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Modelling Trafficking of Proteins within the Mammalian Cell Using Bio-PEPA [chapter]

Vashti Galpin
2012 Lecture Notes in Computer Science  
The model Bio-PEPABio-PEPA is a stochastic process algebra for biological modelling. • It allows multiple forms of analysis, including simulation and ordinary differential equations. • Species are defined  ...  conc of FGF) Both proteins such as Src and endosomes containing Src are modelled as species, using stoichiometric constants for the decrease in Src and increase in endosomes and vice versa. aSrc@mb =  ... 
doi:10.1007/978-3-642-33636-2_24 fatcat:rfvocpvnsba6dehanik5qqkuwy

The glycoprotein of the live-attenuated Junin virus vaccine strain induces ER stress and forms aggregates prior to degradation in the lysosome

John T. Manning, Nadya E. Yun, Alexey V. Seregin, Takaaki Koma, Rachel Sattler, Chiomah Ezeomah, Cheng Huang, Juan C. de la Torre, Slobodan Paessler
2020 Journal of Virology  
While the vaccine strain is approved for use in endemic regions within Argentina, the mechanisms of Can attenuation have not been elucidated.  ...  strain also contribute to aggregation of the GPC within the ER.  ...  Degradation of membrane-associated proteins can occur through two main pathways in mammalian cells, the ubiquitinproteasome pathway and the lysosomal pathway (15) .  ... 
doi:10.1128/jvi.01693-19 pmid:31996435 pmcid:PMC7108856 fatcat:jv4mks7gunbs5gi2srzvumab4u

Quality control of HLA-DR molecules by the lysosomal aspartyl protease, cathepsin D [article]

Nakul Shah, Sarah McDonald, Charles T.A. Parker, Ryan W. M. Robinson, Amin Oomatia, Alessandra De Riva, Michael J. Deery, Elizabeth D. Mellins, Robert Busch
2020 bioRxiv   pre-print
Exposure of immature monocyte-derived dendritic cells (MoDCs) and KG-1 acute myeloid leukaemia cells to the aspartyl protease inhibitor, pepstatin A (PepA), caused accumulation of human leukocyte antigen  ...  Here, we examined the role of aspartyl proteases in MHCII protein degradation and characterised the form of MHCII that is degraded.  ...  Acknowledgements We thank the Phenotyping Hub of the Cambridge Biomedical Research Centre and the Department of Life Sciences, University of Roehampton, for access to flow cytometers.  ... 
doi:10.1101/2020.03.25.004101 fatcat:4fysas6ia5elxnvuifbjxb5zo4

Hybrid semantics for Bio-PEPA

Vashti Galpin
2014 Information and Computation  
Stochastic HYPE and the mapping of Bio-PEPA to stochastic HYPE is given followed by the properties of the HYPE model.  ...  and is only a small constant larger in size than the Bio-PEPA model.  ...  Acknowledgements: The author thanks Jane Hillston for her comments and the reviewers for their useful suggestions on how to improve the paper.  ... 
doi:10.1016/j.ic.2014.01.016 fatcat:4wbcyfznwzbqdfma2z3lgauzsq

Syntaxin-3 Is Required for Melanosomal Localization of Tyrp1 in Melanocytes

Ayaka Yatsu, Norihiko Ohbayashi, Kanako Tamura, Mitsunori Fukuda
2013 Journal of Investigative Dermatology  
in the trafficking of the melanogenic enzyme Tyrp1 (tyrosinase-related protein 1) in mouse melanocytes.  ...  ) proteins, which generally mediate membrane fusion, on melanosomes in the process of melanogenic enzyme trafficking has never been investigated.  ...  ACKNOWLEDGMENTS We thank Dr Dorothy C Bennett (St George's Hospital Medical School, London, UK) for kindly donating melan-a cells, Megumi Aizawa for technical assistance, and members of the Fukuda laboratory  ... 
doi:10.1038/jid.2013.156 pmid:23549422 fatcat:m5ktriu6ejhzff3k2xsdwid7p4

The Sec1/Munc18 (SM) protein Vps45 is involved in iron uptake, mitochondrial function and virulence in the pathogenic fungus Cryptococcus neoformans [article]

Mélissa Caza, Guanggan Hu, Erik David Nielson, Minsu Cho, Won Hee Jung, James W Kronstad
2018 bioRxiv   pre-print
The battle for iron between invading microorganisms and mammalian hosts is a pivotal determinant of the outcome of infection.  ...  In this study, we examined the role of endocytic trafficking in iron uptake by characterizing a mutant defective in the Sec1/Munc18 (SM) protein Vps45.  ...  ACKNOWLEDGEMENTS 701 The authors would like to thank Dr. Arturo Casadevall for the 18b7 antibody, Dr.  ... 
doi:10.1101/356535 fatcat:cutkolvytnbong3fwsiakl3igi

Impaired autophagy bridges lysosomal storage disease and epithelial dysfunction in the kidney

Beatrice Paola Festa, Zhiyong Chen, Marine Berquez, Huguette Debaix, Natsuko Tokonami, Jenny Ann Prange, Glenn van de Hoek, Cremonesi Alessio, Andrea Raimondi, Nathalie Nevo, Rachel H. Giles, Olivier Devuyst (+1 others)
2018 Nature Communications  
The endolysosomal system sustains the reabsorptive activity of specialized epithelial cells.  ...  The endolysosomal system sustains the reabsorptive activity of specialized epithelial cells.  ...  (project grant 16OI06) and the Swiss National Centre of Competence in Research (NCCR) Kidney Control of Homeostasis (Kidney.CH) for support and Junior Grant (to A.L.).  ... 
doi:10.1038/s41467-017-02536-7 pmid:29323117 pmcid:PMC5765140 fatcat:wervvuffrbcqfe6jjoaoz47uqu

Endoplasmic reticulum–associated degradation of the renal potassium channel, ROMK, leads to type II Bartter syndrome

Brighid M. O'Donnell, Timothy D. Mackie, Arohan R. Subramanya, Jeffrey L. Brodsky
2017 Journal of Biological Chemistry  
To translate these findings to a more relevant cell type, we measured the stabilities of WT ROMK and the ROMK Bartter mutants in HEK293 cells.  ...  As in yeast, the Bartter mutant proteins were less stable than the WT protein, and their degradation was slowed in the presence of a proteasome inhibitor.  ...  ., Golgi export of the Kir2.1 channel is driven by a trafficking signal located within its tertiary structure. Cell, 2011. 145(7): p. 1102-15. 25.  ... 
doi:10.1074/jbc.m117.786376 pmid:28630040 pmcid:PMC5546024 fatcat:3h4dq2fkmndofi7a6kafo3kyou

Class III PI3K Vps34 plays an essential role in autophagy and in heart and liver function

N. Jaber, Z. Dou, J.-S. Chen, J. Catanzaro, Y.-P. Jiang, L. M. Ballou, E. Selinger, X. Ouyang, R. Z. Lin, J. Zhang, W.-X. Zong
2012 Proceedings of the National Academy of Sciences of the United States of America  
LC3 | SQSTM1/p62 | 3-MA | epidermal growth factor receptor | transferrin M acroautophagy (referred to as autophagy hereafter) is a dynamic membrane trafficking process that involves the delivery of intracellular  ...  of Vps34 and a frame shift causing a deletion of 755 of the 887 amino acids of Vps34.  ...  Using a conditional loss-offunction mouse model of Vps34, we have examined the role of Vps34 in MEFs, liver, and heart.  ... 
doi:10.1073/pnas.1112848109 pmid:22308354 pmcid:PMC3277541 fatcat:yhyaliyurnan3oqzs53g4bcgte

The class IA phosphatidylinositol 3-kinase p110-β subunit is a positive regulator of autophagy

Zhixun Dou, Mohar Chattopadhyay, Ji-An Pan, Jennifer L. Guerriero, Ya-Ping Jiang, Lisa M. Ballou, Zhenyu Yue, Richard Z. Lin, Wei-Xing Zong
2010 Journal of Cell Biology  
This work is supported by the National Institutes of Health (grants DK62722 and CA136754 to R.Z. Lin; and CA098092 and CA129536 to W.-X. Zong), Susan Komen for the Cure (grant KG081538 to W.-X.  ...  Zong), and the Carol Baldwin Breast Cancer Research Foundation (to W.-X. Zong). Submitted: 9 June 2010 Accepted: 18 October 2010  ...  Protein concentration of the supernatant was determined by Bradford assays (Bio-Rad Laboratories).  ... 
doi:10.1083/jcb.201006056 pmid:21059846 pmcid:PMC2983054 fatcat:k7miulf7u5h2bangldk4p4xnqi

Proteomes of Lactobacillus delbrueckii subsp. bulgaricus LBB.B5 Incubated in Milk at Optimal and Low Temperatures

Xiaochen Yin, Michelle R. Salemi, Brett S. Phinney, Velitchka Gotcheva, Angel Angelov, Maria L. Marco, Korneel Rabaey
2017 mSystems  
Cell-associated proteins were measured by gel-free, shotgun proteomics using high-performance liquid chromatography coupled with tandem mass spectrophotometry.  ...  the consequences of those responses on the use of L. delbrueckii subsp. bulgaricus as a probiotic remain to be elucidated.  ...  The authors declare no conflicts of interest.  ... 
doi:10.1128/msystems.00027-17 pmid:28951887 pmcid:PMC5605880 fatcat:6tcp3squ5jgfnisr5lyw3rqhbu

Hippocampal AMPA Receptor Gating Controlled by Both TARP and Cornichon Proteins

Akihiko S. Kato, Martin B. Gill, Michelle T. Ho, Hong Yu, Yuan Tu, Edward R. Siuda, He Wang, Yue-Wei Qian, Eric S. Nisenbaum, Susumu Tomita, David S. Bredt
2010 Neuron  
However, the potential for interactions of these subunits within an AMPA receptor complex is unknown.  ...  Transmembrane AMPA receptor regulatory proteins (TARPs) and cornichon proteins (CNIH-2/3) independently modulate AMPA receptor trafficking and gating.  ...  SOL-1 is a transmembrane CUB domain protein, unrelated to CNIH (Zheng et al., 2004) . However, another CUB domain protein, Neto2 regulates mammalian kainate receptor trafficking and gating .  ... 
doi:10.1016/j.neuron.2010.11.026 pmid:21172611 pmcid:PMC3034222 fatcat:ji4bpsxivnaxvbb66cilc2e3ju

Revisiting Ehrlichia ruminantium Replication Cycle Using Proteomics: The Host and the Bacterium Perspectives

Isabel Marcelino, Philippe Holzmuller, Ana Coelho, Gabriel Mazzucchelli, Bernard Fernandez, Nathalie Vachiéry
2021 Microorganisms  
Our findings led to the first model of E. ruminantium infection in host cells in vitro, and we highlight potential biomarkers of E. ruminantium infection in endothelial cells (such as ROCK1, TMEM16K, Albumin  ...  Cystoscape integrated data analysis shows that these proteins lead to major changes in host cell immune responses, host cell metabolism and vesicle trafficking, with a clear involvement of inflammation-related  ...  Mass spectrometry (1DE-nLC-MS/MS) was carried out using facilities of the Montpellier Proteomics Platform (BioCampus Montpellier).  ... 
doi:10.3390/microorganisms9061144 pmid:34073568 fatcat:eii2zwjku5evdpxrq6ypr3rbre

The Chlamydia trachomatis Type III Secretion Chaperone Slc1 Engages Multiple Early Effectors, Including TepP, a Tyrosine-phosphorylated Protein Required for the Recruitment of CrkI-II to Nascent Inclusions and Innate Immune Signaling

Yi-Shan Chen, Robert J. Bastidas, Hector A. Saka, Victoria K. Carpenter, Kristian L. Richards, Gregory V. Plano, Raphael H. Valdivia, Joanne N. Engel
2014 PLoS Pathogens  
We propose a model wherein TepP acts downstream of TARP to recruit scaffolding proteins at entry sites to initiate and amplify signaling cascades important for the regulation of innate immune responses  ...  Chlamydia trachomatis, the causative agent of trachoma and sexually transmitted infections, employs a type III secretion (T3S) system to deliver effector proteins into host epithelial cells to establish  ...  Quayle for A2EN epithelial cell lines, A.M. Pendergast for generous gifts of GST-Crk, and A. Xavier for the generation of anti Ct694 antibodies. Author Contributions  ... 
doi:10.1371/journal.ppat.1003954 pmid:24586162 pmcid:PMC3930595 fatcat:zajqt2i2szel7kiuoub4nh7hji

Generation and Characterization of an Attenuated Mutant in a Response Regulator Gene of Francisella tularensis Live Vaccine Strain (LVS)

Wendy L. Sammons-Jackson, Karen McClelland, Jean N. Manch-Citron, Dennis W. Metzger, Chandra Shekhar Bakshi, Emilio Garcia, Amy Rasley, Burt E. Anderson
2008 DNA and Cell Biology  
Compare cell lysate and supernatant proteins in LVS wild type and mutant. ampicillin.  ...  The FTL0552 deletion mutant exhibited slightly reduced rates of extracellular growth but was unable to replicate or survive in mouse macrophages and was avirulent in the mouse model using either BALB/c  ...  The ability of the mutant to invade and replicate within mouse macrophages was assessed using J774A.1 cells and mouse peritoneal macrophages.  ... 
doi:10.1089/dna.2007.0687 pmid:18613792 pmcid:PMC2980773 fatcat:xe2qgprxe5evhnsh5hbdkhwhpe
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