Article
Cell Biology
Ioanna Dagla, Aikaterini Iliou, Dimitra Benaki, Evagelos Gikas, Emmanuel Mikros, Tina Bagratuni, Efstathios Kastritis, Meletios A. Dimopoulos, Evangelos Terpos, Anthony Tsarbopoulos
Summary: Vaccination is highly effective in mitigating the COVID-19 pandemic. However, individual immune responses to mRNA vaccines vary significantly. Metabolomics analysis reveals distinct plasma metabolic profiles associated with immune response levels, indicating the potential of certain metabolites as predictive markers for vaccine response.
Article
Plant Sciences
Ramona Mihaela Ciubotaru, Pietro Franceschi, Silvia Vezzulli, Luca Zulini, Marco Stefanini, Michael Oberhuber, Peter Robatscher, Giulia Chitarrini, Urska Vrhovsek
Summary: Numerous fungicide applications are needed to control Erysiphe necator, the cause of powdery mildew. This study identifies promising disease-resistant varieties carrying mono-locus or pyramided resistant loci. Metabolic profiling reveals changes in primary compounds, lipids, volatile organic compounds, and phenolic compounds in response to pathogen inoculation. Ten up-accumulated metabolites, including three proposed as resistance biomarkers, distinguish resistant from susceptible varieties in powdery mildew response.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemical Research Methods
Ryan A. Groves, Carly C. Y. Chan, Spencer D. Wildman, Daniel B. Gregson, Thomas Rydzak, Ian A. Lewis
Summary: Liquid chromatography mass spectrometry (LC-MS) is a widely used strategy for metabolomics analyses, offering the potential for both biomarker discovery and clinical diagnostics. However, clinical applications of LC-MS require higher throughput, which has been limited by chromatographic gradient lengths. To address this issue, researchers have developed a new analytical strategy called sequential quantification using isotope dilution (SQUID), which enables high-throughput quantification of target biomarkers in complex samples.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Joao P. P. Vieira, Filip Ottosson, Amra Jujic, Vladimir Denisov, Martin Magnusson, Olle Melander, Joao M. N. Duarte
Summary: Combining LC-MS and NMR techniques improves the discrimination of metabolic disease development, including those induced by a high-fat diet. The study confirms that metabolic pathways in mice affected by high-fat diet also impact diabetes in humans.
Article
Agriculture, Multidisciplinary
Siok-Geok Chong, Intan S. Ismail, Amalina Ahmad Azam, Shih-Jen Tan, Khozirah Shaari, Jen-Kit Tan
Summary: This study investigated the chemical profiles of non-organic and organic soybeans, and the changes in metabolites after fermentation. The results showed no significant difference in the chemical profiles between non-organic and organic soybeans. However, the metabolite profile of unfermented soybeans shifted to higher amino acid and organic acid content after fermentation, potentially enhancing their nutritional value.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2023)
Article
Food Science & Technology
Bohai Li, Fan Hui, Zhang Yuan, Qingxiang Shang, Guo Shuai, Yingshu Bao, Yongfu Chen
Summary: This study aimed to investigate the biochemical mechanism of the lipid-lowering effect of consuming koumiss daily by analyzing the fecal metabolomes of hyperlipidemia patients before and after koumiss treatment. Ten significant differential metabolites were detected, showing increased concentrations at days 30 and 60, many of which were involved in lipid metabolism and transport. The metabolites identified were likely associated with the observed lipid-lowering effect.
JOURNAL OF FUNCTIONAL FOODS
(2021)
Article
Immunology
Johanna Hiefner, Johann Rische, Madeleine J. Bunders, Anna Worthmann
Summary: This study presents a method based on HPLC-MS/MS for the quantification of adenine nucleotides, which helps us understand the impact of disturbances in AN balance on cellular function.
FRONTIERS IN IMMUNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Atiah H. Almalki
Summary: Lung cancer is the leading cause of cancer-related death worldwide. This review presents recent trends in the analytical techniques used for metabolome mapping of lung cancer, and discusses the potential applications of these techniques in the analysis of biological samples, providing new avenues for treatment strategies and monitoring drug responses.
Review
Chemistry, Analytical
Muhammad Waris, Engin Kocak, Ekrem Murat Gonulalan, L. Omur Demirezer, Sedef Kir, Emirhan Nemutlu
Summary: Plant-based metabolomics studies aim to discover new active compounds, determine vegetation period, investigate adulteration, evaluate correlation activity and metabolite levels, and monitor quality control of medicinal plants. However, the chemical differences of primary and secondary metabolites in complex natural products present challenges for analysis, ranging from sample collection to preparation, and from analysis to metabolite annotation and quantification. A comprehensive evaluation of current and new trends in plant metabolomics helps researchers in designing their studies holistically.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Wei Li, Pei Zhang, Xiaoying Hou, Tian Tang, Siqi Li, Ruiqi Sun, Zunjian Zhang, Fengguo Xu
Summary: Modified metabolites play crucial roles in disease progression and diagnosis. A new LC-MS/MS method was developed for the simultaneous quantification of prototypes and their modified forms, with improved sensitivity and accuracy. The method was successfully applied to study lung adenocarcinoma cell lines.
ANALYTICA CHIMICA ACTA
(2022)
Article
Chemistry, Analytical
Li Li, Jing Deng, Li-mei Lin, Ya-mei Li, Yan Lin, Bo-hou Xia, Duan-fang Liao
Summary: The study shows that Prunella vulgaris oil can improve inflammation and fibrosis in rats with intrauterine adhesion (IUA) by regulating amino acid metabolism to balance related disorders and control energy metabolism. Metabolomics analysis reveals significant abnormalities in serum metabolism in IUA rats, with 51 differential markers identified and improved after PVO treatment.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2022)
Article
Cell Biology
Juntuo Zhou, Xi Chen, Wei Chen, Lijun Zhong, Ming Cui
Summary: Using plasma metabolomic and lipidomic analysis, this study identified potential biomarkers correlated with different stages of heart failure. Several dysregulated molecules were found, and marker panels were proposed for the diagnosis of heart failure stages. This research provides valuable information for further studies and biomarker development in heart failure.
MOLECULAR AND CELLULAR BIOCHEMISTRY
(2021)
Article
Genetics & Heredity
Penny Makhumbila, Molemi E. Rauwane, Hangwani H. Muedi, Ntakadzeni E. Madala, Sandiswa Figlan
Summary: The causal agent of rust, Uromyces appendiculatus, is a significant constraint for common bean production. This pathogen causes substantial yield losses worldwide. Although breeding for resistance has made progress, U. appendiculatus still poses a major threat due to its ability to mutate and evolve. Understanding plant phytochemical properties can aid in accelerating breeding for rust resistance.
FRONTIERS IN GENETICS
(2023)
Article
Biochemical Research Methods
Samuel Bernardo-Bermejo, Jingchuan Xue, Linh Hoang, Elizabeth Billings, Bill Webb, M. Willy Honders, Sanne Venneker, Bram Heijs, Maria Castro-Puyana, Maria Luisa Marina, Erik B. van den Akker, Marieke Griffioen, Gary Siuzdak, Martin Giera, Elena Sanchez-Lopez
Summary: Analytical techniques with high sensitivity and selectivity are crucial in clinical sample analysis. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the standard method, but it is expensive. This study demonstrates that similar results can be achieved using a simpler single mass spectrometry detector combined with enhanced in-source fragmentation/annotation and correlated ion monitoring. The protocol provides step-by-step instructions for optimizing the conditions for this technique, making it broadly applicable and cost-effective for quantifying small molecules.
Article
Biochemical Research Methods
Kirsten E. E. Overdahl, Justin B. B. Collier, Anton M. M. Jetten, Alan K. K. Jarmusch
Summary: Feature finding is a common method in processing untargeted mass spectrometry data to obtain a list of chemicals present in a sample. This study introduces signal response evaluation as a method to assess the individual features observed in untargeted MS data.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Review
Biology
Si Ying Lim, Sharmelee Selvaraji, Hazel Lau, Sam Fong Yau Li
Summary: Despite significant advancements in disease diagnosis and treatment, coronary heart disease remains the leading cause of death globally. Omics studies, particularly in the fields of metabolomics and lipidomics, offer promising insights and potential biomarkers for CHD research, while glycomics and metallomics have yet to be extensively explored in this field. This study provides a comprehensive overview of the applications of omics beyond the central dogma in CHD research, highlighting areas for further exploration and development.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biochemical Research Methods
Si Ying Lim, Bao Hui Ng, Dhruti Vermulapalli, Hazel Lau, Anna Karen Carrasco Laserna, Xiaoxun Yang, Sock Hwee Tan, Mark Y. Chan, Sam Fong Yau Li
Summary: Bioinformatics and machine learning tools have enabled the integration of data from different omics platforms for novel insights into diseases. A simultaneous dual extraction method has been introduced for efficient and reproducible generation of metabolomic and glycomic profiles. The joint-omics analysis identified mechanistic interactions between metabolites and glycans, revealing the intermodulatory roles of protein-bound carbohydrates or glycoproteins and amino acids in metabolic pathways and the protective role of the glyco-redox network in coronary heart disease.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Environmental Sciences
Gideon Lam, Ludmila Juricek, Hiranya Dayal, Anna Karen Carrasco Laserna, Medhi Hichor, Etienne Blanc, Caroline Chauvet, Phillipe Noirez, Xavier Coumoul, Sam Fong Yau Li
Summary: This study aimed to analyze the long-term effects of maternal exposure to TCDD on skeletal muscles and the impact of re-exposure during adulthood. The study found that TCDD has different effects on different types of skeletal muscles and that the period of exposure is a crucial factor in determining these effects.
ENVIRONMENTAL SCIENCES EUROPE
(2022)
Article
Food Science & Technology
Hazel Lau, Lai Heng Tan, Liang Ying Ee, Hiranya Dayal, Si Ying Lim, Feng Liu, Sam Fong Yau Li
Summary: In this study, the effectiveness of celery preservation techniques was evaluated using 1H NMR spectroscopy coupled with multivariate analyses. The extraction parameters were optimized to achieve high recoveries of metabolites and reduce fluctuations in concentrations and chemical shifts. The results showed that nanocellulose treatment was the most effective preservation method, and LC-MS analysis revealed significant suppression of phenylpropanoid pathway metabolites.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Shilin Zhang, Jinqing Hu, Sam Fong Yau Li, Hongxiu Lu, Gang Wang, Chang Lu, Muhammad Tariq Sarwar, Aidong Tang, Huaming Yang
Summary: Here, we present a novel electrochemical sensing mechanism for ammonium ions (NH4+) which involves the two-electron oxygen reduction reaction (ORR) and the hydrazine reaction. By using a self-supporting Ag/TiO2 nanotube array composite electrode modified with hematite (Ag/Fe2O3/TNTs), NH4+ can be electrooxidized to hydrazine by H2O2 produced from the ORR. The Ag/Fe2O3/TNT sensor exhibits high sensitivity, short response time, fine selectivity, and good reproducibility, making it suitable for accurate detection of NH4+ in real water samples. Moreover, this mechanism shows certain universality in various Ag/transition metal oxide/TNT sensing systems, providing a new design basis for electrochemical ammonia nitrogen sensors that are urgently needed.
CHEMICAL COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Si Ying Lim, Felicia Li Shea Lim, Inmaculada Criado-Navarro, Xin Hao Yeo, Hiranya Dayal, Sri Dhruti Vemulapalli, Song Jie Seah, Anna Karen Carrasco Laserna, Xiaoxun Yang, Sock Hwee Tan, Mark Y. Chan, Sam Fong Yau Li
Summary: This study investigates the translational potential of a multi-omics approach in understanding acute myocardial infarction (AMI). The integration of metabolomic, lipidomic, glycomic, and metallomic profiles reveals new insights into AMI and improves the classifier performance in distinguishing AMI cases from healthy controls.
Article
Chemistry, Analytical
Yong Ying Tay, Xuan Hao Lin, Sam Fong Yau Li
Summary: In this study, a nanoparticle-imprinted hydrogel (NANOGEL) was developed to detect and capture nanoparticles (NPs) in water samples. The NANOGEL demonstrated good repeatability, reproducibility, and stability. It was found to be highly selective for NPs, and the size of cavities and surface characteristics played a role in its selectivity. The NANOGEL is believed to provide a highly selective and sensitive approach for detecting NPs and removing them from contaminated water resources.
Article
Chemistry, Analytical
Xuan Hao Lin, Mann Joe Wong, Sam Fong Yau Li
Summary: In this study, a highly selective arsenite (As(III)) sensor based on gold nanoparticles (AuNPs) and ionic liquids (ILs) was reported. It was discovered that organic ILs can induce the aggregation and precipitation of AuNPs much more efficiently than inorganic electrolytes. By examining the interactions between AuNPs, As(III), and ILs, it was found that ILs and AuNPs can be used as a sensing probe to detect and determine the concentration of arsenite. Six different ILs were evaluated for this purpose, and the sensor sBMP demonstrated a low limit of detection (LOD) of 0.18 ppb, ranking among the second lowest reported arsenite sensors. The sensing of arsenite was also validated with real water samples using ICP-OES.
Article
Environmental Sciences
Gideon Lam, Phillipe Noirez, Haidar Djemai, Layale Youssef, Etienne Blanc, Karine Audouze, Min Ji Kim, Xavier Coumoul, Sam Fong Yau Li
Summary: This study investigates the metabolic changes induced by persistent organic pollutants (POPs) in different organs of mice using GC-MS metabolomics analysis. The results show that POPs significantly affect fatty acid and glyceride metabolism, but this effect diminishes after 21 days post transplantation.
ENVIRONMENTAL POLLUTION
(2023)
Article
Engineering, Environmental
Hengjie Yu, Shiyu Tang, Sam Fong Yau Li, Fang Cheng
Summary: This study collects experimental data to predict the metal/metalloid concentration in maize seedlings after seed priming with different nanoparticles. The findings show that solubility is highly correlated with model performance, and factors such as surface area, concentration, zeta potential, hydrodynamic diameter of nanoparticles, and relative weight of plants play important roles in determining the concentration.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Agriculture, Multidisciplinary
Shan Huang, Si Ying Lim, Sock Hwee Tan, Mark Y. Chan, Wuzhong Ni, Sam Fong Yau Li
Summary: The relationship between TMAO, betaine, and choline with acute myocardial infarction (AMI) is unclear. This study found that high betaine + low TMAO levels are associated with a significant protective effect against AMI. Furthermore, age is positively correlated with TMAO concentration, indicating a potential interplay between age and the risk of AMI associated with metabolite combination.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Hengjie Yu, Dan Luo, Sam Fong Yau Li, Maozhen Qu, Da Liu, Yingchao He, Fang Cheng
Summary: Seed treatment using nanomaterials is a cost-effective and environmentally friendly solution for mitigating environmental stress in crops. This study used 56 seed nanopriming treatments to alleviate stress in maize, with seven treatments significantly increasing stress resistance. Metabolomics data revealed that ZnO nanopriming treatment regulates various metabolic pathways. Interpretable machine learning was used to predict and understand stress mitigation effects, and the dominant factors and interactions affecting root dry weight under salinity stress were explained.
Article
Chemistry, Multidisciplinary
Liang Ying Ee, Yong Kuok Tan, Jiapei Miao, Hui Ting Chu, Sam Fong Yau Li
Summary: Reusable acidic ternary deep eutectic solvents (TDES) composed of alanine, lactic acid, and ethylene glycol were designed for the fractionation of high-purity lignin and augmentation of lignocellulosic biomass. The TDES extraction method yielded lignin free of sulfur and silica, with desirable molecular weight and monomeric yield, which can be beneficial for various applications. This green extraction method provides a new approach for sustainable biomass valorization.
Article
Biochemistry & Molecular Biology
Si Ying Lim, Zhi En Low, Regina Pei Woon Tan, Zhi Chiaw Lim, Wee Han Ang, Tetsuo Kubota, Michiko Yamanaka, Steven Pang, Erhan Simsek, Sam Fong Yau Li
Summary: By utilizing SC-ICP-MS technique, this research precisely defined the accumulation patterns of platinum drugs in cancer cells and provided insights into drug resistance mechanisms and sulfur-iron metabolism. The study not only confirmed the utility of SC-ICP-MS in chemotherapeutic research, but also offered inspirations for the further development of ICP-MS-based analytical capacities.
Article
Biochemistry & Molecular Biology
Hazel Lau, Nengyi Ni, Hiranya Dayal, Si-Ying Lim, Yi Ren, Sam Fong-Yau Li
Summary: The study demonstrated and compared the anti-inflammatory effects of celery leaf and stem extracts, with celery leaf showing higher efficacy. Through metabolomics analysis and identification of metabolites, the mechanisms of celery's impact on inflammatory responses were revealed.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2021)