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PubMed2003

Evolution of novel cooperative swarming in the bacterium Myxococcus xanthus.

Cooperation among individuals is necessary for evolutionary transitions to higher levels of biological organization. In such transitions, groups of individuals at one level (such as single cells) cooperate to form selective units at a higher level (such as multicellular organisms). Though the evolution of cooperation is difficult to observe directly in higher eukaryotes, microorganisms do offer such an opportunity. Here we report the evolution of novel cooperative behaviour in experimental lineages of the bacterium Myxococcus xanthus. Wild-type strains of M. xanthus exhibit socially dependent swarming across soft surfaces by a mechanism known as 'S-motility' that requires the presence of extracellular type IV pili. In lineages of M. xanthus unable to make pili, a new mechanistic basis for cooperative swarming evolved. Evolved swarming is mediated, at least in part, by enhanced production of an extracellular fibril matrix that binds cells-and their evolutionary interests-together. Though costly to individuals, fibril production greatly enhanced population expansion in groups of interconnected cells. These results show that fundamental transitions to primitive cooperation can readily occur in bacteria.

Antigens, Bacterial↗

PubMed1987

[Evolution of hydrocarbons and bacterial activity in the marine sediments contaminated by crude oil overflow and treated].

The fate of an experimental oil pollution of intertidal sediments in a sheltered beach of North Brittany (France) has been investigated over a 16-month period. Chemical treatments were applied to two of the three contaminated plots by pre-mixing oil respectively with dispersant and biodegrading agents. The physico-chemical and bacteriological characteristics of the polluted areas were followed with the purpose of identifying the limiting parameters for oil microbial degradation and the effect of treatment. The concentration of hydrocarbons in the oiled sediments did not change significantly during the experimental period. Spectrofluorimetric and chromatographic data showed that the main evolution of oil concerns the degradation of n-alkanes and the removal of light aromatics. Biodegradation of hydrocarbons occurred at a measurable rate only during the warm seasons (average temperature 18 +/- 2 degrees C) causing after sixteen months the disappearance of more than 80% of the n-alkanes fraction independently of the pollution sediment level and the chemical treatment of the experimental plots. However, the biodegradation of n-alkanes proceeded during the first months, at different rates, inversely depending on oil content in the collected samples. The main limiting factor is dissolved oxygen according to the fact that spilled oil was located at 3-5 cm depth in a poorly oxygenated zone characterized by low redox potential. Nutrients were not a limiting factor probably due to domestic and agricultural inputs in this area. A marked bacterial growth was observed two weeks after the oil spill with a relative increase in hydrocarbon degrading bacteria with respect to total heterotrophs. Degradation rates, based on C14 n-hexadecane experiments, seem to follow the same way than specific bacterial counts (plate technique). Specific bacteria are always high at the end of our 16 months' field experimentation. In the laboratory as well as in the field experiments, the same behaviour of untreated and chemically treated oil was observed in partially anaerobic sediment.

Bacteria↗

PubMed1986

Dietary fat and experimental carcinogenesis: a summary of recent in vivo studies.

Diets high in fat have been demonstrated to enhance carcinogenesis in numerous models. Studies on the relationship between dietary fat and cancer in experimental animals have improved with the evolution in our knowledge of the carcinogenic process and with our ability to formulate better controlled diets. This paper summarizes studies conducted during the past 15-20 years on the effects of dietary fat on in vivo carcinogenesis. Relationships between skin carcinogenesis and dietary fat have received little attention during this time, but tremendous progress has been made in our understanding of mammary and colon carcinogenesis. Studies have been conducted of mammary carcinogenesis induced in various rat strains by several chemical carcinogens or by X-irradiation. Several colon carcinogenesis models have also been used to evaluate dietary fat effects. Recent studies in the lung, liver, and pancreas have shown relationships between the carcinogenic process at these sites and dietary fat; however, further studies are needed. The confounding between high fat intakes and low carbohydrate intakes and the difficulties of separating high fat intake from high caloric intake must be addressed in future research. The mechanism of the observed effects of dietary fat is unknown.

Animals↗

PubMed2000

Biomass evolution in porous media and its effects on permeability under starvation conditions.

The purpose of this study was to understand bacteria profile modification and its applications in subsurface biological operations such as biobarrier formation, in situ bioremediation, and microbial-enhanced oil recovery. Biomass accumulation and evolution in porous media were investigated both experimentally and theoretically. To study both nutrient-rich and carbon-source-depleted conditions, Leuconostoc mesenteroides was chosen because of its rapid growth rate and exopolymer production rate. Porous micromodels were used to study the effects of biomass evolution on the permeability of a porous medium. Bacterial starvation was initiated by switching the feed from a nutrient solution to a buffer solution in order to examine biofilm stability under nutrient-poor conditions. Four different evolution patterns were identified during the nutrient-rich and nutrient-depleted conditions used in the micromodel experiments. In phase I, the permeability of the porous micromodel decreased as a result of biomass accumulation in pore bodies and pore throats. In phase II, starvation conditions were initiated. The depletion of nutrient in the phase II resulted in slower growth of the biofilm causing the permeability to reach a minimum as all the remaining nutrients were consumed. In phase III, permeability began to increase due to biofilm sloughing caused by shear stress. In phase IV, shear stress remained below the critical shear stress for sloughing and the biofilm remained stable for long periods of time during starvation. The critical shear stress for biofilm sloughing provided an indication of biofilm strength. Shear removal of biofilms occurred when shear stress exceeded critical shear stress. A network model was used to describe the biofilm formation phenomenon and the existence of a critical shear stress. Simulations were in qualitative agreement with the experimental results, and demonstrate the existence of a critical shear stress.

Biomass↗

PubMed1994

A hypothesis: reciprocal information transfer between oligoribonucleotides and oligopeptides in prebiotic molecular evolution.

We wish to propose a mechanism for reciprocal information transfer in prebiotic molecular evolution, based on heterologous pairing complex formation between oligoribonucleotides and oligopeptides. In this proposed pairing complex, the bases of the oligoribonucleotide and the side chains of the oligopeptide may form three types of complementary Watson-Crick-type hydrogen bonds. The structural basis for the pairing is the close correspondence of the distances between the side chains in the two molecules. Both the inter-nucleotide spacing of the RNA and the inter-side-chain spacing of the peptide are approximately 3.4 A. The proposed pairing mode would allow both specific and nonspecific interactions required for reciprocal information transfer. Thus, it represents a simple and versatile coding system that could have had significant implications in prebiotic molecular selection and evolution. In addition, we propose several testable experimental approaches based on the pairing mode of oligoribonucleotides and oligopeptides to verify our hypothesis.

Amino Acid Sequence↗

PubMedDate not supplied

Speeding up a genetic algorithm for EPR-based spin label characterization of biosystem complexity.

Complexity of biological systems is one of the toughest problems for any experimental technique. Complex biochemical composition and a variety of biophysical interactions governing the evolution of a state of a biological system imply that the experimental response of the system would be superimposed of many different responses. To obtain a reliable characterization of such a system based on spin-label Electron Paramagnetic Resonance (EPR) spectroscopy, multiple Hybrid Evolutionary Optimization (HEO) combined with spectral simulation can be applied. Implemented as the GHOST algorithm this approach is capable of handling the huge solution space and provides an insight into the "quasicontinuous" distribution of parameters that describe the biophysical properties of an experimental system. However, the analysis procedure requires several hundreds of runs of the evolutionary optimization routine making this algorithm extremely computationally demanding. As only the best parameter sets from each run are assumed to contribute into the final solution, this algorithm appears far from being optimized. The goal of this study is to modify the optimization routine in a way that 20-40 runs would be enough to obtain qualitatively the same characterization. However, to keep the solution diversity throughout the HEO run, fitness sharing and newly developed shaking mechanisms are applied and tested on various test EPR spectra. In addition, other evolutionary optimization parameters such as population size and probability of genetic operators were also varied to tune the algorithm. According to the testing examples a speed-up factor of 5-7 was achieved.

Algorithms↗

PubMed2005

Ancient and recent positive selection transformed opioid cis-regulation in humans.

Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking. We found that positive natural selection altered the cis-regulation of human prodynorphin, the precursor molecule for a suite of endogenous opioids and neuropeptides with critical roles in regulating perception, behavior, and memory. Independent lines of phylogenetic and population genetic evidence support a history of selective sweeps driving the evolution of the human prodynorphin promoter. In experimental assays of chimpanzee-human hybrid promoters, the selected sequence increases transcriptional inducibility. The evidence for a change in the response of the brain's natural opioids to inductive stimuli points to potential human-specific characteristics favored during evolution. In addition, the pattern of linked nucleotide and microsatellite variation among and within modern human populations suggests that recent selection, subsequent to the fixation of the human-specific mutations and the peopling of the globe, has favored different prodynorphin cis-regulatory alleles in different parts of the world.

Alleles↗

PubMed1997

Evolution of male tail development in rhabditid nematodes related to Caenorhabditis elegans.

The evolutionary pathway that has led to male tails of diverse morphology among species of the nematode family Rhabditidae was reconstructed. This family includes the well-studied model species Caenorhabditis elegans. By relating the steps of male tail morphological evolution to the phenotypic changes brought about by developmental mutations induced experimentally in C. elegans, the goal is to identify genes responsible for morphological evolution. The varying morphological characters of the male tails of several rhabiditid species have been described previously (Fitch and Emmons, 1995, Dev. Biol. 170:564-582). The developmental events preceding differentiation of the adult structures have also been analyzed; in many cases the origins of varying adult morphological characters were traced to differences during ontogeny. In the present work, the evolutionary changes producing these differences were reconstructed in the context of the four possible phylogenies supported independently by sequences of 18S ribosomal RNA genes (rDNA). Two or more alternative states were defined for 36 developmental and adult morphological characters. These characters alone do not provide sufficient data to resolve most species relationships; however, when combined with the rDNA characters, they provide stronger support for one of the four rDNA phylogenies. Assuming a model of ordered transformations for multistate developmental characters generally results in greater resolution. Transformations between character states can be assigned unequivocally by parsimony to unambiguous branches for most of the characters. Correlations are thereby revealed for some of the developmental characters, indicating a probability of a shared developmental or genetic regulatory pathway. Four of the unequivocal character state changes on unambiguously supported branches closely resemble the phenotypic changes brought about by known mutations in C. elegans. These mutations define genes that are known to act in genetic regulatory hierarchies controlling pattern formation, differentiation, and morphogenesis. Although these studies are still at an early stage, these results strongly suggest that parallel studies of developmental mutants in C. elegans and of morphological and developmental evolution among related nematodes will help define genetic changes underlying the evolution of form.

Animals↗

PubMed1995

Time evolution of the number of functional murine eccrine sweat glands after irradiation: a quantitative analysis of experimental data using a model of proliferative and functional organization.

The function of eccrine sweat glands in the beta-pad of the mouse foot after irradiation was followed over time. Graded doses of X-rays were given to the foot, either as single doses or in two equal fractions separated by a 24-h interval. A quantitative, non-invasive, functional assay was used allowing repeated evaluation of the animals. Sweat gland function was assessed once a week for the first 6 weeks, and at 8, 10, 14, 18, 28, 38 and 45 weeks after irradiation. The beta-pad of the unirradiated foot was used as a control. The function dropped to a nadir within 8-10 weeks after irradiation, whereafter it gradually recovered, reaching a stable level 20-25 weeks after irradiation. These data were analyzed using a mathematical model of proliferative and functional organization of the sweat pore. The model provides a description of the time evolution of pore function, and its basic features were as follows. The functional subunit is a single sweat pore, which will be assayed as functional provided that it contains a number of functional cells above a critical threshold. The functional cells are capable of self renewal (a so-called 'flexible' tissue), and the proportion of proliferating cells is subject to homeostatic control. Irradiation is assumed to transfer a certain fraction of the cells into a state with a limited probability of successful division. This fraction is assumed to have a linear-quadratic dependence on dose. The values of all free model parameters were optimized by a maximum-likelihood fit to the experimental data. With optimized parameter values, the initial decrease, nadir, and long-term level of tissue function estimated from the model were in close agreement with the experimental observations for all the 28 dose groups. Some of the estimated model parameters are: growth fraction 4.2 +/- 0.2%; cell cycle time, 0.95 +/- 0.04 days; number of functional cells in a single pore in the unirradiated animal, 9.9 +/- 0.5; and alpha/beta ratio, 4.3 Gy (95% confidence interval 3.1-5.0 Gy). It is concluded that the present model, despite its relative mathematical simplicity, provides a close description of the postirradiation kinetics of functional cells in the mouse sweat gland.

Animals↗

PubMed2000

Determination of depolymerization kinetics of amylose, amylopectin, and soluble starch by Aspergillus oryzae alpha-amylase using a fluorimetric 2-p-toluidinylnaphthalene-6-sulfonate/flow-injection analysis system.

This study reports on the determination of the depolymerization kinetics of amylose, amylopectin, and soluble starch by Aspergillus oryzae alpha-amylase using flow-injection analysis with fluorescence detection and 2-p-toluidinylnaphthalene-6-sulfonate as the fluorescent probe. The experimental data points, corresponding to the evolution of the concentration of "detectable" substrate with depolymerization time, were fit to a single exponential decay curve in the case of amylose and to a double exponential decay curve in the cases of amylopectin and soluble starch. For all the assayed substrates, the determined depolymerization rates at time zero correlated well with the initial enzyme and substrate concentrations through the usual Michaelis-Menten hyperbola. Therefore, this methodology allows the determination of alpha-amylase activity using any of these substrates. For amylopectin and soluble starch, the value of the total depolymerization rate at any depolymerization time was the result of the additive contribution of two partial depolymerization rates. In contrast, the total depolymerization rate for amylose was always a single value. These results, in conjunction with the relative time evolution of the two partial depolymerization rates (for amylopectin and soluble starch), are in good agreement with a linear molecular structure for amylose, a "grape-like" cluster molecular structure for amylopectin, and an extensively degraded grape-like cluster structure for soluble starch.

Amylopectin↗

PubMed1997

System peaks in capillary zone electrophoresis. 3. Practical rules for predicting the existence of system peaks in capillary zone electrophoresis of anions using indirect spectrophotometric detection.

A theoretical and experimental study of the existence and evolution of system peaks in capillary zone electrophoresis (CZE) with indirect spectrophotometric detection is presented with respect to the effect of the number of coions present in the background electrolyte (BGE). It is shown that in BGEs having only one coion (i.e., the UV-absorbing probe anion), the sample produces only negative peaks due to each analyte anion and no system peaks, with the number of sample peaks corresponding to the number of analytes present in the sample injected. In BGEs containing two coions, a sample with one analyte anion produces one negative indirect detection peak and one system peak. The transition between BGEs having one coion and those with two coions has also been studied and it has been shown that an addition of ca. 5% of the second coion to a single coion BGE causes the resulting BGE to behave macroscopically as a regular two-coion BGE. A descriptive model is proposed, based on transient isotachophoresis (transient stacking) of the sample species and of the coion from the BGE which has the closest mobility to the sample ion. This model explains qualitatively the formation and evolution of the sample peak (containing the sample species and being detected by indirect detection due to displacement of the UV-absorbing probe in its zone) and the system peak (containing no sample species and being a vacancy in the continuum of coions of the BGE). It is shown that the system peak may be positive or negative as it corresponds to the situation where the vacancy of one component of the BGE results in an enhanced concentration of the other component. It has been demonstrated that the system peak is created by a vacancy of that component of the BGE which has the greatest difference in mobility relative to that of the sample species. On indirect detection in BGEs containing two coions the sample displaces predominantly the BGE coion which has a mobility closest to that of the analyte anion. In systems with BGEs containing two coions, a sample having n analytes produces n sample peaks and one system peak, the sign and magnitude of which are dependent on the sum of the UV absorbances of the analytes involved. The effect of bicarbonate from atmospheric CO2 has also been studied and it has been shown that weakly alkaline BGEs with a single anionic UV-absorbing coion, such as those currently used for anionic analyses with indirect detection, may suffer from the presence of system peaks due to bicarbonate.

Anions↗

PubMed1994

Automated image analyzing system for the quantitative study of living cells in culture.

A fully automated image analyzing system was developed for the quantitative study of cells in culture. It was able to count cells, to classify cells according to their morphological characteristics and to follow cell culture development. A specific procedure was designed to process Hoffman modulation contrast images. It detects local gray level differences while using conditional dilation techniques. We were able to successfully detect aggregated unstained cells, presently a technical limit in image segmentation. Living cells can be studied in a noninvasive and nondestructive way with this system. An improved automatic focusing algorithm was developed which ensured an accurate prediction of the optimal focus position. A strictly defined sampling procedure was applied to estimate unbiasedly cell density and obtain precisely cell contours. The evaluation of the system was carried out on Chinese hamster ovary (CHO-NTR) cell cultures treated with a newly developed neurotensin agonist JMV449. Chinese hamster ovary cell division was found to be retarded 20 hours after the JMV449 treatment, while the morphology of CHO-NTR cells has already undergone significant changes 12 hours after the treatment. This image analyzing system provides the possibility to follow cell culture development (e.g., cell density evolution, cell morphological changes) under various experimental conditions.

Animals↗

PubMedDate not supplied

Experimental myocardial infarction in a closed-chest canine model. Observations of temporal and spatial evolution over 24 hours.

Myocardial infarction was induced in 7 mongrel dogs by transfemoral intraluminal occlusion of the left anterior descending coronary artery. Perfusion area at risk was determined by post-mortem coronarography and infarct size by macrohistological staining with para-nitrophenoltetrazolium. Regional flow was determined by injection of radioactive microspheres 0.2 hours, 12 hours, and 24 hours post occlusion. Infarct size as determined by planimetry of post-mortem angiograms and macrohistological stains at identical magnification revealed 74.5 +/- 12.1% infarcted tissue of the perfusion area at risk. The flow of the necrotic tissue was below 13 Ml/100 g min without exception, indicating a threshold perfusion for maintenance of myocardial viability. Accordingly, a flow of less than or equal to 10 ml/100 g min identified 93% of the entire infarcted myocardium, resulting in 71 +/0 20% as compared to the perfusion area at risk. Based on the good agreement of macrohistological and flow data, the evolution of myocardial injury was determined by flow measurements. The results indicated a different progression of the borders of critical flow in the subendocardial and subepicardial layers, whereas in the subendocardium 85% of the tissue at risk was identified by the critical flow at 0.2 hours and 97% at 12 hours, the subepicardial flow changed at a different pace: only 53% showed subcritical perfusion at 0.2 hours, 61% at 12 hours with a final increase of 39% from 12 to 24 hours.

Animals↗

PubMed1992

Spontaneous mutagenesis: experimental, genetic and other factors.

Spontaneous mutations are "the net result of all that can go wrong with DNA during the life cycle of an organism" (Glickman et al., 1986). Thus, the types and amounts of spontaneous mutations produced are the resultant of all the cellular processes that are mutagenic and those that are antimutagenic. It is not widely appreciated that the types and frequencies of spontaneous mutations change markedly with subtle changes in experimental conditions. All types of mutations are produced spontaneously, i.e., base substitutions, frameshifts, insertions and deletions. However, very few papers have appeared that are devoted exclusively to the study of the mechanisms of spontaneous mutagenesis, and of the subtle experimental factors that affect the types and frequencies of spontaneous mutations. This is unfortunate because spontaneous mutagenesis appears to play a major role in evolution, aging, and carcinogenesis. This review emphasizes subtle experimental variables that markedly affect the results of a spontaneous mutation experiment. A thorough understanding of these variables eliminates the need for a theory of "directed" mutagenesis. The intrinsic instability of DNA, and the types of normal metabolic lesions that are produced in DNA that lead to mutations via errors made in replication, repair, and recombination are reviewed, as is the genetic control of spontaneous mutagenesis. As with spontaneous mutagenesis, spontaneous carcinogenesis can also be considered to be the net result of all that can go wrong with DNA during the life of an organism.

Cell Transformation, Neoplastic↗

PubMedDate not supplied

Prospective and retrospective tests of evolutionary theories of senescence.

Retrospective and prospective methods in the study of the evolution of longevity and senescence are compared. Retrospective studies can provide tests of evolutionary theories of senescence through the interpretation of evolutionary pattern demonstrated by species in nature. Patterns in longevity displayed by African rivulin fishes provide a clear and incisive example of the evolution of longevity and associated life history characters, but such tests are often difficult to find or unclear in the a posteriori interpretation of evolution that they offer. Far more experimentation of the prospective kind has been applied to testing theories of life span. Though prospective tests of evolutionary theory are compromised to a degree by the artificiality of the laboratory environment, experiments performed there are not necessarily invalid. In addition, prospective tests offer the added impetus that theoretical predictions are tested a priori. The use of Drosophila melanogaster as a laboratory model for the study of longevity has provided a number of particularly enlightening recent advances describing the number and distribution of genes controlling longevity, the metabolic pathways by which other characters are physiologically associated with life span, and even the controlling genetic elements affecting those traits. Improvements in longevity shown under programs of selective breeding may be the result of adaptations in the glycolytic pathway altering the ability to utilize the sugar sucrose as a food source.

Journal Article↗

PubMed2005

Fungal biodegradation of naphthalene: microcosms studies.

The present work is aimed to ascertain naphthalene biodegradation capability of P. chrysosporium and T. harzianum in soil microcosms. Considering the high naphthalene volatility, a suitable soil microcosm was set-up and used. Several degradation tests were conducted with different C/N ratio media for the two fungi in order to enquire the best range of working conditions. The kinetic studies were conducted at a maximal naphthalene concentration of 600 mg kg(-1). During experimental time course naphthalene concentration, CO2 evolution as well as phytotoxicity tests were performed as monitoring parameters. The results shown in the current paper, put in evidence that T. harzianum, differently than in liquid culture, is not able to biodegrade naphthalene directly in soil microcosm, while P. chrysosporium in the same conditions biodegrades the PAH till about 600 mg kg(-1). As concern the founded kinetics for P. chrysosporium, a saturation shape in presence of N-limited medium (high C/N ratio) was evaluated while a growing form more than linear in no-N limited medium (normal C/N ratio) was determined.

Basidiomycota↗

PubMed2005

Epitope spreading within lupus-associated ribonucleoprotein antigens.

Autoantibodies reactive with several cellular antigens are present in the sera of patients with systemic lupus erythematosus. Polypeptides within the Ro-RNP complex and the snRNP complex are often targeted by these autoantibodies. One of the mechanisms responsible for their evolution is that of epitope spreading. Experimental animal model systems provide evidence for this. This review discusses the animal model systems of epitope spreading within these ribonucleoprotein antigens, the mechanisms of epitope spreading, and its relevance for disease pathogenesis.

Animals↗

PubMed2005

Linear motifs: evolutionary interaction switches.

Linear motifs are short sequence patterns associated with a particular function. They differ fundamentally from longer, globular protein domains in terms of their binding affinities, evolution and in how they are found experimentally or computationally. In this Minireview, we discuss various aspects of these critically important functional regions.

Amino Acid Motifs↗