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PubMed2002

Lack of canonical E6 and E7 open reading frames in bird papillomaviruses: Fringilla coelebs papillomavirus and Psittacus erithacus timneh papillomavirus.

Determination and analyses of the complete sequence of Fringilla coelebs papillomavirus and Psittacus erithacus timneh papillomavirus indicate that they represent a distinct and distant lineage of papillomaviruses. The lack of canonical E6-E7 open reading frames suggests that they serve adaptive functions during papillomavirus evolution.

Amino Acid Sequence↗

PubMed2003

New hepatitis B virus of cranes that has an unexpected broad host range.

All hepadnaviruses known so far have a very limited host range, restricted to their natural hosts and a few closely related species. This is thought to be due mainly to sequence divergence in the large envelope protein and species-specific differences in host components essential for virus propagation. Here we report an infection of cranes with a novel hepadnavirus, designated CHBV, that has an unexpectedly broad host range and is only distantly evolutionarily related to avihepadnaviruses of related hosts. Direct DNA sequencing of amplified CHBV DNA as well a sequencing of cloned viral genomes revealed that CHBV is most closely related to, although distinct from, Ross' goose hepatitis B virus (RGHBV) and slightly less closely related to duck hepatitis B virus (DHBV). Phylogenetically, cranes are very distant from geese and ducks and are most closely related to herons and storks. Naturally occurring hepadnaviruses in the last two species are highly divergent in sequence from RGHBV and DHBV and do not infect ducks or do so only marginally. In contrast, CHBV from crane sera and recombinant CHBV produced from LMH cells infected primary duck hepatocytes almost as efficiently as DHBV did. This is the first report of a rather broad host range of an avihepadnavirus. Our data imply either usage of similar or identical entry pathways and receptors by DHBV and CHBV, unusual host and virus adaptation mechanisms, or divergent evolution of the host genomes and cellular components required for virus propagation.

Animals↗

PubMed2003

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Animals↗

PubMed1986

Temporal evolution of altered islet neurotransmitter sensitivity after VMH lesion.

It has been suggested that increased insulin secretion after ventromedial hypothalamic (VMH) obesity is mediated by decreased sympathetic and increased parasympathetic neural input. The evolution of pancreatic islet adaptation was studied from 1 to 130 days after VMH lesion in rats by assessing the sensitivity of insulin secretion from incubated isolated islets to 10 mM glucose and selected acetylcholine and norepinephrine concentrations. Insulin secretion in response to glucose increased by 1 day, reaching a twofold plateau from 7 to 130 days. Sensitivity to norepinephrine increased by 1 day, whereas sensitivity to acetylcholine decreased by 2 days, and both remained altered up to 130 days. These data suggest that elevated plasma insulin concentrations characteristic of VMH obesity were associated with increased insulin secretion in response to glucose before decreased sensitivity to acetylcholine and concurrent with increased sensitivity to norepinephrine. We conclude that these compensatory responses, which shift the islet to a new operating point secondary to altered neural input, are essential to pancreatic adaptation in VMH obesity.

Acetylcholine↗

PubMed1992

Differences in optokinetic and vestibular ocular reflex performance in teleosts and their relationship to different life styles.

Horizontal eye movements in response to vestibular and optokinetic stimulation were investigated in 20 species of marine and fresh water teleosts. Most species performed spontaneous saccadic eye movements in light and in darkness. Successive saccades occurred either at irregular intervals and in different directions (few species), or in bursts of smaller saccades in one direction followed by saccades in the opposite direction (majority of species). Thus, in the latter group the lines of sight shifted cyclically from one side to the other about every 10-15 s. Eye movement responses in goldfish and toadfish were prototypical for two major functional groups. Optokinetic and vestibular nystagmus in the goldfish were much more regular and attained significantly higher gains than in the oyster toadfish. Optokinetic afternystagmus (OKAN) and per-/postrotatory nystagmus lasted about 10-12 s in the goldfish, but only 2-3 s in the oyster toadfish. Bilateral labyrinthectomy in goldfish resulted in optokinetic gains and OKAN durations that were very close to those of intact toadfish. These results indicate the presence (in goldfish) and the absence (in toadfish) of a functioning velocity storage network, respectively. Other non-ostariophysan teleosts failed to show a 'goldfish-like' response pattern as well. Ostariophysan species differed in their reflex performance as well. A 'goldfish-like' response pattern was observed in five of the seven cypriniform species and in two of the four characiform species but not in the four siluriform species. Positively correlated, combined response properties suggest that some species are better equipped for gaze stabilization at higher velocities than other species. These behavioral differences may parallel different specializations in locomotor pattern and mode of life. Absence of a functioning velocity storage network in bottom-dwelling teleosts (as in Amphibia) may be related to the sporadic, slow locomotion of these species and the resulting small requirements for continuous gaze stabilization during self-motion at higher velocities.

Animals↗

PubMed1986

Locomotion and feeding postures of spider and howling monkeys: field study and evolutionary interpretation.

Field observations demonstrate clear differences in locomotion and feeding postures between spider monkeys (Ateles) and howling monkeys (Alouatta). When feeding, Ateles employs sitting postures approximately half the time, and a variety of suspensory postures using the tail the other half. Ateles moves quadrupedally during 52% of locomotion, by tail-arm suspension 25%, and various mixed support-suspensory modes the remainder. Tail-arm suspension is practiced more rapidly on thinner supports, and on more negatively inclined supports than is quadrupedal movement. Howlers do not locomote by tail-arm suspension: movement is almost entirely quadrupedal and is slower than that of spider monkeys. The positional behavior of spider monkeys fits closely recent views of major adaptive changes in hominoid evolution emphasizing brachiation and speed during travel. Howler locomotion and also tissue composition appear related to diet and digestive mechanisms.

Alouatta↗

PubMed2003

Omnis definitio periculosa est: on the definition of the term "embryo" in the Human Fertilisation & Embryology Act 1990.

In adopting a purposive interpretation of the definition of the term "embryo" in the Human Fertilisation & Embryology Act 1990, the Court of Appeal judgement in R(on the application of B. Quintavalle on behalf of Pro-Life Alliance) v. Secretary of State for Health effectively stifled democratic debate on the development of therapeutic cloning techniques. Instead of being evidence of the flexibility of of the statute to adapt to the rapid evolution of scientific techniques, the judgment bears witness to a certain dependence of the law on scientific criteria and moreover, raises the question of legitimate judicial function. Indeed, judges should not be seen to be deciding questions of social choice that should ultimately be decided through the democratic process. Although the purposive approach may be objectively justified, it is suggested that the appeal judges erred in their appreciation of the very purpose of the 1990 Act. It is argued that the Parliamentary debates in 1990 illustrate that the purpose of the 1990 Act does not go beyond the area of procreation and embryo research in this context. Consequently, it is claimed that no economy should have been made on a full democratic debate. By preventing such a debate, the Court of Appeal appears to admit that the law has become servile to the scientific, political and a fortiori economic, interests at stake.

Cloning, Organism↗

PubMed2005

IMGT, the international ImMunoGeneTics information system: a standardized approach for immunogenetics and immunoinformatics.

IMGT, the international ImMunoGeneTics information system http://imgt.cines.fr, was created in 1989 by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM) (Université Montpellier II and CNRS) at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) of any species which belong to the immunoglobulin superfamily (IgSF) and to the MHC superfamily (MhcSF). IMGT consists of five databases, ten on-line tools and more than 8,000 HTML pages of Web resources. IMGT provides a common access to standardized data from genome, genetics, proteome and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY comprises six main concepts: IDENTIFICATION, CLASSIFICATION, DESCRIPTION, NUMEROTATION, ORIENTATION and OBTENTION. Based on these concepts, the controlled vocabulary and the annotation rules necessary for the immunogenetics data identification, classification, description and numbering and for the management of IMGT knowledge are defined in the IMGT Scientific chart. IMGT is the international reference in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody sites and of the TR recognition sites in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr.

Journal Article↗

PubMed2004

Vocal mechanics in Darwin's finches: correlation of beak gape and song frequency.

Recent studies of vocal mechanics in songbirds have identified a functional role for the beak in sound production. The vocal tract (trachea and beak) filters harmonic overtones from sounds produced by the syrinx, and birds can fine-tune vocal tract resonance properties through changes in beak gape. In this study, we examine patterns of beak gape during song production in seven species of Darwin's finches of the Galápagos Islands. Our principal goals were to characterize the relationship between beak gape and vocal frequency during song production and to explore the possible influence therein of diversity in beak morphology and body size. Birds were audio and video recorded (at 30 frames s(-1)) as they sang in the field, and 164 song sequences were analyzed. We found that song frequency regressed significantly and positively on beak gape for 38 of 56 individuals and for all seven species examined. This finding provides broad support for a resonance model of vocal tract function in Darwin's finches. Comparison among species revealed significant variation in regression y-intercept values. Body size correlated negatively with y-intercept values, although not at a statistically significant level. We failed to detect variation in regression slopes among finch species, although the regression slopes of Darwin's finch and two North American sparrow species were found to differ. Analysis within one species (Geospiza fortis) revealed significant inter-individual variation in regression parameters; these parameters did not correlate with song frequency features or plumage scores. Our results suggest that patterns of beak use during song production were conserved during the Darwin's finch adaptive radiation, despite the evolution of substantial variation in beak morphology and body size.

Acoustics↗

PubMed2004

Segmentally variable genes: a new perspective on adaptation.

Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes suggests that genes are evolving at many different rates. We have attempted to derive a new classification of genes into three broad categories: lineage-specific genes that evolve rapidly and appear unique to individual species or strains; highly conserved genes that frequently perform housekeeping functions; and partially variable genes that contain highly variable regions, at least 70 amino acids long, interspersed among well-conserved regions. The latter we term segmentally variable genes (SVGs), and we suggest that they are especially interesting targets for biochemical studies. Among these genes are ones necessary to deal with the environment, including genes involved in host-pathogen interactions, defense mechanisms, and intracellular responses to internal and environmental changes. For the most part, the detailed function of these variable regions remains unknown. We propose that they are likely to perform important binding functions responsible for protein-protein, protein-nucleic acid, or protein-small molecule interactions. Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment.

Acclimatization↗

PubMed2026

Codon bias variation in Staphylococcus aureus.

BACKGROUND: Staphylococcus aureus causes a multiplicity of human diseases acquired in community and healthcare settings alike around the globe. While most studies focus on coding changes to assess genome evolution and study genetic adaptation, interrogation of silent mutations in the form of synonymous codon usage bias is less well-studied. As such, understanding of patterns in codon bias at the gene and genome levels, and how codon bias impacts protein expression in S. aureus remains incomplete. METHODS: The codon bias of 2,565 protein encoding genes from NCTC 8325 was queried against all publicly available closed S. aureus genomes. Using public BioSample data, genomes were sorted by disease state, submitting institution, and collection site. Codon bias was assessed at the level of gene and genome using the codon adaptation index (CAI), calculated using 30S and 50S ribosomal genes. Gene set enrichment analysis was applied to determine associations between physiological functions, CAI gene scores, and interquartile ranges. CAI scores were also compared to an in vitro S. aureus proteomics database to correlate codon bias and protein expression. RESULTS: CAI scores varied within and between isolates at the gene and genome levels. Genes with ribosome-associated functions were most enriched among high CAI genes, and had low CAI interquartile ranges (IQR), suggesting selective pressure to maintain high expression of these genes across all S. aureus isolates. Genome sequences submitted by Aga Khan University Hospital, Nairobi, Kenya were most different from others. For the LAC USA 300 strain, CAI and protein expression were moderately positively correlated (cor = 0.534, p < 2.2e-16). CONCLUSIONS: Codon bias in S. aureus was shown to vary between gene, and to be a source of genetic variation between isolates; CAI and in vitro protein expression were positively correlated.

Staphylococcus aureus↗

PubMed2004

Isolation of functional photosystem II core particles from the Cyanobacterium synechocystis sp. PCC 6803.

This chapter contains the description of several methods used for the isolation of functional photosystem (PS)II core particles from wild-type (wt), PSI-less, and CP47 histidine-tagged cells of the cyanobacterium Synechocystis sp. PCC 6803. These protocols discuss the cultivation of PSI-containing and PSI-less cells, isolation of thylakoid membranes, purification of PSII core particles using a weak cation exchange or metal affinity column chromatography, and characterization of the final preparation. The described isolation procedures, which normally yield PSII particles highly active in oxygen evolution, can be easily adapted for obtaining preparations from different types of Synechocystis mutants with modified PSII.

Bacterial Proteins↗

PubMed2005

Fold recognition of the human immunodeficiency virus type 1 V3 loop and flexibility of its crown structure during the course of adaptation to a host.

The third hypervariable (V3) region of the HIV-1 gp120 protein is responsible for many aspects of viral infectivity. The tertiary structure of the V3 loop seems to influence the coreceptor usage of the virus, which is an important determinant of HIV pathogenesis. Hence, the information about preferred conformations of the V3-loop region and its flexibility could be a crucial tool for understanding the mechanisms of progression from an initial infection to AIDS. Taking into account the uncertainty of the loop structure, we predicted the structural flexibility, diversity, and sequence fitness to the V3-loop structure for each of the sequences serially sampled during an asymptomatic period. Structural diversity correlated with sequence diversity. The predicted crown structure usage implied that structural flexibility depended on the patient and that the antigenic character of the virus might be almost uniform in a patient whose immune system is strong. Furthermore, the predicted structural ensemble suggested that toward the end of the asymptomatic period there was a change in the V3-loop structure or in the environment surrounding the V3 loop, possibly because of its proximity to the gp120 core.

Adaptation, Physiological↗

PubMed2006

Nonadditive regulation of FRI and FLC loci mediates flowering-time variation in Arabidopsis allopolyploids.

Allopolyploidy is formed by combining two or more divergent genomes and occurs throughout the evolutionary history of many plants and some animals. Transcriptome analysis indicates that many genes in various biological pathways, including flowering time, are expressed nonadditively (different from the midparent value). However, the mechanisms for nonadditive gene regulation in a biological pathway are unknown. Natural variation of flowering time is largely controlled by two epistatically acting loci, namely FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). FRI upregulates FLC expression that represses flowering in Arabidopsis. Synthetic Arabidopsis allotetraploids contain two sets of FLC and FRI genes originating from Arabidopsis thaliana and A. arenosa, respectively, and flower late. Inhibition of early flowering is caused by upregulation of A. thaliana FLC (AtFLC) that is trans-activated by A. arenosa FRI (AaFRI). Two duplicate FLCs (AaFLC1 and AaFLC2) originating from A. arenosa are expressed in some allotetraploids but silenced in other lines. The expression variation in the allotetraploids is associated with deletions in the promoter regions and first introns of A. arenosa FLCs. The strong AtFLC and AaFLC loci are maintained in natural Arabidopsis allotetraploids, leading to extremely late flowering. Furthermore, FLC expression correlates positively with histone H3-Lys4 methylation and H3-Lys9 acetylation and negatively with H3-Lys9 methylation, epigenetic marks for gene activation and silencing. We provide evidence for interactive roles of regulatory sequence changes, chromatin modification, and trans-acting effects in natural selection of orthologous FLC loci, which determines the fate of duplicate genes and adaptation of allopolyploids during evolution.

Acetylation↗

PubMed2006

Human cytomegalovirus persists in its host and attacks and avoids elimination by the immune system.

Human cytomegalovirus (HCMV) is a herpesvirus that infects, and is carried by, 70%-100% of the world's population. During its evolution, the virus has adapted to survive in an immunocompetent host. For many years, HCMV was not considered to be a major human pathogen because it only caused rare cases of HCMV inclusion disease in neonates. However, HCMV is poorly adapted to survive in the immunosuppressed host and has emerged as an important human pathogen in AIDS patients, and in patients undergoing immunosuppressive therapy after organ or bone marrow transplantation. The virus is also the major infectious cause of birth defects. To coexist with its host, HCMV must avoid elimination by the immune system. Research over the past decade has revealed sophisticated mechanisms that enable the virus to remain invisible to cells of the immune system.

Animals↗

PubMed2006

Cellular organization of the oncosphere of Mosgovoyia ctenoides (Cestoda: Anoplocephalidae).

The ultrastructure of the infective oncosphere of the cestode Mosgovoyia ctenoides (Anoplocephalidae) is described. The surface of the infective oncosphere is covered by a thin cytoplasmic layer of tegument connected by a narrow cytoplasmic process with the binucleate subtegumental cell, situated deeper in the body. Below the basal matrix of the cytoplasmic layer of the tegument are situated wide bands of the peripheral, somatic musculature responsible for body movements. The 3 pairs of hooks and their muscles form a complex hook muscle system, responsible for coordinated hook action. Five major types of cells have been distinguished: (1) a binucleate subtegumental cell, (2) a binucleate penetration gland, (3) 2 nerve cells, (4) numerous somatic cells, and (5) about 6 germinative cells. The approximate number of cells is 24 (26 nuclei, including 2 syncytial structures). The results of this study, when compared with other published reports from other cestode taxa, support previous hypotheses that the progressive reduction of oncosphere cells is an adaptive feature in cestode evolution.

Animals↗

PubMed2005

Myelin tetraspan family proteins but no non-tetraspan family proteins are present in the ascidian (Ciona intestinalis) genome.

Several of the proteins used to form and maintain myelin sheaths in the central nervous system (CNS) and the peripheral nervous system (PNS) are shared among different vertebrate classes. These proteins include one-to-several alternatively spliced myelin basic protein (MBP) isoforms in all sheaths, proteolipid protein (PLP) and DM20 (except in amphibians) in tetrapod CNS sheaths, and one or two protein zero (P0) isoforms in fish CNS and in all vertebrate PNS sheaths. Several other proteins, including 2', 3'-cyclic nucleotide 3'-phosphodiesterase (CNP), myelin and lymphocyte protein (MAL), plasmolipin, and peripheral myelin protein 22 (PMP22; prominent in PNS myelin), are localized to myelin and myelin-associated membranes, though class distributions are less well studied. Databases with known and identified sequences of these proteins from cartilaginous and teleost fishes, amphibians, reptiles, birds, and mammals were prepared and used to search for potential homologs in the basal vertebrate, Ciona intestinalis. Homologs of lipophilin proteins, MAL/plasmolipin, and PMP22 were identified in the Ciona genome. In contrast, no MBP, P0, or CNP homologs were found. These studies provide a framework for understanding how myelin proteins were recruited during evolution and how structural adaptations enabled them to play key roles in myelination.

Amino Acid Sequence↗

PubMed1998

Cell-cell communication in carcinogenesis.

To explain the complex carcinogenic process by which a single normal cell in human beings can be converted to an invasive and metastatic cancer cell, a number of experimental findings, epidemiological observations and their associated hypothesis/theories have been integrated in this review. All cancers have been generally viewed as the result of a disruption of the homeostatic regulation of a cell's ability to respond appropriately to extra-cellular signals of the body which trigger intra-cellular signal transducting mechanisms which modulate gap junctional intercellular communication between the cells within a tissue. Normal homeostatic control of these three forms of cell communication determines whether: (a) the cell remains quiescent (Go); (b) enters into the cell proliferation phase; (c) is induced to differentiate; (d) is committed to apoptose; or (e) if it is already differentiated, it can adaptively respond. During the evolution from single cell organisms to multicellular organisms, new cellular/biological functions appeared, namely, the control of cell proliferation ("contact inhibition"), the appearance of the process of differentiation from committed stem cells of the various tissues and the need for programmed cell death or apoptosis. Interestingly, cancer cells have been characterized as cells: (a) having been derived from a stem-like cell; (b) without their ability to control cell growth or without the ability to contact inhibit; (c) which can not terminally differentiate under normal conditions; and (d) having altered ability to apoptosis under normal conditions. During that evolutionary transition from the single cell organism to the multicellular organism, many new genes appeared to accompany these new cellular functions. One of these new genes was the gene coding for a membrane associated protein channel (the gap junction) which between coupled cells, allowed the passive transfer on ions and small molecular weight molecules. A family of over a dozen of these highly evolutionarily-conserved genes (the connexin genes) coded for the connexin proteins. A hexameric unit of these connexins in one cell (a connexon) couples with a corresponding connexon in a contiguous cell to join the cytoplasms. This serves to synchronize either the metabolic or electrotonic functions of cells within a tissue. Most normal cells within solid tissues have functional gap junctional intercellular communication (GJIC) (exceptions are free-standing cells such as red blood cells, neutrophils, and several, if not all, the stem cells). On the other hand, the cancer cells of solid tissues appear to have either dysfunctional homologous or heterologous GJIC. Therefore, among the many differences between a cancer cell and its normal parental cell, the carcinogenic process involves the transition from a normal, GJIC-competent cell to one that is defective in GJIC. The review examines how GJIC can be either transiently or stably modulated by endogenous or exogenesis chemicals or by oncogenes and tumor suppressor genes at the transcriptional, translational, or posttranslational levels. It also uses the gap junction as the biological structure to facilitate cellular/tissue homeostasis to be the integrator for the "stem cell" theory, "disease of differentiation theory", "initiation/promotion/progression" concepts, nature and nurture concept of carcinogenesis, the mutation/ epigenetic theories of carcinogenesis, and the oncogene/ tumor suppressor gene theories of carcinogenesis. From this background, implications to cancer prevention and cancer therapy are generated.

Cell Communication↗