11-27

442

String Junctions and Holographic Interfaces

Female rats were given tritiated drinking water (3 microCi/ml) from 30 days before mating up to and throughout pregnancy. At this low dose, the course and the outcome of pregnancy were normal. The differences between newborn body and cerebral weights of the treated rats and those of control animals were on the borderline of significance. In contrast, cerebral DNA and cerebral protein were highly significantly lower. In 30-35% of the treated population the DNA and protein values were more than 2 standard deviations (SD) below the mean values for the control population. Thus the number of the progeny of the mothers exposed to tritiated water that were considered to have outstandingly low levels of DNA and protein was 14-17 times greater than in the control group. The irradiated population also had 3-5% of severely affected individuals with cerebral DNA and protein values more than 2 SD below the mean of ...

443

Magnetic resonance imaging: early detection of central nervous system involvement in acquired immunodeficiency syndrome (AIDS)

In this paper we study half-BPS type IIB supergravity solutions with multiple $AdS_3\\times S^3\\times M_4$ asymptotic regions, where $M_4$ is either $T^4$ or $K_3$. These solutions were first constructed in [1] and have geometries given by the warped product of $AdS_2 \\times S^2 \\times M_4 $ over $\\Sigma$, where $\\Sigma$ is a Riemann surface. We show that the holographic boundary has the structure of a star graph, i.e. $n$ half-lines joined at a point. The attractor mechanism and the relation of the solutions to junctions of self-dual strings in six-dimensional supergravity are discussed. The solutions of [1] are constructed introducing two meromorphic and two harmonic functions defined on $\\Sigma$. We focus our analysis on solutions corresponding to junctions of three different conformal field theories and show that the conditions for having a solution charged only under Ramond-Ramond three-form fields reduce to relations involving the ...

2010-01-01

444

Hypothalmic hypopituitarism following cranial irradiation for nasopharyngeal carcinoma

Central Nervous System (CNS) involvement, whether primary by the Human Immunodeficiency Virus - HIV - itself, or secondary (toxoplasmosis or lymphoma) is remarkably frequent in AIDS, in 40 to 70% of cases, depending upon the author. In order to study the natural history of this illness, a cohort of 25 asymptomatic seropositive patients have been established. Every 6 months these patients undergo biological and clinical examinations, as well as Magnetic Resonance brain scans. After two examinations at a 6 month's interval, the first results are reported. Out of these 25 cases, 9 present anomalies: One patient with diffuse cerebral atrophy and 8 others with high signal intensity areas on T2 weighted sequences, like those of the Multiple Sclerosis. No relationship could be demonstrated between the existence of these lesions and various criteria such as age, sex, risk factors and T4 cells count. The nature of these lesions is not lear. They ...

445

Assessment of oral toxicity and safety of pentamethylchromanol (PMCol), a potential chemopreventative agent, in rats and dogs

Eight patients, one male and seven females, with no pre-existing hypothalamic-pituitary disease, who developed symptoms of hypopituitarism following cranial irradiation for nasopharyngeal carcinoma were studied 5 years or more after radiotherapy. All were GH deficient. Four of the patients with no GH response during insulin tolerance tests (ITT) showed increased GH in response to synthetic human growth hormone releasing factor (GRF-44). Four patients had impaired cortisol responses to ITT, and gradual but diminished cortisol responses to ovine corticotrophin releasing factor (CRF-41). There was no significant difference between mean peak increments in response to ITT and those in response to CRF-41. TSH responses to TRH were delayed in five and absent in two patients; four of these had low free T4 index. Prolactin was raised in all seven women and increased further in response to TRH. Two patients had impaired gonadotrophin responses to LHRH. ...

1986-06-01

446

British Library Electronic Table of Contents (United Kingdom)

2,2,5,7,8-Pentamethyl-6-chromanol (PMCol) was administered by gavage in rats for 28 days at dose levels of 0, 100, 500, and 2000mg/kg/day. PMCol administration induced decreases in body weight gains and food consumption, hepatotoxicity (increased TBILI, ALB, ALT, TP; increased relative liver weights; increased T4 and TSH), nephrotoxicity (increased BUN and BUN/CREAT, histopathology lesions), effect on lipid metabolism (increased CHOL), anemia, increase in WBC counts (total and differential), coagulation (FBGNand PTdarr) and hyperkeratosis of the nonglandular stomach in the 2000mg/kg/day dose group (in one or both sexes). In the 500mg/kg/day dose group, toxicity was seen to a lesser extent. In the 100mg/kg/day dose group, only increased CHOL (females) was observed. To assess the toxicity of...

2010-01-01

447

Analytic modelling of tidal effects in the relativistic inspiral of binary neutron stars

2000-centiGray total lymphoid irradiation for refractory rheumatoid arthritis

To detect the gravitational-wave signal from binary neutron stars and extract information about the equation of state of matter at nuclear density, it is necessary to match the signal with a bank of accurate templates. We have performed the longest (to date) general-relativistic simulations of binary neutron stars with different compactnesses and used them to constrain a tidal extension of the effective-one-body model so that it reproduces the numerical waveforms accurately and essentially up to the merger. The typical errors in the phase over the $\\simeq 22$ gravitational-wave cycles are $\\Delta \\phi\\simeq \\pm 0.24$ rad, thus with relative phase errors $\\Delta \\phi/\\phi \\simeq 0.2%$. We also show that with a single choice of parameters, the effective-one-body approach is able to reproduce all of the numerically-computed phase evolutions, in contrast with what found when adopting a tidally corrected post-Newtonian Taylor-T4 expansion.

2010-01-01

448

[Cloning of the gene for thermostable Thermus aquaticus YT1 DNA polymerase and its expression in Escherichia coli].

Because toxicity with the use of 3000 centiGray (cGy) of total lymphoid irradiation (TLI) was observed in an earlier study, 2000-cGy treatments were delivered in a 2-portal format to 7 patients and in a modified 3-portal fashion to 6 patients, as part of a randomized, investigator-blinded trial of TLI treatment for refractory rheumatoid arthritis. Analysis of combined data from the 13 patients revealed statistically significant improvement in 5 clinical indicators of disease activity at the end of TLI and 6 and 12 months later, accompanied by T4-specific immunosuppression. Management considerations resulted in the introduction of prednisone therapy in 5 patients, methotrexate in 4, and azathioprine in 1 during the interval of 8-12 months post-TLI. Herpes zoster occurred in 5 patients prior to the initiation of this additional therapy. These data indicate that, in patients with rheumatoid arthritis, a TLI dose of 2000 cGy is sufficient to ...

449

The Differentially Expressed Genes by Radiotherapy in the Patients with Uterine Cervix Cancer

Using the phasmid vector pSL5, the genomic DNA fragment of T. aquaticus YT1 which contained the thermostable DNA polymerase (Taq-polymerase) gene was cloned. The BglII fragment of this genome locus was subcloned in the BamHI site of the pUC19 plasmid. To optimize the Taq-polymerase gene expression in E. coli cells, the gene was cloned in the correct reading frame regarding the initiation ATG codon of the pPR-TGATG-1 expression vector. The gene expression in this vector was controlled by the phage lambda PR promoter and the temperature-sensitive phage lambda repressor. We used PCR to amplify the short 5'-end fragment of the Taq-polymerase gene coding for the part into which an artificial SacI site was introduced. This site has been used for cloning the PCR product into the pPR-TGATG-1 vector, and the missing gene part was cloned into the KpnI site of the PCR product from the natural cloned gene. The cells of the E. coli PVG-A1 strain, which was ...

450

Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A

Purpose : To detect differentially expressed genes in the patients with uterine cervical cancer during the radiation therapy. Materials and Methods : In patients with biopsy proven uterine cervical cancer, we took a tumor tissue just before radiation therapy and at 40 minutes after external irradiation of 1.8 Gy. Total RNAs isolated from non-irradiated and irradiated tumor tissue samples were analyzed using the differential-display reverse transcription-polymerase chain reaction (DDRT-PCR). Complementary DNA (cDNA) fragments corresponding to differentially expressed messenger RNAs(mRNAs) were eluted, and cloned. The differential expression of the corresponding mRNAs was confirmed by reverse northern blot. Differentially expressed cDNA bands were sequenced. Nucleotide sequence data were analyzed in the Gene Bank and EMBL databases via the BLAST network server to identify homologies to known genes or cDNA ...

2001-12-15

451

Strikingly different penetrance of LHON in two Chinese families with primary mutation G11778A is independent of mtDNA haplogroup background and secondary mutation G13708A

The penetrance of Leber's hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in different affected pedigrees. Here we describe two large Chinese families that show a striking difference in the penetrance of LHON, in which 53.3% and 15.0% of members were affected (P < 0.02), respectively. Analysis of the complete mtDNA genome of the two families revealed the presence of the primary mutation G11778A and several other variants suggesting the same haplogroup status G2a. The family with higher penetrance contained a previously described secondary mutation G13708A, which presents a polymorphism in normal Chinese samples and does not affect in vivo mitochondrial oxidative metabolism as described in a previous study. Evolutionary analysis failed ...

2008-08-25

452

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

The penetrance of Leber's hereditary optic neuropathy (LHON) in families with primary mitochondrial DNA (mtDNA) mutations is very complex. Matrilineal and nuclear genetic background, as well as environmental factors, have been reported to be involved in different affected pedigrees. Here we describe two large Chinese families that show a striking difference in the penetrance of LHON, in which 53.3% and 15.0% of members were affected (P < 0.02), respectively. Analysis of the complete mtDNA genome of the two families revealed the presence of the primary mutation G11778A and several other variants suggesting the same haplogroup status G2a. The family with higher penetrance contained a previously described secondary mutation G13708A, which presents a polymorphism in normal Chinese samples and does not affect in vivo mitochondrial oxidative metabolism as described in a previous study. Evolutionary analysis failed to indicate ...

2008-08-25

453

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

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, ...

1996-12-31

454

cDNA cloning and sequence analysis of preproendothelin-1 (PPET-1) from salmon, Oncorhynchus keta.

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

455

The mitochondrial genome of the entomophagous endoparasite Xenosvesparum (Insecta: Strepsiptera)

The presence of endothelin (ET)-like immunoreactivity and the cardiovascular effects of mammalian ET-1 in fish have been reported. To identify ET-related peptides in fish, we screened the cDNA library of the salmon (Oncorhynchus keta) stomach by means of rapid amplification of cDNA ends, and we cloned cDNAs encoding an ET-related peptide. The salmon ET-related sequence of 21 amino acids is identical to the trout ET-1 peptide recently purified from kidney specimens of Oncorhynchus mykiss. The deduced amino acid sequence of salmon pre-proET-1 (PPET-1) comprises 244 amino acids, including a putative signal sequence and mature ET-1, as well as big ET-1 and ET-1-like sequences. This precursor, the first reported PPET-1 sequence for Salmoniformes, Teleostei, has low homology with the sequences of human, mouse, frog (Xenopus laevis), and zebrafish (Danio rerio) PPET-1 (26%, 29%, 24%, and 39%, respectively). PMID:16740985

2006-06-01

456

Stability and cations coordination of DNA and RNA 14-mer G-quadruplexes: a multiscale computational approach.

In this study, the nearly complete sequence (14,519 bp) of the mitochondrial DNA (mtDNA) of the entomophagous endoparasite Xenos vesparum (Insecta: Strepsiptera) is described. All protein coding genes (PCGs) are in the arrangement known to be ancestral for insects, but three tRNA genes (trnA, trnS(gcu), and trnL(uag)) have transposed to derived positions and there are three tandem copies of trnH, each of which is potentially functional. All of these rearrangements except for that of trnL(uag) is within the short span between nad3 and nad4 and there are numerous blocks of unassignable sequence in this region, perhaps as remnants of larger scale predisposing rearrangements. X. vesparum mtDNA nucleotide composition is strongly biased toward As and Ts, as is typical for insect mtDNAs. There is also significant strand skew in the distribution of these nucleotides, with the J-strand being richer in A than T and in C than G, and ...

2005-12-01

457

Predicting Knot and Catenane Type of Products of Site-specific Recombination on Twist Knot Substrates

Molecular dynamics simulations have been used to study the differences between two DNA and RNA 14-mer quadruplexes of analogous sequences. Their structures present a completely different fold: DNA forms a bimolecular quadruplex containing antiparallel strands and diagonal loops; RNA forms an intrastrand parallel quadruplex containing a G-tetrad and an hexad, which dimerizes by hexad stacking. We used a multiscale computational approach combining classical Molecular dynamics simulations and density functional theory calculations to elucidate the difference in stability of the 2-folds and their ability in coordinating cations. The presence of 2'-OH groups in the RNA promotes the formation of a large number of intramolecular hydrogen bonds that account for the difference in fold and stability of the two 14-mers. We observe that the adenines in the RNA quadruplex play a key role in conserving the geometry of the hexad. We predict the cation ...

2008-09-03

458

Physical mapping of human chromosome 16. Annual progress report

Site-specific recombination is an important cellular process that yields a variety of knotted and catenated DNA products on supercoiled circular DNA. Twist knots are some of the most common conformations of these products. They are also one of the simplest families of knots and catenanes. Yet, our systematic understanding of their implication in DNA and important cellular processes like site-specific recombination is very limited. Here we present a topological model of site-specific recombination characterising all possible products of site-specific recombination on twist knot substrates, extending previous work of Buck and Flapan. We illustrate how to use our model to examine previously uncharacterized experimental data. We show how our model can help determine the sequence of products in multiple rounds of processive recombination and distinguish between products of processive and distributive recombination. Companion ...

2010-01-01

459

Light-dependent regulation of DEL1 is determined by the antagonistic action of E2Fb and E2Fc.

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 ...

1993-08-01

460

Investigation of xenotropic murine leukemia virus-related virus (XMRV) in human and other cell lines.

Endoreduplication represents a cell cycle variant during which multiple rounds of DNA replication occur without subsequent chromosome separation and cytokinesis, resulting into a cellular increase of the DNA content. Although the DNA ploidy level of cells is controlled by external stimuli such as light, currently limited knowledge is available on how environmental signals regulate the endoreduplication cycle at the molecular level. Previously, we have demonstrated that the conversion from the mitotic cell cycle into an endoreduplication cycle is mediated by the atypical E2F transcription factor DEL1 that operates as a repressor of endocycle onset. Here, we identified DEL1 as a transcriptional target of the classical E2Fb and E2Fc transcription factors that antagonistically control DEL1 transcript levels through competition for a single E2F cis-acting binding site. Correspondingly with the reported opposite effect of light ...

2011-09-01

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

461

In vivo hypermutation of xenotropic murine leukemia virus-related virus DNA in peripheral blood mononuclear cells of rhesus macaque by APOBEC3 proteins.

Xenotropic murine leukemia virus-related virus (XMRV) was discovered in human prostate tumors and later in some chronic fatigue syndrome (CFS) patients. However, subsequent studies have identified various sources of potential contamination with XMRV and other murine leukemia virus (MLV)-related sequences in test samples. Biological and nucleotide sequence analysis indicates that XMRV is distinct from known xenotropic MLVs and has a broad host range and cell tropism including human cells. Therefore, it is prudent to minimize the risk of human exposure to infection by evaluating XMRV contamination in cell lines handled in laboratory research and particularly those used in the manufacture of biological products. Nested DNA PCR assays were optimized for investigating XMRV gag and env sequences in various cell lines, which included MRC-5, Vero, HEK-293, MDCK, HeLa, and A549, that may be used in the development of some vaccines and other cell lines broadly used in ...

2011-10-11

462

Hepatic aflatoxin B1-DNA adducts and TP53 mutations in patients with hepatocellular carcinoma despite low exposure to aflatoxin B1 in southern Japan

The gammaretrovirus, xenotropic murine leukemia virus-related virus (XMRV), replicates to high titers in some human cell lines and is able to infect non-human primates. To determine whether APOBEC3 (A3) proteins restrict XMRV infections in a non-human primate model, we sequenced proviral DNA from peripheral blood mononuclear cells of XMRV-infected rhesus macaques. Hypermutation characteristic of A3DE, A3F and A3G activities was observed in the XMRV proviral sequences in vivo. Furthermore, expression of rhesus A3DE, A3F, or A3G in human cells inhibited XMRV infection and caused hypermutation of XMRV DNA. These studies show that some rhesus A3 isoforms are highly effective against XMRV in the blood of a non-human primate model of infection and in cultured human cells. PMID:21982221

2011-10-01

463

British Library Electronic Table of Contents (United Kingdom)

Abstract Background & aims: Hepatitis B or C virus infection is considered to be the main cause of hepatocellular carcinoma (HCC) in Japan. Aflatoxin B1 (AFB1) is a carcinogen associated with HCC in regions with high exposure. Mutations in codon 249, exon 7 are a hallmark of AFB1 exposure. Therefore, to clarify the role of AFB1 in hepatocarcinogenesis, we examined AFB1-DNA in liver tissue and sequenced TP53 in Japanese patients with HCC. Methods: Hepatocyte AFB1-DNA adducts were determined immunohistochemically and direct sequencing of TP53 was done to determine mutations in 188 of 279 patients who underwent hepatic resection for HCC. We assessed hepatitis C virus antibodies (HCV Ab) and HBSAg expression; patients without either were defined as having non-B non-C hepatocellular carcinoma (...

2011-01-01

464

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

First report of the complete sequence of Sida golden yellow vein virus from Jamaica.

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

465

Final report of the specific research. Investigations on the analysis of bio-protective factors against radiation. 1998-2000 FY (Research Group of NIRS)

Begomoviruses are phytopathogens that threaten food security [18]. Sida spp. are ubiquitous weed species found in Jamaica. Sida samples were collected island-wide, DNA was extracted via a modified Dellaporta method, and the viral genome was amplified using degenerate and sequence-specific primers [2, 11]. The amplicons were cloned and sequenced. Sequence analysis revealed that a DNA-A molecule isolated from a plant in Liguanea, St. Andrew, was 90.9% similar to Sida golden yellow vein virus-[United States of America:Homestead:A11], making it a strain of SiGYVV. It was named Sida golden yellow vein virus-[Jamaica:Liguanea 2:2008] (SiGYVV-[JM:Lig2:08]). The cognate DNA-B, previously unreported, was successfully cloned and was most similar to that of Malvastrum yellow mosaic Jamaica virus (MaYMJV). Phylogenetic analysis suggested that this virus was most closely related to begomoviruses that infect malvaceous hosts in Jamaica, ...

2011-05-29

466

Evidence of minimal methanogenic numbers and activity in sediments collected from the JAPEX/JNOC/GSC et al. Mallik 5L-38 gas hydrate production research well

This report concerns investigations in the title conducted by 8 groups of National Institute of Radiological Sciences (NIRS) during the period of 1998-2000. The groups are for investigation of: Effects of p53 tumor suppressor gene in radiation-induced leukemia, Role of atm-gene in dose rate effect of ionizing radiation, Function of DNA-dependent protein kinase catalytic subunit (DNA-PK{sub cs}), Functional complementation of radiation-sensitive mutant M10 cell line by human XRCC4 cDNA expression, Role of radiation-induced apoptosis in digital defects in embryonic mice, Functional analysis of S-phase specific novel nuclear protein NP95 by gene targeting, Role of chemokine in T cell development and lymphomagenesis, and establishment of production techniques of gene-modified mice using embryonic stem cells for genetic analysis of radiation-sensitive genes. The groups describe summaries of their studies and published original ...

2002-03-01

467

Effects of intersegmental transfers on target location by proteins

Gene analysis was used to determined the presence, abundance and phylogenetic affiliation of methanogens that exist in gas-hydrate-bearing sediment samples obtained from 23 drill cores from the JAPEX/JNOC/GSC et al. Mallik 5L-38 gas hydrate research well. Rates of methane production were examined using sediment-inoculated enrichments containing {sup 14}C-labeled carbon substrates, carbon dioxide and acetate. Archaeal 16S rDNA was only detected in 6 of the samples, resulting in 8 sequences with relationships to the Miscellaneous Crenarchaeotic Group (7 clones) and the Subsurface Euryarchaeotic Group (1 clone). The single Euryarchaeota sequence did not appear to be related to methanogens. Subsamples from the cores showed variable results upon DNA extraction and amplification. Methanogenic Coenzyme M (CoM) was detected in 13 of the 20 cores, but methanogenic methyl CoM reductase genes were not amplified from the samples when using a sensitive ...

2005-07-01

468

Assessment of the role of oxygen and mitochondria in heat shock induction of radiation and thermal resistance in Saccharomyces cerevisiae

We study a model for a protein searching for a target, using facilitated diffusion, on a DNA molecule confined in a finite volume. The model includes three distinct pathways for facilitated diffusion: (a) sliding - in which the protein diffuses along the contour of the DNA (b) jumping - where the protein travels between two sites along the DNA by three-dimensional diffusion, and finally (c) intersegmental transfer - which allows the protein to move from one site to another by transiently binding both at the same time. The typical search time is calculated using scaling arguments which are verified numerically. Our results suggest that the inclusion of intersegmental transfer (i) decreases the search time considerably (ii) makes the search time much more robust to variations in the parameters of the model and (iii) that the optimal search time occurs in a regime very different than that found for models which ignore ...

2008-01-01

469

Analysis of the 5{prime} region of PMS2 reveals heterogeneous transcripts and a novel overlapping gene

In response to a heat shock, the yeast Saccharomyces cerevisiae undergoes a large increase in its resistance to heat and, by the induction of its recombinational DNA repair capacity, a corresponding increase in resistance to radiation. Yeast which lack mitochondrial DNA, mitochondria-controlled protein synthetic apparatus, aerobic respiration, and electron transport (rho/sup 0/ strain) were used to assess the role of O/sub 2/, mitochondria, and oxidative processes controlled by mitochondria in the induction of these resistances. We have found that rho/sup 0/ yeast grown and heat shocked in either the presence or absence of O/sub 2/ are capable of developing both radiation and heat resistance. We conclude that neither the stress signal nor its cellular consequences of induced heat and radiation resistance are directly dependent on O/sub 2/, mitochondrial DNA, or mitochondria-controlled protein synthetic or oxidative ...

1983-10-01

470

Accelerator driven assembly

The PMS2 gene encodes a protein that is involved in DNA mismatch repair and is mutated in a subset of patients with hereditary nonpolyposis colon cancer (HNPCC). The previously published PMS2 cDNA sequence lack an upstream in-frame stop codon preceding the presumptive initiating methionine. To evaluate the 5` terminus of the PMS2 coding region further, we isolated additional cDNA clones, RT-PCR products, and the corresponding 5` genomic segment of the PMS2 locus. The PMS2 gene transcripts were found to have heterogeneous but colinear 5` termini, one of which contained an in-frame termination codon preceding the initiating methionine. In addition, a novel gene encoding a 34.5-kDa polypeptide was found to initiate transcriptionally within PMS2 from the opposite strand. 23 refs., 5 figs., 2 tabs.

1995-09-20

471

Monitoring of DNA and cytogenetic damage in lymphocytes from persons with skin cancer diseases

This report addresses a Los Alamos National Laboratory (LANL) proposal to build a pulsed neutron source for simulating nuclear-weapons effects. A point design for the pulsed neutron facility was initiated early in FY94 after hosting a Defense Nuclear Agency (DNA) panel review and after subsequently visiting several potential clients and users. The technical and facility designs contained herein fulfill the Statement of Work (SOW) agreed upon by LANL and DNA. However, our point designs and parametric studies identify a unique, cost-effective, above-ground capability for neutron nuclear-weapons-effects studies at threat levels. This capability builds on existing capital installations and infrastructure at LANL. We believe that it is appropriate for us, together with the DNA, to return to the user community and ask for their comments and critiques. We also realize that the requirements of last year have changed significantly. ...

1997-01-01

472

Transient suppression of MLH1 allows effective single-nucleotide substitution by single-stranded DNA oligonucleotides

There is a lot of interest in the studies that would help to understand whether there is a casual association between cancer and various types of molecular or cytogenetic damage detected in human cells. One major oncogenesis process is activation of proto-oncogenes by point mutations or chromosomal translocation. There are substantial evidence that indicates that the loss of heterozygosity of certain chromosomes is involved in human cancerogenesis. Our study aimed to elicit the possible association between cancer and DNA and cytogenetic abnormalities induced in lymphocytes of people bearing various categories of skin cancer cells. Fresh blood was collected by venipuncture from 25 individuals (including nine prior to cancer treatment). All patients were nonsmoking males, however 42.3 % of them were former smokers. Blood samples were divided into two parts and in the first part of samples cytogenetic studies were performed immediately, while from the second part ...

2004-11-01

473

British Library Electronic Table of Contents (United Kingdom)

Short synthetic single-stranded oligodeoxyribonucleotides (ssODNs) can be used to introduce subtle modifications into the genome of mouse embryonic stem cells (ESCs). We have previously shown that effective application of ssODN-mediated gene targeting in ESC requires (transient) suppression of DNA mismatch repair (MMR). However, whereas transient down-regulation of the mismatch recognition protein MSH2 allowed substitution of 3 or 4 nucleotides, 1 or 2 nucleotide substitutions were still suppressed. We now demonstrate that single- or dinucleotide substitution can effectively be achieved by transient down-regulation of the downstream MMR protein MLH1. By exploiting highly specific real-time PCR, we demonstrate the feasibility of substituting a single basepair in a non-selectable gene. Howev...

2011-01-01

474

Thermal diffusion by Brownian motion induced fluid stress

Studies of human mutation rates

The Ludwig-Soret effect, the migration of a species due to a temperature gradient, has been extensively studied without a complete picture of its cause emerging. Here we investigate the dynamics of DNA and spherical particles sub jected to a thermal gradient using a combination of Brownian dynamics and the lattice Boltzmann method. We observe that the DNA molecules will migrate to colder regions of the channel, an observation also made in the experiments of Duhr, et al[1]. In fact, the thermal diffusion coefficient found agrees quantitatively with the experimental value. We also observe that the thermal diffusion coefficient decreases as the radius of the studied spherical particles increases. Furthermore, we observe that the thermal fluctuations-fluid momentum flux coupling induces a gradient in the stress which leads to thermal migration in both systems.

2007-01-01

475

Report on NCI symposium: comparison of mechanisms of carcinogenesis by radiation and chemical agents. II. Cellular and animal models

November 1989, marked the beginning of a new three-year cycle of DOE grant support, in connection with which the program underwent a major reorganization. This document presents the progress on the three objectives of the present program which are: to isolate by the technique of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), proteins of special interest because of the relative mutability of the corresponding gene, establish the identity of the protein, and, for selected proteins, move to a characterization of the corresponding gene; to develop a more efficient approach, based on 2-D PAGE, for the detection of variants in DNA, with special reference to the identification of mutations in the parents of the individual whose DNA is being examined; and, to continue an effective interface with the genetic studies on the children of atomic bomb survivors in Japan, with reference to both the planning and implementation of new studies at ...

1990-01-01

476

Preliminary crystallographic analysis of a possible transcription factor encoded by the mimivirus L544 gene

The point at which the common final pathway for induction of cancer by chemical carcinogens and ionizing radiation has not been identified. Although common molecular targets are suggested by recent findings about the role of oncogenes, the mechanism by which the deposition of radiation energy and the formation of adducts or other DNA lesions induced by chemicals affects the changes in the relevant targets may be quite different. The damage to DNA that plays no part in the transformation events, but that influences the stability of the genome, and therefore, the probability of subsequent changes that influence tumorigenesis may be more readily induced by some agents than others. Similarly, the degree of cytotoxic effects that disrupt tissue integrity and increase the probability of expression of initiated cells may be dependent on the type of carcinogen. Also, evidence was presented that repair of the initial lesions could be demonstrated after ...

1984-05-20

477

British Library Electronic Table of Contents (United Kingdom)

Mimivirus is the prototype of a new family (the Mimiviridae) of nucleocytoplasmic large DNA viruses (NCLDVs), which already include the Poxviridae, Iridoviridae, Phycodnaviridae and Asfarviridae. Mimivirus specifically replicates in cells from the genus Acanthamoeba. Proteomic analysis of purified mimivirus particles revealed the presence of many subunits of the DNA-directed RNA polymerase II complex. A fully functional pre-transcriptional complex appears to be loaded in the virions, allowing mimivirus to initiate transcription within the host cytoplasm immediately upon infection independently of the host nuclear apparatus. To fully understand this process, a systematic study of mimivirus proteins that are predicted (by bioinformatics) or suspected (by proteomic analysis) to be involved in...

2011-01-01

478

Non-destructive Imaging of Individual Bio-Molecules

Multiple resonances and Coulomb blockade splitting in a quantum dot-DNA composite

Radiation damage is considered to be the major problem that still prevents imaging an individual biological molecule for structural analysis. So far, all known mapping techniques using sufficient short wave-length radiation, be it X-rays or high energy electrons, circumvent this problem by averaging over many molecules. Averaging, however, leaves conformational details uncovered. Even the anticipated use of ultra-short but extremely bright X-ray bursts of a Free Electron Laser shall afford averaging over 10^6 molecules to arrive at atomic resolution. Here we present direct experimental evidence for non-destructive imaging of individual DNA molecules. In fact, we show that DNA withstands coherent low energy electron radiation with deBroglie wavelength in the Angstrom regime despite a vast dose of 10^8 electrons/nm^2 accumulated over more than one hour.

2009-01-01

479

British Library Electronic Table of Contents (United Kingdom)

Inspired by the recent realizations of quantum dot (QD)-DNA conjugation, we study the spectral density of a magnetic impurity coupled to a mesoscopic semiconducting host. Using a combination of exact diagonalization technique and an analytic approach, we demonstrate that various types of resonances occur according to the relative position of impurity levels (IL) with respect to the host levels (HL). While the usual Coulomb peaks appear when the IL lie inside a band gap, with IL approaching HL and hybridization activated, they shift nonlinearly with the repulsion strength and even undergo splitting for a strong hybridization. When IL merge into HL, multiple resonances of a comblike structure are found along with a parity effect.

2011-01-01

480

Microdialysis unit for molecular weight separation

Low cytotoxicity effect of dendrosome as an efficient carrier for rotavirus VP2 gene transferring into a human lung cell line

The present invention relates generally to an apparatus and method for separating high molecular weight molecules from low molecular weight molecules. More specifically, the invention relates to the use of microdialysis for removal of the salt (low molecular weight molecules) from a nucleotide sample (high molecular weight molecules) for ESI-MS analysis. The dialysis or separation performance of the present invention is improved by (1) increasing dialysis temperature thereby increasing desalting efficiency and improving spectrum quality; (2) adding piperidine and imidazole to the dialysis buffer solution and reducing charge states and further increasing detection sensitivity for DNA; (3) using low concentrations of dialysis buffer and shifting the DNA negative ions to higher charge states, producing a nearly 10-fold increase in detection sensitivity and a slightly decreased desalting efficiency, or (4) any combination of (1), (2), and (3).

1999-09-21

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481

British Library Electronic Table of Contents (United Kingdom)

The efficiency of dendrosome (a gene porter) was assessed in transferring recombinant human rotavirus VP2 cDNA into A549, a human lung cell line. After gene transferring, transmission electron microscopy showed core-like particles (CLPs) formation in the transfected cells both with dendrosome and lipofectamine porters. In addition, western blotting analysis showed that the expression of VP2 gene was almost equal in the dendrosome and lipofectamine-transfected cells. Also, the cytotoxicity studies revealed that dendrosome had a lower cytotoxicity than lipofectamine. Therefore, our study may introduce dendrosome as a possible carrier for gene transferring into the human lung cell line, especially, for intranasally administration of DNA vaccines.

2009-01-01

482

Hypomethylation and induction of retinoic acid receptor beta 2 by concurrent action of adenosine analogues and natural compounds in breast cancer cells

British Library Electronic Table of Contents (United Kingdom)

DNA methylation is considered as a potential cause of aberrations in regulation of gene expression during carcinogenesis. Therefore, changes in DNA methylation patterns may be targets for chemoprevention. In the present study, we investigated effects of all-trans retinoic acid (ATRA), vitamin D3, and resveratrol alone and in combination with adenosine analogues: 2-chloro-2'-deoxyadenosine (2CdA) and 9-beta-d-arabinosyl-2-fluoroadenine (F-ara-A), on methylation and expression of retinoic acid receptor beta 2 (RARbeta2) in MCF-7 and MDA-MB-231 breast cancer cell lines. Alterations in methylation and expression levels after treatment of cells with the tested compounds were evaluated by methylation-sensitive restriction analysis (MSRA) and real-time PCR, respectively. RARbeta2 promoter in the ...

2010-01-01

483

Human papillomavirus: science and technologies for the elimination of cervical cancer

British Library Electronic Table of Contents (United Kingdom)

Introduction: Academic research has made a significant advancement in understanding the viral causes of cervical cancer and generating the technology for prevention, both at the primary and secondary levels. Human papillomaviruses (HPVs) have been recognized as the first necessary cause of cervical cancer, the second most common cancer in women worldwide. Areas covered: This paper reviews the epidemiological evidence of the causality of HPV in relation to cervical cancer, other genital tract cancers and some cancers of the oral cavity and oropharynx. The review also covers HPV DNA testing as a screening tool. DNA probes of high-risk HPV types in different formats have been fully validated as primary screening tests, as secondary triage tests and as a prognostic marker following treatment o...

2011-01-01

484

Groundtruth approach to accurate quantitation of fluorescence microarrays

Flow cytometric analysis of respiratory tract cells exposed to oil shale and silica particulates. [Hamsters

To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results significantly closer to the known ground-truth for these samples.

2000-12-01

485

Effects of pre- and postnatal exposure to tritiated water for five generations on postnatal brain development

Flow cytometric techniques were used to measure the cytological and biochemical damage to respiratory tract cells in animals exposed to particulates. Hamsters were exposed to raw and spent oil shale particulates and silica by intratracheal instillation. Exfoliated lung cells were obtained by sacrificing the animals and lavaging the respiratory tract posterior to the trachea with saline. Cell samples were fixed in ethanol and stained with mithramycin for fluorescence analysis of DNA content. DNA content distributions from hamsters exposed to spent oil shale and silica particulates showed atypical changes 28 to 35 days later. Cell counts and total numbers of macrophages, leukocytes, and epithelial cells in the lavage fluid also showed marked changes related to time after exposure.

1979-01-01

486

Effect of Diaporthe RNA virus 1 (DRV1) on growth and pathogenicity of different Diaporthe species

The possible long-term effects of chronic radiation exposure have been studied. Rats were given tritiated drinking water (3 #mu#Ci/ml) before and during pregnancy and thereafter continuously through five generations. The brains were studied at 30 and 120 days postnatally. Significant decreases in weight and DNA and protein contents of specific parts of the brain were found, the most pronounced decreases being in the diencephalon. The decrease in protein content were more pronounced than the decreases in DNA content; the decreases were also more pronounced at 30 days than at 120 days, and more pronounced in the fith generation than in previous generations.

487

British Library Electronic Table of Contents (United Kingdom)

A 4.1?kbp positive-strand RNA virus known as Diaporthe RNA virus 1 (DRV1) occurs in hypovirulent, non-sporulating isolates of the fungal pathogen Diaporthe perjuncta. A full-length cDNA clone of DRV1 was developed and RNA transcribed from the cDNA clone used to transfect different Diaporthe spp. The transfected species included three D. ambigua isolates and an unidentified Phomopsis asexual state of a Diaporthe sp. Successful transfections were confirmed using RT-PCR. Although the in vitro-transcribed positive sense single-stranded RNA used for transfection included vector sequences at both ends, the genomes of progeny virus from DRV1-transfected isolates were free of the vector sequences. Transfection resulted in morphological changes in these fungal pathogens. However, the presence of DR...

2011-01-01

488

Crystal structure of the human centromeric nucleosome containing CENP-A

British Library Electronic Table of Contents (United Kingdom)

In eukaryotes, accurate chromosome segregation during mitosis and meiosis is coordinated by kinetochores, which are unique chromosomal sites for microtubule attachment. Centromeres specify the kinetochore formation sites on individual chromosomes, and are epigenetically marked by the assembly of nucleosomes containing the centromere-specific histone H3 variant, CENP-A. Although the underlying mechanism is unclear, centromere inheritance is probably dictated by the architecture of the centromeric nucleosome. Here we report the crystal structure of the human centromeric nucleosome containing CENP-A and its cognate ?-satellite DNA derivative (147 base pairs). In the human CENP-A nucleosome, the DNA is wrapped around the histone octamer, consisting of two each of histones H2A, H2B, H4 and CENP...

2011-01-01

489

Cloning and characteristics of Brn1 gene in Curvularia lunata causing leaf spot in maize

British Library Electronic Table of Contents (United Kingdom)

The full length cDNA of the Brn1 was first cloned, and then expression of the Brn1 was analyzed and the function was identified by silencing technology. Results show that the full length cDNA of the C. lunata Brn1 gene contains 1001 base pairs and an 801?bp open reading frame encoding 267 amino acids. Semi-quantitative PCR analysis shows that the expression of Brn1 at 96?h is significantly higher than at 24 and 72?h (p?Brn1-silenced transformants were light brown in culture filtrate, and have significantly reduced toxin production relative to the wild-type. These results imply that Brn1 gene in C. lunata is not only involved in 1,8-dihydroxynaphthalene melanin synthesis, but is also relatively associated with toxin biosynthesis of the pathogen.

2011-01-01

490

Chronic irradiation and brain development. Final (4th) progress report

A variable gene delivery carrier-biotinylated chitosan/polyethyleneimine

The possible long term effects of chronic radiation exposure have been studied. Rats were given tritiated drinking water (3#mu#Ci/ml) before pregnancy, during pregnancy and threafter, continuously through 5 generations. The brains were studied at 30 and 120 days postnatally. Significant decreases in weight, DNA and protein contents of specific parts of the brain were found, the most pronounced decreases being in the diencephalon. The decreases in protein content were more pronounced than the decreases in DNA content; the decreases were also more pronounced at 30 days than at 120 days, and more pronounced in the fifth generation than in previous generations. An attempt was made to explain these complex phenomena on the basis of known periods of proliferation of various brain cells, damage to mothers themselves in each generation, and damage and repair of nucleic acids caused by radioactivity.

491

A miniaturized spatial temperature gradient capillary electrophoresis system with radiative heating and automated sample introduction for DNA mutation detection

A variable gene delivery system has been developed based on conjugating chitosan to biotin through a functionalized poly(ethylene glycol) (PEG) spacer, which can be used to further bind different molecules on the outer layer of a polymer/DNA complex by streptavidin (SA)-biotin linkage. In this study, TAT-conjugated SA was used as the model molecule to prove the conjugation function of the prepared complex. In addition, low-molecular-weight poly(ethyleneimine) (PEI) was added into the polymer/DNA complex to increase the transfection efficiency. The results of the luciferase assay show that the transfection efficiency of the prepared complex was significantly correlated with the amount of PEI and was further enhanced when TAT was conjugated to the complex by SA-biotin linkage. Considered to have negligible cytotoxic effects, the variable gene delivery complex prepared in this study would be of considerable potential as carriers for in vitro ...

2010-12-01

492

British Library Electronic Table of Contents (United Kingdom)

Abstract A miniaturized spatial temperature gradient CE system with automated sample introduction for DNA mutation detection was established. Continuous electrokinetic sample injection was achieved by combining an automated slotted vial array sample introduction device to the spatial temperature gradient CE system. The temperature gradient was produced by a radiative heating system with a single graphite block heater, and the stability of the temperature gradient was investigated. The temperature variation of each measure point was 0.12 0.21% RSD (n=7) within 6 h. A 14 cm Teflon AF coated silica capillary was used both as the separation channel and as the liquid core waveguide tube of fluorescence signal. Under a temperature gradient from 54.8 to 59.5 C, a low range control mutation standa...

2010-01-01

493

cDNA Cloning of the Basement Membrane Chondroitin Sulfate Proteoglycan Core Protein, Bamacan: A Five Domain Structure Including Coiled-Coil Motifs

The holographic principle and the language of genes

Basement membranes contain several proteoglycans, and those bearing heparan sulfate glycosaminoglycans such as perlecan and agrin usually predominate. Most mammalian basement membranes also contain...Full Text Available

1997-01-27

494

The Werner syndrome helicase protein is required for cell proliferation, immortalization, and tumorigenesis in Scaffold Attachment Factor B1 deficient mice

We show that the holographic principle in quantum gravity imposes a strong constraint on life. The degrees of freedom of an organism can be estimated according to the theory of Boolean networks, which is constrained by the entropy bound. Hence we can explain the languages in protein sequences or in DNA sequences. The overall evolution of biological complexity can be illustrated. And some general properties of protein length distributions can be explained by a linguistic mechanism.

2008-01-01

495

Terpenoid-based defenses in conifers: cDNA cloning, characterization, and functional expression of wound-inducible (E)-?-bisabolene synthase from grand fir (Abies grandis)

Werner syndrome (WS) is a rare disorder characterized by the premature onset of several pathologies associated with aging. The gene responsible for WS codes for a RecQ-type DNA helicase and is believed...Full Text Available

496

SM Higgs properties measurement at ATLAS

(E)-α-Bisabolene synthase is one of two wound-inducible sesquiterpene synthases of grand fir (Abies grandis), and the olefin product of this cyclization reaction...Full Text Available

1998-06-09

497

Ionising radiation. Part 2

The discovery of a new particle in the Higgs searches being prepared for LHC will not guarantee that the Standard Model Higgs boson has been seen. This paper discusses the possibilities for measuring the spin, parity and couplings of the particle, under the assumption that it does in fact behave like the Standard Model Higgs. The key question, which cannot alas be answered, is: if it looks like a dog, and barks like a dog, how much of the DNA must we analyse to be sure that it is a dog?

2009-01-01

498

Identification of a nuclear-localized nuclease from wheat cells undergoing programmed cell death that is able to trigger DNA fragmentation and apoptotic morphology on nuclei from human cells

A brief tutorial on the health effects of ionising radiation is presented. The distinction between somatic and genetic health effects is explained. The two types of somatic health effects, i.e., acute and chronic effects, are discussed, as well as the concepts of ''deterministic'' and ''stochastic'' (also called ''probabilistic'') health effects. The possibility of cancer caused by DNA damage is discussed. The document ends with the definition of some key radiation terms.

2000-11-01

499

BosR (BB0647) Controls the RpoN-RpoS Regulatory Pathway and Virulence Expression in Borrelia burgdorferi by a Novel DNA-Binding Mechanism

PCD (programmed cell death) in plants presents important morphological and biochemical differences compared with apoptosis in animal cells. This raises the question of whether PCD arose independently...Full Text Available

2006-08-01

500