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PubMed1994

Dictyostelium discoideum, a lower eukaryote model for the study of DNA repair: implications for the role of DNA-damaging chemicals in the evolution of repair proficient cells.

The evolution of the ability of living cells to cope with stress is crucial for the maintenance of their genetic integrity. Yet low levels of mutation must remain to allow adaptation to environmental changes. The cellular slime mold D. discoideum is a good system for studying molecular aspects of the repair of lethal and mutagenic damage to DNA by radiation and chemicals. The wild-type strains of this soil microorganism are extremely resistant to DNA damaging agents. In nature the amoeboid cells in their replicative stage feed on soil bacteria and are exposed to numerous DNA-damaging chemicals produced by various soil microorganisms. It is probable that the evolution of repair systems in this organism and perhaps in others is a consequence of the necessity to cope with chemical damage which also confers resistance to radiation.

Animals↗
PubMed2001

Interstellar matrices: the chemical composition and evolution of interstellar ices as observed by ISO.

Matrix isolation techniques have been developed in the early sixties as a tool for studying the spectroscopic properties of out of equilibrium species (atoms, radicals, ions, reactive molecules), embedded in rare gas inert matrices at low temperatures. Cold interstellar grains surfaces are able to condense out gas phase molecules, routinely observed by radioastronomy. These grain 'mantles' can be considered as 'interstellar matrices'. However, these matrices are not clean and unreactive. They are made principally of dirty ices whose composition must be determined carefully to assess the importance of the solid state chemistry that takes place in the Interstellar Medium. Infrared spectroscopy, both in astronomy and in the laboratory, is the unique tool to determine the chemical composition of these ices. Astronomical spectra can directly be compared with laboratory ones obtained using classical matrix isolation techniques. Furthermore, dedicated experiments may be undertaken to further improve the understanding of the basic physico-chemical processes that take place in cosmic ices.

Astronomical Phenomena↗
PubMed2006

Protocell-like microspheres from thermal polyaspartic acid.

One of the most prominent amino acids to appear in monomer-generating origin-of-life experiments is aspartic acid. Hugo Schiff found in 1897 that aspartic acid polymerizes when heated to form polyaspartylimide which hydrolyzes in basic aqueous solution to form thermal polyaspartic acid which is a branched polypeptide. We recently reported at the ISSOL 2005 Conference that commercially made thermal polyaspartic acid forms microspheres when heated in boiling water and allowed to cool. In a new experiment we heated aspartic acid at 180 degrees C for up to 100 h to form thermal polyaspartylimide which when heated in boiling water without addition of base hydrolyzed to form thermal polyaspartic acid which upon cooling formed microspheres. Thermal polyaspartic acid microspheres appear protocell-like in the sense of being prebiotically plausible lattices or containers that could eventually have been filled with just the right additions of primordial proteins, nucleic acids, lipids, and metabolites so as to constitute protocells capable of undergoing further chemical and biological evolution. Thermal polyaspartic acid microspheres are extremely simple models of protocells that are more amenable to precise quantitative experimental investigation than the proteinoid microspheres of Sidney W. Fox. We present here scanning electron microscope images of such thermal polyaspartic acid microspheres. Figure 1 shows thermal polyaspartic acid microspheres from L: -aspartic acid heated at 180 degrees C for 50 h, at a magnification of 3,500x. Figure 2 shows thermal polyaspartic acid microspheres from the same sample at a magnification of 7,000x. The thermal polyaspartic acid microspheres have a diameter of approximately 1 mum These images were viewed with a Hitachi S2460N scanning electron microscope at 20 kV acceleration voltage. Figure 1 Thermal polyaspartic acid microspheres from L: -aspartic acid heated at 180 degrees C for 50 h, at a magnification of 3,500x. Figure 2 Thermal polyaspartic acid microspheres from L: -aspartic acid heated at 180 degrees C for 50 h, at a magnification of 7,000x.

Evolution, Chemical↗
PubMed2005

The storage of sewage sludge: influence of liming on the evolution of copper chemical fractions.

Sewage sludge re-used in agriculture has to be stabilized and is often stored for several months before land spreading. Stabilization treatment may affect the behaviour of heavy metals such as Cu, which is an element potentially toxic to the environment. In the present study, the chemical forms of copper have been investigated in heaps of limed and unlimed sludge coming from the wastewater treatment plant of Roselies (Belgium). These limed and unlimed aerobically digested sludges were stored during 4 mo in controlled conditions close to field ones. The sequential extraction procedure developed by Tessier was used to determine the copper chemical forms of representative samples taken in the outer shell and in the depth of the heaps. The physico-chemical properties (pH, organic matter, dry matter and temperature) of these samples were also monitored. This study shows that liming transforms part of organically-bound copper into both exchangeable and residual copper. These changes mainly occur during the first 2 wk of storage. After several months of storage, copper passes from the residual fraction to the exchangeable and oxide fractions. During the whole experiment, changes occur faster in the outer shell than in the depth of the heaps. Thus, we demonstrate that the distribution of the copper forms depends on the storage time and it is different in the outer shell from that in the depth of the heaps.

Calcium Compounds↗
PubMed1995

Carbonaceous matter in cometary dust and coma.

The analysis of carbonaceous matter in p/Halley's dust and coma via mass spectrometry of positive ions is reviewed. Dust impact generated ions were analyzed by the PUMA instrument aboard VEGA I, and coma plasma ions by the PICCA instrument aboard GIOTTO. For the organic molecules results an overall C:H:O:N ratio of 1.:1.4:0.6:0.1. Most of this polymer material can formally be understood as an aggregation of monomers C2H2, CH2O, and HCN. Special emphasis is given to possible aromatic, especially heterocyclic, and other unsaturated ions, and their importance for abiotic chemical and prebiotic evolution. Aspects of the potential heterogeneous catalysis in liquid water at the inorganic grain backbone structure found by this analysis, too, are also treated.

Acetylene↗
PubMed2004

Effect of chemicals on the microbial evolution in foods.

In contrast with most chemical hazardous compounds, the concentration of food pathogens changes during processing, storage, and meal preparation, making it difficult to estimate the number of microorganisms or the concentration of their toxins at the moment of ingestion by the consumer. These changes are attributed to microbial proliferation, survival, and/or inactivation and must be considered when exposure to a microbial hazard is assessed. The number of microorganisms can also change as a result of physical removal, mixing of food ingredients, partitioning of a food product, or cross-contamination (M. J. Nauta. 2002. Int. J. Food Microbiol. 73:297-304). Predictive microbiology, i.e., relating these microbial evolutionary patterns to environmental conditions, can therefore be considered a useful tool for microbial risk assessment, especially in the exposure assessment step. During the early development of the field (late 1980s and early 1990s), almost all research was focused on the modeling of microbial growth over time and the influence of temperature on this growth. Later, modeling of the influence of other intrinsic and extrinsic parameters garnered attention. Recently, more attention has been given to modeling of the effects of chemicals on microbial inactivation and survival. This article is an overview of different applied strategies for modeling the effect of chemical compounds on microbial populations. Various approaches for modeling chemical growth inhibition, the growth-no growth interface, and microbial inactivation by chemicals are reviewed.

Bacteria↗
PubMed2006

Olive mill wastewater sludge from evaporation ponds: evolution of physico-chemical parameters during storage and composting process.

The evolution of analytical parameters of olive mill waste water sludge stored in evaporation ponds was investigated after one year and two years of storage. It was observed that some of the phenolic monomer compounds resisted removal and the fraction of water soluble phenols was only slightly polymerised. Co-composting of the sludge was carried out with yard trimming as bulking agent ratio and poultry manure to balance the C/N. Three turned piles with three proportions of 35%, 65% and 80% of olive mill waste water sludge were prepared. Co-composting of the sludge was possible in all the cases. Best results were obtained, however, at a proportion of 35% which permitted a shorter composting time, a higher degree of nitrification and a higher rate of total phenols decreasing. A high polymerisation of the fraction of water soluble phenols was observed at the end of composting in all the piles.

Animals↗
PubMed1997

Chemical ecology and biomolecular evolution .

The belief in the Darwinian theory of evolution appeared to be shaken when one tried to interpret statements of molecular biology in it. As a consequence there arose a theory of non-Darwinian neutral evolution. The supporters of this theory believe that under natural conditions no factors exist which can distinguish and select organisms on their internal (molecular) structure. In the opinion of these neutralists natural selection cannot in principle control the molecular constitution of organisms. Contrary to the viewpoint of the critics of neutralism it is impossible to admit that nucleic acids, proteins and other biomolecules can evolve without the participation of natural selection. This controversy in contemporary theoretical biology can be solved by integrating the conceptions of molecular ecology with Darwinian theory. Molecular ecology acknowledges the interactions of organisms by means of chemical substances synthesized by them. Such chemical ecological factors play a leading part in the selective stages of biomolecular evolution. These diverse chemical ecological interrelations take place intensively when living beings interact with parasitic microbes.

Animals↗
PubMed2004

Directed evolution of a glycosynthase via chemical complementation.

Recently, we reported a general assay for enzyme catalysis based on the yeast three-hybrid assay, Chemical Complementation, which is intended to expand the range of chemical reactions to which directed evolution can be applied. Here, Chemical Complementation was applied to a glycosynthase derived from a retaining glycosidase, an important class of enzymes for carbohydrate synthesis. Using the yeast three-hybrid assay, the glycosynthase activity of the E197A mutant of the Cel7B from Humicola insolens was linked to transcription of a LEU2 reporter gene, making cell growth dependent on glycosynthase activity in the absence of leucine. Then the LEU2 selection was used to isolate the most active glycosynthase from a Glu197 saturation library, yielding an E197S Cel7B variant with a 5-fold increase in glycosynthase activity. These results not only establish Chemical Complementation as a platform for the directed evolution of glycosynthases, but also show the generality of this approach and the ease with which it can be applied to new chemical reactions.

Ascomycota↗
PubMed2005

Creation of GPCR-based chemical sensors by directed evolution in yeast.

G protein-coupled receptors (GPCRs) form a class of biological chemical sensors with an enormous diversity in ligand binding and sensitivity. To explore structural aspects of ligand recognition, we subjected the human UDP-glucose receptor (P2Y14) functionally expressed in the yeast Saccharomyces to directed evolution. We sought to generate new receptor subtypes with ligand-binding properties that would be useful in the development of practical biosensors. Mutagenesis of the entire UDP-glucose receptor gene yielded receptors with increased activity but similar ligand specificities, while random mutagenesis of residues in the immediate vicinity of the ligand-binding pocket yielded mutants with altered ligand specificity. By first sensitizing the P2Y14 receptor and then redirecting ligand specificity, we were able to create mutant receptors suitable for a simple biosensor. Our results demonstrate the feasibility of altering receptor ligand-binding properties via a directed evolution strategy, using standard yeast genetic techniques. The novel receptor mutants can be used to detect chemical ligands in complex mixtures and to discriminate among chemically or stereochemically related compounds. Specifically, we demonstrate how engineered receptors can be applied in a pairwise manner to differentiate among several chemical analytes that would be indistinguishable with a single receptor. These experiments demonstrate the feasibility of a combinatorial approach to detector design based on the principles of olfaction.

Binding Sites↗
PubMed1984

The problem of transition from the chemical to the biological evolution: some possible solutions.

On the basis of evidence that several low-molecular-weight substances as well as enzymes are compartmentalised within the so-called soluble phase of the cell, and other considerations, it is argued that DNA may not contain information for certain types of organisation found in living cells. It may be necessary for a cell to possess the "non-DNA-controlled" organisation for performance of its minimum functions; such organisation would then also serve as a "template" for its appearance in the daughter cell. The problem of transition from chemical to biological evolution (that is, the formation of the "first cell") may be essentially the problem of emergence of such intracellular organisation for which information may not reside in DNA. Two possible mechanisms through which this may have happened are stated.

Animals↗
PubMedDate not supplied

Dependence of the flash-induced oxygen evolution pattern on the chemically and far red light-modulated redox condition in cyanobacterial photosynthetic electron transport.

Flash-induced photosynthetic oxygen evolution was measured in cells and thylakoid preparations from the coccoid cyanobacteria Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7942 and from the filamentous cyanobacterium Oscillatoria chalybea. The resulting characteristic flash patterns from these cyanobacteria can be chemically altered by addition of exogenously added substances like CCCP, DCPiP and inorganic salts. Potassium chloride, manganese sulfate and calcium chloride affected the sequences by specific increases in the flash yield and/or effects on the transition parameters. Chloride appeared to exert the strongest stimulatory effect on the oxygen yield. In comparison to chloride, both manganese and calcium did not significantly stimulate the flash amplitudes as such, but improved the functioning of the oxygen evolving complex by decreasing the miss parameter alpha. Particular effects were observed with respect to the time constants of the relaxation kinetics of the first two flash signals Y1/Y2 of the cyanobacterial patterns. In the presence of the investigated chemicals the amplitudes of the first two flash signals (Y2 in particular) were increased and the relaxation kinetics were enhanced so that the time constant became about identical to the conditions of steady state oxygen flash amplitudes. The results provide further evidence against a possible participation of either PS I or respiratory processes to Y1/Y2 of cyanobacterial flash patterns. Dramatic effects were observed when protoplasts from Oscillatoria chalybea or cells from Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7942 were exposed to weak far red background illumination. Under these conditions, Y2 (and to a smaller extent Y1) of otherwise unchanged flash sequences were specifically modified. Y2 was substantially increased and again the relaxation kinetics were accelerated making the signal indistinguishable from a Y(SS) signal. From the mathematical fit of the sequences we conclude that S2 contributes to 10-20% of the S-state distribution (in comparison to 0% in the control). Thus, far red background illumination might represent a valuable means for photosynthetic investigations where high amounts of S2 are required like e. g. EPR measurements. In such experiments the corresponding EPR signals appeared substantially enhanced following far red preillumination (Ahrling and Bader, unpublished observations). Our results clearly show that the 'controversial results' from parts of the literature suggesting the participation of different mechanisms (net oxygen evolution, inhibited uptake processes etc.) are not required to explain the flash-induced oxygen evolution in cyanobacteria: the seemingly 'incompatible' conditions and conformations can be perfectly interconverted by different modulation techniques (chemicals, far red) of the respective redox condition within the water oxidation complex of photosynthesis.

2,4-Dinitrophenol↗
PubMed2005

Chemical constraints on the evolution of olfactory communication channels of moths.

It is estimated there are over 100,000 moth species (Lepidoptera) that produce sex pheromones comprising communication channels used in specific-mate-recognition systems (SMRS) involved in pre-zygotic mating isolation and speciation. About 1572 moth species have been found to use 377 pheromone components, the majority being alcohols, aldehydes or acetate esters of olefinic chains of 10-22 carbons. Since there are limited numbers of possible unsaturated (double bonded) E- and Z-configured isomers of these chains, there may be constraints on incipient species evolving new pheromone components, especially if they are utilized by existing species. Here I develop algorithms that count and name all possible structures of chains with or without a functional group. The results show that for acetate esters there are only seven or nine monounsaturated isomers of six or seven carbon chains, respectively, suggesting use of these compounds could limit the number of communication channels available for radiation of new species (no moths use these short chains). For commonly used 14-carbon chains with an acetate ester functional group, and 1-3 unsaturations, there are 1039 isomers. A total of 2,096,883 isomers were counted from all multiply unsaturated 10-22-carbon chain acetate esters. The number of possible signals quickly extends into millions when considering pheromone blends of 2-4 components used by most species. There should be little chemical constraint on evolution of new communication channels based on compounds of 10 or more carbons, even for closely related species (e.g. ermine moths, Yponomeuta).

Acetates↗