Effects of oxygen transport on 3-d human mesenchymal stem cell metabolic activity in perfusion and static cultures: experiments and mathematical model

Human mesenchymal stem cells (hMSCs) have unique potential to develop into functional tissue constructs to replace a wide range of tissues damaged by disease or injury. While recent studies have highlighted the necessity for 3-D culture systems to facilitate the proper biological, physiological, and developmental processes of the cells, the effects of the physiological environment on the intrinsic tissue development characteristics in the 3-D scaffolds have not been fully investigated. In this study, experimental results from a 3-D perfusion bioreactor system and the static culture are combined with a mathematical model to assess the effects of oxygen transport on hMSC metabolism and proliferation in 3-D constructs grown in static and perfusion conditions. Cells grown in the perfusion culture had order of magnitude higher metabolic rates, and the perfusion culture supports higher cell density at the end of cultivation. The specific oxygen consumption rate for the constructs in the perfusion bioreactor was found to decrease from 0.012 to 0.0017 micromol/10(6) cells/h as cell density increases, suggesting intrinsic physiological change at high cell density. BrdU staining revealed the noneven spatial distribution of the proliferating cells in the constructs grown under static culture conditions compared to the cells that were grown in the perfusion system. The hypothesis that the constructs in static culture grow under oxygen limitation is supported by higher Y(L/G) in static culture. Modeling results show that the oxygen tension in the static culture is lower than that of the perfusion unit, where the cell density was 4 times higher. The experimental and modeling results show the dependence of cell metabolism and spatial growth patterns on the culture environment and highlight the need to optimize the culture parameters in hMSC tissue engineering.     

Design of a magnetic field generator for experiments on magnetic effects in cell cultures

A magnetic field generator constructed of rare earth-cobalt magnets is proposed for examining the biological effects of static magnetic fields (less than 1 T) on tissue cultures. Important quantities of a magnetic field from a biological-effects viewpoint, ie, its strength and the product of strength and gradient, are analysed. A practical procedure for designing the generator with optimum parameters is given. Also, parameters are determined which will yield a sinusoidal spatial field distribution.     

Testing the purity of cell cultures using clinical diagnostic PCR kits

Cell cultures of higher organisms, especially human cells, are increasingly used in medical, pharmaceutical, and scientific research. The main difficulty for cell cultures is hidden nonlethal contamination by mycoplasmas, viruses, and cross contamination with other cells. We suggest using PCR kits designed and officially employed in clinical diagnostics as an accessible and reliable method for monitoring the purity of cell cultures. We tested 50 human cell lines using commercial diagnostic systems for detection of papillomaviruses, herpes viruses, adenoviruses, Mycoplasma hominis, and total bacterial mass. No contamination was revealed in the cell lines tested. For the cell lines that contained integrated parts of viral genomes, the presence of the corresponding DNA sequences was confirmed. These diagnostic systems can be effectively used to test the purity of cell lines and for qualitative detection of possible contamination, as well as for quantitative evaluations using calculation of viral load, just as is practiced in clinical diagnostics.     

A model of cell cycle control: effects of thymidine on synchronous cell cultures.

Further evidence is presented in support of a model for growth control in which commitment for cell division is determined by an event in the preceding cell cycle. A study was made of conditions affecting synchronous growth following treatment of murine mastocytoma cells with excess thymidine at different phases of the cell cycle. Cells were synchronized by a physical procedure involving velocity sedimentation in a zonal rotor. Pulse treatment of such cultures with thymidine at times corresponding to the S, G2, and M periods had no effect on further growth. However, addition at G1, although having no immediate effect, arrested cell growth in the next cell cycle. This temporal effect may account for the decay of synchrony observed during double thymidine blockade or thymidine-FUdR blockade. When the time interval between two such blocks was 7 hr or less, P815Y cells were arrested after one synchronous division. At this critical time a majority of cells were at, or near, G1. It is suggested that thymidine exerts a hitherto unrecognized effect at the G1 interval.     

Root hair cell enhancement in tissue cultures from soybean roots: a useful model system: in vitro Rhizobium symbiosis

A technique for obtaining large numbers of root hair cells in cell cultures from soybeans is described. The cells were grown on agar containing the Prairie Regional Laboratory B5 (PRL-B5) medium for periods longer than 60 days. Mixed populations of cultured root hair cells and cortical cells were used to study the in vitro association between soybean cells and Rhizobium japonicum. The advantages of these types of root cell cultures in studies of symbiosis are discussed.     

Predicting stability of mixed microbial cultures from single species experiments: 2. Physiological model

In this paper, we study the equilibria of a physiological model describing the continuous culture in which two microbial populations compete for two substitutable resources. This work is an extension of the stability analysis of the phenomenological model of mixed microbial growth [M.M. Ballyk, G.S.K. Wolkowicz, Exploitative competition in the chemostat for two perfectly substitutable resources, Math. Biosci. 118 (1993) 127-180; S.S. Pilyugin, G.T. Reeves, A. Narang, Predicting stability of mixed microbial cultures from single species experiments: 2. Phenomenological model]. Here, we investigate the influence of the peripheral enzymes that catabolize the substrate uptake on the stability of the mixed culture. We show that, under steady state conditions, an increase in the concentration of one substrate inhibits the uptake of the other substrate(s). We present the criteria for existence, uniqueness, and stability of various types of equilibria. We formulate these criteria in terms of growth isoclines and consumption curves for each of the competing species. Since both types of curves can be obtained from a single species experiment, our approach provides a direct connection between theory and experiment and allows one to infer the dynamics of mixed cultures from the dynamics of single species cultures. By expressing the stability criteria in terms of intracellular properties, the model establishes a link between ecology and molecular biology.     

Predicting stability of mixed microbial cultures from single species experiments: 1. Phenomenological model

The growth of mixed microbial cultures on mixtures of substrates is a fundamental problem of both theoretical and practical interest. On the one hand, the literature is abundant with experimental studies of mixed-substrate phenomena [T. Egli, The ecological and physiological significance of the growth of heterotrophic microorganisms with mixtures of substrates, Adv. Microbiol. Ecol. 14 (1995) 305-386]. On the other hand, a number of mathematical models of mixed-substrate growth have been analyzed in the last three decades. These models typically assume specific kinetic expressions for substrate uptake and biomass growth rates and their predictions are formulated in terms of parameters of the model. In this work, we formulate and analyze a general mathematical model of mixed microbial growth on mixtures of substitutable substrates. Using this model, we study the effect of mutual inhibition of substrate uptake rates on the stability of the equilibria of the model. Specifically, we address the following question: How much of the dynamics exhibited by two competing species can be inferred from single species data? We provide geometric criteria for stability of various types of equilibria corresponding to non-competitive exclusion, competitive exclusion, and coexistence of two competing species in terms of growth isoclines and consumption curves. A growth isocline is a curve in the plane of substrate concentrations corresponding to the zero net growth of a given species. In [G.T. Reeves, A. Narang, S.S. Pilyugin, Growth of mixed cultures on mixtures of substitutable substrates: The operating diagram for a structured model, J. Theor. Biol. 226 (2004) 143-157], we introduced consumption curves as sets of all possible combinations of substrate concentrations corresponding to balanced growth of a single microbial species. Both types of curves can be obtained in single species experiments.     

Intelligent bioprocessing for haemotopoietic cell cultures using monitoring and design of experiments

The need for successful ex-vivo expansion and directed differentiation of haematopoietic stem cells (HSCs) for therapeutic applications has increased over the past decade. Haematopoietic cell cultures are complex and full characterisation of the process environment has yet to be achieved. The complexity and transient nature of HSC cultures make the identification, maintenance and control of optimal operating conditions challenging. Application of real-time, on-line monitoring techniques and process control strategies enhances the ability to operate bioprocesses of desired reproducibility and high product quality. In this review, we discussed the methods by which in vitro culture information necessary for bioprocess control may be obtained, including process considerations, monitoring and analytical tools, and design of experiments (DOE). The successful application of these tools may result in time- and cost-effective cultures for directed differentiation and expansion of haematopoietic components intended for clinical use.     

Growth of the chorioallantoic membrane into a rapid-prototyped model pore system: experiments and mathematical model

This paper presents a mathematical model to describe the growth of tissue into a rapid-prototyped porous scaffold when it is implanted onto the chorioallantoic membrane (CAM). The scaffold was designed to study the effects of the size and shape of pores on tissue growth into conventional tissue engineering scaffolds, and consists of an array of pores each having a pre-specified shape. The experimental observations revealed that the CAM grows through each pore as an intact layer of tissue, provided the width of the pore exceeds a threshold value. Based on these results a mathematical model is described to simulate the growth of the membrane, assuming that the growth is a function of the local isotropic membrane tension. The model predictions are compared against measurements of the extent of membrane growth through the pores as a function of time for pores with different dimensions.     

Primary uroepithelial cultures. A model system to analyze umbrella cell barrier function.

Despite almost 25 years of effort, the development of a highly differentiated and functionally equivalent cell culture model of uroepithelial cells has eluded investigators. We have developed a primary cell culture model of rabbit uroepithelium that consists of an underlying cell layer that interacts with a collagen substratum, an intermediate cell layer, and an upper cell layer of large (25-100 micrometer) superficial cells. When examined at the ultrastructural level, the superficial cells formed junctional complexes and had an asymmetric unit membrane, a hallmark of terminal differentiation in bladder umbrella cells. These cultured "umbrella" cells expressed uroplakins and a 27-kDa uroepithelial specific antigen that assembled into detergent-resistant asymmetric unit membrane particles. The cultures had low diffusive permeabilities for water (2.8 x 10(-4) cm/s) and urea (3.0 x 10(-7) cm/s) and high transepithelial resistance (>8000 Omega cm2) was achieved when 1 mM CaCl2 was included in the culture medium. The cell cultures expressed an amiloride-sensitive sodium transport pathway and increases in apical membrane capacitance were observed when the cultures were osmotically stretched. The described primary rabbit cell culture model mimics many of the characteristics of uroepithelium found in vivo and should serve as a useful tool to explore normal uroepithelial function as well as dysfunction as a result of disease.     

Dynamic cell culture system: a new cell cultivation instrument for biological experiments in space

The prototype of a miniaturized cell cultivation instrument for animal cell culture experiments aboard Spacelab is presented (Dynamic cell culture system: DCCS). The cell chamber is completely filled and has a working volume of 200 μl. Medium exchange is achieved with a self-powered osmotic pump (flowrate 1 μl h⁻¹). The reservoir volume of culture medium is 230 μl. The system is neither mechanically stirred nor equipped with sensors. Hamster kidney (Hak) cells growing on Cytodex 3 microcarriers were used to test the biological performance of the DCCS. Growth characteristics in the DCCS, as judged by maximal cell density, glucose consumption, lactic acid secretion and pH, were similar to those in cell culture tubes.     

Molecular hybridization of nucleic acids as a method for the laboratory diagnosis of influenza in model experiments on cell cultures and in research on nasopharyngeal smears obtained from patients

DNA probes containing the nucleotide sequences of the conservative genes of influenza A virus (matrix, nucleoprotein and acidic polymerase genes) show their specificity with respect to the RNA of influenza A viruses in mammal tissue cell cultures (continuous spaniel kidney cell culture and primary calf kidney cell culture). The minimal amount of infected monolayer cells, permitting the detection of viral RNA, is 10(3). The results obtained in the study of nasopharyngeal washings make it possible to recommend the method of molecular hybridization for use in the epidemiological analysis in addition to virological and serological tests. The method of hybridization permits the detection of virus-specific RNA in the allantoic fluid of chick embryos in subculturing the materials under study even in those cases when hemagglutinating influenza virus cannot be isolated.     

Micropatterned cell cultures on elastic membranes as an in vitro model of myocardium

We describe here a new in vitro protocol for structuring cardiac cell cultures to mimic important aspects of the in vivo ventricular myocardial phenotype by controlling the location and mechanical environment of cultured cells. Microlithography is used to engineer microstructured silicon metal wafers. Those are used to fabricate either microgrooved silicone membranes or silicone molds for microfluidic application of extracellular matrix proteins onto elastic membranes (involving flow control at micrometer resolution). The physically or microfluidically structured membranes serve as a cell culture growth substrate that supports cell alignment and allows the application of stretch. The latter is achieved with a stretching device that can deliver isotropic or anisotropic stretch. Neonatal ventricular cardiomyocytes, grown on these micropatterned membranes, develop an in vivo-like morphology with regular sarcomeric patterns. The entire process from fabrication of the micropatterned silicon metal wafers to casting of silicone molds, microfluidic patterning and cell isolation and seeding takes approximately 7 days.     

Comparative studies of the phytochrome system in cell cultures from different plants

Phytochrome contents have been assayed in vivo in cell suspension cultures of Petroselinum hortense, Daucus carota and Glycine max. After transferring the cells to fresh medium phytochrome increased in parallel with the increase in cell number, whereas the amount of phytochrome per cell remained constant. The rate of phytochrome reaccumulation after pretreatment with 15 h red light was very similar in all three systems (2.8–3.6 (e) 10^–5/h). Dark reversion and a fast and slow P_fr destruction were observed in all systems. The rate constants of these reactions varied strongly between the systems. The phytochrome systems of the cell cultures were compared with those of etiolated and light-grown seedlings and it was concluded that the cell suspension cultures of Petroselinum hortense and Daucus carota behaved similarly to light-grown seedlings. In contrast, those of Glycine max behaved similarly to a dark grown seedling.Abbreviations P_r'fr red, far-red absorbing forms of phytochrome - P_tot P_r+P_fr total amount of phytochrome - fwt fresh weight     

The pitfalls of proteomics experiments without the correct use of bioinformatics tools

The elucidation of the entire genomic sequence of various organisms, from viruses to complex metazoans, most recently man, is undoubtedly the greatest triumph of molecular biology since the discovery of the DNA double helix. Over the past two decades, the focus of molecular biology has gradually moved from genomes to proteomes, the intention being to discover the functions of the genes themselves. The postgenomic era stimulated the development of new techniques (e.g. 2-DE and MS) and bioinformatics tools to identify the functions, reactions, interactions and location of the gene products in tissues and/or cells of living organisms. Both 2-DE and MS have been very successfully employed to identify proteins involved in biological phenomena (e.g. immunity, cancer, host-parasite interactions, etc.), although recently, several papers have emphasised the pitfalls of 2-DE experiments, especially in relation to experimental design, poor statistical treatment and the high rate of 'false positive' results with regard to protein identification. In the light of these perceived problems, we review the advantages and misuses of bioinformatics tools - from realisation of 2-DE gels to the identification of candidate protein spots - and suggest some useful avenues to improve the quality of 2-DE experiments. In addition, we present key steps which, in our view, need to be to taken into consideration during such analyses. Lastly, we present novel biological entities named 'interactomes', and the bioinformatics tools developed to analyse the large protein-protein interaction networks they form, along with several new perspectives of the field.     

Application of global sensitivity analysis to determine goals for design of experiments: an example study on antibody-producing cell cultures

Global sensitivity analysis (GSA) can be used to quantify the importance of model parameters and their interactions with respect to model output. In this study, the Sobol' method for GSA is applied to a dynamic model of monoclonal antibody-producing mammalian cell cultures in order to identify the parameters that need to be accurately determined experimentally. Our results show that most parameters have low sensitivity indices and exhibit strong interactions with one another. These parameters can be set at their nominal values and unnecessary experimentation can therefore be avoided. In contrast, certain parameters are identified as sensitive, necessitating their estimation given sufficiently rich experimental data. Moreover, parameter sensitivity varies during culture time in a biologically meaningful manner. In conclusion, GSA can serve as an excellent precursor to optimal experiment design.     

Testing Mendelian inheritance from field-collected parasites: Revealing duplicated loci enables correct inference of reproductive mode and mating system

Cryptic aspects of parasite population biology, e.g., mating systems, are increasingly being inferred from polymorphic and co-dominant genetic markers such as microsatellite loci. Underlying the use of such co-dominant markers is the assumption of Mendelian inheritance. The failure to meet this assumption can lead to artifactual statistics and erroneous population inferences. Here, we illustrate the importance of testing the Mendelian segregation and assortment of genetic markers and demonstrate how field-collected samples can be utilised for this purpose. To examine the reproductive mode and mating system of hermaphroditic parasites, we developed microsatellites for the cestode, Oochoristica javaensis. Among loci, we found a bimodal distribution of F_IS (a fixation index that quantifies the deviation from Hardy–Weinberg equilibrium within subpopulations) values where loci were either highly negative (close to −1) or highly positive (∼0.8). By conducting tests of Mendelian segregation from natural crosses, we determined that loci with negative F_IS values were in fact duplicated loci that were amplified by a single primer pair. Genetic crosses also provided linkage data and indicated that the duplicated loci most likely arose via tandem duplications rather than whole genome/chromosome duplications. By correcting for the duplicated loci, we were able to correctly infer that O. javaensis has sexual reproduction, but the mating system is highly inbred. To assist others in testing Mendelian segregation and independent assortment from natural samples, we discuss the benefits and limitations, and provide guidelines for particular parasite systems amenable to the methods employed here.     

Complex growth dynamics in batch cultures: experiments and cybernetic models

The cybernetic framework developed by Ramkrishna and co-workers is shown to encompass the regulation of nutrient transport processes as well as the effect of nutrient transport on the biotic phase. A structured model which accounts for both an abiotic or environmental phase and a biotic or cellular phase is proposed to describe bacterial growth on lactose as the limiting carbon and energy source. In the presence of lactose, competing uptake mechanisms are proposed. At low lactose concentrations, an energy-requiring transport process is the preferred uptake mechanism. The coupling between cellular energetics and nutrient uptake results in an interesting intermittent growth phenomenon. As the concentration of lactose increases, a nonenergetic transport process is preferred and cellular growth ceases to be intermittent. Model simulations are compared with previously reported experimental results and exhibit good agreement over the entire range of initial lactose concentrations.