Article
Biochemical Research Methods
Peng Zhou, Baisong An, Xiaolei Zhang, Jiming Lv, Baisong Lin
Summary: Metabolomics was employed to investigate the therapeutic effect and mechanism of danshensu (DSS) on coronary heart disease (CHD) model rats. By analyzing the overall metabolic profile and biomarkers, the study revealed the regulatory effect of DSS on metabolic pathways. The results demonstrated that metabolomics could be used to discover biomarkers and metabolic pathways of CHD, and further understand the pharmacological effects and mechanisms of natural products.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2022)
Article
Plant Sciences
Suphitcha Limjiasahapong, Khwanta Kaewnarin, Narumol Jariyasopit, Sakchai Hongthong, Narong Nuntasaen, Jonathan L. Robinson, Intawat Nookaew, Yongyut Sirivatanauksorn, Chutima Kuhakarn, Vichai Reutrakul, Sakda Khoomrung
Summary: Pyranonaphthoquinones (PNQs) are important structural scaffolds found in natural products, and Ventilago harmandiana was found to be a rich source of PNQs. A new method using ultraperformance liquid chromatography-mass spectrometry was developed to quantitatively determine six PNQs in various parts of the plant. Different parts of the plant showed varying concentrations of PNQs, with PNQ-332 being the major compound in most parts except for the root, where PNQ-318A was the most abundant. MS/MS spectra at different collision energies were provided for structural elucidation of the PNQs.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Shubhangi Raskar, Vishwabandhu Purkar, Milind Sardesai, Sirsha Mitra
Summary: The study found that the chemical composition of Embelia varies depending on the location, which is crucial for sustainable selection of herbal trade materials.
Article
Plant Sciences
Cyril Abadie, Julie Lalande, Guillaume Tcherkez
Summary: Plant metabolomics is widely used in plant physiology to study metabolic responses to environmental parameters. Derivatization followed by GC-MS metabolic profiling is a major technique for quantifying primary carbon, sulphur, and nitrogen metabolites. However, routine exact mass GC-MS analyses are not common due to the lack of dedicated databases. In this study, a curated database for exact mass metabolomics focused on primary metabolism was presented. The advantages of exact mass analyses were demonstrated, including resolving isotopic patterns, localizing S-containing metabolites, and avoiding identification errors. A practical example using Arabidopsis leaves showcased how exact mass GC-MS analysis can be used for plant samples and identify metabolic profiles.
PLANT CELL AND ENVIRONMENT
(2022)
Article
Microbiology
Ipsita Mohanty, Subhasish Tapadar, Samuel G. Moore, Jason S. Biggs, Christopher J. Freeman, David A. Gaul, Neha Garg, Vinayak Agarwal
Summary: The study investigates the presence of bromotyrosine alkaloids in marine sponges from different geographical locations, revealing significant correlations between microbiomes and metabolomes. It also demonstrates a conservation of biosynthetic logic between different classes of sponge-derived natural products. Overall, the study highlights the interconnectedness between microbiomes and metabolomes in marine sponges.
Review
Biochemistry & Molecular Biology
Sudha Manickam, Veera Ranjani Rajagopalan, Rohit Kambale, Raghu Rajasekaran, Selvaraju Kanagarajan, Raveendran Muthurajan
Summary: Plant metabolomics is a field that involves comprehensive analyses of small molecules in plant tissues and cells, providing insights into the functional roles of metabolites and their associations with specific traits. Integrating metabolomics data with other omics data enables researchers to understand the complex interactions within organisms.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Nicholas J. J. Morehouse, Trevor N. N. Clark, Emily J. J. McMann, Jeffrey A. A. van Santen, F. P. Jake Haeckl, Christopher A. A. Gray, Roger G. G. Linington
Summary: Spectral matching of MS2 fragmentation spectra has limitations due to instrument differences and limited spectral reference libraries. To overcome this challenge, SNAP-MS uses structural similarity network annotation to assign compound families to molecular networking subnetworks without using experimental or calculated reference spectra. SNAP-MS accurately annotates subnetworks built from both reference spectra and an in-house microbial extract library, and predicts compound families from published molecular networks acquired using different MS instruments.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Yuan Liu, Hua Zhang, William F. Dove, Zicong Wang, Zhijun Zhu, Perry J. Pickhardt, Mark Reichelderfer, Lingjun Li
Summary: A challenge in reducing colorectal cancer deaths is to screen patients using low-invasive testing. This study used a blood test and mass spectrometry to identify changes in metabolite levels of colorectal cancer. By quantifying 40 metabolites in serum samples, the study found decreased levels of threonine and asparagine in patients with growing or high-risk adenomas, as well as decreased levels of glutamine in patients with unknown growth status or high-risk adenomas. Elevated levels of arginine were found in patients with low-risk adenoma. These results suggest that certain metabolites may be useful in distinguishing colorectal patients with growing adenomas.
JOURNAL OF PROTEOME RESEARCH
(2023)
Review
Food Science & Technology
Clara Sousa
Summary: Natural pigments are widely distributed molecules in nature and play a significant role in our daily lives. In addition to their colors, they also have relevant biological properties associated with health benefits. Edible plant leaves, although less known as a source of natural pigments, contain a high variety of chlorophylls, carotenoids, and anthocyanins. This review critically analyzes the workflow used to identify and quantify these pigments in edible plant leaves using tandem mass spectrometry. Consistency issues in the methods used to extract and analyze these compounds are addressed. Mass spectrometry is a widely employed technique in metabolomics and will be discussed in the context of pigment identification and quantification.
Article
Plant Sciences
Serhat Sezai Cicek, Anna Lais Pfeifer Barbosa, Arlette Wenzel-Storjohann, Jorge Federico Orellana Segovia, Roberto Messias Bezerra, Frank Soennichsen, Christian Zidorn, Isamu Kanzaki, Deniz Tasdemir
Summary: This study investigated the phytochemistry and bioactivity of Vouacapoua americana, an economically important tree in the Amazon region. Several potentially pharmacologically active compounds were identified, and the structure of one compound was revised. The findings contribute to the development of drugs from Amazonian medicinal plants.
Article
Biochemistry & Molecular Biology
Maria Pilar Giner, Stefan Christen, Simona Bartova, Mikhail Makarov, Marie E. Migaud, Carles Canto, Sofia Moco
Summary: NAD(+) and its reduced form NADH are essential coenzymes in hundreds of metabolic reactions, serving as substrates for key enzymes. Analyzing the NAD(+) metabolome using liquid chromatography-tandem mass spectrometry can provide insights into NAD(+) biology and its implications for health and disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
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
Biochemistry & Molecular Biology
Don D. Nguyen, Veronika Saharuka, Vitaly Kovalev, Lachlan Stuart, Massimo Del Prete, Kinga Lubowiecka, Rene De Mot, Vittorio Venturi, Theodore Alexandrov
Summary: METASPACE is a fast and accurate tool for annotating microbial specialized metabolites from imaging MS data. It has been shown to successfully annotate a variety of microbial metabolites from data obtained from microbial colonies grown on agar.
Article
Chemistry, Multidisciplinary
Morgane Mauduit, Marie Derrien, Marie Grenier, Stephane Greff, Sacha Molinari, Pierre Chevaldonne, Charlotte Simmler, Thierry Perez
Summary: This study presents a novel underwater hand-held solid-phase extraction device, I-SMEL, which is used to concentrate molecules from seawater and study the chemical composition of marine benthic species. The device was deployed in a sponge-dominated Mediterranean ecosystem and showed promising results in enriching and recovering specialized metabolites from sponges. This research opens up new perspectives in marine chemical ecology and paves the way for sustainable efforts in natural product chemistry.
ACS CENTRAL SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Sanghoon Lee, Jeffrey A. van Santen, Nima Farzaneh, Dennis Y. Liu, Cameron R. Pye, Tim U. H. Baumeister, Weng Ruh Wong, Roger G. Linington
Summary: NP Analyst is an open online platform for integrating bioassay data and mass spectrometry data, with the ability to predict compound bioactivity profiles, support multiple data formats, and integrate with existing workflows.
ACS CENTRAL SCIENCE
(2022)
Correction
Genetics & Heredity
Zequn Chen, Kelly J. Vining, Xiwu Qi, Xu Yu, Ying Zheng, Zhiqi Liu, Hailing Fang, Li Li, Yang Bai, Chengyuan Liang, Weilin Li, Bernd Markus Lange
Article
Microbiology
Fani Ntana, Sean R. Johnson, Bjorn Hamberger, Birgit Jensen, Hans J. L. Jorgensen, David B. Collinge
Summary: Specialised metabolites produced during plant-fungal associations play crucial roles in defining and establishing symbiotic relationships. However, they are often overlooked in studying plant-microbe interactions. This study investigated how the specialised metabolism of tomato plants is regulated during a mutualistic symbiotic association with the root endophyte Serendipita indica. The results showed that the presence of S. indica induced the expression of genes involved in the biosynthesis of specific compounds in both roots and leaves, while the expression levels of other pathways were lower.
Article
Biochemistry & Molecular Biology
Amber N. Parrish, Iris Lange, Dunja Samec, Bernd Markus Lange
Summary: This study analyzed the chemical diversity in three species of the genus Equisetum. The results showed that there were species- and organ-specific patterns of metabolite accumulation. Different metabolites contributed to the separation of shoot and rhizome samples. The findings provide a foundation for further investigation into the metabolism of this ancient land plant lineage.
Article
Biochemistry & Molecular Biology
Francesca Zamolo, Jan Phillip Heinrichs, Matthias Wuest
Summary: This study examined the distribution, translocation, and biosynthetic sites of IBMP in bell pepper plants. The results showed that IBMP was the most abundant pyrazine in all aerial plant parts, with IPMP being dominant in root tissues. The highest levels of IBMP were found in unripe bell pepper fruits. Biosynthesis of IBMP was observed in all plant parts, but not in roots and ripe bell pepper fruits. There was no evidence of phloem translocation of IBMP.
Article
Chemistry, Multidisciplinary
Francesca Zamolo, Matthias Wuest
Summary: 3-Isobutyl-2-methoxypyrazine (IBMP) is a highly potent odorant that gives fruits and vegetables their distinct aroma. Bell peppers, in particular, have high levels of IBMP, making it the compound responsible for their characteristic smell. However, the biosynthesis of methoxypyrazines, including IBMP, has been unknown until now. Through feeding experiments with stable-isotope labeled precursors, it has been discovered that l-Serine plays a key role in the construction of the pyrazine ring in 3-alkyl-2-methoxypyrazines (MPs). Analysis using HS-SPME-GCxGC-TOF-MS revealed that the biosynthetic pathway to IBMP is closely linked to l-Serine derived from photorespiration.
CHEMISTRY-A EUROPEAN JOURNAL
(2023)
Article
Biochemical Research Methods
Jan Leppert, Tillman Brehmer, Matthias Wuest, Peter Boeker
Summary: A fast and reliable method is introduced to evaluate retention parameters for gas chromatography based on the distribution-centric 3-parameter model. The method uses a differentiable model of solute migration in a gas chromatographic system and employs Newton's method with trust region to determine the parameters. The determined retention parameters can be applied in method development and show good agreement with isothermal GC measurements.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Plant Sciences
B. Markus Lange, Narayanan Srividya
Summary: In this article, the authors review all functionally characterized monoterpene synthases (MTSs) and sesquiterpene synthases (STSs) of Cannabis sativa L. They also explore the locations of MTSs and STSs in the chromosome-level assembly of the reference chemovar CBDRx. Computational analyses and literature reviews are combined to lay the foundation for future studies on the determinants of substrate and product specificity in these enzymes.
PHYTOCHEMISTRY REVIEWS
(2023)
Article
Plant Sciences
B. Markus Lange, Narayanan Srividya, Iris Lange, Amber N. Parrish, Lukas R. Benzenberg, Iovanna Pandelova, Kelly J. Vining, Matthias Wuest
Summary: The essential oils extracted from above-ground materials of mint family members are widely used in consumer products. Previous research focused on the characterization of terpenoid oil constituents in mint leaves, but we found that other organs, such as stems, rhizomes, and roots, also emit volatiles with varying compositions. The analysis of volatile quantities released by mint plants treated with Verticillium dahliae-spore suspension or water showed differences in susceptible and resistant species, indicating their involvement in disease resistance.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Multidisciplinary Sciences
Richard Barker, Colin P. S. Kruse, Christina Johnson, Amanda Saravia-Butler, Homer Fogle, Hyun-Seok Chang, Ralph Moller Trane, Noah Kinscherf, Alicia Villacampa, Aranzazu Manzano, Raul Herranz, Laurence B. Davin, Norman G. Lewis, Imara Perera, Chris Wolverton, Parul Gupta, Pankaj Jaiswal, Sigrid S. Reinsch, Sarah Wyatt, Simon Gilroy
Summary: This study compares transcriptomic analysis of 15 Arabidopsis thaliana spaceflight experiments in the GeneLab data repository, revealing that factors such as analysis type and environmental and hardware conditions have important effects on defining plant reactions to spaceflight. The use of a metadata matrix helps reduce complexity in drawing conclusions by selecting studies with high design similarity.
Article
Chemistry, Multidisciplinary
Tillman Brehmer, Benny Duong, Manuela Marquart, Luise Friedemann, Peter J. Faust, Peter Boeker, Matthias Wuest, Jan Leppert
Summary: This study presents an open source database with suitable retention parameters for prediction and simulation of GC separations, and introduces three common retention models. Useful computer simulations are important for saving resources and time in GC method development. The standardized procedure of measurements and calculations presented in this study is beneficial for chromatographers, analytical chemists, and method developers. The main benefits include simulations of temperature-programed GC separations and comparison with measurements, with observed deviation of predicted retention times being less than 1%. The database includes over 900 entries covering a wide range of compounds on more than 20 different GC columns, such as VOCs, PAHs, FAMEs, PCBs, or allergenic fragrances.
Review
Biochemistry & Molecular Biology
Francesca Zamolo, Matthias Wuest
Summary: Pyrazines are widely present in nature and are synthesized by microorganisms, insects, and plants. They have diverse biological functions, including playing a role as semiochemicals and aroma compounds in foods. 3-alkyl-2-methoxypyrazines (MPs) have been the focus of research due to their association with green and earthy attributes and their influence on the aroma of vegetables and wines. The biosynthetic pathway and precursors of MPs have been the subject of discussion and were recently discovered to involve l-leucine and l-serine as important precursors for IBMP.
Article
Agriculture, Multidisciplinary
Marvin Benedikt Brenner, Sandra Flory, Matthias Wuest, Jan Frank, Karl Wagner
Summary: Currently, there is a lack of in vitro dissolution methods that can accurately predict the in vivo bioavailability of compounds from complex mixtures. This study developed an in vivo predictive dissolution method (BiPHa+) using data on the in vivo performance of bioavailability-improved curcumin formulations. Compared with conventional dissolution systems, BiPHa+ demonstrated superior in vivo-relevant formulation characterization and had the highest degree of linearity in predicting bioavailability. It also provided mechanistic information about formulation-dependent release characteristics.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemical Research Methods
Tillman Brehmer, Peter Boeker, Matthias Wuest, Jan Leppert
Summary: The development of new analytical methods that support the optimization process can save resources, time, and costs. In this study, the relationship between the measured elution temperature and the characteristic temperature was investigated for various volatile substances. A novel multivariate curve fit model was developed, which accurately describes the relation between the characteristic temperature T-char and elution temperatures T-elu, expanding the prediction range for high volatile compounds.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Horticulture
Charlotte Hubert, Saskia Tsiaparas, Liane Kahlert, Katharina Luhmer, Marcel Dieter Moll, Maike Passon, Matthias Wuest, Andreas Schieber, Ralf Pude
Summary: This study investigated the effects of two different postharvest processes on the content and composition of essential oils in three different Mentha genotypes. The results showed that the postharvest processing treatments did not significantly affect the essential oil content and composition, but genotype selection and harvest time had a significant impact.
Article
Biochemistry & Molecular Biology
Armando Moreno-Velasco, Mabel Fragoso-Serrano, Pedro de Jesus Flores-Tafoya, Sebastian Carrillo-Rojas, Elihu Bautista, Suzana Guimara Leitao, Jhon F. Castaneda-Gomez, Rogelio Pereda-Miranda
Summary: This study investigated the roots of Operculina hamiltonii, a traditional medicinal plant in Brazil. Three new acyl sugars or resin glycosides were identified and their structures elucidated. The combination of these compounds with other drugs showed enhanced cytotoxic effects on breast cancer cells.
Article
Biochemistry & Molecular Biology
Qian-Qing Liu, Lin-An Xiong, Jia-Yu Qian, Ting-Ting Gong, Lie-Feng Ma, Luo Fang, Zha-Jun Zhan
Summary: A new naturally occurring compound, Linderagatins C-F (1-4), with the structures of diaryltetrahydrofuran-type 7,9'-dinorlignans, was discovered in the roots of Lindera aggregata. The neuroprotective effects of compounds 2 and 3 on erastin-induced ferroptosis in HT-22 cells were found to be significant.
