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PubMed2026

MRE11 suppresses germline mutagenesis at meiotic double-strand breaks in mice.

SPO11 forms hundreds of double-strand breaks (DSBs) to initiate meiotic recombination that is normally error-free. However, SPO11 activity can be mutagenic when one chromatid incurs closely spaced DSBs (double cuts), especially when DSBs are dysregulated by loss of the ATM kinase. De novo indels and structural variants can arise via end joining at double cuts within a single hotspot (microdeletions) or at adjacent hotspots separated by at least 30 kb, as we now show, sometimes accompanied by ectopic insertions of double-cut fragments. Here, we investigate how meiotic DSB end processing influences end joining. In MRE11-deficient mouse spermatocytes, which do not resect their DSBs, deletions at double cuts occur readily, with end-joining breakpoint profiles closely matching SPO11 DSB profiles. Microdeletions suggest that two DSBs can be as close as ∼21 bp. The tyrosyl-DNA phosphodiesterase TDP2 contributes to both deletion formation and ectopic insertion of double-cut fragments, presumably by removing SPO11 from DNA ends prior to joining. Finally, observations suggest a cooperative role for MRE11 and ATM in locally regulating DSB distributions. Our findings provide insight into the mechanism of de novo mutation origin, emphasizing the role of meiotic DSBs in shaping genome evolution.

Animals↗
PubMed1978

Altitudinal field defects and retinal nerve fibre degeneration in optic nerve lesions.

Altitudinal visual field defects in five cases with optic nerve lesions due to optic glioma, compression, and trauma are correlated to retinal nerve fibre degeneration, recorded with ophthalmoscopy and photography in red-free light. In one case the optic nerve was damaged at operation. Repeated fundus photography was used to record the evolution of descending optic atrophy. The results suggest that the findings in funduscopic examination of the retinal nerve fibre layer should be cautiously judged and the method cannot replace careful perimetry in cooperative patients.

Adult↗
PubMed2000

Mutualism, parasitism and competition in the evolution of coviruses.

Coviruses are viruses with the property that their genetic information is divided up among two or more different viral particles. I model the evolution of coviruses using information on both viral virulence and the interactions between viruses and molecules that parasitize them: satellite viruses, satellite RNAs and defective interfering viruses. The model ultimately, and inevitably contains within it single-species dynamics as well as mutualistic, parasitic, cooperative and competitive relationships. The model shows that coexistence between coviruses and the self-sufficient viruses that spawned them is unlikely, in the sense that the quantitative conditions for coexistence are not easy to satisfy I also describe an abrupt transition from mutualistic two-species to single-species dynamics, showing a new sense in which questions such as 'Is a lichen one species or two?' can be given a definite answer.

Animals↗
PubMedDate not supplied

[Cytoembryologic aspects of evolution of specialized electric organs of fishes].

Almost all fish electric organs (EO) developed from the skeletal muscles or from its embryonic rudiments. The only exception is the definite (in contrast to larval) EO of Apteronotidae, formed by motoneurons, whose loss of relation with muscles is secondary. The main feature of all EO of the muscle genesis is cooperative morphological and electrophysiological polarity of their electrocyte cells anterioposteriorly or (in Torpedo, Uranoscopus) of the dorso-ventral axes of the body. In particular, for the EO of muscular origin, unilateral asymmetric innervation of electrocytes by electromotoneurons is characteristic. Such innervation is a prerequisite condition for the summation of electric discharges. It is one of the main distinctions of EO from definitive skeletal muscles. However, in the emryogenesis of all vertebrates the initial innervation of muscle rudiments by the so-called pioneer motoneurons occurs. In teleosts (according to data on Brachidanio rerio available) extending to every myotome are outgrowths of three pioneer motoneurons referred to after their position in the nerotubule as "rostral", "medial" and "caudal". The former two innervate dorsally with the dorsal compartment of the myotome. The third approaches the ventral compartment of the same myotome caudally. In the gymnotic fish the innervation of EO formed from the axial skeletal muscles retains the same nature. The electrocytes of EO from the dorsal and ventral compartments of the myotome, are approached by electromotoneurons, respectively, rostrally and caudally. In compartments, the antipolarity of the innervation of the dorsal and ventral EO compartments leads to a paradoxical effect of generation of anti-polar pulses. The summation of these pulses creates a very short difference electric charge. In Mormyridae the antipolarity of the innervation of the rostral and ventral compartments of EO formed from the axial muscle is not pronounced. However, electroneurons resemble pioneer motoneurons by the following characters: the large size of the bodies and their localization near the central tube, absence of dendrities, electrosynaptic connection, polar (asymmetrical) pattern of electrocyte innervation. Outside EO, the cooperative polarity of the cells is only characteristic of epithelia, particularly, ciliated. At the same time, in some electric fish, the electrogeneratory tissue is similar to epithelium in a number of morphological characters, or the genes expressed in it show the gene of keratin AE-1, typical of epithelia. The above gives grounds to believe that EO of muscle origin are a product of fixation and aggravation by natural selection of hereditary anomalies, manifested in the recovery or in the retaining of the embryonic (i.e., polar nature) of the efferent innervation of some parts of skeletal muscles. Another distinction of EO from the muscles appears to lie in the expression of some individual components of the gene epithelial complex. A method is proposed for electromyographic recording of such anomalies and molecular-genetic approachers to analysis of their nature. The causes of the absence of EO epithelial genesis are discussed and also of the fact that these organs developed only in the evolution of fish.

Animals↗
PubMed2002

Experimental social evolution with Myxococcus xanthus.

Genetically-based social behaviors are subject to evolutionary change in response to natural selection. Numerous microbial systems provide not only the opportunity to understand the genetic mechanisms underlying specific social interactions, but also to observe evolutionary changes in sociality over short time periods. Here we summarize experiments in which behaviors of the social bacterium Myxococcus xanthus changed extensively during evolutionary adaptation to two relatively asocial laboratory environments. M. xanthus moves cooperatively, exhibits cooperative multicellular development upon starvation and also appears to prey cooperatively on other bacteria. Replicate populations of M. xanthus were evolved in both structured (agar plate) and unstructured (liquid) environments that contained abundant resources. The importance of social cooperation for evolutionary fitness in these habitats was limited by the absence of positive selection for starvation-induced spore production or predatory efficiency. Evolved populations showed major losses in all measured categories of social proficiency- motility, predation, fruiting ability, and sporulation. Moreover, several evolved genotypes were observed to exploit the social behavior of their ancestral parent when mixed together during the developmental process. These experiments that resulted in both socially defective and socially exploitative genotypes demonstrate the power of laboratory selection experiments for studying social evolution at the microbial level. Results from additional selection experiments that place positive selection pressure on social phenotypes can be integrated with direct study of natural populations to increase our understanding of principles that underlie the evolution of microbial social behavior.

Biological Evolution↗
PubMed2006

Why we still use intravenous drugs as the basic regimen for neurosurgical anaesthesia.

PURPOSE OF REVIEW: Evolution of neurosurgery mainly trends towards minimally invasive and functional procedures including endoscopies, small-size craniotomies, intraoperative imaging and stereotactic interventions. Consequently, new adjustments of anaesthesia should aim at providing brain relaxation, minimal interference with electrophysiological monitoring, rapid recovery, patients' cooperation during surgery and neuroprotection. RECENT FINDINGS: In brain tumour patients undergoing craniotomy, propofol anaesthesia is associated with lower intracranial pressure and cerebral swelling than volatile anaesthesia. Hyperventilation used to improve brain relaxation may decrease jugular venous oxygen saturation below the critical threshold. It decreases the cerebral perfusion pressure in patients receiving sevoflurane, but not in those receiving propofol. The advantage of propofol over volatile agents has also been confirmed regarding interference with somatosensory, auditory and motor evoked potentials. Excellent and predictable recovery conditions as well as minimal postoperative side-effects make propofol particularly suitable in awake craniotomies. Finally, the potential neuroprotective effect of this drug could be mediated by its antioxidant properties which can play a role in apoptosis, ischaemia-reperfusion injury and inflammatory-induced neuronal damage. SUMMARY: Although all the objectives of neurosurgical anaesthesia cannot be met by one single anaesthetic agent or technique, propofol-based intravenous anaesthesia appears as the first choice to challenge the evolution of neurosurgery in the third millennium.

Anesthesia↗
PubMed2002

Equine infectious anemia virus envelope evolution in vivo during persistent infection progressively increases resistance to in vitro serum antibody neutralization as a dominant phenotype.

Equine infectious anemia virus (EIAV) infection of horses is characterized by well-defined waves of viremia associated with the sequential evolution of distinct viral populations displaying extensive envelope gp90 variation; however, a correlation of in vivo envelope evolution with in vitro serum neutralization phenotype remains undefined. Therefore, the goal of the present study was to utilize a previously defined panel of natural variant EIAV envelope isolates from sequential febrile episodes to characterize the effects of envelope variation during persistent infection on viral neutralization phenotypes and to define the determinants of EIAV envelope neutralization specificity. To assess the neutralization phenotypes of the sequential EIAV envelope variants, we determined the sensitivity of five variant envelopes to neutralization by a longitudinal panel of immune serum from the source infected pony. The results indicated that the evolution of the EIAV envelope sequences observed during sequential febrile episodes produced an increasingly neutralization-resistant phenotype. To further define the envelope determinants of EIAV neutralization specificity, we examined the neutralization properties of a panel of chimeric envelope constructs derived from reciprocal envelope domain exchanges between selected neutralization-sensitive and neutralization-resistant envelope variants. These results indicated that the EIAV gp90 V3 and V4 domains individually conferred serum neutralization resistance while other envelope segments in addition to V3 and V4 were evidently required for conferring total serum neutralization sensitivity. These data clearly demonstrate for the first time the influence of sequential gp90 variation during persistent infection in increasing envelope neutralization resistance, identify the gp90 V3 and V4 domains as the principal determinants of antibody neutralization resistance, and indicate distinct complex cooperative envelope domain interactions in defining sensitivity to serum antibody neutralization.

Amino Acid Sequence↗
PubMedDate not supplied

Two-level evolution of foraging agent communities.

This paper presents simulation results of artificial foraging agent communities. The goal of each agent in the community is to find food. Once a food source is found, agents eat portions of it and carry some other portions to the nest (in a manner similar to ants) until the food is depleted. Agents may also communicate food positions when they are near each other. They are given a set of genes that control several characteristics, such as their activity, memory, scepticism, lying, etc. These genes are recombined and propagated by means of sexual reproduction. When one nest is superpopulated with agents, it can break in two nests. Agents can communicate only with those belonging to the same nest, which gives rise to emergent situations of competition and cooperation between the agents in the same nest, as well as competition between different nests. Other emergent phenomena such as the propagation of rumours are also studied.

Animals↗
PubMed1996

The origin of kinetic cooperativity in prebiotic catalysts.

A polyallylamine carrying long hydrophobic dodecyl groups and adenine residues as side chains (PALAD C12) may be able to catalyze the hydrolysis of N-carbobenzoxy-l-alanine p-nitrophenyl ester (N-Cbz-Ala) as well as p-nitrophenyl acetate (pNPA). The progress curve of hydrolysis of the former displays a long lag and apparently no steady state. After this transient the rate falls off due to the accumulation of the products. Conversely, the hydrolysis of p-nitrophenyl acetate displays classical burst kinetics followed by a slow decline of the reaction rate.Theoretical considerations show that a steady state may be expected to occur only if the concentration of the free catalyst is very small during the reaction. This condition is sufficient to allow the rate of disappearance of the substrate to be equal to the rate of appearance of the products, which is precisely a condition for the existence of a steady state. If the catalyst is poorly active and has a loose affinity for its substrate and product, the measurement of a significant reaction rate will require a much larger concentration of the catalyst. Therefore, under these conditions, one cannot expect a steady state to occur. The mathematical expression of the error made in the steady-state assumption has been derived. This error increases with the catalyst concentration and decreases if the affinity of the substrate for the catalyst is high. Therefore the lack of steady state is associated with the affinity (or the dissociation) of the substrate and the product for the catalyst. When this affinity is low, the free concentration of the catalyst during the reaction is high and one cannot expect a steady state to occur. This is precisely what takes place with N-Cbz-Ala.A mathematical expression of the rate of hydrolysis of N-Cbz-Ala and of any reactant that displays this type of kinetics may be derived at the end of the transient when the rate is close to its maximum value. Under these conditions the rate cannot follow classical Michaelis-Menten kinetics and displays positive cooperativity. It may therefore be speculated that primordial template-like catalysts that were displaying a poor affinity for their substrates and products were already exhibiting apparent positive cooperativity in the kinetic reactions they were able to catalyze.

Alanine↗
PubMed2000

Postsegregational killing does not increase plasmid stability but acts to mediate the exclusion of competing plasmids.

Postsegregational killing (PSK) systems consist of a tightly linked toxin-antitoxin pair. Antitoxin must be continually produced to prevent the longer lived toxin from killing the cell. PSK systems on plasmids are widely believed to benefit the plasmid by ensuring its stable vertical inheritance. However, experimental tests of this "stability" hypothesis were not consistent with its predictions. We suggest an alternative hypothesis to explain the evolution of PSK: that PSK systems have been selected through benefiting host plasmids in environments where plasmids must compete during horizontal reproduction. In this "competition" hypothesis, success of PSK systems is a consequence of plasmid-plasmid competition, rather than from an adaptive plasmid-host relationship. In support of this hypothesis, a plasmid-encoded parDE PSK system mediated the exclusion of an isogenic DeltaparDE plasmid. An understanding of how PSK systems influence plasmid success may provide insight into the evolution of other determinants (e.g., antibiotic resistance and virulence) also rendering a cell potentially dependent on an otherwise dispensable plasmid.

DNA, Bacterial↗
PubMed2000

Evolution of lamivudine-resistant hepatitis B virus and HIV-1 in co-infected individuals: an analysis of the CAESAR study. CAESAR co-ordinating committee.

OBJECTIVES: Lamivudine has potent activity against HIV-1 and hepatitis B virus (HBV). Co-infection with these two viruses is common, and this may therefore influence the choice of antiretroviral therapies. A cohort of co-infected patients treated with lamivudine were studied in order to evaluate the differential effects of lamivudine on the two viral populations within the same individual after 44-52 weeks of therapy. DESIGN AND METHODS: Retrospective virological analysis of an HIV-1/HBV co-infected lamivudine cohort derived from a randomized, placebo-controlled study of lamivudine in HIV infection, the CAESAR study. RESULTS: Five of thirteen patients with HBV viral load > 10,000 copies/ml after 44-52 weeks of lamivudine therapy had genotypic drug resistance. Four of these five had a rebound of viral replication over the period of study and in one case this was associated with an alanine transaminase serum elevation. Ten of the thirteen patients had a 44-52 week HIV viral load > 1000 copies/ml, all of whom also had HIV reverse transcriptase M184V or M184I mutations. CONCLUSIONS: Extrapolating these results to the population yields an estimated 1-year incidence of drug-resistant HBV of at least 14% in lamivudine-treated HIV-1/HBV co-infected patients. The clinical and virological benefit of HBV lamivudine monotherapy in co-infected patients should be balanced against the potential for emergence of drug resistance. Further, these data suggest that the determinants of HIV and HBV drug resistance are different and that parallel evolution, rather than co-evolution of HBV and HIV-1 in co-infected individuals occurs.

CD4 Lymphocyte Count↗
PubMed2003

Animal source foods and human health during evolution.

Animal source foods (ASF) have always been a constituent of human diets. Their pattern of use, however, changed in dramatic ways over the course of human evolution. Before 2 million years ago (mya), meat in particular was acquired opportunistically via hunting of small or young animals and scavenging of animals killed by other species. At some point after that time, humans began to hunt cooperatively, making possible the acquisition of meat from large game. The marked increase in human heights between 2.0 and 1.7 mya may be linked to more efficient means of acquiring meat, namely through hunting. The final pattern of meat (and other ASF) use before the modern era is associated with the shift from hunting and gathering beginning approximately 10,000 y ago. This fundamental dietary change resulted in a narrowing of diet, reduced consumption of meat and increased focus on domesticated grains. The study of archaeological human remains from around the world reveals that this period in human dietary history saw a decline in health, including increased evidence of morbidity (poorer dental health, increased occlusal abnormalities, increased iron deficiency anemia, increased infection and bone loss). Human populations living in developing and developed settings today rely on meats with lipid compositions that when eaten in excess promote cardiovascular disease. As humans become more sedentary and eat more high fat foods, we can expect to see increases in heart disease, osteoporosis and other diseases of "civilization."

Agriculture↗
PubMed2006

Nuclear-mitochondrial genomic profiling reveals a pattern of evolution in epithelial ovarian tumor stem cells.

Analyses of genome orthologs in cancer on the background of tumor heterogeneity, coupled with the recent identification that the tumor propagating capacity resides within a very small fraction of cells (the tumor stem cells-TSCs), has not been achieved. Here, we describe a strategy to explore genetic drift in the mitochondrial genome accompanying varying stem cell dynamics in epithelial ovarian cancer. A major and novel outcome is the identification of a specific mutant mitochondrial DNA profile associated with the TSC lineage that is drastically different from the germ line profile. This profile, however, is often camouflaged in the primary tumor, and sometimes may not be detected even after metastases, questioning the validity of whole tumor profiling towards determining individual prognosis. Continuing mutagenesis in subsets with a mutant mitochondrial genome could result in transformation through a cooperative effect with nuclear genes - a representative example in our study is a tumor suppressor gene viz. cAMP responsive element binding binding protein. This specific profile could be a critical predisposing step undertaken by a normal stem cell to overcome a tightly regulated mutation rate and DNA repair in its evolution towards tumorigenesis. Our findings suggest that varying stem cell dynamics and mutagenesis define TSC progression that may clinically translate into increasing tumor aggression with serious implications for prognosis.

Adenocarcinoma, Papillary↗
PubMed1992

Potential of genetic algorithms in protein folding and protein engineering simulations.

Genetic algorithms are very efficient search mechanisms which mutate, recombine and select amongst tentative solutions to a problem until a near optimal one is achieved. We introduce them as a new tool to study proteins. The identification and motivation for different fitness functions is discussed. The evolution of the zinc finger sequence motif from a random start is modelled. User specified changes of the lambda repressor structure were simulated and critical sites and exchanges for mutagenesis identified. Vast conformational spaces are efficiently searched as illustrated by the ab initio folding of a model protein of a four beta strand bundle. The genetic algorithm simulation which mimicked important folding constraints as overall hydrophobic packaging and a propensity of the betaphilic residues for trans positions achieved a unique fold. Cooperativity in the beta strand regions and a length of 3-5 for the interconnecting loops was critical. Specific interaction sites were considerably less effective in driving the fold.

Algorithms↗
PubMed2002

Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum.

Widespread use of antimalarial agents can profoundly influence the evolution of the human malaria parasite Plasmodium falciparum. Recent selective sweeps for drug-resistant genotypes may have restricted the genetic diversity of this parasite, resembling effects attributed in current debates to a historic population bottleneck. Chloroquine-resistant (CQR) parasites were initially reported about 45 years ago from two foci in southeast Asia and South America, but the number of CQR founder mutations and the impact of chlorquine on parasite genomes worldwide have been difficult to evaluate. Using 342 highly polymorphic microsatellite markers from a genetic map, here we show that the level of genetic diversity varies substantially among different regions of the parasite genome, revealing extensive linkage disequilibrium surrounding the key CQR gene pfcrt and at least four CQR founder events. This disequilibrium and its decay rate in the pfcrt-flanking region are consistent with strong directional selective sweeps occurring over only approximately 20-80 sexual generations, especially a single resistant pfcrt haplotype spreading to very high frequencies throughout most of Asia and Africa. The presence of linkage disequilibrium provides a basis for mapping genes under drug selection in P. falciparum.

Alleles↗
PubMed2003

Limited evolution of HIV antiretroviral drug resistance-associated mutations during the performance of drug resistance testing.

We investigated the evolution of HIV reverse transcriptase (RT)- and protease-associated antiretroviral (ARV) drug resistance mutations during the time taken to perform genotypic drug resistance testing. Thirty treatment-experienced patients who were adherent to therapy and who underwent genotypic drug resistance testing provided blood samples at randomization and when reviewing the test results (baseline). Patients remained on their existing therapy between randomization and baseline. The predominant HIV strains in 10 patients (33%) either lost and/or gained primary RT inhibitor (RTI)- or protease inhibitor (PI)-associated resistance mutations during the testing period. Of the 9 patients with RT mutations, 2 lost, 5 gained, and 2 both lost and gained RTI resistance mutations. One patient gained a significant PI-associated resistance mutation on an existing PI-resistant background. The evolution that occurred in the RT may have altered the effectiveness of subsequent ARV therapy in some patients. Neither viral load at randomization, ARV drug class used at randomization, time between collection of blood samples, duration of current therapy, nor number of ARV drugs used influenced gain or loss of resistance mutations. There was a significant association between duration of previous ARV therapy and gain of RTI-associated resistance mutations ( p =.02), however. In general, our results suggest that patients should continue current therapy until test results are available. A few patients would be expected to gain ARV drug-associated resistance mutations during this time, however.

Adult↗
PubMed2001

Rapid phenotypic change and diversification of a soil bacterium during 1000 generations of experimental evolution.

Evolutionary pathways open to even relatively simple organisms, such as bacteria, may lead to complex and unpredictable phenotypic changes, both adaptive and non-adaptive. The evolutionary pathways taken by 18 populations of Ralstonia strain TFD41 while they evolved in defined environments for 1000 generations were examined. Twelve populations evolved in liquid media, while six others evolved on agar surfaces. Phenotypic analyses of these derived populations identified some changes that were consistent across all populations and others that differed among them. The evolved populations all exhibited morphological changes in their cell envelopes, including reductions of the capsule in each population and reduced prostheca-like surface structures in most populations. Mean cell length increased in most populations (in one case by more than fourfold), although a few populations evolved shorter cells. Carbon utilization profiles were variable among the evolved populations, but two distinct patterns were correlated with genetic markers introduced at the outset of the experiment. Fatty acid methyl ester composition was less variable across populations, but distinct patterns were correlated with the two physical environments. All 18 populations evolved greatly increased sensitivity to bile salts, and all but one had increased adhesion to sand; both patterns consistent with changes in the outer envelope. This phenotypic diversity contrasts with the fairly uniform increases in competitive fitness observed in all populations. This diversity may represent a set of equally probable adaptive solutions to the selective environment; it may also arise from the chance fixation of non-adaptive mutations that hitchhiked with a more limited set of beneficial mutations.

Bacterial Adhesion↗