Mathematical and computational analysis of intracelluar dynamics 3
Mathematical and computational analysis of intracelluar dynamics 3
... Sections 3. 3 and 3. 4 Finally, novel systemic behaviors of the system are inferred and predicted from the simulation results (Sections 3. 5 and 3. 6) 34 3. 2 Formulation of kinetic models Figure 3- 1 Kinetic ... p 53] n1 k [ p 53] v3 = j3n1 + [ p 53] n1 v4 = k [PIP 2] k {[PIPT ] − [PIP3]} = j + [PIP 2] j + [PIPT ] − [PIP3] vm = k m [PTEN ][PIP 3] j m + [PIP3] (3- 3) k [ p 53] n2 v5 = v6 = j5n + [ p 53] n2 k [ ... conserved (Figure 3- 7) p53ss AKT*ss [p53ss] [AKTass ] [AKTT ] Figure 3- 7 Model M3: steady-state bifurcation diagrams of p 53 and AKTa The steady state values of p 53 ([p53ss], gray curve) and AKTa ([AKTass],...
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Mathematical and computational analysis of intracelluar dynamics 2
... skin and brain cortex (Feng et al., 20 07; Wang et al., 20 05; Stambolic et al., 20 01; Trotman and Pandolfi, 20 03; Singh et al., 20 02; Tang and Eng, 20 06a, 20 06b) AKT phosphorylation of MDM2 (AKT-MDM2) ... (CI41) and mouse hippocampal 12 neurons (Gottlieb et al., 20 02; Su et al., 20 03; Wang et al., 20 05; Ogawara et al., 20 02; Zhou et al., 20 01; Singh et al., 20 02; Yamaguchi et al., 20 01; Mayo and ... kidney 14 (29 3T and HEK293), human primary keratinocytes cells, mouse fibroblasts (NIH3T3 and MEF) (Gottlieb et al., 20 02; Mayo et al., 20 02; Mayo and Donner, 20 01; Ashcroft et al., 20 02; Ogawara...
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Mathematical and computational analysis of intracelluar dynamics 4
... damped oscillations of p53 and MDM2 protein levels in cell populations of mouse fibroblasts and human breast cancer epithelial MCF-7 cells, following 5Gy of IR The dynamics of the p53-MDM2 oscillator ... populations of human wild-type and Bloom’s syndrome patients’ fibroblast, following induction of DNA damage either by 20 J/m2 of UV radiation or 2.5 Gy of ionizing radiation (IR) ... following: periods of oscillation are to hrs; peaks of MDM2 oscillations lag behind p53 peak for 1.5 to 2.5 hrs; periods of oscillations decrease with increasing IR intensity; and peaks of p53 pulses...
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Mathematical and computational analysis of intracelluar dynamics 5
... (uM) 1 .5 1. 75 0.2 0. 25 0 .5 0. 75 0 .5 1. 25 [AKTT] (uM) 0. 75 1 .5 1. 75 1 .5 1. 75 120 350 D C 110 300 100 90 250 80 200 0. 25 0 .5 0. 75 1. 25 [AKTT] (uM) 1 .5 1. 75 70 0. 25 1. 25 [AKTT] (uM) Figure 5- 24 Oscillation ... Analog and digital forms of p53 oscillations Digital [TP53] 5. 7.2 [p53] uM Analog Tim e Figure 5- 20 Schematic illustration of analog and digital p53 oscillations Time-courses of analog (blue) and ... interval of 0.02 µM For each combination of k0 and j5, a p53 steady-state curve as a function of ρ is computed; k0,basal is set as 0.1 µM/min and j5 is set as 0 .5 µM in the computation of the p53 steady...
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Mathematical and computational analysis of intracelluar dynamics 6
... 53 55 57 59 61 63 65 67 69 71 73 75 77 79 Figure 6- 1B Percentage length of each exonic region relative to its flanking intronic region To illustrate the fact that the exonic region of the dystrophin ... in Figure 6- 1 121 1,000,000 N u m b e r o f b a s e p a irs 100,000 10,000 1,000 100 10 1 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 Exon 43 45 47 49 51 53 55 57 59 61 63 65 67 69 71 73 75 ... (Pramono et al., 19 96; Matsuo, 19 96; Matsuo and Takeshima, 2005; Wilton and Fletcher, 2005a, 2005b; Wilton et al., 2007; AartsmaRus et al., 2002, 2004, 2005, 20 06; van Deutekom and van Ommen, 2003;...
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Mathematical and computational analysis of intracelluar dynamics 7
... 0 .7 0 .7 0 .7 0.6 0.6 0.6 0.5 0.5 0.5 0.4 0.4 0.4 0.3 0.3 0.3 0.2 0.2 0.2 0.1 0.1 0 90 92 94 96 98 100 102 104 106 108 0.1 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 19 20 21 22 23 24 25 26 27 ... only 17% of target sites of (+) AONs had one or more clusters, they were manifested in 52% of target sites of (++) AONs Set B also exhibited similar trends: 71 %, 70 % and 80% of target sites of (–) ... 5th-percentile of L3 scores of (++) AON target sites (Appendix A-18) On the other hand, target sites of h45AON5 and h46AON4 graded as (+) and target sites of h51AON29, h55AON5 and h77AON2 graded...
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Mathematical and computational analysis of intracelluar dynamics 8
... systematically in place of current trial -and- error means, which could reduce the cost and waiting time of therapy In conclusion, the use of models has greatly aided in the understanding of the two intracellular ... dynamics between the two steady states of the system leads to the understanding of how cells regulate the switch between cell survival and death Interestingly, bistability between apoptotic and ... exhibit oscillatory dynamics under certain conditions The role of these oscillations of intracellular p53 protein levels upon DNA damage in cell survival and death in the context of the p53-AKT network...
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Mathematical and computational analysis of intracelluar dynamics 9
... specific and other known or unknown details of the regulation of p53 and AKT In particular, different forms of p53 are ignored to reduce the number of variables and unknown mechanistic and kinetic ... genetic diseases Examples of such 163 genes are beta-globin gene in thalassemia (Suwanmanee et al., 2002; Gorman et al., 2000; Sazani and Kole, 2003; Dominski and Kole, 199 3) and OA1 gene in ocular ... algorithm, the accuracy of the model is limited by the accuracy of such algorithms However, the use of vast numbers of predicted secondary structures that averaged 44,582 of them per exon (Appendix...
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Mathematical and computational analysis of intracelluar dynamics
... system A system- level understanding of the biological process and elucidating of the systems behaviors can then be obtained from the insights of such analyses The dynamics of two intracellular processes ... not a standalone process Analyses show that dynamics of co-transcriptional binding accessibilities of AON target sites could statistically correlate with efficacy and efficiency of 94% of previously ... physiologies and make novel predictions by analyzing intracellular dynamics based on the known interactions among intracellular components using mathematical and computational models Examples of intracellular...
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Báo cáo khóa học: Mutational and computational analysis of the role of conserved residues in the active site of a family 18 chitinase docx
... residues are not described well and there is no example of mutational analysis of all of these residues in the same enzyme To obtain an insight into how the many conserved residues in the active sites ... circulans, whereas it may be mutated to asparagine without loss of activity in other family 18 chitinases [28,30] Preliminary results of a comparative study of available structures of family 18 chitinases ... bond ˚ and Asp140 is 10.7 A Mutational effects The residues mutated in this study are shown in Fig Asp140, Asp142, Glu144 and Asp215 were mutated individually to asparagine and alanine, Tyr10 and...
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Báo cáo khoa học: "A Linguistic and Computational Analysis of the German "Third Construction"*" potx
... terms of a closely related automaton, the Bottom-up EPDA (BEPDA) ~ The BEPDA consists of a finite-state control and of a stack of stacks There are two types of moves: either an input is read and ... new stack on top of the stack of stacks, or a fixed number of stacks below and above a designated stack on the stack of stacks is removed and a new symbol is pushed on the top of the designated ... popped Then, the remaining noun and verb are simply read and popped If we use any of the metrics proposed in [Joshi 1990] (such as the sum of the number of moves that input elements are stored in the...
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Báo cáo khoa học: Proteomic and biochemical analysis of 14-3-3-binding proteins during C2-ceramide-induced apoptosis pot
... comprehensive proteomics analysis of 14-3-3-binding proteins under physiological conditions as compared with apoptosis stimulation, with the aim of increasing our knowledge of the role of 14-3-3 proteins ... changes in 14-3-3-binding patterns in HeLa cells during C2-ceramideinduced apoptosis With the aim of further analyzing the role of 14-3-3 proteins in apoptosis, an evaluation of the ability of proteins ... role of 14-3-3 proteins in C2-ceramide-induced apoptosis, probably through regulation of already known apoptosis- related 14-3-3-binding proteins, some of them most likely still to be identified 14-3-3-binding...
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Báo cáo khoa học: Structural and functional analysis of ataxin-2 and ataxin-3 potx
... b5 strand) of D3 and F27/Y289 (b2 strand), L67/M324, V70/I327 and L72/L328 (all in b4 strand) of B The second cluster consists of P6/M267, L10/ L271 (both in a-helix), V18/C279 (b1 strand), L32/F293 ... solution structures of the UBL domain of hHR23A/B bound to a UIM peptide of S5a [99,119] could be used to model the complex of hHR23A/B and ataxin-3 Similarly, the complex of a UIM of ataxin-3 with ... detailed analysis of ataxin-2 homologues including the yeast homologue Pbp1, using a structurebased multiple sequence alignment of Sm and Sm-like proteins and a 3D model of the Lsm domain of ataxin-2...
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Báo cáo sinh học: "Review of "Reconstructing Evolution: New mathematical and computational advances" edited by Olivier Gascuel and Mike Steel" potx
... Chapters and are devoted to problems arising in the context of the reconstruction of Trees from Subtrees and Characters In Chapter 7, by M J Sanderson et al., the problem of fragmentation of the ... motivated by the fact that the evolutionary history of some sets of taxa is better represented by a network rather than a tree Chapter 9, by D Huson, first gives a short overview of which types of networks ... that of evolutionary trees constructed from real biological data and, thereby, to better understand the processes that lead to the patterns found in those trees Chapter 6, by K Hartmann and M...
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