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Sequence Similarity (sequence + similarity)
Kinds of Sequence Similarity Selected AbstractsSequence similarities between Raspberry leaf mottle virus, Raspberry leaf spot virus and the closterovirus Raspberry mottle virusANNALS OF APPLIED BIOLOGY, Issue 3 2010W.J. McGavin A sequencing study was performed to determine the relationship between Raspberry mottle virus (RMoV), a newly identified tentative closterovirus found in the United States, and Raspberry leaf mottle virus (RLMV) and Raspberry leaf spot virus (RLSV), which have been known for many years to be components of Raspberry mosaic disease (RMD) in the UK and Europe but which have not been characterised at the molecular level. Cloning and sequencing of cDNAs amplified by reverse transcription-PCR revealed the presence of closteroviruses with high sequence similarity to RMoV in infected plants from the SCRI Rubus virus collection, as well as in a number of samples collected from RMD-symptomatic raspberry plants located at different farms in Scotland and England. These results suggest that RMoV, RLMV and RLSV are isolates of the same virus and we propose that they all should be referred to as RLMV, which was the first of these viruses to be described. Many of the field samples were also infected with a second closterovirus isolate, parts of which could be amplified using RLMV-derived primers. The coat protein amino acid sequences of RLMV and the second virus (PM1) were only 78% identical, even though helicase domain and RNA-dependent RNA polymerase (RDRP) domain sequences were more than 97% identical between RLMV and PM1. [source] Widely distributed Drosophila G-protein-coupled receptor (CG7887) is activated by endogenous tachykinin-related peptidesDEVELOPMENTAL NEUROBIOLOGY, Issue 1 2006Ryan T. Birse Abstract Neuropeptides related to vertebrate tachykinins have been identified in Drosophila. Two Drosophila G-protein-coupled receptors (GPCRs), designated NKD (CG6515) and DTKR (CG7887), cloned earlier, display sequence similarities to mammalian tachykinin receptors. However, they were not characterized with the endogenous Drosophila tachykinins (DTKs). The present study characterizes one of these receptors, DTKR. We determined that HEK-293 cells transfected with DTKR displayed dose-dependent increases in both intracellular calcium and cyclic AMP levels in response to the different DTK peptides. DTK peptides also induced internalization of DTKR-green fluorescent protein (GFP) fusion constructs in HEK-293 cells. We generated specific antireceptor antisera and showed that DTKR is widely distributed in the adult brain and more scarcely in the larval CNS. The distribution of the receptor in brain neuropils corresponds well with the distribution of its ligands, the DTKs. Our findings suggest that DTKR is a DTK receptor in Drosophila and that this ligand-receptor system plays multiple functional roles. © 2005 Wiley Periodicals, Inc. J Neurobiol, 2006 [source] Identification and characterization of the genes for N -acetylglucosamine kinase and N -acetylglucosamine-phosphate deacetylase in the pathogenic fungus Candida albicansFEBS JOURNAL, Issue 8 2001Toshiko Yamada-Okabe Like bacteria and many fungi, the pathogenic fungus Candida albicans can utilize GlcNAc as a carbon source for growth. A cluster of six genes was identified in the C. albicans genome. One of the genes in the cluster was CaNAG1, which is responsible for GlcN6P deaminase and is therefore essential for GlcNAc-dependent growth. The other five genes were designated CaNAG2, CaNAG3, CaNAG4, CaNAG5 and CaNAG6. The mRNA levels of CaNAG1, CaNAG2 and CaNAG5 were significantly induced by GlcNAc, whereas those of CaNAG3, CaNAG4 and CaNAG6 were not. Neither CaNAG2 nor CaNAG5 was essential for growth, but disruption of CaNAG2 or CaNAG5 greatly retarded the growth of cells using GlcNAc as the sole carbon source. Although no homolog of CaNAG2 or CaNAG5 was found in the Saccharomyces cerevisiae genome, CaNag2p displayed sequence similarities to Escherichia coli nagA, and CaNag5p is homologous to a wide variety of hexose kinases. When expressed as a fusion protein with glutathione S -transferase (GST), CaNag5p produced GlcNAc-P from GlcNAc in the presence of ATP, whereas GST alone did not. Furthermore, the recombinant GST,CaNag2p fusion protein converted GlcNAcP, which was produced by CaNag5p, into GlcNP. These results clearly demonstrate that CaNAG2 and CaNAG5 encode GlcNAcP deacetylase and GlcNAc kinase, respectively. CaNag5p recognized glucose and mannose as substrates, whereas the recently identified human GlcNAc kinase was specific to GlcNAc. Deletion of CaNAG2 or CaNAG5 markedly, and that of CaNAG1 moderately, attenuated the virulence of C. albicans in a mouse systemic infection model. Thus, it appears that GlcNAc metabolism of C. albicans is closely associated with its virulence. [source] Cultivation of methanotrophic bacteria in opposing gradients of methane and oxygenFEMS MICROBIOLOGY ECOLOGY, Issue 3 2006Ingeborg Bussmann Abstract In sediments, methane-oxidizing bacteria live in opposing gradients of methane and oxygen. In such a gradient system, the fluxes of methane and oxygen are controlled by diffusion and consumption rates, and the rate-limiting substrate is maintained at a minimum concentration at the layer of consumption. Opposing gradients of methane and oxygen were mimicked in a specific cultivation set-up in which growth of methanotrophic bacteria occurred as a sharp band at either c. 5 or 20 mm below the air-exposed end. Two new strains of methanotrophic bacteria were isolated with this system. One isolate, strain LC 1, belonged to the Methylomonas genus (type I methantroph) and contained soluble methane mono-oxygenase. Another isolate, strain LC 2, was related to the Methylobacter group (type I methantroph), as determined by 16S rRNA gene and pmoA sequence similarities. However, the partial pmoA sequence was only 86% related to cultured Methylobacter species. This strain accumulated significant amounts of formaldehyde in conventional cultivation with methane and oxygen, which may explain why it is preferentially enriched in a gradient cultivation system. [source] Development of species-specific PCR primers on rDNA for the identification of European Armillaria speciesFOREST PATHOLOGY, Issue 5 2003G. Sicoli Summary Attempts to design species-specific PCR primers from six European Armillaria species in the ribosomal RNA genes are reported. Primers were developed on the basis of the nucleotide sequence variability of the internal transcribed spacers (ITS) and the intergenic spacer (IGS1) of the ribosomal DNA. Four sets of primers gave specific PCR products for Armillaria tabescens, Armillaria mellea and Armillaria ostoyae. However, due to the high sequence similarities between Armillaria borealis and Armillaria ostoyae and between Armillaria cepistipes and Armillaria gallica no species specific amplification was obtained for these taxa. Résumé Des essais ont été réalisés pour obtenir des amorces PCR spécifiques de 6 espèces européennes d'Armillaria dans les gènes de l'ARNr. Les amorces ont été développées sur la base de la variabilité de séquence nucléotidique dans les ITS et IGS (IGS1) de l'ADN ribosomal. Quatre couples d'amorces ont permis d'obtenir des produits PCR spécifiques pour A. tabescens, A. mellea et A. ostoyae. Cependant, compte tenu des très fortes similarités de séquence entre A. borealis et A. ostoyae, et entre A. cepistipes et A. gallica, il n'a pas été obtenu d'amplification spécifique pour ces taxons. Zusammenfassung Es wird über Versuche berichtet, artspezifische Primer für sechs europäische Armillariaarten in der Region der ribosomalen RNA-Gene zu entwickeln. Als Grundlage dafür diente die Variabilität der Nukleotidsequenzen der ITS- und der IGS 1-Region der ribosomalen DNA. Vier Primerpaare ergaben spezifische PCR-Produkte für A. tabescens, A. mellea und A. ostoyae. Dagegen wurden aufgrund der grossen Ähnlichkeit der Sequenzen von A. borealis und A. ostoyae sowie von A. cepistipes und A. gallica für diese Taxa keine artspezifischen Amplifikationsprodukte erhalten. [source] CoagMDB: a database analysis of missense mutations within four conserved domains in five vitamin K,dependent coagulation serine proteases using a text-mining tool,HUMAN MUTATION, Issue 3 2008Rebecca E. Saunders Abstract Central repositories of mutations that combine structural, sequence, and phenotypic information in related proteins will facilitate the diagnosis and molecular understanding of diseases associated with them. Coagulation involves the sequential activation of serine proteases and regulators in order to yield stable blood clots while maintaining hemostasis. Five coagulation serine proteases,factor VII (F7), factor IX (F9), factor X (F10), protein C (PROC), and thrombin (F2),exhibit high sequence similarities and all require vitamin K. All five of these were incorporated into an interactive database of mutations named CoagMDB (http://www.coagMDB.org; last accessed: 9 August 2007). The large number of mutations involved (especially for factor IX) and the increasing problem of out-of-date databases required the development of new database management tools. A text mining tool automatically scans full-length references to identify and extract mutations. High recall rates between 96 and 99% and precision rates of 87 to 93% were achieved. Text mining significantly reduces the time and expertise required to maintain the databases and offers a solution to the problem of locus-specific database management and upkeep. A total of 875 mutations were extracted from 1,279 literature sources. Of these, 116 correspond to Gla domains, 86 to the N-terminal EGF domain, 73 to the C-terminal EGF domain, and 477 to the serine protease domain. The combination of text mining and consensus domain structures enables mutations to be correlated with experimentally-measurable phenotypes based on either low protein levels (Type I) or reduced functional activities (Type II), respectively. A tendency for the conservation of phenotype with structural location was identified. Hum Mutat 29(3), 333,344, 2008. © 2007 Wiley-Liss, Inc. [source] Rhesus macaque antibody molecules: sequences and heterogeneity of alpha and gamma constant regionsIMMUNOLOGY, Issue 1 2004Franco Scinicariello Summary Rhesus macaques (Macaca mulatta) are extensively used in vaccine development. Macaques infected with simian immunodeficiency viruses (SIV) or simian-human immunodeficiency viruses (SHIV) are the best animal model currently available for acquired-immune-deficiency-syndrome-related studies. Recent results emphasize the importance of antibody responses in controlling HIV and SIV infection. Despite the increasing attention placed on humoral immunity in these models, very limited information is available on rhesus macaque antibody molecules. Therefore, we sequenced, cloned and characterized immunoglobulin gamma (IGHG) and alpha (IGHA) chain constant region genes from rhesus macaques of Indian and Chinese origin. Although it is currently thought that rhesus macaques express three IgG subclasses, we identified four IGHG genes, which were designated IGHG1, IGHG2, IGHG3 and IGHG4 on the basis of sequence similarities with the four human genes encoding the IgG1, IgG2, IgG3 and IgG4 subclasses. The four genes were expressed at least at the messenger RNA level, as demonstrated by real-time reverse transcription polymerase chain reaction (RT-PCR). The level of intraspecies heterogeneity was very high for IGHA genes, whereas IGHG genes were remarkably similar in all animals examined. However, single amino acid substitutions were present in IGHG2 and IGHG4 genes, indicating the presence of IgG polymorphism possibly resulting in the expression of different allotypes. Two IgA alleles were identified in several animals and RT-PCR showed that both alleles may be expressed. Presence of immunoglobulin gene polymorphism appears to reflect the unusually high levels of intraspecies heterogeneity already demonstrated for major histocompatibility complex genes in this non-human primate species. [source] Aquabirnaviruses isolated from marine organisms form a distinct genogroup from other aquabirnavirusesJOURNAL OF FISH DISEASES, Issue 11 2004C X Zhang Abstract A phylogenetic tree of aquabirnaviruses, including marine birnaviruses (MABV) and infectious pancreatic necrosis virus (IPNV), was developed based on the nucleotide sequences and deduced amino acid sequences of the polyprotein and VP5 genes of genomic segment A. In the polyprotein of MABV strains, the amino acid sequences were very similar, with identities of 98.3,99.7%. Twenty-one unique amino acid residues were found in the deduced amino acid sequences of the polyprotein gene of MABV strains. The phylogenetic tree based on the nucleotide sequence of genomic segment A and polyprotein sequences showed that 31 aquabirnavirus strains were clustered into seven genogroups. All MABV strains isolated in Japan and Korea were clustered into one genogroup which was distinct from other aquabirnaviruses. The seventh genogroup containing all MABV strains showed amino acid sequence similarities of 80.7,90.6% with other genogroups. In VP5, four unique residues were found in MABV strains when compared with IPNV strains. The MABV strains exhibited amino acid sequence similarities of 63.9,86.4% with IPNV strains. The amino acid sequences of VP5 were conserved among MABV strains, but differed from those of IPNV strains. The MABV strains isolated from different host species and different geographical areas were very similar to each other, suggesting that the MABV are distinct from the other genogroups. [source] Mala s 12 is a major allergen in patients with atopic eczema and has sequence similarities to the GMC oxidoreductase family,ALLERGY, Issue 6 2007A. Zargari Background:, Atopic eczema (AE) is a chronic inflammatory skin disorder, characterized by impaired skin barrier and itch. The yeast Malassezia belongs to the normal human skin microflora and can induce IgE- and T-cell-mediated allergic reactions in AE patients. Previously, we have identified several IgE-binding components in Malassezia sympodialis extract. Methods:, Here, we report cloning, production and characterization of a M. sympodialis 67-kDa allergen. Results:, The sequence of the 67-kDa protein, termed Mala s 12, showed sequence similarity to the glucose,methanol,choline (GMC) oxidoreductase enzyme superfamily and was expressed as a recombinant protein in Escherichia coli. The purified protein bound flavin adenine dinucleotide with 1:1 stoichiometry per monomer of protein. The protein-bound flavin showed an extinction coefficient at 451 nm of 11.3 mM,1cm,1. The recombinant 67-kDa protein did not show any enzymatic activity when tested as oxidase or dehydrogenase using choline, glucose, myo-inositol, methanol, ethanol, 1-pentanol, benzyl alcohol, 2-phenylethanol, cholesterol or lauryl alcohol as possible substrates. Recombinant Mala s 12 was recognized by serum IgE from 13 of 21 (62%) M. sympodialis -sensitized AE patients indicating that the 67-kDa component is a major allergen. Conclusions:, The data show that Mala s 12 has sequence similarity to the GMC oxidoreductase family and is a major allergen in AE patients. [source] First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genomePLANT BIOTECHNOLOGY JOURNAL, Issue 6 2003Andreas M. Rickert Summary A panel of 17 tetraploid and 11 diploid potato genotypes was screened by comparative sequence analysis of polymerase chain reaction (PCR) products for single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), in regions of the potato genome where genes for qualitative and/or quantitative resistance to different pathogens have been localized. Most SNP and InDel markers were derived from bacterial artificial chromosome (BAC) insertions that contain sequences similar to the family of plant genes for pathogen resistance having nucleotide-binding-site and leucine-rich-repeat domains (NBS-LRR-type genes). Forty-four such NBS-LRR-type genes containing BAC-insertions were mapped to 14 loci, which tag most known resistance quantitative trait loci (QTL) in potato. Resistance QTL not linked to known resistance-gene-like (RGL) sequences were tagged with other markers. In total, 78 genomic DNA fragments with an overall length of 31 kb were comparatively sequenced in the panel of 28 genotypes. 1498 SNPs and 127 InDels were identified, which corresponded, on average, to one SNP every 21 base pairs and one InDel every 243 base pairs. The nucleotide diversity of the tetraploid genotypes (, = 0.72 × 10,3) was lower when compared with diploid genotypes (, = 2.31 × 10,3). RGL sequences showed higher nucleotide diversity when compared with other sequences, suggesting evolution by divergent selection. Information on sequences, sequence similarities, SNPs and InDels is provided in a database that can be queried via the Internet. [source] The Arabidopsis thaliana ATP-binding cassette proteins: an emerging superfamilyPLANT CELL & ENVIRONMENT, Issue 5 2000T. G. E. Davies ABSTRACT Solute transport systems are one of the major ways in which organisms interact with their environment. Typically, transport is catalysed by integral membrane proteins, of which one of the largest groups is the ATP-binding cassette (ABC) proteins. On the basis of sequence similarities, a large family of ABC proteins has been identified in Arabidopsis. A total of 60 open reading frames (ORFs) encoding ABC proteins were identified by BLAST homology searching of the nuclear genome. These 60 putative proteins include 89 ABC domains. Based on the assignment of transmembrane domains (TMDs), at least 49 of the 60 proteins identified are ABC transporters. Of these 49 proteins, 28 are full-length ABC transporters (eight of which have been described previously), and 21 are uncharacterized half-transporters. Three of the remaining proteins identified appear to be soluble, lacking identifiable TMDs, and most likely have non-transport functions. The eight other ORFs have homology to the nucleotide-binding and transmembrane components of multi-subunit permeases. The majority of ABC proteins found in Arabidopsis can, on the basis of sequence homology, be assigned to subfamilies equivalent to those found in the yeast genome. This assignment of the Arabidopsis ABC proteins into easily recognizable subfamilies (with distinguishable subclusters) is an important first step in the elucidation of their functional role in higher plants. [source] Identification of four proteins from the small subunit of the mammalian mitochondrial ribosome using a proteomics approachPROTEIN SCIENCE, Issue 3 2001Emine Cavdar Koc Abstract Proteins in the small subunit of the mammalian mitochondrial ribosome were separated by two-dimensional polyacrylamide gel electrophoresis. Four individual proteins were subjected to in-gel Endoprotease Lys-C digestion. The sequences of selected proteolytic peptides were obtained by electrospray tandem mass spectrometry. Peptide sequences obtained from in-gel digestion of individual spots were used to screen human, mouse, and rat expressed sequence tag databases, and complete consensus cDNAs for these species were deduced in silico. The corresponding protein sequences were characterized by comparison to known ribosomal proteins in protein databases. Four different classes of mammalian mitochondrial small subunit ribosomal proteins were identified. Only two of these proteins have significant sequence similarities to ribosomal proteins from prokaryotes. These proteins are homologs to Escherichia coli S9 and S5 proteins. The presence of these newly identified mitochondrial ribosomal proteins are also investigated in the Drosophila melanogaster, Caenorhabditis elegans, and in the genomes of several fungi. [source] Two homologous parasitism-specific proteins encoded in Cotesia plutellae bracovirus and their expression profiles in parasitized Plutella xylostellaARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY (ELECTRONIC), Issue 4 2008Sunyoung Lee Abstract A wasp, Cotesia plutellae, parasitizes the diamondback moth, Plutella xylostella, and interrupts host physiology for wasp survival and development. Identification of parasitism-specific factors would be helpful to understand the host,parasitoid interaction. This study focused on identification of a 15-kDa protein found only in plasma of the parasitized P. xylostella. Degenerate primers were designed after N-terminal amino acid sequencing of the parasitism-specific protein and used to clone the corresponding gene from the parasitized P. xylostella by a nested reverse transcriptase-polymerase chain reaction (RT-PCR). Two homologous genes were cloned and identified as "CpBV15," and "CpBV15,," respectively, due to the identical size (158 amino acid residues) of the predicted open reading frames, in which they shared amino acid sequences in both terminal regions, but varied in internal sequences. Southern hybridization analysis indicated that both genes were located on C. plutellae bracovirus genome. Real-time quantitative RT-PCR revealed that both genes were mostly expressed at the late parasitization period, which was further confirmed by an immunoblotting assay using CpBV15 antibody. A recombinant CpBV15 protein was produced from Sf9 cells via a baculovirus expression system. The purified CpBV15 protein could enter hemocytes of P. xylostella and were localized in the cytosol. Along with the sequence similarities of CpBV15s with eukaryotic initiation factors, their putative biological role has been discussed in terms of the host translation inhibitory factor. Arch. Insect Biochem. Physiol. 67:157,171, 2008. © 2008 Wiley-Liss, Inc. [source] Comparative Analysis of Sequence Characteristics among Different Superimposed Stages of the Chelif Basin, AlgeriaACTA GEOLOGICA SINICA (ENGLISH EDITION), Issue 6 2009ZHANG Yuanfu Abstract: Superimposed basins were investigated with respect to tectonic evolution, sediment deposition and petroleum characteristics within a single superposition stage generally. The comparative study was seldom seen. Sequence characteristics were compared for two different superimposed stages , an expanding rifting stage and a depression-foreland transition stage , in the Chelif Basin during the Miocene in this paper. A model and mechanism for sequence evolution of superimposed basins in different dynamic situations are discussed with respect to sequence similarities and differences. The compared characters include sequence thickness, sequence boundaries and system tracts, as well as sediment deposition within sequences and sequence development patterns. Finally, some typical features of sequence development concomitant with changes of superimposed stages in the Chelif Basin are discussed. [source] Cross-reactive and species-specific immunoglobulin E epitopes of plant profilins: an experimental and structure-based analysisCLINICAL & EXPERIMENTAL ALLERGY, Issue 7 2006C. Radauer Summary Background Profilins are cross-reactive plant allergens responsible for multiple pollen sensitization and pollen-associated food allergy. While it is assumed that profilins from different species are immunologically equivalent, some studies suggest partial or even lacking IgE cross-reactivity between certain profilins. Objective We aimed to obtain a semi-quantitative assessment of the contributions of conserved and species-specific epitopes to IgE binding of plant profilins. Methods We compared model structures of profilins from timothy, mugwort, celery and bell pepper with crystal structures of birch and latex profilins. We predicted potential conformational epitopes that consisted of contiguous patches of at least 20% surface-exposed residues. Celery and timothy profilins were purified from their natural sources, and profilins from birch, mugwort, bell pepper and latex were expressed in Escherichia coli. The structural integrity of all purified proteins was confirmed by circular dichroism spectroscopy. IgE ELISAs and ELISA inhibitions using sera from 22 profilin-sensitized allergic patients were carried out. Results Peptide backbone conformations of all six profilins were highly similar. Nine variable epitopes and two containing high proportions of conserved residues were predicted. IgE from all sera bound to all tested profilins and the amounts were highly correlated. However, IgE inhibition experiments revealed that up to 60% of total IgE binding was mediated by species-specific epitopes. The extent of cross-reactivity among profilins from timothy, birch, latex and celery was greater than cross-reactivity to mugwort and bell pepper profilins. This pattern was mirrored by sequence similarities among one of the predicted variable epitopes. Patients with IgE to cross-reactive epitopes displayed allergic reactions to a greater number of plant foods than patients having IgE directed to species-specific epitopes. Conclusion The large extent of cross-reactivity among plant profilins justifies using a single profilin for diagnosis. However, the fine specificity of IgE directed to variable epitopes may influence the clinical manifestation of profilin sensitization. [source] Molecular characterization of Ciona sperm outer arm dynein reveals multiple components related to outer arm docking complex protein 2CYTOSKELETON, Issue 10 2006Akiko Hozumi Abstract Using proteomic and immunochemical techniques, we have identified the light and intermediate chains (IC) of outer arm dynein from sperm axonemes of the ascidian Cionaintestinalis. Ciona outer arm dynein contains six light chains (LC) including a leucine-rich repeat protein, Tctex1- and Tctex2-related proteins, a protein similar to Drosophila roadblock and two components related to Chlamydomonas LC8. No LC with thioredoxin domains is included in Ciona outer arm dynein. Among the five ICs in Ciona, three are orthologs of those in sea urchin dynein: two are WD-repeat proteins and the third one, unique to metazoan sperm flagella, contains both thioredoxin and nucleoside diphosphate kinase modules. The remaining two Ciona ICs have extensive coiled coil structure and show sequence similarity to outer arm dynein docking complex protein 2 (DC2) that was first identified in Chlamydomonas flagella. We recently identified a third DC2-like protein with coiled coil structure, Ci-Axp66.0 that is also associated in substoichiometric amounts with Ciona outer arm dynein. In addition, Oda5p, a component of an additional complex required for assembly of outer arm dynein in Chlamydomonas flagella, also groups with this family of DC2-like proteins. Thus, the assembly of outer arm dynein onto doublet microtubules involves multiple coiled-coil proteins related to DC2. Cell Motil. Cytoskeleton 2006. © 2006 Wiley-Liss, Inc. [source] Arabidopsis thaliana protein, ATK1, is a minus-end directed kinesin that exhibits non-processive movementCYTOSKELETON, Issue 3 2002Adam I. Marcus Abstract The microtubule cytoskeleton forms the scaffolding of the meiotic spindle. Kinesins, which bind to microtubules and generate force via ATP hydrolysis, are also thought to play a critical role in spindle assembly, maintenance, and function. The A. thaliana protein, ATK1 (formerly known as KATA), is a member of the kinesin family based on sequence similarity and is implicated in spindle assembly and/or maintenance. Thus, we want to determine if ATK1 behaves as a kinesin in vitro, and if so, determine the directionality of the motor activity and processivity character (the relationship between molecular "steps" and microtubule association). The results show that ATK1 supports microtubule movement in an ATP-dependent manner and has a minus-end directed polarity. Furthermore, ATK1 exhibits non-processive movement along the microtubule and likely requires at least four ATK1 motors bound to the microtubule to support movement. Based on these results and previous data, we conclude that ATK1 is a non-processive, minus-end directed kinesin that likely plays a role in generating forces in the spindle during meiosis. Cell Motil. Cytoskeleton 52:144,150, 2002. © 2002 Wiley-Liss, Inc. [source] Analysis of Sir2E in the cellular slime mold Dictyostelium discoideum: Cellular localization, spatial expression and overexpressionDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 8 2008Takahiro Katayama It has been reported that Dictyostelium discoideum encodes four silent information regulator 2 (Sir2) proteins (Sir2A,D) showing sequence similarity to human homologues of Sir2 (SIRT1,3). Further screening in a database revealed that D. discoideum encodes an additional Sir2 homologue (Sir2E). The amino acid sequence of Sir2E is not similar to those of SIRTs but is similar to those of proteins encoded by Giardia lamblia, Cryptosporidium hominis and Cryptosporidium parvum. Fluorescence of Sir2E-green fluorescent protein fusion protein was detected in the D. discoideum nucleus, indicating that Sir2E is a nuclear localizing protein. Reverse transcription,polymerase chain reaction and whole-mount in situ hybridization analyses showed that D. discoideum expressed sir2E in amoebae in the growth phase and in prestalk cells in the developmental phase. D. discoideum overexpressing sir2E grew faster than the wild type. These results indicate that Sir2E plays important roles both in the growth phase and developmental phase of D. discoideum. [source] Requirement for ,B1-crystallin promoter of Xenopus laevis in embryonic lens development and lens regenerationDEVELOPMENT GROWTH & DIFFERENTIATION, Issue 3 2005Nobuhiko Mizuno Regulation of the lens-specific ,B1-crystallin promoter in Xenopus laevis was investigated using transgenic larvae and tadpoles. Comparison of the promoter sequence with that of chicken ,B1-crystallin gene indicates significant sequence similarity over a span of several hundred base pairs starting from the transcriptional start site. Remarkably, PL-1 and PL-2 sequences identified in the chicken promoter as essential binding sites of MAF, Pax6 and Prox1 transcription factors were conserved. Mutations of X (Xenopus) PL-1 and XPL-2 sequences eliminated the promoter activity, indicating a conserved mechanism regulating ,B1-crystallin promoter among vertebrate species. A stepwise deletion of the promoter sequence starting from 2800 bp indicated that the proximal 260 bp directly upstream of the transcription initiation site is sufficient for eliciting lens-specific expression, but the 150 bp promoter sequence is inactive despite it containing the XPL-1 and XPL-2 sequences, suggesting the presence of an additional and essential regulatory sequence located between ,150 and ,260 bp. Activity of the ,B1-crystallin promoter during lens regeneration from cornea was examined using transgenic tadpoles and found to have the same dependence on promoter regions as in embryonic lens development, indicating that gene regulation is largely shared by the two lens-generating processes. [source] Maternal expression and function of the Drosophila sox gene Dichaete during oogenesisDEVELOPMENTAL DYNAMICS, Issue 10 2006Ashim Mukherjee Abstract Members of the Sox family of DNA-binding HMG domain proteins have been shown to regulate gene transcription in a wide range of developmental processes, including sex determination, neurogenesis, and chondrogenesis. However, little is known about their potential functions in developing germline tissues. In Drosophila, the Sox protein Dichaete (a.k.a., Fish-hook) is a member of the SoxB subgroup whose HMG domain shares strong sequence similarity to that of vertebrate Sox2. Dichaete exhibits dynamic expression in embryonic and larval stages and has pleiotropic functions in a variety of tissues. In this study, we extend analyses of Dichaete function and show that expression of Dichaete protein is detected in the developing oocyte during early to mid stages of oogenesis. Strikingly, Dichaete exhibits cytoplasmic distribution and is not detected in the oocyte nucleus. Germline mosaic analyses revealed that the Dichaete gene has maternal functions that influence dorsal/ventral patterning of the egg chamber. Dichaete mutant eggs exhibit defects in formation of the dorsal appendages, differentiation of dorsal/anterior follicle cells, and mislocalization of Gurken protein and gurken mRNA. Dichaete protein was shown to possess RNA-binding capabilities, suggesting a direct post-transcriptional role in regulating RNA functions. Developmental Dynamics 235:2828,2835, 2006. © 2006 Wiley-Liss, Inc. [source] A MAGE/NDN-like gene in zebrafishDEVELOPMENTAL DYNAMICS, Issue 3 2003Jocelyn M. Bischof Abstract The human necdin/MAGE gene family has over 50 members, but most of the proteins encoded by these genes are of unknown function. We have now identified a single locus in Danio rerio that encodes a putative protein with significant coding sequence similarity to the mammalian NDN/MAGE genes. Analysis of the complete Fugu ribripes genome sequence also suggests that there is only a single MAGE-like gene in teleost fish. mage is expressed in the larval and adult brain, specifically the retina, the medial region of the telencephalon, periventricular gray zone of the optic tectum, and most highly in the cerebellar corpus. The discovery of a zebrafish NDN/MAGE gene expressed the developing brain facilitates studies of the MAGE homology domain in vertebrate development. Developmental Dynamics, 2003. © 2003 Wiley-Liss, Inc. [source] Characterization of the plasticity-related gene, Arc, in the frog brainDEVELOPMENTAL NEUROBIOLOGY, Issue 12 2010Lisa A. Mangiamele Abstract In mammals, expression of the immediate early gene Arc/Arg3.1 in the brain is induced by exposure to novel environments, reception of sensory stimuli, and production of learned behaviors, suggesting a potentially important role in neural and behavioral plasticity. To date, Arc has only been characterized in a few species of mammals and birds, which limits our ability to understand its role in modifying behavior. To begin to address this gap, we identified Arc in two frog species, Xenopus tropicalis and Physalaemus pustulosus, and characterized its expression in the brain of P. pustulosus. We found that the predicted protein for frog Arc shared 60% sequence similarity with Arc in other vertebrates, and we observed high Arc expression in the forebrain, but not the midbrain or hindbrain, of female túngara frogs sacrificed at breeding ponds. We also examined the time-course of Arc induction in the medial pallium, the homologue of the mammalian hippocampus, in response to a recording of a P. pustulosus mating chorus and found that accumulation of Arc mRNA peaked 0.75 h following stimulus onset. We found that the mating chorus also induced Arc expression in the lateral and ventral pallia and the medial septum, but not in the striatum, hypothalamus, or auditory midbrain. Finally, we examined acoustically induced Arc expression in response to different types of mating calls and found that Arc expression levels in the pallium and septum did not vary with the biological relevance or acoustic complexity of the signal. © 2010 Wiley Periodicals, Inc. Develop Neurobiol 70: 813,825, 2010 [source] Exploring the Phospholipid Biosynthetic Pathways of Aspergillus fumigatus by Computational Genome AnalysisENGINEERING IN LIFE SCIENCES (ELECTRONIC), Issue 6 2005H. Do Abstract Aspergillus fumigatus causes a wide range of diseases that include mycotoxicosis, allergic reactions and systematic diseases (invasive aspergillosis) with high mortality rates. In recent years, considerable progress in the genome sequencing of this fungus has been made by an international consortium, which includes the Wellcome Trust Sanger Institute (UK) and the Institute for Genome Research (USA). A tenfold whole genome shotgun sequence assembly of A. fumigatus has been made publicly available. In this study, it was attempted to identify the genes related to the phospholipid biosynthesis from the A. fumigatus genome by a gene prediction program (GlimmerM) and to reconstruct the metabolic pathway for phospholipids of A. fumigatus. Fifteen genes related to phospholipid pathway were identified in the A. fumigatus genomic sequence. The open reading frames predicted by GlimmerM showed a high amino acid sequence similarity with the other fungal phospholipid biosynthetic genes and well-conserved functional domains. The obtained results also demonstrated that the reconstructed pathway of A. fumigatus in phospholipid biosynthesis was very similar to that of other fungi such as Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, and Neurospora crassa. Therefore it is postulated that the antifungal drugs targeted for the biosynthesis of phospholipids could also be effective against A. fumigatus. [source] Expressed sequence tag analysis of the diapausing queen of the bumblebee Bombus ignitusENTOMOLOGICAL RESEARCH, Issue 4 2006Yeon-Ju KIM Abstract We constructed a full-length cDNA library from diapausing queens of the bumblebee Bombus ignitus. A total of 480 randomly selected clones was sequenced by single-run 5,-end sequencing. Of these, there were 437 high quality clones, 23 poor quality clones and 20 read-fail clones. Each high quality clone sequence was searched against a public protein database. The most frequently found matching genes were ribosomal proteins (12.5%), p10 (3.58%), cytochrome P450 monooxygenase (3.13%) and sensory appendage protein (2.9%). Sequence similarity analysis between bumblebees and other insect species showed that 72 out of 437 (16.5%) bumblebee expressed sequence tags (EST) matched sequences of Apis mellifera, with matches to Drosophila melanogaster (6.6%), Caenorhabditis briggsae (6.2%), Lysiphlebus testaceipes (4.8%), Periplaneta americana (3.7%) and Anopheles gambiae (3.4%) following, suggesting that sequence similarity of bumblebee EST is closest to that of A. mellifera. Functional classification of EST based on Gene Ontology showed that most genes found by sequencing are associated with physiological processes in the bumblebee. The results of sequencing and analysis of our 437 cDNA demonstrated that high-throughput EST sequencing and data analysis are powerful means for identifying novel genes and for expression profiling. Our bumblebee EST collection could be a useful platform for further studies of gene expression in diapausing bumblebees. [source] The structure of bacterial communities in the western Arctic Ocean as revealed by pyrosequencing of 16S rRNA genesENVIRONMENTAL MICROBIOLOGY, Issue 5 2010David L. Kirchman Summary Bacterial communities in the surface layer of the oceans consist of a few abundant phylotypes and many rare ones, most with unknown ecological functions and unclear roles in biogeochemical processes. To test hypotheses about relationships between abundant and rare phylotypes, we examined bacterial communities in the western Arctic Ocean using pyrosequence data of the V6 region of the 16S rRNA gene. Samples were collected from various locations in the Chukchi Sea, the Beaufort Sea and Franklin Bay in summer and winter. We found that bacterial communities differed between summer and winter at a few locations, but overall there was no significant difference between the two seasons in spite of large differences in biogeochemical properties. The sequence data suggested that abundant phylotypes remained abundant while rare phylotypes remained rare between the two seasons and among the Arctic regions examined here, arguing against the ,seed bank' hypothesis. Phylotype richness was calculated for various bacterial groups defined by sequence similarity or by phylogeny (phyla and proteobacterial classes). Abundant bacterial groups had higher within-group diversity than rare groups, suggesting that the ecological success of a bacterial lineage depends on diversity rather than on the dominance of a few phylotypes. In these Arctic waters, in spite of dramatic variation in several biogeochemical properties, bacterial community structure was remarkably stable over time and among regions, and any variation was due to the abundant phylotypes rather than rare ones. [source] Comparative analysis of the widespread and conserved PB1-like viruses infecting Pseudomonas aeruginosaENVIRONMENTAL MICROBIOLOGY, Issue 11 2009Pieter-Jan Ceyssens Summary We examined the genetic diversity of lytic Pseudomonas aeruginosa bacteriophage PB1 and four closely related phages (LBL3, LMA2, 14-1 and SN) isolated throughout Europe. They all encapsulate linear, non-permuted genomes between 64 427 and 66 530 bp within a solid, acid-resistant isometric capsid (diameter: 74 nm) and carry non-flexible, contractile tails of approximately 140 nm. The genomes are organized into at least seven transcriptional blocks, alternating on both strands, and encode between 88 (LBL3) and 95 (LMA2) proteins. Their virion particles are composed of at least 22 different proteins, which were identified using mass spectrometry. Post-translational modifications were suggested for two proteins, and a frameshift hotspot was identified within ORF42, encoding a structural protein. Despite large temporal and spatial separations between phage isolations, very high sequence similarity and limited horizontal gene transfer were found between the individual viruses. These PB1-like viruses constitute a new genus of environmentally very widespread phages within the Myoviridae. [source] Distribution of Roseobacter RCA and SAR11 lineages and distinct bacterial communities from the subtropics to the Southern OceanENVIRONMENTAL MICROBIOLOGY, Issue 8 2009Helge-Ansgar Giebel Summary We assessed the composition of the bacterioplankton in the Atlantic sector of the Southern Ocean in austral fall and winter and in New Zealand coastal waters in summer. The various water masses between the subtropics/Agulhas,Benguela boundary region and the Antarctic coastal current exhibited distinct bacterioplankton communities with the highest richness in the polar frontal region, as shown by denaturing gradient gel electrophoresis of 16S rRNA gene fragments. The SAR11 clade and the Roseobacter clade-affiliated (RCA) cluster were quantified by real-time quantitative PCR. SAR11 was detected in all samples analysed from subtropical waters to the coastal current and to depths of > 1000 m. In fall and winter, this clade constituted < 3% to 48% and 4,28% of total bacterial 16S rRNA genes respectively, with highest fractions in subtropical to polar frontal regions. The RCA cluster was only present in New Zealand coastal surface waters not exceeding 17°C, in the Agulhas,Benguela boundary region (visited only during the winter cruise), in subantarctic waters and in the Southern Ocean. In fall, this cluster constituted up to 36% of total bacterial 16S rRNA genes with highest fractions in the Antarctic coastal current and outnumbered the SAR11 clade at most stations in the polar frontal region and further south. In winter, the RCA cluster constituted lower proportions than the SAR11 clade and did not exceed 8% of total bacterial 16S rRNA genes. In fall, the RCA cluster exhibited significant positive correlations with latitude and ammonium concentrations and negative correlations with concentrations of nitrate, phosphate, and for near-surface samples also with chlorophyll a, biomass production of heterotrophic prokaryotes and glucose turnover rates. The findings show that the various water masses between the subtropics and the Antarctic coastal current harbour distinct bacterioplankton communities. They further indicate that the RCA cluster, despite the narrow sequence similarity of > 98% of its 16S rRNA gene, is an abundant component of the heterotrophic bacterioplankton in the Southern Ocean, in particular in its coldest regions. [source] Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adultsENVIRONMENTAL MICROBIOLOGY, Issue 7 2009-Stojanovi, Mirjana Rajili Summary In this paper we present the in silico assessment of the diversity of variable regions of the small subunit ribosomal RNA (SSU rRNA) gene based on an ecosystem-specific curated database, describe a probe design procedure based on two hypervariable regions with minimal redundancy and test the potential of such probe design strategy for the design of a flexible microarray platform. This resulted in the development and application of a phylogenetic microarray for studying the human gastrointestinal microbiota , referred as the human intestinal tract chip (HITChip). Over 4800 dedicated tiling oligonucleotide probes were designed based on two hypervariable regions of the SSU rRNA gene of 1140 unique microbial phylotypes (< 98% identity) following analysis of over 16 000 human intestinal SSU rRNA sequences. These HITChip probes were hybridized to a diverse set of human intestinal samples and SSU rRNA clones to validate its fingerprinting and quantification potential. Excellent reproducibility (median Pearson's correlation of 0.99) was obtained following hybridization with T7 polymerase transcripts generated in vitro from SSU rRNA gene amplicons. A linear dose,response was observed with artificial mixtures of 40 different representative amplicons with relative abundances as low as 0.1% of total microbiota. Analysis of three consecutively collected faecal samples from ten individuals (five young and five elderly adults) revealed temporal dynamics and confirmed that the adult intestinal microbiota is an individual-specific and relatively stable ecosystem. Further analysis of the stable part allowed for the identification of a universal microbiota core at the approximate genus level (90% sequence similarity). This core consists of members of Actinobacteria, Bacteroidetes and Firmicutes. Used as a phylogenetic fingerprinting tool with the possibility for relative quantification, the HITChip has the potential to bridge the gaps in our knowledge in the quantitative and qualitative description of the human gastrointestinal microbiota composition. [source] Molecular and morphological characterization of the association between bacterial endosymbionts and the marine nematode Astomonema sp. from the BahamasENVIRONMENTAL MICROBIOLOGY, Issue 5 2007Niculina Musat Summary Marine nematode worms without a mouth or functional gut are found worldwide in intertidal sandflats, deep-sea muds and methane-rich pock marks, and morphological studies show that they are associated with endosymbiotic bacteria. While it has been hypothesized that the symbionts are chemoautotrophic sulfur oxidizers, to date nothing is known about the phylogeny or function of endosymbionts from marine nematodes. In this study, we characterized the association between bacterial endosymbionts and the marine nematode Astomonema sp. from coral reef sediments in the Bahamas. Phylogenetic analysis of the host based on its 18S rRNA gene showed that Astomonema sp. is most closely related to non-symbiotic nematodes of the families Linhomoeidae and Axonolaimidae and is not closely related to marine stilbonematinid nematodes with ectosymbiotic sulfur-oxidizing bacteria. In contrast, phylogenetic analyses of the symbionts of Astomonema sp. using comparative 16S rRNA gene sequence analysis revealed that these are closely related to the stilbonematinid ectosymbionts (95,96% sequence similarity) as well as to the sulfur-oxidizing endosymbionts from gutless marine oligochaetes. The closest free-living relatives of these gammaproteobacterial symbionts are sulfur-oxidizing bacteria from the family Chromatiaceae. Transmission electron microscopy and fluorescence in situ hybridization showed that the bacterial symbionts completely fill the gut lumen of Astomonema sp., suggesting that these are their main source of nutrition. The close phylogenetic relationship of the Astomonema sp. symbionts to known sulfur-oxidizing bacteria as well as the presence of the aprA gene, typically found in sulfur-oxidizing bacteria, indicates that the Astomonema sp. symbionts use reduced sulfur compounds as an energy source to provide their hosts with nutrition. [source] Anaerobic redox cycling of iron by freshwater sediment microorganismsENVIRONMENTAL MICROBIOLOGY, Issue 1 2006Karrie A. Weber Summary The potential for microbially mediated anaerobic redox cycling of iron (Fe) was examined in a first-generation enrichment culture of freshwater wetland sediment microorganisms. Most probable number enumerations revealed the presence of significant populations of Fe(III)-reducing (approximately 108 cells ml,1) and Fe(II)-oxidizing, nitrate-reducing organisms (approximately 105 cells ml,1) in the freshwater sediment used to inoculate the enrichment cultures. Nitrate reduction commenced immediately following inoculation of acetate-containing (approximately 1 mM) medium with a small quantity (1% v/v) of wetland sediment, and resulted in the transient accumulation of NO2, and production of a mixture of gaseous end-products (N2O and N2) and NH4+. Fe(III) oxide (high surface area goethite) reduction took place after NO3, was depleted and continued until all the acetate was utilized. Addition of NO3, after Fe(III) reduction ceased resulted in the immediate oxidation of Fe(II) coupled to reduction of NO3, to NH4+. No significant NO2, accumulation was observed during nitrate-dependent Fe(II) oxidation. No Fe(II) oxidation occurred in pasteurized controls. Microbial community structure in the enrichment was monitored by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified 16S rDNA and reverse transcription polymerase chain reaction-amplified 16S rRNA, as well as by construction of 16S rDNA clone libraries for four different time points during the experiment. Strong similarities in dominant members of the microbial community were observed in the Fe(III) reduction and nitrate-dependent Fe(II) oxidation phases of the experiment, specifically the common presence of organisms closely related (, 95% sequence similarity) to the genera Geobacter and Dechloromonas. These results indicate that the wetland sediments contained organisms such as Geobacter sp. which are capable of both dissimilatory Fe(III) reduction and oxidation of Fe(II) with reduction of NO3, to NH4+. Our findings suggest that microbially catalysed nitrate-dependent Fe(II) oxidation has the potential to contribute to a dynamic anaerobic Fe redox cycle in freshwater sediments. [source] | |||||||||||||||||||||||||||||||||||||||||||