BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=curation_notes.txthttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160.pdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=manifest.xmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160.scihttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160.vcmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160-matlab.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=curation_image.jpeghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160_url.sedmlhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160.mhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160.pnghttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=metadata.rdfhttps://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000160?filename=BIOMD0000000160.odeprimaryOK200Harish DharuriManually curatedordinary differential equation modelL2V1https://www.ebi.ac.uk/biomodels/BIOMD000000016017157878falseBioModelsSBMLModelsXie2007 CircClock2007MODEL1029395046Z Xie, Kulasiri DZ Xie17157878, Circadian rhythms of gene activity, metabolism, physiology and behaviour are observed in all the eukaryotes and some prokaryotes. In this study, we present a model to represent the transcriptional regulatory network essential for the circadian rhythmicity in Drosophila. The model incorporates the transcriptional feedback loops revealed so far in the network of the circadian clock (PER/TIM and VRI/PDP1 loops). Conventional Hill functions are not assumed to describe the regulation of genes, instead of the explicit reactions of binding and unbinding processes of transcription factors to promoters are modelled. The model simulates sustained circadian oscillations in mRNA and protein concentrations in constant darkness in agreement with experimental observations. It also simulates entrainment by light-dark cycles, disappearance of the rhythmicity in constant light and the shape of phase response curves resembling that of the experimental results. The model is robust over a wide range of parameter variations. In addition, the simulated E-box mutation, per(S) and per(L) mutants are similar to that observed in the experiments. The deficiency between the simulated mRNA levels and experimental observations in per(01), tim(01) and clk(Jrk) mutants suggests some difference on the part of the model from reality.. 2, 245. Centre for Advanced Computational Solutions (C-fACS), Lincoln University, Canterbury, New Zealand.hdharuri@cds.caltech.eduCalifornia Institute of TechnologyBIOMD0000000160Circadian rhythms of gene activity, metabolism, physiology and behaviour are observed in all the eukaryotes and some prokaryotes. In this study, we present a model to represent the transcriptional regulatory network essential for the circadian rhythmicity in Drosophila. The model incorporates the transcriptional feedback loops revealed so far in the network of the circadian clock (PER/TIM and VRI/PDP1 loops). Conventional Hill functions are not assumed to describe the regulation of genes, instead of the explicit reactions of binding and unbinding processes of transcription factors to promoters are modelled. The model simulates sustained circadian oscillations in mRNA and protein concentrations in constant darkness in agreement with experimental observations. It also simulates entrainment by light-dark cycles, disappearance of the rhythmicity in constant light and the shape of phase response curves resembling that of the experimental results. The model is robust over a wide range of parameter variations. In addition, the simulated E-box mutation, per(S) and per(L) mutants are similar to that observed in the experiments. The deficiency between the simulated mRNA levels and experimental observations in per(01), tim(01) and clk(Jrk) mutants suggests some difference on the part of the model from reality.Modelling of circadian rhythms in Drosophila incorporating the interlocked PER/TIM and VRI/PDP1 feedback loops.Xie Z Z, Kulasiri D Dbiochemical pathways, subgenus>, Hac-1/Dark, Metabolic Process, fruit fly, PDP1epsilon, Materials, Activity, DmelCG6829, Metabolic Concepts, Visible Light, dper, protein, STY, Apaf-1, Social Controls, Mendosicutes, Mutations, GEF5, responsivity, Concepts, Apaf1, Metabolism Concept, dPER, protein aggregate, Phenomenon, ARK, Formal Social Controls, Non Polyadenylated, Flies, dmper, jerky, hac-1, Metabacteria, catabolism, Triose-phosphate isomerase, mel_per, Drosophilas, Polyadenylated Messenger, Fly, KAT13D, CLK|STY, arc, metabolic process resulting in cell growth, pdp1epsilon, mKIAA0334, Eucarya, Pdp1epsilon, ark, T1, eucaryotes, Bacteria Woese et al. 2024, Social, TNFSF14, DmelCG17888, Prokaryotae, biotransformation, Procaryotae, dApaf1, fruit flies, TIM, Tim, Catabolism, single-organism behavior, CG2647, pdp1, Archaebacteria, anatomical protrusion, Radiation, wide/broad, Process, D-Apaf-1, Polyadenylated, UNQ391/PRO726, C77407, metabolism resulting in cell growth, anon-53Fa, l(2)SH0173, Light, JH8., tim, XClock, results, TIM1, Pdp1e, LIGHT, Ritsu, tim1, TPID, Genetic Materials, secretion, prokaryotes, CG6829, Genetic Material, 1823, dark/hac-1/dapaf-1, Polyadenylated Messenger RNA, Visible Radiations, Drosophila <basidiomycete fungi>, Visible Radiation, Non Polyadenylated mRNA, Factors, protein_coding_transcript, HVEML, DmelCG2647, Eukarya, fruit fly <Drosophila>, Control, INSDC_feature:gene, hac1, Controls, PDP, Non-Polyadenylated mRNA, experimental procedures, dapaf-1S, wide, apaf-1, Drosophila, dapaf-1L, Material, spine, Drosophila Fruit Fly, PDP1, Cistron, Feedbacks, Regulation, Poly(A) RNA, PER, Per, Prokaryota, pdp, Drosophila <flies, Drosophila Fruit Flies, Regulations, CLK, Clk, Drosophila Fallen, Dapaf-1/HAC-1, experimental, P60, Processes, Eukaryotes, Gene, Pdp-1, eubacteria, broad, Metabolic Processes, 5330400M04Rik, protein-containing complex, Transcription Factor, EG:155E2.4, rit, hTIM, protrusion, Ly113, Dark/Hac-1/dApaf1, clk, Hac1, Dark/Hac-1/dApaf-1, relational shape quality, Messenger, Metabolism, mel_pdp1, Gene Products, Darknesses, CG3234, Bacteriobiota, Metabolism Phenomena, bHLHe8, study, reactivity, Transcription, methods, Genetic, TPI, experimental section, ligand, dapaf-1, Metabolic Concept, messenger RNA, dapaf, Visible, dark, CG17888, Monera, Drosophila Fruit, Bacteria (ex Cavalier-Smith 1987), template RNA, DARK, Debt69, TR2, Archaebiota, dArk, Dapaf-1, dark/dapaf-1/hac-1, bacteria, RNA, DmelCG3234, Eukaryote, degradation, Formal Social Control, protein complex, 5.3.1.1, dApaf-1, Proteins, Messenger RNA, Eukaryotas, genus>, apaf1, function, Factor, Cistrons, dtim, CD258, Concept, Metabolic Phenomena, eukaryotes, CLK/STY, Metabolism Concepts, APAF1, native protein, Social Control, Hac-1, Pdp1 epsilon, Poly(A)+ mRNA, Protein, Phenomena, INSDC_feature:mRNA, Polyadenylated RNA, Dark, metabolism, dTIM, dTim, Dark/Apaf-I, Metabolic Phenomenon, Radiations, anon-WO0140519.206, multicellular organism metabolic process, bA6J24.6, Poly(A)+ RNA, biodegradation, Metabolic, mRNA, Poly(A) Tail, HVEM-L, not Bacteria Haeckel 1894, archaea, Photoradiation, mel_tim, Non-Polyadenylated, Dark/Dapaf-1/HAC1, dApaf-1/DARK/HAC-1, LTg, Fruit Flies, Protein Gene Products, Gene Proteins, Xclk, Eukaryotae, Photoradiations, PSDP, prokaryote, HEL-S-49, clk-6, Fruit Fly, regulation, Eucaryotae, response, Polyadenylated mRNA, General activity, dAPAF-1, Anabolismextent, Misinformation, Sectors, Public Sectors, YB, AUTSX5, number, Gene, Copyrights, protein, NOVH, protein-containing complex, CCN3, 2210402P09Rik, QM, Personal, Communications, Yb, Messenger, Figs, Gene Products, Misinformations, Miscommunication, Public Enterprise, protein aggregate, Enterprises, Non Polyadenylated, CG2706, fs(1)M104, PIST, DmelCG7615, Personnel, Polyadenylated Messenger, Public Domains, AI844555, messenger RNA, Social Communications, IGFBP9, Public Enterprises, DEPP, Communication, Rubberplants, Social, IBP-9, Communication Programs, Kiaa4053, template RNA, Rubberplant, L10, Fseg, species, NOVh, Enterprise, Personal Communication, Decidual protein induced by progesterone, RNA, Papers, Polyadenylated, Social Communication, completeness, protein complex, DmelCG2706, Proteins, Messenger RNA, DXS648, presence., Programs, Program, Fasting-induced gene protein, count in organism, native protein, IGFBP-9, Public, Public Domain, Poly(A)+ mRNA, Protein, Communications Personnel, CAL, Domains, INSDC_feature:mRNA, NOV, Polyadenylated RNA, PlexA1, GOPC1, Domain, Data Base, Polyadenylated Messenger RNA, Poly(A)+ RNA, Plxn1, Non Polyadenylated mRNA, protein_coding_transcript, mRNA, Poly(A) Tail, Non-Polyadenylated, nov, mKIAA4053, Non-Polyadenylated mRNA, fs(1)Y[b], dJ94G16.2, Miscommunications, Protein Gene Products, Gene Proteins, FIG, Fig, Sector, C130088N23Rik, EG:95B7.8, CG7615, 2600013D04Rik, PLXN1, Communication Program, DXS648E, Polyadenylated mRNA, Poly(A) RNAsubgenus>, pdp1, fruit fly, PDP1epsilon, Drosophila Fallen, DmelCG3234, P60, 5.3.1.1, C77407, genus>, Pdp-1, tim, dtim, Feedbacks., rit, TIM1, hTIM, Pdp1e, Ritsu, GEF5, Pdp1 epsilon, tim1, TPID, mel_pdp1, CG3234, dTIM, dTim, Flies, 1823, anon-WO0140519.206, Drosophila <basidiomycete fungi>, bA6J24.6, TPI, Triose-phosphate isomerase, Drosophilas, Fly, fruit fly <Drosophila>, mel_tim, pdp1epsilon, Pdp1epsilon, CG17888, PDP, Fruit Flies, Drosophila Fruit, Drosophila, DmelCG17888, PSDP, Drosophila Fruit Fly, HEL-S-49, PDP1, Debt69, Fruit Fly, fruit flies, TIM, Tim, pdp, Drosophila <flies, Drosophila Fruit FliesfalseXie2007_CircClock The model reproduces the oscillations for mRNA and protein species as depicted in Fig 3 of the plot. The model differs slightly from that given in the paper and this was made after a communication from the authors. The values of parameters tcvriclkp, tcdvpmt and dccpt are slightly different. Also, although it is not given in the paper, rate laws for reactions re20, re28, re35, re42, re43 and re45 are multiplied by a specie. Model was successfully tested on MathSBML To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92. 2024-08-212024-09-022008-01-30BIOMD0000000160dme0471117157878MODEL1029395046BIOMD0000000160GO:0005623GO:0044257GO:0006351GO:0006402GO:0006412GO:0007623GO:0045187GO:0046982GO:0043624GO:0006357GO:0030528GO:0003700GO:00434337227O61734O61735Q59E16P07663Q9VMS4Q9TW49