Article
Chemistry, Analytical
Ching-Hua Lee, Sung-Chun Tang, Ching-Hua Kuo
Summary: The study developed a sensitive and specific LC-MS/MS-MRM method to accurately identify PC(O-) and PC(P-), and applied it to investigate the regulation of etherPCs in primary neuronal cultures under hypoxic stress. Results revealed that the regulation of etherPCs was related to sn-1 chain length, while concentration changes of diacyl-PCs depended heavily on the degree of unsaturation.
ANALYTICA CHIMICA ACTA
(2021)
Article
Biochemical Research Methods
Alessia Vignoli, Leonardo Tenori, Cristina Morsiani, Paola Turano, Miriam Capri, Claudio Luchinat
Summary: Blood derivatives are commonly used in metabolomic clinical studies due to their low invasiveness and rich biological information. However, the choice of blood collection tubes can affect the metabolic content of plasma and serum. In this study, the metabolomic and lipoprotein profiles of blood samples collected using different tubes were compared. Results showed significant alterations in metabolites and correlations among the three blood matrices. The influence of blood collection tubes on lipoprotein profiles was also observed but to a lesser extent. Overcoming the issue of different collection tubes is crucial for scaling metabolomics and lipoprotein analysis in epidemiological studies. A statistical solution based on regression was proposed to reduce the alterations induced by different collection tubes for both metabolomic and lipoprotein profiles.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Yifan Xu, Haonan Li, Yiqun Han, Teng Wang, Yanwen Wang, Jicheng Gong, Ke Gao, Wu Chen, Weiju Li, Hongyin Zhang, Junxia Wang, Xinghua Qiu, Tong Zhu
Summary: Sphingolipids are a class of lipids with diverse structures and biological functions, and have been proposed as potential biomarkers for cardiometabolic diseases. The current methods for quantifying sphingolipids have limitations in terms of sample pretreatment and volume. In this study, a simple and rapid method using methanol for plasma sphingolipid extraction was developed, and 37 sphingolipids from 8 classes were successfully quantified using liquid chromatography coupled with tandem mass spectrometry. This method showed good performance and was applied successfully in an epidemiological study.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
William Craig Byrdwell, Hari K. Kotapati, Robert Goldschmidt, Pavel Jakubec, Lucie Novakova
Summary: The study demonstrates the use of split-flow two-dimensional liquid chromatography (SF-2D-LC) and quadruple parallel mass spectrometry (LC3MS4) for analyzing NIST SRM 1849a adult/infant formula, achieving successful three-dimensional chromatographic separation with optimized separation space and mass spectrometry methods.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Biochemical Research Methods
Elana A. Slutsky Smith, Soliman Khatib, Andrea Szuchman-Sapir
Summary: In this study, a method for selectively identifying lipid lactones from biological matrices was developed. The results demonstrated that the presented method can detect lactones in a highly selective manner from complex biological matrices, making it a valuable addition to existing lipidomic approaches.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2022)
Article
Food Science & Technology
Jingjing Li, Zhiqiang Li, Jinshan Ran, Chaowu Yang, Zhongzhen Lin, Yiping Liu
Summary: This study used liquid chromatography-mass spectrometry to differentiate between chicken meat and abdominal fat from different sources. Specific lipid markers were identified for different chicken breeds. A total of 209 lipid molecules were determined as marker candidates for abdominal fat and intramuscular fat authentication, with glycerophospholipids being the dominant class. Sphingolipids and PUFA-enriched glycerophospholipids were found in higher abundance in intramuscular fat, contributing to its unique flavor and nutritional value.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Genetics & Heredity
Viviana Floridia, Marta Sfulcini, Enrico D'Alessandro, Luca Cattaneo, Matteo Mezzetti, Luigi Liotta, Erminio Trevisi, Vincenzo Lopreiato, Andrea Minuti
Summary: This study aimed to evaluate the effect of different anticoagulants on the expression of 14 genes in leukocytes from Holstein cows. The results showed that only the SDHA gene had significantly lower expression in Na-citrate tubes compared to Li-heparin and K-EDTA tubes. However, the relative abundance levels of the other genes were not statistically significant among the different anticoagulants. Therefore, the choice of test tube did not affect the gene expression levels caused by the anticoagulant.
Article
Biochemical Research Methods
Xinxin Ye, Bin Zhu, Yang Chen, Yingfeng Wang, Dan Wang, Zhigang Zhao, Zhongfeng Li
Summary: This study performed integrated metabolomics and lipidomics analysis on healthy subjects and cerebral infarction patients, identifying metabolite and lipid biomarkers and enriching disturbed pathways. The results suggest that the approach could contribute to understanding the metabolic dysregulation associated with cerebral infarction pathogenesis and may aid in its early diagnosis.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Xinxin Ye, Bin Zhu, Yang Chen, Yingfeng Wang, Dan Wang, Zhigang Zhao, Zhongfeng Li
Summary: This study integrated metabolomics and lipidomics analysis to identify 49 metabolite and 68 lipid biomarkers associated with the pathogenesis of cerebral infarction. A support vector machine model constructed using these biomarkers showed excellent predictive ability for early diagnosis.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Chemistry, Analytical
Davide Coniglio, Giovanni Ventura, Cosima D. Calvano, Ilario Losito, Tommaso R. I. Cataldi
Summary: Arsenic-containing lipids, or arsenolipids, are organic compounds commonly found in marine organisms. Mass spectrometry techniques, such as ICP-MS and LC-ESI-MS, have played a key role in characterizing these lipids. Negative polarity and tandem MS analyses have further improved the identification of specific ions and the determination of the regiochemistry of these compounds.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2023)
Article
Plant Sciences
Trevor B. Romsdahl, Jean-Christophe Cocuron, Mackenzie J. Pearson, Ana Paula Alonso, Kent D. Chapman
Summary: This study introduces a stepwise targeted lipidomics approach to characterize polar and non-polar lipid classes. By using hydrophilic interaction chromatography and reverse phase chromatography, changes among different lipid molecular species were found, and potential metabolic explanations were discussed.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Applied
Mengyu Chen, Wenjie Huang, Zhibin Yin, Wenyang Zhang, Qian Kong, Shaowen Wu, Wenyan Li, Zhao Bai, Alisdair R. Fernie, Xiaodan Huang, Shijuan Yan
Summary: The research found metabolic differences among black wolfberry fruits grown in different geographical regions, with some samples showing significantly different metabolite profiles with higher levels of beneficial components, providing a new direction for further studies on the health benefits of black wolfberry fruits.
Article
Food Science & Technology
Run Zhang, Man Yang, Xinhua Hou, Renda Hou, Ligang Wang, Lijun Shi, Fuping Zhao, Xin Liu, Qingshi Meng, Lixian Wang, Longchao Zhang
Summary: This study investigated the characterization and difference of lipids and metabolites between JWX and LW pork using metabolomic and lipidomic profiling. The results showed that JWX pork had higher intramuscular fat content and meat redness compared to LW pork. The composition of metabolites and lipids also showed significant differences between the two types of pork.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Biochemical Research Methods
Dorota Garwolinska, Michal Mlynarczyk, Agata Kot-Wasik, Weronika Hewelt-Belka
Summary: The study found that storage of human milk samples at 4 degrees Celsius for 4 days and subjecting them to three freeze-thaw cycles can lead to changes in lipid content. Differences in levels of certain lipid species between samples stored at -20 degrees Celsius and -80 degrees Celsius were not statistically significant, and individual variance remained consistent regardless of sample storage conditions. Storing HM samples at -20 degrees Celsius for up to 3 weeks and at -80 degrees Celsius for up to 12 weeks ensures sample lipidome stability.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Pharmacology & Pharmacy
Weiwei Li, Hui Chen, Yihan Qian, Shouchuan Wang, Zichen Luo, Jinjun Shan, Xiaoni Kong, Yueqiu Gao
Summary: This study used lipidomics and metabolomics techniques to summarize the metabolic characteristics of four commonly used acute intrahepatic cholestasis models. The results showed that the bile acid profile was altered in all models. Additionally, different models exhibited distinct metabolic profiles, revealing the differences in the mechanisms of acute cholestasis.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Naama Karu, Alida Kindt, Adriaan J. van Gammeren, Anton A. M. Ermens, Amy C. Harms, Lutzen Portengen, Roel C. H. Vermeulen, Willem A. Dik, Anton W. Langerak, Vincent H. J. van der Velden, Thomas Hankemeier
Summary: This article is significant in characterizing the biochemical response of COVID-19 patients and identifying therapeutic targets. Through LC-MS platform analysis of plasma samples, the study found certain amino acids and derivatives associated with inflammatory responses, contributing to understanding the metabolic status of severe cases.
Article
Nutrition & Dietetics
Alida Kindt, Yvonne Kraus, David Rasp, Kai M. Foerster, Narges Ahmidi, Andreas W. Flemmer, Susanne Herber-Jonat, Florian Heinen, Heike Weigand, Thomas Hankemeier, Berthold Koletzko, Jan Krumsiek, Juergen Babl, Anne Hilgendorff
Summary: A study found that the use of a novel standardized parenteral nutrition (PN) solution called MUC PREPARE can improve nutritional intake, accelerate termination of parenteral feeding, and positively affect growth in very preterm infants. Infants receiving MUC PREPARE showed improved macro- and micronutrient intake, balanced electrolyte levels, and stable metabolomic profiles. The use of MUC PREPARE also resulted in earlier termination of parenteral feeding and higher weight gain in extremely immature infants. This new standardized PN solution is considered a superior therapeutic strategy for very preterm infants.
Article
Chemistry, Analytical
Thomas Hankemeier, Luojiao Huang, Nicolas Drouin, Jason Causon, Agnieszka Wegrzyn, Jose Castro-Perez, Ronan Fleming, Amy Harms
Summary: Accurate reconstruction of metabolic pathways is crucial for understanding metabolomics changes and biological processes in diseases. A tracer-based metabolomics strategy using stable isotope labeled precursors can trace pathways by measuring the transformation of metabolites. By quantifying labeled metabolite substructures, a new method achieves simultaneous isotopic labeling information at the intact metabolite and moiety level. This method was applied to trace the fate of labeled atoms in human-induced pluripotent stem cell-derived neurons, revealing the pathway reconstruction of de novo glutathione synthesis and its alteration under oxidative stress and neurodegeneration.
ANALYTICAL CHEMISTRY
(2023)
Article
Behavioral Sciences
Fiona A. Hagenbeek, Jenny van Dongen, Rene Pool, Peter J. Roetman, Amy C. Harms, Jouke Jan Hottenga, Cornelis Kluft, Olivier F. Colins, Catharina E. M. van Beijsterveldt, Vassilios Fanos, Erik A. Ehli, Thomas Hankemeier, Robert R. J. M. Vermeiren, Meike Bartels, Sebastien Dejean, Dorret Boomsma
Summary: This study introduces and demonstrates the potential of an integrated multi-omics approach in investigating the biology of childhood aggressive behavior. By using single- and integrative multi-omics models, the researchers identified biomarkers for subclinical aggression and studied the connections among these biomarkers. The study found strong associations between DNA methylation, amino acids, and parental non-transmitted polygenic scores with traits like ADHD, Autism Spectrum Disorder, intelligence, smoking initiation, and self-reported health. Aggression-related omics traits were also linked to known and novel risk factors such as inflammation, carcinogens, and smoking.
Article
Biochemical Research Methods
Lieke Lamont, Darya Hadavi, Andrew P. Bowman, Bryn Flinders, Dale Cooper-Shepherd, Martin Palmer, Jan Jordens, Ynze Mengerink, Maarten Honing, James Langridge, Tiffany Porta Siegel, Rob J. Vreeken, Ron M. A. Heeren
Summary: In this study, high-resolution ion mobility spectrometry (IMS) techniques were used for rapid separation of isomeric prostanoids and their detection in intestinal tissue. The results showed that GT derivatization increased the ionization efficiency of prostanoids, enabling their detection at endogenous concentration levels. The comparison of high-resolution IMS techniques revealed their potential for isomeric analysis of biologically relevant prostanoids.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2023)
Article
Oncology
Lennart Huizing, Lin Chen, Anjali A. A. Roeth, Lara R. R. Heij, Bryn Flinders, Stefan A. W. Bouwense, Benjamin Balluff, Ulf P. P. Neumann, Ron M. A. Heeren, Steven W. M. Olde Damink, Rob J. J. Vreeken, Frank G. G. Schaap
Summary: Sulfatides were found in tumor tissue of patients with intrahepatic cholangiocarcinoma (iCCA), and the abundance and ratio of unsaturated to saturated sulfatides were associated with tumor recurrence in iCCA patients.
Review
Biochemistry & Molecular Biology
Chunyuan Yin, Amy C. C. Harms, Thomas Hankemeier, Alida Kindt, Elizabeth C. M. de Lange
Summary: Alzheimer's disease is an aging-related neurodegenerative disease that leads to progressive memory loss and cognitive decline. Understanding the pathogenesis and etiology of the disease is still limited, and there are no effective treatments available. Metabolomics offers a valuable approach to studying biochemical changes and discovering potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Plant Sciences
Kanchana Pandian, Minami Matsui, Thomas Hankemeier, Ahmed Ali, Emiko Okubo-Kurihara
Summary: Single-cell metabolomics is a powerful tool for understanding cellular heterogeneity and unraveling the mechanisms of biological phenomena. It holds great promise in plant research, especially when cellular heterogeneity affects different biological processes. Metabolomics, as a detailed phenotypic analysis, is expected to provide answers to previously unaddressed questions, leading to improved crop production, better understanding of disease resistance, and other applications.
Review
Biochemistry & Molecular Biology
Laura Ann Hetzel, Ahmed Ali, Vincenzo Corbo, Thomas Hankemeier
Summary: Organoids are a valuable cell model used to study organ development, disease progression, and treatment effectiveness. The use of microfluidic devices is emerging as a solution to overcome challenges and optimize organoid assays. However, the specific features and materials of these devices must be carefully considered based on the intended application and organoid development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Zhengzheng Zhang, Madhulika Singh, Alida Kindt, Agnieszka B. Wegrzyn, Mackenzie J. Pearson, Ahmed Ali, Amy C. Harms, Paul Baker, Thomas Hankemeier
Summary: The importance of lipidomics research in understanding various diseases, including metabolism, cancer, and the recent COVID-19 pandemic, has led to the development of a targeted HILIC-MS/MS method that allows for comprehensive analysis of lipid species. This method overcomes the challenges posed by the diverse structures and properties of lipids in biological systems, and provides accurate quantitation of lipid concentrations at the fatty acyl chain level. The applicability of this method has been demonstrated through the discovery of differential lipid features related to COVID-19 severity, highlighting its potential for future investigations of the lipidome in different disease contexts.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Biochemical Research Methods
Ronan M. T. Fleming, Hulda S. Haraldsdottir, Le Hoai Minh, Phan Tu Vuong, Thomas Hankemeier, Ines Thiele
Summary: Several applications in constraint-based modelling can be formulated as cardinality optimization problems involving the minimization or maximization of the number of nonzeros in a vector. By approximating the zero-norm with nonconvex continuous functions, a set of cardinality optimization problems in constraint-based modelling is reformulated into a difference of convex functions. Novel algorithms are implemented and numerically tested, demonstrating their efficiency and practical utility in various biochemical networks.
Article
Endocrinology & Metabolism
Xinyu Di, Borja Martinez-Tellez, Elke H. J. Krekels, Lucas Jurado-Fasoli, Francisco J. Osuna-Prieto, Lourdes Ortiz-Alvarez, Thomas Hankemeier, Patrick C. N. Rensen, Jonatan R. Ruiz, Isabelle Kohler
Summary: The plasma levels of eCBs and their analogues are associated with higher adiposity and worse cardiometabolic profile.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2023)
Article
Dermatology
Jannik Rousel, Andreea Nadaban, Mahdi Saghari, Lisa Pagan, Ahnjili Zhuparris, Bart Theelen, Tom Gambrah, Hein E. C. van Der Wall, Rob J. Vreeken, Gary L. Feiss, Tessa Niemeyer-van der Kolk, Jacobus Burggraaf, Martijn B. A. van Doorn, Joke A. Bouwstra, Robert Rissmann
Summary: Seborrheic dermatitis is a chronic inflammatory skin disease characterized by skin barrier dysfunction and changes in ceramide composition. This study found a correlation between barrier impairment and inflammation in seborrheic dermatitis, suggesting that restoring the cutaneous barrier could be a potential therapeutic approach.
EXPERIMENTAL DERMATOLOGY
(2023)
Article
Endocrinology & Metabolism
Yi Ding, Marielle C. Haks, Susan J. F. van den Eeden, Tom H. M. Ottenhoff, Amy C. Harms, Thomas Hankemeier, Muhamed N. H. Eeza, Jorg Matysik, A. Alia, Herman P. Spaink
Summary: The leptin signaling pathway plays an important role in regulating glucose homeostasis, metabolism, and systemic inflammatory responses. However, its metabolic effects on infectious diseases like tuberculosis are not well understood. In this study, the researchers investigated the role of leptin in metabolism in zebrafish larvae and mice in the absence and presence of mycobacterial infection. They found that leptin mutation and mycobacterial infection lead to a similar metabolic syndrome characterized by a decrease in 11 amine metabolites. The researchers concluded that leptin and mycobacterial infection impact metabolism independently, without a synergistic effect. They also observed distinct transcriptomic responses in the leptin mutant zebrafish larvae and mycobacterial infection, which can lead to similar metabolic end states.
Article
Computer Science, Information Systems
Erik Schultes, Marco Roos, Luiz Olavo Bonino da Silva Santos, Giancarlo Guizzardi, Jildau Bouwman, Thomas Hankemeier, Arie Baak, Barend Mons
Summary: This article introduces the concept and methodology of Digital Twins (DT) and proposes an architectural design for FAIR Digital Twins (FDT) that supports data intensive research and complies with GDPR requirements for open science.
FRONTIERS IN BIG DATA
(2022)
