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PubMed1990

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↗
PubMed1993

Structural and evolutionary relationships between two families of bacterial extracytoplasmic chaperone proteins which function cooperatively in fimbrial assembly.

Gram-negative purple bacteria possess pairs of extracytoplasmic, ATP-independent, fimbrium-specific chaperone proteins which cooperatively function in the assembly of this extracellular organelle. The two non-homologous families of these proteins have been termed "Fimbrial chaperone family no. 1" (FCF1) and "Fimbrial chaperone family no. 2" (FCF2). The eleven sequenced or partially sequenced members of each of these two protein families were analysed. Their sequences were multiply aligned, and average similarity and hydropathy plots were generated. Statistical analyses of the sequences revealed that the short FCF1 proteins (of about 240 residues) have been better conserved through evolutionary time than have the much larger FCF2 proteins (of about 830 residues). Moreover, the N-terminal thirds of the FCF2 proteins are better conserved than the central or C-terminal thirds of these proteins. Phylogenetic tree construction revealed that, in general, the two proteins which cooperate in the assembly of a particular fimbrial type have similar positions on their respective phylogenetic trees, suggesting that the two proteins evolved in parallel as a functional unit. Two exceptions were noted, however. In one case, a hybrid protein appears to have arisen, possibly by genetic recombination. In another case, the two proteins of a particular pair may have evolved separately and come together late in the evolutionary process to provide their cooperative function.

Amino Acid Sequence↗
PubMed2005

An optimized experimental protocol based on neuro-evolutionary algorithms application to the classification of dyspeptic patients and to the prediction of the effectiveness of their treatment.

OBJECTIVE: This paper aims to present a specific optimized experimental protocol (EP) for classification and/or prediction problems. The neuro-evolutionary algorithms on which it is based and its application with two selected real cases are described in detail. The first application addresses the problem of classifying the functional (FD) or organic (OD) forms of dyspepsia; the second relates to the problem of predicting the 6-month follow-up outcome of dyspeptic patients treated by helicobacter pylori (HP) eradication therapy. METHODS AND MATERIAL: The database built by the multicentre observational study, performed in Italy by the NUD-look Study Group, provided the material studied: a collection of data from 861 patients with previously uninvestigated dyspepsia, being referred for upper gastrointestinal endoscopy to 42 Italian Endoscopic Services. The proposed EP makes use of techniques based on advanced neuro-evolutionary systems (NESs) and is structured in phases and steps. The use of specific input selection (IS) and training and testing (T and T) techniques together with genetic doping (GenD) algorithm is described in detail, as well as the steps taken in the two benchmark and optimization protocol phases. RESULTS: In terms of accuracy results, a value of 79.64% was achieved during optimization, with mean benchmark values of 64.90% for the linear discriminant analysis (LDA) and 68.15% for the multi layer perceptron (MLP), for the classification task. A value of 88.61% was achieved during optimization for the prediction task, with mean benchmark values of 49.32% for the LDA and 70.05% for the MLP. CONCLUSIONS: The proposed EP has led to the construction of inductors that are viable and usable on medical data which is representative but highly not linear. In particular, for the classification problem, these new inductors may be effectively used on the basal examination data to support doctors in deciding whether to avoid endoscopic examinations; whereas, in the prediction problem, they may support doctors' decisions about the advisability of eradication therapy. In both cases the variables selected indicate the possibility of reducing the data collection effort and also of providing information that can be used for general investigations on symptom relevance.

Algorithms↗
PubMed2004

The evolutionary development of the protein complement of photosystem 2.

During the transition from anoxygenic to oxygenic photosynthesis, the Type 2 reaction center underwent many changes, none so dramatic as the remarkable increase in complexity at the protein level, from only three or four subunits in the anoxygenic reaction center to possibly more than 25 in Photosystem 2 (PS2). The evolutionary source of most of these proteins is enigmatic, as they have no apparent homology to any other proteins in existing databases. However, some of the proteins in PS2 have apparent homologies to each other, suggesting ancient gene duplications have played an important role in the development of the complex. These homologies include the well-known examples of the D1 and D2 reaction center core proteins and the CP43 and CP47 core antenna proteins. In addition, PsbE and PsbF, the two subunits comprising cytochrome b-559, show homology to each other, suggesting that a homodimeric cytochrome preceded the heterodimeric one. Other potential homologies that appear to be statistically significant include PsbV with the N-terminal part of D1 and PsbT with PsbI. Most of the proteins that make up the photosynthetic apparatus bear no relation to any other proteins from any source. This suggests that a period of remarkable evolutionary innovation took place when the ability to make oxygen was invented. This was probably a response to the production of highly toxic oxygen and these new proteins served to protect and repair the photosynthetic apparatus from the harmful effects of oxygen.

Cyanobacteria↗
PubMed2005

Identification of an evolutionary conserved SURF-6 domain in a family of nucleolar proteins extending from human to yeast.

The mammalian SURF-6 protein is localized in the nucleolus, yet its function remains elusive in the recently characterized nucleolar proteome. We discovered by searching the Protein families database that a unique evolutionary conserved SURF-6 domain is present in the carboxy-terminal of a novel family of eukaryotic proteins extending from human to yeast. By using the enhanced green fluorescent protein as a fusion protein marker in mammalian cells, we show that proteins from distantly related taxonomic groups containing the SURF-6 domain are localized in the nucleolus. Deletion sequence analysis shows that multiple regions of the SURF-6 protein are capable of nucleolar targeting independently of the evolutionary conserved domain. We identified that the Saccharomyces cerevisiae member of the SURF-6 family, named rrp14 or ykl082c, has been categorized in yeast databases to interact with proteins involved in ribosomal biogenesis and cell polarity. These results classify SURF-6 as a new family of nucleolar proteins in the eukaryotic kingdom and point out that SURF-6 has a distinct domain within the known nucleolar proteome that may mediate complex protein-protein interactions for analogous processes between yeast and mammalian cells.

Amino Acid Sequence↗
PubMed2004

Observability in dynamic evolutionary models.

In the paper observability problems are considered in basic dynamic evolutionary models for sexual and asexual populations. Observability means that from the (partial) knowledge of certain phenotypic characteristics the whole evolutionary process can be uniquely recovered. Sufficient conditions are given to guarantee observability for both sexual and asexual populations near an evolutionarily stable state.

Animals↗
PubMed2005

Evolutionary history of the retinoblastoma gene from archaea to eukarya.

The retinoblastoma gene product (Rb protein) has a role in progression through the cell cycle, regulating the activities of several transcription factors such as E2F. Since its functional loss results in impaired differentiation in the nervous, hematopoietic, and muscular systems, the Rb protein is very important for cell regulation in multicellular eukaryotes. To gain an insight into the evolutionary history of the Rb gene, I have compared the amino acid sequences of Rb proteins in multicellular eukaryotes and unicellular organisms including yeast, archaeotes, and viruses. Two short amino acid sequences, in the N-terminal and pocket A regions of human Rb protein, found to be well conserved, also in a single protein of Saccharomyces cerevisiae. These sequences were also found in proteins of two archaeotes, Archaeoglobus fulgidus and Methanococcus jannaschii. Further, the most conserved sequence in the pocket B region among multicellular eukaryotic Rb proteins was also conserved in several poxviruses. From these data, I conclude that the pocket A and B regions, backbones of the Rb protein, are derived from different organisms, respectively, the ancestors of archaeote and poxvirus, and that the ancestral pocket B region has been lost during evolutionary history of unicellular eukaryotes.

Amino Acid Sequence↗
PubMed2006

Improving the efficiency of evolutionary de novo peptide design: strategies for probing configuration and parameter settings.

Evolutionary molecular design based on genetic algorithms (GAs) has been demonstrated to be a flexible and efficient optimization approach with potential for locating global optima. Its efficacy and efficiency are largely dependent on the operations and control parameters of the GAs. Accordingly, we have explored new operations and probed good parameter setting through simulations. The findings have been evaluated in a helical peptide design according to "Parameter setting by analogy" strategy; highly helical peptides have been successfully obtained with a population of only 16 peptides and 5 iterative cycles. The results indicate that new operations such as multi-step crossover-mutation are able to improve the explorative efficiency and to reduce the sensitivity to crossover and mutation rates (CR-MR). The efficiency of the peptide design has been furthermore improved by setting the GAs at the good CR-MR setting determined through simulation. These results suggest that probing the operations and parameter settings through simulation in combination with "Parameter setting by analogy" strategy provides an effective framework for improving the efficiency of the approach. Consequently, we conclude that this framework will be useful for contributing to practical peptide design, and gaining a better understanding of evolutionary molecular design.

Algorithms↗
PubMed2004

Thermodynamical interpretation of evolutionary dynamics on a fitness landscape in a evolution reactor, I.

A theory for describing evolution as adaptive walks by a finite population with M walkers (M > or = 1) on an anisotropic Mt. Fuji-type fitness landscape is presented, from a thermodynamical point of view. Introducing the 'free fitness' as the sum of a fitness term and an entropy term and 'evolutionary force' as the gradient of free fitness on a fitness coordinate, we demonstrate that the behavior of these theoretical walkers is almost consistent with the thermodynamical schemes. The major conclusions are as follows: (1) an adaptive walk (=evolution) is driven by an evolutionary force in the direction in which free fitness increases; (2) the expectation of the climbing rate obeys an equation analogous to the Einstein relation in Brownian motion; (3) the standard deviation of the climbing rate is a quantity analogous to the mean thermal energy of a particle, kT (x constant). In addition, on the interpretation that the walkers climb the landscape by absorbing 'fitness information' from the surroundings, we succeeded in quantifying the fitness information and formulating a macroscopic scheme from an informational point of view.

Adaptation, Biological↗
PubMed2004

Evolutionary game dynamics in finite populations.

We introduce a model of stochastic evolutionary game dynamics in finite populations which is similar to the familiar replicator dynamics for infinite populations. Our focus is on the conditions for selection favoring the invasion and/or fixation of new phenotypes. For infinite populations, there are three generic selection scenarios describing evolutionary game dynamics among two strategies. For finite populations, there are eight selection scenarios. For a fixed payoff matrix a number of these scenarios can occur for different population sizes. We discuss several examples with unexpected behavior.

Biological Evolution↗
PubMed2005

Evolutionary and mechanistic relationships between glycosidases acting on alpha- and beta-bonds.

Because of the fast accumulation of sequences derived from genome sequencing efforts, the sampling of the sequence space in glycosidase and related enzyme families is such that sensitive sequence similarity detection methods like PSI-BLAST are now able to reveal distant, but clear, structural and evolutionary relations between glycosidases acting on alpha- and beta-bonds. We have observed this trend within groups of glycosidases with completely different folds. We postulate that the evolutionary interconversion between alpha- and beta-acting glycosidases was greatly facilitated by the fact that both types share a similar axial orientation of the glycosidic bond in the reactive bound substrate. Glycosides in the beta anomeric configuration, require a sugar ring distortion, resulting in an axial orientation of the glycosidic bond, equivalent to that of an alpha glycosidic bond, prior to displacement by nucleophilic substitution.

Evolution, Molecular↗
PubMed2026

Epitranscriptomic erasers in bivalves: Evolutionary divergence and species-specific transcriptional plasticity of the ALKBH family under acute thermal stress.

The AlkB homolog (ALKBH) family of Fe(II)/α-ketoglutarate-dependent dioxygenases mediates nucleic acid demethylation, thereby governing RNA metabolism and genomic stability. Despite their pivotal roles in epitranscriptomic regulation across vertebrates, the evolutionary dynamics and functional significance of ALKBH proteins in bivalve mollusks remain largely unexplored. Here, we present a comprehensive phylogenomic analysis of 210 ALKBH genes identified across 35 bivalve species. Our analyses reveal a distinct evolutionary trajectory characterized by the lineage-specific loss of ALKBH4 and the restricted distribution of ALKBH5 to the Mytilidae family, contrasting sharply with vertebrate repertoires. Using the noble scallop (Chlamys nobilis) and Pacific oyster (Crassostrea gigas) as model systems, we demonstrate that ALKBH genes exhibit conserved spatiotemporal expression patterns, with pronounced enrichment in gonadal tissues and during metamorphic transitions, implicating these enzymes in gametogenesis and larval development. Furthermore, comparative thermal stress experiments reveal divergent transcriptional plasticity: the subtropical scallop C. nobilis mounts rapid, transient induction of ALKBH1/2/6 under heat shock, whereas the eurythermal oyster C. gigas maintains sustained ALKBH3 expression, potentially underpinning its superior thermal tolerance. Conversely, cold stress elicits bimodal regulation in C. nobilis, with ALKBH1/2 upregulation contrasting with ALKBH6/7/8 suppression. These findings illuminate the functional diversification of bivalve ALKBH genes and their potential utility as molecular biomarkers for assessing developmental competence and thermal resilience in shellfish aquaculture.

Animals↗
PubMed2026

Evolutionary conservation of heat shock proteins in Blattodea and their roles in wing morphogenesis and ovarian development of Blattella germanica.

Heat shock proteins (Hsps) are essential molecular chaperones for protein homeostasis and stress responses. However, the Hsp repertoires and functions in Blattodea remain underexplored. Our genome-scale survey of nine Blattodea species revealed 37-46 conserved Hsp90, Hsp70, and DNAJ (Hsp40) genes, with DNAJ the most abundant and Hsp90 the least. Phylogenetic analysis confirmed the evolutionary conservation of three Hsp90, seven Hsp70, and 29 DNAJ subclades in Blattodea. Selection pressure analysis revealed predominant purifying selection (dN/dS ≪ 1) across lineages, strongest in DNAJ and highest in Hsp90 conservation. In Blattella germanica, expression of six representative BgHsp genes progressively increased during development, peaking in fifth-instar nymphs. Tissue expression profiling revealed that BgHspA1-2/3/4 were predominantly expressed in legs, BgDNAJB5 and BgHsp90AB1-2 were enriched in the fat body, and BgHsp90AB1 was highly expressed in the head. dsRNA injection targeting conserved Hsp gene regions achieved 61.9-94.1% knockdown of all six target genes. RNAi knockdown of six BgHsp genes disrupted wing morphogenesis, causing distinct phenotypes: wing whitening (56.7%, dsBgHspA1-4), unequal length (66.7%, dsBgHspA1-3; 76.7%, dsBgDNAJB5), and wing wrinkling (70%, dsBgHspA1-2; 63.3%, dsBgHsp90AB1; 76.7%, dsBgHsp90AB1-2). During ovarian formation, the developmental delay was most severe in the dsBgHsp90AB1 group, moderate in the dsBgHsp90AB1-2 and dsBgHspA1-2/3/4 groups, and weakest in the dsBgDNAJB5 group. Besides, knockdown significantly downregulated key developmental genes (apterous-a, nubbin, scalloped, ultrabithorax, wingless, and vitellogenin). These findings provide a reference for understanding the evolutionary patterns of Hsps in Blattodea, and offer mechanistic insights into the developmental regulation mediated by Hsps in this important public-health pest.

Animals↗
PubMed2026

Evolutionary characterization and expression profiling of ACC and FASN genes in Chinese mitten crab Eriocheir sinensis.

Acetyl-CoA carboxylase (ACC) and fatty acid synthase (FASN) are rate-limiting enzymes in the fatty acid biosynthetic pathway, yet their evolutionary relationships, sequence features, and expression profiles remain poorly understood in crustaceans, particularly in the economically important Chinese mitten crab (Eriocheir sinensis). Here, we identified and systematically analyzed ACC and FASN genes in E. sinensis using comparative genomic analyses across 43 species. ACC was highly conserved as a single-copy gene in invertebrates, in contrast to the multiple paralogs observed in vertebrates. Similarly, FASN was generally maintained as a single-copy gene across most taxa but exhibited lineage-specific expansion in certain insect groups. Phylogenetic and structural analysis revealed strong conservation of both genes within crustaceans, supported by multiple conserved motifs and canonical functional domains. Expression profiling showed predominant expression in the hepatopancreas and midgut, suggesting their potential involvement in crustacean lipid metabolism. During the molting cycle, ACC and FASN exhibited higher expression levels during stages C and D, suggesting an increased capacity for fatty acid biosynthesis before molting. In addition, dietary lipid levels experiment revealed that ACC and FASN expression responded dynamically to dietary lipid availability, with increased expression at moderate lipid levels but reduced expression under excessive lipid supplementation, indicating a possible adaptive transcriptional response to lipid status. Collectively, this study provides insights into the evolutionary conservation and expression dynamics of ACC and FASN and improves our understanding of lipid metabolic adaptation in crustaceans.

Animals↗
PubMed2006

Structural and molecular evolutionary analysis of Agouti and Agouti-related proteins.

Agouti (ASIP) and Agouti-related protein (AgRP) are endogenous antagonists of melanocortin receptors that play critical roles in the regulation of pigmentation and energy balance, respectively, and which arose from a common ancestral gene early in vertebrate evolution. The N-terminal domain of ASIP facilitates antagonism by binding to an accessory receptor, but here we show that the N-terminal domain of AgRP has the opposite effect and acts as a prodomain that negatively regulates antagonist function. Computational analysis reveals similar patterns of evolutionary constraint in the ASIP and AgRP C-terminal domains, but fundamental differences between the N-terminal domains. These studies shed light on the relationships between regulation of pigmentation and body weight, and they illustrate how evolutionary structure function analysis can reveal both unique and common mechanisms of action for paralogous gene products.

Agouti Signaling Protein↗
PubMed2004

Scale-free networks versus evolutionary drift.

Recent studies of properties of various biological networks revealed that many of them display scale-free characteristics. Since the theory of scale-free networks is applicable to evolving networks, one can hope that it provides not only a model of a biological network in its current state but also sheds some insight into the evolution of the network. In this work, we investigate the probability distributions and scaling properties underlying some models for biological networks and protein domain evolution. The analysis of evolutionary models for domain similarity networks indicates that models which include evolutionary drift are typically not scale free. Instead they adhere quite closely to the Yule distribution. This finding indicates that the direct applicability of scale-free models in understanding the evolution of biological network may not be as wide as it has been hoped for.

Computational Biology↗
PubMed2005

Evolutionary pressures and a stable world for animals and robots: a commentary on Merker.

In his article on The Liabilities of Mobility, asserts that "Consciousness presents us with a stable arena for our actions-the world ..." and argues for this property as providing evolutionary pressure for the evolution of consciousness. In this commentary, I will explore the implications of Merker's ideas for consciousness in artificial agents as well as animals, and also meet some possible objections to his evolutionary pressure claim.

Animals↗
PubMed2006

Passing thoughts on the evolutionary stability of implicit motor behaviour: performance retention under physiological fatigue.

Heuristics of evolutionary biology (e.g., survival of the fittest) dictate that phylogenetically older processes are inherently more stable and resilient to disruption than younger processes. On the grounds that non-declarative behaviour emerged long before declarative behaviour, Reber (1992) argues that implicit (non-declarative) learning is supported by neural processes that are evolutionarily older than those supporting explicit learning. Reber suggested that implicit learning thus leads to performance that is more robust than explicit learning. Applying this evolutionary framework to motor performance, we examined whether implicit motor learning, relative to explicit motor learning, conferred motor output that was resilient to physiological fatigue and durable over time. In Part One of the study a fatigued state was induced by a double Wingate Anaerobic test protocol. Fatigue had no affect on performance of participants in the implicit condition; whereas, performance of participants in the explicit condition deteriorated significantly. In Part Two of the study a convenience sample of participants was recalled following a one-year hiatus. In both the implicit and the explicit condition retention of performance was seen and, contrary to the findings in Part One, so was resilience to fatigue. The resilient performance in the explicit condition after one year may have resulted from forgetting (the decay of declarative knowledge) or from consolidation of declarative knowledge as implicit memories. In either case, implicit processes were left to more effectively support motor performance.

Adult↗