Search

Your search keyword '"Yates, John R."' showing total 256 results
Start Over Author "Yates, John R." Journal journal of proteome research
256 results on '"Yates, John R."'

1. Venom Composition in a Phenotypically Variable Pit Viper (Trimeresurus insularis) across the Lesser Sunda Archipelago

Author

Jones, Brenda Kathryn, Saviola, Anthony J, Reilly, Sean B, Stubbs, Alexander L, Arida, Evy, Iskandar, Djoko T, McGuire, Jimmy A, Yates, John R, and Mackessy, Stephen P

Subjects
Animals, Antivenins, Conserved Sequence, Crotalid Venoms, Electrophoresis, Polyacrylamide Gel, Fibrinogen, Gelatin, Gene Expression, Indonesia, Islands, L-Amino Acid Oxidase, Lectins, C-Type, Membrane Glycoproteins, Metalloproteases, Phenotype, Phospholipases A2, Phosphoric Diester Hydrolases, Phylogeny, Proteolysis, Serine Proteases, Trimeresurus, Asia, enzyme, evolution, island, proteomics, toxin, venomics, Chemical Sciences, Biological Sciences, Biochemistry & Molecular Biology
Abstract

The genus Trimeresurus comprises a group of venomous pitvipers endemic to Southeast Asia and the Pacific Islands. Of these, Trimeresurus insularis, the White-lipped Island Pitviper, is a nocturnal, arboreal species that occurs on nearly every major island of the Lesser Sunda archipelago. In the current study, venom phenotypic characteristics of T. insularis sampled from eight Lesser Sunda Islands (Flores, Lembata, Lombok, Pantar, Sumba, Sumbawa, Timor, and Wetar) were evaluated via SDS-PAGE, enzymatic activity assays, fibrinogenolytic assays, gelatin zymography, and RP-HPLC, and the Sumbawa sample was characterized by venomic analysis. For additional comparative analyses, venoms were also examined from several species in the Trimeresurus complex, including T. borneensis, T. gramineus, T. puniceus, T. purpureomaculatus, T. stejnegeri, and Protobothrops flavoviridis. Despite the geographical isolation, T. insularis venoms from all eight islands demonstrated remarkable similarities in gel electrophoretic profiles and RP-HPLC patterns, and all populations had protein bands in the mass ranges of phosphodiesterases (PDE), l-amino acid oxidases (LAAO), P-III snake venom metalloproteinases (SVMP), serine proteases, cysteine-rich secretory proteins (CRISP), phospholipases A2 (PLA2), and C-type lectins. An exception was observed in the Lombok sample, which lacked protein bands in the mass range of serine protease and CRISP. Venomic analysis of the Sumbawa venom also identified these protein families, in addition to several proteins of lesser abundance (

Published
2019

4. Quantitative Proteomic Profiling Reveals Differentially Regulated Proteins in Cystic Fibrosis Cells

Author

Rauniyar, Navin, Gupta, Vijay, Balch, William E, and Yates, John R

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Pediatric, Lung, Cystic Fibrosis, Biotechnology, Rare Diseases, 2.1 Biological and endogenous factors, Aetiology, Congenital, Biomarkers, Cystic Fibrosis Transmembrane Conductance Regulator, Gene Expression Regulation, Humans, Proteomics, Systems Biology, cystic fibrosis transmembrane conductance regulator, CFTR, MudPIT, mass spectrometry, NSAF, spectral count, label free, proteomics, Chemical Sciences, Biochemistry & Molecular Biology, Biological sciences, Chemical sciences
Abstract

The most prevalent cause of cystic fibrosis (CF) is the deletion of a phenylalanine residue at position 508 in CFTR (ΔF508-CFTR) protein. The mutated protein fails to fold properly, is retained in the endoplasmic reticulum via the action of molecular chaperones, and is tagged for degradation. In this study, the differences in protein expression levels in CF cell models were assessed using a systems biology approach aided by the sensitivity of MudPIT proteomics. Analysis of the differential proteome modulation without a priori hypotheses has the potential to identify markers that have not yet been documented. These may also serve as the basis for developing new diagnostic and treatment modalities for CF. Several novel differentially expressed proteins observed in our study are likely to play important roles in the pathogenesis of CF and may serve as a useful resource for the CF scientific community.

Published
2014

5. Characterization, Design, and Function of the Mitochondrial Proteome: From Organs to Organisms

Author

Lotz, Christopher, Lin, Amanda J, Black, Caitlin M, Zhang, Jun, Lau, Edward, Deng, Ning, Wang, Yueju, Zong, Nobel C, Choi, Jeong H, Xu, Tao, Liem, David A, Korge, Paavo, Weiss, James N, Hermjakob, Henning, Yates, John R, Apweiler, Rolf, and Ping, Peipei

Subjects
Biochemistry and Cell Biology, Genetics, Biological Sciences, Biotechnology, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Chromatography, Liquid, Drosophila melanogaster, Electrophoresis, Polyacrylamide Gel, Humans, Mice, Mitochondrial Proteins, Proteome, Tandem Mass Spectrometry, mitochondrial proteome, mitochondrial function, heart diseases, intergenomic, intragenomic, proteomic comparisons, Chemical Sciences, Biochemistry & Molecular Biology, Biological sciences, Chemical sciences
Abstract

Mitochondria are a common energy source for organs and organisms; their diverse functions are specialized according to the unique phenotypes of their hosting environment. Perturbation of mitochondrial homeostasis accompanies significant pathological phenotypes. However, the connections between mitochondrial proteome properties and function remain to be experimentally established on a systematic level. This uncertainty impedes the contextualization and translation of proteomic data to the molecular derivations of mitochondrial diseases. We present a collection of mitochondrial features and functions from four model systems, including two cardiac mitochondrial proteomes from distinct genomes (human and mouse), two unique organ mitochondrial proteomes from identical genetic codons (mouse heart and mouse liver), as well as a relevant metazoan out-group (drosophila). The data, composed of mitochondrial protein abundance and their biochemical activities, capture the core functionalities of these mitochondria. This investigation allowed us to redefine the core mitochondrial proteome from organs and organisms, as well as the relevant contributions from genetic information and hosting milieu. Our study has identified significant enrichment of disease-associated genes and their products. Furthermore, correlational analyses suggest that mitochondrial proteome design is primarily driven by cellular environment. Taken together, these results connect proteome feature with mitochondrial function, providing a prospective resource for mitochondrial pathophysiology and developing novel therapeutic targets in medicine.

Published
2014

6. Analysis of the Tropism of SARS-CoV-2 Based on the Host Interactome of the Spike Protein

Author

Bamberger, Casimir, Pankow, Sandra, Martínez-Bartolomé, Salvador, Diedrich, Jolene K., Park, Robin S. K., and Yates, John R.

Abstract

The β-coronavirus SARS-CoV-2 causes severe acute respiratory syndrome (COVID-19) in humans. It enters and infects epithelial airway cells upon binding of the receptor binding domain (RBD) of the virus entry protein spike to the host receptor protein Angiotensin Converting Enzyme 2 (ACE2). Here, we used coimmunoprecipitation coupled with bottom-up mass spectrometry to identify host proteins that engaged with the spike protein in human bronchial epithelial cells (16HBEo–). We found that the spike protein bound to extracellular laminin and thrombospondin and endoplasmatic reticulum (ER)-resident DJB11 and FBX2 proteins. The ER-resident proteins UGGT1, CALX, HSP7A, and GRP78/BiP bound preferentially to the original Wuhan D614 over the mutated G614 spike protein in the more rapidly spreading Alpha SARS-CoV-2 strain. The increase in protein binding to the D614 spike might be explained by higher accessibility of cryptic sites in “RDB open” and “S2 only” D614 spike protein conformations and may enable SARS-CoV-2 to infect additional, ACE2-negative cell types. Moreover, a novel proteome-based cell type set enrichment analysis (pCtSEA) found that host factors like laminin might render additional cell types such as macrophages and epithelial cells in the nephron permissive to SARS-CoV-2 infection.

Published
2023
Full Text
View/download PDF

7. Want to Publish in JPR? This Is What You Need to Know!

Author

Yates, John R., primary, Cristea, Ileana M., additional, Dong, Meng-Qui, additional, Eyers, Claire E., additional, LaBaer, Joshua, additional, Li, Jia V., additional, Nicholson, Jeremy K., additional, Overall, Christopher M., additional, Palmblad, Magnus, additional, and Slavov, Nikolai, additional

Published
2022
Full Text
View/download PDF

9. Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics

Author

Cheng, Li-Chun, primary, Zhang, Xi, additional, Abhinav, Kanishk, additional, Nguyen, Julie A, additional, Baboo, Sabyasachi, additional, Martinez-Bartolomé, Salvador, additional, Branon, Tess C, additional, Ting, Alice Y, additional, Loose, Esther, additional, Yates, John R, additional, and Gerace, Larry, additional

Published
2022
Full Text
View/download PDF

18. Confronting Racism in Chemistry Journals

Author

Burrows, Cynthia J., primary, Huang, Jiaxing, additional, Wang, Shu, additional, Kim, Hyun Jae, additional, Meyer, Gerald J., additional, Schanze, Kirk, additional, Lee, T. Randall, additional, Lutkenhaus, Jodie L., additional, Kaplan, David, additional, Jones, Christopher, additional, Bertozzi, Carolyn, additional, Kiessling, Laura, additional, Mulcahy, Mary Beth, additional, Lindsley, Craig W., additional, Finn, M. G., additional, Blum, Joel D., additional, Kamat, Prashant, additional, Choi, Wonyong, additional, Snyder, Shane, additional, Aldrich, Courtney C., additional, Rowan, Stuart, additional, Liu, Bin, additional, Liotta, Dennis, additional, Weiss, Paul S., additional, Zhang, Deqing, additional, Ganesh, Krishna N., additional, Atwater, Harry A., additional, Gooding, J. Justin, additional, Allen, David T., additional, Voigt, Christopher A., additional, Sweedler, Jonathan, additional, Schepartz, Alanna, additional, Rotello, Vincent, additional, Lecommandoux, Sébastien, additional, Sturla, Shana J., additional, Hammes-Schiffer, Sharon, additional, Buriak, Jillian, additional, Steed, Jonathan W., additional, Wu, Hongwei, additional, Zimmerman, Julie, additional, Brooks, Bryan, additional, Savage, Phillip, additional, Tolman, William, additional, Hofmann, Thomas F., additional, Brennecke, Joan F., additional, Holme, Thomas A., additional, Merz, Kenneth M., additional, Scuseria, Gustavo, additional, Jorgensen, William, additional, Georg, Gunda I., additional, Wang, Shaomeng, additional, Proteau, Philip, additional, Yates, John R., additional, Stang, Peter, additional, Walker, Gilbert C., additional, Hillmyer, Marc, additional, Taylor, Lynne S., additional, Odom, Teri W., additional, Carreira, Erick, additional, Rossen, Kai, additional, Chirik, Paul, additional, Miller, Scott J., additional, Shea, Joan-Emma, additional, McCoy, Anne, additional, Zanni, Martin, additional, Hartland, Gregory, additional, Scholes, Gregory, additional, Loo, Joseph A., additional, Milne, James, additional, Tegen, Sarah B., additional, Kulp, Daniel T., additional, and Laskin, Julia, additional

Published
2020
Full Text
View/download PDF

20. National Cancer Institute Think-Tank Meeting Report on Proteomic Cartography and Biomarkers at the Single-Cell Level: Interrogation of Premalignant Lesions

Author

Kagan, Jacob, primary, Moritz, Robert L., additional, Mazurchuk, Richard, additional, Lee, Je Hyuk, additional, Kharchenko, Peter Vasili, additional, Rozenblatt-Rosen, Orit, additional, Ruppin, Eytan, additional, Edfors, Fredrik, additional, Ginty, Fiona, additional, Goltsev, Yury, additional, Wells, James A., additional, LaCava, John, additional, Riesterer, Jessica L., additional, Germain, Ronald N., additional, Shi, Tujin, additional, Chee, Mark S., additional, Budnik, Bogdan A., additional, Yates, John R., additional, Chait, Brian T., additional, Moffitt, Jeffery R., additional, Smith, Richard D., additional, and Srivastava, Sudhir, additional

Published
2020
Full Text
View/download PDF

29. Proteomic Analysis of Peripheral Blood Mononuclear Cells after a High-Fat, High-Carbohydrate Meal with Orange Juice

Author

Chaves, Daniela F. S., Carvalho, Paulo C., Brasili, Elisa, Rogero, Marcelo M., Hassimotto, Neuza A., Diedrich, Jolene K., Moresco, James J., Yates, John R., and Lajolo, Franco M.

Abstract

Oxidative stress and inflammation play a role in the physiopathology of insulin resistance, diabetes and cardiovascular disease. A single high-fat, high-carbohydrate (HFHC) meal induces an increase in inflammatory and oxidative stress markers in peripheral blood mononuclear cells (PBMC). Previous studies have shown that orange juice is able to prevent this response by inhibiting toll like receptors (TLR) expression and endotoxemia. Our goal was to study the proteome response in PBMC after the consumption of a HFHC meal consumed with water, orange juice or an isocaloric beverage (water with glucose). Twelve healthy individuals completed the protocol in a crossover design, and blood samples were obtained before and 1, 3, and 5 h after consumption. Proteomic profile, glucose, insulin, lipid and cytokines levels were investigated. The glycemic and insulinemic response was higher when the meal was consumed with glucose, while there was no difference in the response between water and orange juice. Proteome analysis in PBMC was carried out using TMT ten-plex. A total of 3813 proteins, originating from 15 662 peptides were identified. Three proteins showed significantly altered expression in the three treatments: apolipoprotein A-II, ceruloplasmin and hemopexin. When the HFHC meal was consumed with water there was an increase in some inflammatory pathways such as the Fc-gamma receptor dependent phagocytosis and the complement cascade, but the immune system as a whole was not significantly altered. However, when the meal was consumed with glucose, the immune system was up regulated. Among the pathways induced after 3 h were those of the adaptive immune system and cytokine signaling. Five hours after the meal, pathways of the complement cascade and classical antibody mediated complement activation were up regulated. When the meal was consumed with orange juice there was an up regulation of proteins involved in signal transduction, DNA replication and cell cycle. The promyelocytic leukemia protein (PML) showed a 28.2-fold increase. This protein was down regulated when the meal was consumed with water. Regarding the immune system, several of the pathways induced by glucose were down regulated when the meal was consumed with orange juice: proteins involved with the adaptive immune system and cytokine signaling. Therefore, we have shown that orange juice can not only suppress diet induced inflammation, but also regulate the expression of proteins such as PML, which may play a key role in the regulation of metabolism.

Published
2024
Full Text
View/download PDF

30. Comparative proteomic analysis of the aging soleus and extensor digitorum longus rat muscles using TMT labeling and mass spectrometry

Author

Chaves, Daniela F. S., Carvalho, Paulo C., Lima, Diogo B., Nicastro, Humberto, Lorenzeti, Fabio M, Filho, Mario S., Hirabara, Sandro M, Alves, Paulo H.M., Moresco, James J, Yates, John R., and Lancha, Antonio H.

Abstract

Sarcopenia describes an age-related decline in skeletal muscle mass, strength, and function that ultimately impairs metabolism, leads to poor balance, frequent falling, limited mobility, and a reduction in quality of life. Here we investigate the pathogenesis of sarcopenia through a proteomic shotgun approach. Briefly, we employed tandem mass tags (TMT) to quantitate and compare the protein profiles obtained from young versus old rat slow-twitch type of muscle (soleus) and a fast-twitch type of muscle (extensor digitorum longus, EDL). Our results disclose 3452 and 1848 proteins identified from soleus and EDL muscles samples of which 78 and 174 were found to be differentially expressed, respectively. In general, most of the proteins were structural related, involved in energy metabolism, oxidative stress, detoxification, or transport. Aging affected soleus and EDL muscles differently and several proteins were regulated in opposite ways. For example, pyruvate kinase had its expression and activity different in both soleus and EDL muscles. We were able to verify with existing literature many of our differentially expressed proteins as candidate aging biomarkers , and most importantly, disclose several new candidate biomarkers such as the glioblastoma amplified sequence (GAS), zero beta-globin, and prolargin.

Published
2024
Full Text
View/download PDF

32. PACOM: A Versatile Tool for Integrating, Filtering, Visualizing, and Comparing Multiple Large Mass Spectrometry Proteomics Data Sets

Author

Martínez-Bartolomé, Salvador, primary, Medina-Aunon, J. Alberto, additional, López-García, Miguel Ángel, additional, González-Tejedo, Carmen, additional, Prieto, Gorka, additional, Navajas, Rosana, additional, Salazar-Donate, Emilio, additional, Fernández-Costa, Carolina, additional, Yates, John R., additional, and Albar, Juan Pablo, additional

Published
2018
Full Text
View/download PDF

35. Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases

Author

Hwang, Heeyoun, primary, Park, Gun Wook, additional, Park, Ji Yeong, additional, Lee, Hyun Kyoung, additional, Lee, Ju Yeon, additional, Jeong, Ji Eun, additional, Park, Sung-Kyu Robin, additional, Yates, John R., additional, Kwon, Kyung-Hoon, additional, Park, Young Mok, additional, Lee, Hyoung-Joo, additional, Paik, Young-Ki, additional, Kim, Jin Young, additional, and Yoo, Jong Shin, additional

Published
2017
Full Text
View/download PDF

37. Temporal Quantitative Profiling of Newly Synthesized Proteins during Aβ Accumulation

Author

Ma, Yuanhui, McClatchy, Daniel B., Martínez-Bartolomé, Salvador, Bamberger, Casimir, and Yates, John R.

Abstract

Accumulation of aggregated amyloid beta (Aβ) in the brain is believed to impair multiple cellular pathways and play a central role in Alzheimer’s disease pathology. However, how this process is regulated remains unclear. In theory, measuring protein synthesis is the most direct way to evaluate a cell’s response to stimuli, but to date, there have been few reliable methods to do this. To identify the protein regulatory network during the development of Aβ deposition in AD, we applied a new proteomic technique to quantitate newly synthesized protein (NSP) changes in the cerebral cortex and hippocampus of 2-, 5-, and 9-month-old APP/PS1 AD transgenic mice. This bio-orthogonal noncanonical amino acid tagging analysis combined PALM (pulse azidohomoalanine labeling in mammals) and HILAQ (heavy isotope labeled AHA quantitation) to reveal a comprehensive dataset of NSPs prior to and post Aβ deposition, including the identification of proteins not previously associated with AD, and demonstrated that the pattern of differentially expressed NSPs is age-dependent. We also found dysregulated vesicle transportation networks including endosomal subunits, coat protein complex I (COPI), and mitochondrial respiratory chain throughout all time points and two brain regions. These results point to a pathological dysregulation of vesicle transportation which occurs prior to Aβ accumulation and the onset of AD symptoms, which may progressively impact the entire protein network and thereby drive neurodegeneration. This study illustrates key pathway regulation responses to the development of AD pathogenesis by directly measuring the changes in protein synthesis and provides unique insights into the mechanisms that underlie AD.

Published
2021
Full Text
View/download PDF

41. Proteomics of Rat Lungs Infected by Cryptococcus gattiiReveals a Potential Warburg-like Effect

Author

Rosa, Rafael L., Berger, Markus, Santi, Lucélia, Driemeier, David, Barros Terraciano, Paula, Campos, Alexandre R., Guimarães, Jorge A., Vainstein, Marilene H., Yates, John R., and Beys-da-Silva, Walter O.

Abstract

Cryptococcus gattiiis the causative agent of cryptococcosis infection that can lead to pneumonia and meningitis in immunocompetent individuals. The molecular basis of the pathogenic process and impact on the host biochemistry are poorly understood and remain largely unknown. In this context, a comparative proteomic analysis was performed to investigate the response of the host during an infection caused by C. gattii. Lungs of experimentally infected rats were analyzed by shotgun proteomics to identify differentially expressed proteins induced by C. gattiiclinical strain. The proteomic results were characterized using bioinformatic tools, and subsequently, the molecular findings were validated in cell culture and lungs of infected animals. A dramatic change was observed in protein expression triggered by C. gattiiinfection, especially related to energy metabolism. The main pathways affected include aerobic glycolysis cycle, TCA cycle, and pyrimidine and purine metabolism. Analyses in human lung fibroblast cells confirmed the altered metabolic status found in infected lungs. Thus, it is clear that C. gattiiinfection triggers important changes in energy metabolism leading to the activation of glycolysis and lactate accumulation in lung cells, culminating in a cancerlike metabolic status known as the Warburg effect. The results presented here provide important insights to better understand C. gattiimolecular pathogenesis.

Published
2019
Full Text
View/download PDF

42. Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate

Author

Park, Gun Wook, primary, Hwang, Heeyoun, additional, Kim, Kwang Hoe, additional, Lee, Ju Yeon, additional, Lee, Hyun Kyoung, additional, Park, Ji Yeong, additional, Ji, Eun Sun, additional, Park, Sung-Kyu Robin, additional, Yates, John R., additional, Kwon, Kyung-Hoon, additional, Park, Young Mok, additional, Lee, Hyoung-Joo, additional, Paik, Young-Ki, additional, Kim, Jin Young, additional, and Yoo, Jong Shin, additional

Published
2016
Full Text
View/download PDF

45. Chromosome-Based Proteomic Study for Identifying Novel Protein Variants from Human Hippocampal Tissue Using Customized neXtProt and GENCODE Databases

Author

Hwang, Heeyoun, primary, Park, Gun Wook, additional, Kim, Kwang Hoe, additional, Lee, Ju Yeon, additional, Lee, Hyun Kyoung, additional, Ji, Eun Sun, additional, Park, Sung-Kyu Robin, additional, Xu, Tao, additional, Yates, John R., additional, Kwon, Kyung-Hoon, additional, Park, Young Mok, additional, Lee, Hyoung-Joo, additional, Paik, Young-Ki, additional, Kim, Jin Young, additional, and Yoo, Jong Shin, additional

Published
2015
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results