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PubMed1996

Rapid retrovirus titration using competitive polymerase chain reaction.

A quantitative polymerase chain reaction (PCR) procedure has been developed for rapid retrovirus titration. This procedure, which is based on the simultaneous amplification of the sample with known amounts of a competitor DNA fragment (competitive PCR), was used for the quantification of viral RNA genomes in retrovirus-producing cell clone supernatants and of proviral DNA molecules formed at 24 h after infection of different reference cell lines. The results obtained from the analysis of several samples indicated that proviral DNA quantification is in complete agreement with the number of selectable colonies in a standard colony assay. Conversely, the number of viral RNA genomes in the producer cell clone supernatants is a poor predictor of the actual efficiency of infection. Repeated competitive PCR experiments for provirus copy number determination at different times after transduction indicated that the number of proviral DNA molecules remains stable over time, suggesting stable integration into the host genome. The developed procedure is rapid and simple, is applicable to retroviral constructs not containing a selectable gene and can be used to directly measure the efficiency of infection of any target cell type, thus overcoming the problem of the dependency of retroviral titer determination on the rate of expression of a selectable gene and on the efficiency of colony formation of a reference cell line.

3T3 Cells↗
PubMed2004

Tropheryma whipplei Infection of an acellular porcine heart valve bioprosthesis in a patient who did not have intestinal Whipple's disease.

Rare cases of culture-negative infective endocarditis are caused by Tropheryma whipplei, the uncommon bacterium of Whipple's disease. We evaluated an 80-year-old woman with valvular heart disease but without intestinal Whipple's disease. The diagnosis of aortic valve xenograft culture-negative infection with T. whipplei was established by multiple molecular assays and by electron microscopy. First, a PCR with broad-range primers identified the complete 16S ribosomal DNA of T. whipplei in bioprosthesis tissue. Novel real-time reverse transcription-PCR assays were developed to detect mRNAs encoding recently identified proteins determined from the T. whipplei genome, specifically Whipplei surface protein (TW113) and a DNA polymerase III subunit (TW727). The positive detection of mRNAs indicated the presence of metabolically active bacteria and suggested the viability of T. whipplei. The quantification of T. whipplei genome equivalents by real-time PCR indicated a high-density bacterial colonization of the valve tissue. Additionally, an ultrastructural examination revealed numerous rod-shaped bacteria consistent in size with T. whipplei in the extracellular collagen matrix of the bioprosthesis. We conclude that extracellular growth of T. whipplei can occur in the microenvironment of biological prosthetic valve tissue and that T. whipplei endocarditis can occur in the absence of intestinal Whipple's disease.

Actinomycetales↗
PubMed2006

Quantification of size distribution of restriction fragments in mitochondrial genome using fluorescence correlation spectroscopy.

A crucial investigation is to quantify restriction fragment length polymorphisms without gel electrophoresis, as the distribution of fragment size is mainly evaluated on the gel, which cannot be easily quantified. We developed a method to determine the fragmentation of the mitochondrial genome caused by restriction enzymes using fluorescence correlation spectroscopy (FCS). Distribution of fragment size was evaluated by the decrease in amplitude of the fluorescence correlation function while the mitochondrial genome PCR product was digested with Hga I or Hae III. Using a multicomponent model, which was considered as a fragment length-weighted correlation function, we calculated the correlation amplitude theoretically expected and compared it to that measured by FCS. These amplitudes for Hga I were coincident, whereas the measured amplitude for Hae III was more than the theoretical one. Because of tetra-nucleotide recognition by Hae III, there were many more fragments than with Hga I. Therefore, the amplitude measured by FCS would be a very useful index for primary screening for alterations in the entire mitochondrial genome with restriction enzymes that have several polymorphic restriction sites in the genome.

Cell Line↗
PubMed2001

Multiple groups of novel retroviral genomes in pigs and related species.

In view of the concern over potential infection hazards in the use of porcine tissues and organs for xenotransplantation to humans, we investigated the diversity of porcine endogenous retrovirus (PERV) genomes in the DNA of domestic pigs and related species. In addition to the three known envelope subgroups of infectious gamma retroviruses (PERV-A, -B, and -C), classed together here as PERV group gamma 1, four novel groups of gamma retrovirus (gamma 2 to gamma 5) and four novel groups of beta retrovirus (beta 1 to beta 4) genomes were detected in pig DNA using generic and specific PCR primers. PCR quantification indicated that the retroviral genome copy number in the Landrace x Duroc F(1) hybrid pig ranged from 2 (beta 2 and gamma 5) to approximately 50 (gamma 1). The gamma 1, gamma 2, and beta 4 genomes were transcribed into RNA in adult kidney tissue. Apart from gamma 1, the retroviral genomes are not known to be infectious, and sequencing of a small number of amplified genome fragments revealed stop codons in putative open reading frames in several cases. Analysis of DNA from wild boar and other species of Old World pigs (Suidae) and New World peccaries (Tayassuidae) showed that one retrovirus group, beta 2, was common to all species tested, while the others were present among all Old World species but absent from New World species. The PERV-C subgroup of gamma1 genomes segregated among domestic pigs and were absent from two African species (red river hog and warthog). Thus domestic swine and their phylogenetic relatives harbor multiple groups of hitherto undescribed PERV genomes.

Animals↗
PubMed2006

Quantification of the retrotransposon BARE-1 reveals the dynamic nature of the barley genome.

We used quantitative real-time PCR analysis to measure the copy number of the BARE-1 retrotransposon in 5 cultivars of barley (Hordeum vulgare), as well as in samples from its wild relative, Hordeum spontaneum. Two sets of PCR primers were used to amplify regions within the long terminal repeat (LTR) and the reverse transcriptase (RT) gene of BARE-1 (GenBank accession Z17327). The LTR primers detected an average of 2.148 x 105 +/- 0.012 x 105 copies per haploid genome among barley samples, whereas the RT primers detected an average of 1.588 x 104 +/- 0.085 x 104 copies. The average ratio of LTR:RT was estimated to be 13.5:1. This finding indicates that more than 7% of the barley genome is occupied by BARE-1 elements in the form of solo LTRs and another 2.6% of the genome is occupied by the full-length element. Taken together, BARE-1 sequences represent approximately 9.6% of the barley genome among the barley plants used in this study. For the above estimation, a genome size of 5.44 x 103 Mb for H. vulgare and 5.39 x 103 Mb for H. spontaneum were assumed. Our study on quantification results of the BARE-1 for a small group of barley cultivars showed that there are significant differences among cultivars in terms of BARE-1 copy number, providing further evidence that BARE-1 is active and has a major role in shaping the barley genome as a result of breeding and selection. Quantification results also showed that most of the elements (> 90%) are present as truncated copies (solo LTRs). These results show that there is a high level of recombination leading to the formation of truncated elements and a subsequent DNA loss from the genome. Taken together, our study provides a glimpse into a dynamic micro-evolutionary process that is the by-product of genome reshuffling and directional selection in barley breeding programs.

Breeding↗
PubMed2006

Policy implications of genetic information on regulation under the Clean Air Act: the case of particulate matter and asthmatics.

The U.S. Clean Air Act (CAA) explicitly guarantees the protection of sensitive human subpopulations from adverse health effects associated with air pollution exposure. Identified subpopulations, such as asthmatics, may carry multiple genetic susceptibilities to disease onset and progression and thus qualify for special protection under the CAA. Scientific advances accelerated as a result of the groundbreaking Human Genome Project enable the quantification of genetic information that underlies such human variability in susceptibility and the cellular mechanisms of disease. In epidemiology and regulatory toxicology, genetic information can more clearly elucidate human susceptibility essential to risk assessment, such as in support of air quality regulation. In an effort to encourage the incorporation of genomic information in regulation, the U.S. Environmental Protection Agency (EPA) has issued an Interim Policy on Genomics. Additional research strategy and policy documents from the National Academy of Science, the U.S. EPA, and the U.S. Department of Health and Human Services further promote the expansion of asthma genetics research for human health risk assessment. Through a review of these government documents, we find opportunities for the inclusion of genetic information in the regulation of air pollutants. In addition, we identify sources of information in recent scientific research on asthma genetics relevant to regulatory standard setting. We conclude with recommendations on how to integrate these approaches for the improvement of regulatory health science and the prerequisites for inclusion of genetic information in decision making.

Air Pollutants↗
PubMed2005

Real-time quantification of microRNAs by stem-loop RT-PCR.

A novel microRNA (miRNA) quantification method has been developed using stem-loop RT followed by TaqMan PCR analysis. Stem-loop RT primers are better than conventional ones in terms of RT efficiency and specificity. TaqMan miRNA assays are specific for mature miRNAs and discriminate among related miRNAs that differ by as little as one nucleotide. Furthermore, they are not affected by genomic DNA contamination. Precise quantification is achieved routinely with as little as 25 pg of total RNA for most miRNAs. In fact, the high sensitivity, specificity and precision of this method allows for direct analysis of a single cell without nucleic acid purification. Like standard TaqMan gene expression assays, TaqMan miRNA assays exhibit a dynamic range of seven orders of magnitude. Quantification of five miRNAs in seven mouse tissues showed variation from less than 10 to more than 30,000 copies per cell. This method enables fast, accurate and sensitive miRNA expression profiling and can identify and monitor potential biomarkers specific to tissues or diseases. Stem-loop RT-PCR can be used for the quantification of other small RNA molecules such as short interfering RNAs (siRNAs). Furthermore, the concept of stem-loop RT primer design could be applied in small RNA cloning and multiplex assays for better specificity and efficiency.

Animals↗
PubMed2003

Frequent infection with a viral pathogen, parvovirus B19, in rheumatic diseases of childhood.

OBJECTIVE: To find further evidence of the association of parvovirus B19 infection with juvenile rheumatic diseases, and to get new insights into the immunopathogenesis of these diseases. METHODS: Paired serum and synovial fluid samples from 74 children with rheumatic disease were analyzed with respect to their content of viral DNA and antibodies directed against the B19 viral proteins VP1, VP2, and NS1. Control sera from 124 children with noninflammatory bone diseases or growth retardation were also analyzed. The sequence of the viral DNA, amplified by polymerase chain reaction (PCR), was determined. IgG-complexed virus was isolated from sera and synovial fluid by adsorption to protein A beads. The amount of free virus versus immunocomplexed virus particles was determined by quantification of the viral genomes by quantitative PCR. RESULTS: Twenty-six of the 74 patients (35%) had detectable amounts of parvovirus B19 DNA in the serum (n = 22 [30%]) and/or the synovial fluid (n = 16 [22%]), whereas only 9 of the 124 control sera (7%) were positive for the viral DNA (P < 0.0001). Forty-six patients (62%) had serum IgG against the structural proteins, indicating past infection with B19. NS1-specific antibodies were detected in sera from 29 patients (39%) and 27 controls (22%) (P < 0.001). In addition, 3 patients (4%) showed VP2-specific IgM. In 15 patients, viral DNA could be repeatedly detected in followup samples of serum and synovial fluid. Sequencing revealed low-degree nucleotide variations that are in the range of genotype 1 of parvovirus B19. Immunocomplexed virus was present in varying amounts, both in the sera and in the synovial fluid samples. CONCLUSION: Parvovirus B19 is frequently found in serum or synovial fluid of children with rheumatism. The rate of persistent B19 infection in these patients is significantly higher than in age-matched controls.

Adolescent↗
PubMed2004

Rapid detection of subtelomeric deletion/duplication by novel real-time quantitative PCR using SYBR-green dye.

Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, miscarriages, and hematological malignancies. Automated detection of subtle deletions and duplications involving telomeres is essential for high-throughput screening procedures, but impractical when conventional cytogenetic methods are used. Novel real-time PCR quantitative genotyping of subtelomeric amplicons using SYBR-green dye allows high-resolution screening of single copy number gains and losses by their relative quantification against a diploid genome. To assess the applicability of the technique in the screening and diagnosis of subtelomeric imbalances, we describe here a blinded study in which DNA from 20 negative controls and 20 patients with known unbalanced cytogenetic abnormalities involving at least one or more telomeres were analyzed using a novel human subtelomere-specific primer set, producing altogether 86 amplicons, in the SYBR-green I-based real-time quantitative PCR screening approach. Screening of the DNA samples from 20 unrelated controls for copy number polymorphism do not detect any polymorphism in the set of amplicons, but single-copy-number gains and losses were accurately detected by quantitative PCR in all patients, except the copy number alterations of the subtelomeric p-arms of the acrocentric chromosomes in two cases. Furthermore, a detailed mapping of the deletion/translocation breakpoint was demonstrated in two cases by novel real-time PCR "primer-jumping." Because of the simplicity and flexibility of the SYBR-green I-based real-time detection, the primer-set can easily be extended, either to perform further detailed molecular characterization of breakpoints or to include amplicons for the detection and/or analysis of syndromes that are associated with genomic copy number alterations, e.g., deletion/duplication-syndromes and malignant cancers.

Benzothiazoles↗
PubMed2025

Clinical and Epidemiological Insights into a Parainfluenza Virus Type 3 Outbreak in Multiple Myeloma Patients.

Human parainfluenza virus type 3 (HPIV-3) can be responsible for mild to severe respiratory infections and hospital epidemics. We investigated an outbreak in a hematology unit. Respiratory viruses were screened using multiplex PCR. HPIV-3 quantification and whole-genome sequencing were performed on HPIV-3 positive respiratory samples. Clinical characteristics, infection progression, incidence rates of respiratory viruses within the hospital and detection of respiratory viruses were documented, along with the reinforcement of infection prevention and control (IPC) measures implemented. Between November 2022, and January 2023, HPIV-3 was identified in 20 of 113 hematology patients (17.7%), of whom 80% had multiple myeloma. A majority of HPIV-3-positive patients developed pneumonia (60%), and mortality was notably higher (35%) compared to patients who were negative (3%, p&#x2009;<&#x2009;0.0001). Respiratory HPIV-3 viral loads were similar between patients with and without pneumonia. In parallel, HPIV-3 incidence in the hospital overall was lower than in the hematology unit (p&#x2009;<&#x2009;0.0001). Air virus screening showed the detection of HPIV-3 in the air in different areas, and whole-genome sequencing confirmed the circulation of a single HPIV-3 strain. Strengthened IPC measures were associated with the containment of the outbreak. HPIV-3 has high epidemic potential in patients with multiple myeloma and causes severe infections. Our findings highlight the need for routine HPIV-3 testing in hematology units.

Humans↗
PubMed2005

High expression of foot-and-mouth disease virus structural protein VP1 in tobacco chloroplasts.

A tobacco chloroplast expression vector, pTRVP1, containing the foot-and-mouth disease virus (FMDV) VP1 gene and the selective marker aadA gene, was constructed and transferred to tobacco by biolistic method. Three resistant lines were obtained through spectinomycin selection, and each transgenic line was subjected to a second round of spectinomycin selection. PCR and PCR southern blot analysis revealed that the VP1 gene had integrated into the chloroplast genome. Western blot and quantification ELISA assays indicated that the VP1 gene was expressed in tobacco chloroplasts and accounted for 2-3% of total soluble protein. This suggested that plant chloroplasts were an efficient expression system for the potential production of recombinant antigens in plants.

Capsid Proteins↗
PubMed2004

High risk HPV load estimated by Hybrid Capture II correlates with HPV16 load measured by real-time PCR in cervical smears of HPV16-infected women.

BACKGROUND: High risk human papillomavirus (HR-HPV) load determined by quantitative methods has already been considered as highly predictive of future development of high grade cervical lesions. Some studies also demonstrated that Hybrid Capture II (HCII) results can be considered as a reflection of HPV DNA load, while others did not. HCI assay, well suited for routine HR-HPV screening, is not especially dedicated for quantitative use. However, we have recently shown that women with high viral loads assessed by HCII were at increased risk of cervical precancer. OBJECTIVES: The aim of the study was to determine if the values given by the HCII assay can be considered as quantitative. STUDY DESIGN: We used a real-time PCR allowing precise quantification of both HPV16 genome and albumin gene to normalize the measuring HPV16 load in cervical cells and to compare the data with those obtained by HCIIin a series of 40 HR-HPV positive samples. RESULTS: Reproducibility of the HPV16 real-time PCR, assessed from nine independent experiments of serial dilutions of SiHa cell DNA, was reflected in coefficients of variation for standard curves of crossing point (Cp) values below 5%. The HPV16 loads with a broad individual variability were significantly related to the cumulative load estimated by HCII and did not depend on the cellularity of samples. CONCLUSIONS: We assume that the HCII values can be used as a quantitative measure of HR-HPV DNA, so long as cervical specimens are collected using standardized protocols.

Base Sequence↗
PubMed2002

The value of microarray techniques for quantitative gene profiling in molecular diagnostics.

There has been an explosion of interest in microarray technologies that allow the quantification of whole-genome RNA expression data. The apparent correlation of expression profiles with clinically relevant parameters such as disease outcome has raised expectations with respect to the clinical usefulness of the data generated. Yet the accuracy and biological relevance of these data remain contentious, even in basic research applications. Therefore, numerous issues related to format, quality, validation and interpretation remain to be resolved before microarray profiling can become a diagnostic tool of clinical relevance for routine work.

Gene Expression Profiling↗
PubMed2004

Development and comparison of four real-time polymerase chain reaction systems for specific detection and quantification of Zea mays L.

Four real-time polymerase chain reaction systems aiming at the specific detection and quantification of maize DNA are described. They have been developed in four independent laboratories targeting different maize sequences, i.e., alcohol dehydrogenase (Adh1), high mobility group protein (hmga), invertase A (ivr1), and zein, respectively. They were all fully specific, showing a very similar quantification accuracy along a number of distantly related maize cultivars and being either single or low copy number genes. They were highly sensitive and exhibited limits of quantification below 100 maize genomic copies. In consequence, they are considered suitable for use as maize specific endogenous reference genes in DNA analyses, including GMO quantitative tests.

Alcohol Dehydrogenase↗
PubMed2001

Molecular and quantitative characterisation of the porcine embryonic myosin heavy chain gene.

The porcine embryonic myosin heavy chain (MyHC) is a major isoform in foetal skeletal muscle, and is the last remaining major porcine skeletal MyHC gene to be isolated and characterised. We report here on its cDNA and genomic isolation, molecular characterisation, quantification and expression. Unlike all other porcine and mammalian skeletal MyHC genes reported to date, the deduced translated start site of the porcine embryonic gene was located in exon 2, instead of exon 3. Its promoter conferred differentiation-specific expression. We found, by quantitative real-time RT-PCR, that for much of gestation the embryonic MyHC was by far the most transcriptionally active gene compared with the slow/I and perinatal MyHC isoforms, and it was consistently more highly expressed than the perinatal isoform throughout gestation. The embryonic MyHC isoform was, however, rapidly down-regulated at around birth. By contrast, 22 weeks after birth, the porcine perinatal isoform remained detectable by PCR. Additionally, we discovered the presence of differential splicing at the 3'-end of the embryonic MyHC gene that resulted in an in-frame deletion, with the consequential loss of 93 amino acids close to the ACD domain, a region that is important for the assembly of myosin filaments. The detection of this truncated variant points to a possible major post-transcriptional mechanism of embryonic MyHC regulation that may be linked to myosin filament formation or turnover.

Alternative Splicing↗
PubMed2002

The -2 bp deletion in exon 6 of the 'alpha 7-like' nicotinic receptor subunit gene is a risk factor for the P50 sensory gating deficit.

Abnormality in the P50 auditory-evoked potential gating is an endophenotype associated with schizophrenia. Biochemical and genetic studies have suggested that the alpha 7 nicotinic acetylcholine receptor (nAChR) is involved in this sensory gating deficit. Two related alpha 7 genes (CHRNA7 and CHRNA7-like gene) resulting from a partial duplication (from exon 5 to exon 10) are present in the human genome. Two types of genetic variation, a large deletion and a -2 base-pair deletion in exon 6 resulting in a truncation of the open reading frame, affect specifically the CHRNA7-like gene. We developed a simple multiplex PCR assay on genomic DNA, allowing the quantification of the number of exons 6 and the distinction of all possible exon 6 genotypes. Genotyping of 70 schizophrenic patients and 77 controls showed that carrying at least one -2 bp deletion of exon 6 did not constitute a risk factor for schizophrenia. In contrast, the distribution of genotypes differed significantly between subjects with normal and abnormal P50 ratios, with an over-representation of genotypes carrying at least one -2 bp deletion of exon 6 among subjects exhibiting an abnormal P50 ratio. We thus conclude that the -2 bp deletion within the CHRNA7-like gene is a risk factor for P50 sensory gating deficit. Interestingly, most of the effect came from the non schizophrenic group, which may suggest that in schizophrenic patients other risk factors account for the large proportion of subjects exhibiting an abnormal P50 ratio.

Adult↗
PubMed2006

Quantification of high-capacity helper-dependent adenoviral vector genomes in vitro and in vivo, using quantitative TaqMan real-time polymerase chain reaction.

First-generation adenoviral (Ad) and high-capacity adenoviral (HC-Ad) vectors are efficient delivery vehicles for transferring therapeutic transgenes in vivo into tissues/organs. The initial successes reported with adenoviral vectors in preclinical trials have been limited by immune-related adverse side effects. This has been, in part, attributed to the use of poorly characterized preparations of adenoviral vectors and also to the untoward immune adverse side effects elicited when high doses of these vectors were used. HC-Ads have several advantages over Ads, including the lack of viral coding sequences, which after infection and uncoating, makes them invisible to the host's immune system. Another advantage is their large cloning capacity (up to approximately 35 kb). However, accurate characterization of HC-Ad vectors, and of contaminating replication-competent adenovirus (RCA) or helper virus, is necessary before these preparations can be used safely in clinical trials. Consequently, the development of accurate, simple, and reproducible methods to standardize and validate adenoviral preparations for the presence of contaminant genomes is required. By using a molecular method that allows accurate, reproducible, and simultaneous determination of HC-Ad, contaminating helper virus, and RCA genome copy numbers based on real-time quantitative PCR, we demonstrate accurate detection of these three genomic entities, within CsCl-purified vector stocks, total DNA isolated from cells transduced in vitro, and from brain tissue infected in vivo. This approach will allow accurate assessment of the levels and biodistribution of HC-Ad and improve the safety and efficacy of clinical trials.

Adenoviridae↗
PubMed2026

Genome-wide survey of spliceosomal snRNA transcripts across hundreds of human biosamples reveals abundant transcription but low maturation level of snRNA variants.

Small nuclear RNAs (snRNAs) are essential components of the spliceosome and are encoded by large, multicopy gene families. However, their genome-wide identification and quantification have remained challenging due to high sequence similarity among family members. To address this, we utilized RAMPAGE (Rapid Amplification of cDNA Ends) data from the ENCODE project to comprehensively profile nascent transcription of spliceosomal snRNAs across 115 human biosamples. We identified 74 expressed snRNA variants, characterized by canonical promoter features including bidirectional transcription flanking a positioned nucleosome, active histone modifications, and evolutionary conservation- features largely absent from unexpressed variants. These transcriptional events were corroborated by total RNA-seq and Bru-seq data, yet the majority of these variants showed extremely low levels in small RNA-seq, indicating post-transcriptional bottlenecks for snRNA processing and maturation. Our findings reveal new layers of regulation in snRNA variant expression and suggest that selective post-transcriptional processing plays a critical role in shaping the functional snRNA repertoire and its contribution to splicing regulation.

Journal Article↗