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3. Mitochondrial hyperfusion via metabolic sensing of regulatory amino acids

Author

Abdullah, Mahmud O., Zeng, Run X., Margerum, Chelsea L., Papadopoli, David, Monnin, Cian, Punter, Kaylee B., Chu, Charles, Al-Rofaidi, Mohammad, Al-Tannak, Naser F., Berardi, Domenica, Rattray, Zahra, Rattray, Nicholas J.W., Abraham, Sheela A., Eskelinen, Eeva-Liisa, Watson, David G., Avizonis, Daina, Topisirovic, Ivan, and Chan, Edmond Y.W.

Published
2022
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4. Urinary Paraben Concentrations and Associations with the Periconceptional Urinary Metabolome: Untargeted and Targeted Metabolomics Analyses of Participants from the Early Pregnancy Study

Author

Vollmar, Ana K. Rosen, Rattray, Nicholas J.W., Cai, Yuping, Jain, Abhishek, Yan, Hong, Deziel, Nicole C., Calafat, Antonia M., Wilcox, Allen J., Jukic, Anne Marie Z., and Johnson, Caroline H.

Subjects
Physiological aspects, Chemical properties, Risk factors, Health aspects, Female infertility -- Risk factors, Endocrine disruptors -- Health aspects -- Physiological aspects, Parabens -- Health aspects -- Physiological aspects, Personal care products -- Chemical properties -- Health aspects, Pregnancy -- Physiological aspects -- Health aspects, Hygiene products -- Chemical properties -- Health aspects, Health and beauty aids -- Chemical properties -- Health aspects, Infertility, Female -- Risk factors
Abstract

Introduction Parabens are common antimicrobial preservatives used in personal care products, cosmetics, foods, and medications since the 1930s. (1-4) Exposure typically occurs through ingestion of foods and medications and dermal [...], Background: Parabens, found in everyday items from personal care products to foods, are chemicals with endocrine- disrupting activity, which has been shown to influence reproductive function. OBJECTIVES: This study investigated whether urinary concentrations of methylparaben, propylparaben, or butylparaben were associated with the urinary metabolome during the periconceptional period, a critical window for female reproductive function. Changes to the periconceptional urinary metabolome could provide insights into the mechanisms by which parabens could impact fertility. Methods: Urinary paraben concentrations were measured in paired pre- and postconception urine samples from 42 participants in the Early Pregnancy Study, a prospective cohort of 221 women attempting to conceive. We performed untargeted and targeted metabolomics analyses using ultrahigh-performance liquid chromatography quadrupole time-of-flight mass spectrometry. We used principal component analysis, orthogonal partial least-squares discriminant analysis, and permutation testing, coupled with univariate statistical analyses, to find metabolites associated with paraben concentration at the two time points. Potential confounders were identified with a directed acyclic graph and used to adjust results with multivariable linear regression. Metabolites were identified using fragmentation data. Results: Seven metabolites were associated with paraben concentration (variable importance to projection score >1, false discovery rate-corrected q-value Discussion: This study identified novel relationships between urinary paraben concentrations and diet-related metabolites but not with metabolites on endocrine-disrupting pathways, as hypothesized. It demonstrates the feasibility of integrating untargeted metabolomics data with environmental exposure information and epidemiological adjustment for confounders. The findings underscore a potentially important connection between diet and paraben exposure, with applications to nutritional epidemiology and dietary exposure assessment. https://doi.org/10.1289/EHP12125

Published
2023
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5. OMICmAge: An integrative multi-omics approach to quantify biological age with electronic medical records

Author

Chen, Qingwen, primary, Dwaraka, Varun B., additional, Carreras-Gallo, Natàlia, additional, Mendez, Kevin, additional, Chen, Yulu, additional, Begum, Sofina, additional, Kachroo, Priyadarshini, additional, Prince, Nicole, additional, Went, Hannah, additional, Mendez, Tavis, additional, Lin, Aaron, additional, Turner, Logan, additional, Moqri, Mahdi, additional, Chu, Su H., additional, Kelly, Rachel S., additional, Weiss, Scott T., additional, Rattray, Nicholas J.W, additional, Gladyshev, Vadim N., additional, Karlson, Elizabeth, additional, Wheelock, Craig, additional, Mathé, Ewy A., additional, Dahlin, Amber, additional, McGeachie, Michae J., additional, Smith, Ryan, additional, and Lasky-Su, Jessica A., additional

Published
2023
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6. Urinary Paraben Concentrations and Associations with the Periconceptional Urinary Metabolome: Untargeted and Targeted Metabolomics Analyses of Participants from the Early Pregnancy Study

Author

Rosen Vollmar, Ana K., primary, Rattray, Nicholas J.W., additional, Cai, Yuping, additional, Jain, Abhishek, additional, Yan, Hong, additional, Deziel, Nicole C., additional, Calafat, Antonia M., additional, Wilcox, Allen J., additional, Jukic, Anne Marie Z., additional, and Johnson, Caroline H., additional

Published
2023
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12. Supplemental Material - Development of an Accessible Gene Expression Bioinformatics Pipeline to Study Driver Mutations of Colorectal Cancer

Author

van den Driest, Lisa, Johnson, Caroline H., Rattray, Nicholas J.W., and Rattray, Zahra

Subjects
FOS: Clinical medicine, 111599 Pharmacology and Pharmaceutical Sciences not elsewhere classified
Abstract

Supplemental Material for Development of an Accessible Gene Expression Bioinformatics Pipeline to Study Driver Mutations of Colorectal Cancer by Lisa van den Driest, Caroline H. Johnson, Nicholas J.W. Rattray and Zahra Rattray in Alternatives to Laboratory Animals

Published
2022
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13. ENT2 facilitates brain endothelial cell penetration and blood-brain barrier transport by a tumor-targeting anti-DNA autoantibody

Author

Rattray, Zahra, primary, Deng, Gang, additional, Zhang, Shenqi, additional, Shirali, Anupama, additional, May, Christopher K., additional, Chen, Xiaoyong, additional, Cuffari, Benedette J., additional, Liu, Jun, additional, Zou, Pan, additional, Rattray, Nicholas J.W., additional, Johnson, Caroline H., additional, Dubljevic, Valentina, additional, Campbell, James A., additional, Huttner, Anita, additional, Baehring, Joachim M., additional, Zhou, Jiangbing, additional, and Hansen, James E., additional

Published
2021
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14. YIV-906 Potentiated anti-PD1 Action Against Hepatocellular Carcinoma by Enhancing Adaptive and Innate Immunity in the Tumor Microenvironment.

Author

Yang, Xiaochen, primary, lam, wing, additional, Jiang, Zaoli, additional, Guan, Fulan, additional, Han, Xue, additional, Hu, Rong, additional, Cai, Wei, additional, Cheng, William, additional, Liu, Shwu-Huey, additional, Cheng, Peikwen, additional, Cai, Yuping, additional, Rattray, Nicholas J.W., additional, Johnson, Caroline H., additional, Chen, Lieping, additional, and Cheng, Yung-Chi, additional

Published
2021
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15. Novel insights into the mode of action of 1,4-dioxane using a systems screening approach

Author

Charkoftaki, Georgia, primary, Golla, Jaya Prakash, additional, Santos-Neto, Alvaro, additional, Orlicky, David J., additional, Garcia-Milian, Rolando, additional, Chen, Ying, additional, Rattray, Nicholas J.W., additional, Cai, Yuping, additional, Wang, Yewei, additional, Shern, Colin T, additional, Mironova, Varvara, additional, Wang, Yensheng, additional, Johnson, Caroline H., additional, Thompson, David C., additional, and Vasiliou, Vasilis, additional

Published
2020
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16. Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli

Author

Jervis, Adrian J., Carbonell, Pablo, Vinaixa, Maria, Dunstan, Mark S., Hollywood, Katherine A., Robinson, Christopher J., Rattray, Nicholas J.W., Yan, Cunyu, Swainston, Neil, Currin, Andrew, Sung, Rehana, Toogood, Helen, Taylor, Sandra, Faulon, Jean Loup, Breitling, Rainer, Takano, Eriko, Scrutton, Nigel S., University of Manchester [Manchester], Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde [Glasgow], MICrobiologie de l'ALImentation au Service de la Santé (MICALIS), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, UK Biotechnology and Biological Sciences Research Council (BBSRC) [BB/M017702/1, BB/L027593/1, BB/M000354/1, BB/J015512/1], French National Research Agency [ANR-15-CE1-0008], Royal Society Wolfson Merit Award, and Engineering and Physical Sciences Research Council (EPSRC) [EP/J020192/1]

Subjects
[SDV]Life Sciences [q-bio], Biomedical Engineering, ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology, Biochemistry, Genetics and Molecular Biology (miscellaneous), machine learning, terpenoids, Manchester Institute of Biotechnology, TA164, ribosome binding site, translational tuning, Escherichia coli, synthetic biology, pathway engineering, Ribosomes
Abstract

International audience; The field of synthetic biology aims to make the design of biological systems predictable, shrinking the huge design space to practical numbers for testing. When designing microbial cell factories, most optimization efforts have focused on enzyme and strain selection/engineering, pathway regulation, and process development. In silico tools for the predictive design of bacterial ribosome binding sites (RBSs) and RBS libraries now allow translational tuning of biochemical pathways; however, methods for predicting optimal RBS combinations in multigene pathways are desirable. Here we present the implementation of machine learning algorithms to model the RBS sequence-phenotype relationship from representative subsets of large combinatorial RBS libraries allowing the accurate prediction of optimal high-producers. Applied to a recombinant monoterpenoid production pathway in Escherichia coli, our approach was able to boost production titers by over 60% when screening under 3% of a library. To facilitate library screening, a multiwell plate fermentation procedure was developed, allowing increased screening throughput with sufficient resolution to discriminate between high and low producers. High producers from one library did not translate during scale-up, but the reduced screening requirements allowed rapid rescreening at the larger scale. This methodology is potentially compatible with any biochemical pathway and provides a powerful tool toward predictive design of bacterial production chassis.

Published
2019
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19. TD/GC–MS analysis of volatile markers emitted from mono- and co-cultures of Enterobacter cloacae and Pseudomonas aeruginosa in artificial sputum

Author

Lawal, Oluwasola, Knobel, Hugo, Weda, Hans, Nijsen, Tamara M.E., Goodacre, Royston, Fowler, Stephen J., Ahmed, Waqar M., Artigas, Antonio, Bannard-Smith, J., Bos, Lieuwe D.J., Camprubi, Marta, Coelho, Luis, Dark, Paul, Davie, Alan, Diaz, Emili, Goma, Gemma, Felton, Timothy, Leopold, Jan Hendrik, van Oort, Pouline M.P., Povoa, Pedro, Portsmouth, Craig, Rattray, Nicholas J.W., Rijnders, Guus, Schultz, Marcus J., Steenwelle, Ruud, Sterk, Peter J., Valles, Jordi, Verhoeckx, Fred, Vink, Anton, White, Iain R., Winters, Tineke, Zakharkina, Tetyana, Inorganic Materials Science, Intensive Care Medicine, ACS - Heart failure & arrhythmias, AII - Infectious diseases, APH - Methodology, Amsterdam Gastroenterology Endocrinology Metabolism, Graduate School, Pulmonology, ACS - Diabetes & metabolism, ACS - Pulmonary hypertension & thrombosis, and ACS - Microcirculation

Subjects
0301 basic medicine, Microbiological culture, Endocrinology, Diabetes and Metabolism, 030106 microbiology, Clinical Biochemistry, UT-Hybrid-D, medicine.disease_cause, Biochemistry, Gas Chromatography-Mass Spectrometry, RS, Microbiology, 03 medical and health sciences, Manchester Institute of Biotechnology, Enterobacter cloacae, medicine, Volatile organic compounds, Axenic, biology, Bacteria, Pseudomonas aeruginosa, Chemistry, biology.organism_classification, Antimicrobial, ResearchInstitutes_Networks_Beacons/manchester_institute_of_biotechnology, 3. Good health, 030104 developmental biology, Sputum, Gas chromatography–mass spectrometry, medicine.symptom, Infection
Abstract

Introduction: Infections such as ventilator-associated pneumonia (VAP) can be caused by one or more pathogens. Current methods for identifying these pathogenic microbes often require invasive sampling, and can be time consuming, due to the requirement for prolonged cultural enrichment along with selective and differential plating steps. This results in delays in diagnosis which in such critically ill patients can have potentially life-threatening consequences. Therefore, a non-invasive and timely diagnostic method is required. Detection of microbial volatile organic compounds (VOCs) in exhaled breath is proposed as an alternative method for identifying these pathogens and may distinguish between mono- and poly-microbial infections. Objectives: To investigate volatile metabolites that discriminate between bacterial mono- and co-cultures. Methods: VAP-associated pathogens Enterobacter cloacae and Pseudomonas aeruginosa were cultured individually and together in artificial sputum medium for 24 h and their headspace was analysed for potential discriminatory VOCs by thermal desorption gas chromatography–mass spectrometry. Results: Of the 70 VOCs putatively identified, 23 were found to significantly increase during bacterial culture (i.e. likely to be released during metabolism) and 13 decreased (i.e. likely consumed during metabolism). The other VOCs showed no transformation (similar concentrations observed as in the medium). Bacteria-specific VOCs including 2-methyl-1-propanol, 2-phenylethanol, and 3-methyl-1-butanol were observed in the headspace of axenic cultures of E. cloacae, and methyl 2-ethylhexanoate in the headspace of P. aeruginosa cultures which is novel to this investigation. Previously reported VOCs 1-undecene and pyrrole were also detected. The metabolites 2-methylbutyl acetate and methyl 2-methylbutyrate, which are reported to exhibit antimicrobial activity, were elevated in co-culture only. Conclusion: The observed VOCs were able to differentiate axenic and co-cultures. Validation of these markers in exhaled breath specimens could prove useful for timely pathogen identification and infection type diagnosis.

Published
2018
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20. Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells

Author

Warth, Benedikt, primary, Palermo, Amelia, additional, Rattray, Nicholas J.W., additional, Lee, Nathan V., additional, Zhu, Zhou, additional, Hoang, Linh T., additional, Cai, Yuping, additional, Mazurek, Anthony, additional, Dann, Stephen, additional, VanArsdale, Todd, additional, Fantin, Valeria R., additional, Shields, David, additional, Siuzdak, Gary, additional, and Johnson, Caroline H., additional

Published
2019
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21. Palbociclib and fulvestrant act in synergy to modulate central carbon metabolism in breast cancer cells

Author

Warth, Benedikt, primary, Palermo, Amelia, additional, Rattray, Nicholas J.W., additional, Lee, Nathan V, additional, Zhu, Zhou, additional, Hoang, Linh T., additional, Mazurek, Anthony, additional, Dann, Stephen, additional, VanArsdale, Todd, additional, Fantin, Valeria, additional, Shields, David, additional, Siuzdak, Gary, additional, and Johnson, Caroline H., additional

Published
2018
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22. SYNBIOCHEM–a SynBio foundry for the biosynthesis and sustainable production of fine and speciality chemicals

Author

Carbonell, Pablo, primary, Currin, Andrew, additional, Dunstan, Mark, additional, Fellows, Donal, additional, Jervis, Adrian, additional, Rattray, Nicholas J.W., additional, Robinson, Christopher J., additional, Swainston, Neil, additional, Vinaixa, Maria, additional, Williams, Alan, additional, Yan, Cunyu, additional, Barran, Perdita, additional, Breitling, Rainer, additional, Chen, George Guo-Qiang, additional, Faulon, Jean-Loup, additional, Goble, Carole, additional, Goodacre, Royston, additional, Kell, Douglas B., additional, Feuvre, Rosalind Le, additional, Micklefield, Jason, additional, Scrutton, Nigel S., additional, Shapira, Philip, additional, Takano, Eriko, additional, and Turner, Nicholas J., additional

Published
2016
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23. Citizen scientists can aid diagnostics

Author

Rattray, Nicholas J.W.

Abstract

Citizen scientists are an underrated source of observations on medical conditions. They frequently offer researchers a head start in the hunt for biomarkers (see, for example, the tentative identification of [...]

Published
2015

24. Exhaled breath VOCs are associated with nocturnal wakening in asthmatic children

Author

Wang, Yuanyue, primary, Hashimoto, Simone, additional, Brinkman, Paul, additional, Vink, Teunis J., additional, Weda, Hans, additional, Knobel, Hugo, additional, Nijsen, Tamara, additional, Rattray, Nicholas J.W., additional, Montuschi, Paolo, additional, Santonico, Marco, additional, Pennazza, Giorgio, additional, D'Amico, Arnaldo, additional, Fleming, Louise, additional, Sousa, Ana R., additional, Murray, Clare, additional, Corfield, Julie, additional, Bisgaard, Hans, additional, Bush, Andrew, additional, Van Aalderen, Wim, additional, Chung, Fan, additional, Shaw, Dominic, additional, Pandis, Ioannis, additional, Bansal, Aruna, additional, Roberts, Graham, additional, Sterk, Peter J., additional, and Fowler, Stephen, additional

Published
2015
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