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PubMed2000

Comparative respiratory morphology: themes and principles in the design and construction of the gas exchangers.

Along the evolutionary continuum, a kaleidoscope of gas exchangers has evolved from the simple cell membrane of the primeval unicells. The most momentous events in this process were: the intensification of molecular oxygen in the biosphere and its appropriation into aerobic metabolism, the rise of multicellular organisms, the development of a circulatory system and carrier pigments in blood, the advocacy of air breathing, adoption of suctional breathing, and the shift to endothermy. To satisfy species-specific needs for oxygen, some constraints were overcome through transactions that obliged certain compromises and trade-offs. Optimal designs of the gas exchangers for particular phylogenetic levels of development, habitat, and lifestyle have developed only so far as to satisfy prescribed needs. The efficiency of the human lung, for example, falls well below those of certain taxa that are considered to be relatively "less advanced." Utilizing different resources and strategies, in fascinating processes of conformity, different groups of animals have developed similar respiratory structures. In most cases, the analogy reflects evolutionary convergence in response to corresponding selective pressures rather than common ancestry. Anat Rec (New Anat) 261:25-44, 2000.

Animals↗
PubMed2006

Born to bind: the BTB protein-protein interaction domain.

The BTB domain is a protein-protein interaction motif that is found throughout eukaryotes. It determines a unique tri-dimensional fold with a large interaction surface. The exposed residues are highly variable and can permit dimerization and oligomerization, as well as interaction with a number of other proteins. BTB-containing proteins are numerous and control cellular processes that range from actin dynamics to cell-cycle regulation. Here, we review findings in the field of transcriptional regulation to illustrate how the high variability of the BTB has allowed related transcription factors to evolve different functional abilities. We then report how recent work has showed that, in spite of their high sequence divergence and apparently unrelated functions, many BTB-containing proteins have at least one shared role: the recruitment of degradation targets to E3 ubiquitin ligase complexes. Taken together, these findings illustrate diverse and convergent functions of a versatile protein-protein interaction domain.

Amino Acid Sequence↗
PubMed2026

Creating bottom-up RNA transfer vehicles from synthetic protein assemblies.

Evolution guides biological systems to populate ecological niches, with viruses among the most successful examples of this principle. Viruses evolved over billions of years to efficiently transfer genetic information. Although viruses are highly diverse, most have converged towards remarkable similarity in the size and shape of their capsids1,2. By contrast, generative models for protein design enable the creation of protein architectures that are absent from nature3-5. Here we investigate whether protein assemblies designed by artificial intelligence can be functionalized to construct nucleic acid transport vehicles that are independent of evolutionary trajectories. By combining natural protein domains with synthetic protein assemblies, we create more than 100 bottom-up RNA transfer vehicles with unique sizes and shapes. These vehicles surpass the RNA transfer efficiency of widely used delivery vehicles by several orders of magnitude. In addition, we demonstrate that their tropism can be programmed by incorporation of computationally designed peptide binders and use them to deliver therapeutically relevant cargo RNAs into a wide range of cellular models. We show the in vivo biodistribution of one of these vehicles in a mouse at near-single-cell resolution, confirm its safety, and use it to perform a gene-editing treatment strategy for Duchenne muscular dystrophy in patient-derived cells and a pig. Our work demonstrates how proteins created by generative artificial intelligence can be harnessed for the rational engineering of RNA transport systems with the desired properties by overcoming the limitations of natural protein diversity.

Journal Article↗
PubMed2005

Syncytin-A and syncytin-B, two fusogenic placenta-specific murine envelope genes of retroviral origin conserved in Muridae.

Recently, we and others have identified two human endogenous retroviruses that entered the primate lineage 25-40 million years ago and that encode highly fusogenic retroviral envelope proteins (syncytin-1 and -2), possibly involved in the formation of the placenta syncytiotrophoblast layer generated by trophoblast cell fusion at the materno-fetal interface. A systematic in silico search throughout mouse genome databases presently identifies two fully coding envelope genes, present as unique copies and unrelated to any known murine endogenous retrovirus, that we named syncytin-A and -B. Quantitative RT-PCR demonstrates placenta-specific expression for both genes, with increasing transcript levels in this organ from 9.5 to 14.5 days postcoitum. In situ hybridization of placenta cryosections further localizes these transcripts in the syncytiotrophoblast-containing labyrinthine zona. Consistently, we show that both genes can trigger cell-cell fusion in ex vivo transfection assays, with distinct cell type specificities suggesting different receptor usage. Genes orthologous to syncytin-A and -B and disclosing a striking conservation of their coding status are found in all Muridae tested (mouse, rat, gerbil, vole, and hamster), dating their entry into the rodent lineage approximately 20 million years ago. Together, these data strongly argue for a critical role of syncytin-A and -B in murine syncytiotrophoblast formation, thus unraveling a rather unique situation where two pairs of endogenous retroviruses, independently acquired by the primate and rodent lineages, would have been positively selected for a convergent physiological role.

Animals↗
PubMed1998

Genetic and morphological analyses reveal a critical interaction between the C-termini of two SNARE proteins and a parallel four helical arrangement for the exocytic SNARE complex.

In a screen for suppressors of a temperature-sensitive mutation in the yeast SNAP-25 homolog, Sec9, we have identified a gain-of-function mutation in the yeast synaptobrevin homolog, Snc2. The genetic properties of this suppression point to a specific interaction between the C-termini of Sec9 and Snc2 within the SNARE complex. Biochemical analysis of interactions between the wild-type and mutant proteins confirms this prediction, demonstrating specific effects of these mutations on interactions between the SNAREs. The location of the mutations suggests that the C-terminal H2 helical domain of Sec9 is likely to be aligned in parallel with Snc2 in the SNARE complex. To test this prediction, we examined the structure of the yeast exocytic SNARE complex by deep-etch electron microscopy. Like the neuronal SNARE complex, it is a rod approximately 14 nm long. Using epitope tags, antibodies and maltose-binding protein markers, we find that the helical domains of Sso, Snc and both halves of Sec9 are all aligned in parallel within the SNARE complex, suggesting that the yeast exocytic SNARE complex consists of a parallel four helix bundle. Finally, we find a similar arrangement for SNAP-25 in the neuronal SNARE complex. This provides strong evidence that the exocytic SNARE complex is a highly conserved structure composed of four parallel helical domains whose C-termini must converge in order to bring about membrane fusion.

Amino Acid Sequence↗
PubMed1999

Traces and determinants of strongly stochastic operators.

Periodic orbit theory allows calculations of long-time properties of chaotic systems from traces, dynamical zeta functions, and spectral determinants of deterministic evolution operators, which are in turn evaluated in terms of periodic orbits. For the case of stochastic dynamics a direct numerical evaluation of the trace of an evolution operator is possible as a multidimensional integral. Techniques for evaluating such path integrals are discussed. Using as an example the logistic map f(x)=lambdax(1-x) with moderate to strong additive Gaussian noise, rapid convergence is demonstrated for all values of lambda with strong noise as well as at fixed lambda=5 for all noise levels.

Journal Article↗
PubMed2001

Convergence in evolutionary programs with self-adaptation.

Evolutionary programs are capable of finding good solutions to difficult optimization problems. Previous analysis of their convergence properties has normally assumed the strategy parameters are kept constant, although in practice these parameters are dynamically altered. In this paper, we propose a modified version of the 1/5-success rule for self-adaptation in evolution strategies (ES). Formal proofs of the long-term behavior produced by our self-adaptation method are included. Both elitist and non-elitist ES variants are analyzed. Preliminary tests indicate an ES with our modified self-adaptation method compares favorably to both a non-adapted ES and a 1/5-success rule adapted ES.

Algorithms↗
PubMed2006

A novel approach to phylogenetic tree construction using stochastic optimization and clustering.

BACKGROUND: The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology. RESULTS: A new phylogenetic tree construction method from a given set of objects (proteins, species, etc.) is presented. As an extension of ant colony optimization, this method proposes an adaptive phylogenetic clustering algorithm based on a digraph to find a tree structure that defines the ancestral relationships among the given objects. CONCLUSION: Our phylogenetic tree construction method is tested to compare its results with that of the genetic algorithm (GA). Experimental results show that our algorithm converges much faster and also achieves higher quality than GA.

Algorithms↗
PubMed2000

[Concomitant radiochemotherapy in cancer of the cervix uteri: modifications of the standards].

For a long time, combined external irradiation and brachytherapy has been considered as the standard treatment in patients with advanced cervical cancers. Recently, five clinical randomized trials assessing the role of cis-platin-based chemotherapy delivered concomitantly to radiotherapy have been conducted in the United States. Another clinical randomized trial assessing the role of epirubicin was conducted by the Queen Mary Hospital in Hong Kong. With more than 2,000 enrolled patients, these studies showed converging results with an overall and disease-free survival improvement in the arms combining cis-platin and epirubicin-based chemotherapy and irradiation. These combinations led to a significant decrease in loco-regional evolution or recurrence rates, or even in pulmonary metastases rates. The relative risk of recurrences was decreased by 50%. The relative risk of death was decreased by 40%. The differences, however, were less significant in patients with advanced stages III or IVA. Hematological and digestive acute toxicity was significantly higher in the radiochemotherapy groups, but long-term complications were comparable. The results of these randomized trials have led to a modification in the standard of treatment in these poor prognosis cervix cancers. Five of the randomized trials evidenced the superiority of cis-platin-based chemotherapy, but the optimal chemotherapeutic regimens remain to be defined.

Adenocarcinoma↗
PubMed2004

The evolution of genes for pigmentation in African cichlid fishes.

The cichlid fishes in the East African Great Lakes exhibit a great diversity of color patterns, presumably as adaptations to species-specific habitats and/or due to the action of sexual selection on color for species discrimination or female mate choice. To elucidate the mechanisms underlying such pigment pattern diversity, we cloned the cichlid homologs of tyrosinase, endothelin receptor b1, mitf, and Aim1 that previously had been cloned and characterized from pigmentation mutants of zebrafish and medaka fish. Gene sequence analysis among five cichlid species from the Great Lakes shows that the evolutionary rate of amino acid replacement in mitf is the highest of these four genes. We then compared the mitf amino acid replacement rates between species from the lacustrine and tilapiine/steatocranus lineages, and between Lake Malawi- and Victoria-haplochromine cichlids and Lake Tanganyika Lamprologini. We show that the evolutionary rate within the lacustrine lineage is twice that of the tilapiine/steatocranus lineage, but that rates for the Malawi-Victoria haplochromine and Lamprologini lineages are almost the same. These results suggest that the accelerated evolution of mitf might have occurred concomitantly with pigment pattern diversification in Great Lakes species, but not necessarily correlated with species under intense sexual selection on male mating color via female mate choice. Finally, we characterized a novel alternatively spliced variant of cichlid mitf that is similar to a mammalian mitf splice variant generated using alternate splice sites. We suggest that this new variant in cichlids, like that in mammals, encodes an MITF transcriptional factor having higher relative DNA binding affinity. These data provide a novel example of functional convergence in which a particular splice variant is independently generated via alternative splicing of a specific gene in different lineages.

Alternative Splicing↗
PubMed1998

Entropy evolution for the Baker map.

Gibbs entropy is invariant for the Baker map. A Jordan basis spectral decomposition of the Baker Frobenius-Perron operator suggests that any initial density evolves to the stationary density that has maximal entropy. This entropy conundrum is resolved by considering the difference between weak and strong convergence. A binary representation is used to make these points transparent. (c) 1998 American Institute of Physics.

Journal Article↗
PubMed2006

Spatially structured superinfection and the evolution of disease virulence.

When pathogen strains differing in virulence compete for hosts, spatial structuring of disease transmission can govern both evolved levels of virulence and patterns in strain coexistence. We develop a spatially detailed model of superinfection, a form of contest competition between pathogen strains; the probability of superinfection depends explicitly on the difference in levels of virulence. We apply methods of adaptive dynamics to address the interplay of spatial dynamics and evolution. The mean-field approximation predicts evolution to criticality; any small increase in virulence capable of dynamical persistence is favored. Both pair approximation and simulation of the detailed model indicate that spatial structure constrains disease virulence. Increased spatial clustering reduces the maximal virulence capable of single-strain persistence and, more importantly, reduces the convergent-stable virulence level under strain competition. The spatially detailed model predicts that increasing the probability of superinfection, for given difference in virulence, increases the likelihood of between-strain coexistence. When strains differing in virulence can coexist ecologically, our results may suggest policies for managing diseases with localized transmission. Comparing equilibrium densities from the pair approximation, we find that introducing a more virulent strain into a host population infected by a less virulent strain can sometimes reduce total host mortality and increase global host density.

Adaptation, Physiological↗
PubMed1997

Labile evolution of display traits in bowerbirds indicates reduced effects of phylogenetic constraint.

Bowerbirds (Ptilonorhynchidae) have among the most exaggerated sets of display traits known, including bowers, decorated display courts and bright plumage, that differ greatly in form and degree of elaboration among species. Mapping bower and plumage traits on an independently derived phylogeny constructed from mitochondrial cytochrome b sequences revealed large differences in display traits between closely related species and convergences in both morphological and behavioural traits. Plumage characters showed no effect of phylogenetic inertia, although bowers exhibited some constraint at the more fundamental level of design, but above which they appeared free of constraint. Bowers and plumage characters, therefore, are poor indicators of phylogenetic relationship in this group. Testing Gilliard's (1969) transferral hypothesis indicated some support for the idea that the focus of display has shifted from bird to bower in avenue-building species, but not in maypole-builders or in bowerbirds as a whole.

Animals↗
PubMed2006

A model for the evolution of paralog families in genomes.

We introduce and analyse a simple probabilistic model of genome evolution. It is based on three fundamental evolutionary events: gene loss, duplication and accumulated change. This is motivated by previous works which consisted in fitting the available genomic data into, what is called paralog distributions. This formalism is described by a system of infinite number of linear equations. We show that this system generates a semigroup of linear operators on the space l (1). We prove that size distribution of paralogous gene families in a genome converges to the equilibrium as time goes to infinity. Moreover we show that when probabilities of gene removal and duplication are close to each other, then the resulting distribution is close to logarithmic distribution. Some empirical results for yeast genomes are presented.

Evolution, Molecular↗
PubMed2004

Identification of the mammalian Not gene via a phylogenomic approach.

Despite the great morphological diversity of early embryos, the underlying mechanisms of gastrulation are known to be broadly conserved in vertebrates. However, a number of genes characterized as fulfilling an essential function in this process in several model organisms display no clear ortholog in mammalian genomes. We have devised an in silico phylogenomic approach, based on exhaustive similarity searches in vertebrate genomes and subsequent bayesian phylogenetic analyses, to identify such missing genes, presumed to be highly divergent. This approach has been used to identify mammalian orthologs of Not, an homeodomain containing gene previously characterized in Xenopus, chick and zebrafish as playing a critical role in the formation of the notochord. This attempt led to the identification of a highly divergent mammalian Not-related gene in the mouse, human and rat. The results from phylogenetic reconstructions, synteny analyses, expression pattern analyses in wild-type and mutant mouse embryos, and overexpression experiments in Xenopus embryos converge to confirm these genes as representatives of the Not family in mammals. The identification of the mammalian Not gene delivers an important component for the understanding of the genetics underlying notochord formation in mammals and its evolution among vertebrates. The phylogenomic method used to retrieve this gene thus provides a tool, which can complement or validate genome annotations in situations when they are weakly supported.

Amino Acid Sequence↗
PubMed2026

Global epidemiology, genomic evolution, and clinical implications of dual- and multiple-carbapenemase-producing Klebsiella pneumoniae: A systematic qualitative review.

BACKGROUND: The global emergence of dual- and multiple-carbapenemase-producing Klebsiella pneumoniae, particularly isolates co-harbouring blaNDM and blaOXA-48/OXA-48-like determinants, represents a critical threat to global health because of limited therapeutic options and expanding genomic complexity. METHODS: This systematic qualitative review synthesized evidence from 44 English-language peer-reviewed studies published between 2017 and 2026 and indexed in Scopus, with a focus on genomic evolution and spatiotemporal distribution. RESULTS: High-risk clones ST147, ST101, and ST11 were identified as major drivers of dissemination. Genomic analysis revealed key adaptive mechanisms, including stable IncL 96-kb fusion plasmids and IS10-mediated truncation of blaNDM-1, potentially reducing fitness costs while preserving resistance. Convergence events were also documented in which dual-carbapenemase-producing isolates acquired additional colistin resistance determinants (mcr-1 or mgrB alterations) and virulence-associated markers such as iuc1. Importantly, related resistance determinants were identified beyond hospital settings, including community, environmental, and food-associated reservoirs. CONCLUSION: The shift from single to dual and multiple carbapenemase production in K. pneumoniae underscores the need for integrated genomic surveillance, improved antimicrobial stewardship, and broader reservoir monitoring to address this evolving public health threat.

Klebsiella pneumoniae↗
PubMed2002

Do convergent developmental mechanisms underlie convergent phenotypes?

Convergence is a pervasive evolutionary process, affecting many aspects of phenotype and even genotype. Relatively little is known about convergence in developmental processes, however, nor about the degree to which convergence in development underlies convergence in anatomy. A switch in the ecology of sea urchins from feeding to nonfeeding larvae illustrates how convergence in development can be associated with convergence in anatomy. Comparisons to more distantly related taxa, however, suggest that this association may be limited to relatively close phylogenetic comparisons. Similarities in gene expression during development provide another window into the association between convergence in developmental processes and convergence in anatomy. Several well-studied transcription factors exhibit likely cases of convergent gene expression in distantly related animal phyla. Convergence in regulatory gene expression domains is probably more common than generally acknowledged, and can arise for several different reasons.

Animals↗
PubMedDate not supplied

The A/P axis in echinoderm ontogeny and evolution: evidence from fossils and molecules.

Even though echinoderms are members of the Bilateria, the location of their anterior/posterior axis has remained enigmatic. Here we propose a novel solution to the problem employing three lines of evidence: the expression of a posterior class Hox gene in the coeloms of the nascent adult body plan within the larva; the anatomy of certain early fossil echinoderms; and finally the relation between endoskeletal plate morphology and the associated coelomic tissues. All three lines of evidence converge on the same answer, namely that the location of the adult mouth is anterior, and the anterior/posterior axis runs from the mouth through the adult coelomic compartments. This axis then orients the animal such that there is but a single plane of symmetry dividing the animal into left and right halves. We tentatively hypothesize that this plane of symmetry is positioned along the dorsal/ventral axis. These axis identifications lead to the conclusion that the five ambulacra are not primary body axes, but instead are outgrowths from the central anterior/posterior axis. These identifications also shed insight into several other evolutionary mysteries of various echinoderm clades such as the independent evolution of bilateral symmetry in irregular echinoids, but do not elucidate the underlying mechanisms of the adult coelomic architecture.

Animals↗