Modeling of Intracellular Transport and Compartmentation

Abstract

The complexity and internal organization of mammalian cells as well as the regulation of intracellular transport processes has increasingly moved into the focus of investigation during the past two decades. Advanced staining and microscopy techniques help to shed light onto spatial cellular compartmentation and regulation, increasing the demand for improved modeling techniques. In this chapter, we summarize recent developments in the field of quantitative simulation approaches and frameworks for the description of intracellular transport processes. Special focus is therefore laid on compartmented and spatiotemporally resolved simulation approaches. The processes considered include free and facilitated diffusion of molecules, active transport via the microtubule and actin filament network, vesicle distribution, membrane transport, cell cycle-dependent cell growth and morphology variation, and protein production. Commercially and freely available simulation packages are summarized as well as model data exchange and harmonization issues.

Objective comparison of particle tracking methods

“…Technological developments in the past two decades have greatly advanced the field of bioimaging and have enabled the investigation of dynamic processes in living cells at unprecedented spatial and temporal resolution. Examples include the study of cell membrane dynamics 1 , cytoskeletal filaments 2 , focal adhesions 3 , viral infection 4 , intracellular transport 5 , gene transcription 6 and genome maintenance 7 . Apart from state-of-the-art light microscopy 8,9 and fluorescent labeling 10,11 , a key technology in the quest for quantitative analysis of intracellular dynamic processes is particle tracking.…”

OMEGA: a software tool for the management, analysis, and dissemination of intracellular trafficking data that incorporates motion type classification and quality control

“…Dynamic intracellular processes, such as viral and bacterial infection (Chenouard et al, 2009a;Brandenburg and Zhuang, 2007;Sun et al, 2013;Mercer et al, 2010;Li et al, 2017;Pereira et al, 2014;Ewers et al, 2005), vesicular trafficking (Siebrasse et al, 2016;Aoyama et al, 2017;Gramlich and Klyachko, 2017;Jandt et al, 2011;Jandt and Zeng, 2012;Loerke et al, 2009), membrane receptors dynamics (Jaqaman et al, 2016;Sergé et al, 2008;Block et al, 2016;Saxton and Jacobson, 1997), cytoskeletal rearrangement (Applegate et al, 2011;Akhmanova and Steinmetz, 2008), focal adhesion reorganization (Berginski et al, 2011), gene transcription (Sinha et al, 2010), and genome maintenance (Agarwal et al, 2011) are important for many clinically relevant fields of study including immune regulation, metabolic disorders, infectious diseases, and cancer. In all of these cases, diverse individual sub-resolution 'particles' (e.g.…”

Polycation‐mediated gene delivery: Challenges and considerations for the process of plasmid DNA transfection

“…Desirably, other components should include mediators that regulate homeostatic processes, as this will enable polyplexes to travel through the cell unhindered as much as possible and vice versa . To further understand the intracellular transport processes in eukaryotic cells during transient infection, increased focus has been given to processes such as free and facilitated diffusion of molecules and active transport via microtubule and actin filament networks .…”