Quantification of global DNA methylation with infrared fluorescence in liver and muscle tissues of differentially fed boars

Methylation of cytosine residues at CpG sites is involved in various biological processes to control gene regulation and gene expression. Global DNA methylation is changed in different tumors and in cloned animals. Global DNA methylation can be accurately quantified by dot blot analysis with infrared (IR) fluorophores. Methylated lambda DNA was used as model DNA to develop and validate an immunochemical assay with IR fluorescence detection. Two different IR fluorophores were used, one to detect 5-methylcytosine and another to account for DNA loading. A sensitive infrared detection method was established which is suitable for accurate and reproducible quantification of global DNA methylation across a wide dynamic range. This method was subsequently employed to quantify global DNA methylation in liver and in muscle tissues of boars which have received either a control diet or a methyl supplemented diet in an ongoing study. A significant difference in global DNA methylation is indicated in muscle but not in liver tissue between the two groups of boars.

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

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.

New methods for quantification and analysis of quantitative real-time polymerase chain reaction data

Quantitative real-time polymerase chain reaction (qPCR) is a sensitive gene quantitation method that has been widely used in the biological and biomedical fields. The currently used methods for PCR data analysis, including the threshold cycle (CT) method, linear and non-linear model fitting methods, all require subtracting background fluorescence. However, the removal of background fluorescence is usually inaccurate, and therefore can distort results. Here, we propose a new method, the taking-difference linear regression method, to overcome this limitation. Briefly, for each two consecutive PCR cycles, we subtracted the fluorescence in the former cycle from that in the later cycle, transforming the n cycle raw data into n-1 cycle data. Then linear regression was applied to the natural logarithm of the transformed data. Finally, amplification efficiencies and the initial DNA molecular numbers were calculated for each PCR run. To evaluate this new method, we compared it in terms of accuracy and precision with the original linear regression method with three background corrections, being the mean of cycles 1-3, the mean of cycles 3-7, and the minimum. Three criteria, including threshold identification, max R2, and max slope, were employed to search for target data points. Considering that PCR data are time series data, we also applied linear mixed models. Collectively, when the threshold identification criterion was applied and when the linear mixed model was adopted, the taking-difference linear regression method was superior as it gave an accurate estimation of initial DNA amount and a reasonable estimation of PCR amplification efficiencies. When the criteria of max R2 and max slope were used, the original linear regression method gave an accurate estimation of initial DNA amount. Overall, the taking-difference linear regression method avoids the error in subtracting an unknown background and thus it is theoretically more accurate and reliable. This method is easy to perform and the taking-difference strategy can be extended to all current methods for qPCR data analysis.^

Mineral quantification of a Jordan Cretaceous outcrop (Section GM3, Ghawr Al Mazar, Ghor al Mazrar)

Cyclic fluctuations in global sea level during epochs of warm greenhouse climate have remained enigmatic, because absence or subordinate presence of polar ice during these periods precludes an explanation by glacio-eustatic forcing. An alternative concept suggests that the water-bearing potential of groundwater aquifers is equal to that of ice caps and that changes in the dynamic balance of aquifer charge versus discharge, as a function of the temperature-related intensity of the hydrological cycle, may have driven eustasy during warm climates. However, this idea has long been neglected for two reasons: 1) the large storage potential of subsurface aquifers was confused with the much smaller capacity of rivers and lakes and 2) empirical data were missing that document past variations in the hydrological cycle in relation to eustasy. In the present study we present the first empirical evidence for changes in precipitation, continental weathering intensity and evaporation that correlate with astronomically (long obliquity) forced sea-level cycles during the warmest period of the Cretaceous (Cenomanian-Turonian). We compare sequence-stratigraphic data with changes in the terrigenous mineral assemblage in a low-latitude marine sedimentary sequence from the equatorial humid belt at the South-Tethyan margin (Levant carbonate platform, Jordan), thereby avoiding uncertainties from land-ocean correlations. Our data indicate covariance between cycles in weathering and sea level: predominantly chemical weathering under wet climate conditions is reflected by dominance of weathering products (clays) in deposits that represent sea-level fall (aquifer charge > discharge). Conversely, preservation of weathering-sensitive minerals (feldspars, epidote and pyroxenes) in transgressive sediments reflects decreased continental weathering due to dryer climate (aquifer discharge > charge). Based on our results we suggest that aquifer-eustasy represents a viable alternative to glacio-eustasy as a driver of cyclic 3rd-order sea-level fluctuations during the middle Cretaceous greenhouse climate, and it may have been a pervasive process throughout Earth history.

Protein quantification from complex protein mixtures using a proteomics methodology with single-cell resolution

We have developed an extremely sensitive technique, termed immuno-detection amplified by T7 RNA polymerase (IDAT) that is capable of monitoring proteins, lipids, and metabolites and their modifications at the single-cell level. A double-stranded oligonucleotide containing the T7 promoter is conjugated to an antibody (Ab), and then T7 RNA polymerase is used to amplify RNA from the double-stranded oligonucleotides coupled to the Ab in the Ab-antigen complex. By using this technique, we are able to detect the p185her2/neu receptor from the crude lysate of T6–17 cells at 10−13 dilution, which is 109-fold more sensitive than the conventional ELISA method. Single-chain Fv fragments or complementarity determining region peptides of the Ab also can be substituted for the Ab in IDAT. In a modified protocol, the oligonucleotide has been coupled to an Ab against a common epitope to create a universal detector species. With the linear amplification ability of T7 RNA polymerase, IDAT represents a significant improvement over immuno-PCR in terms of sensitivity and has the potential to provide a robotic platform for proteomics.

A sensitive HPLC method for measuring bacterial proteolysis and proteinase activity in UHT milk

A sensitive quantitative reversed-phase HPLC method is described for measuring bacterial proteolysis and proteinase activity in UHT milk. The analysis is performed on a TCA filtrate of the milk. The optimum concentration of TCA was found to be 4%; at lower concentrations, non-precipitated protein blocked the HPLC while higher concentrations yielded lower amounts of peptides. The method showed greater sensitivity and reproducibility than a fluorescamine-based method. Quantification of the HPLC method was achieved by use of an external dipeptide standard or a standard proteinase. (c) 2006 Elsevier Ltd. All rights reserved.

Quantification of visual field loss in age-related macular degeneration

Background - An evaluation of standard automated perimetry (SAP) and short wavelength automated perimetry (SWAP) for the central 10–2 visual field test procedure in patients with age-related macular degeneration (AMD) is presented in order to determine methods of quantifying the central sensitivity loss in patients at various stages of AMD. Methods - 10–2 SAP and SWAP Humphrey visual fields and stereoscopic fundus photographs were collected in 27 eyes of 27 patients with AMD and 22 eyes of 22 normal subjects. Results - Mean Deviation and Pattern Standard Deviation (PSD) varied significantly with stage of disease in SAP (both p<0.001) and SWAP (both p<0.001), but post hoc analysis revealed overlap of functional values among stages. In SWAP, indices of focal loss were more sensitive to detecting differences in AMD from normal. SWAP defects were greater in depth and area than those in SAP. Central sensitivity (within 1°) changed by -3.9 and -4.9 dB per stage in SAP and SWAP, respectively. Based on defect maps, an AMD Severity Index was derived. Conclusions - Global indices of focal loss were more sensitive to detecting early stage AMD from normal. The SWAP sensitivity decline with advancing stage of AMD was greater than in SAP. A new AMD Severity Index quantifies visual field defects on a continuous scale. Although not all patients are suitable for SWAP examinations, it is of value as a tool in research studies of visual loss in AMD.

Quantification of visual field loss in age-related macular degeneration

Presentation Purpose:To determine methods of quantifying the sensitivity loss in the central 10o visual field in a cross section of patients at various stages of age-related macular degeneration (AMD). Methods:Standard and short-wavelength automated perimetry (SAP and SWAP) visual fields were collected using program 10-2 of the Humphrey Field Analyzer, in 44 eyes of 27 patients with AMD and 41 eyes of 22 normal subjects. Stereoscopic fundus photographs were graded by two independent observers and the stage of disease determined. Global indices were compared for their ability to delineate the normal visual field from early stages of AMD and to differentiate between stages. Results:Mean Deviation (MD) and Pattern Standard Deviation (PSD) varied significantly with stage of disease in SAP (both p<0.001) and SWAP (both p<0.001), but post-hoc analysis revealed overlap of functional values between stages. Global indices of focal loss, PSD and local spatial variability (LSV) were the most sensitive to detecting differences between normal subjects and early stage AMD patients, in SAP and SWAP, respectively. Overall, defects were confined to the central 5°. SWAP defects were consistently greater in depth and area than those in SAP. The most vulnerable region of the 10° field to sensitivity loss with increasing stage of AMD was the central 1°, in which the sensitivity decline was -4.8dB per stage in SAP and -4.9dB per stage in SWAP. Based on the pattern deviation defect maps, a severity index of AMD visual field loss was derived. Threshold variability was considerably increased in late stage AMD eyes. Conclusions:Global indices of focal loss were more sensitive to the detection of early stage AMD from normal. The sensitivity decline with advancing stage of AMD was greater in SWAP compared to SAP, however the trend was not strong across all stages of disease. The less commonly used index LSV represents relatively statistically unmanipulated summary measure of focal loss. A new severity index is described which is sensitive to visual field change in AMD, measures visual field defects on a continuous scale and may serve as a useful measure of functional change in AMD in longitudinal studies. Keywords: visual fields • age-related macular degeneration • perimetry

A novel dried blood spot-LCMS method for the quantification of methotrexate polyglutamates as a potential marker for methotrexate use in children

Objective: Development and validation of a selective and sensitive LCMS method for the determination of methotrexate polyglutamates in dried blood spots (DBS). Methods: DBS samples [spiked or patient samples] were prepared by applying blood to Guthrie cards which was then dried at room temperature. The method utilised 6-mm disks punched from the DBS samples (equivalent to approximately 12 μl of whole blood). The simple treatment procedure was based on protein precipitation using perchloric acid followed by solid phase extraction using MAX cartridges. The extracted sample was chromatographed using a reversed phase system involving an Atlantis T3-C18 column (3 μm, 2.1x150 mm) preceded by Atlantis guard column of matching chemistry. Analytes were subjected to LCMS analysis using positive electrospray ionization. Key Results: The method was linear over the range 5-400 nmol/L. The limits of detection and quantification were 1.6 and 5 nmol/L for individual polyglutamates and 1.5 and 4.5 nmol/L for total polyglutamates, respectively. The method has been applied successfully to the determination of DBS finger-prick samples from 47 paediatric patients and results confirmed with concentrations measured in matched RBC samples using conventional HPLC-UV technique. Conclusions and Clinical Relevance: The methodology has a potential for application in a range of clinical studies (e.g. pharmacokinetic evaluations or medication adherence assessment) since it is minimally invasive and easy to perform, potentially allowing parents to take blood samples at home. The feasibility of using DBS sampling can be of major value for future clinical trials or clinical care in paediatric rheumatology. © 2014 Hawwa et al.

A simple bioanalytical method for the quantification of antiepileptic drugs in dried blood spots

An increasing number of publications on the dried blood spot (DBS) sampling approach for the quantification of drugs and metabolites have been spurred on by the inherent advantages of this sampling technique. In the present research, a selective and sensitive high-performance liquid chromatography method for the concurrent determination of multiple antiepileptic drugs (AEDs) [levetiracetam (LVT), lamotrigine (LTG), phenobarbital (PHB)], carbamazepine (CBZ) and its active metabolite carbamazepine-10,11 epoxide (CBZE)] in a single DBS has been developed and validated. Whole blood was spotted onto Guthrie cards and dried. Using a standard punch (6 mm diameter), a circular disc was punched from the card and extracted with methanol: acetonitrile (3:1, v/v) containing hexobarbital (Internal Standard) and sonicated prior to evaporation. The extract was then dissolved in water and vortex mixed before undergoing solid phase extraction using HLB cartridges. Chromatographic separation of the AEDs was achieved using Waters XBridge™ C18 column with a gradient system. The developed method was linear over the concentration ranges studied with r ≥ 0.995 for all compounds. The lower limits of quantification (LLOQs) were 2, 1, 2, 0.5 and 1 μg/mL for LVT, LTG, PHB, CBZE and CBZ, respectively. Accuracy (%RE) and precision (%CV) values for within and between day were <20% at the LLOQs and <15% at all other concentrations tested. This method was successfully applied to the analysis of the AEDs in DBS samples taken from children with epilepsy for the assessment of their adherence to prescribed treatments.

Plasma and cold sprayed aluminum carbon nanotube composites: Quantification of nanotube distribution and multi-scale mechanical properties

Carbon nanotubes (CNT) could serve as potential reinforcement for metal matrix composites for improved mechanical properties. However dispersion of carbon nanotubes (CNT) in the matrix has been a longstanding problem, since they tend to form clusters to minimize their surface area. The aim of this study was to use plasma and cold spraying techniques to synthesize CNT reinforced aluminum composite with improved dispersion and to quantify the degree of CNT dispersion as it influences the mechanical properties. Novel method of spray drying was used to disperse CNTs in Al-12 wt.% Si prealloyed powder, which was used as feedstock for plasma and cold spraying. A new method for quantification of CNT distribution was developed. Two parameters for CNT dispersion quantification, namely Dispersion parameter (DP) and Clustering Parameter (CP) have been proposed based on the image analysis and distance between the centers of CNTs. Nanomechanical properties were correlated with the dispersion of CNTs in the microstructure. Coating microstructure evolution has been discussed in terms of splat formation, deformation and damage of CNTs and CNT/matrix interface. Effect of Si and CNT content on the reaction at CNT/matrix interface was thermodynamically and kinetically studied. A pseudo phase diagram was computed which predicts the interfacial carbide for reaction between CNT and Al-Si alloy at processing temperature. Kinetic aspects showed that Al4C3 forms with Al-12 wt.% Si alloy while SiC forms with Al-23wt.% Si alloy. Mechanical properties at nano, micro and macro-scale were evaluated using nanoindentation and nanoscratch, microindentation and bulk tensile testing respectively. Nano and micro-scale mechanical properties (elastic modulus, hardness and yield strength) displayed improvement whereas macro-scale mechanical properties were poor. The inversion of the mechanical properties at different scale length was attributed to the porosity, CNT clustering, CNT-splat adhesion and Al 4C3 formation at the CNT/matrix interface. The Dispersion parameter (DP) was more sensitive than Clustering parameter (CP) in measuring degree of CNT distribution in the matrix.

Plasma And Cold Sprayed Aluminum Carbon Nanotube Composites: Quantification Of Nanotube Distribution And Multi-Scale Mechanical Properties

Carbon nanotubes (CNT) could serve as potential reinforcement for metal matrix composites for improved mechanical properties. However dispersion of carbon nanotubes (CNT) in the matrix has been a longstanding problem, since they tend to form clusters to minimize their surface area. The aim of this study was to use plasma and cold spraying techniques to synthesize CNT reinforced aluminum composite with improved dispersion and to quantify the degree of CNT dispersion as it influences the mechanical properties. Novel method of spray drying was used to disperse CNTs in Al-12 wt.% Si pre-alloyed powder, which was used as feedstock for plasma and cold spraying. A new method for quantification of CNT distribution was developed. Two parameters for CNT dispersion quantification, namely Dispersion parameter (DP) and Clustering Parameter (CP) have been proposed based on the image analysis and distance between the centers of CNTs. Nanomechanical properties were correlated with the dispersion of CNTs in the microstructure. Coating microstructure evolution has been discussed in terms of splat formation, deformation and damage of CNTs and CNT/matrix interface. Effect of Si and CNT content on the reaction at CNT/matrix interface was thermodynamically and kinetically studied. A pseudo phase diagram was computed which predicts the interfacial carbide for reaction between CNT and Al-Si alloy at processing temperature. Kinetic aspects showed that Al4C3 forms with Al-12 wt.% Si alloy while SiC forms with Al-23wt.% Si alloy. Mechanical properties at nano, micro and macro-scale were evaluated using nanoindentation and nanoscratch, microindentation and bulk tensile testing respectively. Nano and micro-scale mechanical properties (elastic modulus, hardness and yield strength) displayed improvement whereas macro-scale mechanical properties were poor. The inversion of the mechanical properties at different scale length was attributed to the porosity, CNT clustering, CNT-splat adhesion and Al4C3 formation at the CNT/matrix interface. The Dispersion parameter (DP) was more sensitive than Clustering parameter (CP) in measuring degree of CNT distribution in the matrix.

Quantification of the effects of architectural traits on dry mass production and light interception of tomato canopy under different temperature regimes using a dynamic functional-structural plant model

There is increasing interest in evaluating the environmental effects on crop architectural traits and yield improvement. However, crop models describing the dynamic changes in canopy structure with environmental conditions and the complex interactions between canopy structure, light interception, and dry mass production are only gradually emerging. Using tomato (Solanum lycopersicum L.) as a model crop, a dynamic functional-structural plant model (FSPM) was constructed, parameterized, and evaluated to analyse the effects of temperature on architectural traits, which strongly influence canopy light interception and shoot dry mass. The FSPM predicted the organ growth, organ size, and shoot dry mass over time with high accuracy (>85%). Analyses of this FSPM showed that, in comparison with the reference canopy, shoot dry mass may be affected by leaf angle by as much as 20%, leaf curvature by up to 7%, the leaf length: width ratio by up to 5%, internode length by up to 9%, and curvature ratios and leaf arrangement by up to 6%. Tomato canopies at low temperature had higher canopy density and were more clumped due to higher leaf area and shorter internodes. Interestingly, dry mass production and light interception of the clumped canopy were more sensitive to changes in architectural traits. The complex interactions between architectural traits, canopy light interception, dry mass production, and environmental conditions can be studied by the dynamic FSPM, which may serve as a tool for designing a canopy structure which is 'ideal' in a given environment.

Biomarkers of Nitrosative Stress: Development and validation of a new analytical method for 3-Nitrotyrosine quantification

Background: The nitration of tyrosine residues in proteins is associated with nitrosative stress, resulting in the formation of 3-nitrotyrosine (3-NT). 3-NT levels in biological samples have been associated with numerous physiological and pathological conditions. For this reason, several attempts have been made in order to develop methods that accurately quantify 3-NT in biological samples. Regarding chromatographic methods, they seem to be very accurate, showing very good sensibility and specificity. However, accurate quantification of this molecule, which is present at very low concentrations both at physiological and pathological states, is always a complex task and a target of intense research. Objectives: We aimed to develop a simple, rapid, low-cost and sensitive 3-NT quantification method for use in medical laboratories as an additional tool for diagnosis and/or treatment monitoring of a wide range of pathologies. We also aimed to evaluate the performance of the HPLC-based method developed here in a wide range of biological matrices. Material and methods: All experiments were performed on a Hitachi LaChrom Elite® HPLC system and separation was carried out using a Lichrocart® 250-4 Lichrospher 100 RP-18 (5μm) column. The method was further validated according to ICH guidelines. The biological matrices tested were serum, whole blood, urine, B16 F-10 melanoma cell line, growth medium conditioned with the same cell line, bacterial and yeast suspensions. Results: From all the protocols tested, the best results were obtained using 0.5% CH3COOH:MeOH:H2O (15:15:70) as the mobile phase, with detection at wavelengths 215, 276 and 356 nm, at 25ºC, and using a flow rate of 1 mL/min. By using this protocol, it was possible to obtain a linear calibration curve (correlation coefficient = 1), limits of detection and quantification in the order of ng/mL, and a short analysis time (<15 minutes per sample). Additionally, the developed protocol allowed the successful detection and quantification of 3-NT in all biological matrices tested, with detection at 356 nm. Conclusion: The method described in this study, which was successfully developed and validated for 3-NT quantification, is simple, cheap and fast, rendering it suitable for analysis in a wide range of biological matrices.

A real-time reverse transcriptase polymerase chain reaction for detection and quantification of Vesiculovirus

Vesiculoviruses (VSV) are zoonotic viruses that cause vesicular stomatitis disease in cattle, horses and pigs, as well as sporadic human cases of acute febrile illness. Therefore, diagnosis of VSV infections by reliable laboratory techniques is important to allow a proper case management and implementation of strategies for the containment of virus spread. We show here a sensitive and reproducible real-time reverse transcriptase polymerase chain reaction (RT-PCR) for detection and quantification of VSV. The assay was evaluated with arthropods and serum samples obtained from horses, cattle and patients with acute febrile disease. The real-time RT-PCR amplified the Piry, Carajas, Alagoas and Indiana Vesiculovirus at a melting temperature 81.02 ± 0.8ºC, and the sensitivity of assay was estimated in 10 RNA copies/mL to the Piry Vesiculovirus. The viral genome has been detected in samples of horses and cattle, but not detected in human sera or arthropods. Thus, this assay allows a preliminary differential diagnosis of VSV infections.