SEARCH · PubMed Health

Results for “Copy Number Variations”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 1,297 records · Page 72Linked to original sources

PubMed1996

Optimal sequencing strategies for surveying molecular genetic diversity.

Two commonly used measures of genetic diversity for intraspecies DNA sequence data are based, respectively, on the number of segregating sites, and on the average number of pairwise nucleotide differences. Expressions are derived for their variance in the presence of intragenic recombination for a panmictic population of fixed size that is at neutral equilibrium at the region sequenced. We show that, in contrast to the slow decrease in variance with increasing sample size, if the recombination rate is nonzero, the asymptotic rate of decrease of variance with increasing sequence length, for fixed sample size, is quite rapid. In particular, it is close to that which would be obtained by sequencing independent chromosome regions. The correlation between measures of diversity from linked regions is also examined. For a given total number of bases sequenced in a particular region, optimal sequencing strategies are derived. These typically involve sequencing relatively few (three to 10) long copies of the region. Under optimal strategies, the variances of the two measures are very similar for most parameter values considered. Results concerning optimal sequencing strategies will be sensitive to gross departures from the underlying assumptions, such as population bottlenecks, selective sweeps, and substantial population substructure.

DNA↗

PubMed2005

Could human papillomaviruses be spread through blood?

The human papillomaviruses (HPVs) are epitheliotropic viruses that require the environment of a differentiating squamous epithelium for their life cycle. HPV infection through abrasion of the skin or sexual intercourse causes benign warts and sometimes cancer. HPV DNA detected in the blood has been interpreted as having originated from metastasized cancer cells. The present study examined HPV DNA in banked, frozen peripheral blood mononuclear cells (PBMCs) from 57 U.S. human immunodeficiency virus (HIV)-infected pediatric patients collected between 1987 and 1996 and in fresh PBMCs from 19 healthy blood donors collected in 2002 to 2003. Eight patients and three blood donors were positive mostly for two subgroups of the HPV type 16 genome. The HPV genome detected in all 11 PBMC samples existed as an episomal form, albeit at a low DNA copy number. Among the eight patients, seven acquired HIV from transfusion (three associated with hemophilia) and one acquired HIV through vertical transmission; this patient also had received a transfusion before sampling. Our data suggest that PBMCs may be HPV carriers and might spread the virus through blood.

Adolescent↗

PubMed1996

Homoplasy for size at microsatellite loci in humans and chimpanzees.

Homoplasy (convergence in the size of different alleles) at microsatellite loci was examined by sequencing multiple alleles of two compound microsatellites and single copies of alleles of the same size at two other compound loci in both chimpanzees and humans. At one of the two loci for which multiple alleles were sequenced, extensive homoplasy for size was uncovered both within and between species. At the three loci for which alleles of the same size were examined in the two species, sequencing demonstrated different internal structures. These results confirm theoretical predictions that a certain fraction of mutations at microsatellite loci should produce alleles that are identical in size but differ by a number of mutations. The sequence data reveal a previously unrecognized class of variation at microsatellites and open up the possibility that DNA sequencing may allow the extraction of more information from these loci, thus increasing their power as variable markers for genetic mapping studies. Conversely, the data also indicate that the assumption that alleles of the same size are identical in sequence, which is implicit in several methods of analysis, is violated in some cases. Therefore, caution should be used when employing microsatellites in phylogenetic and other studies in which the individuals being examined are separated by a great number of generations from a common ancestor.

Alleles↗

PubMed1997

Site-specific in situ amplification of the integrated polyomavirus genome: a case for a context-specific over-replication model of gene amplification.

The fate of the genome of the polyoma (Py) tumor virus following integration in the chromosomes of transformed rat FR3T3 cells was re-examined. The viral sequences were integrated at a single transformant-specific chromosomal site in each of 22 transformants tested. In situ amplification of the viral sequences was observed in 24 of 34 transformants analyzed. Large T antigen, the unique viral function involved in initiating DNA replication from the viral origin, was essential for the amplification process. There was an absolute requirement for a reiteration of viral sequences and the extent of the reiteration affected the degree of amplification. The reiteration may be important for homologous recombination-mediated resolution of in situ amplified sequences. Among 11 transformants harboring a 1 to 2 kb repeat, the degree of amplification was transformant-specific and varied over a wide range. At the high end of the spectrum, the genome copy number increased 1300-fold at steady state, while at the low end, amplification was below twofold. Some aspect of the host chromatin at the site integration that affected viral gene expression, also directly or indirectly modulated the amplification. Use of high-resolution electrophoresis for the analysis of the integrated amplified sequences revealed a recurring novel pattern, consisting of a ladder with numerous bands separated by a constant distance approximately the size of the Py genome. We suggest that this pattern was generated by conversion of the amplified viral genomes to head to tail linear arrays with cell to cell variations in the number of genome repeats at single, transformant-specific, chromosomal sites. In light of the known "out of schedule" firing of the Py origin, we propose an "onion skin" structure intermediate and present a homologous recombination model for the conversion from onion skins to linear arrays. The relevance of the in situ amplification of the Py genome to cellular gene amplification is discussed. Finally, these results clarify our understanding of the integration of the Py genome in rat cells. They suggest that, in most cases, the multiple bands previously described in Py-transformants are likely to reflect genome amplification rather than multiple independent integration events, as assumed in the past. This interpretation is congruent with the accepted view that the integration of the Py genome is a rare and rate-limiting event in transformation.

Animals↗

PubMed2006

A hybrid deterministic-stochastic algorithm for modeling cell signaling dynamics in spatially inhomogeneous environments and under the influence of external fields.

Cell signaling dynamics mediate myriad processes in biology. It has become increasingly clear that inter- and intracellular signaling reactions often occur in a spatially inhomogeneous environment and that it is important to account for stochastic fluctuations of certain species involved in signaling reactions. The importance of these effects enhances the difficulty of gleaning mechanistic information from observations of a few experimental reporters and highlights the significance of synergistic experimental and computational studies. When both stochastic fluctuations and spatial inhomogeneity must be included in a model simultaneously, however, the resulting computational demands quickly become overwhelming. In many situations the failure of standard coarse-graining methods (i.e., ignoring spatial variation or stochastic fluctuations) when applied to all components of a complex system does not exclude the possibility of successfully applying such coarse-graining to some components of the system. Following this approach alleviates computational cost but requires "hybrid" algorithms where some variables are treated at a coarse-grained level while others are not. We present an efficient algorithm for simulation of stochastic, spatially inhomogeneous reaction-diffusion kinetics coupled to coarse-grained fields described by (stochastic or deterministic) partial differential equations (PDEs). The PDEs could represent mean-field descriptions of reactive species present in large copy numbers or evolution of hydrodynamic variables that influence signaling (e.g., membrane shape or cytoskeletal motion). We discuss the approximations made to derive our algorithm and test its efficacy by applying it to problems that include many features typical of realistic cell signaling processes.

Algorithms↗

PubMed2002

Stable heteroplasmy but differential inheritance of a large mitochondrial DNA deletion in nematodes.

Many human mitochondrial diseases are associated with defects in the mitochondrial DNA (mtDNA). Mutated and wild-type forms of mtDNA often coexist in the same cell in a state called heteroplasmy. Here, we report the isolation of a Caenorhabditis elegans strain bearing the 3.1-kb uaDf5 deletion that removes 11 genes from the mtDNA. The uaDf5 deletion is maternally transmitted and has been maintained for at least 100 generations in a stable heteroplasmic state in which it accounts for approximately 60% of the mtDNA content of each developmental stage. Heteroplasmy levels vary between individual animals (from approximately 20 to 80%), but no observable phenotype is detected. The total mtDNA copy number in the uaDf5 mutant is approximately twice that of the wild type. The maternal transmission of the uaDf5 mtDNA is controlled by at least two competing processes: one process promotes the increase in the average proportion of uaDf5 mtDNA in the offspring, while the second promotes a decrease. These two forces prevent the segregation of the mtDNAs to homoplasmy.

Animals↗

PubMed2001

Regional variation in myosin isoforms and phosphorylation at the resting tone in urinary bladder smooth muscle.

Urinary bladder filling and emptying requires coordinated control of bladder body and urethral smooth muscles. Bladder dome, midbladder, base, and urethra showed significant differences in the percentage of 20-kDa myosin light chain (LC20) phosphorylation (35.45 +/- 4.6, 24.7 +/- 2.2, 13.6+/- 2.1, and 12.8 +/- 2.7%, respectively) in resting muscle. Agonist-mediated force was associated with a rise in LC20 phosphorylation, but the extent of phosphorylation at all levels of force was less for urethral than for bladder body smooth muscle. RT-PCR and quantitative competitive RT-PCR analyses of total RNA from bladder body and urethral smooth muscles revealed only a slight difference in myosin heavy chain mRNA copy number per total RNA, whereas mRNA copy numbers for NH2-terminal isoforms SM-B (inserted) and SM-A (noninserted) in these muscles showed a significant difference (2.28 x 10(8) vs. 1.68 x 10(8) for SM-B and 0.12 x 10(8) vs. 0.42 x 10(8) for SM-A, respectively), which was also evident at the protein level. The ratio of COOH-terminal isoforms SM2:SM1 in the urethra was moderately but significantly lower than that in other regions of the bladder body. A high degree of LC20 phosphorylation and SM-B in the bladder body may help to facilitate fast cross-bridge cycling and force generation required for rapid emptying, whereas a lower level of LC20 phosphorylation and the presence of a higher amount of SM-A in urethral smooth muscle may help to maintain the high basal tone of urethra, required for urinary continence.

Animals↗

PubMed2000

Toxoplasma gondii catalase: are there peroxisomes in toxoplasma?

The intracellular protozoan parasite Toxoplasma gondii, like all members of the phylum Apicomplexa, is known to possess many organelles: in addition to mitochondria and the compartments of the secretory pathway, there is a reduced chloroplast (the apicoplast) and the phylum-specific components of the apical complex: dense granules, micronemes and rhoptries. Conspicuously missing so far are microbodies, organelles that can be found in nearly all eukaryotic organisms. Microbodies show a large variation with regard to their size, number and contents, depending on the organism and cell type. One marker enzyme of this single membrane-bound organelle is catalase, which is responsible for the degradation of hydrogen peroxide to water and oxygen. The EST project in T. gondii revealed the existence of two overlapping clones which showed similarity with catalase, and these were used to clone the corresponding gene. The predicted sequence of T. gondii catalase has -AKM at the C terminus, which falls within the consensus of the PTS1 peroxisomal targeting signal. Southern blot analysis confirmed the presence of a single copy gene. Northern and western blot analyses showed that the catalase gene is transcribed and translated. Immunofluorescence assays using an antibody raised against a catalase peptide identified a distinct structure towards the apical end, but other catalase-specific antibodies failed to confirm this localisation. Cell fractionations indicated that the majority of the enzyme was in the cytosol. The fusion of the C-terminal twelve amino acids, including AKM, or the canonical peroxisomal targeting signal, -SKL, to GFP resulted in predominantly cytosolic localization in T. gondii. There was therefore no evidence for membrane-bound peroxisomes in Toxoplasma.

Amino Acids↗

PubMed2004

Assessment of monitor conditions for the display of radiological diagnostic images and ambient lighting.

Diagnostic efficacy is related to viewing conditions. An increasing number of radiology departments are using workstations for reporting and it was the aim of this study to assess monitor performance and ambient lighting in areas allocated to soft-copy reporting and review. The study was performed in 4 Dublin hospitals and 20 monitors were examined. Using a Society of Motion Pictures and Television Engineers' (SMPTE) test pattern, maximum luminance, spatial uniformity of luminance, temporal luminance stability, brightness and contrast resolution (gamma), geometry and ambient lighting was assessed. The results demonstrated that although temporal luminance stability and spatial uniformity appeared to be at acceptable levels, maximum luminance and gamma value variations were noted, with maximum luminance and geometry values often not complying with published guidelines. Cleaning the monitor face had no impact. 90% of viewing areas had acceptable ambient lighting levels. The data presented demonstrate that monitors examined were not operating at optimal levels for all performance parameters and inclusion of regular assessments of monitors should be part of an imaging department's ongoing quality assurance programme.

Computer Terminals↗

PubMedDate not supplied

Antigenic variation in Trypanosoma equiperdum.

Trypanosoma equiperdum is an African trypanosome that causes dourine in horses. Like the other African trypanosomes, T. equiperdum escapes elimination by the immune system of its host by using an elaborate system of antigenic variant. The trypanosomes are covered by a coat consisting of a single protein called the variable surface glycoprotein (VSG) that acts as the major trypanosome immunogen. As the host responds to one VSG, trypanosomes covered with another VSG become dominant. There is a loose order of appearance of these VSG during the infection. The factors that affect the timing of VSG expression and the effective size of the VSG repertoire in T. equiperdum are reviewed. The VSG genes are generally activated by a process of duplicative transposition involving the duplication of a silent VSG gene and inserting a copy of the gene into an expression site. The order of VSG expression is related to the amount of homology between the silent gene and the expression site. The genes expressed late in infection lack extensive homology with the expression site and depend on homology with the gene in the expression site. The genes coding for VSG expressed late in infection are hybrid genes because of this mode of transfer. This transfer mechanism allows the trypanosome to create complex VSG genes from parts of several different silent genes that are each pseudogenes. Additionally, data are presented showing that only a limited portion of the VSG is actually seen by the host immune system. These factors indicate that the effective VSG repertoire is greater than the number of VSG genes in the trypanosome genome.

Animals↗

PubMed2004

PTCH polymorphism is associated with the rate of increase in basal cell carcinoma numbers during follow-up: preliminary data on the influence of an exon 12-exon 23 haplotype.

After first presentation with a basal cell carcinoma (BCC), patients demonstrate interindividual diversity in the rate of development of further BCCs (number/year of follow-up). The mechanism for this variation is unknown. In this study, we evaluated whether PTCH variants mediate this phenomenon. We used negative binomial regression analysis to identify associations between BCC numbers/year and host characteristics, parameters of exposure to ultraviolet radiation (UVR), and PTCH exon 12(1686) C/T, intron 15(2560+9) G/C, and exon 23(3944) C/T genotypes and haplotypes in 279 BCC cases who presented with an initial tumor on the head/neck. PTCH genotypes were not significantly associated with BCCs/year, although cases with two copies of the C1686-C3944 haplotype developed significantly fewer BCCs/year than those without this haplotype (rate ratio = 0.44; 95% CI = 0.27-0.71). Cases with one copy of T1686-T3944 developed more BCCs/year (rate ratio = 2.46; 95% CI = 1.27-3.97) than those without the haplotype. We found no significant associations between BCCs/year and the other PTCH haplotypes studied. We reexamined the association of C1686-C3944 with BCCs/year in a model that included UVR exposure parameters (sunburning in childhood, sunbathing score, intermittency of exposure between 40 and 60 years of age, exposure in hours/year) and skin type, gender, and age at first presentation. The association between C1686-C3944 and BCCs/year remained significant (rate ratio = 0.44; 95% CI = 0.26-0.73 for two copies of the haplotype). The data show that allelic variation in PTCH contributes to the rate of development of BCC.

Adult↗

PubMed2005

Genome-wide prediction of human VNTRs.

Polymorphic minisatellites, also known as variable number of tandem repeats (VNTRs), are tandem repeat regions that show variation in the number of repeat units among chromosomes in a population. Currently, there are no general methods for predicting which minisatellites have a high probability of being polymorphic, given their sequence characteristics. An earlier approach has focused on potentially highly polymorphic and hypervariable minisatellites, which make up only a small fraction of all minisatellites in the human genome. We have developed a model, based on available minisatellite and VNTR sequence data, that predicts the probability that a minisatellite (unit size > or = 6 bp) identified by the computer program Tandem Repeats Finder is polymorphic (VNTR). According to the model, minisatellites with high copy number and high degree of sequence similarity are most likely to be VNTRs. This approach was used to scan the draft sequence of the human genome for VNTRs. A total of 157,549 minisatellite repeats were found, of which 29,224 are predicted to be VNTRs. Contrary to previous results, VNTRs appear to be widespread and abundant throughout the human genome, with an estimated density of 9.1 VNTRs/Mb.

Genome, Human↗

PubMed2000

Stationary-phase variation due to transposition of novel insertion elements in Xanthomonas oryzae pv. oryzae.

Xanthomonas oryzae pv. oryzae causes bacterial leaf blight, a serious disease of rice. Spontaneous mutants which are deficient for virulence and extracellular polysaccharide (Eps) production accumulate in large numbers in stationary-phase cultures of this bacterium, a phenomenon which we have called stationary-phase variation. A clone (pSD1) carrying the Eps biosynthetic gene (gum) cluster of X. oryzae pv. oryzae restored Eps production and virulence to several spv (for stationary-phase variation) mutants. Data from localized recombination analysis, Southern hybridization, PCR amplification, and sequence analysis showed that the mutations are due to insertion of either one of two novel endogenous insertion sequence (IS) elements, namely, ISXo1 and ISXo2, into gumM, the last gene of the gum gene cluster. The results of Southern analysis indicate the presence of multiple copies of both IS elements in the genome of X. oryzae pv. oryzae. These results demonstrate the role of IS elements in stationary-phase variation in X. oryzae pv. oryzae.

Alleles↗

PubMed1990

A partial map of the barley genome incorporating restriction fragment length polymorphism, polymerase chain reaction, isozyme, and morphological marker loci.

Nine low copy number genomic DNA clones, a ribosomal sequence, and seven cDNA clones were found to identify polymorphisms in cultivated barley (Hordeum vulgare L.). An F2 population consisting of 100 plants was produced from a cross between a high-yielding two-rowed feed barley cultivar and a genetic marker stock homozygous for nine recessive and one dominant morphological marker genes. Through the use of these 10 well-distributed marker genes, five previously mapped isozyme loci, and two storage-protein loci, the approximate recombinational location for each of 17 restriction fragment length polymorphism loci was estimated. One clone, pMSU21, identified variation that appeared to be the result of a small insertion-deletion event that differentiated two-rowed and six-rowed genotypes. This difference was characterized, and one allele was sequenced. Oligonucleotide primers that flanked the insertion-deletion event were synthesized, and DNA samples from the F2 population were subjected to polymerase chain reaction sequence amplification. The variation identified by this technique was determined to be allelic to the variation identified using pMSU21 in Southern blot analysis. Maps of previously undescribed informative clones are included.

Base Sequence↗

PubMed2003

[Transposition as a way of existence: phage Mu].

Transposition is a special mode of DNA recombination that produces a transfer of a DNA segment (transposable element, TE) from one chromosome region to a nonhomologous genomic loci. Bacterial TEs have chosen two principal strategies of their movement within and among genomes: conservative transposition (resulting in a simple insertion) and/or replicative transposition (accompanied by complete DNA replication and producing a cointegrate). Variations of transposition strategies concern the number and nature of cuts that sever the transposon from the flanking donor DNA: one-strand break (phage Mu) or double-strand breaks (Tn7, IS10 and members of IS3 family) and the possibility of accompanying TE replication, which leads to different end-products of transposition. Phage Mu combines properties of a temperate phage and a transposable element. Among transposons, it is studied in most detail. As a transposable element phage Mu is remarkable because its life-cycle involves two transposition modes: non-replicative resulting in lysogeny and replicative leading to multiple copying of phage DNA during the lytic growth. There are several levels of transcription regulation (or choice of developmental pathway). The genetic transposition reaction mediated by phage Mu A transposase A in the transpososome complex involves elaborate protein-nucleic acid and protein-protein interactions.

Animals↗

PubMed2002

Molecular and evolutionary analysis of mussel histone genes (Mytilus spp.): possible evidence of an "orphon origin" for H1 histone genes.

Linker histones are a divergent group of histone proteins with an independent evolutionary history in which, besides somatic subtypes, tissue- and differentiation-specific subtypes are included. In the present work H1 histone coding and noncoding segments from five Mytilus mussel species (Mollusca: Bivalvia) widely distributed throughout the world have been determined and characterized. Analysis of promoter regions shows clear homologies among Mytilus H1 genes, sea urchin H1 genes, and vertebrate differentiation-specific H1 subtypes (H5 and H1(o)), all having an H4 box motif in common. The amino acid sequence of the H1 protein central conserved domain is also closely related to that previously defined for the vertebrate divergent subtypes. A phylogenetic tree reconstructed from different H1 genes from several species strengthens the hypothesis of an "orphon" origin for the Mytilus H1 genes, as well as for the H1(o)/H5 genes from vertebrates and the H1D gene from the sea urchin Strongylocentrotus purpuratus, is suggested. As additional data, the average copy number of the H1 genes in the species analyzed was estimated as being 100 to 110 copies per haploid genome, where FISH revealed telomeric chromosomal location for several H1 copies in M. galloprovincialis. The contribution of such proximity to heterochromatic regions over the amount of codon bias detected for H1 genes is discussed.

Amino Acid Sequence↗

PubMed2001

Haplotype-specific sequence encoding the protein kinase, interferon-inducible double-stranded RNA-dependent activator in the human leukocyte antigen class II region.

The protein kinase, interferon-inducible double-stranded (ds)RNA-dependent activator (PRKRA) is a dsRNA-binding protein which activates a protein kinase participating in the antiviral activity of interferon. Our previous studies indicated that the nucleotide sequence encoding PRKRA, which appeared to be an intronless gene, was present in PAC HS265J14 containing the human leukocyte antigen (HLA) DR subregion. In this study, we further investigated and characterized the PRKRA gene on the human genome by means of Southern blotting and polymerase chain reaction with homozygous typing cell lines for HLA genes. Results indicated that the presence of PRKRA in the DR subregion was dependent on the DR53 group. Consistently, fluorescence in situ hybridization profiles with PRKRA as a probe showed that the hybridization signal on Chromosome (Chr) 6p21.3 was seen only in the samples carrying the DR haplotypes that belonged to the DR53 group. Interestingly, another hybridization signal, which was mapped on Chr 2q31.2-q32.1, was always detected in the samples examined, i.e., even in the samples negative for the DR53 group. The outcome of a sequence-database homology search further indicated that the PRKRA gene with introns appeared to be present in a recently opened draft-sequence, RP11-65L3 (GenBank accession number AC009948), which is located between D2S335 and D2S2257. Together, the data presented here indicate that the PRKRA gene in the DR subregion is a processed pseudogene (PRKRApsi), which could have been generated only on the DR53 common ancestor's genome, and that the master copy of PRKRApsi is most probably present on Chr 2q31.2-q32.1.

Alleles↗

PubMed2005

The maize root transcriptome by serial analysis of gene expression.

Serial Analysis of Gene Expression was used to define number and relative abundance of transcripts in the root tip of well-watered maize seedlings (Zea mays cv FR697). In total, 161,320 tags represented a minimum of 14,850 genes, based on at least two tags detected per transcript. The root transcriptome has been sampled to an estimated copy number of approximately five transcripts per cell. An extrapolation from the data and testing of single-tag identifiers by reverse transcription-PCR indicated that the maize root transcriptome should amount to at least 22,000 expressed genes. Frequency ranged from low copy number (2-5, 68.8%) to highly abundant transcripts (100-->1,200; 1%). Quantitative reverse transcription-PCR for selected transcripts indicated high correlation with tag frequency. Computational analysis compared this set with known maize transcripts and other root transcriptome models. Among the 14,850 tags, 7,010 (47%) were found for which no maize cDNA or gene model existed. Comparing the maize root transcriptome with that in other plants indicated that highly expressed transcripts differed substantially; less than 5% of the most abundant transcripts were shared between maize and Arabidopsis (Arabidopsis thaliana). Transcript categories highlight functions of the maize root tip. Significant variation in abundance characterizes transcripts derived from isoforms of individual enzymes in biochemical pathways.

Base Sequence↗