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PubMed2006

Intelligent design and biological complexity.

Before any intelligence can appear, a world endowed with the potential for being experienced as a body of phenomena has to be existent. Indeed, if there is to be an intelligence, there first has to be something intelligible. Hence, when an intelligence is present, "creation" must already have taken place. Nevertheless, biological complexity has been deemed by some to be one of the privileged points of insertion of a supernatural intelligence endowed with temporal and causal primacy. In the course of a critical review, it is pointed out that the spectacle of nature's spontaneous tinkering with the structures and performances of informational macromolecules and with interactive connections among these molecules suggests that intelligence and design are absent from evolution. Nor is intelligent design required for explaining biological complexity, which can increase spontaneously as a byproduct of combinatorial intermolecular gambles and of the restoration of molecular damage wrought by mutations. One of the possible molecular pathways to spontaneous evolutionary increases in complexity is described.

Biological Evolution↗
PubMed2006

Optimisation of halogenase enzyme activity by application of a genetic algorithm.

A genetic algorithm (GA) was applied for the optimisation of an enzyme assay composition respectively the enzyme activity of a recombinantly produced FADH(2)-dependent halogenating enzyme. The examined enzyme belongs to the class of halogenases and is capable to halogenate tryptophan regioselective in position 5. Therefore, the expressed trp-5-halogenase can be an interesting tool in the manufacturing of serotonin precursors. The application of stochastic search strategies (e.g. GAs) is well suited for fast determination of the global optimum in multidimensional search spaces, where statistical approaches or even the popular classical one-factor-at-a-time method often failures by misleading to local optima. The concentrations of six different medium components were optimised and the maximum yield of the halogenated tryptophan could be increased from 3.5 up to 65%.

Algorithms↗
PubMed2005

Recapitulation of protein family divergence using flexible backbone protein design.

We use flexible backbone protein design to explore the sequence and structure neighborhoods of naturally occurring proteins. The method samples sequence and structure space in the vicinity of a known sequence and structure by alternately optimizing the sequence for a fixed protein backbone using rotamer based sequence search, and optimizing the backbone for a fixed amino acid sequence using atomic-resolution structure prediction. We find that such a flexible backbone design method better recapitulates protein family sequence variation than sequence optimization on fixed backbones or randomly perturbed backbone ensembles for ten diverse protein structures. For the SH3 domain, the backbone structure variation in the family is also better recapitulated than in randomly perturbed backbones. The potential application of this method as a model of protein family evolution is highlighted by a concerted transition to the amino acid sequence in the structural core of one SH3 domain starting from the backbone coordinates of an homologous structure.

Evolution, Molecular↗
PubMed2005

A statistical analysis of random mutagenesis methods used for directed protein evolution.

We have developed a statistical method named MAP (mutagenesis assistant program) to equip protein engineers with a tool to develop promising directed evolution strategies by comparing 19 mutagenesis methods. Instead of conventional transition/transversion bias indicators as benchmarks for comparison, we propose to use three indicators based on the subset of amino acid substitutions generated on the protein level: (1) protein structure indicator; (2) amino acid diversity indicator with a codon diversity coefficient; and (3) chemical diversity indicator. A MAP analysis for a single nucleotide substitution was performed for four genes: (1) heme domain of cytochrome P450 BM-3 from Bacillus megaterium (EC 1.14.14.1); (2) glucose oxidase from Aspergillus niger (EC 1.1.3.4); (3) arylesterase from Pseudomonas fluorescens (EC 3.1.1.2); and (4) alcohol dehydrogenase from Saccharomyces cerevisiae (EC 1.1.1.1). Based on the MAP analysis of these four genes, 19 mutagenesis methods have been evaluated and criteria for an ideal mutagenesis method have been proposed. The statistical analysis showed that existing gene mutagenesis methods are limited and highly biased. An average amino acid substitution per residue of only 3.15-7.4 can be achieved with current random mutagenesis methods. For the four investigated gene sequences, an average fraction of amino acid substitutions of 0.5-7% results in stop codons and 4.5-23.9% in glycine or proline residues. An average fraction of 16.2-44.2% of the amino acid substitutions are preserved, and 45.6% (epPCR method) are chemically different. The diversity remains low even when applying a non-biased method: an average of seven amino acid substitutions per residue, 2.9-4.7% stop codons, 11.1-16% glycine/proline residues, 21-25.8% preserved amino acids, and 55.5% are amino acids with chemically different side-chains. Statistical information for each mutagenesis method can further be used to investigate the mutational spectra in protein regions regarded as important for the property of interest.

Amino Acid Substitution↗
PubMed2006

The use of radiotelemetry to evaluate electrographic seizures in rats with kainate-induced epilepsy.

Temporal lobe epilepsy in humans is a chronic condition with a highly variable temporal evolution. Animal models of this disorder have been developed to recapitulate many of the characteristics seen in humans with temporal lobe epilepsy. These animal models generate chronic spontaneous electrographic and motor seizures with a progressive increase in frequency over many months. In order to understand the underlying cellular and molecular mechanisms driving epileptogenesis, a practical means for accurately assessing seizure progression over this extended time period must be devised. In this report, we describe the use of a three-channel radiotelemetry system to record spontaneous electrographic interictal "spikes" and seizure activity from the cortical surface and the two hippocampi. This approach has allowed continuous recording before, during, and several months after kainate-induced status epilepticus. The important advantages of this approach are the potential for long-term continuous electrographic recording with comparatively unrestricted behavior; the disadvantages include increased cost, surgical difficulty and lower frequency-response in the recordings.

Action Potentials↗
PubMed2005

Dynamics of a quantitative character subject only to stabilising selection.

The implications of stabilising selection on a quantitative trait, in the absence of other evolutionary forces, are theoretically investigated in a randomly mating population. The dynamics of various statistics that describe the alleles contributing to the trait are determined and used to infer the behaviour of the trait. Dynamical solutions of the distribution of allelic effects and the distribution of the trait are found when all initial distributions of allelic effects are Gaussian and linkage disequilibria are neglected. Some results for the behaviour of the mean and the variance of genotypic effects of the population, when subject to a moving optimum, are derived. When the initial distributions of allelic effects are not Gaussian, but possess a small asymmetry, the mean and the variance of the allelic effects differ only slightly from the Gaussian results. By contrast, the third central moments of allelic effects, are, at all loci, strictly zero in the Gaussian case but are generally non-zero for non-symmetric initial distributions. To leading order in a quantitative measure of the asymmetry of the distribution, we determine the third central moment of allelic effects.

Alleles↗
PubMed2005

Organization of chromatin in the interphase mammalian cell.

The use of imaging techniques has become an essential tool in cell biology. In particular, advances in fluorescence microscopy and conventional transmission electron microscopy have had a major impact on our understanding of chromatin structure and function. In this review we attempt to chart the conceptual evolution of models describing the organization and function of chromatin in higher eukaryotic cells, in parallel with the advances in light and electron microscopy over the past 50 years. In the last decade alone, the application of energy filtered transmission electron microscopy (EFTEM), also referred to as electron spectroscopic imaging (ESI), has provided many new insights into the organization of chromatin in the interphase nucleus. Based on ESI imaging of chromatin in situ, we propose a 'lattice' model for the organization of chromatin in interphase cells. In this model, the chromatin fibers of 10 and 30nm diameter observed by ESI, produce a meshwork that accommodates an extensive and distributed interchromosomal (IC) space devoid of chromatin. The functional implications of this model for nuclear activity are discussed.

Animals↗
PubMed2005

The quantitative genetics of transcription.

Quantitative geneticists have become interested in the heritability of transcription and detection of expression quantitative trait loci (eQTLs). Linkage mapping methods have identified major-effect eQTLs for some transcripts and have shown that regulatory polymorphisms in cis and in trans affect expression. It is also clear that these mapping strategies have little power to detect polygenic factors, and some new statistical approaches are emerging that paint a more complex picture of transcriptional heritability. Several studies imply pervasive non-additivity of transcription, transgressive segregation and epistasis, and future studies will soon document the extent of genotype-environment interaction and population structure at the transcriptional level. The implications of these findings for genotype-phenotype mapping and modeling the evolution of transcription are discussed.

Chi-Square Distribution↗
PubMed2005

Convergent evolution as a mechanism for pathogenic adaptation.

The survival of human pathogens depends on their ability to modulate defence pathways in human host cells. This was thought to be attained mainly by pathogen specific "virulence factors". However, pathogens are increasingly being discovered that use distant homologs of the human regulatory proteins as virulence factors. We analyzed several cases of this approach, with a particular focus on virulence proteases. The analysis reveals clear cases of bacterial proteases mimicking the specificity of their human counterparts, such as strong similarities in their active and/or binding sites. With more sensitive tools for distant homology recognition, we could expect to discover many more such cases.

Adaptation, Physiological↗
PubMed2004

RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids.

Two, apparently functional, paralogues of the RPB2 gene, which encodes the second largest subunit of RNA polymerase II, are shown to be present in two major groups of asterid plants. Although all other land plants surveyed so far have been found to have only one of these two copies, the RPB2 gene phylogeny inferred from the 3' half of the gene for 35 angiosperm taxa and six other land plants indicates that the duplication of the RPB2 gene occurred earlier than the time for origin of the asterid group, probably near the origin of "core eudicots." The d copy is present in all plants which are unambiguously assigned to the core eudicots, whereas the I copy is retained only in the lamiid clade, Ericales, and Escallonia, all belonging to the asterid group of plants. Both parsimony and likelihood analyses of sequences from the 3' half of the gene give strong bootstrap support for these conclusions. There is no support for monophyly of the taxa having both copies. Thus, numerous losses of one of the copies must be inferred. Structurally, both paralogues appear functional, and transcription is demonstrated for both copies. In the lamiid group, the d copy has lost introns 18-23. The well supported phylogenetic relationships implied by the RPB2 gene phylogeny are largely congruent with well supported phylogenetic hypotheses based on other sequence data. However, Ilex, usually assigned to the campanuliid clade, is instead supported as being a member of the lamiid clade, both from sequence data and the presence of an I copy as well as the loss of introns 18-23 in the d copy. Escallonia, supported as a member of the campanuliid clade both by RPB2-d-sequences and previously published DNA sequence data, has all the introns 18-23 in its d copy, as do all other members studied from the campanuliid group. We used the Markov Chain Monte Carlo (MCMC) approach of the MrBayes program to implement Maximum Likelihood bootstrapping. Under the same model of evolution, bootstrapping frequencies are significantly lower than the Bayesian posterior probabilities inferred from the MCMC chain.

Gene Dosage↗
PubMed2006

Mitochondrial DNA evidence of an early Holocene population expansion of threespine sticklebacks from Scotland.

In this study, we analyzed the cytochrome b gene in threespine stickleback (Gasterosteus aculeatus) populations from Scotland. We found evidence of a postglacial population expansion in Scotland and large differences in genetic diversity estimates among populations. Higher levels of genetic diversity are negatively correlated with distance from the ocean. In addition, distance from the ocean and predation risk both explain variation in plate count in Scottish populations. Overall, the mtDNA data support the racemic model of evolution in threespine stickleback.

Animals↗
PubMed2003

Estrogen receptors in Xenopus: duplicate genes, splice variants, and tissue-specific expression.

The estrogenic steroid hormones, acting primarily through the nuclear estrogen receptors ERalpha and ERbeta, regulate sexual differentiation in a wide variety of vertebrates. In the frog Xenopus laevis, estrogen regulates the strength of vocal neuromuscular synapses and contributes to the physiological basis of sexually differentiated songs. To understand the mechanisms by which estrogen produces these effects, we have characterized the ERs of X. laevis and their expression in laryngeal muscle and other tissues. We found a remarkable molecular diversity in the estrogen receptor population within individuals. First, we have identified two distinct ERalpha genes, xlERalpha1 and xlERalpha2, which represent, to our knowledge, the first discovery of retained duplicates of the ERalpha gene in any species. These two genes are highly conserved at the amino acid level but have distinct nucleotide sequences; moreover, ERalpha2 has no N-terminal domain. Cloning of ERalpha and ERbeta in the related species Xenopus tropicalis and phylogenetic analysis indicate that the two xlERalpha loci were generated by a duplication specific to the X. laevis lineage-most likely the genome duplication that led to a doubling of the X. laevis chromosome number about 30 million years ago. The primary ER expressed in X. laevis laryngeal muscle is the novel gene xlERalpha2; ERalpha1 is primarily expressed in liver, forebrain, and oviduct. Alternatively spliced transcripts of both xlERalpha1 and xlERalpha2 are also expressed in a tissue-specific manner. We propose that complementary spatial expression of these two genes and their alternatively spliced transcripts contributes to their conservation over such a long period of time, consistent with the subfunctionalization model for evolution after gene duplication.

Amino Acid Sequence↗
PubMed1990

Evolutionary relationships between "Q-type" photosynthetic reaction centres: hypothesis-testing using parsimony.

Hypotheses concerning the evolutionary relationships between "Q-type" photosynthetic reaction centres are tested using amino acid parsimony analysis of subunit sequences and an alignment based on dot matrix comparisons. Strong evidence is found for independent gene duplications having produced the L and M subunits of the photosynthetic purple bacterial reaction centre and D1 and D2 of Photosystem-II. Much support is also found for the L and M subunits of the green filamentous bacterium Chloroflexus aurantiacus arising from the same gene duplication as the purple bacterial subunits, suggesting there was an ancestral bacterial heterodimeric reaction centre. These conclusions caution against over-extrapolation from the purple bacterial reaction centre to Photosystem-II, and suggest that the latter is more ancient than previously supposed.

Bacteria↗
PubMed1992

On the origin of the transfer RNA molecule.

Data and arguments are given in favour of the hypothesis that the primitive tRNA molecule may have originated from a direct duplication event involving one of the two halves of the tRNA molecule. It seems that a molecule capable of assuming a hairpin structure was involved as a precursor in this duplication. The two halves of the present tRNAs could, therefore, be considered as paralogous.

Amino Acid Sequence↗
PubMed1984

Coevolution of bacteria and phage: are there endless cycles of bacterial defenses and phage counterdefenses?

The assertion that the coevolution of bacteria and bacteriophage leads to an endless arms race between resistant bacterial mutants and corresponding host-range phage mutants is questioned. In general, structural constraints on the highly site-specific phage adsorption process appear more severe than physiological constraints on resource assimilation by bacteria. Several alternative hypotheses are presented that could account for the persistence of phage, despite this fundamental asymmetry in the coevolutionary potential of bacteria and phage.

Bacterial Physiological Phenomena↗