Article
Immunology
Jian Guo, Juan Chen, Teng Li, Lei Gao, Cizhong Jiang, Wenjuan Wu
Summary: In this study, a mucous-like strain of P. wickerhamii with atypical colony morphology was identified. The transcriptomics, proteomics, and metabolomics of this strain and two other P. wickerhamii strains were analyzed to reveal the morphological differences and molecular basis of pathogenicity. Mannan endo-1,4-beta-mannosidase was found to be significantly downregulated in the mucous-like strain, resulting in a thinner cell wall and reduced toxicity to macrophages. Metabolite analysis suggested that the mucoid appearance may be caused by increased levels of linoleic acid, glycerol, and other metabolites. Further study is needed to understand the ecology, aetiology, and pathogenesis of P. wickerhamii, particularly its transmission between humans, animals, and the environment, from a One Health perspective.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Environmental Sciences
Ruya Huang, Samuel Kumi Okyere, Chenyang Shao, Muhammad Yousif, Fei Liao, Xiaoxuan Wang, Juan Wen, Jianchen Wang, Yanchun Hu
Summary: This study investigated the toxic mechanisms of Ageratina adenophora using a multiomics approach. The main active toxic compounds and differential metabolites in A. adenophora were identified. The results showed that A. adenophora induces liver inflammatory damage by activating specific signaling pathways and affecting nutrient metabolism and neuron conduction.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Environmental Sciences
Na Qiao, Yanyang Yang, Jianzhao Liao, Hui Zhang, Fan Yang, Feiyang Ma, Qingyue Han, Wenlan Yu, Ying Li, Lianmei Hu, Jiaqiang Pan, Riaz Hussain, Zhaoxin Tang
Summary: The study found that high copper diet in pigs led to renal dysfunction, as indicated by elevated serum creatinine levels and renal tubular epithelial cell swelling. Transcriptomics and metabolomics analysis revealed significant changes in genes and metabolites in the kidneys of pigs in the high copper diet group, suggesting disruption in glycerophospholipids and glycosphingolipids metabolism pathways. Furthermore, copper exposure induced mitochondrial apoptosis and inhibited autophagy, highlighting the importance of these mechanisms in copper-induced renal damage.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Biochemistry & Molecular Biology
Nguyen Thi Hai Yen, Jung-Hwa Oh, Nguyen Thi Van Anh, Quoc-Viet Le, Se-Myo Park, Young Jin Park, Yong-Soon Cho, Kyoung-Sik Moon, Huy Truong Nguyen, Jae-Gook Shin, Nguyen Phuoc Long, Dong Hyun
Summary: This study conducted multi-specimen molecular characterization in rats treated with different doses of indomethacin to investigate its toxicity mechanism. The results showed that a dose of 10 mg/kg of indomethacin caused significant metabolic changes and kidney injury. Analysis revealed an oxidant-antioxidant imbalance and dysfunction of mitochondria, which resulted in the dysregulation of metabolites and genes related to the kidney, as well as the suppression of amino acid and fatty acid metabolism. These findings provide insights into the mechanism of indomethacin toxicity and suggest potential targets for reducing its toxicity.
CHEMICO-BIOLOGICAL INTERACTIONS
(2023)
Article
Biotechnology & Applied Microbiology
Chuner Cai, Xuanhong Liu, Hui Zhao, Ting Jiang, Rui Jia, Peimin He
Summary: The study found that exposure of U. prolifera to 10 mg L-1 copper sulfate for 12 hours mainly resulted in a reduction in transcription and translation. However, the resistance, signal transduction, and metabolism of U. prolifera were enhanced to actively respond to acute copper stress.
JOURNAL OF APPLIED PHYCOLOGY
(2021)
Editorial Material
Medicine, Legal
Joshua A. Harrill, Mark R. Viant, Carole L. Yauk, Magdalini Sachana, Timothy W. Gant, Scott S. Auerbach, Richard D. Beger, Mounir Bouhifd, Jason O'Brien, Lyle Burgoon, Florian Caiment, Donatella Carpi, Tao Chen, Brian N. Chorley, John Colbourne, Raffaella Corvi, Laurent Debrauwer, Claire O'Donovan, Timothy M. D. Ebbels, Drew R. Ekman, Frank Faulhammer, Laura Gribaldo, Gina M. Hilton, Stephanie P. Jones, Aniko Kende, Thomas N. Lawson, Sofia B. Leite, Pim E. G. Leonards, Mirjam Luijten, Alberto Martin, Laura Moussa, Serge Rudaz, Oliver Schmitz, Tomasz Sobanski, Volker Strauss, Monica Vaccari, Vikrant Vijay, Ralf J. M. Weber, Antony J. Williams, Andrew Williams, Russell S. Thomas, Maurice Whelan
Summary: Omics methodologies are widely used in toxicological research, but face challenges in gaining widespread regulatory acceptance due to lack of transparency in data processing methods and standardization in reporting. To foster further regulatory use of Omics data, the OECD's EAGMST launched a project to develop guidance for reporting Omics data.
REGULATORY TOXICOLOGY AND PHARMACOLOGY
(2021)
Article
Plant Sciences
Qikun Xing, Lea Cabioch, Antoine Desrut, Gildas Le Corguille, Sylvie Rousvoal, Laurence Dartevelle, Elodie Rolland, Yann Guitton, Philippe Potin, Gabriel V. Markov, Sylvain Faugeron, Catherine Leblanc
Summary: In the marine environment, the brown alga Laminaria digitata exhibits chemical and transcriptomic regulations as well as emission of volatile aldehydes in response to herbivore interactions. Bioassays using the limpet Patella pellucida and L. digitata revealed that incubation with 4-hydroxyhexenal (4-HHE) decreased algal consumption by herbivores. Metabolomic and transcriptomic approaches demonstrated significant modifications to algal molecular responses after treatment with different aldehydes, particularly in fatty acid degradation pathways. This research highlights the potential biological role of algal perception of specific aldehydes in the interactions between kelps and grazers in complex ecosystems.
Article
Environmental Sciences
Yanliang Zhang, Jinqi Zhao, Na Sa, Chenyu Huang, Wenyu Yu, Tianxiao Ma, Hongjun Yang, Fang Ma, Siqi Sun, Chaochun Tang, Weiguo Sang
Summary: This study investigated the effects of copper exposure on earthworms, finding that it disrupts amino acid, lipid, and carbohydrate metabolism, decreases intestinal bacterial diversity, and affects their abundance. These changes lead to decreased energy expenditure, inhibited nutrient absorption and fatty acid synthesis, and weakened antioxidant and detoxification abilities, ultimately inhibiting the growth of earthworms.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biochemistry & Molecular Biology
Panagiota Filippou, Xavier Zarza, Chrystalla Antoniou, Toshihiro Obata, Carlos A. Villarroel, Ioannis Ganopoulos, Vaggelis Harokopos, Gholamreza Gohari, Vassilis Aidinis, Panagiotis Madesis, Anastasis Christou, Alisdair R. Fernie, Antonio F. Tiburcio, Vasileios Fotopoulos
Summary: The study found that salt-tolerant genotypes displayed lower levels of oxidative damage after salt treatment, while salt-sensitive genotypes showed higher oxidative responses. Metabolomics data revealed differences in responses to stress among different genotypes, while global transcriptomic analysis identified previously undiscovered gene expression differences related to salinity.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Review
Biochemical Research Methods
Mohammad Reza Karimi, Amir Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz
Summary: Holistic perspectives are crucial in understanding the complexity of tumors and current single-layer analysis has limitations. Integrative multilayer approaches are emerging as effective tools in achieving systemic views on cancer biology.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Plant Sciences
Jiang Zhang, Xu-Feng Chen, Wei-Tao Huang, Huan-Huan Chen, Ning-Wei Lai, Lin-Tong Yang, Zeng-Rong Huang, Jiuxin Guo, Xin Ye, Li-Song Chen
Summary: This study investigates the adaptive responses of citrus seedlings to different pH and copper concentrations. Increasing pH can alleviate copper toxicity by reducing copper accumulation and oxidative damage, improving leaf growth and metabolism. However, under low pH conditions, the adaptive responses fail to counteract the effects of copper toxicity.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Chemistry, Medicinal
Sophie Guillotin, Nicolas Delcourt
Summary: Harmful algal blooms (HAB) and the release of toxic metabolites pose a threat to marine organisms and human health. The consequences of toxin exposure on gene expression, protein profile, and metabolic pathways are still not well understood, but recent OMICS-based research has provided important insights. This review provides a comprehensive overview of the latest research and discusses the use of OMICS datasets to identify new features in ecotoxicology, food safety, and human health. Future perspectives in OMICS studies are also explored.
Article
Food Science & Technology
Min Zhang, Xiaoying Zou, Yixuan Du, Zhuangguang Pan, Fangqing He, Yuanming Sun, Meiying Li
Summary: This research investigated the anti-hyperlipidemia effects of alliin in vivo and its potential mechanisms using transcriptomics and metabolomics analysis. The results showed that high doses of alliin intervention significantly decreased serum total cholesterol and liver malondialdehyde levels while increasing liver superoxide dismutase and catalase levels. Transcriptomics analysis revealed several genes involved in steroid biosynthesis, triglyceride metabolism, drug metabolism-cytochrome P450, and the PI3K-Akt signaling pathway. Metabolomics analysis identified significant differences in carboxylic acids between the alliin group and the high-fat diet group. The study provides a theoretical framework for understanding the lipid-lowering mechanism of alliin and suggests potential market opportunities for its development and utilization in improving the health status of individuals with hyperlipidemia.
Review
Immunology
Denis A. Mogilenko, Alexey Sergushichev, Maxim N. Artyomov
Summary: Immunometabolism has become a new interdisciplinary field of research in recent years, providing important insights into the regulation of immune responses. Traditional approaches and new technologies, such as spatially resolved metabolic imaging and computational algorithms, have helped us understand the complexity of immunometabolic regulation. This review discusses recent studies and technological developments that aim to capture the interplay between immune responses and metabolism.
ANNUAL REVIEW OF IMMUNOLOGY
(2023)
Editorial Material
Microbiology
Jennifer Geddes-McAlister
Summary: The beauty within biological systems can be revealed through advanced technological platforms. Improvements in genome, transcriptome, proteome, and metabolome investigations, as well as data integration, have accelerated our understanding of diverse biological systems. For fungal pathogens, innovation is driven by exploring mechanisms of antifungal resistance, uncovering new relationships and interactions between host and pathogen, improving characterization of virulence determinants, and discovering new antifungal targets.
Article
Instruments & Instrumentation
Win Cowger, Andy M. Booth, Bonnie M. Hamilton, Clara Thaysen, Sebastian Primpke, Keenan Munno, Amy L. Lusher, Alexandre Dehaut, Vitor P. Vaz, Max Liboiron, Lisa Devriese, Ludovic Hermabessiere, Chelsea Rochman, Samantha N. Athey, Jennifer M. Lynch, Hannah De Frond, Andrew Gray, Oliver A. H. Jones, Susanne Brander, Clare Steele, Shelly Moore, Alterra Sanchez, Holly Nel
APPLIED SPECTROSCOPY
(2020)
Article
Medicine, Legal
Jessica Pandohee, Jeff G. Hughes, James R. Pearson, Oliver A. H. Jones
Article
Environmental Sciences
Yufei Wang, Linhua Fan, Oliver A. H. Jones, Felicity Roddick
Summary: Reactive oxygen species generated in wastewater lagoons upon sunlight exposure play a crucial role in attenuating emerging contaminants. The production of reactive radicals is influenced by both environmental factors and the composition of effluent organic matter in the wastewater. The optical properties of wastewater can serve as indicators for the formation of reactive species under sunlight irradiation.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Engineering, Environmental
W. McCance, O. A. H. Jones, D. I. Cendon, M. Edwards, A. Surapaneni, S. Chadalavada, S. Wang, M. Currell
Article
Chemistry, Multidisciplinary
Oliver A. H. Jones, Paul G. Stevenson, Simone C. Hameka, Dale A. Osborne, Patrick D. Taylor, Michelle J. S. Spencer
Summary: The use of 3D printing in chemistry education has greatly expanded in the past decade, allowing for the creation of physical models to help students better understand complex concepts such as multidimensional spectra and chromatograms. These innovative models can enhance students' understanding of data, particularly benefiting visual and tactile learners.
JOURNAL OF CHEMICAL EDUCATION
(2021)
Article
Medicine, Legal
Simon P. B. Ovenden, Lyndal J. McDowall, Hugh E. McKeown, Nathan W. McGill, Oliver A. H. Jones, James R. Pearson, Marija Petricevic, Michael L. Rogers, Trevor J. Rook, Jilliarne Williams, Renee L. Webster, Shannon D. Zanatta
Summary: In this study, two acylation methods for fentanyl production were investigated using LC-HRMS and MVA, identifying fifty-five impurities and specific CAS for each method. The results provide valuable information for investigating illicit chemical agent use and suggest potential specific CAS for the Valdez method.
FORENSIC SCIENCE INTERNATIONAL
(2021)
Article
Biochemistry & Molecular Biology
Elvina Parlindungan, Chaitali Dekiwadia, Oliver A. H. Jones
Summary: Food waste is a global issue with significant economic costs, leading researchers to explore natural alternatives such as bacteriocin peptides from Lactiplantibacillus plantarum B21 for food preservation. This study shows that nitrogen and Tween sources are essential for bacteriocin production, while carbohydrates are critical for growth. The bacteriocin interacts with cell membranes of target microorganisms, leading to cell leakage and death, providing insight for potential development of L. plantarum B21 as a natural biopreservative.
PROCESS BIOCHEMISTRY
(2021)
Article
Environmental Sciences
W. McCance, O. A. H. Jones, D. I. Cendon, M. Edwards, A. Surapaneni, S. Chadalavada, M. Currell
Summary: Anthropogenic activities in urban environments can impact groundwater quality, especially at Wastewater Treatment Plants(WWTPs). Long-term time-series analysis can help to better understand hydrogeochemical influences and anthropogenic inputs, leading to effective identification and control of environmental and health risks.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Environmental Sciences
Rohan M. Shah, Katie E. Hillyer, Sarah Stephenson, Joseph Crosswell, Avinash Karpe, Enzo A. Palombo, Oliver A. H. Jones, Daniel Gorman, Levente Bodrossy, Jodie van de Kamp, Andrew Bissett, Andrew S. Whiteley, Andy D. L. Steven, David J. Beale
Summary: The study used omics-based approaches to establish blueprints of microbial functionality in healthy estuarine sediment communities in pristine environments, identifying relationships between metabolic pathways and genes with community metabolic potential. An increase in KEGG genes related to metal homeostasis and metal resistance was observed, with correlations found between metal abundance and functional genes related to Fe and Zn metabolism. This research provides a baseline microbial blueprint for the pristine sediment microbiome and lays the groundwork for future ecosystem monitoring comparisons.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Water Resources
Meeruppage Gunawardhana, Ewen Silvester, Oliver A. H. Jones, Samantha Grover
Summary: The study highlights the importance of evapotranspiration in the water budget of mountain peatlands in the Australian Alps, showing that it accounts for 26% of annual precipitation. The seasonally dependent biogeochemical regulation processes observed in this study can serve as a reference for evaluating the condition of peatlands under similar weather conditions.
JOURNAL OF HYDROLOGY-REGIONAL STUDIES
(2021)
Review
Biochemistry & Molecular Biology
David J. Beale, Oliver A. H. Jones, Utpal Bose, James A. Broadbent, Thomas K. Walsh, Jodie van de Kamp, Andrew Bissett
Summary: Current environmental monitoring efforts often ignore the potential effects of unmeasured compounds and environmental factors, hindering effective environmental management. Comprehensive, untargeted monitoring and ecosurveillance can provide more effective monitoring and fill knowledge gaps. Despite being not well known, ecosurveillance has been beneficially applied in various systems.
EMERGING TOPICS IN LIFE SCIENCES
(2022)
Article
Environmental Sciences
Georgia M. Sinclair, Michela Di Giannantonio, Oliver A. H. Jones, Sara M. Long
Summary: Understanding the effects of experimental parameters on ecotoxicology experiments is crucial, especially temperature, light, and food type. However, the influence of substrate type is often assumed to be negligible. This study investigated the metabolic changes in freshwater crustaceans exposed to copper using different substrates and found that substrate alone can elicit different metabolic responses and affect substrate preferences of different life stages. These findings challenge the current paradigm and emphasize the importance of considering substrate as a significant experimental factor.
ENVIRONMENTAL MONITORING AND ASSESSMENT
(2023)
Article
Biochemistry & Molecular Biology
Georgia M. Sinclair, Sara M. Long, Navneet Singh, Timothy L. Coggan, Matthew P. J. Askeland, Oliver A. H. Jones
Summary: In this study, the metabolic response of freshwater amphipod Austrochiltonia subtenuis to per and polyfluoroalkyl substances (PFAS) at environmentally relevant concentrations was assessed using Gas Chromatography-Mass Spectrometry-based metabolomics. The results showed that PFAS induced changes in amino acids, fatty acids, and cholesterol levels. PFOS was found to bioaccumulate, while GenX and PFHxS were eliminated at different rates.
Article
Endocrinology & Metabolism
Georgia M. Sinclair, Sophie M. Oakes, Andrew C. Warden, Amy M. Paten, Oliver A. H. Jones
Summary: This study evaluated the potential of alternative NMR-active nuclei, other than H-1, to generate useful metabolomic data. The results showed that carbon NMR provided useful information but required larger sample sizes. Phosphorus produced overlapping peaks in one-dimensional analysis but showed potential in two-dimensional experiments. N-15 NMR was found to not be sensitive enough for general metabolomic work.
Article
Environmental Sciences
Matthew Currell, William McCance, Oliver A. H. Jones
Summary: The range of synthetic chemicals and our understanding of their potential harm to human and ecological health are both increasing. However, our knowledge about their behavior and associated risks in the environment is still lacking. Therefore, it is important to improve contaminant detection methods and increase understanding of their sources, fate, and transport. This article reviews recent advances in the use of novel molecular tracers for the identification and characterization of groundwater pollution sources.
CURRENT OPINION IN ENVIRONMENTAL SCIENCE & HEALTH
(2022)
