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Heat shock proteins as mediators of aggregation-induced 'danger' signals: implications of the slow evolutionary fine-tuning of sequences for the antigenicity of cancer cells.

Organisms 'tune' to their environment through adaptations which confer a selective advantage. However, in complex systems, a primary change of positive adaptive value might have multiple minor secondary effects, usually of negative adaptive value, which could invoke further counter-adaptations. This 'fine-tuning', a 'debugging', mainly at the intracellular level, would appear an evolutionary burden detracting from the positive nature of the primary change. However, if the primary mutation is in a potential oncogene, secondary, short-term effects may include the recruitment, in an apparently random manner, of unmutated non-oncogene products into the antigenic repertoire of the cancer cell. This 'danger' signal, provided by the co-aggregation of oncogene and non-oncogene products, would be mediated by inducible heat-shock proteins (Hsps), and lead to display of corresponding MHC-peptide complexes. It was argued previously that T cells specific for peptides from most 'self' intracellular antigens are not eliminated during T cell 'education', and so would be available for subsequent immune activation by the corresponding peptides. These considerations might explain why cancer specific antigens have been so elusive, why cancer antigenicity is often individual specific, and why therapeutic approaches involving complexes of peptides with Hsps may be successful.

Antigens, Neoplasm↗

Molecular biology of extremophiles: recent progress on the hyperthermophilic archaeon Sulfolobus.

Extremophiles are microorganisms that flourish in habitats of extreme temperature, pH, salinity, or pressure. All extreme environments are dominated by microorganisms belonging to Archaea, the third domain of life, evolutionary distinct from Bacteria and Eucarya. Over the past few years the biology of extremophilic Archaea has stimulated a lot of interest, aimed at understanding at molecular level the adaptation to their life conditions, as well as their evolutionary relationships to other organisms. Here, we review recent insights in the molecular biology of thermoacidophilic Archaea of the genus Sulfolobus, which has been used as a model system for biochemical, structural, and genetic studies in Archaea and extremophiles in general. With the recent completion of the genome sequence of Sulfolobus solfataricus it is expected that these organisms will contribute new discoveries in the near future.

DNA Replication↗

Recent evolution of the human pathogen Cryptococcus neoformans by intervarietal transfer of a 14-gene fragment.

The availability of the whole-genome sequence from the 2 known varieties of the human pathogenic fungus Cryptococcus neoformans provides an opportunity to study the relative contribution of divergence and introgression during the process of speciation in a genetically tractable organism. At the genomic level, these varieties are nearly completely syntenic, share approximately 85-90% nucleotide identity, and are believed to have diverged approximately 18 MYA. Via a comparative genomic approach, we identified a 14-gene region (approximately 40 kb) that is nearly identical between the 2 varieties that resulted from a nonreciprocal transfer event from var. grubii to var. neoformans approximately 2 MYA. The majority of clinical and environmental var. neoformans strains from around the world contain this sequence obtained from var. grubii. This introgression event likely occurred via an incomplete intervarietal sexual cycle, creating a hybrid intermediate where mobile elements common to both lineages mediated the exchange. The subsequent duplication in laboratory strains of a fragment of this same genomic region supports evolutionary theories that instabilities in subtelomeric regions promote adaptive evolution through gene amplification and subsequent adaptation. Along with a more ancient predicted transfer event in C. neoformans and a recently reported example from Saccharomyces cerevisiae, these data indicate that DNA exchange between closely related sympatric varieties or species may be a recurrent theme in the evolution of fungal species. It further suggests that although evolutionary divergence is the primary force driving speciation, rare introgression events also play a potentially important role.

Chromosome Mapping↗

[The morphological and ontogenetic changes in the Protozoa during the transition to a sessile mode of life].

The morphological adaptations of protozoans to sessile mode life and evolutionary changes in ontogeny are considered. There are main morphotypes of sessile protists: stalked organisms that attached to substrate by the extended base of body (basal disk), and unstalked organisms that are flatted on substrate. The origin of the morphotypes was independent in different taxa and involved nonhomologous structures. Adaptation to the sessile mode of life in the protists was connected with the progressive increase in the body size and intensity of organelle functions by polymerisation, subsequent division of function and change of functions. Evolution of adhesive organelles is characterised by growing intensity of their functions by allometric growth (usually without polymerisation), and in some cases with the subsequent division of functions and change of functions. The evolution manifests itself primarily in the organelles that provide interaction of cell with environment. The organelles that ensuring functioning of cell change due to correlations with the organelles of the first group. These two groups of organelles are similar to A.N. Sewertsoff's ecto- and endosomatic organs in multicellular organisms. The ontogeny of the sessile protists included three stages: formation of the migratory stage, distribution and choice of substrate and metamorphosis of the migratory stage after adhesion. As a rule there are no recapitulations on the first stage. The majority of structures tomotes or zoospores are inherited from the parent cell. Thus the present of some ancestral characteristics at the earlier stages of protistean ontogeny is display of the Baer's law. The main features of ontogeny evolution in sessile protists are the anaboly of the additional stages of life cycle, the displays of archallaxis or deviation during the migratory stage formation, and anaboly at the stage of buds morphogenesis after adhesion. At the last stage, the study of recapitulations is most perspective with the decision of phylogenetic problems in sessile protists.

Adaptation, Physiological↗

A novel evolutionary drug scheduling model in cancer chemotherapy.

In this paper, we introduce a modified optimal control model of drug scheduling in cancer chemotherapy and a new adaptive elitist-population-based genetic algorithm (AEGA) to solve it. Working closely with an oncologist, we first modify the existing model, because its equation for the cumulative drug toxicity is inconsistent with medical knowledge and clinical experience. To explore multiple efficient drug scheduling policies, we propose a novel variable representation--a cycle-wise representation, and modify the elitist genetic search operators in the AEGA. The simulation results obtained by the modified model match well with the clinical treatment experiences, and can provide multiple efficient solutions for oncologists to consider. Moreover, it has been shown that the evolutionary drug scheduling approach is simple, and capable of solving complex cancer chemotherapy problems by adapting multimodal versions of evolutionary algorithms.

Algorithms↗

The evolutionary origin of cooperators and defectors.

Coexistence of cooperators and defectors is common in nature, yet the evolutionary origin of such social diversification is unclear. Many models have been studied on the basis of the assumption that benefits of cooperative acts only accrue to others. Here, we analyze the continuous snowdrift game, in which cooperative investments are costly but yield benefits to others as well as to the cooperator. Adaptive dynamics of investment levels often result in evolutionary diversification from initially uniform populations to a stable state in which cooperators making large investments coexist with defectors who invest very little. Thus, when individuals benefit from their own actions, large asymmetries in cooperative investments can evolve.

Altruism↗

Time-dependent random walks and the theory of complex adaptive systems.

Motivated by novel results in the theory of complex adaptive systems, we analyze the dynamics of random walks in which the jumping probabilities are time dependent. We determine the survival probability in the presence of an absorbing boundary. For an unbiased walk, the survival probability is maximized in the case of large temporal oscillations in the jumping probabilities. On the other hand, a random walker who is drifted towards the absorbing boundary performs best with a constant jumping probability. We use the results to reveal the underlying dynamics responsible for the phenomenon of self-segregation and clustering observed in the evolutionary minority game.

Adaptation, Biological↗

Possible constraints on adaptive variation in sex ratio at birth in humans and other primates.

There is general agreement that adaptive variation of sex ratio at birth has not been decisively demonstrated in primates (including human beings). So some workers have questioned whether it actually exists. Others have conjectured that it exists but is subject to as yet unidentified 'constraints' (factors opposing the modifying influences of selection in the phenotype). Meanwhile though most workers have called for research to reveal the proximate causes of sex ratio variation, few (if any) have directed studies toward that end. Here it is argued that hormonal action is responsible both for much adaptive and non-adaptive sex ratio variation, and for constraints on the adaptive variation. My hypothesis proposes that levels of steroid hormones (testosterone and oestrogen) of both parents around the time of conception are positively associated with offspring sex ratio (proportion male at birth) of mammals including man. Testosterone in men and oestrogen in women are also known to be positively associated with the health, attractiveness and fertility of individual human beings. However, high levels of testosterone in women are frequently associated with adverse medical conditions. It is suggested that for these reasons (and contrary to some adaptive theory) some classes of people (particularly women) in suboptimal health ("condition") produce excesses of sons. It seems that gonadal hormones are responsible for adaptive variation; and that maternal adrenal hormones are responsible for maladaptive variation. In evolutionary terms, gonadal hormones precede adrenal hormones.

Adaptation, Physiological↗

Molecular evolution of vertebrate visual pigments.

Dramatic improvement of our understanding of the genetic basis of vision was brought by the molecular characterization of the bovine rhodopsin gene and the human rhodopsin and color opsin genes (Nathans and Hogness, 1983; Nathans et al., 1984, 1986a,b). The availability of cDNA clones from these studies has facilitated the isolation of retinal and nonretinal opsin genes and cDNA clones from a large variety of species. Today, the number of genomic and cDNA clones of opsin genes isolated from different vertebrate species exceeds 100 and is increasing rapidly. The opsin gene sequences reveal the importance of the origin and differentiation of various opsins and visual pigments. To understand the molecular genetic basis of spectral tuning of visual pigments, it is essential to establish correlations between a series of the sequences of visual pigments and their lambda(max) values. The potentially important amino acid changes identified in this way have to be tested whether they are in fact responsible for the lambda(max)-shifts using site-directed mutagenesis and cultured cells. A major goal of molecular evolutionary genetics is to understand the molecular mechanisms involved in functional adaptations of organisms to different environments, including the mechanisms of the regulation of the spectral absorption. Therefore, both molecular evolutionary analyses of visual pigments and vision science have an important common goal.

Animals↗

Adaptation to seasonal drought in Arabis alpina is linked to the demographic history and climatic changes since the last glacial maximum.

Understanding how species adapt to new environments is a central goal in evolutionary biology, and a topical question in climate change research. Here, we sequenced the genomes of 426 individuals of the perennial, Arctic-alpine herb Arabis alpina to study demography and adaptation, with a focus on populations in Northern Spain, that experience warm and dry summers. Our inference supports a scenario in which A. alpina colonized Northern Spain in a range expansion event that started near the Alps around 216 thousand years ago (kya). During the last glacial episode (115 to 12 kya), this expansion proceeded westward, and effective population sizes were large across Europe, likely due to a larger suitable habitat for A. alpina. These ancient demographic events gave rise to a highly diverged genetic lineage in Northern Spain. In the present interglacial (between 12 kya and present), populations became increasingly fragmented, and lost genetic diversity across Europe. Furthermore, we detected signatures of selection at genes associated with responses to abiotic stress, including drought stress, and regulation of growth, for instance at SC5D and NAC055, which reflects the climatic changes since the last glacial period. Notably, an ancient polymorphism at the gene FRL1 emerged as a candidate for conferring variation in flowering behavior, and for contributing to adaptation to drought. Our study suggests that the combination of ancestral variation in flowering behavior, and positive selection on new mutations involved in drought responses, underlies the evolution of a new trait syndrome, and adaptation to climate change.

Droughts↗

Insights into salt adaptation from comparative genomics of Scirpus mariqueter and a related freshwater species.

The evolutionary mechanisms underlying ecological divergence between closely related species remain a central question in biology. Scirpus mariqueter is a coastal halophyte thriving in the saline intertidal zone and exhibits marked adaptive differences compared to its freshwater relative Bolboschoenus planiculmis. However, the genomic and physiological bases of its salt tolerance remain poorly understood. We generated high-quality genome assemblies for both species and investigated the anatomical and physiological innovations underpinning S. mariqueter's adaptation to extreme environments. Morphological analyses revealed that S. mariqueter evolved specialized traits-including denser leaf palisade tissues, enhanced stem aerenchyma, and compact root cortices-synergistically limiting salt intrusion. Using chromosome-level genomes, we identified lineage-specific expansions in S. mariqueter of gene families critical for salinity tolerance, including those regulating carbohydrate metabolism, photosynthetic fidelity, and reactive oxygen species (ROS) detoxification. Strikingly, germin-like protein (GLP) and wound-induced protein (WIP) families contain tandem repeats mediating ROS scavenging and cell wall integrity, underwent adaptive expansion, paralleling anatomical innovations. Physiological profiling under salt stress confirmed S. mariqueter's unique capacity to maintain photosynthetic activity and carbohydrate production, directly linking genomic adaptations to functional resilience. This study reveals an adaptive strategy whereby structural modifications, diversification of stress-responsive gene families, and metabolic stability collectively enable S. mariqueter to thrive in saline ecosystems.

Salt Tolerance↗

Radiation hormesis: an evolutionary expectation and the evidence.

Fundamental to evolutionary biology is the tendency for organisms to become progressively adapted to those environments to which they are most frequently exposed. Since background radiation is a universal component of our environment, radiation hormesis is an evolutionary expectation. Whole-of-life experiments and more numerous (and evolutionarily more artificial) shorter duration and higher dose-rate experiments are consistent with this expectation. Additional research is needed especially at the molecular level to search for underlying mechanisms, and implications for radiation protection guidelines need to be analyzed.

Adaptation, Physiological↗

Evolutionary conflicts of interest between males and females.

Sexual conflict arises from differences in the evolutionary interests of males and females and can occur over traits related to courtship, mating and fertilisation through to parental investment. Theory shows that sexual conflict can lead to sexually antagonistic coevolution (SAC), where adaptation in one sex can lead to counter-adaptation in the other. Thus, sexual conflict can lead to evolutionary change within species. In addition, SAC can--through its effects on traits related to the probability of mating and of zygote formation--potentially lead to reproductive isolation. In this review, I discuss that, although sexual conflict is ubiquitous, the actual expression of sexual conflict leading to SAC is less frequent. The balance between the benefits and costs of the manipulation of one sex by the other, and the availability of mechanisms by which conflict is expressed, determine whether actual sexual conflict is likely to occur. New insights address the relationship between sexual conflict and conflict resolution, adaptation, sexual selection and fitness. I suggest that it will be useful to examine systematically the parallels and contrasts between sexual and other evolutionary conflicts. Understanding why some traits, but not others, are subject to evolutionary change by SAC will require data on the mechanisms of the traits involved and on the relative benefits and costs of manipulation and resistance to manipulation.

Animals↗

An investigation into the role of phenotypic plasticity in evolution.

Phenotypic plasticity can modify evolutionary pathways and accelerate the course of evolution. This was brought out in a quantitative model by Hinton & Nowlan (1987, Complex Systems 1, 497-502). The present work confirms and extends their results. We consider a population of genetically haploid individuals of fixed size. Genotypes are represented by one-dimensional arrays (strings) of genes. Each gene can be in one of three allelic states, designated 1, 0 and X. 1 and 0 stand for fixed states, that is for states with predetermined effects on the phenotype. X stands for a plastic state: the phenotypic effect of an X can be equivalent to that of a 1 or a 0, the actual choice being realized by a process of random coin-tossing. Our model, in contrast to that of Hinton and Nowlan, assumes a relatively smooth dependence of fitness on distance from a pre-assigned target genotype. From the fitness values, the number of individuals reaching reproductive maturity is determined. Reproduction involves random mating and a single recombinational event, with one of the two progeny genotypes becoming, in turn, a possible parental genotype for the next generation. We find that it is because of the special assumptions in the Hinton and Nowlan model that phenotypic plasticity invariably accelerates evolution. The relationship is not as straightforward with realistic fitness schemes. Instead, the general result is that plasticity, up to a certain optimal level, slows down the rate of evolutionary change but improves the level of adaptation finally reached.

Adaptation, Physiological↗

Identification of crystalline allantoin in the urine of African Cricetidae (Rodentia) and its role in their water economy.

All eleven cricetid species, examined in this investigation, produced an off-white crystalline precipitate in their urine when deprived of water, whereas not one murid examined did so. This crystalline compound was identified as allantoin, a common end product of purine catabolism. The quantity found in the solid precipitate alone accounted for 47% of the total nitrogen excreted and was approximately 14 times greater than the predicted quantity of allantoin from purine degradation. It appears that there is a shift in nitrogen excretion from urea to allantoin in the Cricetidae. Water-deprived cricetids had higher urine osmolalities, urea concentrations and lower daily percentage body water turnovers than the murids. This can be explained by the substantial water savings associated with excreting solid allantoin. The discrepancy in the mode of nitrogen excretion between the two families inhabiting the Namib Desert can be attributed to their different evolutionary histories, the Cricetidae being pre-adapted for survival in deserts.

Adaptation, Physiological↗

Genetic variability and ecological adaptability of hypopus formation in a stored product mite.

Occurrence in Lepidoglyphus destructor of a facultative developmental stage (hypopus) adapted for dispersal and dormancy depends on genotype X environment interaction. Dietary factors affect hypopus formation, but the response of individuals to food quality greatly differs according to genotype. Large genetic variation in the control of hypopus formation exists within as well as between populations. Response to selection is rapid and reversible. The trait has substantial potential for selective adaptation to unpredictably varying environments and for evolutionary change.

Animals↗

The return of the whole organism.

The long trend towards analysis at lower and lower levels is starting to reverse. The new integrative studies must make use of the resources uncovered by molecular biology but should also use the characteristics of whole organisms to measure the outcomes of developmental processes. Two examples are given of how movement between levels of analysis is being used with increasing power and promise. The first is the study of behavioural imprinting in birds where many of the molecular and neural mechanisms involved have been uncovered and are now being integrated to explain the behaviour of the whole animal. The second is the triggering during sensitive periods in early life by environmental events of one of several alternative modes of development leading to different phenotypes. A renewed focus on the whole organism is also starting to change the face of evolutionary biology. The decision-making and adaptability of the organism is recognized an important driver of evolution and is increasingly seen as an alternative to the gene-focused views.

Adaptation, Physiological↗

Eggs-only diet: its implications for the toxin profile changes and ecology of the marbled sea snake (Aipysurus eydouxii).

Studies so far have correlated the variation in the composition of snake venoms with the target prey population and snake's diet. Here we present the first example of an alternative evolutionary link between venom composition and dietary adaptation of snakes. We describe a dinucleotide deletion in the only three finger toxin gene expressed in the sea snake Aipysurus eydouxii (Marbled Sea Snake) venom and how it may have been the result of a significant change in dietary habits. The deletion leads to a frame shift and truncation with an accompanying loss of neurotoxicity. Due to the remarkable streamlining of sea snake venoms, a mutation of a single toxin can have dramatic effects on the whole venom, in this case likely explaining the 50- to 100-fold decrease in venom toxicity in comparison to that of other species in the same genus. This is a secondary result of the adaptation of A. eydouxii to a new dietary habit--feeding exclusively on fish eggs and, thus, the snake no longer using its venom for prey capture. This was parallel to greatly atrophied venom glands and loss of effective fangs. It is interesting to note that a potent venom was not maintained for use in defense, thus reinforcing that the primary use of snake venom is for prey capture.

Amino Acid Sequence↗