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Sequences Alone (sequence + alone)
Selected AbstractsEukaryotic diversity and phylogeny using small- and large-subunit ribosomal RNA genes from environmental samplesENVIRONMENTAL MICROBIOLOGY, Issue 12 2009William Marande Summary The recent introduction of molecular techniques in eukaryotic microbial diversity studies, in particular those based in the amplification and sequencing of small-subunit ribosomal DNA (SSU rDNA), has revealed the existence of an unexpected variety of new phylotypes. The taxonomic ascription of the organisms bearing those sequences is generally deduced from phylogenetic analysis. Unfortunately, the SSU rDNA sequence alone has often not enough phylogenetic information to resolve the phylogeny of fast-evolving or very divergent sequences, leading to their misclassification. To address this problem, we tried to increase the phylogenetic signal by amplifying the complete eukaryotic rDNA cluster [i.e. the SSU rDNA, the internal transcribed spacers, the 5.8S rDNA and the large-subunit (LSU) rDNA] from environmental samples, and sequencing the SSU and LSU rDNA part of the clones. Using marine planktonic samples, we showed that surveys based on either SSU or SSU + LSU rDNA retrieved comparable diversity patterns. In addition, phylogenetic trees based on the concatenated SSU + LSU rDNA sequences showed better resolution, yielding good support for major eukaryotic groups such as the Opisthokonta, Rhizaria and Excavata. Finally, highly divergent SSU rDNA sequences, whose phylogenetic position was impossible to determine with the SSU rDNA data alone, could be placed correctly with the SSU + LSU rDNA approach. These results suggest that this method can be useful, in particular for the analysis of eukaryotic microbial communities rich in phylotypes of difficult phylogenetic ascription. [source] A combinatorial approach to studying protein complex composition by employing size-exclusion chromatography and proteome analysisJOURNAL OF SEPARATION SCIENCE, JSS, Issue 10 2007Shi-Sheng Li Abstract The genome sequences of numerous organisms are available now, but gene sequences alone do not provide sufficient information to accurately deduce protein functions. Protein function is largely dependent on the association of multiple polypeptide chains into large structures with interacting subunits that regulate and support each other. Therefore, the mapping of protein interaction networks in a physiological context is conducive to deciphering protein functions, including those of hypothetical proteins. Although several high-throughput methods to globally identify protein interactions have been reported in recent years, these approaches often have a high rate of nonspecific or artificial interactions detected. For instance, the fraction of false positives of the protein interactions identified by yeast two-hybrid assay has been predicted to be of the order of 50%. We have developed a strategy to globally map Bacillus subtilis protein,protein interactions in a physiological context by fractionating the cell lysates using size-exclusion chromatography (SEC), followed by proteome analysis. Components of both known and unknown protein complexes, multisubunits and multiproteins, have been identified using this strategy. In one case, the partners of the B. subtilis protein complex have been coexpressed in Escherichia coli, and the formation of the overexpressed protein complex has been further confirmed by a pull-down assay. [source] On the systematics of the fungus gnat subfamily Mycetophilinae (Diptera): a combined morphological and molecular approachJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 3 2009E. Rindal Abstract The phylogenetic relationships within the fungus gnat subfamily Mycetophilinae (Diptera) are addressed using a combined morphological and molecular approach. Twenty-four species, representing nine genera of the tribe Mycetophilini and 15 genera of the tribe Exechiini, were included in the study. Analyses include nucleotide sequences of mitochondrial (cytochrome oxidase I and 16S), and nuclear (18S and 28S rDNA) genes, in addition to 65 morphological characters. A combined parsimony analysis, including all characters, supports the monophyly of the subfamily Mycetophilinae and two of its tribes, Exechiini and Mycetophilini. There is also statistical support for a Mycetophila- group and a Phronia- group within the tribe Mycetophilini. The Phronia- group includes the genera Phronia, Macrobrachius and Trichonta. The Mycetophila- group includes the genera Mycetophila, Epicypta, Platurocypta, Sceptonia and Zygomyia. A Bayesian analysis based on the nucleotide sequences alone also support these clades within Mycetophilini except for the position of Dynatosoma which is recovered as the sister taxon to the Phronia- group. A somewhat different pattern, however, is observed for the tribe Exechiini , neither molecular data nor the combined data set support unambiguously any intergeneric relationships within Exechiini. Zusammenfassung Die phylogenetischen Verwandtschaftsbeziehungen innerhalb der Pilzmücken der Unterfamilie Mycetophilinae (Diptera) wurden mit einem kombinierten morphologischen und molekularen Ansatz untersucht. Vierundzwanzig Arten aus 9 Gattungen des Tribus Mycetophilini und 15 Gattungen des Tribus Exechiini wurden in die Untersuchungen einbezogen. Die Ergebnisse einer kombinierten kladistischen Analyse von 65 morphologischen Merkmalen und den Nukleotidsequenzen der mitochondrialen Cytochrom Oxidase I und 16S Gene sowie der 18S und 28S Gene des Kerngenoms stützen die Monophylie der Unterfamilie Mycetophilinae sowie der beiden Tribus Exechiini und Mycetophilini. Weiterhin hatten die Mycetophila- und die Phronia- Gruppe innerhalb des Tribus Mycetophilini hohe statistische Unterstützung. Die Phronia- Gruppe schlie,t die Gattungen Phronia, Macrobrachius und Trichonta und die Mycetophila- Gruppe die Gattungen Mycetophila, Epicypta, Platurocypta, Sceptonia und Zygomyia ein. Die Gattung Dynatosoma gruppierte ebenso in der Mycetophila- Gruppe. Die Bayesische Analyse der Nukleotidsequenzen stützt ebenfalls die Monophylie der oben genannten Gruppen innerhalb des Tribus Mycetophilini. Ein anderes Bild ergab sich für den Tribus Exechiini. Weder die Analysen der molekularen Daten alleine noch in Kombination mit den morphologischen Daten ergaben für die einebezogenen Gattungen zweifelsfreie phylogenetische Verwandschaftsbeziehungen mit hoher statistischer Unterstützung. [source] PRIMER NOTE: Primers for amplifying the hypervariable, male-transmitted COII-COI junction region in amblemine freshwater mussels (Bivalvia: Unionoidea: Ambleminae)MOLECULAR ECOLOGY RESOURCES, Issue 3 2007JENNIFER M. WALKER Abstract Freshwater bivalves in the superfamily Unionoidea possess distinct male (M)- and female (F)-transmitted mitochondrial DNA (mtDNA). The former evolves independently of and at a significantly faster rate than the latter. Thus, population genetic and phylogenetic analyses of M sequences facilitate the generation of independent estimates of genetic variation and evolutionary relationships which are often more robust than those provided by analyses of F sequences alone. However, M mtDNA's rapid substitution rate often renders polymerase chain reaction (PCR) amplification difficult with ,universal' primers. Herein, we report on three pairs of PCR primers that consistently amplify the hypervariable M COII-COI gene junction region in 25 bivalve genera (Unionoidea: Ambleminae). [source] Molecular phylogenetic analyses of the Japanese Ulva and Enteromorpha (Ulvales, Ulvophyceae), with special reference to the free-floating UlvaPHYCOLOGICAL RESEARCH, Issue 2 2003Satoshi Shimada SUMMARY In order to elucidate the species composition of free-floating Ulva that cause green tide in several bays in Japan, and to clarify the generic status of Ulva and Enteromorpha (Ulvales, Ulvophyceae), the nuclear encoded internal transcribed spacer (ITS) region including the 5.8S gene and the plastid encoded large subunit of ribulose-1, 5-bisphosphate carboxylase/ oxgenase (rbcL) gene sequences for 15 species were determined. Both ITS and rbcL analyses indicate that free-floating Ulva samples are divided into four different lineages that correspond to Ulva lactuca Linnaeus, U. pertusa Kjellman, U. armoricana Dion etal. and U. fasciata Delile. These four species are distinguished by cell morphology including the arrangement of cells, the shape and size of cells and the position of chloroplasts. Molecular data also indicated that Ulva and Enteromorpha are not separated as respective monophyletic groups within a large monophyletic clade and congeneric as shown by previous molecular studies using the ITS sequences alone. This strongly suggests that these genera are congeneric and Enteromorpha should be reduced to the synonym of Ulva. [source] | ||||||||||