mathematical tools in cancer signalling systems biology

... chemokines in vitro (Table 2) DPIV in cell biology A number of DPIV-binding proteins have been identified, including adenosine deaminase [78,79], CD45 (protein tyrosine phosphatase) [80], caveolin-1 ... ability to inactivate the incretin hormones glucagon-like peptide-1 and glucose insulinotropic peptide In the treatment of type diabetes, DPIV inhibitors extend incretin action, resulting in improved ... DP9-overexpressing cells of the ECM-interacting molecules discoidin domain receptor 1, a kinase activated by collagen binding, and the MMP inhibitor, tissue inhibitor of matrix metalloproteinase-2,...

Ngày tải lên: 06/03/2014, 09:22

... and indirect physical and functional interactions from peer-reviewed publications The relationships in the network include protein-protein interactions, protein binding to DNA or RNA, protein ... colony-stimulating-factor; HNSCC, head and neck squamous cell carcinoma; IGF, insulin-like growth factor; IκB, inhibitor kappaB; IKK, inhibitor-kappaB kinase; IL, interleukin; IL-R, interleukin receptor; ... (containing only the 10 bp core sequence of the RELA binding motif, Figure 7b, upper left panel), or using oligonucleotides containing a larger 50 bp sequence that included the RELA binding motif...

Ngày tải lên: 14/08/2014, 08:20

... describing systems biology applied to biochemistry in the years 2000–2010 employing the ten most commonly used software tools models, lindo (Lindo Systems Inc., Chicago, IL, USA; www.lindo.com) ... protein kinase; MCF, macrophare chemotactic factor; MCIP, modulatory calcineurin-interacting protein; MDCK, Madin Darby canine kidney; MEF, mouse embryonic fibroblast; MEK, MAP kinase/ERK kinase; ... accurately explain insulin-stimulated changes in the concentration of intracellular species and partitioning of glucose disposal in skeletal muscle Insulin propagates a rather complex coordination of...

Ngày tải lên: 14/02/2014, 14:20

... enzymes analysed included vacuolar invertase (vInv), neutral invertase (nInv), extracellular invertase (eInv), sucrose phosphate synthase (SPS), fructokinase (FrcK) and glucokinase (GlcK) Significant ... activity of vInv in Rsch increased continuously during cold exposure, and became significantly higher than in C24 after days at °C As compared with that of vInv, the activities of nInv and eInv were ... kept in mind that the sink export rate in our model is composed of assimilate export to sink organs and flux into further pools of carbon-containing metabolites and structural components, e.g amino...

Ngày tải lên: 14/02/2014, 22:20

... enzyme of interest should be investigated in the context of the in vivo-like medium Finally, in vivo, the enzymes are present at much higher concentrations than in typical enzyme assays, in which ... at least three independent cell-free extracts from steady-state samples from a single chemostat culture Enzyme In vivo-like Vmax (mmolÆmin)1Æg protein)1) Flux (mmolÆmin)1Æg protein)1) HXK PGI ... obtained in the in vivo-like assay medium, suggesting that the ‘optimized’ conditions are, in reality, not optimal for these enzymes A thorough analysis of the yeast kinetics of phosphofructokinase...

Ngày tải lên: 06/03/2014, 09:22

... crucial in scientic discovery, the pioneering work by Swanson on hypothesis generation [299] is mainly credited with sparking interest in text mining techniques in biology Text mining aids in the ... networks in systems biology, and one that allows one a much better understanding of signalling as signal processing Put another way, and again quoting Henrik Kacser [25,26], But one thing is certain: ... advantage in nucleic acid sequencing [321,322]) Metabolomics, modelling and machine learning systems M IB HOME OF THE MANCHESTER CENTRE FOR INTEGRATIVE SYSTEMS BIOLOGY Fig The Manchester Interdisciplinary...

Ngày tải lên: 07/03/2014, 12:20

... Mapping Protein – Protein Interactions Using Mass Spectrometry Schematic Representation for Inferring Protein – Protein Interactions from Domain Information An Illustrative Example of Two Proteins ... Domain –domain interaction Database of domain interactions and bindings Database of Interacting Proteins Dynamic programming Domain pair exclusion analysis European Bioinformatics Institute Enzyme ... and the information obtained can be incorporated into the basic model [GeH03] Integration Integration has multiple implications, including integrating different data sources, integrating different...

Ngày tải lên: 29/05/2014, 14:34

... types of agents, representing two different kinds of cells (or two kinds of molecules) can move freely and interact within the containing space; e) Interacting state machine: systems are represented ... modelling of intracellular chemical interactions Biosystems 85(1):37–45 Priami C, Ballarini P, Quaglia P (2009) BlenX4Bio–BlenX for Biologists In: Computational Methods in Systems Biology Springer, ... Hillston J (2005) Automatically deriving ODEs from process algebra models of signalling pathways In: Computational Methods in Systems Biology Springer, Berlin Heidelberg, pp 204–215 Calzone L,...

Ngày tải lên: 20/06/2014, 21:20

... through hexokinase enzymes, which have been shown to play a central role in sugar signalling, hormone signalling and plant development [15] Our findings point to a strong influence of hexokinase on ... homeostasis, supporting a crucial role in plant carbohydrate metabolism In addition, a prevailing role of hexokinase in regulating Scr cycling would explain why a strong reduction of invertase activity ... vacuolar invertase AtßFRUCT4 showed a dramatic reduction of cellular invertase activity, whereas the corresponding flux vInv did not decrease in a corresponding manner (Figure 3) This finding indicated...

Ngày tải lên: 21/06/2014, 03:20

... changes in proteome levels of proteins participating in relevant biological processes are shown in Figure 3b Again, in common with the transcriptome data, most of the changes in protein levels lie in ... methionine metabolism; 6, protein biosynthesis; 7, protein folding; 8, purine nucleotide, purine base and pyrimidine base biosynthesis; 9, regulation of transcription; 10, ubiquitindependent protein ... Glutamine Gln1p Leucine, isoleucine, valine Lysine Ilv3p, Leu1p Aco1p, Aco2p, Lys2p, Lys4p Aco1p, aconitase; Aco2p, putative aconitase isozyme; Ado1p; adenosine kinase; Arg1p, arginosuccinate...

Ngày tải lên: 06/08/2014, 18:21

... corresponding decrease in succinate From these observations, an increased flux though the TCA cycle could be inferred 2-Oxoglutarate, an intermediate in the TCA cycle, is critical in coupling carbon ... decrease in levels of glutamate Instead, there was a corresponding trend in the increase in the transcript and protein levels of the mitochondrial 2-oxoglutarate transporters, and an increase in protein ... control of growth rate Initially, they examined changes in transcript levels correlating with increasing growth rates using analysis of covariance (ANCOVA) after a multiple testing correction They...

Ngày tải lên: 06/08/2014, 18:21

... enrichment in RNA metabolism for both AR and ABsensitive proteins and in DNA binding for AR and hydrophilicity-sensitive proteins In addition, charge-sensitive proteins showed an enrichment in transferase ... mirrored by those of their protein targets In order to disrupt a protein’s function, a small molecule must either bind directly to the protein or act indirectly by interfering with another component ... as being particularly effective in modulating these mitochondrial functions [27] Further, we found that AR-sensitive proteins had higher degree in the regulatory interaction network reinforcing...

Ngày tải lên: 09/08/2014, 22:24

... atoms (13C) instead of the normal carbon-12 (12C) When the cells are growing in this medium, they incorporate the heavy arginine into all of their proteins All of the arginine containing peptides ... 2011, 1:26 http://www.jclinbioinformatics.com/content/1/1/26 dependent signalling pathways in the vasopressin signalling network of collecting duct cells, involving several kinases not generally ... phosphoproteins are substrates for protein kinase A, protein kinase C, casein kinase II and DNA-dependent protein kinase The high number of phosphotyrosine residues suggests an important role for tyrosine...

Ngày tải lên: 10/08/2014, 09:22

... yeast genes sharing pairs of binding sites in their promoters were significantly more likely to be co-expressed than genes sharing only single binding sites, to various machine learning methods that ... refine network representations [43,44] In plants, the lignin systems- project is taking this approach to model the lignin biosynthesis pathway [15] http://www.ligninsystems.org Other sources of information ... our systems biology- based network and in the co-expression network, respectively Transcription factors in our systems biology- based network that are not in the co-expression network are marked in...

Ngày tải lên: 11/08/2014, 11:21

... progress in systems biology, it seems likely that a second edition of this book will appear before many years have passed It is to be hoped that these (mostly minor) defects will be eliminated in the ... 168) In places, the writing would have benefited from the assistance of a native English speaker; odd phrasing such as 'negative definite' for 'always negative' (p 74, example 3–10 and surrounding ... might be the most serious imbalance in the book; as the authors admit, the continuum hypothesis is unlikely to be valid in modelling many aspects of signal processing and transcriptional regulation...

Ngày tải lên: 13/08/2014, 23:20

... oscillations in both populations, which slowly disappear and become linear growth Indeed, as the cell population begins to grow, it tends to activate APC signaling owing to overpopulation in the inner ... overpopulation signal, while increasing Tho speeds hypoxia activation Decreasing the initial number of cells has the same effect as increasing Tht, while decreasing the number or the initial strength of ... Chaplain MA: Continuous and discrete mathematical models of tumor-induced angio-genesis Bull Math Biol 1998, 60:857-899 Hahn WC, Weinberg RA: Modelling the molecular circuitry of cancer Nat Rev Cancer...

Ngày tải lên: 13/08/2014, 23:20

... treated in terms of a dynamic exchange, with amino acids constantly being converted into proteins, and proteins being degraded into amino acids His experiments with labeling leucine residues in proteins ... degree of modularity in nature: many separate functions are handled independently, and are only integrated into a single model at the end Moreover, with sufficient understanding of the system under ... identify proteins by fluorescence microscopy Machine-learning techniques can train a program to recognize the subcellular locations of proteins from the morphological features visible in fluorescence...

Ngày tải lên: 14/08/2014, 14:21

... differential equations The combination of these approaches led to interesting insights into the timedependent role of the kinase IKK in the NF-κB pathway in inducing the apoptotic response and ... autocrine loops involving transforming growth factor α and interleukin The question posed by Lauffenburger as to how information about extracellular cues is encoded in intracellular signaling pathways ... is not encoded in a single pathway, but that the information is distributed over the signaling network It also enabled a comparison of different modeling strategies, including principal component...

Ngày tải lên: 14/08/2014, 20:22

... Genome Biology 2008, 9:328 http://genomebiology.com/2008/9/12/328 Genome Biology 2008, models in systems biology using examples from halophilic archaea, including a simple mechanism for regulating ... in developing automated methods for determining the intracellular location of proteins tagged with green fluorescent protein Traditionally, this could only be done by expert microscopic examination ... (University of Edinburgh, UK) introduced compositional definitions of minimal flows in Petri nets and applied them to examples in the Petri-net-based ‘Calculus of Biochemical Systems Being able to...

Ngày tải lên: 14/08/2014, 21:20

... (scanning level, pre/postwashing), location effect (chip, coverslip, washing), dye effect (dye, unequal mixing of mixtures, labeling, intensity), print pin effect, spot effect (amount of DNA in the ... = 0.7(indep.) input calibrated input π0 = 0.9(dep.fix) input calibrated π0 = 0.9(dep.random) Error 0.00 0.05 0.10 0.15 0.20 π0 = 0.9(indep.) calibrated input calibrated input calibrated input ... many difficulties in balancing my job and study At these moments, Prof Choi always encouraged me to keep pursuing my goal and showed great patience in tolerating my delay in making progress I would...

Ngày tải lên: 09/09/2015, 18:56