Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Replication Timing”

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 487 records · Page 27Linked to original sources
PubMed1999

Bacterial lipopolysaccharide inhibits dengue virus infection of primary human monocytes/macrophages by blockade of virus entry via a CD14-dependent mechanism.

Monocytes/macrophages (MO/Mphi) are the major target cells for both dengue virus (DV) and bacterial lipopolysaccharide (LPS), and the aim of this study was to define their interactions. We had found that LPS markedly suppressed DV infection of primary human MO/Mphi when it was added to cultures prior to or together with, but not after, viral adsorption. The inhibitory effect of LPS was direct and specific and was not mediated by LPS-induced secretion of cytokines and chemokines such as tumor necrosis factor alpha, interleukin-1beta (IL-1beta), IL-6, IL-8, IL-12, alpha interferon, MIP-1alpha, and RANTES. In fact, productive DV infection was not blocked but was just postponed by LPS, with a time lag equal to one viral replication cycle. Time course studies demonstrated that LPS was only effective in suppressing DV infection of MO/Mphi that had not been previously exposed to the virus. At various time points after viral adsorption, the level of unbound viruses that remained free in the culture supernatants of LPS-pretreated cultures was much higher than that of untreated controls. These observations suggest that the LPS-induced suppression of DV replication was at the level of virus attachment and/or entry. Blockade of the major LPS receptor, CD14, with monoclonal antibodies MY4 or MoS39 failed to inhibit DV infection but could totally abrogate the inhibitory effect of LPS. Moreover, human serum could significantly enhance the LPS-induced DV suppression in a CD14-dependent manner, indicating that the "binding" of LPS to CD14 was critical for the induction of virus inhibition. Taken together, our results suggest that LPS blocked DV entry into human MO/Mphi via its receptor CD14 and that a CD14-associated cell surface structure may be essential for the initiation of a DV infection.

Adult↗
PubMed1990

Measurement of intraoral muscle forces during functional exercises.

Measurements of intraoral muscle force with foil strain gauges, load cells, and pressure transducers bonded to a Tru-Tain stent and to a lip bumper appliance were tested by means of seven functional exercises in five adult subjects over a 5-day interval. The measuring devices and the functional exercises were tested for replicability and validity. Results showed that the pressure transducer was the superior measuring device with respect to size, sensitivity, thermal compensation, factory uniformity, replicability, and validity. The device most susceptible to error, on the basis of these factors, was the foil strain gauge. Of the seven functional exercises used, the pronunciation of the words "phone," "mom," and "church" and the exercise of swallowing were replicable over time. The other three exercises--chewing gum, sucking, and blowing on a straw--were determined to be unreliable in terms of replicability over time. Overall pressure values recorded were significantly higher than in previous reports. Pressure values were higher for the Tru-Tain stent than for the lip bumper.

Adult↗
PubMed2001

Timely release of both replication forks from oriC requires modulation of origin topology.

Initiation of DNA replication at oriC occurs bidirectionally both in vivo and in vitro. Although the proteins involved in establishing the replication forks are known, little is known about the events that ensure that initiation is bidirectional. We show here that in the absence of DNA gyrase, replication fork progression from oriC on a plasmid template in vitro is unidirectional, although both replication forks have formed at the origin. There was no bias in the release of one fork or the other, ruling out protein blockage of one fork as a possible reason for the asymmetric release. Timely release of both forks required the presence of either DNA gyrase or topoisomerase IV, suggesting that modulation of the topology of the origin region is the governing factor.

Bacterial Proteins↗
PubMed1986

Temporal order of replication of Xenopus laevis 5S ribosomal RNA genes in somatic cells.

The timing of replication of both the somatic and oocyte-type 5S ribosomal RNA genes of Xenopus laevis was determined in cultured cells by using 5-bromodeoxyuridine labeling of DNA coupled with a retroactive synchrony technique employing the fluorescence-activated cell sorter (FACS). The somatic genes replicate very early in S phase, while the oocyte genes replicate very late. These experiments provide direct evidence for a model [Gottesfeld, J. & Bloomer, L. S. (1982) Cell 28, 781-791] in which the transcription-activating factor TFIIIA is required at the time of Xenopus 5S rRNA gene replication to facilitate transcription of these genes.

Animals↗
PubMed2025

A Quantitative Real-Time PCR Assay for Measuring Poxvirus Replication and Cell Binding.

Quantitative real-time PCR (qPCR) is a fast and reliable method to quantify viral genomes as a surrogate to titering on monolayers of cells for measuring virus replication. Whether it be for determining the number of virions released, the total number of genomes produced during infection, or the number of virions bound to a cell, qPCR assays can be adapted to quickly enumerate total viral genomes in a broad range of experiments comparing virus replication under different conditions. In addition, qPCR offers several advantages compared to plaque assays including time, linearity over 9 logs, and scalability from tens-to-hundreds of samples, depending on the qPCR machine. Here we describe a qPCR assay for quantifying vaccinia virus' dsDNA genome that can be used to determine the total number of virions produced. Furthermore, we describe a straightforward protocol for a cell-binding assay that is sensitive enough to use with small concentrations of inoculating virions. This protocol is suitable for measuring the cell-binding ability of mutations that affect virus production and infectivity.

Virus Replication↗
PubMed1979

The effects of an Escherichia coli dnaAts mutation on the replication of the plasmids colE1 pSC101, R100.1 and RTF-TC.

The rate of replication of the plasmids colE1, pSC101, R100.1 and pAR132 (an RTF-TC derivative of the drug resistance factor R100.1) has been investigated directly by DNA:DNA hybridization. These rates have been compared, in a dnaAts strain, to that of various markers of the host chromosome at permissive and non-permissive temperatures. Chromosome initiation in the dnaAts strain stops rapidly after a shift to the non-permissive temperature, but plasmids R100.1 and pAR132 do not seem to be affected directly and continue replication for some time. The colE1 replication rate undergoes a large increase after the temperature shift, followed by a rapid decrease to a very low level 25 min after the shift. In contrast pSC101 replication stops immediately after the shift. ColE1 is able to replicate in an integratively suppressed dnaAts strain at 42 degrees C whereas pSC101 stops replication immediately under these conditions. We conclude that R100.1 and its derivative RTF-TC can replicate without a functional dnaA product; that colE1, while affected by a shift in temperature in a dnaAts strain, does not directly require dnaA; and that the plasmid pSC101 has an absolute requirement for dnaA. The absolute requirement of pSC101 for dnaA in the integratively suppressed Hfr strain provides a useful system for further investigation of the dnaA function.

DNA Replication↗
PubMed1992

Replication of patient isolates of human immunodeficiency virus type 1 in T cells: a spectrum of rates and efficiencies of entry.

Isolates of human immunodeficiency virus type 1 (HIV-1) undergo many different rates of replication, with the time course of replication being determined by the host cell and the virus. Recently, we demonstrated that the permissiveness of four CD4+ T-cell lines for the laboratory strain NL4-3 correlated with the rate and efficiency of virus entry. In this study, we have analyzed the replication of a "slow/low" isolate from the pre-AIDS period of infection and two "rapid/high" isolates from the AIDS period of infection to determine which steps in the virus life cycle determine differences in the growth characteristics of patient isolates. Differences in the growth of the patient isolates correlated with differences in entry but not postentry steps of the virus life cycle. The two rapid/high patient isolates (SF33 and SF216) underwent 50% entry in less than or equal to 0.5 hr in C8166 cells, in less than or equal to 1 hr in mitogen-stimulated peripheral blood mononuclear cells, and in greater than or equal to 2.5 hr in H9 cells. In contrast, a class 3 slow/low patient isolate required 1 hr for 50% entry into C8166 cells, 3 hr for 50% entry into peripheral blood mononuclear cells, and 5-6 hr for 50% entry into H9 cells. Entry efficiency correlated with entry rate, with the rapid/high viruses having a 2-fold higher titer and the slow/low virus having a 5-fold higher titer on C8166 than H9 cells. The laboratory strain NL4-3 displayed intermediate rates and efficiencies of entry. These data demonstrate that entry characteristics are major determinants of the pathogenic potential of patient isolates.

Acquired Immunodeficiency Syndrome↗
PubMed1989

Characterization of the phage phi 29 protein p5 as a single-stranded DNA binding protein. Function in phi 29 DNA-protein p3 replication.

The phage phi 29 protein p5, required in vivo in the elongation step of phi 29 DNA replication, was highly purified from Escherichia coli cells harbouring a gene 5-containing plasmid and from phi 29-infected Bacillus subtilis. The protein was characterized as the gene 5 product by amino acid analysis and NH2-terminal sequence determination. The purified protein p5 was shown to bind to single-stranded DNA and to protect it against nuclease degradation. No effect of protein p5 was observed either on the formation of the p3-dAMP initiation complex or on the rate of elongation. However, protein p5 greatly stimulated phi 29 DNA-protein p3 replication at incubation times where the replication in the absence of p5 leveled off.

Amino Acids↗
PubMed2006

The effect of dietary probiotic supplementation on tibial bone characteristics and strength in broilers.

A 6-wk study with 50 birds was conducted to investigate the effects of a dietary supplemental probiotic on morphometric parameters and yield stress of the tibia. Twenty-five 1-d-old broiler chicks were assigned to a control or an experimental diet containing Bacillus licheniformis and Bacillus subtilis (BioPlus 2B, CHR Hansen BioSystems, Denmark, Ugur Ecza Deposu, Turkiye Distributoru, Adapazari 41400, Turkey; each containing 2.3 x 10(8) cfu/g of spores) supplemented to the starter and finisher diets at 500 g/1000 kg of feed. Each diet was replicated 5 times with 5 birds in each replicate. Tibiotarsi weight, length, and weight/length index, robusticity index, diaphysis diameter, modulus of elasticity, yield stress parameters, and percentage Ca content were not affected by the dietary supplementation of probiotic, whereas thickness of the medial and lateral wall of the tibia, tibiotarsal index, percentage ash, and P content were significantly improved by the probiotic. Medullary canal diameter of the tibia of the birds fed the control diet was significantly greater than that of birds fed the probiotic diet. There was no treatment impact on live performance of the birds throughout the 6-wk feeding trial.

Animal Feed↗
PubMed1984

Reversal of DNA methylation with 5-azacytidine alters chromosome replication patterns in human lymphocyte and fibroblast cultures.

Prior studies demonstrated that developmental or induced methylation of DNA can inactivate associated gene loci. Such DNA methylation can be reversed and specific genes reactivated by treatment with 5-azacytidine (5- azaC ). The present cytogenetic studies using replication banding methods show that 5- azaC treatment also results in an increase or decrease in replication staining at one or more band locations in human lymphocyte and fibroblast chromosomes. New replication band locations are not formed. These changes in replication staining, which reflect changes in timing of replication, are different between these two tissues. However, in both tissues, the delayed onset of replication in the heterocyclic, inactive X is shortened by 5- azaC . A correlation is thus suggested between the induced temporal change to earlier DNA replication, and induced hypomethylation and gene activation. The temporal effect on chromosome replication in 5- azaC -treated cells depends on the portion of the S-period studied. Toward the beginning of S, early-replication patterns are increased in both lymphocytes and fibroblasts. Toward the end of S, late-replication patterns are increased only in lymphocytes, suggesting a differential effect of 5- azaC in: (1) early-vs. late-S, and (2) lymphocytes vs. fibroblasts. Generally, 5- azaC has its greatest effect on the inactive chromosome regions that are typically late-replicating prior to 5- azaC treatment. These observed changes in replication band staining suggest that DNA methylation may modify regional groups of genes in concert.

Azacitidine↗
PubMed1983

Sources of variance in the bioassay of protein value.

A factorial design was used to simultaneously evaluate the relative effect of 8 experimental factors and their interactions on the weanling rat bioassay of protein value: (1) source of protein: ANRC casein, lactalbumin, high-protein wheat flour; (2) protein level of the diet: 5 and 10%; (3) dietary fat level: 10 and 20% corn oil; (4) animal: ARS-Sprague-Dawley, from Taconic Farms; (5) age of animal: 21 and 28 days; (6) acclimation time: 2 and 4 days; (7) replication: 2 complete replications in time; and (8) duration of the test: food consumption and body weights were measured at 3, 7, 10, 14, 17, 21, 24, and 28 days after starting the test diet and converted to the ratio of grams of weight gained per gram of protein consumed for each weigh day. The official AOAC method for determining the protein efficiency ratio was followed with minor modifications. All 8 factors and many of their possible interactions appeared to significantly influence the measured ratios. When the ratios were adjusted by reference to the corresponding value for casein as a control, fat level, rat source, rat age, and acclimation time were no longer significant sources of variation. Plots of measured ratios and their coefficients of variation against time suggest that the optimum assay time varies with the protein but that the assay time should not be less than 21 days. The generally used 28-day assay time seems to offer no increase in precision over 21 days.

Animal Nutritional Physiological Phenomena↗
PubMed1995

Procedures for measuring the quality of heat-treated soybeans.

Soybeans were subjected to 12 heat treatments, differing in temperature and steeping (conditioning) time: control (no heat); 110 degrees C, 0 min; 110 degrees C, 30 min; 123 degrees C, 0 min; 123 degrees C, 30 min; 135 degrees C, 0 min; 135 degrees C, 30 min; 146 degrees C, 0 min; 146 degrees C, 15 min; 146 degrees C, 30 min; 153 degrees C, 30 min; and 160 degrees C, 30 min. These soybean treatments were tested for protein dispersibility index, absorbance at 420 nm, ADIN, pepsin-insoluble N, and in situ and in vitro protein degradation. Seven of these treatments (control; 123 degrees C, 30 min; 135 degrees C, 0 min; 135 degrees C, 30 min; 146 degrees C, 0 min; 146 degrees C, 30 min; and 153 degrees C, 30 min) were used in a feeding study involving 21 Holstein heifers (7 x 7 Latin square design replicated three times) and a lactation experiment (7 x 7 Latin square design replicated two times) using 14 multiparous Holstein cows in early lactation. Concentrations of branched-chain AA in blood plasma were used as indicators of protein uptake from the intestine in the heifer study, and production of 3.5% FCM was used to evaluate soybean treatments in the lactation study. Based on the criteria used, soybeans heated to 146 degrees C for 30 min were considered to be optimal. The protein dispersibility index and absorbance at 420 nm proved useful in evaluation of heat exposure of soybeans, and these procedures are suggested for routine monitoring of quality of commercially heated soybeans.

Amino Acids, Branched-Chain↗
PubMed1979

Time estimation and hyperactivity, replication.

Three groups of boys included 135 of normal IQ, showing normal activity; 6 were hyperactive and of normal IQ, and 6 showed normal activity but low IQ. Their ability to estimate a 30-sec. interval showed only the 6 normally active boys of low IQ had significantly different elapsed and estimated times. Time estimation is not clinically useful for identifying hyperactive boys.

Adolescent↗
PubMed1977

Cell cycle analysis of F'lac replication in Escherichia coli B/r.

The timing and control of replication of an F'lac plasmid was investigated in two substrains of Escherichia coli B/r lac/F'lac growing at a variety of rates. The cellular content of covalently closed circular F'lac deoxyribonucleic acid and the cellular mass at the time of F'lac replication both increased as a function of growth rate. The timing of plasmid replication during the division cycle was determined by measuring the inducibility of beta-galactosidase in cells of different ages in exponentially growing cultures. At all growth rates, the rate of induced beta-galactosidase synthesis increased in a step-wise fashion during the division cycle, indicating that the F'lac plasmid replicated at a discrete time in the cycle. At growth rates greater than one doubling per h, the cell age at F'lac replication was indistinguishable from the cell age at chromosomal lac+ replication in an isogenic F- parent. The ratio of plasmids to chromosomal origins decreased from about 0.7 to 0.4 between growth rates of 1.0 to 2.5 doublings per h. These observations are all consistent with replication of F'lac at about the same time in the division cycle as replication of the homologous chromosomal region at these growth rates. This similarity in timing of replication of homologous deoxyribonucleic acid regions was not evident in slower-growing cells.

Cell Division↗
PubMed2004

Enforcement of late replication origin firing by clusters of short G-rich DNA sequences.

Previous studies in budding yeast suggested that the default firing time of most DNA replication origins is early in S phase and that origins can be forced to fire later by proximity to certain cis-acting sequences. However, these cis-acting sequences were not well defined. We have attempted to characterize cis-acting sequences that affect replication timing in the fission yeast. We identified a stretch of 200 bp that was sufficient to compel nearby origins to fire late. The 200-bp stretch was able to force an origin to fire late whether adjacent to the origin or approximately 800 bp away in opposite orientation. The stretch contains a cluster of three close matches to a G-rich, 10-bp late consensus sequence (LCS). The three LCS elements cooperate with each other and with other sequences within the 200-bp stretch to enforce late replication. Although only a few origins that fire in very late S phase have been identified in fission yeast, all of them are located close to a cluster of LCS elements.

Base Sequence↗