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At least 73 records · Page 4Linked to original sources
PubMed2026

Development of a High-Sensitivity Glycoproteomics Approach for Fc-Specific Quantification of IgG Core Fucosylation in Traumatic Brain Injury.

Traumatic brain injury (TBI) triggers complex neuroinflammatory cascades that involve sustained immune activation and dysregulated antibody effector functions. Immunoglobulin G (IgG) Fc N-glycosylation, particularly core fucosylation, critically modulates immune signaling through altered Fcγ receptor (FcγR) interactions; however, its role in TBI remains unexplored. Here, we developed a high-sensitivity, mass spectrometry-based glycoproteomics method for the systematic analysis of IgG Fc core fucosylation dynamics following TBI. The approach integrates Fc-specific enzymatic truncation with GlycINATOR (EndoS2) and tryptic digestion, followed by high-resolution LC-MS/MS profiling, enabling confident identification of truncated Fc glycopeptides. Furthermore, a targeted parallel reaction monitoring (PRM) strategy allowed direct quantification of core fucosylated and afucosylated glycopeptides from 10 μg of crude serum protein, eliminating the need for IgG purification. Our results reveal time-dependent and subclass-specific remodeling of IgG Fc fucosylation postinjury, characterized by an overall reduction in fucosylated species and a relative increase in afucosylation. Collectively, this study establishes a scalable analytical platform for Fc-specific glycosylation profiling and identifies IgG core fucosylation as a candidate molecular indicator of immune dysregulation in TBI, providing new insights into post-traumatic immune regulation.

Brain Injuries, Traumatic↗
PubMed2026

Chimeric structural isomer fragments as cost-efficient internal standards for amino acid quantification by mass spectrometry.

Amino acid (AA) profiles from body fluids such as blood and urine are clinical indicators for diagnosing metabolic and hepatic diseases. Current quantitative methods, such as liquid chromatography-mass spectrometry (LC-MS) with isotopically labelled internal standards (ISs), are costly and technically demanding. This study proposes a cost-efficient alternative using structural isomers as ISs in a direct liquid infusion (DLI) tandem mass spectrometry (MS/MS) approach. The method leverages chimeric spectra and fragment intensity ratios to quantify AAs, demonstrating high linearity and precision even with a 3D ion trap mass analyser. This approach offers a viable strategy for AA quantification in preventive medicine, particularly for screening metabolic diseases such as phenylketonuria, diabetes, and liver dysfunction.

Amino Acids↗
PubMed1992

Concurrent down-regulation of IP prostanoid receptors and the alpha-subunit of the stimulatory guanine-nucleotide-binding protein (Gs) during prolonged exposure of neuroblastoma x glioma cells to prostanoid agonists. Quantification and functional implications.

Neuroblastoma x glioma hybrid NG108-15 cells express a high-affinity IP prostanoid receptor. Saturation binding analysis of this receptor, using [3H]prostaglandin E1 ([3H]PGE1) as ligand, indicated that it was present at some 1.5 pmol/mg of membrane protein and displayed a dissociation constant for this ligand of 30-40 nM. Prolonged exposure of these cells either to PGE1 or to iloprost, which is a stable analogue of prostacyclin, caused a 40-70% decrease in levels of the receptor. The remaining receptors were capable of interacting with the stimulatory G-protein (Gs) of the adenylate cyclase cascade, as saturation analysis of the binding of [3H]PGE1 indicated that they had a similar affinity for the 3H-labelled ligand, and because the specific binding of [3H]PGE1 to these receptors was still sensitive to the presence of poorly hydrolysed analogues of GTP. We have recently demonstrated that prolonged exposure of NG108-15 ells to PGE1 causes a cyclic AMP-independent loss of Gs alpha-subunit (Gs alpha) from these cells [McKenzie & Milligan (1990) J. Biol. Chem. 265, 17084-17093]. Steady-state concentration of the larger 45 kDa form of Gs alpha (which is the predominant form expressed in these cells) was assessed to be 9.6 pmol/mg of membrane protein, and treatment with iloprost decreased levels of this polypeptide to some 3.0 pmol/mg of protein. Time courses of iloprost-mediated down-regulation of the IP prostanoid receptor, loss of Gs alpha protein as assessed by immunoblotting and loss of Gs alpha activity as assessed by the reconstitution of NaF stimulation of adenylate cyclase activity to membranes of S49 cyc- cells by sodium cholate extracts of NG108-15 cells were identical, suggesting that the loss of the IP prostanoid receptor and G-protein occurred in parallel. Each of these effects was half-maximal between 2 and 3 h of exposure to the agonist. Stoichiometry of loss of Gs alpha and IP prostanoid receptor was unchanged by the percentage receptor occupancy, and quantification indicated the loss of some 7-10 mol of Gs alpha/mol of receptor. This is the first report to demonstrate the temporal concurrence of loss of Gs alpha and of a receptor which interacts with this G-protein. Chronic activation of the IP prostanoid receptor on these cells results in the development of a heterologous form of desensitization to agents which function to activate adenylate cyclase [Kelly, Keen, Nobbs & MacDermot (1990) Br. J. Pharmacol. 99, 306-316]. Agonist regulation of Gs alpha levels in these cells may contribute to this process.

Adenylyl Cyclases↗
PubMed2025

FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data.

SUMMARY: Single molecule footprinting profiles the heterogeneity of TF occupancy at cis-regulatory elements across cell populations at unprecedented resolution. The single molecule nature of the data in principle allows for observing the footprint of individual transcription factors and nucleosomes. However, we currently lack algorithms to quantify these occupancy patterns of chromatin binding factors in an automated way and without prior assumptions on their genomic location. Here we present FootprintCharter, an unsupervised tool to detect and quantify footprints for transcription factors (TFs) and nucleosomes from single molecule footprinting data. After detection, TF footprints can be labeled with orthogonal motif annotations provided by the user. FootprintCharter allows for the quantification of complex molecular states such as positioning of unphased nucleosomes and combinatorial co-binding of multiple TFs. AVAILABILITY AND IMPLEMENTATION: FootprintCharter is freely available on Bioconductor with version 2.2.0 of https://bioconductor.org/packages/SingleMoleculeFootprinting through the functions FootprintCharter, PlotFootprints, and Plot_FootprintCharter_SM.

Transcription Factors↗
PubMed1975

Analysis and quantification of ether lipids by chromatographic methods.

Chromatographic methods, especially thin-layer chromatography (TLC) and gas-liquid chromatography (GLC) are widely used in investigations of the occurrence, molecular structure and metabolism of ether lipids. The application of such techniques to structural analysis and quantification, in combination with methods for the degradation and derivatization of ether lipids, is discussed.

Alkenes↗
PubMed1992

Quantification of fetal antigen 2 (FA2) in supernatants of cultured osteoblasts, normal human serum, and serum from patients with chronic renal failure.

Fetal antigen 2 (FA2) was found within the cytoplasm of osteoblasts and in osteoid material, in a bone biopsy with morphological changes of renal osteodystrophy. An ELISA technique for FA2 quantification was developed, and the specificity confirmed by comparison with electroimmunoassay. The intra- and interassay coefficient of variations (%) were 8.3 and 9.7 respectively, and the detection limit 0.0004 arbitrary units FA2/1 using second-trimester human amniotic fluid as reference (1 AU FA2/1). FA2 was detected in serum-free supernatants from osteoblast cultures. Following size chromatography, the FA2 distribution (two peaks eluted corresponding to Mw 30 kDa and 100 kDa) in serum from a patient with chronic renal failure complicated with secondary hyperparathyroidism and in human amniotic fluid were identical. Probably due to the detection limit, only one peak fraction (30 kDa) was seen in normal human serum. Significantly greater FA2 concentrations were found in sera (n = 14) from patients with chronic renal failure (median: 11.9 mAU FA2/1; range: 5.2-49.0 mAU FA2/1) compared to normal healthy individuals (n = 23) (median: 4.1 mAU FA2/1; range 2.4-9.4 mAU FA2/1) (P less than 0.00001). A close correlation was found between serum FA2 and alkaline phosphatase (R(s) = 0.761; P = 0.006), c-terminal fraction of PTH (R(s) = 0.872; P = 0.003) and intact PTH(1-84) (R(s) = 0.904; P = 0.011) in the haemodialysis patients. These data indicate that FA2 is synthesized by osteoblasts and may represent a new marker for metabolic bone changes.

Cells, Cultured↗
PubMed2026

ClearDepthIAS enables automated high-throughput quantification of roots in soil-grown taproot crops.

Understanding root system architecture is critical for improving crop productivity and resilience, yet phenotyping root traits such as root growth angle and rooting depth remains technically challenging, especially at high throughput. Here, we present ClearDepthIAS, a high-throughput imaging and analysis platform that enables nondestructive, automated quantification of root architecture traits in taproot system crops. By capturing and stitching 360° images of roots growing along the transparent walls of pots and applying deep learning-based segmentation (ClearDepth-WRT), we measured wall root shallowness (WRS)-a proxy for root growth angle-with high precision. We demonstrated for the tap root systems of soybean and canola that the system accurately detects root tips, quantifies their vertical distribution, and extracts biologically meaningful traits such as root area, distribution indices, and growth angles. Validation experiments in canola and soybean demonstrated that WRS can correlate with root crown architecture in mature plants, both in greenhouse and field settings. Furthermore, WRS and root distribution indices derived from ClearDepthIAS are predictors of early root architecture and can be correlated with root biomass distribution across soil depths under field conditions; however, environmental interactions may influence these relationships and weaken or even negate such correlations, as observed when comparing field to field variation in root system architecture. Our system enables efficient phenotyping of genetically diverse populations, with medium to high trait heritability, supporting its utility for genome-wide association studies and breeding. ClearDepthIAS accelerates the development of root ideotypes for improved resource acquisition and carbon sequestration, offering a scalable tool for supporting climate-resilient agriculture.

Plant Roots↗
PubMed1979

Quantification of joint laxity.

We have compared the finger hyperextensometer (Jobbins et al., 1978) and the scoring system of Carter and Wilkinson (1964), modified by Beighton et al. (1973), in the quantification of joint laxity in a population selected to demonstrate a wide range of joint movement. Both systems correlated well (P less than 0.001) with a 'global index' of joint laxity derived by adding the arcs of movement recorded at most joints in the body by the method of the American Academy of Orthopaedic Surgeons (1965). The Carter and Wilkinson system produced better correlations and is the method of choice for assessing generalized joint laxity.

Humans↗
PubMed1979

Quantification of the human orienting response to another human: lesioned and psychiatric patients compared to normals.

A method for eliciting, controlling, and quantifying the alpha suppression response to a human "real-person" stimulus is presented. Improved control is achieved by a feedback from the EEG response to the presentation of the stimulus. Quantification is comprehensive in that initial response and subsequent habituation for both latency and duration are described. Patients who had suffered a focal lesion but who had recovered sufficiently to travel from one hospital to another by taxi were compared with hospitalized psychiatric patients and normal volunteers. Lesioned patients showed less EEG response to visual stimuli than did the other groups, even with an evocative, real-person stimulus. The differences among the three groups were most evident at the onset of stimulation and less so after habituation had occurred.

Adult↗
PubMed1978

Activation of the alternative pathway of complement by grain. I. C3PA conversion and quantification of complement consumption by rye.

Ground whole rye and airborne rye dust of comparable size distribution were tested for their ability to activate the complement cascade via the alternative pathway. Precipitin-negative pooled normal human serum was incubated with increasing amounts of the two rye dusts. Electrophoresis of the resultant supernatant fluids demonstrated the conversion of the proactivator of the third component of complement to the gamma-migrating activator of the third component. This activation was completely prevented by pre-treating the serum with the chelator EDTA, while pre-treatment with EGTA allowed suboptimal arc conversion, strongly implying that complement was activated via the alternative pathway. Quantification of the supernanant fluids showed dose-dependent complement consumption as defined by both CH100 immunodiffusion and CH50 tube haemolytic techniques. Airborne rye dust showed a greater quantitative potential than ground whole rye for activating the alternative pathway. These results indicate the possibility of the direct action of airborne organic dusts on the induction of inflammatory sequelae in the lungs of both sensitized and unsensitized individuals.

Air Pollutants↗
PubMed1978

Quantification and properties of tubulin polymerization in crude brain extracts and preparations of microtubular and purified tubulin.

Removal of assembled tubulin by centrifugation, followed by measurement in the supernatant of the residual colchicine binding capacity of the non-polymerized, non-precipitable tubulin, is a sensitive and reliable method of measuring tubulin polymerization. This method can be used in both crude and purified preparations of brain tubulin and allows the molar quantification of the total, polymerized and non-polymerized tubulin species in each sample. Only 40--50% of the total tubulin present in crude adult brain extracts is capable of polymerizing when incubated with GTP. The percentage of tubulin polymerizing with GTP is slightly higher in crude foetal brain extracts than in the adult. Incubation of first polymerization supernatants, containing exclusively the GTP-insensitive tubulin, with guanosine 5'-[alpha, beta-methylene]triphosphate (GuoP[CH2]PP) but not with 2.4 M glycerol results in tubulin polymerization. High concentrations of glycerol (2.4 M) promote the polymerization of tubulin in adult but not in crude foetal brain extracts. Both ATP and adenosine 5'-[alpha, beta-methylene]triphosphate (AdoP[CH2]PP) are effective in promoting the polymerization of GDP-free (90%) microtubular protein. The microtubular protein assembled with GuoP[CH2]PP or AdoP[CH2]PP has the unique character of being resistant to calcium concentrations (2mM), which cause complete depolymerization of the tubulin assembled with GTP or ATP. Phosphocellulose-purified tubulin significantly assembles when incubated with GuoP[CH2]PP or AdoP[CH2]PP at protein concentrations at which GTP or ATP do not promote polymerization. 2 micrometer tubulin is the minimal concentration required for polymerization in both crude and purified preparations of adult rat brain tubulin.

Animals↗
PubMed1975

Megakaryocyte quantifications in relation to thrombokinetics in primary thrombocythaemia and allied diseases.

Megakaryocyte morphology was studied quantitatively in primary thrombocythaemia (PT) and in chronic myelogenous leukaemia (CML). The relation of thrombokinetics to megakaryocyte quantifications was evaluated in PT and compared to previously obtained results in polycythaemia vera (PV) and idiopathic thrombocytopenic purpura (ITP). Megakaryocyte area, number and volume per mul bone marrow were significantly higher in PT as compared to controls. The nuclear lobe number was significantly increased and the megakaryocytes were shifted towards more mature forms, suggesting a prolonged megakaryocyte generation time. In CML the megakaryocyte number and volume per mul bone marrow were also significantly above normal, but the megakaryocyte area, number of lobes and degree of megakaryocytic maturation were significantly below normal. Platelet production was in PT 6.2 times normal and proportional to the increase in megakaryocyte volume which was 6.8 times normal. In PV with major splenomegaly the mean platelet production rate was higher (9.5 times normal) although their peripheral platelet count was lower than in PT. This discrepancy is explained by the greatly enlarged splenic platelet pool in the PV patients. In ITP the mean platelet production rate was 2.2 to 3 times normal and was significantly lower than in PT and PV.

Adult↗
PubMed1992

A sensitive enzymatic method (SK-013) for detection and quantification of specific periodontopathogens.

Porphyromonas gingivalis, Bacteroides forsythus, and Treponema denticola have been found to predominate in periodontal pockets of patients with adult periodontitis. These microorganisms hydrolyze the synthetic peptide N-benzoyl-DL-arginine-2-naphthylamide (BANA). In this study, we developed an enzymatic method, designated SK-013, to detect the existence of these microorganisms in subgingival plaque bacteria. This enzymatic method was based on the observation of the hydrolysis of N-carbobenzoxy-glycyl-glycyl-arginyl-3,5-dibromo-4-hydroxyaniline (N-CBz-Gly-Gly-Arg-DBHA) and made more sensitive by adding an enhancing system. The SK-013 was specifically positive for P. gingivalis, B. forsythus, T. denticola, and some strains of Capnocytophaga species, but was not specific for any of the other bacterial strains tested. This SK-013 system may be valuable for detection and quantification of periodontal disease-associated bacteria in subgingival plaque and thus for diagnosis of periodontal infections.

Bacteroides↗
PubMed1979

Quantification of tetanus antitoxin in human sera. I. Counter-immunoelectrophoresis.

An extensive sero-epidemiological survey of immunity to tetanus is to be performed in Norway during 1978 and 1979 and thus a simple and reliable method for screening sera for content of tetanus antitoxin is needed. An improved counter-immunoelectrophoretic method for quantification of tetanus antitoxin is described. The toxin neutralization test in mice is considered to correlate well with protection in humans. Counter-immunoelectrophoresis has the advantage of using tetanus toxoid instead of toxin as well as being more rapid and less expensive. Specific antibodies of the IgG, IgM, and IgA classes could be read simultaneously for many sera. This may be of importance, since it is reported in the literature that only antibody of the IgG class is capable of neutralizing tetanus toxin in mice. Counter-immunoelectrophoresis is limited by being less sensitive than the toxin neutralization test in mice.

Chromatography, Gel↗
PubMed1975

Quantification of mouse macrophage chemotaxis in vitro: role of C5 for the production of chemotactic activity.

Delineation of the mechanisms of macrophage accumulation at local tissue sites will further our understanding of immunologically mediated host resistance to infectious and neoplastic diseases. Since mice are frequently used for the study of immune function, we developed a method for the quantification of mouse macrophage chemotaxis in vitro. By this method it was found that the fifth component of complement is necessary for the production of chemotactic activity in mouse serum by inflammatory agents such as endotoxin or aggregated gamma globulin. The majority of macrophage chemotactic activity produced by these agents in mouse serum can be attributed to a low-molecular-weight (ca. 15,000) chemotactic factor. The data suggest that this factor is the biologically active cleavage product of the fifth component of complement, C5a.

Animals↗
PubMed1978

Quantification of obstetric traction.

Measurements of factors involved in the degree of traction exerted during obstetric cases were carried out. Bovine material force was approximately 150 lbs. Maximum manual effort would be approximately four times this and mechanical traction would be at least 50 per cent higher again. A workable maternal fetal ratio was established for use in cases of fetal oversize. Possible quantification of other factors is also discussed.

Animals↗
PubMed1976

Low cost intrathyroidal iodine quantification with a fluorescent scanner.

A thyroid fluorescent scanner has proven to be useful for imaging thyroids in cases where isotope scans are contraindicated. Minor modifications of a commercially available scanner make possible total intrathyroidal quantification, which aids in the differentiation between primary and secondary hypothyroidism and in the diagnosis of thyroiditis.

Costs and Cost Analysis↗
PubMed1976

Quantification of bone mineralization using computed tomography.

Computed tomography was used to find a sensitive parameter for bone mineralization. A precision scanning instrument was constructed for determination of the mineral distribution in sections of the forearm. The quality of the reconstructed images allows separate quantification of compact and spongy bone even when gamma rays are used. Computer simulation and measured of models and macerated human bones showed that under clinical conditions it is possible to quantify spongy bone density within an accuracy of +/-2%.

Adolescent↗