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PubMed2002

The cosmological density of baryons from observations of 3He+ in the Milky Way.

Primordial nucleosynthesis after the Big Bang can be constrained by the abundances of the light elements and isotopes 2H, 3He, 4He and 7Li (ref. 1). The standard theory of stellar evolution predicts that 3He is also produced by solar-type stars, so its abundance is of interest not only for cosmology, but also for understanding stellar evolution and the chemical evolution of the Galaxy. The 3He abundance in star-forming (H II) regions agrees with the present value for the local interstellar medium, but seems to be incompatible with the stellar production rates inferred from observations of planetary nebulae, which provide a direct test of stellar evolution theory. Here we develop our earlier observations, which, when combined with recent theoretical developments in our understanding of light-element synthesis and destruction in stars, allow us to determine an upper limit for the primordial abundance of 3He relative to hydrogen: 3He/H = (1.1 +/- 0.2) x 10(-5). The primordial density of all baryons determined from the 3He data is in excellent agreement with the densities calculated from other cosmological probes. The previous conflict is resolved because most solar-mass stars do not produce enough 3He to enrich the interstellar medium significantly.

Journal Article↗
PubMed1976

Water deficit and ethylene evolution by young cotton bolls.

Ethylene evolution and abscission of young cotton (Gossypium hirsutum L.) bolls were shown, in earlier papers, to increase when plants were subjected to conditions that decreased photosynthesis and sugar content of bolls (dim light, long warm nights). Moisture stress also increased ethylene evolution by young bolls, but it did not decrease their concentrations of fructose, glucose, or sucrose. When detached bolls were incubated for 16 or 24 hours at high or low humidity, their rate of ethylene evolution increased markedly at low humidity and slightly at high humidity. These results suggest that water deficit stimulates ethylene evolution by young bolls directly through partial desiccation, but do not exclude the possibility of a stimulus from moisture-stressed plants. Although attached and detached bolls both lost only a small percentage of their water content, detached bolls lost more for a given rate of ethylene evolution than bolls on moisture-stressed plants. The increased rate of ethylene evolution by young cotton bolls on plants subjected to a water deficit is probably adequate, in many cases, to cause their abscission.

Journal Article↗
PubMed1994

The influence of illness duration on syndrome clarity and stability in functional psychosis: does the diagnosis emerge and stabilise with time?

This review aims to examine the relationship between phase and duration of illness and the clarity and stability of syndromes in psychotic illness. Originating from clinical experience with first episode psychosis, where Neo-Kraepelinian templates and the underlying model have felt especially awkward and ill-fitting, a hypothesis that the clinical picture of functional psychosis might become clearer over time and stabilise in individual patients is proposed which involves the notion of differentiation. A broad range of psychopathological studies and historical papers which refer directly or indirectly to the evolution of the clinical picture in psychosis over time are reviewed. The findings are difficult to interpret, since few studies have focused directly on the issue; however there is evidence of evolution over time of the clinical picture, particularly within the schizophrenia spectrum, and instability beyond this. Further research is needed to clarify the longitudinal patterns of psychopathology in psychotic illness. The capacity for evolution and instability and consequent scope for reclassification of patients has important implications for research and psychoeducation in early psychosis.

Adolescent↗
PubMed2002

Genome shuffling of Lactobacillus for improved acid tolerance.

Fermentation-based bioprocesses rely extensively on strain improvement for commercialization. Whole-cell biocatalysts are commonly limited by low tolerance of extreme process conditions such as temperature, pH, and solute concentration. Rational approaches to improving such complex phenotypes lack good models and are especially difficult to implement without genetic tools. Here we describe the use of genome shuffling to improve the acid tolerance of a poorly characterized industrial strain of Lactobacillus. We used classical strain-improvement methods to generate populations with subtle improvements in pH tolerance, and then shuffled these populations by recursive pool-wise protoplast fusion. We identified new shuffled lactobacilli that grow at substantially lower pH than does the wild-type strain on both liquid and solid media. In addition, we identified shuffled strains that produced threefold more lactic acid than the wild type at pH 4.0. Genome shuffling seems broadly useful for the rapid evolution of tolerance and other complex phenotypes in industrial microorganisms.

Catalysis↗
PubMed2002

Nucleic acid evolution and minimization by nonhomologous random recombination.

We have developed a simple method for exploring nucleic acid sequence space by nonhomologous random recombination (NRR) that enables DNA fragments to randomly recombine in a length-controlled manner without the need for sequence homology. We compared the results of using NRR and error-prone PCR to evolve DNA aptamers that bind streptavidin. Starting with two parental sequences of modest avidin affinity, evolution using NRR resulted in aptamers with 15- to 20-fold higher affinity than the highest-affinity aptamers evolved using error-prone PCR, and 27- or 46-fold higher affinities than parental sequences derived using systematic evolution of ligands by exponential enrichment (SELEX). NRR also facilitates the identification of functional regions within evolved sequences. Inspection of a small number of NRR-evolved clones identified a 40-base DNA sequence, present in multiple copies in each clone, that binds streptavidin. Our findings suggest that NRR may enhance the effectiveness of nucleic acid evolution and the ease of identifying structure-activity relationships among evolved sequences.

Base Sequence↗
PubMed1985

How can quantum mechanics of material evolution be possible? Symmetry and symmetry-breaking in protobiological evolution.

Material self-assembly as a self-organizing process is always accompanied by symmetry-breaking in the material configuration. Self-sequencing of amino acids during their thermal polymerization has lost a certain property of permutation symmetry that was observed in the mixture of free amino acids. The evolutionary precursor state is more symmetrical about its internal material configuration and more degenerate due to the multitude of the indistinguishable individuals. The evolution proceeds in the direction along which the degeneracy in the internal states dissolves owing to the symmetry-breaking originating in material flow equilibrium of open material aggregates. Protobiological information is latent in the material system which is highly symmetrical and highly degenerate in its internal states. Evolution of matter is an endogenous process in which the earlier symmetric property is lost and less degenerate states are approached. Quantum-mechanically, the generation of protobiological information is due to the symmetry-breaking of the Hamiltonian originating in the interaction with the exterior through material flow, in contrast to the Schrödinger equation which preserves a symmetry and the associated invariants.

Biological Evolution↗
PubMedDate not supplied

[The late results of protected goniotrepanation].

The analysis of 737 goniotrepanation with scleral protection shows the higher efficacy of this operation in comparison with other protected fistulizing operations. The normalization of the intraocular pressure persisted in 97% of cases a year after the operation and in 80% five years. According to the evolutive stage of the disease, 50% of the operations were performed in the second stage of glaucoma, 13% in the advanced and quasi-absolute glaucoma stage and only 17% in the initial stage of the disease. The normalization of the intraocular pressure was directly proportional to the evolutive stage of glaucoma. The intraoperative incidents were minimal and the reduced postoperative complications did not influence the visual function. Owing to the simplicity of the technique and to the better results over time, authors prefer protected goniotrepanation to other fistulizing operations.

Age Factors↗
PubMedDate not supplied

The correlation of clinical and laboratory parameters of the acute phase with the evolution of poststreptococcal glomerulonephritis in adults.

Prospective clinical study included the group of 44 patients who had the acute phase of poststreptococcal glomerulonephritis (PSGN) between the age of 18 and 22 during their military service. After the acute phase the patients were followed up to 5 years in order to investigate the influence of some clinical and laboratory parameters in the acute phase of PSGN on the evolution of this disease. The evolution of the disease, estimated on the basis of pathological findings in urine (proteinuria and erhytrocyturia), was found in 61% of patients. It was shown that severity of the clinical picture and the degree of proteinuria in the acute phase of PSGN were in direct correlation with the evolution of disease. On the other hand, the elevated concentrations of circulatory immune complexes (CIC) and cryoglobulin in the acute phase did not significantly affect the evolution of the disease although in some degree it contributed to the severity of pathological findings in the urine.

Acute Disease↗
PubMed2002

Artificial evolution of an enzyme active site: structural studies of three highly active mutants of Escherichia coli alkaline phosphatase.

The crystal structure of three mutants of Escherichia coli alkaline phosphatase with catalytic activity (k(cat)) enhancement as compare to the wild-type enzyme is described in different states. The biological aspects of this study have been reported elsewhere. The structure of the first mutant, D330N, which is threefold more active than the wild-type enzyme, was determined with phosphate in the active site, or with aluminium fluoride, which mimics the transition state. These structures reveal, in particular, that this first mutation does not alter the active site. The second mutant, D153H-D330N, is 17-fold more active than the wild-type enzyme and activated by magnesium, but its activity drops after few days. The structure of this mutant was solved under four different conditions. The phosphate-free enzyme was studied in an inactivated form with zinc at site M3, or after activation by magnesium. The comparison of these two forms free of phosphate illustrates the mechanism of the magnesium activation of the catalytic serine residue. In the presence of magnesium, the structure was determined with phosphate, or aluminium fluoride. The drop in activity of the mutant D153H-D330N could be explained by the instability of the metal ion at M3. The analysis of this mutant helped in the design of the third mutant, D153G-D330N. This mutant is up to 40-fold more active than the wild-type enzyme, with a restored robustness of the enzyme stability. The structure is presented here with covalently bound phosphate in the active site, representing the first phosphoseryl intermediate of a highly active alkaline phosphatase. This study shows how structural analysis may help to progress in the improvement of an enzyme catalytic activity (k(cat)), and explains the structural events associated with this artificial evolution.

Alkaline Phosphatase↗
PubMed2003

[Cryptobiosphere of Mars].

The US Viking missions (1975-1976) failed to discover any biological activity on the surface of Mars. Yet, life may exist in the planet lithosphere which was found to contain a substantial amount of water. Martian interior can also provide microbial cryptolife with sources of carbon (CO, CO2, CH4) and energy (reduced elements and compounds, e.g. H2, CO, H2S, NH4+, CH4, Fe3+). Microorganisms identical to the Earth's anaerobic methanogens, sulfate reducers, acetogens, denitrifiers etc. are the most probable Martian aborigines. Well-balanced continuous functioning of the Martian cryptobiosphere implies closure of biochemical carbon, sulfur and nitrogen cycles which cannot be reached but with participation of organotrophic and anaerobic hydrolytic and zymotic organisms, ammonifiers and denitrifiers. Considering the low intensity of biological and chemical processes in the absence of surface hydrosphere, low-power atmosphere and cryptobiosphere closure on Mars, and slow global energy matter cycles, evolution of the presumable Martian cryptolife should also go at a slack pace and directions and forms of the evolution of living substance can have little in common with those on Earth. Comprehensive investigations of the Martian biota will employ a great variety of geochemical, radi- and stable isotope, microbiological, enzymatic and molecular biology methods.

Aerobiosis↗
PubMed2002

Stable propagation of an ordered array of cracks during directional drying.

We study the appearance and evolution of an array of parallel cracks in a thin slab of material that is directionally dried, and show that the cracks penetrate the material uniformly if the drying front is sufficiently sharp. We also show that cracks have a tendency to become evenly spaced during the penetration. The typical distance between cracks is mainly governed by the typical distance of the pattern at the surface, and it is not modified during the penetration. Our results agree with recent experimental work, and can be extended to three dimensions to describe the properties of columnar polygonal patterns observed in some geological formations.

Journal Article↗
PubMed2005

Genetic variation in laboratory mice.

Characterizing the patterns of genetic variation in an organism provides fundamental insight into the evolutionary history of the organism and defines the scope and nature of studies that must be designed to correlate genotype to phenotype. Given the pre-eminent role of the inbred mouse in biomedical research, considerable effort has been undertaken in recent years to describe more fully the nature and amount of genetic variation among the numerous strains of mice that are in widest use. Here, we discuss recent studies that have contributed to an emerging understanding of the unique variation patterns found in inbred strains of mice and how they have arisen through a combination of natural evolution and human-directed breeding. These preliminary results have ramifications for genetic research into complex biomedical traits and are the basis for the development of future variation resources.

Animals↗
PubMed2004

Use of sequence duplication to engineer a ligand-triggered, long-distance molecular switch in T4 lysozyme.

We have designed a molecular switch in a T4 lysozyme construct that controls a large-scale translation of a duplicated helix. As shown by crystal structures of the construct with the switch on and off, the conformational change is triggered by the binding of a ligand (guanidinium ion) to a site that in the wild-type protein was occupied by the guanidino head group of an Arg. In the design template, a duplicated helix is flanked by two loop regions of different stabilities. In the "on" state, the N-terminal loop is weakly structured, whereas the C-terminal loop has a well defined conformation that is stabilized by means of nonbonded interactions with the Arg head group. The truncation of the Arg to Ala destabilizes this loop and switches the protein to the "off" state, in which the duplicated helix is translocated approximately 20 A. Guanidinium binding restores the key interactions, restabilizes the C-terminal loop, and restores the "on" state. Thus, the presence of an external ligand, which is unrelated to the catalytic activity of the enzyme, triggers the inserted helix to translate 20 A away from the binding site. The results illustrate a proposed mechanism for protein evolution in which sequence duplication followed by point mutation can lead to the establishment of new function.

Bacteriophage T4↗
PubMed1999

A novel ontogenetic pathway in hybrid embryos between species with different modes of development.

To investigate the bases for evolutionary changes in developmental mode, we fertilized eggs of a direct-developing sea urchin, Heliocidaris erythrogramma, with sperm from a closely related species, H. tuberculata, that undergoes indirect development via a feeding larva. The resulting hybrids completed development to form juvenile adult sea urchins. Hybrids exhibited restoration of feeding larval structures and paternal gene expression that have been lost in the evolution of the direct-developing maternal species. However, the developmental outcome of the hybrids was not a simple reversion to the paternal pluteus larval form. An unexpected result was that the ontogeny of the hybrids was distinct from either parental species. Early hybrid larvae exhibited a novel morphology similar to that of the dipleurula-type larva typical of other classes of echinoderms and considered to represent the ancestral echinoderm larval form. In the hybrid developmental program, therefore, both recent and ancient ancestral features were restored. That is, the hybrids exhibited features of the pluteus larval form that is present in both the paternal species and in the immediate common ancestor of the two species, but they also exhibited general developmental features of very distantly related echinoderms. Thus in the hybrids, the interaction of two genomes that normally encode two disparate developmental modes produces a novel but harmonious ontongeny.

Animals↗
PubMed2005

A novel method of screening thrombin-inhibiting DNA aptamers using an evolution-mimicking algorithm.

Thrombin-inhibiting DNA aptamers have already been obtained through the systematic evolution of ligands by exponential enrichment (SELEX). However, SELEX is a method that screens DNA aptamers that bind to their target molecules, and it sometimes fails to screen good inhibitors. Therefore, it is necessary to develop a method of screening DNA aptamers based on their inhibitory effects on the target molecules. We developed a novel method of detecting aptamers using an evolution-mimicking algorithm, and we applied it to the search of new aptamers which inhibit thrombin. First, we randomly designed and synthesized ten 15mer oligonucleotides presumed to form G-quartet structures, and then measured their thrombin-inhibiting activities. The aptamers showing high inhibitory activity were selected, and we shuffled and mutated those sequences in silico to generate 10 new sequences of next-generation aptamers. After repeating the cycle five times, we successfully obtained the same aptamers reported previously, and they showed high inhibitory activity. In addition, we added 8mer oligonucleotides to both the 5' and the 3' end of the selected 15mer aptamers, and then repeated the evolution in silico. After two cycles, we were able to obtain aptamers with higher inhibitory activity than that of the 15mer aptamers.

Algorithms↗
PubMed2005

Characterization and properties of G4X mutants of Ralstonia eutropha PHA synthase for poly(3-hydroxybutyrate) biosynthesis in Escherichia coli.

Modification of the type I polyhydroxyalkanoate synthase of Ralstonia eutropha (PhaC(Re)) was performed through systematic in vitro evolution in order to obtain improved PhaC(Re) having an enhanced activity of poly(3-hydroxybutyrate) (PHB) synthesis in recombinant Escherichia coli. For the first time, a beneficial G4D N-terminal mutation important for the enhancement of both PHB content in dry cells and PhaC(Re) level in vivo was identified. Site-directed saturation mutagenesis at the G4 position enabled us to identify other mutations conferring similar enhanced characteristics. In addition, the PHB homopolymer synthesized by most G4X single mutants also had higher molecular weights than that of the wild-type. In vitro enzymatic assays of purified G4D mutant PhaC(Re) revealed that the mutant enzyme exhibited slightly lower activity and reaction efficiency compared to the wild-type enzyme. [diagram in text].

Acyltransferases↗
PubMed2000

Evolution of parental care and ovulation behavior in oysters.

Approximately half of all living oysters brood offspring in the inhalant chamber of their mantle cavities; the remainder are broadcast spawners which do not engage in parental care of young. Ostreid ovulation involves a complex behavioral sequence that results in the countercurrent passage of newly spawned eggs through the gills (ctenidia) and into the inhalant chamber. We constructed molecular and combined-evidence phylogenetic trees to test hypotheses concerning the directionality of parental care evolution, and the evolutionary significance of the trans-ctenidial ovulation pathway, in the Ostreidae. Representatives of all three ostreid subfamilies, together with gryphaeid and nonostreoidean pterioid outgroups, were sequenced for a 941-nucleotide fragment of the 28S ribosomal gene. Our phylogenetic analyses indicate that (1) the Ostreidae are robustly monophyletic, (2) broadcast spawning and larval planktotrophy are ancestral ostreid traits, (3) trans-ctenidial ovulation predates the evolution of parental care in ostreid lineages, and (4) brooding originated once in the common ancestor of the Ostreinae/Lophinae, involved a modification of the final behavioral step in the ancestral ovulation pathway, and has been retained in all descendent lineages. Our data permit an independent test of fossil-based ostreid phylogenetic hypotheses and provide novel insights into oyster evolution and systematics.

Animals↗
PubMed2004

The use of forced protein evolution to investigate and improve stability of family 10 xylanases. The production of Ca2+-independent stable xylanases.

Metal ions such as calcium often play a key role in protein thermostability. The inclusion of metal ions in industrial processes is, however, problematic. Thus, the evolution of enzymes that display enhanced stability, which is not reliant on divalent metals, is an important biotechnological goal. Here we have used forced protein evolution to interrogate whether the stabilizing effect of calcium in an industrially relevant enzyme can be replaced with amino acid substitutions. Our study has focused on the GH10 xylanase CjXyn10A from Cellvibrio japonicus, which contains an extended calcium binding loop that confers proteinase resistance and thermostability. Three rounds of error-prone PCR and selection identified a treble mutant, D262N/A80T/R347C, which in the absence of calcium is more thermostable than wild type CjXyn10A bound to the divalent metal. D262N influences the properties of the calcium binding site, A80T fills a cavity in the enzyme, increasing the number of hydrogen bonds and van der Waals interactions, and the R347C mutation introduces a disulfide bond that decreases the free energy of the unfolded enzyme. A derivative of CjXyn10A (CfCjXyn10A) in which the calcium binding loop has been replaced with a much shorter loop from Cellulomonas fimi CfXyn10A was also subjected to forced protein evolution to select for thermostablizing mutations. Two amino acid substitutions within the introduced loop and the A80T mutation increased the thermostability of the enzyme. This study demonstrates how forced protein evolution can be used to introduce enhanced stability into industrially relevant enzymes while removing calcium as a major stability determinant.

Binding Sites↗