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Journal of Exposure Science &... Nov 2023Toenails are a promising matrix for chronic metal exposure assessment, but there are currently no standard methods for collection and analysis. Questions remain about...
BACKGROUND
Toenails are a promising matrix for chronic metal exposure assessment, but there are currently no standard methods for collection and analysis. Questions remain about sample mass requirements and the extent to which metals measured in this matrix are representative of chronic body burden.
OBJECTIVE
This study proposes a method to maximize sample conservation for toenail metals analysis using inductively coupled plasma mass spectrometry (ICP-MS). We demonstrate the reliability of an ~25 mg toenail sample (typically 1-2 clippings) for metals analysis and evaluate the intra-individual variability of multiple metals in this matrix over time in men from the Gulf Long-term Follow-up (GuLF) Study.
METHODS
Toenail samples from 123 GuLF Study participants were collected at two visits 3 years apart and analyzed for 18 elements using ICP-MS. Participants with samples exceeding 200 mg at the first visit (n = 29) were selected for triplicate sub-sample analysis. Kendall's coefficient of concordance (W) was used to assess sub-sample reliability and Spearman's correlation coefficients (ρ) were used to evaluate fluctuations in elemental concentrations over time.
RESULTS
Results were not reported for Cd, Co, Mo, Sb, and V (detected in <60% of the samples). There was strong agreement among triplicate samples (Kendall's W: 0.72 (Cu)-0.90 (Cu)) across all elements evaluated, moderate correlations of elemental concentrations (Spearman's ρ: 0.21-0.42) over 3 years for As, Ca, Cr, Fe, Pb, Mn, and Zn, and strong correlations (>0.50) for Se, Cu, and Hg.
IMPACT STATEMENT
This toenail reliability study found that a low-mass (~25 mg) toenail sample (1-2 clippings) is suitable for the determination of most elements using ICP-MS and helps to increase the analytical capacity of limited toenail biospecimens collected in cohort studies. The results highlight differences in the suitability of toenails for chronic metal exposure assessment by element and underscore the need to consider intra-person variability, especially when comparing results across studies. We also provide recommendations for analytical standardization and the partitioning of the total collected toenail sample into multiple analytic sub-samples for future studies using toenail biospecimen for multiple assays.
Topics: Male; Humans; Nails; Reproducibility of Results; Metals; Mercury; Biomarkers; Trace Elements
PubMed: 37296232
DOI: 10.1038/s41370-023-00560-y -
Journal of Periodontal Research Oct 2023To analyse the salivary epitranscriptomic profiles as periodontitis biomarkers using multiplexed mass spectrometry (MS).
OBJECTIVE
To analyse the salivary epitranscriptomic profiles as periodontitis biomarkers using multiplexed mass spectrometry (MS).
BACKGROUND
The field of epitranscriptomics, which relates to RNA chemical modifications, opens new perspectives in the discovery of diagnostic biomarkers, especially in periodontitis. Recently, the modified ribonucleoside N6-methyladenosine (m6A) was revealed as a crucial player in the etiopathogenesis of periodontitis. However, no epitranscriptomic biomarker has been identified in saliva to date.
MATERIALS AND METHODS
Twenty-four saliva samples were collected from periodontitis patients (n = 16) and from control subjects (n = 8). Periodontitis patients were stratified according to stage and grade. Salivary nucleosides were directly extracted and, in parallel, salivary RNA was digested into its constituent nucleosides. Nucleoside samples were then quantified by multiplexed MS.
RESULTS
Twenty-seven free nucleosides were detected and an overlapping set of 12 nucleotides were detected in digested RNA. Among the free nucleosides, cytidine and three other modified nucleosides (inosine, queuosine and m6Am) were significantly altered in periodontitis patients. In digested RNA, only uridine was significantly higher in periodontitis patients. Importantly there was no correlation between free salivary nucleoside levels and the levels of those same nucleotides in digested salivary RNA, except for cytidine, m5C and uridine. This statement implies that the two detection methods are complementary.
CONCLUSION
The high specificity and sensitivity of MS allowed the detection and quantification of multiple nucleosides from RNA and free nucleosides in saliva. Some ribonucleosides appear to be promising biomarkers of periodontitis. Our analytic pipeline opens new perspectives for diagnostic periodontitis biomarkers.
Topics: Humans; Nucleosides; Tandem Mass Spectrometry; Chromatography, Liquid; Nucleotides; Periodontitis; RNA; Cytidine; Uridine; Biomarkers; Saliva
PubMed: 37349891
DOI: 10.1111/jre.13155 -
Journal of Pharmaceutical and... Sep 2023The emergence of new psychoactive substances currently exceeding a thousand is rapidly changing substance prevalence patterns and straining the methods used for...
The emergence of new psychoactive substances currently exceeding a thousand is rapidly changing substance prevalence patterns and straining the methods used for detection, most of which are suitable only for a single class of substances. This study presents a rapid and facile dilute-and-shoot system operated in conjunction with an optimized liquid chromatographic separation system for the high-sensitivity detection of substances across a range of substance classes with 3 isotopes used only. The proposed method based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) is able to identify 68 substance and their metabolites in urine samples as small as 50 μL. Optimal chromatographic conditions including 95% water/methanol ratio with 0.1% added formic acid and a prolonged LC gradient run-time (15 min) improved the peak shape of polar compounds and enhanced signal strength by 5%. Under 4-fold dilution, all analytes were within 80-120% of tolerance response levels, indicating that the matrix effect was insignificant. In experiments, the limit of detection (LOD) ranged from 0.05 to 0.5 ng mL, while the coefficient of determination (R) was > 0.9950. The retention time shift of each peak remained at < 2% with an inter-day relative standard deviation (RSD) of 0.9-14.9% and intra-day RSD of 1.1%- 13.8%. The rapid dilute-and-shoot presents a high-sensitivity, significant stability, robustness and reproducibility without serious interference. To demonstrate the effectiveness of the system, 532 urine samples were collected from suspected drug abusers, and the proposed method was used for rapid analysis. Of these samples, 79.5% contained between one and twelve analytes, and 12.4% tested positive for new psychoactive substances, mostly derivatives of amphetamine and synthetic cathinones. The study presents a high-sensitivity analytic system that is capable of detecting substances from multiple classes and can be used for effective monitoring of substance prevalence in urine.
Topics: Humans; Chromatography, Liquid; Tandem Mass Spectrometry; Reproducibility of Results; Central Nervous System Agents; Amphetamine; Limit of Detection; Chromatography, High Pressure Liquid
PubMed: 37210892
DOI: 10.1016/j.jpba.2023.115443 -
Nature Oct 2023
Topics: Molecular Biology; Cryoelectron Microscopy; Mass Spectrometry; Proteins; Analytic Sample Preparation Methods
PubMed: 37845529
DOI: 10.1038/d41586-023-03236-7 -
Journal of Veterinary Internal Medicine 2023Cytosine arabinoside (Ara-C) is a nucleoside analog prodrug utilized for immunomodulatory effects mediated by its active metabolite Ara-CTP. Optimal dosing protocols for...
BACKGROUND
Cytosine arabinoside (Ara-C) is a nucleoside analog prodrug utilized for immunomodulatory effects mediated by its active metabolite Ara-CTP. Optimal dosing protocols for immunomodulation in dogs have not been defined. Cytarabine ocfosfate (CO) is a lipophilic prodrug of Ara-C that can be administered PO and provides prolonged serum concentrations of Ara-C.
OBJECTIVES
Provide pharmacokinetic data for orally administered CO and determine accumulation and functional consequences of Ara-CTP within peripheral blood leukocytes.
ANIMALS
Three healthy female hound dogs and 1 healthy male Beagle.
METHODS
Prospective study. Dogs received 200 mg/m of CO PO q24h for 7 doses. Serum and cerebrospinal fluid (CSF) CO and Ara-C concentrations were measured by liquid chromatography-tandem mass spectroscopy (LC-MS/MS). Complete blood counts, flow cytometry, and leukocyte activation assays were done up to 21 days. Incorporation of Ara-CTP within leukocyte DNA was determined by LC-MS/MS.
RESULTS
Maximum serum concentration (C ) for Ara-C was 456.1-724.0 ng/mL (1.88-2.98 μM) and terminal half-life was 23.3 to 29.4 hours. Cerebrospinal fluid: serum Ara-C ratios ranged from 0.54 to 1.2. Peripheral blood lymphocyte concentrations remained within the reference range, but proliferation rates poststimulation were decreased at 6 days. Incorporation of Ara-CTP was not saturated and remained >25% of peak concentration at 13 days.
CONCLUSIONS AND CLINICAL IMPORTANCE
Oral CO may produce prolonged serum Ara-C half-lives at concentrations sufficient to induce functional changes in peripheral leukocytes and is associated with prolonged retention of DNA-incorporated Ara-CTP. Application of functional and active metabolite assessment is feasible and may provide more relevant data to determine optimal dosing regimens for Ara-C-based treatments.
Topics: Female; Male; Dogs; Animals; Arabinofuranosylcytosine Triphosphate; Chromatography, Liquid; Prodrugs; Prospective Studies; Tandem Mass Spectrometry; Leukocytes; Biomarkers; Cytarabine; DNA
PubMed: 37670479
DOI: 10.1111/jvim.16842 -
Journal of Medical Screening Dec 2023A rolling circle amplification (RCA) based commercial methodology using cell-free (cf)DNA to screen for common trisomies became available in 2018. Relevant publications...
OBJECTIVE
A rolling circle amplification (RCA) based commercial methodology using cell-free (cf)DNA to screen for common trisomies became available in 2018. Relevant publications documented high detection but with a higher than expected 1% false positive rate. Preliminary evidence suggested assay variability was an issue. A multi-center collaboration was created to explore this further and examine whether subsequent manufacturer changes were effective.
METHODS
Three academic (four devices) and two commercial (two devices) laboratories provided run date, chromosome 21, 18, and 13 run-specific standard deviations, number of samples run, and reagent lot identifications. Temporal trends and between-site/device consistency were explored. Proportions of run standard deviations exceeding pre-specified caps of 0.4%, 0.4% and 0.6% were computed.
RESULTS
Overall, 661 RCA runs between April 2019 and July 30, 2022 tested 39,756 samples. In the first 24, subsequent 9, and final 7 months, proportions of capped chromosome 21 runs dropped from 39% to 22% to 6.0%; for chromosome 18, rates were 76%, 36%, and 4.0%. Few chromosome 13 runs were capped using the original 0.60%, but capping at 0.50%, rates were 28%, 16%, and 7.6%. Final rates occurred after reformulated reagents and imaging software modifications were fully implemented across all devices. Revised detection and false positive rates are estimated at 98.4% and 0.3%, respectively. After repeat testing, failure rates may be as low as 0.3%.
CONCLUSION
Current RCA-based screening performance estimates are equivalent to those reported for other methods, but with a lower test failure rate after repeat testing.
Topics: Pregnancy; Female; Humans; Cell-Free Nucleic Acids; Early Detection of Cancer; Prenatal Diagnosis; Trisomy
PubMed: 37194254
DOI: 10.1177/09691413231173315 -
Biotechnology Journal Dec 2023Bovine serum albumin (BSA) is a globular non-glycoprotein that has gotten a lot of attention because of its unique properties like biocompatibility, biodegradability,... (Review)
Review
Bovine serum albumin (BSA) is a globular non-glycoprotein that has gotten a lot of attention because of its unique properties like biocompatibility, biodegradability, non-immunogenicity, non-toxicity, and strong resemblance to the natural extracellular matrix (ECM). Given its robust mechanical properties, such as interfacial tension, conductivity, swelling resistance, and viscoelasticity, it can be concluded that it is an appropriate matrix for producing novel BSA-based nanoconstructs. Thus, simple analytic methods are required for accurately detecting BSA as a model protein in medical sciences and healthcare. Furthermore, the characteristics mentioned above aid BSA in the electrospinning process, which results in fibers conjugated with other polymers. Electrospun synthesis has recently received much attention for its ability to produce stable, biomimicking, highly porous, 3D BSA-derived nano-fibers. As a result, BSA-based nano-fibers have achieved exclusive developments in the medical sector, such as tissue engineering for the remodeling of damaged tissue or organ repair by creating artificial ones. Meanwhile, they could be used as drug delivery systems (DDS) for target-specific drug delivery, wound dressings, and so on. This study illustrates the structural and physicochemical properties of BSA and the determination of BSA using various methods, by citing recent reports and current developments in the medical field. Furthermore, current challenges and future directions are also highlighted.
Topics: Serum Albumin, Bovine; Polymers; Tissue Engineering; Drug Delivery Systems; Porosity; Nanofibers
PubMed: 37632263
DOI: 10.1002/biot.202300279 -
Accounts of Chemical Research Dec 2023ConspectusThe quantum chemical modeling of organic crystals and other molecular condensed-phase problems requires computationally affordable electronic structure methods...
ConspectusThe quantum chemical modeling of organic crystals and other molecular condensed-phase problems requires computationally affordable electronic structure methods which can simultaneously describe intramolecular conformational energies and intermolecular interactions accurately. To achieve this, we have developed a spin-component-scaled, dispersion-corrected second-order Møller-Plesset perturbation theory (SCS-MP2D) model. SCS-MP2D augments canonical MP2 with a dispersion correction which removes the uncoupled Hartree-Fock dispersion energy present in canonical MP2 and replaces it with a more reliable coupled Kohn-Sham treatment, all evaluated within the framework of Grimme's D3 dispersion model. The spin-component scaling is then used to improve the description of the residual (nondispersion) portion of the correlation energy.The SCS-MP2D model improves upon earlier corrected MP2 models in a few ways. Compared to the highly successful dispersion-corrected MP2C model, which is based solely on intermolecular perturbation theory, the SCS-MP2D dispersion correction improves the description of both inter- and intramolecular interactions. The dispersion correction can also be evaluated with trivial computational cost, and nuclear analytic gradients are computed readily to enable geometry optimizations. In contrast to earlier spin-component scaling MP2 models, the optimal spin-component scaling coefficients are only mildly sensitive to the choice of training data, and a single global parametrization of the model can describe both thermochemistry and noncovalent interactions.The resulting dispersion-corrected, spin-component-scaled MP2 (SCS-MP2D) model predicts conformational energies and intermolecular interactions with accuracy comparable to or better than those of many range-separated and double-hybrid density functionals, as is demonstrated on a variety of benchmark tests. Among the functionals considered here, only the revDSD-PBEP86-D3(BJ) functional gives consistently smaller errors in benchmark tests. The results presented also hint that further improvements of SCS-MP2D may be possible through a more robust fitting procedure for the seven empirical parameters.To demonstrate the performance of SCS-MP2D further, several applications to molecular crystal problems are presented. The three chosen examples all represent cases where density-driven delocalization error causes GGA or hybrid density functionals to artificially stabilize crystals exhibiting more extended π-conjugation. Our pragmatic strategy addresses the delocalization error by combining a periodic density functional theory (DFT) treatment of the infinite lattice with intramolecular/conformational energy corrections computed with SCS-MP2D. For the anticancer drug axitinib, applying the SCS-MP2D conformational energy correction produces crystal polymorph stabilities that are consistent with experiment, in contrast to earlier studies. For the crystal structure prediction of the ROY molecule, so named for its colorful red, orange, and yellow crystals, this approach leads to the first plausible crystal energy landscape, and it reveals that the lowest-energy polymorphs have already been found experimentally. Finally, in the context of photomechanical crystals, which transform light into mechanical work, these techniques are used to predict the structural transformations and extract design principles for maximizing the work performed.
PubMed: 37963266
DOI: 10.1021/acs.accounts.3c00578 -
Journal of Proteome Research Feb 2024The trends of the last 20 years in biotechnology were revealed using artificial intelligence and natural language processing (NLP) of publicly available data.... (Review)
Review
The trends of the last 20 years in biotechnology were revealed using artificial intelligence and natural language processing (NLP) of publicly available data. Implementing this "science-of-science" approach, we capture convergent trends in the field of proteomics in both technology development and application across the phylogenetic tree of life. With major gaps in our knowledge about protein composition, structure, and location over time, we report trends in persistent, popular approaches and emerging technologies across 94 ideas from a corpus of 29 journals in PubMed over two decades. New metrics for clusters of these ideas reveal the progression and popularity of emerging approaches like single-cell, spatial, compositional, and chemical proteomics designed to better capture protein-level chemistry and biology. This analysis of the proteomics literature with advanced analytic tools quantifies the Rate of Rise for a next generation of technologies to better define, quantify, and visualize the multiple dimensions of the proteome that will transform our ability to measure and understand proteins in the coming decade.
Topics: Proteomics; Artificial Intelligence; Phylogeny; Proteome; Technology
PubMed: 38096378
DOI: 10.1021/acs.jproteome.3c00430 -
Pakistan Journal of Pharmaceutical... Sep 2023The study aimed to prepare and characterize biodegradable sustained-release beads of letrozole (LTZ) for treating cancerous disease. The ionotropic gelation method was...
The study aimed to prepare and characterize biodegradable sustained-release beads of letrozole (LTZ) for treating cancerous disease. The ionotropic gelation method was used for the preparation and calcium chloride (CaCl) was used as a gelating agent, while chitosan (CTS) and sodium alginate (NaAlg) as biodegradable polymeric matrices in the blend hydrogel beads. The beads were characterized for their size, surface morphology, drug entrapment efficiency, drug-polymer interaction and crystallinity using different analytic techniques, including optical microscopy, Scanning Electron Microscopy (SEM), UV-spectroscopy, Fourier-transform Infrared Spectroscopy (FTIR), Thermo gravimetric Analysis (TGA), Differential Scanning Calorimetry (DSC) and X-ray Diffraction Analysis (XRD) respectively. In vitro swelling studies were also applied to observe the response of these polymeric networks against different pH (at 1.2, 6.8 and 7.4 pH). The results from TGA and DSC exhibited that the components in the formulation possess better thermal stability. The XRD of polymeric networks displays a minor crystalline and significant amorphous nature. The SEM micrographs revealed that polymeric networks have uneven surfaces and grooves. Better swelling and in vitro outcomes were achieved at a high pH (6.8,7.4), which endorsed the pH-responsive characteristics of the prepared beads. Hence, beads based on chitosan and sodium alginate were successfully synthesized and can be used for the controlled release of letrozole.
Topics: Delayed-Action Preparations; Letrozole; Chitosan; Particle Size; Polymers; Alginates; Spectroscopy, Fourier Transform Infrared; Hexuronic Acids; Microscopy, Electron, Scanning; Glucuronic Acid
PubMed: 38008961
DOI: No ID Found