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6 results on '"Jennifer E. Kyle"'

1. LipidOz enables automated elucidation of lipid carbon–carbon double bond positions from ozone-induced dissociation mass spectrometry data

Author

Dylan H. Ross, Joon-Yong Lee, Aivett Bilbao, Daniel J. Orton, Josie G. Eder, Meagan C. Burnet, Brooke L. Deatherage Kaiser, Jennifer E. Kyle, and Xueyun Zheng

Subjects
Materials Chemistry, Environmental Chemistry, General Chemistry, Biochemistry
Abstract

Lipids play essential roles in many biological processes and disease pathology, but unambiguous identification of lipids is complicated by the presence of multiple isomeric species differing by fatty acyl chain length, stereospecifically numbered (sn) position, and position/stereochemistry of double bonds. Conventional liquid chromatography-mass spectrometry (LC-MS/MS) analyses enable the determination of fatty acyl chain lengths (and in some cases sn position) and number of double bonds, but not carbon-carbon double bond positions. Ozone-induced dissociation (OzID) is a gas-phase oxidation reaction that produces characteristic fragments from lipids containing double bonds. OzID can be incorporated into ion mobility spectrometry (IMS)-MS instruments for the structural characterization of lipids, including additional isomer separation and confident assignment of double bond positions. The complexity and repetitive nature of OzID data analysis and lack of software tool support have limited the application of OzID for routine lipidomics studies. Here, we present an open-source Python tool, LipidOz, for the automated determination of lipid double bond positions from OzID-IMS-MS data, which employs a combination of traditional automation and deep learning approaches. Our results demonstrate the ability of LipidOz to robustly assign double bond positions for lipid standard mixtures and complex lipid extracts, enabling practical application of OzID for future lipidomics.

Published
2023
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2. Insights into pulmonary phosphate homeostasis and osteoclastogenesis emerge from the study of pulmonary alveolar microlithiasis

Author

Yasuaki Uehara, Yusuke Tanaka, Shuyang Zhao, Nikolaos M. Nikolaidis, Lori B. Pitstick, Huixing Wu, Jane J. Yu, Erik Zhang, Yoshihiro Hasegawa, John G. Noel, Jason C. Gardner, Elizabeth J. Kopras, Wendy D. Haffey, Kenneth D. Greis, Jinbang Guo, Jason C. Woods, Kathryn A. Wikenheiser-Brokamp, Jennifer E. Kyle, Charles Ansong, Steven L. Teitelbaum, Yoshikazu Inoue, Göksel Altinişik, Yan Xu, and Francis X. McCormack

Subjects
Lung Diseases, lung disease, Multidisciplinary, General Physics and Astronomy, General Chemistry, bone, respiratory disease, General Biochemistry, Genetics and Molecular Biology, lung, lipid, bone development, Osteogenesis, homeostasis, Humans, human, gene, protein
Abstract

Pulmonary alveolar microlithiasis is an autosomal recessive lung disease caused by a deficiency in the pulmonary epithelial Npt2b sodium-phosphate co-transporter that results in accumulation of phosphate and formation of hydroxyapatite microliths in the alveolar space. The single cell transcriptomic analysis of a pulmonary alveolar microlithiasis lung explant showing a robust osteoclast gene signature in alveolar monocytes and the finding that calcium phosphate microliths contain a rich protein and lipid matrix that includes bone resorbing osteoclast enzymes and other proteins suggested a role for osteoclast-like cells in the host response to microliths. While investigating the mechanisms of microlith clearance, we found that Npt2b modulates pulmonary phosphate homeostasis through effects on alternative phosphate transporter activity and alveolar osteoprotegerin, and that microliths induce osteoclast formation and activation in a receptor activator of nuclear factor-κB ligand and dietary phosphate dependent manner. This work reveals that Npt2b and pulmonary osteoclast-like cells play key roles in pulmonary homeostasis and suggest potential new therapeutic targets for the treatment of lung disease.

Published
2023
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3. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

Author

Jingqui Dai, Alexey V. Melnik, Jenan J. Kharbush, Kenji L. Kurita, Robert A. Keyzers, Katrina M. Waters, Mario Sandoval-Calderón, Ajit Jadhav, Clifford A. Kapono, Charles B. Larson, Evgenia Glukhov, Danielle VanLeer, Daniel P. Demarque, Lars Jelsbak, Yi Zeng, Eve A. Granatosky, Kit Pogliano, Maryam Elfeki, Marcelino Gutiérrez, Jeramie D. Watrous, Katherine R. Duncan, Laura M. Sanchez, Jeremy Carver, Brendan M. Duggan, Thomas O. Metz, Julia A. Vorholt, Pep Charusanti, Paul Shinn, Nuno Bandeira, Pavel A. Pevzner, Amy C. Sims, Nobuhiro Koyama, David Gonzalez, Xueting Liu, Denise Brentan Silva, Venkat R. Macherla, Pieter C. Dorrestein, Andrew R. Johnson, Jörn Piel, Michael J. Meehan, Delphine Parrot, Jehad Almaliti, Don D. Nguyen, Louis-Félix Nothias, Wenyuan Shi, Max Crüsemann, Cristopher A. Boya P., Philip G. Williams, Erin E. Carlson, Ronnie G. Gavilan, Yao Peng, Roland D. Kersten, Jennifer E. Kyle, Bertrand Aigle, Yu-Liang Yang, Mingxun Wang, Amina Bouslimani, Lixin Zhang, Ram P. Neupane, Chih-Chuang Liaw, Tyler Peryea, Eric J. N. Helfrich, Kristian Fog Nielsen, Hans-Ulrich Humpf, Robert A. Quinn, Rolf Müller, Paul R. Jensen, Hailey Houson, Eduardo Esquenazi, Kathleen Dorrestein, Vanessa V. Phelan, Bernhard O. Palsson, Lisa Vuong, Cheng-Chih Hsu, Sophie Tomasi, Trent R. Northen, Laura A. Pace, Marc Litaudon, Samantha J. Mascuch, Chen Zhang, Maria Maansson, Ashley M. Sidebottom, Vinayak Agarwal, Ricardo Pianta Rodrigues da Silva, Ellis C. O’Neill, Tal Luzzatto-Knaan, Florian Ryffel, Oliver B. Vining, Andrés M. C. Rodríguez, Andreas Klitgaard, Enora Briand, Brian T. Murphy, Neha Garg, Norberto Peporine Lopes, Ralph S. Baric, William H. Gerwick, Pierre-Marie Allard, Daniel Torres-Mendoza, Jeffrey S. McLean, Stefan Jenkins, Lena Gerwick, Theodore Alexandrov, Roger G. Linington, Egle Pociute, Christian Sohlenkamp, Joshua R. Gurr, Matthew F. Traxler, Wei-Ting Liu, Rob Knight, Anne Lamsa, Anna Edlund, Bradley S. Moore, Prasad Phapale, Hosein Mohimani, Karin Kleigrewe, Charlotte Frydenlund Michelsen, Lucas Miranda Marques, Niclas Engene, Jean-Luc Wolfender, Thomas Hoffman, Rachel J. Dutton, Dac-Trung Nguyen, Paul D. Boudreau, Dimitrios J. Floros, Kerry L. McPhail, Carla Porto, Brian E. Sedio, Computer Science and Engineering, University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC), Collaborative Mass Spectrometry Innovation Center, KDDI R&D Laboratories Inc. [Saitama], Shandong University of Science and Technology, Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Dynamique des Génomes et Adaptation Microbienne (DynAMic), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Metacohorts Consortium, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Unité mixte de physique CNRS/Thales (UMPhy CNRS/THALES), THALES [France]-Centre National de la Recherche Scientifique (CNRS), Department of Civil Engineering, University of Siegen, Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut de recherches sur la catalyse et l'environnement de Lyon (IRCELYON), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique de l'ENS Lyon (Phys-ENS), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Skaggs School of Pharmacy and Pharmaceutical Sciences [San Diego], CNPq, Conselho Nacional de Desenvolvimento Científico e Tecnológico, 2014/01884-2, FAPESP, São Paulo Research Foundation, DAAD, German Academic Exchange Service, K12 GM068524, NIH, National Institutes of Health, RCSA, Research Corporation for Science Advancement, K99DE024543, NIH, National Institutes of Health, PQ 480 306385/2011-2, CNPq, Conselho Nacional de Desenvolvimento Científico e Tecnológico, T32 GM075762, NIH, National Institutes of Health, U01TW006634-06, NIH, National Institutes of Health, U19-AI106772, NIAID, National Institute of Allergy and Infectious Diseases, U19-AI106772, NIH, National Institutes of Health, DFG, Deutsche Forschungsgemeinschaft, 2013/16496-5, FAPESP, São Paulo Research Foundation, 2014/50265-3, FAPESP, São Paulo Research Foundation, 1F32GM089044, NIH, National Institutes of Health, 1R01DE023810-01, NIH, National Institutes of Health, 1R01GM095373, NIH, National Institutes of Health, 200020-146200, FNS, French Norwegian Foundation, 2012/18031-7, FAPESP, São Paulo Research Foundation, NIAID, National Institute of Allergy and Infectious Diseases, K01 GM103809, NIH, National Institutes of Health, 31125002, NSFC, National Natural Science Foundation of China, 5R21AI085540, NIH, National Institutes of Health, 81102369, NSFC, National Natural Science Foundation of China, CN-12-552, CONACYT, Consejo Nacional de Ciencia y Tecnología, DEB 1010816, NSF, National Science Foundation, Wolfender, Jean-Luc, University of California-University of California, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Lorraine (UL)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), University of Campinas [Campinas] (UNICAMP), Centre National de la Recherche Scientifique (CNRS)-THALES, Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon, Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Chimie de Rennes-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Unité mixte de physique CNRS/Thalès (UMP CNRS/THALES), THALES-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS),Saarland Universitätscampus E8.1, 66123 Saarbrücken, Germany.

Subjects
0301 basic medicine, Internationality, Computer science, Information Dissemination/methods, Information Storage and Retrieval, Bioinformatics, Mass spectrometry data, 01 natural sciences, Applied Microbiology and Biotechnology, Knowledge base, Data driven, Ms libraries, Data Curation, Data Curation/methods, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, ddc:615, Natural products, 3. Good health, Identification (information), Molecular networking, Molecular Medicine, Knowledge based systems, Raw data, Biotechnology, Biological Products/chemistry/classification, Biomedical Engineering, Chemical, Bioengineering, Mass spectrometry, Article, Databases, Open Access, 03 medical and health sciences, Knowledge-based systems, Computational platforms and environments, TA164, MEDICINA, Tandem mass, High through-put characterization, Mass Spectrometry/statistics & numerical data, Biological Products, Data curation, Information Dissemination, Information Storage and Retrieval/methods, Spectrometry, 010405 organic chemistry, business.industry, Data science, 0104 chemical sciences, Data sharing, 030104 developmental biology, ZA, Database Management Systems, business, Databases, Chemical
Abstract

International audience; The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.

Published
2016
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4. Cell type-resolved human lung lipidome reveals cellular cooperation in lung function

Author

Charles Ansong, Yan Xu, Jennifer E. Kyle, Timothy P. Bushnell, John M. Ashton, Kent J. Bloodsworth, Gail H. Deutsch, Jacquelyn Lillis, Thomas J. Mariani, James P. Carson, Gautam Bandyopadhyay, Matthew Cochran, Gloria S. Pryhuber, Erika M. Zink, Jeffrey A. Whitsett, Jason R. Myers, Ravi S. Misra, Geremy Clair, Erin S. Baker, Yina Du, and Anil K. Shukla

Subjects
Male, 0301 basic medicine, Cell type, Cell, lcsh:Medicine, Computational biology, Biology, Proteomics, Article, Human lung, 03 medical and health sciences, Lipidomics, medicine, Humans, lcsh:Science, Databases, Protein, Lung, Multidisciplinary, 030102 biochemistry & molecular biology, lcsh:R, Lipidome, Lipid Metabolism, 030104 developmental biology, medicine.anatomical_structure, Proteome, lcsh:Q, Female, Function (biology)
Abstract

Cell type-resolved proteome analyses of the brain, heart and liver have been reported, however a similar effort on the lipidome is currently lacking. Here we applied liquid chromatography-tandem mass spectrometry to characterize the lipidome of major lung cell types isolated from human donors, representing the first lipidome map of any organ. We coupled this with cell type-resolved proteomics of the same samples (available at Lungmap.net). Complementary proteomics analyses substantiated the functional identity of the isolated cells. Lipidomics analyses showed significant variations in the lipidome across major human lung cell types, with differences most evident at the subclass and intra-subclass (i.e. total carbon length of the fatty acid chains) level. Further, lipidomic signatures revealed an overarching posture of high cellular cooperation within the human lung to support critical functions. Our complementary cell type-resolved lipid and protein datasets serve as a rich resource for analyses of human lung function.

Published
2018
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5. Viruses in granitic groundwater from 69 to 450 m depth of the Äspö hard rock laboratory, Sweden

Author

Jennifer E. Kyle, Karsten Pedersen, F. Grant Ferris, and Hallgerd S C Eydal

Subjects
Sweden, Veterinary medicine, biology, viruses, Microorganism, Mineralogy, Silicon Dioxide, musculoskeletal system, Positive correlation, biology.organism_classification, Microbiology, Bacteriophage, Lytic cycle, Viruses, Prokaryotic cells, Water Microbiology, Ecosystem, Ecology, Evolution, Behavior and Systematics, Groundwater
Abstract

The objectives of this study were to determine if viruses exist in deep granitic groundwater and to analyse their abundance and morphological diversity. Fluorescent microscopy counts on 10 groundwater samples ranging from 69 to 450 m depth were in the range of 10(4)-10(6) TNC ml(-1) (TNC, total number of prokaryotic cells) and 10(5)-10(7) VLP ml(-1) (VLP, virus-like particles). A good positive correlation of VLP with TNC (r=0.91, P=0.0003) was found with an average VLP/TNC ratio of 12. Transmission electron microscopy revealed four distinct bacteriophage groups (polyhedral, tailed, filamentous and pleomorphic) with at least seven phage families of which some are known to be lytic. Our results suggest the presence of viruses in deep granitic groundwater up to 450 m depth. If they are active and lytic, they will constitute an important group of predators that might control the numbers of microorganisms in the analysed groundwater.

Published
2008
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6. Role of smectite in siliceous-sinter formation and microbial-texture preservation: Octopus Spring, Yellowstone National Park, Wyoming, USA

Author

Jennifer E. Kyle and Paul A. Schroeder

Subjects
Pseudobrookite, Opal, Nitrogen, Geochemistry, Soil Science, Mineralogy, Yellowstone National Park, engineering.material, Feldspar, chemistry.chemical_compound, Geochemistry and Petrology, Earth and Planetary Sciences (miscellaneous), Montmorillonite, Water Science and Technology, Calcite, Geyserite, Hematite, chemistry, visual_art, visual_art.visual_art_medium, engineering, Biosignatures, Sedimentary rock, Siliceous Sinter, Clay minerals, Geology, Ilmenite
Abstract

A siliceous sinter collected from Octopus Spring in Yellowstone National Park, USA contains an occluded volcanic rock fragment that has undergone alteration. The sinter piece beyond the fragment is mostly dominated by opal-A with trace amounts of bacterial cells, calcite and detrital quartz. Within the altered rock region, the mineral assemblage is dominated by dioctahedral smectite and quartz with trace amounts of pseudobrookite, ilmenite, rutile and hematite. Onset of opal-CT formation was only found in the outer spicular region of the sinter, which is unexpected given that this outer part represents newest growth. A reaction mechanism is proposed whereby the alteration of feldspar to smectitic clay locally produces excess silica, and alkali metal, and raises pH. As the clay mineral forms, it sequesters ions from pore fluids thereby inhibiting the opal-A phase change to more ordered opal-CT. Ions such as Mg are known to promote the opal-A to opal-CT reaction. Smectite formation therefore may assist microbial-texture preservation processes as excess silica produced increases the rate at which primary opal-A is formed The altered zone also retains the greatest amount of fixed C and fixed N (operationally defined as C and N retained upon combustion at 450°C). The fixed N probably represents ammonium trapped in the exchangeable interlayer site of the smectite. This fixed N may serve as a potential biological signature of microbial activity, in ancient rocks formed in similar environments. Copyright © 2007, The Clay Minerals Society.

Published
2007
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