Abstract:
:The Golgi apparatus has intrigued researchers since its discovery and despite the advances, there are still many open questions in regards to its shape and function. We propose a mechanical model of Golgi apparatus stack and explain its most elementary geometrical properties: the equilibrium number of cisternae, the stack size, and its general equilibrium shape. Combining both analytical and numerical methods we successfully reconstruct the stack morphology within the theory of bending elasticity. We demonstrate that energy-wise the stack prefers an overall bent shape and show strong evidence that the adhesion strength determines the equilibrium number of cisternae per stack. We explore the morphological role of fenestrations and discuss their impact on the overall stack structure. We also comment on the effects of the asymmetry in the composition of membrane leaflets on the shape of the cisternae and thus offer a broad steady-state study of the stack morphology and present a method that can be used also for other membrane-bound organelles.
journal_name
Phys Bioljournal_title
Physical biologyauthors
Jelerčič Udoi
10.1088/1478-3975/ab3766subject
Has Abstractpub_date
2019-09-05 00:00:00pages
066003issue
6eissn
1478-3967issn
1478-3975journal_volume
16pub_type
杂志文章相关文献
PHYSICAL BIOLOGY文献大全abstract::The one-cell amphibian embryo is modeled as a rigid spherical shell containing equal volumes of two immiscible fluids with different densities and viscosities and a surface tension between them. The fluids represent denser yolk in the bottom hemisphere and clearer cytoplasm and the germinal vesicle in the top hemisphe...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/5/1/015006
更新日期:2008-04-10 00:00:00
abstract::Based on recent experimental data, we design a model for neuronal membrane potentials that incorporates the influence of the surrounding glia (dressed neurons). A neurotransmitter released into the synaptic cleft triggers a Ca(2+) response in nearby glial cells that spreads as a Ca(2+) wave and interacts with other sy...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3967/1/1/004
更新日期:2004-06-01 00:00:00
abstract::The important role of cation-chloride co-transporters in epilepsy is being supported by an increasing number of investigations. However, enormous complexity is involved since the action of these co-transporters has effects on the ionic homeostasis influencing directly the neuronal excitability and the tissue propensit...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/5/056008
更新日期:2013-10-01 00:00:00
abstract::Oncolytic virotherapy-the use of viruses that specifically kill tumor cells-is an innovative and highly promising route for treating cancer. However, its therapeutic outcomes are mainly impaired by the host immune response to the viral infection. In this paper, we propose a multiscale mathematical model to study how t...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/2/025005
更新日期:2013-04-01 00:00:00
abstract::In many bacterial species, the protein FtsZ forms a cytoskeletal ring that marks the future division site and scaffolds the division machinery. In rod-shaped bacteria, most frequently membrane-attached FtsZ rings or ring fragments are reported and occasionally helices. By contrast, axial FtsZ clusters have never been ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/9/1/016009
更新日期:2012-02-01 00:00:00
abstract::A central question in eukaryotic cell biology asks, during cell division, how is the growth and distribution of organelles regulated to ensure each daughter cell receives an appropriate amount. For vacuoles in budding yeast, there are well described organelle-to-cell size scaling trends as well as inheritance mechanis...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/aba510
更新日期:2020-10-09 00:00:00
abstract::Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation diagram and characterize the bistable and the monostable regimes. The main focus of...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/3/036005
更新日期:2013-06-01 00:00:00
abstract::Gene-regulation networks contain recurring elementary circuits termed network motifs. It is of interest to understand under which environmental conditions each motif might be selected. To address this, we study one of the most significant network motifs, a three-gene circuit called the coherent feed-forward loop (FFL)...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/2/2/001
更新日期:2005-06-01 00:00:00
abstract::Tissue factor (TF) is a transmembrane glycoprotein cofactor of activated blood coagulation factor VII (FVIIa) that is required for hemostatic thrombin generation at sites of blood vessel injury. Membrane-associated TF detected in circulating blood of healthy subjects, referred to as intravascular or circulating TF has...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/6/066005
更新日期:2011-12-01 00:00:00
abstract::We model the motility of Dictyostelium cells in a systematic data-driven manner. We deduce a minimal dynamical model that reproduces the statistical features of experimental trajectories. These are trajectories of the centroid of the cell perimeter, which is more sensitive to pseudopod activity than the usual tracking...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/4/046006
更新日期:2011-08-01 00:00:00
abstract::The spatial patterning of three cell fates in a row of competent cells is exemplified by vulva development in the nematode Caenorhabditis elegans. The intercellular signaling network that underlies fate specification is well understood, yet quantitative aspects remain to be elucidated. Quantitative models of the netwo...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/9/4/045001
更新日期:2012-08-01 00:00:00
abstract::A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication o...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/7/4/045001
更新日期:2010-12-09 00:00:00
abstract::The asymmetric cell division cycle in Caulobacter crescentus is controlled by an elaborate molecular mechanism governing the production, activation and spatial localization of a host of interacting proteins. In previous work, we proposed a deterministic mathematical model for the spatiotemporal dynamics of six major r...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/13/3/035007
更新日期:2016-06-25 00:00:00
abstract::Cells can often choose among several stably heritable phenotypes. Examples are the expressions of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states that may be associated with positive feedback in dynamic modification of nucleosomes. We generalize thi...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/7/2/026010
更新日期:2010-06-04 00:00:00
abstract::Circular DNA in viruses and bacteria is often knotted. While mathematically problematic, the determination of the knot size is crucial for the study of the physical and biological behaviour of long macromolecules. Here, we review work on the size distribution of these knots under equilibrium conditions. We discuss kno...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/6/2/025012
更新日期:2009-07-01 00:00:00
abstract::Engineering artificial cells to mimic one or multiple fundamental cell biological functions is an emerging area of synthetic biology. Reconstituting functional modules from biological components in vitro is a challenging yet an important essence of bottom-up synthetic biology. Here we describe the concept of building ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/aa9768
更新日期:2017-12-06 00:00:00
abstract::Protein-protein interactions are central to biology and, in this 'post-genomic era', prediction of these interactions has become the goal of many computational efforts. Close inspection of even relatively simple biological regulatory circuitry reveals multiple levels of control of the contributing protein interactions...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/2/2/S07
更新日期:2005-06-01 00:00:00
abstract::This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle-field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale sy...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/10/4/045007
更新日期:2013-08-01 00:00:00
abstract::With the development of next-generation sequencing technologies, many large scale experimental efforts aim to map genotypic variability among individuals. This natural variability in populations fuels many fundamental biological processes, ranging from evolutionary adaptation and speciation to the spread of genetic di...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/11/2/026005
更新日期:2014-04-01 00:00:00
abstract::Efficient nucleotide import is critical to fuel the reverse DNA synthesis that takes place within the HIV-1 capsid. However, the mechanism by which the HIV-1 capsid imports nucleotides is presently unclear. In this work, we carry out a series of Brownian diffusion simulations to elucidate the nucleotide import process...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/abbf32
更新日期:2020-10-07 00:00:00
abstract::Traditionally animal groups have been characterized by the macroscopic patterns that they form. It is now recognised that such patterns convey limited information about the nature of the aggregation as a whole. Aggregate properties cannot be determined by passive observations alone; instead one must interact with them...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/ab12b9
更新日期:2019-04-23 00:00:00
abstract::Intermolecular interactions became an inherent part of the structure-function paradigm. Therefore, the generalized concept of protein stability and interactions should consider the balance of stabilizing forces working in different types of intermolecular interactions. We consider here two 'extremes' of protein intera...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/8/3/035002
更新日期:2011-06-01 00:00:00
abstract::Directed cell migration often involves at least two types of cell motility that include multicellular streaming and chain migration. However, what is unclear is how cell contact dynamics and the distinct microenvironments through which cells travel influence the selection of one migratory mode or the other. The embryo...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/3/035003
更新日期:2013-06-01 00:00:00
abstract::Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts within households and more distant contacts between the households. The epidemic transmission dynamics is significantly modified as a consequence. W...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/abb209
更新日期:2020-10-21 00:00:00
abstract::Bacteria such as Escherichia coli propel themselves by rotating a bundle of helical filaments, each driven by a rotary motor embedded in the cell membrane. Each filament is an assembly of thousands of copies of the protein flagellin which assumes two different states. We model the filament by an elastic network of rig...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/4/046009
更新日期:2011-08-01 00:00:00
abstract::The DFT:B3LYP (6-31G** basis set) method, including the hyperfine and spin-orbit couplings (HFC and SOC, respectively), is used to study the separation of two complementary trinucleotide sequences, (dC-dG-dA)-(dG-dC-dT), upon the action of two Mg(2+) cofactors (a simplified model). The computations reveal a crossing o...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/6/066017
更新日期:2015-12-10 00:00:00
abstract::Cells moving on a two dimensional substrate generate motion by polymerizing actin filament networks inside a flat membrane protrusion. New filaments are generated by branching off existing ones, giving rise to branched network structures. We investigate the force-extension relation of branched filaments, grafted on an...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/4/046007
更新日期:2015-06-04 00:00:00
abstract::Growing evidence suggests that critical cellular processes are profoundly influenced by the cross talk between extracellular nanomechanical forces and the material properties of the cellular microenvironment. Although many studies have examined either the effect of nanomechanical forces or the material properties of t...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/6/066003
更新日期:2013-12-01 00:00:00
abstract::The majority of chronic infections are caused by biofilms, which have higher levels of antibiotic resistance than planktonic growth. Violet-blue 405 nm light has recently emerged as a novel bactericide, but limited studies have been conducted on its effectiveness against biofilms. We found that in response to 405 nm l...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/ab759a
更新日期:2020-03-04 00:00:00
abstract::Asexual reproduction in multicellular organisms is a complex biophysical process that is not yet well understood quantitatively. Here, we report a detailed population study for the asexual freshwater planarian Schmidtea mediterranea, which can reproduce via transverse fission due to a large stem cell contingent. Our l...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/2/026003
更新日期:2011-04-01 00:00:00