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Sample records for agamous ag subfamily

  1. 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

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

    PubMed

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

    2011-08-01

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

  3. Exon skipping of AGAMOUS homolog PrseAG in developing double flowers of Prunus lannesiana (Rosaceae).

    PubMed

    Liu, Zhixiong; Zhang, Dandan; Liu, Di; Li, Fenglan; Lu, Hai

    2013-02-01

    KEY MESSAGE : Two transcript isoforms of AGAMOUS homologs, from single and double flower Prunus lannesiana, respectively, showed different functions. The Arabidopsis floral homeotic C function gene AGAMOUS (AG) confers stamen and carpel identity. Loss of AG function results in homeotic conversions of stamens into petals and formation of double flowers. In order to present a molecular dissection of a double-flower cultivar in Prunus lannesiana (Rosaceae), we isolated and identified a single-copy gene, AG homolog from two genetically cognate P. lannesiana bearing single and double flowers, respectively. Sequence analysis revealed that the AG homolog, prseag-1, from double flowers showed a 170-bp exon skipping as compared to PrseAG (Prunus serrulata AGAMOUS) from the single flowers. Genomic DNA sequence revealed that abnormal splicing resulted in mutant prseag-1 protein with the C-terminal AG motifs I and II deletions. In addition, protein sequence alignment and phylogenetic analyses revealed that the PrseAG was grouped into the euAG lineage. A semi-quantitative PCR analysis showed that the expression of PrseAG was restricted to reproductive organs of stamens and carpels in single flowers of P. lannesiana 'speciosa', while the prseag-1 mRNA was highly transcribed throughout the petals, stamens, and carpels in double flowers from 'Albo-rosea'. The transgenic Arabidopsis containing 35S::PrseAG displayed extremely early flowering, bigger stamens and carpels and homeotic conversion of petals into staminoid organs, but ectopic expression of prseag-1 could not mimic the phenotypic ectopic expression of PrseAG in Arabidopsis. In general, this study provides evidences to show that double flower 'Albo-rosea' is a putative C functional ag mutant in P. lannesiana.

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

    PubMed

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

    2011-01-01

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

  5. 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

  6. Transgenic Suppression of AGAMOUS Genes in Apple Reduces Fertility and Increases Floral Attractiveness

    PubMed Central

    Klocko, Amy L.; Borejsza-Wysocka, Ewa; Brunner, Amy M.; Shevchenko, Olga; Aldwinckle, Herb; Strauss, Steven H.

    2016-01-01

    We investigated the ability of RNA interference (RNAi) directed against two co-orthologs of AGAMOUS (AG) from Malus domestica (domestic apple, MdAG) to reduce the risks of invasiveness and provide genetic containment of transgenes, while also promoting the attractiveness of flowers for ornamental usage. Suppression of two MdAG-like genes, MdMADS15 and MdMADS22, led to the production of trees with highly showy, polypetalous flowers. These “double-flowers” had strongly reduced expression of both MdAG-like genes. Members of the two other clades within in the MdAG subfamily showed mild to moderate differences in gene expression, or were unchanged, with the level of suppression approximately proportional to the level of sequence identity between the gene analyzed and the RNAi fragment. The double-flowers also exhibited reduced male and female fertility, had few viable pollen grains, a decreased number of stigmas, and produced few viable seeds after cross-pollination. Despite these floral alterations, RNAi-AG trees with double-flowers set full-sized fruit. Suppression or mutation of apple AG-like genes appears to be a promising method for combining genetic containment with improved floral attractiveness. PMID:27500731

  7. Determination of Arabidopsis floral meristem identity by AGAMOUS.

    PubMed

    Mizukami, Y; Ma, H

    1997-03-01

    Determinate growth of floral meristems in Arabidopsis requires the function of the floral regulatory gene AGAMOUS (AG). Expression of AG mRNA in the central region of floral meristems relies on the partially overlapping functions of the LEAFY (LFY) and APETALA1 (AP1) genes, which promote initial floral meristem identity. Here, we provide evidence that AG function is required for the final definition of floral meristem identity and that constitutive AG function can promote, independent of LFY and AP1 functions, the determinate floral state in the center of reproductive meristems. Loss-of-function analysis showed that the indeterminate central region of the ag mutant floral meristem undergoes conversion to an inflorescence meristem when long-day-dependent flowering stimulus is removed. Furthermore, gain-of-function analysis demonstrated that ectopic AG function results in precocious flowering and the formation of terminal flowers at apices of both the primary inflorescence and axillary branches of transgenic Arabidopsis plants in which AG expression is under the control of the 35S promoter from cauliflower mosaic virus. Similar phenotypes were also observed in lfy ap1 double mutants carrying a 35S-AG transgene. Together, these results indicate that AG is a principal developmental switch that controls the transition of meristem activity from indeterminate to determinate.

  8. Spatiotemporal expression of duplicate AGAMOUS orthologues during floral development in Phalaenopsis.

    PubMed

    Song, In-Ja; Nakamura, Toru; Fukuda, Tatsuya; Yokoyama, Jun; Ito, Takuro; Ichikawa, Hiroaki; Horikawa, Yoh; Kameya, Toshiaki; Kanno, Akira

    2006-06-01

    The AGAMOUS (AG) family of MADS-box genes plays important roles in controlling the development of the reproductive organs of flowering plants. To understand the molecular mechanisms behind the floral development in the orchid, we isolated and characterized two AG-like genes from Phalaenopsis that we denoted PhalAG1 and PhalAG2. Phylogenetic analysis indicated that PhalAG1 and PhalAG2 fall into different phylogenetic positions in the AG gene family as they belong to the C- and D-lineages, respectively. Reverse transcription-polymerase chair reaction (RT-PCR) analyses showed that PhalAG1 and PhalAG2 transcripts were detected in flower buds but not in vegetative organs. Moreover, in situ hybridization experiments revealed that PhalAG1 and PhalAG2 hybridization signals were observed in the lip, column, and ovule during the floral development of Phalaenopsis, with little difference between the expression patterns of the two genes. These results suggest that both AG-like genes in Phalaenopsis act redundantly with each other in floral development.

  9. Multi-petal cyclamen flowers produced by AGAMOUS chimeric repressor expression.

    PubMed

    Tanaka, Yuri; Oshima, Yoshimi; Yamamura, Tomomichi; Sugiyama, Masao; Mitsuda, Nobutaka; Ohtsubo, Norihiro; Ohme-Takagi, Masaru; Terakawa, Teruhiko

    2013-01-01

    Cyclamen persicum (cyclamen) is a commercially valuable, winter-blooming perennial plant. We cloned two cyclamen orthologues of AGAMOUS (AG), CpAG1 and CpAG2, which are mainly expressed in the stamen and carpel, respectively. Cyclamen flowers have 5 petals, but expression of a chimeric repressor of CpAG1 (CpAG1-SRDX) caused stamens to convert into petals, resulting in a flower with 10 petals. By contrast, CpAG2-SRDX only caused incomplete formation of stamens and carpels. Expression in Arabidopsis thaliana showed similar effects on flower organ specification. Simultaneous expression of CpAG1-SRDX and CpAG2-SRDX in cyclamen induced rose-like, multi-petal flowers, a potentially valuable trait in commercial ornamental varieties. Expression of CpAG2-SRDX in a cyclamen mutant lacking expression of CpAG1 more effectively produced multi-petal flowers. Here, we controlled the number of petals in cyclamen by simple genetic engineering with a chimeric repressor. This strategy may be applicable useful for other ornamental plants with two distinct AG orthologues.

  10. Alternative splicing of the AGAMOUS orthologous gene in double flower of Magnolia stellata (Magnoliaceae).

    PubMed

    Zhang, Bo; Liu, Zhi-Xiong; Ma, Jiang; Song, Yi; Chen, Fa-Ju

    2015-12-01

    Magnolia stellata is a woody ornamental shrub with more petaloid tepals than related plants from family Magnoliaceae. Recent studies revealed that expression changes in an AGAMOUS (AG) orthologous gene could resulted in double flowers with increased numbers of petals. We isolated three transcripts encoding different isoforms of a single AG orthologous gene, MastAG, mastag_2 and mastag_3, from M. stellata. Sequence alignments and Southern blot analyses suggested that MastAG was a single-copy gene in M. stellata genomes, and that mastag_2 and mastag_3 were abnormally spliced isoforms of MastAG. An 144bp exon skipping in MastAG results in the truncated mastag_2 protein lacking the completely I domain and 18 aa of the K1 subdomain, whereas an 165bp exon skipping of MastAG produces a truncated mastag_3 protein lacking 6 aa of the K3 subdomain and the completely C terminal region. Expression analyses showed that three alternative splicing (AS) isoforms expressed only in developing stamens and carpels. Functional analyses revealed that MastAG could mimic the endogenous AG to specify carpel identity, but failed to regulate stamen development in an Arabidopsis ag-1 mutant. Moreover, the key domain or subdomain deletions represented by mastag_2 and mastag_3 resulted in loss of C-function. However, ectopic expression of mastag_2 in Arabidopsis produced flowers with sepals converted into carpeloid organs, but without petals and stamens, whereas ectopic expression of mastag_3 in Arabidopsis could mimic the flower phenotype of the ag mutant and produced double flowers with homeotic transformation of stamens into petals and carpels into another ag flower. Our results also suggest that mastag_3 holds some potential for biotechnical engineering to create multi-petal phenotypes in commercial ornamental cultivars.

  11. Functional domains of the floral regulator AGAMOUS: characterization of the DNA binding domain and analysis of dominant negative mutations.

    PubMed Central

    Mizukami, Y; Huang, H; Tudor, M; Hu, Y; Ma, H

    1996-01-01

    The Arabidopsis MADS box gene AGAMOUS (AG) controls reproductive organ identity and floral meristem determinacy. The AG protein binds in vitro to DNA sequences similar to the targets of known MADS domain transcription factors. Whereas most plant MADS domain proteins begin with the MADS domain, AG and its orthologs contain a region N-terminal to the MADS domain. All plant MADS domain proteins share another region with moderate sequence similarity called the K domain. Neither the region (I region) that lies between the MADS and K domains nor the C-terminal region is conserved. We show here that the AG MADS domain and the I region are necessary and sufficient for DNA binding in vitro and that AG binds to DNA as a dimer. To investigate the in vivo function of the regions of AG not required for in vitro DNA binding, we introduced several AG constructs into wild-type plants and characterized their floral phenotypes. We show that transgenic Arabidopsis plants with a 35S-AG construct encoding an AG protein lacking the N-terminal region produced apetala 2 (ap2)-like flowers similar to those ectopically expressing AG proteins retaining the N-terminal region. This result suggests that the N-terminal region is not required to produce the ap2-like phenotype. In addition, transformants with a 35S-AG construct encoding an AG protein lacking the C-terminal region produced ag-like flowers, indicating that this truncated AG protein inhibits normal AG function. Finally, transformants with a 35S-AG construct encoding an AG protein lacking both K and C regions produced flowers with more stamens and carpels. The phenotypes of the AG transformants demonstrate that both the K domain and the C-terminal region have important and distinct in vivo functions. We discuss possible mechanisms through which AG may regulate downstream genes. PMID:8672883

  12. Control of reproductive floral organ identity specification in Arabidopsis by the C function regulator AGAMOUS.

    PubMed

    ÓMaoiléidigh, Diarmuid S; Wuest, Samuel E; Rae, Liina; Raganelli, Andrea; Ryan, Patrick T; Kwasniewska, Kamila; Das, Pradeep; Lohan, Amanda J; Loftus, Brendan; Graciet, Emmanuelle; Wellmer, Frank

    2013-07-01

    The floral organ identity factor AGAMOUS (AG) is a key regulator of Arabidopsis thaliana flower development, where it is involved in the formation of the reproductive floral organs as well as in the control of meristem determinacy. To obtain insights into how AG specifies organ fate, we determined the genes and processes acting downstream of this C function regulator during early flower development and distinguished between direct and indirect effects. To this end, we combined genome-wide localization studies, gene perturbation experiments, and computational analyses. Our results demonstrate that AG controls flower development to a large extent by controlling the expression of other genes with regulatory functions, which are involved in mediating a plethora of different developmental processes. One aspect of this function is the suppression of the leaf development program in emerging floral primordia. Using trichome initiation as an example, we demonstrate that AG inhibits an important aspect of leaf development through the direct control of key regulatory genes. A comparison of the gene expression programs controlled by AG and the B function regulators APETALA3 and PISTILLATA, respectively, showed that while they control many developmental processes in conjunction, they also have marked antagonistic, as well as independent activities.

  13. Automated Protein Subfamily Identification and Classification

    PubMed Central

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

    2007-01-01

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

  14. Regulatory elements of the floral homeotic gene AGAMOUS identified by phylogenetic footprinting and shadowing.

    SciTech Connect

    Hong, R. L., Hamaguchi, L., Busch, M. A., and Weigel, D.

    2003-06-01

    OAK-B135 In Arabidopsis thaliana, cis-regulatory sequences of the floral homeotic gene AGAMOUS (AG) are located in the second intron. This 3 kb intron contains binding sites for two direct activators of AG, LEAFY (LFY) and WUSCHEL (WUS), along with other putative regulatory elements. We have used phylogenetic footprinting and the related technique of phylogenetic shadowing to identify putative cis-regulatory elements in this intron. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for activity of AG regulatory sequences in A. thaliana. Although there is little obvious sequence similarity outside the Brassicaceae, the intron from cucumber AG has at least partial activity in A. thaliana. Our studies underscore the value of the comparative approach as a tool that complements gene-by-gene promoter dissection, but also highlight that sequence-based studies alone are insufficient for a complete identification of cis-regulatory sites.

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

    PubMed Central

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

    2005-01-01

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

  16. Phylogenetic utility of the nuclear genes AGAMOUS 1 and PHYTOCHROME B in palms (Arecaceae): an example within Bactridinae

    PubMed Central

    Ludeña, Bertha; Chabrillange, Nathalie; Aberlenc-Bertossi, Frédérique; Adam, Hélène; Tregear, James W.; Pintaud, Jean-Christophe

    2011-01-01

    Background and Aims Molecular phylogenetic studies of palms (Arecaceae) have not yet provided a fully resolved phylogeny of the family. There is a need to increase the current set of markers to resolve difficult groups such as the Neotropical subtribe Bactridinae (Arecoideae: Cocoseae). We propose the use of two single-copy nuclear genes as valuable tools for palm phylogenetics. Methods New primers were developed for the amplification of the AGAMOUS 1 (AG1) and PHYTOCHROME B (PHYB) genes. For the AGAMOUS gene, the paralogue 1 of Elaeis guineensis (EgAG1) was targeted. The region amplified contained coding sequences between the MIKC K and C MADS-box domains. For the PHYB gene, exon 1 (partial sequence) was first amplified in palm species using published degenerate primers for Poaceae, and then specific palm primers were designed. The two gene portions were sequenced in 22 species of palms representing all genera of Bactridinae, with emphasis on Astrocaryum and Hexopetion, the status of the latter genus still being debated. Key Results The new primers designed allow consistent amplification and high-quality sequencing within the palm family. The two loci studied produced more variability than chloroplast loci and equally or less variability than PRK, RPBII and ITS nuclear markers. The phylogenetic structure obtained with AG1 and PHYB genes provides new insights into intergeneric relationships within the Bactridinae and the intrageneric structure of Astrocaryum. The Hexopetion clade was recovered as monophyletic with both markers and was weakly supported as sister to Astrocaryum sensu stricto in the combined analysis. The rare Astrocaryum minus formed a species complex with Astrocaryum gynacanthum. Moreover, both AG1 and PHYB contain a microsatellite that could have further uses in species delimitation and population genetics. Conclusions AG1 and PHYB provide additional phylogenetic information within the palm family, and should prove useful in combination with other

  17. AGAMOUS Terminates Floral Stem Cell Maintenance in Arabidopsis by Directly Repressing WUSCHEL through Recruitment of Polycomb Group Proteins[W

    PubMed Central

    Liu, Xigang; Kim, Yun Ju; Müller, Ralf; Yumul, Rae Eden; Liu, Chunyan; Pan, Yanyun; Cao, Xiaofeng; Goodrich, Justin; Chen, Xuemei

    2011-01-01

    Floral stem cells produce a defined number of floral organs before ceasing to be maintained as stem cells. Therefore, floral stem cells offer an ideal model to study the temporal control of stem cell maintenance within a developmental context. AGAMOUS (AG), a MADS domain transcription factor essential for the termination of floral stem cell fate, has long been thought to repress the stem cell maintenance gene WUSCHEL (WUS) indirectly. Here, we uncover a role of Polycomb Group (PcG) genes in the temporally precise repression of WUS expression and termination of floral stem cell fate. We show that AG directly represses WUS expression by binding to the WUS locus and recruiting, directly or indirectly, PcG that methylates histone H3 Lys-27 at WUS. We also show that PcG acts downstream of AG and probably in parallel with the known AG target KNUCKLES to terminate floral stem cell fate. Our studies identify core components of the network governing the temporal program of floral stem cells. PMID:22028461

  18. The F-box-containing protein UFO and AGAMOUS participate in antagonistic pathways governing early petal development in Arabidopsis.

    PubMed

    Durfee, Tim; Roe, Judith L; Sessions, R Allen; Inouye, Carla; Serikawa, Kyle; Feldmann, Kenneth A; Weigel, Detlef; Zambryski, Patricia C

    2003-07-08

    The UNUSUAL FLORAL ORGANS (UFO) gene is required for multiple processes in the developing Arabidopsis flower, including the proper patterning and identity of both petals and stamens. The gene encodes an F-box-containing protein, UFO, which interacts physically and genetically with the Skp1 homolog, ASK1. In this report, we describe four ufo alleles characterized by the absence of petals, which uncover another role for UFO in promoting second whorl development. This UFO-dependent pathway is required regardless of the second whorl organ to be formed, arguing that it affects a basic process acting in parallel with those establishing organ identity. However, the pathway is dispensable in the absence of AGAMOUS (AG), a known inhibitor of petal development. In situ hybridization results argue that AG is not transcribed in the petal region, suggesting that it acts non-cell-autonomously to inhibit second whorl development in ufo mutants. These results are combined into a genetic model explaining early second whorl initiation/proliferation, in which UFO functions to inhibit an AG-dependent activity.

  19. The F-box-containing protein UFO and AGAMOUS participate in antagonistic pathways governing early petal development in Arabidopsis

    PubMed Central

    Durfee, Tim; Roe, Judith L.; Sessions, R. Allen; Inouye, Carla; Serikawa, Kyle; Feldmann, Kenneth A.; Weigel, Detlef; Zambryski, Patricia C.

    2003-01-01

    The UNUSUAL FLORAL ORGANS (UFO) gene is required for multiple processes in the developing Arabidopsis flower, including the proper patterning and identity of both petals and stamens. The gene encodes an F-box-containing protein, UFO, which interacts physically and genetically with the Skp1 homolog, ASK1. In this report, we describe four ufo alleles characterized by the absence of petals, which uncover another role for UFO in promoting second whorl development. This UFO-dependent pathway is required regardless of the second whorl organ to be formed, arguing that it affects a basic process acting in parallel with those establishing organ identity. However, the pathway is dispensable in the absence of AGAMOUS (AG), a known inhibitor of petal development. In situ hybridization results argue that AG is not transcribed in the petal region, suggesting that it acts non-cell-autonomously to inhibit second whorl development in ufo mutants. These results are combined into a genetic model explaining early second whorl initiation/proliferation, in which UFO functions to inhibit an AG-dependent activity. PMID:12826617

  20. Phylogenetic analysis of AGAMOUS sequences reveals the origin of the diploid and tetraploid forms of self-pollinating wild buckwheat, Fagopyrum homotropicum Ohnishi

    PubMed Central

    Tomiyoshi, Mitsuyuki; Yasui, Yasuo; Ohsako, Takanori; Li, Cheng-Yun; Ohnishi, Ohmi

    2012-01-01

    Fagopyrum homotropicum Ohnishi is a self-pollinating wild buckwheat species indigenous to eastern Tibet and the Yunnan and Sichuan Provinces of China. It is useful breeding material for shifting cultivated buckwheat (F. esculentum ssp. esculentum Moench) from out-crossing to self-pollinating. Despite its importance as a genetic resource in buckwheat breeding, the genetic variation of F. homotropicum is poorly understood. In this study, we investigated the genetic variation and phylogenetic relationships of the diploid and tetraploid forms of F. homotropicum based on the nucleotide sequences of a nuclear gene, AGAMOUS (AG). Neighbor-joining analysis revealed that representative individuals clustered into three large groups (Group I, II and III). Each group contained diploid and tetraploid forms of F. homotropicum. We identified tetraploid plants that had two diverged AG sequences; one belonging to Group I and the other belonging to Group II, or one belonging to Group II and the other belonging to Group III. These results suggest that the tetraploid form originated from at least two hybridization events between deeply differentiated diploids. The results also imply that the genetic diversity contributed by tetraploidization of differentiated diploids may have allowed the distribution range of F. homotropicum to expand to the northern areas of China. PMID:23226084

  1. Phylogenetic analysis of AGAMOUS sequences reveals the origin of the diploid and tetraploid forms of self-pollinating wild buckwheat, Fagopyrum homotropicum Ohnishi.

    PubMed

    Tomiyoshi, Mitsuyuki; Yasui, Yasuo; Ohsako, Takanori; Li, Cheng-Yun; Ohnishi, Ohmi

    2012-09-01

    Fagopyrum homotropicum Ohnishi is a self-pollinating wild buckwheat species indigenous to eastern Tibet and the Yunnan and Sichuan Provinces of China. It is useful breeding material for shifting cultivated buckwheat (F. esculentum ssp. esculentum Moench) from out-crossing to self-pollinating. Despite its importance as a genetic resource in buckwheat breeding, the genetic variation of F. homotropicum is poorly understood. In this study, we investigated the genetic variation and phylogenetic relationships of the diploid and tetraploid forms of F. homotropicum based on the nucleotide sequences of a nuclear gene, AGAMOUS (AG). Neighbor-joining analysis revealed that representative individuals clustered into three large groups (Group I, II and III). Each group contained diploid and tetraploid forms of F. homotropicum. We identified tetraploid plants that had two diverged AG sequences; one belonging to Group I and the other belonging to Group II, or one belonging to Group II and the other belonging to Group III. These results suggest that the tetraploid form originated from at least two hybridization events between deeply differentiated diploids. The results also imply that the genetic diversity contributed by tetraploidization of differentiated diploids may have allowed the distribution range of F. homotropicum to expand to the northern areas of China.

  2. Characterization and expression analysis of AGAMOUS-like, SEEDSTICK-like, and SEPALLATA-like MADS-box genes in peach (Prunus persica) fruit.

    PubMed

    Tani, Eleni; Polidoros, Alexios N; Flemetakis, Emmanouil; Stedel, Catalina; Kalloniati, Chrissanthi; Demetriou, Kyproula; Katinakis, Panagiotis; Tsaftaris, Athanasios S

    2009-08-01

    MADS-box genes encode transcriptional regulators that are critical for flowering, flower organogenesis and plant development. Although there are extensive reports on genes involved in flower organogenesis in model and economically important plant species, there are few reports on MADS-box genes in woody plants. In this study, we have cloned and characterized AGAMOUS (AG), SEEDSTICK (STK) and SEPALLATA (SEP) homologs from peach tree (Prunus persica L. Batsch) and studied their expression patterns in different tissues as well as in fruit pericarp during pit hardening. AG- STK- and SEP-like homologs, representative of the C-, D-, E-like MADS-box gene lineages, respectively, play key roles in stamen, carpel, ovule and fruit development in Arabidopsis thaliana. Sequence similarities, phylogenetic analysis and structural characteristics were used to provide classification of the isolated genes in type C (PPERAG), type D (PPERSTK) and type E (PPERSEP1, PPERSEP3, PPERFB9) organ identity genes. Expression patterns were determined and in combination with phylogenetic data provided useful indications on the function of these genes. These data suggest the involvement of MADS-box genes in peach flower and fruit development and provide further evidence for the role of these genes in woody perennial trees that is compatible with their function in model plant species.

  3. Role for the banana AGAMOUS-like gene MaMADS7 in regulation of fruit ripening and quality.

    PubMed

    Liu, Juhua; Liu, Lin; Li, Yujia; Jia, Caihong; Zhang, Jianbin; Miao, Hongxia; Hu, Wei; Wang, Zhuo; Xu, Biyu; Jin, Zhiqiang

    2015-11-01

    MADS-box transcription factors play important roles in organ development. In plants, most studies on MADS-box genes have mainly focused on flower development and only a few concerned fruit development and ripening. A new MADS-box gene named MaMADS7 was isolated from banana fruit by rapid amplification of cDNA ends (RACE) based on a MADS-box fragment obtained from a banana suppression subtractive hybridization (SSH) cDNA library. MaMADS7 is an AGAMOUS-like MADS-box gene that is preferentially expressed in the ovaries and fruits and in tobacco its protein product localizes to the nucleus. This study found that MaMADS7 expression can be induced by exogenous ethylene. Ectopic expression of MaMADS7 in tomato resulted in broad ripening phenotypes. The expression levels of seven ripening and quality-related genes, ACO1, ACS2, E4, E8, PG, CNR and PSY1 in MaMADS7 transgenic tomato fruits were greatly increased while the expression of the AG-like MADS-box gene TAGL1 was suppressed. Compared with the control, the contents of β-carotene, lycopene, ascorbic acid and organic acid in transformed tomato fruits were increased, while the contents of glucose and fructose were slightly decreased. MaMADS7 interacted with banana 1-aminocyclopropane-1-carboxylic acid (ACC) oxidase gene 1 (MaACO1) and tomato phytoene synthase gene (LePSY1) promoters. Our results indicated that MaMADS7 plays an important role in initiating endogenous ethylene biosynthesis and fruit ripening.

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

    PubMed

    Wagner, Rüdiger; Stuckenberg, Brian

    2016-03-15

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

  5. Functional diversification of AGAMOUS lineage genes in regulating tomato flower and fruit development.

    PubMed

    Pan, Irvin L; McQuinn, Ryan; Giovannoni, James J; Irish, Vivian F

    2010-06-01

    AGAMOUS clade genes encode MADS box transcription factors that have been shown to play critical roles in many aspects of flower and fruit development in angiosperms. Tomato possesses two representatives of this lineage, TOMATO AGAMOUS (TAG1) and TOMATO AGAMOUS-LIKE1 (TAGL1), allowing for an analysis of diversification of function after gene duplication. Using RNAi (RNA interference) silencing, transgenic tomato lines that specifically down-regulate either TAGL1 or TAG1 transcript accumulation have been produced. TAGL1 RNAi lines show no defects in stamen or carpel identity, but show defects in fruit ripening. In contrast TAG1 RNAi lines show defects in stamen and carpel development. In addition TAG1 RNAi lines produce red ripe fruit, although they are defective in determinacy and produce ectopic internal fruit structures. e2814, an EMS- (ethyl methane sulphonate) induced mutation that is temperature sensitive and produces fruit phenotypes similar to that of TAG1 RNAi lines, was also characterized. Neither TAG1 nor TAGL1 expression is disrupted in the e2814 mutant, suggesting that the gene corresponding to the e2814 mutant represents a distinct locus that is likely to be functionally downstream of TAG1 and TAGL1. Based on these analyses, possible modes by which these gene duplicates have diversified in terms of their functions and regulatory roles are discussed.

  6. The structural biology of the FGF19 subfamily.

    PubMed

    Beenken, Andrew; Mohammadi, Moosa

    2012-01-01

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

  7. Progress Report for DOE DE-FG03-98ER20317 ''Regulation of the floral homeotic gene AGAMOUS'' Current and Final Funding Period: September 1, 2002, to December 31, 2002

    SciTech Connect

    Weigel, D.

    2003-03-11

    OAK-B135 Results obtained during this funding period: (1) Phylogenetic footprinting of AG regulatory sequences Sequences necessary and sufficient for AGAMOUS (AG) expression in the center of Arabidopsis flowers are located in the second intron, which is about 3 kb in size. This intron contains binding sites for two transcription factors, LEAFY (LFY) and WUSCHEL (WUS), which are direct activators of AG. We used the new method of phylogenetic shadowing to identify new regulatory elements. Among 29 Brassicaceae, several other motifs, but not the LFY and WUS binding sites previously identified, are largely invariant. Using reporter gene analyses, we tested six of these motifs and found that they are all functionally important for activity of AG regulatory sequences in A. thaliana. (2) Repression of AG by MADS box genes A candidate for repressing AG in the shoot apical meristem has been the MADS box gene FUL, since it is expressed in the shoot apical meristem and since an activated version (FUL:VP16) leads to ectopic AG expression in the shoot apical meristem. However, there is no ectopic AG expression in full single mutants. We therefore started to generate VP16 fusions of several other MADS box genes expressed in the shoot apical meristem, to determine which of these might be candidates for FUL redundant genes. We found that AGL6:VP16 has a similar phenotype as FUL:VP16, suggesting that AGL6 and FUL interact. We are now testing this hypothesis. (3) Two candidate AG regulators, WOW and ULA Because the phylogenetic footprinting project has identified several new candidate regulatory motifs, of which at least one (the CCAATCA motif) has rather strong effects, we had decided to put the analysis of WOW and ULA on hold, and to focus on using the newly identified motifs as tools. We conduct ed yeast one-hybrid screen with two of the conserved motifs, and identified several classes of transcription factors that can interact with them. One of these is encoded by the PAN gene

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2015-06-17

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

  10. 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.

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

    PubMed

    Taylor, Kathryn M; Nicholson, Robert I

    2003-04-01

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

  12. The AGAMOUS-LIKE 20 MADS domain protein integrates floral inductive pathways in Arabidopsis

    PubMed Central

    Lee, Horim; Suh, Sung-Suk; Park, Eunsook; Cho, Euna; Ahn, Ji Hoon; Kim, Sang-Gu; Lee, Jong Seob; Kwon, Young Myung; Lee, Ilha

    2000-01-01

    The very late-flowering behavior of Arabidopsis winter-annual ecotypes is conferred mainly by two genes, FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). A MADS-domain gene, AGAMOUS-LIKE 20 (AGL20), was identified as a dominant FRI suppressor in activation tagging mutagenesis. Overexpression of AGL20 suppresses not only the late flowering of plants that have functional FRI and FLC alleles but also the delayed phase transitions during the vegetative stages of plant development. Interestingly, AGL20 expression is positively regulated not only by the redundant vernalization and autonomous pathways of flowering but also by the photoperiod pathway. Our results indicate that AGL20 is an important integrator of three pathways controlling flowering in Arabidopsis. PMID:10995392

  13. Functional characterization of SEPALLATA3 and AGAMOUS orthologues in silver birch.

    PubMed

    Lemmetyinen, Juha; Hassinen, Minna; Elo, Annakaisa; Porali, Ilkka; Keinonen, Kaija; Mäkelä, Hannu; Sopanen, Tuomas

    2004-05-01

    The development of flowers is regulated by a complex network of transcriptional activators and repressors, many of which belong to the MADS box gene family. In this study, we describe two MADS box genes of silver birch (Betula pendula Roth), BpMADS1 and BpMADS6, which are similar to SEPALLATA3 and AGAMOUS in Arabidopsis thaliana, respectively. In situ hybridization showed that BpMADS1 was expressed in the inflorescence meristem at a very early stage, but not later. Both genes were expressed in developing carpels, ovules and stamens but not in tepals or scales. Ectopic expression of BpMADS1 in Arabidopsis resulted in a reduced number of floral organs or whole whorls and in petaloid or carpelloid sepals, a phenotype reminiscent of that of fil mutants. 35S::BpMADS6 caused very early flowering in Arabidopsis. In tobacco, both 35S::BpMADS1 and 35S::BpMADS6 accelerated flowering and, in addition, 35S::BpMADS6 caused changes in sepals and petals. In some transgenic birch plants, 35S::BpMADS1 antisense resulted in the development of both male and female organs in the axil of a single bract and in a change of some inflorescences into vegetative shoots. In two plants, either 35S::BpMADS6 sense or antisense constructs resulted in an increase in the number of tepals and in complete lack of stamens in some male inflorescences. These results suggest that BpMADS1 participates both in inflorescence and in flower formation and BpMADS6 participates in flower formation and that they are functional homologues to SEPALLATA3 and AGAMOUS, respectively.

  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).

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

    PubMed

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

    2010-01-01

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

  16. Sequence evolution and sex-specific expression patterns of the C class floral identity gene, SpAGAMOUS, in dioecious Spinacia oleracea L.

    PubMed

    Sather, D Noah; York, Amber; Pobursky, Kevin J; Golenberg, Edward M

    2005-10-01

    Development in dioecious cultivated spinach, Spinacia oleracea, is distinguished by the absence of alternative reproductive organ primordia in male and female flowers. Given the highly derived floral developmental program in spinach, we wished to characterize a spinach C class floral identity gene and to determine the patterns of sequence evolution as well as compare the spatial and temporal expression patterns with those of AGAMOUS. The isolated cDNA sequence clusters phylogenetically within the AGAMOUS/FARINELLI C class clade. In comparison with the SLM1 sequence from the related Silene latifolia, amino acid replacements are highly conservative and non-randomly distributed, being predominantly found in hinge regions or on exposed surfaces of helices. The spinach gene (SpAGAMOUS) appears to be exclusively expressed in reproductive tissues and not in vegetative organs. Initial expression of SpAGAMOUS is similar in male and female floral primordia. However, upon initiation of the first whorl organs, SpAGAMOUS becomes restricted to meristemic regions from which the reproductive primordia will develop. This results in an early gender-specific pattern. Thus, the spinach C class gene is differentially expressed prior to reproductive organ development and is, at least, correlated with, if not directly involved in, the sexual dimorphism in spinach.

  17. 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

  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).

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

    PubMed

    Buser, Thaddaeus J; Andrés López, J

    2015-05-01

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

  1. Identification and characterization of Piwi subfamily in insects.

    PubMed

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

    2007-10-12

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

  2. 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

  3. Characterization of an AGAMOUS-like MADS box protein, a probable constituent of flowering and fruit ripening regulatory system in banana.

    PubMed

    Roy Choudhury, Swarup; Roy, Sujit; Nag, Anish; Singh, Sanjay Kumar; Sengupta, Dibyendu N

    2012-01-01

    The MADS-box family of genes has been shown to play a significant role in the development of reproductive organs, including dry and fleshy fruits. In this study, the molecular properties of an AGAMOUS like MADS box transcription factor in banana cultivar Giant governor (Musa sp, AAA group, subgroup Cavendish) has been elucidated. We have detected a CArG-box sequence binding AGAMOUS MADS-box protein in banana flower and fruit nuclear extracts in DNA-protein interaction assays. The protein fraction in the DNA-protein complex was analyzed by mass spectrometry and using this information we have obtained the full length cDNA of the corresponding protein. The deduced protein sequence showed ~95% amino acid sequence homology with MA-MADS5, a MADS-box protein described previously from banana. We have characterized the domains of the identified AGAMOUS MADS-box protein involved in DNA binding and homodimer formation in vitro using full-length and truncated versions of affinity purified recombinant proteins. Furthermore, in order to gain insight about how DNA bending is achieved by this MADS-box factor, we performed circular permutation and phasing analysis using the wild type recombinant protein. The AGAMOUS MADS-box protein identified in this study has been found to predominantly accumulate in the climacteric fruit pulp and also in female flower ovary. In vivo and in vitro assays have revealed specific binding of the identified AGAMOUS MADS-box protein to CArG-box sequence in the promoters of major ripening genes in banana fruit. Overall, the expression patterns of this MADS-box protein in banana female flower ovary and during various phases of fruit ripening along with the interaction of the protein to the CArG-box sequence in the promoters of major ripening genes lead to interesting assumption about the possible involvement of this AGAMOUS MADS-box factor in banana fruit ripening and floral reproductive organ development.

  4. Characterization of an AGAMOUS-like MADS Box Protein, a Probable Constituent of Flowering and Fruit Ripening Regulatory System in Banana

    PubMed Central

    Roy Choudhury, Swarup; Roy, Sujit; Nag, Anish; Singh, Sanjay Kumar; Sengupta, Dibyendu N.

    2012-01-01

    The MADS-box family of genes has been shown to play a significant role in the development of reproductive organs, including dry and fleshy fruits. In this study, the molecular properties of an AGAMOUS like MADS box transcription factor in banana cultivar Giant governor (Musa sp, AAA group, subgroup Cavendish) has been elucidated. We have detected a CArG-box sequence binding AGAMOUS MADS-box protein in banana flower and fruit nuclear extracts in DNA-protein interaction assays. The protein fraction in the DNA-protein complex was analyzed by mass spectrometry and using this information we have obtained the full length cDNA of the corresponding protein. The deduced protein sequence showed ∼95% amino acid sequence homology with MA-MADS5, a MADS-box protein described previously from banana. We have characterized the domains of the identified AGAMOUS MADS-box protein involved in DNA binding and homodimer formation in vitro using full-length and truncated versions of affinity purified recombinant proteins. Furthermore, in order to gain insight about how DNA bending is achieved by this MADS-box factor, we performed circular permutation and phasing analysis using the wild type recombinant protein. The AGAMOUS MADS-box protein identified in this study has been found to predominantly accumulate in the climacteric fruit pulp and also in female flower ovary. In vivo and in vitro assays have revealed specific binding of the identified AGAMOUS MADS-box protein to CArG-box sequence in the promoters of major ripening genes in banana fruit. Overall, the expression patterns of this MADS-box protein in banana female flower ovary and during various phases of fruit ripening along with the interaction of the protein to the CArG-box sequence in the promoters of major ripening genes lead to interesting assumption about the possible involvement of this AGAMOUS MADS-box factor in banana fruit ripening and floral reproductive organ development. PMID:22984496

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

    PubMed

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

    2011-01-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

    Fukumoto, Seiji

    2008-03-01

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

  8. Characterization of an AGAMOUS homologue from the conifer black spruce (Picea mariana) that produces floral homeotic conversions when expressed in Arabidopsis.

    PubMed

    Rutledge, R; Regan, S; Nicolas, O; Fobert, P; Côté, C; Bosnich, W; Kauffeldt, C; Sunohara, G; Séguin, A; Stewart, D

    1998-09-01

    Advances in elucidating the molecular processes controlling flower initiation and development have provided unique opportunities to investigate the developmental genetics of non-flowering plants. In addition to providing insights into the evolutionary aspects of seed plants, identification of genes regulating reproductive organ development in gymnosperms could help determine the level of homology with current models of flower induction and floral organ identity. Based upon this, we have searched for putative developmental regulators in conifers with amino acid sequence homology to MADS-box genes. PCR cloning using degenerate primers targeted to the MADS-box domain revealed the presence of over 27 MADS-box genes within black spruce (Picea mariana), including several with extensive homology to either AP1 or AGAMOUS, both known to regulate flower development in Arabidopsis. This indicates that like angiosperms, conifers contain a large and diverse MADS-box gene family that probably includes regulators of reproductive organ development. Confirmation of this was provided by the characterization of an AGAMOUS-like cDNA clone called SAG1, whose conservation of intron position and tissue-specific expression within reproductive organs indicate that it is a homologue of AGAMOUS. Functional homology with AGAMOUS was demonstrated by the ability of SAG1 to produce homeotic conversions of sepals to carpels and petals to stamens when ectopically expressed in transgenic Arabidopsis. This suggests that some of the genetic pathways controlling flower and cone development are homologous, and antedate the 300-million-year-old divergence of angiosperms and gymnosperms.

  9. 40 CFR 1037.230 - Vehicle families, sub-families, and configurations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

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

  10. 40 CFR 1037.230 - Vehicle families, sub-families, and configurations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

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

  11. 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))).

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

    PubMed

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

    2013-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2008-10-31

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

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

    PubMed

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

    2001-07-01

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

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

    PubMed

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

    1998-11-01

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

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

    PubMed

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

    2014-06-01

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

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

    PubMed

    Angel, Martin; Graves, Carol

    2013-01-01

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

  19. 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.

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

    PubMed Central

    2013-01-01

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

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

    PubMed

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

    2005-02-01

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

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

    PubMed Central

    1986-01-01

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

  3. 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.

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

    PubMed Central

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

    2015-01-01

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

  5. 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.

  6. 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.

  7. 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

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

    PubMed

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

    2017-01-04

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

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

    PubMed

    Schodde, Richard; Christidis, Les

    2014-04-14

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

  10. 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

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

    PubMed

    Guidoti, Marcus; Montemayor, Sara I

    2016-08-11

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

  12. The MADS domain protein DIANA acts together with AGAMOUS-LIKE80 to specify the central cell in Arabidopsis ovules.

    PubMed

    Bemer, Marian; Wolters-Arts, Mieke; Grossniklaus, Ueli; Angenent, Gerco C

    2008-08-01

    MADS box genes in plants consist of MIKC-type and type I genes. While MIKC-type genes have been studied extensively, the functions of type I genes are still poorly understood. Evidence suggests that type I MADS box genes are involved in embryo sac and seed development. We investigated two independent T-DNA insertion alleles of the Arabidopsis thaliana type I MADS box gene AGAMOUS-LIKE61 (AGL61) and showed that in agl61 mutant ovules, the polar nuclei do not fuse and central cell morphology is aberrant. Furthermore, the central cell begins to degenerate before fertilization takes place. Although pollen tubes are attracted and perceived by the mutant ovules, neither endosperm development nor zygote formation occurs. AGL61 is expressed in the central cell during the final stages of embryo sac development. An AGL61:green fluorescent protein-beta-glucoronidase fusion protein localizes exclusively to the polar nuclei and the secondary nucleus of the central cell. Yeast two-hybrid analysis showed that AGL61 can form a heterodimer with AGL80 and that the nuclear localization of AGL61 is lost in the agl80 mutant. Thus, AGL61 and AGL80 appear to function together to differentiate the central cell in Arabidopsis. We renamed AGL61 DIANA, after the virginal Roman goddess of the hunt.

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

    PubMed

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

    2012-07-01

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

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

    PubMed

    Ober, Karen A

    2002-08-01

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

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

    PubMed

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

    2007-12-01

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

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

    PubMed

    Nobel, P S; Hartsock, T L

    1986-04-01

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

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

    PubMed

    Ravosa, M J

    1990-06-01

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

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. AGS experiments - 1994, 1995, 1996

    SciTech Connect

    Depken, J.C.

    1997-01-01

    This report contains the following information on the Brookhaven AGS Accelerator complex: FY 1996 AGS schedule as run; FY 1997 AGS schedule (working copy); AGS beams 1997; AGS experimental area FY 1994 physics program; AGS experimental area FY 1995 physics program; AGS experimental area FY 1996 physics program; AGS experimental area FY 1997 physics program (in progress); a listing of experiments by number; two-phage summaries of each experiment begin here, also ordered by number; listing of publications of AGS experiments begins here; and listing of AGS experimenters begins here.

  6. 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.

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

    PubMed

    Terry, R; Brown, G; Olmstead, R

    1997-05-01

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

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

    PubMed

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

    2009-12-01

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

  9. 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.

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

    PubMed

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

    2010-01-01

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

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

    PubMed

    Novikova, T I; Gordienko, N Ia

    2001-01-01

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

  12. 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.

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

    PubMed Central

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

    2010-01-01

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

  14. 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

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2005-01-17

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

  18. 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

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

    PubMed

    Xu, Jian-Hong; Messing, Joachim

    2009-11-01

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

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

    PubMed

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

    2013-02-01

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

  1. 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.

  2. Determination of floral organ identity by Arabidopsis MADS domain homeotic proteins AP1, AP3, PI, and AG is independent of their DNA-binding specificity.

    PubMed Central

    Riechmann, J L; Meyerowitz, E M

    1997-01-01

    The MADS domain homeotic proteins APETALA1 (AP1), APETALA3 (AP3), PISTILLATA (PI), and AGAMOUS (AG) combinatorially specify the identity of Arabidopsis floral organs. AP1/AP1, AG/AG, and AP3/PI dimers bind to similar CArG box sequences; thus, differences in DNA-binding specificity among these proteins do not seem to be the origin of their distinct organ identity properties. To assess the overall contribution that specific DNA binding could make to their biological specificity, we have generated chimeric genes in which the amino-terminal half of the MADS domain of AP1, AP3, PI, and AG was substituted by the corresponding sequences of human SRF and MEF2A proteins. In vitro DNA-binding assays reveal that the chimeric proteins acquired the respective, and distinct, DNA-binding specificity of SRF or MEF2A. However, ectopic expression of the chimeric genes reproduces the dominant gain-of-function phenotypes exhibited by plants ectopically expressing the corresponding Arabidopsis wild-type genes. In addition, both the SRF and MEF2 chimeric genes can complement the pertinent ap1-1, ap3-3, pi-1, or ag-3 mutations to a degree similar to that of AP1, AP3, PI, and AG when expressed under the control of the same promoter. These results indicate that determination of floral organ identity by the MADS domain homeotic proteins AP1, AP3, PI, and AG is independent of their DNA-binding specificity. In addition, the DNA-binding experiments show that either one of the two MADS domains of a dimer can be sufficient to confer a particular DNA-binding specificity to the complex and that sequences outside the amino-terminal basic region of the MADS domain can, in some cases, contribute to the DNA-binding specificity of the proteins. Images PMID:9243505

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

    PubMed Central

    Wu, Wenjie; LoVerde, Philip T.

    2008-01-01

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

  4. 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

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

    PubMed Central

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

    2012-01-01

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

  6. 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.

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

    PubMed

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

    2007-06-01

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

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

    PubMed

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

    1997-07-01

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

  9. 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.

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

    PubMed

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

    2014-10-10

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

  11. 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.

  12. AgRISTARS

    NASA Technical Reports Server (NTRS)

    1984-01-01

    An introduction to the overall AgRISTARS program, a general statement on progress, and separate summaries of the activities of each project, with emphasis on the technical highlights are presented. Organizational and management information on AgRISTARS is included in the appendices, as is a complete bibliography of publication and reports.

  13. AGS experiments: 1993 - 1994 - 1995

    SciTech Connect

    Depken, J.C.

    1996-04-01

    This report contains: FY 1995 AGS Schedule as Run; FY 1996-97 AGE Schedule (working copy); AGS Beams 1995; AGS Experimental Area FY 1993 Physics Program; AGS Experimental Area FY 1994 Physics Program; AGS Experimental Area FY 1995 Physics Program; AGS Experimental Area FY 1996 Physics Program (In progress); A listing of experiments by number; Two-page summaries of each experiment begin here, also ordered by number; Listing of publications of AGS experiments begins here; and Listing of AGS experimenters begins here. This is the twelfth edition.

  14. @AuAg nanostructures

    NASA Astrophysics Data System (ADS)

    Singh, Rina; Soni, R. K.

    2014-09-01

    Bimetallic and trimetallic nanoparticles have attracted significant attention in recent times due to their enhanced electrochemical and catalytic properties compared to monometallic nanoparticles. The numerical calculations using Mie theory has been carried out for three-layered metal nanoshell dielectric-metal-metal (DMM) system consisting of a particle with a dielectric core (Al@Al2O3), a middle metal Ag (Au) layer and an outer metal Au (Ag) shell. The results have been interpreted using plasmon hybridization theory. We have also prepared Al@Al2O3@Ag@Au and Al@Al2O3@AgAu triple-layered core-shell or alloy nanostructure by two-step laser ablation method and compared with calculated results. The synthesis involves temporal separations of Al, Ag, and Au deposition for step-by-step formation of triple-layered core-shell structure. To form Al@Ag nanoparticles, we ablated silver for 40 min in aluminium nanoparticle colloidal solution. As aluminium oxidizes easily in water to form alumina, the resulting structure is core-shell Al@Al2O3. The Al@Al2O3 particle acts as a seed for the incoming energetic silver particles for multilayered Al@Al2O3@Ag nanoparticles is formed. The silver target was then replaced by gold target and ablation was carried out for different ablation time using different laser energy for generation of Al@Al2O3@Ag@Au core-shell or Al@Al2O3@AgAu alloy. The formation of core-shell and alloy nanostructure was confirmed by UV-visible spectroscopy. The absorption spectra show shift in plasmon resonance peak of silver to gold in the range 400-520 nm with increasing ablation time suggesting formation of Ag-Au alloy in the presence of alumina particles in the solution.

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

    PubMed Central

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

    2006-01-01

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

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

    PubMed

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

    2016-12-21

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

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

    PubMed

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

    2010-01-01

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

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

    PubMed

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

    2005-02-01

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

  19. 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

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

    PubMed

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

    2010-07-01

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

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

    PubMed

    Amiche, Mohamed; Ladram, Ali; Nicolas, Pierre

    2008-11-01

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

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

    PubMed

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

    2008-11-01

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

  3. 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

  4. AgSTAR Partners

    EPA Pesticide Factsheets

    AgSTAR’s Partner Program builds stronger relationships with state and non-governmental stakeholders to support all phases of anaerobic digester projects: planning, deployment, and long-term success.

  5. 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.

  6. Ag-Al-Ca

    NASA Astrophysics Data System (ADS)

    Carow-Watamura, U.; Louzguine, D. V.; Takeuchi, A.

    This document is part of Part 1 http://dx.doi.org/10.1007/97.etType="URL"/> 'Systems from Ag-Al-Ca to Au-Pd-Si' of Subvolume B 'Physical Properties of Ternary Amorphous Alloys' of Volume 37 'Phase Diagrams and Physical Properties of Nonequilibrium Alloys' of Landolt-Börnstein - Group III 'Condensed Matter'. It contains the Chapter 'Ag-Al-Ca' with the content:

  7. 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.

  8. 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.

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

    PubMed

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

    2014-03-01

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

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

    PubMed Central

    2013-01-01

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

  11. 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.

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

    PubMed

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

    2010-01-26

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

  13. 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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-04-12

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

  16. 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.

  17. 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...

  18. 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.

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

    PubMed

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

    2007-10-01

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

  20. 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

  1. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2017-01-01

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

  4. 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...

  5. Heterostructured Ag3PO4/AgBr/Ag plasmonic photocatalyst with enhanced photocatalytic activity and stability under visible light

    NASA Astrophysics Data System (ADS)

    Wang, Wan-Sheng; Du, Hong; Wang, Rui-Xia; Wen, Tao; Xu, An-Wu

    2013-03-01

    A heterostructured Ag3PO4/AgBr/Ag plasmonic photocatalyst was prepared by a rational in situ ion exchange reaction between Ag3PO4 micro-cubes and Br- in aqueous solution followed by photoreduction. The photocatalytic activities of obtained photocatalysts were measured by the degradation of methyl orange (MO) and methylene blue (MB) under visible light irradiation (λ >= 400 nm). Compared to AgBr/Ag, Ag3PO4/AgBr heterocrystals and pure Ag3PO4 crystals, the heterostructured Ag3PO4/AgBr/Ag plasmonic photocatalysts exhibit much higher photocatalytic activity and stability. This enhanced photocatalytic activity suggests that the synergetic effects of the heterostructured Ag3PO4/AgBr/Ag and the strong SPR of Ag NPs on the surface result in the high efficiencies of the photocatalytic activity and the improved stability. With the assistance of Ag3PO4/AgBr/Ag heterostructures, only 8 min and 12 min are taken to completely decompose MO and MB molecules under visible-light irradiation, respectively. Furthermore, the photodegradation rate does not show an obvious decrease during ten successive cycles, indicating that our heterostructured Ag3PO4/AgBr/Ag plasmonic photocatalysts are extremely stable under visible-light irradiation.A heterostructured Ag3PO4/AgBr/Ag plasmonic photocatalyst was prepared by a rational in situ ion exchange reaction between Ag3PO4 micro-cubes and Br- in aqueous solution followed by photoreduction. The photocatalytic activities of obtained photocatalysts were measured by the degradation of methyl orange (MO) and methylene blue (MB) under visible light irradiation (λ >= 400 nm). Compared to AgBr/Ag, Ag3PO4/AgBr heterocrystals and pure Ag3PO4 crystals, the heterostructured Ag3PO4/AgBr/Ag plasmonic photocatalysts exhibit much higher photocatalytic activity and stability. This enhanced photocatalytic activity suggests that the synergetic effects of the heterostructured Ag3PO4/AgBr/Ag and the strong SPR of Ag NPs on the surface result in the high

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

    PubMed

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

    2016-04-13

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

  7. 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

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

    PubMed Central

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

    2007-01-01

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

  9. 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

  10. 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

  11. 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.

  12. Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis[OPEN

    PubMed Central

    Penfold, Christopher A.; Jenkins, Dafyd J.; Legaie, Roxane; Lawson, Tracy; Vialet-Chabrand, Silvere R.M.; Subramaniam, Sunitha; Hickman, Richard; Feil, Regina; Bowden, Laura; Hill, Claire; Lunn, John E.; Finkenstädt, Bärbel; Buchanan-Wollaston, Vicky; Beynon, Jim; Wild, David L.; Ott, Sascha

    2016-01-01

    In Arabidopsis thaliana, changes in metabolism and gene expression drive increased drought tolerance and initiate diverse drought avoidance and escape responses. To address regulatory processes that link these responses, we set out to identify genes that govern early responses to drought. To do this, a high-resolution time series transcriptomics data set was produced, coupled with detailed physiological and metabolic analyses of plants subjected to a slow transition from well-watered to drought conditions. A total of 1815 drought-responsive differentially expressed genes were identified. The early changes in gene expression coincided with a drop in carbon assimilation, and only in the late stages with an increase in foliar abscisic acid content. To identify gene regulatory networks (GRNs) mediating the transition between the early and late stages of drought, we used Bayesian network modeling of differentially expressed transcription factor (TF) genes. This approach identified AGAMOUS-LIKE22 (AGL22), as key hub gene in a TF GRN. It has previously been shown that AGL22 is involved in the transition from vegetative state to flowering but here we show that AGL22 expression influences steady state photosynthetic rates and lifetime water use. This suggests that AGL22 uniquely regulates a transcriptional network during drought stress, linking changes in primary metabolism and the initiation of stress responses. PMID:26842464

  13. Transcriptional Activity of the MADS Box ARLEQUIN/TOMATO AGAMOUS-LIKE1 Gene Is Required for Cuticle Development of Tomato Fruit1

    PubMed Central

    Giménez, Estela; Dominguez, Eva; Pineda, Benito; Heredia, Antonio; Moreno, Vicente; Angosto, Trinidad

    2015-01-01

    Fruit development and ripening entail key biological and agronomic events, which ensure the appropriate formation and dispersal of seeds and determine productivity and yield quality traits. The MADS box gene ARLEQUIN/TOMATO AGAMOUS-LIKE1 (hereafter referred to as TAGL1) was reported as a key regulator of tomato (Solanum lycopersicum) reproductive development, mainly involved in flower development, early fruit development, and ripening. It is shown here that silencing of the TAGL1 gene (RNA interference lines) promotes significant changes affecting cuticle development, mainly a reduction of thickness and stiffness, as well as a significant decrease in the content of cuticle components (cutin, waxes, polysaccharides, and phenolic compounds). Accordingly, overexpression of TAGL1 significantly increased the amount of cuticle and most of its components while rendering a mechanically weak cuticle. Expression of the genes involved in cuticle biosynthesis agreed with the biochemical and biomechanical features of cuticles isolated from transgenic fruits; it also indicated that TAGL1 participates in the transcriptional control of cuticle development mediating the biosynthesis of cuticle components. Furthermore, cell morphology and the arrangement of epidermal cell layers, on whose activity cuticle formation depends, were altered when TAGL1 was either silenced or constitutively expressed, indicating that this transcription factor regulates cuticle development, probably through the biosynthetic activity of epidermal cells. Our results also support cuticle development as an integrated event in the fruit expansion and ripening processes that characterize fleshy-fruited species such as tomato. PMID:26019301

  14. The MADS Domain Protein DIANA Acts Together with AGAMOUS-LIKE80 to Specify the Central Cell in Arabidopsis Ovules[W

    PubMed Central

    Bemer, Marian; Wolters-Arts, Mieke; Grossniklaus, Ueli; Angenent, Gerco C.

    2008-01-01

    MADS box genes in plants consist of MIKC-type and type I genes. While MIKC-type genes have been studied extensively, the functions of type I genes are still poorly understood. Evidence suggests that type I MADS box genes are involved in embryo sac and seed development. We investigated two independent T-DNA insertion alleles of the Arabidopsis thaliana type I MADS box gene AGAMOUS-LIKE61 (AGL61) and showed that in agl61 mutant ovules, the polar nuclei do not fuse and central cell morphology is aberrant. Furthermore, the central cell begins to degenerate before fertilization takes place. Although pollen tubes are attracted and perceived by the mutant ovules, neither endosperm development nor zygote formation occurs. AGL61 is expressed in the central cell during the final stages of embryo sac development. An AGL61:green fluorescent protein–β-glucoronidase fusion protein localizes exclusively to the polar nuclei and the secondary nucleus of the central cell. Yeast two-hybrid analysis showed that AGL61 can form a heterodimer with AGL80 and that the nuclear localization of AGL61 is lost in the agl80 mutant. Thus, AGL61 and AGL80 appear to function together to differentiate the central cell in Arabidopsis. We renamed AGL61 DIANA, after the virginal Roman goddess of the hunt. PMID:18713950

  15. Transcriptional Activity of the MADS Box ARLEQUIN/TOMATO AGAMOUS-LIKE1 Gene Is Required for Cuticle Development of Tomato Fruit.

    PubMed

    Giménez, Estela; Dominguez, Eva; Pineda, Benito; Heredia, Antonio; Moreno, Vicente; Lozano, Rafael; Angosto, Trinidad

    2015-07-01

    Fruit development and ripening entail key biological and agronomic events, which ensure the appropriate formation and dispersal of seeds and determine productivity and yield quality traits. The MADS box gene Arlequin/tomato Agamous-like1 (hereafter referred to as TAGL1) was reported as a key regulator of tomato (Solanum lycopersicum) reproductive development, mainly involved in flower development, early fruit development, and ripening. It is shown here that silencing of the TAGL1 gene (RNA interference lines) promotes significant changes affecting cuticle development, mainly a reduction of thickness and stiffness, as well as a significant decrease in the content of cuticle components (cutin, waxes, polysaccharides, and phenolic compounds). Accordingly, overexpression of TAGL1 significantly increased the amount of cuticle and most of its components while rendering a mechanically weak cuticle. Expression of the genes involved in cuticle biosynthesis agreed with the biochemical and biomechanical features of cuticles isolated from transgenic fruits; it also indicated that TAGL1 participates in the transcriptional control of cuticle development mediating the biosynthesis of cuticle components. Furthermore, cell morphology and the arrangement of epidermal cell layers, on whose activity cuticle formation depends, were altered when TAGL1 was either silenced or constitutively expressed, indicating that this transcription factor regulates cuticle development, probably through the biosynthetic activity of epidermal cells. Our results also support cuticle development as an integrated event in the fruit expansion and ripening processes that characterize fleshy-fruited species such as tomato.

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

    PubMed

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

    2009-01-01

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

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

    PubMed

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

    2010-01-01

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

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

    PubMed

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

    1994-12-01

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

  19. 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

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

    PubMed Central

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

    2016-01-01

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

  1. 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.

  2. 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.

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

    PubMed

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

    2005-06-17

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

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

    PubMed

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

    2012-10-01

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

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

    PubMed

    Tan, N H; Ponnudurai, G

    1992-02-01

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

  6. 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.

  7. 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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2005-07-01

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

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

    PubMed Central

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

    2008-01-01

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

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

    PubMed

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

    2003-08-22

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

  12. 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)

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

    PubMed

    Glaberman, Scott; Caccone, Adalgisa

    2008-07-01

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

  14. 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.

  15. AGS experiments -- 1991, 1992, 1993. Tenth edition

    SciTech Connect

    Depken, J.C.

    1994-04-01

    This report contains: (1) FY 1993 AGS schedule as run; (2) FY 1994--95 AGS schedule; (3) AGS experiments {ge} FY 1993 (as of 30 March 1994); (4) AGS beams 1993; (5) AGS experimental area FY 1991 physics program; (6) AGS experimental area FY 1992 physics program; (7) AGS experimental area FY 1993 physics program; (8) AGS experimental area FY 1994 physics program (planned); (9) a listing of experiments by number; (10) two-page summaries of each experiment; (11) listing of publications of AGS experiments; and (12) listing of AGS experiments.

  16. AGS experiments -- 1995, 1996 and 1997

    SciTech Connect

    Depken, J.C.; Presti, P.L.

    1997-12-01

    This report contains (1) FY 1995 AGS schedule as run; (2) FY 1996 AGS schedule as run; (3) FY 1997 AGS schedule as run; (4) FY 1998--1999 AGS schedule (proposed); (5) AGS beams 1997; (6) AGS experimental area FY 1995 physics program; (7) AGS experimental area FY 1996 physics program; (8) AGS experimental area FY 1997 physics program; (9) AGS experimental area FY 1998--1999 physics program (proposed); (10) a listing of experiments by number; (11) two-page summaries of each experiment, in order by number; and (12) listing of publications of AGS experiments.

  17. 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

  18. 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

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

    PubMed

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

    2004-01-01

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

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

    PubMed

    Macas, Jiri; Navrátilová, Alice; Mészáros, Tibor

    2003-10-01

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

  1. 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.

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

    PubMed

    Wallace, R S; Cota, J H

    1996-02-01

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

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

    PubMed

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

    2015-12-01

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

  4. 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.

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  7. 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.

  8. 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.

  9. 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

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

    PubMed

    Bergevin, Christopher

    2011-04-01

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

  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. 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

  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

    2016-01-25

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

  15. Preparation and antibacterial activities of Ag/Ag+/Ag3+ nanoparticle composites made by pomegranate (Punica granatum) rind extract

    NASA Astrophysics Data System (ADS)

    Yang, Hui; Ren, Yan-yu; Wang, Tao; Wang, Chuang

    Nano-silver and its composite materials are widely used in medicine, food and other industries due to their strong conductivity, size effect and other special performances. So far, more microbial researches have been applied, but a plant method is rarely reported. In order to open up a new way to prepare AgNP composites, pomegranate peel extract was used in this work to reduce Ag+ to prepare Ag/Ag+/Ag3+ nanoparticle composites. UV-Vis was employed to detect and track the reduction of Ag+ and the forming process of AgNPs. The composition, structure and size of the crystal were analyzed by XRD and TEM. Results showed that, under mild conditions, pomegranate peel extract reacted with dilute AgNO3 solution to produce Ag/Ag+/Ag3+ nanoparticle composites. At pH = 8 and 10 mmol/L of AgNO3 concentration, the size of the achieved composites ranged between 15 and 35 nm with spherical shapes and good crystallinity. The bactericidal experiment indicated that the prepared Ag/Ag+/Ag3+ nanoparticles had strong antibacterial activity against gram positive bacteria and gram negative bacteria. FTIR analysis revealed that biological macromolecules with groups of sbnd NH2, sbnd OH, and others were distributed on the surface of the newly synthesized Ag/Ag+/Ag3+ nanoparticles. This provided a useful clue to further study the AgNP biosynthesis mechanism.

  16. Ag/AgCl reference electrode in thionyl chloride electrolytes

    NASA Astrophysics Data System (ADS)

    Delnick, F. M.; Cieslak, W. R.

    1985-07-01

    Thionyl chloride is the active cathode and electrolyte solvent in Li/SOCl2 primary battery systems. To evaluate charge-transfer reactions in this solvent system, a reference electrode is required. This report describes the fabrication and characterization of Ag/AgCl microreference electrodes that can be used in SOCl2 battery electrolytes.

  17. Ag-Air Service

    NASA Technical Reports Server (NTRS)

    1981-01-01

    Econ, Inc.'s agricultural aerial application, "ag-air," involves more than 10,000 aircraft spreading insecticides, herbicides, fertilizer, seed and other materials over millions of acres of farmland. Difficult for an operator to estimate costs accurately and decide what to charge or which airplane can handle which assignment most efficiently. Computerized service was designed to improve business efficiency in choice of aircraft and determination of charge rates based on realistic operating cost data. Each subscriber fills out a detailed form which pertains to his needs and then receives a custom-tailored computer printout best suited to his particular business mix.

  18. Construction of Ag/AgCl nanostructures from Ag nanoparticles as high-performance visible-light photocatalysts

    NASA Astrophysics Data System (ADS)

    Yang, Fan; Liu, Dongzhi; Wang, Tianyang; Li, Wei; Hu, Wenping; Zhou, Xueqin

    2016-11-01

    A combined strategy of in situ oxidation and assembly is developed to prepare Ag/AgCl nanospheres and nanocubes from Ag nanoparticles under room temperature. It is a new facile way to fabricate Ag/AgCl with small sizes and defined morphologies. Ag/AgCl nanospheres with an average size of 80 nm were achieved without any surfactants, while Ag/AgCl nanocubes with a mean edge length of 150 nm were obtained by introduction of N-dodecyl- N, N-dimethyl-2-ammonio-acetate. The possible formation mechanism involves the self-assembly of AgCl nanoparticles, Ostwald ripening and photoreduction of Ag+ into Ag0 by the room light. The as-prepared Ag/AgCl nanospheres and nanocubes exhibit excellent photocatalytic activity and stability toward degradation of organic pollutants under visible-light irradiation. It is demonstrated that Ag/AgCl nanocubes display enhanced photocatalytic activity in comparison with Ag/AgCl nanospheres due to the more efficient charge transfer. This work may pave an avenue to construct various functional materials via the assembly strategy using nanoparticles as versatile building blocks.

  19. Communication: Structure, formation, and equilibration of ensembles of Ag-S complexes on an Ag surface

    SciTech Connect

    Russell, Selena M.; Kim, Yousoo; Liu, Da-Jiang; Evans, J. W.; Thiel, P. A.

    2013-02-15

    We have utilized conditions of very low temperature (4.7 K) and very low sulfur coverage to isolate and identify Ag-S complexes that exist on the Ag(111) surface. The experimental conditions are such that the complexes form at temperatures above the temperature of observation. These complexes can be regarded as polymeric chains of varying length, with an Ag4S pyramid at the core of each monomeric unit. Steps may catalyze the formation of the chains and this mechanism may be reflected in the chain length distribution.

  20. AGS Experiments: 1989, 1990, 1991

    SciTech Connect

    Depken, J.C.

    1992-02-01

    This report contains: Experimental areas layout; table of beam parameters and fluxes; experiment schedule as run''; proposed 1992 schedule; a listing of experiments by number; two-page summaries of each experiment begin here, also ordered by number; publications of AGS Experiments begin here; and list of AGS Experimenters begins here.

  1. AGS Experiments: 1989, 1990, 1991

    SciTech Connect

    Depken, J.C.

    1992-02-01

    This report contains: Experimental areas layout; table of beam parameters and fluxes; experiment schedule ``as run``; proposed 1992 schedule; a listing of experiments by number; two-page summaries of each experiment begin here, also ordered by number; publications of AGS Experiments begin here; and list of AGS Experimenters begins here.

  2. What Is Ag-Ed?

    ERIC Educational Resources Information Center

    Lindley, Judy

    Ag-Ed is an agricultural education project aimed at upper primary students, held in conjunction with the Toowoomba Show (similar to a county fair) in Queensland, Australia. The program achieves its purpose of helping children understand the impact and relevance that agriculture has on their everyday lives through two components, an Ag-Ed day and a…

  3. 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.

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

    PubMed

    Aĭbulatov, S V

    2014-01-01

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

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

    PubMed Central

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

    1993-01-01

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

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

    PubMed

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

    2014-10-01

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

  7. 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. 

  8. Plasmonic Ag2MoO4/AgBr/Ag composite: Excellent photocatalytic performance and possible photocatalytic mechanism

    NASA Astrophysics Data System (ADS)

    Wang, Zhongliao; Zhang, Jinfeng; Lv, Jiali; Dai, Kai; Liang, Changhao

    2017-02-01

    Plasmonic Ag2MoO4/AgBr/Ag composite is fabricated by in-situ ion exchange and reduction methods at room temperature. The samples are characterized by X-ray diffraction (XRD), UV-vis diffuse reflectance (DRS), energy-dispersive X-ray spectroscopy (EDS), scanning electron microscope (SEM) and photoluminescence (PL) measurements. The results show that butterfly-like Ag2MoO4 nanosheets served as the precursor, and Ag2MoO4/AgBr/Ag is formed in phase transformation with MoO42- displaced by Br-. The ternary Ag2MoO4/AgBr/Ag composite photocatalysts show greatly enhanced photocatalytic activity in photodegrading methylene blue (MB) under visible light irradiation compared with AgBr and Ag2MoO4. The pseudo-first-order rate constant kapp of Ag2MoO4/AgBr/Ag is 0.602 min-1, which is 11.6 and 18.3 times as high as that of AgBr and Ag2MoO4, respectively. Meanwhile, the efficiency of degradation still kept 90% after ten times cyclic experiments. Eventually, possible photocatalytic mechanism was proposed.

  9. 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.

  10. AgH, Ag/sub 2/, and AgO revisited: Basis set extensions

    SciTech Connect

    Martin, R.L.

    1987-05-01

    An extended basis set has been developed for Ag which significantly improves the agreement between theoretical and experimental spectroscopic parameters for AgH, AgO, and Ag/sub 2/. The major improvement comes about as a result of the improved treatment of electron correlation in the Ag d shell upon the introduction of f functions. Their inclusion produces very slight differences at the SCF level, but significant reductions in r/sub e/ and increases in ..omega../sub e/ and D/sub e/ in the Mo-dash-barller--Plesset perturbation theory expansion. At the MP4(SDTQ) level, typical results are 0.02 A too long for r/sub e/, 4% too low for ..omega../sub e/, and 10 kcal too small for D/sub e/. From a pragmatic standpoint, MP2 give results very similar to this at a much reduced level of effort.

  11. THE AGS ELECTROSTATIC SEPTUM.

    SciTech Connect

    HOCK,J.RUSSO,T.GLEN,J.BROWN,K.

    2003-05-12

    The previous slow beam extraction electro static septum in the AGS was designed in 1981. Research documented at the Fermi Laboratory was used as the base line for this design. The septum consisted of a ground plane of .002 inch diameter wire tungsten-rhenium alloy (75%W 25%Re) with a hollow welded titanium cathode assembly. The vacuum chamber is stationary and the septum is moved with a pair of high vacuum linear feed throughs. After years of beam time, the frequency of failures increased. The vacuum system design was poor by today's standards and resulted in long pump down times after repairs. The failures ranged from broken septum wires to a twisted cathode. In addition to the failures, the mechanical drive system had too much backlash, making the operating position difficult to repeat. The new septum needed to address all of these issues in order to become a more reliable septum.

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

    PubMed

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

    2016-11-23

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

  13. 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

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

    PubMed

    Jung, Jongduk; Choi, Hong-Keun

    2013-05-01

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

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

    PubMed

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

    2014-08-22

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

  16. 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

  17. The AGS-Booster lattice

    SciTech Connect

    Lee, Y.Y.; Barton, D.S.; Claus, J.; Cottingham, J.G.; Courant, E.D.; Danby, G.T.; Dell, G.F.; Forsyth, E.B.; Gupta, R.C.; Kats, J.

    1987-01-01

    The AGS Booster has three objectives. They are to increase the space charge limit of the AGS, to increase the intensity of the polarized proton beam by accumulating many linac pulses (since the intensity is limited by the polarized ion source), and to reaccelerate heavy ions from the BNL Tandem Van de Graaff before injection into the AGS. The machine is capable of accelerating protons at 7.5 Hertz from 200 MeV to 1.5 GeV or to lower final energies at faster repetition rates. The machine will also be able to accelerate heavy ions from as low as 1 MeV/nucleon to a magnetic rigidity as high as 17.6 Tesla-meters with a one second repetition rate. As an accumulator for polarized protons, the Booster should be able to store the protons at 200 MeV for several seconds. We expect that the Booster will increase the AGS proton intensity by a factor of four, polarized proton intensity by a factor of twenty to thirty, and will also enable the AGS to accelerate all species of heavy ions (at present the AGS heavy ion program is limited to the elements lighter than sulfur because it can only accelerate fully stripped ions). The construction project started in FY 1985 and is expected to be completed in 1989. The purpose of this paper is to provide a future reference for the AGS Booster lattice.

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

    PubMed

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

    2016-01-29

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

  19. 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

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

    PubMed Central

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

    2016-01-01

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

  1. Spin dynamics simulations at AGS

    SciTech Connect

    Huang, H.; MacKay, W.W.; Meot, F.; Roser, T.

    2010-05-23

    To preserve proton polarization through acceleration, it is important to have a correct model of the process. It has been known that with the insertion of the two helical partial Siberian snakes in the Alternating Gradient Synchrotron (AGS), the MAD model of AGS can not deal with a field map with offset orbit. The stepwise ray-tracing code Zgoubi provides a tool to represent the real electromagnetic fields in the modeling of the optics and spin dynamics for the AGS. Numerical experiments of resonance crossing, including spin dynamics in presence of the snakes and Q-jump, have been performed in AGS lattice models, using Zgoubi. This contribution reports on various results so obtained.

  2. Ag-Pd-Si (009)

    NASA Astrophysics Data System (ADS)

    Carow-Watamura, U.; Louzguine, D. V.; Takeuchi, A.

    This document is part of Part 1 http://dx.doi.org/10.1007/97.etType="URL"/> 'Systems from Ag-Al-Ca to Au-Pd-Si' of Subvolume B 'Physical Properties of Ternary Amorphous Alloys' of Volume 37 'Phase Diagrams and Physical Properties of Nonequilibrium Alloys' of Landolt-Börnstein - Group III 'Condensed Matter'. It contains the Chapter 'Ag-Pd-Si (009)' with the content:

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

    PubMed

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

    2009-01-01

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

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

    PubMed

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

    2014-02-28

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

  5. Facile synthesis, structure, and properties of Ag2S/Ag heteronanostructure

    NASA Astrophysics Data System (ADS)

    Sadovnikov, S. I.; Gusev, A. I.

    2016-09-01

    Ag2S/Ag heteronanostructure has been produced by a simple one-stage chemical deposition from aqueous solutions of silver nitrate, sodium sulfide, and sodium citrate with the use of monochromatic light irradiation. For simultaneous synthesis of Ag2S and Ag nanoparticles, deposition has been performed from reaction mixtures with reduced sodium sulfide concentration. The size of Ag2S and Ag nanoparticles is 45-50 and 15-20 nm, respectively. It is established that in the contact layer between silver sulfide and silver, nonconducting α-Ag2S acanthite transforms into superionic β-Ag2S argentite under the action of external electric field. The scheme of the operation of a resistive switch based on an Ag2S/Ag heteronanostructure is proposed. The UV-Vis optical absorption spectra of colloidal solutions of Ag2S/Ag heteronanostructures have been studied.

  6. Enhanced photocatalytic activity of Ag-TiO2/Ag heterogeneous films

    NASA Astrophysics Data System (ADS)

    Liang, Ying; Wang, ShaoHua; Guo, PengFeng

    2015-11-01

    Ag-deposited TiO2 and Ag (Ag-TiO2/Ag) films coated on glass substrates were prepared using a simple sol-gel and dip-coating method. The Ag chemical state was investigated through X-ray diffractometry and X-ray photoelectron spectroscopy. Results showed that the Ag mainly exists in metallic state in the Ag-TiO2 film. Ag-TiO2/Ag exhibits higher photocatalytic activity than individual Ag-TiO2 and TiO2/Ag films. This enhanced photocatalytic activity was attributed to high surface plasmon resonance effects and separation rates of photoinduced electron-hole pairs of Ag nanoparticles. Results were verified by photoluminescence and UV-Vis spectroscopy.

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

    PubMed

    Lackner, Tomáš; Gomy, Yves

    2014-01-01

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed

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

    1998-01-23

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

  10. 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.

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

    PubMed

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

    2015-02-01

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

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

    PubMed Central

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

    2013-01-01

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

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

    PubMed

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

    2016-11-01

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

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

    PubMed Central

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

    2016-01-01

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

  15. Study of the oxygen transport through Ag (110), Ag (poly), and Ag 2.0 Zr

    NASA Technical Reports Server (NTRS)

    Outlaw, R. A.; Wu, D.; Davidson, M. R.; Hoflund, Gar B.

    1992-01-01

    The transport of oxygen through high-purity membranes of Ag (110), Ag (poly), Ag (nano), and Ag 2.0 Zr has been studied by an ultrahigh vacuum permeation method over the temperature range of 400-800 C. The data show that there are substantial deviations from ordinary diffusion-controlled transport. A surface limitation has been confirmed by glow-discharge studies where the upstream O2 supply has been partially converted to atoms, which, for the same temperature and pressure, gave rise to over an order of magnitude increase in transport flux. Further, the addition of 2.0 wt percent Zr to the Ag has provided increased dissociative adsorption rates, which, in turn, increased the transport flux by a factor of 2. It was also observed that below a temperature of 630 C, the diffusivity exhibits an increase in activation energy of over 4 kcal/mol, which has been attributed to trapping of the atomic oxygen and/or kinetic barriers at the surface and subsurface of the vacuum interface. Above 630 C, the activation barrier decreases to the accepted value of about 11 kcal/mol for Ag (poly), consistent with zero concentration at the vacuum interface.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. 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.

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

    PubMed

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

    2014-05-01

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

  5. Effect of Ag Templates on the Formation of Au-Ag Hollow/Core-Shell Nanostructures.

    PubMed

    Tsai, Chi-Hang; Chen, Shih-Yun; Song, Jenn-Ming; Haruta, Mitsutaka; Kurata, Hiroki

    2015-12-01

    Au-Ag alloy nanostructures with various shapes were synthesized using a successive reduction method in this study. By means of galvanic replacement, twined Ag nanoparticles (NPs) and single-crystalline Ag nanowires (NWs) were adopted as templates, respectively, and alloyed with the same amount of Au(+) ions. High angle annular dark field-scanning TEM (HAADF-STEM) images observed from different rotation angles confirm that Ag NPs turned into AuAg alloy rings with an Au/Ag ratio of 1. The shifts of surface plasmon resonance and chemical composition reveal the evolution of the alloy ring formation. On the other hand, single-crystalline Ag NWs became Ag@AuAg core-shell wires instead of hollow nanostructure through a process of galvanic replacement. It is proposed that in addition to the ratio of Ag templates and Au ion additives, the twin boundaries of the Ag templates were the dominating factor causing hollow alloy nanostructures.

  6. Probing the rupture of a Ag atomic junction in a Ag-Au mixed electrode

    NASA Astrophysics Data System (ADS)

    Kim, Taekyeong

    2015-09-01

    We probed that the atomic junction in Ag part ruptures during stretching of atomic sized contacts of Ag-Au mixed electrodes, resulting in Ag-Ag electrodes through a scanning tunneling microscope breaking junction (STM-BJ) technique. We observed that the conductance and tunneling decay constant for a series of amine-terminated oligophenyl molecular junctions are essentially the same for the Ag-Au mixed and the Ag-Ag electrodes. We also found the molecular plateau length and the evolution patterns with the Ag-Au mixed electrodes are similar to those with Ag-Ag electrodes rather than the Au-Au electrodes in the molecular junction elongation. This result is attributed to the smaller binding energy of Ag atoms compared to that of Au atoms, so the Ag junction part is more easily broken than that of Au part in stretching of Ag-Au mixed electrodes. Furthermore, we successfully observed that the rupture force of the atomic junction for the Ag-Au mixed electrodes was identical to that for the Ag-Ag electrodes and smaller than that for the Au-Au electrodes. This study may advance the understanding of the electrical and the mechanical properties in molecular devices with Ag and Au electrodes in future.

  7. 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

  8. 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.

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

    PubMed

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

    2017-01-01

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

  10. Localization of 18S ribosomal genes in suckermouth armoured catfishes Loricariidae (Teleostei, Siluriformes) with discussion on the Ag-NOR evolution

    PubMed Central

    Alves, Anderson Luis; de Borba, Rafael Splendore; Pozzobon, Allan Pierre Bonetti; Oliveira, Claudio; Nirchio, Mauro; Granado, Angel; Foresti, Fausto

    2012-01-01

    Abstract The family Loricariidae with about 690 species divided into six subfamilies, is one of the world’s largest fish families. Cytogenetic studies conducted in the family showed that among 90 species analyzed the diploid number ranges from 2n=38 in Ancistrus sp. to 2n=96 in Hemipsilichthys gobio Luetken, 1874. In the present study, fluorescence in situ hybridization (FISH) was employed to determine the chromosomal localization of the 18S rDNA gene in four suckermouth armoured catfishes: Kronichthys lacerta (Nichols, 1919), Pareiorhaphis splendens (Bizerril, 1995), Liposarcus multiradiatus (Hancock, 1828) and Hypostomus prope plecostomus (Linnaeus, 1758). All species analyzed showed one chromosome pair with 18S rDNA sequences, as observed in the previous Ag-NORs analyses. The presence of size and numerical polymorphism was observed and discussed, with proposing a hypothesis of the Ag-NOR evolution in Loricariidae. PMID:24260671

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

    PubMed

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

    2016-12-01

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

  12. 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.

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

    PubMed

    Mayer, Werner; Pavlicev, Mihaela

    2007-09-01

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

  14. AG Draconis - a symbiotic mystery

    NASA Astrophysics Data System (ADS)

    Galis, R.; Hric, L.; Smelcer, L.

    2015-02-01

    Symbiotic system AG Draconis regularly undergoes quiescent and active stages which consist of the series of individual outbursts. The period analysis of new and historical photometric data, as well as radial velocities, confirmed the presence of the two periods. The longer one (~550 d) is related to the orbital motion and the shorter one (~355 d) could be due to pulsation of the cool component of AG Dra. In addition, the active stages change distinctively, but the outbursts are repeated with periods from 359 - 375 d.

  15. Studies of induced radioactivity at the AGS

    SciTech Connect

    Brown, K.A.; Tanaka, M.

    1987-01-01

    With the goals of higher proton intensities, along with the many modes the AGS now runs and those being commissioned to run, we have begun detailed studies of the beam induced radioactivity in the AGS.

  16. Ag nanotubes and Ag/AgCl electrodes in nanoporous membranes.

    PubMed

    Davenport, Matthew; Healy, Ken; Siwy, Zuzanna S

    2011-04-15

    Miniaturization of the entire experimental setup is a key requirement for widespread application of nanodevices. For nanopore biosensing, integrating electrodes onto the nanopore membrane and controlling the pore length is important for reducing the complexity and improving the sensitivity of the system. Here we present a method to achieve these goals, which relies on electroless plating to produce Ag nanotubes in track-etched polymer nanopore templates. By plating from one side only, we create a conductive nanotube that does not span the full length of the pore, and thus can act as a nanoelectrode located inside the nanopore. To give optimal electrochemical behavior for sensing, we coat the Ag nanotube with a layer of AgCl. We characterize the behavior of this nanoelectrode by measuring its current-voltage response and find that, in most cases, the response is asymmetric. The plated nanopores have initial diameters between 100 and 300 nm, thus a range suitable for detection of viruses.

  17. Loading effect of Ag/AgO on the photocatalytic performance of ZnO rods

    NASA Astrophysics Data System (ADS)

    Samsuddin, Aida Fitri; Aziz, Siti Nor Qurratu Aini Abd; Pung, Swee-Yong

    2017-01-01

    The photocatalytic performance of ZnO rods in degradation of Rhodamine B dye under UV light was improved by 7.3% via deposition of Ag/AgO using 1.0 × 10-3 g mL-1 of silver nitrate solution. However, its photodegradation efficiency decreased with the increase in silver nitrate concentration which was used to prepare the Ag/AgO-ZnO rods. This result suggests that the loading of Ag/AgO on the surface of ZnO rods affected the photocatalytic performance differently. The scavenger study indicates that the main reactive species responsible for the degradation of Rhodamine B dye by Ag-/AgO-deposited ZnO rods were holes, followed by superoxide anion free radicals, hydroxyl free radicals and electrons. Based on these findings, a refined photodegradation mechanism of Rhodamine B by Ag/AgO-ZnO rods is proposed.

  18. AGS experiments: 1990, 1991, 1992. Ninth edition

    SciTech Connect

    Depken, J.C.

    1993-04-01

    This report contains a description of the following: AGS Experimental Area - High Energy Physics FY 1993 and Heavy Ion Physics FY 1993; Table of Beam Parameters and Fluxes; Experiment Schedule ``as run``; Proposed 1993 Schedule; A listing of experiments by number; Two-page summaries of each experiment begin here, also ordered by number; Publications of AGS Experiments; and List of AGS Experimenters.

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

    PubMed Central

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

    2015-01-01

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

  20. Activation properties of Ag+-ion conduction in bulk amorphous AgI: estimation from extrapolation of the AgI composition dependence in AgI Ag2O P2O5 glasses

    NASA Astrophysics Data System (ADS)

    Hanaya, M.; Hatate, A.; Oguni, M.

    2003-06-01

    AgI-based fast-ion conducting glasses with very high AgI compositions from the (AgI)x(AgPO3)1-x, (AgI)x(Ag2PO3.5)1-x, and (AgI)x(Ag3PO4)1-x systems were prepared successfully by using a rapid-press quenching and a twin-roller quenching method. The ac dielectric measurements showed common relaxation properties of Ag+-ion conduction in the glasses independently of the species of the glass network formers of AgPO3, Ag2PO3.5, and Ag3PO4, and the activation energies, Δɛa, for Ag+-ion conduction were observed to converge upon the same magnitude of ~26 kJ mol-1 at the AgI composition limit of x = 1. This indicates the formation of amorphous AgI regions in the glasses, and the value of Δɛa = 26 +/- 1 kJ mol-1 estimated at x = 1 was concluded to correspond to that for bulk amorphous AgI which has never been obtained experimentally.

  1. AGS 20th anniversary celebration

    SciTech Connect

    Baggett, N.V.

    1980-05-22

    On May 22, 1980, a symposium was held at Brookhaven to celebrate the 20th birthday of the AGS, to recall its beginnings, and to review major discoveries that have been made with its beams. The talks at the symposium are recorded in this volume.

  2. AGS experiments, 1988, 1989, 1990

    SciTech Connect

    Depken, J.C.

    1991-04-01

    This report contains: experimental areas layout; table of beam parameters and fluxes; experiment schedule as run''; experiment long range schedule; a listing of experiments by number; two-page summaries of each experiment begin here, also ordered by number; publications of AGS experiments; and list of experimenters.

  3. AGS experiments: 1985, 1986, 1987

    SciTech Connect

    Depken, J.C.

    1987-01-01

    This report contains: Experimental areas layout, table of beam parameters and fluxes, experiment schedule ''as run,'' experiment long range schedule, a listing of experiments by number, two-page summaries of each experiment, also ordered by number, and publications of AGS experiments, 1982-1987.

  4. Antibacterial activity and reusability of CNT-Ag and GO-Ag nanocomposites

    NASA Astrophysics Data System (ADS)

    Kim, Ji Dang; Yun, Hyosuk; Kim, Gwui Cheol; Lee, Chul Won; Choi, Hyun Chul

    2013-10-01

    A facile approach to the synthesis of novel CNT-Ag and GO-Ag antibacterial materials, in which thiol groups are utilized as linkers to secure silver (Ag) nanoparticles to the CNT and GO surfaces without agglomeration, is reported. The resulting CNT-Ag and GO-Ag samples were characterized by performing TEM, XRD, Auger, XPS, and Raman measurements, which revealed that in these antibacterial materials size-similar and quasi-spherical Ag nanoparticles are anchored to the CNT and GO surfaces. The Ag nanoparticles in CNT-Ag and GO-Ag have narrow size distributions with average diameters of 2.6 and 3.5 nm respectively. The antibacterial activities of CNT-Ag and GO-Ag against Escherichia coli were assessed with the paper-disk diffusion method and by determining the minimal inhibitory concentrations (MICs). CNT-Ag was found to have higher antibacterial activity than the reference Ag colloid. Moreover, both CNT-Ag and GO-Ag retain more than 50% of their original antibacterial activities after 20 washes with detergent, which indicates their potential as antibacterial materials for laboratory and medical purposes.

  5. Comparative Study of Antimicrobial Activity of AgBr and Ag Nanoparticles (NPs)

    PubMed Central

    Suchomel, Petr; Kvitek, Libor; Panacek, Ales; Prucek, Robert; Hrbac, Jan; Vecerova, Renata; Zboril, Radek

    2015-01-01

    The diverse mechanism of antimicrobial activity of Ag and AgBr nanoparticles against gram-positive and gram-negative bacteria and also against several strains of candida was explored in this study. The AgBr nanoparticles (NPs) were prepared by simple precipitation of silver nitrate by potassium bromide in the presence of stabilizing polymers. The used polymers (PEG, PVP, PVA, and HEC) influence significantly the size of the prepared AgBr NPs dependently on the mode of interaction of polymer with Ag+ ions. Small NPs (diameter of about 60–70 nm) were formed in the presence of the polymer with low interaction as are PEG and HEC, the polymers which interact with Ag+ strongly produce nearly two times bigger NPs (120–130 nm). The prepared AgBr NPs were transformed to Ag NPs by the reduction using NaBH4. The sizes of the produced Ag NPs followed the same trends – the smallest NPs were produced in the presence of PEG and HEC polymers. Prepared AgBr and Ag NPs dispersions were tested for their biological activity. The obtained results of antimicrobial activity of AgBr and Ag NPs are discussed in terms of possible mechanism of the action of these NPs against tested microbial strains. The AgBr NPs are more effective against gram-negative bacteria and tested yeast strains while Ag NPs show the best antibacterial action against gram-positive bacteria strains. PMID:25781988

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2017-01-25

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

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

    PubMed Central

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

    2007-01-01

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

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

    PubMed

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

    2011-02-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2008-09-01

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

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

    PubMed

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

    2017-02-24

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed Central

    Wei, Z M; Beer, S V

    1995-01-01

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

  15. 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

  16. 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

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

    PubMed

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

    2015-03-01

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

  18. 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

  19. Characterization of spark plasma sintered Ag nanopowders.

    PubMed

    Fu, Y Q; Shearwood, C; Xu, B; Yu, L G; Khor, K A

    2010-03-19

    The low temperature sintering behaviour of nanocrystalline Ag powder (with an average size of 70 nm) was characterized. Using spark plasma sintering (SPS), the Ag nanopowders can be successfully sintered at low pressure for only 5 min without external heating, and the sintering density increases and porosity decreases significantly with increase in the sintering temperature. Nanoindentation has been used to characterize the SPS sintered Ag samples. The mechanisms of the low sintering temperature behaviour of the nano-Ag powder and the nanoscale mechanical performance have been discussed. Compression tests were also used to characterize the mechanical properties of the sintered Ag sample with a maximum strain up to 15%.

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

    PubMed

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

    2007-08-01

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

  1. Synergistic effect of interfacial lattice Ag(+) and Ag(0) clusters in enhancing the photocatalytic performance of TiO2.

    PubMed

    Xu, Liming; Zhang, Dandan; Ming, Lufei; Jiao, Yanchao; Chen, Feng

    2014-09-28

    An interfacial lattice Ag(+) doped on TiO2 (Ag(+)/TiO2) was prepared by eluting Ag(0) clusters from a hydrothermally prepared Ag(0)/Ag(+)/TiO2 composite. An Ag(+)/TiO2@Ag(0) composite photocatalyst was subsequently obtained via a secondary Ag(0) clusters loading process to the Ag(+)/TiO2. The photocatalytic activity of Ag(+)/TiO2@Ag(0) was greatly improved compared to Ag(0)/Ag(+)/TiO2 and Ag(+)/TiO2. X-ray photoelectron spectroscopy (XPS) and cyclic voltammetry (CV) testing verified that Ag(+) ions occur as an interfacial lattice Ag(+) species in the composites. The enhancement effect of the interfacial lattice Ag(+) species is exhibited by the newly-formed Ag(+)/TiO2@Ag(0) as the interfacial lattice Ag(+) is fully exposed but not overlapped with the re-loaded Ag(0) clusters. The interfacial lattice Ag(+) ions and Ag(0) clusters are both responsible for the photocatalytic performance improvement of the catalyst, in either the photocatalytic degradation of methyl orange or photocurrent measurement.

  2. 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

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

    PubMed

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

    2016-01-01

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

  4. Enhancing the ag precipitation by surface mechanical attrition treatment on Cu-Ag alloys

    NASA Astrophysics Data System (ADS)

    Liu, Jiabin; Zhang, Lehao; Liu, Jingjing; Huang, Liuyi; Gu, Hao; Fang, Youtong; Meng, Liang; Zhang, Jian

    2016-09-01

    The influence of surface mechanical attrition treatment (SMAT) on Ag precipitation in Cu-Ag alloys was investigated. Cu-6 wt% Ag was melt, cold rolled and solution treated to be Cu-Ag solid solution, which was either aged at 250 and 350 °C for 24 h directly or SMAT-ed before aging. Ag precipitates were hard be found in the directly aged Cu-Ag sample while they were observed clearly in the SMAT-ed counterpart at 250 °C. The Ag precipitates formed in the surface layer by SMAT are much coarser than those in the un-SMAT-ed sample. It is obvious that the precipitating behavior of Ag was promoted significantly by SMAT approach. A large number of defects were generated by SMAT and they were acting as fast atomic diffusion channels that facilitated the atomic diffusion of Ag.

  5. 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

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

    PubMed

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

    2014-04-01

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

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

    SciTech Connect

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

    1996-02-01

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

  8. 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

  9. 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

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

    PubMed

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

    2014-01-01

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

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

    PubMed

    Bochkov, Andre V; Klompen, Hans

    2015-09-01

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

  12. 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

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

    PubMed

    Hara, Hideho

    2016-06-24

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

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

    PubMed

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

    2016-11-01

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

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

    PubMed

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

    2015-12-15

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

  16. Polymorphism of LiAg

    NASA Astrophysics Data System (ADS)

    Pavlyuk, V. V.; Dmytriv, G. S.; Tarasiuk, I. I.; Chumak, I. V.; Pauly, H.; Ehrenberg, H.

    2010-02-01

    A phase transition from the cubic CsCl-type structure (Pm-3m space group) into a tetragonal UPb-type structure (I4 1/amd) is observed for the LiAg binary compound at ambient conditions. The crystal structure of the tetragonal modification of the LiAg binary compound was solved by direct methods in SHELXS on the base of structure factors which were extracted from a powder diffraction pattern and refined by SHELXL and the Rietveld method ( a = 3.9605(1), c = 8.2825(2) Å, Bragg R-factor = 4.81, Rf-factor = 4.87). Elevated temperatures and/or a small Li-excess versus the equimolar composition favour the cubic structure whereas ambient and lower temperatures and/or a small Li-deficiency stabilize the tetragonal structure. This reconstructive transition is reversible but proceeds slowly.

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

    PubMed

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

    2015-09-30

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

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

    PubMed

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

    2002-05-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2017-03-17

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

  2. The class III peroxidase PRX17 is a direct target of the MADS-box transcription factor AGAMOUS-LIKE15 (AGL15) and participates in lignified tissue formation.

    PubMed

    Cosio, Claudia; Ranocha, Philippe; Francoz, Edith; Burlat, Vincent; Zheng, Yumei; Perry, Sharyn E; Ripoll, Juan-Jose; Yanofsky, Martin; Dunand, Christophe

    2017-01-01

    Several physiological functions have been attributed to class III peroxidases (PRXs) in plants, but the in planta role of most members of this family still remains undetermined. Here, we report the first functional characterization of PRX17 (At2g22420), one of the 73 members of this family in Arabidopsis thaliana. Localization of PRX17 was examined by transient expression in Nicotiana benthamiana. Loss- and gain-of-function mutants in A. thaliana were studied. Regulation at the gene and protein levels was analyzed using β-glucuronidase (GUS) activity, quantitative reverse transcriptase (qRT)-PCR, zymography, and chromatin immunoprecipitation. Phenotypes were characterized including lignin and xylan contents. PRX17 was expressed in various tissues, including vascular tissues, and PRX17 was localized to the cell wall. In prx17, the lignin content was reduced in the stem and siliques and bolting was delayed, while the opposite phenotype was observed in 35S:PRX17 plants, together with a significant increase of lignin and xylan immunofluorescence signal. Finally, we demonstrated that the transcription factor AGAMOUS-LIKE15 (AGL15) binds to the PRX17 promoter and regulates PRX17 expression level. This converging set of structural, transcriptomic and physiological data suggests that PRX17, under the control of AGL15, contributes to developmental programs by playing an essential role in regulating age-dependent lignified tissue formation, including changes in cell wall properties.

  3. 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.

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

    PubMed

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

    2016-10-01

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

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

    PubMed

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

    2009-07-03

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

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

    PubMed

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

    2012-01-01

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

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

    PubMed

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

    2016-07-01

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

  8. 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.

  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. 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

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

    PubMed

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

    2005-01-01

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

  12. Capacitive deionization of seawater effected by nano Ag and Ag@C on graphene.

    PubMed

    Cai, P-F; Su, C-J; Chang, W-T; Chang, F-C; Peng, C-Y; Sun, I-W; Wei, Y-L; Jou, C-J; Wang, H Paul

    2014-08-30

    Drinking water shortage has become worse in recent decades. A new capacitive deionization (CDI) method for increasing water supplies through the effective desalination of seawater has been developed. Silver as nano Ag and Ag@C which was prepared by carbonization of the Ag(+)-β-cyclodextrin complex at 573 K for 30 min can add the antimicrobial function into the CDI process. The Ag@C and Ag nanoparticles dispersed on reduced graphene oxide (Ag@C/rGO and nano Ag/rGO) were used as the CDI electrodes. The nano Ag/rGO and Ag@C/rGO electrodes can reduce the charging resistant, and enhance the electrosorption capability. Better CDI efficiencies with the nano Ag/rGO and Ag@C/rGO electrodes can therefore be obtained. When reversed the voltage, the electrodes can be recovered up to 90% within 5 min. This work presents the feasibility for the nano Ag and Ag@C on rGO electrodes applied in CDI process to produce drinking water from seawater or saline water.

  13. Facile synthesis of S-Ag nanocomposites and Ag2S short nanorods by the interaction of sulfur with AgNO3 in PEG400

    NASA Astrophysics Data System (ADS)

    Zhang, Yan-Li; Xie, Xin-Yuan; Liang, Ming; Xie, Shu-Ming; Chen, Jie-Mei; Zheng, Wen-Jie

    2016-06-01

    A facile, eco-friendly and inexpensive method to prepare Ag2S short nanorods and S-Ag nanocomposites using sublimed sulfur, AgNO3, PVP and PEG400 was studied. According to x-ray diffraction and scanning electron microscopy of the Ag2S, the products are highly crystalline and pure Ag2S nanorods with diameters of 70-160 nm and lengths of 200-360 nm. X-ray diffraction of the S-Ag nanocomposites shows that we obtained cubic Ag and S nanoparticles. Transmission electron microscopy shows that the molar ratio of PVP to Ag+ plays an important role in controlling the size and morphology of the S-Ag nanocomposites. When the molar ratio of PVP to Ag+ was 10:1, smaller sizes, better dispersibility and narrower distribution of S-Ag nanocomposites with diameters of 10-40 nm were obtained. The formation mechanism of the S-Ag nanocomposites was studied by designing a series of experiments using ultraviolet-visible measurement, and it was found that S nanoparticles are produced first and act as seed crystals; then Ag+ becomes Ag nanocrystals on the surfaces of the S nanoparticles by the reduction of PVP. PEG400 acts as a catalyzer, accelerating the reaction rate, and protects the S-Ag nanocomposites from reacting to produce Ag2S. The antimicrobial experiments show that the S-Ag nanocomposites have greater antimicrobial activity on Staphylococcus aureus, Aspergillus niger and blue mold than Ag nanoparticles.

  14. AgI/Ag{sub 3}PO{sub 4} hybrids with highly efficient visible-light driven photocatalytic activity

    SciTech Connect

    Katsumata, Hideyuki; Hayashi, Takahiro; Taniguchi, Masanao; Suzuki, Tohru; Kaneco, Satoshi

    2015-03-15

    Highlights: • AgI/Ag{sub 3}PO{sub 4} hybrid was prepared via an in situ anion-exchange method. • AgI/Ag{sub 3}PO{sub 4} displays the excellent photocatalytic activity under visible light. • AgI/Ag{sub 3}PO{sub 4} readily transforms to be Ag@AgI/Ag{sub 3}PO{sub 4} system. • h{sup +} and O{sub 2}{sup ·−} play the major role in the AO 7 decolorization over AgI/Ag{sub 3}PO{sub 4}. • The activity enhancement is ascribed to a Z-scheme system composed of Ag{sub 3}PO{sub 4}, Ag and AgI. - Abstract: Highly efficient visible-light-driven AgI/Ag{sub 3}PO{sub 4} hybrid photocatalysts with different mole ratios of AgI were prepared via an in situ anion-exchange method and characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), UV–vis diffuse reflectance spectroscopy (DRS) and photoluminescence (PL) technique. Under visible light irradiation (>420 nm), the AgI/Ag{sub 3}PO{sub 4} photocatalysts displayed the higher photocatalytic activity than pure Ag{sub 3}PO{sub 4} and AgI for the decolorization of acid orange 7 (AO 7). Among the hybrid photocatalysts, AgI/Ag{sub 3}PO{sub 4} with 80% of AgI exhibited the highest photocatalytic activity for the decolorization of AO 7. X-ray photoelectron spectroscopy (XPS) results revealed that AgI/Ag{sub 3}PO{sub 4} readily transformed to be Ag@AgI/Ag{sub 3}PO{sub 4} system while the photocatalytic activity of AgI/Ag{sub 3}PO{sub 4} remained after 5 recycling runs. In addition, the quenching effects of different scavengers displayed that the reactive h{sup +} and O{sub 2}{sup ·−} play the major role in the AO 7 decolorization. The photocatalytic activity enhancement of AgI/Ag{sub 3}PO{sub 4} hybrids can be ascribed to the efficient separation of electron–hole pairs through a Z-scheme system composed of Ag{sub 3}PO{sub 4}, Ag and AgI, in which Ag nanoparticles act as the charge separation center.

  15. The cardiovascular response to the AGS

    NASA Technical Reports Server (NTRS)

    Cardus, David; Mctaggart, Wesley G.

    1993-01-01

    This paper reports the preliminary results of experiments on human subjects conducted to study the cardiovascular response to various g-levels and exposure times using an artificial gravity simulator (AGS). The AGS is a short arm centrifuge consisting of a turntable, a traction system, a platform and four beds. Data collection hardware is part of the communication system. The AGS provides a steep acceleration gradient in subjects in the supine position.

  16. Multiple Partial Siberian Snakes in the AGS

    NASA Astrophysics Data System (ADS)

    Takano, J.; Ahrens, L. A.; Bai, M.; Brown, K.; Courant, E. D.; Gardner, C. J.; Glenn, J. W.; Hattori, T.; Huang, H.; Lin, F.; Luccio, A. U.; MacKay, W. W.; Okamura, M.; Roser, T.; Tepikian, S.; Tsoupas, N.; Yip, K.; Zelenski, A.; Zeno, K.

    2007-06-01

    Polarized protons are accelerated up to 24.3 GeV in the Alternating Gradient Synchrotron (AGS) at Brookhaven National Laboratory (BNL). To accelerate the beam with preserving the polarization, two different types of helical dipole partial Siberian snake have been installed to the AGS. One is a superconducting magnet (Cold Snake, CSNK), and the other is a normal conducting one (Warm Snake, WSNK). With these snake magnets, the polarization at the AGS extraction achieved 65%. However, the AGS has spin mismatches at the injection and extraction. This description shows calculated results to have better spin matching with using two or three snakes.

  17. Multiple Partial Siberian Snakes in the AGS

    SciTech Connect

    Takano, J.; Ahrens, L. A.; Bai, M.; Brown, K.; Courant, E. D.; Gardner, C. J.; Glenn, J. W.; Huang, H.; Luccio, A. U.; MacKay, W. W.; Okamura, M.; Roser, T.; Tepikian, S.; Tsoupas, N.; Yip, K.; Zelenski, A.; Zeno, K.; Hattori, T.; Lin, F.

    2007-06-13

    Polarized protons are accelerated up to 24.3 GeV in the Alternating Gradient Synchrotron (AGS) at Brookhaven National Laboratory (BNL). To accelerate the beam with preserving the polarization, two different types of helical dipole partial Siberian snake have been installed to the AGS. One is a superconducting magnet (Cold Snake, CSNK), and the other is a normal conducting one (Warm Snake, WSNK). With these snake magnets, the polarization at the AGS extraction achieved 65%. However, the AGS has spin mismatches at the injection and extraction. This description shows calculated results to have better spin matching with using two or three snakes.

  18. Transformation from Ag@Ag3PO4 to Ag@Ag2SO4 hybrid at room temperature: preparation and its visible light photocatalytic activity

    NASA Astrophysics Data System (ADS)

    Wei, Ting; Gao, Shanmin; Wang, Qingyao; Xu, Hui; Wang, Zeyan; Huang, Baibiao; Dai, Ying

    2017-02-01

    In the present study, Ag/Ag2SO4 hybrid photocatalysts were obtained via a facile redox-precipitation reaction approach by using Ag@Ag3PO4 nanocomposite as the precursor and KMnO4 as the oxidant. Multiple techniques, such as X-ray diffraction pattern (XRD), transmission electron microscope (TEM), high-resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS), UV-vis diffuse reflectance spectroscopy (DRS) and Brunauer-Emmett-Teller (BET), photocurrent and electrochemical impedance spectroscopy (EIS), were applied to investigate the structures, morphologies, optical, and electronic properties of as-prepared samples. The photocatalytic activities were evaluated by photodegradation of organic rhodamine B (RhB) and methyl orange (MO) under visible light irradiation. It was found that pure Ag2SO4 can partially transform into metallic Ag during the photocatalytic degradation of organic pollutants, but the Ag/Ag2SO4 hybrids can maintain its structure stability and show enhanced visible light photocatalytic activity because of the surface plasma resonance effect of the metallic Ag.

  19. Toxicokinetics of Ag in the terrestrial isopod Porcellionides pruinosus exposed to Ag NPs and AgNO₃ via soil and food.

    PubMed

    Tourinho, Paula S; van Gestel, Cornelis A M; Morgan, A John; Kille, Peter; Svendsen, Claus; Jurkschat, Kerstin; Mosselmans, J Fred W; Soares, Amadeu M V M; Loureiro, Susana

    2016-03-01

    Silver nanoparticles (Ag NPs) have been used in numerous consumer products and may enter the soil through the land application of biosolids. However, little is known about the relationship between Ag NP exposure and their bioavailability for soil organisms. This study aims at comparing the uptake and elimination kinetics of Ag upon exposures to different Ag forms (NPs and ionic Ag (as AgNO3)) in the isopod Porcellionides pruinosus. Isopods were exposed to contaminated Lufa 2.2 soil or alder leaves as food. Uptake and elimination rate constants for soil exposure did not significantly differ between Ag NPs and ionic Ag at 30 and 60 mg Ag/kg. For dietary exposure, the uptake rate constant was up to 5 times higher for Ag NPs than for AgNO3, but this was related to feeding activity and exposure concentrations, while no difference in the elimination rate constants was found. When comparing both routes, dietary exposure resulted in lower Ag uptake rate constants but elimination rate constants did not differ. A fast Ag uptake was observed from both routes and most of the Ag taken up seemed not to be eliminated. Synchrotron X-ray fluorescence showed Ag in the S-cells of the hepatopancreas, thus supporting the observations from the kinetic experiment (i.e. low elimination). In addition, our results show that isopods have an extremely high Ag accumulation capacity, suggesting the presence of an efficient Ag storage compartment.

  20. Single step electrochemical synthesis of hydrophilic/hydrophobic Ag5 and Ag6 blue luminescent clusters.

    PubMed

    Santiago González, Beatriz; Blanco, M C; López-Quintela, M Arturo

    2012-12-21

    Well-defined Ag(5) and Ag(6) dodecanethiol/tetrabutyl ammonium-protected clusters were prepared by a one-pot electrochemical method. Ag clusters show bright and photostable emissions. The presence of a dual capping renders the silver clusters soluble in both organic and aqueous solvents.

  1. Synthesis of Cu-Ag@Ag particles using hyperbranched polyester as template

    NASA Astrophysics Data System (ADS)

    Han, Wen-Song

    2015-07-01

    In this manuscript, the third-generation hyperbranched polyester was synthesized with 2, 2-dimethylol propionic acid as AB2 monomer and pentaerythrite as core molecule by using step by step polymerization process at first. Then, the Cu-Ag particles were prepared by co-reduction of silver nitrate and copper nitrate with ascorbic acid in the aqueous solution using hyperbranched polyester as template. Finally, the Cu-Ag@Ag particles were prepared by coating silver on the surface of Cu-Ag particles by reduction of silver nitrate. The synthesized hyperbranched polyester and Cu-Ag@Ag particles were characterized by Fourier transform infrared (FT-IR) spectroscopy, UV-vis spectra, x-ray diffraction, Laser light scattering, thermogravimetric analysis (TGA) and SEM. UV-vis spectra results showed that the Cu-Ag@Ag particles had a strong absorption band at around 420 nm. Laser light scattering and SEM studies confirmed that the most frequent particle sizes of Cu-Ag@Ag particles were 1.2 um. TGA results indicated that the Cu-Ag@Ag particles had good thermal stability. [Figure not available: see fulltext.

  2. An Au/AgBr-Ag heterostructure plasmonic photocatalyst with enhanced catalytic activity under visible light.

    PubMed

    Purbia, Rahul; Paria, Santanu

    2017-01-17

    This study reports an easy synthesis protocol of a novel bimetallic silver halide (Au/AgBr-Ag) plasmonic heterostructure as a visible light induced photocatalyst. In this process, first CTAB capped Au NPs were coated with AgBr, and then Ag nanoparticles were formed on the surface of AgBr by photoreduction, while exposing to daylight at room temperature. The presence of Au and Ag improves the visible absorption ability of NPs and avoids charge recombination of the semiconductor AgBr during photoexcitation, which in turn enhances 16 and 8.9 fold the photocatalytic efficiency of Rhodamine B dye degradation under visible light irradiation compared to that of pure AgBr and AgBr/Ag, respectively. The recycling tests of the photocatalyst show only ∼8.7% decrease in efficiency after the 5(th) cycle of reuse without changing the morphology. During the photocatalytic process, active superoxide radicals (O2˙(-)) play a major role, proved through scavenger trapping and photoluminescence experiments. The presence of two plasmonic metals (Au and Ag) in the heterostructure helps to improve visible light absorption as well as avoid charge recombination of the semiconductor AgBr to act as a better photocatalyst. Since this heteronanostructure can be easily synthesized by a one-step method, this study could provide a new approach for the development of efficient bimetallic/semiconductor halide plasmonic photocatalysts with enhanced visible absorption and better charge separation.

  3. Highly efficient visible light plasmonic photocatalyst Ag@Ag(Br,I).

    PubMed

    Wang, Peng; Huang, Baibiao; Zhang, Qianqian; Zhang, Xiaoyang; Qin, Xiaoyan; Dai, Ying; Zhan, Jie; Yu, Jiaoxian; Liu, Haixia; Lou, Zaizhu

    2010-09-03

    The new plasmonic photocatalyst Ag@Ag(Br,I) was synthesized by the ion-exchange process between the silver bromide and potassium iodide, then by reducing some Ag(+) ions in the surface region of Ag(Br,I) particles to Ag(0) species. Ag nanoparticles are formed from Ag(Br,I) by the light-induced chemical reduction reaction. The Ag@Ag(Br,I) particles have irregular shapes with their sizes varying from 83 nm to 1 mum. The as-grown plasmonic photocatalyst shows strong absorption in the visible light region because of the plasmon resonance of Ag nanoparticles. The ability of this compound to reduce Cr(VI) under visible light was compared with those of other reference photocatalyst. The plasmonic photocatalyst is shown to be highly efficient under visible light. The stability of the photocatalyst was examined by X-ray diffraction and X-ray photoelectron spectroscopy. The XRD pattern and XPS spectra prove the stability of the plasmonic photocatalyst Ag@Ag(Br,I).

  4. Negligible shift of 3Ag- potential in longer-chain carotenoids as revealed by a single persistent peak of 3Ag-→1Ag- stimulated emission followed by 3Ag-←1Ag- transient-absorption

    NASA Astrophysics Data System (ADS)

    Li, Chunyong; Miki, Takeshi; Kakitani, Yoshinori; Koyama, Yasushi; Nagae, Hiroyoshi

    2007-12-01

    Upon excitation of lycopene, anhydrorhodovibrin or spirilloxanthin to the 1Bu+(0) state, stimulated emission followed by transient-absorption was observed as a single peak with the 3Ag-(0) energy that had been determined by measurement of resonance-Raman excitation profiles. This observation was explained in terms of negligible shift of the 3Ag- potential, in reference to the 1Ag- potential, where only the 3Ag-(υ)→1Ag-(υ) emission and the 3Ag-(υ)←1Ag-(υ) absorption become allowed during the vibrational relaxation of υ = 2 → 1 → 0, starting from the 3Ag-(2) level generated by diabatic internal conversion from the 1Bu+(0) level, in anhydrorhodovibrin, for example.

  5. Half-life determination for 108Ag and 110Ag

    NASA Astrophysics Data System (ADS)

    Zahn, Guilherme S.; Genezini, Frederico A.

    2014-11-01

    In this work, the half-life of the short-lived silver radionuclides 108Ag and 110Ag were measured by following the activity of samples after they were irradiated in the IEA-R1 reactor. The results were then fitted using a non-paralizable dead time correction to the regular exponential decay and the individual half-life values obtained were then analyzed using both the Normalized Residuals and the Rajeval techniques, in order to reach the most exact and precise final values. To check the validity of dead-time correction, a second correction method was also employed by means of counting a long-lived 60Co radioactive source together with the samples as a livetime chronometer. The final half-live values obtained using both dead-time correction methods were in good agreement, showing that the correction was properly assessed. The results obtained are partially compatible with the literature values, but with a lower uncertainty, and allow a discussion on the last ENSDF compilations' values.

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

    PubMed

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

    1994-02-01

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

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

    PubMed Central

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

    2012-01-01

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

  8. 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

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

    PubMed Central

    2010-01-01

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

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

    PubMed Central

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

    2007-01-01

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

  11. Progress with the AGS Booster

    SciTech Connect

    Weng, W.T.

    1988-01-01

    Rare K-decay, neutrino and heavy ion physics demands that a rapid- cycling high vacuum and high intensity Booster be built for the AGS at Brookhaven. For each mode of operation there are corresponding accelerator physics and design issues needing special attention. Problems pertinent to any single mode of operation have been encountered and solved before, but putting high intensity proton requirements and high vacuum heavy ion requirements into one machine demands careful design considerations and decisions. The lattice design and magnet characteristics will be briefly reviewed. Major design issues will be discussed and design choices explained. Finally, the construction status and schedule will be presented. 6 refs., 6 figs.

  12. Visible light driven photocatalysis and antibacterial activity of AgVO{sub 3} and Ag/AgVO{sub 3} nanowires

    SciTech Connect

    Singh, Anamika; Dutta, Dimple P.; Ballal, A.; Tyagi, A.K.; Fulekar, M.H.

    2014-03-01

    Graphical abstract: - Highlights: • Ag/AgVO{sub 3} and pure AgVO{sub 3} nanowires synthesized by sonochemical process. • Characterization done using XRD, SEM, TEM, EDX and BET analysis. • Visible light degradation of RhB by Ag/AgVO{sub 3} within 45 min. • Antibacterial activity of Ag/AgVO{sub 3} demonstrated. - Abstract: Ag/AgVO{sub 3} nanowires and AgVO{sub 3} nanorods were synthesized in aqueous media via a facile sonochemical route. The as-synthesized products were characterized by X-ray diffraction, Brunauer–Emmett–Teller surface area analysis, scanning electron microscopy together with an energy dispersion X-ray spectrum analysis, transmission electron microscopy and UV–vis diffuse reflectance spectroscopy. The results revealed that inert atmosphere promotes the formation of Ag/AgVO{sub 3} nanowires. The photocatalytic studies revealed that the Ag/AgVO{sub 3} nanowires exhibited complete photocatalytic degradation of Rhodamine B within 45 min under visible light irradiation. The antibacterial activity of Ag/AgVO{sub 3} nanowires was tested against Escherechia coli and Bacillus subtilis. The minimum growth inhibitory concentration value was found to be 50 and 10 folds lower than for the antibiotic ciprofloxacin for E. coli and B. subtilis, respectively. The antibacterial properties of the β-AgVO{sub 3} nanorods prove that in case of the Ag dispersed Ag/AgVO{sub 3} nanowires, the enhanced antibacterial action is also due to contribution from the AgVO{sub 3} support.

  13. Effects of soil and dietary exposures to Ag nanoparticles and AgNO₃ in the terrestrial isopod Porcellionides pruinosus.

    PubMed

    Tourinho, Paula S; van Gestel, Cornelis A M; Jurkschat, Kerstin; Soares, Amadeu M V M; Loureiro, Susana

    2015-10-01

    The effects of Ag-NPs and AgNO3 on the isopod Porcellionides pruinosus were determined upon soil and dietary exposures. Isopods avoided Ag in soil, with EC50 values of ∼16.0 and 14.0 mg Ag/kg for Ag-NPs and AgNO3, respectively. Feeding inhibition tests in soil showed EC50s for effects on consumption ratio of 127 and 56.7 mg Ag/kg, respectively. Although similar EC50s for effects on biomass were observed for nanoparticulate and ionic Ag (114 and 120 mg Ag/kg dry soil, respectively), at higher concentrations greater biomass loss was found for AgNO3. Upon dietary exposure, AgNO3 was more toxic, with EC50 for effects on biomass change being >1500 and 233 mg Ag/kg for Ag-NPs and AgNO3, respectively. The difference in toxicity between Ag-NPs and AgNO3 could not be explained from Ag body concentrations. This suggests that the relation between toxicity and bioavailability of Ag-NPs differs from that of ionic Ag in soils.

  14. Photocatalytic oxidation removal of Hg0 using ternary Ag/AgI-Ag2CO3 hybrids in wet scrubbing process under fluorescent light

    NASA Astrophysics Data System (ADS)

    Zhang, Anchao; Zhang, Lixiang; Chen, Xiaozhuan; Zhu, Qifeng; Liu, Zhichao; Xiang, Jun

    2017-01-01

    A series of ternary Ag/AgI-Ag2CO3 photocatalysts synthesized using a facile coprecipitation method were employed to investigate their performances of Hg0 removal in a wet scrubbing reactor. The hybrids were characterized by N2 adsorption-desorption, XRD, SEM-EDS, HRTEM, XPS, DRS and ESR. The photocatalytic activities of Hg0 removal were evaluated under fluorescent light. The results showed that AgI content, fluorescent light irradiation, reaction temperature all showed significant influences on Hg0 removal. NO exhibited significant effect on Hg0 removal in comparison to SO2. Among these ternary Ag/AgI-Ag2CO3 hybrids, Ag/AgI(0.1)-Ag2CO3 showed the highest Hg0 removal efficiency, which could be ascribed to the effective separation of photogenerated electron-hole pairs between AgI and Ag2CO3 and the surface plasmon resonance (SPR) effect in the visible region by metallic silver nanoparticles (Ag0 NPs). The trapping studies of reactive radicals showed that the superoxide radicals (rad O2-) may play a key role in Hg0 removal under fluorescent light. According to the experimental and characterization results, a possible photocatalytic oxidation mechanism for enhanced Hg0 removal over Ag/AgI(0.1)-Ag2CO3 hybrid under fluorescent light was proposed.

  15. AgRISTARS documents tracking list report

    NASA Technical Reports Server (NTRS)

    Hawkins, J. L.

    1983-01-01

    A quarterly listing of documents issued and placed in the AgRISTARS tracking system is provided. The technical publications are arranged by type of documents. The reference AgRISTARS document number, title and date of publication, the issuing organization, and the National Technical Information Service reference number is given.

  16. The AGS synchrotron with four helical magnets

    SciTech Connect

    Tsoupas N.; Huang, H.; Roser, T.; MacKay, W.W.; Trbojevic, D.

    2012-05-20

    The idea of using two partial helical magnets was applied successfully to the AGS synchrotron to preserve the proton beam polarization. In this paper we explore in details the idea of using four helical magnets placed symmetrically in the AGS ring. The placement of four helical magnets in the AGS ring provides many advantages over the present setup of the AGS which uses two partial helical magnets. First, the symmetric placement of the four helical magnets allows for a better control of the AGS optics with reduced values of the beta functions especially near beam injection, second, the vertical spin direction during beam injection and extraction is closer to vertical, and third, it provides for a larger 'spin tune gap', which allows the vertical and horizontal tunes to be placed, and prevent the horizontal and vertical intrinsic spin resonances of the AGS to occur during the acceleration cycle. Although the same spin gap can be obtained with a single or two partial helices, the required high field strength of a single helix makes its use impractical, and that of the double helix rather difficult. In this paper we will provide results on the spin tune and on the optics of the AGS with four partial helical magnets, and compare these results with the present setup of the AGS that uses two partial helical magnets.

  17. AgPO2F2 and Ag9(PO2F2)14: the first Ag(i) and Ag(i)/Ag(ii) difluorophosphates with complex crystal structures.

    PubMed

    Malinowski, Przemysław J; Kurzydłowski, Dominik; Grochala, Wojciech

    2015-12-07

    The reaction of AgF2 with P2O3F4 yields a mixed valence Ag(I)/Ag(II) difluorophosphate salt with AgAg(PO2F2)14 stoichiometry - the first Ag(ii)-PO2F2 system known. This highly moisture sensitive brown solid is thermally stable up to 120 °C, which points at further feasible extension of the chemistry of Ag(ii)-PO2F2 systems. The crystal structure shows a very complex bonding pattern, comprising of polymeric Ag(PO2F2)14(4-) anions and two types of Ag(I) cations. One particular Ag(II) site present in the crystal structure of Ag9(PO2F2)14 is the first known example of square pyramidal penta-coordinated Ag(ii) in an oxo-ligand environment. Ag(i)PO2F2 - the product of the thermal decomposition of Ag9(PO2F2)14 - has also been characterized by thermal analysis, IR spectroscopy and X-ray powder diffraction. It has a complicated crystal structure as well, which consists of infinite 1D [Ag(I)O4/2] chains which are linked to more complex 3D structures via OPO bridges. The PO2F2(-) anions bind to cations in both compounds as bidentate oxo-ligands. The terminal F atoms tend to point inside the van der Waals cavities in the crystal structure of both compounds. All important structural details of both title compounds were corroborated by DFT calculations.

  18. Ligand and counterion control of Ag(I) architectures: assembly of a {Ag8} ring cluster mediated by hydrophobic and Ag...Ag interactions.

    PubMed

    Fielden, John; Long, De-liang; Slawin, Alexandra M Z; Kögerler, Paul; Cronin, Leroy

    2007-10-29

    A strategy combining ligand design and counterion variation has been used to investigate the assembly of silver(I) complexes. As a result, dinuclear, octanuclear, and polymeric silver(I) species have been synthesized by complexation of the rigid aliphatic amino ligands cis-3,5-diamino-trans-hydroxycyclohexane (DAHC), cis-3,5-diamino-trans-methoxycyclohexane (DAMC), and cis-3,5-diamino-trans-tert-butyldimethylsilylanyloxycyclohexane (DATC) with silver(I) triflate, nitrate, and perchlorate. The compositions of these aggregates, established by X-ray crystallography and elemental analysis, are [{Ag(DAHC)}2](CF3SO3)2 (1), [{Ag(DAMC)}2](CF3SO3)2 (2), [{Ag(DAMC)}2](NO3)2 (3), [{Ag(DATC)}6{Ag(DAHC)}2](NO3)8 (4), and [{Ag(DATC}n](NO3)n (5), where the DAHC present in 4 is formed by in situ hydrolysis of the acid labile silyl ether group. The type of aggregate formed depends both upon the noncoordinating O-substituent of the ligand and the (also noncoordinating) counterion, with the normal preference of the ligand topology for forming Ag2L2 structures being broken by introduction of the bulky, lipophilic O-tert-butyldimethylsilyl (TBDMS) group. Of particular note is the octanuclear silver ring structure 4, which is isolated only when both the O-TBDMS group and the nitrate counteranion are present and is formed from four Ag2L2 dimers connected by Ag...Ag and hydrogen-bonding interactions. Diffusion rate measurement of this {Ag8} complex by 1H NMR (DOSY) indicates dissociation in CD3OD and CD3CN, showing that this supramolecular ring structure is formed upon crystallization, and establishing a qualitative limit to the strength of Ag...Ag interactions in solution. When solutions of the {Ag8} cluster in methanol are kept for several days though, a new UV-vis absorption is observed at around 430 nm, consistent with the formation of silver nanoparticles.

  19. Fluorescent DNA-bound Ag nanoclusters

    NASA Astrophysics Data System (ADS)

    O'Neill, Patrick; Velazquez, Lourdes; Weirich, Kim; Fygenson, Deborah

    2009-03-01

    Few-atom fluorescent Ag nanoclusters self-assemble on short, synthetic DNA strands, and exhibit sequence and structure dependent fluorescence ranging from the blue to the near infrared. Here we report UV excitation as a ubiquitous feature of these emitters. Each emitter thus has two excitation peaks: a visible peak which is cluster-dependent, and a UV peak which has the same wavelength for all DNA-bound Ag clusters. This UV peak corresponds to resonant absorbance by the DNA bases, and produces the same emission spectra as visible excitation, suggesting energy transfer from the DNA bases to the Ag cluster. We make use of this UV excitation to image the emitters in unstained polyacrylamide gels, and show that electrophoresis can be used to create a pure solution of green DNA:Ag11 clusters from an inhomogeneous red solution of DNA:Ag>12 clusters.

  20. Direct electrospinning of Ag/polyvinylpyrrolidone nanocables

    NASA Astrophysics Data System (ADS)

    Song, Jie; Chen, Menglin; Olesen, Mikkel Buster; Wang, Chenxuan; Havelund, Rasmus; Li, Qiang; Xie, Erqing; Yang, Rong; Bøggild, Peter; Wang, Chen; Besenbacher, Flemming; Dong, Mingdong

    2011-12-01

    Core-sheath silver nanowire/polyvinylpyrrolidone (AgNW/PVP) nanocables have been fabricated via an efficient single-spinneret electrospinning method. The core-sheath structure is revealed by combining several characterization methods. A possible formation mechanism of the AgNW/PVP nanocable involving a strong stretching during the electrospinning process is proposed. Further, electrical measurements were performed on AgNW/PVP nanocables as well as bare AgNWs, which indicated the nanocables became insulating due to the isolation of highly conductive AgNWs by insulating PVP sheath. Therefore, the described fabrication method holds potential for the fabrication of low-cost metal/polymer composite materials for nanoelectronic applications in general.

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

    PubMed

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

    2016-12-01

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

  2. 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.

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

    PubMed

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

    2014-08-01

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

  4. Antibacterial biodegradable Mg-Ag alloys.

    PubMed

    Tie, D; Feyerabend, F; Müller, W D; Schade, R; Liefeith, K; Kainer, K U; Willumeit, R

    2013-06-16

    The use of magnesium alloys as degradable metals for biomedical applications is a topic of ongoing research and the demand for multifunctional materials is increasing. Hence, binary Mg-Ag alloys were designed as implant materials to combine the favourable properties of magnesium with the well-known antibacterial property of silver. In this study, three Mg-Ag alloys, Mg2Ag, Mg4Ag and Mg6Ag that contain 1.87 %, 3.82 % and 6.00 % silver by weight, respectively, were cast and processed with solution (T4) and aging (T6) heat treatment. The metallurgical analysis and phase identification showed that all alloys contained Mg4Ag as the dominant β phase. After heat treatment, the mechanical properties of all Mg-Ag alloys were significantly improved and the corrosion rate was also significantly reduced, due to presence of silver. Mg(OH)₂ and MgO present the main magnesium corrosion products, while AgCl was found as the corresponding primary silver corrosion product. Immersion tests, under cell culture conditions, demonstrated that the silver content did not significantly shift the pH and magnesium ion release. In vitro tests, with both primary osteoblasts and cell lines (MG63, RAW 264.7), revealed that Mg-Ag alloys show negligible cytotoxicity and sound cytocompatibility. Antibacterial assays, performed in a dynamic bioreactor system, proved that the alloys reduce the viability of two common pathogenic bacteria, Staphylococcus aureus (DSMZ 20231) and Staphylococcus epidermidis (DSMZ 3269), and the results showed that the killing rate of the alloys against tested bacteria exceeded 90%. In summary, biodegradable Mg-Ag alloys are cytocompatible materials with adjustable mechanical and corrosion properties and show promising antibacterial activity, which indicates their potential as antibacterial biodegradable implant materials.

  5. A multi-locus species phylogeny of African forest duikers in the subfamily Cephalophinae: evidence for a recent radiation in the Pleistocene

    PubMed Central

    2012-01-01

    Background Duikers in the subfamily Cephalophinae are a group of tropical forest mammals believed to have first originated during the late Miocene. However, knowledge of phylogenetic relationships, pattern and timing of their subsequent radiation is poorly understood. Here we present the first multi-locus phylogeny of this threatened group of tropical artiodactyls and use a Bayesian uncorrelated molecular clock to estimate divergence times. Results A total of 4152 bp of sequence data was obtained from two mitochondrial genes and four nuclear introns. Phylogenies were estimated using maximum parsimony, maximum likelihood, and Bayesian analysis of concatenated mitochondrial, nuclear and combined datasets. A relaxed molecular clock with two fossil calibration points was used to estimate divergence times. The first was based on the age of the split between the two oldest subfamilies within the Bovidae whereas the second was based on the earliest known fossil appearance of the Cephalophinae and molecular divergence time estimates for the oldest lineages within this group. Findings indicate strong support for four major lineages within the subfamily, all of which date to the late Miocene/early Pliocene. The first of these to diverge was the dwarf duiker genus Philantomba, followed by the giant, eastern and western red duiker lineages, all within the genus Cephalophus. While these results uphold the recognition of Philantomba, they do not support the monotypic savanna-specialist genus Sylvicapra, which as sister to the giant duikers leaves Cephalophus paraphyletic. BEAST analyses indicate that most sister species pairs originated during the Pleistocene, suggesting that repeated glacial cycling may have played an important role in the recent diversification of this group. Furthermore, several red duiker sister species pairs appear to be either paraphyletic (C.callipygus/C. ogilbyi and C. harveyi/C. natalensis) or exhibit evidence of mitochondrial admixture (C. nigrifrons

  6. Biting midges of the subfamily Forcipomyiinae (Diptera: Ceratopogonidae) from the Middle East, with keys and descriptions of new species.

    PubMed

    Alwin-Kownacka, Alicja; Szadziewski, Ryszard; Szwedo, Jacek

    2016-10-05

    Middle East biting midges of the genera Atrichopogon Kieffer and Forcipomyia Meigen, subfamily Forcipomyiinae Lenz, covering 41 species are reviewed. Two new species are described and illustrated: Forcipomyia (F.) siverekensis Alwin & Szadziewski sp. nov. and Forcipomyia (Microhelea) borkenti Alwin & Szadziewski sp. nov. The list includes 16 species of Atrichopogon and 25 of Forcipomyia. Nine species previously described by Vimmer and Kieffer from the Middle East are treated as nomina dubia and not included in the list.        Keys to identification of Atrichopogon and Forcipomyia species of the Middle East are also provided.

  7. Characterization and Expression Analysis of PtAGL24, a SHORT VEGETATIVE PHASE/AGAMOUS-LIKE 24 (SVP/AGL24)-Type MADS-Box Gene from Trifoliate Orange (Poncirus trifoliata L. Raf.)

    PubMed Central

    Sun, Lei-Ming; Zhang, Jin-Zhi; Hu, Chun-Gen

    2016-01-01

    The transition from vegetative to reproductive growth in perennial woody plants does not occur until after several years of repeated seasonal changes and alternative growth. To better understand the molecular basis of flowering regulation in citrus, a MADS-box gene was isolated from trifoliate orange (precocious trifoliate orange, Poncirus trifoliata L. Raf.). Sequence alignment and phylogenetic analysis showed that the MADS-box gene is more closely related to the homologs of the AGAMOUS-LIKE 24 (AGL24) lineage than to any of the other MADS-box lineages known from Arabidopsis; it is named PtAGL24. Expression analysis indicated that PtAGL24 was widely expressed in the most organs of trifoliate orange, with the higher expression in mature flowers discovered by real-time PCR. Ectopic expression of PtAGL24 in wild-type Arabidopsis promoted early flowering and caused morphological changes in class I transgenic Arabidopsis. Yeast two-hybrid assay revealed that PtAGL24 interacted with Arabidopsis AtAGL24 and other partners of AtAGL24, suggesting that the abnormal morphology of PtAGL24 overexpression in transgenic Arabidopsis was likely due to the inappropriate interactions between exogenous and endogenous proteins. Also, PtAGL24 interacted with SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (PtSOC1) and APETALA1 (PtAP1) of citrus. These results suggest that PtAGL24 may play an important role in the process of floral transition but may have diverse functions in citrus development. PMID:27375669

  8. Photo- and thermo-chemical transformation of AgCl and Ag2S in environmental matrices and its implication.

    PubMed

    Yin, Yongguang; Xu, Wei; Tan, Zhiqiang; Li, Yanbin; Wang, Weidong; Guo, Xiaoru; Yu, Sujuan; Liu, Jingfu; Jiang, Guibin

    2017-01-01

    AgCl and Ag2S prevalently exist in the environment as minerals and/or the chlorination and sulfidation products of ionic silver and elemental silver nanoparticles (AgNPs). In this work, we investigated the chemical transformation of AgCl and Ag2S under simulated sunlight (in water) and incineration (in sludge and simulated municipal solid waste, SMSW). In the presence of natural organic matter, AgCl in river water was observed to be transformed into AgNPs under simulated sunlight, while photo-reduction of Ag2S could not take place under the same experimental conditions. During the course of incineration, pure Ag2S was transformed into elemental silver while AgCl remained stable; however, both Ag2S in sludge and AgCl in SMSW can be transformed to elemental silver under incineration, evident by the results of X-ray absorption spectroscopy and scanning electron microscopy measurements. Incineration temperature played an important role in the transformation of Ag2S and AgCl into elemental silver. These results suggest that chemical transformations of Ag2S and AgCl into elemental silver could be a possible source of naturally occurring or unintentionally produced AgNPs, affecting the fate, transport, bioavailability and toxicity of silver. Therefore, it is necessary to include the contributions of this transformation process when assessing the risk of ionic silver/AgNPs and the utilization and management of incineration residues.

  9. Formation of AgGaS2 nano-pyramids from Ag2S nanospheres through intermediate Ag2S-AgGaS2 heterostructures and AgGaS2 sensitized Mn2+ emission.

    PubMed

    Huang, Feng; Zhou, Jiangcong; Xu, Ju; Wang, Yuansheng

    2014-02-21

    A one-pot solution synthesis of monodisperse AgGaS2 nanocrystals with uniform pyramid-like shape is realized for the first time, in which an interesting phase and shape evolution from monodisperse Ag2S nanospheres to pure AgGaS2 nano-pyramids through an intermediate stage of Ag2S-AgGaS2 heterostructures, is revealed. Evidently, upon introducing Mn(2+) ions into the reaction system, they are incorporated into AgGaS2 nano-pyramids which act as efficient sensitization matrixes for the red emission of Mn(2+) d-d transition under blue excitation. Benefiting from their non-toxicity and facile fabrication, Mn:AgGaS2 nanocrystals may find potential applications in some fields such as blue chip excited LEDs and bio-labeling.

  10. AgS2O6CF3: the first trifluoromethylsulfonylsulfate(VI).

    PubMed

    Malinowski, Przemysław J; Derzsi, Mariana; Grochala, Wojciech

    2013-08-07

    We describe the synthetic route towards a novel class of salts, trifluoromethylsulfonylsulfates, as exemplified by the silver(I) derivative (AgS2O6CF3). Formation proceeds via direct reaction between a triflate precursor, AgSO3CF3, and SO3. The title compound crystallizes in the P2(1)/c unit cell with a = 5.15746(14) Å, b = 25.8563(9) Å, c = 5.53970(14) Å and β = 101.1749(19)°. The structure is layered with the puckered [AgS2O6] 2D sheets; the terminal CF3 groups are separated by the van der Waals gap, as seen also for related metal triflates. The compound is very fragile thermally and it decomposes endothermally to AgSO3CF3 with concomitant evolution of SO3 even at 65 °C or upon grinding in an agate mortar; thus it may serve as a solid store of--otherwise volatile and corrosive--SO3. The IR and Raman spectra of AgS2O6CF3 have been tentatively assigned based on similarities to those of related Ag2S2O7 and AgSO3CF3 and phonon calculations. Synthesis and properties of KS2O6CF3 are also briefly described.

  11. On the measurement of /sup 107/Ag//sup 109/Ag ratios in meteorites

    SciTech Connect

    Kutschera, W.; Faestermann, T.; Gillitzer, A.; Fortuna, G.

    1986-01-01

    The detection of stable Ag isotopes in meteorites at the ppB level was attempted in an AMS experiment using the Munich MP tandem accelerator in conjunction with a time-of-flight detection system. The sensitivity of detecting Ag at this level was established by observing a counting rate of 17 ions of /sup 107/Ag per sec from a Au sample, which had been spiked with the radioisotope /sup 105/Ag (T/sub 1/2/ = 41 d) at a concentration of 1.0 ppB. A blank Ta sample gave no /sup 105/Ag counts in 13 min, which corresponds to a detection limit of 7.5 x 10/sup -5/ ppB. Although this sensitivity was clearly sufficient to perform /sup 107/Ag and /sup 109/Ag measurements in the desired concentration range, experiments with these isotopes were hampered by a currently irreducable background of stable Ag in the ppM range, possibly originating from the ion source itself. Indications of extraordinarily high Ag concentrations, far above this background, were observed in some of the investigated meteorites, but conclusions on their actual existence must await a better understanding of the origin of the general Ag background. 10 refs., 4 figs., 3 tabs.

  12. Study of antibacterial activity of Ag and Ag2CO3 nanoparticles stabilized over montmorillonite

    NASA Astrophysics Data System (ADS)

    Sohrabnezhad, Sh.; Pourahmad, A.; Mehdipour Moghaddam, M. J.; Sadeghi, A.

    2015-02-01

    Silver carbonate and silver nanoparticles (NPs) over of stabilizer montmorillonite (MMT) have been synthesized in aqueous and polyol solvent, respectively. Dispersions of silver nanoparticles have been prepared by the reduction of silver nitrate over of MMT in presence and absence of Na2CO3 compound in ethylene glycol. It was observed that montmorillonite was capable of stabilizing formed Ag nanoparticles through the reduction of Ag+ ions in ethylene glycol. Na2CO3 was used as carbonate source in synthesis of Ag2CO3 NPs in water solvent and also for controlling of Ag nanoparticles size in ethylene glycol medium. The samples were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), transmission electron microscopy (TEM), and ultraviolet-visible diffuse reflectance spectroscopy (DRS). The TEM images showed that Ag NPs size in presence Na2CO3 salts was smaller than without that. The results indicated intercalation of Ag and Ag2CO3 nanoparticles into the montmorillonite clay layers. The diffuse reflectance spectra exhibited a strong surface plasmon resonance (SPR) adsorption peak in the visible region, resulting from Ag nanoparticles. The antibacterial testing results showed that the Ag2CO3-MMT nanocomposite exhibited an antibacterial activity higher than Ag-MMT sample against Escherichia coli.

  13. Hierarchically plasmonic photocatalysts of Ag/AgCl nanocrystals coupled with single-crystalline WO3 nanoplates

    NASA Astrophysics Data System (ADS)

    Chen, Deliang; Li, Tao; Chen, Qianqian; Gao, Jiabing; Fan, Bingbing; Li, Jian; Li, Xinjian; Zhang, Rui; Sun, Jing; Gao, Lian

    2012-08-01

    The hierarchical photocatalysts of Ag/AgCl@plate-WO3 have been synthesized by anchoring Ag/AgCl nanocrystals on the surfaces of single-crystalline WO3 nanoplates that were obtained via an intercalation and topochemical approach. The heterogeneous precipitation process of the PVP-Ag+-WO3 suspensions with a Cl- solution added drop-wise was developed to synthesize AgCl@WO3 composites, which were then photoreduced to form Ag/AgCl@WO3 nanostructures in situ. WO3 nanocrystals with various shapes (i.e., nanoplates, nanorods, and nanoparticles) were used as the substrates to synthesize Ag/AgCl@WO3 photocatalysts, and the effects of the WO3 contents and photoreduction times on their visible-light-driven photocatalytic performance were investigated. The techniques of TEM, SEM, XPS, EDS, XRD, N2 adsorption-desorption and UV-vis DR spectra were used to characterize the compositions, phases and microstructures of the samples. The RhB aqueous solutions were used as the model system to estimate the photocatalytic performance of the as-obtained Ag/AgCl@WO3 nanostructures under visible light (λ >= 420 nm) and sunlight. The results indicated that the hierarchical Ag/AgCl@plate-WO3 photocatalyst has a higher photodegradation rate than Ag/AgCl, AgCl, AgCl@WO3 and TiO2 (P25). The contents and morphologies of the WO3 substrates in the Ag/AgCl@plate-WO3 photocatalysts have important effects on their photocatalytic performance. The related mechanisms for the enhancement in visible-light-driven photodegradation of RhB molecules were analyzed.The hierarchical photocatalysts of Ag/AgCl@plate-WO3 have been synthesized by anchoring Ag/AgCl nanocrystals on the surfaces of single-crystalline WO3 nanoplates that were obtained via an intercalation and topochemical approach. The heterogeneous precipitation process of the PVP-Ag+-WO3 suspensions with a Cl- solution added drop-wise was developed to synthesize AgCl@WO3 composites, which were then photoreduced to form Ag/AgCl@WO3 nanostructures in

  14. The AGS with four helical magnets

    SciTech Connect

    Tsoupas, N.; Huang, H.; MacKay, W.W.; Roser, T.; Trbojevic, D.

    2010-02-25

    The idea of using multiple partial helical magnets was applied successfully to the AGS synchrotron, to preserve the proton beam polarization. In this paper we explore in details the idea of using four helical magnets placed symmetrically in the AGS ring. This modification provides many advantages over the present setup of the AGS that uses two partial helical magnets. First, it provides a larger 'spin tune gap' for the placement of the vertical betatron tune of the AGS during acceleration, second, the vertical spin direction during the beam injection and extraction is closer to vertical, third, the symmetric placement of the snakes allows for a better control of the AGS optics, and for reduced values of the beta and eta functions, especially near injection, fourth, the optical properties of the helical magnets also favor the placement of the horizontal betatron tune in the 'spin tune gap', thus eliminating the horizontal spin resonances. In this paper we provide results on the spin tune and on the optics of the AGS with four partial helical magnets, and we compare these results with the present setup of the AGS that uses two partial helical magnets.

  15. Presence of specific symbiotic bacteria in flies of the subfamily Tephritinae (Diptera Tephritidae) and their phylogenetic relationships: proposal of 'Candidatus Stammerula tephritidis'.

    PubMed

    Mazzon, Luca; Piscedda, Alessia; Simonato, Mauro; Martinez-Sañudo, Isabel; Squartini, Andrea; Girolami, Vincenzo

    2008-06-01

    The presence of symbiotic bacteria in flies belonging to the subfamily Tephritinae, which predominantly infest the flower heads of composite flowers (Asteraceae), was investigated. Twenty-five species of flies, collected mainly in northern Italy, were examined. The bacteria adhered to the midgut epithelium in a space external to the peritrophic membrane and therefore not in direct contact with the gut contents. Specific, unique and live, but unculturable bacteria were consistently found in the majority of the fly species and their presence was also shown to be persistent in flies reared under microbiologically controlled conditions and devoid of any residual culturable intestinal bacteria. Sequencing of the small subunit rRNA gene from the novel bacteria indicated that they belonged to the family Enterobacteriaceae. Three main strongly supported clades were delineated by phylogenetic trees, the first of which featured a coherent set of sequences displaying gene sequence similarities lower than 96 % compared with recognized taxa. The second and third clades featured cases with higher gene sequence similarities to culturable bacteria, including Erwinia persicina and Ewingella americana, respectively. Relative rate tests were supportive of a fast genetic evolution for the majority of the bacterial symbionts of the subfamily Tephritinae. In agreement with the interpretation suggested in 1929 after pioneering observations made by H. J. Stammer, a symbiotic relationship between the novel bacteria and the tephritid flies is postulated. The origin of this apparently polyphyletic relationship is discussed and a novel candidate organism is proposed for the first clade under the designation 'Candidatus Stammerula tephritidis'.

  16. Characterization of a second member of the subfamily of calcium-binding mitochondrial carriers expressed in human non-excitable tissues.

    PubMed Central

    Del Arco, A; Agudo, M; Satrústegui, J

    2000-01-01

    We have recently identified a subfamily of mitochondrial carriers that bind calcium, and cloned ARALAR1, a member of this subfamily expressed in human muscle and brain. We have now cloned a second human ARALAR gene (ARALAR2) coding for a protein 78.3% identical to Aralar1, but expressed in liver and non-excitable tissues. Aralar2 is identical to citrin, the product of the gene mutated in type-II citrullinaemia [Kobayashi, Sinasac, Iijima, Boright, Begum, Lee, Yasuda, Ikeda, Hirano, Terazono et al. (1999) Nat. Genet. 22, 159-163]. A related protein, DmAralar, 69% identical to Aralar1, was found in Drosophila melanogaster, the DMARALAR locus lying on the right arm of the third chromosome, band 99F. The N-terminal half of Aralar2/citrin is able to bind calcium and this requires the presence of the two most distal EF-hands. The localization of Aralar2/citrin expressed in human cell lines is mitochondrial, the C-terminal half containing sufficient information for import and assembly into mitochondria. The C-terminal half of Aralar proteins is related to the yeast YPR020c gene, with a very high sequence conservation (54.3% identity), suggesting that these proteins play an important role. Thus Aralar proteins are probably expressed in all tissues in an isoform-specific fashion, where they function as calcium-regulated metabolite (possibly anionic) carriers. PMID:10642534

  17. Distinct structural and redox properties of the heme active site in bacterial dye decolorizing peroxidase-type peroxidases from two subfamilies: resonance Raman and electrochemical study.

    PubMed

    Sezer, Murat; Santos, Ana; Kielb, Patrycja; Pinto, Tiago; Martins, Ligia O; Todorovic, Smilja

    2013-05-07

    Spectroscopic data of dye decolorizing peroxidases (DyPs) from Bacillus subtilis (BsDyP), an A subfamily member, and Pseudomonas putida (PpDyP), a B subfamily enzyme, reveal distinct heme coordination patterns of the respective active sites. In solution, both enzymes show a heterogeneous spin population, with the six-coordinated low-spin state being the most populated in the former and the five-coordinated quantum mechanically mixed-spin state in the latter. We ascribe the poor catalytic activity of BsDyP to the presence of a catalytically incompetent six-coordinated low-spin population. The spin populations of the two DyPs are sensitively dependent on the pH, temperature, and physical, i.e., solution versus crystal versus immobilized, state of the enzymes. We observe a redox potential for the Fe(2+)/Fe(3+) couple in BsDyP (-40 mV) at pH 7.6 substantially more positive than those reported for the majority of other peroxidases, including PpDyP (-260 mV). Furthermore, we evaluate the potential of the studied enzymes for biotechnological applications on the basis of electrochemical and spectroelectrochemical data.

  18. Crystal structure and biochemical investigations reveal novel mode of substrate selectivity and illuminate substrate inhibition and allostericity in a subfamily of Xaa-Pro dipeptidases.

    PubMed

    Are, Venkat N; Kumar, Ashwani; Kumar, Saurabh; Goyal, Venuka Durani; Ghosh, Biplab; Bhatnagar, Deepak; Jamdar, Sahayog N; Makde, Ravindra D

    2017-02-01

    Xaa-Pro dipeptidase (XPD) catalyzes hydrolysis of iminopeptide bond in dipeptides containing trans-proline as a second residue. XPDs are found in all living organisms and are believed to play an essential role in proline metabolism. Here, we report crystal structures and extensive enzymatic studies of XPD from Xanthomonas campestris (XPDxc), the first such comprehensive study of a bacterial XPD. We also report enzymatic activities of its ortholog from Mycobacterium tuberculosis (XPDmt). These enzymes are strictly dipeptidases with broad substrate specificities. They exhibit substrate inhibition and allostericity, as described earlier for XPD from Lactococcus lactis (XPDll). The structural, mutational and comparative data have revealed a novel mechanism of dipeptide selectivity and substrate binding in these enzymes. Moreover, we have identified conserved sequence motifs that distinguish these enzymes from other prolidases, thus defining a new subfamily. This study provides a suitable structural template for explaining unique properties of this XPDxc subfamily. In addition, we report unique structural features of XPDxc protein like an extended N-terminal tail region and absence of a conserved Tyr residue near the active site.

  19. 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.

  20. pBLA8, from Brevibacterium linens, belongs to a gram-positive subfamily of ColE2-related plasmids.

    PubMed

    Leret, V; Trautwetter, A; Rincé, A; Blanco, C

    1998-10-01

    A 3.1 kb DNA fragment from pBLA8, a Brevibacterium linens cryptic plasmid, containing all the information required for autonomous replication was cloned and sequenced. Using deletion analysis, the fragment essential and sufficient for autonomous replication was delimited to 1.5 kb. This fragment is characterized by the presence of an ori site located upstream of an operon encoding two proteins, RepA and RepB, both essential for replication. Based on structural similarities and a strong conservation of ori, RepA and RepB, pBLA8 was assigned to a new subfamily of the ColE2 plasmid family. This subfamily is distinguished by the requirement for two Rep proteins and the location of an ori site upstream of the repAB operon. RepA is thought to encode primase activity, whereas RepB could be a DNA-binding protein. An Escherichia coli-B. linens shuttle vector, derived from pBLA8, was constructed. Its host spectrum was extended to Arthrobacter species.

  1. 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.

  2. 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.

  3. Ion-exchange synthesis of Ag/Ag2S/Ag3CuS2 ternary hollow microspheres with efficient visible-light photocatalytic activity.

    PubMed

    Xing, Chaosheng; Zhang, Yuan; Wu, Zhudong; Jiang, Deli; Chen, Min

    2014-02-21

    Ternary Ag/Ag2S/Ag3CuS2 hollow microspheres were synthesized via an in situ ion-exchange method using Cu7S4 hollow submicrospheres as the template. The as-obtained Ag/Ag2S/Ag3CuS2 composite exhibited a well-defined uniform hollow microsphere morphology with an average diameter of about 1.3 μm. The photocatalytic property of the as-prepared Ag/Ag2S/Ag3CuS2 hollow microsphere composite was investigated by the decomposition of methyl orange (MO) under visible light irradiation (λ > 420 nm). It was shown that the photocatalytic activity of the Ag/Ag2S/Ag3CuS2 hollow microsphere was higher than those of Ag/Ag2S, Cu2O, Cu7S4 and P25 for the photodegradation of MO under visible light irradiation. Radical scavenger experiments demonstrated that superoxide radicals and holes were the main reactive species for MO degradation.

  4. Agent planning in AgScala

    NASA Astrophysics Data System (ADS)

    Tošić, Saša; Mitrović, Dejan; Ivanović, Mirjana

    2013-10-01

    Agent-oriented programming languages are designed to simplify the development of software agents, especially those that exhibit complex, intelligent behavior. This paper presents recent improvements of AgScala, an agent-oriented programming language based on Scala. AgScala includes declarative constructs for managing beliefs, actions and goals of intelligent agents. Combined with object-oriented and functional programming paradigms offered by Scala, it aims to be an efficient framework for developing both purely reactive, and more complex, deliberate agents. Instead of the Prolog back-end used initially, the new version of AgScala relies on Agent Planning Package, a more advanced system for automated planning and reasoning.

  5. SPIN MATCHING FROM AGS TO RHIC.

    SciTech Connect

    MACKAY,W.W.; TSOUPAS,N.

    2002-11-06

    With a partial Siberian snake in the AGS and transport lines with interspersed horizontal and vertical bends, the incoming spin direction at the injection points of both the collider rings is not likely to match the ideal vertical stable spin direction of RHIC which has two full helical Siberian snakes per ring. In this paper we examine the matching of a polarized beam transferred from the AGS into RHIC. The present 5% partial solenoidal snake as well as a proposed 20% superconducting helical are considered for the AGS. Solutions with retuned snakes in RHIC to better match the incoming beam have been found.

  6. Ozone decomposition on Ag/SiO2 and Ag/clinoptilolite catalysts at ambient temperature.

    PubMed

    Nikolov, Penko; Genov, Krassimir; Konova, Petya; Milenova, Katya; Batakliev, Todor; Georgiev, Vladimir; Kumar, Narendra; Sarker, Dipak K; Pishev, Dimitar; Rakovsky, Slavcho

    2010-12-15

    Silver modified zeolite (Bulgarian natural clinoptilolite) and Ag/silica catalysts were synthesized by ion exchange and incipient wet impregnation method respectively and characterized by different techniques. DC arc-AES was used for Ag detection. XRD spectra show that Ag is loaded over the surface of the SiO(2) sample and that after the ion-exchange process the HEU type structure of clinoptilolite is retained. UV-VIS (specific reflection at 310 nm) and IR (band at 695 cm(-1)) spectroscopy analysis proved that silver is loaded as a T-atom into zeolite channels as Ag(+), instead of Na(+), Ca(2+), or K(+) ions, existing in the natural clinoptilolite form. The samples Ag/SiO(2) and Ag-clinoptilolite were tested as catalysts for decomposition of gas phase ozone. Very high catalytic activity (up to 99%) was observed and at the same time the catalysts remained active over time at room temperature.

  7. Control and performance of the AGS and AGS Booster Main Magnet Power Supplies

    SciTech Connect

    Reece, R.K.; Casella, R.; Culwick, B.; Geller, J.; Marneris, I.; Sandberg, J.; Soukas, A.; Zhang, S.Y.

    1993-01-01

    Techniques for precision control of the main magnet power supplies for the AGS and AGS Booster synchrotron will be discussed. Both synchrotrons are designed to operate in a Pulse-to-Pulse Modulation (PPM) environment with a Supercycle Generator defining and distributing global timing events for the AGS Facility. Details of modelling, real-time feedback and feedforward systems, generation and distribution of real time field data, operational parameters and an overview of performance for both machines are included.

  8. Control and performance of the AGS and AGS Booster Main Magnet Power Supplies

    SciTech Connect

    Reece, R.K.; Casella, R.; Culwick, B.; Geller, J.; Marneris, I.; Sandberg, J.; Soukas, A.; Zhang, S.Y.

    1993-06-01

    Techniques for precision control of the main magnet power supplies for the AGS and AGS Booster synchrotron will be discussed. Both synchrotrons are designed to operate in a Pulse-to-Pulse Modulation (PPM) environment with a Supercycle Generator defining and distributing global timing events for the AGS Facility. Details of modelling, real-time feedback and feedforward systems, generation and distribution of real time field data, operational parameters and an overview of performance for both machines are included.

  9. Effects of Ag on the Kirkendall void formation of Sn-xAg/Cu solder joints

    NASA Astrophysics Data System (ADS)

    Kim, Sunghwan; Yu, Jin

    2010-10-01

    Binary Sn-Ag solders with varying amounts of Ag (0.5, 2.0, and 3.5 wt %) were reacted with Cu under bump metallurgy (UBM) which was electroplated with bis-sodium sulfopropyl-disulfide additive, and the characteristics of Kirkendall void formation at the solder joints were investigated. The results indicate that the propensity to form Kirkendall voids at the solder joint decreased with the Ag content. Subsequent Auger electron spectroscopy analyses showed that Ag dissolved in the Cu UBM reduced the segregation of S to the Cu3Sn/Cu interface, which suppressed the nucleation of Kirkendall voids at the interface.

  10. Nanoporous Ag prepared from the melt-spun Cu-Ag alloys

    NASA Astrophysics Data System (ADS)

    Li, Guijing; Song, Xiaoping; Sun, Zhanbo; Yang, Shengchun; Ding, Bingjun; Yang, Sen; Yang, Zhimao; Wang, Fei

    2011-07-01

    Nanoporous Ag ribbons with different morphology and porosity were achieved by the electrochemical corrosion of the melt-spun Cu-Ag alloys. The Cu-rich phase in the alloys was removed, resulting in the formation of the nanopores distributed across the whole ribbon. It is found that the structures, morphology and porosity of the nanoporous Ag ribbons were dependent on the microstructures of the parent alloys. The most of ligaments presented a rod-like shape due to the formation of pseudoeutectic microstructure in the melt-spun Cu 55Ag 45 and Cu 70Ag 30 alloys. For nanoporous Ag prepared from Cu 85Ag 15 alloys, the ligaments were camber-like because of the appearance of the divorced microstructures. Especially, a novel bamboo-grove-like structure could be observed at the cross-section of the nanoporous Ag ribbons. The experiment reveals that nanoporous Ag ribbons exhibited excellent enhancement of surface-enhanced Raman scattering (SERS) effect, but a slight difference existed due to the discrepancy of their morphology.

  11. Lesson 3: Attorney General (AG) Certification

    EPA Pesticide Factsheets

    The AG Certification is a letter confirming legal authority to implement the electronic reporting covered by the application and enforce the affected programs using the electronic documents received under those programs.

  12. AgRISTARS documents tracking list report

    NASA Technical Reports Server (NTRS)

    Hawkins, J. L.

    1982-01-01

    A quarterly listing of those documents and related publications that have been issued and placed in the AgRISTARS tracking system is presented. The Tracking List Report provides a catalog, by project, of technical publications arranged by type of document and gives the reference AgRISTARS document numbers, title and date of publication, the issuing organization, and the National Technical Information Service reference number.

  13. BNL AGS - a context for kaon factories

    SciTech Connect

    Littenberg, L.S.

    1983-05-01

    Figure 1 shows the Brookhaven site with the AGS-CBA complex highlighted. In this photograph the AGS is dwarfed by CBA and indeed during the past few years future plans for particle physics at BNL have been dominated by this enormous project. However, very recently interest in future physics use of the AGS has undergone a strong revival. Indeed, since the beginning of this year, two projects for augmenting the AGS have been proposed. Such projects could keep the AGS viable as a research machine for many years to come. In general such schemes will also improve the performance and increase the versatility of the CBA, and so are doubly valuable. It should be kept in mind that in spite of the fact the AGS has been perhaps the most fruitful machine in the history of high energy physics, its full capacities have never been exploited. Even without improvements at least one generation of rare K decay experiments beyond those currently launched seems feasible. Beyond that a major effort at any of the experiments discussed above could take it to the point where it would be limited by intrinsic physics background. To pursue a full program of physics at this level one would want to increase the intensity of the AGS as described. A ten-fold increase in K flux would remove such experiments from the category of all-out technological assaults and render them manageable by reasonably small groups of physicists. In addition, certain other, cleaner experiments, e.g., K/sub L//sup 0/ ..-->.. e/sup +/e/sup -/ or e/sup +/e/sup -/..pi../sup 0/, could be pushed to limits unobtainable at the present AGS. The increased flux would also be welcomed by the neutrino and hypernuclear physics programs. Even experiments which do not at present require higher fluxes would benefit through the availability of purer beams and cleaner conditions.

  14. 20% PARTIAL SIBERIAN SNAKE IN THE AGS.

    SciTech Connect

    Huang, H; Bai, M; Brown, K A; Glenn, W; Luccio, A U; Mackay, W W; Montag, C; Ptitsyn, V; Roser, T; Tsoupas, N; Zeno, K; Ranjbar, V; Spinka, H; Underwood, D

    2002-11-06

    An 11.4% partial Siberian snake was used to successfully accelerate polarized proton through a strong intrinsic depolarizing spin resonance in the AGS. No noticeable depolarization was observed. This opens up the possibility of using a 20% to 30% partial Siberian snake in the AGS to overcome all weak and strong depolarizing spin resonances. Some design and operation issues of the new partial Siberian snake are discussed.

  15. AGS polarized proton operation in run 8.

    SciTech Connect

    Huang,H.; Ahrens, L.; Bai, M.; Brown, K.A.; Gardner, C.; Glenn, J.W.; Lin, F.; Luccio, A.U.; MacKay, W.W.; Roser, T.; Tepikian, S.; Tsoupas, N.; Yip, K.; Zeno, K.

    2008-06-23

    Dual partial snake scheme has been used for the Brookhaven AGS (Alternating Gradient Synchrotron) polarized proton operation for several years. It has provided polarized proton beams with 1.5 x 10{sup 11} intensity and 65% polarization for RHIC spin program. There is still residual polarization loss. Several schemes such as putting horizontal tune into the spin tune gap, and injection-on-the-fly were tested in the AGS to mitigate the loss. This paper presents the experiment results and analysis.

  16. Dealloying-driven synthesis and characterization of AgCl/Ag/TiO2 nanocomposites with enhanced photocatalytic properties

    NASA Astrophysics Data System (ADS)

    Wang, Tongyang; Wang, Yan; Zhao, Zhengfeng; Zhang, Lanxiang; Huang, Shifeng

    2017-03-01

    The combination of dealloying with acid treatment was used to fabricate mesoporous anatase TiO2 with high specific surface area of 233 m2/g. Using anatase TiO2 as a matrix, a photoreduction strategy was developed to synthesize AgCl/Ag/TiO2 nanocomposites with different Ti/Ag molar ratios. The morphology and properties of AgCl/Ag/TiO2 nanocomposites were investigated by X-ray diffraction, field emission scanning electron microscopy and transmission electron microscopy. The AgCl/Ag/TiO2 nanocomposites showed an enhanced photocatalytic activity for the degradation of methyl orange solution under visible light irradiation. The optimum Ti/Ag molar ratio in the AgCl/Ag/TiO2 nanocomposites was shown to be 6:1, which was attributed to its high specific surface area of 207 m2/g and the surface plasmon resonance effect.

  17. A visible-light-driven core-shell like Ag2S@Ag2CO3 composite photocatalyst with high performance in pollutants degradation.

    PubMed

    Yu, Changlin; Wei, Longfu; Zhou, Wanqin; Dionysiou, Dionysios D; Zhu, Lihua; Shu, Qing; Liu, Hong

    2016-08-01

    A series of Ag2S-Ag2CO3 (4%, 8%, 16%, 32% and 40% Ag2S), Ag2CO3@Ag2S (32%Ag2S) and Ag2S@Ag2CO3 (32%Ag2S) composite photocatalysts were fabricated by coprecipitation or successive precipitation reaction. The obtained catalysts were analyzed by N2 physical adsorption, powder X-ray diffraction, scanning electron microscopy, transmission electron microscopy, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, Raman spectroscopy, UV-vis diffuse reflectance spectroscopy and photocurrent test. Under visible light irradiation, the influences of Ag2S content and core-shell property on photocatalytic activity and stability were evaluated in studies focused on the degradation of methyl orange (MO) dye, phenol, and bisphenol A. Results showed that excellent photocatalytic performance was obtained over Ag2S/Ag2CO3 composite photocatalysts with respect to Ag2S and Ag2CO3. With optimal content of Ag2S (32 wt%), the Ag2S-Ag2CO3 showed the highest photocatalytic degradation efficiency. Moreover, the structured property of Ag2S/Ag2CO3 greatly influenced the activity. Compared with Ag2S-Ag2CO3 and Ag2CO3@Ag2S, core-shell like Ag2S@Ag2CO3 demonstrated the highest activity and stability. The main reason for the boosting of photocatalytic performance was due to the formation of Ag2S/Ag2CO3 well contacted interface and unique electron structures. Ag2S/Ag2CO3 interface could significantly increase the separation efficiency of the photo-generated electrons (e(-)) and holes (h(+)), and production of OH radicals. More importantly, the low solubility of Ag2S shell could effectively protect the core of Ag2CO3, which further guarantees the stability of Ag2CO3.

  18. 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.

  19. Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity

    PubMed Central

    2011-01-01

    Background Plant HD-Zip transcription factors are modular proteins in which a homeodomain is associated to a leucine zipper. Of the four subfamilies in which they are divided, the tested members from subfamily I bind in vitro the same pseudopalindromic sequence CAAT(A/T)ATTG and among them, several exhibit similar expression patterns. However, most experiments in which HD-Zip I proteins were over or ectopically expressed under the control of the constitutive promoter 35S CaMV resulted in transgenic plants with clearly different phenotypes. Aiming to elucidate the structural mechanisms underlying such observation and taking advantage of the increasing information in databases of sequences from diverse plant species, an in silico analysis was performed. In addition, some of the results were also experimentally supported. Results A phylogenetic tree of 178 HD-Zip I proteins together with the sequence conservation presented outside the HD-Zip domains allowed the distinction of six groups of proteins. A motif-discovery approach enabled the recognition of an activation domain in the carboxy-terminal regions (CTRs) and some putative regulatory mechanisms acting in the amino-terminal regions (NTRs) and CTRs involving sumoylation and phosphorylation. A yeast one-hybrid experiment demonstrated that the activation activity of ATHB1, a member of one of the groups, is located in its CTR. Chimerical constructs were performed combining the HD-Zip domain of one member with the CTR of another and transgenic plants were obtained with these constructs. The phenotype of the chimerical transgenic plants was similar to the observed in transgenic plants bearing the CTR of the donor protein, revealing the importance of this module inside the whole protein. Conclusions The bioinformatical results and the experiments conducted in yeast and transgenic plants strongly suggest that the previously poorly analyzed NTRs and CTRs of HD-Zip I proteins play an important role in their function, hence

  20. The Exiguobacterium sibiricum 255-15 GtfC Enzyme Represents a Novel Glycoside Hydrolase 70 Subfamily of 4,6-α-Glucanotransferase Enzymes

    PubMed Central

    Gangoiti, Joana; Pijning, Tjaard

    2015-01-01

    The glycoside hydrolase 70 (GH70) family originally was established for glucansucrase enzymes found solely in lactic acid bacteria synthesizing α-glucan polysaccharides from sucrose (e.g., GtfA). In recent years, we have characterized GtfB and related Lactobacillus enzymes as 4,6-α-glucanotransferase enzymes. These GtfB-type enzymes constitute the first GH70 subfamily of enzymes that are unable to act on sucrose as a substrate but are active with maltodextrins and starch, cleave α1→4 linkages, and synthesize linear α1→6-glucan chains. The GtfB disproportionating type of activity results in the conversion of malto-oligosaccharides into isomalto/malto-polysaccharides with a relatively high percentage of α1→6 linkages. This paper reports the identification of the members of a second GH70 subfamily (designated GtfC enzymes) and the characterization of the Exiguobacterium sibiricum 255-15 GtfC enzyme, which is also inactive with sucrose and displays 4,6-α-glucanotransferase activity with malto-oligosaccharides. GtfC differs from GtfB in synthesizing isomalto/malto-oligosaccharides. Biochemically, the GtfB- and GtfC-type enzymes are related, but phylogenetically, they clearly constitute different GH70 subfamilies, displaying only 30% sequence identity. Whereas the GtfB-type enzyme largely has the same domain order as glucansucrases (with α-amylase domains A, B, and C plus domains IV and V), this GtfC-type enzyme differs in the order of these domains and completely lacks domain V. In GtfC, the sequence of conserved regions I to IV of clan GH-H is identical to that in GH13 (I-II-III-IV) but different from that in GH70 (II-III-IV-I because of a circular permutation of the (β/α)8 barrel. The GtfC 4,6-α-glucanotransferase enzymes thus represent structurally and functionally very interesting evolutionary intermediates between α-amylase and glucansucrase enzymes. PMID:26590275

  1. High Visible Photoelectrochemical Activity of Ag Nanoparticle-Sandwiched CdS/Ag/ZnO Nanorods.

    PubMed

    Yang, Xu; Li, Hui; Zhang, Wu; Sun, Mingxuan; Li, Lequn; Xu, Ning; Wu, Jiada; Sun, Jian

    2017-01-11

    We report on the sensitizing of CdS-coated ZnO (CdS/ZnO) nanorods (NRs) by Ag nanoparticles (NPs) embedded between the CdS coating and the ZnO nanorod and the improved optical and photoelectrochemical properties of the Ag NP-sandwiched nanostructure CdS/Ag/ZnO NRs. The CdS/Ag/ZnO NRs were fabricated by growing Ag NPs on hydrothermally grown ZnO NRs and subsequently depositing CdS coatings followed by subsequent N2 annealing. The structure of the fabricated CdS/Ag/ZnO NRs was characterized by field-emission scanning electron microscopy, transmission electron microscopy, X-ray diffraction, and Raman backscattering, revealing that the ZnO NRs and the CdS coatings are both structured with hexagonal wurtzite and the Ag NPs contact well with ZnO and CdS. Optical properties were evaluated by measuring optical absorption and photoluminescence, showing that the Ag NPs behave well as sensitizers for optical property improvement and the CdS/Ag/ZnO NRs exhibit better photoresponse in a wide spectral region than CdS/ZnO because of plasmon-enhanced absorption due to the embedment of Ag NPs. The Ag NPs also serve as electron relays from CdS to ZnO, facilitating electron transfer from the CdS coatings to the ZnO NRs. The excellent photoresponse and efficient electron transfer make the CdS/Ag/ZnO NRs highly photoelectrochemically active. The CdS/Ag/ZnO NRs fabricated on indium-tin oxide present much better photoelectrochemical performance as photoanodes working in the visible region than CdS/ZnO NRs without Ag NPs. Under visible illumination, a maximum optical-to-chemical conversion efficiency of 3.13% is obtained for CdS/Ag/ZnO NR photoanodes against 1.35% for CdS/ZnO NR photoanodes.

  2. Electron and Phonon Dynamics in Hexagonal Pd Nanosheets and Ag/Pd/Ag Sandwich Nanoplates.

    PubMed

    Wang, Li; Sagaguchi, Takuya; Okuhata, Tomoki; Tsuboi, Motohiro; Tamai, Naoto

    2017-02-28

    Pd and its hybrid nanostructures have attracted considerable attention over the past decade, with both catalytic and plasmonic properties. The electron and phonon properties directly govern conversion efficiencies in applications such as energy collectors and photocatalysts. We report the dynamic processes of electron-phonon coupling and coherent acoustic phonon vibration in hexagonal Pd nanosheets and Ag/Pd/Ag sandwich nanoplates using transient absorption spectroscopy. The electron-phonon coupling constant of Pd nanosheets, GPd-nanosheet (8.7 × 10(17) W/(m(3)·K)) is larger than that of the bulk GPd (5.0 × 10(17) W/(m(3)·K)). The effective coupling constant Geff of Ag/Pd/Ag nanoplates decreases with increasing Ag shell thickness, finally approaching the bulk GAg. The variation of Geff is explained in terms of reduced density of states near Fermi level of Pd nanosheets with 1.8 nm ultrathin thickness. Coherent acoustic phonon vibration in Pd nanosheets is assigned to a fundamental breathing mode, similar to the vibration of benzene. The period increases with increasing Ag shell thickness. For Ag/Pd/Ag nanoplates with 20 nm thick Ag shells, the vibrational mode is ascribed to a quasi-extensional mode. The results show that the modes of the coherent acoustic phonon vibration transform with the geometric variation of Pd nanosheets and Ag/Pd/Ag nanoplates. Our results represent an understanding of quantum-confinement related electron dynamics and bulk-like phonon kinetics in the ultrathin Pd nanosheets and their hybrid nanostructures.

  3. An Ab Initio Study of the Low-Lying Doublet States of AgO and AgS

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.

    1990-01-01

    Spectroscopic constants (D(sub o), r(sub e), mu(sub e), T(sub e)) are determined for the doublet states of AgO and AgS below approx. = 30000/cm. Large valence basis sets are employed in conjunction with relativistic effective core potentials (RECPs). Electron correlation is included using the modified coupled-pair functional (MCPF) and multireference configuration interaction (MRCI) methods. The A(sup 2)Sigma(sup +) - X(sup 2)Pi band system is found to occur in the near infrared (approx. = 9000/cm) and to be relatively weak with a radiative lifetime of 900 microns for A(sup 2)Sigma(sup +) (upsilon = 0). The weakly bound C(sup 2)Pi state (our notation), the upper state of the blue system, is found to require high levels of theoretical treatment to determine a quantitatively accurate potential. The red system is assigned as a transition from the C(sup 2)Pi state to the previously unobserved A(sup 2)Sigma(sup +) state. Several additional transitions are identified that should be detectable experimentally. A more limited study is performed for the vertical excitation spectrum of AgS. In addition, a detailed all-electron study of the X(sup 2)Pi and A(sup 2)Sigma(sup +) states of AgO is carried out using large atomic natural orbital (ANO) basis sets. Our best calculated D(sub o) value for AgO is significantly less than the experimental value, which suggests that there may be some systematic error in the experimental determination.

  4. 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

  5. Strongly visible-light responsive plasmonic shaped AgX:Ag (X = Cl, Br) nanoparticles for reduction of CO2 to methanol

    NASA Astrophysics Data System (ADS)

    An, Changhua; Wang, Jizhuang; Jiang, Wen; Zhang, Meiyu; Ming, Xijuan; Wang, Shutao; Zhang, Qinhui

    2012-08-01

    Plasmonic shaped AgX:Ag (X = Cl, Br) nanoparticles have been synthesized by a facile and versatile glycerol-mediated solution route. The as-prepared AgX:Ag nanoparticles exhibit regular shapes, i.e., cube-tetrapod-like AgCl:Ag nanoparticles and AgBr:Ag nanoplates. Compared with the pristine AgX, AgX:Ag nanocomposites display stronger absorption in the visible region due to the surface plasmon resonance of silver nanoparticles. The calculation of bandgaps and band positions indicates the as-achieved AgX:Ag nanoparticles can be used as a class of potential photocatalyst for the reduction of CO2. For example, reduction of CO2 under visible light irradiation with the assistance of the anisotropic AgX:Ag nanoparticles yields as much as 100 μmol methanol in the products. Furthermore, the AgX:Ag nanoparticles can maintain its structure and activity after 3 runs of reactions. Therefore, the present route opens an avenue to acquire plasmonic photocatalysts for conversion of CO2 into useful organic compounds.Plasmonic shaped AgX:Ag (X = Cl, Br) nanoparticles have been synthesized by a facile and versatile glycerol-mediated solution route. The as-prepared AgX:Ag nanoparticles exhibit regular shapes, i.e., cube-tetrapod-like AgCl:Ag nanoparticles and AgBr:Ag nanoplates. Compared with the pristine AgX, AgX:Ag nanocomposites display stronger absorption in the visible region due to the surface plasmon resonance of silver nanoparticles. The calculation of bandgaps and band positions indicates the as-achieved AgX:Ag nanoparticles can be used as a class of potential photocatalyst for the reduction of CO2. For example, reduction of CO2 under visible light irradiation with the assistance of the anisotropic AgX:Ag nanoparticles yields as much as 100 μmol methanol in the products. Furthermore, the AgX:Ag nanoparticles can maintain its structure and activity after 3 runs of reactions. Therefore, the present route opens an avenue to acquire plasmonic photocatalysts for conversion of CO2

  6. Calibration of qualitative HBsAg assay results for quantitative HBsAg monitoring.

    PubMed

    Gunning, Hans; Adachi, Dena; Tang, Julian W

    2014-10-01

    Evidence is accumulating that quantitative hepatitis B surface antigen monitoring may be useful in managing patients with chronic HBV infection on certain treatment regimens. Based on these results with the Abbott Architect qualitative and quantitative HBsAg assays, it seems feasible to convert qualitative to quantitative HBsAg values for this purpose.

  7. Ultra-Fast Synthesis for Ag2Se and CuAgSe Thermoelectric Materials

    NASA Astrophysics Data System (ADS)

    DUAN, H. Z.; LI, Y. L.; ZHAO, K. P.; QIU, P. F.; SHI, X.; CHEN, L. D.

    2016-10-01

    Ag2Se and CuAgSe have been recently reported as promising thermoelectric materials at room temperature. The traditional melting-annealing-sintering processes are used to grow Ag2Se and CuAgSe materials with the disadvantages of high costs of energy and time. In this work, phase-pure polycrystalline Ag2Se and CuAgSe compounds were synthesized from raw elemental powders directly by manual mixing followed by spark plasma sintering (MM-SPS) in a few minutes. The influence of SPS heating rate on the phase composition, microstructure, and thermoelectric properties, including Seebeck coefficient, electrical conductivity, and thermal conductivity, were investigated. The zTs of 0.8 at 390 K and 0.6 at 450 K are obtained for Ag2Se and CuAgSe, respectively, which is comparable with the values in the materials prepared by the traditional method. Furthermore, this ultrafast sample synthesis can significantly save material synthesis time and thus has the obvious advantage for large-scale production.

  8. Facile synthesis of sunlight-driven AgCI:Ag plasmonic nanophotocatalyst.

    SciTech Connect

    An, C.; Peng, S.; Sun, Y.; Center for Nanoscale Materials; Univ. of Illinois

    2010-06-18

    Highly efficient plasmonic photocatalysts of AgCl:Ag hybrid nanoparticles are successfully synthesized via a one-pot synthetic approach involving a precipitation reaction followed by polyol reduction. The as-synthesized nanoparticles exhibit high catalytic performance under visible light and sunlight for decomposing organics, such as methylene blue.

  9. Beet Juice-Induced Green Fabrication of Plasmonic AgCl/Ag Nanoparticles

    EPA Science Inventory

    A simple, green, and fast approach (complete within 5 min) was explored for the fabrication of hybrid AgCl/Ag plasmonic nanoparticles under microwave (MW) irradiation. In this method, beet juice served as a reducing reagent, which is an abundant sugar-rich agricultural produce. I...

  10. A novel toxin from the venom of the scorpion Tityus trivittatus, is the first member of a new alpha-KTX subfamily.

    PubMed

    Abdel-Mottaleb, Yousra; Coronas, Fredy V; de Roodt, Adolfo R; Possani, Lourival D; Tytgat, Jan

    2006-01-23

    The first example of a new sub-family of toxins (alpha-KTx20.1) from the scorpion Tityus trivittatus was purified, sequenced and characterized physiologically. It has 29 amino acid residues, three disulfide bridges assumed to adopt the cysteine-stabilized alpha/beta scaffold with a pI value of 8.98. The sequence identities with all the other known alpha-KTx are less than 40%. Its effects were verified using seven different cloned K(+) channels (vertebrate Kv1.1-1.5, Shaker IR and hERG) expressed in Xenopus leavis oocytes. The toxin-induced effects show large differences among the different K(+) channels and a preference towards Kv1.3 (EC50=7.9+/-1.4 nM).

  11. 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

  12. 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

  13. List of primary types of the larentiine moth species (Lepidoptera: Geometridae) described from Indonesia - a starting point for biodiversity assessment of the subfamily in the region

    PubMed Central

    2015-01-01

    Abstract Background The Indonesian geometrid moth fauna is rich and diverse, yet it is poorly studied. This is particularly the case for the second largest geometrid subfamily Larentiinae which comprises moths with predominantly high mountainous distribution in the tropics. The present study provides a first inventory of the primary type specimens of larentiine moth species (Lepidoptera: Geometridae) described from Indonesia. New information The list of species described from Indonesia is arranged alphabetically by the tribe, genus, and species, and presents data on 251 species and subspecies. For each species type status, type locality, depository, and a full reference to the original description are listed. Synonyms with Indonesian type localities are included. The study indicates a large part of the Indonesian geometrid fauna belong to the tribe Eupitheciini. PMID:26311296

  14. Review of the fur-mite genus Soricilichus Fain, 1970 (Acariformes: Chirodiscidae)-symbionts of the African shrews of the subfamily Crocidurinae (Soricomorpha: Soricidae).

    PubMed

    Bochkov, Andre V; Mbalitini, Sylvestre G; Verheyen, Erik

    2016-01-29

    The fur-mite genus Soricilichus Fain, 1970 (3 species) (Acariformes: Chirodiscidae) represented by permanent symbionts of the African shrews of the subfamily Crocidurinae (Soricomorpha: Soricidae) is revised. The external morphology of these species was investigated with light and scanning electron microscopy. Based on the type specimens and newly obtained samples, 2 recognized species, S. scutisorex Fain, 1970 from Scutisorex somereni Thomas and S. kivuensis Fain, 1981 from Crocidura sp.-both are from DR of Congo-are redescribed. A new species S. sylvisorex sp. nov. found on shrews of the genera Sylvisorex (S. granti Thomas (type host), S. lunaris Thomas, S. vulcanorum Hutterer and Verheyen) and Crocidura (C. denti Dollman, C. cf. niobe, Crocidura sp.), collected in the DR Congo is also described. An amended generic diagnosis, including description of female immature stages, and a key to species are provided.

  15. spr-2, a suppressor of the egg-laying defect caused by loss of sel-12 presenilin in Caenorhabditis elegans, is a member of the SET protein subfamily

    PubMed Central

    Wen, Chenhui; Levitan, Diane; Li, Xiajun; Greenwald, Iva

    2000-01-01

    Presenilin plays critical roles in the genesis of Alzheimer's disease and in LIN-12/Notch signaling during development. Here, we describe a screen for genes that influence presenilin level or activity in Caenorhabditis elegans. We identified four spr (suppressor of presenilin) genes by reverting the egg-laying defective phenotype caused by a null allele of the sel-12 presenilin gene. We analyzed the spr-2 gene in some detail. We show that loss of spr-2 activity suppresses the egg-laying defective phenotype of different sel-12 alleles and requires activity of the hop-1 presenilin gene, suggesting that suppression is accomplished by elevating presenilin activity rather than by bypassing the need for presenilin activity. We also show that SPR-2 is a nuclear protein and is a member of a protein subfamily that includes human SET, which has been identified in numerous different biochemical assays and at translocation breakpoints associated with a subtype of acute myeloid leukemia. PMID:11114162

  16. Ag on Si(111) from basic science to application

    SciTech Connect

    Belianinov, Aleksey

    2012-01-01

    In our work we revisit Ag and Au adsorbates on Si(111)-7x7, as well as experiment with a ternary system of Pentacene, Ag and Si(111). Of particular interest to us is the Si(111)-(√3x√3)R30°}–Ag (Ag-Si-√3 hereafter). In this thesis I systematically explore effects of Ag deposition on the Ag-Si-√3 at different temperatures, film thicknesses and deposition fluxes. The generated insight of the Ag system on the Si(111) is then applied to generate novel methods of nanostructuring and nanowire growth. I then extend our expertise to the Au system on the Ag-Si(111) to gain insight into Au-Si eutectic silicide formation. Finally we explore behavior and growth modes of an organic molecule on the Ag-Si interface.

  17. Morphology and mechanical properties of nanocrystalline Cu/Ag alloy

    NASA Astrophysics Data System (ADS)

    Li, Ao; Szlufarska, Izabela

    2017-04-01

    Hybrid Monte Carlo (MC)/molecular dynamics (MD) simulations are conducted to study the microstructures of nanocrystalline (nc) Cu/Ag alloys with various Ag concentrations. When the Ag concentration is below 50 Ag atoms/nm!, an increase in Ag concentration leads to a gradual growth of monolayer grain boundary (GB) complexions into nanolayer complexions. Above the concentration of 50 Ag atoms/nm!, wetting layers with a bulk crystalline phase are observed. The effects of Ag on mechanical properties and deformation mechanisms of nc Cu/Ag alloys are investigated in MD simulations of uniaxial tension. GB sliding resistance is found to first increase and then decrease with an increase in Ag concentration. Surprisingly, we also find that the dislocation density decreases monotonically with an increase in Ag concentration, which suggests that the grain interiors are softened by the introduction of Ag dopants at GBs. In addition, there is a critical Ag concentration that maximizes flow stress of nc Cu/Ag alloys. The flow stress, GB sliding resistance, and the intragranular dislocation densities become less sensitive to Ag dopants when the grain diameter increases from 5nm to 40nm.

  18. A signature motif mediating selective interactions of BCL11A with the NR2E/F subfamily of orphan nuclear receptors

    PubMed Central

    Chan, Chun Ming; Fulton, Joel; Montiel-Duarte, Cristina; Collins, Hilary M.; Bharti, Neetu; Wadelin, Frances R.; Moran, Paula M.; Mongan, Nigel P.; Heery, David M.

    2013-01-01

    Despite their physiological importance, selective interactions between nuclear receptors (NRs) and their cofactors are poorly understood. Here, we describe a novel signature motif (F/YSXXLXXL/Y) in the developmental regulator BCL11A that facilitates its selective interaction with members of the NR2E/F subfamily. Two copies of this motif (named here as RID1 and RID2) permit BCL11A to bind COUP-TFs (NR2F1;NR2F2;NR2F6) and Tailless/TLX (NR2E1), whereas RID1, but not RID2, binds PNR (NR2E3). We confirmed the existence of endogenous BCL11A/TLX complexes in mouse cortex tissue. No interactions of RID1 and RID2 with 20 other ligand-binding domains from different NR subtypes were observed. We show that RID1 and RID2 are required for BCL11A-mediated repression of endogenous γ-globin gene and the regulatory non-coding transcript Bgl3, and we identify COUP-TFII binding sites within the Bgl3 locus. In addition to their importance for BCL11A function, we show that F/YSXXLXXL/Y motifs are conserved in other NR cofactors. A single FSXXLXXL motif in the NR-binding SET domain protein NSD1 facilitates its interactions with the NR2E/F subfamily. However, the NSD1 motif incorporates features of both LXXLL and FSXXLXXL motifs, giving it a distinct NR-binding pattern in contrast to other cofactors. In summary, our results provide new insights into the selectivity of NR/cofactor complex formation. PMID:23975195

  19. 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.

  20. 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

  1. Evolution and Function of the NR1I Nuclear Hormone Receptor Subfamily (VDR, PXR, and CAR) with Respect to Metabolism of Xenobiotics and Endogenous Compounds

    PubMed Central

    Reschly, E.J.; Krasowski, M.D.

    2008-01-01

    The NR1I subfamily of nuclear hormone receptors includes the 1,25-(OH)2-vitamin D3 receptor (VDR; NR1I1), pregnane X receptor (PXR; NR1I2), and constitutive androstane receptor (CAR; NR1I3). PXR and VDR are found in diverse vertebrates from fish to mammals while CAR is restricted to mammals. Current evidence suggests that the CAR gene arose from a duplication of an ancestral PXR gene, and that PXR and VDR arose from duplication of an ancestral gene, represented now by a single gene in the invertebrate Ciona intestinalis. Aside from the high-affinity effects of 1,25-(OH)2-vitamin D3 on VDRs, the NR1I subfamily members are functionally united by the ability to bind potentially toxic endogenous compounds with low affinity and initiate changes in gene expression that lead to enhanced metabolism and elimination (e.g., induction of cytochrome P450 3A4 expression in humans). The detoxification role of VDR seems limited to sensing high concentrations of certain toxic bile salts, such as lithocholic acid, whereas PXR and CAR have the ability to recognize structurally diverse compounds. PXR and CAR show the highest degree of cross-species variation in the ligand-binding domain of the entire vertebrate nuclear hormone receptor superfamily, suggesting adaptation to species-specific ligands. This review examines the insights that phylogenetic and experimental studies provide into the function of VDR, PXR, and CAR, and how the functions of these receptors have expanded to evolutionary advantage in humans and other animals. PMID:16724925

  2. Homology of the internal sac components in the leaf beetle subfamily Criocerinae and evolutionary novelties related to the extremely elongated flagellum.

    PubMed

    Matsumura, Yoko; Yoshizawa, Kazunori

    2012-05-01

    Extremely elongated intromittent organs are found in a wide range of taxa, especially among insects. This phenomenon is generally thought to result from sexual selection, but it is predicted that limited storage space in the body cavity and the difficulty of using the elongated organs should have constrained the evolution of extreme elongation, neutralizing any selective advantage. Therefore, in groups with long intromittent organs, features that overcome these constraints may have evolved or coevolved together with intromittent organ elongation. Using a comparative morphological approach and outgroup comparisons, we identified potential constraints and key novelties that may neutralize such constraints in the leaf beetle subfamily Criocerinae. Observations of the internal sac structure throughout Criocerinae were performed. Comparing the results with preceding studies from outgroups, a ground plan of the criocerine internal sac was constructed. Our analysis also identified specific features that are always correlated with extreme elongation: the rotation of whole internal-sac sclerites and the possession of a pocket in which to store the elongated flagellum. The pocket is thought to be formed by the rotation of the sclerites, markedly altering internal sac shape from the criocerine ground plan. Onlythe clades that have acquired this derived state contain species with an elongated flagellum that distinctly exceeds the median lobe length. It is presumed that these character correlations evolved independently three times. The detected character correlations corroborate the hypothesis that there are latent adaptive constraints for the evolution of extremely elongated intromittent organs. The constraints may have been neutralized by the alteration from the criocerine ground plan resulting in the formation of a storage pocket. In conclusion, deviation from the criocerine ground plan is considered to be the evolutionary innovation that neutralized the latent adaptive

  3. 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.

  4. Molecular modelling of CYP2F substrates: comparison of naphthalene metabolism by human, rat and mouse CYP2F subfamily enzymes.

    PubMed

    Lewis, David F V; Ito, Yuko; Lake, Brian G

    2009-01-01

    We have constructed three-dimensional molecular models of some cytochrome P450 (CYP) CYP2F subfamily forms via homology with CYP2C5 where sequence identities are in the region of 55%, thus representing high degrees of confidence in the accuracy of the models produced. The three-dimensional structures of these CYP2F enzymes have been compared by molecular overlay, especially with regard to the active site regions, and it would appear that the substitution of a lysine (Lys-301) in human CYP2F1 for the usual glutamate (Glu-301) in mouse CYP2F2, goat CYPF3 and rat CYP2F4 prior to the conserved distal threonine residue may well constitute a significant factor in any species differences between these CYP2F enzymes. Both substrate binding to CYP2F2 and metabolic clearance by CYP2F enzymes correlate with the lipophilicity, parameter, log P (where P is the octanol/water partition coefficient of the substrate). Other features of CYP2F substrate binding are likely to include pi-pi stacking interactions between aromatic rings and hydrogen bonding in some cases. The metabolism of the respiratory toxicant naphthalene is compared and contrasted between three mammalian species, namely mouse, rat and human. The CYPs involved in the metabolic activation and detoxification of naphthalene are discussed in the light of current evidence from both experimental and theoretical studies. It is noted that the CYP2F subfamily enzymes are associated with the activation of naphthalene in all three mammalian species, although there are marked differences between man and the two rodent species in the toxicity of this compound.

  5. 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

  6. Structure-function analysis of LIV-1, the breast cancer-associated protein that belongs to a new subfamily of zinc transporters.

    PubMed

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

    2003-10-01

    The LIV-1 gene has been previously associated with oestrogen-positive breast cancer and its metastatic spread to the regional lymph nodes. We have investigated the protein product of this gene as a marker for disease progression of breast cancer. The protein sequence contains a potential metalloprotease motif (HEX P H E XGD), which fits the consensus sequence for the catalytic zinc-binding site motif of the zincin metalloproteases. This motif has identified a new subfamily of ZIP (Zrt-, Irt-like proteins) zinc transporters, which we have termed LZT (LIV-1 subfamily of ZIP zinc transporters). Expression of recombinant LIV-1 in Chinese-hamster ovary cells confirmed the prediction that LZT proteins can act as zinc-influx transporters. Zinc is essential for growth and zinc transporters have an important role in maintaining intracellular zinc homoeostasis, aberrations of which could lead to diseases such as cancer. This is the first report of the expression of a recombinant human LZT protein in mammalian cells. Recombinant LIV-1 locates to the plasma membrane, concentrated in lamellipodiae, similar to membrane-type metalloproteases. Examination of LIV-1 tissue expression located it mainly to hormonally controlled tissues with widespread expression in the brain. Interestingly, the LIV-1 sequence contains a strong PEST site and other potential degradation motifs, which, combined with our evidence that recombinant LIV-1 associates with ubiquitin, may explain the low-level expression of LIV-1. Combining the crucial role that zinc plays in cell growth and the proven role of metalloproteases in metastasis presents an exciting indication of how LIV-1 plays a role in breast cancer progression.

  7. Observation of nonvolatile resistive memory switching characteristics in Ag/graphene-oxide/Ag devices.

    PubMed

    Venugopal, Gunasekaran; Kim, Sang-Jae

    2012-11-01

    In this paper, we report highly stable and bipolar resistive switching effects of Ag/Graphene oxide thinfilm/Ag devices. The graphene-oxide (GO) thinfilms were prepared on Ag/SiO2/Si substrates by spin-coating technique. The Ag/GO/Ag devices showed a steady and bipolar resistive switching characteristic. The resistance switching from low resistance state (LRS) and high resistance state (HRS) with the resistance ratio of HRS to LRS of about 10 which was attained at a voltage bias of 0.1 V. Based on the filamentary conduction model, the dominant conduction mechanism of switching effect was well explained. Our results show GO can be a promising candidate for future development of nonvolatile memory devices.

  8. Noble-metal Ag nanoparticle chains: annealing Ag/Bi superlattice nanowires in vacuum

    NASA Astrophysics Data System (ADS)

    Xu, Shao Hui; Fei, Guang Tao; You, Qiao; Gao, Xu Dong; Huo, Peng Cheng; De Zhang, Li

    2016-09-01

    One-dimensional noble-metal Ag nanoparticle chains have been prepared by electrodepositing Ag/Bi superlattice nanowires in a porous anodic alumina oxide (AAO) template and following an annealing process in vacuum. It is found that Bi, as a sacrificial metal, can be removed completely after annealing at 450 °C with a vacuum degree of 10-5 Torr. The regulation of particle size, shape and interparticle spacing of Ag NP chains has been realized by adjusting the segment length of the Ag/Bi superlattice nanowires and the annealing condition. With an extension of the annealing time, it is observed that Ag particles display the transform trend from ellipsoid to sphere. Our findings could inspire further investigation on the design and fabrication of metal nanoparticle chains.

  9. Noble-metal Ag nanoparticle chains: annealing Ag/Bi superlattice nanowires in vacuum.

    PubMed

    Xu, Shao Hui; Fei, Guang Tao; You, Qiao; Gao, Xu Dong; Huo, Peng Cheng; De Zhang, Li

    2016-09-16

    One-dimensional noble-metal Ag nanoparticle chains have been prepared by electrodepositing Ag/Bi superlattice nanowires in a porous anodic alumina oxide (AAO) template and following an annealing process in vacuum. It is found that Bi, as a sacrificial metal, can be removed completely after annealing at 450 °C with a vacuum degree of 10(-5) Torr. The regulation of particle size, shape and interparticle spacing of Ag NP chains has been realized by adjusting the segment length of the Ag/Bi superlattice nanowires and the annealing condition. With an extension of the annealing time, it is observed that Ag particles display the transform trend from ellipsoid to sphere. Our findings could inspire further investigation on the design and fabrication of metal nanoparticle chains.

  10. Facile synthesis of AgCl/polydopamine/Ag nanoparticles with in-situ laser improving Raman scattering effect

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Zhang, Wenqi; Wang, Lin; Wang, Feng; Yang, Haifeng

    2017-01-01

    We reported a simple and fast method to prepare a composite material of polydopamine (PDA) adlayer covered cubic AgCl core, which was inlaid with Ag nanoparticles (NPs), shortly named as AgCl/PDA/AgNPs. The resultant AgCl/PDA/AgNPs could be employed as surface-enhanced Raman scattering (SERS) substrate for in-situ detection and the SERS activity could be further greatly improved due to the production of more AgNPs upon laser irradiation. With 4-mercaptopyridine (4-Mpy) as the probe molecule, the enhancement factor could reach 107. Additionally, such SERS substrate shows good reproducibility with relative standard deviation of 7.32% and long term stability (after storage for 100 days under ambient condition, SERS intensity decay is less than 25%). In-situ elevating SERS activity of AgCl/PDA/AgNPs induced by laser may be beneficial to sensitive analysis in practical fields.

  11. Spin coating of Ag nanoparticles: Effect of reduction

    SciTech Connect

    Ansari, A. A. Sartale, S. D.

    2014-04-24

    A surfactant free method for the growth of Ag nanoparticles on glass substrate by spin coating of Ag ions solution followed by chemical reduction in aqueous hydrazine hydrate (HyH) solution has been presented. Appearance of surface plasmon resonance confirms the formation of Ag nanoparticles. Morphology and absorbance spectra of Ag nanoparticles films are used to examine effect of hydrazine concentration on the growth of Ag nanoparticles. SEM images show uniformly distributed Ag nanoparticles. Rate constant was found to be dependent on HyH concentration as a consequence influence particle size.

  12. Synthesis, characterization and antimycobacterial activity of Ag(I)-aspartame, Ag(I)-saccharin and Ag(I)-cyclamate complexes.

    PubMed

    Cavicchioli, Maurício; Leite, Clarice Q F; Sato, Daisy N; Massabni, Antonio C

    2007-10-01

    The present work describes the synthesis and antimycobacterial activity of three Ag(I)-complexes with the sweeteners aspartame, saccharin, and cyclamate as ligands, with the aim of finding new candidate substances for fighting tuberculosis and other mycobacterial infections. The minimal inhibitory concentration of these three complexes was investigated in order to determine their in-vitro antimycobacterial activity against Mycobacterium tuberculosis, Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium malmoense, and Mycobacterium kansasii. The MIC values were determined using the Microplate Alamar Blue Assay. The best MIC values found for the complexes were 9.75 microM for Ag(I)-aspartame against M. kansasii and 15.7 microM for Ag(I)-cyclamate against M. tuberculosis.

  13. Template synthesis of Ag/AgCl microrods and their efficient visible light-driven photocatalytic performance

    SciTech Connect

    Chen, Hua; Xiao, Liang; Huang, Jianhua

    2014-09-15

    Highlights: • Preparation ofAg/AgCl microrods by reaction of Ag{sub 2}WO{sub 4} microrods with NaCl solution. • Generation of metallic Ag is induced by the ambient light in the synthesis process. • Ag/AgCl shows excellent visible light-driven photodegradation of organic dyes. - Abstract: Ag/AgCl microrods, aggregated by nanoparticles with a diameter ranging from 100 nm to 2 μm, were prepared by an ion-exchange reaction at 80 °C between Ag{sub 2}WO{sub 4} template and NaCl solution. The existence of metallic Ag species was confirmed by XRD, DRS and XPS measurements. Ag/AgCl microrods showed excellent photocatalytic activity for the degradation of rhodamine B and methylene blue under visible light irradiation. The degradation rate constants of rhodamine B and methylene blue are 0.176 and 0.114 min{sup −1}, respectively. The cycling photodegradation experiments suggest that Ag/AgCl microds could be employed as stable plasmonic photocatalysts for the degradation of organic dyes under visible light irradiation.

  14. BiPO4 photocatalyst employing synergistic action of Ag/Ag3PO4 nanostructure and graphene nanosheets

    NASA Astrophysics Data System (ADS)

    Mohaghegh, N.; Rahimi, E.

    2016-06-01

    Graphene-supported BiPO4/Ag/Ag3PO4 photocatalyst has been fabricated by simple hydrothermal and impregnation reaction. In BiPO4/Ag/Ag3PO4 based on Reduced Graphene Oxide (RGO), this network renders numerous pathways for rapid mass transport, strong adsorption and multireflection of incident light; meanwhile, the interface between BiPO4/Ag/Ag3PO4 and RGO increases the active sites and electron transfer rate. BiPO4/Ag/Ag3PO4 based on RGO noticeably exhibited high photocatalytic activity than that of BiPO4/Ag/Ag3PO4 and P25 under visible light irradiation for cationic dye (Rhodamine B), anionic dye (methyl orange) and 4-chlorophenol (4-CP) as a neutral pollutant, which are usually difficult to be degraded over the other catalysts. This enhanced photocatalytic activity of Graphene-supported BiPO4/Ag/Ag3PO4 for all pollutants could be mainly ascribed to the reinforced charge transfer from BiPO4/Ag/Ag3PO4 to RGO, which suppresses the recombination of electron/hole pairs. Besides that, this photocatalyst can be used repetitively with a high photocatalytic activity and no apparent loss of activity occurs. The results reveal that the RGO nanosheets work as a photocatalyst promoter during the photocatalytic reaction, leading to an improved photocatalytic activity.

  15. Preparation of Ag2O/Ag2CO3/MWNTs composite photocatalysts for enhancement of ciprofloxacin degradation

    NASA Astrophysics Data System (ADS)

    Wang, Huiqin; Li, Jinze; Huo, Pengwei; Yan, Yongsheng; Guan, Qingfeng

    2016-03-01

    The Ag2O/Ag2CO3/multi-walled carbon nanotube (MWNTs) composite photocatalysts were prepared by calcination of the obtained precipitate. The structures and morphology of as-prepared composite photocatalysts were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS), diffuse reflectance spectroscopy (DRS), photoluminescence (PL) spectroscopy, X-ray photoelectron spectroscopy (XPS). The Ag2O/Ag2CO3/MWNTs composite photocatalysts exhibit higher degradation rate of ciprofloxacin (CIP) than the pure Ag2CO3, Ag2O/Ag2CO3 and Ag2CO3/MWNTs under visible light irradiation. The amount of loaded Ag2CO3 onto MWNTs and calcined time for Ag2CO3/MWNTs were systematically investigated, and the optimal amount of loaded Ag2CO3 and calcined time of Ag2CO3/MWNTs are 150 wt% and 10 min, respectively. The highest photocatalytic degradation rate of CIP could reach 76% under optimal conditions. The active species trapping experiments were also analyzed, the results show that the holes are main contributor for the degradation processes of CIP, furthermore the electrons, rad O2- and rad OH are also crucially influenced the photocatalytic degradation processes of CIP. The possible photocatalytic processes of CIP with Ag2O/Ag2CO3/MWNTs composite photocatalyst are also proposed.

  16. Mussel-inspired green synthesis of polydopamine-Ag-AgCl composites with efficient visible-light-driven photocatalytic activity.

    PubMed

    Cai, Aijun; Wang, Xiuping; Guo, Aiying; Chang, Yongfang

    2016-09-01

    Polydopamine-Ag-AgCl composites (PDA-Ag-AgCl) were synthesized using a mussel-inspired method at room temperature, where PDA acts as a reducing agent to obtain the noble Ag nanoparticles from a precursor. The morphologies and structures of the as-prepared PDA-Ag-AgCl were characterized by several techniques including field emission scanning electron microscopy (FESEM), transmission electron microscopy (SEM), Raman spectra, and X-Ray photoelectron spectrum (XPS). The morphological observation depicts formation of nanoparticles with various micrometer size diameters and surface XPS analysis shows presence of various elements including Ag, N, Cl, and O. The enhanced absorbance of the PDA-Ag-AgCl particles in the visible light region is confirmed through UV-Vis diffuse reflectance spectra (DRS), and the charge transfer is demonstrated by photoluminescence (PL) and photocurrent response. The synthesized PDA-Ag-AgCl composites could be used as visible-light-driven photocatalysts for the degradation of Rhodamine B. The elevated photocatalytic activity is ascribed to the effective charge transfer from plasmon-excited Ag to AgCl that can improve the efficiency of the charge separation during the photocatalytic reaction. Furthermore, differences in the photocatalytic performance among the different PDA-Ag-AgCl composites are noticed that could be attributed to the Brunauer-Emmett-Teller (BET) specific surface area, which benefits to capture the visible light efficiently. The PDA-Ag-AgCl exhibits excellent stability without a significant loss in activity after 5cycles. The proposed method is low-cost and environmentally friendly, hence a promising new way to fabricate plasmon photocatalysts.

  17. Effect of cysteine and humic acids on bioavailability of Ag from Ag nanoparticles to a freshwater snail

    USGS Publications Warehouse

    Luoma, Samuel N.; Tasha Stoiber,; Croteau, Marie-Noele; Isabelle Romer,; Ruth Merrifeild,; Lead, Jamie

    2016-01-01

    Metal-based engineered nanoparticles (NPs) will undergo transformations that will affect their bioavailability, toxicity and ecological risk when released to the environment, including interactions with dissolved organic material. The purpose of this paper is to determine how interactions with two different types of organic material affect the bioavailability of silver nanoparticles (AgNPs). Silver uptake rates by the pond snail Lymnaea stagnalis were determined after exposure to 25 nmol l-1 of Ag as PVP AgNPs, PEG AgNPs or AgNO3, in the presence of either Suwannee River humic acid or cysteine, a high-affinity thiol-rich organic ligand. Total uptake rate of Ag from the two NPs was either increased or not strongly affected in the presence of 1 – 10 mg 1-1 humic acid. Humic substances contain relatively few strong ligands for Ag explaining their limited effects on Ag uptake rate. In contrast, Ag uptake rate was substantially reduced by cysteine. Three components of uptake from the AgNPs were quantified in the presence of cysteine using a biodynamic modeling approach: uptake of dissolved Ag released by the AgNPs, uptake of a polymer or large (>3kD) Ag-cysteine complex and uptake of the nanoparticle itself. Addition of 1:1 Ag:cysteine reduced concentrations of dissolved Ag, which contributed to, but did not fully explain the reductions in uptake. A bioavailable Ag-cysteine complex (> 3kD) appeared to be the dominant avenue of uptake from both PVP AgNPs and PEG AgNPs in the presence of cysteine. Quantifying the different avenues of uptake sets the stage for studies to assess toxicity unique to NPs.

  18. One-pot synthesis of ternary Ag₂CO₃/Ag/AgCl photocatalyst in natural geothermal water with enhanced photocatalytic activity under visible light irradiation.

    PubMed

    Yao, Xiaxi; Liu, Xiaoheng

    2014-09-15

    Geothermal water is a clean, cheap and renewable resource and it is widely distributed all over the world. In this work, ternary Ag2CO3/Ag/AgCl photocatalyst has been successfully synthesized via a one-pot precipitation method in natural geothermal water at room temperature, wherein the geothermal water serves as the source of chlorine and carbonate. The results suggest that the Ag/AgCl nanoparticles are anchored on the surface of Ag2CO3 and Ag2CO3/Ag/AgCl composite shows strong absorption ability in the visible light region. The evaluation of the photocatalytic activity indicates that the as-synthesized Ag2CO3/Ag/AgCl photocatalyst exhibits higher photocatalytic performance for the degradation of methylene blue (MB) aqueous solution under visible light irradiation than one-component (Ag2CO3), two-component (Ag/AgCl, Ag2CO3/AgCl) and the mechanical mixture of Ag2CO3 and Ag/AgCl. The trapping experiments confirmed that holes (h(+)) and (•)O2(-) were the two main active species in the photocatalytic process. Finally, a possible Z-scheme photocatalytic mechanism of the charge transfer was proposed for the enhanced photocatalytic performance. This work may open up new insights into the application of cheap geothermal water resources in the word and provide new opportunities for facile fabrication of Ag/AgCl-based photocatalysts.

  19. Ag/ZnO heterostructure nanocrystals: synthesis, characterization, and photocatalysis.

    PubMed

    Zheng, Yuanhui; Zheng, Lirong; Zhan, Yingying; Lin, Xingyi; Zheng, Qi; Wei, Kemei

    2007-08-20

    A high yield of the dimer-type heterostructure of Ag/ZnO nanocrystals with different Ag contents is successfully prepared through a simple solvothermal method in the absence of surfactants. The samples are characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, UV-vis spectroscopy, and IR spectroscopy. The results show that all samples are composed of metallic Ag and ZnO; Ag nanoparticles locate on the surface of ZnO nanorods; the binding energy of Ag 3d(5/2) for the Ag/ZnO sample with a Ag content of 5.0 atom % shifts remarkably to the lower binding energy compared with the corresponding value of pure metallic Ag because of the interaction between Ag and ZnO nanocrystals; the concentration of oxygen vacancy for the as-synthesized samples varies with the increasing Ag content, and the Ag/ZnO sample with a Ag content of 5.0 atom % has the largest density of oxygen vacancy. In addition, the relationship between their structure and photocatalytic property is investigated in detail. It is found that the photocatalytic property is closely related to its structure, such as heterostructure, oxygen defect, and crystallinity. The presence of metallic Ag nanoparticles and oxygen vacancy on the surface of ZnO nanorods promotes the separation of photogenerated electron-hole pairs and thus enhances the photocatalytic activity.

  20. 3D [Ag-Mg] polyanionic frameworks in the La 4Ag 10Mg 3 and La 4Ag 10.3Mg 12 new ternary compounds

    NASA Astrophysics Data System (ADS)

    Solokha, Pavlo; De Negri, Serena; Pavlyuk, Volodymyr; Eck, Bernhard; Dronskowski, Richard; Saccone, Adriana

    2010-12-01

    The crystal structures of two new ternary phases, La 4Ag 10Mg 3 and La 4Ag 10.3Mg 12, were refined from X-ray single crystal diffraction data. La 4Ag 10Mg 3 crystallizes in the Ca 4Au 10In 3 structure type, an ordered variant of the binary Zr 7Ni 10 compound: orthorhombic, Cmce, oS68, a=14.173(5), b=10.266(3), c=10.354(3) Å, Z=4, w R2=0.0826, 676 F2 values, 50 variables. La 4Ag 10.3Mg 12 represents a new structure type: orthorhombic, Cmmm, oS116-10.32, a=9.6130(3), b=24.9663(8), c=9.6333(2) Å, Z=4, w R2=0.0403, 1185 F2 values, 101 variables. The structural analysis of both compounds, highlighting a significant contraction of the Ag-Mg distances, suggests the existence of three-dimensional [Ag-Mg] networks hosting La atoms. LMTO calculations applied to La 4Ag 10Mg 3 indicate that the strongest bonds occur for Ag-Ag and Ag-Mg interactions, and confirm the presence of a 3D ∞[Ag 10Mg 3] δ- polyanionic framework balanced by positively charged La atoms.

  1. Bipolar Ag-Zn battery

    NASA Technical Reports Server (NTRS)

    Giltner, L. John

    1994-01-01

    The silver-zinc (AgZn) battery system has been unique in its ability to safely satisfy high power demand applications with low mass and volume. However, a new generation of defense, aerospace, and commercial applications will impose even higher power demands. These new power demands can be satisfied by the development of a bipolar battery design. In this configuration the power consuming, interelectrode current conductors are eliminated while the current is then conducted via the large cross-section electrode substrate. Negative and positive active materials are applied to opposite sides of a solid silver foil substrate. In addition to reducing the weight and volume required for a specified power level, the output voltage performance is also improved as follows. Reduced weight through: elimination of the plastic cell container; elimination of plate leads and intercell connector; and elimination of internal plate current collector. Increased voltage through: elimination of resistance of current collector; elimination of resistance of plate lead; and elimination of resistance of intercell connector. EPI worked previously on development of a secondary bipolar silver zinc battery. This development demonstrated the electrical capability of the system and manufacturing techniques. One difficulty with this development was mechanical problems with the seals. However, recent improvements in plastics and adhesives should eliminate the major problem of maintaining a seal around the periphery of the bipolar module. The seal problem is not as significant for a primary battery application or for a requirement for only a few discharge cycles. A second difficulty encountered was with activation (introducing electrolyte into the cell) and with venting gas from the cell without loss of electrolyte. During previous work, the following projections for energy density were made from test data for a high power system which demonstrated in excess of 50 discharge/charge cycles. Projected

  2. Bipolar Ag-Zn battery

    NASA Astrophysics Data System (ADS)

    Giltner, L. John

    1994-02-01

    The silver-zinc (AgZn) battery system has been unique in its ability to safely satisfy high power demand applications with low mass and volume. However, a new generation of defense, aerospace, and commercial applications will impose even higher power demands. These new power demands can be satisfied by the development of a bipolar battery design. In this configuration the power consuming, interelectrode current conductors are eliminated while the current is then conducted via the large cross-section electrode substrate. Negative and positive active materials are applied to opposite sides of a solid silver foil substrate. In addition to reducing the weight and volume required for a specified power level, the output voltage performance is also improved as follows. Reduced weight through: elimination of the plastic cell container; elimination of plate leads and intercell connector; and elimination of internal plate current collector. Increased voltage through: elimination of resistance of current collector; elimination of resistance of plate lead; and elimination of resistance of intercell connector. EPI worked previously on development of a secondary bipolar silver zinc battery. This development demonstrated the electrical capability of the system and manufacturing techniques. One difficulty with this development was mechanical problems with the seals. However, recent improvements in plastics and adhesives should eliminate the major problem of maintaining a seal around the periphery of the bipolar module. The seal problem is not as significant for a primary battery application or for a requirement for only a few discharge cycles. A second difficulty encountered was with activation (introducing electrolyte into the cell) and with venting gas from the cell without loss of electrolyte. During previous work, the following projections for energy density were made from test data for a high power system which demonstrated in excess of 50 discharge/charge cycles. Projected

  3. 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...

  4. A novel cluster of mariner-like elements belonging to mellifera subfamily from spiders and insects: implications of recent horizontal transfer on the South-West Islands of Japan.

    PubMed

    Yamada, Kaori; Kawanishi, Yuichi; Yamada, Akinori; Tokuda, Gaku; Gurung, Raj Deep; Sasaki, Takeshi; Nakajima, Yumiko; Maekawa, Hideaki

    2014-04-01

    Mariner-like elements (MLEs) have been isolated from various eukaryotic genomes and they are divided into 15 subfamilies, including main five subfamilies: mauritiana, cecropia, mellifera/capitata, irritans, and elegans/briggsae. In the present study, MLEs belonging to mellifera subfamily were isolated from various spiders and insects (Hymenoptera and Lepidoptera) inhabiting the South-West Islands of Japan and neighboring regions. MLEs isolated from 15 different species formed a distinct novel cluster in mellifera subfamily. MLEs obtained from three different species [i.e., the bee Amegilla senahai subflavescens (Amsmar1), the wasp Campsomeris sp. (Casmar1), and the swallowtail butterfly Pachliopta aristolochiae (Paamar1)] contained an intact open reading frame that encoded a putative transposase. These transposases exhibited high similarity of 97.9% among themselves. In case of Casmar1, the presence of an intact ORF was found in high frequencies (i.e., 11 out of 12 clones). In addition, these transposases also showed the presence of a terminal inverted repeat-binding motif, DD(34)D and two highly conserved amino acid motifs, (W/L)(I/L)PHQL and YSP(D/N)L(A/S)P. These two motifs differed from previously known motifs, WVPHEL and YSPDLAP. MLEs isolated from these three different species may have been inserted into their genomes by horizontal transfer. Furthermore, the presence of an intact ORF suggests that they are still active in habitats along these isolated islands.

  5. 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.

  6. Submission to GenBank of the Tonoplast membrane intrinsic protein (TIP) Subfamily in Cotton – GenBank Accession No. GU998831-GU998839 and GenBank Accession TPA;inferential No. BK007053-BK007060

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The tonoplast intrinsic proteins (TIP) are one of the five aquaporin protein subfamilies. Aquaporin proteins are known to facilitate water transport through biological membranes. In order to identify TIP aquaporin gene candidates in cotton (Gossypium hirsutum L.), in silico and molecular cloning eff...

  7. Submission to GenBank of the Small intrinsic protein (SIP) Subfamily in Cotton – GenBank Accession No. GU998846-GU998848 and GenBank Accession TPA;inferential No. BK007063-BK007064

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The small basic intrinsic proteins (SIP) are one of the five aquaporin protein subfamilies. Aquaporin proteins are known to facilitate water transport through biological membranes. In order to identify SIP aquaporin gene candidates in cotton (Gossypium hirsutum L.), in silico and molecular cloning e...

  8. Submission to GenBank of the Nodulin 26-like intrinsic protein (NIP) Subfamily in Cotton – GenBank Accession No. GU998840-GU998845 and GenBank Accession TPA;inferential No. BK007061-BK007062

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The NOD26-like intrinsic proteins (NIP) are one of the five aquaporin protein subfamilies. Aquaporin proteins are known to facilitate water transport through biological membranes. In order to identify NIP aquaporin gene candidates in cotton (Gossypium hirsutum L.), in silico and molecular cloning ef...

  9. Spectrophotometry of the shell around AG Carinae

    NASA Technical Reports Server (NTRS)

    Mitra, P. Mila; Dufour, Reginald J.

    1990-01-01

    Spatially-resolved long-slit spectrophotometry are presented for two regions of the shell nebula around the P-Cygni variable star AG Carinae. The spectra cover the 3700-6800 A wavelength range. Emission-line diagnostics are used to derive extinction, electron temperatures, and densities for various positions in the nebula. The chemical abundances and ionization structure are calculated and compared with other types of planetary nebulae and shells around other luminous stars. It is found that the N/O and N/S ratios of Ag Car are high compared to solar neighborhood ISM values. The O/H depletion found for the AG Car shell approaches that found in the condensations of the Eta Car system.

  10. Enhanced chemiluminescence of the luminol-AgNO3 system by Ag nanoparticles.

    PubMed

    Li, Shifeng; Sun, Huimin; Wang, Dong; Hong, Jianguo; Tao, Shanjun; Yu, Haiyin; Wang, Xiuhua; Wei, Xianwen

    2012-01-01

    The oxidation reaction of luminol with AgNO(3) can produce chemiluminescence (CL) in the presence of silver nanoparticles (NPs) in alkaline solution. Based on the studies of UV-vis absorption spectra, photoluminescence (PL) spectra and CL spectra, a CL enhancement mechanism is proposed. The CL emission spectrum of the luminol-AgNO(3)-Ag NPs system indicated that the luminophore was still 3-aminophthalate. On injection of silver nanoparticles into the mixture of luminol and AgNO(3), they catalysed the reduction of AgNO(3) by luminol. The product luminol radicals reacted with the dissolved oxygen, to produce a strong CL emission. As a result, the CL intensity was substantially increased. Moreover, the influences of 18 amino acids, e.g. cystine, tyrosine and asparagine, and 25 organic compounds, including gallic acid, tannic acid and hydroquinone, on the luminol-AgNO(3)-Ag NPs CL system were studied by a flow-injection procedure, which led to an effective method for detecting these compounds.

  11. Ag/FeCo/Ag core/shell/shell magnetic nanoparticles with plasmonic imaging capability.

    PubMed

    Takahashi, Mari; Mohan, Priyank; Nakade, Akiko; Higashimine, Koichi; Mott, Derrick; Hamada, Tsutomu; Matsumura, Kazuaki; Taguchi, Tomohiko; Maenosono, Shinya

    2015-02-24

    Magnetic nanoparticles (NPs) have been used to separate various species such as bacteria, cells, and proteins. In this study, we synthesized Ag/FeCo/Ag core/shell/shell NPs designed for magnetic separation of subcellular components like intracellular vesicles. A benefit of these NPs is that their silver metal content allows plasmon scattering to be used as a tool to observe detection by the NPs easily and semipermanently. Therefore, these NPs are considered a potential alternative to existing fluorescent probes like dye molecules and colloidal quantum dots. In addition, the Ag core inside the NPs suppresses the oxidation of FeCo because of electron transfer from the Ag core to the FeCo shell, even though FeCo is typically susceptible to oxidation. The surfaces of the Ag/FeCo/Ag NPs were functionalized with ε-poly-L-lysine-based hydrophilic polymers to make them water-soluble and biocompatible. The imaging capability of the polymer-functionalized NPs induced by plasmon scattering from the Ag core was investigated. The response of the NPs to a magnetic field using liposomes as platforms and applying a magnetic field during observation by confocal laser scanning microscopy was assessed. The results of the magnetophoresis experiments of liposomes allowed us to calculate the magnetic force to which each liposome was subjected.

  12. The axisymmetric stellar wind of AG Carinae

    NASA Technical Reports Server (NTRS)

    Schulte-Ladbeck, Regina E.; Clayton, Geoffrey C.; Hillier, D. John; Harries, Tim J.; Howarth, Ian D.

    1994-01-01

    We present optical linear spectropolarimetry of the Luminous Blue Variable AG Carinae obtained after a recent visual brightness increase. The absence of He II lambda 4686 emission, together with the weakening of the He I spectrum and the appearance of Fe lines in the region around 5300 A, confirm that AG Car has started a new excursion across the HR diagram. The H alpha line profile exhibits very extended line wings that are polarized differently in both amount and position angle from either the continuum or the line core. The polarization changes across H alpha, together with variable continuum polarization, indicate the presence of intrinsic polarization. Coexistence of the line-wing polarization with extended flux-line wings evidences that both are formed by electron scattering in a dense wind. The position angle rotates across the line profiles, in a way that presently available models suggest is due to rotation and expansion of the scattering material. AG Car displays very large variations of its linear polarization with time, Delta P approximately 1.2%, indicating significant variations in envelope opacity. We find that the polarization varies along a preferred position angle of approximately 145 deg (with a scatter of +/- 10 deg) which we interpret as a symmetry axis of the stellar wind (with an ambiguity of 90 deg). This position angle is co-aligned with the major axis of the AG Car ring nebula and perpendicular to the AG Car jet. Our observations thus suggest that the axisymmetric geometry seen in the resolved circumstellar environment at various distances already exists within a few stellar radii of AG Car. From the H alpha polarization profile we deduce an interstellar polarization of Q = 0.31%, U = -1.15% at H alpha. The inferred interstellar polarization implies that the intrinsic polarization is not always of the same sign. This indicates either significant temporal changes in the envelope geometry, or it may arise from effects of multiple scattering

  13. Siberian Snake solenoid for the AGS

    SciTech Connect

    Ratner, L. G.

    1991-01-01

    Recent experiments at the Indiana University Cyclotron Facility (IUCF) have demonstrated that Siberian Snakes'' can be used to preserve the polarization of an accelerated polarized beam in a circular accelerator. Retrofitting full snakes into accelerators such as the Alternating Gradient Synchrotron (AGS) at Brookhaven is almost impossible due to space limitations, but a partial snake that can correct depolarization due to imperfection resonances with 1/20 to 1/30 of a full strength snake seems to present a viable option. We describe such a device for the AGS and give the design criteria in terms of simplicity of accelerator operation and level of achievable polarization. 2 refs., 5 figs., 1 tab.

  14. Facile synthesis of novel Ag/AgI/BiOI composites with highly enhanced visible light photocatalytic performances

    SciTech Connect

    Cao, Jing; Zhao, Yijie; Lin, Haili; Xu, Benyan; Chen, Shifu

    2013-10-15

    Novel Ag/AgI/BiOI composites were controllably synthesized via a facile ion-exchange followed by photoreduction strategy by using hierarchical BiOI microflower as substrate. The as-prepared Ag/AgI/BiOI composites were studied by X-ray powder diffractometer (XRD), scanning electron microscopy (SEM), high-resolution transmission electron microscopy (HRTEM), X-ray photoelectron spectroscopy (XPS), Brunauer–Emmett–Teller (BET) surface area analyzer and UV–vis diffuse reflectance spectroscopy (DRS). Under visible light (λ>420 nm), Ag/AgI/BiOI displayed highly enhanced photocatalytic activities for degradation of methyl orange (MO) compared to the pure hierarchical BiOI, which was mainly ascribed to the highly efficient separation of electrons and holes through the closely contacted interfaces in the Ag/AgI/BiOI ternary system. - Graphical abstract: Ag/AgI/BiOI displayed excellent photocatalytic activities for methyl orange degradation under visible light, which was mainly ascribed to the highly efficient separation of electrons and holes through Z-scheme pathway. Display Omitted - Highlights: • Novel Ag/AgI/BiOI composites were successfully synthesized. • Ag/AgI/BiOI displayed higher visible light activities than those of pure BiOI and AgI. • ·O{sub 2}{sup −} and h{sup +}, especially ·O{sub 2}{sup −}, dominated the photodegradation process of MO. • A Z-scheme pattern was adopted for Ag/AgI/BiOI activity enhancement.

  15. Ag@AgHPW as a plasmonic catalyst for visible-light photocatalytic degradation of environmentally harmful organic pollutants

    SciTech Connect

    Zhou, Wenhui; Cao, Minhua Li, Na; Su, Shuangyue; Zhao, Xinyu; Wang, Jiangqiang; Li, Xianghua; Hu, Changwen

    2013-06-01

    Graphical abstract: Ag@Ag{sub x}H{sub 3−x}PW12O40 (Ag@AgHPW) nanoparticles (NPs), a new visible-light driven plasmonic photocatalyst, are prepared by a green photoreduction strategy without the addition of any surfactant, which show a high activity and stability for the degradation of methyl blue (MB) under visible light irradiation. - Highlights: • A new visible-light driven photocatalyst Ag@Ag{sub x}H{sub 3−x}PW{sub 12}O{sub 40} was designed. • The photocatalyst shows a high activity for the degradation of methyl blue. • The high activity can be ascribed to the synergy of photoexcited AgHPW and Ag. - Abstract: Ag@Ag{sub x}H{sub 3−x}PW{sub 12}O{sub 40} (Ag@AgHPW) nanoparticles (NPs), a new visible-light driven plasmonic photocatalyst, are prepared by a green photoreduction strategy without the addition of any surfactant. They show strong absorption in the visible region because of the localized surface plasmon resonance (LSPR) of Ag NPs. This plasmonic photocatalyst shows a high activity and stability for the degradation of methyl blue (MB) under visible light irradiation, which could be attributed to the highly synergy of photoexcited Ag{sub x}H{sub 3−x}PW{sub 12}O{sub 40} (AgHPW) and plasmon-excited Ag NPs and the confinement effects at interfaces between polyoxometalates (POMs) and silver. POM anions have redox ability and high photocatalytic activity, whereas Ag NPs could effectively accelerate the separation of electrons and holes, both of which contribute to their high activity.

  16. Ag Nanowire Based Transparent Conductor for CIGS PV

    SciTech Connect

    Woods, L. M.; Wolk, J.; Smith, M.; Davande, H.; Ribelin, R. M.; Perkins, C. L.

    2011-01-01

    Coated silver nanowires (AgNW) have been considered as a replacement for transparent conducting oxides (TCOs) in CIGS based photovoltaic devices. The advantages of AgNW over TCOs are discussed, and optical and electrical characteristics of AgNWs on glass are presented. Similarly fabricated AgNWs with varying sheet resistance on CIGS devices were tested against ITO transparent conductor controls. The CIGS was produced using a roll-to-roll technique on a flexible polymer substrate. Variations in the ZnO layer resistivity that are adjacent to the AgNW layer in the CIGS device were also tested. Device results indicate similar Jsc, but a reduced FF for cells made with the AgNWs, and Voc dependence on the resistivity of the coated AgNW and ZnO window layers. FF and Voc losses associated with the use of AgNWs are discussed.

  17. Hierarchical Ag mesostructures for single particle SERS substrate

    NASA Astrophysics Data System (ADS)

    Xu, Minwei; Zhang, Yin

    2017-01-01

    Hierarchical Ag mesostructures with highly rough surface morphology have been synthesized at room temperature through a simple seed-mediated approach. Electron microscopy characterizations indicate that the obtained Ag mesostructures exhibit a textured surface morphology with the flower-like architecture. Moreover, the particle size can be tailored easily in the range of 250-500 nm. For the growth process of the hierarchical Ag mesostructures, it is believed that the self-assembly mechanism is more reasonable rather than the epitaxial overgrowth of Ag seed. The oriented attachment of nanoparticles is revealed during the formation of Ag mesostructures. Single particle surface enhanced Raman spectra (sp-SERS) of crystal violet adsorbed on the hierarchical Ag mesostructures were measured. Results reveal that the hierarchical Ag mesostructures can be highly sensitive sp-SERS substrates with good reproducibility. The average enhancement factors for individual Ag mesostructures are estimated to be about 106.

  18. 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

  19. Effect of Ag+ and PO43- ratios on the microstructure and photocatalytic activity of Ag3PO4

    NASA Astrophysics Data System (ADS)

    Qin, Jiaqian; Zhang, Xinyu; Yang, Chengwu; Song, Aijun; Zhang, Bing; Rajendran, Saravanan; Ma, Mingzhen; Liu, Riping

    2016-09-01

    In this work, the catalyst silver phosphate (Ag3PO4) with different initial ratios of Ag+ and PO43- in aqueous solution was synthesized by a simple precipitation method from AgNO3 and NH4H2PO4 which were used as the precursor. After that, the prepared samples were characterized by different techniques such as field emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), UV-visible diffuse reflectance spectroscopy (UV-DRS) and decomposition evolution of rhodamine B (RhB) solution. The results indicate that the initial ratios of Ag+/PO43- in aqueous solution can modify the morphology and also it can significantly affect the photocatalytic performance. During photocatalytic process, the rich Ag+ ion Ag3PO4 can form the surface plasmon resonance (SPR) of Ag nanoparticles, which inhibit the reduction of Ag3PO4 resulting in higher photocatalytic activity and stability.

  20. The electron paramagnetic resonance spectrum of Ag2 3

    NASA Astrophysics Data System (ADS)

    van der Pol, A.; Reijersen, E. J.; de Boer, E.; Wasowicz, T.; Michalik, J.

    A highly resolved EPR spectrum of the silver trimer 109Ag2+3, present in 109Ag1-NaA zeolite, has been measured. The spectrum is characterized by an axially symmetric spin Hamiltonian having and for each of the 109Ag nuclei tMPH0037_images.

  1. AGS experiments -- 1996, 1997, 1998, 1999. Fifteenth edition

    SciTech Connect

    Lo Presti, P.

    1999-03-01

    This report is a compilation of two-page summaries for AGS experiments for FY 1996, FY 1997, FY 1998, FY 1999. The bulk of the experiments are for high energy physics and nuclear physics programs. Also included are the run schedules for the AGS for each of those years and a listing of publications of AGS experiments for 1982--1999.

  2. Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates.

    PubMed

    Wibberg, Daniel; Rupp, Oliver; Blom, Jochen; Jelonek, Lukas; Kröber, Magdalena; Verwaaijen, Bart; Goesmann, Alexander; Albaum, Stefan; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas

    2015-01-01

    Rhizoctonia solani, a soil-born plant pathogenic basidiomycetous fungus, affects various economically important agricultural and horticultural crops. The draft genome sequence for the R. solani AG1-IB isolate 7/3/14 as well as a corresponding transcriptome dataset (Expressed Sequence Tags--ESTs) were established previously. Development of a specific R. solani AG1-IB gene model based on GMAP transcript mapping within the eukaryotic gene prediction platform AUGUSTUS allowed detection of new genes and provided insights into the gene structure of this fungus. In total, 12,616 genes were recognized in the genome of the AG1-IB isolate. Analysis of predicted genes by means of different bioinformatics tools revealed new genes whose products potentially are involved in degradation of plant cell wall components, melanin formation and synthesis of secondary metabolites. Comparative genome analyses between members of different R. solani anastomosis groups, namely AG1-IA, AG3 and AG8 and the newly annotated R. solani AG1-IB genome were performed within the comparative genomics platform EDGAR. It appeared that only 21 to 28% of all genes encoded in the draft genomes of the different strains were identified as core genes. Based on Average Nucleotide Identity (ANI) and Average Amino-acid Identity (AAI) analyses, considerable sequence differences between isolates representing different anastomosis groups were identified. However, R. solani isolates form a distinct cluster in relation to other fungi of the phylum Basidiomycota. The isolate representing AG1-IB encodes significant more genes featuring predictable functions in secondary metabolite production compared to other completely sequenced R. solani strains. The newly established R. solani AG1-IB 7/3/14 gene layout now provides a reliable basis for post-genomics studies.

  3. Antibacterial Ag/a-C nanocomposite coatings: The influence of nano-galvanic a-C and Ag couples on Ag ionization rates

    NASA Astrophysics Data System (ADS)

    Manninen, N. K.; Calderon, S.; Carvalho, I.; Henriques, M.; Cavaleiro, A.; Carvalho, S.

    2016-07-01

    Biofilm formation has been pointed as a major concern in different industrial applications, namely on biomedical implants and surgical instruments, which has prompted the development of new strategies for production of efficient antimicrobial surfaces. In this work, nano-galvanic couples were created to enhance the antibacterial properties of silver, by embedding it into amorphous carbon (a-C) matrix. The developed Ag/a-C nanocomposite coatings, deposited by magnetron sputtering, revealed an outstanding antibacterial activity against Staphylococcus epidermidis, promoting a total reduction in biofilm formation with no bacteria counts in all dilution. The open circuit potential (OCP) tests in 0.9% NaCl confirmed that a-C shows a positive OCP value, in contrast to Ag coating, thus enhancing the ionization of biocidal Ag+ due to the nano-galvanic couple activation. This result was confirmed by the inductively coupled plasma-optical emission spectroscopy (ICP-OES), which revealed a higher Ag ionization rate in the nanocomposite coating in comparison with the Ag coating. The surface of Ag/a-C and Ag coatings immersed in 0.9% NaCl were monitored by scanning electron microscopy (SEM) over a period of 24 h, being found that the Ag ionization determined by ICP-OES was accompanied by an Ag nanoparticles coalescence and agglomeration in Ag/a-C coating.

  4. Water repellent Ag/Ag2O@bamboo cellulose fiber membrane as bioinspired cargo carriers.

    PubMed

    Wang, Yaru; Zhang, Ximu; Zhang, Xiaofang; Zhao, Jiangqi; Zhang, Wei; Lu, Canhui

    2015-11-20

    Water striders can walk on water. To mimic this function, a porous membrane consisted of bamboo cellulose fiber was hybridized with Ag/Ag2O nanoparticles through a facile in situ method to produce water repellent and well-ventilated materials. Herein, we report the sole surface roughness created by Ag/Ag2O nanoparticles could render the membrane a water contact angle (CA) of 140±3.0°. When floating on water, the hybrid membrane was able to support a heavy load more than 10 times the weight of the membrane itself. Additionally, this membrane demonstrated capabilities for oil sampling under water or oil/water separation and strong antibacterial activity against Escherichia coli. Thus we foresee that this novel hybrid membrane can be potentially utilized as drag-reducing, gas permeable and antibiotic substrates for constructing miniature aquatic devices.

  5. Selectivity control of photosensitivity of Ag-GaP and Ag- AlGaN structures

    NASA Astrophysics Data System (ADS)

    Lamkin, I. A.; Tarasov, S. A.; Solomonov, A. V.; Andreev, M. Y.; Kurin, S. Yu

    2015-12-01

    Design, growth and studies of photosensitive structures based on Ag-GaP and Ag- AlxGa1-xN contacts are reported. Methods for structure selectivity control, which allow changing the sensitivity spectrum half-width in a range of 11-210 nm were worked out. By varying the metal layer thickness, a set of Ag-GaP short-wavelength photodetectors (PD) was fabricated. The set includes PDs from broadband (spectrum half-width Δλ=210 nm, sensitivity SI = 0,19 A/W) to visible-blind (Δλ=15 nm, SI = 0,034 A/W). The use of Ag-AlxGa1-xN structures provided increased sensitivity (SI = 0,071 A/W) and Δλ reduced to 11 nm due to special selection of solid solution composition.

  6. Communication: Kinetics of chemical ordering in Ag-Au and Ag-Ni nanoalloys

    NASA Astrophysics Data System (ADS)

    Calvo, F.; Fortunelli, A.; Negreiros, F.; Wales, D. J.

    2013-09-01

    The energy landscape and kinetics of medium-sized Ag-Au and Ag-Ni nanoalloy particles are explored via a discrete path sampling approach, focusing on rearrangements connecting regions differing in chemical order. The highly miscible Ag27Au28 supports a large number of nearly degenerate icosahedral homotops. The transformation from reverse core-shell to core-shell involves large displacements away from the icosahedron through elementary steps corresponding to surface diffusion and vacancy formation. The immiscible Ag42Ni13 naturally forms an asymmetric core-shell structure, and about 10 eV is required to extrude the nickel core to the surface. The corresponding transformation occurs via a long and smooth sequence of surface displacements. For both systems the rearrangement kinetics exhibit Arrhenius behavior. These results are discussed in the light of experimental observations.

  7. 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

  8. Evolutionary selection across the nuclear hormone receptor superfamily with a focus on the NR1I subfamily (vitamin D, pregnane X, and constitutive androstane receptors)

    PubMed Central

    Krasowski, Matthew D; Yasuda, Kazuto; Hagey, Lee R; Schuetz, Erin G

    2005-01-01

    Background The nuclear hormone receptor (NR) superfamily complement in humans is composed of 48 genes with diverse roles in metabolic homeostasis, development, and detoxification. In general, NRs are strongly conserved between vertebrate species, and few examples of molecular adaptation (positive selection) within this superfamily have been demonstrated. Previous studies utilizing two-species comparisons reveal strong purifying (negative) selection of most NR genes, with two possible exceptions being the ligand-binding domains (LBDs) of the pregnane X receptor (PXR, NR1I2) and the constitutive androstane receptor (CAR, NR1I3), two proteins involved in the regulation of toxic compound metabolism and elimination. The aim of this study was to apply detailed phylogenetic analysis using maximum likelihood methods to the entire complement of genes in the vertebrate NR superfamily. Analyses were carried out both across all vertebrates and limited to mammals and also separately for the two major domains of NRs, the DNA-binding domain (DBD) and LBD, in addition to the full-length sequences. Additional functional data is also reported for activation of PXR and the vitamin D receptor (VDR; NR1I1) to gain further insight into the evolution of the NR1I subfamily. Results The NR genes appear to be subject to strong purifying selection, particularly in the DBDs. Estimates of the ratio of the non-synonymous to synonymous nucleotide substitution rates (the ω ratio) revealed that only the PXR LBD had a sub-population of codons with an estimated ω ratio greater than 1. CAR was also unusual in showing high relative ω ratios in both the DBD and LBD, a finding that may relate to the recent appearance of the CAR gene (presumably by duplication of a pre-mammalian PXR gene) just prior to the evolution of mammals. Functional analyses of the NR1I subfamily show that human and zebrafish PXRs show similar activation by steroid hormones and early bile salts, properties not shared by sea

  9. High Resolution PDF Measurements on Ag Nanoparticles

    SciTech Connect

    Rocha, Tulio C. R.; Martin, Chris; Kycia, Stefan; Zanchet, Daniela

    2009-01-29

    The quantitative analysis of structural defects in Ag nanoparticles was addressed in this work. We performed atomic scale structural characterization by a combination of x-ray diffraction (XRD) using the Pair Distribution Function analysis (PDF) and High Resolution Transmission Electron Microscopy (HRTEM). The XRD measurements were performed using an innovative instrumentation setup to provide high resolution PDF patterns.

  10. Accuracy Assessment for AG500, Electromagnetic Articulograph

    ERIC Educational Resources Information Center

    Yunusova, Yana; Green, Jordan R.; Mefferd, Antje

    2009-01-01

    Purpose: The goal of this article was to evaluate the accuracy and reliability of the AG500 (Carstens Medizinelectronik, Lenglern, Germany), an electromagnetic device developed recently to register articulatory movements in three dimensions. This technology seems to have unprecedented capabilities to provide rich information about time-varying…

  11. Energy loss of 107Ag, 109Ag, and 150Sm in Ni and Au

    NASA Astrophysics Data System (ADS)

    Ribas, R. V.; Seale, W. A.; Roney, W. A.; Szanto, E. M.

    1980-04-01

    The stopping pow´er of 107Ag, 109Ag, and 150Sm in nickel and gold was measured as a preliminary test of a new technique for measuring energy loss based on the γ-ray Doppler shift. The analysis of the data was based on the theories of Lindhard, Scharff, and Schiott for nuclear and electronic stopping. The results are compared with the semiempirical predictions of Northcliffe and Schilling and the Lindhard-Scharff-Schiott theory.

  12. A dry method to synthesize dendritic Ag2Se nanostructures utilizing CdSe quantum dots and Ag thin films

    NASA Astrophysics Data System (ADS)

    Hu, Lian; Zhang, Bingpo; Xu, Tianning; Li, Ruifeng; Wu, Huizhen

    2015-01-01

    Dendritic Ag2Se nanostructures are synthesized in a dry environment by UV irradiating the hybrids composed of CdSe quantum dots (QDs) and silver (Ag). UV irradiation on CdSe QDs induces a photooxidation effect on the QD surface and leads to the formation of SeO2 components. Then SeO2 reacts with the Ag atoms in either Ag film or QD layer to produce the Ag2Se. The growth mechanism of Ag2Se dendrites on solid Ag films is explored and explained by a diffusion limited aggregation model in which the QD layer provides enough freedom for Ag2Se motion. Since the oxidation of the CdSe QDs is the critical step for the Ag2Se dendrites formation this dry chemical interaction between QDs and Ag film can be applied in the study of the QD surface chemical properties. With this dry synthesis method, the Ag2Se dendrites can also be facilely formed at the designed area on Ag substrates.

  13. A dry method to synthesize dendritic Ag2Se nanostructures utilizing CdSe quantum dots and Ag thin films.

    PubMed

    Hu, Lian; Zhang, Bingpo; Xu, Tianning; Li, Ruifeng; Wu, Huizhen

    2015-01-09

    Dendritic Ag2Se nanostructures are synthesized in a dry environment by UV irradiating the hybrids composed of CdSe quantum dots (QDs) and silver (Ag). UV irradiation on CdSe QDs induces a photooxidation effect on the QD surface and leads to the formation of SeO2 components. Then SeO2 reacts with the Ag atoms in either Ag film or QD layer to produce the Ag2Se. The growth mechanism of Ag2Se dendrites on solid Ag films is explored and explained by a diffusion limited aggregation model in which the QD layer provides enough freedom for Ag2Se motion. Since the oxidation of the CdSe QDs is the critical step for the Ag2Se dendrites formation this dry chemical interaction between QDs and Ag film can be applied in the study of the QD surface chemical properties. With this dry synthesis method, the Ag2Se dendrites can also be facilely formed at the designed area on Ag substrates.

  14. New insight into daylight photocatalysis of AgBr@Ag: synergistic effect between semiconductor photocatalysis and plasmonic photocatalysis.

    PubMed

    Jiang, Jing; Li, Hao; Zhang, Lizhi

    2012-05-14

    Noble metal nanoparticles (NPs) are often used as electron scavengers in conventional semiconductor photocatalysis to suppress electron-hole (e(-)-h(+) ) recombination and promote interfacial charge transfer, and thus enhance photocatalytic activity of semiconductors. In this contribution, it is demonstrated that noble metal NPs such as Ag NPs function as visible-light harvesting and electron-generating centers during the daylight photocatalysis of AgBr@Ag. Novel Ag plasmonic photocatalysis could cooperate with the conventional AgBr semiconductor photocatalysis to enhance the overall daylight activity of AgBr@Ag greatly because of an interesting synergistic effect. After a systematic investigation of the daylight photocatalysis mechanism of AgBr@Ag, the synergistic effect was attributed to surface plasmon resonance induced local electric field enhancement on Ag, which can accelerate the generation of e(-)-h(+) pairs in AgBr, so that more electrons are produced in the conduction band of AgBr under daylight irradiation. This study provides new insight into the photocatalytic mechanism of noble metal/semiconductor systems as well as the design and fabrication of novel plasmonic photocatalysts.

  15. Advances of Ag, Cu, and Ag-Cu alloy nanoparticles synthesized via chemical reduction route

    NASA Astrophysics Data System (ADS)

    Tan, Kim Seah; Cheong, Kuan Yew

    2013-04-01

    Silver (Ag) and copper (Cu) nanoparticles have shown great potential in variety applications due to their excellent electrical and thermal properties resulting high demand in the market. Decreasing in size to nanometer scale has shown distinct improvement in these inherent properties due to larger surface-to-volume ratio. Ag and Cu nanoparticles are also shown higher surface reactivity, and therefore being used to improve interfacial and catalytic process. Their melting points have also dramatically decreased compared with bulk and thus can be processed at relatively low temperature. Besides, regularly alloying Ag into Cu to create Ag-Cu alloy nanoparticles could be used to improve fast oxidizing property of Cu nanoparticles. There are varieties methods have been reported on the synthesis of Ag, Cu, and Ag-Cu alloy nanoparticles. This review aims to cover chemical reduction means for synthesis of those nanoparticles. Advances of this technique utilizing different reagents namely metal salt precursors, reducing agents, and stabilizers, as well as their effects on respective nanoparticles have been systematically reviewed. Other parameters such as pH and temperature that have been considered as an important factor influencing the quality of those nanoparticles have also been reviewed thoroughly.

  16. A comparative study about electronic structures at rubrene/Ag and Ag/rubrene interfaces

    SciTech Connect

    Sinha, Sumona Mukherjee, M.

    2015-10-15

    The contact between the electrode and the organic semiconductor is one of the most crucial factors in determining the organic device performance. The development and production technology of different organic devices require the understanding of different types of metal/organic semiconducting thin film interfaces. Comparisons about the electronic structures at Rubrene/Ag and Ag/Rubrene interfaces have been studied using photoemission spectroscopy. The Ag on rubrene interfaces is found to show more interesting and complex natures than its counterpart. The vacuum level (VL) was shifted about 0.51 eV from push back effect for deposition of 5 Å rubrene onto Ag film whereas the electronic features of silver was only suppressed and no energy shift was resulted. While the deposition of 5 Å Ag onto rubrene film leads to the diffusion of the Ag atoms, as a cluster with quantum size effect, inside the film. Angle dependent XPS measurement indicates that diffused metal clusters were present at entire probed depth of the film. Moreover these clusters dope the uppermost surface of the rubrene film which consequences a shift of the electronic states of thick organic film towards higher binding energy. The VL was found to shift about 0.31 eV toward higher binding energy whereas the shift was around 0.21 eV for the electronic states of rubrene layer.

  17. Ag induced electromagnetic interference shielding of Ag-graphite/PVDF flexible nanocomposites thinfilms

    SciTech Connect

    Kumaran, R.; Alagar, M.; Dinesh Kumar, S.; Subramanian, V.; Dinakaran, K.

    2015-09-14

    We report Ag nanoparticle induced Electromagnetic Interference (EMI) shielding in a flexible composite films of Ag nanoparticles incorporated graphite/poly-vinylidene difluoride (PVDF). PVDF nanocomposite thin-films were synthesized by intercalating Ag in Graphite (GIC) followed by dispersing GIC in PVDF. The X-ray diffraction analysis and the high-resolution transmission electron microscope clearly dictate the microstructure of silver nanoparticles in graphite intercalated composite of PVDF matrix. The conductivity values of nanocomposites are increased upto 2.5 times when compared to neat PVDF having a value of 2.70 S/cm at 1 MHz. The presence of Ag broadly enhanced the dielectric constant and lowers the dielectric loss of PVDF matrix proportional to Ag content. The EMI shielding effectiveness of the composites is 29.1 dB at 12.4 GHz for the sample having 5 wt. % Ag and 10 wt. % graphite in PVDF.

  18. The Effect of Ag and Ag+N Ion Implantation on Cell Attachment Properties

    SciTech Connect

    Urkac, Emel Sokullu; Oztarhan, Ahmet; Gurhan, Ismet Deliloglu; Iz, Sultan Gulce; Tihminlioglu, Funda; Oks, Efim; Nikolaev, Alexey; Ila, Daryush

    2009-03-10

    Implanted biomedical prosthetic devices are intended to perform safely, reliably and effectively in the human body thus the materials used for orthopedic devices should have good biocompatibility. Ultra High Molecular Weight Poly Ethylene (UHMWPE) has been commonly used for total hip joint replacement because of its very good properties. In this work, UHMWPE samples were Ag and Ag+N ion implanted by using the Metal-Vapor Vacuum Arc (MEVVA) ion implantation technique. Samples were implanted with a fluency of 1017 ion/cm2 and extraction voltage of 30 kV. Rutherford Backscattering Spectrometry (RBS) was used for surface studies. RBS showed the presence of Ag and N on the surface. Cell attachment properties investigated with model cell lines (L929 mouse fibroblasts) to demonstrate that the effect of Ag and Ag+N ion implantation can favorably influence the surface of UHMWPE for biomedical applications. Scanning electron microscopy (SEM) was used to demonstrate the cell attachment on the surface. Study has shown that Ag+N ion implantation represents more effective cell attachment properties on the UHMWPE surfaces.

  19. Preparation of Ag@Ag₃PO₄@ZnO ternary heterostructures for photocatalytic studies.

    PubMed

    Jin, Chao; Liu, Guanglei; Zu, Lianhai; Qin, Yao; Yang, Jinhu

    2015-09-01

    In this article, we report a novel Ag@Ag3PO4@ZnO ternary heterostructures synthesized through a three-step approach. Firstly, single-crystalline Ag nanorods are fabricated and served as the templates for subsequent Ag3PO4 deposition. Secondly, Ag3PO4 crystals are grown around Ag core nanorods through a solution co-precipitation process, leading to the Ag@Ag3PO4 binary heterostructures. Finally, ZnO nanorod arrays on the surface of the Ag@Ag3PO4 heterostructures are realized via a seeded growth strategy, forming the typical Ag@Ag3PO4@ZnO ternary heterostructures. The photodegradation of rhodamine B under ultraviolet-visible light irradiation indicates that the Ag@Ag3PO4@ZnO ternary heterostructures exhibit much higher activities than pure Ag3PO4 and binary heterostructures of Ag@Ag3PO4. The higher photocatalytic activity of the Ag@Ag3PO4@ZnO composites may be attributed to the effective photogenerated charge separation at heterointerfaces of Ag/Ag3PO4 and Ag3PO4/ZnO, and the rapid electron transport along one-dimensional Ag and ZnO nanorods.

  20. Enhanced thermal stability of Ag nanorods through capping

    SciTech Connect

    Bachenheimer, Lou; Elliott, Paul; Stagon, Stephen; Huang, Hanchen

    2014-11-24

    Ag nanorods may serve as sensors in the detection of trace amounts of chemical agents, even single molecules, through surface enhanced Raman spectroscopy (SERS). However, thermal coarsening of Ag nanorods near room temperature limits their applications. This letter proposes the use of a thin oxide capping layer to enhance the thermal stability of Ag nanorods beyond 100 °C. Using electron microscopy characterization and SERS tests, the authors show that the proposed method is effective in stabilizing both morphology and sensitivity of Ag nanorods. The results of this work extend the applicability of Ag nanorods as chemical sensors to higher temperatures.

  1. 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.

  2. A novel DNMT3B subfamily, DeltaDNMT3B, is the predominant form of DNMT3B in non-small cell lung cancer.

    PubMed

    Wang, Luo; Wang, Jie; Sun, Shiyong; Rodriguez, Marivonne; Yue, Ping; Jang, Se Jin; Mao, Li

    2006-07-01

    De novo promoter DNA methylation represses gene transcription and is a common mechanism to inactivate tumor suppressor genes in tumorigenesis. DNMT3B plays an important role in de novo DNA methylation. We report here the identification of a novel DNMT3B subfamily, termed DeltaDNMT3B, whose expression is initiated through a promoter located at intron 4 and exon 5 of the DNMT3B gene. At least 7 transcriptional variants of DeltaDNMT3B have been observed as the result of alternative pre-mRNA splicing. Predicted proteins derived from these variants suggest that 4 of the variants share a conservative enzymatic domain but contain a variable PWWP motif, a putative DNA binding structure, whereas 3 of the variants lack the enzymatic domain due to predicted premature translational termination. In non-small cell lung cancer (NSCLC) cell lines, DeltaDNMT3B variants are frequently expressed and are the predominant forms of DNMT3B. Similarly, DeltaDNMT3B variants are frequently expressed in primary NSCLC but are not detectable or are expressed at low levels in corresponding normal lung tissue. Our results indicate that DeltaDNMT3B is the major expression form of DNMT3B in NSCLC and may play an important role in the development of aberrant promoter methylation during lung tumorigenesis.

  3. 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

  4. A systematic review of the subfamily Syringophilinae (Acari: Syringophilidae) of the Nearctic region. Part 1: quill mites associated with passerines (Aves: Passeriformes).

    PubMed

    Skoracki, Maciej; Spicer, Greg S; Oconnor, Barry M

    2016-02-29

    Quill mites belonging to the subfamily Syringophilinae Lavoipierre, 1953 associated with the Nearctic passeriform birds are revised. All of the 49 known species, which are grouped in seven genera, are recorded. Among them, four new species are described: Syringophiloidus audubioni sp. nov. from Spizella breweri (Cassini) (Emberizidae), Syringophilopsis catesbyi sp. nov. from Vireo olivaceus (Linnaeus) (Vireonidae), S. wilsoni sp. nov. from Pheucticus melanocephalus (Swainson) (Cardinalidae), and S. bartrami sp. nov. from Spizella passerina (Bechstein) (Emberizidae). The species Syringophilopsis hylocichlae Clark, 1964 syn. nov. is synonymized with Syringophilopsis turdus (Fritsch, 1958), and Syringophiloidus zonotrichia syn. nov. is synonymized with Betasyringophiloidus seiuri (Clark, 1964) comb. nov. Six species are recorded from the Nearctic region for the first time: Syringophiloidus delichonum Bochkov, 2001, S. glandarii (Fritsch, 1958), S. weiszii Skoracki et al., 2001, S. bombycillae Skoracki, 2002, Syringophilopsis mimidus Sikora et al., 2011, and Torotrogla merulae Skoracki et al., 2000. Data on Nearctic syringophiline species, their hosts and distribution are summarized and the keys to all species are constructed.

  5. The membrane-spanning 4-domains, subfamily A (MS4A) gene cluster contains a common variant associated with Alzheimer's disease

    PubMed Central

    2011-01-01

    Background In order to identify novel loci associated with Alzheimer's disease (AD), we conducted a genome-wide association study (GWAS) in the Spanish population. Methods We genotyped 1,128 individuals using the Affymetrix Nsp I 250K chip. A sample of 327 sporadic AD patients and 801 controls with unknown cognitive status from the Spanish general population were included in our initial study. To increase the power of the study, we combined our results with those of four other public GWAS datasets by applying identical quality control filters and the same imputation methods, which were then analyzed with a global meta-GWAS. A replication sample with 2,200 sporadic AD patients and 2,301 controls was genotyped to confirm our GWAS findings. Results Meta-analysis of our data and independent replication datasets allowed us to confirm a novel genome-wide significant association of AD with the membrane-spanning 4-domains subfamily A (MS4A) gene cluster (rs1562990, P = 4.40E-11, odds ratio = 0.88, 95% confidence interval 0.85 to 0.91, n = 10,181 cases and 14,341 controls). Conclusions Our results underscore the importance of international efforts combining GWAS datasets to isolate genetic loci for complex diseases. PMID:21627779

  6. 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

  7. 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.

  8. Inherited surfactant deficiency due to uniparental disomy of rare mutations in the surfactant protein-B and ATP binding cassette, subfamily A, member 3 genes

    PubMed Central

    Hamvas, Aaron; Nogee, Lawrence M.; Wegner, Daniel J.; DePass, Kelcey; Christodoulou, John; Bennetts, Bruce; McQuade, Leon R.; Gray, Peter H.; Deterding, Robin R.; Carroll, Travis R.; Kammesheidt, Anja; Kasch, Laura M.; Kulkarni, Shashikant; Cole, F. Sessions

    2009-01-01

    Objective To characterize inheritance of homozygous, rare, recessive loss-of-function mutations in the surfactant protein-B (SFTPB) or ATP binding cassette, subfamily A, member 3 (ABCA3) genes in newborns with lethal respiratory failure. Study design We resequenced parents whose infants were homozygous for mutations in SFTPB or ABCA3. For infants with only one heterozygous parent, we performed microsatellite analysis for chromosomes 2 (SFTPB) and 16 (ABCA3). Results We identified one infant homozygous for the c.1549C>GAA mutation (121ins2) in SFTPB for whom only the mother was heterozygous and 3 infants homozygous for mutations in ABCA3 (p.K914R, p.P147L, and c.806_7insGCT) for whom only the fathers were heterozygous. For the SP-B deficient infant, microsatellite markers confirmed maternal heterodisomy with segmental isodisomy. Microsatellite analysis confirmed paternal isodisomy for the three ABCA3 deficient infants. Two ABCA3 deficient infants underwent lung transplantation at 3 and 5 months of age, respectively, and two infants died. None exhibited any non-pulmonary phenotype. Conclusions Uniparental disomy should be suspected in infants with rare homozygous mutations in SFTPB or ABCA3. Confirmation of parental carrier status is important to provide recurrence risk and to monitor expression of other phenotypes that may emerge through reduction to homozygosity of recessive alleles. PMID:19647838

  9. 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

  10. 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.

  11. 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

  12. Investigating the properties of infrared PCFs based on AgCl-AgBr, AgBr-TlI, AgCl-AgBr-AgI(TlI) crystals theoretically and experimentally

    NASA Astrophysics Data System (ADS)

    Korsakov, A. S.; Zhukova, L. V.; Vrublevsky, D. S.; Korsakova, E. A.

    2014-12-01

    For operating at the CO2 laser wavelength (10.6 μm), we manufactured single- and double-layered infrared (IR) fibers, as well as those with an enlarged mode field diameter, obtained via extrusion from Ag(Cl) x Br1 - x (0 < x < 1), Ag1 - x Tl x Br1 - x I x (0 < x ≤ 0.08), Ag1 - x Tl x Cl y I z Br1 - y - z (0.003 ≤ x ≤ 0.040; 0.066 ≤ y ≤ 0.246; 0.004 ≤ z ≤ 0.048) crystals. We calculated their fundamental characteristics at 10.6 μm and conducted computer simulation of their structure and mode field beforehand. Optical and mechanical characteristics of IR crystals and fibers, such as transmission range, refractive indices, and durability, were also determined, with the dependence of varying monadic thallium iodide content on them being shown as well. In particular, we demonstrated that the increase of thallium iodide content in the initial silver chloride bromide widens the transparency range to 40 μm and improves the rupture strength up to 200 MPa, which is due to the decrease in average fiber grain size up to 95 nm—nanocrystalline size. Using a CCD camera for the far field investigation at 10.6 μm, we showed the single mode of the fibers obtained.

  13. Biotic and abiotic interactions in aquatic microcosms determine fate and toxicity of Ag nanoparticles: part 2-toxicity and Ag speciation.

    PubMed

    Bone, Audrey J; Colman, Benjamin P; Gondikas, Andreas P; Newton, Kim M; Harrold, Katherine H; Cory, Rose M; Unrine, Jason M; Klaine, Stephen J; Matson, Cole W; Di Giulio, Richard T

    2012-07-03

    To study the effects of complex environmental media on silver nanoparticle (AgNP) toxicity, AgNPs were added to microcosms with freshwater sediments and two species of aquatic plants (Potamogeton diversifolius and Egeria densa), followed by toxicity testing with microcosm surface water. Microcosms were designed with four environmental matrices in order to determine the contribution of each environmental compartment to changes in toxicity: water only (W), water + sediment (WS), water + plants (WP), and water + plants + sediment (WPS). Silver treatments included AgNPs with two different coatings, gum arabic (GA-AgNPs) or polyvinylpyrollidone (PVP-AgNPs), as well as AgNO(3). Water samples taken from the microcosms at 24 h postdosing were used in acute toxicity tests with two standard model organisms, early life stage zebrafish (Danio rerio) and Daphnia magna. Speciation of Ag in these samples was analyzed using Ag L3-edge X-ray absorption near edge spectroscopy (XANES). Silver speciation patterns for the nanoparticle treatments varied significantly by coating type. While PVP-AgNPs were quite stable and resisted transformation across all matrices (>92.4% Ag(0)), GA-AgNP speciation patterns suggest significantly higher transformation rates, especially in treatments with plants (<69.2% and <58.8% Ag(0) in WP and WPS, respectively) and moderately increased transformation with sediments (<85.6% Ag(0)). Additionally, the presence of plants in the microcosms (with and without sediments) reduced both the concentration of Ag in the water column and toxicity for all Ag treatments. Reductions in toxicity may have been related to decreased water column concentrations as well as changes in the surface chemistry of the particles induced by organic substances released from the plants.

  14. Ag@Ag8W4O16 nanoroasted rice beads with photocatalytic, antibacterial and anticancer activity.

    PubMed

    Selvamani, Muthamizh; Krishnamoorthy, Giribabu; Ramadoss, Manigandan; Sivakumar, Praveen Kumar; Settu, Munusamy; Ranganathan, Suresh; Vengidusamy, Narayanan

    2016-03-01

    Increasing resistance of pathogens and cancer cell line towards antibiotics and anticancer agents has caused serious health problems in the past decades. Due to these problems in recent years, researchers have tried to combine nanotechnology with material science to have intrinsic antimicrobial and anticancer activity. The metals and metal oxides were investigated with respect to their antimicrobial and anticancer effects towards bacteria and cancer cell line. In the present work metal@metal tungstate (Ag@Ag8W4O16 nanoroasted rice beads) is investigated for antibacterial activity against Escherichia coli and Staphylococcus aureus using Mueller-Hinton broth and the anticancer activity against B16F10 cell line was studied. Silver decorated silver tungstate (Ag@Ag8W4O16) was synthesized by the microwave irradiation method using Cetyl Trimethyl Ammonium Bromide (CTAB). Ag@Ag8W4O16 was characterized by using various spectroscopic techniques. The phase and crystalline nature were analyzed by using XRD. The morphological analysis was carried out using Field Emission Scanning Electron Microscopy (FE-SEM), and High Resolution Transmission Electron Microscopy (HR-TEM). Further, Fourier Transform Infrared Spectroscopy (FT-IR) and Raman spectral analysis were carried out in order to ascertain the presence of functional groups in Ag@Ag8W4O16. The optical property was investigated using Diffuse Reflectance Ultraviolet-Visible Spectroscopy (DRS-UV-Vis) and the band gap was found to be 3.08eV. Surface area of the synthesized Ag@Ag8W4O16 wasanalyzed by BET analysis and Ag@Ag8W4O16 was utilized for the degradation of organic dyes methylene blue and rhodamine B. The morphology of the Ag@Ag8W4O16 resembles roasted rice beads with breath and length in nm range. The oxidation state of tungsten (W) and silver (Ag) was investigated using X-ray photoelectron spectroscopy (XPS).

  15. Nanojoining of crossed Ag nanowires: a molecular dynamics study

    NASA Astrophysics Data System (ADS)

    Cui, Jianlei; Wang, Xuewen; Barayavuga, Theogene; Mei, Xuesong; Wang, Wenjun; He, Xiaoqiao

    2016-07-01

    Ag nanowires are considered to be the promising candidates for future electronic circuit owing to the excellent electrical and thermal properties, with the miniaturization of electronics devices into nanometer scale. Though interconnect technology between Ag nanowires (Ag NWs) is essential for nanofunctional devices, it lacks sufficient experimental data. Besides, the determination of Ag NW interconnection configuration is experimentally difficult to do for lacking the sufficient investigation of atomic configuration evolution during nanojoining process. So the nanojoining between the crossed Ag NWs with the same diameter of 2 nm and different lengths was performed by molecular dynamics simulation to explain the unclear nanojoining mechanism based on thermal effect. As the simulation results present, when the nanojoining temperature is relatively high, though the Ag NWs are connected with the interpenetration effect of Ag atoms at the crossed nanojunction area, the nanostructures of Ag NWs have been seriously deformed with shorter length and larger diameter, showing relatively more obvious melting characteristics based on the chaotic atomic structures. If the temperature is reduced to 300 K as cold welding, the crossed Ag NWs can be partially contacted with the partial mixture of Ag atoms, and the interstices always exist between the Si surface and the upper Ag nanowire. In addition, the obvious dislocation phenomenon will appear and evolve as time goes on. Consequently, the dominant mechanism was revealed for providing a fundamental understanding of how `hot' and `cold' welding technology affects the atomic contact configuration, respectively.

  16. A novel hexanuclear silver(I) cluster containing a regular Ag6 ring with short Ag-Ag distances and an argentophilic interaction.

    PubMed

    Barreiro, Elena; Casas, José S; Couce, María D; Laguna, Antonio; López-de-Luzuriaga, José M; Monge, Miguel; Sánchez, Agustin; Sordo, José; Vázquez López, Ezequiel M

    2013-04-28

    The hexanuclear complex [HQ][Ag(p-mpspa)] (H2-p-mpspa = 3-(4-methoxyphenyl)-2-sulfanylpropenoic acid) was prepared by reacting the precursor [Ag(H-p-mpspa)] with diisopropylamine (Q). The complex was characterized by spectroscopic techniques and the structure was solved by a single crystal X-ray diffraction study. The crystal contains hydrogen-bonded diisopropylammonium cations and [Ag6(p-mpspa)6](6-) anions that are based on a regular Ag6 ring with each S-donor atom of the sulfanylcarboxylate ligand bridging two Ag atoms. The Ag-Ag bond distances, 2.8036(6) Å, are very short and suggest a closed shell d(10)···d(10) argentophilic interaction. To analyze the relative role of this interaction and that of the S-bridging atom the anionic [Ag6(p-mpspa)6](6-) moiety has been studied theoretically at the Hartree-Fock (HF) and 2(nd) order Møller-Plesset perturbation theory (MP2) levels on a very simple [Ag6(SH)6] A model system. A large model system [Ag6(p-mpspa)6](6-)B has also been studied by applying the ONIOM (QM/MM) approach using HF/UFF and MP2/UFF combinations as levels of theory. The six experimentally observed Ag(I)···Ag(I) supported interactions are reproduced when dispersion-type interactions are considered in the theory levels MP2 and ONIOM MP2/UFF for models A and B, respectively. The use of HF and ONIOM HF/UFF levels led to a similar hexanuclear structure but displayed a large hexagonal disposition without argentophilic contacts for both models A and B. The steric hindrance exerted by the ligands did not preclude the formation of argentophilic interactions, as observed experimentally.

  17. RRR and thermal conductivity of Ag and Ag-0.2 wt.%Mg alloy in Ag/Bi-2212 wires

    NASA Astrophysics Data System (ADS)

    Li, P.; Ye, L.; Jiang, J.; Shen, T.

    2015-12-01

    Residual resistivity ratio (RRR) and thermal conductivity of metal matrix in metal/superconductor composite wires are important parameters for designing superconducting magnets. However, the resistivity of silver in reacted Ag/Bi-2212 wires has yet to be determined over temperature range from 4.2 K to 80 K because Bi-2212 filaments have a critical transition temperature Tc of ∼ 80 K, and because it is unknown whether the RRR of Ag/Bi-2212 degrades with Cu diffusing from Bi-2212 filaments into silver sheathes at elevated temperatures and to what degree it varies with heat treatment. We measured the resistivity of stand-alone Ag and AgMg (Ag-0.2 wt.% Mg) wires as well as the resistivity of Ag and Ag-0.2 wt.% Mg in Ag/Bi- 2212 round wires reacted in 1 bar oxygen at 890 °C for 1, 8, 24 and 48 hours and quickly cooled to room temperature. The heat treatment was designed to reduce the critical current Ic of Bi- 2212 wires to nearly zero while allowing Cu loss to fully manifest itself. We determined that pure silver exhibits a RRR of ∼ 220 while the oxide-dispersion strengthened Ag-Mg exhibits a RRR of ∼ 5 in stand-alone samples. A surprising result is that the RRR of silver in the composite round wires doesn't degrade with extended time at 890 °C for up to 48 hours. This surprising result may be explained by our observation that the Cu that diffuses into silver tends to form Cu2O precipitates in oxidizing atmosphere, instead of forming Ag-Cu solution alloy. We also measured the thermal conductivity and the magneto-resistivity of pure Ag and Ag-0.2 wt. % Mg from 4.2 K to 300 K in magnetic fields up to 14.8 T and summarized them using a Kohler plot.

  18. Interfacial Reactions in Sn-Ag/Co Couples

    NASA Astrophysics Data System (ADS)

    Chen, Sinn-wen; Chen, Tung-Kai; Chang, Jui-shen; Hsu, Chia-ming; Chen, Wei-An

    2014-02-01

    Sn-Ag alloys are important solders, and Co and Co alloys are investigated as barrier layers. Interfacial reactions in Sn-Ag/Co couples were examined in this study for Ag contents of 1.0 wt.%, 2.0 wt.%, and 3.5 wt.% and reaction temperatures of 250°C, 200°C, and 150°C. Only CoSn3 formed in Sn-Ag/Co couples reacted at 250°C, but both CoSn3 and Ag3Sn formed in couples reacted at 200°C and 150°C. The reaction layer was 100 μm thick in Sn-3.5 wt.%Ag/Co couples reacted at 200°C for 110 h. The reaction rates were lower if Ag was added, but remained very fast compared with those for Ni and Ni-based substrates.

  19. Photo-catalytic activity of Plasmonic Ag@AgCl nanoparticles (synthesized via a green route) for the effective degradation of Victoria Blue B from aqueous phase.

    PubMed

    Devi, Th Babita; Begum, Shamima; Ahmaruzzaman, M

    2016-07-01

    This study reports a green process for the fabrication of Ag@AgCl (silver@silver chloride) nanoparticles by using Aquilaria agallocha (AA) leaves juice without using any external reagents. The effect of various reaction parameters, such as reaction temperature, reaction time and concentration of Aquilaria agallocha leaves juice in the formation of nanoparticles have also been investigated. From the FTIR spectra of leaves juice and phytochemicals test, it was found that flavonoids present in the leaves are responsible for the reduction of Ag(+) ions to Ag(0) species and leads to the formation of Ag@AgCl NPs. The synthesized Ag@AgCl NPs were utilized for the removal of toxic and hazardous dyes, such as Victoria Blue B from aqueous phase. Approximately, 99.46% degradation of Victoria Blue B dye were observed with Ag@AgCl NPs. Furthermore, the photocatalytic activity of the Ag@AgCl nanoparticles was unchanged after 5cycles of operation.

  20. New frontiers in water purification: highly stable amphopolycarboxyglycinate-stabilized Ag-AgCl nanocomposite and its newly discovered potential

    NASA Astrophysics Data System (ADS)

    Krutyakov, Yurii A.; Zherebin, Pavel M.; Kudrinskiy, Alexey A.; Zubavichus, Yan V.; Presniakov, Mikhail Yu; Yapryntsev, Alexey D.; Karabtseva, Anastasia V.; Mikhaylov, Dmitry M.; Lisichkin, Georgii V.

    2016-09-01

    A simple synthetic procedure for high-stable dispersions of porous composite Ag/AgCl nanoparticles stabilized with amphoteric surfactant sodium tallow amphopolycarboxyglycinate has been proposed for the first time. The prepared samples were characterized by UV-vis spectroscopy, x-ray powder diffraction (XRD), x-ray photoelectron spectroscopy, small area electron diffraction (SAED), scanning electron microscopy (SEM), transmission electron microscopy (TEM), high-resolution transmission electron microscopy (HRTEM), and electron probe micro-analysis. In addition, measurements (carried out at the Kurchatov synchrotron radiation source stations) of the Ag K-edge extended x-ray absorption fine structure (EXAFS) and x-ray absorption near edge structure (XANES) spectra and XRD of the prepared nanoparticles have been performed. The obtained results suggest that small-sized Ag clusters are homogeneously distributed in the mass of the AgCl nanoparticle (~80 nm) formed during the synthesis. The Ag/AgCl dispersion demonstrates photocatalytic activity (with respect to methyl orange) and high bactericidal activity against E. coli. This activity is superior to the activity of both Ag and AgCl nanoparticles stabilized by the same surfactant. Thus, porous composite Ag/AgCl nanoparticles can be used as a multifunctional agent that is able to remove both pollutants and bacterium from water.

  1. Sequestration of Ag(I) from aqueous solution as Ag(0) nanostructures by nanoscale zero valent iron (nZVI)

    NASA Astrophysics Data System (ADS)

    Zhang, Yalei; Yan, Jing; Dai, Chaomeng; Li, Yuting; Zhu, Yan; Zhou, Xuefei

    2015-11-01

    This study investigates the application of nanoparticle zero valent iron (nZVI) to sequester Ag(I) as Ag(0) nanostructures from aqueous solution. Batch experiments were performed with nZVI exposed to aqueous Ag(I) to investigate the effects of environmental parameters, including nZVI dose, temperature and pH. High temperature facilitates Ag(I) sequestration, and the rate constants are determined to be 0.02, 0.12, and 0.31 mg L/m2 at 30, 50, and 60 °C, respectively. Ag(I) sequestration was adversely affected by adding nitric acid to the solution due to significant acid washing, decreasing the available nZVI active sites. Characterization techniques including TEM, XRD, and HR-XPS revealed that nZVI is oxidized to lepidocrocite and magnetite/maghemite and confirmed the formation of nanocrystalline silver. HR-XPS analysis indicated that Ag2O forms rapidly as an intermediate due to Ag(I) adsorption onto the FeOOH layer. The Ag(0) nanostructures that are formed are fractal, spherical, and dendritic or rod-like, respectively, in morphology by FE-TEM images at different Ag/Fe mass ratios. A general reaction model for the interaction Ag(I) with nZVI is proposed. Our results suggest that nZVI is effective for Ag(I) removal.

  2. Plasmonic Ag@AgCl nanotubes fabricated from copper nanowires as high-performance visible light photocatalyst.

    PubMed

    Sun, Lei; Zhang, Ruizhong; Wang, Yuan; Chen, Wei

    2014-09-10

    In this paper, plasmonic photocatalyst Ag@AgCl nanotubes were prepared by a cost-efficient and template-based method and their photocatalytic properties were studied. In the synthesis, copper nanowires were first synthesized and Ag nanotubes were then obtained through the galvanic reaction between copper and Ag ions. The formation of Ag@AgCl nanotubes was finally achieved by in situ oxidation reaction upon the addition of FeCl3. The crystal structure of the product was characterized by X-ray powder diffraction. The morphology and composition of the composite were studied by scanning electron microscopy, transmission electron microscopy, and X-ray photoelectron spectroscopy measurements. All the structure characterizations showed that the tubulate product was produced by the synthetic processes. By using the obtained product as photocatalyst, the photodegradation of methyl orange (MO) was investigated under visible light. The experimental results showed that the as-prepared Ag@AgCl nanotubes exhibit excellent photocatalytic performance and high stability. Under visible light irradiation, more than 92.58% of the MO dye has been decomposed in 10 min on the product with a 1:1 ratio of Fe/Ag. On the basis of the proposed mechanism, the improved photocatalytic activities of the Ag@AgCl hybrids can be ascribed to the enhanced surface area for dye molecule adsorption, enhanced visible light absorbance, and the efficient charge separation of the hybrid nanostructures.

  3. Mechanisms of Toxicity of Ag Nanoparticles in Comparison to Bulk and Ionic Ag on Mussel Hemocytes and Gill Cells.

    PubMed

    Katsumiti, Alberto; Gilliland, Douglas; Arostegui, Inmaculada; Cajaraville, Miren P

    2015-01-01

    Silver nanoparticles (Ag NPs) are increasingly used in many products and are expected to end up in the aquatic environment. Mussels have been proposed as marine model species to evaluate NP toxicity in vitro. The objective of this work was to assess the mechanis