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PubMed1997

The influence of specific neighboring bases on substitution bias in noncoding regions of the plant chloroplast genome.

Substitutions occurring in noncoding sequences of the plant chloroplast genome violate the independence of sites that is assumed by substitution models in molecular evolution. The probability that a substitution at a site is a transversion, as opposed to a transition, increases significantly with increasing A + T content of the two adjacent nucleotides. In the present study, this dependency of substitutions on local context is examined further in a number of noncoding regions from the chloroplast genome of members of the grass family (Poaceae). Two features were examined; the influence of specific neighboring bases, as opposed to the general A + T content, on transversion proportion and an influence on substitutions by nucleotides other than the two immediately adjacent to the site of substitution. In both cases, a significant effect was found. In the case of specific nucleotides, transversion proportion is significantly higher at sites with a pyrimidine immediately 5' on either strand. Substitutions at sites of the type YNR, where N is the site of substitution, have the highest rate of transversion. This specific effect is secondary to the A + T content effect such that, in terms of proportion of substitutions that are transversions, the nucleotides are ranked T > A > C > G as to their effect when they are immediately 5' to the site of substitution. In the case of nucleotides other than the immediate neighbors, a significant influence on substitution dynamics is observed in the case where the two neighboring bases are both A and/or T. Thus, substitutions are primarily, but not exclusively, influenced by the composition of the two nucleotides that are immediately adjacent. These results indicate that the pattern of molecular evolution of the plant chloroplast genome is extremely complex as a result of a variety of inter-site dependencies.

Chloroplasts↗
PubMed2003

Evolution of the brain tumour spheroid model: transcending current model limitations.

Tumour recurrence and the high mortality and morbidity associated with malignant brain tumours may be attributed to the failure of current therapeutic modalities (surgery, radiation and chemotherapy) to control the invasion of malignant brain tumour cells into healthy brain tissue. Several in vitro and in vivo models have been developed and used to study brain tumour invasion and cell motility. Here, we review some of the traditional in vitro models of brain tumour invasion and the latest adaptations to the widely used spheroid model. Several research groups studying the mechanisms mediating brain tumour invasion have made important contributions to the field by improving in vitro models of tumour migration and invasion. Sharing these advances will hopefully accelerate experimental discovery and the development of novel anti-invasion brain tumour therapies.

Brain Neoplasms↗
PubMed1982

On a global representation of dynamical characteristics in ESS-models.

ESS-models are considered in the frame of adequate dynamical systems. This leads to a method of global representation of the dynamical characteristics, which allows for a comprehensive view on the relations among ESS-matrices. As an extension of ESS-models, the concept of ESS-models with changing matrix is introduced, which, in applications, makes use of such global representations. In particular, structurally stable and "catastrophic" cases can be identified and their significance in the context of ESS-models can be clarified. As a complete result for the case of two strategies a surface representation is obtained, which is an analogue to the elementary "cusp catastrophe". These concepts are applied in a model that describes directed evolution of a behavioural component to a certain limit.

Animals↗
PubMed2005

Mathematical model for optimal control in wastewater discharges: the global performance.

In this work we show how mathematical models and optimal control techniques can help us to solve some problems of environmental engineering, more precisely, water pollution problems arising from wastewater discharges into coastal areas or rivers. We deal with a complete two-dimensional mathematical model for the evolution of pollutant concentration in a shallow water domain. By integrating this model we obtain a zero-dimensional one and we use it to study the global performance of the system in a realistic situation. Finally, by using the two-dimensional model, we recall two optimal control problems related to the wastewater disposal problem.

Models, Theoretical↗
PubMed1992

Evolutionarily stable age at first reproduction in a density-dependent model.

We develop a new model of life history evolution to investigate the evolution of age at first reproduction. Density dependence is taken into account. For a given "species", age of maturity, offspring survival, immature survival, adult survival, fecundity, immature age-classes entering in competition with adults and immature competitive ability are traits adjustable by natural selection, and constitute a particular strategy. On the contrary, the type of intraspecific competition (scramble or contest), strength of competition and inherent net reproductive rate Ro(inh) are fixed (specific) characteristics. As a consequence of fixing Ro(inh), the evolution of any trait will affect trade-offs between others. Evolutionarily stable strategies are determined numerically by using the mathematical concept of Lyapunov exponents. Altogether, we consider 960 different hypothetical "species" (i.e. different combinations of fixed traits). Corresponding ESSs are analyzed with respect to their age at first reproduction, adult survival and immature competitive ability components. They appear to be gathered in three groups. One is intuitive and characterized by a reduction of immature competitive ability and a correlation of age of maturity with adult survival; populations reach mainly equilibria. The two other groups respectively include "species" with low age of maturity but high adult survival, and "species" close to semelparity with delayed maturity; immature competitive ability may not be minimized, and populations possibly exhibit complex dynamics. In conclusion, the hypothesis that the evolution of a demographic parameter modifies trade-offs between others turns out to have important consequences. We argue that life history theory cannot ignore the source and mode-of-operation of density dependence and must regard potential short-term instability as essential.

Animals↗
PubMed2002

An experimental ecotoxicological study and its application to the behavioural study of organic mercury (CH3HgCl) in the environment: influence of temperature and pH.

Laboratory experiments were carried out to study the influence of temperature (24, 28 and 30 degrees C) and pH (1-10) on organic mercury (CH3HgCl) transfer and accumulation in an experimental ecotoxicological model. We followed the evolution of CH3HgCl in a basic model (water + air) by varying temperature and pH. In a second step, we completed the model by adding sediment and fish. We added CH3HgCI to water at the beginning of each experiment which was repeated at least three times. Results demonstrated that mercury was released from methylmercury into the air regardless of water pH and its concentration in the air increased with increasing pH. By contrast, in presence of sediment, almost all the mercury was fixed onto the sediment and no mercury was traced in air or in water. Interestingly, in the presence of sediment, the life span of fish under methylmercury exposure lasted longer despite their higher mercury body level content at their death. These results indicate that water is a bad exposure indicator for aquatic pollution. In case of chronic pollution, sediments, fish and aquatic plants are more appropriate indicators.

Animals↗
PubMed2003

The out of Africa model of varicella-zoster virus evolution: single nucleotide polymorphisms and private alleles distinguish Asian clades from European/North American clades.

Until 1998, varicella-zoster virus (VZV) was generally considered sufficiently stable to allow the use of a single sequenced virus (VZV-Dumas) as a consensual representation of the world VZV genotype. But recent investigations have uncovered a gE mutant virus called VZV-MSP with a second genotype and a distinguishable accelerated cell spread phenotype. A subsequent study suggested that single nucleotide polymorphisms (SNPs) could be applied toward the genetic analysis of the VZV genome. To further assess the scope of genetic variation in the VZV genome on a worldwide basis, we carried out an extensive SNP analysis of structural glycoprotein genes gB, gE, gH, gI, gL, as well as the IE62 regulatory gene in viruses collected from Western Europe, North America and Asia, including the VZV vaccine strain. The SNP data showed segregation of viral isolates of Asian origin from those of Western ancestry into distinct phylogenetic clades. Unexpectedly, however, VZV from Thailand segregated with VZV from Iceland and the United States, i.e. it was more Western than Asian in nature. Further, SNP analysis disclosed strikingly unusual genotypes, e.g. gH genes with up to five missense mutations and gL genes with insertions of an in-frame methionine codon. In summary, these VZV genomic analyses have shown that individual VZV strains, like closely related human beings, have distinctive SNP profiles containing private alleles within just five VZV genes (gB, gH, gE, gL and IE62) that provide a fingerprint to localize ancestry of the viral strain.

Africa↗
PubMed2003

Transfer RNA paralogs: evidence for genetic code-amino acid biosynthesis coevolution and an archaeal root of life.

A search has been performed on 2878 tRNA sequences from 60 different genomes in order to detect the existence of closely related 'alloacceptor' tRNAs accepting dissimilar amino acids that could be paralogs generated by gene duplications. This has led to the identification of extremely conserved tRNA(Phe)-tRNA(Tyr) pairs displaying as high as 94% identity between them, and also other potentially paralogous tRNA pairs in archaeal species. These paralogous pairs are enriched for amino acid pairs belonging to the same amino acid biosynthetic family, thus providing evidence for the coevolution of genetic code and amino acid biosynthesis. Overall, the genetic distances between alloacceptor tRNAs yield estimates of how closely clustered in sequence space are the tRNAs in a genome. Among 34 Bacteria, 18 Archaea and 8 Eukarya, Methanopyrus kandleri and Aeropyrum pernix have yielded the lowest alloacceptor distances and largest number of paralogous pairs. Based on a cluster-dispersion model of tRNA evolution, such tight alloacceptor clustering is a measure of primitiveness of tRNA genotypes, and places last universal common ancestor (LUCA) between the branches leading to these two archaea in the tRNA phylogenetic tree.

Amino Acids↗
PubMed2001

Evolution of the two-step model for UV-mutagenesis.

It is quite remarkable how our understanding of translesion DNA synthesis (TLS) has changed so dramatically in the past 2 years. Until very recently, little was known about the molecular mechanisms of TLS in higher eukaryotes and what we did know, was largely based upon Escherichia coli and Saccharomyces cerevisiae model systems. The paradigm, proposed by Bryn Bridges and I [Mutat. Res. 150 (1985) 133] in 1985, was that error-prone TLS occurred in two steps; namely a misinsertion event opposite a lesion, followed by extension of the mispair so as to facilitate complete bypass of the lesion. The initial concept was that at least for E. coli, the misinsertion event was performed by the cell's main replicase, DNA polymerase III holoenzyme, and that elongation was achieved through the actions of specialized polymerase accessory proteins, such as UmuD and UmuC. Some 15 years later, we now know that this view is likely to be incorrect in that both misinsertion and bypass are performed by the Umu proteins (now called pol V). As pol V is normally a distributive enzyme, pol III may only be required to "fix" the misincorporation as a mutation by completing chromosome duplication. However, while the role of the E. coli proteins involved in TLS have changed, the initial concept of misincorporation followed by extension/bypass remains valid. Indeed, recent evidence suggests that it can equally be applied to TLS in eukaryotic cells where there are many more DNA polymerases to choose from. The aim of this review is, therefore, to provide a historical perspective to the "two-step" model for UV-mutagenesis, how it has recently evolved, and in particular, to highlight the seminal contributions made to it by Bryn Bridges.

DNA Polymerase III↗
PubMed2005

An adaptive radiation model for the origin of new gene functions.

Current models for the evolution of new gene functions after gene duplication presume that the duplication events themselves have no effect on fitness. But those duplications that result in new gene functions are likely to be positively selected from their inception. The evolution of new function may start with the amplification of an existing gene with some level of preadaptation for that function, followed by a period of competitive evolution among the gene copies, resulting in the preservation of the most effective variant and the 'pseudogenization' and eventual loss of the rest.

Adaptation, Physiological↗
PubMed2003

The yersiniae--a model genus to study the rapid evolution of bacterial pathogens.

Yersinia pestis, the causative agent of plague, seems to have evolved from a gastrointestinal pathogen, Yersinia pseudotuberculosis, in just 1,500-20,000 years--an 'eye blink' in evolutionary time. The third pathogenic Yersinia, Yersinia enterocolitica, also causes gastroenteritis but is distantly related to Y. pestis and Y. pseudotuberculosis. Why do the two closely related species cause remarkably different diseases, whereas the distantly related enteropathogens cause similar symptoms? The recent availability of whole-genome sequences and information on the biology of the pathogenic yersiniae have shed light on this paradox, and revealed ways in which new, highly virulent pathogens can evolve.

Animals↗
PubMed2000

The evolutionary dynamics of male-killers and their hosts.

Male-killing bacteria are cytoplasmic sex-ratio distorters that are transmitted vertically through females of their insect hosts. The killing of male hosts by their bacteria is thought to be an adaptive bacterial trait because it augments the fitness of female hosts carrying clonal relatives of those bacteria. Here we attempt to explain observations of multiple male-killers in natural host populations. First we show that such male-killer polymorphism cannot be explained by a classical model of male-killing. We then show that more complicated models incorporating the evolution of resistance in hosts can explain male-killer polymorphism. However, this is only likely if resistance genes are very costly. We also consider the long-term evolutionary dynamics of male-killers, and show that evolution towards progressively more 'efficient' male-killers can be thwarted by the appearance of host resistance. The presence of a resistance gene can allow a less efficient male-killer to outcompete its rival and hence reverse the trend towards more efficient transmission and reduced metabolic load on the host.

Animals↗
PubMed2003

Fat body expressed yolk protein genes in Hyphantria cunea are related to the YP4 follicular epithelium yolk protein subunit gene of pyralid moths.

cDNA clones for two of the yolk proteins, YP1 and YP2, produced by the fat body of the moth, Hyphantria cunea, were sequenced and found to be homologous to the follicular epithelium yolk proteins of pyralid moths. Both cDNA clones coded for polypeptides of 290 residues and the deduced amino acid sequence identity between YP1 and YP2 was very high (79.0%). Analysis of the secondary structure of the predicted polypeptides suggests that YP1 and YP2 do not form heteromeric proteins because of differences in secondary structure due to the lack of alpha helices in YP1. Northern blot analysis showed that the transcripts for YP1 (1.2 kb) and YP2 (1.1 kb) were present primarily in the female fat body with only trace levels detectable in the ovary of the adult female. In a developmental study, the YP1 and YP2 transcripts were first detectable in 10-day-old pupae and increased into the adult stage. These results suggest that the YP1 and YP2 genes in H. cunea have been recruited to replace the vitellogenin gene as the primary source of yolk proteins. During this process they have acquired a modified pattern of expression that is different from homologous genes reported in pyralid moths. The assessment of the evolution of proteinaceous yolk in these moths should serve as an excellent model for the evolution of gene recruitment.

Amino Acid Sequence↗
PubMed2005

Endovascular treatment of aneurysms: gene expression of neointimal cells recruited on the embolic agent and evolution with recurrence in an experimental model.

PURPOSE: The authors attempted to identify genes associated with healing or recurrence after embolization in an aneurysm model in which neointima formation at the neck varies according to flow zones. A better understanding of the relationship between blood flow, molecular events, and healing or recurrence may provide future avenues to improve results of endovascular treatment of aneurysms. METHODS: Bilateral carotid venous pouch aneurysms were constructed in 36 dogs and embolized with gelatin sponges. Angiography and pathological studies were performed at T0 and/or 3 weeks (n=22). Angiographic results and neointima formation were scored using a qualitative index applied to the distal (inflow) and proximal (outflow) zones of the neck. In 14 animals, mRNA expression 1 to 14 days after embolization at the proximal or distal segment of the sponge was analyzed by RT-PCR, attempting to correlate flow zones, gene expression, and neointima formation. RESULTS: Aneurysms recurred at 3 weeks, as shown by significantly worse angiographic scores as compared to T0 (P<.01). Neointimal scores differed at pathology, with a more complete neointima at the proximal as compared to the distal aspect of the sponge at 3 weeks (P=.027). Embolization was followed by migration of CD31+, CD14+, smooth muscle alpha-actin+ (SMA+) cells that progressively expressed metalloproteinases (MMP-9,-12,-14), but stable or lesser, retarded expression of inhibitors (TIMP1-4). Growth factors (PDGF-BB, TGF-beta1, TNF-alpha, MCP-1 and Ang-1) were expressed at increasing levels, maximal at 7 to 14 days. Differences between distal and proximal zones were limited to increased expression of MMP-2 proximally (P<.035). CONCLUSION: Gene expression after embolization is compatible with patterns associated with neointima formation. The authors have not identified key factors involved in recurrence.

Actins↗
PubMed1990

Neurosurgical staff development model: from concept to implementation.

Nurses new to the neuroscience specialty often have fears regarding their expertise in this field. This article describes a staff development model successfully implemented in a 560-bed tertiary care center. The historical evolution of the model is discussed and components of the model in relation to professional development are presented. Future plans for development, evaluation and integration of the model into a clinical ladder program are also discussed.

Career Mobility↗