Dependency of size of Saccharomyces cerevisiae cells on growth rate.

The mean size and percentage of budded cells of a wild-type haploid strain of Saccharomyces cerevisiae grown in batch culture over a wide range of doubling times (tau) have been measured using microscopic measurements and a particle size analyzer. Mean size increased over a 2.5-fold range with increasing growth rate (from tau = 450 min to tau = 75 min). Mean size is principally a function of growth rate and not of a particular carbon source. The duration of the budded phase increased at slow growth rates according to the empirical equation, budded phase = 0.5 tau + 27 (all in minutes). Using a recent model of the cell cycle in which division is thought to be asymmetric, equations have been derived for mean cell age and mean cell volume. The data are consistent with the notion that initiation of the cell cycle occurs at "start" after attainment of a critical cell size, and this size is dependent on growth rate, being, at slow growth rates, 63% of the volume of fast growth rates. Previous reports are reanalyzed in the light of the unequal division model and associated population equations.     

Arthropod orientation in choice chambers as a Markov chain

ABSTRACT. A Markov model of arthropod locomotor behaviour in choice chambers is presented. In the model, the compartments of the choice chamber and the movements of the animals from one compartment to another are treated as the states and the state transitions of a Markov chain, respectively. The model allows one to calculate the transition probabilities and the equilibrium distribution of animals in a choice chamber from direct measurements of displacement speeds and boundary turning reactions in each compartment. The compartment preferences (i.e. the proportion of time spent in each compartment) in two-compartment choice chambers were found to be strongly correlated with the predictions of the model. Klinokinesis is suggested to have negligible significance in some of the experiments reviewed. An equation is given to evaluate quantitatively the relative strength of kinetic and tactic components in the overall preference in the choice chamber; this assessment has not previously been possible.     

Effects of irradiation on the lip mucosa in the mice as a function of rate. Comparison with the effect of fractionation

We have investigated the effect of single doses delivered at various dose rates on the mouse lip mucosa biological system. The dose rates were: 642, 76.8, 14.1, 2.9 and 1.5 Gy/h. The incidence of desquamation in the different groups of mice was used for constructing dose effect curves. The dose leading to desquamation in 50% of the animals (ED50) was obtained by probit analysis. These ED50 were 16.5, 16.7, 19, 30.2 and 33.5 Gy for the respective dose rates. Fractionated irradiations have also been performed in the same biological system (separately published), and we have therefore been able to compare the fractionated and low dose rate irradiations. The recently published model of Dale was used for this comparison. With that mathematical approach a alpha/beta value of 7.4 Gy and a half time of repair of sublethal damage of 47 minutes have been derived. These results compare well with others from the literature on biological systems with similar characteristics (rapidly proliferating systems).     

A stochastic approach for the interpretation of single pulse experiments in morphological multicompartments of renewing and exponentially growing cell populations

A general approach for the interpretation of single pulse experiments in multicompartment systems is presented. It allows an extension of the classical single compartment Barret's methodology, and has been detailed in the pipeline model case to show its capabilities. FLM, FLC, grain count curves, labelling indices and compartment size ratios of each compartment, are fitted into a coherent scheme that fully describes the statistical aspects of the phase durations including possible losses. It is shown that if the compartments are identical, irrespective of the feedback coupling between them, the system may be treated as a single compartment. It is also shown that the FLC information is necessary to identify the existence of losses in the system, and how to correct the "apparent" transit times if losses are present. The pipeline model is treated and a suggestion is made to reconcile the "British" and "American" interpretations of the erythroid system. As a corollary, simple formulae are derived in the deterministic case through a coupling matrix describing the interaction between compartments. Computer codes are described and have been implemented in the J.E.N. Thermoecology Laboratory.     

Evidence that recombination between reiterated sequences in the Bacillus subtilis chromosome does not occur via unequal crossing over.

An experimental system was designed to permit the detection of recombination events occurring via unequal crossing over between sister bacterial chromosomes in Bacillus subtilis. It exploits the fact that during spore development, genetic and metabolic cooperation occurs between two different cell types, only one of which survives. During the early stages of sporulation, the two chromosomes of the developing sporangiole lie in the same cell and recombination between them is possible, in principle. Internal duplications flanking a selectable antibiotic-resistance gene have been introduced into the spoIIIC, spoIVA and spoVJ genes, whose correct expression in the mother cell (non-surviving compartment) is necessary for completion of spore development. After incubation in a sporulation-inducing medium in the absence of selective pressure, these strains sporulate at a low frequency and up to 30% of the progeny are Spo-. They result from mosaic sporangioles, in which only the chromosome segregated into the mother cell compartment of the developing sporangiole contains a reconstituted spo gene. In mosaic sporangioles generated by unequal crossing over between sister bacterial chromosomes, the insertionally inactivated spo gene, segregated into the pre-spore compartment, would carry an extra copy of the duplication initially present. Analysis of the products of 124 independent recombination events giving rise to mosaic sporangioles provided no evidence for the occurrence of unequal crossing over.     

Tissue distribution and pharmacokinetics of an ATWLPPR-conjugated chlorin-type photosensitizer targeting neuropilin-1 in glioma-bearing nude mice.

Destruction of the neovasculature is essential for efficient tumor eradication by photodynamic therapy (PDT). The PDT anti-vascular effect can be promoted by developing addressed photosensitizers localized preferentially to the tumor vascular compartment. A new photosensitizer conjugated to an heptapeptide [H-Ala-Thr-Trp-Leu-Pro-Pro-Arg-OH (ATWLPPR)] targeting neuropilin-1, a Vascular Endothelial Growth Factor (VEGF) co-receptor, has been synthesized. It was administered intravenously for an easier access to endothelial cells lining the vasculature in human malignant glioma-bearing nude mice. Plasma pharmacokinetic parameters were derived from plasma concentration-time data using a non-compartmental analysis and validated a relatively rapid elimination from the blood compartment with an elimination rate constant of 0.062 h(-1) and a biological half-life of 11.0 h. The photosensitizer was mainly concentrated in organs such as liver, spleen and kidneys, which are rich in reticuloendothelial cells. In these organs, the elimination profiles of the photosensitizer were comparable, with half-lives as short as 12.2, 15.1 and 19.7 h, respectively. The peptidic moiety of the conjugated photosensitizer was degraded to various rates depending on the organ considered, most of the degradation process occurred in organs of the reticuloendothelial system. A metabolic product resulting from the enzymatic cleavage of the peptide bond between Ala and Thr was detected in plasma at all the examined time points from 2 h post-injection. The conjugated photosensitizer accumulated rapidly and at high levels in the tumor, with 2.3% of injected dose per gram of tumor tissue at 1 h after injection. Taking into account the aspecific uptake of the degradation product, the tumor levels of total photoactivable compounds might exhibit an interesting photodynamic activity. On the contrary, levels of total photoactivable compounds remained low in the skin. This study provides essential information for the choice of the time interval not to exceed to activate the photosensitizer.     

Multiple heparan sulfate proteoglycans synthesized by a basement membrane producing murine embryonal carcinoma cell line

The murine embryonal carcinoma derived cell line M1536-B3 secretes the basement membrane components laminin and entactin and, when grown in bacteriological dishes, produces and adheres to sacs of basement membrane components. Heparan sulfate proteoglycans have been isolated from these sacs, the cells, and the medium. At least three different heparan sulfate proteoglycans are produced by these cells as determined by proteoglycan size, glycosaminoglycan chain length, and charge density. The positions of the N- and O-sulfate groups in the glycosaminoglycan chains from each proteoglycan appear to be essentially the same despite differences in the size and culture compartment locations of the heparan sulfate proteoglycan. Additionally, small quantities of chondroitin sulfate proteoglycans are found in each fraction and copurify with each heparan sulfate proteoglycan. Because this cell line appears to synthesize at least three different heparan sulfate proteoglycans which are targeted to different final locations (basement membrane, cell surface, and medium), this will be a useful system in which to study the factors which determine final heparan sulfate proteoglycan structures and culture compartment targeting and the possible effects of the protein core(s) on heparan sulfate carbohydrate chain synthesis and secretion.     

Nonsteady-State Three Compartment Tracer Kinetics: I. Theory

A set of differential equations is derived which describes the four unidirectional fluxes of a substance across the boundaries of the central compartment of a serially arranged three compartment system, and the amount of this substance present in the central compartment. An analytic solution is obtained which yields all of these quantities as functions of time. The analysis is associated with a defined set of repetitive experiments from which the necessary data are obtained and during which the two outer compartments must be subject to experimental control. The solution is applicable to both the initial steady state and a transient, time-dependent state created by making a step change in the initial conditions. It describes the fluxes and compartment size without assuming that constant kinetic coefficients relate the fluxes to compartmental quantities but is limited by the requirement that the response of the system be repeatable in time.     

Fuzzy reasoning system for fault diagnosis of physiological activities in a cultivating process.

Aiming at development of a system which supports cultivating operations, a method to diagnose physiological activities in a cultivating process is presented, and a fuzzy expert system for diagnosing Lactobacillus casei cultivating process is implemented in this paper. This system can calculate specific rates of cell growth, substrate consumption, and product formation with measuring cell mass concentration, substrate concentration, and product concentration by using a turbidity sensor and HPLC. A database is implemented, where standard curves on specific rates representing characteristics of microorganisms are stored according to normalized substrate consumption. Comparing the calculated specific rates with standard values derived from the database, the system diagnoses physiological activities of the microorganisms. As a case study, a knowledge base for diagnosing lactic acid production process is implemented. The use of fault diagnosis on pH malfunctions by the expert system proves its reasonable performance.     

Topology of gene expression networks as revealed by data mining and modeling

MOTIVATION: Interpretation of high-throughput gene expression profiling requires a knowledge of the design principles underlying the networks that sustain cellular machinery. Recently a novel approach based on the study of network topologies has been proposed. This methodology has proven to be useful for the analysis of a variety of biological systems, including metabolic networks, networks of protein-protein interactions, and gene networks that can be derived from gene expression data. In the present paper, we focus on several important issues related to the topology of gene expression networks that have not yet been fully studied. RESULTS: The networks derived from gene expression profiles for both time series experiments in yeast and perturbation experiments in cell lines are studied. We demonstrate that independent from the experimental organism (yeast versus cell lines) and the type of experiment (time courses versus perturbations) the extracted networks have similar topological characteristics suggesting together with the results of other common principles of the structural organization of biological networks. A novel computational model of network growth that reproduces the basic design principles of the observed networks is presented. Advantage of the model is that it provides a general mechanism to generate networks with different types of topology by a variation of a few parameters. We investigate the robustness of the network structure to random damages and to deliberate removal of the most important parts of the system and show a surprising tolerance of gene expression networks to both kinds of disturbance.     

On the evaluation of data from flow-dialysis experiments

Flow dialysis can be used to measure (i) ligand binding to macromolecules and (ii) the size of transmembrane ion gradients. Generally an approximate method is used to calculate the binding or gradient parameters from the raw data. Here we present a simple but exact method and evaluate the errors that may arise when the approximate method is used to calculate the magnitude of ion gradients. In addition, equations are presented that allow for a correction for sampling from or additions to the upper compartment of a flow-dialysis vessel during the measurements. Setty and Hendler [(1982) J. Biochem. Biophys. Methods 7, 35-46] have reported artifacts in the measurement of ion-gradients caused by the addition of electron donors to the upper compartment of a flow-dialysis cell. Here we extend their observations and suggest additional methods to prevent such artifacts.     

Epidermal kinetic alterations required to generate the psoriatic phenotype: a reappraisal

Objectives: Although there have been major advances in understanding immunopathogenesis of psoriasis, the basic processes causing psoriatic morphology remain to be identified. Materials and methods: Our group has designed a systematic review of studies (1962–2009) on keratinocyte kinetics in psoriasis. We obtained data from MEDLINE, PubMed, Current Contents, reference lists and specialist textbooks. A general equation for evolution of the differentiated epidermis has been analysed. Necessary conditions for observed qualitative change in homeostasis between normal skin and established psoriatic lesions were determined. Results and discussion: Increase in the number of cell divisions (or imbalance in symmetric division rates of committed progenitor cells) and/or decrease in physiological apoptosis in the germinative compartment, together with feedback loops that limit thickening of the skin, are required to generate psoriatic morphology, that is, to increase the absolute size but decrease relative size of the differentiated cell compartment with respect to the germinative compartment.     

On the time-dependent reversible stochastic compartmental model—II. A class ofn-compartment systems

This paper discusses the solution of a generaln-compartment system with time dependent transition probabilities utilizing the technique described by Cardenas and Matis (1975) (hereafter abbreviated (CM)). In addition, the cumulant generating function is derived for a special class of reversiblen-compartment systems where the time-dependent intensity coefficients corresponding to the migration and death rates are some multiple of each other. The immigration rates can be any integrable function of time. The moments are also obtained and the solution to the two-compartment system is presented explicitly. The solution is illustrated with a linear and a periodic function which forms have been widely reported in the literature.     

The spread of inequality

The causes of socioeconomic inequality have been debated since the time of Plato. Many reasons for the development of stratification have been proposed, from the need for hierarchical control over large-scale irrigation systems to the accumulation of small differences in wealth over time via inheritance processes. However, none of these explains how unequal societies came to completely displace egalitarian cultural norms over time. Our study models demographic consequences associated with the unequal distribution of resources in stratified societies. Agent-based simulation results show that in constant environments, unequal access to resources can be demographically destabilizing, resulting in the outward migration and spread of such societies even when population size is relatively small. In variable environments, stratified societies spread more and are also better able to survive resource shortages by sequestering mortality in the lower classes. The predictions of our simulation are provided modest support by a range of existing empirical studies. In short, the fact that stratified societies today vastly outnumber egalitarian societies may not be due to the transformation of egalitarian norms and structures, but may instead reflect the more rapid migration of stratified societies and consequent conquest or displacement of egalitarian societies over time.     

Regulation and Timing of Deoxyribonucleic Acid Synthesis in Hyphae of Aspergillus nidulans

Pulse labeling of deoxyribonucleic acid (DNA) and radioautography have been used to study the effect of growth rate on nuclear replication in Aspergillus nidulans. When conidia were germinated in media supporting a fast growth rate, the radioactive pulse labeled either all of the nuclei in a cell or none of them. At slower growth rates, hyphae contained both labeled and unlabeled nuclei. Altering the growth rate thus changed nuclear replication from simultaneous to sequential. The time taken to duplicate the DNA in a nucleus, estimated from the ratio of labeled to total nuclei, remained constant at the different doubling times. The distribution of label showed that nuclei in the same hypha spent unequal times in both the postmitotic gap (G1) and the premitotic gap (G2) periods when grown at slow rates. These unequal G1 and G2 periods are considered to cause asynchrony. Once DNA synthesis was out of phase through growth on a poor medium, transferring the hypha to a rich medium did not resynchronize the nuclei. To interpret the data, two initiator mechanisms, one starting DNA synthesis and the other mitosis, are postulated to control nuclear replication in A. nidulans.     

Foundations of stochastic development

A consistent mathematical theory of stochastic poikilotherm development has been derived based upon a minimum set of biological assumptions obtained from the literature. In the subsequent analysis, the resulting developmental rate can be justifiably represented as a random variable. Three cases are considered: (1) developmental rates dependent only on temperature, (2) rates dependent on both temperature and age, and (3) rates dependent on a general function of temperature and time. The analysis provides a mathematical foundation for the current practice of superimposing a probability distribution function on a biological time scale to describe the development of individuals from a population.     

Feto-maternal production and transfer of cortisol in the rhesus (Macaca mulatta)

Four pregnant rhesus monkeys cnd their fetuses. were infused constantly with ¹⁴C-cortisol and ³H-cortisol. Steady state plasma specific activities for ¹⁴C and ³H-cortisol were obtained after 80 to 90 minutes in both mother and fetus. These data and the rates of infusion of radioactivity were used to calculate the following parameters for both mother and fetus: 1) metabolic clearance rates, 2) production rates, 3) mean adrenal secretory rates, 4) transfer rates from mother to fetus and fetus to mother cnd, 5) the fraction of cortisol in each vascular compartment derived from the maternal and fetal edrenals. Plasma cortisone concentrations, as well as the fraction of cortisone derived from fetal and maternal cortisol were determined. Tetrahydrocortisol and tetrahydrocortisone concentrations were calculated. Mean cortisol secretory rates for the maternal and fetal adrenals were 60.0±11.8 and 1.82±0.42 mg/day. Fifty-eight % of the cortisol in the fetal compartment was of maternal origin. During transfer across the placenta to the fetus, cortisol was largely converted to cortisone. In fetal plasma 76% of the cortisone was of maternal origin. Cortisone concentrations in fetal plasma were higher than those of cortisol.     

A simple centrifugal dehydration force method to characterize water compartments in fresh and post-mortem fish muscle

A centrifugal dehydration force (CDF) method to quantify changes in tissue hydration in fresh and in post-mortem muscular fish tail tissue is presented. The data obtained were used to assess fluid flow rate from tissues and the size of hydration compartments expressed in g water/g dry mass (DM). Curve fit analysis demonstrated that muscle tissue has three detectable water compartments. Application of the method to the fresh fish indicated the presence of a large non-bulk water compartment (3.14 g water/g DM) with a much smaller (0.11 g water/g DM) inner non-bulk water sub-compartment in addition to a comparatively small bulk water compartment (0.99 g water/g DM). At 10 min and at 4h post-mortem, no significant change in size or flow rate of the water compartments was observed. At 24h post-mortem the muscular fish tissue, stored in water, swelled with statistically significant increase in total water and in the bulk water compartment but no significant change in the size of the non-bulk water compartments. The water flow rate from the non-bulk water compartment was, however, increased significantly in the 24h dead tissue. This simple CDF method has application for quantization of bulk and non-bulk water compartments in other biological and non-biological systems.     

Investigation of binding mechanisms of nuclear proteins using confocal scanning laser microscopy and FRAP

Fluorescence recovery after photobleaching (FRAP) measurements offer an important tool towards analysing diffusion processes within living biological cells. A model is presented that aims to provide a rigorous theoretical framework from which binding information of proteins from FRAP data can be extracted. A single binding reaction is considered and a set of mathematical equations is introduced that incorporates the concentration of free proteins, vacant binding sites and bound complexes in addition to the on- and off-rates of the proteins. To allow a realistic FRAP model, characteristics of the instruments used to perform FRAP measurements are included in the equation. The proposed model has been designed to be applied to biological samples with a confocal scanning laser microscope (CSLM) equipped with the feature to bleach regions characterised by a radially Gaussian distributed profile. Binding information emerges from FRAP simulations considering the diffusion coefficient, radial extent of the bleached volume and bleach constant as parameters derived from experimental data. The proposed model leads to FRAP curves that depend on the on- and off-rates. Analytical expressions are used to define the boundaries of on- and off-rate parameter space in simplified cases when molecules can move on an infinite domain. A similar approach is ensued when movement is restricted in a compartment with a finite size. The theoretical model can be used in conjunction to experimental data acquired by CSLM to investigate the biophysical properties of proteins in living cells.     

Justified chauvinism: advances in defining meiotic recombination through sperm typing

Sperm typing offers an efficient means of studying the quantitative and qualitative aspects of meiotic recombination that are virtually unapproachable by pedigree analysis. Since the initial development of the technique >10 years ago, several salient findings based on empirically derived recombination data have been described. The precise rates and distributions of recombination have been reported for specific regions of the genome, serving as the prototype for high-resolution genome-wide recombination patterns. Identification and characterization of molecular genetic events, such as unequal crossing over, gene conversion and crossover asymmetry, are under close inspection for the first time as a result of this technology. The influence of these phenomena on the evolution of the genome is of primary interest from a scientific and medical perspective. In this article, we review the novel discoveries in mammalian meiotic recombination that have been revealed through sperm typing.