Agent-based modelling as scientific method: a case study analysing primate social behaviour

A scientific methodology in general should provide two things: first, a means of explanation and, second, a mechanism for improving that explanation. Agent-based modelling (ABM) is a method that facilitates exploring the collective effects of individual action selection. The explanatory force of the model is the extent to which an observed meta-level phenomenon can be accounted for by the behaviour of its micro-level actors. This article demonstrates that this methodology can be applied to the biological sciences; agent-based models, like any other scientific hypotheses, can be tested, critiqued, generalized or specified. We review the state of the art for ABM as a methodology for biology and then present a case study based on the most widely published agent-based model in the biological sciences: Hemelrijk's DomWorld, a model of primate social behaviour. Our analysis shows some significant discrepancies between this model and the behaviour of the macaques, the genus used for our analysis. We also demonstrate that the model is not fragile: its other results are still valid and can be extended to compensate for these problems. This robustness is a standard advantage of experiment-based artificial intelligence modelling techniques over analytic modelling.     

Synthesis and evaluation as MRI probe of the trifluoromethylated p-boronophenylalanine and its alcohol derivative

Boron-neutron capture therapy (BNCT) and magnetic resonance imaging (MRI) are quite attractive techniques for treatment and diagnosis of cancer, respectively. In order to develop practical tools for BNCT and MRI, novel compounds containing both the trifluoromethyl group and 10B atom in a single molecule were designed. In the present study, p-boronophenylalanine and p-boronophenylalaninol with the trifluoromethyl group were synthesized, and 19F NMR measurements of these compounds were carried out.     

Proteinase-activated receptor 4 stimulation-induced epithelial-mesenchymal transition in alveolar epithelial cells

Background

Proteinase-activated receptors (PARs; PAR_1–4) that can be activated by serine proteinases such as thrombin and neutrophil catepsin G are known to contribute to the pathogenesis of various pulmonary diseases including fibrosis. Among these PARs, especially PAR₄, a newly identified subtype, is highly expressed in the lung. Here, we examined whether PAR₄ stimulation plays a role in the formation of fibrotic response in the lung, through alveolar epithelial-mesenchymal transition (EMT) which contributes to the increase in myofibroblast population.

Methods

EMT was assessed by measuring the changes in each specific cell markers, E-cadherin for epithelial cell, α-smooth muscle actin (α-SMA) for myofibroblast, using primary cultured mouse alveolar epithelial cells and human lung carcinoma-derived alveolar epithelial cell line (A549 cells).

Results

Stimulation of PAR with thrombin (1 U/ml) or a synthetic PAR₄ agonist peptide (AYPGKF-NH₂, 100 μM) for 72 h induced morphological changes from cobblestone-like structure to elongated shape in primary cultured alveolar epithelial cells and A549 cells. In immunocytochemical analyses of these cells, such PAR₄ stimulation decreased E-cadherin-like immunoreactivity and increased α-SMA-like immunoreactivity, as observed with a typical EMT-inducer, tumor growth factor-β (TGF-β). Western blot analyses of PAR₄-stimulated A549 cells also showed similar changes in expression of these EMT-related marker proteins. Such PAR₄-mediated changes were attenuated by inhibitors of epidermal growth factor receptor (EGFR) kinase and Src. PAR₄-mediated morphological changes in primary cultured alveolar epithelial cells were reduced in the presence of these inhibitors. PAR₄ stimulation increased tyrosine phosphorylated EGFR or tyrosine phosphorylated Src level in A549 cells, and the former response being inhibited by Src inhibitor.

Conclusion

PAR₄ stimulation of alveolar epithelial cells induced epithelial-mesenchymal transition (EMT) as monitored by cell shapes, and epithelial or myofibroblast marker at least partly through EGFR transactivation via receptor-linked Src activation.     

Identification on Membrane and Characterization of Phosphoproteins Using an Alkoxide-Bridged Dinuclear Metal Complex as a Phosphate-Binding Tag Molecule

We have developed a method for on-membrane direct identification of phosphoproteins, which are detected by a phosphate-binding tag (Phos-tag) that has an affinity to phosphate groups with a chelated Zn2+ ion. This rapid profiling approach for phosphoproteins combines chemical inkjet technology for microdispensing of reagents onto a tiny region of target proteins with mass spectrometry for on-membrane digested peptides. Using this method, we analyzed human epidermoid carcinoma cell lysates of A-431 cells stimulated with epidermal growth factor, and identified six proteins with intense signals upon affinity staining with the phosphate-binding tag. It was already known that these proteins are phosphorylated, and our new approach proved to be effective at rapid profiling of phosphoproteins. Furthermore, we tried to determine their phosphorylation sites by MS/MS analysis after in-gel digestion of the corresponding spots on the 2DE gel to the rapid on-membrane identifications. As one example of use of information gained from the rapid-profiling approach, we successfully characterized a phosphorylation site at Ser-113 on prostaglandin E synthase 3.     

Characterization of proteins expressed abundantly in the fruit-body ofFlammulina velutipes

Chronological changes of protein expression in the vegetative mycelium ofFlammulina velutipes and expression of these proteins in the fruit-body were investigated by two-dimensional polyacrylamide gel electrophoresis. Four proteins (FBA 1-4) expressed abundantly in the fruit-body were found to have different expression patterns in the vegetative mycelium after the fruiting treatment. FBA 1-4 had similar amino acid sequences and displayed a high similarity with the deduced amino acid sequence of theC1 cDNA, which has an Arg-Gly-Asp (RGD) cell-attachment sequence. This suggests that FBA 1-4 may have cell-to-cell attachment activity.     

Crystallization and some properties of acetylpolyamine amidohydrolase from Mycoplana bullata

During the course of investigations on the catabolism of acetylpolyamines by microorganisms, we found that acetylpolyamine amidohydrolase was produced by Mycoplana bullata FERM BP-1845 and isolated the enzyme from the cell-free extract in crystalline form. The enzyme had an apparent molecular weight of 67 kDa and was composed of two identical subunits. The enzyme activity was inhibited by o-oxyquinoline and the crystalline enzyme contained one zinc atom per each subunit. The enzyme had an optimal pH around 8.0 with acetylputrescine as substrate and showed broad substrate specificity and high affinity towards various acetylpolyamines, such as acetylputrescine, acetylcadaverine, acetylspermidine, and acetylspermine.     

Fossil Flowers and Associated Plant Fossils from the Kamikitaba Locality (Ashizawa Formation, Futaba Group, Lower Coniacian, Upper Cretaceous) of Northeast Japan

in situ spores, and megaspores also document the presence of Selaginellaceae and Schizaeaceae. Received 8 February 1999/ Accepted in revised form 7 April 1999     

Isolation and characterization of novel neutral glycolipids from Thermoplasma acidophilum.

Several novel neutral glycolipids (GL-1a, GL-1b, GL-2a, GL-2b and GL-2c) were isolated from Thermoplasma acidophilum by high-performance liquid chromatography using phenylboronic acid-silica and preparative thin-layer chromatography. The tentative structures of these lipids were characterized by the combination of gas-liquid chromatography, the methylation procedure, and (1)H-NMR and FAB-mass spectrometries. The lipophilic portion of the neutral glycolipids was composed of a simple molecular species named caldarchaeol (dibiphytanyl-diglycerol tetraether). The sugar moieties of these glycolipids were composed of gulose and glucose which formed monosaccharide residues on one side or both sides of the core lipids. Gulose was attached to the terminal glycerol OH group of the core lipid with a beta-configuration and glucose being attached with an alpha-configuration. The proposed structure of GL-1a was gulosylcaldarchaeol and that of GL-1b was glucosylcaldarchaeol. The structures of GL-2a, GL-2b, and GL-2c were the analogs of the caldarchaeol derivatives attached by a variety of gulosyl residues or glucosyl residues on both sides of the terminal OH groups.     

SHC-alpha5beta1 integrin interactions regulate breast cancer cell adhesion and motility.

The oncogenic SHC proteins are signaling substrates for most receptor and cytoplasmic tyrosine kinases (TKs) and have been implicated in cellular growth, transformation, and differentiation. In tumor cells overexpressing TKs, the levels of tyrosine phosphorylated SHC are chronically elevated. The significance of amplified SHC signaling in breast tumorigenesis and metastasis remains unknown. Here we demonstrate that seven- to ninefold overexpression of SHC significantly altered interactions of cells with fibronectin (FN). Specifically, in human breast cancer cells overexpressing SHC (MCF-7/SHC) the association of SHC with alpha5beta1 integrin (FN receptor) was increased, spreading on FN was accelerated, and basal growth on FN was reduced. These effects coincided with an early decline of adhesion-dependent MAP kinase activity. Basal motility of MCF-7/SHC cells on FN was inhibited relative to that in several cell lines with normal SHC levels. However, when EGF or IGF-I was used as the chemoattractant, the locomotion of MCF-7/SHC cells was greatly (approx fivefold) stimulated, while it was only minimally altered in the control cells. These data suggest that SHC is a mediator of the dynamic regulation of cell adhesion and motility on FN in breast cancer cells.     

Immunological identification of an inward rectifier K+ channel (Kir4.1) in the intermediate cell (melanocyte) of the cochlear stria vascularis of gerbils and rats

The cochlear stria vascularis produces the positive endocochlear potential (EP) and the endolymph. Both the EP and the endolymph are essential for the physiological function of hair cells. The intermediate cell is one of several cell types constituting the stria vascularis. It is known that inward rectifier K+ channels can play a constitutive role in the determination of the resting membrane potential. Localization of a member of the inward rectifier K+ channel family, Kir4.1, in the stria vascularis of gerbils and rats was investigated by immunological methods. A polyclonal antibody specific to the C-terminus of the rat Kir4.1 channel was raised in rabbits. Immunostaining of dissociated cells revealed that the Kir4.1 channel was localized to the intermediate cell, but not to the epithelial marginal cell. Subcellular localization of the Kir4.1 channel to the plasma membrane of the intermediate cell was confirmed by immunoelectron microscopy. Immunostaining of whole-tissue preparations revealed a network-like structure composed of intermediate cells. It seems likely that the Kir4.1 channel mediates the inwardly rectifying K+ current in the intermediate cell as shown previously by electrophysiological methods, and that this channel plays key roles in the production of the EP and K+ transport in the stria vascularis.