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PubMed1987

Epstein-Barr virus genomes in lymphoid cells: activation in mitosis and chromosomal location.

Biotin-labeled Epstein-Barr virus (EBV)-specific DNA probes have been used to detect viral genomes by in situ hybridization. Immunocytochemically amplified signals produced by the hybridized probe allow visualization of viral DNA even in cells previously reported to contain only one or two EBV genomes. In EBV producer lymphoid cell lines, such as B95-8, P3HR-1, or Daudi, activation of latent EBV DNA could be observed in mitotic cells; in non-virus-producing cells of these same lines, EBV was found to be present in low copy numbers. Noninducible cell lines such as IB4, AW-Ramos, and Namalwa exhibited low but clearly positive hybridization. Unexpectedly, significant variations in the amounts of EBV DNA per cell were observed between individual cells of these lines. The EBV DNA in the cloned IB4 cell line was localized to chromosome 4 in metaphase cells, but in the noncloned converted line AW-Ramos, the location of integrated viral DNA was essentially random.

Cell Line↗

PubMed1999

A 189-bp repeat region within the human cytomegalovirus replication origin contains a sequence dispensable but irreplaceable with other sequences.

The human cytomegalovirus (HCMV) replication origin exhibits a strain-dependent difference in the number of copies of a 189-bp region: the AD169 and Towne strains contain one and three copies of the region, respectively. A nearly complete deletion of the 189-bp repeat region of the Towne strain does not eliminate the origin's ability to initiate DNA synthesis. Here we report that the replication ability of the HCMV replication origin in infected cells disappeared after replacements of an internal sequence (152 bp) of the 189-bp repeat region with lambda DNA of identical and different lengths as well as after introduction of multiple nucleotide substitutions within the 152-bp internal sequence of the 189-bp repeat. In contrast, a variation in the copy number of 189-bp region (either one or two copies) or an inversion of the 152-bp internal sequence of the 189-bp repeat maintained replication abilities similar to those of the wild-type origin of the Towne strain. These results indicate that the 189-bp repeat region within the HCMV replication origin is not just a dispensable spacer sequence but instead contains an irreplaceable sequence that may play a supporting role in HCMV DNA replication.

Amino Acid Substitution↗

PubMed1987

Intraspecific and interspecific variation in the sequence and abundance of highly repeated DNA among mosquitoes of the Aedes albopictus subgroup.

Interspecific variation in abundance of highly repeated DNA sequences has been examined in three species of the Aedes scutellaris and three species of the A. albopictus subgroup of the A. scutellaris group. Sequences from a population of A. albopictus were hybridised with whole genomic content from other species and strains. Copy number estimates were determined by dot-blot hybridisation. Variation in sequence abundance between strains of A. albopictus was as great as between it and the other six species. Two clusters were formed by principal components analysis, each of which contains populations of A. albopictus. Copy numbers of highly repeated sequences do not correlate with genome size. The results indicate extensive sequence divergence and rapid evolution. These findings are discussed in relation to the importance of concerted evolution and natural selection in the evolution of the species group.

Aedes↗

PubMed2005

Human defensin gene copy number polymorphisms: comprehensive analysis of independent variation in alpha- and beta-defensin regions at 8p22-p23.

To investigate defensin gene copy number polymorphisms, a quantitative real-time PCR assay was developed and used to study DNA from 27 unrelated individuals of diverse ethnic and racial backgrounds. The DEFB4 and DEFB103A genes varied in tandem, with copy numbers 2 to 8, with a mode of 6 per diploid genome (PDG). The combined copy numbers of the DEFA1 and DEFA3 genes ranged from 5 to 14, with a mode of 10 copies PDG. The copy numbers of the DEFA1/3 genes varied independently of those of the DEFB4 and DEFB103A genes. The amount of HNP-1 and HNP-3 peptides expressed in neutrophils was found to be proportional to the combined copy number of DEFA1 and DEFA3. The DEFA3 allele was absent in 7/27 subjects. The highly copy-number-variable DEFA1 and DEFA3 genes are flanked by other defensin genes present uniformly at 2 copies PDG. The remarkable variability in defensin gene copy numbers could contribute to differences in individual resistance to infections.

Alleles↗

PubMed1997

PCR analysis of human telomeric repeats present on HHV-6A viral strains.

Human herpesvirus 6 (HHV-6) presents a perfect tandem array of human telomeric repeats (TRS) at both identical direct repeats (DR). Several researchers have reported a different TRS copy number by sequence analysis of HHV-6 DR's cloned fragments so it has been hypothesized that number of TRS is unstable. By PCR we show that the TRS copy number of U1102 HHV-6 variant A strains is stable during viral cultivation in cell lines and each HHV-6 variant A strain, detected in pathologic specimens, is characterized by a specific TRS copy number.

Cell Line↗

PubMed1986

Short repeats cause heterogeneity at genomic terminus of bovine herpesvirus 1.

Analysis of the genomes of different bovine herpesvirus 1 strains revealed a UL terminal HindIII fragment differing in size (from 2.4 to 2.8 kilobases). This fragment polymorphism occurred in the DNA of a wild-type isolate, in highly passaged, apathogenic tissue culture derivatives, and in plaque-purified substrains. This heterogeneity was due to variations in the copy number of a 14-base-pair tandem repeat comprising the base sequence 5'-GCTCCTCCTCCCTC-3', which also exists, with some differences, in other short reiteration sequences of herpes simplex virus type 1, Epstein-Barr virus, and related human cellular DNA. Furthermore, the tandem repeat array was located in close proximity to the left end of the viral genome and may functionally be involved in viral replication.

Animals↗

PubMed2000

Mitochondrial genome variation and the origin of modern humans.

The analysis of mitochondrial DNA (mtDNA) has been a potent tool in our understanding of human evolution, owing to characteristics such as high copy number, apparent lack of recombination, high substitution rate and maternal mode of inheritance. However, almost all studies of human evolution based on mtDNA sequencing have been confined to the control region, which constitutes less than 7% of the mitochondrial genome. These studies are complicated by the extreme variation in substitution rate between sites, and the consequence of parallel mutations causing difficulties in the estimation of genetic distance and making phylogenetic inferences questionable. Most comprehensive studies of the human mitochondrial molecule have been carried out through restriction-fragment length polymorphism analysis, providing data that are ill suited to estimations of mutation rate and therefore the timing of evolutionary events. Here, to improve the information obtained from the mitochondrial molecule for studies of human evolution, we describe the global mtDNA diversity in humans based on analyses of the complete mtDNA sequence of 53 humans of diverse origins. Our mtDNA data, in comparison with those of a parallel study of the Xq13.3 region in the same individuals, provide a concurrent view on human evolution with respect to the age of modern humans.

Africa↗

PubMed1999

Microsatellite variation within the human RHCE gene.

BACKGROUND AND OBJECTIVES: This study provides a unique method for identifying individuals carrying the Rh haplotype cDe, and supports a model for the evolution of Rh haplotypes in which cDe is the progenitor. MATERIALS AND METHODS: DNA from 212 unrelated donors of known Rh serological phenotype was PCR amplified. The resulting products were analysed by denaturing polyacrylamide gel electrophoresis, denaturing gradient gel electrophoresis and DNA sequencing. RESULTS: Two adjacent microsatellite repeat elements of the form (AC)n (GCAC)n were found within the human Rh blood group genes. These display copy number variation which was non-randomly distributed with respect to Rh serological phenotype, and was restricted to alleles of RHCE expressing the c antigen. CONCLUSION: The predominantly Black African allele cDe displayed a unique set of microsatellite alleles, providing a method of identifying individuals carrying this haplotype.

Africa↗

PubMed1992

16S rrn gene copy number in Helicobacter pylori and its application to molecular typing.

The copy number of the genes encoding 16S ribosomal RNA was analysed for the genomes of geographically diverse strains of Helicobacter pylori, and restriction site variation within and around the genes was characterized. A DNA probe of 550 bp was amplified by the polymerase chain reaction from genomic DNA of the type strain NCTC 11637. This probe constituted a sequence internal to the 3' end of the 16S rrn gene. Homology profiles were compared for genomic Southern blots made with four restriction enzymes cutting within and outside the probe sequence. A copy number of two was established for all 12 strains analysed. This approach yielded significantly simpler data than does conventional 'ribotyping ' of H. pylori. It was equally discriminatory, however, and provided strain-specific 16S rrn gene 'signatures'. These represent both fundamental physical-genetic information and a novel approach to typing this gastric pathogen.

Bacterial Typing Techniques↗

PubMed2004

NUMTs in sequenced eukaryotic genomes.

Mitochondrial DNA sequences are frequently transferred to the nucleus giving rise to the so-called nuclear mitochondrial DNA (NUMT). Analysis of 13 eukaryotic species with sequenced mitochondrial and nuclear genomes reveals a large interspecific variation of NUMT number and size. Copy number ranges from none or few copies in Anopheles, Caenorhabditis, Plasmodium, Drosophila, and Fugu to more than 500 in human, rice, and Arabidopsis. The average size is between 62 (baker's yeast) and 647 bps (Neurospora), respectively. A correlation between the abundance of NUMTs and the size of the nuclear or the mitochondrial genomes, or of the nuclear gene density, is not evident. Other factors, such as the number and/or stability of mitochondria in the germline, or species-specific mechanisms controlling accumulation/loss of nuclear DNA, might be responsible for the interspecific diversity in NUMT accumulation.

Cell Nucleus↗

PubMed2025

MarkerMatch: A Proximity-Based Probe-Matching Algorithm for Joint Analysis of Copy-Number Variants from Different Genotyping Arrays.

MOTIVATION: Copy-number variants (CNVs) are a form of genetic structural variation with increasing importance in complex human disorders. Both DNA sequencing and microarray data can be used to call CNVs, which can be used in association tests, such as association between CNV number and disease status. Unlike genotypes, CNV detection in microarrays requires the use of observed intensity signals at each probe, which limits the imputability for analyses that span multiple array types. Thus far, a consensus set of probes (the intersection encompassing the probes that occur in common on all arrays) has been used to circumvent the problem of differing array-specific sensitivities. This has, however, led to excessive reduction in overall sensitivity of CNV calls as arrays can have an undesirably low overlap of probe sets. To overcome this limitation, we developed MarkerMatch, a proximity-based algorithm that matches probes across different genotyping microarrays to maximize the number of probes considered in the CNV calling algorithm, thereby increasing the resolution and sensitivity while preserving precision. RESULTS: By analyzing CNV calls from 4,906 individuals genotyped across three different arrays (Global Screening Array, Omni2.5 array, and Omni Express Exome array), we show that the MarkerMatch approach improves sensitivity by increasing the density of probes available for CNV calling while maintaining precision or improving it relative to the current practice (e.g., use of consensus probes only). We further demonstrate that MarkerMatch exceeds the output from current practice in terms of F1 score, Fowlkes-Mallows index, and Jaccard index. We also optimize MarkerMatch parameters, D MAX and Method, and find an optimal D MAX setting at 10kb, with no clear optimal candidate based on Method, indicating that parameters for this metric should be determined on a use case basis.

Journal Article↗

PubMed1995

Identification of a mariner element from the tsetse fly, Glossina palpalis palpalis.

In the present study, the polymerase chain reaction was used initially to demonstrate the presence of mariner sequences in seven species/subspecies of tsetse flies. DNA hybridization experiments show mariner sequences to be dispersed within the tsetse genome and that there are large variations in copy numbers among the various taxa. A genomic library was used to isolate and characterize a full-length mariner element from G. p. palpalis. The results indicate that this element is 1257 bp in length, flanked by two 32 bp inverted repeats differing at only one position, and belongs to the mellifera subfamily. The nucleotide sequence that is translated into a reading frame of 337 amino acids requires the introduction of two frame shifts and one stop codon to maximize sequence homology with a mariner element from Drosophila erecta. Based on this evidence, we conclude that the G. p. palpalis mariner element clearly represents a non-functional transposable element and that the protein product is not an active transposase.

Amino Acid Sequence↗

PubMed1987

Variable number of tandem repeat (VNTR) markers for human gene mapping.

A large collection of good genetic markers is needed to map the genes that cause human genetic diseases. Although nearly 400 polymorphic DNA markers for human chromosomes have been described, the majority have only two alleles and are thus uninformative for analysis of genetic linkage in many families. A few known marker systems, however, detect loci that respond to restriction enzyme cleavage by producing a fragment that can have many different lengths. This polymorphism is due to variation in the number of tandem repeats of a short DNA sequence. Because most individuals will be heterozygous at such loci, these markers will provide linkage information in almost all families. Ten oligomeric sequences derived from the tandem repeat regions of the myoglobin gene, the zeta-globin pseudogene, the insulin gene, and the X-gene region of hepatitis B virus, were used to develop a series of single-copy probes. These probes revealed new, highly polymorphic genetic loci whose allele sizes reflected variation in the number of tandem repeats.

Chromosome Mapping↗

PubMed1992

Cell phenotype (CD23)-dependent variation in EBV genome copy numbers within lymphoblastoid cell lines (LCL).

Three Epstein-Barr-virus-transformed lymphoblastoid cell lines (LCL) were analysed on the basis of their CD23 expression. Levels of EBV-DNA were compared in the positive and negative subpopulations. Two lines were further analysed with regard to EBNA, cytoplasmic immunoglobulin (cIg) and lytic (EA/VCA) protein expression. Both subpopulations had a similar MHC class-II transcription, but the CD23- subpopulation had a lower plating efficiency and a lower rate of DNA synthesis. In the B6, NAD50 and 0467.3 cell lines, CD23- cells contained 2 +/- 0.2 - 6.4 +/- 3.0 times less EBV DNA than the corresponding CD23+ population. EBNA was expressed in 81 +/- 4.2% - 93 +/- 3.8% of the CD23+ cells and in 0 - 46 +/- 8.0% of the CD23- cells. No CD23+ cells in B6 or NAD50 contained any EA/VCA, while 19 +/- 2.8% - 24 +/- 4.2% of the CD23- cells were positive for the lytic-cycle-associated antigens. Of the CD23- cells, 70 +/- 8.6% - 86 +/- 6.0% were positive for cytoplasmic immunoglobulin compared to 14.7 +/- 2.7% - 14.9 +/- 1.8% in the corresponding CD23+ population. We have previously shown that only 18% of the cIg-positive cells were EBNA-positive in the B6 line compared to 94% in the cIg- population. This was open to 2 alternative interpretations: loss of EBV genomes from a fraction of the cells with subsequent differentiation to secretory immunoglobulin production, or down-regulation of EBNA expression in differentiating, EBV-genome-positive cells. Our present findings speak for the first alternative, indicating that a certain proportion of the cells may lose their EBV genomes in both long-established and freshly transformed LCLs. This is accompanied by a reduced percentage of EBNA-positive cells, the disappearance of at least one activation marker (CD23) associated with the virally induced blast transformation, and an increased synthesis of cIg.

Antibody Formation↗

PubMed2025

SegMantX: A Novel Tool for Detecting DNA Duplications Uncovers Prevalent Duplications in Plasmids.

Segmental duplications play an important role in genome evolution via their contribution to copy-number variation, gene-family diversification, and the emergence of novel functions. The detection of segmental duplications is challenging due to heterogeneous amelioration of sequence similarity among duplicates, which hinders the reconstruction of continuous sequence alignment. Here we introduce SegMantX, a novel approach for the identification of diverged segmental duplications in prokaryote genomes using local alignment chaining. In this approach, local alignments resulting from a preliminary sequence similarity search (e.g. BLASTn) are chained into continuous segments. Evaluating the performance of SegMantX using simulated sequences shows that the tool can detect diverged duplications beyond the sensitivity limits of standard alignment-based methods. Applying SegMantX to 6,784 enterobacterial plasmids, we find that 65% plasmids contain duplicated regions and gene duplications, most of which correspond either to dispersed, noncoding regions or duplicated mobile genetic elements (MGEs; e.g. transposons and insertion sequences). Furthermore, we demonstrate the applicability of SegMantX for the identification of diverged gene transfers between replicons and plasmid hybridization events. Our findings highlight MGEs as drivers of segmental duplications in plasmid evolution, leading to the amplification of their cargo genes, including antibiotic resistance genes. SegMantX provides a powerful framework for reconstructing diverged segmental duplications and other alignment problems.

Plasmids↗

PubMed2026

"Tissue-specific mitochondrial dysfunction in keratoconus: An integrated structural, genomic, and functional analysis".

PURPOSE: Keratoconus (KC) is a progressive corneal ectasia characterized by stromal thinning, conical protrusion, and irregular astigmatism, leading to visual impairment. Although oxidative stress is implicated in KC, the role of mitochondrial dysfunction remains unclear. We evaluated mitochondrial structural, genomic, and functional abnormalities in corneal tissues and blood from KC patients. METHODS: This prospective study enrolled 110 KC patients and 55 controls. Transmission electron microscopy (TEM) and immunohistochemistry (IHC) were performed on epithelial and stromal tissues from 10 KC to 5 control corneas assessing mitochondrial morphology, oxidative phosphorylation (OXPHOS) complexes and pro-apoptotic protein NOXA. Whole mitochondrial DNA (mtDNA) sequencing and relative mtDNA copy number analysis were performed on paired blood and corneal tissues from 50 KC patients and 35 controls including both epithelial and stromal samples. Gene expression of mitochondrial biogenesis and oxidative stress-related genes was analysed by qRT-PCR in corneal epithelium from independent 50 KC patients and 15 controls. RESULTS: TEM revealed cristolysis, membrane disruption, and reduced mitochondrial density in KC corneas. IHC showed reduced expression of OXPHOS complexes and increased NOXA expression (p < 0.05). Sequencing identified 1107 mtDNA variants, with more variants in corneal tissues than matched blood (929 vs. 576; p = 0.0002). Recurrent likely pathogenic variants were enriched in complex I-encoding genes (ND4, ND5). KC corneas showed reduced mtDNA copy number, downregulated POLRMT, upregulated NOX4, and significant downregulation of multiple antioxidant genes (p < 0.0001). CONCLUSION: KC patients exhibit tissue-specific mitochondrial abnormalities and impaired oxidative stress regulation, supporting a role for mitochondrial dysfunction in disease pathogenesis and highlighting potential therapeutic targets.

Corneal pathology↗

PubMed2003

Longitudinal monitoring of 2-long terminal repeat circles in peripheral blood mononuclear cells from patients with chronic HIV-1 infection.

OBJECTIVE: To evaluate the potential use of 2-long terminal repeats (LTR) HIV circular DNA quantification for the monitoring of ongoing virus replication in treated HIV-1-infected patients. DESIGN AND METHODS: In a longitudinal setting, where the natural course of HIV-1 infection was in most cases disrupted by continuous or discontinuous antiviral therapy, 2-LTR circles of HIV-1 DNA were quantified in serial peripheral blood mononuclear cell samples, selected in retrospect from 16 patients with chronic HIV-1 infection, using quantitative real-time PCR. We compared variations of 2-LTR circle level with concomitant variations in plasma viral RNA level and with the frequency of productively infected cells and chromosome associated proviral DNA copy numbers in patient's peripheral blood mononuclear cells. RESULTS: Antiviral treatment led to a sharp decrease in plasma viraemia and infectious cell frequency. In contrast, we found that levels of proviral DNA and 2-LTR circles were significantly lower under treatment only when groups of specimens that were homogeneous, with respect both to plasma viraemia and infectious cell frequency, were compared. Moreover, during the time of undetectable plasma viraemia, scarcely any decline in proviral DNA or 2-LTR circle levels was observed. CONCLUSIONS: The low impact of antiviral treatment on 2-LTR circle levels in vivo, when plasma viraemia and infectious cell frequency both dramatically decline lead us to conclude that 2-LTR circles should not be used for the monitoring of recent viral replication in treated patients.

Anti-HIV Agents↗

PubMed1995

Quantitation of Chlamydia trachomatis by culture, direct immunofluorescence and competitive polymerase chain reaction.

OBJECTIVES: Methods to quantitate Chlamydia trachomatis have never been compared although it would be relevant to periodically evaluate the sensitivity of a detection system. We compared the sensitivity and reproducibility of culture, direct immunofluorescence and the polymerase chain reaction (PCR) to quantitate C trachomatis. METHODS: A competitive semiquantitative PCR procedure was developed. The number of inclusions in culture, particles by direct immunofluorescence and DNA copies by PCR were measured for 12 patient specimens. Variation was determined by measuring a sample 10 times for each method. RESULTS: Patient C trachomatis major outer membrane protein gene DNA was measured semiquantitatively by amplifying together with reference DNA. DNA molecules, particles and infectious units were quantitated in clinical samples with, on average, 595 DNA molecules and 87 immunofluorescent particles observed per inclusion-forming-unit. Similar coefficients of variation (47-52%) were observed for the 3 procedures. CONCLUSION: Competitive PCR and counting immunofluorescent particles provide reproducible and sensitive methods of quantitating C trachomatis.

Bacterial Outer Membrane Proteins↗