High-throughput DNA extraction strategy for fecal microbiome studies

Microbiome studies are becoming larger in size to detect the potentially small effect that environmental factors have on our gut microbiomes, or that the microbiome has on our health. Therefore, fast and reproducible DNA isolation methods are needed to handle thousands of fecal samples. We used the Chemagic 360 chemistry and Magnetic Separation Module I (MSMI) instrument to compare two sample preservatives and four different pre-treatment protocols to find an optimal method for DNA isolation from thousands of fecal samples. The pre-treatments included bead beating, sample handling in tube and plate format, and proteinase K incubation. The optimal method offers a sufficient yield of high-quality DNA without contamination. Three human fecal samples (adult, senior, and infant) with technical replicates were extracted. The extraction included negative controls (OMNIgeneGUT, DNA/RNA shield fluid, and Chemagic Lysis Buffer 1) to detect cross-contamination and ZymoBIOMICS Gut Microbiome Standard as a positive control to mimic the human gut microbiome and assess sensitivity of the extraction method. All samples were extracted using Chemagic DNA Stool 200 H96 kit (PerkinElmer, Finland). The samples were collected in two preservatives, OMNIgeneGUT and DNA/RNA shield fluid. DNA quantity was measured using Qubit-fluorometer, DNA purity and quality using gel electrophoresis, and taxonomic signatures with 16S rRNA gene-based sequencing with V3V4 and V4 regions. Bead beating increased bacterial diversity. The largest increase was detected in gram-positive genera Blautia, Bifidobacterium, and Ruminococcus. Preservatives showed minor differences in bacterial abundances. The profiles between the V3V4 and V4 regions differed considerably with lower diversity samples. Negative controls showed signs from genera abundant in fecal samples. Technical replicates of the Gut Standard and stool samples showed low variation. The selected isolation protocol included recommended steps from manufacturer as well as bead beating. Bead beating was found to be necessary to detect hard-to-lyse bacteria. The protocol was reproducible in terms of DNA yield among different stool replicates and the ZymoBIOMICS Gut Microbiome Standard. The MSM1 instrument and pre-treatment in a 96-format offered the possibility of automation and handling of large sample collections. Both preservatives were feasible in terms of sample handling and had low variation in taxonomic signatures. The 16S rRNA target region had a high impact on the composition of the bacterial profile.

IMPORTANCE

Next-generation sequencing (NGS) is a widely used method for determining the composition of the gut microbiota. Due to the differences in the gut microbiota composition between individuals, microbiome studies have expanded into large population studies to maximize detection of small effects on microbe-host interactions. Thus, the demand for a rapid and reliable microbial profiling is continuously increasing, making the optimization of high-throughput 96-format DNA extraction integral for NGS-based downstream applications. However, experimental protocols are prone to bias and errors from sample collection and storage, to DNA extraction, primer selection and sequencing, and bioinformatics analyses. Methodological bias can contribute to differences in microbiome profiles, causing variability across studies and laboratories using different protocols. To improve consistency and confidence of the measurements, the standardization of microbiome analysis methods has been recognized in many fields.

A Robust HPLC Method for Easily Oxidizable Phosphine Ligand Analysis

Phosphine ligands are widely used in the manufacture of small molecule active pharmaceutical ingredients, for they play a key role in transition-metal-catalyzed cross-coupling. However, chromatographic analysis of phosphine ligands can be challenging because of the easily oxidizable nature of this class of compounds. This manuscript describes an out-of-specification (OOS) investigation study of XPhos raw material analysis by high performance liquid chromatography (LC). It is concluded that on-column degradation/oxidation is the culprit behind this OOS result. In addition, a slightly modified yet much improved new LC method is developed by adding a trace amount of tris(2-carboxyethyl)phosphine (TCEP) into the aqueous mobile phase. TCEP is also a phosphine compound and is commonly used as a reducing reagent in molecular biology. The trace amount of TCEP serves as a surrogate reagent to passivate the LC column and eliminate the on-column degradation/oxidation. As a result, a much more robust performance is achieved with greatly improved method precision and sensitivity. This is a general approach and can be applied to the LC analysis of many other phosphine ligands in the same manner.

A high performance thin layer chromatography (HPTLC) method for the quality assessment of agarwood (Aquilaria malaccensis) oil from Northeast India

The high-value agarwood oil, largely used in perfumery is generally graded by the traditional method of sensorial assessment. The compositional complexity and variation made its quality control challenging. Besides, non-volatile contaminants and adulterants are the bottlenecks in gas-chromatographic detection. Herein, a HPTLC based technique was developed for the quality assessment of agarwood oil from Northeast India. A 'marker band' (anisylacetone and oxygenated sesquiterpene rich) on HPTLC profile, containing major peaks of the oil and characteristic agarwood aroma was quantified to assess the quality. The developed method was validated in terms of specificity, linearity, sensitivity, recovery and precision. The application of the method in test samples of three different grades indicated a positive correlation between 'marker band' quantity and oil quality. Its abundance in the superior grade oil was >50% and <20% in poor grade. It can be an efficient analytical tool for the quality assessment and grading of agarwood oil.

Enhancing Odor Analysis with Gas Chromatography-Olfactometry (GC-O): Recent Breakthroughs and Challenges

Gas chromatography-olfactometry (GC-O) has made significant advancements in recent years, with breakthroughs in its applications and the identification of its limitations. This technology is widely used for analyzing complex odor patterns. The review begins by explaining the principles of GC-O, including sample preparation, separation methods, and olfactory evaluation techniques. It then explores the diverse range of applications where GC-O has found success, such as food and beverage industries, environmental monitoring, perfume and aroma development, and forensic analysis. One of the major breakthroughs in GC-O analysis is the improvement in separation power and resolution of odorants. Techniques like rapid GC, comprehensive two-dimensional GC, and multidimensional GC have enhanced the identification and quantification of odor-active chemicals. However, GC-O also has limitations. These include the challenges in detecting and quantifying trace odorants, dealing with matrix effects, and ensuring the repeatability and consistency of results across laboratories. The review examines these limitations closely and discusses potential solutions and future directions for improvement in GC-O analysis. Overall, this review presents a comprehensive overview of the recent advances in GC-O, covering breakthroughs, applications, and limitations. It aims to promote the wider usage of GC-O analysis in odor analysis and related industries. Researchers, practitioners, and anyone interested in leveraging the capabilities of GC-O in analyzing complex odor patterns will find this review a valuable resource. The article highlights the potential of GC-O and encourages further research and development in the field.

A stability-indicating method development and validation for the determination of related substances in novel synthetic decapeptide by HPLC

In the present scenario, peptide is an emerging field of research having vast therapeutic applications. Diverse impurities may rise from various stages of the synthesis process and storage of the peptides. Because these contaminants may have an impact on the therapeutic safety and effectiveness of peptides in their approaching applications, they must be identified and carefully monitored. Considering the pharmaceutical importance of the extent of peptides, we were motivated to synthesize a decapeptide and establish a novel gradient reversed-phase high-performance liquid chromatography (RP-HPLC) method for its analysis along with efficient separation of its six related impurities. Different buffers, organic modifiers, and columns were used in the tests for good separation of these impurities. To establish a stability-indicating method, a stress study was also conducted. The International Conference on Harmonization (ICH) guidelines have been followed for validation of the developed analytical method. The validated method revealed sufficient accuracy, specificity, linearity, robustness, precision, and high sensitivity for its intended use. The proposed method could be appropriate for routine analysis and stability assessment of the decapeptide, which might be useful for further scientific investigation.

Development of a Simultaneous Normal-Phase HPLC Analysis of Lignans, Tocopherols, Phytosterols, and Squalene in Sesame Oil Samples

The objective of this study was to develop a simultaneous analytical method for the determination of lignans, tocols, phytosterols, and squalene using high-performance liquid chromatography coupled with a diode array and fluorescence detector (HPLC-DAD-FLD). The method employed a VertisepTM UPS silica HPLC column (4.6 × 250 mm, 5 µm) with a mobile phase mixture of n-hexane/tetrahydrofuran/2-propanol. This approach enabled the simultaneous analysis of ten compounds within 22 min. The linear correlation (R2) exceeded 0.9901. The limit of detection (LOD) and limit of quantitation (LOQ) were up to 0.43 µg mL-1 for lignans and tocopherols and up to 326.23 µg mL-1 for phytosterol and squalene. The precision and accuracy of the intra-day and inter-day variation were less than 1.09 and 3.32% relative standard deviations (RSDs). Furthermore, the developed method was applied for the analysis of targeted compounds in twenty-eight sesame oil samples (1775-8965 µg g-1 total lignans, 29.7-687.9 µg g-1 total tocopherols, 2640-9500 µg g-1 phytosterol, and 245-4030 µg g-1 squalene). The HPLC method that has been developed was proven to be a reliable and effective tool for the determination of those functional compounds among sesame oil samples.

Development and Validation of Novel HPLC Methods for Quantitative Determination of Vitamin D3 in Tablet Dosage Form

In the present work, an efficient isocratic HPLC method was developed for the precise and accurate estimation of vitamin D3 in tablet form. The chromatographic conditions comprised an L3 silica column (5 µm in particle size, 4.6 mm × 250 mm) with a mobile phase n-hexane/ethyl acetate (85:15 v/v) with a flow rate of 2.0 mL/min and a detection wavelength of 292 nm. The new methodology was validated for accuracy, precision, specificity, robustness, and quantification limits according to an official monograph of USP/BP and ICH guidelines. The peak areas of the six replicates of the homogeneous sample were recorded. The mean value obtained was 67,301, and the relative standard deviation (RSD) was 0.1741. The linearity and range were in the acceptable bounds, i.e., 0.999, which was calculated using regression line analysis. The results show that the method is truly acceptable as the RSD, as the flow rate was 0.81%, while for the mobile phase composition, it was 0.72%, which lies in the acceptable range. The limit of detection (LOD) and the limit of quantification (LOQ) values were 0.0539 µg/mL and 0.1633 µg/mL, respectively. The % RSD of the intra and inter-day precision of the method was deemed acceptable according to the international commission for harmonization guidelines. The developed method has potential to be used for the detection and quantification of vitamin D3 during routine analysis for tablets in dosage form.

Novel LC-MS/MS Method for Simultaneous Determination of Monoamine Neurotransmitters and Metabolites in Human Samples

For the simultaneous determination of monoamine neurotransmitters (NTs) like dopamine, serotonin, noradrenaline, and epinephrine, and their metabolites (metanephrine, normetanephrine, 3-methoxytyramine, vanillylmandelic acid, 3,4-dihydroxyphenylacetic acid, homovanillic acid, and 5-hydroxyindoleacetic acid), a robust liquid chromatography method coupled with tandem mass spectrometry (LC-MS/MS) was introduced as the analytical method. This analytical method proved to be accurate for the simultaneous measurement of the amounts of 11 NTs and their metabolites in biological samples. The method proved to be more efficient and better than the previously reported method in terms of precision, recovery, sample requirement, and extraction procedure. The reported method requires only 100 μL of blood and 200 μL of urine, and the extraction procedure requires acetonitrile precipitation, filtration, drying, and reconstitution in water. The separation of all analytes was performed on an C18 column (4.6 mm × 150 mm and 1.8 μm). A 10 min gradient elution program with a mobile phase consisting of phase A (0.2% formic acid in water) and phase B (methanol) was used. The positive ionization mode was used for the detection of all analytes in multiple reaction monitoring (MRM). The proposed method was validated with an internal standard and yielded lower limits of detection and quantification ranges of 0.0182-0.0797 ng/mL and 0.0553-0.2415 ng/mL, respectively, with a good linearity (R2) between 0.9959 and 0.9994. The recoveries ranged from 73.37% to 116.63% in blood and from 80.9% to 115.33% in urine. For the NTs and metabolites, the intra- and interday % CV were 0.24-9.36 and 0.85-9.67, respectively. The developed LC-MS/MS method was successfully used for the determination of trace amounts of endogenous compounds in human blood and urine samples.

Liquid chromatography-tandem mass spectrometry determination of bumetanide in human plasma and application to a clinical pharmacokinetic study

Determining a drug's bioavailability and bioequivalence is important for developing and approving a drug product. The procedure supports applications for generic drug products and novel therapeutic substances, makes important decisions regarding safety and efficacy, and measures a drug's concentration in biological matrices. This study aimed to develop and validate a specific, simple, sensitive, and accurate method using liquid chromatography-tandem mass spectrometry (LC-MS) for measuring bumetanide (BUM) in human plasma. Chromatographic separation was achieved using a Hypurity C18 column (4.6 × 50 mm, 5 μm) under isocratic conditions, and LC-MS detected positive ionization acquisition modes. Protonated precursor to product ion transitions were observed at m/z 365.08 → 240.10 and 370.04 → 244.52 for BUM and internal standard, respectively. The linear range of BUM in plasma samples was 3.490-401.192 ng/mL. The inter-precision value ranged from 1.76% to 4.75%. The inter-accuracy value ranged from 96.46% to 99.95%. The method was adequately validated per the U.S. Food and Drug Administration guidelines, and the results were within permissible bounds. The Cmax and Tmax values were ~53.097 ± 13.537 ng/mL and 1.25 (0.67-5.00) h, respectively. The new approach showed satisfactory results for studying BUM in human plasma with potential use in pharmacokinetic and bioequivalence investigations.

Does the Quantification of Δ9-Tetrahydrocannabinolic Acid A in Serum/Plasma Provide Any Additional Information About Consumption Pattern from Drivers Under the Influence of Cannabis?

Introduction: Δ9-tetrahydrocannabinolic acid A (THCA-A) is one of the main ingredients of cannabis plants and is converted to the psychoactive substance Δ9-tetrahydrocannabinol (THC) by decarboxylation during heating above ∼90°C. During the consumption of cannabis, a varying proportion of THCA-A is absorbed into the body. Therefore, the quantification of THCA-A in serum/plasma might provide additional information on consumption behavior in driving under the influence of cannabis cases. Materials and Methods: In this study, an already established gas-chromatography mass-spectrometry (GC-MS) method for the quantification of THC, 11-OH-THC, and THC-COOH in serum and plasma samples was extended to include THCA-A. This validated method was then applied to 1228 routinely achieved serum/plasma samples from drivers suspected of cannabis consumption in Western Saxony. Two different grouping systems for chronic/occasional consumption, one system for acute/subacute consumption, Huestis formulas, and the cannabis influence factor (CIF) were used for evaluation. Results: Method validation showed appropriate results for forensic toxicological routine analysis. Limit of detection and lower limit of quantification (LLOQ) for THCA-A were 0.3 and 1.0 ng/mL, respectively. Reproducibility was <11% and accuracy ranged between 104% and 107%. THCA-A was stable in native samples at least for 2 weeks at room temperature or 4°C as well as 1 month at -20°C. Freeze-thaw stability for three cycles and processed sample stability over 3 days was proven. A total of 865 cases with a THC concentration above the German analytical cutoff of 1 ng/mL as well as the analytical LLOQs of 0.9 and 2.5 ng/mL for 11-OH-THC and THC-COOH, respectively, were included in further statistical analysis. In 407 (47.1%) of these samples, THCA-A was quantifiable. Different statistical analyses indicated a correlation between THCA-A and THC concentrations in cases of chronic and acute consumption. In addition, an increase of chronic and acute cases with increasing THCA-A concentrations was observed. However, no correlation between THCA-A and CIF was found. Discussion: These data show that THCA-A might be an additional indicative marker to provide information about consumption frequency and acuteness. Additional studies with known consumption frequencies and times are required to verify these findings.

GC-MS/MS analysis of synthetic cannabinoids 5F-MDMB-PICA and 5F-CUMYL-PICA in forensic cases

Aim: Validate a method to quantify 1-(5-fluoropentyl)-N-(2-phenylpropan-2-yl)-1H-indole-3-carboxamide (5F-CUMYL-PICA) and methyl 2-[[1-(5-fluoropentyl) indole-3-carbonyl] amino]-3,3-dimethyl-butanoate (5F-MDMB-PICA) in blood samples using GC-MS/MS. Materials & methods: A solid-phase extraction (SPE) method has been developed to quantify 5F-MDMB-PICA and 5F-CUMYL-PICA in authentic human blood samples. Results & conclusion: The limit of detection (LOD) was 0.1 and 0.11 ng/ml for 5F-CUMYL-PICA and 5F-MDMB-PICA, respectively, while the limit of quantification (LOQ) was 0.50 ng/ml for both two compounds. Recovery was 91.40, 82.54 and 85.10% for SPE, supported liquid extraction (SLE) and ISOLUTE C18; matrix effects 15, 24 and 22.5% for SPE, SLE and ISOLUTE C18; accuracy was 2.4-5.5 and 3.9-7.3% for SPE, SLE and ISOLUTE C18, while precision was 4.6-7.7 and 6.4-8.3% for SPE, SLE and ISOLUTE C18, respectively. The concentrations of 5F-CUMYL-PICA and 5F-MDMB-PICA in the authentic human blood samples were 2.18 and 3.07 ng/ml, respectively. The validated method was successfully used in supporting the quantification of analytes in blood.

Efficient retrosynthetic planning with MCTS exploration enhanced A* search

Retrosynthetic planning, which aims to identify synthetic pathways for target molecules from starting materials, is a fundamental problem in synthetic chemistry. Computer-aided retrosynthesis has made significant progress, in which heuristic search algorithms, including Monte Carlo Tree Search (MCTS) and A* search, have played a crucial role. However, unreliable guiding heuristics often cause search failure due to insufficient exploration. Conversely, excessive exploration also prevents the search from reaching the optimal solution. In this paper, MCTS exploration enhanced A* (MEEA*) search is proposed to incorporate the exploratory behavior of MCTS into A* by providing a look-ahead search. Path consistency is adopted as a regularization to improve the generalization performance of heuristics. Extensive experimental results on 10 molecule datasets demonstrate the effectiveness of MEEA*. Especially, on the widely used United States Patent and Trademark Office (USPTO) benchmark, MEEA* achieves a 100.0% success rate. Moreover, for natural products, MEEA* successfully identifies bio-retrosynthetic pathways for 97.68% test compounds.

Development of an Untargeted LC-MS Metabolomics Method with Postcolumn Infusion for Matrix Effect Monitoring in Plasma and Feces

Untargeted metabolomics based on reverse phase LC-MS (RPLC-MS) plays a crucial role in biomarker discovery across physiological and disease states. Standardizing the development process of untargeted methods requires paying attention to critical factors that are under discussed or easily overlooked, such as injection parameters, performance assessment, and matrix effect evaluation. In this study, we developed an untargeted metabolomics method for plasma and fecal samples with the optimization and evaluation of these factors. Our results showed that optimizing the reconstitution solvent and sample injection amount was critical for achieving the balance between metabolites coverage and signal linearity. Method validation with representative stable isotopically labeled standards (SILs) provided insights into the analytical performance evaluation of our method. To tackle the issue of the matrix effect, we implemented a postcolumn infusion (PCI) approach to monitor the overall absolute matrix effect (AME) and relative matrix effect (RME). The monitoring revealed distinct AME and RME profiles in plasma and feces. Comparing RME data obtained for SILs through postextraction spiking with those monitored using PCI compounds demonstrated the comparability of these two methods for RME assessment. Therefore, we applied the PCI approach to predict the RME of 305 target compounds covered in our in-house library and found that targets detected in the negative polarity were more vulnerable to the RME, regardless of the sample matrix. Given the value of this PCI approach in identifying the strengths and weaknesses of our method in terms of the matrix effect, we recommend implementing a PCI approach during method development and applying it routinely in untargeted metabolomics.

A comprehensive approach for evaluating the virucidal performance of domestic laundry detergents under practical conditions

AIMS

We aimed to develop a method to assess the virucidal performance of domestic laundry in a lab-scale washing machine (Rotawash) based on EN 17658.

METHODS AND RESULTS

For method development, virus recovery was investigated after drying on cotton carriers for three test viruses murine norovirus (MNV), modified vaccinia virus Ankara (MVA), and bovine coronavirus (BCoV), followed by washing simulations in flasks and Rotawash. MNV and MVA demonstrated sufficient recovery from carriers after drying and washing (up to 40°C and 60 min). BCoV exhibited lower recovery, indicating less relevance as a test virus. Rotawash efficacy tests conducted with MNV, a resistant, non-enveloped virus, showed limited efficacy of a bleach-free detergent, aligning with results from a domestic washing machine. Rotawash washes achieved higher reductions in infectious virus titers than suspension tests, indicating the role of washing mechanics in virus removal.

CONCLUSIONS

This study established a practical method to test the virucidal efficacy of laundry detergents in Rotawash, simulating domestic washing.

A novel, high-performance, low-volume, rapid luciferase immunoprecipitation system (LIPS) assay to detect autoantibodies to zinc transporter 8

BACKGROUND

Zinc transporter 8 autoantibodies (ZnT8A) are thought to appear close to type 1 diabetes (T1D) onset and can identify high-risk multiple (≥2) autoantibody positive individuals. Radiobinding assays (RBA) are widely used for ZnT8A measurement but have limited sustainability. We sought to develop a novel, high-performance, non-radioactive luciferase immunoprecipitation system (LIPS) assay to replace RBA.

METHODS

A custom dual C-terminal ZnT8 (aa268-369; R325/W325) heterodimeric antigen, tagged with a NanoluciferaseTM (Nluc-ZnT8) reporter, and LIPS assay was developed. Assay performance was evaluated by testing sera from new onset T1D (n = 573), healthy schoolchildren (n = 521), and selected first-degree relatives (FDRs) from the Bart's Oxford family study (n = 617; 164 progressed to diabetes).

RESULTS

In new-onset T1D, ZnT8A levels by LIPS strongly correlated with RBA (Spearman's r = 0.89; P < 0.0001), and positivity was highly concordant (94.3%). At a high specificity (95%), LIPS and RBA had comparable assay performance [LIPS pROC-AUC(95) 0.032 (95% CI: 0.029-0.036); RBA pROC-AUC(95) 0.031 (95% CI: 0.028-0.034); P = 0.376]. Overall, FDRs found positive by LIPS or RBA had a comparable 20-year diabetes risk (52.6% and 59.7%, respectively), but LIPS positivity further stratified T1D risk in FDRs positive for at least one other islet autoantibody detected by RBA (P = 0.0346).

CONCLUSION

This novel, high-performance, cheaper, quicker, higher throughput, low blood volume Nluc-ZnT8 LIPS assay is a safe, non-radioactive alternative to RBA with enhanced sensitivity and ability to discriminate T1D progressors. This method offers an advanced approach to current strategies to screen the general population for T1D risk for immunotherapy trials and to reduce rates of diabetic ketoacidosis at diagnosis.

Comparison of colorimetric, spectroscopic and electrochemical techniques for quantification of hydrogen sulfide

Background: Hydrogen sulfide (H2S), an endogenous gasotransmitter, has potential applications in several conditions. However, its quantification in simulated physiological solutions is a major challenge due to its gaseous nature and other physicochemical properties. Aim: This study was designed to compare four commonly used H2S detection and quantification methods in aqueous solutions. Methods: The four techniques compared were one colorimetric, one chromatographic and two electrochemical methods. Results: Colorimetric and chromatographic methods quantified H2S in millimolar and micromole ranges, respectively. The electrochemical methods quantified H2S in the nanomole and picomole ranges and were less time-consuming. Conclusion: The H2S quantification method should be selected based on the specific requirements of a research project in terms of sensitivity, response time and cost-effectiveness.

Time-lapse confocal microscopy to study in vitro Streptococcus mutans surface colonization

The cariogenicity of Streptococcus mutans relates to its ability to form biofilms on dental surfaces. The aim of this work was to develop a flowcell system compatible with time-lapse confocal microscopy to compare the adhesion and accumulation of S. mutans cells on surfaces in unsupplemented media against media containing sucrose or sucralose (a non-metabolized sweetener) over a short period of time. Fluorescent S. mutans 3209/pVMCherry was suspended in unsupplemented media or media supplemented with 1% sucrose or 1% sucralose and passed through a 3D-printed flowcell system. Flowcells were imaged over 60 minutes using a confocal microscope. Image analysis was performed, including a newly developed object-movement-based method to measure biomass adhesion. Streptococcus mutans 3209/pVMCherry grown in 1% sucrose-supplemented media formed small, dense, relatively immobile clumps in the flowcell system measured by biovolume, surface area, and median object centroid movement. Sucralose-supplemented and un-supplemented media yielded large, loose, mobile aggregates. Architectural metrics and per-object movement were significantly different (P < 0.05) when comparing sucrose-supplemented media to either unsupplemented or sucralose-supplemented media. These results demonstrate the utility of a flowcell system compatible with time-lapse confocal microscopy and image analysis when studying initial biofilm formation and adhesion under different nutritional conditions.

Combining stochastic resetting with Metadynamics to speed-up molecular dynamics simulations

Metadynamics is a powerful method to accelerate molecular dynamics simulations, but its efficiency critically depends on the identification of collective variables that capture the slow modes of the process. Unfortunately, collective variables are usually not known a priori and finding them can be very challenging. We recently presented a collective variables-free approach to enhanced sampling using stochastic resetting. Here, we combine the two methods, showing that it can lead to greater acceleration than either of them separately. We also demonstrate that resetting Metadynamics simulations performed with suboptimal collective variables can lead to speedups comparable with those obtained with optimal collective variables. Therefore, applying stochastic resetting can be an alternative to the challenging task of improving suboptimal collective variables, at almost no additional computational cost. Finally, we propose a method to extract unbiased mean first-passage times from Metadynamics simulations with resetting, resulting in an improved tradeoff between speedup and accuracy. This work enables combining stochastic resetting with other enhanced sampling methods to accelerate a broad range of molecular simulations.

Towards a transferable fermionic neural wavefunction for molecules

Deep neural networks have become a highly accurate and powerful wavefunction ansatz in combination with variational Monte Carlo methods for solving the electronic Schrödinger equation. However, despite their success and favorable scaling, these methods are still computationally too costly for wide adoption. A significant obstacle is the requirement to optimize the wavefunction from scratch for each new system, thus requiring long optimization. In this work, we propose a neural network ansatz, which effectively maps uncorrelated, computationally cheap Hartree-Fock orbitals, to correlated, high-accuracy neural network orbitals. This ansatz is inherently capable of learning a single wavefunction across multiple compounds and geometries, as we demonstrate by successfully transferring a wavefunction model pre-trained on smaller fragments to larger compounds. Furthermore, we provide ample experimental evidence to support the idea that extensive pre-training of such a generalized wavefunction model across different compounds and geometries could lead to a foundation wavefunction model. Such a model could yield high-accuracy ab-initio energies using only minimal computational effort for fine-tuning and evaluation of observables.

Concepts and principles for new rapid simple liquid chromatography method for quantification of antioxidants resveratrol, vitamin E, and coenzyme Q10 in capsules with high-performance liquid chromatography with a photo-diode array detector

Principles and problems in the development of simultaneous liquid chromatography (LC) analytical methods for potent antioxidative molecules resveratrol, tocopherol, and coenzyme Q10 in capsules, have been investigated and systematically compared and summarized. For these purposes, experiments within the full polarity spectrum of LC techniques. were tested and recorded. The whole range of polarities included: Alkyl C18 bonded reversed phase, phenyl, cyanopropyl, diol, and the most polar base silica-filled column matrixes have been used. The summarized results concluded that all mentioned LC techniques could be used for the determination of the mentioned group of the three analytes with different run characteristics and efficiency. These successes could be achieved after careful analyses of molecular physicochemical data of analytes. They are especially organic solubilities. The ultraviolet spectral absorption characteristics of each analyte and the mobile phase constituents for appropriate separation were very important to be known. The ultimate targets were the development method with the isocratic mode of separation yielding symmetrical peak shapes for the best sensitivity and accuracy, with the shortest run time and best reproducibility. From an analytical point of view important for LC, the three analytes have quite distinct characteristics that contribute to successful method development. These features are their organic solvent and water solubility, molecular polarities, and ultraviolet-absorption characteristics, like spectra and absorptivities. All these mentioned parameters were taken into account for solving complications appearing in the development of rapid LC methods for the simultaneous determination of three antioxidant molecules.

HILIC UPLC/ QTof MS Method Development for the Quantification of AGEs Inhibitors - Trouble Shooting Protocol

OBJECTIVE

The paper reports an attempt to develop and validate a HILIC UPLC/ QTof MS method for quantifying N-ε-carboxymethyl-L-lysine (CML) in vitro, testing N-ε- carboxy[D2]methyl-L-lysine (d2-CML), and N-ε-carboxy[4,4,5,5-D4]methyl-L-lysine (d4-CML) as internal standards.

METHODS

During the method development, several challenging questions occurred that hindered the successful completion of the method. The study emphasizes the impact of issues, generally overlooked in the development of similar analytical protocols. For instance, the use of glassware and plasticware was critical for the accurate quantification of CML. Moreover, the origin of atypical variation in the response of the deuterated internal standards, though widely used in other experimental procedures, was investigated.

RESULT

A narrative description of the systematic approach used to address the various drawbacks during the analytical method development and validation is presented.

CONCLUSION

Reporting those findings can be considered beneficial while bringing an insightful notion about critical factors and potential interferences. Therefore, some conclusion and ideas can be drawn from these trouble-shooting questions, which might help other researchers to develop more reliable bioanalytical methods, or to raise their awareness of stumbling blocks along the way.

LC-MS/MS methods for direct measurement of sepiapterin and tetrahydrobiopterin in human plasma and clinical applications

Aim: Tetrahydrobiopterin (BH4), a natural cofactor of aromatic amino acid hydroxylases, and sepiapterin, a natural precursor of BH4, are endogenously present in human plasma. This is the first report on methods for direct quantification of sepiapterin and BH4 in human plasma by LC-MS/MS for pharmacokinetic assessment. Materials & methods: The analytes in plasma were harvested from blood that were treated with 10% ascorbic acid (AA) to a final concentration of 1% AA. Results & conclusion: The quantification methods were validated for calibration ranges of 0.75-500 ng/ml and 0.5-500 ng/ml for sepiapterin and BH4, respectively. Quantification of analytes was challenging due to their susceptibility to redox reactions. The validated methods were utilized successfully to support clinical development of sepiapterin.

Assessment of biomarker stability and assay performance parameters for medical diagnosis: a case study of diagnosis of major depressive disorder

Aim: Assessing the stability profiles and assay performance of 24 biomarker assays in 32 biomarker/body fluid combinations identified as relevant for prediction of major depressive disorder. Materials & methods: Combinations were tested for stability and assay performance with ELISA at different storage and freeze-thaw conditions in pooled samples of 40 patients. Results: Stability and assay performance issues were found in almost all cases except three biomarkers in urine and three in serum. Conclusion: This study shows that, to produce reliable measurement data, assessments of stability and assay performance are essential. In development, other quality assurance parameters might be implemented to increase the level of measurement reliability by increasing assay performance control.

A rapid, sensitive method for clinical monitoring of ketamine and norketamine by ultra-high-performance reverse-phase liquid chromatography tandem mass spectrometry

BACKGROUND

Ketamine is an NMDAR antagonist with aggregating use across many areas of medicine. P450 enzymes heavily metabolise ketamine, where norketamine is a first pass formed metabolite following initial N-demethylation. Serum ketamine monitoring is becoming increasingly important, requiring a sensitive method with a robust lower limit of quantitation.

METHODS

Samples were prepared using protein precipitation or solid phase extraction. Ion suppression was investigated to optimise sample preparation technique, followed by reverse-phase chromatography coupled with tandem mass spectrometry to analyse extractions using a Waters Xevo TQ-S Micro and associated Acquity chromatography systems. Performance characteristics were analysed to validate the assay.

RESULTS

Ketamine and norketamine retention times were 1.28 and 1.23 min, respectively. Ketamine and norketamine precursor ions fragmented into 2 distinguishable product ions (238.14 > 207.18/125.06 and 224.1 > 178.96/124.86). Performance characteristics include an assay recovery of 103.7% (ketamine) and 96.3% (norketamine), lower limit of quantitation 36.2 µg/L (ketamine) and 38.9 µg/L (norketamine), and intra-assay imprecision ≤ 7.04% on average.

CONCLUSIONS

A robust and reproducible assay with limited sample preparation has been designed and validated. The linearity of the assay covers all ranges of interest reported in the literature. Ion suppression was clearly reduced via use of solid phase extraction. The method will form the basis of ketamine monitoring and providing valuable patient information on tolerance and metabolism.

Development and Application of an Atomic Absorption Spectrometry-Based Method to Quantify Magnesium in Leaves of Dioscorea polystachya

The Chinese yam (Dioscorea polystachya, DP) is known for the nutritional value of its tuber. Nevertheless, DP also has promising pharmacological properties. Compared with the tuber, the leaves of DP are still very little studied. However, it may be possible to draw conclusions about the plant quality based on the coloration of the leaves. Magnesium, as a component of chlorophyll, seems to play a role. Therefore, the aim of this research work was to develop an atomic absorption spectrometry-based method for the analysis of magnesium (285.2125 nm) in leaf extracts of DP following the graphite furnace sub-technique. The optimization of the pyrolysis and atomization temperatures resulted in 1500 °C and 1800 °C, respectively. The general presence of flavonoids in the extracts was detected and could explain the high pyrolysis temperature due to the potential complexation of magnesium. The elaborated method had linearity in a range of 1-10 µg L-1 (R2 = 0.9975). The limits of detection and quantification amounted to 0.23 µg L-1 and 2.00 µg L-1, respectively. The characteristic mass was 0.027 pg, and the recovery was 96.7-102.0%. Finally, the method was applied to extracts prepared from differently colored leaves of DP. Similar magnesium contents were obtained for extracts made of dried and fresh leaves. It is often assumed that the yellowing of the leaves is associated with reduced magnesium content. However, the results indicated that yellow leaves are not due to lower magnesium levels. This stimulates the future analysis of DP leaves considering other essential minerals such as molybdenum or manganese.