Dynamic cellular automata: an alternative approach to cellular simulation

A wide variety of approaches, ranging from Petri nets to systems of partial differential equations, have been used to model very specific aspects of cellular or biochemical functions. Here we describe how an agent-based or dynamic cellular automata (DCA) approach can be used as a very simple, yet very general method to model many different kinds of cellular or biochemical processes. Specifically, using simple pairwise interaction rules coupled with random object moves to simulate Brownian motion, we show how the DCA approach can be used to easily and accurately model diffusion, viscous drag, enzyme rate processes, metabolism (the Kreb's cycle), and complex genetic circuits (the repressilator). We also demonstrate how DCA approaches are able to accurately capture the stochasticity of many biological processes. The success and simplicity of this technique suggests that many other physical properties and significantly more complicated aspects of cellular behavior could be modeled using DCA methods. An easy-to-use, graphically-based computer program, called SimCell, was developed to perform the DCA simulations described here. It is available at http://wishart.biology.ualberta.ca/SimCell/.     

Waiting to inhale: HIF-1 modulates aerobic respiration

The hypoxia-inducible factor HIF-1 is known to promote anaerobic respiration during low oxygen conditions (hypoxia). In this issue, Fukuda et al. (2007) expand the range of HIF-1's functions by showing that it modulates aerobic respiration as well.     

Thermal genetic adaptation in the water flea Daphnia and its impact: an evolving metacommunity approach

Genetic adaptation to temperature change can impact responses of populations and communities to global warming. Here we integrate previously published results on experimental evolution trials with follow-up experiments involving the water flea Daphnia as a model system. Our research shows (1) the capacity of natural populations of this species to genetically adapt to changes in temperature in a time span of months to years, (2) the context-dependence of these genetic changes, emphasizing the role of ecology and community composition on evolutionary responses to climatic change, and (3) the impact of micro-evolutionary changes on immigration success of preadapted genotypes. Our study involves (1) experimental evolution trials in the absence and presence of the community of competitors, predators, and parasites, (2) life-table and competition experiments to assess the fitness consequences of micro-evolution, and (3) competition experiments with putative immigrant genotypes. We use these observations as building blocks of an evolving metacommunity to understand biological responses to climatic change. This approach integrates both local and regional responses at both the population and community levels. Finally, we provide an outline of current gaps in knowledge and suggest fruitful avenues for future research.     

A simplified technique to measure respiration rates of aerobic heterotrophic populations

A simplified technique to trap respired carbon dioxide in a closed bottle system was developed from the technique introduced by Hobbie & Crawford in 1969. In this technique carbon dioxide was trapped in ethanolamine in a glass cup without the use of chromatographic paper. The results show that there is no need to enlarge the absorption surface with filter paper as practically complete recovery was achieved with ethanolamine alone in the cup.     

Regulatory mechanisms of cellular respiration; the role of cell membranes; uranium inhibition of cellular respiration

Uranium as UO(2)(NO(3))(2) combines reversibly with proteins. The degree of dissociation of this combination depends, among other factors, on the H(+) concentration. At pH 7.3 the U-albumin complex was easily dissociated on addition of citrate, while at pH 3.8 it was not. Uranium inhibited reversibly a number of enzyme systems. Uranium enzyme inhibitions could be reversed on addition of certain hydroxypolycarboxylic acids (citric acid, alpha-hydroxyaspartic acid, malic acid); in no case, however, did phosphate have any effect. In cell-free yeast juice, the fermentation of glucose-hexosediphosphate was inhibited by UO(2)(NO(3))(2). Slight reactivation occurred on addition of phosphate. In living yeast cells, the fermentation and oxidation of glucose was inhibited by small amounts of UO(2)(NO(3))(2) (7,7 micrograms per mg. dry weight), while the oxidation of acetic acid, ethyl alcohol, malic and citric acids, was not affected at all. U inhibition in living yeast cells at pH 7.3 was completely released on addition of small amounts of phosphate, adenosinetriphosphate, and citrate, while at pH 3.8 U inhibition was not released by phosphate and citrate. At saturation, one yeast cell contained 7.06 x 10(6) molecules of uranium. Lactic dehydrogenase was not inhibited by U while the oxidation of lactic acid by gonococci was inhibited. Addition of phosphate released this inhibition. The U inhibition of liver succinoxidase was unaffected by phosphate, while the U inhibition of the oxidation of succinate by E. coli was released by phosphate. It has been concluded from these experiments that U inhibition of cell metabolism is due to combination of the metal with the protein portion of the cell membrane. Uranium is presented as an example of surface inhibition.     

A teaching exercise for the identification of bacteria using an interactive computer program

An interactive computer program written in Fortran is described which provides an exercise in the identification of bacteria. The program, IDEN, provides a novel way of enhancing a student's approach to systematic bacteriology and numerical identification procedures. An unknown bacterium is assigned to a student who is provided with a list of possible species and a list of tests which may be carried out. The student's objective is the correct identification of the unknown in the most economical manner. An indication is given concerning the way in which this program can be used to enhance theoretical instruction and practical investigation.     

Uncoupler resistance in Escherichia coli: the role of cellular respiration

Bioenergetic properties of a mutant strain of Escherichia coli K12 designated TUV, which is resistant to the protonophoric uncoupling agent 4,5,6,7-tetrachloro-2-trifluoromethylbenzimidiazole (TTFB) have been compared with those of its non-resistant parent, E. coli K12 Doc-S. Strain TUV grew and respired some 20-30% faster than strain Doc-S, and was cross-resistant to carbonylcyanide p-(trifluoromethoxy)phenylhydrazone and triphenyltin, but not to 2,4-dinitrophenol. Phosphorus nuclear magnetic resonance demonstrated the TTFB-mediated collapse of the transmembrane pH gradient at identical rates in starved cells of both strains, indicating that uncoupler access and function were unimpaired in the mutant under these conditions. Strain TUV displayed enhanced uncoupler resistance and maintained intracellular pH and ATP levels only when respiring. On the other hand, strain TUV also showed increased resistance to novobiocin, implying that its outer wall permeability had been lowered. We suggest that the active resistance of strain TUV results from the exclusion of uncoupler by the interaction of inner and outer membrane components in a manner modulated by the degree of cellular energization.     

The effect of the laser on cellular respiration

Summary A frequency of 5300 Å, derived from a frequency-doubled Q-switched neodymium laser was observed to produce progressive injury and death of cells from a culture of newborn rat cerebellum. A subsequent observation that the green laser frequency (but not 6943 Å of the same intensity from a Q-switched ruby laser) could reduce the rate of oxygen consumption of rat brain cell suspensions suggested that the cytochromes may serve as chromophores. This hypothesis was confirmed by a demonstration that cytochromes c+c₁ failed to act as hydrogen acceptors following 10 impacts of 1 Mw/cm² each of the green laser frequency and cytochromes a+a₃ showed a similar response when a brain cell suspension was irradiated (200 kw) with frequencies of 6096 and 6013 Å. These data illustrate the principle that laser frequencies which are appropriately matched to the absorption characteristics of target molecules can selectively inhibit specific molecular components in intact cells, if a controlled energy density range is used.This work was supported in part by the U.S. Army Medical Research and Development Command, Office of the Surgeon General, under Contract No. DA-49-193-MD-2564, and in part by Electro-Optical Systems, Inc.     

Merging nano-genotoxicology with eco-genotoxicology: an integrated approach to determine interactive genotoxic and sub-lethal toxic effects of C(60) fullerenes and fluoranthene in marine mussels, Mytilus sp

Whilst there is growing concern over the potential detrimental impact of engineered nanoparticles (ENPs) on the natural environment, little is known about their interactions with other contaminants. In the present study, marine mussels (Mytilus sp.) were exposed for 3 days to C(60) fullerenes (C(60); 0.10-1 mg l(-1)) and a model polycyclic aromatic hydrocarbon (PAH), fluoranthene (32-100 μg l(-1)), either alone or in combination. The first two experiments were conducted by exposing the organisms to different concentrations of C(60) and fluoranthene alone, in order to determine the effects on total glutathione levels (as a measure of generic oxidative stress), genotoxicity (DNA strand breaks using Comet assay in haemocytes), DNA adduct analyses (using (32)P-postlabelling method) in different organs, histopathological changes in different tissues (i.e. adductor muscle, digestive gland and gills) and physiological effects (feeding or clearance rate). Subsequently, in the third experiment, a combined exposure of C(60) plus fluoranthene (0.10 mg l(-1) and 32 μg l(-1), respectively) was carried out to evaluate all endpoints mentioned above. Both fluoranthene and C(60) on their own caused concentration-dependent increases in DNA strand breaks as determined by the Comet assay. Formation of DNA adducts however could not be detected for any exposure conditions. Combined exposure to C(60) and fluoranthene additively enhanced the levels of DNA strand breaks along with a 2-fold increase in the total glutathione content. In addition, significant accumulation of C(60) was observed in all organs, with highest levels in digestive gland (24.90 ± 4.91μg C(60) g(-1) ww). Interestingly, clear signs of abnormalities in adductor muscle, digestive gland and gills were observed by histopathology. Clearance rates indicated significant differences compared to the control with exposure to C(60), and C(60)/fluoranthene combined treatments, but not after fluoranthene exposure alone. This study demonstrated that at the selected concentrations, both C(60) and fluoranthene evoke toxic responses and genetic damage. The combined exposure produced enhanced damage with additive rather than synergistic effects.     

Characterisation of the microbial 16S rDNA diversity of an aerobic phosphorus-removal ecosystem and monitoring of its transition to nitrate respiration

The microbial community of a conventional anaerobic-aerobic sequencing batch reactor was investigated by cloning and sequencing bacterial 16S rDNA. The 92 16S rDNA sequences analysed ranged across 50 different operational taxonomic units (OTU). The majority of these sequences were not closely related to known species. They belonged to 12 different groups, but essentially to the Cytophagales and the Proteobacteria beta, which represented 38% and 17% of the retrieved sequences respectively. No OTU numerically outnumbered the others. However, similarities were observed with previous reports on molecular characterisation of phosphorus-accumulating ecosystems, suggesting an enrichment in microorganisms belonging to the Rhodocyclus group. Thereafter, the ability of this anaerobic-aerobic microbial community to accumulate phosphorus with nitrate as its energy source was investigated. The reactor was shifted from anaerobic-aerobic running conditions to anaerobic-anoxic conditions by injection of nitrate; and its microbial community was monitored by PCR-single strand conformation polymorphism (SSCP). The reactor maintained a good phosphorus accumulation and similar SSCP microbial community patterns for a period of 17 days, suggesting that the same microbial community was able to respire both oxygen and nitrate. However, this situation was unstable, since a breakdown in phosphorus accumulation occurred thereafter.     

SOMAP: a novel interactive approach to multiple protein sequences alignment

A novel interactive method for generating multiple protein sequencealignments is described. The program has no internal limit tothe number or length of sequences it can handle and is designedfor use with DEC VAX processors running the VMS operating system.The approach used is essentially one of manual sequence manipulation,aided by built-in symbolic displays of identities and similarities,and strict and ‘fuzzy’ (ambiguous) pattern-matchingfacilities. Additional flexibility is provided by means of aninterface to a publicly available automatic alignment systemand to a comprehensive sequence analysis package. Received on August 28, 1990; accepted on November 20, 1990     

Bioturbation enhances the aerobic respiration of lake sediments in warming lakes

While lakes occupy less than 2% of the total surface of the Earth, they play a substantial role in global biogeochemical cycles. For instance, shallow lakes are important sites of carbon metabolism. Aerobic respiration is one of the important drivers of the carbon metabolism in lakes. In this context, bioturbation impacts of benthic animals (biological reworking of sediment matrix and ventilation of the sediment) on sediment aerobic respiration have previously been underestimated. Biological activity is likely to change over the course of a year due to seasonal changes of water temperatures. This study uses microcosm experiments to investigate how the impact of bioturbation (by Diptera, Chironomidae larvae) on lake sediment respiration changes when temperatures increase. While at 5°C, respiration in sediments with and without chironomids did not differ, at 30°C sediment respiration in microcosms with 2000 chironomids per m² was 4.9 times higher than in uninhabited sediments. Our results indicate that lake water temperature increases could significantly enhance lake sediment respiration, which allows us to better understand seasonal changes in lake respiration and carbon metabolism as well as the potential impacts of global warming.     

Cyanide-resistant respiration is frequent, but confined to yeasts incapable of aerobic fermentation

In Pichia membranifaciens, cyanide-resistant respiration (CRR) sensitive to salicylhydroxamic acid emerged after forced aeration of starved cells for 4 h. Surveying a large number of species by this simple methodology, we found that CRR is very frequent among yeasts. Remarkably, considering our results together with previous data in the literature, CRR was present in 24 out of 28 non-fermentative or Crabtree-negative yeasts and absent in 10 out of 12 Crabtree-positive yeasts. We submit that, as alternatives to cytochromic respiration, yeasts developed two strategies: either aerobic fermentation in Crabtree-positive yeasts or CRR in non-fermentative or Crabtree-negative yeasts.