Article
Plant Sciences
Sunil S. Gangurde, Aamir W. Khan, Pasupuleti Janila, Murali T. Variath, Surendra S. Manohar, Prashant Singam, Annapurna Chitikineni, Rajeev K. Varshney, Manish K. Pandey
Summary: Seed weight has a direct impact on the yield and market price of groundnut. Marker-based early generation selection can accelerate breeding for large-seeded varieties. QTL-seq was used to identify candidate genes and develop markers for seed weight in groundnut.
Article
Chemistry, Physical
Xinxing Li, Anuja Shreeram Kulkarni, Xun Liu, Wei-Qiang Gao, Lin Huang, Zhiqian Hu, Kun Qian
Summary: A novel molecular tool based on metal-organic framework (MOF) hybrids is developed for metabolic analysis in colorectal cancer (CRC), providing direct metabolic fingerprints in seconds. A machine learning algorithm is utilized to construct a diagnostic prediction model to discriminate CRC patients from normal controls, with an average area under the curve of 0.947 for the discovery cohort and 0.912 for the independent validation cohort. Additionally, a CRC-specific metabolic signature consisting of 34 potential biomarkers is identified based on the diagnostic model.
Article
Immunology
Seda Yerlikaya, Ewurama D. A. Owusu, Augustina Frimpong, Robert Kirk DeLisle, Xavier C. Ding
Summary: This study identified two novel malaria diagnostic biomarkers, glyceraldehyde 3-phosphate dehydrogenase and dihydrofolate reductase-thymidylate synthase, through a systematic review and in silico analysis. These candidates have favorable diagnostic features and partially de-risked product development prospects, paving the way for next-generation malaria rapid diagnostic tests.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Pharmacology & Pharmacy
Dawei Deng, Chen Pan, Zeming Wu, Yujiao Sun, Chang Liu, Hong Xiang, Peiyuan Yin, Dong Shang
Summary: Osteoporosis is increasingly common among the global elderly population, and serum metabolite markers are crucial for its treatment and prevention. Metabolomics and lipidomics analysis revealed that lipids metabolism, including glycerol phospholipids, sphingolipids, fatty acids, and bile acids, is deregulated in osteoporosis. Bile acids, particularly hyocholic acids, were found to play essential roles and may serve as potential markers for diagnosis and treatment.
FRONTIERS IN PHARMACOLOGY
(2021)
Review
Chemistry, Medicinal
Luis A. R. Carvalho, Goncalo J. L. Bernardes
Summary: Activity-based protein profiling (ABPP) is a widely used method in malaria research that utilizes small molecular probes to study enzymatic activity, achieving significant advancements in the study of Plasmodium proteases, metabolic pathways, and target identification for antimalarials.
Article
Multidisciplinary Sciences
David Charles, Lee A. Gethings, James F. Potts, Peter G. J. Burney, Vanessa Garcia-Larsen
Summary: This study aimed to identify potential candidate markers of polyphenol intake in human serum and found that serum profiling for these compounds might improve the accuracy of determining flavonoid intake.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Shuai Zeng, Ziting Mao, Yijie Ren, Duolin Wang, Dong Xu, Trupti Joshi
Summary: G2PDeep is an open-access web server that provides a deep-learning framework for quantitative phenotype prediction and genomic marker discovery. It allows researchers to create and train models through an interactive web interface, monitor training process, and compare model performance. Additionally, G2PDeep integrates multiple datasets, including the soybean nested association mapping data, for predictions of quantitative phenotypes and genomic markers.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Statistics & Probability
Chen Lin, Kevin Wang, Samuel Mueller
Summary: This article explores traditional collinearity indices and proposes a new framework called mcvis, which uses resampling techniques to learn from these conventional indices repeatedly to better understand the causes of collinearity. It includes new collinearity measures and visualizations, particularly a bipartite plot to inform on the degree and structure of collinearity.
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
(2021)
Article
Infectious Diseases
Xiaola Guo, Shuai Wang, Junmei Zhang, Rui Li, Yong'e Zhang, Zhengrong Wang, Qingming Kong, William C. Cho, Xianghong Ju, Yujuan Shen, Lingqiang Zhang, Haining Fan, Jianping Cao, Yadong Zheng
Summary: This study identified three parasite-origin proteins released by echinococcus parasites into the sera during infection, which showed potential as promising diagnostic candidates for echinococcosis and for evaluating treatment prognosis.
PLOS NEGLECTED TROPICAL DISEASES
(2022)
Review
Pharmacology & Pharmacy
Hongbo Wang, Qinghai Meng, Jinjun Qian, Muxi Li, Chunyan Gu, Ye Yang
Summary: This review provides an overview of different types of RNAs in cancer diagnostics and treatment, discussing their unique characteristics and potential applications. It highlights the increasing use of mRNAs, lncRNAs, circRNAs, and miRNAs as diagnostic markers or therapeutic targets in various cancers. The review also explores the mechanisms by which these RNAs regulate and participate in cancer development, as well as their potential in cancer prediction and treatment.
PHARMACOLOGY & THERAPEUTICS
(2022)
Article
Oncology
Dapeng Li, Lei Zhang, Jinming Fu, Hao Huang, Yanlong Liu, Lin Zhu, Hongru Sun, Simin Sun, Ding Zhang, Tian Tian, Fan Wang, Fulan Hu, Xiaolin Peng, Gairui Li, Liyuan Zhao, Ting Zheng, Xuan Wang, Binbin Cui, Yashuang Zhao
Summary: This study discovered and validated a panel of methylation-based markers that specifically detect colorectal cancer (CRC) with high accuracy rates. These markers have the potential to be used as noninvasive cfDNA markers for the diagnosis of CRC.
CLINICAL EPIGENETICS
(2022)
Review
Biochemistry & Molecular Biology
John Oloche Onuh, Hongyu Qiu
Summary: Detecting pathogenesis early through metabolomics profiling offers new insights on disease mechanisms and potential in diagnosing clinical hypertension early. This review summarizes the latest progress in metabolomics and discusses current trends in applying it to clinical hypertension, exploring associated mechanisms and research challenges for future perspectives. The information enhances understanding of hypertension development and encourages clinical application of metabolomics in hypertension and cardiovascular complications.
Article
Chemistry, Multidisciplinary
Giulio Brunetti, Francesco Padovani, Annalisa De Pastina, Chiara Rotella, Amy Monahan, Stephen L. Hoffman, Said A. Jongo, Salim Abdulla, Giampietro Corradin, Gerd Pluschke, Claudia Daubenberger, Martin Hegner
Summary: Malaria, a life-threatening epidemic disease affecting half of the world's population, has seen a stagnation in incidence rate in recent years. New fast and optimized tools are critical for malaria vaccine research, and a clinical diagnostic device based on nanotechnology has been developed to accurately detect immune responses to malaria vaccines.
Article
Oncology
Ratna Priya, Vaishali Jain, Javed Akhtar, Neeraj Saklani, Puja Sakhuja, Anil Kumar Agarwal, Ravindra Varma Polisetty, Ravi Sirdeshmukh, Sudeshna Kar, Poonam Gautam
Summary: This study analyzed the protein content of extracellular vesicles derived from gallbladder cancer cell lines, identifying potential biomarkers for the detection of gallbladder cancer. Haptoglobin (HP) levels were found to be increased in gallbladder cancer, suggesting its potential as a biomarker.
FRONTIERS IN ONCOLOGY
(2022)
Article
Chemistry, Applied
Evangelos Karagiannis, Eirini Sarrou, Michail Michailidis, Georgia Tanou, Ioannis Ganopoulos, Christos Bazakos, Konstantinos Kazantzis, Stefan Martens, Aliki Xanthopoulou, Athanassios Molassiotis
Summary: This study characterized the physicochemical, sensory, and bioactive compound traits of twenty-two sweet cherry accessions in Greece, revealing significant differences in color, taste, and polyphenol content among the evaluated accessions. Certain cultivars showed higher consumer acceptance and polyphenol levels, providing valuable resources for future breeding efforts to improve the nutritional quality traits of sweet cherry cultivars.
Article
Surgery
Richmond T. Bergner, Sarah Onida, Rahul Velineni, Konstantina Spagou, Manjit S. Gohel, Marielle Bouschbacher, Serge Bohbot, Joseph Shalhoub, Elaine Holmes, Alun H. Davies
Summary: The study aimed to identify potential biomarkers predictive of healing or failure to heal in venous leg ulceration. It found that serum biofluids could differentiate between healing and nonhealing patients, and the ratio of carnitine to ceramide could differentiate between healing phenotypes with 100% sensitivity, 79% specificity, and 91% accuracy. This metabolic signature has potential applications for disease prognostication and development of targeted therapies for venous leg ulceration.
Article
Pathology
Lucy M. V. Gee, Ben Barron-Millar, Jack Leslie, Claire Richardson, Marco Y. W. Zaki, Saimir Luli, Rachel A. Burgoyne, Rainie I. T. Cameron, Graham R. Smith, John G. Brain, Barbara Innes, Laura Jopson, Jessica K. Dyson, Katherine R. C. McKay, Alexandros Pechlivanis, Elaine Holmes, Rolando Berlinguer-Palmini, Stella Victorelli, George F. Mells, Richard N. Sandford, Jeremy Palmer, John A. Kirby, Christos Kiourtis, Joao Mokochinski, Zoe Hall, Thomas G. Bird, Lee A. Borthwick, Christopher M. Morris, Peter S. Hanson, Diana Jurk, Elizabeth A. Stoll, Fiona E. N. LeBeau, David E. J. Jones, Fiona Oakley
Summary: Patients with cholestatic liver disease can experience cognitive impairments, but the underlying cellular mechanisms are poorly understood. This study used a rodent model and human neuronal cell cultures to explore the neurocognitive symptoms and potential therapies. The results showed that obeticholic acid, a second-line anti-cholestatic agent, could normalize memory function and reverse neuronal senescence.
AMERICAN JOURNAL OF PATHOLOGY
(2023)
Article
Gastroenterology & Hepatology
Francesca M. Trovato, Rabiya Zia, Florent Artru, Salma Mujib, Ellen Jerome, Anna Cavazza, Muireann Coen, Ian Wilson, Elaine Holmes, Phillip Morgan, Arjuna Singanayagam, Christine Bernsmeier, Salvatore Napoli, William Bernal, Julia Wendon, Rosa Miquel, Krishna Menon, Vishal C. Patel, John Smith, Stephen R. Atkinson, Evangelos Triantafyllou, Mark J. W. McPhail
Summary: A metabolome study found that ALF patients have dysregulated metabolism and immune responses, potentially mediated by the LPC-ATX-LPA pathway.
JOURNAL OF HEPATOLOGY
(2023)
Article
Immunology
Helene Ruffieux, Aimee L. Hanson, Samantha Lodge, Nathan G. Lawler, Luke Whiley, Nicola Gray, Tui H. Nolan, Laura Bergamaschi, Federica Mescia, Lorinda Turner, Aloka de Sa, Victoria S. Pelly, Prasanti Kotagiri, Nathalie R. Kingston, John Bradley, Elaine Holmes, Julien K. Wist, Jeremy A. Nicholson, Paul Lyons, Kenneth G. C. Smith, Sylvia Richardson, Glenn Bantug, Christoph Hess
Summary: We analyzed detailed longitudinal phenotyping data from 215 individuals with varying disease severities to understand the biology behind individual patient responses to SARS-CoV-2 infection. Our findings revealed distinct profiles of 'systemic recovery', including the progression and resolution of inflammatory, immune cell, metabolic, and clinical responses. We identified strong correlations between innate immune cell numbers, kynurenine metabolites, and lipid metabolites, which have implications for homeostasis restoration, risk of death, and long COVID.
Article
Cell Biology
Ruby White, Javier Sotillo, Maria Eugenia Ancarola, Anne Borup, Anders Toftegaard Boysen, Paul J. Brindley, Edit Buzas, Serena Cavallero, Sujittra Chaiyadet, Iain W. Chalmers, Marcela A. Cucher, Maude Dagenais, Chelsea N. Davis, Eileen Devaney, Maria A. Duque-Correa, Ramon Marc Eichenberger, Santiago Fontenla, Thomas A. Gasan, Cornelis H. Hokke, Maja Kosanovic, Marije E. Kuipers, Thewarach Laha, Alex Loukas, Rick M. Maizels, Antonio Marcilla, Hynek Mazanec, Russell M. Morphew, Kyriaki Neophytou, Linh Thuy Nguyen, Esther Nolte-'t Hoen, Michael Povelones, Mark W. Robinson, Alicia Rojas, Irma Schabussova, Hermelijn H. Smits, Sivapong Sungpradit, Lucienne Tritten, Bradley Whitehead, Amin Zakeri, Peter Nejsum, Amy H. Buck, Karl F. Hoffmann
Summary: Over the past decade, there has been a growing research interest in studying how extracellular vesicles (EVs) shape cross-species communication. In particular, helminths, which are parasitic worm species, have been found to manipulate the immune function and physiology of their hosts. This article highlights the challenges and best practices for studying helminth-derived EVs, complementing existing guidelines for mammalian EV research.
JOURNAL OF EXTRACELLULAR VESICLES
(2023)
Article
Gastroenterology & Hepatology
Munirah Alsaleh, Paiboon Sithithaworn, Narong Khuntikeo, Watcharin Loilome, Puangrat Yongvanit, Thomas Hughes, Thomas O'Connor, Ross H. Andrews, Christopher A. Wadsworth, Roger Williams, Larry Koomson, Isobel Jane Cox, Elaine Holmes, Simon D. Taylor-Robinson
Summary: This study used LC-MS profiling to analyze urinary metabolites in a Thai population and identified metabolic characteristics of Opisthorchis viverrini-induced cholangiocarcinoma (CCA). Utilizing a larger sample size, this study confirmed the diagnostic potential of certain metabolites.
JOURNAL OF CLINICAL AND EXPERIMENTAL HEPATOLOGY
(2023)
Article
Chemistry, Applied
Sung-Tong Chin, Gerhard Hoerlendsberger, Kok Wai Wong, Sirui Li, Sze How Bong, Luke Whiley, Julien Wist, Reika Masuda, Johan Greeff, Elaine Holmes, Jeremy K. Nicholson, Ruey Leng Loo
Summary: In this study, a one-step isopropanol method and a two-step methyl-tert-butyl ether method were compared for extracting lipid species in chicken egg yolks before LC-MS/MS analysis. The isopropanol method showed high reproducibility in extracting 937 lipid species from 20 major lipid subclasses. Machine learning techniques successfully differentiated cage, barn, and free-range eggs with high accuracy. The lipid profiles of these eggs were found to be characteristic and could be used for verifying the provenance of conventional chicken eggs.
Review
Agriculture, Multidisciplinary
David Felipe Garcia Mendez, Janeth Sanabria, Julien Wist, Elaine Holmes
Summary: Since the early 1980s, researchers have developed in vitro models of the human gastrointestinal system for studying the gut microbiome ecology. Simulating all features and conditions of the gastrointestinal system using a bioreactor is a significant challenge. Despite advances in simulating functionalities such as temperature and pH control, more work is needed to make the models closer to in vivo conditions. In this review, the impact of key operational parameters on gut microbial ecology is discussed, highlighting the advantages and limitations of current bioreactor systems.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Review
Immunology
Rory Doolan, Namitha Putananickal, Lucienne Tritten, Tiffany Bouchery
Summary: Soil-transmitted helminths affect approximately 1.5 billion people worldwide, but no human vaccine is currently available. The current strategy for elimination relies on preventive chemotherapy. Traditional vaccine approaches focusing on peptide antigens have had limited success, and mucosal and cellular-based vaccines may be a better alternative in fighting against helminth infection.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Gastroenterology & Hepatology
Laura Martinez-Gili, Alexandros Pechlivanis, Julie A. K. McDonald, Sofina Begum, Jonathan Badrock, Jessica K. Dyson, Rebecca Jones, Gideon Hirschfield, Stephen D. Ryder, Richard Sandford, Simon Rushbrook, Douglas Thorburn, Simon D. Taylor-Robinson, Mary M. E. Crossey, Julian R. Marchesi, George Mells, Elaine Holmes, David Jones
Summary: A study on patients with primary biliary cholangitis (PBC) showed that there is variation in response to ursodeoxycholic acid (UDCA) treatment. Responders exhibited high levels of secondary and tertiary bile acids, while non-responders had lower urinary bile acid levels and higher levels of 12-dehydrocholic acid. Additionally, non-responders showed lower gut microbiota diversity and lower capacity for bile acid deconjugation.
Article
Public, Environmental & Occupational Health
Sofina Begum, Samantha Lodge, Drew Hall, Blair Z. Johnson, Sze How Bong, Luke Whiley, Nicola Gray, Vanessa S. Fear, Mark W. Fear, Elaine Holmes, Fiona M. Wood, Jeremy K. Nicholson
Summary: Burn injury in children has long-term effects on metabolism and physiology, leading to increased morbidity and mortality. However, little is known about the metabolic trajectory and specific health outcomes.
FRONTIERS IN PUBLIC HEALTH
(2023)
Meeting Abstract
Peripheral Vascular Disease
Joram M. Posma, Isabel Garcia Perez, Ibrahim Karaman, He Gao, Queenie Chan, Martha Daviglus, Linda Van Horn, Elaine Holmes, Jeremy K. Nicholson, Paul Elliott
JOURNAL OF HYPERTENSION
(2023)
Retraction
Food Science & Technology
Isabel Garcia-Perez, Joram M. Posma, Edward S. Chambers, John C. Mathers, John Draper, Manfred Beckmann, Jeremy K. Nicholson, Elaine Holmes, Gary Frost
Article
Emergency Medicine
Eva Kierath, Monique Ryan, Elaine Holmes, Jeremy K. Nicholson, Mark W. Fear, Fiona M. Wood, Luke Whiley, Nicola Gray
Summary: Background: Non-severe paediatric burns can result in poor long-term health outcomes, even in cases with good acute burn-related outcomes. The mechanisms underlying this transition from non-severe burn to sustained negative long-term health impacts remain unknown. This study aimed to investigate the role of plasma lipidome changes in reflecting underlying changes in health status and linking to long-term health after burn trauma in children. Methods: The lipidome was analyzed in children who had previously experienced a non-severe burn, compared to non-injured controls. Results: The analysis revealed significantly higher concentrations of lysophosphatidylethanolamines and phosphatidylethanolamines, and significantly lower concentrations of myristic, palmitic, and palmitoleic acids in the plasma of burn-injured children compared to controls. Conclusion: Long-term changes in the lipid profile may provide insight into the mechanisms underlying poor long-term health after non-severe burn injury. Further investigation is needed to understand the relationship between long-term pathology and lipidomic changes for clinical intervention to reduce the long-term health burden post-burn trauma.
Article
Biophysics
Jose Ivan Serrano-Contreras, John C. Lindon, Gary Frost, Elaine Holmes, Jeremy K. Nicholson, Isabel Garcia-Perez
Summary: NMR spectroscopy is an important technique in metabolic profiling, but metabolite identification is often hindered by peak overlap. Recently developed pure shift NMR spectroscopy has the potential to simplify complex proton NMR spectra and aid metabolite identification. In this study, two complementary approaches to spectral simplification were evaluated, and both methods were found to improve resolution of resonances and enhance metabolite identification. These methods are easy to implement and the strong coupling artifacts contain latent connectivity information that can be used to enhance metabolite identification.
NMR IN BIOMEDICINE
(2023)