Insulin-transferrin-selenous acid in growth medium alters the expression of PKC isoforms in mesangial cells

Glomerular mesangial cells (MCs) have been used as an in vitro model for glomerular disease. The culture conditions used for these cells vary and include the use of insulin or insulin-transferrin-selenous acid (ITS) in the growth medium. We studied the effect of ITS in the growth medium containing either normal or high glucose on the expression of protein kinase C (PKC) isoforms in MCs. In the presence of ITS in the medium, MCs expressed lower levels of both PKC isoforms in their cytosol in comparison to MCs grown in medium without ITS. Upon stimulation with PMA, both isoforms were translocated to the particulate (nucleus/cytoskeleton) compartment in MCs grown in presence of ITS. However, in the absence of ITS in the growth medium, both PKC isoforms were primarily translocated to the membrane compartment upon PMA stimulation. These results indicate that insulin in the growth medium may activate MCs resulting in translocation of PKC from the cytosol to other subcellular compartments. This effect is even evident in MCs grown in normal glucose concentration. Our data indicate that the use of ITS in growth medium and eventual interpretation from such experiments involving primary mesangial cells grown in culture needs careful evaluation.     

Constrained proteome allocation affects coexistence in models of competitive microbial communities

Microbial communities are ubiquitous and play crucial roles in many natural processes. Despite their importance for the environment, industry and human health, there are still many aspects of microbial community dynamics that we do not understand quantitatively. Recent experiments have shown that the structure and composition of microbial communities are intertwined with the metabolism of the species that inhabit them, suggesting that properties at the intracellular level such as the allocation of cellular proteomic resources must be taken into account when describing microbial communities with a population dynamics approach. In this work, we reconsider one of the theoretical frameworks most commonly used to model population dynamics in competitive ecosystems, MacArthur’s consumer-resource model, in light of experimental evidence showing how proteome allocation affects microbial growth. This new framework allows us to describe community dynamics at an intermediate level of complexity between classical consumer-resource models and biochemical models of microbial metabolism, accounting for temporally-varying proteome allocation subject to constraints on growth and protein synthesis in the presence of multiple resources, while preserving analytical insight into the dynamics of the system. We first show with a simple experiment that proteome allocation needs to be accounted for to properly understand the dynamics of even the simplest microbial community, i.e. two bacterial strains competing for one common resource. Then, we study our consumer-proteome-resource model analytically and numerically to determine the conditions that allow multiple species to coexist in systems with arbitrary numbers of species and resources.Subject terms: Biodiversity, Microbial ecology, Microbial ecology, Bacterial physiology     

Inoculation and growth conditions for high-cell-density expansion of mammalian neural stem cells in suspension bioreactors

Inoculation and growth conditions for the large-scale expansion of mammalian neural stem cells (NSC) have been determined. We examined suspension culture bioreactors of murine NSC, and concluded that the oxygen level should be kept high (20%), and the osmolarity of the medium should be kept low (below 400 mOsm/kg). The pH of the medium was found to have a large effect on cell proliferation, and the best growth characteristics were obtained within an optimum pH range of 7. 1 to 7.5. The inoculation conditions were also seen to have a large effect not only on the growth characteristics, but also on the number of cells that die in the initial stages of the culture. For large expansion of cells, low inoculum levels (10(4) cells/mL) and single-cell suspensions proved superior, whereas, for fast expansion of cells, higher inoculum levels (10(5) cells/mL) and spheroid inoculum forms were preferred. The inoculum temperature of the medium did not have a large effect on growth characteristics, but the pH greatly influenced cell proliferation. Inoculum pH levels should also be kept between 7.1 and 7.5. If these protocols are followed, high multiplication ratios and viabilities can be obtained in a 5-day batch suspension culture bioreactor run. A large number of cells could then be used in animal models for testing of neural drugs and in research and development toward cures for neurodegenerative disorders such as multiple sclerosis (MS) and Huntington's and Parkinson's disease. The results presented here also point the way toward studies on in vitro expansion of human neural stem cells.     

RESPONSES OF THE PHYTOPLANKTON COMMUNITY GROWTH RATE TO NUTRIENT PULSES IN VARIABLE ESTUARINE ENVIRONMENTS

In estuaries, phytoplankton are exposed to rapidly changing conditions that may have profound effects on community structure and function. In these experiments, we evaluated the growth, productivity, and compositional responses of natural phytoplankton communities exposed to limiting nutrient additions and incubation conditions typical of estuarine habitats. Mesocosm bioassays were used to measure the short-term (2-day) growth rate, primary productivity, and group-specific biomass responses of the phytoplankton community in the Neuse River Estuary, North Carolina. A three-factor (mixing, sediment addition, and nutrient addition) experimental design was applied using 55-L mesocosm tanks. Growth rates were determined using the ¹⁴C photopigment radiolabeling method, and the abundance of algal groups was based on quantification of chemosystematic photopigments by HPLC. For Neuse River Estuary phytoplankton communities, stratified (nonmixed), turbid, and low-nitrate conditions favored increases in cryptomonad biomass. Mixed, turbid, high-nitrate conditions were favorable for increased primary productivity and chlorophytes, diatoms, and cyanobacteria. The highest community growth rates occurred under calm, high-nitrate conditions. This approach provided an assessment of the community-level phytoplankton responses and insights into the mechanisms driving blooms and bloom species in estuarine waters. The ability to rapidly alter growth rates to capitalize on conditions conducive for growth may play an important role in the timing, extent, and species involved with blooms in estuarine waters. Adaptive growth rate responses of individual species, as well as the community as a whole, further illustrate the sensitivity of estuarine ecosystems to excessive N inputs.     

The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high‐throughput environmental sequencing to show that S. paradoxus is a very rare member of the oak bark microbial community. We find that S. paradoxus can grow well on sterile medium made from oak bark, but that its growth is strongly suppressed when the other members of the community are present. We purified a set of twelve common fungal and bacterial species from the oak bark community and tested how each affected the growth of S. paradoxus in direct competition on oak bark medium at summer and winter temperatures, identifying both positive and negative interactions. One Pseudomonas species produces a diffusible toxin that suppresses S. paradoxus as effectively as either the whole set of twelve species together or the complete community present in nonsterilized oak medium. Conversely, one of the twelve species, Mucilaginibacter sp., had the opposite effect and promoted S. paradoxus growth at low temperatures. We conclude that, in its natural oak tree habitat, S. paradoxus is a rare species whose success depends on the much more abundant microbial species surrounding it.     

An integrated agent-mathematical model of the effect of intercellular signalling via the epidermal growth factor receptor on cell proliferation

We have previously developed Epitheliome, a software agent representation of the growth and repair characteristics of epithelial cell populations, where cell behaviour is governed by a number of simple rules. In this paper, we describe how this model has been extended to incorporate an example of a molecular 'mechanism' behind a rule-in this case, how signalling by both endogenous and exogenous ligands of the epidermal growth factor receptor (EGFR) can impact on the proliferation of cell agents. We have developed a mathematical model representing release of endogenous ligand by cells, three-dimensional diffusion of the secreted molecules through a volume of cell culture medium, ligand-receptor binding, and bound receptor internalization and trafficking. Information relating to quantities of molecular species associated with each cell agent is frequently exchanged between the agent and signalling models, and the ratio of bound to free receptors determines cell cycle progression and hence the proliferative behaviour of the cell agents. We have applied this integrated model to examine the effect of plating density on tissue growth via autocrine/paracrine signalling. This predicts that cell growth is dependent on the concentration of exogenous ligand, but where this is limited, then growth becomes dependent on cell density and the availability of endogenous ligand. We have further modified the calcium concentration of the medium to modulate the formation of intercellular bonds between cells and shown that the increased propensity for cells to form colonies in physiological calcium does not result in significantly different patterns of receptor occupancy. In conclusion, our approach demonstrates that by combining agent-based and mathematical modelling paradigms, it is possible to probe the complex feedback relationship between the behaviour of individual cells and their interaction with one another and their environment.     

The potential of production of sulfated polysaccharides from Porphyridium

Summary The environmental conditions prevailing in Israel make marine algae an attractive crop for the production of valuable chemicals. A marine species of Porphyridium seems to fit this purpose.The unicellular red alga Porphyridium is encapsulated by a polysaccharide envelope that is present in the gel state. This polysaccharide is an acidic heteropolymer composed of sulfated sugars. It forms ionic bridges through divalent cations, thus reaching a very high molecular weight. The thickness of the polysaccharide capsule varies according to the phase of growth and the growth conditions. Its outer part dissolves in the growth medium, which becomes progressively more viscous. Sulfated polysaccharides form theramlly reversible gels similar to agar and carrageenan, which are usually extracted from marine macroalgae. These gels have been finding increasing use in commercial applications as gelling agents, thickeners, stabilizers, and emulsifiers.We have done experiments on the cultivation of a marine species of Porphyridium for the production of polysaccharides. This unicellular alga has an advantage over the macroalgae due to its relatively faster growth rate and the possibility to regulate its growth. The potential for production of the polysaccharide, both that dissolved in the external medium and that attached to the cell (including an intracellular fraction), and the effects of growth conditions on productivity were suudied in the laboratory. Porphyridium was also cultivated outdoors in seawater in 1-m² ponds and its growth potential investigated.     

Predicting community characteristics from habitat conditions: fluvial fish and hydraulics

1. One current approach to the prediction of community characteristics is to use models of key local-scale processes (e.g. niche dimensions) affecting individuals and to estimate the effects of these attributes over larger scales. We tested this approach, focusing on how the hydraulic habitat structures fluvial fish communities. 2. We used a recent statistical habitat model to predict fish community characteristics in eleven reaches in the Rhône river basin in France. Predictions were made ‘blindly’ since most reaches were not used to calibrate the model. The model reflects species preferences for local hydraulics. We made predictions of the fish community from the local hydraulic conditions found in the reaches under low flow conditions. The overall abundance and the relative abundance (both as indices) of fish species, specific size classes and species traits (i.e. reproductive, trophic, morphological and others) were predicted. We summarized our predictions of the relative abundance of species as two ‘community structure indices’ using Principal Component Analysis. 3. Our predictions from low-flow hydraulics were compared with long-term observations of fish communities. The relative abundance of species actually observed depended largely on zoogeographic factors within the Rhône basin which could not be predicted by the model. The model predicted 13% of the variance in the indices of relative abundance at the species level and 23% of this variance at the trait level for all zoogeographic regions combined. However, when focused on reaches within a geographic region, the model explained up to 47% of the same variance. Therefore, geographic regions act as ‘filters’ on the relative abundance of species, but hydraulics do affect fish communities within a given geographical context. 4. For the synthetic ‘community structure indices’, we obtained good predictions from hydraulics independently of the geographical context (variance explained up to 95%). These indices were linked to simple key hydraulic characteristics of river reaches (Froude and/or Reynolds number). The indices enabled interpretations of the links between hydraulics, geomorphology, discharge and community patterns. These links were consistent with existing knowledge of species and their traits. 5. In addition to the above validations, the habitat model partly explained the observed effects of impoundment on fish communities. 6. The present results show that stream hydraulics strongly impact fish community structure. Consequently, our findings confirm that community characteristics can be predicted using models of the local-scale habitat requirements of the species forming the community.     

Species sorting and neutral processes are both important during the initial assembly of bacterial communities

Many studies have shown that species sorting, that is, the selection by local environmental conditions is important for the composition and assembly of bacterial communities. On the other hand, there are other studies that could show that bacterial communities are neutrally assembled. In this study, we implemented a microcosm experiment with the aim to determine, at the same time, the importance of species sorting and neutral processes for bacterial community assembly during the colonisation of new, that is, sterile, habitats, by atmospheric bacteria. For this we used outdoor microcosms, which contained sterile medium from three different rock pools representing different environmental conditions, which were seeded by rainwater bacteria. We found some evidence for neutral assembly processes, as almost every 4th taxon growing in the microcosms was also detectable in the rainwater sample irrespective of the medium. Most of these taxa belonged to widespread families with opportunistic growth strategies, such as the Pseudomonadaceae and Comamonadaceae, indicating that neutrally assembled taxa may primarily be generalists. On the other hand, we also found evidence for species sorting, as one out of three media selected a differently composed bacterial community. Species sorting effects were relatively weak and established themselves via differences in relative abundance of generalists among the different media, as well as media-specific occurrences of a few specific taxa. In summary, our results suggest that neutral and species sorting processes interact during the assembly of bacterial communities and that their importance may differ depending on how many generalists and specialists are present in a community.     

Spatio-temporal Processes in a Calcareous Grassland

Abstract The herbaceous plant communities occurring on nutrient-poor calcareous soils of north-western Europe are typically rich in species, with as many as 30–40 species m^-2. It is an open question as to what dynamic properties allow this diversity. We review evidence that we have collected on the spatial and temporal processes operating in a calcareous grassland community in England to address this issue. Our data indicate spatial aggregation of individuals within species consistent with the modular growth of the species concerned, but there is little evidence to suggest spatial structure generated by interactions between species, and we have been unable to separate most species tested into different niches. The development of spatial structure of the community through time is also consistent with dynamics that depend principally on the modular growth patterns of the different species. We suggest that there is a nonlinearity in the per capita rate of increase with the property that the community is no more than weakly dependent on densities of the species under natural conditions. The dynamic of the community is then driven more by forces external to the community than by density-dependent effects within the community.     

In vitro characterization of proliferation and differentiation of trout satellite cells

Fish satellite cells have been extracted from various species, but the myogenic characteristics of these cells in culture remain largely unknown. We show here that 60%-70% of the adherent cells are myogenic based on their immunoreactivity for the myogenic regulatory factor MyoD. In DMEM containing 10% fetal calf serum (FCS), trout myoblasts display rapid expression of myogenin (18% of myogenin-positive cells at day 2) combined with rapid fusion into myotubes (50% of myogenin-positive nuclei and 30% nuclei in myosin heavy chain [MyHC]-positive cells at day 7). These kinetics of differentiation are reminiscent of the behavior of fetal myoblasts in mammals. However, not all the myogenic cells differentiate; this subpopulation of cells might correspond to the previously named “reserve” cells. More than 90% of the BrdU-positive cells are also positive for MyoD, indicating that myogenic cells proliferate in vitro. By contrast, less than 1% of myogenin-positive cells are positive for BrdU suggesting that myogenin expression occurs only in post-mitotic cells. In order to maximize either the proliferation or the differentiation of cells, we have defined new culture conditions based on the use of a proliferation medium (F10+10%FCS) and a differentiation medium (DMEM+2%FCS). Three days after switching the medium, the differentiation index (% MyHC-positive nuclei) is 40-fold higher than that in proliferation medium, whereas the proliferation index (% BrdU-positive nuclei) is three-fold lower. Stimulation of cell proliferation by insulin-like growth factor 1 (IGF1), IGF2, and FGF2 is greater in F10 medium. The characterization of these extracted muscle cells thus validates the use of this in vitro system of myogenesis in further studies of the myogenic activity of growth factors in trout.     

Improved culture-based isolation of differentiating endothelial progenitor cells from mouse bone marrow mononuclear cells

Numerous endothelial progenitor cell (EPC)-related investigations have been performed in mouse experiments. However, defined characteristics of mouse cultured EPC have not been examined. We focused on fast versus slow adherent cell population in bone marrow mononuclear cells (BMMNCs) in culture and examined their characteristics. After 24 h-culture of BMMNCs, attached (AT) cells and floating (FL) cells were further cultured in endothelial differentiation medium separately. Immunological and molecular analyses exhibited more endothelial-like and less monocyte/macrophage-like characteristics in FL cells compared with AT cells. FL cells formed thick/stable tube and hypoxia or shear stress overload further enhanced these endothelial-like features with increased angiogenic cytokine/growth factor mRNA expressions. Finally, FL cells exhibited therapeutic potential in a mouse myocardial infarction model showing the specific local recruitment to ischemic border zone and tissue preservation. These findings suggest that slow adherent (FL) but not fast attached (AT) BMMNCs in culture are EPC-rich population in mouse.     

Copper toxicity: evidence for the conversion of cupric to cuprous copper in vivo under anaerobic conditions.

We have determined the toxicity to cells of Escherichia coli B of cupric copper applied under aerobic and anaerobic conditions in two ways. The growth of cells in liquid medium incorporating cupric copper shows differential inhibition, comparing aerobic and anaerobic conditions--toxicity being greater under anoxia. The growth of colonies upon agar plates incorporating cupric copper does not show such a differential effect. We conclude that colonies on plates are largely anoxic even when incubated aerobically. EPR spectra of cells obtained at various times after application of cupric copper under anoxic conditions indicate the conversion of a considerable proportion of the Cu(II) to a non-paramagnetic species, probably Cu(I). We demonstrate that Cu(I) is more toxic than Cu(II) to cells when applied under anoxic conditions and conclude that the difference in toxicity of Cu(II) applied to cells under aerobic and anaerobic conditions results from the greater extent of reduction of Cu(II) to Cu(I) under anaerobic conditions.     

Development of standardized cell culture conditions for tumor cells with potential clinical application

BACKGROUND: Tumor cell lines have enormous value for the study of different aspects of cancer biology and have also recently gained great importance in autologous cell-based anti-tumor therapies. However, the use of these cells is still limited because in vitro growth is hampered by suboptimal culture conditions and current media contain fetal bovine serum (FBS), which poses serious safety concerns regarding clinical application. METHODS: To address this drawback, we aimed to develop a strategy for optimization of the culture medium for human medullary thyroid carcinoma (MTC) cell lines as a model system. We combined the general cell screening system (GCSS), which continuously measured the growth behavior of cells in a 96-well plate format, with statistically based experimental designs. RESULTS: The results obtained clearly demonstrated that, just by changing the composition of the basal medium, a significantly enhanced growth rate could be observed, and by subsequent addition of several substances a serum-free cell culture medium could be developed. This medium allowed the propagation of two MTC cell lines comparable with conventionally used serum-supplemented medium. DISCUSSION: We present a fast and easy way to screen for substances that are essential for tumor cell growth in vitro. Furthermore, these tumor cells can be adapted to culture conditions that allow the use of the cells in safe cell-based therapies. This is of utmost importance because of increasing regulatory requirements.     

Investigating the community consequences of competition among clonal plants

Although clonal plants comprise most of the biomass of several widespread ecosystems, including many grasslands, wetlands, and tundra, our understanding of the effects of clonal attributes on community patterns and processes is weak. Here we present the conceptual basis for experiments focused on manipulating clonal attributes in a community context to determine how clonal characteristics affect interactions among plants at both the individual and community levels. All treatments are replicated at low and high density in a community density series to compare plant responses in environments of different competitive intensity. We examine clonal integration, the sharing of resources among ramets, by severing ramets from one another and comparing their response to ramets with intact connections. Ramet aggregation, the spacing of ramets relative to each other, is investigated by comparing species that differ in their natural aggregation (either clumped growth forms, with ramets tightly packed together, or runner growth forms, with ramets loosely spread) and by planting individual ramets of all species evenly spaced throughout a mesocosm. We illustrate how to test predictions to examine the influence of these two clonal traits on competitive interactions at the individual and community levels. To evaluate the effect of clonal integration on competition, we test two predictions: at the individual level, species with greater clonal integration will be better individual-level competitors, and at the community level, competition will cause a greater change in community composition when ramets are integrated (connected) than when they are not. For aggregation we test at the individual level: clumped growth forms are better competitors than runner growth forms because of their ability to resist invasion, and at the community level: competition will have a greater effect on community structure when ramets are evenly planted. An additional prediction connects the individual- and community-level effects of competition: resistance ability better predicts the effects of competition on relative abundance in a community than does invasion ability. We discuss additional experimental design considerations as revealed by our ongoing studies. Examining how clonal attributes affect both the individual- and community-level effects of competition requires new methods and metrics such as those presented here, and is vital to understanding the role of clonality in community structure of many ecosystems.     

Self-thinning and community persistence in a simple size-structured dynamical model of plant growth

This paper presents a size-structured dynamical model of plant growth. The model takes the form of a partial differential-integral equation and includes the effects of self- shading by leaves. Closed form solutions are presented for the equilibrium size density distribution. Analytic conditions are derived for community persistence, and the self-thinning exponent is obtained as a function of species characteristics and environmental conditions.     

Community structure and the evolution of aposematic coloration

Studies on the evolution of aposematic coloration (prey coloration advertising for unpalatability) have mainly focused on predator psychology in simplified single-prey species systems. We chose, instead, to model population dynamics on the community level. We studied the invasion by an aposematic phenotype in the presence and absence of another prey species. The single-prey and two-prey models differed in two major ways. First, with two prey species the invasion was possible only with a weak aposematic signal, whereas with a single prey species there was no such an upper limit for signal strength. Second, with a single prey species, increase of the aposematic phenotype always resulted in rapid extinction of the predator. Resource value and growth rate of the alternative prey species affected the invasion. These results suggest that community structure is an important determinant of the conditions for invasion of aposematism, and may have contributed to its initial evolution.     

Identifying mechanisms that structure ecological communities by snapping model parameters to empirically observed tradeoffs

Theory predicts that interspecific tradeoffs are primary determinants of coexistence and community composition. Using information from empirically observed tradeoffs to augment the parametrisation of mechanism‐based models should therefore improve model predictions, provided that tradeoffs and mechanisms are chosen correctly. We developed and tested such a model for 35 grassland plant species using monoculture measurements of three species characteristics related to nitrogen uptake and retention, which previous experiments indicate as important at our site. Matching classical theoretical expectations, these characteristics defined a distinct tradeoff surface, and models parameterised with these characteristics closely matched observations from experimental multi‐species mixtures. Importantly, predictions improved significantly when we incorporated information from tradeoffs by ‘snapping’ characteristics to the nearest location on the tradeoff surface, suggesting that the tradeoffs and mechanisms we identify are important determinants of local community structure. This ‘snapping’ method could therefore constitute a broadly applicable test for identifying influential tradeoffs and mechanisms.     

Global analysis of endothelial cell line proliferation patterns based on nutrient-depletion models: implications for a standardization of cell proliferation assays

It is known that cell populations growing in different environmental conditions may exhibit different proliferation patterns. However, it is not clear if, despite the diversity of the so-observed patterns, inherent cellular growth characteristics of the population can nevertheless be determined. This study quantifies the proliferative behaviour of the permanent endothelial human cell line, Eahy926, and establishes to which extent the estimation of the cell proliferation rate depends on variations of the experimental protocols. Cell proliferation curves were obtained for cells cultured over 16 days and the influences of cell seeding densities, foetal bovine serum content and frequency of culture medium changes were investigated. Quantitative dynamic modelling was conducted to evaluate the kinetic characteristics of this cell population. We proposed successive models and retained a nutrient-depletion toxicity dependant model, which takes into account the progressive depletion of nutrients, as well as the increase of toxicity in the cell culture medium. This model is shown to provide a very good and robust prediction of the experimental proliferation curves, whatever are the considered frequency of culture medium changes and serum concentrations. Thus, the model enables an intrinsic quantification of the parameters driving in vitro EAhy926 proliferation, including proliferation, nutrient consumption and toxicity increase rates, rather independently of the experiments design. We therefore propose that such models could provide a basis for a standardized quantification of intrinsic cell proliferation kinetics.