Data from a multi-year targeted proteomics study of a longitudinal birth cohort of type 1 diabetes

Authors: Lisa M. Bramer, Ernesto S. Nakayasu, Javier E. Flores, Jennifer E. Van Eyk, Michael J. MacCoss, Hemang M. Parikh, Thomas O. Metz, Bobbie-Jo M. Webb-Robertson

Source: Scientific Data, Vol 12, Iss 1, Pp 1-8 (2025)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2052-4463

Access URL: https://doaj.org/article/a1089d7936d945fba003a1bfb3f4901d

The human plasma lipidome response to exertional heat tolerance testing

Authors: Igor L. Estevao, Josh B. Kazman, Lisa M. Bramer, Carrie Nicora, Ming Qiang Ren, Nyamkhishig Sambuughin, Nathalie Munoz, Young-Mo Kim, Kent Bloodsworth, Maile Richert, Justin Teeguarden, Kristin Burnum-Johnson, Patricia A. Deuster, Ernesto S. Nakayasu, Gina Many

Source: Lipids in Health and Disease, Vol 23, Iss 1, Pp 1-12 (2024)

Subject Terms: Heat stress, Plasma lipidomics, Biomarkers, Heat tolerance testing, Physiological strain index, Nutritional diseases. Deficiency diseases, RC620-627

File Description: electronic resource

Relation: https://doaj.org/toc/1476-511X

Access URL: https://doaj.org/article/aad8a64ea9334f3eb1e4e7e5fb9a25ea

Protein carbamylation and proteomics: from artifacts to elucidation of biological functions

Authors: Youngki You, Gina Many, Ernesto S. Nakayasu

Source: Frontiers in Analytical Science, Vol 4 (2025)

Subject Terms: carbamylation, post-translational modification, proteomics, function, disease, Analytical chemistry, QD71-142

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/frans.2024.1512573/full; https://doaj.org/toc/2673-9283

Access URL: https://doaj.org/article/3d0c6d6eff614cdca6e7d89215d336c8

Regulation of bacterial stringent response by an evolutionarily conserved ribosomal protein L11 methylation

Authors: Hanna E. Walukiewicz, Yuliya Farris, Meagan C. Burnet, Sarah C. Feid, Youngki You, Hyeyoon Kim, Thomas Bank, David Christensen, Samuel H. Payne, Alan J. Wolfe, Christopher V. Rao, Ernesto S. Nakayasu

Source: mBio, Vol 15, Iss 10 (2024)

Subject Terms: lysine methylation, arginine methylation, phyloproteomics, post-translational modification, evolutionarily conservation, stringent response, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/1735fe52424741cba0a5cc8935e3d006

Regulation of β-cell death by ADP-ribosylhydrolase ARH3 via lipid signaling in insulitis

Authors: Soumyadeep Sarkar, Cailin Deiter, Jennifer E. Kyle, Michelle A. Guney, Dylan Sarbaugh, Ruichuan Yin, Xiangtang Li, Yi Cui, Mireia Ramos-Rodriguez, Carrie D. Nicora, Farooq Syed, Jonas Juan-Mateu, Charanya Muralidharan, Lorenzo Pasquali, Carmella Evans-Molina, Decio L. Eizirik, Bobbie-Jo M. Webb-Robertson, Kristin Burnum-Johnson, Galya Orr, Julia Laskin, Thomas O. Metz, Raghavendra G. Mirmira, Lori Sussel, Charles Ansong, Ernesto S. Nakayasu

Source: Cell Communication and Signaling, Vol 22, Iss 1, Pp 1-17 (2024)

Subject Terms: Medicine, Cytology, QH573-671

File Description: electronic resource

Relation: https://doaj.org/toc/1478-811X

Access URL: https://doaj.org/article/6b57b4f4064a4390ae8f0840effa40ac

A proteomic meta-analysis refinement of plasma extracellular vesicles

Authors: Milene C. Vallejo, Soumyadeep Sarkar, Emily C. Elliott, Hayden R. Henry, Samantha M. Powell, Ivo Diaz Ludovico, Youngki You, Fei Huang, Samuel H. Payne, Sasanka Ramanadham, Emily K. Sims, Thomas O. Metz, Raghavendra G. Mirmira, Ernesto S. Nakayasu

Source: Scientific Data, Vol 10, Iss 1, Pp 1-14 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2052-4463

Access URL: https://doaj.org/article/a7d72d2c446c44ff926f2c19bd0e61eb

Elucidating regulatory processes of intense physical activity by multi-omics analysis

Authors: Ernesto S. Nakayasu, Marina A. Gritsenko, Young-Mo Kim, Jennifer E. Kyle, Kelly G. Stratton, Carrie D. Nicora, Nathalie Munoz, Kathleen M. Navarro, Daniel Claborne, Yuqian Gao, Karl K. Weitz, Vanessa L. Paurus, Kent J. Bloodsworth, Kelsey A. Allen, Lisa M. Bramer, Fernando Montes, Kathleen A. Clark, Grant Tietje, Justin Teeguarden, Kristin E. Burnum-Johnson

Source: Military Medical Research, Vol 10, Iss 1, Pp 1-21 (2023)

Subject Terms: Multi-omics analysis, Intense exercise, Human performance, Biofluids, Metabolism, Immunity, Medicine (General), R5-920, Military Science

File Description: electronic resource

Relation: https://doaj.org/toc/2054-9369

Access URL: https://doaj.org/article/8d95b24435db469bbedea100bc80ed20

Comprehensive characterization of extracellular vesicles produced by environmental (Neff) and clinical (T4) strains of Acanthamoeba castellanii

Authors: Elisa Gonçalves Medeiros, Michele Ramos Valente, Leandro Honorato, Marina da Silva Ferreira, Susana Ruiz Mendoza, Diego de Souza Gonçalves, Lucas Martins Alcântara, Kamilla Xavier Gomes, Marcia Ribeiro Pinto, Ernesto S. Nakayasu, Geremy Clair, Isadora Filipaki Munhoz da Rocha, Flavia C. G. dos Reis, Marcio L. Rodrigues, Lysangela R. Alves, Leonardo Nimrichter, Arturo Casadevall, Allan Jefferson Guimarães

Source: mSystems, Vol 9, Iss 6 (2024)

Subject Terms: Acanthamoeba castellanii, extracelular vesicles, mPLEX, Neff, T4, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2379-5077

Access URL: https://doaj.org/article/6d88a4b62eab476089b31eb9bf95d733

Analysis of a macrophage carbamylated proteome reveals a function in post-translational modification crosstalk

Authors: Youngki You, Chia-Feng Tsai, Rishi Patel, Soumyadeep Sarkar, Geremy Clair, Mowei Zhou, Tao Liu, Thomas O. Metz, Chittaranjan Das, Ernesto S. Nakayasu

Source: Cell Communication and Signaling, Vol 21, Iss 1, Pp 1-12 (2023)

Subject Terms: Lysine carbamylation, Post-translational modification cross-talk, Multi-omics, Cell signaling, Post-translational modification, Medicine, Cytology, QH573-671

File Description: electronic resource

Relation: https://doaj.org/toc/1478-811X

Access URL: https://doaj.org/article/9726e3ddedfd445f827b3fc5a5232449

Decrease in multiple complement proteins associated with development of islet autoimmunity and type 1 diabetes

Authors: Bobbie-Jo M. Webb-Robertson, Ernesto S. Nakayasu, Fran Dong, Kathy C. Waugh, Javier E. Flores, Lisa M. Bramer, Athena A. Schepmoes, Yuqian Gao, Thomas L. Fillmore, Suna Onengut-Gumuscu, Ashley Frazer-Abel, Stephen S. Rich, V. Michael Holers, Thomas O. Metz, Marian J. Rewers

Source: iScience, Vol 27, Iss 2, Pp 108769- (2024)

Subject Terms: Immunology, Diabetology, Proteomics, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004223028468; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/acc4fc3a7d7e468abe5144f230ae4843

Rapid remodeling of the soil lipidome in response to a drying-rewetting event

Authors: Sneha P. Couvillion, Robert E. Danczak, Dan Naylor, Montana L. Smith, Kelly G. Stratton, Vanessa L. Paurus, Kent J. Bloodsworth, Yuliya Farris, Darren J. Schmidt, Rachel E. Richardson, Lisa M. Bramer, Sarah J. Fansler, Ernesto S. Nakayasu, Jason E. McDermott, Thomas O. Metz, Mary S. Lipton, Janet K. Jansson, Kirsten S. Hofmockel

Source: Microbiome, Vol 11, Iss 1, Pp 1-20 (2023)

Subject Terms: Soil, Lipidomics, Summer drought, Drying-rewetting, Metabolomics, Microbial ecology, QR100-130

File Description: electronic resource

Relation: https://doaj.org/toc/2049-2618

Access URL: https://doaj.org/article/911829cd983242c7847f34849a073ec4

Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections

Authors: Lisa M. Bramer, Robert D. Hontz, Amie J. Eisfeld, Amy C. Sims, Young-Mo Kim, Kelly G. Stratton, Carrie D. Nicora, Marina A. Gritsenko, Athena A. Schepmoes, Osamu Akasaka, Michiko Koga, Takeya Tsutsumi, Morio Nakamura, Ichiro Nakachi, Rie Baba, Hiroki Tateno, Shoji Suzuki, Hideaki Nakajima, Hideaki Kato, Kazunari Ishida, Makoto Ishii, Yoshifumi Uwamino, Keiko Mitamura, Vanessa L. Paurus, Ernesto S. Nakayasu, Isaac K. Attah, Andrew G. Letizia, Katrina M. Waters, Thomas O. Metz, Karen Corson, Yoshihiro Kawaoka, Vincent R. Gerbasi, Hiroshi Yotsuyanagi, Kiyoko Iwatsuki-Horimoto

Source: Heliyon, Vol 9, Iss 3, Pp e13795- (2023)

Subject Terms: CNDP1, Carnosinase, COVID-19, SARS-CoV-2, NETs, ROS, Science (General), Q1-390, Social sciences (General), H1-99

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2405844023010022; https://doaj.org/toc/2405-8440

Access URL: https://doaj.org/article/53d6cd1dfc184584aa9c45e5874a5dd0

Interrogating the role of the milk microbiome in mastitis in the multi-omics era

Authors: Sneha P. Couvillion, Katie E. Mostoller, Janet E. Williams, Ryan M. Pace, Izabel L. Stohel, Haley K. Peterson, Carrie D. Nicora, Ernesto S. Nakayasu, Bobbie-Jo M. Webb-Robertson, Mark A. McGuire, Michelle K. McGuire, Thomas O. Metz

Source: Frontiers in Microbiology, Vol 14 (2023)

Subject Terms: milk, multi-omics, mastitis, metagenomics, metatranscriptomics, metaproteomics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fmicb.2023.1105675/full; https://doaj.org/toc/1664-302X

Access URL: https://doaj.org/article/07303f6497a64c2285eaea06e9447874

EMC3 regulates mesenchymal cell survival via control of the mitotic spindle assembly

Authors: Xiaofang Tang, Wei Wei, John M. Snowball, Ernesto S. Nakayasu, Sheila M. Bell, Charles Ansong, Xinhua Lin, Jeffrey A. Whitsett

Source: iScience, Vol 26, Iss 1, Pp 105667- (2023)

Subject Terms: Biological sciences, Cell biology, Molecular biology, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004222019393; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/4ca76f27195f4bcba447222a1f873aa2

Extracellular vesicles in β cell biology: Role of lipids in vesicle biogenesis, cargo, and intercellular signaling

Authors: Rebecca S. Aguirre, Abhishek Kulkarni, Matthew W. Becker, Xiaoyong Lei, Soumyadeep Sarkar, Sasanka Ramanadham, Edward A. Phelps, Ernesto S. Nakayasu, Emily K. Sims, Raghavendra G. Mirmira

Source: Molecular Metabolism, Vol 63, Iss , Pp 101545- (2022)

Subject Terms: Islet, Diabetes, Extracellular vesicles, Lipids, Internal medicine, RC31-1245

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2212877822001144; https://doaj.org/toc/2212-8778

Access URL: https://doaj.org/article/678c7a50544c41d5811309036b14ae85

Transcriptional and translational landscape of Candida auris in response to caspofungin

Authors: Daniel Zamith-Miranda, Rafaela F. Amatuzzi, Isadora F. Munhoz da Rocha, Sharon T. Martins, Aline C.R. Lucena, Alexandre Z. Vieira, Gabriel Trentin, Fausto Almeida, Marcio L. Rodrigues, Ernesto S. Nakayasu, Joshua D. Nosanchuk, Lysangela R. Alves

Source: Computational and Structural Biotechnology Journal, Vol 19, Iss , Pp 5264-5277 (2021)

Subject Terms: Candida auris, Transcriptomics, Proteomics, Drug resistance, Stress response, Biotechnology, TP248.13-248.65

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2001037021003925; https://doaj.org/toc/2001-0370

Access URL: https://doaj.org/article/1a54674d336b4b93b4c3be1456c7a484

An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells

Authors: Maikel L. Colli, Mireia Ramos-Rodríguez, Ernesto S. Nakayasu, Maria I. Alvelos, Miguel Lopes, Jessica L. E. Hill, Jean-Valery Turatsinze, Alexandra Coomans de Brachène, Mark A. Russell, Helena Raurell-Vila, Angela Castela, Jonàs Juan-Mateu, Bobbie-Jo M. Webb-Robertson, Lars Krogvold, Knut Dahl-Jorgensen, Lorella Marselli, Piero Marchetti, Sarah J. Richardson, Noel G. Morgan, Thomas O. Metz, Lorenzo Pasquali, Décio L. Eizirik

Source: Nature Communications, Vol 11, Iss 1, Pp 1-17 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/7ba57ffc94954c2897c0cf413d87e02a

Regulation of Translation by Lysine Acetylation in Escherichia coli

Authors: Sarah C. Feid, Hanna E. Walukiewicz, Xiaoyi Wang, Ernesto S. Nakayasu, Christopher V. Rao, Alan J. Wolfe

Source: mBio, Vol 13, Iss 3 (2022)

Subject Terms: acetylation, metabolism, ribosomes, translation, polysomal profiling, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/d84ac070263343a3a09991c137ed9f64

A Histoplasma capsulatum Lipid Metabolic Map Identifies Antifungal Targets

Authors: Daniel Zamith-Miranda, Heino M. Heyman, Meagan C. Burnet, Sneha P. Couvillion, Xueyun Zheng, Nathalie Munoz, William C. Nelson, Jennifer E. Kyle, Erika M. Zink, Karl K. Weitz, Kent J. Bloodsworth, Geremy Clair, Jeremy D. Zucker, Jeremy R. Teuton, Samuel H. Payne, Young-Mo Kim, Morayma Reyes Gil, Erin S. Baker, Erin L. Bredeweg, Joshua D. Nosanchuk, Ernesto S. Nakayasu

Source: mBio, Vol 12, Iss 6 (2021)

Subject Terms: Histoplasma capsulatum, drug targets, lipid metabolism, lipidomics, metabolic map, proteomics, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/8eb7759b9e454abfae77ea9cf8f38aa8

The Legionella Effector SdjA Is a Bifunctional Enzyme That Distinctly Regulates Phosphoribosyl Ubiquitination

Authors: Lei Song, Yongchao Xie, Chuang Li, Lidong Wang, Chunlin He, Yong Zhang, Jingya Yuan, Jingjing Luo, Xi Liu, Yu Xiu, Hang Li, Marina Gritsenko, Ernesto S. Nakayasu, Yue Feng, Zhao-Qing Luo

Source: mBio, Vol 12, Iss 5 (2021)

Subject Terms: Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/d0411fb8407348c58ad85a0e40018ea1