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 1,315 records · Page 73Linked to original sources
PubMed2005

Construction, detection and microarray analysis on the Shigella flexneri 2a sitC mutant.

In order to overcome the defects of difficult gene operations in low-copy suicide plasmid pCVD442, Gateway technology was applied in the construction process of recombinant plasmid for gene knockout in this study. With this improved knockout system, we inactivated sitC gene, which is associated with iron transport in Shigella flexneri 2a strain 301, to yield the mutant, MTS. The functional detection of the mutant was performed at the level of culture medium, cell and animal experiment, respectively. The gene expression profiles were compared with DNA microarray between the mutant and the wild type under iron-restricted conditions. The results showed that MTS grew obviously less well than the wild-type strains in L broth containing 150 micromol/L iron chelator DIP (2,2'-dipyridyl). Addition of iron or manganese to the cultures stimulated the growth of MTS to wild-type levels in rich culture medium. In either the experiment on the ability of intracellular multiplication and cell-to-cell spread in HeLa and U937 cell lines, or the experiment on keratoconjunctivitis in guinea pigs, MTS showed no obvious changes in virulence compared with the parental strain Sf301. When 65 micromol/L DIP was added to the cultured HeLa cells, the ability of intracellular multiplication of MTS reduced about 51.6% as compared with that of Sf301. The analysis of expression profiles under iron-limited condition showed that MTS was more sensitive for the change of iron deficiency than Sf301. There are 106 more up-regulated genes in MTS than in wild-type strains, which are involved in membrane transportation, amino acid metabolism and uncategorized function genes, while down-regulated genes are mainly involved in energy and carbohydrate metabolism. Under low iron conditions, the expression levels of known iron-transport associated genes generally increased. Additionally, the number of these genes and their increase amplitude in MTS are more than those in Sf301. Together, these results confirmed that Sit iron-transport system is important for the growth of Shigella.

ATP-Binding Cassette Transporters↗
PubMed2002

Nht2, a copia LTR retrotransposon from a conditionally dispensable chromosome in Nectria haematococca.

In the plant pathogenic ascomycete Nectria haematococca mating population (MP) VI, the conditionally dispensable chromosomes are unstable during sexual reproduction. During mapping of such a chromosome, three dispersed repeats were identified. Nht2, one of these repeated elements, is a long terminal repeat (LTR) retrotransposon that is 5.9 kb in length. Its deduced amino acid sequence is homologous to the four enzymatic domains characteristic of copia retrotransposons, but it contains multiple stop codons and probably is no longer able to transpose autonomously. Nht2's LTRs differ at ten positions and the characteristics of these differences resemble the changes induced by repeat-induced point mutation (RIP) in Neurospora crassa. The likelihood that Nectria haematococca MP VI has a RIP-like process, however, is reduced by the fact that a multi-copy transposon cloned from the same ascospore isolate as Nht2 encodes an intact open reading frame. Nht2 is broadly distributed among isolates collected from a variety of host plants. A limited survey of three field isolates suggests that Nht2 is on only one or a few chromosomes in every genome. Nht2's degeneracy and its widespread distribution within the species both suggest that it is an ancient element within N. haematococca MP VI.

Amino Acid Sequence↗
PubMed2001

Detecting errors in mtDNA data by phylogenetic analysis.

Sequencing and documenting a sample of homologous DNA stretches is prone to copying errors in a way rather analogous to the biological replication process. Previous attempts at obtaining representative mtDNA sequences, typically of the control region, for evolutionary studies or forensic purposes have yielded rather unsatisfactory results in many cases. The key ingredient in pinpointing problems with given data is the phylogenetic analysis of closely related mtDNAs within the framework of an established worldwide phylogeny that is supported by coding region information. We develop some general rules by which likely errors in data tables can readily be detected without rereading whole sequences repeatedly. Following these guidelines, one can expect to lower the error rate by at least an order of magnitude, although it will still be hard to beat the mitochondrial gamma polymerase in precision.

DNA, Mitochondrial↗
PubMed1995

Zebrafish cyclin D1 is differentially expressed during early embryogenesis.

We have isolated and determined the nucleotide sequence of a cDNA containing the complete coding region of cyclin D1 from embryonic zebrafish cDNA library. The cyclin D1 gene is a single copy gene within the zebrafish genome, which undergoes an alternative polyadenylation process. The initial expression of cyclin D1 transcript occurs at the presumed onset of G1 phase in the developing zebrafish embryo.

Amino Acid Sequence↗
PubMed1986

Induction of differentiation in Friend erythroleukemia cells with dimethyl sulfoxide, hexamethylene bisacetamide and sodium butyrate is not accompanied by changes in proviral DNA or its expression.

The integration pattern, copy number and DNA expression of the Friend virus genome was examined in Friend erythroleukemia cells induced to differentiate with dimethyl sulfoxide, hexamethylene bisacetamide and sodium butyrate. The integrated proviral DNA in Friend erythroleukemia cells was examined by Southern hybridization with a cloned Friend virus (F-MuLV) probe at days 1 and 4 following inducer treatment, as well as on day 6 at which time the cells had remained for 48 h in inducer free medium. KpnI fragments 9 and 5.7 kb long were observed. The copy number of each fragment remained constant throughout the erythroid differentiation process. EcoRI digestion of DNA isolated from cells at different times following the inducer treatment demonstrated multiple integration sites of the proviral genome, which also remained constant during the differentiation process. Proviral DNA expression was examined at 4 h and 4 days following inducer treatment as well as on day 6 by which time cells remained for 48 h in inducer free medium. Northern blot hybridization to the F-MuLV probe indicated no change in the provirus gene expression independent of the class of inducers. These observations reinforce our conclusions that the viral genome and its transcription product do not play a major role in the differentiation process of Friend erythroleukemic cells.

Acetamides↗
PubMed1996

Cat proenkephalin-A does not contain the opioid octapeptide.

The sequence of a large cDNA fragment of proenkephalin-A from the cat adrenal medulla was obtained using reverse transcription followed by polymerase chain reaction, and cloning. This cDNA encompasses the region normally containing all the opioid peptides, except the C-terminal heptapeptide. As with other species, cat proenkephalin-A contains four conserved copies of (Met5)-enkephalin, and one of (Leu5)-enkephalin, flanked by processing sites of paired basic amino acids. However, significant differences were found in the nucleotide and deduced amino acid sequences in the region of the octapeptide. In particular, the essential tyrosyl residue is substituted by a histidyl residue, making it unlikely that the cat equivalent would have opioid activity. Furthermore, the peptide is not flanked by paired basic residues, suggesting it is not processed.

Adrenal Medulla↗
PubMed1999

Phospholipase D as an effector for ADP-ribosylation factor in the regulation of vesicular traffic.

A mammalian phospholipase D (PLD) activity that is stimulated by ADP-ribosylation factor (ARF) has been identified in Golgi-enriched membrane fractions. This activity is due to the PLD1 isoform and evidence from several laboratories indicates that PLD1 is important for the polymerization of vesicle coat proteins on membranes. When expressed in Chinese hamster ovary cells, PLD1 localized to dispersed small vesicles that overlapped with the location of the ERGIC53 protein, a marker for the endoplasmic reticulum (ER)-Golgi intermediate compartment. Cells having increased PLD1 expression had accelerated anterograde and retrograde transport between the ER and Golgi. Membranes from cells having elevated PLD1 activity bound more COPI, ARF, and ARF-GTPase activating protein. These membranes also produced more COPI vesicles than did membranes from control cells. It is likely that PLD1 participates in both positive and negative feedback regulation of the formation of COPI vesicles and is important for controlling the rate of this process.

ADP-Ribosylation Factors↗
PubMedDate not supplied

The patient and practitioner as co-authors of the medical record.

Health care professionals traditionally have resisted patient access to medical records. There is evidence, however, that the patient's medical record can promote improved communication between patient and practitioner. In an exploratory study, patients in a primary care office practice collaborated with their health care professionals in the authorship of their records. Co-authorship was effective in conveying more complete, accurate, and mutually understandable information. The patient-held copy of the record served as an adjunct to this collaborative process. The potential problems and prospects arising from this strategy are discussed.

Ambulatory Care↗
PubMed1993

Variation and genetic control of surface antigen expression in mycoplasmas: the Vlp system of Mycoplasma hyorhinis.

Surface antigenic diversity in the swine pathogen Mycoplasma hyorhinis is generated by random combinatorial expression and high-frequency phase variation of multiple, size-variant membrane surface lipoproteins (Vlps) which represent the major coat proteins of this wall-less procaryote. The distinctive structural basis for Vlp variation was revealed in a family of several related but divergent vlp genes. These occur in one cluster as single chromosomal copies, each encoding a conserved domain for membrane insertion and lipoprotein processing, and a divergent external domain that changes size by deletion or insertion of repetitive intragenic coding sequences while retaining a distinctive charge motif. Lack of detectable changes in restriction fragment patterns or DNA sequence of vlp structural genes during phase transitions between ON and OFF expression states ruled out long range genomic rearrangements and frameshift mutations as a means of controlling Vlp phase variation. However, highly homologous vlp promoter regions contain a homopolymeric tract of contiguous adenine residues [poly(A)] upstream of the transcriptional start site which is subject to frequent mutations altering its length. These mutations are the only sequence changes detected during phase transitions, and are highly correlated with the expression state of each vlp gene. This suggests a mechanism of transcriptional control regulating Vlp phase variation by critical changes within the poly(A) region affecting the spacing between the -10 and -35 hexamers or a putative regulator binding site. The multiple levels of structural and antigenic diversity embodied in the vlp gene family may provide essential adaptive capabilities for this wall-less microbial pathogen.

Animals↗
PubMed2003

Detours and shortcuts to transcription reinitiation.

Gene transcription is repetitive, enabling the synthesis of multiple copies of identical RNA molecules from the same template. The cyclic process of RNA synthesis from active genes, referred to as transcription reinitiation, contributes significantly to the level of RNAs in living cells. Contrary to the perception that multiple transcription cycles are a mere iteration of mechanistically identical steps, a large body of evidence indicates that, in most transcription systems, reinitiation involves highly specific and regulated pathways. These pathways influence the availability for reinitiation of template DNA and/or transcription proteins, and represent an important yet poorly characterized aspect of gene regulation.

Genes, Bacterial↗
PubMed1991

Primer terminus recognition and highly processive replication by Epstein-Barr virus DNA polymerase.

The Epstein-Barr virus (EBV) DNA polymerase is essential for viral DNA replication in the lytic phase of the EBV life cycle. It efficiently extends RNA primers on the template DNA, suggesting the possible involvement of the EBV DNA polymerase in synthesizing Okazaki fragments from RNA primers on the lagging strand template. Competition experiments revealed that the EBV DNA polymerase had significantly higher affinity for primer termini hybridized to the template DNA than for the single-stranded DNA template or the single-stranded primer itself. ATP was not required either for primer terminus recognition or for sustainment of polymerization. The stimulation of the enzyme by (NH4)2SO4 was dependent on the template/primers utilized. These observations suggest that the primary and secondary structure of the template/primers are important factors for primer terminus recognition by the EBV DNA polymerase. The enzyme elongated synthetic RNA primer annealed to circular single-stranded M13 DNA coated with Escherichia coli single-stranded DNA-binding protein without dissociation. The processivity of the EBV DNA polymerase was strikingly high (greater than 7200 nucleotides) and the rate of polymerization was 12 nucleotides/s per polymerase molecule. The high processing capacity is a desirable feature in the synthesis of multiple copies of the EBV genome in rolling-circle DNA replication.

Adenosine Triphosphate↗
PubMed2000

The salience of visuospatial and organizational skills in reproducing the Rey-Osterreith Complex Figure in subjects with high and low IQs.

The salience of visuospatial and organizational skills in copying the Rey-Osterreith Complex Figure (ROCF) was examined in 44 adults diagnosed with Attention Deficit Hyperactivity Disorder (ADHD). Subjects were divided into a high average and above IQ group (n = 21) and an average and below IQ group (n = 23). Multiple regressions were conducted for both groups, with the ROCF copy as the dependent variable and WAIS-R Block Design and Stern Fragmentation scores as predictor variables. Results indicated that, for the high IQ group, visuospatial skills were more salient in predicting ROCF copy scores. By contrast, for the low IQ group, organizational skills were more salient for predicting ROCF copy score. Our findings are discussed in relation to the Boston Process Approach.

Adult↗
PubMed1988

Molecular cloning of the major surface antigen of leishmania.

The gene encoding gp63, the major surface glycoprotein of Leishmania promastigotes, was isolated from Leishmania major using a synthetic oligonucleotide probe based on the NH2-terminal protein sequence of purified gp63. DNA sequence analysis and the translated amino acid sequence indicate that gp63 is synthesized as precursor molecule having both an NH2-terminal preregion (signal peptide) and an adjacent proregion. This structure is consistent with the protease activity of gp63 since many other proteases are synthesized as precursor forms requiring processing for enzymatic activity. Hybridization studies demonstrated that there are multiple copies of the gp63 gene in the genome of L. major and other Leishmania species. The conservation of the coding sequence of gp63 amongst diverse species of Leishmania provides further support for the importance of gp63 during the life cycle of Leishmania.

Amino Acid Sequence↗
PubMed2003

Neuropsychological long-term sequelae after posterior fossa tumour resection during childhood.

The importance of the cerebellum for non-motor functions is becoming more and more evident. The influence on cognitive functions from acquired cerebellar lesions during childhood, however, is not well known. We present follow-up data from 24 patients, who were operated upon during childhood for benign cerebellar tumours. The benign histology of these tumours required neither radiotherapy nor chemotherapy. Post-operatively, these children were of normal intelligence with a mean IQ of 99.1, performance intelligence quotient (PIQ) of 101.3 and verbal intelligence quotient (VIQ) of 96.8. However, 57% of patients showed abnormalities in subtesting. In addition, more extensive neuropsychological testing revealed significant problems for attention, memory, processing speed and interference. Visuo-constructive problems were marked for copying the Rey figure, but less pronounced for recall of the figure. Verbal fluency was more affected than design fluency. Behavioural deficits could be detected in 33% of patients. Attention deficit problems were marked in 12.5%, whereas others demonstrated psychiatric symptoms such as mutism, addiction problems, anorexia, uncontrolled temper tantrums and phobia. Age at tumour operation and size of tumour had no influence on outcome. Vermis involvement was related to an increase in neuropsychological and psychiatric problems. The observation that patients with left-sided cerebellar tumours were more affected than patients with right-sided tumours is probably also influenced by a more pronounced vermian involvement in the former group. In summary, this study confirms the importance of the cerebellum for cognitive development and points to the necessity of careful follow-up for these children to provide them with the necessary help to achieve full integration into professional life.

Adolescent↗
PubMed2005

Socially transmitted mate preferences in a monogamous bird: a non-genetic mechanism of sexual selection.

There is increasing evidence that animals can acquire mate preferences through the use of public information, notably by observing (and copying) the mate preferences of others in the population. If females acquire preferences through social mechanisms, sexual selection could act very rapidly to spread the preference and drive elaboration of the preferred trait(s). Although there are reports of 'mate-choice copying' in polygynous species, there is no clear evidence for this process in monogamous species. Here, we investigated whether adult female zebra finches Taeniopygia guttata can socially acquire sexual preferences for individual males and, in a separate study, for a generalized trait (coloured leg bands) of males. In both studies, test females observed males in two simultaneous conditions: a ('chosen') mixed-sex situation in which a male was paired with a (model) female, and a ('unchosen') same-sex situation in which a male was paired with another male. In the first experiment, after two weeks of females observing males, test females significantly preferred individual males who had been paired with another female (i.e. chosen males). In the second experiment, test females significantly preferred novel males that were wearing the same leg band colour as the apparently chosen males. Our findings are consistent with the conclusion that female zebra finches' mate preferences are altered by public information. Our study implies that mate preferences can spread rapidly through populations by social mechanisms, affecting the strength of sexual selection in a monogamous species.

Animals↗
PubMed2005

Alteration of the fatty acid profile of Streptomyces coelicolor by replacement of the initiation enzyme 3-ketoacyl acyl carrier protein synthase III (FabH).

The first elongation step of fatty acid biosynthesis by a type II dissociated fatty acid synthases is catalyzed by 3-ketoacyl-acyl carrier protein (ACP) synthase III (KASIII, FabH). This enzyme, encoded by the fabH gene, catalyzes a decarboxylative condensation between an acyl coenzyme A (CoA) primer and malonyl-ACP. In organisms such as Escherichia coli, which generate only straight-chain fatty acids (SCFAs), FabH has a substrate preference for acetyl-CoA. In streptomycetes and other organisms which produce a mixture of both SCFAs and branched-chain fatty acids (BCFAs), FabH has been shown to utilize straight- and branched-chain acyl-CoA substrates. We report herein the generation of a Streptomyces coelicolor mutant (YL/ecFabH) in which the chromosomal copy of the fabH gene has been replaced and the essential process of fatty acid biosynthesis is initiated by plasmid-based expression of the E. coli FabH (bearing only 35% amino acid identity to the Streptomyces enzyme). The YL/ecFabH mutant produces predominantly SCFAs (86%). In contrast, BCFAs predominate (approximately 70%) in both the S. coelicolor parental strain and S. coelicolor YL/sgFabH (a deltafabH mutant carrying a plasmid expressing the Streptomyces glaucescens FabH). These results provide the first unequivocal evidence that the substrate specificity of FabH observed in vitro is a determinant of the fatty acid made in an organism. The YL/ecFabH strain grows significantly slower on both solid and liquid media. The levels of FabH activity in cell extracts of YL/ecFabH were also significantly lower than those in cell extracts of YL/sgFabH, suggesting that a decreased rate of fatty acid synthesis may account for the observed decreased growth rate. The production of low levels of BCFAs in YL/ecFabH suggests either that the E. coli FabH is more tolerant of different acyl-CoAs substrates than previously thought or that there is an additional pathway for initiation of BCFA biosynthesis in Streptomyces coelicolor.

3-Oxoacyl-(Acyl-Carrier-Protein) Synthase↗
PubMed2006

Pausing during reverse transcription increases the rate of retroviral recombination.

Retroviruses package two copies of genomic RNA into viral particles. During the minus-sense DNA synthesis step of reverse transcription, the nascent DNA can transfer multiple times between the two copies of the genome, resulting in recombination. The mechanism for this process is similar to the process of obligate strand transfers mediated by the repeat and primer binding site sequences. The location at which the DNA 3' terminus completely transfers to the second RNA strand defines the point of crossover. Previous work in vitro demonstrated that reverse transcriptase pausing has a significant impact on the location of the crossover, with a proportion of complete transfer events occurring very close to pause sites. The role of pausing in vivo, however, is not clearly understood. By employing a murine leukemia virus-based single-cycle infection assay, strong pausing was shown to increase the probability of recombination, as reflected in the reconstitution of green fluorescent protein expression. The infection assay results were directly correlated with the presence of strong pause sites in reverse transcriptase primer extension assays in vitro. Conversely, when pausing was diminished in vitro, without changing the sequence of the RNA template involved in recombination, there was a significant reduction in recombination in vivo. Together, these data demonstrate that reverse transcriptase pausing, as observed in vitro, directly correlates with recombination during minus-sense DNA synthesis in vivo.

DNA, Viral↗
PubMed1996

Disruption of the NAD(+)-specific glutamate dehydrogenase gene of Neurospora crassa by means of the RIP (repeat-induced point mutations) process.

The structural gene for the catabolite-repressed, substrate-induced NAD(+)-specific glutamate dehydrogenase (gdh-1) of Neurospora crassa was disrupted using the process of repeat-induced point mutation (RIP). Plasmids containing incomplete copies of the gene, along with selectable markers, were introduced into germinated conidia by electroporation. The sexual progeny of a transformant containing an ectopically integrated copy of a plasmid, harbouring the 5' flanking region and a part of the coding sequence of gdh-1 DNA, was examined for the occurrence of RIP by (i) Southern blot analysis of the genomic DNA digested with the isoschizomers MboI and Sau3A, (ii) Northern blot analysis of total RNA in cultures subjected to repression and induction conditions for NAD-GDH, (iii) direct assessment of enzymatic activity, and (iv) evaluation of protein levels by Western blot analysis using a polyclonal anti-GDH IgG preparation. Attempts were made at delineating different regions of the gene exhibiting RIP by using 32P-labelled DNA probes, corresponding to (i) the complete gene, (ii) a fragment containing the 5' flanking region plus two-thirds of the coding sequence, and (iii) the 5' flanking segment alone. The extent and relative location of RIP, as revealed by these hybridization probes, appeared to correlate with changes in specific activity under repression and derepression conditions. Mutant progeny, thus recovered, included isolates with altered regulatory features, such as constitutive expression, inability to elicit derepression, higher-than-wildtype GDH levels under derepression and inefficient repression.

Blotting, Northern↗