Journal: Molecular Systems Biology

Article Title: Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico

doi: 10.1038/msb.2011.91

Figure Lengend Snippet: The very low limit for spg1 is due to dosage imbalance with byr4 . ( A ) To trigger cellular septation, GTPase Spg1 and its GAP Byr4 function in an antagonistic manner. The molecular interactions are given with Systems Biology Graphical Notation (SBGN) using CellDesigner 4.1 ( http://www.celldesigner.org ). ( B ) 2D-gTOW experiment between spg1 and byr4 . The copy numbers of spg1 and byr4 can be increased only when both gene copy numbers are balanced (dotted line). Extra copies of spg1 + are supplied by the pA6R plasmid, and extra copies of byr4 + are supplied by the pTOWsp-M plasmid. ( C ) Microscopic image of cells by 2D-gTOW experiment involving spg1 and byr4 . Sp286h+ cells with pTOWsp-M with byr4 and pA6R with spg1 were cultivated in EMM with leucine. GFP (reflecting the byr4 copy number), RFP (reflecting the spg1 copy number), the nucleus, and the septum were observed. Expected phenotypes of the cells within the dosage balance between spg1 and byr4 , and the indices within the image are shown.

Article Snippet: The SBML file of the gTOW model shown in can be obtained from BioModels database ( http://www.ebi.ac.uk/biomodels-main/ ) (ID: MODEL1111040000).

Techniques: Plasmid Preparation

Journal: Molecular Systems Biology

Article Title: Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico

doi: 10.1038/msb.2011.91

Figure Lengend Snippet: Mathematical model reproducing gTOW data. ( A ) Whole structure of the mathematical model of the fission yeast cell cycle developed in this study (gTOW model) given with Systems Biology Graphical Notation (SBGN) using CellDesigner 4.1. Pink colored components are the ones added to the ‘basic model' to make the ‘gTOW model'. CellDesigner file and Systems Biology Markup Language (SBML) file are provided in . ( B ) Comparison of the copy number limits of cell-cycle regulators between the data obtained by gTOW and prediction of the mathematical model. Scale of the axis=log2. ( C ) Time-course simulation result of the gTOW model.

Article Snippet: The SBML file of the gTOW model shown in can be obtained from BioModels database ( http://www.ebi.ac.uk/biomodels-main/ ) (ID: MODEL1111040000).

Techniques: Comparison

Journal: Molecular Systems Biology

Article Title: Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico

doi: 10.1038/msb.2011.91

Figure Lengend Snippet: Testing the gTOW model with 2D-gTOW experiments. ( A ) Comparison of upper limits of cell-cycle regulators in clp1 Δ, cig1 Δ, puc1 Δ, and srw1 Δ strains between the model prediction (orange) and experimental data (blue). The percentage of mutant/wild type is shown. Yellow marker indicates that the upper limit in the mutant strain is significantly less than the wild type (copy number is < 30% and P -value is <0.05). The large discrepancy between the model and experiment in the upper limit of pyp3 + in the srw1 Δ is also shown in yellow marker. The complete experimental data set is shown in . ( B ) Regulatory interactions among cell-cycle regulators in the fission yeast cell-cycle control network mathematically reconstituted in the gTOW model. Arrows and blocked end lines represent the simulation of synthesis (or activation) and repression of synthesis (or inhibition). Red lines indicate the potential novel regulations proposed by comparison of the gTOW model and 2D-gTOW data shown in (A). Red question marks refer the regulations with uncertain strengths in the model. Possible mechanisms for these regulations are described in Discussion.

Article Snippet: The SBML file of the gTOW model shown in can be obtained from BioModels database ( http://www.ebi.ac.uk/biomodels-main/ ) (ID: MODEL1111040000).

Techniques: Comparison, Mutagenesis, Marker, Control, Activation Assay, Inhibition

Journal: Briefings in Bioinformatics

Article Title: Harmonizing semantic annotations for computational models in biology

doi: 10.1093/bib/bby087

Figure Lengend Snippet: Example RDF-based annotation from SBML model BIOMD0000000239 in BioModels. The annotation block (indicated by a curly brace) defines the biological meaning of a physical compartment in the model. The RDF block within the element links the compartment’s metadata identifier ‘metaid_MT_IMS’ to the Gene Ontology term GO:0005758, which represents the mitochondrial intermembrane space. The use of the bqbiol:is predicate in this link indicates that the compartment is defined as the mitochondrial intermembrane space.

Article Snippet: One of the archives contains an SBML model retrieved from BioModels (BIOMD0000000176) that simulates glycolysis in yeast [ ].

Techniques: Blocking Assay

Journal: BMC Systems Biology

Article Title: A model reduction method for biochemical reaction networks

doi: 10.1186/1752-0509-8-52

Figure Lengend Snippet: Schematic of the original and reduced yeast-glycolysis networks. The left-hand panel is a schematic representation of the yeast glycolysis model used for model reduction. The full model description and an explanation of all the abbreviations is found in . The right-hand panel represents the reduced model after deleting 5 complexes (F6P, P2G, P3G, G6P and PEP). The blue arrows in the two panels indicate external fluxes.

Article Snippet: We have submitted to Biomodels two SBML files corresponding to the original and the reduced yeast glycolysis models (submission identifiers MODEL1403250001 and MODEL1403250002 respectively).

Techniques:

Journal: BMC Systems Biology

Article Title: A model reduction method for biochemical reaction networks

doi: 10.1186/1752-0509-8-52

Figure Lengend Snippet: Reduction of the yeast glycolysis model. Left-hand panel: minimum error integral versus number of deleted complexes (we have taken T =1.5 min for the computation of the error integral). Right-hand panel: identity of the deleted complexes and their convergence times.

Article Snippet: We have submitted to Biomodels two SBML files corresponding to the original and the reduced yeast glycolysis models (submission identifiers MODEL1403250001 and MODEL1403250002 respectively).

Techniques:

Journal: BMC Systems Biology

Article Title: A model reduction method for biochemical reaction networks

doi: 10.1186/1752-0509-8-52

Figure Lengend Snippet: Comparison of concentration profiles of yeast-glycolysis metabolites between the full and reduced models.

Article Snippet: We have submitted to Biomodels two SBML files corresponding to the original and the reduced yeast glycolysis models (submission identifiers MODEL1403250001 and MODEL1403250002 respectively).

Techniques: Comparison, Concentration Assay