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Sample records for sider retroposon subfamilies

  1. Genomic cartography and proposal of nomenclature for the repeated, interspersed elements of the Leishmania major SIDER2 family and identification of SIDER2-containing transcripts.

    PubMed

    Requena, Jose M; Rastrojo, Alberto; Garde, Esther; López, Manuel C; Thomas, M Carmen; Aguado, Begoña

    2017-03-01

    The genomes of most eukaryotic organisms contain a large number of transposable elements that are able to move from one genomic site to another either by transferring of DNA mobile elements (transposons) or transpose via reverse transcription of an RNA intermediate (retroposons). An exception to this rule is found in protists of the subgenus Leishmania, in which active retroposons degenerated after a flourishing era, leaving only retroposon remains; these have been classified into two families: SIDER1 and SIDER2. In this work, we have re-examined the elements belonging to the family SIDER2 present in the genome of Leishmania major with the aim of providing a nomenclature that will facilitate a future reference to particular elements. According to sequence conservation, the 1100 SIDER2 elements have been grouped into subfamilies, and the inferred taxonomic relationships have also been incorporated into the nomenclature. Additionally, we are providing detailed data regarding the genomic distribution of these elements and their association with specific transcripts, based on the recently established transcriptome for L. major. Thus, the presented data can help to study and better understand the roles played by these degenerated retroposons in both regulation of gene expression and genome plasticity.

  2. [Domain organization of the ORF2 C-terminal region of the German cockroach retroposon R1].

    PubMed

    Kagramanova, A S; Kapelinskaia, T V; Korolev, A L; Mukha, D V

    2010-08-01

    Using cosmid vector, a gene library of German cockroach Blattella germanica was constructed. From this library, clones containing full-length copies of two subfamilies of R1 retroposons were selected. Retroposons R1 of German cockroach belonging to different subfamilies were shown to be different in domain organization of the ORF2 C-terminal region. For the first time, retroposons transmembrane domains were identified in the sequences of R1. It was demonstrated that two retroposon R1 subfamilies of German cockroach arose as a result of intragenomic divergence rather than via horizontal transfer of alien mobile element into cockroach genome. The differences in domain organization appeared not as a result of saltatory recombination processes, but as a consequence of gradual mutation accumulation, which led to either degeneration, or to domain formation.

  3. Mosaic retroposon insertion patterns in placental mammals.

    PubMed

    Churakov, Gennady; Kriegs, Jan Ole; Baertsch, Robert; Zemann, Anja; Brosius, Jürgen; Schmitz, Jürgen

    2009-05-01

    One and a half centuries after Charles Darwin and Alfred Russel Wallace outlined our current understanding of evolution, a new scientific era is dawning that enables direct observations of genetic variation. However, pure sequence-based molecular attempts to resolve the basal origin of placental mammals have so far resulted only in apparently conflicting hypotheses. By contrast, in the mammalian genomes where they were highly active, the insertion of retroelements and their comparative insertion patterns constitute a neutral, virtually homoplasy-free archive of evolutionary histories. The "presence" of a retroelement at an orthologous genomic position in two species indicates their common ancestry in contrast to its "absence" in more distant species. To resolve the placental origin controversy we extracted approximately 2 million potentially phylogenetically informative, retroposon-containing loci from representatives of the major placental mammalian lineages and found highly significant evidence challenging all current single hypotheses of their basal origin. The Exafroplacentalia hypothesis (Afrotheria as the sister group to all remaining placentals) is significantly supported by five retroposon insertions, the Epitheria hypothesis (Xenarthra as the sister group to all remaining placentals) by nine insertion patterns, and the Atlantogenata hypothesis (a monophyletic clade comprising Xenarthra and Afrotheria as the sister group to Boreotheria comprising all remaining placentals) by eight insertion patterns. These findings provide significant support for a "soft" polytomy of the major mammalian clades. Ancestral successive hybridization events and/or incomplete lineage sorting associated with short speciation intervals are viable explanations for the mosaic retroposon insertion patterns of recent placental mammals and for the futile search for a clear root dichotomy.

  4. Mosaic retroposon insertion patterns in placental mammals

    PubMed Central

    Churakov, Gennady; Kriegs, Jan Ole; Baertsch, Robert; Zemann, Anja; Brosius, Jürgen; Schmitz, Jürgen

    2009-01-01

    One and a half centuries after Charles Darwin and Alfred Russel Wallace outlined our current understanding of evolution, a new scientific era is dawning that enables direct observations of genetic variation. However, pure sequence-based molecular attempts to resolve the basal origin of placental mammals have so far resulted only in apparently conflicting hypotheses. By contrast, in the mammalian genomes where they were highly active, the insertion of retroelements and their comparative insertion patterns constitute a neutral, virtually homoplasy-free archive of evolutionary histories. The “presence” of a retroelement at an orthologous genomic position in two species indicates their common ancestry in contrast to its “absence” in more distant species. To resolve the placental origin controversy we extracted ∼2 million potentially phylogenetically informative, retroposon-containing loci from representatives of the major placental mammalian lineages and found highly significant evidence challenging all current single hypotheses of their basal origin. The Exafroplacentalia hypothesis (Afrotheria as the sister group to all remaining placentals) is significantly supported by five retroposon insertions, the Epitheria hypothesis (Xenarthra as the sister group to all remaining placentals) by nine insertion patterns, and the Atlantogenata hypothesis (a monophyletic clade comprising Xenarthra and Afrotheria as the sister group to Boreotheria comprising all remaining placentals) by eight insertion patterns. These findings provide significant support for a “soft” polytomy of the major mammalian clades. Ancestral successive hybridization events and/or incomplete lineage sorting associated with short speciation intervals are viable explanations for the mosaic retroposon insertion patterns of recent placental mammals and for the futile search for a clear root dichotomy. PMID:19261842

  5. A universal method for the study of CR1 retroposons in nonmodel bird genomes.

    PubMed

    Suh, Alexander; Kriegs, Jan Ole; Donnellan, Stephen; Brosius, Jürgen; Schmitz, Jürgen

    2012-10-01

    Presence/absence patterns of retroposon insertions at orthologous genomic loci constitute straightforward markers for phylogenetic or population genetic studies. In birds, the convenient identification and utility of these markers has so far been mainly restricted to the lineages leading to model birds (i.e., chicken and zebra finch). We present an easy-to-use, rapid, and cost-effective method for the experimental isolation of chicken repeat 1 (CR1) insertions from virtually any bird genome and potentially nonavian genomes. The application of our method to the little grebe genome yielded insertions belonging to new CR1 subfamilies that are scattered all across the phylogenetic tree of avian CR1s. Furthermore, presence/absence analysis of these insertions provides the first retroposon evidence grouping flamingos + grebes as Mirandornithes and several markers for all subsequent branching events within grebes (Podicipediformes). Five markers appear to be species-specific insertions, including the hitherto first evidence in birds for biallelic CR1 insertions that could be useful in future population genetic studies.

  6. Multiple Lineages of Ancient CR1 Retroposons Shaped the Early Genome Evolution of Amniotes

    PubMed Central

    Suh, Alexander; Churakov, Gennady; Ramakodi, Meganathan P.; Platt, Roy N.; Jurka, Jerzy; Kojima, Kenji K.; Caballero, Juan; Smit, Arian F.; Vliet, Kent A.; Hoffmann, Federico G.; Brosius, Jürgen; Green, Richard E.; Braun, Edward L.; Ray, David A.; Schmitz, Jürgen

    2015-01-01

    Chicken repeat 1 (CR1) retroposons are long interspersed elements (LINEs) that are ubiquitous within amniote genomes and constitute the most abundant family of transposed elements in birds, crocodilians, turtles, and snakes. They are also present in mammalian genomes, where they reside as numerous relics of ancient retroposition events. Yet, despite their relevance for understanding amniote genome evolution, the diversity and evolution of CR1 elements has never been studied on an amniote-wide level. We reconstruct the temporal and quantitative activity of CR1 subfamilies via presence/absence analyses across crocodilian phylogeny and comparative analyses of 12 crocodilian genomes, revealing relative genomic stasis of retroposition during genome evolution of extant Crocodylia. Our large-scale phylogenetic analysis of amniote CR1 subfamilies suggests the presence of at least seven ancient CR1 lineages in the amniote ancestor; and amniote-wide analyses of CR1 successions and quantities reveal differential retention (presence of ancient relics or recent activity) of these CR1 lineages across amniote genome evolution. Interestingly, birds and lepidosaurs retained the fewest ancient CR1 lineages among amniotes and also exhibit smaller genome sizes. Our study is the first to analyze CR1 evolution in a genome-wide and amniote-wide context and the data strongly suggest that the ancestral amniote genome contained myriad CR1 elements from multiple ancient lineages, and remnants of these are still detectable in the relatively stable genomes of crocodilians and turtles. Early mammalian genome evolution was thus characterized by a drastic shift from CR1 prevalence to dominance and hyperactivity of L2 LINEs in monotremes and L1 LINEs in therians. PMID:25503085

  7. Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions

    PubMed Central

    Nilsson, Maria A.; Churakov, Gennady; Sommer, Mirjam; Tran, Ngoc Van; Zemann, Anja; Brosius, Jürgen; Schmitz, Jürgen

    2010-01-01

    The Australasian and South American marsupial mammals, such as kangaroos and opossums, are the closest living relatives to placental mammals, having shared a common ancestor around 130 million years ago. The evolutionary relationships among the seven marsupial orders have, however, so far eluded resolution. In particular, the relationships between the four Australasian and three South American marsupial orders have been intensively debated since the South American order Microbiotheria was taxonomically moved into the group Australidelphia. Australidelphia is significantly supported by both molecular and morphological data and comprises the four Australasian marsupial orders and the South American order Microbiotheria, indicating a complex, ancient, biogeographic history of marsupials. However, the exact phylogenetic position of Microbiotheria within Australidelphia has yet to be resolved using either sequence or morphological data analysis. Here, we provide evidence from newly established and virtually homoplasy-free retroposon insertion markers for the basal relationships among marsupial orders. Fifty-three phylogenetically informative markers were retrieved after in silico and experimental screening of ∼217,000 retroposon-containing loci from opossum and kangaroo. The four Australasian orders share a single origin with Microbiotheria as their closest sister group, supporting a clear divergence between South American and Australasian marsupials. In addition, the new data place the South American opossums (Didelphimorphia) as the first branch of the marsupial tree. The exhaustive computational and experimental evidence provides important insight into the evolution of retroposable elements in the marsupial genome. Placing the retroposon insertion pattern in a paleobiogeographic context indicates a single marsupial migration from South America to Australia. The now firmly established phylogeny can be used to determine the direction of genomic changes and

  8. The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads

    PubMed Central

    Doronina, Liliya; Matzke, Andreas; Churakov, Gennady; Stoll, Monika; Huge, Andreas; Schmitz, Jürgen

    2017-01-01

    Solving problematic phylogenetic relationships often requires high quality genome data. However, for many organisms such data are still not available. Among rodents, the phylogenetic position of the beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy-free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data). PMID:28256552

  9. Determining the Position of Storks on the Phylogenetic Tree of Waterbirds by Retroposon Insertion Analysis

    PubMed Central

    Kuramoto, Tae; Nishihara, Hidenori; Watanabe, Maiko; Okada, Norihiro

    2015-01-01

    Despite many studies on avian phylogenetics in recent decades that used morphology, mitochondrial genomes, and/or nuclear genes, the phylogenetic positions of several birds (e.g., storks) remain unsettled. In addition to the aforementioned approaches, analysis of retroposon insertions, which are nearly homoplasy-free phylogenetic markers, has also been used in avian phylogenetics. However, the first step in the analysis of retroposon insertions, that is, isolation of retroposons from genomic libraries, is a costly and time-consuming procedure. Therefore, we developed a high-throughput and cost-effective protocol to collect retroposon insertion information based on next-generation sequencing technology, which we call here the STRONG (Screening of Transposons Obtained by Next Generation Sequencing) method, and applied it to 3 waterbird species, for which we identified 35,470 loci containing chicken repeat 1 retroposons (CR1). Our analysis of the presence/absence of 30 CR1 insertions demonstrated the intra- and interordinal phylogenetic relationships in the waterbird assemblage, namely 1) Loons diverged first among the waterbirds, 2) penguins (Sphenisciformes) and petrels (Procellariiformes) diverged next, and 3) among the remaining families of waterbirds traditionally classified in Ciconiiformes/Pelecaniformes, storks (Ciconiidae) diverged first. Furthermore, our genome-scale, in silico retroposon analysis based on published genome data uncovered a complex divergence history among pelican, heron, and ibis lineages, presumably involving ancient interspecies hybridization between the heron and ibis lineages. Thus, our retroposon-based waterbird phylogeny and the established phylogenetic position of storks will help to understand the evolutionary processes of aquatic adaptation and related morphological convergent evolution. PMID:26527652

  10. [A family of short retroposons (Squaml) from squamate reptiles (Reptilia: Squamata): structure, evolution and correlation with phylogeny].

    PubMed

    Kosushkin, S A; Borodulina, O R; Solov'eva, E N; Grechko, V V

    2008-01-01

    We have isolated and characterised sequences of a SINE family specific for squamate reptiles from a genome of lacertid lizard that we called Squam1. Copies are 360-390 bp in length and share a significant similarity with tRNA gene sequence on its 5'-end. This family was also detected by us in DNA of representatives of varanids, iguanids (anolis), gekkonids, and snakes. No signs of it were found in DNA of mammals, birds, amphibians, and crocodiles. Detailed analysis of primary structure of the retroposons obtained by us from genomic libraries or GenBank sequences was carried out. Most taxa possess 2-3 subfamilies of the SINE in their genomes with specific diagnostic features in their primary structure. Individual variability of copies in different families is about 85% and is just slightly lower on the genera level. Comparison of consensus sequences on family level reveals a high degree of structural similarity with a number of specific apomorphic features which makes it a useful marker of phylogeny for this group of reptiles. Snakes do not show specific affinity to varanids when compared to other lizards, as it was suggested earlier.

  11. Activity of ancient RTE retroposons during the evolution of cows, spiral-horned antelopes, and Nilgais (Bovinae).

    PubMed

    Nilsson, M A; Klassert, D; Bertelsen, M F; Hallström, B M; Janke, A

    2012-10-01

    In the genome of Artiodactyla (cow, sheep, pigs, camels, and whales), a major retroposon group originated from a presumable horizontal transfer of BovB, a retrotransposon-like element retroposon, between 52 and 70 million years ago. Since then, BovB retroposons have proliferated and today occupy a quarter of the cow's genome sequence. The BovB-related short interspersed elements (SINEs) were used for resolving the phylogeny of Bovinae (cows, spiral-horned antelopes, and nilgais) and their relatives. In silico screening of 55,000 intronic retroposon insertions in the cow genome and experimental validation of 126 introns resulted in 29 informative retroposon markers for resolving bovine evolutionary relationships. A transposition-in-transposition analysis identifies three different phases of SINE activity and show how BovB elements have expanded in the cattle genome.

  12. Sidereal variations deep underground in Tasmania

    NASA Technical Reports Server (NTRS)

    Humble, J. E.; Fenton, A. G.; Fenton, K. B.

    1985-01-01

    Data from the deep underground vertically directed muon telescopes at Poatina, Tasmania, have been used since 1972 for a number of investigations, including the daily intensity variations, atmospheric influences, and checking for possible effects due to the interplanetary magnetic field. These telescopes have a total sensitive area of only 3 square meters, with the result that the counting rate is low (about 1680 events per hour) and the statistical errors on the results are rather large. Consequently, it was decided several years ago to construct larger detectors for this station. The first of these telescopes has been in operation for two complete years, and the results from it are presented. Results from the new, more stable equipment at Poatina appear to confirm the existence of a first harmonic in the daily variations in sidereal time reported earlier, and are consistent with small or non-existent first harmonics in solar and anti-sidereal time. All the second harmonics appear to be small, if not zero at these energies.

  13. Evolutionary origins of retroposon lineages of Mhc class II Ab alleles.

    PubMed

    Lu, C C; Ye, Y; She, J X; Bonhomme, F; Wakeland, E K

    1996-01-01

    Major histocompatibility complex (Mhc) class II Ab genes have evolved into three distinct lineages. While lineage 2 alleles differ from lineage 1 alleles by the insertion of a retroposon in intron 2, the basis for the extremely large intron 2 in lineage 3 alleles has heretofore been undetermined. In this report, we demonstrate by nucleotide sequencing that the genomic sequences of prototypic alleles from all three lineages diverge significantly and that lineage 3 is derived from lineage 2 by two insertional events in intron 2. One insert, composed of a member of B1 short interspersed repetitive elements (SINEs), occurs 508 base pairs (bp) 3' of exon 2, and the other, 1141 bp 3' of exon 2 within the retroposon that distinguishes lineage 2 from lineage 1. To assess the evolutionary stability of these lineages and the extent of ancestral polymorphisms of Ab within Mus species, we extended our restriction site polymorphism analysis to include 86 alleles from 120 independently derived H2 haplotypes from 12 separate species and subspecies of Mus. A phylogenetic tree revealing the relationships of these Ab alleles with respect to restriction site polymorphisms, but excluding the retroposon insertions, demonstrated that these lineages have distinctive genomic structures beyond the retroposon polymorphisms. In summary, these mouse Ab genes were produced from successive retroposon insertion events. Lineage 1 and 2 were detected in a variety of Mus species, including Mus caroli, indicating that these lineages diverged more than 2 million years ago. Lineage 3 alleles were found only in the Mus musculus subspecies, suggesting that it diverged from lineage 2 more recently. These results indicate that all three lineages of Ab have persisted through several speciation events in the genus Mus.

  14. Diterpenes and phenolic compounds from Sideritis pullulans.

    PubMed

    Faiella, Laura; Piaz, Fabrizio Dal; Bader, Ammar; Braca, Alessandra

    2014-10-01

    Phytochemical investigation of Sideritis pullulans aerial part and root extracts allowed to isolate six ent-kaurane diterpenes, two phenylpropanoids, and one coumarin, identified as 1α,3α,7β,18-tetrahydroxy-ent-kaur-16-ene (sideripullol A) (1), 3α,11α,18-trihydroxy-ent-kaur-16-ene (sideripullol B) (2), 3α,7β,18-trihydroxy-17-nor-ent-kauran-16-one (sideritone A) (3), 3α,7β-dihydroxy-18-acetyloxy-17-nor-ent-kauran-16-one (sideritone B) (4), 3α,7β,16α,17-tetrahydroxy-18-acetyloxy-ent-kaurane (sideripullol C) (5), 7β,16α,17,18-tetrahydroxy-ent-kaurane (sideripullol D) (6), β-(3-methoxy-4-hydroxyphenyl)-ethyl-O-α-l-arabinopiranosyl-(1→2)-α-l-rhamnopyranosyl-(1→3)-6-O-t-feruloyl-β-d-glucopyranoside (sideritiside A) (7), β-(3,4-dihydroxyphenyl)-ethyl-O-α-l-arabinopiranosyl-(1→2)-α-l-rhamnopyranosyl-(1→3)-6-O-t-feruloyl-β-d-glucopyranoside (sideritiside B) (8), and 7-demethyl-8-methoxycoumarsabin (9), respectively. Twenty known compounds, including phenolics, flavonol glycosides, iridoids, diterpenes, sesquiterpenes, lignans, coumarins, and phenylpropanoids were also isolated and characterized. All diterpenes were evaluated for their cytotoxic activity.

  15. [Analysis of the inheritance patterns of 5'-truncated copies of the German cockroach R2 retroposons in individual crosses].

    PubMed

    Kagramanova, A S; Korolev, A L; Mukha, D V

    2010-11-01

    The inheritance patterns of the 5'-truncated copies of R2 retroposons were analyzed in individual crosses of the German cockroach. The recombination level within the cluster of ribosomal RNA genes was determined. It was demonstrated that only the frequencies of individual variants of 5'-truncated retroposon copies are appropriate for population analysis rather than the patterns characterizing individual X chromosomes. The methodical approach used in the work is convenient for studying the genetic variation in ribosomal DNA multigene families.

  16. Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds.

    PubMed

    Suh, Alexander; Paus, Martin; Kiefmann, Martin; Churakov, Gennady; Franke, Franziska Anni; Brosius, Jürgen; Kriegs, Jan Ole; Schmitz, Jürgen

    2011-08-23

    The relationships of passerines (such as the well-studied zebra finch) with non-passerine birds is one of the great enigmas of avian phylogenetic research, because decades of extensive morphological and molecular studies yielded highly inconsistent results between and within data sets. Here we show the first application of the virtually homoplasy-free retroposon insertions to this controversy. Our study examined ~200,000 retroposon-containing loci from various avian genomes and retrieved 51 markers resolving early bird phylogeny. Among these, we obtained statistically significant evidence that parrots are the closest and falcons the second-closest relatives of passerines, together constituting the Psittacopasserae and the Eufalconimorphae, respectively. Our new and robust phylogenetic framework has substantial implications for the interpretation of various conclusions drawn from passerines as model organisms. This includes insights of relevance to human neuroscience, as vocal learning (that is, birdsong) probably evolved in the psittacopasseran ancestor, >30 million years earlier than previously assumed.

  17. Mesozoic retroposons reveal parrots as the closest living relatives of passerine birds

    PubMed Central

    Suh, Alexander; Paus, Martin; Kiefmann, Martin; Churakov, Gennady; Franke, Franziska Anni; Brosius, Jürgen; Kriegs, Jan Ole; Schmitz, Jürgen

    2011-01-01

    The relationships of passerines (such as the well-studied zebra finch) with non-passerine birds is one of the great enigmas of avian phylogenetic research, because decades of extensive morphological and molecular studies yielded highly inconsistent results between and within data sets. Here we show the first application of the virtually homoplasy-free retroposon insertions to this controversy. Our study examined ~200,000 retroposon-containing loci from various avian genomes and retrieved 51 markers resolving early bird phylogeny. Among these, we obtained statistically significant evidence that parrots are the closest and falcons the second-closest relatives of passerines, together constituting the Psittacopasserae and the Eufalconimorphae, respectively. Our new and robust phylogenetic framework has substantial implications for the interpretation of various conclusions drawn from passerines as model organisms. This includes insights of relevance to human neuroscience, as vocal learning (that is, birdsong) probably evolved in the psittacopasseran ancestor, >30 million years earlier than previously assumed. PMID:21863010

  18. Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons

    PubMed Central

    Franchini, Lucía F.; López-Leal, Rodrigo; Nasif, Sofía; Beati, Paula; Gelman, Diego M.; Low, Malcolm J.; de Souza, Flávio J. S.; Rubinstein, Marcelo

    2011-01-01

    The proopiomelanocortin gene (POMC) is expressed in a group of neurons present in the arcuate nucleus of the hypothalamus. Neuron-specific POMC expression in mammals is conveyed by two distal enhancers, named nPE1 and nPE2. Previous transgenic mouse studies showed that nPE1 and nPE2 independently drive reporter gene expression to POMC neurons. Here, we investigated the evolutionary mechanisms that shaped not one but two neuron-specific POMC enhancers and tested whether nPE1 and nPE2 drive identical or complementary spatiotemporal expression patterns. Sequence comparison among representative genomes of most vertebrate classes and mammalian orders showed that nPE1 is a placental novelty. Using in silico paleogenomics we found that nPE1 originated from the exaptation of a mammalian-apparent LTR retrotransposon sometime between the metatherian/eutherian split (147 Mya) and the placental mammal radiation (≈90 Mya). Thus, the evolutionary origin of nPE1 differs, in kind and time, from that previously demonstrated for nPE2, which was exapted from a CORE-short interspersed nucleotide element (SINE) retroposon before the origin of prototherians, 166 Mya. Transgenic mice expressing the fluorescent markers tomato and EGFP driven by nPE1 or nPE2, respectively, demonstrated coexpression of both reporter genes along the entire arcuate nucleus. The onset of reporter gene expression guided by nPE1 and nPE2 was also identical and coincidental with the onset of Pomc expression in the presumptive mouse diencephalon. Thus, the independent exaptation of two unrelated retroposons into functional analogs regulating neuronal POMC expression constitutes an authentic example of convergent molecular evolution of cell-specific enhancers. PMID:21876128

  19. Inexpensive Clock for Displaying Planetary or Sidereal Time

    NASA Technical Reports Server (NTRS)

    Lux, James

    2007-01-01

    An inexpensive wall clock has been devised for displaying solar time or sidereal time as it would be perceived on a planet other than the Earth, or for displaying sidereal time on the Earth. The concept of a wall clock synchronized to a period other than the terrestrial mean solar day is not new in itself. What is new here is that the clock is realized through a relatively simple electronic modification of a common battery-powered, quartz-crystal-oscillator-driven wall clock. The essence of the modification is to shut off the internal oscillator of the clock and replace the internal-oscillator output signal with a signal of the required frequency generated by an external oscillator. The unmodified clock electronic circuitry includes a quartz crystal connected to an integrated circuit (IC) that includes, among other parts, a buffer amplifier that conditions the oscillator output. The modification is effected by removing the quartz crystal and connecting the output terminal of the external oscillator, via a capacitor, to the input terminal of the buffer amplifier

  20. Automated Protein Subfamily Identification and Classification

    PubMed Central

    Brown, Duncan P; Krishnamurthy, Nandini; Sjölander, Kimmen

    2007-01-01

    Function prediction by homology is widely used to provide preliminary functional annotations for genes for which experimental evidence of function is unavailable or limited. This approach has been shown to be prone to systematic error, including percolation of annotation errors through sequence databases. Phylogenomic analysis avoids these errors in function prediction but has been difficult to automate for high-throughput application. To address this limitation, we present a computationally efficient pipeline for phylogenomic classification of proteins. This pipeline uses the SCI-PHY (Subfamily Classification in Phylogenomics) algorithm for automatic subfamily identification, followed by subfamily hidden Markov model (HMM) construction. A simple and computationally efficient scoring scheme using family and subfamily HMMs enables classification of novel sequences to protein families and subfamilies. Sequences representing entirely novel subfamilies are differentiated from those that can be classified to subfamilies in the input training set using logistic regression. Subfamily HMM parameters are estimated using an information-sharing protocol, enabling subfamilies containing even a single sequence to benefit from conservation patterns defining the family as a whole or in related subfamilies. SCI-PHY subfamilies correspond closely to functional subtypes defined by experts and to conserved clades found by phylogenetic analysis. Extensive comparisons of subfamily and family HMM performances show that subfamily HMMs dramatically improve the separation between homologous and non-homologous proteins in sequence database searches. Subfamily HMMs also provide extremely high specificity of classification and can be used to predict entirely novel subtypes. The SCI-PHY Web server at http://phylogenomics.berkeley.edu/SCI-PHY/ allows users to upload a multiple sequence alignment for subfamily identification and subfamily HMM construction. Biologists wishing to provide their own

  1. Retroposon analysis and recent geological data suggest near-simultaneous divergence of the three superorders of mammals

    PubMed Central

    Nishihara, Hidenori; Maruyama, Shigenori; Okada, Norihiro

    2009-01-01

    As a consequence of recent developments in molecular phylogenomics, all extant orders of placental mammals have been grouped into 3 lineages: Afrotheria, Xenarthra, and Boreotheria, which originated in Africa, South America, and Laurasia, respectively. Despite this advancement, the order of divergence of these 3 lineages remains unresolved. Here, we performed extensive retroposon analysis with mammalian genomic data. Surprisingly, we identified a similar number of informative retroposon loci that support each of 3 possible phylogenetic hypotheses: the basal position for Afrotheria (22 loci), Xenarthra (25 loci), and Boreotheria (21 loci). This result indicates that the divergence of the placental common ancestor into the 3 lineages occurred nearly simultaneously. Thus, we examined whether these molecular data could be integrated into the geological context by incorporating recent geological data. We obtained firm evidence that complete separation of Gondwana into Africa and South America occurred 120 ± 10 Ma. Accordingly, the previous reported time frame (division of Pangea into Gondwana and Laurasia at 148–138 Ma and division of Gondwana at 105 Ma) cannot be used to validate mammalian divergence order. Instead, we use our retroposon results and the recent geological data to propose that near-simultaneous divisions of continents leading to isolated Africa, South America, and Laurasia caused nearly concomitant divergence of the ancient placental ancestor into 3 lineages, Afrotheria, Xenarthra, and Boreotheria, ≈120 Ma. PMID:19286970

  2. Fish retroposons related to the Penelope element of Drosophila virilis define a new group of retrotransposable elements.

    PubMed

    Volff, J N; Hornung, U; Schartl, M

    2001-06-01

    Poseidon and Neptune are two ancient lineages of retroposons related to the Penelope element from Drosophila virilis. They have been identified in various teleost fish species, including the medakafish (Oryzias latipes), and the pufferfishes Fugu rubripes and Tetraodon nigroviridis, whose genomes are currently being sequenced. Some of these elements are highly reiterated in fish genomes. Penelope-related elements were also identified in blood fluke, shrimp, sea urchin, cichlid fish and frog, showing that they are widespread in animals. Penelope-related retroposons were not detected among sequences from the Drosophila melanogaster and human genome projects, suggesting that they have been lost from certain animal lineages. A sequence encoding a putative Uri (also called GIY-YIG) endonuclease domain was detected downstream from the gene for reverse transcriptase. To the best of our knowledge, this type of endonuclease sequence has previously been identified in group I introns and in genes for prokaryotic excinucleases but not in retrotransposable elements. Penelope-related elements are frequently truncated at their 5' ends and can also be flanked by long terminal repeat-like structures. Phylogenetic analysis of the reverse transcriptase domain failed to assign Penelope-related retroposons to one of the major groups of retroelements. Overall, therefore, the evidence strongly suggests that these sequences represent a new group of retrotransposable elements.

  3. When Will It Be ...?: U.S. Naval Observatory Sidereal Time and Julian Date Calculators

    NASA Astrophysics Data System (ADS)

    Chizek Frouard, Malynda R.; Lesniak, Michael V.; Bartlett, Jennifer L.

    2017-01-01

    Sidereal time and Julian date are two values often used in observational astronomy that can be tedious to calculate. Fortunately, the U.S. Naval Observatory (USNO) has redesigned its on-line Sidereal Time and Julian Date (JD) calculators to provide data through an Application Programming Interface (API). This flexible interface returns dates and times in JavaScript Object Notation (JSON) that can be incorporated into third-party websites or applications.Via the API, Sidereal Time can be obtained for any location on Earth for any date occurring in the current, previous, or subsequent year. Up to 9999 iterations of sidereal time data with intervals from 1 second to 1095 days can be generated, as long as the data doesn’t extend past the date limits. The API provides the Gregorian calendar date and time (in UT1), Greenwich Mean Sidereal Time, Greenwich Apparent Sidereal Time, Local Mean Sidereal Time, Local Apparent Sidereal Time, and the Equation of the Equinoxes.Julian Date can be converted to calendar date, either Julian or Gregorian as appropriate, for any date between JD 0 (January 1, 4713 BCE proleptic Julian) and JD 5373484 (December 31, 9999 CE Gregorian); the reverse calendar date to Julian Date conversion is also available. The calendar date and Julian Date are returned for all API requests; the day of the week is also returned for Julian Date to calendar date conversions.On-line documentation for using all USNO API-enabled calculators, including sample calls, is available (http://aa.usno.navy.mil/data/docs/api.php).For those who prefer using traditional data input forms, Sidereal Time can still be accessed at http://aa.usno.navy.mil/data/docs/siderealtime.php, and the Julian Date Converter at http://aa.usno.navy.mil/data/docs/JulianDate.php.

  4. Identification of CR1 retroposons in Arborophila rufipectus and their application to Phasianidae phylogeny.

    PubMed

    Cui, Yaoyao; Yan, Chaochao; Sun, Tianlin; Li, Jing; Yue, Bisong; Zhang, Xiuyue; Li, Jing

    2016-07-01

    Chicken repeat 1 (CR1), a member of non-LTR retroposon, is an important phylogenetic marker in avian systematics. In this study, we reported several characteristics of CR1 elements in a draft genome of Arborophila rufipectus (Sichuan partridge). According to the analyses of RepeatMasker, approximately 254 966 CR1 elements were identified in A. rufipectus, covering 6.7% of the genome. Subsequently, we selected eighteen novel CR1 elements by comparing the chicken genome, turkey genome and assembled A. rufipectus scaffolds. Here, a combined data set comprising of 22 CR1 loci, mitochondrial genomes and eight unlinked introns was analysed to infer the evolutionary relationships of twelve Phasianidae species. The applicability of CR1 sequences for inferring avian phylogeny relative to mtDNA and intron sequences was investigated as well. Our results elucidated the position of A. rufipectus in Phasianidae with robust supports that it presented a sister clade to Arborophila ardens/Arborophila brunneopectus, and implied that genus Arborophila was in a basal phylogenetic position within Phasianidae and a phylogenetic affinity between Meleagris gallopavo and Pucrasia macrolopha. Therefore, this work not only resolved some of the confounding relationships among Phasianidae, but also suggested CR1 sequences could provide powerful complementary data for phylogeny reconstruction.

  5. Testis-specific expression of a functional retroposon encoding glucose-6-phosphate dehydrogenase in the mouse

    SciTech Connect

    Hendriksen, P.J.M. |; Hoogerbrugge, J.W.; Baarends, W.M.

    1997-05-01

    The X-chromosomal gene glucose-6-phosphate dehydrogenase (G6pd) is known to be expressed in most cell types of mammalian species. In the mouse, we have detected a novel gene, designated G6pd-2, encoding a G6PD isoenzyme. G6pd-2 does not contain introns and appears to represent a retroposed gene. This gene is uniquely transcribed in postmeiotic spermatogenic cells in which the X-encoded G6pd gene is not transcribed. Expression of the G6pd-2 sequence in a bacterial system showed that the encoded product is an active enzyme. Zymogramic analysis demonstrated that recombinant G6PD-2, but not recombinant G6PD-1 (the X-chromosome-encoded G6PD), formed tetramers under reducing conditions. Under the same conditions, G6PD tetramers were also found in extracts of spermatids and spermatozoa, indicating the presence of G6pd-2-encoded isoenzyme in these cell types. G6pd-2 is one of the very few known expressed retroposons encoding a functional protein, and the presence of this gene is probably related to X chromosome inactivation during spermatogenesis. 62 refs., 7 figs.

  6. Dataset for distribution of SIDER2 elements in the Leishmania major genome and transcriptome.

    PubMed

    Requena, Jose M; Rastrojo, Alberto; Garde, Esther; López, Manuel C; Thomas, M Carmen; Aguado, Begoña

    2017-04-01

    This paper contains data related to the research article entitled "Genomic cartography and proposal of nomenclature for the repeated, interspersed elements of the Leishmania major SIDER2 family and identification of SIDER2-containing transcripts" [1]. SIDER2 elements are repeated sequences, derived from, nowadays, extinct retrotransposons, that populate the genomes of protist of the genera Leishmania. This dataset (Supplementary file 1), an inventory of 1100 SIDER2 elements, was generated by surveying the L. major complete genome using bioinformatics tools with further manual refinements. In addition to the genomic distribution of these elements (summarized in Fig. 1), this dataset contains information regarding their association with specific transcripts, based on the recently established transcriptome for L. major[2].

  7. Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data.

    PubMed

    Kuritzin, Andrej; Kischka, Tabea; Schmitz, Jürgen; Churakov, Gennady

    2016-03-01

    Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p<0.05) for the branching of the third from the other two, if all three of the given species are screened equally for genome or experimental data. Five elements are necessary for significant support (p<0.05) if a diagnostic locus derived from only one of three species is screened, and no conflicting markers are detected. Most potentially conflicting patterns can be evaluated for their significance and ancestral hybridization can be distinguished from incomplete lineage sorting by considering symmetric or asymmetric distribution of rare genomic changes among possible tree configurations. Additionally, we provide an R-application to make the new KKSC insertion significance test available for the scientific

  8. Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

    PubMed Central

    Kuritzin, Andrej; Kischka, Tabea

    2016-01-01

    Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p<0.05) for the branching of the third from the other two, if all three of the given species are screened equally for genome or experimental data. Five elements are necessary for significant support (p<0.05) if a diagnostic locus derived from only one of three species is screened, and no conflicting markers are detected. Most potentially conflicting patterns can be evaluated for their significance and ancestral hybridization can be distinguished from incomplete lineage sorting by considering symmetric or asymmetric distribution of rare genomic changes among possible tree configurations. Additionally, we provide an R-application to make the new KKSC insertion significance test available for the scientific

  9. A distal enhancer and an ultraconserved exon are derived from a novel retroposon.

    PubMed

    Bejerano, Gill; Lowe, Craig B; Ahituv, Nadav; King, Bryan; Siepel, Adam; Salama, Sofie R; Rubin, Edward M; Kent, W James; Haussler, David

    2006-05-04

    Hundreds of highly conserved distal cis-regulatory elements have been characterized so far in vertebrate genomes. Many thousands more are predicted on the basis of comparative genomics. However, in stark contrast to the genes that they regulate, in invertebrates virtually none of these regions can be traced by using sequence similarity, leaving their evolutionary origins obscure. Here we show that a class of conserved, primarily non-coding regions in tetrapods originated from a previously unknown short interspersed repetitive element (SINE) retroposon family that was active in the Sarcopterygii (lobe-finned fishes and terrestrial vertebrates) in the Silurian period at least 410 million years ago (ref. 4), and seems to be recently active in the 'living fossil' Indonesian coelacanth, Latimeria menadoensis. Using a mouse enhancer assay we show that one copy, 0.5 million bases from the neuro-developmental gene ISL1, is an enhancer that recapitulates multiple aspects of Isl1 expression patterns. Several other copies represent new, possibly regulatory, alternatively spliced exons in the middle of pre-existing Sarcopterygian genes. One of these, a more than 200-base-pair ultraconserved region, 100% identical in mammals, and 80% identical to the coelacanth SINE, contains a 31-amino-acid-residue alternatively spliced exon of the messenger RNA processing gene PCBP2 (ref. 6). These add to a growing list of examples in which relics of transposable elements have acquired a function that serves their host, a process termed 'exaptation', and provide an origin for at least some of the many highly conserved vertebrate-specific genomic sequences.

  10. [First open reading frame protein (ORF1p) of the Blattella germanica R1 retroposon and phylogenetically close GAG-like proteins of insects and fungi contain RRM domains].

    PubMed

    Kapelinskaia, T V; Kagramanova, A S; Korolev, A L; Mukha, D V

    2011-02-01

    The rDNA locus of insects and other arthropods contains non-LTR retrotransposons (retroposons) that are specifically inserted into 28S rRNA genes. The most frequent retroposons are R1 and R2, but the mechanism of insertion and the functions of these mobile elements have not been studied in detail. A clone containing a full-length R1 retroposon copy was islated from the cosmid library of Blattella germanica genes and sequenced. The amino acid sequences encoded by ORF1 of the R1 retroposon were subjected to bioinformatic analysis. It was found that ORF1 of this mobile element encodes a protein (ORF1p) belonging to the superfamily of zinc finger (CCHC) retroviral nucleocapsid proteins and contains two conserved RRM domains (RNA-recognizing motifs) identified on the basis of analysis of the secondary structure of this protein. The discovery of RRM domains in ORF1p of R1 retroposons can contribute to the understanding of the mechanisms of their retrotransposition. We revealed a coiled-coil motif in the N-terminal region of R1 ORF1p, which is similar to the coiled-coil domain involved in homo- or heteromultimerization of proteins and in protein-protein interactions. The domain organization of homologous Gag-like proteins of retroposons in some insects and fungi was found to be similar to the structure established by us for R1 ORF1p of B. germanica.

  11. Cosmic ray sidereal diurnal variation of galactic origin observed by neutron monitors

    NASA Technical Reports Server (NTRS)

    Ishida, Y.; Nagashima, K.; Mori, S.; Morishita, I.

    1985-01-01

    Cosmic ray sidereal diurnal variations observed by neutron monitors are analyzed for the period 1961 to 1978, by adding 134 station years data to the previous paper (Nagashima, et al., 1983). Also the dependence of the sidereal variations on Sun's polar magnetic field polarity is examined for two periods; the period of negative polarity in the northern region, 1961 to 1969 and the period of positive polarity, 1970 to 1978. It is obtained that for the former period, the amplitude A=0.0203 + or 0.0020% and the phase phi=6.1 + or - 0.4 h LST and for the latter period, 0.0020% and phi=8.6 + or - 4 h LST, respectively.

  12. Traditional uses, chemical composition and biological activities of Sideritis raeseri Boiss. & Heldr.

    PubMed

    Romanucci, Valeria; Di Fabio, Giovanni; D'Alonzo, Daniele; Guaragna, Annalisa; Scapagnini, Giovanni; Zarrelli, Armando

    2017-01-01

    Sideritis species have been used in folk medicine for their antimicrobial, antiulcerogenic, digestive and anti-inflammatory properties. Over the years, the phytochemistry of the genus Sideritis has been studied, and various terpenoids, sterols, coumarins and especially flavonoid aglycones and glycosides have been identified. In particular, species from the Balkan Peninsula have been studied and were found to be rich in flavonoids, with valuable antioxidant activity. In the folk medicine of the Balkan countries, Sideritis raeseri is used as a herbal tea in the treatment of inflammation, gastrointestinal disorders and coughs, and also as a tonic, whereas extracts are used as a component of dietary supplements for anaemia. Its dried inflorescences are used to prepare a beverage called 'mountain tea'. In light of the considerable interest generated in the chemistry, pharmacological properties and commercial value of S. raeseri Boiss. & Heldr., we review and summarise the available literature on these plants. The review details the chemical composition of the essential oil, its mineral and polyphenol contents, the naming of these plants and their physicochemical characterisation, and the nuclear magnetic resonance spectral data and biological properties associated with the plant extracts, with a focus on their potential chemotherapeutic applications. © 2016 Society of Chemical Industry.

  13. An Enhancer Near ISL1 and an Ultraconserved Exon of PCBP2 areDerived from a Retroposon

    SciTech Connect

    Bejerano, Gill; Lowe, Craig; Ahituv, Nadav; King, Bryan; Siepel,Adam; Salama, Sofie; Rubin, Edward M.; Kent, W. James; Haussler, David

    2005-11-27

    Hundreds of highly conserved distal cis-regulatory elementshave been characterized to date in vertebrate genomes1. Many thousandsmore are predicted based on comparative genomics2,3. Yet, in starkcontrast to the genes they regulate, virtually none of these regions canbe traced using sequence similarity in invertebrates, leaving theirevolutionary origin obscure. Here we show that a class of conserved,primarily non-coding regions in tetrapods originated from a novel shortinterspersed repetitive element (SINE) retroposon family that was activein Sarcopterygii (lobe-finned fishes and terrestrial vertebrates) in theSilurian at least 410 Mya4, and, remarkably, appears to be recentlyactive in the "living fossil" Indonesian coelacanth, Latimeriamenadoensis. We show that one copy is a distal enhancer, located 500kbfrom the neuro-developmental gene ISL1. Several others represent new,possibly regulatory, alternatively spliced exons in the middle ofpre-existing Sarcopterygian genes. One of these is the>200bpultraconserved region5, 100 percent identical in mammals, and 80 percentidentical to the coelacanth SINE, that contains a 31aa alternativelyspliced exon of the mRNA processing gene PCBP26. These add to a growinglist of examples7 in which relics of transposable elements have acquireda function that serves their host, a process termed "exaptation"8, andprovide an origin for at least some of the highly-conservedvertebrate-specific genomic sequences recently discovered usingcomparative genomics.

  14. Expression of the woodchuck N-myc2 retroposon in brain and in liver tumors is driven by a cryptic N-myc promoter.

    PubMed Central

    Fourel, G; Transy, C; Tennant, B C; Buendia, M A

    1992-01-01

    The woodchuck intronless proto-oncogene N-myc2 was initially discovered as a frequent target site for hepadnavirus integration in hepatocellular carcinoma. N-myc2 possesses characteristics of a functional retroposon derived from the woodchuck N-myc gene. We have investigated the regulatory signals governing N-myc2 expression and found that a short promoter, including a variant TATA box and potential binding sites for several transcription factors, is localized in the N-myc2 sequences homologous to the 5' untranslated region of the second N-myc exon. The corresponding region in the intron-containing woodchuck N-myc gene also exhibited promoter activity in transient transfection assays. The high evolutionary conservation of these sequences in mammalian N-myc genes suggests that they contain a cryptic N-myc promoter which may be unmasked in the particular context provided by the N-myc2 retroposon. Although N-myc2, like the woodchuck N-myc gene, contributes to an extended CpG island and was found constitutively hypomethylated, it presents a highly restricted expression pattern in adult animals. Whereas the intron-containing N-myc gene is expressed at low levels in different tissues, N-myc2 mRNA was detected only in brain tissue, raising questions about the functional significance of the maintenance of a second N-myc gene in the woodchuck genome. Images PMID:1333041

  15. Search for a Lorentz-violating sidereal signal with atmospheric neutrinos in IceCube

    SciTech Connect

    IceCube; etal, Abbasi, R,

    2010-11-11

    A search for sidereal modulation in the flux of atmospheric muon neutrinos in IceCube was performed. Such a signal could be an indication of Lorentz-violating physics. Neutrino oscillationmodels, derivable from extensions to the Standard Model, allow for neutrino oscillations that depend on the neutrino's direction of propagation. No such direction-dependent variation was found. Adiscrete Fourier transform method was used to constrain the Lorentz and CPT-violating coefficients in one of these models. Due to the unique high energy reach of IceCube, it was possible to improveconstraints on certain Lorentz-violating oscillations by three orders of magnitude with respect to limits set by other experiments.

  16. Cladistic analysis of Subfamily Bruchomyiinae (Diptera: Psychodidae).

    PubMed

    Wagner, Rüdiger; Stuckenberg, Brian

    2016-03-15

    Subfamily Bruchomyiinae is comprised of 60 species and has been referred to as the most primitive within the Psychodidae. The assumed sister-group relationship with Phlebotominae is based on ecological constraints of their environment. A cladistics analysis based on 29 characters and 52 species revealed the distinction of an Old World clade characterized by males with elongate, narrow vasa deferentia, and a New World clade with males having shorter and basally widened vasa deferentia. The Old World clade consists of the genera Nemopalpus Macquart (9 species), and Eutonnoiria Alexander (1 species). The New World clade includes Bruchomyia Alexander (10 species), Boreofairchildia genus nov. (13 species), Laurenceomyia genus nov. (5 species), and Notofairchildia genus nov. (15 species). Parsimony and Bayesian analyses resulted in trees that generally support this generic classification; however, with some species groups less resolved. Diagnostic features for genera are provided. In contrast to the other New World genera, Notofairchildia is paraphyletic with the provisional inclusion of at least the Australasian taxa.

  17. Antibacterial and antioxidant activities in Sideritis italica (Miller) Greuter et Burdet essential oils.

    PubMed

    Basile, Adriana; Senatore, Felice; Gargano, Rosalba; Sorbo, Sergio; Del Pezzo, Marisa; Lavitola, Alfredo; Ritieni, Alberto; Bruno, Maurizio; Spatuzzi, Daniela; Rigano, Daniela; Vuotto, Maria Luisa

    2006-09-19

    Sideritis italica (Miller) Greuter et Burdet is a widespread Lamiacea in the Mediterranean region used in traditional medicine. Essential oils were antibacterial against nine ATCC and as many clinically isolated Gram-positive and Gram-negative bacterial strains. Antibacterial activity was also found against Helicobacter pylori: a dose-dependant inhibition was shown between 5 and 25 microg/ml. The antibacterial activity of the oils was expressed as MICs (minimum inhibitory concentrations) and MBCs (minimum bactericidal concentrations). At a concentration between 3.9 and 250 microg/ml the oils showed a significant antibacterial effect against both Gram-negative and Gram-positive bacteria. In particular the ATCC strains Pseudomonas aeruginosa (MIC=3.9 microg/ml and 7.8 for flowerheads and leaves, respectively), Proteus mirabilis (MIC=15.6 and 7.8 microg/ml), Salmonella typhi (MIC=7.8 microg/ml) and Proteus vulgaris (MIC=15.6 microg/ml) were the most inhibited. Only Pseudomonas aeruginosa showed MBC at a concentration between 62.6 and 125 microg/ml. The antioxidant activity of the essential oils was evaluated by two cell free colorimetric methods: ABTS and DMPD; leaf oil is more active (4.29 +/- 0.02 trolox equivalents and 4.53 +/- 0.67 ascorbic acid equivalents by ABTS and DMPD, respectively). Finally the antioxidant activity of the essential oils was also evaluated by their effects on human whole blood leukocytes (WB) and on isolated polymorphonucleate (PMN) chemiluminescence. Comparing the effects of the oils from leaves and flowerheads on both PMN and WB chemiluminescence emission, we found no significant differences. Essential oils showed a dose-dependent and linear inhibitory activity on isolated PMN as well as on WB CL emission when PMA-stimulated. On the contrary, the inhibitory activity on resting cells was nonlinear. Our data represent an answer to the continual demand for new antibiotics and antioxidants for the continuous emergence of antibiotic

  18. The structural biology of the FGF19 subfamily.

    PubMed

    Beenken, Andrew; Mohammadi, Moosa

    2012-01-01

    The ability of the Fibroblast Growth Factor (FGF) 19 subfamily to signal in an endocrine fashion sets this subfamily apart from the remaining five FGF subfamilies known for their paracrine functions during embryonic development. Compared to the members of paracrine FGF subfamiles, the three members of the FGF19 subfamily, namely FGF19, FGF21 and FGF23, have poor affinity for heparan sulfate (HS) and therefore can diffuse freely in the HS-rich extracellular matrix to enter into the bloodstream. In further contrast to paracrine FGFs, FGF19 subfamily members have unusually poor affinity for their cognate FGF receptors (FGFRs) and therefore cannot bind and activate them in a solely HS-dependent fashion. As a result, the FGF19 subfamily requires α/βklotho coreceptor proteins in order to bind, dimerize and activate their cognate FGFRs. This klotho-dependency also determines the tissue specificity of endocrine FGFs. Recent structural and biochemical studies have begun to shed light onto the molecular basis for the klotho-dependent endocrine mode of action of the FGF19 subfamily. Crystal structures of FGF19 and FGF23 show that the topology of the HS binding site (HBS) of FGF19 subfamily members deviates drastically from the common topology adopted by the paracrine FGFs. The distinct topologies of the HBS of FGF19 and FGF23 prevent HS from direct hydrogen bonding with the backbone atoms of the HBS of these ligands and accordingly decrease the HS binding affinity of this subfamily. Recent biochemical data reveal that the ?klotho ectodomain binds avidly to the ectodomain of FGFR1c, the main cognate FGFR of FGF23, creating a de novo high affinity binding site for the C-terminal tail of FGF23. The isolated FGF23 C-terminus can be used to effectively inhibit the formation of the FGF23-FGFR1c-αklotho complex and alleviate hypophosphatemia in renal phosphate disorders due to elevated levels of FGF23.

  19. The sidereal anisotropy of cosmic rays around 3 x 10 (15) eV observed at a middle north latitude

    NASA Technical Reports Server (NTRS)

    Murakami, K.; Kifune, T.; Hayashida, N.

    1985-01-01

    The sidereal time variation of cosmic rays (median primary energy : 3 10 to the 15th power eV) is investigated with air shower observations at Akeno, Japan (900 m a.s.l.) which started in September 1981. Air showers are detected by a coincidence requirement on several muon detectors. The result obtained for three years is suggestive of a big semi-diurnal variation (0.37 % in amplitude). On the other hand, the diurnal variation is rather small than the semi-diurnal one. The feature of the sidereal anisotropy supposed from the present result looks quite different from that below 10 to the 14th power eV.

  20. Variability in the essential-oil composition of Sideritis scardica GRISEB. from native Bulgarian populations.

    PubMed

    Trendafilova, Antoaneta B; Todorova, Milka N; Evstatieva, Ljuba N; Antonova, Daniela V

    2013-03-01

    The essential-oil composition of six native populations of Sideritis scardica from Bulgaria was studied by GC-FID and GC/MS analyses. Altogether, 37 components, representing 73.1 to 79.2% of the total oil content were identified. Among them, α-pinene (4.4-25.1%), β-pinene (2.8-18.0%), oct-1-en-3-ol (2.3-8.0%), phenylacetaldehyde (0.5-9.5%), β-bisabolene (1.3-11.0%), benzyl benzoate (1.1-14.3%), and m-camphorene (1; 0.3-12.4%) were the main compounds. All samples were characterized by low contents of oxygenated mono- and sesquiterpenes (≤1.6 and 2.3%, resp.). Principal component analysis (PCA) and cluster analysis (CA) showed a significant variability in the chemical composition of the studied samples as well as a correlation between the oil profiles and the ecological conditions of the natural habitats of S. scardica.

  1. Annual dormancy cycles in buried seeds of shrub species: germination ecology of Sideritis serrata (Labiatae).

    PubMed

    Copete, M A; Herranz, J M; Ferrandis, P; Copete, E

    2015-07-01

    The germination ecology of Sideritis serrata was investigated in order to improve ex-situ propagation techniques and management of their habitat. Specifically, we analysed: (i) influence of temperature, light conditions and seed age on germination patterns; (ii) phenology of germination; (iii) germinative response of buried seeds to seasonal temperature changes; (iv) temperature requirements for induction and breaking of secondary dormancy; (v) ability to form persistent soil seed banks; and (vi) seed bank dynamics. Freshly matured seeds showed conditional physiological dormancy, germinating at low and cool temperatures but not at high ones (28/14 and 32/18 °C). Germination ability increased with time of dry storage, suggesting the existence of non-deep physiological dormancy. Under unheated shade-house conditions, germination was concentrated in the first autumn. S. serrata seeds buried and exposed to natural seasonal temperature variations in the shade-house, exhibited an annual conditional dormancy/non-dormancy cycle, coming out of conditional dormancy in summer and re-entering it in winter. Non-dormant seeds were clearly induced into dormancy when stratified at 5 or 15/4 °C for 8 weeks. Dormant seeds, stratified at 28/14 or 32/18 °C for 16 weeks, became non-dormant if they were subsequently incubated over a temperature range from 15/4 to 32/18 °C. S. serrata is able to form small persistent soil seed banks. The maximum seed life span in the soil was 4 years, decreasing with burial depth. This is the second report of an annual conditional dormancy/non-dormancy cycle in seeds of shrub species.

  2. Aroma compounds of mountain tea (Sideritis scardica and S. raeseri) from western Balkan.

    PubMed

    Qazimi, Bujar; Stefkov, Gjoshe; Karapandzova, Marija; Cvetkovikj, Ivana; Kulevanova, Svetlana

    2014-09-01

    The composition of the volatile aroma components was defined in the dried and fresh aerial parts of Sideritis scardica Griseb. from R. Macedonia and S. raeseri Boiss. & Heldr. from R. Macedonia, Albania and Greece. Analysis was made by gas chromatography (GC/FID/MS) equipped with a headspace (HS) sampler. Thirty-two components (15 monoterpenes representing 33.2- 62.8% and 17 sesquiterpenes representing 25.2- 51.2% of the entire volatiles) were identified as aroma components of dried plant material of S. scardica. Thirty components {14 monoterpenes (19.3-74.2%), 2 alcohols (6.2- 38.4%) and 14 sesquiterpenes (18.2- 33.5%)} were identified as aroma components in the fresh aerial parts of S. scardica. The predominant components were trans-caryophyllene, β-pinene, α-pinene and 1-octen-3-ol, which were found only in the fresh samples. In the aerial parts of S. rteseri, 43 components were identified in the dried samples {22 monoterpenes (65.7-94.3%) and 21 sesquiterpenes (5.4- 27.8%)} and 29 components {15 monoterpenes (77.3-90.7%) and 14 sesquiterpenes (6.3- 18.2%)} in the respective fresh samples. Prevailing components in all tested samples of S. raeseri were β-pinene, α-pinene, α-copaene, sabinene and limonene. Only minor differences were revealed in the qualitative composition of the aroma volatiles between the dried and fresh plant material of both species. Furthermore there was almost no difference in the chemical profiles of the aroma compounds between S. scardica and S. raeseri, except for 1- octen-3-ol, which was present only in fresh S. scardica.

  3. Anti-inflammatory, gastroprotective, and cytotoxic effects of Sideritis scardica extracts.

    PubMed

    Tadić, Vanja M; Jeremic, Ivica; Dobric, Silva; Isakovic, Aleksandra; Markovic, Ivanka; Trajkovic, Vladimir; Bojovic, Dragica; Arsic, Ivana

    2012-03-01

    Sideritis scardica Griseb. (ironwort, mountain tea), an endemic plant of the Balkan Peninsula, has been used in traditional medicine in the treatment of gastrointestinal complaints, inflammation, and rheumatic disorders. This study aimed to evaluate its gastroprotective and anti-inflammatory activities. Besides, continuously increasing interest in assessing the role of the plant active constituents preventing the risk of cancer was a reason to make a detailed examination of the investigated ethanol, diethyl ether, ethyl acetate, and N-butanol extracts regarding cytotoxicity. Oral administration of the investigated extracts caused a dose-dependent anti-inflammatory effect in a model of carrageenan-induced rat paw edema. Gastroprotective activity of the extracts was investigated using an ethanol-induced acute stress ulcer in rats. The cytotoxic activity of plant extracts was assessed on PBMC, B16, and HL-60 cells and compared to the cytotoxicity of phenolic compounds identified in extracts. Apoptotic and necrotic cell death were analyzed by double staining with fluoresceinisothiocyanate (FITC)-conjugated annexin V and PI. The developed HPLC method enabled qualitative fingerprint analysis of phenolic compounds in the investigated extracts. Compared to the effect of the positive control, the anti-inflammatory drug indomethacine (4 mg/kg), which produced a 50 % decrease in inflammation, diethyl ether and N-butanol extracts exhibited about the same effect in doses of 200 and 100 mg/kg (53.6 and 48.7 %; 48.4 and 49.9 %, respectively). All investigated extracts produced dose-dependent gastroprotective activity with the efficacy comparable to that of the reference drug ranitidine. The diethyl ether extract showed significant dose-dependent cytotoxicity on B16 cells and HL-60 cells, decreasing cell growth to 51.3 % and 77.5 % of control, respectively, when used at 100 µg/mL. It seems that phenolic compounds (apigenin, luteolin, and their corresponding glycosides) are

  4. Rit Subfamily Small GTPases: Regulators in Neuronal Differentiation and Survival

    PubMed Central

    Shi, Geng-Xian; Cai, Weikang; Andres, Douglas A.

    2013-01-01

    Ras family small GTPases serve as binary molecular switches to regulate a broad array of cellular signaling cascades, playing essential roles in a vast range of normal physiological processes, with dysregulation of numerous Ras-superfamily G-protein-dependent regulatory cascades underlying the development of human disease. However, the physiological function for many “orphan” Ras-related GTPases remain poorly characterized, including members of the Rit subfamily GTPases. Rit is the founding member of a novel branch of the Ras subfamily, sharing close homology with the neuronally expressed Rin and Drosophila Ric GTPases. Here, we highlight recent studies using transgenic and knockout animal models which have begun to elucidate the physiological roles for the Rit subfamily, including emerging roles in the regulation of neuronal morphology and cellular survival signaling, and discuss new genetic data implicating Rit and Rin signaling in disorders such as cancer, Parkinson’s disease, autism, and schizophrenia. PMID:23770287

  5. A review of the subfamily Rogadinae (Hymenoptera: Braconidae) from Iran.

    PubMed

    Farahani, Samira; Talebi, Ali Asghar; Achterberg, Cornelis Van; Rakhshani, Ehsan

    2015-06-17

    Specimens of the subfamily Rogadinae (Hymenoptera: Braconidae) were collected in northern Iran during 2010-2011 with a series of Malaise traps. Twelve species belonging to three genera (Aleiodes Wesmael, 1838, Heterogamus Wesmael, 1838 and Clinocentrus Haliday, 1833) were identified, with one genus (Heterogamus) and seven species new for the fauna of Iran. An updated checklist of the genera and species of the subfamily Rogadinae is included. A total of 26 species belonging to four genera are listed for Iran after correction for misidentifications. A key to the genera and the species of Rogadinae known from Iran is provided.

  6. First molecular phylogeny of the subfamily Polycerinae (Mollusca, Nudibranchia, Polyceridae)

    NASA Astrophysics Data System (ADS)

    Palomar, Gemma; Pola, Marta; Garcia-Vazquez, Eva

    2014-03-01

    The subfamily Polycerinae includes four genera with around 46 species described to date. This subfamily is characterized by a limaciform body, which may have simple tentacular processes on the margin of the oral veil. Phylogenetic relationships between the genera of the subfamily Polycerinae (Polyceridae) have not yet been studied, and therefore, the only available information is based on morphological descriptions. The present study reports the first phylogenetic analysis of Polycerinae based on the mitochondrial genes cytochrome oxidase subunit I and the large ribosomal subunit (16S rRNA) using maximum likelihood and Bayesian methods. Our results showed that Polycerinae is monophyletic, but the relationships within the subfamily as well as within Polycera remain unresolved. A key finding of this study is that there are clearly two sympatric species of Polycera present in South Africa: Polycera capensis Quoy and Gaimard, 1824 also found in Australia and an undescribed Polycera sp. On the other hand, the studied specimens of the genus Gymnodoris were clustered within Polycerinae, reopening the problem of the systematic position of this genus. Additional genes and species of Polycerinae and Gymnodoris would provide more information and probably fully resolve this situation.

  7. The LZT proteins; the LIV-1 subfamily of zinc transporters.

    PubMed

    Taylor, Kathryn M; Nicholson, Robert I

    2003-04-01

    Zinc is an essential ion for cells with a vital role to play in controlling the cellular processes of the cell, such as growth, development and differentiation. Specialist proteins called zinc transporters control the level of intracellular zinc in cells. In mammals, the ZIP family of zinc transporters has a pivotal role in maintaining the correct level of intracellular zinc by their ability to transport zinc into cells from outside, although they may also transport metal ions other than zinc. There are now recognised to be four subfamilies of the ZIP transporters, including the recently discovered LIV-1 subfamily which has similarity to the oestrogen-regulated gene LIV-1, previously implicated in metastatic breast cancer. We call this new subfamily LZT, for LIV-1 subfamily of ZIP zinc Transporters. Here we document current knowledge of this previously uncharacterised group of proteins, which includes the KE4 proteins. LZT proteins are similar to ZIP transporters in secondary structure and ability to transport metal ions across the plasma membrane or intracellular membranes. However, LZT proteins have a unique motif (HEXPHEXGD) with conserved proline and glutamic acid residues, unprecedented in other zinc transporters. The localisation of LZT proteins to lamellipodiae mirrors cellular location of the membrane-type matrix metalloproteases. These differences to other zinc transporters may be consistent with an alternative role for LZT proteins in cells, particularly in diseases such as cancer.

  8. Sideritis spp. Extracts Enhance Memory and Learning in Alzheimer’s β-Amyloidosis Mouse Models and Aged C57Bl/6 Mice

    PubMed Central

    Hofrichter, Jacqueline; Krohn, Markus; Schumacher, Toni; Lange, Cathleen; Feistel, Bjöorn; Walbroel, Bernd; Pahnke, Jens

    2016-01-01

    Nowadays, Alzheimer’s disease is the most prevalent epiphenomenon of the aging population. Although soluble amyloid-β (Aβ) species (monomers, oligomers) are recognized triggers of the disease, no therapeutic approach is able to stop it. Herbal medicines are used to treat different diseases in many regions of the world. On the Balkan Peninsula, at the eastern Mediterranean Sea, and adjacent regions, Sideritis species are used as traditional medicine to prevent age-related problems in elderly. To evaluate this traditional knowledge in controlled experiments, we tested extracts of two commonly used Sideritis species, Sideritis euboea and Sideritis scardica, with regard to their effects on cognition in APP-transgenic and aged, non-transgenic C57Bl/6 mice. Additionally, histomorphological and biochemical changes associated with Aβ deposition and treatment were assessed. We found that daily oral treatment with Sideritis spp. extracts highly enhanced cognition in aged, non-transgenic as well as in APP-transgenic mice, an effect that was even more pronounced when extracts of both species were applied in combination. The treatment strongly reduced Aβ42 load in APP-transgenic mice, accompanied by increased phagocytic activity of microglia, and increased expression of the α-secretase ADAM10. Moreover, the treatment was able to fully rescue neuronal loss of APP-transgenic mice to normal levels as seen in non-transgenic controls. Having the traditional knowledge in mind, our results imply that treatment with Sideritis spp. extracts might be a potent, well-tolerated option for treating symptoms of cognitive impairment in elderly and with regard to Alzheimer’s disease by affecting its most prominent hallmarks: Aβ pathology and cognitive decline. PMID:27258424

  9. The mechanisms of in vitro cytotoxicity of mountain tea, Sideritis scardica, against the C6 glioma cell line.

    PubMed

    Jeremic, Ivica; Tadic, Vanja; Isakovic, Andjelka; Trajkovic, Vladimir; Markovic, Ivanka; Redzic, Zoran; Isakovic, Aleksandra

    2013-11-01

    Sideritis scardica (mountain tea) is an endemic plant on the Balkan Peninsula traditionally used for treating different conditions, mainly of inflammatory nature. This study was aimed to examine the cytotoxic activity of different S. scardica extracts against the rat glioma C6 line and rat astrocytes in primary culture. The obtained data revealed that diethyl ether (extract 2) and ethyl acetate (extract 3) extracts of S. scardica exerted a cytotoxic effect on C6 rat glioma cells. Diethyl ether extract induced an increase in reactive oxygen species production, leading to apoptotic and autophagic cell death. Ethyl acetate extract induced G2 M cell cycle arrest and autophagy. None of the tested extracts was cytotoxic to rat astrocytes in primary culture. Cytotoxic effects of S. scardica extracts were, at least in part, mediated by their flavonoid constituents apigenin and luteolin that, when applied alone, induced cell cycle arrest, apoptosis, and autophagy.

  10. Sidereal time analysis as a tool for detection of gravitational and neutrino signals from the core-collapse SN explosions in the inhomogeneous Local Universe

    NASA Astrophysics Data System (ADS)

    Baryshev, Yu. V.; Paturel, G.; Sokolov, V. V.

    2016-06-01

    The core-collapse supernova explosion produces both neutrino and gravitational wave (tensor-transversal plus possible scalar-longitudinal) bursts. In the case of GW detectors, which have low angular resolution, the method of sidereal time analysis of output signals was applied for extraction of GW signals from high level noise. This method was suggested by Joseph Weber in 1970 for analysis of signals from his bar detector and later was developed for existing bar and interferometric GW detectors. The same sidereal time approach can be also used for low energy neutrino detectors which have many years of observational time (e.g. Super-Kamiokande, LVD, Baksan). This method is based on: 1) difference between sidereal and mean solar time (which help to delete noises related to day-night solar time), 2) directivity diagram (antenna pattern) of a detector (which chooses a particular sky region in a particular sidereal time), and 3) known position on the sky of spatial inhomogeneities of GW and neutrino sources in the Local Universe (distances less than 100 Mpc), such as the Galactic plane, the Galaxy center, closest galaxies, the Virgo galaxy cluster, the Super-galactic plane, the Great Attractor.

  11. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae).

    PubMed

    Comer, Jason R; Zomlefer, Wendy B; Barrett, Craig F; Stevenson, Dennis Wm; Heyduk, Karolina; Leebens-Mack, James H

    2016-04-01

    Palms (Arecaceae) include economically important species such as coconut, date palm, and oil palm. Resolution of the palm phylogeny has been problematic due to rapid diversification and slow rates of molecular evolution. The focus of this study is on relationships of the 14 tribes of subfamily Arecoideae and their inferred ancestral areas. A targeted sequencing approach was used to generate a data set of 168 single/low copy nuclear genes for 34 species representing the Arecoideae tribes and the other palm subfamilies. Species trees from the concatenated and coalescent based analyses recovered largely congruent topologies. Three major tribal clades were recovered: the POS clade (Podococceae, Oranieae, Sclerospermeae), the RRC clade (Roystoneeae, Reinhardtieae, Cocoseae), and the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae, Pelagodoxeae). Leopoldinieae was sister to the rest of the core arecoids (Geonomateae, Manicarieae+Pelagodoxeae, and Areceae+Euterpeae). The nuclear phylogeny supported a North American origin for subfamily Arecoideae, with most tribal progenitors diversifying within the Americas. The POS clade may have dispersed from the Americas into Africa, with tribe Oranieae subsequently spreading into the Indo-Pacific. Two independent dispersals into the Indo-Pacific were inferred for two tribes within the core arecoids (tribes Areceae and Pelagodoxeae).

  12. Cytogenetics and genome evolution in the subfamily Triatominae (Hemiptera, Reduviidae).

    PubMed

    Panzera, F; Pérez, R; Panzera, Y; Ferrandis, I; Ferreiro, M J; Calleros, L

    2010-01-01

    The subfamily Triatominae (Hemiptera, Reduviidae), vectors of Chagas disease, includes over 140 species. Karyotypic information is currently available for 80 of these species. This paper summarizes the chromosomal variability of the subfamily and how it may reveal aspects of genome evolution in this group. The Triatominae present a highly conserved chromosome number. All species, except 3, present 20 autosomes. The differences in chromosome number are mainly caused by variation in the number of sex chromosomes, due to the existence of 3 sex systems in males (XY, X(1)X(2)Y and X(1)X(2)X(3)Y). However, inter- and intraspecific differences in the position, quantity and meiotic behavior of constitutive heterochromatin, in the total genome size, and in the location of ribosomal 45S rRNA clusters, have revealed considerable cytogenetic variability within the subfamily. This cytogenetic diversity offers the opportunity to perform cytotaxonomic and phylogenetic studies, as well as structural, evolutionary, and functional analyses of the genome. The imminent availability of the complete genome of Rhodnius prolixus also opens new perspectives for understanding the evolution and genome expression of triatomines. The application of fluorescence in situ hybridization for the mapping of genes and sequences, as well as comparative analyses of genome homology by comparative genomic hybridization will be useful tools for understanding the genomic changes in relation to evolutionary processes such as speciation and adaptation to different environments.

  13. Generic revision of the ant subfamily Dorylinae (Hymenoptera, Formicidae)

    PubMed Central

    Borowiec, Marek L.

    2016-01-01

    Abstract The generic classification of the ant subfamily Dorylinae is revised, with the aim of facilitating identification of easily-diagnosable monophyletic genera. The new classification is based on recent molecular phylogenetic evidence and a critical reappraisal of doryline morphology. New keys and diagnoses based on workers and males are provided, along with reviews of natural history and phylogenetic relationships, distribution maps, and a list of valid species for each lineage. Twenty-eight genera (27 extant and 1 extinct) are recognized within the subfamily, an increase from 20 in the previous classification scheme. Species classified in the polyphyletic Cerapachys and Sphinctomyrmex prior to this publication are here distributed among 9 and 3 different genera, respectively. Amyrmex and Asphinctanilloides are synonymized under Leptanilloides and the currently recognized subgenera are synonymized for Dorylus. No tribal classification is proposed for the subfamily, but several apparently monophyletic genus-groups are discussed. Valid generic names recognized here include: Acanthostichus (= Ctenopyga), Aenictogiton, Aenictus (= Paraenictus, Typhlatta), Cerapachys (= Ceratopachys), Cheliomyrmex, Chrysapace gen. rev., Cylindromyrmex (= Holcoponera, Hypocylindromyrmex, Metacylindromyrmex), Dorylus (= Alaopone syn. n., Anomma syn. n., Cosmaecetes, Dichthadia syn. n., Rhogmus syn. n., Shuckardia, Sphecomyrmex, Sphegomyrmex, Typhlopone syn. n.), Eburopone gen. n., Eciton (= Camptognatha, Holopone, Mayromyrmex), Eusphinctus gen. rev., Labidus (= Nycteresia, Pseudodichthadia), Leptanilloides (= Amyrmex syn. n., Asphinctanilloides syn. n.), Lioponera gen. rev. (= Neophyracaces syn. n., Phyracaces syn. n.), Lividopone, Neivamyrmex (= Acamatus, Woitkowskia), Neocerapachys gen. n., Nomamyrmex, Ooceraea gen. rev. (= Cysias syn. n.), Parasyscia gen. rev., †Procerapachys, Simopone, Sphinctomyrmex, Syscia gen. rev., Tanipone, Vicinopone, Yunodorylus gen. rev., Zasphinctus

  14. Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering

    PubMed Central

    Boari de Lima, Elisa; Meira, Wagner; de Melo-Minardi, Raquel Cardoso

    2016-01-01

    As increasingly more genomes are sequenced, the vast majority of proteins may only be annotated computationally, given experimental investigation is extremely costly. This highlights the need for computational methods to determine protein functions quickly and reliably. We believe dividing a protein family into subtypes which share specific functions uncommon to the whole family reduces the function annotation problem’s complexity. Hence, this work’s purpose is to detect isofunctional subfamilies inside a family of unknown function, while identifying differentiating residues. Similarity between protein pairs according to various properties is interpreted as functional similarity evidence. Data are integrated using genetic programming and provided to a spectral clustering algorithm, which creates clusters of similar proteins. The proposed framework was applied to well-known protein families and to a family of unknown function, then compared to ASMC. Results showed our fully automated technique obtained better clusters than ASMC for two families, besides equivalent results for other two, including one whose clusters were manually defined. Clusters produced by our framework showed great correspondence with the known subfamilies, besides being more contrasting than those produced by ASMC. Additionally, for the families whose specificity determining positions are known, such residues were among those our technique considered most important to differentiate a given group. When run with the crotonase and enolase SFLD superfamilies, the results showed great agreement with this gold-standard. Best results consistently involved multiple data types, thus confirming our hypothesis that similarities according to different knowledge domains may be used as functional similarity evidence. Our main contributions are the proposed strategy for selecting and integrating data types, along with the ability to work with noisy and incomplete data; domain knowledge usage for detecting

  15. Revision of the monogenean subfamily Neothoracocotylinae Lebedev, 1969 (Polyopisthocotylea: Thoracocotylidae).

    PubMed

    Hayward, C J; Rohde, K

    1999-11-01

    Members of the subfamily Neothoracocotylinae are gastrocotylinean monogeneans on the gills of scombrid fishes of the genera Scomberomorus and Acanthocybium, and reportedly of a coryphaenid fish belonging to the genus Coryphaena. We revise the diagnosis of the subfamily and its two genera and accept only two species as valid. Neothoracocotyle acanthocybii (Meserve, 1938) Hargis, 1956 is known from Acanthocybium solandri throughout the Pacific Ocean and in the western Atlantic. N. coryphaenae (Yamaguti, 1938) Hargis, 1956, known only from a single specimen and described from Coryphaena hippurus in Japan, is synonymised with N. acanthocybii. The sole member of Scomberocotyle, S. scomberomori (Koratha, 1955) Hargis, 1956, infects five species of Scomberomorus in the eastern Pacific Ocean and the western and castern Atlantic. We record this worm from several new hosts and/or localities, including S. sierra and S. concolor in the eastern Pacific (Mexico to Colombia), S. maculatus and S. cavalla in the western Atlantic (USA to Brazil), and S. tritor in the eastern Atlantic (Sierra Leone to Nigeria).

  16. Molecular phylogenetics of sculpins of the subfamily Oligocottinae (Cottidae).

    PubMed

    Buser, Thaddaeus J; Andrés López, J

    2015-05-01

    The sculpin subfamily Oligocottinae includes 18-20 species of nearshore benthic fishes with a diverse array of reproductive strategies. As a first step toward understanding the evolution of that diversity, we conducted a phylogenetic study based on DNA sequences from eight genomic regions from 31 sculpin species aimed at testing monophyly and relationships of the Oligocottinae. Representatives from the perciform families Agonidae, Cottidae, Hemitripteridae, Hexagrammidae, Psychrolutidae, and Rhamphocottidae served as outgroups. The sequence data were analyzed in maximum likelihood and Bayesian phylogenetic inference frameworks. Results of these analyses show that a systematic revision of the group is warranted. The genus Clinocottus is a polyphyletic assemblage of three distinct lineages, which should be indicated by resurrection of the subgenera Blennicottus, Clinocottus, and Oxycottus; Leiocottus hirundo is more closely related to Clinocottus analis than C. analis is related to any other member of Clinocottus; the composition of the tribe Oligocottini should be revised to include only the genera Oligocottus, Clinocottus, and Orthonopias; and the genus Sigmistes should be removed from the subfamily Oligocottinae.

  17. Identification and characterization of Piwi subfamily in insects.

    PubMed

    Zhou, Xue; Liao, Zhen; Jia, Qidong; Cheng, Luogen; Li, Fei

    2007-10-12

    As a subfamily of Argonaute proteins, Piwi is poorly understood compared with Ago subfamily until recent discovery of Piwi protein interacting with piRNA. We did a large scale screening of insect genomes to identify piwi-like genes. Full or partial cDNA sequences were obtained by EST elongation and GENSCAN. We found that the exon numbers were totally different between vertebrates and invertebrates, approximately 20 exons in mammals but only 6-9 exons in insects. This infers either intron insertion or loss occurred during evolution. Characterized PAZ, c-terminal PIWI domains exist in almost all predicted Piwi-like proteins. We found six conserved motifs, which contain active catalytic triad "Asp-Asp-His/Lys" required for slicer activity. The expression of siwi1 and siwi2 in Bombyx mori were verified with RT-PCR. Phylogenetic tree inferred by Bayesian algorithm indicates invertebrate Piwi-like proteins are classified into three clades, of which Ago3 clade is closer to mammalian Piwi proteins.

  18. Evolutionary and biogeographic history of the subfamily Neoplecostominae (Siluriformes: Loricariidae)

    PubMed Central

    Roxo, Fábio F; Zawadzki, Cláudio H; Alexandrou, Markos A; Costa Silva, Guilherme J; Chiachio, Marcio C; Foresti, Fausto; Oliveira, Claudio

    2012-01-01

    Freshwater fish evolution has been shaped by changes in the earth's surface involving changes in the courses of rivers and fluctuations in sea level. The main objective of this study is to improve our knowledge of the evolution of loricariids, a numerous and adaptive group of freshwater catfish species, and the role of geological changes in their evolution. We use a number of different phylogenetic methods to test the relationships among 52 representative taxa within the Neoplecostominae using 4676 bps of mitochondrial and nuclear DNA. Our analysis revealed that the subfamily Neoplecostominae is monophyletic, including Pseudotocinclus, with three lineages recognized. The first lineage is composed of part of Pareiorhina rudolphi, P. cf. rudolphi, and Pseudotocinclus; the second is composed of Isbrueckerichthys, Pareiorhaphis, Kronichthys, and the species Neoplecostomus ribeirensis; and the third is composed of Pareiorhina carrancas, P. cf. carrancas, Pareiorhina sp. 1, a new genus, and all the species of the genus Neoplecostomus, except N. ribeirensis. The relaxed molecular clock calibration provides a temporal framework for the evolution of the group, which we use for a likelihood-based historical biogeographic analysis to test relevant hypotheses on the formation of southeast Brazil. We hypothesize that headwater capture events and marine regressions have shaped the patterns of distribution within the subfamily Neoplecostominae throughout the distinct basins of southeast Brazil. PMID:23145330

  19. Systematic Study of the Time-Dependence of the Sidereal Cosmic-Ray Anisotropy and Solar Dipole with IceCube

    NASA Astrophysics Data System (ADS)

    Lukasik, Michael; IceCube Collaboration Collaboration

    2017-01-01

    Between 2009 and 2016, the IceCube Detector located deep within the ice at the South Pole has detected nearly 380 billion cosmic rays. The large statistics of the data set allows us to observe the large- and small-scale anisotropy in their arrival direction distribution and the solar dipole caused by the orbital motion of the Earth. In this talk, we present a detailed systematic study of the sidereal anisotropy and the solar dipole. In particular, we search for a possible seasonal modulation in amplitude. Any statistically significant seasonal variation of the amplitude over the course of one orbital rotation could indicate the presence of a directional dependence, for example the Compton-Getting effect. To study the time dependence, the effect of the sidereal anisotropy on the solar dipole and vice versa need to be carefully studied and simulated.

  20. Moving out: from sterol transport to drug resistance - the ABCG subfamily of efflux pumps.

    PubMed

    Moitra, Karobi; Silverton, Latoya; Limpert, Katy; Im, Kate; Dean, Michael

    2011-01-01

    The ATP binding cassette (ABC) proteins are typically ATP-driven transmembrane pumps that have been evolutionarily conserved from bacteria to humans. In humans these transporters are subdivided into seven subfamilies, ranging from A to G. The ABCG subfamily of transporters is the primary focus of this review. This subfamily of proteins has been conserved throughout evolution and plays a central role in several cellular processes, such as sterol homeostasis and multidrug resistance. Functional polymorphisms/mutations in some of these G-subfamily transporters have clinical consequences in humans.

  1. Phylogeny of seed dormancy in Convolvulaceae, subfamily Convolvuloideae (Solanales)

    PubMed Central

    Jayasuriya, K. M. G. Gehan; Baskin, Jerry M.; Geneve, Robert L.; Baskin, Carol C.

    2009-01-01

    Background and Aims The water gap is an important morphoanatomical structure in seeds with physical dormancy (PY). It is an environmental signal detector for dormancy break and the route of water into the non-dormant seed. The Convolvulaceae, which consists of subfamilies Convolvuloideae (11 tribes) and Humbertoideae (one tribe, monotypic Humberteae), is the only family in the asterid clade known to produce seeds with PY. The primary aim of this study was to compare the morphoanatomical characteristics of the water gap in seeds of species in the 11 tribes of the Convolvuloideae and to use this information, and that on seed dormancy and storage behaviour, to construct a phylogenetic tree of seed dormancy for the subfamily. Methods Scanning electron microscopy (SEM) was used to define morphological changes in the hilum area during dormancy break; hand and vibratome sections were taken to describe the anatomy of the water gap, hilum and seed coat; and dye tracking was used to identify the initial route of water entry into the non-dormant seed. Results were compared with a recent cladogram of the family. Key Results Species in nine tribes have (a) layer(s) of palisade cells in the seed coat, a water gap and orthodox storage behaviour. Erycibe (Erycibeae) and Maripa (Maripeae) do not have a palisade layer in the seed coat or a water gap, and are recalcitrant. The hilar fissure is the water gap in relatively basal Cuscuteae, and bulges adjacent to the micropyle serve as the water gap in the Convolvuloideae, Dicranostyloideae (except Maripeae) and the Cardiochlamyeae clades. Seeds from the Convolvuloideae have morphologically prominent bulges demarcated by cell shape in the sclereid layer, whereas the Dicranostyloideae and Cardiochlamyeae have non-prominent bulges demarcated by the number of sub-cell layers. The anatomy and morphology of the hilar pad follow the same pattern. Conclusions PY in the subfamily Convolvuloideae probably evolved in the aseasonal tropics from an

  2. Actions and mode of actions of FGF19 subfamily members.

    PubMed

    Fukumoto, Seiji

    2008-03-01

    Fibroblast growth factors (FGFs) are humoral factors with diverse biological functions. While most FGFs were shown to work as local factors regulating cell growth and differentiation, recent investigations indicated that FGF19 subfamily members, FGF15/19, FGF21 and FGF23 work as systemic factors. FGF15/19 produced by intestine inhibits bile acid synthesis and FGF21from liver is involved in carbohydrate and lipid metabolism. In addition, FGF23 was shown to be produced by bone and regulate phosphate and vitamin D metabolism. Furthermore, these FGFs require klotho or betaklotho for their actions in addition to canonical FGF receptors. It is possible that these FGFs together with their receptor systems might be targets for novel therapeutic measures in the future.

  3. 40 CFR 1037.230 - Vehicle families, sub-families, and configurations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... vehicles to greenhouse gas standards, divide your product line into families of vehicles as specified in... greenhouse gas vehicle families into subfamilies that include vehicles with identical FELs. Note that you may... 40 Protection of Environment 34 2013-07-01 2013-07-01 false Vehicle families, sub-families,...

  4. 40 CFR 1037.230 - Vehicle families, sub-families, and configurations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... vehicles to greenhouse gas standards, divide your product line into families of vehicles as specified in... greenhouse gas vehicle families into subfamilies that include vehicles with identical FELs. Note that you may... 40 Protection of Environment 34 2012-07-01 2012-07-01 false Vehicle families, sub-families,...

  5. Phylogenetic relationships of subfamilies in the family Hesperiidae (Lepidoptera: Hesperioidea) from China.

    PubMed

    Yuan, Xiangqun; Gao, Ke; Yuan, Feng; Wang, Ping; Zhang, Yalin

    2015-06-10

    Hesperiidae is one of the largest families of butterflies. Our knowledge of the higher systematics on hesperiids from China is still very limited. We infer the phylogenetic relationships of the subfamilies of Chinese skippers based on three mitochondrial genes (cytochrome b (Cytb), the NADH dehydrogenase subunit 1 (ND1) and cytochrome oxidase I (COI)). In this study, 30 species in 23 genera were included in the Bayesian and maximum likelihood analyses. The subfamily Coeliadinae, Eudaminae, Pyrginae and Heteropterinae were recovered as a monophyletic clade with strong support. The subfamily Hesperiinae formed a clade, but support for monophyly was weak. Our results imply that the five subfamilies of Chinese Hesperiidae should be divided into: Coeliadinae, Eudaminae, Pyrginae, Heteropterinae and Hesperiinae. The relationships of the five subfamilies should be as follows: Coeliadinae + (Eudaminae + (Pyrginae + (Heteropterinae + Hesperiinae))).

  6. MMTS, a new subfamily of Tc1-like transposons.

    PubMed

    Ahn, Sang Jung; Kim, Moo-Sang; Jang, Jae Ho; Lim, Sang Uk; Lee, Hyung Ho

    2008-10-31

    A novel Tc1-like transposable element has been identified as a new DNA transposon in the mud loach, Misgurnus mizolepis. The M. mizolepis Tc1-like transposon (MMTS) is comprised of inverted terminal repeats and a single gene that codes Tc1-like transposase. The deduced amino acid sequence of the transposase-encoding region of MMTS transposon contains motifs including DDE motif, which was previously recognized in other Tc1-like transposons. However, putative MMTS transposase has only 34-37% identity with well-known Tc1, PPTN, and S elements at the amino acid level. In dot-hybridization analysis used to measure the copy numbers of the MMTS transposon in genomes of the mud loach, it was shown that the MMTS transposon is present at about 3.36 x 104 copies per 2 x 109 bp, and accounts for approximately 0.027% of the mud loach genome. Here, we also describe novel MMTS-like transposons from the genomes of carp-like fishes, flatfish species, and cichlid fishes, which bear conserved inverted repeats flanking an apparently intact transposase gene. Additionally, BLAST searches and phylogenetic analysis indicated that MMTS-like transposons evolved uniquely in fishes, and comprise a new subfamily of Tc1-like transposons, with only modest similarity to Drosophila melanogaster (foldback element FB4, HB2, HB1), Xenopus laevis, Xenopus tropicalis, and Anopheles gambiae (Frisky).

  7. Molecular phylogeny of the subfamilies in Geometridae (Geometroidea: Lepidoptera).

    PubMed

    Abraham, D; Ryrholm, N; Wittzell, H; Holloway, J D; Scoble, M J; Löfstedt, C

    2001-07-01

    Molecular sequence data from three gene fragments were used to examine critically a provisional phylogenetic classification based on morphological characters of the Geometridae, one of the most species-rich families of moths. The sister group relationship between Geometridae and Drepanidae gained further support from the molecular analysis, which was based on the ND1 mitochondrial gene and the first and second expansion segments of the 28S ribosomal RNA gene. Although the alignment of the second expansion segment contained regions with many gaps, it provided the most resolution of the gene fragments. Parsimony analysis of the combined data resulted in a cladogram in which species belonging to Drepanidae, Larentiinae, and Sterrhinae formed monophyletic groups. The Ennominae did not form a monophyletic group but rather were contained within a broader monophyletic group including Archiearinae, Geometrinae, and Alsophilinae (represented by only one species per group in the present study). The molecular results were used to explore further the relationship between Sterrhinae and Larentiinae, the question as to whether Ennominae actually represent a monophyletic group, and the relationships between Ennominae and some of the other subfamilies.

  8. A novel subfamily of LINE-derived elements in mice.

    PubMed

    Flood, W D; Rogozin, I B; Ruvinsky, A

    1998-11-01

    Hybrid sequences have been described previously that consist of a 5' region homologous to ORF2 of LINEs and a 3' end that shares homology with a sequence located in the first intron of Cepsilon immunoglobulin. The present investigation has revealed 14 new sequences from seven murine species, that show high homology to those observed earlier. Database search has found several new homologous hybrid sequences including one located in the mouse T-cell receptor (Tcra) locus. Several interesting features of this sequence include identical 15-bp flanking short direct repeats as well as poly-A signal and A-rich sequence at the 3' end. We have classified this set of sequences as LINE-derived elements (LDEs), which constitute a newly observed subfamily. Comparative analysis of these sequences suggests that a single recombination event was responsible for the production of an LDE progenitor. The phylogenetic tree shows a number of elements that pre-existed in the common ancestor of murine species and displays different evolutionary rates. The time of LDE origin is estimated at approximately 10-15 MYA.

  9. Linsitinib (OSI-906) antagonizes ATP-binding cassette subfamily G member 2 and subfamily C member 10-mediated drug resistance.

    PubMed

    Zhang, Hui; Kathawala, Rishil J; Wang, Yi-Jun; Zhang, Yun-Kai; Patel, Atish; Shukla, Suneet; Robey, Robert W; Talele, Tanaji T; Ashby, Charles R; Ambudkar, Suresh V; Bates, Susan E; Fu, Li-Wu; Chen, Zhe-Sheng

    2014-06-01

    In this study we investigated the effect of linsitinib on the reversal of multidrug resistance (MDR) mediated by the overexpression of the ATP-binding cassette (ABC) subfamily members ABCB1, ABCG2, ABCC1 and ABCC10. Our results indicate for the first time that linsitinib significantly potentiate the effect of anti-neoplastic drugs mitoxantrone (MX) and SN-38 in ABCG2-overexpressing cells; paclitaxel, docetaxel and vinblastine in ABCC10-overexpressing cells. Linsitinib moderately enhanced the cytotoxicity of vincristine in cell lines overexpressing ABCB1, whereas it did not alter the cytotoxicity of substrates of ABCC1. Furthermore, linsitinib significantly increased the intracellular accumulation and decreased the efflux of [(3)H]-MX in ABCG2-overexpressing cells and [(3)H]-paclitaxel in ABCC10-overexpressing cells. However, linsitinib, at a concentration that reversed MDR, did not significantly alter the expression levels of either the ABCG2 or ABCC10 transporter proteins. Furthermore, linsitinib did not significantly alter the intracellular localization of ABCG2 or ABCC10. Moreover, linsitinib stimulated the ATPase activity of ABCG2 in a concentration-dependent manner. Overall, our study suggests that linsitinib attenuates ABCG2- and ABCC10-mediated MDR by directly inhibiting their function as opposed to altering ABCG2 or ABCC10 protein expression.

  10. Bathyconchoeciinae, a new subfamily of deep oceanic planktonic halocyprid Ostracod (Myodocopa, Ostracoda).

    PubMed

    Angel, Martin; Graves, Carol

    2013-01-01

    Species of the genera Bathyconchoecia and Scottoecia are currently classified in the subfamily Euconchoeciinae together with species of the genus Euconchoecia. The morphological and ecological characteristics of many of the species currently attributable to these two taxa are compared with a range of Euconchoecia species and are shown to differ extensively. These differences are sufficient to separate these taxa at the subfamily level. Therefore, a new subfamily, the Bathyconchoeciinae is proposed to accommodate all the species currently classified in the genera Bathyconchoecia and Scottoecia.

  11. Chemical composition, antimicrobial and antioxidant activities of the essential oils of Sideritis erythrantha Boiss. and Heldr. (var. erythrantha and var. cedretorum P.H. Davis) endemic in Turkey.

    PubMed

    Köse, Elif Odabaş; Deniz, Ismail Gökhan; Sarıkürkçü, Cengiz; Aktaş, Ozgür; Yavuz, Mustafa

    2010-10-01

    In the present study, chemical compositions, antimicrobial and antioxidant activities of the essential oils of Sideritis erythrantha var. erythrantha (SE) and Sideritis erythrantha var. cedretorum (SC), which are endemic taxa in Turkey, were investigated. The essential oils obtained by hydrodistillation were analyzed by gas chromatography-mass spectrometry (GC-MS). α-Pinene was the major component of the essential oils of SC and SE. SC essential oil was as effective as antibiotic against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin resistant Enterococcus faecalis (VRE), ampicillin resistant Haemophilusinfluenzae and vancomycin sensitive E. faecalis. Similarly, SE essential oil was also as effective as antibiotic against VRE and ampicillin resistant H. influenzae. Antioxidant activities of the essential oils of SC and SE were determined by 1,1-diphenyl-2-picrylhydrazyl (DPPH), β-carotene/linoleic acid and reducing power. Both essential oils exhibited weak antioxidant activity. This is the first report on antimicrobial and antioxidant activities of the essential oils of SC and SE.

  12. Comparison of human and mouse T-cell receptor variable gene segment subfamilies

    SciTech Connect

    Clark, S.P.; Arden, B.; Kabelitz, D.; Mak, T.W.

    1995-10-01

    Like the immunoglobulin Igh-V and Igk-V gene families, the human or mouse TCRV gene families may be grouped into subfamilies displaying {ge} 75% nucleic acid sequence similarity among their members. Systematic interspecies sequence comparisons reveal that most mouse Tcr-V subfamilies exhibit clear homology to human TCRV subfamilies ({ge}60% amino acid sequence similarity). Homologous paris of TCRV genes in mice and humans show higher sequence similarity than TCRV genes from different subfamilies within either species, indicating trans-species evolution of TCRV genes. Mouse and human homologues show conservation of their relative map order, particularly in the 3{prime} region and a similar sequential and developmentally programmed expression. When the V regions from both species were analyzed together, local length differences and conserved residues in the loop regions were revealed, characteristic of each of the four TCRV families. 31 refs., 4 figs.

  13. Evolutionary age of repetitive element subfamilies and sensitivity of DNA methylation to airborne pollutants

    PubMed Central

    2013-01-01

    Background Repetitive elements take up >40% of the human genome and can change distribution through transposition, thus generating subfamilies. Repetitive element DNA methylation has associated with several diseases and environmental exposures, including exposure to airborne pollutants. No systematic analysis has yet been conducted to examine the effects of exposures across different repetitive element subfamilies. The purpose of the study is to evaluate sensitivity of DNA methylation in differentially‒evolved LINE, Alu, and HERV subfamilies to different types of airborne pollutants. Methods We sampled a total of 120 male participants from three studies (20 high-, 20 low-exposure in each study) of steel workers exposed to metal-rich particulate matter (measured as PM10) (Study 1); gas-station attendants exposed to air benzene (Study 2); and truck drivers exposed to traffic-derived elemental carbon (Study 3). We measured methylation by bisulfite-PCR-pyrosequencing in 10 differentially‒evolved repetitive element subfamilies. Results High-exposure groups exhibited subfamily-specific methylation differences compared to low-exposure groups: L1PA2 showed lower DNA methylation in steel workers (P=0.04) and gas station attendants (P=0.03); L1Ta showed lower DNA methylation in steel workers (P=0.02); AluYb8 showed higher DNA methylation in truck drivers (P=0.05). Within each study, dose–response analyses showed subfamily-specific correlations of methylation with exposure levels. Interaction models showed that the effects of the exposures on DNA methylation were dependent on the subfamily evolutionary age, with stronger effects on older LINEs from PM10 (p‒interaction=0.003) and benzene (p‒interaction=0.04), and on younger Alus from PM10 (p-interaction=0.02). Conclusions The evolutionary age of repetitive element subfamilies determines differential susceptibility of DNA methylation to airborne pollutants. PMID:23855992

  14. The role of keratin subfamilies and keratin pairs in the formation of human epidermal intermediate filaments

    PubMed Central

    1986-01-01

    The four major keratins of normal human epidermis (molecular mass 50, 56.5, 58, and 65-67 kD) can be subdivided on the basis of charge into two subfamilies (acidic 50-kD and 56.5-kD keratins vs. relatively basic 58-kD and 65-67-kD keratins) or subdivided on the basis of co- expression into two "pairs" (50-kD/58-kD keratin pair synthesized by basal cells vs. 56.5-kD/65-67-kD keratin pair expressed in suprabasal cells). Acidic and basic subfamilies were separated by ion exchange chromatography in 8.5 M urea and tested for their ability to reassemble into 10-nm filaments in vitro. The two keratins in either subfamily did not reassemble into 10-nm filaments unless combined with members of the other subfamily. While electron microscopy of acidic and basic keratins equilibrated in 4.5 M urea showed that keratins within each subfamily formed distinct oligomeric structures, possibly representing precursors in filament assembly, chemical cross-linking followed by gel analysis revealed dimers and larger oligomers only when subfamilies were combined. In addition, among the four major keratins, the acidic 50-kD and basic 58-kD keratins showed preferential association even in 8.5 M urea, enabling us to isolate a 50-kD/58-kD keratin complex by gel filtration. This isolated 50-kD/58-kD keratin pair readily formed 10-nm filaments in vitro. These results demonstrate that in tissues containing multiple keratins, two keratins are sufficient for filament assembly, but one keratin from each subfamily is required. More importantly, these data provide the first evidence for the structural significance of specific co-expressed acidic/basic keratin pairs in the formation of epithelial 10-nm filaments. PMID:2422179

  15. The sidereal semi-diurnal variation observed at high zenith angles at Mawson, 1968-1984, and the polarity of the solar main field

    NASA Technical Reports Server (NTRS)

    Jacklyn, R. M.; Duldig, M. L.

    1985-01-01

    High zenith-angle North/South telescopes viewing equatorially and at midlatitudes through 40 MWE of atmosphere have been operating at Mawson since early 1968. It is evident that a sidereal semi-diurnal component of galactic origin has been observed, over and above a possible spurious component proposed by Nagashima, arising from a bi-directional component of the solar anisotropy. Although a very pronounced reduction in the semi-diurnal galactic response followed the reversal of polarity of the solar main field during 1969 to 1971, so far the observations indicate that there has been no recurrence of a larger galactic response following the reversal of polarity around 1981. The possible role of the latitudional extent lambda omicron of the wavy neutral sheet is discussed.

  16. Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project.

    PubMed

    Konkel, Miriam K; Walker, Jerilyn A; Hotard, Ashley B; Ranck, Megan C; Fontenot, Catherine C; Storer, Jessica; Stewart, Chip; Marth, Gabor T; Batzer, Mark A

    2015-08-29

    The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic "young" Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages.

  17. Sequence Analysis and Characterization of Active Human Alu Subfamilies Based on the 1000 Genomes Pilot Project

    PubMed Central

    Konkel, Miriam K.; Walker, Jerilyn A.; Hotard, Ashley B.; Ranck, Megan C.; Fontenot, Catherine C.; Storer, Jessica; Stewart, Chip; Marth, Gabor T.; Batzer, Mark A.

    2015-01-01

    The goal of the 1000 Genomes Consortium is to characterize human genome structural variation (SV), including forms of copy number variations such as deletions, duplications, and insertions. Mobile element insertions, particularly Alu elements, are major contributors to genomic SV among humans. During the pilot phase of the project we experimentally validated 645 (611 intergenic and 34 exon targeted) polymorphic “young” Alu insertion events, absent from the human reference genome. Here, we report high resolution sequencing of 343 (322 unique) recent Alu insertion events, along with their respective target site duplications, precise genomic breakpoint coordinates, subfamily assignment, percent divergence, and estimated A-rich tail lengths. All the sequenced Alu loci were derived from the AluY lineage with no evidence of retrotransposition activity involving older Alu families (e.g., AluJ and AluS). AluYa5 is currently the most active Alu subfamily in the human lineage, followed by AluYb8, and many others including three newly identified subfamilies we have termed AluYb7a3, AluYb8b1, and AluYa4a1. This report provides the structural details of 322 unique Alu variants from individual human genomes collectively adding about 100 kb of genomic variation. Many Alu subfamilies are currently active in human populations, including a surprising level of AluY retrotransposition. Human Alu subfamilies exhibit continuous evolution with potential drivers sprouting new Alu lineages. PMID:26319576

  18. Phylogenetic relationships and protein modelling revealed two distinct subfamilies of group II HKT genes between crop and model grasses.

    PubMed

    Ariyarathna, H A Chandima K; Francki, Michael G

    2016-07-01

    Molecular evolution of large protein families in closely related species can provide useful insights on structural functional relationships. Phylogenetic analysis of the grass-specific group II HKT genes identified two distinct subfamilies, I and II. Subfamily II was represented in all species, whereas subfamily I was identified only in the small grain cereals and possibly originated from an ancestral gene duplication post divergence from the coarse grain cereal lineage. The core protein structures were highly analogous despite there being no more than 58% amino acid identity between members of the two subfamilies. Distinctly variable regions in known functional domains, however, indicated functional divergence of the two subfamilies. The subsets of codons residing external to known functional domains predicted signatures of positive Darwinian selection potentially identifying new domains of functional divergence and providing new insights on the structural function and relationships between protein members of the two subfamilies.

  19. Datziinae as a new subfamily name for the unavailable name Protopsychodinae Stebner et al., 2015, (Diptera: Psychodidae).

    PubMed

    Stebner, Frauke; Solórzano Kraemer, Mónica M; Ibáñez-Bernal, Sergio; Wagner, Rüdiger

    2015-01-01

    In a recent paper a new subfamily of Psychodidae was inadequately named Protopsychodinae. This nomenclatural act cannot be considered as a valid name under ICZN regulations because the subfamily name is not based on the type genus Datzia Stebner et al., 2015, and furthermore the fossil genus Protopsychoda Azar et al., 1999 was originally described under the subfamily Psychodinae. Therefore, the new family-group name Datziinae is herein proposed.

  20. Datziinae as a new subfamily name for the unavailable name Protopsychodinae Stebner et al., 2015, (Diptera: Psychodidae)

    PubMed Central

    Solórzano Kraemer, Mónica M.; Ibáñez-Bernal, Sergio; Wagner, Rüdiger

    2015-01-01

    In a recent paper a new subfamily of Psychodidae was inadequately named Protopsychodinae. This nomenclatural act cannot be considered as a valid name under ICZN regulations because the subfamily name is not based on the type genus Datzia Stebner et al., 2015, and furthermore the fossil genus Protopsychoda Azar et al., 1999 was originally described under the subfamily Psychodinae. Therefore, the new family-group name Datziinae is herein proposed. PMID:26623188

  1. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.

    PubMed

    Marchler-Bauer, Aron; Bo, Yu; Han, Lianyi; He, Jane; Lanczycki, Christopher J; Lu, Shennan; Chitsaz, Farideh; Derbyshire, Myra K; Geer, Renata C; Gonzales, Noreen R; Gwadz, Marc; Hurwitz, David I; Lu, Fu; Marchler, Gabriele H; Song, James S; Thanki, Narmada; Wang, Zhouxi; Yamashita, Roxanne A; Zhang, Dachuan; Zheng, Chanjuan; Geer, Lewis Y; Bryant, Stephen H

    2017-01-04

    NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families. CDD also supports comparative analyses of protein families via conserved domain architectures, and a recent curation effort focuses on providing functional characterizations of distinct subfamily architectures using SPARCLE: Subfamily Protein Architecture Labeling Engine. CDD can be accessed at https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml.

  2. Relicts from Tertiary Australasia: undescribed families and subfamilies of songbirds (Passeriformes) and their zoogeographic signal.

    PubMed

    Schodde, Richard; Christidis, Les

    2014-04-14

    A number of hitherto unrecognized, deeply divergent taxa of Australasian songbirds have been revealed by DNA sequence studies in the last decade. Differentiation among them is at levels equivalent to family and subfamily rank among songbirds generally. Accordingly, the purpose of this paper is to name and describe eleven of them formally under Articles 13.1, 13.2, 16.1 and 16.2 of the International Code of Zoological Nomenclature so that they are made available for use in zoology. The taxa are: families Oreoicidae, Eulacestomatidae, Rhagologidae, Ifritidae and Melampittidae, and subfamilies Pachycareinae, Oreoscopinae, Toxorhamphinae, Oedistomatinae, Peltopsinae and Lamproliinae. The families to which the subfamilies belong are documented. Morphological and behavioural traits of the new family-group taxa are discussed; reasons for taxonomic rankings are summarized; and grounds for the geographic origin of corvoid songbirds, to which all the new families belong, are briefly addressed. One new genus,Megalampitta in Melampittidae, is also described.

  3. Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)

    PubMed Central

    2012-01-01

    Background The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on β-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5. Results About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data. Examination of subfamilies with catalytically-active members revealed that one third are monospecific (containing a single enzyme activity), although new functions may be discovered with biochemical characterization in the future. Furthermore, twenty subfamilies presently have no characterization whatsoever and many others have only limited structural and biochemical data. Mapping of functional knowledge onto the GH5 phylogenetic tree revealed that the sequence space of this historical and industrially important family is far from well dispersed, highlighting targets in need of further study. The analysis also uncovered a number of GH5 proteins which have lost their catalytic machinery, indicating evolution towards novel functions. Conclusion Overall, the subfamily division of GH5 provides an actively curated resource for large-scale protein sequence annotation for glycogenomics; the subfamily assignments are openly accessible via the Carbohydrate-Active Enzyme database at http://www.cazy.org/GH5.html. PMID:22992189

  4. A new macropterous species of a rarely collected subfamily (Heteroptera, Tingidae, Vianaidinae).

    PubMed

    Guidoti, Marcus; Montemayor, Sara I

    2016-08-11

    Pterovianaida duckensis n. sp., a new macropterous species of the rarely collected subfamily Vianaidinae is here described. The group currently comprises nine species, two of them fossils. Pterovianaida Montemayor and Carpintero is a recent monotypic genus described for a macropterous species collected in Peru. Here, a new macropterous species of Pterovianaida is described, and characters of the head, pronotum and hemelytra distinguish this species from the type species. This is the first record of a macropterous Vianaidinae for Brazil. A key to all extant species of this subfamily is provided.

  5. New Drosophila P-like elements and reclassification of Drosophila P-elements subfamilies.

    PubMed

    Loreto, Elgion L S; Zambra, Francis M B; Ortiz, Mauro F; Robe, Lizandra J

    2012-07-01

    Genomic searches for P-like transposable elements were performed (1) in silico in the 12 available Drosophila genomes and (2) by PCR using degenerate primers in 21 Neotropical Drosophila species. In silico searches revealed P-like sequences only in Drosophila persimilis and Drosophila willistoni. Sixteen new P-like elements were obtained by PCR. These sequences were added to sequences of previously described P-like elements, and a phylogenetic analysis was performed. The subfamilies of P-elements described in the literature (Canonical, M, O, T, and K) were included in the reconstructed tree, and all were monophyletic. However, we suggest that some subfamilies can be enlarged, other subdivided, and some new subfamilies may be proposed, totalizing eleven subfamilies, most of which contain new P-like sequences. Our analyses support the monophyly of P-like elements in Drosophilidae. We suggest that, once these elements need host-specific factors to be mobilizable, the horizontal transfer (HT) of P-like elements may be inhibited among more distant taxa. Nevertheless, HT among Drosophilidae species appears to be a common phenomenon.

  6. Phylogenetic relationships of the carabid subfamily Harpalinae (Coleoptera) based on molecular sequence data.

    PubMed

    Ober, Karen A

    2002-08-01

    The carabid subfamily Harpalinae contains most of the species of carabid beetles. This subfamily, with over 19,000 species, radiated in the Cretaceous to yield a large clade that is diverse in morphological form and ecological habit. While there are several morphological, cytological, and chemical characters that unite most harpalines, the placement of some tribes within the subfamily remains controversial, as does the sister group relationships to this large group. In this study, DNA sequences from the 28S rDNA gene and the wingless nuclear protein-coding gene were collected from 52 carabid genera representing 31 harpaline tribes in addition to more than 21 carabid outgroup taxa to reconstruct the phylogeny of this group. Molecular sequence data from these genes, along with additional data from the 18S rDNA gene, were analyzed with a variety of phylogenetic analysis methods, separately for each gene and in a combined data approach. Results indicated that the subfamily Harpalinae is monophyletic with the enigmatic tribes of Morionini, Peleciini, and Pseudomorphini included within it. Brachinine bombardier beetles are closely related to Harpalinae as they form the sister group to harpalines or, in some analyses, are included within it or with austral psydrines. The austral psydrines are the sister group to Harpalinae+Brachinini clade in most analyses and austral psydrines+Brachinini+Harpalinae clade is strongly supported.

  7. Structures of the four subfamilies of phosphodiesterase-4 provide insight into the selectivity of their inhibitors.

    PubMed

    Wang, Huanchen; Peng, Ming-Sheng; Chen, Yi; Geng, Jie; Robinson, Howard; Houslay, Miles D; Cai, Jiwen; Ke, Hengming

    2007-12-01

    PDE4 (phosphodiesterase-4)-selective inhibitors have attracted much attention as potential therapeutics for the treatment of both depression and major inflammatory diseases, but their practical application has been compromised by side effects. A possible cause for the side effects is that current PDE4-selective inhibitors similarly inhibit isoforms from all four PDE4 subfamilies. The development of PDE4 subfamily-selective inhibitors has been hampered by a lack of structural information. In the present study, we rectify this by providing the crystal structures of the catalytic domains of PDE4A, PDE4B and PDE4D in complex with the PDE4 inhibitor NVP {4-[8-(3-nitrophenyl)-[1,7]naphthyridin-6-yl]benzoic acid} as well as the unliganded PDE4C structure. NVP binds in the same conformation to the deep cAMP substrate pocket and interacts with the same residues in each instance. However, detailed structural comparison reveals significant conformational differences. Although the active sites of PDE4B and PDE4D are mostly comparable, PDE4A shows significant displacements of the residues next to the invariant glutamine residue that is critical for substrate and inhibitor binding. PDE4C appears to be more distal from other PDE4 subfamilies, with certain key residues being disordered. Our analyses provide the first structural basis for the development of PDE4 subfamily-selective inhibitors.

  8. Leaf and Stem CO(2) Uptake in the Three Subfamilies of the Cactaceae.

    PubMed

    Nobel, P S; Hartsock, T L

    1986-04-01

    Net CO(2) uptake over 24-hour periods was examined for the leaves and for the stems of 11 species of cacti representing all three subfamilies. For Pereskia aculeata, Pereskia grandifolia, and Maihuenia poeppigii (subfamily Pereskioideae), all the net shoot CO(2) uptake was by the leaves and during the daytime. In contrast, for the leafless species Carnegiea gigantea, Ferocactus acanthodes, Coryphantha vivipara, and Mammillaria dioica (subfamily Cactoideae), all the shoot net CO(2) uptake was by the stems and at night. Similarly, for leafless Opuntia ficus-indica (subfamily Opuntioideae), all net CO(2) uptake occurred at night. For leafy members of the Opuntioideae (Pereskiopsis porteri, Quiabentia chacoensis, Austrocylindropuntia subulata), at least 88% of the shoot CO(2) uptake over 24 hours was by the leaves and some CO(2) uptake occurred at night. Leaves responded to the instantaneous level of photosynthetically active radiation (PAR) during the daytime, as occurs for C(3) plants, whereas nocturnal CO(2) uptake by stems of O. ficus-indica and F. acanthodes responded to the total daily PAR, as occurs for Crassulacean acid metabolism (CAM) plants. Thus, under the well-watered conditions employed, the Pereskioideae behaved as C(3) plants, the Cactoideae behaved as CAM plants, and the Opuntioideae exhibited characteristics of both pathways.

  9. Functional assessment of subfamily variation in maxillomandibular morphology among Old World monkeys.

    PubMed

    Ravosa, M J

    1990-06-01

    Among Old World monkeys, subfamily variation in maxillomandibular form is commonly attributed to divergent dietary and social behaviors. However, our knowledge of any musculoskeletal adaptations for gape in cercopithecines, and folivory in colobines, is incomplete. Such data are requisite to a more informed perspective on the evolutionary morphology of these taxa. Structural analyses of gape and biomechanical efficiency were applied to a representative sample of adult cercopithecids. Factors pertaining to the biomechanical scaling of cranial structures were evaluated with least-squares bivariate regression techniques. To assess subfamily differences in masticatory efficiency, analyses of covariance were made between relevant factors. Cercopithecines achieve increased gape and relative canine size mainly with strong positive allometry of the facial skull, combined with a larger gonial angle. Colobines possess a relatively long masseter lever arm and short facial skull, as well as an enlargened masseter-medial pterygoid complex. Subfamily differences in temporalis lever arm scaling are negligible. Biomechanical comparisons within and between subfamilies suggest that the mechanical advantage of the temporalis is relatively greater than that of the masseter, while the mechanical advantage of both muscles increases with face length. Evidence is presented to stress the need for adequate consideration of the dependent variable in allometric investigations of skull form.

  10. Leaf and Stem CO2 Uptake in the Three Subfamilies of the Cactaceae 1

    PubMed Central

    Nobel, Park S.; Hartsock, Terry L.

    1986-01-01

    Net CO2 uptake over 24-hour periods was examined for the leaves and for the stems of 11 species of cacti representing all three subfamilies. For Pereskia aculeata, Pereskia grandifolia, and Maihuenia poeppigii (subfamily Pereskioideae), all the net shoot CO2 uptake was by the leaves and during the daytime. In contrast, for the leafless species Carnegiea gigantea, Ferocactus acanthodes, Coryphantha vivipara, and Mammillaria dioica (subfamily Cactoideae), all the shoot net CO2 uptake was by the stems and at night. Similarly, for leafless Opuntia ficus-indica (subfamily Opuntioideae), all net CO2 uptake occurred at night. For leafy members of the Opuntioideae (Pereskiopsis porteri, Quiabentia chacoensis, Austrocylindropuntia subulata), at least 88% of the shoot CO2 uptake over 24 hours was by the leaves and some CO2 uptake occurred at night. Leaves responded to the instantaneous level of photosynthetically active radiation (PAR) during the daytime, as occurs for C3 plants, whereas nocturnal CO2 uptake by stems of O. ficus-indica and F. acanthodes responded to the total daily PAR, as occurs for Crassulacean acid metabolism (CAM) plants. Thus, under the well-watered conditions employed, the Pereskioideae behaved as C3 plants, the Cactoideae behaved as CAM plants, and the Opuntioideae exhibited characteristics of both pathways. PMID:16664741

  11. Structures of the Four Subfamilies of Phosphodiesterase-4 Provide Insight into the Selectivity of Their Inhibitors

    SciTech Connect

    Wang, H.; Peng, M; Chen , Y; Geng, J; Robinson, H; Houslay , M; Cai, J; Ke, H

    2007-01-01

    PDE4 (phosphodiesterase-4)-selective inhibitors have attracted much attention as potential therapeutics for the treatment of both depression and major inflammatory diseases, but their practical application has been compromised by side effects. A possible cause for the side effects is that current PDE4-selective inhibitors similarly inhibit isoforms from all four PDE4 subfamilies. The development of PDE4 subfamily-selective inhibitors has been hampered by a lack of structural information. In the present study, we rectify this by providing the crystal structures of the catalytic domains of PDE4A, PDE4B and PDE4D in complex with the PDE4 inhibitor NVP 4-[8-(3-nitrophenyl)-[1,7]naphthyridin-6-yl]benzoic acid as well as the unliganded PDE4C structure. NVP binds in the same conformation to the deep cAMP substrate pocket and interacts with the same residues in each instance. However, detailed structural comparison reveals significant conformational differences. Although the active sites of PDE4B and PDE4D are mostly comparable, PDE4A shows significant displacements of the residues next to the invariant glutamine residue that is critical for substrate and inhibitor binding. PDE4C appears to be more distal from other PDE4 subfamilies, with certain key residues being disordered. Our analyses provide the first structural basis for the development of PDE4 subfamily-selective inhibitors.

  12. Seed morphology and anatomy and its utility in recognizing subfamilies and tribes of Zingiberaceae

    SciTech Connect

    Benedict, John C.; Smith, Selena Y.; Collinson, Margaret E.; Leong-Skornickova, Jana; Specht, Chelsea D.; Marone, Federica; Xiao, Xianghui; Parkinson, Dilworth Y.

    2015-11-01

    PREMISE OF THE STUDY: Recent phylogenetic analyses based on molecular data suggested that the monocot family Zingiberaceae be separated into four subfamilies and four tribes. Robust morphological characters to support these clades are lacking. Seeds were analyzed in a phylogenetic context to test independently the circumscription of clades and to better understand evolution of seed characters within Zingiberaceae. METHODS: Seventy-five species from three of the four subfamilies were analyzed using synchrotron based x-ray tomographic microscopy (SRXTM) and scored for 39 morphoanatomical characters. KEY RESULTS: Zingiberaceae seeds are some of the most structurally complex seeds in angiosperms. No single seed character was found to distinguish each subfamily, but combinations of characters were found to differentiate between the subfamilies. Recognition of the tribes based on seeds was possible for Globbeae, but not for Alpinieae, Riedelieae, or Zingibereae, due to considerable variation. CONCLUSIONS: SRXTM is an excellent, nondestructive tool to capture morphoanatomical variation of seeds and allows for the study of taxa with limited material available. Alpinioideae, Siphonochiloideae, Tamijioideae, and Zingiberoideae are well supported based on both molecular and morphological data, including multiple seed characters. Globbeae are well supported as a distinctive tribe within the Zingiberoideae, but no other tribe could be differentiated using seeds due to considerable homoplasy when compared with currently accepted relationships based on molecular data. Novel seed characters suggest tribal affinities for two currently unplaced Zingiberaceae taxa: Siliquamomum may be related to Riedelieae and Monolophus to Zingibereae, but further work is needed before formal revision of the family.

  13. The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages

    PubMed Central

    Johnson, Deborah A; Hill, Jeffrey P; Thomas, Michael A

    2006-01-01

    Background In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of gene duplication and protein sequence evolution. Here, we utilize expressed sequence tag (EST) data to study gene duplication and expression patterns in the monosaccharide transporter (MST) gene family across the land plants. In Arabidopsis, there are 53 MST genes that form seven distinct subfamilies. We created profile hidden Markov models of each subfamily and searched EST databases representing diverse land plant lineages to address the following questions: 1) Are homologs of each Arabidopsis subfamily present in the earliest land plants? 2) Do expression patterns among subfamilies and individual genes within subfamilies differ across lineages? 3) Has gene duplication within each lineage resulted in lineage-specific expansion patterns? We also looked for correlations between relative EST database representation in Arabidopsis and similarity to orthologs in early lineages. Results Homologs of all seven MST subfamilies were present in land plants at least 400 million years ago. Subfamily expression levels vary across lineages with greater relative expression of the STP, ERD6-like, INT and PLT subfamilies in the vascular plants. In the large EST databases of the moss, gymnosperm, monocot and eudicot lineages, EST contig construction reveals that MST subfamilies have experienced lineage-specific expansions. Large subfamily expansions appear to be due to multiple gene duplications arising from single ancestral genes. In Arabidopsis, one or a few genes within most subfamilies have much higher EST database representation than others. Most highly represented (broadly expressed) genes in Arabidopsis have best match orthologs in early divergent lineages. Conclusion The seven

  14. Is the large-scale sidereal anisotropy of the galactic cosmic-ray intensity really instable at TeV energies?

    NASA Astrophysics Data System (ADS)

    Amenomori, M.; Bi, X. J.; Chen, D.; Chen, W. Y.; Cui, S. W.; Danzengluobu; Ding, L. K.; Ding, X. H.; Feng, C. F.; Feng, Zhaoyang; Feng, Z. Y.; Gou, Q. B.; Guo, H. W.; Guo, Y. Q.; He, H. H.; He, Z. T.; Hibino, K.; Hotta, N.; Hu, Haibing; Hu, H. B.; Huang, J.; Jia, H. Y.; Jiang, L.; Kajino, F.; Kasahara, K.; Katayose, Y.; Kato, C.; Kawata, K.; Labaciren; Le, G. M.; Li, A. F.; Li, W. J.; Liu, C.; Liu, J. S.; Lu, H.; Meng, X. R.; Mizutani, K.; Munakata, K.; Nanjo, H.; Nishizawa, M.; Ohnishi, M.; Ohta, I.; Ozawa, S.; Qian, X. L.; Qu, X. B.; Saito, T.; Saito, T. Y.; Sakata, M.; Sako, T. K.; Shao, J.; Shibata, M.; Shiomi, A.; Shirai, T.; Sugimoto, H.; Takita, M.; Tan, Y. H.; Tateyama, N.; Torii, S.; Tsuchiya, H.; Udo, S.; Wang, H.; Wu, H. R.; Xue, L.; Yamamoto, Y.; Yang, Z.; Yasue, S.; Yuan, A. F.; Yuda, T.; Zhai, L. M.; Zhang, H. M.; Zhang, J. L.; Zhang, X. Y.; Zhang, Y.; Zhang, Yi; Zhang, Ying; Zhaxisangzhu; Zhou, X. X.

    2012-08-01

    The sidereal cosmic-ray anisotropy at TeV energies has a large-scale deficit region distributed between 150 and 240 degrees in right ascension, which is called the "loss-cone". The Milagro experiment reported the detection of a steady increase in the loss-cone amplitude at 6 TeV from July 2000 to July 2007. In this paper, we examine Milagro's claim using the data collected by the Tibet air-shower experiment from November 1999 through December 2008. No time dependence was found in the loss-cone amplitude at 4.4, 6.2, and 11 TeV. If the increase in the loss-cone amplitude were, as Milagro argued, due to variations in the heliosphere in relation to solar activities, the same tendency would be seen at sub-TeV energies where the anisotropy is far more sensitive to solar activities. At 0.6 TeV, however, Matsushiro underground muon observatory reported no significant increase in the loss-cone amplitude during the corresponding period.

  15. Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories

    NASA Technical Reports Server (NTRS)

    Nakayama, S.; Moncrief, N. D.; Kretsinger, R. H.

    1992-01-01

    In the first report in this series we described the relationships and evolution of 152 individual proteins of the EF-hand subfamilies. Here we add 66 additional proteins and define eight (CDC, TPNV, CLNB, LPS, DGK, 1F8, VIS, TCBP) new subfamilies and seven (CAL, SQUD, CDPK, EFH5, TPP, LAV, CRGP) new unique proteins, which we assume represent new subfamilies. The main focus of this study is the classification of individual EF-hand domains. Five subfamilies--calmodulin, troponin C, essential light chain, regulatory light chain, CDC31/caltractin--and three uniques--call, squidulin, and calcium-dependent protein kinase--are congruent in that all evolved from a common four-domain precursor. In contrast calpain and sarcoplasmic calcium-binding protein (SARC) each evolved from its own one-domain precursor. The remaining 19 subfamilies and uniques appear to have evolved by translocation and splicing of genes encoding the EF-hand domains that were precursors to the congruent eight and to calpain and to SARC. The rates of evolution of the EF-hand domains are slower following formation of the subfamilies and establishment of their functions. Subfamilies are not readily classified by patterns of calcium coordination, interdomain linker stability, and glycine and proline distribution. There are many homoplasies indicating that similar variants of the EF-hand evolved by independent pathways.

  16. Dramatic Number Variation of R Genes in Solanaceae Species Accounted for by a Few R Gene Subfamilies.

    PubMed

    Wei, Chunhua; Chen, Jiongjiong; Kuang, Hanhui

    2016-01-01

    Most disease resistance genes encode nucleotide-binding-site (NBS) and leucine-rich-repeat (LRR) domains, and the NBS-LRR encoding genes are often referred to as R genes. Using newly developed approach, 478, 485, 1,194, 1,665, 2,042 and 374 R genes were identified from the genomes of tomato Heinz1706, wild tomato LA716, potato DM1-3, pepper Zunla-1 and wild pepper Chiltepin and tobacco TN90, respectively. The majority of R genes from Solanaceae were grouped into 87 subfamilies, including 16 TIR-NBS-LRR (TNL) and 71 non-TNL subfamilies. Each subfamily was annotated manually, including identification of intron/exon structure and intron phase. Interestingly, TNL subfamilies have similar intron phase patterns, while the non-TNL subfamilies have diverse intron phase due to frequent gain of introns. Prevalent presence/absence polymorphic R gene loci were found among Solanaceae species, and an integrated map with 427 R loci was constructed. The pepper genome (2,042 in Chiltepin) has at least four times of R genes as in tomato (478 in Heinz1706). The high number of R genes in pepper genome is due to the amplification of R genes in a few subfamilies, such as the Rpi-blb2 and BS2 subfamilies. The mechanism underlying the variation of R gene number among different plant genomes is discussed.

  17. Dramatic Number Variation of R Genes in Solanaceae Species Accounted for by a Few R Gene Subfamilies

    PubMed Central

    Wei, Chunhua; Chen, Jiongjiong; Kuang, Hanhui

    2016-01-01

    Most disease resistance genes encode nucleotide-binding-site (NBS) and leucine-rich-repeat (LRR) domains, and the NBS-LRR encoding genes are often referred to as R genes. Using newly developed approach, 478, 485, 1,194, 1,665, 2,042 and 374 R genes were identified from the genomes of tomato Heinz1706, wild tomato LA716, potato DM1-3, pepper Zunla-1 and wild pepper Chiltepin and tobacco TN90, respectively. The majority of R genes from Solanaceae were grouped into 87 subfamilies, including 16 TIR-NBS-LRR (TNL) and 71 non-TNL subfamilies. Each subfamily was annotated manually, including identification of intron/exon structure and intron phase. Interestingly, TNL subfamilies have similar intron phase patterns, while the non-TNL subfamilies have diverse intron phase due to frequent gain of introns. Prevalent presence/absence polymorphic R gene loci were found among Solanaceae species, and an integrated map with 427 R loci was constructed. The pepper genome (2,042 in Chiltepin) has at least four times of R genes as in tomato (478 in Heinz1706). The high number of R genes in pepper genome is due to the amplification of R genes in a few subfamilies, such as the Rpi-blb2 and BS2 subfamilies. The mechanism underlying the variation of R gene number among different plant genomes is discussed. PMID:26849045

  18. Odontomariinae, a new middle paleozoic subfamily of slit-bearing euophaloidean gastropods (Euophalomorpha, Gastropoda)

    USGS Publications Warehouse

    Fryda, J.; Heidelberger, D.; Blodgett, R.B.

    2006-01-01

    A new subfamily, the Odontomariinae subfam. nov., is established herein for a distinctive group of uncoiled, slit-bearing Middle Devonian euomphalid gastropods. Its taxonomic position is based on the recent discovery of open coiled protoconchs and it is placed within the Euomphalomorpha. The genera Odontomaria Odontomaria C. F. Roemer and Tubiconcha n. gen. belonging to this new subfamily are enlarged based on studies on new material of the following species: Odontomaria semiplicata (Sandberger & Sandberger), Odontomaria gracilis n. sp., Odontomaria jankei n. sp., Odontomaria cheeneetnukensis n. sp., Odontomaria cindiprellerae n. sp. and Tubiconcha leunissi (Heidelberger, 2001). Members of the Odontomariinae were mainly sedentary organisms in high-energy, moderately shallow water. ?? 2006 E. Schweizerbart'sche Verlagsbuchhandlung.

  19. Examination of subfamilial phylogeny in Bromeliaceae using comparative sequencing of the plastid locus ndhF.

    PubMed

    Terry, R; Brown, G; Olmstead, R

    1997-05-01

    Parsimony analysis of 31 sequences of the chloroplast locus ndhF was used to address questions of subfamilial phylogeny in Bromeliaceae. Results presented here are congruent with those from chloroplast DNA restriction site analysis in recognizing a clade containing Bromelioideae and Pitcairnioideae, and in resolving Tillandsioideae near the base of the family. Placements of several taxonomically difficult genera (e.g., Glomeropitcairnia and Navia) corroborate those of traditional treatments; however, these data suggest that Brocchinia (Pitcairnioideae) is the sister group to the remainder of Bromeliaceae. Further evidence for the paraphyly of Pitcairnioideae includes the resolution of Puya as the sister group to Bromelioideae. Implications for taxonomic realignment at the subfamily level are considered.

  20. The gymnosperm Pinus pinea contains both AOX gene subfamilies, AOX1 and AOX2.

    PubMed

    Frederico, António Miguel; Zavattieri, Maria Amely; Campos, Maria Doroteia; Cardoso, Hélia Guerra; McDonald, Allison E; Arnholdt-Schmitt, Birgit

    2009-12-01

    The gymnosperm Pinus pinea L. (stone pine) is a typical Mediterranean pine used for nuts and timber production, and as an ornamental around the world. Pine genomes are large in comparison to other species. The hypothesis that retrotransposons, such as gymny, made a large contribution to this alteration in genome size was recently confirmed. However, P. pinea is unique in other various aspects. P. pinea demonstrates a different pattern of gymny organization than other Pinus subgenera. Additionally, P. pinea has a highly recalcitrant behaviour in relation to standard conifer protocols for the induction of somatic embryogenesis or rooting. Because such types of cell reprogramming can be explained as a reaction of plant cells to external stress, it is of special interest to study sequence peculiarities in stress-inducible genes, such as the alternative oxidase (AOX). This is the first report containing molecular evidence for the existence of AOX in gymnosperms at the genetic level. P. pinea AOXs were isolated by a polymerase chain reaction (PCR) approach and three genes were identified. Two of the genes belong to the AOX1 subfamily and one belongs to the AOX2 subfamily. The existence of both AOX subfamilies in gymnosperms is reported here for the first time. This discovery supports the hypothesis that AOX1 and AOX2 subfamilies arose prior to the separation of gymnosperms and angiosperms, and indicates that the AOX2 is absent in monocots because of subsequent gene loss events. Polymorphic P. pinea AOX1 sequences from a selected genetic clone are presented indicating non-allelic, non-synonymous and synonymous translation products.

  1. Predaceous diving beetles in Maine: Faunal list and keys to subfamilies

    USGS Publications Warehouse

    Boobar, L.R.; Spangler, P.J.; Gibbs, K.E.; Longcore, J.R.; Hopkins, K.M.

    1998-01-01

    Records of predaceous diving beetles (Coleoptera: Dytiscidae) collected in Maine are summarized. These records are augmented by field surveys of beetles in Aroostook Co., Maine during 1993-95. Keys to subfamilies are presented with color plates for selected species. A list of diving beetles that have been collected near Maine (state or province) is presented so that investigators will know what additional species might be expected in Maine. Basic taxonomy is presented to facilitate use of keys.

  2. Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies.

    PubMed

    Lin, Ching-Ping; Huang, Jen-Pan; Wu, Chung-Shien; Hsu, Chih-Yao; Chaw, Shu-Miaw

    2010-01-01

    As the largest and the basal-most family of conifers, Pinaceae provides key insights into the evolutionary history of conifers. We present comparative chloroplast genomics and analysis of concatenated 49 chloroplast protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, to address the long-standing controversy about Pinaceae phylogeny. The complete cpDNAs of Cathaya argyrophylla and Cedrus deodara (Abitoideae) and draft cpDNAs of Larix decidua, Picea morrisonicola, and Pseudotsuga wilsoniana are reported. We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae. Our phylogenetic analyses reveal that Cedrus is clustered with Abies-Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix-Pseudotsuga. Topology and structural change tests and indel-distribution comparisons lend further evidence to our phylogenetic finding. Our molecular datings suggest that Pinaceae first evolved during Early Jurassic, and diversification of Pinaceous subfamilies and genera took place during Mid-Jurassic and Lower Cretaceous, respectively. Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix-Pseudotsuga-Piceae-Cathaya-Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, and Piceae-Cathaya-Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix-Pseudotsuga, Picea, and Cathaya-Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae. Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies.

  3. [Study of the root nodules in some species of the Papilionaceae subfamily by scanning electron microscopy].

    PubMed

    Novikova, T I; Gordienko, N Ia

    2001-01-01

    Nitrogen-fixing nodules from 16 species in 6 tribes of the sub-family Papilionaceae have been examined by scanning electron microscopy. The structure of infection threads was similar in all the studied papilionoid species except Lupinus polyphillus. In this species the infection threads were found in young nodules only. The morphology of bacterioids and the character of their "package" are determined by the host plant genotype. The obtained results are discussed in relation to the evolution of the legumes.

  4. Data supporting the nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae).

    PubMed

    Comer, Jason R; Zomlefer, Wendy B; Barrett, Craig F; Stevenson, Dennis Wm; Heyduk, Karolina; Leebens-Mack, James H

    2016-06-01

    This data article provides data and supplemental materials referenced in "Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae)" (Comer et al., 2016) [1]. Raw sequence reads generated for this study are available through the Sequence Read Archive (SRA Study Accession: SRP061467). An aligned supermatrix of 168 nuclear genes for 35 taxa (34 palms and one outgroup taxon) is provided. Also provided are individual maximum likelihood gene trees used for the coalescent based analyses, output from the maximum parsimony analyses, and two figures.

  5. Comparative Chloroplast Genomics Reveals the Evolution of Pinaceae Genera and Subfamilies

    PubMed Central

    Lin, Ching-Ping; Huang, Jen-Pan; Wu, Chung-Shien; Hsu, Chih-Yao; Chaw, Shu-Miaw

    2010-01-01

    As the largest and the basal-most family of conifers, Pinaceae provides key insights into the evolutionary history of conifers. We present comparative chloroplast genomics and analysis of concatenated 49 chloroplast protein-coding genes common to 19 gymnosperms, including 15 species from 8 Pinaceous genera, to address the long-standing controversy about Pinaceae phylogeny. The complete cpDNAs of Cathaya argyrophylla and Cedrus deodara (Abitoideae) and draft cpDNAs of Larix decidua, Picea morrisonicola, and Pseudotsuga wilsoniana are reported. We found 21- and 42-kb inversions in congeneric species and different populations of Pinaceous species, which indicates that structural polymorphics may be common and ancient in Pinaceae. Our phylogenetic analyses reveal that Cedrus is clustered with Abies–Keteleeria rather than the basal-most genus of Pinaceae and that Cathaya is closer to Pinus than to Picea or Larix–Pseudotsuga. Topology and structural change tests and indel-distribution comparisons lend further evidence to our phylogenetic finding. Our molecular datings suggest that Pinaceae first evolved during Early Jurassic, and diversification of Pinaceous subfamilies and genera took place during Mid-Jurassic and Lower Cretaceous, respectively. Using different maximum-likelihood divergences as thresholds, we conclude that 2 (Abietoideae and Larix–Pseudotsuga–Piceae–Cathaya–Pinus), 4 (Cedrus, non-Cedrus Abietoideae, Larix–Pseudotsuga, and Piceae–Cathaya–Pinus), or 5 (Cedrus, non-Cedrus Abietoideae, Larix–Pseudotsuga, Picea, and Cathaya–Pinus) groups/subfamilies are more reasonable delimitations for Pinaceae. Specifically, our views on subfamilial classifications differ from previous studies in terms of the rank of Cedrus and with recognition of more than two subfamilies. PMID:20651328

  6. DNA Barcoding of the parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) from Chamela, Mexico

    PubMed Central

    Gutiérrez-Arellano, Daniela; Gutiérrez-Arellano, Claudia Renata

    2015-01-01

    Abstract Background and aims. The Doryctinae is a considerably diverse, poorly studied group of parasitoid wasps and one of the most diverse subfamilies within Braconidae. Taxonomic knowledge of this group remains highly incomplete, specially in the tropics. In Mexico, it has been reported as the subfamily with the highest number of recorded genera. A preliminary Barcoding study carried out in the Chamela region, located near the Mexican pacific coast in Jalisco, identified 185 barcoding species of Dorytinae assigned to 19 identified doryctine genera. This work updates the later study, representing a three years effort to assess the species richness of this subfamily for the Chamela region. Materials and methods. Ten collecting field trips of 5 to 10 days each were carried out from June 2009 to May 2011. A 2% divergence criterion using the BIN system implemented in BOLD was followed in order to establish species boundaries among the specimens that were collected. Results and conclusions. A total of 961 specimens were collected, from which 883 COI sequences were obtained. The sequences generated corresponded to 289 barcoding species and 30 identified genera. The most speciose genera were Heterospilus Haliday (170 spp.), Ecphylus Förster (19 spp.), Allorhogas Gahan (15 spp.) and Callihormius Ashmead (14 spp.). Addition of previously collected material increased the diversity of the subfamily in the region to 34 genera and 290 species. Paraphyly of Heterospilus with respect to Neoheterospilus and Heterospathius was again recovered. Twenty new species and two new genera (Sabinita Belokobylskij, Zaldívar-Riverón et Martínez, Ficobolus Martínez, Belokobylskij et Zaldívar-Riverón) have been described so far from the material collected in this work. PMID:26023287

  7. DNA Barcoding of the parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) from Chamela, Mexico.

    PubMed

    Gutiérrez-Arellano, Daniela; Gutiérrez-Arellano, Claudia Renata; Zaldívar-Riverón, Alejandro

    2015-01-01

    Background and aims. The Doryctinae is a considerably diverse, poorly studied group of parasitoid wasps and one of the most diverse subfamilies within Braconidae. Taxonomic knowledge of this group remains highly incomplete, specially in the tropics. In Mexico, it has been reported as the subfamily with the highest number of recorded genera. A preliminary Barcoding study carried out in the Chamela region, located near the Mexican pacific coast in Jalisco, identified 185 barcoding species of Dorytinae assigned to 19 identified doryctine genera. This work updates the later study, representing a three years effort to assess the species richness of this subfamily for the Chamela region. Materials and methods. Ten collecting field trips of 5 to 10 days each were carried out from June 2009 to May 2011. A 2% divergence criterion using the BIN system implemented in BOLD was followed in order to establish species boundaries among the specimens that were collected. Results and conclusions. A total of 961 specimens were collected, from which 883 COI sequences were obtained. The sequences generated corresponded to 289 barcoding species and 30 identified genera. The most speciose genera were Heterospilus Haliday (170 spp.), Ecphylus Förster (19 spp.), Allorhogas Gahan (15 spp.) and Callihormius Ashmead (14 spp.). Addition of previously collected material increased the diversity of the subfamily in the region to 34 genera and 290 species. Paraphyly of Heterospilus with respect to Neoheterospilus and Heterospathius was again recovered. Twenty new species and two new genera (Sabinita Belokobylskij, Zaldívar-Riverón et Martínez, Ficobolus Martínez, Belokobylskij et Zaldívar-Riverón) have been described so far from the material collected in this work.

  8. Ancient Complexity, Opisthokont Plasticity, and Discovery of the 11th Subfamily of Arf GAP Proteins

    PubMed Central

    Schlacht, Alexander; Mowbrey, Kevin; Elias, Marek; Kahn, Richard A.; Dacks, Joel B.

    2013-01-01

    The organelle paralogy hypothesis is one model for the acquisition of non-endosymbiotic organelles, generated from molecular evolutionary analyses of proteins encoding specificity in the membrane traffic system. GTPase Activating Proteins (GAPs) for the ADP-ribosylation factor (Arfs) GTPases are additional regulators of the kinetics and fidelity of membrane traffic. Here we describe molecular evolutionary analyses of Arf GAP protein family. Of the ten subfamilies previously defined in humans, we find that five were likely present in the Last Eukaryotic Common Ancestor (LECA). Of the three more recently derived subfamilies, one was likely present in the ancestor of opisthokonts (animals and fungi) and apusomonads (flagellates classified as the sister lineage to opisthokonts), while two arose in the holozoan lineage. We also propose to have identified a novel ancient subfamily (ArfGAPC2), present in diverse eukaryotes but which is lost frequently, including in the opisthokonts. Surprisingly few ancient domains accompanying the ArfGAP domain were identified, in marked contrast to the extensively decorated human Arf GAPs. Phylogenetic analyses of the subfamilies reveal patterns of single and multiple gene duplications specific to the Holozoa, to some degree mirroring evolution of Arf GAP targets, the Arfs. Conservation, and lack thereof, of various residues in the ArfGAP structure provide contextualization of previously identified functional amino acids and their application to Arf GAP biology in general. Overall, our results yield insights into current Arf GAP biology, reveal complexity in the ancient eukaryotic ancestor, and integrate the Arf GAP family into a proposed mechanism for the evolution of non-endosymbiotic organelles. PMID:23433073

  9. Structure-function analysis of a novel member of the LIV-1 subfamily of zinc transporters, ZIP14.

    PubMed

    Taylor, K M; Morgan, H E; Johnson, A; Nicholson, R I

    2005-01-17

    Here, we report the first investigation of a novel member of the LZT (LIV-1 subfamily of ZIP zinc Transporters) subfamily of zinc influx transporters. LZT subfamily sequences all contain a unique and highly conserved metalloprotease motif (HEXPHEXGD) in transmembrane domain V with both histidine residues essential for zinc transport by ZIP (Zrt-, Irt-like Proteins) transporters. We investigate here whether ZIP14 (SLC39A14), lacking the initial histidine in this motif, is still able to transport zinc. We demonstrate that this plasma membrane located glycosylated protein functions as a zinc influx transporter in a temperature-dependant manner.

  10. A large-scale chloroplast phylogeny of the Lamiaceae sheds new light on its subfamilial classification

    PubMed Central

    Li, Bo; Cantino, Philip D.; Olmstead, Richard G.; Bramley, Gemma L. C.; Xiang, Chun-Lei; Ma, Zhong-Hui; Tan, Yun-Hong; Zhang, Dian-Xiang

    2016-01-01

    Lamiaceae, the sixth largest angiosperm family, contains more than 7000 species distributed all over the world. However, although considerable progress has been made in the last two decades, its phylogenetic backbone has never been well resolved. In the present study, a large-scale phylogenetic reconstruction of Lamiaceae using chloroplast sequences was carried out with the most comprehensive sampling of the family to date (288 species in 191 genera, representing approximately 78% of the genera of Lamiaceae). Twelve strongly supported primary clades were inferred, which form the phylogenetic backbone of Lamiaceae. Six of the primary clades correspond to the current recognized subfamilies Ajugoideae, Lamioideae, Nepetoideae, Prostantheroideae, Scutellarioideae, and Symphorematoideae, and one corresponds to a portion of Viticoideae. The other five clades comprise: 1) Acrymia and Cymaria; 2) Hymenopyramis, Petraeovitex, Peronema, and Garrettia; 3) Premna, Gmelina, and Cornutia; 4) Callicarpa; and 5) Tectona. Based on these results, three new subfamilies—Cymarioideae, Peronematoideae, and Premnoideae—are described, and the compositions of other subfamilies are updated based on new findings from the last decade. Furthermore, our analyses revealed five strongly supported, more inclusive clades that contain subfamilies, and we give them phylogenetically defined, unranked names: Cymalamiina, Scutelamiina, Perolamiina, Viticisymphorina, and Calliprostantherina. PMID:27748362

  11. Amplification of prolamin storage protein genes in different subfamilies of the Poaceae.

    PubMed

    Xu, Jian-Hong; Messing, Joachim

    2009-11-01

    Prolamins are seed storage proteins in cereals and represent an important source of essential amino acids for feed and food. Genes encoding these proteins resulted from dispersed and tandem amplification. While previous studies have concentrated on protein sequences from different grass species, we now can add a new perspective to their relationships by asking how their genes are shared by ancestry and copied in different lineages of the same family of species. These differences are derived from alignment of chromosomal regions, where collinearity is used to identify prolamin genes in syntenic positions, also called orthologous gene copies. New or paralogous gene copies are inserted in tandem or new locations of the same genome. More importantly, one can detect the loss of older genes. We analyzed chromosomal intervals containing prolamin genes from rice, sorghum, wheat, barley, and Brachypodium, representing different subfamilies of the Poaceae. The Poaceae commonly known as the grasses includes three major subfamilies, the Ehrhartoideae (rice), Pooideae (wheat, barley, and Brachypodium), and Panicoideae (millets, maize, sorghum, and switchgrass). Based on chromosomal position and sequence divergence, it becomes possible to infer the order of gene amplification events. Furthermore, the loss of older genes in different subfamilies seems to permit a faster pace of divergence of paralogous genes. Change in protein structure affects their physical properties, subcellular location, and amino acid composition. On the other hand, regulatory sequence elements and corresponding transcriptional activators of new gene copies are more conserved than coding sequences, consistent with the tissue-specific expression of these genes.

  12. The Evolution of the SEPALLATA Subfamily of MADS-Box Genes

    PubMed Central

    Zahn, Laura M.; Kong, Hongzhi; Leebens-Mack, James H.; Kim, Sangtae; Soltis, Pamela S.; Landherr, Lena L.; Soltis, Douglas E.; dePamphilis, Claude W.; Ma, Hong

    2005-01-01

    Members of the SEPALLATA (SEP) MADS-box subfamily are required for specifying the “floral state” by contributing to floral organ and meristem identity. SEP genes have not been detected in gymnosperms and seem to have originated since the lineage leading to extant angiosperms diverged from extant gymnosperms. Therefore, both functional and evolutionary studies suggest that SEP genes may have been critical for the origin of the flower. To gain insights into the evolution of SEP genes, we isolated nine genes from plants that occupy phylogenetically important positions. Phylogenetic analyses of SEP sequences show that several gene duplications occurred during the evolution of this subfamily, providing potential opportunities for functional divergence. The first duplication occurred prior to the origin of the extant angiosperms, resulting in the AGL2/3/4 and AGL9 clades. Subsequent duplications occurred within these clades in the eudicots and monocots. The timing of the first SEP duplication approximately coincides with duplications in the DEFICIENS/GLOBOSA and AGAMOUS MADS-box subfamilies, which may have resulted from either a proposed genome-wide duplication in the ancestor of extant angiosperms or multiple independent duplication events. Regardless of the mechanism of gene duplication, these pairs of duplicate transcription factors provided new possibilities of genetic interactions that may have been important in the origin of the flower. PMID:15687268

  13. PICKLE is a CHD subfamily II ATP-dependent chromatin remodeling factor.

    PubMed

    Ho, Kwok Ki; Zhang, Heng; Golden, Barbara L; Ogas, Joe

    2013-02-01

    PICKLE plays a critical role in repression of genes that regulate development identity in Arabidopsis thaliana. PICKLE codes for a putative ATP-dependent chromatin remodeler that exhibits sequence similarity to members of subfamily II of animal CHD remodelers, which includes remodelers such as CHD3/Mi-2 that also restrict expression of developmental regulators. Whereas animal CHD3 remodelers are a component of the Mi-2/NuRD complex that promotes histone deacetylation, PICKLE promotes trimethylation of histone H3 lysine 27 suggesting that it acts via a distinct epigenetic pathway. Here, we examine whether PICKLE is also a member of a multisubunit complex and characterize the biochemical properties of recombinant PICKLE protein. Phylogenetic analysis indicates that PICKLE-related proteins in plants share a common ancestor with members of subfamily II of animal CHD remodelers. Biochemical characterization of PICKLE in planta, however, reveals that PICKLE primarily exists as a monomer. Recombinant PICKLE protein is an ATPase that is stimulated by ssDNA and mononucleosomes and binds to both naked DNA and mononucleosomes. Furthermore, recombinant PICKLE exhibits ATP-dependent chromatin remodeling activity. These studies demonstrate that subfamily II CHD proteins in plants, such as PICKLE, retain ATP-dependent chromatin remodeling activity but act through a mechanism that does not involve the ubiquitous Mi-2/NuRD complex.

  14. Genesis of the vertebrate FoxP subfamily member genes occurred during two ancestral whole genome duplication events.

    PubMed

    Song, Xiaowei; Tang, Yezhong; Wang, Yajun

    2016-08-22

    The vertebrate FoxP subfamily genes play important roles in the construction of essential functional modules involved in physiological and developmental processes. To explore the adaptive evolution of functional modules associated with the FoxP subfamily member genes, it is necessary to study the gene duplication process. We detected four member genes of the FoxP subfamily in sea lampreys (a representative species of jawless vertebrates) through genome screenings and phylogenetic analyses. Reliable paralogons (i.e. paralogous chromosome segments) have rarely been detected in scaffolds of FoxP subfamily member genes in sea lampreys due to the considerable existence of HTH_Tnp_Tc3_2 transposases. However, these transposases did not alter gene numbers of the FoxP subfamily in sea lampreys. The coincidence between the "1-4" gene duplication pattern of FoxP subfamily genes from invertebrates to vertebrates and two rounds of ancestral whole genome duplication (1R- and 2R-WGD) events reveal that the FoxP subfamily of vertebrates was quadruplicated in the 1R- and 2R-WGD events. Furthermore, we deduced that a synchronous gene duplication process occurred for the FoxP subfamily and for three linked gene families/subfamilies (i.e. MIT family, mGluR group III and PLXNA subfamily) in the 1R- and 2R-WGD events using phylogenetic analyses and mirror-dendrogram methods (i.e. algorithms to test protein-protein interactions). Specifically, the ancestor of FoxP1 and FoxP3 and the ancestor of FoxP2 and FoxP4 were generated in 1R-WGD event. In the subsequent 2R-WGD event, these two ancestral genes were changed into FoxP1, FoxP2, FoxP3 and FoxP4. The elucidation of these gene duplication processes shed light on the phylogenetic relationships between functional modules of the FoxP subfamily member genes.

  15. Schistosoma mansoni: Identification of SmNR4A, a member of nuclear receptor subfamily 4

    PubMed Central

    Wu, Wenjie; LoVerde, Philip T.

    2008-01-01

    A cDNA encoding a member of nuclear receptor subfamily 4 (SmNR4A) was isolated from the trematode Schistosoma mansoni. The open reading frame (ORF) of SmNR4A cDNA is 2481 base pairs long encoding an 827 amino acid protein. Alignment of the deduced protein sequence showed the DNA binding domain (DBD) of SmNR4A is highly conserved. Like human and Drosophila members in NR subfamily 4, SmNR4A possess an atypical ligand binding domain (LBD), the conserved lysine in helix H3 is replaced by a glutamic acid, and three of the four phenylalanines which fill the entire surface of the ligand binding pocket (LBP) are conserved in SmNR4A. A phylogenetic tree of SmNR4A was constructed using the conserved protein sequence of the DBD, the C-terminal-extension of DBD (CTE) and the LBD. The results show that the SmNR4A is a member of NR subfamily 4 from S. mansoni. The SmNR4A gene contains six exons spanning more than 50 kbp. The relative mRNA expression levels of SmNR4A were evaluated in fourteen different developmental stages by quantitative real-time reverse-transcriptase polymerase chain reaction (qPCR). The results demonstrated that SmNR4A expression was regulated throughout development. It was highly expressed in daughter sporocysts and 35-day worms, but barely expressed in cercariae and 1-hour and 3-day schistosomules. PMID:18682251

  16. Reassessment of Species Diversity of the Subfamily Denticollinae (Coleoptera: Elateridae) through DNA Barcoding

    PubMed Central

    Lee, Seunghwan; Park, In Gyun; Park, Haechul

    2016-01-01

    The subfamily Denticollinae is a taxonomically diverse group in the family Elateridae. Denticollinae includes many morphologically similar species and crop pests, as well as many undescribed species at each local fauna. To construct a rapid and reliable identification system for this subfamily, the effectiveness of molecular species identification was assessed based on 421 cytochrome c oxidase subunit I (COI) sequences of 84 morphologically identified species. Among the 84 morphospecies, molecular species identification of 60 species (71.4%) was consistent with their morphological identifications. Six cryptic and/or pseudocryptic species with large genetic divergence (>5%) were confirmed by their sympatric or allopatric distributions. However, 18 species, including a subspecies, had ambiguous genetic distances and shared overlapping intra- and interspecific genetic distances (range: 2.12%–3.67%) suggesting incomplete lineage sorting, introgression of mitochondrial genome, or affection by endosymbionts, such as Wolbachia infection, between species and simple genetic variation within species. In this study, we propose a conservative threshold of 3.6% for convenient molecular operational taxonomic unit (MOTU) identification in the subfamily Denticollinae based on the results of pairwise genetic distances analyses using neighbor-joining, mothur, Automatic Barcode Gap Discovery analysis, and tree-based species delimitation by Poisson Tree Processes analysis. Using the 3.6% threshold, we identified 87 MOTUs and found 8 MOTUs in the interval between 2.5% to 3.5%. Evaluation of MOTUs identified in this range requires integrative species delimitation, including review of morphological and ecological differences as well as sensitive genetic markers. From this study, we confirmed that COI sequence is useful for reassessing species diversity for polymorphic and polytypic species occurring in sympatric and allopatric distributions, and for a single species having an

  17. Phylogeny and Evolutionary Patterns in the Dwarf Crayfish Subfamily (Decapoda: Cambarellinae)

    PubMed Central

    Pedraza-Lara, Carlos; Doadrio, Ignacio; Breinholt, Jesse W.; Crandall, Keith A.

    2012-01-01

    The Dwarf crayfish or Cambarellinae, is a morphologically singular subfamily of decapod crustaceans that contains only one genus, Cambarellus. Its intriguing distribution, along the river basins of the Gulf Coast of United States (Gulf Group) and into Central México (Mexican Group), has until now lacked of satisfactory explanation. This study provides a comprehensive sampling of most of the extant species of Cambarellus and sheds light on its evolutionary history, systematics and biogeography. We tested the impact of Gulf Group versus Mexican Group geography on rates of cladogenesis using a maximum likelihood framework, testing different models of birth/extinction of lineages. We propose a comprehensive phylogenetic hypothesis for the subfamily based on mitochondrial and nuclear loci (3,833 bp) using Bayesian and Maximum Likelihood methods. The phylogenetic structure found two phylogenetic groups associated to the two main geographic components (Gulf Group and Mexican Group) and is partially consistent with the historical structure of river basins. The previous hypothesis, which divided the genus into three subgenera based on genitalia morphology was only partially supported (P = 0.047), resulting in a paraphyletic subgenus Pandicambarus. We found at least two cases in which phylogenetic structure failed to recover monophyly of recognized species while detecting several cases of cryptic diversity, corresponding to lineages not assigned to any described species. Cladogenetic patterns in the entire subfamily are better explained by an allopatric model of speciation. Diversification analyses showed similar cladogenesis patterns between both groups and did not significantly differ from the constant rate models. While cladogenesis in the Gulf Group is coincident in time with changes in the sea levels, in the Mexican Group, cladogenesis is congruent with the formation of the Trans-Mexican Volcanic Belt. Our results show how similar allopatric divergence in

  18. ARGONAUTE SUBFAMILY GENES IN THE SMALL BROWN PLANTHOPPER, Laodelphax striatellus (HEMIPTERA: DELPHACIDAE).

    PubMed

    Zhou, Yan-Ru; Li, Lin-Ying; Li, Jun-Min; Sun, Zong-Tao; Xie, Li; Chen, Jian-Ping

    2016-01-01

    Argonaute (AGO) proteins are essential catalytic components of the RNA-induced silencing complex and play central roles in RNA interference. Using a combination of bioinformatics and rapid amplification of cDNA ends (RACE) methods, putative AGO subfamily members, ls-AGO1 and ls-AGO2, were cloned and characterized from the small brown planthopper, Laodelphax striatellus. The open reading frame (ORF) of ls-AGO1 is 2,820 bp long, encoding a putative protein of 939 amino acid residues, and ls-AGO2 contains an ORF of 2,490 bp, encoding 829 amino acid residues. The expected conserved PAZ and PIWI domains, and the conserved Asp-Asp-His (DDH) catalytic triad motif in the PIWI domain were observed in both ls-AGO1 and ls-AGO2. Reverse transcription-qPCR (RT-qPCR) results showed that both ls-AGO1 and ls-AGO2 were expressed in all developmental stages of L. striatellus with highest mRNA abundance in eggs. Expression of ls-AGO1 and ls-AGO2 was significantly decreased in adult insects in response to acquisition of rice black-streaked dwarf virus by second instar nymphs. mRNA expression of ls-AGO1 was significantly downregulated in response to low and high temperatures, but expression of ls-AGO2 was only affected by low temperature. ls-AGO1 and ls-AGO2 were initially downregulated when insects were transferred from rice to maize and to the wild grass Brachypodium distachyon, but expression showed partial or complete recovery 7 days after transfer. These results document that AGO subfamily members of L. striatellus are ubiquitously expressed at different developmental stages and respond to various stresses. Thus, AGO subfamily may act in regulating the stress-response of L. striatellus by controlling related gene expression.

  19. The formation of the polyploid hybrids from different subfamily fish crossings and its evolutionary significance.

    PubMed

    Liu, Shaojun; Qin, Qinbo; Xiao, Jun; Lu, Wenting; Shen, Jiamin; Li, Wei; Liu, Jifang; Duan, Wei; Zhang, Chun; Tao, Min; Zhao, Rurong; Yan, Jinpeng; Liu, Yun

    2007-06-01

    This study provides genetic evidences at the chromosome, DNA content, DNA fragment and sequence, and morphological levels to support the successful establishment of the polyploid hybrids of red crucian carp x blunt snout bream, which belonged to a different subfamily of fish (Cyprininae subfamily and Cultrinae subfamily) in the catalog. We successfully obtained the sterile triploid hybrids and bisexual fertile tetraploid hybrids of red crucian carp (RCC) (female symbol) x blunt snout bream (BSB) (male symbol) as well as their pentaploid hybrids. The triploid hybrids possessed 124 chromosomes with two sets from RCC and one set from BSB; the tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from BSB. The females of tetraploid hybrids produced unreduced tetraploid eggs that were fertilized with the haploid sperm of BSB to generate pentaploid hybrids with 172 chromosomes with three sets from BSB and two sets from RCC. The ploidy levels of triploid, tetraploid, and pentaploid hybrids were confirmed by counting chromosomal number, forming chromosomal karyotype, and measuring DNA content and erythrocyte nuclear volume. The similar and different DNA fragments were PCR amplified and sequenced in triploid, tetraploid hybrids, and their parents, indicating their molecular genetic relationship and genetic markers. In addition, this study also presents results about the phenotypes and feeding habits of polyploid hybrids and discusses the formation mechanism of the polyploid hybrids. It is the first report on the formation of the triploid, tetraploid, and pentaploid hybrids by crossing parents with a different chromosome number in vertebrates. The formation of the polyploid hybrids is potentially interesting in both evolution and fish genetic breeding.

  20. A novel subfamily of Hsp70s in the endoplasmic reticulum.

    PubMed

    A, R; Tyson, J R; Stirling, C J

    1997-07-01

    The endoplasmic reticulum contains a number of proteins involved in the processing of secretory polypeptides. These include BiP, which is an Hsp70-family member highly conserved throughout evolution. BiP is known to be intimately involved in several aspects of protein biogenesis, but our understanding of these events has been complicated by the recent description of a novel Hsp70-related protein in yeast, Lhauthorp, whose functions overlap with those of BiP. Current indications are that this protein is distributed widely among eukaryotes and that it represents a distinct subfamily of the Hsp70 class of molecular chaperones.

  1. Dimorphic chloroplasts in the epidermis of Podostemoideae, a subfamily of the unique aquatic angiosperm family Podostemaceae.

    PubMed

    Fujinami, Rieko; Yoshihama, Isao; Imaichi, Ryoko

    2011-09-01

    Plants of the Podostemoideae, a subfamily of the unique aquatic angiosperm family Podostemaceae, which are found in rapids and waterfalls of the tropics and subtropics, have two different sizes of chloroplasts in their epidermis. These small and large chloroplasts are located separately in each epidermal cell along its upper and inner tangential walls, respectively. This is the first case of the chloroplast dimorphism in a single epidermal cell of angiosperms. While the large chloroplasts have well developed starch grains, the small chloroplasts have a normal granal ultrastructure but very few starch grains. This suggests that the small chloroplasts mainly function in CO(2) uptake for photosynthesis from torrential water.

  2. Phthiria sharafi sp. nov., a new record of the subfamily Phthiriinae (Bombyliidae, Diptera) from Saudi Arabia.

    PubMed

    El-Hawagry, Magdi S; Al Dhafer, Hathal M

    2014-10-10

    This new species (Phthiria sharafi sp. nov.) represents the first record of the subfamily Phthiriinae (Bombyliidae, Diptera) from Saudi Arabia. The species was collected from Garf Raydah Protected Area, Abha, Asir Province, south-western part of Saudi Arabia, using a Malaise trap erected in a site rich in olive, cactus and Juniper trees. The type locality has an Afrotropical influence, with the Afrotropical elements predominant, and a closer affiliation to the Afrotropical region than to the Palearctic region or the Eremic zone. 

  3. Current status of subfamily Ichneumoninae (Hymenoptera: Ichneumonidae) from Malaysia and Singapore

    NASA Astrophysics Data System (ADS)

    Norhafiza, A. F.; Idris, A. B.

    2013-11-01

    In this paper, 25 genera and 38 species under 10 tribes (Alomyini, Compsophorini, Goedartiini, Heresiarchini, Ichneumonini, Ischnojoppini, Joppocryptini, Listrodromini, Oedicephalini and Platylabini) of the subfamily Ichneumoninae housed in the Centre for Insect Systematics, UKM and Raffles Museum of Biodiversity Research (National University of Singapore) are reported from Malaysia and Singapore. The tribe Heresiarchini has the greatest number of species (13) followed by Ichneumonini with six species. Imeria is the largest genus which contains five species recorded. Six species in this study are new records for Malaysia.

  4. Identification of multiple distinct Snf2 subfamilies with conserved structural motifs

    PubMed Central

    Flaus, Andrew; Martin, David M. A.; Barton, Geoffrey J.; Owen-Hughes, Tom

    2006-01-01

    The Snf2 family of helicase-related proteins includes the catalytic subunits of ATP-dependent chromatin remodelling complexes found in all eukaryotes. These act to regulate the structure and dynamic properties of chromatin and so influence a broad range of nuclear processes. We have exploited progress in genome sequencing to assemble a comprehensive catalogue of over 1300 Snf2 family members. Multiple sequence alignment of the helicase-related regions enables 24 distinct subfamilies to be identified, a considerable expansion over earlier surveys. Where information is known, there is a good correlation between biological or biochemical function and these assignments, suggesting Snf2 family motor domains are tuned for specific tasks. Scanning of complete genomes reveals all eukaryotes contain members of multiple subfamilies, whereas they are less common and not ubiquitous in eubacteria or archaea. The large sample of Snf2 proteins enables additional distinguishing conserved sequence blocks within the helicase-like motor to be identified. The establishment of a phylogeny for Snf2 proteins provides an opportunity to make informed assignments of function, and the identification of conserved motifs provides a framework for understanding the mechanisms by which these proteins function. PMID:16738128

  5. The AFL subfamily of B3 transcription factors: evolution and function in angiosperm seeds.

    PubMed

    Carbonero, Pilar; Iglesias-Fernández, Raquel; Vicente-Carbajosa, Jesús

    2016-12-21

    Seed development follows zygotic embryogenesis; during the maturation phase reserves accumulate and desiccation tolerance is acquired. This is tightly regulated at the transcriptional level and the AFL (ABI3/FUS3/LEC2) subfamily of B3 transcription factors (TFs) play a central role. They alter hormone biosynthesis, mainly in regards to abscisic acid and gibberellins, and also regulate the expression of other TFs and/or modulate their downstream activity via protein-protein interactions. This review deals with the origin of AFL TFs, which can be traced back to non-vascular plants such as Physcomitrella patens and achieves foremost expansion in the angiosperms. In green algae, like the unicellular Chlamydomonas reinhardtii or the pluricellular Klebsormidium flaccidum, a single B3 gene and four B3 paralogous genes are annotated, respectively. However, none of them present with the structural features of the AFL subfamily, with the exception of the B3 DNA-binding domain. Phylogenetic analysis groups the AFL TFs into four Major Clusters of Ortologous Genes (MCOGs). The origin and function of these genes is discussed in view of their expression patterns and in the context of major regulatory interactions in seeds of monocotyledonous and dicotyledonous species.

  6. GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains.

    PubMed

    Lee, David A; Rentzsch, Robert; Orengo, Christine

    2010-01-01

    GeMMA (Genome Modelling and Model Annotation) is a new approach to automatic functional subfamily classification within families and superfamilies of protein sequences. A major advantage of GeMMA is its ability to subclassify very large and diverse superfamilies with tens of thousands of members, without the need for an initial multiple sequence alignment. Its performance is shown to be comparable to the established high-performance method SCI-PHY. GeMMA follows an agglomerative clustering protocol that uses existing software for sensitive and accurate multiple sequence alignment and profile-profile comparison. The produced subfamilies are shown to be equivalent in quality whether whole protein sequences are used or just the sequences of component predicted structural domains. A faster, heuristic version of GeMMA that also uses distributed computing is shown to maintain the performance levels of the original implementation. The use of GeMMA to increase the functional annotation coverage of functionally diverse Pfam families is demonstrated. It is further shown how GeMMA clusters can help to predict the impact of experimentally determining a protein domain structure on comparative protein modelling coverage, in the context of structural genomics.

  7. Phylogenetic relationships in subfamily Tillandsioideae (Bromeliaceae) based on DNA sequence data from seven plastid regions.

    PubMed

    Barfuss, Michael H J; Samuel, Rosabelle; Till, Walter; Stuessy, Tod F

    2005-02-01

    Molecular phylogenetic studies of seven plastid DNA regions were used to resolve circumscriptions at generic and infrageneric levels in subfamily Tillandsioideae of Bromeliaceae. One hundred and ten tillandsioid samples were analyzed, encompassing 10 genera, 104 species, and two cultivars. Two species of Bromelioideae, eight species of the polymorphic Pitcairnioideae, and two species of Rapateaceae were selected as outgroups. Parsimony analysis was based on sequence variation of five noncoding (partial 5' and 3' trnK intron, rps16 intron, trnL intron, trnL-trnF intergenic spacer, atpB-rbcL intergenic spacer) and two coding plastid regions (rbcL and matK). Phylogenetic analyses of individual regions produced congruent, but mostly weakly supported or unresolved clades. Results of the combined data set, however, clearly show that subfamily Tillandsioideae is monophyletic. The earliest divergence separates a lineage comprised of Glomeropitcairnia and Catopsis from the "core" tillandsioids. In their present circumscriptions, genera Vriesea and Tillandsia, and their subgenera or sections, as well as Guzmania and Mezobromelia, are poly- and/or paraphyletic. Genera Alcantarea, Werauhia, Racinaea, and Viridantha appear monophyletic, but separation of these from Vriesea and Tillandsia makes the remainder paraphyletic. Nevertheless, Tillandsioideae separates into four main clades, which are proposed as tribes, viz., Catopsideae, Glomeropitcairnieae, Vrieseeae, and Tillandsieae.

  8. A novel member of glycoside hydrolase family 30 subfamily 8 with altered substrate specificity

    PubMed Central

    St John, Franz J.; Dietrich, Diane; Crooks, Casey; Pozharski, Edwin; González, Javier M.; Bales, Elizabeth; Smith, Kennon; Hurlbert, Jason C.

    2014-01-01

    Endoxylanases classified into glycoside hydrolase family 30 subfamily 8 (GH30-8) are known to hydrolyze the hemicellulosic polysaccharide glucuronoxylan (GX) but not arabinoxylan or neutral xylooligosaccharides. This is owing to the specificity of these enzymes for the α-1,2-linked glucuronate (GA) appendage of GX. Limit hydrolysis of this substrate produces a series of aldouronates each containing a single GA substituted on the xylose penultimate to the reducing terminus. In this work, the structural and biochemical characterization of xylanase 30A from Clostridium papyro­solvens (CpXyn30A) is presented. This xylanase possesses a high degree of amino-acid identity to the canonical GH30-8 enzymes, but lacks the hallmark β8–α8 loop region which in part defines the function of this GH30 subfamily and its role in GA recognition. CpXyn30A is shown to have a similarly low activity on all xylan substrates, while hydrolysis of xylohexaose revealed a competing transglycosylation reaction. These findings are directly compared with the model GH30-8 enzyme from Bacillus subtilis, XynC. Despite its high sequence identity to the GH30-8 enzymes, CpXyn30A does not have any apparent specificity for the GA appendage. These findings confirm that the typically conserved β8–α8 loop region of these enzymes influences xylan substrate specificity but not necessarily β-1,4-xylanase function. PMID:25372685

  9. Phylogenetic relationships between flies of the Tephritinae subfamily (Diptera, Tephritidae) and their symbiotic bacteria.

    PubMed

    Mazzon, Luca; Martinez-Sañudo, Isabel; Simonato, Mauro; Squartini, Andrea; Savio, Claudia; Girolami, Vincenzo

    2010-07-01

    The Tephritinae is considered the most specialized subfamily of fruit flies, predominantly infesting flowerheads of Asteraceae. Some species are known to host specific non-culturable symbiont bacteria ("Candidatus Stammerula spp.") in the midgut. In this work we (i) examined the phylogenetic relationships among the insect hosts, (ii) investigated the presence of bacteria in other hitherto unexamined species, and (iii) evaluated the phylogenetic congruence between insects and symbionts. A total of 33 Tephritinae species in 17 different genera were analyzed. Two regions of the mitochondrial DNA (16S rDNA and COI-tRNALeu-COII) were examined in the insect host, while the 16S was analyzed in the bacteria. From the phylogenetic trees, four of the five tribes considered were statistically supported by each of the clustering methods used. Species belonging to the tribe Noeetini never clustered at significant levels. The phylogenetic COI-tRNALeu-COII tree showed internal nodes more highly supported than the 16S phylogeny. The analysis of the distribution of symbiosis across the subfamily has highlighted the presence of bacteria only in the tribe Tephritini and in the genus Noeeta from the tribe Noeetini. A cophylogenetic analysis revealed a substantial congruence between hosts and symbionts. The interesting exceptions can be justified by events like losses, duplications and hosts switching opportunities, which are likely to arise during the biological cycle of the fly in consideration of the extracellular status of these symbionts.

  10. A consistent nomenclature of antimicrobial peptides isolated from frogs of the subfamily Phyllomedusinae.

    PubMed

    Amiche, Mohamed; Ladram, Ali; Nicolas, Pierre

    2008-11-01

    A growing number of cationic antimicrobial peptides have been isolated from the skin of hylid frogs belonging to the Phyllomedusinae subfamily. The amino acid sequences of these peptides are currently located in several databases under identifiers with no consistent system of nomenclature to describe them. In order to provide a workable terminology for antimicrobial peptides from Phyllomedusid frogs, we have made a systematic effort to collect, analyze, and classify all the Phyllomedusid peptide sequences available in databases. We propose that frogs belonging to the Phyllomedusinae subfamily should be described by the species names set out in Amphibian Species of the World: http://research.amnh.org/herpetology/amphibia/index.php, American Museum of Natural History, New York, USA. Multiple alignments analysis of at least 80 antimicrobial peptides isolated from 12 Phyllomedusinae species were distributed in seven distinct peptide families including dermaseptin, phylloseptin, plasticin, dermatoxin, phylloxin, hyposin and orphan peptides, and will be considered as the name of the headgroup of each family. The parent peptide's name should be followed by the first upper letter of the species for orthologous peptides and publication date determines priority. For example, the abbreviation B for bicolor and H for hypochondrialis. When two species begin with the same letter, two letters in upper case should be used (the first letter followed by the second or the third letter and so on). For example, the abbreviation DI for distincta, DU for duellmani, VA for vaillanti and VN for vanzolinii. Paralogous peptides should bear letter(s) in upper case followed by numbers.

  11. Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts.

    PubMed

    Asakura, Yukari; Bayraktar, Omer Ali; Barkan, Alice

    2008-11-01

    Chloroplast genomes in angiosperms encode approximately 20 group II introns, approximately half of which are classified as subgroup IIB. The splicing of all but one of the subgroup IIB introns requires a heterodimer containing the peptidyl-tRNA hydrolase homolog CRS2 and one of two closely related proteins, CAF1 or CAF2, that harbor a recently recognized RNA binding domain called the CRM domain. Two CRS2/CAF-dependent introns require, in addition, a CRM domain protein called CFM2 that is only distantly related to CAF1 and CAF2. Here, we show that CFM3, a close relative of CFM2, associates in vivo with those CRS2/CAF-dependent introns that are not CFM2 ligands. Mutant phenotypes in rice and Arabidopsis support a role for CFM3 in the splicing of most of the introns with which it associates. These results show that either CAF1 or CAF2 and either CFM2 or CFM3 simultaneously bind most chloroplast subgroup IIB introns in vivo, and that the CAF and CFM subunits play nonredundant roles in splicing. These results suggest that the expansion of the CRM protein family in plants resulted in two subfamilies that play different roles in group II intron splicing, with further diversification within a subfamily to accommodate multiple intron ligands.

  12. The Evolutionary History of R2R3-MYB Proteins Across 50 Eukaryotes: New Insights Into Subfamily Classification and Expansion

    PubMed Central

    Du, Hai; Liang, Zhe; Zhao, Sen; Nan, Ming-Ge; Phan Tran, Lam-Son; Lu, Kun; Huang, Yu-Bi; Li, Jia-Na

    2015-01-01

    R2R3-MYB proteins (2R-MYBs) are one of the main transcription factor families in higher plants. Since the evolutionary history of this gene family across the eukaryotic kingdom remains unknown, we performed a comparative analysis of 2R-MYBs from 50 major eukaryotic lineages, with particular emphasis on land plants. A total of 1548 candidates were identified among diverse taxonomic groups, which allowed for an updated classification of 73 highly conserved subfamilies, including many newly identified subfamilies. Our results revealed that the protein architectures, intron patterns, and sequence characteristics were remarkably conserved in each subfamily. At least four subfamilies were derived from early land plants, 10 evolved from spermatophytes, and 19 from angiosperms, demonstrating the diversity and preferential expansion of this gene family in land plants. Moreover, we determined that their remarkable expansion was mainly attributed to whole genome and segmental duplication, where duplicates were preferentially retained within certain subfamilies that shared three homologous intron patterns (a, b, and c) even though up to 12 types of patterns existed. Through our integrated distributions, sequence characteristics, and phylogenetic tree analyses, we confirm that 2R-MYBs are old and postulate that 3R-MYBs may be evolutionarily derived from 2R-MYBs via intragenic domain duplication. PMID:26047035

  13. Altered NR4A Subfamily Gene Expression Level in Peripheral Blood of Parkinson's and Alzheimer's Disease Patients.

    PubMed

    Montarolo, Francesca; Perga, Simona; Martire, Serena; Navone, Désirée Nicole; Marchet, Alberto; Leotta, Daniela; Bertolotto, Antonio

    2016-10-01

    Parkinson's disease (PD) is a neurodegenerative pathology characterized by the degeneration of midbrain dopamine neurons, whose development and maintenance in brain is related to the transcription factor NR4A2 (also called Nurr1). Notably, NR4A2 is a neuroprotective agent with anti-inflammatory role in microglia and astrocytes. Furthermore, mutations in NR4A2 gene are associated to the familial form of PD, and its gene expression level is down-regulated in blood obtained from PD patients. NR4A2 belongs to the NR4A subfamily consisting of three members: NR4A1, NR4A2, and NR4A3. The NR4A subfamily shares high degree of homology in their molecular structure and cooperates in a spectrum of functions ranging from central nervous system to immune control during physiological and pathological conditions. Considering the close functional link between the member of NR4A subfamily, we performed a gene expression analysis of NR4A1, NR4A2, and NR4A3 in peripheral blood obtained from PD patients and healthy controls (HC). Then, in order to evaluate possible involvement of the NR4A subfamily in other neurodegenerative processes, we carried out the same analysis on blood obtained from Alzheimer's disease (AD) patients. A correlation between clinical features and gene expression was also evaluated. We found a marked down-regulated gene expression of the NR4A subfamily obtained from PD patients, but only a NR4A1 decrease in AD patients compared to HC. This study reports that the entire NR4A subfamily and not only NR4A2 could be systemically involved in PD suggesting that the study of these factors could be a promising approach to develop PD therapy.

  14. Molecular phylogeny of moth-specialized spider sub-family Cyrtarachninae, which includes bolas spiders.

    PubMed

    Tanikawa, Akio; Shinkai, Akira; Miyashita, Tadashi

    2014-11-01

    The evolutionary process of the unique web architectures of spiders of the sub-family Cyrtarachninae, which includes the triangular web weaver, bolas spider, and webless spider, is thought to be derived from reduction of orbicular 'spanning-thread webs' resembling ordinal orb webs. A molecular phylogenetic analysis was conducted to explore this hypothesis using orbicular web spiders Cyrtarachne, Paraplectana, Poecilopachys, triangular web spider Pasilobus, bolas spiders Ordgarius and Mastophora, and webless spider Celaenia. The phylogeny inferred from partial sequences of mt-COI, nuclear 18S-rRNA and 28S-rRNA showed that the common ancestor of these spiders diverged into two clades: a spanning-thread web clade and a bolas or webless clade. This finding suggests that the triangular web evolved by reduction of an orbicular spanning web, but that bolas spiders evolved in the early stage, which does not support the gradual web reduction hypothesis.

  15. Nasal mites of the subfamily Speleognathinae (Ereynetidae) from birds in Texas.

    PubMed

    Pence, D B; Casto, S D

    1976-06-01

    Nasal mites of the subfamily Speleognathinae were recovered from several species of birds in Texas. New host records include Ophthalmophagus striatus (Crossley) 1952 from Columbigallina passerina, Boydaia clarki Fain 1963 from Callipepla squamata, Boydaia falconis Fain 1956 from Falco sparverius, and Boydaia tyrannus Ford 1959 from Myiarchus cinerascens. Also recovered was Astrida coccyzae Pence 1972 from Coccyzus americanus. Boydaia pheucticola sp. n. from Pheucticus melanocephalus is described. It differs from similar species in the adult female by having the coxal setae formula 2-1-2-0, sensillae clavate but not globose or subglobose, and interior seta on coxa I reduced in size but not vestigial. The larva is differentiated by the modified legs II with one long recurved hooklike claw and a shorter curved claw.

  16. Quill mites of the subfamily Picobiinae (Acari: Syringophilidae) associated with woodpeckers (Aves: Piciformes: Picidae).

    PubMed

    Skoracki, Maciej; Unsoeld, Markus; Kavetska, Katarzyna; Kaszewska, Katarzyna

    2014-03-01

    The paper contains a review of quill mites of the subfamily Picobiinae (Acari: Prostigmata: Syringophilidae) associated with woodpeckers (Aves: Piciformes: Picidae). Three new species are described: Picobia mentalis Skoracki et Unsoeld sp. nov. from Picus mentalis Temminck, Neopicobia ea Skoracki et Unsoeld sp. nov. from Celeus flavus (St. Mueller) (type host), C. elegans (St. Mueller), C. torquatus (Boddaert), and Neopicobia freya Skoracki et Unsoeld sp. nov. from Dryocopus galeatus (Temminck) (type host) and Piculus rubiginosus (Swainson). Additionally, six new host species for Picobia heeri Haller, 1878 and 12 new host species for Picobia dryobatis (Fritsch, 1956) are reported. A complete list of the picobiines parasitising birds of the family Picidae is presented in the tabular form.

  17. Identification of the KDM2/7 Histone Lysine Demethylase Subfamily Inhibitor and its Antiproliferative Activity

    PubMed Central

    2013-01-01

    Histone Nε-methyl lysine demethylases KDM2/7 have been identified as potential targets for cancer therapies. On the basis of the crystal structure of KDM7B, we designed and prepared a series of hydroxamate analogues bearing an alkyl chain. Enzyme assays revealed that compound 9 potently inhibits KDM2A, KDM7A, and KDM7B, with IC50s of 6.8, 0.2, and 1.2 μM, respectively. While inhibitors of KDM4s did not show any effect on cancer cells tested, the KDM2/7-subfamily inhibitor 9 exerted antiproliferative activity, indicating the potential for KDM2/7 inhibitors as anticancer agents. PMID:23964788

  18. That awkward age for butterflies: insights from the age of the butterfly subfamily Nymphalinae (Lepidoptera: Nymphalidae).

    PubMed

    Wahlberg, Niklas

    2006-10-01

    The study of the historical biogeography of butterflies has been hampered by a lack of well-resolved phylogenies and a good estimate of the temporal span over which butterflies have evolved. Recently there has been surge of phylogenetic hypotheses for various butterfly groups, but estimating ages of divergence is still in its infancy for this group of insects. The main problem has been the sparse fossil record for butterflies. In this study I have used a surprisingly good fossil record for the subfamily Nymphalinae (Lepidoptera: Nymphalidae) to estimate the ages of diversification of major lineages using Bayesian relaxed clock methods. I have investigated the effects of varying priors on posterior estimates in the analyses. For this data set, it is clear that the prior of the rate of molecular evolution at the ingroup node had the largest effect on the results. Taking this into account, I have been able to arrive at a plausible history of lineage splits, which appears to be correlated with known paleogeological events. The subfamily appears to have diversified soon after the K/T event about 65 million years ago. Several splits are coincident with major paleogeological events, such as the connection of the African and Asian continents about 21 million years ago and the presence of a peninsula of land connecting the current Greater Antilles to the South American continent 35 to 33 million years ago. My results suggest that the age of Nymphalidae is older than the 70 million years speculated to be the age of butterflies as a whole.

  19. Relevant use of Klotho in FGF19 subfamily signaling system in vivo.

    PubMed

    Tomiyama, Ken-ichi; Maeda, Ryota; Urakawa, Itaru; Yamazaki, Yuji; Tanaka, Tomohiro; Ito, Shinji; Nabeshima, Yoko; Tomita, Tsutomu; Odori, Shinji; Hosoda, Kiminori; Nakao, Kazuwa; Imura, Akihiro; Nabeshima, Yo-ichi

    2010-01-26

    Alpha-Klotho (alpha-Kl) and its homolog, beta-Klotho (beta-Kl) are key regulators of mineral homeostasis and bile acid/cholesterol metabolism, respectively. FGF15/ humanFGF19, FGF21, and FGF23, members of the FGF19 subfamily, are believed to act as circulating metabolic regulators. Analyses of functional interactions between alpha- and beta-Kl and FGF19 factors in wild-type, alpha-kl(-/-), and beta-kl(-/-) mice revealed a comprehensive regulatory scheme of mineral homeostasis involving the mutually regulated positive/negative feedback actions of alpha-Kl, FGF23, and 1,25(OH)(2)D and an analogous regulatory network composed of beta-Kl, FGF15/humanFGF19, and bile acids that regulate bile acid/cholesterol metabolism. Contrary to in vitro data, beta-Kl is not essential for FGF21 signaling in adipose tissues in vivo, because (i) FGF21 signals are transduced in the absence of beta-Kl, (ii) FGF21 could not be precipitated by beta-Kl, and (iii) essential phenotypes in Fgf21(-/-) mice (decreased expressions of Hsl and Atgl in WAT) were not replicated in beta-kl(-/-) mice. These findings suggest the existence of Klotho-independent FGF21 signaling pathway(s) where undefined cofactors are involved. One-to-one functional interactions such as alpha-Klotho/FGF23, beta-Klotho/FGF15 (humanFGF19), and undefined cofactor/FGF21 would result in tissue-specific signal transduction of the FGF19 subfamily.

  20. Comparative Mitogenomic Analysis of Species Representing Six Subfamilies in the Family Tenebrionidae

    PubMed Central

    Zhang, Hong-Li; Liu, Bing-Bing; Wang, Xiao-Yang; Han, Zhi-Ping; Zhang, Dong-Xu; Su, Cai-Na

    2016-01-01

    To better understand the architecture and evolution of the mitochondrial genome (mitogenome), mitogenomes of ten specimens representing six subfamilies in Tenebrionidae were selected, and comparative analysis of these mitogenomes was carried out in this study. Ten mitogenomes in this family share a similar gene composition, gene order, nucleotide composition, and codon usage. In addition, our results show that nucleotide bias was strongly influenced by the preference of codon usage for A/T rich codons which significantly correlated with the G + C content of protein coding genes (PCGs). Evolutionary rate analyses reveal that all PCGs have been subjected to a purifying selection, whereas 13 PCGs displayed different evolution rates, among which ATPase subunit 8 (ATP8) showed the highest evolutionary rate. We inferred the secondary structure for all RNA genes of Tenebrio molitor (Te2) and used this as the basis for comparison with the same genes from other Tenebrionidae mitogenomes. Some conserved helices (stems) and loops of RNA structures were found in different domains of ribosomal RNAs (rRNAs) and the cloverleaf structure of transfer RNAs (tRNAs). With regard to the AT-rich region, we analyzed tandem repeat sequences located in this region and identified some essential elements including T stretches, the consensus motif at the flanking regions of T stretch, and the secondary structure formed by the motif at the 3′ end of T stretch in major strand, which are highly conserved in these species. Furthermore, phylogenetic analyses using mitogenomic data strongly support the relationships among six subfamilies: ((Tenebrionidae incertae sedis + (Diaperinae + Tenebrioninae)) + (Pimeliinae + Lagriinae)), which is consistent with phylogenetic results based on morphological traits. PMID:27258256

  1. Heterodimerization within the TREK channel subfamily produces a diverse family of highly regulated potassium channels

    PubMed Central

    Levitz, Joshua; Royal, Perrine; Comoglio, Yannick; Wdziekonski, Brigitte; Schaub, Sébastien; Clemens, Daniel M.; Isacoff, Ehud Y.; Sandoz, Guillaume

    2016-01-01

    Twik-related K+ channel 1 (TREK1), TREK2, and Twik-related arachidonic-acid stimulated K+ channel (TRAAK) form the TREK subfamily of two-pore-domain K+ (K2P) channels. Despite sharing up to 78% sequence homology and overlapping expression profiles in the nervous system, these channels show major differences in their regulation by physiological stimuli. For instance, TREK1 is inhibited by external acidification, whereas TREK2 is activated. Here, we investigated the ability of the members of the TREK subfamily to assemble to form functional heteromeric channels with novel properties. Using single-molecule pull-down (SiMPull) from HEK cell lysate and subunit counting in the plasma membrane of living cells, we show that TREK1, TREK2, and TRAAK readily coassemble. TREK1 and TREK2 can each heterodimerize with TRAAK, but do so less efficiently than with each other. We functionally characterized the heterodimers and found that all combinations form outwardly rectifying potassium-selective channels but with variable voltage sensitivity and pH regulation. TREK1-TREK2 heterodimers show low levels of activity at physiological external pH but, unlike their corresponding homodimers, are activated by both acidic and alkaline conditions. Modeling based on recent crystal structures, along with mutational analysis, suggests that each subunit within a TREK1-TREK2 channel is regulated independently via titratable His. Finally, TREK1/TRAAK heterodimers differ in function from TRAAK homodimers in two critical ways: they are activated by both intracellular acidification and alkalinization and are regulated by the enzyme phospholipase D2. Thus, heterodimerization provides a means for diversifying functionality through an expansion of the channel types within the K2P channels. PMID:27035963

  2. Heterodimerization within the TREK channel subfamily produces a diverse family of highly regulated potassium channels.

    PubMed

    Levitz, Joshua; Royal, Perrine; Comoglio, Yannick; Wdziekonski, Brigitte; Schaub, Sébastien; Clemens, Daniel M; Isacoff, Ehud Y; Sandoz, Guillaume

    2016-04-12

    Twik-related K(+) channel 1 (TREK1), TREK2, and Twik-related arachidonic-acid stimulated K(+) channel (TRAAK) form the TREK subfamily of two-pore-domain K(+) (K2P) channels. Despite sharing up to 78% sequence homology and overlapping expression profiles in the nervous system, these channels show major differences in their regulation by physiological stimuli. For instance, TREK1 is inhibited by external acidification, whereas TREK2 is activated. Here, we investigated the ability of the members of the TREK subfamily to assemble to form functional heteromeric channels with novel properties. Using single-molecule pull-down (SiMPull) from HEK cell lysate and subunit counting in the plasma membrane of living cells, we show that TREK1, TREK2, and TRAAK readily coassemble. TREK1 and TREK2 can each heterodimerize with TRAAK, but do so less efficiently than with each other. We functionally characterized the heterodimers and found that all combinations form outwardly rectifying potassium-selective channels but with variable voltage sensitivity and pH regulation. TREK1-TREK2 heterodimers show low levels of activity at physiological external pH but, unlike their corresponding homodimers, are activated by both acidic and alkaline conditions. Modeling based on recent crystal structures, along with mutational analysis, suggests that each subunit within a TREK1-TREK2 channel is regulated independently via titratable His. Finally, TREK1/TRAAK heterodimers differ in function from TRAAK homodimers in two critical ways: they are activated by both intracellular acidification and alkalinization and are regulated by the enzyme phospholipase D2. Thus, heterodimerization provides a means for diversifying functionality through an expansion of the channel types within the K2P channels.

  3. Three new species in the subfamily Eriopeltinae Sulc from Italy (Hemiptera, Coccoidea, Coccidae) with comments on the genus Lecanopsis.

    PubMed

    Pellizzari, Giuseppina

    2013-01-01

    Three new coccid species, namely Hadzibejliaspis ferenci Pellizzari n. sp., Lecanopsis sicula Pellizzari n. sp. and L. salvatorei Pellizzari n. sp. are described and illustrated. Identification keys for the genera in the subfamily Eriopeltinae Sulc and to species in the genera Hadzibejliaspis Koteja and Lecanopsis Targioni Tozzetti are provided.

  4. THE GRK4 SUBFAMILY OF G PROTEIN-COUPLED RECEPTOR KINASES: ALTERNATIVE SPLICING, GENE ORGANIZATION, AND SEQUENCE CONSERVATION

    EPA Science Inventory

    The GRK4 subfamily of G protein-coupled receptor kinases. Alternative splicing, gene organization, and sequence conservation.

    Premont RT, Macrae AD, Aparicio SA, Kendall HE, Welch JE, Lefkowitz RJ.

    Department of Medicine, Howard Hughes Medical Institute, Duke Univer...

  5. Highly conserved salt bridge stabilizes a proteinase K subfamily enzyme, Aqualysin I, from Thermus aquaticus YT-1.

    PubMed

    Sakaguchi, Masayoshi; Osaku, Kanae; Maejima, Susumu; Ohno, Nao; Sugahara, Yasusato; Oyama, Fumitaka; Kawakita, Masao

    2014-01-01

    The proteinase K subfamily enzymes, thermophilic Aqualysin I (AQN) from Thermus aquaticus YT-1 and psychrophilic serine protease (VPR) from Vibrio sp. PA-44, have six and seven salt bridges, respectively. To understand the possible significance of salt bridges in the thermal stability of AQN, we prepared mutant proteins in which amino acid residues participating in salt bridges common to proteinase K subfamily members and intrinsic to AQN were replaced to disrupt the bridges one at a time. Disruption of a salt bridge common to proteinase K subfamily enzymes in the D183N mutant resulted in a significant reduction in thermal stability, and a massive change in the content of the secondary structure was observed, even at 70°C, in the circular dichroism (CD) analysis. These results indicate that the common salt bridge Asp183-Arg12 is important in maintaining the conformation of proteinase K subfamily enzymes and suggest the importance of proximity between the regions around Asp183 and the N-terminal region around Arg12. Of the three mutants that lack an AQN intrinsic salt bridge, D212N was more prone to unfolding at 80°C than the wild-type enzyme. Similarly, D17N and E237Q were less thermostable than the wild-type enzyme, although this may be partially due to increased autolysis. The AQN intrinsic salt bridges appear to confer additional thermal stability to this enzyme. These findings will further our understanding of the factors involved in stabilizing protein structure.

  6. Mid-Tertiary dispersal, not Gondwanan vicariance explains distribution patterns in the wax palm subfamily (Ceroxyloideae: Arecaceae).

    PubMed

    Trénel, Philipp; Gustafsson, Mats H G; Baker, William J; Asmussen-Lange, Conny B; Dransfield, John; Borchsenius, Finn

    2007-10-01

    The Ceroxyloideae is a small but heterogeneous subfamily of palms (Arecaceae, Palmae). It includes a Caribbean lineage (tribe Cyclospathae), a southern hemisphere disjunction (tribe Ceroxyleae), and an amphi-Andean element (tribe Phytelepheae), until recently considered a distinct subfamily (Phytelephantoideae) due to its highly derived morphology. A variety of hypotheses have been proposed to account for the biogeography of the subfamily, involving Gondwanan vicariance, austral interplate dispersal from South America to Australia via Antarctica, Andean orogeny, and Pleistocene refuges. We assessed the systematic classification and biogeography of the group based on a densely sampled phylogeny using >5.5kb of DNA sequences from three plastid and two nuclear genomic regions. The subfamily and each of its three tribes were resolved as monophyletic with high support. Divergence time estimates based on penalized likelihood and Bayesian dating methods indicate that Gondwanan vicariance is highly unlikely as an explanation for basic disjunctions in tribe Ceroxyleae. Alternative explanations include a mid-Tertiary trans-Atlantic/trans-African dispersal track and the "lemurian stepping stones" hypothesis. Austral interplate dispersal of Oraniopsis to Australia could have occurred, but apparently only in the mid-Eocene/early Oligocene interval after global cooling had begun. Our data do not support Pleistocene climatic changes as drivers for speciation in the Andean-centered Phytelepheae as previously proposed. Radiation in this tribe coincides largely with the major uplift of the Andes, favoring Andean orogeny over Pleistocene climatic changes as a possible speciation-promoting factor in this tribe.

  7. Evolutionary origin of the NCSI gene subfamily encoding norcoclaurine synthase is associated with the biosynthesis of benzylisoquinoline alkaloids in plants

    PubMed Central

    Vimolmangkang, Sornkanok; Deng, Xianbao; Owiti, Albert; Meelaph, Thitirat; Ogutu, Collins; Han, Yuepeng

    2016-01-01

    Sacred lotus is rich in biologically active compounds, particularly benzylisoquinoline alkaloids (BIAs). Here, we report on isolation of genes encoding (S)-norcoclaurine synthase (NCS) in sacred lotus, which is a key entry-enzyme in BIA biosynthesis. Seven NCS genes, designated NnNCS1 through NnNCS7, were identified in the sacred lotus genome, and five are located next to each other within a 83 kb region on scaffold 8. The NCS genes are divided into two subfamilies, designated NCSI and NCSII. The NCSII genes are universal in plants, while the NCSI genes are only identified in a limited number of dicotyledonous taxa that produce BIAs. In sacred lotus, only NnNCS4 belongs to the NCSII subfamily, whilst the rest NCS genes within the NCSI subfamily. Overall, the NnNCS7 gene was predominantly expressed in all tested tissues, and its expression is significantly correlated with alkaloid content in leaf. In contrast, the NnNCS4 expression shows no significant correlation with alkaloid accumulation in leaf, and its lack of expression cannot inhibit alkaloid accumulation. Taken together, these results suggest that the NCSI subfamily is crucial for BIA biosynthesis, and its origin may represent an important evolutionary event that allows certain plant taxa to produce BIAs. PMID:27189519

  8. Proteins with an alpha/beta hydrolase fold: Relationships between subfamilies in an ever-growing superfamily.

    PubMed

    Lenfant, Nicolas; Hotelier, Thierry; Bourne, Yves; Marchot, Pascale; Chatonnet, Arnaud

    2013-03-25

    Alpha/beta hydrolases function as hydrolases, lyases, transferases, hormone precursors or transporters, chaperones or routers of other proteins. The amount of structural and functional available data related to this protein superfamily expands exponentially, as does the number of proteins classified as alpha/beta hydrolases despite poor sequence similarity and lack of experimental data. However the superfamily can be rationally divided according to sequence or structural homologies, leading to subfamilies of proteins with potentially similar functions. Since the discovery of proteins homologous to cholinesterases but devoid of enzymatic activity (e.g., the neuroligins), divergent functions have been ascribed to members of other subfamilies (e.g., lipases, dipeptidylaminopeptidase IV, etc.). To study the potentially moonlighting properties of alpha/beta hydrolases, the ESTHER database (for ESTerase and alpha/beta Hydrolase Enzymes and Relatives; http://bioweb.ensam.inra.fr/esther), which collects, organizes and disseminates structural and functional information related to alpha/beta hydrolases, has been updated with new tools and the web server interface has been upgraded. A new Overall Table along with a new Tree based on HMM models has been included to tentatively group subfamilies. These tools provide starting points for phylogenetic studies aimed at pinpointing the origin of duplications leading to paralogous genes (e.g., acetylcholinesterase versus butyrylcholinesterase, or neuroligin versus carboxylesterase). Another of our goals is to implement new tools to distinguish catalytically active enzymes from non-catalytic proteins in poorly studied or annotated subfamilies.

  9. Patterns of gene duplication and functional evolution during the diversification of the AGAMOUS subfamily of MADS box genes in angiosperms.

    PubMed Central

    Kramer, Elena M; Jaramillo, M Alejandra; Di Stilio, Verónica S

    2004-01-01

    Members of the AGAMOUS (AG) subfamily of MIKC-type MADS-box genes appear to control the development of reproductive organs in both gymnosperms and angiosperms. To understand the evolution of this subfamily in the flowering plants, we have identified 26 new AG-like genes from 15 diverse angiosperm species. Phylogenetic analyses of these genes within a large data set of AG-like sequences show that ancient gene duplications were critical in shaping the evolution of the subfamily. Before the radiation of extant angiosperms, one event produced the ovule-specific D lineage and the well-characterized C lineage, whose members typically promote stamen and carpel identity as well as floral meristem determinacy. Subsequent duplications in the C lineage resulted in independent instances of paralog subfunctionalization and maintained functional redundancy. Most notably, the functional homologs AG from Arabidopsis and PLENA (PLE) from Antirrhinum are shown to be representatives of separate paralogous lineages rather than simple genetic orthologs. The multiple subfunctionalization events that have occurred in this subfamily highlight the potential for gene duplication to lead to dissociation among genetic modules, thereby allowing an increase in morphological diversity. PMID:15020484

  10. Regulation of development and cancer by the R2B subfamily of RPTPs and the implications of proteolysis

    PubMed Central

    Craig, Sonya E.L.; Brady-Kalnay, Susann M.

    2014-01-01

    The initial cloning of receptor protein tyrosine phosphatases (RPTPs) was met with excitement because of their hypothesized function in counterbalancing receptor tyrosine kinase signaling. In recent years, members of a subfamily of RPTPs with homophilic cell-cell adhesion capabilities, known as the R2B subfamily, have been shown to have functions beyond that of counteracting tyrosine kinase activity, by independently influencing cell signaling in their own right and by regulating cell adhesion. The R2B subfamily is composed of four members: PTPmu (PTPRM), PTPrho (PTPRT), PTPkappa (PTPRK), and PCP-2 (PTPRU). The effects of this small subfamily of RPTPs is far reaching, influencing several developmental processes and cancer. In fact, R2B RPTPs are predicted to be tumor suppressors and are among the most frequently mutated protein tyrosine phosphatases (PTPs) in cancer. Confounding these conclusions are more recent studies suggesting that proteolysis of the full-length R2B RPTPs result in oncogenic extracellular and intracellular protein fragments. This review discusses the current knowledge of the role of R2B RPTPs in development and cancer, with special detail given to the mechanisms and implications that proteolysis has on R2B RPTP function. We also touch upon the concept of exploiting R2B proteolysis to develop cancer imaging tools, and consider the effects of R2B proteolysis on axon guidance, perineural invasion and collective cell migration. PMID:25223585

  11. Phylogeny of the most species-rich freshwater bivalve family (Bivalvia: Unionida: Unionidae): Defining modern subfamilies and tribes.

    PubMed

    Lopes-Lima, Manuel; Froufe, Elsa; Do, Van Tu; Ghamizi, Mohamed; Mock, Karen E; Kebapçı, Ümit; Klishko, Olga; Kovitvadhi, Satit; Kovitvadhi, Uthaiwan; Paulo, Octávio S; Pfeiffer, John M; Raley, Morgan; Riccardi, Nicoletta; Şereflişan, Hülya; Sousa, Ronaldo; Teixeira, Amílcar; Varandas, Simone; Wu, Xiaoping; Zanatta, David T; Zieritz, Alexandra; Bogan, Arthur E

    2017-01-01

    Freshwater mussels of the order Unionida are key elements of freshwater habitats and are responsible for important ecological functions and services. Unfortunately, these bivalves are among the most threatened freshwater taxa in the world. However, conservation planning and management are hindered by taxonomic problems and a lack of detailed ecological data. This highlights the urgent need for advances in the areas of systematics and evolutionary relationships within the Unionida. This study presents the most comprehensive phylogeny to date of the larger Unionida family, i.e., the Unionidae. The phylogeny is based on a combined dataset of 1032bp (COI+28S) of 70 species in 46 genera, with 7 of this genera being sequenced for the first time. The resulting phylogeny divided the Unionidae into 6 supported subfamilies and 18 tribes, three of which are here named for the first time (i.e., Chamberlainiini nomen novum, Cristariini nomen novum and Lanceolariini nomen novum). Molecular analyses were complemented by investigations of selected morphological, anatomical and behavioral characters used in traditional phylogenetic studies. No single morphological, anatomical or behavioral character was diagnostic at the subfamily level and few were useful at the tribe level. However, within subfamilies, many tribes can be recognized based on a subset of these characters. The geographical distribution of each of the subfamilies and tribes is also presented. The present study provides important advances in the systematics of these extraordinary taxa with implications for future ecological and conservation studies.

  12. ROLE OF ATP BINDING CASSETTE SUB-FAMILY MEMBER 2 (ABCG2) IN MOUSE EMBRYONIC STEM CELL DEVELOPMENT.

    EPA Science Inventory

    ATP binding cassette sub-family member 2 (ABCG2), is a member of the ABC transporter superfamily and a principal xenobiotic transporter. ABCG2 is also highly expressed in certain stem cell populations where it is thought to be related to stem cell plasticity, although the role o...

  13. Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds.

    PubMed

    Almeida, Daniela; Maldonado, Emanuel; Khan, Imran; Silva, Liliana; Gilbert, M Thomas P; Zhang, Guojie; Jarvis, Erich D; O'Brien, Stephen J; Johnson, Warren E; Antunes, Agostinho

    2016-04-13

    The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 avian whole genomes representing all major extant bird clades. Overall, 12 CYP2 subfamilies were identified, including the first description of the CYP2F, CYP2G, and several CYP2AF genes in avian genomes. Some of the CYP2 genes previously described as being lineage-specific, such as CYP2K and CYP2W, are ubiquitous to all avian groups. Furthermore, we identified a large number of CYP2J copies, which have been associated previously with water reabsorption. We detected positive selection in the avian CYP2C, CYP2D, CYP2H, CYP2J, CYP2K, and CYP2AC subfamilies. Moreover, we identified new substrate recognition sites (SRS0, SRS2_SRS3, and SRS3.1) and heme binding areas that influence CYP2 structure and function of functional importance as under significant positive selection. Some of the positively selected sites in avian CYP2D are located within the same SRS1 region that was previously linked with the metabolism of plant toxins. Additionally, we find that selective constraint variations in some avian CYP2 subfamilies are consistently associated with different feeding habits (CYP2H and CYP2J), habitats (CYP2D, CYP2H, CYP2J, and CYP2K), and migratory behaviors (CYP2D, CYP2H, and CYP2J). Overall, our findings indicate that there has been active enzyme site selection on CYP2 subfamilies and differential selection associated with different life history traits among birds.

  14. Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes

    PubMed Central

    Saarela, Jeffery M.; Wysocki, William P.; Barrett, Craig F.; Soreng, Robert J.; Davis, Jerrold I.; Clark, Lynn G.; Kelchner, Scot A.; Pires, J. Chris; Edger, Patrick P.; Mayfield, Dustin R.; Duvall, Melvin R.

    2015-01-01

    Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some ‘early-diverging’ tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae–Meliceae and Ampelodesmeae–Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae–Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae–Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a

  15. Yeast gain-of-function mutations reveal structure–function relationships conserved among different subfamilies of transient receptor potential channels

    PubMed Central

    Su, Zhenwei; Zhou, Xinliang; Haynes, W. John; Loukin, Stephen H.; Anishkin, Andriy; Saimi, Yoshiro; Kung, Ching

    2007-01-01

    Transient receptor potential (TRP) channels found in animals, protists, and fungi are primary chemo-, thermo-, or mechanosensors. Current research emphasizes the characteristics of individual channels in each animal TRP subfamily but not the mechanisms common across subfamilies. A forward genetic screen of the TrpY1, the yeast TRP channel, recovered gain-of-function (GOF) mutations with phenotype in vivo and in vitro. Single-channel patch-clamp analyses of these GOF-mutant channels show prominent aberrations in open probability and channel kinetics. These mutations revealed functionally important aromatic amino acid residues in four locations: at the intracellular end of the fifth transmembrane helix (TM5), at both ends of TM6, and at the immediate extension of TM6. These aromatics have counterparts in most TRP subfamilies. The one in TM5 (F380L) aligns precisely with an exceptional Drosophila mutant allele (F550I) that causes constitutive activity in the canonical TRP channel, resulting in rapid and severe retinal degeneration beyond mere loss of phototaxis. Thus, this phenylalanine maintains the balance of various functional states (conformations) of a channel for insect phototransduction as well as one for fungal mechanotransduction. This residue is among a small cluster of phenylalanines found in all known subfamilies of TRP channels. This unique case illustrates that GOF mutations can reveal structure–function principles that can be generalized across different TRP subfamilies. It appears that the conserved aromatics in the four locations have conserved functions in most TRP channels. The possible mechanistic roles of these aromatics and the further use of yeast genetics to dissect TRP channels are discussed. PMID:18042709

  16. Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds

    PubMed Central

    Almeida, Daniela; Maldonado, Emanuel; Khan, Imran; Silva, Liliana; Gilbert, M. Thomas P.; Zhang, Guojie; Jarvis, Erich D.; O’Brien, Stephen J.; Johnson, Warren E.; Antunes, Agostinho

    2016-01-01

    The cytochrome P450 (CYP) superfamily defends organisms from endogenous and noxious environmental compounds, and thus is crucial for survival. However, beyond mammals the molecular evolution of CYP2 subfamilies is poorly understood. Here, we characterized the CYP2 family across 48 avian whole genomes representing all major extant bird clades. Overall, 12 CYP2 subfamilies were identified, including the first description of the CYP2F, CYP2G, and several CYP2AF genes in avian genomes. Some of the CYP2 genes previously described as being lineage-specific, such as CYP2K and CYP2W, are ubiquitous to all avian groups. Furthermore, we identified a large number of CYP2J copies, which have been associated previously with water reabsorption. We detected positive selection in the avian CYP2C, CYP2D, CYP2H, CYP2J, CYP2K, and CYP2AC subfamilies. Moreover, we identified new substrate recognition sites (SRS0, SRS2_SRS3, and SRS3.1) and heme binding areas that influence CYP2 structure and function of functional importance as under significant positive selection. Some of the positively selected sites in avian CYP2D are located within the same SRS1 region that was previously linked with the metabolism of plant toxins. Additionally, we find that selective constraint variations in some avian CYP2 subfamilies are consistently associated with different feeding habits (CYP2H and CYP2J), habitats (CYP2D, CYP2H, CYP2J, and CYP2K), and migratory behaviors (CYP2D, CYP2H, and CYP2J). Overall, our findings indicate that there has been active enzyme site selection on CYP2 subfamilies and differential selection associated with different life history traits among birds. PMID:26979796

  17. Bimodal regulation of an Elk subfamily K+ channel by phosphatidylinositol 4,5-bisphosphate.

    PubMed

    Li, Xiaofan; Anishkin, Andriy; Liu, Hansi; van Rossum, Damian B; Chintapalli, Sree V; Sassic, Jessica K; Gallegos, David; Pivaroff-Ward, Kendra; Jegla, Timothy

    2015-11-01

    Phosphatidylinositol 4,5-bisphosphate (PIP2) regulates Shaker K+ channels and voltage-gated Ca2+ channels in a bimodal fashion by inhibiting voltage activation while stabilizing open channels. Bimodal regulation is conserved in hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, but voltage activation is enhanced while the open channel state is destabilized. The proposed sites of PIP2 regulation in these channels include the voltage-sensor domain (VSD) and conserved regions of the proximal cytoplasmic C terminus. Relatively little is known about PIP2 regulation of Ether-á-go-go (EAG) channels, a metazoan-specific family of K+ channels that includes three gene subfamilies, Eag (Kv10), Erg (Kv11), and Elk (Kv12). We examined PIP2 regulation of the Elk subfamily potassium channel human Elk1 to determine whether bimodal regulation is conserved within the EAG K+ channel family. Open-state stabilization by PIP2 has been observed in human Erg1, but the proposed site of regulation in the distal C terminus is not conserved among EAG family channels. We show that PIP2 strongly inhibits voltage activation of Elk1 but also stabilizes the open state. This stabilization produces slow deactivation and a mode shift in voltage gating after activation. However, removal of PIP2 has the net effect of enhancing Elk1 activation. R347 in the linker between the VSD and pore (S4-S5 linker) and R479 near the S6 activation gate are required for PIP2 to inhibit voltage activation. The ability of PIP2 to stabilize the open state also requires these residues, suggesting an overlap in sites central to the opposing effects of PIP2 on channel gating. Open-state stabilization in Elk1 requires the N-terminal eag domain (PAS domain + Cap), and PIP2-dependent stabilization is enhanced by a conserved basic residue (K5) in the Cap. Our data shows that PIP2 can bimodally regulate voltage gating in EAG family channels, as has been proposed for Shaker and HCN channels. PIP2 regulation

  18. Quantitative Polymerase Chain Reaction Analysis of the Mouse Cyp2j Subfamily: Tissue Distribution and Regulation.

    PubMed

    Graves, Joan P; Gruzdev, Artiom; Bradbury, J Alyce; DeGraff, Laura M; Li, Huiling; House, John S; Hoopes, Samantha L; Edin, Matthew L; Zeldin, Darryl C

    2015-08-01

    Members of the cytochrome P450 CYP2J subfamily are expressed in multiple tissues in mice and humans. These enzymes are active in the metabolism of fatty acids to generate bioactive compounds. Herein we report new methods and results for quantitative polymerase chain reaction (qPCR) analysis for the seven genes (Cyp2j5, Cyp2j6, Cyp2j8, Cyp2j9, Cyp2j11, Cyp2j12, and Cyp2j13) of the mouse Cyp2j subfamily. SYBR Green primer sets were developed and compared with commercially available TaqMan primer/probe assays for specificity toward mouse Cyp2j cDNA, and analysis of tissue distribution and regulation of Cyp2j genes. Each TaqMan primer/probe set and SYBR Green primer set were shown to be specific for their intended mouse Cyp2j cDNA. Tissue distribution of the mouse Cyp2j isoforms confirmed similar patterns of expression between the two qPCR methods. Cyp2j5 and Cyp2j13 were highly expressed in male kidneys, and Cyp2j11 was highly expressed in both male and female kidneys. Cyp2j6 was expressed in multiple tissues, with the highest expression in the small intestine and duodenum. Cyp2j8 was detected in various tissues, with highest expression found in the skin. Cyp2j9 was highly expressed in the brain, liver, and lung. Cyp2j12 was predominately expressed in the brain. We also determined the Cyp2j isoform expression in Cyp2j5 knockout mice to determine whether there was compensatory regulation of other Cyp2j isoforms, and we assessed Cyp2j isoform regulation during various inflammatory models, including influenza A, bacterial lipopolysaccharide, house dust mite allergen, and corn pollen. Both qPCR methods detected similar suppression of Cyp2j6 and Cyp2j9 during inflammation in the lung.

  19. [Supraspecies relationships in the subfamily (Rodentia, Cricetidae, Arvicolinae): unexpexted result of nuclear genes analysis].

    PubMed

    Abramson, N I; Lebedev, V S; Tesakov, A S; Bannikova, A A

    2009-01-01

    Phylogenetic analysis of supraspecies relationships in one of the most young and species rich group of myomorph rodents - subfamily Arvicolinae was carried out on the base of two nuclear genes. Results have shown that mole-voles - Ellobiusini, steppe voles - (Lagurini) and grey voles (Arvicolini) are sister groups. This divergence is the most late, third wave of radiation within the family. The sister clade to this group is the tribe of red-back voles - Myodini (=Clethrionomini) - "second radiation". The order of divergence for earliest radiation remains still unresolved (Ondatrini, Prometheomyini, Dicrostonychini, Lemmini). New data on the close relationships of mole voles, grey voles and steppe voles are unexpected one and contradict to the conventional views. The latter ideas on the significant ancientry and separation of Ellobiusini from all other voles is based on extreme simplicity of their rooted molars and very peculiar structure of the skull and postcranial skeleton. However, many of these characters most likely indicate on significant degree of adaptation to the subterranean life and have no phylogenetic signal.

  20. Sequence analysis and mapping of the Sry gene in species of the subfamily Arvicolinae (rodentia).

    PubMed

    Acosta, M J; Marchal, J A; Romero-Fernández, I; Megías-Nogales, B; Modi, W S; Sánchez Baca, Antonio

    2010-01-01

    The rodent subfamily Arvicolinae, which contains about 125 species, presents some interesting exceptions concerning Sry, the sex determining gene in mammals. In some species multiple Sry copies have been described on the Y chromosome and in the Iberian vole, Microtus cabrerae, several Sry sequences have been cloned and mapped not only on the Y but also on the X chromosome. Here we present a comparative analysis of Sry sequences from a total of 22 species. Our study demonstrates for the first time that for most North American species, as previously reported for the European species, multiple copies of the Sry gene exist on the Y chromosome. Furthermore, we have sequenced and analyzed the full sequence of Sry from several European species, showing that the sequence and structure of the gene in this group of species present the main features described for Sry in other mammals. Finally, FISH analyses on some of these species demonstrated that all Sry sequences, despite their functional status, mapped on the euchromatic short arm of the Y chromosome.

  1. Specific interactions of Mss4 with members of the Rab GTPase subfamily.

    PubMed

    Burton, J L; Burns, M E; Gatti, E; Augustine, G J; De Camilli, P

    1994-12-01

    Mss4 is a mammalian protein that was identified as a suppressor of a yeast secretory mutant harboring a mutation in the GTPase Sec4 and was found to stimulate GDP release from this protein. We have now performed a biochemical characterization of the Mss4 protein and examined the specificity of its association with mammalian GTPases. Mss4 is primarily a soluble protein with a widespread tissue distribution. Recombinant Mss4 binds GTPases present in tissue extracts, and by a gel overlay assay binds specifically Rab Rab10proteins. We further define the Mss4-GTPase interaction to a subset of Rabs belonging to the same subfamily branch which include Rab1, Rab3, Rab8, Rab10, Sec4 and Ypt1 but not Rab2, Rab4, Rab5, Rab6, Rab9 and Rab11. Accordingly, Mss4 co-precipitates from a brain extract with Rab3a but not Rab5. Mss4 only stimulates GDP release from, and the association of GTP gamma S with, this Rab subset. Recombinant Mss4 and Rab3a form a stable complex in solution that is dissociated with either GDP or GTP gamma S. Injection of Mss4 into the squid giant nerve terminal enhances neurotransmitter release. These results suggest that Mss4 behaves as a guanylnucleotide exchange factor (GEF) for a subset of Rabs to influence distinct vesicular transport steps along the secretory pathway.

  2. Effect of Habitat Conditions and Plant Traits on Leaf Damage in the Carduoideae Subfamily

    PubMed Central

    Münzbergová, Zuzana; Skuhrovec, Jiří

    2013-01-01

    Plant traits are the key factors that determine herbivore foraging selection. The traits serving as defense traits against herbivores represent a wide range of traits, such as chemical, physiological, morphological and life-history traits. While many studies considered plant defense traits at the within-species scale, much less is known from comparisons of a wide range of closely related species. The aim of this study was to identify factors responsible for the intensity of leaf damage in the Carduoideae subfamily of Asteraceae, which hosts many invasive species and thus is potential candidate plant species that could be controlled by biological control. Specifically, we wanted to see the relative importance of habitat characteristics, plant size and plants traits in determining the degree of folivory. The study identified several defense traits able to explain differences in herbivory between species after accounting for differences in the habitats in which the species occur and the plant size. Specifically, the most important traits were traits related to the quality of the leaf tissue expressed as the content of phosphorus, water and specific leaf area, which suggests that the leaf quality had a more important effect on the degree of herbivory than the presence of specific defense mechanisms such as spines and hair. Leaf quality is thus a candidate factor that drives herbivore choice when selecting which plant to feed on and should be considered when assessing the danger that a herbivore will switch hosts when introduced to a new range. PMID:23717643

  3. The Eucalyptus Tonoplast Intrinsic Protein (TIP) Gene Subfamily: Genomic Organization, Structural Features, and Expression Profiles

    PubMed Central

    Rodrigues, Marcela I.; Takeda, Agnes A. S.; Bravo, Juliana P.; Maia, Ivan G.

    2016-01-01

    Plant aquaporins are water channels implicated in various physiological processes, including growth, development and adaptation to stress. In this study, the Tonoplast Intrinsic Protein (TIP) gene subfamily of Eucalyptus, an economically important woody species, was investigated and characterized. A genome-wide survey of the Eucalyptus grandis genome revealed the presence of eleven putative TIP genes (referred as EgTIP), which were individually assigned by phylogeny to each of the classical TIP1–5 groups. Homology modeling confirmed the presence of the two highly conserved NPA (Asn-Pro-Ala) motifs in the identified EgTIPs. Residue variations in the corresponding selectivity filters, that might reflect differences in EgTIP substrate specificity, were observed. All EgTIP genes, except EgTIP5.1, were transcribed and the majority of them showed organ/tissue-enriched expression. Inspection of the EgTIP promoters revealed the presence of common cis-regulatory elements implicated in abiotic stress and hormone responses pointing to an involvement of the identified genes in abiotic stress responses. In line with these observations, additional gene expression profiling demonstrated increased expression under polyethylene glycol-imposed osmotic stress. Overall, the results obtained suggest that these novel EgTIPs might be functionally implicated in eucalyptus adaptation to stress. PMID:27965702

  4. Molecular phylogeny and biogeography of the weevil subfamily Platypodinae reveals evolutionarily conserved range patterns.

    PubMed

    Jordal, Bjarte H

    2015-11-01

    Platypodinae is a peculiar weevil subfamily of species that cultivate fungi in tunnels excavated in dead wood. Their geographical distribution is generally restricted, with genera confined to a single continent or large island, which provides a useful system for biogeographical research. This study establishes the first detailed molecular phylogeny of the group, with the aim of testing hypotheses on classification, diversification, and biogeography. A phylogeny was reconstructed based on 3648 nucleotides from COI, EF-1α, CAD, ArgK, and 28S. Tree topology was well resolved and indicated a strong correlation with geography, more so than predicted by previous morphology-based classifications. Tesserocerini was paraphyletic, with Notoplatypus as the sister group to a clade consisting of three main lineages of Tesserocerini and the recently evolved Platypodini. Austroplatypus formed the sister group to all remaining Platypodini and hence confirmed its separate status from Platypus. The Indo-Australian genera of Platypodini were strikingly paraphyletic, suggesting that the taxonomy of this tribe needs careful revision. Ancestral-area reconstructions in Lagrange and S-DIVA were ambiguous for nodes roughly older than 80 Ma. More recent events were firmly assessed and involved post-Gondwanan long-distance dispersal. The Neotropics was colonized three times, all from the Afrotropical region, with the latest event less than 25 Ma that included the ancestor of all Neotropical Platypodini.

  5. A review of the subfamily Picobiinae Johnston and Kethley, 1973 (Acariformes: Prostigmata: Syringophilidae).

    PubMed

    Skoracki, Maciej; Sikora, Bozena; Spicer, Greg S

    2016-05-19

    The fauna of quill mites of the subfamily Picobiinae Johnston and Kethley, 1973 (Acariformes: Cheyletoidea: Syringophilidae) is comprehensively revised. All of 78 known species, which are grouped into 11 genera, are examined and diagnosed or redescribed. Data on picobiine hosts and distribution are summarized, including new host and locality records. The following new species are described: Charadriineopicobia apricaria sp. nov. ex Pluvialis apricaria (Linnaeus) (Charadriiformes: Charadriidae) from France, Neopicobia pari sp. nov. ex Periparus venustulus Swinhoe (type host) (Passeriformes: Paridae) from China, Parus major Linnaeus (Paridae) from Macedonia and Finland, and Poecile varius Temminck and Schlegel (Paridae) from Japan, Picobia magellani sp. nov. ex Scytalopus magellanicus (Gmelin) (Passeriformes: Rhinocryptidae) from Colombia, Picobia lonchura sp. nov. ex Lonchura leucogastra (Blyth) (Passeriformes: Estrildidae) from Indonesia, Picobia makoli sp. nov. ex Xiphocolaptes promeropirhynchus (Lesson) (Passeriformes: Furnariidae) from Colombia. The species Picobia polonica Skoracki, Magowski and Dabert, 2001 syn. nov. is a junior synonym of C. khulkhaskhani Kivganov and Sharafat, 1995. The following new combinations are proposed: Neopicobia ictericus (Skoracki and Glowska, 2010) comb. nov., Rafapicobia brotogeris (Fain, Bochkov and Mironov, 2000) comb. nov., and Rafapicobia ramphastos (Fain, Bochkov and Mironov, 2000) comb. nov. Keys to the all picobiine genera and species are presented, along with a check-list of picobiine species and their hosts.

  6. The new vertebrate CYP1C family: cloning of new subfamily members and phylogenetic analysis.

    PubMed

    Godard, Celine A J; Goldstone, Jared V; Said, Maya R; Dickerson, Richard L; Woodin, Bruce R; Stegeman, John J

    2005-06-17

    Two novel CYP1 genes from teleost fish constituting a new subfamily have been cloned. These paralogous sequences are designated CYP1C1 and CYP1C2. Both genes were initially obtained from untreated scup Stenotomus chrysops tissues by RT-PCR and RACE. Scup CYP1C1 and CYP1C2 code for 524 and 525 amino acids, respectively, and share 80-81% identity at the nucleotide and amino acid levels. Orthologues of CYP1C1 and CYP1C2 were identified in genome databases for other fish species, and both CYP1B1 and CYP1C1 were cloned from zebrafish (Danio rerio). Phylogenetic analysis shows that CYP1Cs and CYP1Bs constitute a sister clade to the CYP1As. Analysis of sequence domains likely to have functional significance suggests that the two CYP1Cs in scup may have catalytic functions and/or substrate specificity that differ from each other and from those of mammalian CYP1Bs or CYP1As. RT-PCR results indicate that CYP1C1 and CYP1C2 are variously expressed in several scup organs.

  7. The global phylogeny of the subfamily Sycoryctinae (Pteromalidae): parasites of an obligate mutualism.

    PubMed

    Segar, Simon T; Lopez-Vaamonde, Carlos; Rasplus, Jean-Yves; Cook, James M

    2012-10-01

    The inflorescences of fig trees (Ficus, Moraceae) host well-defined, host plant specific wasp communities that lend themselves to tests of hypotheses on insect diversification. We provide the first estimate of the global molecular phylogeny for the Sycoryctinae - a large subfamily of fig wasps consisting mainly of parasitoids of fig-pollinating wasps. We find strong support for a large Old World clade that contains eight of the eleven genera, in the tribes Sycoryctini and Philotrypesini. The sister taxon is tribe Apocryptini, comprising the genera Apocrypta and Bouceka. Finally, a new tribe, Critogastrini, is raised for the genus Critogaster, sister to all other sycoryctines. At the genus level, we found a general pattern of strong host conservatism, in which closely related wasps associate with closely related figs. Despite this, there is also evidence for multiple host shifts between more distantly related figs in some wasp genera (especially Philotrypesis). We estimate Sycoryctinae to have originated 49-64 Ma, after the initial co-radiation of the host figs and pollinators. Further, conservative assumptions in our analyses probably overestimate the age of the sycoryctines. Together, patterns of host association, evidence for a mix of host constraints and host shifting, and molecular dating suggest that sycoryctine parasites radiated through delayed phylogenetic tracking of their hosts. This contributes to the growing body of literature suggesting that coevolving parasites often radiate after their hosts.

  8. A comparative study of the biological properties of venoms of some old world vipers (subfamily viperinae).

    PubMed

    Tan, N H; Ponnudurai, G

    1992-02-01

    1. The hemorrhagic, procoagulant, anticoagulant, phosphodiesterase, hyaluronidase, alkaline phosphomonoesterase, 5'-nucleotidase, arginine ester hydrolase, phospholipase A, L-amino acid oxidase and protease activities of 30 samples of venoms from nine species (12 taxa) of the old world vipers (Subfamily Viperinae) including snakes from the genera Bitis, Causus, Cerastes, Echis, Eristicophis and Pseudocerastes, were determined and the Sephadex G-75 gel filtration patterns for some of the venoms were also examined. 2. Examination of the biological properties of the venoms of the Viperinae tested indicates the presence of common venom biological characteristics at the various phylogenic levels. 3. Venoms of most species of the Viperinae examined exhibited characteristic biological properties at the species level, and this allows the differentiation of the Viperinae species by differences in their biological properties. 4. Particularly useful for this purpose, are the effects of venom on kaolin-cephalin clotting time of platelet poor rabbit plasma and the Sephadex G-75 gel filtration pattern and arginine ester hydrolase activity of the venom.

  9. Molecular phylogeny and conservation priorities of the subfamily Acheilognathinae (Teleostei: Cyprinidae).

    PubMed

    Cheng, Peilin; Yu, Dan; Liu, Siqing; Tang, Qiongying; Liu, Huanzhang

    2014-05-01

    It is increasingly accepted that conservation work should consider the evolutionary history of target species. Fishes in the subfamily Acheilognathinae, family Cyprinidae, are, with the exception of three species exclusively distributed in Europe, restricted to Asia and show a distinct spawning behavior in laying their eggs in gill chambers of freshwater mussels. At present, many of the 70 species recognized in this group are facing with serious population decline in China and Japan, and their phylogenetic relationships are not well resolved. In the present study, based on mtDNA cyt b and 12S rRNA gene sequences, we reconstructed a more detailed species-level phylogenetic tree of this group, and assessed species conservation priorities based on their evolutionary distinctiveness. Molecular phylogenetic analyses showed that the Acheilognathinae contains two major clades: Acheilognathus clade and Tanakia-Rhodeus clade. Based on this phylogenetic result, conservation priority analyses were conducted using ED (evolutionary distinctiveness)/HED (heightened evolutionary distinctiveness), and EDGE (evolutionary distinctiveness and global endangeredness)/HEDGE (heightened evolutionary distinctiveness and global endangeredness) methods. The results suggested that T. himantegus, T. lanceolata, A. gracilis, A. imberbis, T. tanago, and A. longipinnis should be ranked as the top-priority species for conservation. According to our results, we also discussed the current conservation efforts of the bitterling fishes and gave suggestions for future work.

  10. Sinocoelotes gen. n., a new genus of the subfamily Coelotinae (Araneae, Agelenidae) from Southeast Asia

    PubMed Central

    Chen, Lu; Zhao, Zhe; Li, Shuqiang

    2016-01-01

    Abstract A new genus of the spider subfamily Coelotinae, Sinocoelotes gen. n., with nine new species, is described from Yunnan and Sichuan Provinces in southern China. The new species are: Sinocoelotes cangshanensis sp. n. (♀), Sinocoelotes hehuaensis sp. n. (♂♀), Sinocoelotes luoshuiensis sp. n. (♀), Sinocoelotes mangbangensis sp. n. (♀) from Yunnan; Sinocoelotes kangdingensis sp. n. (♀), Sinocoelotes ludingensis sp. n. (♂♀), Sinocoelotes mahuanggouensis sp. n. (♀), Sinocoelotes muliensis sp. n. (♀), and Sinocoelotes yanyuanensis sp. n. (♂) from Sichuan. In addition, six Coelotes species are transferred to the new genus: Sinocoelotes acicularis (Wang, Griswold & Ubick, 2009), comb. n. (♂♀), Sinocoelotes forficatus (Liu & Li, 2010), comb. n. (♂♀), Sinocoelotes guangxian (Zhang, Yang, Zhu & Song, 2003), comb. n. (♂♀), Sinocoelotes pseudoterrestris (Schenkel, 1963), comb. n. (♂♀), Sinocoelotes pseudoyunnanensis (Wang, Griswold & Ubick, 2009), comb. n. (♂♀) and Sinocoelotes thailandensis (Dankittipakul & Wang, 2003), comb. n. (♂♀). DNA barcodes of all the species were documented for future use. PMID:27667932

  11. Phylogeny and historical biogeography of leafhopper subfamily Evacanthinae (Hemiptera: Cicadellidae) based on morphological and molecular data

    PubMed Central

    Wang, Yang; Dietrich, Christopher H.; Zhang, Yalin

    2017-01-01

    Phylogenetic relationships among major lineages of the Evacanthinae, a highly diverse leafhopper subfamily distributed worldwide, were explored by analysing a dataset of 100 discrete morphological characters and DNA sequence data from five gene regions. Sixty-seven taxa representing all evacanthine tribes and all regional faunas, and fourteen putative outgroup taxa were included. Maximum-likelihood and Bayesian analyses yielded similar tree topologies that were well resolved with strong support for the monophyly of Evacanthinae and its four previously included tribes, but indicated that Draconirvana Dietrich, was incorrectly placed to tribe and that Sophonia Walker, Evacanthus Le Peletier & Serville, Bundera Distant, Paraonukia Ishihara and Onukia Matsumura are not monophyletic. Divergence time analysis suggests that the deepest divergences coincided with breakup of Gondwana but that more recent divergences occurred largely within a single biogeographic realm during the Paleogene, with a few long-distance dispersal events. Biogeographical analyses suggest that Evacanthinae originated in Neotropical region. A new tribe, Pentoffiini trib.n., is established to include Pentoffia Kramer and Evanirvana Hill, the genus Draconirvana Dietrich, placement n. is transferred to Evacanthini from Nirvanini, a key to tribes is also given and illustrations of representative genera are provided. PMID:28368039

  12. Adaptive evolution after gene duplication in alpha-KT x 14 subfamily from Buthus martensii Karsch.

    PubMed

    Cao, Zhijian; Mao, Xin; Xu, Xiuling; Sheng, Jiqun; Dai, Chao; Wu, Yingliang; Luo, Feng; Sha, Yonggang; Jiang, Dahe; Li, Wenxin

    2005-07-01

    A series of isoforms of alpha-KT x 14 (short chain potassium channel scorpion toxins) were isolated from the venom of Buthus martensii Karsch by RACE and screening cDNA library methods. These isoforms adding BmKK1--3 and BmSKTx1--2 together shared high homology (more than 97%) with each other. The result of genomic sequence analysis showed that a length 79 bp intron is inserted Ala codes between the first and the second base at the 17th amino acid of signal peptide. The introns of these isoforms also share high homology with those of BmKK2 and BmSKT x 1 reported previously. Sequence analysis of many clones of cDNA and genomic DNA showed that a species population or individual polymorphism of alpha-KT x 14 genes took place in scorpion Buthus martensii Karsch and accelerated evolution played an important role in the forming process of alpha-KT x 14 scorpion toxins subfamily. The result of southern hybridization indicated that alpha-KT x 14 toxin genes existed in scorpion chromosome with multicopies. All findings maybe provided an important evidence for an extensive evolutionary process of the scorpion "pharmacological factory": at the early course of evolution, the ancestor toxic gene duplicated into a series of multicopy genes integrated at the different chromosome; at the late course of evolution, subsequent functional divergence of duplicate genes was generated by mutations, deletions and insertion.

  13. Floral Development in the Tribe Cedreleae (Meliaceae, Sub-family Swietenioideae): Cedrela and Toona

    PubMed Central

    Gouvêa, Cantídio Fernando; Dornelas, Marcelo Carnier; Rodriguez, Adriana Pinheiro Martinelli

    2008-01-01

    Background and Aims Floral development of Cedrela and Toona, the genera comprising the basal tribe Cedreleae of the sub-family Swietenioideae of Meliaceae, is described. The focus was on three endangered, ecologically and economically important species: Cedrela fissilis, Cedrela odorata and Toona ciliata. The aims of the study were to characterize the patterns of floral development in the tribe and to establish apomorphic and plesiomorphic floral characters in relation to other taxa within the family based on the current molecular phylogeny of Meliaceae. Methods A detailed floral structural and developmental study was completed using both scanning electron microscopy and visualization of microtome sections with a light microscope. Key Results Twelve floral developmental stages were identified. The initial development of the pentamerous flowers of both Toona and Cedrela is strikingly similar. The morphological differences observed between them are due to differential patterns of organ elongation and adnation/connation occurring late in development. Additionally, the formation of functionally male and female flowers was found to occur at specific positions within the inflorescence. Conclusions Due to the basal position of the tribe Cedreleae in the phylogeny of Meliaceae, functionally either male or female pentamerous flowers and the presence of (at least partially) free stamens may be considered plesiomorphic traits within the family. In contrast, sympetaly and the absence of nectaries in Cedrela species are synapomorphies. PMID:17981877

  14. Human leukocyte-derived arginine aminopeptidase. The third member of the oxytocinase subfamily of aminopeptidases.

    PubMed

    Tanioka, Toshihiro; Hattori, Akira; Masuda, Shinako; Nomura, Yoshihiro; Nakayama, Hiroshi; Mizutani, Shigehiko; Tsujimoto, Masafumi

    2003-08-22

    In this study we report the cloning and characterization of a novel human aminopeptidase, which we designate leukocyte-derived arginine aminopeptidase (L-RAP). The sequence encodes a 960-amino acid protein with significant homology to placental leucine aminopeptidase and adipocyte-derived leucine aminopeptidase. The predicted L-RAP contains the HEXXH(X)18E zinc-binding motif, which is characteristic of the M1 family of zinc metallopeptidases. Phylogenetic analysis indicates that L-RAP forms a distinct subfamily with placental leucine aminopeptidase and adipocyte-derived leucine aminopeptidase in the M1 family. Immunocytochemical analysis indicates that L-RAP is located in the lumenal side of the endoplasmic reticulum. Among various synthetic substrates tested, L-RAP revealed a preference for arginine, establishing that the enzyme is a novel arginine aminopeptidase with restricted substrate specificity. In addition to natural hormones such as angiotensin III and kallidin, L-RAP cleaved various N-terminal extended precursors to major histocompatibility complex class I-presented antigenic peptides. Like other proteins involved in antigen presentation, L-RAP is induced by interferon-gamma. These results indicate that L-RAP is a novel aminopeptidase that can trim the N-terminal extended precursors to antigenic peptides in the endoplasmic reticulum.

  15. The exodus subfamily of CC chemokines inhibits the proliferation of chronic myelogenous leukemia progenitors.

    PubMed

    Hromas, R; Cripe, L; Hangoc, G; Cooper, S; Broxmeyer, H E

    2000-02-15

    Chemokines are a family of related proteins that regulate leukocyte infiltration into inflamed tissue and play important roles in disease processes. Among the biologic activities of chemokines is inhibition of proliferation of normal hematopoietic progenitors. However, chemokines that inhibit normal progenitors rarely inhibit proliferation of hematopoietic progenitors from patients with chronic myelogenous leukemia (CML). We and others recently cloned a subfamily of CC chemokines that share similar amino-terminal peptide sequences and a remarkable ability to chemoattract T cells. These chemokines, Exodus-1/LARC/MIP-3alpha, Exodus-2/SLC/6Ckine/TCA4, and Exodus-3/CKbeta11/MIP-3beta, were found to inhibit proliferation of normal human marrow progenitors. The study described here found that these chemokines also inhibited the proliferation of progenitors in every sample of marrow from patients with CML that was tested. This demonstration of consistent inhibition of CML progenitor proliferation makes the 3 Exodus chemokines unique among chemokines. (Blood. 2000;95:1506-1508)

  16. Species-specific evolution of class I MHC genes in iguanas (order: Squamata; subfamily: Iguaninae).

    PubMed

    Glaberman, Scott; Caccone, Adalgisa

    2008-07-01

    Over the last few decades, the major histocompatibility complex (MHC) has emerged as a model for understanding the influence of natural selection on genetic diversity in populations as well as for investigating the genetic basis of host resistance to pathogens. However, many vertebrate taxa remain underrepresented in the field of MHC research, preventing its application to studies of disease, evolution, and conservation genetics in these groups. This is particularly true for squamates, which are by far the most diversified order of non-avian reptiles but have not been the subject of any recent MHC studies. In this paper, we present MHC class I complementary DNA data from three squamate species in the subfamily Iguaninae (iguanas): the Galápagos marine iguana (Amblyrhynchus cristatus), the Galápagos land iguana (Conolophus subcristatus), and the green iguana (Iguana iguana). All sequences obtained are related to the few published class I genes from other squamates. There is evidence for multiple loci in each species, and the conserved alpha-3 domain appears to be evolving in a species-specific manner. Conversely, there is some indication of shared polymorphism between species in the peptide-binding alpha-1 and alpha-2 domains, suggesting that these two regions have different phylogenetic histories. The great similarity between alpha-3 sequences in marine iguanas in particular suggests that concerted evolution is acting to homogenize class I loci within species. However, while less likely, the data are also compatible with a birth and death model of evolution.

  17. Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification.

    PubMed

    Covain, Raphaël; Fisch-Muller, Sonia; Oliveira, Claudio; Mol, Jan H; Montoya-Burgos, Juan I; Dray, Stéphane

    2016-01-01

    The Loricariinae belong to the Neotropical mailed catfish family Loricariidae, the most species-rich catfish family. Among loricariids, members of the Loricariinae are united by a long and flattened caudal peduncle and the absence of an adipose fin. Despite numerous studies of the Loricariidae, there is no comprehensive phylogeny of this morphologically highly diversified subfamily. To fill this gap, we present a molecular phylogeny of this group, including 350 representatives, based on the analysis of mitochondrial and nuclear genes (8426 positions). The resulting phylogeny indicates that Loricariinae are distributed into two sister tribes: Harttiini and Loricariini. The Harttiini tribe, as classically defined, constitutes a paraphyletic assemblage and is here restricted to the three genera Harttia, Cteniloricaria, and Harttiella. Two subtribes are distinguished within Loricariini: Farlowellina and Loricariina. Within Farlowellina, the nominal genus formed a paraphyletic group, as did Sturisoma and Sturisomatichthys. Within Loricariina, Loricaria, Crossoloricaria, and Apistoloricaria are also paraphyletic. To solve these issues, and given the lack of clear morphological diagnostic features, we propose here to synonymize several genera (Quiritixys with Harttia; East Andean members of Crossoloricaria, and Apistoloricaria with Rhadinoloricaria; Ixinandria, Hemiloricaria, Fonchiiichthys, and Leliella with Rineloricaria), to restrict others (Crossoloricaria, and Sturisomatichthys to the West Andean members, and Sturisoma to the East Andean species), and to revalidate the genus Proloricaria.

  18. Structure-function analysis of HKE4, a member of the new LIV-1 subfamily of zinc transporters.

    PubMed Central

    Taylor, Kathryn M; Morgan, Helen E; Johnson, Andrea; Nicholson, Robert I

    2004-01-01

    The KE4 proteins are an emerging group of proteins with little known functional data. In the present study, we report the first characterization of the recombinant human KE4 protein in mammalian cells. The KE4 sequences are included in the subfamily of ZIP (Zrt-, Irt-like Proteins) zinc transporters, which we have termed LZT (LIV-1 subfamily of ZIP zinc Transporters). All these LZT sequences contain similarities to ZIP transporters, including the consensus sequence in transmembrane domain IV, which is essential for zinc transport. However, the new LZT subfamily can be separated from other ZIP transporters by the presence of a highly conserved potential metalloprotease motif (HEXPHEXGD) in transmembrane domain V. Here we report the location of HKE4 on intracellular membranes, including the endoplasmic reticulum, and its ability to increase the intracellular free zinc as measured with the zinc-specific fluorescent dye, Newport Green, in a time-, temperature- and concentration-dependent manner. This is in contrast with the zinc influx ability of another LZT protein, LIV-1, which was due to its plasma membrane location. Therefore we have added to the functionality of LZT proteins by reporting their ability to increase intracellular-free zinc, whether they are located on the plasma membrane or on intracellular membranes. This result, in combination with the crucial role that zinc plays in cell growth, emphasizes the importance of this new LZT subfamily, including the KE4 sequences, in the control of intracellular zinc homoeostasis, aberrations of which can lead to diseases such as cancer, immunological disorders and neurological dysfunction. PMID:14525538

  19. Molecular phylogenetics of subfamily Ornithogaloideae (Hyacinthaceae) based on nuclear and plastid DNA regions, including a new taxonomic arrangement

    PubMed Central

    Martínez-Azorín, Mario; Crespo, Manuel B.; Juan, Ana; Fay, Michael F.

    2011-01-01

    Background and Aims The taxonomic arrangement within subfamily Ornithogaloideae (Hyacinthaceae) has been a matter of controversy in recent decades: several new taxonomic treatments have been proposed, based exclusively on plastid DNA sequences, and these have resulted in classifications which are to a great extent contradictory. Some authors have recognized only a single genus Ornithogalum for the whole subfamily, including 250–300 species of variable morphology, whereas others have recognized many genera. In the latter case, the genera are inevitably much smaller and they are better defined morphologically. However, some are not monophyletic as circumscribed. Methods Phylogenetic analyses of Ornithogaloideae were based on nucleotide sequences of four plastid regions (trnL intron, trnL-F spacer, rbcL and matK) and a nuclear region (ITS). Eighty species covering all relevant taxonomic groups previously recognized in the subfamily were sampled. Parsimony and Bayesian analyses were performed. The molecular data were compared with a matrix of 34 morphological characters. Key Results Combinations of plastid and nuclear data yielded phylogenetic trees which are better resolved than those obtained with any plastid region alone or plastid regions in combination. Three main clades are found, corresponding to the previously recognized tribes Albuceae, Dipcadieae and Ornithogaleae. In these, up to 19 clades are described which are definable by morphology and biogeography. These mostly correspond to previously described taxa, though some need recircumscription. Morphological characters are assessed for their diagnostic value for taxonomy in the subfamily. Conclusions On the basis of the phylogenetic analyses, 19 monophyletic genera are accepted within Ornithogaloideae: Albuca, Avonsera, Battandiera, Cathissa, Coilonox, Dipcadi, Eliokarmos, Elsiea, Ethesia, Galtonia, Honorius, Loncomelos, Melomphis, Neopatersonia, Nicipe, Ornithogalum, Pseudogaltonia, Stellarioides and

  20. Structure-function analysis of HKE4, a member of the new LIV-1 subfamily of zinc transporters.

    PubMed

    Taylor, Kathryn M; Morgan, Helen E; Johnson, Andrea; Nicholson, Robert I

    2004-01-01

    The KE4 proteins are an emerging group of proteins with little known functional data. In the present study, we report the first characterization of the recombinant human KE4 protein in mammalian cells. The KE4 sequences are included in the subfamily of ZIP (Zrt-, Irt-like Proteins) zinc transporters, which we have termed LZT (LIV-1 subfamily of ZIP zinc Transporters). All these LZT sequences contain similarities to ZIP transporters, including the consensus sequence in transmembrane domain IV, which is essential for zinc transport. However, the new LZT subfamily can be separated from other ZIP transporters by the presence of a highly conserved potential metalloprotease motif (HEXPHEXGD) in transmembrane domain V. Here we report the location of HKE4 on intracellular membranes, including the endoplasmic reticulum, and its ability to increase the intracellular free zinc as measured with the zinc-specific fluorescent dye, Newport Green, in a time-, temperature- and concentration-dependent manner. This is in contrast with the zinc influx ability of another LZT protein, LIV-1, which was due to its plasma membrane location. Therefore we have added to the functionality of LZT proteins by reporting their ability to increase intracellular-free zinc, whether they are located on the plasma membrane or on intracellular membranes. This result, in combination with the crucial role that zinc plays in cell growth, emphasizes the importance of this new LZT subfamily, including the KE4 sequences, in the control of intracellular zinc homoeostasis, aberrations of which can lead to diseases such as cancer, immunological disorders and neurological dysfunction.

  1. Sequence subfamilies of satellite repeats related to rDNA intergenic spacer are differentially amplified on Vicia sativa chromosomes.

    PubMed

    Macas, Jiri; Navrátilová, Alice; Mészáros, Tibor

    2003-10-01

    We cloned and sequenced the Vicia sativa 25S-18S rDNA intergenic spacer (IGS) and the satellite repeat S12, thought to be related to the spacer sequence. The spacer was shown to contain three types of subrepeats (A, B, and C) with monomers of 173 bp (A), 10 bp (B), and 66 bp (C), separated by unique or partially duplicated sequences. Two spacer variants were detected in V. sativa that differed in length (2990 and 3168 bp) owing to an extra copy of the subrepeat A. The A subrepeats were also shown to be highly homologous to the satellite repeat S12, which is located in large clusters on chromosomes 4, 5, and 6, and is not associated with the rDNA loci. Sequencing of additional S12 clones retrieved from a shotgun genomic library allowed definition of three subfamilies of this repeat based on minor differences in their nucleotide sequences. Two of these subfamilies could be discriminated from the rest of the S12 sequences as well as from the IGS A subrepeats using specific oligonucleotide primers that labeled only a subset of the S12 loci when used in the primed in situ DNA labeling (PRINS) reaction on mitotic chromosomes. These experiments showed that, in spite of the high overall similarity of the IGS A subrepeats and the S12 satellite repeats, there are S12 subfamilies that are divergent from the common consensus and are present at only some of the chromosomes containing the S12 loci. Thus, the subfamilies may have evolved at these loci following the spreading of the A subrepeats from the IGS to genomic regions outside the rDNA clusters.

  2. The first record of the wolf spider subfamily Zoicinae from China (Araneae: Lycosidae), with the description of two new species.

    PubMed

    Li, Zongxu; Wang, Lu-yu; Zhangi, Zhi-sheng

    2013-01-01

    The subfamily Zoicinae Lehtinen & Hippa, 1979 is here first recorded from China with the description of a new species in the genus Zoica Simon, 1898, Z. unciformis sp. nov. from Wild Elephant Valley (Yunnan) and a new species in the genus Lysania Thorell, 1890, L. deangia sp. nov., from a rubber plantation in Nangsang Village (Yunnan). Lysania pygmaea Thorell, 1890 is recorded for the first time in China, from three localities in Yunnan and Guangxi and is redescribed here.

  3. An intron loss in the chloroplast gene rpoC1 supports a monophyletic origin for the subfamily Cactoideae of the Cactaceae.

    PubMed

    Wallace, R S; Cota, J H

    1996-02-01

    The deletion of an approximately 700-bp intron in the chloroplast-encoded gene rpoC1 was shown in 21 representative species of the subfamily Cactoideae of the angiosperm family Cactaceae. Members of the subfamilies Pereskioideae and Opuntioideae were found to possess the intron, as did members of the related families Aizoaceae, Basellaceae, Didiereaceae, Phytolaccaceae, and Portulacaceae. These results support a monophyletic origin for the most-speciose subfamily of the cactus family, and represent a first report of the loss of this intron in dicots.

  4. Type 2 diabetes - Tuberculosis co-morbidity is associated with diminished circulating levels of IL-20 subfamily of cytokines.

    PubMed

    Kumar, Nathella Pavan; Banurekha, Vaithilingam V; Nair, Dina; Kumaran, Paul; Dolla, Chandra Kumar; Babu, Subash

    2015-12-01

    IL-20 subfamily of cytokines play an important role in both host defense mechanisms and glucose metabolism. Since, the interaction between tuberculosis (TB) and diabetes (DM) involves both of the above processes, we examined the association of IL-20 subfamily of cytokines in TB-DM co-morbidity. We examined circulating plasma cytokine levels in individuals with active TB with (PTB-DM) or without (PTB) diabetes and also those with latent TB with (LTB-DM) or without (LTB) diabetes. PTB-DM is characterized by diminished circulating levels of IL-19, IL-20, IL-22 and IL-24 but increased levels of IL-10. Similarly, LTB-DM was also characterized by diminished circulating levels of IL-10, IL-19, IL-20 and IL-24 but increased levels of IL-22. Moreover, there was a significant negative correlation of IL-10, IL-19, IL-20, IL-22 and IL-24 levels with hemoglobin A1C (HbA1c) levels in both PTB and/or LTB individuals. Finally, PTB is characterized by diminished levels of IL-19, IL-20, IL-22 and IL-24 in comparison to LTB individuals. Our data reveal that coincident diabetes in either PTB or LTB is characterized by decreased production of the IL-20 subfamily of cytokines and suggest that these cytokines might play an important role in pathogenesis or protection.

  5. Identification and Structure-Function Analysis of Subfamily Selective G Protein-Coupled Receptor Kinase Inhibitors

    SciTech Connect

    Homan, Kristoff T.; Larimore, Kelly M.; Elkins, Jonathan M.; Szklarz, Marta; Knapp, Stefan; Tesmer, John J.G.

    2015-02-13

    Selective inhibitors of individual subfamilies of G protein-coupled receptor kinases (GRKs) would serve as useful chemical probes as well as leads for therapeutic applications ranging from heart failure to Parkinson’s disease. To identify such inhibitors, differential scanning fluorimetry was used to screen a collection of known protein kinase inhibitors that could increase the melting points of the two most ubiquitously expressed GRKs: GRK2 and GRK5. Enzymatic assays on 14 of the most stabilizing hits revealed that three exhibit nanomolar potency of inhibition for individual GRKs, some of which exhibiting orders of magnitude selectivity. Most of the identified compounds can be clustered into two chemical classes: indazole/dihydropyrimidine-containing compounds that are selective for GRK2 and pyrrolopyrimidine-containing compounds that potently inhibit GRK1 and GRK5 but with more modest selectivity. The two most potent inhibitors representing each class, GSK180736A and GSK2163632A, were cocrystallized with GRK2 and GRK1, and their atomic structures were determined to 2.6 and 1.85 Å spacings, respectively. GSK180736A, developed as a Rho-associated, coiled-coil-containing protein kinase inhibitor, binds to GRK2 in a manner analogous to that of paroxetine, whereas GSK2163632A, developed as an insulin-like growth factor 1 receptor inhibitor, occupies a novel region of the GRK active site cleft that could likely be exploited to achieve more selectivity. However, neither compound inhibits GRKs more potently than their initial targets. This data provides the foundation for future efforts to rationally design even more potent and selective GRK inhibitors.

  6. Dynamic Distribution and Interaction of the Arabidopsis SRSF1 Subfamily Splicing Factors1

    PubMed Central

    Stankovic, Nancy; Schloesser, Marie; Joris, Marine; Sauvage, Eric; Hanikenne, Marc; Motte, Patrick

    2016-01-01

    Ser/Arg-rich (SR) proteins are essential nucleus-localized splicing factors. Our prior studies showed that Arabidopsis (Arabidopsis thaliana) RSZ22, a homolog of the human SRSF7 SR factor, exits the nucleus through two pathways, either dependent or independent on the XPO1 receptor. Here, we examined the expression profiles and shuttling dynamics of the Arabidopsis SRSF1 subfamily (SR30, SR34, SR34a, and SR34b) under control of their endogenous promoter in Arabidopsis and in transient expression assay. Due to its rapid nucleocytoplasmic shuttling and high expression level in transient assay, we analyzed the multiple determinants that regulate the localization and shuttling dynamics of SR34. By site-directed mutagenesis of SR34 RNA-binding sequences and Arg/Ser-rich (RS) domain, we further show that functional RRM1 or RRM2 are dispensable for the exclusive protein nuclear localization and speckle-like distribution. However, mutations of both RRMs induced aggregation of the protein whereas mutation in the RS domain decreased the stability of the protein and suppressed its nuclear accumulation. Furthermore, the RNA-binding motif mutants are defective for their export through the XPO1 (CRM1/Exportin-1) receptor pathway, but retain nucleocytoplasmic mobility. We performed a yeast two hybrid screen with SR34 as bait and discovered SR45 as a new interactor. SR45 is an unusual SR splicing factor bearing two RS domains. These interactions were confirmed in planta by FLIM-FRET and BiFC and the roles of SR34 domains in protein-protein interactions were further studied. Altogether, our report extends our understanding of shuttling dynamics of Arabidopsis SR splicing factors. PMID:26697894

  7. The SAUR19 subfamily of SMALL AUXIN UP RNA genes promote cell expansion

    PubMed Central

    Spartz, Angela K.; Lee, Sang H.; Wenger, Jonathan P.; Gonzalez, Nathalie; Itoh, Hironori; Inzé, Dirk; Peer, Wendy A.; Murphy, Angus S.; Overvoorde, Paul J.; Gray, William M.

    2012-01-01

    SUMMARY The plant hormone auxin controls numerous aspects of plant growth and development by regulating the expression of hundreds of genes. SMALL AUXIN UP RNA (SAUR) genes comprise the largest family of auxin-responsive genes, but their function is unknown. Although prior studies have correlated the expression of some SAUR genes with auxin-mediated cell expansion, genetic evidence implicating SAURs in cell expansion has not been reported. The Arabidopsis SAUR19, SAUR20, SAUR21, SAUR22, SAUR23, and SAUR24 (SAUR19– 24) genes encode a subgroup of closely related SAUR proteins. We demonstrate that these SAUR proteins are highly unstable in Arabidopsis. However, the addition of an N-terminal GFP or epitope tag dramatically increases the stability of SAUR proteins. Expression of these stabilized SAUR fusion proteins in Arabidopsis confers numerous auxin-related phenotypes indicative of increased and/or unregulated cell expansion, including increased hypocotyl and leaf size, defective apical hook maintenance, and altered tropic responses. Furthermore, seedlings expressing an artificial microRNA targeting multiple members of the SAUR19–24 subfamily exhibit short hypocotyls and reduced leaf size. Together, these findings demonstrate that SAUR19– 24 function as positive effectors of cell expansion. This regulation may be achieved through the modulation of auxin transport, as SAUR gain-of-function and loss-of-function seedlings exhibit increased and reduced basipetal indole-3-acetic acid transport, respectively. Consistent with this possibility, SAUR19–24 proteins predominantly localize to the plasma membrane. PMID:22348445

  8. The Crystal Structure of Streptococcus pyogenes Uridine Phosphorylase Reveals a Distinct Subfamily of Nucleoside Phosphorylases

    SciTech Connect

    Tran, Timothy H.; Christoffersen, S.; Allan, Paula W.; Parker, William B.; Piskur, Jure; Serra, I.; Terreni, M.; Ealick, Steven E.

    2011-09-20

    Uridine phosphorylase (UP), a key enzyme in the pyrimidine salvage pathway, catalyzes the reversible phosphorolysis of uridine or 2'-deoxyuridine to uracil and ribose 1-phosphate or 2'-deoxyribose 1-phosphate. This enzyme belongs to the nucleoside phosphorylase I superfamily whose members show diverse specificity for nucleoside substrates. Phylogenetic analysis shows Streptococcus pyogenes uridine phosphorylase (SpUP) is found in a distinct branch of the pyrimidine subfamily of nucleoside phosphorylases. To further characterize SpUP, we determined the crystal structure in complex with the products, ribose 1-phosphate and uracil, at 1.8 {angstrom} resolution. Like Escherichia coli UP (EcUP), the biological unit of SpUP is a hexamer with an ?/? monomeric fold. A novel feature of the active site is the presence of His169, which structurally aligns with Arg168 of the EcUP structure. A second active site residue, Lys162, is not present in previously determined UP structures and interacts with O2 of uracil. Biochemical studies of wild-type SpUP showed that its substrate specificity is similar to that of EcUP, while EcUP is {approx}7-fold more efficient than SpUP. Biochemical studies of SpUP mutants showed that mutations of His169 reduced activity, while mutation of Lys162 abolished all activity, suggesting that the negative charge in the transition state resides mostly on uracil O2. This is in contrast to EcUP for which transition state stabilization occurs mostly at O4.

  9. Evolutionary relationships among primary endosymbionts of the mealybug subfamily phenacoccinae (hemiptera: Coccoidea: Pseudococcidae).

    PubMed

    Gruwell, Matthew E; Hardy, Nate B; Gullan, Penny J; Dittmar, Katharina

    2010-11-01

    Mealybugs (Coccoidea: Pseudococcidae) are sap-sucking plant parasites that harbor bacterial endosymbionts within specialized organs. Previous studies have identified two subfamilies, Pseudococcinae and Phenacoccinae, within mealybugs and determined the primary endosymbionts (P-endosymbionts) of the Pseudococcinae to be Betaproteobacteria ("Candidatus Tremblaya princeps") containing Gammaproteobacteria secondary symbionts. Here, the P-endosymbionts of phenacoccine mealybugs are characterized based on 16S rRNA from the bacteria of 20 species of phenacoccine mealybugs and four outgroup Puto species (Coccoidea: Putoidae) and aligned to more than 100 published 16S rRNA sequences from symbiotic and free-living bacteria. Phylogenetic analyses recovered three separate lineages of bacteria from the Phenacoccinae, and these are considered to be the P-endosymbionts of their respective mealybug hosts, with those from (i) the mealybug genus Rastrococcus belonging to the Bacteroidetes, (ii) the subterranean mealybugs, tribe Rhizoecini, also within Bacteroidetes, in a clade sister to cockroach endosymbionts (Blattabacterium), and (iii) the remaining Phenacoccinae within the Betaproteobacteria, forming a well-supported sister group to "Candidatus Tremblaya princeps." Names are proposed for two strongly supported lineages: "Candidatus Brownia rhizoecola" for P-endosymbionts of Rhizoecini and "Candidatus Tremblaya phenacola" for P-endosymbionts of Phenacoccinae excluding Rastrococcus and Rhizoecini. Rates of nucleotide substitution among lineages of Tremblaya were inferred to be significantly faster than those of free-living Betaproteobacteria. Analyses also recovered a clade of Gammaproteobacteria, sister to the P-endosymbiont lineage of aphids ("Candidatus Buchnera aphidicola"), containing the endosymbionts of Putoidae, the secondary endosymbionts of pseudococcine mealybugs, and the endosymbionts of several other insect groups.

  10. Comparative genome analysis between Agrostis stolonifera and members of the Pooideae subfamily, including Brachypodium distachyon.

    PubMed

    Araneda, Loreto; Sim, Sung-Chur; Bae, Jin-Joo; Chakraborty, Nanda; Curley, Joe; Chang, Taehyun; Inoue, Maiko; Warnke, Scott; Jung, Geunhwa

    2013-01-01

    Creeping bentgrass (Agrostis stolonifera, allotetraploid 2n = 4x = 28) is one of the major cool-season turfgrasses. It is widely used on golf courses due to its tolerance to low mowing and aggressive growth habit. In this study, we investigated genome relationships of creeping bentgrass relative to the Triticeae (a consensus map of Triticum aestivum, T. tauschii, Hordeum vulgare, and H. spontaneum), oat, rice, and ryegrass maps using a common set of 229 EST-RFLP markers. The genome comparisons based on the RFLP markers revealed large-scale chromosomal rearrangements on different numbers of linkage groups (LGs) of creeping bentgrass relative to the Triticeae (3 LGs), oat (4 LGs), and rice (8 LGs). However, we detected no chromosomal rearrangement between creeping bentgrass and ryegrass, suggesting that these recently domesticated species might be closely related, despite their memberships to different Pooideae tribes. In addition, the genome of creeping bentgrass was compared with the complete genome sequence of Brachypodium distachyon in Pooideae subfamily using both sequences of the above-mentioned mapped EST-RFLP markers and sequences of 8,470 publicly available A. stolonifera ESTs (AgEST). We discovered large-scale chromosomal rearrangements on six LGs of creeping bentgrass relative to B. distachyon. Also, a total of 24 syntenic blocks based on 678 orthologus loci were identified between these two grass species. The EST orthologs can be utilized in further comparative mapping of Pooideae species. These results will be useful for genetic improvement of Agrostis species and will provide a better understanding of evolution within Pooideae species.

  11. Evolutionary Relationships among Primary Endosymbionts of the Mealybug Subfamily Phenacoccinae (Hemiptera: Coccoidea: Pseudococcidae) ▿

    PubMed Central

    Gruwell, Matthew E.; Hardy, Nate B.; Gullan, Penny J.; Dittmar, Katharina

    2010-01-01

    Mealybugs (Coccoidea: Pseudococcidae) are sap-sucking plant parasites that harbor bacterial endosymbionts within specialized organs. Previous studies have identified two subfamilies, Pseudococcinae and Phenacoccinae, within mealybugs and determined the primary endosymbionts (P-endosymbionts) of the Pseudococcinae to be Betaproteobacteria (“Candidatus Tremblaya princeps”) containing Gammaproteobacteria secondary symbionts. Here, the P-endosymbionts of phenacoccine mealybugs are characterized based on 16S rRNA from the bacteria of 20 species of phenacoccine mealybugs and four outgroup Puto species (Coccoidea: Putoidae) and aligned to more than 100 published 16S rRNA sequences from symbiotic and free-living bacteria. Phylogenetic analyses recovered three separate lineages of bacteria from the Phenacoccinae, and these are considered to be the P-endosymbionts of their respective mealybug hosts, with those from (i) the mealybug genus Rastrococcus belonging to the Bacteroidetes, (ii) the subterranean mealybugs, tribe Rhizoecini, also within Bacteroidetes, in a clade sister to cockroach endosymbionts (Blattabacterium), and (iii) the remaining Phenacoccinae within the Betaproteobacteria, forming a well-supported sister group to “Candidatus Tremblaya princeps.” Names are proposed for two strongly supported lineages: “Candidatus Brownia rhizoecola” for P-endosymbionts of Rhizoecini and “Candidatus Tremblaya phenacola” for P-endosymbionts of Phenacoccinae excluding Rastrococcus and Rhizoecini. Rates of nucleotide substitution among lineages of Tremblaya were inferred to be significantly faster than those of free-living Betaproteobacteria. Analyses also recovered a clade of Gammaproteobacteria, sister to the P-endosymbiont lineage of aphids (“Candidatus Buchnera aphidicola”), containing the endosymbionts of Putoidae, the secondary endosymbionts of pseudococcine mealybugs, and the endosymbionts of several other insect groups. PMID:20851962

  12. Comparison of otoacoustic emissions within gecko subfamilies: morphological implications for auditory function in lizards.

    PubMed

    Bergevin, Christopher

    2011-04-01

    Otoacoustic emissions (OAEs) are sounds emitted by the ear and provide a non-invasive probe into mechanisms underlying peripheral auditory transduction. This study focuses upon a comparison of emission properties in two phylogenetically similar pairs of gecko: Gekko gecko and Hemidactylus turcicus and Eublepharis macularius and Coleonyx variegatus. Each pair consists of two closely related species within the same subfamily, with quantitatively known morphological properties at the level of the auditory sensory organ (basilar papilla) in the inner ear. Essentially, the comparison boils down to an issue of size: how does overall body size, as well as the inner-ear dimensions (e.g., papilla length and number of hair cells), affect peripheral auditory function as inferred from OAEs? Estimates of frequency selectivity derived from stimulus-frequency emissions (emissions evoked by a single low-level tone) indicate that tuning is broader in the species with fewer hair cells/shorter papilla. Furthermore, emissions extend outwards to higher frequencies (for similar body temperatures) in the species with the smaller body size/narrower interaural spacing. This observation suggests the smaller species have relatively improved high-frequency sensitivity, possibly related to vocalizations and/or aiding azimuthal sound localization. For one species (Eublepharis), emissions were also examined in both juveniles and adults. Qualitatively similar emission properties in both suggests that inner-ear function is adult like soon after hatching and that external body size (e.g., middle-ear dimensions and interaural spacing) has a relatively small impact upon emission properties within a species.

  13. Nepenthesin, a unique member of a novel subfamily of aspartic proteinases: enzymatic and structural characteristics.

    PubMed

    Takahashi, Kenji; Athauda, Senarath B P; Matsumoto, Koji; Rajapakshe, Sanath; Kuribayashi, Masayuki; Kojima, Masaki; Kubomura-Yoshida, Nobuko; Iwamatsu, Akihiro; Shibata, Chiaki; Inoue, Hideshi

    2005-12-01

    Carnivorous plants are known to secrete acid proteinases to digest prey, mainly insects, for nitrogen uptake. In our recent study, we have purified, for the first time, to homogeneity two acid proteinases, nepenthesin I (Nep I) and nepenthesin II (Nep II) from the pitcher fluid of Nepenthes distillatoria and investigated their enzymatic and structural characteristics. Both enzymes were optimally active at pH approx. 2.6 toward acid-denatured hemoglobin; the specificity of Nep I toward oxidized insulin B chain appears to be similar, but slightly wider than those of other aspartic proteinases (APs). At or below 50 degrees C both enzymes were remarkably stable; especially Nep I was extremely stable over a wide range of pH from 3 to 10 for over 30 days. This suggests an evolutionary adaptation of the enzymes to their specific habitat. We have also cloned the cDNAs and deduced the complete amino acid sequences of the precursors of Nep I and Nep II from the pitcher tissue of Nepenthes gracilis. Although the corresponding mature enzymes are homologous with ordinary pepsin-type APs, both enzymes had a high content of cysteine residues (12 residues per molecule), which are assumed to form six unique disulfide bonds as suggested by computer modeling and are thought to contribute toward the remarkable stability of Neps. Moreover, the amino acid sequence identity of Neps with ordinary APs, including plant vacuolar APs, are remarkably low (approx. 20%), and phylogenetic comparison shows that Neps are distantly related to them to form a novel subfamily of APs with a high content of cysteine residues and a characteristic insertion, named 'the Nep-type AP (NAP)-specific insertion', including a large number of novel, orthologous plant APs emerging in the gene/protein databases.

  14. Enzymic and structural characterization of nepenthesin, a unique member of a novel subfamily of aspartic proteinases.

    PubMed

    Athauda, Senarath B P; Matsumoto, Koji; Rajapakshe, Sanath; Kuribayashi, Masayuki; Kojima, Masaki; Kubomura-Yoshida, Nobuko; Iwamatsu, Akihiro; Shibata, Chiaki; Inoue, Hideshi; Takahashi, Kenji

    2004-07-01

    Carnivorous plants are known to secrete acid proteinases to digest prey, mainly insects, for nitrogen uptake. In the present study, we have purified, for the first time, to homogeneity two acid proteinases (nepenthesins I and II) from the pitcher fluid of Nepenthes distillatoria (a pitcher-plant known locally as badura) and investigated their enzymic and structural characteristics. Both enzymes were optimally active at pH approx. 2.6 towards acid-denatured haemoglobin; the specificity of nepenthesin I towards oxidized insulin B chain appears to be similar, but slightly wider than those of other APs (aspartic proteinases). Among the enzymic properties, however, the most notable is their unusual stability: both enzymes were remarkably stable at or below 50 degrees C, especially nepenthesin I was extremely stable over a wide range of pH from 3 to 10 for over 30 days. This suggests an evolutionary adaptation of the enzymes to their specific habitat. We have also cloned the cDNAs and deduced the complete amino acid sequences of the precursors of nepenthesins I and II (437 and 438 residues respectively) from the pitcher tissue of N. gracilis. Although the corresponding mature enzymes (each 359 residues) are homologous with ordinary pepsin-type APs, both enzymes had a high content of cysteine residues (12 residues/molecule), which are assumed to form six unique disulphide bonds as suggested by computer modelling and are supposed to contribute towards the remarkable stability of nepenthesins. Moreover, the amino acid sequence identity of nepenthesins with ordinary APs, including plant vacuolar APs, is remarkably low (approx. 20%), and phylogenetic comparison shows that nepenthesins are distantly related to them to form a novel subfamily of APs with a high content of cysteine residues and a characteristic insertion, named 'the nepenthesin-type AP-specific insertion', that includes a large number of novel, orthologous plant APs emerging in the gene/protein databases.

  15. Comparative Genome Analysis between Agrostis stolonifera and Members of the Pooideae Subfamily, including Brachypodium distachyon

    PubMed Central

    Bae, Jin-Joo; Chakraborty, Nanda; Curley, Joe; Chang, Taehyun; Inoue, Maiko; Warnke, Scott; Jung, Geunhwa

    2013-01-01

    Creeping bentgrass (Agrostis stolonifera, allotetraploid 2n = 4x = 28) is one of the major cool-season turfgrasses. It is widely used on golf courses due to its tolerance to low mowing and aggressive growth habit. In this study, we investigated genome relationships of creeping bentgrass relative to the Triticeae (a consensus map of Triticum aestivum, T. tauschii, Hordeum vulgare, and H. spontaneum), oat, rice, and ryegrass maps using a common set of 229 EST-RFLP markers. The genome comparisons based on the RFLP markers revealed large-scale chromosomal rearrangements on different numbers of linkage groups (LGs) of creeping bentgrass relative to the Triticeae (3 LGs), oat (4 LGs), and rice (8 LGs). However, we detected no chromosomal rearrangement between creeping bentgrass and ryegrass, suggesting that these recently domesticated species might be closely related, despite their memberships to different Pooideae tribes. In addition, the genome of creeping bentgrass was compared with the complete genome sequence of Brachypodium distachyon in Pooideae subfamily using both sequences of the above-mentioned mapped EST-RFLP markers and sequences of 8,470 publicly available A. stolonifera ESTs (AgEST). We discovered large-scale chromosomal rearrangements on six LGs of creeping bentgrass relative to B. distachyon. Also, a total of 24 syntenic blocks based on 678 orthologus loci were identified between these two grass species. The EST orthologs can be utilized in further comparative mapping of Pooideae species. These results will be useful for genetic improvement of Agrostis species and will provide a better understanding of evolution within Pooideae species. PMID:24244501

  16. Structural and Functional Interactions between Transient Receptor Potential Vanilloid Subfamily 1 and Botulinum Neurotoxin Serotype A

    PubMed Central

    2016-01-01

    Background Botulinum neurotoxins are produced by Clostridium botulinum bacteria. There are eight serologically distinct botulinum neurotoxin isoforms (serotypes A–H). Currently, botulinum neurotoxin serotype A (BoNT⁄A) is commonly used for the treatment of many disorders, such as hyperactive musculoskeletal disorders, dystonia, and pain. However, the effectiveness of BoNT⁄A for pain alleviation and the mechanisms that mediate the analgesic effects of BoNT⁄A remain unclear. To define the antinociceptive mechanisms by which BoNT/A functions, the interactions between BoNT⁄A and the transient receptor potential vanilloid subfamily 1 (TRPV1) were investigated using immunofluorescence, co-immunoprecipitation, and western blot analysis in primary mouse embryonic dorsal root ganglion neuronal cultures. Results 1) Three-week-old cultured dorsal root ganglion neurons highly expressed transient TRPV1, synaptic vesicle 2A (SV2A) and synaptosomal-associated protein 25 (SNAP-25). SV2A and SNAP-25 are the binding receptor and target protein, respectively, of BoNT⁄A. 2) TRPV1 colocalized with both BoNT⁄A and cleaved SNAP-25 when BoNT⁄A was added to dorsal root ganglia neuronal cultures. 3) After 24 hours of BoNT⁄A treatment (1 nmol⁄l), both TRPV1 and BoNT⁄A positive bands were detected in western blots of immunoprecipitated pellets. 4) Blocking TRPV1 with a specific antibody decreased the cleavage of SNAP-25 by BoNT⁄A. Conclusion BoNT/A interacts with TRPV1 both structurally and functionally in cultured mouse embryonic dorsal root ganglion neurons. These results suggest that an alternative mechanism is used by BoNT⁄A to mediate pain relief. PMID:26745805

  17. Cephalocteinae Mulsant et Rey, 1866 (Hemiptera, Heteroptera), a subfamily of Cydnidae new for the Italian fauna: first record of Cephalocteus scarabaeoides (Fabricius, 1807) from Sardinia.

    PubMed

    Fancello, Luca; Cillo, Davide; Bazzato, Erika

    2016-01-25

    Cephalocteus scarabaeoides is recorded from the south-western coast of Sardinia, in sandy habitat (marine dunes near the beach), for the first time. The species and the subfamily are new for the Italian fauna.

  18. Alu Sb2 subfamily is present in all higher primates but was most succesfully amplified in humans

    SciTech Connect

    Richer, C.; Zietkiewicz, E.; Labuda, D.

    1994-09-01

    Alu repeats can be classified into subfamilies which amplified in primate genomes at different evolutionary time periods. A young Alu subfamily, Sb2, with a characteristic 7-nucleotide duplication at position 256, has been described in seven human loci. An Sb2 insertion found near the HD gene was unique to two HD families, indicating that Sb2 was still retropositionally active. Here, we have shown that the Sb2 insertion in the CHOL locus was similarly rare, being absent in 120 individuals of Caucasian, Oriental and Black origin. In contrast, Sb2 inserts in five other loci were found fixed (non-polymorphic), based on measurements in the same population sample, but absent from orthologous positions in higher apes. This suggest that Sb2 repeats spread relatively early in the human lineage following divergence from other primates and that these elements may be human-specific. By quantitative PCR, we investigated the presence of Sb2 sequences in different primate DNA, using one PCR primer anchored at the 5{prime} Alu-end and the other complementary to the duplicated Sb2-specific segment. With an Sb2-containing plasmid as a standard, we estimated the number of Sb2 repeats at 1500-1800 copies per human haploid equivalent; corresponding numbers in chimpanzee and gorilla were almost two orders of magnitude lower, while the signal observed in orangutan and gibbon DNAs was consistent with the presence of a single copy. The analysis of 22 human, 11 chimpanzee and 10 gorilla sequences indicates that the Alu Sb2 dispersed independently in these three primate lineages; gorilla consensus differs from the human Sb2 sequence by one position, while all chimpanzee repeats have their linker expanded by up to eight A-residues. Should they be thus considered as separate subfamilies? It is possible that sequence modifications with respect to the human consensus are responsible for poor retroposition of Sb2 in apes.

  19. [Contribution to the black fly fauna of the subfamily Prosimuliinae (Diptera: Simuliidae) of the Sakha Republik (Yakutia)].

    PubMed

    Aĭbulatov, S V

    2014-01-01

    Examination of river basins of Yakutia and the study of the previously collected material resulted in revealing of 34 species of the subfamily Prosimuliinae belonging to 8 genera (Gymnopais, Prosimulium, Helodon, Stegopterna, Greniera, Cnephia, Metacnephia, and Sulcicnephia). The fauna of Yakutia was supplemented with two black fly species Cnephia angarensis Rubzov, 1956 and Gymnopais frontatus Yankovsky, 1982. The distribution of the species Prosimulium tridentatum, Helodon alpestris, H. irkutensis, H. rubicundus, Stegopterna asema, and Cnephia lyra) was clarified. The combined table of species distribution with GPS coordinates of collecting sites has been composed.

  20. Two Drosophila retrotransposon gypsy subfamilies differ in ability to produce new DNA copies via reverse transcription in Drosophila cultured cells.

    PubMed Central

    Lyubomirskaya, N V; Avedisov, S N; Surkov, S A; Ilyin, Y V

    1993-01-01

    Plasmid DNA constructs containing 5' end truncated retrotransposon gypsy were introduced into Drosophila cultured cells. Appearance of new complete DNA copies with reconstructed via reverse transcription 5'LTR were detected by PCR after transient expression and by Southern blot analysis of genome DNA of stably transformed cells. Two gypsy subfamilies supposed to be different in transpositional activity were analyzed in terms of their ability to produce new DNA copies via reverse transcription in D. hydei cultured cells. It was demonstrated that both gypsy variants undergo retrotransposition but with different efficiency. Images PMID:7688116

  1. New species and records of the mite genus Prolistrophorus (Acariformes: Listrophoridae) from rodents of the subfamily Sigmodontinae (Rodentia: Cricetidae).

    PubMed

    Bochkov, Andre V; Lareschi, Marcela; Barreto, Mauricio

    2014-10-01

    Six fur-mite species of the genus Prolistrophorus Fain, 1970 (Acariformes: Listrophoridae) were recorded from Central and South American rodents of the subfamily Sigmodontinae (Rodentia: Cricetidae). Among them, Prolistrophorus (Aprolistrophorus) parabidentatus sp. nov. from Akodon azarae from Argentina and Prolistrophorus (Aprolistrophorus) tylomys sp. nov. from Tylomys nudicaudus from Guatemala are described as new for science. New hosts are recorded for the following species: Prolistrophorus (Prolistrophorus) grassii (Radford, 1954) from Zygodontomys brevicauda from Colombia, P. (P.) frontalis (Hirst, 1921) from Oligoryzomys sp. from Argentina, P. (P.) argentinus (Hirst, 1921) from Melanomys caliginosus, Akodon affinis from Colombia and Scapteromys aquaticus from Argentina, Prolistrophorus (Beprolistrophorus) hirstianus Fain, 1973 from Scapteromys aquaticus from Argentina.

  2. Sea snakes in Australian waters (Serpentes: subfamilies Hydrophiinae and Laticaudinae)--a review with an updated identification key.

    PubMed

    Rasmussen, Arne Redsted; Sanders, Kate Laura; Guinea, Michael L; Amey, Andrew P

    2014-10-02

    Sea snakes (Elapidae, subfamilies Hydrophiinae and Laticaudinae) reach high species richness in the South China Sea and in the Australian region; however, most countries in the two regions still lack up-to-date checklists and identification tools for these snakes. We present an updated reviewed checklist and a new complete identification key to sea snakes in Australian waters. The identification key includes 29 species documented and 4 possibly occurring taxa and is based mostly on easy-to-use external characters. We find no evidence for breeding populations of Laticauda in Australian waters, but include the genus on the list of possibly occurring taxa. 

  3. A genomic view of the NOD-like receptor family in teleost fish: Identification of a novel NLR subfamily in zebrafish

    USGS Publications Warehouse

    Laing, K.J.; Purcell, M.K.; Winton, J.R.; Hansen, J.D.

    2008-01-01

    Background. A large multigene family of NOD-like receptor (NLR) molecules have been described in mammals and implicated in immunity and apoptosis. Little information, however, exists concerning this gene family in non-mammalian taxa. This current study, therefore, provides an in-depth investigation of this gene family in lower vertebrates including extensive phylogenetic comparison of zebrafish NLRs with orthologs in tetrapods, and analysis of their tissue-specific expression. Results. Three distinct NLR subfamilies were identified by mining genome databases of various non-mammalian vertebrates; the first subfamily (NLR-A) resembles mammalian NODs, the second (NLR-B) resembles mammalian NALPs, while the third (NLR-C) appears to be unique to teleost fish. In zebrafish, NLR-A and NLR-B subfamilies contain five and six genes respectively. The third subfamily is large, containing several hundred NLR-C genes, many of which are predicted to encode a C-terminal B30.2 domain. This subfamily most likely evolved from a NOD3-like molecule. Gene predictions for zebrafish NLRs were verified using sequence derived from ESTs or direct sequencing of cDNA. Reverse-transcriptase (RT)-PCR analysis confirmed expression of representative genes from each subfamily in selected tissues. Conclusion. Our findings confirm the presence of multiple NLR gene orthologs, which form a large multigene family in teleostei. Although the functional significance of the three major NLR subfamilies is unclear, we speculate that conservation and abundance of NLR molecules in all teleostei genomes, reflects an essential role in cellular control, apoptosis or immunity throughout bony fish. ?? 2008 Laing et al; licensee BioMed Central Ltd.

  4. Testing the reliability of standard and complementary DNA barcodes for the monocot subfamily Alooideae from South Africa.

    PubMed

    Daru, Barnabas H; van der Bank, Michelle; Bello, Abubakar; Yessoufou, Kowiyou

    2016-11-23

    Although a standard DNA barcode has been identified for plants, it does not always provide species-level specimen identifications for investigating important ecological questions. In this study, we assessed the species-level discriminatory power of standard (rbcLa + matK) and complementary barcodes (ITS1 and trnH-psbA) within the subfamily Alooideae (Asphodelaceae), a large and recent plant radiation, whose species are important in horticulture yet are threatened. Alooideae has its centre of endemism in southern Africa, with some outlier species occurring elsewhere in Africa and Madagascar. We sampled 360 specimens representing 235 species within all 11 genera of the subfamily. With three distance-based methods, all markers performed poorly for our combined data set, with the highest proportion of correct species-level specimen identifications (30%) found for ITS1. However, when performance was assessed across genera, the discriminatory power varied from 0% for all single markers and combinations in Gasteria to 63% in Haworthiopsis, again for ITS1, suggesting that DNA barcoding success may be related to the evolutionary history of the lineage considered. Although ITS1 could be a good barcode for Haworthiopsis, the generally poor performance of all markers suggests that Alooideae remains a challenge. As species boundaries within Alooideae remain controversial, we call for continued search for suitable markers or the use of genomics approaches to further explore species discrimination in the group.

  5. Structural and Functional Elucidation of Peptide Ts11 Shows Evidence of a Novel Subfamily of Scorpion Venom Toxins

    PubMed Central

    Cremonez, Caroline M.; Maiti, Mohitosh; Peigneur, Steve; Cassoli, Juliana Silva; Dutra, Alexandre A. A.; Waelkens, Etienne; Lescrinier, Eveline; Herdewijn, Piet; de Lima, Maria Elena; Pimenta, Adriano M. C.; Arantes, Eliane C.; Tytgat, Jan

    2016-01-01

    To date, several families of peptide toxins specifically interacting with ion channels in scorpion venom have been described. One of these families comprise peptide toxins (called KTxs), known to modulate potassium channels. Thus far, 202 KTxs have been reported, belonging to several subfamilies of KTxs (called α, β, γ, κ, δ, and λ-KTxs). Here we report on a previously described orphan toxin from Tityus serrulatus venom, named Ts11. We carried out an in-depth structure-function analysis combining 3D structure elucidation of Ts11 and electrophysiological characterization of the toxin. The Ts11 structure is highlighted by an Inhibitor Cystine Knot (ICK) type scaffold, completely devoid of the classical secondary structure elements (α-helix and/or β-strand). This has, to the best of our knowledge, never been described before for scorpion toxins and therefore represents a novel, 6th type of structural fold for these scorpion peptides. On the basis of their preferred interaction with voltage-gated K channels, as compared to all the other targets tested, it can be postulated that Ts11 is the first member of a new subfamily, designated as ε-KTx. PMID:27706049

  6. Functional analysis of all AGAMOUS subfamily members in rice reveals their roles in reproductive organ identity determination and meristem determinacy.

    PubMed

    Dreni, Ludovico; Pilatone, Alessandro; Yun, Dapeng; Erreni, Stefano; Pajoro, Alice; Caporali, Elisabetta; Zhang, Dabing; Kater, Martin M

    2011-08-01

    Reproductive organ development is one of the most important steps in the life cycle of plants. Studies using core eudicot species like thale cress (Arabidopsis thaliana) and snapdragon (Antirrhinum majus) have shown that MADS domain transcription factors belonging to the AGAMOUS (AG) subfamily regulate the identity of stamens, carpels, and ovules and that they are important for floral meristem determinacy. Here, we investigate the genetic interactions between the four rice (Oryza sativa) AG subfamily members, MADS3, MADS13, MADS21, and MADS58. Our data show that, in contrast with previous reports, MADS3 and MADS58 determine stamen and carpel identity and, together with MADS13, are important for floral meristem determinacy. In the mads3 mads58 double mutant, we observed a complete loss of reproductive organ identity and massive accumulation of lodicules in the third and fourth floral whorls. MADS21 is an AGL11 lineage gene whose expression is not restricted to ovules. Instead, its expression profile is similar to those of class C genes. However, our genetic analysis shows that MADS21 has no function in stamen, carpel, or ovule identity determination.

  7. Recognition of two major clades and early diverged groups within the subfamily Cyperoideae (Cyperaceae) including Korean sedges.

    PubMed

    Jung, Jongduk; Choi, Hong-Keun

    2013-05-01

    We aim to present phylogenetic major groups within the subfamily Cyperoideae (Cyperaceae) on the basis of three molecular data sets; nuclear ribosomal internal transcribed spacer and 5.8S ribosomal RNA region, the ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene, and trnL intron and trnL-F intergenic spacer. Three molecular data and two combined data sets were used to obtain robust and detailed phylogenetic trees by using maximum parsimony and Bayesian inference, respectively. We analyzed 81 genera and 426 species of Cyperaceae, including Korean species. We suggest one early diverged group (EDGs), and two major clades (FAEC and SDC) within the subfamily Cyperoideae. And the clade EDGs comprises six tribes (Schoeneae, Bisboeckelereae, Sclerieae, Cryptangieae, Trilepideae, and Rhynchosporeae) at the basal nodes of Cyperoideae. The FAEC clade (posterior probability [PP]/bootstrap value [BS] = 1.00/85) comprises four tribes (Fuireneae, Abildgaardieae, Eleocharideae, Cypereae), and the SDC clade (PP/BS = 1.00/86) comprises three tribes (Scirpeae, Dulichieae, Cariceae). These three clades used for phylogenetic groups in our study will be useful for establishing the major lineage of the sedge family. The phylogeny of Korean sedges was also investigated within the whole phylogeny of Cyperaceae. The 20 genera of Korean sedges were placed in 10 tribes forming 14 clades.

  8. Checklist of helminth parasites of Goodeinae (Osteichthyes: Cyprinodontiformes: Goodeidae), an endemic subfamily of freshwater fishes from Mexico.

    PubMed

    Martínez-Aquino, Andrés; Mendoza-Palmero, Carlos A; Aguilar-Aguilar, Rogelio; Pérez-Ponce de León, Gerardo

    2014-08-22

    From August 2008 to July 2010, 1,471 fish belonging to the subfamily Goodeinae (representing 28 species) were collected from 47 localities across central Mexico and analyzed for helminth parasites. In addition, a database with all available published accounts of the helminth parasite fauna of goodeines was assembled. Based on both sources of information, a checklist containing all the records was compiled as a necessary first step to address future questions in the areas of ecology, evolutionary biology and biogeography of this host-parasite association. The checklist is presented in two tables, a parasite-host list and a host-parasite list. The checklist contains 51 nominal species, from 34 genera and 26 families of helminth parasites. It includes 8 species of adult digeneans, 9 metacercarie, 6 monogeneans, 3 adult cestodes, 9 metacestodes, 1 adult acanthocephalan, 1 cystacanth, 6 adult nematodes and 8 larval nematodes. Based on the amount of information contained in the checklist, we pose that goodeines, a subfamily of viviparous freshwater fishes endemic to central Mexico, might be regarded as the first group of wildlife vertebrate for which a complete inventory of their helminth parasite fauna has been completed.

  9. Analysis of Comparative Sequence and Genomic Data to Verify Phylogenetic Relationship and Explore a New Subfamily of Bacterial Lipases

    PubMed Central

    Salleh, Abu Bakar; Basri, Mahiran

    2016-01-01

    Thermostable and organic solvent-tolerant enzymes have significant potential in a wide range of synthetic reactions in industry due to their inherent stability at high temperatures and their ability to endure harsh organic solvents. In this study, a novel gene encoding a true lipase was isolated by construction of a genomic DNA library of thermophilic Aneurinibacillus thermoaerophilus strain HZ into Escherichia coli plasmid vector. Sequence analysis revealed that HZ lipase had 62% identity to putative lipase from Bacillus pseudomycoides. The closely characterized lipases to the HZ lipase gene are from thermostable Bacillus and Geobacillus lipases belonging to the subfamily I.5 with ≤ 57% identity. The amino acid sequence analysis of HZ lipase determined a conserved pentapeptide containing the active serine, GHSMG and a Ca2+-binding motif, GCYGSD in the enzyme. Protein structure modeling showed that HZ lipase consisted of an α/β hydrolase fold and a lid domain. Protein sequence alignment, conserved regions analysis, clustal distance matrix and amino acid composition illustrated differences between HZ lipase and other thermostable lipases. Phylogenetic analysis revealed that this lipase represented a new subfamily of family I of bacterial true lipases, classified as family I.9. The HZ lipase was expressed under promoter Plac using IPTG and was characterized. The recombinant enzyme showed optimal activity at 65°C and retained ≥ 97% activity after incubation at 50°C for 1h. The HZ lipase was stable in various polar and non-polar organic solvents. PMID:26934700

  10. Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3.

    PubMed

    Floor, Stephen N; Condon, Kendall J; Sharma, Deepak; Jankowsky, Eckhard; Doudna, Jennifer A

    2016-01-29

    DEAD-box proteins utilize ATP to bind and remodel RNA and RNA-protein complexes. All DEAD-box proteins share a conserved core that consists of two RecA-like domains. The core is flanked by subfamily-specific extensions of idiosyncratic function. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest as members function during protein translation, are essential for viability, and are frequently altered in human malignancies. Here, we define the function of the subfamily-specific extensions of the human DEAD-box protein DDX3. We describe the crystal structure of the subfamily-specific core of wild-type DDX3 at 2.2 Å resolution, alone and in the presence of AMP or nonhydrolyzable ATP. These structures illustrate a unique interdomain interaction between the two ATPase domains in which the C-terminal domain clashes with the RNA-binding surface. Destabilizing this interaction accelerates RNA duplex unwinding, suggesting that it is present in solution and inhibitory for catalysis. We use this core fragment of DDX3 to test the function of two recurrent medulloblastoma variants of DDX3 and find that both inactivate the protein in vitro and in vivo. Taken together, these results redefine the structural and functional core of the DDX3 subfamily of DEAD-box proteins.

  11. Molecular Evidence that Only Two Opsin Subfamilies, the Blue Light- (SWS2) and Green Light-Sensitive (RH2), Drive Color Vision in Atlantic Cod (Gadus morhua)

    PubMed Central

    Søviknes, Anne Mette; Drivenes, Øyvind; Helvik, Jon Vidar

    2014-01-01

    Teleosts show a great variety in visual opsin complement, due to both gene duplication and gene loss. The repertoire ranges from one subfamily of visual opsins (scotopic vision) including rod opsin only retinas seen in many deep-sea species to multiple subfamilies of visual opsins in some pelagic species. We have investigated the opsin repertoire of Atlantic cod (Gadus morhua) using information in the recently sequenced cod genome and found that despite cod not being a deep sea species it lacks visual subfamilies sensitive towards the most extreme parts of the light spectra representing UV and red light. Furthermore, we find that Atlantic cod has duplicated paralogs of both blue-sensitive SWS2 and green-sensitive RH2 subfamilies, with members belonging to each subfamily linked in tandem within the genome (two SWS2-, and three RH2A genes, respectively). The presence of multiple cone opsin genes indicates that there have been duplication events in the cod ancestor SWS2 and RH2 opsins producing paralogs that have been retained in Atlantic. Our results are supported by expressional analysis of cone opsins, which further revealed an ontogenetic change in the array of cone opsins expressed. These findings suggest life stage specific programs for opsin regulation which could be linked to habitat changes and available light as the larvae is transformed into an early juvenile. Altogether we provide the first molecular evidence for color vision driven by only two families of cone opsins due to gene loss in a teleost. PMID:25551396

  12. Autoinhibitory Interdomain Interactions and Subfamily-specific Extensions Redefine the Catalytic Core of the Human DEAD-box Protein DDX3*

    PubMed Central

    Floor, Stephen N.; Condon, Kendall J.; Sharma, Deepak; Jankowsky, Eckhard; Doudna, Jennifer A.

    2016-01-01

    DEAD-box proteins utilize ATP to bind and remodel RNA and RNA-protein complexes. All DEAD-box proteins share a conserved core that consists of two RecA-like domains. The core is flanked by subfamily-specific extensions of idiosyncratic function. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest as members function during protein translation, are essential for viability, and are frequently altered in human malignancies. Here, we define the function of the subfamily-specific extensions of the human DEAD-box protein DDX3. We describe the crystal structure of the subfamily-specific core of wild-type DDX3 at 2.2 Å resolution, alone and in the presence of AMP or nonhydrolyzable ATP. These structures illustrate a unique interdomain interaction between the two ATPase domains in which the C-terminal domain clashes with the RNA-binding surface. Destabilizing this interaction accelerates RNA duplex unwinding, suggesting that it is present in solution and inhibitory for catalysis. We use this core fragment of DDX3 to test the function of two recurrent medulloblastoma variants of DDX3 and find that both inactivate the protein in vitro and in vivo. Taken together, these results redefine the structural and functional core of the DDX3 subfamily of DEAD-box proteins. PMID:26598523

  13. The Arabidopsis A4 subfamily of lectin receptor kinases negatively regulates abscisic acid response in seed germination.

    PubMed

    Xin, Zeyu; Wang, Anyou; Yang, Guohua; Gao, Peng; Zheng, Zhi-Liang

    2009-01-01

    Abscisic acid (ABA) is an important plant hormone for a wide array of growth and developmental processes and stress responses, but the mechanism of ABA signal perception on the plasma membrane remains to be dissected. A previous GeneChip analysis revealed that a member of the A4 subfamily of lectin receptor kinases (LecRKs) of Arabidopsis (Arabidopsis thaliana), At5g01540 (designated LecRKA4.1), is up-regulated in response to a low dose of ABA in the rop10-1 background. Here, we present functional evidence to support its role in ABA response. LecRKA4.1 is expressed in seeds and leaves but not in roots, and the protein is localized to the plasma membrane. A T-DNA knockout mutant, lecrka4.1-1, slightly enhanced ABA inhibition of seed germination. Interestingly, LecRKA4.1 is adjacent to two other members of the A4 subfamily of LecRK genes, At5g01550 (LecRKA4.2) and At5g01560 (LecRKA4.3). We found that loss-of-function mutants of LecRKA4.2 and LecRKA4.3 exhibited similarly weak enhancement of ABA response in seed germination inhibition. Furthermore, LecRKA4.2 suppression by RNA interference in lecrka4.1-1 showed stronger ABA inhibition of seed germination than lecrka4.1-1, while the response to gibberellic acid was not affected in lecrka4.1-1 and lecrka4.1-1; LecRKA4.2 (RNAi) lines. Expression studies, together with network-based analysis, suggest that LecRKA4.1 and LecRKA4.2 regulate some of the ABA-responsive genes. Taken together, our results demonstrate that the A4 subfamily of LecRKs has a redundant function in the negative regulation of ABA response in seed germination.

  14. Preliminary study of the clonal characteristics of the TCR BV subfamilies in T cells in the peripheral blood from patients with uveitis.

    PubMed

    Zou, H-Y; Yu, W-Z; Zhang, Q; Yang, H-C; Huang, H-Y; Jiao, M

    2014-02-28

    The aim of this study was to investigate the characteristics and polymorphisms of the T-cell receptor BV complementarity-determining region 3 (TCR BV CDR3) gene in peripheral blood mononuclear cells (PBMCs) from patients with uveitis to provide an experimental basis for studying the pathogenesis of this disease. RT-PCR amplification of 26 subfamilies of the TCR BV CDR3 gene and immune spectratyping analysis were used to study the pedigree drift of TCR BV CDR3 in PBMCs from the uveitis patients. The following results were obtained: 1) the vast majority of the TCR BV CDR3 spectra in PBMCs in 5 healthy subjects fit the normal (or Gaussian) distribution. The distributions of the TCR BV CDR3 spectra in 4 patients with uveitis were non-normal and showed an abnormal peak including a widowed peak trend, a partial peak, and an irregular abnormal peak. 2) In the 26 TCR BV subfamilies, the abnormal peak frequency was different in the various subfamilies. The BV2 and BV17 (both 3/4) subfamilies had higher frequencies of the non-normally distributed abnormal peak. The BV5.2, BV6, BV15, and BV18 subfamilies showed no abnormal peaks. 3) TCR BV2 and BV17 yielded an abnormal peak in 3 HLA-B27-negative patients; however, no such abnormalities were detected in HLA-B27-positive patients. The abnormal expression of some TCR BV subfamilies in PBMCs from patients with uveitis may be associated with the immune pathogenesis of the disease. Our study provides the basis for further investigations into the pathogenesis of uveitis.

  15. Sarandibrinus, a new genus of Saprininae subfamily from Madagascar (Coleoptera, Histeridae) (Second contribution to the knowledge of the Histeridae of Madagascar).

    PubMed

    Lackner, Tomáš; Gomy, Yves

    2014-01-01

    Sarandibrinus araceliae, a new genus and species of the Saprininae subfamily is described from southern Madagascar. The new taxon exhibits autapomorphic characters for the Saprininae subfamily and is unusual especially for its large and deep prosternal foveae and the shape of spiculum gastrale. The description is accompanied by color habitus images, SEM micrographs, mouthparts and antenna line drawings and drawings of the male genitalia. Key to the genera of the Saprininae of Madagascar and the adjacent archipelagos is given. Hypocaccus (Baeckmanniolus) rubiciliae (Lewis, 1899) is newly reported from Madagascar and Hypocaccus (Nessus) perparvulus (Desbordes, 1916) is new to Mauritius.

  16. New species of insect trypanosomatids from Costa Rica and the proposal for a new subfamily within the Trypanosomatidae.

    PubMed

    Jirků, Milan; Yurchenko, Vyacheslav Y; Lukeš, Julius; Maslov, Dmitri A

    2012-01-01

    Several new species of trypanosomatids (Euglenozoa, Kinetoplastea, Trypanosomatidae), isolated from the intestines of Neotropical insects (Heteroptera), were genotyped on the basis of spliced leader RNA, and also defined phylogenetically using gene sequences of small subunit ribosomal RNA and glycosomal glyceraldehyde phosphate dehydrogenase. The taxonomic descriptions also included characterization using morphometry and electron microscopy. Our phylogenetic analyses placed the new species within the clade, previously designated "SE" for "Slowly Evolving" sequences of ribosomal RNA genes, a clade that also includes numerous monoxenous parasites of insects from the genera Crithidia, Leptomonas, and Wallaceina, as well as the dixenous genus Leishmania. Based on the high phylogenetic support for this clade, which is consistently recovered in all recent phylogenetic reconstructions, a proposal is put forward to recognize this natural taxon as a new subfamily, Leishmaniinae, within the family Trypanosomatidae.

  17. Roundabout controls axon crossing of the CNS midline and defines a novel subfamily of evolutionarily conserved guidance receptors.

    PubMed

    Kidd, T; Brose, K; Mitchell, K J; Fetter, R D; Tessier-Lavigne, M; Goodman, C S; Tear, G

    1998-01-23

    The robo gene in Drosophila was identified in a large-scale mutant screen for genes that control the decision by axons to cross the CNS midline. In robo mutants, too many axons cross and recross the midline. Here we show that robo encodes an axon guidance receptor that defines a novel subfamily of immunoglobulin superfamily proteins that is highly conserved from fruit flies to mammals. For those axons that never cross the midline, Robo is expressed on their growth cones from the outset; for the majority of axons that do cross the midline, Robo is expressed at high levels on their growth cones only after they cross the midline. Transgenic rescue experiments reveal that Robo can function in a cell-autonomous fashion. Robo appears to function as the gatekeeper controlling midline crossing.

  18. Analysis of the murine Dtk gene identifies conservation of genomic structure within a new receptor tyrosine kinase subfamily

    SciTech Connect

    Lewis, P.M.; Crosier, K.E.; Crosier, P.S.

    1996-01-01

    The receptor tyrosine kinase Dtk/Tyro 3/Sky/rse/brt/tif is a member of a new subfamily of receptors that also includes Axl/Ufo/Ark and Eyk/Mer. These receptors are characterized by the presence of two immunoglobulin-like loops and two fibronectin type III repeats in their extracellular domains. The structure of the murine Dtk gene has been determined. The gene consists of 21 exons that are distributed over 21 kb of genomic DNA. An isoform of Dtk is generated by differential splicing of exons from the 5{prime} region of the gene. The overall genomic structure of Dtk is virtually identical to that determined for the human UFO gene. This particular genomic organization is likely to have been duplicated and closely maintained throughout evolution. 38 refs., 3 figs., 1 tab.

  19. The structure of SAV1646 from Staphylococcus aureus belonging to a new `ribosome-associated' subfamily of bacterial proteins.

    PubMed

    Chirgadze, Yuri N; Clarke, Teresa E; Romanov, Vladimir; Kisselman, Gera; Wu-Brown, Jean; Soloveychik, Maria; Chan, Tiffany S Y; Gordon, Roni D; Battaile, Kevin P; Pai, Emil F; Chirgadze, Nickolay Y

    2015-02-01

    The crystal structure of the SAV1646 protein from the pathogenic microorganism Staphylococcus aureus has been determined at 1.7 Å resolution. The 106-amino-acid protein forms a two-layer sandwich with α/β topology. The protein molecules associate as dimers in the crystal and in solution, with the monomers related by a pseudo-twofold rotation axis. A sequence-homology search identified the protein as a member of a new subfamily of yet uncharacterized bacterial `ribosome-associated' proteins with at least 13 members to date. A detailed analysis of the crystal protein structure along with the genomic structure of the operon containing the sav1646 gene allowed a tentative functional model of this protein to be proposed. The SAV1646 dimer is assumed to form a complex with ribosomal proteins L21 and L27 which could help to complete the assembly of the large subunit of the ribosome.

  20. Citrus (Rutaceae) SNP markers based on Competitive Allele-Specific PCR; transferability across the Aurantioideae subfamily1

    PubMed Central

    Garcia-Lor, Andres; Ancillo, Gema; Navarro, Luis; Ollitrault, Patrick

    2013-01-01

    • Premise of the study: Single nucleotide polymorphism (SNP) markers based on Competitive Allele-Specific PCR (KASPar) were developed from sequences of three Citrus species. Their transferability was tested in 63 Citrus genotypes and 19 relative genera of the subfamily Aurantioideae to estimate the potential of SNP markers, selected from a limited intrageneric discovery panel, for ongoing broader diversity analysis at the intra- and intergeneric levels and systematic germplasm bank characterization. • Methods and Results: Forty-two SNP markers were developed using KASPar technology. Forty-one were successfully genotyped in all of the Citrus germplasm, where intra- and interspecific polymorphisms were observed. The transferability and diversity decreased with increasing taxonomic distance. • Conclusions: SNP markers based on the KASPar method developed from sequence data of a limited intrageneric discovery panel provide a valuable molecular resource for genetic diversity analysis of germplasm within a genus and should be useful for germplasm fingerprinting at a much broader diversity level. PMID:25202535

  1. Cloning and Expression of a Subfamily 1.4 Lipase from Bacillus licheniformis IBRL-CHS2.

    PubMed

    Reddy, Nidyaletchmy Subba; Rahim, Rashidah Abdul; Ibrahim, Darah; Kumar, K Sudesh

    2016-11-01

    We report on the cloning of the lipase gene from Bacillus licheniformis IBRL-CHS2 and the expression of the recombinant lipase. DNA sequencing analysis of the cloned lipase gene showed that it shares 99% identity with the lipase gene from B. licheniformis ATCC 14580 and belongs to subfamily 1.4 of true lipases based on amino acid sequence alignment of various Bacillus lipases. The 612 bp lipase gene was then cloned into the pET-15b(+) expression vector and the construct was transformed into E. coli BL21 (DE3) for bulk expression of the lipase. Expression was analysed by SDS-PAGE where the lipase was found to have a molecular weight of about 23 kDa.

  2. Cloning and Expression of a Subfamily 1.4 Lipase from Bacillus licheniformis IBRL-CHS2

    PubMed Central

    Reddy, Nidyaletchmy Subba; Rahim, Rashidah Abdul; Ibrahim, Darah; Kumar, K. Sudesh

    2016-01-01

    We report on the cloning of the lipase gene from Bacillus licheniformis IBRL-CHS2 and the expression of the recombinant lipase. DNA sequencing analysis of the cloned lipase gene showed that it shares 99% identity with the lipase gene from B. licheniformis ATCC 14580 and belongs to subfamily 1.4 of true lipases based on amino acid sequence alignment of various Bacillus lipases. The 612 bp lipase gene was then cloned into the pET-15b(+) expression vector and the construct was transformed into E. coli BL21 (DE3) for bulk expression of the lipase. Expression was analysed by SDS-PAGE where the lipase was found to have a molecular weight of about 23 kDa. PMID:27965753

  3. Distinct annexin subfamilies in plants and protists diverged prior to animal annexins and from a common ancestor.

    PubMed

    Morgan, R O; Pilar Fernandez, M

    1997-02-01

    Annexin homologues in the kingdoms of Planta and Protista were characterized by molecular sequence analysis to determine their phylogenetic and structural relationship with annexins of Animalia. Sequence fragments from 19 plant annexins were identified in sequence databases and composite sequences were also assembled from expressed sequence tags for Arabidopsis thaliana. Length differences in protein aminotermini and evidence for unique exon splice sites indicated that plant annexins were distinct from those of animals. A third annexin gene of Giardia lamblia (Anx21-Gla) was identified as a distant relative to other protist annexins and to those of higher eukaryotes, thus providing a suitable outgroup for evolutionary reconstruction of the family tree. Rooted evolutionary trees portrayed protist, plant, and Dictyostelium annexins as early, monophyletic ramifications prior to the appearance of closely related animal annexin XIII. Molecular phylogenetic analyses of DNA and protein sequence alignments revealed at least seven separate plant subfamilies, represented by Anx18 (alfalfa, previously classified), Anx22 (thale cress), Anx23 (thale cress, cotton, rape and cabbage), Anx24 (bell pepper and tomato p34), Anx25 (strawberry, horseradish, pea, soybean, and castor bean), Anx26-Zma, and Anx27-Zma (maize). Other unique subfamilies may exist for rice, tomato p35, apple, and celery annexins. Consensus sequences compiled for each eukaryotic kingdom showed some breakdown of the "annexin-fold" motif in repeats 2 and 3 of protist and plant annexins and a conserved codon deletion in repeat 3 of plants. The characterization of distinct annexin genes in plants and protists reflects their comparable diversity among animal species and offers alternative models for the comparative study of structure-function relationships within this important gene family.

  4. Two exo-β-D-glucosaminidases/exochitosanases from actinomycetes define a new subfamily within family 2 of glycoside hydrolases

    PubMed Central

    Côté, Nathalie; Fleury, Alain; Dumont-Blanchette, Émilie; Fukamizo, Tamo; Mitsutomi, Masaru; Brzezinski, Ryszard

    2005-01-01

    A GlcNase (exo-β-D-glucosaminidase) was purified from culture supernatant of Amycolatopsis orientalis subsp. orientalis grown in medium with chitosan. The enzyme hydrolysed the terminal GlcN (glucosamine) residues in oligomers of GlcN with transglycosylation observed at late reaction stages. 1H-NMR spectroscopy revealed that the enzyme is a retaining glycoside hydrolase. The GlcNase also behaved as an exochitosanase against high-molecular-mass chitosan with Km and kcat values of 0.16 mg/ml and 2832 min−1. On the basis of partial amino acid sequences, PCR primers were designed and used to amplify a DNA fragment which then allowed the cloning of the GlcNase gene (csxA) associated with an open reading frame of 1032 residues. The GlcNase has been classified as a member of glycoside hydrolase family 2 (GH2). Sequence alignments identified a group of CsxA-related protein sequences forming a distinct GH2 subfamily. Most of them have been annotated in databases as putative β-mannosidases. Among these, the SAV1223 protein from Streptomyces avermitilis has been purified following gene cloning and expression in a heterologous host and shown to be a GlcNase with no detectable β-mannosidase activity. In CsxA and all relatives, a serine-aspartate doublet replaces an asparagine residue and a glutamate residue, which were strictly conserved in previously studied GH2 members with β-galactosidase, β-glucuronidase or β-mannosidase activity and shown to be directly involved in various steps of the catalytic mechanism. Alignments of several other GH2 members allowed the identification of yet another putative subfamily, characterized by a novel, serine-glutamate doublet at these positions. PMID:16316314

  5. Structural and Functional Analysis of a New Subfamily of Glycosyltransferases Required for Glycosylation of Serine-rich Streptococcal Adhesins

    SciTech Connect

    Zhu, Fan; Erlandsen, Heidi; Ding, Lei; Li, Jingzhi; Huang, Ying; Zhou, Meixian; Liang, Xiaobo; Ma, Jinbiao; Wu, Hui

    2011-09-16

    Serine-rich repeat glycoproteins (SRRPs) are a growing family of bacterial adhesins found in many streptococci and staphylococci; they play important roles in bacterial biofilm formation and pathogenesis. Glycosylation of this family of adhesins is essential for their biogenesis. A glucosyltransferase (Gtf3) catalyzes the second step of glycosylation of a SRRP (Fap1) from an oral streptococcus, Streptococcus parasanguinis. Although Gtf3 homologs are highly conserved in SRRP-containing streptococci, they share minimal homology with functionally known glycosyltransferases. We report here the 2.3 {angstrom} crystal structure of Gtf3. The structural analysis indicates that Gtf3 forms a tetramer and shares significant structural homology with glycosyltransferases from GT4, GT5, and GT20 subfamilies. Combining crystal structural analysis with site-directed mutagenesis and in vitro glycosyltransferase assays, we identified residues that are required for UDP- or UDP-glucose binding and for oligomerization of Gtf3 and determined their contribution to the enzymatic activity of Gtf3. Further in vivo studies revealed that the critical amino acid residues identified by the structural analysis are crucial for Fap1 glycosylation in S. parasanguinis in vivo. Moreover, Gtf3 homologs from other streptococci were able to rescue the gtf3 knock-out mutant of S. parasanguinis in vivo and catalyze the sugar transfer to the modified SRRP substrate in vitro, demonstrating the importance and conservation of the Gtf3 homologs in glycosylation of SRRPs. As the Gtf3 homologs only exist in SRRP-containing streptococci, we conclude that the Gtf3 homologs represent a unique subfamily of glycosyltransferases.

  6. Phylogenetic analysis and expression patterns of Pax genes in the onychophoran Euperipatoides rowelli reveal a novel bilaterian Pax subfamily.

    PubMed

    Franke, Franziska Anni; Schumann, Isabell; Hering, Lars; Mayer, Georg

    2015-01-01

    Pax family genes encode a class of transcription factors that regulate various developmental processes. To shed light on the evolutionary history of these genes in Panarthropoda (Onychophora + Tardigrada + Arthropoda), we analyzed the Pax repertoire in the embryonic and adult transcriptomes of the onychophoran Euperipatoides rowelli. Our data revealed homologs of all five major bilaterian Pax subfamilies in this species, including Pax2/5/8, Pax4/6, Pox-neuro, Pax1/9/Pox-meso, and Pax3/7. In addition, we identified a new Pax member, pax-α, which does not fall into any other known Pax subfamily but instead clusters in the heterogenic Pax-α/β clade containing deuterostome, ecdysozoan, and lophotrochozoan gene sequences. These findings suggest that the last common bilaterian ancestor possessed six rather than five Pax genes, which have been retained in the panarthropod lineage. The expression data of Pax orthologs in the onychophoran embryo revealed distinctive patterns, some of which might be related to their ancestral roles in the last common panarthropod ancestor, whereas others might be specific to the onychophoran lineage. The derived roles include, for example, an involvement of pax2/5/8, pox-neuro, and pax3/7 in onychophoran nephridiogenesis, and an additional function of pax2/5/8 in the formation of the ventral and preventral organs. Furthermore, our transcriptomic analyses suggest that at least some Pax genes, including pax6 and pax-α, are expressed in the adult onychophoran head, although the corresponding functions remain to be clarified. The remarkable diversity of the Pax expression patterns highlights the functional and evolutionary plasticity of these genes in panarthropods.

  7. Sonorensin: an Antimicrobial Peptide, Belonging to the Heterocycloanthracin Subfamily of Bacteriocins, from a New Marine Isolate, Bacillus sonorensis MT93

    PubMed Central

    Chopra, Lipsy; Singh, Gurdeep; Choudhary, Vikas

    2014-01-01

    Marine environments are the greatest fronts of biodiversity, representing a resource of unexploited or unknown microorganisms and new substances having potential applications. Among microbial products, antimicrobial peptides (AMPs) have received great attention recently due to their applications as food preservatives and therapeutic agents. A new marine soil isolate producing an AMP was identified as Bacillus sonorensis based on 16S rRNA gene sequence analysis. It produced an AMP that showed a broad spectrum of activity against both Gram-positive and Gram-negative bacteria. The peptide, named sonorensin, was purified to homogeneity using a combination of chromatographic techniques. The intact molecular mass of the purified peptide, 6,274 Da, as revealed by matrix-assisted laser desorption ionization–time of flight (MALDI-TOF), was in agreement with Tricine-SDS-PAGE analysis. A PCR array of primers was used to identify AMP structural genes, which allowed the successful amplification of the related genes from strain MT93. The putative open reading frame of sonorensin was amplified, cloned into the pET-32a(+) vector, expressed as a thioredoxin (Trx) fusion protein in Escherichia coli, and then purified. Sequence alignment analysis revealed that the bacteriocin being reported could belong to new subfamily of bacteriocins, heterocycloanthracin. The peptide indicated its potential as a biocontrol agent or food antimicrobial agent, due to its antimicrobial activity against bacteria such as Listeria monocytogenes and Staphylococcus aureus. This is the first report of the production, purification, and characterization of wild-type and recombinant bacteriocin by B. sonorensis and the first bacteriocin of the heterocycloanthracin subfamily to be characterized. PMID:24610839

  8. Multilocus phylogenetic inference in subfamily Chlorogaloideae and related genera of Agavaceae - informing questions in taxonomy at multiple ranks.

    PubMed

    Archibald, Jenny K; Kephart, Susan R; Theiss, Kathryn E; Petrosky, Anna L; Culley, Theresa M

    2015-03-01

    A series of taxonomic questions at the subfamilial, generic, and intrageneric levels have remained within subfamily Chlorogaloideae s.s. (comprising Camassia, Chlorogalum, Hastingsia, and Schoenolirion) and relatives in Agavaceae. We present the first phylogenetic hypotheses focused on Chlorogaloideae that are based on multiple independent loci and include a wide sampling of outgroups across Agavaceae. In addition to chloroplast regions ndhF and trnL-trnF, we used nrDNA ITS for phylogenetic inference. Incomplete concerted evolution of the latter is indicated by intra-individual site polymorphisms for nearly half of the individuals. Comparisons of four coding and analysis methods for these characters indicate that the region remains phylogenetically informative. Our results confirm that Chlorogaloideae s.s. is not monophyletic, due to the close relationship of Schoenolirion with Hesperaloe and Hesperoyucca, as well as the likely sister relationship between Hesperocallis and core Chlorogaloideae (Camassia, Chlorogalum, and Hastingsia). Chlorogalum is also not monophyletic, being divided with strong support into vespertine and diurnal clades. This study produced the first phylogenetic hypotheses across Hesperaloe, allowing initial tests of several taxonomic disagreements within this genus. Our results reveal the lack of cohesion of H. funifera, indicating that H. funifera ssp. funifera may be more closely related to H. campanulata than to H. funifera ssp. chiangii (=H. chiangii). With potential gene flow between many members of Hesperaloe and a possible hybrid origin for H. campanulata, the genetic relationships within this genus appear complex. Further population-level investigation of many of the taxa in Chlorogaloideae s.l. would benefit our understanding of the evolution and taxonomy of these groups; Camassia and Hastingsia are the current focus of ongoing study.

  9. A Species-Level Phylogeny of Extant Snakes with Description of a New Colubrid Subfamily and Genus

    PubMed Central

    McKelvy, Alexander D.; Grismer, L. Lee; Bell, Charles D.; Lailvaux, Simon P.

    2016-01-01

    Background With over 3,500 species encompassing a diverse range of morphologies and ecologies, snakes make up 36% of squamate diversity. Despite several attempts at estimating higher-level snake relationships and numerous assessments of generic- or species-level phylogenies, a large-scale species-level phylogeny solely focusing on snakes has not been completed. Here, we provide the largest-yet estimate of the snake tree of life using maximum likelihood on a supermatrix of 1745 taxa (1652 snake species + 7 outgroup taxa) and 9,523 base pairs from 10 loci (5 nuclear, 5 mitochondrial), including previously unsequenced genera (2) and species (61). Results Increased taxon sampling resulted in a phylogeny with a new higher-level topology and corroborate many lower-level relationships, strengthened by high nodal support values (> 85%) down to the species level (73.69% of nodes). Although the majority of families and subfamilies were strongly supported as monophyletic with > 88% support values, some families and numerous genera were paraphyletic, primarily due to limited taxon and loci sampling leading to a sparse supermatrix and minimal sequence overlap between some closely-related taxa. With all rogue taxa and incertae sedis species eliminated, higher-level relationships and support values remained relatively unchanged, except in five problematic clades. Conclusion Our analyses resulted in new topologies at higher- and lower-levels; resolved several previous topological issues; established novel paraphyletic affiliations; designated a new subfamily, Ahaetuliinae, for the genera Ahaetulla, Chrysopelea, Dendrelaphis, and Dryophiops; and appointed Hemerophis (Coluber) zebrinus to a new genus, Mopanveldophis. Although we provide insight into some distinguished problematic nodes, at the deeper phylogenetic scale, resolution of these nodes may require sampling of more slowly-evolving nuclear genes. PMID:27603205

  10. In silico cloning and characterization of the TGA (TGACG MOTIF-BINDING FACTOR) transcription factors subfamily in Carica papaya.

    PubMed

    Idrovo Espín, Fabio Marcelo; Peraza-Echeverria, Santy; Fuentes, Gabriela; Santamaría, Jorge M

    2012-05-01

    The TGA transcription factors belong to the subfamily of bZIP group D that play a major role in disease resistance and development. Most of the TGA identified in Arabidopsis interact with the master regulator of SAR, NPR1 that controls the expression of PR genes. As a first approach to determine the possible involvement of these transcription factors in papaya defense, we characterized Arabidopsis TGA orthologs from the genome of Carica papaya cv. SunUp. Six orthologs CpTGA1 to CpTGA6, were identified. The predicted CpTGA proteins were highly similar to AtTGA sequences and probably share the same DNA binding properties and transcriptional regulation features. The protein sequences alignment evidenced the presence of conserved domains, characteristic of this group of transcription factors. The phylogeny showed that CpTGA evolved into three different subclades associated with defense and floral development. This is the first report of basal expression patterns assessed by RT-PCR, from the whole subfamily of CpTGA members in different tissues from papaya cv. Maradol mature plants. Overall, CpTGA1, CpTGA3 CpTGA6 and CpTGA4 showed a basal expression in all tissues tested; CpTGA2 expressed strongly in all tissues except in petioles while CpTGA5 expressed only in petals and to a lower extent in petioles. Although more detailed studies in anthers and other floral structures are required, we suggest that CpTGA5 might be tissue-specific, and it might be involved in papaya floral development. On the other hand, we report here for the first time, the expression of the whole family of CpTGA in response to salicylic acid (SA). The expression of CpTGA3, CpTGA4 and CpTGA6 increased in response to SA, what would suggest its involvement in the SAR response in papaya.

  11. Sonorensin: an antimicrobial peptide, belonging to the heterocycloanthracin subfamily of bacteriocins, from a new marine isolate, Bacillus sonorensis MT93.

    PubMed

    Chopra, Lipsy; Singh, Gurdeep; Choudhary, Vikas; Sahoo, Debendra K

    2014-05-01

    Marine environments are the greatest fronts of biodiversity, representing a resource of unexploited or unknown microorganisms and new substances having potential applications. Among microbial products, antimicrobial peptides (AMPs) have received great attention recently due to their applications as food preservatives and therapeutic agents. A new marine soil isolate producing an AMP was identified as Bacillus sonorensis based on 16S rRNA gene sequence analysis. It produced an AMP that showed a broad spectrum of activity against both Gram-positive and Gram-negative bacteria. The peptide, named sonorensin, was purified to homogeneity using a combination of chromatographic techniques. The intact molecular mass of the purified peptide, 6,274 Da, as revealed by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF), was in agreement with Tricine-SDS-PAGE analysis. A PCR array of primers was used to identify AMP structural genes, which allowed the successful amplification of the related genes from strain MT93. The putative open reading frame of sonorensin was amplified, cloned into the pET-32a(+) vector, expressed as a thioredoxin (Trx) fusion protein in Escherichia coli, and then purified. Sequence alignment analysis revealed that the bacteriocin being reported could belong to new subfamily of bacteriocins, heterocycloanthracin. The peptide indicated its potential as a biocontrol agent or food antimicrobial agent, due to its antimicrobial activity against bacteria such as Listeria monocytogenes and Staphylococcus aureus. This is the first report of the production, purification, and characterization of wild-type and recombinant bacteriocin by B. sonorensis and the first bacteriocin of the heterocycloanthracin subfamily to be characterized.

  12. Prevalent Exon-Intron Structural Changes in the APETALA1/FRUITFULL, SEPALLATA, AGAMOUS-LIKE6, and FLOWERING LOCUS C MADS-Box Gene Subfamilies Provide New Insights into Their Evolution

    PubMed Central

    Yu, Xianxian; Duan, Xiaoshan; Zhang, Rui; Fu, Xuehao; Ye, Lingling; Kong, Hongzhi; Xu, Guixia; Shan, Hongyan

    2016-01-01

    AP1/FUL, SEP, AGL6, and FLC subfamily genes play important roles in flower development. The phylogenetic relationships among them, however, have been controversial, which impedes our understanding of the origin and functional divergence of these genes. One possible reason for the controversy may be the problems caused by changes in the exon-intron structure of genes, which, according to recent studies, may generate non-homologous sites and hamper the homology-based sequence alignment. In this study, we first performed exon-by-exon alignments of these and three outgroup subfamilies (SOC1, AG, and STK). Phylogenetic trees reconstructed based on these matrices show improved resolution and better congruence with species phylogeny. In the context of these phylogenies, we traced evolutionary changes of exon-intron structures in each subfamily. We found that structural changes have occurred frequently following gene duplication and speciation events. Notably, exons 7 and 8 (if present) suffered more structural changes than others. With the knowledge of exon-intron structural changes, we generated more reasonable alignments containing all the focal subfamilies. The resulting trees showed that the SEP subfamily is sister to the monophyletic group formed by AP1/FUL and FLC subfamily genes and that the AGL6 subfamily forms a sister group to the three abovementioned subfamilies. Based on this topology, we inferred the evolutionary history of exon-intron structural changes among different subfamilies. Particularly, we found that the eighth exon originated before the divergence of AP1/FUL, FLC, SEP, and AGL6 subfamilies and degenerated in the ancestral FLC-like gene. These results provide new insights into the origin and evolution of the AP1/FUL, FLC, SEP, and AGL6 subfamilies. PMID:27200066

  13. Design Factors That Influence the Performance of Flight Intercept Traps for the Capture of Longhorned Beetles (Coleoptera: Cerambycidae) from the Subfamilies Lamiinae and Cerambycinae

    PubMed Central

    Allison, Jeremy D.; Bhandari, Basu D.; McKenney, Jessica L.; Millar, Jocelyn G.

    2014-01-01

    In North America, cerambycid beetles can have significant ecological and economic effects on forest ecosystems, and the rate of introduction and/or detection of exotic species is increasing. Detection and survey programs rely on semiochemical-baited intercept traps which are often ineffective for large woodborers like cerambycid beetles. This study examined the effects of flight intercept trap design on the capture of cerambycid beetles in the subfamilies Lamiinae and Cerambycinae. These subfamilies are the two largest in the Cerambycidae and they include many of the most damaging cerambycid pests and species on regulatory watch lists in North America. This study demonstrates that intercept trap design, treatment of trap surfaces with a lubricant, and the type of collection cup all influence the capture of beetles from the subfamilies Lamiinae and Cerambycinae. It also demonstrates that the addition of a large lubricant-treated collar to the bottom funnel of a multiple-funnel trap significantly increases the capture of some Lamiinae. The best trap design for both subfamilies was a lubricant treated multiple-funnel [MF] trap equipped with a wet cup and lubricant treated large collar on the bottom funnel. This design captured between 4 and 14 times more Lamiinae and Cerambycinae than commercially-available MF and panel traps. PMID:24671147

  14. Design factors that influence the performance of flight intercept traps for the capture of longhorned beetles (Coleoptera: Cerambycidae) from the subfamilies Lamiinae and Cerambycinae.

    PubMed

    Allison, Jeremy D; Bhandari, Basu D; McKenney, Jessica L; Millar, Jocelyn G

    2014-01-01

    In North America, cerambycid beetles can have significant ecological and economic effects on forest ecosystems, and the rate of introduction and/or detection of exotic species is increasing. Detection and survey programs rely on semiochemical-baited intercept traps which are often ineffective for large woodborers like cerambycid beetles. This study examined the effects of flight intercept trap design on the capture of cerambycid beetles in the subfamilies Lamiinae and Cerambycinae. These subfamilies are the two largest in the Cerambycidae and they include many of the most damaging cerambycid pests and species on regulatory watch lists in North America. This study demonstrates that intercept trap design, treatment of trap surfaces with a lubricant, and the type of collection cup all influence the capture of beetles from the subfamilies Lamiinae and Cerambycinae. It also demonstrates that the addition of a large lubricant-treated collar to the bottom funnel of a multiple-funnel trap significantly increases the capture of some Lamiinae. The best trap design for both subfamilies was a lubricant treated multiple-funnel [MF] trap equipped with a wet cup and lubricant treated large collar on the bottom funnel. This design captured between 4 and 14 times more Lamiinae and Cerambycinae than commercially-available MF and panel traps.

  15. New case of lateral asymmetry in fishes: A new subfamily, genus and species of deep water clingfishes from Papua New Guinea, western Pacific Ocean.

    PubMed

    Fricke, Ronald; Chen, Jhen-Nien; Chen, Wei-Jen

    2017-01-01

    The unusual clingfish Protogobiesox asymmetricus n. gen, n. sp. is described on the basis of four specimens collected in deep water off the north coast of Papua New Guinea in 2012. The species is characterized by its 9-10 dorsal rays, 8 anal rays, 17-24 pectoral-fin rays, 15 principal caudal-fin rays, 3 gills, third arch with 3 gill rakers, 34-35 total vertebrae, with asymmetrical lateral bending starting behind the skull, bent at an angle of 85°-92°; skull asymmetrical in frontal view; skin naked, surface of head and body without striae; disc without adhesive papillae. A new subfamily Protogobiesocinae is described for this species and Lepadicyathus mendeleevi Prokofiev, 2005, which is redescribed. The new subfamily is compared within the family; keys to the subfamilies of Gobiesocidae and the species within the new subfamily are presented; its phylogenetic relationship to other gobiesocids is inferred based on a multi-locus DNA dataset.

  16. Molecular determinants of substrate specificity revealed by the structure of Clostridium thermocellum arabinofuranosidase 43A from glycosyl hydrolase family 43 subfamily 16.

    PubMed

    Goyal, Arun; Ahmed, Shadab; Sharma, Kedar; Gupta, Vikas; Bule, Pedro; Alves, Victor D; Fontes, Carlos M G A; Najmudin, Shabir

    2016-12-01

    The recent division of the large glycoside hydrolase family 43 (GH43) into subfamilies offers a renewed opportunity to develop structure-function studies aimed at clarifying the molecular determinants of substrate specificity in carbohydrate-degrading enzymes. α-L-Arabinofuranosidases (EC 3.2.1.55) remove arabinose side chains from heteropolysaccharides such as xylan and arabinan. However, there is some evidence suggesting that arabinofuranosidases are substrate-specific, being unable to display a debranching activity on different polysaccharides. Here, the structure of Clostridium thermocellum arabinofuranosidase 43A (CtAbf43A), which has been shown to act in the removal of arabinose side chains from arabinoxylan but not from pectic arabinan, is reported. CtAbf43A belongs to GH43 subfamily 16, the members of which have a restricted capacity to attack xylans. The crystal structure of CtAbf43A comprises a five-bladed β-propeller fold typical of GH43 enzymes. CtAbf43A displays a highly compact architecture compatible with its high thermostability. Analysis of CtAbf43A along with the other member of GH43 subfamily 16 with known structure, the Bacillus subtilis arabinofuranosidase BsAXH-m2,3, suggests that the specificity of subfamily 16 for arabinoxylan is conferred by a long surface substrate-binding cleft that is complementary to the xylan backbone. The lack of a curved-shaped carbohydrate-interacting platform precludes GH43 subfamily 16 enzymes from interacting with the nonlinear arabinan scaffold and therefore from deconstructing this polysaccharide.

  17. Phylogeny of Bromelioideae (Bromeliaceae) inferred from nuclear and plastid DNA loci reveals the evolution of the tank habit within the subfamily.

    PubMed

    Schulte, Katharina; Barfuss, Michael H J; Zizka, Georg

    2009-05-01

    Phylogenetic relationships within subfamily Bromelioideae (Bromeliaceae, Poales) were inferred using DNA sequence data from the low-copy nuclear gene phosphoribulokinase (PRK) and five plastid loci (matK gene, 3'trnK intron, trnL intron, trnL-trnF spacer, atpB-rbcL spacer). The PRK dataset exhibited a considerably higher proportion of potentially informative characters than the plastid dataset (16.9% vs. 3.1%), leading to a higher resolution and improved nodal support of the resulting phylogenies. Bromelia is resolved as sister to the remainder of the subfamily, albeit this relationship receives only weak nodal support. The basal position of Bromelia, as well as Deinacanthon, Greigia, Ochagavia, Fascicularia and Fernseea within the subfamily is corroborated and the remainder of the subfamily forms a highly supported clade (the eu-bromelioids). By the inclusion of nuclear data the sister group position of Fernseea to the eu-bromelioids is now highly supported. Within the eu-bromelioids the resolution of the clade representing the more advanced core bromelioids has increased and further demonstrates the highly problematic generic concept of Aechmea as well as Quesnelia. Moreover, the data were used to examine the evolution of sepal symmetry and the tank habit. Tracing of character transitions onto the molecular phylogeny implies that both characters have undergone only few transitions within the subfamily and thus are not as homoplasious as previously assumed. The character state reconstruction reveals the great importance of the evolution of the tank habit for the diversification of the core bromelioids.

  18. The phylogeny of the family Lacertidae (Reptilia) based on nuclear DNA sequences: convergent adaptations to arid habitats within the subfamily Eremiainae.

    PubMed

    Mayer, Werner; Pavlicev, Mihaela

    2007-09-01

    The family Lacertidae encompasses more than 250 species distributed in the Palearctis, Ethiopis and Orientalis. Lacertids have been subjected in the past to several morphological and molecular studies to establish their phylogeny. However, the problems of convergent adaptation in morphology and of excessively variable molecular markers have hampered the establishment of well supported deeper phylogenetic relationships. Particularly the adaptations to xeric environments have often been used to establish a scenario for the origin and radiation of major lineages within lacertids. Here we present a molecular phylogenetic study based on two nuclear marker genes and representatives of 37 lacertid genera and distinct species groups (as in the case of the collective genus Lacerta). Roughly 1600 bp of the nuclear rag1 and c-mos genes were sequenced and analyzed. While the results provide good support to the hitherto suggested main subfamilies of Gallotiinae (Gallotia and Psammodromus), Eremiainae and Lacertinae [Harris, D.J., Arnold, E.N., Thomas, R.H., 1998. Relationships of lacertid lizards (Reptilia: Lacertidae) estimated from mitochondrial DNA sequences and morphology. Proc. R. Soc. Lond. B 265, 1939-1948], they also suggest unexpected relationships. In particular, the oriental genus Takydromus, previously considered the sister-group to the three subfamilies, is nested within Lacertinae. Moreover, the genera within the Eremiainae are further divided into two groups, roughly corresponding to their respective geographical distributions in the Ethiopian and the Saharo-Eurasian ranges. The results support an independent origin of adaptations to xeric conditions in different subfamilies. The relationships within the subfamily Lacertinae could not be resolved with the markers used. The species groups of the collective genus Lacerta show a bush-like topology in the inferred Bayesian tree, suggesting rapid radiation. The composition of the subfamilies Eremiainae and Lacertinae

  19. Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transporter Subfamily A Protein

    PubMed Central

    Tay, Wee Tek; Mahon, Rod J.; Heckel, David G.; Walsh, Thomas K.; Downes, Sharon; James, William J.; Lee, Sui-Fai; Reineke, Annette; Williams, Adam K.; Gordon, Karl H. J.

    2015-01-01

    The use of conventional chemical insecticides and bacterial toxins to control lepidopteran pests of global agriculture has imposed significant selection pressure leading to the rapid evolution of insecticide resistance. Transgenic crops (e.g., cotton) expressing the Bt Cry toxins are now used world wide to control these pests, including the highly polyphagous and invasive cotton bollworm Helicoverpa armigera. Since 2004, the Cry2Ab toxin has become widely used for controlling H. armigera, often used in combination with Cry1Ac to delay resistance evolution. Isolation of H. armigera and H. punctigera individuals heterozygous for Cry2Ab resistance in 2002 and 2004, respectively, allowed aspects of Cry2Ab resistance (level, fitness costs, genetic dominance, complementation tests) to be characterised in both species. However, the gene identity and genetic changes conferring this resistance were unknown, as was the detailed Cry2Ab mode of action. No cross-resistance to Cry1Ac was observed in mutant lines. Biphasic linkage analysis of a Cry2Ab-resistant H. armigera family followed by exon-primed intron-crossing (EPIC) marker mapping and candidate gene sequencing identified three independent resistance-associated INDEL mutations in an ATP-Binding Cassette (ABC) transporter gene we named HaABCA2. A deletion mutation was also identified in the H. punctigera homolog from the resistant line. All mutations truncate the ABCA2 protein. Isolation of further Cry2Ab resistance alleles in the same gene from field H. armigera populations indicates unequal resistance allele frequencies and the potential for Bt resistance evolution. Identification of the gene involved in resistance as an ABC transporter of the A subfamily adds to the body of evidence on the crucial role this gene family plays in the mode of action of the Bt Cry toxins. The structural differences between the ABCA2, and that of the C subfamily required for Cry1Ac toxicity, indicate differences in the detailed mode

  20. TP0262 is a modulator of promoter activity of tpr Subfamily II genes of Treponema pallidum subsp. pallidum

    PubMed Central

    Giacani, Lorenzo; Godornes, Charmie; Puray-Chavez, Maritza; Guerra-Giraldez, Cristina; Tompa, Martin; Lukehart, Sheila A.; Centurion-Lara, Arturo

    2009-01-01

    Transcriptional regulation in Treponema pallidum subsp. pallidum is poorly understood, primarily because this organism cannot be cultivated in vitro or genetically manipulated. We have recently shown a phase variation mechanism controlling transcription initiation of Subfamily II tpr (T. pallidum repeat) genes (tprE, tprG, and tprJ), a group of virulence factor candidates. Furthermore, the same study suggested that additional mechanisms might influence the level of transcription of these tprs. The T. pallidum genome sequence has revealed a few open reading frames (ORFs) with similarity to known bacterial transcription factors (TFs), including four catabolite activator protein (CAP) homologs. In this work, sequences matching the E. coli cAMP receptor protein (CRP) binding motif were identified in silico upstream of tprE, tprG, and tprJ. Using elecrophoretic mobility shift assay (EMSA) and DNaseI footprinting assay, recombinant TP0262, a T. pallidum CRP homolog, was shown to bind specifically to amplicons obtained from the tpr promoters containing putative CRP binding motifs. Using a heterologous reporter system, binding of TP0262 to these promoters was shown to either increase (tprE and tprJ) or decrease (tprG) tpr promoter activity. This is the first characterization of a T. pallidum transcriptional modulator which influences tpr promoter activity. PMID:19432808

  1. Modulating the function of ATP-binding cassette subfamily G member 2 (ABCG2) with inhibitor cabozantinib.

    PubMed

    Zhang, Guan-Nan; Zhang, Yun-Kai; Wang, Yi-Jun; Barbuti, Anna Maria; Zhu, Xi-Jun; Yu, Xin-Yue; Wen, Ai-Wen; Wurpel, John N D; Chen, Zhe-Sheng

    2017-01-25

    Cabozantinib (XL184) is a small molecule tyrosine kinase receptor inhibitor, which targets c-Met and VEGFR2. Cabozantinib has been approved by the Food and Drug Administration to treat advanced medullary thyroid cancer and renal cell carcinoma. In the present study, we evaluated the ability of cabozantinib to modulate the function of the ATP-binding cassette subfamily G member 2 (ABCG2) by sensitizing cells that are resistant to ABCG2 substrate antineoplastic drugs. We used a drug-selected resistant cell line H460/MX20 and three ABCG2 stable transfected cell lines ABCG2-482-R2, ABCG2-482-G2, and ABCG2-482-T7, which overexpress ABCG2. Cabozantinib, at non-toxic concentrations (3 or 5μM), sensitized the ABCG2-overexpressing cells to mitoxantrone, SN-38, and topotecan. Our results indicate that cabozantinib reverses ABCG2-mediated multidrug resistance by antagonizing the drug efflux function of the ABCG2 transporter instead of downregulating its expression. The molecular docking analysis indicates that cabozantinib binds to the drug-binding site of the ABCG2 transporter. Overall, our findings demonstrate that cabozantinib inhibits the ABCG2 transporter function and consequently enhances the effect of the antineoplastic agents that are substrates of ABCG2. Cabozantinib may be a useful agent in anticancer treatment regimens for patients who are resistant to ABCG2 substrate drugs.

  2. Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases

    PubMed Central

    Avila, César L; Rapisarda, Viviana A; Farías, Ricardo N; De Las Rivas, Javier; Chehín, Rosana

    2007-01-01

    Background The pyridine nucleotide disulfide reductase (PNDR) is a large and heterogeneous protein family divided into two classes (I and II), which reflect the divergent evolution of its characteristic disulfide redox active site. However, not all the PNDR members fit into these categories and this suggests the need of further studies to achieve a more comprehensive classification of this complex family. Results A workflow to improve the clusterization of protein families based on the array of linear conserved motifs is designed. The method is applied to the PNDR large family finding two main groups, which correspond to PNDR classes I and II. However, two other separate protein clusters, previously classified as class I in most databases, are outgrouped: the peroxide reductases (NAOX, NAPE) and the type II NADH dehydrogenases (NDH-2). In this way, two novel PNDR classes III and IV for NAOX/NAPE and NDH-2 respectively are proposed. By knowledge-driven biochemical and functional data analyses done on the new class IV, a linear array of motifs putatively related to Cu(II)-reductase activity is detected in a specific subset of NDH-2. Conclusion The results presented are a novel contribution to the classification of the complex and large PNDR protein family, supporting its reclusterization into four classes. The linear array of motifs detected within the class IV PNDR subfamily could be useful as a signature for a particular subgroup of NDH-2. PMID:17367536

  3. Molecular and enzymatic characterization of a subfamily I.4 lipase from an edible oil-degrader Bacillus sp. HH-01.

    PubMed

    Kamijo, Takashi; Saito, Akihiro; Ema, Sadaharu; Yoh, Inchi; Hayashi, Hiroko; Nagata, Ryo; Nagata, Yoshiho; Ando, Akikazu

    2011-02-01

    An edible-oil degrading bacterial strain HH-01 was isolated from oil plant gummy matter and was classified as a member of the genus Bacillus on the basis of the nucleotide sequence of the 16S rRNA gene. A putative lipase gene and its flanking regions were cloned from the strain based on its similarity to lipase genes from other Bacillus spp. The deduced product was composed of 214 amino acids and the putative mature protein, consisting of 182 amino acids, exhibited 82% amino acid sequence identity with the subfamily I.4 lipase LipA of Bacillus subtilis 168. The recombinant product was successfully overproduced as a soluble form in Escherichia coli and showed lipase activity. The gene was, therefore, designated as lipA of HH-01. HH-01 LipA was stable at pH 4-11 and up to 30°C, and its optimum pH and temperature were 8-9 and 30°C, respectively. The enzyme showed preferential hydrolysis of the 1(3)-position ester bond in trilinolein. The activity was, interestingly, enhanced by supplementing with 1 mM CoCl(2), in contrast to other Bacillus lipases. The lipA gene seemed to be constitutively transcribed during the exponential growth phase, regardless of the presence of edible oil.

  4. Characterization and genomic analyses of two newly isolated Morganella phages define distant members among Tevenvirinae and Autographivirinae subfamilies

    PubMed Central

    Oliveira, Hugo; Pinto, Graça; Oliveira, Ana; Noben, Jean-Paul; Hendrix, Hanne; Lavigne, Rob; Łobocka, Małgorzata; Kropinski, Andrew M.; Azeredo, Joana

    2017-01-01

    Morganella morganii is a common but frequent neglected environmental opportunistic pathogen which can cause deadly nosocomial infections. The increased number of multidrug-resistant M. morganii isolates motivates the search for alternative and effective antibacterials. We have isolated two novel obligatorily lytic M. morganii bacteriophages (vB_MmoM_MP1, vB_MmoP_MP2) and characterized them with respect to specificity, morphology, genome organization and phylogenetic relationships. MP1’s dsDNA genome consists of 163,095 bp and encodes 271 proteins, exhibiting low DNA (<40%) and protein (<70%) homology to other members of the Tevenvirinae. Its unique property is a >10 kb chromosomal inversion that encompass the baseplate assembly and head outer capsid synthesis genes when compared to other T-even bacteriophages. MP2 has a dsDNA molecule with 39,394 bp and encodes 55 proteins, presenting significant genomic (70%) and proteomic identity (86%) but only to Morganella bacteriophage MmP1. MP1 and MP2 are then novel members of Tevenvirinae and Autographivirinae, respectively, but differ significantly from other tailed bacteriophages of these subfamilies to warrant proposing new genera. Both bacteriophages together could propagate in 23 of 27 M. morganii clinical isolates of different origin and antibiotic resistance profiles, making them suitable for further studies on a development of bacteriophage cocktail for potential therapeutic applications. PMID:28387353

  5. Hepatic cytochrome P450 enzymes belonging to the CYP2C subfamily from an Australian marsupial, the koala (Phascolarctos cinereus).

    PubMed

    Jones, Brett R; El-Merhibi, Adaweyah; Ngo, Suong N T; Stupans, Ieva; McKinnon, Ross A

    2008-09-01

    Cytochromes P450 (CYPs) are critically important in the oxidative metabolism of a diverse array of xenobiotics and endogenous substrates. We have previously reported that the obligate Eucalyptus feeder koala (Phascolarctos cinereus) exhibits a higher hepatic CYP2C activity as compared to non-Eucalyptus feeders human or rat, with stimulation of CYP2C activity by cineole. In the present study, we examine CYP2C expression by immunohistochemistry and describe the identification and cloning of koala CYP2Cs. Utilising anti-rat CYP2C6 antibody, the expression of CYP2C was found to be uniform across the hepatic sections, being consistent with that observed in human and rat. Two 1647 and 1638 bp koala liver CYP2C complete cDNAs, designated CYP2C47 and CYP2C48 respectively, were cloned by cDNA library screening. The koala CYP2C cDNAs encode a protein of 495 amino acids. Three additional partial CYP2C sequences were also identified from the koala, indicating the multiplicity of the CYP2C subfamily in this unique marsupial species. The results of this study demonstrate the presence of koala hepatic CYP2Cs that share several common features with other published CYP2Cs; however CYP2C47 and CYP2C48 contain four extra amino acid residues at the NH2-terminal, a transmembrane anchor which was reported being a fundamentally conserved structure core of all eukaryote CYP enzymes.

  6. Testosterone metabolism of equine single CYPs of the 3A subfamily compared to the human CYP3A4.

    PubMed

    Vimercati, S; Büchi, M; Zielinski, J; Peduto, N; Mevissen, M

    2017-02-24

    Cytochrome P450 enzymes (CYPs) are responsible for the phase I metabolism of drugs, xenobiotics and endogenous substances. Knowledge of single CYPs and their substrates is important for drug metabolism, helps to predict adverse effects and may prevent reduced drug efficacy in polypharmacy. In this study, three equine isoenzymes of the 3A subfamily, the equine flavoprotein NADPH-P450 oxidoreductase (POR), and the cytochrome b5 (CYB5) were cloned, sequenced and heterologously expressed in a baculovirus expression system. Testosterone, the standard compound for characterization of the human CYP3A4, was used to characterize the newly expressed equine CYPs. The metabolite pattern was similar in equine and the human CYPs, but the amounts of metabolites were isoform-dependent. All equine CYPs produced 2-hydroxytestosterone (2-OH-TES), a metabolite never described in equines. The main metabolite of CYP3A4 6β-hydroxytestosterone (6β-OH-TES) was measured in CYPs 3A95 and 3A97 with levels close to the detection limit. Ketoconazole inhibited 2-OH-TES in the human CYP3A4 and the equine CYP3A94 and CYP3A97 completely, whereas a 70% inhibition was found in CYP3A95. Testosterone 6β- and 2-hydroxylation was significantly different in the equine CYPs compared to CYP3A4. The expression of single equine CYPs allows characterizing drug metabolism and may allow prevention of drug-drug interactions.

  7. Hydrophobic Residues near the Bilin Chromophore-Binding Pocket Modulate Spectral Tuning of Insert-Cys Subfamily Cyanobacteriochromes

    PubMed Central

    Cho, Sung Mi; Jeoung, Sae Chae; Song, Ji-Young; Song, Ji-Joon; Park, Youn-Il

    2017-01-01

    Cyanobacteriochromes (CBCRs) are a subfamily of phytochrome photoreceptors found exclusively in photosynthetic cyanobacteria. Four CBCRs containing a second Cys in the insert region (insert-Cys) have been identified from the nonheterocystous cyanobacterium Microcoleus B353 (Mbr3854g4 and Mbl3738g2) and the nitrogen fixing, heterocystous cyanobacterium Nostoc punctiforme (NpF2164g3 and NpR1597g2). These insert-Cys CBCRs can sense light in the near-UV to orange range, but key residues responsible for tuning their colour sensitivity have not been reported. In the present study, near-UV/Green (UG) photosensors Mbr3854g4 (UG1) and Mbl3738g2 (UG2) were chosen for further spectroscopic analysis of their spectral sensitivity and tuning. Consistent with most dual-Cys CBCRs, both UGs formed a second thioether linkage to the phycocyanobilin (PCB) chromophore via the insert-Cys. This bond is subject to breakage and relinkage during forward and reverse photoconversions. Variations in residues equivalent to Phe that are in close contact with the PCB chromophore D-ring in canonical red/green CBCRs are responsible for tuning the light absorption peaks of both dark and photoproducts. This is the first time these key residues that govern light absorption in insert-Cys family CBCRs have been identified and characterised. PMID:28094296

  8. hrpL activates Erwinia amylovora hrp gene transcription and is a member of the ECF subfamily of sigma factors.

    PubMed Central

    Wei, Z M; Beer, S V

    1995-01-01

    hrpL of Erwinia amylovora Ea321 encodes a 21.7-kDa regulatory protein, similar to members of the ECF (extra cytoplasmic functions) subfamily of eubacterial RNA polymerase sigma factors. hrpL is a single-gene operon in complementation group VI of the E. amylovora hrp gene cluster. Its product is required by Ea321 to elicit the hypersensitive response (HR) and to cause disease. HrpL controls the expression of five independent hrp loci, including hrpN, which encodes harpin, a proteinaceous elicitor of the HR. hrpL is environmentally regulated, and its expression is affected by hrpS, another regulatory gene of the hrp gene cluster of E. amylovora. pCPP1078, a multicopy plasmid carrying hrpL, is able to restore HR-eliciting ability to hrpS mutants. A conserved motif was identified upstream of the hrpI and hrpN operons, which are transcriptionally regulated by hrpL. This conserved motif shares a high degree of similarity with other biochemically defined or putative ECF-dependent promoter sequences, including sequences upstream of Streptomyces coelicolor dagA P2, Pseudomonas aeruginosa algD, Pseudomonas syringae pv. syringae 61 hrpZ, and P. syringae pv. tomato avrD. In spite of the similarity between the hrpL genes of E. amylovora and P. syringae 61, no functional cross-complementation was observed. PMID:7592386

  9. The phylogeny of the social wasp subfamily Polistinae: evidence from microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters

    PubMed Central

    Arévalo, Elisabeth; Zhu, Yong; Carpenter, James M; Strassmann, Joan E

    2004-01-01

    Background Social wasps in the subfamily Polistinae (Hymenoptera: Vespidae) have been important in studies of the evolution of sociality, kin selection, and within colony conflicts of interest. These studies have generally been conducted within species, because a resolved phylogeny among species is lacking. We used nuclear DNA microsatellite flanking sequences, mitochondrial COI sequence, and morphological characters to generate a phylogeny for the Polistinae (Hymenoptera) using 69 species. Results Our phylogeny is largely concordant with previous phylogenies at higher levels, and is more resolved at the species level. Our results support the monophyly of the New World subgenera of Polistini, while the Old World subgenera are a paraphyletic group. All genera for which we had more than one exemplar were supported as monophyletic except Polybia which is not resolved, and may be paraphyletic. Conclusion The combination of DNA sequences from flanks of microsatellite repeats with mtCOI sequences and morphological characters proved to be useful characters establishing relationships among the different subgenera and species of the Polistini. This is the first detailed hypothesis for the species of this important group. PMID:15070433

  10. Genome-Wide Identification and Expression Analysis of Homeodomain Leucine Zipper Subfamily IV (HDZ IV) Gene Family from Musa accuminata

    PubMed Central

    Pandey, Ashutosh; Misra, Prashant; Alok, Anshu; Kaur, Navneet; Sharma, Shivani; Lakhwani, Deepika; Asif, Mehar H.; Tiwari, Siddharth; Trivedi, Prabodh K.

    2016-01-01

    The homeodomain zipper family (HD-ZIP) of transcription factors is present only in plants and plays important role in the regulation of plant-specific processes. The subfamily IV of HDZ transcription factors (HD-ZIP IV) has primarily been implicated in the regulation of epidermal structure development. Though this gene family is present in all lineages of land plants, members of this gene family have not been identified in banana, which is one of the major staple fruit crops. In the present work, we identified 21 HDZIV encoding genes in banana by the computational analysis of banana genome resource. Our analysis suggested that these genes putatively encode proteins having all the characteristic domains of HDZIV transcription factors. The phylogenetic analysis of the banana HDZIV family genes further confirmed that after separation from a common ancestor, the banana, and poales lineages might have followed distinct evolutionary paths. Further, we conclude that segmental duplication played a major role in the evolution of banana HDZIV encoding genes. All the identified banana HDZIV genes expresses in different banana tissue, however at varying levels. The transcript levels of some of the banana HDZIV genes were also detected in banana fruit pulp, suggesting their putative role in fruit attributes. A large number of genes of this family showed modulated expression under drought and salinity stress. Taken together, the present work lays a foundation for elucidation of functional aspects of the banana HDZIV encoding genes and for their possible use in the banana improvement programs. PMID:26870050

  11. Differential expression of cytochrome P450 enzymes from the CYP2C subfamily in the human brain.

    PubMed

    Booth Depaz, Iris M; Toselli, Francesca; Wilce, Peter A; Gillam, Elizabeth M J

    2015-03-01

    Cytochrome P450 enzymes from the CYP2C subfamily play a prominent role in the metabolic clearance of many drugs. CYP2C enzymes have also been implicated in the metabolism of arachidonic acid to vasoactive epoxyeicosatrienoic acids. CYP2C8, CYP2C9, and CYP2C19 are expressed in the adult liver at significant levels; however, the expression of CYP2C enzymes in extrahepatic tissues such as the brain is less well characterized. Form-specific antibodies to CYP2C9 and CYP2C19 were prepared by affinity purification of antibodies raised to unique peptides. CYP2C9 and CYP2C19 were located in microsomal fractions of all five human brain regions examined, namely the frontal cortex, hippocampus, basal ganglia, amygdala, and cerebellum. Both CYP2C9 and CYP2C19 were detected predominantly within the neuronal soma but with expression extending down axons and dendrites in certain regions. Finally, a comparison of cortex samples from alcoholics and age-matched controls suggested that CYP2C9 expression was increased in alcoholics.

  12. Blockade of transient receptor potential cation channel subfamily V member 1 promotes regeneration after sciatic nerve injury

    PubMed Central

    Ren, Fei; Zhang, Hong; Qi, Chao; Gao, Mei-ling; Wang, Hong; Li, Xia-qing

    2015-01-01

    The transient receptor potential cation channel subfamily V member 1 (TRPV1) provides the sensation of pain (nociception). However, it remains unknown whether TRPV1 is activated after peripheral nerve injury, or whether activation of TRPV1 affects neural regeneration. In the present study, we established rat models of unilateral sciatic nerve crush injury, with or without pretreatment with AMG517 (300 mg/kg), a TRPV1 antagonist, injected subcutaneously into the ipsilateral paw 60 minutes before injury. At 1 and 2 weeks after injury, we performed immunofluorescence staining of the sciatic nerve at the center of injury, at 0.3 cm proximal and distal to the injury site, and in the dorsal root ganglia. Our results showed that Wallerian degeneration occurred distal to the injury site, and neurite outgrowth and Schwann cell regeneration occurred proximal to the injury. The number of regenerating myelinated and unmyelinated nerve clusters was greater in the AMG517-pretreated rats than in the vehicle-treated group, most notably 2 weeks after injury. TRPV1 expression in the injured sciatic nerve and ipsilateral dorsal root ganglia was markedly greater than on the contralateral side. Pretreatment with AMG517 blocked this effect. These data indicate that TRPV1 is activated or overexpressed after sciatic nerve crush injury, and that blockade of TRPV1 may accelerate regeneration of the injured sciatic nerve. PMID:26487864

  13. The solution structure of BmTx3B, a member of the scorpion toxin subfamily alpha-KTx 16.

    PubMed

    Wang, Yuefeng; Chen, Xiang; Zhang, Naixia; Wu, Gong; Wu, Houming

    2005-02-01

    This article reports the solution structure of BmTx3B (alpha-KTx16.2), a potassium channel blocker belonging to the subfamily alpha-KTx16, purified from the venom of the Chinese scorpion Buthus martensi Karsch. In solution, BmTx3B assumes a typical CSalphabeta motif, with an alpha-helix connected to a triple-stranded beta-sheet by 3 disulfide bridges, which belongs to the first structural group of short-chain scorpion toxins. On the other hand, BmTx3B is quite different from other toxins (such as ChTx and AgTx2) of this group in terms of the electrostatic and hydrophobic surface distribution. The functional surface (beta-face) of the molecule is characterized by less basic residues (only 2: Lys28 and Arg35) and extra aromatic residues (Phe1, Phe9, Trp15, and Tyr37). The peptide shows a great preference for the Kca1.1 channel over the Kv channel (about a 10(3)-fold difference). The model of BmTx3B/Kca1.1 channel complex generated by docking and dynamic simulation reveals that the stable binding between the BmTx3B and Kca1.1 channel is favored by a number of aromatic pi-pi stacking interactions. The influences of these structural features on the kinetic behavior of the toxin binding to Kca1.1 channel are also discussed.

  14. Evaluation of TCR Vbeta subfamily T cell expansion in NOD/SCID mice transplanted with human cord blood hematopoietic stem cells.

    PubMed

    Lin, Chen; Chen, Shaohua; Yang, Lijian; Tan, Yubo; Bai, Xue; Li, Yangqiu

    2007-08-01

    Examination of the T cell receptor (TCR) gene repertoire is important in the analysis of the immune status of models, because clonal expansion of T cells permits the identification of specific antigen responses of T cells. Little is known about T-cell immunity in the humanized NOD/SCID mouse model. TCR Vbeta repertoire usage and clonality were analyzed to investigate the distribution and clonal expansion of TCR Vbeta subfamily T cells in NOD/SCID mice transplanted with human cord blood (CB) hematopoietic stem cells. The NOD/SCID mice were sublethally irradiated ((60)Co, 300cGy) to eliminate residual innate immunity in the host. The experimental mice were transplanted intravenously with CB CD34(+) cells sorted by MACS. After 6 weeks, RNA was obtained from peripheral blood, bone marrow and thymus of the study animals. The gene expression and clonality of the TCR Vbeta repertoire were determined by RT-PCR and GeneScan techniques. A restricted range of TCR Vbeta usage was exhibited in the bone marrow of mice, which included TCR Vbeta 1, 2, 9, 13 and 19. Further, oligoclonal expression of some TCR Vbeta subfamilies (Vbeta9, 13, 19) was identified by GeneScan technique. To investigate the reason for oligoclonal expansion of the TCR Vbeta subfamily T cells from CB in mouse models, the T-cell culture with tissue-antigen of NOD/SCID mouse was performed in vitro. The cells from peripheral blood mononuclear cells and bone marrow, spleen, thymus in NOD/SCID mice were frozen and thawed, and used as tissue-antigen. CB mononuclear cells were separately cultured with the component from those murine cells for 15-20 days. Oligoclonal expression or oligoclonal trend of some TCR Vbeta subfamilies (Vbeta10, 11 and Vbeta2, 15, 16, 19) was detected in T cells after stimulation with tissue-antigen of NOD/SCID mouse. Interestingly, a similar clonal expansion of the TCR Vbeta11 subfamily was found in T cells cultured with peripheral blood, bone marrow and spleen respectively. The TCR Vbeta

  15. Estrous Cycle and Gestational Age-Dependent Expression of Members of the Interleukin-36 Subfamily in a Semi-Allogeneic Model of Infected and Non-Infected Murine Pregnancy

    PubMed Central

    Murrieta-Coxca, José Martin; Gómez-Chávez, Fernando; Baeza-Martínez, Damariz Adriana; Cancino-Diaz, Mario Eugenio; Cancino-Diaz, Juan Carlos; Pérez-Tapia, Sonia Mayra; Reyes-Maldonado, Elba; Rodríguez-Martínez, Sandra

    2016-01-01

    The IL-36 subfamily is a recently described group of cytokines with pro-inflammatory behavior, comprising three agonists (α, β, and γ), its receptor (R), and one antagonist (Ra). The expression and function of IL-36 subfamily members in the estrous cycle in healthy and infected pregnancy has not been described. We evaluated mRNA and protein expression of IL-36 family members during the estrous cycle, implantation, fetal development, and post-labor periods in a model of allogenic pregnancy in mice. We also explored the ability of Listeria monocytogenes to modulate the expression of IL-36 subfamily members during pregnancy. Expression of IL-36 subfamily members showed different expression during the estrous cycle and pregnancy but was induced at estrous, 16.5 days post coitum (dpc), 18.5 dpc, and labor. IL-36 subfamily members showed a characteristic distribution in the glandular epithelium, perimetrium, myometrium, and stratum vasculare. Infection with L. monocytogenes during pregnancy induced strong production of IL-36 subfamily members, an observation that correlated with an increasing prevalence of fetal loss. In conclusion, IL-36 agonists showed specific patterns of mRNA and protein expression that might suggest functional specialization or specific target cells. Infection with L. monocytogenes during pregnancy induced strong production of IL-36 subfamily members. PMID:27713746

  16. Estrous Cycle and Gestational Age-Dependent Expression of Members of the Interleukin-36 Subfamily in a Semi-Allogeneic Model of Infected and Non-Infected Murine Pregnancy.

    PubMed

    Murrieta-Coxca, José Martin; Gómez-Chávez, Fernando; Baeza-Martínez, Damariz Adriana; Cancino-Diaz, Mario Eugenio; Cancino-Diaz, Juan Carlos; Pérez-Tapia, Sonia Mayra; Reyes-Maldonado, Elba; Rodríguez-Martínez, Sandra

    2016-01-01

    The IL-36 subfamily is a recently described group of cytokines with pro-inflammatory behavior, comprising three agonists (α, β, and γ), its receptor (R), and one antagonist (Ra). The expression and function of IL-36 subfamily members in the estrous cycle in healthy and infected pregnancy has not been described. We evaluated mRNA and protein expression of IL-36 family members during the estrous cycle, implantation, fetal development, and post-labor periods in a model of allogenic pregnancy in mice. We also explored the ability of Listeria monocytogenes to modulate the expression of IL-36 subfamily members during pregnancy. Expression of IL-36 subfamily members showed different expression during the estrous cycle and pregnancy but was induced at estrous, 16.5 days post coitum (dpc), 18.5 dpc, and labor. IL-36 subfamily members showed a characteristic distribution in the glandular epithelium, perimetrium, myometrium, and stratum vasculare. Infection with L. monocytogenes during pregnancy induced strong production of IL-36 subfamily members, an observation that correlated with an increasing prevalence of fetal loss. In conclusion, IL-36 agonists showed specific patterns of mRNA and protein expression that might suggest functional specialization or specific target cells. Infection with L. monocytogenes during pregnancy induced strong production of IL-36 subfamily members.

  17. Checklist of the subfamily Adoncholaiminae Gerlach and Riemann, 1974 (Nematoda: Oncholaimida: Oncholaimidae) of the world: genera, species, distribution, and reference list for taxonomists and ecologists

    PubMed Central

    2016-01-01

    Abstract Background Adoncholaiminae is one of the seven subfamilies in the free-living aquatic nematode family Oncholaimidae. Nematodes in Adoncholaiminae are found from various water environment of the world. However, a checklist of all Adoncholaiminae species including full literature, especially information of experimental (not taxonomic) works, has not been updated for more than 40 years. New information A revised checklist of the subfamily Adoncholaiminae of the world is provided. It contains 31 valid and 13 invalid species names in four genera with synonyms, collection records, and full literature from 1860's to 2015 for each species. A literature survey of total 477 previous papers was conducted in this work, and 362 of them are newly added to checklist. PMID:26929708

  18. The StarD4 subfamily of steroidogenic acute regulatory-related lipid transfer (START) domain proteins: new players in cholesterol metabolism.

    PubMed

    Calderon-Dominguez, Maria; Gil, Gregorio; Medina, Miguel Angel; Pandak, William M; Rodríguez-Agudo, Daniel

    2014-04-01

    Cholesterol levels in the body are maintained through the coordinated regulation of its uptake, synthesis, distribution, storage and efflux. However, the way cholesterol is sorted within cells remains poorly defined. The discovery of the newly described StarD4 subfamily, part of the steroidogenic acute regulatory lipid transfer (START) domain family of proteins, affords an opportunity for the study of intracellular cholesterol movement, metabolism and its disorders. The three members of this intracellular subfamily of proteins (StarD4, StarD5 and StarD6) have a similar lipid binding pocket specific for sterols (cholesterol in particular), but differing regulation and localization. The ability to bind and transport cholesterol through a non-vesicular mean suggests that they play a previously unappreciated role in cholesterol homeostasis.

  19. Mus spretus LINE-1s in the Mus musculus domesticus inbred strain C57BL/6J are from two different Mus spretus LINE-1 subfamilies

    SciTech Connect

    Zhao, Yingping; Daggett, L.P.; Hardies, S.C.

    1996-02-01

    A LINE-1 element, L1C105, was found in the Mus musculus domesticus inbred strain, C57BL/6J. Upon sequencing, this element was found to belong to a M. spretus LINE-1 subfamily originating within the last 0.2 million years. This is the second spretus-specific LINE-1 subfamily found to be represented in C57BL/6J. Although it is unclear how these M. spretus LINE-1s transferred from M. spretus to M. m. domesticus, it is now clear that at least two different spretus LINE-1 sequences have recently transferred. The limited divergence between the C57BL/6J spretus-like LINE-1s and their closest spretus ancestors suggests that the transfer did not involve an exceptionally long lineage of sequential transpositions. 54 refs., 6 figs.

  20. A review of Cunaxidae (Acariformes, Trombidiformes): Histories and diagnoses of subfamilies and genera, keys to world species, and some new locality records

    PubMed Central

    Skvarla, Michael J.; Fisher, J. Ray; Dowling, Ashley P. G.

    2014-01-01

    Abstract Cunaxidae are predaceous mites found in a variety of habitats. This work provides comprehensive keys to world subfamilies, genera, and species. Diagnoses and historical reviews are provided for subfamilies and genera. Cunaxa boneti, C. denmarki, C. exoterica, C. floridanus, C. lehmanae, C. lukoschusi, C. metzi, C. myabunderensis, C newyorkensis, C. rackae, C. reevesi, and C. reticulatus are moved to Rubroscirus and C. otiosus, C. valentis, and C. rasile are returned to Rubroscirus. Cunaxoides neopectinatus is moved to Pulaeus. Neocunaxoides pradhani and N. gilbertoi are transferred to Scutopalus. Pulaeus minutus and P. subterraneus are moved to Lupaeus. Pseudobonzia bakari, P. malookensis, and P. shamshadi are transferred to Neobonzia. Dactyloscirus bifidus is transferred to Armascirus. Scirula papillata is reported from the Western Hemisphere for the first time. Armascirus ozarkensis, A. primigenius, and Dactyloscirus dolichosetosus are reported from new localities. PMID:25061358

  1. The Discovery of phiAGATE, A Novel Phage Infecting Bacillus pumilus, Leads to New Insights into the Phylogeny of the Subfamily Spounavirinae

    PubMed Central

    Barylski, Jakub; Nowicki, Grzegorz; Goździcka-Józefiak, Anna

    2014-01-01

    The Bacillus phage phiAGATE is a novel myovirus isolated from the waters of Lake Góreckie (a eutrophic lake in western Poland). The bacteriophage infects Bacillus pumilus, a bacterium commonly observed in the mentioned reservoir. Analysis of the phiAGATE genome (149844 base pairs) resulted in 204 predicted protein-coding sequences (CDSs), of which 53 could be functionally annotated. Further investigation revealed that the bacteriophage is a member of a previously undescribed cluster of phages (for the purposes of this study we refer to it as “Bastille group”) within the Spounavirinae subfamily. Here we demonstrate that these viruses constitute a distinct branch of the Spounavirinae phylogenetic tree, with limited similarity to phages from the Twortlikevirus and Spounalikevirus genera. The classification of phages from the Bastille group into any currently accepted genus proved extremely difficult, prompting concerns about the validity of the present taxonomic arrangement of the subfamily. PMID:24466180

  2. The discovery of phiAGATE, a novel phage infecting Bacillus pumilus, leads to new insights into the phylogeny of the subfamily Spounavirinae.

    PubMed

    Barylski, Jakub; Nowicki, Grzegorz; Goździcka-Józefiak, Anna

    2014-01-01

    The Bacillus phage phiAGATE is a novel myovirus isolated from the waters of Lake Góreckie (a eutrophic lake in western Poland). The bacteriophage infects Bacillus pumilus, a bacterium commonly observed in the mentioned reservoir. Analysis of the phiAGATE genome (149844 base pairs) resulted in 204 predicted protein-coding sequences (CDSs), of which 53 could be functionally annotated. Further investigation revealed that the bacteriophage is a member of a previously undescribed cluster of phages (for the purposes of this study we refer to it as "Bastille group") within the Spounavirinae subfamily. Here we demonstrate that these viruses constitute a distinct branch of the Spounavirinae phylogenetic tree, with limited similarity to phages from the Twortlikevirus and Spounalikevirus genera. The classification of phages from the Bastille group into any currently accepted genus proved extremely difficult, prompting concerns about the validity of the present taxonomic arrangement of the subfamily.

  3. Two new mite species of the subfamily Harpirhynchinae Dubinin, 1957 (Acariformes: Harpirhynchidae), parasites of the passerine birds (Aves: Passeriformes) in Australia and South Asia.

    PubMed

    Bochkov, Andre V; Klompen, Hans

    2015-09-01

    Two new mite species of the subfamily Harpirhynchinae Dubinin, 1957 (Acariformes: Harpirhynchidae) are described from passerine birds (Aves: Passeriformes): Harpirhynchoides artamus n. sp. from Artamus fuscus Vieillot (Artamidae) from an unknown locality in South Asia and Neharpyrhynchus domrowi n. sp. from three host species of the family Meliphagidae, Acanthorhynchus tenuirostris (Latham) (type-host) from Australia (New South Walles), Ptiloprora perstriata (De Vis) and Myzomela rosenbergii Schlegel from Papua New Guinea.

  4. Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing

    PubMed Central

    Richardson, Dale N.; Rogers, Mark F.; Labadorf, Adam; Ben-Hur, Asa; Guo, Hui; Paterson, Andrew H.; Reddy, Anireddy S. N.

    2011-01-01

    Alternative splicing (AS) of pre-mRNA is a fundamental molecular process that generates diversity in the transcriptome and proteome of eukaryotic organisms. SR proteins, a family of splicing regulators with one or two RNA recognition motifs (RRMs) at the N-terminus and an arg/ser-rich domain at the C-terminus, function in both constitutive and alternative splicing. We identified SR proteins in 27 eukaryotic species, which include plants, animals, fungi and “basal” eukaryotes that lie outside of these lineages. Using RNA recognition motifs (RRMs) as a phylogenetic marker, we classified 272 SR genes into robust sub-families. The SR gene family can be split into five major groupings, which can be further separated into 11 distinct sub-families. Most flowering plants have double or nearly double the number of SR genes found in vertebrates. The majority of plant SR genes are under purifying selection. Moreover, in all paralogous SR genes in Arabidopsis, rice, soybean and maize, one of the two paralogs is preferentially expressed throughout plant development. We also assessed the extent of AS in SR genes based on a splice graph approach (http://combi.cs.colostate.edu/as/gmap_SRgenes). AS of SR genes is a widespread phenomenon throughout multiple lineages, with alternative 3′ or 5′ splicing events being the most prominent type of event. However, plant-enriched sub-families have 57%–88% of their SR genes experiencing some type of AS compared to the 40%–54% seen in other sub-families. The SR gene family is pervasive throughout multiple eukaryotic lineages, conserved in sequence and domain organization, but differs in gene number across lineages with an abundance of SR genes in flowering plants. The higher number of alternatively spliced SR genes in plants emphasizes the importance of AS in generating splice variants in these organisms. PMID:21935421

  5. The North African sawfly genus Prionomeion (Hymenoptera, Diprionidae), with a key to the Palaearctic genera of the subfamily Diprioninae.

    PubMed

    Hara, Hideho

    2016-06-24

    The diagnostic characters are discussed for the North African genus Prionomeion Benson, 1939 (Hymenoptera, Diprionidae, Diprioninae). The type species, Prionomeion gaullei (Konow, 1906), is redescribed based on the holotype (female) and one male, both from Algeria. The second species of the genus, P. maghrebense sp. nov. is described based on one female from Morocco and one male from Algeria. A key to the Palaearctic genera of the subfamily Diprioninae is given.

  6. Rapid Identification of OXA-48 and OXA-163 Subfamilies in Carbapenem-Resistant Gram-Negative Bacilli with a Novel Immunochromatographic Lateral Flow Assay.

    PubMed

    Pasteran, Fernando; Denorme, Laurence; Ote, Isabelle; Gomez, Sonia; De Belder, Denise; Glupczynski, Youri; Bogaerts, Pierre; Ghiglione, Barbara; Power, Pablo; Mertens, Pascal; Corso, Alejandra

    2016-11-01

    We assessed a novel immunochromatographic lateral flow assay for direct identification of OXA-48-like carbapenemases and accurate differentiation of allele variants with distinct substrate profiles (OXA-48 or OXA-163 subfamilies). The assay allowed rapid (less than 4 min) and reliable direct confirmation of OXA-163- and/or OXA-48-like enzymes (with 100% sensitivity and 100% specificity) from cultured colonies that were recovered from both solid medium and spiked blood culture bottles.

  7. The first southwest Asian record of the subfamily Microdontinae, and the description of a new species of Metadon Reemer from Iran (Diptera: Syrphidae).

    PubMed

    Gilasian, Ebrahim; Reemer, Menno; Parchami-Araghi, Mehrdad

    2015-12-15

    Metadon persicus Gilasian & Reemer sp. nov. is described, based on a single female specimen from the Zagros mountains in Iran. Morphological variation among the members of the genus Metadon Reemer and their distribution in the world are discussed. Photographs of the new species are provided. The subfamily Microdontinae represents a new taxon for southwestern Asia and the genus Metadon is reported from the western Palaearctic region for the first time.

  8. A review of the mite subfamily Harpirhynchinae (Acariformes: Harpirhynchidae)--parasites of New World birds (Aves: Neognathae).

    PubMed

    Bochkov, Andre V; OConnor, Barry M; Klompen, Hans

    2015-09-30

    Mites of the subfamily Harpirhynchinae (Acariformes: Cheyletoidea: Harpirhynchidae) associated with neognathous birds (Aves: Neognathae) in the New World are revised. In all, 68 species in 8 genera are recorded. Among them, 27 new species and 1 new genus are described as new for science: Harpyrhynchoides gallowayi Bochkov, OConnor and Klompen sp. nov. from Columba livia (Columbiformes: Columbidae) from Canada (Manitoba), H. zenaida Bochkov, OConnor and Klompen sp. nov. from Zenaida macroura (Columbiformes: Columbidae) from USA (Michigan), H. calidris Bochkov, OConnor and Klompen sp. nov. from Calidris minutilla (Charadriiformes: Scolopacidae) from USA (Kansas), H. actitis Bochkov, OConnor and Klompen sp. nov. from Actitis macularius (Charadriiformes: Scolopacidae) from Canada (British Columbia), H. charadrius Bochkov, OConnor and Klompen sp. nov. from Charadrius vociferus (Charadriiformes: Charadriidae) from USA (Texas), H. pluvialis Bochkov, OConnor and Klompen sp. nov. from Pluvialis dominica (Charadriiformes: Charadriidae) from USA (Ohio), H. bubulcus Bochkov, OConnor and Klompen sp. nov. from Bubulcus ibis (Pelecaniformes: Ardeidae) from USA (Florida), H. ixobrychus Bochkov, OConnor and Klompen sp. nov. from Ixobrychus exilis (Pelecaniformes: Ardeidae) from USA (Michigan), H. puffinus Mertins sp. nov. from Puffinus gravis (Procellariformes: Procellariidae) from USA (Florida), H. megascops Bochkov, OConnor and Klompen sp. nov. from Megascops asio (Strigiformes: Strigidae) from USA (Michigan), H. athene Bochkov, OConnor and Klompen sp. nov. from Athene canicularia (Strigiformes: Strigidae) from USA (Texas), H. coccyzus Bochkov, OConnor and Klompen sp. nov. from Coccyzus americanus (Cuculiformes: Cuculidae) from USA (Michigan), H. crotophaga Bochkov, OConnor and Klompen sp. nov. from Crotophaga ani (Cuculiformes: Cuculidae) from Suriname; Crassacarus Bochkov, OConnor and Klompen, gen. nov.: Crassacarus alexfaini Bochkov, OConnor and Klompen sp. nov. (type of genus

  9. Characterization of PREP2, a paralog of PREP1, which defines a novel sub-family of the MEINOX TALE homeodomain transcription factors.

    PubMed

    Fognani, C; Kilstrup-Nielsen, C; Berthelsen, J; Ferretti, E; Zappavigna, V; Blasi, F

    2002-05-01

    TALE (three amino acid loop extension) homeodomain proteins include the PBC and the MEINOX sub-families. MEINOX proteins form heterodimer complexes with PBC proteins. Heterodimerization is crucial to DNA binding and for nuclear localization. PBC-MEINOX heterodimers bind DNA also in combination with HOX proteins, thereby modulating their DNA-binding specificity. TALE proteins therefore play crucial roles in multiple developmental and differentiation pathways in vivo. We report the identification and characterization of a novel human gene homologous to PREP1, called PREP2. Sequence comparisons indicate that PREP1 and PREP2 define a novel sub-family of MEINOX proteins, distinct from the MEIS sub-family. PREP2 is expressed in a variety of human adult tissues and displays a more restricted expression pattern than PREP1. PREP2 is capable of heterodimerizing with PBC proteins. Heterodimerization with PBX1 appears to be essential for nuclear localization of both PREP2 and PBX1. A comparison between the functional properties of PREP1 and PREP2 reveals that PREP2-PBX display a faster DNA-dissociation rate than PREP1-PBX heterodimers, suggesting different roles in controlling gene expression. Like PREP1, PREP2-PBX heterodimers are capable of forming ternary complexes with HOXB1. The analysis of some PREP2 in vitro properties suggests a functional diversification among PREP and between PREP and MEIS MEINOX proteins.

  10. NRfamPred: A proteome-scale two level method for prediction of nuclear receptor proteins and their sub-families

    PubMed Central

    Kumar, Ravindra; Kumari, Bandana; Srivastava, Abhishikha; Kumar, Manish

    2014-01-01

    Nuclear receptor proteins (NRP) are transcription factor that regulate many vital cellular processes in animal cells. NRPs form a super-family of phylogenetically related proteins and divided into different sub-families on the basis of ligand characteristics and their functions. In the post-genomic era, when new proteins are being added to the database in a high-throughput mode, it becomes imperative to identify new NRPs using information from amino acid sequence alone. In this study we report a SVM based two level prediction systems, NRfamPred, using dipeptide composition of proteins as input. At the 1st level, NRfamPred screens whether the query protein is NRP or non-NRP; if the query protein belongs to NRP class, prediction moves to 2nd level and predicts the sub-family. Using leave-one-out cross-validation, we were able to achieve an overall accuracy of 97.88% at the 1st level and an overall accuracy of 98.11% at the 2nd level with dipeptide composition. Benchmarking on independent datasets showed that NRfamPred had comparable accuracy to other existing methods, developed on the same dataset. Our method predicted the existence of 76 NRPs in the human proteome, out of which 14 are novel NRPs. NRfamPred also predicted the sub-families of these 14 NRPs. PMID:25351274

  11. Crystal structure of a raw-starch-degrading bacterial α-amylase belonging to subfamily 37 of the glycoside hydrolase family GH13

    PubMed Central

    Liu, Yanhong; Yu, Jigang; Li, Fudong; Peng, Hui; Zhang, Xuecheng; Xiao, Yazhong; He, Chao

    2017-01-01

    Subfamily 37 of the glycoside hydrolase family GH13 was recently established on the basis of the discovery of a novel α-amylase, designated AmyP, from a marine metagenomic library. AmyP exhibits raw-starch-degrading activity and consists of an N-terminal catalytic domain and a C-terminal starch-binding domain. To understand this newest subfamily, we determined the crystal structure of the catalytic domain of AmyP, named AmyPΔSBD, complexed with maltose, and the crystal structure of the E221Q mutant AmyPΔSBD complexed with maltotriose. Glu221 is one of the three conserved catalytic residues, and AmyP is inactivated by the E221Q mutation. Domain B of AmyPΔSBD forms a loop that protrudes from domain A, stabilizes the conformation of the active site and increases the thermostability of the enzyme. A new calcium ion is situated adjacent to the -3 subsite binding loop and may be responsible for the increased thermostability of the enzyme after the addition of calcium. Moreover, Tyr36 participates in both stacking and hydrogen bonding interactions with the sugar motif at subsite -3. This work provides the first insights into the structure of α-amylases belonging to subfamily 37 of GH13 and may contribute to the rational design of α-amylase mutants with enhanced performance in biotechnological applications. PMID:28303907

  12. Crystal structure of a raw-starch-degrading bacterial α-amylase belonging to subfamily 37 of the glycoside hydrolase family GH13.

    PubMed

    Liu, Yanhong; Yu, Jigang; Li, Fudong; Peng, Hui; Zhang, Xuecheng; Xiao, Yazhong; He, Chao

    2017-03-17

    Subfamily 37 of the glycoside hydrolase family GH13 was recently established on the basis of the discovery of a novel α-amylase, designated AmyP, from a marine metagenomic library. AmyP exhibits raw-starch-degrading activity and consists of an N-terminal catalytic domain and a C-terminal starch-binding domain. To understand this newest subfamily, we determined the crystal structure of the catalytic domain of AmyP, named AmyPΔSBD, complexed with maltose, and the crystal structure of the E221Q mutant AmyPΔSBD complexed with maltotriose. Glu221 is one of the three conserved catalytic residues, and AmyP is inactivated by the E221Q mutation. Domain B of AmyPΔSBD forms a loop that protrudes from domain A, stabilizes the conformation of the active site and increases the thermostability of the enzyme. A new calcium ion is situated adjacent to the -3 subsite binding loop and may be responsible for the increased thermostability of the enzyme after the addition of calcium. Moreover, Tyr36 participates in both stacking and hydrogen bonding interactions with the sugar motif at subsite -3. This work provides the first insights into the structure of α-amylases belonging to subfamily 37 of GH13 and may contribute to the rational design of α-amylase mutants with enhanced performance in biotechnological applications.

  13. Morphological "primary homology" and expression of AG-subfamily MADS-box genes in pines, podocarps, and yews.

    PubMed

    Englund, Marie; Carlsbecker, Annelie; Engström, Peter; Vergara-Silva, Francisco

    2011-01-01

    The morphological variation among reproductive organs of extant gymnosperms is remarkable, especially among conifers. Several hypotheses concerning morphological homology between various conifer reproductive organs have been put forward, in particular in relation to the pine ovuliferous scale. Here, we use the expression patterns of orthologs of the ABC-model MADS-box gene AGAMOUS (AG) for testing morphological homology hypotheses related to organs of the conifer female cone. To this end, we first developed a tailored 3'RACE procedure that allows reliable amplification of partial sequences highly similar to gymnosperm-derived members of the AG-subfamily of MADS-box genes. Expression patterns of two novel conifer AG orthologs cloned with this procedure-namely PodAG and TgAG, obtained from the podocarp Podocarpus reichei and the yew Taxus globosa, respectively-are then further characterized in the morphologically divergent female cones of these species. The expression patterns of PodAG and TgAG are compared with those of DAL2, a previously discovered Picea abies (Pinaceae) AG ortholog. By treating the expression patterns of DAL2, PodAG, and TgAG as character states mapped onto currently accepted cladogram topologies, we suggest that the epimatium-that is, the podocarp female cone organ previously postulated as a "modified" ovuliferous scale-and the canonical Pinaceae ovuliferous scale can be legitimally conceptualized as "primary homologs." Character state mapping for TgAG suggests in turn that the aril of Taxaceae should be considered as a different type of organ. This work demonstrates how the interaction between developmental-genetic data and formal cladistic theory could fruitfully contribute to gymnosperm systematics.

  14. Association between genetic variations of NMDA receptor NR3 subfamily genes and heroin addiction in male Han Chinese.

    PubMed

    Xie, Xiaohu; Liu, Huifen; Zhang, Jianbing; Chen, Weisheng; Zhuang, Dingding; Duan, Shiwei; Zhou, Wenhua

    2016-09-19

    Growing amounts of evidence suggest that N-Methyl-d-aspartate (NMDA) receptor mediated glutamate neurotransmission may be involved in the pathophysiology of drug dependence. The NMDA receptor consists of three subfamilies (NR1, NR2, and NR3). The ability of subunit NR3 to negatively modulate the NMDA receptor function makes it an attractive candidate gene of heroin addiction. The purpose of this study is to explore the association between four single nucleotide polymorphisms (SNPs) of NR3 gene and heroin addiction. Genotyping of two SNPs (rs3739722 and rs17189632) in GRIN3A and two SNPs (rs4807399 and rs2240158) in GRIN3B was performed using TaqMan SNP genotyping method. The association between heroin addiction and these SNPs was assessed among 332 male heroin dependent patients and 400 male normal control subjects. The results showed the genotype and allele frequencies of rs17189632 and rs2240158 were significantly different between the cases and the controls (nominal P values were 0.0284, 0.0136 for rs17189632; 0.0048, 0.0013 for rs2240158, respectively). After Bonferroni correction, rs2240158 of GRIN3B was still found to be associated with heroin addiction. The frequencies of haplotype C-A at GRIN3A (rs3739722-rs17189632) and of C-C and C-T at GRIN3B (rs4807399-rs2240158) differed significantly between the cases and the controls. The genotype and allele distributions of rs3739722 and rs4807399 were not significantly different between in the cases and in the controls (P>0.05). These results suggest that GRIN3A rs17189632 and GRIN3B rs2240158 may contribute to the susceptibility of heroin addiction.

  15. Stereochemistry of Fuscumol and Fuscumol Acetate Influences Attraction of Longhorned Beetles (Coleoptera: Cerambycidae) of the Subfamily Lamiinae.

    PubMed

    Hughes, G P; Meier, L R; Zou, Y; Millar, J G; Hanks, L M; Ginzel, M D

    2016-10-01

    The chemical structures of aggregation-sex pheromones of longhorned beetles (Coleoptera: Cerambycidae) are often conserved among closely related taxa. In the subfamily Lamiinae, adult males and females of several species are attracted by racemic blends of (E)-6,10-dimethyl-5,9-undecadien-2-ol (termed fuscumol) and the structurally related (E)-6,10-dimethyl-5,9-undecadien-2-yl acetate (fuscumol acetate). Both compounds have a chiral center, so each can exist in two enantiomeric forms. Males of many species of longhorned beetles only produce one stereoisomer of each pheromone component, and attraction may be reduced by the presence of stereoisomers that are not produced by a particular species. In a previous publication, analysis of headspace volatiles of adult beetles of the lamiine species Astyleiopus variegatus (Haldeman) revealed that males sex-specifically produced (S)-fuscumol and (S)-fuscumol acetate. Here, we describe field trials which tested attraction of this species to single enantiomers of fuscumol and fuscumol acetate, or to blends of enantiomers. We confirmed attraction of A. variegatus to its species-specific blend, but during the course of the trials, found that several other species also were attracted. These included Aegomorphus modestus (Gyllenhall), attracted to (S)-fuscumol acetate; Astylidius parvus (LeConte), attracted to (R)-fuscumol; Astylopsis macula (Say), attracted to (S)-fuscumol; and Graphisurus fasciatus (DeGeer), attracted to a blend of (R)-fuscumol and (R)-fuscumol acetate. These results suggest that chirality may be important in the pheromone chemistry of lamiines, and that specific stereoisomers or mixtures of stereoisomers are likely produced by each species.

  16. Identification and characterization of RBEL1 subfamily of GTPases in the Ras superfamily involved in cell growth regulation.

    PubMed

    Montalbano, JoAnne; Lui, Ki; Sheikh, M Saeed; Huang, Ying

    2009-07-03

    Recently, we reported the identification of a novel gene named RBEL1 (Rab-like protein 1) and characterized its two encoded isoforms, RBEL1A and RBEL1B, that function as novel GTPases of Ras superfamily. Here we report the identification of two additional splice variants of RBEL1 that we have named RBEL1C and -D. All four RBEL1 isoforms (A, B, C, and D) have identical N termini harboring the Rab-like GTPase domains but contain variable C termini. Although all isoforms can be detected in both cytoplasm and nucleus, RBEL1A is predominantly cytoplasmic, whereas RBEL1B is mostly nuclear. RBEL1C and -D, by contrast, are evenly distributed between the cytoplasm and nucleus. Furthermore, all four RBEL1 proteins are also capable of associating with cellular membrane. The RBEL1 proteins also exhibit a unique nucleotide-binding potential and, whereas the larger A and B isoforms are mainly GTP-bound, the smaller C and D variants bind to both GTP and GDP. Furthermore, a regulatory region at amino acid position 236-302 immediately adjacent to the GTP-binding domain is important for GTP-binding potential of RBEL1A, because deletion of this region converts RBEL1A from predominantly GTP-bound to GDP-bound. RBEL1 knockdown via RNA interference results in marked cell growth suppression, which is associated with morphological and biochemical features of apoptosis as well as inhibition of extracellular signal-regulated kinase phosphorylation. Taken together, our results indicate that RBEL1 proteins are linked to cell growth and survival and possess unique biochemical, cellular, and functional characteristics and, therefore, appear to form a novel subfamily of GTPases within the Ras superfamily.

  17. Convergent, parallel and correlated evolution of trophic morphologies in the subfamily schizothoracinae from the Qinghai-Tibetan plateau.

    PubMed

    Qi, Delin; Chao, Yan; Guo, Songchang; Zhao, Lanying; Li, Taiping; Wei, Fulei; Zhao, Xinquan

    2012-01-01

    Schizothoracine fishes distributed in the water system of the Qinghai-Tibetan plateau (QTP) and adjacent areas are characterized by being highly adaptive to the cold and hypoxic environment of the plateau, as well as by a high degree of diversity in trophic morphology due to resource polymorphisms. Although convergent and parallel evolution are prevalent in the organisms of the QTP, it remains unknown whether similar evolutionary patterns have occurred in the schizothoracine fishes. Here, we constructed for the first time a tentative molecular phylogeny of the schizothoracine fishes based on the complete sequences of the cytochrome b gene. We employed this molecular phylogenetic framework to examine the evolution of trophic morphologies. We used Pagel's maximum likelihood method to estimate the evolutionary associations of trophic morphologies and food resource use. Our results showed that the molecular and published morphological phylogenies of Schizothoracinae are partially incongruent with respect to some intergeneric relationships. The phylogenetic results revealed that four character states of five trophic morphologies and of food resource use evolved at least twice during the diversification of the subfamily. State transitions are the result of evolutionary patterns including either convergence or parallelism or both. Furthermore, our analyses indicate that some characters of trophic morphologies in the Schizothoracinae have undergone correlated evolution, which are somewhat correlated with different food resource uses. Collectively, our results reveal new examples of convergent and parallel evolution in the organisms of the QTP. The adaptation to different trophic niches through the modification of trophic morphologies and feeding behaviour as found in the schizothoracine fishes may account for the formation and maintenance of the high degree of diversity and radiations in fish communities endemic to QTP.

  18. The Hevea brasiliensis XIP aquaporin subfamily: genomic, structural and functional characterizations with relevance to intensive latex harvesting.

    PubMed

    Lopez, David; Amira, Maroua Ben; Brown, Daniel; Muries, Beatriz; Brunel-Michac, Nicole; Bourgerie, Sylvain; Porcheron, Benoit; Lemoine, Remi; Chrestin, Hervé; Mollison, Ewan; Di Cola, Alessandra; Frigerio, Lorenzo; Julien, Jean-Louis; Gousset-Dupont, Aurélie; Fumanal, Boris; Label, Philippe; Pujade-Renaud, Valérie; Auguin, Daniel; Venisse, Jean-Stéphane

    2016-07-01

    X-Intrinsic Proteins (XIP) were recently identified in a narrow range of plants as a full clade within the aquaporins. These channels reportedly facilitate the transport of a wide range of hydrophobic solutes. The functional roles of XIP in planta remain poorly identified. In this study, we found three XIP genes (HbXIP1;1, HbXIP2;1 and HbXIP3;1) in the Hevea brasiliensis genome. Comprehensive bioinformatics, biochemical and structural analyses were used to acquire a better understanding of this AQP subfamily. Phylogenetic analysis revealed that HbXIPs clustered into two major groups, each distributed in a specific lineage of the order Malpighiales. Tissue-specific expression profiles showed that only HbXIP2;1 was expressed in all the vegetative tissues tested (leaves, stem, bark, xylem and latex), suggesting that HbXIP2;1 could take part in a wide range of cellular processes. This is particularly relevant to the rubber-producing laticiferous system, where this isoform was found to be up-regulated during tapping and ethylene treatments. Furthermore, the XIP transcriptional pattern is significantly correlated to latex production level. Structural comparison with SoPIP2;1 from Spinacia oleracea species provides new insights into the possible role of structural checkpoints by which HbXIP2;1 ensures glycerol transfer across the membrane. From these results, we discuss the physiological involvement of glycerol and HbXIP2;1 in water homeostasis and carbon stream of challenged laticifers. The characterization of HbXIP2;1 during rubber tree tapping lends new insights into molecular and physiological response processes of laticifer metabolism in the context of latex exploitation.

  19. The ZNF75 zinc finger gene subfamily: Isolation and mapping of the four members in humans and great apes

    SciTech Connect

    Villa, A.; Strina, D.; Frattini, A.

    1996-07-15

    We have previously reported the characterization of the human ZNF75 gene located on Xq26, which has only limited homology (less than 65%) to other ZF genes in the databases. Here, we describe three human zinc finger genes with 86 to 95% homology to ZNF75 at the nucleotide level, which represent all the members of the human ZNF75 subfamily. One of these, ZNF75B, is a pseudogene mapped to chromosome 12q13. The other two, ZNF75A and ZNF75C, maintain on ORF in the sequenced region, and at least the latter is expressed in the U937 cell line. They were mapped to chromosomes 16 and 11, respectively. All these genes are conserved in chimpanzees, gorillas, and orangutans. The ZNF75B homologue is a pseudogene in all three great apes, and in chimpanzee it is located on chromosome 10 (phylogenetic XII), at p13 (corresponding to the human 12q13). The chimpanzee homologue of ZNF75 is also located on the Xq26 chromosome, in the same region, as detected by in situ hybridization. As expected, nucleotide changes were clearly more abundant between human and organutan than between human and chimpanzee or gorilla homologues. Members of the same class were more similar to each other than to the other homologues within the same species. This suggests that the duplication and/or retrotranscription events occurred in a common ancestor long before great ape speciation. This, together with the existance of at least two genes in cows and horses, suggests a relatively high conservation of this gene family. 20 refs., 5 figs., 1 tab.

  20. A novel fractal approach for predicting G-protein-coupled receptors and their subfamilies with support vector machines.

    PubMed

    Nie, Guoping; Li, Yong; Wang, Feichi; Wang, Siwen; Hu, Xuehai

    2015-01-01

    G-protein-coupled receptors (GPCRs) are seven membrane-spanning proteins and regulate many important physiological processes, such as vision, neurotransmission, immune response and so on. GPCRs-related pathways are the targets of a large number of marketed drugs. Therefore, the design of a reliable computational model for predicting GPCRs from amino acid sequence has long been a significant biomedical problem. Chaos game representation (CGR) reveals the fractal patterns hidden in protein sequences, and then fractal dimension (FD) is an important feature of these highly irregular geometries with concise mathematical expression. Here, in order to extract important features from GPCR protein sequences, CGR algorithm, fractal dimension and amino acid composition (AAC) are employed to formulate the numerical features of protein samples. Four groups of features are considered, and each group is evaluated by support vector machine (SVM) and 10-fold cross-validation test. To test the performance of the present method, a new non-redundant dataset was built based on latest GPCRDB database. Comparing the results of numerical experiments, the group of combined features with AAC and FD gets the best result, the accuracy is 99.22% and Matthew's correlation coefficient (MCC) is 0.9845 for identifying GPCRs from non-GPCRs. Moreover, if it is classified as a GPCR, it will be further put into the second level, which will classify a GPCR into one of the five main subfamilies. At this level, the group of combined features with AAC and FD also gets best accuracy 85.73%. Finally, the proposed predictor is also compared with existing methods and shows better performances.

  1. How pH Modulates the Dimer-Decamer Interconversion of 2-Cys Peroxiredoxins from the Prx1 Subfamily*

    PubMed Central

    Morais, Mariana A. B.; Giuseppe, Priscila O.; Souza, Tatiana A. C. B.; Alegria, Thiago G. P.; Oliveira, Marcos A.; Netto, Luis E. S.; Murakami, Mario T.

    2015-01-01

    2-Cys peroxiredoxins belonging to the Prx1 subfamily are Cys-based peroxidases that control the intracellular levels of H2O2 and seem to assume a chaperone function under oxidative stress conditions. The regulation of their peroxidase activity as well as the observed functional switch from peroxidase to chaperone involves changes in their quaternary structure. Multiple factors can modulate the oligomeric transitions of 2-Cys peroxiredoxins such as redox state, post-translational modifications, and pH. However, the molecular basis for the pH influence on the oligomeric state of these enzymes is still elusive. Herein, we solved the crystal structure of a typical 2-Cys peroxiredoxin from Leishmania in the dimeric (pH 8.5) and decameric (pH 4.4) forms, showing that conformational changes in the catalytic loop are associated with the pH-induced decamerization. Mutagenesis and biophysical studies revealed that a highly conserved histidine (His113) functions as a pH sensor that, at acidic conditions, becomes protonated and forms an electrostatic pair with Asp76 from the catalytic loop, triggering the decamerization. In these 2-Cys peroxiredoxins, decamer formation is important for the catalytic efficiency and has been associated with an enhanced sensitivity to oxidative inactivation by overoxidation of the peroxidatic cysteine. In eukaryotic cells, exposure to high levels of H2O2 can trigger intracellular pH variations, suggesting that pH changes might act cooperatively with H2O2 and other oligomerization-modulator factors to regulate the structure and function of typical 2-Cys peroxiredoxins in response to oxidative stress. PMID:25666622

  2. Phylogenetic analysis of the myostatin gene sub-family and the differential expression of a novel member in zebrafish.

    PubMed

    Kerr, Tovah; Roalson, Eric H; Rodgers, Buel D

    2005-01-01

    The myostatin (MSTN)-null phenotype in mammals is characterized by extreme gains in skeletal muscle mass or "double muscling" as the cytokine negatively regulates skeletal muscle growth. Recent attempts, however, to reproduce a comparable phenotype in zebrafish have failed. Several aspects of MSTN biology in the fishes differ significantly from those in mammals and at least two distinct paralogs have been identified in some species, which possibly suggests functional divergence between the different vertebrate classes or between fish paralogs. We therefore conducted a phylogenetic analysis of the entire MSTN gene sub-family. Maximum likelihood, Bayesian inference, and bootstrap analyses indicated a monophyletic distribution of all MSTN genes with two distinct fish clades: MSTN-1 and -2. These analyses further indicated that all Salmonid genes described are actually MSTN-1 orthologs and that additional MSTN-2 paralogs may be present in most, if not all, teleosts. An additional zebrafish homolog was identified by BLAST searches of the zebrafish Hierarchical Tets Generation System database and was subsequently cloned. Comparative sequence analysis of both genes (zebrafish MSTN (zfMSTN)-1 and -2) revealed many differences, primarily within the latency-associated peptide regions, but also within the bioactive domains. The 2-kb promoter region of zfMSTN-2 contained many putative cis regulatory elements that are active during myogenesis, but are lacking in the zfMSTN-1 promoter. In fact, zfMSTN-2 expression was limited to the early stages of somitogenesis, whereas zfMSTN-1 was expressed throughout embryogenesis. These data suggest that zfMSTN-2 may be more closely associated with skeletal muscle growth and development. They also resolve the previous ambiguity in classification of fish MSTN genes.

  3. Isolation of two novel ras genes in Dictyostelium discoideum; evidence for a complex, developmentally regulated ras gene subfamily.

    PubMed

    Daniel, J; Bush, J; Cardelli, J; Spiegelman, G B; Weeks, G

    1994-02-01

    In Dictyostelium discoideum, three ras genes (rasD, rasG and rasB) and one ras-related gene (rap1) have been previously isolated and characterized, and the deduced amino acid sequence of their predicted protein products share at least 50% sequence identity with the human H-Ras protein. We have now cloned and characterized two additional members of the ras gene subfamily in Dictyostelium, rasC and rasS. These genes are developmentally regulated and unlike the previously isolated Dictyostelium ras genes, maximum levels of their transcripts were detected during aggregation, suggesting that the encoded proteins have distinct functions during aggregation. The rasC cDNA encodes a 189 amino acid protein that is 65% identical to the Dictyostelium RasD and RasG proteins and 56% identical to the human H-Ras protein. The predicted 194 amino acid gene product encoded by rasS is 60% identical to the Dictyostelium RasD and RasG proteins and 54% identical to the human H-Ras protein. Whereas RasD, RasG, RasB and Rap1 are totally conserved in their putative effector domains relative to H-Ras, RasC and RasS have single amino acid substitutions in their effector domains, consistent with the idea that they have unique functions. In RasC, aspartic acid-38 has been replaced by asparagine (D38N), and in RasS, isoleucine-36 has been replaced by leucine (I36L). In addition, both proteins have several differences in the effector-proximal domain, a domain which is believed to play a role in Ras target activation. In RasC, there is a single conservative amino acid change in the canonical sequence of the binding site for the Ras-specific monoclonal antibody Y13-259, and consequently, RasC is less immunoreactive with the antibody than either of the Dictyostelium RasD or RasG proteins. In contrast, RasS, which has three substitutions in the Y13-259 binding site, does not react with the Y13-259 antibody.

  4. Crystal Structures of Two Transcriptional Regulators from Bacillus cereus Define the Conserved Structural Features of a PadR Subfamily

    PubMed Central

    Fibriansah, Guntur; Kovács, Ákos T.; Pool, Trijntje J.; Boonstra, Mirjam; Kuipers, Oscar P.; Thunnissen, Andy-Mark W. H.

    2012-01-01

    PadR-like transcriptional regulators form a structurally-related family of proteins that control the expression of genes associated with detoxification, virulence and multi-drug resistance in bacteria. Only a few members of this family have been studied by genetic, biochemical and biophysical methods, and their structure/function relationships are still largely undefined. Here, we report the crystal structures of two PadR-like proteins from Bacillus cereus, which we named bcPadR1 and bcPadR2 (products of gene loci BC4206 and BCE3449 in strains ATCC 14579 and ATCC 10987, respectively). BC4206, together with its neighboring gene BC4207, was previously shown to become significantly upregulated in presence of the bacteriocin AS-48. DNA mobility shift assays reveal that bcPadR1 binds to a 250 bp intergenic region containing the putative BC4206–BC4207 promoter sequence, while in-situ expression of bcPadR1 decreases bacteriocin tolerance, together suggesting a role for bcPadR1 as repressor of BC4206–BC4207 transcription. The function of bcPadR2 (48% identical in sequence to bcPadR1) is unknown, but the location of its gene just upstream from genes encoding a putative antibiotic ABC efflux pump, suggests a role in regulating antibiotic resistance. The bcPadR proteins are structurally similar to LmrR, a PadR-like transcription regulator in Lactococcus lactis that controls expression of a multidrug ABC transporter via a mechanism of multidrug binding and induction. Together these proteins define a subfamily of conserved, relatively small PadR proteins characterized by a single C-terminal helix for dimerization. Unlike LmrR, bcPadR1 and bcPadR2 lack a central pore for ligand binding, making it unclear whether the transcriptional regulatory roles of bcPadR1 and bcPadR2 involve direct ligand recognition and induction. PMID:23189126

  5. Identification and characterization of three TLR1 subfamily members from the orange-spotted grouper, Epinephelus coioides.

    PubMed

    Li, Yan-Wei; Xu, Dong-Dong; Li, Xia; Mo, Ze-Quan; Luo, Xiao-Chun; Li, An-Xing; Dan, Xue-Ming

    2016-08-01

    Toll-like receptors (TLRs), which play important roles in host defense against pathogen infection, are the most intensively studied pattern recognition receptors (PRRs). In this study, we identified three novel TLR1 subfamily members, including TLR1 (EcTLR1b), TLR2 (EcTLR2b) and TLR14 (EcTLR14), from the orange-spotted grouper (Epinephelus coioides). EcTLR1b and EcTLR2b displayed low sequence identity with the previously reported grouper TLR1 (EcTLR1a) and TLR2 (EcTLR2a), respectively. The open reading frames (ORFs) of EcTLR1b, EcTLR2b and EcTLR14 contain 2484 bp, 2394 bp and 2640 bp, which encode the corresponding 827 amino acids (aa), 797 aa and 879 aa, respectively. All three TLRs have leucine-rich repeat (LRR) domains (including an LRR-NT (except for EcTLR1b), several LRR motifs and an LRR-CT), a trans-membrane region and a Toll/interleukin-1 receptor (TIR) domain. The TIR domains of the three TLRs exhibited conserved boxes, namely box1, box2 and box3, and their 3D models were similar to those of human TLR1 or TLR2. Sequence alignment demonstrated that the TIR domains of the three TLRs shared higher sequence identity with those of other species than the full-length receptors. Phylogenetic analysis indicated that EcTLR1s and EcTLR2s are characterized by their differing evolutionary status, whereas EcTLR14 was found to be in the same group as other piscine TLR14/18s. The three TLRs were ubiquitously expressed in seven tested tissues of healthy groupers, although their expression profiles were different. Post Cryptocaryon irritans infection, TLR1s expression was up-regulated in the gills. The expression of TLR2b was mainly increased in the spleen, but decreased in the gills, which was similar to the expression pattern of TLR2a post C. irritans infection. Unlike EcTLR1b and EcTLR2b, however, the grouper TLR14 transcript was substantially induced in both tissues post challenge. These findings may be helpful in understanding the innate immune mechanism of host

  6. Phylogenetic relationships and biogeographical patterns in Circum-Mediterranean subfamily Leuciscinae (Teleostei, Cyprinidae) inferred from both mitochondrial and nuclear data

    PubMed Central

    2010-01-01

    Background Leuciscinae is a subfamily belonging to the Cyprinidae fish family that is widely distributed in Circum-Mediterranean region. Many efforts have been carried out to deciphering the evolutionary history of this group. Thus, different biogeographical scenarios have tried to explain the colonization of Europe and Mediterranean area by cyprinids, such as the "north dispersal" or the "Lago Mare dispersal" models. Most recently, Pleistocene glaciations influenced the distribution of leuciscins, especially in North and Central Europe. Weighing up these biogeographical scenarios, this paper constitutes not only the first attempt at deciphering the mitochondrial and nuclear relationships of Mediterranean leuciscins but also a test of biogeographical hypotheses that could have determined the current distribution of Circum-Mediterranean leuciscins. Results A total of 4439 characters (mitochondrial + nuclear) from 321 individuals of 176 leuciscine species rendered a well-supported phylogeny, showing fourteen main lineages. Analyses of independent mitochondrial and nuclear markers supported the same main lineages, but basal relationships were not concordant. Moreover, some incongruence was found among independent mitochondrial and nuclear phylogenies. The monophyly of some poorly known genera such as Pseudophoxinus and Petroleuciscus was rejected. Representatives of both genera belong to different evolutionary lineages. Timing of cladogenetic events among the main leuciscine lineages was gained using mitochondrial and all genes data set. Conclusions Adaptations to a predatory lifestyle or miniaturization have superimposed the morphology of some species. These species have been separated into different genera, which are not supported by a phylogenetic framework. Such is the case of the genera Pseudophoxinus and Petroleuciscus, which real taxonomy is not well known. The diversification of leuciscine lineages has been determined by intense vicariant events following the

  7. Evolution of a novel subfamily of nuclear receptors with members that each contain two DNA binding domains

    PubMed Central

    Wu, Wenjie; Niles, Edward G; Hirai, Hirohisa; LoVerde, Philip T

    2007-01-01

    Background Nuclear receptors (NRs) are important transcriptional modulators in metazoans which regulate transcription through binding to the promoter region of their target gene by the DNA binding domain (DBD) and activation or repression of mRNA synthesis through co-regulators bound to the ligand binding domain (LBD). NRs typically have a single DBD with a LBD. Results Three nuclear receptors named 2DBD-NRs, were identified from the flatworm Schistosoma mansoni that each possess a novel set of two DBDs in tandem with a LBD. They represent a novel NR modular structure: A/B-DBD-DBD-hinge-LBD. The 2DBD-NRs form a new subfamily of NRs, VII. By database mining, 2DBD-NR genes from other flatworm species (Schmidtea mediterranea and Dugesia japonica), from Mollusks (Lottia gigantean) and from arthropods (Daphnia pulex) were also identified. All 2DBD-NRs possess a P-box sequence of CEACKK in the first DBD, which is unique to 2DBD-NRs, and a P-box sequence of CEGCKG in the second DBD. Phylogenetic analyses of both DBD and ligand binding domain sequences showed that 2DBD-NR genes originate from a common two DBD-containing ancestor gene. A single 2DBD-NR orthologue was found in Arthropoda, Platyhelminths and Mollusca. Subsequent 2DBD-NR gene evolution in Mollusks and Platyhelminths involved gene duplication. Chromosome localization of S. mansoni 2DBD-NR genes by Fluorescent in situ hybridization (FISH) suggests that 2DBD-NR genes duplicated on different chromosomes in the Platyhelminths. Dimerization of Sm2DBDα indicates that 2DBD-NRs may act as homodimers, suggesting either that two repeats of a half-site are necessary for each DBD of 2DBD-NRs to bind to its target gene, or that each 2DBD-NR can recognize multiple sites. Conclusion 2DBD-NRs share a common ancestor gene which possessed an extra DBD that likely resulted from a recombination event. After the split of the Arthropods, Mollusks and Platyhelminths, 2DBD-NR underwent a recent duplication in a common ancestor of

  8. Subcellular location of Arabidopsis thaliana subfamily a1 β-galactosidases and developmental regulation of transcript levels of their coding genes.

    PubMed

    Moneo-Sánchez, María; Izquierdo, Lucía; Martín, Ignacio; Labrador, Emilia; Dopico, Berta

    2016-12-01

    The aim of this work is to gain insight into the six members of the a1 subfamily of the β-galactosidases (BGAL) from Arabidopsis thaliana. First, the subcellular location of all these six BGAL proteins from a1 subfamily has been established in the cell wall by the construction of transgenic plants producing the enhanced green fluorescent protein (eGFP) fused to the BGAL proteins. BGAL12 is also located in the endoplasmic reticulum. Our study of the AtBGAL transcript accumulation along plant development indicated that all AtBGAL transcript appeared in initial stages of development, both dark- and light-grown seedlings, being AtBGAL1, AtBGAL2 and AtBGAL3 transcripts the predominant ones in the latter condition, mainly in the aerial part and with levels decreasing with age. The high accumulation of transcript of AtBGAL4 in basal internodes and in leaves at the end of development, and their strong increase after treatment both with BL and H3BO3 point to an involvement of BGAL4 in cell wall changes leading to the cease of elongation and increased rigidity. The changes of AtBGAL transcript accumulation in relation to different stages and conditions of plant development, suggest that each of the different gene products have a plant-specific function and provides support for the proposed function of the subfamily a1 BGAL in plant cell wall remodelling for cell expansion or for cell response to stress conditions.

  9. Fourfold polyphyly of the genus formerly known as Upucerthia, with notes on the systematics and evolution of the avian subfamily Furnariinae

    USGS Publications Warehouse

    Chesser, R.T.; Barker, F.K.; Brumfield, R.T.

    2007-01-01

    The traditional avian subfamily Furnariinae, a group of terrestrial ovenbirds typical of the Andean and Patagonian arid zones, consists of the genera Furnarius, Cinclodes, Geositta, Upucerthia, Chilia, and Eremobius. We investigated phylogenetic relationships within the Furnariinae, with particular attention to the nine species of the genus Upucerthia, using nuclear and mitochondrial DNA sequences from all genera in the subfamily. Upucerthia was found to be highly polyphyletic, its constituent species forming four non-sister clades: (1) a basal lineage consisting of two Upucerthia species, U. ruficaudus and U. andaecola, as well as the monotypic genera Eremobius and Chilia; (2) a lineage consisting of U. harterti and U. certhioides, two species behaviorally divergent from other Upucerthia species; (3) a lineage consisting of U. serrana, which is not closely related to any other Upucerthia species; and (4) a lineage, sister to Cinclodes, consisting of the four Upucerthia species U. dumetaria, U. albigula, U. validirostris, and U. jelskii. The larger Furnariinae was also found to be highly polyphyletic; the terrestrial open country ecotype characteristic of this subfamily occurs in four unrelated clades in the family Furnariidae, including a basal lineage as well as derived lineages. Although the large degree of divergence among Upucerthia clades was not previously recognized, owing to ecological, behavioral, and morphological similarities, the groupings correspond closely to relationships suggested by plumage. This is in contrast to studies of other avian genera in which plumage patterns have been shown to be extensively convergent. The generic names Upucerthia and Ochetorhynchus are available for two of the former Upucerthia clades; new generic names may be warranted for the other two.

  10. Cross-priming of microsatellite loci in subfamily cyprininae (family Cyprinidae): their utility in finding markers for population genetic analysis in three Indian major carps.

    PubMed

    Masih, Prachi; Luhariya, Rupesh K; Das, Rakhi; Gupta, Arti; Mohindra, Vindhya; Singh, Rajeev K; Srivastava, Rohit; Chauhan, U K; Jena, J K; Lal, Kuldeep K

    2014-08-01

    This study is aimed to identify polymorphic microsatellite markers and establish their potential for population genetics studies in three carp (family cyprinidae; subfamily cyprininae) species, Labeo rohita, Catla catla and Cirrhinus mrigala through use of cyprinid primers. These species have high commercial value and knowledge of genetic variation is important for management of farmed and wild populations. We tested 108 microsatellite primers from 11 species belonging to three different cyprinid subfamilies, Cyprininae, Barbinae and Leuciscinae out of which 63 primers (58.33%) successfully amplified orthologous loci in three focal species. Forty-two loci generated from 29 primers were polymorphic in these three carp species. Sequencing of amplified product confirmed the presence of SSRs in these 42 loci and orthologous nature of the loci. To validate potential of these 42 polymorphic loci in determining the genetic variation, we analyzed 486 samples of three focal species collected from Indus, Ganges and Brahmaputra river systems. Results indicated significant genetic variation, with mean number of alleles per locus ranging from 6.80 to 14.40 and observed heterozygosity ranging from 0.50 to 0.74 in the three focal species. Highly significant (P < 0.00001) allelic homogeneity values revealed that the identified loci can be efficiently used in population genetics analysis of these carp species. Further, thirty-two loci from 19 primers were useful for genotyping in more than one species. The data from the present study was compiled with cross-species amplification data from previous results on eight species of subfamily cyprininae to compare cross-transferability of microsatellite loci. It was revealed that out of 226 heterologous loci amplified, 152 loci that originated from 77 loci exhibited polymorphism and 45 primers were of multispecies utility, common for 2-7 species.

  11. A multi-locus species phylogeny of African forest duikers in the subfamily Cephalophinae: evidence for a recent radiation in the Pleistocene

    PubMed Central

    2012-01-01

    Background Duikers in the subfamily Cephalophinae are a group of tropical forest mammals believed to have first originated during the late Miocene. However, knowledge of phylogenetic relationships, pattern and timing of their subsequent radiation is poorly understood. Here we present the first multi-locus phylogeny of this threatened group of tropical artiodactyls and use a Bayesian uncorrelated molecular clock to estimate divergence times. Results A total of 4152 bp of sequence data was obtained from two mitochondrial genes and four nuclear introns. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analysis of concatenated mitochondrial, nuclear and combined datasets. A relaxed molecular clock with two fossil calibration points was used to estimate divergence times. The first was based on the age of the split between the two oldest subfamilies within the Bovidae whereas the second was based on the earliest known fossil appearance of the Cephalophinae and molecular divergence time estimates for the oldest lineages within this group. Findings indicate strong support for four major lineages within the subfamily, all of which date to the late Miocene/early Pliocene. The first of these to diverge was the dwarf duiker genus Philantomba, followed by the giant, eastern and western red duiker lineages, all within the genus Cephalophus. While these results uphold the recognition of Philantomba, they do not support the monotypic savanna-specialist genus Sylvicapra, which as sister to the giant duikers leaves Cephalophus paraphyletic. BEAST analyses indicate that most sister species pairs originated during the Pleistocene, suggesting that repeated glacial cycling may have played an important role in the recent diversification of this group. Furthermore, several red duiker sister species pairs appear to be either paraphyletic (C.callipygus/C. ogilbyi and C. harveyi/C. natalensis) or exhibit evidence of mitochondrial admixture (C. nigrifrons

  12. Biting midges of the subfamily Forcipomyiinae (Diptera: Ceratopogonidae) from the Middle East, with keys and descriptions of new species.

    PubMed

    Alwin-Kownacka, Alicja; Szadziewski, Ryszard; Szwedo, Jacek

    2016-10-05

    Middle East biting midges of the genera Atrichopogon Kieffer and Forcipomyia Meigen, subfamily Forcipomyiinae Lenz, covering 41 species are reviewed. Two new species are described and illustrated: Forcipomyia (F.) siverekensis Alwin & Szadziewski sp. nov. and Forcipomyia (Microhelea) borkenti Alwin & Szadziewski sp. nov. The list includes 16 species of Atrichopogon and 25 of Forcipomyia. Nine species previously described by Vimmer and Kieffer from the Middle East are treated as nomina dubia and not included in the list.        Keys to identification of Atrichopogon and Forcipomyia species of the Middle East are also provided.

  13. Presence of specific symbiotic bacteria in flies of the subfamily Tephritinae (Diptera Tephritidae) and their phylogenetic relationships: proposal of 'Candidatus Stammerula tephritidis'.

    PubMed

    Mazzon, Luca; Piscedda, Alessia; Simonato, Mauro; Martinez-Sañudo, Isabel; Squartini, Andrea; Girolami, Vincenzo

    2008-06-01

    The presence of symbiotic bacteria in flies belonging to the subfamily Tephritinae, which predominantly infest the flower heads of composite flowers (Asteraceae), was investigated. Twenty-five species of flies, collected mainly in northern Italy, were examined. The bacteria adhered to the midgut epithelium in a space external to the peritrophic membrane and therefore not in direct contact with the gut contents. Specific, unique and live, but unculturable bacteria were consistently found in the majority of the fly species and their presence was also shown to be persistent in flies reared under microbiologically controlled conditions and devoid of any residual culturable intestinal bacteria. Sequencing of the small subunit rRNA gene from the novel bacteria indicated that they belonged to the family Enterobacteriaceae. Three main strongly supported clades were delineated by phylogenetic trees, the first of which featured a coherent set of sequences displaying gene sequence similarities lower than 96 % compared with recognized taxa. The second and third clades featured cases with higher gene sequence similarities to culturable bacteria, including Erwinia persicina and Ewingella americana, respectively. Relative rate tests were supportive of a fast genetic evolution for the majority of the bacterial symbionts of the subfamily Tephritinae. In agreement with the interpretation suggested in 1929 after pioneering observations made by H. J. Stammer, a symbiotic relationship between the novel bacteria and the tephritid flies is postulated. The origin of this apparently polyphyletic relationship is discussed and a novel candidate organism is proposed for the first clade under the designation 'Candidatus Stammerula tephritidis'.

  14. Characterization of a second member of the subfamily of calcium-binding mitochondrial carriers expressed in human non-excitable tissues.

    PubMed Central

    Del Arco, A; Agudo, M; Satrústegui, J

    2000-01-01

    We have recently identified a subfamily of mitochondrial carriers that bind calcium, and cloned ARALAR1, a member of this subfamily expressed in human muscle and brain. We have now cloned a second human ARALAR gene (ARALAR2) coding for a protein 78.3% identical to Aralar1, but expressed in liver and non-excitable tissues. Aralar2 is identical to citrin, the product of the gene mutated in type-II citrullinaemia [Kobayashi, Sinasac, Iijima, Boright, Begum, Lee, Yasuda, Ikeda, Hirano, Terazono et al. (1999) Nat. Genet. 22, 159-163]. A related protein, DmAralar, 69% identical to Aralar1, was found in Drosophila melanogaster, the DMARALAR locus lying on the right arm of the third chromosome, band 99F. The N-terminal half of Aralar2/citrin is able to bind calcium and this requires the presence of the two most distal EF-hands. The localization of Aralar2/citrin expressed in human cell lines is mitochondrial, the C-terminal half containing sufficient information for import and assembly into mitochondria. The C-terminal half of Aralar proteins is related to the yeast YPR020c gene, with a very high sequence conservation (54.3% identity), suggesting that these proteins play an important role. Thus Aralar proteins are probably expressed in all tissues in an isoform-specific fashion, where they function as calcium-regulated metabolite (possibly anionic) carriers. PMID:10642534

  15. Distinct structural and redox properties of the heme active site in bacterial dye decolorizing peroxidase-type peroxidases from two subfamilies: resonance Raman and electrochemical study.

    PubMed

    Sezer, Murat; Santos, Ana; Kielb, Patrycja; Pinto, Tiago; Martins, Ligia O; Todorovic, Smilja

    2013-05-07

    Spectroscopic data of dye decolorizing peroxidases (DyPs) from Bacillus subtilis (BsDyP), an A subfamily member, and Pseudomonas putida (PpDyP), a B subfamily enzyme, reveal distinct heme coordination patterns of the respective active sites. In solution, both enzymes show a heterogeneous spin population, with the six-coordinated low-spin state being the most populated in the former and the five-coordinated quantum mechanically mixed-spin state in the latter. We ascribe the poor catalytic activity of BsDyP to the presence of a catalytically incompetent six-coordinated low-spin population. The spin populations of the two DyPs are sensitively dependent on the pH, temperature, and physical, i.e., solution versus crystal versus immobilized, state of the enzymes. We observe a redox potential for the Fe(2+)/Fe(3+) couple in BsDyP (-40 mV) at pH 7.6 substantially more positive than those reported for the majority of other peroxidases, including PpDyP (-260 mV). Furthermore, we evaluate the potential of the studied enzymes for biotechnological applications on the basis of electrochemical and spectroelectrochemical data.

  16. Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro dipeptidases.

    PubMed

    Are, Venkat N; Kumar, Ashwani; Kumar, Saurabh; Goyal, Venuka Durani; Ghosh, Biplab; Bhatnagar, Deepak; Jamdar, Sahayog N; Makde, Ravindra D

    2017-02-01

    Xaa-Pro dipeptidase (XPD) catalyzes hydrolysis of iminopeptide bond in dipeptides containing trans-proline as a second residue. XPDs are found in all living organisms and are believed to play an essential role in proline metabolism. Here, we report crystal structures and extensive enzymatic studies of XPD from Xanthomonas campestris (XPDxc), the first such comprehensive study of a bacterial XPD. We also report enzymatic activities of its ortholog from Mycobacterium tuberculosis (XPDmt). These enzymes are strictly dipeptidases with broad substrate specificities. They exhibit substrate inhibition and allostericity, as described earlier for XPD from Lactococcus lactis (XPDll). The structural, mutational and comparative data have revealed a novel mechanism of dipeptide selectivity and substrate binding in these enzymes. Moreover, we have identified conserved sequence motifs that distinguish these enzymes from other prolidases, thus defining a new subfamily. This study provides a suitable structural template for explaining unique properties of this XPDxc subfamily. In addition, we report unique structural features of XPDxc protein like an extended N-terminal tail region and absence of a conserved Tyr residue near the active site.

  17. Phylogenic analysis revealed an expanded C₂H₂-homeobox subfamily and expression profiles of C₂H₂ zinc finger gene family in Verticillium dahliae.

    PubMed

    Xiong, Dianguang; Wang, Yonglin; Deng, Chenglin; Hu, Ruowen; Tian, Chengming

    2015-05-15

    C2H2 zinc finger (CZF) proteins are a major class of transcription factors that play crucial roles in fungal growth, development, various stress responses, and virulence. Little genome-wide data is available regarding the roles of CZF proteins in Verticillium dahliae, a destructive pathogen that causes vascular wilt disease in more than 200 plant species. We identified a total of 79 typical CZF genes in V. dahliae. Comparative analysis revealed that four plant pathogenic fungi, V. dahliae, Fusarium oxysporum, Magnaporthe oryzae, and Botrytis cinerea, have comparable numbers of predicted CZF genes with similar characteristics. Phylogenetic analysis identified a C2H2-homeobox subfamily in V. dahliae containing seven genes with similar gene structures. V. dahliae and F. oxysporum (Hypocreomycetidae) have more genes of this subfamily than M. oryzae (Sordariomycetidae) and B. cinerea (Leotiomycetes). Furthermore, gene-expression analysis of the smoke tree wilt fungus V. dahliae strain XS11 using digital gene-expression profiling and RT-qPCR revealed that a number of CZF genes were differentially expressed during microsclerotia formation, nutritional starvation, and simulated in planta conditions. Furthermore, the expression profiles revealed that some CZF genes were overrepresented during multiple stages, indicating that they might play diverse roles. Our results provide useful information concerning the functions of CZF genes in microsclerotia formation, nutritional stress responses, and pathogenicity in V. dahliae, and form a basis for future functional studies of these genes.

  18. pBLA8, from Brevibacterium linens, belongs to a gram-positive subfamily of ColE2-related plasmids.

    PubMed

    Leret, V; Trautwetter, A; Rincé, A; Blanco, C

    1998-10-01

    A 3.1 kb DNA fragment from pBLA8, a Brevibacterium linens cryptic plasmid, containing all the information required for autonomous replication was cloned and sequenced. Using deletion analysis, the fragment essential and sufficient for autonomous replication was delimited to 1.5 kb. This fragment is characterized by the presence of an ori site located upstream of an operon encoding two proteins, RepA and RepB, both essential for replication. Based on structural similarities and a strong conservation of ori, RepA and RepB, pBLA8 was assigned to a new subfamily of the ColE2 plasmid family. This subfamily is distinguished by the requirement for two Rep proteins and the location of an ori site upstream of the repAB operon. RepA is thought to encode primase activity, whereas RepB could be a DNA-binding protein. An Escherichia coli-B. linens shuttle vector, derived from pBLA8, was constructed. Its host spectrum was extended to Arthrobacter species.

  19. The distribution of glutathione and homoglutathione in leaf, root and seed tissue of 73 species across the three sub-families of the Leguminosae.

    PubMed

    Colville, Louise; Sáez, Clara M Blanco; Lewis, Gwilym P; Kranner, Ilse

    2015-07-01

    Homoglutathione (γ-glutamyl-cysteinyl-β-alanine) is a homologue of glutathione (γ-glutamyl-cysteinyl-glycine), which is a ubiquitous and indispensable tripeptide in eukaryotes with multi-facetted functions, many of which relate to cellular redox regulation. Homoglutathione is unique to the Leguminosae family, but studies of its occurrence have been restricted to the Papilionoideae subfamily, and almost exclusively to crop species. To determine whether the distribution of homoglutathione in the Leguminosae has a phylogenetic basis the occurrence of homoglutathione was investigated in the leaves, roots and seeds of 73 wild species of Leguminosae, representing 30 tribes across the Caesalpinioideae, Mimosoideae and Papilionoideae subfamilies. Homoglutathione was found only in the Papilionoideae, and was generally restricted to the 'Old World Clade'. It is proposed that homoglutathione may have arisen following a whole genome duplication event after the divergence of the Old World Clade. Homoglutathione is believed to fulfil the same functional roles as glutathione, but this study showed that homoglutathione and glutathione have different tissue-specific distribution patterns. Homoglutathione tended to occur more frequently in root tissue, and higher concentrations were found in leaves and roots, whereas glutathione tended to be present at the highest concentrations in seeds. This may reflect a distinct role for homoglutathione, particularly in roots, or an inability of homoglutathione to functionally replace glutathione in reproductive tissues. However, no relationships with environmental factors or nodulation were observed. Greater understanding of the factors that influence homoglutathione distribution may help to elucidate its unique function in some legume species.

  20. A subfamily of putative cytokinin receptors is revealed by an analysis of the evolution of the two-component signaling system of plants.

    PubMed

    Gruhn, Nijuscha; Halawa, Mhyeddeen; Snel, Berend; Seidl, Michael F; Heyl, Alexander

    2014-05-01

    The two-component signaling system--the major signaling pathway of bacteria--is found among higher eukaryotes only in plants, where it regulates diverse processes, such as the signaling of the phytohormone cytokinin. Cytokinin is perceived by a hybrid histidine (His) kinase receptor, and the signal is transduced by a multistep phosphorelay system of His phosphotransfer proteins and different classes of response regulators (RRs). To shed light on the origin and evolution of the two-component signaling system members in plants, we conducted a comprehensive domain-based phylogenetic study across the relevant kingdoms, including Charophyceae algae, the group of green algae giving rise to land plants. Surprisingly, we identified a subfamily of cytokinin receptors with members only from the early diverging land plants Marchantia polymorpha and Physcomitrella patens and then experimentally characterized two members of this subfamily. His phosphotransfer proteins of Charophyceae seemed to be more closely related to land plants than to other groups of green algae. Farther down the signaling pathway, the type-B RRs were found across all plant clades, but many members lack either the canonical Asp residue or the DNA binding domain. In contrast, the type-A RRs seemed to be limited to land plants. Finally, the analysis provided hints that one additional group of RRs, the type-C RRs, might be degenerated receptors and thus, of a different evolutionary origin than bona fide RRs.

  1. The Exiguobacterium sibiricum 255-15 GtfC Enzyme Represents a Novel Glycoside Hydrolase 70 Subfamily of 4,6-α-Glucanotransferase Enzymes.

    PubMed

    Gangoiti, Joana; Pijning, Tjaard; Dijkhuizen, Lubbert

    2015-11-20

    The glycoside hydrolase 70 (GH70) family originally was established for glucansucrase enzymes found solely in lactic acid bacteria synthesizing α-glucan polysaccharides from sucrose (e.g., GtfA). In recent years, we have characterized GtfB and related Lactobacillus enzymes as 4,6-α-glucanotransferase enzymes. These GtfB-type enzymes constitute the first GH70 subfamily of enzymes that are unable to act on sucrose as a substrate but are active with maltodextrins and starch, cleave α1→4 linkages, and synthesize linear α1→6-glucan chains. The GtfB disproportionating type of activity results in the conversion of malto-oligosaccharides into isomalto/malto-polysaccharides with a relatively high percentage of α1→6 linkages. This paper reports the identification of the members of a second GH70 subfamily (designated GtfC enzymes) and the characterization of the Exiguobacterium sibiricum 255-15 GtfC enzyme, which is also inactive with sucrose and displays 4,6-α-glucanotransferase activity with malto-oligosaccharides. GtfC differs from GtfB in synthesizing isomalto/malto-oligosaccharides. Biochemically, the GtfB- and GtfC-type enzymes are related, but phylogenetically, they clearly constitute different GH70 subfamilies, displaying only 30% sequence identity. Whereas the GtfB-type enzyme largely has the same domain order as glucansucrases (with α-amylase domains A, B, and C plus domains IV and V), this GtfC-type enzyme differs in the order of these domains and completely lacks domain V. In GtfC, the sequence of conserved regions I to IV of clan GH-H is identical to that in GH13 (I-II-III-IV) but different from that in GH70 (II-III-IV-I because of a circular permutation of the (β/α)8 barrel. The GtfC 4,6-α-glucanotransferase enzymes thus represent structurally and functionally very interesting evolutionary intermediates between α-amylase and glucansucrase enzymes.

  2. Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity

    PubMed Central

    2011-01-01

    Background Plant HD-Zip transcription factors are modular proteins in which a homeodomain is associated to a leucine zipper. Of the four subfamilies in which they are divided, the tested members from subfamily I bind in vitro the same pseudopalindromic sequence CAAT(A/T)ATTG and among them, several exhibit similar expression patterns. However, most experiments in which HD-Zip I proteins were over or ectopically expressed under the control of the constitutive promoter 35S CaMV resulted in transgenic plants with clearly different phenotypes. Aiming to elucidate the structural mechanisms underlying such observation and taking advantage of the increasing information in databases of sequences from diverse plant species, an in silico analysis was performed. In addition, some of the results were also experimentally supported. Results A phylogenetic tree of 178 HD-Zip I proteins together with the sequence conservation presented outside the HD-Zip domains allowed the distinction of six groups of proteins. A motif-discovery approach enabled the recognition of an activation domain in the carboxy-terminal regions (CTRs) and some putative regulatory mechanisms acting in the amino-terminal regions (NTRs) and CTRs involving sumoylation and phosphorylation. A yeast one-hybrid experiment demonstrated that the activation activity of ATHB1, a member of one of the groups, is located in its CTR. Chimerical constructs were performed combining the HD-Zip domain of one member with the CTR of another and transgenic plants were obtained with these constructs. The phenotype of the chimerical transgenic plants was similar to the observed in transgenic plants bearing the CTR of the donor protein, revealing the importance of this module inside the whole protein. Conclusions The bioinformatical results and the experiments conducted in yeast and transgenic plants strongly suggest that the previously poorly analyzed NTRs and CTRs of HD-Zip I proteins play an important role in their function, hence

  3. The Exiguobacterium sibiricum 255-15 GtfC Enzyme Represents a Novel Glycoside Hydrolase 70 Subfamily of 4,6-α-Glucanotransferase Enzymes

    PubMed Central

    Gangoiti, Joana; Pijning, Tjaard

    2015-01-01

    The glycoside hydrolase 70 (GH70) family originally was established for glucansucrase enzymes found solely in lactic acid bacteria synthesizing α-glucan polysaccharides from sucrose (e.g., GtfA). In recent years, we have characterized GtfB and related Lactobacillus enzymes as 4,6-α-glucanotransferase enzymes. These GtfB-type enzymes constitute the first GH70 subfamily of enzymes that are unable to act on sucrose as a substrate but are active with maltodextrins and starch, cleave α1→4 linkages, and synthesize linear α1→6-glucan chains. The GtfB disproportionating type of activity results in the conversion of malto-oligosaccharides into isomalto/malto-polysaccharides with a relatively high percentage of α1→6 linkages. This paper reports the identification of the members of a second GH70 subfamily (designated GtfC enzymes) and the characterization of the Exiguobacterium sibiricum 255-15 GtfC enzyme, which is also inactive with sucrose and displays 4,6-α-glucanotransferase activity with malto-oligosaccharides. GtfC differs from GtfB in synthesizing isomalto/malto-oligosaccharides. Biochemically, the GtfB- and GtfC-type enzymes are related, but phylogenetically, they clearly constitute different GH70 subfamilies, displaying only 30% sequence identity. Whereas the GtfB-type enzyme largely has the same domain order as glucansucrases (with α-amylase domains A, B, and C plus domains IV and V), this GtfC-type enzyme differs in the order of these domains and completely lacks domain V. In GtfC, the sequence of conserved regions I to IV of clan GH-H is identical to that in GH13 (I-II-III-IV) but different from that in GH70 (II-III-IV-I because of a circular permutation of the (β/α)8 barrel. The GtfC 4,6-α-glucanotransferase enzymes thus represent structurally and functionally very interesting evolutionary intermediates between α-amylase and glucansucrase enzymes. PMID:26590275

  4. A novel toxin from the venom of the scorpion Tityus trivittatus, is the first member of a new alpha-KTX subfamily.

    PubMed

    Abdel-Mottaleb, Yousra; Coronas, Fredy V; de Roodt, Adolfo R; Possani, Lourival D; Tytgat, Jan

    2006-01-23

    The first example of a new sub-family of toxins (alpha-KTx20.1) from the scorpion Tityus trivittatus was purified, sequenced and characterized physiologically. It has 29 amino acid residues, three disulfide bridges assumed to adopt the cysteine-stabilized alpha/beta scaffold with a pI value of 8.98. The sequence identities with all the other known alpha-KTx are less than 40%. Its effects were verified using seven different cloned K(+) channels (vertebrate Kv1.1-1.5, Shaker IR and hERG) expressed in Xenopus leavis oocytes. The toxin-induced effects show large differences among the different K(+) channels and a preference towards Kv1.3 (EC50=7.9+/-1.4 nM).

  5. The unusual Afrotropical and Oriental leafhopper subfamily Signoretiinae (Hemiptera, Cicadellidae): taxonomic notes, new distributional records, and description of two new Signoretia species

    PubMed Central

    Takiya, Daniela M.; Dietrich, Christopher H.; Viraktamath, Chandra A.

    2013-01-01

    Abstract The leafhopper subfamily Signoretiinae is redescribed and includes two tribes: Signoretiini Baker and Phlogisini Linnavuori. Redescriptions of included tribes, diagnoses and a taxonomic key to genera are provided. New records for genera of Signoretiinae are as follows: Phlogis in Central African Republic, Malaysia and Thailand; Preta in Thailand; and Signoretia in the Republic of the Congo, Zambia, Thailand, Vietnam, and Taiwan (China). Signoretia pacifica is newly recorded from Cameroon. In addition, detailed illustrations of the male genitalia of the previously described species, Chouious tianzeus, Preta gratiosa,and Signoretia yangli are provided; the male genitalia of Signoretia malaya are described for the first time; and two new species of Signoretia are described, Signoretia delicata sp. n. from the Philippinesand Signoretia kintendela sp. n. from the Republic of the Congo. PMID:24039527

  6. Targeting kinases with anilinopyrimidines: discovery of N-phenyl-N’-[4-(pyrimidin-4-ylamino)phenyl]urea derivatives as selective inhibitors of class III receptor tyrosine kinase subfamily

    PubMed Central

    Gandin, Valentina; Ferrarese, Alessandro; Dalla Via, Martina; Marzano, Cristina; Chilin, Adriana; Marzaro, Giovanni

    2015-01-01

    Kinase inhibitors are attractive drugs/drug candidates for the treatment of cancer. The most recent literature has highlighted the importance of multi target kinase inhibitors, although a correct balance between specificity and non-specificity is required. In this view, the discovery of multi-tyrosine kinase inhibitors with subfamily selectivity is a challenging goal. Herein we present the synthesis and the preliminary kinase profiling of a set of novel 4-anilinopyrimidines. Among the synthesized compounds, the N-phenyl-N’-[4-(pyrimidin-4-ylamino)phenyl]urea derivatives selectively targeted some members of class III receptor tyrosine kinase family. Starting from the structure of hit compound 19 we synthesized a further compound with an improved affinity toward the class III receptor tyrosine kinase members and endowed with a promising antitumor activity both in vitro and in vivo in a murine solid tumor model. Molecular modeling simulations were used in order to rationalize the behavior of the title compounds. PMID:26568452

  7. List of primary types of the larentiine moth species (Lepidoptera: Geometridae) described from Indonesia - a starting point for biodiversity assessment of the subfamily in the region

    PubMed Central

    2015-01-01

    Abstract Background The Indonesian geometrid moth fauna is rich and diverse, yet it is poorly studied. This is particularly the case for the second largest geometrid subfamily Larentiinae which comprises moths with predominantly high mountainous distribution in the tropics. The present study provides a first inventory of the primary type specimens of larentiine moth species (Lepidoptera: Geometridae) described from Indonesia. New information The list of species described from Indonesia is arranged alphabetically by the tribe, genus, and species, and presents data on 251 species and subspecies. For each species type status, type locality, depository, and a full reference to the original description are listed. Synonyms with Indonesian type localities are included. The study indicates a large part of the Indonesian geometrid fauna belong to the tribe Eupitheciini. PMID:26311296

  8. Review of the fur-mite genus Soricilichus Fain, 1970 (Acariformes: Chirodiscidae)-symbionts of the African shrews of the subfamily Crocidurinae (Soricomorpha: Soricidae).

    PubMed

    Bochkov, Andre V; Mbalitini, Sylvestre G; Verheyen, Erik

    2016-01-29

    The fur-mite genus Soricilichus Fain, 1970 (3 species) (Acariformes: Chirodiscidae) represented by permanent symbionts of the African shrews of the subfamily Crocidurinae (Soricomorpha: Soricidae) is revised. The external morphology of these species was investigated with light and scanning electron microscopy. Based on the type specimens and newly obtained samples, 2 recognized species, S. scutisorex Fain, 1970 from Scutisorex somereni Thomas and S. kivuensis Fain, 1981 from Crocidura sp.-both are from DR of Congo-are redescribed. A new species S. sylvisorex sp. nov. found on shrews of the genera Sylvisorex (S. granti Thomas (type host), S. lunaris Thomas, S. vulcanorum Hutterer and Verheyen) and Crocidura (C. denti Dollman, C. cf. niobe, Crocidura sp.), collected in the DR Congo is also described. An amended generic diagnosis, including description of female immature stages, and a key to species are provided.

  9. spr-2, a suppressor of the egg-laying defect caused by loss of sel-12 presenilin in Caenorhabditis elegans, is a member of the SET protein subfamily

    PubMed Central

    Wen, Chenhui; Levitan, Diane; Li, Xiajun; Greenwald, Iva

    2000-01-01

    Presenilin plays critical roles in the genesis of Alzheimer's disease and in LIN-12/Notch signaling during development. Here, we describe a screen for genes that influence presenilin level or activity in Caenorhabditis elegans. We identified four spr (suppressor of presenilin) genes by reverting the egg-laying defective phenotype caused by a null allele of the sel-12 presenilin gene. We analyzed the spr-2 gene in some detail. We show that loss of spr-2 activity suppresses the egg-laying defective phenotype of different sel-12 alleles and requires activity of the hop-1 presenilin gene, suggesting that suppression is accomplished by elevating presenilin activity rather than by bypassing the need for presenilin activity. We also show that SPR-2 is a nuclear protein and is a member of a protein subfamily that includes human SET, which has been identified in numerous different biochemical assays and at translocation breakpoints associated with a subtype of acute myeloid leukemia. PMID:11114162

  10. A signature motif mediating selective interactions of BCL11A with the NR2E/F subfamily of orphan nuclear receptors

    PubMed Central

    Chan, Chun Ming; Fulton, Joel; Montiel-Duarte, Cristina; Collins, Hilary M.; Bharti, Neetu; Wadelin, Frances R.; Moran, Paula M.; Mongan, Nigel P.; Heery, David M.

    2013-01-01

    Despite their physiological importance, selective interactions between nuclear receptors (NRs) and their cofactors are poorly understood. Here, we describe a novel signature motif (F/YSXXLXXL/Y) in the developmental regulator BCL11A that facilitates its selective interaction with members of the NR2E/F subfamily. Two copies of this motif (named here as RID1 and RID2) permit BCL11A to bind COUP-TFs (NR2F1;NR2F2;NR2F6) and Tailless/TLX (NR2E1), whereas RID1, but not RID2, binds PNR (NR2E3). We confirmed the existence of endogenous BCL11A/TLX complexes in mouse cortex tissue. No interactions of RID1 and RID2 with 20 other ligand-binding domains from different NR subtypes were observed. We show that RID1 and RID2 are required for BCL11A-mediated repression of endogenous γ-globin gene and the regulatory non-coding transcript Bgl3, and we identify COUP-TFII binding sites within the Bgl3 locus. In addition to their importance for BCL11A function, we show that F/YSXXLXXL/Y motifs are conserved in other NR cofactors. A single FSXXLXXL motif in the NR-binding SET domain protein NSD1 facilitates its interactions with the NR2E/F subfamily. However, the NSD1 motif incorporates features of both LXXLL and FSXXLXXL motifs, giving it a distinct NR-binding pattern in contrast to other cofactors. In summary, our results provide new insights into the selectivity of NR/cofactor complex formation. PMID:23975195

  11. The Atypical Response Regulator Protein ChxR Has Structural Characteristics and Dimer Interface Interactions That Are Unique within the OmpR/PhoB Subfamily

    SciTech Connect

    Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Hu, Lei; Middaugh, C. Russell; Hefty, P. Scott

    2013-05-29

    Typically as a result of phosphorylation, OmpR/PhoB response regulators form homodimers through a receiver domain as an integral step in transcriptional activation. Phosphorylation stabilizes the ionic and hydrophobic interactions between monomers. Recent studies have shown that some response regulators retain functional activity in the absence of phosphorylation and are termed atypical response regulators. The two currently available receiver domain structures of atypical response regulators are very similar to their phospho-accepting homologs, and their propensity to form homodimers is generally retained. An atypical response regulator, ChxR, from Chlamydia trachomatis, was previously reported to form homodimers; however, the residues critical to this interaction have not been elucidated. We hypothesize that the intra- and intermolecular interactions involved in forming a transcriptionally competent ChxR are distinct from the canonical phosphorylation (activation) paradigm in the OmpR/PhoB response regulator subfamily. To test this hypothesis, structural and functional studies were performed on the receiver domain of ChxR. Two crystal structures of the receiver domain were solved with the recently developed method using triiodo compound I3C. These structures revealed many characteristics unique to OmpR/PhoB subfamily members: typical or atypical. Included was the absence of two {alpha}-helices present in all other OmpR/PhoB response regulators. Functional studies on various dimer interface residues demonstrated that ChxR forms relatively stable homodimers through hydrophobic interactions, and disruption of these can be accomplished with the introduction of a charged residue within the dimer interface. A gel shift study with monomeric ChxR supports that dimerization through the receiver domain is critical for interaction with DNA.

  12. Structure-function analysis of LIV-1, the breast cancer-associated protein that belongs to a new subfamily of zinc transporters.

    PubMed Central

    Taylor, Kathryn M; Morgan, Helen E; Johnson, Andrea; Hadley, Lisa J; Nicholson, Robert I

    2003-01-01

    The LIV-1 gene has been previously associated with oestrogen-positive breast cancer and its metastatic spread to the regional lymph nodes. We have investigated the protein product of this gene as a marker for disease progression of breast cancer. The protein sequence contains a potential metalloprotease motif (HEX P H E XGD), which fits the consensus sequence for the catalytic zinc-binding site motif of the zincin metalloproteases. This motif has identified a new subfamily of ZIP (Zrt-, Irt-like proteins) zinc transporters, which we have termed LZT (LIV-1 subfamily of ZIP zinc transporters). Expression of recombinant LIV-1 in Chinese-hamster ovary cells confirmed the prediction that LZT proteins can act as zinc-influx transporters. Zinc is essential for growth and zinc transporters have an important role in maintaining intracellular zinc homoeostasis, aberrations of which could lead to diseases such as cancer. This is the first report of the expression of a recombinant human LZT protein in mammalian cells. Recombinant LIV-1 locates to the plasma membrane, concentrated in lamellipodiae, similar to membrane-type metalloproteases. Examination of LIV-1 tissue expression located it mainly to hormonally controlled tissues with widespread expression in the brain. Interestingly, the LIV-1 sequence contains a strong PEST site and other potential degradation motifs, which, combined with our evidence that recombinant LIV-1 associates with ubiquitin, may explain the low-level expression of LIV-1. Combining the crucial role that zinc plays in cell growth and the proven role of metalloproteases in metastasis presents an exciting indication of how LIV-1 plays a role in breast cancer progression. PMID:12839489

  13. Evolution and Function of the NR1I Nuclear Hormone Receptor Subfamily (VDR, PXR, and CAR) with Respect to Metabolism of Xenobiotics and Endogenous Compounds

    PubMed Central

    Reschly, E.J.; Krasowski, M.D.

    2008-01-01

    The NR1I subfamily of nuclear hormone receptors includes the 1,25-(OH)2-vitamin D3 receptor (VDR; NR1I1), pregnane X receptor (PXR; NR1I2), and constitutive androstane receptor (CAR; NR1I3). PXR and VDR are found in diverse vertebrates from fish to mammals while CAR is restricted to mammals. Current evidence suggests that the CAR gene arose from a duplication of an ancestral PXR gene, and that PXR and VDR arose from duplication of an ancestral gene, represented now by a single gene in the invertebrate Ciona intestinalis. Aside from the high-affinity effects of 1,25-(OH)2-vitamin D3 on VDRs, the NR1I subfamily members are functionally united by the ability to bind potentially toxic endogenous compounds with low affinity and initiate changes in gene expression that lead to enhanced metabolism and elimination (e.g., induction of cytochrome P450 3A4 expression in humans). The detoxification role of VDR seems limited to sensing high concentrations of certain toxic bile salts, such as lithocholic acid, whereas PXR and CAR have the ability to recognize structurally diverse compounds. PXR and CAR show the highest degree of cross-species variation in the ligand-binding domain of the entire vertebrate nuclear hormone receptor superfamily, suggesting adaptation to species-specific ligands. This review examines the insights that phylogenetic and experimental studies provide into the function of VDR, PXR, and CAR, and how the functions of these receptors have expanded to evolutionary advantage in humans and other animals. PMID:16724925

  14. Homology of the internal sac components in the leaf beetle subfamily Criocerinae and evolutionary novelties related to the extremely elongated flagellum.

    PubMed

    Matsumura, Yoko; Yoshizawa, Kazunori

    2012-05-01

    Extremely elongated intromittent organs are found in a wide range of taxa, especially among insects. This phenomenon is generally thought to result from sexual selection, but it is predicted that limited storage space in the body cavity and the difficulty of using the elongated organs should have constrained the evolution of extreme elongation, neutralizing any selective advantage. Therefore, in groups with long intromittent organs, features that overcome these constraints may have evolved or coevolved together with intromittent organ elongation. Using a comparative morphological approach and outgroup comparisons, we identified potential constraints and key novelties that may neutralize such constraints in the leaf beetle subfamily Criocerinae. Observations of the internal sac structure throughout Criocerinae were performed. Comparing the results with preceding studies from outgroups, a ground plan of the criocerine internal sac was constructed. Our analysis also identified specific features that are always correlated with extreme elongation: the rotation of whole internal-sac sclerites and the possession of a pocket in which to store the elongated flagellum. The pocket is thought to be formed by the rotation of the sclerites, markedly altering internal sac shape from the criocerine ground plan. Onlythe clades that have acquired this derived state contain species with an elongated flagellum that distinctly exceeds the median lobe length. It is presumed that these character correlations evolved independently three times. The detected character correlations corroborate the hypothesis that there are latent adaptive constraints for the evolution of extremely elongated intromittent organs. The constraints may have been neutralized by the alteration from the criocerine ground plan resulting in the formation of a storage pocket. In conclusion, deviation from the criocerine ground plan is considered to be the evolutionary innovation that neutralized the latent adaptive

  15. A multi-locus analysis of phylogenetic relationships within grass subfamily Pooideae (Poaceae) inferred from sequences of nuclear single copy gene regions compared with plastid DNA.

    PubMed

    Hochbach, Anne; Schneider, Julia; Röser, Martin

    2015-06-01

    To investigate phylogenetic relationships within the grass subfamily Pooideae we studied about 50 taxa covering all recognized tribes, using one plastid DNA (cpDNA) marker (matK gene-3'trnK exon) and for the first time four nuclear single copy gene loci. DNA sequence information from two parts of the nuclear genes topoisomerase 6 (Topo6) spanning the exons 8-13 and 17-19, the exons 9-13 encoding plastid acetyl-CoA-carboxylase (Acc1) and the partial exon 1 of phytochrome B (PhyB) were generated. Individual and nuclear combined data were evaluated using maximum parsimony, maximum likelihood and Bayesian methods. All of the phylogenetic results show Brachyelytrum and the tribe Nardeae as earliest diverging lineages within the subfamily. The 'core' Pooideae (Hordeeae and the Aveneae/Poeae tribe complex) are also strongly supported, as well as the monophyly of the tribes Brachypodieae, Meliceae and Stipeae (except PhyB). The beak grass tribe Diarrheneae and the tribe Duthieeae are not monophyletic in some of the analyses. However, the combined nuclear DNA (nDNA) tree yields the highest resolution and the best delimitation of the tribes, and provides the following evolutionary hypothesis for the tribes: Brachyelytrum, Nardeae, Duthieeae, Meliceae, Stipeae, Diarrheneae, Brachypodieae and the 'core' Pooideae. Within the individual datasets, the phylogenetic trees obtained from Topo6 exon 8-13 shows the most interesting results. The divergent positions of some clone sequences of Ampelodesmos mauritanicus and Trikeraia pappiformis, for instance, may indicate a hybrid origin of these stipoid taxa.

  16. Molecular modelling of CYP2F substrates: comparison of naphthalene metabolism by human, rat and mouse CYP2F subfamily enzymes.

    PubMed

    Lewis, David F V; Ito, Yuko; Lake, Brian G

    2009-01-01

    We have constructed three-dimensional molecular models of some cytochrome P450 (CYP) CYP2F subfamily forms via homology with CYP2C5 where sequence identities are in the region of 55%, thus representing high degrees of confidence in the accuracy of the models produced. The three-dimensional structures of these CYP2F enzymes have been compared by molecular overlay, especially with regard to the active site regions, and it would appear that the substitution of a lysine (Lys-301) in human CYP2F1 for the usual glutamate (Glu-301) in mouse CYP2F2, goat CYPF3 and rat CYP2F4 prior to the conserved distal threonine residue may well constitute a significant factor in any species differences between these CYP2F enzymes. Both substrate binding to CYP2F2 and metabolic clearance by CYP2F enzymes correlate with the lipophilicity, parameter, log P (where P is the octanol/water partition coefficient of the substrate). Other features of CYP2F substrate binding are likely to include pi-pi stacking interactions between aromatic rings and hydrogen bonding in some cases. The metabolism of the respiratory toxicant naphthalene is compared and contrasted between three mammalian species, namely mouse, rat and human. The CYPs involved in the metabolic activation and detoxification of naphthalene are discussed in the light of current evidence from both experimental and theoretical studies. It is noted that the CYP2F subfamily enzymes are associated with the activation of naphthalene in all three mammalian species, although there are marked differences between man and the two rodent species in the toxicity of this compound.

  17. Analysis of the grape MYB R2R3 subfamily reveals expanded wine quality-related clades and conserved gene structure organization across Vitis and Arabidopsis genomes

    PubMed Central

    Matus, José Tomás; Aquea, Felipe; Arce-Johnson, Patricio

    2008-01-01

    Background The MYB superfamily constitutes the most abundant group of transcription factors described in plants. Members control processes such as epidermal cell differentiation, stomatal aperture, flavonoid synthesis, cold and drought tolerance and pathogen resistance. No genome-wide characterization of this family has been conducted in a woody species such as grapevine. In addition, previous analysis of the recently released grape genome sequence suggested expansion events of several gene families involved in wine quality. Results We describe and classify 108 members of the grape R2R3 MYB gene subfamily in terms of their genomic gene structures and similarity to their putative Arabidopsis thaliana orthologues. Seven gene models were derived and analyzed in terms of gene expression and their DNA binding domain structures. Despite low overall sequence homology in the C-terminus of all proteins, even in those with similar functions across Arabidopsis and Vitis, highly conserved motif sequences and exon lengths were found. The grape epidermal cell fate clade is expanded when compared with the Arabidopsis and rice MYB subfamilies. Two anthocyanin MYBA related clusters were identified in chromosomes 2 and 14, one of which includes the previously described grape colour locus. Tannin related loci were also detected with eight candidate homologues in chromosomes 4, 9 and 11. Conclusion This genome wide transcription factor analysis in Vitis suggests that clade-specific grape R2R3 MYB genes are expanded while other MYB genes could be well conserved compared to Arabidopsis. MYB gene abundance, homology and orientation within particular loci also suggests that expanded MYB clades conferring quality attributes of grapes and wines, such as colour and astringency, could possess redundant, overlapping and cooperative functions. PMID:18647406

  18. Structure-function analysis of LIV-1, the breast cancer-associated protein that belongs to a new subfamily of zinc transporters.

    PubMed

    Taylor, Kathryn M; Morgan, Helen E; Johnson, Andrea; Hadley, Lisa J; Nicholson, Robert I

    2003-10-01

    The LIV-1 gene has been previously associated with oestrogen-positive breast cancer and its metastatic spread to the regional lymph nodes. We have investigated the protein product of this gene as a marker for disease progression of breast cancer. The protein sequence contains a potential metalloprotease motif (HEX P H E XGD), which fits the consensus sequence for the catalytic zinc-binding site motif of the zincin metalloproteases. This motif has identified a new subfamily of ZIP (Zrt-, Irt-like proteins) zinc transporters, which we have termed LZT (LIV-1 subfamily of ZIP zinc transporters). Expression of recombinant LIV-1 in Chinese-hamster ovary cells confirmed the prediction that LZT proteins can act as zinc-influx transporters. Zinc is essential for growth and zinc transporters have an important role in maintaining intracellular zinc homoeostasis, aberrations of which could lead to diseases such as cancer. This is the first report of the expression of a recombinant human LZT protein in mammalian cells. Recombinant LIV-1 locates to the plasma membrane, concentrated in lamellipodiae, similar to membrane-type metalloproteases. Examination of LIV-1 tissue expression located it mainly to hormonally controlled tissues with widespread expression in the brain. Interestingly, the LIV-1 sequence contains a strong PEST site and other potential degradation motifs, which, combined with our evidence that recombinant LIV-1 associates with ubiquitin, may explain the low-level expression of LIV-1. Combining the crucial role that zinc plays in cell growth and the proven role of metalloproteases in metastasis presents an exciting indication of how LIV-1 plays a role in breast cancer progression.

  19. Cymapamphantus valentineorum, a new genus and species of Pamphantinae (Heteroptera: Lygaeoidea: Geocoridae) from the British Virgin Islands, with a checklist of the species and keys to the tribes and genera of the subfamily

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The new genus and new species Cymapamphantus valentineorum, belonging to the geocorid subfamily Pamphantinae, is described from one brachypterous male and six brachypterous females taken on Guana Island, British Virgin Islands. A dorsal habitus illustration, dorsal and lateral photographs of the ma...

  20. A novel cluster of mariner-like elements belonging to mellifera subfamily from spiders and insects: implications of recent horizontal transfer on the South-West Islands of Japan.

    PubMed

    Yamada, Kaori; Kawanishi, Yuichi; Yamada, Akinori; Tokuda, Gaku; Gurung, Raj Deep; Sasaki, Takeshi; Nakajima, Yumiko; Maekawa, Hideaki

    2014-04-01

    Mariner-like elements (MLEs) have been isolated from various eukaryotic genomes and they are divided into 15 subfamilies, including main five subfamilies: mauritiana, cecropia, mellifera/capitata, irritans, and elegans/briggsae. In the present study, MLEs belonging to mellifera subfamily were isolated from various spiders and insects (Hymenoptera and Lepidoptera) inhabiting the South-West Islands of Japan and neighboring regions. MLEs isolated from 15 different species formed a distinct novel cluster in mellifera subfamily. MLEs obtained from three different species [i.e., the bee Amegilla senahai subflavescens (Amsmar1), the wasp Campsomeris sp. (Casmar1), and the swallowtail butterfly Pachliopta aristolochiae (Paamar1)] contained an intact open reading frame that encoded a putative transposase. These transposases exhibited high similarity of 97.9% among themselves. In case of Casmar1, the presence of an intact ORF was found in high frequencies (i.e., 11 out of 12 clones). In addition, these transposases also showed the presence of a terminal inverted repeat-binding motif, DD(34)D and two highly conserved amino acid motifs, (W/L)(I/L)PHQL and YSP(D/N)L(A/S)P. These two motifs differed from previously known motifs, WVPHEL and YSPDLAP. MLEs isolated from these three different species may have been inserted into their genomes by horizontal transfer. Furthermore, the presence of an intact ORF suggests that they are still active in habitats along these isolated islands.

  1. Leaf and stem CO/sub 2/ uptake in the three subfamilies of the Cactaceae. [Pereskia aculeata; Pereskia grandifolia; Maihuenia poeppigii; Carnegiea gigantea; Ferocactus acanthodes; Coryphantha vivipara; Mammillaria dioica; Opuntia ficus-inidica; Pereskiopsis porteri; Quiabentia chacoensis; Austrocylindropuntia subulata

    SciTech Connect

    Nobel, P.S.; Hartsock, T.L.

    1986-04-01

    Net CO/sub 2/ uptake over 24-hour periods was examined for the leaves and for the stems of 11 species of cacti representing all three subfamilies. For Pereskia aculeata, Pereskia grandifolia, and Maihuenia poeppigii (subfamily Pereskioideae), all the net shoot CO/sub 2/ uptake was by the leaves and during the daytime. In contrast, for the leafless species Carnegiea gigantea, Ferocactus acanthodes, Coryphantha vivipara, and Mammillaria dioica (subfamily Cactoideae), all the shoot net CO/sub 2/ uptake was by the stems and at night. Similarly, for leafless Opuntia ficus-indica (subfamily Opuntioideae), all net CO/sub 2/ uptake occurred at night. For leafy members of the Opuntioideae (Pereskiopsis porteri, Quiabentia chacoensis, Austrocylindropuntia subulata), at least 88% of the shoot CO/sub 2/ uptake over 24 hours was by the leaves and some CO/sub 2/ uptake occurred at night. Leaves responded to the instantaneous level of photosynthetically active radiation (PAR) during the daytime, as occurs for C/sub 3/ plants, whereas nocturnal CO/sub 2/ uptake by stems of O. ficus-indica and F. acanthodes responded to the total daily PAR, as occurs for Crassulacean acid metabolism (CAM) plants. Thus, under the well-watered conditions employed, the Pereskioideae behaved as C/sub 3/ plants, the Cactoideae behaved as CAM plants, and the Opuntioideae exhibited characteristics of both pathways.

  2. Submission to GenBank of the Tonoplast membrane intrinsic protein (TIP) Subfamily in Cotton – GenBank Accession No. GU998831-GU998839 and GenBank Accession TPA;inferential No. BK007053-BK007060

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The tonoplast intrinsic proteins (TIP) are one of the five aquaporin protein subfamilies. Aquaporin proteins are known to facilitate water transport through biological membranes. In order to identify TIP aquaporin gene candidates in cotton (Gossypium hirsutum L.), in silico and molecular cloning eff...

  3. Submission to GenBank of the Small intrinsic protein (SIP) Subfamily in Cotton – GenBank Accession No. GU998846-GU998848 and GenBank Accession TPA;inferential No. BK007063-BK007064

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The small basic intrinsic proteins (SIP) are one of the five aquaporin protein subfamilies. Aquaporin proteins are known to facilitate water transport through biological membranes. In order to identify SIP aquaporin gene candidates in cotton (Gossypium hirsutum L.), in silico and molecular cloning e...

  4. Submission to GenBank of the Nodulin 26-like intrinsic protein (NIP) Subfamily in Cotton – GenBank Accession No. GU998840-GU998845 and GenBank Accession TPA;inferential No. BK007061-BK007062

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The NOD26-like intrinsic proteins (NIP) are one of the five aquaporin protein subfamilies. Aquaporin proteins are known to facilitate water transport through biological membranes. In order to identify NIP aquaporin gene candidates in cotton (Gossypium hirsutum L.), in silico and molecular cloning ef...

  5. Chilean Pitavia more closely related to Oceania and Old World Rutaceae than to Neotropical groups: evidence from two cpDNA non-coding regions, with a new subfamilial classification of the family

    PubMed Central

    Groppo, Milton; Kallunki, Jacquelyn A.; Pirani, José Rubens; Antonelli, Alexandre

    2012-01-01

    Abstract The position of the plant genus Pitavia within an infrafamilial phylogeny of Rutaceae (rue, or orange family) was investigated with the use of two non-coding regions from cpDNA, the trnL-trnF region and the rps16 intron. The only species of the genus, Pitavia punctata Molina, is restricted to the temperate forests of the Coastal Cordillera of Central-Southern Chile and threatened by loss of habitat. The genus traditionally has been treated as part of tribe Zanthoxyleae (subfamily Rutoideae) where it constitutes the monogeneric tribe Pitaviinae. This tribe and genus are characterized by fruits of 1 to 4 fleshy drupelets, unlike the dehiscent fruits typical of the subfamily. Fifty-five taxa of Rutaceae, representing 53 genera (nearly one-third of those in the family) and all subfamilies, tribes, and almost all subtribes of the family were included. Parsimony and Bayesian inference were used to infer the phylogeny; six taxa of Meliaceae, Sapindaceae, and Simaroubaceae, all members of Sapindales, were also used as out-groups. Results from both analyses were congruent and showed Pitavia as sister to Flindersia and Lunasia, both genera with species scattered through Australia, Philippines, Moluccas, New Guinea and the Malayan region, and phylogenetically far from other Neotropical Rutaceae, such as the Galipeinae (Galipeeae, Rutoideae) and Pteleinae (Toddalieae, former Toddalioideae). Additionally, a new circumscription of the subfamilies of Rutaceae is presented and discussed. Only two subfamilies (both monophyletic) are recognized: Cneoroideae (including Dictyolomatoideae, Spathelioideae, Cneoraceae, and Ptaeroxylaceae) and Rutoideae (including not only traditional Rutoideae but also Aurantioideae, Flindersioideae, and Toddalioideae). As a consequence, Aurantioideae (Citrus and allies) is reduced to tribal rank as Aurantieae. PMID:23717188

  6. Cytochrome P450 CYP3A in marsupials: cloning and characterisation of the second identified CYP3A subfamily member, isoform 3A78 from koala (Phascolarctos cinereus).

    PubMed

    El-Merhibi, Adaweyah; Ngo, Suong N T; Crittenden, Tamara A; Marchant, Ceilidh L; Stupans, Ieva; McKinnon, Ross A

    2011-11-01

    Cytochromes P450 (CYPs) are critically important in the oxidative metabolism of a diverse array of xenobiotics and endogenous substrates. Previously, we cloned and characterised the CYP2C, CYP4A, and CYP4B gene subfamilies from marsupials and demonstrated important species-differences in both activity and tissue expression of these CYP enzymes. Recently, we isolated the Eastern grey kangaroo CYP3A70. Here we have cloned and characterised the second identified member of marsupial CYP3A gene subfamily, CYP3A78 from the koala (Phascolarctos cinereus). In addition, we have examined the gender-differences in microsomal erythromycin N-demethylation activity (a CYP3A marker) and CYP3A protein expression across test marsupial species. Significant differences in hepatic erythromycin N-demethylation activity were observed between male and female koalas, with the activity detected in female koalas being 2.5-fold higher compared to that in male koalas (p<0.01). No gender-differences were observed in tammar wallaby or Eastern grey kangaroo. Immunoblot analysis utilising anti-human CYP3A4 antibody detected immunoreactive proteins in liver microsomes from all test male and female marsupials including the koala, tammar wallaby, and Eastern grey kangaroo, with no gender-differences detected across test marsupials. A 1610 bp koala hepatic CYP3A complete cDNA, designated CYP3A78, was cloned by reverse transcription-polymerase chain reaction approaches. It displays 64% nucleotide and 57% amino acid sequence identity to the Eastern grey kangaroo CYP3A70. The CYP3A78 cDNA encodes a protein of 515 amino acids, shares approximately 68% nucleotide and 56% amino acid sequence identity to human CYP3A4, and displays high sequence similarity to other published mammalian CYP3As from human, monkey, cow, pig, dog, rat, rabbit, mouse, hamster, and guinea pig. Collectively, this study provides primary molecular data regarding koala hepatic CYP3A78 gene and enables further functional analyses of CYP

  7. Evolutionary selection across the nuclear hormone receptor superfamily with a focus on the NR1I subfamily (vitamin D, pregnane X, and constitutive androstane receptors)

    PubMed Central

    Krasowski, Matthew D; Yasuda, Kazuto; Hagey, Lee R; Schuetz, Erin G

    2005-01-01

    Background The nuclear hormone receptor (NR) superfamily complement in humans is composed of 48 genes with diverse roles in metabolic homeostasis, development, and detoxification. In general, NRs are strongly conserved between vertebrate species, and few examples of molecular adaptation (positive selection) within this superfamily have been demonstrated. Previous studies utilizing two-species comparisons reveal strong purifying (negative) selection of most NR genes, with two possible exceptions being the ligand-binding domains (LBDs) of the pregnane X receptor (PXR, NR1I2) and the constitutive androstane receptor (CAR, NR1I3), two proteins involved in the regulation of toxic compound metabolism and elimination. The aim of this study was to apply detailed phylogenetic analysis using maximum likelihood methods to the entire complement of genes in the vertebrate NR superfamily. Analyses were carried out both across all vertebrates and limited to mammals and also separately for the two major domains of NRs, the DNA-binding domain (DBD) and LBD, in addition to the full-length sequences. Additional functional data is also reported for activation of PXR and the vitamin D receptor (VDR; NR1I1) to gain further insight into the evolution of the NR1I subfamily. Results The NR genes appear to be subject to strong purifying selection, particularly in the DBDs. Estimates of the ratio of the non-synonymous to synonymous nucleotide substitution rates (the ω ratio) revealed that only the PXR LBD had a sub-population of codons with an estimated ω ratio greater than 1. CAR was also unusual in showing high relative ω ratios in both the DBD and LBD, a finding that may relate to the recent appearance of the CAR gene (presumably by duplication of a pre-mammalian PXR gene) just prior to the evolution of mammals. Functional analyses of the NR1I subfamily show that human and zebrafish PXRs show similar activation by steroid hormones and early bile salts, properties not shared by sea

  8. A review of New Zealand and southeast Australian echinothurioids (Echinodermata: Echinothurioida)-excluding the subfamily Echinothuriinae-with a description of a new species of Tromikosoma.

    PubMed

    Anderson, Owen F

    2016-03-17

    An examination of a large collection of echinothurioid echinoids (excluding the subfamily Echinothuriinae Thomson) from museum collections in New Zealand and Australia has expanded the known diversity of the group in New Zealand from three species in two genera to seven species in five genera, and revealed a new species in the genus Tromikosoma Mortensen.New records for New Zealand and Australia are reported for Sperosoma obscurum Agassiz and Clark, 1907 and S. nudum Shigei, 1978 and new records for New Zealand are reported for Tromikosoma australe (Koehler, 1922) and Kamptosoma asterias (A. Agassiz, 1881). Tromikosoma rugosum sp. nov., remarkable for its unusual wrinkled appearance and exceedingly thin test, is described from deep water in the northeast of New Zealand. No evidence for the existence of Phormosoma rigidum A. Agassiz, 1881 as a species separate from P. bursarium A. Agassiz, 1881 was found, and synonymy with P. bursarium is proposed.Previous records of these echinoid species were rare, as they live mostly in deep water (>1000 m), and three species were previously known from the type material alone. Tromikosoma rugosum sp. nov. now falls into that category, but new material of the other species greatly expands both the number of known records and their geographical distribution. The majority of these new records are from the New Zealand region, with several additional records from south-east Australia.An updated key to the echinothurioids of New Zealand is provided.

  9. A novel DNMT3B subfamily, DeltaDNMT3B, is the predominant form of DNMT3B in non-small cell lung cancer.

    PubMed

    Wang, Luo; Wang, Jie; Sun, Shiyong; Rodriguez, Marivonne; Yue, Ping; Jang, Se Jin; Mao, Li

    2006-07-01

    De novo promoter DNA methylation represses gene transcription and is a common mechanism to inactivate tumor suppressor genes in tumorigenesis. DNMT3B plays an important role in de novo DNA methylation. We report here the identification of a novel DNMT3B subfamily, termed DeltaDNMT3B, whose expression is initiated through a promoter located at intron 4 and exon 5 of the DNMT3B gene. At least 7 transcriptional variants of DeltaDNMT3B have been observed as the result of alternative pre-mRNA splicing. Predicted proteins derived from these variants suggest that 4 of the variants share a conservative enzymatic domain but contain a variable PWWP motif, a putative DNA binding structure, whereas 3 of the variants lack the enzymatic domain due to predicted premature translational termination. In non-small cell lung cancer (NSCLC) cell lines, DeltaDNMT3B variants are frequently expressed and are the predominant forms of DNMT3B. Similarly, DeltaDNMT3B variants are frequently expressed in primary NSCLC but are not detectable or are expressed at low levels in corresponding normal lung tissue. Our results indicate that DeltaDNMT3B is the major expression form of DNMT3B in NSCLC and may play an important role in the development of aberrant promoter methylation during lung tumorigenesis.

  10. A 20(S)-protopanoxadiol derivative overcomes multi-drug resistance by antagonizing ATP-binding cassette subfamily B member 1 transporter function

    PubMed Central

    Chen, Wantao; Xu, Qin; Xiao, Meng; Hu, Lihong; Mao, Li; Wang, Xu

    2016-01-01

    In cancer cells, failure of chemotherapy is often caused by the ATP-binding cassette subfamily B member 1 (ABCB1), and few drugs have been successfully developed to overcome ABCB1-mediated multi-drug resistance (MDR). To suppress ABCB1 activity, we previously designed and synthesized a new series of derivatives based on 20(S)-protopanoxadiol (PPD). In the present study, we investigated the role of PPD derivatives in the function of ABC transporters. Non-toxic concentrations of the PPD derivative PPD12 sensitized ABCB1-overexpressing cells to their anti-cancer substrates better than either the parental PPD or inactive PPD11. PPD12 increased intracellular accumulation of adriamycin and rhodamine123 in resistant cancer cells. Although PPD12 did not suppress the expression of ABCB1 mRNA or protein, it stimulated the activity of ABCB1 ATPase. Because PPD12 is a competitive inhibitor, it was predicted to bind to the large hydrophobic cavity of homology-modeled human ABCB1. PPD12 also enhanced the efficacy of adriamycin against ABCB1-overexpressing KB/VCR xenografts in nude mice. In conclusion, PPD12 enhances the efficacy of substrate drugs in ABCB1-overexpressing cancer cells. These findings suggest that a combination therapy consisting of PPD12 with conventional chemotherapeutic agents may be an effective treatment for ABCB1-mediated MDR cancer patients. PMID:26824187

  11. A systematic review of the subfamily Syringophilinae (Acari: Syringophilidae) of the Nearctic region. Part 1: quill mites associated with passerines (Aves: Passeriformes).

    PubMed

    Skoracki, Maciej; Spicer, Greg S; Oconnor, Barry M

    2016-02-29

    Quill mites belonging to the subfamily Syringophilinae Lavoipierre, 1953 associated with the Nearctic passeriform birds are revised. All of the 49 known species, which are grouped in seven genera, are recorded. Among them, four new species are described: Syringophiloidus audubioni sp. nov. from Spizella breweri (Cassini) (Emberizidae), Syringophilopsis catesbyi sp. nov. from Vireo olivaceus (Linnaeus) (Vireonidae), S. wilsoni sp. nov. from Pheucticus melanocephalus (Swainson) (Cardinalidae), and S. bartrami sp. nov. from Spizella passerina (Bechstein) (Emberizidae). The species Syringophilopsis hylocichlae Clark, 1964 syn. nov. is synonymized with Syringophilopsis turdus (Fritsch, 1958), and Syringophiloidus zonotrichia syn. nov. is synonymized with Betasyringophiloidus seiuri (Clark, 1964) comb. nov. Six species are recorded from the Nearctic region for the first time: Syringophiloidus delichonum Bochkov, 2001, S. glandarii (Fritsch, 1958), S. weiszii Skoracki et al., 2001, S. bombycillae Skoracki, 2002, Syringophilopsis mimidus Sikora et al., 2011, and Torotrogla merulae Skoracki et al., 2000. Data on Nearctic syringophiline species, their hosts and distribution are summarized and the keys to all species are constructed.

  12. The membrane-spanning 4-domains, subfamily A (MS4A) gene cluster contains a common variant associated with Alzheimer's disease

    PubMed Central

    2011-01-01

    Background In order to identify novel loci associated with Alzheimer's disease (AD), we conducted a genome-wide association study (GWAS) in the Spanish population. Methods We genotyped 1,128 individuals using the Affymetrix Nsp I 250K chip. A sample of 327 sporadic AD patients and 801 controls with unknown cognitive status from the Spanish general population were included in our initial study. To increase the power of the study, we combined our results with those of four other public GWAS datasets by applying identical quality control filters and the same imputation methods, which were then analyzed with a global meta-GWAS. A replication sample with 2,200 sporadic AD patients and 2,301 controls was genotyped to confirm our GWAS findings. Results Meta-analysis of our data and independent replication datasets allowed us to confirm a novel genome-wide significant association of AD with the membrane-spanning 4-domains subfamily A (MS4A) gene cluster (rs1562990, P = 4.40E-11, odds ratio = 0.88, 95% confidence interval 0.85 to 0.91, n = 10,181 cases and 14,341 controls). Conclusions Our results underscore the importance of international efforts combining GWAS datasets to isolate genetic loci for complex diseases. PMID:21627779

  13. Modelling and mutational analysis of Aspergillus nidulans UreA, a member of the subfamily of urea/H+ transporters in fungi and plants

    PubMed Central

    Sanguinetti, Manuel; Amillis, Sotiris; Pantano, Sergio; Scazzocchio, Claudio; Ramón, Ana

    2014-01-01

    We present the first account of the structure–function relationships of a protein of the subfamily of urea/H+ membrane transporters of fungi and plants, using Aspergillus nidulans UreA as a study model. Based on the crystal structures of the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT) and of the Nucleobase-Cation-Symport-1 benzylhydantoin transporter from Microbacterium liquefaciens (Mhp1), we constructed a three-dimensional model of UreA which, combined with site-directed and classical random mutagenesis, led to the identification of amino acids important for UreA function. Our approach allowed us to suggest roles for these residues in the binding, recognition and translocation of urea, and in the sorting of UreA to the membrane. Residues W82, Y106, A110, T133, N275, D286, Y388, Y437 and S446, located in transmembrane helixes 2, 3, 7 and 11, were found to be involved in the binding, recognition and/or translocation of urea and the sorting of UreA to the membrane. Y106, A110, T133 and Y437 seem to play a role in substrate selectivity, while S446 is necessary for proper sorting of UreA to the membrane. Other amino acids identified by random classical mutagenesis (G99, R141, A163, G168 and P639) may be important for the basic transporter's structure, its proper folding or its correct traffic to the membrane. PMID:24966243

  14. Role of NH{sub 2}-terminal hydrophobic motif in the subcellular localization of ATP-binding cassette protein subfamily D: Common features in eukaryotic organisms

    SciTech Connect

    Lee, Asaka; Asahina, Kota; Okamoto, Takumi; Kawaguchi, Kosuke; Kostsin, Dzmitry G.; Kashiwayama, Yoshinori; Takanashi, Kojiro; Yazaki, Kazufumi; Imanaka, Tsuneo; Morita, Masashi

    2014-10-24

    Highlights: • ABCD proteins classifies based on with or without NH{sub 2}-terminal hydrophobic segment. • The ABCD proteins with the segment are targeted peroxisomes. • The ABCD proteins without the segment are targeted to the endoplasmic reticulum. • The role of the segment in organelle targeting is conserved in eukaryotic organisms. - Abstract: In mammals, four ATP-binding cassette (ABC) proteins belonging to subfamily D have been identified. ABCD1–3 possesses the NH{sub 2}-terminal hydrophobic region and are targeted to peroxisomes, while ABCD4 lacking the region is targeted to the endoplasmic reticulum (ER). Based on hydropathy plot analysis, we found that several eukaryotes have ABCD protein homologs lacking the NH{sub 2}-terminal hydrophobic segment (H0 motif). To investigate whether the role of the NH{sub 2}-terminal H0 motif in subcellular localization is conserved across species, we expressed ABCD proteins from several species (metazoan, plant and fungi) in fusion with GFP in CHO cells and examined their subcellular localization. ABCD proteins possessing the NH{sub 2}-terminal H0 motif were localized to peroxisomes, while ABCD proteins lacking this region lost this capacity. In addition, the deletion of the NH{sub 2}-terminal H0 motif of ABCD protein resulted in their localization to the ER. These results suggest that the role of the NH{sub 2}-terminal H0 motif in organelle targeting is widely conserved in living organisms.

  15. Inherited surfactant deficiency due to uniparental disomy of rare mutations in the surfactant protein-B and ATP binding cassette, subfamily A, member 3 genes

    PubMed Central

    Hamvas, Aaron; Nogee, Lawrence M.; Wegner, Daniel J.; DePass, Kelcey; Christodoulou, John; Bennetts, Bruce; McQuade, Leon R.; Gray, Peter H.; Deterding, Robin R.; Carroll, Travis R.; Kammesheidt, Anja; Kasch, Laura M.; Kulkarni, Shashikant; Cole, F. Sessions

    2009-01-01

    Objective To characterize inheritance of homozygous, rare, recessive loss-of-function mutations in the surfactant protein-B (SFTPB) or ATP binding cassette, subfamily A, member 3 (ABCA3) genes in newborns with lethal respiratory failure. Study design We resequenced parents whose infants were homozygous for mutations in SFTPB or ABCA3. For infants with only one heterozygous parent, we performed microsatellite analysis for chromosomes 2 (SFTPB) and 16 (ABCA3). Results We identified one infant homozygous for the c.1549C>GAA mutation (121ins2) in SFTPB for whom only the mother was heterozygous and 3 infants homozygous for mutations in ABCA3 (p.K914R, p.P147L, and c.806_7insGCT) for whom only the fathers were heterozygous. For the SP-B deficient infant, microsatellite markers confirmed maternal heterodisomy with segmental isodisomy. Microsatellite analysis confirmed paternal isodisomy for the three ABCA3 deficient infants. Two ABCA3 deficient infants underwent lung transplantation at 3 and 5 months of age, respectively, and two infants died. None exhibited any non-pulmonary phenotype. Conclusions Uniparental disomy should be suspected in infants with rare homozygous mutations in SFTPB or ABCA3. Confirmation of parental carrier status is important to provide recurrence risk and to monitor expression of other phenotypes that may emerge through reduction to homozygosity of recessive alleles. PMID:19647838

  16. Identification of proliferation-induced genes in Arabidopsis thaliana. Characterization of a new member of the highly evolutionarily conserved histone H2A.F/Z variant subfamily.

    PubMed Central

    Callard, D; Mazzolini, L

    1997-01-01

    The changes in gene expression associated with the reinitiation of cell division and subsequent progression through the cell cycle in Arabidopsis thaliana cell-suspension cultures were investigated. Partial synchronization of cells was achieved by a technique combining phosphate starvation and a transient treatment with the DNA replication inhibitor aphidicolin. Six cDNAs corresponding to genes highly induced in proliferating cells and showing cell-cycle-regulated expression were obtained by the mRNA differential display technique. Full-length cDNA clones (cH2BAt and cH2AvAt) corresponding to two of the display products were subsequently isolated. The cH2BAt clone codes for a novel histone H2B protein, whereas the cH2AvAt cDNA corresponds to a gene encoding a new member of the highly conserved histone H2A.F/Z subfamily of chromosomal proteins. Further studies indicated that H2AvAt mRNA expression is tightly correlated with cell proliferation in cell-suspension cultures, and that closely related analogs of the encoded protein exist in Arabidopsis. The implications of the conservation of histone H2A.F/Z variants in plants are discussed. PMID:9414552

  17. Giant panda (Ailuropoda melanoleuca) population dynamics and bamboo (subfamily Bambusoideae) life history: a structured population approach to examining carrying capacity when the prey are semelparous

    USGS Publications Warehouse

    Carter, J.; Ackleh, A.S.; Leonard, B.P.; Wang, Hongfang

    1999-01-01

    The giant panda, Ailuropoda melanoleuca, is a highly specialized Ursid whose diet consists almost entirely of various species of bamboo. Bamboo (Bambusoideae) is a grass subfamily whose species often exhibit a synchronous semelparity. Synchronous semelparity can create local drops in carrying capacity for the panda. We modeled the interaction of pandas and their bamboo food resources with an age structured panda population model linked to a natural history model of bamboo biomass dynamics based on literature values of bamboo biomass, and giant panda life history dynamics. This paper reports the results of our examination of the interaction between pandas and their bamboo food resource and its implications for panda conservation. In the model all panda populations were well below the carrying capacity of the habitat. The giant panda populations growth was most sensitive to changes in birth rates and removal of reproductive aged individuals. Periodic starvation that has been documented in conjunction with bamboo die-offs is probably related to the inability to move to other areas within the region where bamboo is still available. Based on the results of this model, giant panda conservation should concentrate on keeping breeding individuals in the wild, keep corridors to different bamboo species open to pandas, and to concentrate research on bamboo life history.

  18. ABC Transporter Subfamily D: Distinct Differences in Behavior between ABCD1–3 and ABCD4 in Subcellular Localization, Function, and Human Disease

    PubMed Central

    2016-01-01

    ATP-binding cassette (ABC) transporters are one of the largest families of membrane-bound proteins and transport a wide variety of substrates across both extra- and intracellular membranes. They play a critical role in maintaining cellular homeostasis. To date, four ABC transporters belonging to subfamily D have been identified. ABCD1–3 and ABCD4 are localized to peroxisomes and lysosomes, respectively. ABCD1 and ABCD2 are involved in the transport of long and very long chain fatty acids (VLCFA) or their CoA-derivatives into peroxisomes with different substrate specificities, while ABCD3 is involved in the transport of branched chain acyl-CoA into peroxisomes. On the other hand, ABCD4 is deduced to take part in the transport of vitamin B12 from lysosomes into the cytosol. It is well known that the dysfunction of ABCD1 results in X-linked adrenoleukodystrophy, a severe neurodegenerative disease. Recently, it is reported that ABCD3 and ABCD4 are responsible for hepatosplenomegaly and vitamin B12 deficiency, respectively. In this review, the targeting mechanism and physiological functions of the ABCD transporters are summarized along with the related disease. PMID:27766264

  19. Genetic association of aromatic hydrocarbon receptor (AHR) and cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) polymorphisms with dioxin blood concentrations among pregnant Japanese women.

    PubMed

    Kobayashi, Sumitaka; Sata, Fumihiro; Sasaki, Seiko; Ban, Susumu; Miyashita, Chihiro; Okada, Emiko; Limpar, Mariko; Yoshioka, Eiji; Kajiwara, Jumboku; Todaka, Takashi; Saijo, Yasuaki; Kishi, Reiko

    2013-06-07

    Dioxins are metabolized by cytochrome P450, family 1 (CYP1) via the aromatic hydrocarbon receptor (AHR). We determined whether different blood dioxin concentrations are associated with polymorphisms in AHR (dbSNP ID: rs2066853), AHR repressor (AHRR; rs2292596), CYP1 subfamily A polypeptide 1 (CYP1A1; rs4646903 and rs1048963), CYP1 subfamily A polypeptide 2 (CYP1A2; rs762551), and CYP1 subfamily B polypeptide 1 (CYP1B1; rs1056836) in pregnant Japanese women. These six polymorphisms were detected in 421 healthy pregnant Japanese women. Differences in dioxin exposure concentrations in maternal blood among the genotypes were investigated. Comparisons among the GG, GA, and AA genotypes of AHR showed a significant difference (genotype model: P=0.016 for the mono-ortho polychlorinated biphenyl concentrations and toxicity equivalence quantities [TEQs]). Second, we found a significant association with the dominant genotype model ([TT+TC] vs. CC: P=0.048 for the polychlorinated dibenzo-p-dioxin TEQs; P=0.035 for polychlorinated dibenzofuran TEQs) of CYP1A1 (rs4646903). No significant differences were found among blood dioxin concentrations and polymorphisms in AHRR, CYP1A1 (rs1048963), CYP1A2, and CYP1B1. Thus, polymorphisms in AHR and CYP1A1 (rs4646903) were associated with maternal dioxin concentrations. However, differences in blood dioxin concentrations were relatively low.

  20. Potential role of melastatin-related transient receptor potential cation channel subfamily M gene expression in the pathogenesis of urinary bladder cancer

    PubMed Central

    Ceylan, Gülay Güleç; Önalan, Ebru Etem; Kuloğlu, Tuncay; Aydoğ, Gülten; Keleş, İbrahim; Tonyali, Şenol; Ceylan, Cavit

    2016-01-01

    Urinary bladder cancer is one of the most common malignancies of the urinary tract. Ion channels and calcium homeostasis are involved in almost all basic cellular mechanisms. The transient receptor potential cation channel subfamily M (TRPM) takes its name from the melastatin protein, which is classified as potential tumor suppressor. To the best of our knowledge, there have been no previous studies in the literature investigating the role of these ion channels in bladder cancer. The present study aimed to determine whether bladder cancer is associated with mRNA expression levels of TRPM ion channel genes, and whether there is the potential to conduct further studies to establish novel treatment modalities. The present study included a total of 47 subjects, of whom 40 were bladder cancer patients and 7 were controls. Following the histopathological evaluation for bladder carcinoma, the mRNA and protein expression of TRPM were examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry in tumor and normal tissues, in order to determine whether there is a difference in the expression of these channels in tumor and normal tissues. Immunoreactivity for TRPM2, TRPM4, TRPM7 and TRPM8 was observed in epithelial bladder cells in the two groups. RT-qPCR revealed a significant increase in TRPM7 expression in bladder cancer tissue compared to the controls (healthy bladder tissue), whereas no differences in TRPM2 or TRPM4 expression levels were observed. There were significant reductions in the expression levels of TRPM5 and TRPM8 in bladder cancer tissues. In the present study, the effects of TRP ion channels on the formation of bladder cancer was investigated. This study is instructive for TRPM2, TRPM4, TRPM5, TRPM7 and TRPM8 and their therapeutic role in bladder cancer. The results support the fact that these gens can be novel targets and can also be tested for during the treatment of bladder cancer. PMID:28101241

  1. Over-expression in Escherichia coli, purification and reconstitution in liposomes of the third member of the OCTN sub-family: The mouse carnitine transporter OCTN3

    SciTech Connect

    Scalise, Mariafrancesca; Galluccio, Michele; Pochini, Lorena; Indiveri, Cesare

    2012-05-25

    Highlights: Black-Right-Pointing-Pointer mOCTN3 transport protein has been cloned in pET-21a(+) and over-expressed in Escherichia coli. Black-Right-Pointing-Pointer The expressed mOCTN3 has been purified to homogeneity by Ni-chelating chromatography. Black-Right-Pointing-Pointer The protein solubilised in Triton X-100 has been reconstituted in liposomes. Black-Right-Pointing-Pointer Recombinant mOCTN3 catalyses transport of carnitine by a uniport mode. -- Abstract: pET-21a(+)-mOCTN3-6His was constructed and used for over-expression in Escherichia coli Rosetta(DE3)pLysS. After IPTG induction a protein with apparent molecular mass of 53 kDa was collected in the insoluble fraction of the cell lysate and purified by Ni{sup 2+}-chelating chromatography with a yield of 2 mg/l of cell culture. The over-expressed protein was identified with mOCTN3 by anti-His antibody and reconstitution in liposomes. mOCTN3 required peculiar conditions for optimal expression and reconstitution in liposomes. The protein catalyzed a time dependent [{sup 3}H]carnitine uptake which was stimulated by intraliposomal ATP and nearly independent of the pH. The K{sub m} for carnitine was 36 {mu}M. [{sup 3}H]carnitine transport was inhibited by carnitine analogues and some Cys and NH{sub 2} reagents. This paper represents the first outcome in over-expressing, in active form, the third member of the OCTN sub-family, mOCTN3, in E. coli.

  2. Alona iheringula Sinev & Kotov, 2004 (Crustacea, Anomopoda, Chydoridae, Aloninae): Life Cycle and DNA Barcode with Implications for the Taxonomy of the Aloninae Subfamily

    PubMed Central

    Silva, Erika dos Santos; de Abreu, Cínthia Bruno; Orlando, Tereza Cristina; Wisniewski, Célio; dos Santos-Wisniewski, Maria José

    2014-01-01

    Knowledge of reproductive rates and life cycle of the Cladocera species is essential for population dynamic studies, secondary production and food webs, as well as the management and preservation of aquatic ecosystems. The present study aimed to understand the life cycle and growth of Alona iheringula Kotov & Sinev, 2004 (Crustacea, Anomopoda, Chydoridae), a Neotropical species, as well as its DNA barcoding, providing new information on the Aloninae taxonomy. The specimens were collected in the dammed portion of the Cabo Verde River (21°26′05″ S and 46°10′57″ W), in the Furnas Reservoir, Minas Gerais State, Brazil. Forty neonates were observed individually two or three times a day under controlled temperature (25±1°C), photoperiod (12 h light/12 h dark) and feeding (Pseudokirchneriella subcapitata at a concentration of 105 cells.mL−1 and a mixed suspension of yeast and fish feed in equal proportion). Individual body growth was measured daily under optical microscope using a micrometric grid and 40× magnification. The species had a mean size of 413(±29) µm, a maximum size of 510 µm and reached maturity at 3.24(±0.69) days of age. Mean fecundity was 2 eggs per female per brood and the mean number of eggs produced per female during the entire life cycle was 47.6(±6.3) eggs per female. The embryonic development time was 1.79(±0.23) days and the maximum longevity was 54 days. The species had eight instars throughout its life cycle and four instars between neonate and primipara stage. The present study using molecular data (a 461 bp smaller COI fragment) demonstrated a deep divergence in the Aloninae subfamily. PMID:24878503

  3. Association with the Plasma Membrane Is Sufficient for Potentiating Catalytic Activity of Regulators of G Protein Signaling (RGS) Proteins of the R7 Subfamily.

    PubMed

    Muntean, Brian S; Martemyanov, Kirill A

    2016-03-25

    Regulators of G protein Signaling (RGS) promote deactivation of heterotrimeric G proteins thus controlling the magnitude and kinetics of responses mediated by G protein-coupled receptors (GPCR). In the nervous system, RGS7 and RGS9-2 play essential role in vision, reward processing, and movement control. Both RGS7 and RGS9-2 belong to the R7 subfamily of RGS proteins that form macromolecular complexes with R7-binding protein (R7BP). R7BP targets RGS proteins to the plasma membrane and augments their GTPase-accelerating protein (GAP) activity, ultimately accelerating deactivation of G protein signaling. However, it remains unclear if R7BP serves exclusively as a membrane anchoring subunit or further modulates RGS proteins to increase their GAP activity. To directly answer this question, we utilized a rapidly reversible chemically induced protein dimerization system that enabled us to control RGS localization independent from R7BP in living cells. To monitor kinetics of Gα deactivation, we coupled this strategy with measuring changes in the GAP activity by bioluminescence resonance energy transfer-based assay in a cellular system containing μ-opioid receptor. This approach was used to correlate changes in RGS localization and activity in the presence or absence of R7BP. Strikingly, we observed that RGS activity is augmented by membrane recruitment, in an orientation independent manner with no additional contributions provided by R7BP. These findings argue that the association of R7 RGS proteins with the membrane environment provides a major direct contribution to modulation of their GAP activity.

  4. Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases.

    PubMed

    Han, Yun-Bin; Chen, Liu-Qing; Li, Zhuo; Tan, Yu-Meng; Feng, Yan; Yang, Guang-Yu

    2017-03-24

    Endoglycoceramidases (EGCases) specifically hydrolyze the glycosidic linkage between the oligosaccharide and the ceramide moieties of various glycosphingolipids, and they have received substantial attention in the emerging field of glycosphingolipidology. However, the mechanism regulating the strict substrate specificity of these GH5 glycosidases has not been identified. In this study, we report a novel EGCase I from Rhodococcus equi 103S (103S_EGCase I) with remarkably broad substrate specificity. Based on phylogenetic analyses, the enzyme may represent a new subfamily of GH5 glycosidases. The X-ray crystal structures of 103S_EGCase I alone and in complex with its substrates monosialodihexosylganglioside (GM3) and monosialotetrahexosylganglioside (GM1) enabled us to identify several structural features that may account for its broad specificity. Compared with EGCase II from Rhodococcus sp. M-777 (M777_EGCase II), which possesses strict substrate specificity, 103S_EGCase I possesses a longer α7-helix and a shorter loop 4, which forms a larger substrate-binding pocket that could accommodate more extended oligosaccharides. In addition, loop 2 and loop 8 of the enzyme adopt a more open conformation, which also enlarges the oligosaccharide-binding cavity. Based on this knowledge, a rationally designed experiment was performed to examine the substrate specificity of EGCase II. The truncation of loop 4 in M777_EGCase II increased its activity toward GM1 (163%). Remarkably, the S63G mutant of M777_EGCase II showed a broader substrate spectra and significantly increased activity toward bulky substrates (up to >1370-fold for fucosyl-GM1). Collectively, the results presented here reveal the exquisite substrate recognition mechanism of EGCases and provide an opportunity for further engineering of these enzymes.

  5. Kranz and single-cell forms of C4 plants in the subfamily Suaedoideae show kinetic C4 convergence for PEPC and Rubisco with divergent amino acid substitutions

    PubMed Central

    Rosnow, Josh J.; Evans, Marc A.; Kapralov, Maxim V.; Cousins, Asaph B.; Edwards, Gerald E.; Roalson, Eric H.

    2015-01-01

    The two carboxylation reactions performed by phosphoenolpyruvate carboxylase (PEPC) and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) are vital in the fixation of inorganic carbon for C4 plants. The abundance of PEPC is substantially elevated in C4 leaves, while the location of Rubisco is restricted to one of two chloroplast types. These differences compared with C3 leaves have been shown to result in convergent enzyme optimization in some C4 species. Investigation into the kinetic properties of PEPC and Rubisco from Kranz C4, single cell C4, and C3 species in Chenopodiaceae s. s. subfamily Suaedoideae showed that these major carboxylases in C4 Suaedoideae species lack the same mutations found in other C4 systems which have been examined; but still have similar convergent kinetic properties. Positive selection analysis on the N-terminus of PEPC identified residues 364 and 368 to be under positive selection with a posterior probability >0.99 using Bayes empirical Bayes. Compared with previous analyses on other C4 species, PEPC from C4 Suaedoideae species have different convergent amino acids that result in a higher K m for PEP and malate tolerance compared with C3 species. Kinetic analysis of Rubisco showed that C4 species have a higher catalytic efficiency of Rubisco (k catc in mol CO2 mol–1 Rubisco active sites s–1), despite lacking convergent substitutions in the rbcL gene. The importance of kinetic changes to the two-carboxylation reactions in C4 leaves related to amino acid selection is discussed. PMID:26417023

  6. Phylogeny and biogeography of African Murinae based on mitochondrial and nuclear gene sequences, with a new tribal classification of the subfamily

    PubMed Central

    2008-01-01

    Background Within the subfamily Murinae, African murines represent 25% of species biodiversity, making this group ideal for detailed studies of the patterns and timing of diversification of the African endemic fauna and its relationships with Asia. Here we report the results of phylogenetic analyses of the endemic African murines through a broad sampling of murine diversity from all their distribution area, based on the mitochondrial cytochrome b gene and the two nuclear gene fragments (IRBP exon 1 and GHR). Results A combined analysis of one mitochondrial and two nuclear gene sequences consistently identified and robustly supported ten primary lineages within Murinae. We propose to formalize a new tribal arrangement within the Murinae that reflects this phylogeny. The diverse African murine assemblage includes members of five of the ten tribes and clearly derives from multiple faunal exchanges between Africa and Eurasia. Molecular dating analyses using a relaxed Bayesian molecular clock put the first colonization of Africa around 11 Mya, which is consistent with the fossil record. The main period of African murine diversification occurred later following disruption of the migration route between Africa and Asia about 7–9 Mya. A second period of interchange, dating to around 5–6.5 Mya, saw the arrival in Africa of Mus (leading to the speciose endemic Nannomys), and explains the appearance of several distinctive African lineages in the late Miocene and Pliocene fossil record of Eurasia. Conclusion Our molecular survey of Murinae, which includes the most complete sampling so far of African taxa, indicates that there were at least four separate radiations within the African region, as well as several phases of dispersal between Asia and Africa during the last 12 My. We also reconstruct the phylogenetic structure of the Murinae, and propose a new classification at tribal level for this traditionally problematic group. PMID:18616808

  7. Sex difference in induction of hepatic CYP2B and CYP3A subfamily enzymes by nicardipine and nifedipine in rats.

    PubMed

    Konno, Yoshihiro; Sekimoto, Masashi; Nemoto, Kiyomitsu; Degawa, Masakuni

    2004-04-01

    Male and female of F344 rats were treated per os with nicardipine (Nic) and nifedipine (Nif), and changes in the levels of mRNA and protein of hepatic cytochrome P450 (P450) enzymes, CYP2B1, CYP2B2, CYP3A1, CYP3A2, CYP3A9, and CYP3A18 were examined. Furthermore, hepatic microsomal activities for pentoxyresorufin O-dealkylation (PROD) and nifedipine oxidation, which are mainly mediated by CYP2B and CYP3A subfamily enzymes, respectively, were measured. Analyses of RT-PCR and Western blotting revealed that Nic and Nif induced predominantly CYP3A and CYP2B enzymes, respectively. As for the gene activation of CYP2B enzymes, especially CYP2B1, Nif showed high capacity in both sexes of rats, whereas Nic did a definite capacity in the males but little in the females. Gene activations of CYP3A1, CYP3A2, and CYP3A18 by Nic occurred in both sexes of rats, although that of CYP3A9 did only in the male rats. Although gene activations of CYP3A1 and CYP3A2 by Nif were observed in both sexes of rats, a slight activation of the CYP3A9 gene occurred only in female rats, and the CYP3A18 gene activation, in neither male nor female rats. Thus, changes in levels of the mRNA or protein of CYP2B and CYP3A enzymes, especially CYP2B1 and CYP3A2, were closely correlated with those in hepatic PROD and nifedipine oxidation activities, respectively. The present findings demonstrate for the first time the sex difference in the Nic- and Nif-mediated induction of hepatic P450 enzymes in rats and further indicate that Nic and Nif show different specificities and sex dependencies in the induction of hepatic P450 enzymes.

  8. Hom s 4, an IgE-reactive autoantigen belonging to a new subfamily of calcium-binding proteins, can induce Th cell type 1-mediated autoreactivity.

    PubMed

    Aichberger, Karl J; Mittermann, Irene; Reininger, Renate; Seiberler, Susanne; Swoboda, Ines; Spitzauer, Susanne; Kopp, Tamara; Stingl, Georg; Sperr, Wolfgang R; Valent, Peter; Repa, Andreas; Bohle, Barbara; Kraft, Dietrich; Valenta, Rudolf

    2005-07-15

    Skin inflammation in atopic dermatitis starts with Th2 and IgE-mediated responses against exogenous allergens and, for unknown reasons, resembles features of a Th1-driven reaction in the chronic stages. We report the characterization of a human protein, Hom s 4, recognized by IgE autoantibodies from atopic dermatitis patients. The complete Hom s 4 cDNA codes for a 54-kDa basic protein containing two typical calcium-binding domains separated by an unusually long alpha-helical domain. Therefore, Hom s 4 and homologous proteins found by sequence comparison in mice, fruit flies, and nematodes constitute a novel subfamily of calcium-binding proteins. Using Hom s 4-specific Abs, it is demonstrated that the protein is strongly expressed within epidermal keratinocytes and dermal endothelial cells. Purified Hom s 4 showed IgE cross-reactivity with exogenous calcium-binding allergens from plants and fish but, in contrast to the exogenous allergens, induced only weak histamine release from patient basophils. However, the analysis of Hom s 4-specific cytokine and humoral immune responses indicated that Hom s 4 strongly induces Th1 responses which are accompanied by the release of IFN-gamma, a cytokine implicated in epithelial cell damage. Hom s 4-induced IFN-gamma production was found in normal individuals, in patients with chronic inflammatory skin diseases and in Th2-prone atopic persons, suggesting that Hom s 4 represents a protein with an intrinsic property to induce Th1-mediated autoreactivity. It may thus contribute to chronic skin inflammation in atopic as well as in nonatopic persons.

  9. Brother of the regulator of the imprinted site (BORIS) variant subfamily 6 is a novel target of lung cancer stem-like cell immunotherapy.

    PubMed

    Horibe, Ryota; Hirohashi, Yoshihiko; Asano, Takuya; Mariya, Tasuku; Suzuki, Takeshi; Takaya, Akari; Saijo, Hiroshi; Shionoya, Yosuke; Kubo, Terufumi; Nakatsugawa, Munehide; Kanaseki, Takayuki; Tsukahara, Tomohide; Watanabe, Kazue; Atsuyama, Eri; Toji, Shingo; Hirano, Hiroshi; Hasegawa, Tadashi; Takahashi, Hiroki; Sato, Noriyuki; Torigoe, Toshihiko

    2017-01-01

    Lung cancer is one of the most common malignancies with a high rate of mortality. Lung cancer stem-like cells (CSCs)/ cancer-initiating cells (CICs) play major role in resistance to treatments, recurrence and distant metastasis and eradication of CSCs/CICs is crucial to improve recent therapy. Cytotoxic T lymphocytes (CTLs) are major effectors of cancer immunotherapy, and CTLs recognize antigenic peptides derived from antigens that are presented by major histocompatibility complex (MHC) class I molecules. In this study, we analyzed the potency of a cancer-testis (CT) antigen, brother of the regulator of the imprinted site variant subfamily 6 (BORIS sf6), in lung CSC/CIC immunotherapy. BORIS sf6 mRNA was expressed in lung carcinoma cells (9/19), especially in sphere-cultured lung cancer stem-like cells, and in primary lung carcinoma tissues (4/9) by RT-PCR. Immunohistochemical staining using BORIS sf6-specific antibody revealed that high expression of BORIS sf6 is related to poorer prognosis. CTLs could be induced by using a human leukocyte antigen, (HLA)-A2 restricted antigenic peptide (BORIS C34_24(9)), from all of 3 HLA-A2-positive individuals, and CTL clone cells specific for BORIS C34_24(9) peptide could recognize BORIS sf6-positive, HLA-A2-positive lung carcinoma cells. These results indicate that BORIS sf6 is a novel target of lung cancer immunotherapy that might be useful for targeting treatment-resistant lung cancer stem-like cells.

  10. Brother of the regulator of the imprinted site (BORIS) variant subfamily 6 is a novel target of lung cancer stem-like cell immunotherapy

    PubMed Central

    Horibe, Ryota; Hirohashi, Yoshihiko; Asano, Takuya; Mariya, Tasuku; Suzuki, Takeshi; Takaya, Akari; Saijo, Hiroshi; Shionoya, Yosuke; Kubo, Terufumi; Nakatsugawa, Munehide; Kanaseki, Takayuki; Tsukahara, Tomohide; Watanabe, Kazue; Atsuyama, Eri; Toji, Shingo; Hirano, Hiroshi; Hasegawa, Tadashi; Takahashi, Hiroki; Sato, Noriyuki; Torigoe, Toshihiko

    2017-01-01

    Lung cancer is one of the most common malignancies with a high rate of mortality. Lung cancer stem-like cells (CSCs)/ cancer-initiating cells (CICs) play major role in resistance to treatments, recurrence and distant metastasis and eradication of CSCs/CICs is crucial to improve recent therapy. Cytotoxic T lymphocytes (CTLs) are major effectors of cancer immunotherapy, and CTLs recognize antigenic peptides derived from antigens that are presented by major histocompatibility complex (MHC) class I molecules. In this study, we analyzed the potency of a cancer-testis (CT) antigen, brother of the regulator of the imprinted site variant subfamily 6 (BORIS sf6), in lung CSC/CIC immunotherapy. BORIS sf6 mRNA was expressed in lung carcinoma cells (9/19), especially in sphere-cultured lung cancer stem-like cells, and in primary lung carcinoma tissues (4/9) by RT-PCR. Immunohistochemical staining using BORIS sf6-specific antibody revealed that high expression of BORIS sf6 is related to poorer prognosis. CTLs could be induced by using a human leukocyte antigen, (HLA)-A2 restricted antigenic peptide (BORIS C34_24(9)), from all of 3 HLA-A2-positive individuals, and CTL clone cells specific for BORIS C34_24(9) peptide could recognize BORIS sf6-positive, HLA-A2-positive lung carcinoma cells. These results indicate that BORIS sf6 is a novel target of lung cancer immunotherapy that might be useful for targeting treatment-resistant lung cancer stem-like cells. PMID:28248963

  11. Aberrant expression of aldehyde dehydrogenase 1A (ALDH1A) subfamily genes in acute lymphoblastic leukaemia is a common feature of T-lineage tumours.

    PubMed

    Longville, Brooke A C; Anderson, Denise; Welch, Mathew D; Kees, Ursula R; Greene, Wayne K

    2015-01-01

    The class 1A aldehyde dehydrogenase (ALDH1A) subfamily of genes encode enzymes that function at the apex of the retinoic acid (RA) signalling pathway. We detected aberrant expression of ALDH1A genes, particularly ALDH1A2, in a majority (72%) of primary paediatric T cell acute lymphoblastic leukaemia (T-ALL) specimens. ALDH1A expression was almost exclusive to T-lineage, but not B-lineage, ALL. To determine whether ALDH1A expression may have relevance to T-ALL cell growth and survival, the effect of inhibiting ALDH1A function was measured on a panel of human ALL cell lines. This revealed that T-ALL proliferation had a higher sensitivity to modulation of ALDH1A activity and RA signalling as compared to ALL cell lines of B-lineage. Consistent with these findings, the genes most highly correlated with ALDH1A2 expression were involved in cell proliferation and apoptosis. Evidence that such genes may be targets of regulation via RA signalling initiated by ALDH1A activity was provided by the TNFRSF10B gene, encoding the apoptotic death receptor TNFRSF10B (also termed TRAIL-R2), which negatively correlated with ALDH1A2 and showed elevated transcription following treatment of T-ALL cell lines with the ALDH1A inhibitor citral (3,7-dimethyl-2,6-octadienal). These data indicate that ALDH1A expression is a common event in T-ALL and supports a role for these enzymes in the pathobiology of this disease.

  12. An Essential Subfamily of Drs2p-related P-Type ATPases Is Required for Protein Trafficking between Golgi Complex and Endosomal/Vacuolar System

    PubMed Central

    Hua, Zhaolin; Fatheddin, Parvin; Graham, Todd R.

    2002-01-01

    The Saccharomyces cerevisiae genome contains five genes encoding P-type ATPases that are potential aminophospholipid translocases (APTs): DRS2, NEO1, and three uncharacterized open reading frames that we have named DNF1, DNF2, and DNF3 for DRS2/NEO1 family. NEO1 is the only essential gene in APT family and seems to be functionally distinct from the DRS2/DNF genes. The drs2Δ dnf1Δ dnf2Δ dnf3Δ quadruple mutant is inviable, although any one member of this group can maintain viability, indicating that there is a substantial functional overlap between the encoded proteins. We have previously implicated Drs2p in clathrin function at the trans-Golgi network. In this study, we constructed strains carrying all possible viable combinations of null alleles from this group and analyzed them for defects in protein transport. The drs2Δ dnf1Δ mutant grows slowly, massively accumulates intracellular membranes, and exhibits a substantial defect in the transport of alkaline phosphatase to the vacuole. Transport of carboxypeptidase Y to the vacuole is also perturbed, but to a lesser extent. In addition, the dnf1Δ dnf2Δ dnf3Δ mutant exhibits a defect in recycling of GFP-Snc1p in the early endocytic-late secretory pathways. Drs2p and Dnf3p colocalize with the trans-Golgi network marker Kex2p, whereas Dnf1p and Dnf2p seem to localize to the plasma membrane and late exocytic or early endocytic membranes. We propose that eukaryotes express multiple APT subfamily members to facilitate protein transport in multiple pathways. PMID:12221123

  13. Structural and Functional Characterization of a Ruminal β-Glycosidase Defines a Novel Subfamily of Glycoside Hydrolase Family 3 with Permuted Domain Topology*

    PubMed Central

    Ramírez-Escudero, Mercedes; del Pozo, Mercedes V.; Marín-Navarro, Julia; González, Beatriz; Golyshin, Peter N.; Polaina, Julio; Ferrer, Manuel; Sanz-Aparicio, Julia

    2016-01-01

    Metagenomics has opened up a vast pool of genes for putative, yet uncharacterized, enzymes. It widens our knowledge on the enzyme diversity world and discloses new families for which a clear classification is still needed, as is exemplified by glycoside hydrolase family-3 (GH3) proteins. Herein, we describe a GH3 enzyme (GlyA1) from resident microbial communities in strained ruminal fluid. The enzyme is a β-glucosidase/β-xylosidase that also shows β-galactosidase, β-fucosidase, α-arabinofuranosidase, and α-arabinopyranosidase activities. Short cello- and xylo-oligosaccharides, sophorose and gentibiose, are among the preferred substrates, with the large polysaccharide lichenan also being hydrolyzed by GlyA1. The determination of the crystal structure of the enzyme in combination with deletion and site-directed mutagenesis allowed identification of its unusual domain composition and the active site architecture. Complexes of GlyA1 with glucose, galactose, and xylose allowed picturing the catalytic pocket and illustrated the molecular basis of the substrate specificity. A hydrophobic platform defined by residues Trp-711 and Trp-106, located in a highly mobile loop, appears able to allocate differently β-linked bioses. GlyA1 includes an additional C-terminal domain previously unobserved in GH3 members, but crystallization of the full-length enzyme was unsuccessful. Therefore, small angle x-ray experiments have been performed to investigate the molecular flexibility and overall putative shape. This study provided evidence that GlyA1 defines a new subfamily of GH3 proteins with a novel permuted domain topology. Phylogenetic analysis indicates that this topology is associated with microbes inhabiting the digestive tracts of ruminants and other animals, feeding on chemically diverse plant polymeric materials. PMID:27679487

  14. Solution Structure of the Cuz1 AN1 Zinc Finger Domain: An Exposed LDFLP Motif Defines a Subfamily of AN1 Proteins

    PubMed Central

    Sun, Zhen-Yu J.; Bhanu, Meera K.; Allan, Martin G.; Arthanari, Haribabu; Wagner, Gerhard; Hanna, John

    2016-01-01

    Zinc binding domains are common and versatile protein structural motifs that mediate diverse cellular functions. Among the many structurally distinct families of zinc finger (ZnF) proteins, the AN1 domain remains poorly characterized. Cuz1 is one of two AN1 ZnF proteins in the yeast S. cerevisiae, and is a stress-inducible protein that functions in protein degradation through direct interaction with the proteasome and Cdc48. Here we report the solution structure of the Cuz1 AN1 ZnF which reveals a compact C6H2 zinc-coordinating domain that resembles a two-finger hand holding a tri-helical clamp. A central phenylalanine residue sits between the two zinc-coordinating centers. The position of this phenylalanine, just before the penultimate zinc-chelating cysteine, is strongly conserved from yeast to man. This phenylalanine shows an exceptionally slow ring-flipping rate which likely contributes to the high rigidity and stability of the AN1 domain. In addition to the zinc-chelating residues, sequence analysis of Cuz1 indicates a second highly evolutionarily conserved motif. This LDFLP motif is shared with three human proteins—Zfand1, AIRAP, and AIRAP-L—the latter two of which share similar cellular functions with Cuz1. The LDFLP motif, while embedded within the zinc finger domain, is surface exposed, largely uninvolved in zinc chelation, and not required for the overall fold of the domain. The LDFLP motif was dispensable for Cuz1's major known functions, proteasome- and Cdc48-binding. These results provide the first structural characterization of the AN1 zinc finger domain, and suggest that the LDFLP motif may define a sub-family of evolutionarily conserved AN1 zinc finger proteins. PMID:27662200

  15. Lavellodrilus notosetosus sp. nov. (Annelida, Crassiclitellata, Acanthodrilidae): a new Mexican earthworm with uncommon characters, revealed by a preliminary revision of subfamily Acanthodrilinae.

    PubMed

    Fragoso, Carlos; Rojas, Patricia

    2016-08-19

    A new acanthodriline earthworm species, Lavellodrilus notosetosus sp. nov., is described from tropical rain forests of southern Mexico. The new species is placed within the genus Lavellodrilus by the presence of mesial spermathecal pores. It is separated from other species of the genus by the dorsal location of setae cd in most of the body, last hearts in segment 13, first intestinal segment in 20 and genital setae in segment 12. A preliminary morphological revision of all genera and species of Acanthodrilinae was undertaken in order to: i) evaluate if the mesial spermathecal pores justify the status of Lavellodrilus, ii) determine how common (expressed as percentages of species having the character) the diagnostic characters of the new species are in the subfamily, iii) clarify if these characters exhibit a geographical pattern, and iv) contribute towards a comprehensive analysis of the Acanthodrilinae. In this revision, species were separated in nine geographical regions: USA, northern Mexico, southern Mexico, Caribbean Islands (northern hemisphere), and South America, South Africa, Madagascar, Australia, New Zealand, New Caledonia and Antarctic Islands (southern hemisphere). As a result of the revision it was found that among the 511 recognized species of Acanthodrilinae only 11 species have a mesial location of the spermathecal pores, in two cases probably representing monophyletic groups (Lavellodrilus and a group of South African Parachilota species). It was also found that the distinguishing characters in L. notosetosus sp. nov., notably the location of last hearts, genital setae and the first intestinal segment, are uncommon characters in the acanthodriline earthworm fauna of southern Mexico and Central America, but more frequent in North America, the Caribbean, and the southern hemisphere. We conclude that the acanthodrilines from the northern hemisphere are morphologically more similar to those from Australia, New Zealand, and New Caledonia than to those

  16. Molecular and morphological description of Haemoproteus (Parahaemoproteus) bukaka (species nova), a haemosporidian associated with the strictly Australo-Papuan host subfamily Cracticinae.

    PubMed

    Goulding, W; Adlard, R D; Clegg, S M; Clark, N J

    2016-09-01

    Linking morphological studies with molecular phylogeny is important to understanding cryptic speciation and the evolution of host-parasite relationships. Haemosporidian parasites of the Australo-Papuan bird family Artamidae are relatively unstudied. Only one parasite species from the subfamily Cracticinae has been described, and this was based solely on morphological description. This is despite many Cracticinae species being easily observed and abundant over large ranges and in close proximity to human populations. We used morphological and molecular methods to describe a new Haemoproteus species (H. bukaka sp. nov.) from an endemic Butcherbird host (Cracticus louisiadensis) in a relatively unstudied insular area of high avian endemism (Papua New Guinea's Louisiade Archipelago). Phylogenetic reconstructions using parasite cyt-b gene sequences placed the proposed Haemoproteus bukaka sp. nov. close to other host-specialist Haemoproteus species that infect meliphagid honeyeater hosts in the region, e.g. H. ptilotis. Distinct morphological characters of this haemosporidian include macrogametocytes with characteristic large vacuoles opposing a subterminal nucleus on the host cell envelope. Among 27 sampled individuals, prevalence of H. bukaka sp.nov. was high (74 % infection rate) but strongly variable across four islands in the archipelago (ranging from 0 to 100 % prevalence). Parasitaemia levels were low across all infected individuals (0.1-0.6 %). We suspect host density may play a role in maintaining high prevalence given the close proximity and similar physical environments across islands. The findings are discussed in the context of the host genus Cracticus and theory relating to parasite-host evolution and its conservation implications in Papua New Guinea.

  17. Pole orientation, sidereal period, and sense of rotation of asteroids

    NASA Technical Reports Server (NTRS)

    Taylor, R. C.; Gehrels, T.

    1986-01-01

    Pole orientations of asteroids were determined. The method, called photometric astrometry, takes precise epochs of lightcurves into account. Pole determination research on asteroids 532 Herculina, 45 Eugenia, and 3 Juno continues. Discrepancies between various pole determination techniques presently being used are analyzed. The study of asteroid shapes and creating a generalized master pole determination technique also continues which will incorporate the best features of several current methods.

  18. Unusual evolutionary conservation and further species-specific adaptations of a large family of nonclassical MHC class Ib genes across different degrees of genome ploidy in the amphibian subfamily Xenopodinae.

    PubMed

    Edholm, Eva-Stina; Goyos, Ana; Taran, Joseph; De Jesús Andino, Francisco; Ohta, Yuko; Robert, Jacques

    2014-06-01

    Nonclassical MHC class Ib (class Ib) genes are a family of highly diverse and rapidly evolving genes wherein gene numbers, organization, and expression markedly differ even among closely related species rendering class Ib phylogeny difficult to establish. Whereas among mammals there are few unambiguous class Ib gene orthologs, different amphibian species belonging to the anuran subfamily Xenopodinae exhibit an unusually high degree of conservation among multiple class Ib gene lineages. Comparative genomic analysis of class Ib gene loci of two divergent (~65 million years) Xenopodinae subfamily members Xenopus laevis (allotetraploid) and Xenopus tropicalis (diploid) shows that both species possess a large cluster of class Ib genes denoted as Xenopus/Silurana nonclassical (XNC/SNC). Our study reveals two distinct phylogenetic patterns among these genes: some gene lineages display a high degree of flexibility, as demonstrated by species-specific expansion and contractions, whereas other class Ib gene lineages have been maintained as monogenic subfamilies with very few changes in their nucleotide sequence across divergent species. In this second category, we further investigated the XNC/SNC10 gene lineage that in X. laevis is required for the development of a distinct semi-invariant T cell population. We report compelling evidence of the remarkable high degree of conservation of this gene lineage that is present in all 12 species of the Xenopodinae examined, including species with different degrees of ploidy ranging from 2, 4, 8 to 12 N. This suggests that the critical role of XNC10 during early T cell development is conserved in amphibians.

  19. Expression, purification, crystallization and preliminary X-ray analysis of the DNA-binding domain of a Chlamydia trachomatis OmpR/PhoB-subfamily response regulator homolog, ChxR.

    PubMed

    Hickey, John M; Hefty, P Scott; Lamb, Audrey L

    2009-08-01

    Two-component signal transduction systems in bacteria are a primary mechanism for responding to environmental stimuli and adjusting gene expression accordingly. Generally in these systems a sensor kinase phosphorylates a response regulator that regulates transcription. Response regulators contain two domains: a receiver domain and an effector domain. The receiver domain is typically phosphorylated and as a result facilitates the DNA-binding and transcriptional activity of the effector domain. The OmpR/PhoB subfamily is the largest of the response-regulator subfamilies and is primarily defined by the winged helix-turn-helix DNA-binding motif within the effector domain. The overall structure of effector domains is highly conserved and contains three defined elements that are critical for transcriptional regulation: a DNA major-groove binding helix, a DNA minor-groove binding wing and a transcriptional activation loop. These functional elements are often diverse in sequence and conformation and reflect the functional differences observed between individual subfamily members. ChxR from Chlamydia trachomatis is an atypical OmpR/PhoB response regulator homolog that has transcriptional activity in the absence of phosphorylation. To facilitate the precise identification of the functional elements of the ChxR effector domain, this protein was cloned, expressed, purified and crystallized. Crystals were obtained from two separate mother liquors, producing two morphologically distinct crystals. The space group of both crystals was P4(3)2(1)2 (or its enantiomorph P4(1)2(1)2) with isomorphous unit-cell parameters; the crystals diffracted to 2.2-2.5 A resolution.

  20. Amphibious Shelter-Builder Oniscidea Species from the New World with Description of a New Subfamily, a New Genus and a New Species from Brazilian Cave (Isopoda, Synocheta, Styloniscidae)

    PubMed Central

    2015-01-01

    The new subfamily Iuiuniscinae, Styloniscidae, is erected for the new genus Iuiuniscus and the new species I. iuiuensis, which is described from cave of the State of Bahia, Northeastern Brazil. A special ecological character is shown here for the first time for a New World Oniscidea: the construction of mud shelters. An introduction addressing the systematics of Synocheta with emphasis on Styloniscidae Vandel, 1952 is provided, as well as general comments about the dependence of water in some Oniscidea and ecological traits of amphibious Synocheta. The problems referring to nomenclature, taxonomy and the interrelationships in Styloniscidae are discussed. PMID:25992909

  1. Amphibious shelter-builder Oniscidea species from the New World with description of a new subfamily, a new genus and a new species from Brazilian cave (Isopoda, Synocheta, Styloniscidae).

    PubMed

    Souza, Leila A; Ferreira, Rodrigo L; Senna, André R

    2015-01-01

    The new subfamily Iuiuniscinae, Styloniscidae, is erected for the new genus Iuiuniscus and the new species I. iuiuensis, which is described from cave of the State of Bahia, Northeastern Brazil. A special ecological character is shown here for the first time for a New World Oniscidea: the construction of mud shelters. An introduction addressing the systematics of Synocheta with emphasis on Styloniscidae Vandel, 1952 is provided, as well as general comments about the dependence of water in some Oniscidea and ecological traits of amphibious Synocheta. The problems referring to nomenclature, taxonomy and the interrelationships in Styloniscidae are discussed.

  2. [Revision of of the subfamily of Metaracoelophryinae de Puytorac 1972 (Oligohymenophora: Hoplytophryida: Hoplytophryidae), astome ciliates of the digestive tract of Oligochaeta worms of Africa: description of five new species].

    PubMed

    Fokam, Z; Ngassam, P; Nana, P A; Bricheux, G; Bouchard, P; Sime Ngando, T

    2012-02-01

    Five new species belonging to the astome ciliates, living in the digestive tract of Oligochaeta worms belonging to the genus Alma from Cameroon, have been described. The techniques used are: vital staining, staining of the nucleus with Diamidino Phenyl Indol (DAPI), scanning electron microscopy and silver staining method (Fernandez Galiano, 1976, 1994). This work confirms the presence of the genus Paracoelophrya and Dicoelophrya in the digestive track of the oligochaete Alma from Gabon and Cameroon; it helps to understand the general taxonomy of this Metaracoelophryinae subfamily. Moreover, the homogeneity of this group is confirmed and the phylogenetic relationship inside the Hoplitophryida order need more studies to be solved.

  3. Can SINEs: a family of tRNA-derived retroposons specific to the superfamily Canoidea.

    PubMed Central

    Coltman, D W; Wright, J M

    1994-01-01

    A repetitive element of approximately 200 bp was cloned from harbour seal (Phoca vitulina concolour) genomic DNA. The sequence of the element revealed putative RNA polymerase III control boxes, a poly A tail and direct terminal repeats characteristic of SINEs. Sequence and secondary structural similarities suggest that the SINE is derived from a tRNA, possibly tRNA-alanine. Southern blot analysis indicated that the element is predominately dispersed in unique regions of the seal genome, but may also be present in other repetitive sequences, such as tandemly arrayed satellite DNA. Based on slot-blot hybridization analysis, we estimate that 1.3 x 10(6) copies of the SINE are present in the harbour seal genome; SINE copy number based on the number of clones isolated from a size-selected library, however, is an order of magnitude lower (1-3 x 10(5) copies), an estimate consistent with the abundance of SINEs in other mammalian genomes. Database searches found similar sequences have been isolated from dog (Canis familiaris) and mink (Mustela vison). These, and the seal SINE sequences are characterized by an internal CT dinucleotide microsatellite in the tRNA-unrelated region. Hybridization of genomic DNA from representative species of a wide range of mammalian orders to an oligonucleotide (30mer) probe complementary to a conserved region of the SINE confirmed that the element is unique to carnivores of the superfamily Canoidea. Images PMID:8052527

  4. The current source of human Alu retroposons is a conserved gene shared with Old World monkey

    SciTech Connect

    Britten, R.J.; Stout, D.B.; Davidson, E.H. )

    1989-05-01

    A significant fraction of human Alu repeated sequences are members of the precise, recently inserted class. A cloned member of this class has been used as a probe for interspecies hybridization and thermal stability determination. The probe was reassociated with human, mandrill, and spider monkey DNA under conditions such that only almost perfectly matching duplexes could form. Equally precise hybrids were formed with human and mandrill DNA (Old World monkey) but not with spider monkey DNA (New World). These measurements as well as reassociation kinetics show the presence in mandrill DNA of many precise class Alu sequences that are very similar or identical in quantity and sequence to those in human DNA. Human and mandrill are moderately distant species with a single-copy DNA divergence of about 6%. Nevertheless, their recently inserted Alu sequences arise by retroposition of transcripts of source genes with nearly identical sequences. Apparently a gene present in our common ancestor at the time of branching was inherited and highly conserved in sequence in both the lineage of Old World monkeys and the lineage of apes and man.

  5. Molecular evidence from retroposons that whales form a clade within even-toed ungulates.

    PubMed

    Shimamura, M; Yasue, H; Ohshima, K; Abe, H; Kato, H; Kishiro, T; Goto, M; Munechika, I; Okada, N

    1997-08-14

    The origin of whales and their transition from terrestrial life to a fully aquatic existence has been studied in depth. Palaeontological, morphological and molecular studies suggest that the order Cetacea (whales, dolphins and porpoises) is more closely related to the order Artiodactyla (even-toed ungulates, including cows, camels and pigs) than to other ungulate orders. The traditional view that the order Artiodactyla is monophyletic has been challenged by molecular analyses of variations in mitochondrial and nuclear DNA. We have characterized two families of short interspersed elements (SINEs) that were present exclusively in the genomes of whales, ruminants and hippopotamuses, but not in those of camels and pigs. We made an extensive survey of retropositional events that might have occurred during the divergence of whales and even-toed ungulates. We have characterized nine retropositional events of a SINE unit, each of which provides phylogenetic resolution of the relationships among whales, ruminants, hippopotamuses and pigs. Our data provide evidence that whales, ruminants and hippopotamuses form a monophyletic group.

  6. The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers

    PubMed Central

    Smeets, Aude; Loumaye, Eléonore; Clippe, André; Rees, Jean-François; Knoops, Bernard; Declercq, Jean-Paul

    2008-01-01

    The peroxiredoxins (PRDXs) define a superfamily of thiol-dependent peroxidases able to reduce hydrogen peroxide, alkyl hydroperoxides, and peroxynitrite. Besides their cytoprotective antioxidant function, PRDXs have been implicated in redox signaling and chaperone activity, the latter depending on the formation of decameric high-molecular-weight structures. PRDXs have been mechanistically divided into three major subfamilies, namely typical 2-Cys, atypical 2-Cys, and 1-Cys PRDXs, based on the number and position of cysteines involved in the catalysis. We report the structure of the C45S mutant of annelid worm Arenicola marina PRDX6 in three different crystal forms determined at 1.6, 2.0, and 2.4 Å resolution. Although A. marina PRDX6 was cloned during the search of annelid homologs of mammalian 1-Cys PRDX6s, the crystal structures support its assignment to the mechanistically typical 2-Cys PRDX subfamily. The protein is composed of two distinct domains: a C-terminal domain and an N-terminal domain exhibiting a thioredoxin fold. The subunits are associated in dimers compatible with the formation of intersubunit disulfide bonds between the peroxidatic and the resolving cysteine residues in the wild-type enzyme. The packing of two crystal forms is very similar, with pairs of dimers associated as tetramers. The toroid-shaped decamers formed by dimer association and observed in most typical 2-Cys PRDXs is not present. Thus, A. marina PRDX6 presents structural features of typical 2-Cys PRDXs without any formation of toroid-shaped decamers, suggesting that it should function more like a cytoprotective antioxidant enzyme or a modulator of peroxide-dependent cell signaling rather than a molecular chaperone. PMID:18359859

  7. Revision of the Oriental subfamily Heteropteryginae Kirby, 1896, with a re-arrangement of the family Heteropterygidae and the descriptions of five new species of Haaniella Kirby, 1904. (Phasmatodea: Areolatae: Heteropterygidae).

    PubMed

    Hennemann, Frank H; Conle, Oskar V; Brock, Paul D; Seow-Choen, Francis

    2016-09-01

    The areolate Oriental family Heteropterygidae Kirby, 1893 is critically reviewed and the results of the present study contradict the arrangement suggested by Zompro (2004), but in most aspects agree with a molecular study presented by Whiting et al (2003) and a phylogenetic study presented by Bradler (2009). The family is critically discussed and new hypotheses are presented for the phylogeny and intra-familiar relationships, placing the subfamily Dataminae Rehn & Rehn, 1939 as the basalmost clade of Heteropterygidae. The subfamilies Obriminae Brunner v. Wattenwyl, 1893 and Heteropteryginae Kirby, 1893 together represent the sister-group of Dataminae. Arguments and a tree are presented to support this hypothesis. New diagnoses and lists of genera are provided for all three subfamilies contained in Heteropterygidae, along with keys to distinguish between them.        The subfamily Obriminae is critically reviewed and the distinction between the three tribes Obrimini Brunner v. Wattenwyl, 1893, Eubulidini Zompro, 2004 and Miroceramiini Zompro, 2004 introduced by Zompro (2004) is shown to be poorly supported. While Obrimini sensu Zompro, 2004 is generally accepted (but now also contains genera that were placed in Eubulidini or Miroceramiini by Zompro (2004)), the tribes Eubulidini and Miroceramiini are not supported. A new arrangement is introduced, which is based on morphological characters neglected or overlooked by Zompro (2004) but were partly discussed by Bradler (2009). The genus Mearnsiana Rehn & Rehn, 1939 is removed from Miroceramiini and transferred to Obrimini. The genera Eubulides Stål, 1877, Heterocopus Redtenbacher, 1906, Theramenes Stål, 1875 and Stenobrimus Redtenbacher, 1906 are removed from Eubulidini and also transferred to Obrimini. Consequently, Eubulidini is synonymised with Obrimini (n. syn.). Miroceramiini is a monotypical tribe and only includes the Wallacean genus Miroceramia Günther, 1934. The new tribe Tisamenini n. trib. is

  8. ETL, a novel seven-transmembrane receptor that is developmentally regulated in the heart. ETL is a member of the secretin family and belongs to the epidermal growth factor-seven-transmembrane subfamily.

    PubMed

    Nechiporuk, T; Urness, L D; Keating, M T

    2001-02-09

    Using differential display of rat fetal and postnatal cardiomyocytes, we have identified a novel seven-transmembrane receptor, ETL. The cDNA-predicted amino acid sequence of ETL indicated that it encodes a 738-aa protein composed of a large extracellular domain with epidermal growth factor (EGF)-like repeats, a seven-transmembrane domain, and a short cytoplasmic tail. ETL belongs to the secretin family of G-protein-coupled peptide hormone receptors and the EGF-TM7 subfamily of receptors. The latter are characterized by a variable number of extracellular EGF and cell surface domains and conserved seven transmembrane-spanning regions. ETL mRNA expression is up-regulated in the adult rat and human heart. In situ hybridization analyses revealed expression in rat cardiomyocytes and abundant expression in vascular and bronchiolar smooth muscle cells. In COS-7 cells transfected with Myc-tagged rat ETL, rat ETL exists as a stable dimer and undergoes endoproteolytic cleavage of the extracellular domain. The proteolytic activity can be abolished by a specific mutation, T455A, in this domain. In transfected mammalian cells, ETL is associated with cell membranes and is also observed in cytoplasmic vesicles. ETL is the first seven-transmembrane receptor containing EGF-like repeats that is developmentally regulated in the heart.

  9. In Silico/In Vivo Insights into the Functional and Evolutionary Pathway of Pseudomonas aeruginosa Oleate-Diol Synthase. Discovery of a New Bacterial Di-Heme Cytochrome C Peroxidase Subfamily

    PubMed Central

    Estupiñán, Mónica; Álvarez-García, Daniel; Barril, Xavier; Diaz, Pilar; Manresa, Angeles

    2015-01-01

    As previously reported, P. aeruginosa genes PA2077 and PA2078 code for 10S-DOX (10S-Dioxygenase) and 7,10-DS (7,10-Diol Synthase) enzymes involved in long-chain fatty acid oxygenation through the recently described oleate-diol synthase pathway. Analysis of the amino acid sequence of both enzymes revealed the presence of two heme-binding motifs (CXXCH) on each protein. Phylogenetic analysis showed the relation of both proteins to bacterial di-heme cytochrome c peroxidases (Ccps), similar to Xanthomonas sp. 35Y rubber oxidase RoxA. Structural homology modelling of PA2077 and PA2078 was achieved using RoxA (pdb 4b2n) as a template. From the 3D model obtained, presence of significant amino acid variations in the predicted heme-environment was found. Moreover, the presence of palindromic repeats located in enzyme-coding regions, acting as protein evolution elements, is reported here for the first time in P. aeruginosa genome. These observations and the constructed phylogenetic tree of the two proteins, allow the proposal of an evolutionary pathway for P. aeruginosa oleate-diol synthase operon. Taking together the in silico and in vivo results obtained we conclude that enzymes PA2077 and PA2078 are the first described members of a new subfamily of bacterial peroxidases, designated as Fatty acid-di-heme Cytochrome c peroxidases (FadCcp). PMID:26154497

  10. Ig-hepta, a novel member of the G protein-coupled hepta-helical receptor (GPCR) family that has immunoglobulin-like repeats in a long N-terminal extracellular domain and defines a new subfamily of GPCRs.

    PubMed

    Abe, J; Suzuki, H; Notoya, M; Yamamoto, T; Hirose, S

    1999-07-09

    A novel member of the G protein-coupled receptor (GPCR) family was cloned and characterized, which is unique, among the members, in its long extracellular domain comprising Ig-like repeats and in its high expression predominantly in the lung. The clone (Ig-Hepta) was first identified as a polymerase chain reaction product generated with primers designed to amplify secretin receptor family members including the parathyroid hormone-related peptide receptors. Analysis of the open reading frame of cDNAs isolated from a rat lung cDNA library indicated that Ig-Hepta is a protein of 1389 amino acid residues and has two Ig-like repeats in the N-terminal extracellular domain (exodomain) of 1053 amino acid residues and 7 transmembrane spans in the C-terminal region. Northern blot analysis revealed very high expression of its mRNA in the lung and low but detectable levels in the kidney and heart. The mRNA expression in the lung was found to be strongly induced postnatally. Biochemical analysis indicated that Ig-Hepta is a highly glycosylated protein and exists as a disulfide-linked dimer. Immunohistochemistry on rat lung and kidney sections revealed dense localization of Ig-Hepta in alveolar walls and intercalated cells in the collecting duct, respectively, suggesting a role in the regulation of acid-base balance. Ig-Hepta defines a new subfamily of GPCRs.

  11. Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales.

    PubMed

    Nikaido, M; Matsuno, F; Abe, H; Shimamura, M; Hamilton, H; Matsubayashi, H; Okada, N

    2001-12-01

    Short interspersed repetitive elements (SINEs) are a kind of retroposons dispersed among the eukaryotic genomes. Previously, we isolated and characterized a new SINE family, named CHR-2, members of which are distributed in the genomes of cetaceans, hippopotamuses, and ruminants. We analyzed systematically more than a hundred members of the CHR-2 SINEs, which were isolated from the genomes of cetaceans and cow, together with the additional data available in the DNA databases, and showed that these SINEs are divided into at least five distinct subfamilies that share diagnostic nucleotides and/or deletions. A hybridization analysis clearly demonstrated that, among these five subfamilies, two subfamilies, named CD and CDO, are specific to cetaceans and toothed whales, respectively. We reconstruct the evolutionary history of the CHR-2 SINEs during evolution of cetartiodactyl genomes.

  12. Phylogenetic Analysis of the Spider Mite Sub-Family Tetranychinae (Acari: Tetranychidae) Based on the Mitochondrial COI Gene and the 18S and the 5′ End of the 28S rRNA Genes Indicates That Several Genera Are Polyphyletic

    PubMed Central

    Matsuda, Tomoko; Morishita, Maiko; Hinomoto, Norihide; Gotoh, Tetsuo

    2014-01-01

    The spider mite sub-family Tetranychinae includes many agricultural pests. The internal transcribed spacer (ITS) region of nuclear ribosomal RNA genes and the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA have been used for species identification and phylogenetic reconstruction within the sub-family Tetranychinae, although they have not always been successful. The 18S and 28S rRNA genes should be more suitable for resolving higher levels of phylogeny, such as tribes or genera of Tetranychinae because these genes evolve more slowly and are made up of conserved regions and divergent domains. Therefore, we used both the 18S (1,825–1,901 bp) and 28S (the 5′ end of 646–743 bp) rRNA genes to infer phylogenetic relationships within the sub-family Tetranychinae with a focus on the tribe Tetranychini. Then, we compared the phylogenetic tree of the 18S and 28S genes with that of the mitochondrial COI gene (618 bp). As observed in previous studies, our phylogeny based on the COI gene was not resolved because of the low bootstrap values for most nodes of the tree. On the other hand, our phylogenetic tree of the 18S and 28S genes revealed several well-supported clades within the sub-family Tetranychinae. The 18S and 28S phylogenetic trees suggest that the tribes Bryobiini, Petrobiini and Eurytetranychini are monophyletic and that the tribe Tetranychini is polyphyletic. At the genus level, six genera for which more than two species were sampled appear to be monophyletic, while four genera (Oligonychus, Tetranychus, Schizotetranychus and Eotetranychus) appear to be polyphyletic. The topology presented here does not fully agree with the current morphology-based taxonomy, so that the diagnostic morphological characters of Tetranychinae need to be reconsidered. PMID:25289639

  13. Villin promoter-mediated transgenic expression of transient receptor potential cation channel, subfamily V, member 6 (TRPV6) increases intestinal calcium absorption in wild-type and vitamin D receptor knockout mice.

    PubMed

    Cui, Min; Li, Qiang; Johnson, Robert; Fleet, James C

    2012-10-01

    Transient receptor potential cation channel, subfamily V, member 6 (TRPV6) is an apical membrane calcium (Ca) channel in the small intestine proposed to be essential for vitamin D-regulated intestinal Ca absorption. Recent studies have challenged the proposed role for TRPV6 in Ca absorption. We directly tested intestinal TRPV6 function in Ca and bone metabolism in wild-type (WT) and vitamin D receptor knockout (VDRKO) mice. TRPV6 transgenic mice (TG) were made with intestinal epithelium-specific expression of a 3X Flag-tagged human TRPV6 protein. TG and VDRKO mice were crossed to make TG-VDRKO mice. Ca and bone metabolism was examined in WT, TG, VDRKO, and TG-VDRKO mice. TG mice developed hypercalcemia and soft tissue calcification on a chow diet. In TG mice fed a 0.25% Ca diet, Ca absorption was more than three-fold higher and femur bone mineral density (BMD) was 26% higher than WT. Renal 1α hydroxylase (CYP27B1) mRNA and intestinal expression of the natural mouse TRPV6 gene were reduced to <10% of WT but small intestine calbindin-D(9k) expression was elevated >15 times in TG mice. TG-VDRKO mice had high Ca absorption that prevented the low serum Ca, high renal CYP27B1 mRNA, low BMD, and abnormal bone microarchitecture seen in VDRKO mice. In addition, small intestinal calbindin D(9K) mRNA and protein levels were elevated in TG-VDRKO. Transgenic TRPV6 expression in intestine is sufficient to increase Ca absorption and bone density, even in VDRKO mice. VDR-independent upregulation of intestinal calbindin D(9k) in TG-VDRKO suggests this protein may buffer intracellular Ca during Ca absorption. © 2012 American Society for Bone and Mineral Research.

  14. Hedyotis diffusa Willd overcomes 5-fluorouracil resistance in human colorectal cancer HCT-8/5-FU cells by downregulating the expression of P-glycoprotein and ATP-binding casette subfamily G member 2

    PubMed Central

    LI, QIONGYU; WANG, XIANGFENG; SHEN, ALING; ZHANG, YUCHEN; CHEN, YOUQIN; SFERRA, THOMAS J.; LIN, JIUMAO; PENG, JUN

    2015-01-01

    Previous studies have demonstrated that Hedyotis diffusa Willd (HDW), a traditional Chinese herbal medicine, exhibits potent anticancer activity in models of colorectal cancer (CRC). Aggressive forms of CRC exhibit resistance to widely used chemotherapeutic drugs, including the antimetabolite, 5-fluorouracil (5-FU); however, less is known with regard to the activity of HDW against 5-FU-resistant cancer. In the present study, the mechanism of action and the potency of ethanol extracts of HDW (EEHDW) were investigated on a multidrug-resistant CRC HCT-8/5-FU cell line. Using an MTT cell proliferation assay, EEHDW treatment was shown to significantly reduce the cell viability of HCT-8/5-FU cells in a dose- and time-dependent manner. Furthermore, EEHDW significantly increased the retention of the ATP-binding cassette (ABC) transporter substrate, rhodamine-123, as compared with the untreated controls. To further investigate the molecular mechanisms targeted by EEHDW in the resistant cells, the expression levels of the ABC drug transporter protein, P-glycoprotein (P-gp), and ABC subfamily G member 2 (ABCG2), were analyzed using reverse-transcription polymerase chain reaction and western blot analysis. The mRNA and protein expression levels of P-gp and ABCG2 were reduced in the HCT-8/5-FU cells following EEHDW treatment, indicating that EEHDW inhibits ABCG2-mediated drug resistance by downregulating the expression of ABCG2 and P-gp. Therefore, the potential application of EEHDW as a chemotherapeutic adjuvant represents a promising alternative approach to the treatment of drug-resistant CRC. PMID:26640560

  15. Hedyotis diffusa Willd overcomes 5-fluorouracil resistance in human colorectal cancer HCT-8/5-FU cells by downregulating the expression of P-glycoprotein and ATP-binding casette subfamily G member 2.

    PubMed

    Li, Qiongyu; Wang, Xiangfeng; Shen, Aling; Zhang, Yuchen; Chen, Youqin; Sferra, Thomas J; Lin, Jiumao; Peng, Jun

    2015-11-01

    Previous studies have demonstrated that Hedyotis diffusa Willd (HDW), a traditional Chinese herbal medicine, exhibits potent anticancer activity in models of colorectal cancer (CRC). Aggressive forms of CRC exhibit resistance to widely used chemotherapeutic drugs, including the antimetabolite, 5-fluorouracil (5-FU); however, less is known with regard to the activity of HDW against 5-FU-resistant cancer. In the present study, the mechanism of action and the potency of ethanol extracts of HDW (EEHDW) were investigated on a multidrug-resistant CRC HCT-8/5-FU cell line. Using an MTT cell proliferation assay, EEHDW treatment was shown to significantly reduce the cell viability of HCT-8/5-FU cells in a dose- and time-dependent manner. Furthermore, EEHDW significantly increased the retention of the ATP-binding cassette (ABC) transporter substrate, rhodamine-123, as compared with the untreated controls. To further investigate the molecular mechanisms targeted by EEHDW in the resistant cells, the expression levels of the ABC drug transporter protein, P-glycoprotein (P-gp), and ABC subfamily G member 2 (ABCG2), were analyzed using reverse-transcription polymerase chain reaction and western blot analysis. The mRNA and protein expression levels of P-gp and ABCG2 were reduced in the HCT-8/5-FU cells following EEHDW treatment, indicating that EEHDW inhibits ABCG2-mediated drug resistance by downregulating the expression of ABCG2 and P-gp. Therefore, the potential application of EEHDW as a chemotherapeutic adjuvant represents a promising alternative approach to the treatment of drug-resistant CRC.

  16. A factor that regulates the class II major histocompatibility complex gene DPA is a member of a subfamily of zinc finger proteins that includes a Drosophila developmental control protein.

    PubMed Central

    Sugawara, M; Scholl, T; Ponath, P D; Strominger, J L

    1994-01-01

    A novel DNA sequence element termed the J element involved in the regulated expression of class II major histocompatibility complex genes was recently described. To study this element and its role in class II gene regulation further, a cDNA library was screened with oligonucleotide probes containing both the S element and the nearby J element of the human DPA gene. Several DNA clones were obtained by this procedure, one of which, clone 18, is reported and characterized here. It encodes a protein predicted to contain 688 amino acid residues, including 11 zinc finger motifs of the C2H2 type in the C-terminal region, that are Krüppel-like in the conservation of the H/C link sequence connecting them. The 160 N-terminal amino acids in the nonfinger region of clone 18 are highly homologous with similar regions of several other human, mouse, and Drosophila sequences, defining a subfamily of Krüppel-like zinc finger proteins termed TAB (tramtrack [ttk]-associated box) here. One of the Drosophila sequences, ttk, is a developmental control gene, while a second does not contain a zinc finger region but encodes a structure important in oocyte development. An acidic activation domain is located between the N-terminal conserved region of clone 18 and its zinc fingers. This protein appears to require both the S and J elements, which are separated by 10 bp for optimal binding. Antisense cDNA to clone 18 inhibited the expression of a reporter construct containing the DPA promoter, indicating its functional importance in the expression of this class II gene. Images PMID:7969177

  17. Functional analysis of basic transcription element (BTE)-binding protein (BTEB) 3 and BTEB4, a novel Sp1-like protein, reveals a subfamily of transcriptional repressors for the BTE site of the cytochrome P4501A1 gene promoter.

    PubMed Central

    Kaczynski, Joanna A; Conley, Abigail A; Fernandez Zapico, Martin; Delgado, Sharon M; Zhang, Jin-San; Urrutia, Raul

    2002-01-01

    The Sp1-like family of transcription factors is emerging as an integral part of the cellular machinery involved in the control of gene expression. Members of this family of proteins contain three highly homologous C-terminal zinc-finger motifs that bind GC-rich sequences found in the promoters of a diverse number of genes, such as the basic transcription element (BTE) in the promoter of the carcinogen-metabolizing cytochrome P4501A1 (CYP1A1) gene. In the present study, we report the molecular and functional characterization of BTE-binding protein (BTEB) 4, a novel ubiquitously expressed member of the Sp1-like proteins family. This protein represents a new homologue of BTEB1, originally described as a regulator of the BTE site in the CYP1A1 gene promoter. Similarly to the recently described BTEB3, we demonstrate that the N-terminal region of BTEB4 directly represses transcription and binds the co-repressor mSin3A. In addition, we show that the C-terminal zinc-finger domain of BTEB4 binds specifically the BTE site of the CYP1A1 promoter, similar to BTEB1 and BTEB3. Also, we show that both BTEB3 and BTEB4 repress the CYP1A1 gene promoter via the BTE site in HepG2 and BxPC3 cells. Thus the identification of this protein expands the repertoire of BTEB-like members of the Sp1-like protein family involved in transcriptional repression. Furthermore, our results demonstrate that the BTEB subfamily can repress the CYP1A1 gene promoter via the BTE site. PMID:12036432

  18. Upregulated Expression of Transient Receptor Potential Cation Channel Subfamily V Receptors in Mucosae of Patients with Oral Squamous Cell Carcinoma and Patients with a History of Alcohol Consumption or Smoking

    PubMed Central

    Sakakibara, Akiko; Sakakibara, Shunsuke; Kusumoto, Junya; Takeda, Daisuke; Hasegawa, Takumi; Akashi, Masaya; Minamikawa, Tsutomu; Hashikawa, Kazunobu; Terashi, Hiroto; Komori, Takahide

    2017-01-01

    Objectives Transient receptor potential cation channel (subfamily V, members 1–4) (TRPV1–4) are expressed in skin and neurons and activated by external stimuli in normal mucosae of all oral cavity sites. The oral cavity is exposed to various stimuli, including temperature, mechanical stimuli, chemical substances, and changes in pH, and, notably, the risk factors for oncogenic transformation in oral squamous epithelium are the same as the external stimuli received by TRPV1–4 receptors. Hence, we examined the relationship between oral squamous cell carcinoma (SCC) and TRPV1–4 expression. Materials and Methods Oral SCC patients (n = 37) who underwent surgical resection were included in this study. We investigated the expression of TRPV1–4 by immunohistochemical staining and quantification of TRPV1–4 mRNA in human oral mucosa. In addition, we compared the TRPV1–4 levels in mucosa from patients with SCC to those in normal oral mucosa. Results The receptors were expressed in oral mucosa at all sites (tongue, buccal mucosa, gingiva, and oral floor) and the expression was stronger in epithelia from patients with SCC than in normal epithelia. Furthermore, alcohol consumption and tobacco use were strongly associated with the occurrence of oral cancer and were found to have a remarkable influence on TRPV1–4 receptor expression in normal oral mucosa. In particular, patients with a history of alcohol consumption demonstrated significantly higher expression levels. Conclusion Various external stimuli may influence the behavior of cancer cells. Overexpression of TRPV1-4 is likely to be a factor in enhanced sensitivity to external stimuli. These findings could contribute to the establishment of novel strategies for cancer therapy or prevention. PMID:28081185

  19. Characterization of the starch-acting MaAmyB enzyme from Microbacterium aurum B8.A representing the novel subfamily GH13_42 with an unusual, multi-domain organization

    PubMed Central

    Valk, Vincent; van der Kaaij, Rachel M.; Dijkhuizen, Lubbert

    2016-01-01

    The bacterium Microbacterium aurum strain B8.A degrades granular starches, using the multi-domain MaAmyA α-amylase to initiate granule degradation through pore formation. This paper reports the characterization of the M. aurum B8.A MaAmyB enzyme, a second starch-acting enzyme with multiple FNIII and CBM25 domains. MaAmyB was characterized as an α-glucan 1,4-α-maltohexaosidase with the ability to subsequently hydrolyze maltohexaose to maltose through the release of glucose. MaAmyB also displays exo-activity with a double blocked PNPG7 substrate, releasing PNP. In M. aurum B8.A, MaAmyB may contribute to degradation of starch granules by rapidly hydrolyzing the helical and linear starch chains that become exposed after pore formation by MaAmyA. Bioinformatics analysis showed that MaAmyB represents a novel GH13 subfamily, designated GH13_42, currently with 165 members, all in Gram-positive soil dwelling bacteria, mostly Streptomyces. All members have an unusually large catalytic domain (AB-regions), due to three insertions compared to established α-amylases, and an aberrant C-region, which has only 30% identity to established GH13 C-regions. Most GH13_42 members have three N-terminal domains (2 CBM25 and 1 FNIII). This is unusual as starch binding domains are commonly found at the C-termini of α-amylases. The evolution of the multi-domain M. aurum B8.A MaAmyA and MaAmyB enzymes is discussed. PMID:27808246

  20. Cytochrome P450 CYP3A in marsupials: cloning and identification of the first CYP3A subfamily member, isoform 3A70 from Eastern gray kangaroo (Macropus giganteus).

    PubMed

    El-Merhibi, Adaweyah; Ngo, Suong N T; Marchant, Ceilidh L; Height, Tamara A; Stupans, Ieva; McKinnon, Ross A

    2012-09-15

    Australian marsupials are unique fauna that have evolved and adapted to unique environments and thus it is likely that their detoxification systems differ considerably from those of well-studied eutherian mammals. Knowledge of these processes in marsupials is therefore vital to understanding the consequences of exposure to xenobiotics. Cytochromes P450 (CYPs) are critically important in the oxidative metabolism of a diverse array of both xenobiotics and endogenous substrates. In this study we have cloned and characterized CYP3A70, the first identified member of the CYP3A gene subfamily from Eastern gray kangaroo (Macropus giganteus). A 1665 base pair kangaroo hepatic CYP3A complete cDNA, designated CYP3A70, was cloned by reverse transcription-polymerase chain reaction approaches, which encodes a protein of 506 amino acids. The CYP3A70 cDNA shares approximately 71% nucleotide and 65% amino acid sequence homology to human CYP3A4 and displays high sequence similarity to other published mammalian CYP3As from human, monkey, cow, pig, dog, rat, rabbit, mouse, hamster, and guinea pig. Transfection of the CYP3A70 cDNAs into 293T cells resulted in stable cell lines expressing a CYP3A immuno-reactive protein that was recognized by a goat anti-human CYP3A4 polyclonal antibody. The anti-human CYP3A4 antibody also detected immunoreactive proteins in liver microsomes from all test marsupials, including the kangaroo, koala, wallaby, and wombat, with multiple CYP3A immunoreactive bands observed in kangaroo and wallaby tissues. Relatively, very low CYP catalytic activity was detected for the kangaroo CYP3A70 cDNA-expressed proteins (19.6 relative luminescent units/μg protein), which may be due to low protein expression levels. Collectively, this study provides primary molecular data regarding the Eastern kangaroo hepatic CYP3A70 gene and enables further functional analyses of CYP3A enzymes in marsupials.

  1. Nuclear/nucleolar GTPase 2 proteins as a subfamily of YlqF/YawG GTPases function in pre-60S ribosomal subunit maturation of mono- and dicotyledonous plants.

    PubMed

    Im, Chak Han; Hwang, Sung Min; Son, Young Sim; Heo, Jae Bok; Bang, Woo Young; Suwastika, I Nengah; Shiina, Takashi; Bahk, Jeong Dong

    2011-03-11

    The YlqF/YawG families are important GTPases involved in ribosome biogenesis, cell proliferation, or cell growth, however, no plant homologs have yet to be characterized. Here we isolated rice (Oryza sativa) and Arabidopsis nuclear/nucleolar GTPase 2 (OsNug2 and AtNug2, respectively) that belong to the YawG subfamily and characterized them for pre-60S ribosomal subunit maturation. They showed typical intrinsic YlqF/YawG family GTPase activities in bacteria and yeasts with k(cat) values 0.12 ± 0.007 min(-1) (n = 6) and 0.087 ± 0.002 min(-1) (n = 4), respectively, and addition of 60S ribosomal subunits stimulated their activities in vitro. In addition, OsNug2 rescued the lethality of the yeast nug2 null mutant through recovery of 25S pre-rRNA processing. By yeast two-hybrid screening five clones, including a putative one of 60S ribosomal proteins, OsL10a, were isolated. Subcellular localization and pulldown assays resulted in that the N-terminal region of OsNug2 is sufficient for nucleolar/nuclear targeting and association with OsL10a. OsNug2 is physically associated with pre-60S ribosomal complexes highly enriched in the 25S, 5.8S, and 5S rRNA, and its interaction was stimulated by exogenous GTP. Furthermore, the AtNug2 knockdown mutant constructed by the RNAi method showed defective growth on the medium containing cycloheximide. Expression pattern analysis revealed that the distribution of AtNug2 mainly in the meristematic region underlies its potential role in active plant growth. Finally, it is concluded that Nug2/Nog2p GTPase from mono- and didicotyledonous plants is linked to the pre-60S ribosome complex and actively processed 27S into 25S during the ribosomal large subunit maturation process, i.e. prior to export to the cytoplasm.

  2. Co-expression of pregnane X receptor and ATP-binding cassette sub-family B member 1 in peripheral blood: A prospective indicator for drug resistance prediction in non-small cell lung cancer

    PubMed Central

    KONG, QINGNUAN; HAN, ZENGLEI; ZUO, XIAOLI; WEI, HONGJUN; HUANG, WEIQING

    2016-01-01

    The aim of the present study was to investigate the protein expression profiling of pregnane X receptor (PXR) and ATP-binding cassette sub-family B member 1 (ABCB1; also known as MDR1 or P-gp), present in the peripheral blood mononuclear cells (PBMCs) and cancerous tissues of cases of non-small cell lung cancer (NSCLC). Furthermore, the study aimed to assess the feasibility of predicting drug resistance through the medium of PBMCs. Of the subjects included in the study, 37 were histopathologically diagnosed with NSCLC and 17 were control patients without cancer. ThinPrep liquid-based smears with cytosine were applied in the examination of the PBMCs and proved quite effective in preserving the morphology and surface antigens of the lymphocytes. Measurements of expression levels in the PBMCs and cancerous tissues were obtained by immunohistochemical means. The results showed that, with the exception of the selective PXR expression in the normal lung tissues, the two types of proteins existed extensively throughout the PBMCs, normal tissues and tumors. Among the cancer patients, prior to chemotherapy, a significant rise in ABCB1 expression could be observed in the PBMCs, together with a similar rise in ABCB1 and PXR expression in the tumor specimens. Marked upregulation of the two proteins was detected in the PBMCs following 1 cycle of first-line chemotherapy. ABCB1 expression, correlated with PXR, persisted mostly in the PBMCs and tissue samples. When bound to and activated by ligands, PXR translocates from the cytoplasm to the nucleus of the cells. PXR subsequently binds to its DNA response elements as a heterodimer with the retinoid X receptor. A PXR translocation of moderate or low differentiation was identified in 3 cases of adenocarcinoma, which were co-expressing the two genes in the PBMCs prior to chemotherapy. During follow-up visits, tumor recurrence was observed within 3 months in 5 cases, which were characterized by PXR translocation. These findings

  3. Co-expression of pregnane X receptor and ATP-binding cassette sub-family B member 1 in peripheral blood: A prospective indicator for drug resistance prediction in non-small cell lung cancer.

    PubMed

    Kong, Qingnuan; Han, Zenglei; Zuo, Xiaoli; Wei, Hongjun; Huang, Weiqing

    2016-05-01

    The aim of the present study was to investigate the protein expression profiling of pregnane X receptor (PXR) and ATP-binding cassette sub-family B member 1 (ABCB1; also known as MDR1 or P-gp), present in the peripheral blood mononuclear cells (PBMCs) and cancerous tissues of cases of non-small cell lung cancer (NSCLC). Furthermore, the study aimed to assess the feasibility of predicting drug resistance through the medium of PBMCs. Of the subjects included in the study, 37 were histopathologically diagnosed with NSCLC and 17 were control patients without cancer. ThinPrep liquid-based smears with cytosine were applied in the examination of the PBMCs and proved quite effective in preserving the morphology and surface antigens of the lymphocytes. Measurements of expression levels in the PBMCs and cancerous tissues were obtained by immunohistochemical means. The results showed that, with the exception of the selective PXR expression in the normal lung tissues, the two types of proteins existed extensively throughout the PBMCs, normal tissues and tumors. Among the cancer patients, prior to chemotherapy, a significant rise in ABCB1 expression could be observed in the PBMCs, together with a similar rise in ABCB1 and PXR expression in the tumor specimens. Marked upregulation of the two proteins was detected in the PBMCs following 1 cycle of first-line chemotherapy. ABCB1 expression, correlated with PXR, persisted mostly in the PBMCs and tissue samples. When bound to and activated by ligands, PXR translocates from the cytoplasm to the nucleus of the cells. PXR subsequently binds to its DNA response elements as a heterodimer with the retinoid X receptor. A PXR translocation of moderate or low differentiation was identified in 3 cases of adenocarcinoma, which were co-expressing the two genes in the PBMCs prior to chemotherapy. During follow-up visits, tumor recurrence was observed within 3 months in 5 cases, which were characterized by PXR translocation. These findings

  4. Evolution of the Twist Subfamily Vertebrate Proteins: Discovery of a Signature Motif and Origin of the Twist1 Glycine-Rich Motifs in the Amino-Terminus Disordered Domain

    PubMed Central

    Rodriguez, Yacidzohara; Gonzalez-Mendez, Ricardo R.

    2016-01-01

    Twist proteins belong to the basic helix-loop-helix (bHLH) family of multifunctional transcriptional factors. These factors are known to use domains other than the common bHLH in protein-protein interactions. There has been much work characterizing the bHLH domain and the C-terminus in protein-protein interactions but despite a few attempts more focus is needed at the N-terminus. Since the region of highest diversity in Twist proteins is the N-terminus, we analyzed the conservation of this region in different vertebrate Twist proteins and study the sequence differences between Twist1 and Twist2 with emphasis on the glycine-rich regions found in Twist1. We found a highly conserved sequence motif in all Twist1 (SSSPVSPADDSLSNSEEE) and Twist2 (SSSPVSPVDSLGTSEEE) mammalian species with unknown function. Through sequence comparison we demonstrate that the Twist protein family ancestor was “Twist2-like” and the two glycine-rich regions found in Twist1 sequences were acquired late in evolution, apparently not at the same time. The second glycine-rich region started developing first in the fish vertebrate group, while the first glycine region arose afterwards within the reptiles. Disordered domain and secondary structure predictions showed that the amino acid sequence and disorder feature found at the N-terminus is highly evolutionary conserved and could be a functional site that interacts with other proteins. Detailed examination of the glycine-rich regions in the N-terminus of Twist1 demonstrate that the first region is completely aliphatic while the second region contains some polar residues that could be subject to post-translational modification. Phylogenetic and sequence space analysis showed that the Twist1 subfamily is the result of a gene duplication during Twist2 vertebrate fish evolution, and has undergone more evolutionary drift than Twist2. We identified a new signature motif that is characteristic of each Twist paralog and identified important residues

  5. Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins

    PubMed Central

    Nikaido, Masato; Matsuno, Fumio; Hamilton, Healy; Brownell, Robert L.; Cao, Ying; Ding, Wang; Zuoyan, Zhu; Shedlock, Andrew M.; Fordyce, R. Ewan; Hasegawa, Masami; Okada, Norihiro

    2001-01-01

    SINE (short interspersed element) insertion analysis elucidates contentious aspects in the phylogeny of toothed whales and dolphins (Odontoceti), especially river dolphins. Here, we characterize 25 informative SINEs inserted into unique genomic loci during evolution of odontocetes to construct a cladogram, and determine a total of 2.8 kb per taxon of the flanking sequences of these SINE loci to estimate divergence times among lineages. We demonstrate that: (i) Odontocetes are monophyletic; (ii) Ganges River dolphins, beaked whales, and ocean dolphins diverged (in this order) after sperm whales; (iii) three other river dolphin taxa, namely the Amazon, La Plata, and Yangtze river dolphins, form a monophyletic group with Yangtze River dolphins being the most basal; and (iv) the rapid radiation of extant cetacean lineages occurred some 28–33 million years B.P., in strong accord with the fossil record. The combination of SINE and flanking sequence analysis suggests a topology and set of divergence times for odontocete relationships, offering alternative explanations for several long-standing problems in cetacean evolution. PMID:11416211

  6. Differential alu mobilization and polymorphism among the human and chimpanzee lineages.

    PubMed

    Hedges, Dale J; Callinan, Pauline A; Cordaux, Richard; Xing, Jinchuan; Barnes, Erin; Batzer, Mark A

    2004-06-01

    Alu elements are primate-specific members of the SINE (short interspersed element) retroposon family, which comprise approximately 10% of the human genome. Here we report the first chromosomal-level comparison examining the Alu retroposition dynamics following the divergence of humans and chimpanzees. We find a twofold increase in Alu insertions in humans in comparison to the common chimpanzee (Pan troglodytes). The genomic diversity (polymorphism for presence or absence of the Alu insertion) associated with these inserts indicates that, analogous to recent nucleotide diversity studies, the level of chimpanzee Alu diversity is approximately 1.7 times higher than that of humans. Evolutionarily recent Alu subfamily structure differs markedly between the human and chimpanzee lineages, with the major human subfamilies remaining largely inactive in the chimpanzee lineage. We propose a population-based model to account for the observed fluctuation in Alu retroposition rates across primate taxa.

  7. The Sidereal Time Variations of the Lorentz Force and Maximum Attainable Speed of Electrons

    NASA Astrophysics Data System (ADS)

    Nowak, Gabriel; Wojtsekhowski, Bogdan; Roblin, Yves; Schmookler, Barak

    2016-09-01

    The Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab produces electrons that orbit through a known magnetic system. The electron beam's momentum can be determined through the radius of the beam's orbit. This project compares the beam orbit's radius while travelling in a transverse magnetic field with theoretical predictions from special relativity, which predict a constant beam orbit radius. Variations in the beam orbit's radius are found by comparing the beam's momentum entering and exiting a magnetic arc. Beam position monitors (BPMs) provide the information needed to calculate the beam momentum. Multiple BPM's are included in the analysis and fitted using the method of least squares to decrease statistical uncertainty. Preliminary results from data collected over a 24 hour period show that the relative momentum change was less than 10-4. Further study will be conducted including larger time spans and stricter cuts applied to the BPM data. The data from this analysis will be used in a larger experiment attempting to verify special relativity. While the project is not traditionally nuclear physics, it involves the same technology (the CEBAF accelerator) and the same methods (ROOT) as a nuclear physics experiment. DOE SULI Program.

  8. Computer Simulation of Replaceable Many Sider Plates (RMSP) with Enhanced Chip-Breaking Characteristics

    NASA Astrophysics Data System (ADS)

    Korchuganova, M.; Syrbakov, A.; Chernysheva, T.; Ivanov, G.; Gnedasch, E.

    2016-08-01

    Out of all common chip curling methods, a special tool face form has become the most widespread which is developed either by means of grinding or by means of profile pressing in the production process of RMSP. Currently, over 15 large tool manufacturers produce tools using instrument materials of over 500 brands. To this, we must add a large variety of tool face geometries, which purpose includes the control over form and dimensions of the chip. Taking into account all the many processed materials, specific tasks of the process planner, requirements to the quality of manufactured products, all this makes the choice of a proper tool which can perform the processing in the most effective way significantly harder. Over recent years, the nomenclature of RMSP for lathe tools with mechanical mounting has been considerably broadened by means of diversification of their faces

  9. Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths).

    PubMed

    Möller-Krull, Maren; Delsuc, Frédéric; Churakov, Gennady; Marker, Claudia; Superina, Mariella; Brosius, Jürgen; Douzery, Emmanuel J P; Schmitz, Jürgen

    2007-11-01

    Armadillos, anteaters, and sloths (Order Xenarthra) comprise 1 of the 4 major clades of placental mammals. Isolated in South America from the other continental landmasses, xenarthrans diverged over a period of about 65 Myr, leaving more than 200 extinct genera and only 31 living species. The presence of both ancestral and highly derived anatomical features has made morphoanatomical analyses of the xenarthran evolutionary history difficult, and previous molecular analyses failed to resolve the relationships within armadillo subfamilies. We investigated the presence/absence patterns of retroposons from approximately 7,400 genomic loci, identifying 35 phylogenetically informative elements and an additional 39 informative rare genomic changes (RGCs). DAS-short interspersed elements (SINEs), previously described only in the Dasypus novemcinctus genome, were found in all living armadillo genera, including the previously unsampled Chlamyphorus, but were noticeably absent in sloths. The presence/absence patterns of the phylogenetically informative retroposed elements and other RGCs were then compared with data from the DNA sequences of the more than 12-kb flanking regions of these retroposons. Together, these data provide the first fully resolved genus tree of xenarthrans. Interestingly, multiple evidence supports the grouping of Chaetophractus and Zaedyus as a sister group to Euphractus within Euphractinae, an association that was not previously demonstrated. Also, flanking sequence analyses favor a close phylogenetic relationship between Cabassous and Tolypeutes within Tolypeutinae. Finally, the phylogenetic position of the subfamily Chlamyphorinae is resolved by the noncoding sequence data set as the sister group of Tolypeutinae. The data provide a stable phylogenetic framework for further evolutionary investigations of xenarthrans and important information for defining conservation priorities to save the diversity of one of the most curious groups of mammals.

  10. Expansion of CORE-SINEs in the genome of the Tasmanian devil

    PubMed Central

    2012-01-01

    Background The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species’ survival. To better understand the Tasmanian devil genome, we screened it for transposable elements and investigated the dynamics of short interspersed element (SINE) retroposons. Results The temporal history of Tasmanian devil SINEs, elucidated using a transposition in transposition analysis, indicates that WSINE1, a CORE-SINE present in around 200,000 copies, is the most recently active element. Moreover, we discovered a new subtype of WSINE1 (WSINE1b) that comprises at least 90% of all Tasmanian devil WSINE1s. The frequencies of WSINE1 subtypes differ in the genomes of two of the other Australian marsupial orders. A co-segregation analysis indicated that at least 66 subfamilies of WSINE1 evolved during the evolution of Dasyuromorphia. Using a substitution rate derived from WSINE1 insertions, the ages of the subfamilies were estimated and correlated with a newly established phylogeny of Dasyuromorphia. Phylogenetic analyses and divergence time estimates of mitochondrial genome data indicate a rapid radiation of the Tasmanian devil and the closest relative the quolls (Dasyurus) around 14 million years ago. Conclusions The radiation and abundance of CORE-SINEs in marsupial genomes indicates that they may be a major player in the evolution of marsupials. It is evident that the early phases of evolution of the carnivorous marsupial order Dasyuromorphia was characterized by a burst of SINE activity. A correlation between a speciation event and a major burst of retroposon activity is for the first time shown in a marsupial genome. PMID:22559330

  11. MicroRNA-320a and microRNA-4496 attenuate Helicobacter pylori cytotoxin-associated gene A (CagA)-induced cancer-initiating potential and chemoresistance by targeting β-catenin and ATP-binding cassette, subfamily G, member 2.

    PubMed

    Kang, Dong Woo; Yang, Eun Sun; Noh, Yu Na; Hwang, Won Chan; Jo, Se-Young; Suh, Young-Ah; Park, Won Sang; Choi, Kang-Yell; Min, Do Sik

    2017-04-01

    Infection with Helicobacter pylori is closely linked to an increased risk of gastric cancer. Although cytotoxin-associated gene A (CagA), a major virulence factor of H. pylori, is known to be a causal factor for gastric carcinogenesis, the molecular link between CagA and gastric cancer-initiating cell (CIC)-like properties remains elusive. Here, we demonstrate that CagA is required for increased expression of β-catenin and its target CIC markers via downregulation of microRNA (miR)-320a and miR-4496. CagA promoted gastric CIC properties and was responsible for chemoresistance. miR-320a and miR-4496 attenuated the in vitro self-renewal and tumour-initiating capacity of CagA-expressing CICs by targeting β-catenin. Moreover, miR-320a and miR-4496 decreased CagA-induced chemoresistance by targeting ATP-binding cassette, subfamily G, member 2 (ABCG2) at the transcriptional and post-transcriptional levels, respectively. Combination therapy with 5-fluorouracil and miR-320a/miR-4496 suppressed gastric tumourigenesis and metastatic potential in an orthotopic mouse model, probably via suppression of CagA-induced CIC properties and chemoresistance. Our results provide novel evidence that CIC properties, chemoresistance and tumourigenesis associated with H. pylori are linked to CagA-induced upregulation of β-catenin and ABCG2. These data provide novel insights into the molecular mechanisms of CagA-induced carcinogenisis and the therapeutic potential of of miR-320a and miR-4496. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  12. Observations of Large Scale Sidereal Anisotropy in 1 and 11 TeV cosmic rays from the MINOS experiment

    SciTech Connect

    de Jong, J.K.

    2012-01-01

    The MINOS Near and Far Detectors are two large, functionally-identical, steel-scintillating sampling calorimeters located at depths of 220 mwe and 2100 mwe respectively. The detectors observe the muon component of hadronic showers produced from cosmic ray interactions with nuclei in the earth's atmosphere. From the arrival direction of these muons, the anisotropy in arrival direction of the cosmic ray primaries can be determined. The MINOS Near and Far Detector have observed anisotropy on the order of 0.1% at 1 and 11 TeV respectively. The amplitude and phase of the first harmonic at 1 TeV are 8.2 {+-} 1.7(stat.) x 10{sup -4} and (8.9 {+-} 12.1(stat.)){sup o}, and at 11 TeV are 3.8 {+-} 0.5(stat.) x 10{sup -4} and (27.2 {+-} 7.2(stat.)){sup o}.

  13. Pr77 and L1TcRz

    PubMed Central

    Sánchez-Luque, Francisco; López, Manuel C.; Macias, Francisco; Alonso, Carlos; Thomas, M. Carmen

    2012-01-01

    The sequence corresponding to the first 77 nucleotides of the L1Tc and NARTc non-LTR retrotransposons from Trypanosoma cruzi is an internal promoter (Pr77) that generates abundant, although poorly translatable, un-spliced transcripts. It has been recently described that L1TcRz, an HDV-like ribozyme, resides within the 5′-end of the RNA from the L1Tc and NARTc retrotransposons. Remarkably, the same first 77 nucleotides of L1Tc/NARTc elements comprise both the Pr77 internal promoter and the HDV-like L1TcRz. The L1TcRz cleaves on the 5′-side of the +1 nucleotide of the L1Tc element insuring that the promoter and the ribozyme functions travel with the transposon during retrotransposition. The ribozyme activity would prevent the mobilization of upstream sequences and insure the individuality of the L1Tc/NARTc copies transcribed from associated tandems. The Pr77/L1TcRz sequence is also found in other trypanosomatid’s non-LTR retrotransposons and degenerated retroposons. The possible conservation of the ribozyme activity in a widely degenerated retrotransposon, as the Leishmania SIDERs, could indicate that the presence of this element and the catalytic activity could play some favorable genetic regulation. The functional implications of the Pr77/L1TcRz dual system in the regulation of the L1Tc/NARTc retrotransposons and in the gene expression of trypanosomatids are also discussed in this paper. PMID:22754746

  14. Spatiotemporal dynamics of immature culicines (subfamily Culicinae) and their larval habitats in Mwea Rice Scheme, Kenya.

    PubMed

    Muturi, Ephantus J; Mwangangi, Joseph M; Jacob, Benjamin G; Shililu, Josephat I; Mbogo, Charles M; Githure, John I; Novak, Robert J

    2009-03-01

    An ecological study was conducted at three study sites in Mwea Rice Scheme, Kenya to identify the diverse aquatic habitats in which culicine mosquitoes thrived and to explore the best strategies for mosquito control in the area. During the 11-month study period, ten habitat categories and 11 culicine species mainly dominated by Culex quinquefasciatus (72.0%) and Culex annulioris (17.9%) were identified from pupae and late instars larval samples. Two of the 11 culicine species, Ficalbia (Mimomyia) plumosa and Uranotaenia spp., have not been reported previously in the study area. Rurumi had more habitat types than either of the other study sites but the least number of mosquito species. In contrast, Karima had the least number of habitat types but significantly higher density of early instars than the other study sites. The relative abundance of late instars and pupae did not vary significantly among study sites. The contribution of different habitat types to larval production varied markedly between seasons and among study sites. Paddies and canals were perennial contributors of culicine mosquito larvae while the other habitat types were important mainly during the wet season. Some habitat types such as ditches, seeps, marshes, and fishpond were absent in some study sites but of great significance in other study sites. C. quinquefasciatus was positively associated with turbidity at all study sites and also negatively associated with emergent vegetation and distance to the nearest homestead in Karima, emergent vegetation in Kiuria, and other aquatic invertebrates in Rurumi. C. annulioris was positively associated with emergent vegetation at all study sites and also with depth in Kiuria. These findings indicate that besides rice fields and associated habitats, a diversity of other aquatic habitats contribute to culicine adult mosquito production in the study area and that environmental factors that determine the occurrence of a particular mosquito species may vary significantly even among areas of similar land use. This information is critical when designing and implementing mosquito larval control programs.

  15. A QUICK KEY TO THE SUBFAMILIES AND GENERA OF ANTS OF THE SAVANNAH RIVER SITE

    SciTech Connect

    Martin, D

    2007-09-04

    This taxonomic key was devised to support development of a Rapid Bioassessment Protocol using ants at the Savannah River Site. The emphasis is on 'rapid' and, because the available keys contained a very large number of genera not known to occur at the Savannah River Site, we found that the available keys were unwieldy. Because these keys contained many more genera than we would ever encounter and because this larger number of genera required more couplets in the key and often required examination of characters that are difficult to assess without higher magnifications (60X or higher), more time was required to process samples. In developing this set of keys I emphasized character states that are easier for nonspecialists to recognize. I recognize that the character sets used may lead to some errors but I believe that the error rate will be small and, for the purpose of rapid bioassessment, this error rate will be acceptable provided that overall sample sizes are adequate. Oliver and Beattie (1996a, 1996b) found that for rapid assessment of biodiversity the same results were found when identifications were done to morphospecies by people with minimal expertise as when the same data sets were identified by subject matter experts. Basset et al. (2004) concluded that it was not as important to correctly identify all species as it was to be sure that the study included as many functional groups as possible. If your study requires high levels of accuracy, it is highly recommended that, when you key out a specimen and have any doubts concerning the identification, you should refer to keys in Bolton (1994) or to the other keys used to develop this area specific taxonomic key.

  16. Intergeneric hybrids in Rosaceae subtribe Pyrinae (formerly subfamily Maloideae) at USDA genebank

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The USDA Agricultural Research Service maintains clonal germplasm collections representing world diversity of Pyrus, Cydonia and Mespilus at its National Clonal Germplasm Repository in Corvallis, Oregon, USA. Smaller collections of Amelanchier, Aronia, Crataegus, Sorbus and other genera in Rosaceae ...

  17. Attraction of tortricid moths of subfamily olethreutinae to field traps baited with dodecadienes.

    PubMed

    Chisholm, M D; Reed, D W; Underhill, E W; Palaniswamy, P; Wong, J W

    1985-02-01

    All four geometrical isomers of 7,9- and 8,10-dodecadienes with acetate, alcohol, and aldehyde functional groups were synthesized and field tested. The field survey produced sex attractant lures for 14 insect species. Species in the generaCydia, Grapholita, Eucosma, Pelochrista, Petrova, Phenta, Hedya, and Pseudosciaphila were captured. Defined lures were developed for some of the species captured. Gas chromatographie retention times for all geometrical isomers of 7,9- and 8,10-dodecadienes with acetate, alcohol, and aldehyde functional groups are reported. A study of the isomerization of 8,10-dodecadienyl acetates and aldehydes impregnated in rubber septa is reported.

  18. Phylogeny and evolution of the auks (subfamily Alcinae) based on mitochondrial DNA sequences

    USGS Publications Warehouse

    Moum, Truls; Johansen, Steinar; Erikstad, Kjell Einar; Piatt, John F.

    1994-01-01

    The genetic divergence and phylogeny of the auks was assessed by mitochondrial DNA sequence comparisons in a study using 19 of the 22 auk species and two outgroup representatives. We compared more than 500 nucleotides from each of two mitochondrial genes encoding 12S rRNA and the NADH dehydrogenase subunit 6. Divergence times were estimated from transversional substitutions. The dovekie (Alle alle) is related to the razorbill (Alca torda) and the murres (Uria spp). Furthermore, the Xantus's murrelet (Synthliboramphus hypoleucus) and the ancient (Synthliboramphus antiquus) and Japanese murrelets (Synthliboramphus wumizusume) are genetically distinct members of the same main lineage, whereas brachyramphine and synthliboramphine murrelets are not closely related. An early adaptive radiation of six main species groups of auks seems to trace back to Middle Miocene. Later speciation probably involved ecological differentiations and geographical isolations.

  19. The subfamily Mendesellinae (Hymenoptera: Braconidae) in Brazil, with the description of six new species.

    PubMed

    Bortoni, Marco Aurélio; Souza-Gessner, Carolina DA Silva; Penteado-Dias, Angélica Maria

    2016-11-29

    In this paper, we study the Mendesellinae wasps from Brazil deposited at Departamento de Ecologia e Biologia Evolutiva da Universidade Federal de São Carlos, São Carlos, SP, Brazil collection. Two new species of Epsilogaster (E. masoni sp. n. and E. whitfieldi sp. n.) and four new species of Mendesella (M. albipleura sp. n., M. itatiaia sp. n., M. japi sp. n., M. yamadai sp. n.) are described and illustrated.

  20. Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis

    DOE PAGES

    Prigozhin, Daniil M.; Krieger, Inna V.; Huizar, John P.; ...

    2014-12-31

    Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows thatmore » Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.« less

  1. Quaternary Structure of Fur Proteins, a New Subfamily of Tetrameric Proteins.

    PubMed

    Pérard, Julien; Covès, Jacques; Castellan, Mathieu; Solard, Charles; Savard, Myriam; Miras, Roger; Galop, Sandra; Signor, Luca; Crouzy, Serge; Michaud-Soret, Isabelle; de Rosny, Eve

    2016-03-15

    The ferric uptake regulator (Fur) belongs to the family of the DNA-binding metal-responsive transcriptional regulators. Fur is a global regulator found in all proteobacteria. It controls the transcription of a wide variety of genes involved in iron metabolism but also in oxidative stress or virulence factor synthesis. When bound to ferrous iron, Fur can bind to specific DNA sequences, called Fur boxes. This binding triggers the repression or the activation of gene expression, depending on the regulated genes. As a general view, Fur proteins are considered to be dimeric proteins both in solution and when bound to DNA. In this study, we have purified Fur from four pathogenic strains (Pseudomonas aeruginosa, Francisella tularensis, Yersinia pestis, and Legionella pneumophila) and compared them to Fur from Escherichia coli (EcFur), the best characterized of this family. By using a series of "in solution" techniques, including multiangle laser light scattering and small-angle X-ray scattering, as well as cross-linking experiments, we have shown that the Fur proteins can be classified into two groups, according to their quaternary structure. The group of dimers is represented by EcFur and YpFur and the group of very stable tetramers by PaFur, FtFur, and LpFur. Using PaFur as a case study, we also showed that the dissociation of the tetramers into dimers is necessary for binding of Fur to DNA, and that this dissociation requires the combined effect of metal ion binding and DNA proximity.

  2. The subfamily Cheloninae (Hymenoptera, Braconidae) from Egypt, with the description of two new species

    PubMed Central

    Edmardash, Yusuf Abd-Elaziz; Abdel-Dayem, Mahmoud Saleh; Gadallah, Neveen Samy

    2011-01-01

    Abstract A key to the chelonine species (Braconidae) (both recorded and recently collected) from Egypt is given. It includes 16 species, of which five species are new to the Egyptian fauna and two (Phanerotoma (Phanerotoma) elbaiensis sp. n. and Phanerotoma (Bracotritoma) ponti sp. n.) are new for science. A faunistic list and the description for the two new species are added. PMID:21977002

  3. Firefly luciferase genes from the subfamilies Psilocladinae and Ototretinae (Lampyridae, Coleoptera).

    PubMed

    Oba, Yuichi; Yoshida, Mayumi; Shintani, Takeru; Furuhashi, Mana; Inouye, Satoshi

    2012-02-01

    Firefly luciferase genes have been isolated from approximately 20 species of Lampyrinae, Luciolinae, and Photurinae. These are mostly nocturnal luminescent species that use light signals for sexual communication. In this study, we isolated three cDNAs for firefly luciferase from Psilocladinae (Cyphonocerus ruficollis) and Ototretinae (Drilaster axillaris and Stenocladius azumai), which are diurnal non-luminescent or weakly luminescent species that may use pheromones for communication. The amino acid sequences deduced from the three cDNAs showed 81-89% identities to each other and 60-81% identities with known firefly luciferases. The three purified recombinant proteins showed luminescence and fatty acyl-CoA synthetic activities, as observed in other firefly luciferases. The emission maxima by the three firefly luciferases (λmax, 545-546nm) were shorter than those by known luciferases from the nocturnal fireflies (λmax, 550-568nm). These results suggest that the primary structures and enzymatic properties of luciferases are conserved in Lampyridae, but the luminescence colors were red-shifted in nocturnal species compared to diurnal species.

  4. A new fish species of the subfamily Serraninae (Perciformes, Serranidae) from the Philippines.

    PubMed

    Williams, Jeffrey T; Carpenter, Kent E

    2015-01-19

    A new species of serranine fish is described from the Philippine Islands. A single specimen of a new species, Chelidoperca santosi, captured by fishermen working in Palawan waters was discovered in the public fish market in Iloilo City, Panay, Philippines. Two additional specimens of the new species, also from the Philippines, were subsequently discovered in the collections of the Museum Victoria, Australia. The new species is currently known only from the Philippines and is characterized by its distinctive coloration with a row of four small dark spots on the snout (two in front of each eye) and two dark spots on the chin (one on each side of the symphysis of the dentaries), a white anal fin with six large yellow spots separated by broad white interspaces and a narrow yellow distal border, caudal fin with narrow yellow bars and a yellowish distal margin and no dark spots, and a combination of meristic and morphological characters. 

  5. 40 CFR 1037.230 - Vehicle families, sub-families, and configurations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... characteristics: (1) Method of vapor storage, including the number of vapor storage devices, the working material, and the total working capacity of vapor storage (as determined under 40 CFR 86.132-96(h)(1)(iv))....

  6. Prestonellinae-validation of the name as a new subfamily of Bothriembryontidae (Mollusca, Gastropoda, Orthalicoidea).

    PubMed

    Bruggen, A C Van; Herbert, David G; Breure, Abraham S H

    2016-02-29

    The affinities of the enigmatic South African land snail genus Prestonella Connolly, 1929 were discussed by Herbert (2007) and Herbert & Mitchell (2009), who showed, on the basis of morphological and molecular data, that the genus is referable to the superfamily Orthalicoidea. Currently, the three described species of Prestonella are the only known African representatives of this diverse superfamily. Earlier, van Bruggen (1978) had recognized that these species formed a distinct group and had placed them in the (new) family Prestonellidae. However, as noted by Bouchet & Rocroi (2005: 140), no diagnosis was provided by van Bruggen; the name Prestonellidae thus does not meet the requirements of ICZN Art. 13.1, and is not an available name. In this paper we will redress this issue, also taking into account more recent research which has shed light on the systematic position of this genus within the Orthalicoidea.

  7. Characterization of new transposable element sub-families from white clover (Trifolium repens) using PCR amplification.

    PubMed

    Becker, Kailey E; Thomas, Mary C; Martini, Samer; Shuipys, Tautvydas; Didorchuk, Volodymyr; Shanker, Rachyl M; Laten, Howard M

    2016-10-01

    Transposable elements (TEs) dominate the landscapes of most plant and animal genomes. Once considered junk DNA and genetic parasites, these interspersed, repetitive DNA elements are now known to play major roles in both genetic and epigenetic processes that sponsor genome variation and regulate gene expression. Knowledge of TE consensus sequences from elements in species whose genomes have not been sequenced is limited, and the individual TEs that are encountered in clones or short-reads rarely represent potentially canonical, let alone, functional representatives. In this study, we queried the Repbase database with eight BAC clones from white clover (Trifolium repens), identified a large number of candidate TEs, and used polymerase chain reaction and Sanger sequencing to create consensus sequences for three new TE families. The results show that TE family consensus sequences can be obtained experimentally in species for which just a single, full-length member of a TE family has been sequenced.

  8. Calibration of mutation rates reveals diverse subfamily structure of galliform CR1 repeats

    Technology Transfer Automated Retrieval System (TEKTRAN)

    CR1 repeats are the most abundant family of repeats in the chicken genome, with more than 200,000 copies accounting for ~80% of the chicken interspersed repeats. CR1 repeats are believed to have arisen from the retrotransposition of a small number of master elements, which gave rise to the 22 CR1 su...

  9. Structural basis for controlling the dimerization and stability of the WW domains of an atypical subfamily.

    PubMed

    Ohnishi, Satoshi; Tochio, Naoya; Tomizawa, Tadashi; Akasaka, Ryogo; Harada, Takushi; Seki, Eiko; Sato, Manami; Watanabe, Satoru; Fujikura, Yukiko; Koshiba, Seizo; Terada, Takaho; Shirouzu, Mikako; Tanaka, Akiko; Kigawa, Takanori; Yokoyama, Shigeyuki

    2008-09-01

    The second WW domain in mammalian Salvador protein (SAV1 WW2) is quite atypical, as it forms a beta-clam-like homodimer. The second WW domain in human MAGI1 (membrane associated guanylate kinase, WW and PDZ domain containing 1) (MAGI1 WW2) shares high sequence similarity with SAV1 WW2, suggesting comparable dimerization. However, an analytical ultracentrifugation study revealed that MAGI1 WW2 (Leu355-Pro390) chiefly exists as a monomer at low protein concentrations, with an association constant of 1.3 x 10(2) M(-1). We determined its solution structure, and a structural comparison with the dimeric SAV1 WW2 suggested that an Asp residue is crucial for the inhibition of the dimerization. The substitution of this acidic residue with Ser resulted in the dimerization of MAGI1 WW2. The spin-relaxation data suggested that the MAGI1 WW2 undergoes a dynamic process of transient dimerization that is limited by the charge repulsion. Additionally, we characterized a longer construct of this WW domain with a C-terminal extension (Leu355-Glu401), as the formation of an extra alpha-helix was predicted. An NMR structural determination confirmed the formation of an alpha-helix in the extended C-terminal region, which appears to be independent from the dimerization regulation. A thermal denaturation study revealed that the dimerized MAGI1 WW2 with the Asp-to-Ser mutation gained apparent stability in a protein concentration-dependent manner. A structural comparison between the two constructs with different lengths suggested that the formation of the C-terminal alpha-helix stabilized the global fold by facilitating contacts between the N-terminal linker region and the main body of the WW domain.

  10. Comparing Linear Conjunctive Languages to Subfamilies of the Context-Free Languages

    NASA Astrophysics Data System (ADS)

    Okhotin, Alexander

    Linear conjunctive grammars define the same family of languages as one-way real-time cellular automata (Okhotin, "On the equivalence of linear conjunctive grammars to trellis automata", RAIRO ITA, 2004), and this family is known to be incomparable to the context-free languages (Terrier, "On real-time one-way cellular array", Theoret. Comput. Sci., 1995). This paper investigates subclasses of the context-free languages for possible containment in this class. It is shown that every visibly pushdown automaton (Alur, Madhusudan, "Visibly pushdown languages", STOC 2004) can be simulated by a one-way real-time cellular automaton, but already for LL(1) context-free languages and for one-counter DPDAs no simulation is possible.

  11. The evolutionarily conserved Krueppel-associated box domain defines a subfamily of eukaryotic multifingered proteins

    SciTech Connect

    Bellefroid, E.J.; Poncelet, D.A.; Lecocq, P.J.; Revelant, O.; Martial, J.A. )

    1991-05-01

    The authors have previously shown that the human genome includes hundreds of genes coding for putative factors related to the Krueppel zinc-finger protein, which regulates Drosophila segmentation. They report herein that about one-third of these genes code for proteins that share a very conserved region of about 75 amino acids in their N-terminal nonfinger portion. Homologous regions are found in a number of previously described finger proteins, including mouse Zfp-1 and Xenopus Xfin. They named this region the Krueppel-associated box (KRAB). This domain has the potential to form two amphipathic {alpha}-helices. Southern blot analysis of zoo blots suggests that the Krueppel-associated box is highly conserved during evolution. Northern blot analysis shows that these genes are expressed in most adult tissues and are down-regulated during in vitro terminal differentiation of human myeloid cells.

  12. Two new fish species of the subfamily Anthiinae (Perciformes, Serranidae) from the Marquesas.

    PubMed

    Williams, Jeffrey T; Delrieu-Trottin, Erwan; Planes, Serge

    2013-01-01

    Two new species of anthiine fishes are described from the Marquesas Islands, French Polynesia. Plectranthias flammeus was found at depths from 20-45 m and is characterized by dorsal rays X, 14 or 15, with spines 1-6 bearing fleshy white tabs at their tips, longest fleshy tab on spine 4; 14 unbranched pectoral rays; lateral line incomplete with 16-17 tubed scales; preopercle with 8-10 small spines along posterior margin and 2 antrorse spines on ventral margin; broad, fiery red-orange streak across lower cheek; head and body with irregularly spaced maroon-ringed yellow blotches on a white background; pair of small dark oblong spots (red with black centers in life) on the bases of the middle rays of the caudal fin. Pseudanthias oumati was found on the outer reef slope of Fatu Hiva at a depth of 50-55 m and is characterized by 3rd dorsal spine elongate and tipped with fleshy yellow filament extending beyond tip of spine; lateral-line scales 43; gill rakers 10 + 28; no papillae on posterior edge of orbit; front of upper lip not thickened (male condition unknown); caudal fin lunate; color of female yellow, all fins yellow with narrow magenta margin (except pectoral fin, which lacks magenta); no stripe from snout to pectoral base; small scales located on basal quarter of soft-dorsal fin from segmented rays 1-12; dorsal profile of head slightly concave.

  13. Regulation of human natural killer cell migration and proliferation by the exodus subfamily of CC chemokines.

    PubMed

    Robertson, M J; Williams, B T; Christopherson, K; Brahmi, Z; Hromas, R

    2000-01-10

    Natural killer (NK) cells play an important role in innate and adaptive immune responses to obligate intracellular pathogens. Nevertheless, the regulation of NK cell trafficking and migration to inflammatory sites is poorly understood. Exodus-1/MIP-3alpha/LARC, Exodus-2/6Ckine/SLC, and Exodus-3/MIP-3beta/ELC/CKbeta-11 are CC chemokines that share a unique aspartate-cysteine-cysteine-leucine motif near their amino terminus and preferentially stimulate the migration of T lymphocytes. The effects of Exodus chemokines on human NK cells were examined. Exodus-1, -2, and -3 did not induce detectable chemotaxis of resting peripheral blood NK cells. In contrast, Exodus-2 and -3 stimulated migration of polyclonal activated peripheral blood NK cells in a dose-dependent fashion. Exodus-2 and -3 also induced dose-dependent chemotaxis of NKL, an IL-2-dependent human NK cell line. Results of modified checkerboard assays indicate that migration of NKL cells in response to Exodus-2 and -3 represents true chemotaxis and not simply chemokinesis. Exodus-1, -2, and -3 did not induce NK cell proliferation in the absence of other stimuli. Nevertheless, Exodus-2 and -3 significantly augmented IL-2-induced proliferation of normal human CD56(dim) NK cells. In contrast, Exodus-1, -2, and -3 did not affect the cytolytic activity of resting or activated peripheral blood NK cells. Expression of message for CCR7, a shared receptor for Exodus-2 and -3, was detected in activated polyclonal NK cells and NKL cells but not resting NK cells. Taken together, these results indicate that Exodus-2 and -3 can participate in the recruitment and proliferation of activated NK cells. Exodus-2 and -3 may regulate interactions between T cells and NK cells that are crucial for the generation of optimal immune responses.

  14. Discrimination against major groove adducts by Y-family polymerases of the DinB subfamily.

    PubMed

    Walsh, Jason M; Ippoliti, Paul J; Ronayne, Erin A; Rozners, Eriks; Beuning, Penny J

    2013-09-01

    Y-family DNA polymerases bypass DNA adducts in a process known as translesion synthesis (TLS). Y-family polymerases make contacts with the minor groove side of the DNA substrate at the nascent base pair. The Y-family polymerases also contact the DNA major groove via the unique little finger domain, but they generally lack contacts with the major groove at the nascent base pair. Escherichia coli DinB efficiently and accurately copies certain minor groove guanosine adducts. In contrast, we previously showed that the presence in the DNA template of the major groove-modified base 1,3-diaza-2-oxophenothiazine (tC) inhibits the activity of E. coli DinB. Even when the DNA primer is extended up to three nucleotides beyond the site of the tC analog, DinB activity is strongly inhibited. These findings prompted us to investigate discrimination against other major groove modifications by DinB and its orthologs. We chose a set of pyrimidines and purines with modifications in the major groove and determined the activity of DinB and several orthologs with these substrates. DinB, human pol kappa, and Sulfolobus solfataricus Dpo4 show differing specificities for the major groove adducts pyrrolo-dC, dP, N(6)-furfuryl-dA, and etheno-dA. In general, DinB was least efficient for bypass of all of these major groove adducts, whereas Dpo4 was most efficient. DinB activity was essentially completely inhibited by the presence of etheno-dA, while pol kappa activity was strongly inhibited. All three of these DNA polymerases were able to bypass N(6)-furfuryl-dA with modest efficiency, with DinB being the least efficient. We also determined that the R35A variant of DinB enhances bypass of N(6)-furfuryl-dA but not etheno-dA. In sum, we find that whereas DinB is specific for bypass of minor groove adducts, it is specifically inhibited by major groove DNA modifications.

  15. CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs

    PubMed Central

    Schneider, Tim; Hung, Lee-Hsueh; Schreiner, Silke; Starke, Stefan; Eckhof , Heinrich; Rossbach, Oliver; Reich, Stefan; Medenbach, Jan; Bindereif , Albrecht

    2016-01-01

    Circular RNAs (circRNAs) constitute a new class of noncoding RNAs in higher eukaryotes generated from pre-mRNAs by alternative splicing. Here we investigated in mammalian cells the association of circRNAs with proteins. Using glycerol gradient centrifugation, we characterized in cell lysates circRNA-protein complexes (circRNPs) of distinct sizes. By polysome-gradient fractionation we found no evidence for efficient translation of a set of abundant circRNAs in HeLa cells. To identify circRNPs with a specific protein component, we focused on IMP3 (IGF2BP3, insulin-like growth factor 2 binding protein 3), a known tumor marker and RNA-binding protein. Combining RNA-seq analysis of IMP3-co-immunoprecipitated RNA and filtering for circular-junction reads identified a set of IMP3-associated circRNAs, which were validated and characterized. In sum, our data suggest that specific circRNP families exist defined by a common protein component. In addition, this provides a general approach to identify circRNPs with a given protein component. PMID:27510448

  16. Distorted octahedral coordination of tungstate in a subfamily of specific binding proteins.

    PubMed

    Hollenstein, Kaspar; Comellas-Bigler, Mireia; Bevers, Loes E; Feiters, Martin C; Meyer-Klaucke, Wolfram; Hagedoorn, Peter-Leon; Locher, Kaspar P

    2009-06-01

    Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). These substrates are captured by an external, high-affinity binding protein, and delivered to ATP binding cassette transporters, which move them across the cell membrane. We have recently reported a crystal structure of the molybdate/tungstate binding protein ModA/WtpA from Archaeoglobus fulgidus, which revealed an octahedrally coordinated central metal atom. By contrast, the previously determined structures of three bacterial homologs showed tetracoordinate molybdenum and tungsten atoms in their binding pockets. Until then, coordination numbers above four had only been found for molybdenum/tungsten in metalloenzymes where these metal atoms are part of the catalytic cofactors and coordinated by mostly non-oxygen ligands. We now report a high-resolution structure of A. fulgidus ModA/WtpA, as well as crystal structures of four additional homologs, all bound to tungstate. These crystal structures match X-ray absorption spectroscopy measurements from soluble, tungstate-bound protein, and reveal the details of the distorted octahedral coordination. Our results demonstrate that the distorted octahedral geometry is not an exclusive feature of the A. fulgidus protein, and suggest distinct binding modes of the binding proteins from archaea and bacteria.

  17. Diverse functions of PHD fingers of the MLL/KMT2 subfamily.

    PubMed

    Ali, Muzaffar; Hom, Robert A; Blakeslee, Weston; Ikenouye, Larissa; Kutateladze, Tatiana G

    2014-02-01

    Five members of the KMT2 family of lysine methyltransferases, originally named the mixed lineage leukemia (MLL1-5) proteins, regulate gene expression during embryogenesis and development. Each KMT2A-E contains a catalytic SET domain that methylates lysine 4 of histone H3, and one or several PHD fingers. Over the past few years a growing number of studies have uncovered diverse biological roles of the KMT2A-E PHD fingers, implicating them in binding to methylated histones and other nuclear proteins, and in mediating the E3 ligase activity and dimerization. Mutations in the PHD fingers or deletion of these modules are linked to human diseases including cancer and Kabuki syndrome. In this work, we summarize recently identified biological functions of the KMT2A-E PHD fingers, discuss mechanisms of their action, and examine preference of these domains for histone and non-histone ligands.

  18. Comparative human-horse sequence analysis of the CYP3A subfamily gene cluster.

    PubMed

    Schmitz, A; Demmel, S; Peters, L M; Leeb, T; Mevissen, M; Haase, B

    2010-12-01

    Cytochrome P450 enzymes (CYP450s) represent a superfamily of haem-thiolate proteins. CYP450s are most abundant in the liver, a major site of drug metabolism, and play key roles in the metabolism of a variety of substrates, including drugs and environmental contaminants. Interaction of two or more different drugs with the same enzyme can account for adverse effects and failure of therapy. Human CYP3A4 metabolizes about 50% of all known drugs, but little is known about the orthologous CYP450s in horses. We report here the genomic organization of the equine CYP3A gene cluster as well as a comparative analysis with the human CYP3A gene cluster. The equine CYP450 genes of the 3A family are located on ECA 13 between 6.97-7.53 Mb, in a region syntenic to HSA 7 99.05-99.35 Mb. Seven potential, closely linked equine CYP3A genes were found, in contrast to only four genes in the human genome. RNA was isolated from an equine liver sample, and the approximately 1.5-kb coding sequence of six CYP3A genes could be amplified by RT-PCR. Sequencing of the RT-PCR products revealed numerous hitherto unknown single nucleotide polymorphisms (SNPs) in these six CYP3A genes, and one 6-bp deletion compared to the reference sequence (EquCab2.0). The presence of the variants was confirmed in a sample of genomic DNA from the same horse. In conclusion, orthologous genes for the CYP3A family exist in horses, but their number differs from those of the human CYP3A gene family. CYP450 genes of the same family show high homology within and between mammalian species, but can be highly polymorphic.

  19. Cloning and characterization of human ORNT2: a second mitochondrial ornithine transporter that can rescue a defective ORNT1 in patients with the hyperornithinemia-hyperammonemia-homocitrullinuria syndrome, a urea cycle disorder.

    PubMed

    Camacho, José A; Rioseco-Camacho, Natalia; Andrade, Dario; Porter, John; Kong, Jin

    2003-08-01

    We recently characterized the mitochondrial ornithine transporter (ORNT1), the gene defective in the hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome, a urea cycle disorder. Despite the apparent functional ablation of ORNT1 in 10 French-Canadian probands with the ORNT1-F188 Delta allele, these patients are mildly affected when compared to patients with other urea cycle disorders such as deficiency of ornithine transcarbamylase. Given that the inner mitochondrial membrane is impermeable to solutes, we hypothesize that other unidentified carriers have some degree of functional redundancy with ORNT1. Using conserved sequences of mammalian and fungal mitochondrial ornithine transporters, we screened the Expressed Sequence Tag database for additional transporters belonging to the ORNT subfamily. Here we identify a new intronless gene, ORNT2, located on chromosome 5. The gene product of ORNT2 is 88% identical to ORNT1, targets to the mitochondria and is expressed in human liver, pancreas, kidney, and cultured fibroblasts from control and HHH patients. When ORNT2 is overexpressed transiently in cultured fibroblasts from HHH patients, it rescues the deficient ornithine metabolism in these cells. Our results suggest that ORNT2 may in part be responsible for the milder phenotype in HHH patients secondary to a gene redundancy effect. We believe ORNT2 arose from a retrotransposition event. To our knowledge, this is the first report of a functional retroposon (ORNT2) that can rescue the disease phenotype of the gene it arose from, ORNT1. As such, ORNT2 may eventually become a candidate for pharmacological-based approaches to correct a urea cycle disorder.

  20. Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms.

    PubMed

    Fischer, Iris; Diévart, Anne; Droc, Gaetan; Dufayard, Jean-François; Chantret, Nathalie

    2016-03-01

    Gene duplications are an important factor in plant evolution, and lineage-specific expanded (LSE) genes are of particular interest. Receptor-like kinases expanded massively in land plants, and leucine-rich repeat receptor-like kinases (LRR-RLK) constitute the largest receptor-like kinases family. Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced flowering plant genomes, the complex evolutionary dynamics of this family was characterized in depth. We studied the involvement of selection during the expansion of this family among angiosperms. LRR-RLK subgroups harbor extremely contrasting rates of duplication, retention, or loss, and LSE copies are predominantly found in subgroups involved in environmental interactions. Expansion rates also differ significantly depending on the time when rounds of expansion or loss occurred on the angiosperm phylogenetic tree. Finally, using a dN/dS-based test in a phylogenetic framework, we searched for selection footprints on LSE and single-copy LRR-RLK genes. Selective constraint appeared to be globally relaxed at LSE genes, and codons under positive selection were detected in 50% of them. Moreover, the leucine-rich repeat domains, and specifically four amino acids in them, were found to be the main targets of positive selection. Here, we provide an extensive overview of the expansion and evolution of this very large gene family.

  1. The first complete mitochondrial genome for the subfamily Limacodidae and implications for the higher phylogeny of Lepidoptera

    PubMed Central

    Liu, Qiu-Ning; Xin, Zhao-Zhe; Bian, Dan-Dan; Chai, Xin-Yue; Zhou, Chun-Lin; Tang, Bo-Ping

    2016-01-01

    The mitochondrial genome (mitogenome) provides important information for understanding molecular evolution and phylogeny. To determine the systematic status of the family Limacodidae within Lepidoptera, we infer a phylogenetic hypothesis based on the complete mitogenome of Monema flavescens (Lepidoptera: Limacodidae). The mitogenome of M. flavescens is 15,396 base pairs (bp), and includes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The AT skew of this mitogenome is slightly negative and the nucleotide composition is also biased towards A + T nucleotides (80.5%). All PCGs are initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which is initiated by CGA. All tRNAs display the typical clover-leaf structure characteristic of mitochondrial tRNAs, with the exception of trnS1 (AGN). The mitogenome CR is 401 bp and consists of several features common to Lepidoptera. Phylogenetic analysis using Bayesian Inference (BI) and Maximum Likelihood (ML) based on nucleotide and amino acid sequences of 13 mitochondrial PCGs indicates that M. flavescens belongs to Zygaenoidea. We obtain a well-supported phylogenetic tree consisting of Yponomeutoidea + (Tortricoidea + Zygaenoidea + (Papilionoidea + (Pyraloidea + (Noctuoidea + (Geometroidea + Bombycoidea))))). PMID:27767191

  2. Typification of species names in Adenocaulon and Eriachaenium (Compositae/Asteraceae, Subfamily Mutisioideae, Tribe Mutisieae, Subtribe Adenocaulinae).

    PubMed

    Funk, Vicki A; Hind, D J Nicholas

    2016-01-01

    During the course of a recent research project on Adenocaulon and Eriachaenium it became apparent that some of the species names had not been typified. In this study we located and designated as much type material as possible for these two genera. We indicate holotypes or lectotypes where appropriate, including one for the type of the genus Adenocaulon.

  3. A QUICK KEY TO THE SUBFAMILIES AND GENERA OF ANTS OF THE SAVANNAH RIVER SITE, AIKEN, SC

    SciTech Connect

    Martin, D

    2006-10-04

    This taxonomic key was devised to support development of a Rapid Bioassessment Protocol using ants at the Savannah River Site. The emphasis is on ''rapid'' and, because the available keys contained a large number of genera not known to occur at the Savannah River Site, we found that the available keys were unwieldy. Because these keys contained more genera than we would likely encounter and because this larger number of genera required both more couplets in the key and often required examination of characters that are difficult to assess without higher magnifications (60X or higher) more time was required to process samples. In developing this set of keys I recognize that the character sets used may lead to some errors but I believe that the error rate will be small and, for the purpose of rapid bioassessment, this error rate will be acceptable provided that overall sample sizes are adequate. Oliver and Beattie (1996a, 1996b) found that for rapid assessment of biodiversity the same results were found when identifications were done to morphospecies by people with minimal expertise as when the same data sets were identified by subject matter experts. Basset et al. (2004) concluded that it was not as important to correctly identify all species as it was to be sure that the study included as many functional groups as possible. If your study requires high levels of accuracy, it is highly recommended that when you key out a specimen and have any doubts concerning the identification, you should refer to keys in Bolton (1994) or to the other keys used to develop this area specific taxonomic key.

  4. Molecular properties of the class III subfamily of acyl-coenyzme A binding proteins from tung tree (Vernicia fordii)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Acyl-CoA binding proteins (ACBPs) have been identified in most branches of life. A single prototypical ACBP was first discovered in yeast, and was found to play a signficant role in lipid metabolism, among other functions. Plants also contain the prototype small, soluble ACBP, but have also evolve...

  5. Characterization of the rbcS multigene family in wheat: subfamily classification, determination of chromosomal location and evolutionary analysis.

    PubMed

    Sasanuma, T

    2001-03-01

    To elucidate the evolution of a multigene family in plants, nucleotide sequences of members of the rbcS multigene family encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase in wheat were determined. Five genomic clones containing rbcS sequences were isolated. The known members of the rbcS family of common wheat, including the clones reported here, were categorized into two Classes (I and II), which, in turn, were classified into three (A, B and E) and two (C and D) subtypes, respectively. The sequences of the intron and the 3' flanking region were divergent between the classes but not among the types within a class. The differences among the types within a class were caused by large indels (about 100-350 bp) in the intron. The members of Classes I and II were located on homeologous group 2 and 5 chromosomes, respectively. The Southern hybridization data indicated that all types of rbcS were present in the ancestral species of wheat. Thus, it is concluded that the divergence between the classes originated from an interchromosomal duplication and that several intrachromosomal duplications followed; these events occurred before the speciation of diploids. The detection of nonfunctional genes and the elimination of fragments suggests that several mechanisms were involved in reducing the copy number of rbcS during the evolution of wheat.

  6. Repeated sequence homogenization between the control and pseudo-control regions in the mitochondrial genomes of the subfamily Aquilinae.

    PubMed

    Cadahía, Luis; Pinsker, Wilhelm; Negro, Juan José; Pavlicev, Mihaela; Urios, Vicente; Haring, Elisabeth

    2009-05-15

    In birds, the noncoding control region (CR) and its flanking genes are the only parts of the mitochondrial (mt) genome that have been modified by intragenomic rearrangements. In raptors, two noncoding regions are present: the CR has shifted to a new position with respect to the "ancestral avian gene order," whereas the pseudo-control region (PsiCR) is located at the original genomic position of the CR. As possible mechanisms for this rearrangement, duplication and transposition have been considered. During characterization of the mt gene order in Bonelli's eagle Hieraaetus fasciatus, we detected intragenomic sequence similarity between the two regions supporting the duplication hypothesis. We performed intra- and intergenomic sequence comparisons in H. fasciatus and other falconiform species to trace the evolution of the noncoding mtDNA regions in Falconiformes. We identified sections displaying different levels of similarity between the CR and PsiCR. On the basis of phylogenetic analyses, we outline an evolutionary scenario of the underlying mutation events involving duplication and homogenization processes followed by sporadic deletions. Apparently, homogenization may easily occur if sufficient sequence similarity between the CR and PsiCR exists. Moreover, homogenization itself allows perpetuation of this continued equalization, unless this process is stopped by deletion. The Pandionidae and the Aquilinae seem to be the only two lineages of Falconiformes where homology between both regionsis still detectable, whereas in other raptors no similarity was found so far. In these two lineages, the process of sequence degeneration may have slowed down by homogenization events retaining high sequence similarity at least in some sections.

  7. Subfamily-specific adaptations in the structures of two penicillin-binding proteins from Mycobacterium tuberculosis

    SciTech Connect

    Prigozhin, Daniil M.; Krieger, Inna V.; Huizar, John P.; Mavrici, Daniela; Waldo, Geoffrey S.; Hung, Li -Wei; Sacchettini, James C.; Terwilliger, Thomas C.; Alber, Tom; Mayer, Claudine

    2014-12-31

    Beta-lactam antibiotics target penicillin-binding proteins including several enzyme classes essential for bacterial cell-wall homeostasis. To better understand the functional and inhibitor-binding specificities of penicillin-binding proteins from the pathogen, Mycobacterium tuberculosis, we carried out structural and phylogenetic analysis of two predicted D,D-carboxypeptidases, Rv2911 and Rv3330. Optimization of Rv2911 for crystallization using directed evolution and the GFP folding reporter method yielded a soluble quadruple mutant. Structures of optimized Rv2911 bound to phenylmethylsulfonyl fluoride and Rv3330 bound to meropenem show that, in contrast to the nonspecific inhibitor, meropenem forms an extended interaction with the enzyme along a conserved surface. Phylogenetic analysis shows that Rv2911 and Rv3330 belong to different clades that emerged in Actinobacteria and are not represented in model organisms such as Escherichia coli and Bacillus subtilis. Clade-specific adaptations allow these enzymes to fulfill distinct physiological roles despite strict conservation of core catalytic residues. The characteristic differences include potential protein-protein interaction surfaces and specificity-determining residues surrounding the catalytic site. Overall, these structural insights lay the groundwork to develop improved beta-lactam therapeutics for tuberculosis.

  8. Transcriptional regulation of rat P-450 2C gene subfamily members by the sexually dimorphic pattern of growth hormone secretion.

    PubMed

    Legraverend, C; Mode, A; Westin, S; Ström, A; Eguchi, H; Zaphiropoulos, P G; Gustafsson, J A

    1992-02-01

    The onset of the sexually dimorphic pattern of GH secretion and increased hepatic GH-binding capacity in rats at puberty is temporally correlated with the developmental induction of three hepatic cytochrome P-450s with steroid hydroxylase activity, P-450 IIC11, P-450 IIC12, and P-450 IIC13, and one cytochrome P-450 with vitamin A hydroxylase activity, P-450 IIC7. In this study we demonstrate that expression of the 2C11, 2C12, and 2C13 genes is modulated by GH at the level of transcriptional initiation both in vivo and in primary cultures of adult hepatocytes. In an effort to define the minimum sequence responsible for the inductive effects of GH, we have analyzed the ability of a 0.7-kilobase fragment isolated from the 5'-flank of the 2C12 gene, including the natural promoter, to drive transcription of a 320-basepair G-less cassette in vitro. We were unable to detect any substantial difference in RNA polymerase-II-dependent transcriptional efficiency toward the 2C12 promoter between liver nuclear extracts from normal and hypophysectomized rats of both sexes. This observation supports the assumption that the sequence information contained between bases -700 and 1 is sufficient to support basal transcription of the 2C12 gene. Sequence information residing 5' or 3' of the 0.7-kilobase 5'-flank or a higher ordered chromatin structure may be necessary for the sex-specific transcriptional activation of the 2C12 gene.

  9. Molecular Phylogeny and Biogeographic History of the Armored Neotropical Catfish Subfamilies Hypoptopomatinae, Neoplecostominae and Otothyrinae (Siluriformes: Loricariidae)

    PubMed Central

    Roxo, Fábio F.; Albert, James S.; Silva, Gabriel S. C.; Zawadzki, Cláudio H.; Foresti, Fausto; Oliveira, Claudio

    2014-01-01

    The main objectives of this study are estimate a species-dense, time-calibrated molecular phylogeny of Hypoptopomatinae, Neoplecostominae, and Otothyrinae, which together comprise a group of armoured catfishes that is widely distributed across South America, to place the origin of major clades in time and space, and to demonstrate the role of river capture on patterns of diversification in these taxa. We used maximum likelihood and Bayesian methods to estimate a time-calibrated phylogeny of 115 loricariid species, using three mitochondrial and one nuclear genes to generate a matrix of 4,500 base pairs, and used parametric biogeographic analyses to estimate ancestral geographic ranges and to infer the effects of river capture events on the geographic distributions of these taxa. Our analysis recovered Hypoptopomatinae, Neoplecostominae, and Otothyrinae as monophyletic with strong statistical support, and Neoplecostominae as more closely related to Otothyrinae than to Hypoptopomatinae. Our time-calibrated phylogeny and ancestral-area estimations indicate an origin of Hypoptopomatinae, Neoplecostominae, and Otothyrinae during the Lower Eocene in the Atlantic Coastal Drainages, from which it is possible to infer several dispersal events to adjacent river basins during the Neogene. In conclusion we infer a strong influence of river capture in: (1) the accumulation of modern clade species-richness values; (2) the formation of the modern basin-wide species assemblages, and (3) the presence of many low-diversity, early-branching lineages restricted to the Atlantic Coastal Drainages. We further infer the importance of headwater stream capture and marine transgressions in shaping patterns in the distributions of Hypoptopomatinae, Neoplecostominae and Otothyrinae throughout South America. PMID:25148406

  10. Gating currents from a Kv3 subfamily potassium channel: charge movement and modification by BDS-II toxin.

    PubMed

    Wang, Zhuren; Robertson, Brian; Fedida, David

    2007-11-01

    Kv3 channels have a major role in determining neuronal excitability, and are characterized by ultra-rapid kinetics of gating and a high activation threshold. However, the gating currents, which occur as a result of positional changes of the charged elements in the channel structure during activation, are not well understood. Here we report a study of gating currents from wild-type Kv3.2b channels, expressed in human embryonic kidney (HEK) cells to facilitate high time-resolution recording. On-gating currents (I(g,on)) had extremely rapid kinetics such that at +80 mV, the time constant for the decay of I(g,on) was only approximately 0.3 ms. Decay of I(g,on) appeared mono-exponential at all potentials studied, and in support of this, the charge-voltage (Q-V) relationship was fitted with a single Boltzmann function, supporting the idea that only one charge system is required to account for the time course of I(g,on) and the voltage dependence of Q(on). The voltage (V((1/2))) for half movement of gating charge was -8.4 +/- 4.0 mV (n = 6), which closely matches the voltage dependence of activation of Kv3.2b ionic currents reported before. Depolarizations to more positive potentials than 0 mV decreased the amplitude and slowed the decay of the off-gating currents (I(g,off)), suggesting that a rate-limiting step in opening was present in Kv3 channels as in Shaker and other Kv channels. Return of charge was negatively shifted along the potential axis with a V((1/2)) of Q(off) of -80.9 +/- 0.8 mV (n = 3), which allowed approximately 90% charge return upon repolarization to -100 mV. BDS-II toxin apparently reduced I(g,on), and greatly slowed the kinetics of I(g,on), while shifting the Q-V relationship in the depolarizing direction. However, the Q-V relationship remained well fitted by a single Boltzmann function. These data provide the first description of Kv3 gating currents and give further insight into the interaction of BDS toxins and Kv3 channels.

  11. Modulation of Kv3 subfamily potassium currents by the sea anemone toxin BDS: significance for CNS and biophysical studies.

    PubMed

    Yeung, Shuk Yin M; Thompson, Dawn; Wang, Zhuren; Fedida, David; Robertson, Brian

    2005-09-21

    Kv3 potassium channels, with their ultra-rapid gating and high activation threshold, are essential for high-frequency firing in many CNS neurons. Significantly, the Kv3.4 subunit has been implicated in the major CNS disorders Parkinson's and Alzheimer's diseases, and it is claimed that selectively targeting this subunit will have therapeutic utility. Previous work suggested that BDS toxins ("blood depressing substance," from the sea anemone Anemonia sulcata) were specific blockers for rapidly inactivating Kv3.4 channels, and consequently these toxins are increasingly used as diagnostic agents for Kv3.4 subunits in central neurons. However, precisely how selective are these toxins for this important CNS protein? We show that BDS is not selective for Kv3.4 but markedly inhibits current through Kv3.1 and Kv3.2 channels. Inhibition comes about not by "pore block" but by striking modification of Kv3 gating kinetics and voltage dependence. Activation and inactivation kinetics are slowed by BDS-I and BDS-II, and V(1/2) for activation is shifted to more positive voltages. Alanine substitution mutagenesis around the S3b and S4 segments of Kv3.2 reveals that BDS acts via voltage-sensing domains, and, consistent with this, ON gating currents from nonconducting Kv3.2 are markedly inhibited. The altered kinetics and gating properties, combined with lack of subunit selectivity with Kv3 subunits, seriously affects the usefulness of BDS toxins in CNS studies. Furthermore, our results do not easily fit with the voltage sensor "paddle" structure proposed recently for Kv channels. Our data will be informative for experiments designed to dissect out the roles of Kv3 subunits in CNS function and dysfunction.

  12. Site-directed mutation studies of human liver cytochrome P-450 isoenzymes in the CYP2C subfamily.

    PubMed Central

    Veronese, M E; Doecke, C J; Mackenzie, P I; McManus, M E; Miners, J O; Rees, D L; Gasser, R; Meyer, U A; Birkett, D J

    1993-01-01

    Evidence from human studies in vivo and in vitro strongly suggests that the methylhydroxylation of tolbutamide and the 4-hydroxylation of phenytoin, the major pathways in the elimination of these two drugs, are catalysed by the same cytochrome P-450 isoenzyme(s). In the present study we used site-directed mutagenesis and cDNA expression in COS cells to characterize in detail the kinetics of tolbutamide and phenytoin hydroxylations by seven CYP2C proteins (2C8, 2C9 and variants, and 2C10) in order to define the effects of small changes in amino acid sequences and the likely proteins responsible in the metabolism of these two drugs in man. Tolbutamide was hydroxylated to varying extents by all expressed cytochrome P-450 isoenzymes, although activity was much lower for the expressed 2C8 protein. While the apparent Km values for the 2C9/10 isoenzymes (71.6-131.7 microM) were comparable with the range of apparent Km values previously observed in human liver microsomes, the apparent Km for 2C8 (650.5 microM) was appreciably higher. The 2C8 enzyme also showed quite different sulphaphenazole inhibition characteristics. The 4-hydroxylation of phenytoin was also more efficiently catalysed by the 2C9/10 enzymes. These enzymes showed similarities in kinetics of phenytoin hydroxylation and sulphaphenazole inhibition compared with human liver phenytoin hydroxylase. Also of interest was the observation that, among the 2C9 variants, small differences in amino acid composition could appreciably affect both tolbutamide and phenytoin hydroxylations. The amino acid substitution Cys-144-->Arg increased both the rates of tolbutamide and phenytoin hydroxylations, while the Leu-359-->Ile change had a greater effect on phenytoin hydroxylation. We conclude that: (1) although 2C8 and 2C9/10 proteins metabolize tolbutamide. only 2C9/10 proteins play a major role in human liver; (2) 2C9/10 proteins also appear to be chiefly responsible for phenytoin hydroxylation; and (3) subtle differences in the amino acid composition of these 2C9/10 proteins can affect the functional specificities towards both tolbutamide and phenytoin. Images Figure 2 PMID:8424795

  13. A distinct subfamily of papain-like cystein proteinases regulated by senescence and stresses in Glycine max.

    PubMed

    Esteban-García, Belén; Garrido-Cárdenas, José Antonio; Alonso, Diego López; García-Maroto, Federico

    2010-09-01

    GMCP3 encodes a cystein proteinase of Glycine max belonging to the papain-like family (C1A in MEROPS database) that was previously found to be involved in the mobilization of protein reserves during seed germination. Here, we report that GMCP3 is induced by senescence and diverse stresses in non-seed tissues, thus indicating a more general function in plants. Cladistic analysis of papain-like proteins of plants indicated that GMCP3, along with related proteases of other species, belongs to a distinct new group within the C1A family, which can also be distinguished by the four-exon structure of the gene. We also describe the genomic organization of GMCP3 revealing the presence of two closely related copies that are transcriptionally regulated in a similar way, although only one appears to be functional.

  14. Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms1[OPEN

    PubMed Central

    Dufayard, Jean-François; Chantret, Nathalie

    2016-01-01

    Gene duplications are an important factor in plant evolution, and lineage-specific expanded (LSE) genes are of particular interest. Receptor-like kinases expanded massively in land plants, and leucine-rich repeat receptor-like kinases (LRR-RLK) constitute the largest receptor-like kinases family. Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced flowering plant genomes, the complex evolutionary dynamics of this family was characterized in depth. We studied the involvement of selection during the expansion of this family among angiosperms. LRR-RLK subgroups harbor extremely contrasting rates of duplication, retention, or loss, and LSE copies are predominantly found in subgroups involved in environmental interactions. Expansion rates also differ significantly depending on the time when rounds of expansion or loss occurred on the angiosperm phylogenetic tree. Finally, using a dN/dS-based test in a phylogenetic framework, we searched for selection footprints on LSE and single-copy LRR-RLK genes. Selective constraint appeared to be globally relaxed at LSE genes, and codons under positive selection were detected in 50% of them. Moreover, the leucine-rich repeat domains, and specifically four amino acids in them, were found to be the main targets of positive selection. Here, we provide an extensive overview of the expansion and evolution of this very large gene family. PMID:26773008

  15. Diramus, a new genus of the leafhopper subfamily Evacanthinae (Hemiptera: Cicadellidae), with description of three new species from Thailand.

    PubMed

    Wang, Yang; Wei, Cong; Zhang, Yalin

    2013-01-01

    Diramus, gen. nov. (Hemiptera: Cicadellidae: Evacanthinae), and three new species, Diramus khaokus sp. nov., Diramus nigromaculatus sp. nov. and Diramus uncatus sp. nov., are described from Thailand. The differences between the new genus and the closely related genus Bundera Distant is discussed.

  16. UBC1 encodes a novel member of an essential subfamily of yeast ubiquitin-conjugating enzymes involved in protein degradation.

    PubMed Central

    Seufert, W; McGrath, J P; Jentsch, S

    1990-01-01

    The covalent attachment of ubiquitin to cellular proteins is catalyzed by members of a family of ubiquitin-conjugating enzymes. These enzymes participate in a variety of cellular processes, including selective protein degradation, DNA repair, cell cycle control, and sporulation. In the yeast Saccharomyces cerevisiae, two closely related ubiquitin-conjugating enzymes, UBC4 and UBC5, have recently been shown to mediate the selective degradation of short-lived and abnormal proteins. We have now identified a third distinct member of this class of ubiquitin-conjugating enzymes, UBC1. UBC1, UBC4 and UBC5 are functionally overlapping and constitute an enzyme family essential for cell growth and viability. All three mediate selective protein degradation, however, UBC1 appears to function primarily in the early stages of growth after germination of spores. ubc1 mutants generated by gene disruption display only a moderate slow growth phenotype, but are markedly impaired in growth following germination. Moreover, yeast carrying the ubc1ubc4 double mutation are viable as mitotic cells, however, these cells fail to survive after undergoing sporulation and germination. This specific requirement for UBC1 after a state of quiescence suggests that degradation of certain proteins may be crucial at this transition point in the yeast life cycle. Images Fig. 1. Fig. 4. Fig. 5. Fig. 6. PMID:2265617

  17. Intercontinental biogeography of subfamily Orontioideae (Symplocarpus, Lysichiton, and Orontium) of Araceae in Eastern Asia and North America.

    PubMed

    Nie, Ze-Long; Sun, Hang; Li, Heng; Wen, Jun

    2006-07-01

    Symplocarpus, Lysichiton, and Orontium (Orontioideae) are three of the few north temperate genera of the primarily tropical Araceae. Symplocarpus is disjunctly distributed in eastern Asia (3 spp.) and eastern North America (1 sp.); Lysichiton has an intercontinental discontinuous distribution in eastern Asia (1 sp.) and northwestern North America (1 sp.); and the monotypic Orontium is restricted to eastern North America. Phylogenetic analysis of the trnL-F and ndhF sequences supports (1) the monophyly of both Symplocarpus and Lysichiton, (2) the sister-group relationship of Symplocarpus and Lysichiton, and (3) the clade of Orontium, Symplocarpus, and Lysichiton. Although Symplocarpus shows a much wider disjunction than Lysichiton, the estimated divergence time of the former [4.49+/-1.69 or 6.88+/-4.18 million years ago (mya)] was similar to that of the latter (4.02+/-1.60 or 7.18+/-4.33 mya) based on the penalized likelihood and the Bayesian dating methods, respectively. Eastern Asia was suggested to be the ancestral area of the Symplocarpus-Lysichiton clade based on the dispersal-vicariance analysis. Our biogeographic results support independent migrations of Symplocarpus and Lysichiton across the Bering land bridge in the late Tertiary (Pliocene/late Miocene). Fossil evidence suggests Orontioideae dated back to the late Cretaceous in the temperate Northern Hemisphere (72 mya). The relative rate test shows similar substitution rates of the trnL-F sequences between the proto and the true aroids, although the latter has substantially higher species diversity. The proto Araceae perhaps suffered from a higher rate of extinction in the temperate zone associated with periods of climatic cooling in the Tertiary.

  18. Molecular variability of the COI fragment supports the systematic position of Enarmoniini within the subfamily Olethreutinae (Lepidoptera: Tortricidae).

    PubMed

    Razowski, Józef; Tarcz, Sebastian

    2014-01-01

    The Tortricidae, a globally distributed family of Lepidoptera, consists of approximately 10,000 described species, of which a large number do not have clearly defined taxonomic positions. In the present paper the systematics of Enarmoniini based on molecular data is compared to systematics based on morphology. Two genera of Enarmoniini were used for analysis: the type-genus Enarmonia (one species examined) and Ancylis (7 species examined). A comparison of a 606 bp homologous fragment of the COI mitochondrial gene revealed that Enarmoniini form a cluster distinct from Olethreutini (3 genera and 7 species examined), Eucosmini (2 genera, 4 species) and Grapholitini (4 genera, 9 species). In our opinion the molecular studies combined with previously obtained morphological data should facilitate a more natural classification system of this relatively poorly explored family of Microlepidoptera. Altogether, 30 species of Tortricidae were examined.

  19. Typification of species names in Adenocaulon and Eriachaenium (Compositae/Asteraceae, Subfamily Mutisioideae, Tribe Mutisieae, Subtribe Adenocaulinae)

    PubMed Central

    Funk, Vicki A.; Hind, D. J. Nicholas

    2016-01-01

    Abstract During the course of a recent research project on Adenocaulon and Eriachaenium it became apparent that some of the species names had not been typified. In this study we located and designated as much type material as possible for these two genera. We indicate holotypes or lectotypes where appropriate, including one for the type of the genus Adenocaulon. PMID:27698588

  20. Modulation of Kv3 Subfamily Potassium Currents by the Sea Anemone Toxin BDS: Significance for CNS and Biophysical Studies

    PubMed Central

    Yeung, Shuk Yin M.; Thompson, Dawn; Wang, Zhuren; Fedida, David; Robertson, Brian

    2005-01-01

    Kv3 potassium channels, with their ultra-rapid gating and high activation threshold, are essential for high-frequency firing in many CNS neurons. Significantly, the Kv3.4 subunit has been implicated in the major CNS disorders Parkinson’s and Alzheimer’s diseases, and it is claimed that selectively targeting this subunit will have therapeutic utility. Previous work suggested that BDS toxins (“blood depressing substance,” from the sea anemone Anemonia sulcata) were specific blockers for rapidly inactivating Kv3.4 channels, and consequently these toxins are increasingly used as diagnostic agents for Kv3.4 subunits in central neurons. However, precisely how selective are these toxins for this important CNS protein? We show that BDS is not selective for Kv3.4 but markedly inhibits current through Kv3.1 and Kv3.2 channels. Inhibition comes about not by “pore block” but by striking modification of Kv3 gating kinetics and voltage dependence. Activation and inactivation kinetics are slowed by BDS-I and BDS-II, and V1/2 for activation is shifted to more positive voltages. Alanine substitution mutagenesis around the S3b and S4 segments of Kv3.2 reveals that BDS acts via voltage-sensing domains, and, consistent with this, ON gating currents from nonconducting Kv3.2 are markedly inhibited. The altered kinetics and gating properties, combined with lack of subunit selectivity with Kv3 subunits, seriously affects the usefulness of BDS toxins in CNS studies. Furthermore, our results do not easily fit with the voltage sensor “paddle” structure proposed recently for Kv channels. Our data will be informative for experiments designed to dissect out the roles of Kv3 subunits in CNS function and dysfunction. PMID:16177043

  1. Catalog of the coleoptera of America North of Mexico. Family: Curculionidae. Subfamily: Polydrosinae. Tribe: Tanymecini. Agriculture handbook (Research)

    SciTech Connect

    Howden, A.T.

    1993-09-01

    The Coleoptera, or beetles, are represented in the world by about 220,000 described species, of which about 24,000 occur in the United States and Canada. A comprehensive taxonomic catalog of beetles for this area has not been available except the series of world-based 'Coleopterorum Catalogus' volumes (1909-present, Junk, Berlin).

  2. Karyotypic variation in Rhinophylla pumilio Peters, 1865 and comparative analysis with representatives of two subfamilies of Phyllostomidae (Chiroptera)

    PubMed Central

    Gomes, Anderson José Baia; Nagamachi, Cleusa Yoshiko; Rodrigues, Luís Reginaldo Ribeiro; Farias, Solange Gomes; Rissino, Jorge Dores; Pieczarka, Julio Cesar

    2012-01-01

    Abstract The family Phyllostomidae belongs to the most abundant and diverse group of bats in the Neotropics with more morphological traits variation at the family level than any other group within mammals. In this work, we present data of chromosome banding (G, C and Ag-NOR) and Fluorescence In Situ Hybridization (FISH) for representatives of Rhinophylla pumilio Peters, 1865 collected in four states of Brazil (Amazonas, Bahia, Mato Grosso and Pará). Two karyomorphs were found in this species: 2n=34, FN=64 in populations from western Pará and Mato Grosso states and 2n=34, FN=62 from Amazonas, Bahia, and northeastern Pará and Marajó Island (northern). Difference in the Fundamental Number is determined by variation in the size of the Nucleolar Organizer Region (NOR) accompanied with heterochromatin on chromosomes of pair 16 or, alternatively, a pericentric inversion. The C-banding technique detected constitutive heterochromatin in the centromeric regions of all chromosomes and on the distal part of the long arm of pair 15 of specimens from all localities. FISH with a DNA telomeric probe did not show any interstitial sequence, and an 18S rDNA probe and silver staining revealed the presence of NOR in the long arm of the pair 15, associated with heterochromatin, and in the short arm of the pair 16 for all specimens. The intra-specific analysis using chromosome banding did not show any significant difference between the samples. The comparative analyses using G-banding have shown that nearly all chromosomes of Rhinophylla pumilio were conserved in the chromosome complements of Glossophaga soricina Pallas, 1766, Phyllostomus hastatus Pallas, 1767, Phyllostomus discolor Wagner, 1843 and Mimon crenulatum Geoffroy, 1801, with a single chromosomal pair unique to Rhinophylla pumilio (pair 15). However, two chromosomes of Mimon crenulatum are polymorphic for two independent pericentric inversions. The karyotype with 2n=34, NF=62 is probably the ancestral one for the other karyotypes described for Rhinophylla pumilio. PMID:24260663

  3. Molecular Insights into the Klotho-Dependent, Endocrine Mode of Action of Fibroblast Growth Factor 19 Subfamily Members

    SciTech Connect

    Goetz,R.; Beenken, A.; Ibrahimi, O.; Kalinina, J.; Olsen, S.; Eliseenkova, A.; Xu, C.; Neubert, T.; Zhang, F.; et al.

    2007-01-01

    Unique among fibroblast growth factors (FGFs), FGF19, -21, and -23 act in an endocrine fashion to regulate energy, bile acid, glucose, lipid, phosphate, and vitamin D homeostasis. These FGFs require the presence of Klotho/{beta}Klotho in their target tissues. Here, we present the crystal structures of FGF19 alone and FGF23 in complex with sucrose octasulfate, a disaccharide chemically related to heparin. The conformation of the heparin-binding region between {beta} strands 10 and 12 in FGF19 and FGF23 diverges completely from the common conformation adopted by paracrine-acting FGFs. A cleft between this region and the {beta}1-{beta}2 loop, the other heparin-binding region, precludes direct interaction between heparin/heparan sulfate and backbone atoms of FGF19/23. This reduces the heparin-binding affinity of these ligands and confers endocrine function. Klotho/{beta}Klotho have evolved as a compensatory mechanism for the poor ability of heparin/heparan sulfate to promote binding of FGF19, -21, and -23 to their cognate receptors.

  4. On cockroaches of the subfamily Epilamprinae (Dictyoptera: Blaberidae) from South India and Sri Lanka, with descriptions of new taxa.

    PubMed

    Anisyutkin, Leonid N

    2014-08-08

    The new genus Indoapterolampra, gen. nov. and two new species (I. rugosiuscula sp. nov. and Morphna lucida sp. nov.) are described. Rhabdoblatta praecipua (Walker, 1868) is removed from the synonymy with 'Polyzosteria' terranea Walker, 1868. The latter species is considered Epilamprinae gen. sp. The lectotype of Phoraspis (Thorax) porcellana Saussure, 1862 is designated. A key for the genera of Epilamprinae from South India and Sri Lanka is provided. Detailed morphological descriptions of the studied taxa are given. The structure of the male genitalia of I. rugosiuscula sp. nov., M. lucida sp. nov., M. plana (Brunner von Wattenwyl, 1865), M. decolyi (Bolivar, 1897) and R. praecipua and that of the female genital complex of M. decolyi, P. (T.) porcellana and Phlebonotus anomalus (Saussure, 1863) are described for the first time. Some aspects of the cockroach evolution are briefly discussed. 

  5. Systematic Analysis of the Maize PHD-Finger Gene Family Reveals a Subfamily Involved in Abiotic Stress Response.

    PubMed

    Wang, Qianqian; Liu, Jinyang; Wang, Yu; Zhao, Yang; Jiang, Haiyang; Cheng, Beijiu

    2015-09-30

    Plant homeodomain (PHD)-finger proteins were found universally in eukaryotes and known as key players in regulating transcription and chromatin structure. Many PHD-finger proteins have been well studied on structure and function in animals. Whereas, only a few of plant PHD-finger factors had been characterized, and majority of PHD-finger proteins were functionally unclear. In this study, a complete comprehensive analysis of maize PHD family is presented. Sixty-seven PHD-finger genes in maize were identified and further divided into ten groups according to phylogenetic analysis that was supported by motif and intron/exon analysis. These genes were unevenly distributed on ten chromosomes and contained 12 segmental duplication events, suggesting that segmental duplications were the major contributors in expansion of the maize PHD family. The paralogous genes mainly experienced purifying selection with restrictive functional divergence after the duplication events on the basis of the Ka/Ks ratio. Gene digital expression analysis showed that the PHD family had a wide expression profile in maize development. In addition, 15 potential stress response genes were detected by promoter cis-element and expression analysis. Two proteins ZmPHD14 and ZmPHD19 were located in the nucleus. These results provided a solid base for future functional genome study of the PHD-finger family in maize and afforded important clues for characterizing and cloning potentially important candidates in response to abiotic stresses.

  6. Glycosyltransferase Family 43 Is Also Found in Early Eukaryotes and Has Three Subfamilies in Charophycean Green Algae

    PubMed Central

    Taujale, Rahil; Yin, Yanbin

    2015-01-01

    The glycosyltransferase family 43 (GT43) has been suggested to be involved in the synthesis of xylans in plant cell walls and proteoglycans in animals. Very recently GT43 family was also found in Charophycean green algae (CGA), the closest relatives of extant land plants. Here we present evidence that non-plant and non-animal early eukaryotes such as fungi, Haptophyceae, Choanoflagellida, Ichthyosporea and Haptophyceae also have GT43-like genes, which are phylogenetically close to animal GT43 genes. By mining RNA sequencing data (RNA-Seq) of selected plants, we showed that CGA have evolved three major groups of GT43 genes, one orthologous to IRX14 (IRREGULAR XYLEM14), one orthologous to IRX9/IRX9L and the third one ancestral to all land plant GT43 genes. We confirmed that land plant GT43 has two major clades A and B, while in angiosperms, clade A further evolved into three subclades and the expression and motif pattern of A3 (containing IRX9) are fairly different from the other two clades likely due to rapid evolution. Our in-depth sequence analysis contributed to our overall understanding of the early evolution of GT43 family and could serve as an example for the study of other plant cell wall-related enzyme families. PMID:26023931

  7. Glycosyltransferase family 43 is also found in early eukaryotes and has three subfamilies in Charophycean green algae.

    PubMed

    Taujale, Rahil; Yin, Yanbin

    2015-01-01

    The glycosyltransferase family 43 (GT43) has been suggested to be involved in the synthesis of xylans in plant cell walls and proteoglycans in animals. Very recently GT43 family was also found in Charophycean green algae (CGA), the closest relatives of extant land plants. Here we present evidence that non-plant and non-animal early eukaryotes such as fungi, Haptophyceae, Choanoflagellida, Ichthyosporea and Haptophyceae also have GT43-like genes, which are phylogenetically close to animal GT43 genes. By mining RNA sequencing data (RNA-Seq) of selected plants, we showed that CGA have evolved three major groups of GT43 genes, one orthologous to IRX14 (IRREGULAR XYLEM14), one orthologous to IRX9/IRX9L and the third one ancestral to all land plant GT43 genes. We confirmed that land plant GT43 has two major clades A and B, while in angiosperms, clade A further evolved into three subclades and the expression and motif pattern of A3 (containing IRX9) are fairly different from the other two clades likely due to rapid evolution. Our in-depth sequence analysis contributed to our overall understanding of the early evolution of GT43 family and could serve as an example for the study of other plant cell wall-related enzyme families.

  8. Microsatellite spreading in the human genome: evolutionary mechanisms and structural implications.

    PubMed

    Nadir, E; Margalit, H; Gallily, T; Ben-Sasson, S A

    1996-06-25

    Microsatellites are tandem repeat sequences abundant in the genomes of higher eukaryotes and hitherto considered as "junk DNA." Analysis of a human genome representative data base (2.84 Mb) reveals a distinct juxtaposition of A-rich microsatellites and retroposons and suggests their coevolution. The analysis implies that most microsatellites were generated by a 3'-extension of retrotranscripts, similar to mRNA polyadenylylation, and that they serve in turn as "retroposition navigators," directing the retroposons via homology-driven integration into defined sites. Thus, they became instrumental in the preservation and extension of primordial genomic patterns. A role is assigned to these reiterating A-rich loci in the higher-order organization of the chromatin. The disease-associated triplet repeats are mostly found in coding regions and do not show an association with retroposons, constituting a unique set within the family of microsatellite sequences.

  9. Structure of Human B12 Trafficking Protein CblD Reveals Molecular Mimicry and Identifies a New Subfamily of Nitro-FMN Reductases.

    PubMed

    Yamada, Kazuhiro; Gherasim, Carmen; Banerjee, Ruma; Koutmos, Markos

    2015-12-04

    In mammals, B12 (or cobalamin) is an essential cofactor required by methionine synthase and methylmalonyl-CoA mutase. A complex intracellular pathway supports the assimilation of cobalamin into its active cofactor forms and delivery to its target enzymes. MMADHC (the methylmalonic aciduria and homocystinuria type D protein), commonly referred to as CblD, is a key chaperone involved in intracellular cobalamin trafficking, and mutations in CblD cause methylmalonic aciduria and/or homocystinuria. Herein, we report the first crystal structure of the globular C-terminal domain of human CblD, which is sufficient for its interaction with MMADHC (the methylmalonic aciduria and homocystinuria type C protein), or CblC, and for supporting the cytoplasmic cobalamin trafficking pathway. CblD contains an α+β fold that is structurally reminiscent of the nitro-FMN reductase superfamily. Two of the closest structural relatives of CblD are CblC, a multifunctional enzyme important for cobalamin trafficking, and the activation domain of methionine synthase. CblD, CblC, and the activation domain of methionine synthase share several distinguishing features and, together with two recently described corrinoid-dependent reductive dehalogenases, constitute a new subclass within the nitro-FMN reductase superfamily. We demonstrate that CblD enhances oxidation of cob(II)alamin bound to CblC and that disease-causing mutations in CblD impair the kinetics of this reaction. The striking structural similarity of CblD to CblC, believed to be contiguous in the cobalamin trafficking pathway, suggests the co-option of molecular mimicry as a strategy for achieving its function.

  10. Cytogenetic analyses of five amazon lizard species of the subfamilies Teiinae and Tupinambinae and review of karyotyped diversity the family Teiidae.

    PubMed

    Carvalho, Natália Dayane Moura; Arias, Federico José; da Silva, Francijara Araújo; Schneider, Carlos Henrique; Gross, Maria Claudia

    2015-01-01

    Lizards of the family Teiidae (infraorder Scincomorpha) were formerly known as Macroteiidae. There are 13 species of such lizards in the Amazon, in the genera Ameiva (Meyer, 1795), Cnemidophorus (Wagler, 1830), Crocodilurus (Spix, 1825), Dracaena (Daudin, 1801), Kentropyx (Spix, 1825) and Tupinambis (Daudin, 1802). Cytogenetic studies of this group are restricted to karyotype macrostructure. Here we give a compilation of cytogenetic data of the family Teiidae, including classic and molecular cytogenetic analysis of Ameiva ameiva (Linnaeus, 1758), Cnemidophorus sp.1, Kentropyx calcarata (Spix, 1825), Kentropyx pelviceps (Cope, 1868) and Tupinambis teguixin (Linnaeus, 1758) collected in the state of Amazonas, Brazil. Ameiva ameiva, Kentropyx calcarata and Kentropyx pelviceps have 2n=50 chromosomes classified by a gradual series of acrocentric chromosomes. Cnemidophorus sp.1 has 2n=48 chromosomes with 2 biarmed chromosomes, 24 uniarmed chromosomes and 22 microchromosomes. Tupinambis teguixin has 2n=36 chromosomes, including 12 macrochromosomes and 24 microchromosomes. Constitutive heterochromatin was distributed in the centromeric and terminal regions in most chromosomes. The nucleolus organizer region was simple, varying in its position among the species, as evidenced both by AgNO3 impregnation and by hybridization with 18S rDNA probes. The data reveal a karyotype variation with respect to the diploid number, fundamental number and karyotype formula, which reinforces the importance of increasing chromosomal analyses in the Teiidae.

  11. The RNA binding protein HuR determines the differential translation of autism-associated FoxP subfamily members in the developing neocortex

    PubMed Central

    Popovitchenko, T.; Thompson, K.; Viljetic, B.; Jiao, X.; Kontonyiannis, D. L.; Kiledjian, M.; Hart, R. P.; Rasin, M. R.

    2016-01-01

    Forkhead-box domain (Fox) containing family members are known to play a role in neocorticogenesis and have also been associated with disorders on the autism spectrum. Here we show that a single RNA-binding protein, Hu antigen R (HuR), dictates translation specificity of bound mRNAs and is sufficient to define distinct Foxp-characterized subpopulations of neocortical projection neurons. Furthermore, distinct phosphorylation states of HuR differentially regulate translation of Foxp mRNAs in vitro. This demonstrates the importance of RNA binding proteins within the framework of the developing brain and further confirms the role of mRNA translation in autism pathogenesis. PMID:27383233

  12. Evolution of a Neotropical marine fish lineage (Subfamily Chaenopsinae, Suborder Blennioidei) based on phylogenetic analysis of combined molecular and morphological data.

    PubMed

    Lin, Hsiu-Chin; Hastings, Philip A

    2011-08-01

    Phylogenetic relationships within tube blennies (Chaenopsinae) were reconstructed using Bayesian, maximum parsimony and likelihood analyses of multiple molecular markers (mitochondrial DNA: COI; nuclear DNA: TMO-4C4, RAG1, Rhodopsin, and Histone H3) and 148 morphological characters. This total-evidence based topology is well-resolved and congruent across analytical methods with strong support for the monophyly of the Chaenopsinae, all included genera and several internal nodes. A rapid radiation in the early evolution of chaenopsins is inferred from the relatively poor support values for relationships among basal lineages and their divergence into different habitats (rocky reefs, coral reefs and the reef/sand interface). Rates of molecular evolution in chaenopsins, as inferred by divergence among four putative transisthmian geminate species pairs, are rapid compared to other fishes. Conflicts among genetic markers and morphology are especially evident within the genus Coralliozetus, with different species relationships supported by morphology, TMO-4C4, and RAG1 plus Rhodopsin. This study hypothesizes a novel sistergroup relationship between Ekemblemaria and Hemiemblemaria, consistent with morphological, molecular and habitat use data. Our total evidence phylogenetic hypothesis indicates that previously hypothesized morphological characters supporting a close relationship between Hemiemblemaria and Chaenopsis plus Lucayablennius resulted from convergent evolution in these relatively free-swimming blennies.

  13. Species diversity and peptide toxins blocking selectivity of ether-a-go-go-related gene subfamily K+ channels in the central nervous system.

    PubMed

    Restano-Cassulini, Rita; Korolkova, Yuliya V; Diochot, Sylvie; Gurrola, Georgina; Guasti, Leonardo; Possani, Lourival D; Lazdunski, Michel; Grishin, Eugene V; Arcangeli, Annarosa; Wanke, Enzo

    2006-05-01

    The ether-à-go-go-related gene (erg) K+ channels are known to be crucial for life in Caenorhabditis elegans (mating), Drosophila melanogaster (seizure), and humans (LQT syndrome). The erg genes known to date (erg1, erg2, and erg3) are highly expressed in various areas of the rat and mouse central nervous system (CNS), and ERG channel blockers alter firing accommodation. To assign physiological roles to each isoform, it is necessary to design pharmacological strategies to distinguish individual currents. To this purpose, we have investigated the blocking properties of specific peptide inhibitors of hERG1 channels on the human and rat isoforms. In particular, we have tested ErgTx1 (from the scorpion Centruroides noxious), BeKm-1 (from the scorpion Buthus eupeus), and APETx1 (from the sea anemone Anthopleura elegantissima). Because these peptides had different species-specific effects on the six different channels, we have also carried out a biophysical characterization of hERG2 and hERG3 channels that turned out to be different from the rat homologs. It emerged that APETx1 is exquisitely selective for ERG1 and does not compete with the other two toxins. BeKm-1 discriminates well among the three rat members. ErgTx1 is unable to block hERG2, but blocks rERG2 and has the lowest KD for hERG3. BeKm-1 and ErgTx1 compete for hERG3 but not for rERG2 blockade. Our findings should be helpful for structure-function studies and for novel CNS ERG-specific drug design.

  14. Structure of Human B12 Trafficking Protein CblD Reveals Molecular Mimicry and Identifies a New Subfamily of Nitro-FMN Reductases*

    PubMed Central

    Yamada, Kazuhiro; Gherasim, Carmen; Banerjee, Ruma; Koutmos, Markos

    2015-01-01

    In mammals, B12 (or cobalamin) is an essential cofactor required by methionine synthase and methylmalonyl-CoA mutase. A complex intracellular pathway supports the assimilation of cobalamin into its active cofactor forms and delivery to its target enzymes. MMADHC (the methylmalonic aciduria and homocystinuria type D protein), commonly referred to as CblD, is a key chaperone involved in intracellular cobalamin trafficking, and mutations in CblD cause methylmalonic aciduria and/or homocystinuria. Herein, we report the first crystal structure of the globular C-terminal domain of human CblD, which is sufficient for its interaction with MMADHC (the methylmalonic aciduria and homocystinuria type C protein), or CblC, and for supporting the cytoplasmic cobalamin trafficking pathway. CblD contains an α+β fold that is structurally reminiscent of the nitro-FMN reductase superfamily. Two of the closest structural relatives of CblD are CblC, a multifunctional enzyme important for cobalamin trafficking, and the activation domain of methionine synthase. CblD, CblC, and the activation domain of methionine synthase share several distinguishing features and, together with two recently described corrinoid-dependent reductive dehalogenases, constitute a new subclass within the nitro-FMN reductase superfamily. We demonstrate that CblD enhances oxidation of cob(II)alamin bound to CblC and that disease-causing mutations in CblD impair the kinetics of this reaction. The striking structural similarity of CblD to CblC, believed to be contiguous in the cobalamin trafficking pathway, suggests the co-option of molecular mimicry as a strategy for achieving its function. PMID:26364851

  15. TRPA5, an Ankyrin Subfamily Insect TRP Channel, is Expressed in Antennae of Cydia pomonella (Lepidoptera: Tortricidae) in Multiple Splice Variants

    PubMed Central

    Cattaneo, Alberto Maria; Bengtsson, Jonas Martin; Montagné, Nicolas; Jacquin-Joly, Emmanuelle; Rota-Stabelli, Omar; Salvagnin, Umberto; Bassoli, Angela; Witzgall, Peter; Anfora, Gianfranco

    2016-01-01

    Transient receptor potential (TRP) channels are an ancient family of cation channels, working as metabotropic triggers, which respond to physical and chemical environmental cues. Perception of chemical signals mediate reproductive behaviors and is therefore an important target for sustainable management tactics against the codling moth Cydia pomonella L. (Lepidoptera: Tortricidae). However, olfactory behavior strongly depends on diel periodicity and correlation of chemical with physical cues, like temperature, and physical cues thus essentially contribute to the generation of behavioral response. From an antennal transcriptome generated by next generation sequencing, we characterized five candidate TRPs in the codling moth. The coding DNA sequence of one of these was extended to full length, and phylogenetic investigation revealed it to be orthologous of the TRPA5 genes, reported in several insect genomes as members of the insect TRPA group with unknown function but closely related to the thermal sensor pyrexia. Reverse transcription PCR revealed the existence of five alternate splice forms of CpTRPA5. Identification of a novel TRPA and its splice forms in codling moth antennae open for investigation of their possible sensory roles and implications in behavioral responses related to olfaction. PMID:27638948

  16. Involvement of the CYP78A subfamily of cytochrome P450 monooxygenases in protonema growth and gametophore formation in the moss Physcomitrella patens.

    PubMed

    Katsumata, Takumi; Fukazawa, Jutarou; Magome, Hiroshi; Jikumaru, Yusuke; Kamiya, Yuji; Natsume, Masahiro; Kawaide, Hiroshi; Yamaguchi, Shinjiro

    2011-01-01

    CYP78 is a plant-specific family of cytochrome P450 monooxygenases, some members of which regulate the plastochron length and organ size in angiosperms. The CYP78 family appears to be highly conserved in land plants, but there have been no reports on the role of CYP78s in bryophytes. The moss, Physcomitrella patens, possesses two CYP78As, CYP78A27 and CYP78A28. We produced single and double mutants and overexpression lines for CYP78A27 and CYP78A28 by gene targeting to investigate the function of CYP78As in P. patens. Neither the cyp78a27 nor cyp78a28 single mutant showed any obvious phenotype, while the double mutant exhibited severely retarded protonemal growth and gametophore development. The endogenous levels of some plant hormones were also altered in the double mutant. Transgenic lines that overexpressed CYP78A27 or CYP78A28 showed delayed and reduced bud formation. Our results suggest that CYP78As participate in the synthesis of a critical growth regulator in P. patens.

  17. A revision of the haploporinae nicoll, 1914 (digenea: haploporidae) from mullets (mugilidae): two new haploporine genera and a key to the genera of the subfamily.

    PubMed

    Blasco-Costa, Isabel; Montero, Francisco E; Gibson, David I; Balbuena, Juan Antonio; Kostadinova, Aneta

    2009-03-01

    Two new haploporine genera are established for parasites of mullets. Ragaia n. g. is erected for R. lizae n. sp. from Liza ramado in the Ebro Delta on the Mediterranean Coast of Spain. This new genus is distinguished by the unique combination of the following characters: a strongly muscular ventral sucker which is twice as large as the oral sucker; a large, muscular hermaphroditic sac similar in length to the ventral sucker; a saccular, thick-walled internal seminal vesicle which is larger than the external seminal vesicle; and the ovary and vitellarium located rather close to the posterior extremity. Pseudodicrogaster n. g. is erected to accommodate Dicrogaster japonica Machida, 1996, as P. japonica (Machida, 1996) n. comb., a parasite of Mugil cephalus L. off Fukaura, Japan. This genus is recognised on the basis of: the tubular condition of both the internal and external seminal vesicles, the latter being much shorter than the former; the sucker ratio; the massive pyriform hermaphroditic sac; the location of the testis; and the presence of two eye-spots in developed miracidia. A key to the nine recognised genera of the Haploporinae is presented.

  18. Keylimepie peckorum gen. n. and sp. n., (Hymenoptera, Braconidae) from southern Florida, U.S., the first known brachypterous member of the subfamily Microgastrinae.

    PubMed

    Fernandez-Triana, Jose; Boudreault, Caroline

    2016-01-01

    Keylimepie peckorum Fernandez-Triana, gen. n. and sp. n., are described from southern Florida, U.S. Females have the shortest wings (0.6-0.7 × body length) of any known microgastrine wasp. The genus can also be recognized on features of the head, propodeum and first three metasomal tergites. All specimens were collected in hammock forests of the Florida Keys and Everglades National Park, but their host caterpillar is unknown. Because its morphology is unique and it is the first new microgastrine genus discovered in North America since 1985, the potential for future conservation of the species is discussed.

  19. New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium

    SciTech Connect

    Michalska, Karolina; Brown, Roslyn N.; Li, Hui; Jedrzejczak, Robert; Niemann, George; Heffron, Fred; Cort, John R.; Adkins, Joshua N.; Babnigg, Gyorgy; Joachimiak, Andrzej

    2013-03-01

    Phage viruses that infect prokaryotes integrate their genome into the host chromosome; thus, microbial genomes typically contain genetic remnants of both recent and ancient phage infections. Often phage genes occur in clusters of atypical G+C content that reflect integration of the foreign DNA. However, some phage genes occur in isolation without other phage gene neighbors, probably resulting from horizontal gene transfer. In these cases, the phage gene product is unlikely to function as a component of a mature phage particle, and instead may have been co-opted by the host for its own benefit. The product of one such gene from Salmonella enterica serovar Typhimurium, STM3605, encodes a protein with modest sequence similarity to phage-like lysozyme (N-acetylmuramidase) but appears to lack essential catalytic residues that are strictly conserved in all lysozymes. Close homologs in other bacteria share this characteristic. The structure of the STM3605 protein was characterized by X-ray crystallography, and functional assays showed that it is a stable, folded protein whose structure closely resembles lysozyme. However, this protein is unlikely to hydrolyze peptidoglycan. Instead, STM3605 is presumed to have evolved an alternative function because it shows some lytic activity and partitions to micelles.

  20. Differential expression of human cytochrome P450 enzymes from the CYP3A subfamily in the brains of alcoholic subjects and drug-free controls.

    PubMed

    Booth Depaz, Iris M; Toselli, Francesca; Wilce, Peter A; Gillam, Elizabeth M J

    2013-06-01

    Cytochrome P450 enzymes are responsible for the metabolism of most commonly used drugs. Among these enzymes, CYP3A forms mediate the clearance of around 40-50% of drugs and may also play roles in the biotransformation of endogenous compounds. CYP3A forms are expressed both in the liver and extrahepatically. However, little is known about the expression of CYP3A proteins in specific regions of the human brain. In this study, form-selective antibodies raised to CYP3A4 and CYP3A5 were used to characterize the expression of these forms in the human brain. Both CYP3A4 and CYP3A5 immunoreactivity were found to varying extents in the microsomal fractions of cortex, hippocampus, basal ganglia, amygdala, and cerebellum. However, only CYP3A4 expression was observed in the mitochondrial fractions of these brain regions. N-terminal sequencing confirmed the principal antigen detected by the anti-CYP3A4 antibody in cortical microsomes to be CYP3A4. Immunohistochemical analysis revealed that CYP3A4 and CYP3A5 expression was primarily localized in the soma and axonal hillock of neurons and varied according to cell type and cell layer within brain regions. Finally, analysis of the frontal cortex of chronic alcohol abusers revealed elevated expression of CYP3A4 in microsomal but not mitochondrial fractions; CYP3A5 expression was unchanged. The site-specific expression of CYP3A4 and CYP3A5 in the human brain may have implications for the role of these enzymes in both normal brain physiology and the response to drugs.

  1. A PPR protein in the PLS subfamily stabilizes the 5′-end of processed rpl16 mRNAs in maize chloroplasts

    PubMed Central

    Hammani, Kamel; Takenaka, Mizuki; Miranda, Rafael; Barkan, Alice

    2016-01-01

    Pentatricopeptide repeat (PPR) proteins are a large family of helical-repeat proteins that bind RNA in mitochondria and chloroplasts. Precise RNA targets and functions have been assigned to only a small fraction of the >400 members of the PPR family in plants. We used the amino acid code governing the specificity of RNA binding by PPR repeats to infer candidate-binding sites for the maize protein PPR103 and its ortholog Arabidopsis EMB175. Genetic and biochemical data confirmed a predicted binding site in the chloroplast rpl16 5′UTR to be a site of PPR103 action. This site maps to the 5′ end of transcripts that fail to accumulate in ppr103 mutants. A small RNA corresponding to the predicted PPR103 binding site accumulates in a PPR103-dependent fashion, as expected of PPR103's in vivo footprint. Recombinant PPR103 bound specifically to this sequence in vitro. These observations imply that PPR103 stabilizes rpl16 mRNA by impeding 5′→3′ RNA degradation. Previously described PPR proteins with this type of function consist of canonical PPR motifs. By contrast, PPR103 is a PLS-type protein, an architecture typically associated with proteins that specify sites of RNA editing. However, PPR103 is not required to specify editing sites in chloroplasts. PMID:27095196

  2. Lenticellaria and Hillerella, new kraussinoid genera (Kraussinoidea, Brachiopoda) from Indo-Pacific and Red Sea waters: evolution in the subfamily Megerliinae.

    PubMed

    Simon, Eric G; Logan, Alan; Zuschin, Martin; Mainguy, Jerome; Mottequin, Bernard

    2016-07-08

    Two new kraussinid brachiopod genera, namely Lenticellaria gen. nov. and Hillerella gen. nov. are described from Pacific waters in the sub-equatorial zone in the Indonesian Archipelago, from Indian Ocean waters in Madagascar and from Red Sea waters in Egypt (Gulf of Aqaba) and Sudan. This fills the equatorial gap in the distribution of the superfamily Kraussinoidea, known from higher latitudes in both hemispheres. The micromorphic new material described is an excellent example of homeomorphy in brachiopods. It also provides new information on the distribution of the genus Megerlia sensu stricto and illustrates subtle variations in the evolutionary process of the reduced brachidium in Kraussinoidea.

  3. Description of Oculogryphus shuensis sp. n. (Coleoptera, Lampyridae), the first species of the genus in the Sino-Japanese realm, with a modified key to the subfamily Ototretinae

    PubMed Central

    Jeng, Ming-Luen; Engel, Michael S.

    2014-01-01

    Abstract A new species of the lampyrid genus Oculogryphus Jeng, Engel, and Yang, O. shuensis sp. n. from China (Sichuan Province) is described and figured. The genus previously was known only from Vietnam, and the new species is the first representative of the genus in the Sino-Japanese zoogeographic realm. Some morphological variations of Oculogryphus and the allied genus Stenocladius are discussed and a modification to the most recent key to ototretine genera is proposed to accommodate Oculogryphus. PMID:24574852

  4. Characterization of cDNAs of the human pregnancy-specific beta1-glycoprotein family, a new subfamily of the immunoglobulin gene superfamily

    SciTech Connect

    Zheng, Q.X.; Tease, L.A.; Shupert, W.L.; Chan, W.Y. )

    1990-03-20

    Three highly homologous cDNAs encoding human pregnancy-specific {beta}1-glycoprotein (SP1) were isolated from a human placental cDNA library. These cDNAs share >90% nucleotide homology in their coding sequences, and >79% of the encoded amino acids are homologous. Proteins encoded by these cDNAs are very similar to members of the carcinoembryonic antigen family and contain repeating domains, conserved disulfided bridges, and {beta}-sheet structure typical of the immunoglobulin gene superfamily. However, the high degree of sequence homology and relatively lesser degree of glycosylation among the SP1 proteins suggest that they exist as a unique family instead of being members of the CEA family. Both soluble and potentially membrane-bound forms of SP1 proteins were present in the placenta. Northern blot analysis using specific probes confirmed the expression of multiple mRNA species in human term placenta.

  5. Review and new subfamily placement of the plant bug genus Isometocoris Carvalho and Sailer, 1954 (Hemiptera: Heteroptera: Miridae), with the description of a new species from Brazil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The genus Isometocoris Carvalho and Sailer is reviewed and I. penicillus, new species, from Brazil is described. Diagnoses of the genus and included species I. blantoni Carvalho and Sailer and I. penicillus, n. sp., are given; a color adult habitus photo of both Isometocoris species, male genitalic ...

  6. Systematics of Australian Thrasorinae (Hymenoptera: Cynipoidea: Figitidae) with a description of Mikeiinae, new subfamily, and two new genera and three new species

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new systematics of Australian Thrasorinae is proposed herein. The genus Mikeius is transferred from Thrasorinae to Mikeiinae Paretas-Martínez & Pujade-Villar n. subf and M. clavata Pujade-Villar & Restrepo-Ortiz n. sp. is described. Two new genera of Thrasorinae are erected: Cicatrix Paretas-Martí...

  7. The members of M20D peptidase subfamily from Burkholderia cepacia, Deinococcus radiodurans and Staphylococcus aureus (HmrA) are carboxydipeptidases, primarily specific for Met-X dipeptides.

    PubMed

    Jamdar, Sahayog N; Are, Venkata N; Navamani, Mallikarjunan; Kumar, Saurabh; Nagar, Vandan; Makde, Ravindra D

    2015-12-01

    Three members of peptidase family M20D from Burkholderia cepacia (BcepM20D; Uniprot accession no. A0A0F7GQ23), Deinococcus radiodurans R1 (DradM20D; Uniprot accession no. Q9RTP6) and Staphylococcus aureus (HmrA; Uniprot accession no. Q99Q45) were characterized in terms of their preference for various substrates. The results thus reveal that all the enzymes including HmrA lack endopeptidase as well as aminopeptidase activities and possess strong carboxypeptidase activity. Further, the amidohydrolase activity exerted on other substrates like N-Acetyl-Amino acids, N-Carbobenzoxyl-Amino acids and Indole acetic acid (IAA)-Amino acids is due to the ability of these enzymes to accommodate different types of chemical groups other than the amino acid at the S1 pocket. Further, data on peptide hydrolysis strongly suggests that all the three enzymes are primarily carboxydipeptidases exhibiting highest catalytic efficiency (kcat/Km 5-36 × 10(5) M(-1) s(-1)) for Met-X substrates, where -X could be Ala/Gly/Ser/Tyr/Phe/Leu depending on the source organism. The supportive evidence for the substrate specificities was also provided with the molecular docking studies carried out using structure of SACOL0085 and homology modelled structure of BcepM20D. The preference for different substrates, their binding at active site of the enzyme and possible role of these enzymes in recycling of methionine are discussed in this study.

  8. Characterization of Non-Specific Cytotoxic Cell Receptor Protein 1: A New Member of the Lectin-Type Subfamily of F-Box Proteins

    PubMed Central

    Kallio, Heini; Tolvanen, Martti; Jänis, Janne; Pan, Pei-wen; Laurila, Eeva; Kallioniemi, Anne; Kilpinen, Sami; Tuominen, Vilppu J.; Isola, Jorma; Valjakka, Jarkko; Pastorekova, Silvia; Pastorek, Jaromir; Parkkila, Seppo

    2011-01-01

    Our previous microarray study showed that the non-specific cytotoxic cell receptor protein 1 (Nccrp1) transcript is significantly upregulated in the gastric mucosa of carbonic anhydrase IX (CA IX)-deficient (Car9−/−) mice. In this paper, we aimed to characterize human NCCRP1 and to elucidate its relationship to CA IX. Recombinant NCCRP1 protein was expressed in Escherichia coli, and a novel polyclonal antiserum was raised against the purified full-length protein. Immunocytochemistry showed that NCCRP1 is expressed intracellularly, even though it has previously been described as a transmembrane protein. Using bioinformatic analyses, we identified orthologs of NCCRP1 in 35 vertebrate genomes, and up to five paralogs per genome. These paralogs are FBXO genes whose protein products are components of the E3 ubiquitin ligase complexes. NCCRP1 proteins have no signal peptides or transmembrane domains. NCCRP1 has mainly been studied in fish and was thought to be responsible for the cytolytic function of nonspecific cytotoxic cells (NCCs). Our analyses showed that in humans, NCCRP1 mRNA is expressed in tissues containing squamous epithelium, whereas it shows a more ubiquitous tissue expression pattern in mice. Neither human nor mouse NCCRP1 expression is specific to immune tissues. Silencing CA9 using siRNAs did not affect NCCRP1 levels, indicating that its expression is not directly regulated by CA9. Interestingly, silencing NCCRP1 caused a statistically significant decrease in the growth of HeLa cells. These studies provide ample evidence that the current name, “non-specific cytotoxic cell receptor protein 1,” is not appropriate. We therefore propose that the gene name be changed to FBXO50. PMID:22087255

  9. Biophysical characterization of the honeybee DSC1 orthologue reveals a novel voltage-dependent Ca2+ channel subfamily: CaV4

    PubMed Central

    Gosselin-Badaroudine, Pascal; Moreau, Adrien; Simard, Louis; Cens, Thierry; Rousset, Matthieu; Collet, Claude; Charnet, Pierre

    2016-01-01

    Bilaterian voltage-gated Na+ channels (NaV) evolved from voltage-gated Ca2+ channels (CaV). The Drosophila melanogaster Na+ channel 1 (DSC1), which features a D-E-E-A selectivity filter sequence that is intermediate between CaV and NaV channels, is evidence of this evolution. Phylogenetic analysis has classified DSC1 as a Ca2+-permeable Na+ channel belonging to the NaV2 family because of its sequence similarity with NaV channels. This is despite insect NaV2 channels (DSC1 and its orthologue in Blatella germanica, BSC1) being more permeable to Ca2+ than Na+. In this study, we report the cloning and molecular characterization of the honeybee (Apis mellifera) DSC1 orthologue. We reveal several sequence variations caused by alternative splicing, RNA editing, and genomic variations. Using the Xenopus oocyte heterologous expression system and the two-microelectrode voltage-clamp