M2986 Pancreas TurnoverModel ID: https://identifiers.org/morpheus/M2986
Full title: Beta Cell Turnover in Pancreatic Islet
Date: 20.09.2024
Authors: M. N. Akhtar, L. Brusch, N. Ninov
BioModels: https://www.ebi.ac.uk/biomodels/MODEL2503030004
Species: https://identifiers.org/taxonomy:7955
Tissue: https://identifiers.org/UBERON:0000006
Cells: https://identifiers.org/CL:0000169, https://identifiers.org/CL:0000445
Units: [time] = 1 d
[space] = 1 µm
Software: Morpheus (open source). Download from: https://morpheus.gitlab.io
Reference: This Morpheus model was developed and analyzed in the original publication:
M. N. Akhtar, A. Hnatiuk, L. Delgadillo-Silva, S. Geravandi, K. Sameith, S. Reinhardt, K. Bernhardt, S. P. Singh, K. Maedler, L. Brusch, N. Ninov (2025). Developmental beta-cell death orchestrates the islet’s inflammatory milieu by regulating immune system crosstalk. The EMBO Journal 44 (4), 1131 - 1153, https://doi.org/10.1038/s44318-024-00332-w
Submitters: L. Brusch
Curators: D. Jahn
optimalSurrounding tissue with fluid-like properties, hence no interactions with CellTypes.Cycling beta cell in WT condition (https://identifiers.org/CL:0000169)time >= time.birth+Tcexp(rand_norm(Tc.ln_mean,Tc.ln_std))timerand_uni(0,1)<(k.inact*mcs_duration) and time>time.starttime(rand_uni(0,1)<(v*celltype.Cell_WT_p.size/N_WT*mcs_duration)) and (time>time.start)space.z==0 and ((space.x-size.x/2)^2+(space.y-size.y/2)^2)<20^2time(time>=time.onset) and (time<time.onset+time.duration) and rand_uni(0,1)<(d*mcs_duration)timeQuiescent beta cell in WT condition (https://identifiers.org/CL:0000169)rand_uni(0,1)<(k.act*mcs_duration) and time>time.starttime-(time.inact-time.birth)(rand_uni(0,1)<(v*celltype.Cell_WT_q.size/N_WT*mcs_duration)) and (time>time.start)space.z==0 and ((space.x-size.x/2)^2+(space.y-size.y/2)^2)<20^2time(time>=time.onset) and (time<time.onset+time.duration) and rand_uni(0,1)<(d*mcs_duration)timeCycling beta cell in p35 mutant condition (https://identifiers.org/CL:0000169)time >= time.birth+Tcexp(rand_norm(Tc.ln_mean,Tc.ln_std))timerand_uni(0,1)<(k.inact*mcs_duration) and time>time.starttime(rand_uni(0,1)<(v*celltype.Cell_p35_p.size/N_p35*mcs_duration)) and (time>time.start)space.z==2 and ((space.x-size.x/2)^2+(space.y-size.y/2)^2)<20^2timeQuiescent beta cell in p35 mutant condition (https://identifiers.org/CL:0000169)rand_uni(0,1)<(k.act*mcs_duration) and time>time.starttime-(time.inact-time.birth)(rand_uni(0,1)<(v*celltype.Cell_p35_q.size/N_p35*mcs_duration)) and (time>time.start)space.z==2 and ((space.x-size.x/2)^2+(space.y-size.y/2)^2)<20^2timeStatic dummy object to separate two conditions in z-layers above and below.1Apoptotic beta cell (https://identifiers.org/CL:0000445)time>=time.birth+time.apoptoticoptimaloptimalMean cell cycle duration.Recruitment flux per day of de-novo beta cells into the islet.Apoptotic death rate per day for beta cells.Onset time of apoptosis for beta cells.Duration in days of apoptosis phase.Rate of cell cycle activation per day (quiescence -> cycling).Rate of cell cycle inactivation per day (cycling -> quiescence).Cell dynamics, plotting and exp. data start from time.start=5dpf. The CPM model uses the burn-in phase from 0 to 5dpf to equilibrate cell shapes.Duration in days when apoptotic cells remain observable before clearance by immune cells.ode.Np_WT+ode.Nq_WTode.Np_p35+ode.Nq_p35(time>=5.0)*(v*ode.Np_WT/ode.Nsum_WT + k.act*ode.Nq_WT - k.inact*ode.Np_WT + ln(2)/Tc.mean*ode.Np_WT - d*(time>=time.onset)*(time<(time.onset+time.duration))*ode.Np_WT)(time>=5.0)*(v*ode.Nq_WT/ode.Nsum_WT - k.act*ode.Nq_WT + k.inact*ode.Np_WT - d*(time>=time.onset)*(time<(time.onset+time.duration))*ode.Nq_WT)(time>=5.0)*(v*ode.Np_p35/ode.Nsum_p35 + k.act*ode.Nq_p35 - k.inact*ode.Np_p35 + ln(2)/Tc.mean*ode.Np_p35)(time>=5.0)*(v*ode.Nq_p35/ode.Nsum_p35 - k.act*ode.Nq_p35 + k.inact*ode.Np_p35)Target cell size in number of lattice nodes.celltype.Cell_WT_p.size+celltype.Cell_WT_q.sizecelltype.Cell_p35_p.size+celltype.Cell_p35_q.size