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PubMed2005

Eyeshine and spectral tuning of long wavelength-sensitive rhodopsins: no evidence for red-sensitive photoreceptors among five Nymphalini butterfly species.

Spectral tuning of rhodopsins commonly refers to the effects of opsin amino acid substitutions on the wavelength for peak sensitivity of the rhodopsin absorption spectrum. Nymphalini butterflies provide an opportunity for identifying some of the amino acid substitutions responsible for insect rhodopsin spectral tuning because the majority of photoreceptor cells (R3-9) in the adult retina express only a single long wavelength-sensitive (LWS) opsin mRNA transcript. Therefore, the opsin genotype can be directly correlated with its phenotype. We determined the LWS opsin gene sequence from cDNA of the mourning cloak Nymphalis antiopa, and from genomic DNA of the malachite Siproeta stelenes and the peacock Inachis io. Using an epi-microspectrophotometer we examined each butterfly's eyeshine for photochemical evidence of multiple LWS rhodopsins and found only one. We then performed partial-bleaching experiments to obtain absorbance spectra for the LWS rhodopsins of all three species as well as from another nymphalid, the buckeye Junonia coenia. The isolated LWS opsin gene sequences varied in length from 1437-1612 bp and encode rhodopsins R522 (S. stelenes), R530 (I. io), R534 (N. antiopa) and, together with a previously published sequence, R510 (J. coenia). Comparative sequence analysis indicates that the S. stelenes rhodopsin is slightly blue-shifted compared to the typical 530 nm lepidopteran rhodopsin because of the presence of a S138A substitution at a homologous site that in mammalian MWS/LWS rhodopsins causes a 5 nm blue-shift. The difference in peak absorption between R522 of S. stelenes and R530 of Inachis io is therefore largely accounted for by this substitution. This suggests that spectral tuning mechanisms employing the S138A may have evolved in parallel in mammalian and butterfly MWS/LWS rhodopsins across 500 million years of evolution.

Amino Acid Sequence↗

PubMed2005

Jules Verne's Journey to the centre of the Earth: the secret of counterdepressive narratives.

The author interprets Jules Verne's Journey to the centre of the Earth with the help of Matte Blanco's theoretical framework, which describes the principle of symmetry and the principle of generalization. The first states that, from the moment an element or a proposition becomes conscious, it coexists in the unconscious with its symmetrically opposite form. The second refers to the confusion of elements once they have been apprehended by thought as containing a common point; they are put into larger and larger groups which merge into an indivisible whole. Verne's novel is built on paired elements which become symmetrized (e.g. distinct minerals vs molten lava; scientific rationality vs madness; the living vs the dead, etc.). These elements in turn become confused with one another, thanks largely to the novel's atmosphere of oral incorporation. This allows the fusion between subject and object, and, in particular, between the orphaned hero and his dead (Earth) mother. The novel's narrative evolution through three stages (separation, fusion and de-fusion, which are paralleled by rational, irrational and rational thought) can thus be understood as a mourning process. Similar processes can be found in other literary works.

Delusions↗

PubMed1984

Comparative biology of mnemonic processes: conditioned defensive reflexes and conditioned immune reactions.

Analogies in considerable detail hold between essential characteristics of classical conditioned defensive reflexes and immune reactions. The analogies become evident when combined conditioned and unconditioned stimuli are formally set into correspondence with combined hapten and carrier immunogens. Learning is elaborated also in the immune system when the transfer of information from the unconditioned to the conditional immuno-stimuli concurrently occurs. The analogies are regarded as having been evolved by adaptation of fundamentally parallel functions for survival against attack or invasion in the course of evolution, one on the macro- and the other on the micro- or molecular scale.

Biological Evolution↗

PubMed2003

[Renal damage during type I cryoglobulinemia].

UNLABELLED: CHARACTERISTICS OF THE RENAL DAMAGE: Type I cryoglobulinemia, composed of a single monoclonal immunoglobulin, may be responsible for a glomerulopathy with clinical presentation and histological characteristics close to those of mixed cryoglobulinemia. CONTEXT: Type I cryoglobulins complicate a malignant haematological disease, chronic lymphoid leukaemia or non-Hodgkin's malignant lymphoma in 60% of cases. EVOLUTION: Treatment with corticosteroids and immunosuppressors or antimitotics often leads to the parallel stabilisation or remission of the renal manifestations and the haematological disease

Acute Disease↗

PubMed1985

A homologue of alpha 2-macroglobulin purified from the hemolymph of the horseshoe crab Limulus polyphemus.

A high molecular weight protease inhibitor has been purified from the cell-free plasma of the horseshoe crab Limulus polyphemus using high speed centrifugation, polyethylene glycol precipitation, and gel filtration. The inhibitor is sensitive to mild acidification, methylamine treatment, and inhibits the proteolytic activity of a variety of endopeptidases. The molecule does not inhibit trypsin-mediated hydrolysis of low molecular weight substrates and protects the active site of trypsin from inactivation by soybean trypsin inhibitor. These properties are diagnostic of the alpha 2-macroglobulin (alpha 2M) class of protease inhibitors found in vertebrates. Like vertebrate alpha 2M the Limulus alpha 2M molecule is composed of subunits of molecular weight 180,000-185,000 as determined by polyacrylamide gel electrophoresis under reducing conditions. The apparent native molecular weight for the Limulus molecule as determined by both gel filtration and gel electrophoresis under nonreducing conditions is 500,000-550,000, compared to a native molecular weight of 700,000-750,000 for human alpha 2M, determined in parallel under identical conditions. These results suggest that alpha 2M appeared in evolution at least 550 million years ago before the divergence of the lineages that gave rise to present-day arthropods and mammals.

Amino Acids↗

PubMed1989

[The sociobiological ideas of Arthur Schopenhauer].

Starting from the basic ideas of sociobiology we prove that Schopenhauer, in his "Metaphysics of Sexual Love", has to pass for a precursor of sociobiological thinking. Several consequences of this parallel are discussed: The quest for strategic principles of organismic growth and evolution as a positive characteristic of both approaches--the hypothesis of a dominant genetic determination of human behaviour as an outcome of a typical bourgeois view of mankind connecting Schopenhauer and sociobiologists--the necessity of taking into consideration biological predispositions of flexible (learned) behaviour as elements of sociobiological models enjoying the same rights as genetical ones--the utility of Schopenhauer's natural philosophy for the purpose of complementing historical knowledge of many disciplines (also psychology).

Biology↗

PubMed1973

Studies in rheumatic fever. VI. Ultrastructure of chronic rheumatic heart disease.

The fine structure alterations in the atrium and atrial appendage, mitral valve and papillary muscle are described in 11 matched patients with chronic rheumatic heart disease. The muscle changes consisted of loss of myofilaments and accumulation of lipid and osmiophilic dense bodies. The connective tissue stroma of the atrium and the mitral valve showed extensive deposition of collagen and elastic fibers. There were numerous foci of collagen degeneration, characterized by fraying of the collagen fibers and accumulation of homogeneous granular material at these sites. Although the muscle changes were more striking, the connective tissue alterations appear important in the evolution of the chronic disease. The extent of collagen degeneration appeared to parallel the degree of collagen formation. The muscle fiber degeneration and connective tissue alterations did not correlate with the clinical findings. At the resolution of the electron microscope, the continuing process in the rheumatic heart appears to be primarily collagen formation and degradation rather than primary degeneration of the muscle fibers. It is the balance of these processes which determine the clinical state of the patient. Acute muscle damage along with evidence of inflammation do not seem to be associated with progressive, chronic rheumatic heart disease.

Adult↗

PubMed2004

Gene expression profiling of human adrenocortical tumors using complementary deoxyribonucleic Acid microarrays identifies several candidate genes as markers of malignancy.

The aim of this study was to identify predictor sets of genes whose over- or underexpression in human sporadic adrenocortical tumors would help to identify malignant vs. benign tumors and to predict postsurgical metastatic recurrence. For this, we analyzed the expression of 230 candidate genes using cDNA microarrays in a series of 57 well-characterized human sporadic adrenocortical tumors (33 adenomas and 24 carcinomas). We identified two clusters of genes (the IGF-II cluster containing eight genes, including IGF-II, and the steroidogenesis cluster containing six genes encoding steroidogenic enzymes plus eight other genes) whose combined levels of expression appeared to be good predictors of malignancy. This predictive value was as strong as that of the pathological score of Weiss. The analysis of the population of carcinomas (13 tumors) for genes whose expression would be strongly different between recurring and nonrecurring tumors allowed identification of 14 genes meeting these criteria. Among these genes, there are probably new markers of tumor evolution that will deserve additional validation on a larger scale. Taken together, these results show that the parallel analysis of the expression levels of a selected group of genes on microgram quantities of tumor RNA (a quantity that can be obtained from fine needle aspirations) appears as a complementary method to histopathology for the diagnosis and prognosis of evolution of adrenocortical carcinomas.

Adolescent↗

PubMed2006

Conversion of hydroxyphenylpyruvate dioxygenases into hydroxymandelate synthases by directed evolution.

Hydroxymandelate synthase (HmaS) and hydroxyphenylpyruvate dioxygenase (HppD) are non-heme iron-dependent dioxygenases, which share a common substrate and first catalytic step. The catalytic pathways then diverge to yield hydroxymandelate for secondary metabolism, or homogentisate in tyrosine catabolism. To probe the differences between these related active sites that channel a common intermediate down alternative pathways, we attempted to interconvert their activities by directed evolution. HmaS activity was readily introduced to HppD by just two amino acid changes. A parallel attempt to engineer HppD activity in HmaS was unsuccessful, suggesting that homogentisate synthesis places greater chemical and steric demands on the active site.

Catalysis↗

PubMed1991

Murine genes related to the Drosophila AbdB homeotic genes are sequentially expressed during development of the posterior part of the body.

The cloning, characterization and developmental expression patterns of two novel murine Hox genes, Hox-4.6 and Hox-4.7, are reported. Structural data allow us to classify the four Hox-4 genes located in the most upstream (5') position in the HOX-4 complex as members of a large family of homeogenes related to the Drosophila homeotic gene Abdominal B (AbdB). It therefore appears that these vertebrate genes are derived from a selective amplification of an ancestral gene which gave rise, during evolution, to the most posterior of the insect homeotic genes so far described. In agreement with the structural colinearity, these genes have very posteriorly restricted expression profiles. In addition, their developmental expression is temporally regulated according to a cranio-caudal sequence which parallels the physical ordering of these genes along the chromosome. We discuss the phylogenetic alternative in the evolution of genetic complexity by amplifying either genes or regulatory sequences, as exemplified by this system in the mouse and Drosophila. Furthermore, the possible role of 'temporal colinearity' in the ontogeny of all coelomic (metamerized) metazoans showing a temporal anteroposterior morphogenetic progression is addressed.

Amino Acid Sequence↗

PubMed2025

Characterisation of a persistent SARS-CoV-2 infection lasting more than 750 days in a person living with HIV: a genomic analysis.

BACKGROUND: People who are immunocompromised can develop persistent SARS-CoV-2 infections. Several viral mutations accumulated during the course of such persistent infections have also been observed in prominent variants of concern (VOCs). Here, we characterise persistent infection and viral evolution of SARS-CoV-2 lasting more than 750 days in a person with advanced HIV-1 infection. METHODS: Between March, 2021, and July, 2022, eight clinical specimens were collected from a person living with HIV, neither receiving antiretroviral therapy nor virally suppressed, and presumed to have been initially infected with SARS-CoV-2 in mid-May, 2020. Viral RNA was extracted from each swab and an amplicon-based sequencing approach was used for genomic analysis of SARS-CoV-2. Variable sites were characterised at the consensus and subconsensus levels, and phylogenetic tools were applied to analyse viral evolution. Publicly available SARS-CoV-2 sequences from GenBank were leveraged to contextualise our sequenced samples and identify any potential evidence of transmission. FINDINGS: Genomes formed a monophyletic cluster in the B.1 lineage. 68 consensus and 67 subconsensus single nucleotide variants were observed over the course of infection. The intrahost clock rate remained similar to that of the interhost rate in contemporaneous community sequences (6·74 × 10-4 [95% credible interval 5·05 × 10-4 to 8·54 × 10-4] substitutions per site per year vs 6·11 × 10-4 [5·54 × 10-5 to 6·66 × 10-4]). Mutations grouped into two distinct subpopulations present throughout infection. 10 non-synonymous mutations in the spike protein gene were at positions in common with those defining the omicron lineage (BA.1 or BA.2), of which nine were present before November, 2021. Nine of 18 substitutions present throughout infection were rare in online databases, suggesting a lack of long transmission chains descending from this individual. INTERPRETATION: Convergent SARS-CoV-2 evolution, both in and outside the spike protein, observed in this study suggests parallels with the evolutionary process leading to emergence of the omicron VOC. The inferred absence of onward infections might indicate a loss of transmissibility during adaptation to a single host. Our results underscore the importance of appropriate treatment to cure persistent SARS-CoV-2 infections and monitoring them to understand how mutations contribute to viral adaptation. FUNDING: National Institute of General Medical Sciences of the National Institutes of Health, Centers for Disease Control and Prevention, the National Institute of Allergy and Infectious Diseases, MassCPR, and Morris Singer Foundation.

Humans↗

PubMed1978

Generalized microscopic reversibility, kinetic co-operativity of enzymes and evolution.

Generalized microscopic reversibility implies that the apparent rate of any catalytic process in a complex mechanism is paralleled by substrate desorption in such a way that this ratio is held constant within the reaction mechanism [Whitehead (1976) Biochem. J. 159, 449--456]. The physical and evolutionary significances of this concept, for both polymeric and monomeric enzymes, are discussed. For polymeric enzymes, generalized microscopic reversibility of necessity occurs if, within the same reaction sequence, the substrate stabilizes one type of conformation of the active site only. Generalized microscopic reversibility suppresses the kinetic co-operativity of the slow transition model [Ainslie, Shill & Neet (1972) J. Biol. Chem. 247, 7088--7096]. This situation is obtained if the free-energy difference between the corresponding transition states of the two enzyme forms is held constant along the reaction co-ordinate. This situation implies that the 'extra costs' of energy (required to pass each energy barrier) that are not covered by the corresponding binding energies of the transition states vary in a similar way along the two reaction co-ordinates. The regulatory behaviour of monomeric enzymes is discussed in the light of the concept of 'catalytic perfection' proposed by Albery & Knowles [(1976) Biochemistry 15, 5631--5640]. These authors claim that an enzyme will be catalytically 'perfect' when its catalytic efficiency is maximum. If this situation occurs for a monomeric enzyme obeying either the slow transition or the mnemonical model, it can be shown that the kinetic co-operativity disappears. In other words, kinetic co-operativity of a monomeric enzyme is 'paid for' at the expense of catalytic efficiency, and the monomeric enzyme cannot be simultaneously co-operative and catalytically very efficient. This is precisely what has been found experimentally in a number of cases.

Biological Evolution↗

PubMed2001

Parallel gigantism and complex colonization patterns in the Cape Verde scincid lizards Mabuya and Macroscincus (Reptilia: Scincidae) revealed by mitochondrial DNA sequences.

The scincid lizards of the Cape Verde islands comprise the extinct endemic giant Macroscincus coctei and at least five species of Mabuya, one of which, Mabuya vaillanti, also had populations with large body size. Phylogenetic analysis based on DNA sequences derived from the mitochondrial cytochrome b, cytochrome oxidase I and 12S rRNA genes (711, 498 and 378 base pairs (bp), respectively) corroborates morphological evidence that these species constitute a clade and that Macroscincus is unrelated to very large skinks in other areas. The relationships are ((M. vaillanti and Mabuya delalandii) (Mabuya spinalis and Macroscincus coctei (Mabuya fogoensis nicolauensis (Mabuya fogoensis antaoensis and Mabuya stangeri)))). The Cape Verde archipelago was colonized from West Africa, probably in the Late Miocene or Early Pliocene period. The north-eastern islands were probably occupied first, after which the ancestor of M. vaillanti and M. delalandii may have originated on Boavista, the ancestor of the latter species arriving on Santiago or Fogo later. The M. fogoensis--M. stangeri clade colonized the islands of Branco, Razo, Santa Luzia and São Vicente from São Nicolau and reached Santo Antão after this. Colonization of these northeastern islands was slow, perhaps because the recipient islands had not developed earlier or because colonization cut across the path of the Canary Current and the Northeast Trade Winds, the main dispersing agents in the region. Rapid extension of range into the southwestern islands occurred later in M. spinalis and then in M. vaillanti and M. delalandii. The long apparent delay between the origin of these species and their southwestern dispersal may have been because there were earlier colonizations of the southern islands which excluded later ones until the earlier inhabitants were exterminated by volcanic or climatic events. The evolution of large size in Macroscincus occurred in the northwestern islands and was paralleled in the eastern and southern islands by populations of M. vaillanti. Both cases of size increase in Cape Verde skinks were accompanied by the development of herbivory.

Animals↗

PubMed1992

Gastrulation and the evolution of development.

The original eukaryotic cell may have possessed the key processes necessary for metazoan development--cell differentiation, patterning and motility--and these are present in the cell cycle. Protozoa also possess key patterning processes. It remains a problem as to why there should be two main modes of development--one based on asymmetric cell division and the other on cellular interactions. The latter may be related to asexual reproduction. The morphogenetic movements of gastrulation--as distinct from specifying the body plan--are highly conserved in a wide variety of organisms. This may reflect the requirement for patterning being specified in two dimensions, sheets of cells, and a third dimension being created by cell infolding. The origin of the gastrula can be accounted for in terms of Haeckel's gastrea theory--an early metazoan resembling the gastrula. Gastrulation in Cnidaria may resemble the primitive condition but there is nevertheless considerable diversity. While this may reflect, for example, yolkiness, it seems that there is little selection on developmental processes other than for reliability. Thus it is possible that the embryo is privileged with respect to selection and this may help account for the evolution of novel processes like the origin of the neural crest. Reliability is the key demand made on development. This may be provided by apparent redundancy. Since many developmental processes involve switches and spatial patterning reliability is provided by parallel buffering mechanisms and not by negative feedback.

Animals↗

PubMed1997

Evolution of male tail development in rhabditid nematodes related to Caenorhabditis elegans.

The evolutionary pathway that has led to male tails of diverse morphology among species of the nematode family Rhabditidae was reconstructed. This family includes the well-studied model species Caenorhabditis elegans. By relating the steps of male tail morphological evolution to the phenotypic changes brought about by developmental mutations induced experimentally in C. elegans, the goal is to identify genes responsible for morphological evolution. The varying morphological characters of the male tails of several rhabiditid species have been described previously (Fitch and Emmons, 1995, Dev. Biol. 170:564-582). The developmental events preceding differentiation of the adult structures have also been analyzed; in many cases the origins of varying adult morphological characters were traced to differences during ontogeny. In the present work, the evolutionary changes producing these differences were reconstructed in the context of the four possible phylogenies supported independently by sequences of 18S ribosomal RNA genes (rDNA). Two or more alternative states were defined for 36 developmental and adult morphological characters. These characters alone do not provide sufficient data to resolve most species relationships; however, when combined with the rDNA characters, they provide stronger support for one of the four rDNA phylogenies. Assuming a model of ordered transformations for multistate developmental characters generally results in greater resolution. Transformations between character states can be assigned unequivocally by parsimony to unambiguous branches for most of the characters. Correlations are thereby revealed for some of the developmental characters, indicating a probability of a shared developmental or genetic regulatory pathway. Four of the unequivocal character state changes on unambiguously supported branches closely resemble the phenotypic changes brought about by known mutations in C. elegans. These mutations define genes that are known to act in genetic regulatory hierarchies controlling pattern formation, differentiation, and morphogenesis. Although these studies are still at an early stage, these results strongly suggest that parallel studies of developmental mutants in C. elegans and of morphological and developmental evolution among related nematodes will help define genetic changes underlying the evolution of form.

Animals↗

PubMed1995

Mitochondrial portraits of human populations using median networks.

Analysis of variation in the hypervariable region of mitochondrial DNA (mtDNA) has emerged as an important tool for studying human evolution and migration. However, attempts to reconstruct optimal intraspecific mtDNA phylogenies frequently fail because parallel mutation events partly obscure the true evolutionary pathways. This makes it inadvisable to present a single phylogenetic tree at the expense of neglecting equally acceptable ones. As an alternative, we propose a novel network approach for portraying mtDNA relationships. For small sample sizes (< approximately 50), an unmodified median network contains all most parsimonious trees, displays graphically the full information content of the sequence data, and can easily be generated by hand. For larger sample sizes, we reduce the complexity of the network by identifying parallelisms. This reduction procedure is guided by a compatibility argument and an additional source of phylogenetic information: the frequencies of the mitochondrial haplotypes. As a spin-off, our approach can also assist in identifying sequencing errors, which manifest themselves in implausible network substructures. We illustrate the advantages of our approach with several examples from existing data sets.

Biological Evolution↗

PubMed2002

Deep insight from simple models of evolution.

On one hand, people admire the often strikingly efficient results of organic evolution. On the other hand, however, they decry mutation and selection to be a rather prodigal, inefficient trial-and-error strategy. Taking into account the parallel information processing in a heterogeneous population and sexual propagation with recombination, as well as the genetic control of the reproduction accuracy, computer simulated evolution reveals a couple of interesting, sometimes surprising, properties of nature's learning-by-doing algorithm. Survival of the fittest, Spencer's résumé of Darwin's view, turns out to be a bad advice if taken literally. Individual death, forgetting, and even regression show up to be necessary ingredients of the life game. Whether the process should be named gradualistic or punctualistic, is a matter of the observer's point of view.

Algorithms↗

PubMed2000

Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards.

DNA sequences from 195 squamate reptiles indicate that mitochondrial gene order is the most reliable phylogenetic character establishing monophyly of acrodont lizards and of the snake families Boidae, Colubridae, and Viperidae. Gene order shows no evidence of evolutionary parallelisms or reversals in these taxa. Derived secondary structures of mitochondrial tRNAs also prove to be useful phylogenetic characters showing no reversals. Parallelisms for secondary structures of tRNAs are restricted to deep lineages that are separated by at least 200 million years of independent evolution. Presence of a stem-and-loop structure between the genes encoding tRNA(Asn) and tRNA(Cys), where the replication origin for light-strand synthesis is typically located in vertebrate mitochondrial genomes, is found to undergo at least three and possibly as many as seven evolutionary shifts, most likely parallel losses. This character is therefore a less desirable phylogenetic marker than the other structural changes examined. Sequencing regions that contain multiple genes, including tRNA genes, may be preferable to the common practice of obtaining single-gene fragments for phylogenetic inference because it permits observation of major structural changes in the mitochondrial genome. Such characters may occasionally provide phylogenetic information on relatively short internal branches for which base substitutional changes are expected to be relatively uninformative.

Animals↗