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Genome Sequence (genome + sequence)
Kinds of Genome Sequence Terms modified by Genome Sequence Selected AbstractsComplete Genome Sequence of a Slovak Isolate of Zucchini Yellow Mosaic Virus (ZYMV) Provides Further Evidence of a Close Molecular Relationship Among Central European ZYMV Isolates,JOURNAL OF PHYTOPATHOLOGY, Issue 7-8 2006M. Glasa Abstract The complete nucleotide sequence of a Slovak isolate of Zucchini yellow mosaic virus (ZYMV-Kuchyna) was determined. The viral genome contains 9593 nucleotides, excluding the poly(A) tail, and encodes a putative polyprotein of 3080 amino acid residues. All characteristic motifs of potyviral proteins' fundamental viral properties and vector transmission are conserved in the ZYMV-Kuchyna genome. The entire sequence shares identities of 90.4,98.8% and 78,98.8% with 12 sequenced ZYMV isolates at the nucleotide and amino acid levels, respectively. Phylogenetic analysis of the complete capsid protein (CP) sequences of more than 50 geographically different ZYMV isolates has shown that Central European isolates are closely related and form a phylogenetically homogeneous group. [source] Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxideENVIRONMENTAL MICROBIOLOGY, Issue 5 2009Axel W. Strittmatter Summary Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp,1) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood,Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO2 but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII- c3, Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2. [source] Genome sequences of two novel phages infecting marine roseobactersENVIRONMENTAL MICROBIOLOGY, Issue 8 2009Yanlin Zhao Summary Two bacteriophages, DSS3,2 and EE36,1, which infect marine roseobacters Silicibacter pomeroyi DSS-3 and Sulfitobacter sp. EE-36, respectively, were isolated from Baltimore Inner Harbor water. These two roseophages resemble bacteriophage N4, a large, short-tailed phage infecting Escherichia coli K12, in terms of their morphology and genomic structure. The full genome sequences of DSS3,2 and EE36,1 reveal that their genome sizes are 74.6 and 73.3 kb, respectively, and they both contain a highly conserved N4-like DNA replication and transcription system. Both roseophages contain a large virion-encapsidated RNA polymerase gene (> 10 kb), which was first discovered in N4. DSS3,2 and EE36,1 also possess several genes (i.e. ribonucleotide reductase and thioredoxin) that are most similar to the genes in roseobacters. Overall, the two roseophages are highly closely related, and share 80,94% nucleotide sequence identity over 85% of their ORFs. This is the first report of N4-like phages infecting marine bacteria and the second report of N4-like phage since the discovery of phage N4 40 years ago. The finding of these two N4-like roseophages will allow us to further explore the specific phage,host interaction and evolution for this unique group of bacteriophages. [source] Caenorhabditis elegans expresses three functional profilins in a tissue-specific mannerCYTOSKELETON, Issue 1 2006D. Polet Abstract Profilins are actin binding proteins, which also interact with polyphosphoinositides and proline-rich ligands. On the basis of the genome sequence, three diverse profilin homologues (PFN) are predicted to exist in Caenorhabditis elegans. We show that all three isoforms PFN-1, PFN-2, and PFN-3 are expressed in vivo and biochemical studies indicate they bind actin and influence actin dynamics in a similar manner. In addition, they bind poly(L -proline) and phosphatidylinositol 4,5-bisphosphate micelles. PFN-1 is essential whereas PFN-2 and PFN-3 are nonessential. Immunostainings revealed different expression patterns for the profilin isoforms. In embryos, PFN-1 localizes in the cytoplasm and to the cell,cell contacts at the early stages, and in the nerve ring during later stages. During late embryogenesis, expression of PFN-3 was specifically detected in body wall muscle cells. In adult worms, PFN-1 is expressed in the neurons, the vulva, and the somatic gonad, PFN-2 in the intestinal wall, the spermatheca, and the pharynx, and PFN-3 localizes in a striking dot-like fashion in body wall muscle. Thus the model organism Caenorhabditis elegans expresses three profilin isoforms and is the first invertebrate animal with tissue-specific profilin expression. Cell Motil. Cytoskeleton, 2006.© 2005 Wiley-Liss, Inc. [source] Piloting the zebrafish genome browserDEVELOPMENTAL DYNAMICS, Issue 3 2006Anthony DiBiase Abstract This correspondence is a primer for the zebrafish research community on zebrafish tracks available in the UCSC Genome Browser at http://genome.ucsc.edu based on Sanger's Zv4 assembly. A primary capability of this facility is comparative informatics between humans (as well as many other model organisms) and zebrafish. The zebrafish genome sequencing project has played important roles in mutant mapping and cloning, and comparative genomic research projects. This easy-to-use genome browser aims to display and download useful genome sequence information for zebrafish mutant mapping and cloning projects. Its user-friendly interface expedites annotation of the zebrafish genome sequence. Developmental Dynamics 235:747,753, 2006. © 2005 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] From genomes to morphology: a view from amphioxusACTA ZOOLOGICA, Issue 1 2010Peter W. H. Holland Abstract Holland, P.W.H. 2010. From genomes to morphology: a view from amphioxus. ,Acta Zoologica (Stockholm) 91: 81,86 As complete genome sequences are determined from an ever-increasing number of animal species, new opportunities are arising for comparative biology. For zoologists interested in the evolution of shape and form, however, there is a problem. The link between genome sequence and morphology is not direct and is obfuscated by complex and evolving genetic pathways, even when conserved regulatory genes are considered. Nonetheless, a large-scale comparison of genome sequences between extant chordates reveals an intriguing parallel between genotypic and phenotypic evolution. Tunicates have highly altered genomes, with loss of ancestral genes and shuffled genetic arrangements, while vertebrate genomes are also derived through gene loss and genome duplication. The recently sequenced amphioxus genome, in contrast, reveals much greater stasis on the cephalochordate lineage, in parallel to a less derived body plan. The opportunities and challenges for relating genome evolution to morphological evolution are discussed. [source] Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxideENVIRONMENTAL MICROBIOLOGY, Issue 5 2009Axel W. Strittmatter Summary Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp,1) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood,Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO2 but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII- c3, Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2. [source] Reverse dissimilatory sulfite reductase as phylogenetic marker for a subgroup of sulfur-oxidizing prokaryotesENVIRONMENTAL MICROBIOLOGY, Issue 2 2009Alexander Loy Summary Sulfur-oxidizing prokaryotes (SOP) catalyse a central step in the global S-cycle and are of major functional importance for a variety of natural and engineered systems, but our knowledge on their actual diversity and environmental distribution patterns is still rather limited. In this study we developed a specific PCR assay for the detection of dsrAB that encode the reversely operating sirohaem dissimilatory sulfite reductase (rDSR) and are present in many but not all published genomes of SOP. The PCR assay was used to screen 42 strains of SOP (most without published genome sequence) representing the recognized diversity of this guild. For 13 of these strains dsrAB was detected and the respective PCR product was sequenced. Interestingly, most dsrAB -encoding SOP are capable of forming sulfur storage compounds. Phylogenetic analysis demonstrated largely congruent rDSR and 16S rRNA consensus tree topologies, indicating that lateral transfer events did not play an important role in the evolutionary history of known rDSR. Thus, this enzyme represents a suitable phylogenetic marker for diversity analyses of sulfur storage compound-exploiting SOP in the environment. The potential of this new functional gene approach was demonstrated by comparative sequence analyses of all dsrAB present in published metagenomes and by applying it for a SOP census in selected marine worms and an alkaline lake sediment. [source] Identification of genes involved in the biosynthesis of the cytotoxic compound glidobactin from a soil bacteriumENVIRONMENTAL MICROBIOLOGY, Issue 7 2007Barbara Schellenberg Summary Glidobactins (syn. cepafungins) are a family of structurally related cytotoxic compounds that were isolated from the soil bacterial strain K481-B101 (ATCC 53080; DSM 7029) originally assigned to Polyangium brachysporum and, independently, from an undefined species related to Burkholderia cepacia. Glidobactins are acylated tripeptide derivatives that contain a 12-membered ring structure consisting of the two unique non-proteinogenic amino acids erythro -4-hydroxy- l -lysine and 4(S)-amino-2(E)-pentenoic acid. Here we report the cloning and functional analysis of a gene cluster (glbA,glbH) involved in glidobactin synthesis from K481-B101, which according to its 16S rRNA sequence belongs to the Burkholderiales. The putative encoded proteins include a mixed non-ribosomal peptide/polyketide synthetase whose structure and architecture allowed to build a biosynthetic pathway model explaining the biosynthesis of the unique peptide part of glidobactins. Intriguingly, among the more than 600 bacterial strains whose genome sequence is currently available, homologous gene clusters were found in Burkholderia pseudomallei, the causing agent of melioidosis, and in the insect pathogen Photorhabdus luminescens, strongly suggesting that these organisms are capable to synthesize compounds similar to glidobactins. In addition, a glb gene cluster that was inactivated by transposon-mediated rearrangements was also present in Burkholderia mallei, a very close relative of B. pseudomallei and the causing agent of glanders in horse-like animals. [source] Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440ENVIRONMENTAL MICROBIOLOGY, Issue 7 2003K. E. Nelson No abstract is available for this article. [source] Evolution of astacin-like metalloproteases in animals and their function in developmentEVOLUTION AND DEVELOPMENT, Issue 2 2006Frank Möhrlen SUMMARY Astacin-like metalloproteases are ubiquitous in the animal kingdom but their phylogenetic relationships and ancient functions within the Metazoa are unclear. We have cloned and characterized four astacin-like cDNAs from the marine hydroid Hydractinia echinata and performed a database search for related genes in the draft genome sequence of the sea anemone Nematostella vectensis. These sequences and those of higher animals' astacins were subjected to phylogenetic analysis revealing five clusters within the Eumetazoa. The bone morphogenetic protein-1/tolloid-like astacins were represented in all eumetazoan phyla studied. The meprins were only found in vertebrates and cnidarians. Two clusters were taxon-specific, and one cluster represented astacins, which probably evolved after the split of the Cnidaria. Interestingly, grouping of astacins according to the protease catalytic domain alone resulted in clusters of proteins with similar overall domain architecture. The Hydractinia astacins were expressed in distinct cells during metamorphosis and some also during wound healing. Previously characterized cnidarian astacins also act during development. Based on our phylogeny, however, we propose that the developmental function of most of them is not homologous to the developmental function assigned to higher animals' astacins. [source] Characterization of a eukaryotic type serine/threonine protein kinase and protein phosphatase of Streptococcus pneumoniae and identification of kinase substratesFEBS JOURNAL, Issue 5 2005Linda Nováková Searching the genome sequence of Streptococcus pneumoniae revealed the presence of a single Ser/Thr protein kinase gene stkP linked to protein phosphatase phpP. Biochemical studies performed with recombinant StkP suggest that this protein is a functional eukaryotic-type Ser/Thr protein kinase. In vitro kinase assays and Western blots of S. pneumoniae subcellular fractions revealed that StkP is a membrane protein. PhpP is a soluble protein with manganese-dependent phosphatase activity in vitro against a synthetic substrate RRA(pT)VA. Mutations in the invariant aspartate residues implicated in the metal binding completely abolished PhpP activity. Autophosphorylated form of StkP was shown to be a substrate for PhpP. These results suggest that StkP and PhpP could operate as a functional pair in vivo. Analysis of phosphoproteome maps of both wild-type and stkP null mutant strains labeled in vivo and subsequent phosphoprotein identification by peptide mass fingerprinting revealed two possible substrates for StkP. The evidence is presented that StkP can phosphorylate in vitro phosphoglucosamine mutase GlmM which catalyzes the first step in the biosynthetic pathway leading to the formation of UDP- N -acetylglucosamine, an essential common precursor to cell envelope components. [source] Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134FEMS MICROBIOLOGY REVIEWS, Issue 5 2008Danilo Pérez-Pantoja Abstract Cupriavidus necator JMP134 is a model for chloroaromatics biodegradation, capable of mineralizing 2,4-D, halobenzoates, chlorophenols and nitrophenols, among other aromatic compounds. We performed the metabolic reconstruction of aromatics degradation, linking the catabolic abilities predicted in silico from the complete genome sequence with the range of compounds that support growth of this bacterium. Of the 140 aromatic compounds tested, 60 serve as a sole carbon and energy source for this strain, strongly correlating with those catabolic abilities predicted from genomic data. Almost all the main ring-cleavage pathways for aromatic compounds are found in C. necator: the ,-ketoadipate pathway, with its catechol, chlorocatechol, methylcatechol and protocatechuate ortho ring-cleavage branches; the (methyl)catechol meta ring-cleavage pathway; the gentisate pathway; the homogentisate pathway; the 2,3-dihydroxyphenylpropionate pathway; the (chloro)hydroxyquinol pathway; the (amino)hydroquinone pathway; the phenylacetyl-CoA pathway; the 2-aminobenzoyl-CoA pathway; the benzoyl-CoA pathway and the 3-hydroxyanthranilate pathway. A broad spectrum of peripheral reactions channel substituted aromatics into these ring cleavage pathways. Gene redundancy seems to play a significant role in the catabolic potential of this bacterium. The literature on the biochemistry and genetics of aromatic compounds degradation is reviewed based on the genomic data. The findings on aromatic compounds biodegradation in C. necator reviewed here can easily be extrapolated to other environmentally relevant bacteria, whose genomes also possess a significant proportion of catabolic genes. [source] The archaeal flagellum: a different kind of prokaryotic motility structureFEMS MICROBIOLOGY REVIEWS, Issue 2 2001Nikhil A Thomas Abstract The archaeal flagellum is a unique motility apparatus distinct in composition and likely in assembly from the bacterial flagellum. Gene families comprised of multiple flagellin genes co-transcribed with a number of conserved, archaeal-specific accessory genes have been identified in several archaea. However, no homologues of any bacterial genes involved in flagella structure have yet been identified in any archaeon, including those archaea in which the complete genome sequence has been published. Archaeal flagellins possess a highly conserved hydrophobic N-terminal sequence that is similar to that of type IV pilins and clearly unlike that of bacterial flagellins. Also unlike bacterial flagellins but similar to type IV pilins, archaeal flagellins are initially synthesized with a short leader peptide that is cleaved by a membrane-located peptidase. With recent advances in genetic transfer systems in archaea, knockouts have been reported in several genes involved in flagellation in different archaea. In addition, techniques to isolate flagella with attached hook and anchoring structures have been developed. Analysis of these preparations is under way to identify minor structural components of archaeal flagella. This and the continued isolation and characterization of flagella mutants should lead to significant advances in our knowledge of the composition and assembly of archaeal flagella. [source] Impact of Human Genome Project on treatment of frail and edentulous patients,GERODONTOLOGY, Issue 1 2004Ichiro Nishimura Objective:, Because of ongoing increases in life expectancy and deferment of edentulousness to older age, dentists are facing a different challenge to satisfy elderly denture wearers with a higher prevalence of chronic diseases. This discussion introduces the Human Genome databases as novel and powerful resources to re-examine the core problems experienced by frail and edentulous patients. Background:, Recent studies demonstrated that mandibular implant overdentures do not necessarily increase masticatory function, perception and satisfaction in denture wearers with adequate edentulous residual ridges. It has been demonstrated that the rate of edentulous residual ridge resorption significantly varies among individuals. The prognosis and cost-effectiveness of denture treatment, with or without implants, may largely depend on how the edentulous ridge is maintained. However, reliable clinical methods permitting dentists to predict the long-term health of the edentulous residual ridge are lacking. Materials and methods:, With the completion of the Human Genome Project, the genomic sequence database from this multinational consortium will provide a unique resource to determine the genetic basis of similarity and diversity of humans. Results:, One base pair in every 100 to 300 base pairs of the genome sequence varies among humans, suggesting that genetic diagnosis using the single nucleotide polymorphisms (SNPs) may provide a novel opportunity to differentiate our edentulous patients. Conclusions:, Future dental service for the elderly will require a personalized care paradigm, using highly sensitive diagnostic technology such as SNP genomic analysis, for recommending the treatment with greatest potential benefit. [source] Pathogenesis of Helicobacter pylori infectionHELICOBACTER, Issue 2002Markus Gerhard Five years after publication of the complete genome sequence of Helicobacter pylori, research interest is shifting from the descriptive association of virulence factors with clinical outcome in infected patients to the molecular mechanisms of virulence factor action. This is particularly noticeable for VacA and CagA, for both of which detailed understanding of the interaction with host signalling pathways has accumulated over the last year. The role of H. pylori Lewis antigens for clinical outcome was further substantiated. Various strategies of H. pylori to fool or evade the human immune system are described, which all lead to the dysfunction of specific compartments of the host cellular immune system. Finally, a number of animal models indicate that inflammation is a key factor for gastric carcinogenesis, which is finally supported by a large prospective study identifying corpus atrophy and intestinal metaplasia as precancerous conditions. [source] The malaria vector mosquito Anopheles gambiae expresses a suite of larval-specific defensin genesINSECT MOLECULAR BIOLOGY, Issue 2 2008J. M. Meredith Abstract cDNAs of Anopheles gambiae Defensin 2 (AgDef2), Defensin 3 (AgDef3) and Defensin 4 (AgDef4), identified in the genome sequence, have been characterized and their expression profiles investigated. In contrast to both typical defensins and insect antimicrobial peptides generally, the newly identified defensins were not upregulated with acute-phase kinetics following immune challenge in insects or cell culture. However, mRNA abundance of AgDef2, AgDef3 and AgDef4 increased significantly during the larval stages. Promoter analysis of all three genes failed to identify putative immune response elements previously identified in other mosquito defensin genes. As previous studies failed to identify these larval-specific defensins, it seems likely that further antimicrobial peptide genes with nontypical expression profiles will be identified as more genome sequences become available. [source] The case for sequencing the genome of the electric eel Electrophorus electricusJOURNAL OF FISH BIOLOGY, Issue 2 2008J. S. Albert A substantial international community of biologists have proposed the electric eel Electrophorus electricus (Teleostei: Gymnotiformes) as an important candidate for genome sequencing. In this study, the authors outline the unique advantages that a genome sequencing project of this species would offer society for developing new ways of producing and storing electricity. Over tens of millions of years, electric fish have evolved an exceptional capacity to generate a weak (millivolt) electric field in the water near their body from specialized muscle-derived electric organs, and simultaneously, to sense changes in this field that occur when it interacts with foreign objects. This electric sense is used both to navigate and orient in murky tropical waters and to communicate with other members of the same species. Some species, such as the electric eel, have also evolved a strong voltage organ as a means of stunning prey. This organism, and a handful of others scattered worldwide, convert chemical energy from food directly into workable electric energy and could provide important clues on how this process could be manipulated for human benefit. Electric fishes have been used as models for the study of basic biological and behavioural mechanisms for more than 40 years by a large and growing research community. These fishes represent a rich source of experimental material in the areas of excitable membranes, neurochemistry, cellular differentiation, spinal cord regeneration, animal behaviour and the evolution of novel sensory and motor organs. Studies on electric fishes also have tremendous potential as a model for the study of developmental or disease processes, such as muscular dystrophy and spinal cord regeneration. Access to the genome sequence of E. electricus will provide society with a whole new set of molecular tools for understanding the biophysical control of electromotive molecules, excitable membranes and the cellular production of weak and strong electric fields. Understanding the regulation of ion channel genes will be central for efforts to induce the differentiation of electrogenic cells in other tissues and organisms and to control the intrinsic electric behaviours of these cells. Dense genomic sequence information of E. electricus will also help elucidate the genetic basis for the origin and adaptive diversification of a novel vertebrate tissue. The value of existing resources within the community of electric fish research will be greatly enhanced across a broad range of physiological and environmental sciences by having a draft genome sequence of the electric eel. [source] Absence of detectable measles virus genome sequence in blood of autistic children who have had their MMR vaccination during the routine childhood immunization schedule of UKJOURNAL OF MEDICAL VIROLOGY, Issue 5 2006M.A. Afzal Abstract Leukocyte preparations from children with documented evidence of MMR vaccination and confirmed diagnosis of autism were examined by several assays designed to target multiple regions of the measles virus genome sequence. No sample was found positive by any method. The assays applied were highly sensitive, specific and robust in nature, and were based on the amplification of measles virus RNA transcripts by real-time quantitative RT-PCR (QRT-PCR) as well as by conventional RT-PCR-nested PCR. The assays applied were potentially able to detect measles virus RNA down to single figure copy numbers per reaction. The amount of total nucleic acid extract of leukocytes subjected to various measles virus-specific investigations was several fold higher than minimally required of a sample where measles virus persistence is well documented. This study failed to substantiate reports of the persistence of measles virus in autistic children with development regression. J. Med. Virol. 78:623,630, 2006. © 2006 Wiley-Liss, Inc. [source] A previously unrecognized sixth genotype of GB virus C revealed by analysis of 5,-untranslated region sequencesJOURNAL OF MEDICAL VIROLOGY, Issue 1 2006A. Scott Muerhoff Abstract GB virus C (GBV-C) is a positive-strand RNA virus that infects a large proportion of the world's human population. It has been classified tentatively as a member of the Flaviviridae family and has been shown to exist as a group of five closely related genotypes. Recently, we reported the first full-length genome sequence of a genotype 5 isolate from South Africa [Muerhoff et al. (2005): J Gen Virol 86: 1729,1735]. As part of the analysis of that sequence, a phylogenetic tree was elucidated from the 5,-untranslated region (UTR) that showed excellent congruence to the tree produced by analysis of complete open reading frame sequences. When 5,-UTR analysis was broadened subsequently to include additional isolates from around the globe, a heretofore unrecognized GBV-C genotype was discovered in Indonesia. When first reported in 2000 [Handajani et al. (2000): J Clin Microbiol 38:662,668], these isolates were described as constituting a novel fifth genotype. However, comparison to isolates from the then-known fourth and fifth genotypes (from Myanmar/Vietnam and South Africa, respectively) was not performed. A dataset of 121 GBV-C 5,-UTR sequences was complied and included representatives of the fourth and fifth genotypes as well as the "novel" Indonesian sequences and demonstrated, with strong support via bootstrap analysis, the existence of a sixth GBV-C genotype among infected individuals in Indonesia. The discovery of this sixth genotype emphasizes the diverse nature of GBV-C isolates and may have important implications for the interpretation of studies involving GBV-C/HIV co-infected individuals. J. Med. Virol. 78:105,111, 2006. © 2005 Wiley-Liss, inc. [source] MOLECULAR GENETIC MANIPULATION OF THE DIATOM THALASSIOSIRA PSEUDONANA (BACILLARIOPHYCEAE),JOURNAL OF PHYCOLOGY, Issue 5 2006Nicole Poulsen Here, we describe the first system for genetic transformation of Thalassiosira pseudonana (Hustedt) Hasle et Heimdal, the only diatom for which a complete genome sequence is presently available. This method is based on microparticle bombardment followed by selection of transformants using the antibiotic nourseothricin. It exhibits the highest transformation efficiency compared with transformation systems for other diatom species. To achieve the high transformation efficiency, it is important to allow recovery of the bombarded T. pseudonana cells in non-selective suspension culture before spreading on nourseothricin containing agar plates. It is demonstrated that T. pseudonana is readily susceptible to co-transformation allowing for the simultaneous introduction of a non-selective gene together with the selection marker gene. Both introduced genes are stably inherited even in the absence of the antibiotic selection pressure. We have developed two T. pseudonana -specific expression vectors that can drive constitutive expression (vector pTpfcp) and inducible expression (vector pTpNR) of introduced genes. In combination with the available genome data the T. pseudonana transformation system is expected to provide a powerful tool for functional genomics in diatoms. [source] Parallel separations of oligonucleotides with optically gated sample introduction on multi-channel microchipsJOURNAL OF SEPARATION SCIENCE, JSS, Issue 1-2 2004Hongwei Xu Abstract With the release of the human genome sequence, there has been increasing attention given to other genetic analyses, including the detection of genetic variations and fast sequencing of multiple samples for pharmacogenomics studies. Rapid injections of samples in multiplexed separation channels by optically gated sample introduction are shown here for DNA separation. Serial separations of four amino acids are shown in less than four seconds on a microchip with four multiplexed channels. Five short oligonucleotides have also been rapidly separated in 2% LPA with four channels using this technique. In addition, multiple unique samples have been simultaneously separated and five-base resolution has been demonstrated. [source] Hemagglutinating activity and corresponding putative sequence identity from Curcuma aromatica rhizomeJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 6 2008Ponpimol Tiptara Abstract BACKGROUND:Curcuma aromatica is a medicinal plant belonging to the Zingiberaceae family with an incomplete genome sequence. It has been reported that extract from the rhizome of this plant contains haemagglutinating activity. In this study the profile of fractions containing hemagglutinating activity is described. RESULTS: Following extraction with saline buffer, the protein solution was fractionated by ammonium sulfate precipitation. Ion-exchange chromatography was completed on fast-flow SP-Sepharose, as well as gel filtration chromatography on Superdex 75. The active fractions were then separated by one-dimensional sodium dodecyl sulfate,polyacrylamide gel electrophoresis and labeled proteins were digested with trypsin. The digest bands were analyzed by reversed-phase liquid chromatography,tandem mass spectrometry. Inferred peptide sequences were used in Mascot searching and mass spectrometry-driven BLAST (MS-BLAST) homology searches allowed the recognition of related proteins in other species of Viridiplantae. Six putative proteins from nine bands showed similarity with lectin sequences. CONCLUSION: This study reports the identification of six lectins from the Curcuma aromatica rhizome achieved by mass spectrometry using MS-BLAST algorithms to search for homology between de novo determined peptide sequences and protein sequences available in sequence databases. Copyright © 2008 Society of Chemical Industry [source] Advances in Campylobacter biology and implications for biotechnological applicationsMICROBIAL BIOTECHNOLOGY, Issue 3 2010Byeonghwa Jeon Summary Campylobacter jejuni is a major foodborne pathogen of animal origin and a leading cause of bacterial gastroenteritis in humans. During the past decade, especially since the publication of the first C. jejuni genome sequence, major advances have been made in understanding the pathobiology and physiology of this organism. It is apparent that C. jejuni utilizes sophisticated mechanisms for effective colonization of the intestinal tracts in various animal species. Although Campylobacter is fragile in the environment and requires fastidious growth conditions, it exhibits great flexibility in the adaptation to various habitats including the gastrointestinal tract. This high adaptability is attributable to its genetically, metabolically and phenotypically diverse population structure and its ability to change in response to various challenges. Unlike other enteric pathogens, such as Escherichia coli and Salmonella, Campylobacter is unable to utilize exogenous glucose and mainly depends on the catabolism of amino acids as a carbon source. Campylobacter proves highly mutable in response to antibiotic treatments and possesses eukaryote-like dual protein glycosylation systems, which modify flagella and other surface proteins with specific sugar structures. In this review we will summarize the distinct biological traits of Campylobacter and discuss the potential biotechnological approaches that can be developed to control this enteric pathogen. [source] Admixture facilitates adaptation from standing variation in the European aspen (Populus tremula L.), a widespread forest treeMOLECULAR ECOLOGY, Issue 8 2010DULCINEIA DE CARVALHO Abstract Adaptation to new environments can start from new mutations or from standing variation already present in natural populations. Whether admixture constrains or facilitates adaptation from standing variation is largely unknown, especially in ecological keystone or foundation species. We examined patterns of neutral and adaptive population divergence in Populus tremula L., a widespread forest tree, using mapped molecular genetic markers. We detected the genetic signature of postglacial admixture between a Western and an Eastern lineage of P. tremula in Scandinavia, an area suspected to represent a zone of postglacial contact for many species of animals and plants. Stringent divergence-based neutrality tests provided clear indications for locally varying selection at the European scale. Six of 12 polymorphisms under selection were located less than 1 kb away from the nearest gene predicted by the Populus trichocarpa genome sequence. Few of these loci exhibited a signature of ,selective sweeps' in diversity-based tests, which is to be expected if adaptation occurs primarily from standing variation. In Scandinavia, admixture explained genomic patterns of ancestry and the nature of clinal variation and strength of selection for bud set, a phenological trait of great adaptive significance in temperate trees, measured in a common garden trial. Our data provide a hitherto missing direct link between past range shifts because of climatic oscillations, and levels of standing variation currently available for selection and adaptation in a terrestrial foundation species. [source] Characterization of HMW-PBPs from the rod-shaped actinomycete Corynebacterium glutamicum: peptidoglycan synthesis in cells lacking actin-like cytoskeletal structuresMOLECULAR MICROBIOLOGY, Issue 3 2007Noelia Valbuena Summary Analysis of the complete genome sequence of Corynebacterium glutamicum indicated that, in addition to ftsI, there are eight proteins with sequence motifs that are strongly conserved in penicillin binding proteins (PBPs): four genes that code for high-molecular-weight (HMW)-PBPs (PBP1a, PBP1b, PBP2a and PBP2b), two genes encoding low-molecular-weight PBPs (PBP4 and PBP4b) and two probable ,-lactamases (PBP5 and PBP6). Here, the function of the four HMW-PBPs in C. glutamicum was investigated using a combination of genetic knockouts, enhanced green fluorescent protein 2 (EGFP2) fusions and penicillin staining of membrane preparations. The four HMW-PBPs were expressed in a growing culture of C. glutamicum, but none of four pbp genes was individually essential for the growth of the bacterium, and only the simultaneous disruption of both pbp1b and pbp2b was lethal. The fused EGFP2,PBP proteins were functional in vivo, which allowed correct determination of their cellular localization. EGFP2 fusions to PBP1a, PBP1b and PBP2b localized at the poles and at the septum, whereas EGFP2,PBP2a was predominantly found at the septum. Cefsulodin treatment specifically delocalized PBP1a and PBP1b (class A HMW-PBPs), whereas mecillinam caused the specific delocalization of PBP2b and PBP2a (class B HMW-PBPs). The results provide new insight into the mechanisms involved in the synthesis of the cell wall in this bacterial species, which lacks a known actin-like cytoskeletal structure. [source] Glycosomes: parasites and the divergence of peroxisomal purposeMOLECULAR MICROBIOLOGY, Issue 3 2004Marilyn Parsons Summary Peroxisomes are membrane-bounded organelles that compartmentalize a variety of metabolic functions. Perhaps the most divergent peroxisomes known are the glycosomes of trypanosomes and their relatives. The glycolytic pathway of these organisms resides within the glycosome. The development of robust molecular genetic and proteomic approaches coupled with the completion of the genome sequence of the pathogens Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major provides an opportunity to determine the complement of proteins within the glycosome and the function of compartmentation. Studies now suggest that regulation of glycolysis is a strong driving force for maintenance of the glycosome. [source] Cross-species hybridization of a Borrelia burgdorferi DNA array reveals infection- and culture-associated genes of the unsequenced genome of the relapsing fever agent Borrelia hermsiiMOLECULAR MICROBIOLOGY, Issue 3 2004Jianmin Zhong Summary The known genome sequence of Borrelia burgdorferi, an agent of Lyme borreliosis, was used to study the genetic content and gene expression in B. hermsii, another spirochete pathogen and a cause of relapsing fever. Cross-species hybridization of a DNA array representing 1628 open reading frames (ORF) of B. burgdorferi with genomic DNA of B. hermsii indicated that the latter organism has at least 81% of the chromosomal genes and 43% of the plasmid genes of B. burgdorferi. We then carried out quantitative hybridization of the arrays with multiple replicates of cDNA produced from B. hermsii cells growing in the blood of infected mice or in culture medium that was adjusted to the same pH, temperature and a spirochete density as infected blood. Of 642 B. burgdorferi ORFs hybridized by all replicates under both conditions, 12 (1.9%) demonstrated differential expression by a regularized t -test and stringent criteria. BBP07 and BBG30, two plasmid-borne ORFs with the greatest measurable difference in expression between in vivo and in vitro conditions, putatively encode proteins of unknown function. Orthologues of BBP07 in B. hermsii were identified, and increased expression in infected mice was demonstrated by quantitative reverse-transcriptase polymerase chain reaction. [source] Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfAMOLECULAR MICROBIOLOGY, Issue 6 2003Eliane Milohanic Summary PrfA is the major regulator of Listeria virulence gene expression. This protein is a member of the Crp/Fnr family of transcription regulators. To gain a deeper understanding of the PrfA regulon, we constructed a whole-genome array based on the complete genome sequence of Listeria monocytogenes strain EGDe and evaluated the expression profiles of the wild-type EGDe and a prfA -deleted mutant (EGDe ,prfA). Both strains were grown at 37°C in brain,heart infusion broth (BHI) and BHI supplemented with either activated charcoal, a compound known to enhance virulence gene expression, or cellobiose, a sugar reported to downregulate virulence gene expression in spite of full expression of PrfA. We identified three groups of genes that are regulated differently. Group I comprises, in addition to the 10 already known genes, two new genes, lmo2219 and lmo0788, both positively regulated and preceded by a putative PrfA box. Group II comprises eight negatively regulated genes: lmo0278 is preceded by a putative PrfA box, and the remaining seven genes (lmo0178,lmo0184) are organized in an operon. Group III comprises 53 genes, of which only two (lmo0596 and lmo2067) are preceded by a putative PrfA box. Charcoal addition induced upregulation of group I genes but abolished regulation by PrfA of most group III genes. In the presence of cellobiose, all the group I genes were downregulated, whereas group III genes remained fully activated. Group II genes were repressed in all conditions tested. A comparison of the expression profiles between a second L. monocytogenes strain (P14), its spontaneous mutant expressing a constitutively active PrfA variant (P14prfA*) and its corresponding prfA -deleted mutant (P14,prfA) and the EGDe strain revealed interesting strain-specific differences. Sequences strongly similar to a sigma B-dependent promoter were identified upstream of 22 group III genes. These results suggest that PrfA positively regulates a core set of 12 genes preceded by a PrfA box and probably expressed from a sigma A-dependent promoter. In contrast, a second set of PrfA-regulated genes lack a PrfA box and are expressed from a sigma B-dependent promoter. This study reveals that PrfA can act as an activator or a repressor and suggests that PrfA may directly or indirectly activate different sets of genes in association with different sigma factors. [source] | |||||||||||||||||||||||||||||||||||||