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PubMed2004

Prolinks: a database of protein functional linkages derived from coevolution.

The advent of whole-genome sequencing has led to methods that infer protein function and linkages. We have combined four such algorithms (phylogenetic profile, Rosetta Stone, gene neighbor and gene cluster) in a single database--Prolinks--that spans 83 organisms and includes 10 million high-confidence links. The Proteome Navigator tool allows users to browse predicted linkage networks interactively, providing accompanying annotation from public databases. The Prolinks database and the Proteome Navigator tool are available for use online at http://dip.doe-mbi.ucla.edu/pronav.

ATP Synthetase Complexes↗
PubMed2005

Coevolution of the relaxin-like peptides and their receptors.

Currently, four relaxin peptide family receptors are known: LGR7 is the relaxin receptor, although it also interacts specifically with relaxin-3; LGR8 is the insulin-like factor 3 (INSL3) receptor; and GPCR135 or the somatostatin- and angiotensin-like peptide receptor (SALPR) and GPCR142 are both specific relaxin-3 receptors. Because these receptors coevolved together with their relaxin ligands, phylogenetic analysis of these sequences can provide insight into peptide-receptor interactions and even predict interacting partners for INSL4, INSL5, and INSL6, the receptors for which are unknown.

Animals↗
PubMed2006

Trauma surgery and traffic policy in Germany in the 1930s: a case study in the coevolution of modern surgery and society.

This paper analyzes how in Germany in the first half of the twentieth century the development of surgery and modern automobile traffic were intertwined. It describes the mutual influence of traffic policy and trauma surgery under the conditions of National Socialist politics of modernization. This coevolutionary development provides an example of how the rise of much of modern surgery can be better understood by taking into account other, nonmedical developments in society.

Accidents, Traffic↗
PubMed1995

Evidence of the coevolution of a snake toxin and its endogenous antitoxin cloning, sequence and expression of a serum albumin cDNA of the Chinese cobra.

A full-length cDNA of the serum albumin (CSA) of the cobra (Naja naja kaouthia) was cloned from a lambda gt 11 library. It encodes a mature protein of 614 amino-acid residues homologous to the precursor of mammalian serum albumins. The 1 degree and 2 degrees structures of the CSA resemble those of the human variety. The putative toxin binding sites are mainly located in the subdomains IIA and IIIA. The relation between structural homology and function of the serum albumins (SA) is discussed. An analysis of their evolutionary tree revealed that anti-toxicity arose by < 90 amino-acid exchanges. The rate of substitution is much higher in the SA than in cytochrome C, which probably reflects the difference in evolutionary driving forces. The evolutionary period of the SA (6.7 +/- 0.1 M.Y.) significantly exceeds that of hemoglobin (5.8 M.Y.). Eight tripeptides in the nicotinic acetylcholine receptor (ACR), all flanking the putative toxin binding site, are also found in the CSA where they join to form 1 octa-, 1 penta- and 4 tripeptides, thus indicating the concerted evolution of two functionally linked proteins: toxin and antitoxin (CSA).

Amino Acid Sequence↗
PubMed2003

Convergence and coevolution in a mutualism: evidence from a molecular phylogeny of Ficus.

The interaction between Ficus (Moraceae) and their pollinating wasps (Chalcidoidea: Agaonidae; more than 700 species-specific couples) is one of the most specialized mutualisms found in nature. Both partners of this interaction show extensive variation in their respective biology. Here we investigate Ficus life-history trait evolution and fig/fig wasp coadaptation in the context of a well-resolved molecular phylogeny. Mapping out variations in Ficus life-history traits on an independently derived phylogeny constructed from ribosomal DNA sequences (external and internal transcribed spacer) reveals several parallel transitions in Ficus growth habit and breeding system. Convergent trait evolution might explain the discrepancies between morphological analyses and our molecular reconstruction of the genus. Morphological characters probably correlate with growth habit and breeding system and could therefore be subject to convergent evolution. Furthermore, we reconstruct the evolution of Ficus inflorescence characters that are considered adaptations to the pollinators. Our phylogeny reveals convergences in ostiole shape, stigma morphology, and stamen:ovule ratio. Statistical tests taking into account the phylogenetic relationship of the species show that transitions in ostiole shape are correlated with variation in wasp pollinator head shape, and evolutionary changes in stigma morphology and stamen:ovule ratio correlate with changes in the pollination behavior of the associated wasp. These correlations provide evidence for reciprocal adaptations of morphological characters between these mutualistic partners that have interacted over a long evolutionary time. In light of previous ecological studies on mutualism, we discuss the adaptive significance of these correlations and what they can tell us about the coevolutionary process occurring between figs and their pollinators.

Adaptation, Biological↗
PubMed1992

Coevolution of hosts and microorganisms: an analysis of the involvement of cytokines in host-parasite interactions.

Parasites may employ particular strategies of eluding an immune response by taking advantage of those mechanisms that normally guarantee immunological self-tolerance. Much in the way as it occurs during the establishment of self-tolerance, live pathogens may induce clonal deletion, functional inactivation (anergy) and immunosuppression. At this latter level, it appears that certain pathogens produce immunosuppressive cytokine-like mediators or provoke the host to secrete cytokines that will compromise the anti-parasite immune response. It appears that immune responses that preferentially involve T helper 1 cells (secretors of interleukin-2-and interferon-gamma) tend to be protective, whereas T helper 2 cells (secretors of IL-4, IL-5, IL-6, and IL-10), a population that antagonizes T helper cells, mediate disease susceptibility and are involved in immunopathological reactions. Cytokines produced by T helper 2 cells mediate many symptoms of infection, including eosinophilia, mastocytosis, hyperimmunoglobulinemia, and elevated IgE levels. Administration of IL-2 and IFN-gamma has beneficial effects in many infections mediated by viruses, bacteria, and protozoa. The use of live vaccinia virus might be an avenue for the treatment of or the vaccination against infection. We have found that a vaccinia virus expressing the gene for human IL-2, though attenuated, precipitates autoimmune disease in immunodeficient, athymic mice. Thus, although T helper 1 cytokines may have desired immunostimulatory properties, they also may lead to unwarranted autoaggressive responses.

Animals↗
PubMed2005

Coevolution and biogeography among Nematodirinae (Nematoda: Trichostrongylina) Lagomorpha and Artiodactyla (Mammalia): exploring determinants of history and structure for the northern fauna across the holarctic.

Nematodes of the subfamily Nematodirinae are characteristic components of a Holarctic fauna. The topology of a generic-level phylogenetic hypothesis, patterns of diversity, and geographic distributions for respective nematode taxa in conjunction with data for host occurrence are consistent with primary distributions determined across Beringia for species of Murielus, Rauschia, Nematodirus, and Nematodirella. Ancestral hosts are represented by Lagomorpha, with evidence for a minimum of 1 host-switching-event and subsequent radiation in the Artiodactyla. Diversification may reflect vicariance of respective faunas along with episodic or cyclical range expansion and isolation across Beringia during the late Tertiary and Quaternary. Secondarily, species of Nematodirus attained a distribution in the Neotropical region with minimal diversification of an endemic fauna represented by Nematodirus molini among tayassuids, Nematodirus lamae among camelids and Nematodirus urichi in cervids during the Pleistocene. Nematodirines are a core component of an Arctic-Boreal fauna of zooparasitic nematodes (defined by latitude and altitude) adapted to transmission in extreme environments characterized by seasonally low temperatures and varying degrees of desiccation. The history and distribution of this fauna is examined in the context of biotic and abiotic determinants for geographic colonization and host switching with an exploration of predicted responses of complex host-parasite systems to ecological perturbation under a regime of global climate change.

Animals↗
PubMed2002

NK cell receptors of the orangutan (Pongo pygmaeus): a pivotal species for tracking the coevolution of killer cell Ig-like receptors with MHC-C.

CD94, NKG2, Ly49, and killer cell Ig-like receptor (KIR) expressed by orangutan peripheral blood cells were examined by cloning and sequencing cDNA from a panel of individuals. Orthologs of human CD94, NKG2A, D, and F were defined. NKG2C and E are represented by one gene, Popy-NKG2CE, that is equidistant from the two human genes. Several Popy-CD94, NKG2A, and NKG2CE alleles were defined. Popy-Ly49L is expressed in cultured NK cells and has a sequence consistent with it encoding a functional receptor. Orangutan KIR corresponding to the three KIR lineages expressed in humans and chimpanzees were defined. Popy-KIR2DL4 of lineage I is the only ortholog of a human or chimpanzee KIR, but in all individuals examined, the transcripts of this gene produced premature termination, either in the D2 domain or at the beginning of the cytoplasmic domain. Ten Popy-KIR3DL and one Popy-KIR3DS of lineage II are all closely related, but represent the products of at least two genes. The two Popy-KIR2DL and four Popy-KIR2DS of lineage III also represent two genes, both being more related to KIR2DS4 than to other human and chimpanzee KIR of lineage III. The Popy-KIR2D include ones predicted to be specific for the C1 epitope of MHC-C, but none specific for C2. This correlates with the observation that all orangutan MHC-C allotypes examined have the C1 motif.

Alleles↗
PubMed2003

Coevolution of markers of innate and adaptive immunity in skin and peripheral blood of patients with erythema migrans.

We used multiparameter flow cytometry to characterize leukocyte immunophenotypes and cytokines in skin and peripheral blood of patients with erythema migrans (EM). Dermal leukocytes and cytokines were assessed in fluids aspirated from epidermal suction blisters raised over EM lesions and skin of uninfected controls. Compared with corresponding peripheral blood, EM infiltrates were enriched for T cells, monocytes/macrophages, and dendritic cells (DCs), contained lower proportions of neutrophils, and were virtually devoid of B cells. Enhanced expression of CD14 and HLA-DR by lesional neutrophils and macrophages indicated that these innate effector cells were highly activated. Staining for CD45RO and CD27 revealed that lesional T lymphocytes were predominantly Ag-experienced cells; furthermore, a subset of circulating T cells also appeared to be neosensitized. Lesional DC subsets, CD11c(+) (monocytoid) and CD11c(-) (plasmacytoid), expressed activation/maturation surface markers. Patients with multiple EM lesions had greater symptom scores and higher serum levels of IFN-alpha, TNF-alpha, and IL-2 than patients with solitary EM. IL-6 and IFN-gamma were the predominant cytokines in EM lesions; however, greater levels of both mediators were detected in blister fluids from patients with isolated EM. Circulating monocytes displayed significant increases in surface expression of Toll-like receptor (TLR)1 and TLR2, while CD11c(+) DCs showed increased expression of TLR2 and TLR4; lesional macrophages and CD11c(+) and CD11c(-) DCs exhibited increases in expression of all three TLRs. These results demonstrate that Borrelia burgdorferi triggers innate and adaptive responses during early Lyme disease and emphasize the interdependence of these two arms of the immune response in the efforts of the host to contain spirochetal infection.

Adult↗
PubMed2000

Erhaia (Gastropoda: Rissooidea): phylogenetic relationships and the question of Paragonimus coevolution in Asia.

The human lung fluke Paragonimus is transmitted by gastropod taxa of two superfamilies: Ceritheoidea and Rissooidea. The question whether or not Paragonimus shows the same specificity of host-parasite coevolved relationship as the human blood fluke Schistosoma was inspired by the finding of two sympatric snail species as hosts for Paragonimus skrjabini in Fujian Province, China: Gammatricula and Erhaia. The former species can clearly be classified as Pomatiopsidae: Triculinae. The latter has previously been classified as Pomatiopsidae: Pomatiopsinae. However, this classification based on anatomical characteristics is uncertain. In order to obtain a robust phylogenetic hypothesis for Erhaia, we have studied three gene fragments from this taxon as well as from twelve related taxa. The data show that the species involved represent four families: Pomatiopsidae, Hydrobiidae, Cochliopidae (here raised to family status), and Amnicolidae. Erhaia fits securely into the Amnicolidae. This indicates that P. skrjabini has not coevolved with snail lineages. However, P. skrjabini has so far only been reported from rissooidean snails, whereas members of the Paragonimus westermani complex have only been found in ceritheoidean snails. The implication is that there is a host specificity on the superfamily level. However, Asian freshwater species of the Ceritheoidea and Rissooidea usually are not sympatric and often prefer different habitats. It is therefore possible that ecological niche partitioning plays the primary role for Paragonimus evolution.

Animals↗
PubMed1999

Evolutionary relationships among the protostrongylidae (Nematoda: Metastrongyloidea) as inferred from morphological characters, with consideration of parasite-host coevolution.

The phylogeny of nematodes in the family Protostrongylidae (Nematoda: Metastrongyloidea) was reconstructed by cladistic analysis of 28 binary and multistate characters derived from comparative morphology. Analyses were hierarchical, and examined (1) relationships among genera, including 13 ingroup taxa and Metastrongylidae as an outgroup (single tree, 78 steps, consistency index [CI] = 0.705); and (2) relationships among genera and species groups, including 21 ingroup taxa and Metastrongylus apri as an outgroup (single tree, 76 steps, CI = 0.582). In the species-level tree, Protostrongylidae was divided into 2 major clades, 1 containing the subfamilies Muelleriinae (including the recently described Umingmtakstrangylus pallikuukensis), Elaphostrongylinae, and the Varestrongylinae (excluding Pneumocaulus kadenazii). Varestrongylus was paraphyletic as it included Pneumostrongylus calcaratus. The second major clade consisted of a paraphyletic group containing Protostrongylus spp. and Spiculocaulus leuckarti and, basal to this subclade, several other individual protostrongylid lineages. The various subclades generally correspond to the subfamilial divisions of the Protostrongylidae. The Neostrongylinae, however, is not supported as Neostrongylus and Orthostrongylus are not sister groups. Based on a large number of hypothesized synapomorphies, the elaphostrongylines appear to be a highly derived group of protostrongylids, a feature potentially correlated with their habitat localization in muscular and nervous tissues. The generic-level tree retained most of the primary structure revealed among the species but excluded the varestrongylines from the Muelleriinae + Elaphostrongylinae subclade. Artiodactyles of the family Cervidae are considered basal hosts for protostrongylids; secondary colonization in Caprini, Rupicaprini, and among lagomorphs is postulated.

Animals↗
PubMed1990

Examination of protein sequence homologies. VII. The complementary molecular coevolution of ribosomal proteins equivalent to Escherichia coli L7/L12 and L10.

Recently reported P1, P2 and metabacteria line sequences of transposition-type 'A' proteins, equivalent to Escherichia coli ribosomal protein L7/L12, were examined using a correlation method which evaluates the sequence similarity quantitatively. As the sequences could be aligned along the alignment previously constructed for 25 various 'A' proteins, the inclusive alignment further supports the previous claims concerning the rule of "preservation units" and the transpositional regeneration for metabacterial and eukaryotic 'A' proteins. Yeasts contain multispecies of P1 and P2 line genes and their P1 line sequences show low correlation coefficient values compared to other P1 line sequences, indicating a great evolutionary distance between lower and higher eukaryotes. Five sequences of protein P0 from metabacteria, yeast, and human, of which about 20 residues at the C termini are homologous with those of their own transposition-type 'A' proteins, were similarly examined. The N-terminal three-quarters of the sequences align naturally and the first two-thirds of the alignment could involve the E. coli L10 (EL10) sequence. An alignment of the remaining sequences at the C termini was established, relying on the well-matching sequence similarities between the metabacteria 'A' protein and their P0 protein sequences. Finally, the C-terminal halves of P0 protein sequences corresponded with almost overall sequences of the transposition-type 'A' proteins. The gene fusion of a protein might have resulted in the formation of the P0 proteins. A coupling of this gene fusion and the transposition of prototype 'A' proteins may have given rise to the complementary molecular transformations required for the development toward higher organism cells.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMedDate not supplied

[The coevolution of ixodid ticks and terrestrial vertebrates].

Paleontologic and zoogeographic data speak in favour of Mesozoic origin of ixodid ticks. The absence of strict restrictions for the feeding on unusual species of hosts has caused the domination of polyphagy and oligophagy over monophagy among ixodid ticks. The same peculiarities of ixodid ecology are responsible for a restricted part or absence of phylogenetic parallelism with hosts in their evolution. Primary food relations with reptiles are, apparently, preserved only in the genus Aponomma and in many species of Amblyomma while hosts for most species of other genera are mammals and, to a lesser extent, birds. The number of potential hosts in these species can be much greater than that of real ones. Restrictions in the distribution of some species are connected rather with direct effect of unfavourable environmental factors on their nonparasitic stages of the life cycle than with the absence of suitable hosts. During the evolution of natural landscapes and at a shorter stages under the influence of successions or anthropogenic factors ixodids easily adapt themselves to feeding on new species of hosts. So the differentiation of primary and secondary hosts of these parasites is rather difficult.

Adaptation, Physiological↗