Science.gov

Sample records for sider retroposon subfamilies

  1. Molecular evolution. Retroposon revivals.

    PubMed

    Brookfield, J F

    1995-03-01

    Phylogenetic studies of the mouse L1 retroposon family show that the elements evolve through successively active subfamilies, which differ from each other by complete replacements of their promoter sequences.

  2. Members of a large retroposon family are determinants of post-transcriptional gene expression in Leishmania.

    PubMed

    Bringaud, Frédéric; Müller, Michaela; Cerqueira, Gustavo Coutinho; Smith, Martin; Rochette, Annie; El-Sayed, Najib M A; Papadopoulou, Barbara; Ghedin, Elodie

    2007-09-01

    Trypanosomatids are unicellular protists that include the human pathogens Leishmania spp. (leishmaniasis), Trypanosoma brucei (sleeping sickness), and Trypanosoma cruzi (Chagas disease). Analysis of their recently completed genomes confirmed the presence of non-long-terminal repeat retrotransposons, also called retroposons. Using the 79-bp signature sequence common to all trypanosomatid retroposons as bait, we identified in the Leishmania major genome two new large families of small elements--LmSIDER1 (785 copies) and LmSIDER2 (1,073 copies)--that fulfill all the characteristics of extinct trypanosomatid retroposons. LmSIDERs are approximately 70 times more abundant in L. major compared to T. brucei and are found almost exclusively within the 3'-untranslated regions (3'UTRs) of L. major mRNAs. We provide experimental evidence that LmSIDER2 act as mRNA instability elements and that LmSIDER2-containing mRNAs are generally expressed at lower levels compared to the non-LmSIDER2 mRNAs. The considerable expansion of LmSIDERs within 3'UTRs in an organism lacking transcriptional control and their role in regulating mRNA stability indicate that Leishmania have probably recycled these short retroposons to globally modulate the expression of a number of genes. To our knowledge, this is the first example in eukaryotes of the domestication and expansion of a family of mobile elements that have evolved to fulfill a critical cellular function.

  3. Rapid decay of unstable Leishmania mRNAs bearing a conserved retroposon signature 3′-UTR motif is initiated by a site-specific endonucleolytic cleavage without prior deadenylation

    PubMed Central

    Müller, Michaela; Padmanabhan, Prasad K.; Rochette, Annie; Mukherjee, Debdutta; Smith, Martin; Dumas, Carole; Papadopoulou, Barbara

    2010-01-01

    We have previously shown that the Leishmania genome possess two widespread families of extinct retroposons termed Short Interspersed DEgenerated Retroposons (SIDER1/2) that play a role in post-transcriptional regulation. Moreover, we have demonstrated that SIDER2 retroposons promote mRNA degradation. Here we provide new insights into the mechanism by which unstable Leishmania mRNAs harboring a SIDER2 retroposon in their 3′-untranslated region are degraded. We show that, unlike most eukaryotic transcripts, SIDER2-bearing mRNAs do not undergo poly(A) tail shortening prior to rapid turnover, but instead, they are targeted for degradation by a site-specific endonucleolytic cleavage. The main cleavage site was mapped in two randomly selected SIDER2-containing mRNAs in vivo between an AU dinucleotide at the 5′-end of the second 79-nt signature (signature II), which represents the most conserved sequence amongst SIDER2 retroposons. Deletion of signature II abolished endonucleolytic cleavage and deadenylation-independent decay and increased mRNA stability. Interestingly, we show that overexpression of SIDER2 anti-sense RNA can increase sense transcript abundance and stability, and that complementarity to the cleavage region is required for protecting SIDER2-containing transcripts from degradation. These results establish a new paradigm for how unstable mRNAs are degraded in Leishmania and could serve as the basis for a better understanding of mRNA decay pathways in general. PMID:20453029

  4. Computational identification of 69 retroposons in Arabidopsis.

    PubMed

    Zhang, Yujun; Wu, Yongrui; Liu, Yilei; Han, Bin

    2005-06-01

    Retroposition is a shot-gun strategy of the genome to achieve evolutionary diversities by mixing and matching coding sequences with novel regulatory elements. We have identified 69 retroposons in the Arabidopsis (Arabidopsis thaliana) genome by a computational approach. Most of them were derivatives of mature mRNAs, and 20 genes contained relics of the reverse transcription process, such as truncations, deletions, and extra sequence additions. Of them, 22 are processed pseudogenes, and 52 genes are likely to be actively transcribed, especially in tissues from apical meristems (roots and flowers). Functional compositions of these retroposon parental genes imply that not the mRNA itself but its expression in gamete cells defines a suitable template for retroposition. The presence/absence patterns of retroposons can be used as cladistic markers for biogeographic research. Effects of human and the Mediterranean Pleistocene refugia in Arabidopsis biogeographic distributions were revealed based on two recent retroposons (At1g61410 and At5g52090). An evolutionary rate of new gene creation by retroposition was calculated as 0.6 genes per million years. Retroposons can also be used as molecular fossils of the parental gene expressions in ancient time. Extensions of 3' untranslated regions for those expressed parental genes are revealed as a possible trend of plant transcriptome evolution. In addition, we reported the first plant functional chimeric gene that adapts to intercompartmental transport by capturing two additional exons after retroposition. PMID:15923328

  5. Corrected sidereal anisotropy for underground moons

    NASA Technical Reports Server (NTRS)

    Swinson, D. B.; Nagashima, K.

    1985-01-01

    Data from underground muon telescopes in New Mexico and Bolivia are analyzed in sidereal time and anti-sidereal time in the rigidity range 20 GV to a few 100's of GV. Using both vertical and north- and south- pointing telescopes in both hemispheres, a latitude range of 70 N to 50 S is covered. It is shown that there is an anti-sidereal variation of the P 1 over 2 type, having opposite phase in the Northern and Southern Hemispheres, and maximum amplitude at mid latitudes. The anti-sidereal data are used to correct the sidereal data, using the Nagashima method (Nagashima, 1984); the resulting corrected sidereal vectors for northern hemisphere telescopes have their sidereal maxima close to 3h sidereal time, in reasonable agreement with sidereal data at higher energies from small air showers. The Nagashima correction also eliminates effects due to the reversal of the Sun's polar magnetic field which show up in the uncorrected sidereal data.

  6. 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

  7. 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. PMID:19261842

  8. 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.

  9. 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.

  10. A retroposon analysis of Afrotherian phylogeny.

    PubMed

    Nishihara, Hidenori; Satta, Yoko; Nikaido, Masato; Thewissen, J G M; Stanhope, Michael J; Okada, Norihiro

    2005-09-01

    Recent comprehensive studies of DNA sequences support the monophyly of Afrotheria, comprising elephants, sirenians (dugongs and manatees), hyraxes, tenrecs, golden moles, aardvarks, and elephant shrews, as well as that of Paenungulata, comprising elephants, sirenians, and hyraxes. However, phylogenetic relationships among paenungulates, as well as among nonpaenungulates, have remained ambiguous. Here we applied an extensive retroposon analysis to these problems to support the monophyly of aardvarks, tenrecs, and golden moles, with elephant shrews as their sister group. Regarding phylogenetic relationships in Paenungulata, we could characterize only one informative locus, although we could isolate many insertions specific to each of three lineages, namely, Proboscidea, Sirenia, and Hyracoidea. These data prompted us to reexamine phylogenetic relationships among Paenungulata using 19 nuclear gene sequences resulting in three different analyses, namely, short interspersed element (SINE) insertions, nuclear sequence analyses, and morphological cladistics, supporting different respective phylogenies. We concluded that these three lineages diverged very rapidly in a very short evolutionary period, with the consequence that ancestral polymorphism present in the last common ancestor of Paenungulata results in such incongruence. Our results suggest the rapid fixation of many large-scale morphological synapomorphies for Tethytheria; implications of this in relation to the morphological evolution in Paenungulata are discussed. PMID:15930154

  11. Multiple lineages of ancient CR1 retroposons shaped the early genome evolution of amniotes.

    PubMed

    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

  12. 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

  13. A retroposon-based view on the temporal differentiation of sex chromosomes

    PubMed Central

    Suh, Alexander

    2012-01-01

    Retroposon presence/absence patterns in orthologous genomic loci are known to be strong and almost homoplasy-free phylogenetic markers of common ancestry. This is evidenced by the comprehensive reconstruction of various species trees of vertebrate lineages in recent years, as well as the inference of the evolution of genes via retroposon-based gene trees of paralogous genes. Recently, it has been shown that retroposon markers are also suitable for the inference of differentiation events of gametologous genes, i.e., homologous genes on opposite sex chromosomes. This is because sex chromosomes evolved via stepwise cessation of recombination, making the presence or absence of a particular retroposon insertion among the two different gametologs in more or less closely related species a clear-cut indicator of the timing of differentiation events. Here, I examine the advantages and current limitations of this novel perspective for understanding avian sex chromosome evolution, compare the retroposon-based and sequence-based insights into gametolog differentiation and show that retroposons promise to be equally applicable to other sex chromosomal systems, such as the human X and Y chromosomes. PMID:23061025

  14. 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

  15. 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.

  16. Retroposon insertions and the chronology of avian sex chromosome evolution.

    PubMed

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

    2011-11-01

    The vast majority of extant birds possess highly differentiated Z and W sex chromosomes. Nucleotide sequence data from gametologs (homologs on opposite sex chromosomes) suggest that this divergence occurred throughout early bird evolution via stepwise cessation of recombination between identical sex chromosomal regions. Here, we investigated avian sex chromosome differentiation from a novel perspective, using retroposon insertions and random insertions/deletions for the reconstruction of gametologous gene trees. Our data confirm that the CHD1Z/CHD1W genes differentiated in the ancestor of the neognaths, whereas the NIPBLZ/NIPBLW genes diverged in the neoavian ancestor and independently within Galloanserae. The divergence of the ATP5A1Z/ATP5A1W genes in galloanserans occurred independently in the chicken, the screamer, and the ancestor of duck-related birds. In Neoaves, this gene pair differentiated in each of the six sampled representatives, respectively. Additionally, three of our investigated loci can be utilized as universal, easy-to-use independent tools for molecular sexing of Neoaves or Neognathae. PMID:21633113

  17. 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.

  18. Genomic expansion of the Bov-A2 retroposon relating to phylogeny and breed management.

    PubMed

    Onami, Jun-ichi; Nikaido, Masato; Mannen, Hideyuki; Okada, Norihiro

    2007-03-01

    Bov-A2 is a retroposon that is widely distributed among the genomes of ruminants (e.g., cow, deer, giraffe, pronghorn, musk deer, and chevrotain). This retroposon is composed of two monomers, called Bov-A units, which are joined by a linker sequence. The structure and origin of Bov-A2 has been well characterized but a genome-level exploration of this retroposon has not been implemented. In this study we performed an extensive search for Bov-A2 using all available genome sequence data on Bos taurus. We found unique Bov-A2-derived sequences that were longer than Bov-A2 due to amplification of three to six Bov-A units arranged in tandem. Detailed analysis of these elongated Bov-A2-derived sequences revealed that they originated through unequal crossing-over of Bov-A2. We found a large number of these elongated Bov-A2-derived sequences in cattle genomes, indicating that unequal crossing-over of Bov-A2 occurred very frequently. We found that this type of elongation is not observed in wild bovine and is therefore specific to the domesticated cattle genome. Furthermore, at specific loci, the number of Bov-A units was also polymorphic between alleles, implying that the elongation of Bov-A units might have occurred very recently. For these reasons, we speculate that genomic instability in bovine genomes can lead to extensive unequal crossing-over of Bov-A2 and levels of polymorphism might be generated in part by repeated outbreeding. PMID:17436038

  19. GABAA receptor modulation by terpenoids from Sideritis extracts

    PubMed Central

    Kessler, Artur; Sahin-Nadeem, Hilal; Lummis, Sarah C R; Weigel, Ingrid; Pischetsrieder, Monika; Buettner, Andrea; Villmann, Carmen

    2014-01-01

    Scope GABAA receptors are modulated by Sideritis extracts. The aim of this study was to identify single substances from Sideritis extracts responsible for GABAA receptor modulation. Methods and results Single volatile substances identified by GC have been tested in two expression systems, Xenopus oocytes and human embryonic kidney cells. Some of these substances, especially carvacrol, were highly potent on GABAA receptors composed of α1β2 and α1β2γ2 subunits. All effects measured were independent from the presence of the γ2 subunit. As Sideritis extracts contain a high amount of terpenes, 13 terpenes with similar structure elements were tested in the same way. Following a prescreening on α1β2 GABAA receptors, a high-throughput method was used for identification of the most effective terpenoid substances on GABA-affinity of α1β2γ2 receptors expressed in transfected cell lines. Isopulegol, pinocarveol, verbenol, and myrtenol were the most potent modifiers of GABAA receptor function. Conclusion Comparing the chemical structures, the action of terpenes on GABAA receptors is most probably due to the presence of hydroxyl groups and a bicyclic character of the substances tested. We propose an allosteric modulation independent from the γ2 subunit and similar to the action of alcohols and anesthetics. PMID:24273211

  20. The SIDER database of drugs and side effects.

    PubMed

    Kuhn, Michael; Letunic, Ivica; Jensen, Lars Juhl; Bork, Peer

    2016-01-01

    Unwanted side effects of drugs are a burden on patients and a severe impediment in the development of new drugs. At the same time, adverse drug reactions (ADRs) recorded during clinical trials are an important source of human phenotypic data. It is therefore essential to combine data on drugs, targets and side effects into a more complete picture of the therapeutic mechanism of actions of drugs and the ways in which they cause adverse reactions. To this end, we have created the SIDER ('Side Effect Resource', http://sideeffects.embl.de) database of drugs and ADRs. The current release, SIDER 4, contains data on 1430 drugs, 5880 ADRs and 140 064 drug-ADR pairs, which is an increase of 40% compared to the previous version. For more fine-grained analyses, we extracted the frequency with which side effects occur from the package inserts. This information is available for 39% of drug-ADR pairs, 19% of which can be compared to the frequency under placebo treatment. SIDER furthermore contains a data set of drug indications, extracted from the package inserts using Natural Language Processing. These drug indications are used to reduce the rate of false positives by identifying medical terms that do not correspond to ADRs.

  1. Analgesic and antiinflammatory properties of Sideritis lotsyi var. Mascaensis.

    PubMed

    Hernández-Pérez, Margarita; Rabanal Gallego, Rosa M

    2002-05-01

    The antiinflammatory, analgesic and antimicrobial activities of crude ethanol extracts of Sideritis lotsyi var. mascaensis (Lamiaceae), and chloroform and aqueous fractions were evaluated in mice using paw and ear oedema induced by carrageenan and 12-o-tetradecanoyl-phorbol-acetate (TPA), respectively, as inflammation models, the writhing test induced by acetic acid for evaluating analgesic activity and the disk-diffusion method for testing antimicrobial actions. The results obtained demonstrated significant topical antiinflammatory and analgesic activities for the ethanol extract and chloroform fraction, but no relevant antimicrobial activity against the microorganisms tested.

  2. To the theory of mechanisms subfamilies

    NASA Astrophysics Data System (ADS)

    Fomin, A.; Dvornikov, L.; Paramonov, M.; Jahr, A.

    2016-04-01

    The principles of formation of mechanisms subfamilies based on the usage of different kinds of kinematic pairs within the families of mechanisms are substantiated in the current paper. The division of mechanisms into subfamilies allows defining not only fundamental differences in the structure of mechanisms, but also provides the necessary foundation for the synthesis of new structures. 57 subfamilies of mechanisms have been totally distinguished. Among them, 31 subfamilies - within the zero family, 15 subfamilies - within the first family, 7 subfamilies - within the second family, 3 subfamilies - within the third family and 1 subfamily-within the fourth family. There were separately viewed planar mechanisms of the third family with three general imposed constraints and spatial mechanisms of the second family with two general imposed constraints in terms of their subfamilies. New methods of kinematical and dynamical investigations of mechanisms might be developed according to their analytical equations describing structural organization of different subfamilies of mechanisms.

  3. 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

  4. 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

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

    PubMed

    Nishihara, Hidenori; Maruyama, Shigenori; Okada, Norihiro

    2009-03-31

    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, approximately 120 Ma.

  6. 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

  7. 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.

  8. 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

    2006-05-01

    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.

  9. 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

  10. 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

  11. Effectiveness of Observation-Domain Sidereal Filtering for GPS Precise Point Positioning

    NASA Astrophysics Data System (ADS)

    Atkins, C.; Ziebart, M. K.

    2014-12-01

    Global navigation satellite systems (GNSS) are increasingly being used in earthquake monitoring and tsunami warning systems. However, the ability of GNSS to measure potentially small ground displacements is limited by a number of error sources, one of which is multipath interference, which affects the measurements made by a GNSS receiver.Sidereal filtering is a technique sometimes used to reduce errors caused by multipath in the positioning of static receivers via GPS in particular. It relies upon the receiver and its surrounding environment remaining static from one day to the next and takes advantage of the approximately sidereal repeat time of the GPS constellation geometry. The repeating multipath error can thus be identified, usually in the position domain, and largely removed from the following day.We have developed an observation-domain sidereal filter (ODSF) algorithm that operates on un-differenced ionosphere-free GPS carrier phase observations to reduce errors caused by multipath. It is applied in the context of high-rate 1 Hz precise point positioning (PPP) of a static receiver. An ODSF is able to account for the slightly different repeat times of each GPS satellite, unlike a position-domain sidereal filter, and can hence be more effective at reducing high-frequency multipath error.Using eight-hour long datasets of GPS observations from two different receivers with different antenna types and contrasting environments, the ODSF algorithm is shown overall to yield a position time series 10% to 45% more stable, in terms of Allan deviation, than a position-domain sidereal filter over time intervals of between 20 s and 300 s in length. This would be particularly useful for earthquake and tsunami early warning systems where the accurate measurement of small displacements of the ground over the period of just a few minutes is crucial. However, the sidereal filters have also been applied to a third dataset during which two short episodes of particularly high

  12. Gamergates in the Australian ant subfamily Myrmeciinae

    NASA Astrophysics Data System (ADS)

    Dietemann, Vincent; Peeters, Christian; Hölldobler, Bert

    2004-09-01

    Ant workers can mate and reproduce in a few hundreds of species belonging to the phylogenetically basal poneromorph subfamilies (sensu Bolton 2003). We report the first occurrence of gamergates (i.e. mated reproductive workers) in a myrmeciomorph subfamily. In a colony of Myrmecia pyriformis that was collected without a queen, workers continued to be produced over a period of 3 years in the laboratory. Behavioural observations and ovarian dissections indicated that three workers were mated and produced the diploid offspring. The Myrmeciinae are thus another taxon in which the selective benefits of sexual reproduction by workers can be investigated.

  13. 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.

  14. Observation of cosmic ray sidereal time variation by Grapes III muon telescope at Ooty

    NASA Astrophysics Data System (ADS)

    Kojima, H.; Fujimoto, K.; Gupta, S. K.; Hayashi, Y.; Ito, N.; Jain, Kawakami S.; Mohanty, D. K.; Nonaka, T.; Noto, S.; Ravindran, K. C.; Satomi, K.; Sivaprasad, K.; Tanaka, H.; Tonwar, S. C.; Toyofuku, T.; Viswanathan, K.; Yoshikoshi, T.

    2001-08-01

    We analyzed the sidereal time variation on the data of muons counting rate observed by the large muon telescope of GRAPES III ( total area 560 m2 , muon's energy > 1GeV) over 3 years at Ooty ( 11.4deg latitude, 76.7deg longitude). Their counting rate is around 53,000 counts /sec and this high counting rate is great advantage for modulation measurement. The analysis based on the data of such high-statistics enable us to compare the sidereal diurnal variation even with each single year's result. We observed the Tail-in and Loss corn anisotropies through detailed analysis. We newly started the measurement of direction of individual muons with accuracy of about 8 degrees from 1999. We present some results on the siderealdailyvariation obtained by this systemtoo.

  15. A proposed new bacteriophage subfamily: "Jerseyvirinae".

    PubMed

    Anany, Hany; Switt, Andrea I Moreno; De Lappe, Niall; Ackermann, Hans-Wolfgang; Reynolds, Darren M; Kropinski, Andrew M; Wiedmann, Martin; Griffiths, Mansel W; Tremblay, Denise; Moineau, Sylvain; Nash, John H E; Turner, Dann

    2015-04-01

    Based on morphology and comparative nucleotide and protein sequence analysis, a new subfamily of the family Siphoviridae is proposed, named "Jerseyvirinae" and consisting of three genera, "Jerseylikevirus", "Sp3unalikevirus" and "K1glikevirus". To date, this subfamily consists of 18 phages for which the genomes have been sequenced. Salmonella phages Jersey, vB_SenS_AG11, vB_SenS-Ent1, vB_SenS-Ent2, vB_SenS-Ent3, FSL SP-101, SETP3, SETP7, SETP13, SE2, SS3e and wksl3 form the proposed genus "Jerseylikevirus". The proposed genus "K1glikevirus" consists of Escherichia phages K1G, K1H, K1ind1, K1ind2 and K1ind3. The proposed genus "Sp3unalikevirus" contains one member so far. Jersey-like phages appear to be widely distributed, as the above phages were isolated in the UK, Canada, the USA and South Korea between 1970 and the present day. The distinguishing features of this subfamily include a distinct siphovirus morphotype, genomes of 40.7-43.6 kb (49.6-51.4 mol % G+C), a syntenic genome organisation, and a high degree of nucleotide sequence identity and shared proteins. All known members of the proposed subfamily are strictly lytic. PMID:25663216

  16. Mouse mammary tumor proviruses from a T-cell lymphoma are associated with the retroposon L1Md.

    PubMed Central

    Dudley, J P

    1988-01-01

    Four Charon 4A clones containing mouse mammary tumor virus (MMTV) proviruses and their cellular flanking sequences were obtained from partial EcoRI libraries of a C57BL/6 T-cell lymphoma with both endogenous and newly acquired MMTV proviruses. The cellular flanking sequences of three of four MMTV proviruses contained DNA homologous to the 3' end of the long interspersed retroposon L1Md. Two of the three proviruses were newly acquired in the lymphoma DNA, and these MMTV proviruses appeared to be 5 kilobases downstream and in the same transcriptional orientation as the L1 sequence. The third provirus was endogenous Mtv-9 and was located less than 500 base pairs from the 3' end of L1. Seven additional clones containing MMTV proviruses were isolated from partial MboI libraries of a B6 T-cell lymphoma. Five of the seven clones contained L1 elements in the cellular DNA flanking MMTV DNA. At least two clones (including one with the Mtv-8 provirus) had multiple L1 copies flanking the MMTV provirus, and one clone contained a single MMTV long terminal repeat directly integrated into a truncated L1 sequence. Although the frequencies of B1 and L1 in random library clones were similar, only one MMTV-containing clone hybridized to the abundant repetitive element B1. These data suggest a nonrandom association between MMTV and L1Md. Images PMID:2826809

  17. Multiple nuclear genes and retroposons support vicariance and dispersal of the palaeognaths, and an Early Cretaceous origin of modern birds

    PubMed Central

    Haddrath, Oliver; Baker, Allan J.

    2012-01-01

    The origin and timing of the diversification of modern birds remains controversial, primarily because phylogenetic relationships are incompletely resolved and uncertainty persists in molecular estimates of lineage ages. Here, we present a species tree for the major palaeognath lineages using 27 nuclear genes and 27 archaic retroposon insertions. We show that rheas are sister to the kiwis, emu and cassowaries, and confirm ratite paraphyly because tinamous are sister to moas. Divergence dating using 10 genes with broader taxon sampling, including emu, cassowary, ostrich, five kiwis, two rheas, three tinamous, three extinct moas and 15 neognath lineages, suggests that three vicariant events and possibly two dispersals are required to explain their historical biogeography. The age of crown group birds was estimated at 131 Ma (95% highest posterior density 122–138 Ma), similar to previous molecular estimates. Problems associated with gene tree discordance and incomplete lineage sorting in birds will require much larger gene sets to increase species tree accuracy and improve error in divergence times. The relatively rapid branching within neoaves pre-dates the extinction of dinosaurs, suggesting that the genesis of the radiation within this diverse clade of birds was not in response to the Cretaceous–Paleogene extinction event. PMID:22977150

  18. 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.

  19. Evaluation of the antinflammatory and analgesic activity of Sideritis canariensis var. pannosa in mice.

    PubMed

    Hernández-Pérez, Margarita; Rabanal, Rosa M

    2002-06-01

    A previous chemical study of Sideritis canariensis var. pannosa demonstrated the presence of some important classes of related organic compounds with anti-inflammatory activities. In the present study, the crude ethanol extract and the chloroformic and aqueous fractions of S. canariensis have been examined for their antimicrobial actions through the disk-diffusion method and for their anti-inflammatory and analgesic effects in several animal models. No relevant antimicrobial activity against the tested microorganisms was found. The chloroformic fraction was the most interesting, exhibiting a good analgesic and anti-inflammatory activity.

  20. Tetrahymena Metallothioneins Fall into Two Discrete Subfamilies

    PubMed Central

    Campos, Virginia; Benítez, Laura; Martín-González, Ana; Hamilton, Eileen P.; Orias, Eduardo; Gutiérrez, Juan C.

    2007-01-01

    Background Metallothioneins are ubiquitous small, cysteine-rich, multifunctional proteins which can bind heavy metals. Methodology/Principal Findings We report the results of phylogenetic and gene expression analyses that include two new Tetrahymena thermophila metallothionein genes (MTT3 and MTT5). Sequence alignments of all known Tetrahymena metallothioneins have allowed us to rationalize the structure of these proteins. We now formally subdivide the known metallothioneins from the ciliate genus Tetrahymena into two well defined subfamilies, 7a and 7b, based on phylogenetic analysis, on the pattern of clustering of Cys residues, and on the pattern of inducibility by the heavy metals Cd and Cu. Sequence alignment also reveals a remarkably regular, conserved and hierarchical modular structure of all five subfamily 7a MTs, which include MTT3 and MTT5. The former has three modules, while the latter has only two. Induction levels of the three T. thermophila genes were determined using quantitative real time RT-PCR. Various stressors (including heavy metals) brought about dramatically different fold-inductions for each gene; MTT5 showed the highest fold-induction. Conserved DNA motifs with potential regulatory significance were identified, in an unbiased way, upstream of the start codons of subfamily 7a MTs. EST evidence for alternative splicing in the 3′ UTR of the MTT5 mRNA with potential regulatory activity is reported. Conclusion/Significance The small number and remarkably regular structure of Tetrahymena MTs, coupled with the experimental tractability of this model organism for studies of in vivo function, make it an attractive system for the experimental dissection of the roles, structure/function relationships, regulation of gene expression, and adaptive evolution of these proteins, as well as for the development of biotechnological applications for the environmental monitoring of toxic substances. PMID:17356700

  1. Impact of GPS Satellite Antenna Phase Center Variations and Modified Sidereal Filtering on Reference Frame Determination.

    NASA Astrophysics Data System (ADS)

    Owen, S. E.; Webb, F.

    2005-12-01

    Errors in the satellite and ground station antenna phase center variations are among the limiting sources of error in high precision GPS positioning. Recent determinations of phase-center variations (PCV) for both the transmitting satellite and receiving ground station antennas have shown promise for improving geodetic estimates of reference frame parameters, such as scale. While the PCV for the transmitting antennas is reasonably well determined and includes some variation from satellite to satellite, the apparent PCV at ground station antennas are likely to be site specific and dominated by local environmental effects, such as signal multipath. To mitigate these effects, we implement a modified sidereal filter (MSF). The MSF is applied as a correction to the phase and range data. The correction is based on stacking several days of phase and range residuals where each day is shifted by the actual orbital period of each satellite, rather than sidereal time. We will evaluate the effect of stacking several days to 1 month of residuals on such metrics as phase rms and point positioning repeatability. We will present an evaluation the impact of these PCV and MSF corrections on reference frame parameters. The corrections will be applied to several years of observations from a global set of IGS stations.

  2. Studies on Cosmic Ray Sidereal Anisotropy with the Multidirectional Muon Telescope at Ooty

    NASA Astrophysics Data System (ADS)

    Kojima, H.; Fujimoto, K.; Gupta, S. K.; Hayashi, Y.; Ishida, Y.; Ito, N.; Jain, A.; Kawakami, S.; Nonaka, T.; Oshima, A.; Sivaprasad, K.; Tamaki, S.; Tanaka, H.; Tonwar, S. C.; Yoshikoshi, T.

    2003-07-01

    We have developed a multidirectional telescope capable of recording individual muons with angular accuracy of about 5 degrees. This muon telescope consists of ˜ 3000 proportional counters with total area of ˜ 420 m2 with threshold energy > 1 GeV. The telescope is a component of the GRAPES-3 experiment at Ooty in southern India (N 11.4, E 76.7 and 2200m altitude). The very large muon counting rate ˜ 1.8 × 108 per hour, achieved due to the very large area of the telescope, gives us great advantage for cosmic ray modulation studies. The analysis of data with such high statistics enables us to have a sensitive measurement of sidereal variation within a single year of observation. Further, since our telescope is located near the Equator, we are able to observe both the Northern and the Southern hemispheres simultaneously. We present here the results on the sidereal variation obtained with this multidirectional muon telescope for the observational period, 2000-2001. We report here on Tail-in and Loss-corn anisotropies through detailed analysis. We also discuss other possible explanations for the present observations.

  3. Comparative Chemical Composition and Antioxidant Properties of the Essential Oils of three Sideritis libanotica Subspecies.

    PubMed

    Formisano, Carmen; Oliviero, Filomena; Rigano, Daniela; Arnold, Nelly Apostolides; Senatore, Felice

    2015-06-01

    The phytochemical composition of the essential oils of three Sideritis libanotica subspecies, namely S. libanotica ssp. libanotica, S. libanotica ssp. linearis and S. libanotica ssp. michroclamys, all collected in Lebanon, was analyzed by GC and GC-MS. The diterpene sideridiol was recognized as the main constituent of both S. libanotica ssp. libanotica (50.8%) and S. libanotica ssp. michroclamys (18.4%) oils, while hexadecanoic acid (10.5%) prevailed in S. libanotica ssp. linearis. The antioxidant activity of the oils was studied in two cell free systems by DPPH radical scavenging and ferric ion reduction (FRAP) assays; only S. libanotica ssp. linearis showed a moderate activity when assayed by the FRAP test (0.6 ± 0.01 mmol TE/mL). PMID:26197555

  4. 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.

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

    PubMed

    Wagner, Rüdiger; Stuckenberg, Brian

    2016-01-01

    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. PMID:27394447

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

    PubMed

    Wagner, Rüdiger; Stuckenberg, Brian

    2016-01-01

    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.

  7. 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.

  8. The antioxidant role of Sideritis caesarea infusion against TCA toxicity in rats.

    PubMed

    Celik, Ismail; Kaya, Mehmet Salih

    2011-03-01

    Sideritis caesarea (SC) Duman, Aytac & Baser is a member of the Lamiaceae family. The present study was designed to investigate the antioxidant properties of the aerial parts of island green tea SC against TCA effects in rats. Biomarkers selected for monitoring antioxidant capacity were the activities of glutathione reductase (GR), superoxide dismutase (SOD), glutathione-S-transferase, catalase (CAT), GSH level and malondialdehyde (MDA) content in various organs of rats. Three experimental groups, A (untreated = control), B (only TCA-treated) and C (TCA+SC-treated), were studied. At the end of the 50 d experiment, the MDA content in tissues increased significantly in group B, whereas no significant changes were observed in group C as compared with that of the control group. Antioxidant enzyme activities such as SOD and CAT increased significantly in the brain, liver and kidneys of group B but decreased significantly in group C as compared with group B. The GSH level and GR activity increased significantly in the brain and liver of group C as compared with the control and TCA-exposed rats. Hence, the study reveals that the constituents present in SC impart protection against chemical-induced oxidative injury that may result in the development of cancer. PMID:21078212

  9. 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.

  10. Acrosome reaction is subfamily specific in sea star fertilization.

    PubMed

    Nakachi, Mia; Moriyama, Hideaki; Hoshi, Motonori; Matsumoto, Midori

    2006-10-15

    In the fertilization process of sea stars, sperm is activated to go through the acrosome reaction before cell fusion. We focused on induction of the acrosome reaction as a key process in fertilization. Six species of sea stars were used in this study: Asterias amurensis, Asterias rubens, Asterias forbesi, Aphelasterias japonica, Distolasterias nipon, and Asterina pectinifera. Acrosome reaction assays indicate that the acrosome reaction can be induced across species within Asteriinae subfamily. However, cross-fertilization assays indicate that sea stars have species specificity in fertilization. Therefore, steps after the acrosome reaction are responsible for the species specificity. To explain acrosome reaction subfamily specificity at the molecular level, the sugar components of egg jelly were examined and analyzed by principal component analysis. A. amurensis and A. forbesi belong to the same induction group of the acrosome reaction. D. nipon and An. pectinifera are in a unique group. Enzyme-linked immunosorbent assays indicate that Asteriinae subfamily share a common glycan structure, the Fragment 1 of Acrosome Reaction-Inducing Substance from A. amurensis. Fragment 1 plays an important role in the subfamily specificity of acrosome reaction induction. In addition, A. amurensis sperm activating peptide was recognized by sperm from the same superorder. These results demonstrate that the specificity of acrosome reaction induction is present at the subfamily level in sea stars.

  11. Phycoviolobilin formation and spectral tuning in the DXCF cyanobacteriochrome subfamily.

    PubMed

    Rockwell, Nathan C; Martin, Shelley S; Gulevich, Alexander G; Lagarias, J Clark

    2012-02-21

    Phytochromes are red/far-red photosensory proteins that regulate adaptive responses to light via photoswitching of cysteine-linked linear tetrapyrrole (bilin) chromophores. The related cyanobacteriochromes (CBCRs) extend the photosensory range of the phytochrome superfamily to shorter wavelengths of visible light. CBCRs and phytochromes share a conserved Cys residue required for bilin attachment. In one CBCR subfamily, often associated with a blue/green photocycle, a second Cys lies within a conserved Asp-Xaa-Cys-Phe (DXCF) motif and is essential for the blue/green photocycle. Such DXCF CBCRs use isomerization of the phycocyanobilin (PCB) chromophore into the related phycoviolobilin (PVB) to shorten the conjugated system for sensing green light. We here use recombinant expression of individual CBCR domains in Escherichia coli to survey the DXCF subfamily from the cyanobacterium Nostoc punctiforme. We describe ten new photoreceptors with well-resolved photocycles and three additional photoproteins with overlapping dark-adapted and photoproduct states. We show that the ability of this subfamily to form PVB or retain PCB provides a powerful mechanism for tuning the photoproduct absorbance, with blue-absorbing dark states leading to a broad range of photoproducts absorbing teal, green, yellow, or orange light. Moreover, we use a novel green/teal CBCR that lacks the blue-absorbing dark state to demonstrate that PVB formation requires the DXCF Cys residue. Our results demonstrate that this subfamily exhibits much more spectral diversity than had been previously appreciated. PMID:22279972

  12. 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.

  13. 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

  14. 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). PMID:26748268

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

    PubMed

    Borowiec, Marek L

    2016-01-01

    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 gen. rev

  16. 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

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

    PubMed

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

    2016-06-01

    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

  18. 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

  19. 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). PMID:10629726

  20. 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

  1. Assay of urinary excretion of polyphenols after ingestion of a cup of mountain tea (Sideritis scardica) measured by HPLC-DAD-ESI-MS/MS.

    PubMed

    Petreska Stanoeva, Jasmina; Stefova, Marina

    2013-11-01

    Flavonoids and phenolic acid metabolites excreted in human urine after ingestion of Sideritis scardica decoction with characterized polyphenolic composition were studied. A feeding study was carried out with 10 human volunteers, and urine samples were collected for 24 h after ingestion of the Sidertis decoction. Polyphenol metabolites were identified and quantified in urine samples by HPLC with tandem mass spectrometric detection. Thirty-one different metabolites of hypolaetin, methylhypolaetin, isoscutellarein, methylisoscutellarein, and apigenin and 32 phenolic acid metabolites were detected and quantified using a method validated for this purpose. The urinary excretion of polyphenol metabolites corresponded to 5% (n/n) of the intake of polyphenols from the Sideritis decoction. Flavonoid metabolites were dominant in urine samples with 87-94% of total polyphenolic metabolites content. The most abundant metabolites were methylhypolaetin and methylisoscutellarein glucuronides. Urinary excretion of isoscutellarein (35.61%) was 10 times higher than that of hypolaetin (3.67%). Apigenin also showed high urinary excretion (32.46%).

  2. Flavonoids from Sideritis Species: Human Monoamine Oxidase (hMAO) Inhibitory Activities, Molecular Docking Studies and Crystal Structure of Xanthomicrol.

    PubMed

    Turkmenoglu, Fatma Pinar; Baysal, İpek; Ciftci-Yabanoglu, Samiye; Yelekci, Kemal; Temel, Hamdi; Paşa, Salih; Ezer, Nurten; Çalış, İhsan; Ucar, Gulberk

    2015-04-23

    The inhibitory effects of flavonoids on monoamine oxidases (MAOs) have attracted great interest since alterations in monoaminergic transmission are reported to be related to neurodegenerative diseases such as Parkinson's and Alzheimer's diseases and psychiatric disorders such as depression and anxiety, thus MAOs may be considered as targets for the treatment of these multi-factorial diseases. In the present study, four Sideritis flavonoids, xanthomicrol (1), isoscutellarein 7-O-[6'''-O-acetyl-β-D-allopyranosyl-(1→2)]-β-D-glucopyranoside (2), isoscutellarein 7-O-[6'''-O-acetyl-β-D-allopyranosyl-(1→2)]-6''-O-acetyl-β-D-glucopyranoside (3) and salvigenin (4) were docked computationally into the active site of the human monoamine oxidase isoforms (hMAO-A and hMAO-B) and were also investigated for their hMAO inhibitory potencies using recombinant hMAO isoenzymes. The flavonoids inhibited hMAO-A selectively and reversibly in a competitive mode. Salvigenin (4) was found to be the most potent hMAO-A inhibitor, while xanthomicrol (1) appeared as the most selective hMAO-A inhibitor. The computationally obtained results were in good agreement with the corresponding experimental values. In addition, the x-ray structure of xanthomicrol (1) has been shown. The current work warrants further preclinical studies to assess the potential of xanthomicrol (1) and salvigenin (4) as new selective and reversible hMAO-A inhibitors for the treatment of depression and anxiety.

  3. Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

    PubMed Central

    Mewis, Keith; Lombard, Vincent

    2016-01-01

    The rapid rise in DNA sequencing has led to an expansion in the number of glycoside hydrolase (GH) families. The GH43 family currently contains α-l-arabinofuranosidase, β-d-xylosidase, α-l-arabinanase, and β-d-galactosidase enzymes for the debranching and degradation of hemicellulose and pectin polymers. Many studies have revealed finer details about members of GH43 that necessitate the division of GH43 into subfamilies, as was done previously for the GH5 and GH13 families. The work presented here is a robust subfamily classification that assigns over 91% of all complete GH43 domains into 37 subfamilies that correlate with conserved sequence residues and results of biochemical assays and structural studies. Furthermore, cooccurrence analysis of these subfamilies and other functional modules revealed strong associations between some GH43 subfamilies and CBM6 and CBM13 domains. Cooccurrence analysis also revealed the presence of proteins containing up to three GH43 domains and belonging to different subfamilies, suggesting significant functional differences for each subfamily. Overall, the subfamily analysis suggests that the GH43 enzymes probably display a hitherto underestimated variety of subtle specificity features that are not apparent when the enzymes are assayed with simple synthetic substrates, such as pNP-glycosides. PMID:26729713

  4. 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))).

  5. A Novel MSCRAMM Subfamily in Coagulase Negative Staphylococcal Species

    PubMed Central

    Arora, Srishtee; Uhlemann, Anne-Catrin; Lowy, Franklin D.; Hook, Magnus

    2016-01-01

    Coagulase negative staphylococci (CoNS) are important opportunistic pathogens. Staphylococcus epidermidis, a coagulase negative staphylococcus, is the third leading cause of nosocomial infections in the US. Surface proteins like Microbial Surface Components Recognizing Adhesive Matrix Molecules (MSCRAMMs) are major virulence factors of pathogenic gram positive bacteria. Here, we identified a new chimeric protein in S. epidermidis, that we call SesJ. SesJ represents a prototype of a new subfamily of MSCRAMMs. Structural predictions show that SesJ has structural features characteristic of a MSCRAMM along with a N-terminal repeat region and an aspartic acid containing C-terminal repeat region, features that have not been previously observed in staphylococcal MSCRAMMs but have been found in other surface proteins from gram positive bacteria. We identified and analyzed structural homologs of SesJ in three other CoNS. These homologs of SesJ have an identical structural organization but varying sequence identities within the domains. Using flow cytometry, we also show that SesJ is expressed constitutively on the surface of a representative S. epidermidis strain, from early exponential to stationary growth phase. Thus, SesJ is positioned to interact with protein targets in the environment and plays a role in S. epidermidis virulence. PMID:27199900

  6. Systematics and evolution of the subfamily Gerbillinae (Mammalia, Rodentia, Muridae).

    PubMed

    Chevret, Pascale; Dobigny, Gauthier

    2005-06-01

    Although they represent a quarter of the mammalian species, the evolutionary relationships among as well as within, the main murid lineages are still controversial. The subfamily Gerbillinae is no exception as previous studies based on morphological, karyotypical, and allozyme characters are highly incongruent. Here, we present the first molecular phylogeny for gerbils based on cytochrome b and 12S rRNA mitochondrial genes. Results are largely congruent between the two genes as well as with the concatenated data set with most of the nodes being well-supported. Based on the topologies retrieved here, we (1) propose the identification of three main clades, (2) support the split of Tatera genus into an Asian and an African group, the latter including Gerbillurus species, and (3) provide some evidence towards the inaccuracy of subgeneric divisions within both Gerbillus and Meriones. In addition, the sharp contrast between the genetic characters and morphological data sets suggest high levels of convergence, probably as a result of strong environmental constraints imposed on these rodents adapted to arid and semi-arid regions. Finally, molecular datings for the various cladogenetic events are in good agreement with the known gerbilline fossil record and support an African origin with subsequent migrations to Asia.

  7. Receptive range analysis of a mouse odorant receptor subfamily

    PubMed Central

    Li, Jingyi; Haddad, Rafi; Santos, Vanessa; Bavan, Selvan; Luetje, Charles W.

    2015-01-01

    Mammals deploy a large array of odorant receptors (ORs) to detect and distinguish a vast number of odorant molecules. ORs vary widely in the type of odorant structures recognized and in the breadth of molecular receptive range (MRR), with some ORs recognizing a small group of closely related molecules and other ORs recognizing a wide range of structures. While closely related ORs have been shown to have similar MRRs, the functional relationships among less closely related ORs are unclear. We screened a small group of ORs with a diverse odorant panel to identify a new odorant-OR pairing (unsaturated aldehydes and MOR263-3). We then extensively screened MOR263-3 and a series of additional MORs related to MOR263-3 in various ways. MORs related by phylogenetic analysis (several other members of the MOR263 subfamily) had MRRs that overlapped with the MRR of MOR263-3, even with amino acid identity as low as 48% (MOR263-2). MOR171-17, predicted to be functionally related to MOR263-3 by an alternative bioinformatic analysis, but with only 39% amino acid identity, had a distinct odorant specificity. Our results support the use of phylogenetic analysis to predict functional relationships among ORs with relatively low amino acid identity. PMID:25772782

  8. VAMP subfamilies identified by specific R-SNARE motifs.

    PubMed

    Rossi, Valeria; Picco, Raffaella; Vacca, Marcella; D'Esposito, Maurizio; D'Urso, Michele; Galli, Thierry; Filippini, Francesco

    2004-05-01

    In eukaryotes, interactions among the alpha-helical coiled-coil domains (CCDs) of soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) play a pivotal role in mediating the fusion among vesicles and target membranes. Surface residues of such CCDs are major candidates to regulate the specificity of membrane fusion, as they may alter local charge at the interaction layers and surface of the fusion complex, possibly modulating its formation and/or the binding of non-SNARE regulatory factors. Based on alternate patterns in surface residues, we have identified two motifs which group vesicular SNAREs in two novel subfamilies: RG-SNAREs and RD-SNAREs. The RG-SNARE CCD is common to all members of the widely conserved family of long VAMPs or longins and to yeast and non-neuronal VAMPs, possibly mediating "basic" fusion mechanisms; instead, only synaptobrevins from Bilateria share an RD-SNARE CCD, which is likely to mediate interactions to specific, yet unknown, regulatory factors and/or be the landmark of rapid fusion reactions like that mediating the release of neurotransmitters.

  9. 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.

  10. 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.

  11. 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.

  12. 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. PMID:27203707

  13. 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.

  14. 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

  15. Identification and phylogenetic characterization of a new subfamily of α-amylase enzymes from marine microorganisms.

    PubMed

    Liu, Yang; Lei, Yin; Zhang, Xuecheng; Gao, Yi; Xiao, Yazhong; Peng, Hui

    2012-06-01

    A gene encoding a starch-hydrolyzing enzyme was isolated from a marine metagenomic library and overexpressed in Escherichia coli. The enzyme, designated AmyP, shows very low similarity to full-length sequences of known α-amylases, although a catalytic domain correlated with the α-amylase superfamily was identified. Based on the range of substrate hydrolysis and the product profile, the protein was clearly defined as a saccharifying-type α-amylase. Sequence comparison indicated that AmyP was related to four putative glycosidases previously identified only in bacterial genome sequences. They were all from marine bacteria and formed a new subfamily of glycoside hydrolase GH13. Moreover, this subfamily was closely related to the probable genuine bacterial α-amylases (GH13_19). The results suggested that the subfamily may be an independent clade of ancestral marine bacterial α-amylases.

  16. 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

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

    PubMed

    Guidoti, Marcus; Montemayor, Sara I

    2016-01-01

    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. PMID:27515654

  18. Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships

    PubMed Central

    2010-01-01

    Background Nonribosomal peptide synthetases (NRPSs) are multimodular enzymes, found in fungi and bacteria, which biosynthesize peptides without the aid of ribosomes. Although their metabolite products have been the subject of intense investigation due to their life-saving roles as medicinals and injurious roles as mycotoxins and virulence factors, little is known of the phylogenetic relationships of the corresponding NRPSs or whether they can be ranked into subgroups of common function. We identified genes (NPS) encoding NRPS and NRPS-like proteins in 38 fungal genomes and undertook phylogenomic analyses in order to identify fungal NRPS subfamilies, assess taxonomic distribution, evaluate levels of conservation across subfamilies, and address mechanisms of evolution of multimodular NRPSs. We also characterized relationships of fungal NRPSs, a representative sampling of bacterial NRPSs, and related adenylating enzymes, including α-aminoadipate reductases (AARs) involved in lysine biosynthesis in fungi. Results Phylogenomic analysis identified nine major subfamilies of fungal NRPSs which fell into two main groups: one corresponds to NPS genes encoding primarily mono/bi-modular enzymes which grouped with bacterial NRPSs and the other includes genes encoding primarily multimodular and exclusively fungal NRPSs. AARs shared a closer phylogenetic relationship to NRPSs than to other acyl-adenylating enzymes. Phylogenetic analyses and taxonomic distribution suggest that several mono/bi-modular subfamilies arose either prior to, or early in, the evolution of fungi, while two multimodular groups appear restricted to and expanded in fungi. The older mono/bi-modular subfamilies show conserved domain architectures suggestive of functional conservation, while multimodular NRPSs, particularly those unique to euascomycetes, show a diversity of architectures and of genetic mechanisms generating this diversity. Conclusions This work is the first to characterize subfamilies of fungal

  19. 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

  20. Four new species of the subfamily Gryllacridinae (Orthoptera: Gryllacrididae) from China.

    PubMed

    Li, Miaomiao; Liu, Xianwei; Li, Kai

    2016-01-01

    A taxonomic study of the subfamily Gryllacridinae is presented. Four new species belonging to two genera are described: Larnaca sinica sp. nov., Larnaca hainanica sp. nov.; Prosopogryllacris chinensis sp. nov., Prosopogryllacris incisa sp. nov.. A revised key and distributional data are given. PMID:27615930

  1. 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.

  2. Four new species of the subfamily Psilodercinae (Araneae: Ochyroceratidae) from Southwest China.

    PubMed

    Wang, Chunxia; Li, Shuqiang

    2013-01-01

    Four new species of the family Ochyroceratidae are described from Southwest China: Althepus christae sp. nov., Lecler- cera undulatus sp. nov., Psiloderces incomptus sp. nov. from Yunnan; and P. exilis sp. nov. from Guangxi. The four spe- cies belong to the subfamily Psilodercinae.

  3. 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.

  4. Evolution of the Secondary Symbiont “Candidatus Serratia symbiotica” in Aphid Species of the Subfamily Lachninae ▿†

    PubMed Central

    Lamelas, Araceli; Pérez-Brocal, Vicente; Gómez-Valero, Laura; Gosalbes, María José; Moya, Andrés; Latorre, Amparo

    2008-01-01

    Buchnera aphidicola BCc, the primary endosymbiont of the aphid Cinara cedri (subfamily Lachninae), is losing its symbiotic capacity and might be replaced by the coresident “Candidatus Serratia symbiotica.” Phylogenetic and morphological analyses within the subfamily Lachninae indicate two different “Ca. Serratia symbiotica” lineages and support the longtime coevolution of both symbionts in C. cedri. PMID:18502932

  5. 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

  6. Members of a recently discovered subfamily of cytokinin receptors display differences and similarities to their classical counterparts.

    PubMed

    Gruhn, Nijuscha; Seidl, Michael F; Halawa, Mhyeddeen; Heyl, Alexander

    2015-01-01

    Cytokinins represent a group of plant hormones that have been shown to be essential for plant growth and development. A recent large-scale phylogenetic analysis of components of the cytokinin signal transduction pathway revealed, among other findings, the existence of a second, previously unknown subfamily of cytokinin receptors. Here we report that the cytokinin binding domains of the members of the 2 subfamilies contain residues that are highly conserved in either or in both subfamilies. Experiments using fluorescence microscopy hint at an ER and a plasma membrane localization for 2 members of the newly identified subfamily. These data provide new insights in the conservation of sequence and localization properties among the 2 subfamilies. PMID:25826259

  7. Phylogenetic relationships of Rutaceae: a cladistic analysis of the subfamilies using evidence from RBC and ATP sequence variation.

    PubMed

    Chase, M W; Morton, C M; Kallunki, J A

    1999-08-01

    Sequence data for plastid rbcL and atpB from members of Anacardiaceae, Burseraceae, Cneoraceae, Meliaceae, Ptaeroxylaceae, Rutaceae, and Simaroubaceae were analyzed cladistically to evaluate the familial and subfamilial circumscriptions of Rutaceae. Taxa representing all subfamilies and tribes were sampled. The analysis shows that Rutaceae are paraphyletic, with Spathelia and Dictyoloma (Rutaceae), Harrisonia (Simaroubaceae), Cneorum (Cneoraceae), and Ptaeroxylon (Ptaeroxylaceae) forming a clade sister to all other Rutaceae. Circumscription of Rutaceae to include all of these taxa is recommended. This analysis indicates that Simaroubaceae and Meliaceae are the outgroups closest to Rutaceae. Correlation of the molecular phylogenies with biochemical data indicates that chemotaxonomic information is more reliable than fruit type as an indicator of familial and subfamilial circumscriptions. The subfamilial classification needs revision; none of the subfamilies of more than one genus is monophyletic.

  8. Members of a recently discovered subfamily of cytokinin receptors display differences and similarities to their classical counterparts

    PubMed Central

    Gruhn, Nijuscha; Seidl, Michael F; Halawa, Mhyeddeen; Heyl, Alexander

    2015-01-01

    Cytokinins represent a group of plant hormones that have been shown to be essential for plant growth and development. A recent large-scale phylogenetic analysis of components of the cytokinin signal transduction pathway revealed, among other findings, the existence of a second, previously unknown subfamily of cytokinin receptors. Here we report that the cytokinin binding domains of the members of the 2 subfamilies contain residues that are highly conserved in either or in both subfamilies. Experiments using fluorescence microscopy hint at an ER and a plasma membrane localization for 2 members of the newly identified subfamily. These data provide new insights in the conservation of sequence and localization properties among the 2 subfamilies. PMID:25826259

  9. Simultaneous determination of polyphenols and major purine alkaloids in Greek Sideritis species, herbal extracts, green tea, black tea, and coffee by high-performance liquid chromatography-diode array detection.

    PubMed

    Samanidou, Victoria; Tsagiannidis, Anastasios; Sarakatsianos, Ioannis

    2012-02-01

    Herein, a high-performance liquid chromatography-diode array detection method has been developed for the simultaneous determination of 15 phenolic antioxidants: flavan-3-ols, (-)-epigallocatechin, (+)-catechin, (-)-epigallocatechin gallate, (-)-epicatechin, (-)-epicatechin gallate, (-)-gallocatechin, a phenolic acid (gallic acid), a hydroxycinnamic acid (chlorogenic acid), flavones (apigenin), flavonols (kaempferol, quercetin, and myricetin), and purine alkaloids (caffeine theophylline, theobromine) in different herb extracts, tea, and coffee varieties. The developed method was validated and successfully applied in order to determine the polyphenolic content to estimate the antioxidant activity of the Sideritis species commonly known as Greek mountain tea. To the best of our knowledge, this is the first report on the quantitative determination of catechins and other polyphenols in Greek mountain tea. Acidic hydrolysis was necessary for the simultaneous determination of the aglycones of the target analytes. According to our results, chlorogenic acid, myricetin, apigenin, catechin, and epicatechin gallate are found in the Sideritis species.

  10. Subclassification and Biochemical Analysis of Plant Papain-Like Cysteine Proteases Displays Subfamily-Specific Characteristics1[C][W

    PubMed Central

    Richau, Kerstin H.; Kaschani, Farnusch; Verdoes, Martijn; Pansuriya, Twinkal C.; Niessen, Sherry; Stüber, Kurt; Colby, Tom; Overkleeft, Hermen S.; Bogyo, Matthew; Van der Hoorn, Renier A.L.

    2012-01-01

    Papain-like cysteine proteases (PLCPs) are a large class of proteolytic enzymes associated with development, immunity, and senescence. Although many properties have been described for individual proteases, the distribution of these characteristics has not been studied collectively. Here, we analyzed 723 plant PLCPs and classify them into nine subfamilies that are present throughout the plant kingdom. Analysis of these subfamilies revealed previously unreported distinct subfamily-specific functional and structural characteristics. For example, the NPIR and KDEL localization signals are distinctive for subfamilies, and the carboxyl-terminal granulin domain occurs in two PLCP subfamilies, in which some individual members probably evolved by deletion of the granulin domains. We also discovered a conserved double cysteine in the catalytic site of SAG12-like proteases and two subfamily-specific disulfides in RD19A-like proteases. Protease activity profiling of representatives of the PLCP subfamilies using novel fluorescent probes revealed striking polymorphic labeling profiles and remarkably distinct pH dependency. Competition assays with peptide-epoxide scanning libraries revealed common and unique inhibitory fingerprints. Finally, we expand the detection of PLCPs by identifying common and organ-specific protease activities and identify previously undetected proteases upon labeling with cell-penetrating probes in vivo. This study provides the plant protease research community with tools for further functional annotation of plant PLCPs. PMID:22371507

  11. 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

  12. 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.

  13. 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. PMID:26849045

  14. 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.

  15. 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.

  16. Identifying the catalytic acid/base in GH29 α-L-fucosidase subfamilies.

    PubMed

    Shaikh, F Aidha; Lammerts van Bueren, Alicia; Davies, Gideon J; Withers, Stephen G

    2013-08-27

    While the catalytic nucleophile in the configuration-retaining α-L-fucosidases from family GH29 is fully conserved with respect to sequence, there is no fully sequence-conserved acid/base residue candidate across the family. X-ray crystallographic studies and kinetic characterizations have allowed the identification of this residue in a few cases, and a recent combination of phylogenetic tree analyses with substrate specificity data has allowed the division of GH29 enzymes into two subfamilies, A and B, allowing the probable assignment of these residues. Here, we perform detailed kinetic and mechanistic characterizations of the corresponding alanine mutants and other candidates. Through comparison of kinetic parameters obtained for the hydrolysis of fucosyl substrates with activated leaving groups by these mutants with those of the corresponding wild-type enzymes, in conjunction with the demonstration of azide rescue, we largely confirm the acid/base residue predictions for the GH29 fucosidases from the two subfamilies.

  17. A Ras subfamily GTPase shows cell cycle-dependent nuclear localization

    PubMed Central

    Sutherland, Brent W.; Spiegelman, George B.; Weeks, Gerald

    2001-01-01

    Previously characterized Ras subfamily proteins have been found to be predominantly associated with the plasma membrane where they function in signal transduction pathways to convey extracellular signals to intracellular targets. Here, we provide evidence that the Dictyostelium Ras subfamily protein RasB has a novel subcellular localization and function. The protein is predominantly localized in the nucleus during most of the cell cycle. Furthermore, during mitosis and cytokinesis RasB assumes a diffuse cellular localization despite the fact that the nuclear membrane stays intact. The linkage between the position of RasB in the cell and division suggests that it may have a role in nuclear division. Consistent with this idea, rasB– cells exhibit severe growth defects and cells overexpressing an activated version of RasB are multinucleate. PMID:11606416

  18. 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.

  19. 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

  20. A review of the subfamily Acaenitinae Förster, 1869 (Hymenoptera, Ichneumonidae) from Ukrainian Carpathians

    PubMed Central

    2013-01-01

    Abstract Ichneumonid wasps of the subfamily Acaenitinae Förster, 1869 are reviewed for the first time from the Ukrainian Carpathians. Two species, Coleocentrus exareolatus Kriechbaumer, 1894 and Coleocentrus heteropus Thomson, 1894 are new records for Ukraine. Arotes annulicornis Kriechbaumer, 1894 is considered to be a junior synonym of Arotes albicinctus Gravenhorst, 1829 (syn. nov.). A key to species of Coleocentrus of the Carpathians is provided. PMID:24723751

  1. Molecular Evolutionary Characterization of a V1R Subfamily Unique to Strepsirrhine Primates

    PubMed Central

    Yoder, Anne D.; Chan, Lauren M.; dos Reis, Mario; Larsen, Peter A.; Campbell, C. Ryan; Rasoloarison, Rodin; Barrett, Meredith; Roos, Christian; Kappeler, Peter; Bielawski, Joseph; Yang, Ziheng

    2014-01-01

    Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vomeronasal receptor class 1 (V1R) sequences ever generated for a diverse yet phylogenetically coherent group of mammals, the tooth-combed primates (suborder Strepsirrhini). Phylogenetic analysis confirms our intensive sampling from a single V1R subfamily, apparently unique to the strepsirrhine primates. We designate this subfamily as V1Rstrep. The subfamily retains extensive repertoires of gene copies that descend from an ancestral gene duplication that appears to have occurred prior to the diversification of all lemuriform primates excluding the basal genus Daubentonia (the aye-aye). We refer to the descendent clades as V1Rstrep-α and V1Rstrep-β. Comparison of the two clades reveals different amino acid compositions corresponding to the predicted ligand-binding site and thus potentially to altered functional profiles between the two. In agreement with previous studies of the mouse lemur (genus, Microcebus), the majority of V1Rstrep gene copies appear to be intact and under strong positive selection, particularly within transmembrane regions. Finally, despite the surprisingly high number of gene copies identified in this study, it is nonetheless probable that V1R diversity remains underestimated in these nonmodel primates and that complete characterization will be limited until high-coverage assembled genomes are available. PMID:24398377

  2. Rice shoot branching requires an ATP-binding cassette subfamily G protein.

    PubMed

    Yasuno, Naoko; Takamure, Itsuro; Kidou, Shin-ichiro; Tokuji, Yoshihiko; Ureshi, An-na; Funabiki, Atsushi; Ashikaga, Kazunori; Yamanouchi, Utako; Yano, Masahiro; Kato, Kiyoaki

    2009-01-01

    * Shoot branching is important for the establishment of plant architecture and productivity. * Here, characterization of rice (Oryza sativa) reduced culm number 1 (rcn1) mutants revealed that Rcn1 positively controls shoot branching by promoting the outgrowth of lateral shoots. Molecular studies revealed that Rcn1 encodes a novel member of ATP-binding cassette protein subfamily G (ABCG subfamily), also known as the white-brown complex (WBC) subfamily, and is designated OsABCG5. * Rcn1 is expressed in leaf primordia of main and axillary shoots, and in the vascular cells and leaf epidermis of older leaves. In addition, Rcn1 is expressed in the crown root primordia, endodermis, pericycle and stele in the root. No effect on Rcn1 expression in shoots or roots was seen when the roots were treated with auxins. Phenotypic analyses of rcn1 and tillering dwarf 3 (d3) double mutants at the seedling stage clarified that Rcn1 works independently of D3 in the branching inhibitor pathway. * Rcn1 is the first functionally defined plant ABCG protein gene that controls shoot branching and could thus be significant in future breeding for high-yielding rice. PMID:19140940

  3. Molecular evolutionary characterization of a V1R subfamily unique to strepsirrhine primates.

    PubMed

    Yoder, Anne D; Chan, Lauren M; dos Reis, Mario; Larsen, Peter A; Campbell, C Ryan; Rasoloarison, Rodin; Barrett, Meredith; Roos, Christian; Kappeler, Peter; Bielawski, Joseph; Yang, Ziheng

    2014-01-01

    Vomeronasal receptor genes have frequently been invoked as integral to the establishment and maintenance of species boundaries among mammals due to the elaborate one-to-one correspondence between semiochemical signals and neuronal sensory inputs. Here, we report the most extensive sample of vomeronasal receptor class 1 (V1R) sequences ever generated for a diverse yet phylogenetically coherent group of mammals, the tooth-combed primates (suborder Strepsirrhini). Phylogenetic analysis confirms our intensive sampling from a single V1R subfamily, apparently unique to the strepsirrhine primates. We designate this subfamily as V1Rstrep. The subfamily retains extensive repertoires of gene copies that descend from an ancestral gene duplication that appears to have occurred prior to the diversification of all lemuriform primates excluding the basal genus Daubentonia (the aye-aye). We refer to the descendent clades as V1Rstrep-α and V1Rstrep-β. Comparison of the two clades reveals different amino acid compositions corresponding to the predicted ligand-binding site and thus potentially to altered functional profiles between the two. In agreement with previous studies of the mouse lemur (genus, Microcebus), the majority of V1Rstrep gene copies appear to be intact and under strong positive selection, particularly within transmembrane regions. Finally, despite the surprisingly high number of gene copies identified in this study, it is nonetheless probable that V1R diversity remains underestimated in these nonmodel primates and that complete characterization will be limited until high-coverage assembled genomes are available. PMID:24398377

  4. 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

  5. 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.

  6. 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

  7. Phylogeny and evolutionary patterns in the Dwarf crayfish subfamily (Decapoda: Cambarellinae).

    PubMed

    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

  8. 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. PMID:26446351

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

    PubMed

    Han, Taeman; Lee, Wonhoon; 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 extensively

  10. Candidate chemoreceptor subfamilies differentially expressed in the chemosensory organs of the mollusc Aplysia

    PubMed Central

    Cummins, Scott F; Erpenbeck, Dirk; Zou, Zhihua; Claudianos, Charles; Moroz, Leonid L; Nagle, Gregg T; Degnan, Bernard M

    2009-01-01

    Background Marine molluscs, as is the case with most aquatic animals, rely heavily on olfactory cues for survival. In the mollusc Aplysia californica, mate-attraction is mediated by a blend of water-borne protein pheromones that are detected by sensory structures called rhinophores. The expression of G protein and phospholipase C signaling molecules in this organ is consistent with chemosensory detection being via a G-protein-coupled signaling mechanism. Results Here we show that novel multi-transmembrane proteins with similarity to rhodopsin G-protein coupled receptors are expressed in sensory epithelia microdissected from the Aplysia rhinophore. Analysis of the A. californica genome reveals that these are part of larger multigene families that possess features found in metazoan chemosensory receptor families (that is, these families chiefly consist of single exon genes that are clustered in the genome). Phylogenetic analyses show that the novel Aplysia G-protein coupled receptor-like proteins represent three distinct monophyletic subfamilies. Representatives of each subfamily are restricted to or differentially expressed in the rhinophore and oral tentacles, suggesting that they encode functional chemoreceptors and that these olfactory organs sense different chemicals. Those expressed in rhinophores may sense water-borne pheromones. Secondary signaling component proteins Gαq, Gαi, and Gαo are also expressed in the rhinophore sensory epithelium. Conclusion The novel rhodopsin G-protein coupled receptor-like gene subfamilies identified here do not have closely related identifiable orthologs in other metazoans, suggesting that they arose by a lineage-specific expansion as has been observed in chemosensory receptor families in other bilaterians. These candidate chemosensory receptors are expressed and often restricted to rhinophores and oral tentacles, lending support to the notion that water-borne chemical detection in Aplysia involves species- or lineage

  11. Control of postnatal apoptosis in the neocortex by RhoA-subfamily GTPases determines neuronal density.

    PubMed

    Sanno, Hitomi; Shen, Xiao; Kuru, Nilgün; Bormuth, Ingo; Bobsin, Kristin; Gardner, Humphrey A R; Komljenovic, Dorde; Tarabykin, Victor; Erzurumlu, Reha S; Tucker, Kerry L

    2010-03-24

    Apoptosis of neurons in the maturing neocortex has been recorded in a wide variety of mammals, but very little is known about its effects on cortical differentiation. Recent research has implicated the RhoA GTPase subfamily in the control of apoptosis in the developing nervous system and in other tissue types. Rho GTPases are important components of the signaling pathways linking extracellular signals to the cytoskeleton. To investigate the role of the RhoA GTPase subfamily in neocortical apoptosis and differentiation, we have engineered a mouse line in which a dominant-negative RhoA mutant (N19-RhoA) is expressed from the Mapt locus, such that all neurons of the developing nervous system are expressing the N19-RhoA inhibitor. Postnatal expression of N19-RhoA led to no major changes in neocortical anatomy. Six layers of the neocortex developed and barrels (whisker-related neural modules) formed in layer IV. However, the density and absolute number of neurons in the somatosensory cortex increased by 12-26% compared with wild-type littermates. This was not explained by a change in the migration of neurons during the formation of cortical layers but rather by a large decrease in the amount of neuronal apoptosis at postnatal day 5, the developmental maximum of cortical apoptosis. In addition, overexpression of RhoA in cortical neurons was seen to cause high levels of apoptosis. These results demonstrate that RhoA-subfamily members play a major role in developmental apoptosis in postnatal neocortex of the mouse but that decreased apoptosis does not alter cortical cytoarchitecture and patterning. PMID:20335457

  12. Control of postnatal apoptosis in the neocortex by RhoA-subfamily GTPases determines neuronal density

    PubMed Central

    Sanno, Hitomi; Shen, Xiao; Kuru, Nilgün; Bormuth, Ingo; Bobsin, Kristin; Komljenovic, Dorde; Tarabykin, Victor; Erzurumlu, Reha S.; Tucker, Kerry L.

    2010-01-01

    Apoptosis of neurons in the maturing neocortex has been recorded in a wide variety of mammals, but very little is known about its effects on cortical differentiation. Recent research has implicated the RhoA GTPase subfamily in the control of apoptosis in the developing nervous system and in other tissue types. Rho GTPases are important components of the signaling pathways linking extracellular signals to the cytoskeleton. To investigate the role of the RhoA GTPase subfamily in neocortical apoptosis and differentiation, we have engineered a mouse line in which a dominant-negative RhoA mutant (N19-RhoA) is expressed from the Mapt locus, such that all neurons of the developing nervous system are expressing the N19-RhoA inhibitor. Postnatal expression of N19-RhoA led to no major changes in neocortical anatomy. Six layers of the neocortex developed and barrels (whisker-related neural modules) formed in layer IV. However, the density and absolute number of neurons in the somatosensory cortex increased by 12 - 26%, as compared to wildtype littermates. This was not explained by a change in the migration of neurons during the formation of cortical layers, but rather by a large decrease in the amount of neuronal apoptosis at P5, the developmental maximum of cortical apoptosis. In addition, overexpression of RhoA in cortical neurons was seen to cause high levels of apoptosis. These results demonstrate that RhoA-subfamily members play a major role in developmental apoptosis in postnatal neocortex of the mouse, but that decreased apoptosis does not alter cortical cytoarchitecture and patterning. PMID:20335457

  13. 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.

  14. 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. PMID:21120679

  15. 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.

  16. 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. PMID:27054154

  17. 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.

  18. Functional analysis of putative genes encoding the PIP2 water channel subfamily in Populus trichocarpa.

    PubMed

    Secchi, Francesca; MacIver, Bryce; Zeidel, Mark L; Zwieniecki, Maciej A

    2009-11-01

    We located fully sequenced putative genes of the plasma membrane intrinsic proteins (PIPs) family in the Populus trichocarpa (Torr. Gray), genome. Of 23 gene candidates, we assigned eight genes to the PIP2 subfamily. All eight putative genes were expressed in vegetative tissues (roots, leaves, bark and wood), and all of them showed water channel activity after being expressed in Xenopus oocytes. Six of eight proteins were affected by mercury ions. No proteins were affected by the presence of nickel or tungsten ions, or by lowering the pH of bathing external solution from 7.4 to 6.5. The presence of copper ions caused seven of eight PIP2 proteins to increase their water transport capacity by as much as 50%. This systematic study of the PIP2 subfamily of proteins in P. trichocarpa provides a basic overview of their activity as water channels and will be a useful reference for future physiological studies of plant water relations that use P. trichocarpa as a model system. PMID:19808706

  19. Karyotype differentiation patterns in species of the subfamily Scarabaeinae (Scarabaeidae, Coleoptera).

    PubMed

    Cabral-de-Mello, Diogo Cavalcanti; de Oliveira, Sárah Gomes; Ramos, Ituza Celeste; de Moura, Rita de Cássia

    2008-12-01

    The aim of this study was to describe the karyotype of species belonging to the subfamily Scarabaeinae (Coleoptera, Scarabaeidae) and to compile the conventional cytogenetic data available in the literature for this group. The karyotypes of ten species belonging to the tribes Canthonini, Coprini, Onthophagini and Phanaeini were analyzed by conventional staining. Eight of these species were described for the first time (Canthon aff carbonarius, Canthon chalybaeus, Coprophanaeus dardanus, Deltochilum aff amazonicum, Dichotomius geminatus, Oxysternon silenus, Phanaeus chalcomelas and Malagoniella aff astyanax) and two were redescribed (Diabroctis mimas and Digitonthophagus gazella) since their karyotypes differed from those previously published in the literature. Four species studied showed a diploid number of 2n=20 and a parachute type sex determining system and the karyotype was 2n=20,Xy in two species and 2n=18,Xy(p), 2n=19,X0, 2n=12,XY and 2n=14,neoXY in one each. The chromosome morphology of the different species varied, with the observation of metacentric, submetacentric, subacrocentric and acrocentric chromosomes. The X chromosome was predominantly meta or submetacentric in the species analyzed, whereas the y chromosome presented two arms or was punctiform. In conclusion, the subfamily Scarabaeinae comprises 120 species analyzed cytogenetically, and are observed the occurrence of five chromosome rearrangements (autosome-autosome and X-autosome fusions, pericentric inversions, fissions and loss of the y chromosome) that are related to the chromosome variability and evolution in the group. PMID:18495484

  20. 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

  1. Two members of a widely expressed subfamily of hormone-stimulated adenylyl cyclases.

    PubMed Central

    Premont, R T; Chen, J; Ma, H W; Ponnapalli, M; Iyengar, R

    1992-01-01

    cDNA encoding a hormone- and guanine nucleotide-stimulated adenylyl cyclase [ATP pyrophosphate-lyase (cyclizing), EC 4.6.1.1] (type 6) from rat liver and kidney has been cloned and expressed. This enzyme is stimulated by forskolin, guanosine 5'-[gamma-thio]triphosphate, and isoproterenol plus GTP but is not stimulated by beta gamma subunits of guanine nucleotide-binding proteins. A second form (type 5), which is 75% similar to type 6, has also been cloned. Both types 5 and 6 cDNAs have multiple messages. PCR-based detection of the mRNA for the type 5 and 6 enzymes indicates that both are widely distributed. Homology analyses indicate at least four distinct subfamilies of guanine nucleotide stimulatory protein-regulated adenylyl cyclases. Types 5 and 6 enzymes define one distinct subfamily of mammalian adenylyl cyclases. Diversity of one guanine nucleotide-binding protein-regulated effector may allow different modes of regulation of cell-surface signal transmission. Images PMID:1409703

  2. Nonlinear interaction of intense hypergeometric Gaussian subfamily laser beams in plasma

    NASA Astrophysics Data System (ADS)

    Sobhani, H.; Vaziri (Khamedi), M.; Rooholamininejad, H.; Bahrampour, A. R.

    2016-07-01

    Propagation of Hypergeometric-Gaussian laser beam in a nonlinear plasma medium is investigated by considering the Source Dependent Expansion method. A subfamily of Hypergeometric-Gaussian beams with a non-negative, even and integer radial index, can be expressed as the linear superposition of finite number of Laguerre-Gaussian functions. Propagation of Hypergeometric-Gaussian beams in a nonlinear plasma medium depends on the value of radial index. The bright rings' number of these beams is changed during the propagation in plasma medium. The effect of beam vortex charge number l and initial (input) beam intensity on the self-focusing of Hypergeometric-Gaussian beams is explored. Also, by choosing the suitable initial conditions, Hypergeometric-Gaussian subfamily beams can be converted to one or more mode components that a typical of mode conversion may be occurred. The self-focusing of these winding beams can be used to control the focusing force and improve the electron bunch quality in laser plasma accelerators.

  3. A cladistic analysis of the genera in the subfamily Pudicinae (Nematoda, Trichostrongyloidea, Heligmonellidae).

    PubMed

    Durette-Desset, M C; Justine, J L

    1991-09-01

    A parsimony analysis was performed on 37 specific taxa belonging to the subfamily Pudicinae (family Heligmonellidae), which contains parasites mainly from South American caviomorph rodents. Thirteen characters were used from the synlophe (rotation of axis, presence of carene, carene asymmetry, presence of comaretes, single ventral comarete length, ridge discontinuity, ventral ridge numbers, presence of a peculiar posterior synlophe, presence of supernumerary spines) and the male caudal bursa (relative length of rays 9 and 10, caudal bursa type, division of the dorsal ray, divergence of the 10th rays). The cladogram shows a consistency index of 1.0. The subfamily Pudicinae has two synapomorphies. Two suprageneric groups are recognized. Suprageneric group 1 shows one synapomorphy and contains Heligmostrongylus, Fuellebornema, Sciurodendrium and Pseudoheligmosomum; suprageneric group 2 shows two synapomorphies and contains Pudica, Acanthostrongylus, Justinema and Durettestrongylus. Five genera are defined on the basis of synapomorphies. The genera Heligmostrongylus, Sciurodendrium and Pudica which are considered paraphyletic, however, are retained due to lack of knowledge as to their relationships.

  4. Expression Profiling of Nuclear Receptors Identifies Key Roles of NR4A Subfamily in Uterine Fibroids

    PubMed Central

    Yin, Hanwei; Lo, Jay H.; Kim, Ji-Young; Marsh, Erica E.; Kim, J. Julie; Ghosh, Asish K.; Bulun, Serdar

    2013-01-01

    Uterine fibroids (UFs), also known as uterine leiomyomas, are benign, fibrotic smooth muscle tumors. Although the GnRH analog leuprolide acetate that suppresses gonadal steroid hormones is used as a treatment, it has significant side effects, thereby limiting its use. Availability of more effective therapy is limited because of a lack of understanding of molecular underpinnings of the disease. Although ovarian steroid hormones estrogen and progesterone and their receptors are clearly involved, the role of other nuclear receptors (NRs) in UFs is not well defined. We used quantitative real-time PCR to systematically profile the expression of 48 NRs and identified several NRs that were aberrantly expressed in UFs. Among others, expression of NR4A subfamily members including NGFIB (NR4A1), NURR1 (NR4A2), and NOR1 (NR4A3) were dramatically suppressed in leiomyoma compared with the matched myometrium. Restoration of expression of each of these NR4A members in the primary leiomyoma smooth muscle cells decreased cell proliferation. Importantly, NR4As regulate expressions of the profibrotic factors including TGFβ3 and SMAD3, and several collagens that are key components of the extracellular matrix. Finally, we identify NR4A members as targets of leuprolide acetate treatment. Together, our results implicate several NRs including the NR4A subfamily in leiomyoma etiology and identify NR4As as potential therapeutic targets for treating fibrotic diseases. PMID:23550059

  5. A subfamily of PLP-dependent enzymes specialized in handling terminal amines.

    PubMed

    Schiroli, Davide; Peracchi, Alessio

    2015-09-01

    The present review focuses on a subfamily of pyridoxal phosphate (PLP)-dependent enzymes, belonging to the broader fold-type I structural group and whose archetypes can be considered ornithine δ-transaminase and γ-aminobutyrate transaminase. These proteins were originally christened "subgroup-II aminotransferases" (AT-II) but are very often referred to as "class-III aminotransferases". As names suggest, the subgroup includes mainly transaminases, with just a few interesting exceptions. However, at variance with most other PLP-dependent enzymes, catalysts in this subfamily seem specialized at utilizing substrates whose amino function is not adjacent to a carboxylate group. AT-II enzymes are widespread in biology and play mostly catabolic roles. Furthermore, today several transaminases in this group are being used as bioorganic tools for the asymmetric synthesis of chiral amines. We present an overview of the biochemical and structural features of these enzymes, illustrating how they are distinctive and how they compare with those of the other fold-type I enzymes. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications. PMID:25770684

  6. Phylogenetic status of insect parasitism in the subfamily Entaphelenchinae Nickle with description of Peraphelenchus orientalis n. sp. (Tylenchomorpha: Aphelenchoididae).

    PubMed

    Kanzaki, Natsumi; Tanaka, Ryusei; Ikeda, Hiroshi; Taki, Hisatomo; Sugiura, Shinji; Matsumoto, Kazuma

    2013-08-01

    The nematode family Aphelenchoididae is a highly divergent group that contains plant parasites, predators, fungal feeders, and insect parasites. It is taxonomically separated into 7 subfamilies. Although molecular phylogenetic relationships among 6 of the subfamilies have been clarified, the phylogenetic position of the subfamily Entaphelenchinae, which is composed of endoparasites of insects, remains unclear. Here, a new entaphelenchid species, Peraphelenchus orientalis n. sp., was isolated from the body cavities of burying beetles, Nicrophorus quadripunctatus, with a 14% prevalence (5 out of 36). The phylogenetic position of the subfamily within the family Aphelenchoididae was determined using morphological and molecular data for the new species. The rRNA sequences suggested that the new species belongs to Clade 3 of Aphelenchoididae, which mostly consists of predators and insect parasites. Although molecular sequences from other entaphelenchid species were not available, the subfamily appears to be monophyletic. The new species is characterized by the absence of a functional rectum and anus and by the presence of 3 pairs of male genital papillae, a loosely coiled male body, and a W-shaped male spicule. Compared with the original description of Peraphelenchus necrophori, P. orientalis n. sp. has significant typological differences, possibly because of misinterpretations during the original description of P. necrophori. Excluding these questionable characters, i.e., presence-absence of functional rectum and anus and number of male genital papillae, the new species is distinguished from P. necrophori by minor morphological characters and morphometric values.

  7. 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

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

    PubMed

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

    2015-06-05

    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.

  9. Soybean (Glycine max) expansin gene superfamily origins: segmental and tandem duplication events followed by divergent selection among subfamilies

    PubMed Central

    2014-01-01

    Background Expansins are plant cell wall loosening proteins that are involved in cell enlargement and a variety of other developmental processes. The expansin superfamily contains four subfamilies; namely, α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). Although the genome sequencing of soybeans is complete, our knowledge about the pattern of expansion and evolutionary history of soybean expansin genes remains limited. Results A total of 75 expansin genes were identified in the soybean genome, and grouped into four subfamilies based on their phylogenetic relationships. Structural analysis revealed that the expansin genes are conserved in each subfamily, but are divergent among subfamilies. Furthermore, in soybean and Arabidopsis, the expansin gene family has been mainly expanded through tandem and segmental duplications; however, in rice, segmental duplication appears to be the dominant process that generates this superfamily. The transcriptome atlas revealed notable differential expression in either transcript abundance or expression patterns under normal growth conditions. This finding was consistent with the differential distribution of the cis-elements in the promoter region, and indicated wide functional divergence in this superfamily. Moreover, some critical amino acids that contribute to functional divergence and positive selection were detected. Finally, site model and branch-site model analysis of positive selection indicated that the soybean expansin gene superfamily is under strong positive selection, and that divergent selection constraints might have influenced the evolution of the four subfamilies. Conclusion This study demonstrated that the soybean expansin gene superfamily has expanded through tandem and segmental duplication. Differential expression indicated wide functional divergence in this superfamily. Furthermore, positive selection analysis revealed that divergent selection constraints might have

  10. 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. PMID:27159982

  11. Unusual molecular pattern in Ajugoideae subfamily: the case of Ajuga genevensis L. from Dolomites.

    PubMed

    Venditti, A; Frezza, C; Riccardelli, M; Foddai, S; Nicoletti, M; Serafini, M; Bianco, A

    2016-01-01

    We analysed the ethanolic extract from Ajuga genevensis L. (Lamiaceae) growing in Dolomites, part of Italian Alps. Three new compounds for this species were identified: rosmarinic acid (1), oleanolic acid (2) and maslinic acid (3), representative of two different classes of chemical compounds (phenylpropanoids and pentacyclic triterpenes). A. genevensis resulted to be a valuable source of these compounds endowed with interesting biological activities (i.e. antioxidant, neuroprotective, anti-inflammatory, antiproliferative). The recognition of compounds (1), (2) and (3) may also confirm the ethnomedicinal uses of this plant. From a chemotaxonomical point of view, it is worth noting that iridoids were not evidenced in this accession. Iridoids are considered chemotaxonomic marker in Lamiales, and, in contrast with a previous study on this species, the presence of aucubin was not confirmed. In addition, the presence of large amounts of rosmarinic acid (1) was unexpected for a species that does not belong to subfamily Nepetoideae.

  12. Characterization of mariner-like transposons of the mauritiana Subfamily in seven tree aphid species.

    PubMed

    Kharrat, Imen; Mezghani, Maha; Casse, Nathalie; Denis, Françoise; Caruso, Aurore; Makni, Hanem; Capy, Pierre; Rouault, Jacques-Deric; Chénais, Benoît; Makni, Mohamed

    2015-02-01

    Mariner-like elements (MLEs) are Class II transposons present in all eukaryotic genomes in which MLEs have been searched for. This article reports the detection of MLEs in seven of the main fruit tree aphid species out of eight species studied. Deleted MLE sequences of 916-919 bp were characterized, using the terminal-inverted repeats (TIRs) of mariner elements belonging to the mauritiana Subfamily as primers. All the sequences detected were deleted copies of full-length elements that included the 3'- and 5'-TIRs but displayed internal deletions affecting Mos1 activity. Networks based on the mtDNA cytochrome oxidase subunit-I (CO-I) and MLE sequences were incongruent, suggesting that mutations in transposon sequences had accumulated before speciation of tree aphid species occurred, and that they have been maintained in this species via vertical transmissions. This is the first evidence of the widespread occurrence of MLEs in aphids.

  13. Unrelated sequences at the 5' end of mouse LINE-1 repeated elements define two distinct subfamilies.

    PubMed Central

    Wincker, P; Jubier-Maurin, V; Roizès, G

    1987-01-01

    Some full length members of the mouse long interspersed repeated DNA family L1Md have been shown to be associated at their 5' end with a variable number of tandem repetitions, the A repeats, that have been suggested to be transcription controlling elements. We report that the other type of repeat, named F, found at the 5' end of a few L1 elements is also an integral part of full length L1 copies. Sequencing shows that the F repeats are GC rich, and organized in tandem. The L1 copies associated with either A or F repeats can be correlated with two different subsets of L1 sequences distinguished by a series of variant nucleotides specific to each and by unassociated but frequent restriction sites. These findings suggest that sequence replacement has occurred at least once in 5' of L1Md, and is related to the generation of specific subfamilies. Images PMID:3684566

  14. TSH increases synthesis of hepatic ATP-binding cassette subfamily A member 1 in hypercholesterolemia.

    PubMed

    Zhang, Tiantian; Zhou, Lingyan; Li, Cong Cong; Shi, Hong; Zhou, Xinli

    2016-07-22

    Epidemiological evidence suggests that thyrotropin (TSH) levels are closely correlated with the severity of hypercholesterolemia. Reverse cholesterol transfer (RCT) plays an important role in regulating bloodcholesterol. However, the molecular mechanism of hypercholesterolemia in subclinical hypothyroidism (SCH) has not been fully clarified. The SCH mouse model, which is characterized by elevated serum TSH but not thyroid hormone levels, demonstrated a significant increase in plasma cholesterol compared with controls. Interestingly, Tshr KO mice, with normal thyroid hormone levels after thyroid hormone supplementation, showed lower plasma cholesterol levels compared with their wild-type littermates. ATP binding cassette subfamily A member 1(ABCA1) is a member of the ABC superfamily, which induces transfer of intracellular cholesterol to extracellular apolipoprotein. TSH upregulated hepatic ABCA1 to promote the efflux of intercellular cumulative cholesterol, resulting in increased plasma cholesterol. These data might partially explain the pathogenesis of hypercholesterolemia in SCH. PMID:27179782

  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. PMID:932921

  16. 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.

  17. The complete mitochondrial genome of the Zacco platypus, Huangshan, China (Cypriniformes: Cyprinidae, subfamily Daninninae).

    PubMed

    Cheng, Shuang-Huai; Yan, Jin-Jin; Yan, Yun-Zhi; Zhang, Yi; Xia, Meng-Ning; Liu, Ying-Long; Lu, Yan-Mei

    2015-01-01

    The mitochondrial genome of Zacco platypus (Cypriniformes: Cyprinidae, subfamily Daninninae) is a circular molecule of 16,611 bp in length, containing 37 typical animal mitochondrial genes: 13 protein-coding genes (PCGs), 2 ribosomal RNAs, 22 transfer RNAs and a D-loop region. Its gene order and arrangement are identical to the common type found in most fish mitogenomes. All PCGs start with a typical ATG codon except for COI which use GTG as start codon; all PCGs terminate in the common stop codon TAA or TAG, except for the COII which use single T as stop codon. The D-loop region is 928 bp long, located between tRNAPro and tRNAPhe genes. It contains some structures of repeated motifs and microsatellite-like elements characteristic of the Cyprinidae. PMID:24409889

  18. Subfamily-Specific Fluorescent Probes for Cysteine Proteases Display Dynamic Protease Activities during Seed Germination1

    PubMed Central

    Lu, Haibin; Chandrasekar, Balakumaran; Oeljeklaus, Julian; Misas-Villamil, Johana C.; Wang, Zheming; Shindo, Takayuki; Bogyo, Matthew; Kaiser, Markus; van der Hoorn, Renier A.L.

    2015-01-01

    Cysteine proteases are an important class of enzymes implicated in both developmental and defense-related programmed cell death and other biological processes in plants. Because there are dozens of cysteine proteases that are posttranslationally regulated by processing, environmental conditions, and inhibitors, new methodologies are required to study these pivotal enzymes individually. Here, we introduce fluorescence activity-based probes that specifically target three distinct cysteine protease subfamilies: aleurain-like proteases, cathepsin B-like proteases, and vacuolar processing enzymes. We applied protease activity profiling with these new probes on Arabidopsis (Arabidopsis thaliana) protease knockout lines and agroinfiltrated leaves to identify the probe targets and on other plant species to demonstrate their broad applicability. These probes revealed that most commercially available protease inhibitors target unexpected proteases in plants. When applied on germinating seeds, these probes reveal dynamic activities of aleurain-like proteases, cathepsin B-like proteases, and vacuolar processing enzymes, coinciding with the remobilization of seed storage proteins. PMID:26048883

  19. The RhsD-E subfamily of Escherichia coli K-12.

    PubMed Central

    Sadosky, A B; Gray, J A; Hill, C W

    1991-01-01

    The Escherichia coli K-12 chromosome contains a family of five large, unlinked sequences known as the Rhs elements. They share several complex homologies, the most prominent being a 3.7 kb Rhs core. The elements are divided into two subfamilies, RhsA-B-C and RhsD-E, according to the sequence similarities of the cores. The RhsD core is 3747 bp long compared to 3714 bp for RhsA. Despite a 22% sequence divergence, the RhsD core conserves features previously noted for RhsA. Similar to RhsA, the RhsD core maintains a single ORF, the start codon coinciding with the first nucleotide of the homology. The RhsD core-ORF continues 177 codons beyond the homology, resulting in a carboxy terminal extension unrelated to that of RhsA. The RhsD core retains all 28 copies of the repeated motif GxxxRYxYDxxGRL(I/T) seen in RhsA. The other member of the RhsD-E subfamily, RhsE, has been mapped to minute 32 of the E. coli map. It appears defective in that it contains only the last 1550 bp of the 3.7 kb core. Its sequence is more closely related to that of RhsD than RhsA. In addition, RhsE and RhsB share a 1.3 kb homology, known as the H-repeat. The H-repeats from RhsE and RhsB are more closely related than their cores, showing only 1% nucleotide divergence. PMID:1766878

  20. The assassin bug subfamily Harpactorinae (Hemiptera: Reduviidae) from Vietnam: an annotated checklist of species.

    PubMed

    Lam, Truong Xuan; Cai, Wanzhi; Tomokuni, Masaaki; Ishikawa, Tadashi

    2015-01-01

    A checklist of all known Vietnamese species of the assassin bug subfamily Harpactorinae (Hemiptera: Heteroptera: Reduviidae) is presented with distributional and taxonomic notes. Sixty-five species in 35 genera of the subfamily are recognized in Vietnam. Eleven genera and 32 species are reported herein for the first time from this country. Newly recorded genera are Henricohahnia Breddin, 1900, Kalonotocoris Miller, 1941, Lingnania China, 1940, Lopodytes Stål, 1853, Macracanthopsis Reuter, 1881, Sclomina Stål, 1861, Serendiba Distant, 1906, Serendus Hsiao, 1979, Vesbius Stål, 1866, Villanovanus Distant, 1904, and Yolinus Amyot & Serville, 1843. New record species are Biasticus confusus Hsiao, 1979, B. flavinotus (Matsumura, 1913), Cosmolestes annulipes Distant, 1879, C. pulcher Hsiao, 1979, Cydnocoris fasciatus Reuter, 1881, C. gilvus (Burmeister, 1838), Endochus nigricornis Stål, 1859, Henricohahnia vittata Miller, 1954, Isyndus heros (Fabricius, 1803), I. pilosipes Reuter, 1881, Kalonotocoris curvipes Miller, 1941, Lingnania braconiformis China, 1940, Lopodytes spectabilis Miller, 1941, Macracanthopsis nodipes Reuter, 1881, Sclomina erinacea Stål, 1861, Serendiba nigrospina Hsiao, 1979, S. staliana (Horváth, 1879), Serendus geniculatus Hsiao, 1979, Sphedanolestes annulipes Distant, 1903, S. gularis Hsiao, 1979, S. impressicollis (Stål, 1861), S. pubinotus Reuter, 1881, S. trichrous Stål, 1874, S. xiongi Cai & Cai, 2004, Sycanus croceus Hsiao, 1979, Velinus annulatus Distant, 1879, V. malayus (Stål, 1863), V. rufiventris Hsiao, 1979, Vesbius purpureus (Thunberg, 1784), V. sanguinosus Stål, 1874, Villanovanus nigrorufus Hsiao, 1979, and Yolinus albopustulatus China, 1940. All the species are examined with Vietnamese materials except for Agriosphodrus dohrni (Signoret, 1862), Cydnocoris russatus Stål, 1867, and Sycanus atrocoeruleus Signoret, 1862. PMID:25781817

  1. 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.

  2. 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

  3. Membrane-integral pyrophosphatase subfamily capable of translocating both Na+ and H+.

    PubMed

    Luoto, Heidi H; Baykov, Alexander A; Lahti, Reijo; Malinen, Anssi M

    2013-01-22

    One of the strategies used by organisms to adapt to life under conditions of short energy supply is to use the by-product pyrophosphate to support cation gradients in membranes. Transport reactions are catalyzed by membrane-integral pyrophosphatases (PPases), which are classified into two homologous subfamilies: H(+)-transporting (found in prokaryotes, protists, and plants) and Na(+)-transporting (found in prokaryotes). Transport activities have been believed to require specific machinery for each ion, in accordance with the prevailing paradigm in membrane transport. However, experiments using a fluorescent pH probe and (22)Na(+) measurements in the current study revealed that five bacterial PPases expressed in Escherichia coli have the ability to simultaneously translocate H(+) and Na(+) into inverted membrane vesicles under physiological conditions. Consistent with data from phylogenetic analyses, our results support the existence of a third, dual-specificity bacterial Na(+),H(+)-PPase subfamily, which apparently evolved from Na(+)-PPases. Interestingly, genes for Na(+),H(+)-PPase have been found in the major microbes colonizing the human gastrointestinal tract. The Na(+),H(+)-PPases require Na(+) for hydrolytic and transport activities and are further activated by K(+). Based on ionophore effects, we conclude that the Na(+) and H(+) transport reactions are electrogenic and do not result from secondary antiport effects. Sequence comparisons further disclosed four Na(+),H(+)-PPase signature residues located outside the ion conductance channel identified earlier in PPases using X-ray crystallography. Our results collectively support the emerging paradigm that both Na(+) and H(+) can be transported via the same mechanism, with switching between Na(+) and H(+) specificities requiring only subtle changes in the transporter structure.

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

    PubMed

    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

  5. Identification of a novel human subfamily of mitochondrial carriers with calcium-binding domains.

    PubMed

    del Arco, Araceli; Satrústegui, Jorgina

    2004-06-01

    Aralar1 and citrin were identified as calcium binding aspartate/glutamate carriers (AGC) in mitochondria. The presence of calcium binding motifs facing the extramitochondrial space allows the regulation of the transport activity of these carriers by cytosolic calcium and provides a new mechanism to transduce calcium signals in mitochondria without the requirement of calcium entry in the organelle. We now report the complete characterization of a second subfamily of human calcium binding mitochondrial carriers named SCaMC (short calcium-binding mitochondrial carriers). We have identified three SCaMC genes in the human genome. All code for highly conserved proteins (about 70-80% identity), of about 500 amino acids with a characteristic mitochondrial carrier domain at the C terminus, and an N-terminal extension harboring four EF-hand binding motifs with high similarity to calmodulin. All SCaMC proteins were found to be located exclusively in mitochondria, and their N-terminal extensions were dispensable for the correct mitochondrial targeting of the polypeptides. SCaMC-1 is the human orthologue of the rabbit Efinal protein, which was reported to be located in peroxisomes, and SCaMC-2 is the human orthologue of the rat MCSC protein, described as up-regulated by dexamethasone in AR42J cells. One of the SCaMC genes, SCaMC-2, has four variants generated by alternative splicing, resulting in proteins with a common C terminus but with variations in their N-terminal halves, including the loss of one to three EF-hand motifs. These results make SCaMC one of most complex subfamilies of mitochondrial carriers and suggest that the large number of isoforms and splice variants may confer different calcium sensitivity to the transport activity of these carriers.

  6. 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

  7. 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...

  8. 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...

  9. The involvement of a PPR protein of the P subfamily in partial RNA editing of an Arabidopsis mitochondrial transcript.

    PubMed

    Doniwa, Yoko; Ueda, Minoru; Ueta, Masami; Wada, Akira; Kadowaki, Koh-ichi; Tsutsumi, Nobuhiro

    2010-04-01

    C-to-U RNA editing (i.e., alteration of a C in the genomic sequence to U in the transcript) has been confirmed widely in angiosperm organellar genomes. During the C-to-U RNA editing event, incomplete edited transcripts have been observed at many sites in the steady-state mRNA population (partial editing). Here, by using coexpression analysis and the surveillance of whole editing status on the mitochondrial genome, we have revealed that a pentatricopeptide repeat (PPR) protein classified into the P subfamily (PPR596) has site-specific influence on the efficiency of C-to-U RNA editing events at partial editing sites on the Arabidopsis thaliana mitochondrial genome. Previous works have revealed that PPR proteins classified into the PLS subfamily containing the E or E and DYW motif are involved in RNA editing as trans-factors; they are believed to recruit deaminase at editing sites. In contrast with the mutant analyses of PLS-subfamily PPR proteins, the editing efficiency at rps3eU1344SS was revealed to be significantly increased in ppr596 mutants. Our study implies P-subfamily PPR protein is involved in the control of the degree of partial editing.

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Positive Selection Shaped the Convergent Evolution of Independently Expanded Kallikrein Subfamilies Expressed in Mouse and Rat Saliva Proteomes

    PubMed Central

    Karn, Robert C.; Laukaitis, Christina M.

    2011-01-01

    We performed proteomics studies of salivas from the genome mouse (C57BL/6 strain) and the genome rat (BN/SsNHsd/Mcwi strain). Our goal was to identify salivary proteins with one or more of three characteristics that may indicate that they have been involved in adaptation: 1) rapid expansion of their gene families; 2) footprints of positive selection; and/or 3) sex-limited expression. The results of our proteomics studies allow direct comparison of the proteins expressed and their levels between the sexes of the two rodent species. Twelve members of the Mus musculus species-specific kallikrein subfamily Klk1b showed sex-limited expression in the mouse saliva proteomes. By contrast, we did not find any of the Rattus norvegicus species-specific kallikrein subfamily Klk1c proteins in male or female genome rat, nor transcripts in their submandibular glands. On the other hand, we detected expression of this family as transcripts in the submandibular glands of both sexes of Sprague-Dawley rats. Using the CODEML program in the PAML package, we demonstrate that the two rodent kallikrein subfamilies have apparently evolved rapidly under the influence of positive selection that continually remodeled the amino acid sites on the same face in the members of the subfamilies. Thus, although their kallikrein subfamily expansions were independent, this evolutionary pattern has occurred in parallel in the two rodent species, suggesting a form of convergent evolution at the molecular level. On the basis of this new data, we suggest that the previous speculative function of the species-specific rodent kallikreins as important solely in wound healing in males be investigated further. In addition to or instead of that function, we propose that their sex-limited expression, coupled with their rapid evolution may be clues to an as-yet-undetermined interaction between the sexes. PMID:21695125

  15. 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

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

    PubMed

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

    2007-12-01

    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.

  17. 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

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

    PubMed Central

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

    2015-01-01

    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

  19. 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.

  20. 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

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

    PubMed

    Chen, Lu; Zhao, Zhe; Li, Shuqiang

    2016-01-01

    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

  2. Moderate halophilic bacteria colonizing the phylloplane of halophytes of the subfamily Salicornioideae (Amaranthaceae).

    PubMed

    Mora-Ruiz, Merit del Rocío; Font-Verdera, Francisca; Díaz-Gil, Carlos; Urdiain, Mercedes; Rodríguez-Valdecantos, Gustavo; González, Bernardo; Orfila, Alejandro; Rosselló-Móra, Ramon

    2015-09-01

    Halophytes accumulate large amounts of salt in their tissues, and thus are susceptible to colonization by halotolerant and halophilic microorganisms that might be relevant for the growth and development of the plant. Here, the study of 814 cultured strains and 14,189 sequences obtained by 454 pyrosequencing were combined in order to evaluate the presence, abundance and diversity of halophilic, endophytic and epiphytic microorganisms in the phytosphere of leaves of members of the subfamily Salicornioideae from five locations in Spain and Chile. Cultures were screened by the tandem approach of MALDI-TOF/MS and 16S rRNA gene sequencing. In addition, differential centrifugation was used to enrich endophytes for further DNA isolation, 16S rRNA gene amplification and 454 pyrosequencing. Culturable and non-culturable data showed strong agreement with a predominance of Proteobacteria, Firmicutes and Actinobacteria. The most abundant isolates corresponded to close relatives of the species Chromohalobacter canadensis and Salinicola halophilus that comprised nearly 60% of all isolates and were present in all plants. Up to 66% of the diversity retrieved by pyrosequencing could be brought into pure cultures and the community structures were highly dependent on the compartment where the microorganisms thrived (plant surface or internal tissues). PMID:26164126

  3. 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.

  4. 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.

  5. 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

  6. 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. PMID:26516029

  7. 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.

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

    PubMed

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

    2016-01-01

    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. PMID:27395108

  9. 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

  10. Molecular phylogeny, divergence times and biogeography of spiders of the subfamily Euophryinae (Araneae: Salticidae).

    PubMed

    Zhang, Jun-Xia; Maddison, Wayne P

    2013-07-01

    We investigate phylogenetic relationships of the jumping spider subfamily Euophryinae, diverse in species and genera in both the Old World and New World. DNA sequence data of four gene regions (nuclear: 28S, Actin 5C; mitochondrial: 16S-ND1, COI) were collected from 263 jumping spider species. The molecular phylogeny obtained by Bayesian, likelihood and parsimony methods strongly supports the monophyly of a Euophryinae re-delimited to include 85 genera. Diolenius and its relatives are shown to be euophryines. Euophryines from different continental regions generally form separate clades on the phylogeny, with few cases of mixture. Known fossils of jumping spiders were used to calibrate a divergence time analysis, which suggests most divergences of euophryines were after the Eocene. Given the divergence times, several intercontinental dispersal events are required to explain the distribution of euophryines. Early transitions of continental distribution between the Old and New World may have been facilitated by the Antarctic land bridge, which euophryines may have been uniquely able to exploit because of their apparent cold tolerance. Two hot-spots of diversity of euophryines are discovered: New Guinea and the Caribbean Islands. Implications of the molecular phylogeny on the taxonomy of euophryines, and on the evolution of unusual genitalic forms and myrmecophagy, are also briefly discussed. PMID:23542001

  11. Modulation of the Rat Hepatic Cytochrome P4501A Subfamily Using Biotin Supplementation

    PubMed Central

    Ronquillo-Sánchez, M. D.; Camacho-Carranza, R.; Fernandez-Mejia, C.; Hernández-Ojeda, S.; Elinos-Baez, M.; Espinosa-Aguirre, J. J.

    2013-01-01

    Studies have found that biotin favors glucose and lipid metabolism, and medications containing biotin have been developed. Despite the use of biotin as a pharmacological agent, few studies have addressed toxicity aspects including the possible interaction with cytochrome P450 enzyme family. This study analyzed the effects of pharmacological doses of biotin on the expression and activity of the cytochrome P4501A subfamily involved in the metabolism of xenobiotics. Wistar rats were treated daily with biotin (2 mg/kg, i.p.), while the control groups were treated with saline. All of the rats were sacrificed by cervical dislocation after 1, 3, 5, or 7 days of treatment. CYP1A1 and CYP1A2 mRNAs were modified by biotin while enzyme activity and protein concentration were not affected. The lack of an effect of biotin on CYP1A activity was confirmed using other experimental strategies, including (i) cotreatment of the animals with biotin and a known CYP1A inducer; (ii) the addition of biotin to the reaction mixtures for the measurement of CYP1A1 and CYP1A2 activities; and (iii) the use of an S9 mixture that was prepared from control and biotin-treated rats to analyze the activation of benzo[a]pyrene (BaP) into mutagenic metabolites using the Ames test. The results suggest that biotin does not influence the CYP1A-mediated metabolism of xenobiotics. PMID:23984390

  12. 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. PMID:26190520

  13. 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)

  14. A cladistic analysis and classification of the subfamily Bembicinae (Hymenoptera: Crabronidae), with a key to the genera.

    PubMed

    Nemkov, Pavel G; Lelej, Arkady S

    2013-01-01

    A cladistic analysis of the digger wasp subfamily Bembicinae based on morphological characters is presented. The underlying data matrix comprises 83 terminal taxa (coded on genus-level) and 64 morphological characters. The resulting strict consensus tree was used as the basis for a revised tribal and subtribal classification of the Bembicinae. Based on a previously published classification, we herewith propose a change: the tribe Heliocausini Handlirsch 1925, stat. resurr. (composed of Acanthocausus Fritz & Toro 1977, Heliocausus Kohl 1892, and Tiguipa Fritz & Toro 1976) is separated from Bembicini Latreille 1802. Four tribes are recognized within the subfamily Bembicinae and seven subtribes within the tribe Gorytini and two subtribes in the tribe Nyssonini, based on the present cladistic analysis.The subtribe Nurseina Nemkov & Lelej, subtrib. nov. (comprising of Nippononysson Yasumatsu & Maidl 1936 and Nursea Cameron 1902) is separated from other genera in the tribe Nyssonini Latreille 1804. An new identification key to the genera of the Bembicinae is provided.

  15. 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

  16. 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

  17. On the phylogeny of Mustelidae subfamilies: analysis of seventeen nuclear non-coding loci and mitochondrial complete genomes

    PubMed Central

    2011-01-01

    Background Mustelidae, as the largest and most-diverse family of order Carnivora, comprises eight subfamilies. Phylogenetic relationships among these Mustelidae subfamilies remain argumentative subjects in recent years. One of the main reasons is that the mustelids represent a typical example of rapid evolutionary radiation and recent speciation event. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence and nuclear protein-coding data, herein we employ 17 nuclear non-coding loci (>15 kb), in conjunction with mt complete genome data (>16 kb), to clarify these enigmatic problems. Results The combined nuclear intron and mt genome analyses both robustly support that Taxidiinae diverged first, followed by Melinae. Lutrinae and Mustelinae are grouped together in all analyses with strong supports. The position of Helictidinae, however, is enigmatic because the mt genome analysis places it to the clade uniting Lutrinae and Mustelinae, whereas the nuclear intron analysis favores a novel view supporting a closer relationship of Helictidinae to Martinae. This finding emphasizes a need to add more data and include more taxa to resolve this problem. In addition, the molecular dating provides insights into the time scale of the origin and diversification of the Mustelidae subfamilies. Finally, the phylogenetic performances and limits of nuclear introns and mt genes are discussed in the context of Mustelidae phylogeny. Conclusion Our study not only brings new perspectives on the previously obscured phylogenetic relationships among Mustelidae subfamilies, but also provides another example demonstrating the effectiveness of nuclear non-coding loci for reconstructing evolutionary histories in a group that has undergone rapid bursts of speciation. PMID:21477367

  18. 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.

  19. Systematics of Australian Thrasorinae (Hymenoptera, Cynipoidea, Figitidae) with descriptions of Mikeiinae, new subfamily, two new genera, and three new species

    PubMed Central

    Paretas-Martínez, J.; Restrepo-Ortiz, C.; Buffington, M.; Pujade-Villar, J.

    2011-01-01

    Abstract The Australian Thrasorinae are revised and Mikeius is transferred to Mikeiinae Paretas-Martínez & Pujade-Villar, subfam. n., and Mikeius clavatus Pujade-Villar & Restrepo-Ortiz, sp. n., is described. Two new genera of Thrasorinae are erected: Cicatrix Paretas-Martínez, gen. n., including Cicatrix pilosiscutum(Girault), comb. n. from Amblynotus, Cicatrix schauffi (Buffington), comb. n. from Mikeius, and Cicatrix neumannoides Paretas-Martínez & Restrepo-Ortiz, sp. n.; and Palmiriella Pujade-Villar & Paretas-Martínez, gen. n., including Palmiriella neumanni (Buffington), comb. n. from Mikeius, Thrasorus rieki Paretas-Martínez & Pujade-Villar, sp. n., is also described. A phylogenetic analysis of 176 morphological and biological characters, including all these new taxa and all genera previously included in Thrasorinae, was conducted. All subfamilies were recovered as monophyletic, with the following relationships: Parnipinae (Euceroptrinae (Mikeiinae (Plectocynipinae (Thrasorinae)))). A worldwide key to the subfamilies of Figitidae is provided that includes the new subfamily, as well as a key to genera Thrasorinae. PMID:21852926

  20. Sphingomonas paucimobilis beta-glucosidase Bgl1: a member of a new bacterial subfamily in glycoside hydrolase family 1.

    PubMed

    Marques, Ana Rita; Coutinho, Pedro M; Videira, Paula; Fialho, Arsénio M; Sá-Correia, Isabel

    2003-03-15

    The Sphingomonas paucimobilis beta-glucosidase Bgl1 is encoded by the bgl1 gene, associated with an 1308 bp open reading frame. The deduced protein has a potential signal peptide of 24 amino acids in the N-terminal region, and experimental evidence is consistent with the processing and export of the Bgl1 protein through the inner membrane to the periplasmic space. A His(6)-tagged 44.3 kDa protein was over-produced in the cytosol of Escherichia coli from a recombinant plasmid, which contained the S. paucimobilis bgl1 gene lacking the region encoding the putative signal peptide. Mature beta-glucosidase Bgl1 is specific for aryl-beta-glucosides and has no apparent activity with oligosaccharides derived from cellulose hydrolysis and other saccharides. A structure-based alignment established structural relations between S. paucimobilis Bgl1 and other members of the glycoside hydrolase (GH) family 1 enzymes. At subsite -1, the conserved residues required for catalysis by GH1 enzymes are present in Bgl1 with only minor differences. Major differences are found at subsite +1, the aglycone binding site. This alignment seeded a sequence-based phylogenetic analysis of GH1 enzymes, revealing an absence of horizontal transfer between phyla. Bootstrap analysis supported the definition of subfamilies and revealed that Bgl1, the first characterized beta-glucosidase from the genus Sphingomonas, represents a very divergent bacterial subfamily, closer to archaeal subfamilies than to others of bacterial origin.

  1. 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.

  2. 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.

  3. 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

  4. Uclacyanins, stellacyanins, and plantacyanins are distinct subfamilies of phytocyanins: plant-specific mononuclear blue copper proteins.

    PubMed Central

    Nersissian, A. M.; Immoos, C.; Hill, M. G.; Hart, P. J.; Williams, G.; Herrmann, R. G.; Valentine, J. S.

    1998-01-01

    The cDNAs encoding plantacyanin from spinach were isolated and characterized. In addition, four new cDNA sequences from Arabidopsis ESTs were identified that encode polypeptides resembling phytocyanins, plant-specific proteins constituting a distinct family of mononuclear blue copper proteins. One of them encodes plantacyanin from Arabidopsis, while three others, designated as uclacyanin 1, 2, and 3, encode protein precursors that are closely related to precursors of stellacyanins and a blue copper protein from pea pods. Comparative analyses with known phytocyanins allow further classification of these proteins into three distinct subfamilies designated as uclacyanins, stellacyanins, and plantacyanins. This specification is based on (1) their spectroscopic properties, (2) their glycosylation state, (3) the domain organization of their precursors, and (4) their copper-binding amino acids. The recombinant copper binding domain of Arabidopsis uclacyanin 1 was expressed, purified, and shown to bind a copper atom in a fashion known as "blue" or type 1. The mutant of cucumber stellacyanin in which the glutamine axial ligand was substituted by a methionine (Q99M) was purified and shown to possess spectroscopic properties similar to uclacyanin 1 rather than to plantacyanins. Its redox potential was determined by cyclic voltammetry to be +420 mV, a value that is significantly higher than that determined for the wild-type protein (+260 mV). The available structural data suggest that stellacyanins (and possibly other phytocyanins) might not be diffusible electron-transfer proteins participating in long-range electron-transfer processes. Conceivably, they are involved in redox reactions occurring during primary defense responses in plants and/or in lignin formation. PMID:9761472

  5. Identification and structure-function analysis of subfamily selective G protein-coupled receptor kinase inhibitors.

    PubMed

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

    2015-01-16

    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. Multilocus molecular phylogeny of the suckermouth armored catfishes (Siluriformes: Loricariidae) with a focus on subfamily Hypostominae.

    PubMed

    Lujan, Nathan K; Armbruster, Jonathan W; Lovejoy, Nathan R; López-Fernández, Hernán

    2015-01-01

    The Neotropical catfish family Loricariidae is the fifth most species-rich vertebrate family on Earth, with over 800 valid species. The Hypostominae is its most species-rich, geographically widespread, and ecomorphologically diverse subfamily. Here, we provide a comprehensive molecular phylogenetic reappraisal of genus-level relationships in the Hypostominae based on our sequencing and analysis of two mitochondrial and three nuclear loci (4293bp total). Our most striking large-scale systematic discovery was that the tribe Hypostomini, which has traditionally been recognized as sister to tribe Ancistrini based on morphological data, was nested within Ancistrini. This required recognition of seven additional tribe-level clades: the Chaetostoma Clade, the Pseudancistrus Clade, the Lithoxus Clade, the 'Pseudancistrus' Clade, the Acanthicus Clade, the Hemiancistrus Clade, and the Peckoltia Clade. Results of our analysis, which included type- and non-type species for every valid genus in Hypostominae, support the reevaluation and restriction of several historically problematic genera, including Baryancistrus, Cordylancistrus, Hemiancistrus, and Peckoltia. Much of the deep lineage diversity in Hypostominae is restricted to Guiana Shield and northern Andean drainages, with three tribe-level clades still largely restricted to the Guiana Shield. Of the six geographically widespread clades, a paraphyletic assemblage of three contain lineages restricted to drainages west of the Andes Mountains, suggesting that early diversification of the Hypostominae predated the late Miocene surge in Andean uplift. Our results also highlight examples of trophic ecological diversification and convergence in the Loricariidae, including support for three independent origins of highly similar and globally unique morphological specializations for eating wood.

  7. 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. PMID

  8. 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. PMID:16381601

  9. Dynamic Distribution and Interaction of the Arabidopsis SRSF1 Subfamily Splicing Factors.

    PubMed

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

    2016-02-01

    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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

    2016-01-01

    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. PMID:27395887

  15. Structural Basis for Dimerization and Catalysis of a Novel Esterase from the GTSAG Motif Subfamily of the Bacterial Hormone-sensitive Lipase Family*

    PubMed Central

    Li, Ping-Yi; Ji, Peng; Li, Chun-Yang; Zhang, Yi; Wang, Guang-Long; Zhang, Xi-Ying; Xie, Bin-Bin; Qin, Qi-Long; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhang, Yu-Zhong

    2014-01-01

    Hormone-sensitive lipases (HSLs) are widely distributed in microorganisms, plants, and animals. Microbial HSLs are classified into two subfamilies, an unnamed new subfamily and the GDSAG motif subfamily. Due to the lack of structural information, the detailed catalytic mechanism of the new subfamily is not yet clarified. Based on sequence analysis, we propose to name the new subfamily as the GTSAG motif subfamily. We identified a novel HSL esterase E25, a member of the GTSAG motif subfamily, by functional metagenomic screening, and resolved its structure at 2.05 Å. E25 is mesophilic (optimum temperature at 50 °C), salt-tolerant, slightly alkaline (optimum pH at 8.5) for its activity, and capable of hydrolyzing short chain monoesters (C2–C10). E25 tends to form dimers both in the crystal and in solution. An E25 monomer contains an N-terminal CAP domain, and a classical α/β hydrolase-fold domain. Residues Ser186, Asp282, and His312 comprise the catalytic triad. Structural and mutational analyses indicated that E25 adopts a dimerization pattern distinct from other HSLs. E25 dimer is mainly stabilized by an N-terminal loop intersection from the CAP domains and hydrogen bonds and salt bridges involving seven highly conserved hydrophilic residues from the catalytic domains. Further analysis indicated that E25 also has some catalytic profiles different from other HSLs. Dimerization is essential for E25 to exert its catalytic activity by keeping the accurate orientation of the catalytic Asp282 within the catalytic triad. Our results reveal the structural basis for dimerization and catalysis of an esterase from the GTSAG motif subfamily of the HSL family. PMID:24867954

  16. Freyinae, a major new subfamily of Neotropical jumping spiders (Araneae: Salticidae).

    PubMed

    Edwards, G B

    2015-01-01

    Freyinae, new subfamily, is described for a group of genera of Neotropical jumping spiders that can be distinguished from other non-ant mimic salticoid Neotropical salticids by having the following three morphological features: a slightly more elongate carapace, a distinctive prolateral tibial macrosetae arrangement (medially placed subdistal and subproximal macrosetae, with a subdorsal medial macroseta in some males), and an unusual dorsoventrally thick tegulum basal division (although one or two of these features are sometimes lost). It includes 20 genera previously considered valid, of which 19 are retained: Akela Peckham & Peckham, 1896, Aphirape C.L. Koch, 1850, Asaracus C.L. Koch, 1846, Capidava Simon, 1902, Chira Peckham & Peckham, 1896, Edilemma Ruiz & Brescovit, 2006, Eustiromastix Simon, 1902, Freya C.L. Koch, 1850, Frigga C.L. Koch, 1850, Kalcerrytus Galiano, 2000, Nycerella Galiano, 1982, Onofre Ruiz & Brescovit, 2007, Pachomius Peckham & Peckham, 1896, Phiale C.L. Koch, 1846, Rishaschia Makhan, 2006, Sumampattus Galiano, 1983, Trydarssus Galiano, 1995, Tullgrenella Mello‑Leitão, 1941, and Wedoquella Galiano, 1984. Romitia Caporiacco, 1947 (and its synonym Uspachus Galiano, 1995) is synonymized with Pachomius, new synonymy. New genera described in the subfamily are: Drizztius, Leptofreya, Megafreya, Philira, Tarkas, Triggella, and Xanthofreya. The following nomenclatorial changes are made: New synonyms: Freya demarcata Chamberlin & Ivie, 1936 = Freya (sub Cyrene) albosignata (F.O.P.-Cambridge, 1901); Freya (sub Cyrene) grisea (F.O.P.-Cambridge, 1901) = Freya (sub Cyrene) infuscata (F.O.P.-Cambridge, 1901); Freya (sub Cyrene) emarginata (F.O.P.-Cambridge, 1901) and Nycerella (sub Heraclea) sanguinea paradoxa (Peckham & Peckham, 1896) = Nycerella (sub Heraclea) sanguinea (Peckham & Peckham, 1896); Pachomius (sub Phiale) maculosus (Chickering, 1946) = Phiale (sub Cyrene) bilobata (F.O.P.-Cambridge, 1901); Phiale (sub Cyrene) mediocava (F

  17. 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.

  18. Members of rice plasma membrane intrinsic proteins subfamily are involved in arsenite permeability and tolerance in plants.

    PubMed

    Mosa, Kareem A; Kumar, Kundan; Chhikara, Sudesh; Mcdermott, Joseph; Liu, Zijuan; Musante, Craig; White, Jason C; Dhankher, Om Parkash

    2012-12-01

    Rice accumulates high level of arsenic (As) in its edible parts and thus plays an important role in the transfer of As into the food chain. However, the mechanisms of As uptake and its detoxification in rice are not well understood. Recently, members of the Nodulin 26-like intrinsic protein (NIP) subfamily of plant aquaporins were shown to transport arsenite in rice and Arabidopsis. Here we report that members of the rice plasma membrane intrinsic protein (PIP) subfamily are also involved in As tolerance and transport. Based on the homology search with the mammalian AQP9 and yeast Fps1 arsenite transporters, we identified and cloned five rice PIP gene subfamily members. qRT-PCR analysis of PIPs in rice root and shoot tissues revealed a significant down regulation of transcripts encoding OsPIP1;2, OsPIP1;3, OsPIP2;4, OsPIP2;6, and OsPIP2;7 in response to arsenite treatment. Heterologous expression of OsPIP2;4, OsPIP2;6, and OsPIP2;7 in Xenopus laevis oocytes significantly increased the uptake of arsenite. Overexpression of OsPIP2;4, OsPIP2;6, and OsPIP2;7 in Arabidopsis yielded enhanced arsenite tolerance and higher biomass accumulation. Further, these transgenic plants showed no significant accumulation of As in shoot and root tissues in long term uptake assays. Whereas, short duration exposure to arsenite caused both active influx and efflux of As in the roots. The data suggests a bidirectional arsenite permeability of rice PIPs in plants. These rice PIPs genes will be highly useful for engineering important food and biofuel crops for enhanced crop productivity on contaminated soils without increasing the accumulation of toxic As in the biomass or edible tissues. PMID:22350764

  19. Members of rice plasma membrane intrinsic proteins subfamily are involved in arsenite permeability and tolerance in plants.

    PubMed

    Mosa, Kareem A; Kumar, Kundan; Chhikara, Sudesh; Mcdermott, Joseph; Liu, Zijuan; Musante, Craig; White, Jason C; Dhankher, Om Parkash

    2012-12-01

    Rice accumulates high level of arsenic (As) in its edible parts and thus plays an important role in the transfer of As into the food chain. However, the mechanisms of As uptake and its detoxification in rice are not well understood. Recently, members of the Nodulin 26-like intrinsic protein (NIP) subfamily of plant aquaporins were shown to transport arsenite in rice and Arabidopsis. Here we report that members of the rice plasma membrane intrinsic protein (PIP) subfamily are also involved in As tolerance and transport. Based on the homology search with the mammalian AQP9 and yeast Fps1 arsenite transporters, we identified and cloned five rice PIP gene subfamily members. qRT-PCR analysis of PIPs in rice root and shoot tissues revealed a significant down regulation of transcripts encoding OsPIP1;2, OsPIP1;3, OsPIP2;4, OsPIP2;6, and OsPIP2;7 in response to arsenite treatment. Heterologous expression of OsPIP2;4, OsPIP2;6, and OsPIP2;7 in Xenopus laevis oocytes significantly increased the uptake of arsenite. Overexpression of OsPIP2;4, OsPIP2;6, and OsPIP2;7 in Arabidopsis yielded enhanced arsenite tolerance and higher biomass accumulation. Further, these transgenic plants showed no significant accumulation of As in shoot and root tissues in long term uptake assays. Whereas, short duration exposure to arsenite caused both active influx and efflux of As in the roots. The data suggests a bidirectional arsenite permeability of rice PIPs in plants. These rice PIPs genes will be highly useful for engineering important food and biofuel crops for enhanced crop productivity on contaminated soils without increasing the accumulation of toxic As in the biomass or edible tissues.

  20. 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. 

  1. 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.

  2. 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

  3. Length of guanosine homopolymeric repeats modulates promoter activity of subfamily II tpr genes of Treponema pallidum ssp. pallidum.

    PubMed

    Giacani, Lorenzo; Lukehart, Sheila; Centurion-Lara, Arturo

    2007-11-01

    In Treponema pallidum, homopolymeric guanosine repeats of varying length are present upstream of both Subfamily I (tprC, D, F and I) and II (tprE, G and J) tpr genes, a group of potential virulence factors, immediately upstream of the +1 nucleotide. To investigate the influence of these poly-G sequences on promoter activity, tprE, G, J, F and I promoter regions containing homopolymeric tracts with different numbers of Gs, the ribosomal binding site and start codon were cloned in frame with the green fluorescent protein reporter gene (GFP), and promoter activity was measured both as fluorescence emission from Escherichia coli cultures transformed with the different plasmid constructs and using quantitative RT-PCR. For tprJ, G and E-derived clones, fluorescence was significantly higher with constructs containing eight Gs or fewer, while plasmids containing the same promoters with none or more Gs gave modest or no signal above the background. In contrast, tprF/I-derived clones induced similar levels of fluorescence regardless of the number of Gs within the promoter. GFP mRNA quantification showed that all of the promoters induced measurable transcription of the GFP gene; however, only for Subfamily II promoters was message synthesis inversely correlated to the number of Gs in the construct.

  4. Molecular tests of phylogenetic taxonomies: a general procedure and example using four subfamilies of the lizard family Iguanidae.

    PubMed

    Schulte, J A; Macey, J R; Larson, A; Papenfuss, T J

    1998-12-01

    A general procedure is described for examining when results of molecular phylogenetic analyses warrant formal revision of taxonomies constructed using morphological characters. We illustrate this procedure with tests of monophyly for four subfamilies in the lizard family Iguanidae using 1561 aligned base positions (838 phylogenetically informative) of mitochondrial DNA sequences, representing coding regions for eight tRNAs, ND2, and portions of ND1 and COI. Ten new sequences ranging in length from 1732 to 1751 bases are compared with 12 previously reported sequences and 67 morphological characters (54 phylogenetically informative) from the literature. New morphological character states are provided for Sator. Phylogenies derived from the molecular and combined data are in agreement but both conflict with phylogenetic inferences from the morphological data alone. Strong support is found for the monophyly of the subfamilies Crotaphytinae and Phrynosomatinae. Monophyly of the Iguaninae is weakly supported in each analysis. All analyses suggest that the Tropidurinae is not monophyletic but the hypothesis of monophyly cannot be rejected. A phylogenetic taxonomy is proposed in which the Tropidurinae* is maintained as a metataxon (denoted with an asterisk), for which monophyly has not been demonstrated. Within the Phrynosomatinae, the close relationship of Sator and Sceloporus is questioned and an alternative hypothesis in which Sator is the sister taxon to a clade comprising Petrosaurus, Sceloporus, and Urosaurus is presented. Statistical tests of monophyly provide a powerful way to evaluate support for taxonomic groupings. Use of the metataxon prevents premature taxonomic rearrangements where support is lacking.

  5. Length of guanosine homopolymeric repeats modulates promoter activity of subfamily II tpr genes of Treponema pallidum ssp. pallidum

    PubMed Central

    Giacani, Lorenzo; Lukehart, Sheila; Centurion-Lara, Arturo

    2010-01-01

    In Treponema pallidum, homopolymeric guanosine repeats of varying length are present upstream of both Subfamily I (tprC, D, F and I) and II (tprE, G and J) tpr genes, a group of potential virulence factors, immediately upstream of the +1 nucleotide. To investigate the influence of these poly-G sequences on promoter activity, tprE, G, J, F and I promoter regions containing homopolymeric tracts with different numbers of Gs, the ribosomal binding site and start codon were cloned in frame with the green fluorescent protein reporter gene (GFP), and promoter activity was measured both as fluorescence emission from Escherichia coli cultures transformed with the different plasmid constructs and using quantitative RT-PCR. For tprJ, G and E-derived clones, fluorescence was significantly higher with constructs containing eight Gs or fewer, while plasmids containing the same promoters with none or more Gs gave modest or no signal above the background. In contrast, tprF/I-derived clones induced similar levels of fluorescence regardless of the number of Gs within the promoter. GFP mRNA quantification showed that all of the promoters induced measurable transcription of the GFP gene; however, only for Subfamily II promoters was message synthesis inversely correlated to the number of Gs in the construct. PMID:17683506

  6. 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

  7. Members of the Francisella tularensis Phagosomal Transporter Subfamily of Major Facilitator Superfamily Transporters Are Critical for Pathogenesis

    PubMed Central

    Marohn, Mark E.; Santiago, Araceli E.; Shirey, Kari Ann; Lipsky, Michael; Vogel, Stefanie N.

    2012-01-01

    Francisella tularensis is the causative agent of tularemia. Due to its aerosolizable nature and low infectious dose, F. tularensis is classified as a category A select agent and, therefore, is a priority for vaccine development. Survival and replication in macrophages and other cell types are critical to F. tularensis pathogenesis, and impaired intracellular survival has been linked to a reduction in virulence. The F. tularensis genome is predicted to encode 31 major facilitator superfamily (MFS) transporters, and the nine-member Francisella phagosomal transporter (Fpt) subfamily possesses homology with virulence factors in other intracellular pathogens. We hypothesized that these MFS transporters may play an important role in F. tularensis pathogenesis and serve as good targets for attenuation and vaccine development. Here we show altered intracellular replication kinetics and attenuation of virulence in mice infected with three of the nine Fpt mutant strains compared with wild-type (WT) F. tularensis LVS. The vaccination of mice with these mutant strains was protective against a lethal intraperitoneal challenge. Additionally, we observed pronounced differences in cytokine profiles in the livers of mutant-infected mice, suggesting that alterations in in vivo cytokine responses are a major contributor to the attenuation observed for these mutant strains. These results confirm that this subset of MFS transporters plays an important role in the pathogenesis of F. tularensis and suggest that a focus on the development of attenuated Fpt subfamily MFS transporter mutants is a viable strategy toward the development of an efficacious vaccine. PMID:22508856

  8. PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification.

    PubMed

    Thomas, Paul D; Kejariwal, Anish; Campbell, Michael J; Mi, Huaiyu; Diemer, Karen; Guo, Nan; Ladunga, Istvan; Ulitsky-Lazareva, Betty; Muruganujan, Anushya; Rabkin, Steven; Vandergriff, Jody A; Doremieux, Olivier

    2003-01-01

    The PANTHER database was designed for high-throughput analysis of protein sequences. One of the key features is a simplified ontology of protein function, which allows browsing of the database by biological functions. Biologist curators have associated the ontology terms with groups of protein sequences rather than individual sequences. Statistical models (Hidden Markov Models, or HMMs) are built from each of these groups. The advantage of this approach is that new sequences can be automatically classified as they become available. To ensure accurate functional classification, HMMs are constructed not only for families, but also for functionally distinct subfamilies. Multiple sequence alignments and phylogenetic trees, including curator-assigned information, are available for each family. The current version of the PANTHER database includes training sequences from all organisms in the GenBank non-redundant protein database, and the HMMs have been used to classify gene products across the entire genomes of human, and Drosophila melanogaster. The ontology terms and protein families and subfamilies, as well as Drosophila gene c;assifications, can be browsed and searched for free. Due to outstanding contractual obligations, access to human gene classifications and to protein family trees and multiple sequence alignments will temporarily require a nominal registration fee. PANTHER is publicly available on the web at http://panther.celera.com.

  9. New subfamilies of major intrinsic proteins in fungi suggest novel transport properties in fungal channels: implications for the host-fungal interactions

    PubMed Central

    2014-01-01

    Background Aquaporins (AQPs) and aquaglyceroporins (AQGPs) belong to the superfamily of Major Intrinsic Proteins (MIPs) and are involved in the transport of water and neutral solutes across the membranes. MIP channels play significant role in plant-fungi symbiotic relationship and are believed to be important in host-pathogen interactions in human fungal diseases. In plants, at least five major MIP subfamilies have been identified. Fungal MIP subfamilies include orthodox aquaporins and five subgroups within aquaglyceroporins. XIP subfamily is common to both plants and fungi. In this study, we have investigated the extent of diversity in fungal MIPs and explored further evolutionary relationships with the plant MIP counterparts. Results We have extensively analyzed the available fungal genomes and examined nearly 400 fungal MIPs. Phylogenetic analysis and homology modeling exhibit the existence of a new MIP cluster distinct from any of the known fungal MIP subfamilies. All members of this cluster are found in microsporidia which are unicellular fungal parasites. Members of this family are small in size, charged and have hydrophobic residues in the aromatic/arginine selectivity filter and these features are shared by small and basic intrinsic proteins (SIPs), one of the plant MIP subfamilies. We have also found two new subfamilies (δ and γ2) within the AQGP group. Fungal AQGPs are the most diverse and possess the largest number of subgroups. We have also identified distinguishing features in loops E and D in the newly identified subfamilies indicating their possible role in channel transport and gating. Conclusions Fungal SIP-like MIP family is distinct from any of the known fungal MIP families including orthodox aquaporins and aquaglyceroporins. After XIPs, this is the second MIP subfamily from fungi that may have possible evolutionary link with a plant MIP subfamily. AQGPs in fungi are more diverse and possess the largest number of subgroups. The aromatic

  10. 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

  11. VP22 core domain from Herpes simplex virus 1 reveals a surprising structural conservation in both the Alpha- and Gammaherpesvirinae subfamilies

    PubMed Central

    Hew, Kelly; Pan, Lucy Xin; Cornvik, Tobias; Nordlund, Pär

    2015-01-01

    The viral tegument is a layer of proteins between the herpesvirus capsid and its outer envelope. According to phylogenetic studies, only a third of these proteins are conserved amongst the three subfamilies (Alpha-, Beta- and Gammaherpesvirinae) of the family Herpesviridae. Although some of these tegument proteins have been studied in more detail, the structure and function of the majority of them are still poorly characterized. VP22 from Herpes simplex virus 1 (subfamily Alphaherpesvirinae) is a highly interacting tegument protein that has been associated with tegument assembly. We have determined the crystal structure of the conserved core domain of VP22, which reveals an elongated dimer with several potential protein–protein interaction regions and a peptide-binding site. The structure provides us with the structural basics to understand the numerous functional mutagenesis studies of VP22 found in the literature. It also establishes an unexpected structural homology to the tegument protein ORF52 from Murid herpesvirus 68 (subfamily Gammaherpesvirinae). Homologues for both VP22 and ORF52 have been identified in their respective subfamilies. Although there is no obvious sequence overlap in the two subfamilies, this structural conservation provides compelling structural evidence for shared ancestry and functional conservation. PMID:26068188

  12. Human and rodent aldo-keto reductases from the AKR1B subfamily and their specificity with retinaldehyde

    PubMed Central

    Ruiz, F. Xavier; Moro, Armando; Gallego, Oriol; Ardèvol, Albert; Rovira, Carme; Petrash, J. Mark; Parés, Xavier; Farrés, Jaume

    2011-01-01

    NADP(H)-dependent cytosolic aldo-keto reductases (AKR) are mostly monomeric enzymes which fold into a typical (α/β)8-barrel structure. Substrate specificity and inhibitor selectivity are determined by interaction with residues located in three highly variable loops (A, B, and C). Based on sequence identity, AKR have been grouped into families, namely AKR1–AKR15, containing multiple subfamilies. Two human enzymes from the AKR1B subfamily (AKR1B1 and AKR1B10) are of special interest. AKR1B1 (aldose reductase) is related to secondary diabetic complications, while AKR1B10 is induced in cancer cells and is highly active with all-trans-retinaldehyde. Residues interacting with all-trans-retinaldehyde and differing between AKR1B1 and AKR1B10 are Leu125Lys and Val131Ala (loop A), Leu301Val, Ser303Gln, and Cys304Ser (loop C). Recently, we demonstrated the importance of Lys125 as a determinant of AKR1B10 specificity for retinoids. Residues 301 and 304 are also involved in interactions with substrates or inhibitors, and thus we checked their contribution to retinoid specificity. We also extended our study with retinoids to rodent members of the AKR1B subfamily: AKR1B3 (aldose reductase), AKR1B7 (mouse vas deferens protein), AKR1B8 (fibroblast-growth factor 1-regulated protein), and AKR1B9 (Chinese hamster ovary reductase), which were tested against all-trans isomers of retinaldehyde and retinol. All enzymes were active with retinaldehyde, but with kcat values (0.02–0.52 min−1) much lower than that of AKR1B10 (27 min−1). None of the enzymes showed oxidizing activity with retinol. Since these enzymes (except AKR1B3) have Lys125, other residues should account for retinaldehyde specificity. Here, by using site-directed mutagenesis and molecular modeling, we further delineate the contribution of residues 301 and 304. We demonstrate that besides Lys125, Ser304 is a major structural determinant for all-trans-retinaldehyde specificity of AKR1B10. PMID:21329680

  13. NR-2L: a two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features.

    PubMed

    Wang, Pu; Xiao, Xuan; Chou, Kuo-Chen

    2011-01-01

    Nuclear receptors (NRs) are one of the most abundant classes of transcriptional regulators in animals. They regulate diverse functions, such as homeostasis, reproduction, development and metabolism. Therefore, NRs are a very important target for drug development. Nuclear receptors form a superfamily of phylogenetically related proteins and have been subdivided into different subfamilies due to their domain diversity. In this study, a two-level predictor, called NR-2L, was developed that can be used to identify a query protein as a nuclear receptor or not based on its sequence information alone; if it is, the prediction will be automatically continued to further identify it among the following seven subfamilies: (1) thyroid hormone like (NR1), (2) HNF4-like (NR2), (3) estrogen like, (4) nerve growth factor IB-like (NR4), (5) fushi tarazu-F1 like (NR5), (6) germ cell nuclear factor like (NR6), and (7) knirps like (NR0). The identification was made by the Fuzzy K nearest neighbor (FK-NN) classifier based on the pseudo amino acid composition formed by incorporating various physicochemical and statistical features derived from the protein sequences, such as amino acid composition, dipeptide composition, complexity factor, and low-frequency Fourier spectrum components. As a demonstration, it was shown through some benchmark datasets derived from the NucleaRDB and UniProt with low redundancy that the overall success rates achieved by the jackknife test were about 93% and 89% in the first and second level, respectively. The high success rates indicate that the novel two-level predictor can be a useful vehicle for identifying NRs and their subfamilies. As a user-friendly web server, NR-2L is freely accessible at either http://icpr.jci.edu.cn/bioinfo/NR2L or http://www.jci-bioinfo.cn/NR2L. Each job submitted to NR-2L can contain up to 500 query protein sequences and be finished in less than 2 minutes. The less the number of query proteins is, the shorter the time will

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

    PubMed Central

    Lackner, Tomáš; Gomy, Yves

    2014-01-01

    Abstract 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. PMID:25147466

  15. Cyclophilins of a novel subfamily interact with SNW/SKIP coregulator in Dictyostelium discoideum and Schizosaccharomyces pombe.

    PubMed

    Skruzný, M; Ambrozková, M; Fuková, I; Martínková, K; Blahůsková, A; Hamplová, L; Půta, F; Folk, P

    2001-10-31

    We screened the Dictyostelium discoideum two-hybrid cDNA library with the SNW/SKIP transcription coregulator SnwA and identified a novel cyclophilin CypE. Independently, the Schizosaccharomyces pombe cDNA library was screened with the SnwA ortholog Snw1 and the ortholog of CypE (named Cyp2) was found. Both cyclophilins bind the respective SNW protein in their autologous systems. The interaction was localized to the N-terminal part of SnwA as well as of Snw1. CypE was confirmed in vitro to be a cyclosporin A-sensitive peptidyl-prolyl cis-trans isomerase. Remarkably, both SNW proteins bind the cyclophilins in a cyclosporin A independent manner, possibly serving as adaptors for these novel isomerases. These results are the first characterization of the members of a novel cyclophilin subfamily, which includes the human CGI-124/PPIL1 protein. PMID:11690648

  16. Recent advances regarding the role of ABC subfamily C member 10 (ABCC10) in the efflux of antitumor drugs

    PubMed Central

    Kathawala, Rishil J.; Wang, Yi-Jun; Ashby, Charles R.; Chen, Zhe-Sheng

    2014-01-01

    ABCC10, also known as multidrug-resistant protein 7 (MRP7), is the tenth member of the C subfamily of the ATP-binding cassette (ABC) superfamily. ABCC10 mediates multidrug resistance (MDR) in cancer cells by preventing the intracellular accumulation of certain antitumor drugs. The ABCC10 transporter is a 171-kDa protein that is localized on the basolateral cell membrane. ABCC10 is a broad-specificity transporter of xenobiotics, including antitumor drugs, such as taxanes, epothilone B, vinca alkaloids, and cytarabine, as well as modulators of the estrogen pathway, such as tamoxifen. In recent years, ABCC10 inhibitors, including cepharanthine, lapatinib, erlotinib, nilotinib, imatinib, sildenafil, and vardenafil, have been reported to overcome ABCC10-mediated MDR. This review discusses some recent and clinically relevant aspects of the ABCC10 drug efflux transporter from the perspective of current chemotherapy, particularly its inhibition by tyrosine kinase inhibitors and phosphodiesterase type 5 inhibitors. PMID:24103790

  17. Recent advances regarding the role of ABC subfamily C member 10 (ABCC10) in the efflux of antitumor drugs.

    PubMed

    Kathawala, Rishil J; Wang, Yi-Jun; Ashby, Charles R; Chen, Zhe-Sheng

    2014-05-01

    ABCC10, also known as multidrug-resistant protein 7 (MRP7), is the tenth member of the C subfamily of the ATP-binding cassette (ABC) superfamily. ABCC10 mediates multidrug resistance (MDR) in cancer cells by preventing the intracellular accumulation of certain antitumor drugs. The ABCC10 transporter is a 171-kDa protein that is localized on the basolateral cell membrane. ABCC10 is a broad-specificity transporter of xenobiotics, including antitumor drugs, such as taxanes, epothilone B, vinca alkaloids, and cytarabine, as well as modulators of the estrogen pathway, such as tamoxifen. In recent years, ABCC10 inhibitors, including cepharanthine, lapatinib, erlotinib, nilotinib, imatinib, sildenafil, and vardenafil, have been reported to overcome ABCC10-mediated MDR. This review discusses some recent and clinically relevant aspects of the ABCC10 drug efflux transporter from the perspective of current chemotherapy, particularly its inhibition by tyrosine kinase inhibitors and phosphodiesterase type 5 inhibitors. PMID:24103790

  18. Kbot55, purified from Buthus occitanus tunetanus venom, represents the first member of a novel α-KTx subfamily.

    PubMed

    ElFessi-Magouri, Rym; Peigneur, Steve; Khamessi, Oussema; Srairi-Abid, Najet; ElAyeb, Mohamed; Mille, Bea Garcia; Cuypers, Eva; Tytgat, Jan; Kharrat, Riadh

    2016-06-01

    Kbot55 is a 39 amino acid peptide isolated from the venom of the Tunisian scorpion Buthus occitanus tunetanus. This peptide is cross-linked by 3 disulfide bridges and has a molecular mass of 4128.65Da. Kbot55 is very low represented in the venom and thus represents a challenge for biochemical characterization. In this study, Kbot55 has been subjected to a screening on ion channels expressed in Xenopus laevis oocytes. It was found that Kbot55 targets voltage-gated potassium channels with high affinity. Kbot55 shows very low amino acid identity with other scorpion potassium toxins and therefore was considered a bona fide novel type of scorpion toxin. Sequence alignment analysis indicated that Kbot55 is the first representative of the new α-Ktx31 subfamily and therefore was classified as α-Ktx31.1. PMID:26079392

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. The Search for Therapeutic Bacteriophages Uncovers One New Subfamily and Two New Genera of Pseudomonas-Infecting Myoviridae

    PubMed Central

    Henry, Marine; Bobay, Louis-Marie; Chevallereau, Anne; Saussereau, Emilie; Ceyssens, Pieter-Jan; Debarbieux, Laurent

    2015-01-01

    In a previous study, six virulent bacteriophages PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5 and CHA_P1 were evaluated for their in vivo efficacy in treating Pseudomonas aeruginosa infections using a mouse model of lung infection. Here, we show that their genomes are closely related to five other Pseudomonas phages and allow a subdivision into two clades, PAK_P1-like and KPP10-like viruses, based on differences in genome size, %GC and genomic contents, as well as number of tRNAs. These two clades are well delineated, with a mean of 86% and 92% of proteins considered homologous within individual clades, and 25% proteins considered homologous between the two clades. By ESI-MS/MS analysis we determined that their virions are composed of at least 25 different proteins and electron microscopy revealed a morphology identical to the hallmark Salmonella phage Felix O1. A search for additional bacteriophage homologs, using profiles of protein families defined from the analysis of the 11 genomes, identified 10 additional candidates infecting hosts from different species. By carrying out a phylogenetic analysis using these 21 genomes we were able to define a new subfamily of viruses, the Felixounavirinae within the Myoviridae family. The new Felixounavirinae subfamily includes three genera: Felixounalikevirus, PAK_P1likevirus and KPP10likevirus. Sequencing genomes of bacteriophages with therapeutic potential increases the quantity of genomic data on closely related bacteriophages, leading to establishment of new taxonomic clades and the development of strategies for analyzing viral genomes as presented in this article. PMID:25629728

  4. 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

  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. 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

  7. 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.

  8. 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. PMID:25627710

  9. 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.

  10. 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

    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.

  11. 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

  12. 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.

  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. The molecular phylogeny of the digenean family Opecoelidae Ozaki, 1925 and the value of morphological characters, with the erection of a new subfamily.

    PubMed

    Bray, Rodney A; Cribb, Thomas H; Littlewood, D Timothy J; Waeschenbach, Andrea

    2016-01-01

    Large and small rDNA sequences of 41 species of the family Opecoelidae are utilised to produce phylogenetic inference trees, using brachycladioids and lepocreadioids as outgroups. Sequences were newly generated for 13 species. The resulting Bayesian trees show a monophyletic Opecoelidae. The earliest divergent group is the Stenakrinae, based on two species which are not of the type-genus. The next well-supported clade to diverge is constituted of three species of Helicometra Odhner, 1902. Based on this tree and the characters of the egg and uterus, a new subfamily, the Helicometrinae, is erected and defined to include the genera Helicometra, Helicometrina Linton, 1910 and Neohelicometra Siddiqi et Cable, 1960. The subfamily Opecoelinae is found to be monophyletic, but the Plagioporinae is paraphyletic. The single representative of the Opecoelininae (not of the type genus) is nested within a group of deep-sea 'plagioporines'. The two representatives of the Opistholebetidae are embedded within a group of shallow-water 'plagioporine' species. The Opistholebetidae is reduced to subfamily status pro tem as its morphological and biological characteristics are distinctive. This implies that as opecoelid systematics develops with more molecular evidence, several further subfamilies will be recognised. Many of the morphological characters were found to be homoplasious, but the characters defining the Helicometrinae and Opecoelinae, such as filamented eggs, reduced cirrus-sac and uterine seminal receptacle, are closely correlated with the inferred phylogeny. PMID:27189270

  15. 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.

  16. The feature of distribution and clonality of TCR γ/δ subfamilies T cells in patients with B-cell non-Hodgkin lymphoma.

    PubMed

    Wang, Liang; Xu, Meng; Wang, Chunyan; Zhu, Lihua; Hu, Junyan; Chen, Shaohua; Wu, Xiuli; Li, Bo; Li, Yangqiu

    2014-01-01

    Restricted T-cell receptor (TCR) Vα/Vβ repertoire expression and clonal expansion of αβ T cells especially for putative tumor-associated antigens were observed in patients with hematological malignancies. To further characterize the γδ T-cell immune status in B-cell non-Hodgkin lymphoma (B-NHL), we investigated the distribution and clonality of TCR Vγ/Vδ repertoire in peripheral blood (PB), bone marrow (BM), and lymph node (LN) from patients with B-NHL. Four newly diagnosed B-NHL cases, including three with diffuse large B-cell lymphoma (DLBCL) and one with small lymphocytic lymphoma (SLL), were enrolled. The restrictive expression of TCR Vγ/Vδ subfamilies with different distribution patterns could be detected in PB, BM, or LN from all of four patients, and partial subfamily T cells showed clonal proliferation. At least one clonally expanded Vδ subfamily member was found in PB from each patient. However, the expression pattern and clonality of TCR Vγ/Vδ changed in different immune organs and showed individual feature in different patients. The clonally expanded Vδ5, Vδ6, and Vδ8 were detected only in PB but neither in BM nor LN while clonally expanded Vδ2 and Vδ3 could be detected in both PB and BM/LN. In conclusion, the results provide a preliminary profile of distribution and clonality of TCR γ/δ subfamilies T cells in PB, BM, and LN from B-NHL; similar clonally expanded Vδ subfamily T cells in PB and BM may be related to the same B-cell lymphoma-associated antigens, while the different reactive clonally expanded Vγ/Vδ T cells may be due to local immune response. PMID:24963496

  17. 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

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

    PubMed

    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

    2015-11-01

    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

  19. 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

  20. New Transient Receptor Potential Vanilloid Subfamily Member 1 Positron Emission Tomography Radioligands: Synthesis, Radiolabeling, and Preclinical Evaluation

    PubMed Central

    2013-01-01

    The transient receptor potential vanilloid subfamily member 1 (TRPV1) cation channel is known to be involved in pain nociception and neurogenic inflammation, and accumulating evidence suggests that it plays an important role in several central nervous system (CNS)-related disorders. TRPV1-specific positron emission tomography (PET) radioligands can serve as powerful tools in TRPV1-related (pre)clinical research and drug design. We have synthesized several potent TRPV1 antagonists and accompanying precursors for radiolabeling with carbon-11 or fluorine-18. The cinnamic acid derivative [11C]DVV24 and the aminoquinazoline [18F]DVV54 were successfully synthesized, and their biological behavior was studied. In addition, the in vivo behavior of a 123I-labeled analogue of iodo-resiniferatoxin (I-RTX), a well-known TRPV1 antagonist, was evaluated. The binding affinities of DVV24 and DVV54 for human TRPV1 were 163 ± 28 and 171 ± 48 nM, respectively. [11C]DVV24, but not [18F]DVV54 or 123I-RTX, showed retention in the trigeminal nerve, known to abundantly express TRPV1. Nevertheless, it appears that ligands with higher binding affinities will be required to allow in vivo imaging of TRPV1 via PET. PMID:23421633

  1. Cyanide-insensitive quinol oxidase (CIO) from Gluconobacter oxydans is a unique terminal oxidase subfamily of cytochrome bd.

    PubMed

    Miura, Hiroshi; Mogi, Tatsushi; Ano, Yoshitaka; Migita, Catharina T; Matsutani, Minenosuke; Yakushi, Toshiharu; Kita, Kiyoshi; Matsushita, Kazunobu

    2013-06-01

    Cyanide-insensitive terminal quinol oxidase (CIO) is a subfamily of cytochrome bd present in bacterial respiratory chain. We purified CIO from the Gluconobacter oxydans membranes and characterized its properties. The air-oxidized CIO showed some or weak peaks of reduced haemes b and of oxygenated and ferric haeme d, differing from cytochrome bd. CO- and NO-binding difference spectra suggested that haeme d serves as the ligand-binding site of CIO. Notably, the purified CIO showed an extraordinary high ubiquinol-1 oxidase activity with the pH optimum of pH 5-6. The apparent Vmax value of CIO was 17-fold higher than that of G. oxydans cytochrome bo3. In addition, compared with Escherichia coli cytochrome bd, the quinol oxidase activity of CIO was much more resistant to cyanide, but sensitive to azide. The Km value for O2 of CIO was 7- to 10-fold larger than that of G. oxydans cytochrome bo3 or E. coli cytochrome bd. Our results suggest that CIO has unique features attributable to the structure and properties of the O2-binding site, and thus forms a new sub-group distinct from cytochrome bd. Furthermore, CIO of acetic acid bacteria may play some specific role for rapid oxidation of substrates under acidic growth conditions.

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

    PubMed

    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.

  3. The unique ligand binding features of subfamily-II iLBPs with respect to bile salts and related drugs.

    PubMed

    Favretto, Filippo; Ceccon, Alberto; Zanzoni, Serena; D'Onofrio, Mariapina; Ragona, Laura; Molinari, Henriette; Assfalg, Michael

    2015-04-01

    Intracellular lipid binding proteins (iLBPs) are a family of evolutionarily related small cytoplasmic proteins implicated in the transcellular transport of lipophilic ligands. Subfamily-II iLBPs include the liver fatty acid binding protein (L-FABP), and the ileal and the liver and ileal bile acid binding proteins (L-BABP and I-BABP). Atomic-level investigations during the past 15-20 years have delivered relevant information on bile acid binding by this protein group, revealing unique features including binding cooperativity, promiscuity, and site selectivity. Using NMR spectroscopy and other biophysical techniques, our laboratories have contributed to an understanding of the molecular determinants of some of these properties and their generality among proteins from different animal species. We focused especially on formation of heterotypic complexes, considering the mixed compositions of physiological bile acid pools. Experiments performed with synthetic bile acid derivatives showed that iLBPs could act as targets for cell-specific contrast agents and, more generally, as effective carriers of amphiphilic drugs. This review collects the major findings related to bile salt interactions with iLBPs aiming to provide keys for a deeper understanding of protein-mediated intracellular bile salt trafficking. PMID:25468388

  4. TP0262 is a modulator of promoter activity of tpr Subfamily II genes of Treponema pallidum ssp. pallidum.

    PubMed

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

    2009-06-01

    Transcriptional regulation in Treponema pallidum ssp. 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. pallidumrepeat) 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 with similarity to known bacterial transcription factors, including four catabolite activator protein homologues. In this work, sequences matching the Escherichia coli cAMP receptor protein (CRP) binding motif were identified in silico upstream of tprE, tprG and tprJ. Using elecrophoretic mobility shift assay and DNaseI footprinting assay, recombinant TP0262, a T. pallidum CRP homologue, 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 that influences tpr promoter activity.

  5. DNA topoisomerase VIII: a novel subfamily of type IIB topoisomerases encoded by free or integrated plasmids in Archaea and Bacteria.

    PubMed

    Gadelle, Danièle; Krupovic, Mart; Raymann, Kasie; Mayer, Claudine; Forterre, Patrick

    2014-07-01

    Type II DNA topoisomerases are divided into two families, IIA and IIB. Types IIA and IIB enzymes share homologous B subunits encompassing the ATP-binding site, but have non-homologous A subunits catalyzing DNA cleavage. Type IIA topoisomerases are ubiquitous in Bacteria and Eukarya, whereas members of the IIB family are mostly present in Archaea and plants. Here, we report the detection of genes encoding type IIB enzymes in which the A and B subunits are fused into a single polypeptide. These proteins are encoded in several bacterial genomes, two bacterial plasmids and one archaeal plasmid. They form a monophyletic group that is very divergent from archaeal and eukaryotic type IIB enzymes (DNA topoisomerase VI). We propose to classify them into a new subfamily, denoted DNA topoisomerase VIII. Bacterial genes encoding a topoisomerase VIII are present within integrated mobile elements, most likely derived from conjugative plasmids. Purified topoisomerase VIII encoded by the plasmid pPPM1a from Paenibacillus polymyxa M1 had ATP-dependent relaxation and decatenation activities. In contrast, the enzyme encoded by mobile elements integrated into the genome of Ammonifex degensii exhibited DNA cleavage activity producing a full-length linear plasmid and that from Microscilla marina exhibited ATP-independent relaxation activity. Topoisomerases VIII, the smallest known type IIB enzymes, could be new promising models for structural and mechanistic studies.

  6. 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

  7. MOAT-E (ARA) is a full-length MRP/cMOAT subfamily transporter expressed in kidney and liver

    PubMed Central

    Belinsky, M G; Kruh, G D

    1999-01-01

    Multidrug resistance-associated protein (MRP) and the canalicular multispecific organic anion transporter (cMOAT) are organic anion pumps that have been linked to cytotoxic drug resistance. We previously reported the isolation of three human MRP/cMOAT-related transporters, MOAT-B (MRP4), MOAT-C (MRP5) and MOAT-D (MRP3). In the present study we describe the fourth MRP/cMOAT-related transporter. We analysed ARA, a human cDNA reported to encode a 453 residue MRP-related transporter, and found that it represents a fused transcript composed of MRP sequences and partial sequences of a novel transporter. The complete coding sequence of this novel transporter, which we designated MOAT-E, was isolated. MOAT-E encodes a 1503 residue transporter that is most closely related to MRP (45%), MOAT-D (44%) and cMOAT (39%), both in terms of amino acid identity and sharing a common topology in which ∼ 17 transmembrane spanning helices are distributed within three membrane spanning domains. RNA blot analysis indicated that MOAT-E expression is restricted to kidney and liver. These observations suggest that MOAT-E may function as an organic anion transporter involved in cellular detoxification and possibly in the hepatobiliary and renal excretion of xenobiotics and/or endogenous metabolites. Isolation of MOAT-E helps to define the MRP/cMOAT subfamily of transporters. © 1999 Cancer Research Campaign PMID:10424734

  8. Cloning of the mitogen-activated S6 kinase from rat liver reveals an enzyme of the second messenger subfamily

    SciTech Connect

    Kozma, S.C.; Ferrari, S. Bassand, P.; Siegmann, M.; Thomas, G. ); Totty, N. )

    1990-10-01

    Recently the authors reported the purification of a mitogen-activated S6 kinase from Swiss mouse 3T3 fibroblasts and rat liver. The rat liver protein was cleaved with cyanogen bromide or trypsin and 17 of the resulting peptides were sequenced. DNA primers were generated from 3 peptides that had homology to sequences of the conserved catalytic domain of protein kinases. These primers were used in the polymerase chain reaction to obtain a 0.4-kilobase DNA fragment. This fragment was either radioactively labeled and hybridized to Northern blots of poly(A){sup {sup plus}} mRNA or used to screen a rat liver cDNA library. Northern blot analysis revealed four transcripts of 2.5, 3.2, 4.0, and 6.0 kilobases, and five S6 kinase clones were obtained by screening the library. Only two of the clones, which were identical, encoded a full-length protein. This protein had a molecular weight of 56,160, which correlated closely to that of the dephosphorylated kinase determined by SDS/PAGE. The catalytic domain of the kinase resembles that of other serine/threonine kinases belonging to the second messenger subfamily of protein kinases.

  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. 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

  11. 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

  12. 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

  13. 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

  14. Evolution of SINE S1 retroposons in Cruciferae plant species.

    PubMed

    Lenoir, A; Cournoyer, B; Warwick, S; Picard, G; Deragon, J M

    1997-09-01

    The S1 element is a plant short interspersed element (SINE) that was first described and studied in Brassica napus. In this work, we investigated the distribution and the molecular phylogeny of the S1 element within the Cruciferae (= Brassicaceae). S1 elements were found to be widely distributed within the Cruciferae, especially in species of the tribe Brassiceae. The molecular phylogeny of S1 elements in eight Cruciferae species (Brassica oleracea, Brassica rapa, Brassica napus, Brassica nigra, Sinapis, arvensis, Sinapis pubescens, Coincya monensis, and Vella spinosa) was inferred using 14-36 elements per species. Significant neighbor-joining and maximum-parsimony phylogenetic clusters, supported by high bootstrap P values and/or represented in 100% of the most-parsimonious trees, were observed for each species. Most of these clusters probably correspond to recent species-specific bursts of S1 amplification. Since these species diverged recently, S1 amplification in Cruciferae plants is proposed to be a highly dynamic process that could contribute to genome rearrangements and eventually lead to reproductive isolation. S1 sequence analysis also revealed putative gene conversion events that occurred between different S1 elements of a given species. These events suggest that gene conversion is a minor but significant component of the molecular drive governing S1 concerted evolution.

  15. 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

  16. Molecular Evolution of the CYP2D Subfamily in Primates: Purifying Selection on Substrate Recognition Sites without the Frequent or Long-Tract Gene Conversion

    PubMed Central

    Yasukochi, Yoshiki; Satta, Yoko

    2015-01-01

    The human cytochrome P450 (CYP) 2D6 gene is a member of the CYP2D gene subfamily, along with the CYP2D7P and CYP2D8P pseudogenes. Although the CYP2D6 enzyme has been studied extensively because of its clinical importance, the evolution of the CYP2D subfamily has not yet been fully understood. Therefore, the goal of this study was to reveal the evolutionary process of the human drug metabolic system. Here, we investigate molecular evolution of the CYP2D subfamily in primates by comparing 14 CYP2D sequences from humans to New World monkey genomes. Window analysis and statistical tests revealed that entire genomic sequences of paralogous genes were extensively homogenized by gene conversion during molecular evolution of CYP2D genes in primates. A neighbor-joining tree based on genomic sequences at the nonsubstrate recognition sites showed that CYP2D6 and CYP2D8 genes were clustered together due to gene conversion. In contrast, a phylogenetic tree using amino acid sequences at substrate recognition sites did not cluster the CYP2D6 and CYP2D8 genes, suggesting that the functional constraint on substrate specificity is one of the causes for purifying selection at the substrate recognition sites. Our results suggest that the CYP2D gene subfamily in primates has evolved to maintain the regioselectivity for a substrate hydroxylation activity between individual enzymes, even though extensive gene conversion has occurred across CYP2D coding sequences. PMID:25808902

  17. Identification of a GH110 subfamily of alpha 1,3-galactosidases: novel enzymes for removal of the alpha 3Gal xenotransplantation antigen.

    PubMed

    Liu, Qiyong P; Yuan, Huaiping; Bennett, Eric P; Levery, Steven B; Nudelman, Edward; Spence, Jean; Pietz, Greg; Saunders, Kristen; White, Thayer; Olsson, Martin L; Henrissat, Bernard; Sulzenbacher, Gerlind; Clausen, Henrik

    2008-03-28

    In search of alpha-galactosidases with improved kinetic properties for removal of the immunodominant alpha1,3-linked galactose residues of blood group B antigens, we recently identified a novel prokaryotic family of alpha-galactosidases (CAZy GH110) with highly restricted substrate specificity and neutral pH optimum (Liu, Q. P., Sulzenbacher, G., Yuan, H., Bennett, E. P., Pietz, G., Saunders, K., Spence, J., Nudelman, E., Levery, S. B., White, T., Neveu, J. M., Lane, W. S., Bourne, Y., Olsson, M. L., Henrissat, B., and Clausen, H. (2007) Nat. Biotechnol. 25, 454-464). One member of this family from Bacteroides fragilis had exquisite substrate specificity for the branched blood group B structure Galalpha1-3(Fucalpha1-2)Gal, whereas linear oligosaccharides terminated by alpha1,3-linked galactose such as the immunodominant xenotransplantation epitope Galalpha1-3Galbeta1-4GlcNAc did not serve as substrates. Here we demonstrate the existence of two distinct subfamilies of GH110 in B. fragilis and thetaiotaomicron strains. Members of one subfamily have exclusive specificity for the branched blood group B structures, whereas members of a newly identified subfamily represent linkage specific alpha1,3-galactosidases that act equally well on both branched blood group B and linear alpha1,3Gal structures. We determined by one-dimensional (1)H NMR spectroscopy that GH110 enzymes function with an inverting mechanism, which is in striking contrast to all other known alpha-galactosidases that use a retaining mechanism. The novel GH110 subfamily offers enzymes with highly improved performance in enzymatic removal of the immunodominant alpha3Gal xenotransplantation epitope.

  18. 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

    2015-01-01

    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.

  19. 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

    2015-01-01

    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

  20. Comparative genomic evidence for duplication of TLR1 subfamily and miiuy croaker TLR1 perceives LPS stimulation via MyD88 and TIRAP.

    PubMed

    Xu, Tianjun; Wang, Yanjin; Li, Jinrui; Shu, Chang; Han, Jingjing; Chu, Qing

    2016-09-01

    Being indispensable pattern recognition receptors in innate immune responses in host protection, Toll-like receptors (TLRs) play an important role in pathogen recognition. Fish TLRs exhibit high variety and distinct features, although little is known about their function on ligand recognition and signaling pathway in fish. This paper reports the evolutionary spectrum of the TLR1 subfamily (referred to as TLR1, TLR6, and TLR10) as determined using the comparative genomic approach. We hypothesized that the TLR1 subfamily underwent two rounds of gene duplication events; the first duplication occurred prior to the divergence of amphibians, and the second one occurred prior to the divergence of eutherians. To further study the function of fish TLR1, we identified miiuy croaker (Miichthys miiuy) TLR1 (mmiTLR1) and determined its potential ability to perceive Vibrio anguillarum and lipopolysaccharide stimulation. Data further suggested that mmiTLR1 is dependent on TIRAP and MyD88 for signal transmission. In addition, immunocytochemistry showed the speculative interaction between MyD88 and mmiTLR1 TIR domain. Overall, we systematically and comprehensively analyzed evolution of TLR1 subfamily and the function of mmiTLR1, which will provide the basis for future scientific research on fish TLRs. PMID:27431585

  1. Quantification of subfamily I.2.C catechol 2,3-dioxygenase mRNA transcripts in groundwater samples of an oxygen-limited BTEX-contaminated site.

    PubMed

    Táncsics, András; Szoboszlay, Sándor; Szabó, István; Farkas, Milán; Kovács, Balázs; Kukolya, József; Mayer, Zoltán; Kriszt, Balázs

    2012-01-01

    Low dissolved oxygen concentration of subsurface environments is a limiting factor for microbial aromatic hydrocarbon degradation, and to date, there are only a limited number of available reports on functional genes and microbes that take part in the degradation of aromatic hydrocarbons under hypoxic conditions. Recent discoveries shed light on the prevalence of subfamily I.2.C catechol 2,3-dioxygenases in petroleum hydrocarbon contaminated hypoxic groundwaters, and their considerable environmental importance was suggested. Here, we report on a Hungarian aromatic hydrocarbon (methyl-substituted benzene derivatives, mostly xylenes) contaminated site where we investigated this presumption. Groundwater samples were taken from the center and the edge of the contaminant plume and beyond the plume. mRNA transcripts of subfamily I.2.C catechol 2,3-dioxygenases were detected in considerable amounts in the contaminated samples by qPCR analysis, while activity of subfamily I.2.A, which includes the largest group of extradiol dioxygenases described by culture-dependent studies and thought to be widely distributed in BTEX-contaminated environments, was not observed. Bacterial community structure analyses showed the predominance of genus Rhodoferax related species in the contaminated samples.

  2. 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.

  3. How pH modulates the dimer-decamer interconversion of 2-Cys peroxiredoxins from the Prx1 subfamily.

    PubMed

    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

    2015-03-27

    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 (His(113)) functions as a pH sensor that, at acidic conditions, becomes protonated and forms an electrostatic pair with Asp(76) 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.

  4. How pH modulates the dimer-decamer interconversion of 2-Cys peroxiredoxins from the Prx1 subfamily.

    PubMed

    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

    2015-03-27

    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 (His(113)) functions as a pH sensor that, at acidic conditions, becomes protonated and forms an electrostatic pair with Asp(76) 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

  5. 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

  6. Suppression of aberrant transient receptor potential cation channel, subfamily V, member 6 expression in hyperproliferative colonic crypts by dietary calcium.

    PubMed

    Peleg, Sara; Sellin, Joseph H; Wang, Yu; Freeman, Michael R; Umar, Shahid

    2010-09-01

    Dietary calcium is believed to reduce colon cancer risk, but the mechanism by which this occurs is poorly understood. Employing the Citrobacter rodentium-induced transmissible murine colonic hyperplasia (TMCH) model, we previously showed that a high-calcium diet (hCa) significantly abrogated hyperplasia in the distal colons of NIH-Swiss mice. Here, we explored the mechanism of dietary protection by hCa by analyzing the expression of genes involved in the regulation of Ca uptake/flux in the intestinal epithelium, including the Ca-sensing receptor, vitamin D receptor, Ca binding protein, and transient receptor potential cation channels, subfamily V, members 5 and 6 (TRPV5/6). Interestingly, while TRPV6 expression increased significantly during TMCH, the expression of the other gene products was unchanged. This elevated TRPV6 expression was significantly abrogated by a hCa diet. Immunofluorescence revealed apical membrane localization of TRPV6 in the normal colon, whereas during TMCH we observed intense apical pole and cytoplasmic staining along the entire longitudinal crypt axis, including the expanded proliferating zone. The hCa diet reversed this effect. In humans, overexpression of TRPV6 was associated with early-stage colon cancer, and in colon carcinoma cells, inhibition of TRPV6 expression by small interfering RNA inhibited their proliferation and induced apoptosis. TRPV6 small interfering RNA also diminished the transcriptional activity of the calcium-dependent nuclear factors in activated T cells. Thus the aberrant overexpression of TRPV6 contributes to colonic crypt hyperplasia in mice and to colon cancer cell proliferation in humans. Therefore, it is likely that suppression of TRPV6 by a hCa diet is required for its protective effects in the colon.

  7. Species discrimination in the subfamily Ostertagiinae of Northern China: assessment of DNA barcode in a taxonomically challenging group.

    PubMed

    Lv, Jizhou; Zhang, Yongning; Feng, Chunyan; Yuan, Xiangfen; Sun, Degang; Deng, Junhua; Wang, Caixia; Wu, Shaoqiang; Lin, Xiangmei

    2016-03-01

    Gastrointestinal nematodes within the subfamily Ostertagiinae (Teladorsagia, Ostertagia, and Marshallagia et al.) are among the most common infections of domesticated livestock. These parasites are of particular interest, as many of the species within this group are of economic importance worldwide. Traditionally, nematode species designations have been based on morphological criteria. However, this group possesses poorly defined species. There is an urgent need to develop a reliable technique that can distinguish species of Ostertagiinae. DNA barcoding has been proved to be a powerful tool to identify species of birds, mammals, and arthropods, but this technique has not yet been examined for identifying species of Ostertagiinae. In this study, a total of 138 mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) sequences from individuals representing 11 species of Ostertagiinae were acquired by PCR for the first time. The specimens were collected from pastoral area of northern China. Genetic divergence analyses showed that mean interspecific Kimura two-parameter distances of COI (13.61 %) were about four times higher than the mean value of the intraspecific divergence (3.69 %). Then, the performance of the COI to identify species of Ostertagiinae was evaluated by identification success rates using nearest neighbor (NN) and BLASTn. The results indicated that the rates of correct sequence identification for COI were high (>80 %) when using the NN and BLASTn methods. Besides, the deep lineage divergences are detected in Teladorsagia circumcincta. Meanwhile, the analyses also detected no genetic differentiation between some species such as Ostertagia hahurica and Ostertagia buriatica. These results indicate that the traditional status of species within Ostertagiinae should be closely examined based on the molecular data.

  8. Structural Features and Functional Dependency on β-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL.

    PubMed

    Fukui, Kenji; Baba, Seiki; Kumasaka, Takashi; Yano, Takato

    2016-08-12

    In early reactions of DNA mismatch repair, MutS recognizes mismatched bases and activates MutL endonuclease to incise the error-containing strand of the duplex. DNA sliding clamp is responsible for directing the MutL-dependent nicking to the newly synthesized/error-containing strand. In Bacillus subtilis MutL, the β-clamp-interacting motif (β motif) of the C-terminal domain (CTD) is essential for both in vitro direct interaction with β-clamp and in vivo repair activity. A large cluster of negatively charged residues on the B. subtilis MutL CTD prevents nonspecific DNA binding until β clamp interaction neutralizes the negative charge. We found that there are some bacterial phyla whose MutL endonucleases lack the β motif. For example, the region corresponding to the β motif is completely missing in Aquifex aeolicus MutL, and critical amino acid residues in the β motif are not conserved in Thermus thermophilus MutL. We then revealed the 1.35 Å-resolution crystal structure of A. aeolicus MutL CTD, which lacks the β motif but retains the metal-binding site for the endonuclease activity. Importantly, there was no negatively charged cluster on its surface. It was confirmed that CTDs of β motif-lacking MutLs, A. aeolicus MutL and T. thermophilus MutL, efficiently incise DNA even in the absence of β-clamp and that β-clamp shows no detectable enhancing effect on their activity. In contrast, CTD of Streptococcus mutans, a β motif-containing MutL, required β-clamp for the digestion of DNA. We propose that MutL endonucleases are divided into three subfamilies on the basis of their structural features and dependence on β-clamp. PMID:27369079

  9. 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.

  10. 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. PMID:27542340

  11. The Relationship between Diet Breadth and Geographic Range Size in the Butterfly Subfamily Nymphalinae – A Study of Global Scale

    PubMed Central

    Slove, Jessica; Janz, Niklas

    2011-01-01

    The “oscillation hypothesis” has been proposed as a general explanation for the exceptional diversification of herbivorous insect species. The hypothesis states that speciation rates are elevated through repeated correlated changes – oscillations – in degree of host plant specificity and geographic range. The aim of this study is to test one of the predictions from the oscillation hypothesis: a positive correlation between diet breadth (number of host plants used) and geographic range size, using the globally distributed butterfly subfamily Nymphalinae. Data on diet breadth and global geographic range were collected for 182 Nymphalinae butterflies species and the size of the geographic range was measured using a GIS. We tested both diet breadth and geographic range size for phylogenetic signal to see if species are independent of each other with respect to these characters. As this test gave inconclusive results, data was analysed both using cross-species comparisons and taking phylogeny into account using generalised estimating equations as applied in the APE package in R. Irrespective of which method was used, we found a significant positive correlation between diet breadth and geographic range size. These results are consistent for two different measures of diet breadth and removal of outliers. We conclude that the global range sizes of Nymphalinae butterflies are correlated to diet breadth. That is, butterflies that feed on a large number of host plants tend to have larger geographic ranges than do butterflies that feed on fewer plants. These results lend support for an important step in the oscillation hypothesis of plant-driven diversification, in that it can provide the necessary fuel for future population fragmentation and speciation. PMID:21246054

  12. Identification of AHK2- and AHK3-like cytokinin receptors in Brassica napus reveals two subfamilies of AHK2 orthologues.

    PubMed

    Kuderová, Alena; Gallová, Lucia; Kuricová, Katarína; Nejedlá, Eliška; Čurdová, Anna; Micenková, Lenka; Plíhal, Ondřej; Šmajs, David; Spíchal, Lukáš; Hejátko, Jan

    2015-01-01

    Cytokinin (CK) signalling is known to play key roles in the regulation of plant growth and development, crop yields, and tolerance to both abiotic stress and pathogen defences, but the mechanisms involved are poorly characterized in dicotyledonous crops. Here the identification and functional characterization of sensor histidine kinases homologous to Arabidopsis CK receptors AHK2 and AHK3 in winter oilseed rape are presented. Five CHASE-containing His kinases were identified in Brassica napus var. Tapidor (BnCHK1-BnCHK5) by heterologous hybridization of its genomic library with gene-specific probes from Arabidopsis. The identified bacterial artificial chromosome (BAC) clones were fingerprinted and representative clones in five distinct groups were sequenced. Using a bioinformatic approach and cDNA cloning, the precise gene and putative protein domain structures were determined. Based on phylogenetic analysis, four AHK2 (BnCHK1-BnCHK4) homologues and one AHK3 (BnCHK5) homologue were defined. It is further suggested that BnCHK1 and BnCHK3, and BnCHK5 are orthologues of AHK2 and AHK3, originally from the B. rapa A genome, respectively. BnCHK1, BnCHK3, and BnCHK5 displayed high affinity for trans-zeatin (1-3nM) in a live-cell competitive receptor assay, but not with other plant hormones (indole acetic acid, GA3, and abscisic acid), confirming the prediction that they are genuine CK receptors. It is shown that BnCHK1 and BnCHK3, and BnCHK5 display distinct preferences for various CK bases and metabolites, characteristic of their AHK counterparts, AHK2 and AHK3, respectively. Interestingly, the AHK2 homologues could be divided into two subfamilies (BnCHK1/BnCK2 and BnCHK3/BnCHK4) that differ in putative transmembrane domain topology and CK binding specificity, thus implying potential functional divergence.

  13. 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

  14. Overexpression of Transient Receptor Protein Cation Channel Subfamily A Member 1, Confers an Independent Prognostic Indicator in Nasopharyngeal Carcinoma

    PubMed Central

    Wu, You-Ting; Yen, Shao-Lun; Li, Chien-Feng; Chan, Ti-Chun; Chen, Tzu-Ju; Lee, Sung-Wei; He, Hong-Lin; Chang, I-Wei; Hsing, Chung-Hsi; Shiue, Yow-Ling

    2016-01-01

    Background: Detection of oncogenes provides chances to understand tumor development and progression. Transient receptor protein cation channel subfamily A, member 1 (TRPA1) transcript was significantly upregulated in nasopharyngeal carcinoma (NPC) with a stepwise upregulation from low- to high-stage NPCs from a preliminary data analysis in the Gene Expression Omnibus database. The TRPA1 gene is a member of the TRP channel family, encoding integral membrane proteins that functions as cation channels. Loss of calcium homeostasis takes place in cancer cells. Methods: Immunostaining of TRPA1 was analyzed on 124 biopsies from NPC patients retrospectively. The H-score method was used to evaluate the immunoexpression of TRPA1. The correlations between H-score of TRPA1 protein level and clinicopathological factors, as well as the significances of TRPA1 protein level for disease-specific, distal-metastasis-free and local recurrence-free survivals were assessed. Results: These patients were characterized to be no initial metastasis and medicated with the traditional procedure. The TRPA1 score was found to be associated with clinicopathological parameters and patient survivals. Along with the guideline of 7th edition of the American Joint Committee on Cancer, we found that TRPA1 upregulation (50%) was associated with advanced primary tumor (P = 0.009) and overall clinical stage (P = 0.019). In univariate log-rank testing, primary tumor, nodal status, stage and TRPA1 protein level significantly contributed to worse disease-specific survival, distal metastasis-free survival and local recurrence-free survival. In multivariate analysis, high TRPA1 protein level and tumor stage emerged as independent prognostic indicators for inferior disease-specific survival (P = 0.014; P = 0.003), distal metastasis-free survival (P = 0.004; P = 0.034) and recurrence-free survival (P = 0.017; P = 0.015). Conclusions: The upregulation of TRPA1 protein level is frequently correlated to unfavorable

  15. 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

  16. Identification of AHK2- and AHK3-like cytokinin receptors in Brassica napus reveals two subfamilies of AHK2 orthologues.

    PubMed

    Kuderová, Alena; Gallová, Lucia; Kuricová, Katarína; Nejedlá, Eliška; Čurdová, Anna; Micenková, Lenka; Plíhal, Ondřej; Šmajs, David; Spíchal, Lukáš; Hejátko, Jan

    2015-01-01

    Cytokinin (CK) signalling is known to play key roles in the regulation of plant growth and development, crop yields, and tolerance to both abiotic stress and pathogen defences, but the mechanisms involved are poorly characterized in dicotyledonous crops. Here the identification and functional characterization of sensor histidine kinases homologous to Arabidopsis CK receptors AHK2 and AHK3 in winter oilseed rape are presented. Five CHASE-containing His kinases were identified in Brassica napus var. Tapidor (BnCHK1-BnCHK5) by heterologous hybridization of its genomic library with gene-specific probes from Arabidopsis. The identified bacterial artificial chromosome (BAC) clones were fingerprinted and representative clones in five distinct groups were sequenced. Using a bioinformatic approach and cDNA cloning, the precise gene and putative protein domain structures were determined. Based on phylogenetic analysis, four AHK2 (BnCHK1-BnCHK4) homologues and one AHK3 (BnCHK5) homologue were defined. It is further suggested that BnCHK1 and BnCHK3, and BnCHK5 are orthologues of AHK2 and AHK3, originally from the B. rapa A genome, respectively. BnCHK1, BnCHK3, and BnCHK5 displayed high affinity for trans-zeatin (1-3nM) in a live-cell competitive receptor assay, but not with other plant hormones (indole acetic acid, GA3, and abscisic acid), confirming the prediction that they are genuine CK receptors. It is shown that BnCHK1 and BnCHK3, and BnCHK5 display distinct preferences for various CK bases and metabolites, characteristic of their AHK counterparts, AHK2 and AHK3, respectively. Interestingly, the AHK2 homologues could be divided into two subfamilies (BnCHK1/BnCK2 and BnCHK3/BnCHK4) that differ in putative transmembrane domain topology and CK binding specificity, thus implying potential functional divergence. PMID:25336686

  17. WXG100 Protein Superfamily Consists of Three Subfamilies and Exhibits an α-Helical C-Terminal Conserved Residue Pattern

    PubMed Central

    Poulsen, Christian; Panjikar, Santosh; Holton, Simon J.; Wilmanns, Matthias; Song, Young-Hwa

    2014-01-01

    Members of the WXG100 protein superfamily form homo- or heterodimeric complexes. The most studied proteins among them are the secreted T-cell antigens CFP-10 (10 kDa culture filtrate protein, EsxB) and ESAT-6 (6 kDa early secreted antigen target, EsxA) from Mycobacterium tuberculosis. They are encoded on an operon within a gene cluster, named as ESX-1, that encodes for the Type VII secretion system (T7SS). WXG100 proteins are secreted in a full-length form and it is known that they adopt a four-helix bundle structure. In the current work we discuss the evolutionary relationship between the homo- and heterodimeric WXG100 proteins, the basis of the oligomeric state and the key structural features of the conserved sequence pattern of WXG100 proteins. We performed an iterative bioinformatics analysis of the WXG100 protein superfamily and correlated this with the atomic structures of the representative WXG100 proteins. We find, firstly, that the WXG100 protein superfamily consists of three subfamilies: CFP-10-, ESAT-6- and sagEsxA-like proteins (EsxA proteins similar to that of Streptococcus agalactiae). Secondly, that the heterodimeric complexes probably evolved from a homodimeric precursor. Thirdly, that the genes of hetero-dimeric WXG100 proteins are always encoded in bi-cistronic operons and finally, by combining the sequence alignments with the X-ray data we identify a conserved C-terminal sequence pattern. The side chains of these conserved residues decorate the same side of the C-terminal α-helix and therefore form a distinct surface. Our results lead to a putatively extended T7SS secretion signal which combines two reported T7SS recognition characteristics: Firstly that the T7SS secretion signal is localized at the C-terminus of T7SS substrates and secondly that the conserved residues YxxxD/E are essential for T7SS activity. Furthermore, we propose that the specific α-helical surface formed by the conserved sequence pattern including YxxxD/E motif is a key

  18. Structure, evolution and expression of a second subfamily of protein phosphatase 2A catalytic subunit genes in the rice plant (Oryza sativa L.).

    PubMed

    Yu, Richard Man Kit; Wong, Minnie Man Lai; Jack, Ralph Wilson; Kong, Richard Yuen Chong

    2005-11-01

    Protein phosphatase 2A (PP2A) is one of the major serine/threonine protein phosphatases in the cell and plays a variety of regulatory roles in metabolism and signal transduction. Previously, we described the structure and expression of two genes encoding PP2A catalytic subunits (PP2Ac)--OsPP2A-1 and OsPP2A-3--in the rice plant (Yu et al. 2003). Here, we report the isolation and characterisation of a second structurally distinguishable PP2Ac subfamily comprised of three additional isogenes, OsPP2A-2, OsPP2A-4 (each containing ten introns) and OsPP2A-5 (which contains nine introns). Northern blot analysis demonstrated that the three isogenes are ubiquitously expressed in all rice tissues during plant development, and differentially expressed in response to high salinity and the combined stresses of drought and heat. Phylogenetic analyses indicated that the two PP2Ac subfamilies are descended from two ancient lineages, which derived from gene duplications that occurred after the monocotyledon-dicotyledon split. In the second subfamily, it is proposed that two duplication events were involved; in which, the initial duplication of a ten-intron primordial gene yielded OsPP2A-2 and the progenitor of OsPP2A-4 and OsPP2A-5. The OsPP2A-4/OsPP2A-5 progenitor, in turn, underwent a second duplication event, resulting in the present day OsPP2A-4 and OsPP2A-5. It is proposed that loss of the 5'-most intron from OsPP2A-5 occurred after these two duplication events. PMID:16021503

  19. Two ways of legumin-precursor processing in conifers. Characterization and evolutionary relationships of Metasequoia cDNAs representing two divergent legumin gene subfamilies.

    PubMed

    Häger, K P; Wind, C

    1997-06-15

    Subunit monomers and oligomers of crystalloid-type legumins are major components of SDS-soluble fractions from Metasequoia glyptostroboides (Dawn redwood, Taxodiaceae) seed proteins. The subunits are made up of disulfide linked alpha-polypeptides and beta-polypeptides with molecular masses of 33 kDa and 23-25 kDa, respectively. Unusually for legumins, those from Metasequoia are glycosylated and the carbohydrate moieties are residing in the C-terminal region of the respective beta-polypeptides. A Metasequoia endosperm cDNA library has been constructed and legumin-encoding transcripts representing two divergent gene subfamilies have been characterized. Intersubfamily comparisons reveal 75% identity at the amino acid level and the values range from 53-35% when the legumin precursors deduced were compared with those from angiosperms. The predicted sequences together with data from amino acid sequencing prove that post-translational processing of Metasequoia prolegumins is directed to two different processing sites, each of them specific for one of the legumin subfamilies. The sites involved differ in their relative position and in the junction to be cleaved: Metasequoia legumin precursors MgLeg18 and MgLeg26 contain the conventional post-translational Asn-Gly processing site, which is generally regarded as highly conserved. In contrast, the MgLeg4 precursor is lacking this site and post-translational cleavage is directed to an unusual Asn-Thr processing site located in its hypervariable region, causing N-terminal extension of the beta-polypeptide relative to those hitherto known. Evidence is given that the unusual variant of processing also occurs in other conifers. Phylogenetic analysis reveals the precursors concerned as representatives of a distinct legumin subfamily, originating from duplication of an ancestral gene prior to or at the beginning of Taxodiaceae diversification.

  20. 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.

  1. Distinct biochemical properties of the native members of the G12 G-protein subfamily. Characterization of G alpha 12 purified from rat brain.

    PubMed Central

    Harhammer, R; Nürnberg, B; Harteneck, C; Leopoldt, D; Exner, T; Schultz, G

    1996-01-01

    G12 and G13 are insufficiently characterized pertussis toxin-insensitive G-proteins. Here, we describe the isolation of G alpha 12 from rat brain membranes. G alpha 12 was purified to apparent homogeneity by three steps of conventional chromatography, followed by two cycles of subunit-exchange chromatography on immobilized G subunits. Purified G alpha 12 bound guanosine 5'-[gamma-thio]triphosphate slowly and substoichiometrically. For isolation of functionally active G alpha 12, it was mandatory to use sucrose monolaurate as a detergent. Comparative studies of both rat-brain-derived members of the G12 subfamily revealed differences in the affinity of G alpha 12 and G alpha 13 for G beta gamma. G alpha 12 required a higher Mg2+ concentration for AlF4- -induced dissociation from immobilized G beta gamma than did G alpha 13. In addition, the G12 subfamily members differed in their sedimentation velocities, as determined by sucrose-density-gradient centrifugation. Analysis of sedimentation coefficients revealed a higher tendency of G12 to form supramolecular structures in comparison to G13 and other G-proteins. These G13 structures were stabilized by sucrose monolaurate, which in turn may explain the necessity for this detergent for purification of functionally active G alpha 12. Despite these distinct biochemical characteristics of G12 and G13, both purified G-proteins coupled to a recombinant thromboxane A2 (TXA2) receptor reconstituted into phospholipid vesicles. These data indicate, (1) significant differences in the biochemical properties of native members of the G12 subfamily, and (2) their specific coupling to TXA2 receptors. PMID:8870664

  2. The Subfamily-Specific Interaction between Kv2.1 and Kv6.4 Subunits Is Determined by Interactions between the N- and C-termini

    PubMed Central

    Bocksteins, Elke; Mayeur, Evy; Van Tilborg, Abbi; Regnier, Glenn; Timmermans, Jean-Pierre; Snyders, Dirk J.

    2014-01-01

    The “silent” voltage-gated potassium (KvS) channel subunit Kv6.4 does not form electrically functional homotetramers at the plasma membrane but assembles with Kv2.1 subunits, generating functional Kv2.1/Kv6.4 heterotetramers. The N-terminal T1 domain determines the subfamily-specific assembly of Kv1-4 subunits by preventing interactions between subunits that belong to different subfamilies. For Kv6.4, yeast-two-hybrid experiments showed an interaction of the Kv6.4 N-terminus with the Kv2.1 N-terminus, but unexpectedly also with the Kv3.1 N-terminus. We confirmed this interaction by Fluorescence Resonance Energy Transfer (FRET) and co-immunoprecipitation (co-IP) using N-terminal Kv3.1 and Kv6.4 fragments. However, full-length Kv3.1 and Kv6.4 subunits do not form heterotetramers at the plasma membrane. Therefore, additional interactions between the Kv6.4 and Kv2.1 subunits should be important in the Kv2.1/Kv6.4 subfamily-specificity. Using FRET and co-IP approaches with N- and C-terminal fragments we observed that the Kv6.4 C-terminus physically interacts with the Kv2.1 N-terminus but not with the Kv3.1 N-terminus. The N-terminal amino acid sequence CDD which is conserved between Kv2 and KvS subunits appeared to be a key determinant since charge reversals with arginine substitutions abolished the interaction between the N-terminus of Kv2.1 and the C-terminus of both Kv2.1 and Kv6.4. In addition, the Kv6.4(CKv3.1) chimera in which the C-terminus of Kv6.4 was replaced by the corresponding domain of Kv3.1, disrupted the assembly with Kv2.1. These results indicate that the subfamily-specific Kv2.1/Kv6.4 heterotetramerization is determined by interactions between Kv2.1 and Kv6.4 that involve both the N- and C-termini in which the conserved N-terminal CDD sequence plays a key role. PMID:24901643

  3. A new species in the genus Alectorolophus Brunner von Wattenwyl, 1898 from Indonesia with discussion on its position compared to allied genera in subfamily Catantopinae (Orthoptera: Acrididae).

    PubMed

    Storozhenko, Sergey Yu; Kim, Taewoo

    2016-01-01

    Alectorolophus impunctus Storozhenko et Kim, sp. nov. from Sulawesi Island, Indonesia, is described here. Keys to both sexes of all known species and subspecies of Alectorolophus are also provided in this report. The position of genus Alectorolophus in the systematics of grasshoppers is clarified. It belongs to subtribe Ecphantina (Catantopinae: Catantopini) consisting of nine genera distributed in Australia and Oriental regions. The diagnosis of Ecphantina is clarified and a key to genera is provided. An annotated list of the genera and species of Ecphantina is given. Moreover, the correct name of the subfamily Coptacridinae is Coptacrinae Brunner von Wattenwyl, 1893. PMID:27395214

  4. Schizosaccharomyces pombe pfh1+ Encodes an Essential 5′ to 3′ DNA Helicase That Is a Member of the PIF1 Subfamily of DNA Helicases

    PubMed Central

    Zhou, Jin-Qiu; Qi, Haiyan; Schulz, Vincent P.; Mateyak, Maria K.; Monson, Ellen K.; Zakian, Virginia A.

    2002-01-01

    The Saccharomyces cerevisiae Pif1p DNA helicase is the prototype member of a helicase subfamily conserved from yeast to humans. S. cerevisiae has two PIF1-like genes, PIF1 itself and RRM3, that have roles in maintenance of telomeric, ribosomal, and mitochondrial DNA. Here we describe the isolation and characterization of pfh1+, a Schizosaccharomyces pombe gene that encodes a Pif1-like protein. Pfh1p was the only S. pombe protein with high identity to Saccharomyces Pif1p. Unlike the two S. cerevisiae Pif1 subfamily proteins, the S. pombe Pfh1p was essential. Like Saccharomyces Pif1p, a truncated form of the S. pombe protein had 5′ to 3′ DNA helicase activity. Point mutations in an invariant lysine residue in the ATP binding pocket of Pfh1p had the same phenotype as deleting pfh1+, demonstrating that the ATPase/helicase activity of Pfh1p was essential. Although mutant spores depleted for Pfh1p proceeded through S phase, they arrested with a terminal cellular phenotype consistent with a postinitiation defect in DNA replication. Telomeric DNA was modestly shortened in the absence of Pfh1p. However, genetic analysis demonstrated that maintenance of telomeric DNA was not the sole essential function of S. pombe Pfh1p. PMID:12058079

  5. Mutations in CGI-58, the gene encoding a new protein of the esterase/lipase/thioesterase subfamily, in Chanarin-Dorfman syndrome.

    PubMed

    Lefèvre, C; Jobard, F; Caux, F; Bouadjar, B; Karaduman, A; Heilig, R; Lakhdar, H; Wollenberg, A; Verret, J L; Weissenbach, J; Ozgüc, M; Lathrop, M; Prud'homme, J F; Fischer, J

    2001-11-01

    Chanarin-Dorfman syndrome (CDS) is a rare autosomal recessive form of nonbullous congenital ichthyosiform erythroderma (NCIE) that is characterized by the presence of intracellular lipid droplets in most tissues. We previously localized a gene for a subset of NCIE to chromosome 3 (designated "the NCIE2 locus"), in six families. Lipid droplets were found in five of these six families, suggesting a diagnosis of CDS. Four additional families selected on the basis of a confirmed diagnosis of CDS also showed linkage to the NCIE2 locus. Linkage-disequilibrium analysis of these families, all from the Mediterranean basin, allowed us to refine the NCIE2 locus to an approximately 1.3-Mb region. Candidate genes from the interval were screened, and eight distinct mutations in the recently identified CGI-58 gene were found in 13 patients from these nine families. The spectrum of gene variants included insertion, deletion, splice-site, and point mutations. The CGI-58 protein belongs to a large family of proteins characterized by an alpha/beta hydrolase fold. CGI-58 contains three sequence motifs that correspond to a catalytic triad found in the esterase/lipase/thioesterase subfamily. Interestingly, CGI-58 differs from other members of the esterase/lipase/thioesterase subfamily in that its putative catalytic triad contains an asparagine in place of the usual serine residue. PMID:11590543

  6. Revision of the monogenean subfamily Thoracocotylinae price, 1936 (Polyopisthocotylea: Thoracocotylidae), with the description of a new species of the genus Pseudothoracocotyla Yamaguti, 1963.

    PubMed

    Hayward, C J; Rohde, K

    1999-11-01

    Members of the subfamily Thoracocotylinae are gastrocotylid monogeneans of Spanish mackerels (scombrid fishes of the genus Scomberomorus) from warm to warm-temperate seas around the world. We revise the diagnosis of the subfamily and recognise two genera and three species as valid. The genus Paradawesia Bravo Hollis & Lamothe Argumedo, 1976 is synonymised with Thoracocotyle MacCallum, 1913, and Dawesia Unnithan, 1965 and Methoracocotyle Lebedev, 1984 are synonymised with Pseudothoracocotyla Yamaguti, 1963. Thoracocotyle crocea MacCallum, 1913 (syns T. paradoxica Meserve, 1938 and Paradawesia bychowskyi Bravo Hollis & Lamothe Argumedo, 1976) is recorded from two species of Scomberomorus in the eastern Pacific (California to Peru) and four in the western Atlantic (South Carolina to Brazil). Pseudothoracocotyla ovalis (Tripathi, 1956) Yamaguti, 1963 (new syns Dawesia indica Unnithan, 1965, D. incisa Lebedev, 1970, Methoracocotyle scomberomori (Young, 1968) Lebedev, 1984, M. gigantica (Rohde, 1976) Lebedev, 1984 and Thoracotyle indica (Unnithan, 1965) Murugesh, 1995) is recorded from the gills of seven species of Scomberomorus from the Indo-west Pacific (eastern South Africa north to the Persian Gulf, and east to Fiji). Pseudothoracocotyla whittingtoni n. sp. is described from an eighth Indo-west Pacific scomberomorid, S. munroi, in Australian waters.

  7. 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. PMID:24520157

  8. 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.

  9. The CC-NBS-LRR Subfamily in Pinus monticola: Targeted Identification, Gene Expression, and Genetic Linkage with Resistance to Cronartium ribicola.

    PubMed

    Liu, Jun-Jun; Ekramoddoullah, Abul K M

    2007-06-01

    ABSTRACT To investigate disease resistance gene analogs (RGAs) encoding coiled-coil-nucelotide-binding site-leucine-rich repeats (CC-NBS-LRR) proteins in western white pine, degenerate primers targeting the conserved motifs in the NBS domain were designed to amplify RGAs from genomic DNA and cDNA. Sixty-one distinct RGAs were identified with identities to well-known R proteins of the CC-NBS-LRR subfamily. These RGAs exhibited variation of putative amino acid sequences from 13% to 98%, representing a complex CC-NBS-LRR subfamily. A phylogenetic tree constructed from the amino acid sequence alignment revealed that these 61 RGAs were grouped with other CC-NBS-LRR members from angiosperms, and could be further divided into six classes with an identity threshold of 68%. To map RGAs, RGA polymorphisms and a modified amplified fragment length polymorphism (AFLP) method with incorporated sequences from the NBS domain were used to reveal NBS or NBS-AFLP markers. RGA polymorphism study revealed that three off the identified RGAs were not linked to the Cr2 gene imparting resistance to white pine blister rust. However, the AFLP strategy, using bulk segregant analysis (BSA) and haploid segregation analysis, identified 11 NBS-AFLP markers localized in the Cr2 linkage, the closest two to the gene being 0.41 cM and 1.22 cM away at either side. Eight of these markers showed significant amino acid sequence homologies with RGAs. PMID:18943604

  10. iDPF-PseRAAAC: A Web-Server for Identifying the Defensin Peptide Family and Subfamily Using Pseudo Reduced Amino Acid Alphabet Composition.

    PubMed

    Zuo, Yongchun; Lv, Yang; Wei, Zhuying; Yang, Lei; Li, Guangpeng; Fan, Guoliang

    2015-01-01

    Defensins as one of the most abundant classes of antimicrobial peptides are an essential part of the innate immunity that has evolved in most living organisms from lower organisms to humans. To identify specific defensins as interesting antifungal leads, in this study, we constructed a more rigorous benchmark dataset and the iDPF-PseRAAAC server was developed to predict the defensin family and subfamily. Using reduced dipeptide compositions were used, the overall accuracy of proposed method increased to 95.10% for the defensin family, and 98.39% for the vertebrate subfamily, which is higher than the accuracy from other methods. The jackknife test shows that more than 4% improvement was obtained comparing with the previous method. A free online server was further established for the convenience of most experimental scientists at http://wlxy.imu.edu.cn/college/biostation/fuwu/iDPF-PseRAAAC/index.asp. A friendly guide is provided to describe how to use the web server. We anticipate that iDPF-PseRAAAC may become a useful high-throughput tool for both basic research and drug design. PMID:26713618

  11. Ligation of members of the beta 1 or the beta 2 subfamilies of integrins by antibodies triggers eosinophil respiratory burst and spreading.

    PubMed Central

    Laudanna, C; Melotti, P; Bonizzato, C; Piacentini, G; Boner, A; Serra, M C; Berton, G

    1993-01-01

    Eosinophils interact with extracellular matrix proteins and endothelial cells through adhesion proteins belonging to the beta 1 and beta 2 subfamilies of integrins. Extending previous observations, we found that tumour necrosis factor (TNF) and granulocyte-macrophage colony-stimulating factor stimulated generation of superoxide anion by eosinophils plated on fibronectin-coated surfaces. As studies with adherent neutrophils indicated that TNF might act as activating leucocyte integrins to deliver signals involved in activation of cell functions, we investigated the effects of monoclonal antibodies (mAb) directed against VLA-4 (CD49d/CD29), LFA-1 (CD11a/CD18), CR3 (CD11b/CD18) or the common beta 2 subunit (CD18) on generation of eosinophil toxic oxygen molecules and spreading. We show that cross-linking of members of both the beta 1 and the beta 2 integrin subfamilies triggers eosinophil respiratory burst and spreading. Evidence for the selectivity of anti-integrin mAb effects is derived from the findings that isotype-matched mAb of other specificities (anti-class I MHC Ag, anti-beta 2-microglobulin, anti-CD4) did not trigger eosinophil functions. The findings presented in this paper suggest that integrin-dependent, eosinophil adhesion in sites of allergic reaction may be accompanied by release of toxic oxygen molecules involved in tissue damage. Images Figure 6 PMID:7903278

  12. 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.

  13. 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.

  14. iDPF-PseRAAAC: A Web-Server for Identifying the Defensin Peptide Family and Subfamily Using Pseudo Reduced Amino Acid Alphabet Composition

    PubMed Central

    Zuo, Yongchun; Lv, Yang; Wei, Zhuying; Yang, Lei; Li, Guangpeng; Fan, Guoliang

    2015-01-01

    Defensins as one of the most abundant classes of antimicrobial peptides are an essential part of the innate immunity that has evolved in most living organisms from lower organisms to humans. To identify specific defensins as interesting antifungal leads, in this study, we constructed a more rigorous benchmark dataset and the iDPF-PseRAAAC server was developed to predict the defensin family and subfamily. Using reduced dipeptide compositions were used, the overall accuracy of proposed method increased to 95.10% for the defensin family, and 98.39% for the vertebrate subfamily, which is higher than the accuracy from other methods. The jackknife test shows that more than 4% improvement was obtained comparing with the previous method. A free online server was further established for the convenience of most experimental scientists at http://wlxy.imu.edu.cn/college/biostation/fuwu/iDPF-PseRAAAC/index.asp. A friendly guide is provided to describe how to use the web server. We anticipate that iDPF-PseRAAAC may become a useful high-throughput tool for both basic research and drug design. PMID:26713618

  15. Revision of the subfamily Opiinae (Hymenoptera, Braconidae) from Hunan (China), including thirty-six new species and two new genera

    PubMed Central

    Li, Xi-Ying; van Achterberg, Cornelis; Tan, Ji-Cai

    2013-01-01

    Abstract The species of the subfamily Opiinae (Hymenoptera: Braconidae) from Hunan (Oriental China) are revised and illustrated. Thirty-six new species are described: Apodesmia bruniclypealis Li & van Achterberg, sp. n., Apodesmia melliclypealis Li & van Achterberg, sp. n., Areotetes albiferus Li & van Achterberg, sp. n., Areotetes carinuliferus Li & van Achterberg, sp. n., Areotetes striatiferus Li & van Achterberg, sp. n., Coleopioides diversinotum Li & van Achterberg, sp. n., Coleopioides postpectalis Li & van Achterberg, sp. n., Fopius dorsopiferus Li, van Achterberg & Tan, sp. n., Indiopius chenae Li & van Achterberg, sp. n., Opiognathus aulaciferus Li & van Achterberg, sp. n., Opiognathus brevibasalis Li & van Achterberg, sp. n., Opius crenuliferus Li & van Achterberg, sp. n., Opius malarator Li, van Achterberg & Tan, sp. n., Opius monilipalpis Li & van Achterberg, sp. n., Opius pachymerus Li & van Achterberg, sp. n., Opius songi Li & van Achterberg, sp. n., Opius youi Li & van Achterberg, sp. n., Opius zengi Li & van Achterberg, sp. n., Phaedrotoma acuticlypeata Li & van Achterberg, sp. n., Phaedrotoma angiclypeata Li & van Achterberg, sp. n., Phaedrotoma antenervalis Li & van Achterberg, sp. n., Phaedrotoma depressiclypealis Li & van Achterberg, sp. n., Phaedrotoma flavisoma Li & van Achterberg, sp. n., Phaedrotoma nigrisoma Li & van Achterberg, sp. n., Phaedrotoma protuberator Li & van Achterberg, sp. n., Phaedrotoma rugulifera Li & van Achterberg, sp. n., Li & van Achterberg,Phaedrotoma striatinota Li & van Achterberg, sp. n., Phaedrotoma vermiculifera Li & van Achterberg, sp. n., Rhogadopsis latipennis Li & van Achterberg, sp. n., Rhogadopsis longicaudifera Li & van Achterberg, sp. n., Rhogadopsis maculosa Li, van Achterberg & Tan, sp. n., Rhogadopsis obliqua Li & van Achterberg, sp. n., Rhogadopsis sculpturator Li & van Achterberg, sp. n., Utetes longicarinatus Li & van Achterberg, sp. n. and Xynobius notauliferus Li & van Achterberg, sp. n. Areotetes

  16. 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.

  17. 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

  18. Morphological features, ecology, and distribution of poorly studied molluscan genera of the Colinae subfamily (Bastropoda, Buccinidae) from the far eastern seas of Russia

    NASA Astrophysics Data System (ADS)

    Kosyan, A. R.

    2007-08-01

    Data on the distribution of six genera of poorly studied buccinids of the Colinae subfamily (Neogastropoda, Buccinidae), namely, Colus Röding, 1799; Plicifusus Dall, 1902; Retifusus Dall, 1916; Aulacofusus Dall, 1918; Pararetifusus Kosuge, 1967; and Latisipo Dall, 1916, are presented. These mollusks are widely spread in the North Pacific region dwelling predominantly over loose sediments in a wide range of sea depths. Based on the morphology and contents of their digestive tracts, it is assumed that the representatives of the genera studied are predators with diverse diets. It is supposed that the increase in the dwelling depths had no significant influence on the feeding ecology of the species studied. Meanwhile, the lower abundance of preys at greater depths caused the lower population densities and modifications in the proboscis structure of selected taxa.

  19. 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

  20. In planta biocatalysis screen of P450s identifies 8-methoxypsoralen as a substrate for the CYP82C subfamily, yielding original chemical structures.

    PubMed

    Kruse, Tanya; Ho, Kwongling; Yoo, Hye-Dong; Johnson, Thomas; Hippely, Matt; Park, Joon-Hyun; Flavell, Richard; Bobzin, Steve

    2008-02-01

    An in vivo plant screen that allows for the analysis of exogenously applied substrates against transgenic Arabidopsis lines overexpressing individual cytochrome P450s has been developed. By deploying this screen with a subset of 91 P450s, we have identified an original substrate for members of the CYP82C subfamily. The therapeutic compound 8-methoxypsoralen was hydroxylated by plants overexpressing CYP82C2 or CYP82C4, forming 5-hydroxy-8-methoxypsoralen. Additionally, plants further modified this product to create a glycosylated compound, likely the compound 5-O-beta-D-glucopyranosyl-8-methoxypsoralen. The discovery of adducts of therapeutic compounds demonstrates the potential of this biocatalysis screening approach to create compounds that may be of pharmacological value. Additionally, this platform provides a means to expand the general knowledge base of P450 enzyme/substrate combinations and may provide valuable tools for a vast array of biocatalytic and bioremediation processes. PMID:18291319

  1. The target gene of tae-miR164, a novel NAC transcription factor from the NAM subfamily, negatively regulates resistance of wheat to stripe rust.

    PubMed

    Feng, Hao; Duan, Xiaoyuan; Zhang, Qiong; Li, Xiaorui; Wang, Bing; Huang, Lili; Wang, Xiaojie; Kang, Zhensheng

    2014-04-01

    microRNA (miRNA) participates in various physiological and biochemical processes in plants by regulating corresponding target genes. NAC [NAM (no apical meristem), ATAF (Arabidopsis transcription activation factor) and CUC (cup-shaped cotyledon)] transcription factors, usually as the targets of miR164, play important roles in the regulation of plant development and responses to abiotic and biotic stresses. In a previous study, the target gene of tae-miR164 in wheat was sequenced through degradome sequencing. In this study, we isolated the full-length cDNA of the candidate target gene, which is a NAC transcription factor gene in the NAM subfamily, and designated it as TaNAC21/22 after bioinformatics analysis. The interaction between TaNAC21/22 and tae-miR164 was confirmed experimentally through co-transformation of both genes in tobacco leaves. Transcript accumulation of TaNAC21/22 and tae-miR164 showed contrasting divergent expression patterns in wheat response to Puccinia striiformis f. sp. tritici (Pst). TaNAC21/22 was confirmed to be located in the nucleus and could function as a transcriptional activator. Silencing of the individual gene showed that TaNAC21/22 negatively regulates resistance to stripe rust. These results indicate that the target of tae-miR164, a novel NAC transcription factor from the NAM subfamily of wheat, plays an important role in regulating the resistance of host plants to stripe rust.

  2. Two-stage gene assembly/cloning of a member of the TspDTI subfamily of bifunctional restriction endonucleases, TthHB27I.

    PubMed

    Krefft, Daria; Zylicz-Stachula, Agnieszka; Mulkiewicz, Ewa; Papkov, Aliaksei; Jezewska-Frackowiak, Joanna; Skowron, Piotr M

    2015-01-20

    The Thermus sp. family of bifunctional type IIS/IIG/IIC restriction endonucleases (REase)-methyltransferases (MTase) comprises thermo-stable TaqII, TspGWI, TspDTI, TsoI, Tth111II/TthHB27I enzymes as well as a number of putative enzymes/open reading frames (ORFs). All of the family members share properties including a large protein size (ca. 120kDa), amino acid (aa) sequence homologies, enzymatic activity modulation by S-adenosylmethionine (SAM), recognition of similar asymmetric cognate DNA sites and cleavage at a distance of 11/9 nt. Analysis of the enzyme aa sequences and domain/motif organisation led to further Thermus sp. family division into the TspDTI and TspGWI subfamilies. The latter exhibits an unprecedented phenomenon of DNA recognition change upon substitution of SAM by its analogue, sinefungin (SIN), towards a very frequent DNA cleavage. We report cloning in Escherichia coli (E. coli), using a two-stage procedure and a putative tthHB27IRM gene, detected by bioinformatics analysis of the Thermus thermophilus HB27 (T. thermophilus) genome. The functionality of a 3366 base pair (bp)-/1121 aa-long, high GC content ORF was validated experimentally through the expression in E. coli. Protein features corroborated with the reclassification of TthHB27I into the TspDTI subfamily, which manifested in terms of aa-sequence/motif homologies and insensitivity to SIN-induced specificity shift. However, both SAM and SIN stimulated the REase DNA cleavage activity by at least 16-32 times; the highest was observed for the Thermus sp. family. The availability of TthHB27I and the need to include SAM or SIN in the reaction in order to convert the enzyme from "hibernation" status to efficient DNA cleavage is of practical significance in molecular biotechnology, extending the palette of available REase specificities.

  3. 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

  4. Have giant lobelias evolved several times independently? Life form shifts and historical biogeography of the cosmopolitan and highly diverse subfamily Lobelioideae (Campanulaceae)

    PubMed Central

    2009-01-01

    Background The tendency of animals and plants to independently develop similar features under similar evolutionary pressures - convergence - is a widespread phenomenon in nature. In plants, convergence has been suggested to explain the striking similarity in life form between the giant lobelioids (Campanulaceae, the bellflower family) of Africa and the Hawaiian Islands. Under this assumption these plants would have developed the giant habit from herbaceous ancestors independently, in much the same way as has been suggested for the giant senecios of Africa and the silversword alliance of Hawaii. Results Phylogenetic analyses based on plastid (rbcL, trnL-F) and nuclear (internal transcribed spacer [ITS]) DNA sequences for 101 species in subfamily Lobelioideae demonstrate that the large lobelioids from eastern Africa the Hawaiian Islands, and also South America, French Polynesia and southeast Asia, form a strongly supported monophyletic group. Ancestral state reconstructions of life form and distribution, taking into account phylogenetic uncertainty, indicate their descent from a woody ancestor that was probably confined to Africa. Molecular dating analyses using Penalized Likelihood and Bayesian relaxed clock approaches, and combining multiple calibration points, estimate their first diversification at ~25-33 million years ago (Ma), shortly followed by several long-distance dispersal events that resulted in the current pantropical distribution. Conclusion These results confidently show that lobelioid species, commonly called 'giant', are very closely related and have not developed their giant form from herbaceous ancestors independently. This study, which includes the hitherto largest taxon sampling for subfamily Lobelioideae, highlights the need for a broad phylogenetic framework for testing assumptions about morphological development in general, and convergent evolution in particular. PMID:19941635

  5. Brother of the regulator of the imprinted site (BORIS) variant subfamily 6 is involved in cervical cancer stemness and can be a target of immunotherapy.

    PubMed

    Asano, Takuya; Hirohashi, Yoshihiko; Torigoe, Toshihiko; Mariya, Tasuku; Horibe, Ryota; Kuroda, Takafumi; Tabuchi, Yuta; Saijo, Hiroshi; Yasuda, Kazuyo; Mizuuchi, Masahito; Takahashi, Akari; Asanuma, Hiroko; Hasegawa, Tadashi; Saito, Tsuyoshi; Sato, Noriyuki

    2016-03-01

    Cervical cancer is a major cause of cancer death in females worldwide. Cervical cancer stem-like cells (CSCs)/cancer-initiating cells (CICs) are resistant to conventional radiotherapy and chemotherapy, and CSCs/CICs are thought to be responsible for recurrence. Eradication of CSCs/CICs is thus essential to cure cervical cancer. In this study, we isolated cervical CSCs/CICs by sphere culture, and we identified a cancer testis (CT) antigen, CTCFL/BORIS, that is expressed in cervical CSCs/CICs. BORIS has 23 mRNA isoform variants classified by 6 subfamilies (sfs), and they encode 17 different BORIS peptides. BORIS sf1 and sf4 are expressed in both CSCs/CICs and non-CSCs/CICs, whereas BORIS sf6 is expressed only in CSCs/CICs. Overexpression of BORIS sf6 in cervical cancer cells increased sphere formation and tumor-initiating ability compared with those in control cells, whereas overexpression of BORIS sf1 and BORIS sf4 resulted in only slight increases. Thus, BORIS sf6 is a cervical CSC/CIC-specific subfamily and has a role in the maintenance of cervical CSCs/CICs. BORIS sf6 contains a specific c-terminal domain (C34), and we identified a human leukocyte antigen (HLA)-A2-restricted antigenic peptide, BORIS C34_24(9) encoded by BORIS sf6. A BORIS C34_24(9)-specific cytotoxic T cell (CTL) clone showed cytotoxicity for BORIS sf6-overexpressing cervical cancer cells. Furthermore, the CTL clone significantly suppressed sphere formation of CaSki cells. Taken together, the results indicate that the CT antigen BORIS sf6 is specifically expressed in cervical CSCs/CICs, that BORIS sf6 has a role in the maintenance of CSCs/CICs, and that BORIS C34_24(9) peptide is a promising candidate for cervical CSC/CIC-targeting immunotherapy. PMID:26849232

  6. 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.

  7. Crystal structure of perakine reductase, founding member of a novel aldo-keto reductase (AKR) subfamily that undergoes unique conformational changes during NADPH binding.

    PubMed

    Sun, Lianli; Chen, Yixin; Rajendran, Chitra; Mueller, Uwe; Panjikar, Santosh; Wang, Meitian; Mindnich, Rebekka; Rosenthal, Cindy; Penning, Trevor M; Stöckigt, Joachim

    2012-03-30

    Perakine reductase (PR) catalyzes the NADPH-dependent reduction of the aldehyde perakine to yield the alcohol raucaffrinoline in the biosynthetic pathway of ajmaline in Rauvolfia, a key step in indole alkaloid biosynthesis. Sequence alignment shows that PR is the founder of the new AKR13D subfamily and is designated AKR13D1. The x-ray structure of methylated His(6)-PR was solved to 2.31 Å. However, the active site of PR was blocked by the connected parts of the neighbor symmetric molecule in the crystal. To break the interactions and obtain the enzyme-ligand complexes, the A213W mutant was generated. The atomic structure of His(6)-PR-A213W complex with NADPH was determined at 1.77 Å. Overall, PR folds in an unusual α(8)/β(6) barrel that has not been observed in any other AKR protein to date. NADPH binds in an extended pocket, but the nicotinamide riboside moiety is disordered. Upon NADPH binding, dramatic conformational changes and movements were observed: two additional β-strands in the C terminus become ordered to form one α-helix, and a movement of up to 24 Å occurs. This conformational change creates a large space that allows the binding of substrates of variable size for PR and enhances the enzyme activity; as a result cooperative kinetics are observed as NADPH is varied. As the founding member of the new AKR13D subfamily, PR also provides a structural template and model of cofactor binding for the AKR13 family. PMID:22334702

  8. Brother of the regulator of the imprinted site (BORIS) variant subfamily 6 is involved in cervical cancer stemness and can be a target of immunotherapy

    PubMed Central

    Asano, Takuya; Hirohashi, Yoshihiko; Torigoe, Toshihiko; Mariya, Tasuku; Horibe, Ryota; Kuroda, Takafumi; Tabuchi, Yuta; Saijo, Hiroshi; Yasuda, Kazuyo; Mizuuchi, Masahito; Takahashi, Akari; Asanuma, Hiroko; Hasegawa, Tadashi; Saito, Tsuyoshi; Sato, Noriyuki

    2016-01-01

    Cervical cancer is a major cause of cancer death in females worldwide. Cervical cancer stem-like cells (CSCs)/cancer-initiating cells (CICs) are resistant to conventional radiotherapy and chemotherapy, and CSCs/CICs are thought to be responsible for recurrence. Eradication of CSCs/CICs is thus essential to cure cervical cancer. In this study, we isolated cervical CSCs/CICs by sphere culture, and we identified a cancer testis (CT) antigen, CTCFL/BORIS, that is expressed in cervical CSCs/CICs. BORIS has 23 mRNA isoform variants classified by 6 subfamilies (sfs), and they encode 17 different BORIS peptides. BORIS sf1 and sf4 are expressed in both CSCs/CICs and non-CSCs/CICs, whereas BORIS sf6 is expressed only in CSCs/CICs. Overexpression of BORIS sf6 in cervical cancer cells increased sphere formation and tumor-initiating ability compared with those in control cells, whereas overexpression of BORIS sf1 and BORIS sf4 resulted in only slight increases. Thus, BORIS sf6 is a cervical CSC/CIC-specific subfamily and has a role in the maintenance of cervical CSCs/CICs. BORIS sf6 contains a specific c-terminal domain (C34), and we identified a human leukocyte antigen (HLA)-A2-restricted antigenic peptide, BORIS C34_24(9) encoded by BORIS sf6. A BORIS C34_24(9)-specific cytotoxic T cell (CTL) clone showed cytotoxicity for BORIS sf6-overexpressing cervical cancer cells. Furthermore, the CTL clone significantly suppressed sphere formation of CaSki cells. Taken together, the results indicate that the CT antigen BORIS sf6 is specifically expressed in cervical CSCs/CICs, that BORIS sf6 has a role in the maintenance of CSCs/CICs, and that BORIS C34_24(9) peptide is a promising candidate for cervical CSC/CIC-targeting immunotherapy. PMID:26849232

  9. 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

  10. 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.

  11. Regulation of Protease-activated Receptor 1 Signaling by the Adaptor Protein Complex 2 and R4 Subfamily of Regulator of G Protein Signaling Proteins*

    PubMed Central

    Chen, Buxin; Siderovski, David P.; Neubig, Richard R.; Lawson, Mark A.; Trejo, JoAnn

    2014-01-01

    The G protein-coupled protease-activated receptor 1 (PAR1) is irreversibly proteolytically activated by thrombin. Hence, the precise regulation of PAR1 signaling is important for proper cellular responses. In addition to desensitization, internalization and lysosomal sorting of activated PAR1 are critical for the termination of signaling. Unlike most G protein-coupled receptors, PAR1 internalization is mediated by the clathrin adaptor protein complex 2 (AP-2) and epsin-1, rather than β-arrestins. However, the function of AP-2 and epsin-1 in the regulation of PAR1 signaling is not known. Here, we report that AP-2, and not epsin-1, regulates activated PAR1-stimulated phosphoinositide hydrolysis via two different mechanisms that involve, in part, a subset of R4 subfamily of “regulator of G protein signaling” (RGS) proteins. A significantly greater increase in activated PAR1 signaling was observed in cells depleted of AP-2 using siRNA or in cells expressing a PAR1 420AKKAA424 mutant with defective AP-2 binding. This effect was attributed to AP-2 modulation of PAR1 surface expression and efficiency of G protein coupling. We further found that ectopic expression of R4 subfamily members RGS2, RGS3, RGS4, and RGS5 reduced activated PAR1 wild-type signaling, whereas signaling by the PAR1 AKKAA mutant was minimally affected. Intriguingly, siRNA-mediated depletion analysis revealed a function for RGS5 in the regulation of signaling by the PAR1 wild type but not the AKKAA mutant. Moreover, activation of the PAR1 wild type, and not the AKKAA mutant, induced Gαq association with RGS3 via an AP-2-dependent mechanism. Thus, AP-2 regulates activated PAR1 signaling by altering receptor surface expression and through recruitment of RGS proteins. PMID:24297163

  12. Regulation of protease-activated receptor 1 signaling by the adaptor protein complex 2 and R4 subfamily of regulator of G protein signaling proteins.

    PubMed

    Chen, Buxin; Siderovski, David P; Neubig, Richard R; Lawson, Mark A; Trejo, Joann

    2014-01-17

    The G protein-coupled protease-activated receptor 1 (PAR1) is irreversibly proteolytically activated by thrombin. Hence, the precise regulation of PAR1 signaling is important for proper cellular responses. In addition to desensitization, internalization and lysosomal sorting of activated PAR1 are critical for the termination of signaling. Unlike most G protein-coupled receptors, PAR1 internalization is mediated by the clathrin adaptor protein complex 2 (AP-2) and epsin-1, rather than β-arrestins. However, the function of AP-2 and epsin-1 in the regulation of PAR1 signaling is not known. Here, we report that AP-2, and not epsin-1, regulates activated PAR1-stimulated phosphoinositide hydrolysis via two different mechanisms that involve, in part, a subset of R4 subfamily of "regulator of G protein signaling" (RGS) proteins. A significantly greater increase in activated PAR1 signaling was observed in cells depleted of AP-2 using siRNA or in cells expressing a PAR1 (420)AKKAA(424) mutant with defective AP-2 binding. This effect was attributed to AP-2 modulation of PAR1 surface expression and efficiency of G protein coupling. We further found that ectopic expression of R4 subfamily members RGS2, RGS3, RGS4, and RGS5 reduced activated PAR1 wild-type signaling, whereas signaling by the PAR1 AKKAA mutant was minimally affected. Intriguingly, siRNA-mediated depletion analysis revealed a function for RGS5 in the regulation of signaling by the PAR1 wild type but not the AKKAA mutant. Moreover, activation of the PAR1 wild type, and not the AKKAA mutant, induced Gαq association with RGS3 via an AP-2-dependent mechanism. Thus, AP-2 regulates activated PAR1 signaling by altering receptor surface expression and through recruitment of RGS proteins. PMID:24297163

  13. The Atypical Response Regulator Protein ChxR Has Structural Characteristics and Dimer Interface Interactions That Are Unique within the OmpR/PhoB Subfamily*

    PubMed Central

    Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Hu, Lei; Middaugh, C. Russell; Hefty, P. Scott

    2011-01-01

    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 α-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. PMID:21775428

  14. 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...

  15. 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.

  16. 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

  17. The ligand-binding domains of the thyroid hormone/retinoid receptor gene subfamily function in vivo to mediate heterodimerization, gene silencing, and transactivation.

    PubMed Central

    Qi, J S; Desai-Yajnik, V; Greene, M E; Raaka, B M; Samuels, H H

    1995-01-01

    The ligand-binding domains (LBDs) of the thyroid/retinoid receptor gene subfamily contain a series of heptad motifs important for dimeric interactions. This subfamily includes thyroid hormone receptors (T3Rs), all-trans retinoic acid (RA) receptors (RARs), 9-cis RA receptors (RARs and retinoid X receptors [RXRs]), the 1,25-dihydroxyvitamin D3 receptor (VDR), and the receptors that modulate the peroxisomal beta-oxidation pathway (PPARs). These receptors bind to their DNA response elements in vitro as heterodimers with the RXRs. Unliganded receptors in vivo, in particular the T3Rs, can mediate gene silencing and ligand converts these receptors into a transcriptionally active form. The in vivo interactions of these receptors with RXR were studied by using a GAL4-RXR chimera containing the yeast GAL4 DNA-binding domain and the LBD of RXR beta. GAL4-RXR activates transcription from GAL4 response elements in the presence of 9-cis RA. Unliganded T3R, which does not bind or activate GAL4 elements, represses the activation of GAL4-RXR by 9-cis RA in HeLa cells. However, addition of T3 alone leads to transcriptional activation. These findings suggest that T3R can repress or activate transcription while tethered to the LBD of GAL4-RXR and that heterodimerization can occur in vivo without stabilization by hormone response elements. Similar ligand-dependent activation was observed in HeLa cells expressing RAR, VDR, or PPAR and in GH4C1 cells from endogenous receptors. Replacement of the last 17 amino acids of the LBD of RXRbeta with the 90-amino-acid transactivating domain of the herpes simplex virus VP16 protein leads to a GAL4 constitutive activator that is repressed by wild-type T3R but not by a ninth heptad mutant that does not form heterodimers. This finding suggests that the ninth heptad or T3R is important for gene silencing and that the LBD of RXR does not exhibit silencing activity. This conclusion was verified with GAL4-LBD chimeras and with wild-type receptors in

  18. 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

  19. 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

    2016-01-01

    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. PMID:27394276

  20. Bile acids of snakes of the subfamily Viperinae and the biosynthesis of C-23-hydroxylated bile acids in liver homogenate fractions from the adder, Vipera berus (Linn.).

    PubMed Central

    Ikawa, S; Tammar, A R

    1976-01-01

    1. Analysis of bile salts of four snakes of the subfamily Viperinae showed that their bile acids consisted mainly of C-23-hydroxylated bile acids. 2. Incubations of 14C-labelled sodium cholate (3 alpha, 7 alpha, 12 alpha-trihydroxy-5 beta-cholan-24-oate) and deoxycholate (3 alpha, 12 alpha-dihydroxy-5 beta-cholan-24-oate) with whole and fractionated adder liver homogenates were carried out in the presence of molecular oxygen and NADPH or an NADPH-generating system. The formation of C-23-hydroxylated bile acids, namely bitocholic acid (3 alpha, 12 alpha, 23xi-trihydroxy-5 beta-cholan-24-oic acid) and 3 alpha, 7 alpha, 12 alpha, 23 xi-tetrahydroxy-cholanic acid (3 alpha, 7 alpha, 12 alpha, 23 xi-tetrahydroxy-5 beta-cholan-24-oic acid), was observed mainly in the microsomal fraction and partly in the mitochondrial fraction. 3. Biosynthetic pathways of C-23-hydroxylated bile acids are discussed. PMID:6007

  1. Analysis of the formation of flower shapes in wild species and cultivars of tree peony using the MADS-box subfamily gene.

    PubMed

    Shu, Qingyan; Wang, Liangsheng; Wu, Jie; Du, Hui; Liu, Zheng'an; Ren, Hongxu; Zhang, Jingjing

    2012-02-01

    Tree peony (Paeonia suffricotisa) cultivars have a unique character compared with wild species; the stamen petalody results in increased whorls of petals and generates different flower forms, which are one of the most important traits for cultivar classification. In order to investigate how petaloid stamens are formed, we obtained the coding sequence (666 bp) and genomic DNA sequence of the PsTM6 genes (belongs to B subfamily of MADS-box gene family) from 23 tree peony samples, Five introns and six exons consisted of the genomic DNA sequence. The analysis of cis-acting regulatory elements in the third and fourth intron indicated that they were highly conserved in all samples. Partial putative amino acids were analyzed and the results suggested that functional differentiation of PsTM6 paralogs apparently affected stamen petalody and flower shape formation due to due to amino acid substitution caused by differences in polarity and electronic charge. Sliding window analysis indicated that the different regions of PsTM6 were subjected to different selection forces, especially in the K domain. This is the first attempt to investigate genetic control of the stamen petalody based on the PsTM6 sequence. This will provide a basis for understanding the evolution of PsTM6 and its the function of in determining stamen morphology of tree peony.

  2. 3,4-diaminobenzoic acid derivatives as inhibitors of the oxytocinase subfamily of M1 aminopeptidases with immune-regulating properties.

    PubMed

    Papakyriakou, Athanasios; Zervoudi, Efthalia; Tsoukalidou, Sofia; Mauvais, Francois-Xavier; Sfyroera, Georgia; Mastellos, Dimitrios C; van Endert, Peter; Theodorakis, Emmanuel A; Vourloumis, Dionisios; Stratikos, Efstratios

    2015-02-12

    Members of the oxytocinase subfamily of M1 aminopeptidases (ERAP1, ERAP2, and IRAP) play important roles in both the adaptive and innate human immune responses. Their enzymatic activity can contribute to the pathogenesis of several major human diseases ranging from viral and parasitic infections to autoimmunity and cancer. We have previously demonstrated that diaminobenzoic acid derivatives show promise as selective inhibitors for this group of aminopeptidases. In this study, we have thoroughly explored a series of 3,4-diaminobenzoic acid derivatives as inhibitors of this class of enzymes, achieving submicromolar inhibitors for ERAP2 (IC50 = 237 nM) and IRAP (IC50 = 105 nM). Cell-based analysis indicated that the lead compounds can be effective in downregulating macrophage activation induced by lipopolysaccharide and interferon-γ as well as cross-presentation by bone marrow-derived dendritic cells. Our results indicate that this class of inhibitors may be useful for the targeted downregulation of immune responses.

  3. GintABC1 encodes a putative ABC transporter of the MRP subfamily induced by Cu, Cd, and oxidative stress in Glomus intraradices.

    PubMed

    González-Guerrero, Manuel; Benabdellah, Karim; Valderas, Ascensión; Azcón-Aguilar, Concepción; Ferrol, Nuria

    2010-02-01

    A full-length cDNA sequence putatively encoding an ATP-binding cassette (ABC) transporter (GintABC1) was isolated from the extraradical mycelia of the arbuscular mycorrhizal fungus Glomus intraradices. Bioinformatic analysis of the sequence indicated that GintABC1 encodes a 1513 amino acid polypeptide, containing two six-transmembrane clusters (TMD) intercalated with sequences characteristics of the nucleotide binding domains (NBD) and an extra N-terminus extension (TMD0). GintABC1 presents a predicted TMD0-(TMD-NBD)(2) topology, typical of the multidrug resistance-associated protein subfamily of ABC transporters. Gene expression analyses revealed no difference in the expression levels of GintABC1 in the extra- vs the intraradical mycelia. GintABC1 was up-regulated by Cd and Cu, but not by Zn, suggesting that this transporter might be involved in Cu and Cd detoxification. Paraquat, an oxidative agent, also induced the transcription of GintABC1. These data suggest that redox changes may be involved in the transcriptional regulation of GintABC1 by Cd and Cu.

  4. 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.

  5. Physical mapping of 18S and 5S rDNA loci and histone H3 gene in grasshopper species of the subfamily Gomphocerinae (Acrididae).

    PubMed

    Silva-Neto, L C; Bernardino, A C S; Loreto, V; Moura, R C

    2015-01-01

    In this study, fluorescence in situ hybridization (FISH) analysis was used to determine and compare the numbers and chromosomal locations of two multigene families (rDNA and histone H3) in four Neotropical species of gomphocerine grasshoppers. FISH using the 18S rDNA probe identified a single site on the S9 chromosome of Amblytropidia sp and Cauratettix borelli, a single site on chromosome M6 of Compsacris pulcher, and two sites (chromosomes L1 and L2) in Orphulella punctata. By contrast, FISH with a 5S rDNA probe identified dispersion of this sequence in the genomes of the four species, with evidence of intraspecific variations. Amblytropidia sp had six to eight FISH signals on autosomal chromosomes, while C. pulcher exhibited a signal only on the M5 bivalent. The histone H3 gene was less variable and was restricted to a single pair in all species. The conservation of the numbers and locations of 18S rDNA and H3 genes in conjunction with data from the literature was useful for evaluating karyotype evolution in this subfamily. The variation in the number and sizes of 5S rDNA sites indicates a process of recent dispersion that might have been mediated by transposition. PMID:26634462

  6. First record of the ant subfamily Aenictinae (Hymenoptera, Formicidae) from Saudi Arabia, with the description of a new species.

    PubMed

    Sharaf, Mostafa R; Aldawood, Abdulrahman S; El-Hawagry, Magdi S

    2012-01-01

    The ant subfamily Aenictinae is recorded for the first time from the Kingdom of Saudi Arabia and for the second time from the Arabian Peninsula. A new species Aenictus arabicussp. n., is described from the worker caste. Aenictus arabicus belongs to the Aenictus wroughtonii-group and appears to be most closely related to Aenictus rhodiensis Menozzi, but can be easily distinguished from the latter by the following characters: overall smaller size; cephalic index (head width/head length) small; occipital corners in lateral view rounded; antennal scape when laid back surpassing approximately two-thirds of head length; funicular segments 2-8 each at least 2× as long as broad; subpetiolar process well developed; petiole and postpetiole distinctly imbricate; gaster and clypeus entirely yellow, teeth of mandibles reddish- brown. Aenictus arabicus was collected from leaf litter, next to a tree of Psidium guajava L. The new species also is similar to Aenictus sagei and Aenictus wroughtonii. Affinities and a key to related species of the species group are given. PMID:23166469

  7. 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.

  8. Application of molecular modeling to analysis of inhibition of kinesin motor proteins of the BimC subfamily by monastrol and related compounds.

    PubMed

    Bevan, David R; Garst, James F; Osborne, Caroline K; Sims, Angela M

    2005-11-01

    Application of molecular modeling approaches has potential to contribute to rational drug design. These approaches may be especially useful when attempting to elucidate the structural features associated with novel drug targets. In this study, molecular docking and molecular dynamics were applied to studies of inhibition of the human motor protein denoted HsEg5 and other homologues in the BimC subfamily. These proteins are essential for mitosis, so compounds that inhibit their activity may have potential as anticancer therapeutics. The discovery of a small-molecule cell-permeable inhibitor, monastrol, has stimulated research in this area. Interestingly, monastrol is reported to inhibit the human and Xenopus forms of Eg5, but not those from Drosophila and Aspergillus. In this study, homology modeling was used to generate models of the Xenopus, Drosophila, and Aspergillus homologues, using the crystal structure of the human protein in complex with monastrol as a template. A series of known inhibitors was docked into each of the homologues, and the differences in binding energies were consistent with reported experimental data. Molecular dynamics revealed significant changes in the structure of the Aspergillus homologue that may contribute to its relative insensitivity to monastrol and related compounds. PMID:17191952

  9. 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

    2016-01-01

    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. PMID:27394469

  10. 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

  11. 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

  12. The assassin bug subfamily Tribelocephalinae (Hemiptera: Heteroptera: Reduviidae) from Japan, with descriptions of eight new species in the genera Opistoplatys and Abelocephala.

    PubMed

    Ishikawa, Tadashi; Cai, Wanzhi; Tomokuni, Masaaki

    2015-01-01

    We examined the Japanese species of the reduviid subfamily Tribelocephalinae. We identified two species of Opistoplatys Westwood, which is the genus with the second largest number of species, and six species of Abelocephala Maldonado, which to date has been referred to as a monotypic genus. All the identified species represent new species and they are described herein under the following names: Opistoplatys minimus sp. nov., Opistoplatys flavolineatus sp. nov., Abelocephala albula sp. nov., Abelocephala araiorum sp. nov., Abelocephala nakatai sp. nov., Abelocephala yaeyamensis sp. nov., Abelocephala major sp. nov., and Abelocephala longiceps sp. nov. Species of Abelocephala can be distinguished from each other based on multiple morphological characters such as body length, ratio of the length to the width of the head, color of the posterior pronotal lobe, shading and pattern of color in the hemelytral basal part, and acuteness or roundness in the apical angle of the outer (larger) cell on the hemelytral membranes. We confirmed that the Japanese tribelocephalines are ground inhabitants living under and within the forest leaf litter. Our results inferred that species of Opistoplatys have positive phototaxis but generally move by walking, whereas species of Abelocephala have negative phototaxis but frequently fly above the forest floor. PMID:25947429

  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. Physical mapping of 18S and 5S rDNA loci and histone H3 gene in grasshopper species of the subfamily Gomphocerinae (Acrididae).

    PubMed

    Silva-Neto, L C; Bernardino, A C S; Loreto, V; Moura, R C

    2015-11-25

    In this study, fluorescence in situ hybridization (FISH) analysis was used to determine and compare the numbers and chromosomal locations of two multigene families (rDNA and histone H3) in four Neotropical species of gomphocerine grasshoppers. FISH using the 18S rDNA probe identified a single site on the S9 chromosome of Amblytropidia sp and Cauratettix borelli, a single site on chromosome M6 of Compsacris pulcher, and two sites (chromosomes L1 and L2) in Orphulella punctata. By contrast, FISH with a 5S rDNA probe identified dispersion of this sequence in the genomes of the four species, with evidence of intraspecific variations. Amblytropidia sp had six to eight FISH signals on autosomal chromosomes, while C. pulcher exhibited a signal only on the M5 bivalent. The histone H3 gene was less variable and was restricted to a single pair in all species. The conservation of the numbers and locations of 18S rDNA and H3 genes in conjunction with data from the literature was useful for evaluating karyotype evolution in this subfamily. The variation in the number and sizes of 5S rDNA sites indicates a process of recent dispersion that might have been mediated by transposition.

  15. Four carcinoembryonic antigen subfamily members, CEA, NCA, BGP and CGM2, selectively expressed in the normal human colonic epithelium, are integral components of the fuzzy coat.

    PubMed

    Frängsmyr, L; Baranov, V; Hammarström, S

    1999-01-01

    To elucidate which of the seven transcriptionally active genes of the carcinoembryonic antigen (CEA) subfamily are expressed in human colon, we first examined mRNA expression using reverse transcriptase PCR. The result showed the CEA, nonspecific crossreacting antigen 50/90 (NCA), biliary glycoprotein (BGP), and carcinoembryonic antigen gene family member 2 (CGM2) mRNAs were expressed in the colon. To determine the cellular sources of these members within normal colonic mucosa, in situ hybridization and immunocytochemistry were then performed. CEA and NCA mRNAs were clearly detectable in the cytoplasm of columnar and goblet cells at the free luminal surface and the upper crypts with low hybridization in the mid crypt and the crypt base. In contrast, BGP and CGM2 mRNAs were restricted only to columnar cells at the upper third of the crypts and the luminal surface. Colon epithelium expression of CEA, NCA, BGP and CGM2 coincided with that of corresponding mRNAs. Ultrastructurally, CEA, NCA, BGP and CGM2 were localized mainly to the apical surface glycocalyx, the fuzzy coat, of columnar cells. Interestingly, these molecules were localized in different microdomains within the fuzzy coat. Furthermore, BGP was highly expressed in the fuzzy coat of cryptal caveolated cells. As integral components of the fuzzy coat, CEA, NCA, BGP and CGM2 can hardly function as intercellular adhesion molecules; they possibly play an important role in epithelial-microbial interactions.

  16. Newly identified motifs in Candida albicans Cdr1 protein nucleotide binding domains are pleiotropic drug resistance subfamily-specific and functionally asymmetric

    PubMed Central

    Rawal, Manpreet Kaur; Banerjee, Atanu; Shah, Abdul Haseeb; Khan, Mohammad Firoz; Sen, Sobhan; Saxena, Ajay Kumar; Monk, Brian C.; Cannon, Richard D.; Bhatnagar, Rakesh; Mondal, Alok Kumar; Prasad, Rajendra

    2016-01-01

    An analysis of Candida albicans ABC transporters identified conserved related α-helical sequence motifs immediately C-terminal of each Walker A sequence. Despite the occurrence of these motifs in ABC subfamilies of other yeasts and higher eukaryotes, their roles in protein function remained unexplored. In this study we have examined the functional significance of these motifs in the C. albicans PDR transporter Cdr1p. The motifs present in NBD1 and NBD2 were subjected to alanine scanning mutagenesis, deletion, or replacement of an entire motif. Systematic replacement of individual motif residues with alanine did not affect the function of Cdr1p but deletion of the M1-motif in NBD1 (M1-Del) resulted in Cdr1p being trapped within the endoplasmic reticulum. In contrast, deletion of the M2-motif in NBD2 (M2-Del) yielded a non-functional protein with normal plasma membrane localization. Replacement of the motif in M1-Del with six alanines (M1-Ala) significantly improved localization of the protein and partially restored function. Conversely, replacement of the motif in M2-Del with six alanines (M2-Ala) did not reverse the phenotype and susceptibility to antifungal substrates of Cdr1p was unchanged. Together, the M1 and M2 motifs contribute to the functional asymmetry of NBDs and are important for maturation of Cdr1p and ATP catalysis, respectively. PMID:27251950

  17. 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

  18. 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.

  19. Improvement of the cellular quality of cryopreserved bovine blastocysts accompanied by enhancement of the ATP-binding cassette sub-family B member 1 expression.

    PubMed

    Mori, Miyuki; Kasa, Shojiro; Isozaki, Yoshihiro; Kamori, Tsugumitsu; Yamaguchi, Shoichiro; Ueda, Shuji; Kuwano, Toshio; Eguchi, Minako; Isayama, Keishiro; Nishimura, Shotaro; Tabata, Shoji; Yamauchi, Nobuhiko; Hattori, Masa-aki

    2013-01-01

    The ATP-binding cassette sub-family B member 1 (ABCB1) plays a critical role in maintaining the metabolic capability of cells as an efflux transporter that pumps xenobiotics out of cells. We investigated the effects of highly expressed ABCB1 on the development and viability of cryopreserved bovine embryos. The ABCB1 level in cultured bovine embryos was decreased during development to blastocyst-stage compared to germinal vesicle- and second metaphase-stage oocytes. When bovine embryos were cultured with forskolin and/or rifampicin, the ABCB1 level was significantly increased in blastocysts but embryo development was not significantly improved. After embryo cryopreservation, highly ABCB1-expressed blastocysts exhibited significant increases in viability and hatching rates. The high viability of the cryopreserved blastocysts was accompanied by a significant increase in cell proliferation during culture for 48 h. Thus, ABCB1 is expressed in bovine oocytes and embryos, and the cellular quality of bovine blastocysts is improved by the enhancement of ABCB1 expression. PMID:23164983

  20. An ethoxyquin-inducible aldehyde reductase from rat liver that metabolizes aflatoxin B1 defines a subfamily of aldo-keto reductases.

    PubMed

    Ellis, E M; Judah, D J; Neal, G E; Hayes, J D

    1993-11-01

    Protection of liver against the toxic and carcinogenic effects of aflatoxin B1 (AFB1) can be achieved through the induction of detoxification enzymes by chemoprotectors such as the phenolic antioxidant ethoxyquin. We have cloned and sequenced a cDNA encoding an aldehyde reductase (AFB1-AR), which is expressed in rat liver in response to dietary ethoxyquin. Expression of the cDNA in Escherichia coli and purification of the recombinant enzyme reveals that the protein exhibits aldehyde reductase activity and is capable of converting the protein-binding dialdehyde form of AFB1-dihydrodiol to the nonbinding dialcohol metabolite. We show that the mRNA encoding this enzyme is markedly elevated in the liver of rats fed an ethoxyquin-containing diet, correlating with acquisition of resistance to AFB1. AFB1-AR represents the only carcinogen-metabolizing aldehyde reductase identified to date that is induced by a chemoprotector. Alignment of the amino acid sequence of AFB1-AR with other known and putative aldehyde reductases shows that it defines a subfamily within the aldo-keto reductase superfamily. PMID:8234296

  1. The human CYP2F gene subfamily: Identification of a cDNA encoding a new cytochrome P450, cDNA-directed expression, and chromosome mapping

    SciTech Connect

    Nhamburo, P.T.; Kimura, Shioko; McBride, O.W.; Kozak, C.A.; Gelboin, H.V.; Gonzalez, F.J. )

    1990-06-12

    A cDNA coding for a P450, designated IIF1, was isolated from a human lung {lambda}gt11 library by screening with a human IIC9 cDNA probe. The cDNA-encoded IIF1 protein had 491 amino acids and a calculated molecular weight of 55,507. IIF1 cDNA, expressed by using a vaccinia virus vector, produced a cytochrome with a {lambda}{sub max} of 454 nm when reduced and complexed with carbon monoxide. This enzyme was able to dealkylate ethoxycoumarin, propoxycoumarin, and pentoxyresorufin but possessed no activity toward ethoxyresorufin and only trace dearylation activity toward benzyloxyresorufin. A variant cDNA, designated IIF1v, was isolated that was identical with IIF1 except for the loss of two segments of 161 and 388 bp within the cDNA coding region. Two mRNAs, consistent with the predicted size of the IIF1 and IIF1v transcripts, were found at very low abundance in lung specimens by Northern blot analysis. A 2-kb transcript, hybridizing with the human IIF1, was also detected as an abundant mRNA in rat lung. The CYP2F gene subfamily was localized to human chromosome 19 and mouse chromosome 7. On the basis of southern blotting analysis with multiple restriction enzymes, the authors conclude that the CYP2F1 gene is flanked by a second highly similar gene.

  2. The mammalian Rab family of small GTPases: definition of family and subfamily sequence motifs suggests a mechanism for functional specificity in the Ras superfamily.

    PubMed

    Pereira-Leal, J B; Seabra, M C

    2000-08-25

    The Rab/Ypt/Sec4 family forms the largest branch of the Ras superfamily of GTPases, acting as essential regulators of vesicular transport pathways. We used the large amount of information in the databases to analyse the mammalian Rab family. We defined Rab-conserved sequences that we designate Rab family (RabF) motifs using the conserved PM and G motifs as "landmarks". The Rab-specific regions were used to identify new Rab proteins in the databases and suggest rules for nomenclature. Surprisingly, we find that RabF regions cluster in and around switch I and switch II regions, i.e. the regions that change conformation upon GDP or GTP binding. This finding suggests that specificity of Rab-effector interaction cannot be conferred solely through the switch regions as is usually inferred. Instead, we propose a model whereby an effector binds to RabF (switch) regions to discriminate between nucleotide-bound states and simultaneously to other regions that confer specificity to the interaction, possibly Rab subfamily (RabSF) specific regions that we also define here. We discuss structural and functional data that support this model and its general applicability to the Ras superfamily of proteins.

  3. 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

    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.

  4. 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

    2013-06-01

    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. PMID:23528250

  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. 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.

  7. Nuclear receptor subfamily 4, group A, member 1 inhibits extrinsic apoptosis and reduces caspase-8 activity in H2O2-induced human HUC-F2 fibroblasts

    PubMed Central

    Shimizu, Yuri; Miyakura, Reiko; Otsuka, Yuzuru

    2015-01-01

    Objective: Apoptosis is characterized by distinct morphological and biochemical changes that occur upon activation of a family of serine proteases known as caspases. Reactive oxygen species (ROS) induce apoptosis in many cell systems. Nuclear receptor subfamily 4, group A, member 1 (NR4A1) has been shown to induce apoptosis in a number of cell lineages, but can also paradoxically act as a death inhibitory factor. In the current study, we focused on the potential role of NR4A1 in hydrogen peroxide (H2O2)-induced apoptosis of normal human umbilical cord fibroblast (HUC-F2) cells. Methods: Growth of HUC-F2 cells treated with H2O2 was measured by MTT assay. Analysis of gene expression was performed with a STEP ONE PLUS Real Time PCR system. Inactivation of NR4A1 was treated with siRNA. Apoptosis was measured by Beckman Coulter flow cytometer after inhibition of NR4A1 with siRNA and H2O2 treatment. Caspase -3, -8 and -9 was measured by caspase assay kit. Results: H2O2 treatment led to enhanced NR4A1 expression. Moreover inhibition of NR4A1 with specific siRNA in HUC-F2 cells triggered an increase in apoptosis and caspase-8 and -3 activities following the addition of H2O2. Discussion: Our results collectively suggest that NR4A1 is a regulator that inhibits extrinsic apoptosis in HUC-F2 cells during oxidative stress through reduction of caspase-8 and -3 activities. PMID:25330024

  8. 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. PMID:27169863

  9. 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

    2016-01-01

    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

  10. The compromised recognition of turnip crinkle virus1 subfamily of microrchidia ATPases regulates disease resistance in barley to biotrophic and necrotrophic pathogens.

    PubMed

    Langen, Gregor; von Einem, Sabrina; Koch, Aline; Imani, Jafargholi; Pai, Subhash B; Manohar, Murli; Ehlers, Katrin; Choi, Hyong Woo; Claar, Martina; Schmidt, Rebekka; Mang, Hyung-Gon; Bordiya, Yogendra; Kang, Hong-Gu; Klessig, Daniel F; Kogel, Karl-Heinz

    2014-02-01

    MORC1 and MORC2, two of the seven members of the Arabidopsis (Arabidopsis thaliana) Compromised Recognition of Turnip Crinkle Virus1 subfamily of microrchidia Gyrase, Heat Shock Protein90, Histidine Kinase, MutL (GHKL) ATPases, were previously shown to be required in multiple layers of plant immunity. Here, we show that the barley (Hordeum vulgare) MORCs also are involved in disease resistance. Genome-wide analyses identified five MORCs that are 37% to 48% identical on the protein level to AtMORC1. Unexpectedly, and in clear contrast to Arabidopsis, RNA interference-mediated knockdown of MORC in barley resulted in enhanced basal resistance and effector-triggered, powdery mildew resistance locus A12-mediated resistance against the biotrophic powdery mildew fungus (Blumeria graminis f. sp. hordei), while MORC overexpression decreased resistance. Moreover, barley knockdown mutants also showed higher resistance to Fusarium graminearum. Barley MORCs, like their Arabidopsis homologs, contain the highly conserved GHKL ATPase and S5 domains, which identify them as members of the MORC superfamily. Like AtMORC1, barley MORC1 (HvMORC1) binds DNA and has Mn2+-dependent endonuclease activities, suggesting that the contrasting function of MORC1 homologs in barley versus Arabidopsis is not due to differences in their enzyme activities. In contrast to AtMORCs, which are involved in silencing of transposons that are largely restricted to pericentromeric regions, barley MORC mutants did not show a loss-of-transposon silencing regardless of their genomic location. Reciprocal overexpression of MORC1 homologs in barley and Arabidopsis showed that AtMORC1 and HvMORC1 could not restore each other's function. Together, these results suggest that MORC proteins function as modulators of immunity, which can act negatively (barley) or positively (Arabidopsis) dependent on the species. PMID:24390392

  11. 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

  12. Atypical OmpR/PhoB Subfamily Response Regulator GlnR of Actinomycetes Functions as a Homodimer, Stabilized by the Unphosphorylated Conserved Asp-focused Charge Interactions*

    PubMed Central

    Lin, Wei; Wang, Ying; Han, Xiaobiao; Zhang, Zilong; Wang, Chengyuan; Wang, Jin; Yang, Huaiyu; Lu, Yinhua; Jiang, Weihong; Zhao, Guo-Ping; Zhang, Peng

    2014-01-01

    The OmpR/PhoB subfamily protein GlnR of actinomycetes is an orphan response regulator that globally coordinates the expression of genes related to nitrogen metabolism. Biochemical and genetic analyses reveal that the functional GlnR from Amycolatopsis mediterranei is unphosphorylated at the potential phosphorylation Asp50 residue in the N-terminal receiver domain. The crystal structure of this receiver domain demonstrates that it forms a homodimer through the α4-β5-α5 dimer interface highly similar to the phosphorylated typical response regulator, whereas the so-called “phosphorylation pocket” is not conserved, with its space being occupied by an Arg52 from the β3-α3 loop. Both in vitro and in vivo experiments confirm that GlnR forms a functional homodimer via its receiver domain and suggest that the charge interactions of Asp50 with the highly conserved Arg52 and Thr9 in the receiver domain may be crucial in maintaining the proper conformation for homodimerization, as also supported by molecular dynamics simulations of the wild type GlnR versus the deficient mutant GlnR(D50A). This model is backed by the distinct phenotypes of the total deficient GlnR(R52A/T9A) double mutant versus the single mutants of GlnR (i.e. D50N, D50E, R52A and T9A), which have only minor effects upon both dimerization and physiological function of GlnR in vivo, albeit their DNA binding ability is weakened compared with that of the wild type. By integrating the supportive data of GlnRs from the model Streptomyces coelicolor and the pathogenic Mycobacterium tuberculosis, we conclude that the actinomycete GlnR is atypical with respect to its unphosphorylated conserved Asp residue being involved in the critical Arg/Asp/Thr charge interactions, which is essential for maintaining the biologically active homodimer conformation. PMID:24733389

  13. 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

  14. Functional Analysis of the Small Component of the 4-Hydroxyphenylacetate 3-Monooxygenase of Escherichia coli W: a Prototype of a New Flavin:NAD(P)H Reductase Subfamily

    PubMed Central

    Galán, Beatriz; Díaz, Eduardo; Prieto, María A.; García, José L.

    2000-01-01

    Escherichia coli W uses the aromatic compound 4-hydroxyphenylacetate (4-HPA) as a sole source of carbon and energy for growth. The monooxygenase which converts 4-HPA into 3,4-dihydroxyphenylacetate, the first intermediate of the pathway, consists of two components, HpaB (58.7 kDa) and HpaC (18.6 kDa), encoded by the hpaB and hpaC genes, respectively, that form a single transcription unit. Overproduction of the small HpaC component in E. coli K-12 cells has facilitated the purification of the protein, which was revealed to be a homodimer that catalyzes the reduction of free flavins by NADH in preference to NADPH. Subsequently, the reduced flavins diffuse to the large HpaB component or to other electron acceptors such as cytochrome c and ferric ion. Amino acid sequence comparisons revealed that the HpaC reductase could be considered the prototype of a new subfamily of flavin:NAD(P)H reductases. The construction of a fusion protein between the large HpaB oxygenase component and the choline-binding domain of the major autolysin of Streptococcus pneumoniae allowed us to develop a rapid method to efficiently purify this highly unstable enzyme as a chimeric CH-HpaB protein, which exhibited a 4-HPA hydroxylating activity only when it was supplemented with the HpaC reductase. These results suggest the 4-HPA 3-monooxygenase of E. coli W as a representative member of a novel two-component flavin-diffusible monooxygenase (TC-FDM) family. Relevant features on the evolution and structure-function relationships of these TC-FDM proteins are discussed. PMID:10633095

  15. The Compromised Recognition of Turnip Crinkle Virus1 Subfamily of Microrchidia ATPases Regulates Disease Resistance in Barley to Biotrophic and Necrotrophic Pathogens1[C][W][OPEN

    PubMed Central

    Langen, Gregor; von Einem, Sabrina; Koch, Aline; Imani, Jafargholi; Pai, Subhash B.; Manohar, Murli; Ehlers, Katrin; Choi, Hyong Woo; Claar, Martina; Schmidt, Rebekka; Mang, Hyung-Gon; Bordiya, Yogendra; Kang, Hong-Gu; Klessig, Daniel F.; Kogel, Karl-Heinz

    2014-01-01

    MORC1 and MORC2, two of the seven members of the Arabidopsis (Arabidopsis thaliana) Compromised Recognition of Turnip Crinkle Virus1 subfamily of microrchidia Gyrase, Heat Shock Protein90, Histidine Kinase, MutL (GHKL) ATPases, were previously shown to be required in multiple layers of plant immunity. Here, we show that the barley (Hordeum vulgare) MORCs also are involved in disease resistance. Genome-wide analyses identified five MORCs that are 37% to 48% identical on the protein level to AtMORC1. Unexpectedly, and in clear contrast to Arabidopsis, RNA interference-mediated knockdown of MORC in barley resulted in enhanced basal resistance and effector-triggered, powdery mildew resistance locus A12-mediated resistance against the biotrophic powdery mildew fungus (Blumeria graminis f. sp. hordei), while MORC overexpression decreased resistance. Moreover, barley knockdown mutants also showed higher resistance to Fusarium graminearum. Barley MORCs, like their Arabidopsis homologs, contain the highly conserved GHKL ATPase and S5 domains, which identify them as members of the MORC superfamily. Like AtMORC1, barley MORC1 (HvMORC1) binds DNA and has Mn2+-dependent endonuclease activities, suggesting that the contrasting function of MORC1 homologs in barley versus Arabidopsis is not due to differences in their enzyme activities. In contrast to AtMORCs, which are involved in silencing of transposons that are largely restricted to pericentromeric regions, barley MORC mutants did not show a loss-of-transposon silencing regardless of their genomic location. Reciprocal overexpression of MORC1 homologs in barley and Arabidopsis showed that AtMORC1 and HvMORC1 could not restore each other’s function. Together, these results suggest that MORC proteins function as modulators of immunity, which can act negatively (barley) or positively (Arabidopsis) dependent on the species. PMID:24390392

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. World Time (Solar and Sidereal): An Astronomy Teaching Aid.

    ERIC Educational Resources Information Center

    Hutton, Don; Coates, Denis

    1999-01-01

    Describes a simple model that illustrates concepts about time and its relation to terrestrial longitude. The model also simulates the diurnal motion of the sun and moon and their changing positions against the background stars. (Author/WRM)

  1. 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 Central

    Edholm, Eva-Stina; Goyos, Ana; Taran, Joseph; De Jesús Andino, Francisco; Ohta, Yuko; Robert, Jacques

    2014-01-01

    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 X. laevis (allotetraploid) and X. 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 12N. This suggests that the critical role of XNC10 during early T cell development is conserved in amphibians. PMID:24771209

  2. 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.

  3. 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

  4. 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. PMID:25992909

  5. Expression of LINE-1 retroposons is essential for murine preimplantation development.

    PubMed

    Beraldi, Rosanna; Pittoggi, Carmine; Sciamanna, Ilaria; Mattei, Elisabetta; Spadafora, Corrado

    2006-03-01

    In higher eukaryotes, reverse transcriptase (RT) activities are encoded by a variety of endogenous retroviruses and retrotransposable elements. We previously found that mouse preimplantation embryos are endowed with an endogenous RT activity. Inhibition of that activity by the non nucleosidic inhibitor nevirapine or by microinjection of anti-RT antibody caused early embryonic developmental arrest. Those experiments indicated that RT is required for early development, but did not identify the responsible coding elements. We now show that microinjection of morpholino-modified antisense oligonucleotides targeting the 5' end region of active LINE-1 retrotransposons in murine zygotes irreversibly arrests preimplantation development at the two- and four-cell stages; the overall level of functional RT is concomitantly downregulated in arrested embryos. Furthermore, we show that the induction of embryo developmental arrest is associated with a substantial reprogramming of gene expression. Together, these results support the conclusion that expression of LINE-1 retrotransposons is required for early embryo preimplantation development.

  6. 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.

  7. 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

  8. Mouse Macrophages Completely Lacking Rho Subfamily GTPases (RhoA, RhoB, and RhoC) Have Severe Lamellipodial Retraction Defects, but Robust Chemotactic Navigation and Altered Motility*

    PubMed Central

    Königs, Volker; Jennings, Richard; Vogl, Thomas; Horsthemke, Markus; Bachg, Anne C.; Xu, Yan; Grobe, Kay; Brakebusch, Cord; Schwab, Albrecht; Bähler, Martin; Knaus, Ulla G.; Hanley, Peter J.

    2014-01-01

    RhoA is thought to be essential for coordination of the membrane protrusions and retractions required for immune cell motility and directed migration. Whether the subfamily of Rho (Ras homolog) GTPases (RhoA, RhoB, and RhoC) is actually required for the directed migration of primary cells is difficult to predict. Macrophages isolated from myeloid-restricted RhoA/RhoB (conditional) double knock-out (dKO) mice did not express RhoC and were essentially “pan-Rho”-deficient. Using real-time chemotaxis assays, we found that retraction of the trailing edge was dissociated from the advance of the cell body in dKO cells, which developed extremely elongated tails. Surprisingly, velocity (of the cell body) was increased, whereas chemotactic efficiency was preserved, when compared with WT macrophages. Randomly migrating RhoA/RhoB dKO macrophages exhibited multiple small protrusions and developed large “branches” due to impaired lamellipodial retraction. A mouse model of peritonitis indicated that monocyte/macrophage recruitment was, surprisingly, more rapid in RhoA/RhoB dKO mice than in WT mice. In comparison with dKO cells, the phenotypes of single RhoA- or RhoB-deficient macrophages were mild due to mutual compensation. Furthermore, genetic deletion of RhoB partially reversed the motility defect of macrophages lacking the RhoGAP (Rho GTPase-activating protein) myosin IXb (Myo9b). In conclusion, the Rho subfamily is not required for “front end” functions (motility and chemotaxis), although both RhoA and RhoB are involved in pulling up the “back end” and resorbing lamellipodial membrane protrusions. Macrophages lacking Rho proteins migrate faster in vitro, which, in the case of the peritoneum, translates to more rapid in vivo monocyte/macrophage recruitment. PMID:25213860

  9. Investigation of drug-drug interactions caused by human pregnane X receptor-mediated induction of CYP3A4 and CYP2C subfamilies in chimeric mice with a humanized liver.

    PubMed

    Hasegawa, Maki; Tahara, Harunobu; Inoue, Ryo; Kakuni, Masakazu; Tateno, Chise; Ushiki, Junko

    2012-03-01

    The induction of cytochrome P450 (P450) enzymes is one of the risk factors for drug-drug interactions (DDIs). To date, the human pregnane X receptor (PXR)-mediated CYP3A4 induction has been well studied. In addition to CYP3A4, the expression of CYP2C subfamily is also regulated by PXR, and the DDIs caused by the induction of CYP2C enzymes have been reported to have a major clinical impact. The purpose of the present study was to investigate whether chimeric mice with a humanized liver (PXB mice) can be a suitable animal model for investigating the PXR-mediated induction of CYP2C subfamily, together with CYP3A4. We evaluated the inductive effect of rifampicin (RIF), a typical human PXR ligand, on the plasma exposure to the four P450 substrate drugs (triazolam/CYP3A4, pioglitazone/CYP2C8, (S)-warfarin/CYP2C9, and (S)-(-)-mephenytoin/CYP2C19) by cassette dosing in PXB mice. The induction of several drug-metabolizing enzymes and transporters in the liver was also examined by measuring the enzyme activity and mRNA expression levels. Significant reductions in the exposure to triazolam, pioglitazone, and (S)-(-)-mephenytoin, but not to (S)-warfarin, were observed. In contrast to the in vivo results, all the four P450 isoforms, including CYP2C9, were elevated by RIF treatment. The discrepancy in the (S)-warfarin results between in vivo and in vitro studies may be attributed to the relatively small contribution of CYP2C9 to (S)-warfarin elimination in the PXB mice used in this study. In summary, PXB mice are a useful animal model to examine DDIs caused by PXR-mediated induction of CYP2C and CYP3A4. PMID:22126990

  10. One-year monitoring of meta-cleavage dioxygenase gene expression and microbial community dynamics reveals the relevance of subfamily I.2.C extradiol dioxygenases in hypoxic, BTEX-contaminated groundwater.

    PubMed

    Táncsics, András; Farkas, Milán; Szoboszlay, Sándor; Szabó, István; Kukolya, József; Vajna, Balázs; Kovács, Balázs; Benedek, Tibor; Kriszt, Balázs

    2013-07-01

    Aromatic hydrocarbons including benzene, toluene, ethyl-benzene, and xylene (BTEX) are frequent contaminants of groundwater, the major drinking water resource. Bioremediation is the only sustainable process to clean up these environments. Microbial degradation of BTEX compounds occurs rapidly under aerobic conditions but, in subsurface environments, the availability of oxygen is commonly restricted. Even so, the microaerobic degradation of aromatic compounds is still poorly understood. Hence, the dynamics of a bacterial community and the expression of meta-cleavage dioxygenase genes, with particular emphasis on subfamily I.2.C extradiol dioxygenase genes, were assessed over a 13-month period in a hypoxic, aromatic hydrocarbon-contaminated shallow groundwater by using sequence-aided terminal-restriction fragment length polymorphism (T-RFLP) and single-nucleotide primer extension (SNuPE), respectively. The bacterial 16S rRNA fingerprinting revealed the predominance of members of Rhodoferax, Azoarcus, Pseudomonas, and unknown bacteria related to Rhodocyclaceae. It was observed that mRNA transcripts of subfamily I.2.C extradiol dioxygenase genes were detected constantly over the monitoring period, and the detected sequences clustered into six distinct clusters. In order to reveal changes in the expression of these clusters over the monitoring period a SNuPE assay was developed. This quasi fingerprinting of functional gene expression provided the opportunity to link the investigated function to specific microbial populations. The results obtained can improve our understanding of aromatic hydrocarbon degradation under oxygen limitation and may benefit bioremediation research by demonstrating the usefulness of SNuPE for the monitoring of microbial populations involved in degradation process.

  11. A single amino acid substitution in IIIf subfamily of basic helix-loop-helix transcription factor AtMYC1 leads to trichome and root hair patterning defects by abolishing its interaction with partner proteins in Arabidopsis.

    PubMed

    Zhao, Hongtao; Wang, Xiaoxue; Zhu, Dandan; Cui, Sujuan; Li, Xia; Cao, Ying; Ma, Ligeng

    2012-04-20

    Plant trichomes and root hairs are powerful models for the study of cell fate determination. In Arabidopsis thaliana, trichome and root hair initiation requires a combination of three groups of proteins, including the WD40 repeat protein transparent TESTA GLABRA1 (TTG1), R2R3 repeat MYB protein GLABRA1 (GL1), or werewolf (WER) and the IIIf subfamily of basic helix-loop-helix (bHLH) protein GLABRA3 (GL3) or enhancer of GLABRA3 (EGL3). The bHLH component acts as a docking site for TTG1 and MYB proteins. Here, we isolated a mutant showing defects in trichome and root hair patterning that carried a point mutation (R173H) in AtMYC1 that encodes the fourth member of IIIf bHLH family protein. Genetic analysis revealed partial redundant yet distinct function between AtMYC1 and GL3/EGL3. GLABRA2 (GL2), an important transcription factor involved in trichome and root hair control, was down-regulated in Atmyc1 plants, suggesting the requirement of AtMYC1 for appropriate GL2 transcription. Like its homologs, AtMYC1 formed a complex with TTG1 and MYB proteins but did not dimerized. In addition, the interaction of AtMYC1 with MYB proteins and TTG1 was abrogated by the R173H substitution in Atmyc1-1. We found that this amino acid (Arg) is conserved in the AtMYC1 homologs GL3/EGL3 and that it is essential for their interaction with MYB proteins and for their proper functions. Our findings indicate that AtMYC1 is an important regulator of trichome and root hair initiation, and they reveal a novel amino acid necessary for protein-protein interactions and gene function in IIIf subfamily bHLH transcription factors.

  12. 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

    2016-01-01

    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

  13. 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

    2016-01-01

    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

  14. Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes.

    PubMed

    Chung, Dae-Hwan; Huddleston, Jennifer R; Farkas, Joel; Westpheling, Janet

    2011-11-01

    Potent HaeIII-like DNA restriction activity was detected in cell-free extracts of Caldicellulosiruptor bescii DSM 6725 using plasmid DNA isolated from Escherichia coli as substrate. Incubation of the plasmid DNA in vitro with HaeIII methyltransferase protected it from cleavage by HaeIII nuclease as well as cell-free extracts of C. bescii. The gene encoding the putative restriction enzyme was cloned and expressed in E. coli with a His-tag at the C-terminus. The purified protein was 38 kDa as predicted by the 981-bp nucleic acid sequence, was optimally active at temperatures between 75°C and 85°C, and was stable for more than 1 week when stored at 35°C. The cleavage sequence was determined to be 5'-GG/CC-3', indicating that CbeI is an isoschizomer of HaeIII. A search of the C. bescii genome sequence revealed the presence of both a HaeIII-like restriction endonuclease (Athe 2438) and DNA methyltransferase (Athe 2437). Preliminary analysis of other Caldicellulosiruptor species suggested that this restriction/modification activity is widespread in this genus. A phylogenetic analysis based on sequence alignment and conserved motif searches identified features of CbeI distinct from other members of this group and classified CbeI as a member of a novel subfamily of HaeIII-like enzymes.

  15. 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

  16. 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

  17. Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs.

    PubMed

    Horton, Amy C; Mahadevan, Navin R; Minguillon, Carolina; Osoegawa, Kazutoyo; Rokhsar, Daniel S; Ruvinsky, Ilya; de Jong, Pieter J; Logan, Malcolm P; Gibson-Brown, Jeremy J

    2008-12-01

    T-box genes encode a family of DNA-binding transcription factors implicated in numerous developmental processes in all metazoans. The Tbx2/3/4/5 subfamily genes are especially interesting because of their key roles in the evolution of vertebrate appendages, eyes, and the heart, and, like the Hox genes, the longevity of their chromosomal linkage. A BAC library derived from the single male amphioxus (Branchiostoma floridae) used to sequence the amphioxus genome was screened for AmphiTbx2/3 and AmphiTbx4/5, yielding two independent clones containing both genes. Using comparative expression, genomic linkage, and phylogenetic analyses, we have reconstructed the evolutionary histories of these members of the T-box gene family. We find that the Tbx2-Tbx4 and Tbx3-Tbx5 gene pairs have maintained tight linkage in most animal lineages since their birth by tandem duplication, long before the divergence of protostomes and deuterostomes (e.g., arthropods and vertebrates) at least 600 million years ago, and possibly before the divergence of poriferans and cnidarians (e.g., sponges and jellyfish). Interestingly, we find that the gene linkage detected in all vertebrate genomes has been maintained in the primitively appendage-lacking, basal chordate, amphioxus. Although all four genes have been involved in the evolution of developmental programs regulating paired fin and (later) limb outgrowth and patterning, and most are also implicated in eye and heart development, linkage maintenance--often considered due to regulatory constraints imposed by limb, eye, and/or heart associated gene expression--is undoubtedly a consequence of other, much more ancient functional constraints. PMID:18815807

  18. The mouse S100A15 ortholog parallels genomic organization, structure, gene expression, and protein-processing pattern of the human S100A7/A15 subfamily during epidermal maturation.

    PubMed

    Wolf, Ronald; Voscopoulos, Christopher J; FitzGerald, Peter C; Goldsmith, Paul; Cataisson, Christophe; Gunsior, Michele; Walz, Markus; Ruzicka, Thomas; Yuspa, Stuart H

    2006-07-01

    The calcium-binding proteins of the human S100A7/A15 (hS100A7/A15) subfamily are differentially expressed in normal and pathological epidermis. The hS100A7 (psoriasin) and S100A15 reside in a chromosomal cluster of highly similar paralogs. To exploit the power of mouse models for determining functions of gene products, the corresponding S100A7/A15 ortholog was cloned and examined in murine skin. The single mouse S100A15 (mS100A15) gene encodes a protein of 104 amino acids with a predicted molecular weight of 12,870 Da and two EF-hand calcium binding sites. Using gene-specific primers and specific antibodies, expression of mS100A15 in both skin and isolated keratinocytes is confined to differentiating granular and cornified epidermal cells. Immunoblotting of epidermal extracts revealed a series of high molecular weight bands that are also recognized by an antibody for transglutaminase-mediated protein crosslinks. mS100A15 expression is upregulated in cultured keratinocytes induced to differentiate by calcium or phorbol esters. Maximal induction occurs concordantly with expression of late differentiation markers. Induction is enhanced in keratinocytes overexpressing protein kinase Calpha and is dependent on activator protein-1 transcription factors. The regulation, expression pattern and crosslinking of mS100A15 are consistent with the characteristics of the human orthologs, providing a valid surrogate model to study changes in these proteins associated with cutaneous pathologies.

  19. Faster clearance of omeprazole in rats with acute renal failure induced by uranyl nitrate: contribution of increased expression of hepatic cytochrome P450 (CYP) 3A1 and intestinal CYP1A and 3A subfamilies.

    PubMed

    Lee, Dae Y; Jung, Young S; Shin, Hyun S; Lee, Inchul; Kim, Young C; Lee, Myung G

    2008-07-01

    It has been reported that omeprazole is mainly metabolized via hepatic cytochrome P450 (CYP) 1A1/2, CYP2D1 and CYP3A1/2 in male Sprague-Dawley rats, and the expression of hepatic CYP3A1 is increased in male Sprague-Dawley rats with acute renal failure induced by uranyl nitrate (U-ARF rats). Thus, the metabolism of omeprazole would be expected to increase in U-ARF rats. After intravenous administration of omeprazole (20 mgkg(-1)) to U-ARF rats, the area under the plasma concentration-time curve from time zero to infinity (AUC) was significantly reduced (371 vs 494 microg min mL(-1)), possibly due to the significantly faster non-renal clearance (56.6 vs 41.2 mL min(-1) kg(-1)) compared with control rats. This could have been due to increased expression of hepatic CYP3A1 in U-ARF rats. After oral administration of omeprazole (40 mgkg(-1)) to U-ARF rats, the AUC was also significantly reduced (89.3 vs 235 microg min mL(-1)) compared with control rats. The AUC difference after oral administration (62.0% decrease) was greater than that after intravenous administration (24.9% decrease). This may have been primarily due to increased intestinal metabolism of omeprazole caused by increased expression of intestinal CYP1A and 3A subfamilies in U-ARF rats, in addition to increased hepatic metabolism.

  20. 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

  1. 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

    Rodriguez, Yacidzohara; Gonzalez-Mendez, Ricardo R; Cadilla, Carmen L

    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 within

  2. 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.

  3. MIR retroposon exonization promotes evolutionary variability and generates species-specific expression of IGF-1 splice variants.

    PubMed

    Annibalini, Giosuè; Bielli, Pamela; De Santi, Mauro; Agostini, Deborah; Guescini, Michele; Sisti, Davide; Contarelli, Serena; Brandi, Giorgio; Villarini, Anna; Stocchi, Vilberto; Sette, Claudio; Barbieri, Elena

    2016-05-01

    Insulin-like growth factor (IGF) -1 is a pleiotropic hormone exerting mitogenic and anti-apoptotic effects. Inclusion or exclusion of exon 5 into the IGF-1 mRNA gives rise to three transcripts, IGF-1Ea, IGF-1Eb and IGF-1Ec, which yield three different C-terminal extensions called Ea, Eb and Ec peptides. The biological significance of the IGF-1 splice variants and how the E-peptides affect the actions of mature IGF-1 are largely unknown. In this study we investigated the origin and conservation of the IGF-1 E-peptides and we compared the pattern of expression of the IGF-1 isoforms in vivo, in nine mammalian species, and in vitro using human and mouse IGF-1 minigenes. Our analysis showed that only IGF-1Ea is conserved among all vertebrates, whereas IGF-1Eb and IGF-1Ec are an evolutionary novelty originated from the exonization of a mammalian interspersed repetitive-b (MIR-b) element. Both IGF-1Eb and IGF-1Ec mRNAs were constitutively expressed in all mammalian species analyzed but their expression ratio varies greatly among species. Using IGF-1 minigenes we demonstrated that divergence in cis-acting regulatory elements between human and mouse conferred species-specific features to the exon 5 region. Finally, the protein-coding sequences of exon 5 showed low rate of synonymous mutations and contain disorder-promoting amino acids, suggesting a regulatory role for these domains. In conclusion, exonization of a MIR-b element in the IGF-1 gene determined gain of exon 5 during mammalian evolution. Alternative splicing of this novel exon added new regulatory elements at the mRNA and protein level potentially able to regulate the mature IGF-1 across tissues and species. PMID:27048986

  4. [Line class retroposon is the component of the DNA polymorphic fragments pattern of trematode Himasthla elongata parthenitae].

    PubMed

    Solov'eva, A I; Galaktionov, N K; Podgornaia, O I

    2013-01-01

    We have determined that S-SAP method (Sequence specific amplification polymorphism) reveals clonal variability in the genomes of larvae of flatworm Himasthla elongata (Trematoda, Echinostomatidae). Being parthenogenetic the larvae were previously considered to be genetically homogeneous. Cloning and sequencing of a -500 bp conservative fragment (B1) from the fragments' pattern has been performed. Sequence analysis of B1 has shown that this fragment has maximum homology with LINE elements from CR1 family of Hydra and sparrow. In situ hybridization (FISH) has detected dispersed distribution of B1. Several other fragments cloned from the same lane of agarose electrophoresis correspond to conservative domain of reverse transcriptase (RT) from CR1 family. Thus, we have shown that 1) cercariae of trematode H. elongata have clonal variability; 2) the S-SAP method allows to obtaining patterns of fragment distribution characteristic of individual cercariae; 3) conservative domain of RT of CR1 family participates in the pattern of polymorphic fragments generation. Identification of the CR1 transcripts in cercariae of H. elongata transcriptome is the aim of the future work. Cloning of the variable fragments from the fragments' pattern is in progress. PMID:25509118

  5. 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

  6. 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.

  7. 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

  8. 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}.

  9. Studies on Neotropical Phasmatodea XVI: Revision of Haplopodini Günther, 1953 (rev. stat.), with notes on the subfamily Cladomorphinae Bradley & Galil, 1977 and the descriptions of a new tribe, four new genera and nine new species (Phasmatodea: "Anareolatae": Phasmatidae: Cladomorphinae).

    PubMed

    Hennemann, Frank H; Conle, Oskar V; Perez-Gelabert, Daniel E

    2016-01-01

    The anareolate New World subfamily Cladomorphinae Bradley & Galil, 1977 is reviewed and keys to the six tribes currently included are presented; these are: Cladomorphini Bradley & Galil, 1977, Cladoxerini Karny, 1923, Cranidiini Günther, 1953, Pterinoxylini n. trib., Hesperophasmatini Bradley & Galil, 1977 and Haplopodini Günther, 1953 rev. stat.. New diagnoses are presented for all these tribes and possible relationships within Cladomorphinae are discusssed. Morphology of the genitalia and egg-structures indicate Cladomorphinae as presently treated to be polyphyletic. Two subordinate groups are recognized within present Cladomorphinae, which differ considerably in numerous morphological characters of the insects and eggs. The first group and here regarded as Cladomorphinae sensu stricto is formed by the mostly South American Cladomorphini + Cranidiini + Cladoxerini, while the second group is formed by the predominantly Caribbean Hesperophasmatini + Pterinoxylini n. trib. + Haplopodini.        Members of the first group (= Cladomorphini sensu stricto) share the dorsally carinate basitarsus in which the two dorsal carinae are melted with another, increasingly elongated gonapophyses VIII of females which are noticeably longer than gonapophyses IX and lamellate as well as strongly displaced medioventral carina of the profemora. Cranidiini + Cladomorphini share the strongly elongated and filiform gonapophyses VIII and presence of gonoplacs in the females, specialized poculum of males and presence of a median line in the eggs. Cranidiini differs from all other tribes of Cladomorphinae by the entirely unarmed legs of both sexes, distinctly broadened and leaf-like body and prominent longitudinal keel of the mesosternum of females, prominently enlarged poculum and spinulose phallus of males as well as the conspicuous narrowing of the posteromedian gap of the internal micropylar plate of the eggs and noticeably separated median line. Cladomorphini is characteristic

  10. Polyphyletic origin of cultivated rice: based on the interspersion pattern of SINEs.

    PubMed

    Cheng, Chaoyang; Motohashi, Reiko; Tsuchimoto, Suguru; Fukuta, Yoshimichi; Ohtsubo, Hisako; Ohtsubo, Eiichi

    2003-01-01

    The wild rice species Oryza rufipogon with wide intraspecific variation is thought to be the progenitor of the cultivated rice species Oryza sativa with two ecotypes, japonica and indica. To determine the origin of cultivated rice, subfamily members of the rice retroposon p-SINE1, which show insertion polymorphism in the O. sativa -O. rufipogon population, were identified and used to "bar code" each of 101 cultivated and wild rice strains based on the presence or absence of the p-SINE1 members at the respective loci. A phylogenetic tree constructed based on the bar codes given to the rice strains showed that O. sativa strains were classified into two groups corresponding to japonica and indica, whereas O. rufipogon strains were in four groups, in which annual O. rufipogon strains formed a single group, differing from the perennial O. rufipogon strains of the other three groups. Japonica strains were closely related to the O. rufipogon perennial strains of one group, and the indica strains were closely related to the O. rufipogon annual strains, indicating that O. sativa has been derived polyphyletically from O. rufipogon. The subfamily members of p-SINE1 constitute a powerful tool for studying the classification and relationship of rice strains, even when one has limited knowledge of morphology, taxonomy, physiology, and biochemistry of rice strains. PMID:12519908

  11. Evolutionary paths of the cAMP-dependent protein kinase (PKA) catalytic subunits.

    PubMed

    Søberg, Kristoffer; Jahnsen, Tore; Rognes, Torbjørn; Skålhegg, Bjørn S; Laerdahl, Jon K

    2013-01-01

    3',5'-cyclic adenosine monophosphate (cAMP) dependent protein kinase or protein kinase A (PKA) has served as a prototype for the large family of protein kinases that are crucially important for signal transduction in eukaryotic cells. The PKA catalytic subunits Cα and Cβ, encoded by the two genes PRKACA and PRKACB, respectively, are among the best understood and characterized human kinases. Here we have studied the evolution of this gene family in chordates, arthropods, mollusks and other animals employing probabilistic methods and show that Cα and Cβ arose by duplication of an ancestral PKA catalytic subunit in a common ancestor of vertebrates. The two genes have subsequently been duplicated in teleost fishes. The evolution of the PRKACG retroposon in simians was also investigated. Although the degree of sequence conservation in the PKA Cα/Cβ kinase family is exceptionally high, a small set of signature residues defining Cα and Cβ subfamilies were identified. These conserved residues might be important for functions that are unique to the Cα or Cβ clades. This study also provides a good example of a seemingly simple phylogenetic problem which, due to a very high degree of sequence conservation and corresponding weak phylogenetic signals, combined with problematic nonphylogenetic signals, is nontrivial for state-of-the-art probabilistic phylogenetic methods. PMID:23593352

  12. Identification and characterization of a member of Rab subfamily, Rab8, from Clonorchis sinensis.

    PubMed

    Liang, Pei; He, Lei; Yu, Jinyun; Xie, Zhizhi; Chen, Xueqing; Mao, Qiang; Liang, Chi; Huang, Yan; Lu, Gang; Yu, Xinbing

    2015-05-01

    The Rabs act as a binary molecular switch that utilizes the conformational changes associated with the GTP/GDP cycle to elicit responses from target proteins. It regulates a broad spectrum of cellular processes including cell proliferation, cytoskeletal assembly, and intracellular membrane trafficking in eukaryotes. The Rab8 from Clonorchis sinensis (CsRab8) was composed of 199 amino acids. The deduced amino acid sequence shared above 50% identities with other species from trematode, tapeworm, mammal, insecta, nematode, and reptile, respectively. The homologous analysis of sequences showed the conservative domains: G1 box (GDSGVGKS), G2 box (T), G3 box (DTAG), G4 box (GNKCDL), and G5 box. In addition, the structure modeling had also shown other functional domains: GTP/Mg(2+) binding sites, switch I region, and switch II region. A phylogenic tree analysis indicated that the CsRab8 was clustered with the Rab from Schistosoma japonicum, and trematode and tapeworm came from the same branch, which was different from an evolutional branch built by other species, such as mammal animal, insecta, nematode, and reptile. The recombinant CsRab8 protein was expressed in Escherichia coli and the purified protein was a soluble molecule by 12% sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis. CsRab8 was identified as a component of excretory/secretory products of C. sinensis by western blot analysis. The transcriptional level of CsRab8 at metacercaria stage was the highest at the four stages and higher by 56.49-folds than that at adult worm, 1.23-folds than that at excysted metacercaria, and 2.69-folds than that at egg stage. Immunohistochemical localization analysis showed that CsRab8 was specifically distributed in the tegument, vitellarium, eggs, and testicle of adult worms, and detected on the vitellarium and tegument of metacercaria. Combined with the results, CsRab8 is indispensable for survival and development of parasites, especially for regulating excretory/secretory products secretion. PMID:25773178

  13. 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.

  14. 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

  15. 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.; 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 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

  16. 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.

  17. CircRNA-protein complexes: IMP3 protein component defines subfamily of circRNPs.

    PubMed

    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

  18. A molecular phylogeny of the orange subfamily(Rutaceae: Aurantioideae) using nine cpDNA sequences.

    PubMed

    Bayer, Randall J; Mabberley, David J; Morton, Cynthia; Miller, Cathy H; Sharma, Ish K; Pfeil, Bernard E; Rich, Sarah; Hitchcock, Roberta; Sykes, Steve

    2009-03-01

    The breeding of new, high-quality citrus cultivars depends on dependable information about the relationships of taxa within the tribe Citreae; therefore, it is important to have a well-supported phylogeny of the relationships between species not only to advance breeding strategies, but also to advance conservation strategies for the wild taxa. The recent history of the systematics of Citrus (Rutaceae: Aurantioideae) and its allies, in the context of Rutaceae taxonomy as a whole, is reviewed. The most recent classification is tested using nine cpDNA sequence regions in representatives of all genera of the subfam. Aurantioideae (save Limnocitrus) and numerous species and hybrids referred to Citrus s.l. Aurantioideae are confirmed as monophyletic. Within Aurantioideae, tribe Clauseneae are not monophyletic unless Murraya s.s. and Merrillia are removed to Aurantieae. Within tribe Aurantieae, the three traditionally recognized subtribes are not monophyletic. Triphasiinae is not monophyletic unless Oxanthera is returned to Citrus (Citrinae). Balsamocitrinae is polyphyletic. Feroniella, traditionally considered allied closely to Limonia (=Feronia), is shown to be nested in Citrus. The proposed congenericity of Severinia and Atalantia is confirmed. The most recent circumscription of Citrus is strongly supported by this analysis, with hybrids appearing with their putative maternal parents. The genus was resolved into two clades, one comprising wild species from New Guinea, Australia, and New Caledonia (formerly Clymenia, Eremocitrus, Microcitrus, Oxanthera), but surprisingly also Citrus medica, traditionally believed to be native in India. The second clade is largely from the Asian mainland (including species formerly referred to Fortunella and Poncirus).

  19. Stability, redox parameters and electrocatalytic activity of a cytochrome domain from a new subfamily.

    PubMed

    Molinas, María F; Benavides, Leandro; Castro, María A; Murgida, Daniel H

    2015-10-01

    We report a spectroscopic, electrochemical and spectroelectrochemical characterization of the soluble cytochrome c domain (Cyt-D) from the Rhodothermus marinus caa3 terminal oxygen reductase and its putative electron donor, a high potential [4Fe-4S] protein (HiPIP). Cyt-D exhibits superior stability, particularly at the level of the heme pocket, compared to archetypical cytochromes in terms of thermal and chemical denaturation, alkaline transition and oxidative bleaching of the heme, which is further increased upon adsorption on biomimetic electrodes. Therefore, this protein is proposed as a suitable building block for electrochemical biosensing. As a proof of concept, we show that the immobilized Cyt-D exhibits good electrocatalytic activity towards H2O2 reduction. Relevant thermodynamic and kinetic electron transfer parameters for Cyt-D and HiPIP are also reported, including reorganization energies of 0.33 eV and 0.42 eV, respectively.

  20. 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 ...

  1. 40 CFR 1037.230 - Vehicle families, sub-families, and configurations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ..., and the total working capacity of vapor storage (as determined under 40 CFR 86.132-96(h)(1)(iv)). You... significantly affect drag areas. Note that this allowance does not apply for substantial differences, even if the vehicles have the same measured drag areas....

  2. 40 CFR 1037.230 - Vehicle families, sub-families, and configurations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... have very small body hardware differences that do not significantly affect drag areas. Note that this allowance does not apply for substantial differences, even if the vehicles have the same measured drag...

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

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... small body hardware differences that do not significantly affect drag areas. Note that this allowance does not apply for substantial differences, even if the vehicles have the same measured drag areas....

  4. Parotocinclus planicauda, a new species of the subfamily Hypoptopomatinae from southeastern Brazil (Ostariophysi: Loricariidae).

    PubMed

    Garavello, J C; Britski, H A

    2003-05-01

    Parotocinclus planicauda, a new species from a tributary of the Doce River drainage in Minas Gerais State, Brazil, is distinguished from all other species of the genus by the presence of a caudal peduncle almost quadrangular in cross section; the anterior position of the adipose fin, close to the dorsal fin insertion; and very small orbits. A key to the Parotocinclus species of eastern Brazilian coastal rivers south of the São Francisco River is provided.

  5. 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.

  6. 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.

  7. 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

    2016-01-01

    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. PMID:27394284

  8. 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.

  9. 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.

  10. 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. 

  11. A new addition to the subfamily Anabropsinae (Orthoptera: Anostostomatidae) from China.

    PubMed

    Shi, Fuming; Bian, Xun

    2016-01-01

    The paper describes one very interesting genus and species, Brevipenna Shi & Bian gen. nov. and B. falcata Shi & Bian sp. nov.. The genus shares similar characters with macropterous genus Pteranabropsis Gorochov, 1988 and apterous or subapterous genus Apteranabropsis Gorochov, 1988 in following: distributed in Asia, presence both tympana, male ninth abdominal tergite with 1 pair of lobes, which continue with the paired hooks of tenth abdominal tergite, and paraproct specialized with 2 long sclerotized processes. The tegmina and hind wings are short, and right and left ones overlapped. Therefore, we conclude the new genus may be intermediate state between the Pteranabropsis and Apteranabropsis. Perhaps, future study will suggest the three genera be combined. All the material is deposited in the Museum of Hebei University. PMID:27394213

  12. Subfamily-Specific Adaptations in the Structures of Two Penicillin-Binding Proteins from Mycobacterium tuberculosis

    PubMed Central

    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

    2014-01-01

    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. PMID:25551456

  13. Subfamily Limoniinae Speiser, 1909 (Diptera, Limoniidae) from Baltic amber (Eocene): the genus Elephantomyia Osten Sacken, 1860.

    PubMed

    Kania, Iwona

    2015-01-01

    A revision of the genus Elephantomyia Osten Sacken (Diptera: Limoniidae) from Baltic amber (Eocene) is presented. Four species--E. baltica Alexander, E. brevipalpa Loew, E. longirostris Loew, and E. pulchella Loew--are redescribed and documented with photographs and drawings. In addition, two new species of the genus are described: Elephantomyia bozenae sp. nov., and Elephantomyia irinae sp. nov. All these fossil species are placed within the subgenus Elephantomyia. A key to the extinct species of Elephantomyia is provided, and the genus' ecological pattern and evolutionary aspects are discussed. PMID:25706127

  14. Subfamily Limoniinae Speiser, 1909 (Diptera, Limoniidae) from Baltic Amber (Eocene): The Genus Elephantomyia Osten Sacken, 1860

    PubMed Central

    Kania, Iwona

    2015-01-01

    A revision of the genus Elephantomyia Osten Sacken (Diptera: Limoniidae) from Baltic amber (Eocene) is presented. Four species—E. baltica Alexander, E. brevipalpa Loew, E. longirostris Loew, and E. pulchella Loew—are redescribed and documented with photographs and drawings. In addition, two new species of the genus are described: Elephantomyia bozenae sp. nov., and Elephantomyia irinae sp. nov. All these fossil species are placed within the subgenus Elephantomyia. A key to the extinct species of Elephantomyia is provided, and the genus’ ecological pattern and evolutionary aspects are discussed. PMID:25706127

  15. 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. PMID:26886069

  16. 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

    2016-01-01

    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.

  17. A new fish species of the subfamily Serraninae (Perciformes, Serranidae) from the Philippines.

    PubMed

    Williams, Jeffrey T; Carpenter, Kent E

    2015-01-01

    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.  PMID:25661613

  18. 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. PMID:12948741

  19. RPT2/NCH1 subfamily of NPH3-like proteins is essential for the chloroplast accumulation response in land plants.

    PubMed

    Suetsugu, Noriyuki; Takemiya, Atsushi; Kong, Sam-Geun; Higa, Takeshi; Komatsu, Aino; Shimazaki, Ken-Ichiro; Kohchi, Takayuki; Wada, Masamitsu

    2016-09-13

    In green plants, the blue light receptor kinase phototropin mediates various photomovements and developmental responses, such as phototropism, chloroplast photorelocation movements (accumulation and avoidance), stomatal opening, and leaf flattening, which facilitate photosynthesis. In Arabidopsis, two phototropins (phot1 and phot2) redundantly mediate these responses. Two phototropin-interacting proteins, NONPHOTOTROPIC HYPOCOTYL 3 (NPH3) and ROOT PHOTOTROPISM 2 (RPT2), which belong to the NPH3/RPT2-like (NRL) family of BTB (broad complex, tramtrack, and bric à brac) domain proteins, mediate phototropism and leaf flattening. However, the roles of NRL proteins in chloroplast photorelocation movement remain to be determined. Here, we show that another phototropin-interacting NRL protein, NRL PROTEIN FOR CHLOROPLAST MOVEMENT 1 (NCH1), and RPT2 redundantly mediate the chloroplast accumulation response but not the avoidance response. NPH3, RPT2, and NCH1 are not involved in the chloroplast avoidance response or stomatal opening. In the liverwort Marchantia polymorpha, the NCH1 ortholog, MpNCH1, is essential for the chloroplast accumulation response but not the avoidance response, indicating that the regulation of the phototropin-mediated chloroplast accumulation response by RPT2/NCH1 is conserved in land plants. Thus, the NRL protein combination could determine the specificity of diverse phototropin-mediated responses. PMID:27578868

  20. 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.

  1. 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.

  2. Phylogenetic analysis of hampala fishes (subfamily Cyprininae) in Malaysia inferred from partial mitochondrial cytochrome B DNA sequences.

    PubMed

    Ryan, Jeffrine R J; Esa, Yuzine B

    2006-10-01

    This study examined 396 base pairs of the mitochondrial cytochrome b gene from 110 individuals belonging to the genus Hampala, a group of freshwater cyprinids that inhabit Southeast Asia. The samples were taken from various locations throughout Sarawak, Sabah, and peninsular Malaysia. The nucleotide sequences were subjected to phylogenetic analyses by using the neighbor-joining, maximum parsimony, and maximum likelihood methods. All three methods revealed the reciprocally monophyletic relationship of Hampala macrolepidota to the other Hampala forms, thus strongly supporting its status as a distinct species. Phylogenetic analysis also discovered the existence of two H. bimaculata lineages endemic to Borneo: (1) a newly identified species from the southern and central part of Sarawak assigned as H. bimaculata Type A and (2) the previously described H. bimaculata from northern Sarawak and the west coast of Sabah assigned as H. bimaculata Type B. However, the status of H. sabana and an intermediate form were not elucidated. The results suggest that the intermediate form from the Tawau population is actually a subpopulation of H. sabana, while the highly divergent intermediate form from Kalabakan could represent a cryptic species. The sharing of H. macrolepidota haplotypes in the southern peninsular Malaysia and southern and central Sarawak samples (Hm1 and Hm2) reflected the recent disconnection of the two regions, during the late Pleistocene. Overall, the partial sequence of the mitochondrial cytochrome b gene was useful for resolving the phylogenetic relationships among Hampala fishes in Malaysia.

  3. Systematic analysis of maize class III peroxidase gene family reveals a conserved subfamily involved in abiotic stress response.

    PubMed

    Wang, Yu; Wang, Qianqian; Zhao, Yang; Han, Guomin; Zhu, Suwen

    2015-07-15

    Class III peroxidases (PRXs) are plant-specific enzymes that play key roles in the responses to biotic and abiotic stress during plant growth and development. In this study, we identified 119 nonredundant PRX genes (designated ZmPRXs). These PRX genes were divided into 18 groups based on their phylogenetic relationships. We performed systematic bioinformatics analysis of the PRX genes, including analysis of gene structures, conserved motifs, phylogenetic relationships and gene expression profiles. The ZmPRXs are unevenly distributed on the 10 maize chromosomes. In addition, these genes have undergone 16 segmental duplication and 12 tandem duplication events, indicating that both segmental and tandem duplication were the main contributors to the expansion of the maize PRX family. Ka/Ks analysis suggested that most duplicated ZmPRXs experienced purifying selection, with limited functional divergence during the duplication events, and comparative analysis among maize, sorghum and rice revealed that there were independent duplication events besides the whole-genome duplication of the maize genome. Furthermore, microarray analysis indicated that most highly expressed genes might play significant roles in root. We examined the expression of five candidate ZmPRXs under H2O2, SA, NaCl and PEG stress conditions using quantitative real-time PCR (qRT-PCR), revealing differential expression patterns. This study provides useful information for further functional analysis of the PRX gene family in maize.

  4. 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.

  5. Molecular insights into the klotho-dependent, endocrine mode of action of fibroblast growth factor 19 subfamily members.

    PubMed

    Goetz, Regina; Beenken, Andrew; Ibrahimi, Omar A; Kalinina, Juliya; Olsen, Shaun K; Eliseenkova, Anna V; Xu, ChongFeng; Neubert, Thomas A; Zhang, Fuming; Linhardt, Robert J; Yu, Xijie; White, Kenneth E; Inagaki, Takeshi; Kliewer, Steven A; Yamamoto, Masaya; Kurosu, Hiroshi; Ogawa, Yasushi; Kuro-o, Makoto; Lanske, Beate; Razzaque, Mohammed S; Mohammadi, Moosa

    2007-05-01

    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/betaKlotho 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 beta1-beta2 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/betaKlotho 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. PMID:17339340

  6. 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

  7. A primate subfamily of galectins expressed at the maternal–fetal interface that promote immune cell death

    PubMed Central

    Than, Nandor Gabor; Romero, Roberto; Goodman, Morris; Weckle, Amy; Xing, Jun; Dong, Zhong; Xu, Yi; Tarquini, Federica; Szilagyi, Andras; Gal, Peter; Hou, Zhuocheng; Tarca, Adi L.; Kim, Chong Jai; Kim, Jung-Sun; Haidarian, Saied; Uddin, Monica; Bohn, Hans; Benirschke, Kurt; Santolaya-Forgas, Joaquin; Grossman, Lawrence I.; Erez, Offer; Hassan, Sonia S.; Zavodszky, Peter; Papp, Zoltan; Wildman, Derek E.

    2009-01-01

    Galectins are proteins that regulate immune responses through the recognition of cell-surface glycans. We present evidence that 16 human galectin genes are expressed at the maternal–fetal interface and demonstrate that a cluster of 5 galectin genes on human chromosome 19 emerged during primate evolution as a result of duplication and rearrangement of genes and pseudogenes via a birth and death process primarily mediated by transposable long interspersed nuclear elements (LINEs). Genes in the cluster are found only in anthropoids, a group of primate species that differ from their strepsirrhine counterparts by having relatively large brains and long gestations. Three of the human cluster genes (LGALS13, -14, and -16) were found to be placenta-specific. Homology modeling revealed conserved three-dimensional structures of galectins in the human cluster; however, analyses of 24 newly derived and 69 publicly available sequences in 10 anthropoid species indicate functional diversification by evidence of positive selection and amino acid replacements in carbohydrate-recognition domains. Moreover, we demonstrate altered sugar-binding capacities of 6 recombinant galectins in the cluster. We show that human placenta-specific galectins are predominantly expressed by the syncytiotrophoblast, a primary site of metabolic exchange where, early during pregnancy, the fetus comes in contact with immune cells circulating in maternal blood. Because ex vivo functional assays demonstrate that placenta-specific galectins induce the apoptosis of T lymphocytes, we propose that these galectins reduce the danger of maternal immune attacks on the fetal semiallograft, presumably conferring additional immune tolerance mechanisms and in turn sustaining hemochorial placentation during the long gestation of anthropoid primates. PMID:19497882

  8. 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).

  9. Analysis of 5S rDNA organization and variation in polyploid hybrids from crosses of different fish subfamilies.

    PubMed

    Qin, Qinbo; He, Weiguo; Liu, Shaojun; Wang, Jing; Xiao, Jun; Liu, Yun

    2010-07-15

    In this article, sequence analysis of the coding region (5S) and adjacent nontranscribed spacer (NTS) were conducted in red crucian carp (RCC), blunt snout bream (BSB), and their polyploid offspring. Three monomeric 5S rDNA classes (designated class I: 203 bp; class II: 340 bp; and class III: 477 bp) of RCC were characterized by distinct NTS types (designated NTS-I, II, and III for the 83, 220, and 357 bp monomers, respectively). In BSB, only one monomeric 5S rDNA was observed (designated class IV: 188 bp), which was characterized by one NTS type (designated NTS-IV: 68 bp). In the polyploid offspring, the tetraploid (4nRB) hybrids partially inherited 5S rDNA classes from their female parent (RCC); however, they also possessed a unique 5S rDNA sequence (designated class I-L: 203 bp) with a novel NTS sequence (designated NTS-I-L: 83 bp). The characteristic paternal 5S rDNA sequences (class IV) were not observed. The 5S rDNA of triploid (3nRB) hybrids was completely inherited from the parental species, and generally preserved the parental 5S rDNA structural organization. These results first revealed the influence of polyploidy on the organization and evolution of the multigene family of 5S rDNA of fish, and are also useful in clarifying aspects of vertebrate genome evolution.

  10. 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. PMID:26023931

  11. 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

  12. 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

  13. 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. 

  14. [Interlineage distribution and characteristics of the structure of two subfamilies of Drosophila melanogaster MDG4 (gypsy) retrotransposon].

    PubMed

    Razorenova, O V; Karpova, N N; Smirnova, Iu B; Kusulidu, L K; Reneva, N K; Subocheva, E A; Kim, A I; Liubomirskaia, N V; Il'in, Iu V

    2001-02-01

    The distribution of two variants of MDG4 (gypsy) was analyzed in several Drosophila melanogaster strains. Southern blot hybridization revealed the inactive variant of MDG4 in all strains examined and active MDG4 only in some of them. Most of the strains harboring the active MDG4 variant were recently isolated from natural populations. It is of interest that the active MDG4 prevailed over the inactive one only in strains carrying the mutant flamenco gene. Several lines were analyzed in more detail. The number of MDG4 sites on salivary-gland polytene chromosomes was established via in situ hybridization, and MDG4 was tested for transposition using the ovoD test. PMID:11253423

  15. Five new feather mites of the subfamily Pterodectinae (Acariformes: Astigmata: Proctophyllodidae) from passerines and hummingbirds (Aves) of Brazil.

    PubMed

    Hernandes, Fabio Akashi; Pedroso, Luiz Gustavo A; Oniki-Willis, Yoshika

    2016-01-01

    Five new species of feather mites (Proctophyllodidae: Pterodectinae) are described from passerines and hummingbirds of Brazil: Amerodectes longifuscus sp. nov. from Poospiza lateralis (Nordmann, 1835) (Passeriformes: Emberizidae), A. vireonis sp. nov. from Vireo olivaceus (Linnaeus, 1766) (Passeriformes: Vireonidae), Tyrannidectes synallaxis sp. nov. from Synallaxis ruficapilla Vieillot, 1819 (Passeriformes: Furnariidae), Trochilodectes willisi sp. nov. from Phaethornis eurynome (Lesson, 1832) (Apodiformes: Trochilidae), and Xynonodectes phaethornis sp. nov. from Ph. pretrei (Lesson & Delattre, 1839) (Apodiformes: Trochilidae). PMID:27615933

  16. 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...

  17. Five new feather mites of the subfamily Pterodectinae (Acariformes: Astigmata: Proctophyllodidae) from passerines and hummingbirds (Aves) of Brazil.

    PubMed

    Hernandes, Fabio Akashi; Pedroso, Luiz Gustavo A; Oniki-Willis, Yoshika

    2016-09-06

    Five new species of feather mites (Proctophyllodidae: Pterodectinae) are described from passerines and hummingbirds of Brazil: Amerodectes longifuscus sp. nov. from Poospiza lateralis (Nordmann, 1835) (Passeriformes: Emberizidae), A. vireonis sp. nov. from Vireo olivaceus (Linnaeus, 1766) (Passeriformes: Vireonidae), Tyrannidectes synallaxis sp. nov. from Synallaxis ruficapilla Vieillot, 1819 (Passeriformes: Furnariidae), Trochilodectes willisi sp. nov. from Phaethornis eurynome (Lesson, 1832) (Apodiformes: Trochilidae), and Xynonodectes phaethornis sp. nov. from Ph. pretrei (Lesson & Delattre, 1839) (Apodiformes: Trochilidae).

  18. 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

  19. 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.

  20. Fructose-1,6-bisphosphate aldolases in amitochondriate protists constitute a single protein subfamily with eubacterial relationships.

    PubMed

    Sánchez, Lidya; Horner, David; Moore, Dorothy; Henze, Katrin; Embley, T; Müller, Miklós

    2002-07-24

    Sequences of putative fructose-1,6-bisphospate aldolases (FBA) in five amitochondriate unicellular eukaryotes, the diplomonads Giardia intestinalis (published earlier) and Spironucleus barkhanus, the pelobiont Mastigamoeba balamuthi,the entamoebid Entamoeba histolytica, and the parabasalid Trichomonas vaginalis all belong to Class II of FBAs and are highly similar to each other (>48% amino acid identity). The five protist sequences, however, do not form a monophyletic group. Diplomonad FBAs share a most recent common ancestor, while FBAs of the three other protist species are part of a lineage that also includes sequences from a few eubacteria (Clostridium difficile, Treponema pallidum, Chlorobium tepidum). Both clades are part of the Type B of Class II aldolases, a complex that contains at least three additional lineages (subgroups) of enzymes. Type B enzymes are distant from Type A Class II aldolases, which consists of a number of bacterial and fungal enzymes and also contains the cytosolic FBA of Euglena gracilis. Class II aldolases are not homologous to Class I enzymes, to which animal and plant enzymes belong. The results indicate that amitochondriate protists acquired their FBAs from separate and different sources, involving lateral gene transfer from eubacteria, than did all other eukaryotes studied so far and underscore the complex composition of the glycolytic machinery in unicellular eukaryotes.

  1. 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.

  2. Molecular Characterization of a Newly Identified Subfamily Member of Penaeidin from two Penaeid Shrimps, Fenneropenaeus indicus and Metapenaeus monoceros.

    PubMed

    Afsal, V V; Antony, Swapna P; Philip, Rosamma; Bright Singh, I S

    2016-03-01

    Penaeidins are a major group of antimicrobial peptides found in penaeid shrimps. This study reports a new isoform of penaeidin from the hemocytes of Indian white shrimp, Fenneropenaeus indicus (Fi-PEN, JX657680), and the pink shrimp, Metapenaeus monoceros (Mm-PEN, KF275674). Mm-PEN is also the first antimicrobial peptide to be identified from M. monoceros. The complete coding sequences of the newly identified Fi-PEN and Mm-PEN consisted of an ORF of 338 bp encoding 71 amino acids with a predicted molecular weight of 5.66 kDa and a pI of 9.38. The penaeidins had its characteristic signal peptide region (19 amino acids), which was followed by a mature peptide with a proline-rich domain (24 amino acids) at the N-terminal region and a cysteine-rich domain (28 amino acids) at the C-terminal region, designating it to penaeidin-3 subgroup. Structural analysis revealed an alpha-helix in its secondary structure and an extended structure at the proline-rich domain. The newly identified penaeidin isoform showed maximum similarity of 63 % to a penaeidin-3 isoform of P. monodon, which further proves it to be a new isoform. Phylogenetic analysis showed that it possessed similar evolutionary status like other penaeidins, which has subsequently diverged at different phases of evolution. The wide distribution of penaeidins in penaeid shrimps indicates the importance of these AMPs in the innate immunity. PMID:26607699

  3. 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.

  4. Three subfamilies of pheromone and receptor genes generate multiple B mating specificities in the mushroom Coprinus cinereus.

    PubMed Central

    Halsall, J R; Milner, M J; Casselton, L A

    2000-01-01

    The B mating type locus of the basidiomycete Coprinus cinereus encodes a large family of lipopeptide pheromones and their seven transmembrane domain receptors. Here we show that the B42 locus, like the previously described B6 locus, derives its unique specificity from nine multiallelic genes that are organized into three subgroups each comprising a receptor and two pheromone genes. We show that the three genes within each group are kept together as a functional unit by being embedded in an allele-specific DNA sequence. Using a combination of sequence analysis, Southern blotting, and DNA-mediated transformation with cloned genes, we demonstrate that different B loci may share alleles of one or two groups of genes. This is consistent with the prediction that the three subgroups of genes are functionally redundant and that it is the different combinations of their alleles that generate the multiple B mating specificities found in nature. The B42 locus was found to contain an additional gene, mfs1, that encodes a putative multidrug transporter belonging to the major facilitator family. In strains with other B mating specificities, this gene, whose functional significance was not established, lies in a region of shared homology flanking the B locus. PMID:10757757

  5. 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.

  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. 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

  8. Crystal structure of 3,4a,7,7,10a-penta­methyl-3-vinyl­dodeca­hydro-1H-benzo[f]chromen-9-ol isolated from Sideritis perfoliata

    PubMed Central

    Çelik, Ísmail; Ersanlı, Cem Cüneyt; Köseoğlu, Rahmi; Akşit, Hüseyin; Erenler, Ramazan; Demirtaş, Ibrahim; Akkurt, Mehmet

    2016-01-01

    The asymmetric unit of the title compound, C20H34O2, contains two crystallographically independent mol­ecules (1 and 2) with similar conformations. In both mol­ecules, the cyclo­hexane rings adopt a chair conformation, while the oxane rings are also puckered. In the crystal, O—H⋯O hydrogen bonds connect adjacent mol­ecules, forming C(6) helical chains located around a 21 screw axis and running along the crystallographic a axis. The packing of these chains is governed only by van der Waals inter­actions. Semi-empirical PM3 quantum chemical calculations are in a satisfactory agreement with the structural results of the X-ray structure analysis. The absolute structure was indeterminate in the present experiment. PMID:27746923

  9. Ingi, a 5.2-kb dispersed sequence element from Trypanosoma brucei that carries half of a smaller mobile element at either end and has homology with mammalian LINEs.

    PubMed Central

    Kimmel, B E; ole-MoiYoi, O K; Young, J R

    1987-01-01

    A dispersed repetitive element named ingi, which is present in the genome of the protozoan parasite Trypanosoma brucei, is described. One complete 5.2-kilobase element and the ends of two others were sequenced. There were no direct or inverted terminal repeats. Rather, the ends consisted of two halves of a previously described 512-base-pair transposable element (G. Hasan, M.J. Turner, and J.S. Cordingley, Cell 37:333-341, 1984). Oligo(dA) tails and possible insertion site duplications suggested that ingi is a retroposon. The sequenced element appears to be a pseudogene copy of an original retroposon with one or more open reading frames occupying most of its length. Significant homologies of the encoded amino acid sequences with reverse transcriptases and mammalian long interpersed nuclear element sequences suggest a remote evolutionary origin for this kind of retroposon. Images PMID:3037321

  10. 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.

  11. HET-E and HET-D belong to a new subfamily of WD40 proteins involved in vegetative incompatibility specificity in the fungus Podospora anserina.

    PubMed Central

    Espagne, Eric; Balhadère, Pascale; Penin, Marie-Louise; Barreau, Christian; Turcq, Béatrice

    2002-01-01

    Vegetative incompatibility, which is very common in filamentous fungi, prevents a viable heterokaryotic cell from being formed by the fusion of filaments from two different wild-type strains. Such incompatibility is always the consequence of at least one genetic difference in specific genes (het genes). In Podospora anserina, alleles of the het-e and het-d loci control heterokaryon viability through genetic interactions with alleles of the unlinked het-c locus. The het-d2(Y) gene was isolated and shown to have strong similarity with the previously described het-e1(A) gene. Like the HET-E protein, the HET-D putative protein displayed a GTP-binding domain and seemed to require a minimal number of 11 WD40 repeats to be active in incompatibility. Apart from incompatibility specificity, no other function could be identified by disrupting the het-d gene. Sequence comparison of different het-e alleles suggested that het-e specificity is determined by the sequence of the WD40 repeat domain. In particular, the amino acids present on the upper face of the predicted beta-propeller structure defined by this domain may confer the incompatible interaction specificity. PMID:12019224

  12. High prevalence and diversity of viruses of the subfamily Gammaherpesvirinae, family Herpesviridae, in fecal specimens from bats of different species in southern China.

    PubMed

    Zheng, Xue-yan; Qiu, Min; Chen, Shao-wei; Xiao, Jian-peng; Ma, Li-zhen; Liu, Shan; Zhou, Jun-hua; Zhang, Qiong-hua; Li, Xing; Chen, Zhong; Wu, Yi; Chen, Hui-fang; Jiang, Li-na; Xiong, Yi-quan; Ma, Shu-juan; Zhong, Xue-shan; Huo, Shu-ting; Ge, Jing; Cen, Shu-wen; Chen, Qing

    2016-01-01

    Several studies have reported the detection of herpesviruses (HVs) in bats. However, the prevalence and phylogenetic characteristics of HVs in bats are still poorly understood. To elucidate the epidemiological characteristics of bat HVs in southern China, 520 fecal samples from eight bat species were collected in four geographic regions of southern China. Of these samples, 73 (14.0 %) tested positive for HVs using nested polymerase chain reaction assay. Phylogenetic analysis revealed a high degree of molecular diversity of HVs in bats of different species from different geographic regions. Our study provides evidence for co-evolution of bats and HVs.

  13. 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 ...

  14. 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. PMID:27199597

  15. A PPR protein in the PLS subfamily stabilizes the 5'-end of processed rpl16 mRNAs in maize chloroplasts.

    PubMed

    Hammani, Kamel; Takenaka, Mizuki; Miranda, Rafael; Barkan, Alice

    2016-05-19

    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.

  16. 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

  17. The RNA binding protein HuR determines the differential translation of autism-associated FoxP subfamily members in the developing neocortex.

    PubMed

    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

  18. 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

  19. ERCC6, a member of a subfamily of putative helicases, is involved in Cockayne's syndrome and preferential repair of active genes.

    PubMed

    Troelstra, C; van Gool, A; de Wit, J; Vermeulen, W; Bootsma, D; Hoeijmakers, J H

    1992-12-11

    Cells from patients with the UV-sensitive nucleotide excision repair disorder Cockayne's syndrome (CS) have a specific defect in preferential repair of lesions from the transcribed strand of active genes. This system permits quick resumption of transcription after UV exposure. Here we report the characterization of ERCC6, a gene involved in preferential repair in eukaryotes. ERCC6 corrects the repair defect of CS complementation group B (CS-B). It encodes a protein of 1493 amino acids, containing seven consecutive domains conserved between DNA and RNA helicases. The entire helicase region bears striking homology to segments in recently discovered proteins involved in transcription regulation, chromosome stability, and DNA repair. Mutation analysis of a CS-B patient indicates that the gene is not essential for cell viability and is specific for preferential repair of transcribed sequences. PMID:1339317

  20. Cytogenetic analyses of five amazon lizard species of the subfamilies Teiinae and Tupinambinae and review of karyotyped diversity the family Teiidae

    PubMed Central

    Carvalho, Natália Dayane Moura; Arias, Federico José; da Silva, Francijara Araújo; Schneider, Carlos Henrique; Gross, Maria Claudia

    2015-01-01

    Abstract 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. PMID:26753079

  1. 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. PMID:26753079

  2. Keylimepie peckorum gen. n. and sp. n., (Hymenoptera, Braconidae) from southern Florida, U.S., the first known brachypterous member of the subfamily Microgastrinae

    PubMed Central

    Fernandez-Triana, Jose; Boudreault, Caroline

    2016-01-01

    Abstract 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. PMID:27199597

  3. The diversity and evolutionary relationships of the pregnancy-associated glycoproteins, an aspartic proteinase subfamily consisting of many trophoblast-expressed genes

    PubMed Central

    Xie, Sancai; Green, Jonathan; Bixby, James B.; Szafranska, Bozena; DeMartini, James C.; Hecht, Steven; Roberts, R. Michael

    1997-01-01

    The pregnancy-associated glycoproteins (PAGs) are structurally related to the pepsins, thought to be restricted to the hooved (ungulate) mammals and characterized by being expressed specifically in the outer epithelial cell layer (chorion/trophectoderm) of the placenta. At least some PAGs are catalytically inactive as proteinases, although each appears to possess a cleft capable of binding peptides. By cloning expressed genes from ovine and bovine placental cDNA libraries, by Southern genomic blotting, by screening genomic libraries, and by using PCR to amplify portions of PAG genes from genomic DNA, we estimate that cattle, sheep, and most probably all ruminant Artiodactyla possess many, possibly 100 or more, PAG genes, many of which are placentally expressed. The PAGs are highly diverse in sequence, with regions of hypervariability confined largely to surface-exposed loops. Nonsynonymous (replacement) mutations in the regions of the genes coding for these hypervariable loop segments have accumulated at a higher rate than synonymous (silent) mutations. Construction of distance phylograms, based on comparisons of PAG and related aspartic proteinase amino acid sequences, suggests that much diversification of the PAG genes occurred after the divergence of the Artiodactyla and Perissodactyla, but that at least one gene is represented outside the hooved species. The results also suggest that positive selection of duplicated genes has acted to provide considerable functional diversity among the PAGs, whose presence at the interface between the placenta and endometrium and in the maternal circulation indicates involvement in fetal–maternal interactions. PMID:9371757

  4. TRPA5, an Ankyrin Subfamily Insect TRP Channel, is Expressed in Antennae of Cydia pomonella (Lepidoptera: Tortricidae) in Multiple Splice Variants.

    PubMed

    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

  5. Influence of Cytochrome P450, Family 2, Subfamily D, Polypeptide 6 (CYP2D6) polymorphisms on pain sensitivity and clinical response to weak opioid analgesics.

    PubMed

    Zahari, Zalina; Ismail, Rusli

    2014-01-01

      CYP2D6 polymorphisms show large geographical and interethnic differences. Variations in CYP2D6 activity may impact upon a patient's pain level and may contribute to interindividual variations in the response to opioids. This paper reviews the evidence on how CYP2D6 polymorphisms might influence pain sensitivity and clinical response to codeine and tramadol. For example, it is shown that (1) CYP2D6 poor metabolizers (PMs) may be less efficient at synthesizing endogenous morphine compared with other metabolizers. In contrast, ultra-rapid metabolizers (UMs) may be more efficient than other metabolizers at synthesizing endogenous morphine, thus strengthening endogenous pain modulation. Additionally, for codeine and tramadol that are bioactivated by CYP2D6, PMs may undergo no metabolite formation, leading to inadequate analgesia. Conversely, UMs may experience quicker analgesic effects but be prone to higher mu-opioid-related toxicity. The literature suggested the potential usefulness of the determination of CYP2D6 polymorphisms in elucidating serious adverse events and in preventing subsequent inappropriate selection or doses of codeine and tramadol. Notably, even though many studies investigated a possible role of the CYP2D6 polymorphisms on pain sensitivity, pharmacokinetics and pharmacodynamics of these drugs, the results of analgesia and adverse effects are conflicting. More studies are required to demonstrate genetically determined unresponsiveness and risk of developing serious adverse events for patients with pain and these should involve larger numbers of patients in different population types. PMID:23759977

  6. Positive selection pressure within teleost Toll-like receptors tlr21 and tlr22 subfamilies and their response to temperature stress and microbial components in zebrafish.

    PubMed

    Sundaram, Arvind Y M; Consuegra, Sonia; Kiron, Viswanath; Fernandes, Jorge M O

    2012-09-01

    Toll-like receptors (TLRs) play a crucial role in host defence, since they trigger immune response following recognition of pathogen-associated molecular patterns (PAMPs) in potential infectious agents. TLRs have been found in numerous organisms, including mammals, birds and teleosts. Some TLR members are commonly retained across all species, whilst others were lost, gained or diverged independently during evolution. Our knowledge about the evolution and specific functions of tlr21, tlr22 and tlr23 in teleosts are still scarce. Phylogenetic analysis of 18 tlr13, tlr21, tlr22 and tlr23 genes from 9 different fish species divided them in two groups. All tlr21 genes were under the first clade, while the second comprised tlr22, tlr23 and tlr13 from Atlantic salmon. Evidence of positive selection was detected at three sites within the leucine-rich repeat regions of Tlr22, which may influence PAMP recognition. Immunostimulation experiments revealed that expression of zebrafish tlr22 is modulated by several unrelated PAMPs. Up to a 3-fold increase in tlr21 and tlr22 expression was detected in larvae exposed to immunostimulants such as lipopolysaccharide, peptidoglycan or poly I:C. We found that zebrafish tlrs are expressed mainly in immune-related organs, such as spleen and kidney as well as in testis and temperature stress did not have an effect on the expression of tlr21 and tlr22 in the early stages of development in zebrafish larvae. Our data indicates that these teleost tlrs may play a role in innate host defence. In particular, tlr22 is evolving under positive selection, which indicates functional diversification and adaptation of the response to different PAMPs.

  7. 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...

  8. Systematic nomenclature for the PLUNC/PSP/BSP30/SMGB proteins as a subfamily of the BPI fold-containing superfamily.

    PubMed

    Bingle, Colin D; Seal, Ruth L; Craven, C Jeremy

    2011-08-01

    We present the BPIFAn/BPIFBn systematic nomenclature for the PLUNC (palate lung and nasal epithelium clone)/PSP (parotid secretory protein)/BSP30 (bovine salivary protein 30)/SMGB (submandibular gland protein B) family of proteins, based on an adaptation of the SPLUNCn (short PLUNCn)/LPLUNCn (large PLUNCn) nomenclature. The nomenclature is applied to a set of 102 sequences which we believe represent the current reliable data for BPIFA/BPIFB proteins across all species, including marsupials and birds. The nomenclature will be implemented by the HGNC (HUGO Gene Nomenclature Committee).

  9. Human serotonin 1D receptor is encoded by a subfamily of two distinct genes: 5-HT1D alpha and 5-HT1D beta.

    PubMed Central

    Weinshank, R L; Zgombick, J M; Macchi, M J; Branchek, T A; Hartig, P R

    1992-01-01

    The serotonin 1D (5-HT1D) receptor is a pharmacologically defined binding site and functional receptor site. Observed variations in the properties of 5-HT1D receptors in different tissues have led to the speculation that multiple receptor proteins with slightly different properties may exist. We report here the cloning, deduced amino acid sequences, pharmacological properties, and second-messenger coupling of a pair of human 5-HT1D receptor genes, which we have designated 5-HT1D alpha and 5-HT1D beta due to their strong similarities in sequence, pharmacological properties, and second-messenger coupling. Both genes are free of introns in their coding regions, are expressed in the human cerebral cortex, and can couple to inhibition of adenylate cyclase activity. The pharmacological binding properties of these two human receptors are very similar, and match closely the pharmacological properties of human, bovine, and guinea pig 5-HT1D sites. Both receptors exhibit high-affinity binding of sumatriptan, a new anti-migraine medication, and thus are candidates for the pharmacological site of action of this drug. Images PMID:1565658

  10. 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. PMID:21550409

  11. 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.

  12. Lymphocyte function-associated antigen-1 binding residues in intercellular adhesion molecule-2 (ICAM-2) and the integrin binding surface in the ICAM subfamily

    PubMed Central

    Casasnovas, José M.; Pieroni, Cristiana; Springer, Timothy A.

    1999-01-01

    The crystal structure of intercellular adhesion molecule-2 (ICAM-2) revealed significant differences in the presentation of the critical acidic residue important for integrin binding between I and non-I-domain integrin ligands. Based on this crystal structure, we mutagenized ICAM-2 to localize the binding site for the integrin lymphocyte function-associated antigen-1 (LFA-1). The integrin binding site runs diagonally across the GFC β-sheet and includes residues on the CD edge of the β-sandwich. The site is oblong and runs along a flat ridge on the upper half of domain 1, which is proposed to dock to a groove in the I domain of LFA-1, with the critical Glu-37 residue ligating the Mg2+ in the I domain. Previous mutagenesis of ICAM-1 and ICAM-3, interpreted in light of the recently determined ICAM-1 and ICAM-2 structures, suggests similar binding sites. By contrast, major differences are seen with vascular cell adhesion molecule-1 (VCAM-1), which binds α4 integrins that lack an I domain. The binding site on VCAM-1 includes the lower portion of domain 1 and the upper part of domain 2, whereas the LFA-1 binding site on ICAM is confined to the upper part of domain 1. PMID:10077629

  13. Pulmonary cytochrome P450 enzymes belonging to the CYP4B subfamily from an Australian marsupial, the tammar wallaby (Macropus eugenii).

    PubMed

    Milic, Natalie L; Ngo, Suong N T; Marchant, Ceilidh L; Height, Tamara A; McKinnon, Ross A

    2011-01-01

    Cytochromes P450 (CYPs) are critically important in the oxidative metabolism of a diverse array of xenobiotics and endogenous substrates. We have previously reported the cloning and characterisation of the koala CYP4A15, the first reported member of the CYP4 family from marsupials, and have demonstrated important species differences in CYP4A activity and tissue expression. In the present study, the cloning of CYP4B1 in the wallaby (Macropus eugenii) and their expression across marsupials is described. Rabbit anti-mouse CYP4B1 antibody detected immunoreactive proteins in lung and liver microsomes from all test marsupials, with relative weak signal detected from the koala, suggesting a species-specific expression. Microsomal 2-aminofluorene bio-activation (a CYP4B1 marker) in wallaby lung was comparable to that of rabbit, with significant higher activities detected in wallaby liver and kidneys compared to rabbit. A 1548bp wallaby lung CYP4B complete cDNA, designated CYP4B1, which encodes a protein of 510 amino acids and shares 72% nucleotide and 69% amino acid sequence identity to human CYP4B1, was cloned by polymerase chain reaction approaches. The results demonstrate the presence of wallaby CYP4B1 that shares several common features with other published CYP4Bs; however the wallaby CYP4B1 cDNA contains four extra amino acid residues at the NH₂-terminal, a fundamentally conserved transmembrane anchor of all eukaryote CYPs.

  14. 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.

  15. Cyclic transmission of Sarcocystis gerbilliechis n. sp. by the Arabian saw-scaled viper, Echis coloratus, to rodents of the subfamily gerbillinae.

    PubMed

    Jäkel, T

    1995-08-01

    Infection experiments with rodents and snakes were performed to elucidate the life cycle of a Sarcocystis isolate found in an Arabian saw-scaled viper, Echis coloratus. Oocytes in feces of the naturally infected and of 2 experimentally infected Arabian saw-scaled vipers were already sporulated and contained 2 sporocysts each, measuring 12.7 (12.3-13.3) microns x 11.0 (10.7-11.4) microns. After oral inoculation of various rodent species with these sporocysts, sarcocysts developed in the esophagus and skeletal muscles of gerbils and related genera. Mature sarcocysts were filiform in shape and reached a maximum length of 11.7 mm after 5 mo postinoculation (PI), whereas the width did not exceed 190 microns. The primary cyst wall formed small, knoblike protrusions, which were up to 180 nm long and 120 nm wide. Mature schizonts were present in the liver and other organs of gerbils between 11 and 14 days PI. After inoculation of vipers of 3 different genera with mature sarcocysts from gerbils, oocysts developed in the intestine of Arabian saw-scaled vipers. A comparison of these data with those from previously described Sarcocystis species with snake-rodent life cycles suggests that Sarcocystis gerbilliechis is a new species. PMID:7623207

  16. Influence of Cytochrome P450, Family 2, Subfamily D, Polypeptide 6 (CYP2D6) polymorphisms on pain sensitivity and clinical response to weak opioid analgesics.

    PubMed

    Zahari, Zalina; Ismail, Rusli

    2014-01-01

      CYP2D6 polymorphisms show large geographical and interethnic differences. Variations in CYP2D6 activity may impact upon a patient's pain level and may contribute to interindividual variations in the response to opioids. This paper reviews the evidence on how CYP2D6 polymorphisms might influence pain sensitivity and clinical response to codeine and tramadol. For example, it is shown that (1) CYP2D6 poor metabolizers (PMs) may be less efficient at synthesizing endogenous morphine compared with other metabolizers. In contrast, ultra-rapid metabolizers (UMs) may be more efficient than other metabolizers at synthesizing endogenous morphine, thus strengthening endogenous pain modulation. Additionally, for codeine and tramadol that are bioactivated by CYP2D6, PMs may undergo no metabolite formation, leading to inadequate analgesia. Conversely, UMs may experience quicker analgesic effects but be prone to higher mu-opioid-related toxicity. The literature suggested the potential usefulness of the determination of CYP2D6 polymorphisms in elucidating serious adverse events and in preventing subsequent inappropriate selection or doses of codeine and tramadol. Notably, even though many studies investigated a possible role of the CYP2D6 polymorphisms on pain sensitivity, pharmacokinetics and pharmacodynamics of these drugs, the results of analgesia and adverse effects are conflicting. More studies are required to demonstrate genetically determined unresponsiveness and risk of developing serious adverse events for patients with pain and these should involve larger numbers of patients in different population types.

  17. A PPR protein in the PLS subfamily stabilizes the 5'-end of processed rpl16 mRNAs in maize chloroplasts.

    PubMed

    Hammani, Kamel; Takenaka, Mizuki; Miranda, Rafael; Barkan, Alice

    2016-05-19

    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