danio rerio phylogenetic: Topics by WorldWideScience.org

cDNA cloning and sequence analysis of preproendothelin-1 (PPET-1) from salmon, Oncorhynchus keta.

Polycystic kidney disease (PKD) is one of the leading causes of end-stage renal disease in humans and is characterized by progressive cyst formation, renal enlargement, and abnormal tubular development....Full Text Available

2010-04-01

Cryopreservation of isolated blastomeres and embryonic stem-like cells of Leopard danio, Brachydanio frankei

The presence of endothelin (ET)-like immunoreactivity and the cardiovascular effects of mammalian ET-1 in fish have been reported. To identify ET-related peptides in fish, we screened the cDNA library of the salmon (Oncorhynchus keta) stomach by means of rapid amplification of cDNA ends, and we cloned cDNAs encoding an ET-related peptide. The salmon ET-related sequence of 21 amino acids is identical to the trout ET-1 peptide recently purified from kidney specimens of Oncorhynchus mykiss. The deduced amino acid sequence of salmon pre-proET-1 (PPET-1) comprises 244 amino acids, including a putative signal sequence and mature ET-1, as well as big ET-1 and ET-1-like sequences. This precursor, the first reported PPET-1 sequence for Salmoniformes, Teleostei, has low homology with the sequences of human, mouse, frog (Xenopus laevis), and zebrafish (Danio rerio) PPET-1 (26%, 29%, 24%, and 39%, respectively). PMID:16740985

2006-06-01

British Library Electronic Table of Contents (United Kingdom)

Abstract This study aimed at developing a suitable cryopreservation protocol for embryonic stem (ES)-like cells of a tiny freshwater fish Leopard danio (Brachydanio frankei). Embryonic stem (ES)-like cells derived from blastomeres of the early blastulae stage of the developing embryo were cultured in vitro in a medium containing Leibowitz-15 supplemented with 10% foetal bovine serum, leopard danio embryo extract, sodium bicarbonate, sodium selenite, basic fibroblast growth factor, epidermal growth factor and leukaemia inhibitory factor. The ES-like cells showed properties similar to ES cells in other species. They were morphologically small, round to polygonal and present in patches and extensively expressed alkaline phosphatase and stage-specific embryonic antigen. The toxicity and chilli...

2010-01-01

Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer

Phylogenetic Network for European mtDNA

BackgroundThe phylogenetic relationships among the holoparasites of Rafflesiales have remained enigmatic for over a century. Recent molecular phylogenetic studies using the mitochondrial...Full Text Available

Molecular phylogenetics and molecular dating of the New Zealand Gleicheniaceae

The sequence in the first hypervariable segment (HVS-I) of the control region has been used as a source of evolutionary information in most phylogenetic analyses of mtDNA. Population genetic inference...Full Text Available

2001-06-01

Unearthing the Phylogenetic Roots of Sleep

... Symonds, G. J. Wilson, and H. Zhu. 1997. Seismic stratigraphy and structural history of the Reinga Basin and ... ...

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

Why we sleep remains one of the enduring unanswered questions in biology. At its core, sleep can be defined behaviorally as a homeostatically regulated state of reduced movement and sensory...Full Text Available

2008-08-05

Phylogenetic relationships in Cortinarius, section Calochroi, inferred from nuclear DNA sequences

BackgroundOrthology analysis is an important part of data analysis in many areas of bioinformatics such as comparative genomics and molecular phylogenetics. The ever-increasing flood...Full Text Available

Phylogenetic Relationships in Pterodroma Petrels Are Obscured by Recent Secondary Contact and Hybridization

BackgroundSection Calochroi is one of the most species-rich lineages in the genus Cortinarius (Agaricales, Basidiomycota) and is widely distributed...Full Text Available

Phylogenetic Characterization of Virulence and Resistance Phenotypes of Pseudomonas syringae

The classification of petrels (Pterodroma spp.) from Round Island, near Mauritius in the Indian Ocean, has confounded researchers since their...Full Text Available

Evaluating Phylogenetic Congruence in the Post-Genomic Era

Individual strains of the plant pathogenic bacterium Pseudomonas syringae vary in their ability to produce toxins, nucleate ice, and resist antimicrobial compounds. These phenotypes...Full Text Available

2005-09-01

Empirical tests of life-history evolution theory using phylogenetic analysis of plant demography

Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for...Full Text Available

2011-01-01

British Library Electronic Table of Contents (United Kingdom)

Summary 1. A primary goal of evolutionary ecology is to understand factors selecting for the diversity of life histories. Life-history components, such as time-to-reproduction, adult survivorship and fecundity, might differ among species because of variation in direct and indirect benefits of these life histories in different environments or might have lower-than-expected variability because of phylogenetic constraints. Here, we present a phylogenetic examination of demography and life histories using a data base of 204 terrestrial plant species. 2. Overall, statistical models without phylogeny were preferred to models with phylogeny for vital rates and elasticities, suggesting that they lacked phylogenetic signal and are evolutionarily labile. However, the effect of phylogeny was signific...

2010-01-01

Comparative and phylogenomic studies on the mitochondrial genomes of Pentatomomorpha (Insecta: Hemiptera: Heteroptera)

A PRELIMINARY PHYLOGENETIC ANALYSIS OF METAPENAEOPSIS (DECAPODA: PENAEIDAE) BASED ON MITOCHONDRIAL DNA SEQUENCES OF ...

BackgroundNucleotide sequences and the gene arrangements of mitochondrial genomes are effective tools for resolving phylogenetic problems. Hemipteroid insects are known to possess...Full Text Available

Molecular phylogenetic analysis of tropical freshwater mussels (Mollusca: Bivalvia: Unionoida) resolves the position of Coelatura and supports a monophyletic Unionidae.

... each species studied are listed in Table 1. Penaeus monodon Fabricius, 1798 (family Penaeidae) and Solenocera koelbeli De Man, ... ...

Molecular phylogenetic relationships and phenotypic diversity in miniaturized toadlets, genus Brachycephalus (Amphibia: Anura: Brachycephalidae)

In previous molecular phylogenetic analyses of the freshwater mussel family Unionidae (Bivalvia: Unionoida), the Afrotropical genus Coelatura had been recovered in various positions, generally indicating a paraphyletic Unionidae. However that result was typically poorly supported and in conflict with morphology-based analyses. We set out to test the phylogenetic position of Coelatura by sampling tropical lineages omitted from previous studies. Forty-one partial 28S nuclear rDNA and partial COI mtDNA sequences (1130 total aligned nucleotides) were analyzed separately and in combination under both maximum parsimony and likelihood, as well as Bayesian inference. There was significant phylogenetic incongruence between the character sets (partition homogeneity test, p<0.01), but a novel heuristic for comparing bootstrap values among character sets analyzed separately and in combination illustrated that the observed conflict ...

2011-07-30

British Library Electronic Table of Contents (United Kingdom)

Toadlets of the genus Brachycephalus are endemic to the Atlantic rainforests of southeastern and southern Brazil. The 14 species currently described have snout-vent lengths less than 18mm and are thought to have evolved through miniaturization: an evolutionary process leading to an extremely small adult body size. Here, we present the first comprehensive phylogenetic analysis for Brachycephalus, using a multilocus approach based on two nuclear (Rag-1 and Tyr) and three mitochondrial (Cyt b, 12S, and 16S rRNA) gene regions. Phylogenetic relationships were inferred using a partitioned Bayesian analysis of concatenated sequences and the hierarchical Bayesian method (BEST) that estimates species trees based on the multispecies coalescent model. Individual gene trees showed conflict and also va...

2011-01-01

Virulence Factors of Escherichia coli Isolates That Produce CTX-M-Type Extended-Spectrum ?-Lactamases

The complete mitochondrial genome of the stomatopod crustacean Squilla mantis

This study determined the phylogenetic groups and virulence factors of 37 Escherichia coli isolates producing types of CTX-M compared with those of 19 isolates producing different types...Full Text Available

2005-11-01

Tandem repeats analysis for the high resolution phylogenetic analysis of Yersinia pestis

BackgroundAnimal mitochondrial genomes are physically separate from the much larger nuclear genomes and have proven useful both for phylogenetic studies and for understanding genome...Full Text Available

1 2 3 4

Sexual Dimorphism in Primate Aerobic Capacity: A Phylogenetic Test

BackgroundYersinia pestis, the agent of plague, is a young and highly monomorphic species. Three biovars, each one thought to be associated with the last three Y....Full Text Available

Scintillation proximity assay for measurement of RNA methylation

Male intrasexual competition should favour increased male physical prowess. This should in turn result in greater aerobic capacity in males than in females (i.e., sexual dimorphism), and a correlation...Full Text Available

2010-06-01

Phylogenetic and Evolutionary Relationships among Yellow Fever Virus Isolates in Africa

Methylation of RNA by methyltransferases is a phylogenetically ubiquitous post-transcriptional modification that occurs most extensively in transfer RNA (tRNA) and ribosomal RNA (rRNA). Biochemical...Full Text Available

2009-03-01

Genetic evidence of illegal trade in protected whales links Japan with the US and South Korea

Previous studies with a limited number of strains have indicated that there are two genotypes of yellow fever (YF) virus in Africa, one in west Africa and the other in east and central Africa. We have...Full Text Available

2001-08-01

Evolution of feeding specialization in Tanganyikan scale-eating cichlids: a molecular phylogenetic approach

We report on genetic identification of ‘whale meat’ purchased in sushi restaurants in Los Angeles, CA (USA) in October 2009 and in Seoul, South Korea in June and September 2009. Phylogenetic...Full Text Available

2010-10-23

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae

BackgroundCichlid fishes in Lake Tanganyika exhibit remarkable diversity in their feeding habits. Among them, seven species in the genus Perissodus are known for...Full Text Available

Analysis of European mtDNAs for Recombination

BackgroundOncidium spp. produce commercially important orchid cut flowers. However, they are amenable to intergeneric and inter-specific crossing making phylogenetic...Full Text Available

Comparison of acute toxicity of process chemicals used in the oil refinery industry, tested with the diatom Chaetoceros gracilis, the flagellate Isochrysis galbana, and the zebra fish, Brachydanio rerio

The standard paradigm postulates that the human mitochondrial genome (mtDNA) is strictly maternally inherited and that, consequently, mtDNA lineages are clonal. As a result of mtDNA clonality, phylogenetic...Full Text Available

2001-01-01

Network structure and phylogenetic signal in an artificially assembled plant-pollinator community

Chemicals under the trade names Nalco 537-DA, Nalco 625, Nalco 7607, Nalco 5165, Ivamin, and technical monoethanolamine are used extensively in the oil refinery industry. Aquatic toxicity tests were conducted using zebra fish fry (Brachydanio rerio) and the unicellular algae Isochrysis galbana (a flagellate) and Chaetoceros gracilis (a diatom). Inhibition of cell division, chlorophyll content, and "1"4CO_2 uptake in the algae were sensitive end points. The effective concentrations (EC50s) of growth inhibition were 0.1 mg/L (Ivamin; I. galbana), 0.8 mg/L (Nalco 7607; I. galbana), 6 mg/L (Nalco 625; I. galbana), 10 mg/L (Nalco 5165; C. gracilis), and 15 mg/L (Nalco 537-DA; C. gracilis). The lethal concentrations (LC50s) (96 h) toward zebra fish fry was 1 mg/L for Nalco 7607, 6.5 mg/L for Nalco 537-DA, 7.1 mg/L for Nalco 625, and 20 mg/L for Ivamin 803. Monoethanolamine had an LC50 higher than 5,000 mg/L. Nalco 5165 was not tested on fish fry. The heartbeat frequency ...

CERN Document Server

Community ecologists are principally occupied with the proposition that natural assemblages of species exhibit orderliness and with identifying its causes. Plant-pollinator networks exhibit a variety of orderly properties, one of which is 'nestedness'. Nestedness has been attributed to various causes, but we propose a further influence arising from the phylogenetic structure of the biochemical constraints on the pollen diets of bees. We use an artificial assemblage as an opportunity to isolate the action of this mechanism. The properties of the network that we studied are consistent with the proposition that nestedness is caused by the phylogeny of diet range in bees, but the claim is preliminary and we propose that valuable progress in understanding plant-pollinator systems may be made through applying the techniques of chemical ecology at the community scale.

2011-01-01

The complete mitochondrial genome of Atelura formicaria (Hexapoda: Zygentoma) and the phylogenetic relationships of basal insects.

Complete genome sequence of Actinosynnema mirum type strain (101T)

In this study, the complete sequence of the mitochondrial DNA (mtDNA) of Atelura formicaria (Hexapoda: Zygentoma) is described. The molecule is 15.205 bp in length and it is the third complete mt genome sequenced from the Zygentoma. The genome organization conforms with the putative ancestral insect gene arrangement. All protein coding genes use standard initiation codons (methionine and isoleucine). The exception is nad4 that starts with GTG, a codon used for this purpose in other insect species. A peculiar strand skew bias is observed, given that the PCGs encoded on the J-strand contain more thymines than adenines and more cytosines than guanines. This trend in nucleotide composition has been observed also in the "firebrat" Thermobia domestica (Zygentoma, Lepismatidae), but differs from that of the majority of hexapod species, including Tricholepidion gertschi (Zygentoma, Lepidotrichidae), where adenines and cytosines outnumber thymines and guanines. The presence of structural ...

2009-03-11

Ultrastructure of the spermatozoon of the digenean Cricocephalus albus (Kuhl & van Hasselt, 1822) Looss, 1899 (Platyhelminthes, Pronocephaloidea, Pronocephalidae), parasite of ''the hawksbill sea turtle''Eretmochelys imbricata (Linnaeus, 1766) in Senegal

Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 ...

2009-05-20

British Library Electronic Table of Contents (United Kingdom)

The mature spermatozoon of Cricocephalus albus is filiform, tapered at both ends and shows the following features: 2 axonemes of different lengths presenting the 9+''1'' trepaxonematan pattern, 2 bundles of parallel cortical microtubules, a mitochondrion and a nucleus. Nevertheless, the particularity of the spermatozoon of C. albus is its anterior extremity with an apical electron-dense material associated with extramembranar ornamentation, a cytoplasmic dorsolateral expansion and spine-like bodies. To our knowledge, such an anterior extremity of the spermatozoon has not previously been described from a species of the superfamily Pronocephaloidea. Our study provides new data on the mature gamete of C. albus in order to improve our understanding of the pronocephaloidean phylogenetic relatio...

2011-01-01

The morphology and systematics of Mammalodon colliveri (Cetacea: Mysticeti), a toothed mysticete from the Oligocene of Australia

British Library Electronic Table of Contents (United Kingdom)

Mammalodon colliveri is an unusual toothed archaic mysticete (Cetacea) from the Upper Oligocene Jan Juc Formation of south-east Australia. The morphology of the holotype skull and postcrania are described in detail. Superimposed on the generally plesiomorphic archaeocete-like morphology of Mammalodon are subtle mysticete synapomorphies. Derived features of Mammalodon include a short and bluntly rounded rostrum, reduced premaxillae, and anterodorsally directed orbits. Within Mysticeti, this suite of features is unique. The aberrant rostral morphology of Mammalodon suggests specialization for suction feeding. Janjucetus hunderi is placed in an expanded family Mammalodontidae. Phylogenetic analysis corroborates the monophyly of Basilosauridae, Neoceti, Odontoceti, and Mysticeti, and yields a ...

2010-01-01

The Morphology, Ontogeny, and Small Subunit rRNA Gene Sequence Analysis of Diophrys parappendiculata n. sp. (Protozoa, Ciliophora, Euplotida), a New Marine Ciliate from Coastal Waters of Southern China

British Library Electronic Table of Contents (United Kingdom)

ABSTRACT. The morphology, morphogenesis, and phylogeny of Diophrys parappendiculata n. sp., a large marine ciliate isolated from the coastal waters of Daya Bay, southern China, were investigated. This new species is characterized by a combination of its large size, appendiculata-pattern of ciliature, and bipartite adoral zone of membranelles. The main stages of morphogenesis during binary fission were also recorded and described. Comparisons of morphological characteristics with similar congeners support the validity of the new species. The small subunit rRNA gene sequence of D. parappendiculata is 96.3-99.94% similar to those of four other congeners; it differs in four nucleotides from that of Diophrys appendiculata (i.e. structural similarity was 99.94%). Phylogenetic analysis indicates ...

2011-01-01

Phylogeography of rabies virus isolated from dogs in Brazil between 1985 and 2006

British Library Electronic Table of Contents (United Kingdom)

To establish the phylogeographic relationships in rabies viruses in Brazil, we studied a dataset retrieved from GenBank consisting of 71 genetic sequences from the coding region of the N gene of rabies viruses isolated in dogs over a period of 22?years. The Bayesian Markov chain Monte Carlo method available in the BEAST package was used with the GTR+G+?4 evolutionary model in conjunction with the relaxed uncorrelated lognormal molecular clock model and an exponential growth tree prior. A discrete phylogeographic diffusion model was also analyzed using a standard continuous-time Markov chain viewed with Google Earth to provide a spatial projection of the diffusion of genetic lineages based on their phylogeographic relationships. The topology of the time and substitution phylogenetic trees a...

2011-01-01

Phylogenetic constraints on digesta separation: Variation in fluid throughput in the digestive tract in mammalian herbivores

British Library Electronic Table of Contents (United Kingdom)

The relevance of the mean retention time (MRT) of particles through the gastrointestinal tract (GIT) is well understood and MRTparticleGIT is an important parameter in digestion models. Solute markers have been used to estimate MRTsoluteGIT (or 'fluid passage') in animals, but the relevance of this measure is less evident and is usually sought in its relation to MRTparticleGIT. The ratio between the two measures indicates the degree of 'digesta washing', with little washing occurring at ratios of 1, aborad washing at ratios >1 (where the solute marker travels faster than the particle marker), and orad (retrograde) washing at ratios <1 (where the solute marker travels slower than the particle marker). We analysed digesta washing in a dataset of 98 mammalian species including man of differen...

2011-01-01

Oxidation of Elemental Sulfur by Fusarium solani Strain THIF01 Harboring Endobacterium Bradyrhizobium sp.

British Library Electronic Table of Contents (United Kingdom)

Nineteen fungal strains having an ability to oxidize elemental sulfur in mineral salts medium were isolated from deteriorated sandstones of Angkor monuments. These fungi formed clearing zone on agar medium supplemented with powder sulfur due to the dissolution of sulfur. Representative of the isolates, strain THIF01, was identified as Fusarium solani on the basis of morphological characteristics and phylogenetic analyses. PCR amplification targeting 16S rRNA gene and analyses of full 16S rRNA gene sequence indicated strain THIF01 harbors an endobacterium Bradyrhizobium sp.; however, involvement of the bacterium in the sulfur oxidation is still unclear. Strain THIF01 oxidized elemental sulfur to thiosulfate and then sulfate. Germination of the spores of strain THIF01 was observed in a liqui...

2010-01-01

Immunofluorescence analysis of the internal brain anatomy of Nereis diversicolor (Polychaeta, Annelida)

British Library Electronic Table of Contents (United Kingdom)

Comparative analyses of neuroanatomical characters can make valuable contributions to the inference of phylogenetic relationships. Whereas investigations in this field are numerous for arthropods, in-depth studies on other protostomes are sparse. Here, we provide a survey of the internal neuroarchitecture of the brain of the aciculate ragworm Nereis diversicolor (Polychaeta, Annelida). Descriptions are based on confocal laser scanning microscope analyses of brain sections labeled with the nuclear marker DAPI and antibodies raised against FMRF-amide, serotonin, and histamine. Autofluorescence of the nervous tissue has been utilized to further elucidate the anatomical structures of the brain. The architecture of two major brain compartments, i.e., the paired mushroom bodies and the central o...

2008-01-01

Identification and characterization of retinoid-active short-chain dehydrogenases/reductases in Drosophila melanogaster

British Library Electronic Table of Contents (United Kingdom)

Background In chordates, retinoid metabolism is an important target of short-chain dehydrogenases/reductases (SDRs). It is not known whether SDRs play a role in retinoid metabolism of protostomes, such as Drosophila melanogaster. Methods Drosophila genome was searched for genes encoding proteins with ?50% identity to human retinol dehydrogenase 12 (RDH12). The corresponding proteins were expressed in Sf9 cells and biochemically characterized. Their phylogenetic relationships were analyzed using PHYLIP software. Results A total of six Drosophila SDR genes were identified. Five of these genes are clustered on chromosome 2 and one is located on chromosome X. The deduced proteins are 300 to 406 amino acids long and are associated with microsomal membranes. They recognize all-trans-retinaldehyd...

2009-01-01

1 2 3 4

Functional adaptation of microbial communities from jet fuel-contaminated soil under bioremediation treatment: simulation of pollutant rebound

British Library Electronic Table of Contents (United Kingdom)

Abstract To investigate the link between the functionality and the diversity of microbial communities under strong selective pressure from pollutants, two types of mesocosms that simulate natural attenuation and phytoremediation were generated using soil from a site highly contaminated with jet fuel and under air-sparging treatment. An increase in the petroleum hydrocarbon concentration from 4900 to 18-500-mg-kg-1-dw soil simulated a pollutant rebound (postremediation pollutant reversal due to residual contamination). Analysis of soil bacterial communities by denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments showed stronger changes and selection for a phylogenetically diverse microbial population in the mesocosms with pollutant-tolerant willow trees. Enumerat...

2011-01-01

Differential expression of farnesyl diphosphate synthase gene from Withania somnifera in different chemotypes and in response to elicitors

British Library Electronic Table of Contents (United Kingdom)

Withania somnifera (L.) Dunal (Family, Solanaceae), commonly known as Ashwagandha is one of the most valuable medicinal plants synthesizing large number of pharmacologically active secondary metabolites known as withanolides. Though the plant has been well characterized in terms of phytochemical profiles as well as pharmaceutical activities, not much is known about the genes responsible for biosynthesis of these compounds. In this study, we have characterized a gene encoding farnesyl diphosphate synthase (FPPS; EC 2.5.1.10), a key enzyme in the pathway of biosynthesis of isoprenoids, from W. somnifera. The full-length cDNA of Withania somnifera FPPS (WsFPPS) of 1,253?bps encodes a polypeptide of 343 amino acids. The amino acid sequence homology and phylogenetic analysis suggest that WsFPPS...

2011-01-01

Decolorization of textile azo dyes by newly isolated halophilic and halotolerant bacteria

British Library Electronic Table of Contents (United Kingdom)

Studies were carried out on the decolorization of textile azo dyes by newly isolated halophilic and halotolerant bacteria. Among the 27 strains of halophilic and halotolerant bacteria isolated from effluents of textile industries, three showed remarkable ability in decolorizing the widely utilized azo dyes. Phenotypic characterization and phylogenetic analysis based on 16S rDNA sequence comparisons indicate that these strains belonged to the genus Halomonas. The three strains were able to decolorize azo dyes in a wide range of NaCl concentration (up to 20%w/v), temperature (25-40degreeC), and pH (5-11) after 4 days of incubation in static culture. They could decolorize the mixture of dyes as well as pure dyes. These strains also readily grew in and decolorized the high concentrations of dy...

2007-01-01

Associations between a highly invasive species and native macrophytes differ across spatial scales

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The association between invasive and native species varies across spatial scales and is affected by phylogenetic relatedness, but these issues have rarely been addressed in aquatic ecosystems. In this study, we used a non-native, highly invasive species of Poaceae (tropical signalgrass) to test the hypotheses that (i) tropical signalgrass success correlates negatively with success of most native species of macrophytes at fine spatial scales, but its success correlates positively or at random with natives at coarse spatial scales, and that (ii) tropical signalgrass is less associated with native species belonging to the family Poaceae than with species belonging to other families (Darwin?s naturalization hypothesis). We used a dataset obtained at fine (0.25?m2) and coarse (ca. 1,000?m2) sca...

2011-01-01

Adjustment of sperm allocation under high risk of sperm competition across taxa: a meta-analysis

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Abstract Sperm competition theory predicts that under high risk of sperm competition, males will increase the number of sperm that they allocate to a female. This prediction has been supported by some experimental studies but not by others. Here, I conducted a meta-analysis to determine whether the increase in sperm allocation under high risk of sperm competition is a generalized response across taxa. I collected data from 39 studies and 37 species. Across taxa, males under a high risk of sperm competition respond by increasing their sperm allocation (mean effect size-=-0.32). Number of offspring did not explain a significant portion of the variation in effect sizes. A traditional meta-analysis (i.e. without phylogenetic information) described the variation among effect sizes better than a...

2011-01-01

Sequences, geographic variations and molecular phylogeny of venom phospholipases and threefinger toxins of eastern India Bungarus fasciatus and kinetic analyses of its Pro31 phospholipases A2.

Energetics and kinetics of anaerobic aromatic and fatty acid degradation

Eight phospholipases A2 (PLAs) and four three-finger-toxins (3FTx) from the pooled venom of Bungarus fasciatus (Bf) were previously studied and sequenced, but their expression pattern in individual Bf venom and possible geographic variations remained to be investigated. We herein analyze the individual venom of two Bf specimens from Kolkata (designated as KBf) to address this question. Seven PLAs and five 3FTx were purified from the KBf venoms, and respective cDNAs were cloned from venom glands of one of the snakes. Comparison of their mass and N-terminal sequence revealed that all the PLAs were conserved in both KBf venoms, but that two of their 3FTx isoforms were variable. When comparing the sequences of these KBf-PLAs with those published, only one was found to be identical to that of Bf Vb-2, and the other five were 94-98% identical to those of Bf II, III, Va, VI and XI-2, respectively. Notably, the most abundant PLA isoforms of Bf and KBf venoms contain Pro31 substitution. They ...

2006-12-08

Zoonotic Bartonella Species in Fleas and Blood from Red Foxes in Australia.

The kinetics of benzoate degradation by the anaerobic syntrophic bacterium, Syntrophus buswellii, was studied in coculture with Desulfovibrio strain G11. The threshold value for benzoate degradation was dependent on the acetate concentration with benzoate threshold values ranging from 2.4 [mu]M at 20 mM acetate to 30.0 [mu]M at 65 mM acetate. Increasing acetate concentrations also inhibited the rate of benzoate degradation with a apparent K[sub i] for acetate inhibition of 7.0 mM. Lower threshold values were obtained when nitrate rather than sulfate was the terminal electron acceptor. These data are consistent with a thermodynamic explanation for the threshold, and suggest that there is a minimum Gibbs free energy value required for the degradation of benzoate. An acetoacetyl-CoA thiolase has been isolated from Syntrophomonas wolfei; it is apparently a key enzyme controlling the synthesis of poly-B-hydroxyalkanoate from acetyl-CoA in this organism. Kinetic characterization of the ...

1992-11-16

The frontal weapon of the termite Armitermes euamignathus Silvestri (Isoptera, Termitidae, Nasutitermitinae)

Abstract Bartonella are arthropod-borne, fastidious, Gram-negative, and aerobic bacilli distributed by fleas, lice, sand flies, and, possibly, ticks. The zoonotic Bartonella species, Bartonella henselae and Bartonella clarridgeiae, which are the causes of cat scratch disease and endocarditis in humans, have been reported from cats, cat fleas, and humans in Australia. However, to date, there has been no report of B. henselae or B. clarridgeiae in Australian wild animals and their ectoparasites. B. henselae and B. clarridgeiae were detected in fleas (Ctenocephalides felis) from red foxes (Vulpes vulpes), an introduced pest animal species in Australia, and only B. clarridgeiae was detected in blood from one red fox. Phylogenetic analysis of the ribosomal intergenic spacer region revealed that the B. henselae detected in the current study were related to B. henselae strain Houston-1, a major pathogenic strain in humans in Australia, and confirmed the genetic ...

2011-09-15

Scientific Electronic Library Online (English)

Abstract in english Frontal weapon is the term used to designate the apparatus consisting of frontal gland and associated structures that participate in the chemical defense of termite soldiers. The ultra structure of the frontal gland and the scanning microscopy of the soldier head was investigated in the termite Amiitermes euamignathus Silvestri, 1901.Campaniform sensilla was not observed but there were 80 to100 sensory bristles around the frontal pore. The glandular epithelium shows only (more) class 1 cells according 10 the classification of NOIROT & QUENNEDEY (1974, 1991). The glandular cells are characterized by apical microvilli, a basal labyrinth and a large quantity of smooth endoplasmic reticulum which forms dense zones throughout the cytoplasm. The secretion is concentrated mainly in the basal pole of the cell and consists of large lipid droplets. The secretory epithelium is covered by a thick apical cuticle composed of a thin outer epicuticle, a layer of epicuticular ...

2001-06-01

Sympatric Distribution of Three Human Taenia Tapeworms Collected between 1935 and 2005 in Korea

High genetic diversity of HIV-1 was found in men who have sex with men in Shijiazhuang, China

Taeniasis has been known as one of the prevalent parasitic infections in Korea. Until recently, Taenia saginata had long been considered a dominant, and widely distributed species but epidemiological profiles of human Taenia species in Korea still remain unclear. In order to better understand distribution patterns of human Taenia tapeworms in Korea, partial nucleotide sequences of mitochondrial cox1 and ITS2 (internal transcribed spacer 2) were determined, along with morphological examinations, on 68 Taenia specimens obtained from university museum collections deposited since 1935. Genomic DNA was extracted from formalin-preserved specimens. Phylogenetic relationships among the genotypes (cox1 haplotype) detected in this study were inferred using the neighbor-joining method as a tree building method. Morphological and genetic analyses identified 3 specimens as T. solium, 51 specimens as T. asiatica, and 14 specimens as T. saginata. Our results indicate that all 3 ...

2008-12-20

British Library Electronic Table of Contents (United Kingdom)

Men who have sex with men (MSM) have become one of the populations with severely HIV prevalence in China. However, very few genetic studies have been done on HIV-1 spreading in this population. In this study, the genetic characterization of HIV-1 strains prevalent in the MSM in Shijiazhuang, China, was analyzed basing on the HIV-1 full-length gag, pol, and partial env gene. 21 drug-naive HIV-1 sero-positive patients were enrolled into the study. Full length gag, pol, partial env genes and some near full length genomes were amplified with nest RT-PCR followed by sequencing. Multiple subtypes, including CRF01_AE (52.9%), subtype B (35.3%) and CRF07_BC (11.8%), were found in the population. Phylogenetic analysis showed close relationship between our strains with those from Beijing MSM but not...

2011-01-01

First report of the complete sequence of Sida golden yellow vein virus from Jamaica.

Evolutionary dynamics of Newcastle disease virus

Begomoviruses are phytopathogens that threaten food security [18]. Sida spp. are ubiquitous weed species found in Jamaica. Sida samples were collected island-wide, DNA was extracted via a modified Dellaporta method, and the viral genome was amplified using degenerate and sequence-specific primers [2, 11]. The amplicons were cloned and sequenced. Sequence analysis revealed that a DNA-A molecule isolated from a plant in Liguanea, St. Andrew, was 90.9% similar to Sida golden yellow vein virus-[United States of America:Homestead:A11], making it a strain of SiGYVV. It was named Sida golden yellow vein virus-[Jamaica:Liguanea 2:2008] (SiGYVV-[JM:Lig2:08]). The cognate DNA-B, previously unreported, was successfully cloned and was most similar to that of Malvastrum yellow mosaic Jamaica virus (MaYMJV). Phylogenetic analysis suggested that this virus was most closely related to begomoviruses that infect malvaceous hosts in Jamaica, Cuba and Florida in the United States. ...

2011-05-29

Evidence of minimal methanogenic numbers and activity in sediments collected from the JAPEX/JNOC/GSC et al. Mallik 5L-38 gas hydrate production research well

A comprehensive dataset of NDV genome sequences was evaluated using bioinformatics to characterize the evolutionary forces affecting NDV genomes. Despite evidence of recombination in most genes, only one event in the fusion gene of genotype V viruses produced evolutionarily viable progenies. The codon-associated rate of change for the six NDV proteins revealed that the highest rate of change occurred at the fusion protein. All proteins were under strong purifying (negative) selection; the fusion protein displayed the highest number of amino acids under positive selection. Regardless of the phylogenetic grouping or the level of virulence, the cleavage site motif was highly conserved implying that mutations at this site that result in changes of virulence may not be favored. The coding sequence of the fusion gene and the genomes of viruses from wild birds displayed higher yearly rates of change in virulent viruses than in viruses of low virulence, suggesting that an ...

2009-08-15

Elimination of a new ampelovirus (GLRaV-Pr) and Grapevine rupestris stem pitting associated virus (GRSPaV) from two Vitis vinifera cultivars combining in vitro thermotherapy with shoot tip culture

Gene analysis was used to determined the presence, abundance and phylogenetic affiliation of methanogens that exist in gas-hydrate-bearing sediment samples obtained from 23 drill cores from the JAPEX/JNOC/GSC et al. Mallik 5L-38 gas hydrate research well. Rates of methane production were examined using sediment-inoculated enrichments containing {sup 14}C-labeled carbon substrates, carbon dioxide and acetate. Archaeal 16S rDNA was only detected in 6 of the samples, resulting in 8 sequences with relationships to the Miscellaneous Crenarchaeotic Group (7 clones) and the Subsurface Euryarchaeotic Group (1 clone). The single Euryarchaeota sequence did not appear to be related to methanogens. Subsamples from the cores showed variable results upon DNA extraction and amplification. Methanogenic Coenzyme M (CoM) was detected in 13 of the 20 cores, but methanogenic methyl CoM reductase genes were not amplified from the samples when using a sensitive quantitative polymerase ...

2005-07-01

British Library Electronic Table of Contents (United Kingdom)

A new virus species designated as Grapevine leafroll associated virus-Pr (GLRaV-Pr), which is classified in a distinct phylogenetic group of the genus Ampelovirus (Closteroviridae), was recently characterized from Greek grapevine cultivars. Elimination studies of GLRaV-Pr were carried out in two grapevine cultivars, 'Mantilaria' and 'Prevezaniko', co-infected with Grapevine rupestris stem pitting associated virus (GRSPaV, Flexiviridae). Both viruses were detected by nested RT-PCR assays. Virus elimination was achieved by combining in vitro thermotherapy with meristem ( 0.2mm) or shoot tip culture ( 0.5cm). The survival and regeneration rate of meristems was very low. On the other hand, high survival rates were observed in the cultured shoot tips accompanied with high elimination rates for ...

2009-01-01

Partial preservation of the Tentaculites Crotalinus shell from Ponta Grossa Formation (Devonian)

Origin of XMRV and its Demise as a Human Pathogen Associated with Chronic Fatigue Syndrome.

This paper deals with an analysis of a single specimen of Tentaculites crotalinus SALTER emend. CIGUEL et al. (1984) that present a possible partial preservation of the shell. It comes from an outcrop of the Grossa Formation (Devonian) near Jaguariaiva, State of Parana. The skeletal microstructure of the Tentaculitoidea shell rather poorly Known. Thus, the phylogenetic relationships of these invertebrates still uncertain. Tentaculitids are very common fossils in Devonian Ponta Grossa Formation (Parana Basin) but so far Known only from external and internal moulds. The objective of this study is to demonstrate wheter the layer found in between the internal and external mould is or not a case shell preservation. The chemical composition of this layer and of the external mould was analysed by X rays. X rays difratometry was applied only to the matrix (at the external mould). The structure of the supposed shell remain was studied by binocular stereomicroscope and ...

N"v"a"r"-"e"p"s"i"l"o"n-acetyl-#beta#-lysine: An osmolyte synthesized by mothanogenic archaebacteria

Retroviruses are well known pathogens of mammals, birds and fish. Their potential to induce cancer in chickens was already described almost 100 years ago and murine retroviruses have been a subject of study for 50 years. The first human retroviruses, HTLV and HIV, were discovered more than 30 years ago, surprising researchers and physicians by the profound differences in the diseases they cause. HTLV-1 is able to induce, after decades of infection, lymphomas/leukemia or neuroimmune disorders whereas untreated HIV infection leads almost inevitably to AIDS. The recently described XMRV (xenotropic murine leukemia virus-related virus) appeared to possess many of the features known for HTLV and was regarded by some to be the third human retrovirus. However, recent publications by Knox et al. [1] and Paprotka et al. [2] have shed new light on this gammaretrovirus. Knox and colleagues clearly demonstrate that XMRV is absent in patients belonging to a chronic fatigue syndrome cohort who had ...

2011-07-27

Genomic analysis of the symbiotic marine crenarchaeon, Cenarchaeumsymbiosum

Methanosarcina thermophila, a nonmarine methanogenic archaebacterium, can grow in a range of saline concentrations. At less than 0.4 M NaCl, Ms. thermophila accumulated glutamate in response to increasing osmotic stress. At greater than 0.4 M NaCl, this organism synthesized a modified #beta#-amino acid that was identified as N"v"a"r"-"e"p"s"i"l"o"n-acetyl-#beta#-lysine by NMR spectroscopy and ion-exchange HPLC. This #beta#-amino acid derivative accumulated to high intracellular concentrations (up to 0.6 M) in Ms. thermophila and in another methanogen examined - Methanogenium cariaci, a marine species. The compound has features that are characteristic of a compatible solute: it is neutrally charged at physiological pH and it is highly soluble. When the cells were grown in the presence of exogenous glycine betaine, a physiological pH and it is highly soluble. When the cells were grown in the presence of exogenous glycine betaine, a physiological compatible solute, ...

Dating divergences in the Fungal Tree of Life: review and new analyses.

Crenarchaea are ubiquitous and abundant microbial constituents of soils, sediments, lakes and ocean waters, yet relatively little is known about their fundamental evolutionary, ecological, and physiological properties. To better describe the ubiquitous nonthermophilic Crenarchaea, we analyzed the genome sequence of one representative, the uncultivated sponge symbiont, Cenarchaeum symbiosum. C. symbiosum genotypes coinhabiting the same host partitioned into two dominant populations, corresponding to previously described a- and b-type ribosomal RNA variants. Although synthetic, overlapping a- and b-type ribotypes harbored significant genetic variability. A single tiling path comprising the dominant a-type genotype was assembled, and used to explore the biological properties of C. symbiosum and its planktonic relatives. Out of a total of 2,066 predicted open reading frames, 36% were more highly conserved with other Archaea. The remainder partitioned between bacteria (18%), eukaryotes ...

2006-06-24

Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park

The collection of papers in this issue of Mycologia documents considerable improvements in taxon sampling and phylogenetic resolution regarding the Fungal Tree of Life. The new data will stimulate new attempts to date divergences and correlate events in fungal evolution with those of other organisms. Here, we review the history of dating fungal divergences by nucleic acid variation and then use a dataset of 50 genes for 25 selected fungi, plants and animals to investigate divergence times in kingdom Fungi. In particular, we test the choice of fossil calibration points on dating divergences in fungi. At the scale of our analysis, substitution rates varied without showing significant within-lineage correlation, so we used the Langley-Fitch method in the R8S package of computer programs to estimate node ages. Different calibration points had a dramatic effect on estimated divergence dates. The estimate for the age of the Ascomycota/Basidiomycota split was 1808000000 y ...

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Phylogeny of iguanian lizards inferred from 29 nuclear loci, and a comparison of concatenated and species-tree approaches for an ancient, rapid radiation.

A novel, obligately anaerobic, extremely thermophilic, cellulolytic bacterium, designated OB47T, was isolated from Obsidian Pool, Yellowstone National Park, WY, USA. The isolate was a non-motile, non-spore forming, Gram-positive rod approximately 2 m long by 0.2 m wide and grew at temperatures between 55-85oC with the optimum at 78oC. The pH range for growth was 6.0-8.0 with values of near 7.0 being optimal. Growth on cellobiose produced the fastest specific growth rates at 0.75 hr-1. The organism also displayed fermentative growth on glucose, maltose, arabinose, fructose, starch, lactose, mannose, sucrose, galactose, xylose, arabinogalactan, Avicel, xylan, filter paper, processed cardboard, pectin, dilute acid-pretreated switchgrass and Populus. OB47T was unable to grow on mannitol, fucose, lignin, Gelrite, acetate, glycerol, ribose, sorbital, carboxymethylcellulose and casein. Yeast extract stimulated growth and thiosulfate, sulfate, nitrate, and sulfur were not reduced. Fermentation ...

2010-02-01