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PubMed1995

Gerontogenes: real or virtual?

The view that the life span of an organism is intrinsically limited and is largely species-specific necessarily involves certain notions of genetic elements of regulation. The term gerontogenes refers to any such genetic elements that are involved in the regulation of aging and life span. The existence of genes for programmed aging is generally discounted on the basis of evolutionary arguments against the notion of the adaptive nature of aging. It is suggested here that the concept of gerontogenes be linked with the idea of genes involved in homeostasis and longevity assurance, which is not contradictory to the nonadaptive nature of aging. Because these genes were not originally selected as real genes for aging, their involvement in aging is an emergent property making them virtual gerontogenes. Some experimental evidence is available that suggests that sets of genes involved in the maintenance and repair of various cellular functions are the primary candidates qualifying as virtual gerontogenes.

Aging↗

PubMed2004

Sex determination and the evolution of dioecy from monoecy in Sagittaria latifolia (Alismataceae).

The role of mutations of small versus large effect in adaptive evolution is of considerable interest to evolutionary biologists. The major evolutionary pathways for the origin of dioecy in plants (the gynodioecy and monoecy-paradioecy pathways) are often distinguished by the number of mutations involved and the magnitude of their effects. Here, we investigate the genetic and environmental determinants of sex in Sagittaria latifolia, a species with both monoecious and dioecious populations, and evaluate evidence for the evolution of dioecy via gynodioecy or monoecy-paradioecy. We crossed plants of the two sexual systems to generate F1, F2 and backcross progeny, and grew clones from dioecious populations in low-and high-fertilizer conditions to examine sex inconstancy in females and males. Several lines of evidence implicate two-locus control of the sex phenotypes. In dioecious populations sex is determined by Mendelian segregation of alleles, with males heterozygous at both the male- and female-sterility loci. In monoecious populations, plants are homozygous for alleles dominant to male sterility in females and recessive to female sterility in males. Experimental manipulation of resources revealed sex inconstancy in males but not females. These results are consistent with predictions for the evolution of dioecy via gynodioecy, rather than the expected monoecy-paradioecy pathway, given the ancestral monoecious condition.

Biological Evolution↗

PubMed2003

Approaches to the structural modelling of insect wings.

Insect wings lack internal muscles, and the orderly, necessary deformations which they undergo in flight and folding are in part remotely controlled, in part encoded in their structure. This factor is crucial in understanding their complex, extremely varied morphology. Models have proved particularly useful in clarifying the facilitation and control of wing deformation. Their development has followed a logical sequence from conceptual models through physical and simple analytical to numerical models. All have value provided their limitations are realized and constant comparisons made with the properties and mechanical behaviour of real wings. Numerical modelling by the finite element method is by far the most time-consuming approach, but has real potential in analysing the adaptive significance of structural details and interpreting evolutionary trends. Published examples are used to review the strengths and weaknesses of each category of model, and a summary is given of new work using finite element modelling to investigate the vibration properties and response to impact of hawkmoth wings.

Animals↗

PubMed1999

Early parental preoccupations and behaviors and their possible relationship to the symptoms of obsessive-compulsive disorder.

This study focuses on early parental preoccupations and behaviors (EPPB) surrounding the birth of a new family member. An interview instrument was developed to assess EPPB at eight months prepartum and two weeks and three months postpartum. Measures with adequate psychometric and conceptual properties were used to assess the overall level of parental preoccupations and associated actions as well as three content domains: caregiving (CARE), relationship building (RELATIONSHIP), and anxious intrusive thoughts associated with harm avoidant behaviors (AITHAB). The hypothesis that preoccupations and behaviors would peak for both parents close to the birth of the child was confirmed. Measures of EPPB were distinguished from symptoms of depression and generalized anxiety. Consistent with our a priori hypothesis the content and character of the AITHAB was found to resemble the symptoms of obsessive-compulsive disorder (OCD). The study findings suggest the potential adaptive significance of EPPB and the possible evolutionary origins of OCD.

Adult↗

PubMed1996

Discontinuous gas exchange in insects.

Many insects exchange respiratory gases cyclically and discontinuously. A typical discontinuous gas exchange cycle (DGC) starts with a closed-spiracle (C) phase, during which little external gas exchange takes place, followed by a fluttering-spiracle (F) phase, which is usually dominated by diffusive oxygen uptake. The DGC is terminated by an open-spiracle (O) phase, during which accumulated CO2 escapes. This review critically examines the applicability of the DGC to insect gas exchange in general, discusses the primary mechanisms of gas exchange in the F and O phases, evaluates the widespread hypothesis that the DGC lowers respiratory water loss rates adaptively, and proposes new hypotheses concerning the evolutionary genesis of the DGC in insects and other tracheate arthropods.

Animals↗

PubMed2006

Free radical biology and medicine: it's a gas, man!

We review gases that can affect oxidative stress and that themselves may be radicals. We discuss O(2) toxicity, invoking superoxide, hydrogen peroxide, and the hydroxyl radical. We also discuss superoxide dismutase (SOD) and both ground-state, triplet oxygen ((3)O(2)), and the more energetic, reactive singlet oxygen ((1)O(2)). Nitric oxide ((*)NO) is a free radical with cell signaling functions. Besides its role as a vasorelaxant, (*)NO and related species have other functions. Other endogenously produced gases include carbon monoxide (CO), carbon dioxide (CO(2)), and hydrogen sulfide (H(2)S). Like (*)NO, these species impact free radical biochemistry. The coordinated regulation of these species suggests that they all are used in cell signaling. Nitric oxide, nitrogen dioxide, and the carbonate radical (CO(3)(*-)) react selectively at moderate rates with nonradicals, but react fast with a second radical. These reactions establish "cross talk" between reactive oxygen (ROS) and reactive nitrogen species (RNS). Some of these species can react to produce nitrated proteins and nitrolipids. It has been suggested that ozone is formed in vivo. However, the biomarkers that were used to probe for ozone reactions may be formed by non-ozone-dependent reactions. We discuss this fascinating problem in the section on ozone. Very low levels of ROS or RNS may be mitogenic, but very high levels cause an oxidative stress that can result in growth arrest (transient or permanent), apoptosis, or necrosis. Between these extremes, many of the gasses discussed in this review will induce transient adaptive responses in gene expression that enable cells and tissues to survive. Such adaptive mechanisms are thought to be of evolutionary importance.

Free Radicals↗

PubMed1995

Cholesterol content of trout plasma membranes varies with acclimation temperature.

Involvement of cholesterol in thermally induced restructuring of biological membranes was investigated in several tissues of rainbow trout (Oncorhynchus mykiss). Cholesterol-rich plasma membranes (PM) were isolated from erythrocytes, liver, kidney, and gill of fish acclimated to 5 and 20 degrees C. Mean PM cholesterol-to-phospholipid molar ratios (C/P) from warm-acclimated animals were significantly higher than those of cold-acclimated fish in liver (0.26 vs. 0.18; P < 0.01), kidney (0.49 vs. 0.40; P < 0.02), and gill (0.66 vs. 0.60; P < 0.05); erythrocyte C/P did not differ significantly with acclimation temperature (0.28 vs. 0.25; P = 0.25). In light of the ordering effects of cholesterol on fluid-phase membranes, these results are consistent with a role for cholesterol in the homeoviscous response of some poikilotherm PMs. Tissue differences in both PM cholesterol levels and the magnitude of thermally evoked cholesterol changes may reflect tissue-specific membrane functions. Lower PM C/P of trout tissues relative to corresponding data available for homeotherms also support a possible evolutionary relationship between cholesterol content and thermal adaptation of the PM.

Acclimatization↗

PubMed2006

Distinguishing HIV-1 drug resistance, accessory, and viral fitness mutations using conditional selection pressure analysis of treated versus untreated patient samples.

BACKGROUND: HIV can evolve drug resistance rapidly in response to new drug treatments, often through a combination of multiple mutations 123. It would be useful to develop automated analyses of HIV sequence polymorphism that are able to predict drug resistance mutations, and to distinguish different types of functional roles among such mutations, for example, those that directly cause drug resistance, versus those that play an accessory role. Detecting functional interactions between mutations is essential for this classification. We have adapted a well-known measure of evolutionary selection pressure (Ka/Ks) and developed a conditional Ka/Ks approach to detect important interactions. RESULTS: We have applied this analysis to four independent HIV protease sequencing datasets: 50,000 clinical samples sequenced by Specialty Laboratories, Inc.; 1800 samples from patients treated with protease inhibitors; 2600 samples from untreated patients; 400 samples from untreated African patients. We have identified 428 mutation interactions in Specialty dataset with statistical significance and we were able to distinguish primary vs. accessory mutations for many well-studied examples. Amino acid interactions identified by conditional Ka/Ks matched 80 of 92 pair wise interactions found by a completely independent study of HIV protease (p-value for this match is significant: 10-70). Furthermore, Ka/Ks selection pressure results were highly reproducible among these independent datasets, both qualitatively and quantitatively, suggesting that they are detecting real drug-resistance and viral fitness mutations in the wild HIV-1 population. CONCLUSION: Conditional Ka/Ks analysis can detect mutation interactions and distinguish primary vs. accessory mutations in HIV-1. Ka/Ks analysis of treated vs. untreated patient data can distinguish drug-resistance vs. viral fitness mutations. Verification of these results would require longitudinal studies. The result provides a valuable resource for AIDS research and will be available for open access upon publication at http://www.bioinformatics.ucla.edu/HIV.

Journal Article↗

PubMed2006

Thymus-dependent T cell tolerance of neuroendocrine functions: principles, reflections, and implications for tolerogenic/negative self-vaccination.

Under the evolutionary pressure exerted by the emergence of adaptive immunity and its inherent risk of horror autotoxicus, the thymus appeared some 500 million years ago as a novel lymphoid structure able to prevent autoimmunity and to orchestrate self-tolerance as a cornerstone in the physiology of the immune system. Also, the thymus plays a prominent role in T cell education to neuroendocrine principles. Some self-antigens (oxytocin, neurotensin, insulin-like growth factor 2 [IGF-2]) have been selected to be predominantly expressed in thymic epithelium and to be presented to thymus T cells for educating them to tolerate other antigens related to them. In the insulin family, IGF2 is dominantly transcribed in cortical (c) and medullary (m) thymic epithelial cells (TECs), whereas the insulin gene (INS) is expressed at low level by only a few subsets of mTECs. Intrathymic transcription of both IGF2 and INS is under the control of the autoimmune regulator (Aire) gene. The highest concentrations of IGF-2 in the thymus explain why this peptide is much more tolerated than insulin, and why tolerance to IGF-2 is so difficult to break by active immunization. The high level of tolerance to IGF-2 is correlated to the development of a tolerogenic/regulatory profile when the sequence B11-25 of IGF-2 (homologous to the autoantigen insulin B9-23) is presented to DQ8+ type 1 diabetic patients. Since subcutaneous and oral insulin does not exert any tolerogenic properties, IGF-2 and other thymus self-antigens related to type 1 diabetes (T1D) should be preferred to insulin for the design of novel specific antigen-based preventive approaches against T1D.

Animals↗

PubMed2006

Analysis of core housekeeping and virulence genes reveals cryptic lineages of Clostridium perfringens that are associated with distinct disease presentations.

Clostridium perfringens is an important human and animal pathogen that causes a number of diseases that vary in their etiology and severity. Differences between strains regarding toxin gene composition and toxin production partly explain why some strains cause radically different diseases than others. However, they do not provide a complete explanation. The purpose of this study was to determine if there is a phylogenetic component that explains the variance in C. perfringens strain virulence by assessing patterns of genetic polymorphism in genes (colA gyrA, plc, pfoS, and rplL) that form part of the core genome in 248 type A strains. We found that purifying selection plays a central role in shaping the patterns of nucleotide substitution and polymorphism in both housekeeping and virulence genes. In contrast, recombination was found to be a significant factor only for the virulence genes plc and colA and the housekeeping gene gyrA. Finally, we found that the strains grouped into five distinct evolutionary lineages that show evidence of host adaptation and the early stages of speciation. The discovery of these previously unknown lineages and their association with distinct disease presentations carries important implications for human and veterinary clostridial disease epidemiology and provides important insights into the pathways through which virulence has evolved in C. perfringens.

Animals↗

PubMed2006

Genomewide evolutionary rates in laboratory and wild yeast.

As wild organisms adapt to the laboratory environment, they become less relevant as biological models. It has been suggested that a commonly used S. cerevisiae strain has rapidly accumulated mutations in the lab. We report a low-to-intermediate rate of protein evolution in this strain relative to wild isolates.

Evolution, Molecular↗

PubMed1999

Convergence and correlations among leaf size and function in seed plants: a comparative test using independent contrasts.

Prior studies of a broad array of seed plants have reported strong correlations among leaf life span, specific leaf area, nitrogen concentration, and carbon assimilation rates, which have been interpreted as evidence of coordinated leaf physiological strategies. However, it is not known whether these relationships reflect patterns of evolutionary convergence, or whether they are due to contrasting characteristics of major seed plant lineages. We reevaluated a published data set for these seven traits measured in over 100 species, using phylogenetic independent contrasts calculated over a range of alternative seed plant phylogenies derived from recent molecular systematic analyses. In general, pairwise correlations among these seven traits were similar with and without consideration of phylogeny, and results were robust over a range of alternative phylogenies. We also evaluated relationships between these seven traits and lamina area, another important aspect of leaf function, and found moderate correlations with specific leaf area (0.64), mass-based photosynthesis (0.54), area-based nitrogen (-0.56), and leaf life span (-0.42). However, several of these correlations were markedly reduced using independent contrasts; for example, the correlation between leaf life span and lamina area was reduced to close to zero. This change reflects the large differences in both these traits between conifers and angiosperms and the absence of a relationship between the traits within these groups. This analysis illustrates that most interspecific relationships among leaf functional traits, considered across a broad range of seed plant taxa, reflect significant patterns of correlated evolutionary change, lending further support to the adaptive interpretation of these relationships.

Journal Article↗

PubMed2003

An evolutionary model of carcinogenesis.

A quantitative model of carcinogenesis based on methods from population biology and game theory demonstrates normal cells in vivo occupy a ridge-shaped maximum in a well-defined tissue fitness landscape, a novel configuration that allows cooperative coexistence of multiple cellular populations. This state, although necessary for development of functioning multicellular organisms, is subject to invasion by fitter, mutant phenotypes permitting somatic evolution of cancer. The model demonstrates carcinogenesis is an emergent phenomenon requiring a sequence of evolutionary steps as cellular proliferation follows successful adaptation to varying environmental constraints. In the initial development of preneoplastic lesions, cellular proliferation is controlled exclusively by interactions with other cells, the extracellular matrix, and soluble or insoluble growth factors so that gain of function mutations in oncogenes, loss of function mutations in tumor suppressor genes, and disruption of normal senescence pathways will permit clonal expansion. This provides explicit selection mechanisms for the mutations depicted in the classical Fearon-Vogelstein model of colorectal carcinogenesis. The model demonstrates neoplastic cellular proliferation can also be promoted by alterations in the somatic landscape that reduce inhibitory signals produced by the normal cells and extracellular matrix. This is consistent with experimental evidence for a strong microenvironmental influence in tumorigenesis independent of genomic changes in the neoplastic populations. However, we find that these changes alone produce only self-limited neoplastic growth because cellular crowding alters system dynamics so that proliferation is dependent on substrate availability. Consequent cellular competition for critical nutrients results in Darwinian selection pressures favoring phenotypes that increase substrate delivery (e.g., angiogenesis) or uptake (e.g., amplify membrane transporters). These previously unknown substrate dynamics in the later stages of carcinogenesis provide a mechanism for evolution of cellular properties typically found in invasive cancers including the angiogenic and glycolytic phenotypes.

Animals↗

PubMed2004

[Arctic and southern freshwater pearl mussel Margaritifera margaritifera with long and short life span as a model system for testing longevity mechanisms].

The freshwater pearl mussel (Margaritifera margartifera) is one of the longest lived animals, attaining ages in excess of 150 years in polar climates. Because of its long life, the species may be useful for studying genetic and physiological mechanisms contributing to longevity. An ongoing study is comparing 6 southern populations in Spain, with maximum recorded ages of 28-40 years, to 3 Arctic populations in northwest Russia, with maximum ages of 114-190 years. Within Arctic populations, 40% of mussels live more than 100 years in rivers that are pristine. Possible evolutionary significance of northern longevity is an adaptation to severe cold and unstable environments in high gradient rivers. During winter, mussels have a near-famine existence during the Polar Night, and experience some shell damage from ice formation and flows. In summer, periodic droughts result in exposure and desiccation. In response to adversity, pearl mussels have acquired effective mechanisms for shell reparation and tissue healing and regeneration. Northern populations have low metabolic rates, reducing energy expenditure for growth under normal as well as extreme conditions. However, this species is capable of increasing metabolic rate for tissue regeneration and self-healing. The physiological adaptations to sustain longevity may provide useful clues to impedence of the aging process.

Aging↗

PubMedDate not supplied

[The prevalence of disseminated sclerosis in Ukraine].

Both geoclimatic factors and environmental contamination due to human activity in agriculture and industry have been implicated in the onset and course of disseminated sclerosis in Ukraine, according to epidemiological investigations. On the basis of the results obtained a conception has been advocated of the demyelinization process development as a consequence of the myelin protein metabolism control getting upset in the most differentiated system of those individuals genetically predisposed to the condition owing to aggravation of the endocrine disorders tending to occur in male subjects predominantly under the influence of geoclimatic factors while in females because of the environmental contamination. Peculiarities of formation in the evolutionary time scale of sex-related adaptive defence mechanisms are thought to account for the above observation.

Adult↗

PubMed2026

A chromosome-level genome of the Nicobar pigeon, Caloenas nicobarica.

The Nicobar pigeon (Caloenas nicobarica), the closest living relative of the extinct Dodo (Raphus cucullatus), is endemic to Southeast Asia with a fragmented distribution across numerous small islands. It suffers from habitat loss, hunting, and predation from invasive species, resulting in its classification as Near Threatened by the International Union for the Conservation of Nature. We have generated a haplotype-resolved and chromosome-level genome assembly of the Nicobar pigeon using a combination of PacBio HiFi long-read sequencing and Arima Hi-C chromatin interaction mapping. This assembly includes two haplotypes, each spanning approximately 1.2 Gb. Haplotype 1 has a contig N50 of 25.2 Mb and a scaffold N50 of 79.7 Mb, whereas haplotype 2 has a contig N50 of 24.7 Mb and a scaffold N50 of 107.9 Mb. As the first high-quality genome assembly of any bird in the Columbidae Indo-Pacific clade, this resource provides valuable insights for phylogenetic studies. Furthermore, the phylogenetic proximity of the Nicobar pigeon to the Dodo (R. cucullatus) and the Rodrigues Solitaire (Pezophaps solitaria) offers a unique opportunity to study these extinct species, making this assembly a critical resource for evolutionary studies. It also offers a unique model for studying genetic diversity, adaptation, and speciation in island environments. This genomic resource will not only enhance our understanding of the evolutionary history of the Nicobar pigeon but also serve as a valuable tool for future conservation efforts aimed at preserving this unique species and its fragile island ecosystem.

Animals↗

PubMed1994

Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations.

We followed evolutionary change in 12 populations of Escherichia coli propagated for 10,000 generations in identical environments. Both morphology (cell size) and fitness (measured in competition with the ancestor) evolved rapidly for the first 2000 generations or so after the populations were introduced into the experimental environment, but both were nearly static for the last 5000 generations. Although evolving in identical environments, the replicate populations diverged significantly from one another in both morphology and mean fitness. The divergence in mean fitness was sustained and implies that the populations have approached different fitness peaks of unequal height in the adaptive landscape. Although the experimental time scale and environment were microevolutionary in scope, our experiments were designed to address questions concerning the origin as well as the fate of genetic and phenotypic novelties, the repeatability of adaptation, the diversification of lineages, and thus the causes and consequences of the uniqueness of evolutionary history. In fact, we observed several hallmarks of macroevolutionary dynamics, including periods of rapid evolution and stasis, altered functional relationships between traits, and concordance of anagenetic and cladogenetic trends. Our results support a Wrightian interpretation, in which chance events (mutation and drift) play an important role in adaptive evolution, as do the complex genetic interactions that underlie the structure of organisms.

Adaptation, Physiological↗

PubMedDate not supplied

An adaptive ant colony system algorithm for continuous-space optimization problems.

Ant colony algorithms comprise a novel category of evolutionary computation methods for optimization problems, especially for sequencing-type combinatorial optimization problems. An adaptive ant colony algorithm is proposed in this paper to tackle continuous-space optimization problems, using a new objective-function-based heuristic pheromone assignment approach for pheromone update to filtrate solution candidates. Global optimal solutions can be reached more rapidly by self-adjusting the path searching behaviors of the ants according to objective values. The performance of the proposed algorithm is compared with a basic ant colony algorithm and a Square Quadratic Programming approach in solving two benchmark problems with multiple extremes. The results indicated that the efficiency and reliability of the proposed algorithm were greatly improved.

Algorithms↗