-
1دورية أكاديمية
المؤلفون: Peterson, Joseph R.Aff1, IDs1305802301654z_cor1, Cole, John A., Pfeiffer, John R., Norris, Gregory H., Zhang, Yuhan, Lopez-Ramos, Dorys, Pandey, Tushar, Biancalana, Matthew, Esslinger, Hope R., Antony, Anuja K., Takiar, Vinita
المصدر: Breast Cancer Research. 25(1)
-
2دورية أكاديمية
المؤلفون: Howard, Frederick M.Aff1, IDs10549022067220_cor1, He, Gong, Peterson, Joseph R., Pfeiffer, J. R., Earnest, Tyler, Pearson, Alexander T., Abe, Hiroyuki, Cole, John A., Nanda, Rita
المصدر: Breast Cancer Research and Treatment. 196(1):57-66
-
3مؤتمر
المؤلفون: Stone, John E., Hallock, Michael J., Phillips, James C., Peterson, Joseph R., Luthey-Schulten, Zaida, Schulten, Klaus
المصدر: 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) Parallel and Distributed Processing Symposium Workshops, 2016 IEEE International. :89-100 May, 2016
Relation: 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW)
-
4دورية أكاديمية
المؤلفون: Earnest, Tyler M, Cole, John A, Peterson, Joseph R, Hallock, Michael J, Kuhlman, Thomas E, Luthey‐Schulten, Zaida
المصدر: Biopolymers. 105(10)
مصطلحات موضوعية: Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Genetics, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Cell Division, DNA Replication, DNA, Bacterial, Escherichia coli, Models, Biological, Ribosomes, bacterial cell division, ribosome biogenesis, stochastic gene expression, Chemical Sciences, Biophysics, Biological sciences, Chemical sciences
الوصف: Ribosomes-the primary macromolecular machines responsible for translating the genetic code into proteins-are complexes of precisely folded RNA and proteins. The ways in which their production and assembly are managed by the living cell is of deep biological importance. Here we extend a recent spatially resolved whole-cell model of ribosome biogenesis in a fixed volume [Earnest et al., Biophys J 2015, 109, 1117-1135] to include the effects of growth, DNA replication, and cell division. All biological processes are described in terms of reaction-diffusion master equations and solved stochastically using the Lattice Microbes simulation software. In order to determine the replication parameters, we construct and analyze a series of Escherichia coli strains with fluorescently labeled genes distributed evenly throughout their chromosomes. By measuring these cells' lengths and number of gene copies at the single-cell level, we could fit a statistical model of the initiation and duration of chromosome replication. We found that for our slow-growing (120 min doubling time) E. coli cells, replication was initiated 42 min into the cell cycle and completed after an additional 42 min. While simulations of the biogenesis model produce the correct ribosome and mRNA counts over the cell cycle, the kinetic parameters for transcription and degradation are lower than anticipated from a recent analytical time dependent model of in vivo mRNA production. Describing expression in terms of a simple chemical master equation, we show that the discrepancies are due to the lack of nonribosomal genes in the extended biogenesis model which effects the competition of mRNA for ribosome binding, and suggest corrections to parameters to be used in the whole-cell model when modeling expression of the entire transcriptome. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 735-751, 2016.
وصف الملف: application/pdf
URL الوصول: https://escholarship.org/uc/item/12q6s853
-
5دورية أكاديمية
المصدر: Proceedings of the National Academy of Sciences of the United States of America, 2015 Dec . 112(52), 15886-15891.
URL الوصول: https://www.jstor.org/stable/26466252
-
6دورية أكاديمية
لا يتم عرض هذه النتيجة على الضيوف.
تسجيل الدخول للوصول الكامل. -
7كتاب إلكتروني
المؤلفون: Hobart, David E., Peterson, Joseph R.
المساهمون: Morss, Lester R., editorAff1, Edelstein, Norman M., editorAff2, Fuger, Jean, editorAff3
المصدر: The Chemistry of the Actinide and Transactinide Elements. :1444-1498
-
8كتاب إلكتروني
المؤلفون: Hobart, David E.Aff4, Peterson, Joseph R.Aff5
المساهمون: Morss, Lester R., editorAff1, Edelstein, Norman M., editorAff2, Fuger, Jean, editorAff3
المصدر: The Chemistry of the Actinide and Transactinide Elements. :1444-1498
-
9دورية أكاديمية
المؤلفون: Peterson, Joseph R., Wight, Charles A., Berzins, Martin
المصدر: In Procedia Computer Science 2013 18:2259-2268
-
10دورية أكاديمية
لا يتم عرض هذه النتيجة على الضيوف.
تسجيل الدخول للوصول الكامل.