VBL: Virtual Biophysics Lab

VBL (Virtual Biophysics Lab) is a computational project to develop a basic numerical model of tumor spheroids. This paper is a status report that describes the structure of the code that implements the model, and the progress made up to February 2008, and also some recent results in modeling the effects of radiations on cells in a bioreactor

A quantitative study on the growth variability of tumour cell clones in vitro

Objectives: In this study, we quantify the growth variability of tumour cell clones from a human leukemia cell line. Materials and methods: We have used microplate spectrophotometry to measure the growth kinetics of hundreds of individual cell clones from the Molt3 cell line. The growth rate of each clonal population has been estimated by fitting experimental data with the logistic equation. Results: The growth rates were observed to vary among different clones. Up to six clones with a growth rate above or below the mean growth rate of the parent population were further cloned and the growth rates of their offsprings were measured. The distribution of the growth rates of the subclones did not significantly differ from that of the parent population thus suggesting that growth variability has an epigenetic origin. To explain the observed distributions of clonal growth rates we have developed a probabilistic model assuming that the fluctuations in the number of mitochondria through successive cell cycles are the leading cause of growth variability. For fitting purposes, we have estimated experimentally by flow cytometry the maximum average number of mitochondria in Molt3 cells. The model fits nicely the observed distributions of growth rates, however, cells in which the mitochondria were rendered non functional (rho-0 cells) showed only a 30% reduction in the clonal growth variability with respect to normal cells. Conclusions: A tumor cell population is a dynamic ensemble of clones with highly variable growth rate. At least part of this variability is due to fluctuations in the number of mitochondria.Comment: 31 pages, 5 figure

Judicial disagreement need not be political: dissent on the Estonian Supreme Court

I investigate the non-unanimous decisions of judges on the Estonian Supreme Court. I argue that since judges on the court enjoy high de jure independence, dissent frequently, and are integrated in the normal judicial hierarchy, the Estonian Supreme Court is a crucial case for the presumption that judicial disagreement reveals policy preferences. I analyse dissenting opinions using an ideal point response model. Examining the characteristics of cases which discriminated with respect to the recovered dimension, I show that this dimension cannot be interpreted as a meaningful policy dimension, but instead reflects disagreement about the proper scope of constitutional redress

Microplate spectrophotometry for the high-throughput screening of cytotoxic molecules

Objectives: High-throughput chemical and biochemi- cal technologies are now exploited by modern phar- macology and toxicology to synthesize a multitude of new molecules with bioactive potential, or to isolate them from living matter. Testing molecules in cell sys- tems on a large scale, however, is a rate-limiting step in drug discovery or in toxicity assessment. In this study, we developed a low-cost high-throughput method for first-level screening of cytotoxic molecules. Materials and methods: We used microplate spectro- photometry to measure growth kinetics of human tumour cells that grow in suspension (Molt3) or adherent to the plastic surface of culture wells (HeLa) in standard RPMI medium. Cells were trea- ted with colchicin, idarubicin or paclitaxel under var- ious treatment schedules. The effects were quantified and compared with those measured by optical microscopy using the trypan blue dye exclusion method to reveal dead cells. Results: Proliferation kinetics of tumour cells can be quantified by measuring variations in optical densi- ties of cell samples at 410 and 560 nm wavelengths. For cells that grow in suspension, one single reading at 730 nm may be sufficient to reconstruct growth curves that parallel those obtained by direct cell counting. Effects of the cytotoxic treatments could also be quantified and results compared very favour- ably with those obtained using standard techniques. Conclusions: Microplate spectrophotometry is a robust and sensitive method to monitor growth of animal cell populations both in the absence and in the presence of cytotoxic drugs. This method imple- ments existing technologies and can be fully auto- mated

Statistical approach to the analysis of cell desynchronization data

Experimental measurements on semi-synchronous tumor cell populations show that after a few cell cycles they desynchronize completely, and this desynchronization reflects the intercell variability of cell-cycle duration. It is important to identify the sources of randomness that desynchronize a population of cells living in a homogeneous environment: for example, being able to reduce randomness and induce synchronization would aid in targeting tumor cells with chemotherapy or radiotherapy. Here we describe a statistical approach to the analysis of the desynchronization measurements that is based on minimal modeling hypotheses, and can be derived from simple heuristics. We use the method to analyze existing desynchronization data and to draw conclusions on the randomness of cell growth and proliferation

Thresholds, long delays and stability from generalized allosteric effect in protein networks

Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation are well known to play a pivotal role in the intracellular transduction of activation and death signals. A protein can have multiple sites where chemical groups can reversibly attach in processes such as phosphorylation or nitrosylation. A microscopic description of these processes must take into account the intrinsic probabilistic nature of the underlying reactions. We apply combinatorial considerations to standard enzyme kinetics and in this way we extend to the dynamic regime a simplified version of the traditional models on the allosteric regulation of protein functions. We link a generic modification chain to a downstream Michaelis\u2013Menten enzymatic reaction and we demonstrate numerically that this accounts both for thresholds and long time delays in the conversion of the substrate by the enzyme. The proposed mechanism is stable and robust and the higher the number of modification sites, the greater the stability. We show that a high number of modification sites converts a fast reaction into a slow process, and the slowing down depends on the number of sites and may span many orders of magnitude; in this way multisite modification of proteins stands out as a general mechanism that allows the transfer of information from the very short time scales of enzyme reactions (milliseconds) to the long time scale of cell response (hours)

Plant lectins as carriers for oral drugs: is wheat germ agglutinin a suitable candidate?

Wheat germ agglutinin (WGA) is a plant protein that binds specifically to sugars expressed also by gastrointestinal epithelial cells. WGA is currently investigated as an anti-tumor drug and as a carrier for oral drugs. Information on whether it can cross the gastrointestinal epithelium and on its possible effects on the integrity of the epithelial layer is however scanty or lacking, and herein we address these issues. Differentiated Caco2 cells have been used as a model of polarized intestinal epithelium. WGA concentration at both the apical and the basolateral side of the epithelium has been quantified using a sensitive ELISA assay (sensitivity threshold 0.84 nM). Trans epithelial electrical resistance (TEER) has been measured to evaluate the integrity of the epithelium upon treatments with WGA. 3H-Mannitol (182.2 Da) and FITC-dextran (3000 Da) have been used to measure the permeability of the epithelium. Cell viability has been measured by the MTT, by 7-AAD uptake, and Annexin-V binding assays. Up to a concentration of 5.6 AM, c0.1% of intact WGA molecules only could cross the epithelial layer. WGA perturbed the integrity of the epithelium and increased the permeability of the tissue in a dose- and timedependent manner. WGA did not induce cell death but increased the permeability of individual cells to 7-AAD which is normally not uptaken by viable cells. These data allowed us to define a toxicity threshold for WGA on epithelial cells. WGA suitability as a carrier for oral drugs can therefore be evaluated on a rational basis