Modelling of fluid-phase endocytosis kinetics in the amoebae of the cellular slime mouldDictyostelium discoideum. A multicompartmental approach

Curating models from BioModels: Developing a workflow for creating OMEX files

The reproducibility of computational biology models can be greatly facilitated by widely adopted standards and public repositories. We examined 50 models from the BioModels Database and attempted to validate the original curation and correct some of them if necessary. For each model, we reproduced these published results using Tellurium. Once reproduced we manually created a new set of files, with the model information stored by the Systems Biology Markup Language (SBML), and simulation instructions stored by the Simulation Experiment Description Markup Language (SED-ML), and everything included in an Open Modeling EXchange (OMEX) file, which could be used with a variety of simulators to reproduce the same results. On the one hand, the validation procedure of 50 models developed a manual workflow that we would use to build an automatic platform to help users more easily curate and verify models in the future. On the other hand, these exercises allowed us to find the limitations and possible enhancement of the current curation and tooling to verify and curate models.

Synthesis, Self-Assembly and In Vitro Cellular Uptake Kinetics of Nanosized Drug Carriers Based on Aggregates of Amphiphilic Oligomers of N-Vinyl-2-pyrrolidone

Development of nanocarrier-based drug delivery systems is a major breakthrough in pharmacology, promising targeted delivery and reduction in drug toxicity. On the cellular level, encapsulation of a drug substantially affects the endocytic processes due to nanocarrier–membrane interaction. In this study we synthesized and characterized nanocarriers assembled from amphiphilic oligomers of N-vinyl-2-pyrrolidone with a terminal thiooctadecyl group (PVP-OD). It was found that the dissolution free energy of PVP-OD depends linearly on the molecular mass of its hydrophilic part up to M¯n = 2 × 10⁴, leading to an exponential dependence of critical aggregation concentration (CAC) on the molar mass. A model hydrophobic compound (DiI dye) was loaded into the nanocarriers and exhibited slow release into the aqueous phase on a scale of 18 h. Cellular uptake of the loaded nanocarriers and that of free DiI were compared in vitro using glioblastoma (U87) and fibroblast (CRL2429) cells. While the uptake of both DiI/PVP-OD nanocarriers and free DiI was inhibited by dynasore, indicating a dynamin-dependent endocytic pathway as a major mechanism, a decrease in the uptake rate of free DiI was observed in the presence of wortmannin. This suggests that while macropinocytosis plays a role in the uptake of low-molecular components, this pathway might be circumvented by incorporation of DiI into nanocarriers.

Conserved features of endocytosis in Dictyostelium

Endocytosis in protozoa is often regarded as largely different from the pathways operating in mammalian cells. Experiments in the amoeba Dictyostelium, one of the genetically tractable single-celled organisms, have allowed us to manipulate the flow through endocytic compartments and to study the dynamic distribution of molecules by means of green fluorescent protein fusions. This review attempts to compile the molecular data available from Dictyostelium and assign them to specific steps of internalization by phagocytosis or macropinocytosis and to subsequent stages of the endocytic pathway. Parallels to phagocytes of the mammalian immune system are emphasized. The major distinctive feature between mammalian phagocytes and free-living cells is the need for osmoregulation. Therefore Dictyostelium cells possess a contractile vacuole that has occasionally obscured analysis of endocytosis but is now found to be entirely separate from endocytic organelles. In conclusion, the potential of Dictyostelium amoebas to provide a model system of mammalian phagocytes is ever increasing.

Fusion and fission events in the endocytic pathway of Dictyostelium

The endocytic pathway in Dictyostelium appears as a short circuit between endocytosis and exocytosis. Within the hour that elapses between internalization of nutrients and release of remnants, digestion by lysosomal enzymes occurs. Meanwhile, the maturing endosome undergoes a complex series of fusion and fission events, which change its character profoundly and which are far from being fully understood. This review attempts to order the dynamic events into a sequence of stages that is most consistent with present knowledge.

Targeted gene disruption reveals a role for vacuolin B in the late endocytic pathway and exocytosis

Cells of Dictyostelium discoideum take up fluid by macropinocytosis. The contents of macropinosomes are acidified and digested by lysosomal enzymes. Thereafter, an endocytic marker progresses in an F-actin dependent mechanism from the acidic lysosomal phase to a neutral post-lysosomal phase. From the post-lysosomal compartment indigestible remnants are released by exocytosis. This compartment is characterised by two isoforms of vacuolin, A and B, which are encoded by different genes. Fusions of the vacuolin isoforms to the green fluorescent protein associate with the cytoplasmic side of post-lysosomal vacuoles in vivo. Vacuolin isoforms also localise to patches at the plasma membrane. Since vacuolins have no homologies to known proteins and do not contain domains of obvious function, we investigated their role by knocking out the genes separately. Although the sequences of vacuolins A and B are about 80% identical, only deletion of the vacuolin B gene results in a defect in the endocytic pathway; the vacuolin A knock-out appeared to be phenotypically normal. In vacuolin B- mutants endocytosis is normal, but the progression of fluid-phase marker from acidic to neutral pH is impaired. Furthermore, in the mutants post-lysosomal vacuoles are dramatically increased in size and accumulate endocytic marker, suggesting a role for vacuolin B in targeting the vacuole for exocytosis.

Coronin and vacuolin identify consecutive stages of a late, actin-coated endocytic compartment in Dictyostelium

Cells of the unicellular eukaryote Dictyostelium discoideum take up all their nutrients by endocytosis. Both particle- and fluid-containing vacuoles are transiently surrounded by a cytoskeletal coat [1] [2]. When this coat has dissociated, acidification and digestion of the vesicle contents occur, followed by exocytosis of the indigestible remnants after 60-90 minutes. At least nine compartments are needed for mathematical modelling of endocytic transit [3], suggesting that markers associate for only a few minutes with a specific endocytic compartment. Among the proteins that have been identified as components of endocytic vesicles are actin, subunits of the V-H+ ATPase and small GTP-binding proteins of the Rab family [4] [5] [6] [7]. Using a monoclonal antibody produced against Dictyostelium endocytic vesicles, we have isolated a cDNA corresponding to a novel protein that we have named vacuolin. In order to determine the precise step along the endocytic pathway that involves vacuolin, we generated a fusion protein of the green fluorescent protein (GFP) and vacuolin. GFP-vacuolin-decorated vesicles were identified as a post-lysosomal compartment that acquires endocytic markers shortly before exocytosis. At earlier stages, this post-lysosomal compartment was identified by the binding of a tagged cytoskeletal protein, coronin-GFP. Vacuoles were coated with filamentous actin along the entire post-lysosomal pathway, and the integrity of the actin coat was required for exocytosis.