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Sequence
Kinds of Sequence Terms modified by Sequence Selected AbstractsCOMPLETE NUCLEOTIDE SEQUENCE OF SPHEROIDIN GENES OF CALLIPTAMUS IT ALICUS ENTOMOPOXVIRUS(CIEPV) AND GOMPHOCERUS SIBIRICUS ENTOMOPOXVIRUS(GSEPV)INSECT SCIENCE, Issue 3 2004Yong-dan Li Abstract, The spheroidin genes of Calliptamus italicus entomopoxvirus (CiEPV) and Gomphocerus sibiricus entomopoxvirus (GsEPV) were obtained by PCR, and the fragments were cloned, se-quenced and analyzed. The CiEPV and GsEPV spheroidin genes respectively harbored ORFs of 2 922 bps and 2 967 bps that were capable of coding polypeptides of 109.2 and 111.1 kDa. Computer analysis indicated that CiEPV and GsEPV spheroidins shared less than 20% amino acid identities with lepidopteran AmEPV and coleopteran AcEPV spheroidins, but more than 80% amino acid identities with orthopteran OaEPV, MsEPV and AaEPV spheroidins. The CiEPV and GsEPV spheroidins respectively contained 19 and 21 cysteine residues that were particularly abundant at the C-termini, as is the case with those of the other orthopteran EPV spheroidins. The numbers and locations of the cysteine residues of the spheroidins were most similar to those of the spheroidins of EPVs that are virulent on the same insect orders. The promoter regions of the two spheroidin genes were highly conserved (99%) among the orthopteran EPVs and also contained the typical very A+T rich and TAAATG signal mediating transcription of poxvirus late genes. We also sequenced an incomplete ORF downstream of the pheroidin gene of CiEPV and GsEPV. The ORF was in the opposite direction to the spheroidin gene and was homologous to MSV072 putative protein of MsEPV. [source] SEQUENCE AND STRUCTURAL ANALYSIS OF ,-CARRAGEENAN-DERIVED OLIGOSACCHARIDES BY TWO-DIMENSIONAL NUCLEAR MAGNETIC RESONANCE,JOURNAL OF PHYCOLOGY, Issue 4 2010Wei Zhang ,-Carrageenan was hydrolyzed with mild hydrochloric acid and separated into a series of oligosaccharides, the sequences and structures of which were investigated by double-quantum filtered correlation spectroscopy (DQF-COSY), total correlation spectroscopy (TOCSY), heteronuclear multiple-quantum coherence (HMQC), and heteronuclear multiple-bond correlation (HMBC) techniques, respectively. The chemical structures and conformations of the individual sugar residues were identified, as well as the sequential connectivity of the oligosaccharides. The interresidue nuclear Overhauser effects (NOEs)/rotating frame Overhauser effects (ROEs) revealed an ordered helical structure of the carrageenan oligosaccharide chains. Therefore, a general two-dimensional (2-D) NMR methodology for the unambiguous sequence and structure analysis of ,-carrageenan-derived oligosaccharides was established in this study. [source] SYSTEMATICS OF THE HILDENBRANDIALES (RHODOPHYTA): GENE SEQUENCE AND MORPHOMETRIC ANALYSES OF GLOBAL COLLECTIONS,JOURNAL OF PHYCOLOGY, Issue 2 2003Alison R. Sherwood Fifty-seven collections of marine and freshwater Hildenbrandia from North America, South America, Europe, and Africa were compared with 21 type and historically important specimens using multivariate morphometrics. Additionally, phylogenetic analyses of 48 specimens of Hildenbrandia and two specimens of Apophlaea were carried out based on sequences of the rbcL chloroplast gene and the nuclear 18S rRNA gene. Morphometric analyses based on vegetative cell and filament dimensions distinguished two groups of freshwater Hildenbrandia specimens, the first corresponding to those collections from North America and the Philippines and the second to those from Europe and the Canary Islands. The first group had smaller mean cell and filament dimensions (cells 4.0 × 4.4 ,m, filaments 46.5 ,m) and corresponded to H. angolensis, whereas the second group had larger mean dimensions (cells 5.8 × 6.6 ,m, filaments 55.3 ,m) and represented H. rivularis. Marine specimens were morphometrically distinguishable into two groups based on tetrasporangial division pattern as well as other thallus characters. However, measurements and character determinations of some type specimens differed greatly from the original descriptions, and thus further work to determine the stability of these characters is required. Phylogenetic reconstruction based on the 18S rRNA gene and rbcL gene sequence data generally demonstrated separation of the marine and freshwater forms of Hildenbrandia, with some marine taxa forming monophyletic groups (e.g. H. lecannellieri and H. occidentalis) and others forming paraphyletic groups (e.g. H. rubra). The two specimens of Apophlaea formed a monophyletic group within the paraphyletic genus Hildenbrandia. [source] THE DATE AND SEQUENCE OF USE OF NEOLITHIC FUNERARY MONUMENTS: NEW AMS DATING EVIDENCE FROM THE COTSWOLD-SEVERN REGIONOXFORD JOURNAL OF ARCHAEOLOGY, Issue 4 2006MARTIN SMITH Summary. In this paper we discuss 26 new Neolithic AMS dates obtained from human and animal bone from four previously undated funerary monuments in the Cotswold-Severn region. By strategically targeting particular portions of these skeletal assemblages, a number of valuable inferences are made concerning the extent of variation in apparently co-existing burial practices both within and between monuments. Of particular interest is the observation that variations in the extent to which interments have become disarticulated cannot necessarily be equated with chronological relationships regarding their deposition. This project has also obtained dates from cremated bone, which establish that the range of funerary treatments in practice during the earlier Neolithic also included cremation. Additionally it is observed that whilst some, apparently primary, deposits may in fact be later insertions, other material in apparently secondary contexts may actually return earlier Neolithic dates. [source] THE POPULATION GENETICS OF ADAPTATION: THE ADAPTATION OF DNA SEQUENCESEVOLUTION, Issue 7 2002H. Allen Orr Abstract I describe several patterns characterizing the genetics of adaptation at the DNA level. Following Gillespie (1983, 1984, 1991), I consider a population presently fixed for the ith best allele at a locus and study the sequential substitution of favorable mutations that results in fixation of the fittest DNA sequence locally available. Given a wild type sequence that is less than optimal, I derive the fitness rank of the next allele typically fixed by natural selection as well as the mean and variance of the jump in fitness that results when natural selection drives a substitution. Looking over the whole series of substitutions required to reach the best allele, I show that the mean fitness jumps occurring throughout an adaptive walk are constrained to a twofold window of values, assuming only that adaptation begins from a reasonably fit allele. I also show that the first substitution and the substitution of largest effect account for a large share of the total fitness increase during adaptation. I further show that the distribution of selection coefficients fixed throughout such an adaptive walk is exponential (ignoring mutations of small effect), a finding reminiscent of that seen in Fisher's geometric model of adaptation. Last, I show that adaptation by natural selection behaves in several respects as the average of two idealized forms of adaptation, perfect and random. [source] DNA BARCODING OF CHLORARACHNIOPHYTES USING NUCLEOMORPH ITS SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 4 2010Gillian H. Gile Chlorarachniophytes are a small group of marine photosynthetic protists. They are best known as examples of an intermediate stage of secondary endosymbiosis: their plastids are derived from green algae and retain a highly reduced nucleus, called a nucleomorph, between the inner and outer pairs of membranes. Chlorarachniophytes can be challenging to identify to the species level, due to their small size, complex life cycles, and the fact that even genus-level diagnostic morphological characters are observable only by EM. Few species have been formally described, and many available culture collection strains remain unnamed. To alleviate this difficulty, we have developed a barcoding system for rapid and accurate identification of chlorarachniophyte species in culture, based on the internal transcribed spacer (ITS) region of the nucleomorph rRNA cistron. Although this is a multicopy locus, encoded in both subtelomeric regions of each chromosome, interlocus variability is low due to gene conversion by homologous recombination in this region. Here, we present barcode sequences for 39 cultured strains of chlorarachniophytes (>80% of currently available strains). Based on barcode data, other published molecular data, and information from culture records, we were able to recommend names for 21 out of the 24 unidentified, partially identified, or misidentified chlorarachniophyte strains in culture. Most strains could be assigned to previously described species, but at least two to as many as five new species may be present among cultured strains. [source] PHYLOGENY OF FOUR DINOPHYSIACEAN GENERA (DINOPHYCEAE, DINOPHYSIALES) BASED ON rDNA SEQUENCES FROM SINGLE CELLS AND ENVIRONMENTAL SAMPLES,JOURNAL OF PHYCOLOGY, Issue 5 2009Sara M. Handy Dinoflagellates are a highly diverse and environmentally important group of protists with relatively poor resolution of phylogenetic relationships, particularly among heterotrophic species. We examined the phylogeny of several dinophysiacean dinoflagellates using samples collected from four Atlantic sites. As a rule, 3.5 kb of sequence including the nuclear ribosomal genes SSU, 5.8S, LSU, plus their internal transcribed spacer (ITS) 1 and 2 regions were determined for 26 individuals, including representatives of two genera for which molecular data were previously unavailable, Ornithocercus F. Stein and Histioneis F. Stein. In addition, a clone library targeting the dinophysiacean ITS2 and LSU sequences was constructed from bulk environmental DNA from three sites. Three phylogenetic trees were inferred from the data, one using data from this study for cells identified to genus or species (3.5 kb, 28 taxa); another containing dinoflagellate SSU submissions from GenBank and the 12 new dinophysiacean sequences (1.9 kb, 56 taxa) from this study; and the third tree combing data from identified taxa, dinophysiacean GenBank submissions, and the clone libraries from this study (2.1 kb, 136 taxa). All trees were congruent and indicated a distinct division between the genera Phalacroma F. Stein and Dinophysis Ehrenb. The cyanobionts containing genera Histioneis and Ornithocercus were also monophyletic. This was the largest molecular phylogeny of dinophysoid taxa performed to date and was consistent with the view that the genus Phalacroma may not be synonymous with Dinophysis. [source] UREASE GENE SEQUENCES FROM ALGAE AND HETEROTROPHIC BACTERIA IN AXENIC AND NONAXENIC PHYTOPLANKTON CULTURES,JOURNAL OF PHYCOLOGY, Issue 3 2009Kristopher M. Baker While urea has long been recognized as an important form of nitrogen in planktonic ecosystems, very little is known about how many or which phytoplankton and bacteria can use urea as a nitrogen source. We developed a method, targeting the gene encoding urease, for the direct detection and identification of ureolytic organisms and tested it on seven axenic phytoplankton cultures (three diatoms, two prymnesiophytes, a eustigmatophyte, and a pelagophyte) and on three nonaxenic Aureococcus anophagefferens Hargraves et Sieburth cultures (CCMP1784 and two CCMP1708 cultures from different laboratories). The urease amplicon sequences from axenic phytoplankton cultures were consistent with genomic data in the three species for which both were available. Seven of 12 phytoplankton species have one or more introns in the amplified region of their urease gene(s). The 63 urease amplicons that were cloned and sequenced from nonaxenic A. anophagefferens cultures grouped into 17 distinct sequence types. Eleven types were related to ,-Proteobacteria, including three types likely belonging to the genus Roseovarius. Four types were related to ,-Proteobacteria, including two likely belonging to the genus Marinobacter, and two types were related to ,-Proteobacteria. Terminal restriction fragment length polymorphism (TRFLP) analyses suggested that the sequenced amplicons represented approximately half of the diversity of bacterial urease genes present in the nonaxenic cultures. While many of the bacterial urease sequence types were apparently lab- or culture-specific, others were found in all three nonaxenic cultures, suggesting the possibility of specific relationships between these bacteria and A. anophagefferens. [source] PHYLOGENY OF THE EUGLENALES INFERRED FROM PLASTID LSU rDNA SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 4 2008Jong Im Kim To gain insights into the phylogeny of the Euglenales, we analyzed the plastid LSU rDNA sequences from 101 strains of the photosynthetic euglenoids belonging to nine ingroup genera (Euglena, Trachelomonas, Strombomonas, Monomorphina, Cryptoglena, Colacium, Discoplastis, Phacus, and Lepocinclis) and two outgroup genera (Eutreptia and Eutreptiella). Bayesian and maximum-likelihood (ML) analyses resulted in trees of similar topologies and four major clades: a Phacus and Lepocinclis clade; a Colacium clade; a Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade; and a Euglena clade. The Phacus and Lepocinclis clade was the sister group of all other euglenalian genera, followed by Discoplastis spathirhyncha (Skuja) Triemer and the Colacium clade, respectively, which was inconsistent with their placement based on nuclear rDNA genes. The Trachelomonas, Strombomonas, Monomorphina, and Cryptoglena clade was sister to the Euglena clade. The loricate genera, Trachelomonas and Strombomonas, were closely related to each other, while Monomorphina and Cryptoglena also grouped together. The Euglena clade formed a monophyletic lineage comprising most species from taxa formerly allocated to the subgenera Calliglena and Euglena. However, within this genus, none of the subgenera was monophyletic. [source] OLIGONUCLEOTIDE PRIMERS FOR THE DETECTION OF BIOLUMINESCENT DINOFLAGELLATES REVEAL NOVEL LUCIFERASE SEQUENCES AND INFORMATION ON THE MOLECULAR EVOLUTION OF THIS GENE,JOURNAL OF PHYCOLOGY, Issue 2 2008Andrea Baker Bioluminescence is reported in members of 18 dinoflagellate genera. Species of dinoflagellates are known to have different bioluminescent signatures, making it difficult to assess the presence of particular species in the water column using optical tools, particularly when bioluminescent populations are in nonbloom conditions. A "universal" oligonucleotide primer set, along with species and genus-specific primers specific to the luciferase gene were developed for the detection of bioluminescent dinoflagellates. These primers amplified luciferase sequences from bioluminescent dinoflagellate cultures and from environmental samples containing bioluminescent dinoflagellate populations. Novel luciferase sequences were obtained for strains of Alexandrium cf. catenella (Whedon et Kof.) Balech and Alexandrium fundyense Balech, and also from a strain of Gonyaulax spinifera (Clap. et Whitting) Diesing, which produces bioluminescence undetectable to the naked eye. The phylogeny of partial luciferase sequences revealed five significant clades of the dinoflagellate luciferase gene, suggesting divergence among some species and providing clues on their molecular evolution. We propose that the primers developed in this study will allow further detection of low-light-emitting bioluminescent dinoflagellate species and will have applications as robust indicators of dinoflagellate bioluminescence in natural water samples. [source] TAXONOMIC REEXAMINATION OF 17 SPECIES OF NITELLA SUBGENUS TIEFFALLENIA (CHARALES, CHAROPHYCEAE) BASED ON INTERNAL MORPHOLOGY OF THE OOSPORE WALL AND MULTIPLE DNA MARKER SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 1 2005Hidetoshi Sakayama In an attempt to reconstruct the natural taxonomic system for Nitella, 17 species of Nitella subgenus Tieffallenia were reexamined using SEM observations of the internal morphology of the oospore wall (IMOW) and phylogenetic analyses of 4553 base pairs from multiple DNA markers (atpB, rbcL, psaB, and ITS-5.8S rRNA genes). Our SEM observations identified three types of IMOW: homogeneous (HG), weakly spongy (W-SG), and strongly spongy (S-SG) types. Based on differences in the IMOW, species with reticulate or tuberculate oospore wall ornamentation in the external morphology of the oospore wall (EMOW) were subdivided into two distinct groups (characterized by the HG or S-SG types of IMOW, respectively), which were robustly separated from each other in our molecular phylogenetic analyses. In our molecular phylogeny, the subgenus Tieffallenia consisted of four robust monophyletic groups,three clades of the HG type and a spongy (S-SG and W-SG) type clade,that were characterized by differences in the IMOW and EMOW. In addition, our SEM observations and sequence data verified the distinct status of five species (N. japonica Allen, N. oligospira A. Braun, N. vieillardii stat. nov., N. imperialis stat. nov., and N. morongii Allen) that R. D. Wood had assigned as infraspecific taxa. Moreover, our SEM observations of the IMOW also suggested that N. megaspora (J. Groves) Sakayama originally identified by LM includes at least two distinct species, characterized by W-SG and S-SG types of IMOW, respectively. [source] PHYLOGENY OF THE DASYCLADALES (CHLOROPHYTA, ULVOPHYCEAE) BASED ON ANALYSES OF RUBISCO LARGE SUBUNIT (rbcL) GENE SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 4 2003Frederick W. Zechman The phylogeny of the green algal Order Dasycladales was inferred by maximum parsimony and Bayesian analyses of chloroplast-encoded rbcL sequence data. Bayesian analysis suggested that the tribe Acetabularieae is monophyletic but that some genera within the tribe, such as Acetabularia Lamouroux and Polyphysa Lamouroux, are not. Bayesian analysis placed Halicoryne Harvey as the sister group of the Acetabularieae, a result consistent with limited fossil evidence and monophyly of the family Acetabulariaceae but was not supported by significant posterior probability. Bayesian analysis further suggested that the family Dasycladaceae is a paraphyletic assemblage at the base of the Dasycladales radiation, casting doubt on the current family-level classification. The genus Cymopolia Lamouroux was inferred to be the basal-most dasycladalean genus, which is also consistent with limited fossil evidence. Unweighted parsimony analyses provided similar results but primarily differed by the sister relationship between Halicoryne Lamouroux and Bornetella Munier-Chalmas, thus supporting the monophyly of neither the families Acetabulariaceae nor Dasycladaceae. This result, however, was supported by low bootstrap values. Low transition-to-transversion ratios, potential loss of phylogenetic signal in third codon positions, and the 550 million year old Dasycladalean lineage suggest that dasyclad rbcL sequences may be saturated due to deep time divergences. Such factors may have contributed to inaccurate reconstruction of phylogeny, particularly with respect to potential inconsistency of parsimony analyses. Regardless, strongly negative g1 values were obtained in analyses including all codon positions, indicating the presence of considerable phylogenetic signal in dasyclad rbcL sequence data. Morphological features relevant to the separation of taxa within the Dasycladales and the possible effects of extinction on phylogeny reconstruction are discussed relative to the inferred phylogenies. [source] PHYLOGENETIC SYSTEMATICS OF THE ULVACEAE (ULVALES, ULVOPHYCEAE) USING CHLOROPLAST AND NUCLEAR DNA SEQUENCES,JOURNAL OF PHYCOLOGY, Issue 6 2002Hillary S. Hayden Systematic hypotheses for the Ulvaceae were tested using phylogenetic analysis of sequences for the gene encoding the large subunit of RUBISCO, small subunit rDNA and a combined data matrix. Representatives of eight putative ulvaceous genera and twelve additional taxa from the Ulvophyceae and Trebouxiophyceae were included in analyses using maximum parsimony and maximum likelihood criteria. Molecular data supported hypotheses for the Ulvaceae that are based on the early development of vegetative thalli and motile cell ultrastructure. Ulvaceae sensu Floyd and O'Kelly, including Percursaria Bory de Saint-Vincent, Ulvaria Ruprecht and a complex of closely related species of Chloropelta Tanner, Enteromorpha Link and Ulva L. was supported; however, monophyly of Enteromorpha and Ulva was not supported. The Ulvales and Ulotrichales sensu Floyd and O'Kelly were monophyletic. Blidingia Kylin and Kornmannia Bliding were allied with the former and Capsosiphon Gobi with the latter, although relationships among these and other taxa in these orders remain uncertain. The Ulvales are characterized by an isomorphic life history pattern, gametangia and sporangia that are identical in structure and development, motile cells with bilobed terminal caps and proximal sheaths consisting of two equal subunits. Method of motile cell release and the gross morphology of vegetative thalli are not systematically reliable characters. [source] SPECIES PHYLOGENY OF COSMARIUM AND STAURASTRUM (DESMIDIACEAE) BASED ON RBC L SEQUENCESJOURNAL OF PHYCOLOGY, Issue 2000O.-M. Lee Cosmarium and Staurastrum are the two most diverse genera of placoderm desmids (Family Desmidiaceae), with approximately 1100 and 800 species, respectively. Phylogenetic analysis of relationships of species has been extremely difficult. In a monograph of North American placoderm desmids, Prescott et al. described early phylogenetic work that concluded Staurastrum to be polyphyletic and certainly polymorphic. Likewise, Cosmarium has also been viewed as polyphyletic, and a number of workers have proposed splitting these genera. The classical view of West and West grouped species within each genus into two divisions and 6,8 sections based on wall features and semicell shape. We sequenced rbcL from 18 species of Cosmarium (2 divisions, 7 sections) and 12 species of Staurastrum (2 divisions and 7 sections) and performed a phylogenetic analysis (parsimony, maximum likelihood, bootstrap) using other placoderm desmids and Zygnematales as outgroups. The results exhibit little support for the monophyly of sections or divisions of the two genera. Furthermore, although there is support for the monophyly of clades within each genus, there is also support for a separate clade containing species from both genera. [source] THE PHYLOGENY OF CAULERPA BASED ON RDNA INTERNAL TRANSCRIBED SPACER SEQUENCESJOURNAL OF PHYCOLOGY, Issue 2000S. Nemeth Phylogenetic hypotheses for the pantropical marine green algal genus, Caulerpa, were inferred based on analyses of nuclear-encoded rDNA internal transcribed spacer (ITS) sequences. Results of these analyses were used to assess the correspondence between rDNA phylogeny and traditional sectional taxonomy, to identify synapomorphic morphological characters (including assimilator morphology and chloroplast ultrastructure), and to examine marine biogeographic hypotheses for the genus. Ribosomal DNA ITS sequences were aligned for thirty-three species and intraspecific taxa of Caulerpa. Results indicate limited correspondence between phylogeny and sectional taxonomy for the genus, (e.g., the sections Filicoideae and Sedoideae were not monophyletic). In contrast, chloroplast morphology could be mapped to the tree topology with limited homoplasy. Pantropical isolates of the filicoidean species, Caulerpa sertularioides and Caulerpa mexicana each formed monophyletic groups. Caulerpa reyesii was included as a derived taxon within the Caulerpa taxifolia clade, suggesting that these species were conspecific and affirmed the lack of correspondence between phylogeny and assimilator morphology. Isolates and various intraspecific taxa of Caulerpa racemosa did not form a monophyletic group. Instead, these taxa formed a heterogeneous assemblage with other sedoidean and filicoidean taxa. Within the C. sertularioides clade, Caribbean and Atlantic isolates formed a basal paraphyletic group, whereas eastern and western Pacific isolates formed a more derived monophyletic group. Therefore, these results are not consistent with an Indo-West Pacific origin of this species. [source] A CANDID ASSESSMENT OF SYSTEMATICS IN THE LAMINARIALES: MUDDLED MORPHOLOGIES AND SKETCHY SEQUENCESJOURNAL OF PHYCOLOGY, Issue 2000G.W. Saunders Algae of the Alariaceae, Laminariaceae and Lessoniaceae are the largest, most complex, and, arguably, most fascinating of the seaweeds. It is, therefore, a profound paradox that these species remain in taxonomic chaos despite the contemporary emphases on systematics. Setchell and Gardner established the classification system in 1925, recognizing these families on the basis of clear morphological features. At that time, however, they acknowledged that some species had features consistent with placement in two families, or that obscured logical placement in any of the families. Ironically, the problems noted by Setchell and Gardner have been ignored and the system has become entrenched in kelp literature. Initial molecular studies highlighted the shortcomings noted by Setchell and Gardner, and further indicated that little of the morphology-based system was natural. It was obvious that the diagnostic morphological features, presence or absence of sporophylls and ontogenetic splitting, were ,noisy' being gained and lost independently many times in kelp evolution. Despite the insights of the initial molecular studies, they had limitations and key relationships remained unresolved. The investigations used the Internal Transcribed Spacers (ITS) of the ribosomal cistron that have phylogenetic limitations owing to their short length, which is exacerbated by the many variable regions that can't be aligned confidently and must be removed prior to phylogenetic analyses. Many molecular publications have appeared subsequent to the first ITS results, and their contribution towards elucidating kelp phylogeny will be assessed. Current investigations using the Large Subunit ribosomal DNA (LSU) for kelp systematics will also be discussed. [source] POPULATION GENETIC STRUCTURE OF FINLESS PORPOISES, NEOPHOCAENA PHOCAENOIDES, IN CHINESE WATERS, INFERRED FROM MITOCHONDRIAL CONTROL REGION SEQUENCESMARINE MAMMAL SCIENCE, Issue 2 2002Guang Yang Abstract Seven hundred and twenty base pairs (bp) of the mitochondrial control region from 73 finless porpoises, Neophocaena phocaenoides, in Chinese waters were sequenced. Thirteen variable sites were determined and 17 haplotypes were defined. Of these, 5 and 7 were found only in the Yellow Sea population and the South China Sea population, respectively, whereas no specific haplo-type was found in the Yangtze River population. Phylogenetic analyses using NJ and ML algorithm did not divide the haplotypes into monophyletic clades representing recognized geographic populations of finless porpoises in Chinese waters, suggesting the existence of migration and gene flow among populations. Analysis of molecular variance showed the obvious population genetic structure (,st= 0.41, P < 0.05); however, the structure was mainly between either the Yangtze River population or the Yellow Sea population and the South China Sea population. The genetic diversity (nucleotide diversity and haplotypic diversity) of the Yellow Sea population was significantly higher than those of the Yangtze River population and the South China Sea population, suggesting the relatively later divergence of the latter two populations and supporting the Yellow Sea population as the original center of Neophocaena. [source] MOLECULAR SYSTEMATICS OF RIVER DOLPHINS INFERRED FROM COMPLETE MITOCHONDRIAL CYTOCHROME- B GENE SEQUENCESMARINE MAMMAL SCIENCE, Issue 1 2002Guang Yang Abstract 1,140 bp of the complete mitochondrial cytochrome- b gene sequences of baiji (Lipotes vexillifer), franciscana (Pontoporia blainvillei), and Ganges river dolphin (Platanista gangetica gangetica) were determined to address the systematic position and phylogeny of extant river dolphins with combination of homologous sequences of other cetaceans. The neighbor-joining (NJ), maximum parsimony (MP), and maximum likelihood (ML) phylogenetic analyses all identified the river dolphins into three lineages, i. e., Platanista, Lipotes, and Inia+Pontoporia. The Lipotes did not have sister relationship with either Platanista or Inia+Pontoporia, which strongly supported the referral of Lipotes to a separate family, i. e., Lipotidae. There were very high sequence divergences between all river dolphin genera, suggesting a relatively longer period of separation time than those among other odontocete families. [source] MINIMAL VALID AUTOMATA OF SAMPLE SEQUENCES FOR DISCRETE EVENT SYSTEMSASIAN JOURNAL OF CONTROL, Issue 2 2004Sheng-Luen Chung ABSTRACT Minimal valid automata (MVA) refer to valid automata models that fit a given input-output sequence sample from a Mealy machine model. They are minimal in the sense that the number of states in these automata is minimal. Critical to system identification problems of discrete event systems, MVA can be considered as a special case of the minimization problem for incompletely specified sequential machine (ISSM). While the minimization of ISSM in general is an NP-complete problem, various approaches have been proposed to alleviate computational requirement by taking special structural properties of the ISSM at hand. In essence, MVA is to find the minimal realization of an ISSM where each state only has one subsequent state transition defined. This paper presents an algorithm that divides the minimization process into two phases: first to give a reduced machine for the equivalent sequential machine, and then to minimize the reduced machine into minimal realization solutions. An example with comprehensive coverage on how the associated minimal valid automata are derived is also included. [source] ON THE STRONG LAW OF LARGE NUMBERS UNDER REARRANGEMENTS FOR SEQUENCES OF BLOCKWISE ORTHOGONAL RANDOM ELEMENTS IN BANACH SPACESAUSTRALIAN & NEW ZEALAND JOURNAL OF STATISTICS, Issue 4 2007Nguyen Van Quang Summary The condition of the strong law of large numbers is obtained for sequences of random elements in type p Banach spaces that are blockwise orthogonal. The current work extends a result of Chobanyan & Mandrekar (2000)[On Kolmogorov SLLN under rearrangements for orthogonal random variables in a B -space. J. Theoret. Probab. 13, 135,139.] Special cases of the main results are presented as corollaries, and illustrative examples are provided. [source] Sequence learning in infancy: the independent contributions of conditional probability and pair frequency informationDEVELOPMENTAL SCIENCE, Issue 6 2009Stuart Marcovitch The ability to perceive sequences is fundamental to cognition. Previous studies have shown that infants can learn visual sequences as early as 2 months of age and it has been suggested that this ability is mediated by sensitivity to conditional probability information. Typically, conditional probability information has covaried with frequency information in these studies, raising the possibility that each type of information may have contributed independently to sequence learning. The current study explicitly investigated the independent contribution of each type of information. We habituated 2.5-, 4.5-, and 8.5-month-old infants to a sequence of looming visual shapes whose ordering was defined independently by specific conditional probability relations among pair elements and by the frequency of occurrence of such pairs. During test trials, we tested infants' sensitivity to each type of information and found that both types of information independently influenced sequence learning by 4.5 months of age. [source] Regiospecific Three-Component Access to Fluorescent 2,4-Disubstituted Quinolines via One-Pot Coupling-Addition-Cyclocondensation-Sulfur Extrusion Sequence,EUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 18 2010Sven Rotzoll Abstract 2,4-Di- and 2,4,7-trisubstituted quinolines are readily synthesized in a regioselective fashion from acyl chlorides, terminal alkynes, and 2-aminothiophenols by a consecutive, microwave-assisted one-pot three-component Sonogashira coupling-Michael addition,cyclocondensation sequence and following sulfur extrusion in moderate to good yields. The terminal sulfur extrusion step was studied by DFT computations. The absorption spectra of 2,4-disubstituted quinolines can be rationalized by DFT-ZINDO-CI calculations and all derivatives show intense blue emission upon UV excitation. [source] Stereodefined Access to 3-Deoxy Sugars Through a Tandem Baylis,Hillman and Lewis Acid Catalyzed Reaction SequenceEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 5 2010Palakodety Radha Krishna Abstract An innovative synthetic protocol is reported for the ready access to 3-deoxy sugars in both D and L forms as exclusive products (des >95,%) in high yields through a stereodefined Lewis acid catalyzed reaction sequence of the sugar-derived Baylis,Hillman adducts. [source] One-Pot Synthesis of Fluorinated 1-Benzoyl-3,4-dihydroisoquinolines from [2-(o -Alkynylphenyl)ethyl]amines by a Hydroamination/Oxidation SequenceEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 1 2010René Severin Abstract Fluorinated 1-benzoyl-3,4-dihydroisoquinolines can easily be synthesized by a new one-pot procedure from corresponding fluorinated [2-(o -alkynylphenyl)ethyl]amines in high yields. The one-pot process consists of an initial [Ind2TiMe2]-catalyzed intramolecular alkyne hydroamination and a subsequent Pd-catalyzed oxidation of the benzyl side chain of the resulting hydroamination product. The process tolerates electron-donating and -withdrawing substituents on the benzene ring that is converted into the benzoyl side chain of the products as well as ortho -substitution. [source] [4+2]/HyBRedOx Approach to C -Naphthyl Glycosides: Failure in the Projuglone Series and Reinvestigation of the HyBRedOx SequenceEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 3 2009Lucie Maingot Abstract C -Naphthyl glycosides displaying a 1,5-difunctionality on the naphthalene ring that can undergo oxidation to bromonaphthoquinone are key intermediates in the synthesis of natural C -aryl glycoside analogues. In this area, sugar-modified derivatives are of specific interest, but their synthesis is challenging. The de novo access to such compounds has been investigated through a [4+2] heterocycloaddition route, previously validated in a model series. For this purpose, two new dienophiles, conveniently protected at the phenolic positions, were synthesized. From an extensive study of their reactivity towards a range of 4-hetero-substituted ("prosugar") heterodienes, the expected heteroadducts were stereoselectively obtained in acceptable yields. Application of the hydroboration/reduction/oxidation sequence did not afford the target C -glycosides from the reduced adducts. The negative effect of the conformational bias of the substrate on this tandem reaction is discussed.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] A New, Expeditious Entry to the Benzophenanthrofuran Framework by a Pd-Catalyzed C - and O -Arylation/PIFA-Mediated Oxidative Coupling SequenceEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 12 2005Fátima Churruca Abstract The synthesis of a series of 2,3-diarylbenzo[b]furans starting from 1,2-diarylethanones and 1,2-dibromoarenes proceeds by means of both homogeneous and polymer-anchored palladium catalysts. This tandem process can be effectively halted at the C -arylation step, thus providing key o -bromoarylated deoxybenzoin intermediates in good yields. The efficient oxidative coupling leading to benzo[b]phenanthro[9,10- d]furans is carried out using the safer hypervalent iodine reagent PIFA. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Emergence of a subfamily of xylanase inhibitors within glycoside hydrolase family 18FEBS JOURNAL, Issue 7 2005Anne Durand The xylanase inhibitor protein I (XIP-I), recently identified in wheat, inhibits xylanases belonging to glycoside hydrolase families 10 (GH10) and 11 (GH11). Sequence and structural similarities indicate that XIP-I is related to chitinases of family GH18, despite its lack of enzymatic activity. Here we report the identification and biochemical characterization of a XIP-type inhibitor from rice. Despite its initial classification as a chitinase, the rice inhibitor does not exhibit chitinolytic activity but shows specificities towards fungal GH11 xylanases similar to that of its wheat counterpart. This, together, with an analysis of approximately 150 plant members of glycosidase family GH18 provides compelling evidence that xylanase inhibitors are largely represented in this family, and that this novel function has recently emerged based on a common scaffold. The plurifunctionality of GH18 members has major implications for genomic annotations and predicted gene function. This study provides new information which will lead to a better understanding of the biological significance of a number of GH18 ,inactivated' chitinases. [source] Acylation of lysophosphatidylcholine plays a key role in the response of monocytes to lipopolysaccharideFEBS JOURNAL, Issue 13 2003Bernhard Schmid Mononuclear phagocytes play a pivotal role in the progression of septic shock by producing tumor necrosis factor-, (TNF-,) and other inflammatory mediators in response to lipopolysaccharide (LPS) from Gram-negative bacteria. Our previous studies have shown monocyte and macrophage activation correlate with changes in membrane phospholipid composition, mediated by acyltransferases. Interferon-, (IFN-,), which activates and primes these cells for enhanced inflammatory responses to LPS, was found to selectively activate lysophosphatidylcholine acyltransferase (LPCAT) (P < 0.05) but not lysophosphatidic acid acyltransferase (LPAAT) activity. When used to prime the human monocytic cell line MonoMac 6, the production of TNF-, and interleukin-6 (IL-6) was approximately five times greater in cells primed with IFN-, than unprimed cells. Two LPCAT inhibitors SK&F 98625 (diethyl 7-(3,4,5-triphenyl-2-oxo2,3-dihydro-imidazole-1-yl)heptane phosphonate) and YM 50201 (3-hydroxyethyl 5,3,-thiophenyl pyridine) strongly inhibited (up to 90%) TNF-, and IL-6 production in response to LPS in both unprimed MonoMac-6 cells and in cells primed with IFN-,. In similar experiments, these inhibitors also substantially decreased the response of both primed and unprimed peripheral blood mononuclear cells to LPS. Sequence-based amplification methods showed that SK&F 98625 inhibited TNF-, production by decreasing TNF-, mRNA levels in MonoMac-6 cells. Taken together, the data from these studies suggest that LPCAT is a key enzyme in both the pathways of activation (priming) and the inflammatory response to LPS in monocytes. [source] Early Carboniferous (Mississippian) calciturbidites in the northern Rhenish Mountains (Germany)GEOLOGICAL JOURNAL, Issue 2-3 2008D. Korn Abstract Viséan calciturbidites occur in two separate turbidite sequences at the northern margin of the Rhenish Mountains: (1) the Herdringen Sequence (Becke-Oese, Retringen and Herdringen formations), and (2) the Hellefeld Sequence (Hellefeld, Linnepe and Wennemen formations). Both sequences show temporal fluctuations in the carbonate content, which can be related to global eustatic fluctuations. Two peaks of carbonate sedimentation which occurred during lowstands in the Holkerian to early Asbian and in the Brigantian are interrupted by a late Asbian decline of carbonate deposition during a transgressive interval. Patterns of bed thickness and carbonate content in the Herdringen Sequence indicate a sediment source to the north; it shifted during the Late Viséan from the northeast to the northwest. Coeval sediments in the Hellefeld Sequence were derived from a source to the southeast. Detailed analyses of Asbian sections show the high potential for fine-scaled correlation. Copyright © 2007 John Wiley & Sons, Ltd. [source] A Novel Coupling 1,3-Dipolar Cycloaddition Sequence as a Three-Component Approach to Highly Fluorescent IndolizinesHELVETICA CHIMICA ACTA, Issue 7 2005Alexandru Indolizines 4 and biindolizines 6 can be synthesized in moderate yields in a consecutive one-pot three-component process by a coupling/1,3-dipolar cycloaddition sequence of a (hetero)arenecarbonyl chloride 1, a terminal alkyne 2, and a suitable 1-(2-oxoethyl) pyridinium bromide 3 or 5, respectively (Schemes,1 and 2). After the Sonogashira coupling, a [2+3] cycloaddition of the in situ formed pyridinium ylide, an allyl-type 1,3-dipole, furnishes a cycloadduct that is instantaneously oxidatively aromatized to give the highly fluorescent indolizine derivatives that were unambiguously characterized by an X-ray-structure analysis of compound 4d (Fig.,1). Additionally, fluorescence studies with pyridinyl-substituted representatives reveal not only that indolizines and biindolizines are highly interesting fluorescence dyes but that their fluorescence color can also be reversibly switched upon altering the pH of the medium. [source] | |||||||||||||||||||||||||||||||||||||||||||||||||