Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Origin cell mapping”

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 235 records · Page 13Linked to original sources
PubMed1995

Initiation of latent DNA replication in the Epstein-Barr virus genome can occur at sites other than the genetically defined origin.

Our laboratory has previously shown that replication of a small plasmid, p174, containing the genetically defined Epstein-Barr virus (EBV) latent origin of replication, oriP, initiates within oriP at or near a dyad symmetry (DS) element and terminates specifically at a family of repeated sequences (FR), also located within oriP. We describe here an analysis of the replication of intact approximately 170-kb EBV genomes in four latently infected cell lines that uses two-dimensional gel replicon mapping. Initiation was detected at oriP in all EBV genomes examined; however, some replication forks appear to originate from alternative initiation sites. In addition, pausing of replication forks was observed at the two clusters of EBV nuclear antigen 1 binding sites within oriP and at or near two highly expressed viral genes 0.5 to 1 kb upstream of oriP, the EBV-encoded RNA (EBER) genes. In the Raji EBV genome, the relative abundance of these stalled forks and the direction in which they are stalled indicate that most replication forks originate upstream of oriP. We thus searched for additional initiation sites in the Raji EBV and found that the majority of initiation events were distributed over a broad region to the left of oriP. This delocalized pattern of initiation resembles initiation of replication in several well-characterized mammalian chromosomal loci and is the first described for any viral genome. EBV thus provides a unique model system with which to investigate factors influencing the selection of replication initiation and termination sites in mammalian cells.

Antigens, Viral↗
PubMed1986

Replication of a plasmid bearing a human Alu-family repeat in monkey COS-7 cells.

Monkey COS-7 cells were transformed with BLUR8 DNA, a pBR322 plasmid containing a human Alu-family sequence at the BamHI site. Within 24 hr of transformation 2-5% of the BLUR8 molecules recovered resisted cleavage by Dpn I, indicating they had replicated. Electron microscopy revealed appropriately sized circular molecules with replication bubbles whose centers were mapped to the Alu insert. A 16-base-pair deletion within the Alu sequence prevented replication. The results indicate that certain Alu sequences can serve as origins of replication in COS-7 cells.

Animals↗
PubMed2001

RAGE expression and AGE-induced MAP kinase activation in Caco-2 cells.

RAGE (receptor for advanced glycation end products) is a multiligand cell surface molecule of the immunoglobulin superfamily. It was originally described as a receptor for protein adducts formed by glycoxidation (AGEs) that accumulate in diseases such as diabetes and renal failure. Performing RT-PCR and Western blot analysis we intended to determine RAGE expression in the human colon adenocarcinoma cell line Caco-2. Moreover, Caco-2 cells were incubated in the presence of AGEs. Since RAGE ligation triggers the p21(ras) signal transduction pathway the activation state of p44/42 (ERK1/2) MAP kinases was determined. Here we demonstrate for the first time that Caco-2 cells express RAGE and that administration of the food-derived casein-linked AGE N(epsilon)-(carboxymethyl)lysine (Cas-CML) results in Caco-2 p44/42 (ERK1/2) MAP kinase activation.

Adenocarcinoma↗
PubMed1982

Temporal patterns of human cytomegalovirus transcription: mapping the viral RNAs synthesized at immediate early, early, and late times after infection.

The transcription of the human cytomegalovirus genome was investigated at immediate early, early, and late times after infection. Viral RNAs associated with either the whole cell, the nucleus, the cytoplasm, or the polyribosomes were analyzed. At immediate early times, i.e., in the absence of de novo viral protein synthesis, the viral RNA in high abundance originated from a region of the long unique section of the prototype arrangement of the viral genome (0.660 to 0.770 map units). The viral RNA in low abundance originated from the long repeat sequences (0.010 to 0.035 and 0.795 to 0.825 map units) and a region in the long unique section (0.201 to 0.260 map units). Viral RNAs associated with the polyribosomes as polyadenylated RNA were mapped to these restricted regions of the viral genome and characterized according to size class in kilobases. At 24 h after infection in the presence of an inhibitor of viral DNA replication, i.e., at early times, the stable viral RNAs in highest abundance mapped in the long repeat sequences. Viral RNAs at intermediate abundance under these conditions mapped in two regions of the long unique section of the viral genome (0.325 to 0.460 and 0.685 to 0.770 map units). Stable viral RNAs that were associated with the polyribosomes in high abundance as polyadenylated RNA orginated from the long repeat sequences, but not from the long unique section of the viral genome. An analysis of whole-cell RNA at late times (72 h) indicated that the abundant transcription was in the regions of the long unique sequences (0.325 to 0.460 and 0.660 to 0.685 map units), and transcription of intermediate abundance was from the long repeat sequences. However, stable viral mRNA's derived from the long repeat sequences were associated with the polyribosomes at late times after infection. In addition, mRNA's originating from the long and short unique sequences were found associated with the polyribosomes at higher relative concentration than at early times after infection. It is proposed that expression of the immediate early viral genes is required to transcribe the early viral genes in the long repeat and adjacent sequences. These sequences are also transcribed at late times after infection while viral DNA synthesis continues. The expression of viral genes in most of the long and short unique sequences appears to require viral DNA replication.

Cell Nucleus↗
PubMed1978

Biological properties and physical map of the genome of a new papovavirus, HD virus.

The superhelical DNA of the HD papovavirus is heterogeneous and consists of two discrete size classes with molecular weights of 3.45 X 10(6) and 3.25 X 10(6). Both size classes of DNA are encapsidated into HD virion particles. Their relative intracellular amounts differ, depending on the cell system. Vero-76 carrier cultures in which HD virus was detected contain both size classes of DNA, with the larger molecules prevailing by a factor of 10. Five clonal lines derived from Vero-76 cell cultures contain exclusively the larger DNA. On the other hand, after cocultivation of Vero-76 with CV-1 cells for several passages, minicircular DNA is accumulated such that both size classes are synthesized in equal amounts. Any of the originally viral DNA-producing cell lines may, upon subcultivation, cease yielding virus. The RITA cell line of Cercopithecus aethiops origin is the only cell line among numerous ones tested which upon infection permits the establishment of a one-step growth cycle. However, between 6 and 8 days after infection, viral DNA synthesis is discontinued, and a persistent viral infection cannot be established. Physical maps of the genomes were constructed, and it could be shown that the smaller, minicircular DNA had originated from the larger DNA as the result of a deletion. The sequences missing in the minicircular DNA are confined to the relative map position 0.15 to 0.21.

Cell Line↗
PubMed1983

Biochemical activities of T-antigen proteins encoded by simian virus 40 A gene deletion mutants.

We have analyzed T antigens produced by a set of simian virus 40 (SV40) A gene deletion mutants for ATPase activity and for binding to the SV40 origin of DNA replication. Virus stocks of nonviable SV40 A gene deletion mutants were established in SV40-transformed monkey COS cells. Mutant T antigens were produced in mutant virus-infected CV1 cells. The structures of the mutant T antigens were characterized by immunoprecipitation with monoclonal antibodies directed against distinct regions of the T-antigen molecule. T antigens in crude extracts prepared from cells infected with 10 different mutants were immobilized on polyacrylamide beads with monoclonal antibodies, quantified by Coomassie blue staining, and then assayed directly for T antigen-specific ATPase activity and for binding to the SV40 origin of DNA replication. Our results indicate that the T antigen coding sequences required for origin binding map between 0.54 and 0.35 map units on the SV40 genome. In contrast, sequences closer to the C terminus of T antigen (between 0.24 and 0.20 map units) are required for ATPase activity. The presence of the ATPase activity correlated closely with the ability of the mutant viruses to replicate and to transform nonpermissive cells. The origin binding activity was retained, however, by three mutants that lacked these two functions, indicating that this activity is not sufficient to support either cellular transformation or viral replication. Neither the ATPase activity nor the origin binding activity correlated with the ability of the mutant DNA to activate silent rRNA genes or host cell DNA synthesis.

Adenosine Triphosphatases↗
PubMed1979

Purification and mapping of specific mRNAs by hybridization-selection and cell-free translation.

We describe a simple procedure for isolating specific mRNAs and for mapping them to the regions of the DNA from which they originate. The method involves hybridization of total cytoplasmic RNA to restriction fragments of DNA that have been fractionated in agarose gels and immobilized on nitrocellulose filters. The hybridization-selected RNAs are eluted and translated in a cell-free system in order to identify their encoded polypeptides. Optimal hybridization and filter washing conditions are given for selection of mRNAs from adenovirus 2-infected cells and transformed cells.

Adenoviridae↗
PubMed1983

Brachial muscles in the chick embryo: the fate of individual somites.

The wing and wing-associated muscles of the shoulder and thorax in the bird all cleave from common myogenic masses in the developing wing bud and are referred to collectively as brachial muscles. In this study the precise embryonic origin of the brachial muscles was determined using chick-quail chimaeras. Such chimaeras consisted of a graft of one somite taken from a 2-day quail donor embryo transplanted to the equivalent location in a 2-day chick host embryo. The chimaeras were analysed at 9.5-10.0 days in ovo to determine the location of the grafted cells and therefore the structures that were derived from the transplanted somite. The somites that were studied in this matter were somites 13 to 23 inclusive. The results show that only somites 16 to 21 inclusive contribute cells to the brachial musculature; moreover, the cells from a given somite are not distributed randomly among the brachial muscles but populate specific muscles only: thus it has been possible to map the somitic origin of individual brachial muscles. Moreover, there is an indication that each somite plays a unique role in the development of the brachial muscles.

Animals↗
PubMed2000

Enhanced flexibility and aphidicolin-induced DNA breaks near mammalian replication origins: implications for replicon mapping and chromosome fragility.

Common fragile sites are chromosomal loci prone to breakage and rearrangement that can be induced by aphidicolin, an inhibitor of DNA polymerases. Within these loci, sites of preferential DNA breaks were proposed to correlate with peaks of enhanced DNA flexibility, the function of which remains elusive. Here we show that mammalian DNA replication origins are enriched in peaks of enhanced flexibility. This finding suggests that the search for these features may help in the mapping of replication origins, and we present evidence supporting this hypothesis. The association of peaks of flexibility with replication origins also suggests that some origins may associate with minor levels of fragility. As shown here, an increased sensitivity to aphidicolin was found near two mammalian DNA replication origins.

Animals↗
PubMed2002

Primitive and definitive blood share a common origin in Xenopus: a comparison of lineage techniques used to construct fate maps.

Primitive blood constitutes the ventralmost mesoderm in amphibians, and its cleavage-stage origin reveals important clues about the orientation of the dorsal/ventral axis in the embryo. In recent years, investigators employing various lineage-labeling strategies have reported disparate results for the origin of primitive blood in Xenopus [W. D. Tracey, Jr., M. E. Pepling, G. H. Thomsen, and J. P. Gergen (1998). Development 125, 1371-1380; M. C. Lane W. C. Smith (1999). Development 126, 423-434; K. R. Mills, D. Kruep, and M. S. Saha (1999). Dev. Biol. 209, 352-368; A. Ciau-Uitz, M. Walmsley, and R. Patient (2000). Cell 102, 787-796]. These discrepancies must be resolved in order to elucidate early embryonic patterning mechanisms in vivo. We directly compared two of the techniques used to determine the origin of the ventral blood islands and primitive blood, injection of either beta-galactosidase mRNA or conjugated dextrans, by coinjecting both tracers simultaneously into individual blastomeres in cleavage-stage embryos. We find that dextrans label progeny efficiently, while beta-galactosidase activity is not present in many of the progeny of an injected blastomere, suggesting that mRNA fails to diffuse throughout a blastomere. This result demonstrates that beta-galactosidase mRNA fails to meet the criterion for a true lineage label, namely efficient detection of the progeny of a blastomere, and raises questions about interpretations based on mapping the ventral blood islands using Lac Z mRNA as a tracer. We examined the origins of the ventral blood islands and primitive blood from the vegetal region of the marginal zone in regularly cleaving embryos by coinjecting both reporters into C-tier blastomeres. Our results demonstrate that both the ventral blood islands and primitive blood routinely arise from all C-tier blastomeres. Our data, in combination with published mapping results for the dorsal aorta, demonstrate that primitive and definitive blood do not have separate origins at the 32-cell stage in Xenopus. In addition, these results support a proposal to align the dorsal/ventral axis of the mesendoderm with the animal/vegetal axis in pregastrula Xenopus.

Animals↗
PubMed1979

Novel acriflavin resistance genes, acrC and acrD, in Escherichia coli K-12.

Acriflavine-resistant mutants were isolated from an acriflavine-sensitive (acrA) strain of Escherichia coli K-12 and then tested for temperature sensitivity of cell division. Genetic analysis characterized two new genetic loci, acrC and acrD. The former was mapped between tonA and proA, and the latter between the origin of genetic transfer of HfrH and serB. acrC and acrD mutants could divide but did not initiate a new round of deoxyribonucleic acid (DNA) replication at 43 degrees C. DNA synthesis of the acrC mutant cells ceased after a period of time following temperature shift-up, and thereafter DNA degradation occurred. However, cell mass continued to increase for a long time at the nonpermissive temperature. On the other hand, DNA synthesis of the acrD mutant cells ceased soon after the shift-up, and the cell mass did not appreciably increase during the prolonged incubation.

Acridines↗
PubMed1997

Deletion analysis of ors12, a centromeric, early activated, mammalian origin of DNA replication.

We have generated a panel of deletion mutants of ors12 (812-bp), a mammalian origin of DNA replication previously isolated by nascent strand extrusion from early replicating African Green monkey (CV-1) DNA. The deletion mutants were tested for their replication activity in vivo by the bromodeoxyuridine substitution assay, after transfection into HeLa cells, and in vitro by the Dpnl resistance assay, using extracts from HeLa cells. We identified a 215-bp internal fragment as essential for the autonomous replication activity of ors12. When subcloned into the vector pML2 and similarly tested, this subfragment was capable of autonomous replication in vivo and in vitro. Several repeated sequence motifs are present in this 215-bp fragment, such as TGGG(A) and G(A)AG (repeated four times each); TTTC, AGG, and CTTA (repeated 3 times each); the motifs CACACA and CTCTCT, and two imperfect inverted repeats. 22 and 16 bp long, respectively. The overall sequence of the 215-bp fragment is G/C-rich (50.2%), by comparison to the 186-bp (33.5% G/C-rich) minimal sequence required for the autonomous replication activity of ors8, another functional ors that was similarly isolated and characterized.

Base Sequence↗
PubMed1984

Scanning electron-stimulated desorption microscopy of red blood cells.

Scanning electron-stimulated desorption (SESD) has been used to image the surface of unfixed red blood cells with high surface specificity and with a lateral spatial resolution of less than or equal to 1 micron. The micrographs were obtained using a scanning Auger microprobe with an appended secondary ion mass spectrometer (SIMS). The instrument was operated at low electron beam energies (2 kV) to maximize electron-stimulated desorption probabilities and minimize the interaction of the electrons with the biological substrate. ESD spectra from the surface of red blood cells prepared from smears of whole blood show H+ as the predominant desorbed positive ion and O+, OH+, H3O+, Na+, and Cl+ as secondary species. SESD images and line-scans obtained with the above ion signals demonstrate that SESD can be used to map the surface chemistry of cells at submicron resolution. The parent molecules contributing to the desorbed ion signals are shown to originate from the first few atomic layers of the cell surface and are believed to be components of the blood plasma (H2O, NaCl, etc.) which coalesced onto the cells as they dehydrated in the vacuum chamber of the microprobe. An interesting extension of this work is the possibility of mapping the concentration of adsorption sites of specific cell-surface binding species using ESD labels.

Animals↗
PubMedDate not supplied

Transplantation of polymer-encapsulated fetal hippocampal cells into ischemic lesions of adult rat hippocampus.

In a previous study we demonstrated that fetal hippocampal cells, when transplanted into ischemic lesions of the adult rat hippocampus, can survive in large numbers in the host brain and show the innervation of the transplants by cholinergic fibers originated from the host brain. The present study was undertaken in an attempt to elucidate the hypothesis that the fiber connections forming synapses between the transplanted fetal neurons and the host brain play an important role in the survival of the transplanted cells. We transplanted the polymer-encapsulated fetal hippocampal cells prepared from E17-18 rat fetuses into the ischemic lesions in the adult rat hippocampus at which the CA1 pyramidal cells selectively died, and examined both histochemically or immunohistochemically for their survival and the expression of the synaptic vesicle protein, synaptophysin, and dendritic cytoskeltal protein, microtubule-associated protein 2 (MAP 2) within them. In addition, the cholinergic fibers originated from the host brain were examined by acetylcholine esterase (AChE) histochemistry. The results demonstrated that the polymer-encapsulated hippocampal cells could survive in the brain; however, the number of surviving cells markedly decreased following the transplantation, whereas no host-derived cholinergic fibers penetrated the polymer membrane of the capsules following the transplantation. In the cluster of surviving cells, only slight synaptophysin expression and no extensive growth of the dendrites were detected. The present results indicate that the direct contact between the host brain tissue and the transplant play an important role in the survival of such allografted neurons.

Acetylcholinesterase↗
PubMed1979

Genetic mapping of the chromosomal replication origin of Salmonella typhimurium.

Two hundred strains of Escherichia coli harboring Filv+ plasmids which carry a segment of the Salmonella typhimurium chromosome were isolated independently. Among them, two strains were found to harbor F' plasmids that are able to replicate in Hfr cells of E. coli; i.e., they carry a site designated poh (permissive on Hfr) of the S. typhimurium chromosome. The poh site is presumably identical with the replication origin (oriC) of the bacterial chromosome. These two plasmids carry the dnaA-uncA-rbs-ilv-cya-metE region of the chromosome of S. typhimurium. Other F' plasmids which only carried the ilv-cya-metE region were unable to be maintained in Hfr cells. The poh site (= oriC) of S. typhimurium thus is located in the uhp-ilv region of the chromosome. The two plasmids carrying the poh site of S. typhimurium can suppress the temperature-sensitive character of an E. coli mutant that carries the temperature-sensitive dnaA46 allele, when the plasmids exist in the mutant cells. This suggests that the dnaA chromosome in place of the dnaA gene product of E. coli itself. The ability of the plasmids carrying the poh site of S. typhimurium to replicate in Hfr cells of E. coli suggests that the replication system of E. coli can recognize the Salmonella replication origin.

Chromosome Mapping↗
PubMed2003

Dynamics of DNA replication in mammalian somatic cells: nucleotide pool modulates origin choice and interorigin spacing.

Selection of active origins and regulation of interorigin spacing are poorly understood in mammalian cells. Using tricolor analysis of combed DNA molecules, we studied an amplified locus containing the known origin, oriGNAI3. We visualized replication firing events at this and other discrete regions and established a strict correlation between AT richness and initiation sites. We found that oriGNAI3 is the prominent origin of the domain, the firing of which correlates with silencing of neighboring sites and establishes large interorigin distances. We demonstrate that cells reversibly respond to a reduction in nucleotide availability by slowing the rate of replication fork progression; in addition, the efficiency of initiation at oriGNAI3 is lowered while other normally dormant origins in the region are activated, which results in an overall increase in the density of initiation events. Thus, nucleotide pools are involved in the specification of active origins, which in turn defines their density along chromosomes.

AMP Deaminase↗
PubMed1996

ORC- and Cdc6-dependent complexes at active and inactive chromosomal replication origins in Saccharomyces cerevisiae.

We have developed a genomic footprinting protocol which allows us to examine protein-DNA interactions at single copy chromosomal origins of DNA replication in the budding yeast Saccharomyces cerevisiae. We show that active replication origins oscillate between two chromatin states during the cell cycle: an origin recognition complex (ORC)-dependent post-replicative state and a Cdc6p-dependent pre-replicative state. Furthermore, we show that both post- and pre-replicative complexes can form efficiently on closely apposed replicators. Surprisingly, ARS301 which is active as an origin on plasmids but not in its normal chromosomal location, forms ORC- and Cdc6p-dependent complexes in both its active and inactive contexts. Thus, although ORC and Cdc6p are essential for initiation, their binding is not sufficient to dictate origin use.

Base Sequence↗
PubMed2004

Cardiac neural crest of the mouse embryo: axial level of origin, migratory pathway and cell autonomy of the splotch (Sp2H) mutant effect.

A sub-population of the neural crest is known to play a crucial role in development of the cardiac outflow tract. Studies in avians have mapped the complete migratory pathways taken by 'cardiac' neural crest cells en route from the neural tube to the developing heart. A cardiac neural crest lineage is also known to exist in mammals, although detailed information on its axial level of origin and migratory pattern are lacking. We used focal cell labelling and orthotopic grafting, followed by whole embryo culture, to determine the spatio-temporal migratory pattern of cardiac neural crest in mouse embryos. Axial levels between the post-otic hindbrain and somite 4 contributed neural crest cells to the heart, with the neural tube opposite somite 2 being the most prolific source. Emigration of cardiac neural crest from the neural tube began at the 7-somite stage, with cells migrating in pathways dorsolateral to the somite, medial to the somite, and between somites. Subsequently, cardiac neural crest cells migrated through the peri-aortic mesenchyme, lateral to the pharynx, through pharyngeal arches 3, 4 and 6, and into the aortic sac. Colonisation of the outflow tract mesenchyme was detected at the 32-somite stage. Embryos homozygous for the Sp2H mutation show delayed onset of cardiac neural crest emigration, although the pathways of subsequent migration resembled wild type. The number of neural crest cells along the cardiac migratory pathway was significantly reduced in Sp2H/Sp2H embryos. To resolve current controversy over the cell autonomy of the splotch cardiac neural crest defect, we performed reciprocal grafts of premigratory neural crest between wild type and splotch embryos. Sp2H/Sp2H cells migrated normally in the +/+ environment, and +/+ cells migrated normally in the Sp2H/Sp2H environment. In contrast, retarded migration along the cardiac route occurred when either Sp2H/+ or Sp2H/Sp2H neural crest cells were grafted into the Sp2H/Sp2H environment. We conclude that the retardation of cardiac neural crest migration in splotch mutant embryos requires the genetic defect in both neural crest cells and their migratory environment.

Animals↗