Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “structural phylogenetics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,783 records · Page 99Linked to original sources
PubMed2004

Genetic relationships and evolution of genotypes of yellow fever virus and other members of the yellow fever virus group within the Flavivirus genus based on the 3' noncoding region.

Genetic relationships among flaviviruses within the yellow fever (YF) virus genetic group were investigated by comparing nucleotide sequences of the 3' noncoding region (3'NCR). Size heterogeneity was observed between members and even among strains of the same viral species. Size variation between YF strains was due to duplications and/or deletions of repeated nucleotide sequence elements (RYF). West African genotypes had three copies of the RYF (RYF1, RYF2, and RYF3); the Angola and the East and Central African genotypes had two copies (RYF1 and RYF3); and South American genotypes had only a single copy (RYF3). Nucleotide sequence analyses suggest a deletion within the 3'NCR of South American genotypes, including RYF1 and RYF2. Based on studies with the French neurotropic vaccine strain, passage of a YF virus strain in cell culture can result in deletion of RYF1 and RYF2. Taken together, these observations suggest that South American genotypes of YF virus evolved from West African genotypes and that the South American genotypes lost RYF1 and RYF2, possibly in a single event. Repeated sequence elements were found within the 3'NCR of other members of the YF virus genetic group, suggesting that it is probably characteristic for members of the YF virus genetic group. A core sequence of 15 nucleotides, containing two stem-loops, was found within the 3'NCR of all members of the YF genetic group and may represent the progenitor repeat sequence. Secondary structure predictions of the 3'NCR showed very similar structures for viruses that were closely related phylogenetically.

Africa, Western↗
PubMed2000

trans splicing of polycistronic Caenorhabditis elegans pre-mRNAs: analysis of the SL2 RNA.

Genes in Caenorhabditis elegans operons are transcribed as polycistronic pre-mRNAs in which downstream gene products are trans spliced to a specialized spliced leader, SL2. SL2 is donated by a 110-nucleotide RNA, SL2 RNA, present in the cell as an Sm-bound snRNP. SL2 RNA can be conceptually folded into a phylogenetically conserved three-stem-loop secondary structure. Here we report an in vivo mutational analysis of the SL2 RNA. Some sequences can be changed without consequence, while other changes result in a substantial loss of trans splicing. Interestingly, the spliced leader itself can be dramatically altered, such that the first stem-loop cannot form, with only a relatively small loss in trans-splicing efficiency. However, the primary sequence of stem II is crucial for SL2 trans splicing. Similarly, the conserved primary sequence of the third stem-loop plays a key role in trans splicing. While mutations in stem-loop III allow snRNP formation, a single nucleotide substitution in the loop prevents trans splicing. In contrast, the analogous region of SL1 RNA is not highly conserved, and its mutation does not abrogate function. Thus, stem-loop III appears to confer a specific function to SL2 RNA. Finally, an upstream sequence, previously predicted to be a proximal sequence element, is shown to be required for SL2 RNA expression.

Animals↗
PubMed1988

Frontal and lateral visual system in birds. Frontal and lateral gaze.

Birds exhibit a variable retinal organization in terms of foveas and areas of high cell density. The distribution of these retinal structures in different species does not follow phylogenetic lines. In order to study this phenomenon, we presented chickens and pigeons with a luminous bar that could be moved at different speeds and directions in the visual field and could be located at various distances from the animal; head movements were monitored during the presentations. The results show that for a static or slow-moving stimulus the birds adopted a frontal gaze that stabilized the image in the retina, and for a fast-moving stimulus they adopted a lateral gaze that allowed the image to move across the retina. These results reveal that: (a) these two ways of looking correlate with the retinal anatomy, not with the phylogeny, of the species, and (b) these two ways of looking reflect two different sensorimotor systems that involve different anatomical features and neurophysiological properties of the visual system in birds.

Animals↗
PubMed2001

Evolution and phylogeny of insect endogenous retroviruses.

BACKGROUND: The genome of invertebrates is rich in retroelements which are structurally reminiscent of the retroviruses of vertebrates. Those containing three open reading frames (ORFs), including an env-like gene, may well be considered as endogenous retroviruses. Further support to this similarity has been provided by the ability of the env-like gene of DmeGypV (the Gypsy endogenous retrovirus of Drosophila melanogaster) to promote infection of Drosophila cells by a pseudotyped vertebrate retrovirus vector. RESULTS: To gain insights into their evolutionary story, a sample of thirteen insect endogenous retroviruses, which represents the largest sample analysed until now, was studied by computer-assisted comparison of the translated products of their gag, pol and env genes, as well as their LTR structural features. We found that the three phylogenetic trees based respectively on Gag, Pol and Env common motifs are congruent, which suggest a monophyletic origin for these elements. CONCLUSIONS: We showed that most of the insect endogenous retroviruses belong to a major clade group which can be further divided into two main subgroups which also differ by the sequence of their primer binding sites (PBS). We propose to name IERV-K and IERV-S these two major subgroups of Insect Endogenous Retro Viruses (or Insect ERrantiVirus, according to the ICTV nomenclature) which respectively use Lys and Ser tRNAs to prime reverse transcription.

Amino Acid Motifs↗
PubMed2004

Identification of a stanniocalcin paralog, stanniocalcin-2, in fish and the paracrine actions of stanniocalcin-2 in the mammalian ovary.

Stanniocalcin is a glycoprotein hormone important in the maintenance of calcium and phosphate homeostasis in fish. Two related mammalian stanniocalcin genes, STC1 and STC2, were found to be expressed in various tissues as paracrine regulators. We have demonstrated the existence of a second stanniocalcin gene in fish, designated fish STC2, with only 30% identity to fish STC1. However, phylogenetic analysis and comparison of the genomic structure of STC genes in vertebrates indicated that STC1 and STC2 genes were probably derived from a common ancestor gene. Based on the prominent expression of mammalian STC1 in the ovary, we tested STC2 expression in rat ovary and the regulation of STC2 expression by gonadotropins. Treatment of immature rats with pregnant mare serum gonadotropin increased STC2 transcripts, whereas subsequent treatment with human chorionic gonadotropin suppressed STC2 expression. Real-time PCR analyses also demonstrated that STC2 is expressed mainly in thecal layers. In situ hybridization studies also revealed that STC2 is expressed in thecal cell layers of antral and preovulatory follicles after gonadotropin stimulation. To elucidate the physiological functions of STC2, recombinant human and fish STC2 proteins were generated and found to be N-glycosylated homodimers. In cultured granulosa cells, treatment with human or fish STC2 suppressed FSH-induced progesterone, but not estradiol or cAMP, production. The STC2 suppression of progesterone production was associated with the inhibition of FSH-induced CYP11A and 3beta-hydroxysteroid dehydrogenase expression. Thus, STC2 is a functional homodimeric glycoprotein, and thecal cell-derived STC2 could play a paracrine role during follicular development.

Animals↗
PubMed2005

The single AmphiTrk receptor highlights increased complexity of neurotrophin signalling in vertebrates and suggests an early role in developing sensory neuroepidermal cells.

Neurotrophins (Nt) and their tyrosine kinase Trk receptors play an essential role in the development and maintenance of the complex vertebrate nervous system. Invertebrate genome sequencing projects have suggested that the Nt/Trk system is a vertebrate innovation. We describe the isolation and characterisation of the amphioxus Trk receptor, AmphiTrk. Its ancestral link to vertebrate Trk receptors is supported by phylogenetic analysis and domain characterisation. The genomic structure of AmphiTrk strongly suggests that a ProtoTrk gene emerged by means of exon-shuffling prior to the cephalochordate/vertebrate split. We also examined the physiological response of AmphiTrk to vertebrate neurotrophins, and found that despite 500 million years of divergence, AmphiTrk transduces signals mediated by NGF, BDNF, NT3 and NT4. Markedly, AmphiTrk is able to activate survival and differentiation pathways, but fails to activate the PLCgamma pathway, which is involved in synaptic plasticity in higher vertebrates. AmphiTrk is expressed during amphioxus embryogenesis in sensory neural precursors in the epidermis, which possesses single migratory cells. We propose that the duplication and divergence of the Nt/Trk system, in tandem with recruitment of the PLCgamma pathway, may have provided the genetic basis for a key aspect of vertebrate evolution: the complexity of the nervous system.

Amino Acid Sequence↗
PubMed2006

Molecular-genetic biodiversity in a natural population of the yeast Saccharomyces cerevisiae from "Evolution Canyon": microsatellite polymorphism, ploidy and controversial sexual status.

The yeast S. cerevisiae is a central model organism in eukaryotic cell studies and a major component in many food and biotechnological industrial processes. However, the wide knowledge regarding genetics and molecular biology of S. cerevisiae is based on an extremely narrow range of strains. Studies of natural populations of S. cerevisiae, not associated with human activities or industrial fermentation environments, are very few. We isolated a panel of S. cerevisiae strains from a natural microsite, "Evolution Canyon" at Mount Carmel, Israel, and studied their genomic biodiversity. Analysis of 19 microsatellite loci revealed high allelic diversity and variation in ploidy level across the panel, from diploids to tetraploids, confirmed by flow cytometry. No significant differences were found in the level of microsatellite variation between strains derived from the major localities or microniches, whereas strains of different ploidy showed low similarity in allele content. Maximum genetic diversity was observed among diploids and minimum among triploids. Phylogenetic analysis revealed clonal, rather than sexual, structure of the triploid and tetraploid subpopulations. Viability tests in tetrad analysis also suggest that clonal reproduction may predominate in the polyploid subpopulations.

Alleles↗
PubMed2001

Molecular phylogeny of the other tissue coccidia: Lankesterella and Caryospora.

Nearly complete sequences were obtained from the 18S rDNA genes of Eimeria falciformis (the type species of the genus), Caryospora bigenetica, and Lankesterella minima. Two clones of the rDNA gene from C. higenetica varied slightly in primary structure. Parsimony-based and maximum likelihood phylogenetic reconstructions with a number of other apicomplexan taxa support 2 major clades within the Eucoccidiorida, i.e., the isosporoid coccidia (consisting of Toxoplasma, Neospora, Isospora [in part], and Sarcocystis spp.) and a second clade containing Lankesterella and Caryospora spp., as well as the eimeriid coccidia (Cyclospora, Isospora [in part], and Eimeria spp.). Our observations suggest that Caryospora spp. may not belong in the family Eimeriidae but rather may be allied with the family Lankesterellidae with which they share molecular and life history similarities. This may be a third lineage of coccidian parasites that has independently evolved a unique heteroxenous transmission strategy.

Animals↗
PubMed2026

Genome-Wide Identification and Characterization of the TBL Gene Family and Temporal Expression Dynamics During Powdery Mildew Infection in Cucumber (Cucumis sativus).

Cell-wall polysaccharide O-acetylation contributes to cell-wall assembly, organ development, and plant-pathogen interactions, but the cucumber TBL gene family remains poorly characterized. Here, 37 CsTBL genes were identified genome-wide and analyzed using phylogenetic, syntenic, conserved-motif, gene-structure, promoter, protein-structure, Gene Ontology, and transcriptome approaches, followed by RT-qPCR analysis after powdery mildew inoculation. All CsTBL proteins contained the conserved GDS and DxxH motifs, whereas accessory motifs and predicted structural features varied among clades. Intraspecific analysis identified dispersed, WGD/segmental, and tandem duplication categories, and cross-species synteny was more extensive with melon than with Arabidopsis. Homology-derived annotations associated CsTBL genes with cell-wall polysaccharide metabolism, Golgi/endomembrane compartments, and O-acetyltransferase activity, including six genes assigned to xylan O-acetyltransferase-related annotations. Expression profiling revealed tissue- and developmental-stage-dependent patterns, whereas the publicly available powdery mildew RNA-seq dataset provided descriptive temporal expression profiles in Podosphaera xanthii-inoculated samples. Independent RT-qPCR analysis using time-matched mock controls revealed distinct post-inoculation responses among six selected genes. Relative to the corresponding mock controls, CsTBL2 was consistently repressed; CsTBL15 showed transient induction at 1 dpi followed by repression; CsTBL24 exhibited a biphasic response; CsTBL25 was induced at all sampled post-inoculation time points; CsTBL26 showed progressive induction; and CsTBL30 reached its highest observed expression level at 3 dpi. Integrated functional annotation and expression evidence highlighted CsTBL26 as a priority candidate for further functional characterization, while CsTBL24 and CsTBL25 represented fruit-associated candidates with distinct powdery mildew responses; CsTBL30 remained an additional strongly infection-responsive candidate. These findings provide an evolutionary and expression-based framework for the functional characterization of the cucumber TBL gene family.

O-acetylation↗
PubMed1999

Expression of human blood group antigens A and B in stomach cells of C. carpio, C. auratus, R. ridibunda and H. sapiens.

Human blood group ABH antigens are found not only on red blood cell membranes, but in many other cell types as well. Their biological functions still remain unclear. The aim of the present study was to examine the cellular expression of these antigens in the stomach of representatives of different Vertebrates--Pisces and Amphibia and to compare it with their expression found in Man. The immunohistochemical technique applied was based on the biotinstreptavidin-peroxidase complex. Monoclonal antibodies to human A and B antigens were used as primary antibodies in the system. Stomach paraffin sections from Cyprinus carpio, Carassius auratus, Rana ridibunda and Homo sapiens were examined. Blood group antigens were found mainly in tunica mucosa of C. carpio, C. auratus and R. ridibunda. Tunica muscularis and tunica serosa were always immunonegative. The antigens were localized in the apical part of the cytoplasm of epithelial cells in lamina epithelialis. Strong positive reaction was seen in secretory granules of the stomach of C. auratus, while in R. ridibunda the antigens were expressed by single epithelial cells in cardial stomach glands. A and B antigens were not found in human stomach sections most probably due to the negative secretor status of the individuals studied. Our results show that ABH human blood group antigens are evolutionary conserved structures similarly expressed by different Vertebrates. The phylogenetic stability in their cellular expression possibly results from the important biological role they have. Future large scale systematic investigations could elucidate the undefined and disputable physiological functions of human blood group antigens.

ABO Blood-Group System↗
PubMed1992

The genomic organization of a novel regulatory myosin light chain gene (MYL5) that maps to chromosome 4p16.3 and shows different patterns of expression between primates.

Myosin participates in a varying repertoire of cellular functions ranging from cytokinesis, receptor capping and secretion to sarcomere contraction. In vertebrates this functional complexity is achieved through the regulated expression of gene families encoding isoproteins for each of the myosin subunits. We report here the identification and characterization of a gene (MYL5) that encodes a novel regulatory myosin light chain isoprotein and maps 700 kb from the human chromosome 4p telomere. Identical cDNAs have been isolated from human adult retina and fetal muscle cDNA libraries. A full length 519 bp open reading frame was identified in the cDNA sequence encoding a predicted protein of 173 residues. Sequence analysis of a 5.6 kb genomic region that encodes these cDNAs revealed the presence of 7 exons which span 4 kb. Expression of this gene has been detected in human adult retina, cerebellum, basal ganglia and fetal skeletal muscle. Whereas Northern analysis fails to detect transcription of this gene in human adult skeletal muscle it reveals an abundant transcript in monkey skeletal muscle. Phylogenetic comparison of the predicted proteins primary structure to those of related myosin light chains from Drosophila, rat and human reveal evolutionarily conserved structural motifs important for both calcium binding and phosphorylation.

Adult↗
PubMed1987

Evolutionary aspects of reptilian and mammalian enamel structure.

The evolution of enamel structure is dealt with here on the basis of fossil reptiles and mammals ranging from the Triassic to the present. The evidence suggests that prismatic enamel had developed in some therapsid reptiles and the mammal, Eozostrodon about 180 million years ago. For the next 100 million years, mammalian evolutionary history is sparingly documented and this is reflected in the poor record of enamel evolution during this period. The few Jurassic reptiles and mammals studied suggest a preprismatic structure. In the Late Cretaceous (80 to 65 million years ago) when the fossil record improves, mammalian enamel investigated from North American localities, are found to be prismatic; allotherian (multituberculate) and metatherian (marsupial) enamels are usually tubular, while eutherian (placental) ones are not. Prism structure in Tertiary mammals in general, conforms to that of their present day descendants, but there are discernible exceptions. The record of evolutionary change in Tertiary mammals is obscured by functional modifications related to biomechanical stresses. Enamel structure may be secondarily modified; similar in phylogenetically unrelated groups (eg., pauciserial enamel of early rodents) or dissimilar at the intra-familial level (eg., rodent families Ctenodactylidae and Ischryomyicae). Prismatic enamel is recorded from the tooth of a hatchling of the gavial, Gavialis gangeticus.

Animals↗
PubMed1987

Tandem scanning reflected light microscopy of primate enamel.

Studies of the cross sectional packing arrangements of primate enamel prisms have been used in a number of recent studies in attempts to determine their taxonomic utility. Credibility of the results has been greatly influenced by the methods employed to examine enamel prism packing patterns and also by the limited sampling. We report here the use of a technique for the non destructive examination, in depth, of enamel prism packing patterns in modern and fossil primate teeth which has considerable advantages over any others so far used, and the preliminary results of a survey of enamel structural diversity in the Order Primates. The phylogenetic implications of these findings are also discussed. A novel microscope, the Tandem Scanning Reflected Light Microscope (TSM) has been used. This instrument has allowed these data to be obtained non destructively which has permitted the inclusion of rare fossil primates in this survey. The technique has many advantages relating to the interpretation of the results as the specimens are not etched or otherwise prepared. Primates exhibit all three major prism packing arrangements known for recent mammals. The distribution of these permits the recognition of haplorhine from strepsirhine primates and also cercopithecoid monkeys from other catarrhines.

Animals↗
PubMed1986

Neurochemical significance of the red nucleus.

This study reviews some of the more prominent reports related to neuromelanin and the physiological significance of the substantia nigra and the red nucleus. The phylogenetic and ontogenetic parallelism between these two structures is considered. The presence of dopachrome in the red nucleus and of neuromelanin in the substantia nigra is discussed. An experimental study in four human brains in which the red nucleus was injected with zinc sulfate showed the presence of neuromelanin in the red nucleus. This is the first reported demonstration that dopachrome present in the red nucleus is the precursor of neuromelanin.

Adult↗
PubMed1986

Cyclophilin: distribution and variant properties in normal and neoplastic tissues.

The cytosolic concentration, Mr, and isoforms of cyclophilin (CyP), a specific cytosolic binding protein for cyclosporin A (CsA), were determined in normal and neoplastic human tissues as well as tissues from species of diverse phylogeny. CyP was present in all tissues examined; however, concentrations varied significantly among different tissue types. The CyP concentration was highest in lymphoblasts from a patient with T cell acute lymphocytic leukemia (1.15 micrograms/mg protein) and Hodgkin's and non-Hodgkin's lymphomas. CyP concentration in colon adenocarcinomas was twofold to threefold greater than that found in adjacent normal tissue. CyP from all normal and neoplastic human tissues examined had an apparent Mr of 17,000 determined by gel filtration HPLC. Major (pI 8.6 to 8.7) and minor (pI 6.7 to 6.9) CyP isoforms were identified in all human and murine tissue extracts by column sucrose gradient isoelectrofocusing; however, the ratio of the major to minor isoform varied widely. Among other species examined, significant concentrations of CyP were detected in cytosol extracts from sponges (Microciona prolifera), yeast (Saccharomyces cerevisiae), mushrooms, the giant cockroach (Blaberus discoidalis), and a trematode (Schistosoma mansoni). By contrast, CyP was not detectable in extracts of Escherichia coli. A twofold to threefold elevation in the CyP content of murine splenocytes was detected 72 hr after Con A stimulation. A survey of a variety of natural products, synthetic compounds, and immunoregulating agents has failed thus far to identify compounds capable of competing with CsA for binding to CyP. The broad tissue and phylogenetic distribution of CyP, its highly conserved structure, and its increased content after mitogenic stimulation suggest a fundamental role in cellular metabolism.

Animals↗
PubMed1994

Characterization of a glucose-repressible ADP-ribosylation factor 3 (ARF3) from Saccharomyces cerevisiae.

ADP-ribosylation factors (ARFs) are highly conserved approximately 20-kDa guanine nucleotide-binding proteins that enhance the ADP-ribosyltransferase activity of cholera toxin, and are believed to participate in vesicular transport in both exocytic and endocytic pathways. Based on size, phylogenetic analysis, amino acid sequence, and gene structure, mammalian ARFs fall into three classes (class I, ARFs 1, 2, 3; class II, ARFs 4, 5; class III, ARF6). Two ARF genes (yARF1, yARF2) are known in Saccharomyces cerevisiae and believed to participate in vesicular trafficking in the Golgi system; the double deletion mutant is not viable. A third yeast ARF (yARF3) cDNA has been cloned by polymerase chain reaction-based procedures. It contains an open reading frame of 549 bases encoding a protein of 183 amino acids, with a deduced amino acid sequence more identical (60%) to that of the class III mammalian ARF than to those of the other two classes (52-56%). The yARF3 protein, however, reacted poorly with antibodies against any of the three classes of mammalian ARFs. In the presence of GTP, recombinant yARF3 protein stimulated cholera toxin-catalyzed auto-ADP-ribosylation. yARF3 gene transcription, similar to that of yARF2, was repressed by glucose. As yARF3 was not essential for cell viability and was not required for endoplasmic reticulum to Golgi protein transport, it may provide an opportunity to define an ARF function in another kind of vesicular trafficking.

ADP-Ribosylation Factors↗
PubMed1994

Characterization of class II and class III ADP-ribosylation factor genes and proteins in Drosophila melanogaster.

ADP-ribosylation factors (ARFs) are ubiquitous approximately 20-kDa guanine nucleotide-binding proteins that enhance the ADP-ribosyltransferase activity of cholera toxin and are involved in intracellular vesicular transport. Based on size, phylogenetic analysis, amino acid identity, and gene structure, mammalian ARFs fall into three classes (class I, ARF1, -2, and -3; class II, ARF4 and -5; class III, ARF6). A class I ARF had been identified in Drosophila melanogaster. To search for ARFs of other classes in Drosophila, polymerase chain reaction-based techniques were used, resulting in cloning of Drosophila ARF (dARF) II and dARF III with deduced amino acid sequences similar to those of class II and class III mammalian ARFs, respectively. The three Drosophila ARF genes map to different chromosomes and the coding regions have different splicing sites. dARF II mRNA, like ARF I mRNA, is fairly uniformly distributed throughout adult flies, whereas dARF III mRNA is significantly more abundant in heads than in legs or bodies. Recombinant dARF II and dARF III have biochemical and immunological properties similar to those of human ARF5 (hARF5) and hARF6, respectively. These observations are consistent with the conclusion that the three classes of ARFs are present in non-mammalian as well as mammalian species.

ADP-Ribosylation Factor 1↗
PubMed1996

Interspecies cross-reactivity of a monoclonal antibody directed against wheat chloroplast fructose-1,6-bisphosphatase.

The primary structure of several chloroplast fructose-1,6-bisphosphatase (CFBPase) was deduced from DNA sequences, but only spinach, pea and rapeseed enzymes have been characterized structurally. We analyzed whether CFBPases from different phylogenetic origin contain a common epitope. To this end a DNA fragment of 1200 base pairs encoding 338 amino acid residues of wheat CFBPase (38 kDa) was cloned in the expression plasmid pGEX-1 in frame with the gene coding for glutathione S-transferase (GT) of Schistosoma japonicun (26.5 kDa). Upon transformation of Escherichia coli and induction with isopropyl-beta-D-thiogalactopyranoside, centrifugation of the lysate partitioned 10% of the fusion protein in the supernatant fraction and the remaining 90% in the precipitate. The expected 65 kDa protein was purified from both the soluble and the particulate fraction by affinity chromatography on columns of glutathione-agarose. This fusion protein was successfully used to produce a monoclonal antibody that specifically recognized the CFBPase region of the fusion protein but not the GT moiety. Moreover, the monoclonal antibody immunoreacted not only with polypeptides (ca. 40 kDa) present in leaf crude extracts of other varieties of wheat (Triticum spelta, T. aestivum and T. durum), but also with homogeneous preparations of the spinach (Spinacia oleracea) and rapeseed (Brassica napus) enzymes. Thus, the cross reaction of this monoclonal antibody with counterparts from different plant species indicates the persistency of a common epitope through biological evolution.

Amino Acid Sequence↗