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Protein-coding Genes (protein-coding + gene)
Selected AbstractsA Fundamental Problem with Amino-Acid-Sequence Characters for Phylogenetic AnalysesCLADISTICS, Issue 3 2000Mark P. Simmons Protein-coding genes may be analyzed in phylogenetic analyses using nucleotide-sequence characters and/or amino-acid-sequence characters. Although amino-acid-sequence characters "correct" for saturation (parallelism), amino-acid-sequence characters are subject to convergence and ignore phylogenetically informative variation. When all nucleotide-sequence characters have a consistency index of 1, characters coded using the amino acid sequence may have a consistency index of less than 1. The reason for this is that most amino acids are specified by more than one codon. If two different codons that both code for the same amino acid are derived independent of one another in divergent lineages, nucleotide-sequence characters may not be homoplasious when amino-acid-sequence characters may be homoplasious. Not only may amino-acid-sequence characters support groupings that are not supported by nucleotide-sequence characters, they may support contradictory groupings. Because this convergence is a problem of character delimitation, it affects the results of all tree-construction methods (maximum likelihood, neighbor joining, parsimony, etc.). In effect, coding amino-acid-sequence characters instead of nucleotide-sequence characters putatively corrects for saturation and definitely causes a convergence problem. An empirical example from the Mhc locus is given. [source] THE EVOLUTION OF DIOECY, HETERODICHOGAMY, AND LABILE SEX EXPRESSION IN ACEREVOLUTION, Issue 11 2007S. S. Renner The northern hemisphere tree genus Acer comprises 124 species, most of them monoecious, but 13 dioecious. The monoecious species flower dichogamously, duodichogamously (male, female, male), or in some species heterodichogamously (two morphs that each produce male and female flowers but at reciprocal times). Dioecious species cannot engage in these temporal strategies. Using a phylogeny for 66 species and subspecies obtained from 6600 nucleotides of chloroplast introns, spacers, and a protein-coding gene, we address the hypothesis (Pannell and Verdú, Evolution 60: 660,673. 2006) that dioecy evolved from heterodichogamy. This hypothesis was based on phylogenetic analyses (Gleiser and Verdú, New Phytol. 165: 633,640. 2005) that included 29,39 species of Acer coded for five sexual strategies (duodichogamous monoecy, heterodichogamous androdioecy, heterodichogamous trioecy, dichogamous subdioecy, and dioecy) treated as ordered states or as a single continuous variable. When reviewing the basis for these scorings, we found errors that together with the small taxon sample, cast doubt on the earlier inferences. Based on published studies, we coded 56 species of Acer for four sexual strategies, dioecy, monoecy with dichogamous or duodichogamous flowering, monoecy with heterodichogamous flowering, or labile sex expression, in which individuals reverse their sex allocation depending on environment,phenotype interactions. Using Bayesian character mapping, we infer an average of 15 transformations, a third of them involving changes from monoecy-cum-duodichogamy to dioecy; less frequent were changes from this strategy to heterodichogamy; dioecy rarely reverts to other sexual systems. Contra the earlier inferences, we found no switches between heterodichogamy and dioecy. Unexpectedly, most of the species with labile sex expression are grouped together, suggesting that phenotypic plasticity in Acer may be a heritable sexual strategy. Because of the complex flowering phenologies, however, a concern remains that monoecy in Acer might not always be distinguishable from labile sex expression, which needs to be addressed by long-term monitoring of monoecious trees. The 13 dioecious species occur in phylogenetically disparate clades that date back to the Late Eocene and Oligocene, judging from a fossil-calibrated relaxed molecular clock. [source] The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae)INSECT MOLECULAR BIOLOGY, Issue 2 2006I. Kim Abstract We determined the complete nucleotide sequences of the mitochondrial genome (mitogenome) of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). The entire mitochondrial DNA (mtDNA) molecule was 15 314 bp long. The C. raphaelis genes were in the same order and orientation as the completely sequenced mitogenomes of other lepidopteran species, except for the presence of an extra copy of tRNASer(AGN). High similarity in primary sequence and secondary structure between the two tandemly located copies of the tRNASer(AGN) suggest a recent duplication of an original single tRNASer(AGN). The DHU arm of the two copies of tRNASer(AGN) formed a simple loop as seen in many other metazoan mt tRNASer(AGN). The putative initiation codon for the C. raphaelis COI gene appears to be a tetranucleotide, TTAG, found commonly in the sequenced lepidopterans. ATPase8, ATPase6, ND4L and ND6 genes, which are next to another protein-coding gene at their 3, end all had the sequences potential to form a hairpin structure, suggesting the importance of such a structure for precise cleavage of the mature protein-coding genes. [source] Phylogenetic relationships within the tropical soft coral genera Sarcophyton and Lobophytum (Anthozoa, Octocorallia)INVERTEBRATE BIOLOGY, Issue 4 2006Catherine S. McFadden Abstract. The alcyonacean soft coral genera Sarcophyton and Lobophytum are conspicuous, ecologically important members of shallow reef communities throughout the Indo-West Pacific. Study of their ecology is, however, hindered by incomplete knowledge of their taxonomy: most species cannot be identified in the field and the two genera cannot always be distinguished reliably. We used a 735-bp fragment of the octocoral-specific mitochondrial protein-coding gene msh1 to construct a phylogeny for 92 specimens identified to 19 species of Lobophytum and 16 species of Sarcophyton. All phylogenetic methods used recovered a tree with three strongly supported clades. One clade included only morphologically typical Sarcophyton species with a stalk distinct from the polypary, poorly formed club-shaped sclerites in the colony surface, and large spindles in the interior of the stalk. A second clade included only morphologically typical Lobophytum colonies with lobes and ridges on the colony surface, poorly formed clubs in the colony surface, and interior sclerites consisting of oval forms with regular girdles of ornamental warts. The third distinct clade included a mix of Sarcophyton and Lobophytum nominal species with intermediate morphologies. Most of the species in this mixed clade had a polypary that was not distinct from the stalk, and the sclerites in the colony surface were clubs with well-defined heads. Within the Sarcophyton clade, specimens identified as Sarcophyton glaucum belonged to six very distinct genetic sub-clades, suggesting that this morphologically heterogeneous species is actually a cryptic species complex. Our results highlight the need for a complete taxonomic revision of these genera, using molecular data to help confirm species boundaries as well as to guide higher taxonomic decisions. [source] Evidence from a protein-coding gene that acanthocephalans are rotifersINVERTEBRATE BIOLOGY, Issue 1 2000David B. Mark Welch Abstract. Rotifera and Acanthocephala are generally regarded as separate phyla sharing a basal position among triploblast protostomes. This paper presents the first molecular phylogenetic examination of the relationship of Acanthocephala to all three rotifer classes, Seisonidea, Monogononta, and Bdelloidea. Inclusion of Acanthocephala within Rotifera, probably as a sister-taxon to a clade composed of Bdelloidea and Monogononta (the Eurotatoria), is strongly supported by both parsimony and distance methods, using a region of the nuclear coding gene hsp82. Previous molecular evidence for the inclusion of Acanthocephala in the Rotifera suggested that Acanthocephala is a sister-taxon of Bdelloidea, forming the clade Lemniscea. No support is found for this clade, and evidence is presented that the monogonont rotifer used in those analyses, Brachionus plicatilis, may be evolving in an anomalous manner. [source] Phylogeographic analysis detects congruent biogeographic patterns between a woodland agamid and Australian wet tropics taxa despite disparate evolutionary trajectoriesJOURNAL OF BIOGEOGRAPHY, Issue 8 2010Danielle L. Edwards Abstract Aim, To test the congruence of phylogeographic patterns and processes between a woodland agamid lizard (Diporiphora australis) and well-studied Australian wet tropics fauna. Specifically, to determine whether the biogeographic history of D. australis is more consistent with a history of vicariance, which is common in wet tropics fauna, or with a history of dispersal with expansion, which would be expected for species occupying woodland habitats that expanded with the increasingly drier conditions in eastern Australia during the Miocene,Pleistocene. Location, North-eastern Australia. Methods, Field-collected and museum tissue samples from across the entire distribution of D. australis were used to compile a comprehensive phylo-geographic dataset based on c. 1400 bp of mitochondrial DNA (mtDNA), incorporating the ND2 protein-coding gene. We used phylogenetic methods to assess biogeographic patterns within D. australis and relaxed molecular clock analyses were conducted to estimate divergence times. Hierarchical Shimodaira,Hasegawa tests were used to test alternative topologies representing vicariant, dispersal and mixed dispersal/vicariant biogeographic hypotheses. Phylogenetic analyses were combined with phylogeographic analyses to gain an insight into the evolutionary processes operating within D. australis. Results, Phylogenetic analyses identified six major mtDNA clades within D. australis, with phylogeographic patterns closely matching those seen in many wet tropics taxa. Congruent phylogeographic breaks were observed across the Black Mountain Corridor, Burdekin and St Lawrence Gaps. Divergence amongst clades was found to decrease in a north,south direction, with a trend of increasing population expansion in the south. Main conclusions, While phylogeographic patterns in D australis reflect those seen in many rain forest fauna of the wet tropics, the evolutionary processes underlying these patterns appear to be very different. Our results support a history of sequential colonization of D. australis from north to south across major biogeographic barriers from the late Miocene,Pleistocene. These patterns are most likely in response to expanding woodland habitats. Our results strengthen the data available for this iconic region in Australia by exploring the understudied woodland habitats. In addition, our study shows the importance of thorough investigations of not only the biogeographic patterns displayed by species but also the evolutionary processes underlying such patterns. [source] Role and therapeutic potential of microRNAs in diabetesDIABETES OBESITY & METABOLISM, Issue 2009I. G. M. Kolfschoten The discovery in mammalian cells of hundreds of small RNA molecules, called microRNAs, with the potential to modulate the expression of the majority of the protein-coding genes has revolutionized many areas of biomedical research, including the diabetes field. MicroRNAs function as translational repressors and are emerging as key regulators of most, if not all, physiological processes. Moreover, alterations in the level or function of microRNAs are associated with an increasing number of diseases. Here, we describe the mechanisms governing the biogenesis and activities of microRNAs. We present evidence for the involvement of microRNAs in diabetes mellitus, by outlining the contribution of these small RNA molecules in the control of pancreatic ,-cell functions and by reviewing recent studies reporting changes in microRNA expression in tissues isolated from diabetes animal models. MicroRNAs hold great potential as therapeutic targets. We describe the strategies developed for the delivery of molecules mimicking or blocking the function of these tiny regulators of gene expression in living animals. In addition, because changes in serum microRNA profiles have been shown to occur in association with different human diseases, we also discuss the potential use of microRNAs as blood biomarkers for prevention and management of diabetes. [source] Conflicting phylogenetic signals at the base of the metazoan treeEVOLUTION AND DEVELOPMENT, Issue 4 2003Antonis Rokas Summary A phylogenetic framework is essential for under-standing the origin and evolution of metazoan development. Despite a number of recent molecular studies and a rich fossil record of sponges and cnidarians, the evolutionary relationships of the early branching metazoan groups to each other and to a putative outgroup, the choanoflagellates, remain uncertain. This situation may be the result of the limited amount of phylogenetic information found in single genes and the small number of relevant taxa surveyed. To alleviate the effect of these analytical factors in the phylogenetic recons-truction of early branching metazoan lineages, we cloned multiple protein-coding genes from two choanoflagellates and diverse sponges, cnidarians, and a ctenophore. Comparisons of sequences for ,-tubulin, ,-tubulin, elongation factor 2, HSP90, and HSP70 robustly support the hypothesis that choanoflagellates are closely affiliated with animals. However, analyses of single and concatenated amino acid sequences fail to resolve the relationships either between early branching metazoan groups or between Metazoa and choano-flagellates. We demonstrate that variable rates of evolution among lineages, sensitivity of the analyses to taxon selection, and conflicts in the phylogenetic signal contained in different amino acid sequences obscure the phylogenetic associations among the early branching Metazoa. These factors raise concerns about the ability to resolve the phylogenetic history of animals with molecular sequences. A consensus view of animal evolution may require investigations of genome-scale characters. [source] Identification of protein-coding genes in the genome of Vibrio cholerae with more than 98% accuracy using occurrence frequencies of single nucleotidesFEBS JOURNAL, Issue 15 2001Ju Wang The published sequence of the Vibrio cholerae genome indicates that, in addition to the genes that encode proteins of known and unknown function, there are 1577 ORFs identified as conserved hypothetical or hypothetical gene candidates. Because the annotation is not 100% accurate, it is not known which of the 1577 ORFs are true protein-coding genes. In this paper, an algorithm based on the Z curve method, with sensitivity, specificity and accuracy greater than 98%, is used to solve this problem. Twenty-fold cross-validation tests show that the accuracy of the algorithm is 98.8%. A detailed discussion of the mechanism of the algorithm is also presented. It was found that 172 of the 1577 ORFs are unlikely to be protein-coding genes. The number of protein-coding genes in the V. cholerae genome was re-estimated and found to be ,,3716. This result should be of use in microarray analysis of gene expression in the genome, because the cost of preparing chips may be somewhat decreased. A computer program was written to calculate a coding score called VCZ for gene identification in the genome. Coding/noncoding is simply determined by VCZ > 0/VCZ < 0. The program is freely available on request for academic use. [source] The mitochondrial genome of the wine yeast Hanseniaspora uvarum: a unique genome organization among yeast/fungal counterpartsFEMS YEAST RESEARCH, Issue 1 2006Paraskevi V. Pramateftaki Abstract The complete sequence of the apiculate wine yeast Hanseniaspora uvarum mtDNA has been determined and analysed. It is an extremely compact linear molecule containing the shortest functional region ever found in fungi (11 094 bp long), flanked by Type 2 telomeric inverted repeats. The latter contained a 2704-bp-long subterminal region and tandem repeats of 839-bp units. In consequence, a population of mtDNA molecules that differed at the number of their telomeric reiterations was detected. The functional region of the mitochondrial genome coded for 32 genes, which included seven subunits of respiratory complexes and ATP synthase (the genes encoding for NADH oxidoreductase subunits were absent), two rRNAs and 23 tRNA genes which recognized codons for all amino acids. A single intron interrupted the cytochrome oxidase subunit 1 gene. A number of reasons contributed towards its strikingly small size, namely: (1) the remarkable size reduction (by >40%) of the rns and rnl genes; (2) that most tRNA genes and five of the seven protein-coding genes were the shortest among known yeast homologs; and (3) that the noncoding regions were restricted to 5.1% of the genome. In addition, the genome showed multiple changes in the orientation of transcription and the gene order differed drastically from other yeasts. When all protein coding gene sequences were considered as one unit and were compared with the corresponding molecules from all other complete mtDNAs of yeasts, the phylogenetic trees constructed robustly supported its placement basal to the yeast species of the ,Saccharomyces complex', demonstrating the advantage of this approach over single-gene or multigene approaches of unlinked genes. [source] The mitochondrial genome of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae)INSECT MOLECULAR BIOLOGY, Issue 2 2006I. Kim Abstract We determined the complete nucleotide sequences of the mitochondrial genome (mitogenome) of the Korean hairstreak, Coreana raphaelis (Lepidoptera: Lycaenidae). The entire mitochondrial DNA (mtDNA) molecule was 15 314 bp long. The C. raphaelis genes were in the same order and orientation as the completely sequenced mitogenomes of other lepidopteran species, except for the presence of an extra copy of tRNASer(AGN). High similarity in primary sequence and secondary structure between the two tandemly located copies of the tRNASer(AGN) suggest a recent duplication of an original single tRNASer(AGN). The DHU arm of the two copies of tRNASer(AGN) formed a simple loop as seen in many other metazoan mt tRNASer(AGN). The putative initiation codon for the C. raphaelis COI gene appears to be a tetranucleotide, TTAG, found commonly in the sequenced lepidopterans. ATPase8, ATPase6, ND4L and ND6 genes, which are next to another protein-coding gene at their 3, end all had the sequences potential to form a hairpin structure, suggesting the importance of such a structure for precise cleavage of the mature protein-coding genes. [source] Monophyletic groups within ,higher land birds', comparison of morphological and molecular dataJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 4 2003G. Mayr Abstract The relationships within the ,higher land birds' and putatively related taxa are analysed in a study using 89 morphological characters and DNA sequences of three nuclear, protein-coding genes, c- myc, RAG-1, and myoglobin intron II. Separate analyses of the different data sets and a ,total evidence' analysis in which the data sets of the morphological and molecular analyses were combined are compared. All three analyses support the hitherto disputed sister group relationship between Pici (Ramphastidae, Indicatoridae and Picidae) and Galbulae (Galbulidae and Bucconidae). Previously unrecognized osteological synapomorphies of this clade are presented. All analyses further resulted in monophyly of the taxon [Aegothelidae + (Apodidae/Hemiprocnidae + Trochilidae)]. Analysis of the morphological data and of the combined data set also supported monophyly of the taxon [Strigiformes + (Falconidae + Accipitridae)]. The morphological data further support monophyly of the taxon (Upupidae + Bucerotidae). Other placements in the three analyses received either no or only weak bootstrap support. [source] Clades within the ‘higher land birds’, evaluated by nuclear DNA sequencesJOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 1-2 2001Johansson In this study we investigated the phylogenetic relationships within the ‘higher land birds’ by parsimony analysis of nucleotide DNA sequences obtained from the two nuclear, protein-coding genes, c- myc and RAG-1. Nuclear genes have not previously been used to address this phylogenetic question. The results include high jackknife support for a monophyletic Apodiformes (including the Trochilidae). This arrangement was further supported by the observation of an insertion of four amino acids in the c- myc gene in all apodiform taxa. Monophyly was also inferred for each of the two piciform groups Galbulae and Pici. Within Pici, the Capitonidae was found to be paraphyletic, with the New World barbets more closely related to the Ramphastidae than to the Old World barbets. Another clade with high jackknife support consists of the Upupidae, Phoeniculidae and Bucerotidae. The families Momotidae and Todidae, and Coraciidae and Brachypteraciidae, respectively, also form well supported monophyletic clades. The results are inconclusive regarding the monophyly of the orders Coraciiformes and Piciformes, respectively. Die von nuklearen DNA-Sequenzen abgeleiten Kladen bei den ‘Höheren and vögeln’ Es wurde eine Studie über die phylogenetischen Beziehungen bei den ‘höheren Landvögeln’ mit Hilfe einer Parsimonie-Analyse von DNA-Kernsequenzen zweier proteincodierender Genen, c-myc und RAG-1, durchgeführt. Kerngene wurden bisher noch nicht für die Untersuchung dieser phylogentischen Frage eingesetzt. Die Ergebnisse unterstützen mit hohen Jackknife-Werten eine Monophylie der Apodiformes (einschließlich der Trochilidae). Eine solche Einordnung wird auch durch die Beobachtung einer Einfüngung von vier Aminosäuren im c-myc -Gen bei allen apodiformen Taxa unterstützt. Eine Monophylie konnte ebenso für die beiden picidiformen Gruppen, Glabulae und Pici, bestätigt werden. Bei den Pici erweisen sich die Capitonidae als paraphyletisch, wobei die Bartvögel der NeuenWelt näher mit den Ramphistidae verwandt sind als mit den Bartvögeln der Alten Welt. Eine weitere Klade, die durch hohe Jackknife-Werte unterstützt wird, besteht aus den Upupidae, Phoeniculidae und Bucerotidae. Die Familien Momotidae und Todidae bzw. Coraciidae und Brachypteraciidae bilden ebenfalls gut unterstützte Kladen. Über die Monophylie der Ordnungen Coraciiformes und Piciformes können die Ergebnisse jedoch keine Entscheidung herbeiführen. [source] Evolutionary genetics and biogeographic structure of Rhizobium gallicum sensu lato, a widely distributed bacterial symbiont of diverse legumesMOLECULAR ECOLOGY, Issue 13 2005CLAUDIA SILVA Abstract We used phylogenetic and population genetics approaches to evaluate the importance of the evolutionary forces on shaping the genetic structure of Rhizobium gallicum and related species. We analysed 54 strains from several populations distributed in the Northern Hemisphere, using nucleotide sequences of three ,core' chromosomal genes (rrs, glnII and atpD) and two ,auxiliary' symbiotic genes (nifH and nodB) to elucidate the biogeographic history of the species and symbiotic ecotypes (biovarieties) within species. The analyses revealed that strains classified as Rhizobium mongolense and Rhizobium yanglingense belong to the chromosomal evolutionary lineage of R. gallicum and harbour symbiotic genes corresponding to a new biovar; we propose their reclassification as R. gallicum bv. orientale. The comparison of the chromosomal and symbiotic genes revealed evidence of lateral transfer of symbiotic information within and across species. Genetic differentiation analyses based on the chromosomal protein-coding genes revealed a biogeographic pattern with three main populations, whereas the 16S rDNA sequences did not resolve that biogeographic pattern. Both the phylogenetic and population genetic analyses showed evidence of recombination at the rrs locus. We discuss our results in the light of the contrasting views of bacterial species expressed by microbial taxonomist and evolutionary biologists. [source] Three nuclear genes for phylogenetic, SNP and population genetic studies of molluscs and other invertebratesMOLECULAR ECOLOGY RESOURCES, Issue 1 2010A. AUDZIJONYTE Abstract The study reports new primers capable of amplifying fragments from three nuclear protein-coding genes in a variety of deep-sea molluscs and annelids , adenine nucleotide translocase (Ant), calmodulin (Cal) and cyclophilin A (CycA). The Ant primers appear to be restricted to bivalve molluscs, whereas the Cal and CycA primers also amplified appropriate gene fragments from Lepetodrilus gastropod molluscs and Osedax polychaete worms. The amplified fragment of Cal contains an intron in the molluscs, but no intron was detected in the Ant and CycA fragments from any of the tested animals. DNA sequences generated by the three primer sets exhibited one to 15 single nucleotide polymorphism sites in deep-sea vesicomyid clams and Osedax boneworms. The observed levels of polymorphism indicate that the genes are likely to be useful in both population genetic and phylogenetic analyses of different invertebrate taxa. [source] Expression of microRNAs and protein-coding genes associated with perineural invasion in prostate cancer,THE PROSTATE, Issue 11 2008Robyn L. Prueitt Abstract Background Perineural invasion (PNI) is the dominant pathway for local invasion in prostate cancer. To date, only few studies have investigated the molecular differences between prostate tumors with PNI and those without it. Methods To evaluate the involvement of both microRNAs and protein-coding genes in PNI, we determined their genome-wide expression with a custom microRNA microarray and Affymetrix GeneChips in 50 prostate adenocarcinomas with PNI and 7 without it. In situ hybridization (ISH) and immunohistochemistry was used to validate candidate genes. Results Unsupervised classification of the 57 adenocarcinomas revealed two clusters of tumors with distinct global microRNA expression. One cluster contained all non-PNI tumors and a subgroup of PNI tumors. Significance analysis of microarray data yielded a list of microRNAs associated with PNI. At a false discovery rate (FDR) <10%, 19 microRNAs were higher expressed in PNI tumors than in non-PNI tumors. The most differently expressed microRNA was miR-224. ISH showed that this microRNA is expressed by perineural cancer cells. The analysis of protein-coding genes identified 34 transcripts that were differently expressed by PNI status (FDR,<,10%). These transcripts were down-regulated in PNI tumors. Many of those encoded metallothioneins and proteins with mitochondrial localization and involvement in cell metabolism. Consistent with the microarray data, perineural cancer cells tended to have lower metallothionein expression by immunohistochemistry than nonperineural cancer cells. Conclusions Although preliminary, our findings suggest that alterations in microRNA expression, mitochondrial function, and cell metabolism occur at the transition from a noninvasive prostate tumor to a tumor with PNI. Prostate 68: 1152,1164, 2008. Published 2008 Wiley-Liss, Inc. [source] The complete mitochondrial genome of the domestic red deer (Cervus elaphus) of New Zealand and its phylogenic position within the family CervidaeANIMAL SCIENCE JOURNAL, Issue 5 2010Kenta WADA ABSTRACT We determined the complete nucleotide sequence of the mitochondrial genome of the semidomestic red deer (Cervus elaphus) of New Zealand. The genome was 16 357 bp long and contained 13 protein-coding genes, 12SrRNA, 16SrRNA, 22 tRNAs and a D-loop as found in other mammals. Database homology searches showed that the mitochondrial DNA (mtDNA) sequence from the New Zealand semidomestic deer was similar to partial mtDNA sequences from the European, Norwegian (C. e. atlanticus) and Spanish red deer (C. e. hispanicus). Phylogenetic analysis of the mitochondrial protein-coding regions revealed two well-defined monophyletic clades in subfamilies Cervinae and Muntiacinae. However, red deer and Sika deer were not found to be close relatives. The analysis did identify the red deer as a sister taxon of a Samber/Sika deer clade, although it was more closely related to the Samber than the Sika group. [source] Structure,function studies of the RNA polymerase II elongation complexACTA CRYSTALLOGRAPHICA SECTION D, Issue 2 2009Florian Brueckner RNA polymerase II (Pol II) is the eukaryotic enzyme that is responsible for transcribing all protein-coding genes into messenger RNA (mRNA). The mRNA-transcription cycle can be divided into three stages: initiation, elongation and termination. During elongation, Pol II moves along a DNA template and synthesizes a complementary RNA chain in a processive manner. X-ray structural analysis has proved to be a potent tool for elucidating the mechanism of Pol II elongation. Crystallographic snapshots of different functional states of the Pol II elongation complex (EC) have elucidated mechanistic details of nucleotide addition and Pol II translocation. Further structural studies in combination with in vitro transcription experiments led to a mechanistic understanding of various additional features of the EC, including its inhibition by the fungal toxin ,-amanitin, the tunability of the active site by the elongation factor TFIIS, the recognition of DNA lesions and the use of RNA as a template. [source] The spliceosome: the most complex macromolecular machine in the cell?BIOESSAYS, Issue 12 2003Timothy W. Nilsen The primary transcripts, pre-mRNAs, of almost all protein-coding genes in higher eukaryotes contain multiple non-coding intervening sequences, introns, which must be precisely removed to yield translatable mRNAs. The process of intron excision, splicing, takes place in a massive ribonucleoprotein complex known as the spliceosome. Extensive studies, both genetic and biochemical, in a variety of systems have revealed that essential components of the spliceosome include five small RNAs,U1, U2, U4, U5 and U6, each of which functions as a RNA, protein complex called an snRNP (small nuclear ribonucleoprotein). In addition to snRNPs, splicing requires many non-snRNP protein factors, the exact nature and number of which has been unclear. Technical advances, including new affinity purification methods and improved mass spectrometry techniques, coupled with the completion of many genome sequences, have now permitted a number of proteomic analyses of purified spliceosomes. These studies, recently reviewed by Jurica and Moore,1 reveal that the spliceosome is composed of as many as 300 distinct proteins and five RNAs, making it among the most complex macromolecular machines known. BioEssays 25:1147,1149, 2003. © 2003 Wiley Periodicals, Inc. [source] The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequencesBIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 3 2005MASAKI MIYA In a previous study based on 100 whole mitochondrial genome (mitogenome) sequences, we sought to provide a new perspective on the ordinal relationships of higher ray-finned fish (Actinopterygii). The study left unexplored the phylogenetic ,position, of, toadfishes, (order, Batrachoidiformes),, as, data, were, unavailable, owing, to, technical, difficulties. In the present study, we successfully determined mitogenomic sequences for two toadfish species (Batrachomoeus trispinosus and Porichthys myriaster) and found that the difficulties resulted from unusual gene arrangements and associated repetitive non-coding sequences. Unambiguously aligned, concatenated mitogenomic sequences (13 461 bp) from 102 higher actinopterygians (excluding the ND6 gene and control region) were divided into five partitions (1st, 2nd and 3rd codon positions of the protein-coding genes, tRNA genes and rRNA genes) and partitioned Bayesian analyses were conducted. The resultant phylogenies strongly suggest that the toadfishes are not members of relatively primitive higher actinopterygians (Paracanthopterygii), but belong to a crown group of actinopterygians (Percomorpha), as was demonstrated for ophidiiform eels (Ophidiiformes) and anglerfishes (Lophiiformes) in the previous study. We propose revised limits of major unranked categories for higher actinopterygians and a new name (Berycomorpha) for a clade comprising two reciprocally paraphyletic orders (Beryciformes and Stephanoberyciformes) based on the present mitogenomic phylogenies. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 85, 289,306. [source] MicroRNAs in the pathogeny of chronic lymphocytic leukaemiaBRITISH JOURNAL OF HAEMATOLOGY, Issue 5 2007Milena S. Nicoloso Summary MicroRNAs (miRNAs) have been linked to the initiation and progression of chronic lymphocytic leukaemia (CLL). The main molecular alterations are represented by variations in gene expression, usually mild and with consequences for a vast number of target protein-coding genes. Recent studies have shown that miRNAs are the main candidates for the elusive class of CLL predisposing genes. These discoveries could be exploited for the development of useful markers for diagnosis and prognosis, as well as for the development of new RNA-based cancer therapies. [source] Phylogenetic relationships of the spider family Tetragnathidae (Araneae, Araneoidea) based on morphological and DNA sequence dataCLADISTICS, Issue 2 2009Fernando Álvarez-Padilla The monophyly of Tetragnathidae including the species composition of the family (e.g., Are Nephila and their relatives part of this lineage?), the phylogenetic relationships of its various lineages, and the exact placement of Tetragnathidae within Araneoidea have been three recalcitrant problems in spider systematics. Most studies on tetragnathid phylogeny have focused on morphological and behavioral data, but little molecular work has been published to date. To address these issues we combine previous morphological and behavioral data with novel molecular data including nuclear ribosomal RNA genes 18S and 28S, mitochondrial ribosomal RNA genes 12S and 16S and protein-coding genes from the mitochondrion [cytochrome c oxidase subunit I (COI)] and from the nucleus (histone H3), totaling ca. 6.3 kb of sequence data per taxon. These data were analyzed using direct optimization and static homology using both parsimony and Bayesian methods. Our results indicate monophyly of Tetragnathidae, Tetragnathinae, Leucauginae, the "Nanometa clade" and the subfamily Metainae, which, with the exception of the later subfamily, received high nodal support. Morphological synapomorphies that support these clades are also discussed. The position of tetragnathids with respect to the rest of the araneoid spiders remains largely unresolved but tetragnathids and nephilids were never recovered as sister taxa. The combined dataset suggests that Nephilidae is sister to Araneidae; furthermore, the sister group of Nephila is the clade composed by Herennia plus Nephilengys and this pattern has clear implications for understanding the comparative biology of the group. Tetragnathidae is most likely sister to some members of the "reduced piriform clade" and nephilids constitute the most-basal lineage of araneids. [source] | ||||||||||||||||||||||||||||