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Results for “Absolute quantification”

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PubMed2006

Real-time polymerase chain reaction and melting curve analysis.

Monitoring polymerase chain reaction (PCR) once each cycle is a powerful method to detect and quantify the presence of nucleic acid sequences and has become known as "real-time" PCR. Absolute quantification of initial template copy number can be obtained, although quantification relative to a control sample or second sequence is often adequate. Melting analysis following PCR monitors duplex hybridization as the temperature is changed and is a simple method for sequence verification and genotyping. Melting analysis is often conveniently performed immediately after PCR in the same reaction tube. The fluorescence of either DNA dyes that are specific to double-strands or fluorescently labeled oligonucleotide probes can be monitored for both real-time quantification and melting analysis. When used together with rapid temperature control, these methods allow amplification and genotyping in less than a half hour.

DNA↗

PubMed1997

Transcranial cerebral oximetry in the hyperbaric environment.

Continuous monitoring of dynamic changes of transcranial regional cerebral oxygenation (rSO2) was performed in 7 healthy volunteers (mean age 40.9 +/- 12.6 years; range 25-62 years) during normo- and hyperbaric oxygenation (HBO at 2.5 and at 1.95 ATA) using an INVOS 3100 cerebral oximeter. A significant change between HBO and control phase could be found in rSO2, alterations (p < 0.05; ANOVA, Tukey test). The results suggest that the calculation of rSO2 may be a useful method to monitor changes of oxygen saturation under hyperbaric conditions. However, the absolute quantification of rSO2 is useless at the moment and needs further investigation.

Adult↗

PubMed2023

Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.

Translation efficiency has been mainly studied by ribosome profiling, which only provides an incomplete picture of translation kinetics. Here, we integrated the absolute quantifications of tRNAs, mRNAs, RNA half-lives, proteins, and protein half-lives with ribosome densities and derived the initiation and elongation rates for 475 genes (67% of all genes), 73 with high precision, in the bacterium Mycoplasma pneumoniae (Mpn). We found that, although the initiation rate varied over 160-fold among genes, most of the known factors had little impact on translation efficiency. Local codon elongation rates could not be fully explained by the adaptation to tRNA abundances, which varied over 100-fold among tRNA isoacceptors. We provide a comprehensive quantitative view of translation efficiency, which suggests the existence of unidentified mechanisms of translational regulation in Mpn.

RNA, Transfer↗

PubMed2006

Proteomic analyses to identify novel therapeutic targets for the treatment of advanced prostate cancer.

At present there is no cure for advanced prostate cancer once it progresses to an androgen independent stage. Hormonal therapy, radiotherapy, and chemotherapy all have limited durations of efficacy for men diagnosed with androgen independent disease and patients will succumb over a period of several months to two years. The androgen receptor (AR) has been suspected to play an important role in the mechanism of progression to androgen independence. This is because the AR is a transcription factor that 'normally' mediates the effects of androgen to regulate expression of genes involved in proliferation and survival of prostate cells. Thus identifying and characterizing the proteins that interact with the AR to facilitate an activated receptor is of critical importance. Proteomic approaches such as isotope-coded affinity tags (ICAT), isotope Tags for Relative and Absolute Quantification (iTRAQ)(TM), Stable Isotope Labeling with Amino acids in Cell culture (SILAC), Tandem Affinity Purification (TAP) of tagged proteins (TAP-tag) and Multidimensional Protein Identification Technology (MudPIT) provide large scale unbiased strategies and have not been previously applied to identify proteins that interact with the AR. Here an example of the power of these proteomic approaches to identify potential therapeutic targets for prostate cancer is provided. Application of MudPIT identified 82 peptides in endogenous complexes immunoprecipitated with the AR from prostate cancer cells. Identification of these novel proteins may ultimately lead to the development of better therapies for the treatment or prevention of advanced prostate cancer.

Journal Article↗

PubMed1997

Continuous fluorescence monitoring of rapid cycle DNA amplification.

Rapid cycle DNA amplification was continuously monitored by three different fluorescence techniques. Fluorescence was monitored by (i) the double-strand-specific dye SYBR Green I, (ii) a decrease in fluorescein quenching by rhodamine after exonuclease cleavage of a dual-labeled hydrolysis probe and (iii) resonance energy transfer of fluorescein to Cy5 by adjacent hybridization probes. Fluorescence data acquired once per cycle provides rapid absolute quantification of initial template copy number. The sensitivity of SYBR Green I detection is limited by nonspecific product formation. Use of a single exonuclease hydrolysis probe or two adjacent hybridization probes offers increasing levels of specificity. In contrast to fluorescence measurement once per cycle, continuous monitoring throughout each cycle monitors the temperature dependence of fluorescence. The cumulative, irreversible signal of hydrolysis probes can be distinguished easily from the temperature-dependent, reversible signal of hybridization probes. By using SYBR Green I, product denaturation, annealing and extension can be followed within each cycle. Substantial product-to-product annealing occurs during later amplification cycles, suggesting that product annealing is a major cause of the plateau effect. Continuous within-cycle monitoring allows rapid optimization of amplification conditions and should be particularly useful in developing new, standardized clinical assays.

Benzothiazoles↗

PubMed1998

Expression of interleukin-6 (IL-6) receptor gene in acute myeloblastic leukemia and response of leukemic cells to exogenous IL-6. A comparative study between cell line cells and corresponding native cells.

As interleukin (IL-6) ahs been reported to have diverse effects on acute myeloblastic leukemia (AML) blast cell growth, we investigated whether the level of IL-6 receptor (IL-6R) expression by blast cells is associated with their susceptibility to proliferate in response to exogenous IL-6. For absolute quantification of IL-6R transcript numbers, we established a quantitative IL-6R reverse transcription polymerase chain reaction (RT-PCR) method with an internal RNA standard. In the present work, two types of AML blast cells were investigated, namely autonomously growing cell line cells (n = 8) and non cultured native blast cells (n = 20), including those from which the cell lines originate. The native blast cells expressed an average of 2.8 x 10(7) +/- 1.9 x 10(7) IL-6R transcripts in one microgram of total cellular RNA, whereas the expression by the cell line cells was significantly more abundant, the value being 8.3 x 10(7) +/- 2.8 X 10(7) (P < 0.001). The proliferation responses were evaluated by exposing the cells to IL-6 (1000 U/ml) in a clonogenic cell culture assay and, in the case of the cell line cells, in a long-term suspension culture assay as well. None of the autonomously growing cell lines responded to exogenous IL-6, whereas the native blast cell showed either stimulatory, inhibitory or neutral responses. Thus, the IL-6R expression level did not predict whether the cells proliferated in response to exogenous IL-6, which shows that IL-6R quantification cannot be used as a screening test prior to possibly applying this cytokine to clinical use in AML therapy.

Adolescent↗

PubMed2003

Flow cytometric detection of minimal residual disease in acute lymphoblastic leukemia.

Assessment of minimal residual disease (MRD) during the first months of therapy gives information on the timely response to treatment, and proves to be a powerful and independent indicator of treatment outcome in patients with acute lymphoblastic leukemia (ALL). Immunological evaluation by flow cytometry (FCM) is one of the most attractive approaches to this. The present review summarizes the historical development of this approach over the last 20 years, and shows that current methodology is based on the existence of leukemia-associated patterns of derangement in antigen expression with respect to normal differentiation or location of occurrence. Recent clinical studies are summarized which proved that FCM is applicable to more than 90% of patients with ALL and gives prognostic information comparable to polymerase chain-reaction (PCR)-based technology. Ongoing efforts based on parallel application of both technologies are explained which are designed to clarify which approach bears the best cost-relevance ratio in order to be broadly used in the future for risk assessment and tailoring of treatment modalities. Concluding perspectives relate to further technical developments like usage of peripheral blood (PB) instead of bone marrow (BM), absolute quantification, or strategic placement of investigative time-points, which may allow to simplify the MRD approach and thus augment it's economic efficiency.

Adult↗

PubMed2004

Short communication: amino acid transporters in porcine mammary gland during lactation.

The objective of this study was to determine whether mRNA transcripts for the amino acid (AA) transporter proteins CAT-1, CAT-2B, B(0,+), and ASCT1 are present in porcine mammary tissue (MT). Transcript abundance on d 7 and 17 of lactation was determined by Northern blot analysis, and absolute quantification was performed by real-time polymerase chain reaction. Porcine MT expresses CAT-1, CAT-2B, B(0,+), and ASCT1 during lactation. Preliminary findings indicate that B(0,+) mRNA abundance tended to decrease on d 17 compared with that on d 7.

Amino Acid Transport System y+↗

PubMed2026

Protein Profiling Identifies Biomarkers for Predicting Disease Severity in Anti-NMDAR Encephalitis.

Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is a severe autoimmune neurological disorder characterized by pathogenic antibodies against the NMDAR. A systematic protein profiling approach is warranted to identify biomarkers capable of predicting disease status. An Olink proximity extension assay (PEA) profiled 91 inflammation-related proteins from anti-NMDAR encephalitis patients. Disease severity or prognosis were assessed by CASE score or mRS score at 6-month follow-up. Patients were stratified into distinct molecular clusters using unsupervised clustering. Logistic regression models incorporating selected biomarkers were developed to predict disease severity and prognosis, followed by absolute quantification using ELISA. Patients were classified into four consensus clusters. Clusters 1 and 2 corresponded to the mild group, while Cluster 3 represented the severe group, consistent with CASE score above 6. Cluster 4 showed heterogeneous clinical features. Elevated serum levels of IL-10, IL-6, and SIRT2, as well as increased CSF levels of CXCL10, CXCL11, and MMP10, were positively associated with severe disease. Conversely, several proteins including LTA and CCL11, CCL8, TGFB1, CXCL6 were associated with severe disease or unfavorable 6-month outcomes. A logistic regression model combining serum CXCL6 and CCL11 with CSF MMP10 achieved an area under the curve (AUC) of 0.95 for predicting disease severity. Serum CCL11 alone showed predictive value for 6-month prognosis, with an AUC of 0.79. These findings delineate distinct protein signatures associated with clinical heterogeneity of anti-NMDAR encephalitis. Prediction models incorporating multiple biomarkers may provide an approach for disease severity stratification and prognosis forecast.

Humans↗

PubMed2026

[Laryngeal squamous cell carcinoma-derived exosomes promote neuronal axonal growth by remodeling the neural microenvironment].

Objective: Perineural invasion (PNI) is a critical determinant of poor prognosis in laryngeal squamous cell carcinoma (LSCC), but its underlying mechanisms remain unclear. This study aimed to investigate whether LSCC-derived exosomes induce axonal growth by delivering neuroactive molecules, thereby contributing to tumor perineural invasion. Methods: Clinical data from the laryngeal cancer cohort of The Cancer Genome Atlas Head and Neck Squamous Cell Carcinoma (TCGA-HNSC) dataset were analyzed. Propensity score matching (PSM) and Cox regression were used to evaluate the prognostic value of nerve density, and these findings were validated using 35 pairs of laryngeal cancer and adjacent normal tissue specimens collected at Yantai Yuhuangding Hospital between 2022 and 2026 to assess neural morphological changes. Exosomes were isolated from the human LSCC cell line AMC-HN-8, characterized by quality-control assays, and co-cultured with PC12 cells. A rescue experiment using GW4869, a specific inhibitor of neutral sphingomyelinase, was performed to confirm the exosome-dependent effect. Neurite outgrowth was evaluated by immunofluorescence, and the expression of axonal growth-related genes was measured by RT-qPCR. Targeted metabolomics was employed for the absolute quantification of neuroactive metabolites within the vesicles and for pathway enrichment analysis. Results: After PSM adjustment, high nerve density was identified as an independent poor prognostic factor in LSCC patients (HR=2.10, P=0.035), with particularly pronounced prognostic value in the early-stage node-negative (N0) subgroup (HR=4.07, P=0.001). Pathological sections showed high expression of the neural markers βIII-tubulin and PGP9.5 in LSCC tissues (βIII-tubulin: t=2.234, P<0.05; PGP9.5: t=2.575, P<0.05). Exosomes were successfully isolated from AMC-HN-8 cells and passed quality control. In vitro assays showed that LSCC-derived exosomes significantly promoted neurite extension and branching in PC12 cells (t=4.147, P<0.000 1) and upregulated core axonal growth genes, including GAP-43, NEFL, and NEFM (GAP-43: t=3.698, P<0.05; NEFL: t=5.113, P<0.01; NEFM: t=5.263, P<0.01); this effect was completely reversed by the exosome-release inhibitor GW4869 (t=3.535, P<0.001). Targeted metabolomics revealed a specific enrichment of 12 neurotransmitters and metabolites within LSCC exosomes, centered on glutamine (83.411 μmol/L, FC=1.88) and glutamate (18.461 μmol/L, FC=1.21), which were significantly enriched in signaling pathways such as "central carbon metabolism in cancer" and "glutamatergic synapse". Conclusion: Nerve density is a potential adverse prognostic factor in patients with LSCC. LSCC-derived exosomes can directly induce axonal growth in neuron-like cells, suggesting that tumor cells actively remodel the neural microenvironment and drive axonal growth through exosome-mediated long-range signaling.

Exosomes↗

PubMed2005

Quantitative detection of species-specific DNA in feedstuffs and fish meals.

A sensitive and rapid method for the quantitative detection of bovine-, ovine-, swine-, and chicken-specific mitochondrial DNA sequences based on real-time PCR has been developed. The specificity of the primers and probes for real-time PCR has been tested using DNA samples of other vertebrate species that may also be present in rendered products. The quantitative detection was performed with dual-labeled probes (TaqMan) using absolute quantification with external standards of single species meat-and-bone meals. This method facilitates the detection of 0.01% of the target species-derived material in concentrate feed mixtures and fish meals.

Animal Feed↗

PubMed2000

Quantitative analysis of gene amplification in insecticide-resistant Culex mosquitoes.

The amplification of carboxylesterase structural genes followed by their overexpression is the most common mechanism of resistance to organophosphorus insecticides in Culex mosquitoes. Most resistant Culex quinquefasciatus mosquitoes have co-amplified estalpha2(1) and estbeta2(1) genes. Recently, Southern, DNA dot-blot analysis and phosphorimaging technology were used to quantify the est gene copy number in aphids and mosquitoes. Although more accurate than autoradiography, this method relies on probe hybridization, which can be variable. We have directly measured gene and mRNA copy number by using real-time quantitative PCRs in mosquitoes. The acquisition of fluorescence from incorporation of the double-strand-specific dye SYBR GreenI into a PCR product once per cycle is used to provide an absolute quantification of the initial template copy number. Thus it has been possible to show that estalpha2(1) and estbeta2(1) are co-amplified approx. 80-fold in the genome of the resistant PelRR strain of C. quinquefasciatus. The two genes, although co-amplified in a 1:1 ratio, are differentially transcribed: the estbeta2(1) gene from this amplicon has greater transcription than estalpha2(1) in all individual mosquito larvae tested, with an average ratio of 10:1. Purified esterases from mosquito homogenates were found in a ratio of 3:1, which, combined with the quantitative mRNA data, suggests the operation of both transcriptional and translational control mechanisms to regulate the expression of the amplified genes in C. quinquefasciatus insecticide-resistant mosquitoes.

Animals↗

PubMed2000

[Magnetic tomography--new imaging techniques and future perspectives].

BACKGROUND: From the very introduction of MRI into medicine, the modality has presented the user a long list of theoretical tissue contrast parameters. The development of MRI has been aimed at turning these theoretical possibilities into practical options. MATERIAL AND METHODS: We give an overview of the new MRI techniques and perspectives for the future based on a literature search and our own experience. RESULTS: Today, the modality offers state-of-the-art anatomical details as well as visualisation of several functional parameters such as perfusion, diffusion, blood oxygen saturation, and tissue temperature. In the near future, MRI may provide absolute quantification of regional perfusion and rate of oxygen consumption in a clinical setting. New vascular and gastrointestinal contrast media will further increase the sensitivity and specificity of MRI. A continuous increase in imaging speed has made MRI capable of providing adequate "fluoroscopic" guidance during interventional procedures, and real-time diagnostic imaging is only few years ahead. INTERPRETATION: The spread of MRI installations will increase as a result of increasing demand for the best and least harmful diagnostic procedure. The main challenge to the MRI community will be to exploit the vast diagnostic possibilities.

Blood Circulation↗

PubMed2000

Immunoquantitation of FMO1 in human liver, kidney, and intestine.

To determine the level of FMO1 protein present in human liver tissues, a monospecific antibody was prepared and a sensitive Western blotting procedure with enhanced chemiluminescence detection was developed. Human FMO1, purified from insect cells expressing the recombinant protein, was used as a protein standard for absolute quantification. The average concentrations of FMO1 in microsomes prepared from human liver, kidney, intestine, and fetal liver were found to be <1, 47 +/- 9, 2.9 +/- 1.9, and 14.4 +/- 3.5 pmol/mg, respectively. Quantitation in intestinal microsomes was complicated by variable degrees of proteolytic degradation of FMO1, not seen in microsomes prepared from liver or kidney. Recombinant human FMO1 and detergent-solubilized human duodenal microsomes both metabolized p-tolyl methyl sulfide stereoselectively to the (R)-sulfoxide, indicating the expression of functional FMO1 in human intestine. The relatively high levels of immunoquantifiable FMO1 in human kidney and fetal liver complement our previous catalytic studies in these tissues, which also demonstrated preferential (R)-p-tolyl methyl sulfoxide formation. These data demonstrate a profound ontogenic change in expression of hepatic FMO1 in humans, such that in adult life FMO1 is exclusively an extrahepatic drug-metabolizing enzyme. The marked expression levels of FMO1 found in human kidney coupled to the high catalytic activity of this isoform toward a diverse array of sulfides and tertiary amines suggest the possibility that human renal FMO1 is a significant contributor to the metabolic clearance of drugs and other xenobiotics bearing these functionalities.

Adolescent↗

PubMed2000

Serial proton MR spectroscopy of contrast-enhancing multiple sclerosis plaques: absolute metabolic values over 2 years during a clinical pharmacological study.

BACKGROUND AND PURPOSE: The time courses of total creatine (Cr), N-acetylaspartate (NAA), choline (Cho), and myo-inositol have not previously been investigated in the follow-up of contrast-enhancing multiple sclerosis (MS) plaques. Therefore, over a period of 2 years, we compared the absolute concentrations of these metabolites between patients treated with a placebo or 15 +/- deoxyspergualin (DSG) and between clinical groups with relapsing-remitting or secondary-progressive MS. METHODS: Sixteen patients, recruited from a pharmacological study of DSG, and 11 healthy control subjects were investigated by a stimulated-echo acquisition mode sequence (TR/TE = 3000/20). The selected volume initially contained a contrast-enhancing plaque, which was followed up for a period of 2 years. RESULTS: In contrast-enhancing plaques, Cho was significantly elevated and showed a significant reduction after both 3 and 12 months. The initially normal Cr significantly increased between 3 and 12 months, and was negatively correlated with plaque volume on T1-weighted MR images. NAA initially showed normal values, a significant decrease at 1 month, and a slow recovery over 2 years. Myo-inositol did not show a clear tendency. The placebo group did not differ from the treated group, nor did the relapsing-remitting group differ from the secondary-progressive group. CONCLUSION: The contradictory time courses of Cr and NAA show that an absolute quantification in proton MR spectroscopy in MS is necessary to avoid a false interpretation of reduced NAA/Cr ratios. The increase in Cr is probably due to remyelination. The initial dip and later recovery of NAA seem to be related to diminishing edema and remyelination.

Adult↗

PubMed1992

[Positron emission tomography in cardiological diagnosis: principles and clinical application].

Positron emission tomography (PET) is an emerging new cardiac imaging modality which allows sophisticated tissue characterization using radiopharmaceuticals. This technique provides absolute quantification of regional tracer concentration using short-lived isotopes such as carbon-11, oxygen-15 and nitrogen-13, which can be easily incorporated in many compounds without changing their biological behaviour. These technical advantages are somewhat offset by the high cost of this technology which includes camera as well as on site cyclotron required for the preparation of radiopharmaceuticals. Recent clinical dates suggest that unique information can be obtained with PET. Using blood flow tracers in combination with PET, coronary artery disease can be detected and localized with high diagnostic accuracy. First studies comparing Tl-201 SPECT and PET in the same patient population indicate diagnostic superiority of PET. In combination with tracer kinetic models, regional myocardial blood flow can be quantitated and the functional significance of coronary artery stenosis defined by regional coronary reserve measurements. The assessment of regional glucose metabolism by PET with the tracer F-18 deoxyglucose has received wide clinical acceptance. Metabolic imaging in patients with advanced coronary artery disease allows the delineation of ischemically compromised but viable myocardium. Selection of patients for revascularization based on this scintigraphy tissue characterization has been shown to have a high predictive value for subsequent tissue recovery. Comparison of PET/FDG imaging with thallium-201 scintigraphy for assessment of tissue viability indicate that, in patients with fixed thallium-201 defects, additional diagnostic information can be obtained by this more expensive technology.(ABSTRACT TRUNCATED AT 250 WORDS)

Cardiomyopathies↗

PubMed2004

Constant-infusion H(2)15O PET and acetazolamide challenge in the assessment of cerebral perfusion status.

UNLABELLED: Assessing the baseline perfusion and perfusion reserve after acetazolamide (ACZ) challenge is a common method for the evaluation of patients with cerebrovascular disease. Most previous studies using H(2)(15)O PET applied the bolus injection technique. There is considerable discrepancy regarding the optimal time point of imaging after ACZ injection. The purpose of this study was to continuously monitor cerebral blood flow (CBF) after ACZ using constant-infusion H(2)(15)O PET. METHODS: Four patients with stenoses of an internal carotid artery and 6 with moyamoya disease were studied. H(2)(15)O was continuously infused, and data were recorded in 1-min frames. After equilibration of H(2)(15)O, 5 min of baseline data were acquired, and then 1 g of ACZ was administered intravenously and data collection continued for 10-22 min. Arterial blood was continuously drawn for absolute quantification of CBF. RESULTS: The arterial (15)O concentration remained generally stable during scanning, and the cerebellar blood flow fluctuations of the 5 baseline scans were small. The scan-to-scan difference was 6% (difference of 2 successive scans/mean). In the nonpathologic areas, the increase in CBF started 1-2 min after administration of ACZ. The largest fraction of the increase occurred from 0 to 10 min. The ratio of CBF in pathologic areas to CBF in cerebellum showed an initial decrease that stabilized after 5 min. CONCLUSION: A continuous-infusion protocol is a viable alternative to single bolus injections for the assessment of cerebral perfusion status. Such a protocol is advantageous when the time course of CBF after an intervention is not known. With continuous monitoring, the optimal time point for evaluation of a certain parameter can be chosen post hoc. Furthermore, the time course of CBF itself may allow the definition of new parameters for evaluating perfusion status in cerebrovascular patients, both for assessment before a revascularization procedure and for follow-up. A limitation of the present study is the relatively small number of patients with each type of cerebrovascular disease and the lack of healthy subjects.

Acetazolamide↗

PubMed2004

Evaluation of a real-time polymerase-chain reaction for severe acute respiratory syndrome (SARS) associated coronavirus in patients with hospitalised exacerbation of COPD.

One year after the first outbreak infections with SARS associated coronavirus were again reported and the clinical picture varied. Because health care facilities will have to initiate immediate preventive action in cases of probable SARS we tested the potential of PCR to exclude SARS associated coronavirus in patients hospitalized with respiratory symptoms. Based on primers published recently a real time Taqman PCR was established and evaluated. Lower respiratory tract specimens of patients with acute exacerbation of COPD were investigated. 141 patients with mild to moderate COPD were included. The assay was specific, sensitive, precise and reproducible and allowed absolute quantification without cross-reactivity to other respiratory viruses. None of the samples were positive for SARS associated coronavirus. Our RT-PCR for SARS associated coronavirus is a valid and practicable method to further exclude SARS in X-ray negative patients with respiratory symptoms, even in the presence of other respiratory RNA viruses.

Aged↗