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Sample records for reference tissue quantification

  1. Quantification of brain mu-opioid receptors with [11C]carfentanil: reference-tissue methods.

    PubMed

    Endres, Christopher J; Bencherif, Badreddine; Hilton, John; Madar, Igal; Frost, J James

    2003-02-01

    [(11)C]Carfentanil (CFN) is a mu-opioid agonist used for in vivo positron emission tomography (PET) studies of mu-opioid receptors. Previously, a tissue-ratio method was validated for the quantification of CFN binding. However, since that initial validation, several other blood independent (reference-tissue) methods have become available. To evaluate these methods, CFN PET studies with arterial blood sampling were acquired in six healthy male control subjects. Specific binding estimates obtained from reference-tissue methods were compared to those obtained with a more rigorous blood input modeling technique. It was determined that both a graphical method, and a simplified reference tissue model, were more accurate than the tissue-ratio method for quantification of CFN binding.

  2. Quantification of absolute fat mass using an adipose tissue reference signal model.

    PubMed

    Hu, Houchun H; Nayak, Krishna S

    2008-12-01

    To develop a method for quantifying absolute fat mass, and to demonstrate its feasibility in phantoms and in ex vivo swine specimens at 3 Tesla. Chemical-shift-based fat-water decomposition was used to first reconstruct fat-only images. Our proposed model used a reference signal from fat in pure adipose tissue to calibrate and normalize the fat signal intensities from the fat-only images. Fat mass was subsequently computed on a voxel-by-voxel basis and summed across each sample. Feasibility of the model was tested in six ex vivo swine samples containing varying mixtures of fat (adipose) and lean tissues. The samples were imaged using 1.5-mm isotropic voxels and a single-channel birdcage head coil at 3 Tesla. Lipid assay was independently performed to determine fat mass, and served as the comparison standard. Absolute fat mass values (in grams) derived by our proposed model were in excellent agreement with lipid assay results, with a 5% to 7% difference (r > 0.99; P < 0.001). Preliminary results in ex vivo swine samples demonstrated the feasibility of computing absolute fat mass as a quantitative endpoint using chemical-shift fat-water MRI with a signal model based on reference fat from pure adipose tissue. (c) 2008 Wiley-Liss, Inc.

  3. Dual time point method for the quantification of irreversible tracer kinetics: A reference tissue approach applied to [(18)F]-FDOPA brain PET.

    PubMed

    Alves, Isadora L; Meles, Sanne K; Willemsen, Antoon Tm; Dierckx, Rudi A; Marques da Silva, Ana M; Leenders, Klaus L; Koole, Michel

    2016-01-01

    The Patlak graphical analysis (PGAREF) for quantification of irreversible tracer binding with a reference tissue model was approximated by a dual time point imaging approach (DTPREF). The DTPREF was applied to 18 [(18)F]-FDOPA brain scans using the occipital cortex as reference region (DTPOCC) and compared to both PGAOCC and striatal-to-occipital ratios (SOR). Pearson correlation analysis and Bland-Altman plots showed an excellent correlation and good agreement between DTPOCC and PGAOCC, while correlations between SOR and PGAOCC were consistently lower. Linear discriminant analysis (LDA) demonstrated a similar performance for all methods in differentiating patients with Parkinson's disease (PD) from healthy controls (HC). Specifically for [(18)F]-FDOPA brain imaging, these findings validate DTPOCC as an approximation for PGAOCC, providing the same quantitative information while reducing the acquisition time to two short static scans. For PD patients, this approach can greatly improve patient comfort while reducing motion artifacts and increasing image quality. In general, DTPREF can improve the clinical applicability of tracers with irreversible binding characteristics when a reference tissue is available.

  4. Bone to pick: the importance of evaluating reference genes for RT-qPCR quantification of gene expression in craniosynostosis and bone-related tissues and cells.

    PubMed

    Yang, Xianxian; Hatfield, Jodie T; Hinze, Susan J; Mu, Xiongzheng; Anderson, Peter J; Powell, Barry C

    2012-05-08

    RT-qPCR is a common tool for quantification of gene expression, but its accuracy is dependent on the choice and stability (steady state expression levels) of the reference gene/s used for normalization. To date, in the bone field, there have been few studies to determine the most stable reference genes and, usually, RT-qPCR data is normalised to non-validated reference genes, most commonly GAPDH, ACTB and 18 S rRNA. Here we draw attention to the potential deleterious impact of using classical reference genes to normalise expression data for bone studies without prior validation of their stability. Using the geNorm and Normfinder programs, panels of mouse and human genes were assessed for their stability under three different experimental conditions: 1) disease progression of Crouzon syndrome (craniosynostosis) in a mouse model, 2) proliferative culture of cranial suture cells isolated from craniosynostosis patients and 3) osteogenesis of a mouse bone marrow stromal cell line. We demonstrate that classical reference genes are not always the most 'stable' genes and that gene 'stability' is highly dependent on experimental conditions. Selected stable genes, individually or in combination, were then used to normalise osteocalcin and alkaline phosphatase gene expression data during cranial suture fusion in the craniosynostosis mouse model and strategies compared. Strikingly, the expression trends of alkaline phosphatase and osteocalcin varied significantly when normalised to the least stable, the most stable or the three most stable genes. To minimise errors in evaluating gene expression levels, analysis of a reference panel and subsequent normalization to several stable genes is strongly recommended over normalization to a single gene. In particular, we conclude that use of single, non-validated "housekeeping" genes such as GAPDH, ACTB and 18 S rRNA, currently a widespread practice by researchers in the bone field, is likely to produce data of questionable

  5. Quantification of adipose tissue insulin sensitivity.

    PubMed

    Søndergaard, Esben; Jensen, Michael D

    2016-06-01

    In metabolically healthy humans, adipose tissue is exquisitely sensitive to insulin. Similar to muscle and liver, adipose tissue lipolysis is insulin resistant in adults with central obesity and type 2 diabetes. Perhaps uniquely, however, insulin resistance in adipose tissue may directly contribute to development of insulin resistance in muscle and liver because of the increased delivery of free fatty acids to those tissues. It has been hypothesized that insulin adipose tissue resistance may precede other metabolic defects in obesity and type 2 diabetes. Therefore, precise and reproducible quantification of adipose tissue insulin sensitivity, in vivo, in humans, is an important measure. Unfortunately, no consensus exists on how to determine adipose tissue insulin sensitivity. We review the methods available to quantitate adipose tissue insulin sensitivity and will discuss their strengths and weaknesses. Copyright © 2016 American Federation for Medical Research.

  6. QUANTIFICATION OF TISSUE PROPERTIES IN SMALL VOLUMES

    SciTech Connect

    J. MOURANT; ET AL

    2000-12-01

    The quantification of tissue properties by optical measurements will facilitate the development of noninvasive methods of cancer diagnosis and detection. Optical measurements are sensitive to tissue structure which is known to change during tumorigenesis. The goals of the work presented in this paper were to verify that the primary scatterers of light in cells are structures much smaller than the nucleus and then to develop an optical technique that can quantify parameters of structures the same size as the scattering features in cells. Polarized, elastic back-scattering was found to be able to quantify changes in scattering properties for turbid media consisting of scatterers of the size found in tissue.

  7. Ultrasound strain imaging for quantification of tissue function: cardiovascular applications

    NASA Astrophysics Data System (ADS)

    de Korte, Chris L.; Lopata, Richard G. P.; Hansen, Hendrik H. G.

    2013-03-01

    With ultrasound imaging, the motion and deformation of tissue can be measured. Tissue can be deformed by applying a force on it and the resulting deformation is a function of its mechanical properties. Quantification of this resulting tissue deformation to assess the mechanical properties of tissue is called elastography. If the tissue under interrogation is actively deforming, the deformation is directly related to its function and quantification of this deformation is normally referred as `strain imaging'. Elastography can be used for atherosclerotic plaques characterization, while the contractility of the heart or skeletal muscles can be assessed with strain imaging. We developed radio frequency (RF) based ultrasound methods to assess the deformation at higher resolution and with higher accuracy than commercial methods using conventional image data (Tissue Doppler Imaging and 2D speckle tracking methods). However, the improvement in accuracy is mainly achieved when measuring strain along the ultrasound beam direction, so 1D. We further extended this method to multiple directions and further improved precision by using compounding of data acquired at multiple beam steered angles. In arteries, the presence of vulnerable plaques may lead to acute events like stroke and myocardial infarction. Consequently, timely detection of these plaques is of great diagnostic value. Non-invasive ultrasound strain compounding is currently being evaluated as a diagnostic tool to identify the vulnerability of plaques. In the heart, we determined the strain locally and at high resolution resulting in a local assessment in contrary to conventional global functional parameters like cardiac output or shortening fraction.

  8. Fat quantification in skeletal muscle using multigradient-echo imaging: Comparison of fat and water references.

    PubMed

    Peterson, Pernilla; Romu, Thobias; Brorson, Håkan; Dahlqvist Leinhard, Olof; Månsson, Sven

    2016-01-01

    To investigate the precision, accuracy, and repeatability of water/fat imaging-based fat quantification in muscle tissue using a large flip angle (FA) and a fat reference for the calculation of the proton density fat fraction (FF). Comparison is made to a small FA water reference approach. An Intralipid phantom and both forearms of six patients suffering from lymphedema and 10 healthy volunteers were investigated at 1.5T. Two multigradient-echo sequences with eight echo times and FAs of 10° and 85° were acquired. For healthy volunteers, the acquisition of the right arm was performed twice with repositioning. From each set, water reference FF and fat reference FF images were reconstructed and the average FF and the standard deviation were calculated within the subfascial compartment. The small FA water reference was considered the reference standard. A high agreement was found between the small FA water reference and large FA fat reference methods (FF bias = 0.31%). In this study, the large FA fat reference approach also resulted in higher precision (38% smaller FF standard deviation in homogenous muscle tissue), but no significant difference in repeatability between the various methods was detected (coefficient of repeatability of small FA water reference approach 0.41%). The precision of fat quantification in muscle tissue can be increased with maintained accuracy using a larger flip angle, if a fat reference instead of a water reference is used. © 2015 Wiley Periodicals, Inc.

  9. Determination of reference microRNAs for relative quantification in grass carp (Ctenopharyngodon idella).

    PubMed

    Xu, Xiao-Yan; Shen, Yu-Bang; Fu, Jian-Jun; Lu, Li-Qun; Li, Jia-Le

    2014-02-01

    Relative quantification is the strategy of choice for processing real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) data in microRNA (miRNA) expression studies. Normalization of relative quantification data is performed by comparison to reference genes. In teleost species, such as grass carp (Ctenopharyngodon idella), the determination of reference miRNAs and the optimal numbers of these that should be used has not been widely studied. In the present study, the stability of seven miRNAs (miR-126-3p, miR-101a, miR-451, miR-22a, miR-146, miR-142a-5p and miR-192) was investigated by RT-qPCR in different tissues and in different development stages of grass carp. Stability values were calculated with geNorm, NormFinder, BestKeeper and Delta CT algorithms. The results showed that tissue type is an important variability factor for miRNA expression stability. All seven miRNAs had good stability values and, therefore, could be used as reference miRNAs. When all tissues and developmental stages were considered, miR-101a was the most stable miRNA. When each tissue type was considered separately, the most stable miRNAs were 126-3p in blood and liver, 101a in the gills, 192 in the kidney, 451 in the intestine and 22a in the brain, head kidney, spleen, heart, muscle, skin and fin. 126-3p was the most stable reference miRNA gene during developmental stages 1-5, while 22a was the most stable during developmental stages 6-18. Overall, this study provides valuable information about the reference miRNAs that can be used to perform appropriate normalizations when undertaking relative quantification in RT-qPCR studies of grass carp.

  10. Toward a reference standard for tissue phantoms

    NASA Astrophysics Data System (ADS)

    Di Ninni, Paola; Martelli, Fabrizio; Zaccanti, Giovanni

    2011-03-01

    A reference standard for tissue-simulating phantoms, i.e., a phantom with well known and stable optical properties, reproducible, and easy to be found, would be very useful for many applications based on measurements of diffused light. Although many tissue-equivalent phantoms have been proposed, to our knowledge none of them has been characterized sufficiently well to be suggested as a reference standard. Based on the results of measurements of optical properties we carried out at visible and NIR wavelengths, the use of Intralipid 20% diluted in water as diffusive medium, and of India ink as absorber, is here suggested as a first step towards a diffusive reference standard for tissue-simulating phantoms. As for Intralipid 20%, measurements carried out on samples from nine different batches with expiry dates spreading over ten years showed surprisingly small batch-to-batch variations. For the reduced scattering coefficient the maximum deviation from the value averaged over the nine batches was of about 2%, and the results for the absorption coefficient were very close to those for pure water. As for India ink measurements on samples from different batches and from five different brands showed large inter-brand and inter-batch variations for both the absorption and the extinction coefficient. On the contrary, small variations have been observed for the ratio between the absorption and the extinction coefficient. Intralipid 20% and Indian ink can be therefore easily mixed to obtain liquid phantoms with well known optical properties. This phantom can be a first step towards a reference standard for optical tissue phantoms.

  11. Multiscale quantification of tissue behavior during amniote embryo axis elongation.

    PubMed

    Bénazéraf, Bertrand; Beaupeux, Mathias; Tchernookov, Martin; Wallingford, Allison; Salisbury, Tasha; Shirtz, Amelia; Shirtz, Andrew; Huss, David; Pourquié, Olivier; François, Paul; Lansford, Rusty

    2017-08-23

    Embryonic axis elongation is a complex multi-tissue morphogenetic process responsible for the formation of the posterior part of the amniote body. How movements and growth are coordinated between the different posterior tissues (e.g. neural tube, axial and paraxial mesoderm, lateral plate, ectoderm, endoderm) to drive axis morphogenesis remain largely unknown. Here, we use quail embryos to quantify cell behavior and tissue movements during elongation. We quantify the tissue-specific contribution to axis elongation by using 3D volumetric techniques, then quantify tissue-specific parameters such as cell density and proliferation. To study cell behavior at a multi-tissue scale, we used high-resolution 4D imaging of transgenic quail embryos expressing fluorescent proteins. We developed specific tracking and image analysis techniques to analyze cell motion and compute tissue deformations in 4D. This analysis reveals extensive sliding between tissues during axis extension. Further quantification of tissue tectonics showed patterns of rotations, contractions and expansions, which are coherent with the multi-tissue behavior observed previously. Our approach defines a quantitative and multiscale method to analyze the coordination between tissue behaviors during early vertebrate embryo morphogenetic events. © 2017. Published by The Company of Biologists Ltd.

  12. Image quantification of high-throughput tissue microarray

    NASA Astrophysics Data System (ADS)

    Wu, Jiahua; Dong, Junyu; Zhou, Huiyu

    2006-03-01

    Tissue microarray (TMA) technology allows rapid visualization of molecular targets in thousands of tissue specimens at a time and provides valuable information on expression of proteins within tissues at a cellular and sub-cellular level. TMA technology overcomes the bottleneck of traditional tissue analysis and allows it to catch up with the rapid advances in lead discovery. Studies using TMA on immunohistochemistry (IHC) can produce a large amount of images for interpretation within a very short time. Manual interpretation does not allow accurate quantitative analysis of staining to be undertaken. Automatic image capture and analysis has been shown to be superior to manual interpretation. The aims of this work is to develop a truly high-throughput and fully automated image capture and analysis system. We develop a robust colour segmentation algorithm using hue-saturation-intensity (HSI) colour space to provide quantification of signal intensity and partitioning of staining on high-throughput TMA. Initial segmentation results and quantification data have been achieved on 16,000 TMA colour images over 23 different tissue types.

  13. Segmentation and quantification of adipose tissue by magnetic resonance imaging

    PubMed Central

    Chen, Jun; Shen, Wei

    2016-01-01

    In this brief review, introductory concepts in animal and human adipose tissue segmentation using proton magnetic resonance imaging (MRI) and computed tomography are summarized in the context of obesity research. Adipose tissue segmentation and quantification using spin relaxation-based (e.g., T1-weighted, T2-weighted), relaxometry-based (e.g., T1-, T2-, T2*-mapping), chemical-shift selective, and chemical-shift encoded water–fat MRI pulse sequences are briefly discussed. The continuing interest to classify subcutaneous and visceral adipose tissue depots into smaller sub-depot compartments is mentioned. The use of a single slice, a stack of slices across a limited anatomical region, or a whole body protocol is considered. Common image post-processing steps and emerging atlas-based automated segmentation techniques are noted. Finally, the article identifies some directions of future research, including a discussion on the growing topic of brown adipose tissue and related segmentation considerations. PMID:26336839

  14. Applications of 'TissueQuant'- a color intensity quantification tool for medical research.

    PubMed

    Prasad, Keerthana; P, Bhagath Kumar; Chakravarthy, Marx; Prabhu, Gopalakrishna

    2012-04-01

    This paper demonstrates the use of TissueQuant - an image analysis tool for quantification of color intensities which was developed for use in medical research where the stained biological specimen such as tissue or antigen needs to be quantified. TissueQuant provides facilities for user interaction to choose and quantify the color of interest and its shades. Gaussian weighting functions are used to provide a color score which quantifies how close the shade is to the user specified reference color. We describe two studies in medical research which use TissueQuant for quantification. The first study evaluated the effect of petroleum-ether extract of Cissus quadrangularis (CQ) on osteoporotic rats. It was found that the analysis results correlated well with the manual evaluation, p < 0.001. The second study evaluated the nerve morphometry and it was found that the adipose and non adipose tissue content was maximum in radial nerve among the five nerves studied. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  15. Quantification of Carbohydrates in Grape Tissues Using Capillary Zone Electrophoresis

    PubMed Central

    Zhao, Lu; Chanon, Ann M.; Chattopadhyay, Nabanita; Dami, Imed E.; Blakeslee, Joshua J.

    2016-01-01

    Soluble sugars play an important role in freezing tolerance in both herbaceous and woody plants, functioning in both the reduction of freezing-induced dehydration and the cryoprotection of cellular constituents. The quantification of soluble sugars in plant tissues is, therefore, essential in understanding freezing tolerance. While a number of analytical techniques and methods have been used to quantify sugars, most of these are expensive and time-consuming due to complex sample preparation procedures which require the derivatization of the carbohydrates being analyzed. Analysis of soluble sugars using capillary zone electrophoresis (CZE) under alkaline conditions with direct UV detection has previously been used to quantify simple sugars in fruit juices. However, it was unclear whether CZE-based methods could be successfully used to quantify the broader range of sugars present in complex plant extracts. Here, we present the development of an optimized CZE method capable of separating and quantifying mono-, di-, and tri-saccharides isolated from plant tissues. This optimized CZE method employs a column electrolyte buffer containing 130 mM NaOH, pH 13.0, creating a current of 185 μA when a separation voltage of 10 kV is employed. The optimized CZE method provides limits-of-detection (an average of 1.5 ng/μL) for individual carbohydrates comparable or superior to those obtained using gas chromatography–mass spectrometry, and allows resolution of non-structural sugars and cell wall components (structural sugars). The optimized CZE method was successfully used to quantify sugars from grape leaves and buds, and is a robust tool for the quantification of plant sugars found in vegetative and woody tissues. The increased analytical efficiency of this CZE method makes it ideal for use in high-throughput metabolomics studies designed to quantify plant sugars. PMID:27379118

  16. A novel enzyme immunoassay specific for ABCA1 protein quantification in human tissues and cells.

    PubMed

    Paul, Vijay; Meyer, Heinrich H D; Leidl, Katharina; Soumian, Soni; Albrecht, Christiane

    2008-10-01

    ATP-binding cassette transporter A1 (ABCA1) mediates the transport of cholesterol and phospholipids from cells to lipid-poor HDL and maintains cellular lipid homeostasis. Impaired ABCA1 function plays a role in lipid disorders, cardiovascular disease, atherosclerosis, and metabolic disorders. Despite the clinical importance of ABCA1, no method is available for quantifying ABCA1 protein. We developed a sensitive indirect competitive ELISA for measuring ABCA1 protein in human tissues using a commercial ABCA1 peptide and a polyclonal anti-ABCA1 antibody. The ELISA has a detection limit of 8 ng/well (0.08 mg/l) with a working range of 9-1000 ng/well (0.09-10 mg/l). Intra- and interassay coefficient of variations (CVs) were 6.4% and 9.6%, respectively. Good linearity (r = 0.97-0.99) was recorded in serial dilutions of human arterial and placental crude membrane preparations, and fibroblast lysates. The ELISA measurements for ABCA1 quantification in reference arterial tissues corresponded well with immunoblot analysis. The assay performance and clinical utility was evaluated with arterial tissues obtained from 15 controls and 44 patients with atherosclerotic plaques. ABCA1 protein concentrations in tissue lysates were significantly lower in patients (n = 24) as compared with controls (n = 5; 9.37 +/- 0.82 vs. 17.03 +/- 4.25 microg/g tissue; P < 0.01). The novel ELISA enables the quantification of ABCA1 protein in human tissues and confirms previous semiquantitative immunoblot results.

  17. En route to traceable reference standards for surface group quantifications by XPS, NMR and fluorescence spectroscopy.

    PubMed

    Hennig, Andreas; Dietrich, Paul M; Hemmann, Felix; Thiele, Thomas; Borcherding, Heike; Hoffmann, Angelika; Schedler, Uwe; Jäger, Christian; Resch-Genger, Ute; Unger, Wolfgang E S

    2015-03-21

    The fluorine content of polymer particles labelled with 2,2,2-trifluoroethylamine was reliably quantified with overlapping sensitivity ranges by XPS and solid-state NMR. This provides a first step towards reference materials for the metrological traceability of surface group quantifications. The extension of this concept to fluorescence spectroscopy is illustrated.

  18. The simplified reference tissue model with 18F-fallypride positron emission tomography: choice of reference region.

    PubMed

    Ishibashi, Kenji; Robertson, Chelsea L; Mandelkern, Mark A; Morgan, Andrew T; London, Edythe D

    2013-01-01

    The development of high-affinity radiotracers for positron emission tomography (PET) has allowed for quantification of dopamine receptors in extrastriatal and striatal regions of the brain. As these new radiotracers have distinctly different kinetic properties than their predecessors, it is important to examine the suitability of kinetic models to represent their uptake, distribution, and in vivo washout. Using the simplified reference tissue model, we investigated the influence of reference region choice on the striatal binding potential of 18F-fallypride, a high-affinity dopamine D2/D3 receptor ligand. We compared the use of the visual cortex and a white matter region (superior longitudinal fasciculus) to the cerebellum, a commonly used reference tissue, in a PET-fallypride study of healthy and methamphetamine-dependent subjects. Compared to the cerebellum, use of the visual cortex produced significantly greater sample variance in binding potential relative to nondisplaceable uptake (BP(ND)). Use of the white matter region was associated with BP(ND) values and sample variance similar to those obtained with the cerebellum and a larger effect size for the group differences in striatal BP(ND) between healthy and methamphetamine-dependent subjects. Our results do not support the use of the visual cortex as a reference region in 18F-fallypride studies and suggest that white matter may be a reasonable alternative to the cerebellum as it displays similar statistical and kinetic properties.

  19. Quantification of adipose tissue in a rodent model of obesity

    NASA Astrophysics Data System (ADS)

    Johnson, David H.; Flask, Chris; Wan, Dinah; Ernsberger, Paul; Wilson, David L.

    2006-03-01

    Obesity is a global epidemic and a comorbidity for many diseases. We are using MRI to characterize obesity in rodents, especially with regard to visceral fat. Rats were scanned on a 1.5T clinical scanner, and a T1W, water-spoiled image (fat only) was divided by a matched T1W image (fat + water) to yield a ratio image related to the lipid content in each voxel. The ratio eliminated coil sensitivity inhomogeneity and gave flat values across a fat pad, except for outlier voxels (> 1.0) due to motion. Following sacrifice, fat pad volumes were dissected and measured by displacement in canola oil. In our study of 6 lean (SHR), 6 dietary obese (SHR-DO), and 9 genetically obese rats (SHROB), significant differences in visceral fat volume was observed with an average of 29+/-16 ml increase due to diet and 84+/-44 ml increase due to genetics relative to lean control with a volume of 11+/-4 ml. Subcutaneous fat increased 14+/-8 ml due to diet and 198+/-105 ml due to genetics relative to the lean control with 7+/-3 ml. Visceral fat strongly correlated between MRI and dissection (R2 = 0.94), but MRI detected over five times the subcutaneous fat found with error-prone dissection. Using a semi-automated images segmentation method on the ratio images, intra-subject variation was very low. Fat pad composition as estimated from ratio images consistently differentiated the strains with SHROB having a greater lipid concentration in adipose tissues. Future work will include in vivo studies of diet versus genetics, identification of new phenotypes, and corrective measures for obesity; technical efforts will focus on correction for motion and automation in quantification.

  20. Reference Materials for Calibration of Analytical Biases in Quantification of DNA Methylation

    PubMed Central

    Yu, Hannah; Hahn, Yoonsoo; Yang, Inchul

    2015-01-01

    Most contemporary methods for the quantification of DNA methylation employ bisulfite conversion and PCR amplification. However, many reports have indicated that bisulfite-mediated PCR methodologies can result in inaccurate measurements of DNA methylation owing to amplification biases. To calibrate analytical biases in quantification of gene methylation, especially those that arise during PCR, we utilized reference materials that represent exact bisulfite-converted sequences with 0% and 100% methylation status of specific genes. After determining relative quantities using qPCR, pairs of plasmids were gravimetrically mixed to generate working standards with predefined DNA methylation levels at 10% intervals in terms of mole fractions. The working standards were used as controls to optimize the experimental conditions and also as calibration standards in melting-based and sequencing-based analyses of DNA methylation. Use of the reference materials enabled precise characterization and proper calibration of various biases during PCR and subsequent methylation measurement processes, resulting in accurate measurements. PMID:26368560

  1. Mouse spleen tissue as a staining intensity reference for immunohistochemistry.

    PubMed

    Moon, Yeonsook; Park, Gyeongsin; Han, Kyungja; Kang, Chang-Suk; Lee, Wonbae

    2008-01-01

    Immunohistochemistry (IHC) is widely used in diagnostic practice and research, but it is limited due to its subjective nature and weakness in reproducibility. For successful interpretation, IHC requires an internal reference system that controls for procedural variables and provides a staining intensity reference. We investigated the feasibility of using mouse spleen tissue as an intensity reference in conventional IHC. Formalin-fixed, paraffin-embedded mouse (BALB/c) spleen tissue was stained with variable procedural conditions including primary antibody (Ab) types, antigen retrieval methods, chromogen exposure times, and secondary Ab concentrations. Mouse spleen tissue showed identical staining intensity regardless of primary Ab types, even without primary Ab, and showed minimal differences according to retrieval methods. However, it showed various staining intensities according to chromogen exposure time and secondary Ab concentration. When mouse spleen was included in tissue microarrays and compared with the c-erbB2 IHC scoring system, splenic B cells showed weak membrane staining compatible with score 1+, whereas splenic plasma cells showed strong staining intensity compatible with score 3+. These results show that mouse spleen tissue can serve as a staining intensity reference for the interpretation of IHC.

  2. Development of automated quantification of visceral and subcutaneous adipose tissue volumes from abdominal CT scans

    NASA Astrophysics Data System (ADS)

    Mensink, Sanne D.; Spliethoff, Jarich W.; Belder, Ruben; Klaase, Joost M.; Bezooijen, Roland; Slump, Cornelis H.

    2011-03-01

    This contribution describes a novel algorithm for the automated quantification of visceral and subcutaneous adipose tissue volumes from abdominal CT scans of patients referred for colorectal resection. Visceral and subcutaneous adipose tissue volumes can accurately be measured with errors of 1.2 and 0.5%, respectively. Also the reproducibility of CT measurements is good; a disadvantage is the amount of radiation. In this study the diagnostic CT scans in the work - up of (colorectal) cancer were used. This implied no extra radiation. For the purpose of segmentation alone, a low dose protocol can be applied. Obesity is a well known risk factor for complications in and after surgery. Body Mass Index (BMI) is a widely accepted indicator of obesity, but it is not specific for risk assessment of colorectal surgery. We report on an automated method to quantify visceral and subcutaneous adipose tissue volumes as a basic step in a clinical research project concerning preoperative risk assessment. The outcomes are to be correlated with the surgery results. The hypothesis is that the balance between visceral and subcutaneous adipose tissue together with the presence of calcifications in the major bloodvessels, is a predictive indicator for post - operatieve complications such as anastomotic leak. We start with four different computer simulated humanoid abdominal volumes with tissue values in the appropriate Hounsfield range at different dose levels. With satisfactory numerical results for this test, we have applied the algorithm on over a 100 patient scans and have compared results with manual segmentations by an expert for a smaller pilot group. The results are within a 5% difference. Compared to other studies reported in the literature, reliable values are obtained for visceral and subcutaneous adipose tissue areas.

  3. Reference genes for quantitative PCR in the adipose tissue of mice with metabolic disease.

    PubMed

    Almeida-Oliveira, Fernanda; Leandro, João G B; Ausina, Priscila; Sola-Penna, Mauro; Majerowicz, David

    2017-04-01

    Obesity and diabetes are metabolic diseases and they are increasing in prevalence. The dynamics of gene expression associated with these diseases is fundamental to identifying genes involved in related biological processes. qPCR is a sensitive technique for mRNA quantification and the most commonly used method in gene-expression studies. However, the reliability of these results is directly influenced by data normalization. As reference genes are the major normalization method used, this work aims to identify reference genes for qPCR in adipose tissues of mice with type-I diabetes or obesity. We selected 12 genes that are commonly used as reference genes. The expression of these genes in the adipose tissues of mice was analyzed in the context of three different experimental protocols: 1) untreated animals; 2) high-fat-diet animals; and 3) streptozotocin-treated animals. Gene-expression stability was analyzed using four different algorithms. Our data indicate that TATA-binding protein is stably expressed across adipose tissues in control animals. This gene was also a useful reference when the brown adipose tissues of control and obese mice were analyzed. The mitochondrial ATP synthase F1 complex gene exhibits stable expression in subcutaneous and perigonadal adipose tissue from control and obese mice. Moreover, this gene is the best reference for qPCR normalization in adipose tissue from streptozotocin-treated animals. These results show that there is no perfect stable gene suited for use under all experimental conditions. In conclusion, the selection of appropriate genes is a prerequisite to ensure qPCR reliability and must be performed separately for different experimental protocols.

  4. Evaluation of the reliability of maize reference assays for GMO quantification.

    PubMed

    Papazova, Nina; Zhang, David; Gruden, Kristina; Vojvoda, Jana; Yang, Litao; Buh Gasparic, Meti; Blejec, Andrej; Fouilloux, Stephane; De Loose, Marc; Taverniers, Isabel

    2010-03-01

    A reliable PCR reference assay for relative genetically modified organism (GMO) quantification must be specific for the target taxon and amplify uniformly along the commercialised varieties within the considered taxon. Different reference assays for maize (Zea mays L.) are used in official methods for GMO quantification. In this study, we evaluated the reliability of eight existing maize reference assays, four of which are used in combination with an event-specific polymerase chain reaction (PCR) assay validated and published by the Community Reference Laboratory (CRL). We analysed the nucleotide sequence variation in the target genomic regions in a broad range of transgenic and conventional varieties and lines: MON 810 varieties cultivated in Spain and conventional varieties from various geographical origins and breeding history. In addition, the reliability of the assays was evaluated based on their PCR amplification performance. A single base pair substitution, corresponding to a single nucleotide polymorphism (SNP) reported in an earlier study, was observed in the forward primer of one of the studied alcohol dehydrogenase 1 (Adh1) (70) assays in a large number of varieties. The SNP presence is consistent with a poor PCR performance observed for this assay along the tested varieties. The obtained data show that the Adh1 (70) assay used in the official CRL NK603 assay is unreliable. Based on our results from both the nucleotide stability study and the PCR performance test, we can conclude that the Adh1 (136) reference assay (T25 and Bt11 assays) as well as the tested high mobility group protein gene assay, which also form parts of CRL methods for quantification, are highly reliable. Despite the observed uniformity in the nucleotide sequence of the invertase gene assay, the PCR performance test reveals that this target sequence might occur in more than one copy. Finally, although currently not forming a part of official quantification methods, zein and SSIIb

  5. Identification of Reference Genes for RT-qPCR Data Normalization in Cannabis sativa Stem Tissues

    PubMed Central

    Mangeot-Peter, Lauralie; Legay, Sylvain; Hausman, Jean-Francois; Esposito, Sergio; Guerriero, Gea

    2016-01-01

    Gene expression profiling via quantitative real-time PCR is a robust technique widely used in the life sciences to compare gene expression patterns in, e.g., different tissues, growth conditions, or after specific treatments. In the field of plant science, real-time PCR is the gold standard to study the dynamics of gene expression and is used to validate the results generated with high throughput techniques, e.g., RNA-Seq. An accurate relative quantification of gene expression relies on the identification of appropriate reference genes, that need to be determined for each experimental set-up used and plant tissue studied. Here, we identify suitable reference genes for expression profiling in stems of textile hemp (Cannabis sativa L.), whose tissues (isolated bast fibres and core) are characterized by remarkable differences in cell wall composition. We additionally validate the reference genes by analysing the expression of putative candidates involved in the non-oxidative phase of the pentose phosphate pathway and in the first step of the shikimate pathway. The goal is to describe the possible regulation pattern of some genes involved in the provision of the precursors needed for lignin biosynthesis in the different hemp stem tissues. The results here shown are useful to design future studies focused on gene expression analyses in hemp. PMID:27649158

  6. Identification of Reference Genes for RT-qPCR Data Normalization in Cannabis sativa Stem Tissues.

    PubMed

    Mangeot-Peter, Lauralie; Legay, Sylvain; Hausman, Jean-Francois; Esposito, Sergio; Guerriero, Gea

    2016-09-15

    Gene expression profiling via quantitative real-time PCR is a robust technique widely used in the life sciences to compare gene expression patterns in, e.g., different tissues, growth conditions, or after specific treatments. In the field of plant science, real-time PCR is the gold standard to study the dynamics of gene expression and is used to validate the results generated with high throughput techniques, e.g., RNA-Seq. An accurate relative quantification of gene expression relies on the identification of appropriate reference genes, that need to be determined for each experimental set-up used and plant tissue studied. Here, we identify suitable reference genes for expression profiling in stems of textile hemp (Cannabis sativa L.), whose tissues (isolated bast fibres and core) are characterized by remarkable differences in cell wall composition. We additionally validate the reference genes by analysing the expression of putative candidates involved in the non-oxidative phase of the pentose phosphate pathway and in the first step of the shikimate pathway. The goal is to describe the possible regulation pattern of some genes involved in the provision of the precursors needed for lignin biosynthesis in the different hemp stem tissues. The results here shown are useful to design future studies focused on gene expression analyses in hemp.

  7. A regularized full reference tissue model for PET neuroreceptor mapping.

    PubMed

    Mandeville, Joseph B; Sander, Christin Y M; Wey, Hsiao-Ying; Hooker, Jacob M; Hansen, Hanne D; Svarer, Claus; Knudsen, Gitte M; Rosen, Bruce R

    2016-06-27

    The full reference tissue model (FRTM) is a PET analysis framework that includes both free and specifically bound compartments within tissues, together with rate constants defining association and dissociation from the specifically bound compartment. The simplified reference tissue model (SRTM) assumes instantaneous exchange between tissue compartments, and this "1-tissue" approximation reduces the number of parameters and enables more robust mapping of non-displaceable binding potentials. Simulations based upon FRTM have shown that SRTM exhibits biases that are spatially dependent, because biases depend upon binding potentials. In this work, we describe a regularized model (rFRTM) that employs a global estimate of the dissociation rate constant from the specifically bound compartment (k4). The model provides an internal calibration for optimizing k4 through the reference-region outflow rate k2', a model parameter that should be a global constant but varies regionally in SRTM. Estimates of k4 by rFRTM are presented for four PET radioligands. We show that SRTM introduces bias in parameter estimates by assuming an infinite value for k4, and that rFRTM ameliorates bias with an appropriate choice of k4. Theoretical considerations and simulations demonstrate that rFRTM reduces bias in non-displaceable binding potentials. A two-parameter reduction of the model (rFRTM2) provides robust mapping at a voxel-wise level. With a structure similar to SRTM, the model is easily implemented and can be applied as a PET reference region analysis that reduces parameter bias without substantially altering parameter variance.

  8. [Quantification of carotenoids of spirilloxanthin series from anoxygenic phototrophic bacteria by substitute reference standard calibration function method].

    PubMed

    Zhao, Chungui; Zhuo, Minquan; Yang, Suping

    2014-02-04

    In this study, we developed a strategy for accurate, rapid and simultaneous quantification of six carotenoids by substitute reference standard. We prepared six carotenoid standards of spirilloxanthin series from Rhodopesudomonnas palustris CQV97 by spectrophotometry, thin layer chromatography and HPLC. The simultaneous quantification method for six carotenoids was established by HPLC using tartrazine and lycopene as substitute reference standards. We established the HPLC fingerprinting of carotenoids of spirilloxanthin series. The quantitative calibration function relationships between two substitute reference standards and six carotenoids were explored. Based on the quantitative calibration function relationships, we quantitatively analyzed carotenoid contents of two samples of CQV97 and YL28 strains. The RSD and recovery of carotenoid contents determined by substitute reference standards method were consistent with quantitative analysis of carotenoid standards method. The substitute reference standards were capable of accurately transmitting the quantitative relationship of tested samples. The method could realize the simultaneous quantification of six carotenoids.

  9. Quantification of tissue oxygenation levels using diffuse reflectance spectroscopy

    NASA Astrophysics Data System (ADS)

    B. S., Suresh Anand; N., Sujatha

    2010-12-01

    Tumor growth is characterized by increased metabolic activity. The light absorption profile of hemoglobin in dysplastic tissue is different from a normal tissue. Neovascularization is a hallmark of many diseases and can serve as a predictive biomarker for the detection of cancers. Spectroscopic techniques can provide information about the metabolic and morphological changes related to the progression of neoplasia. Diffuse reflectance spectroscopy (DRS) measures the absorption and scattering properties of a biological tissue and this method can provide clinically useful information for the early diagnosis of epithelial precancers. We used tissue simulating phantoms with absorbing and scattering molecules for the determination of total hemoglobin concentration, hemoglobin oxygen saturation and intensity difference between the deoxy and oxy hemoglobin bands. The results show promising approach for the differentiating normal and malignant states of a tissue.

  10. Quantification of tissue oxygenation levels using diffuse reflectance spectroscopy

    NASA Astrophysics Data System (ADS)

    B. S., Suresh Anand; N., Sujatha

    2011-08-01

    Tumor growth is characterized by increased metabolic activity. The light absorption profile of hemoglobin in dysplastic tissue is different from a normal tissue. Neovascularization is a hallmark of many diseases and can serve as a predictive biomarker for the detection of cancers. Spectroscopic techniques can provide information about the metabolic and morphological changes related to the progression of neoplasia. Diffuse reflectance spectroscopy (DRS) measures the absorption and scattering properties of a biological tissue and this method can provide clinically useful information for the early diagnosis of epithelial precancers. We used tissue simulating phantoms with absorbing and scattering molecules for the determination of total hemoglobin concentration, hemoglobin oxygen saturation and intensity difference between the deoxy and oxy hemoglobin bands. The results show promising approach for the differentiating normal and malignant states of a tissue.

  11. Quantification of petroleum-type hydrocarbons in avian tissue

    USGS Publications Warehouse

    Gay, M.L.; Belisle, A.A.; Patton, J.F.

    1980-01-01

    Summary: Methods were developed for the analysis of 16 hydrocarbons in avian tissue. Mechanical extraction with pentane was followed by clean-up on Florisil and Silicar. Residues were determined by gas--liquid chromatography and gas-liquid, chromatography-mass spectrometry. The method was applied to the analysis of liver, kidney, fat, and brain tissue of mallard ducks (Anas platyrhynchos) fed a mixture of hydrocarbons. Measurable concentrations of all compounds analyzed were present in all tissues except brain. Highest concentrations were in fat.

  12. Evaluation of the ERETIC method as an improved quantitative reference for 1H HR-MAS spectroscopy of prostate tissue.

    PubMed

    Albers, Mark J; Butler, Thomas N; Rahwa, Iman; Bao, Nguyen; Keshari, Kayvan R; Swanson, Mark G; Kurhanewicz, John

    2009-03-01

    The Electronic REference To access In vivo Concentrations (ERETIC) method was applied to (1)H HR-MAS spectroscopy. The accuracy, precision, and stability of ERETIC as a quantitative reference were evaluated in solution and human prostate tissue samples. For comparison, the reliability of 3-(trimethylsilyl)propionic-2,2,3,3-d(4) acid (TSP) as a quantitation reference was also evaluated. The ERETIC and TSP peak areas were found to be stable in solution over the short-term and long-term, with long-term relative standard deviations (RSDs) of 4.10% and 2.60%, respectively. Quantification of TSP in solution using the ERETIC peak as a reference and a calibrated, rotor-dependent conversion factor yielded results with a precision < or =2.9% and an accuracy error < or =4.2% when compared with the expected values. The ERETIC peak area reproducibility was superior to TSP's reproducibility, corrected for mass, in both prostate surgical and biopsy samples (4.53% vs. 21.2% and 3.34% vs. 31.8%, respectively). Furthermore, the tissue TSP peaks exhibited only 27.5% of the expected area, which would cause an overestimation of metabolite concentrations if used as a reference. The improved quantification accuracy and precision provided by ERETIC may enable the detection of smaller metabolic differences that may exist between individual tissue samples and disease states.

  13. Quantification and Segmentation of Brain Tissues from MR Images: A Probabilistic Neural Network Approach

    PubMed Central

    Wang, Yue; Adalý, Tülay; Kung, Sun-Yuan; Szabo, Zsolt

    2007-01-01

    This paper presents a probabilistic neural network based technique for unsupervised quantification and segmentation of brain tissues from magnetic resonance images. It is shown that this problem can be solved by distribution learning and relaxation labeling, resulting in an efficient method that may be particularly useful in quantifying and segmenting abnormal brain tissues where the number of tissue types is unknown and the distributions of tissue types heavily overlap. The new technique uses suitable statistical models for both the pixel and context images and formulates the problem in terms of model-histogram fitting and global consistency labeling. The quantification is achieved by probabilistic self-organizing mixtures and the segmentation by a probabilistic constraint relaxation network. The experimental results show the efficient and robust performance of the new algorithm and that it outperforms the conventional classification based approaches. PMID:18172510

  14. Evaluation of endogenous references for gene expression profiling in different tissues of the oriental fruit fly Bactrocera dorsalis (Diptera: Tephritidae)

    PubMed Central

    2010-01-01

    Background Quantitative real-time reverse transcriptase PCR (RT-qPCR) has been widely used for quantification of mRNA as a way to determine key genes involved in different biological processes. For accurate gene quantification analysis, normalization of RT-qPCR data is absolutely essential. To date, normalization is most frequently achieved by the use of internal controls, often referred to as reference genes. However, several studies have shown that the reference genes used for the quantification of mRNA expression can be affected by the experimental set-up or cell type resulting in variation of the expression level of these key genes. Therefore, the evaluation of reference genes is critical for gene expression profiling, which is often neglected in gene expression studies of insects. For this purpose, ten candidate reference genes were investigated in three different tissues (midgut, Malpighian tubules, and fat body) of the oriental fruit fly, Bactrocera dorsalis (Hendel). Results Two different programs, geNorm and Normfinder, were used to analyze the data. According to geNorm, α-TUB + ACT5 are the most appropriate reference genes for gene expression profiling across the three different tissues in the female flies, while ACT3 + α-TUB are considered as the best for males. Furthermore, we evaluated the stability of the candidate reference genes to determine the sexual differences in the same tissue. In the midgut and Malpighian tubules, ACT2 + α-TUB are the best choice for both males and females. However, α-TUB + ACT1 are the best pair for fat body. Meanwhile, the results calculated by Normfinder are quite the same as the results with geNorm; α-TUB is always one of the most stable genes in each sample validated by the two programs. Conclusions In this study, we validated the suitable reference genes for gene expression profiling in different tissues of B. dorsalis. Moreover, appropriate reference genes were selected out for gene expression profiling of the

  15. Proposal for C-Hordein as Reference Material in Gluten Quantification.

    PubMed

    Huang, Xin; Kanerva, Päivi; Salovaara, Hannu; Stoddard, Frederick L; Sontag-Strohm, Tuula

    2017-03-15

    The concentration of residual barley prolamin (hordein) in gluten-free products is overestimated by the R5 ELISA method when calibrated against the wheat gliadin standard. The reason for this may be that the composition of the gliadin standard is different from the composition of hordeins. This study showed that the recognition of whole hordein by R5 antibody mainly came from C-hordein, which is more reactive than the other hordeins. The proportion of C-hordein in total hordein ranged from 16 to 33% of common Finnish barley cultivars used in this study and was always higher than that of ω-gliadin, the homologous protein class in the gliadin standard, which may account for the overestimation. Thus, a hordein standard is needed for barley prolamin quantification instead of the gliadin standard. When gluten-free oat flour was spiked with barley flour, the prolamin concentration was overestimated 1.8-2.5 times with the gliadin standard, whereas estimates in the correct range were obtained when the standard was 40% C-hordein mixed with an inert protein. A preparative-scale method was developed to isolate and purify C-hordein, and C-hordein is proposed as a reference material to calibrate barley prolamin quantification in R5-based assays.

  16. Quantification of tissue texture with photoacoustic spectrum analysis

    NASA Astrophysics Data System (ADS)

    Wang, Xueding; Xu, Guan; Meng, Zhuo-Xian; Lin, Jiandie; Carson, Paul

    2014-05-01

    Photoacoustic (PA) imaging is an emerging technology that could map the functional contrasts in deep biological tissues in high resolution by "listening" to the laser induced thermoelastic waves. Almost all of the current studies in PA imaging are focused on the intensity of the PA signals as an indication of the optical absorbance of the biological tissues. Our group has for the first time demonstrated that the frequency domain power distribution of the broadband PA signals encode the texture information within the regions-of-interest (ROI). Following the similar method of ultrasound spectral analysis (USSA), photoacoustic spectrum analysis (PASA) could evaluate the relative concentrations and, more importantly, the dimensions of microstructures of the optically absorbing materials in biological tissues, including lipid, collagen, water and hemoglobin. By providing valuable insights into tissue pathology, PASA should benefit basic research and clinical management of many diseases, and may help achieve eventual "noninvasive biopsy". In this work, taking advantage of the optical absorption contrasts contributed by lipid and hemoglobin at 1200-nm and 532-nm wavelengths respectively, we investigated the capability of PASA in identifying histological changes corresponding to fat accumulation livers through the study on ex vivo and in situ mouse models. The PA signals from the mouse livers were acquired using our PA and US dual-modality imaging system, and analyzed in the frequency domain. After quantifying the power spectrum by fitting it to a first order model, three spectral parameters, including the intercept, the midband fit and the slope, were extracted and used to differentiate fatty livers from normal livers. The comparison between the PASA parameters from the normal and the fatty livers supports our hypotheses that PASA can quantitatively identify the microstructure changes in liver tissues for differentiating normal and fatty livers.

  17. Automatic Segmentation and Quantification of White and Brown Adipose Tissues from PET/CT Scans.

    PubMed

    Hussein, Sarfaraz; Green, Aileen; Watane, Arjun; Reiter, David; Chen, Xinjian; Papadakis, Georgios Z; Wood, Bradford; Cypess, Aaron; Osman, Medhat; Bagci, Ulas

    2016-12-06

    In this paper, we investigate the automatic detection of white and brown adipose tissues using Positron Emission Tomography/ Computed Tomography (PET/CT) scans, and develop methods for the quantification of these tissues at the whole-body and body-region levels. We propose a patient-specific automatic adiposity analysis system with two modules. In the first module, we detect white adipose tissue (WAT) and its two sub-types from CT scans: Visceral Adipose Tissue (VAT) and Subcutaneous Adipose Tissue (SAT). This process relies conventionally on manual or semi-automated segmentation, leading to inefficient solutions. Our novel framework addresses this challenge by proposing an unsupervised learning method to separate VAT from SAT in the abdominal region for the clinical quantification of central obesity. This step is followed by a context driven label fusion algorithm through sparse 3D Conditional Random Fields (CRF) for volumetric adiposity analysis. In the second module, we automatically detect, segment, and quantify brown adipose tissue (BAT) using PET scans because unlike WAT, BAT is metabolically active. After identifying BAT regions using PET, we perform a co-segmentation procedure utilizing asymmetric complementary information from PET and CT. Finally, we present a new probabilistic distance metric for differentiating BAT from non-BAT regions. Both modules are integrated via an automatic body-region detection unit based on one-shot learning. Experimental evaluations conducted on 151 PET/CT scans achieve state-of-the-art performances in both central obesity as well as brown adiposity quantification.

  18. Quantification of pork, chicken and beef by using a novel reference molecule.

    PubMed

    Sakai, Yumiko; Kotoura, Satoshi; Yano, Takeo; Kurihara, Takashi; Uchida, Kouji; Miake, Kiyotaka; Akiyama, Hiroshi; Tanabe, Soichi

    2011-01-01

    A standard plasmid was constructed as a novel reference molecule for use in real-time quantitative PCR assays to verify the identity of beef, pork, chicken, mutton, and horseflesh. The plasmid contained a target domain of the cytochrome b (cyt b) gene and an artificial DNA sequence. Primers CO-F and CO-R, and probe CO-P were specifically designed to detect the artificial sequence. The calculated R² values of the standard curves (10³-10⁷ copies per reaction) for the five species ranged between 0.998 and 0.999 in the quantification analysis. The constructed plasmid provides a universal method for measuring the copy number of cyt b DNA in minced meat. This method would be a useful procedure for verifying food labels.

  19. Quantification of Histamine and Carcinine in Drosophila melanogaster Tissues.

    PubMed

    Denno, Madelaine E; Privman, Eve; Borman, Ryan P; Wolin, Danielle C; Venton, B Jill

    2016-03-16

    Histamine is a neurotransmitter crucial to the visual processing of Drosophila melanogaster. It is inactivated by metabolism to carcinine, a β-alanyl derivative, and the same enzyme that controls that process also converts dopamine to N-β-alanyl-dopamine. Direct detection of histamine and carcinine has not been reported in single Drosophila brains. Here, we quantify histamine, carcinine, dopamine, and N-β-alanyl-dopamine in Drosophila tissues by capillary electrophoresis coupled to fast-scan cyclic voltammetry (CE-FSCV). Limits of detection were low, 4 ± 1 pg for histamine, 10 ± 4 pg for carcinine, 2.8 ± 0.3 pg for dopamine, and 9 ± 3 pg for N-β-alanyl-dopamine. Tissue content was compared in the brain, eyes, and cuticle from wild-type (Canton S) and mutant (tan(3) and ebony(1)) strains. In tan(3) mutants, the enzyme that produces histamine from carcinine is nonfunctional, whereas in ebony(1) mutants, the enzyme that produces carcinine from histamine is nonfunctional. In all fly strains, the neurotransmitter content was highest in the eyes and there were no strain differences for tissue content in the cuticle. The main finding was that carcinine levels changed significantly in the mutant flies, whereas histamine levels did not. In particular, tan(3) flies had significantly higher carcinine levels in the eyes and brain than Canton S or ebony(1) flies. N-β-Alanyl-dopamine was detected in tan(3) mutants but not in other strains. These results show the utility of CE-FSCV for sensitive detection of histamine and carcinine, which allows a better understanding of their content and metabolism in different types of tissues to be obtained.

  20. Quantification of human body fat tissue percentage by MRI.

    PubMed

    Müller, Hans-Peter; Raudies, Florian; Unrath, Alexander; Neumann, Heiko; Ludolph, Albert C; Kassubek, Jan

    2011-01-01

    The MRI-based evaluation of the quantity and regional distribution of adipose tissue is one objective measure in the investigation of obesity. The aim of this article was to report a comprehensive and automatic analytical method for the determination of the volumes of subcutaneous fat tissue (SFT) and visceral fat tissue (VFT) in either the whole human body or selected slices or regions of interest. Using an MRI protocol in an examination position that was convenient for volunteers and patients with severe diseases, 22 healthy subjects were examined. The software platform was able to merge MRI scans of several body regions acquired in separate acquisitions. Through a cascade of image processing steps, SFT and VFT volumes were calculated. Whole-body SFT and VFT distributions, as well as fat distributions of defined body slices, were analysed in detail. Complete three-dimensional datasets were analysed in a reproducible manner with as few operator-dependent interventions as possible. In order to determine the SFT volume, the ARTIS (Adapted Rendering for Tissue Intensity Segmentation) algorithm was introduced. The advantage of the ARTIS algorithm was the delineation of SFT volumes in regions in which standard region grow techniques fail. Using the ARTIS algorithm, an automatic SFT volume detection was feasible. MRI data analysis was able to determine SFT and VFT volume percentages using new analytical strategies. With the techniques described, it was possible to detect changes in SFT and VFT percentages of the whole body and selected regions. The techniques presented in this study are likely to be of use in obesity-related investigations, as well as in the examination of longitudinal changes in weight during various medical conditions.

  1. Quantification of the edge effect in calcified bioprosthetic tissues.

    PubMed

    Wika, K E; Utoh, J; Brown, J; Harasaki, H

    1993-10-01

    In bioprosthetic tissue samples that had been implanted in the subcutaneous space of rats, and recurring pattern of calcification was observed. In this pattern, which we call the edge effect, the interior of the tissue is calcified and is surrounded and separated from the subcutaneous fluid by a zone that is free from calcification. The edge effect has been qualitatively described in the literature for subcutaneous implants and for valve leaflets, and it may be related to the mechanism of calcification for these materials. The thickness of the calcification free outer layer was quantified for glutaraldehyde treated bovine pericardium, glycerol treated bovine pericardium, glutaraldehyde treated human dura mater, and glycerol treated human dura mater. The edge effect values were found to be unique and consistent for each material type, and they were inversely related to the shrinkage temperatures and the calcium contents of the materials. It was determined that the chemical treatment was more important than the tissue type in determining the edge effect value.

  2. Quantification of retinoid concentrations in human serum and brain tumor tissues.

    PubMed

    Ali, Ramadan; Campos, Benito; Dyckhoff, Gerhard; Haefeli, Walter E; Herold-Mende, Christel; Burhenne, Jürgen

    2012-05-06

    Retinoic acid signaling is essential for central nervous system (CNS) differentiation and appears to be impaired in tumors. Thus far, there are no established methods to quantify relevant retinoids (all-trans-retinoic acid, 9-cis-retinoic acid, 13-cis retinoic acid, and retinol) in human brain tumors. We developed a single step extraction and quantification procedure for polar and apolar retinoids in normal tissue, lipid-rich brain tumor tissues, and serum. This quantification procedure is based on high performance liquid chromatography (HPLC) with diode-array detection (DAD) using all-trans-acitretin as an internal standard and extraction by liquid-liquid partition with ethyl acetate and borate buffer at pH 9. Recovery with this extraction procedure was higher than earlier (two-step) liquid-liquid extraction procedures based on hexane, NaOH, and HCl. The overall quantification procedure was validated according to Food and Drug Administration (FDA) guidelines and fulfilled all criteria of accuracy, precision, selectivity, recovery, and stability. The overall method accuracy varied between -5.6% and +5.4% for serum and -3.8% and +6.2% for tissues, and overall precision ranged from 3.1% to 6.9% for serum and 2.1% to 8.3% for tissues (%CV batch-to-batch). The lower limit of quantification for all compounds in tumor tissue (and serum) was 3.9 ng g(-1) (ng mL(-1)). Using this assay, photodegradation of the retinoids was evaluated and endogenous polar and apolar retinoids were quantified in sera and brain tumor tissues of patients and compared with serum and tonsil tissue concentrations of controls. It may thus serve as a suitable method for the characterization of retinoid uptake and metabolism in the respective compartments. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Comparison of Virtual Touch Tissue Quantification and Virtual Touch Tissue Imaging Quantification for diagnosis of solid breast tumors of different sizes.

    PubMed

    Chen, Ying-Pei; Han, Ting; Wu, Rong; Yao, Ming-Hua; Xu, Guang; Zhao, Li-Xia; Liu, Hui; Pu, Huan; Fang, Yan

    2016-11-25

    Acoustic radiation force impulse imaging (ARFI) with Virtual Touch Tissue Quantification (VTQ) or Virtual Touch Tissue Imaging Quantification (VTIQ) measures shear wave velocity (SWV), which is proportional to tissue stiffness, a diagnostic parameter for malignancy. To compare the performance of VTQ and VTIQ in diagnosing solid breast tumors. Conventional ultrasound, VTQ and VTIQ were used to examine 246 solid breast tumors from 230 patients. Tumors were grouped according to size: <10 mm, 10-20 mm, >20 mm. Pathological diagnoses were via histological examination of biopsies. ROC curves were used to assess diagnostic performance and optimal cut-off points for VTQ and VTIQ. For all sizes, SWVVTQ and SWVVTIQ were higher for malignant versus benign tumors (P < 0.05). SWVVTQ and SWVVTIQ were both higher for tumors≥10 mm (P < 0.05). Areas under the ROC curves (diagnostic performance index; 0.860-0.952) did not differ significantly between VTQ and VTIQ. Optimal cut-off values for SWVVTQ and SWVVTIQ were higher for tumors≥10 mm. The diagnostic performance of VTQ and VTIQ was moderate to good for solid breast tumors. Although both methods have higher sensitivities in tumors≥10 mm, their overall diagnostic performance was similar for all sizes.

  4. 18O-labeled proteome reference as global internal standards for targeted quantification by selected reaction monitoring-mass spectrometry.

    PubMed

    Kim, Jong-Seo; Fillmore, Thomas L; Liu, Tao; Robinson, Errol; Hossain, Mahmud; Champion, Boyd L; Moore, Ronald J; Camp, David G; Smith, Richard D; Qian, Wei-Jun

    2011-12-01

    Selected reaction monitoring (SRM)-MS is an emerging technology for high throughput targeted protein quantification and verification in biomarker discovery studies; however, the cost associated with the application of stable isotope-labeled synthetic peptides as internal standards can be prohibitive for screening a large number of candidate proteins as often required in the preverification phase of discovery studies. Herein we present a proof of concept study using an (18)O-labeled proteome reference as global internal standards (GIS) for SRM-based relative quantification. The (18)O-labeled proteome reference (or GIS) can be readily prepared and contains a heavy isotope ((18)O)-labeled internal standard for every possible tryptic peptide. Our results showed that the percentage of heavy isotope ((18)O) incorporation applying an improved protocol was >99.5% for most peptides investigated. The accuracy, reproducibility, and linear dynamic range of quantification were further assessed based on known ratios of standard proteins spiked into the labeled mouse plasma reference. Reliable quantification was observed with high reproducibility (i.e. coefficient of variance <10%) for analyte concentrations that were set at 100-fold higher or lower than those of the GIS based on the light ((16)O)/heavy ((18)O) peak area ratios. The utility of (18)O-labeled GIS was further illustrated by accurate relative quantification of 45 major human plasma proteins. Moreover, quantification of the concentrations of C-reactive protein and prostate-specific antigen was illustrated by coupling the GIS with standard additions of purified protein standards. Collectively, our results demonstrated that the use of (18)O-labeled proteome reference as GIS provides a convenient, low cost, and effective strategy for relative quantification of a large number of candidate proteins in biological or clinical samples using SRM.

  5. 18O-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry*

    PubMed Central

    Kim, Jong-Seo; Fillmore, Thomas L.; Liu, Tao; Robinson, Errol; Hossain, Mahmud; Champion, Boyd L.; Moore, Ronald J.; Camp, David G.; Smith, Richard D.; Qian, Wei-Jun

    2011-01-01

    Selected reaction monitoring (SRM)-MS is an emerging technology for high throughput targeted protein quantification and verification in biomarker discovery studies; however, the cost associated with the application of stable isotope-labeled synthetic peptides as internal standards can be prohibitive for screening a large number of candidate proteins as often required in the preverification phase of discovery studies. Herein we present a proof of concept study using an 18O-labeled proteome reference as global internal standards (GIS) for SRM-based relative quantification. The 18O-labeled proteome reference (or GIS) can be readily prepared and contains a heavy isotope (18O)-labeled internal standard for every possible tryptic peptide. Our results showed that the percentage of heavy isotope (18O) incorporation applying an improved protocol was >99.5% for most peptides investigated. The accuracy, reproducibility, and linear dynamic range of quantification were further assessed based on known ratios of standard proteins spiked into the labeled mouse plasma reference. Reliable quantification was observed with high reproducibility (i.e. coefficient of variance <10%) for analyte concentrations that were set at 100-fold higher or lower than those of the GIS based on the light (16O)/heavy (18O) peak area ratios. The utility of 18O-labeled GIS was further illustrated by accurate relative quantification of 45 major human plasma proteins. Moreover, quantification of the concentrations of C-reactive protein and prostate-specific antigen was illustrated by coupling the GIS with standard additions of purified protein standards. Collectively, our results demonstrated that the use of 18O-labeled proteome reference as GIS provides a convenient, low cost, and effective strategy for relative quantification of a large number of candidate proteins in biological or clinical samples using SRM. PMID:21988777

  6. Certification of methylmercury content in two fresh-frozen reference materials: SRM 1947 Lake Michigan fish tissue and SRM 1974b organics in mussel tissue (Mytilus edulis).

    PubMed

    Davis, W Clay; Christopher, S J; Pugh, Rebecca S; Donard, O F X; Krupp, Eva A; Point, David; Horvat, Milena; Gibicar, D; Kljakovic-Gaspic, Z; Porter, Barbara J; Schantz, Michele M

    2007-04-01

    This paper describes the development of two independent analytical methods for the extraction and quantification of methylmercury from marine biota. The procedures involve microwave extraction, followed by derivatization and either headspace solid-phase microextraction (SPME) with a polydimethylsiloxane (PDMS)-coated silica fiber or back-extraction into iso-octane. The identification and quantification of the extracted compounds is carried out by capillary gas chromatography/mass spectrometric (GC/MS) and inductively coupled plasma mass spectrometric (GC/ICP-MS) detection. Both methods were validated for the determination of methylmercury (MeHg) concentrations in a variety of biological standard reference materials (SRMs) including fresh-frozen tissue homogenates of SRM 1946 Lake Superior fish tissue and SRM 1974a organics in mussel tissue (Mytilus edulis) and then applied to the certification effort of SRM 1947 Lake Michigan fish tissue and SRM 1974b organics in mussel tissue (Mytilus edulis). While past certifications of methylmercury in tissue SRMs have been based on two independent methods from the National Institute of Standards and Technology (NIST) and participating laboratories, the methods described within provide improved protocols and will allow future certification efforts to be based on at least two independent analytical methods within NIST.

  7. Quantification of progesterone binding in mammary tissue of pregnant ewes

    SciTech Connect

    Smith, J.J.; Capuco, A.V.; Akers, R.M.

    1987-06-01

    Progestin-binding sites in mammary tissue from 14 prepartum, multiparous ewes at 50, 80, 115, and 140 d of gestation were demonstrated by the binding of (/sup 3/H) R5020 (17,21-dimethyl-19-nor-4,9-pregnadiene-3,20-dione) to ovine mammary cytosol in the presence of sodium molybdate and excess cortisol. Homogenization extracted 89% of total mammary receptors (nuclear) into cytosol. Binding was specific for progestins and was of high affinity. The average dissociation constant for (/sup 3/H) R5020 specifically bound to receptors extracted into mammary cytosol was 1.9 (+/- .4) x 10/sup -9/ M (n = 14) and did not change significantly over the test period. However, binding capacities (fmol/mg cytosolic protein) differed according to stage of gestation with averages of 125 +/- 53, 149 +/- 26, 656 +/- 216, 57 +/- 22 at 50, 80, 115, and 140 d of pregnancy, respectively. Increased number of progestin-binding sites at 115 d of gestation (whether data are expressed per unit of tissue weight, DNA, or cytosolic protein) suggests that an increase per mammary epithelial cell may be necessary to produce the full lobuloalveolar proliferation observed at this stage of gestation.

  8. Diagnostic performance of amyloid A protein quantification in fat tissue of patients with clinical AA amyloidosis.

    PubMed

    Hazenberg, Bouke P C; Bijzet, Johan; Limburg, Pieter C; Skinner, Martha; Hawkins, Philip N; Butrimiene, Irena; Livneh, Avi; Lesnyak, Olga; Nasonov, Evgeney L; Filipowicz-Sosnowska, Anna; Gül, Ahmet; Merlini, Giampaolo; Wiland, Piotr; Ozdogan, Huri; Gorevic, Peter D; Maïz, Hédi Ben; Benson, Merrill D; Direskeneli, Haner; Kaarela, Kalevi; Garceau, Denis; Hauck, Wendy; Van Rijswijk, Martin H

    2007-06-01

    Amyloid A protein quantification in fat tissue is a new immunochemical method for detecting AA amyloidosis, a rare but serious disease. The objective was to assess diagnostic performance in clinical AA amyloidosis. Abdominal subcutaneous fat tissue of patients with AA amyloidosis was studied at the start of an international clinical trial with eprodisate (NC-503; 1,3-propanedisulfonate; Kiacta), an antiamyloid compound. All patients had renal findings, i.e. proteinuria (> or =1 g/day) or reduced creatinine clearance (20 - 60 ml/min). Controls were patients with other types of amyloidosis and arthritic patients without amyloidosis. Amyloid A protein was quantified by ELISA using monoclonal antihuman serum amyloid A antibodies. Congo red stained slides were scored by light microscopy in a semiquantitative way (0 to 4+). Ample fat tissue (>50 mg) was available for analysis in 154 of 183 patients with AA amyloidosis and in 354 controls. The sensitivity of amyloid A protein quantification for detection of AA amyloidosis (>11.6 ng/mg fat tissue) was 84% (95% CI: 77 - 89%) and specificity 99% (95% CI: 98 - 100%). Amyloid A protein quantification and semiquantitative Congo red scoring were concordant. Men had lower amyloid A protein values than women (p < 0.0001) and patients with familial Mediterranean fever had lower values than patients with arthritis (p < 0.001) or other inflammatory diseases (p < 0.01). Amyloid A protein quantification in fat tissue is a sensitive and specific method for detection of clinical AA amyloidosis. Advantages are independence from staining quality and observer experience, direct confirmation of amyloid AA type, and potential for quantitative monitoring of tissue amyloid over time.

  9. Nondestructive quantification of permeability of hyperosmotic agent in normal and tumor tissues

    NASA Astrophysics Data System (ADS)

    Xiong, Honglian; Guo, Zhouyi; Zeng, Changchun; Wang, Like; He, Yonghong; Liu, Songhao

    2008-12-01

    Noninvasive tumor imaging could lead to the early detection and timely treatment of cancer. Previous investigations have suggested that optical coherence tomography (OCT) is an ideal diagnostic tool distinguishing normal tissues from tumor tissues based on structural imaging because of the high resolution. In the study, the capability of OCT for functional imaging of normal and tumor tissues based on time and depth resolved quantification of the permeability of biomolecules through these tissues is investigated. An OCT system at 830 nm central wavelength was used in this study. Diffusion of 20% aqueous solution of glucose was monitored and quantified in normal stomach tissues and tumor tissues using OCT. The orthotopic graft model of gastric cancer in nude mice was used. Permeability coefficients were calculated as a function of time and tissue depth. The permeability coefficient was (9.44+/-0.42) ×10-6 cm/s in normal stomach tissues and (5.32+/-0.17)×10-5 cm/s in tumor tissues. The tumor tissues had a higher permeability coefficient compared to normal tissues. From the experimental results, it is found that the accurate and sensitive assessment of the permeability coefficients of normal and tumor tissues offer an effective OCT image method for clinical diagnosis and detection of tumor tissues.

  10. Evaluation of Reference Genes for the Relative Quantification of Apple stem grooving virus and Apple mosaic virus in Apple Trees.

    PubMed

    Gadiou, S; Kundu, J K

    2012-06-01

    A SYBR Green(®)-based one step RT-qPCR assay was developed for the detection and quantification of Apple stem grooving virus (ASGV) and Apple mosaic virus (ApMV). The RT-qPCR assay employed seven plant-expressed genes-glyceraldehyde 3-phosphate dehydrogenase (GAPDH), 18S ribosomal RNA, ubiquitin, ribosomal protein S19, Rubisco, RNA polymerase subunit II and β-actin-as internal reference housekeeping genes in a relative quantification system in three apple cultivars (i.e. Idared, Champion, Fragrance). The average expression stability (M) found by GeNorm software suggest that GAPDH and S19 were the most stable reference genes. We propose employing GAPDH and S19 as housekeeping genes for accurate quantification of ASGV and ApMV in apple leaf samples. The detection limit for both viruses was found around 70 copies of viral genome by one-step RT-qPCR.

  11. Quantification of titanium from TiO2 particles in biological tissue.

    PubMed

    Faucher, Stéphane; Lespes, Gaëtane

    2015-10-01

    This study presents the development of a strategy for the quantification of titanium from titanium dioxide polydisperse particles (TiO2) in dry biological tissue. Calf liver was chosen as laboratory testing material. The challenge was to (i) obtain a complete mineralization of the solid material (biological tissue and TiO2) and (ii) ensure the accuracy of the determined concentrations with a sufficient sensitivity. Mineralization was performed using a mixture of concentrated nitric and hydrofluoric acids. Atomic mass spectrometry associated with light-scattering technique was used to control the physical state (dissolved and particle forms) of titanium and reliably estimate the total titanium concentration in calf liver. The monitoring of (46)Ti and (49)Ti, operating in helium collision/reaction cell mode, and using external calibration with internal standard addition, allowed the quantification of Ti while removing isobaric interferences. The limit of detection and quantification were 0.7 and 2.3μg (Ti)g(-1) (tissue) respectively. The mean analytical recovery over the whole procedure was (103±6)% in a range of concentrations from LOD to 200μg(Ti)g(-1) (tissue). Copyright © 2015 Elsevier GmbH. All rights reserved.

  12. Quantification of pelvic soft tissue artifact in multiple static positions.

    PubMed

    Hara, Reiko; Sangeux, Morgan; Baker, Richard; McGinley, Jennifer

    2014-02-01

    Soft tissue artifact (STA) has been identified as the most critical source of error in clinical gait analysis. Multiple calibration is a technique to reduce the impact of STA on kinematic data, which involves several static calibrations through the range of motion of the joint of interest. This study investigated how skin markers at the pelvis were displaced in relation to anatomical body landmarks in multiple static calibration positions. The magnitude and direction of the pelvic marker displacement was assessed in nine different body positions including 90° and 45° hip flexion, maximum hip extension, and pelvic tilt in 20 healthy young adults. ASIS markers were found to be more susceptible to relative displacement than PSIS markers, with displacement particularly evident in positions where the hip was flexed (up to 17 mm). A strong correlation was found between the hip flexion angle and marker displacement (r(2) = 0.70). While the estimated impact of pelvic STA on gait kinematics was relatively small, the findings suggest that activities with large hip flexion would cause larger STA with a greater impact on pelvic kinematics. The skin surface located over the ASIS differed by a mean of 17 mm between standing and supine positions, which could affect the inter-ASIS distance and the location of hip joint center (HJC) by up to 20mm and 10mm, respectively.

  13. Tissue viability imaging for quantification of skin erythema and blanching

    NASA Astrophysics Data System (ADS)

    Nilsson, Gert E.; Leahy, Martin J.

    2010-02-01

    Naked eye observation has up to recently been the main method of determining skin erythema (vasodilatation) and blanching (vasoconstriction) in skin testing. Since naked eye observation is a highly subjective and investigatordependent method, it is difficult to attain reproducibility and to compare results reported by different researchers performing their studies at different laboratories. Consequently there is a need for more objective, quantitative and versatile methods in the assessment of alterations in skin erythema and blanching caused by internal and external factors such as the intake of vasoactive drugs, application of agents on the skin surface and by constituents in the environment. Since skin microcirculation is sensitive to applied pressure and heat, such methods should preferably be noninvasive and designed for remote use without touching the skin. As skin microcirculation further possesses substantial spatial variability, imaging techniques are to be preferred before single point measurements. An emerging technology based on polarization digital camera spectroscopy - Tissue Viability Imaging (TiVi) - fulfills these requirements. The principles of TiVi (1) and some of its early applications (2-5) are addressed in this paper.

  14. Identification and quantification of selected chemicals in laser pyrolysis products of mammalian tissues

    NASA Astrophysics Data System (ADS)

    Spleiss, Martin; Weber, Lothar W.; Meier, Thomas H.; Treffler, Bernd

    1995-01-01

    Liver and muscle tissue have been irradiated with a surgical CO2-laser. The prefiltered fumes were adsorbed on different sorbents (activated charcoal type NIOSH and Carbotrap) and desorbed with different solvents (carbondisulphide and acetone). Analysis was done by gas chromatography/mass spectrometry. An updated list of identified substances is shown. Typical Maillard reaction products as found in warmed over flavour as aldehydes, aromatics, heterocyclic and sulphur compounds were detected. Quantification of some toxicological relevant substances is presented. The amounts of these substances are given in relation to the laser parameters and different tissues for further toxicological assessment.

  15. Absolute ultrasound perfusion parameter quantification of a tissue-mimicking phantom using bolus tracking [Correspondence].

    PubMed

    Mezl, Martin; Jirik, Radovan; Harabis, Vratislav; Kolar, Radim; Standara, Michal; Nylund, Kim; Gilja, Odd Helge; Taxt, Torfinn

    2015-05-01

    This study presents three methods for absolute quantification in ultrasound perfusion analysis based on bolus tracking. The first two methods deconvolve the perfusion time sequence with a measured AIF, using a nonparametric or a parametric model of the tissue residue function, respectively. The third method is a simplified approach avoiding deconvolution by assuming a narrow AIF. A phantom with a dialyzer filter as a tissue-mimicking model was used for evaluation. Estimated mean transit times and blood volumes were compared with the theoretical values. A match with a maximum error of 12% was achieved.

  16. Fully automatic and nonparametric quantification of adipose tissue in fat-water separation MR imaging.

    PubMed

    Wang, Defeng; Shi, Lin; Chu, Winnie C W; Hu, Miao; Tomlinson, Brian; Huang, Wen-Hua; Wang, Tianfu; Heng, Pheng Ann; Yeung, David K W; Ahuja, Anil T

    2015-11-01

    Despite increasing demand and research efforts, currently there is no consensus on the protocol for automated and reliable quantification of adipose tissue (AT) and visceral adipose tissue (VAT) using MRI. The purpose of this study was to propose a novel computational method with enhanced objectiveness for the quantification of AT and VAT in fat-water separation MRI. 3T data from IDEAL were acquired for the fat-water separation. Fat tissues were separated from nonfat regions (background air, bone, water, and other nonfat tissues) using K-means clustering (K = 2). From the binary fat mask, arm regions were separated from body based on the relative size of connected component. AT was obtained from the binary body fat mask. With the initial contour as the outer boundary of body fat, the subcutaneous adipose tissue (SAT) and VAT were separated using deformable model driven by a specifically generated deformation field pointing to the inner boundary of SAT. The proposed method was tested on 16 patients with dyslipidemia and evaluated by comparing the correlation with semi-automatic segmentation results. Good robustness was also observed in the proposed method from the Bland-Altman plots. Compared to other established fat segmentation methods, the proposed method is highly objective for fat-water separation MRI with minimal variability induced by subjective parameter settings.

  17. Simple quantification of multiplexed quantum dot staining in clinical tissue samples.

    PubMed

    Caldwell, Matthew L; Moffitt, Richard A; Liu, Jian; Parry, R Mitchell; Sharma, Yachna; Wang, May D

    2008-01-01

    In this paper, we present a simple method for the processing and quantification of multiplexed Quantum Dot (QD) labeled images of clinical cancer tissue samples. QDs provide several features which make them ideal for reliable quantification, including long-term signal stability, high signal-to-noise ratios, as well as narrow emission bandwidths. Deconvolution of QD spectra is accomplished in a batch mode in which unmixing parameters are preserved across samples to allow for quantitative and reproducible comparisons. After unmixing the QD images, we segment each one to exclude acellular regions. We use a simple average intensity to quantify the level of QD staining for each image. We illustrate the viability of this approach by testing it on 28 tissue samples using a tissue microarray. We show that using as few as two QD protein targets (MDM-2, and B-actin), the Renal Cell Carcinoma (RCC) samples are distinguishable from adjacent normal tissue samples. A simple linear discriminant results in 100% classification of 25 RCC samples and 3 normal samples. This suggests that multiplexed QDs can be used to properly diagnose RCC from otherwise healthy tissue. We expect to apply this work to larger panels of more robust QD biomarker targets to aid in clinical decision-making for the diagnosis and prognosis of diseases, such as cancer.

  18. Histological quantification of brain tissue inflammatory cell infiltration after focal cerebral infarction: a systematic review.

    PubMed

    Russek, Natanya S; Jensen, Matthew B

    2014-03-01

    Ischemic stroke is a leading cause of death and disability, and current treatments to limit tissue injury and improve recovery are limited. Cerebral infarction is accompanied by intense brain tissue inflammation involving many inflammatory cell types that may cause both negative and positive effects on outcomes. Many potential neuroprotective and neurorestorative treatments may affect, and be affected by, this inflammatory cell infiltration, so that accurate quantification of this tissue response is needed. We performed a systematic review of histological methods to quantify brain tissue inflammatory cell infiltration after cerebral infarction. We found reports of multiple techniques to quantify different inflammatory cell types. We found no direct comparison studies and conclude that more research is needed to optimize the assessment of this important stroke outcome.

  19. Fat emulsions as diffusive reference standards for tissue simulating phantoms?

    PubMed

    Di Ninni, Paola; Bérubé-Lauzière, Yves; Mercatelli, Luca; Sani, Elisa; Martelli, Fabrizio

    2012-10-20

    Intralipid 20% was recently suggested as a diffusive reference standard for tissue simulating phantoms. In this work, we extend previously obtained results to other fat emulsions, specifically Intralipid 10%, Intralipid 30%, Lipovenoes 10%, Lipovenoes 10% PhosphoLipid Reduced, Lipovenoes 20%, Lipofundin S 10%, and Lipofundin S 20%. Of particular importance for practical applications, our measurements carried out at a wavelength of 751 nm show the following features. First, these products show high stability and small batch-to-batch variations in their diffusive optical properties, similar to Intralipid 20%. Second, the absorption coefficient of Intralipid, Lipovenoes, and Lipofundin S are very similar and their measured values are within the experimental errors; moreover the reduced scattering coefficient of Intralipid 20%, Lipovenoes 20%, and Lipofundin S 20% are similar and their measured values are within 5%. Third, the reduced scattering coefficient of Intralipid 10% and Intralipid 30% can be scaled from that of Intralipid 20% with an error of 9% and 2%, respectively. A similar scaling property is valid for Lipovenoes and Lipofundin S. We have verified that this scaling property depends on the composition of the fat emulsions: If the ingredients exactly scale with the concentration then the reduced scattering coefficient almost exactly scale as well.

  20. Ultra-trace quantification method for chlordecone in human fluids and tissues.

    PubMed

    Bichon, Emmanuelle; Guiffard, Ingrid; Vénisseau, Anaïs; Marchand, Philippe; Antignac, Jean-Philippe; Le Bizec, Bruno

    2015-08-21

    Chlordecone is an organochlorine pesticide (OCP) considered as a Persistent Organic Pollutant (POP) as it persists in the environment, bio-accumulates through the food web, causes adverse effects to human health and the environment and transports across international boundaries far from its sources. The atypical physico-chemical properties of chlordecone make its inclusion in classical analytical approaches non applicable. The aim of our work was to include chlordecone in a multi organochlorine residue method preventing any degradation during the analytical process and thus allowing quantification at ppt (ngkg(-1) or ngL(-1)) levels for a wide range of OCPs in breast milk, human serum and adipose tissue. After GC-HRMS vs. MS/MS and EI vs. APCI comparisons, the major improvement in terms of sensitivity was found in decreasing the length and film thickness of the gas chromatography column. Thanks to a linear correlation between relative response and quantity of chlordecone injected, LC-(ESI-)-MS/MS was finally preferred. An acetonitrile based gradient optimized on a C30 coreshell HPLC column has led to reaching limits of quantification as low as 8ngL(-1), 25pgmL(-1) and 0.2ngg(-1) fat for breast milk, serum and adipose tissue, respectively, allowing multiresidue OCP quantification at concentration levels compatible with biomonitoring purposes and pre-requisites. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Methods of RNA preparation affect mRNA abundance quantification of reference genes in pig maturing oocytes.

    PubMed

    Wang, Y-K; Li, X; Song, Z-Q; Yang, C-X

    2017-10-01

    To ensure accurate normalization and quantification of target RNA transcripts using reverse transcription quantitative polymerase chain reaction (RT-qPCR), most studies focus on the identification of stably expressed gene(s) as internal reference. However, RNA preparation methods could also be an important factor, especially for test samples of limited quantity (e.g. oocytes). In this study, we aimed to select appropriate reference gene(s), and evaluate the effect of RNA preparation methods on gene expression quantification in porcine oocytes and cumulus cells during in vitro maturation. Expression profiles of seven genes (GAPDH, 18S, YWHAG, BACT, RPL4, HPRT1 and PPIA) were examined, on RNA samples extracted from cumulus cells (RNeasy Kit) and oocytes (RNeasy Kit and Lysis Kit) during in vitro maturation, respectively. Interestingly, different RNA preparation methods were found to potentially affect the quantification of reference gene expression in pig oocytes cultured in vitro. After geNorm analyses, the most suitable genes for normalization were identified, GAPDH/18S for cumulus cells and YWHAG/BACT for oocytes, respectively. Thus, our results provide useful data and information on the selection of better reference genes and RNA preparation method for related functional studies. © 2017 Blackwell Verlag GmbH.

  2. ID-SERS Based Reference Method for Quantification of Large Biomolecules on a Single Chip

    SciTech Connect

    Yaghobian, Fatemeh; Stosch, Rainer; Henrion, Andre; Guettler, Bernd

    2010-08-06

    Accuracy and precision of quantitative SERS results have been significantly increased by applying a method based on the so-called isotope-dilution (ID) principle. In this ID-SERS approach, an isotopically labeled analogue of the target molecule (isotopologue) is spiked to the sample at a known concentration. Due to the slight difference in their molar masses, some Raman bands of the heavier isotopologue are red-shifted with respect to the same signals resulting from the unlabelled compound. As a result, spectra evaluation is reduced to the determination of intensity ratios rather than absolute intensities, and the unknown quantity of the analyte can be calculated from the known quantity of the standard. This procedure is of particular interest in the development of highly accurate reference procedures for metrology in chemistry. Because the sample is spiked prior to any further treatment, potential loss of material or matrix effects would equally affect both isotopologues, without influencing the final result. The method has been successfully applied for quantifying small diagnostic marker molecules like creatinine at their relevant serum concentration levels using silver colloids as SERS substrates. Now, the ID-SERS approach has been realized as a 'one-chip' approach using 'Bio-chips' made of intrinsically grown spherical silver nanoparticles with gaps less than 10 nm in between (Fig. 1). In addition, the scope of the method has been extended to larger biomolecules like peptides which will be shown using the example of the human growth-hormone (hGH) peptide T12 at physiologically relevant serum concentration levels (Fig. 2). Further developments towards the quantification of full proteins will also be reported.

  3. ID-SERS Based Reference Method for Quantification of Large Biomolecules on a Single Chip

    NASA Astrophysics Data System (ADS)

    Yaghobian, Fatemeh; Stosch, Rainer; Henrion, André; Güttler, Bernd

    2010-08-01

    Accuracy and precision of quantitative SERS results have been significantly increased by applying a method based on the so-called isotope-dilution (ID) principle. In this ID-SERS approach, an isotopically labeled analogue of the target molecule (isotopologue) is spiked to the sample at a known concentration. Due to the slight difference in their molar masses, some Raman bands of the heavier isotopologue are red-shifted with respect to the same signals resulting from the unlabelled compound. As a result, spectra evaluation is reduced to the determination of intensity ratios rather than absolute intensities, and the unknown quantity of the analyte can be calculated from the known quantity of the standard. This procedure is of particular interest in the development of highly accurate reference procedures for metrology in chemistry. Because the sample is spiked prior to any further treatment, potential loss of material or matrix effects would equally affect both isotopologues, without influencing the final result. The method has been successfully applied for quantifying small diagnostic marker molecules like creatinine at their relevant serum concentration levels using silver colloids as SERS substrates. Now, the ID-SERS approach has been realized as a "one-chip" approach using "Bio-chips" made of intrinsically grown spherical silver nanoparticles with gaps less than 10 nm in between (Fig. 1). In addition, the scope of the method has been extended to larger biomolecules like peptides which will be shown using the example of the human growth-hormone (hGH) peptide T12 at physiologically relevant serum concentration levels (Fig. 2). Further developments towards the quantification of full proteins will also be reported.

  4. [Temporal-spatial variations of reference evapotranspiration in Anhui Province and the quantification of the causes].

    PubMed

    Cao, Wen; Duan, Chun-feng; Yao, Yun; Yue, Wei

    2014-12-01

    In this paper, daily reference evapotranspiration (ET0) was computed with the recommended FAO-56 Penman-Monteith equation for Anhui Province using data collected 60 weather stations during 1961 to 2010 and its temporal-spatial variations were characterized. The determining factors in ET0 trends were inquired into through partial derivative quantification analysis for the study region. Results showed that the mean annual ET0 was 878.58 mm x a(-1) over the whole region during the study period. ET0 was the highest in summer and the lowest in winter. The mean annual ET0 decreased from the north to the south and from low altitude regions to high altitude regions. Both sunshine duration and wind speed were the dominant factors contributing to the interannual change of ET0, with less contribution from air temperature or relative humidity. The annual ET0 showed a general decline at a rate of -1.61 mm x a(-1) owing to a more negative contribution of sunshine duration and wind speed than a positive contribution of air temperature and relative humidity. ET0 increased insignificantly in spring and decreased slightly in both autumn and winter. However, it decreased significantly at a rate of -1.37 mm x a(-1) in summer. The main impacting factor was wind speed in spring, autumn and winter, but it was sunshine duration in summer. Great differences in the determining factors of the mean annual ET0 existed from area to area in Anhui Province. The wind speed was the determining factor for 36.7% of the whole stations distributing in the southern part of the area north to the Huaihe River and the area along the Huaihe River, while the sunshine duration was the determining factor for the other regions.

  5. Novel Methods of Automated Quantification of Gap Junction Distribution and Interstitial Collagen Quantity from Animal and Human Atrial Tissue Sections

    PubMed Central

    Yan, Jiajie; Thomson, Justin K.; Wu, Xiaomin; Zhao, Weiwei; Pollard, Andrew E.; Ai, Xun

    2014-01-01

    Background Gap junctions (GJs) are the principal membrane structures that conduct electrical impulses between cardiac myocytes while interstitial collagen (IC) can physically separate adjacent myocytes and limit cell-cell communication. Emerging evidence suggests that both GJ and interstitial structural remodeling are linked to cardiac arrhythmia development. However, automated quantitative identification of GJ distribution and IC deposition from microscopic histological images has proven to be challenging. Such quantification is required to improve the understanding of functional consequences of GJ and structural remodeling in cardiac electrophysiology studies. Methods and Results Separate approaches were employed for GJ and IC identification in images from histologically stained tissue sections obtained from rabbit and human atria. For GJ identification, we recognized N-Cadherin (N-Cad) as part of the gap junction connexin 43 (Cx43) molecular complex. Because N-Cad anchors Cx43 on intercalated discs (ID) to form functional GJ channels on cell membranes, we computationally dilated N-Cad pixels to create N-Cad units that covered all ID-associated Cx43 pixels on Cx43/N-Cad double immunostained confocal images. This approach allowed segmentation between ID-associated and non-ID-associated Cx43. Additionally, use of N-Cad as a unique internal reference with Z-stack layer-by-layer confocal images potentially limits sample processing related artifacts in Cx43 quantification. For IC quantification, color map thresholding of Masson's Trichrome blue stained sections allowed straightforward and automated segmentation of collagen from non-collagen pixels. Our results strongly demonstrate that the two novel image-processing approaches can minimize potential overestimation or underestimation of gap junction and structural remodeling in healthy and pathological hearts. The results of using the two novel methods will significantly improve our understanding of the molecular and

  6. Novel methods of automated quantification of gap junction distribution and interstitial collagen quantity from animal and human atrial tissue sections.

    PubMed

    Yan, Jiajie; Thomson, Justin K; Wu, Xiaomin; Zhao, Weiwei; Pollard, Andrew E; Ai, Xun

    2014-01-01

    Gap junctions (GJs) are the principal membrane structures that conduct electrical impulses between cardiac myocytes while interstitial collagen (IC) can physically separate adjacent myocytes and limit cell-cell communication. Emerging evidence suggests that both GJ and interstitial structural remodeling are linked to cardiac arrhythmia development. However, automated quantitative identification of GJ distribution and IC deposition from microscopic histological images has proven to be challenging. Such quantification is required to improve the understanding of functional consequences of GJ and structural remodeling in cardiac electrophysiology studies. Separate approaches were employed for GJ and IC identification in images from histologically stained tissue sections obtained from rabbit and human atria. For GJ identification, we recognized N-Cadherin (N-Cad) as part of the gap junction connexin 43 (Cx43) molecular complex. Because N-Cad anchors Cx43 on intercalated discs (ID) to form functional GJ channels on cell membranes, we computationally dilated N-Cad pixels to create N-Cad units that covered all ID-associated Cx43 pixels on Cx43/N-Cad double immunostained confocal images. This approach allowed segmentation between ID-associated and non-ID-associated Cx43. Additionally, use of N-Cad as a unique internal reference with Z-stack layer-by-layer confocal images potentially limits sample processing related artifacts in Cx43 quantification. For IC quantification, color map thresholding of Masson's Trichrome blue stained sections allowed straightforward and automated segmentation of collagen from non-collagen pixels. Our results strongly demonstrate that the two novel image-processing approaches can minimize potential overestimation or underestimation of gap junction and structural remodeling in healthy and pathological hearts. The results of using the two novel methods will significantly improve our understanding of the molecular and structural remodeling associated

  7. Quantification of two isomeric flavones in rat colon tissue using reverse phase high performance liquid chromatography.

    PubMed

    Whitted, Crystal L; Palau, Victoria E; Torrenegra, Ruben D; Rodriguez, Oscar E; Harirforoosh, Sam

    2017-01-07

    Antineoplastic activity has been previously shown for two isomeric flavones, 5,7-dihydroxy-3,6,8-trimethoxy flavone (flavone A) and 3,5-dihydroxy-6,7,8-trimethoxy flavone (flavone B), against colon cancer cell lines (Thomas et al. in PLoS ONE 7:e39806, 5). Here, we present modified methods for the extraction and quantification of flavones A and B in rat colon tissue after intravenous dosing via high performance liquid chromatography, from the originally described procedure for extraction and quantification in rat plasma (Whitted et al. in J Chromatogr B Analyt Technol Biomed Life Sci 1001:150-155, 7). Modifications included tissue homogenization (1 g tissue: 2 mL water), filtration of the supernatant with a PVDF membrane, and the use of only one calibration curve to determine the concentration of each flavone in colon tissue. Good separation was achieved and representative equations were linear with r (2)  ≥ 0.99 for both flavones. Precision and accuracy for flavone A ranged from 0.88-24.03 and 109-116%. Precision and accuracy for flavone B ranged from 1.62-33.56 and 98-113%. Concentrations of 1639 ± 601 ng/g flavone A and 5975 ± 2480 ng/g of flavone B were detected in rat colon tissue 6 h post dosing. Modifications to the extraction methods for flavone A and flavone B from rat colon tissue had good separation, precision, and accuracy.

  8. Polarized light spatial frequency domain imaging for non-destructive quantification of soft tissue fibrous structures

    PubMed Central

    Yang, Bin; Lesicko, John; Sharma, Manu; Hill, Michael; Sacks, Michael S.; Tunnell, James W.

    2015-01-01

    The measurement of soft tissue fiber orientation is fundamental to pathophysiology and biomechanical function in a multitude of biomedical applications. However, many existing techniques for quantifying fiber structure rely on transmitted light, limiting general applicability and often requiring tissue processing. Herein, we present a novel wide-field reflectance-based imaging modality, which combines polarized light imaging (PLI) and spatial frequency domain imaging (SFDI) to rapidly quantify preferred fiber orientation on soft collagenous tissues. PLI utilizes the polarization dependent scattering property of fibers to determine preferred fiber orientation; SFDI imaging at high spatial frequency is introduced to reject the highly diffuse photons and to control imaging depth. As a result, photons scattered from the superficial layer of a multi-layered sample are highlighted. Thus, fiber orientation quantification can be achieved for the superficial layer with optical sectioning. We demonstrated on aortic heart valve leaflet that, at spatial frequency of f = 1mm−1, the diffuse background can be effectively rejected and the imaging depth can be limited, thus improving quantification accuracy. PMID:25909033

  9. Reference genes for real-time PCR quantification of messenger RNAs and microRNAs in mouse model of obesity.

    PubMed

    Matoušková, Petra; Bártíková, Hana; Boušová, Iva; Hanušová, Veronika; Szotáková, Barbora; Skálová, Lenka

    2014-01-01

    Obesity and metabolic syndrome is increasing health problem worldwide. Among other ways, nutritional intervention using phytochemicals is important method for treatment and prevention of this disease. Recent studies have shown that certain phytochemicals could alter the expression of specific genes and microRNAs (miRNAs) that play a fundamental role in the pathogenesis of obesity. For study of the obesity and its treatment, monosodium glutamate (MSG)-injected mice with developed central obesity, insulin resistance and liver lipid accumulation are frequently used animal models. To understand the mechanism of phytochemicals action in obese animals, the study of selected genes expression together with miRNA quantification is extremely important. For this purpose, real-time quantitative PCR is a sensitive and reproducible method, but it depends on proper normalization entirely. The aim of present study was to identify the appropriate reference genes for mRNA and miRNA quantification in MSG mice treated with green tea catechins, potential anti-obesity phytochemicals. Two sets of reference genes were tested: first set contained seven commonly used genes for normalization of messenger RNA, the second set of candidate reference genes included ten small RNAs for normalization of miRNA. The expression stability of these reference genes were tested upon treatment of mice with catechins using geNorm, NormFinder and BestKeeper algorithms. Selected normalizers for mRNA quantification were tested and validated on expression of quinone oxidoreductase, biotransformation enzyme known to be modified by catechins. The effect of selected normalizers for miRNA quantification was tested on two obesity- and diabetes- related miRNAs, miR-221 and miR-29b, respectively. Finally, the combinations of B2M/18S/HPRT1 and miR-16/sno234 were validated as optimal reference genes for mRNA and miRNA quantification in liver and 18S/RPlP0/HPRT1 and sno234/miR-186 in small intestine of MSG mice. These

  10. White adipose tissue reference network: a knowledge resource for exploring health-relevant relations.

    PubMed

    Kelder, Thomas; Summer, Georg; Caspers, Martien; van Schothorst, Evert M; Keijer, Jaap; Duivenvoorde, Loes; Klaus, Susanne; Voigt, Anja; Bohnert, Laura; Pico, Catalina; Palou, Andreu; Bonet, M Luisa; Dembinska-Kiec, Aldona; Malczewska-Malec, Malgorzata; Kieć-Wilk, Beata; Del Bas, Josep M; Caimari, Antoni; Arola, Lluis; van Erk, Marjan; van Ommen, Ben; Radonjic, Marijana

    2015-01-01

    Optimal health is maintained by interaction of multiple intrinsic and environmental factors at different levels of complexity-from molecular, to physiological, to social. Understanding and quantification of these interactions will aid design of successful health interventions. We introduce the reference network concept as a platform for multi-level exploration of biological relations relevant for metabolic health, by integration and mining of biological interactions derived from public resources and context-specific experimental data. A White Adipose Tissue Health Reference Network (WATRefNet) was constructed as a resource for discovery and prioritization of mechanism-based biomarkers for white adipose tissue (WAT) health status and the effect of food and drug compounds on WAT health status. The WATRefNet (6,797 nodes and 32,171 edges) is based on (1) experimental data obtained from 10 studies addressing different adiposity states, (2) seven public knowledge bases of molecular interactions, (3) expert's definitions of five physiologically relevant processes key to WAT health, namely WAT expandability, Oxidative capacity, Metabolic state, Oxidative stress and Tissue inflammation, and (4) a collection of relevant biomarkers of these processes identified by BIOCLAIMS ( http://bioclaims.uib.es ). The WATRefNet comprehends multiple layers of biological complexity as it contains various types of nodes and edges that represent different biological levels and interactions. We have validated the reference network by showing overrepresentation with anti-obesity drug targets, pathology-associated genes and differentially expressed genes from an external disease model dataset. The resulting network has been used to extract subnetworks specific to the above-mentioned expert-defined physiological processes. Each of these process-specific signatures represents a mechanistically supported composite biomarker for assessing and quantifying the effect of interventions on a

  11. Preclinical In vivo Imaging for Fat Tissue Identification, Quantification, and Functional Characterization

    PubMed Central

    Marzola, Pasquina; Boschi, Federico; Moneta, Francesco; Sbarbati, Andrea; Zancanaro, Carlo

    2016-01-01

    Localization, differentiation, and quantitative assessment of fat tissues have always collected the interest of researchers. Nowadays, these topics are even more relevant as obesity (the excess of fat tissue) is considered a real pathology requiring in some cases pharmacological and surgical approaches. Several weight loss medications, acting either on the metabolism or on the central nervous system, are currently under preclinical or clinical investigation. Animal models of obesity have been developed and are widely used in pharmaceutical research. The assessment of candidate drugs in animal models requires non-invasive methods for longitudinal assessment of efficacy, the main outcome being the amount of body fat. Fat tissues can be either quantified in the entire animal or localized and measured in selected organs/regions of the body. Fat tissues are characterized by peculiar contrast in several imaging modalities as for example Magnetic Resonance Imaging (MRI) that can distinguish between fat and water protons thank to their different magnetic resonance properties. Since fat tissues have higher carbon/hydrogen content than other soft tissues and bones, they can be easily assessed by Computed Tomography (CT) as well. Interestingly, MRI also discriminates between white and brown adipose tissue (BAT); the latter has long been regarded as a potential target for anti-obesity drugs because of its ability to enhance energy consumption through increased thermogenesis. Positron Emission Tomography (PET) performed with 18F-FDG as glucose analog radiotracer reflects well the metabolic rate in body tissues and consequently is the technique of choice for studies of BAT metabolism. This review will focus on the main, non-invasive imaging techniques (MRI, CT, and PET) that are fundamental for the assessment, quantification and functional characterization of fat deposits in small laboratory animals. The contribution of optical techniques, which are currently regarded with

  12. 18O-Labeled Proteome Reference as Global Internal Standards for Targeted Quantification by Selected Reaction Monitoring-Mass Spectrometry

    SciTech Connect

    Kim, Jong Seo; Fillmore, Thomas L.; Liu, Tao; Robinson, Errol W.; Hossain, Mahmud; Champion, Boyd L.; Moore, Ronald J.; Camp, David G.; Smith, Richard D.; Qian, Weijun

    2011-10-11

    Selected reaction monitoring-mass spectrometry (SRM-MS) is an emerging technology for high throughput targeted protein quantification and verification in biological and biomarker discovery studies; however, the cost associated with the use of stable isotope labeled synthetic peptides as internal standards is prohibitive for quantitatively screening large numbers of candidate proteins as often required in the pre-verification phase of biomarker discovery. Herein we present the proof-of-concept experiments of using an 18O-labeled 'universal' reference as comprehensive internal standards for quantitative SRM-MS analysis. With an 18O-labeled whole proteome sample as reference, every peptide of interest will have its own corresponding heavy isotope labeled internal standard, thus providing an ideal approach for quantitative screening of a large number of candidates using SRM-MS. Our results showed that the 18O incorporation efficiency using a recently improved protocol was >99.5% for most peptides investigated, a level comparable to 13C/15N labeled synthetic peptides in terms of heavy isotope incorporation. The accuracy, reproducibility, and linear dynamic range of quantification were further assessed based on known ratios of standard proteins spiked into mouse plasma with an 18O-labeled mouse plasma reference. A dynamic range of four orders of magnitude in relative concentration was obtained with high reproducibility (i.e., coefficient of variance <10%) based on the 16O/18O peak area ratios. Absolute and relative quantification of C-reactive protein and prostate-specific antigen were demonstrated by coupling an 18O-labeled reference with standard additions of protein standards. Collectively, our results demonstrated that the use of 18O-labeled reference provides a convenient and effective strategy for quantitative SRM screening of large number of candidate proteins.

  13. X-ray fluorescence and energy dispersive x-ray diffraction for the quantification of elemental concentrations in breast tissue.

    PubMed

    Geraki, K; Farquharson, M J; Bradley, D A

    2004-01-07

    This paper presents improvements on a previously reported method for the measurement of elements in breast tissue specimens (Geraki et al 2002 Phys. Med. Biol. 47 2327-39). A synchrotron-based system was used for the detection of the x-ray fluorescence (XRF) emitted from iron, copper, zinc and potassium in breast tissue specimens, healthy and cancerous. Calibration models resulting from the irradiation of standard aqueous solutions were used for the quantification of the elements. The present developments concentrate on increasing the convergence between the tissue samples and the calibration models, therefore improving accuracy. For this purpose the composition of the samples in terms of adipose and fibrous tissue was evaluated, using an energy dispersive x-ray diffraction (EDXRD) system. The relationships between the attenuation and scatter properties of the two tissue components and water were determined through Monte Carlo simulations. The results from the simulations and the EDXRD measurements allowed the XRF data from each specimen to be corrected according to its composition. The statistical analysis of the elemental concentrations of the different groups of specimens reveals that all four elements are found in elevated levels in the tumour specimens. The increase is less pronounced for iron and copper and most for potassium and zinc. Other observed features include the substantial degree of inhomogeneity of elemental distributions within the volume of the specimens, varying between 4% and 36% of the mean, depending on the element and the type of the sample. The accuracy of the technique, based on the measurement of a standard reference material, proved to be between 3% and 22% depending on the element, which presents only a marginal improvement (1%-3%) compared to the accuracy of the previously reported results. The measurement precision was between 1% and 9% while the calculated uncertainties on the final elemental concentrations ranged between 10% and 16%.

  14. Quantification of microRNA-21 and microRNA-125b in melanoma tissue.

    PubMed

    Wandler, Anne; Riber-Hansen, Rikke; Hager, Henrik; Hamilton-Dutoit, Stephen J; Schmidt, Henrik; Nielsen, Boye S; Stougaard, Magnus; Steiniche, Torben

    2017-10-01

    Although microRNAs (miRNAs) have emerged as potent mediators of melanoma development and progression, a precise understanding of their oncogenic role remains unclear. In this study, we analysed formalin-fixed and paraffin-embedded tissues from two separate melanoma cohorts and from a series of benign melanocytic nevi. Using three different quantification methods [array analysis, quantitative PCR (qPCR) and in-situ hybridization (ISH) quantified by digital image analysis], we found considerable miRNA dysregulation in tumours. Using array analysis, samples mainly clustered according to their biological group (benign vs. malignant) and 77 miRNAs differed significantly between nevi and melanoma samples. Increase of miR-21 and miR-142, and decrease of miR-125b, miR-211, miR-101 and miR-513c in the melanomas were verified in both cohorts using qPCR, whereas the decrease of miR-205 observed with array analysis could not be confirmed using qPCR. ISH with digital quantification showed expression of miR-21 and miR-125b in the melanocytic lesions. miR-21 ISH was increased in melanomas, whereas quantification of miR-125b showed uniform ISH expression across nevi and melanomas. Our results support the important involvement of different miRNAs in melanoma biology and may serve as solid basics for further miRNA investigations in melanoma formalin-fixed and paraffin-embedded tissue. In particular, there is increased expression of miR-21 in melanomas compared with benign nevi.

  15. Evaluation of Four Endogenous Reference Genes and Their Real-Time PCR Assays for Common Wheat Quantification in GMOs Detection

    PubMed Central

    Huang, Huali; Cheng, Fang; Wang, Ruoan; Zhang, Dabing; Yang, Litao

    2013-01-01

    Proper selection of endogenous reference genes and their real-time PCR assays is quite important in genetically modified organisms (GMOs) detection. To find a suitable endogenous reference gene and its real-time PCR assay for common wheat (Triticum aestivum L.) DNA content or copy number quantification, four previously reported wheat endogenous reference genes and their real-time PCR assays were comprehensively evaluated for the target gene sequence variation and their real-time PCR performance among 37 common wheat lines. Three SNPs were observed in the PKABA1 and ALMT1 genes, and these SNPs significantly decreased the efficiency of real-time PCR amplification. GeNorm analysis of the real-time PCR performance of each gene among common wheat lines showed that the Waxy-D1 assay had the lowest M values with the best stability among all tested lines. All results indicated that the Waxy-D1 gene and its real-time PCR assay were most suitable to be used as an endogenous reference gene for common wheat DNA content quantification. The validated Waxy-D1 gene assay will be useful in establishing accurate and creditable qualitative and quantitative PCR analysis of GM wheat. PMID:24098735

  16. Evaluation of four endogenous reference genes and their real-time PCR assays for common wheat quantification in GMOs detection.

    PubMed

    Huang, Huali; Cheng, Fang; Wang, Ruoan; Zhang, Dabing; Yang, Litao

    2013-01-01

    Proper selection of endogenous reference genes and their real-time PCR assays is quite important in genetically modified organisms (GMOs) detection. To find a suitable endogenous reference gene and its real-time PCR assay for common wheat (Triticum aestivum L.) DNA content or copy number quantification, four previously reported wheat endogenous reference genes and their real-time PCR assays were comprehensively evaluated for the target gene sequence variation and their real-time PCR performance among 37 common wheat lines. Three SNPs were observed in the PKABA1 and ALMT1 genes, and these SNPs significantly decreased the efficiency of real-time PCR amplification. GeNorm analysis of the real-time PCR performance of each gene among common wheat lines showed that the Waxy-D1 assay had the lowest M values with the best stability among all tested lines. All results indicated that the Waxy-D1 gene and its real-time PCR assay were most suitable to be used as an endogenous reference gene for common wheat DNA content quantification. The validated Waxy-D1 gene assay will be useful in establishing accurate and creditable qualitative and quantitative PCR analysis of GM wheat.

  17. Identification of Reliable Reference Genes for Quantification of MicroRNAs in Serum Samples of Sulfur Mustard-Exposed Veterans

    PubMed Central

    Gharbi, Sedigheh; Shamsara, Mehdi; Khateri, Shahriar; Soroush, Mohammad Reza; Ghorbanmehr, Nassim; Tavallaei, Mahmood; Nourani, Mohammad Reza; Mowla, Seyed Javad

    2015-01-01

    Objective In spite of accumulating information about pathological aspects of sulfur mustard (SM), the precise mechanism responsible for its effects is not well understood. Circulating microRNAs (miRNAs) are promising biomarkers for disease diagnosis and prognosis. Accurate normalization using appropriate reference genes, is a critical step in miRNA expression studies. In this study, we aimed to identify appropriate reference gene for microRNA quantification in serum samples of SM victims. Materials and Methods In this case and control experimental study, using quantitative real-time polymerase chain reaction (qRT-PCR), we evaluated the suitability of a panel of small RNAs including SNORD38B, SNORD49A, U6, 5S rRNA, miR-423-3p, miR-191, miR-16 and miR-103 in sera of 28 SM-exposed veterans of Iran-Iraq war (1980-1988) and 15 matched control volunteers. Different statistical algorithms including geNorm, Normfinder, best-keeper and comparative delta-quantification cycle (Cq) method were employed to find the least variable reference gene. Results miR-423-3p was identified as the most stably expressed reference gene, and miR- 103 and miR-16 ranked after that. Conclusion We demonstrate that non-miRNA reference genes have the least stabil- ity in serum samples and that some house-keeping miRNAs may be used as more reliable reference genes for miRNAs in serum. In addition, using the geometric mean of two reference genes could increase the reliability of the normalizers. PMID:26464821

  18. Identification of Reliable Reference Genes for Quantification of MicroRNAs in Serum Samples of Sulfur Mustard-Exposed Veterans.

    PubMed

    Gharbi, Sedigheh; Shamsara, Mehdi; Khateri, Shahriar; Soroush, Mohammad Reza; Ghorbanmehr, Nassim; Tavallaei, Mahmood; Nourani, Mohammad Reza; Mowla, Seyed Javad

    2015-01-01

    In spite of accumulating information about pathological aspects of sulfur mustard (SM), the precise mechanism responsible for its effects is not well understood. Circulating microRNAs (miRNAs) are promising biomarkers for disease diagnosis and prognosis. Accurate normalization using appropriate reference genes, is a critical step in miRNA expression studies. In this study, we aimed to identify appropriate reference gene for microRNA quantification in serum samples of SM victims. In this case and control experimental study, using quantitative real-time polymerase chain reaction (qRT-PCR), we evaluated the suitability of a panel of small RNAs including SNORD38B, SNORD49A, U6, 5S rRNA, miR-423-3p, miR-191, miR-16 and miR-103 in sera of 28 SM-exposed veterans of Iran-Iraq war (1980-1988) and 15 matched control volunteers. Different statistical algorithms including geNorm, Normfinder, best-keeper and comparative delta-quantification cycle (Cq) method were employed to find the least variable reference gene. miR-423-3p was identified as the most stably expressed reference gene, and miR- 103 and miR-16 ranked after that. We demonstrate that non-miRNA reference genes have the least stabil- ity in serum samples and that some house-keeping miRNAs may be used as more reliable reference genes for miRNAs in serum. In addition, using the geometric mean of two reference genes could increase the reliability of the normalizers.

  19. Wheat Germ Agglutinin Staining as a Suitable Method for Detection and Quantification of Fibrosis in Cardiac Tissue after Myocardial Infarction

    PubMed Central

    Emde, B.; Heinen, A.; Gödecke, A.; Bottermann, K.

    2014-01-01

    The quantification of fibrotic tissue is an important task in the analysis of cardiac remodeling. The use of established fibrosis staining techniques is limited on frozen cardiac tissue sections due to a reduced color contrast compared to paraffin embedded sections. We therefore used FITC-labeled wheat germ agglutinin (WGA), which marks fibrotic tissue in comparable quality as the established picrosirius red (SR) staining, for the staining of post myocardial infarction scar tissue. The fibrosis amount was quantified in a histogram-based approach using the non-commercial image processing program ImageJ. Our results clearly demonstrate that WGA-FITC is a suitable marker for cardiac fibrosis in frozen tissue sections. In combination with the histogram-based analysis, this new quantification approach is i) easy and fast to perform; ii) suitable for raw frozen tissue sections; and iii) allows the use of additional antibodies in co-immunostaining. PMID:25578975

  20. Tissue-dependent VEGF and GLUT1 induction in a rat hemorrhage model: With regard to diagnostic application of mRNA quantification in forensic pathology.

    PubMed

    Zhao, Dong; Michiue, Tomomi; Maeda, Hitoshi

    2015-10-01

    Systemic hypoxia is inevitably involved in the death process to a varying extent. Hypoxia-response factors proved useful in forensic pathology in previous studies; however, fundamental investigations using animal models are expected to reinforce the findings from autopsy practice. An animal experiment using a rat model of fixed-volume hemorrhage was performed to apply basic insight into quantitative mRNA analyses in forensic pathology. Male Sprague-Dawley rats (n=5) were anesthetized, bled from the femoral artery (24ml/kg; about 30% of total circulating blood volume), and decapitated after 1 or 2h. Tissue samples of the heart, brain (hippocampus), kidney, liver, lung and skeletal muscle were collected for RNA and protein analyses. Quantitative analyses of VEGF, GLUT1 and GAPDH mRNAs were performed with TaqMan real-time RT-PCR assay. In the sham control without bleeding, mRNA quantification revealed the tissue-dependent mRNA levels in physiological condition. Relative quantification of VEGF and GLUT1 showed significant inductions under hemorrhage at the mRNA level, using GAPDH as endogenous reference. In conclusion, tissue-dependent induction patterns of VEGF and GLUT1 were revealed in the volume-fixed hemorrhage rat model. This study could practically guide the selection of mRNA markers and tissue samples in forensic pathology related to tissue ischemia and cellular hypoxia for autopsy cases.

  1. Absolute Quantification of Lipophilic Shellfish Toxins by Quantitative Nuclear Magnetic Resonance Using Removable Internal Reference Substance with SI Traceability.

    PubMed

    Kato, Tsuyoshi; Saito, Maki; Nagae, Mika; Fujita, Kazuhiro; Watai, Masatoshi; Igarashi, Tomoji; Yasumoto, Takeshi; Inagaki, Minoru

    2016-01-01

    Okadaic acid (OA), a lipophilic shellfish toxin, was accurately quantified using quantitative nuclear magnetic resonance with internal standards for the development of an authentic reference standard. Pyridine and the residual proton in methanol-d4 were used as removable internal standards to limit any contamination. They were calibrated based on a maleic acid certified reference material. Thus, the concentration of OA was traceable to the SI units through accurate quantitative NMR with an internal reference substance. Signals from the protons on the oxygenated and unsaturated carbons of OA were used for quantification. A reasonable accuracy was obtained by integrating between the lower and upper (13)C satellite signal range when more than 4 mg of OA was used. The best-determined purity was 97.4% (0.16% RSD) when 20 mg of OA was used. Dinophysistoxin-1, a methylated analog of OA having an almost identical spectrum, was also quantified by using the same methodology.

  2. Extraction and Quantification of Carbon Nanotubes in Biological Matrices with Application to Rat Lung Tissue

    PubMed Central

    Doudrick, Kyle; Corson, Nancy; Oberdörster, Günter; Elder, Alison; Herckes, Pierre; Halden, Rolf U.; Westerhoff, Paul

    2013-01-01

    Extraction of carbon nanotubes (CNTs) from biological matrices such as rat lung tissue is integral to developing a quantification method for evaluating the environmental and human health exposure and toxicity of CNTs. The ability of various chemical treatment methods, including Solvable (2.5% sodium hydroxide/surfactant mixture), ammonium hydroxide, nitric acid, sulfuric acid, hydrochloric acid, hydrofluoric acid, hydrogen peroxide, and proteinase K, to extract CNTs from rat lung tissue was evaluated. CNTs were quantified using programmed thermal analysis (PTA). Two CNTs were used to represent the lower (500°C) and upper (800°C) PTA limit of CNT thermal stability. The recovery efficiency of each of the eight chemical reagents evaluated was found to depend on the ability to (1) minimize oxidation of CNTs, (2) remove interfering background carbon from the rat lung tissue, and (3) separate the solid-phase CNTs from the liquid-phase dissolved tissue via centrifugation. A two-step extraction method using Solvable and proteinase K emerged as the optimal approach, enabling a recovery of 98 ± 15% of a 2.9 ± 0.19 µg CNT loading that was spiked into whole rat lungs. Due to its high yield and applicability to low organ burdens of nanomaterials, this extraction method is particularly well suited for in vivo studies to quantify clearance rates and retained CNTs in lungs and other organs. PMID:23992048

  3. Point-of-care device for quantification of bilirubin in skin tissue.

    PubMed

    Alla, Suresh K; Huddle, Adam; Butler, Joshua D; Bowman, Peggy S; Clark, Joseph F; Beyette, Fred R

    2011-03-01

    Steady state diffuse reflectance spectroscopy is a nondestructive method for obtaining biochemical and physiological information from skin tissue. In medical conditions such as neonatal jaundice excess bilirubin in the blood stream diffuses into the surrounding tissue leading to a yellowing of the skin. Diffuse reflectance measurement of the skin tissue can provide real time assessment of the progression of a disease or a medical condition. Here we present a noninvasive point-of-care system that utilizes diffuse reflectance spectroscopy to quantifying bilirubin from skin reflectance spectra. The device consists of an optical system integrated with a signal processing algorithm. The device is then used as a platform to study two different spectral databases. The first spectral database is a jaundice animal model in which the jaundice reflectance spectra are synthesized from normal skin. The second spectral database is the spectral measurements collected on human volunteers to quantify the different chromophores and other physical properties of the tissue such as Hematocrit, Hemoglobin, etc. The initial trials from each of these spectral databases have laid the foundation to verify the performance of this bilirubin quantification device.

  4. The effect of tissue-segmented attenuation maps on PET quantification with a special focus on large arteries.

    PubMed

    Mota-Cobian, A; Alonso-Farto, J C; Fernández-Friera, L; Sánchez-González, J; López-Melgar, B; Jiménez-Borreguero, L J; Fuster, V; Ruiz-Cabello, J; España, S

    2017-06-19

    Accuracy on quantitative PET image analysis relies on the correct application of attenuation correction which is one of the major challenges for PET/MRI that remains to be solved. The purpose of this study is to evaluate the effect of MRI-based attenuation maps and the use of flexible coils on the quantitative accuracy of PET images with a special focus on large arteries. PET/CT data from eight oncologic patients was used. PET data was reconstructed using attenuation maps with different level of detail emulating several approaches available on current PET/MRI scanners. PET images obtained with CT-based and MRI-based attenuation maps were compared to evaluate the quantitative biases obtained. The quantitative effect produced by flexible MRI receiver coils on the attenuation maps was also studied. The use of simpler attenuation maps produced increased biases between PET data reconstructed with CT-based and MRI-based attenuation maps for fat, non-fat soft-tissues and bone. Biases in lung were very high due to the large heterogeneity and inter-patient variability of the lung. The quantification on large arteries had small deviations except for the case when flexible coils were used. The TBR provided smaller biases in all cases as it cancelled out the similar deviations obtained for arteries and reference veins. Simplified attenuation maps used on PET/MRI significantly increase the quantitative variability of PET images especially on lungs and bones. The quantification of PET images acquired with PET/MRI scanners applied to studies of atherosclerosis has small deviations, especially when the TBR is considered. Copyright © 2017 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

  5. Evaluation of Reference Genes for Quantitative Real-Time PCR in Oil Palm Elite Planting Materials Propagated by Tissue Culture

    PubMed Central

    Chan, Pek-Lan; Rose, Ray J.; Abdul Murad, Abdul Munir; Zainal, Zamri; Leslie Low, Eng-Ti; Ooi, Leslie Cheng-Li; Ooi, Siew-Eng; Yahya, Suzaini; Singh, Rajinder

    2014-01-01

    Background The somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels. Results In this study, eight candidate reference genes selected from cDNA microarray study and literature review were evaluated comprehensively across 26 tissue culture samples using RT-qPCR. These samples were collected from two tissue culture lines and media treatments, which consisted of leaf explants cultures, callus and embryoids from consecutive developmental stages. Three statistical algorithms (geNorm, NormFinder and BestKeeper) confirmed that the expression stability of novel reference genes (pOP-EA01332, PD00380 and PD00569) outperformed classical housekeeping genes (GAPDH, NAD5, TUBULIN, UBIQUITIN and ACTIN). PD00380 and PD00569 were identified as the most stably expressed genes in total samples, MA2 and MA8 tissue culture lines. Their applicability to validate the expression profiles of a putative ethylene-responsive transcription factor 3-like gene demonstrated the importance of using the geometric mean of two genes for normalization. Conclusions Systematic selection of the most stably expressed reference genes for RT-qPCR was established in oil palm tissue culture samples. PD00380 and PD00569 were selected for accurate and reliable normalization of gene expression data from RT-qPCR. These data will be valuable to the research associated with the tissue culture process. Also, the method described here will facilitate the selection of appropriate

  6. Optimization of supervised cluster analysis for extracting reference tissue input curves in (R)-[11C]PK11195 brain PET studies

    PubMed Central

    Yaqub, Maqsood; van Berckel, Bart NM; Schuitemaker, Alie; Hinz, Rainer; Turkheimer, Federico E; Tomasi, Giampaolo; Lammertsma, Adriaan A; Boellaard, Ronald

    2012-01-01

    Performance of two supervised cluster analysis (SVCA) algorithms for extracting reference tissue curves was evaluated to improve quantification of dynamic (R)-[11C]PK11195 brain positron emission tomography (PET) studies. Reference tissues were extracted from images using both a manually defined cerebellum and SVCA algorithms based on either four (SVCA4) or six (SVCA6) kinetic classes. Data from controls, mild cognitive impairment patients, and patients with Alzheimer's disease were analyzed using various kinetic models including plasma input, the simplified reference tissue model (RPM) and RPM with vascular correction (RPMVb). In all subject groups, SVCA-based reference tissue curves showed lower blood volume fractions (Vb) and volume of distributions than those based on cerebellum time-activity curve. Probably resulting from the presence of specific signal from the vessel walls that contains in normal condition a significant concentration of the 18 kDa translocation protein. Best contrast between subject groups was seen using SVCA4-based reference tissues as the result of a lower number of kinetic classes and the prior removal of extracerebral tissues. In addition, incorporation of Vb in RPM improved both parametric images and binding potential contrast between groups. Incorporation of Vb within RPM, together with SVCA4, appears to be the method of choice for analyzing cerebral (R)-[11C]PK11195 neurodegeneration studies. PMID:22588187

  7. Optimization of supervised cluster analysis for extracting reference tissue input curves in (R)-[(11)C]PK11195 brain PET studies.

    PubMed

    Yaqub, Maqsood; van Berckel, Bart N M; Schuitemaker, Alie; Hinz, Rainer; Turkheimer, Federico E; Tomasi, Giampaolo; Lammertsma, Adriaan A; Boellaard, Ronald

    2012-08-01

    Performance of two supervised cluster analysis (SVCA) algorithms for extracting reference tissue curves was evaluated to improve quantification of dynamic (R)-[(11)C]PK11195 brain positron emission tomography (PET) studies. Reference tissues were extracted from images using both a manually defined cerebellum and SVCA algorithms based on either four (SVCA4) or six (SVCA6) kinetic classes. Data from controls, mild cognitive impairment patients, and patients with Alzheimer's disease were analyzed using various kinetic models including plasma input, the simplified reference tissue model (RPM) and RPM with vascular correction (RPMV(b)). In all subject groups, SVCA-based reference tissue curves showed lower blood volume fractions (V(b)) and volume of distributions than those based on cerebellum time-activity curve. Probably resulting from the presence of specific signal from the vessel walls that contains in normal condition a significant concentration of the 18 kDa translocation protein. Best contrast between subject groups was seen using SVCA4-based reference tissues as the result of a lower number of kinetic classes and the prior removal of extracerebral tissues. In addition, incorporation of V(b) in RPM improved both parametric images and binding potential contrast between groups. Incorporation of V(b) within RPM, together with SVCA4, appears to be the method of choice for analyzing cerebral (R)-[(11)C]PK11195 neurodegeneration studies.

  8. Quantification of DNA Extracted from Formalin Fixed Paraffin-Embeded Tissue Comparison of Three Techniques: Effect on PCR Efficiency

    PubMed Central

    Panigrahi, Manoj Kumar; Suryavanshi, Moushumi; Mehta, Anurag; Saikia, Kandarpa Kumar

    2016-01-01

    Introduction Mutation detection from Formalin Fixed Paraffin-Embedding (FFPE) tissue in molecular lab became a necessary tool for defining potential targeted drug. Accurate quantification of DNA extracted from FFPE tissue is necessary for downstream applications like Polymerase Chain Reaction (PCR), sequencing etc. Aim To check and define which method for FFPE DNA quantification is suitable for downstream processes. Materials and Methods In this experimental experience study Biorad Smartspec Plus spectrophotomery, Qubit Fluorometer, and Qiagen Rotorgene qPCR was used to compare 20 FFPE DNA quantification in Rajiv Gandhi Cancer Institute and Research Centre, in 2015 and quantified amount of DNA used for PCR reaction. Results The average concentration of DNA extracted from FFPE tissue measured using the spectrophotometer was much higher than the concentration measured using the Qubit Fluorometer and qPCR. Conclusion Results varied depending upon the technique used. A fluorometric analysis may be more suitable for quantification of DNA samples extracted from FFPE tissue compared with spectrophotometric analysis. But qPCR is the best technique because it details DNA quantity along with quality of amplifiable DNA from FFPE tissue. PMID:27790419

  9. Quantification of Confocal Images Using LabVIEW for Tissue Engineering Applications.

    PubMed

    Sfakis, Lauren; Kamaldinov, Tim; Larsen, Melinda; Castracane, James; Khmaladze, Alexander

    2016-11-01

    Quantifying confocal images to enable location of specific proteins of interest in three-dimensional (3D) is important for many tissue engineering (TE) applications. Quantification of protein localization is essential for evaluation of specific scaffold constructs for cell growth and differentiation for application in TE and tissue regeneration strategies. Although obtaining information regarding protein expression levels is important, the location of proteins within cells grown on scaffolds is often the key to evaluating scaffold efficacy. Functional epithelial cell monolayers must be organized with apicobasal polarity with proteins specifically localized to the apical or basolateral regions of cells in many organs. In this work, a customized program was developed using the LabVIEW platform to quantify protein positions in Z-stacks of confocal images of epithelial cell monolayers. The program's functionality is demonstrated through salivary gland TE, since functional salivary epithelial cells must correctly orient many proteins on the apical and basolateral membranes. Bio-LabVIEW Image Matrix Evaluation (Bio-LIME) takes 3D information collected from confocal Z-stack images and processes the fluorescence at each pixel to determine cell heights, nuclei heights, nuclei widths, protein localization, and cell count. As a demonstration of its utility, Bio-LIME was used to quantify the 3D location of the Zonula occludens-1 protein contained within tight junctions and its change in 3D position in response to chemical modification of the scaffold with laminin. Additionally, Bio-LIME was used to demonstrate that there is no advantage of sub-100 nm poly lactic-co-glycolic acid nanofibers over 250 nm fibers for epithelial apicobasal polarization. Bio-LIME will be broadly applicable for quantification of proteins in 3D that are grown in many different contexts.

  10. Virtual Touch Tissue Imaging and Quantification in the Evaluation of Thyroid Nodules.

    PubMed

    Zhou, Hang; Zhou, Xian-Li; Xu, Hui-Xiong; Li, Dan-Dan; Liu, Bo-Ji; Zhang, Yi-Feng; Xu, Jun-Mei; Bo, Xiao-Wan; Li, Xiao-Long; Guo, Le-Hang; Qu, Shen

    2017-02-01

    To investigate the diagnostic performance of a 2-dimensional shear wave elastographic technique (Virtual Touch tissue imaging and quantification [VTIQ]; Siemens Medical Solutions, Mountain View, CA) for predicting thyroid malignancy. A total of 302 thyroid nodules underwent conventional sonography and VTIQ before fine-needle aspiration examination or surgery. Compared with histopathologic or cytologic results in combination with follow-up, the diagnostic performance of various shear wave speed (SWS) indices (minimum [SWSmin ], maximum [SWSmax ], and mean [SWSmean ]) on VTIQ as well as conventional sonographic features for predicting thyroid malignancy was evaluated in all of the nodules. Sixty-five malignant and 237 benign thyroid nodules were histopathologically or cytologically confirmed. All SWS indices on VTIQ were lower in benign nodules than thyroid malignancy (all P < .001). For discrimination between malignant and benign nodules, all VTIQ SWS indices were better than conventional sonographic features, such as a solid component, a taller-than-wide shape, microcalcification, a poorly defined margin and hypoechogenicity, in predicting thyroid malignancy (all P < .05). By applying a cutoff SWSmean value of 2.60 m/s, VTIQ achieved sensitivity and negative predictive values of 84.6% and 94.3%, respectively, for differentiating nodules. The areas under the receiver operating characteristic curve of SWSmax (0.862 versus 0.717), SWSmin (0.866 versus 0.717), and SWSmean (0.891 versus 0.725) for nodules larger than 10 mm were higher than those for nodules of 10 mm or smaller (all P < .05). Interoperator and intraoperator reproducibility was proven to be excellent, with all interclass correlation coefficient values higher than 0.80 (range, 0.813-0.905) CONCLUSIONS: Virtual Touch tissue imaging and quantification is a useful and reproducible tool for predicting thyroid malignancy. © 2016 by the American Institute of Ultrasound in Medicine.

  11. mTRAQ-based quantification of potential endometrial carcinoma biomarkers from archived formalin-fixed paraffin-embedded tissues.

    PubMed

    DeSouza, Leroi V; Krakovska, Olga; Darfler, Marlene M; Krizman, David B; Romaschin, Alexander D; Colgan, Terence J; Siu, K W Michael

    2010-09-01

    Formalin-fixed paraffin-embedded (FFPE) tissues are the primary and preferred medium for archiving patients' samples. Here we demonstrate relative quantifications of protein biomarkers in extracts of laser microdissected epithelial cells from FFPE endometrial carcinoma tissues versus those from normal proliferative endometria by means of targeted proteomic analyses using LC-multiple reaction monitoring (MRM) MS with MRM Tags for Relative and Absolute Quantitation (mTRAQ) labeling. Comparable results of differential expressions for pyruvate kinase isoform M2 (PK-M2) and polymeric Ig receptor were observed between analyses on laser microdissected epithelial cells from FFPE tissues and corresponding homogenates from frozen tissues of the same individuals that had previously been analyzed and reported. We also identified PK-M2 in the normal proliferative phase of the endometrium. Other biomarkers in addition to PK-M2 and polymeric Ig receptor were also observed but not consistently and/or were at levels below the threshold for quantification.

  12. A validation of 10 feline reference genes for gene expression measurements in snap-frozen tissues.

    PubMed

    Penning, Louis C; Vrieling, Henriette E; Brinkhof, Bas; Riemers, Frank M; Rothuizen, Jan; Rutteman, Gerard R; Hazewinkel, Herman A W

    2007-12-15

    For a proper determination of relative mRNA expression levels with real-time quantitative PCR (Q-PCR) internal standards, such as the expression of reference genes, are of utmost importance. For cats, in contrast to dogs, no validation of reference genes has been published. Our goal was to evaluate frequently used reference genes for the analysis of relative mRNA levels from feline tissues in a SYBR Green-based Q-PCR protocol. First, primers were optimized on mRNA-derived cDNA from liver and kidney tissues of randomly chosen (healthy and diseased) cats. Then, the expression variation and stability of each reference gene within a specific tissue was determined. Dental roots and crowns, heart (left ventricle), renal, liver, lung, and mammary gland tissues from 3 to 11 cats of different breeds, sexes, ages, and disease status were included in this study. Averaging relative stabilities over these six tissues revealed the usefulness of each tested gene as reference gene. In order to compensate for the expression variation of a reference gene within a specific tissue, as much as six reference genes (e.g. RPL17, RPL30, RPS7, YWHAZ, and HPRT) were required to obtain highly reliable data in cat tissues. The optimal set of reference genes depended on the tissue analyzed and should, ideally, be selected and evaluated at the start of each experimental condition. A comparison with a similar evaluation in dogs revealed three issues: (i) most ribosomal genes are suitable in both species; (ii) good non-ribosomal reference genes differ; (iii) more feline than canine reference genes are required for proper analysis.

  13. Analysis of dissected tissues with digital holographic microscopy: quantification of inflammation mediated tissue alteration, influence of sample preparation, and reliability of numerical autofocusing

    NASA Astrophysics Data System (ADS)

    Kemper, Björn; Lenz, Philipp; Bettenworth, Dominik; Krausewitz, Philipp; Domagk, Dirk; Ketelhut, Steffi

    2015-03-01

    Quantitative phase imaging with digital holographic microscopy (DHM) allows label-free imaging of tissue sections and quantification of the spatial refractive index distribution, which is of interest for applications in digital pathology. We show that DHM allows quantitative imaging of different layers in unstained tissue samples by detection of refractive index changes. In addition, we evaluate the automated refocussing feature of DHM for application on dissected tissues and could achieve highly reproducible holographic autofocusing for unstained and moderately stained samples. Finally, it is demonstrated that in human ulcerative colitis patients the average tissue refractive index is reduced significantly in all parts of the inflamed colonic wall in comparison to patients in remission.

  14. Quantification of in vivo fluorescence decoupled from the effects of tissue optical properties using fiber-optic spectroscopy measurements

    NASA Astrophysics Data System (ADS)

    Kim, Anthony; Khurana, Mamta; Moriyama, Yumi; Wilson, Brian C.

    2010-11-01

    We present a method for tissue fluorescence quantification in situ using a handheld fiber optic probe that measures both the fluorescence and diffuse reflectance spectra. A simplified method to decouple the fluorescence spectrum from distorting effects of the tissue optical absorption and scattering is developed, with the objective of accurately quantifying the fluorescence in absolute units. The primary motivation is measurement of 5-aminolevulinic acid-induced protoporphyrin IX (ALA-PpIX) concentration in tissue during fluorescence-guided resection of malignant brain tumors. This technique is validated in phantoms and ex vivo mouse tissues, and tested in vivo in a rabbit brain tumor model using ALA-PpIX fluorescence contrast.

  15. Feasibility study on measuring selected proteins in malignant melanoma tissue by SRM quantification.

    PubMed

    Welinder, Charlotte; Jönsson, Göran; Ingvar, Christian; Lundgren, Lotta; Baldetorp, Bo; Olsson, Håkan; Breslin, Thomas; Rezeli, Melinda; Jansson, Bo; Laurell, Thomas; Fehniger, Thomas E; Wieslander, Elisabet; Pawlowski, Krzysztof; Marko-Varga, György

    2014-03-07

    Currently there are no clinically recognized molecular biomarkers for malignant melanoma (MM) for either diagnosing disease stage or measuring response to therapy. The aim of this feasibility study was to develop targeted selected reaction monitoring (SRM) assays for identifying candidate protein biomarkers in metastatic melanoma tissue lysate. In a pilot study applying the SRM assay, the tissue expression of nine selected proteins [complement 3 (C3), T-cell surface glycoprotein CD3 epsilon chain E (CD3E), dermatopontin, minichromosome maintenance complex component (MCM4), premelanosome protein (PMEL), S100 calcium binding protein A8 (S100A8), S100 calcium binding protein A13 (S100A13), transgelin-2 and S100B] was quantified in a small cohort of metastatic malignant melanoma patients. The SRM assay was developed using a TSQ Vantage triple quadrupole mass spectrometer that generated highly accurate peptide quantification. Repeated injection of internal standards spiked into matrix showed relative standard deviation (RSD) from 6% to 15%. All nine target proteins were identified in tumor lysate digests spiked with heavy peptide standards. The multiplex SRM peptide assay panel was then measured and quantified on a set of frozen MM tissue samples obtained from the Malignant Melanoma Biobank collected in Lund, Sweden. All nine proteins could be accurately quantified using the new SRM assay format. This study provides preliminary data on the heterogeneity of biomarker expression within MM patients. The S100B protein, which is clinically used as the pathology identifier of MM, was identified in 9 out of 10 MM tissue lysates. The use of the targeted SRM assay provides potential advancements in the diagnosis of MM that can aid in future assessments of disease in melanoma patients.

  16. Non-Invasive, Simultaneous Quantification of Vascular Oxygenation and Glucose Uptake in Tissue

    PubMed Central

    Rajaram, Narasimhan; Reesor, Andrew F.; Mulvey, Christine S.; Frees, Amy E.; Ramanujam, Nirmala

    2015-01-01

    We report the development of non-invasive, fiber-based diffuse optical spectroscopy for simultaneously quantifying vascular oxygenation (SO2) and glucose uptake in solid tumors in vivo. Glucose uptake was measured using a fluorescent glucose analog, 2-[N-(7-nitrobenz-2-oxa-1,3-diaxol-4-yl)amino]-2-deoxyglucose (2-NBDG). Quantification of label-free SO2 and 2-NBDG-fluorescence-based glucose uptake 60 minutes after administration of the tracer (2-NBDG60) was performed using computational models of light-tissue interaction. This study was carried out on normal tissue and 4T1 and 4T07 murine mammary tumor xenografts in vivo. Injection of 2-NBDG did not cause a significant change in optical measurements of SO2, demonstrating its suitability as a functional reporter of tumor glucose uptake. Correction of measured 2-NBDG-fluorescence for the effects of absorption and scattering significantly improved contrast between tumor and normal tissue. The 4T1 and 4T07 tumors showed significantly decreased SO2, and 4T1 tumors demonstrated increased 2-NBDG60 compared with normal tissue (60 minutes after the administration of 2-NBDG when perfusion-mediated effects have cleared). 2-NBDG-fluorescence was found to be highly sensitive to food deprivation-induced reduction in blood glucose levels, demonstrating that this endpoint is indeed sensitive to glycolytic demand. 2-NBDG60 was also found to be linearly related to dose, underscoring the importance of calibrating for dose when comparing across animals or experiments. 4T1 tumors demonstrated an inverse relationship between 2-NBDG60 and SO2 that was consistent with the Pasteur effect, particularly when exposed to hypoxic gas breathing. Our results illustrate the potential of optical spectroscopy to provide valuable information about the metabolic status of tumors, with important implications for cancer prognosis. PMID:25635865

  17. Bovine muscle 20S proteasome. III: Quantification in tissue crude extracts using ELISA and radial immunodiffusion techniques and practical applications.

    PubMed

    Aubry, L; Sentandreu, M A; Levieux, D; Ouali, A; Dutaud, D

    2006-10-01

    The 20S proteasome is a large complex (700kDa) that exhibits endo- and exo-peptidase activities with wide specificity. In postmortem muscles, several sets of evidence suggest a possible significant contribution of proteasome to meat tenderisation. Hence, an accurate and rapid quantification procedure is needed to attest that new function during the ageing of meat. In the present work, we developed an ELISA test enabling the quantification of nM concentrations of the 20S proteasome. We further tested the radial immunodiffusion (RID) technique described as a more simple method that can quantitatively determine the concentration of an antigen in a complex mixture. The ELISA test allowed us to quantify the 20S protesome in tissue homogenates and fluids with a recovery of 100%, a coefficient of variation lower than 5% and a detection limit of 9ng/ml. Quantification of the 20S proteasome in various bovine tissue by ELISA showed the highest concentration in liver followed by spleen and kidney, with muscles exhibiting the lowest concentrations. In addition, measurement of the proteasome concentration in eight different bovine muscles with various metabolic profiles led to the conclusion that the relationship between muscle metabolic properties and proteasome concentration is rather complex. Nevertheless, heart muscle exhibited the highest proteasome content (331μg/g wet tissue) whereas the lowest values were found for M. Tensor Fascia Latae (213μg/g wet tissue), a fast twitch white muscle, M. Supraspinatus (209μg/g wet tissue), a slow twitch red muscle and M. Pectoralis profondus (203μg/g wet tissue), an intermediate muscle. As compared to other endogenous peptidases, muscle tissue contains relatively high amounts of proteasome. Hence this complex can be quantified using the RID, which allows quantification of protein in the μg range. Plotting the concentration values determined with both methods for all bovine tissues tested gave a straight line with a correlation

  18. Quantification of amounts and (13)C content of metabolites in brain tissue using high- resolution magic angle spinning (13)C NMR spectroscopy.

    PubMed

    Risa, Oystein; Melø, Torun Margareta; Sonnewald, Ursula

    2009-04-01

    Metabolic pathway mapping using (13)C NMR spectroscopy has been used extensively to study interactions between neurons and glia in the brain. Established extraction procedures of brain tissue are time consuming and may result in degradation of labile substances. We examined the potential of mapping (13)C-enriched compounds in intact brain tissue using high-resolution magic angle spinning (HR-MAS) NMR spectroscopy. Sprague-Dawley rats received an intraperitoneal injection of [1,6-(13)C]glucose, and 15 min later the animals were subjected to microwave fixation of the brain. Quantification of concentration and (13)C labelling of metabolites in intact rat thalamus were carried out based on exogenous ethylene glycol concentrations measured from (1)H NMR spectra using an ERETIC (Electronic REference To access In vivo Concentrations) signal. The results from intact tissue were compared with those from perchloric acid-extracted brain tissue. Amounts of (13)C labelling at different positions (C2, C3 and C4) in glutamate, glutamine, gamma-aminobutyric acid and aspartate measured in either intact tissue or perchloric acid extracts were not significantly different. Proton NMR spectra were used for quantification of six different amino acids plus lactate, inositol, N-acetylaspartate, creatine and phosphocreatine. Again, results were very similar when comparing the methods. To our knowledge, this is the first time quantitative (13)C NMR spectroscopy measurements have been carried out on intact brain tissue ex vivo using the HR-MAS technique. The results show that HR-MAS (13)C NMR spectroscopy in combination with (1)H NMR spectroscopy and the ERETIC method is useful for metabolic studies of intact brain tissue ex vivo.

  19. Characterization of reference genes for qPCR analysis in various tissues of the Fujian oyster Crassostrea angulata

    NASA Astrophysics Data System (ADS)

    Pu, Fei; Yang, Bingye; Ke, Caihuan

    2015-07-01

    Accurate quantification of transcripts using quantitative real-time polymerase chain reaction (qPCR) depends on the identification of reliable reference genes for normalization. This study aimed to identify and validate seven reference genes, including actin-2 ( ACT-2), elongation factor 1 alpha ( EF-1α), elongation factor 1 beta ( EF-1β), glyceraldehyde-3-phosphate dehydrogenase ( GAPDH), ubiquitin ( UBQ), β-tubulin ( β-TUB), and 18S ribosomal RNA, from Crassostrea angulata, a valuable marine bivalve cultured worldwide. Transcript levels of the candidate reference genes were examined using qPCR analysis and showed differential expression patterns in the mantle, gill, adductor muscle, labial palp, visceral mass, hemolymph and gonad tissues. Quantitative data were analyzed using the geNorm software to assess the expression stability of the candidate reference genes, revealing that β-TUB and UBQ were the most stable genes. The commonly used GAPDH and 18S rRNA showed low stability, making them unsuitable candidates in this system. The expression pattern of the G protein β-subunit gene ( Gβ) across tissue types was also examined and normalized to the expression of each or both of UBQ and β-TUB as internal controls. This revealed consistent trends with all three normalization approaches, thus validating the reliability of UBQ and β-TUB as optimal internal controls. The study provides the first validated reference genes for accurate data normalization in transcript profiling in Crassostrea angulata, which will be indispensable for further functional genomics studies in this economically valuable marine bivalve.

  20. Establishing a reliable multiple reaction monitoring-based method for the quantification of obesity-associated comorbidities in serum and adipose tissue requires intensive clinical validation.

    PubMed

    Oberbach, Andreas; Schlichting, Nadine; Neuhaus, Jochen; Kullnick, Yvonne; Lehmann, Stefanie; Heinrich, Marco; Dietrich, Arne; Mohr, Friedrich Wilhelm; von Bergen, Martin; Baumann, Sven

    2014-12-05

    Multiple reaction monitoring (MRM)-based mass spectrometric quantification of peptides and their corresponding proteins has been successfully applied for biomarker validation in serum. The option of multiplexing offers the chance to analyze various proteins in parallel, which is especially important in obesity research. Here, biomarkers that reflect multiple comorbidities and allow monitoring of therapy outcomes are required. Besides the suitability of established MRM assays for serum protein quantification, it is also feasible for analysis of tissues secreting the markers of interest. Surprisingly, studies comparing MRM data sets with established methods are rare, and therefore the biological and clinical value of most analytes remains questionable. A MRM method using nano-UPLC-MS/MS for the quantification of obesity related surrogate markers for several comorbidities in serum, plasma, visceral and subcutaneous adipose tissue was established. Proteotypic peptides for complement C3, adiponectin, angiotensinogen, and plasma retinol binding protein (RBP4) were quantified using isotopic dilution analysis and compared to the standard ELISA method. MRM method variabilities were mainly below 10%. The comparison with other MS-based approaches showed a good correlation. However, large differences in absolute quantification for complement C3 and adiponectin were obtained compared to ELISA, while less marked differences were observed for angiotensinogen and RBP4. The verification of MRM in obesity was performed to discriminate first lean and obese phenotype and second to monitor excessive weight loss after gastric bypass surgery in a seven-month follow-up. The presented MRM assay was able to discriminate obese phenotype from lean and monitor weight loss related changes of surrogate markers. However, inclusion of additional biomarkers was necessary to interpret the MRM data on obesity phenotype properly. In summary, the development of disease-related MRMs should include a

  1. Quantification of effects of cancer on elastic properties of breast tissue by Atomic Force Microscopy.

    PubMed

    Ansardamavandi, Arian; Tafazzoli-Shadpour, Mohammad; Omidvar, Ramin; Jahanzad, Iisa

    2016-07-01

    Different behaviors of cells such as growth, differentiation and apoptosis widely differ in case of diseases. The mechanical properties of cells and tissues can be used as a clue for diagnosis of pathological conditions. Here, we implemented Atomic Force Microscopy to evaluate the extent of alteration in mechanical stiffness of tissue layers from patients affected by breast cancer and investigated how data can be categorized based on pathological observations. To avoid predefined categories, Fuzzy-logic algorithm as a novel method was used to divide and categorize the derived Young׳s modulus coefficients (E). Such algorithm divides data among groups in such way that data of each group are mostly similar while dissimilar with other groups. The algorithm was run for different number of categories. Results showed that three (followed by two with small difference) groups categorized data best. Three categories were defined as (E<3000Pa, 30007000Pa) among which data were allocated. The first cluster was assumed as the cellular region while the last cluster was referred to the fibrous parts of the tissue. The intermediate region was due to other non-cellular parts. Results indicated 50% decline of average Young׳s modulus of cellular region of cancerous tissues compared to healthy tissues. The average Young׳s modulus of non-cellular area of normal tissues was slightly lower than that of cancerous tissues, although the difference was not statistically different. Through clustering, the measured Young׳s moduli of different locations of cancerous tissues, a quantified approach was developed to analyze changes in elastic modulus of a spectrum of components of breast tissue which can be applied in diagnostic mechanisms of cancer development, since in cancer progression the softening cell body facilitates the migration of cancerous cells through the original tumor and endothelial junctions.

  2. Comparison of Methods for Quantification of Global DNA Methylation in Human Cells and Tissues

    PubMed Central

    Tomaszewski, Bartłomiej; De Prins, Sofie; Jacobs, Griet; Koppen, Gudrun; Mathers, John C.; Langie, Sabine A. S.

    2013-01-01

    DNA methylation is a key epigenetic modification which, in mammals, occurs mainly at CpG dinucleotides. Most of the CpG methylation in the genome is found in repetitive regions, rich in dormant transposons and endogenous retroviruses. Global DNA hypomethylation, which is a common feature of several conditions such as ageing and cancer, can cause the undesirable activation of dormant repeat elements and lead to altered expression of associated genes. DNA hypomethylation can cause genomic instability and may contribute to mutations and chromosomal recombinations. Various approaches for quantification of global DNA methylation are widely used. Several of these approaches measure a surrogate for total genomic methyl cytosine and there is uncertainty about the comparability of these methods. Here we have applied 3 different approaches (luminometric methylation assay, pyrosequencing of the methylation status of the Alu repeat element and of the LINE1 repeat element) for estimating global DNA methylation in the same human cell and tissue samples and have compared these estimates with the “gold standard” of methyl cytosine quantification by HPLC. Next to HPLC, the LINE1 approach shows the smallest variation between samples, followed by Alu. Pearson correlations and Bland-Altman analyses confirmed that global DNA methylation estimates obtained via the LINE1 approach corresponded best with HPLC-based measurements. Although, we did not find compelling evidence that the gold standard measurement by HPLC could be substituted with confidence by any of the surrogate assays for detecting global DNA methylation investigated here, the LINE1 assay seems likely to be an acceptable surrogate in many cases. PMID:24260150

  3. Novel comprehensive approach for accessible biomarker identification and absolute quantification from precious human tissues.

    PubMed

    Turtoi, Andrei; Dumont, Bruno; Greffe, Yannick; Blomme, Arnaud; Mazzucchelli, Gabriel; Delvenne, Philippe; Mutijima, Eugène Nzaramba; Lifrange, Eric; De Pauw, Edwin; Castronovo, Vincent

    2011-07-01

    The identification of specific biomarkers obtained directly from human pathological lesions remains a major challenge, because the amount of tissue available is often very limited. We have developed a novel, comprehensive, and efficient method permitting the identification and absolute quantification of potentially accessible proteins in such precious samples. This protein subclass comprises cell membrane associated and extracellular proteins, which are reachable by systemically deliverable substances and hence especially suitable for diagnosis and targeted therapy applications. To isolate such proteins, we exploited the ability of chemically modified biotin to label ex vivo accessible proteins and the fact that most of these proteins are glycosylated. This approach consists of three successive steps involving first the linkage of potentially accessible proteins to biotin molecules followed by their purification. The remaining proteins are then subjected to glycopeptide isolation. Finally, the analysis of the nonglycosylated peptides and their involvement in an in silico method increased the confident identification of glycoproteins. The value of the technique was demonstrated on human breast cancer tissue samples originating from 5 individuals. Altogether, the method delivered quantitative data on more than 400 potentially accessible proteins (per sample and replicate). In comparison to biotinylation or glycoprotein analysis alone, the sequential method significantly increased the number (≥30% and ≥50% respectively) of potentially therapeutically and diagnostically valuable proteins. The sequential method led to the identification of 93 differentially modulated proteins, among which several were not reported to be associated with the breast cancer. One of these novel potential biomarkers was CD276, a cell membrane-associated glycoprotein. The immunohistochemistry analysis showed that CD276 is significantly differentially expressed in a series of breast cancer

  4. Localization and quantification of drugs in animal tissues by use of desorption electrospray ionization mass spectrometry imaging.

    PubMed

    Vismeh, Ramin; Waldon, Daniel J; Teffera, Yohannes; Zhao, Zhiyang

    2012-06-19

    Mass spectrometric imaging (MSI) has emerged as a powerful technique to obtain spatial arrangement of individual molecular ions in animal tissues. Ambient desorption electrospray ionization (DESI) technique is uniquely suited for such imaging experiments, as it can be performed on animal tissues in their native environment without prior treatments. Although MSI has become a rapid growing technique for localization of proteins, lipids, drugs, and endogenous compounds in different tissues, quantification of imaged targets has not been explored extensively. Here we present a novel MSI approach for localization and quantification of drugs in animal thin tissue sections. DESI-MSI using an Orbitrap mass analyzer in full scan mode was performed on 6 μm coronal brain sections from rats that were administered 2.5 mg/kg clozapine. Clozapine was localized and quantified in individual brain sections 45 min postdose. External calibration curves were prepared by micropipetting standards with internal standard (IS) on top of the tissues, and average response factors were calculated for the scans in which both clozapine and IS were detected. All response factors were normalized to area units. Quantifications from DESI-MSI revealed 0.2-1.2 ng of clozapine in individual brain sections, results that were further confirmed by extraction and liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis.

  5. Technical evaluation of Virtual Touch™ tissue quantification and elastography in benign and malignant breast tumors.

    PubMed

    Jiang, Quan; Zhang, Yuan; Chen, Jian; Zhang, Yun-Xiao; He, Zhu

    2014-10-01

    The aim of this study was to investigate the diagnostic value of the Virtual Touch™ tissue quantification (VTQ) and elastosonography technologies in benign and malignant breast tumors. Routine preoperative ultrasound, elastosonography and VTQ examinations were performed on 86 patients with breast lesions. The elastosonography score and VTQ speed grouping of each lesion were measured and compared with the pathological findings. The difference in the elastosonography score between the benign and malignant breast tumors was statistically significant (P<0.05). The detection rate for an elastosonography score of 1-3 points in benign tumors was 68.09% and that for an elastosonography score of 4-5 points in malignant tumors was 82.05%. The difference in VTQ speed values between the benign and malignant tumors was also statistically significant (P<0.05). In addition, the diagnostic accuracy of conventional ultrasound, elastosonography, VTQ technology and the combined methods showed statistically significant differences (P<0.05). The use of the three technologies in combination significantly improved the diagnostic accuracy to 91.86%. In conclusion, the combination of conventional ultrasound, elastosonography and VTQ technology can significantly improve accuracy in the diagnosis of breast cancer.

  6. In vivo quantification of motion in liver parenchyma and its application in shistosomiasis tissue characterization

    NASA Astrophysics Data System (ADS)

    Badawi, Ahmed M.; Hashem, Ahmed M.; Youssef, Abou-Bakr M.; Abdel-Wahab, Mohamed F.

    1995-03-01

    Schistosomiasis is a major problem in Egypt, despite an active control program it is estimated to exist in about 1/3 of the population. Deposition of less functioning fibrous tissues in the liver is the major contributory factor to the hepatic pathology. Fibrous tissues consist of a complex array of connective matrix material and a variety of collagen isotopes. As a result of an increased stromal density (collagen content), the parenchyma became more ectogenic and less elastic (hard). In this study we investigated the effect of cardiac mechanical impulses from the heart and aorta on the kinetics of the liver parenchyma. Under conditions of controlled patient movements and suspended respiration, a 30 frame per second of 588 X 512 ultrasound images (cineloop, 32 pels per cm) are captured from an aTL ultrasound machine then digitized. The image acquisition is triggered by the R wave of the ECG of the patient. The motion that has a forced oscillation form in the liver parenchyma is quantified by tracking of small box (20 - 30 pels) in 16 directions for all the successive 30 frames. The tracking was done using block matching techniques (the max correlation between boxes in time, frequency domains, and the minimum SAD (sum absolute difference) between boxes). The motion is quantified for many regions at different positions within the liver parenchyma for 80 cases of variable degrees of schisto., cirrhotic livers, and for normal livers. The velocity of the tissue is calculated from the displacement (quantified motion), time between frames, and the scan time for the ultrasound scanner. We found that the motion in liver parenchyma is small in the order of very few millimeters, and the attenuation of the mechanical wave for one ECG cycle is higher in the schisto. and cirrhotic livers than in the normal ones. Finally quantification of motion in liver parenchyma due to cardiac impulses under controlled limb movement and respiration may be of value in the characterization of

  7. Detection, identification, and quantification of selenoproteins in a candidate human plasma standard reference material.

    PubMed

    Ballihaut, Guillaume; Kilpatrick, Lisa E; Davis, W Clay

    2011-11-15

    To understand the effect of Se supplementation on health, it is critical to accurately assess the Se status in the human body by measuring reliable biomarkers. The preferred biomarkers of the Se status are selenoprotein P (SelP) and glutathione peroxidase 3 (GPx3) along with selenoalbumin (SeAlb), but there is still a real need for reference methods and reference materials to validate their measurements. Therefore, this work presents a systematic approach to provide quality control data in selenoprotein measurements. This approach combines online isotope dilution affinity liquid chromatography (LC) coupled to inductively coupled plasma mass spectrometry (ICPMS), laser ablation ICPMS, and tandem mass spectrometry (MS/MS) to identify and quantify SelP, GPx3, and SeAlb in a human plasma reference material SRM 1950. Quantitative determinations of SelP, GPx3, and SeAlb were 50.2 ± 4.3, 23.6 ± 1.3, and 28.2 ± 2.6 ng g(-1) as Se, respectively. The subsequent identification of the selenoproteins included nine SelP peptides, including two selenopeptides and nine GPx3 peptides, while albumin was identified with a protein coverage factor >95%. The structural elucidation of selenoproteins in the target Se affinity fractions in SRM 1950 provides information needed for method validation and quality control measurements of selenoproteins and therefore the selenium status in human plasma.

  8. Deep-Dive Targeted Quantification for Ultrasensitive Analysis of Proteins in Nondepleted Human Blood Plasma/Serum and Tissues.

    PubMed

    Nie, Song; Shi, Tujin; Fillmore, Thomas L; Schepmoes, Athena A; Brewer, Heather; Gao, Yuqian; Song, Ehwang; Wang, Hui; Rodland, Karin D; Qian, Wei-Jun; Smith, Richard D; Liu, Tao

    2017-09-05

    Mass spectrometry-based targeted proteomics (e.g., selected reaction monitoring, SRM) is emerging as an attractive alternative to immunoassays for protein quantification. Recently we have made significant progress in SRM sensitivity for enabling quantification of low nanograms per milliliter to sub-naograms per milliliter level proteins in nondepleted human blood plasma/serum without affinity enrichment. However, precise quantification of extremely low abundance proteins (e.g., ≤ 100 pg/mL in blood plasma/serum) using targeted proteomics approaches still remains challenging, especially for these samples without available antibodies for enrichment. To address this need, we have developed an antibody-independent deep-dive SRM (DD-SRM) approach that capitalizes on multidimensional high-resolution reversed-phase liquid chromatography (LC) separation for target peptide separation and enrichment combined with precise selection of target peptide fractions of interest, significantly improving SRM sensitivity by ∼5 orders of magnitude when compared to conventional LC-SRM. Application of DD-SRM to human serum and tissue provides precise quantification of endogenous proteins at the ∼10 pg/mL level in nondepleted serum and at <10 copies per cell level in tissue. Thus, DD-SRM holds great promise for precisely measuring extremely low abundance proteins or protein modifications, especially when high-quality antibodies are not available.

  9. Multiscale quantification of tissue spiculation and distortion for detection of architectural distortion and spiculated mass in mammography

    NASA Astrophysics Data System (ADS)

    Lao, Zhiqiang; Zheng, Xin

    2011-03-01

    This paper proposes a multiscale method to quantify tissue spiculation and distortion in mammography CAD systems that aims at improving the sensitivity in detecting architectural distortion and spiculated mass. This approach addresses the difficulty of predetermining the neighborhood size for feature extraction in characterizing lesions demonstrating spiculated mass/architectural distortion that may appear in different sizes. The quantification is based on the recognition of tissue spiculation and distortion pattern using multiscale first-order phase portrait model in texture orientation field generated by Gabor filter bank. A feature map is generated based on the multiscale quantification for each mammogram and two features are then extracted from the feature map. These two features will be combined with other mass features to provide enhanced discriminate ability in detecting lesions demonstrating spiculated mass and architectural distortion. The efficiency and efficacy of the proposed method are demonstrated with results obtained by applying the method to over 500 cancer cases and over 1000 normal cases.

  10. Development of apple certified reference material for quantification of organophosphorus and pyrethroid pesticides.

    PubMed

    Otake, Takamitsu; Yarita, Takashi; Aoyagi, Yoshie; Kuroda, Youko; Numata, Masahiko; Iwata, Hitoshi; Watai, Masatoshi; Mitsuda, Hitoshi; Fujikawa, Takashi; Ota, Hidekazu

    2013-06-01

    An apple certified reference material for the analysis of pesticide residues was issued by the National Metrology Institute of Japan. Organophosphorus and pyrethroid pesticides were sprayed on apples, and these were used as raw materials of certified reference material. The harvested apples were cut into small pieces, freeze-dried, pulverized, sieved, placed into 200 brown glass bottles (3g each), and sterilized by γ-irradiation. Stability and homogeneity assessment was performed, and the relative uncertainties due to instability (for an expiry date of 32 months) and inhomogeneity were 10.3-25.0% and 4.0-6.8%, respectively. The characterization was carried out using multiple analytical methods to ensure the reliability of analytical results; the values of target pesticides were obtained by isotope dilution mass spectrometry. Certified values were 2.28 ± 0.82 mg/kg for diazinon, 3.14 ± 0.79 mg/kg for fenitrothion, 1.55 ± 0.81 mg/kg for cypermethrin, and 2.81 ± 0.70 mg/kg for permethrin. Copyright © 2012 Elsevier Ltd. All rights reserved.

  11. Quantification of Calcified Particles in Human Valve Tissue Reveals Asymmetry of Calcific Aortic Valve Disease Development.

    PubMed

    Yabusaki, Katsumi; Hutcheson, Joshua D; Vyas, Payal; Bertazzo, Sergio; Body, Simon C; Aikawa, Masanori; Aikawa, Elena

    2016-01-01

    Recent studies indicated that small calcified particles observable by scanning electron microscopy (SEM) may initiate calcification in cardiovascular tissues. We hypothesized that if the calcified particles precede gross calcification observed in calcific aortic valve disease (CAVD), they would exhibit a regional asymmetric distribution associated with CAVD development, which always initiates at the base of aortic valve leaflets adjacent to the aortic outflow in a region known as the fibrosa. Testing this hypothesis required counting the calcified particles in histological sections of aortic valve leaflets. SEM images, however, do not provide high contrast between components within images, making the identification and quantification of particles buried within tissue extracellular matrix difficult. We designed a new unique pattern-matching based technique to allow for flexibility in recognizing particles by creating a gap zone in the detection criteria that decreased the influence of non-particle image clutter in determining whether a particle was identified. We developed this flexible pattern particle-labeling (FpPL) technique using synthetic test images and human carotid artery tissue sections. A conventional image particle counting method (preinstalled in ImageJ) did not properly recognize small calcified particles located in noisy images that include complex extracellular matrix structures and other commonly used pattern-matching methods failed to detect the wide variation in size, shape, and brightness exhibited by the particles. Comparative experiments with the ImageJ particle counting method demonstrated that our method detected significantly more (p < 2 × 10(-7)) particles than the conventional method with significantly fewer (p < 0.0003) false positives and false negatives (p < 0.0003). We then applied the FpPL technique to CAVD leaflets and showed a significant increase in detected particles in the fibrosa at the base of the leaflets (p

  12. Quantification of Calcified Particles in Human Valve Tissue Reveals Asymmetry of Calcific Aortic Valve Disease Development

    PubMed Central

    Yabusaki, Katsumi; Hutcheson, Joshua D.; Vyas, Payal; Bertazzo, Sergio; Body, Simon C.; Aikawa, Masanori; Aikawa, Elena

    2016-01-01

    Recent studies indicated that small calcified particles observable by scanning electron microscopy (SEM) may initiate calcification in cardiovascular tissues. We hypothesized that if the calcified particles precede gross calcification observed in calcific aortic valve disease (CAVD), they would exhibit a regional asymmetric distribution associated with CAVD development, which always initiates at the base of aortic valve leaflets adjacent to the aortic outflow in a region known as the fibrosa. Testing this hypothesis required counting the calcified particles in histological sections of aortic valve leaflets. SEM images, however, do not provide high contrast between components within images, making the identification and quantification of particles buried within tissue extracellular matrix difficult. We designed a new unique pattern-matching based technique to allow for flexibility in recognizing particles by creating a gap zone in the detection criteria that decreased the influence of non-particle image clutter in determining whether a particle was identified. We developed this flexible pattern particle-labeling (FpPL) technique using synthetic test images and human carotid artery tissue sections. A conventional image particle counting method (preinstalled in ImageJ) did not properly recognize small calcified particles located in noisy images that include complex extracellular matrix structures and other commonly used pattern-matching methods failed to detect the wide variation in size, shape, and brightness exhibited by the particles. Comparative experiments with the ImageJ particle counting method demonstrated that our method detected significantly more (p < 2 × 10−7) particles than the conventional method with significantly fewer (p < 0.0003) false positives and false negatives (p < 0.0003). We then applied the FpPL technique to CAVD leaflets and showed a significant increase in detected particles in the fibrosa at the base of the leaflets (p

  13. Identification of reference genes and validation for gene expression studies in diverse axolotl (Ambystoma mexicanum) tissues.

    PubMed

    Guelke, Eileen; Bucan, Vesna; Liebsch, Christina; Lazaridis, Andrea; Radtke, Christine; Vogt, Peter M; Reimers, Kerstin

    2015-04-10

    For the precise quantitative RT-PCR normalization a set of valid reference genes is obligatory. Moreover have to be taken into concern the experimental conditions as they bias the regulation of reference genes. Up till now, no reference targets have been described for the axolotl (Ambystoma mexicanum). In a search in the public database SalSite for genetic information of the axolotl we identified fourteen presumptive reference genes, eleven of which were further tested for their gene expression stability. This study characterizes the expressional patterns of 11 putative endogenous control genes during axolotl limb regeneration and in an axolotl tissue panel. All 11 reference genes showed variable expression. Strikingly, ACTB was to be found most stable expressed in all comparative tissue groups, so we reason it to be suitable for all different kinds of axolotl tissue-type investigations. Moreover do we suggest GAPDH and RPLP0 as suitable for certain axolotl tissue analysis. When it comes to axolotl limb regeneration, a validated pair of reference genes is ODC and RPLP0. With these findings, new insights into axolotl gene expression profiling might be gained.

  14. CCQM-K86/P113.1: Relative quantification of genomic DNA fragments extracted from a biological tissue

    NASA Astrophysics Data System (ADS)

    Corbisier, P.; Vincent, S.; Schimmel, H.; Kortekaas, A.-M.; Trapmann, S.; Burns, M.; Bushell, C.; Akgoz, M.; Akyürek, S.; Dong, L.; Fu, B.; Zhang, L.; Wang, J.; Pérez Urquiza, M.; Bautista, J. L.; Garibay, A.; Fuller, B.; Baoutina, A.; Partis, L.; Emslie, K.; Holden, M.; Chum, W. Y.; Kim, H.-H.; Phunbua, N.; Milavec, M.; Zel, J.; Vonsky, M.; Konopelko, L. A.; Lau, T. L. T.; Yang, B.; Hui, M. H. K.; Yu, A. C. H.; Viroonudomphol, D.; Prawettongsopon, C.; Wiangnon, K.; Takabatake, R.; Kitta, K.; Kawaharasaki, M.; Parkes, H.

    2012-01-01

    Key comparison CCQM-K86 was performed to demonstrate and document the capacity of interested national metrology institutes (NMIs) and designated institutes (DIs) in the determination of the relative quantity of two specific genomic DNA fragments present in a biological tissue. The study provides the support for the following measurement claim: "Quantification of the ratio of the number of copies of specified intact sequence fragments of a length in the range of 70 to 100 nucleotides in a single genomic DNA extract from ground maize seed materials". The study was carried out under the auspices of the Bioanalysis Working Group (BAWG) of the Comité Consultatif pour la Quantité de Matière (CCQM) and was piloted by the Institute for Reference Materials and Methods (IRMM) in Geel (Belgium). The following laboratories (in alphabetical order) participated in this key comparison: AIST (Japan), CENAM (Mexico), DMSc (Thailand), GLHK (Hong Kong), IRMM (European Union), KRISS (Republic of Korea), LGC (United Kingdom), MIRS/NIB (Slovenia), NIM (PR China), NIST (USA), NMIA (Australia), TÜBITAK UME (Turkey) and VNIIM (Russian Federation). The following laboratories (in alphabetical order) participated in a pilot study that was organized in parallel: LGC (United Kingdom), PKU (PR China), NFRI (Japan) and NIMT (Thailand). Good agreement was observed between the reported results of eleven participants. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by the CCQM, according to the provisions of the CIPM Mutual Recognition Arrangement (MRA).

  15. A method to obtain reference images for evaluation of ultrasonic tissue characterization techniques.

    PubMed

    Jensen, M S; Wilhjelm, J E; Sahl, B; Brandt, T; Martinsen, K; Jespersen, S K; Falk, E

    2002-05-01

    A general problem when evaluating ultrasonic methods for tissue characterization is that "a golden standard" is seldom known. This paper describes a manual method to obtain a reference image, with the same geometry as the ultrasound image, indicating spatial location of the different tissue types present in the biological tissue scanned in vitro. A 30 x 10 x 2 mm3 piece of formalin fixed porcine tissue was molded into an agar block, which on the top surface, contained a set of fiducial markers, spaced 2.5 mm. The block was submerged into 20 degrees C water and a set of parallel 7.5 MHz spatial compound ultrasound images of tissue and fiducial markers were recorded each 0.5 mm. Guided by the fiducial markers, the agar block was subsequently cut into slices 2.5 mm thick, photographed and finally analyzed histologically identifying these tissues: collagen rich, collagen poor, micro vessels and muscle fibres. Due to: (1) the cutting procedure, (2) the finite size of the ultrasound beam and (3) the spatial variation in propagation velocity, the macroscopic photographs did not align completely with the ultrasound images. Likewise, the histological image is a geometrically distorted version of the macroscopic photograph, due to the histological preparation process. The histological information was "mapped back" into the format of the ultrasound images the following way: On the macroscopic images, outlines were drawn manually which defined the border of the tissue. These outlines were superimposed on the corresponding ultrasound images (identified via the fiducial markers) and modified to encompass what appeared to be tissue regions on the ultrasound images and subsequently re-applied to the macroscopic image. This modified macroscopic outline was used as guideline when drawing outlines identifying regions of the various tissue types. Specifically, the macroscopic image revealed the borders between the different tissues, while the histological image identified the four

  16. Evaluation of penile erection rigidity in healthy men using virtual touch tissue quantification

    PubMed Central

    Zheng, Xiaozhi; Ji, Ping; Mao, Hongwei; Wu, Jing

    2012-01-01

    Background The aim of the study was to describe the shear wave velocity (SWV) values of the penis by virtual touch tissue quantification (VTTQ) and to examine the clinical usefulness of this procedure in evaluation of the rigidity changes in penile erection. Patients and methods. VTTQ was performed in 37 healthy volunteers. In the course of erection, SWV values of glans penis, corpus penis and radix penis were quantified and grades of erection were documented. The SWV values at different grades of erection were compared. Results The axial and radial SWV values of glans penis, corpus penis and radix penis all significantly decreased from Grade 0 to Grade 4 of erection. At Grade 4, they were less than one-third of that at Grade 0 (axial direction: 0.79 ± 0.13 vs. 2.79 ± 0.32 for glans penis, P<0.001; 0.77 ± 0.19 vs. 2.84 ± 0.30 for corpus penis, P<0.001 and 0.76 ± 0.15 vs. 2.81 ± 0.34 for radix penis, P<0.001; radial direction: 0.82 ± 0.15 vs. 2.83 ± 0.31 for glans penis, P<0.001; 0.79 ± 0.18 vs. 2.81 ± 0.27 for corpus penis, P<0.001 and 0.81 ± 0.16 vs. 2.82 ± 0.33 for radix penis, P<0.001). Conclusions VTTQ can provide numerical measurements of penile rigidity and can effectively and sensitively indicate the axial and radial rigidity changes in penile erection, which provide a new approach to assessing the erectile function. PMID:23077447

  17. Development of palm-based reference materials for the quantification of fatty acids composition.

    PubMed

    Tarmizi, Azmil Haizam Ahmad; Lin, Siew Wai; Kuntom, Ainie

    2008-01-01

    Characterisation of fatty acids composition of three palm-based reference materials was carried out through inter-laboratory proficiency tests. Twelve laboratories collaborated in these tests and the fatty acids compositions of palm oil, palm olein and palm stearin were determined by applying the MPOB Test Methods p3.4:2004 and p3.5:2004. Determination of consensus values and their uncertainties were based on the acceptable statistical agreement of results obtained from the collaborating laboratories. The consensus values and uncertainties (%) for each palm oil reference material produced are listed as follows : 0.20% (C12:0), 1.66+/-0.05% (C14:0), 43.39+/-0.39% (C16:0), 0.14+/-0.06% (C16:1), 3.90+/-0.11% (C18:0), 40.95+/-0.23% (C18:1), 9.68+/-0.21% (C18:2), 0.16+/-0.07% (C18:3) and 0.31+/-0.08% (C20:0) for fatty acids composition of palm oil; 0.23+/-0.04% (C12:0), 1.02+/-0.04% (C14:0), 39.66+/-0.19% (C16:0), 0.18+/-0.07% (C16:1), 3.81+/-0.04% (C18:0), 44.01+/-0.08% (C18:1), 10.73+/-0.08% (C18:2), 0.20+/-0.06% (C18:3) and 0.34+/-0.04% (C20:0) for fatty acids composition of palm olein; and 0.20% (C12:0), 1.14+/-0.05% (C14:0), 49.42+/-0.25% (C16:0), 0.16+/-0.08% (C16:1), 4.15+/-0.10% (C18:0), 36.14+/-0.77% (C18:1), 7.95+/-0.29% (C18:2), 0.11+/-0.07% (C18:3) and 0.30+/-0.08% (C20:0) for fatty acids composition of palm stearin.

  18. Determination of reference genes for circadian studies in different tissues and mouse strains

    PubMed Central

    2010-01-01

    Background Circadian rhythms have a profound effect on human health. Their disruption can lead to serious pathologies, such as cancer and obesity. Gene expression studies in these pathologies are often studied in different mouse strains by quantitative real time polymerase chain reaction (qPCR). Selection of reference genes is a crucial step of qPCR experiments. Recent studies show that reference gene stability can vary between species and tissues, but none has taken circadian experiments into consideration. Results In the present study the expression of ten candidate reference genes (Actb, Eif2a, Gapdh, Hmbs, Hprt1, Ppib, Rn18s, Rplp0, Tbcc and Utp6c) was measured in 131 liver and 97 adrenal gland samples taken from three mouse strains (C57BL/6JOlaHsd, 129Pas plus C57BL/6J and Crem KO on 129Pas plus C57BL/6J background) every 4 h in a 24 h period. Expression stability was evaluated by geNorm and NormFinder programs. Differences in ranking of the most stable reference genes were observed both between individual mouse strains as well as between tissues within each mouse strain. We show that selection of reference gene (Actb) that is often used for analyses in individual mouse strains leads to errors if used for normalization when different mouse strains are compared. We identified alternative reference genes that are stable in these comparisons. Conclusions Genetic background and circadian time influence the expression stability of reference genes. Differences between mouse strains and tissues should be taken into consideration to avoid false interpretations. We show that the use of a single reference gene can lead to false biological conclusions. This manuscript provides a useful reference point for researchers that search for stable reference genes in the field of circadian biology. PMID:20712867

  19. Characterization of certified reference material for quantification of polychlorinated biphenyls and organochlorine pesticides in fish.

    PubMed

    Otake, Takamitsu; Aoyagi, Yoshie; Yarita, Takashi; Numata, Masahiko

    2010-07-01

    Fish certified reference material (CRM), NMIJ CRM 7404-a, for the analysis of polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) was developed by the National Metrology Institute of Japan, part of the National Institute of Advanced Industrial Science and Technology. Fish samples (Japanese seabass) used for the preparation of the CRM were collected from Tokyo Bay, and the edible part was freeze-dried, pulverized, sieved, homogenized, and sterilized by gamma-irradiation. This sample is in the form of a powder comprising approximately 10 g stored in a brown glass bottle. The certification was carried out using multiple analytical methods such as pressurized liquid extraction, Soxhlet extraction, saponification, and homogenization to ensure the reliability of analytical results; the certified values of target PCBs (PCB 28, PCB 70, PCB 105, PCB 153, and PCB 170) and OCPs (trans-nonachlor, dieldrin, p,p'-DDE, p,p'-DDT, and p,p'-DDD) were 1.05-14.0 microg kg(-1) and 1.57-18.0 microg kg(-1) for PCBs and OCPs, respectively. This is the first fish powder CRM in which PCBs and OCPs were determined by isotope dilution mass spectrometry.

  20. High Resolution Multi-Detector CT Aided Tissue Analysis and Quantification of Lung Fibrosis

    PubMed Central

    Zavaletta, Vanessa A.; Bartholmai, Brian J.; Robb, Richard A

    2009-01-01

    class discrimination: Normal, Reticular, Honeycombing, and Emphysema. Experiment 3 consisted of a five class discrimination: Normal, Ground glass, Reticular, Honeycombing, and Emphysema. 2.) The remaining four scans were used to further test the algorithm on new data in the context of a whole lung analysis. Each of the four datasets was manually segmented by three experts. These datasets included Normal, Reticular and Honeycombing regions and did not include Ground glass or Emphysema. The accuracy of the classification algorithm was then compared with results from experts. Results Independent VOIs: 1.) Two class discrimination problem (sensitivity, specificity): Normal versus Abnormal (92.96%,93.78%). 2.) Four class discrimination problem: Normal (92%,95%), Reticular (86%,87%), Honeycombing (74%,98%), and Emphysema (93%,98%). 3.) Five class discrimination problem: Normal(92%,95%), Ground glass (75%,89%), Reticular (22%,92%), Honeycombing (74%,91%), and Emphysema (94%,98%). Whole lung datasets: 1.) William's Index shows that algorithm classification of lungs agrees with the experts as well as the experts agree with themselves. 2.) Student-T test between overlap measures of algorithm and expert (AE) and expert and expert (EE) : Normal (t=-1.20, p = 0.230), Reticular (t=-1.44, p = 0.155), Honeycombing (t=-3.15, p = 0.003). 3.) Lung Volumes Intra-class correlation: Dataset 1 (ICC = 0.9984, F = 0.0007); Dataset 2 (ICC = 0.9559, F = 0); Dataset 3 (ICC = 0.8623, F= 0.0015); Dataset 4 (ICC = 0.7807, F = 0.0136). Conclusions We have demonstrated that our novel method is computationally efficient and produces results comparable to expert radiologic judgment. It is effective in the classification of normal versus abnormal tissue and performs as well as the experts in distinguishing among typical pathologies present in lungs with UIP/IPF. The continuing development of quantitative metrics will improve quantification of disease and provide objective measures of disease progression

  1. Quantification of PrPC in bovine peripheral tissues: Analysis in wild-type and PrPC-deficient cattle.

    PubMed

    Kobayashi, Shin-Ichi; Ano, Yasuhisa; Sakudo, Akikazu; Yukawa, Masayoshi; Sigiura, Katsuaki; Manabe, Noboru; Nakayama, Hiroyuki; Onodera, Takashi

    2009-01-01

    Cellular PrP (PrPC) is necessary for bovine spongiform encephalopathy (BSE) infection. The purpose of the present experiment was the quantification of PrPC in peripheral tissues to assess the risk of BSE infection from these tissues. The tissue distribution of PrPC was examined by a sandwich enzyme-linked immunosorbent assay (sELISA) and histochemical analysis. PrPC-deficient cows were used as a negative control. The sELISA revealed that the brain contained the highest PrPC content (10.7 µg/g tissue), while other organs/tissues harbored lower amounts, in decreasing order as follows: longissimus capitis muscle, iliocostalis thoracis muscle, splenius muscle, biceps femoris muscle, triceps brachii muscle, longissimus thoracis muscle, ileum, jejunum, duodenum, colon, cecum, apex linguae, omotransversarius muscle, posterior part of the corpus linguae, anterior part of the corpus linguae and radix linguae (5.2- to 31-fold less PrPC than the brain). In the tissue/organs of PrP-deficient cows, PrPC levels were under the limit of detection. Histochemical analysis showed that PrPC was expressed in nerve cells in intestinal tissues. The presence of PrPC in the bovine tongue, skeletal muscles and intestines raises the possibility of PrPSc accumulation in these tissues, indicating that these organs/tissues may serve as potential sources of BSE infection.

  2. Validation of a Radiography-Based Quantification Designed to Longitudinally Monitor Soft Tissue Calcification in Skeletal Muscle

    PubMed Central

    Moore, Stephanie N.; Hawley, Gregory D.; Smith, Emily N.; Mignemi, Nicholas A.; Ihejirika, Rivka C.; Yuasa, Masato; Cates, Justin M. M.; Liu, Xulei; Schoenecker, Jonathan G.

    2016-01-01

    Introduction Soft tissue calcification, including both dystrophic calcification and heterotopic ossification, may occur following injury. These lesions have variable fates as they are either resorbed or persist. Persistent soft tissue calcification may result in chronic inflammation and/or loss of function of that soft tissue. The molecular mechanisms that result in the development and maturation of calcifications are uncertain. As a result, directed therapies that prevent or resorb soft tissue calcifications remain largely unsuccessful. Animal models of post-traumatic soft tissue calcification that allow for cost-effective, serial analysis of an individual animal over time are necessary to derive and test novel therapies. We have determined that a cardiotoxin-induced injury of the muscles in the posterior compartment of the lower extremity represents a useful model in which soft tissue calcification develops remote from adjacent bones, thereby allowing for serial analysis by plain radiography. The purpose of the study was to design and validate a method for quantifying soft tissue calcifications in mice longitudinally using plain radiographic techniques and an ordinal scoring system. Methods Muscle injury was induced by injecting cardiotoxin into the posterior compartment of the lower extremity in mice susceptible to developing soft tissue calcification. Seven days following injury, radiographs were obtained under anesthesia. Multiple researchers applied methods designed to standardize post-image processing of digital radiographs (N = 4) and quantify soft tissue calcification (N = 6) in these images using an ordinal scoring system. Inter- and intra-observer agreement for both post-image processing and the scoring system used was assessed using weighted kappa statistics. Soft tissue calcification quantifications by the ordinal scale were compared to mineral volume measurements (threshold 450.7mgHA/cm3) determined by μCT. Finally, sample-size calculations necessary

  3. Reference-tissue correction of T2-weighted signal intensity for prostate cancer detection

    NASA Astrophysics Data System (ADS)

    Peng, Yahui; Jiang, Yulei; Oto, Aytekin

    2014-03-01

    The purpose of this study was to investigate whether correction with respect to reference tissue of T2-weighted MRimage signal intensity (SI) improves its effectiveness for classification of regions of interest (ROIs) as prostate cancer (PCa) or normal prostatic tissue. Two image datasets collected retrospectively were used in this study: 71 cases acquired with GE scanners (dataset A), and 59 cases acquired with Philips scanners (dataset B). Through a consensus histology- MR correlation review, 175 PCa and 108 normal-tissue ROIs were identified and drawn manually. Reference-tissue ROIs were selected in each case from the levator ani muscle, urinary bladder, and pubic bone. T2-weighted image SI was corrected as the ratio of the average T2-weighted image SI within an ROI to that of a reference-tissue ROI. Area under the receiver operating characteristic curve (AUC) was used to evaluate the effectiveness of T2-weighted image SIs for differentiation of PCa from normal-tissue ROIs. AUC (+/- standard error) for uncorrected T2-weighted image SIs was 0.78+/-0.04 (datasets A) and 0.65+/-0.05 (datasets B). AUC for corrected T2-weighted image SIs with respect to muscle, bladder, and bone reference was 0.77+/-0.04 (p=1.0), 0.77+/-0.04 (p=1.0), and 0.75+/-0.04 (p=0.8), respectively, for dataset A; and 0.81+/-0.04 (p=0.002), 0.78+/-0.04 (p<0.001), and 0.79+/-0.04 (p<0.001), respectively, for dataset B. Correction in reference to the levator ani muscle yielded the most consistent results between GE and Phillips images. Correction of T2-weighted image SI in reference to three types of extra-prostatic tissue can improve its effectiveness for differentiation of PCa from normal-tissue ROIs, and correction in reference to the levator ani muscle produces consistent T2-weighted image SIs between GE and Phillips MR images.

  4. Comparison of four digital PCR platforms for accurate quantification of DNA copy number of a certified plasmid DNA reference material

    PubMed Central

    Dong, Lianhua; Meng, Ying; Sui, Zhiwei; Wang, Jing; Wu, Liqing; Fu, Boqiang

    2015-01-01

    Digital polymerase chain reaction (dPCR) is a unique approach to measurement of the absolute copy number of target DNA without using external standards. However, the comparability of different dPCR platforms with respect to measurement of DNA copy number must be addressed before dPCR can be classified fundamentally as an absolute quantification technique. The comparability of four dPCR platforms with respect to accuracy and measurement uncertainty was investigated by using a certified plasmid reference material. Plasmid conformation was found to have a significant effect on droplet-based dPCR (QX100 and RainDrop) not shared with chip-based QuantStudio 12k or BioMark. The relative uncertainty of partition volume was determined to be 0.7%, 0.8%, 2.3% and 2.9% for BioMark, QX100, QuantStudio 12k and RainDrop, respectively. The measurements of the certified pNIM-001 plasmid made using the four dPCR platforms were corrected for partition volume and closely consistent with the certified value within the expended uncertainty. This demonstrated that the four dPCR platforms are of comparable effectiveness in quantifying DNA copy number. These findings provide an independent assessment of this method of determining DNA copy number when using different dPCR platforms and underline important factors that should be taken into consideration in the design of dPCR experiments. PMID:26302947

  5. Quantification of arsenolipids in the certified reference material NMIJ 7405-a (Hijiki) using HPLC/mass spectrometry after chemical derivatization.

    PubMed

    Glabonjat, Ronald A; Raber, Georg; Jensen, Kenneth B; Ehgartner, Josef; Francesconi, Kevin A

    2014-10-21

    Arsenic-containing lipids (arsenolipids) are novel natural products recently shown to be widespread in marine animals and algae. Research interest in these arsenic compounds lies in their possible role in the membrane chemistry of organisms and, because they occur in many popular seafoods, their human metabolism and toxicology. Progress has been restricted, however, by the lack of standard arsenolipids and of a quantitative method for their analysis. We report that the certified reference material CRM 7405-a (Hijiki) is a rich source of arsenolipids, and we describe a method based on HPLC-ICPMS/ESMS to quantitatively measure seven of the major arsenolipids present. Sample preparation involved extraction with DCM/methanol, a cleanup step with silica, and conversion of the (oxo)arsenolipids originally present to thio analogues by brief treatment with H2S. Compared to their oxo analogues, the thioarsenolipids showed much sharper peaks on reversed-phase HPLC, which facilitated their resolution and quantification. The compounds were determined by HPLC-ICPMS and HPLC-ESMS, which provided both arsenic-selective detection and high resolution molecular mass detection of the arsenolipids. In this way, the concentrations of two arsenic-containing hydrocarbons and five arsenosugar phospholipids are reported in the CRM Hijiki. This material may serve as a convenient source of characterized arsenolipids to delineate the presence of these compounds in seafoods and to facilitate research in a new era of arsenic biochemistry.

  6. Quantification of Arsenolipids in the Certified Reference Material NMIJ 7405-a (Hijiki) using HPLC/Mass Spectrometry after Chemical Derivatization

    PubMed Central

    2014-01-01

    Arsenic-containing lipids (arsenolipids) are novel natural products recently shown to be widespread in marine animals and algae. Research interest in these arsenic compounds lies in their possible role in the membrane chemistry of organisms and, because they occur in many popular seafoods, their human metabolism and toxicology. Progress has been restricted, however, by the lack of standard arsenolipids and of a quantitative method for their analysis. We report that the certified reference material CRM 7405-a (Hijiki) is a rich source of arsenolipids, and we describe a method based on HPLC-ICPMS/ESMS to quantitatively measure seven of the major arsenolipids present. Sample preparation involved extraction with DCM/methanol, a cleanup step with silica, and conversion of the (oxo)arsenolipids originally present to thio analogues by brief treatment with H2S. Compared to their oxo analogues, the thioarsenolipids showed much sharper peaks on reversed-phase HPLC, which facilitated their resolution and quantification. The compounds were determined by HPLC-ICPMS and HPLC-ESMS, which provided both arsenic-selective detection and high resolution molecular mass detection of the arsenolipids. In this way, the concentrations of two arsenic-containing hydrocarbons and five arsenosugar phospholipids are reported in the CRM Hijiki. This material may serve as a convenient source of characterized arsenolipids to delineate the presence of these compounds in seafoods and to facilitate research in a new era of arsenic biochemistry. PMID:25241916

  7. Development of real-time PCR method for the detection and the quantification of a new endogenous reference gene in sugar beet "Beta vulgaris L.": GMO application.

    PubMed

    Chaouachi, Maher; Alaya, Akram; Ali, Imen Ben Haj; Hafsa, Ahmed Ben; Nabi, Nesrine; Bérard, Aurélie; Romaniuk, Marcel; Skhiri, Fethia; Saïd, Khaled

    2013-01-01

    KEY MESSAGE : Here, we describe a new developed quantitative real-time PCR method for the detection and quantification of a new specific endogenous reference gene used in GMO analysis. The key requirement of this study was the identification of a new reference gene used for the differentiation of the four genomic sections of the sugar beet (Beta vulgaris L.) (Beta, Corrollinae, Nanae and Procumbentes) suitable for quantification of genetically modified sugar beet. A specific qualitative polymerase chain reaction (PCR) assay was designed to detect the sugar beet amplifying a region of the adenylate transporter (ant) gene only from the species of the genomic section I of the genus Beta (cultivated and wild relatives) and showing negative PCR results for 7 species of the 3 other sections, 8 related species and 20 non-sugar beet plants. The sensitivity of the assay was 15 haploid genome copies (HGC). A quantitative real-time polymerase chain reaction (QRT-PCR) assay was also performed, having high linearity (R (2) > 0.994) over sugar beet standard concentrations ranging from 20,000 to 10 HGC of the sugar beet DNA per PCR. The QRT-PCR assay described in this study was specific and more sensitive for sugar beet quantification compared to the validated test previously reported in the European Reference Laboratory. This assay is suitable for GMO quantification in routine analysis from a wide variety of matrices.

  8. Update on Controls for Isolation and Quantification Methodology of Extracellular Vesicles Derived from Adipose Tissue Mesenchymal Stem Cells

    PubMed Central

    Franquesa, Marcella; Hoogduijn, Martin J.; Ripoll, Elia; Luk, Franka; Salih, Mahdi; Betjes, Michiel G. H.; Torras, Juan; Baan, Carla C.; Grinyó, Josep M.; Merino, Ana Maria

    2014-01-01

    The research field on extracellular vesicles (EV) has rapidly expanded in recent years due to the therapeutic potential of EV. Adipose tissue human mesenchymal stem cells (ASC) may be a suitable source for therapeutic EV. A major limitation in the field is the lack of standardization of the challenging techniques to isolate and characterize EV. The aim of our study was to incorporate new controls for the detection and quantification of EV derived from ASC and to analyze the applicability and limitations of the available techniques. ASC were cultured in medium supplemented with 5% of vesicles-free fetal bovine serum. The EV were isolated from conditioned medium by differential centrifugation with size filtration (0.2 μm). As a control, non-conditioned culture medium was used (control medium). To detect EV, electron microscopy, conventional flow cytometry, and western blot were used. The quantification of the EV was by total protein quantification, ExoELISA immunoassay, and Nanosight. Cytokines and growth factors in the EV samples were measured by multiplex bead array kit. The EV were detected by electron microscope. Total protein measurement was not useful to quantify EV as the control medium showed similar protein contents as the EV samples. The ExoELISA kits had technical troubles and it was not possible to quantify the concentration of exosomes in the samples. The use of Nanosight enabled quantification and size determination of the EV. It is, however, not possible to distinguish protein aggregates from EV with this method. The technologies for quantification and characterization of the EV need to be improved. In addition, we detected protein contaminants in the EV samples, which make it difficult to determine the real effect of EV in experimental models. It will be crucial in the future to optimize design novel methods for purification and characterization of EV. PMID:25374572

  9. Epigenomic footprints across 111 reference epigenomes reveal tissue-specific epigenetic regulation of lincRNAs.

    PubMed

    Amin, Viren; Harris, R Alan; Onuchic, Vitor; Jackson, Andrew R; Charnecki, Tim; Paithankar, Sameer; Lakshmi Subramanian, Sai; Riehle, Kevin; Coarfa, Cristian; Milosavljevic, Aleksandar

    2015-02-18

    Tissue-specific expression of lincRNAs suggests developmental and cell-type-specific functions, yet tissue specificity was established for only a small fraction of lincRNAs. Here, by analysing 111 reference epigenomes from the NIH Roadmap Epigenomics project, we determine tissue-specific epigenetic regulation for 3,753 (69% examined) lincRNAs, with 54% active in one of the 14 cell/tissue clusters and an additional 15% in two or three clusters. A larger fraction of lincRNA TSSs is marked in a tissue-specific manner by H3K4me1 than by H3K4me3. The tissue-specific lincRNAs are strongly linked to tissue-specific pathways and undergo distinct chromatin state transitions during cellular differentiation. Polycomb-regulated lincRNAs reside in the bivalent state in embryonic stem cells and many of them undergo H3K27me3-mediated silencing at early stages of differentiation. The exquisitely tissue-specific epigenetic regulation of lincRNAs and the assignment of a majority of them to specific tissue types will inform future studies of this newly discovered class of genes.

  10. Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) Breast Cancer Tissues.

    PubMed

    Steiner, Carine; Tille, Jean-Christophe; Lamerz, Jens; Kux van Geijtenbeek, Sabine; McKee, Thomas A; Venturi, Miro; Rubbia-Brandt, Laura; Hochstrasser, Denis; Cutler, Paul; Lescuyer, Pierre; Ducret, Axel

    2015-10-01

    The ability to accurately quantify proteins in formalin-fixed paraffin-embedded tissues using targeted mass spectrometry opens exciting perspectives for biomarker discovery. We have developed and evaluated a selectedreaction monitoring assay for the human receptor tyrosine-protein kinase erbB-2 (HER2) in formalin-fixed paraffin-embedded breast tumors. Peptide candidates were identified using an untargeted mass spectrometry approach in relevant cell lines. A multiplexed assay was developed for the six best candidate peptides and evaluated for linearity, precision and lower limit of quantification. Results showed a linear response over a calibration range of 0.012 to 100 fmol on column (R(2): 0.99-1.00).The lower limit of quantification was 0.155 fmol on column for all peptides evaluated. The six HER2 peptides were quantified by selected reaction monitoring in a cohort of 40 archival formalin-fixed paraffin-embedded tumor tissues from women with invasive breast carcinomas, which showed different levels of HER2 gene amplification as assessed by standard methods used in clinical pathology. The amounts of the six HER2 peptides were highly and significantly correlated with each other, indicating that peptide levels can be used as surrogates of protein amounts in formalin-fixed paraffin-embedded tissues. After normalization for sample size, selected reaction monitoring peptide measurements were able to correctly predict 90% of cases based on HER2 amplification as defined by the American Society of Clinical Oncology and College of American Pathologists. In conclusion, the developed assay showed good analytical performance and a high agreement with immunohistochemistry and fluorescence in situ hybridization data. This study demonstrated that selected reaction monitoring allows to accurately quantify protein expression in formalin-fixed paraffin-embedded tissues and represents therefore a powerful approach for biomarker discovery studies. The untargeted mass spectrometry

  11. Quantification of Complex Polycyclic Aromatic Hydrocarbon Mixtures in Standard Reference Materials Using GC×GC/ToF-MS

    PubMed Central

    Manzano, Carlos; Hoh, Eunha; Massey Simonich, Staci L.

    2014-01-01

    This research is the first to quantify complex PAH mixtures in NIST SRMs using comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (GC×GC/ToF-MS), with and without extract cleanup, and reports previously unidentified PAH isomers in the NIST SRMs. We tested a novel, high orthogonality GC column combination (LC-50×NSP-35), as well as with a commonly used column combination (Rtx-5ms×Rxi-17) for the quantification of a complex mixture of 85 different PAHs, including parent (PAHs), alkyl- (MPAHs), nitro- (NPAHs), oxy- (OPAHs), thio- (SPAHs), bromo- (BrPAHs), and chloro-PAHs (ClPAHs) in extracts from two standard reference materials: NIST SRM1650b (diesel particulate matter), with cleanup and NIST SRM1975 (diesel particulate extract), with and without extract cleanup. The LC-50×NSP-35 column combination resulted in an average absolute percent difference of 33.8%, 62.2% and 30.8% compared to the NIST certified PAH concentrations for NIST SRM1650b, NIST SRM1975 with cleanup and NIST SRM1975 without cleanup, while the Rtx-5ms×Rxi-17 resulted in an absolute percent difference of 38.6%, 67.2% and 79.6% for NIST SRM1650b, NIST SRM1975 with cleanup and NIST SRM1975 without cleanup, respectively. This GC×GC/ToF-MS method increases the number of PAHs detected and quantified in complex environmental extracts using a single chromatographic run. Without clean-up, 7 additional compounds were detected and quantified in NIST SRM1975 using the LC-50×NSP-35 column combination. These results suggest that the use of the LC-50×NSP-35 column combination in GC×GC/ToF-MS not only results in better chromatographic resolution and greater orthogonality for the separation of complex PAH mixtures, but can also be used for the accurate quantification of complex PAH mixtures in environmental extracts without cleanup. PMID:23932031

  12. Determination of polychlorinated biphenyl congeners and chlorinated pesticides in a fish tissue standard reference material.

    PubMed

    Poster, Dianne L; Kucklick, John R; Schantz, Michele M; Porter, Barbara J; Leigh, Stefan D; Wise, Stephen A

    2003-01-01

    The concentrations of a wide range of polychlorinated biphenyl congeners (PCBs) and chlorinated pesticides in a fish tissue Standard Reference Material (SRM) have been determined using multiple methods of analysis. This material, SRM 1946, Lake Superior Fish Tissue, was recently issued by the National Institute of Standards and Technology (NIST) and complements a suite of marine environmental natural-matrix SRMs that are currently available from NIST for the determination of organic contaminants such as aliphatic hydrocarbons, polycyclic aromatic hydrocarbons (PAHs), PCBs, and chlorinated pesticides. SRM 1946 is a fresh tissue homogenate (frozen) prepared from filleted adult lake trout (Salvelinus namaycush namaycush) collected from the Apostle Islands region of Lake Superior. SRM 1946 has certified and reference concentrations for PCB congeners, including the three non- ortho PCB congeners, and chlorinated pesticides. Certified concentrations are available for 30 PCB congeners and 15 chlorinated pesticides. Reference concentrations are available for 12 PCB congeners and 2 chlorinated pesticides. In addition, SRM 1946 is characterized for additional chemical constituents and properties: fatty acids, extractable fat, methylmercury, total mercury, selected trace elements, proximates, and caloric content. The characterization of chlorinated compounds is described in this paper with an emphasis on the approach used for the certification of the concentrations of PCB congeners and chlorinated pesticides. The PCB congener and chlorinated pesticide data are also compared to concentrations in other marine natural-matrix reference materials available from NIST (fish oil, mussel tissue, whale blubber, and a second fresh frozen fish tissue homogenate prepared from filleted adult lake trout collected from Lake Michigan) and from other organizations such as the National Research Council Canada (ground whole carp), the International Atomic Energy Agency (fish homogenate), and the

  13. Influence of skin tissue properties on the radial reference point for glucose measurement

    NASA Astrophysics Data System (ADS)

    Yang, Yue; Xu, Kexin; Ding, Lijun; Shi, Zhenzhi; Chen, Wenliang

    2009-02-01

    A reference position where the diffuse reflectance light intensity is insensitive to the variation of glucose concentration exists in the radial detection space for glucose measurement in the scattering medium such as skin. The signal measured in this position could be used as an inside reference to evaluate the influence on spectrum caused by other interferential factors. The relationship between the position of radial reference point and the skin tissue property is studied in this paper. Three-layer skin models with different optical parameters are designed to get sample sets at 1200~1700nm. In these sets, μa, μs and g of dermis varies respectively, so does the depth of epidermis or dermis. The distribution rule of dispersion of diffuse reflectance light intensity in the radial space is confirmed with the glucose concentration changes. And the distribution property of the radial reference position in every sample set is obtained through Monte Carlo simulation. The result shows that the distance of radial reference position from light source is insensitive to the variation of absorption coefficient or the depth of dermis, but an increased scattering coefficient will shorten the distance; an increased anisotropy coefficient or depth of epidermis will lengthen it. On the basis of that, the optical probes with different structures are designed according to the skin tissue properties. So they could be used for the measurement of corresponding patients, which enhances the practicability of floating reference method greatly.

  14. The other mechanism of muscular referred pain: the "connective tissue" theory.

    PubMed

    Han, Dong-Gyun

    2009-09-01

    Muscular referred pain, that is, pain perceived in a somatic area other than the site of the noxious stimulation, takes place on a specific place to each muscle in constant and predictable pattern. The central hyperexcitability theory focused on spinal cord, the most proper theory at present, can explain well the segmental pattern of referred pain showing delayed onset. But it is hard to explain the non segmental pattern of referred pain areas of superficial-seated or limb girdle and limb muscles. Referred pain areas of limb girdle and limb muscles appear on the skin above a belt of synergistic muscles beyond the segmental areas. In the case of forearm and calf muscles, referred pain shows up on the palm and sole, the point of force application to the outer object. This finding reflects biomechanical relationship between muscle and its referred pain area. From the phylogenetic perspective, aquatic vertebrated animals (e.g. fish) use myoseptum surrounding myomere, connected to skin to keep tensile strength with it for effective swimming. Likewise, in terrestrial vertebrated animals, there are skin parts weakly interconnected with muscles, though the tensile property of nearly all the skin devolutes except the points of action with the outside. These points are dynamic maximal skin tension areas connected with muscles through superficial fascia, in other words, referred pain areas. Referred pain of deep-seated or truncal muscles appears on the trunk segmentally via spinal cord (the central hyperexcitability theory), but superficial-seated or limb girdle and limb muscles elicit referred pain on dynamic maximal skin tension area through connective tissue (the "connective tissue" theory).

  15. Alarm symptoms of soft-tissue and bone sarcoma in patients referred to a specialist center

    PubMed Central

    Dyrop, Heidi B; Vedsted, Peter; Safwat, Akmal; Maretty-Nielsen, Katja; Hansen, Bjarne H; Jørgensen, Peter H; Baad-Hansen, Thomas; Keller, Johnny

    2014-01-01

    Background and purpose — The Danish Cancer Patient Pathway for sarcoma defines a set of alarm symptoms as criteria for referral to a sarcoma center. This may exclude cancer patients without alarm symptoms, so we investigated the presence of alarm symptoms (defined as being indicative of a sarcoma) in patients who had been referred to the Aarhus Sarcoma Center. Patients and methods — We reviewed the medical records of all 1,126 patients who had been referred, with suspected sarcoma, from other hospitals in the period 2007–2010 for information on symptoms, clinical findings, and diagnosis. Alarm symptoms were analyzed for predictive values in diagnosing sarcoma. Results — 179 (69%) of 258 sarcoma patients were referred with alarm symptoms (soft-tissue tumor > 5 cm or deep-seated, fast-growing soft-tissue tumor, palpable bone tumor, or deep persisting bone pain). The remaining 79 sarcomas were found accidentally. “Size over 5 cm” for soft-tissue tumors, and “deep persisting bone pain” for bone tumors had the highest sensitivity and positive predictive value. Of the 79 sarcoma patients who were referred without alarm symptoms, 7 were found accidentally on imaging, 5 were referred with suspected recurrence of a sarcoma, 64 were referred with a confirmed histological diagnosis, and 3 were referred for other reasons. Interpretation — Defined alarm symptoms are predictive of sarcoma, but one-third of the patients were found accidentally. Further studies on presenting symptoms in primary care are needed to assess the true value of alarm symptoms. PMID:25175662

  16. In-vivo assessment of tissue metabolite levels using 1H MRS and the Electric REference To access In vivo Concentrations (ERETIC) method.

    PubMed

    Heinzer-Schweizer, S; De Zanche, N; Pavan, M; Mens, G; Sturzenegger, U; Henning, A; Boesiger, P

    2010-05-01

    Quantitative values of metabolite concentrations in (1)H magnetic resonance spectroscopy have been obtained using the Electric REference To access In vivo Concentrations (ERETIC) method, whereby a synthetic reference signal is injected during the acquisition of spectra. The method has been improved to enable quantification of metabolite concentrations in vivo. Optical signal transmission was used to eliminate random fluctuations in ERETIC signal coupling to the receiver coil due to changes in position of cables and highly dielectric human tissue. Stability and reliability of the signal were tested in vitro, achieving stability with a mean error of 2.83%. Scaling of the signal in variable loading conditions was demonstrated and in-vivo measurements of brain were acquired on a 3T Philips system using a transmit/receive coil. The quantitative brain water and metabolite concentration values are in good agreement with those in the literature.

  17. The importance of selecting the appropriate reference genes for quantitative real time PCR as illustrated using colon cancer cells and tissue

    PubMed Central

    Walsh, Dara; Coffey, John C.

    2016-01-01

    Quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR) remains the most sensitive technique for nucleic acid quantification. Its popularity is reflected in the remarkable number of publications reporting RT-qPCR data. Careful normalisation within RT-qPCR studies is imperative to ensure accurate quantification of mRNA levels. This is commonly achieved through the use of reference genes as an internal control to normalise the mRNA levels between different samples. The selection of appropriate reference genes can be a challenge as transcript levels vary with physiology, pathology and development, making the information within the transcriptome flexible and variable. In this study, we examined the variation in expression of a panel of nine candidate reference genes in HCT116 and HT29 2-dimensional and 3-dimensional cultures, as well as in normal and cancerous colon tissue. Using normfinder we identified the top three most stable genes for all conditions. Further to this we compared the change in expression of a selection of PKC coding genes when the data was normalised to one reference gene and three reference genes. Here we demonstrated that there is a variation in the fold changes obtained dependent on the number of reference genes used. As well as this, we highlight important considerations namely; assay efficiency tests, inhibition tests and RNA assessment which should also be implemented into all RT-qPCR studies. All this data combined demonstrates the need for careful experimental design in RT-qPCR studies to help eliminate false interpretation and reporting of results. PMID:26962435

  18. 3D geometry-based quantification of colocalizations in multichannel 3D microscopy images of human soft tissue tumors.

    PubMed

    Wörz, Stefan; Sander, Petra; Pfannmöller, Martin; Rieker, Ralf J; Joos, Stefan; Mechtersheimer, Gunhild; Boukamp, Petra; Lichter, Peter; Rohr, Karl

    2010-08-01

    We introduce a new model-based approach for automatic quantification of colocalizations in multichannel 3D microscopy images. The approach uses different 3D parametric intensity models in conjunction with a model fitting scheme to localize and quantify subcellular structures with high accuracy. The central idea is to determine colocalizations between different channels based on the estimated geometry of the subcellular structures as well as to differentiate between different types of colocalizations. A statistical analysis was performed to assess the significance of the determined colocalizations. This approach was used to successfully analyze about 500 three-channel 3D microscopy images of human soft tissue tumors and controls.

  19. Evaluation of reference genes for gene expression studies in human brown adipose tissue.

    PubMed

    Taube, Magdalena; Andersson-Assarsson, Johanna C; Lindberg, Kristin; Pereira, Maria J; Gäbel, Markus; Svensson, Maria K; Eriksson, Jan W; Svensson, Per-Arne

    2015-01-01

    Human brown adipose tissue (BAT) has during the last 5 year been subjected to an increasing research interest, due to its putative function as a target for future obesity treatments. The most commonly used method for molecular studies of human BAT is the quantitative polymerase chain reaction (qPCR). This method requires normalization to a reference gene (genes with uniform expression under different experimental conditions, e.g. similar expression levels between human BAT and WAT), but so far no evaluation of reference genes for human BAT has been performed. Two different microarray datasets with samples containing human BAT were used to search for genes with low variability in expression levels. Seven genes (FAM96B, GNB1, GNB2, HUWE1, PSMB2, RING1 and TPT1) identified by microarray analysis, and 8 commonly used reference genes (18S, B2M, GAPDH, LRP10, PPIA, RPLP0, UBC, and YWHAZ) were selected and further analyzed by quantitative PCR in both BAT containing perirenal adipose tissue and subcutaneous adipose tissue. Results were analyzed using 2 different algorithms (Normfinder and geNorm). Most of the commonly used reference genes displayed acceptably low variability (geNorm M-values <0.5) in the samples analyzed, but the novel reference genes identified by microarray displayed an even lower variability (M-values <0.25). Our data suggests that PSMB2, GNB2 and GNB1 are suitable novel reference genes for qPCR analysis of human BAT and we recommend that they are included in future gene expression studies of human BAT.

  20. Parametric quantification of myocardial ischaemia using real-time perfusion adenosine stress echocardiography images, with SPECT as reference method.

    PubMed

    Gudmundsson, P; Shahgaldi, K; Winter, R; Dencker, M; Kitlinski, M; Thorsson, O; Ljunggren, L; Willenheimer, R

    2010-01-01

    Real-time perfusion (RTP) adenosine stress echocardiography (ASE) can be used to visually evaluate myocardial ischaemia. The RTP power modulation technique, provides images for off-line parametric perfusion quantification using Qontrast software. From replenishment curves, this generates parametric images of peak signal intensity (A), myocardial blood flow velocity (beta) and myocardial blood flow (Axbeta) at rest and stress. This may be a tool for objective myocardial ischaemia evaluation. We assessed myocardial ischaemia by RTP-ASE Qontrast((R))-generated images, using 99mTc-tetrofosmin single-photon emission computed tomography (SPECT) as reference. Sixty-seven patients admitted to SPECT underwent RTP-ASE (SONOS 5500) during Sonovue infusion, before and throughout adenosine stress, also used for SPECT. Quantitative off-line analyses of myocardial perfusion by RTP-ASE Qontrast-generated A, beta and Axbeta images, at different time points during rest and stress, were blindly compared to SPECT. We analysed 201 coronary territories [corresponding to the left anterior descendent (LAD), left circumflex (LCx) and right coronary (RCA) arteries] from 67 patients. SPECT showed ischaemia in 18 patients. Receiver operator characteristics and kappa values showed that A, beta and Axbeta image interpretation significantly identified ischaemia in all territories (area under the curve 0.66-0.80, P = 0.001-0.05). Combined A, beta and Axbeta image interpretation gave the best results and the closest agreement was seen in the LAD territory: 89% accuracy; kappa 0.63; P<0.001. Myocardial isachemia can be evaluated in the LAD territory using RTP-ASE Qontrast-generated images, especially by combined A, beta and Axbeta image interpretation. However, the technique needs improvements regarding the LCx and RCA territories.

  1. Nuquantus: Machine learning software for the characterization and quantification of cell nuclei in complex immunofluorescent tissue images

    NASA Astrophysics Data System (ADS)

    Gross, Polina; Honnorat, Nicolas; Varol, Erdem; Wallner, Markus; Trappanese, Danielle M.; Sharp, Thomas E.; Starosta, Timothy; Duran, Jason M.; Koller, Sarah; Davatzikos, Christos; Houser, Steven R.

    2016-03-01

    Determination of fundamental mechanisms of disease often hinges on histopathology visualization and quantitative image analysis. Currently, the analysis of multi-channel fluorescence tissue images is primarily achieved by manual measurements of tissue cellular content and sub-cellular compartments. Since the current manual methodology for image analysis is a tedious and subjective approach, there is clearly a need for an automated analytical technique to process large-scale image datasets. Here, we introduce Nuquantus (Nuclei quantification utility software) - a novel machine learning-based analytical method, which identifies, quantifies and classifies nuclei based on cells of interest in composite fluorescent tissue images, in which cell borders are not visible. Nuquantus is an adaptive framework that learns the morphological attributes of intact tissue in the presence of anatomical variability and pathological processes. Nuquantus allowed us to robustly perform quantitative image analysis on remodeling cardiac tissue after myocardial infarction. Nuquantus reliably classifies cardiomyocyte versus non-cardiomyocyte nuclei and detects cell proliferation, as well as cell death in different cell classes. Broadly, Nuquantus provides innovative computerized methodology to analyze complex tissue images that significantly facilitates image analysis and minimizes human bias.

  2. Nuquantus: Machine learning software for the characterization and quantification of cell nuclei in complex immunofluorescent tissue images.

    PubMed

    Gross, Polina; Honnorat, Nicolas; Varol, Erdem; Wallner, Markus; Trappanese, Danielle M; Sharp, Thomas E; Starosta, Timothy; Duran, Jason M; Koller, Sarah; Davatzikos, Christos; Houser, Steven R

    2016-03-23

    Determination of fundamental mechanisms of disease often hinges on histopathology visualization and quantitative image analysis. Currently, the analysis of multi-channel fluorescence tissue images is primarily achieved by manual measurements of tissue cellular content and sub-cellular compartments. Since the current manual methodology for image analysis is a tedious and subjective approach, there is clearly a need for an automated analytical technique to process large-scale image datasets. Here, we introduce Nuquantus (Nuclei quantification utility software) - a novel machine learning-based analytical method, which identifies, quantifies and classifies nuclei based on cells of interest in composite fluorescent tissue images, in which cell borders are not visible. Nuquantus is an adaptive framework that learns the morphological attributes of intact tissue in the presence of anatomical variability and pathological processes. Nuquantus allowed us to robustly perform quantitative image analysis on remodeling cardiac tissue after myocardial infarction. Nuquantus reliably classifies cardiomyocyte versus non-cardiomyocyte nuclei and detects cell proliferation, as well as cell death in different cell classes. Broadly, Nuquantus provides innovative computerized methodology to analyze complex tissue images that significantly facilitates image analysis and minimizes human bias.

  3. Nuquantus: Machine learning software for the characterization and quantification of cell nuclei in complex immunofluorescent tissue images

    PubMed Central

    Gross, Polina; Honnorat, Nicolas; Varol, Erdem; Wallner, Markus; Trappanese, Danielle M.; Sharp, Thomas E.; Starosta, Timothy; Duran, Jason M.; Koller, Sarah; Davatzikos, Christos; Houser, Steven R.

    2016-01-01

    Determination of fundamental mechanisms of disease often hinges on histopathology visualization and quantitative image analysis. Currently, the analysis of multi-channel fluorescence tissue images is primarily achieved by manual measurements of tissue cellular content and sub-cellular compartments. Since the current manual methodology for image analysis is a tedious and subjective approach, there is clearly a need for an automated analytical technique to process large-scale image datasets. Here, we introduce Nuquantus (Nuclei quantification utility software) - a novel machine learning-based analytical method, which identifies, quantifies and classifies nuclei based on cells of interest in composite fluorescent tissue images, in which cell borders are not visible. Nuquantus is an adaptive framework that learns the morphological attributes of intact tissue in the presence of anatomical variability and pathological processes. Nuquantus allowed us to robustly perform quantitative image analysis on remodeling cardiac tissue after myocardial infarction. Nuquantus reliably classifies cardiomyocyte versus non-cardiomyocyte nuclei and detects cell proliferation, as well as cell death in different cell classes. Broadly, Nuquantus provides innovative computerized methodology to analyze complex tissue images that significantly facilitates image analysis and minimizes human bias. PMID:27005843

  4. Multivariate reference technique for quantitative analysis of fiber-optic tissue Raman spectroscopy.

    PubMed

    Bergholt, Mads Sylvest; Duraipandian, Shiyamala; Zheng, Wei; Huang, Zhiwei

    2013-12-03

    We report a novel method making use of multivariate reference signals of fused silica and sapphire Raman signals generated from a ball-lens fiber-optic Raman probe for quantitative analysis of in vivo tissue Raman measurements in real time. Partial least-squares (PLS) regression modeling is applied to extract the characteristic internal reference Raman signals (e.g., shoulder of the prominent fused silica boson peak (~130 cm(-1)); distinct sapphire ball-lens peaks (380, 417, 646, and 751 cm(-1))) from the ball-lens fiber-optic Raman probe for quantitative analysis of fiber-optic Raman spectroscopy. To evaluate the analytical value of this novel multivariate reference technique, a rapid Raman spectroscopy system coupled with a ball-lens fiber-optic Raman probe is used for in vivo oral tissue Raman measurements (n = 25 subjects) under 785 nm laser excitation powers ranging from 5 to 65 mW. An accurate linear relationship (R(2) = 0.981) with a root-mean-square error of cross validation (RMSECV) of 2.5 mW can be obtained for predicting the laser excitation power changes based on a leave-one-subject-out cross-validation, which is superior to the normal univariate reference method (RMSE = 6.2 mW). A root-mean-square error of prediction (RMSEP) of 2.4 mW (R(2) = 0.985) can also be achieved for laser power prediction in real time when we applied the multivariate method independently on the five new subjects (n = 166 spectra). We further apply the multivariate reference technique for quantitative analysis of gelatin tissue phantoms that gives rise to an RMSEP of ~2.0% (R(2) = 0.998) independent of laser excitation power variations. This work demonstrates that multivariate reference technique can be advantageously used to monitor and correct the variations of laser excitation power and fiber coupling efficiency in situ for standardizing the tissue Raman intensity to realize quantitative analysis of tissue Raman measurements in vivo, which is particularly appealing in

  5. Uncovering Suitable Reference Proteins for Expression Studies in Human Adipose Tissue with Relevance to Obesity

    PubMed Central

    Pérez-Pérez, Rafael; López, Juan A.; García-Santos, Eva; Camafeita, Emilio; Gómez-Serrano, María; Ortega-Delgado, Francisco J.; Ricart, Wifredo; Fernández-Real, José M.; Peral, Belén

    2012-01-01

    Background Protein expression studies based on the two major intra-abdominal human fat depots, the subcutaneous and the omental fat, can shed light into the mechanisms involved in obesity and its co-morbidities. Here we address, for the first time, the identification and validation of reference proteins for data standardization, which are essential for accurate comparison of protein levels in expression studies based on fat from obese and non-obese individuals. Methodology and Findings To uncover adipose tissue proteins equally expressed either in omental and subcutaneous fat depots (study 1) or in omental fat from non-obese and obese individuals (study 2), we have reanalyzed our previously published data based on two-dimensional fluorescence difference gel electrophoresis. Twenty-four proteins (12 in study 1 and 12 in study 2) with similar expression levels in all conditions tested were selected and identified by mass spectrometry. Immunoblotting analysis was used to confirm in adipose tissue the expression pattern of the potential reference proteins and three proteins were validated: PARK7, ENOA and FAA. Western Blot analysis was also used to test customary loading control proteins. ENOA, PARK7 and the customary loading control protein Beta-actin showed steady expression profiles in fat from non-obese and obese individuals, whilst FAA maintained steady expression levels across paired omental and subcutaneous fat samples. Conclusions ENOA, PARK7 and Beta-actin are proper reference standards in obesity studies based on omental fat, whilst FAA is the best loading control for the comparative analysis of omental and subcutaneous adipose tissues either in obese and non-obese subjects. Neither customary loading control proteins GAPDH and TBB5 nor CALX are adequate standards in differential expression studies on adipose tissue. The use of the proposed reference proteins will facilitate the adequate analysis of proteins differentially expressed in the context of obesity

  6. Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV

    NASA Astrophysics Data System (ADS)

    Endres, Christopher J.; Hammoud, Dima A.; Pomper, Martin G.

    2011-04-01

    When applicable, it is generally preferred to evaluate positron emission tomography (PET) studies using a reference tissue-based approach as that avoids the need for invasive arterial blood sampling. However, most reference tissue methods have been shown to have a bias that is dependent on the level of tracer binding, and the variability of parameter estimates may be substantially affected by noise level. In a study of serotonin transporter (SERT) binding in HIV dementia, it was determined that applying parameter coupling to the simplified reference tissue model (SRTM) reduced the variability of parameter estimates and yielded the strongest between-group significant differences in SERT binding. The use of parameter coupling makes the application of SRTM more consistent with conventional blood input models and reduces the total number of fitted parameters, thus should yield more robust parameter estimates. Here, we provide a detailed evaluation of the application of parameter constraint and parameter coupling to [11C]DASB PET studies. Five quantitative methods, including three methods that constrain the reference tissue clearance (kr2) to a common value across regions were applied to the clinical and simulated data to compare measurement of the tracer binding potential (BPND). Compared with standard SRTM, either coupling of kr2 across regions or constraining kr2 to a first-pass estimate improved the sensitivity of SRTM to measuring a significant difference in BPND between patients and controls. Parameter coupling was particularly effective in reducing the variance of parameter estimates, which was less than 50% of the variance obtained with standard SRTM. A linear approach was also improved when constraining kr2 to a first-pass estimate, although the SRTM-based methods yielded stronger significant differences when applied to the clinical study. This work shows that parameter coupling reduces the variance of parameter estimates and may better discriminate between

  7. Spatially resolved quantification of gadolinium(III)-based magnetic resonance agents in tissue by MALDI imaging mass spectrometry after in vivo MRI.

    PubMed

    Aichler, Michaela; Huber, Katharina; Schilling, Franz; Lohöfer, Fabian; Kosanke, Katja; Meier, Reinhard; Rummeny, Ernst J; Walch, Axel; Wildgruber, Moritz

    2015-03-27

    Gadolinium(III)-based contrast agents improve the sensitivity and specificity of magnetic resonance imaging (MRI), especially when targeted contrast agents are applied. Because of nonlinear correlation between the contrast agent concentration in tissue and the MRI signal obtained in vivo, quantification of certain biological or pathophysiological processes by MRI remains a challenge. Up to now, no technology has been able to provide a spatially resolved quantification of MRI agents directly within the tissue, which would allow a more precise verification of in vivo imaging results. MALDI imaging mass spectrometry for spatially resolved in situ quantification of gadolinium(III) agents, in correlation to in vivo MRI, were evaluated. Enhanced kinetics of Gadofluorine M were determined dynamically over time in a mouse model of myocardial infarction. MALDI imaging was able to corroborate the in vivo imaging MRI signals and enabled in situ quantification of the gadolinium probe with high spatial resolution.

  8. A specific endogenous reference for genetically modified common bean (Phaseolus vulgaris L.) DNA quantification by real-time PCR targeting lectin gene.

    PubMed

    Venturelli, Gustavo L; Brod, Fábio C A; Rossi, Gabriela B; Zimmermann, Naíra F; Oliveira, Jaison P; Faria, Josias C; Arisi, Ana C M

    2014-11-01

    The Embrapa 5.1 genetically modified (GM) common bean was approved for commercialization in Brazil. Methods for the quantification of this new genetically modified organism (GMO) are necessary. The development of a suitable endogenous reference is essential for GMO quantification by real-time PCR. Based on this, a new taxon-specific endogenous reference quantification assay was developed for Phaseolus vulgaris L. Three genes encoding common bean proteins (phaseolin, arcelin, and lectin) were selected as candidates for endogenous reference. Primers targeting these candidate genes were designed and the detection was evaluated using the SYBR Green chemistry. The assay targeting lectin gene showed higher specificity than the remaining assays, and a hydrolysis probe was then designed. This assay showed high specificity for 50 common bean samples from two gene pools, Andean and Mesoamerican. For GM common bean varieties, the results were similar to those obtained for non-GM isogenic varieties with PCR efficiency values ranging from 92 to 101 %. Moreover, this assay presented a limit of detection of ten haploid genome copies. The primers and probe developed in this work are suitable to detect and quantify either GM or non-GM common bean.

  9. Role of Anterior Neck Soft Tissue Quantifications by Ultrasound in Predicting Difficult Laryngoscopy

    PubMed Central

    Wu, Jinhong; Dong, Jing; Ding, Yingchun; Zheng, Jijian

    2014-01-01

    Background The aim of this study was to determine if ultrasound (US) measurements of anterior neck soft tissue thickness at hyoid bone (DSHB), thyrohyoid membrane (DSEM), and anterior commissure (DSAC) levels can be used to predict difficult laryngoscopy. Material/Methods We included 203 patients age 20–65 years scheduled to undergo general anesthesia in this prospective observational study. Correlation analysis and receiver operating characteristic curve (ROC) analysis were used to determine the roles of screening tests [interincisor gap (IIG), thyromental distance (TMD), modified Mallampati score (MMS)] and US measurements (DSHB, DSEM, DSAC) in predicting difficult laryngoscopy. Results There were 28 out of 203 patients categorized as difficult laryngoscopy. DSHB, DSEM, DSAC, and MMS were greater in the difficult laryngoscopy group (P<0.0001). There was a strong positive correlation between DSEM and DSHB (r=0.74); moderate positive correlations between DSEM and DSAC (r=0.60), DSHB and DSAC (r=0.69); small positive correlations between MMS and DSHB (r=0.32), MMS and DSEM (r=0.27), MMS and DSAC (r=0.32), all P values ≤0.0001; very small positive correlation between TMD and IIG (r=0.18, P=0.0089); small negative correlation between IIG and MMS (r=−0.27, P=0.0001); and very small negative correlations between MMS and TMD (r=−0.20, P=0.004), IIG and DSAC (r=−0.18, P=0.011), IIG and DSHB (r=−0.15, P=0.034). The areas under the ROC curve (AUCs) of MMS, DSHB, DSEM, and DSAC were significantly larger compared with the reference line (P<0.0001). Conclusions Anterior neck soft tissue thicknesses measured by US at hyoid bone, thyrohyoid membrane, and anterior commissure levels are independent predictors of difficult laryngoscopy. Combinations of those screening tests or risk factors with US measurements might increase the ability to predict difficult laryngoscopy. PMID:25403231

  10. Quantification of mucosal mononuclear cells in tissues with a fluorescent bead-based polychromatic flow cytometry assay.

    PubMed

    Reeves, R Keith; Evans, Tristan I; Gillis, Jacqueline; Wong, Fay E; Connole, Michelle; Carville, Angela; Johnson, R Paul

    2011-03-31

    Since the vast majority of infections occur at mucosal surfaces, accurate characterization of mucosal immune cells is critically important for understanding transmission and control of infectious diseases. Standard flow cytometric analysis of cells obtained from mucosal tissues can provide valuable information on the phenotype of mucosal leukocytes and their relative abundance, but does not provide absolute cell counts of mucosal cell populations. We developed a bead-based flow cytometry assay to determine the absolute numbers of multiple mononuclear cell types in colorectal biopsies of rhesus macaques. Using 10-color flow cytometry panels and pan-fluorescent beads, cells were enumerated in biopsy specimens by adding a constant ratio of beads per mg of tissue and then calculating cell numbers/mg of tissue based on cell-to-bead ratios determined at the time of sample acquisition. Testing in duplicate specimens showed the assay to be highly reproducible (Spearman R=0.9476, P<0.0001). Using this assay, we report enumeration of total CD45(+) leukocytes, CD4(+) and CD8(+) T cells, B cells, NK cells, CD14(+) monocytes, and myeloid and plasmacytoid dendritic cells in colorectal biopsies, with cell numbers in normal rhesus macaques varying from medians of 4486 cells/mg (T cells) to 3 cells/mg (plasmacytoid dendritic cells). This assay represents a significant advancement in rapid, accurate quantification of mononuclear cell populations in mucosal tissues and could be applied to provide absolute counts of a variety of different cell populations in diverse tissues.

  11. Quantification of Toxoplasma gondii in tissue samples of experimentally infected goats by magnetic capture and real-time PCR.

    PubMed

    Juránková, Jana; Opsteegh, Marieke; Neumayerová, Helena; Kovařčík, Kamil; Frencová, Anita; Baláž, Vojtěch; Volf, Jiří; Koudela, Břetislav

    2013-03-31

    Undercooked meat containing tissue cysts is one of the most common sources of Toxoplasma gondii infection in humans. Goats are very susceptible to clinical toxoplasmosis, and especially kids are common food animals, thereby representing a risk for human infection. A sequence-specific magnetic capture method was used for isolation of T. gondii DNA from tissue samples from experimentally infected goat-kids and real-time PCR for the 529 bp repeat element allowed quantification of T. gondii DNA. The contamination level in different types of tissue and in two groups of goats euthanized 30 and 90 dpi was compared. The highest concentration of T. gondii DNA in both groups of goats was found in lung tissue, but only the higher parasite count in lung tissue compared to other organs in group A (euthanized 30 dpi) was statistically significant. T. gondii concentrations were higher in liver and dorsal muscle samples from goats euthanized 90 dpi than in goats euthanized at 30 dpi, while the T. gondii concentration in hearts decreased. This study describes for the first time distribution of T. gondii parasites in post-weaned goat kids. New information about T. gondii predilection sites in goats and about the progression of infection between 30 and 90 dpi was achieved. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. An image-based skeletal tissue model for the ICRP reference newborn.

    PubMed

    Pafundi, Deanna; Lee, Choonsik; Watchman, Christopher; Bourke, Vincent; Aris, John; Shagina, Natalia; Harrison, John; Fell, Tim; Bolch, Wesley

    2009-07-21

    Hybrid phantoms represent a third generation of computational models of human anatomy needed for dose assessment in both external and internal radiation exposures. Recently, we presented the first whole-body hybrid phantom of the ICRP reference newborn with a skeleton constructed from both non-uniform rational B-spline and polygon-mesh surfaces (Lee et al 2007 Phys. Med. Biol. 52 3309-33). The skeleton in that model included regions of cartilage and fibrous connective tissue, with the remainder given as a homogenous mixture of cortical and trabecular bone, active marrow and miscellaneous skeletal tissues. In the present study, we present a comprehensive skeletal tissue model of the ICRP reference newborn to permit a heterogeneous representation of the skeleton in that hybrid phantom set-both male and female-that explicitly includes a delineation of cortical bone so that marrow shielding effects are correctly modeled for low-energy photons incident upon the newborn skeleton. Data sources for the tissue model were threefold. First, skeletal site-dependent volumes of homogeneous bone were obtained from whole-cadaver CT image analyses. Second, selected newborn bone specimens were acquired at autopsy and subjected to micro-CT image analysis to derive model parameters of the marrow cavity and bone trabecular 3D microarchitecture. Third, data given in ICRP Publications 70 and 89 were selected to match reference values on total skeletal tissue mass. Active marrow distributions were found to be in reasonable agreement with those given previously by the ICRP. However, significant differences were seen in total skeletal and site-specific masses of trabecular and cortical bone between the current and ICRP newborn skeletal tissue models. The latter utilizes an age-independent ratio of 80%/20% cortical and trabecular bone for the reference newborn. In the current study, a ratio closer to 40%/60% is used based upon newborn CT and micro-CT skeletal image analyses. These changes in

  13. An image-based skeletal tissue model for the ICRP reference newborn

    NASA Astrophysics Data System (ADS)

    Pafundi, Deanna; Lee, Choonsik; Watchman, Christopher; Bourke, Vincent; Aris, John; Shagina, Natalia; Harrison, John; Fell, Tim; Bolch, Wesley

    2009-07-01

    Hybrid phantoms represent a third generation of computational models of human anatomy needed for dose assessment in both external and internal radiation exposures. Recently, we presented the first whole-body hybrid phantom of the ICRP reference newborn with a skeleton constructed from both non-uniform rational B-spline and polygon-mesh surfaces (Lee et al 2007 Phys. Med. Biol. 52 3309-33). The skeleton in that model included regions of cartilage and fibrous connective tissue, with the remainder given as a homogenous mixture of cortical and trabecular bone, active marrow and miscellaneous skeletal tissues. In the present study, we present a comprehensive skeletal tissue model of the ICRP reference newborn to permit a heterogeneous representation of the skeleton in that hybrid phantom set—both male and female—that explicitly includes a delineation of cortical bone so that marrow shielding effects are correctly modeled for low-energy photons incident upon the newborn skeleton. Data sources for the tissue model were threefold. First, skeletal site-dependent volumes of homogeneous bone were obtained from whole-cadaver CT image analyses. Second, selected newborn bone specimens were acquired at autopsy and subjected to micro-CT image analysis to derive model parameters of the marrow cavity and bone trabecular 3D microarchitecture. Third, data given in ICRP Publications 70 and 89 were selected to match reference values on total skeletal tissue mass. Active marrow distributions were found to be in reasonable agreement with those given previously by the ICRP. However, significant differences were seen in total skeletal and site-specific masses of trabecular and cortical bone between the current and ICRP newborn skeletal tissue models. The latter utilizes an age-independent ratio of 80%/20% cortical and trabecular bone for the reference newborn. In the current study, a ratio closer to 40%/60% is used based upon newborn CT and micro-CT skeletal image analyses. These

  14. Origin and quantification of differences between normal and tumor tissues observed by terahertz spectroscopy

    NASA Astrophysics Data System (ADS)

    Yamaguchi, Sayuri; Fukushi, Yasuko; Kubota, Oichi; Itsuji, Takeaki; Ouchi, Toshihiko; Yamamoto, Seiji

    2016-09-01

    The origin of the differences in the refractive index observed between normal and tumor tissues using terahertz spectroscopy has been described quantitatively. To estimate water content differences in tissues, we prepared fresh and paraffin-embedded samples from rats. An approximately 5% increase of water content in tumor tissues was calculated from terahertz time domain spectroscopy measurements compared to normal tissues. A greater than 15% increase in percentage of cell nuclei per unit area in tumor tissues was observed by hematoxylin and eosin stained samples, which generates a higher refractive index of biological components other than water. Both high water content and high cell density resulted in higher refractive index by approximately 0.05 in tumor tissues. It is predicted that terahertz spectroscopy can also be used to detect brain tumors in human tissue due to the same underlying mechanism as in rats.

  15. Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) Breast Cancer Tissues*

    PubMed Central

    Steiner, Carine; Tille, Jean-Christophe; Lamerz, Jens; Kux van Geijtenbeek, Sabine; McKee, Thomas A.; Venturi, Miro; Rubbia-Brandt, Laura; Hochstrasser, Denis; Cutler, Paul; Lescuyer, Pierre; Ducret, Axel

    2015-01-01

    The ability to accurately quantify proteins in formalin-fixed paraffin-embedded tissues using targeted mass spectrometry opens exciting perspectives for biomarker discovery. We have developed and evaluated a selectedreaction monitoring assay for the human receptor tyrosine-protein kinase erbB-2 (HER2) in formalin-fixed paraffin-embedded breast tumors. Peptide candidates were identified using an untargeted mass spectrometry approach in relevant cell lines. A multiplexed assay was developed for the six best candidate peptides and evaluated for linearity, precision and lower limit of quantification. Results showed a linear response over a calibration range of 0.012 to 100 fmol on column (R2: 0.99–1.00).The lower limit of quantification was 0.155 fmol on column for all peptides evaluated. The six HER2 peptides were quantified by selected reaction monitoring in a cohort of 40 archival formalin-fixed paraffin-embedded tumor tissues from women with invasive breast carcinomas, which showed different levels of HER2 gene amplification as assessed by standard methods used in clinical pathology. The amounts of the six HER2 peptides were highly and significantly correlated with each other, indicating that peptide levels can be used as surrogates of protein amounts in formalin-fixed paraffin-embedded tissues. After normalization for sample size, selected reaction monitoring peptide measurements were able to correctly predict 90% of cases based on HER2 amplification as defined by the American Society of Clinical Oncology and College of American Pathologists. In conclusion, the developed assay showed good analytical performance and a high agreement with immunohistochemistry and fluorescence in situ hybridization data. This study demonstrated that selected reaction monitoring allows to accurately quantify protein expression in formalin-fixed paraffin-embedded tissues and represents therefore a powerful approach for biomarker discovery studies. The untargeted mass spectrometry

  16. Reliability of soft tissue references for anteroposterior measurement of dental bases.

    PubMed

    Ferrario, V F; Sforza, C; Serrao, G; Colombo, A; Ciusa, V; Bignotto, M

    1998-01-01

    The aims of the present investigation were to devise a new anteroposterior measurement of maxillomandibular discrepancies that would consider both hard and soft tissue contributions, and to verify the correlation of this measurement to a well-established linear assessment of anteroposterior discrepancy. On the pretreatment lateral cephalographs of 300 orthodontic patients (162 males, 138 females) aged between 6 and 50 years, the Wits appraisal and a new "soft tissue" Wits appraisal (linear distance between the projections of soft tissue A and B points on the bisecting occlusal plane) were measured. In the analyzed sample, the former was more variable than the latter. The two measurements were significantly correlated to each other without sex- or age-characteristic patterns. From the correlation, reference values for the new measurement were estimated and found to be between -1.9 mm and 5.4 mm for individuals with a normal occlusion. The new measurement could allow a more careful evaluation of the soft tissue drape together with the underlying hard tissue structure.

  17. Investigating reference genes for quantitative real-time PCR analysis across four chicken tissues.

    PubMed

    Bagés, S; Estany, J; Tor, M; Pena, R N

    2015-04-25

    Accurate normalization of data is required to correct for different efficiencies and errors during the processing of samples in reverse transcription PCR analysis. The chicken is one of the main livestock species and its genome was one of the first reported and used in large scale transcriptomic analysis. Despite this, the chicken has not been investigated regarding the identification of reference genes suitable for the quantitative PCR analysis of growth and fattening genes. In this study, five candidate reference genes (B2M, RPL32, SDHA, TBP and YWHAZ) were evaluated to determine the most stable internal reference for quantitative PCR normalization in the two main commercial muscles (pectoralis major (breast) and biceps femoris (thigh)), liver and abdominal fat. Four statistical methods (geNorm, NormFinder, CV and BestKeeper) were used in the evaluation of the most suitable combination of reference genes. Additionally, a comprehensive ranking was established with the RefFinder tool. This analysis identified YWHAZ and TBP as the recommended combination for the analysis of biceps femoris and liver, YWHAZ and RPL32 for pectoralis major and RPL32 and B2M for abdominal fat and across-tissue studies. The final ranking for each tool changed slightly but overall the results, and most particularly the ability to discard the least robust candidates, were consistent between tools. The selection and number of reference genes were validated using SCD, a target gene related to fat metabolism. Overall, the results can be directly used to quantitate target gene expression in different tissues or in validation studies from larger transcriptomic experiments. Copyright © 2015 Elsevier B.V. All rights reserved.

  18. Automated quantification of epicardial adipose tissue using CT angiography: evaluation of a prototype software.

    PubMed

    Spearman, James V; Meinel, Felix G; Schoepf, U Joseph; Apfaltrer, Paul; Silverman, Justin R; Krazinski, Aleksander W; Canstein, Christian; De Cecco, Carlo Nicola; Costello, Philip; Geyer, Lucas L

    2014-02-01

    This study evaluated the performance of a novel automated software tool for epicardial fat volume (EFV) quantification compared to a standard manual technique at coronary CT angiography (cCTA). cCTA data sets of 70 patients (58.6 ± 12.9 years, 33 men) were retrospectively analysed using two different post-processing software applications. Observer 1 performed a manual single-plane pericardial border definition and EFVM segmentation (manual approach). Two observers used a software program with fully automated 3D pericardial border definition and EFVA calculation (automated approach). EFV and time required for measuring EFV (including software processing time and manual optimization time) for each method were recorded. Intraobserver and interobserver reliability was assessed on the prototype software measurements. T test, Spearman's rho, and Bland-Altman plots were used for statistical analysis. The final EFVA (with manual border optimization) was strongly correlated with the manual axial segmentation measurement (60.9 ± 33.2 mL vs. 65.8 ± 37.0 mL, rho = 0.970, P < 0.001). A mean of 3.9 ± 1.9 manual border edits were performed to optimize the automated process. The software prototype required significantly less time to perform the measurements (135.6 ± 24.6 s vs. 314.3 ± 76.3 s, P < 0.001) and showed high reliability (ICC > 0.9). Automated EFVA quantification is an accurate and time-saving method for quantification of EFV compared to established manual axial segmentation methods. • Manual epicardial fat volume quantification correlates with risk factors but is time-consuming. • The novel software prototype automates measurement of epicardial fat volume with good accuracy. • This novel approach is less time-consuming and could be incorporated into clinical workflow.

  19. Genome-wide quantification of rare somatic mutations in normal human tissues using massively parallel sequencing

    PubMed Central

    Hoang, Margaret L.; Kinde, Isaac; Tomasetti, Cristian; McMahon, K. Wyatt; Rosenquist, Thomas A.; Grollman, Arthur P.; Kinzler, Kenneth W.; Vogelstein, Bert; Papadopoulos, Nickolas

    2016-01-01

    We present the bottleneck sequencing system (BotSeqS), a next-generation sequencing method that simultaneously quantifies rare somatic point mutations across the mitochondrial and nuclear genomes. BotSeqS combines molecular barcoding with a simple dilution step immediately before library amplification. We use BotSeqS to show age- and tissue-dependent accumulations of rare mutations and demonstrate that somatic mutational burden in normal human tissues can vary by several orders of magnitude, depending on biologic and environmental factors. We further show major differences between the mutational patterns of the mitochondrial and nuclear genomes in normal tissues. Lastly, the mutation spectra of normal tissues were different from each other, but similar to those of the cancers that arose in them. This technology can provide insights into the number and nature of genetic alterations in normal tissues and can be used to address a variety of fundamental questions about the genomes of diseased tissues. PMID:27528664

  20. Simultaneous identification and quantification of new psychoactive substances in blood by GC-APCI-QTOFMS coupled to nitrogen chemiluminescence detection without authentic reference standards.

    PubMed

    Ojanperä, Ilkka; Mesihää, Samuel; Rasanen, Ilpo; Pelander, Anna; Ketola, Raimo A

    2016-05-01

    A novel platform is introduced for simultaneous identification and quantification of new psychoactive substances (NPS) in blood matrix, without the necessity of using authentic reference standards. The instrumentation consisted of gas chromatography (GC) coupled to nitrogen chemiluminescence detection (NCD) and atmospheric pressure chemical ionization quadrupole time-of-flight mass spectrometry (APCI-QTOFMS). In this concept, the GC flow is divided in appropriate proportions between NCD for single-calibrant quantification, utilizing the detector's equimolar response to nitrogen, and QTOFMS for accurate mass-based identification. The principle was proven by analyzing five NPS, bupropion, desoxypipradrol (2-DPMP), mephedrone, methylone, and naphyrone, in sheep blood. The samples were spiked with the analytes post-extraction to avoid recovery considerations at this point. All the NPS studies produced a protonated molecule in APCI resulting in predictable fragmentation with high mass accuracy. The N-equimolarity of quantification by NCD was investigated by using external calibration with the secondary standard caffeine at five concentration levels between 0.17 and 1.7 mg/L in blood matrix as five replicates. The equimolarity was on average 98.7%, and the range of individual equimolarity determinations was 76.7-130.1%. The current analysis platform affords a promising approach to instant simultaneous qualitative and quantitative analysis of drugs in the absence of authentic reference standards, not only in forensic and clinical toxicology but also in other bioanalytical applications.

  1. A mussel tissue certified reference material for multiple phycotoxins. Part 1: design and preparation.

    PubMed

    McCarron, Pearse; Emteborg, Håkan; Nulty, Cíara; Rundberget, Thomas; Loader, Jared I; Teipel, Katharina; Miles, Christopher O; Quilliam, Michael A; Hess, Philipp

    2011-05-01

    The development of multi-analyte methods for lipophilic shellfish toxins based on liquid chromatography-mass spectrometry permits rapid screening and analysis of samples for a wide variety of toxins in a single run. Validated methods and appropriate certified reference materials (CRMs) are required to ensure accuracy of results. CRMs are essential for accurate instrument calibration, for assessing the complete analytical method from sample extraction to data analysis and for verifying trueness. However, CRMs have hitherto only been available for single toxin groups. Production of a CRM containing six major toxin groups was achieved through an international collaboration. Preparation of this material, CRM-FDMT1, drew on information from earlier studies as well as improved methods for isolation of toxins, handling bulk tissues and production of reference materials. Previous investigations of stabilisation techniques indicated freeze-drying to be a suitable procedure for preparation of shellfish toxin reference materials and applicable to a wide range of toxins. CRM-FDMT1 was initially prepared as a bulk wet tissue homogenate containing domoic acid, okadaic acid, dinophysistoxins, azaspiracids, pectenotoxin-2, yessotoxin and 13-desmethylspirolide C. The homogenate was then freeze-dried, milled and bottled in aliquots suitable for distribution and analysis. The moisture content and particle size distribution were measured, and determined to be appropriate. A preliminary toxin analysis of the final material showed a comprehensive toxin profile.

  2. An alpha autoradiographic technique for spatial quantification of sup 10 B concentrations in tissue

    SciTech Connect

    Woollard, J.E.; Blue, T.E.; Curran, J.F.; Dobelbower, M.C.; Busby, H.R. ); Barth, R.F. )

    1992-01-01

    This paper reports on boron neutron capture therapy (BNCT) which is an experimental radiation therapy that is being developed for the treatment of malignant tumors. One requirement for successful BNCT is that a sufficient amount of {sup 10}B concentrates in the tumor while clearing from normal tissues and blood. Many pharmaceuticals are currently being developed to selectively deliver {sup 10}B to a tumor. To evaluate the effectiveness of various {sup 10}B delivery agents, the concentrations of boron in blood, tumor, and normal tissues must be known. Using the solid-state nuclear track detector CR-39, a tissue assay technique has been developed to spatially determine {sup 10}B concentrations in tissue samples. The technique has been used to quantify {sup 10}B concentrations in tumor and normal tissue on lines across rat brain tissue sections. This was done by combining {sup 10}B concentrations measured on lines across the CR-39 with color digital images of the tissue section. Coupling the methodology that was developed for tissue samples with an existing analytical technique for blood-{sup 10}B concentration measurements allows for complete evaluation of {sup 10}B distributions in blood, tumor, and normal tissues and should be useful in evaluating various {sup 10}B delivery agents for use in BNCT.

  3. Quantification of nucleic acid quality in postmortem tissues from a cancer research autopsy program

    PubMed Central

    Fan, Jun; Khanin, Raya; Sakamoto, Hitomi; Zhong, Yi; Michael, Chelsea; Pena, Derwin; Javier, Breanna; Wood, Laura D.; Iacobuzio-Donahue, Christine A.

    2016-01-01

    The last decade has seen a marked rise in the use of cancer tissues obtained from research autopsies. Such resources have been invaluable for studying cancer evolution or the mechanisms of therapeutic resistance to targeted therapies. Degradation of biomolecules is a potential challenge to usage of cancer tissues obtained in the post-mortem setting and remains incompletely studied. We analysed the nucleic acid quality in 371 different frozen tissue samples collected from 80 patients who underwent a research autopsy, including eight normal tissue types, primary and metastatic tumors. Our results indicate that RNA integrity number (RIN) of normal tissues decline with the elongation of post-mortem interval (PMI) in a tissue-type specific manner. Unlike normal tissues, the RNA quality of cancer tissues is highly variable with respect to post-mortem interval. The kinetics of DNA damage also has tissue type-specific features. Moreover, while DNA degradation is an indicator of low RNA quality, the converse is not true. Finally, we show that despite RIN values as low as 5.0, robust data can be obtained by RNA sequencing that reliably discriminates expression signatures. PMID:27602498

  4. A microsatellite based method for quantification of fungi in decomposing plant material elucidates the role of Fusarium graminearum DON production in the saprophytic competition with Trichoderma atroviride in maize tissue microcosms.

    PubMed

    Naef, Andreas; Senatore, Mauro; Défago, Geneviève

    2006-02-01

    Common PCR assays for quantification of fungi in living plants cannot be used to study saprophytic colonization of fungi because plant decomposition releases PCR-inhibiting substances and saprophytes degrade the plant DNA which could serve as internal standard. The microsatellite PCR assays presented here overcome these problems by spiking samples prior to DNA extraction with mycelium of a reference strain. PCR with fluorescent primers co-amplifies microsatellite fragments of different length from target and reference strains. These fragments were separated in a capillary sequencer with fluorescence detection. The target/reference ratio of fluorescence signal was used to calculate target biomass in the sample. Such PCR assays were developed for the mycotoxin deoxynivalenol (DON)-producing wheat and maize pathogen Fusarium graminearum and the biocontrol agent Trichoderma atroviride, using new microsatellite markers. In contrast to real-time PCR assays, the novel PCR assays showed reliable fungal biomass quantification in samples with differentially decomposed plant tissue. The PCR assays were used to quantify the two fungi after competitive colonization of autoclaved maize leaf tissue in microcosms. Using a DON-producing F. graminearum wild-type strain and its nontoxigenic mutant we found no evidence for a role of DON production in F. graminearum defense against T. atroviride. The presence of T. atroviride resulted in a 36% lower wild-type DON production per biomass.

  5. Accuracy of dual-energy computed tomography for the quantification of iodine in a soft tissue-mimicking phantom.

    PubMed

    Li, Jung-Hui; Du, Yeh-Ming; Huang, Hsuan-Ming

    2015-09-01

    The objective of this study was to evaluate the accuracy of dual-energy CT (DECT) for quantifying iodine using a soft tissue-mimicking phantom across various DECT acquisition parameters and dual-source CT (DSCT) scanners. A phantom was constructed with plastic tubes containing soft tissue-mimicking materials with known iodine concentrations (0-20 mg/mL). Experiments were performed on two DSCT scanners, one equipped with an integrated detector and the other with a conventional detector. DECT data were acquired using two DE modes (80 kV/Sn140 kV and 100 kV/Sn140 kV) with four pitch values (0.6, 0.8, 1.0, and 1.2). Images were reconstructed using a soft tissue kernel with and without beam hardening correction (BHC) for iodine. Using the dedicated DE software, iodine concentrations were measured and compared to true concentrations. We also investigated the effect of reducing gantry rotation time on the DECT-based iodine measurement. At iodine concentrations higher than 10 mg/mL, the relative error in measured iodine concentration increased slightly. This error can be decreased by using the kernel with BHC, compared with the kernel without BHC. Both 80 kV/Sn140 kV and 100 kV/Sn140 kV modes could provide accurate quantification of iodine content. Increasing pitch value or reducing gantry rotation time had only a minor impact on the DECT-based iodine measurement. The DSCT scanner, equipped with the new integrated detector, showed more accurate iodine quantification for all iodine concentrations higher than 10 mg/mL. An accurate quantification of iodine can be obtained using the second-generation DSCT scanner in various DE modes with pitch values up to 1.2 and gantry rotation time down to 0.28 s. For iodine concentrations ≥10 mg/mL, using the new integrated detector and the kernel with BHC can improve the accuracy of DECT-based iodine measurements. PACS number: 87.57.Q.

  6. Accuracy of dual-energy computed tomography for the quantification of iodine in a soft tissue-mimicking phantom.

    PubMed

    Li, Jung-Hui; Du, Yeh-Ming; Huang, Hsuan-Ming

    2015-09-08

    The objective of this study was to evaluate the accuracy of dual-energy CT (DECT) for quantifying iodine using a soft tissue-mimicking phantom across various DECT acquisition parameters and dual-source CT (DSCT) scanners. A phantom was constructed with plastic tubes containing soft tissue-mimicking materials with known iodine concentrations (0-20 mg/mL). Experiments were performed on two DSCT scanners, one equipped with an integrated detector and the other with a conventional detector. DECT data were acquired using two DE modes (80 kV/Sn140 kV and 100 kV/Sn140 kV) with four pitch values (0.6, 0.8, 1.0, and 1.2). Images were reconstructed using a soft tissue kernel with and without beam hardening correction (BHC) for iodine. Using the dedicated DE software, iodine concentrations were measured and compared to true concentrations. We also investigated the effect of reducing gantry rotation time on the DECT-based iodine measurement. At iodine concentrations higher than 10 mg/mL, the relative error in measured iodine concentration increased slightly. This error can be decreased by using the kernel with BHC, compared with the kernel without BHC. Both 80 kV/Sn140 kV and 100 kV/Sn140 kV modes could provide accurate quantification of iodine content. Increasing pitch value or reducing gantry rotation time had only a minor impact on the DECT-based iodine measurement. The DSCT scanner, equipped with the new integrated detector, showed more accurate iodine quantification for all iodine concentrations higher than 10 mg/mL. An accurate quantification of iodine can be obtained using the second-generation DSCT scanner in various DE modes with pitch values up to 1.2 and gantry rotation time down to 0.28 s. For iodine concentrations ≥ 10 mg/mL, using the new integrated detector and the kernel with BHC can improve the accuracy of DECT-based iodine measurements.

  7. Comprehensive qualification and quantification of triacylglycerols with specific fatty acid chain composition in horse adipose tissue, human plasma and liver tissue.

    PubMed

    Guan, Ming; Dai, Dongsheng; Li, Lin; Wei, Jinchao; Yang, Hui; Li, Shilei; Zhang, Yangyang; Lin, Yu; Xiong, Shaoxiang; Zhao, Zhenwen

    2017-09-01

    High levels of triacylglycerols (TGs) have been linked to cardiovascular disease and liver diseases. Comprehensively analyzing TGs is helpful to understand the TGs functions in these diseases. However, due to the existence of a large number of isomers TGs and the lack of commercial standards, precise analysis of individual triacylglycerol (TG) with specific fatty acid chain composition is full of challenge. In this work, ultra-performance liquid chromatography (UPLC) coupled with electrospray ionization (ESI) mass spectrometry (MS) were employed for comprehensive qualification and quantification of TGs with specific fatty acid chain composition in horse adipose tissue, human plasma and liver tissues including hepatocellular carcinoma (HCC) and para-carcinoma tissues. Multiple MS detection modes from QTRAP MS and FT-ICR MS were utilized, and hundreds of TG species (including many oxidized TG species) with their specific fatty acid chain compositions have been qualified and quantified. The isomer TGs interference, the isobaric interference, and oxidized TG species interference were firstly indicated. Several isomer TGs, for example, 18:1/20:1/18:2 TG and 20:3/18:1/18:0 TG, which were all 56:4 TG, demonstrated different trends in HCC tissue compared with para-carcinoma tissue, which showed the importance of analysis of TG with specific fatty acid chain composition. In addition, 10 TGs with the degree of unsaturation beyond three were significantly decreased, while 16:0/17:0/18:0 TG, no double bond, was significantly increased in the HCC tissue, which firstly revealed aberrant specific TG metabolism in HCC. This is a systematic report about comprehensive analysis of TGs by UPLC-ESI-MS, which is of significance for accurate analysis of these lipids. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Magnetic Nanoparticle Location and Quantification in Mice Tissues after Intravenous Injection

    NASA Astrophysics Data System (ADS)

    Gutiérrez, Lucía; Cabrera, Lourdes I.; Mejías, Raquel; Barber, Domingo F.; Serna, Carlos J.; Morales, M. Puerto

    2010-10-01

    DMSA-coated magnetic nanoparticles have been used for drug delivery, in particular to transport cytokines towards an induced tumour in a murine model. In this work, the use of transmission electron microscopy and AC magnetic susceptibility measurements of the tissue have allowed the detection of the particles within the target tissue.

  9. Optimization and evaluation of MALDI TOF mass spectrometric imaging for quantification of orally dosed octreotide in mouse tissues.

    PubMed

    Rao, Tai; Shen, Boyu; Zhu, Zhangpei; Shao, Yuhao; Kang, Dian; Li, Xinuo; Yin, Xiaoxi; Li, Haofeng; Xie, Lin; Wang, Guangji; Liang, Yan

    2017-04-01

    Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry imaging (MALDI-TOF-MSI) has received considerable attention in recent years since it allows molecular mapping of diverse bimolecular in animal/plant tissue sections, although some barriers still exist in absolute pixel-to-pixel quantification. Octreotide, a synthetic somatostatin analogue, has been widely used to prevent gastrointestine bleeding in the clinic. The aim of the present study is to develop a MALDI-TOF-MSI method for quantitatively visualizing spatial distribution of octreotide in mouse tissues. In this process, a structurally similar internal standard was spotted onto tissue section together with matrix solution to minimize signal variation and give excellent quantitative results. The 2,5-dihydroxybenzoic acid was chosen as the most suitable matrix via comparing the signal/noise generated by MALDI-TOF-MSI after cocrystallization of octreotide with different matrix candidates. The reliability of MALDI-TOF-MSI, with respect to linearity, sensitivity and precision, was tested via measuring octreotide in fresh tissue slices at different concentrations. The validated method was then successfully applied to visualize the distribution of octreotide in mouse tissues after oral administration of octreotide at 20mg/kg. The results demonstrated that MALDI-TOF-MSI could not only clearly visualize the spatial distribution of octreotide, but also make the calculation of the key pharmacokinetic parameters (Tmax and t1/2) possible. More importantly, the tissue concentration-time curves of octreotide determined by MALDI-TOF-MSI agreed well with those measured based on LC-MS/MS.These findings illustrate the potential of MALDI-TOF-MSI in pharmacokinetic profiling during drug development.

  10. Detection and quantification of Flavobacterium psychrophilum in water and fish tissue samples by quantitative real time PCR

    PubMed Central

    2014-01-01

    Background Flavobacterium psychrophilum is the agent of Bacterial Cold Water Disease and Rainbow Trout Fry Syndrome, two diseases leading to high mortality. Pathogen detection is mainly carried out using cultures and more rapid and sensitive methods are needed. Results We describe a qPCR technique based on the single copy gene β’ DNA-dependent RNA polymerase (rpoC). Its detection limit was 20 gene copies and the quantification limit 103 gene copies per reaction. Tests on spiked spleens with known concentrations of F. psychrophilum (106 to 101 cells per reaction) showed no cross-reactions between the spleen tissue and the primers and probe. Screening of water samples and spleens from symptomless and infected fishes indicated that the pathogen was already present before the outbreaks, but F. psychrophilum was only quantifiable in spleens from diseased fishes. Conclusions This qPCR can be used as a highly sensitive and specific method to detect F. psychrophilum in different sample types without the need for culturing. qPCR allows a reliable detection and quantification of F. psychrophilum in samples with low pathogen densities. Quantitative data on F. psychrophilum abundance could be useful to investigate risk factors linked to infections and also as early warning system prior to potential devastating outbreak. PMID:24767577

  11. New biological reference materials - in vivo incorporated toxic metals in water hyacinth tissues

    SciTech Connect

    Austin, J.R.; Simon, S.J.; Williams, L.R.; Beckert, W.F.

    1985-06-01

    The purpose of this study was to demonstrate that high-quality reference materials, containing high levels of multiple toxic elements, can be produced with in vivo incorporation procedures. The approach taken was to produce water hyacinth tissue materials - leaves and stems containing high levels of arsenic, cadmium, lead, and mercury - as follows: apply a hydroponic feeding procedure for the in vivo incorporation of toxic elements into water hyacinths; dry, blend, and homogenize the plant materials and determine the levels of the incorporated elements and the homogeneity of the generated plant material; demonstrate that low-level control materials can be successfully blended with high-level materials to yield a homogeneous material with intermediate toxicant levels; evaluate the precision of the analytical methods used to determine toxic element levels in the materials; and evaluate the stability of the resulting materials. Sufficient quantities of the parent materials were produced so that characterized reference materials can now be made available on request. Levels of the toxic elements incorporated in water hyacinth leaves were 100, 300, 60, and 27 times the levels present in the control leaves for arsenic, cadmium, lead, and mercury, respectively. Overall precision of sampling, subsampling, and digestion, and chemical analysis of the treated materials, ranged from 3 to 10% relative standard deviation and was generally comparable to that of three NBS biological reference materials tested. 3 references, 1 figure, 4 tables.

  12. Development of potential candidate reference materials for drugs in bottom sediment, cod and herring tissues.

    PubMed

    Baranowska, Irena; Buszewski, Bogusław; Namieśnik, Jacek; Konieczka, Piotr; Magiera, Sylwia; Polkowska-Motrenko, Halina; Kościelniak, Paweł; Gadzała-Kopciuch, Renata; Woźniakiewicz, Aneta; Samczyński, Zbigniew; Kochańska, Kinga; Rutkowska, Małgorzata

    2017-02-01

    Regular use of a reference material and participation in a proficiency testing program can improve the reliability of analytical data. This paper presents the preparation of candidate reference materials for the drugs metoprolol, propranolol, carbamazepine, naproxen, and acenocoumarol in freshwater bottom sediment and cod and herring tissues. These reference materials are not available commercially. Drugs (between 7 ng/g and 32 ng/g) were added to the samples, and the spiked samples were freeze-dried, pulverized, sieved, homogenized, bottled, and sterilized by γ-irradiation to prepare the candidate materials. Procedures for extraction and liquid chromatography coupled with tandem mass spectrometry were developed to determine the drugs of interest in the studied material. Each target drug was quantified using two analytical procedures, and the results obtained from these two procedures were in good agreement with each other. Stability and homogeneity assessments were performed, and the relative uncertainties due to instability (for an expiration date of 12 months) and inhomogeneity were 10-25% and 4.0-6.8%, respectively. These procedures will be useful in the future production of reference materials. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Reference values for pulse wave Doppler and tissue Doppler imaging in pediatric echocardiography.

    PubMed

    Dallaire, Frederic; Slorach, Cameron; Hui, Wei; Sarkola, Taisto; Friedberg, Mark K; Bradley, Timothy J; Jaeggi, Edgar; Dragulescu, Andreea; Har, Ronnie L H; Cherney, David Z I; Mertens, Luc

    2015-02-01

    In pediatric echocardiography, pulse wave Doppler, and tissue Doppler imaging velocities are widely used to assess cardiac function. Current reference values and Z scores, allowing adjustment for growth are limited by inconsistent methodologies and small sample size. Using a standardized approach for parametric modeling and Z score quality assessment, we propose new pediatric reference values and Z score equations for most left ventricular pulse wave Doppler and tissue Doppler imaging measurements. Two hundred thirty-three healthy pediatric subjects 1 to 18 years of age were prospectively recruited. Thirteen pulse wave Doppler and 14 tissue Doppler imaging measurements were recorded. Normalization for growth was done via a complete and standardized approach for parametric nonlinear regression modeling. Several analyses were performed to ensure adequate Z score distribution and to detect potential residual associations with growth or residual heteroscedasticity. Most measurements adopted a nonlinear relationship with growth and displayed significant heteroscedasticity. Compared with age, height, and weight, normalization for body surface area was most efficient in removing the effect of growth. Generally, polynomial and allometric models yielded adequate goodness-of-fit. Residual values for several measurements had significant departure from the normal distribution, which could be corrected using logarithmic or reciprocal transformation. Overall, weighted parametric nonlinear models allowed us to compute Z score equations with adequate normal distribution and without residual association with growth. We present Z scores for normalized pulse wave Doppler and tissue Doppler imaging in pediatric echocardiography. Further studies are needed to define the threshold beyond which health becomes a disease by integrating other important factors such as ventricular morphology, loading conditions, and heart rate. © 2015 American Heart Association, Inc.

  14. High-performance capillary electrophoretic method for the quantification of 5-methyl 2'-deoxycytidine in genomic DNA: application to plant, animal and human cancer tissues.

    PubMed

    Fraga, Mario F; Uriol, Esther; Borja Diego, L; Berdasco, María; Esteller, Manel; Cañal, María Jesús; Rodríguez, Roberto

    2002-06-01

    A new approach to the evaluation of the relative degree of genomic DNA methylation through the quantification of 2'-deoxynucleosides is proposed. Detection and quantification of 5-methyl 2'-deoxycytidine in genomic DNA has been performed using micellar high-performance capillary electrophoresis (HPCE) with UV-Vis detection. This approach has been demonstrated to be more sensitive and specific than other HPCE methods for the quantification of DNA methylation degree and also to be faster than other HPLC-based methods. The detection and quantification of nucleosides through enzymatic hydrolyses notably increases the specificity of the technique and allows its exploitation in the analysis of poorly purified and/or concentrated DNA samples such as those obtained from meristematic plant regions and paraffin-embedded tissues.

  15. A ratiometric method of autofluorescence correction used for the quantification of Evans blue dye fluorescence in rabbit arterial tissues.

    PubMed

    Murphy, Christopher L; Lever, M John

    2002-03-01

    Evans blue dye (EBD) conjugates with albumin in the circulation and is frequently used to measure vascular protein leakage. The fluorescence of the dye from tissue sections can be used to measure its uptake at very specific anatomical locations, but problems arise with dye quantification because tissue components also fluoresce; so-called autofluorescence. We have measured uptake of EBD by blood vessel walls at various points around the aorto-renal branch of rabbits. High resolution, digitised, fluorescence images of histological sections of artery wall allowed detailed microscopic analysis of EBD accumulation; and a ratiometric method was developed to enable autofluorescence to be separated from EBD fluorescence. When EBD-free tissue sections were illuminated with blue light, the ratio of red to green fluorescence was constant throughout the tissue (0.59 +/- 0.03, mean +/- S.D., n = 32). Therefore, at each individual pixel, the level of red autofluorescence could be determined by multiplying the green intensity at that pixel by the calculated red to green ratio. Since EBD fluorescence was detected only in the red region of the spectrum, intensity values of the dye alone were obtained from EBD-exposed tissue by subtracting the red autofluorescence estimated by this ratiometric method. In such cases the red to green fluorescence ratio was measured from adjacent sites known to be free of EDB (0.59 +/- 0.02, mean +/- S.D., n = 56). We were therefore able to increase the sensitivity of tracer quantification by complete elimination of background autofluorescence on a pixel-by-pixel basis. Use of EBD standards allowed calibration of corrected fluorescence intensities and calculation of mass transfer coefficients for albumin into the artery wall. Spatial variations in the permeability of the artery wall around the renal ostium were detected with the present high resolution technique, with an average mass transfer coefficient of (6.8 +/- 0.9) x 10(-8) cm s(-1) for all

  16. Quantification of Regional Interstitial Lung Disease from CT-derived Fractional Tissue Volume: A Lung Tissue Research Consortium Study

    PubMed Central

    Yilmaz, Cuneyt; Watharkar, Snehal S.; de Leon, Alberto Diaz; Garcia, Christine K.; Patel, Nova C.; Jordan, Kirk G.; Hsia, Connie C.W.

    2011-01-01

    Rationale and Objectives Evaluation of chest CT is usually qualitative or semi-quantitative, resulting in subjective descriptions often by different observers over time and imprecise determinations of disease severity within distorted lobes. There is a need for standardized imaging biomarkers to quantify regional disease, maximize diagnostic yield, and facilitate multi-center comparisons. We applied lobe-based voxelwise image analysis to derive regional air (Vair) and tissue (Vtissue) volumes and fractional tissue volume (FTV=tissue/[tissue+air] volume) as internally standardized parameter for assessing interstitial lung disease (ILD). Materials and Methods High-resolution CT was obtained at supine and prone end-inspiration and supine end-expiration in 29 patients with ILD and 20 normal subjects. Lobar Vair, Vtissue, and FTV were expressed along standard coordinate axes. Results In normal subjects from end-inspiration to end-expiration, total Vair declined 43%, FTV increased ~80% while Vtissue remained unchanged. With increasing ILD, Vair declined and Vtissue rose in all lobes; FTV increased with a peripheral-to-central progression inversely correlated to spirometry and lung diffusing capacity (R2=0.57–0.75, prone end-inspiration). Inter- and intra-lobar coefficients of variation (CVs) of FTV increased 84–148% in mild-to-moderate ILD, indicating greater spatial heterogeneity, then normalized in severe ILD. Analysis of discontinuous images incurs <3% error compared to consecutive images. Conclusions These regional attenuation-based biomarkers could quantify heterogeneous parenchymal disease in distorted lobes, detect mild ILD involvement in all lobes and describe the pattern of disease progression. The next step would be to study a larger series, examine reproducibility and follow longitudinal changes in correlation with clinical and functional indices. PMID:21596593

  17. Contribution of neuroinflammation to changes in [(11)C]flumazenil binding in the rat brain: Evaluation of the inflamed pons as reference tissue.

    PubMed

    Parente, Andrea; Vállez García, David; Shoji, Alexandre; Lopes Alves, Isadora; Maas, Bram; Zijlma, Rolf; Dierckx, Rudi Ajo; Buchpiguel, Carlos A; de Vries, Erik Fj; Doorduin, Janine

    2017-06-01

    [(11)C]Flumazenil is a well-known PET tracer for GABAA receptors and is mainly used as an imaging biomarker for neuronal loss. Recently, GABAA receptors on immune cells have been investigated as target for modulation of inflammation. Since neuronal loss is often accompanied by neuroinflammation, PET imaging with [(11)C]flumazenil is potentially affected by infiltrating immune cells. This may also compromise the validity of using the pons as reference tissue in quantitative pharmacokinetic analysis. This study aims to evaluate whether inflammatory processes in the brain can influence [(11)C]flumazenil uptake and affect the outcome of pharmacokinetic modeling when the pons is used as reference tissue. The herpes simplex encephalitis (HSE) rat model is known to cause neuroinflammation in the brainstem. Dynamic [(11)C]flumazenil PET scans of 60-min, accompanied by arterial blood sampling and metabolite analysis, were acquired at day 6-7days post-infection of male Wistar rats (HSE, n=5 and control, n=6). Additionally, the GABAA receptor was saturated by injection of unlabeled flumazenil prior to the tracer injection in 4 rats per group. PET data were analyzed by pharmacokinetic modeling. No statistically significant differences were found in the volume of distribution (VT) or non-displaceable binding potential (BPND) between control and HSE rats in any of the brain regions. Pre-saturation with unlabeled flumazenil resulted in a statistically significant reduction in [(11)C]flumazenil VT in all brain regions. The BPND obtained from SRTM exhibited a good correlation to DVR - 1 values from the two-tissue compartment model, coupled with some level of underestimation. Reliable quantification of [(11)C]flumazenil binding in rats can be obtained by pharmacokinetic analysis using the pons as a pseudo-reference tissue even in the presence of strong acute neuroinflammation. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Quantification of Extracellular Matrix Proteins from a Rat Lung Scaffold to Provide a Molecular Readout for Tissue Engineering*

    PubMed Central

    Hill, Ryan C.; Calle, Elizabeth A.; Dzieciatkowska, Monika; Niklason, Laura E.; Hansen, Kirk C.

    2015-01-01

    The use of extracellular matrix (ECM)1 scaffolds, derived from decellularized tissues for engineered organ generation, holds enormous potential in the field of regenerative medicine. To support organ engineering efforts, we developed a targeted proteomics method to extract and quantify extracellular matrix components from tissues. Our method provides more complete and accurate protein characterization than traditional approaches. This is accomplished through the analysis of both the chaotrope-soluble and -insoluble protein fractions and using recombinantly generated stable isotope labeled peptides for endogenous protein quantification. Using this approach, we have generated 74 peptides, representing 56 proteins to quantify protein in native (nondecellularized) and decellularized lung matrices. We have focused on proteins of the ECM and additional intracellular proteins that are challenging to remove during the decellularization procedure. Results indicate that the acellular lung scaffold is predominantly composed of structural collagens, with the majority of these proteins found in the insoluble ECM, a fraction that is often discarded using widely accepted proteomic methods. The decellularization procedure removes over 98% of intracellular proteins evaluated and retains, to varying degrees, proteoglycans and glycoproteins of the ECM. Accurate characterization of ECM proteins from tissue samples will help advance organ engineering efforts by generating a molecular readout that can be correlated with functional outcome to drive the next generation of engineered organs. PMID:25660013

  19. Image-based quantification of fiber alignment within electrospun tissue engineering scaffolds is related to mechanical anisotropy.

    PubMed

    Fee, Timothy; Downs, Crawford; Eberhardt, Alan; Zhou, Yong; Berry, Joel

    2016-07-01

    It is well documented that electrospun tissue engineering scaffolds can be fabricated with variable degrees of fiber alignment to produce scaffolds with anisotropic mechanical properties. Several attempts have been made to quantify the degree of fiber alignment within an electrospun scaffold using image-based methods. However, these methods are limited by the inability to produce a quantitative measure of alignment that can be used to make comparisons across publications. Therefore, we have developed a new approach to quantifying the alignment present within a scaffold from scanning electron microscopic (SEM) images. The alignment is determined by using the Sobel approximation of the image gradient to determine the distribution of gradient angles with an image. This data was fit to a Von Mises distribution to find the dispersion parameter κ, which was used as a quantitative measure of fiber alignment. We fabricated four groups of electrospun polycaprolactone (PCL) + Gelatin scaffolds with alignments ranging from κ = 1.9 (aligned) to κ = 0.25 (random) and tested our alignment quantification method on these scaffolds. It was found that our alignment quantification method could distinguish between scaffolds of different alignments more accurately than two other published methods. Additionally, the alignment parameter κ was found to be a good predictor the mechanical anisotropy of our electrospun scaffolds. The ability to quantify fiber alignment within and make direct comparisons of scaffold fiber alignment across publications can reduce ambiguity between published results where cells are cultured on "highly aligned" fibrous scaffolds. This could have important implications for characterizing mechanics and cellular behavior on aligned tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1680-1686, 2016.

  20. A sensitive high performance liquid chromatography assay for the quantification of doxorubicin associated with DNA in tumor and tissues.

    PubMed

    Lucas, Andrew T; O'Neal, Sara K; Santos, Charlene M; White, Taylor F; Zamboni, William C

    2016-02-05

    Doxorubicin, a widely used anticancer agent, exhibits antitumor activity against a wide variety of malignancies. The drug exerts its cytotoxic effects by binding to and intercalating within the DNA of tumor and tissue cells. However, current assays are unable to accurately determine the concentration of the intracellular active form of doxorubicin. Thus, the development of a sample processing method and a high-performance liquid chromatography (HPLC) methodology was performed in order to quantify doxorubicin that is associated with DNA in tumors and tissues, which provided an intracellular cytotoxic measure of doxorubicin exposure after administration of small molecule and nanoparticle formulations of doxorubicin. The assay uses daunorubicin as an internal standard; liquid-liquid phase extraction to isolate drug associated with DNA; a Shimadzu HPLC with fluorescence detection equipped with a Phenomenex Luna C18 (2μm, 2.0×100mm) analytical column and a gradient mobile phase of 0.1% formic acid in water or acetonitrile for separation and quantification. The assay has a lower limit of detection (LLOQ) of 10ng/mL and is shown to be linear up to 3000ng/mL. The intra- and inter-day precision of the assay expressed as a coefficient of variation (CV%) ranged from 4.01 to 8.81%. Furthermore, the suitability of this assay for measuring doxorubicin associated with DNA in vivo was demonstrated by using it to quantify the doxorubicin concentration within tumor samples from SKOV3 and HEC1A mice obtained 72h after administration of PEGylated liposomal doxorubicin (Doxil(®); PLD) at 6mg/kg IV x 1. This HPLC assay allows for sensitive intracellular quantification of doxorubicin and will be an important tool for future studies evaluating intracellular pharmacokinetics of doxorubicin and various nanoparticle formulations of doxorubicin. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Noninvasive Evaluation of Benign and Malignant Superficial Lymph Nodes by Virtual Touch Tissue Quantification: A Pilot Study.

    PubMed

    Chen, Shaoqi; Lin, Xiaoming; Chen, Xiaoxia; Zheng, Baoqun

    2016-03-01

    The purpose of this study was to investigate the value of Virtual Touch tissue quantification (Siemens Medical Solutions, Erlangen, Germany) for differentiation of benign and malignant superficial lymph node lesions. Shear wave velocity (SWV) values were analyzed in 113 patients, who also had diagnoses by pathologic examination. The diagnostic performance of the SWV was evaluated by sensitivity and specificity at the optimum cutoff value and the area under the receiver operating characteristic curve (AUROC). A total of 60 benign lesions (32 reactive hyperplasia and 28 tuberculosis) and 53 malignant lesions (27 lymphomas and 26 metastatic carcinomas) were studied. The SWV was significantly different between benign (mean ± SD, 3.137 ± 0.857 m/s) and malignant (7.042 ± 1.427 m/s) lesions (P< .001) and yielded sensitivity of 92.5% (95% confidence interval [CI], 81.8%-97.9%) and specificity of 96.7% (95% CI, 88.5%-99.6%) at an optimum cutoff value of 4.645 m/s. The AUROC was 0.973 (95% CI, 0.924-0.994). To separate reactive hyperplasia from tuberculosis within benign lesions, a cutoff value of 2.978 m/s provided sensitivity of 92.9% (95% CI, 76.5%-99.1%) and a specificity of 100% (95% CI, 89.1%-100%), with an AUROC of 0.989 (95% CI, 0.920-1.000). To separate lymphoma from metastatic carcinoma within malignant lesions, a cutoff value of 7.302 m/s provided sensitivity of 88.5% (95% CI, 69.8%-97.6%) and specificity of 81.5% (95% CI, 61.9%-93.7%), with an AUROC of 0.906 (95% CI, 0.764-0.969). Virtual Touch tissue quantification provides a promising noninvasive strategy for differentiation of benign and malignant superficial lymph node lesions. © 2016 by the American Institute of Ultrasound in Medicine.

  2. Time domain diffuse optical spectroscopy: In vivo quantification of collagen in breast tissue

    NASA Astrophysics Data System (ADS)

    Taroni, Paola; Pifferi, Antonio; Quarto, Giovanna; Farina, Andrea; Ieva, Francesca; Paganoni, Anna Maria; Abbate, Francesca; Cassano, Enrico; Cubeddu, Rinaldo

    2015-05-01

    Time-resolved diffuse optical spectroscopy provides non-invasively the optical characterization of highly diffusive media, such as biological tissues. Light pulses are injected into the tissue and the effects of light propagation on re-emitted pulses are interpreted with the diffusion theory to assess simultaneously tissue absorption and reduced scattering coefficients. Performing spectral measurements, information on tissue composition and structure is derived applying the Beer law to the measured absorption and an empiric approximation to Mie theory to the reduced scattering. The absorption properties of collagen powder were preliminarily measured in the range of 600-1100 nm using a laboratory set-up for broadband time-resolved diffuse optical spectroscopy. Optical projection images were subsequently acquired in compressed breast geometry on 218 subjects, either healthy or bearing breast lesions, using a portable instrument for optical mammography that operates at 7 wavelengths selected in the range 635-1060 nm. For all subjects, tissue composition was estimated in terms of oxy- and deoxy-hemoglobin, water, lipids, and collagen. Information on tissue microscopic structure was also derived. Good correlation was obtained between mammographic breast density (a strong risk factor for breast cancer) and an optical index based on collagen content and scattering power (that accounts mostly for tissue collagen). Logistic regression applied to all optically derived parameters showed that subjects at high risk for developing breast cancer for their high breast density can effectively be identified based on collagen content and scattering parameters. Tissue composition assessed in breast lesions with a perturbative approach indicated that collagen and hemoglobin content are significantly higher in malignant lesions than in benign ones.

  3. Quantification of Protein Signatures in Archived Human Prostate Tissues Using Shotgun Proteomic Methods

    DTIC Science & Technology

    2012-05-01

    Fig. 2). The detergent-solubilized proteins were subsequently incubated with wheat - germ agglutinin (WGA) and concanavalin-A (ConA) beads, washed...optimizing protocols to extract and profile proteins in matched normal and diseased tissue samples using directed mass spectrometry methods. The ultimate...able to extract up to 100 micrograms of total protein using whole- mount FFPE RP tissue block samples. This Figure 2. Silver-stained SDS-PAGE gel

  4. Quantification of Cardiomyocyte Alignment from Three-Dimensional (3D) Confocal Microscopy of Engineered Tissue.

    PubMed

    Kowalski, William J; Yuan, Fangping; Nakane, Takeichiro; Masumoto, Hidetoshi; Dwenger, Marc; Ye, Fei; Tinney, Joseph P; Keller, Bradley B

    2017-08-01

    Biological tissues have complex, three-dimensional (3D) organizations of cells and matrix factors that provide the architecture necessary to meet morphogenic and functional demands. Disordered cell alignment is associated with congenital heart disease, cardiomyopathy, and neurodegenerative diseases and repairing or replacing these tissues using engineered constructs may improve regenerative capacity. However, optimizing cell alignment within engineered tissues requires quantitative 3D data on cell orientations and both efficient and validated processing algorithms. We developed an automated method to measure local 3D orientations based on structure tensor analysis and incorporated an adaptive subregion size to account for multiple scales. Our method calculates the statistical concentration parameter, κ, to quantify alignment, as well as the traditional orientational order parameter. We validated our method using synthetic images and accurately measured principal axis and concentration. We then applied our method to confocal stacks of cleared, whole-mount engineered cardiac tissues generated from human-induced pluripotent stem cells or embryonic chick cardiac cells and quantified cardiomyocyte alignment. We found significant differences in alignment based on cellular composition and tissue geometry. These results from our synthetic images and confocal data demonstrate the efficiency and accuracy of our method to measure alignment in 3D tissues.

  5. Validation of a digital PCR method for quantification of DNA copy number concentrations by using a certified reference material.

    PubMed

    Deprez, Liesbet; Corbisier, Philippe; Kortekaas, Anne-Marie; Mazoua, Stéphane; Beaz Hidalgo, Roxana; Trapmann, Stefanie; Emons, Hendrik

    2016-09-01

    Digital PCR has become the emerging technique for the sequence-specific detection and quantification of nucleic acids for various applications. During the past years, numerous reports on the development of new digital PCR methods have been published. Maturation of these developments into reliable analytical methods suitable for diagnostic or other routine testing purposes requires their validation for the intended use. Here, the results of an in-house validation of a droplet digital PCR method are presented. This method is intended for the quantification of the absolute copy number concentration of a purified linearized plasmid in solution with a nucleic acid background. It has been investigated which factors within the measurement process have a significant effect on the measurement results, and the contribution to the overall measurement uncertainty has been estimated. A comprehensive overview is provided on all the aspects that should be investigated when performing an in-house method validation of a digital PCR method.

  6. Digital separation of diaminobenzidine-stained tissues via an automatic color-filtering for immunohistochemical quantification

    PubMed Central

    Fu, Rong; Ma, Xiaomian; Bian, Zhaoying; Ma, Jianhua

    2015-01-01

    The digital separation of diaminobenzidine (DAB)-stained tissues from hematoxylin background is an important pre-processing step to analyze immunostains. In most stain separation methods, specific color channels (for example: RGB, HSI, CMYK) or color deconvolution matrices are used to obtain different tissue contrasts between DAB- and hematoxylin-stained areas. However, these methods could produce incomplete separation or color changes because the color spectra of stains and co-localized stains overlap in histological images. Therefore, we proposed an automatic color-filtering to separate hematoxylin- and DAB-stained tissues. In implantation, the RGB images of DAB-labeled immunostains are first converted to 8-bit BN images by a mathematical translation to produce the largest contrast between brown DAB-stained tissues and blue hematoxylin-stained tissues. The first valley in the histogram revised by nonuniform quantization is set as the cut-off point to obtain a brown filter. DAB-stained tissues are accurately delineated from the background counterstain, resulting in DAB-only-image and De-DAB-image. Subsequently, a blue filter is designed in the CIE-Lab color space to further delineate the hematoxylin-stained tissues from the De-DAB-image. Finally, the average values of the remaining pixels of the De-DAB-image are set as the background color of the DAB-only-image to manage uneven dyeing and provide DAB-stained-image for adaptive immunohistochemistry quantitation. Extensive experimental results demonstrated that the proposed method has significant advantages compared with existing methods in terms of complete stain separation without changing the color in DAB-stained areas. PMID:25780744

  7. Digital separation of diaminobenzidine-stained tissues via an automatic color-filtering for immunohistochemical quantification.

    PubMed

    Fu, Rong; Ma, Xiaomian; Bian, Zhaoying; Ma, Jianhua

    2015-02-01

    The digital separation of diaminobenzidine (DAB)-stained tissues from hematoxylin background is an important pre-processing step to analyze immunostains. In most stain separation methods, specific color channels (for example: RGB, HSI, CMYK) or color deconvolution matrices are used to obtain different tissue contrasts between DAB- and hematoxylin-stained areas. However, these methods could produce incomplete separation or color changes because the color spectra of stains and co-localized stains overlap in histological images. Therefore, we proposed an automatic color-filtering to separate hematoxylin- and DAB-stained tissues. In implantation, the RGB images of DAB-labeled immunostains are first converted to 8-bit BN images by a mathematical translation to produce the largest contrast between brown DAB-stained tissues and blue hematoxylin-stained tissues. The first valley in the histogram revised by nonuniform quantization is set as the cut-off point to obtain a brown filter. DAB-stained tissues are accurately delineated from the background counterstain, resulting in DAB-only-image and De-DAB-image. Subsequently, a blue filter is designed in the CIE-Lab color space to further delineate the hematoxylin-stained tissues from the De-DAB-image. Finally, the average values of the remaining pixels of the De-DAB-image are set as the background color of the DAB-only-image to manage uneven dyeing and provide DAB-stained-image for adaptive immunohistochemistry quantitation. Extensive experimental results demonstrated that the proposed method has significant advantages compared with existing methods in terms of complete stain separation without changing the color in DAB-stained areas.

  8. Quantification of phenylethylamine and p-tyramine in rat tissues using a new radioenzymatic assay

    SciTech Connect

    Hamburger, S.A.; Henry, D.P.

    1986-03-05

    Phenylethylamine (PEA) and p-tyramine (p-tym) are biologically active aralkylamines that are found in a number of mammalian tissues, including brain and plasma. The investigation of the biological role of these substances has been hampered by the lack of accessible assay methodology. They have developed a new radioenzymatic assay using barley root tyramine N-methyltransferase and tritiated S-adenosylmethionine. The products formed by the reaction are isolated by TLC. The assay sensitivity was 2.1 and 1.0 pg/tube for PEA and p-tym, respectively. The concentration of PEA and p-tym was determined simultaneously in tissues from Sprague-Dawley rats (280 gm). Plasma PEA and p-tym were 478 +/- 66 and 309 +/- 69 pg/ml, respectively. They conclude that this new procedure is applicable to all tissues examined in that all tissues contain both PEA and p-tym and that these amines are heterogeneously distributed in rat tissues.

  9. Model-independent quantification of soft tissue viscoelasticity with dynamic optical coherence elastography

    NASA Astrophysics Data System (ADS)

    Leartprapun, Nichaluk; Iyer, Rishyashring; Adie, Steven G.

    2017-02-01

    Mechanical properties of cells and tissues play an important role in governing both normal and diseased biological processes. Recent findings in mechanobiology have demonstrated that viscosity, independent of elasticity, of extracellular matrix (ECM) can alter cellular behaviors. To obtain a comprehensive understanding of the mechanical properties of viscoelastic biological tissues for biomedical applications and mechanobiology research, both the elasticity and the viscosity must be characterized. Although optical coherence elastography (OCE) has emerged as a promising tool for probing the mechanical properties of biological tissues, quantitative OCE methods have mostly been limited to elasticity reconstruction or relied on the use of a presumed mechanical model, which may or may not adequately describe the response of a given tissue type. We present the first experimental demonstration of a mechanical model-independent reconstruction of complex shear modulus from direct measurement of surface wave propagation in viscoelastic media with dynamic acoustic radiation force (ARF)-OCE. Our results suggest that elasticity imaging based on shear wave speed alone could overlook potentially significant variations in the viscoelastic properties of biological tissues.

  10. Widespread expression of SAA and Hp RNA in bovine tissues after evaluation of suitable reference genes.

    PubMed

    Lecchi, Cristina; Dilda, Francesca; Sartorelli, Paola; Ceciliani, Fabrizio

    2012-01-15

    The serum amyloid A (SAA) and haptoglobin (Hp) are the most prominent acute phase proteins (APPs) in cow. Liver mainly produces APPs, but extra hepatic expression has also been demonstrated in some tissues. The major aim of the present study was to assess the constitutive SAA and Hp mRNA expression by quantitative PCR (qPCR) in a wide panel of 33 bovine tissues, including gastrointestinal tract, respiratory system, urogenital system, mammary gland, hematopoietic system, central nervous system, eye, thyroid and heart. Normalization of gene expression in different samples requires reference genes, which are stably expressed. Therefore, seven reference genes were investigated (ACTB, GAPDH, HMBS, SDHA, YWHAZ, SF3A1, EEF1A2) and three genes, namely SF3A1, HMBS and ACTB, were selected after assessing their stability with geNorm™ and NormFinder(©) softwares. The qPCR analysis confirmed liver as the principal source of SAA and Hp, but also identified both APPs' mRNA in almost all tissues. The highest expression rate of SAA was found in thyroid, followed by pancreas and submandibulary gland. Hp mRNA expression was detected at high concentration in pancreas and submandibulary gland. The present data indicated a widespread expression of SAA and Hp also in non pathological conditions, thus envisaging a possible role as immunomodulatory and protective molecules. To understand where SAA and Hp come from is the prerequisite to their utilization as Acute Phase Reaction biomarkers. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Quantification of genetically modified soybeans using a combination of a capillary-type real-time PCR system and a plasmid reference standard.

    PubMed

    Toyota, Akie; Akiyama, Hiroshi; Sugimura, Mitsunori; Watanabe, Takahiro; Kikuchi, Hiroyuki; Kanamori, Hisayuki; Hino, Akihiro; Esaka, Muneharu; Maitani, Tamio

    2006-04-01

    Because the labeling of grains and feed- and foodstuffs is mandatory if the genetically modified organism (GMO) content exceeds a certain level of approved genetically modified varieties in many countries, there is a need for a rapid and useful method of GMO quantification in food samples. In this study, a rapid detection system was developed for Roundup Ready Soybean (RRS) quantification using a combination of a capillary-type real-time PCR system, a LightCycler real-time PCR system, and plasmid DNA as the reference standard. In addition, we showed for the first time that the plasmid and genomic DNA should be similar in the established detection system because the PCR efficiencies of using plasmid DNA and using genomic DNA were not significantly different. The conversion factor (Cf) to calculate RRS content (%) was further determined from the average value analyzed in three laboratories. The accuracy and reproducibility of this system for RRS quantification at a level of 5.0% were within a range from 4.46 to 5.07% for RRS content and within a range from 2.0% to 7.0% for the relative standard deviation (RSD) value, respectively. This system rapidly monitored the labeling system and had allowable levels of accuracy and precision.

  12. Bone Tissue Properties Measurement by Reference Point Indentation in Glucocorticoid-Induced Osteoporosis.

    PubMed

    Mellibovsky, Leonardo; Prieto-Alhambra, Daniel; Mellibovsky, Fernando; Güerri-Fernández, Roberto; Nogués, Xavier; Randall, Connor; Hansma, Paul K; Díez-Perez, Adolfo

    2015-09-01

    Glucocorticoids, widely used in inflammatory disorders, rapidly increase bone fragility and, therefore, fracture risk. However, common bone densitometry measurements are not sensitive enough to detect these changes. Moreover, densitometry only partially recognizes treatment-induced fracture reductions in osteoporosis. Here, we tested whether the reference point indentation technique could detect bone tissue property changes early after glucocorticoid treatment initiation. After initial laboratory and bone density measurements, patients were allocated into groups receiving calcium + vitamin D (Ca+D) supplements or anti-osteoporotic drugs (risedronate, denosumab, teriparatide). Reference point indentation was performed on the cortical bone layer of the tibia by a handheld device measuring bone material strength index (BMSi). Bone mineral density was measured by dual-energy X-ray absorptiometry (DXA). Although Ca+D-treated patients exhibited substantial and significant deterioration, risedronate-treated patients exhibited no significant change, and both denosumab- and teriparatide-treated participants exhibited significantly improved BMSi 7 weeks after initial treatment compared with baseline; these trends remained stable for 20 weeks. In contrast, no densitometry changes were observed during this study period. In conclusion, our study is the first to our knowledge to demonstrate that reference point indentation is sensitive enough to reflect changes in cortical bone indentation after treatment with osteoporosis therapies in patients newly exposed to glucocorticoids.

  13. Single cell analysis in native tissue: Quantification of the retinoid content of hepatic stellate cells

    PubMed Central

    Galler, Kerstin; Requardt, Robert Pascal; Glaser, Uwe; Markwart, Robby; Bocklitz, Thomas; Bauer, Michael; Popp, Jürgen; Neugebauer, Ute

    2016-01-01

    Hepatic stellate cells (HSCs) are retinoid storing cells in the liver: The retinoid content of those cells changes depending on nutrition and stress level. There are also differences with regard to a HSC’s anatomical position in the liver. Up to now, retinoid levels were only accessible from bulk measurements of tissue homogenates or cell extracts. Unfortunately, they do not account for the intercellular variability. Herein, Raman spectroscopy relying on excitation by the minimally destructive wavelength 785 nm is introduced for the assessment of the retinoid state of single HSCs in freshly isolated, unprocessed murine liver lobes. A quantitative estimation of the cellular retinoid content is derived. Implications of the retinoid content on hepatic health state are reported. The Raman-based results are integrated with histological assessments of the tissue samples. This spectroscopic approach enables single cell analysis regarding an important cellular feature in unharmed tissue. PMID:27063397

  14. Single cell analysis in native tissue: Quantification of the retinoid content of hepatic stellate cells.

    PubMed

    Galler, Kerstin; Requardt, Robert Pascal; Glaser, Uwe; Markwart, Robby; Bocklitz, Thomas; Bauer, Michael; Popp, Jürgen; Neugebauer, Ute

    2016-04-11

    Hepatic stellate cells (HSCs) are retinoid storing cells in the liver: The retinoid content of those cells changes depending on nutrition and stress level. There are also differences with regard to a HSC's anatomical position in the liver. Up to now, retinoid levels were only accessible from bulk measurements of tissue homogenates or cell extracts. Unfortunately, they do not account for the intercellular variability. Herein, Raman spectroscopy relying on excitation by the minimally destructive wavelength 785 nm is introduced for the assessment of the retinoid state of single HSCs in freshly isolated, unprocessed murine liver lobes. A quantitative estimation of the cellular retinoid content is derived. Implications of the retinoid content on hepatic health state are reported. The Raman-based results are integrated with histological assessments of the tissue samples. This spectroscopic approach enables single cell analysis regarding an important cellular feature in unharmed tissue.

  15. Single cell analysis in native tissue: Quantification of the retinoid content of hepatic stellate cells

    NASA Astrophysics Data System (ADS)

    Galler, Kerstin; Requardt, Robert Pascal; Glaser, Uwe; Markwart, Robby; Bocklitz, Thomas; Bauer, Michael; Popp, Jürgen; Neugebauer, Ute

    2016-04-01

    Hepatic stellate cells (HSCs) are retinoid storing cells in the liver: The retinoid content of those cells changes depending on nutrition and stress level. There are also differences with regard to a HSC’s anatomical position in the liver. Up to now, retinoid levels were only accessible from bulk measurements of tissue homogenates or cell extracts. Unfortunately, they do not account for the intercellular variability. Herein, Raman spectroscopy relying on excitation by the minimally destructive wavelength 785 nm is introduced for the assessment of the retinoid state of single HSCs in freshly isolated, unprocessed murine liver lobes. A quantitative estimation of the cellular retinoid content is derived. Implications of the retinoid content on hepatic health state are reported. The Raman-based results are integrated with histological assessments of the tissue samples. This spectroscopic approach enables single cell analysis regarding an important cellular feature in unharmed tissue.

  16. In vivo quantification of spatially-varying mechanical properties in developing tissues

    PubMed Central

    Serwane, Friedhelm; Mongera, Alessandro; Rowghanian, Payam; Kealhofer, David A.; Lucio, Adam A.; Hockenbery, Zachary M.; Campàs, Otger

    2017-01-01

    It is generally believed that the mechanical properties of the cellular microenvironment and their spatiotemporal variations play a central role in sculpting embryonic tissues, maintaining organ architecture and controlling cell behavior, including cell differentiation. However, no direct in vivo and in situ measurement of mechanical properties within developing 3D tissues and organs has been performed yet. Here we introduce a technique that employs biocompatible ferrofluid microdroplets as local mechanical actuators and allows quantitative spatiotemporal measurements of mechanical properties in vivo. Using this technique, we show that vertebrate body elongation entails spatially-varying tissue mechanics along the anteroposterior axis. Specifically, we find that the zebrafish tailbud is viscoelastic (elastic below a few seconds and fluid after just one minute) and displays decreasing stiffness and increasing fluidity towards its posterior elongating region. This method opens new avenues to study mechanobiology in vivo, both in embryogenesis and in disease processes, including cancer. PMID:27918540

  17. Inference of Cell Mechanics in Heterogeneous Epithelial Tissue Based on Multivariate Clone Shape Quantification

    PubMed Central

    Tsuboi, Alice; Umetsu, Daiki; Kuranaga, Erina; Fujimoto, Koichi

    2017-01-01

    Cell populations in multicellular organisms show genetic and non-genetic heterogeneity, even in undifferentiated tissues of multipotent cells during development and tumorigenesis. The heterogeneity causes difference of mechanical properties, such as, cell bond tension or adhesion, at the cell–cell interface, which determine the shape of clonal population boundaries via cell sorting or mixing. The boundary shape could alter the degree of cell–cell contacts and thus influence the physiological consequences of sorting or mixing at the boundary (e.g., tumor suppression or progression), suggesting that the cell mechanics could help clarify the physiology of heterogeneous tissues. While precise inference of mechanical tension loaded at each cell–cell contacts has been extensively developed, there has been little progress on how to distinguish the population-boundary geometry and identify the cause of geometry in heterogeneous tissues. We developed a pipeline by combining multivariate analysis of clone shape with tissue mechanical simulations. We examined clones with four different genotypes within Drosophila wing imaginal discs: wild-type, tartan (trn) overexpression, hibris (hbs) overexpression, and Eph RNAi. Although the clones were previously known to exhibit smoothed or convoluted morphologies, their mechanical properties were unknown. By applying a multivariate analysis to multiple criteria used to quantify the clone shapes based on individual cell shapes, we found the optimal criteria to distinguish not only among the four genotypes, but also non-genetic heterogeneity from genetic one. The efficient segregation of clone shape enabled us to quantitatively compare experimental data with tissue mechanical simulations. As a result, we identified the mechanical basis contributed to clone shape of distinct genotypes. The present pipeline will promote the understanding of the functions of mechanical interactions in heterogeneous tissue in a non-invasive manner. PMID

  18. Quantification of plasmid DNA reference materials for Shiga toxin-producing Escherichia coli based on UV, HR-ICP-MS and digital PCR.

    PubMed

    Liang, Wen; Xu, Li; Sui, Zhiwei; Li, Yan; Li, Lanying; Wen, Yanli; Li, Chunhua; Ren, Shuzhen; Liu, Gang

    2016-01-01

    The accuracy and metrology traceability of DNA quantification is becoming a critical theme in many fields, including diagnosis, forensic analysis, microorganism detection etc. Thus the research of DNA reference materials (RMs) and consistency of DNA quantification methods has attracted considerable research interest. In this work, we developed 3 plasmid candidate RMs, containing 3 target genes of Escherichia coli O157:H7 (E. coli O157:H7) and other Shiga toxin-producing Escherichia coli (STEC): stx1, stx2, and fliC (h7) respectively. Comprehensive investigation of the plasmid RMs was performed for their sequence, purity, homogeneity and stability, and then the concentration was quantified by three different methods: ultraviolet spectrophotometer (UV), high resolution inductively coupled plasma mass spectrometry (HR-ICP-MS) and digital PCR. As a routinely applied method for DNA analysis, UV was utilized for the quantification (OD260) and purity analysis for the plasmids. HR-ICP-MS quantified the plasmid DNA through analysing the phosphorus in DNA molecules. Digital PCR distributed the DNA samples onto a microarray chip containing thousands of reaction chambers, and quantified the DNA copy numbers by analysing the number of positive signals without any calibration curves needed. Based on the high purification of the DNA reference materials and the optimization of dPCR analysis, we successfully achieved good consistency between UV, HR-ICP-MS and dPCR, with relative deviations lower than 10 %. We then performed the co-quantification of 3 DNA RMs with three different methods together, and the uncertainties of their concentration were evaluated. Finally, the certified values and expanded uncertainties for 3 DNA RMs (pFliC, pStx1 and pStx2) were (1.60 ± 0.10) × 10(10) copies/μL, (1.53 ± 0.10) × 10(10) copies/μL and (1.70 ± 0.11) × 10(10) copies/μL respectively.Graphical abstractWe developed 3 plasmid candidate RMs, containing 3 target genes of

  19. An HPLC-ECD method for monoamines and metabolites quantification in cuttlefish (cephalopod) brain tissue.

    PubMed

    Bidel, Flavie; Corvaisier, Sophie; Jozet-Alves, Christelle; Pottier, Ivannah; Dauphin, François; Naud, Nadège; Bellanger, Cécile

    2016-08-01

    The cuttlefish belongs to the mollusk class Cephalopoda, considered as the most advanced marine invertebrates and thus widely used as models to study the biology of complex behaviors and cognition, as well as their related neurochemical mechanisms. Surprisingly, methods to quantify the biogenic monoamines and their metabolites in cuttlefish brain remain sparse and measure a limited number of analytes. This work aims to validate an HPLC-ECD method for the simultaneous quantification of dopamine, serotonin, norepinephrine and their main metabolites in cuttlefish brain. In comparison and in order to develop a method suitable to answer both ecological and biomedical questions, the validation was also carried out on a phylogenetically remote species: mouse (mammals). The method was shown to be accurate, precise, selective, repeatable and sensitive over a wide range of concentrations for 5-hydroxyindole-3-acetic acid, serotonin, dopamine, 3,4-dihydroxyphenylacetic acid and norepinephrine in the both extracts of cuttlefish and mouse brain, though with low precision and recovery for 4-hydroxy-3-methoxyphenylethylene glycol. Homovanillic acid, accurately studied in rodents, was not detectable in the brain of cuttlefish. Overall, we described here the first fully validated HPLC method for the routine measurement of both monoamines and metabolites in cuttlefish brain. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  20. Quantification of cell surface receptor expression in live tissue culture media using a dual-tracer stain and rinse approach

    NASA Astrophysics Data System (ADS)

    Xu, Xiaochun; Sinha, Lagnojita; Singh, Aparna; Yang, Cynthia; Xiang, Jialing; Tichauer, Kenneth M.

    2015-03-01

    Immunofluorescence staining is a robust way to visualize the distribution of targeted biomolecules invasively in in fixed tissues and tissue culture. Despite the fact that these methods has been a well-established method in fixed tissue imaging for over 70 years, quantification of receptor concentration still simply assumes that the signal from the targeted fluorescent marker after incubation and sufficient rinsing is directly proportional to the concentration of targeted biomolecules, thus neglecting the experimental inconsistencies in incubation and rinsing procedures and assuming no, nonspecific binding of the fluorescent markers. This work presents the first imaging approach capable of quantifying the concentration of cell surface receptor on cancer cells grown in vitro based on compartment modeling in a nondestructive way. The approach utilizes a dual-tracer protocol where any non-specific retention or variability in incubation and rinsing of a receptor-targeted imaging agent is corrected by simultaneously imaging the retention of a chemically similar, "untargeted" imaging agent. Various different compartment models were used to analyze the data in order to find the optimal procedure for extracting estimates of epidermal growth factor receptor (EGFR) concentration (a receptor overexpressed in many cancers and a key target for emerging molecular therapies) in tissue cultures with varying concentrations of human glioma cells (U251). Preliminary results demonstrated a need to model nonspecific binding of both the targeted and untargeted imaging agents used. The approach could be used to carry out the first repeated measures of cell surface receptor dynamics during 3D tumor mass development, in addition to the receptor response to therapies.

  1. Quantification of Interfibrillar Shear Stress in Aligned Soft Collagenous Tissues via Notch Tension Testing

    PubMed Central

    Szczesny, Spencer E.; Caplan, Jeffrey L.; Pedersen, Pal; Elliott, Dawn M.

    2015-01-01

    The mechanical function of soft collagenous tissues is largely determined by their hierarchical organization of collagen molecules. While collagen fibrils are believed to be discontinuous and transfer load through shearing of the interfibrillar matrix, interfibrillar shear stresses have never been quantified. Scaling traditional shear testing procedures down to the fibrillar length scale is impractical and would introduce substantial artifacts. Here, through the use of a novel microscopic variation of notch tension testing, we explicitly demonstrate the existence of interfibrillar shear stresses within tendon fascicles and provide the first measurement of their magnitude. Axial stress gradients along the sample length generated by notch tension testing were measured and used to calculate a value of 32 kPa for the interfibrillar shear stress. This estimate is comparable to the interfibrillar shear stress predicted by previous multiscale modeling of tendon fascicles, which supports the hypothesis that fibrils are discontinuous and transmit load through interfibrillar shear. This information regarding the structure-function relationships of tendon and other soft collagenous tissues is necessary to identify potential causes for tissue impairment with degeneration and provide the foundation for developing regenerative repair strategies or engineering biomaterials for tissue replacement. PMID:26469396

  2. Optical spectroscopy for quantification of bulk breast tissue properties in adolescent girls: preliminary observations

    NASA Astrophysics Data System (ADS)

    Dick, Samantha N.; Lilge, Lothar

    2005-09-01

    Optical technology holds considerable promise to improve early detection, diagnosis and risk assessment of breast cancer. Unlike current clinical risk assessment tools such as the Gail model, the most widely accepted risk assessment tool, optical risk assessment technology can be applied to the entire female population of all ages. This study is investigating the use of optical reflectance spectroscopy (ORS) as a possible breast tissue development monitoring tool for adolescent girls. Changes in breast development due to proliferation of mammary gland and the surrounding stroma are reflected in changes in breast tissue density and composition which can be interrogated optically. Modifications of development influenced by micronutrients and hormonal status from exposures (e.g. toxins), lifestyle and diet effects, may ultimately be tracked. Preliminary data suggests that ORS has the ability to detect differences in bulk tissue properties in the developing breast of adolescent girls when compared to developmental stages assessed by Tanner, regional variation within breast tissue structure and asymmetries between left and right breast size and shape. Spectral comparison of unilateral breast development permits adjusting the optode separation as function of developmental breast size to minimize optical sampling of pectoral muscle.

  3. Quantification of collagen I in airway tissues using second harmonic generation.

    PubMed

    Tjin, Gavin; Xu, Paul; Kable, Scott H; Kable, Eleanor P W; Burgess, Janette K

    2014-03-01

    Extracellular matrix (ECM) remodeling contributes to the pathogenic changes in chronic obstructive pulmonary disease (COPD) and is both complex and not well understood. Collagen I, a component of the ECM altered in COPD airways, has second harmonic generation (SHG) properties. The SHG signal is coherent, propagating both forward (F) (primarily organized/mature collagen fibrils) and backward (B) (primarily disorganized/immature collagen fibrils) parallel to the incident light. The F/B SHG ratio was used to determine the proportion of organized to disorganized collagen, with lower variation in F/B ratio between sampling regions within the same patient and between patients in the same disease group compared with analyzing F and B data alone. The F/B ratio was independent of laser power drift, regions analyzed within a tissue and tissue orientation during analysis. Using this method, we identified a significant difference in collagen organization in airway tissue between COPD and non diseased. We have developed a robust optimization and calibration methodology that will allow direct comparison of data obtained at different times and from multiple microscopes, which is directly adaptable for use with other tissue types. We report a powerful new tool for advancing our understanding of pathological ECM remodeling that may uncover new therapeutic targets in the future.

  4. Quantification of Interfibrillar Shear Stress in Aligned Soft Collagenous Tissues via Notch Tension Testing

    NASA Astrophysics Data System (ADS)

    Szczesny, Spencer E.; Caplan, Jeffrey L.; Pedersen, Pal; Elliott, Dawn M.

    2015-10-01

    The mechanical function of soft collagenous tissues is largely determined by their hierarchical organization of collagen molecules. While collagen fibrils are believed to be discontinuous and transfer load through shearing of the interfibrillar matrix, interfibrillar shear stresses have never been quantified. Scaling traditional shear testing procedures down to the fibrillar length scale is impractical and would introduce substantial artifacts. Here, through the use of a novel microscopic variation of notch tension testing, we explicitly demonstrate the existence of interfibrillar shear stresses within tendon fascicles and provide the first measurement of their magnitude. Axial stress gradients along the sample length generated by notch tension testing were measured and used to calculate a value of 32 kPa for the interfibrillar shear stress. This estimate is comparable to the interfibrillar shear stress predicted by previous multiscale modeling of tendon fascicles, which supports the hypothesis that fibrils are discontinuous and transmit load through interfibrillar shear. This information regarding the structure-function relationships of tendon and other soft collagenous tissues is necessary to identify potential causes for tissue impairment with degeneration and provide the foundation for developing regenerative repair strategies or engineering biomaterials for tissue replacement.

  5. Prediction of Difficult Laryngoscopy in Obese Patients by Ultrasound Quantification of Anterior Neck Soft Tissue1

    PubMed Central

    Ezri, T.; Gewürtz, G.; Sessler, D.I.; Medalion, B.; Szmuk, P.; Hagberg, C.; Susmallian, S.

    2005-01-01

    Prediction of difficult laryngoscopy in obese patients is challenging. In 50 morbidly obese patients, we quantified the neck soft tissue from skin to anterior aspect of trachea at the vocal cords using ultrasound. Thyromental distance <6 cm, mouth opening <4 cm, limited neck mobility, Mallampati score >2, abnormal upper teeth, neck circumference >45 cm, and sleep apnoea were considered predictors of difficult laryngoscopy. Of the nine (18%) difficult laryngoscopy cases, seven had obstructive sleep apnoea history; whereas, only 2 of the 41 easy laryngoscopy patients did (P<0.001). Difficult laryngoscopy patients had larger neck circumference [50 (3.8) vs. 43.5 (2.2) cm; P<0.001] and more pre-tracheal soft tissue [28 (2.7) mm vs. 17.5 (1.8) mm; P<0.001] [mean (SD)]. Soft tissue values completely separated difficult and easy laryngoscopies. None of the other predictors correlated with difficult laryngoscopy. Thus, an abundance of pretracheal soft tissue at the level of vocal cords is a good predictor of difficult laryngoscopy in obese patients. PMID:14616599

  6. Detection and quantification of virulent Aeromonas hydrophila in channel catfish tissues following waterborne challenge

    USDA-ARS?s Scientific Manuscript database

    The aim of this study was to understand the pathogenesis of motile aeromonas septicemia caused by virulent A. hydrophila (vAh) in channel catfish, Ictalurus punctatus. Adipose fin clipped catfish were challenged with vAh using waterborne challenge method and the distribution of vAh in catfish tissue...

  7. Quantification of the tissue-culture induced variation in barley (Hordeum vulgare L.)

    PubMed Central

    Bednarek, Piotr T; Orłowska, Renata; Koebner, Robert MD; Zimny, Janusz

    2007-01-01

    Background When plant tissue is passaged through in vitro culture, many regenerated plants appear to be no longer clonal copies of their donor genotype. Among the factors that affect this so-called tissue culture induced variation are explant genotype, explant tissue origin, medium composition, and the length of time in culture. Variation is understood to be generated via a combination of genetic and/or epigenetic changes. A lack of any phenotypic variation between regenerants does not necessarily imply a concomitant lack of genetic (or epigenetic) change, and it is therefore of interest to assay the outcomes of tissue culture at the genotypic level. Results A variant of methylation sensitive AFLP, based on the isoschizomeric combinations Acc65I/MseI and KpnI/MseI was applied to analyze, at both the sequence and methylation levels, the outcomes of regeneration from tissue culture in barley. Both sequence mutation and alteration in methylation pattern were detected. Two sets of regenerants from each of five DH donor lines were compared. One set was derived via androgenesis, and the other via somatic embryogenesis, developed from immature embryos. These comparisons delivered a quantitative assessment of the various types of somaclonal variation induced. The average level of variation was 6%, of which almost 1.7% could be accounted for by nucleotide mutation, and the remainder by changes in methylation state. The nucleotide mutation rates and the rate of epimutations were substantially similar between the andro- and embryo-derived sets of regenerants across all the donors. Conclusion We have developed an AFLP based approach that is capable of describing the qualitative and quantitative characteristics of the tissue culture-induced variation. We believe that this approach will find particular value in the study of patterns of inheritance of somaclonal variation, since non-heritable variation is of little interest for the improvement of plant species which are sexually

  8. Automated quantification of epicardial adipose tissue (EAT) in coronary CT angiography; comparison with manual assessment and correlation with coronary artery disease.

    PubMed

    Mihl, Casper; Loeffen, Daan; Versteylen, Mathijs O; Takx, Richard A P; Nelemans, Patricia J; Nijssen, Estelle C; Vega-Higuera, Fernando; Wildberger, Joachim E; Das, Marco

    2014-01-01

    Epicardial adipose tissue (EAT) is emerging as a risk factor for coronary artery disease (CAD). The aim of this study was to determine the applicability and efficiency of automated EAT quantification. EAT volume was assessed both manually and automatically in 157 patients undergoing coronary CT angiography. Manual assessment consisted of a short-axis-based manual measurement, whereas automated assessment on both contrast and non-contrast-enhanced data sets was achieved through novel prototype software. Duration of both quantification methods was recorded, and EAT volumes were compared with paired samples t test. Correlation of volumes was determined with intraclass correlation coefficient; agreement was tested with Bland-Altman analysis. The association between EAT and CAD was estimated with logistic regression. Automated quantification was significantly less time consuming than automated quantification (17 ± 2 seconds vs 280 ± 78 seconds; P < .0001). Although manual EAT volume differed significantly from automated EAT volume (75 ± 33 cm(³) vs 95 ± 45 cm(³); P < .001), a good correlation between both assessments was found (r = 0.76; P < .001). For all methods, EAT volume was positively associated with the presence of CAD. Stronger predictive value for the severity of CAD was achieved through automated quantification on both contrast-enhanced and non-contrast-enhanced data sets. Automated EAT quantification is a quick method to estimate EAT and may serve as a predictor for CAD presence and severity. Copyright © 2014 Society of Cardiovascular Computed Tomography. Published by Elsevier Inc. All rights reserved.

  9. Non-Invasive Quantification of White and Brown Adipose Tissues and Liver Fat Content by Computed Tomography in Mice

    PubMed Central

    Lubura, Marko; Hesse, Deike; Neumann, Nancy; Scherneck, Stephan; Wiedmer, Petra; Schürmann, Annette

    2012-01-01

    Objectives Obesity and its distribution pattern are important factors for the prediction of the onset of diabetes in humans. Since several mouse models are suitable to study the pathophysiology of type 2 diabetes the aim was to validate a novel computed tomograph model (Aloka-Hitachi LCT-200) for the quantification of visceral, subcutaneous, brown and intrahepatic fat depots in mice. Methods Different lean and obese mouse models (C57BL/6, B6.V-Lepob, NZO) were used to determine the most adequate scanning parameters for the detection of the different fat depots. The data were compared with those obtained after preparation and weighing the fat depots. Liver fat content was determined by biochemical analysis. Results The correlations between weights of fat tissues on scale and weights determined by CT were significant for subcutaneous (r2 = 0.995), visceral (r2 = 0.990) and total white adipose tissue (r2 = 0.992). Moreover, scans in the abdominal region, between lumbar vertebrae L4 to L5 correlated with whole-body fat distribution allowing experimenters to reduce scanning time and animal exposure to radiation and anesthesia. Test-retest reliability and measurements conducted by different experimenters showed a high reproducibility in the obtained results. Intrahepatic fat content estimated by CT was linearly related to biochemical analysis (r2 = 0.915). Furthermore, brown fat mass correlated well with weighted brown fat depots (r2 = 0.952). In addition, short-term cold-expose (4°C, 4 hours) led to alterations in brown adipose tissue attributed to a reduction in triglyceride content that can be visualized as an increase in Hounsfield units by CT imaging. Conclusion The 3D imaging of fat by CT provides reliable results in the quantification of total, visceral, subcutaneous, brown and intrahepatic fat in mice. This non-invasive method allows the conduction of longitudinal studies of obesity in mice and therefore enables experimenters to investigate

  10. Non-invasive quantification of white and brown adipose tissues and liver fat content by computed tomography in mice.

    PubMed

    Lubura, Marko; Hesse, Deike; Neumann, Nancy; Scherneck, Stephan; Wiedmer, Petra; Schürmann, Annette

    2012-01-01

    Obesity and its distribution pattern are important factors for the prediction of the onset of diabetes in humans. Since several mouse models are suitable to study the pathophysiology of type 2 diabetes the aim was to validate a novel computed tomograph model (Aloka-Hitachi LCT-200) for the quantification of visceral, subcutaneous, brown and intrahepatic fat depots in mice. Different lean and obese mouse models (C57BL/6, B6.V-Lep(ob), NZO) were used to determine the most adequate scanning parameters for the detection of the different fat depots. The data were compared with those obtained after preparation and weighing the fat depots. Liver fat content was determined by biochemical analysis. The correlations between weights of fat tissues on scale and weights determined by CT were significant for subcutaneous (r(2) = 0.995), visceral (r(2) = 0.990) and total white adipose tissue (r(2) = 0.992). Moreover, scans in the abdominal region, between lumbar vertebrae L4 to L5 correlated with whole-body fat distribution allowing experimenters to reduce scanning time and animal exposure to radiation and anesthesia. Test-retest reliability and measurements conducted by different experimenters showed a high reproducibility in the obtained results. Intrahepatic fat content estimated by CT was linearly related to biochemical analysis (r(2) = 0.915). Furthermore, brown fat mass correlated well with weighted brown fat depots (r(2) = 0.952). In addition, short-term cold-expose (4 °C, 4 hours) led to alterations in brown adipose tissue attributed to a reduction in triglyceride content that can be visualized as an increase in Hounsfield units by CT imaging. The 3D imaging of fat by CT provides reliable results in the quantification of total, visceral, subcutaneous, brown and intrahepatic fat in mice. This non-invasive method allows the conduction of longitudinal studies of obesity in mice and therefore enables experimenters to investigate the onset of complex diseases such as diabetes

  11. Real-time PCR strategy for parasite quantification in blood and tissue samples of experimental Trypanosoma cruzi infection.

    PubMed

    Caldas, Sérgio; Caldas, Ivo Santana; Diniz, Lívia de Figueiredo; Lima, Wanderson Geraldo de; Oliveira, Riva de Paula; Cecílio, Alzira Batista; Ribeiro, Isabela; Talvani, André; Bahia, Maria Terezinha

    2012-09-01

    The lack of an accurate diagnosis has been a serious obstacle to the advancement of the anti-Trypanosoma cruzi chemotherapy and long-term infection can result in different health risks to human. PCRs are alternative methods, more sensitive than conventional parasitological techniques, which due to their low sensitivities are considered unsuitable for these purposes. The aim of this study was to investigate a sensitive diagnostic strategy to quantify blood and cardiac tissues parasites based on real-time PCR tools during acute and chronic phases of murine Chagas disease, as well as to monitor the evolution of infection in those mice under specific treatment. In parallel, fresh blood examination, immunological analysis and quantification of cardiac inflammation were also performed to confront and improve real-time PCR data. Similar profiles of parasitemia curves were observed in both quantification techniques during the acute phase of the infection. In contrast, parasites could be quantified only by real-time PCR at 60 and 120 days of infection. In cardiac tissue, real-time PCR detected T. cruzi DNA in 100% of infected mice, and using this tool a significant Pearson correlation between parasite load in peripheral blood and in cardiac tissue during acute and chronic phases was observed. Levels of serum CCL2, CCL5 and nitric oxide were coincident with parasite load but focal and diffuse mononuclear infiltrates was observed, even with significant (p<0.05) reduction of parasitism after 60 days of infection. Later, this methodology was used to monitor the evolution of infection in animals treated with itraconazole (Itz). Itz-treatment induced a reduction of parasite load in both blood and cardiac muscle at the treatment period, but after the end of chemotherapy an increase of parasitism was detected. Interestingly, inflammatory mediators levels and heart inflammation intensity had similar evolution to the parasite load, in the group of animals treated. Taken together, our

  12. Quantification of anandamide, oleoylethanolamide and palmitoylethanolamide in rodent brain tissue using high performance liquid chromatography-electrospray mass spectroscopy.

    PubMed

    Liput, Daniel J; Tsakalozou, Eleftheria; Hammell, Dana C; Paudel, Kalpana S; Nixon, Kimberly; Stinchcomb, Audra L

    2014-08-01

    Reported concentrations for endocannabinoids and related lipids in biological tissues can vary greatly; therefore, methods used to quantify these compounds need to be validated. This report describes a method to quantify anandamide (AEA), oleoylethanolamide (OEA) and palmitoylethanolamide (PEA) from rodent brain tissue. Analytes were extracted using acetonitrile without further sample clean up, resolved on a C18 reverse-phase column using a gradient mobile phase and detected using electrospray ionization in positive selected ion monitoring mode on a single quadrupole mass spectrometer. The method produced high recovery rates for AEA, OEA and PEA, ranging from 98.1% to 106.2%, 98.5% to 102.2% and 85.4% to 89.5%, respectively. The method resulted in adequate sensitivity with a lower limit of quantification for AEA, OEA and PEA of 1.4 ng/mL, 0.6 ng/mL and 0.5 ng/mL, respectively. The method was reproducible as intraday and interday accuracies and precisions were under 15%. This method was suitable for quantifying AEA, OEA and PEA from rat brain following pharmacological inhibition of fatty acid amide hydrolase.

  13. An LC-MS/MS based candidate reference method for the quantification of total gentamicin in human serum and plasma using NMR characterized calibrator material.

    PubMed

    Lucha, Stephanie; Taibon, Judith; Pongratz, Stephan; Geletneky, Christian; Huber, Erasmus; Wintterle-Roehm, Christine; Lang, Robert; Grimm, Stefanie H; Duelffer, Thomas; Tarasov, Kirill; Zander, Johannes; Vogeser, Michael; Kobold, Uwe

    2017-01-01

    Accurate measurement of gentamicin concentration in serum and plasma is required for therapeutic drug monitoring to ensure appropriate treatment of patients. In this work, we present a validated LC-MS/MS-based candidate reference measurement procedure for total gentamicin quantification to be used for standardization and harmonization of routine assays applied for therapeutic drug monitoring of this compound. Total gentamicin is the sum of the concentrations of five known congeners C1, C1a, C2, C2a and C2b. To our knowledge, there is so far no LC-MS method for quantification of total gentamicin in human serum described in literature. Sample preparation was based on sample dilution with an aqueous internal standard solution followed by protein precipitation. Stable derivatives of gentamicin-glycine congeners were prepared by chemical synthesis and used as internal standards. The primary calibration material used in this assay was characterized by NMR spectroscopy and the pattern of the gentamicin congeners was determined. The total gentamicin was reported as the sum of the congeners which were quantified individually by LC-MS/MS. The method allows the measurement of total gentamicin in human serum and plasma in the concentration range of 0.1 to 12.0μg/ml with an assay imprecision of ≤6% CV and an assay accuracy between 96% and 114%. LOD and LOQ for the total gentamicin were 0.04μg/ml and 0.13μg/ml, respectively. Comparative measurement of 128 native patient samples using this method implemented at two laboratory sites showed an excellent agreement. Validation results proved that this protocol describes a robust and reliable method which is suggested as reference measurement procedure for the standardization and harmonization of routine assays for the quantification of total gentamicin. Copyright © 2016. Published by Elsevier B.V.

  14. Towards absolute quantification of allergenic proteins in food--lysozyme in wine as a model system for metrologically traceable mass spectrometric methods and certified reference materials.

    PubMed

    Cryar, Adam; Pritchard, Caroline; Burkitt, William; Walker, Michael; O'Connor, Gavin; Burns, Duncan Thorburn; Quaglia, Milena

    2013-01-01

    Current routine food allergen quantification methods, which are based on immunochemistry, offer high sensitivity but can suffer from issues of specificity and significant variability of results. MS approaches have been developed, but currently lack metrological traceability. A feasibility study on the application of metrologically traceable MS-based reference procedures was undertaken. A proof of concept involving proteolytic digestion and isotope dilution MS for quantification of protein allergens in a food matrix was undertaken using lysozyme in wine as a model system. A concentration of lysozyme in wine of 0.95 +/- 0.03 microg/g was calculated based on the concentrations of two peptides, confirming that this type of analysis is viable at allergenically meaningful concentrations. The challenges associated with this promising method were explored; these included peptide stability, chemical modification, enzymatic digestion, and sample cleanup. The method is suitable for the production of allergen in food certified reference materials, which together with the achieved understanding of the effects of sample preparation and of the matrix on the final results, will assist in addressing the bias of the techniques routinely used and improve measurement confidence. Confirmation of the feasibility of MS methods for absolute quantification of an allergenic protein in a food matrix with results traceable to the International System of Units is a step towards meaningful comparison of results for allergen proteins among laboratories. This approach will also underpin risk assessment and risk management of allergens in the food industry, and regulatory compliance of the use of thresholds or action levels when adopted.

  15. Enhancing the quantification of tissue sodium content by MRI: time-efficient sodium B1 mapping at clinical field strengths.

    PubMed

    Lommen, Jonathan; Konstandin, Simon; Krämer, Philipp; Schad, Lothar R

    2016-02-01

    Tissue sodium content (TSC) is a sensitive measure of pathological changes and can be detected non-invasively by MRI. For the absolute quantification of TSC, B1 inhomogeneities must be corrected, which is not well established beyond research applications. An in-depth analysis of B1 mapping methods which are suitable for application in TSC quantification is presented. On the basis of these results, a method for simultaneous B1 mapping and imaging is proposed in order to enhance accuracy and to reduce measurement time at clinical field strengths. The B1 mapping techniques used were phase-sensitive (PS), Bloch-Siegert shift (BSS), double-angle (DAM) and actual flip-angle imaging (AFI) methods. Experimental and theoretical comparisons demonstrated that the PS technique yields the most accurate field profiles and exhibits the highest signal-to-noise ratio (SNR). Simultaneous B1 mapping and imaging was performed for the PS method, employing both degrees of freedom of the MR signal: the B1 field is encoded into signal phase and the amplitude provides the concentration information. In comparison with the more established DAM, a 13% higher SNR was obtained and field effects could be corrected more accurately without the need for additional measurement time. The protocol developed was applied to measure TSC in the healthy human head at an isotropic resolution of 4 mm. TSC was determined to be 35 ± 1 mM in white matter and 134 ± 3 mM in vitreous humor. By employing the proposed simultaneous characterization of the B1 field and acquisition of the spin density-weighted sodium signal, the accuracy of the non-invasive measurement of TSC is enhanced and the measurement time is reduced. This should allow (23)Na MRI to be better incorporated into clinical studies and routine.

  16. Quantification of phase retardation in corneal tissues using a femtosecond laser

    NASA Astrophysics Data System (ADS)

    Calhoun, William R.; Beylin, Alexander; Weiblinger, Richard; Ilev, Ilko

    2013-03-01

    The use of femtosecond lasers (FSL) in ophthalmic procedures, such as LASIK, lens replacement (cataract surgery), as well as several other treatments, is growing rapidly. The treatment effect is based on photo ablation of ocular tissues by a series of ultra-short laser pulses. However, the laser beam characteristics change dynamically due to interactions with birefringent corneal tissue, which may affect the outcome of the laser treatment. To better understand the effect the cornea has on the laser characteristics, we developed a system for measuring retardation and validated it with precise, standard phase retarders. Then we measured the phase retardation of FSLs through bovine corneas and found that there is a considerable, location dependent, variation in retardation values. This information can potentially help optimize FSL parameters to make their application in ophthalmic procedures safer and more effective.

  17. Quantification of virus-like particles suggests viral infection in corals affected by Porites tissue loss

    NASA Astrophysics Data System (ADS)

    Lawrence, Scott A.; Davy, Joanne E.; Aeby, Greta S.; Wilson, William H.; Davy, Simon K.

    2014-09-01

    Porites tissue loss is a common disease of Porites compressa on Hawaiian reefs. Despite its prevalence, to date, the aetiological agent of the disease has not been found. The apparent lack of a microbial causative agent in the similar disease Porites bleaching with tissue loss, as well as increasing evidence of viral infections in scleractinian corals and Symbiodinium, led us to hypothesise that a virus may be responsible. Electron microscopy revealed the presence of numerous and varied virus-like particles (VLPs) in healthy and diseased P. compressa colonies. While overall virus numbers were similar in all samples, the abundance of a group of icosahedral VLPs differed significantly between healthy and diseased colonies. While not conclusive, these results suggest that viruses may play a role in this disease, and provide a basis for further studies.

  18. Quantification of Protein Signatures in Archived Human Prostate Tissues Using Shotgun Proteomic Methods

    DTIC Science & Technology

    2011-06-01

    proteins were subsequently incubated with wheat - germ agglutinin (WGA) and con canavalin- A (ConA) beads, washed, and el uted with sol uble n-acetyl...prostate radial prostatectomies and have focused on optimizing protocols to extract and profile proteins in matched normal and dise ased tissue s...human prostate cancer using label-free, quantitative mass spectrometry. Last year we were able to extract up to 1 00 micrograms of total protein

  19. Evaluation and quantification of spectral information in tissue by confocal microscopy

    NASA Astrophysics Data System (ADS)

    Maeder, Ulf; Marquardt, Kay; Beer, Sebastian; Bergmann, Thorsten; Schmidts, Thomas; Heverhagen, Johannes T.; Zink, Klemens; Runkel, Frank; Fiebich, Martin

    2012-10-01

    A confocal imaging and image processing scheme is introduced to visualize and evaluate the spatial distribution of spectral information in tissue. The image data are recorded using a confocal laser-scanning microscope equipped with a detection unit that provides high spectral resolution. The processing scheme is based on spectral data, is less error-prone than intensity-based visualization and evaluation methods, and provides quantitative information on the composition of the sample. The method is tested and validated in the context of the development of dermal drug delivery systems, introducing a quantitative uptake indicator to compare the performances of different delivery systems is introduced. A drug penetration study was performed in vitro. The results show that the method is able to detect, visualize and measure spectral information in tissue. In the penetration study, uptake efficiencies of different experiment setups could be discriminated and quantitatively described. The developed uptake indicator is a step towards a quantitative assessment and, in a more general view apart from pharmaceutical research, provides valuable information on tissue composition. It can potentially be used for clinical in vitro and in vivo applications.

  20. New method of dynamic color doppler signal quantification in metastatic lymph nodes compared to direct polarographic measurements of tissue oxygenation.

    PubMed

    Scholbach, Thomas; Scholbach, Jakob; Krombach, Gabriele A; Gagel, Bernd; Maneschi, Payam; Di Martino, Ercole

    2005-05-10

    Tumor growth depends on sufficient blood and oxygen supply. Hypoxia stimulates neovascularization and is a known cause for radio- and chemoresistance. The objective of this study was to investigate the use of a novel ultrasound technique for the dynamic assessment of vascularization and oxygenation in metastatic lymph nodes. Twenty-four patients (age 44-78 years) with cervical lymph node metastases of squamous cell head and neck cancer were investigated by color duplex sonography and 17 (age 46-78 years) were investigated additionally with polarography. Sonography was performed after contrast enhancer infusion under defined conditions. Intranodal perfusion data (color hue, colored area) were measured automatically by a novel software technique. This allows an evaluation of blood flow dynamics by calculating perfusion intensity--velocity, perfused area, as well as the novel parameters tissue resistance index (TRI) and tissue pulsatility index (TPI)--for each point of a complete heart cycle. Tumor tissue pO(2) was measured by means of polarographic needle electrodes placed intranodally. The sonographic and polarographic data were correlated using Pearson's test. Sonography demonstrated a statistically significant inverse correlation between hypoxia and perfusion and significant TPI and TRI changes with different N-stages. The percentage of nodal fraction with less than 10 mmHg oxygen saturation was significantly inversely correlated with lymph node perfusion (r = -0.551; p = 0.021). Nodes with a perfusion of less than 0.05 cm/sec flow velocity showed significantly larger hypoxic areas (p = 0.006). Significant differences of TPI and TRI existed between nodes in stage N(1) and N(2)/N(3) (p = 0.028 and 0.048, respectively). This new method of dynamic signal quantification allows a noninvasive and quantitative assessment of tumor and metastatic lymph node perfusion by means of commonly available ultrasound equipment.

  1. Three-dimensional pore space quantification of apple tissue using X-ray computed microtomography.

    PubMed

    Mendoza, Fernando; Verboven, Pieter; Mebatsion, Hibru K; Kerckhofs, Greet; Wevers, Martine; Nicolaï, Bart

    2007-08-01

    The microstructure and the connectivity of the pore space are important variables for better understanding of the complex gas transport phenomena that occur in plant tissues. In this study, we present an experimental procedure for image acquisition and image processing to quantitatively characterize in 3D the pore space of apple tissues (Malus domestica Borkh.) for two cultivars (Jonagold and Braeburn) taken from the fleshy part of the cortex using X-ray computer microtomography. Preliminary sensitivity analyses were performed to determine the effect of the resolution and the volume size (REV, representative elementary volume analysis) on the computed porosity of apple samples. For comparison among cultivars, geometrical properties such as porosity, specific surface area, number of disconnected pore volumes and their distribution parameters were extracted and analyzed in triplicate based on the 3D skeletonization of the pore space (medial axis analysis). The results showed that microtomography provides a resolution at the micrometer level to quantitatively analyze and characterize the 3D topology of the pore space in apple tissue. The computed porosity was confirmed to be highly dependent of the resolution used, and the minimum REV of the cortical flesh of apple fruit was estimated to be 1.3 mm(3). Comparisons among the two cultivars using a resolution of 8.5 mum with a minimum REV cube showed that in spite of the complexity and variability of the pore space network observed in Jonagold and Braeburn apples, the extracted parameters from the medial axis were significantly different (P-value < 0.05). Medial axis parameters showed potential to differentiate the microstructure between the two evaluated apple cultivars.

  2. Quantification of major flavonoids in carnation tissues (Dianthus caryophyllus) as a tool for cultivar discrimination.

    PubMed

    Galeotti, Francesco; Barile, Elisa; Lanzotti, Virginia; Dolci, Marcello; Curir, Paolo

    2008-01-01

    One flavone-C-glycoside and two flavonol-O-glycosides were recognized and isolated as the main flavonoidal components in nine different carnation cultivars, and their chemical structures have been determined by spectroscopic methods, including UV detection, MS and NMR. The distribution of these three compounds in flowers, leaves, stems, young sprouts, and roots of each cultivar was evaluated by a simple HPLC-UV method: the graphic representation of their content in the different tissues allows to identify and characterize unambiguously each considered carnation cultivar. The presented method could be an easy, inexpensive and reliable tool for carnation cultivar discrimination.

  3. Extraction and quantification of adenosine triphosphate in mammalian tissues and cells.

    PubMed

    Chida, Junji; Kido, Hiroshi

    2014-01-01

    Adenosine 5'-triphosphate (ATP) is the "energy currency" of organisms and plays central roles in bioenergetics, whereby its level is used to evaluate cell viability, proliferation, death, and energy transmission. In this chapter, we describe an improved and efficient method for extraction of ATP from tissues and cells using phenol-based reagents. The chaotropic extraction reagents reported so far co-precipitate ATP with insoluble proteins during extraction and with salts during neutralization. In comparison, the phenol-based reagents extract ATP well without the risks of co-precipitation. The extracted ATP can be quantified by the luciferase assay or high-performance liquid chromatography.

  4. Laser-induced Breakdown Spectroscopy: A New Approach for Nanoparticle's Mapping and Quantification in Organ Tissue

    PubMed Central

    Sancey, Lucie; Motto-Ros, Vincent; Kotb, Shady; Wang, Xiaochun; Lux, François; Panczer, Gérard; Yu, Jin; Tillement, Olivier

    2014-01-01

    Emission spectroscopy of laser-induced plasma was applied to elemental analysis of biological samples. Laser-induced breakdown spectroscopy (LIBS) performed on thin sections of rodent tissues: kidneys and tumor, allows the detection of inorganic elements such as (i) Na, Ca, Cu, Mg, P, and Fe, naturally present in the body and (ii) Si and Gd, detected after the injection of gadolinium-based nanoparticles. The animals were euthanized 1 to 24 hr after intravenous injection of particles. A two-dimensional scan of the sample, performed using a motorized micrometric 3D-stage, allowed the infrared laser beam exploring the surface with a lateral resolution less than 100 μm. Quantitative chemical images of Gd element inside the organ were obtained with sub-mM sensitivity. LIBS offers a simple and robust method to study the distribution of inorganic materials without any specific labeling. Moreover, the compatibility of the setup with standard optical microscopy emphasizes its potential to provide multiple images of the same biological tissue with different types of response: elemental, molecular, or cellular. PMID:24962015

  5. Detection and quantification of virulent Aeromonas hydrophila in channel catfish tissues following waterborne challenge.

    PubMed

    Zhang, Dunhua; Moreira, Gabriel S A; Shoemaker, Craig; Newton, Joseph C; Xu, De-Hai

    2016-05-01

    The aim of this study was to understand the pathogenesis of motile aeromonas septicemia caused by an emergent, high virulent Aeromonas hydrophila (vAh) in channel catfish, Ictalurus punctatus Adipose fin clipped catfish were challenged with vAh using a waterborne challenge method, and the distribution of vAh over a time course was detected and quantified using real-time polymerase chain reaction. The results showed that 77.8% of fish died within 48 h post challenge with mean day to death of 1.5 days. At 2 h post challenge, vAh (inferred from genomic DNA copies or genome equivalents) was detected in all external and internal tissues sampled. Gill had the highest vAh cells at 1 h post challenge. Spleen harbored the most vAh cells among internal organs at 4 h post challenge. The tissues/organs with most vAh cells detected at 8 h post challenge were adipose fin, blood, intestine, kidney and skin, while liver showed the highest vAh cells at 24 h post challenge. These results suggest that vAh was able to rapidly proliferate and spread, following wound infection, through the fish blood circulation system and cause mortality within 8-24 h.

  6. Laser-induced breakdown spectroscopy: a new approach for nanoparticle's mapping and quantification in organ tissue.

    PubMed

    Sancey, Lucie; Motto-Ros, Vincent; Kotb, Shady; Wang, Xiaochun; Lux, François; Panczer, Gérard; Yu, Jin; Tillement, Olivier

    2014-06-18

    Emission spectroscopy of laser-induced plasma was applied to elemental analysis of biological samples. Laser-induced breakdown spectroscopy (LIBS) performed on thin sections of rodent tissues: kidneys and tumor, allows the detection of inorganic elements such as (i) Na, Ca, Cu, Mg, P, and Fe, naturally present in the body and (ii) Si and Gd, detected after the injection of gadolinium-based nanoparticles. The animals were euthanized 1 to 24 hr after intravenous injection of particles. A two-dimensional scan of the sample, performed using a motorized micrometric 3D-stage, allowed the infrared laser beam exploring the surface with a lateral resolution less than 100 μm. Quantitative chemical images of Gd element inside the organ were obtained with sub-mM sensitivity. LIBS offers a simple and robust method to study the distribution of inorganic materials without any specific labeling. Moreover, the compatibility of the setup with standard optical microscopy emphasizes its potential to provide multiple images of the same biological tissue with different types of response: elemental, molecular, or cellular.

  7. Measurement and quantification of fluorescent changes in ocular tissue using a novel confocal instrument

    NASA Astrophysics Data System (ADS)

    Buttenschoen, Kim K.; Girkin, John M.; Daly, Daniel J.

    2014-05-01

    Our sight is a major contributor to our quality of life. The treatment of diseases like macular degeneration and glaucoma, however, presents a challenge as the delivery of medication to ocular tissue is not well understood. The instrument described here will help quantify targeted delivery by non-invasively and simultaneously measuring light reflected from and fluorescence excited in the eye, used as position marker and to track compounds respectively. The measurement concept has been proven by monitoring the diffusion of fluorescein and a pharmaceutical compound for treating open angle glaucoma in vitro in a cuvette and in ex vivo porcine eyes. To obtain a baseline of natural fluorescence we measured the change in corneal and crystalline lens autofluorescence in volunteers over a week. We furthermore present data on 3D ocular autofluorescence. Our results demonstrate the capability to measure the location and concentration of the compound of interest with high axial and temporal resolution of 178 μm and 0.6 s respectively. The current detection limit is 2 nM for fluorescein, and compounds with a quantum yield as low as 0.01 were measured to concentrations below 1 μM. The instrument has many applications in assessing the diffusion of fluorescent compounds through the eye and skin in vitro and in vivo, measuring autofluorescence of ocular tissues and reducing the number of animals needed for research. The instrument has the capability of being used both in the clinical and home care environment opening up the possibility of measuring controlled drug release in a patient friendly manner.

  8. Insights into reference point indentation involving human cortical bone: sensitivity to tissue anisotropy and mechanical behavior.

    PubMed

    Granke, Mathilde; Coulmier, Aurélie; Uppuganti, Sasidhar; Gaddy, Jennifer A; Does, Mark D; Nyman, Jeffry S

    2014-09-01

    Reference point indentation (RPI) is a microindentation technique involving 20 cycles of loading in "force-control" that can directly assess a patient׳s bone tissue properties. Even though preliminary clinical studies indicate a capability for fracture discrimination, little is known about what mechanical behavior the various RPI properties characterize and how these properties relate to traditional mechanical properties of bone. To address this, the present study investigated the sensitivity of RPI properties to anatomical location and tissue organization as well as examined to what extent RPI measurements explain the intrinsic mechanical properties of human cortical bone. Multiple indents with a target force of 10N were done in 2 orthogonal directions (longitudinal and transverse) per quadrant (anterior, medial, posterior, and lateral) of the femoral mid-shaft acquired from 26 donors (25-101 years old). Additional RPI measurements were acquired for 3 orthogonal directions (medial only). Independent of age, most RPI properties did not vary among these locations, but they did exhibit transverse isotropy such that resistance to indentation is greater in the longitudinal (axial) direction than in the transverse direction (radial or circumferential). Next, beam specimens (~2mm×5mm×40mm) were extracted from the medial cortex of femoral mid-shafts, acquired from 34 donors (21-99 years old). After monotonically loading the specimens in three-point bending to failure, RPI properties were acquired from an adjacent region outside the span. Indent direction was orthogonal to the bending axis. A significant inverse relationship was found between resistance to indentation and the apparent-level mechanical properties. Indentation distance increase (IDI) and a linear combination of IDI and the loading slope, averaged over cycles 3 through 20, provided the best explanation of the variance in ultimate stress (r(2)=0.25, p=0.003) and toughness (r(2)=0.35, p=0.004), respectively

  9. High-Throughput Confocal Imaging of Intact Live Tissue Enables Quantification of Membrane Trafficking in Arabidopsis1[W

    PubMed Central

    Salomon, Susanne; Grunewald, Dorit; Stüber, Kurt; Schaaf, Sebastian; MacLean, Dan; Schulze-Lefert, Paul; Robatzek, Silke

    2010-01-01

    Membrane compartmentalization and trafficking within and between cells is considered an essential cellular property of higher eukaryotes. We established a high-throughput imaging method suitable for the quantitative detection of membrane compartments at subcellular resolution in intact epidermal tissue. Whole Arabidopsis (Arabidopsis thaliana) cotyledon leaves were subjected to quantitative confocal laser microscopy using automated image acquisition, computational pattern recognition, and quantification of membrane compartments. This revealed that our method is sensitive and reliable to detect distinct endomembrane compartments. We applied quantitative confocal laser microscopy to a transgenic line expressing GFP-2xFYVE as a marker for endosomal compartments during biotic or abiotic stresses, and detected markedly quantitative adaptations in response to changing environments. Using a transgenic line expressing the plasma membrane-resident syntaxin GFP-PEN1, we quantified the pathogen-inducible extracellular accumulation of this fusion protein at fungal entry sites. Our protocol provides a platform to study the quantitative and dynamic changes of endomembrane trafficking, and potential adaptations of this machinery to physiological stress. PMID:20841454

  10. Diagnostic Value of Virtual Touch Tissue Imaging Quantification for Evaluating Median Nerve Stiffness in Carpal Tunnel Syndrome.

    PubMed

    Zhang, Chen; Li, Miao; Jiang, Jue; Zhou, Qi; Xiang, Li; Huang, Yajuan; Ban, Wenrui; Peng, Wei

    2017-09-01

    To measure the shear wave velocity (SWV) of the median nerve by Virtual Touch tissue imaging quantification (VTIQ; Siemens AG, Erlangen, Germany) through the beginning of the carpal tunnel and to determine whether VTIQ could be used to diagnose carpal tunnel syndrome. This study recruited 49 consecutive patients (72 wrists) with a definitive diagnosis of carpal tunnel syndrome and 23 healthy volunteers (46 wrists). We measured the median nerve diameter and cross-sectional area by 2-dimensional sonography and the SWV by VTIQ. The interobserver variability was analyzed, and diagnostic values were evaluated by drawing a receiver operating characteristic curve. The median nerve SWV was significantly higher in the carpal tunnel syndrome group (3.857 m/s) than the control group (2.542 m/s; P < .05). A 3.0-m/s SWV cutoff value revealed sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of 83.3%, 91.3%, 93.8%, 77.8%, and 86.4%, respectively. The interobserver agreement was excellent for the SWV measurements. The median nerve SWV at the carpal tunnel inlet is significantly higher in patients with carpal tunnel syndrome, for whom VTIQ appears to be a highly reproducible diagnostic technique. © 2017 by the American Institute of Ultrasound in Medicine.

  11. Model-based cell number quantification using online single-oxygen sensor data for tissue engineering perfusion bioreactors.

    PubMed

    Lambrechts, T; Papantoniou, I; Sonnaert, M; Schrooten, J; Aerts, J-M

    2014-10-01

    Online and non-invasive quantification of critical tissue engineering (TE) construct quality attributes in TE bioreactors is indispensable for the cost-effective up-scaling and automation of cellular construct manufacturing. However, appropriate monitoring techniques for cellular constructs in bioreactors are still lacking. This study presents a generic and robust approach to determine cell number and metabolic activity of cell-based TE constructs in perfusion bioreactors based on single oxygen sensor data in dynamic perfusion conditions. A data-based mechanistic modeling technique was used that is able to correlate the number of cells within the scaffold (R(2)  = 0.80) and the metabolic activity of the cells (R(2)  = 0.82) to the dynamics of the oxygen response to step changes in the perfusion rate. This generic non-destructive measurement technique is effective for a large range of cells, from as low as 1.0 × 10(5) cells to potentially multiple millions of cells, and can open-up new possibilities for effective bioprocess monitoring.

  12. Implementation of an absolute brain 1H-MRS quantification method to assess different tissue alterations in multiple sclerosis.

    PubMed

    Bagory, Matthieu; Durand-Dubief, Françoise; Ibarrola, Danielle; Comte, Jean-Christophe; Cotton, François; Confavreux, Christian; Sappey-Marinier, Dominique

    2012-10-01

    Magnetic resonance spectroscopy has emerged as a sensitive modality to detect early and diffuse alterations in multiple sclerosis. Recently, the hypothesis of neurodegenerative pathogenesis has highlightened the interest for measurement of metabolites concentrations, to gain specificity, in a large brain volume encompassing different tissue alterations. Therefore, we proposed in this paper the implementation of an absolute quantification method based on localized spectroscopy at short (30 ms) and long (135 ms) echo time of a volume including normal appearing white matter, cortical gray matter, and lesions. First, methodological developments were implemented including external calibration, and corrections of phased-array coil sensitivity and cerebrospinal fluid volume contribution. Second, these improvements were validated and optimized using an original methodology based on simulations of brain images with lesions. Finally, metabolic alterations were assessed in 65 patients including 26 relapsing-remitting, 17 primary-progressive (PP), 22 secondary-progressive (SP) patients, and in 23 normal subjects. Results showed increases of choline, creatine, and myo-inositol concentrations in PP and SP patients compared to controls, whereas the concentration of N-acetyl compounds remained constant. The major finding of this study was the identification of Cho concentration and Cho/tNA ratio as putative markers of progressive onset, suggesting interesting perspectives in detection and followup of neurodegenerative processes.

  13. Evaluation of virtual touch tissue imaging quantification, a new shear wave velocity imaging method, for breast lesion assessment by ultrasound.

    PubMed

    Golatta, Michael; Schweitzer-Martin, Mirjam; Harcos, Aba; Schott, Sarah; Gomez, Christina; Stieber, Anne; Rauch, Geraldine; Domschke, Christoph; Rom, Joachim; Schütz, Florian; Sohn, Christof; Heil, Jörg

    2014-01-01

    To evaluate virtual touch tissue imaging quantification (VTIQ) as a new elastography method concerning its intra- and interexaminer reliability and its ability to differentiate benign from malignant breast lesions in comparison to and in combination with ultrasound (US) B-mode breast imaging reporting and data system (BI-RADS) assessment. US and VTIQ were performed by two examiners in 103 women with 104 lesions. Intra- and interexaminer reliability of VTIQ was assessed. The area under the receiver operating curve (AUC), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of BIRADS, VTIQ, and combined data were compared. Fifty-four of 104 lesions were malignant. Intraexaminer reliability was consistent, and interexaminer agreement showed a strong positive correlation (r = 0.93). The mean VTIQ values in malignant lesions were significantly higher than those in benign (7.73 m/s ± 1.02 versus 4.46 m/s ± 1.87; P < 0.0001). The combination of US-BIRADS with the optimal cut-off for clinical decision making of 5.18 m/s yielded a sensitivity of 98%, specificity of 82%, PPV of 86%, and NPV of 98%. The combination of BIRADS and VTIQ led to improved test validity. VTIQ is highly reliable and reproducible. There is a significant difference regarding the mean maximum velocity of benign and malignant lesions. Adding VTIQ to BIRADS assessment improves the specificity.

  14. Identification of stable reference genes for gene expression analysis of three-dimensional cultivated human bone marrow-derived mesenchymal stromal cells for bone tissue engineering.

    PubMed

    Rauh, Juliane; Jacobi, Angela; Stiehler, Maik

    2015-02-01

    The principles of tissue engineering (TE) are widely used for bone regeneration concepts. Three-dimensional (3D) cultivation of autologous human mesenchymal stromal cells (MSCs) on porous scaffolds is the basic prerequisite to generate newly formed bone tissue. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a specific and sensitive analytical tool for the measurement of mRNA-levels in cells or tissues. For an accurate quantification of gene expression levels, stably expressed reference genes (RGs) are essential to obtain reliable results. Since the 3D environment can affect a cell's morphology, proliferation, and gene expression profile compared with two-dimensional (2D) cultivation, there is a need to identify robust RGs for the quantification of gene expression. So far, this issue has not been adequately investigated. The aim of this study was to identify the most stably expressed RGs for gene expression analysis of 3D-cultivated human bone marrow-derived MSCs (BM-MSCs). For this, we analyzed the gene expression levels of n=31 RGs in 3D-cultivated human BM-MSCs from six different donors compared with conventional 2D cultivation using qRT-PCR. MSCs isolated from bone marrow aspirates were cultivated on human cancellous bone cube scaffolds for 14 days. Osteogenic differentiation was assessed by cell-specific alkaline phosphatase (ALP) activity and expression of osteogenic marker genes. Expression levels of potential reference and target genes were quantified using commercially available TaqMan(®) assays. mRNA expression stability of RGs was determined by calculating the coefficient of variation (CV) and using the algorithms of geNorm and NormFinder. Using both algorithms, we identified TATA box binding protein (TBP), transferrin receptor (p90, CD71) (TFRC), and hypoxanthine phosphoribosyltransferase 1 (HPRT1) as the most stably expressed RGs in 3D-cultivated BM-MSCs. Notably, genes that are routinely used as RGs, for example, beta actin

  15. A comparison of virtual touch tissue quantification and digital rectal examination for discrimination between prostate cancer and benign prostatic hyperplasia.

    PubMed

    Zheng, Xiaozhi; Ji, Ping; Mao, Hongwei; Hu, Jianqun

    2012-03-01

    Virtual touch tissue quantification (VTTQ) is a new, promising technique for detecting the stiffness of tissues. The aim of this study is to compare the performance of VTTQ and digital rectal examination (DRE) in discrimination between prostate cancer and benign prostatic hyperplasia (BPH). VTTQ was performed in 209 prostate nodular lesions of 107 patients with BPH and suspected prostate cancer before the prostate histopathologic examination. The shear wave velocity (SWV) at each nodular lesion was quantified by implementing an acoustic radiation force impulse (ARFI). The performance of VTTQ and DRE in discrimination between prostate cancer and BPH was compared. The diagnostic value of VTTQ and DRE for prostate cancer was evaluated in terms of the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy. Prostate cancer was detected in 57 prostate nodular lesions by histopathologic examination. The SWV values (m/s) were significantly greater in prostate cancer and BPH than in normal prostate (2.37 ± 0.94, 1.98 ± 0.82 vs. 1.34 ± 0.47). The area under the receiver operating characteristic curve (AUC) for VTTQ (SWV>2.5m/s) to differentiate prostate nodules as benign hyperplasia or malignancy was 0.86, while it was 0.67 for DRE. The diagnostic sensitivity, specificity, PPV, NPV and accuracy were 71.93 %, 87.5 %, 68.33 %, 89.26 %, 83.25 %, respectively for VTTQ (SWV>2.5m/s), whereas they were 33.33 %, 81.57 %, 40.43 %, 76.54 %, 68.42 % respectively for DRE. VTTQ can effectively detect the stiffness of prostate nodular lesions, which has a significantly higher performance than DRE in discrimination between prostate cancer and BPH.

  16. Quantification of C4d deposition and hepatitis C virus RNA in tissue in cases of graft rejection and hepatitis C recurrence after liver transplantation

    PubMed Central

    Song, Alice Tung Wan; de Mello, Evandro Sobroza; Alves, Venâncio Avancini Ferreira; Cavalheiro, Norma de Paula; Melo, Carlos Eduardo; Bonazzi, Patricia Rodrigues; Tengan, Fatima Mitiko; Freire, Maristela Pinheiro; Barone, Antonio Alci; D'Albuquerque, Luiz Augusto Carneiro; Abdala, Edson

    2015-01-01

    Histology is the gold standard for diagnosing acute rejection and hepatitis C recurrence after liver transplantation. However, differential diagnosis between the two can be difficult. We evaluated the role of C4d staining and quantification of hepatitis C virus (HCV) RNA levels in liver tissue. This was a retrospective study of 98 liver biopsy samples divided into four groups by histological diagnosis: acute rejection in patients undergoing liver transplant for hepatitis C (RejHCV+), HCV recurrence in patients undergoing liver transplant for hepatitis C (HCVTx+), acute rejection in patients undergoing liver transplant for reasons other than hepatitis C and chronic hepatitis C not transplanted (HCVTx-). All samples were submitted for immunohistochemical staining for C4d and HCV RNA quantification. Immunoexpression of C4d was observed in the portal vessels and was highest in the HCVTx- group. There was no difference in C4d expression between the RejHCV+ and HCVTx+ groups. However, tissue HCV RNA levels were higher in the HCVTx+ group samples than in the RejHCV+ group samples. Additionally, there was a significant correlation between tissue and serum levels of HCV RNA. The quantification of HCV RNA in liver tissue might prove to be an efficient diagnostic test for the recurrence of HCV infection. PMID:25742264

  17. Optical Quantification of Harmonic Acoustic Radiation Force Excitation in a Tissue-Mimicking Phantom.

    PubMed

    Suomi, Visa; Edwards, David; Cleveland, Robin

    2015-12-01

    Optical tracking was used to characterize acoustic radiation force-induced displacements in a tissue-mimicking phantom. Amplitude-modulated 3.3-MHz ultrasound was used to induce acoustic radiation force in the phantom, which was embedded with 10-μm microspheres that were tracked using a microscope objective and high-speed camera. For sine and square amplitude modulation, the harmonic components of the fundamental and second and third harmonic frequencies were measured. The displacement amplitudes were found to increase linearly with acoustic radiation force up to 10 μm, with sine modulation having 19.5% lower peak-to-peak amplitude values than square modulation. Square modulation produced almost no second harmonic, but energy was present in the third harmonic. For the sine modulation, energy was present in the second harmonic and low energy in the third harmonic. A finite-element model was used to simulate the deformation and was both qualitatively and quantitatively in agreement with the measurements. Copyright © 2015 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

  18. A kinetic aggregation assay allowing selective and sensitive amyloid-β quantification in cells and tissues.

    PubMed

    Du, Deguo; Murray, Amber N; Cohen, Ehud; Kim, Hyun-Eui; Simkovsky, Ryan; Dillin, Andrew; Kelly, Jeffery W

    2011-03-15

    The process of amyloid-β (Aβ) fibril formation is genetically and pathologically linked to Alzheimer's disease (AD). Thus, a selective and sensitive method for quantifying Aβ fibrils in complex biological samples allows a variety of hypotheses to be tested. Herein, we report the basis for a quantitative in vitro kinetic aggregation assay that detects seeding-competent Aβ aggregates in mammalian cell culture media, in Caenorhabditis elegans lysate, and in mouse brain homogenate. Sonicated, proteinase K-treated Aβ fibril-containing tissue homogenates or cell culture media were added to an initially monomeric Aβ(1-40) reporter peptide to seed an in vitro nucleated aggregation reaction. The reduction in the half-time (t(50)) of the amyloid growth phase is proportional to the quantity of seeding-competent Aβ aggregates present in the biological sample. An ion-exchange resin amyloid isolation strategy from complex biological samples is demonstrated as an alternative for improving the sensitivity and linearity of the kinetic aggregation assay.

  19. Automatic quantification of mitochondrial fragmentation from two-photon microscope images of mouse brain tissue.

    PubMed

    Lihavainen, E; Kislin, M; Toptunov, D; Khiroug, L; Ribeiro, A S

    2015-12-01

    The morphology of mitochondria can inform about their functional state and, thus, about cell vitality. For example, fragmentation of the mitochondrial network is associated with many diseases. Recent advances in neuronal imaging have enabled the observation of mitochondria in live brains for long periods of time, enabling the study of their dynamics in animal models of diseases. To aid these studies, we developed an automatic method, based on supervised learning, for quantifying the degree of mitochondrial fragmentation in tissue images acquired via two-photon microscopy from transgenic mice, which exclusively express Enhanced cyan fluorescent protein (ECFP) under Thy1 promoter, targeted to the mitochondrial matrix in subpopulations of neurons. We tested the method on images prior to and after cardiac arrest, and found it to be sensitive to significant changes in mitochondrial morphology because of the arrest. We conclude that the method is useful in detecting morphological abnormalities in mitochondria and, likely, in other subcellular structures as well. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  20. Identification and Validation of Reference Genes for Quantification of Target Gene Expression with Quantitative Real-time PCR for Tall Fescue under Four Abiotic Stresses

    PubMed Central

    Hu, Baoyun; Tan, Zhiqun; Huang, Bingru

    2015-01-01

    Tall fescue (Festuca arundinacea Schreb.) is widely utilized as a major forage and turfgrass species in the temperate regions of the world and is a valuable plant material for studying molecular mechanisms of grass stress tolerance due to its superior drought and heat tolerance among cool-season species. Selection of suitable reference genes for quantification of target gene expression is important for the discovery of molecular mechanisms underlying improved growth traits and stress tolerance. The stability of nine potential reference genes (ACT, TUB, EF1a, GAPDH, SAND, CACS, F-box, PEPKR1 and TIP41) was evaluated using four programs, GeNorm, NormFinder, BestKeeper, and RefFinder. The combinations of SAND and TUB or TIP41 and TUB were most stably expressed in salt-treated roots or leaves. The combinations of GAPDH with TIP41 or TUB were stable in roots and leaves under drought stress. TIP41 and PEPKR1 exhibited stable expression in cold-treated roots, and the combination of F-box, TIP41 and TUB was also stable in cold-treated leaves. CACS and TUB were the two most stable reference genes in heat-stressed roots. TIP41 combined with TUB and ACT was stably expressed in heat-stressed leaves. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) assays of the target gene FaWRKY1 using the identified most stable reference genes confirmed the reliability of selected reference genes. The selection of suitable reference genes in tall fescue will allow for more accurate identification of stress-tolerance genes and molecular mechanisms conferring stress tolerance in this stress-tolerant species. PMID:25786207

  1. Identification and validation of reference genes for quantification of target gene expression with quantitative real-time PCR for tall fescue under four abiotic stresses.

    PubMed

    Yang, Zhimin; Chen, Yu; Hu, Baoyun; Tan, Zhiqun; Huang, Bingru

    2015-01-01

    Tall fescue (Festuca arundinacea Schreb.) is widely utilized as a major forage and turfgrass species in the temperate regions of the world and is a valuable plant material for studying molecular mechanisms of grass stress tolerance due to its superior drought and heat tolerance among cool-season species. Selection of suitable reference genes for quantification of target gene expression is important for the discovery of molecular mechanisms underlying improved growth traits and stress tolerance. The stability of nine potential reference genes (ACT, TUB, EF1a, GAPDH, SAND, CACS, F-box, PEPKR1 and TIP41) was evaluated using four programs, GeNorm, NormFinder, BestKeeper, and RefFinder. The combinations of SAND and TUB or TIP41 and TUB were most stably expressed in salt-treated roots or leaves. The combinations of GAPDH with TIP41 or TUB were stable in roots and leaves under drought stress. TIP41 and PEPKR1 exhibited stable expression in cold-treated roots, and the combination of F-box, TIP41 and TUB was also stable in cold-treated leaves. CACS and TUB were the two most stable reference genes in heat-stressed roots. TIP41 combined with TUB and ACT was stably expressed in heat-stressed leaves. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) assays of the target gene FaWRKY1 using the identified most stable reference genes confirmed the reliability of selected reference genes. The selection of suitable reference genes in tall fescue will allow for more accurate identification of stress-tolerance genes and molecular mechanisms conferring stress tolerance in this stress-tolerant species.

  2. Freeze-drying for the stabilisation of shellfish toxins in mussel tissue (Mytilus edulis) reference materials.

    PubMed

    McCarron, Pearse; Emteborg, Håkan; Hess, Philipp

    2007-04-01

    Aliquots of freeze-dried and wet mussel tissue reference materials containing the various shellfish toxins examined in the study.

  3. Selection of suitable reference genes for gene expression studies in normal human ovarian tissues, borderline ovarian tumours and ovarian cancer.

    PubMed

    Ofinran, Olumide; Bose, Ujjal; Hay, Daniel; Abdul, Summi; Tufatelli, Cristina; Khan, Raheela

    2016-12-01

    The use of reference genes is the most common method of controlling the variation in mRNA expression during quantitative polymerase chain reaction, although the use of traditional reference genes, such as β‑actin, glyceraldehyde‑3‑phosphate dehydrogenase or 18S ribosomal RNA, without validation occasionally leads to unreliable results. Therefore, the present study aimed to evaluate a set of five commonly used reference genes to determine the most suitable for gene expression studies in normal ovarian tissues, borderline ovarian and ovarian cancer tissues. The expression stabilities of these genes were ranked using two gene stability algorithms, geNorm and NormFinder. Using geNorm, the two best reference genes in ovarian cancer were β‑glucuronidase and β‑actin. Hypoxanthine phosphoribosyltransferase‑1 and β‑glucuronidase were the most stable in ovarian borderline tumours, and hypoxanthine phosphoribosyltransferase‑1 and glyceraldehyde‑3‑phosphate dehydrogenase were the most stable in normal ovarian tissues. NormFinder ranked β‑actin the most stable in ovarian cancer, and the best combination of two genes was β‑glucuronidase and β‑actin. In borderline tumours, hypoxanthine phosphoribosyltransferase‑1 was identified as the most stable, and the best combination was hypoxanthine phosphoribosyltransferase‑1 and β‑glucuronidase. In normal ovarian tissues, β‑glucuronidase was recommended as the optimum reference gene, and the most optimum pair of reference genes was hypoxanthine phosphoribosyltransferase‑1 and β‑actin. To the best of our knowledge, this is the first study to investigate the selection of a set of reference genes for normalisation in quantitative polymerase chain reactions in different ovarian tissues, and therefore it is recommended that β‑glucuronidase, β‑actin and hypoxanthine phosphoribosyltransferase‑1 are the most suitable reference genes for such analyses.

  4. Development and evaluation of a secondary reference panel for BCR-ABL1 quantification on the International Scale

    PubMed Central

    Cross, N C P; White, H E; Ernst, T; Welden, L; Dietz, C; Saglio, G; Mahon, F-X; Wong, C C; Zheng, D; Wong, S; Wang, S-S; Akiki, S; Albano, F; Andrikovics, H; Anwar, J; Balatzenko, G; Bendit, I; Beveridge, J; Boeckx, N; Cerveira, N; Cheng, S-M; Colomer, D; Czurda, S; Daraio, F; Dulucq, S; Eggen, L; El Housni, H; Gerrard, G; Gniot, M; Izzo, B; Jacquin, D; Janssen, J J W M; Jeromin, S; Jurcek, T; Kim, D-W; Machova-Polakova, K; Martinez-Lopez, J; McBean, M; Mesanovic, S; Mitterbauer-Hohendanner, G; Mobtaker, H; Mozziconacci, M-J; Pajič, T; Pallisgaard, N; Panagiotidis, P; Press, R D; Qin, Y-Z; Radich, J; Sacha, T; Touloumenidou, T; Waits, P; Wilkinson, E; Zadro, R; Müller, M C; Hochhaus, A; Branford, S

    2016-01-01

    Molecular monitoring of chronic myeloid leukemia patients using robust BCR-ABL1 tests standardized to the International Scale (IS) is key to proper disease management, especially when treatment cessation is considered. Most laboratories currently use a time-consuming sample exchange process with reference laboratories for IS calibration. A World Health Organization (WHO) BCR-ABL1 reference panel was developed (MR1–MR4), but access to the material is limited. In this study, we describe the development of the first cell-based secondary reference panel that is traceable to and faithfully replicates the WHO panel, with an additional MR4.5 level. The secondary panel was calibrated to IS using digital PCR with ABL1, BCR and GUSB as reference genes and evaluated by 44 laboratories worldwide. Interestingly, we found that >40% of BCR-ABL1 assays showed signs of inadequate optimization such as poor linearity and suboptimal PCR efficiency. Nonetheless, when optimized sample inputs were used, >60% demonstrated satisfactory IS accuracy, precision and/or MR4.5 sensitivity, and 58% obtained IS conversion factors from the secondary reference concordant with their current values. Correlation analysis indicated no significant alterations in %BCR-ABL1 results caused by different assay configurations. More assays achieved good precision and/or sensitivity than IS accuracy, indicating the need for better IS calibration mechanisms. PMID:27109508

  5. AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.

    PubMed

    Zhang, Runxuan; Calixto, Cristiane P G; Tzioutziou, Nikoleta A; James, Allan B; Simpson, Craig G; Guo, Wenbin; Marquez, Yamile; Kalyna, Maria; Patro, Rob; Eyras, Eduardo; Barta, Andrea; Nimmo, Hugh G; Brown, John W S

    2015-10-01

    RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed a comprehensive, nonredundant Arabidopsis reference transcript dataset (AtRTD) containing over 74 000 transcripts for use with algorithms to quantify AS transcript isoforms in RNA-seq. The AtRTD was formed by merging transcripts from TAIR10 and novel transcripts identified in an AS discovery project. We have estimated transcript abundance in RNA-seq data using the transcriptome-based alignment-free programmes Sailfish and Salmon and have validated quantification of splicing ratios from RNA-seq by high resolution reverse transcription polymerase chain reaction (HR RT-PCR). Good correlations between splicing ratios from RNA-seq and HR RT-PCR were obtained demonstrating the accuracy of abundances calculated for individual transcripts in RNA-seq. The AtRTD is a resource that will have immediate utility in analysing Arabidopsis RNA-seq data to quantify differential transcript abundance and expression.

  6. A survey of clearing techniques for 3D imaging of tissues with special reference to connective tissue.

    PubMed

    Azaripour, Adriano; Lagerweij, Tonny; Scharfbillig, Christina; Jadczak, Anna Elisabeth; Willershausen, Brita; Van Noorden, Cornelis J F

    2016-08-01

    For 3-dimensional (3D) imaging of a tissue, 3 methodological steps are essential and their successful application depends on specific characteristics of the type of tissue. The steps are 1° clearing of the opaque tissue to render it transparent for microscopy, 2° fluorescence labeling of the tissues and 3° 3D imaging. In the past decades, new methodologies were introduced for the clearing steps with their specific advantages and disadvantages. Most clearing techniques have been applied to the central nervous system and other organs that contain relatively low amounts of connective tissue including extracellular matrix. However, tissues that contain large amounts of extracellular matrix such as dermis in skin or gingiva are difficult to clear. The present survey lists methodologies that are available for clearing of tissues for 3D imaging. We report here that the BABB method using a mixture of benzyl alcohol and benzyl benzoate and iDISCO using dibenzylether (DBE) are the most successful methods for clearing connective tissue-rich gingiva and dermis of skin for 3D histochemistry and imaging of fluorescence using light-sheet microscopy. Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.

  7. A new method for quantification and assessment of epileptiform activity in EEG with special reference to focal nocturnal epileptiform activity.

    PubMed

    Larsson, Pål G; Wilson, J; Eeg-Olofsson, O

    2009-06-01

    Quantification of epileptiform activity in EEG has been applied for decades. This has mainly been done by visual inspection of the recorded EEG. There have been many attempts using computers to quantify the activity, usually with moderate success. In a row of contexts, including Landau-Kleffner syndrome and the syndrome of epilepsy with continuous spike wave during slow sleep, the spike index (SI) has been applied to quantify [Symbol: see text]interictal nocturnal focal epileptiform activity', which is suggested as a general term for the epileptiform activity enhanced by sleep. However, the SI has been implemented differently by different authors and has usually not been well described and never properly defined. This study suggests a definition of SI that gives a semiautomatic and relatively robust algorithm for assessment. The method employs spike detection by means of template matching of the current source density estimate. The percentage of time within an epoch with interspike interval (ISI) below a given limit, usually 3 s, is returned as the SI. This is calculated during daytime and in non-REM sleep. The standard epoch length is 10 min. The parameter selection is discussed in the context of the influence of spikes and bursts on cognition. The described method gives reproducible results in routine use, gives clinical valuable information, and is easily implemented in a clinical setting. There is only a minor added workload for the electroencephalographer.

  8. DAKOTA, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis:version 4.0 reference manual

    SciTech Connect

    Griffin, Joshua D. (Sandai National Labs, Livermore, CA); Eldred, Michael Scott; Martinez-Canales, Monica L.; Watson, Jean-Paul; Kolda, Tamara Gibson; Adams, Brian M.; Swiler, Laura Painton; Williams, Pamela J.; Hough, Patricia Diane; Gay, David M.; Dunlavy, Daniel M.; Eddy, John P.; Hart, William Eugene; Guinta, Anthony A.; Brown, Shannon L.

    2006-10-01

    The DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. DAKOTA contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic finite element methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the DAKOTA toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a reference manual for the commands specification for the DAKOTA software, providing input overviews, option descriptions, and example specifications.

  9. DAKOTA : a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis. Version 5.0, user's reference manual.

    SciTech Connect

    Eldred, Michael Scott; Dalbey, Keith R.; Bohnhoff, William J.; Adams, Brian M.; Swiler, Laura Painton; Hough, Patricia Diane; Gay, David M.; Eddy, John P.; Haskell, Karen H.

    2010-05-01

    The DAKOTA (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a flexible and extensible interface between simulation codes and iterative analysis methods. DAKOTA contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quantification with sampling, reliability, and stochastic finite element methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components required for iterative systems analyses, the DAKOTA toolkit provides a flexible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a reference manual for the commands specification for the DAKOTA software, providing input overviews, option descriptions, and example specifications.

  10. Poly(ADP-ribose): Structure, Physicochemical Properties and Quantification In Vivo, with Special Reference to Poly(ADP-ribose) Binding Protein Modules.

    PubMed

    Miwa, Masanao; Ida, Chieri; Yamashita, Sachiko; Tanaka, Masakazu; Fujisawa, Junichi

    2016-01-01

    PolyADP-ribosylation is a unique posttranslational modification of proteins, involved in various cellular functions including stability of chromatin. PolyADP-ribosylation modifies acceptor proteins with a large negatively charged poly(ADP-ribose) (PAR) to greatly change the structure and function of the acceptor proteins. In addition various specific motifs of proteins were recently found to interact non-covalently with PAR thereby changing the spaciotemporal activity of protein-protein interaction in cells. However, the structure of PAR to which specific protein motifs should bind is not fully characterized. The present work will review the structure, physicochemical properties and quantification of PAR in vivo, with special reference to PAR binding protein modules.

  11. Quantification of the predominant monomeric catechins in baking chocolate standard reference material by LC/APCI-MS.

    PubMed

    Nelson, Bryant C; Sharpless, Katherine E

    2003-01-29

    Catechins are polyphenolic plant compounds (flavonoids) that may offer significant health benefits to humans. These benefits stem largely from their anticarcinogenic, antioxidant, and antimutagenic properties. Recent epidemiological studies suggest that the consumption of flavonoid-containing foods is associated with reduced risk of cardiovascular disease. Chocolate is a natural cocoa bean-based product that reportedly contains high levels of monomeric, oligomeric, and polymeric catechins. We have applied solid-liquid extraction and liquid chromatography coupled with atmospheric pressure chemical ionization-mass spectrometry to the identification and determination of the predominant monomeric catechins, (+)-catechin and (-)-epicatechin, in a baking chocolate Standard Reference Material (NIST Standard Reference Material 2384). (+)-Catechin and (-)-epicatechin are detected and quantified in chocolate extracts on the basis of selected-ion monitoring of their protonated [M + H](+) molecular ions. Tryptophan methyl ester is used as an internal standard. The developed method has the capacity to accurately quantify as little as 0.1 microg/mL (0.01 mg of catechin/g of chocolate) of either catechin in chocolate extracts, and the method has additionally been used to certify (+)-catechin and (-)-epicatechin levels in the baking chocolate Standard Reference Material. This is the first reported use of liquid chromatography/mass spectrometry for the quantitative determination of monomeric catechins in chocolate and the only report certifying monomeric catechin levels in a food-based Standard Reference Material.

  12. A candidate reference method for quantification of low concentrations of plasmid DNA by exhaustive counting of single DNA molecules in a flow stream

    NASA Astrophysics Data System (ADS)

    Yoo, Hee-Bong; Oh, Donggeun; Song, Jae Yong; Kawaharasaki, Mamoru; Hwang, Jeeseong; Yang, In Chul; Park, Sang-Ryoul

    2014-10-01

    This work demonstrates accurate measurement of the amount of substance concentration of low concentration plasmid DNA by counting individual DNA molecules using a high-sensitivity flow cytometric setup. Plasmid DNA is a widely used form of DNA, and its quantity often needs to be accurately determined. This work establishes a reference analytical method for direct quantification of low concentration plasmid DNA prepared as reference standards for polymerase chain reaction-based DNA quantification. The model plasmid DNA pBR322 (4361 bp) was stained with a fluorescent dye and was detected in a flow stream in a micro-fluidic channel with laser-induced fluorescence detection, for which the DNA flow was electro-hydrodynamically focused at the centre of the channel. 200 to 8000 DNA molecules in a ˜1 µL sample volume were counted within 2 min in an ‘exhaustive counting’ manner, which facilitated quantitation without calibration. The sample volume was measured and validated from the close agreement of the results of two independent measurement methods, gravimetric determination of water filling the capillary and graphical estimation of actual cross sectional area of the capillary tubing with the image of calibrated scanning electron microscopy. Within the given concentration range, an excellent measurement linearity (R2 = 0.999) was achieved with appropriate data processing for the correction of the events of double molecules (detection of double molecules opposed to single molecule detection assumed, which occurs due to their coincidental passing of the detection zone). The validity of the proposed method was confirmed from the close agreement with the results of quantitation of enzymatically released nucleotides using capillary electrophoresis.

  13. Evaluation of candidate reference genes for normalization of quantitative RT-PCR in soybean tissues under various abiotic stress conditions.

    PubMed

    Le, Dung Tien; Aldrich, Donavan L; Valliyodan, Babu; Watanabe, Yasuko; Ha, Chien Van; Nishiyama, Rie; Guttikonda, Satish K; Quach, Truyen N; Gutierrez-Gonzalez, Juan J; Tran, Lam-Son Phan; Nguyen, Henry T

    2012-01-01

    Quantitative RT-PCR can be a very sensitive and powerful technique for measuring differential gene expression. Changes in gene expression induced by abiotic stresses are complex and multifaceted, which make determining stably expressed genes for data normalization difficult. To identify the most suitable reference genes for abiotic stress studies in soybean, 13 candidate genes collected from literature were evaluated for stability of expression under dehydration, high salinity, cold and ABA (abscisic acid) treatments using delta CT and geNorm approaches. Validation of reference genes indicated that the best reference genes are tissue- and stress-dependent. With respect to dehydration treatment, the Fbox/ABC, Fbox/60s gene pairs were found to have the highest expression stability in the root and shoot tissues of soybean seedlings, respectively. Fbox and 60s genes are the most suitable reference genes across dehydrated root and shoot tissues. Under salt stress the ELF1b/IDE and Fbox/ELF1b are the most stably expressed gene pairs in roots and shoots, respectively, while 60s/Fbox is the best gene pair in both tissues. For studying cold stress in roots or shoots, IDE/60s and Fbox/Act27 are good reference gene pairs, respectively. With regard to gene expression analysis under ABA treatment in either roots, shoots or across these tissues, 60s/ELF1b, ELF1b/Fbox and 60s/ELF1b are the most suitable reference genes, respectively. The expression of ELF1b/60s, 60s/Fbox and 60s/Fbox genes was most stable in roots, shoots and both tissues, respectively, under various stresses studied. Among the genes tested, 60s was found to be the best reference gene in different tissues and under various stress conditions. The highly ranked reference genes identified from this study were proved to be capable of detecting subtle differences in expression rates that otherwise would be missed if a less stable reference gene was used.

  14. Quantification of the Iodine Content of Perigastric Adipose Tissue by Dual-Energy CT: A Novel Method for Preoperative Diagnosis of T4-Stage Gastric Cancer

    PubMed Central

    Shi, Gaofeng; Li, Yang; Li, Yong

    2015-01-01

    This study investigated the utility of quantifying iodine concentration (IC) in perigastric adipose tissue, using dual-energy computed tomography (DECT), for the detection of T4a-stage gastric cancer. Fifty-four patients with gastric cancer were enrolled at the Fourth Hospital of Hebei Medical University between January and June 2013. Patients were imaged preoperatively with conventional computed tomography (CT) scans and DECT, and the IC in perigastric fat adjacent to the tumor calculated from arterial phase (AP) and portal venous phase (PVP) images. The patients subsequently received surgical treatment (gastrectomy), and histologic analysis of resected specimens was used as a ‘gold standard’ reference for cancer staging. Receiver operating characteristic (ROC) curve analysis was employed to assess the utility of DECT for identifying T4a-stage gastric cancer, with optimal IC thresholds determined from the area under the ROC curve (AUC). Postoperative histology revealed that 32 patients had serosal invasion (group A), and 22 did not (group B). The accuracy of conventional CT for distinguishing stage T4 from non-T4 stages was 68.5% (37/54). IC was significantly higher in group A than in group B (AP: 0.60±0.34 vs. 0.09±0.19 mg/mL, p<0.001; PVP: 0.83±0.41 vs. 0.27±0.21 mg/mL, p<0.001). The sensitivity, specificity and AUC for detecting serosal invasion were 77.1%, 79.2% and 0.89 at an IC threshold of 0.25 mg/mL for AP images; and 80.0%, 79.2% and 0.90 at an IC threshold of 0.45 mg/mL for PVP images. These results indicated that Iodine quantification in perigastric fat using DECT is an accurate method for detecting serosal invasion by gastric cancer. PMID:26372042

  15. Selection of Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Three Types of Rat Adipose Tissue.

    PubMed

    Zhang, Wan-Xia; Fan, Jie; Ma, Jing; Rao, Yi-Song; Zhang, Li; Yan, You-E

    2016-06-22

    Quantitative real-time PCR (qRT-PCR) is the most classical technique in the field of gene expression study. This method requires an appropriate reference gene to normalize mRNA levels. In this study, the expression stability of four frequently-used reference genes in epididymal white adipose tissue (eWAT), inguinal beige adipose tissue (iBeAT) and brown adipose tissue (BAT) from obese and lean rats were evaluated by geNorm, NormFinder and BestKeeper. Based on the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, the two most stable reference genes were recommended in each type of adipose tissue. Two target genes were applied to test the stability of the reference genes. The geNorm and NormFinder results revealed that GAPDH and 36B4 exhibited the highest expression stabilities in eWAT, while 36B4 and β-actin had the highest expression stabilities in iBeAT and BAT. According to the results of the BestKeeper analysis, 36B4 was the most stable gene in eWAT, iBeAT and BAT, in terms of the coefficient of variance. In terms of the coefficient of correlation, GAPDH, 36B4 and β-actin were the most stable genes in eWAT, iBeAT and BAT, respectively. Additionally, expected results and statistical significance were obtained using a combination of two suitable reference genes for data normalization. In conclusion, 36B4 and GAPDH, in combination, are the best reference genes for eWAT, while 36B4 and β-actin are two most suitable reference genes for both iBeAT and BAT. We recommend using these reference genes accordingly.

  16. A single standardized practical training for surgical scrubbing according to EN1500: Effect Quantification, value of the standardized method and comparison with clinical reference groups

    PubMed Central

    Fichtner, Andreas; Haupt, Elke; Karwath, Tobias; Wullenk, Katharina; Pöhlmann, Christoph; Jatzwauk, Lutz

    2013-01-01

    The standardized training of practical competences in skills labs is relatively new among German Medical Faculties. The broad acceptance and outstanding evaluation results do not provide objective data on the efficiency and cost-efficiency of these trainings. This study aims on the quantification of the teaching effect of the surgical scrubbing technique EN1500 and its comparison with clinical references of OR personnel. Methods: 161 4th year medical students were randomized into intervention and control group. The intervention group received a 45 minute standardized peer-teaching training of practical competences necessary in the OR including the scrubbing according to EN1500. Fluorescence dye was mixed in the disinfectant solution. After hand disinfection, standardized fotographs and semi-automated digital processing resulted in quantification of the insufficiently covered hand area. These results were compared with the control group that received the training after the test. In order to provide information on the achieved clinical competence level, the results were compared with the two clinical reference groups. Results: The intervention group remained with 4,99% (SD 2,34) insufficiently covered hand area after the training compared to the control group 7,33% (SD 3,91), p<0,01. There was no significant difference between control group and reference groups: surgeons 9,32% (SD 4,97), scrub nurses 8,46% (SD 4,66). The student intervention group showed results that were significantly better than the clinical references. The methodic mistake remained negligible. In the sub-group analysis, the students with low or medium experience in surgical scrubbing and hand disinfection derived highest benefit from the training, whereas students with no or high experience did benefit less. All participants showed better results on hand palms compared to back of hand areas. Discussion: A single standardized peer-teaching of surgical scrubbing and hand disinfection according to EN

  17. Reference-free quantification of EEG spectra: combining current source density (CSD) and frequency principal components analysis (fPCA).

    PubMed

    Tenke, Craig E; Kayser, Jürgen

    2005-12-01

    Definition of appropriate frequency bands and choice of recording reference limit the interpretability of quantitative EEG, which may be further compromised by distorted topographies or inverted hemispheric asymmetries when employing conventional (non-linear) power spectra. In contrast, fPCA factors conform to the spectral structure of empirical data, and a surface Laplacian (2-dimensional CSD) simplifies topographies by minimizing volume-conducted activity. Conciseness and interpretability of EEG and CSD fPCA solutions were compared for three common scaling methods. Resting EEG and CSD (30 channels, nose reference, eyes open/closed) from 51 healthy and 93 clinically-depressed adults were simplified as power, log power, and amplitude spectra, and summarized using unrestricted, Varimax-rotated, covariance-based fPCA. Multiple alpha factors were separable from artifact and reproducible across subgroups. Power spectra produced numerous, sharply-defined factors emphasizing low frequencies. Log power spectra produced fewer, broader factors emphasizing high frequencies. Solutions for amplitude spectra showed optimal intermediate tuning, particularly when derived from CSD rather than EEG spectra. These solutions were topographically distinct, detecting multiple posterior alpha generators but excluding the dorsal surface of the frontal lobes. Instead a low alpha/theta factor showed a secondary topography along the frontal midline. CSD amplitude spectrum fPCA solutions provide simpler, reference-independent measures that more directly reflect neuronal activity. A new quantitative EEG approach affording spectral components is developed that closely parallels the concept of an ERP component in the temporal domain.

  18. High-throughput Method Development for Sensitive, Accurate and Reproducible Quantification of Therapeutic Monoclonal Antibodies in Tissues Using Orthogonal Array Optimization and Nano-LC/SRM-MS

    PubMed Central

    Duan, Xiaotao; Abuqayyas, Lubna; Dai, Lipeng; Balthasar, Joseph P.; Qu, Jun

    2012-01-01

    Although liquid chromatography/mass spectrometry using selected reaction monitoring (LC/SRM-MS) holds great promise for targeted protein analysis, quantification of therapeutic monoclonal antibody (mAb) in tissues represents a daunting challenge due to the extremely-low tissue levels, complexity of tissue matrices, and the absence of an efficient strategy to develop an optimal LC/SRM-MS method. Here we describe a high-throughput, streamlined strategy for the development of sensitive, selective and reliable quantitative methods of mAb in tissue matrices. A sensitive nano-LC/nanospray-MS method was employed to achieve a low lower limit of quantification (LOQ). For selection of signature peptides (SP), the SP candidates were identified by a high-resolution Orbitrap and then optimal SRM conditions for each candidate were obtained using a high-throughput, on-the-fly orthogonal array optimization (OAO) strategy, which is capable of optimizing a large set of SP candidates within a single nano-LC/SRM-MS run. Using the optimized conditions, the candidates were experimentally evaluated for both sensitivity and stability in the target matrices and SP selection was based on the results of the evaluation. Two unique SPs, respectively from the light and heavy chain, were chosen for quantification of each mAb. The use of two SP improves the quantitative reliability by gauging possible degradation/modification of the mAb. Standard mAb proteins with verified purities were utilized for calibration curves, to prevent the quantitative biases that may otherwise occur when synthesized peptides were used as calibrators. We showed a proof of concept by rapidly developing sensitive nano-LC/SRM-MS methods for quantifying two mAb (8c2 and cT84.66) in multiple preclinical tissues. High sensitivity was achieved for both mAb with LOQ ranged from 0.156 to 0.312 μg/g across different tissues, and the overall procedure showed a wide dynamic range (≥500 fold), good accuracy (RE<18.8%) and

  19. A micro-QuEChERS method coupled to GC-MS for the quantification of pesticides in specific maternal and fetal tissues.

    PubMed

    Brandhonneur, N; De Sousa Mendes, M; Lepvrier, E; Flejou Esseiva, E; Chevanne, F; Le Corre, P

    2015-02-01

    The aim of this study was to establish a new QuEChERS (quick, easy, cheap, effective, rugged and safe) method coupled to gas chromatography-mass spectrometry (GC-MS) detection for the evaluation of the pesticide biodistribution in specific maternal and fetal tissues. This method was validated for the quantification of pesticides such as chlorotriazines (atrazine, simazine and propazine), their chlorinated metabolites (DIA, DEA and DACT). This new QuEChERS method was developed to facilitate extraction from small tissues such as fetal tissues (mean value: 200mg). The limits of detection, quantification, recovery, precision and accuracy were evaluated for different tissues (liver and brain) and blood. LOD and LOQ ranged between 0.34 and 3.27 ng/g and 1.04 to 9.91 ng/g, respectively. Recovery exceeded 80% for all pesticides, except DACT, with an associated RSD<15%. Precision and accuracy satisfied the criteria usually applied in the validation of bioanalytical methods. The results obtained indicate that this technique is suitable for use in studies of the biodistribution of pesticides in fetal tissues and can be used to evaluate the risk of exposure to pesticides during gestation. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Laser capture microdissection of intestinal tissue from sea bass larvae using an optimized RNA integrity assay and validated reference genes.

    PubMed

    Schaeck, M; De Spiegelaere, W; De Craene, J; Van den Broeck, W; De Spiegeleer, B; Burvenich, C; Haesebrouck, F; Decostere, A

    2016-02-17

    The increasing demand for a sustainable larviculture has promoted research regarding environmental parameters, diseases and nutrition, intersecting at the mucosal surface of the gastrointestinal tract of fish larvae. The combination of laser capture microdissection (LCM) and gene expression experiments allows cell specific expression profiling. This study aimed at optimizing an LCM protocol for intestinal tissue of sea bass larvae. Furthermore, a 3'/5' integrity assay was developed for LCM samples of fish tissue, comprising low RNA concentrations. Furthermore, reliable reference genes for performing qPCR in larval sea bass gene expression studies were identified, as data normalization is critical in gene expression experiments using RT-qPCR. We demonstrate that a careful optimization of the LCM procedure allows recovery of high quality mRNA from defined cell populations in complex intestinal tissues. According to the geNorm and Normfinder algorithms, ef1a, rpl13a, rps18 and faua were the most stable genes to be implemented as reference genes for an appropriate normalization of intestinal tissue from sea bass across a range of experimental settings. The methodology developed here, offers a rapid and valuable approach to characterize cells/tissues in the intestinal tissue of fish larvae and their changes following pathogen exposure, nutritional/environmental changes, probiotic supplementation or a combination thereof.

  1. Laser capture microdissection of intestinal tissue from sea bass larvae using an optimized RNA integrity assay and validated reference genes

    PubMed Central

    Schaeck, M.; De Spiegelaere, W.; De Craene, J.; Van den Broeck, W.; De Spiegeleer, B.; Burvenich, C.; Haesebrouck, F.; Decostere, A.

    2016-01-01

    The increasing demand for a sustainable larviculture has promoted research regarding environmental parameters, diseases and nutrition, intersecting at the mucosal surface of the gastrointestinal tract of fish larvae. The combination of laser capture microdissection (LCM) and gene expression experiments allows cell specific expression profiling. This study aimed at optimizing an LCM protocol for intestinal tissue of sea bass larvae. Furthermore, a 3′/5′ integrity assay was developed for LCM samples of fish tissue, comprising low RNA concentrations. Furthermore, reliable reference genes for performing qPCR in larval sea bass gene expression studies were identified, as data normalization is critical in gene expression experiments using RT-qPCR. We demonstrate that a careful optimization of the LCM procedure allows recovery of high quality mRNA from defined cell populations in complex intestinal tissues. According to the geNorm and Normfinder algorithms, ef1a, rpl13a, rps18 and faua were the most stable genes to be implemented as reference genes for an appropriate normalization of intestinal tissue from sea bass across a range of experimental settings. The methodology developed here, offers a rapid and valuable approach to characterize cells/tissues in the intestinal tissue of fish larvae and their changes following pathogen exposure, nutritional/environmental changes, probiotic supplementation or a combination thereof. PMID:26883391

  2. A certified plasmid reference material for the standardisation of BCR-ABL1 mRNA quantification by real-time quantitative PCR.

    PubMed

    White, H; Deprez, L; Corbisier, P; Hall, V; Lin, F; Mazoua, S; Trapmann, S; Aggerholm, A; Andrikovics, H; Akiki, S; Barbany, G; Boeckx, N; Bench, A; Catherwood, M; Cayuela, J-M; Chudleigh, S; Clench, T; Colomer, D; Daraio, F; Dulucq, S; Farrugia, J; Fletcher, L; Foroni, L; Ganderton, R; Gerrard, G; Gineikienė, E; Hayette, S; El Housni, H; Izzo, B; Jansson, M; Johnels, P; Jurcek, T; Kairisto, V; Kizilors, A; Kim, D-W; Lange, T; Lion, T; Polakova, K M; Martinelli, G; McCarron, S; Merle, P A; Milner, B; Mitterbauer-Hohendanner, G; Nagar, M; Nickless, G; Nomdedéu, J; Nymoen, D A; Leibundgut, E O; Ozbek, U; Pajič, T; Pfeifer, H; Preudhomme, C; Raudsepp, K; Romeo, G; Sacha, T; Talmaci, R; Touloumenidou, T; Van der Velden, V H J; Waits, P; Wang, L; Wilkinson, E; Wilson, G; Wren, D; Zadro, R; Ziermann, J; Zoi, K; Müller, M C; Hochhaus, A; Schimmel, H; Cross, N C P; Emons, H

    2015-02-01

    Serial quantification of BCR-ABL1 mRNA is an important therapeutic indicator in chronic myeloid leukaemia, but there is a substantial variation in results reported by different laboratories. To improve comparability, an internationally accepted plasmid certified reference material (CRM) was developed according to ISO Guide 34:2009. Fragments of BCR-ABL1 (e14a2 mRNA fusion), BCR and GUSB transcripts were amplified and cloned into pUC18 to yield plasmid pIRMM0099. Six different linearised plasmid solutions were produced with the following copy number concentrations, assigned by digital PCR, and expanded uncertainties: 1.08±0.13 × 10(6), 1.08±0.11 × 10(5), 1.03±0.10 × 10(4), 1.02±0.09 × 10(3), 1.04±0.10 × 10(2) and 10.0±1.5 copies/μl. The certification of the material for the number of specific DNA fragments per plasmid, copy number concentration of the plasmid solutions and the assessment of inter-unit heterogeneity and stability were performed according to ISO Guide 35:2006. Two suitability studies performed by 63 BCR-ABL1 testing laboratories demonstrated that this set of 6 plasmid CRMs can help to standardise a number of measured transcripts of e14a2 BCR-ABL1 and three control genes (ABL1, BCR and GUSB). The set of six plasmid CRMs is distributed worldwide by the Institute for Reference Materials and Measurements (Belgium) and its authorised distributors (https://ec.europa.eu/jrc/en/reference-materials/catalogue/; CRM code ERM-AD623a-f).

  3. Validated comprehensive analytical method for quantification of coenzyme A activated compounds in biological tissues by online solid-phase extraction LC/MS/MS.

    PubMed

    Magnes, Christoph; Suppan, Maria; Pieber, Thomas R; Moustafa, Tarek; Trauner, Michael; Haemmerle, Guenter; Sinner, Frank M

    2008-08-01

    We report a robust, reliable, and comprehensive analytical method for the identification and quantification of the entire class of coenzyme A (CoA) activated substances, particularly short-, medium-, and long-chain acyl-CoAs derived from various biological tissues. This online SPE-LC/MS/MS-based method is characterized by a simple three-step sample preparation: (1) addition of buffer, organic solvents, and internal standards; (2) homogenization; and (3) centrifugation. The supernatant is injected directly into the SPE-LC/MS/MS system. Identification of CoA activated compounds is performed by accurate mass determination within the HPLC run. Method validation for short-, medium-, and long-chain acyl-CoA fatty acids revealed excellent quality. Accuracy was found to be between 87 and 107% and precision was between 0.1 and 12.8% in mouse skeletal muscle. The lower limit of quantification for all investigated compounds was well below 3.1% of estimated physiological levels in 200 mg of mouse tissue. Comparable results were obtained for mouse liver, mouse brown white adipose tissue and rat liver. For all investigated tissues, no matrix effect was observed.

  4. X-ray microtomography (micro-CT): a reference technology for high-resolution quantification of xylem embolism in trees.

    PubMed

    Cochard, H; Delzon, S; Badel, E

    2015-01-01

    As current methods for measuring xylem embolism in trees are indirect and prone to artefacts, there is an ongoing controversy over the capacity of trees to resist or recover from embolism. The debate will not end until we get direct visualization of the vessel content. Here, we propose desktop X-ray microtomography (micro-CT) as a reference direct technique to quantify xylem embolism and thus validate more widespread measurements based upon either hydraulic or acoustic methods. We used desktop micro-CT to measure embolism levels in dehydrated or centrifuged shoots of laurel - a long-vesseled species thought to display daily cycles of embolism formation and refilling. Our direct observations demonstrate that this Mediterranean species is highly resistant to embolism and is not vulnerable to drought-induced embolism in a normal range of xylem tensions. We therefore recommend that embolism studies in long-vesseled species should be validated by direct methods such as micro-CT to clear up any misunderstandings on their physiology.

  5. Preparation and analysis of a frozen mussel tissue reference material for the determination of trace organic constituents

    SciTech Connect

    Wise, S.A.; Benner, B.A. Jr.; Christensen, R.G.; Koster, B.J.; Kurz, J.; Schantz, M.M.; Zeisler, R. )

    1991-10-01

    A new mussel tissue Standard Reference Material (SRM) has been prepared and analyzed for trace organic and inorganic constituents. SRM 1974 (Organics in Mussel Tissue (Mytilus edulis)) is a frozen mussel tissue homogenate that has been certified for the concentrations of nine polycyclic aromatic hydrocarbons (PAHs) from results obtained from gas chromatography-mass spectrometry and reversed-phase liquid chromatography with fluorescence detection. Noncertified concentrations for 19 additional PAHs are also reported. Gas chromatography with electron capture detection and gas chromatography with mass spectrometric detection were used to provide noncertified concentrations for 13 polychlorinated biphenyl congeners and 9 chlorinated pesticides. In addition to the organic contaminants, noncertified concentrations for 36 trace elements were determined primarily by instrumental neutron activation analysis. SRM 1974 is the first frozen tissue SRM for environmental measurements of organic and inorganic constituents.

  6. Different extent of hypoxic-ischemic brain damage in newborn rats: histopathology, hemodynamic, virtual touch tissue quantification and neurobehavioral observation.

    PubMed

    Wang, Si-Da; Liang, Shu-Yuan; Liao, Xin-Hong; Deng, Xiang-Fa; Chen, Yuan-Yuan; Liao, Chun-Yan; Wang, Lei; Tang, Shi; Li, Zhi-Xian

    2015-01-01

    To explore the correlation between pathological and ultrasound changes applying conventional ultrasound, Color Doppler ultrasound andVirtual Touch Tissue Quantification (VTQ) technique in newborn hypoxic-ischemic brain damage (HIBD) rat models. To provide theoretical basis for early diagnosis and treatment of HIBD neonatal. A total of 90 newborn Wistar rats were divided into ischemia, asphyxia and control group according to different HIBD molding methods. Conventional ultrasound, Color Doppler ultrasound and VTQ were applied on 3 h, 12 h, 24 h, 48 h and 72 h postoperative. After the observation of 72 h, 10 rats in each group were randomly selected for pathological specimens production. The rest rats were raised for 30 days for neuroethology detection. In ischemia group and asphyxia group, there were 4 deaths and 6 deaths in the modeling process; the mortality rate was 13.33% (4/30) and 20.00% (6/30) respectively. For ischemia group, the systoli velocity (Vs), diastolic velocity (Vd) and resistance index (RI) of right middle cerebral artery (MCA) were significantly decreased after operation (P<0.05). For asphyxia group, the Vs and RI of right MCA were significantly decreased after operation (P<0.05), while the Vd of right MCA was significantly increased after operation (P<0.05), which lead to the postoperative RI value in each time point was all significantly lower than that in ischemia group (P<0.05). For ischemia group and asphyxia group, the VTQ results increased significantly postoperative (P<0.05), and compared with ischemia group and control group, the postoperative VTQ value in each time point was all significantly higher in asphyxia group (P<0.05). The neuroethology results were significantly lower in the ischemia group and asphyxia group (P<0.05), and the results in ischemia group were significantly higher than those of asphyxia group (P<0.05). And the results are consistent with the pathological findings. There is a consistent correlation among

  7. SPM analysis of parametric (R)-[11C]PK11195 binding images: plasma input versus reference tissue parametric methods.

    PubMed

    Schuitemaker, Alie; van Berckel, Bart N M; Kropholler, Marc A; Veltman, Dick J; Scheltens, Philip; Jonker, Cees; Lammertsma, Adriaan A; Boellaard, Ronald

    2007-05-01

    (R)-[11C]PK11195 has been used for quantifying cerebral microglial activation in vivo. In previous studies, both plasma input and reference tissue methods have been used, usually in combination with a region of interest (ROI) approach. Definition of ROIs, however, can be labourious and prone to interobserver variation. In addition, results are only obtained for predefined areas and (unexpected) signals in undefined areas may be missed. On the other hand, standard pharmacokinetic models are too sensitive to noise to calculate (R)-[11C]PK11195 binding on a voxel-by-voxel basis. Linearised versions of both plasma input and reference tissue models have been described, and these are more suitable for parametric imaging. The purpose of this study was to compare the performance of these plasma input and reference tissue parametric methods on the outcome of statistical parametric mapping (SPM) analysis of (R)-[11C]PK11195 binding. Dynamic (R)-[11C]PK11195 PET scans with arterial blood sampling were performed in 7 younger and 11 elderly healthy subjects. Parametric images of volume of distribution (Vd) and binding potential (BP) were generated using linearised versions of plasma input (Logan) and reference tissue (Reference Parametric Mapping) models. Images were compared at the group level using SPM with a two-sample t-test per voxel, both with and without proportional scaling. Parametric BP images without scaling provided the most sensitive framework for determining differences in (R)-[11C]PK11195 binding between younger and elderly subjects. Vd images could only demonstrate differences in (R)-[11C]PK11195 binding when analysed with proportional scaling due to intersubject variation in K1/k2 (blood-brain barrier transport and non-specific binding).

  8. Identification of a reference gene for the quantification of mRNA and miRNA expression during skin wound healing.

    PubMed

    Etich, Julia; Bergmeier, Vera; Pitzler, Lena; Brachvogel, Bent

    2017-03-01

    Wound healing is a coordinated process to restore tissue homeostasis and reestablish the protective barrier of the skin. miRNAs may modulate the expression of target genes to contribute to repair processes, but due to the complexity of the tissue it is challenging to quantify gene expression during the distinct phases of wound repair. Here, we aimed to identify a common reference gene to quantify changes in miRNA and mRNA expression during skin wound healing. Quantitative real-time PCR and bioinformatic analysis tools were used to identify suitable reference genes during skin repair and their reliability was tested by studying the expression of mRNAs and miRNAs. Morphological assessment of wounds showed that the injury model recapitulates the distinct phases of skin repair. Non-degraded RNA could be isolated from skin and wounds and used to study the expression of non-coding small nuclear RNAs during wound healing. Among those, RNU6B was most constantly expressed during skin repair. Using this reference gene we could confirm the transient upregulation of IL-1β and PTPRC/CD45 during the early phase as well as the increased expression of collagen type I at later stages of repair and validate the differential expression of miR-204, miR-205, and miR-31 in skin wounds. In contrast to Gapdh the normalization to multiple reference genes gave a similar outcome. RNU6B is an accurate alternative normalizer to quantify mRNA and miRNA expression during the distinct phases of skin wound healing when analysis of multiple reference genes is not feasible.

  9. Evaluation of candidate reference genes for QPCR during ontogenesis and of immune-relevant tissues of European seabass (Dicentrarchus labrax).

    PubMed

    Mitter, Karin; Kotoulas, Georgios; Magoulas, Antonios; Mulero, Victor; Sepulcre, Pilar; Figueras, Antonio; Novoa, Beatrice; Sarropoulou, Elena

    2009-08-01

    The expression level of mRNA can vary significantly in different experimental conditions, such as stress, infection, developmental stage or tissue. Suitable reference genes are expected to exhibit constant expression levels. However no single gene is constitutively expressed in all cell types and under all experimental conditions. It has become clear that expression stability of the intended reference gene has to be examined before each experiment. For expression studies using quantitative real-time PCR (qPCR) at least two reference genes have to be applied. So far expression studies in the European seabass (Dicentrarchus labrax) as well as in the Gilthead seabream (Sparus aurata) have been performed with only one reference gene (S18, Ef-1 alpha or Gapdh). Though significant variations showed up in other teleost species such as the Atlantic halibut and the zebrafish affirming the need for proper normalization strategies, the present study aims at identifying suitable reference genes among nine candidates [glyceraldehyde-phosphate-dehydrogenase (Gapdh), beta-actin (two regions of beta-actin), 40S ribosomal protein S30 (Fau), ribosomal protein L13 a (L13a), beta2-tubulin (Tubb2) and tyrosine 3 monooxygenase/tryptophan 5-monooxygenase activation protein (Tyr)] for expression analysis of 8 developmental stages and a tissue panel (spleen, liver, kidney and brain) with samples infected with Nodavirus and Vibrio anguillarum in D. labrax. Besides the analysis of raw Ct-values, the gene expression stability was determined using two different software applications BestKeeper and NormFinder. According to both algorithms the best two reference genes for an appropriate normalization approach during D. labrax development are Ef-1 alpha and L13a whereas in the tissue panel Fau and L13a are recommended for qPCR normalization.

  10. Selection of Reference Genes for Gene Expression Normalization in Peucedanum praeruptorum Dunn under Abiotic Stresses, Hormone Treatments and Different Tissues.

    PubMed

    Zhao, Yucheng; Luo, Jun; Xu, Sheng; Wang, Wei; Liu, Tingting; Han, Chao; Chen, Yijun; Kong, Lingyi

    2016-01-01

    Peucedanum praeruptorum Dunn is one of the main traditional Chinese medicines producing coumarins and plenty of literatures are focused on the biosynthesis of coumarins. Quantitative real-time reverse transcription PCR (qRT-PCR) is a widely used method in studying the biosynthesis pathway and the selection of reference genes plays a crucial role in accurate normalization. To facilitate biosynthesis study of coumarins, twelve candidate reference genes were selected from the transcriptome database of P. praeruptorum according to previous studies. Then, BestKeeper, geNoFrm and NormFinder were used for selecting stably expressed reference genes in different tissues and under various stress treatments. The results indicated that, among the twelve candidate reference genes, the SAND family protein (SAND), actin 2 (ACT2), ubiquitin-conjugating enzyme 9 (UBC9), protein phosphatase 2A gene (PP2A) and polypyrimidine tract-binding protein (PTBP1) were the most stable reference genes under different experimental treatments, while glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and tubulin beta-6 (TUB6) were the least stable genes. In addition, the suitability of SAND, TIP41-like protein (TIP41), UBC9, ACT2, TUB6 and their combination as reference genes were confirmed by normalizing the expression of 1-aminocyclopropane-1-carboxylate oxidase (ACO) in different treatments. This work is the first survey of the stability of reference genes in P. praeruptorum and provides guidelines to obtain more accurate qRT-PCR results in P. praeruptorum and other plant species.

  11. Selection of Reference Genes for Gene Expression Normalization in Peucedanum praeruptorum Dunn under Abiotic Stresses, Hormone Treatments and Different Tissues

    PubMed Central

    Zhao, Yucheng; Luo, Jun; Xu, Sheng; Wang, Wei; Liu, Tingting; Han, Chao; Chen, Yijun; Kong, Lingyi

    2016-01-01

    Peucedanum praeruptorum Dunn is one of the main traditional Chinese medicines producing coumarins and plenty of literatures are focused on the biosynthesis of coumarins. Quantitative real-time reverse transcription PCR (qRT-PCR) is a widely used method in studying the biosynthesis pathway and the selection of reference genes plays a crucial role in accurate normalization. To facilitate biosynthesis study of coumarins, twelve candidate reference genes were selected from the transcriptome database of P. praeruptorum according to previous studies. Then, BestKeeper, geNoFrm and NormFinder were used for selecting stably expressed reference genes in different tissues and under various stress treatments. The results indicated that, among the twelve candidate reference genes, the SAND family protein (SAND), actin 2 (ACT2), ubiquitin-conjugating enzyme 9 (UBC9), protein phosphatase 2A gene (PP2A) and polypyrimidine tract-binding protein (PTBP1) were the most stable reference genes under different experimental treatments, while glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and tubulin beta-6 (TUB6) were the least stable genes. In addition, the suitability of SAND, TIP41-like protein (TIP41), UBC9, ACT2, TUB6 and their combination as reference genes were confirmed by normalizing the expression of 1-aminocyclopropane-1-carboxylate oxidase (ACO) in different treatments. This work is the first survey of the stability of reference genes in P. praeruptorum and provides guidelines to obtain more accurate qRT-PCR results in P. praeruptorum and other plant species. PMID:27022972

  12. Novel DNA staining method and processing technique for the quantification of undamaged double-stranded DNA in epidermal tissue sections by PicoGreen probe staining and microspectrophotometry.

    PubMed

    Gagna, Claude E; Kuo, Hon-Reen; Chan, Norman J; Mitacek, Eugene J; Spivak, Alla; Pasquariello, Tiffany D; Balgobin, Chandrika; Mukhi, Ruhayna; Lambert, W Clark

    2007-10-01

    Histotechnological processing of DNA can cause damage to and loss of DNA and can change its structure. DNA probes have severe tissue-staining limitations. New DNA probes and improved histotechnology are needed to enhance the characterization of fixed tissue-bound DNA. Our team developed a novel DNA staining technique and histotechnological processing procedure that improves tissue-bound DNA retention and the qualification and quantification of intact double-stranded (ds)-B-DNA. We used the ultrasensitive PicoGreen ds-DNA probe for the histochemical characterization of ds-DNA. Fifteen fixatives were examined to determine which were best for preventing DNA denaturation and retaining original DNA content and structures. Our use of a microwave-vacuum oven reduced heating temperatures, shortened heating and processing times, and enhanced fixation. We achieved better qualitative and quantitative results by using superior tissue-acquisition techniques (e.g., reduced prefixation times) and improved histotechnology. We also compared our novel approach with archival tissues, delayed fixation, less sophisticated and conventional histological processing techniques, and by experimenting with preservation of tissue-bound ds-Z-DNA. Results demonstrate that our histotechnological procedure and nucleic acid staining method significantly improve the retention of intact, undamaged ds-DNA which, in turn, allows the investigator to more precisely quantify the content and structures of unaltered and undamaged tissue-bound ds-B-DNA.

  13. Reference Tissue-Based Kinetic Evaluation of 18F-AV-1451 for Tau Imaging.

    PubMed

    Baker, Suzanne L; Lockhart, Samuel N; Price, Julie C; He, Mark; Huesman, Ronald H; Schonhaut, Daniel; Faria, Jamie; Rabinovici, Gil; Jagust, William J

    2017-02-01

    The goal of this paper was to evaluate the in vivo kinetics of the novel tau-specific PET radioligand (18)F-AV-1451 in cognitively healthy control (HC) and Alzheimer disease (AD) subjects, using reference region analyses.

  14. Combined quantification of corticotropin-releasing hormone, cortisol-to-cortisone ratio and progesterone by liquid chromatography-Tandem mass spectrometry in placental tissue.

    PubMed

    Fahlbusch, Fabian B; Ruebner, Matthias; Rascher, Wolfgang; Rauh, Manfred

    2013-09-01

    With mid-gestation the production of placental corticotropin-releasing hormone (CRH) starts to steadily increase. The fetal peptide CRH excerts direct functions at the feto-maternal interface (vasodilatation, timing of birth) via its interaction with progesterone and indirectly ensures maturation and growth of fetal organ systems for delivery by driving fetal cortisol production via its induction of adrenocorticotropic hormone release. This feedback loop is tightly controlled by the amount of enzymatic cortisol/cortisone turnover in the placental syncytiotrophoblast by 11β-hydroxy-steroid dehydrogenase type 2 (11β-HSD2). Traditionally, placental tissue hormones have been quantified by immunological methods (e.g. RIA or ELISA), which have the drawback of possible cross-reactivity and tissue perturbations. Most importantly, it is not possible to quantify CRH and steroid hormones, such as cortisol, cortisone and progesterone together in the same sample with these methods. Hence, we aimed to develop and validate a quantitative mass spectrometry (MS) method for multi-modal quantification of these placental hormones: While CRH was readily detectable throughout the placenta, the placental levels of progesterone and especially cortisol and cortisone were higher at the placental base facing the maternal side. The HPLC-MS/MS procedure showed excellent selectivity and sufficient limit of quantification in placental tissue homogenates to allow for simultaneous detection of CRH, cortisol and cortisone, and progesterone. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Reference tissue normalization in longitudinal (18)F-florbetapir positron emission tomography of late mild cognitive impairment.

    PubMed

    Shokouhi, Sepideh; Mckay, John W; Baker, Suzanne L; Kang, Hakmook; Brill, Aaron B; Gwirtsman, Harry E; Riddle, William R; Claassen, Daniel O; Rogers, Baxter P

    2016-01-15

    Semiquantitative methods such as the standardized uptake value ratio (SUVR) require normalization of the radiotracer activity to a reference tissue to monitor changes in the accumulation of amyloid-β (Aβ) plaques measured with positron emission tomography (PET). The objective of this study was to evaluate the effect of reference tissue normalization in a test-retest (18)F-florbetapir SUVR study using cerebellar gray matter, white matter (two different segmentation masks), brainstem, and corpus callosum as reference regions. We calculated the correlation between (18)F-florbetapir PET and concurrent cerebrospinal fluid (CSF) Aβ1-42 levels in a late mild cognitive impairment cohort with longitudinal PET and CSF data over the course of 2 years. In addition to conventional SUVR analysis using mean and median values of normalized brain radiotracer activity, we investigated a new image analysis technique-the weighted two-point correlation function (wS2)-to capture potentially more subtle changes in Aβ-PET data. Compared with the SUVRs normalized to cerebellar gray matter, all cerebral-to-white matter normalization schemes resulted in a higher inverse correlation between PET and CSF Aβ1-42, while the brainstem normalization gave the best results (high and most stable correlation). Compared with the SUVR mean and median values, the wS2 values were associated with the lowest coefficient of variation and highest inverse correlation to CSF Aβ1-42 levels across all time points and reference regions, including the cerebellar gray matter. The selection of reference tissue for normalization and the choice of image analysis method can affect changes in cortical (18)F-florbetapir uptake in longitudinal studies.

  16. Cricoarytenoid Articulation in Elderly Japanese With Special Reference to Morphology of the Synovial Tissue.

    PubMed

    Kawamoto-Hirano, Ai; Honkura, Yohei; Shibata, Shunichi; Abe, Shin-ichi; Murakami, Gen; Katori, Yukio

    2016-03-01

    To clarify composite fibers and cells in the synovial tissues of the cricoarytenoid joint (CA joint). Routine histology and immunohistrochemistry using sagittal or nearly sagittal sections obtained from 18 elderly cadaveric specimens. The CA joint capsule was thin and contained few elastic fibers. A limited supportive ligament, namely, a thickened fascia of the posterior cricoarytenoid muscles, was sometimes evident on the lateral aspect of the CA joint. However, even in the weaker medial aspect of the joint, no marked destruction of the synovial tissues was found. The CA joint always contained synovial folds--a short medial fold and long lateral folds--but these contained no or few macrophages, lymphocytes, and blood capillaries. In 2 exceptional specimens showing inflammatory cell infiltration in the submucosal tissue of the larynx, the macrophage-rich area extended toward the capsule and medial synovial fold. The lateral aspect of the CA joint was likely to be supported mechanically by the muscle-associated tissues. Strong support of the arytenoid by muscles might reduce the degree of CA joint injury with age. However, some patients with hoarseness due to mucosal inflammation of the larynx might have accompanying synovitis and subsequent cartilage injury in the CA joint. © The Author(s) 2015.

  17. Development of an indirect competitive enzyme-linked immunosorbent assay applied to the Botrytis cinerea quantification in tissues of postharvest fruits

    PubMed Central

    2011-01-01

    Background Botrytis cinerea is a phytopathogenic fungus responsible for the disease known as gray mold, which causes substantial losses of fruits at postharvest. This fungus is present often as latent infection and an apparently healthy fruit can deteriorate suddenly due to the development of this infection. For this reason, rapid and sensitive methods are necessary for its detection and quantification. This article describes the development of an indirect competitive enzyme-linked immunosorbent assay (ELISA) for quantification of B. cinerea in apple (Red Delicious), table grape (pink Moscatel), and pear (William's) tissues. Results The method was based in the competition for the binding site of monoclonal antibodies between B. cinerea antigens present in fruit tissues and B. cinerea purified antigens immobilized by a crosslinking agent onto the surface of the microtiter plates. The method was validated considering parameters such as selectivity, linearity, precision, accuracy and sensibility. The calculated detection limit was 0.97 μg mL-1 B. cinerea antigens. The immobilized antigen was perfectly stable for at least 4 months assuring the reproducibility of the assay. The fungus was detected and quantified in any of the fruits tested when the rot was not visible yet. Results were compared with a DNA quantification method and these studies showed good correlation. Conclusions The developed method allowed detects the presence of B. cinerea in asymptomatic fruits and provides the advantages of low cost, easy operation, and short analysis time determination for its possible application in the phytosanitary programs of the fruit industry worldwide. PMID:21970317

  18. How important is tumour shape? Quantification of the epithelial-connective tissue interface in oral lesions using local connected fractal dimension analysis.

    PubMed

    Landini, G; Rippin, J W

    1996-06-01

    Quantification of the local complexity of the epithelial-connective tissue interface (ECTI) in normal mucosa, epithelial dysplasia, and squamous cell carcinoma of the floor of the mouth was investigated by estimating the local connected fractal dimension in tissue profiles from histological sections. The use of certain parameters of the distribution of the local connected fractal dimensions of the ECTI classifies the cases belonging to these three histopathological diagnoses with 85 per cent accuracy by means of linear discriminant analysis. The values of the local fractal dimension were also used to produce colour-coded dimensional images of the ECTI, to highlight locations with higher irregularity that may correlate with locally invasive 'higher-risk' areas.

  19. Dual energy computed tomography for quantification of tissue urate deposits in tophaceous gout: help from modern physics in the management of an ancient disease.

    PubMed

    Bacani, A Kirstin; McCollough, Cynthia H; Glazebrook, Katrina N; Bond, Jeffrey R; Michet, Clement J; Milks, Jeffrey; Manek, Nisha J

    2012-01-01

    Gout has been recognized for centuries but is also a modern day scourge. It is the most common type of inflammatory arthritis in men and appears to be increasing in both incidence and prevalence (Arromdee et al. in J Rheumatol 29(11):2403-2406, 2002). Despite these facts, few advances have been made in the diagnosis and treatment of gout for over 50 years. Difficult cases of gout challenge available therapeutic options. It is only recently that the Food and Drug Administration has approved febuxostat as a treatment option for patients intolerant of allopurinol. We describe a difficult case of tophaceous gout notable for several reasons: utilization of rasburicase as uricolytic treatment to dramatically reduce tissue urate burden; treatment of gout flares with interleukin-1β inhibition; and quantification of tissue urate with novel dual energy computed tomography technology before and after uricolytic therapy.

  20. Stable isotope dilution HILIC-MS/MS method for accurate quantification of glutamic acid, glutamine, pyroglutamic acid, GABA and theanine in mouse brain tissues.

    PubMed

    Inoue, Koichi; Miyazaki, Yasuto; Unno, Keiko; Min, Jun Zhe; Todoroki, Kenichiro; Toyo'oka, Toshimasa

    2016-01-01

    In this study, we developed the stable isotope dilution hydrophilic interaction liquid chromatography with tandem mass spectrometry (HILIC-MS/MS) technique for the accurate, reasonable and simultaneous quantification of glutamic acid (Glu), glutamine (Gln), pyroglutamic acid (pGlu), γ-aminobutyric acid (GABA) and theanine in mouse brain tissues. The quantification of these analytes was accomplished using stable isotope internal standards and the HILIC separating mode to fully correct the intramolecular cyclization during the electrospray ionization. It was shown that linear calibrations were available with high coefficients of correlation (r(2)  > 0.999, range from 10 pmol/mL to 50 mol/mL). For application of the theanine intake, the determination of Glu, Gln, pGlu, GABA and theanine in the hippocampus and central cortex tissues was performed based on our developed method. In the region of the hippocampus, the concentration levels of Glu and pGlu were significantly reduced during reality-based theanine intake. Conversely, the concentration level of GABA increased. This result showed that transited theanine has an effect on the metabolic balance of Glu analogs in the hippocampus. Copyright © 2015 John Wiley & Sons, Ltd.

  1. Wavefront aberration measurements and corrections through thick tissue using fluorescent microsphere reference beacons.

    PubMed

    Azucena, Oscar; Crest, Justin; Cao, Jian; Sullivan, William; Kner, Peter; Gavel, Donald; Dillon, Daren; Olivier, Scot; Kubby, Joel

    2010-08-02

    We present a new method to directly measure and correct the aberrations introduced when imaging through thick biological tissue. A Shack-Hartmann wavefront sensor is used to directly measure the wavefront error induced by a Drosophila embryo. The wavefront measurements are taken by seeding the embryo with fluorescent microspheres used as "artificial guide-stars." The wavefront error is corrected in ten millisecond steps by applying the inverse to the wavefront error on a micro-electro-mechanical deformable mirror in the image path of the microscope. The results show that this new approach is capable of improving the Strehl ratio by 2 times on average and as high as 10 times when imaging through 100 microm of tissue. The results also show that the isoplanatic half-width is approximately 19 microm resulting in a corrected field of view 38 microm in diameter around the guide-star.

  2. Wavefront aberration measurements and corrections through thick tissue using fluorescent microsphere reference beacons

    PubMed Central

    Azucena, Oscar; Crest, Justin; Cao, Jian; Sullivan, William; Kner, Peter; Gavel, Donald; Dillon, Daren; Olivier, Scot; Kubby, Joel

    2010-01-01

    We present a new method to directly measure and correct the aberrations introduced when imaging through thick biological tissue. A Shack-Hartmann wavefront sensor is used to directly measure the wavefront error induced by a Drosophila embryo. The wavefront measurements are taken by seeding the embryo with fluorescent microspheres used as “artificial guide-stars.” The wavefront error is corrected in ten millisecond steps by applying the inverse to the wavefront error on a micro-electro-mechanical deformable mirror in the image path of the microscope. The results show that this new approach is capable of improving the Strehl ratio by 2 times on average and as high as 10 times when imaging through 100 μm of tissue. The results also show that the isoplanatic half-width is approximately 19 μm resulting in a corrected field of view 38 μm in diameter around the guide-star. PMID:20721137

  3. Cricothyroid Articulation in Elderly Japanese With Special Reference to Morphology of the Synovial and Capsular Tissues.

    PubMed

    Kawamoto, Ai; Honkura, Yohei; Suzuki, Ryoji; Abe, Hiroshi; Abe, Shin-Ichi; Murakami, Gen; Katori, Yukio

    2016-09-01

    The present study aimed to clarify individual variations in the cricothyroid joint (CT joint). Using 30 specimens of the CT joint obtained from elderly donated cadavers, we examined the composite fibers of the capsular ligament as well as the morphology of the synovial tissue. The capsular ligament consistently contained abundant thick elastic fiber bundles on the anterior side of the joint (anterior band) and an elastic fiber-made mesh on the posterior side (posterior mesh). The synovial membrane, lined by synovial macrophages, was usually restricted to the recesses in the medial or inferior end of the joint cavity. Without the synovial lining, elastic fibers of the capsular ligament were subsequently detached, dispersed, and exposed to the joint cavity. We also observed a folded and thickened synovial membrane and a hypertrophic protrusion of the capsular ligament. In six specimens, the joint cavity was obliterated by debris of synovial folds and elastic fiber-rich tissues continuous with the usual capsular ligament. Notably, with the exception of two specimens, we did not find lymphocyte infiltration in the degenerative synovial tissue. We considered the CT joint degeneration to be a specific, silent form of osteoarthritis from the absence of lymphocyte infiltration. For high-pitched phonation, the elderly CT joint seemed to maintain its anterior gliding and rotation with the aid of elastic fiber-rich tissues compensating for the loss of congruity between the joint cartilage surfaces. Conversely, however, high-pitched phonation may accelerate obliteration of the joint. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  4. NOISE 2 imaging system: seeing through scattering tissue with a reference point

    NASA Astrophysics Data System (ADS)

    Abookasis, David; Rosen, Joseph

    2004-05-01

    We propose a fly-eye-like imaging system for seeing objects embedded in scattering media. Objects are recovered from many speckled images observed by a digital camera through a microlens array. Each microlens in the array generates a speckle image of the object buried between two layers of chicken breast tissue. In the computer each image is Fourier transformed jointly with an image of the speckled pointlike source captured under the same conditions. A set of the squared magnitudes of the Fourier-transformed pictures is accumulated to form a single average picture. This final picture is again Fourier transformed, resulting in the reconstruction of the hidden object.

  5. Identification of Reference Genes for Quantitative Real Time PCR Assays in Aortic Tissue of Syrian Hamsters with Bicuspid Aortic Valve

    PubMed Central

    Rueda-Martínez, Carmen; Fernández, M. Carmen; Soto-Navarrete, María Teresa; Jiménez-Navarro, Manuel; Durán, Ana Carmen; Fernández, Borja

    2016-01-01

    Bicuspid aortic valve (BAV) is the most frequent congenital cardiac malformation in humans, and appears frequently associated with dilatation of the ascending aorta. This association is likely the result of a common aetiology. Currently, a Syrian hamster strain with a relatively high (∼40%) incidence of BAV constitutes the only spontaneous animal model of BAV disease. The characterization of molecular alterations in the aorta of hamsters with BAV may serve to identify pathophysiological mechanisms and molecular markers of disease in humans. In this report, we evaluate the expression of ten candidate reference genes in aortic tissue of hamsters in order to identify housekeeping genes for normalization using quantitative real time PCR (RT-qPCR) assays. A total of 51 adult (180–240 days old) and 56 old (300–440 days old) animals were used. They belonged to a control strain of hamsters with normal, tricuspid aortic valve (TAV; n = 30), or to the affected strain of hamsters with TAV (n = 45) or BAV (n = 32). The expression stability of the candidate reference genes was determined by RT-qPCR using three statistical algorithms, GeNorm, NormFinder and Bestkeeper. The expression analyses showed that the most stable reference genes for the three algorithms employed were Cdkn1β, G3pdh and Polr2a. We propose the use of Cdkn1β, or both Cdkn1β and G3pdh as reference genes for mRNA expression analyses in Syrian hamster aorta. PMID:27711171

  6. Identification of Reference Genes for Quantitative Real Time PCR Assays in Aortic Tissue of Syrian Hamsters with Bicuspid Aortic Valve.

    PubMed

    Rueda-Martínez, Carmen; Fernández, M Carmen; Soto-Navarrete, María Teresa; Jiménez-Navarro, Manuel; Durán, Ana Carmen; Fernández, Borja

    2016-01-01

    Bicuspid aortic valve (BAV) is the most frequent congenital cardiac malformation in humans, and appears frequently associated with dilatation of the ascending aorta. This association is likely the result of a common aetiology. Currently, a Syrian hamster strain with a relatively high (∼40%) incidence of BAV constitutes the only spontaneous animal model of BAV disease. The characterization of molecular alterations in the aorta of hamsters with BAV may serve to identify pathophysiological mechanisms and molecular markers of disease in humans. In this report, we evaluate the expression of ten candidate reference genes in aortic tissue of hamsters in order to identify housekeeping genes for normalization using quantitative real time PCR (RT-qPCR) assays. A total of 51 adult (180-240 days old) and 56 old (300-440 days old) animals were used. They belonged to a control strain of hamsters with normal, tricuspid aortic valve (TAV; n = 30), or to the affected strain of hamsters with TAV (n = 45) or BAV (n = 32). The expression stability of the candidate reference genes was determined by RT-qPCR using three statistical algorithms, GeNorm, NormFinder and Bestkeeper. The expression analyses showed that the most stable reference genes for the three algorithms employed were Cdkn1β, G3pdh and Polr2a. We propose the use of Cdkn1β, or both Cdkn1β and G3pdh as reference genes for mRNA expression analyses in Syrian hamster aorta.

  7. Feasibility studies into the production of gamma-irradiated oyster tissue reference materials for paralytic shellfish poisoning toxins.

    PubMed

    Turner, Andrew D; Lewis, Adam M; Hatfield, Robert G; Powell, Andy L; Higman, Wendy A

    2013-09-01

    A study was conducted to assess the feasibility for the production of sterile, stable and homogenous shellfish reference materials containing known concentrations of paralytic shellfish poisoning (PSP) toxins. Pacific oysters were contaminated with toxins following mass culturing of toxic algae and shellfish feeding experiments. Live oysters were shucked and tissues homogenised, before measuring into multiple aliquots, with one batch subjected to gamma irradiation treatment and the other remaining untreated. The homogeneity of both batches of samples was assessed using a pre-column oxidation liquid chromatography with fluorescence detection (Pre-COX LC-FLD) method and shown to be within the limits of normal within-batch repeatability. A twelve-month stability experiment was conducted for both untreated and gamma irradiated batches, specifically examining the effects of long term storage at -20 °C, +4 °C and +40 °C. Results indicated mostly good stability of PSP toxins in both materials when stored frozen at -20 °C, but with the instability of GTX2&3 concentrations in the untreated tissues eliminated in the irradiated tissues. Analysis using a post-column oxidation (PCOX) LC-FLD method also showed epimerisation in both GTX1&4 and GTX2&3 epimeric pairs in untreated samples after only 6 months frozen storage. This issue was not present in the tissues irradiated before long term storage. Biological activity testing confirmed the absence of bacteria in the irradiated samples throughout the 12 month study period. With such results there was clear evidence for the potential of increasing the scale of the mass culturing and shellfish feeding for the production of large batches of tissue suitable for the preparation of a certified matrix reference material. Overall results demonstrated the feasibility for production of oyster reference materials for PSTs, with evidence for prolonged stability following gamma irradiation treatment and storage at -20 °C. Crown

  8. A new formalism for the quantification of tissue perfusion by the destruction-replenishment method in contrast ultrasound imaging.

    PubMed

    Arditi, Marcel; Frinking, Peter J A; Zhou, Xiang; Rognin, Nicolas G

    2006-06-01

    A new formalism is presented for the destruction-replenishment perfusion quantification approach at low mechanical index. On the basis of physical considerations, best-fit methods should be applied using perfusion functions with S-shape characteristics. These functions are first described for the case of a geometry with a single flow velocity, then extended to the case of vascular beds with blood vessels having multiple flow velocity values and directions. The principles guiding the analysis are, on one hand, a linearization of video echo signals to overcome the log-compression of the imaging instrument, and, on the other hand, the spatial distribution of the transmit-receive ultrasound beam in the elevation direction. An in vitro model also is described; it was used to confirm experimentally the validity of the approach using a commercial contrast agent. The approach was implemented in the form of a computer program, taking as input a sequence of contrast-specific images, as well as parameters related to the ultrasound imaging equipment used. The generated output is either flow-parameter values computed in regions-of-interest, or parametric flow-images (e.g., mean velocity, mean transit time, mean flow, flow variance, or skewness). This approach thus establishes a base for extracting information about the morphology of vascular beds in vivo, and could allow absolute quantification provided that appropriate instrument calibration is implemented.

  9. Automated quantification of adipose and skeletal muscle tissue in whole-body MRI data for epidemiological studies

    NASA Astrophysics Data System (ADS)

    Wald, Diana; Teucher, Birgit; Dinkel, Julien; Kaaks, Rudolf; Delorme, Stefan; Meinzer, Hans-Peter; Heimann, Tobias

    2012-03-01

    The ratio between the amount of adipose and skeletal muscle tissue is an important determinant of metabolic health. Recent developments in MRI technology allow whole body scans to be performed for accurate assessment of body composition. In the present study, a total of 194 participants underwent a 2-point Dixon MRI sequence of the whole body. A fully automated image segmentation method quantifies the amount of adipose and skeletal muscle tissue by applying standard image processing techniques including thresholding, region growing and morphological operators. The adipose tissue is further divided into subcutaneous and visceral adipose tissue by using statistical shape models. All images were visually inspected. The quantitative analysis was performed on 44 whole-body MRI data using manual segmentations as ground truth data. We achieved 3.3% and 6.3% of relative volume difference between the manual and automated segmentation of subcutaneous and visceral adipose tissue, respectively. The validation of skeletal muscle tissue segmentation resulted in a relative volume difference of 7.8 +/- 4.2% and a volumetric overlap error of 6.4 +/- 2.3 %. To our knowledge, we are first to present a fully automated method which quantifies adipose and skeletal muscle tissue in whole-body MRI data. Due to the fully automated approach, results are deterministic and free of user bias. Hence, the software can be used in large epidemiological studies for assessing body fat distribution and the ratio of adipose to skeletal muscle tissue in relation to metabolic disease risk.

  10. Quantification of Arachidonic Acid and Its Metabolites in Rat Tissues by UHPLC-MS/MS: Application for the Identification of Potential Biomarkers of Benign Prostatic Hyperplasia

    PubMed Central

    Bian, Qiaoxia; Wang, Weihui; Wang, Nannan; Peng, Yan; Ma, Wen; Dai, Ronghua

    2016-01-01

    To evaluate the potential relationship between benign prostatic hyperplasia (BPH) and the arachidonic acid (AA) metabolome, a UHPLC—MS/MS method has been developed and validated for simultaneous determination of AA and its cyclooxygenase(COX) and lipoxygenase(LOX) pathway metabolites (15-HETE, 12-HETE, TXA2, 5-HETE, AA, PGI2, PGF2α, 8-HETE, PGD2, PGE2 and LTB4) in rat tissues. The analytes were extracted from tissue samples with a protein precipitation procedure and then separated on a Shim-pack XR-ODSC18 column with 0.05% formic acid in water (pH adjusted with dilute ammonia) and methanol:acetonitrile (20:80, v/v). Detection was performed on a UHPLC—MS/MS system with electrospray negative ionization (ESI) and a multiple reaction-monitoring mode. The lower limits of quantification (LLOQ) were 0.25–50 ng/mL for all of the analytes in the prostate, seminal, bladder, liver and kidney tissues. The absolute recoveries of the analytes from all of the tissues were more than 50%. By means of the method developed, the AA metabolites in tissue samples from Sham and BPH group rats were determined. The eleven biomarkers in the BPH group prostate, seminal, bladder, liver and kidney tissues were significantly higher than those of the sham group, indicating that BPH fortified the inducible expression of COX and LOX, as well as increased the production of AA and eicosanoids. The method described here offers a useful tool for the evaluation of complex regulatory eicosanoids responses in vivo. PMID:27893755

  11. High resolution systematic digital histological quantification of cardiac fibrosis and adipose tissue in phospholamban p.Arg14del mutation associated cardiomyopathy.

    PubMed

    Gho, Johannes M I H; van Es, René; Stathonikos, Nikolas; Harakalova, Magdalena; te Rijdt, Wouter P; Suurmeijer, Albert J H; van der Heijden, Jeroen F; de Jonge, Nicolaas; Chamuleau, Steven A J; de Weger, Roel A; Asselbergs, Folkert W; Vink, Aryan

    2014-01-01

    Myocardial fibrosis can lead to heart failure and act as a substrate for cardiac arrhythmias. In dilated cardiomyopathy diffuse interstitial reactive fibrosis can be observed, whereas arrhythmogenic cardiomyopathy is characterized by fibrofatty replacement in predominantly the right ventricle. The p.Arg14del mutation in the phospholamban (PLN) gene has been associated with dilated cardiomyopathy and recently also with arrhythmogenic cardiomyopathy. Aim of the present study is to determine the exact pattern of fibrosis and fatty replacement in PLN p.Arg14del mutation positive patients, with a novel method for high resolution systematic digital histological quantification of fibrosis and fatty tissue in cardiac tissue. Transversal mid-ventricular slices (n = 8) from whole hearts were collected from patients with the PLN p.Arg14del mutation (age 48±16 years; 4 (50%) male). An in-house developed open source MATLAB script was used for digital analysis of Masson's trichrome stained slides (http://sourceforge.net/projects/fibroquant/). Slides were divided into trabecular, inner and outer compact myocardium. Per region the percentage of connective tissue, cardiomyocytes and fatty tissue was quantified. In PLN p.Arg14del mutation associated cardiomyopathy, myocardial fibrosis is predominantly present in the left posterolateral wall and to a lesser extent in the right ventricular wall, whereas fatty changes are more pronounced in the right ventricular wall. No difference in distribution pattern of fibrosis and adipocytes was observed between patients with a clinical predominantly dilated and arrhythmogenic cardiomyopathy phenotype. In the future, this novel method for quantifying fibrosis and fatty tissue can be used to assess cardiac fibrosis and fatty tissue in animal models and a broad range of human cardiomyopathies.

  12. The use of a reference tissue arterial input function with low-temporal-resolution DCE-MRI data

    NASA Astrophysics Data System (ADS)

    Heisen, M.; Fan, X.; Buurman, J.; van Riel, N. A. W.; Karczmar, G. S.; ter Haar Romeny, B. M.

    2010-08-01

    Pharmacokinetic modeling is a promising quantitative analysis technique for cancer diagnosis. However, diagnostic dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) of the breast is commonly performed with low temporal resolution. This limits its clinical utility. We investigated for a range of temporal resolutions whether pharmacokinetic parameter estimation is impacted by the use of data-derived arterial input functions (AIFs), obtained via analysis of dynamic data from a reference tissue, as opposed to the use of a standard AIF, often obtained from the literature. We hypothesized that the first method allows the use of data at lower temporal resolutions than the second method. Test data were obtained by downsampling high-temporal-resolution rodent data via a k-space-based strategy. To fit the basic Tofts model, either the data-derived or the standard AIF was used. The resulting estimates of Ktrans and ve were compared with the standard estimates obtained by using the original data. The deviations in Ktrans and ve, introduced when lowering temporal resolution, were more modest using data-derived AIFs compared with using a standard AIF. Specifically, lowering the resolution from 5 to 60 s, the respective changes in Ktrans were 2% (non-significant) and 18% (significant). Extracting the AIF from a reference tissue enables accurate pharmacokinetic parameter estimation for low-temporal-resolution data.

  13. Optimization of a gas chromatography-mass spectrometry method with methyl chloroformate derivatization for quantification of amino acids in plant tissue.

    PubMed

    Vancompernolle, Bram; Croes, Kim; Angenon, Geert

    2016-04-01

    Rapid, easy and reliable quantification of amino acids is crucial in research on plant amino acid metabolism and nutritional improvement of crops via enrichment of essential amino acids. A recently reported analysis method, based on solid phase extraction (SPE), derivatization with methyl chloroformate and gas chromatography-mass spectrometry was optimized and tested on three-week-old Arabidopsis thaliana leaf tissues. Optimization of the SPE cleanup yielded recovery rates of minimum 95% for all amino acids (except arginine). Variations in accuracy and precision did not exceed 12.5%, except for cysteine, histidine and tryptophane, which were excluded from analysis. Quantification of overlapping peaks for isoleucine/threonine and proline/asparagine was possible by selection of two specific fragment ions for each amino acid. Of the 16 selected amino acids, 14 were quantified successfully in at least 75% of the samples, while methionine and tyrosine were only quantifiable in 6% and 42%, respectively. A case study on the aspartate super pathway confirmed the applicability of the optimized method on wild type and genetically modified plants: external supplementation of methionine or lysine yielded a 146-fold or 27-fold increase in the respective absolute amino acid levels compared with the control treatment. Induced expression of dhdps-r1 (a mutated lysine biosynthesis gene encoding a feedback insensitive enzyme) caused an 83-fold increase in absolute lysine levels.

  14. Quantification of vitamin D and 25-hydroxyvitamin D in soft tissues by liquid chromatography-tandem mass spectrometry.

    PubMed

    Lipkie, Tristan E; Janasch, Amber; Cooper, Bruce R; Hohman, Emily E; Weaver, Connie M; Ferruzzi, Mario G

    2013-08-01

    Inadequate data on tissue distribution of vitamin D and its metabolites remains a barrier to defining health outcomes of vitamin D intake and 25-hydroxyvitamin D (25(OH)D) status. The purpose of this study was to develop a method for the analysis of vitamin D2 (ergocalciferol), vitamin D3 (cholecalciferol), 25(OH)D2, and 25(OH)D3 in soft tissues, and determine distribution in select tissues from a dose-response study of vitamin D2 and vitamin D3 in rats. Liver, gastrocnemius muscle, and epididymal fat homogenates were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) with electrospray ionization following liquid-liquid extraction, solid-phase extraction, and derivatization with 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD). A dose-response was observed in most tissues for vitamin D and 25(OH)D from both vitamers. Vitamin D concentration was greater in epididymal fat than gastrocnemius muscle and liver, but 25(OH)D concentration was not significantly different between tissues. Soft tissues of rats fed crystalline vitamin D3 had higher concentrations of total vitamin D than those of rats fed yeast-derived vitamin D2, while total 25(OH)D concentrations were similar between vitamin D sources. This method is well suited to more complete studies of vitamin D bioavailability and metabolite tissue distribution.

  15. Quantification of vitamin D and 25-hydroxyvitamin D in soft tissues by liquid chromatography—tandem mass spectrometry

    PubMed Central

    Lipkie, Tristan E.; Janasch, Amber; Cooper, Bruce R.; Hohman, Emily E.; Weaver, Connie M.; Ferruzzi, Mario G.

    2013-01-01

    Inadequate data on tissue distribution of vitamin D and its metabolites remains a barrier to defining health outcomes of vitamin D intake and 25-hydroxyvitamin D (25(OH)D) status. The purpose of this study was to develop a method for the analysis of vitamin D2 (ergocalciferol), vitamin D3 (cholecalciferol), 25(OH)D2, and 25(OH)D3 in soft tissues, and determine distribution in select tissues from a dose-response study of vitamin D2 and vitamin D3 in rats. Liver, gastrocnemius muscle, and epididymal fat homogenates were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) with electrospray ionization following liquid-liquid extraction, solid-phase extraction, and derivatization with 4-phenyl-1,2,4-triazoline-3,5-dione (PTAD). A dose-response was observed in most tissues for vitamin D and 25(OH)D from both vitamers. Vitamin D concentration was greater in epididymal fat than gastrocnemius muscle and liver, but 25(OH)D concentration was not significantly different between tissues. Soft tissues of rats fed crystalline vitamin D3 had higher concentrations of total vitamin D than those of rats fed yeast-derived vitamin D2, while total 25(OH)D concentrations were similar between vitamin D sources. This method is well suited to more complete studies of vitamin D bioavailability and metabolite tissue distribution. PMID:23811497

  16. Tissue-specific Calibration of Real-time PCR Facilitates Absolute Quantification of Plasmid DNA in Biodistribution Studies

    PubMed Central

    Ho, Joan K; White, Paul J; Pouton, Colin W

    2016-01-01

    Analysis of the tissue distribution of plasmid DNA after administration of nonviral gene delivery systems is best accomplished using quantitative real-time polymerase chain reaction (qPCR), although published strategies do not allow determination of the absolute mass of plasmid delivered to different tissues. Generally, data is expressed as the mass of plasmid relative to the mass of genomic DNA (gDNA) in the sample. This strategy is adequate for comparisons of efficiency of delivery to a single site but it does not allow direct comparison of delivery to multiple tissues, as the mass of gDNA extracted per unit mass of each tissue is different. We show here that by constructing qPCR standard curves for each tissue it is possible to determine the dose of intact plasmid remaining in each tissue, which is a more useful parameter when comparing the fates of different formulations of DNA. We exemplify the use of this tissue-specific qPCR method by comparing the delivery of naked DNA, cationic DNA complexes, and neutral PEGylated DNA complexes after intramuscular injection. Generally, larger masses of intact plasmid were present 24 hours after injection of DNA complexes, and neutral complexes resulted in delivery of a larger mass of intact plasmid to the spleen. PMID:27701400

  17. Reference ranges for regional cerebral tissue oxygen saturation and fractional oxygen extraction in neonates during immediate transition after birth.

    PubMed

    Pichler, Gerhard; Binder, Corinna; Avian, Alexander; Beckenbach, Elisabeth; Schmölzer, Georg M; Urlesberger, Berndt

    2013-12-01

    To define reference ranges for regional cerebral tissue oxygen saturation (crSO2) and regional cerebral fractional tissue oxygen extraction (cFTOE) during the first 15 minutes after birth in neonates requiring no medical support. The crSO2 was measured using near infrared spectroscopy (Invos 5100 cerebral/somatic oximeter monitor; Somanetics Corp, Troy, Michigan) during the first 15 minutes after birth for term and preterm neonates. The near infrared spectroscopy sensor was placed on the left forehead. Peripheral oxygen saturation and heart rate were continuously measured by pulse oximetry, and cFTOE was calculated. Neonates were excluded if they required any medical support. A total of 381 neonates were included: 82 term neonates after vaginal delivery, 272 term neonates after cesarean delivery, and 27 preterm neonates after cesarean delivery. In all neonates, median (10th-90th percentiles) crSO2 was 41% (23-64) at 2 minutes, 68% (45-85) at 5 minutes, 79% (65-90) at 10 minutes, and 77% (63-89) at 15 minutes of age. In all neonates, median (10th-90th percentiles) cFTOE was 33% (11-70) at 2 minutes, 21% (6-45) at 5 minutes, 15% (5-31) at 10 minutes, and 18% (7-34) at 15 minutes of age. We report reference ranges of crSO2 and cFTOE in neonates requiring no medical support during transition immediately after birth. The use of cerebral oxygenation monitoring and use of these reference ranges in neonates during transition may help to guide oxygen delivery and avoid cerebral hypo-oxygenation and hyperoxygenation. Copyright © 2013 Mosby, Inc. All rights reserved.

  18. Reliable quantification of mRNA in archived formalin-fixed tissue with or without paraffin embedding.

    PubMed

    Wang, Zhibin; Lebron, Jose A; Wolf, Jayanthi J

    2015-01-01

    Formalin fixation and paraffin embedding (FFPE) is a standard method for tissue sample storage and preservation in pathology archives. The Reverse Transcriptase Quantitative Polymerase Chain Reaction (RT-qPCR) is a useful method for gene expression analysis, but its sensitivity is significantly decreased in FFPE tissue due to the fixation process. This process results in chemical modifications of RNA, cross-links proteins to RNA, and degrades RNA in these archived samples, hindering the reverse transcription step of the conventional RT-pPCR method and preventing generation of a cDNA that is long enough for the subsequent quantitative PCR step. In this study, we used a multi-species RT-qPCR method originally developed to detect mRNA in tissue homogenate samples (Wang et al., 2011) and applied it to effectively detect a specific mRNA in formalin-fixed tissues with or without paraffin-embedding by targeting mRNA sequences as short as 24 nucleotides. Target sizes ranging from 24 to 91 nucleotides were evaluated using this multi-species RT-qPCR assay. Data generated with FFPE tissues demonstrated that use of short target sequences relieved the dependence on RNA quality and could reliably quantify mRNA. This method was highly sensitive, reproducible, and had a dynamic range of five orders of magnitude. Importantly, this method could quantify mRNA in prolonged formalin-fixed and FFPE tissue, where conventional RT-qPCR assays failed. Moreover, a similar result for small interfering RNA (siRNA)-mediated Apob mRNA knockdown was obtained from tissues fixed in formalin solution for 3months to 4years, and was found to be comparable to results obtained with frozen liver tissues. Therefore, the method presented here allows for preclinical and clinical retrospective and prospective studies on mRNA derived from archived FFPE and prolonged formalin-fixed tissue. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Long-term stability and temporal trends of organic contaminants in four collections of mussel tissue frozen standard reference materials.

    PubMed

    Schantz, Michele M; Pugh, Rebecca S; Pol, Stacy S Vander; Wise, Stephen A

    2015-04-01

    The stability of polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and chlorinated pesticides in frozen mussel tissue Standard Reference Materials (SRMs) stored at -80 °C was assessed by analyzing samples of SRM 1974, SRM 1974a, and SRM 1974b Organics in Mussel Tissue (Mytilus edulis) periodically over 25 y, 20 y, and 12 y, respectively. The most recent analyses were performed during the certification of the fourth release of this material, SRM 1974c. Results indicate the concentrations of these persistent organic pollutants have not changed during storage at -80 °C. In addition, brominated diphenyl ethers (BDEs) were quantified in each of the materials during this study. The stability information is important for on-going monitoring studies collecting large quantities of samples for future analyses (i.e., formally established specimen banking programs). Since all four mussel tissue SRMs were prepared from mussels collected at the same site in Dorchester Bay, MA, USA, the results provide a temporal trend study for these contaminants over a 17 year period (1987 to 2004).

  20. Selection of reliable reference genes for normalization of quantitative RT-PCR from different developmental stages and tissues in amphioxus

    PubMed Central

    Zhang, Qi-Lin; Zhu, Qian-Hua; Liao, Xin; Wang, Xiu-Qiang; Chen, Tao; Xu, Han-Ting; Wang, Juan; Yuan, Ming-Long; Chen, Jun-Yuan

    2016-01-01

    Amphioxus is a closest living proxy to the ancestor of cephalochordates with vertebrates, and key animal for novel understanding in the evolutionary origin of vertebrate body plan, genome, tissues and immune system. Reliable analyses using quantitative real-time PCR (qRT-PCR) for answering these scientific questions is heavily dependent on reliable reference genes (RGs). In this study, we evaluated stability of thirteen candidate RGs in qRT-PCR for different developmental stages and tissues of amphioxus by four independent (geNorm, NormFinder, BestKeeper and deltaCt) and one comparative algorithms (RefFinder). The results showed that the top two stable RGs were the following: (1) S20 and 18 S in thirteen developmental stages, (2) EF1A and ACT in seven normal tissues, (3) S20 and L13 in both intestine and hepatic caecum challenged with lipopolysaccharide (LPS), and (4) S20 and EF1A in gill challenged with LPS. The expression profiles of two target genes (EYA and HHEX) in thirteen developmental stages were used to confirm the reliability of chosen RGs. This study identified optimal RGs that can be used to accurately measure gene expression under these conditions, which will benefit evolutionary and functional genomics studies in amphioxus. PMID:27869224

  1. Separation and quantification of monothiols and phytochelatins from a wide variety of cell cultures and tissues of trees and other plants using high performance liquid chromatography.

    PubMed

    Minocha, Rakesh; Thangavel, P; Dhankher, Om Parkash; Long, Stephanie

    2008-10-17

    The HPLC method presented here for the quantification of metal-binding thiols is considerably shorter than most previously published methods. It is a sensitive and highly reproducible method that separates monobromobimane tagged monothiols (cysteine, glutathione, gamma-glutamylcysteine) along with polythiols (PC(2), PC(3), PC(4) and PC(5)) within 23min from a wide variety of samples. Total run time of the method is 35min. Detection limits for thiols is 33fmol for 10microlL injection. This method will be applicable to study the metal detoxification mechanisms for a wide variety of cell cultures and tissues of plants and trees including algae, Arabidopsis, crambe, rice, and red spruce.

  2. Calibration-free absolute quantification of optical absorption coefficients using acoustic spectra in 3D photoacoustic microscopy of biological tissue.

    PubMed

    Guo, Zijian; Hu, Song; Wang, Lihong V

    2010-06-15

    Optical absorption is closely associated with many physiological important parameters, such as the concentration and oxygen saturation of hemoglobin, and it can be used to quantify the concentrations of nonfluorescent molecules. We propose a method to use acoustic spectra of photoacoustic signals to quantify the absolute optical absorption. This method is self-calibrating and thus insensitive to variations in the optical fluence. Factors such as system bandwidth and acoustic attenuation can affect the quantification but can be canceled by dividing the acoustic spectra measured at two optical wavelengths. Using optical-resolution photoacoustic microscopy, we quantified the absolute optical absorption of black ink samples with various concentrations. We also quantified both the concentration and oxygen saturation of hemoglobin in a live mouse in absolute units.

  3. Localisation and quantification of benzalkonium chloride in eye tissue by TOF-SIMS imaging and liquid chromatography mass spectrometry.

    PubMed

    Desbenoit, Nicolas; Schmitz-Afonso, Isabelle; Baudouin, Christophe; Laprévote, Olivier; Touboul, David; Brignole-Baudouin, Françoise; Brunelle, Alain

    2013-05-01

    Benzalkonium (BAK) chloride is the most commonly used preservative in eye drops. It is generally composed of benzyldimethyldodecylammonium C12 and benzyldimethyltetradecylammonium C14 and is supposed to increase penetration of active compounds. However, numerous studies have reported its toxic effect to ocular surface especially in long-term treatments like against glaucoma, a sight-threatening disease. Albino rabbits were treated with a hyperosmolar solution and a high concentration of BAK solution for 1 month. Enucleated eyes were cryo-sectioned and analysed by mass spectrometry. Mass spectrometry imaging using time-of-flight secondary ion mass spectrometry (TOF-SIMS) has been used to characterize the spatial distribution and to determine the relative quantity of BAK at the surface of rabbit eye sections. Liquid chromatography coupled with mass spectrometry (LC-MS) using a hybrid linear ion trap-Orbitrap® mass spectrometer was used to obtain relative quantification of BAK at the sample surface. TOF-SIMS images of BAK ions indicated a distribution at the ocular surface and in deeper structures. Didecyldimethylammonium (DDMAC), which is used in hospitals as a substitute for BAK, was also detected and showed an accumulation around the eyes. After extraction with acetonitrile and chromatographic separation using a Gemini C18 column and an original elution gradient, the relative quantities of BAK and DDMAC present in the whole eye section surface were determined. This LC-MS method was validated in terms of limits of quantification, linearity, repeatability and reproducibility and its feasibility was evaluated in surgically obtained human samples. Specimens of iris, lens capsule or trabecular meshwork were found with significant levels of BAK and DDMAC, thus confirming the penetration of BAK in deep ocular structures, with potential deleterious effects induced by this cytotoxic compound. The analytical method developed here could therefore be of primary interest in

  4. Plasma, blood and liver tissue sample preparation methods for the separate quantification of liposomal-encapsulated prednisolone phosphate and non-encapsulated prednisolone.

    PubMed

    Smits, Evelien A W; Soetekouw, José A; Bakker, Peter F A; Baijens, Bart J H; Vromans, Herman

    2015-03-01

    Besides the development of sample preparation methods for the determination of separate liposomal-encapsulated prednisolone phosphate and non-encapsulated prednisolone concentrations in murine plasma and blood, this article also presents the first description of an accurate sample preparation method for the determination of such separate concentrations in the murine liver. The quantitative differentiation is based on the immediate hydrolysis of prednisolone phosphate (PP) into prednisolone (P) after its release from the liposomes in vivo: PP represents the encapsulated drug, while P represents the non-encapsulated drug. The use of 10 ml methanol/g tissue during homogenization of liver tissue ensures complete liposome rupture, prevention of the dephosphorylation of PP released during homogenization, sufficient clean supernatants, excellent extraction of P and sufficient extraction of PP and excellent accuracies and precision complying with the internal guidelines for pre-clinical studies (80-120% and maximal 20%, respectively). Similarly, the matching sample preparation methods for plasma and blood involve protein precipitation with four equivalents of methanol also ensuring accuracies and precision complying with the internal guidelines for pre-clinical studies. Application of these sample preparation methods is going to generate the first pharmacokinetic (PK) profile of a liposomal preparation, in which the encapsulated and non-encapsulated drug concentrations in a tissue are measured separately. Such separated concentration profiles can gain important insights into the PKs of liposomal PP and probably also with regard to liposomal formulations in general, like the quantification of the in vivo drug release from the liposomes.

  5. Quantification of the full length leptin receptor (OB-Rb) in human brown and white adipose tissue.

    PubMed

    Kutoh, E; Boss, O; Levasseur, F; Giacobino, J P

    1998-01-01

    Levels of expression of the leptin receptor (OB-R) splice variants have been studied in human omental white and perirenal brown adipose tissues by reverse transcription-PCR. The level of mRNA expression of the full length form (OB-Rb) was approximately 15% of that of the sum of all splice variants in white or brown adipose tissue. In an attempt to quantify the gene expression of OB-Rb in human white adipose tissue, a quantitative competitive PCR technique was developed, using oligonucleotide primers designed for OB-Rb and an internal standard for a "MIMIC" competition strategy. The levels of expression of OB-Rb mRNA in the omental fat of lean and obese patients were compared and no difference could be observed between the two groups. The quantitative RT-PCR technique allows for a fast and accurate measurement of the expression of the OB-Rb mRNA in small tissue samples.

  6. Abdominal adipose tissue quantification on water-suppressed and non-water-suppressed MRI at 3T using semi-automated FCM clustering algorithm

    NASA Astrophysics Data System (ADS)

    Valaparla, Sunil K.; Peng, Qi; Gao, Feng; Clarke, Geoffrey D.

    2014-03-01

    Accurate measurements of human body fat distribution are desirable because excessive body fat is associated with impaired insulin sensitivity, type 2 diabetes mellitus (T2DM) and cardiovascular disease. In this study, we hypothesized that the performance of water suppressed (WS) MRI is superior to non-water suppressed (NWS) MRI for volumetric assessment of abdominal subcutaneous (SAT), intramuscular (IMAT), visceral (VAT), and total (TAT) adipose tissues. We acquired T1-weighted images on a 3T MRI system (TIM Trio, Siemens), which was analyzed using semi-automated segmentation software that employs a fuzzy c-means (FCM) clustering algorithm. Sixteen contiguous axial slices, centered at the L4-L5 level of the abdomen, were acquired in eight T2DM subjects with water suppression (WS) and without (NWS). Histograms from WS images show improved separation of non-fatty tissue pixels from fatty tissue pixels, compared to NWS images. Paired t-tests of WS versus NWS showed a statistically significant lower volume of lipid in the WS images for VAT (145.3 cc less, p=0.006) and IMAT (305 cc less, p<0.001), but not SAT (14.1 cc more, NS). WS measurements of TAT also resulted in lower fat volumes (436.1 cc less, p=0.002). There is strong correlation between WS and NWS quantification methods for SAT measurements (r=0.999), but poorer correlation for VAT studies (r=0.845). These results suggest that NWS pulse sequences may overestimate adipose tissue volumes and that WS pulse sequences are more desirable due to the higher contrast generated between fatty and non-fatty tissues.

  7. Dystrophin quantification

    PubMed Central

    Anthony, Karen; Arechavala-Gomeza, Virginia; Taylor, Laura E.; Vulin, Adeline; Kaminoh, Yuuki; Torelli, Silvia; Feng, Lucy; Janghra, Narinder; Bonne, Gisèle; Beuvin, Maud; Barresi, Rita; Henderson, Matt; Laval, Steven; Lourbakos, Afrodite; Campion, Giles; Straub, Volker; Voit, Thomas; Sewry, Caroline A.; Morgan, Jennifer E.; Flanigan, Kevin M.

    2014-01-01

    Objective: We formed a multi-institution collaboration in order to compare dystrophin quantification methods, reach a consensus on the most reliable method, and report its biological significance in the context of clinical trials. Methods: Five laboratories with expertise in dystrophin quantification performed a data-driven comparative analysis of a single reference set of normal and dystrophinopathy muscle biopsies using quantitative immunohistochemistry and Western blotting. We developed standardized protocols and assessed inter- and intralaboratory variability over a wide range of dystrophin expression levels. Results: Results from the different laboratories were highly concordant with minimal inter- and intralaboratory variability, particularly with quantitative immunohistochemistry. There was a good level of agreement between data generated by immunohistochemistry and Western blotting, although immunohistochemistry was more sensitive. Furthermore, mean dystrophin levels determined by alternative quantitative immunohistochemistry methods were highly comparable. Conclusions: Considering the biological function of dystrophin at the sarcolemma, our data indicate that the combined use of quantitative immunohistochemistry and Western blotting are reliable biochemical outcome measures for Duchenne muscular dystrophy clinical trials, and that standardized protocols can be comparable between competent laboratories. The methodology validated in our study will facilitate the development of experimental therapies focused on dystrophin production and their regulatory approval. PMID:25355828

  8. Quantification of total mercury in liver and heart tissue of Harbor Seals (Phoca vitulina) from Alaska USA

    SciTech Connect

    Marino, Kady B.; Hoover-Miller, Anne; Conlon, Suzanne; Prewitt, Jill; O'Shea, Stephen K.

    2011-11-15

    This study quantified the Hg levels in the liver (n=98) and heart (n=43) tissues of Harbor Seals (Phoca vitulina) (n=102) harvested from Prince William Sound and Kodiak Island Alaska. Mercury tissue dry weight (dw) concentrations in the liver ranged from 1.7 to 393 ppm dw, and in the heart from 0.19 to 4.99 ppm dw. Results of this study indicate liver and heart tissues' Hg ppm dw concentrations significantly increase with age. Male Harbor Seals bioaccumulated Hg in both their liver and heart tissues at a significantly faster rate than females. The liver Hg bioaccumulation rates between the harvest locations Kodiak Island and Prince William Sound were not found to be significantly different. On adsorption Hg is transported throughout the Harbor Seal's body with the partition coefficient higher for the liver than the heart. No significant differences in the bio-distribution (liver:heart Hg ppm dw ratios (n=38)) values were found with respect to either age, sex or geographic harvest location. In this study the age at which Hg liver and heart bioaccumulation levels become significantly distinct in male and female Harbor Seals were identified through a Tukey's analysis. Of notably concern to human health was a male Harbor Seal's liver tissue harvested from Kodiak Island region. Mercury accumulation in this sample tissue was determined through a Q-test to be an outlier, having far higher Hg concentrarion (liver 392 Hg ppm dw) than the general population sampled. - Highlights: Black-Right-Pointing-Pointer Mercury accumulation in the liver and heart of seals exceed food safety guidelines. Black-Right-Pointing-Pointer Accumulation rate is greater in males than females with age. Black-Right-Pointing-Pointer Liver mercury accumulation is greater than in the heart tissues. Black-Right-Pointing-Pointer Mercury determination by USA EPA Method 7473 using thermal decomposition.

  9. Agouti revisited: transcript quantification of the ASIP gene in bovine tissues related to protein expression and localization.

    PubMed

    Albrecht, Elke; Komolka, Katrin; Kuzinski, Judith; Maak, Steffen

    2012-01-01

    Beside its role in melanogenesis, the agouti signaling protein (ASIP) has been related to obesity. The potentially crucial role in adipocyte development makes it a tempting candidate for economic relevant, fat related traits in farm animals. The objective of our study was to characterize the mRNA expression of different ASIP transcripts and of putative targets in different bovine tissues, as well as to study consequences on protein abundance and localization. ASIP mRNA abundance was determined by RT-qPCR in adipose and further tissues of cattle representing different breeds and crosses. ASIP mRNA was up-regulated more than 9-fold in intramuscular fat of Japanese Black cattle compared to Holstein (p<0.001). Further analyses revealed that a transposon-derived transcript was solely responsible for the increased ASIP mRNA abundance. This transcript was observed in single individuals of different breeds indicating a wide spread occurrence of this insertion at the ASIP locus in cattle. The protein was detected in different adipose tissues, skin, lung and liver, but not in skeletal muscle by Western blot with a bovine-specific ASIP antibody. However, the protein abundance was not related to the observed ASIP mRNA over-expression. Immuno-histochemical analyses revealed a putative nuclear localization of ASIP additionally to the expected cytosolic signal in different cell types. The expression of melanocortin receptors (MCR) 1 to 5 as potential targets for ASIP was analyzed by RT-PCR in subcutaneous fat. Only MC1R and MC4R were detected indicating a similar receptor expression like in human adipose tissue. Our results provide evidence for a widespread expression of ASIP in bovine tissues at mRNA and, for the first time, at protein level. ASIP protein is detectable in adipocytes as well as in further cells of adipose tissue. We generated a basis for a more detailed investigation of ASIP function in peripheral tissues of various mammalian species.

  10. Analysis and quantification of collagen organization with the structure tensor in second harmonic microscopy images of ocular tissues.

    PubMed

    Ávila, Francisco J; Bueno, Juan M

    2015-11-20

    The important biological role of collagen-based tissues and the changes produced in the fiber distribution under particular situations (surgery, pathology, external damage, etc.) require tools for the analysis of the collagen organization that might potentially help in early diagnoses. Since collagen structures provide efficient second harmonic generation (SHG) signals, SHG microscopy has emerged as a powerful technique to visualize collagen fibers and qualitatively discriminate normal from abnormal tissues. Here we propose a quantitative method based on the structure tensor to quantify the different organization of collagen patterns in SHG images of ocular tissues. Results show that well-organized collagen distributions present a high degree of isotropy (DoI), a dominant orientation (PO), and a low structural dispersion (SD). On the other hand, the PO vanishes when the collagen tissue is not organized as a consequence of an increase in the SD and a decrease in the DoI. The proposed method is also able to discriminate partially organized samples. The combination of SHG microscopy and the structure tensor is a useful method to objectively classify collagen distributions. Clinical applications of this technique could help in the diagnosis and tracking of pathologies related to collagen disorders in connective tissue.

  11. Single-cell screening and quantification of transcripts in cancer tissues by second-harmonic generation microscopy

    PubMed Central

    Liu, Jing; Damayanti, Nur P.; Cho, Il-Hoon; Polar, Yesim; Badve, Sunil; Irudayaraj, Joseph M. K.

    2015-01-01

    Abstract. Fluorescence-based single molecule techniques to interrogate gene expression in tissues present a very low signal-to-noise ratio due to the strong autofluorescence and other background signals from tissue sections. This report presents a background-free method using second-harmonic generation (SHG) nanocrystals as probes to quantify the messenger RNA (mRNA) of human epidermal growth receptor 2 (Her2) at single molecule resolution in specific phenotypes at single-cell resolution directly in tissues. Coherent SHG emission from individual barium titanium oxide (BTO) nanoprobes was demonstrated, allowing for a stable signal beyond the autofluorescence window. Her2 surface marker and Her2 mRNA were specifically labeled with BTO probes, and Her2 mRNA was quantified at single copy sensitivity in Her2 expressing phenotypes directly in cancer tissues. Our approach provides the first proof of concept of a cross-platform strategy to probe tissues at single-cell resolution in situ. PMID:26405822

  12. A rapid cation-exchange HPLC method for detection and quantification of pyridinium oximes in plasma and tissue.

    PubMed

    Singh, Harry; Moorad-Doctor, Deborah; Ratcliffe, Ruthie H; Wachtel, Katie; Castillo, Andres; Garcia, Gregory E

    2007-03-01

    A rapid and sensitive assay for pyridinium oximes in plasma and tissue was developed. The method was suitable for the analysis of mono- and di-pyridinium oximes and utilizes ultrafiltration followed by cation-exchange high-performance liquid chromatography with UV detection. The assay was originally developed for the measurement of the oxime MMB-4 in plasma for which the lower limit of detection was 0.0005 pg and the limit of quantitation was 0.001 to 2.5 microg. The assay required as little as 50 microL of whole blood or 30 pL of tissue homogenate, and it was used for a pharmacokinetic study from a single intramuscular injection of MMB-4 (dichloride or dimethylsulfonate salt) in the guinea pig. Both salts were found to have similar pharmacokinetic properties in the plasma with a T1/2 of about 34 to 42 min and the area-under-the-curve values increased dose dependently. MMB-4 tissue concentrations were much lower than the plasma. The tissue levels peaked at 5-20 min depending on the tissue. A rank of concentration was diaphragm > heart > thigh muscle.

  13. Enzyme alterations in brain tissue during the early postmortal interval with reference to the histomorphology: review of the literature.

    PubMed

    Oehmichen, M

    1980-01-01

    The state of research on enzyme alterations in brain tissue during the early postmortal interval is surveyed with special reference to the histomorphology; the questions currently discussed in the literature are given special consideration. The type of alterations appearing during the postmortal interval and their dependency on the length of the interval are described so that practically applicable conclusions may be drawn. The findings on enzyme alterations presented in the literature (enzymes of the oxidative metabolism, transmitter, enzymes) are compiled in tables. It could be shown that important structural alterations ascertainable with light microscopy and quantitative alterations in enzyme activity ascertainable with biochemical methods do not usually occur during a 6- to 8-h postmortal interval. Qualitative investigations (i.e., histoenzymatic studies) with longer postmortal intervals and with positive findings are applicable.

  14. Analytical and numerical quantification and comparison of the local electric field in the tissue for different electrode configurations

    PubMed Central

    Čorović, Selma; Pavlin, Mojca; Miklavčič, Damijan

    2007-01-01

    Background Electrochemotherapy and gene electrotransfer are novel promising treatments employing locally applied high electric pulses to introduce chemotherapeutic drugs into tumor cells or genes into target cells based on the cell membrane electroporation. The main focus of this paper was to calculate analytically and numerically local electric field distribution inside the treated tissue in two dimensional (2D) models for different plate and needle electrode configurations and to compare the local electric field distribution to parameter U/d, which is widely used in electrochemotherapy and gene electrotransfer studies. We demonstrate the importance of evaluating the local electric field distribution in electrochemotherapy and gene electrotransfer. Methods We analytically and numerically analyze electric field distribution based on 2D models for electrodes and electrode configurations which are most widely used in electrochemotherapy and gene electrotransfer. Analytical calculations were performed by solving the Laplace equation and numerical calculations by means of finite element method in two dimensions. Results We determine the minimal and maximal E inside the target tissue as well as the maximal E over the entire treated tissue for the given electrode configurations. By comparing the local electric field distribution calculated for different electrode configurations to the ratio U/d, we show that the parameter U/d can differ significantly from the actual calculated values of the local electric field inside the treated tissue. By calculating the needed voltage to obtain E > U/d inside the target tissue, we showed that better electric field distribution can be obtained by increasing the number and changing the arrangement of the electrodes. Conclusion Based on our analytical and numerical models of the local electric field distribution we show that the applied voltage, configuration of the electrodes and electrode position need to be chosen specifically for

  15. UPLC-MS method for quantification of pterostilbene and its application to comparative study of bioavailability and tissue distribution in normal and Lewis lung carcinoma bearing mice.

    PubMed

    Deng, Li; Li, Yongzhi; Zhang, Xinshi; Chen, Bo; Deng, Yulin; Li, Yujuan

    2015-10-10

    A UPLC-MS method was developed for determination of pterostilbene (PTS) in plasma and tissues of mice. PTS was separated on Agilent Zorbax XDB-C18 column (50 × 2.1 mm, 1.8 μm) with gradient mobile phase at the flow rate of 0.2 ml/min. The detection was performed by negative ion electrospray ionization in multiple reaction monitoring mode. The linear calibration curve of PTS in mouse plasma and tissues ranged from 1.0 to 5000 and 0.50 to 500 ng/ml (r(2)>0.9979), respectively, with lowest limits of quantification (LLOQ) were between 0.5 and 2.0 ng/ml, respectively. The accuracy and precision of the assay were satisfactory. The validated method was applied to the study of bioavailability and tissue distribution of PTS in normal and Lewis lung carcinoma (LLC) bearing mice. The bioavailability of PTS (dose 14, 28 and 56 mg/kg) in normal mice were 11.9%, 13.9% and 26.4%, respectively; and the maximum level (82.1 ± 14.2 μg/g) was found in stomach (dose 28 mg/kg). The bioavailability, peak concentration (Cmax), time to peak concentration (Tmax) of PTS in LLC mice was increased compared with normal mice. The results indicated the UPLC-MS method is reliable and bioavailability and tissue distribution of PTS in normal and LLC mice were dramatically different. Copyright © 2015 Elsevier B.V. All rights reserved.

  16. Development of a novel DNA extraction method for identification and quantification of Mycobacterium avium subsp. paratuberculosis from tissue samples by real-time PCR.

    PubMed

    Park, Kun Taek; Allen, Andrew J; Davis, William C

    2014-04-01

    Mycobacterium avium subsp. paratuberculosis (Map) is the causative agent of Johne's disease in ruminants and possibly associated with human Crohn's disease. One impediment in furthering our understanding of this potential association has been the lack of an accurate method for detection of Map in affected tissues. Real time polymerase chain reaction (RT-PCR) methods have been reported to have different sensitivities in detection of Map. This is in part attributable to the difficulties of extracting Map DNA and removing PCR inhibitors from the clinical specimens. The maximum efficiency of RT-PCR can only be achieved by using high quality DNA samples. In this study, we present a novel pre-treatment method which significantly increases Map DNA recovery and decreases PCR inhibitors (p<0.05). When the pre-treatment method was combined with the DNeasy Blood and Tissue kit (Qiagen), PCR inhibition was not detected in any of three different RT-PCR methods tested in this study. The results obtained with the IS900 probe showed an excellent Kappa value (0.849) and a high correlation coefficient r (0.940) compared to the results of culture method. When used to examine unknown field samples (n=15), more positive tissues were identified with DNA extracts prepared with pre-treatment method than without (5 vs 3). This improved Map DNA extraction method from tissue samples will make RT-PCR a more powerful tool for a wide range of applications for Map identification and quantification. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Quantification of inflammation in colonic tissue sections and wound healing in-vitro with digital holographic microscopy

    NASA Astrophysics Data System (ADS)

    Bettenworth, Dominik; Lenz, Philipp; Krausewitz, Philipp; Brückner, Markus; Ketelhut, Steffi; von Bally, Gert; Domagk, Dirk; Kemper, Björn

    2013-06-01

    We show that the tissue refractive index, obtained from quantitative digital holographic microscopy (DHM) phase contrast images of unstained histological colonic sections, is directly related to the degree of inflammation in experimental colitis. In addition, it is demonstrated that quantitative DHM phase contrast is capable to quantify in-vitro wound healing assays.

  18. Detection and Quantification of CWD Prions in Fixed Paraffin Embedded Tissues by Real-Time Quaking-Induced Conversion

    PubMed Central

    Hoover, Clare E.; Davenport, Kristen A.; Henderson, Davin M.; Pulscher, Laura A.; Mathiason, Candace K.; Zabel, Mark D.; Hoover, Edward A.

    2016-01-01

    Traditional diagnostic detection of chronic wasting disease (CWD) relies on immunodetection of misfolded CWD prion protein (PrPCWD) by western blotting, ELISA, or immunohistochemistry (IHC). These techniques require separate sample collections (frozen and fixed) which may result in discrepancies due to variation in prion tissue distribution and assay sensitivities that limit detection especially in early and subclinical infections. Here, we harness the power of real-time quaking induced conversion (RT-QuIC) to amplify, detect, and quantify prion amyloid seeding activity in fixed paraffin-embedded (FPE) tissue sections. We show that FPE RT-QuIC has greater detection sensitivity than IHC in tissues with low PrPCWD burdens, including those that are IHC-negative. We also employ amyloid formation kinetics to yield a semi-quantitative estimate of prion concentration in a given FPE tissue. We report that FPE RT-QuIC has the ability to enhance diagnostic and investigative detection of disease-associated PrPRES in prion, and potentially other, protein misfolding disease states. PMID:27157060

  19. Agouti Revisited: Transcript Quantification of the ASIP Gene in Bovine Tissues Related to Protein Expression and Localization

    PubMed Central

    Albrecht, Elke; Komolka, Katrin; Kuzinski, Judith; Maak, Steffen

    2012-01-01

    Beside its role in melanogenesis, the agouti signaling protein (ASIP) has been related to obesity. The potentially crucial role in adipocyte development makes it a tempting candidate for economic relevant, fat related traits in farm animals. The objective of our study was to characterize the mRNA expression of different ASIP transcripts and of putative targets in different bovine tissues, as well as to study consequences on protein abundance and localization. ASIP mRNA abundance was determined by RT-qPCR in adipose and further tissues of cattle representing different breeds and crosses. ASIP mRNA was up-regulated more than 9-fold in intramuscular fat of Japanese Black cattle compared to Holstein (p<0.001). Further analyses revealed that a transposon-derived transcript was solely responsible for the increased ASIP mRNA abundance. This transcript was observed in single individuals of different breeds indicating a wide spread occurrence of this insertion at the ASIP locus in cattle. The protein was detected in different adipose tissues, skin, lung and liver, but not in skeletal muscle by Western blot with a bovine-specific ASIP antibody. However, the protein abundance was not related to the observed ASIP mRNA over-expression. Immuno-histochemical analyses revealed a putative nuclear localization of ASIP additionally to the expected cytosolic signal in different cell types. The expression of melanocortin receptors (MCR) 1 to 5 as potential targets for ASIP was analyzed by RT-PCR in subcutaneous fat. Only MC1R and MC4R were detected indicating a similar receptor expression like in human adipose tissue. Our results provide evidence for a widespread expression of ASIP in bovine tissues at mRNA and, for the first time, at protein level. ASIP protein is detectable in adipocytes as well as in further cells of adipose tissue. We generated a basis for a more detailed investigation of ASIP function in peripheral tissues of various mammalian species. PMID:22530003

  20. Optimising the quantification of cytokines present at low concentrations in small human mucosal tissue samples using Luminex assays☆

    PubMed Central

    Staples, Emily; Ingram, Richard James Michael; Atherton, John Christopher; Robinson, Karen

    2013-01-01

    Sensitive measurement of multiple cytokine profiles from small mucosal tissue biopsies, for example human gastric biopsies obtained through an endoscope, is technically challenging. Multiplex methods such as Luminex assays offer an attractive solution but standard protocols are not available for tissue samples. We assessed the utility of three commercial Luminex kits (VersaMAP, Bio-Plex and MILLIPLEX) to measure interleukin-17A (IL-17) and interferon-gamma (IFNγ) concentrations in human gastric biopsies and we optimised preparation of mucosal samples for this application. First, we assessed the technical performance, limits of sensitivity and linear dynamic ranges for each kit. Next we spiked human gastric biopsies with recombinant IL-17 and IFNγ at a range of concentrations (1.5 to 1000 pg/mL) and assessed kit accuracy for spiked cytokine recovery and intra-assay precision. We also evaluated the impact of different tissue processing methods and extraction buffers on our results. Finally we assessed recovery of endogenous cytokines in unspiked samples. In terms of sensitivity, all of the kits performed well within the manufacturers' recommended standard curve ranges but the MILLIPLEX kit provided most consistent sensitivity for low cytokine concentrations. In the spiking experiments, the MILLIPLEX kit performed most consistently over the widest range of concentrations. For tissue processing, manual disruption provided significantly improved cytokine recovery over automated methods. Our selected kit and optimised protocol were further validated by measurement of relative cytokine levels in inflamed and uninflamed gastric mucosa using Luminex and real-time polymerase chain reaction. In summary, with proper optimisation Luminex kits (and for IL-17 and IFNγ the MILLIPLEX kit in particular) can be used for the sensitive detection of cytokines in mucosal biopsies. Our results should help other researchers seeking to quantify multiple low concentration cytokines in

  1. Reference charts of gestation-specific tissue Doppler imaging indices of systolic and diastolic functions in the normal fetal heart.

    PubMed

    Chan, Louis Yik-si; Fok, Wing Yee; Wong, John Tai-hung; Yu, Cheuk Man; Leung, Tse Ngong; Lau, Tze Kin

    2005-10-01

    Assessment of fetal cardiac function is difficult because of limited accessibility. Tissue Doppler imaging (TDI) is a promising technique in assessing diastolic function in adults. There has been sparseness concerning the use of TDI in assessing fetal cardiac function. The aim of this study was to construct reference charts of TDI indices of systolic and diastolic functions of the normal fetal heart. Ventricular myocardial velocities at the left ventricular (LV) wall, right ventricular (RV) wall, and interventricular septum (IVS) were assessed by TDI in 302 subjects. From 19 to 37 weeks of gestation, peak myocardial velocities during early diastole (Em) increased from 3.3 to 7.2, 3.9 to 8.3, and 3.2 to 5.0 m/s at the LV wall, RV wall, and IVS, respectively. Peak myocardial velocities during atrial contraction (Am) also increased throughout gestation, but the magnitude of increase was smaller (6.3 to 7.9, 7.7 to 10.6, and 5.5 to 5.9 m/s for the LV wall, RV wall, and IVS, respectively). As a consequence, the Em/Am ratio increased from 0.51 to 0.61 at midtrimester to 0.76 to 0.91 at term. Similar to Em, peak myocardial velocities during systole (Sm) also increased by almost 2 times from 18 to 37 weeks of gestation (3.8 to 6.0, 4.2 to 7.6, and 3.3 to 5.6 for the LV wall, RV wall, and IVS, respectively). Reference charts of gestation-specific Em, Am, Em/Am ratio, Sm, and E/Em were constructed accordingly. In midtrimester, fetal diastolic function is predominantly contributed by atrial contraction. As gestation advances, ventricular relaxation becomes increasingly mature. Reference charts for TDI indices were constructed, these will allow identification of fetuses with an abnormal diastolic function.

  2. An Improved Simplified High-Sensitivity Quantification Method for Determining Brassinosteroids in Different Tissues of Rice and Arabidopsis1[C][W

    PubMed Central

    Xin, Peiyong; Yan, Jijun; Fan, Jinshi; Chu, Jinfang; Yan, Cunyu

    2013-01-01

    Quantification of brassinosteroids is essential and extremely important to study the molecular mechanisms of their physiological roles in plant growth and development. Herein, we present a simple, material and cost-saving high-performance method for determining endogenous brassinosteroids (BRs) in model plants. This new method enables simultaneous enrichment of a wide range of bioactive BRs such as brassinolide, castasterone, teasterone, and typhasterol with ion exchange solid-phase extraction and high-sensitivity quantitation of these BRs based on isotope dilution combined with internal standard approach. For routine analysis, the consumption of plant materials was reduced to one-twentieth of previously reported and the overall process could be completed within 1 day compared with previous 3 to 4 days. The strategy was validated by profiling BRs in different ecotypes and mutants of rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana), and the BR distributions in different model plants tissues were determined with the new method. The method allows plant physiologists to monitor the dynamics and distributions of BRs with 1 gram fresh weight of model plant tissues, which will speed up the process for the molecular mechanism research of BRs with these model plants in future work. PMID:23800992

  3. A strategy for designing multi-taxa specific reference gene systems. example of application--ppi phosphofructokinase (ppi-PPF) used for the detection and quantification of three taxa: maize (Zea mays), cotton (Gossypium hirsutum) and rice (Oryza sativa).

    PubMed

    Chaouachi, Maher; Giancola, Sandra; Romaniuk, Marcel; Laval, Valérie; Bertheau, Yves; Brunel, Dominique

    2007-10-03

    In the first part of the paper, we report the description of a new strategy for the development of a plant reference gene system that can be used for genetically modified organism (GMO) analysis. On the basis of in silico research for candidate genes, the design of degenerate primers allowed the obtention of genomic sequences of the selected gene ppi-phosphofructokinase ( ppi-PPF) for nine taxa in which GMOs have been developed. The comparison and the analysis of inter- and intraspecies sequence variability were performed using a large number of species and cultivars. As an example of application following the detection of single nucleotide polymorphism, we designed specific conventional and real-time polymerase chain reaction tests for the detection and quantification of three taxa, namely, maize, cotton, and rice. This system was highly specific and sensitive. The gene copy number conservation among different cultivars was analyzed and confirmed with a sequencing step. This reference gene system is adequate for use in routine assays for the quantification of GMOs. We then explain briefly the constraints faced and propose recommendations when designing a reference gene system depending on the species to be targeted.

  4. Quantification of thrombus hounsfield units on noncontrast CT predicts stroke subtype and early recanalization after intravenous recombinant tissue plasminogen activator.

    PubMed

    Puig, J; Pedraza, S; Demchuk, A; Daunis-I-Estadella, J; Termes, H; Blasco, G; Soria, G; Boada, I; Remollo, S; Baños, J; Serena, J; Castellanos, M

    2012-01-01

    Little is known about the factors that determine recanalization after intravenous thrombolysis. We assessed the value of thrombus Hounsfield unit quantification as a predictive marker of stroke subtype and MCA recanalization after intravenous rtPA treatment. NCCT scans and CTA were performed on patients with MCA acute stroke within 4.5 hours of symptom onset. Demographics, stroke severity, vessel hyperattenuation, occlusion site, thrombus length, and time to thrombolysis were recorded. Stroke origin was categorized as LAA, cardioembolic, or indeterminate according to TOAST criteria. Two blinded neuroradiologists calculated the Hounsfield unit values for the thrombus and contralateral MCA segment. We used ROC curves to determine the rHU cutoff point to discriminate patients with successful recanalization from those without. We assessed the accuracy (sensitivity, specificity, and positive and negative predictive values) of rHU in the prediction of recanalization. Of 87 consecutive patients, 45 received intravenous rtPA and only 15 (33.3%) patients had acute recanalization. rHU values and stroke mechanism were the highest predictive factors of recanalization. The Matthews correlation coefficient was highest for rHU (0.901). The sensitivity, specificity, and positive and negative predictive values for lack of recanalization after intravenous rtPA for rHU ≤ 1.382 were 100%, 86.67%, 93.75%, and 100%, respectively. LAA thrombi had lower rHU than cardioembolic and indeterminate stroke thrombi (P = .004). The Hounsfield unit thrombus measurement ratio can predict recanalization with intravenous rtPA and may have clinical utility for endovascular treatment decision making.

  5. PCR assay based on a microsatellite-containing locus for detection and quantification of Epichloë endophytes in grass tissue.

    PubMed Central

    Groppe, K; Boller, T

    1997-01-01

    A PCR assay which allows detection and quantification of Epichloë endophytes in tissues of the grass Bromus erectus is described. PCR with specific primers flanking a microsatellite-containing locus (MS primers) amplified fragments 300 to 400 bp in length from as little as 1.0 pg of fungal genomic DNA in 100 ng of DNA from infected plant material. When annealing temperatures were optimized, all Epichloë and Acremonium strains tested, representing many of the known taxonomic groups, yielded an amplification product, indicating that the MS primers may be useful for in planta detection of a variety of related species, including agronomically important Acremonium coenophialum and Acremonium lolii. No fragments were generated from DNA isolates from uninfected plant material or from unrelated fungi isolated from B. erectus. For diagnostic applications, a B. erectus-specific primer pair was designed for use in multiplex PCR to allow simultaneous amplification of plant and fungal DNA sequences, providing an internal control for PCR failure caused by inhibitory plant compounds present in DNA extracts. For quantitative applications, a heterologous control template in primer binding sites complementary to the MS primers was constructed for use in competitive PCR, allowing direct quantification of Epichloë in plant DNA extracts. The fungal DNA present in infected leaves of B. erectus between 1 and 20 pg per 100 ng of leaf DNA, but the amounts of fungal DNA present in the sheath and blade of a given leaf were correlated, indicating that the degree of infection varied between plant individuals but that leaves were colonized in a uniform way. PMID:9097449

  6. Feasibility of epicardial adipose tissue quantification in non-ECG-gated low-radiation-dose CT: comparison with prospectively ECG-gated cardiac CT.

    PubMed

    Simon-Yarza, Isabel; Viteri-Ramírez, Guillermo; Saiz-Mendiguren, Ramón; Slon-Roblero, Pedro J; Paramo, María; Bastarrika, Gorka

    2012-06-01

    Epicardial adipose tissue (EAT) is an important indicator of cardiovascular risk. This parameter is generally assessed on ECG-gated computed tomography (CT) images. To evaluate feasibility and reliability of EAT quantification on non-gated thoracic low-radiation-dose CT examinations with respect to prospectively ECG-gated cardiac CT acquisition. Sixty consecutive asymptomatic smokers (47 men; mean age 64 ± 9.8 years) underwent low-dose CT of the chest and prospectively ECG-gated cardiac CT acquisitions (64-slice dual-source CT). The two examinations were reconstructed with the same range, field of view, slice thickness, and convolution algorithm. Two independent observers blindly quantified EAT volume using commercially available software. Data were compared with paired sample Student t-test, concordance correlation coefficients (CCC), and Bland-Altman plots. No statistically significant difference was observed for EAT volume quantification with low-dose-CT (141.7 ± 58.3 mL) with respect to ECG-gated CT (142.7 ± 57.9 mL). Estimation of CCC showed almost perfect concordance between the two techniques for EAT-volume assessment (CCC, 0.99; mean difference, 0.98 ± 5.1 mL). Inter-observer agreement for EAT volume estimation was CCC: 0.96 for low-dose-CT examinations and 0.95 for ECG-gated CT. Non-gated low-dose CT allows quantifying EAT with almost the same concordance and reliability as using dedicated prospectively ECG-gated cardiac CT acquisition protocols.

  7. Development and validation of a high performance liquid chromatography quantification method of levo-tetrahydropalmatine and its metabolites in plasma and brain tissues: application to a pharmacokinetic study.

    PubMed

    Abdallah, Inas A; Huang, Peng; Liu, Jing; Lee, David Y; Liu-Chen, Lee-Yuan; Hassan, Hazem E

    2017-04-01

    Levo-tetrahydropalmatine (l-THP) is an alkaloid isolated from Chinese medicinal herbs of the Corydalis and Stephania genera. It has been used in China for more than 40 years mainly as an analgesic with sedative/hypnotic effects. Despite its extensive use, its metabolism has not been quantitatively studied, nor there a sensitive reliable bioanalytical method for its quantification simultaneously with its metabolites. As such, the objective of this study was to develop and validate a sensitive and selective HPLC method for simultaneous quantification of l-THP and its desmethyl metabolites l-corydalmine (l-CD) and l-corypalmine (l-CP) in rat plasma and brain tissues. Rat plasma and brain samples were processed by liquid-liquid extraction using ethyl acetate. Chromatographic separation was achieved on a reversed-phase Symmetry® C18 column (4.6 × 150 mm, 5 μm) at 25°C. The mobile phase consisted of acetonitrile-methanol-10 mm ammonium phosphate (pH 3) (10:30:60, v/v) and was used at a flow rate of 0.8 mL/min. The column eluent was monitored at excitation and emission wavelengths of 230 and 315 nm, respectively. The calibration curves were linear over the concentration range of 1-10,000 ng/mL. The intra- and interday reproducibility studies demonstrated accuracy and precision within the acceptance criteria of bioanalytical guidelines. The validated HPLC method was successfully applied to analyze samples from a pharmacokinetic study of l-THP in rats. Taken together, the developed method can be applied for bioanalysis of l-THP and its metabolites in rodents and potentially can be transferred for bioanalysis of human samples.

  8. Evaluation of EDXRF configurations to improve the limit of detection and exposure for in vivo quantification of gadolinium in tumor tissue

    NASA Astrophysics Data System (ADS)

    Santibáñez, M.; Vásquez, M.; Figueroa, R. G.; Valente, M.

    2016-05-01

    In this paper the configuration of an Energy Dispersive X-Ray Fluorescence (EDXRF) system optimized for in vivo quantification of gadolinium in tumor tissue was studied. The system was configured using XMI-MSIM software designed to predict the XRF spectral response using Monte Carlo simulations. The studied setup is comprised of an X-ray tube, tuned to different voltages, and a copper filter system configured with variable thickness, which emits a spectrally narrow beam centered on the specific excitation energy. The values for the central energy excitation and the spectral width were adjusted to optimize the system, using like figures of merit: minimization of the limit of detection, measurement uncertainty and radiation exposure. These values were obtained in two stages. The first was successive simulations of incident spectra with central energy in the range of 50-70 keV. The second was comprised of simulations with incident spectra of different widths (8-29 keV), all with the same determined central energy, evaluating the limit of detection depending on the exposure. This made it possible to find the best balance between system sensitivity and the delivered dose. The obtained results were compared with those produced by radioactive sources of 241Am whose activity was set to produce the same exposure as the proposed setup. To evaluate the feasibility of in vivo quantification, a set of tumor phantoms of 1-6 cm3 at different depths and labeled with a gadolinium concentration of 250 ppm was evaluated. From the resulting spectrum, calibration curves were obtained in function of the size and depth of the tumor, allowing for the evaluation of the potential of the methodology.

  9. Quantification of PARP activity in human tissues: ex vivo assays in blood cells, and immunohistochemistry in human biopsies

    PubMed Central

    Horvath, Eszter M; Zsengellér, Zsuzsanna K.; Szabo, Csaba

    2015-01-01

    Summary Poly (ADP-ribosyl)ation of proteins is a post-translational modification mediated by poly (ADP-ribose) polymerases (PARPs), that uses NAD+ as substrate to form the negatively charged polymer of poly (ADP-ribose) (PAR). After DNA damage, PARP-1 is responsible for approximately 90% of the total cellular PARylation activity. Numerous studies showed activation of PARP-1 in various conditions associated with oxidative and nitrosative stress, such as ischemia-reperfusion injury, diabetes mellitus, and inflammation and also proved the beneficial effects of PARP inhibitors. Pharmacological inhibitors of PARP move toward clinical testing for a variety of indications, including cardioprotection and malignant tumors. Some of the compounds are already in clinical trials. These advances necessitate the detection of PARP activation in human tissues. In the present chapter, we review specific methods used to detect PARP activation in human circulating leukocytes and in human tissue sections. PMID:21870266

  10. Quantification of fluorophore concentration in tissue-simulating media by fluorescence measurements with a single optical fiber.

    PubMed

    Diamond, Kevin R; Patterson, Michael S; Farrell, Thomas J

    2003-05-01

    Quantifying fluorescent compounds in turbid media such as tissue is made difficult by the effects of multiple scattering and absorption of the excitation and emission light. The approach that we used was to measure fluorescence using a single 200-microm optical fiber as both the illumination source and the detector. Fluorescence of aluminum phthalocyanine tetrasulfonate (AlPcS4) was measured over a wide range of fluorophore concentrations and optical properties in tissue-simulating phantoms. A root-mean-square accuracy of 10.6% in AlPcS4 concentration was attainable when fluorescence was measured either interstitially or at the phantom surface. The individual effects of scattering, absorption, and the scattering phase function on the fluorescence signal were also studied by experiments and Monte Carlo simulations.

  11. Computerized Automated Quantification of Subcutaneous and Visceral Adipose Tissue From Computed Tomography Scans: Development and Validation Study

    PubMed Central

    Kim, Young Jae; Park, Ji Won; Kim, Jong Wan; Park, Chan-Soo; Gonzalez, John Paul S; Lee, Seung Hyun

    2016-01-01

    Background Computed tomography (CT) is often viewed as one of the most accurate methods for measuring visceral adipose tissue (VAT). However, measuring VAT and subcutaneous adipose tissue (SAT) from CT is a time-consuming and tedious process. Thus, evaluating patients’ obesity levels during clinical trials using CT scans is both cumbersome and limiting. Objective To describe an image-processing-based and automated method for measuring adipose tissue in the entire abdominal region. Methods The method detects SAT and VAT levels using a separation mask based on muscles of the human body. The separation mask is the region that minimizes the unnecessary space between a closed path and muscle area. In addition, a correction mask, based on bones, corrects the error in VAT. Results To validate the method, the volume of total adipose tissue (TAT), SAT, and VAT were measured for a total of 100 CTs using the automated method, and the results compared with those from manual measurements obtained by 2 experts. Dice’s similarity coefficients (DSCs) between the first manual measurement and the automated result for TAT, SAT, and VAT are 0.99, 0.98, and 0.97, respectively. The DSCs between the second manual measurement and the automated result for TAT, SAT, and VAT are 0.98, 0.98, and 0.97, respectively. Moreover, intraclass correlation coefficients (ICCs) between the automated method and the results of the manual measurements indicate high reliability as the ICCs for the items are all .99 (P<.001). Conclusions The results described in this paper confirm the accuracy and reliability of the proposed method. The method is expected to be both convenient and useful in the clinical evaluation and study of obesity in patients who require SAT and VAT measurements. PMID:26846251

  12. Computerized Automated Quantification of Subcutaneous and Visceral Adipose Tissue From Computed Tomography Scans: Development and Validation Study.

    PubMed

    Kim, Young Jae; Park, Ji Won; Kim, Jong Wan; Park, Chan-Soo; Gonzalez, John Paul S; Lee, Seung Hyun; Kim, Kwang Gi; Oh, Jae Hwan

    2016-02-04

    Computed tomography (CT) is often viewed as one of the most accurate methods for measuring visceral adipose tissue (VAT). However, measuring VAT and subcutaneous adipose tissue (SAT) from CT is a time-consuming and tedious process. Thus, evaluating patients' obesity levels during clinical trials using CT scans is both cumbersome and limiting. To describe an image-processing-based and automated method for measuring adipose tissue in the entire abdominal region. The method detects SAT and VAT levels using a separation mask based on muscles of the human body. The separation mask is the region that minimizes the unnecessary space between a closed path and muscle area. In addition, a correction mask, based on bones, corrects the error in VAT. To validate the method, the volume of total adipose tissue (TAT), SAT, and VAT were measured for a total of 100 CTs using the automated method, and the results compared with those from manual measurements obtained by 2 experts. Dice's similarity coefficients (DSCs) between the first manual measurement and the automated result for TAT, SAT, and VAT are 0.99, 0.98, and 0.97, respectively. The DSCs between the second manual measurement and the automated result for TAT, SAT, and VAT are 0.98, 0.98, and 0.97, respectively. Moreover, intraclass correlation coefficients (ICCs) between the automated method and the results of the manual measurements indicate high reliability as the ICCs for the items are all .99 (P<.001). The results described in this paper confirm the accuracy and reliability of the proposed method. The method is expected to be both convenient and useful in the clinical evaluation and study of obesity in patients who require SAT and VAT measurements.

  13. Computational cell quantification in the human brain tissues based on hard x-ray phase-contrast tomograms

    NASA Astrophysics Data System (ADS)

    Hieber, Simone E.; Bikis, Christos; Khimchenko, Anna; Schulz, Georg; Deyhle, Hans; Thalmann, Peter; Chicherova, Natalia; Rack, Alexander; Zdora, Marie-Christine; Zanette, Irene; Schweighauser, Gabriel; Hench, Jürgen; Müller, Bert

    2016-10-01

    Cell visualization and counting plays a crucial role in biological and medical research including the study of neurodegenerative diseases. The neuronal cell loss is typically determined to measure the extent of the disease. Its characterization is challenging because the cell density and size already differs by more than three orders of magnitude in a healthy cerebellum. Cell visualization is commonly performed by histology and fluorescence microscopy. These techniques are limited to resolve complex microstructures in the third dimension. Phase- contrast tomography has been proven to provide sufficient contrast in the three-dimensional imaging of soft tissue down to the cell level and, therefore, offers the basis for the three-dimensional segmentation. Within this context, a human cerebellum sample was embedded in paraffin and measured in local phase-contrast mode at the beamline ID19 (ESRF, Grenoble, France) and the Diamond Manchester Imaging Branchline I13-2 (Diamond Light Source, Didcot, UK). After the application of Frangi-based filtering the data showed sufficient contrast to automatically identify the Purkinje cells and to quantify their density to 177 cells per mm3 within the volume of interest. Moreover, brain layers were segmented in a region of interest based on edge detection. Subsequently performed histological analysis validated the presence of the cells, which required a mapping from the two- dimensional histological slices to the three-dimensional tomogram. The methodology can also be applied to further tissue types and shows potential for the computational tissue analysis in health and disease.

  14. Sources of variability in the quantification of tissue optical properties by multidiameter single-fiber reflectance and fluorescence spectroscopy

    NASA Astrophysics Data System (ADS)

    Brooks, Sander; Hoy, Christopher L.; Amelink, Arjen; Robinson, Dominic J.; Nijsten, Tamar E.

    2015-05-01

    Recently, a multidiameter single-fiber reflectance and fluorescence spectroscopy device has been developed that enabled us to extract the autofluorescence of tissue that is corrected for the optical properties. Such a system has been incorporated in the population-based Rotterdam Study to investigate the autofluorescence of the skin. Since the device will be used by different operators over many years, it is essential that the results are comparable between users. It is, however, unclear how different methods of handling the probe might influence the outcome. Variability of blood oxygen saturation, blood volume fraction and vessel diameter, average gamma, reduced scattering coefficient at 800 nm, and integrated intrinsic fluorescence measured in three volunteers were assessed within and between eight untrained users. A variability of less than one standard deviation from the group mean was defined as an acceptable limit. Three mature volunteers were also included to assess the intrauser variability of mature skin. The variation in the measured parameters suggests that variation is dominated by tissue heterogeneity. Most users measured within one standard deviation of the group mean. Notably, corrected intrinsic fluorescence showed low intra- and interuser variability. These results strongly suggest that variability is mostly caused by tissue heterogeneity and is not user induced.

  15. Total iodine quantification in fluids and tissues from iodine- or iodide-supplemented rats by ion chromatography following microwave-assisted digestion.

    PubMed

    Delgado, Guadalupe; Muñoz-Torres, Carolina; Orozco-Esquivel, Teresa; Anguiano, Brenda; Aceves, Carmen

    2015-03-01

    Iodine is a crucial component of thyroid hormones, and several reports have shown that iodine per se is implicated in the physiopathology of other organs. Innovative ion chromatography detection following a four-step temperature ramp microwave digestion in 25-50 mM nitric acid was developed to measure total iodine in biological fluids and tissue samples from female Sprague-Dawley rats supplemented with 0.05% molecular iodine (I2) or 0.05% potassium iodide (I(-)) in drinking water. The reported method allows the measurement of total iodine with a limit of quantification of 13.7 μg L(-1), recoveries of 96.3-100.3%, and intra- and inter-assay variations, of 3.5% and 7.4% respectively. Analysis of biological fluids showed that after 48 hours, iodine-supplemented animals exhibited significantly higher levels of total iodine in both serum and urine compared with those supplemented with iodide. The half-life of iodine in serum and urine measured over the first 48 h showed similar patterns for both the I2 (7.89 and 7.76 hours) and I(-) (8.27 and 8.90 hours) supplements. Differential uptake patterns were observed in tissues after 6 days of supplements, with I(-) preferentially retained by thyroid, lactating mammary gland, and milk, and a slightly but significantly higher capture of I2 in pituitary, ovary, and virgin mammary gland. We developed a rapid, selective, and accurate digestion method to process fluid and tissue samples that permits reproducible measurements of total iodine by ion chromatography; iodine or iodide supplement show a similar serum and urine half-life, but organ-specific uptake depends on the chemical form of the iodine supplement.

  16. Quantification of Anaplastic Lymphoma Kinase Protein Expression in Non-Small Cell Lung Cancer Tissues from Patients Treated with Crizotinib.

    PubMed

    Hembrough, Todd; Liao, Wei-Li; Hartley, Christopher P; Ma, Patrick C; Velcheti, Vamsidhar; Lanigan, Christopher; Thyparambil, Sheeno; An, Eunkyung; Monga, Manish; Krizman, David; Burrows, Jon; Tafe, Laura J

    2016-01-01

    Crizotinib has antitumor activity in ALK (anaplastic lymphoma receptor tyrosine kinase)-rearranged non-small cell lung cancer (NSCLC). The current diagnostic test for ALK rearrangement is breakapart fluorescence in situ hybridization (FISH), but FISH has low throughput and is not always reflective of protein concentrations. The emergence of multiple clinically relevant biomarkers in NSCLC necessitates efficient testing of scarce tissue samples. We developed an anaplastic lymphoma kinase (ALK) protein assay that uses multiplexed selected reaction monitoring (SRM) to quantify absolute amounts of ALK in formalin-fixed paraffin-embedded (FFPE) tumor tissue. After validation in formalin-fixed cell lines, the SRM assay was used to quantify concentrations of ALK in 18 FFPE NSCLC samples that had been tested for ALK by FISH and immunohistochemistry. Results were correlated with patient response to crizotinib. We detected ALK in 11 of 14 NSCLC samples with known ALK rearrangements by FISH. Absolute ALK concentrations correlated with clinical response in 5 of 8 patients treated with crizotinib. The SRM assay did not detect ALK in 3 FISH-positive patients who had not responded to crizotinib. In 1 of these cases, DNA sequencing revealed a point mutation that predicts a nonfunctional ALK fusion protein. The SRM assay did not detect ALK in any tumor tissue with a negative ALK status by FISH or immunohistochemistry. ALK concentrations measured by SRM correlate with crizotinib response in NSCLC patients. The ALK SRM proteomic assay, which may be multiplexed with other clinically relevant proteins, allows for rapid identification of patients potentially eligible for targeted therapies. © 2015 American Association for Clinical Chemistry.

  17. Quantification of Anaplastic Lymphoma Kinase Protein Expression in Non–Small Cell Lung Cancer Tissues from Patients Treated with Crizotinib

    PubMed Central

    Hembrough, Todd; Liao, Wei-Li; Hartley, Christopher P.; Ma, Patrick C.; Velcheti, Vamsidhar; Lanigan, Christopher; Thyparambil, Sheeno; An, Eunkyung; Monga, Manish; Krizman, David; Burrows, Jon; Tafe, Laura J.

    2016-01-01

    BACKGROUND Crizotinib has antitumor activity in ALK (anaplastic lymphoma receptor tyrosine kinase)-rearranged non–small cell lung cancer (NSCLC). The current diagnostic test for ALK rearrangement is breakapart fluorescence in situ hybridization (FISH), but FISH has low throughput and is not always reflective of protein concentrations. The emergence of multiple clinically relevant biomarkers in NSCLC necessitates efficient testing of scarce tissue samples. We developed an anaplastic lymphoma kinase (ALK) protein assay that uses multiplexed selected reaction monitoring (SRM) to quantify absolute amounts of ALK in formalin-fixed paraffin-embedded (FFPE) tumor tissue. METHODS After validation in formalin-fixed cell lines, the SRM assay was used to quantify concentrations of ALK in 18 FFPE NSCLC samples that had been tested for ALK by FISH and immunohistochemistry. Results were correlated with patient response to crizotinib. RESULTS We detected ALK in 11 of 14 NSCLC samples with known ALK rearrangements by FISH. Absolute ALK concentrations correlated with clinical response in 5 of 8 patients treated with crizotinib. The SRM assay did not detect ALK in 3 FISH-positive patients who had not responded to crizotinib. In 1 of these cases, DNA sequencing revealed a point mutation that predicts a nonfunctional ALK fusion protein. The SRM assay did not detect ALK in any tumor tissue with a negative ALK status by FISH or immunohistochemistry. CONCLUSIONS ALK concentrations measured by SRM correlate with crizotinib response in NSCLC patients. The ALK SRM proteomic assay, which may be multiplexed with other clinically relevant proteins, allows for rapid identification of patients potentially eligible for targeted therapies. PMID:26585927

  18. Surfactant-aided precipitation/on-pellet-digestion (SOD) procedure provides robust and rapid sample preparation for reproducible, accurate and sensitive LC/MS quantification of therapeutic protein in plasma and tissues.

    PubMed

    An, Bo; Zhang, Ming; Johnson, Robert W; Qu, Jun

    2015-04-07

    For targeted protein quantification by liquid chromatography mass spectrometry (LC/MS), an optimal approach for efficient, robust and hi-throughput sample preparation is critical, but often remains elusive. Here we describe a straightforward surfactant-aided-precipitation/on-pellet-digestion (SOD) strategy that provides effective sample cleanup and enables high and constant peptide yields in various matrices, allowing reproducible, accurate and sensitive protein quantification. This strategy was developed using quantification of monocolnocal antibody in tissues and plasma as the model system. Surfactant treatment before precipitation substantially increased peptide recovery and reproducibility from plasma/tissue, likely because surfactant permits extensive denaturation/reduction/alkylation of proteins and inactivation of endogenous protease inhibitors, and facilitates removal of matrix components. The subsequent precipitation procedure effectively eliminates the surfactant and nonprotein matrix components, and the thorough denaturation by both surfactant and precipitation enabled very rapid on-pellet-digestion (45 min at 37 °C) with high peptide recovery. The performance of SOD was systematically compared against in-solution-digestion, in-gel-digestion and filter-aided-sample-preparation (FASP) in plasma/tissues, and then examined in a full pharmacokinetic study in rats. SOD achieved the best peptide recovery (∼21.0-700% higher than the other three methods across various matrices), reproducibility (3.75-10.9%) and sensitivity (28-30 ng/g across plasma and tissue matrices), and its performance was independent of matrix types. Finally, in validation and pharmacokinetic studies in rats, SOD outperformed other methods and provided highly accurate and precise quantification in all plasma samples without using stable isotope labeled (SIL)-protein internal standard (I.S.). In summary, the SOD method has proven to be highly robust, efficient and rapid, making it readily

  19. Validation of a fast method for quantification of intra-abdominal and subcutaneous adipose tissue for large-scale human studies.

    PubMed

    Borga, Magnus; Thomas, E Louise; Romu, Thobias; Rosander, Johannes; Fitzpatrick, Julie; Dahlqvist Leinhard, Olof; Bell, Jimmy D

    2015-12-01

    Central obesity is the hallmark of a number of non-inheritable disorders. The advent of imaging techniques such as MRI has allowed for a fast and accurate assessment of body fat content and distribution. However, image analysis continues to be one of the major obstacles to the use of MRI in large-scale studies. In this study we assess the validity of the recently proposed fat-muscle quantitation system (AMRA(TM) Profiler) for the quantification of intra-abdominal adipose tissue (IAAT) and abdominal subcutaneous adipose tissue (ASAT) from abdominal MR images. Abdominal MR images were acquired from 23 volunteers with a broad range of BMIs and analysed using sliceOmatic, the current gold-standard, and the AMRA(TM) Profiler based on a non-rigid image registration of a library of segmented atlases. The results show that there was a highly significant correlation between the fat volumes generated by the two analysis methods, (Pearson correlation r = 0.97, p < 0.001), with the AMRA(TM) Profiler analysis being significantly faster (~3 min) than the conventional sliceOmatic approach (~40 min). There was also excellent agreement between the methods for the quantification of IAAT (AMRA 4.73 ± 1.99 versus sliceOmatic 4.73 ± 1.75 l, p = 0.97). For the AMRA(TM) Profiler analysis, the intra-observer coefficient of variation was 1.6% for IAAT and 1.1% for ASAT, the inter-observer coefficient of variation was 1.4% for IAAT and 1.2% for ASAT, the intra-observer correlation was 0.998 for IAAT and 0.999 for ASAT, and the inter-observer correlation was 0.999 for both IAAT and ASAT. These results indicate that precise and accurate measures of body fat content and distribution can be obtained in a fast and reliable form by the AMRA(TM) Profiler, opening up the possibility of large-scale human phenotypic studies.

  20. Quantification of Estrogen Receptor Expression in Normal Breast Tissue in Postmenopausal Women With Breast Cancer and Association With Tumor Subtypes.

    PubMed

    Gulbahce, H Evin; Blair, Cindy K; Sweeney, Carol; Salama, Mohamed E

    2017-09-01

    Estrogen exposure is important in the pathogenesis of breast cancer and is a contributing risk factor. In this study we quantified estrogen receptor (ER) alpha expression in normal breast epithelium (NBR) in women with breast cancer and correlated it with breast cancer subtypes. Tissue microarrays were constructed from 204 breast cancer patients for whom normal breast tissue away from tumor was available. Slides stained with ER were scanned and expression in normal terminal duct lobular epithelium was quantitated using computer-assisted image analysis. ER expression in normal terminal duct lobular epithelium of postmenopausal women with breast cancer was significantly associated with estrogen and triple (estrogen, progesterone receptors, and HER2) negative phenotypes. Also increased age at diagnosis was significantly associated with ER expression in NBR. ER positivity in normal epithelium did not vary by tumor size, lymph node status, tumor grade, or stage. On the basis of quantitative image analysis, we confirm that ER expression in NBR increases with age in women with breast cancer, and report for the first time, a significant association between ER expression in NBR with ER-negative and triple-negative cancers in postmenopausal women.

  1. Quantification of particles of lethal mercury in mouse viscera: high-resolution study of mercury in cells and tissues.

    PubMed

    Cunha, Elisabete M; Cherdwongcharoensuk, D; Aguas, Artur P

    2003-07-01

    To investigate the early visceral distribution of mercury (Hg), we have intraperitoneally injected a lethal dose of HgCl2 that killed BALB/c mice within 2-4 min. Scanning electron microscopy coupled with X-ray microanalysis (SEM-XRM) was used to detect and quantify Hg in situ in different organs. The highest density of Hg was seen in the liver (60.9+/-24.9 Hg particles per mm2 of tissue); this density was three and six times higher than those of renal or splenic Hg, respectively. Hg was scarce in the lungs and absent in the brain. Considering the relative weights of mouse viscera, our quantitative data show that the liver captured 89% of the visceral Hg; the kidneys captured 8.5% and the spleen just 1.7%. SEM-XRM revealed that most of the visceral Hg was associated with resident macrophages, a few Hg dots being detected on the surface of erythrocytes. We conclude that: (i) most intraperitoneally injected Hg was captured by liver Kupffer cells within minutes of injection; (ii) a 10-fold lower density of Hg particles was observed in the kidneys, and a 50-fold lower deposition of Hg was found in the spleen; (iii) SEM-XRM is an adequate method to quantify microparticles of Hg in tissues and cells.

  2. Quantification of telomere features in tumor tissue sections by an automated 3D imaging-based workflow.

    PubMed

    Gunkel, Manuel; Chung, Inn; Wörz, Stefan; Deeg, Katharina I; Simon, Ronald; Sauter, Guido; Jones, David T W; Korshunov, Andrey; Rohr, Karl; Erfle, Holger; Rippe, Karsten

    2017-02-01

    The microscopic analysis of telomere features provides a wealth of information on the mechanism by which tumor cells maintain their unlimited proliferative potential. Accordingly, the analysis of telomeres in tissue sections of patient tumor samples can be exploited to obtain diagnostic information and to define tumor subgroups. In many instances, however, analysis of the image data is conducted by manual inspection of 2D images at relatively low resolution for only a small part of the sample. As the telomere feature signal distribution is frequently heterogeneous, this approach is prone to a biased selection of the information present in the image and lacks subcellular details. Here we address these issues by using an automated high-resolution imaging and analysis workflow that quantifies individual telomere features on tissue sections for a large number of cells. The approach is particularly suited to assess telomere heterogeneity and low abundant cellular subpopulations with distinct telomere characteristics in a reproducible manner. It comprises the integration of multi-color fluorescence in situ hybridization, immunofluorescence and DNA staining with targeted automated 3D fluorescence microscopy and image analysis. We apply our method to telomeres in glioblastoma and prostate cancer samples, and describe how the imaging data can be used to derive statistically reliable information on telomere length distribution or colocalization with PML nuclear bodies. We anticipate that relating this approach to clinical outcome data will prove to be valuable for pretherapeutic patient stratification.

  3. Quantification of endogenous retinoids.

    PubMed

    Kane, Maureen A; Napoli, Joseph L

    2010-01-01

    Numerous physiological processes require retinoids, including development, nervous system function, immune responsiveness, proliferation, differentiation, and all aspects of reproduction. Reliable retinoid quantification requires suitable handling and, in some cases, resolution of geometric isomers that have different biological activities. Here we describe procedures for reliable and accurate quantification of retinoids, including detailed descriptions for handling retinoids, preparing standard solutions, collecting samples and harvesting tissues, extracting samples, resolving isomers, and detecting with high sensitivity. Sample-specific strategies are provided for optimizing quantification. Approaches to evaluate assay performance also are provided. Retinoid assays described here for mice also are applicable to other organisms including zebrafish, rat, rabbit, and human and for cells in culture. Retinoid quantification, especially that of retinoic acid, should provide insight into many diseases, including Alzheimer's disease, type 2 diabetes, obesity, and cancer.

  4. Quantification of visceral adipose tissue in polycystic ovary syndrome: dual-energy X-ray absorptiometry versus magnetic resonance imaging.

    PubMed

    Frøssing, Signe; Nylander, Malin Chatarina; Chabanova, Elizaveta; Kistorp, Caroline; Skouby, Sven O; Faber, Jens

    2017-01-01

    Background Polycystic ovary syndrome (PCOS) is associated with frequent overweight and abdominal obesity. Quantifying visceral adipose tissue (VAT) in PCOS patients can be a tool to assess metabolic risk and monitor effects of treatment. The latest dual-energy X-ray absorptiometry (DXA) technology can measure VAT and subcutaneous adipose tissue (SAT) in a clinical setting. Purpose To compare DXA-measurements of VAT and SAT with the gold standard MRI in women with PCOS. Material and Methods A cross-sectional study of 67 overweight women with PCOS was performed. Measurements of VAT and SAT were performed by DXA in a 5-cm thick transverse slice at the L4/L5 level and by MRI in a 1-cm thick transverse slice at the L3 level. Results Mean (SD) DXA-VAT was 81 (34) cm(3), DXA-SAT was 498 (118) cm(3), MRI-VAT was 117 (48) cm(3), and MRI-SAT was 408 (122) cm(3). MRI and DXA measures of VAT (r = 0.82, P < 0.001) and SAT (r = 0.92, P < 0.001) correlated closely, and DXA-VAT was stronger correlated with MRI-VAT than BMI (r = 0.62, P < 0.001) and waist circumference (r = 0.60, P < 0.001). DXA-VAT coefficient of variance was 6.7% and inter correlation coefficient was 0.98. Bland-Altman analyses showed DXA to slightly underestimate VAT and SAT measurements compared with MRI. Conclusion DXA and MRI measurements of VAT and SAT correlated closely despite different size of region of interest, and DXA-VAT was superior to waist circumference and BMI in estimating MRI-VAT. DXA showed high reproducibility making it is suitable for repeated measurements in the same individual over time.

  5. Quantification of collagen fiber organization in biological tissues at cellular and molecular scales using second-harmonic generation imaging

    NASA Astrophysics Data System (ADS)

    Ambekar Ramachandra Rao, Raghu

    Collagen is the most abundant structural protein found in the human body, and is responsible for providing structure and function to tissues. Collagen molecules organize naturally into structures called fibers on the scale of the wavelength of light and lack inversion symmetry, thus allowing for the process of second harmonic generation (SHG) when exposed to intense incident light. We have developed two quantitative techniques: Fourier transform-second-harmonic generation (FT-SHG) imaging and generalized chi2 second-harmonic generation (chi2-SHG) imaging. In order to show that FT-SHG imaging can be used as a valuable diagnostic tool for real-world biological problems, we first investigate collagenase-induced injury in horse tendons. Clear differences in collagen fiber organization between normal and injured tendon are quantified. In particular, we observe that the regularly oriented organization of collagen fibers in normal tendons is disrupted in injured tendons leading to a more random organization. We also observe that FT-SHG microscopy is more sensitive in assessing tendon injury compared to the conventional polarized light microscopy. The second study includes quantifying collagen fibers in cortical bone using FT-SHG imaging and comparing it with scanning electron microscopy (SEM). Further, as an example study, we show how FT-SHG imaging could be used to quantify changes in bone structure as a function of age. Some initial work and future directions for extending FT-SHG to 3D are also discussed. The second technique, chi2-SHG imaging, takes advantage of the coherent nature of SHG and utilizes polarization to extract the second-order susceptibility (d elements) which provides information on molecular organization, i.e., it provides access to sub-diffractional changes "optically". We use chi2-SHG in combination with FT-SHG imaging to investigate a couple of biological problems. First, we quantify differences in collagen fiber organization between cornea and

  6. Choice of LC-MS methods for the absolute quantification of drug-metabolizing enzymes and transporters in human tissue: a comparative cost analysis.

    PubMed

    Al Feteisi, Hajar; Achour, Brahim; Barber, Jill; Rostami-Hodjegan, Amin

    2015-03-01

    The quantification of drug-metabolizing enzymes and transporters is important for in vitro-in vivo extrapolation (IVIVE) of xenobiotic clearance, which has become an integral part of drug development. There are different mass spectrometry-based techniques used for quantitative proteomics, and as more laboratories are opting for the use of these methods, selecting the most appropriate tool is becoming a concern. For the first time, we attempt to determine the significance of cost of different LC-MS methods of quantitative analysis of these proteins and to present a framework to objectively assess the choice of the techniques. Based on our analysis, quantification using labeled internal standards is more expensive per sample but provides higher quality data than label-free quantification. Quantification using absolute quantification synthetic peptides is the approach of choice for analyzing less than nine proteins, whereas when quantifying a defined set of proteins (10-50), such as enzymes, in a reasonably large number of samples (20-100), the quantification concatemer technique is more economical, followed by label-free quantification. When analyzing proteomes or sub-proteomes (≥500 proteins), label-free quantification is more cost-effective than the use of labeled internal standards. A cost-benefit approach is described to assess the choice of the most appropriate mass spectrometry-based approach for the quantification of proteins relevant to IVIVE.

  7. Quantification of β-Catenin Signaling Components in Colon Cancer Cell Lines, Tissue Sections, and Microdissected Tumor Cells using Reaction Monitoring Mass Spectrometry

    PubMed Central

    Chen, Yi; Gruidl, Mike; Remily-Wood, Elizabeth; Liu, Richard Z.; Eschrich, Steven; Lloyd, Mark; Nasir, Aejaz; Bui, Marilyn M.; Huang, Emina; Shibata, David; Yeatman, Timothy; Koomen, John M.

    2010-01-01

    Reaction monitoring mass spectrometry has emerged as a powerful tool for targeted detection and quantification of proteins in clinical samples. Here, we report the use of gel electrophoresis for protein fractionation and liquid chromatography coupled to multiple reaction monitoring mass spectrometry (LC-MRM) screening for quantitative analysis of components from the Wnt/β-catenin signaling pathway, which contributes to colon tumor formation and progression. In silico tools are used to design LC-MRM screens for each target protein. Following successful peptide detection, stable isotope labeled peptides are synthesized and developed as internal standards. Then, the assays are implemented in colon cancer cell lines to achieve detection in minimal amounts of cells, compatible with direct translation to clinical specimens. Selected assays are compared with qualitative results from immunoblotting (Westerns) and translated to individual frozen colon tissue sections and laser capture microdissected tumor cells. This LC-MRM platform has been translated from in vitro models to clinical specimens, forming the basis for future experiments in patient assessment. PMID:20590165

  8. Quantification of Candesartan in Mouse Plasma by MALDI-TOFMS and in Tissue Sections by MALDI-Imaging Using the Stable-Isotope Dilution Technique

    PubMed Central

    Nakanishi, Toyofumi; Takai, Shinji; Jin, Denan; Takubo, Takayuki

    2013-01-01

    To determine the contents of candesartan in mouse plasma, and blood vessel and kidney sliced sections and also better understand its pharmacokinetics, we applied matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) and MALDI-imaging mass spectrometry (IMS) with the selected reaction monitoring (SRM) mode using a labeled-internal standard. The results of fundamental examinations showed that the slope of the resulting curves of candesartan in the plasma from the equation was 0.91 and the y-intercept was 0.02. Both intra- and inter-day accuracies (n=10) and the precision of candesartan in the plasma by MALDI-TOFMS with the SRM mode were in the range of 3.4 to 17.3% and 93.2%, respectively. The detection limit of candesartan in spiked plasma was 0.2 nmol/L. IMS analysis enabled us to clarify distinct spacial time-distribution images in sliced mouse blood vessel and kidney sections although it still needed to improve a protocol of quantification. Typical pharmacokinetic patterns of candesartan were obtained in the plasma and sliced kidney sections, but those in the blood vessel sections gradually increased 24 h after administration. MALDI-TOFMS and IMS with the SRM mode are powerful tools to identify the spacial distribution and traceability of candesartan in sliced blood vessel and tissue sections as well as in the plasma. PMID:24860711

  9. Development of a rapid method for the sequential extraction and subsequent quantification of fatty acids and sugars from avocado mesocarp tissue.

    PubMed

    Meyer, Marjolaine D; Terry, Leon A

    2008-08-27

    Methods devised for oil extraction from avocado (Persea americana Mill.) mesocarp (e.g., Soxhlet) are usually lengthy and require operation at high temperature. Moreover, methods for extracting sugars from avocado tissue (e.g., 80% ethanol, v/v) do not allow for lipids to be easily measured from the same sample. This study describes a new simple method that enabled sequential extraction and subsequent quantification of both fatty acids and sugars from the same avocado mesocarp tissue sample. Freeze-dried mesocarp samples of avocado cv. Hass fruit of different ripening stages were extracted by homogenization with hexane and the oil extracts quantified for fatty acid composition by GC. The resulting filter residues were readily usable for sugar extraction with methanol (62.5%, v/v). For comparison, oil was also extracted using the standard Soxhlet technique and the resulting thimble residue extracted for sugars as before. An additional experiment was carried out whereby filter residues were also extracted using ethanol. Average oil yield using the Soxhlet technique was significantly (P < 0.05) higher than that obtained by homogenization with hexane, although the difference remained very slight, and fatty acid profiles of the oil extracts following both methods were very similar. Oil recovery improved with increasing ripeness of the fruit with minor differences observed in the fatty acid composition during postharvest ripening. After lipid removal, methanolic extraction was superior in recovering sucrose and perseitol as compared to 80% ethanol (v/v), whereas mannoheptulose recovery was not affected by solvent used. The method presented has the benefits of shorter extraction time, lower extraction temperature, and reduced amount of solvent and can be used for sequential extraction of fatty acids and sugars from the same sample.

  10. Virtual touch tissue imaging and quantification (VTIQ) in the evaluation of thyroid nodules: the associated factors leading to misdiagnosis

    PubMed Central

    Sun, Cheng-Yu; Lei, Kai-Rong; Liu, Bo-Ji; Bo, Xiao-Wan; Li, Xiao-Long; He, Ya-Ping; Wang, Dan; Ren, Wei-Wei; Zhao, Chong-Ke; Xu, Hui-Xiong

    2017-01-01

    To evaluate the associated factors leading to misdiagnosis with VTIQ for differentiation between benign from malignant thyroid nodules (TNs). The study included 238 benign TNs and 150 malignant TNs. Conventional ultrasound (US) features and VTIQ parameters were obtained and compared with the reference standard of histopathological and/or cytological results. Binary logistic regression analysis was performed to select independent variables leading to misdiagnosis. The maximum shear wave speed (SWS) (SWS-max), mean SWS (SWS-mean), SWS-ratio and standard deviation of SWS (SWS-SD) were significantly higher for malignant TNs compared with benign TNs (all P < 0.001). SWS-mean achieved the highest diagnostic performance with a cut-off value of 3.15 m/s. False positive rate was 13.4% (32/238) while false negative rate was 35.3% (53/150). Intranodular calcification (OR: 1.715) was significantly associated with false positive VTIQ findings, while nodule size (OR: 0.936) and echotexture of the thyroid gland (OR: 0.033) were negatively associated with them. Nodule depth (OR: 0.881) and TI-RADS category (OR: 0.563) were negatively associated with false negative VTIQ findings. These US characteristic of TNs should be taken into consideration when interpreting the results of VTIQ examinations. PMID:28157195

  11. Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

    USGS Publications Warehouse

    Chase, D.M.; Elliott, D.G.; Pascho, R.J.

    2006-01-01

    Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

  12. Quantification of radiation dose from short-lived positron emitters formed in human tissue under proton therapy conditions

    NASA Astrophysics Data System (ADS)

    Kettern, K.; Coenen, H. H.; Qaim, S. M.

    2009-06-01

    The dose distribution in proton therapy is mainly due to primary particles and secondary electrons. The contribution of short-lived β + emitters formed in the interactions of protons with the light mass elements C, N and O has hitherto not been considered. We estimated the formation of 11C, 13N and 15O in irradiation of tissue with 200 MeV protons. The integral yields at 150 MeV were compared with a literature phantom measurement. The results for 11C and 15O agreed very well; for 13N, however, appreciable deviation was observed. The activities were also calculated in the region around the Bragg peak as well as over the path length after entrance of the beam. Dose calculations were then done using the medical internal radiation dose (MIRD) formalism. Furthermore, a dose calculation was simulated for a 150 MeV proton beam (2 nA, 2 min) in a brain tumour. The dose deposited by the positron emitters in the Bragg peak region was found to be about 1.5 mGy, i.e. less than 1% of the dose estimated from the electronic interactions of protons. The absorbed dose in the whole brain amounted to 5.5 mGy.

  13. A new method of infrared thermography for quantification of brown adipose tissue activation in healthy adults (TACTICAL): a randomized trial.

    PubMed

    Ang, Qi Yan; Goh, Hui Jen; Cao, Yanpeng; Li, Yiqun; Chan, Siew-Pang; Swain, Judith L; Henry, Christiani Jeyakumar; Leow, Melvin Khee-Shing

    2017-05-01

    The ability to alter the amount and activity of brown adipose tissue (BAT) in human adults is a potential strategy to manage obesity and related metabolic disorders associated with food, drug, and environmental stimuli with BAT activating/recruiting capacity. Infrared thermography (IRT) provides a non-invasive and inexpensive alternative to the current methods (e.g. (18)F-FDG PET) used to assess BAT. We have quantified BAT activation in the cervical-supraclavicular (C-SCV) region using IRT video imaging and a novel image computational algorithm by studying C-SCV heat production in healthy young men after cold stimulation and the ingestion of capsinoids in a prospective double-blind placebo-controlled randomized trial. Subjects were divided into low-BAT and high-BAT groups based on changes in IR emissions in the C-SCV region induced by cold. The high-BAT group showed significant increases in energy expenditure, fat oxidation, and heat output in the C-SCV region post-capsinoid ingestion compared to post-placebo ingestion, but the low-BAT group did not. Based on these results, we conclude that IRT is a promising tool for quantifying BAT activity.

  14. Prediction of recurrence by quantification of p185neu protein in non-small-cell lung cancer tissue.

    PubMed Central

    Diez, M.; Pollán, M.; Maestro, M.; Torres, A.; Ortega, D.; Gómez, A.; Sánchez, A.; Hernando, F.; Balibrea, J. L.

    1997-01-01

    The concentration of c-erbB-2 oncogene-encoded protein (p185neu) in fresh tumour samples obtained at the time of surgery from 94 non-small-cell lung cancer patients (NSCLC) was determined by an enzyme immunoassay. The relative prognostic importance was estimated, and the influence of other predictors was assessed by means of a Cox's proportional regression model. Median concentration of p185 in tumour tissues was 206 U mg(-1) (range 21-1050 U mg(-1)). p185 level did not differ significantly among subgroups defined by TNM classification, histological type, sex and age. Categorization of patients by p185 level, with 206 U mg(-1) and 343 U mg(-1) taken as cut-off values (corresponding to the 50th and 80th percentiles of the frequency distribution), showed that the recurrence rate, cumulative disease-free likelihood at the 36-month follow-up and median time from surgery to the diagnosis of recurrence worsened progressively as the level of p185 increased. Multivariate analysis confirmed the independent prognostic value of p185 level. Risk of recurrence increased by 1.304 for every increase of 100 units in p185 concentration (95% CI 1.141-1.490) (P<0.001). These findings encourage the inclusion of p185 concentration assay in a future predictive multifactorial prognostic index in NSCLC. PMID:9043025

  15. Heavy Metal Quantification in Renal Tissue of Patients in the State of Yucatan and Its Association with Urolithiasis

    PubMed Central

    May-Ix, Luis A.; Rosado-Rubio, J. Gabriel; Medina-Escobedo, Martha; Castellanos-Ruelas, Arturo F.; Chel-Guerrero, Luis A.; Betancur-Ancona, David A.

    2012-01-01

    A possible cause associated with urinary lithiasis (UL) is the bioaccumulation of heavy metals in the kidney. The aim of this study was to evaluate the content of Cu, Pb, and Cd in kidney tissues removed from patients with nephrological problems and associate it with UL. Samples of 50 kidney sections from patients were analyzed. Results were statistically analyzed using a fixed effects model including the overall mean, the effect of the health status of patients (with or without UL), gender (male and female), the interaction between both factors and the random error (NID  (0, σ 2)). Cu level was 8.8 ± 4.4 mg/kg (mean ± DS) and 25.5% of samples had levels above normal. Lead content in 97.9% of the samples (3.6 ± 1.5 mg/kg) was above normal. All results of Cd (13.2 ± 16.6 mg/kg) were below the maximum permissible limits. There was no difference in the amount of heavy metals on patients with or without UL (P > 0.05) nor depending on the gender (P > 0.05). It was concluded that there is no apparent relationship between a very elevated level of Cu or Pb in the kidney on the development of UL. PMID:23762635

  16. Ultrasonographic tissue characterisation of human Achilles tendons: quantification of tendon structure through a novel non-invasive approach.

    PubMed

    van Schie, H T M; de Vos, R J; de Jonge, S; Bakker, E M; Heijboer, M P; Verhaar, J A N; Tol, J L; Weinans, H

    2010-12-01

    To assess whether three-dimensional imaging of the Achilles tendon by ultrasonographic tissue characterisation (UTC) can differentiate between symptomatic and asymptomatic tendons. Case-control study. Sports Medical Department of the Hague Medical Centre. Twenty-six tendons from patients with chronic midportion Achilles tendinopathy were included. The "matched" control group consisted of 26 asymptomatic tendons. Symptomatic and asymptomatic tendons were scanned using the UTC procedure. One researcher performed the ultrasonographic data collection. These blinded data were randomised, and outcome measures were determined by two independent observers. The raw ultrasonographic images were analysed with a custom-designed algorithm that quantifies the three-dimensional stability of echo patterns, qua intensity and distribution over contiguous transverse images. This three-dimensional stability was related to tendon structure in previous studies. UTC categorises four different echotypes that represent (I) highly stable; (II) medium stable; (III) highly variable and (IV) constantly low intensity and variable distribution. The percentages of echo-types were calculated, and the maximum tendon thickness was measured. Finally, the inter-observer reliability of UTC was determined. Symptomatic tendons showed less pixels in echo-types I and II than asymptomatic tendons (51.5% vs 76.6%, p<0.001), thus less three-dimensional stability of the echo pattern. The mean maximum tendon thickness was 9.2 mm in the symptomatic group and 6.8 mm in the asymptomatic group (p<0.001). The Intraclass Correlation Coefficient (ICC) for the interobserver reliability of determining the echo-types I+II was 0.95. The ICC for tendon thickness was 0.84. UTC can quantitatively evaluate tendon structure and thereby discriminate symptomatic and asymptomatic tendons. As such, UTC might be useful to monitor treatment protocols.

  17. Validation of reference genes for gene expression analysis in olive (Olea europaea) mesocarp tissue by quantitative real-time RT-PCR

    PubMed Central

    2014-01-01

    Background Gene expression analysis using quantitative reverse transcription PCR (qRT-PCR) is a robust method wherein the expression levels of target genes are normalised using internal control genes, known as reference genes, to derive changes in gene expression levels. Although reference genes have recently been suggested for olive tissues, combined/independent analysis on different cultivars has not yet been tested. Therefore, an assessment of reference genes was required to validate the recent findings and select stably expressed genes across different olive cultivars. Results A total of eight candidate reference genes [glyceraldehyde 3-phosphate dehydrogenase (GAPDH), serine/threonine-protein phosphatase catalytic subunit (PP2A), elongation factor 1 alpha (EF1-alpha), polyubiquitin (OUB2), aquaporin tonoplast intrinsic protein (TIP2), tubulin alpha (TUBA), 60S ribosomal protein L18-3 (60S RBP L18-3) and polypyrimidine tract-binding protein homolog 3 (PTB)] were chosen based on their stability in olive tissues as well as in other plants. Expression stability was examined by qRT-PCR across 12 biological samples, representing mesocarp tissues at various developmental stages in three different olive cultivars, Barnea, Frantoio and Picual, independently and together during the 2009 season with two software programs, GeNorm and BestKeeper. Both software packages identified GAPDH, EF1-alpha and PP2A as the three most stable reference genes across the three cultivars and in the cultivar, Barnea. GAPDH, EF1-alpha and 60S RBP L18-3 were found to be most stable reference genes in the cultivar Frantoio while 60S RBP L18-3, OUB2 and PP2A were found to be most stable reference genes in the cultivar Picual. Conclusions The analyses of expression stability of reference genes using qRT-PCR revealed that GAPDH, EF1-alpha, PP2A, 60S RBP L18-3 and OUB2 are suitable reference genes for expression analysis in developing Olea europaea mesocarp tissues, displaying the highest level

  18. Validation of reference genes for gene expression analysis in olive (Olea europaea) mesocarp tissue by quantitative real-time RT-PCR.

    PubMed

    Ray, Debashree L; Johnson, Joshua C

    2014-05-18

    Gene expression analysis using quantitative reverse transcription PCR (qRT-PCR) is a robust method wherein the expression levels of target genes are normalised using internal control genes, known as reference genes, to derive changes in gene expression levels. Although reference genes have recently been suggested for olive tissues, combined/independent analysis on different cultivars has not yet been tested. Therefore, an assessment of reference genes was required to validate the recent findings and select stably expressed genes across different olive cultivars. A total of eight candidate reference genes [glyceraldehyde 3-phosphate dehydrogenase (GAPDH), serine/threonine-protein phosphatase catalytic subunit (PP2A), elongation factor 1 alpha (EF1-alpha), polyubiquitin (OUB2), aquaporin tonoplast intrinsic protein (TIP2), tubulin alpha (TUBA), 60S ribosomal protein L18-3 (60S RBP L18-3) and polypyrimidine tract-binding protein homolog 3 (PTB)] were chosen based on their stability in olive tissues as well as in other plants. Expression stability was examined by qRT-PCR across 12 biological samples, representing mesocarp tissues at various developmental stages in three different olive cultivars, Barnea, Frantoio and Picual, independently and together during the 2009 season with two software programs, GeNorm and BestKeeper. Both software packages identified GAPDH, EF1-alpha and PP2A as the three most stable reference genes across the three cultivars and in the cultivar, Barnea. GAPDH, EF1-alpha and 60S RBP L18-3 were found to be most stable reference genes in the cultivar Frantoio while 60S RBP L18-3, OUB2 and PP2A were found to be most stable reference genes in the cultivar Picual. The analyses of expression stability of reference genes using qRT-PCR revealed that GAPDH, EF1-alpha, PP2A, 60S RBP L18-3 and OUB2 are suitable reference genes for expression analysis in developing Olea europaea mesocarp tissues, displaying the highest level of expression stability across

  19. Certification of methylmercury in cod fish tissue certified reference material by species-specific isotope dilution mass spectrometric analysis.

    PubMed

    Inagaki, Kazumi; Kuroiwa, Takayoshi; Narukawa, Tomohiro; Yarita, Takashi; Takatsu, Akiko; Okamoto, Kensaku; Chiba, Koichi

    2008-07-01

    A new cod fish tissue certified reference material, NMIJ CRM 7402-a, for methylmercury analysis was certified by the National Metrological Institute of Japan in the National Institute of Advanced Industrial Science and Technology (NMIJ/AIST). Cod fish was collected from the sea close to Japan. The cod muscle was powdered by freeze-pulverization and was placed into 600 glass bottles (10 g each), which were sterilized with gamma-ray irradiation. The certification was carried out using species-specific isotope dilution gas chromatography inductively coupled plasma mass spectrometry (SSID-GC-ICPMS), where (202)Hg-enriched methylmercury (MeHg) was used as the spike compound. In order to avoid any possible analytical biases caused by nonquantitative extraction, degradation and/or formation of MeHg in sample preparations, two different extraction methods (KOH/methanol and HCl/methanol extractions) were performed, and one of these extraction methods utilized two different derivatization methods (ethylation and phenylation). A double ID method was adopted to minimize the uncertainty arising from the analyses. In order to ensure not only the reliability of the analytical results but also traceability to SI units, the standard solution of MeHg used for the reverse-ID was prepared from high-purity MeHg chloride and was carefully assayed as follows: the total mercury was determined by ID-ICPMS following aqua regia digestion, and the ratio of Hg as MeHg to the total Hg content was estimated by GC-ICPMS. The certified value given for MeHg is 0.58 +/- 0.02 mg kg(-1) as Hg.

  20. Evaluation of Sorghum [Sorghum bicolor (L.)] Reference Genes in Various Tissues and under Abiotic Stress Conditions for Quantitative Real-Time PCR Data Normalization.

    PubMed

    Sudhakar Reddy, Palakolanu; Srinivas Reddy, Dumbala; Sivasakthi, Kaliamoorthy; Bhatnagar-Mathur, Pooja; Vadez, Vincent; Sharma, Kiran K

    2016-01-01

    Accurate and reliable gene expression data from qPCR depends on stable reference gene expression for potential gene functional analyses. In this study, 15 reference genes were selected and analyzed in various sample sets including abiotic stress treatments (salt, cold, water stress, heat, and abscisic acid) and tissues (leaves, roots, seedlings, panicle, and mature seeds). Statistical tools, including geNorm, NormFinder and RefFinder, were utilized to assess the suitability of reference genes based on their stability rankings for various sample groups. For abiotic stress, PP2A and CYP were identified as the most stable genes. In contrast, EIF4α was the most stable in the tissue sample set, followed by PP2A; PP2A was the most stable in all the sample set, followed by EIF4α. GAPDH, and UBC1 were the least stably expressed in the tissue and all the sample sets. These results also indicated that the use of two candidate reference genes would be sufficient for the optimization of normalization studies. To further verify the suitability of these genes for use as reference genes, SbHSF5 and SbHSF13 gene expression levels were normalized using the most and least stable sorghum reference genes in root and water stressed-leaf tissues of five sorghum varieties. This is the first systematic study of the selection of the most stable reference genes for qPCR-related assays in Sorghum bicolor that will potentially benefit future gene expression studies in sorghum and other closely related species.

  1. Evaluation of Sorghum [Sorghum bicolor (L.)] Reference Genes in Various Tissues and under Abiotic Stress Conditions for Quantitative Real-Time PCR Data Normalization

    PubMed Central

    Sudhakar Reddy, Palakolanu; Srinivas Reddy, Dumbala; Sivasakthi, Kaliamoorthy; Bhatnagar-Mathur, Pooja; Vadez, Vincent; Sharma, Kiran K.

    2016-01-01

    Accurate and reliable gene expression data from qPCR depends on stable reference gene expression for potential gene functional analyses. In this study, 15 reference genes were selected and analyzed in various sample sets including abiotic stress treatments (salt, cold, water stress, heat, and abscisic acid) and tissues (leaves, roots, seedlings, panicle, and mature seeds). Statistical tools, including geNorm, NormFinder and RefFinder, were utilized to assess the suitability of reference genes based on their stability rankings for various sample groups. For abiotic stress, PP2A and CYP were identified as the most stable genes. In contrast, EIF4α was the most stable in the tissue sample set, followed by PP2A; PP2A was the most stable in all the sample set, followed by EIF4α. GAPDH, and UBC1 were the least stably expressed in the tissue and all the sample sets. These results also indicated that the use of two candidate reference genes would be sufficient for the optimization of normalization studies. To further verify the suitability of these genes for use as reference genes, SbHSF5 and SbHSF13 gene expression levels were normalized using the most and least stable sorghum reference genes in root and water stressed-leaf tissues of five sorghum varieties. This is the first systematic study of the selection of the most stable reference genes for qPCR-related assays in Sorghum bicolor that will potentially benefit future gene expression studies in sorghum and other closely related species. PMID:27200008

  2. Reference gene selection for quantitative gene expression studies during biological invasions: A test on multiple genes and tissues in a model ascidian Ciona savignyi.

    PubMed

    Huang, Xuena; Gao, Yangchun; Jiang, Bei; Zhou, Zunchun; Zhan, Aibin

    2016-01-15

    As invasive species have successfully colonized a wide range of dramatically different local environments, they offer a good opportunity to study interactions between species and rapidly changing environments. Gene expression represents one of the primary and crucial mechanisms for rapid adaptation to local environments. Here, we aim to select reference genes for quantitative gene expression analysis based on quantitative Real-Time PCR (qRT-PCR) for a model invasive ascidian, Ciona savignyi. We analyzed the stability of ten candidate reference genes in three tissues (siphon, pharynx and intestine) under two key environmental stresses (temperature and salinity) in the marine realm based on three programs (geNorm, NormFinder and delta Ct method). Our results demonstrated only minor difference for stability rankings among the three methods. The use of different single reference gene might influence the data interpretation, while multiple reference genes could minimize possible errors. Therefore, reference gene combinations were recommended for different tissues - the optimal reference gene combination for siphon was RPS15 and RPL17 under temperature stress, and RPL17, UBQ and TubA under salinity treatment; for pharynx, TubB, TubA and RPL17 were the most stable genes under temperature stress, while TubB, TubA and UBQ were the best under salinity stress; for intestine, UBQ, RPS15 and RPL17 were the most reliable reference genes under both treatments. Our results suggest that the necessity of selection and test of reference genes for different tissues under varying environmental stresses. The results obtained here are expected to reveal mechanisms of gene expression-mediated invasion success using C. savignyi as a model species.

  3. Evaluation of candidate reference genes for RT-qPCR studies in three metabolism related tissues of mice after caloric restriction

    PubMed Central

    Gong, Huan; Sun, Liang; Chen, Beidong; Han, Yiwen; Pang, Jing; Wu, Wei; Qi, Ruomei; Zhang, Tie-mei

    2016-01-01

    Reverse transcription quantitative-polymerase chain reaction (RT-qPCR) is a routine method for gene expression analysis, and reliable results depend on proper normalization by stable reference genes. Caloric restriction (CR) is a robust lifestyle intervention to slow aging and delay onset of age-associated diseases via inducing global changes in gene expression. Reliable normalization of RT-qPCR data becomes crucial in CR studies. In this study, the expression stability of 12 candidate reference genes were evaluated in inguinal white adipose tissue (iWAT), skeletal muscle (Sk.M) and liver of CR mice by using three algorithms, geNorm, NormFinder, and Bestkeeper. Our results showed β2m, Ppia and Hmbs as the most stable genes in iWAT, Sk.M and liver, respectively. Moreover, two reference genes were sufficient to normalize RT-qPCR data in each tissue and the suitable pair of reference genes was β2m-Hprt in iWAT, Ppia-Gusb in Sk.M and Hmbs-β2m in liver. By contrast, the least stable gene in iWAT or Sk.M was Gapdh, and in liver was Pgk1. Furthermore, the expression of Leptin and Ppar-γ were profiled in these tissues to validate the selected reference genes. Our data provided a basis for gene expression analysis in future CR studies. PMID:27922100

  4. Selection of reference genes for quantitative RT-PCR (RT-qPCR) analysis of rat tissues under physiological and toxicological conditions.

    PubMed

    Svingen, Terje; Letting, Heidi; Hadrup, Niels; Hass, Ulla; Vinggaard, Anne Marie

    2015-01-01

    In biological research the analysis of gene expression levels in cells and tissues can be a powerful tool to gain insights into biological processes. For this, quantitative RT-PCR (RT-qPCR) is a popular method that often involve the use of constitutively expressed endogenous reference (or 'housekeeping') gene for normalization of data. Thus, it is essential to use reference genes that have been verified to be stably expressed within the specific experimental setting. Here, we have analysed the expression stability of 12 commonly used reference genes (Actb, B2m, Gapdh, Hprt, Pgk1, Rn18s, Rpl13a, Rps18, Rps29, Sdha, Tbp and Ubc) across several juvenile and adult rat tissues (liver, adrenal, prostate, fat pad, testis and ovaries), both under normal conditions and following exposure to various chemicals during development. Employing NormFinder and BestKeeper softwares, we found Hprt and Sdha to be amongst the most stable genes across normal and manipulated tissues, with several others also being suitable for most tissues. Tbp and B2m displayed highest variability in transcript levels between tissues and developmental stages. It was also observed that the reference genes were most unstable in liver and testis following toxicological exposure. For future studies, we propose the use of more than one verified reference gene and the continuous monitoring of their suitability under various experimental conditions, including toxicological studies, based on changes in threshold (Ct) values from cDNA samples having been reverse-transcribed from a constant input concentration of RNA.

  5. High-throughput method development for sensitive, accurate, and reproducible quantification of therapeutic monoclonal antibodies in tissues using orthogonal array optimization and nano liquid chromatography/selected reaction monitoring mass spectrometry.

    PubMed

    Duan, Xiaotao; Abuqayyas, Lubna; Dai, Lipeng; Balthasar, Joseph P; Qu, Jun

    2012-05-15

    Although liquid chromatography/mass spectrometry using selected reaction monitoring (LC/SRM-MS) holds great promise for targeted protein analysis, quantification of therapeutic monoclonal antibody (mAb) in tissues represents a daunting challenge due to the extremely low tissue levels, complexity of tissue matrixes, and the absence of an efficient strategy to develop an optimal LC/SRM-MS method. Here we describe a high-throughput, streamlined strategy for the development of sensitive, selective, and reliable quantitative methods of mAb in tissue matrixes. A sensitive nano-LC/nanospray-MS method was employed to achieve a low lower limit of quantification (LOQ). For selection of signature peptides (SP), the SP candidates were identified by a high-resolution Orbitrap and then optimal SRM conditions for each candidate were obtained using a high-throughput, on-the-fly orthogonal array optimization (OAO) strategy, which is capable of optimizing a large set of SP candidates within a single nano-LC/SRM-MS run. Using the optimized conditions, the candidates were experimentally evaluated for both sensitivity and stability in the target matrixes, and SP selection was based on the results of the evaluation. Two unique SP, respectively from the light and heavy chain, were chosen for quantification of each mAb. The use of two SP improves the quantitative reliability by gauging possible degradation/modification of the mAb. Standard mAb proteins with verified purities were utilized for calibration curves, to prevent the quantitative biases that may otherwise occur when synthesized peptides were used as calibrators. We showed a proof of concept by rapidly developing sensitive nano-LC/SRM-MS methods for quantifying two mAb (8c2 and cT84.66) in multiple preclinical tissues. High sensitivity was achieved for both mAb with LOQ ranged from 0.156 to 0.312 μg/g across different tissues, and the overall procedure showed a wide dynamic range (≥500-fold) and good accuracy [relative error

  6. Precise simultaneous quantification of methadone and cocaine in rat serum and brain tissue samples following their successive i.p. administration.

    PubMed

    Nakhla, David S; Hussein, Lobna A; Magdy, N; Abdallah, Inas A; Hassan, Hazem E

    2017-03-24

    A sensitive high-performance liquid chromatography (HPLC) assay with dual UV detection has been developed and validated for the simultaneous quantification of methadone and cocaine in rat serum and brain tissue samples. Liquid-liquid extraction using hexanes was applied for samples extraction with Levo-Tetrahydropalmatine (L-THP) as the internal standard. Chromatographic separation of the analytes was achieved on a reversed-phase Waters Symmetry(®) C18 column (150mm×4.6mm, 5μm). A gradient elution was employed with a mobile phase consisting of 5mM potassium phosphate containing 0.1% triethylamine (pH=6.5) (A) and acetonitrile (B) with a flow rate of 1mL/min. UV detection was employed at 215nm and 235nm for the determination of methadone and cocaine, respectively. The calibration curves were linear over the range of 0.05-10μg/mL for both methadone and cocaine. The assay was validated according to FDA guidelines for bioanalytical method validation and results were satisfactory and met FDA criteria. Inter-day accuracy values of serum and brain samples ranged from 96.97 to 105.59% while intra-day accuracy values ranged from 91.49 to 111.92%. Stability assays showed that both methadone and cocaine were stable during sample storage, preparation, and analytical procedures. The method was successfully used to analyze biological samples obtained from a drug- drug interaction pharmacokinetics (PK) study conducted in rats to investigate the effect of methadone on cocaine PK. Our method not only can be used for bioanalysis of samples obtained from rats but also can potentially be applied to human biological serum samples to monitor compliance to methadone maintenance therapy (MMT) and to detect possible cocaine-methadone co-abuse.

  7. The use of laser microdissection in the identification of suitable reference genes for normalization of quantitative real-time PCR in human FFPE epithelial ovarian tissue samples.

    PubMed

    Cai, Jing; Li, Tao; Huang, Bangxing; Cheng, Henghui; Ding, Hui; Dong, Weihong; Xiao, Man; Liu, Ling; Wang, Zehua

    2014-01-01

    Quantitative real-time PCR (qPCR) is a powerful and reproducible method of gene expression analysis in which expression levels are quantified by normalization against reference genes. Therefore, to investigate the potential biomarkers and therapeutic targets for epithelial ovarian cancer by qPCR, it is critical to identify stable reference genes. In this study, twelve housekeeping genes (ACTB, GAPDH, 18S rRNA, GUSB, PPIA, PBGD, PUM1, TBP, HRPT1, RPLP0, RPL13A, and B2M) were analyzed in 50 ovarian samples from normal, benign, borderline, and malignant tissues. For reliable results, laser microdissection (LMD), an effective technique used to prepare homogeneous starting material, was utilized to precisely excise target tissues or cells. One-way analysis of variance (ANOVA) and nonparametric (Kruskal-Wallis) tests were used to compare the expression differences. NormFinder and geNorm software were employed to further validate the suitability and stability of the candidate genes. Results showed that epithelial cells occupied a small percentage of the normal ovary indeed. The expression of ACTB, PPIA, RPL13A, RPLP0, and TBP were stable independent of the disease progression. In addition, NormFinder and geNorm identified the most stable combination (ACTB, PPIA, RPLP0, and TBP) and the relatively unstable reference gene GAPDH from the twelve commonly used housekeeping genes. Our results highlight the use of homogeneous ovarian tissues and multiple-reference normalization strategy, e.g. the combination of ACTB, PPIA, RPLP0, and TBP, for qPCR in epithelial ovarian tissues, whereas GAPDH, the most commonly used reference gene, is not recommended, especially as a single reference gene.

  8. Development of a Pacific oyster (Crassostrea gigas) 31,918-feature microarray: identification of reference genes and tissue-enriched expression patterns

    PubMed Central

    2011-01-01

    Background Research using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies. As many as 56,268 EST sequences have been sequenced to date, representing a genome-wide resource that can be used for transcriptomic investigations. Results In this paper, we developed a Pacific oyster microarray containing oligonucleotides representing 31,918 transcribed sequences selected from the publicly accessible GigasDatabase. This newly designed microarray was used to study the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglia, hemocytes, labial palps and digestive gland. Statistical analyses identified genes differentially expressed among tissues and clusters of tissue-enriched genes. These genes reflect major tissue-specific functions at the molecular level, such as tissue formation in the mantle, filtering in the gills and labial palps, and reproduction in the gonads. Hierarchical clustering predicted the involvement of unannotated genes in specific functional pathways such as the insulin/NPY pathway, an important pathway under study in our model species. Microarray data also accurately identified reference genes whose mRNA level appeared stable across all the analyzed tissues. Adp-ribosylation factor 1 (arf1) appeared to be the most robust reference for normalizing gene expression data across different tissues and is therefore proposed as a relevant reference gene for further gene expression analysis in the Pacific oyster. Conclusions This study provides a new transcriptomic tool for studies of oyster biology, which will help in the annotation of its genome and which identifies candidate reference genes for gene expression analysis. PMID:21951653

  9. Evaluation of Appropriate Reference Genes for Reverse Transcription-Quantitative PCR Studies in Different Tissues of a Desert Poplar via Comparision of Different Algorithms

    PubMed Central

    Wang, Hou-Ling; Li, Lan; Tang, Sha; Yuan, Chao; Tian, Qianqian; Su, Yanyan; Li, Hui-Guang; Zhao, Lin; Yin, Weilun; Zhao, Rui; Xia, Xinli

    2015-01-01

    Despite the unshakable status of reverse transcription-quantitative PCR in gene expression analysis, it has certain disadvantages, including that the results are highly dependent on the reference genes selected for data normalization. Since inappropriate endogenous control genes will lead to inaccurate target gene expression profiles, the validation of suitable internal reference genes is essential. Given the increasing interest in functional genes and genomics of Populus euphratica, a desert poplar showing extraordinary adaptation to salt stress, we evaluated the expression stability of ten candidate reference genes in P. euphratica roots, stems, and leaves under salt stress conditions. We used five algorithms, namely, ΔCt, NormFinder, geNorm, GrayNorm, and a rank aggregation method (RankAggreg) to identify suitable normalizers. To support the suitability of the identified reference genes and to compare the relative merits of these different algorithms, we analyzed and compared the relative expression levels of nine P. euphratica functional genes in different tissues. Our results indicate that a combination of multiple reference genes recommended by GrayNorm algorithm (e.g., a combination of Actin, EF1α, GAPDH, RP, UBQ in root) should be used instead of a single reference gene. These results are valuable for research of gene identification in different P. euphratica tissues. PMID:26343648

  10. Quantification of brain lipids by FTIR spectroscopy and partial least squares regression

    NASA Astrophysics Data System (ADS)

    Dreissig, Isabell; Machill, Susanne; Salzer, Reiner; Krafft, Christoph

    2009-01-01

    Brain tissue is characterized by high lipid content. Its content decreases and the lipid composition changes during transformation from normal brain tissue to tumors. Therefore, the analysis of brain lipids might complement the existing diagnostic tools to determine the tumor type and tumor grade. Objective of this work is to extract lipids from gray matter and white matter of porcine brain tissue, record infrared (IR) spectra of these extracts and develop a quantification model for the main lipids based on partial least squares (PLS) regression. IR spectra of the pure lipids cholesterol, cholesterol ester, phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol, sphingomyelin, galactocerebroside and sulfatide were used as references. Two lipid mixtures were prepared for training and validation of the quantification model. The composition of lipid extracts that were predicted by the PLS regression of IR spectra was compared with lipid quantification by thin layer chromatography.

  11. Quantification of five compounds with heterogeneous physicochemical properties (morphine, 6-monoacetylmorphine, cyamemazine, meprobamate and caffeine) in 11 fluids and tissues, using automated solid-phase extraction and gas chromatography-tandem mass spectrometry.

    PubMed

    Bévalot, Fabien; Bottinelli, Charline; Cartiser, Nathalie; Fanton, Laurent; Guitton, Jérôme

    2014-06-01

    An automated solid-phase extraction (SPE) protocol followed by gas chromatography coupled with tandem mass spectrometry was developed for quantification of caffeine, cyamemazine, meprobamate, morphine and 6-monoacetylmorphine (6-MAM) in 11 biological matrices [blood, urine, bile, vitreous humor, liver, kidney, lung and skeletal muscle, brain, adipose tissue and bone marrow (BM)]. The assay was validated for linearity, within- and between-day precision and accuracy, limits of quantification, selectivity, extraction recovery (ER), sample dilution and autosampler stability on BM. For the other matrices, partial validation was performed (limits of quantification, linearity, within-day precision, accuracy, selectivity and ER). The lower limits of quantification were 12.5 ng/mL(ng/g) for 6-MAM, morphine and cyamemazine, 100 ng/mL(ng/g) for meprobamate and 50 ng/mL(ng/g) for caffeine. Analysis of real-case samples demonstrated the performance of the assay in forensic toxicology to investigate challenging cases in which, for example, blood is not available or in which analysis in alternative matrices could be relevant. The SPE protocol was also assessed as an extraction procedure that could target other relevant analytes of interest. The extraction procedure was applied to 12 molecules of forensic interest with various physicochemical properties (alimemazine, alprazolam, amitriptyline, citalopram, cocaine, diazepam, levomepromazine, nordazepam, tramadol, venlafaxine, pentobarbital and phenobarbital). All drugs were able to be detected at therapeutic concentrations in blood and in the alternate matrices.

  12. Quantification of drugs in plasma without primary reference standards by liquid chromatography-chemiluminescence nitrogen detection: application to tramadol metabolite ratios.

    PubMed

    Ojanperä, Suvi; Rasanen, Ilpo; Sistonen, Johanna; Pelander, Anna; Vuori, Erkki; Ojanperä, Ilkka

    2007-08-01

    Lack of availability of reference standards for drug metabolites, newly released drugs, and illicit drugs hinders the analysis of these substances in biologic samples. To counter this problem, an approach is presented here for quantitative drug analysis in plasma without primary reference standards by liquid chromatography-chemiluminescence nitrogen detection (LC-CLND). To demonstrate the feasibility of the method, metabolic ratios of the opioid drug tramadol were determined in the setting of a pharmacogenetic study. Four volunteers were given a single 100-mg oral dose of tramadol, and a blood sample was collected from each subject 1 hour later. Tramadol, O-desmethyltramadol, and nortramadol were determined in plasma by LC-CLND without reference standards and by a gas chromatography-mass spectrometry reference method. In contrast to previous CLND studies lacking an extraction step, a liquid-liquid extraction system was created for 5-mL plasma samples using n-butyl chloride-isopropyl alcohol (98 + 2) at pH 10. Extraction recovery estimation was based on model compounds chosen according to their similar physicochemical characteristics (retention time, pKa, logD). Instrument calibration was performed with a single secondary standard (caffeine) using the equimolar response of the detector to nitrogen. The mean differences between the results of the LC-CLND and gas chromatography-mass spectrometry methods for tramadol, O-desmethyltramadol, and nortramadol were 8%, 32%, and 19%, respectively. The sensitivity of LC-CLND was sufficient for therapeutic concentrations of tramadol and metabolites. A good correlation was obtained between genotype, expressed by the number of functional genes, and the plasma metabolite ratios. This experiment suggests that a recovery-corrected LC-CLND analysis produces sufficiently accurate results to be useful in a clinical context, particularly in instances in which reference standards are not readily accessible.

  13. Dynamic modeling of breast tissue with application of model reference adaptive system identification technique based on clinical robot-assisted palpation.

    PubMed

    Keshavarz, M; Mojra, A

    2015-11-01

    Accurate identification of breast tissue's dynamic behavior in physical examination is critical to successful diagnosis and treatment. In this study a model reference adaptive system identification (MRAS) algorithm is utilized to estimate the dynamic behavior of breast tissue from mechanical stress-strain datasets. A robot-assisted device (Robo-Tac-BMI) is going to mimic physical palpation on a 45 year old woman having a benign mass in the left breast. Stress-strain datasets will be collected over 14 regions of both breasts in a specific period of time. Then, a 2nd order linear model is adapted to the experimental datasets. It was confirmed that a unique dynamic model with maximum error about 0.89% is descriptive of the breast tissue behavior meanwhile mass detection may be achieved by 56.1% difference from the normal tissue.

  14. Establishment of a Reliable Horizontal Reference Plane for 3-Dimensional Facial Soft Tissue Evaluation Before and After Orthognathic Surgery.

    PubMed

    Chortrakarnkij, Peerasak; Lonic, Daniel; Lin, Hsiu-Hsia; Lo, Lun-Jou

    2017-03-01

    This study aims to demonstrate the reliability of our proposed facial reference system in the horizontal axis using 3-dimensional photogrammetry and to find a correlation between this plane and the Frankfurt horizontal (FH) plane. Forty-one patients were enrolled. Three-dimensional facial images were taken before and 6 months after orthognathic surgery. Superimposition was carried out, and differences in landmark position were evaluated. Two constant landmarks were selected to construct a reference system within a standardized reference frame. Cone-beam computed tomography and 3-dimensional facial images were superimposed. Two reference lines were identified, and the angle between these lines was calculated. For landmark reliability, 5 landmarks [gnathion, nasion, exocanthion (Ex), endocanthion, and tragion (T)] were constant. Two landmarks (Ex and T) were selected to construct a reference system within a standardized reference frame. For angular measurement, the mean angle between this reference plane and the skeletal FH plane was 17.6 ± 2.0 degrees. There was no statistical difference between sex, side, and preoperative/postoperative timing of photography. Our proposed reference plane is constructed from reliable facial Ex and T landmarks. This plane is consistent and crosses the FH plane at 17.6 degrees.

  15. Quantification of acylglycines in human urine by HPLC electrospray ionization-tandem mass spectrometry and the establishment of pediatric reference interval in local Chinese.

    PubMed

    Fong, Bonnie Mei-Wah; Tam, Sidney; Leung, Kelvin Sze-Yin

    2012-01-15

    Urinary organic acids, plasma amino acids and acylcarnitine profile analyses are the main tools used to diagnose inborn errors of metabolisms (IEMs). However, without metabolic decompensation, these parameters are often not helpful. On the other hand, in cases of IEM, acylglycines are consistently raised even when patients appear to be in remission. This study aims to set-up a simple liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) method for the determination of urine acylglycines, complementary to organic acid and acylcarnitine profiles, for the diagnosis of IEM. In addition, local reference intervals for various acylglycines are established by using this method. Acylglycines were isolated by solid-phase extraction, derivatized with n-butanol, separated by HPLC, and detected by ESI-MS/MS. Acylglycines were quantified with deuterated internal standards. Mean recoveries of acylglycines ranged from 90.2 to 109.3%. Within- and between-run imprecisions for all acylglycines have CVs less than 10%. Linear regression coefficients were greater than 0.99. Reference intervals were established according to CLSI guidelines by analyzing 204 samples from apparently healthy individuals less than 18 years of age. The distributions of AG in the "normal" urine were skewed towards the right. After log transformation, all the results were normally distributed. Partitioning into age group reference intervals was not indicated, according to the Harris and Boyd approach. In this context, a single reference interval for each acylglycine could be used. This method of urine acylglycines analysis is a powerful diagnostic tool, complementary to urine organic acids and plasma acylcarnitine profiling, for detecting certain inborn errors of metabolism.

  16. SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence.

    PubMed

    Lopez-Maestre, Hélène; Brinza, Lilia; Marchet, Camille; Kielbassa, Janice; Bastien, Sylvère; Boutigny, Mathilde; Monnin, David; Filali, Adil El; Carareto, Claudia Marcia; Vieira, Cristina; Picard, Franck; Kremer, Natacha; Vavre, Fabrice; Sagot, Marie-France; Lacroix, Vincent

    2016-11-02

    SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot be applied to non-model species. They are also mostly tailored for whole genome (re-)sequencing experiments, whereas in many cases, transcriptome sequencing can be used as a cheaper alternative which already enables to identify SNPs located in transcribed regions. In this paper, we propose a method that identifies, quantifies and annotates SNPs without any reference genome, using RNA-seq data only. Individuals can be pooled prior to sequencing, if not enough material is available from one individual. Using pooled human RNA-seq data, we clarify the precision and recall of our method and discuss them with respect to other methods which use a reference genome or an assembled transcriptome. We then validate experimentally the predictions of our method using RNA-seq data from two non-model species. The method can be used for any species to annotate SNPs and predict their impact on the protein sequence. We further enable to test for the association of the identified SNPs with a phenotype of interest.

  17. SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence

    PubMed Central

    Lopez-Maestre, Hélène; Brinza, Lilia; Marchet, Camille; Kielbassa, Janice; Bastien, Sylvère; Boutigny, Mathilde; Monnin, David; Filali, Adil El; Carareto, Claudia Marcia; Vieira, Cristina; Picard, Franck; Kremer, Natacha; Vavre, Fabrice; Sagot, Marie-France; Lacroix, Vincent

    2016-01-01

    SNPs (Single Nucleotide Polymorphisms) are genetic markers whose precise identification is a prerequisite for association studies. Methods to identify them are currently well developed for model species, but rely on the availability of a (good) reference genome, and therefore cannot be applied to non-model species. They are also mostly tailored for whole genome (re-)sequencing experiments, whereas in many cases, transcriptome sequencing can be used as a cheaper alternative which already enables to identify SNPs located in transcribed regions. In this paper, we propose a method that identifies, quantifies and annotates SNPs without any reference genome, using RNA-seq data only. Individuals can be pooled prior to sequencing, if not enough material is available from one individual. Using pooled human RNA-seq data, we clarify the precision and recall of our method and discuss them with respect to other methods which use a reference genome or an assembled transcriptome. We then validate experimentally the predictions of our method using RNA-seq data from two non-model species. The method can be used for any species to annotate SNPs and predict their impact on the protein sequence. We further enable to test for the association of the identified SNPs with a phenotype of interest. PMID:27458203

  18. Development and reproducibility of a 3D stereophotogrammetric reference frame for facial soft tissue growth of babies and young children with and without orofacial clefts.

    PubMed

    Brons, S; van Beusichem, M E; Maal, T J J; Plooij, J M; Bronkhorst, E M; Bergé, S J; Kuijpers-Jagtman, A M

    2013-01-01

    The aim of this study was to develop a reference frame for three dimensional (3D) facial soft tissue growth analysis in children and to determine its reproducibility. Two observers twice placed the reference frame on 39 3D-stereophotogrammetry facial images of children with orofacial clefts and control children. The observers' performances were analyzed by calculating mean distance, distance variability, and P95 between the same facial surfaces at two different time points. Correlations between observers were analyzed with Pearson's correlation coefficient. The influence of presence of a cleft, absence of one ear in the photograph, and age on the reproducibility of the reference frame was checked using Student's t test. Results of intraobserver comparisons showed a mean distance of <0.40 mm, distance variability of <0.51 mm, and P95 of <0.80 mm. For interobserver reliability, the mean distance was <0.52 mm, distance variability was <0.53 mm, and P95 was <1.10 mm. Presence of a cleft, age, and absence of one ear on the 3D photograph did not have a significant influence on the reproducibility of placing the reference frame. The children's reference frame is a reproducible method to superimpose on 3D soft tissue stereophotogrammetry photographs of growing individuals with and without orofacial clefts.

  19. Selection of reference genes is critical for miRNA expression analysis in human cardiac tissue. A focus on atrial fibrillation

    PubMed Central

    Masè, Michela; Grasso, Margherita; Avogaro, Laura; D’Amato, Elvira; Tessarolo, Francesco; Graffigna, Angelo; Denti, Michela Alessandra; Ravelli, Flavia

    2017-01-01

    MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached. This work aims to assess reference genes stability in human cardiac tissue with a focus on AF investigation. We evaluated the stability of five reference genes (U6, SNORD48, SNORD44, miR-16, and 5S) in atrial tissue samples from eighteen cardiac-surgery patients in sinus rhythm and AF. Stability was quantified by combining BestKeeper, delta-Cq, GeNorm, and NormFinder statistical tools. All methods assessed SNORD48 as the best and U6 as the worst reference gene. Applications of different normalization strategies significantly impacted miRNA expression profiles in the study population. Our results point out the necessity of a consensus on data normalization in AF studies to avoid the emergence of divergent biological conclusions. PMID:28117343

  20. Structure-function relationships in radiation-induced cell and tissue lesions: special references to the contributions of scanning electron microscopy and hematopoietic tissue responses

    SciTech Connect

    Seed, T.M.

    1987-03-01

    Contributions of scanning electron microscopy to the field of radiation biology are briefly reviewed and presented in terms of an overall goal to identify and characterize the structural features of radiation-induced lesions in vital cell and tissue targets. In the context of lesion production, the major radiation-elicited response sequences, the types and nature of measured end points, and governing temporal and radiobiological parameters are discussed and illustrated by using results derived from both in vitro cell systems and in vivo studies that measured tissue responses from various organ systems (respiratory, digestive, circulatory, and central nervous systems). Work in our laboratory on the nature of early and late hematopathologic tissue responses (aplastic anemia and myeloid leukemia) induced by protracted radiation exposure and the bridging effect of repair processes relative to the expression of these pathologies is highlighted.

  1. Quantification of brown and white adipose tissue based on Gaussian mixture model using water-fat and T2* MRI in adolescents.

    PubMed

    Hui, Steve C N; Ko, Jacky K L; Zhang, Teng; Shi, Lin; Yeung, David K W; Wang, Defeng; Chan, Queenie; Chu, Winnie C W

    2017-09-01

    To develop a technique for the separation and quantification of brown adipose tissue (BAT) and white adipose tissue (WAT) using fat fraction and T2* intensity based on the Gaussian mixture model (GMM). Chemical-shift water-fat and T2* images were acquired at the neck, supraclavicular, interscapular, and paravertebral regions in 24 volunteers (Obese: n = 12, female/male = 6/6, body mass index [BMI] = 31.3 ± 2.3 kg/m(2) , age = 16.1 ± 0.6; Normal weight: n = 12, female/male = 6/6, BMI = 21.2 ± 2.4 kg/m(2) , age = 12.9 ± 2.4) using a 3T scanner with the chemical-shift water-fat mDixon sequence. BAT and WAT were clustered based on the Gaussian mixture model using the expectation-maximization algorithm. Results and reproducibility were compared and assessed using independent t-tests and intraclass correlation coefficient. BAT in obese participants was predominately found at the supraclavicular region and in normal-weight participants it was more scattered and distributed in interscapular-supraclavicular, axillary, and spine regions. Absolute volume of BAT was higher in the obese group (Obese: 315.2 mL [±89.1], Normal weight: 248.5 mL [±86.4]), but BAT/WAT ratios were significantly higher (P = 0.029) in the normal group. T2* of BAT (P = 0.04) and volume of WAT (P < 0.001) were significantly lower in the normals. Within-group comparison between male and female indicated no significant differences were found in volume (P = 0.776 (normal), 0.501 [obese]), T2* (P = 0.908 [normal], 0.249 [obese]) and fat-fraction of BAT (P = 0.985 [normal], 0.108 [obese]). The intraclass correlation coefficient showed a good reproducibility in volume (BAT: 0.997, WAT: 0.948), T2* (BAT: 0.969, WAT: 0.983), and fat-fraction (BAT: 0.952, WAT: 0.517). BAT identified by this method was in agreement with other studies in terms of location, fat-fraction value, and T2* intensity. The proposed GMM-based segmentation

  2. The Circulatory and Metabolic Responses to Hypoxia in Humans – With Special Reference to Adipose Tissue Physiology and Obesity

    PubMed Central

    Heinonen, Ilkka H. A.; Boushel, Robert; Kalliokoski, Kari K.

    2016-01-01

    Adipose tissue metabolism and circulation play an important role in human health. It is well-known that adipose tissue mass is increased in response to excess caloric intake leading to obesity and further to local hypoxia and inflammatory signaling. Acute exercise increases blood supply to adipose tissue and mobilization of fat stores for energy. However, acute exercise during systemic hypoxia reduces subcutaneous blood flow in healthy young subjects, but the response in overweight or obese subjects remains to be investigated. Emerging evidence also indicates that exercise training during hypoxic exposure may provide additive benefits with respect to many traditional cardiovascular risk factors as compared to exercise performed in normoxia, but unfavorable effects of hypoxia have also been documented. These topics will be covered in this brief review dealing with hypoxia and adipose tissue physiology. PMID:27621722

  3. Selection of reference genes as internal controls for gene expression in tissues of red abalone Haliotis rufescens (Mollusca, Vetigastropoda; Swainson, 1822).

    PubMed

    López-Landavery, Edgar A; Portillo-López, Amelia; Gallardo-Escárate, Cristian; Del Río-Portilla, Miguel A

    2014-10-10

    The red abalone Haliotis rufescens is one of the most important species for aquaculture in Baja California, México, and despite this, few gene expression studies have been done in tissues such as gill, head and gonad. For this purpose, reverse transcription and quantitative real time PCR (RT-qPCR) is a powerful tool for gene expression evaluation. For a reliable analysis, however, it is necessary to select and validate housekeeping genes that allow proper transcription quantification. Stability of nine housekeeping genes (ACTB, BGLU, TUBB, CY, GAPDH, HPRTI, RPL5, SDHA and UBC) was evaluated in different tissues of red abalone (gill, head and gonad/digestive gland). Four-fold serial dilutions of cDNA (from 25 ngμL(-1) to 0.39 ngμL(-1)) were used to prepare the standard curve, and it showed gene efficiencies between 0.95 and 0.99, with R(2)=0.99. geNorm and NormFinder analysis showed that RPL5 and CY were the most stable genes considering all tissues, whereas in gill HPRTI and BGLU were most stable. In gonad/digestive gland, RPL5 and TUBB were the most stable genes with geNorm, while SDHA and HPRTI were the best using NormFinder. Similarly, in head the best genes were RPL5 and UBC with geNorm, and GAPDH and CY with NormFinder. The technical variability analysis with RPL5 and abalone gonad/digestive gland tissue indicated a high repeatability with a variation coefficient within groups ≤ 0.56% and between groups ≤ 1.89%. These results will help us for further research in reproduction, thermoregulation and endocrinology in red abalone.

  4. Upper incisor to Soft Tissue Plane (UI-STP): a new reference for diagnosis and planning in dentofacial deformities.

    PubMed

    Hernandez-Alfaro, Federico

    2010-09-01

    Planning in orthognathic surgery has been and still is an open issue. We have evolved from 2D classical cephalometric hard-tissue planning to 2D soft tissue planning, and finally to 3D and hard and soft tissue evaluation. This, to our knowledge, is the first description of a new Soft Tissue Plane (STP) and its relationship with the anterior position of the upper incisor (UI). Profile photographs of 110 "attractive individuals" with lips at rest or smiling and with upper incisor shown were used. The photographs used were of 65 professional models from two international agencies and 45 individuals considered most attractive in the internet forums, which included catwalk models and actors. In 86 cases (78.18 %), the incisor was located in front of the STP (A). In 15 cases (13.63%), it was on the plane (N); and in the remaining 9 cases (8.18%), it was behind (P). Despite the limitations of this study and based on our series, we can conclude that the upper incisor is located at or in front of the Soft Tissue Plane (STP) in 91.81% of the attractive facial profiles studied. On the other hand, the relative position of the upper incisor to the soft tissue plane (UI-STP) could be a useful diagnostic and planning tool in orthodontic and surgical management of dentofacial deformities.

  5. Certification of NIST standard reference material 2389a, amino acids in 0.1 mol/L HCl--quantification by ID LC-MS/MS.

    PubMed

    Lowenthal, Mark S; Yen, James; Bunk, David M; Phinney, Karen W

    2010-05-01

    An isotope-dilution liquid chromatography-tandem mass spectrometry (ID LC-MS/MS) measurement procedure was developed to accurately quantify amino acid concentrations in National Institute of Standards and Technology (NIST) Standard Reference Material (SRM) 2389a-amino acids in 0.1 mol/L hydrochloric acid. Seventeen amino acids were quantified using selected reaction monitoring on a triple quadrupole mass spectrometer. LC-MS/MS results were compared to gravimetric measurements from the preparation of SRM 2389a-a reference material developed at NIST and intended for use in intra-laboratory calibrations and quality control. Quantitative mass spectrometry results and gravimetric values were statistically combined into NIST-certified mass fraction values with associated uncertainty estimates. Coefficients of variation (CV) for the repeatability of the LC-MS/MS measurements among amino acids ranged from 0.33% to 2.7% with an average CV of 1.2%. Average relative expanded uncertainty of the certified values including Types A and B uncertainties was 3.5%. Mean accuracy of the LC-MS/MS measurements with gravimetric preparation values agreed to within |1.1|% for all amino acids. NIST SRM 2389a will be available for characterization of routine methods for amino acid analysis and serves as a standard for higher-order measurement traceability. This is the first time an ID LC-MS/MS methodology has been applied for quantifying amino acids in a NIST SRM material.

  6. Identification of reliable reference genes for quantitative gene expression studies in oral squamous cell carcinomas compared to adjacent normal tissues in the F344 rat model.

    PubMed

    Peng, Xinjian; McCormick, David L

    2016-08-01

    Oral squamous cell carcinomas (OSCCs) induced in F344 rats by 4-nitroquinoline-1-oxide (4-NQO) demonstrate considerable phenotypic similarity to human oral cancers and the model has been widely used for carcinogenesis and chemoprevention studies. Molecular characterization of this model needs reliable reference genes (RGs) to avoid false- positive and -negative results for proper interpretation of gene expression data between tumor and adjacent normal tissues. Microarray analysis of 11 pairs of OSCC and site-matched phenotypically normal oral tissues from 4-NQO-treated rats identified 10 stably expressed genes in OSCC compared to adjacent normal tissues (p>0.5, CV<15%) that could serve as potential RGs in this model. The commonly used 27 RGs in the rat were also analyzed based on microarray data and most of them were found unsuitable for RGs in this model. Traditional RGs such as ACTB and GAPDH were significantly altered in OSCC compared to adjacent normal tissues (p<0.01, n=11); however, the Hsp90ab1 was ranked as the best RG candidate and the combination of Hsp90ab1 and HPRT1 was identified by NormFinder to be a superior reference for gene normalization among the commonly used RGs. This result was also validated by RT-PCR based on the selected top RG candidate pool. These data suggest that there are no common RGs suitable for different models and RG(s) should be identified before gene expression analysis. We successfully identified Hsp90ab1 as a stable RG in 4-NQO-induced OSCC compared to adjacent normal tissues in F344 rats. The combination of two stably expressed genes may be a better option for gene normalization in tissue samples.

  7. Separation and quantification of monothiols and phytochelatins from a wide variety of cell cultures and tissues of trees and other plants using high performance liquid chromatography

    Treesearch

    Rakesh Minocha; P. Thangavel; Om Parkash Dhankher; Stephanie Long

    2008-01-01

    The HPLC method presented here for the quantification of metal-binding thiols is considerably shorter than most previously published methods. It is a sensitive and highly reproducible method that separates monobromobimane tagged monothiols (cysteine, glutathione, γ-glutamylcysteine) along with polythiols (PC2, PC3...

  8. Development of certified matrix-based reference material of genetically modified rice event TT51-1 for real-time PCR quantification.

    PubMed

    Jiang, Yu; Yang, Hui; Quan, Sheng; Liu, Yinan; Shen, Ping; Yang, Litao

    2015-09-01

    In 2009, the genetically modified (GM) rice event TT51-1 with an engineered insect resistance trait became the first GM rice event to be granted certification for safe production in China, and its derivative lines Bt 63 and Huahui No.1 are expected to be commercialized soon. The development of certified reference material (CRM) for TT51-1 is necessary to monitor and inspect the TT51-1 event and its derivates. In this work, we developed four matrix-based TT51-1 rice CRMs (TT51-1a, TT51-1b, TT51-1c, and TT51-1d) with different TT51-1 mass fraction ratios by blending seed powders of homozygous TT51-1 and its recipient cultivar Minghui 63. The between-bottle homogeneity and the within-bottle homogeneity were tested, and good results were obtained. The potential degradation during transportation and shelf life were evaluated, and demonstrated an expiration period of at least 36 months. The characterization values of the four TT51-1 CRMs based on the mass fraction ratio were 1000.000 ± 51.430 g/kg, 49.940 ± 4.620 g/kg, 9.990 ± 1.110 g/kg, and 4.990 ± 0.620 g/kg, respectively. The characterization values based on the copy number ratio were certified by digital PCR analysis as 97.442 ± 5.253 %, 4.851 ± 0.486 %, 1.042 ± 0.135 %, and 0.556 ± 0.073 %, respectively. These results suggested that the TT51-1 matrix-based CRMs developed are of high quality and can be used as potential calibrators for TT51-1 GM rice inspection and monitoring.

  9. Use of diagnostic accuracy as a metric for evaluating laboratory proficiency with microarray assays using mixed-tissue RNA reference samples.

    PubMed

    Pine, P S; Boedigheimer, M; Rosenzweig, B A; Turpaz, Y; He, Y D; Delenstarr, G; Ganter, B; Jarnagin, K; Jones, W D; Reid, L H; Thompson, K L

    2008-11-01

    Effective use of microarray technology in clinical and regulatory settings is contingent on the adoption of standard methods for assessing performance. The MicroArray Quality Control project evaluated the repeatability and comparability of microarray data on the major commercial platforms and laid the groundwork for the application of microarray technology to regulatory assessments. However, methods for assessing performance that are commonly applied to diagnostic assays used in laboratory medicine remain to be developed for microarray assays. A reference system for microarray performance evaluation and process improvement was developed that includes reference samples, metrics and reference datasets. The reference material is composed of two mixes of four different rat tissue RNAs that allow defined target ratios to be assayed using a set of tissue-selective analytes that are distributed along the dynamic range of measurement. The diagnostic accuracy of detected changes in expression ratios, measured as the area under the curve from receiver operating characteristic plots, provides a single commutable value for comparing assay specificity and sensitivity. The utility of this system for assessing overall performance was evaluated for relevant applications like multi-laboratory proficiency testing programs and single-laboratory process drift monitoring. The diagnostic accuracy of detection of a 1.5-fold change in signal level was found to be a sensitive metric for comparing overall performance. This test approaches the technical limit for reliable discrimination of differences between two samples using this technology. We describe a reference system that provides a mechanism for internal and external assessment of laboratory proficiency with microarray technology and is translatable to performance assessments on other whole-genome expression arrays used for basic and clinical research.

  10. Identification of reference genes for RT-qPCR in ovine mammary tissue during late pregnancy and lactation and in response to maternal nutritional programming.

    PubMed

    Paten, A M; Pain, S J; Peterson, S W; Blair, H T; Kenyon, P R; Dearden, P K; Duncan, E J

    2014-08-01

    The mammary gland is a complex tissue consisting of multiple cell types which, over the lifetime of an animal, go through repeated cycles of development associated with pregnancy, lactation and involution. The mammary gland is also known to be sensitive to maternal programming by environmental stimuli such as nutrition. The molecular basis of these adaptations is of significant interest, but requires robust methods to measure gene expression. Reverse-transcription quantitative PCR (RT-qPCR) is commonly used to measure gene expression, and is currently the method of choice for validating genome-wide expression studies. RT-qPCR requires the selection of reference genes that are stably expressed over physiological states and treatments. In this study we identify suitable reference genes to normalize RT-qPCR data for the ovine mammary gland in two physiological states; late pregnancy and lactation. Biopsies were collected from offspring of ewes that had been subjected to different nutritional paradigms during pregnancy to examine effects of maternal programming on the mammary gland of the offspring. We evaluated eight candidate reference genes and found that two reference genes (PRPF3 and CUL1) are required for normalising RT-qPCR data from pooled RNA samples, but five reference genes are required for analyzing gene expression in individual animals (SENP2, EIF6, MRPL39, ATP1A1, CUL1). Using these stable reference genes, we showed that TET1, a key regulator of DNA methylation, is responsive to maternal programming and physiological state. The identification of these novel reference genes will be of utility to future studies of gene expression in the ovine mammary gland.

  11. What is the best reference site for a single MRI slice to assess whole-body skeletal muscle and adipose tissue volumes in healthy adults?

    PubMed

    Schweitzer, Lisa; Geisler, Corinna; Pourhassan, Maryam; Braun, Wiebke; Glüer, Claus-Christian; Bosy-Westphal, Anja; Müller, Manfred J

    2015-07-01

    Whole-body magnetic resonance imaging (MRI) is the gold standard for the assessment of skeletal muscle (SM) and adipose tissue volumes. It is unclear whether single-slice estimates can replace whole-body data. We evaluated the accuracy of the best single lumbar and midthigh MRI slice to assess whole-body SM, visceral adipose tissue (VAT), and subcutaneous adipose tissue (SAT). Whole-body MRI was performed in 142 healthy adults aged 19-65 y [mean ± SD age: 37.0 ± 11.8 y; BMI (in kg/m(2)): 25.3 ± 5.9]. Single slices were taken at lumbar vertebrae L1-L5 plus intervertebral discs and the thigh (midthigh, 10 cm distally from the midthigh, and 10 cm proximally from the midthigh). The value of single-slice areas was also tested in a longitudinal study on 48 healthy volunteers during weight loss (8.2 ± 5.2 kg). Cross-sectionally, all SM and adipose tissue single-slice areas correlated with total tissue volumes (P < 0.01). Because of the close associations between L3 areas and corresponding tissue volumes (r = 0.832-0.986, P < 0.01), this location was identified as the reference to estimate SM and adipose tissue in both sexes. SM, SAT, and VAT areas at L3 explained most of the variance of total tissue volumes (69-97%, with SEs of estimation of 1.96 and 2.03 L for SM, 0.23 and 0.61 L for VAT, and 4.44 and 2.47 L for SAT for men and women, respectively. There was no major effect on the explained variance compared with that for optimal slices. For SM, the optimal slice area was shown at midthigh. With weight-loss changes in total SM, VAT, and SAT, volumes were significantly different from those at baseline (SM changes: -2.8 ± 2.9 L; VAT changes: -0.7 ± 1.0 L; SAT changes: -5.1 ± 6.0 L). The area at L3 reflected changes in total VAT and SAT. To assess changes in total SM volumes, areas at midthigh showed the best evidence. In both sexes, a single MRI scan at the level of L3 is the best compromise site to assess total tissue volumes of SM, VAT, and SAT. By contrast, L3

  12. A new specific reference gene based on growth hormone gene (GH1) used for detection and relative quantification of Aquadvantage® GM salmon (Salmo salar L.) in food products.

    PubMed

    Ben Hafsa, Ahmed; Nabi, Nesrine; Zellama, Mohamed Salem; Said, Khaled; Chaouachi, Maher

    2016-01-01

    Genetic transformation of fish is mainly oriented towards the improvement of growth for the benefit of the aquaculture. Actually, Atlantic salmon (Salmo salar) is the species most transformed to achieve growth rates quite large compared to the wild. To anticipate the presence of contaminations with GM salmon in fish markets and the lack of labeling regulations with a mandatory threshold, the proper methods are needed to test the authenticity of the ingredients. A quantitative real-time polymerase chain reaction (QRT-PCR) method was used in this study. Ct values were obtained and validated using 15 processed food containing salmon. The relative and absolute limits of detection were 0.01% and 0.01 ng/μl of genomic DNA, respectively. Results demonstrate that the developed QRT-PCR method is suitable specifically for identification of S. salar in food ingredients based on the salmon growth hormone gene 1 (GH1). The processes used to develop the specific salmon reference gene case study are intended to serve as a model for performing quantification of Aquadvantage® GM salmon on future genetically modified (GM) fish to be commercialized.

  13. Reference genes for high-throughput quantitative reverse transcription-PCR analysis of gene expression in organs and tissues of Eucalyptus grown in various environmental conditions.

    PubMed

    Cassan-Wang, Hua; Soler, Marçal; Yu, Hong; Camargo, Eduardo Leal O; Carocha, Victor; Ladouce, Nathalie; Savelli, Bruno; Paiva, Jorge A P; Leplé, Jean-Charles; Grima-Pettenati, Jacqueline

    2012-12-01

    Interest in the genomics of Eucalyptus has skyrocketed thanks to the recent sequencing of the genome of Eucalyptus grandis and to a growing number of large-scale transcriptomic studies. Quantitative reverse transcription-PCR (RT-PCR) is the method of choice for gene expression analysis and can now also be used as a high-throughput method. The selection of appropriate internal controls is becoming of utmost importance to ensure accurate expression results in Eucalyptus. To this end, we selected 21 candidate reference genes and used high-throughput microfluidic dynamic arrays to assess their expression among a large panel of developmental and environmental conditions with a special focus on wood-forming tissues. We analyzed the expression stability of these genes by using three distinct statistical algorithms (geNorm, NormFinder and ΔCt), and used principal component analysis to compare methods and rankings. We showed that the most stable genes identified depended not only on the panel of biological samples considered but also on the statistical method used. We then developed a comprehensive integration of the rankings generated by the three methods and identified the optimal reference genes for 17 distinct experimental sets covering 13 organs and tissues, as well as various developmental and environmental conditions. The expression patterns of Eucalyptus master genes EgMYB1 and EgMYB2 experimentally validated our selection. Our findings provide an important resource for the selection of appropriate reference genes for accurate and reliable normalization of gene expression data in the organs and tissues of Eucalyptus trees grown in a range of conditions including abiotic stresses.

  14. Effect of addition of antibiotics and an antioxidant on the stability of tissue reference materials for domoic acid, the amnesic shellfish poison.

    PubMed

    McCarron, Pearse; Burrell, Stephen; Hess, Philipp

    2007-04-01

    Five separate reference materials (RMs) were prepared from a mussel (Mytilus edulis) tissue containing domoic acid (DA) from scallop hepatopancreas (Pecten maximus). Homogenates were separately spiked with antibiotics, an antioxidant, or a combination of both. Control materials did not contain any additives and were prepared from lightly cooked and autoclaved mussel tissues. Stability studies were run over a 148-day period at three different temperature conditions: -20 degrees C, +4 degrees C and +40 degrees C. DA contents in all materials were characterised by HPLC-UV. Homogeneities were demonstrated at the beginning of the study, with coefficients of variance of less than 4% (n = 9). DA was stable at -20 degrees C in all materials. The control materials showed significant degradation after two days at +40 degrees C, and after eight days at +4 degrees C. Each of the materials containing additives demonstrated better stability during the initial period of the study. In addition there was no significant degradation in any of the materials with additives stored at +4 degrees C over the duration of the study. The material containing a combination of the antibiotics and the antioxidant displayed the best stability of all the materials. There was no significant reduction in DA concentration at all temperature conditions after eight days, and after 32 days the decrease at +40 degrees C was still <20 %. Following this, a DA laboratory reference material (LRM) was prepared and, based on previous results, spiked with both the antioxidant and antibiotics. A short-term stability study on this material gave similar results to the corresponding material in the additives study. This study shows that combined use of the additives investigated in the preparation of a mussel tissue reference material for DA ensures analyte stability for a period of up to eight days at temperatures of up to +40 degrees C, a condition that is particularly important when shipping test materials

  15. Estimation of drug receptor occupancy when non-displaceable binding differs between brain regions – extending the simplified reference tissue model.

    PubMed

    Kågedal, Matts; Varnäs, Katarina; Hooker, Andrew C; Karlsson, Mats O

    2015-07-01

    The simplified reference tissue model (SRTM) is used for estimation of receptor occupancy assuming that the non-displaceable binding in the reference region is identical to the brain regions of interest. The aim of this work was to extend the SRTM to also account for inter-regional differences in non-displaceable concentrations, and to investigate if this model allowed estimation of receptor occupancy using white matter as reference. It was also investigated if an apparent higher affinity in caudate compared with other brain regions, could be better explained by a difference in the extent of non-displaceable binding. The analysis was based on a PET study in six healthy volunteers using the 5-HT1B receptor radioligand [(11)C]-AZ10419369. The radioligand was given intravenously as a tracer dose alone and following different oral doses of the 5-HT1B receptor antagonist AZD3783. Non-linear mixed effects models were developed where differences between regions in non-specific concentrations were accounted for. The properties of the models were also evaluated by means of simulation studies. The estimate (95% CI) of Ki(PL) was 10.2 ng ml(-1) (5.4, 15) and 10.4 ng ml(-1) (8.1, 13.6) based on the extended SRTM with white matter as reference and based on the SRTM using cerebellum as reference, respectively. The estimate (95% CI) of Ki(PL) for caudate relative to other brain regions was 55% (48, 62%). The extended SRTM allows consideration of white matter as reference region when no suitable grey matter region exists. AZD3783 affinity appears to be higher in the caudate compared with other brain regions. © 2014 The British Pharmacological Society.

  16. Selection of Suitable Reference Genes for Normalization of Quantitative Real-Time PCR in Cartilage Tissue Injury and Repair in Rabbits

    PubMed Central

    Peng, Xiao-Xiang; Zhao, Rong-Lan; Song, Wei; Chu, Hai-Rong; Li, Meng; Song, Shu-Ya; Li, Guang-Zhou; Liang, Dong-Chun

    2012-01-01

    When studying the altered expression of genes associated with cartilage regeneration by quantitative real-time RT-PCR (RT-qPCR), reference genes with highly stable expression during different stages of chondrocyte developmental are necessary to normalize gene expression accurately. Until now, no reports evaluating expression changes of commonly used reference genes in rabbit articular cartilage have been published. In this study, defects were made in rabbit articular cartilage, with or without insulin-like growth factor 1 (IGF-1) treatment, to create different chondrocyte living environments. The stability and intensity of the expressions of the candidate reference genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 18S Ribosomal RNA (18S rRNA), cyclophilin (CYP), hypoxanthine phosphoribosyl transferase (HPRT1), and β-2-microglobulin (B2M) were evaluated. The data were analyzed by geNorm and NormFinder. B2M and 18S rRNA were identified to be suitable reference genes for rabbit cartilage tissues. PMID:23203068

  17. Marrow Adipose Tissue Quantification of the Lumbar Spine by Using Dual-Energy CT and Single-Voxel 1H MR Spectroscopy: A Feasibility Study

    PubMed Central

    Daley, Scott M.; Kalra, Mannudeep K.; Brown, J. Keenan; Miller, Karen K.; Torriani, Martin

    2015-01-01

    Purpose To test the performance of dual-energy computed tomography (CT) in the assessment of marrow adipose tissue (MAT) content of the lumbar spine by using proton (hydrogen 1 [1H]) magnetic resonance (MR) spectroscopy as a reference standard and to determine the influence of MAT on the assessment of bone mineral density (BMD). Materials and Methods This study was institutional review board approved and complied with HIPAA guidelines. Written informed consent was obtained. Twelve obese osteopenic but otherwise healthy subjects (mean age ± standard deviation, 43 years ± 13) underwent 3-T 1H MR spectroscopy of the L2 vertebra by using a point-resolved spatially localized spectroscopy sequence without water suppression. The L2 vertebra was scanned with dual-energy CT (80 and 140 kV) by using a dual-source multi–detector row CT scanner with a calibration phantom. Mean basis material composition relative to the phantom was estimated in the L2 vertebra. Volumetric BMD was measured with and without correction for MAT. Bland-Altman 95% limits of agreement and Pearson correlation coefficients were calculated. Results There was excellent agreement between 1H MR spectroscopy and dual-energy CT, with a mean difference in fat fraction of −0.02 between the techniques, with a 95% confidence interval of −0.24, 0.20. There was a strong correlation between marrow fat fraction obtained with 1H MR spectroscopy and that obtained with dual-energy CT (r = 0.91, P < .001). The presence of MAT led to underestimation of BMD, and this bias increased with increasing MAT content (P < .001). Conclusion Dual-energy CT can be used to assess MAT content and BMD of the lumbar spine in a single examination and provides data that closely agree and correlate with 1H MR spectroscopy data. © RSNA, 2015 PMID:25988401

  18. Color correction for automatic fibrosis quantification in liver biopsy specimens

    PubMed Central

    Murakami, Yuri; Abe, Tokiya; Hashiguchi, Akinori; Yamaguchi, Masahiro; Saito, Akira; Sakamoto, Michiie

    2013-01-01

    Context: For a precise and objective quantification of liver fibrosis, quantitative evaluations through image analysis have been utilized. However, manual operations are required in most cases for extracting fiber areas because of color variation included in digital pathology images. Aims: The purpose of this research is to propose a color correction method for whole slide images (WSIs) of Elastica van Gieson (EVG) stained liver biopsy tissue specimens and to realize automated operation of image analysis for fibrosis quantification. Materials and Methods: Our experimental dataset consisted of 38 WSIs of liver biopsy specimens collected from 38 chronic viral hepatitis patients from multiple medical facilities, stained with EVG and scanned at ×20 using a Nano Zoomer 2.0 HT (Hamamatsu Photonics K.K., Hamamatsu, Japan). Color correction was performed by modifying the color distribution of a target WSI so as to fit to the reference, where the color distribution was modeled by a set of two triangle pyramids. Using color corrected WSIs; fibrosis quantification was performed based on tissue classification analysis. Statistical Analysis Used: Spearman's rank correlation coefficients were calculated between liver stiffness measured by transient elastography and median area ratio of collagen fibers calculated based on tissue classification results. Results: Statistical analysis results showed a significant correlation r = 0.61-0.68 even when tissue classifiers were trained by using a subset of WSIs, while the correlation coefficients were reduced to r = 0.40-0.50 without color correction. Conclusions: Fibrosis quantification accompanied with the proposed color correction method could provide an objective evaluation tool for liver fibrosis, which complements semi-quantitative histologic evaluation systems. PMID:24524002

  19. Comparison of Positron Emission Tomography Quantification Using Magnetic Resonance- and Computed Tomography-Based Attenuation Correction in Physiological Tissues and Lesions: A Whole-Body Positron Emission Tomography/Magnetic Resonance Study in 66 Patients.

    PubMed

    Seith, Ferdinand; Gatidis, Sergios; Schmidt, Holger; Bezrukov, Ilja; la Fougère, Christian; Nikolaou, Konstantin; Pfannenberg, Christina; Schwenzer, Nina

    2016-01-01

    Attenuation correction (AC) in fully integrated positron emission tomography (PET)/magnetic resonance (MR) systems plays a key role for the quantification of tracer uptake. The aim of this prospective study was to assess the accuracy of standardized uptake value (SUV) quantification using MR-based AC in direct comparison with computed tomography (CT)-based AC of the same PET data set on a large patient population. Sixty-six patients (22 female; mean [SD], 61 [11] years) were examined by means of combined PET/CT and PET/MR (11C-choline, 18F-FDG, or 68Ga-DOTATATE) subsequently. Positron emission tomography images from PET/MR examinations were corrected with MR-derived AC based on tissue segmentation (PET(MR)). The same PET data were corrected using CT-based attenuation maps (μ-maps) derived from PET/CT after nonrigid registration of the CT to the MR-based μ-map (PET(MRCT)). Positron emission tomography SUVs were quantified placing regions of interest or volumes of interest in 6 different body regions as well as PET-avid lesions, respectively. The relative differences of quantitative PET values when using MR-based AC versus CT-based AC were varying depending on the organs and body regions assessed. In detail, the mean (SD) relative differences of PET SUVs were as follows: -7.8% (11.5%), blood pool; -3.6% (5.8%), spleen; -4.4% (5.6%)/-4.1% (6.2%), liver; -0.6% (5.0%), muscle; -1.3% (6.3%), fat; -40.0% (18.7%), bone; 1.6% (4.4%), liver lesions; -6.2% (6.8%), bone lesions; and -1.9% (6.2%), soft tissue lesions. In 10 liver lesions, distinct overestimations greater than 5% were found (up to 10%). In addition, overestimations were found in 2 bone lesions and 1 soft tissue lesion adjacent to the lung (up to 28.0%). Results obtained using different PET tracers show that MR-based AC is accurate in most tissue types, with SUV deviations generally of less than 10%. In bone, however, underestimations can be pronounced, potentially leading to inaccurate SUV quantifications. In

  20. Selection of reference genes for quantitative real-time PCR expression studies of microdissected reproductive tissues in apomictic and sexual Boechera

    PubMed Central

    2011-01-01

    Background Apomixis, a natural form of asexual seed production in plants, is considered to have great biotechnological potential for agriculture. It has been hypothesised that de-regulation of the sexual developmental pathway could trigger apomictic reproduction. The genus Boechera represents an interesting model system for understanding apomixis, having both sexual and apomictic genotypes at the diploid level. Quantitative qRT-PCR is the most extensively used method for validating genome-wide gene expression analyses, but in order to obtain reliable results, suitable reference genes are necessary. In this work we have evaluated six potential reference genes isolated from a 454 (FLX) derived cDNA library of Boechera. RNA from live microdissected ovules and anthers at different developmental stages, as well as vegetative tissues of apomictic and sexual Boechera, were used to validate the candidates. Results Based on homologies with Arabidopsis, six genes were selected from a 454 cDNA library of Boechera: RPS18 (Ribosomal sub protein 18), Efalpha1 (Elongation factor 1 alpha), ACT 2 (Actin2), UBQ (polyubiquitin), PEX4 (Peroxisomal ubiquitin conjugating enzyme) and At1g09770.1 (Arabidopsis thaliana cell division cycle 5). Total RNA was extracted from 17 different tissues, qRT-PCRs were performed, and raw Ct values were analyzed for primer efficiencies and gene ratios. The geNorm and normFinder applications were used for selecting the most stable genes among all tissues and specific tissue groups (ovule, anthers and vegetative tissues) in both apomictic and sexual plants separately. Our results show that BoechRPS18, BoechEfα1, BoechACT2 and BoechUBQ were the most stable genes. Based on geNorm, the combinations of BoechRPS18 and BoechEfα1 or BoechUBQ and BoechEfα1 were the most stable in the apomictic plant, while BoechRPS18 and BoechACT2 or BoechUBQ and BoechACT2 performed best in the sexual plant. When subgroups of tissue samples were analyzed, different optimal

  1. Proteome Reference Maps of Vegetative Tissues in Pea. An Investigation of Nitrogen Mobilization from Leaves during Seed Filling1

    PubMed Central

    Schiltz, Séverine; Gallardo, Karine; Huart, Myriam; Negroni, Luc; Sommerer, Nicolas; Burstin, Judith

    2004-01-01

    A proteomic approach was used to analyze protein changes during nitrogen mobilization (N mobilization) from leaves to filling seeds in pea (Pisum sativum). First, proteome reference maps were established for mature leaves and stems. They displayed around 190 Coomassie Blue-stained spots with pIs from 4 to 7. A total of 130 spots were identified by mass spectrometry as corresponding to 80 different proteins implicated in a variety of cellular functions. Although the leaf proteome map contained more abundant spots, corresponding to proteins involved in energy/carbon metabolism, than the stem map, their comparison revealed a highly similar protein profile. Second, the leaf proteome map was used to analyze quantitative variations in leaf proteins during N mobilization. Forty percent of the spots showed significant changes in their relative abundance in the total protein extract. The results confirmed the importance of Rubisco as a source of mobilizable nitrogen, and suggested that in pea leaves the rate of degradation of Rubisco may vary throughout N mobilization. Correlated with the loss of Rubisco was an increase in relative abundance of chloroplastic protease regulatory subunits. Concomitantly, the relative abundance of some proteins related to the photosynthetic apparatus (Rubisco activase, Rubisco-binding proteins) and of several chaperones increased. A role for these proteins in the maintenance of a Rubisco activation state and in the PSII repair during the intense proteolytic activity within the chloroplasts was proposed. Finally, two 14-3-3-like proteins, with a potential regulatory role, displayed differential expression patterns during the massive remobilization of nitrogen. PMID:15299134

  2. Proteome reference maps of vegetative tissues in pea. An investigation of nitrogen mobilization from leaves during seed filling.

    PubMed

    Schiltz, Séverine; Gallardo, Karine; Huart, Myriam; Negroni, Luc; Sommerer, Nicolas; Burstin, Judith

    2004-08-01

    A proteomic approach was used to analyze protein changes during nitrogen mobilization (N mobilization) from leaves to filling seeds in pea (Pisum sativum). First, proteome reference maps were established for mature leaves and stems. They displayed around 190 Coomassie Blue-stained spots with pIs from 4 to 7. A total of 130 spots were identified by mass spectrometry as corresponding to 80 different proteins implicated in a variety of cellular functions. Although the leaf proteome map contained more abundant spots, corresponding to proteins involved in energy/carbon metabolism, than the stem map, their comparison revealed a highly similar protein profile. Second, the leaf proteome map was used to analyze quantitative variations in leaf proteins during N mobilization. Forty percent of the spots showed significant changes in their relative abundance in the total protein extract. The results confirmed the importance of Rubisco as a source of mobilizable nitrogen, and suggested that in pea leaves the rate of degradation of Rubisco may vary throughout N mobilization. Correlated with the loss of Rubisco was an increase in relative abundance of chloroplastic protease regulatory subunits. Concomitantly, the relative abundance of some proteins related to the photosynthetic apparatus (Rubisco activase, Rubisco-binding proteins) and of several chaperones increased. A role for these proteins in the maintenance of a Rubisco activation state and in the PSII repair during the intense proteolytic activity within the chloroplasts was proposed. Finally, two 14-3-3-like proteins, with a potential regulatory role, displayed differential expression patterns during the massive remobilization of nitrogen.

  3. Evaluation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in Pyrus pyrifolia using different tissue samples and seasonal conditions.

    PubMed

    Imai, Tsuyoshi; Ubi, Benjamin E; Saito, Takanori; Moriguchi, Takaya

    2014-01-01

    We have evaluated suitable reference genes for real time (RT)-quantitative PCR (qPCR) analysis in Japanese pear (Pyrus pyrifolia). We tested most frequently used genes in the literature such as β-Tubulin, Histone H3, Actin, Elongation factor-1α, Glyceraldehyde-3-phosphate dehydrogenase, together with newly added genes Annexin, SAND and TIP41. A total of 17 primer combinations for these eight genes were evaluated using cDNAs synthesized from 16 tissue samples from four groups, namely: flower bud, flower organ, fruit flesh and fruit skin. Gene expression stabilities were analyzed using geNorm and NormFinder software packages or by ΔCt method. geNorm analysis indicated three best performing genes as being sufficient for reliable normalization of RT-qPCR data. Suitable reference genes were different among sample groups, suggesting the importance of validation of gene expression stability of reference genes in the samples of interest. Ranking of stability was basically similar between geNorm and NormFinder, suggesting usefulness of these programs based on different algorithms. ΔCt method suggested somewhat different results in some groups such as flower organ or fruit skin; though the overall results were in good correlation with geNorm or NormFinder. Gene expression of two cold-inducible genes PpCBF2 and PpCBF4 were quantified using the three most and the three least stable reference genes suggested by geNorm. Although normalized quantities were different between them, the relative quantities within a group of samples were similar even when the least stable reference genes were used. Our data suggested that using the geometric mean value of three reference genes for normalization is quite a reliable approach to evaluating gene expression by RT-qPCR. We propose that the initial evaluation of gene expression stability by ΔCt method, and subsequent evaluation by geNorm or NormFinder for limited number of superior gene candidates will be a practical way of finding out

  4. Quantification of differences in the effective atomic numbers of healthy and cancerous tissues: A discussion in the context of diagnostics and dosimetry

    SciTech Connect

    Taylor, M. L.

    2012-09-15

    Purpose: There are a range of genetic and nongenetic factors influencing the elemental composition of different human tissues. The elemental composition of cancerous tissues frequently differs from healthy tissue of the same organ, particularly in high-Z trace element concentrations. For this reason, one could suggest that this may be exploited in diagnostics and perhaps even influence dosimetry. Methods: In this work, for the first time, effective atomic numbers are computed for common cancerous and healthy tissues using a robust, energy-dependent approach between 10 keV and 100 MeV. These are then quantitatively compared within the context of diagnostics and dosimetry. Results: Differences between effective atomic numbers of healthy and diseased tissues are found to be typically less than 10%. Fibrotic tissues and calcifications of the breast exhibit substantial (tens to hundreds of percent) differences to healthy tissue. Expectedly, differences are most pronounced in the photoelectric regime and consequently most relevant for kV imaging/therapy and radionuclides with prominent low-energy peaks. Cancerous tissue of the testes and stomach have lower effective atomic numbers than corresponding healthy tissues, while diseased tissues of the other organ sites typically have higher values. Conclusions: As dose calculation approaches improve in accuracy, there may be an argument for the explicit inclusion of pathologies. This is more the case for breast, penile, prostate, nasopharyngeal, and stomach cancer, less so for testicular and kidney cancer. The calculated data suggest dual-energy computed tomography could potentially improve lesion identification in the aforementioned organs (with the exception of testicular cancer), with most import in breast imaging. Ultimately, however, the differences are very small. It is likely that the assumption of a generic 'tissue ramp' in planning will be sufficient for the foreseeable future, and that the Z differences do not

  5. Quantification of the humoral immune response and hemoplasma blood and tissue loads in cats coinfected with 'Candidatus Mycoplasma haemominutum' and feline leukemia virus.

    PubMed

    Wolf-Jäckel, Godelind A; Cattori, Valentino; Geret, Catrina P; Novacco, Marilisa; Meli, Marina L; Riond, Barbara; Boretti, Felicitas S; Lutz, Hans; Hofmann-Lehmann, Regina

    2012-08-01

    'Candidatus Mycoplasma haemominutum' (CMhm) is a hemotropic mycoplasma (aka hemoplasma) of domestic cats and wild felids. In a transmission study, we exposed eight specified pathogen-free cats to blood from Iberian lynxes (Lynx pardinus) infected with CMhm. The cats were coinfected with feline leukemia virus (FeLV) from an Iberian lynx or with a prototype FeLV. The goal of the present study was to quantify the humoral immune response to CMhm and to identify potential target tissues and sequestration sites. Antibodies were measured by a recombinant antigen-based enzyme-linked immunosorbent assay, and blood and tissue loads were quantified using real-time PCR. Seven out of eight cats became CMhm-infected; all of these cats seroconverted between 3 and 13 weeks after inoculation. Antibody levels correlated with the CMhm blood loads. The peak CMhm blood loads were inversely correlated with the incubation period. PCR-positive results were found in all 24 tissues tested but not for all samples. Although all tissues were PCR-positive in one cat euthanized ten weeks after infection, many tissues tested negative in six cats euthanized at week 20 after infection. In several cats, the spleen, lung, liver, heart and aorta contained more copies than expected given the tissue's blood supply, but most tissues contained fewer copies than expected. In conclusion, this is the first study to quantify the humoral immune response and tissue loads in CMhm-FeLV-coinfected cats. The tissue loads appeared to correlate with the duration of infection and with the blood loads, but no evidence of significant CMhm tissue sequestration was found. Copyright © 2012 Elsevier Ltd. All rights reserved.

  6. Accurate quantification of sphingosine-1-phosphate in normal and Fabry disease plasma, cells and tissues by LC-MS/MS with (13)C-encoded natural S1P as internal standard.

    PubMed

    Mirzaian, Mina; Wisse, Patrick; Ferraz, Maria J; Marques, André R A; Gabriel, Tanit L; van Roomen, Cindy P A A; Ottenhoff, Roelof; van Eijk, Marco; Codée, Jeroen D C; van der Marel, Gijsbert A; Overkleeft, Herman S; Aerts, Johannes M

    2016-08-01

    We developed a mass spectrometric procedure to quantify sphingosine-1-phosphate (S1P) in biological materials. The use of newly synthesized (13)C5 C18-S1P and commercial C17-S1P as internal standards rendered very similar results with respect to linearity, limit of detection and limit of quantitation. Caution is warranted with determination of plasma S1P levels. Earlier it was reported that S1P is elevated in plasma of Fabry disease patients. We investigated this with the improved quantification. No clear conclusion could be drawn for patient plasma samples given the lack of uniformity of blood collection and plasma preparation. To still obtain insight, plasma and tissues were identically collected from α-galactosidase A deficient Fabry mice and matched control animals. No significant difference was observed in plasma S1P levels. A significant 2.3 fold increase was observed in kidney of Fabry mice, but not in liver and heart. Comparative analysis of S1P in cultured fibroblasts from normal subjects and classically affected Fabry disease males revealed no significant difference. In conclusion, accurate quantification of S1P in biological materials is feasible by mass spectrometry using the internal standards (13)C5 C18-S1P or C17-S1P. Significant local increases of S1P in the kidney might occur in Fabry disease as suggested by the mouse model.

  7. Application of selected reaction monitoring for multiplex quantification of clinically validated biomarkers in formalin-fixed, paraffin-embedded tumor tissue.

    PubMed

    Hembrough, Todd; Thyparambil, Sheeno; Liao, Wei-Li; Darfler, Marlene M; Abdo, Joseph; Bengali, Kathleen M; Hewitt, Stephen M; Bender, Richard A; Krizman, David B; Burrows, Jon

    2013-07-01

    One of the critical gaps in the clinical diagnostic space is the lack of quantitative proteomic methods for use on formalin-fixed, paraffin-embedded (FFPE) tissue. Herein, we describe the development of a quantitative, multiplexed, mass spectrometry-based selected reaction monitoring (SRM) assay for four therapeutically important targets: epidermal growth factor receptor, human EGF receptor (HER)-2, HER3, and insulin-like growth factor-1 receptor. These assays were developed using the Liquid Tissue-SRM technology platform, in which FFPE tumor tissues were microdissected, completely solubilized, and then subjected to multiplexed quantitation by SRM mass spectrometry. The assays were preclinically validated by comparing Liquid Tissue-SRM quantitation of FFPE cell lines with enzyme-linked immunosorbent assay/electrochemiluminescence quantitation of fresh cells (R(2) > 0.95). Clinical performance was assessed on two cohorts of breast cancer tissue: one cohort of 10 samples with a wide range of HER2 expression and a second cohort of 19 HER2 IHC 3+ tissues. These clinical data demonstrate the feasibility of quantitative, multiplexed clinical analysis of proteomic markers in FFPE tissue. Our findings represent a significant advancement in cancer tissue analysis because multiplexed, quantitative analysis of protein targets in FFPE tumor tissue can be tailored to specific oncological indications to provide the following: i) complementary support for anatomical pathological diagnoses, ii) patient stratification to optimize treatment outcomes and identify drug resistance, and iii) support for the clinical development of novel therapies. Copyright © 2013 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

  8. Detection of West Nile virus using formalin fixed paraffin embedded tissues in crows and horses: quantification of viral transcripts by real-time RT-PCR.

    PubMed

    Tewari, Deepanker; Kim, Hyun; Feria, Willard; Russo, Brigite; Acland, Helen

    2004-08-01

    West Nile virus (WNV) RNA was quantified in WNV infected crows and horses with the help of a real-time reverse transcriptase-PCR assay. A 5' nuclease assay, based on NS5 gene detection with a fluorescent probe was used for quantifying WNV RNA using formalin fixed paraffin embedded tissue specimens. Quantitative detection of WNV RNA showed the presence of a higher amount of the viral RNA in crow tissues compared to equine tissues and these results correlated well with the detection of WNV antigen by immunostaining. In crows, the highest amount of virus was seen in the intestine and in horses in the brain.

  9. Double stable isotope ultra performance liquid chromatographic-tandem mass spectrometric quantification of tissue content and activity of phenylethanolamine N-methyltransferase, the crucial enzyme responsible for synthesis of epinephrine.

    PubMed

    Qin, Nan; Peitzsch, Mirko; Menschikowski, Mario; Siegert, Gabriele; Pacak, Karel; Eisenhofer, Graeme

    2013-02-01

    Here, we describe a novel method utilizing double stable isotope ultra performance liquid chromatography-tandem mass spectrometry to measure tissue contents and activity of phenylethanolamine N-methyltransferase (PNMT), the enzyme responsible for synthesis of the stress hormone, epinephrine. The method is based on measurement of deuterium-labeled epinephrine produced from the reaction of norepinephrine with deuterium-labeled S-adenosyl-L-methionine as the methyl donor. In addition to enzyme activity, the method allows for determination of tissue contents of PNMT using human recombinant enzyme for calibration. The calibration curve for epinephrine was linear over the range of 0.1 to 5,000 pM, with 0.5 pM epinephrine representing the lower limit of quantification. The calibration curve relating PNMT to production of deuterium-labeled epinephrine was also linear from 0.01 to 100 ng PNMT. Intra- and inter-assay coefficients of variation were respectively 12.8 % (n = 10) and 10.9 to 13.6 % (n = 10). We established utility of the method by showing induction of the enzyme by dexamethasone in mouse pheochromocytoma cells and strong relationships to PNMT gene expression and tissue epinephrine levels in human pheochromocytomas. Development of this assay provides new possibilities for investigations focusing on regulation of PNMT, the crucial final enzyme responsible for synthesis of epinephrine, the primary fight-or-flight stress hormone.

  10. Multiresidue method for identification and quantification of avermectins, benzimidazoles and nitroimidazoles residues in bovine muscle tissue by ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) using a QuEChERS approach.

    PubMed

    Silva, Guilherme Resende da; Lima, Josefa Abucater; Souza, Leonardo Francisco de; Santos, Flávio Alves; Lana, Mary Ane Gonçalves; Assis, Débora Cristina Sampaio de; Cançado, Silvana de Vasconcelos

    2017-08-15

    A quantitative and confirmatory multiresidue method for determining the presence of avermectins, benzimidazoles and nitroimidazoles in bovine muscle tissue by ultra-high performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) was developed, optimized and validated, using a QuEChERS extraction. The evaluated performance parameters were linearity, selectivity, matrix effect, decision limits (CCα), detection capability (CCβ), limits of detection (LOD), limits of quantification (LOQ), accuracy, precision and robustness. The validated method exhibited linearity with coefficient of determination (R(2)) higher than 0.90 in the working range from 0.5 to 2.0 times the maximum residue limit (MRL) or the minimum required performance level (MRPL) for the studied analytes, except for closantel, for which the linear study range was defined from 50 to 200µgkg(-1). The method was selective in the presence of macrolides and lincosamides for all the studied analytes. The LOD varied from 0.007 to 66.715µgkg(-1), whereas LOQ values ranging from 0.011 to 113.674µgkg(-1) were found. The results of the evaluation of the accuracy and precision were satisfactory for all the studied analytes, and according to the assessment of the robustness, the method was not robust only for the analytes abamectin, moxidectin, doramectin fenbendazole sulfone, closantel, thiabendazole, hydroxyl-metronidazole and ronidazole. The performance parameters demonstrated total method adequacy for the detection and quantification of avermectins, benzimidazoles and nitroimidazoles residues in bovine muscle tissues. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. In situ quantification and evaluation of ClO(-)/H2S homeostasis in inflammatory gastric tissue by applying a rationally designed dual-response fluorescence probe featuring a novel H(+)-activated mechanism.

    PubMed

    Fu, Qiang; Chen, Guang; Liu, Yuxia; Cao, Ziping; Zhao, Xianen; Li, Guoliang; Yu, Fabiao; Chen, Lingxin; Wang, Hua; You, Jinmao

    2017-05-02

    Homeostasis of ClO(-)/H2S plays a crucial role in the damage and repair of gastric tissue, but has rarely been investigated due to the challenge of in situ analysis in the highly acidic gastric environment. Herein, we designed a new H(+)-activated optical mechanism, involving controllable photoinduced electron transfer (PET) and switch of electron push-pull (SEPP), to develop the simple yet multifunctional probe (Z)-4-(2-benzylidenehydrazinyl)-7-nitrobenzo[c][1,2,5]oxadiazole (BNBD). First, the BNBD probe (Off) was protonated by the highly acidic media to trigger strong fluorescence (On). Then, the analytes ClO(-) and H2S reacted with the protonated BNBD, leading to ultrasensitive (ClO(-): 2.7 nM and H2S: 6.9 nM) fluorescence quenching via the rapid oxidation of C[double bond, length as m-dash]N (50 s) and nitro reduction (10 s), respectively. With the logical discrimination by absorbance/colour (ClO(-): 300 nm/colorless and H2S: 400 nm/orange), a strategy for the in situ quantification of ClO(-)/H2S in gastric mucosa and juice was developed. For the first time, the in situ quantitative monitoring of endogenous H2S and ClO(-)/H2S homeostasis as well as the pathologic manifestation in gastric mucosa were realized, thus overcoming the challenge of ClO(-)/H2S analysis under highly acidic conditions and enabling the in situ tissue quantification of ClO(-)/H2S. In combination with the assessment of mucosal damage, this study confirms the injurious/rehabilitative effects of ClO(-)/H2S on gastric mucosa (at 50-90 μm depth), which may facilitate the auxiliary diagnosis of stomach diseases induced by oxidative stress.

  12. Proteomic analysis of breast cancer tissues to identify biomarker candidates by gel-assisted digestion and label-free quantification methods using LC-MS/MS.

    PubMed

    Song, Mi-Na; Moon, Pyong-Gon; Lee, Jeong-Eun; Na, MinKyun; Kang, Wonku; Chae, Yee Soo; Park, Ji-Young; Park, Hoyong; Baek, Moon-Chang

    2012-10-01

    This study presents a proteomic method that differentiates between matched normal and breast tumor tissues from ductal carcinoma in situ (DCIS) and invasive carcinoma from Korean women, to identify biomarker candidates and to understand pathogenesis of breast cancer in protein level. Proteins from tissues obtained by biopsy were extracted by RIPA buffer, digested by the gel-assisted method, and analyzed by nano-UPLC-MS/MS. From proteomic analysis based on label-free quantitation strategy, a non-redundant list of 298 proteins was identified from the normal and tumor tissues, and 244 proteins were quantified using IDEAL-Q software. Hierarchical clustering analysis showed two patterns classified as two groups, invasive carcinoma and DCIS, suggesting a difference between two carcinoma at the protein expression level as expected. Differentially expressed proteins in tumor tissues compared to the corresponding normal tissues were related to three biological pathways: antigen-processing and presentation, glycolysis/gluconeogenesis, and complement and coagulation cascades. Among them, the up-regulation of calreticulin (CRT) and protein disulfide isomerase A3 (PDIA3) was confirmed by Western blot analysis. In conclusion, this study showed the possibility of identifying biomarker candidates for breast cancer using tissues and might help to understand the pathophysiology of this cancer at the protein level.

  13. Dynamic OCT monitoring and quantification of light penetration enhancement for normal, benign and cancerous human lung tissues at different concentrations of glycerol

    SciTech Connect

    Shu-wen Tan; Ying Jin; Hui Yu; Guo-yong Wu

    2013-10-31

    We have evaluated the dynamic effects of the analyte diffusion on the 1/e light penetration depths of normal, benign and cancerous human lung tissue in vitro, as well as have monitored and quantified the dynamic change in the light penetration depths of the mentioned human lung tissue after application of 25 % and 50 % glycerol solution, respectively. The light penetration depths of the analyte diffusion in the lung tissue are measured using the Fourierdomain optical coherence tomography (FD-OCT). Experimental results show that the application of glycerol as a chemical agent can significantly enhance light penetration depths into the human normal lung (NL), lung benign granulomatosis (LBG) and lung squamous cell carcinoma (LSCC) tissue. In-depth transport of the glycerol molecules in the NL, LBG and LSCC tissue at a lower glycerol concentration (25 %) are faster than those at a higher glycerol concentration (50 %), and the 1/e light penetration depths at a lower glycerol concentration (25 %) are smaller than those at a higher glycerol concentration (50 %), respectively. Their differences in the maximal 1/e light penetration depths of the NL, LBG and LSCC tissue at a higher and a lower glycerol concentrations were only 8.8 %, 6.8 % and 4.7 %, respectively. (biophotonics)

  14. Immunohistochemical quantification of the cobalamin transport protein, cell surface receptor and Ki-67 in naturally occurring canine and feline malignant tumors and in adjacent normal tissues

    PubMed Central

    Sysel, Annette M.; Valli, Victor E.; Bauer, Joseph A.

    2015-01-01

    Cancer cells have an obligate need for cobalamin (vitamin B12) to enable DNA synthesis necessary for cellular replication. This study quantified the immunohistochemical expression of the cobalamin transport protein (transcobalamin II; TCII), cell surface receptor (transcobalamin II-R; TCII-R) and proliferation protein (Ki-67) in naturally occurring canine and feline malignant tumors, and compared these results to expression in corresponding adjacent normal tissues. All malignant tumor tissues stained positively for TCII, TCII-R and Ki-67 proteins; expression varied both within and between tumor types. Expression of TCII, TCII-R and Ki-67 was significantly higher in malignant tumor tissues than in corresponding adjacent normal tissues in both species. There was a strong correlation between TCII and TCII-R expression, and a modest correlation between TCII-R and Ki-67 expression in both species; a modest association between TCII and Ki-67 expression was present in canine tissues only. These results demonstrate a quantifiable, synchronous up-regulation of TCII and TCII-R expression by proliferating canine and feline malignant tumors. The potential to utilize these proteins as biomarkers to identify neoplastic tissues, streamline therapeutic options, evaluate response to anti-tumor therapy and monitor for recurrent disease has important implications in the advancement of cancer management for both human and companion animal patients. PMID:25633912

  15. Heat treatment and the use of additives to improve the stability of paralytic shellfish poisoning toxins in shellfish tissue reference materials for internal quality control and proficiency testing.

    PubMed

    Burrell, Stephen; Clion, Valentin; Auroy, Virginie; Foley, Barry; Turner, Andrew D

    2015-06-01

    The need for homogenous reference materials stable for paralytic shellfish toxins is vital for the monitoring and quality assurance of these potent neurotoxins in shellfish. Two stabilisation techniques were investigated, heat treatment through autoclaving and the addition of preserving additives into the tissue matrix. Short and long-term stability experiments as well as homogeneity determination were conducted on materials prepared by both techniques in comparison with an untreated control using two LC-FLD methods. Both techniques improved the stability of the matrix and the PSP toxins present compared to the controls. A material was prepared using the combined techniques of heat treatment followed by spiking with additives and data is presented from this optimised reference material as used over a two year period in the Irish national monitoring program and in a development exercise as part of a proficiency testing scheme operated by QUASIMEME (Quality Assurance of Information for Marine Environmental Monitoring in Europe) since 2011. The results were indicative of the long-term stability of the material as evidenced through consistent assigned values in the case of the proficiency testing scheme and a low relative standard deviation of 10.5% for total toxicity data generated over 24 months. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Direct 4D PET MLEM reconstruction of parametric images using the simplified reference tissue model with the basis function method for [¹¹C]raclopride.

    PubMed

    Gravel, Paul; Reader, Andrew J

    2015-06-07

    This work assesses the one-step late maximum likelihood expectation maximization (OSL-MLEM) 4D PET reconstruction algorithm for direct estimation of parametric images from raw PET data when using the simplified reference tissue model with the basis function method (SRTM-BFM) for the kinetic analysis. To date, the OSL-MLEM method has been evaluated using kinetic models based on two-tissue compartments with an irreversible component. We extend the evaluation of this method for two-tissue compartments with a reversible component, using SRTM-BFM on simulated 3D + time data sets (with use of [(11)C]raclopride time-activity curves from real data) and on real data sets acquired with the high resolution research tomograph. The performance of the proposed method is evaluated by comparing voxel-level binding potential (BPND) estimates with those obtained from conventional post-reconstruction kinetic parameter estimation. For the commonly chosen number of iterations used in practice, our results show that for the 3D + time simulation, the direct method delivers results with lower (%)RMSE at the normal count level (decreases of 9-10 percentage points, corresponding to a 38-44% reduction), and also at low count levels (decreases of 17-21 percentage points, corresponding to a 26-36% reduction). As for the real 3D data set, the results obtained follow a similar trend, with the direct reconstruction method offering a 21% decrease in (%)CV compared to the post reconstruction method at low count levels. Thus, based on the results presented herein, using the SRTM-BFM kinetic model in conjunction with the OSL-MLEM direct 4D PET MLEM reconstruction method offers an improvement in performance when compared to conventional post reconstruction methods.

  17. Evaluating a set of reference genes for expression normalization in multiple tissues and skeletal muscle at different development stages in pigs using quantitative real-time polymerase chain reaction.

    PubMed

    Zhang, Jing; Tang, Zhonglin; Wang, Ning; Long, Liangqi; Li, Kui

    2012-01-01

    Gene expression analysis requires the use of reference genes consistently expressed under various conditions. In many cases, however, the commonly used reference genes are not uniformly expressed independently of tissues or environmental conditions. To provide a set of reliable reference genes in pigs, we used quantitative polymerase chain reaction to examine expression of six common reference genes (GAPDH, ACTB, H3F3A, HPRT1, RPL32, and RPS18) in adult tissues and prenatal skeletal muscles at 33, 65, and 90 days postcopulation from Tongcheng (obese-type) and Landrace (lean-type) pigs. The expression stability of these reference genes was evaluated by NormFinder, BestKeeper, and geNorm methods. Our data suggest that the reference genes were expressed variably in different tissues, developmental stages and breeds. RPS18, PRL32, and H3F3A could be used as internal controls to normalize gene expression in pig tissues and developmental skeletal muscle. The combination of internal control genes was necessary for accurate expression normalization. During skeletal muscle development, H3F3A and RPS18 would be the most appropriate combination to normalize gene expression in Tongcheng pigs, whereas the combination of PRL32 and RPS18 would be more suitable in Landrace pigs. In different tissues, the expression of PRL32 and RPS18 was the most consistent, and the combination of three genes (RPL32, RPS18, and H3F3A) is the most suitable for accurate normalization.

  18. Concurrent