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PubMed2003

Quantitative detection of agar-cultivated and rhizotron-grown Piloderma croceum Erikss. & Hjortst. by ITS1-based fluorescent PCR.

A real-time quantitative TaqMan-PCR was established for the absolute quantification of extramatrical hyphal biomass of the ectomycorrhizal fungus Piloderma croceum in pure cultures as well as in rhizotron samples with non-sterile peat substrate. After cloning and sequencing of internal transcribed spacer (ITS) sequences ITS1/ITS2 and the 5.8S rRNA gene from several fungi, including Tomentellopsis submollis, Paxillus involutus, and Cortinarius obtusus, species-specific primers and a dual-labelled fluorogenic probe were designed for Piloderma croceum. The dynamic range of the TaqMan assay spans seven orders of magnitude, producing an online-detectable fluorescence signal during the cycling run that is directly related to the starting number of ITS copies present. To test the confidence of the PCR-based quantification results, the hyphal length of Piloderma croceum was counted under the microscope to determine the recovery from two defined but different amounts of agar-cultivated mycelia. Inspection of the registered Ct values (defined as that cycle number at which a statistically significant increase in the reporter fluorescence can first be detected) in a 10-fold dilution series of template DNA represents a suitable and stringent quality control standard for exclusion of false PCR-based quantification results. The fast real-time PCR approach enables high throughput of samples, making this method well suited for quantitative analysis of ectomycorrhizal fungi in communities of natural and artificial ecosystems, so long as applicable DNA extraction protocols exist for different types of soil.

Base Sequence↗

PubMed2004

1H NMR relaxation times of skeletal muscle metabolites at 3 T.

This study reports proton relaxation times of water and metabolites in soleus and tibialis anterior muscles of young healthy volunteers at 3 T. The results are in agreement with data reported for 1.5 and 4 T, showing a steady increase of spin-lattice relaxation times of water, creatine and lipids with B(0) and no effect of B(0) on spin-spin relaxation. Comparison between muscles revealed a longer spin-spin relaxation time of water in soleus than in tibialis anterior muscle (31+/-1 ms vs. 28+/-1 ms, p<0.05). These data can be applied to relaxation correction for the absolute quantification of skeletal muscle metabolite concentrations and further sequence optimization.

Adult↗

PubMed2003

Cardiac magnetic resonance spectroscopy.

This review describes recent advances in cardiac magnetic resonance spectroscopy (MRS). MRS allows noninvasive characterization of the metabolic state of cardiac muscle, in both animal and human models. Recent experimental MRS studies have allowed new insights into the essential role of energetics in heart failure. Various new studies suggest a rapidly growing role of MRS for phenotyping new genetically modified mouse models, and recent methodologic advances include development of absolute quantification of high-energy phosphates, measurement of ATP turnover rates and thermodynamic parameters (such as free ADP and free energy change of ATP hydrolysis), and improved acquisition sequences. New patient studies demonstrate the potential value of MRS as a clinical diagnostic tool in patients with ischemic heart disease, heart failure, cardiac transplantation, valve disease, and genetic cardiomyopathy.

Animals↗

PubMed2006

Imaging cardiac neuronal function and dysfunction.

In recent years, the importance of alterations of cardiac autonomic nerve function in the pathophysiology of heart diseases including heart failure, arrhythmia, ische-mic heart disease, and diabetes has been increasingly recognized. Several radiolabeled compounds have been synthesized for noninvasive imaging, including single photon emission CT and positron emission tomography (PET). The catecholamine analogue I-123 metaiodobenzylguanidine (MIBG) is the most commonly used tracer for mapping of myocardial presynaptic sympathetic innervation on a broad clinical basis. In addition, radiolabeled catecholamines and catecholamine analogues are available for PET imaging, which allows absolute quantification and tracer kinetics modeling. Postsynaptic receptor PET imaging added new insights into mechanisms of heart disease. These advanced imaging techniques provide noninvasive, repeatable in vivo information of autonomic nerve function in the human heart and are promising for providing profound insights into molecular pathophysiology, monitoring of treatment, and determination of individual outcome.

Arrhythmias, Cardiac↗

PubMed2006

Neuroproteomics: relevance to anxiety disorders.

Despite advances in the treatment of anxiety disorders, there is a need for medications with greater efficacy and fewer side effects. Advances in techniques to facilitate high throughput, mass analysis of proteins potentially allows for new drug targets, with a shift in focus from membrane receptor proteins and enzymes of neurotransmitter metabolism to molecules in intracellular signal transduction and other pathways. A computerized literature search was done to collect studies on recently developed proteomic techniques and their application in psychiatric research. Particular techniques, such as two-dimensional electrophoresis, two-dimensional differential gel electrophoresis, isotope-coded affinity tags, and isotope tags for relative and absolute quantification, are reviewed. In addition, a combination of these techniques with MALDI-TOF/TOF and ESI-Q-TOF mass spectrometry analysis is discussed in relation to possible novel signaling pathways relevant to anxiety disorders, and to the development of biomarkers for the evaluation of these conditions.

Animals↗

PubMed1993

Searching for replication origins in mammalian DNA.

The attempts at identifying precise replication origins (ori) in mammalian DNA have been pursued mainly through physico-chemical and biochemical approaches, in view of the essential failure of the search for autonomously replicating sequences in cultured cells. These approaches involve the mapping of short stretches of nascent DNA, the identification of the regions where either leading or lagging strands switch polarity, or the localization of replication intermediates by two-dimensional gel electrophoresis. Due to the complexity of animal cell genomes, most of these studies have been performed on amplified domains and with the use of synchronization procedures. The results obtained have been controversial. In order to avoid the use of experimental procedures potentially affecting the physiological mechanism of DNA replication, we have developed a method for the localization of ori in single-copy loci in exponentially growing cells. This method entails the absolute quantification of the abundance of selected DNA fragments along a genomic region within samples of newly synthesized DNA by competitive polymerase chain reaction (PCR); the latter is immune to all the uncontrollable variables which severely affect the reproducibility of conventional PCR. The application of this method to SV40 ori-driven plasmid replication precisely identifies the known ori localization. Using the same approach, we have mapped an ori for bi-directional DNA replication in a 13.7-kb locus of human chromosome 19 encoding lamin B2.

Animals↗

PubMed1993

Determination of peptide 520 in human plasma using post-column photolysis with electrochemical detection in liquid chromatography.

A simple LC method for the determination of peptide 520 in human plasma was developed. Based on micellar chromatography, sodium octyl sulphate (SOS) was added into the mobile phase in order to separate the peptide from human plasma components. The procedure was fast and sensitive for the determination of the peptide in untreated human plasma. The electrochemical (EC) detection limit for peptide 520 in human plasma was 0.5 microgram ml-1. Linearity of the calibration plot for peptide 520 in human plasma was 0.999. This approach represents a direct injection technique for the potential detection and analysis of numerous peptides in biofluids, besides just plasma, with absolute quantification.

Chromatography, Liquid↗

PubMed2004

NEUROD1 acts in vitro as an upstream regulator of NEUROD2 in trophoblast cells.

The basic helix-loop-helix (bHLH) transcription factors NEUROD1, NEUROD2 and ATH2 are expressed during first trimester human placental development. We determined the transactivation potential of each of these factors in trophoblasts by measuring changes in the endogenous gene activity using absolute quantification by real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) after transient transfection. In these assays, NEUROD1 was found to transiently transactivate NEUROD2 in trophoblast cells. Promotor truncation assays, using luciferase constructs, showed the presence of two domains in the NEUROD2 promotor, which showed increased activity after NeuroD1 transfection. Each of these NeuroD1-responsive domains contains an E-box sequence. The NEUROD2 transactivation data fit with the spatial expression pattern of NEUROD1 and NEUROD2, since they are expressed in endovascular trophoblasts. This expression pattern, as well as the present transactivation results, might suggest the presence of a NEUROD differentiation cascade during first trimester human placental development.

Basic Helix-Loop-Helix Proteins↗

PubMed2006

Quantitative analysis of template-based attenuation compensation in 3D brain PET.

An atlas-guided attenuation correction method was recently proposed for 3D brain positron emission tomography (PET) imaging eliminating the need for acquisition of a patient-specific measured transmission scan. The algorithm was validated through comparison to transmission-based attenuation correction (gold standard) using voxelwise statistical parametric mapping (SPM) analysis of clinical data. In contrast to brain 'activation' studies for which SPM is primarily developed, brain PET research studies often involve absolute quantification. In the preliminary validation study published earlier, there is no validation as to how such quantification can be affected by the two methods as the assessment was carried out by an SPM group analysis alone. It is quite important to demonstrate how the proposed method performs individually, particularly for diagnostic applications or individual quantification. In this study, we assess the quantitative accuracy of this method in clinical setting using automated volume of interest (VOI)-based analysis by means of the commercially available BRASS software. There is a very good correlation (R(2)=0.91) between the atlas-guided and measured transmission-guided attenuation correction techniques and the regression line agreed well with the line of identity (slope=0.96) for the grouped analysis of patient data. The mean relative difference between the two methods for all VOIs across the whole population is 2.3% whereas the maximum difference is less than 7%. No proof of statistically significant differences could be verified for all regions. These encouraging results provide further confidence in the adequacy of the proposed approach demonstrating its performance particularly for research studies or diagnostic applications involving quantification.

Aged↗

PubMed2026

Comprehensive quality profiling and comparative metabolic characterization of seven dominant fresh-eating Chinese olive (Canarium album Lour.) cultivars in Southern China.

Fresh-eating Chinese olive (Canarium album Lour.) is a subtropical fruit endemic to southern China with considerable commercial value, yet systematic quality characterization of dominant cultivars remains scarce. This study established a multi-dimensional quality dataset for seven dominant cultivars from Fujian and Guangdong provinces, integrating nutritional components, soluble sugars, organic acids, mineral elements, volatile profiles, and non-targeted metabolomics. Significant cultivar-specific differences were observed across all evaluated dimensions: "Lingfeng" exhibited a sugar-dominant low-acid profile, whereas "Sanleng" showed elevated phenolic constituents accumulation. Volatile profiling identified terpenoid-based candidate discriminatory biomarkers, and metabolomic analysis revealed phenylpropanoid biosynthesis, tryptophan metabolism, and starch and sucrose metabolism as the most variable pathways. Correlations between untargeted profiling and targeted absolute quantification validated untargeted result reliability and revealed their complementarity in nutritional evaluation. These findings provide baseline data for FECO germplasm evaluation and targeted industrial utilization.

China↗

PubMed2026

Quantitative proteomics of molybdenum cofactor biosynthesis and utilization in Caenorhabditis elegans.

The molybdenum cofactor (Moco) is a chemically labile prosthetic group required by a small but essential set of metazoan enzymes, including sulfite oxidase, xanthine dehydrogenase, aldehyde oxidases, and the mitochondrial amidoxime reducing components (MARC). Disruption of Moco biosynthesis in humans causes Molybdenum Cofactor Deficiency (MoCD), a severe neonatal encephalopathy. Caenorhabditis elegans is unique among animals studied so far in that it can meet its Moco requirement through both endogenous biosynthesis and direct uptake of mature Moco from its bacterial diet. However, the organism-wide abundance of the Moco biosynthetic machinery and Moco-dependent enzymes, and their response to altered Moco supply, have remained unknown. Here, using data independent acquisition proteomics with histone anchored absolute quantification, we generated an organism wide quantitative atlas of Moco biosynthesis and utilization in C. elegans under standard and Moco limiting conditions. Components of the biosynthetic pathway showed a strikingly asymmetric abundance. The mitochondrial enzyme MOC-5, which catalyzes the first committed step in Moco biosynthesis, was present at only about 120 copies per genome equivalent, roughly fifty-fold below the downstream cytoplasmic biosynthetic machinery, which ranged from about 5,000 to 8,500 copies per genome equivalent, identifying MOC-5 as a stoichiometric bottleneck. On the utilization side, the MARC paralogs were the dominant Moco consumers, with MARC-1 exceeding 20,000 copies per genome equivalent. Loss of dietary or endogenous Moco selectively depleted the nonsulfurated clients SUOX-1 and MARC-1, whereas biosynthetic proteins remained unchanged, indicating that protein stability, rather than compensatory expression, is the main response to Moco limitation.

Caenorhabditis elegans↗

PubMed2005

Specific and quantitative detection of human polyomaviruses BKV, JCV, and SV40 by real time PCR.

BACKGROUND: The polyomaviruses that infect humans, BK virus (BKV), JC virus (JCV), and simian virus 40 (SV40), typically establish subclinical persistent infections. However, reactivation of these viruses in immunocompromised hosts is associated with renal nephropathy and hemorrhagic cystitis (HC) caused by BKV and with progressive multifocal leukoencephalopathy (PML) caused by JCV. Additionally, SV40 is associated with several types of human cancers including primary brain and bone cancers, mesotheliomas, and non-Hodgkin's lymphoma. Advancements in detection of these viruses may contribute to improved diagnosis and treatment of affected patients. OBJECTIVE: To develop sensitive and specific real time quantitative polymerase chain reaction (RQ-PCR) assays for the detection of T-antigen DNA sequences of the human polyomaviruses BKV, JCV, and SV40 using the ABI Prism 7000 Sequence Detection System. STUDY DESIGN: Assays for absolute quantification of the viral T-ag sequences were designed and the sensitivity and specificity were evaluated. A quantitative assay to measure the single copy human RNAse P gene was also developed and evaluated in order to normalize viral gene copy numbers to cell numbers. RESULTS: Quantification of the target genes is sensitive and specific over a 7 log dynamic range. Ten copies each of the viral and cellular genes are reproducibly and accurately detected. The sensitivity of detection of the RQ-PCR assays is increased 10- to 100-fold compared to conventional PCR and agarose gel protocols. The primers and probes used to detect the viral genes are specific for each virus and there is no cross reactivity within the dynamic range of the standard dilutions. The sensitivity of detection for these assays is not reduced in human cellular extracts; however, different DNA extraction protocols may affect quantification. CONCLUSION: These assays provide a technique for rapid and specific quantification of polyomavirus genomes per cell in human samples.

BK Virus↗

PubMed2006

Fast and simple DNA extraction from saliva and sperm cells obtained from the skin or isolated from swabs.

The forensic scientist often has to cope with problematic samples from the crime scene due to their minute size and thus the low amount of extractable DNA. The retrieval of DNA from swabs taken from the surface of the skin, for example, in cases of strangulation, can be especially difficult. We systematically investigated swabs taken from the skin (to obtain a genetic profile from the victim and also from a possible offender) and from sperm cell containing swabs using two extraction kits: the Invisorb forensic and the Invisorb spin swab kit (both Invitek, Germany). DNA quality and quantity were tested on ethidium bromide containing agarose gels and in a highly sensitive duplex-PCR, which amplifies fragments specific for mitochondrial and nuclear DNA. Absolute quantification was done using real time PCR. Samples, which were positive in the duplex-PCR, were also employed to genetic fingerprinting using the Powerplex ES and the AmpFlSTRIdentifiler(TM) kits. Our study shows that the easy-to-use Invisorb spin swab kit is very suitable for DNA isolation from swabs taken from the skin and also from sperm cells. Retrieval of cells from the skin with swabs moistened in extraction buffer, not in distilled water, led to a significant higher DNA yield.

DNA↗

PubMed2004

Age-related changes in cardiac adenosine receptor expression.

Adenosine is an important cardioprotective agent that works via several adenosine receptor (ADOR) subtypes to regulate cardiovascular activity. It is well established that functional responses to adenosine decline with age. What is unclear, though, is whether these changes occur at the receptor, second messenger or translational level. In this study we determined the effect of age on cardiac adenosine receptor expression using the housekeeping gene 18S rRNA versus the adenosine A(2B) receptor gene as internal controls. Absolute quantification showed that no age-related changes occurred in the expression of 18S rRNA or adenosine A(2B) receptor internal control genes. Subsequently, relative analysis of the adenosine receptor subtypes using 18S rRNA found a significant age-related reduction in the expression of the adenosine A(1) receptor (5.5-fold), with no changes in the expression of the adenosine A(2A), A(2B) and A(3) receptors. When using the expression of the adenosine A(2B) receptor as the internal control gene, a significant down regulation of both the adenosine A(1) (5.4-fold) and A(2A) (2.2-fold) receptors with no change in the expression of adenosine A(3) receptor was found. Therefore, the high level of expression of the 18S rRNA housekeeping gene was found to mask a significant change in expression of the adenosine A(2A) receptor with age. Ultimately, these findings show an age-related reduction in adenosine A(1) and A(2A) receptor expression in rat heart.

Aging↗

PubMed2004

Optimised real-time quantitative PCR assays for RANKL regulated genes.

Osteoclasts are multinucleated giant cells that differentiate from precursors of the monocyte-macrophage lineage. We used receptor activator of NF-kappa B ligand (RANKL) and macrophage colony stimulating factor (M-CSF) to differentiate authentic human osteoclasts from peripheral blood mononuclear cells (PBMCs). We previously described a series of genes that are strongly regulated by RANKL. Here, we provide a set of reliable quantitative real-time PCR based assays of RANKL regulated genes as reference genes that may prove useful in the study of human osteoclasts. The SYBR-green I assays are free of primer dimer and other artefacts, and are designed to amplify in parallel, thus permitting simultaneous analysis of 12 genes. Optimised primers for 18S rRNA provide a valid housekeeping reference gene. Standard curves have been constructed for all assays, thus allowing for absolute quantification of mRNA transcript copy number. As an example, the regulation of expression of the chemokine RANTES in osteoclasts is demonstrated. These gene assays have potential utility in a variety of cell types, tissues and organs, in addition to macrophages and osteoclasts.

Benzothiazoles↗

PubMed2003

Assessment of the impact of model-based scatter correction on [18F]-FDG 3D brain PET in healthy subjects using statistical parametric mapping.

It is recognized that scatter correction can supply more accurate absolute quantification, and that iterative reconstruction results in better noise properties and significantly reduces streak artefacts; however, it is not entirely clear whether they produce significant changes in [18F]-FDG distribution of reconstructed 3D brain PET images relative to not scatter corrected images and analytic reconstruction procedures. The current study assesses the effect of model-based scatter correction using the single-scatter simulation algorithm and iterative reconstruction in 3D brain PET studies, using statistical parametric mapping (SPM) analysis. The study population consisted of 14 healthy volunteers (6 males, 8 females; age 63-80 years). PET images were reconstructed using an analytic 3DRP reprojection algorithm with (SC) and without explicit scatter correction (NSC), as well as using an iterative ordered subset-expectation maximization (OSEM) algorithm. Calculated attenuation correction was performed assuming uniform attenuation (mu = 0.096 cm(-1)) for brain tissues when data are precorrected for scatter. The broad-beam attenuation coefficient (mu = 0.06 cm(-1)) determined from phantom studies was applied to NSC images. The images were coregistered and normalized using the default [15O]-H2O template supplied with SPM99 and an [18F]-FDG template. A t statistic image for the contrast condition effect was then constructed. The contrast comparing SC to NSC images suggest that regional brain metabolic activity decreases significantly in the frontal gyri, in addition to the middle temporal and postcentral gyri. On the other hand, activity increases in the cerebellum, thalamus, insula, brainstem, temporal lobe, and the frontal cortex. No significant changes were detected when comparing images reconstructed using analytic and iterative algorithms. It is concluded that, for some cerebral areas, significant differences in [18F]-FDG distribution arise when images are reconstructed with and without explicit SC. This needs to be considered when interpreting [18F]-FDG 3D brain PET images after applying SC.

Adult↗

PubMed2006

Dynamic susceptibility-weighted contrast-enhanced perfusion MR imaging in pediatric patients.

Dynamic susceptibility-weighted contrast-enhanced (DSC) perfusion MR (pMR) imaging provides hemodynamic information that complements traditional structural MR imaging and is becoming increasingly used in clinical practice to diagnose, manage, and understand brain tumors in the pediatric patient group. pMR imaging-derived regional cerebral blood volume (rCBV) maps provide quantitative estimates of rCBV that can be used to grade gliomas, differentiate between different brain tumor types, and distinguish tumor from nonneoplastic lesions. There are a few minor limitations of the DSC pMR imaging technique, such as susceptibility artifacts, relative rather than absolute quantification of cerebral blood volume (CBV), and inaccurate estimation of CBV in situations of severe disruption or absence of the blood-brain barrier. Recognizing its strengths and potential pitfalls, pMR imaging can be used as part of the routine evaluation of brain tumors to improve the diagnostic accuracy, understand tumor pathophysiology, detect and quantify tumor angiogenesis, and, with further work, serve as an arbiter to assess existing and novel cancer therapies that target blood vessels.

Brain Neoplasms↗

PubMedDate not supplied

Assessment of cardiac sympathetic neuronal function using PET imaging.

The autonomic nervous system plays a key role for regulation of cardiac performance, and the importance of alterations of innervation in the pathophysiology of various heart diseases has been increasingly emphasized. Nuclear imaging techniques have been established that allow for global and regional investigation of the myocardial nervous system. The guanethidine analog iodine 123 metaiodobenzylguanidine (MIBG) has been introduced for scintigraphic mapping of presynaptic sympathetic innervation and is available today for imaging on a broad clinical basis. Not much later than MIBG, positron emission tomography (PET) has also been established for characterizing the cardiac autonomic nervous system. Although PET is methodologically demanding and less widely available, it provides substantial advantages. High spatial and temporal resolution along with routinely available attenuation correction allows for detailed definition of tracer kinetics and makes noninvasive absolute quantification a reality. Furthermore, a series of different radiolabeled catecholamines, catecholamine analogs, and receptor ligands are available. Those are often more physiologic than MIBG and well understood with regard to their tracer physiologic properties. PET imaging of sympathetic neuronal function has been successfully applied to gain mechanistic insights into myocardial biology and pathology. Available tracers allow dissection of processes of presynaptic and postsynaptic innervation contributing to cardiovascular disease. This review summarizes characteristics of currently available PET tracers for cardiac neuroimaging along with the major findings derived from their application in health and disease.

3-Iodobenzylguanidine↗