Sequence Comparison (sequence + comparison)

Distribution by Scientific Domains
Distribution within Life Sciences

Kinds of Sequence Comparison

  • acid sequence comparison
  • amino acid sequence comparison
  • dna sequence comparison
  • nucleotide sequence comparison


  • Selected Abstracts


    PHYLOGENY OF THE EUGLENALES BASED UPON COMBINED SSU AND LSU RDNA SEQUENCE COMPARISONS AND DESCRIPTION OF DISCOPLASTIS GEN.

    JOURNAL OF PHYCOLOGY, Issue 3 2006
    NOV. (EUGLENOPHYTA)
    A Bayesian analysis, utilizing a combined data set developed from the small subunit (SSU) and large subunit (LSU) rDNA gene sequences, was used to resolve relationships and clarify generic boundaries among 84 strains of plastid-containing euglenophytes representing 11 genera. The analysis produced a tree with three major clades: a Phacus and Lepocinlis clade, a Discoplastis clade, and a Euglena, Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade. The majority of the species in the genus Euglena formed a well-supported clade, but two species formed a separate clade near the base of the tree. A new genus, Discoplastis, was erected to accommodate these taxa, thus making the genus Euglena monophyletic. The analysis also supported the monophyly of Colacium, Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena, which formed two subclades sister to the Euglena clade. Colacium, Trachelomonas, and Strombomonas, all of which produce copious amounts of mucilage to form loricas or mucilaginous stalks, formed a well-supported lineage. Our analysis supported retaining Strombomonas and Trachelomonas as separate genera. Monomorphina and Cryptoglena formed two well-supported clades that were sister to the Colacium, Trachelomonas, and Strombomonas clade. Phacus and Lepocinclis, both of which have numerous small discoid chloroplasts without pyrenoids and lack peristaltic euglenoid movement (metaboly), formed a well-supported monophyletic lineage that was sister to the larger Euglena through Cryptoglena containing clade. This study demonstrated that increased taxon sampling, multiple genes, and combined data sets provided increased support for internal nodes on the euglenoid phylogenetic tree and resolved relationships among the major genera in the photosynthetic euglenoid lineage. [source]


    Detection and molecular characterization of foamy viruses in Central African chimpanzees of the Pan troglodytes troglodytes and Pan troglodytes vellerosus subspecies

    JOURNAL OF MEDICAL PRIMATOLOGY, Issue 2 2006
    Sara Calattini
    Abstract Background, Foamy viruses are exogenous retroviruses that are highly endemic in non-human primates (NHPs). Recent studies, mainly performed in North America, indicated frequent simian foamy virus (SFV) infection in persons occupationally exposed to NHPs. This zoonotic infection was demonstrated mainly after bites by chimpanzees [Pan troglodytes (P. t.)] of the West African P. t. verus subspecies in primatology centers or zoos in the USA. Methods, We studied 32 chimpanzees from the Central African subspecies P. t. troglodytes and P. t. vellerosus, originating from Cameroon (29 cases) or Gabon (3 cases). We screened first plasma or sera of the animals with a Western blot detecting the SFVs Gag doublet proteins. Then, we performed two nested polymerase chain reactions (PCRs) amplifying a fragment of the integrase and LTR regions and, finally, we made phylogenetical analyses on the sequences obtained from the integrase PCR products. Results, By serological and/or molecular assays, we detected foamy viruses (FVs) infection in 14 chimpanzees. Sequence comparison and phylogenetic analyses of a 425 bp fragment of the integrase gene obtained for 10 of the 14 positive apes, demonstrated a wide diversity of new FVs strains that belong phylogenetically either to the P. t. troglodytes or P. t. vellerosus foamy viral clade. Conclusions, This study shows that chimpanzees living in these areas of Central Africa are infected by several specific foamy viruses. This raises, in such regions, the potential risk of a human retroviral infection of zoonotic origin linked to chimpanzees contacts, as already exemplified for STLV-1 and SIV infections. [source]


    Rapid diversification of measles virus genotypes circulating in Morocco during 2004,2005 epidemics,

    JOURNAL OF MEDICAL VIROLOGY, Issue 11 2006
    Amal Alla
    Abstract Measles virus strains circulating in six different regions in Morocco during 2004,2005 were analysed. They were genotyped using two different methods: the recently developed method based on real-time PCR amplification and melting curve analyses, and the conventional method based on nucleic acid sequencing and phylogenetic analysis of 456 nucleotides of the 3,-region of the nucleoprotein (N) gene sequence. Five genotypes (A, B3.2, C2, D7 and D8) were shown to be circulating during this period. Previous studies on measles virus genotypes in Morocco (1998,2003) showed that only the genotype C2 was present and was considered to be endemic. Sequence comparison of the 2004,2005 viruses with other measles strains suggests that measles strains belonging to genotype B3.2 were probably imported from West Africa, whereas those belonging to genotypes D7 and D8 were imported from Europe. These studies which identify the route of importation of measles are important for developing strategies for measles elimination in Morocco. J. Med. Virol. 78:1465,1472, 2006. © 2006 Wiley-Liss, Inc. [source]


    Sequence Variations of the Human MPDZ Gene and Association With Alcoholism in Subjects With European Ancestry

    ALCOHOLISM, Issue 4 2009
    Victor M. Karpyak
    Background:,Mpdz gene variations are known contributors of acute alcohol withdrawal severity and seizures in mice. Methods:, To investigate the relevance of these findings for human alcoholism, we resequenced 46 exons, exon,intron boundaries, and 2 kilobases in the 5, region of the human MPDZ gene in 61 subjects with a history of alcohol withdrawal seizures (AWS), 59 subjects with a history of alcohol withdrawal without AWS, and 64 Coriell samples from self-reported nonalcoholic subjects [all European American (EA) ancestry] and compared with the Mpdz sequences of 3 mouse strains with different propensity to AWS. To explore potential associations of the human MPDZ gene with alcoholism and AWS, single SNP and haplotype analyses were performed using 13 common variants. Results:, Sixty-seven new, mostly rare variants were discovered in the human MPDZ gene. Sequence comparison revealed that the human gene does not have variations identical to those comprising Mpdz gene haplotype associated with AWS in mice. We also found no significant association between MPDZ haplotypes and AWS in humans. However, a global test of haplotype association revealed a significant difference in haplotype frequencies between alcohol-dependent subjects without AWS and Coriell controls (p = 0.015), suggesting a potential role of MPDZ in alcoholism and/or related phenotypes other than AWS. Haplotype-specific tests for the most common haplotypes (frequency > 0.05), revealed a specific high-risk haplotype (p = 0.006, maximum statistic p = 0.051), containing rs13297480G allele also found to be significantly more prevalent in alcoholics without AWS compared with nonalcoholic Coriell subjects (p = 0.019). Conclusions:, Sequencing of MPDZ gene in individuals with EA ancestry revealed no variations in the sites identical to those associated with AWS in mice. Exploratory haplotype and single SNP association analyses suggest a possible association between the MPDZ gene and alcohol dependence but not AWS. Further functional genomic analysis of MPDZ variants and investigation of their association with a broader array of alcoholism-related phenotypes could reveal additional genetic markers of alcoholism. [source]


    Characterization and functional analysis of PorB, a Chlamydia porin and neutralizing target

    MOLECULAR MICROBIOLOGY, Issue 4 2000
    Aya Kubo
    A predicted protein (CT713) with weak sequence similarity to the major outer membrane protein (20.4% identity) in Chlamydia trachomatis was identified by Chlamydia genome analysis. We show that this protein is expressed, surface accessible, localized to the chlamydial outer membrane complex and functions as a porin. This protein, PorB, was highly conserved among different serovars, with nearly identical sequences between serovars D, B, C and L2. Sequence comparison between C. trachomatis and Chlamydia pneumoniae showed less conservation between species with 59.3% identity. Immunofluorescence staining with monospecific antisera to purified PorB revealed antigen localized within chlamydial inclusions and found throughout the developmental cycle. Antibodies to PorB neutralized infectivity of C. trachomatis in an in vitro neutralization assay confirming that PorB is surface exposed. As PorB was found to be in the outer membrane, as well as having weak structural characteristics similar to major outer membrane protein (MOMP) and other porins, a liposome-swelling assay was used to determine whether this protein had pore-forming capabilities. PorB had pore-forming activity and was shown to be different from MOMP porin activity. [source]


    A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family

    MOLECULAR REPRODUCTION & DEVELOPMENT, Issue 2 2008
    Martin A. Hansen
    Abstract Many testis-specific genes from the sex chromosomes are subject to rapid evolution, which can make it difficult to identify murine genes in the human genome. The murine CYPT gene family includes 15 members, but orthologs were undetectable in the human genome. However, using refined homology search, sequences corresponding to the shared promoter region of the CYPT family were identified at 39 loci. Most loci were located immediately upstream of genes belonging to the VCX/Y, SPANX, or CSAG gene families. Sequence comparison of the loci revealed a conserved CYPT promoter-like (CPL) element featuring TATA and CCAAT boxes. The expression of members of the three families harboring the CPL resembled the murine expression of the CYPT family, with weak expression in late pachytene spermatocytes and predominant expression in spermatids, but some genes were also weakly expressed in somatic cells and in other germ cell types. The genomic regions harboring the gene families were rich in direct and inverted segmental duplications (SD), which may facilitate gene conversion and rapid evolution. The conserved CPL and the common expression profiles suggest that the human VCX/Y, SPANX, and CSAG2 gene families together with the murine SPANX gene and the CYPT family may share a common ancestor. Finally, we present evidence that VCX/Y and SPANX may be paralogs with a similar protein structure consisting of C terminal acidic repeats of variable lengths. Mol. Reprod. Dev. 75: 219,229, 2008. © 2007 Wiley-Liss, Inc. [source]


    Continuous expression in tobacco leaves of a Brassica napus PEND homologue blocks differentiation of plastids and development of palisade cells

    THE PLANT JOURNAL, Issue 1 2005
    Paul Wycliffe
    Summary Brassica napus complementary deoxyribonucleic acid (cDNA) clones encoding a DNA-binding protein, BnPEND, were isolated by Southwestern screening. A distinctive feature of the protein was a bZIP-like sequence in the amino-terminal portion, which, after expression in Escherichia coli, bound DNA. BnPEND transcripts were present in B. napus roots and flower buds, and to a lesser extent in stems, flowers and young leaves. Treatment in the dark for 72 h markedly increased the amount of BnPEND transcript in leaves of all ages. Sequence comparison showed that BnPEND was similar to a presumed transcription factor from B. napus, GSBF1, a protein deduced from an Arabidopsis thaliana cDNA (BX825084) and the PEND protein from Pisum sativum, believed to anchor the plastid DNA to the envelope early during plastid development. Homology to expressed sequence tag (EST) sequences from additional species suggested that BnPEND homologues are widespread among the angiosperms. Transient expression of BnPEND fused with green fluorescent protein (GFP) in Nicotiana benthamiana epidermal cells showed that BnPEND is a plastid protein, and that the 15 amino acids at the amino-terminal contain information about plastid targeting. Expression of BnPEND in Nicotiana tabacum from the Cauliflower Mosaic Virus 35S promoter gave stable transformants with different extents of white to light-green areas in the leaves, and even albino plants. In the white areas, but not in adjacent green tissue, the development of palisade cells and chloroplasts was disrupted. Our data demonstrate that the BnPEND protein, when over-expressed at an inappropriate stage, functionally blocks the development of plastids and leads to altered leaf anatomy, possibly by preventing the release of plastid DNA from the envelope. [source]


    Endothelin receptor B2 (EDNRB2) is associated with the panda plumage colour mutation in Japanese quail

    ANIMAL GENETICS, Issue 2 2007
    M. Miwa
    Summary The panda mutant in Japanese quail (Coturnix japonica) displays spots of wild-type plumage on a white background and is controlled by an autosomal recessive allele (s). The dotted white is controlled by a third allele (sdw) of the s locus with sdw/sdw quail having less pigmentation than s/s quail. We mapped the s locus to the Japanese quail chromosome 4 (CJA04) in a previous study. The orthologous region of the chicken (Gallus gallus) genome includes endothelin receptor B2 (EDNRB2), an avian-specific paralog of endothelin receptor B (EDNRB). EDNRB mutations in mammals retard the migration of neural crest cells (NCCs), which results in a spotted coat colour and an enteric nervous defect. In the present study, we investigated the association between the s locus and EDNRB2 in Japanese quail. Sequence comparison among transcripts from livers of wild-type, panda and dotted white quail revealed a nucleotide substitution (c.995G>A) leading to a p.R332H amino acid change that was specific to panda, whereas no amino acid substitution was found in dotted white birds. The amino acid position 332 is located in the sixth transmembrane domain and is highly conserved in both avian and mammalian endothelin receptors. The A allele at nucleotide position 995 was specific to panda (s/s) birds among 10 strains, and was mapped to the same chromosomal region as the s locus. Quantitative RT-PCR revealed that EDNRB2 transcripts were reduced in both panda and dotted white mutants compared with wild-type. However, there was no difference between the early embryos of wild-type and panda with respect to the migration of NCCs. The genetic association of EDNRB2 with plumage colour in birds was found for the first time in this study. [source]


    Six cadm/synCAM genes are expressed in the nervous system of developing zebrafish

    DEVELOPMENTAL DYNAMICS, Issue 1 2008
    Thomas Pietri
    Abstract The Cadm (cell adhesion molecule) family of cell adhesion molecules (also known as IGSF4, SynCAM, Necl and TSLC) has been implicated in a multitude of physiological and pathological processes, such as spermatogenesis, synapse formation and lung cancer. The precise mechanisms by which these adhesion molecules mediate these diverse functions remain unknown. To investigate mechanisms of action of these molecules during development, we have identified zebrafish orthologs of Cadm family members and have examined their expression patterns during development and in the adult. Zebrafish possess six cadm genes. Sequence comparisons and phylogenetic analysis suggest that four of the zebrafish cadm genes represent duplicates of two tetrapod Cadm genes, whereas the other two cadm genes are single orthologs of tetrapod Cadm genes. All six zebrafish cadms are expressed throughout the nervous system both during development and in the adult. The spatial and temporal patterns of expression suggest multiple roles for Cadms during nervous system development. Developmental Dynamics 237:233,246, 2008. © 2007 Wiley-Liss, Inc. [source]


    Developmental expression and comparative genomic analysis of Xenopus cardiac myosin heavy chain genes

    DEVELOPMENTAL DYNAMICS, Issue 4 2005
    Robert J. Garriock
    Abstract Myosin heavy chains (MHC) are cytoskeletal motor proteins essential to the process of muscle contraction. We have determined the complete sequences of the Xenopus cardiac MHC genes, ,-MHC and ventricular MHC (vMHC), and have characterized their developmental expression profiles. Whereas ,-MHC is expressed from the earliest stages of cardiac differentiation, vMHC transcripts are not detected until the heart has undergone chamber formation. Early expression of vMHC appears to mark the cardiac conduction system, but expression expands to include the ventricle and outflow tract myocardium during subsequent development. Sequence comparisons, transgenic expression analysis, and comparative genomic studies indicate that Xenopus ,-MHC is the true orthologue of the mammalian ,-MHC gene. On the other hand, we show that the Xenopus vMHC gene is most closely related to chicken ventricular MHC (vMHC1) not the mammalian ,-MHC. Comparative genomic analysis has allowed the detection of a mammalian MHC gene (MyH15) that appears to be the orthologue of vMHC, but evidence suggests that this gene is no longer active. Developmental Dynamics 233:1287,1293, 2005. © 2005 Wiley-Liss, Inc. [source]


    Hev b 9, an enolase and a new cross-reactive allergen from Hevea latex and molds

    FEBS JOURNAL, Issue 24 2000
    Purification, characterization, cloning, expression
    Natural rubber latex allergy is an IgE-mediated disease that is caused by proteins that elute from commercial latex products. A complementary DNA (cDNA) coding for Hev b 9, an enolase (2-phospho- d -glycerate hydrolyase) and allergen from latex of the rubber tree Hevea brasiliensis, was amplified by PCR. The PCR primers were designed according to conserved regions of enolases from plants. The obtained cDNA amplification product consisted of 1651 bp and encoded a protein of 445 amino-acid residues with a calculated molecular mass of 47.6 kDa. Sequence comparisons revealed high similarities of the Hevea latex enolase to mold enolases that have been identified as important allergens. In addition, the crucial amino-acid residues that participate in the formation of the catalytic site and the Mg2+ binding site of enolases were also conserved. Hevea latex enolase was produced as a recombinant protein in Escherichia coli with an N-terminal hexahistidyl tag, and purified by affinity chromatography. The yield amounted to 110 mg of purified Hev b 9 per litre of bacterial culture. The recombinant allergen bound IgE from latex, as well as mold-allergic patients, in immunoblot and ELISA experiments. The natural enolase was isolated from Hevea latex by (NH4)2SO4 precipitation and ion exchange chromatography. The natural and the recombinant (r)Hev b 9 showed equivalent enzymatic activity. Patients' IgE-antibodies preincubated with rHev b 9 lost their ability to bind to natural (n) Hev b 9, indicating the identity of the B-cell epitopes on both molecules. Cross-reactivity with two enolases from Cladosporium herbarum and Alternaria alternata was determined by inhibition of IgE-binding to these enolases by rHev b 9. Therefore, enolases may represent another class of highly conserved enzymes with allergenic potentials. [source]


    Identification of Lophodermium seditiosum and L. pinastri in Swedish forest nurseries using species-specific PCR primers from the ribosomal ITS region

    FOREST PATHOLOGY, Issue 3 2005
    E. Stenström
    Summary Lophodermium seditiosum is a serious needle pathogen on pine, particularly in nurseries, and there is a need to detect the pathogen during its latent phase. The internal transcribed spacer (ITS) regions of the rDNA of L. seditiosum and L. pinastri were amplified with universal primers and sequenced. Sequence comparisons of the two species allowed the design of species-specific primers for the ITS regions. The primers were between 18 and 24 bp long with a minimum of 3 bp differences between the species. These primer pairs did not give any amplification of DNA from any other of the examined fungal species or from healthy Pinus sylvestris needles. It was also possible to identify either L. seditiosum or L. pinastri in infected needles with and without signs of infection using these primer pairs. The method was found to be very useful for detection of latent infections of L. seditiosum in P. sylvestris needles in nurseries. Résumé Lophodermium seditiosum est un pathogène important des aiguilles sur pins, particulièrement en pépinières, et il serait nécessaire de détecter le pathogène dans sa phase latente. Les régions ITS de L. seditiosum et L. pinastri ont été amplifiées avec des amorces universelles et séquencées. La comparaison de la séquence des deux espèces a permis de développer des amorces spécifiques pour chaque espèce dans la région ITS. Les amorces ont une longueur de 18 à 24 paires de bases avec un minimum de 3 paires de bases de différence entre espèces. Ces amorces n'ont produit aucune amplification avec l'ADN des autres espèces de champignons testées ou les aiguilles saines de Pinus sylvestris. Il a également été possible de détecter L. seditiosum ou L. pinastri avec ces amorces dans des aiguilles infectées avec ou sans signe d'infection. Cette méthode s'avère très utile pour la détection d'infections latentes de L. seditiosum dans les aiguilles de P. sylvestris en pépinières. Zusammenfassung Lophodermium seditiosum ist ein starkes Nadelpathogen an Kiefern, speziell in Baumschulen. Für den Einsatz von Bekämpfungsmassnahmen wäre es von Vorteil, wenn man das Pathogen bereits während der Latenzperiode nachweisen könnte. Die ITS Regionen der ribosomalen DNA von L. seditiosum und L. pinastri wurden mit Standardprimern amplifiziert und sequenziert. Vergleiche der Sequenzen der beiden Arten erlaubten die Entwicklung von artspezifischen Primern für die ITS Regionen. Die Primerpaare waren zwischen 18 and 24 Basenpaaren lang und wiesen einen Unterschied von mindestens drei Nukleotiden auf. Die DNA von allen anderen untersuchten Pilzarten und von gesunden Pinus sylvestris Nadeln liessen sich mit keinem dieser Primerpaare amplifiziern. Lophodermium seditiosum und L. pinastri konnten mit den Primerpaaren in infizierten Nadeln mit und ohne Symptome direkt nachgewiesen werden. Die Methode eignete sich vorzüglich zum Nachweis von latenten Infektionen von L. seditiosum in P. sylvestris Nadeln in Baumschulen. [source]


    Cloning and Expression of Low Molecular Weight Glutenin Genes from the Chinese Elite Wheat Cultivar "Xiaoyan 54"

    JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 2 2006
    Xin-Yu Wang
    Abstract The low molecular weight (LMW) glutenin subunits account for 40% of wheat gluten protein content by mass and these proteins are considered to significantly affect dough quality characteristics. Five new full-length LMW glutenin genes (designated LMW-5, LMW-7, LMW-42, LMW-58, and LMW-34) were isolated from the Chinese elite wheat cultivar "Xiaoyan 54" by PCR amplification of genomic DNA using a pair of degenerate primers designed from the conserved sequences of the N- and C-terminal regions of published LMW glutenin genes. Deduced amino acid sequence analysis showed that LMW-5 belongs to the LMW-i type genes and that the other four belong to LMW-m type genes. Sequence comparisons revealed that point mutations occasionally occurred in signal peptide and N-terminus domains and often existed in domain III and domain V. Small insertions and deletions are represented in the repetitive domain. There is a stop codon after amino acid position 110 in the repetitive domain of LMW-34, indicating that it is a pseudogene. The other four genes have complete open reading frames and the putative mature regions of these genes were subcloned into pET-30a expression vector and successfully expressed in Escherichia coli. Protein sodium dodecyl sulfate-polyacrylamide gel electro-phoresis analysis showed that all proteins expressed in E. coli by the four genes could be related to B-group LMW glutenin subunits of wheat. (Managing editor: Li-Hui Zhao) [source]


    Molecular Characterization of two Distinct Begomoviruses from Ageratum conyzoides and Malvastrum coromandelianum in China

    JOURNAL OF PHYTOPATHOLOGY, Issue 11-12 2006
    J. F. Huang
    Abstract Two weed samples, G52 from Ageratum conyzoides and G87 from Malvastrum coromandelianum, showing leaf curling and vein thickening symptoms were collected in Nanning, Guangxi Province, China. The complete nucleotide sequences of DNA-A-like molecules of G52 and G87 were determined to be 2735 and 2745 nucleotides respectively. Both DNA-A molecules have a genomic organization typical of begomoviruses and share 73.4% sequence identity with each other. Sequence comparisons showed that the DNA-A of G52 and G87 were most closely related to those of Ageratum yellow vein virus (AYVV; 85% sequence identity) and Tobacco leaf curl Yunnanvirus (75.7% sequence identity) respectively. Further sequence comparisons showed that G52 has arisen by recombination among viruses related to AYVV, Papaya leaf curl China virus and an unidentified Begomovirus species. The molecular data suggest that G52 and G87 are two distinct begomoviruses, for which the names Ageratum leaf curl virus for G52 and Malvastrum leaf curl virus for G87 are proposed. The satellite DNA, molecule was only found to be associated with G87. G87 DNA, consists of 1354 nucleotides, and shares the highest nucleotide sequence identity (68.9%) with that associated with Sida yellow vein China virus. A defective DNA, molecule was also found to be associated with G87. [source]


    Molecular phylogeny of the freshwater sponges in Lake Baikal

    JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 2 2003
    H. C. Schröder
    Abstract The phylogenetic relationship of the freshwater sponges (Porifera) in Lake Baikal is not well understood. A polyphyletic and/or monophyletic origin have been proposed. The (endemic) Baikalian sponges have been subdivided into two families: endemic Lubomirskiidae and cosmopolitan Spongillidae. In the present study, two new approaches have been made to resolve the phylogenetic relationship of Baikalian sponges; analysis of (1) nucleotide sequences from one mitochondrial gene, the cytochrome oxidase subunit I (COI) and of (2) one selected intron from the tubulin gene. Specimens from the following endemic Baikalian sponge species have been studied; Lubomirskia baicalensis , Baikalospongia intermedia, Baikalospongia recta , Baikalospongia bacillifera and Swartschewskia papyracea . They are all grouped to the family of Lubomirskiidae. Sequence comparisons were performed with the ubiquitously distributed freshwater sponge Spongilla lacustris (family Spongillidae) as well as with one marine sponge, Suberites domuncula . A sequence comparison, of the mitochondrial COI gene revealed a monophyletic grouping of the endemic Baikalian sponges with S. lacustris as the most related species to the common ancestor. The sequences of the COI gene from B. recta , B. intermedia , B. bacillifera and L. baicalensis were found to be identical and separated from those of S. lacustris and S. papyracea . In a second approach, the exon/intron sequences framing the intron-2 of the sponge tubulin gene were chosen for the phylogenetic analysis. The intron sequences were aligned and used for construction of a phylogenetic tree. This analysis revealed again a monophyletic grouping with S. lacustris as the closest related species to the common ancestor. It is concluded that the Baikalian sponges, which have been studied here, are of monophyletic origin. Furthermore, the data suggest that the endemic species S. papyracea is the phylogenetically oldest, extant, endemic Baikalian sponge species. Zusammenfassung Die phylogenetischen Beziehungen der Süßwasserschwämme [Porifera] des Baikalsees sind nur wenig verstanden; sowohl ein polyphyletischer als auch monophyletischer Urspung werden vermutet. Die Baikalschwämme werden in zwei Familien, Lubomirskiidae und Spongillidae, eingeteilt. In der vorliegenden Arbeit wird versucht, die phylogenetischen Beziehungen der Baikalschwämme über zwei Wege aufzuklären: über (i) eine Analyse der Nukleotidsequenzen eines Teils des mitochondrialen Gens der Cytochromoxidase-Untereinheit I (COI) und (ii) eines ausgewählten Introns des Tubulingens. Folgende endemischen Spezies wurden untersucht: Lubomirskia baicalensis , Baikalospongia intermedia , Baikalospongia recta , Baikalospongia bacillifera und Swartschewskia papyracea . Sie werden alle der Familie der Lubomirskiidae zugerechnet. Die Sequenzen wurden mit den entsprechenden Sequenzen des ubiquitär vorkommenden Süßwasserschwammes Spongilla lacustris sowie des Meeresschwammes Suberites domuncula verglichen. Die Sequenzvergleiche der mitochondrialen COI-Gene zeigten, daß die Baikalschwämme monophyletischen Ursprungs sind und zusammen mit S. lacustris von einem gemeinsamen Vorfahren abstammen. Die Sequenzen des COI-Gens von B. recta , B. intermedia , B. bacillifera und L. baicalensis sind identisch und trennen sich phylogenetisch von S. lacustris und S. papyracea ab. Bei dem zweiten von uns gewählten Weg wurden die Sequenzen des zweiten Introns des Schwamm-Tubulingens zur phylogenetischen Analyse herangezogen. Auch dabei konnte gezeigt werden, daß die Baikalschwämme , zusammen mit S. lacustris als dem nächsten verwandten gemeinsamen Vorfahren , einen monophyletischen Ursprung haben. S. papyracea stellt den phylogenetisch ältesten endemischen Baikalschwamm dar. [source]


    Validity of species status of the parasitic mite Otodectes cynotis

    MEDICAL AND VETERINARY ENTOMOLOGY, Issue 2 2002
    J. Lohse
    Abstract A combined molecular and phenotypic approach was used to determine whether ear mites of the genus Otodectes (Acari: Psoroptidae) belong to a single species. The second internal transcribed spacer (ITS 2) of the rDNA of 16 isolates from 11 cats, two dogs, one arctic fox and two ferrets originating from four different continents was characterized. In addition, mites from dog, cat and arctic fox were investigated morphologically. Sequence comparisons revealed five different, but closely related genotypes which did not segregate according to host species or geographical origin. Morphologically, mites of the three host species did not differ significantly in their body or leg sizes. These investigations support the view that ear mites of the genus Otodectes from different hosts and geographical origins belong to a single species, Otodectes cynotis (Hering). [source]


    Pyruvate Formate Lyase (PFL) and PFL Activating Enzyme in the Chytrid Fungus Neocallimastix frontalis: A Free-Radical Enzyme System Conserved Across Divergent Eukaryotic Lineages,

    THE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2004
    GABRIEL GELIUS-DIETRICH
    ABSTRACT Fermentative formate production involves the activity of pyruvate formate lyase, an oxygen-sensitive enzyme that employs a glycyl radical in its reaction mechanism. While common among anaerobic prokaryotes, this enzyme has so far been found in only two distantly related eukaryotic lineages, anaerobic chytridiomycetes and chlorophytes. Sequence comparisons of homologues from the chytridiomycetes Piromyces and Neocallimastix, the chlorophyte Chlamydomonas, and numerous prokaryotes suggest a single, eubacterial origin of eukaryotic pyruvate formate lyases. Pyruvate formate lyase activating enzyme introduces the glycyl radical into the pyruvate formate lyase protein chain. We discovered this enzyme, which had not previously been reported from eukaryotes, in the same two eukaryotic lineages and show that it shares a similar evolutionary history to pyruvate formate lyase. Sequences with high homology to pyruvate formate lyase activating enzyme were identified in the genomes of the anaerobic protozoan parasites Trichomonas vaginalis, Entamoeba histolytica, and Giardia intestinalis. While the occurrence of pyruvate formate lyase activating enzyme together with pyruvate formate lyase in fungi and chlorophytes was to be expected, the target protein of a glycyl radical enzyme-activating enzyme in these protozoa remains to be identified. [source]


    Detailed analysis of the DNA recognition motifs of the Xanthomonas type III effectors AvrBs3 and AvrBs3,rep16

    THE PLANT JOURNAL, Issue 6 2009
    Sabine Kay
    Summary The Gram-negative phytopathogenic bacterium Xanthomonas campestris pv. vesicatoria (Xcv) employs a type III secretion system to translocate effector proteins into plant cells where they modulate host signaling pathways to the pathogen's benefit. The effector protein AvrBs3 acts as a eukaryotic transcription factor and induces the expression of plant genes termed UPA (up-regulated by AvrBs3). Here, we describe 11 new UPA genes from bell pepper that are induced by AvrBs3 early after infection with Xcv. Sequence comparisons revealed the presence of a conserved AvrBs3-responsive element, the UPA box, in all UPA gene promoters analyzed. Analyses of UPA box mutant derivatives confirmed its importance for gene induction by AvrBs3. We show that DNA binding and gene activation were strictly correlated. DNase I footprint studies demonstrated that the UPA box corresponds to the center of the AvrBs3-protected DNA region. Type III delivery of AvrBs3 and mutant derivatives showed that some UPA genes are induced by the AvrBs3 deletion derivative AvrBs3,rep16, which lacks four repeats. We show that AvrBs3,rep16 recognizes a mutated UPA box with two nucleotide exchanges in positions that are not essential for binding and activation by AvrBs3. [source]


    Histone H1-like, lysine-rich low complexity amino acid extensions in mosquito ribosomal proteins RpL23a and RpS6 have evolved independently

    ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 2 2007
    Vida P. Hernandez
    Abstract Histone H1-like amino acid extensions have been described at the amino terminus of Drosophila RpL22 and RpL23a, and at the carboxyl terminus of mosquito ribosomal protein RpS6. An in silico search suggested that RpL23a, but not RpL22, in Anopheles gambiae has an amino-terminal extension. Because low complexity amino acid extensions are not common on eukaryotic ribosomal proteins, and their functions are unknown, we cloned cDNAs encoding RpL23a from Aedes albopictus and Anopheles stephensi mosquito cell lines. RpL23a proteins in Aedes and Anopheles mosquitoes are rich in lysine (,25%), alanine (,21%), and proline (,8%), have a mass of ,40 kDa, a pI of 11.4 to 11.5, and contain an N-terminal extension of approximately 260 amino acid residues. The N-terminal extension in mosquito RpL23a is about 100 amino acids longer than that in the Drosophila RpL23a homolog, and contains several repeated amino acid motifs. Analysis of exon-intron organization in the An. gambiae and in D. melanogaster genes suggests that a short first exon encodes a series of 11 amino acid residues conserved in RpL23a proteins from Drosophila, mosquitoes, and the moth, Bombyx mori. The histone H1-like sequence in RpL23a is encoded entirely within the second exon. The C-terminal 126 amino acid residues of the RpL23a protein, encoded by exon 3 in Drosophila, and by exons 3 and 4 in Anopheles gambiae, are well conserved, and correspond to Escherichia coli RpL23 with the addition of the eukaryotic N-terminal nuclear localization sequence. Sequence comparisons indicate that the histone H1-like extensions on mosquito RpS6 and RpL23a have evolved independently of each other, and of histone H1 proteins. Arch. Insect Biochem. Physiol. 64:100,110, 2007. © 2007 Wiley-Liss, Inc. [source]


    Isolation and characterization of Tn -Dha1, a transposon containing the tetrachloroethene reductive dehalogenase of Desulfitobacterium hafniense strain TCE1

    ENVIRONMENTAL MICROBIOLOGY, Issue 1 2005
    Julien Maillard
    Summary A new 9.9 kb catabolic transposon, Tn -Dha1, containing the gene responsible for tetrachloroethene (PCE) reductive dechlorination activity, was isolated from Desulfitobacterium hafniense strain TCE1. Two fully identical copies of the insertion sequence ISDha1, a new member of the IS256 family, surround the gene cluster pceABCT, a truncated gene for another transposase and a short open reading frame with homology to a member of the twin-arginine transport system (tatA). Evidence was obtained by Southern blot for an alternative form of the transposon element as a circular molecule containing only one copy of ISDha1. This latter structure most probably represents a dead-end product of the transposition of Tn -Dha1. Strong indications for the transposition activity of ISDha1 were given by polymerase chain reaction (PCR) amplification and sequencing of the intervening sequence located between both inverted repeats (IR) of ISDha1 (IR junction). A stable genomic ISDha1 tandem was excluded by quantitative real-time PCR. Promoter mapping of the pceA gene, encoding the reductive dehalogenase, revealed the presence of a strong promoter partially encoded in the right inverted repeat of ISDha1. A sequence comparison with pce gene clusters from Desulfitobacterium sp. strains PCE-S and Y51 and from Dehalobacter restrictus, all of which show 100% identity for the pceAB genes, indicated that both Desulfitobacterium strains seem to possess the same transposon structure, whereas only the pceABCT gene cluster is conserved in D. restrictus. [source]


    Application of nr-DNA ITS sequence for identification of Fusarium culmorum isolates,

    EPPO BULLETIN, Issue 3-4 2000
    P. K. Mishra
    Variation within the internal transcribed spacers (ITS1 and ITS2) and 5.8S ribosomal DNA region of 60 Fusarium culmorum isolates (section Discolor), representing different hosts and diverse geographical origins was examined by polymerase chain reaction (PCR), coupled with sequencing. Phylogenetic relationships of these F. culmorum isolates were estimated in relation to Fusarium spp. from this and other sections of the form-genus, using sequences available from Genbank. The amplified ITS region was approximately 570 bp long in 56 isolates and approximately 585 bp in four other isolates. The inferred phylogeny distinguished clearly four isolates supplied as F. culmorum. These isolates differed in both morphology and sequence from the remaining F. culmorum material. Sequence analysis revealed that the remaining 56 isolates were divided into three ITS types, within which the divergence was extremely low. ITS sequence comparison among the Fusarium isolates showed two major clades, one comprising sections Discolor, Sporotrichiella and Gibbosum and the other comprising Elegans, Liseola, Martiella and Roseum. These results demonstrate the use of the ITS region to resolve the identification and taxonomic problems of Fusarium spp. especially at sectional level but demonstrate the need to develop some other molecular markers for identification at the level of species or race. [source]


    Toll-like receptor 9 binds single-stranded CpG-DNA in a sequence- and pH-dependent manner

    EUROPEAN JOURNAL OF IMMUNOLOGY, Issue 9 2004
    Mark Rutz
    Abstract Toll-like receptors (TLR) recognize bacterial and viral components, but direct interaction of receptor and ligand is unclear. Here, we demonstrate that TLR9 binds directly and sequence-specifically to single-stranded unmethylated CpG-DNA containing a phosphodiester backbone. TLR9-CpG-DNA interaction occurs at the acidic pH (6.5,5.0) found in endosomes and lysosomes. By sequence comparison we identified a potential CpG-DNA binding domain homologous to that described for methyl-CpG-DNA binding proteins. Amino acid substitutions in this region abrogated CpG-DNA binding and led to loss of NF-,B activation. Furthermore, chloroquine and quinacrine, therapeutic agents for autoimmune diseases like rheumatoid arthritis and systemic lupus erythematosus, directly blocked TLR9-CpG-DNA interaction but not TLR2-Pam3Cys binding. Our results demonstrate direct binding of TLR9 to CpG-DNA and suggest that the therapeutic activity of chloroquine and quinacrine in autoimmune diseases may be due to its activity as a TLR9 antagonist and inhibitor of endosomal acidification. [source]


    Comparative genomics of the Mill family: a rapidly evolving MHC class,I gene family

    EUROPEAN JOURNAL OF IMMUNOLOGY, Issue 6 2004
    Yutaka Watanabe
    Abstract Mill (MHC class,I-like located near the leukocyte receptor complex) is a novel family of class,I genes identified in mice that is most closely related to the human MICA/B family. In the present study, we isolated Mill cDNA from rats and carried out a comparative genomic analysis. Rats have two Mill genes orthologous to mouse Mill1 and Mill2 near the leukocyte receptor complex, with expression patterns similar to those of their mouse counterparts. Interspecies sequence comparison indicates that Mill is one of the most rapidly evolving class,I gene families and that non-synonymous substitutions occur more frequently than synonymous substitutions in its ,,1 domain, implicating the involvement of Mill in immune defenses. Interestingly, the ,,2 domain of rat Mill2 contains a premature stop codon in many inbred strains, indicating that Mill2 is not essential for survival. A computer search of the database identified a horse Mill -like expressed sequence tag, indicating that Mill emerged before the radiation of mammals. Hence, the failure to find Mill in human indicates strongly that it was lost from the human lineage. Our present work provides convincing evidence that Mill is akin to the MICA/B family, yet constitutes a distinctgene family. [source]


    Membrane orientation of laminin binding protein

    FEBS JOURNAL, Issue 18 2003
    An extracellular matrix bridging molecule of Leishmania donovani
    Earlier we presented several lines of evidence that a 67-kDa laminin binding protein (LBP) in Leishmania donovani, that is different from the putative mammalian 67-kDa laminin receptor, may play an important role in the onset of leishmaniasis, as these parasites invade macrophages in various organs after migrating through the extracellular matrix. Here we describe the membrane orientation of this Leishmania laminin receptor. Flow cytometric analysis using anti-LBP Ig revealed its surface localization, which was further confirmed by enzymatic radiolabeling of Leishmania surface proteins, autoradiography and Western blotting. Efficient incorporation of LBP into artificial lipid bilayer, as well as its presence in the detergent phase after Triton X-114 membrane extraction, suggests that it may be an integral membrane protein. Limited trypsinization of intact parasite and subsequent immunoblotting of trypsin released material using laminin as primary probe revealed that a major part of this protein harbouring the laminin binding site is oriented extracellularly. Carboxypeptidase Y treatment of the whole cell, as well as the membrane preparation, revealed that a small part of the C-terminal is located in the cytosol. A 34-kDa transmembrane part of LBP could be identified using the photoactive probe, 3-(trifluoromethyl)-3-(m -iodophenyl)diazirine (TID). Partial sequence comparison of the intact protein to that with the trypsin-released fragment indicated that N-terminal may be located extracellularly. Together, these results suggest that LBP may be an integral membrane protein, having significant portion of N-terminal end as well as the laminin binding site oriented extracellularly, a membrane spanning domain and a C-terminal cytosolic end. [source]


    Evaluating low level sequence identities

    FEBS JOURNAL, Issue 2 2001
    AROM homologous?, Are Aspergillus QUTA
    A review published several years ago [Hawkins, A.R. & Lamb, H.K. (1995) Eur. J. Biochem. 232, 7,18] proposed that genetic, biochemical and physiological data can override sequence comparison in the determination of homology in instances where structural information is unavailable. Their lead example was the hypothesis that the transcriptional activator protein for quinate catabolism in Aspergillus nidulans, QUTA, is derived from the pentafunctional AROM protein by a gene duplication followed by cleavage [Hawkins, A.R., Lamb, H.K., Moore, J.D. & Roberts, C.F. (1993) Gene136, 49,54]. We tested this hypothesis by a sensitive combination of position-specific log-odds scoring matrix methods. The position-specific log-odds scoring matrices were derived from a large number of 3-dehydroquinate synthase and 5- enolpyruvylshikimate-3-phosphate synthase domains that were proposed to be the domains from the AROM protein that gave rise to the transcriptional activator protein for quinate metabolism. We show that the degree and pattern of similarity between these position-specific log-odds scoring matrices and the transcriptional activator protein for quinate catabolism in A. nidulans is that expected for random sequences of the same composition. This level of similarity provides no support for the suggested gene duplication and cleavage. The lack of any trace of evidence for homology following a comprehensive sequence analysis indicates that the homology hypothesis is without foundation, underlining the necessity to accept only similarity of sequence and/or structure as evidence of evolutionary relatedness. Further, QUTA is homologous throughout its entire length to an extended family of fungal transcriptional regulatory proteins, rendering the hypothesized QUTA,AROM homology even more problematic. [source]


    Variation in Galr1 expression determines susceptibility to excitotoxin-induced cell death in mice

    GENES, BRAIN AND BEHAVIOR, Issue 5 2008
    S. Kong
    Inbred strains of mice differ in their susceptibility to excitotoxin-induced cell death, but the genetic basis of individual variation in differential susceptibility is unknown. Previously, we identified a highly significant quantitative trait locus (QTL) on chromosome 18 that influenced susceptibility to kainic acid-induced cell death (Sicd1). Comparison of susceptibility to seizure-induced cell death between reciprocal congenic lines for Sicd1 and parental background mice indicates that genes influencing this trait were captured in both strains. Two positional gene candidates, Galr1 and Mbp, map to 55 cM, where the Sicd1 QTL had been previously mapped. Thus, this study was undertaken to determine if Galr1 and/or Mbp could be considered as candidate genes. Genomic sequence comparison of these two functional candidate genes from the C57BL/6J (resistant at Sicd1) and the FVB/NJ (susceptible at Sicd1) strains showed no single-nucleotide polymorphisms. However, expression studies confirmed that Galr1 shows significant differential expression in the congenic and parental inbred strains. Galr1 expression was downregulated in the hippocampus of C57BL/6J mice and FVB.B6- Sicd1 congenic mice when compared with FVB/NJ or B6.FVB- Sicd1 congenic mice. A survey of Galr1 expression among other inbred strains showed a significant effect such that ,susceptible' strains showed a reduction in Galr1 expression as compared with ,resistant' strains. In contrast, no differences in Mbp expression were observed. In summary, these results suggest that differential expression of Galr1 may contribute to the differences in susceptibility to seizure-induced cell death between cell death-resistant and cell death-susceptible strains. [source]


    Identification of evolutionarily conserved regulatory elements in the mouse Fgf8 locus

    GENESIS: THE JOURNAL OF GENETICS AND DEVELOPMENT, Issue 1 2006
    Friedrich Beermann
    Abstract The secreted signaling molecule fibroblast growth factor 8 (Fgf8) is an essential component of certain embryonic signaling centers including the mid-hindbrain (isthmic) organizer, the first branchial arch (BA1), and the apical ectodermal ridge (AER). In these signaling centers Fgf8 transcripts are expressed in a dynamic and transient fashion, but the mechanism by which this highly specific expression pattern is established remains largely unknown. We used DNA sequence comparisons coupled to transgenic approaches to obtain insight into the structure and function of regulatory elements in the Fgf8 locus. First, a bacterial artificial chromosome (BAC) containing the mouse Fgf8 gene partially rescues the embryonic lethality of Fgf8- deficient mice and controls Fgf8 -specific gene expression of a coinjected lacZ reporter transgene. Second, sequence comparison of vertebrate Fgf8 loci revealed evolutionarily highly conserved noncoding sequences that were unexpectedly located mainly 3, of the Fgf8 coding region. Third, in transgenic mice some of these elements were sufficient to target expression to the AER, tail bud, and brain, including the isthmic organizer, indicating that they may represent Fgf8 cis-acting elements. Collectively, these data identify novel regulatory elements of the Fgf8 gene sufficient to drive expression to regions of known Fgf8 activity. genesis 44:1,6, 2006. © 2006 Wiley-Liss, Inc. [source]


    Understanding the recent evolution of the human genome: insights from human,chimpanzee genome comparisons,

    HUMAN MUTATION, Issue 2 2007
    Hildegard Kehrer-Sawatzki
    Abstract The sequencing of the chimpanzee genome and the comparison with its human counterpart have begun to reveal the spectrum of genetic changes that has accompanied human evolution. In addition to gross karyotypic rearrangements such as the fusion that formed human chromosome 2 and the human-specific pericentric inversions of chromosomes 1 and 18, there is considerable submicroscopic structural variation involving deletions, duplications, and inversions. Lineage-specific segmental duplications, detected by array comparative genomic hybridization and direct sequence comparison, have made a very significant contribution to this structural divergence, which is at least three-fold greater than that due to nucleotide substitutions. Since structural genomic changes may have given rise to irreversible functional differences between the diverging species, their detailed analysis could help to identify the biological processes that have accompanied speciation. To this end, interspecies comparisons have revealed numerous human-specific gains and losses of genes as well as changes in gene expression. The very considerable structural diversity (polymorphism) evident within both lineages has, however, hampered the analysis of the structural divergence between the human and chimpanzee genomes. The concomitant evaluation of genetic divergence and diversity at the nucleotide level has nevertheless served to identify many genes that have evolved under positive selection and may thus have been involved in the development of human lineage-specific traits. Genes that display signs of weak negative selection have also been identified and could represent candidate loci for complex genomic disorders. Here, we review recent progress in comparing the human and chimpanzee genomes and discuss how the differences detected have improved our understanding of the evolution of the human genome. Hum Mutat 28(2), 99,130, 2007. © 2006 Wiley-Liss, Inc. [source]


    A putative hexamerin from a Campodea sp. suggests an independent origin of haemocyanin-related storage proteins in Hexapoda

    INSECT MOLECULAR BIOLOGY, Issue 5 2009
    C. Pick
    Abstract Haemocyanins are copper-containing respiratory proteins in the arthropod haemolymph. In hexapods, haemocyanins gave rise to hexamerins, which have lost the ability to bind copper and thus oxygen. Hexamerins are thought to act mainly as storage proteins in nonfeeding periods. So far, hexamerins have only been identified in ectognathan hexapods, but not in Entognatha. Here we report the identification of a putative hexamerin from Campodea sp. (Diplura). The full-length cDNA of Campodea sp. hexamerin 1 (CspHex1) measures 2188 bp and translates into a native polypeptide of 667 amino acids. As in other hexamerins, the six copper-coordinating histidines are not conserved. However, sequence comparison and phylogenetic analyses demonstrated that CspHex1 is not closely related to other hexapod hexamerins, which derive from hexapod type 1 haemocyanin subunits in the ectognathan lineage, but rather resembles a derivative of hexapod type 2 haemocyanin subunits. Hence, haemocyanin-related storage proteins emerged at least two times independently in Hexapoda. [source]


    Partial genomic organization of ribosomal protein S7 gene from malaria vector Anopheles stephensi

    INSECT SCIENCE, Issue 2 2007
    RAJNIKANT DIXIT
    Abstract In this study, we describe the partial genomic organization of ribosomal protein S7 gene isolated from the mosquito Anopheles stephensi. Initially a 558 bp partial cDNA sequence was amplified as precursor mRNA sequence containing 223 bp long intron. 5, and 3, end sequences were recovered using end specific rapid amplification of cDNA ends (RACE) polymerase chain reaction. The full-length cDNA sequence was 914 nucleotide long with an open reading frame capable of encoding 192 amino acid long protein with calculated molecular mass of 22 174 Da and a pI point of 9.94. Protein homology search revealed > 75% identity to other insect's S7 ribosomal proteins. Analysis of sequence alignment revealed several highly conserved domains, one of which is related to nuclear localization signal (NLS) region of human rpS7. Interestingly, intron nucleotide sequence comparison with A. gambiae showed a lesser degree of conservation as compared to coding and untranslated regions. Like this, early studies on the genomic organization and cDNA/ Expressed sequence tag analysis (EST) could help in genome annotation of A. stephensi, and would be likely to be sequenced in the future. [source]