Review
Biochemistry & Molecular Biology
Shuwen Lei, Song Chen, Qingping Zhong
Summary: Digital PCR (dPCR) has gained considerable attention for its ability to quantitate different types of pathogens with desired accuracy, sensitivity, and reproducibility, using end-point measurement for absolute quantification without the need for standard curves. It provides guidance for further genetic analysis and molecular diagnosis, contributing to the quantification of low level of nucleic acid and early detection of pathogenic diseases. The benefits, challenges, and future prospects of dPCR have been highlighted in this review, showcasing its potential as a powerful tool for pathogen detection and control.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Mirjana Radomirovic, Nikola Gligorijevic, Dragana Stanic-Vucinic, Andreja Rajkovic, Tanja Cirkovic Velickovic
Summary: An ultrasensitive immuno-PCR method was developed for quantifying crustacean tropomyosin in foods. It showed high specificity and precision, with a quantification sensitivity 20-fold higher than ELISA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Gillean C. C. Miller, David Barker, Lisa I. I. Pilkington, Rebecca C. C. Deed
Summary: This study synthesized a novel isotopologue of gamma-nonalactone, (H2C2)-H-2-C-13-gamma-nonalactone, for the first time and developed a stable isotope dilution assay (SIDA) for quantification of gamma-nonalactone in NZ Pinot noir wines. The compound showed excellent stability as an internal standard, and the analysis of 12 NZ Pinot noir wines revealed a concentration range of gamma-nonalactone close to its odor detection threshold.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Zehang Gao, Laidi Jin, Chunping Jia, Xiaodong Wang, Jianlong Zhao, Shilun Feng, Xuguang Guo
Summary: An all-in-one microfluidic chip that integrates various functions such as emulsification, passive bubble removal, droplet storage, nucleic acid amplification, and fluorescence signal readout is proposed in this study. The optimized ddPCR device effectively removes bubbles between droplets and has a dead volume of less than 1%. This innovative ddPCR device can accurately quantify nucleic acids and is expected to increase the popularity of dPCR.
SENSORS AND ACTUATORS B-CHEMICAL
(2023)
Article
Dentistry, Oral Surgery & Medicine
Ramya Sekar, Preethi Murali, Mohammed Junaid
Summary: The objective of this study was to investigate the presence of Helicobacter pylori (H. pylori) and its oncogenic and virulent proteins CagA and VacA in patients with gingivitis, periodontitis, oral cancer, and gastric cancer. The results showed a high prevalence of H. pylori in the subgingival plaque samples of the study cohort, but the proportions of CagA and VacA were lower in individuals with periodontal inflammation and oral cancer compared to those with gastric cancer. The study suggests that the oral cavity may serve as a potential niche for H. pylori and that further research is needed to explore the pathogenicity of CagA and VacA proteins in the oral cavity.
Article
Chemistry, Physical
Yuanyuan Wei, Syed Muhammad Tariq Abbasi, Nawaz Mehmood, Luoquan Li, Fuyang Qu, Guangyao Cheng, Dehua Hu, Yi-Ping Ho, Wu Yuan, Ho-Pui Ho
Summary: The study presents a deep learning-aided algorithm called Deep-qGFP for real-time absolute quantification. It enables automated detection and classification of fluorescent-labeled microreactors, accurately measuring their sizes and occupancy status. Deep-qGFP achieves high accuracy and remarkable speed, making it applicable to various GFP-labeling scenarios. It can be seamlessly integrated into common fluorescence microscopes and different microreactor formats, optimizing laboratory practices and potentially transforming GFP-labeled microreactor analysis.
Article
Food Science & Technology
Caterina Villa, Joana Costa, Isabel Mafra
Summary: This study developed a highly sensitive and specific real-time PCR method for sesame detection and quantification in complex matrices. By evaluating multiple molecular markers, two markers with the best performance were identified. The methods showed excellent detection performance for white sesame, black sesame, and sesame-containing biscuits.
Article
Multidisciplinary Sciences
Manuel Loskyll, Daniel Podbiel, Andreas Guber, Jochen Hoffmann
Summary: This study provides a detailed statistical description of the effects of partitioning and subsampling on the relative uncertainty of test results. The current binomial model is not accurate for analyzing the nucleic acid content of single cells. This study separately addresses partitioning and subsampling effects and combines them to calculate the relative uncertainty of a test system, comparing it for single cell content analysis and body fluid analysis.
Article
Biochemistry & Molecular Biology
Cindy Bay, Gzona Bajraktari-Sylejmani, Walter E. Haefeli, Juergen Burhenne, Johanna Weiss, Max Sauter
Summary: LAT-1 is a viable target for drug delivery to the central nervous system (CNS) and tumors, and the study established a UPLC-MS/MS assay for stable isotopically labeled leucine to determine LAT-1 activity and inhibition capacity of new compounds.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Mathilde Aubret, Maud Savonnet, Patricia Laurent, Yoann Roupioz, Myriam Cubizolles, Arnaud Buhot
Summary: A sensitive and antibody-free molecular quantification assay combining aptamers' specificity with loop-mediated isothermal amplification (LAMP) sensitivity was developed for detecting different types of biomarkers and quantifying them at physiological levels. This innovative aptamero-LAMP assay shows potential for paving the way for antibody-free molecular assays.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Ziqing Yu, Lei Xu, Weiyuan Lyu, Feng Shen
Summary: Digital biological analysis compartmentalizes targets of interest and performs detection and investigation. This study presents a parallel multistep digital analysis SlipChip, which enables the manipulation of a large number of droplets for digital biological analysis. The SlipChip utilizes a self-partitioning droplet formation mechanism and can perform digital loop-mediated isothermal amplification and digital CRISPR detection in parallel.
Article
Pharmacology & Pharmacy
Jill Barber, Zubida M. Al-Majdoub, Narciso Couto, Areti-Maria Vasilogianni, Annika Tillmann, Sarah Alrubia, Amin Rostami-Hodjegan, Brahim Achour
Summary: This study evaluated the performance of three widely used label-free proteomic methods in quantifying enzymes and transporters in human liver microsomal samples. The findings showed that the HiN and iBAQ methods had good agreement in measuring absolute abundances, while the TPA method overestimated abundances. The relative abundance distribution of enzymes was similar among the three methods, but differences were observed with the TPA method in the case of transporters. The variability and between-sample relative quantification were consistent across methods. The study also demonstrated overall agreement between the HiN method and a standard protein in the samples.
DRUG METABOLISM AND DISPOSITION
(2022)
Article
Microbiology
So-Young Lee, Jihye Yang, Ju-Hoon Lee
Summary: In this study, fecal samples from 139 humans and 89 animals were collected to detect the presence of crAssphage using quantitative real-time PCR. The results showed that the detection rate of crAssphage in human fecal samples ranged from 23.0% to 30.9%, with the highest detection rate observed using the CrAssPFL2 combination. Furthermore, the detection limit of crAssphage in sewage samples and contaminated food samples was determined, confirming the usefulness of the optimized qPCR method for identifying the source of human fecal contamination.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Plant Sciences
Andrea Corona Ramirez, Sarah Symanczik, Tabea Gallusser, Natacha Bodenhausen
Summary: Quantitative polymerase chain reaction (qPCR) is a reliable and high-throughput method for assessing the symbiotic relationship between arbuscular mycorrhizal fungi (AMF) and plants. This study compared qPCR with the traditional microscopy method and found a strong correlation between the two methods for wheat (cv. Colmetta and Wiwa) and tomato, but not for leek, highlighting the importance of testing the primer pair for each specific crop.
Article
Chemistry, Applied
Joana Costa, Caterina Villa, Liliana Grazina, Isabel Mafra
Summary: This study proposes two highly sensitive and specific single-tube nested real-time PCR methods for the analysis of cashew nut as an allergenic food. The method targeting the Ana o 3 gene showed the highest relative sensitivity in dough/biscuit and was successfully validated for precision and accuracy.
Article
Chemistry, Analytical
Cedric Delvaux, Philippe Massonnet, Christopher Kune, Jean R. N. Haler, Gregory Upert, Gilles Mourier, Nicolas Gilles, Loic Quinton, Edwin De Pauw, Johann Far
ANALYTICAL CHEMISTRY
(2020)
Article
Biochemical Research Methods
Jean R. N. Haler, Vincent Lemaur, Johann Far, Christopher Kune, Pascal Gerbaux, Jerome Cornil, Edwin De Pauw
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2020)
Article
Biochemical Research Methods
Jean R. N. Haler, Philippe Massonnet, Johann Far, Gregory Upert, Nicolas Gilles, Gilles Mourier, Loic Quinton, Edwin De Pauw
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2020)
Article
Biochemical Research Methods
Denis Morsa, Emeline Hanozin, Gauthier Eppe, Edwin De Pauw
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2020)
Article
Biochemical Research Methods
Frederic Dewez, Janina Oejten, Corinna Henkel, Romano Hebeler, Heiko Neuweger, Edwin De Pauw, Ron M. A. Heeren, Benjamin Balluff
Article
Chemistry, Analytical
Cedric Delvaux, Marjorie Dauvin, Madeleine Boulanger, Loic Quinton, Dominique Mengin-Lecreulx, Bernard Joris, Edwin De Pauw, Johann Far
Summary: Peptidoglycan (PGN) is a crucial structure in bacterial cell walls, continuously synthesized and degraded during bacterial life cycle for growth and division. PGN fragments act as messenger molecules in bacterial cell wall stress response and triggering mammalian innate immune response. Bacteria modulate their PGN degradation or recognition by chemically modifying PGN, such as amidating the epsilon-carboxyl group of meso-diaminopimelic acid in the PGN peptide chain. The quantitation of PGN-derived peptides is challenging due to their hydrophilic nature, but capillary zone electrophoresis coupled with high-resolution mass spectrometry shows excellent repeatability in quantitation of PGN peptides and their derivatives in bacterial cytoplasmic extracts.
ANALYTICAL CHEMISTRY
(2021)
Editorial Material
Chemistry, Analytical
Denis Morsa, Emeline Hanozin, Valerie Gabelica, Edwin De Pauw
ANALYTICAL CHEMISTRY
(2020)
Article
Chemistry, Analytical
Frederic Dewez, Edwin De Pauw, Ron M. A. Heeren, Benjamin Balluff
Summary: The multilabel approach in quantitative mass spectrometry imaging provides more accurate quantitation compared to a single-label approach, particularly when the target compound is unevenly distributed at a wide concentration range in the tissue.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Jean R. N. Haler, Johann Far, Victor R. de la Rosa, Christopher Kune, Richard Hoogenboom, Edwin De Pauw
Summary: Researchers have developed an automatable method to fit IM data without the need for computational chemistry. By monitoring the relationship between collision cross sections and the degree of polymerization, they explored physicochemical properties of polymers and their monomer units and identified several remarkable points in the evolution of CCS with DP. These remarkable points can be extracted from raw IM data without accurate calibration, leading to predictions on fit parameters based on the nature of the monomer unit.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Chemistry, Analytical
Raphael La Rocca, Christopher Kune, Mathieu Tiquet, Lachlan Stuart, Gauthier Eppe, Theodore Alexandrov, Edwin De Pauw, Loic Quinton
Summary: Mass spectrometry imaging (MSI) is a powerful method for revealing the spatial chemical composition of different biological samples, but the accuracy of molecular annotation can be affected by mass shifts. Internal calibration is known to be the best solution to reduce mass shifts. This study introduces an algorithm that recalibrates each spectrum individually to mitigate the impact of mass shift and demonstrates its broad applicability in improving data analysis.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Jean R. N. Haler, Eric Bechet, Christopher Kune, Johann Far, Edwin De Pauw
Summary: This study investigates the extraction of structural information from experimental ion mobility-mass spectrometry (IM-MS) data sets using trends-based analyses. The modeled shape evolutions based on computer-aided design software show favorable comparison to experimental collision cross-section (CCS) trends, indicating the effective modeling of ion-drift gas interactions. The relationship between CCS and surface area holds not only for convex shapes but also for moderately concave shapes.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemical Research Methods
Elodie Grifnee, Christopher Kune, Cedric Delvaux, Loic Quinton, Johann Far, Gabriel Mazzucchelli, Edwin De Pauw
Summary: Protein structural analysis has been a focus for decades, with X-ray crystallography, nuclear magnetic resonance, and mass spectrometry being important methods for determining 3D structures. Mass spectrometry has become powerful due to its selectivity and sensitivity, requiring combination with computational chemistry and bioinformatics for full structure assignment. Temperature-dependent digestion experiments provide insights into secondary structures around cleavage sites.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemical Research Methods
Andrea McCann, Christopher Kune, Philippe Massonnet, Johann Far, Marc Ongena, Gauthier Eppe, Loic Quinton, Edwin De Pauw
Summary: With improved ion mobility resolution, it is now possible to separate small protomeric tautomers. This study observed the presence of protomers in the molecule surfactin, supporting the idea that protomeric tautomerism can still be observed in molecules above 1000 Da.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biochemical Research Methods
Justine Hustin, Christopher Kune, Johann Far, Gauthier Eppe, Delphine Debois, Loic Quinton, Edwin De Pauw
Summary: Lipidomics has seen rapid development in the past decade. The analysis of non-targeted lipidomics from biological samples presents challenges due to the diverse structures, concentration ranges, and complexity of lipids. In this study, the authors introduce the use of differential Kendrick's plots as a rapid visualization tool for qualitative non-targeted lipid analysis. They demonstrate that this tool can be applied using liquid chromatography-mass spectrometry (LC-MS) or direct infusion (nESI-MS) data. The authors also provide a software tool, MSKendrickFilter, and utilize the LIPID MAPS database for lipid identification. The study shows that direct infusion is a fast qualitative screening method and can be used for chromatogram analysis.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Analytical
Hugo B. Muller, Georges Scholl, Johann Far, Edwin De Pauw, Gauthier Eppe
Summary: This paper introduces the concept of sliding windows in ion mobility (SWIM) for chromatography hyphenated TIMS applications and demonstrates that using SWIM mode can significantly improve ion mobility resolving power in complex sample analysis.
ANALYTICAL CHEMISTRY
(2023)
