Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Copying Processes”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 811 records · Page 45Linked to original sources
PubMed2005

A graphical simulation model of the entire DNA process associated with the analysis of short tandem repeat loci.

The use of expert systems to interpret short tandem repeat DNA profiles in forensic, medical and ancient DNA applications is becoming increasingly prevalent as high-throughput analytical systems generate large amounts of data that are time-consuming to process. With special reference to low copy number (LCN) applications, we use a graphical model to simulate stochastic variation associated with the entire DNA process starting with extraction of sample, followed by the processing associated with the preparation of a PCR reaction mixture and PCR itself. Each part of the process is modelled with input efficiency parameters. Then, the key output parameters that define the characteristics of a DNA profile are derived, namely heterozygote balance (Hb) and the probability of allelic drop-out p(D). The model can be used to estimate the unknown efficiency parameters, such as pi(extraction). 'What-if' scenarios can be used to improve and optimize the entire process, e.g. by increasing the aliquot forwarded to PCR, the improvement expected to a given DNA profile can be reliably predicted. We demonstrate that Hb and drop-out are mainly a function of stochastic effect of pre-PCR molecular selection. Whole genome amplification is unlikely to give any benefit over conventional PCR for LCN.

Computer Graphics↗
PubMed2001

The ability to execute saccades on the basis of efference copy: impairments in double-step saccade performance in children with developmental co-ordination disorder.

The double-step saccade task (DSST) was used to test the hypothesis that children with developmental co-ordination disorder (DCD) who experience deficits in motor imagery have difficulty processing the visual spatial consequences of intended movements using efference copy signals. In order to ensure that the second saccade in the DSST was executed in the absence of visual cues and had to be programmed on the basis of extra-retinal information (efference copy), we analysed only those double-step ensembles where latency plus duration of first saccades was greater than 240 ms (total presentation time of the targets). No significant differences between DCD and control children were evident on measures of latency of first saccades, intersaccadic interval and first saccade error. As predicted, children with DCD who have impaired motor imagery demonstrated specific deficits on the DSST where efference copy had been used to program the saccade sequence. More specifically, these children were less accurate in terms of final eye position on second saccades. Our results raise the possibility that abnormalities in the processing of efference copy signals could underlie motor clumsiness in the majority of children with DCD. Furthermore, the origin of this deficit in efference copy probably exists at the level of the parietal lobe.

Child↗
PubMed1995

Automatic vessel segmentation and quantification of the rat aortic ring assay of angiogenesis.

BACKGROUND: Pharmacologic control of angiogenesis is a promising new approach to the treatment of a variety of pathologic conditions including cancer. The recently developed in vitro rat aortic ring model provides a simple, reproducible assay for discovering angiogenic agonists and antagonists. However, quantification of results in this assay is time consuming, tedious, and subjective, because it involves visual inspection of images and manually counting the newly formed microvessels extending from the cultured aortic ring. This report describes an automated image analysis-based procedure for quantification of this assay that overcomes these difficulties. EXPERIMENTAL DESIGN: The designed image processing algorithm segments the vessels from gray scale images. A high-pass filter is used, and the results are separated into nonvascular and vessel compartments based on object size and shape. Quantification relies on identification of vessels intersecting a closed transect set a fixed distance from the aortic ring. The number and the total area of these vessels are determined. The entire operation has been automated and packaged in an application called Vessels. RESULTS: The correlation between computer-determined vessel area/vessel number and visual microvessel count is high (r2 = 0.91 and r2 = 0.86, respectively). CONCLUSION: Vessels offers high-speed, fully automatic batch processing including production of a hard copy for documentation. The application runs on the Apple family of computers. On a Quadra 800, the application can process approximately 30 images/hour, which is approximately 2.5 times faster than manual quantification of this assay.

Animals↗
PubMed1999

A set of highly conserved RNA-binding proteins, alphaCP-1 and alphaCP-2, implicated in mRNA stabilization, are coexpressed from an intronless gene and its intron-containing paralog.

Gene families normally expand by segmental genomic duplication and subsequent sequence divergence. Although copies of partially or fully processed mRNA transcripts are occasionally retrotransposed into the genome, they are usually nonfunctional ("processed pseudogenes"). The two major cytoplasmic poly(C)-binding proteins in mammalian cells, alphaCP-1 and alphaCP-2, are implicated in a spectrum of post-transcriptional controls. These proteins are highly similar in structure and are encoded by closely related mRNAs. Based on this close relationship, we were surprised to find that one of these proteins, alphaCP-2, was encoded by a multiexon gene, whereas the second gene, alphaCP-1, was identical to and colinear with its mRNA. The alphaCP-1 and alphaCP-2 genes were shown to be single copy and were mapped to separate chromosomes. The linkage groups encompassing each of the two loci were concordant between mice and humans. These data suggested that the alphaCP-1 gene was generated by retrotransposition of a fully processed alphaCP-2 mRNA and that this event occurred well before the mammalian radiation. The stringent structural conservation of alphaCP-1 and its ubiquitous tissue distribution suggested that the retrotransposed alphaCP-1 gene was rapidly recruited to a function critical to the cell and distinct from that of its alphaCP-2 progenitor.

3' Untranslated Regions↗
PubMed2005

Effect of tissue fixatives on telomere length determination by quantitative PCR.

Telomere length is a well established marker of cellular senescence and thus biological age. Quantitative PCR allows the determination even from very low amounts of tissue by using telomere specific and single copy gene primers. Comparing a directly processed tissue sample to a 4% formaldehyde fixed one showed a significantly reduced efficiency of PCR reactions (mainly in single copy gene experiments) in a storage time-dependent manner resulting in an artificial increase in reported relative telomere length. This effect was not seen when the tissue was stored in RNA later solution. In summary, telomere length determination from formaldehyde fixed material by quantitative PCR is not a reliable method. Unfortunately therefore, many easily accessible tissue samples from pathology laboratories are unsuitable for this technique.

Cellular Senescence↗
PubMed1991

Evaluation of a facsimile (fax) transfer system for medication order delivery.

Delivery of medication orders for initial processing is often slowed by distance between the nursing unit and the pharmacy. Messengers and pneumatic tubes are not always available or reliable. Facsimile (fax) machines are able to transmit photocopies of medication orders in seconds. An initial evaluation of available fax machines led to selection of three models for a trial installation. Criteria for fax evaluation included medication order turnaround time (TAT), percentage of orders requiring more than 2 hours to be received by the nursing unit, and number of orders recopied by nursing personnel for pharmacy use. An initial review identified the time required for order processing using a reliable pneumatic tube system to deliver orders to the central pharmacy. The number of orders recopied by nurses into the chart to provide working copies of misplaced or lost orders for pharmacy was also recorded. The fax system was installed and the initial data collection process was repeated. Statistics focused on the total time required to transmit an order to pharmacy and provide the initial dose to the nursing unit. Analysis of the mean (+/- SD) showed an initial TAT of 1.59 (+/- 1.30) hours (n = 92). TAT after initiation of fax transmission was 1.36 (+/- 1.15) hours, P = 0.20 (n = 104). This improvement is greater than it appears because 1.10 hours of both of these times are fixed times involving pharmacy order processing. The percentage of orders that required more than two hours to provide medication to the nursing unit was reduced from 29% (27/92) to 18% (19/104) P less than 0.05. The average number of nursing recopies into the chart was reduced.

Copying Processes↗
PubMed2005

Evolutionary forces generating sequence homogeneity and heterogeneity within retrotransposon families.

Genome projects allow us to sample copies of a retrotransposon sequence family residing in a host genome. The variation in DNA sequence between these individual copies will reflect the evolutionary process that has spread the sequences through the genome. Here I review quantitatively the expected diversity of elements belonging to a transposable genetic element family. I use a simple neutral model for replicative mobile DNAs such as retrotransposons to predict the extent of sequence variability between members of a single family of transposable elements, both within and between species. The effects of horizontal transfer are also explored. I also consider the impact on these distributions of an increase in transposition rate arising from a mutational change in copy of the sequence. In addition, I consider the question of the interaction between retrotransposons and their hosts, and the causes of the abundance of transposable elements in the genomes that they occupy.

Animals↗
PubMed1988

The cDNA sequence coding for prepro-PGS (prepro-magainins) and aspects of the processing of this prepro-polypeptide.

Amphibian skin is well known as a source of peptides homologous to bioactive peptides found in mammalian gut and brain. A systematic investigation of the skin secretions from Xenopus laevis revealed several peptides not derivable from known precursors. The sequence elucidation, utilizing fast atom bombardment/mass spectrometry, of two peptides, PGS and PGS Gly-10;Lys-22, is reported. These have been independently characterized and named magainins and found to have antimicrobial activity. A mixed sequence oligonucleotide probe complementary to the mRNA sequence coding for PGS was synthesized and used to screen a Xenopus skin cDNA library. A full length cDNA species encoding prepro-PGS was isolated and characterized, and its sequence is reported. The deduced precursor sequence was found to contain one copy of PGS Gly-10;Lys-22 and five copies of PGS. The proteolytic processing of this prepro-polypeptide is discussed.

Amino Acid Sequence↗
PubMed1992

Strand displacement amplification--an isothermal, in vitro DNA amplification technique.

Strand Displacement Amplification (SDA) is an isothermal, in vitro nucleic acid amplification technique based upon the ability of HincII to nick the unmodified strand of a hemiphosphorothioate form of its recognition site, and the ability of exonuclease deficient klenow (exo- klenow) to extend the 3'-end at the nick and displace the downstream DNA strand. Exponential amplification results from coupling sense and antisense reactions in which strands displaced from a sense reaction serve as target for an antisense reaction and vice versa. In the original design (G. T. Walker, M. C. Little, J. G. Nadeau and D. D. Shank (1992) Proc. Natl. Acad. Sci 89, 392-396), the target DNA sample is first cleaved with a restriction enzyme(s) in order to generate a double-stranded target fragment with defined 5'- and 3'-ends that can then undergo SDA. Although effective, target generation by restriction enzyme cleavage presents a number of practical limitations. We report a new target generation scheme that eliminates the requirement for restriction enzyme cleavage of the target sample prior to amplification. The method exploits the strand displacement activity of exo- klenow to generate target DNA copies with defined 5'- and 3'-ends. The new target generation process occurs at a single temperature (after initial heat denaturation of the double-stranded DNA). The target copies generated by this process are then amplified directly by SDA. The new protocol improves overall amplification efficiency. Amplification efficiency is also enhanced by improved reaction conditions that reduce nonspecific binding of SDA primers. Greater than 10(7)-fold amplification of a genomic sequence from Mycobacterium tuberculosis is achieved in 2 hours at 37 degrees C even in the presence of as much as 10 micrograms of human DNA per 50 microL reaction. The new target generation scheme can also be applied to techniques separate from SDA as a means of conveniently producing double-stranded fragments with 5'- and 3'-sequences modified as desired.

Base Sequence↗
PubMedDate not supplied

[Production of full length DNA copies of genomic segments of influenza virus using DNA recombination in the process of polymerase chain reaction].

The case study comprises a description of a method used for producing the full-length cDNA complementary to influenza virus segments made through the recombination of homologous DNA fragments in the process of polymerase chain reaction (PCR). The detailed protocol of the method is presented alongside with a discussion of the advantages of the suggested approach.

Base Sequence↗
PubMed1996

Escherichia coli RNase HI inhibits murine leukaemia virus reverse transcription in vitro and yeast retrotransposon Ty1 transposition in vivo.

BACKGROUND: Reverse transcription, which converts an RNA genome into double-stranded DNA, requires both the polymerase and RNase H activities of reverse transcriptase (RT). In vitro, poorly processive RT dissociates from partially copied RNA-DNA hybrids, that are usually extended by a second RT molecule. Despite similar structures, RNase HI of Escherichia coli can degrade RNA-DNA hybrids that are resistant to RNase H of RT. E. coli RNase HI is used to determine the accessibility to and requirement for RNA-DNA hybrids in reverse transcription in vivo and in vitro. RESULTS: In the presence of E. coli RNase HI, reverse transcription yields incomplete cDNA molecules due to degradation of RNA-DNA hybrids. Delivery of E. coli RNase HI to Ty1 particles via fusion to the capsid protein can reduce retrotransposition by more than 99%, also indicating inhibition of DNA synthesis in vivo. CONCLUSION: Inhibition of both reverse transcription in vitro and retrotransposition in vivo by E. coli RNase HI indicates that the poor processivity of RT exposes RNA-DNA hybrids critical for reverse transcription to degradation. Targeting a cellular RNase H to HIV may help define the site(s) of RNA-DNA hybrids that are susceptible to nonretroviral RNase H and may be useful for gene therapy to inhibit retroviral replication.

Animals↗
PubMed2005

Design considerations for array CGH to oligonucleotide arrays.

BACKGROUND: Representational oligonucleotide microarray analysis has been developed for detection of single nucleotide polymorphisms and/or for genome copy number changes. In this process, the intensity of hybridization to oligonucleotides arrays is increased by hybridizing a polymerase chain reaction (PCR)-amplified representation of reduced genomic complexity. However, hybridization to some oligonucleotides is not sufficiently high to allow precise analysis of that portion of the genome. METHODS: In an effort to identify aspects of oligonucleotide hybridization affecting signal intensity, we explored the importance of the PCR product strand to which each oligonucleotide is homologous and the sequence of the array oligonucleotides. We accomplished this by hybridizing multiple PCR-amplified products to oligonucleotide arrays carrying two sense and two antisense 50-mer oligonucleotides for each PCR amplicon. RESULTS: In some cases, hybridization intensity depended more strongly on the PCR amplicon strand (i.e., sense vs. antisense) than on the detection oligonucleotide sequence. In other cases, the oligonucleotide sequence seemed to dominate. CONCLUSION: Oligonucleotide arrays for analysis of DNA copy number or for single nucleotide polymorphism content should be designed to carry probes to sense and antisense strands of each PCR amplicon to ensure sufficient hybridization and signal intensity.

Aneuploidy↗
PubMed1986

A temperature-dependent pBR322 copy number mutant resulting from a Tn5 position effect.

In the process of randomly mutagenizing a recombinant pBR322 clone with transposon Tn5, a high copy number plasmid mutant, pLO88, has been isolated. The copy number phenotype of pLO88 is observed only at elevated temperatures, greater than or equal to 37 degrees C, and is due to the precise position of a Tn5 insertion. Nucleotide sequence of the Tn5-pBR322 junction reveals that Tn5-88 has inserted into an open reading frame that codes for a 63 amino acid protein previously shown to negatively regulate pBR322 plasmid copy number. By deleting portions of the Tn5 it is shown that the copy number phenotype is due not only to the insertion of Tn5 in pBR322 but also to the requirement that some Tn5 sequences remain intact. It appears that an outwardly directed Tn5 promoter initiates the synthesis of a transcript (RNA X) that interferes with the normal repressor RNA (RNA I)-primer RNA (RNA II) interaction at elevated temperatures.

DNA Replication↗
PubMed2005

Coupling and decoupling of evolutionary mode between X- and Y-chromosomal red-green opsin genes in owl monkeys.

We previously discovered Y-chromosomal red-green opsin genes in two types of owl monkeys with different chromosomal characteristics. In one type, the Y-linked opsin gene is a single-copy intact gene and in the other, the genes exist as multiple pseudogenes on a Y/autosome fusion chromosome. In the present study, we first distinguished the two types of monkeys as distinct allopatric species on the basis of karyotypic characteristics: Aotus lemurinus griseimembra (Karyotype III, diploid chromosome number [2n]=53) and Aotus azarae boliviensis (Karyotype VI; male 2n=49; female 2n=50), belonging to the northern and southern species groups, respectively, separated by the Amazon River system. Our sequence analysis revealed a common L1-Alu-Alu insertion between the two species in the 3'-flanking region of the X-linked opsin genes. The insertion was absent in the Y-linked opsin genes and in the human red and green opsin genes, indicating that it occurred in the X copy before the split into northern and southern species and after the X to Y duplication, i.e. duplication preceded speciation. We also show that in the northern species, the Y-linked opsin gene has evolved concomitantly with the X-linked copy whereas in the southern species, the Y-autosome fusion possibly led to decoupling evolutionary processes between X- and Y-linked copies and subsequent degeneration and duplications of the Y-linked opsin gene.

Alu Elements↗
PubMed1999

Fidelity probes for DNA arrays.

One current approach to quality control in DNA array manufacturing is to synthesize a small set of test probes that detect variation in the manufacturing process. These fidelity probes consist of identical copies of the same probe, but they are deliberately manufactured using different steps of the manufacturing process. A known target is hybridized to these probes, and those hybridization results are indicative of the quality of the manufacturing process. It is not only desirable to detect variations, but also to analyze the variations that occur, indicating in what process step the manufacture changed. We describe a combinatorial approach which constructs a small set of fidelity probes that not only detect variations, but also point out the manufacturing step in which a variation has occurred. This algorithm is currently being used in mass-production of DNA arrays at Affyetrix.

Algorithms↗
PubMed2000

A phosphatidylinositol 3-kinase of Candida albicans influences adhesion, filamentous growth and virulence.

To determine if cellular functions of the phosphatidylinositol 3-kinase CaVps34p are related to processes governing Candida albicans pathogenicity, both copies of the gene were sequentially disrupted. Homozygous deletion of C. albicans VPS34 resulted in a mutant strain which exhibited defects not only in intracellular vesicle transport processes but also in morphogenesis. The CaVPS34 null mutant was unable to form hyphae on different solid media whilst showing a significantly delayed yeast-to-hyphae transition in liquid media. In addition, the mutant was rendered hypersensitive to temperature and osmotic stresses and had a strongly decreased ability to adhere to mouse fibroblast cells compared to the wild-type strain SC5314. Finally, evidence was obtained that CaVPS34 is essential for pathogenicity of C. albicans as the CaVPS34 null mutant was shown to be avirulent in a mouse model of systemic infection. C. albicans pathogenicity was restored to a near wild-type degree upon reintroduction of CaVPS34 into the chromosome of the null mutant, demonstrating that the observed avirulence corresponded to the loss of CaVPS34. Thus, the results suggest that CaVPS34 may serve as a potential target for antifungal drugs.

Animals↗
PubMed1979

Specificity of chromatin transcription in vitro. Anomalies due to RNA-dependent RNA synthesis.

In the presence of Mn2+, globin mRNA can be transcribed into a partial RNA copy by Escherichia coli RNA polymerase. This process also occurs when the mRNA is transcribed together with chromatin. A fraction, at least, of the newly synthesized RNA copy (anti-globin RNA) can serve as a template for the synthesis of globin sequences of the same polarity as the original mRNA. This process is sufficient to explain the specific synthesis of a subset of the globin RNA on mouse foetal liver chromatin. It also accounts for the synthesis of double-stranded RNA sequence by E. coli RNA polymerase, on chromatin as well as on pure mRNA. Results are presented suggesting that the poly(A) tract of the mRNA could be preferentially transcribed. In the presence of Mg2+, the RNA-dependent transcription is strongly inhibited, as well as the synthesis of double-stranded RNA. Under these conditions, the transcription on chromatin appears to be largely DNA dependent, and the synthesis of globin sequences is completely asymmetric. Spermine (0.3 mM) seems to improve the specificity of transcription. The transcription of chromatin in vitro is thus largely dependent on the nature of the divalent cation present in the in the incubation mixture.

Animals↗
PubMed2004

Replication of a unit-copy plasmid F in the bacterial cell cycle: a replication rate function analysis.

For stability, the replication of unit-copy plasmids ought to occur by a highly controlled process. We have characterized the replication dynamics of a unit-copy plasmid F by a replication rate function defined as the probability per unit age interval of the cell cycle that a plasmid will initiate replication. Analysis of baby-machine data [J. Bacteriol. 170 (1988) 1380; J. Bacteriol. 179 (1997) 1393] by stochastics that make no detailed reference to underlying mechanism revealed that this rate function increased monotonically over the cell cycle with rapid increase near cell division. This feature is highly suggestive of a replication control mechanism that is designed to force most plasmids to replicate before cells undergo division. The replication rate function is developed anew from a mechanistic model incorporating the hypotheses that initiators are limiting and that steric hindrance of origins by handcuffing control initiation of replication. The model is based on correctly folded initiator protein monomers arising from an inactive dimer pool via chaperones in limiting amounts, their random distribution to high affinity sites (iterons) at the origin (ori) and an outside locus (incC), the statistical mechanics of bound monomer participation in pairing the two loci (cis-handcuffing), and initiation probability as proportional to the number of non-handcuffed ori-saturated plasmids. Provided cis-handcuffing is present, this model closely accounts for the shape of the replication rate function derived from experiment, and reproduces the observation that replication occurs throughout the cell cycle. Present concepts of iteron-based molecular mechanisms thus appear capable of yielding a quantitative description of unit-copy-number plasmid replication dynamics.

Cell Cycle↗