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Sample records for reveals functional divergence

  1. Analysis of the Petunia TM6 MADS box gene reveals functional divergence within the DEF/AP3 lineage.

    PubMed

    Rijpkema, Anneke S; Royaert, Stefan; Zethof, Jan; van der Weerden, Gerard; Gerats, Tom; Vandenbussche, Michiel

    2006-08-01

    Antirrhinum majus DEFICIENS (DEF) and Arabidopsis thaliana APETALA3 (AP3) MADS box proteins are required to specify petal and stamen identity. Sampling of DEF/AP3 homologs revealed two types of DEF/AP3 proteins, euAP3 and TOMATO MADS BOX GENE6 (TM6), within core eudicots, and we show functional divergence in Petunia hybrida euAP3 and TM6 proteins. Petunia DEF (also known as GREEN PETALS [GP]) is expressed mainly in whorls 2 and 3, and its expression pattern remains unchanged in a blind (bl) mutant background, in which the cadastral C-repression function in the perianth is impaired. Petunia TM6 functions as a B-class organ identity protein only in the determination of stamen identity. Atypically, Petunia TM6 is regulated like a C-class rather than a B-class gene, is expressed mainly in whorls 3 and 4, and is repressed by BL in the perianth, thereby preventing involvement in petal development. A promoter comparison between DEF and TM6 indicates an important change in regulatory elements during or after the duplication that resulted in euAP3- and TM6-type genes. Surprisingly, although TM6 normally is not involved in petal development, 35S-driven TM6 expression can restore petal development in a def (gp) mutant background. Finally, we isolated both euAP3 and TM6 genes from seven solanaceous species, suggesting that a dual euAP3/TM6 B-function system might be the rule in the Solanaceae. PMID:16844905

  2. Playing RNase P Evolution: Swapping the RNA Catalyst for a Protein Reveals Functional Uniformity of Highly Divergent Enzyme Forms

    PubMed Central

    Weber, Christoph; Hartig, Andreas; Hartmann, Roland K.; Rossmanith, Walter

    2014-01-01

    The RNase P family is a diverse group of endonucleases responsible for the removal of 5′ extensions from tRNA precursors. The diversity of enzyme forms finds its extremes in the eukaryal nucleus where RNA-based catalysis by complex ribonucleoproteins in some organisms contrasts with single-polypeptide enzymes in others. Such structural contrast suggests associated functional differences, and the complexity of the ribonucleoprotein was indeed proposed to broaden the enzyme's functionality beyond tRNA processing. To explore functional overlap and differences between most divergent forms of RNase P, we replaced the nuclear RNase P of Saccharomyces cerevisiae, a 10-subunit ribonucleoprotein, with Arabidopsis thaliana PRORP3, a single monomeric protein. Surprisingly, the RNase P-swapped yeast strains were viable, displayed essentially unimpaired growth under a wide variety of conditions, and, in a certain genetic background, their fitness even slightly exceeded that of the wild type. The molecular analysis of the RNase P-swapped strains showed a minor disturbance in tRNA metabolism, but did not point to any RNase P substrates or functions beyond that. Altogether, these results indicate the full functional exchangeability of the highly dissimilar enzymes. Our study thereby establishes the RNase P family, with its combination of structural diversity and functional uniformity, as an extreme case of convergent evolution. It moreover suggests that the apparently gratuitous complexity of some RNase P forms is the result of constructive neutral evolution rather than reflecting increased functional versatility. PMID:25101763

  3. Molecular evolution analysis of WUSCHEL-related homeobox transcription factor family reveals functional divergence among clades in the homeobox region.

    PubMed

    Segatto, Ana Lúcia A; Thompson, Claudia E; Freitas, Loreta B

    2016-07-01

    Gene families have been shown to play important roles in plant evolution and are associated with diversification and speciation. Genes of WUSCHEL-related homeobox family of transcription factors have important functions in plant development and are correlated with the appearance of evolutionary novelties. There are several published studies related to this family, but little is known about the relationships among the main clades in the phylogeny and the molecular evolution of the family. In this study, we obtained a well-resolved Bayesian phylogenetic tree establishing the relationships among the main clades and determining the position of Selaginella moellendorffii WOX genes. Moreover, a correlation was identified between the number of genes in the genomes and the events of whole-genome duplications. The intron-exon structure is more consistent across the modern clade, which appeared more recently in the WOX evolutionary history, and coincides with the development of higher complexity in plant species. No positive selection was detected among sites through the branches in the tree. However, with regard to the main clades, functional divergence among certain amino acids in the homeodomain region was found. Relaxed purifying selection could be the main driving force in the evolution of these genes and in agreement with some genes have been demonstrated to be functionally redundant. PMID:27150824

  4. Functional Divergence of the Glutathione S-Transferase Supergene Family in Physcomitrella patens Reveals Complex Patterns of Large Gene Family Evolution in Land Plants1[W][OA

    PubMed Central

    Liu, Yan-Jing; Han, Xue-Min; Ren, Lin-Ling; Yang, Hai-Ling; Zeng, Qing-Yin

    2013-01-01

    Plant glutathione S-transferases (GSTs) are multifunctional proteins encoded by a large gene family that play major roles in the detoxification of xenobiotics and oxidative stress metabolism. To date, studies on the GST gene family have focused mainly on vascular plants (particularly agricultural plants). In contrast, little information is available on the molecular characteristics of this large gene family in nonvascular plants. In addition, the evolutionary patterns of this family in land plants remain unclear. In this study, we identified 37 GST genes from the whole genome of the moss Physcomitrella patens, a nonvascular representative of early land plants. The 37 P. patens GSTs were divided into 10 classes, including two new classes (hemerythrin and iota). However, no tau GSTs were identified, which represent the largest class among vascular plants. P. patens GST gene family members showed extensive functional divergence in their gene structures, gene expression responses to abiotic stressors, enzymatic characteristics, and the subcellular locations of the encoded proteins. A joint phylogenetic analysis of GSTs from P. patens and other higher vascular plants showed that different class GSTs had distinct duplication patterns during the evolution of land plants. By examining multiple characteristics, this study revealed complex patterns of evolutionary divergence among the GST gene family in land plants. PMID:23188805

  5. Reconstitution of Protein Translation of Mycobacterium Reveals Functional Conservation and Divergence with the Gram-Negative Bacterium Escherichia coli

    PubMed Central

    Srivastava, Aashish; Asahara, Haruichi; Zhang, Meng; Zhang, Weijia; Liu, Haiying; Cui, Sheng; Jin, Qi; Chong, Shaorong

    2016-01-01

    Protein translation is essential for all bacteria pathogens. It has also been a major focus of structural and functional studies and an important target of antibiotics. Here we report our attempts to biochemically reconstitute mycobacterial protein translation in vitro from purified components. This mycobacterial translation system consists of individually purified recombinant translation factors from Mycobacterium tuberculosis (M. tuberculosis), purified tRNAs and ribosomes from Mycobacterium smegmatis (M. smegmatis), and an aminoacyl-tRNA synthetase (AARS) mixture from the cell-extract of M. smegmatis. We demonstrate that such mycobacterial translation system was efficient in in vitro protein synthesis, and enabled functional comparisons of translational components between the gram-positive Mycobacterium and the gram-negative E. coli. Although mycobacterial translation factors and ribosomes were highly compatible with their E. coli counterparts, M. smegmatis tRNAs were not properly charged by the E. coli AARSs to allow efficient translation of a reporter. In contrast, both E. coli and M. smegmatis tRNAs exhibited similar activity with the semi-purified M. smegmatis AARSs mixture for in vitro translation. We further demonstrated the use of both mycobacterial and E. coli translation systems as comparative in vitro assays for small-molecule antibiotics that target protein translation. While mycobacterial and E. coli translation were both inhibited at the same IC50 by the antibiotic spectinomycin, mycobacterial translation was preferentially inhibited by the antibiotic tetracycline, suggesting that there may be structural differences at the antibiotic binding sites between the ribosomes of Mycobacterium and E. coli. Our results illustrate an alternative approach for antibiotic discovery and functional studies of protein translation in mycobacteria and possibly other bacterial pathogens. PMID:27564552

  6. Reconstitution of Protein Translation of Mycobacterium Reveals Functional Conservation and Divergence with the Gram-Negative Bacterium Escherichia coli.

    PubMed

    Srivastava, Aashish; Asahara, Haruichi; Zhang, Meng; Zhang, Weijia; Liu, Haiying; Cui, Sheng; Jin, Qi; Chong, Shaorong

    2016-01-01

    Protein translation is essential for all bacteria pathogens. It has also been a major focus of structural and functional studies and an important target of antibiotics. Here we report our attempts to biochemically reconstitute mycobacterial protein translation in vitro from purified components. This mycobacterial translation system consists of individually purified recombinant translation factors from Mycobacterium tuberculosis (M. tuberculosis), purified tRNAs and ribosomes from Mycobacterium smegmatis (M. smegmatis), and an aminoacyl-tRNA synthetase (AARS) mixture from the cell-extract of M. smegmatis. We demonstrate that such mycobacterial translation system was efficient in in vitro protein synthesis, and enabled functional comparisons of translational components between the gram-positive Mycobacterium and the gram-negative E. coli. Although mycobacterial translation factors and ribosomes were highly compatible with their E. coli counterparts, M. smegmatis tRNAs were not properly charged by the E. coli AARSs to allow efficient translation of a reporter. In contrast, both E. coli and M. smegmatis tRNAs exhibited similar activity with the semi-purified M. smegmatis AARSs mixture for in vitro translation. We further demonstrated the use of both mycobacterial and E. coli translation systems as comparative in vitro assays for small-molecule antibiotics that target protein translation. While mycobacterial and E. coli translation were both inhibited at the same IC50 by the antibiotic spectinomycin, mycobacterial translation was preferentially inhibited by the antibiotic tetracycline, suggesting that there may be structural differences at the antibiotic binding sites between the ribosomes of Mycobacterium and E. coli. Our results illustrate an alternative approach for antibiotic discovery and functional studies of protein translation in mycobacteria and possibly other bacterial pathogens. PMID:27564552

  7. Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata.

    PubMed

    Yao, Qiu-Yang; Xia, En-Hua; Liu, Fei-Hu; Gao, Li-Zhi

    2015-02-15

    WRKY transcription factors (TFs), one of the ten largest TF families in higher plants, play important roles in regulating plant development and resistance. To date, little is known about the WRKY TF family in Brassica oleracea. Recently, the completed genome sequence of cabbage (B. oleracea var. capitata) allows us to systematically analyze WRKY genes in this species. A total of 148 WRKY genes were characterized and classified into seven subgroups that belong to three major groups. Phylogenetic and synteny analyses revealed that the repertoire of cabbage WRKY genes was derived from a common ancestor shared with Arabidopsis thaliana. The B. oleracea WRKY genes were found to be preferentially retained after the whole-genome triplication (WGT) event in its recent ancestor, suggesting that the WGT event had largely contributed to a rapid expansion of the WRKY gene family in B. oleracea. The analysis of RNA-Seq data from various tissues (i.e., roots, stems, leaves, buds, flowers and siliques) revealed that most of the identified WRKY genes were positively expressed in cabbage, and a large portion of them exhibited patterns of differential and tissue-specific expression, demonstrating that these gene members might play essential roles in plant developmental processes. Comparative analysis of the expression level among duplicated genes showed that gene expression divergence was evidently presented among cabbage WRKY paralogs, indicating functional divergence of these duplicated WRKY genes. PMID:25481634

  8. Proterozoic microfossils revealing the time of algal divergences

    NASA Astrophysics Data System (ADS)

    Moczydlowska-Vidal, Malgorzata

    2010-05-01

    Proterozoic microfossils revealing the time of algal divergences Małgorzata Moczydłowska-Vidal Uppsala University, Department of Earth Sciences, Palaeobiology, Villavägen 16, SE 752 36 Uppsala, Sweden (malgo.vidal@pal.uu.se) Morphological and reproductive features and cell wall ultrastructure and biochemistry of Proterozoic acritarchs are used to determine their affinity to modern algae. The first appearance datum of these microbiota is traced to infer a minimum age of the divergence of the algal classes to which they may belong. The chronological appearance of microfossils that represent phycoma-like and zygotic cysts and vegetative cells and/or aplanospores, respectively interpreted as prasinophyceaen and chlorophyceaen microalgae, is related to the Viridiplantae phylogeny. These divergence times differ from molecular clock estimates, and the palaeontological evidence suggests that they are older. The best examples of unicellular, organic-walled microfossils (acritarchs) from the Mesoproterozoic to Early Ordovician are reviewed to demonstrate features, which are indicative of their affinity to photosynthetic microalgae. The first indication that a microfossil may be algal is a decay- and acid-resistant cell wall, which reflects its biochemistry and ultrastructure, and probably indicates the ability to protect a resting/reproductive cyst. The biopolymers synthesized in the cell walls of algae and in land plants ("plant cells"), such as sporopollenin/algaenan, are diagnostic for photosynthetic taxa and were inherited from early unicellular ancestors. These preservable cell walls are resistant to acetolysis, hydrolysis and acids, and show diagnostic ultrastructures such as the trilaminar sheath structure (TLS). "Plant cell" walls differ in terms of chemical compounds, which give high preservation potential, from fungal and animal cell walls. Fungal and animal cells are fossilized only by syngenetic permineralization, whereas "plant cells" are fossilized as body

  9. Functional Conservation and Divergence of Four Ginger AP1/AGL9 MADS–Box Genes Revealed by Analysis of Their Expression and Protein–Protein Interaction, and Ectopic Expression of AhFUL Gene in Arabidopsis

    PubMed Central

    Song, Juanjuan; Sun, Wei; Xia, Kuaifei; Liao, Jingping; Zhang, Mingyong

    2014-01-01

    Alpinia genus are known generally as ginger–lilies for showy flowers in the ginger family, Zingiberaceae, and their floral morphology diverges from typical monocotyledon flowers. However, little is known about the functions of ginger MADS–box genes in floral identity. In this study, four AP1/AGL9 MADS–box genes were cloned from Alpinia hainanensis, and protein–protein interactions (PPIs) and roles of the four genes in floral homeotic conversion and in floral evolution are surveyed for the first time. AhFUL is clustered to the AP1lineage, AhSEP4 and AhSEP3b to the SEP lineage, and AhAGL6–like to the AGL6 lineage. The four genes showed conserved and divergent expression patterns, and their encoded proteins were localized in the nucleus. Seven combinations of PPI (AhFUL–AhSEP4, AhFUL–AhAGL6–like, AhFUL–AhSEP3b, AhSEP4–AhAGL6–like, AhSEP4–AhSEP3b, AhAGL6–like–AhSEP3b, and AhSEP3b–AhSEP3b) were detected, and the PPI patterns in the AP1/AGL9 lineage revealed that five of the 10 possible combinations are conserved and three are variable, while conclusions cannot yet be made regarding the other two. Ectopic expression of AhFUL in Arabidopsis thaliana led to early flowering and floral organ homeotic conversion to sepal–like or leaf–like. Therefore, we conclude that the four A. hainanensis AP1/AGL9 genes show functional conservation and divergence in the floral identity from other MADS–box genes. PMID:25461565

  10. Parametric R-norm directed-divergence convex function

    NASA Astrophysics Data System (ADS)

    Garg, Dhanesh; Kumar, Satish

    2016-06-01

    In this paper, we define parametric R-norm directed-divergence convex function and discuss their special cases and prove some properties similar to Kullback-Leibler information measure. From R-norm divergence measure new information measures have also been derived and their relations with different measures of entropy have been obtained and give its application in industrial engineering.

  11. Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy

    PubMed Central

    Halley, Yvette A.; Oldeschulte, David L.; Bhattarai, Eric K.; Hill, Joshua; Metz, Richard P.; Johnson, Charles D.; Presley, Steven M.; Ruzicka, Rebekah E.; Rollins, Dale; Peterson, Markus J.; Murphy, William J.; Seabury, Christopher M.

    2015-01-01

    Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution tests (D, FS) and phylogenetic analyses (RAxML) provide no evidence for positive selection or hybridization with the sympatric scaled quail (Callipepla

  12. Northern Bobwhite (Colinus virginianus) Mitochondrial Population Genomics Reveals Structure, Divergence, and Evidence for Heteroplasmy.

    PubMed

    Halley, Yvette A; Oldeschulte, David L; Bhattarai, Eric K; Hill, Joshua; Metz, Richard P; Johnson, Charles D; Presley, Steven M; Ruzicka, Rebekah E; Rollins, Dale; Peterson, Markus J; Murphy, William J; Seabury, Christopher M

    2015-01-01

    Herein, we evaluated the concordance of population inferences and conclusions resulting from the analysis of short mitochondrial fragments (i.e., partial or complete D-Loop nucleotide sequences) versus complete mitogenome sequences for 53 bobwhites representing six ecoregions across TX and OK (USA). Median joining (MJ) haplotype networks demonstrated that analyses performed using small mitochondrial fragments were insufficient for estimating the true (i.e., complete) mitogenome haplotype structure, corresponding levels of divergence, and maternal population history of our samples. Notably, discordant demographic inferences were observed when mismatch distributions of partial (i.e., partial D-Loop) versus complete mitogenome sequences were compared, with the reduction in mitochondrial genomic information content observed to encourage spurious inferences in our samples. A probabilistic approach to variant prediction for the complete bobwhite mitogenomes revealed 344 segregating sites corresponding to 347 total mutations, including 49 putative nonsynonymous single nucleotide variants (SNVs) distributed across 12 protein coding genes. Evidence of gross heteroplasmy was observed for 13 bobwhites, with 10 of the 13 heteroplasmies involving one moderate to high frequency SNV. Haplotype network and phylogenetic analyses for the complete bobwhite mitogenome sequences revealed two divergent maternal lineages (dXY = 0.00731; FST = 0.849; P < 0.05), thereby supporting the potential for two putative subspecies. However, the diverged lineage (n = 103 variants) almost exclusively involved bobwhites geographically classified as Colinus virginianus texanus, which is discordant with the expectations of previous geographic subspecies designations. Tests of adaptive evolution for functional divergence (MKT), frequency distribution tests (D, FS) and phylogenetic analyses (RAxML) provide no evidence for positive selection or hybridization with the sympatric scaled quail (Callipepla

  13. Functional Analysis of HIV/AIDS Stigma: Consensus or Divergence?

    ERIC Educational Resources Information Center

    Hosseinzadeh, Hassan; Hossain, Syeda Zakia

    2011-01-01

    Functional theory proposes that attitudes may serve a variety of purposes for individuals. This study aimed to determine whether stigmatized attitudes toward HIV/AIDS serve the same function for all (consensus function) or serve different functions for different individuals (divergence function) by assessing various aspects of HIV/AIDS stigma…

  14. Collective Dynamics Differentiates Functional Divergence in Protein Evolution

    PubMed Central

    Glembo, Tyler J.; Farrell, Daniel W.; Gerek, Z. Nevin; Thorpe, M. F.; Ozkan, S. Banu

    2012-01-01

    Protein evolution is most commonly studied by analyzing related protein sequences and generating ancestral sequences through Bayesian and Maximum Likelihood methods, and/or by resurrecting ancestral proteins in the lab and performing ligand binding studies to determine function. Structural and dynamic evolution have largely been left out of molecular evolution studies. Here we incorporate both structure and dynamics to elucidate the molecular principles behind the divergence in the evolutionary path of the steroid receptor proteins. We determine the likely structure of three evolutionarily diverged ancestral steroid receptor proteins using the Zipping and Assembly Method with FRODA (ZAMF). Our predictions are within ∼2.7 Å all-atom RMSD of the respective crystal structures of the ancestral steroid receptors. Beyond static structure prediction, a particular feature of ZAMF is that it generates protein dynamics information. We investigate the differences in conformational dynamics of diverged proteins by obtaining the most collective motion through essential dynamics. Strikingly, our analysis shows that evolutionarily diverged proteins of the same family do not share the same dynamic subspace, while those sharing the same function are simultaneously clustered together and distant from those, that have functionally diverged. Dynamic analysis also enables those mutations that most affect dynamics to be identified. It correctly predicts all mutations (functional and permissive) necessary to evolve new function and ∼60% of permissive mutations necessary to recover ancestral function. PMID:22479170

  15. Unexpected divergence and lack of divergence revealed in continental Asian Cyornis flycatchers (Aves: Muscicapidae).

    PubMed

    Zhang, Zhen; Wang, Xiaoyang; Huang, Yuan; Olsson, Urban; Martinez, Jonathan; Alström, Per; Lei, Fumin

    2016-01-01

    The flycatcher genus Cyornis (Aves: Muscicapidae) comprises 25 species with Oriental distributions. Their relationships are poorly known. We analyzed the phylogenetic relationships of 70 individuals from 12 species and several subspecies of Cyornis based on three mitochondrial genes and five nuclear introns, with special focus on Chinese and Vietnamese populations of the monotypic C. hainanus and polytypic C. rubeculoides. We found no support for inclusion of C. concretus in Cyornis. Deep divergences were observed among different subspecies of C. banyumas and C. rubeculoides. C. rubeculoides glaucicomans was also shown to have a highly distinctive song, and we propose that it is treated as a distinctive Chinese endemic species, C. glaucicomans. In contrast, the south Vietnamese C. rubeculoides klossi, which has a disjunct distribution from the other subspecies of C. rubeculoides, along with a recently discovered population in Guangdong Province (China) with several plumage features reminiscent of C. r. klossi, were indistinguishable in all loci analyzed from the phenotypically markedly different C. hainanus. More research is needed to elucidate the reasons for this unexpected pattern. PMID:26358612

  16. Evolution of the class C GPCR Venus flytrap modules involved positive selected functional divergence

    PubMed Central

    Cao, Jianhua; Huang, Siluo; Qian, Ji; Huang, Jinlin; Jin, Li; Su, Zhixi; Yang, Ji; Liu, Jianfeng

    2009-01-01

    Background Class C G protein-coupled receptors (GPCRs) represent a distinct group of the GPCR family, which structurally possess a characteristically distinct extracellular domain inclusive of the Venus flytrap module (VFTM). The VFTMs of the class C GPCRs is responsible for ligand recognition and binding, and share sequence similarity with bacterial periplasmic amino acid binding proteins (PBPs). An extensive phylogenetic investigation of the VFTMs was conducted by analyzing for functional divergence and testing for positive selection for five typical groups of the class C GPCRs. The altered selective constraints were determined to identify the sites that had undergone functional divergence via positive selection. In order to structurally demonstrate the pattern changes during the evolutionary process, three-dimensional (3D) structures of the GPCR VFTMs were modelled and reconstructed from ancestral VFTMs. Results Our results show that the altered selective constraints in the VFTMs of class C GPCRs are statistically significant. This implies that functional divergence played a key role in characterizing the functions of the VFTMs after gene duplication events. Meanwhile, positive selection is involved in the evolutionary process and drove the functional divergence of the VFTMs. Our results also reveal that three continuous duplication events occurred in order to shape the evolutionary topology of class C GPCRs. The five groups of the class C GPCRs have essentially different sites involved in functional divergence, which would have shaped the specific structures and functions of the VFTMs. Conclusion Taken together, our results show that functional divergence involved positive selection and is partially responsible for the evolutionary patterns of the class C GPCR VFTMs. The sites involved in functional divergence will provide more clues and candidates for further research on structural-function relationships of these modules as well as shedding light on the

  17. Global expression profiling reveals genetic programs underlying the developmental divergence between mouse and human embryogenesis

    PubMed Central

    2013-01-01

    Background Mouse has served as an excellent model for studying human development and diseases due to its similarity to human. Advances in transgenic and knockout studies in mouse have dramatically strengthened the use of this model and significantly improved our understanding of gene function during development in the past few decades. More recently, global gene expression analyses have revealed novel features in early embryogenesis up to gastrulation stages and have indeed provided molecular evidence supporting the conservation in early development in human and mouse. On the other hand, little information is known about the gene regulatory networks governing the subsequent organogenesis. Importantly, mouse and human development diverges during organogenesis. For instance, the mouse embryo is born around the end of organogenesis while in human the subsequent fetal period of ongoing growth and maturation of most organs spans more than 2/3 of human embryogenesis. While two recent studies reported the gene expression profiles during human organogenesis, no global gene expression analysis had been done for mouse organogenesis. Results Here we report a detailed analysis of the global gene expression profiles from egg to the end of organogenesis in mouse. Our studies have revealed distinct temporal regulation patterns for genes belonging to different functional (Gene Ontology or GO) categories that support their roles during organogenesis. More importantly, comparative analyses identify both conserved and divergent gene regulation programs in mouse and human organogenesis, with the latter likely responsible for the developmental divergence between the two species, and further suggest a novel developmental strategy during vertebrate evolution. Conclusions We have reported here the first genome-wide gene expression analysis of the entire mouse embryogenesis and compared the transcriptome atlas during mouse and human embryogenesis. Given our earlier observation that genes

  18. Divergence of multimodular polyketide synthases revealed by a didomain structure.

    PubMed

    Zheng, Jianting; Gay, Darren C; Demeler, Borries; White, Mark A; Keatinge-Clay, Adrian T

    2012-07-01

    The enoylreductase (ER) is the final common enzyme from modular polyketide synthases (PKSs) to be structurally characterized. The 3.0 Å-resolution structure of the didomain comprising the ketoreductase (KR) and ER from the second module of the spinosyn PKS reveals that ER shares an ∼600-Å(2) interface with KR distinct from that of the related mammalian fatty acid synthase (FAS). In contrast to the ER domains of the mammalian FAS, the ER domains of the second module of the spinosyn PKS do not make contact across the two-fold axis of the synthase. This monomeric organization may have been necessary in the evolution of multimodular PKSs to enable acyl carrier proteins to access each of their cognate enzymes. The isolated ER domain showed activity toward a substrate analog, enabling us to determine the contributions of its active site residues. PMID:22634636

  19. Divergence of multimodular polyketide synthases revealed by a didomain structure

    PubMed Central

    Zheng, Jianting; Gay, Darren C.; Demeler, Borries; White, Mark A.; Keatinge-Clay, Adrian T.

    2012-01-01

    The enoylreductase (ER) is the final common enzyme from modular polyketide synthases (PKSs) to be structurally characterized. The 3.0 Å resolution structure of the didomain comprised of the ketoreductase (KR) and ER from the second module of the spinosyn PKS reveals that ER shares an ~600 Å2 interface with KR distinct from that of the related mammalian fatty acid synthase (FAS). In contrast to the ER domains of the mammalian FAS, the ER domains of the second module of the spinosyn PKS do not make contact across the twofold axis of the synthase. This monomeric organization may have been necessary in the evolution of multimodular PKSs to enable acyl carrier proteins (ACPs) to access each of their cognate enzymes. The isolated ER domain showed activity towards a substrate analog, enabling the contributions of its active site residues to be determined. PMID:22634636

  20. Functional divergence in tandemly duplicated Arabidopsis thaliana trypsin inhibitor genes.

    PubMed Central

    Clauss, M J; Mitchell-Olds, T

    2004-01-01

    In multigene families, variation among loci and alleles can contribute to trait evolution. We explored patterns of functional and genetic variation in six duplicated Arabidopsis thaliana trypsin inhibitor (ATTI) loci. We demonstrate significant variation in constitutive and herbivore-induced transcription among ATTI loci that show, on average, 65% sequence divergence. Significant variation in ATTI expression was also found between two molecularly defined haplotype classes. Population genetic analyses for 17 accessions of A. thaliana showed that six ATTI loci arranged in tandem within 10 kb varied 10-fold in nucleotide diversity, from 0.0009 to 0.0110, and identified a minimum of six recombination events throughout the tandem array. We observed a significant peak in nucleotide and indel polymorphism spanning ATTI loci in the interior of the array, due primarily to divergence between the two haplotype classes. Significant deviation from the neutral equilibrium model for individual genes was interpreted within the context of intergene linkage disequilibrium and correlated patterns of functional differentiation. In contrast to the outcrosser Arabidopsis lyrata for which recombination is observed even within ATTI loci, our data suggest that response to selection was slowed in the inbreeding, annual A. thaliana because of interference among functionally divergent ATTI loci. PMID:15082560

  1. Interspecific Comparison of the Transformer Gene of Drosophila Reveals an Unusually High Degree of Evolutionary Divergence

    PubMed Central

    O'Neil, M. T.; Belote, J. M.

    1992-01-01

    The transformer (tra) gene of Drosophila melanogaster occupies an intermediate position in the regulatory pathway controlling all aspects of somatic sexual differentiation. The female-specific expression of this gene's function is regulated by the Sex lethal (Sxl) gene, through a mechanism involving sex-specific alternative splicing of tra pre-mRNA. The tra gene encodes a protein that is thought to act in conjunction with the transformer-2 (tra-2) gene product to control the sex-specific processing of doublesex (dsx) pre-mRNA. The bifunctional dsx gene carries out opposite functions in the two sexes, repressing female differentiation in males and repressing male differentiation in females. Here we report the results from an evolutionary approach to investigate tra regulation and function, by isolating the tra-homologous genes from selected Drosophila species, and then using the interpecific DNA sequence comparisons to help identify regions of functional significance. The tra-homologous genes from two Sophophoran subgenus species, Drosophila simulans and Drosophila erecta, and two Drosophila subgenus species, Drosophila hydei and Drosophila virilis, were cloned, sequenced and compared to the D. melanogaster tra gene. This comparison reveals an unusually high degree of evolutionary divergence among the tra coding sequences. These studies also highlight a highly conserved sequence within intron one that probably defines a cis-acting regulator of the sex-specific alternative splicing event. PMID:1592233

  2. Basis Functions With Divergence Constraints For The Finite Element Method

    NASA Astrophysics Data System (ADS)

    Pinciuc, Christopher Michael

    Maxwell's equations are a system of partial differential equations of vector fields. Imposing the constitutive relations for material properties yields equations for the curl and divergence of the electric and magnetic fields. The curl and divergence equations must be solved simultaneously, which is not the same as solving three separate scalar problems in each component of the vector field. This thesis describes a new method for solving partial differential equations of vector fields using the finite element method. New basis functions are used to solve the curl equation while allowing the divergence to be set as a constraint. The basis functions are defined on a mesh of bricks and the method is applicable for geometries that conform to a Cartesian coordinate system. The basis functions are a combination of cubic Hermite splines and second order Lagrange interpolation polynomials. The method yields a linearly independent set of constraints for the divergence, which is modelled to second order accuracy within each brick. Mesh refinement is accomplished by dividing selected bricks into 2 x 2 x 2 smaller bricks of equal size. The change in the node pattern at an interface where mesh refinement occurs necessitates a modified implementation of the divergence constraints as well as additional constraints for hanging nodes. The mesh can be refined to an arbitrary number of levels. The basis functions can exactly model the discontinuity in the normal component of the field at a planar interface. The method is modified to solve problems with singularities at material boundaries that form 90° edges and corners. The primary test problem of the new basis functions is to obtain the resonant frequencies and fields of three-dimensional cavities. The new basis functions can resolve physical solutions and non-physical, spurious modes. The eigenvalues obtained with the new method are in good agreement with exact solutions and experimental values in cases where they exist. There is

  3. Genome-wide identification of conserved regulatory function in diverged sequences

    PubMed Central

    Taher, Leila; McGaughey, David M.; Maragh, Samantha; Aneas, Ivy; Bessling, Seneca L.; Miller, Webb; Nobrega, Marcelo A.; McCallion, Andrew S.; Ovcharenko, Ivan

    2011-01-01

    Plasticity of gene regulatory encryption can permit DNA sequence divergence without loss of function. Functional information is preserved through conservation of the composition of transcription factor binding sites (TFBS) in a regulatory element. We have developed a method that can accurately identify pairs of functional noncoding orthologs at evolutionarily diverged loci by searching for conserved TFBS arrangements. With an estimated 5% false-positive rate (FPR) in approximately 3000 human and zebrafish syntenic loci, we detected approximately 300 pairs of diverged elements that are likely to share common ancestry and have similar regulatory activity. By analyzing a pool of experimentally validated human enhancers, we demonstrated that 7/8 (88%) of their predicted functional orthologs retained in vivo regulatory control. Moreover, in 5/7 (71%) of assayed enhancer pairs, we observed concordant expression patterns. We argue that TFBS composition is often necessary to retain and sufficient to predict regulatory function in the absence of overt sequence conservation, revealing an entire class of functionally conserved, evolutionarily diverged regulatory elements that we term “covert.” PMID:21628450

  4. Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses

    PubMed Central

    2012-01-01

    Background Gene duplications play an important role in the evolution of functional protein diversity. Some models of duplicate gene evolution predict complex forms of paralog divergence; orthologous proteins may diverge as well, further complicating patterns of divergence among and within gene families. Consequently, studying the link between protein sequence evolution and duplication requires the use of flexible substitution models that can accommodate multiple shifts in selection across a phylogeny. Here, we employed a variety of codon substitution models, primarily Clade models, to explore how selective constraint evolved following the duplication of a green-sensitive (RH2a) visual pigment protein (opsin) in African cichlids. Past studies have linked opsin divergence to ecological and sexual divergence within the African cichlid adaptive radiation. Furthermore, biochemical and regulatory differences between the RH2aα and RH2aβ paralogs have been documented. It thus seems likely that selection varies in complex ways throughout this gene family. Results Clade model analysis of African cichlid RH2a opsins revealed a large increase in the nonsynonymous-to-synonymous substitution rate ratio (ω) following the duplication, as well as an even larger increase, one consistent with positive selection, for Lake Tanganyikan cichlid RH2aβ opsins. Analysis using the popular Branch-site models, by contrast, revealed no such alteration of constraint. Several amino acid sites known to influence spectral and non-spectral aspects of opsin biochemistry were found to be evolving divergently, suggesting that orthologous RH2a opsins may vary in terms of spectral sensitivity and response kinetics. Divergence appears to be occurring despite intronic gene conversion among the tandemly-arranged duplicates. Conclusions Our findings indicate that variation in selective constraint is associated with both gene duplication and divergence among orthologs in African cichlid RH2a opsins. At

  5. Mitochondrial and nuclear DNA sequences reveal recent divergence in morphologically indistinguishable petrels.

    PubMed

    Welch, Andreanna J; Yoshida, Allison A; Fleischer, Robert C

    2011-04-01

    Often during the process of divergence, genetic markers will only gradually obtain the signal of isolation. Studies of recently diverged taxa utilizing both mitochondrial and nuclear data sets may therefore yield gene trees with differing levels of phylogenetic signal as a result of differences in coalescence times. However, several factors can lead to this same pattern, and it is important to distinguish between them to gain a better understanding of the process of divergence and the factors driving it. Here, we employ three nuclear intron loci in addition to the mitochondrial Cytochrome b gene to investigate the magnitude and timing of divergence between two endangered and nearly indistinguishable petrel taxa: the Galapagos (GAPE) and Hawaiian (HAPE) petrels (Pterodroma phaeopygia and P. sandwichensis). Phylogenetic analyses indicated reciprocal monophyly between these two taxa for the mitochondrial data set, but trees derived from the nuclear introns were unresolved. Coalescent analyses revealed effectively no migration between GAPE and HAPE over the last 100,000 generations and that they diverged relatively recently, approximately 550,000 years ago, coincident with a time of intense ecological change in both the Galapagos and Hawaiian archipelagoes. This indicates that recent divergence and incomplete lineage sorting are causing the difference in the strength of the phylogenetic signal of each data set, instead of insufficient variability or ongoing male-biased dispersal. Further coalescent analyses show that gene flow is low even between islands within each archipelago suggesting that divergence may be continuing at a local scale. Accurately identifying recently isolated taxa is becoming increasingly important as many clearly recognizable species are already threatened by extinction. PMID:21324012

  6. Extensive Local Gene Duplication and Functional Divergence among Paralogs in Atlantic Salmon

    PubMed Central

    Warren, Ian A.; Ciborowski, Kate L.; Casadei, Elisa; Hazlerigg, David G.; Martin, Sam; Jordan, William C.; Sumner, Seirian

    2014-01-01

    Many organisms can generate alternative phenotypes from the same genome, enabling individuals to exploit diverse and variable environments. A prevailing hypothesis is that such adaptation has been favored by gene duplication events, which generate redundant genomic material that may evolve divergent functions. Vertebrate examples of recent whole-genome duplications are sparse although one example is the salmonids, which have undergone a whole-genome duplication event within the last 100 Myr. The life-cycle of the Atlantic salmon, Salmo salar, depends on the ability to produce alternating phenotypes from the same genome, to facilitate migration and maintain its anadromous life history. Here, we investigate the hypothesis that genome-wide and local gene duplication events have contributed to the salmonid adaptation. We used high-throughput sequencing to characterize the transcriptomes of three key organs involved in regulating migration in S. salar: Brain, pituitary, and olfactory epithelium. We identified over 10,000 undescribed S. salar sequences and designed an analytic workflow to distinguish between paralogs originating from local gene duplication events or from whole-genome duplication events. These data reveal that substantial local gene duplications took place shortly after the whole-genome duplication event. Many of the identified paralog pairs have either diverged in function or become noncoding. Future functional genomics studies will reveal to what extent this rich source of divergence in genetic sequence is likely to have facilitated the evolution of extreme phenotypic plasticity required for an anadromous life-cycle. PMID:24951567

  7. Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering

    PubMed Central

    2010-01-01

    Background Fungal infections are an emerging health risk, especially those involving yeast that are resistant to antifungal agents. To understand the range of mechanisms by which yeasts can respond to anti-fungals, we compared gene expression patterns across three evolutionarily distant species - Saccharomyces cerevisiae, Candida glabrata and Kluyveromyces lactis - over time following fluconazole exposure. Results Conserved and diverged expression patterns were identified using a novel soft clustering algorithm that concurrently clusters data from all species while incorporating sequence orthology. The analysis suggests complementary strategies for coping with ergosterol depletion by azoles - Saccharomyces imports exogenous ergosterol, Candida exports fluconazole, while Kluyveromyces does neither, leading to extreme sensitivity. In support of this hypothesis we find that only Saccharomyces becomes more azole resistant in ergosterol-supplemented media; that this depends on sterol importers Aus1 and Pdr11; and that transgenic expression of sterol importers in Kluyveromyces alleviates its drug sensitivity. Conclusions We have compared the dynamic transcriptional responses of three diverse yeast species to fluconazole treatment using a novel clustering algorithm. This approach revealed significant divergence among regulatory programs associated with fluconazole sensitivity. In future, such approaches might be used to survey a wider range of species, drug concentrations and stimuli to reveal conserved and divergent molecular response pathways. PMID:20653936

  8. Analysis of intestinal microbiota in hybrid house mice reveals evolutionary divergence in a vertebrate hologenome

    PubMed Central

    Wang, Jun; Kalyan, Shirin; Steck, Natalie; Turner, Leslie M.; Harr, Bettina; Künzel, Sven; Vallier, Marie; Häsler, Robert; Franke, Andre; Oberg, Hans-Heinrich; Ibrahim, Saleh M.; Grassl, Guntram A.; Kabelitz, Dieter; Baines, John F.

    2015-01-01

    Recent evidence suggests that natural selection operating on hosts to maintain their microbiome contributes to the emergence of new species, that is, the ‘hologenomic basis of speciation’. Here we analyse the gut microbiota of two house mice subspecies, Mus musculus musculus and M. m. domesticus, across their Central European hybrid zone, in addition to hybrids generated in the lab. Hybrid mice display widespread transgressive phenotypes (that is, exceed or fall short of parental values) in a variety of measures of bacterial community structure, which reveals the importance of stabilizing selection operating on the intestinal microbiome within species. Further genetic and immunological analyses reveal genetic incompatibilities, aberrant immune gene expression and increased intestinal pathology associated with altered community structure among hybrids. These results provide unique insight into the consequences of evolutionary divergence in a vertebrate ‘hologenome’, which may be an unrecognized contributing factor to reproductive isolation in this taxonomic group. PMID:25737238

  9. Complex Selection on Human Polyadenylation Signals Revealed by Polymorphism and Divergence Data.

    PubMed

    Kainov, Yaroslav A; Aushev, Vasily N; Naumenko, Sergey A; Tchevkina, Elena M; Bazykin, Georgii A

    2016-01-01

    Polyadenylation is a step of mRNA processing which is crucial for its expression and stability. The major polyadenylation signal (PAS) represents a nucleotide hexamer that adheres to the AATAAA consensus sequence. Over a half of human genes have multiple cleavage and polyadenylation sites, resulting in a great diversity of transcripts differing in function, stability, and translational activity. Here, we use available whole-genome human polymorphism data together with data on interspecies divergence to study the patterns of selection acting on PAS hexamers. Common variants of PAS hexamers are depleted of single nucleotide polymorphisms (SNPs), and SNPs within PAS hexamers have a reduced derived allele frequency (DAF) and increased conservation, indicating prevalent negative selection; at the same time, the SNPs that "improve" the PAS (i.e., those leading to higher cleavage efficiency) have increased DAF, compared to those that "impair" it. SNPs are rarer at PAS of "unique" polyadenylation sites (one site per gene); among alternative polyadenylation sites, at the distal PAS and at exonic PAS. Similar trends were observed in DAFs and divergence between species of placental mammals. Thus, selection permits PAS mutations mainly at redundant and/or weakly functional PAS. Nevertheless, a fraction of the SNPs at PAS hexamers likely affect gene functions; in particular, some of the observed SNPs are associated with disease. PMID:27324920

  10. Comparative Analysis of Wolbachia Genomes Reveals Streamlining and Divergence of Minimalist Two-Component Systems

    PubMed Central

    Christensen, Steen; Serbus, Laura Renee

    2015-01-01

    Two-component regulatory systems are commonly used by bacteria to coordinate intracellular responses with environmental cues. These systems are composed of functional protein pairs consisting of a sensor histidine kinase and cognate response regulator. In contrast to the well-studied Caulobacter crescentus system, which carries dozens of these pairs, the streamlined bacterial endosymbiont Wolbachia pipientis encodes only two pairs: CckA/CtrA and PleC/PleD. Here, we used bioinformatic tools to compare characterized two-component system relays from C. crescentus, the related Anaplasmataceae species Anaplasma phagocytophilum and Ehrlichia chaffeensis, and 12 sequenced Wolbachia strains. We found the core protein pairs and a subset of interacting partners to be highly conserved within Wolbachia and these other Anaplasmataceae. Genes involved in two-component signaling were positioned differently within the various Wolbachia genomes, whereas the local context of each gene was conserved. Unlike Anaplasma and Ehrlichia, Wolbachia two-component genes were more consistently found clustered with metabolic genes. The domain architecture and key functional residues standard for two-component system proteins were well-conserved in Wolbachia, although residues that specify cognate pairing diverged substantially from other Anaplasmataceae. These findings indicate that Wolbachia two-component signaling pairs share considerable functional overlap with other α-proteobacterial systems, whereas their divergence suggests the potential for regulatory differences and cross-talk. PMID:25809075

  11. Complex Selection on Human Polyadenylation Signals Revealed by Polymorphism and Divergence Data

    PubMed Central

    Kainov, Yaroslav A.; Aushev, Vasily N.; Naumenko, Sergey A.; Tchevkina, Elena M.; Bazykin, Georgii A.

    2016-01-01

    Polyadenylation is a step of mRNA processing which is crucial for its expression and stability. The major polyadenylation signal (PAS) represents a nucleotide hexamer that adheres to the AATAAA consensus sequence. Over a half of human genes have multiple cleavage and polyadenylation sites, resulting in a great diversity of transcripts differing in function, stability, and translational activity. Here, we use available whole-genome human polymorphism data together with data on interspecies divergence to study the patterns of selection acting on PAS hexamers. Common variants of PAS hexamers are depleted of single nucleotide polymorphisms (SNPs), and SNPs within PAS hexamers have a reduced derived allele frequency (DAF) and increased conservation, indicating prevalent negative selection; at the same time, the SNPs that “improve” the PAS (i.e., those leading to higher cleavage efficiency) have increased DAF, compared to those that “impair” it. SNPs are rarer at PAS of “unique” polyadenylation sites (one site per gene); among alternative polyadenylation sites, at the distal PAS and at exonic PAS. Similar trends were observed in DAFs and divergence between species of placental mammals. Thus, selection permits PAS mutations mainly at redundant and/or weakly functional PAS. Nevertheless, a fraction of the SNPs at PAS hexamers likely affect gene functions; in particular, some of the observed SNPs are associated with disease. PMID:27324920

  12. Tumor-Associated Neutrophils Show Phenotypic and Functional Divergence in Human Lung Cancer.

    PubMed

    Saha, Shilpi; Biswas, Subhra K

    2016-07-11

    Studies in murine cancer models have demonstrated the phenotypic and functional divergence of neutrophils; however, their role in pro- or anti-tumor responses in human remains elusive. In this issue of Cancer Cell, Singhal et al. report the existence of specialized subsets of neutrophils in human lung cancer with diverging functions. PMID:27411583

  13. Probing functional divergence of 5-aminoimidazole ribonucleotide carboxylases

    NASA Astrophysics Data System (ADS)

    Youn, Hasik

    The conversion of AIR to CAIR catalyzed by AIR carboxylase represents the only carbon-carbon bond formation step in de novo purine biosynthesis. Prokaryotic and most eukaryotic AIR carboxylases utilize two proteins, PurK and PurE to accomplish the conversion of AIR to CAIR via N5-CAIR from AIR, ATP, and bicarbonate. In vertebrates, AIR carboxylases utilizes AIR and CO2 directly to produce CAIR without a free intermediate. NAIR is a slow-tight binding inhibitor for G. gallus AIR carboxylase while this compound is a simple competitive inhibitor in the case of the Escherichia coli system. The tight binding nature of NAIR suggested that this compound represents a transition state analog. A structure- activity study was extended in order to understand the role of ring electronics and substituents of NAIR for the tight-binding phenomenon. The analysis of inhibition data of azole nucleotide inhibitors was summarized as follows; (1) N3 of NAIR is not critical for binding, (2) ring electronics are important for binding in the nitro azole derivatives while they are not critical in the series of carboxy amino azole nucleotides, (3) the nitro group is a critical binding element for the tight-binding of NAIR, (4) the exocyclic amino group contributes to the optimum display of charge density of NAIR for tight-binding, (5) the carboxyl group of CAIR plays an import role for initial binding through electrostatic interactions. The fact that the gene for AIR carboxylase from both avian and methanogen can functionally complement E. coli purK and purE mutants despite the lack of any sequence homology with purK raised questions about the divergent functions of AIR carboxylases. The M. thermoautotrophicum AIR carboxylase was overexpressed and the catalytic function was established. Based on the stoichimetry of the ATP consumption, substrate specificities, and NAIR inhibition pattern, the methanogen AIR carboxylase is proposed to be distinctive from the E. coli and vertebrate forms and

  14. Genetic interactions of separase regulatory subunits reveal the diverged Drosophila Cenp-C homolog

    PubMed Central

    Heeger, Sebastian; Leismann, Oliver; Schittenhelm, Ralf; Schraidt, Oliver; Heidmann, Stefan; Lehner, Christian F.

    2005-01-01

    Faithful transmission of genetic information during mitotic divisions depends on bipolar attachment of sister kinetochores to the mitotic spindle and on complete resolution of sister-chromatid cohesion immediately before the metaphase-to-anaphase transition. Separase is thought to be responsible for sister-chromatid separation, but its regulation is not completely understood. Therefore, we have screened for genetic loci that modify the aberrant phenotypes caused by overexpression of the regulatory separase complex subunits Pimples/securin and Three rows in Drosophila. An interacting gene was found to encode a constitutive centromere protein. Characterization of its centromere localization domain revealed the presence of a diverged CENPC motif. While direct evidence for an involvement of this Drosophila Cenp-C homolog in separase activation at centromeres could not be obtained, in vivo imaging clearly demonstrated that it is required for normal attachment of kinetochores to the spindle. PMID:16140985

  15. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders.

    PubMed

    Gómez-Marín, Carlos; Tena, Juan J; Acemel, Rafael D; López-Mayorga, Macarena; Naranjo, Silvia; de la Calle-Mustienes, Elisa; Maeso, Ignacio; Beccari, Leonardo; Aneas, Ivy; Vielmas, Erika; Bovolenta, Paola; Nobrega, Marcelo A; Carvajal, Jaime; Gómez-Skarmeta, José Luis

    2015-06-16

    Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply evolutionarily conserved 3D chromatin organization that predates the Cambrian explosion. This chromatin architecture generates two largely independent regulatory landscapes (RLs) contained in two adjacent topological associating domains (TADs). By disrupting the conserved TAD border in one of the zebrafish Six clusters, we demonstrate that this border is critical for preventing competition between promoters and enhancers located in separated RLs, thereby generating different expression patterns in genes located in close genomic proximity. Moreover, evolutionary comparison of Six-associated TAD borders reveals the presence of CCCTC-binding factor (CTCF) sites with diverging orientations in all studied deuterostomes. Genome-wide examination of mammalian HiC data reveals that this conserved CTCF configuration is a general signature of TAD borders, underscoring that common organizational principles underlie TAD compartmentalization in deuterostome evolution. PMID:26034287

  16. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders

    PubMed Central

    Gómez-Marín, Carlos; Tena, Juan J.; Acemel, Rafael D.; López-Mayorga, Macarena; Naranjo, Silvia; de la Calle-Mustienes, Elisa; Maeso, Ignacio; Beccari, Leonardo; Aneas, Ivy; Vielmas, Erika; Bovolenta, Paola; Nobrega, Marcelo A.; Carvajal, Jaime; Gómez-Skarmeta, José Luis

    2015-01-01

    Increasing evidence in the last years indicates that the vast amount of regulatory information contained in mammalian genomes is organized in precise 3D chromatin structures. However, the impact of this spatial chromatin organization on gene expression and its degree of evolutionary conservation is still poorly understood. The Six homeobox genes are essential developmental regulators organized in gene clusters conserved during evolution. Here, we reveal that the Six clusters share a deeply evolutionarily conserved 3D chromatin organization that predates the Cambrian explosion. This chromatin architecture generates two largely independent regulatory landscapes (RLs) contained in two adjacent topological associating domains (TADs). By disrupting the conserved TAD border in one of the zebrafish Six clusters, we demonstrate that this border is critical for preventing competition between promoters and enhancers located in separated RLs, thereby generating different expression patterns in genes located in close genomic proximity. Moreover, evolutionary comparison of Six-associated TAD borders reveals the presence of CCCTC-binding factor (CTCF) sites with diverging orientations in all studied deuterostomes. Genome-wide examination of mammalian HiC data reveals that this conserved CTCF configuration is a general signature of TAD borders, underscoring that common organizational principles underlie TAD compartmentalization in deuterostome evolution. PMID:26034287

  17. Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison

    PubMed Central

    Chen, Luonan; Wu, Ling-Yun; Wang, Yong; Zhang, Shihua; Zhang, Xiang-Sun

    2006-01-01

    Background Protein structure comparison is one of the most important problems in computational biology and plays a key role in protein structure prediction, fold family classification, motif finding, phylogenetic tree reconstruction and protein docking. Results We propose a novel method to compare the protein structures in an accurate and efficient manner. Such a method can be used to not only reveal divergent evolution, but also identify circular permutations and further detect active-sites. Specifically, we define the structure alignment as a multi-objective optimization problem, i.e., maximizing the number of aligned atoms and minimizing their root mean square distance. By controlling a single distance-related parameter, theoretically we can obtain a variety of optimal alignments corresponding to different optimal matching patterns, i.e., from a large matching portion to a small matching portion. The number of variables in our algorithm increases with the number of atoms of protein pairs in almost a linear manner. In addition to solid theoretical background, numerical experiments demonstrated significant improvement of our approach over the existing methods in terms of quality and efficiency. In particular, we show that divergent evolution, circular permutations and active-sites (or structural motifs) can be identified by our method. The software SAMO is available upon request from the authors, or from and . Conclusion A novel formulation is proposed to accurately align protein structures in the framework of multi-objective optimization, based on a sequence order-independent strategy. A fast and accurate algorithm based on the bipartite matching algorithm is developed by exploiting the special features. Convergence of computation is shown in experiments and is also theoretically proven. PMID:16948858

  18. Compound liquid crystal microlens array with convergent and divergent functions.

    PubMed

    Kang, Shengwu; Zhang, Xinyu

    2016-04-20

    Based on the common liquid crystal microlens, a new compound structure for a liquid crystal (LC) microlens array is proposed. The structure consists of two sub LC microlens arrays with properties of light divergence and convergence. The structure has two LC layers: one to form the positive sub lens, one for the negative. The patterned electrode and plane electrode are used in both sub microlens arrays. When two sub microlens arrays are electrically controlled separately, they can diverge or converge the incident light, respectively. As two sub microlens arrays are both applied on the voltage, the focal length of the compound LC microlens becomes larger than that of the LC microlens with a single LC layer. Another feature of a compound LC microlens array is that it can make the target contour become visible under intense light. The mechanisms are described in detail, and the experimental data are given. PMID:27140107

  19. Functional overlap between conserved and diverged KH domains in Saccharomyces cerevisiae SCP160

    PubMed Central

    Brykailo, Melissa A.; Corbett, Anita H.; Fridovich-Keil, Judith L.

    2007-01-01

    The K homology (KH) domain is a remarkably versatile and highly conserved RNA-binding motif. Classical KH domains include a characteristic pattern of hydrophobic residues, a Gly-X-X-Gly (GXXG) segment, and a variable loop. KH domains typically occur in clusters, with some retaining their GXXG sequence (conserved), while others do not (diverged). As a first step towards addressing whether GXXG is essential for KH-domain function, we explored the roles of conserved and diverged KH domains in Scp160p, a multiple-KH-domain-containing protein in Saccharomyces cerevisiae. We specifically wanted to know (1) whether diverged KH domains were essential for Scp160p function, and (2) whether diverged KH domains could functionally replace conserved KH domains. To address these questions, we deleted and/or interchanged conserved and diverged KH domains of Scp160p and expressed the mutated alleles in yeast. Our results demonstrated that the answer to each question was yes. Both conserved and diverged KH domains are essential for Scp160p function, and diverged KH domains can function in place of conserved KH domains. These findings challenge the prevailing notions about the requisite features of a KH domain and raise the possibility that there may be more functional KH domains in the proteome than previously appreciated. PMID:17264125

  20. Comparative Genomics and Transcriptomics Analyses Reveal Divergent Lifestyle Features of Nematode Endoparasitic Fungus Hirsutella minnesotensis

    PubMed Central

    Lai, Yiling; Liu, Keke; Zhang, Xinyu; Zhang, Xiaoling; Li, Kuan; Wang, Niuniu; Shu, Chi; Wu, Yunpeng; Wang, Chengshu; Bushley, Kathryn E.; Xiang, Meichun; Liu, Xingzhong

    2014-01-01

    Hirsutella minnesotensis [Ophiocordycipitaceae (Hypocreales, Ascomycota)] is a dominant endoparasitic fungus by using conidia that adhere to and penetrate the secondary stage juveniles of soybean cyst nematode. Its genome was de novo sequenced and compared with five entomopathogenic fungi in the Hypocreales and three nematode-trapping fungi in the Orbiliales (Ascomycota). The genome of H. minnesotensis is 51.4 Mb and encodes 12,702 genes enriched with transposable elements up to 32%. Phylogenomic analysis revealed that H. minnesotensis was diverged from entomopathogenic fungi in Hypocreales. Genome of H. minnesotensis is similar to those of entomopathogenic fungi to have fewer genes encoding lectins for adhesion and glycoside hydrolases for cellulose degradation, but is different from those of nematode-trapping fungi to possess more genes for protein degradation, signal transduction, and secondary metabolism. Those results indicate that H. minnesotensis has evolved different mechanism for nematode endoparasitism compared with nematode-trapping fungi. Transcriptomics analyses for the time-scale parasitism revealed the upregulations of lectins, secreted proteases and the genes for biosynthesis of secondary metabolites that could be putatively involved in host surface adhesion, cuticle degradation, and host manipulation. Genome and transcriptome analyses provided comprehensive understanding of the evolution and lifestyle of nematode endoparasitism. PMID:25359922

  1. Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast

    PubMed Central

    McManus, C. Joel; May, Gemma E.; Spealman, Pieter; Shteyman, Alan

    2014-01-01

    Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of post-transcriptional gene regulatory evolution are largely unknown. Here we used ribosome profiling to compare transcript abundance and translation efficiency in two closely related yeast species (S. cerevisiae and S. paradoxus). By comparing translation regulatory divergence to interspecies differences in mRNA sequence features, we show that differences in transcript leaders and codon bias substantially contribute to divergent translation. Globally, we find that translation regulatory divergence often buffers species differences in mRNA abundance, such that ribosome occupancy is more conserved than transcript abundance. We used allele-specific ribosome profiling in interspecies hybrids to compare the relative contributions of cis- and trans-regulatory divergence to species differences in mRNA abundance and translation efficiency. The mode of gene regulatory divergence differs for these processes, as trans-regulatory changes play a greater role in divergent mRNA abundance than in divergent translation efficiency. Strikingly, most genes with aberrant transcript abundance in F1 hybrids (either over- or underexpressed compared to both parent species) did not exhibit aberrant ribosome occupancy. Our results show that interspecies differences in translation contribute substantially to the evolution of gene expression. Compensatory differences in transcript abundance and translation efficiency may increase the robustness of gene regulation. PMID:24318730

  2. Microsatellite markers reveal genetic divergence among wild and cultured populations of Chinese sucker Myxocyprinus asiaticus.

    PubMed

    Cheng, W W; Wang, D Q; Wang, C Y; Du, H; Wei, Q W

    2016-01-01

    Studies of genetic diversity and genetic population structure are critical for the conservation and management of endangered species. The Chinese sucker Myxocyprinus asiaticus is a vulnerable monotypic species in China, which is at a risk of decline owing to fluctuations in effective population size and other demographic and environmental factors. We screened 11 microsatellite loci in 214 individuals to assess genetic differentiation in both wild and cultured populations. The single extant wild population had a higher number of alleles (13) than the cultured populations (average 7.3). High levels of genetic diversity, expressed as observed and expected heterozygosity (HO = 0.771, HE = 0.748, respectively), were found in both wild and cultured populations. We also report significant differentiation among wild and cultured populations (global FST = 0.023, P < 0.001). Both STRUCTURE analysis and neighbor-joining tree revealed three moderately divergent primary genetic clusters: the wild Yangtze population and the Sichuan population were each identified as an individual cluster, with the remaining populations clustered together. Twenty-two samples collected from the Yangtze River were assigned to the cultured population, demonstrating the efficacy of artificial propagation to avoid drastic reduction in the population size of M. asiaticus. These genetic data support the endangered status of the M. asiaticus and have implications for conservation management planning. PMID:27173283

  3. Metabolomic profiling reveals deep chemical divergence between two morphotypes of the zoanthid Parazoanthus axinellae

    NASA Astrophysics Data System (ADS)

    Cachet, Nadja; Genta-Jouve, Grégory; Ivanisevic, Julijana; Chevaldonné, Pierre; Sinniger, Frédéric; Culioli, Gérald; Pérez, Thierry; Thomas, Olivier P.

    2015-02-01

    Metabolomics has recently proven its usefulness as complementary tool to traditional morphological and genetic analyses for the classification of marine invertebrates. Among the metabolite-rich cnidarian order Zoantharia, Parazoanthus is a polyphyletic genus whose systematics and phylogeny remain controversial. Within this genus, one of the most studied species, Parazoanthus axinellae is prominent in rocky shallow waters of the Mediterranean Sea and the NE Atlantic Ocean. Although different morphotypes can easily be distinguished, only one species is recognized to date. Here, a metabolomic profiling approach has been used to assess the chemical diversity of two main Mediterranean morphotypes, the ``slender'' and ``stocky'' forms of P. axinellae. Targeted profiling of their major secondary metabolites revealed a significant chemical divergence between the morphotypes. While zoanthoxanthin alkaloids and ecdysteroids are abundant in both morphs, the ``slender'' morphotype is characterized by the presence of additional and bioactive 3,5-disubstituted hydantoin derivatives named parazoanthines. The absence of these specific compounds in the ``stocky'' morphotype was confirmed by spatial and temporal monitoring over an annual cycle. Moreover, specimens of the ``slender'' morphotype are also the only ones found as epibionts of several sponge species, particularly Cymbaxinella damicornis thus suggesting a putative ecological link.

  4. Sex reversal assessments reveal different vulnerability to endocrine disruption between deeply diverged anuran lineages

    PubMed Central

    Tamschick, Stephanie; Rozenblut-Kościsty, Beata; Ogielska, Maria; Lehmann, Andreas; Lymberakis, Petros; Hoffmann, Frauke; Lutz, Ilka; Kloas, Werner; Stöck, Matthias

    2016-01-01

    Multiple anthropogenic stressors cause worldwide amphibian declines. Among several poorly investigated causes is global pollution of aquatic ecosystems with endocrine disrupting compounds (EDCs). These substances interfere with the endocrine system and can affect the sexual development of vertebrates including amphibians. We test the susceptibility to an environmentally relevant contraceptive, the artificial estrogen 17α-ethinylestradiol (EE2), simultaneously in three deeply divergent systematic anuran families, a model-species, Xenopus laevis (Pipidae), and two non-models, Hyla arborea (Hylidae) and Bufo viridis (Bufonidae). Our new approach combines synchronized tadpole exposure to three EE2-concentrations (50, 500, 5,000 ng/L) in a flow-through-system and pioneers genetic and histological sexing of metamorphs in non-model anurans for EDC-studies. This novel methodology reveals striking quantitative differences in genetic-male-to-phenotypic-female sex reversal in non-model vs. model species. Our findings qualify molecular sexing in EDC-analyses as requirement to identify sex reversals and state-of-the-art approaches as mandatory to detect species-specific vulnerabilities to EDCs in amphibians. PMID:27029458

  5. Sex reversal assessments reveal different vulnerability to endocrine disruption between deeply diverged anuran lineages.

    PubMed

    Tamschick, Stephanie; Rozenblut-Kościsty, Beata; Ogielska, Maria; Lehmann, Andreas; Lymberakis, Petros; Hoffmann, Frauke; Lutz, Ilka; Kloas, Werner; Stöck, Matthias

    2016-01-01

    Multiple anthropogenic stressors cause worldwide amphibian declines. Among several poorly investigated causes is global pollution of aquatic ecosystems with endocrine disrupting compounds (EDCs). These substances interfere with the endocrine system and can affect the sexual development of vertebrates including amphibians. We test the susceptibility to an environmentally relevant contraceptive, the artificial estrogen 17α-ethinylestradiol (EE2), simultaneously in three deeply divergent systematic anuran families, a model-species, Xenopus laevis (Pipidae), and two non-models, Hyla arborea (Hylidae) and Bufo viridis (Bufonidae). Our new approach combines synchronized tadpole exposure to three EE2-concentrations (50, 500, 5,000 ng/L) in a flow-through-system and pioneers genetic and histological sexing of metamorphs in non-model anurans for EDC-studies. This novel methodology reveals striking quantitative differences in genetic-male-to-phenotypic-female sex reversal in non-model vs. model species. Our findings qualify molecular sexing in EDC-analyses as requirement to identify sex reversals and state-of-the-art approaches as mandatory to detect species-specific vulnerabilities to EDCs in amphibians. PMID:27029458

  6. Metabolomic profiling reveals deep chemical divergence between two morphotypes of the zoanthid Parazoanthus axinellae

    PubMed Central

    Cachet, Nadja; Genta-Jouve, Grégory; Ivanisevic, Julijana; Chevaldonné, Pierre; Sinniger, Frédéric; Culioli, Gérald; Pérez, Thierry; Thomas, Olivier P.

    2015-01-01

    Metabolomics has recently proven its usefulness as complementary tool to traditional morphological and genetic analyses for the classification of marine invertebrates. Among the metabolite-rich cnidarian order Zoantharia, Parazoanthus is a polyphyletic genus whose systematics and phylogeny remain controversial. Within this genus, one of the most studied species, Parazoanthus axinellae is prominent in rocky shallow waters of the Mediterranean Sea and the NE Atlantic Ocean. Although different morphotypes can easily be distinguished, only one species is recognized to date. Here, a metabolomic profiling approach has been used to assess the chemical diversity of two main Mediterranean morphotypes, the “slender” and “stocky” forms of P. axinellae. Targeted profiling of their major secondary metabolites revealed a significant chemical divergence between the morphotypes. While zoanthoxanthin alkaloids and ecdysteroids are abundant in both morphs, the “slender” morphotype is characterized by the presence of additional and bioactive 3,5-disubstituted hydantoin derivatives named parazoanthines. The absence of these specific compounds in the “stocky” morphotype was confirmed by spatial and temporal monitoring over an annual cycle. Moreover, specimens of the “slender” morphotype are also the only ones found as epibionts of several sponge species, particularly Cymbaxinella damicornis thus suggesting a putative ecological link. PMID:25655432

  7. A systems biology approach using metabolomic data reveals genes and pathways interacting to modulate divergent growth in cattle

    PubMed Central

    2013-01-01

    Background Systems biology enables the identification of gene networks that modulate complex traits. Comprehensive metabolomic analyses provide innovative phenotypes that are intermediate between the initiator of genetic variability, the genome, and raw phenotypes that are influenced by a large number of environmental effects. The present study combines two concepts, systems biology and metabolic analyses, in an approach without prior functional hypothesis in order to dissect genes and molecular pathways that modulate differential growth at the onset of puberty in male cattle. Furthermore, this integrative strategy was applied to specifically explore distinctive gene interactions of non-SMC condensin I complex, subunit G (NCAPG) and myostatin (GDF8), known modulators of pre- and postnatal growth that are only partially understood for their molecular pathways affecting differential body weight. Results Our study successfully established gene networks and interacting partners affecting growth at the onset of puberty in cattle. We demonstrated the biological relevance of the created networks by comparison to randomly created networks. Our data showed that GnRH (Gonadotropin-releasing hormone) signaling is associated with divergent growth at the onset of puberty and revealed two highly connected hubs, BTC and DGKH, within the network. Both genes are known to directly interact with the GnRH signaling pathway. Furthermore, a gene interaction network for NCAPG containing 14 densely connected genes revealed novel information concerning the functional role of NCAPG in divergent growth. Conclusions Merging both concepts, systems biology and metabolomic analyses, successfully yielded new insights into gene networks and interacting partners affecting growth at the onset of puberty in cattle. Genetic modulation in GnRH signaling was identified as key modifier of differential cattle growth at the onset of puberty. In addition, the benefit of our innovative concept without prior

  8. Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila

    PubMed Central

    Macpherson, J. Michael; Sella, Guy; Davis, Jerel C.; Petrov, Dmitri A.

    2007-01-01

    The effect of recurrent selective sweeps is a spatially heterogeneous reduction in neutral polymorphism throughout the genome. The pattern of reduction depends on the selective advantage and recurrence rate of the sweeps. Because many adaptive substitutions responsible for these sweeps also contribute to nonsynonymous divergence, the spatial distribution of nonsynonymous divergence also reflects the distribution of adaptive substitutions. Thus, the spatial correspondence between neutral polymorphism and nonsynonymous divergence may be especially informative about the process of adaptation. Here we study this correspondence using genomewide polymorphism data from Drosophila simulans and the divergence between D. simulans and D. melanogaster. Focusing on highly recombining portions of the autosomes, at a spatial scale appropriate to the study of selective sweeps, we find that neutral polymorphism is both lower and, as measured by a new statistic QS, less homogeneous where nonsynonymous divergence is higher and that the spatial structure of this correlation is best explained by the action of strong recurrent selective sweeps. We introduce a method to infer, from the spatial correspondence between polymorphism and divergence, the rate and selective strength of adaptation. Our results independently confirm a high rate of adaptive substitution (∼1/3000 generations) and newly suggest that many adaptations are of surprisingly great selective effect (∼1%), reducing the effective population size by ∼15% even in highly recombining regions of the genome. PMID:18073425

  9. Field Studies Reveal Strong Postmating Isolation between Ecologically Divergent Butterfly Populations

    PubMed Central

    McBride, Carolyn S.; Singer, Michael C.

    2010-01-01

    Gene flow between populations that are adapting to distinct environments may be restricted if hybrids inherit maladaptive, intermediate phenotypes. This phenomenon, called extrinsic postzygotic isolation (EPI), is thought to play a critical role in the early stages of speciation. However, despite its intuitive appeal, we know surprisingly little about the strength and prevalence of EPI in nature, and even less about the specific phenotypes that tend to cause problems for hybrids. In this study, we searched for EPI among allopatric populations of the butterfly Euphydryas editha that have specialized on alternative host plants. These populations recall a situation thought typical of the very early stages of speciation. They lack consistent host-associated genetic differentiation at random nuclear loci and show no signs of reproductive incompatibility in the laboratory. However, they do differ consistently in diverse host-related traits. For each of these traits, we first asked whether hybrids between populations that use different hosts (different-host hybrids) were intermediate to parental populations and to hybrids between populations that use the same host (same-host hybrids). We then conducted field experiments to estimate the effects of intermediacy on fitness in nature. Our results revealed strong EPI under field conditions. Different-host hybrids exhibited an array of intermediate traits that were significantly maladaptive, including four behaviors. Intermediate foraging height slowed the growth of larvae, while intermediate oviposition preference, oviposition site height, and clutch size severely reduced the growth and survival of the offspring of adult females. We used our empirical data to construct a fitness surface on which different-host hybrids can be seen to fall in an adaptive valley between two peaks occupied by same-host hybrids. These findings demonstrate how ecological selection against hybrids can create a strong barrier to gene flow at the early

  10. Dissecting comimetic radiations in Heliconius reveals divergent histories of convergent butterflies

    PubMed Central

    Quek, Swee-Peck; Counterman, Brian A.; Albuquerque de Moura, Priscila; Cardoso, Marcio Z.; Marshall, Charles R.; McMillan, W. Owen; Kronforst, Marcus R.

    2010-01-01

    Mimicry among Heliconius butterflies provides a classic example of coevolution but unresolved relationships among mimetic subspecies have prevented examination of codiversification between species. We present amplified fragment length polymorphism and mtDNA datasets for the major comimetic races of Heliconius erato and H. melpomene. The AFLP data reveal unprecedented resolution, clustering samples by geography and race in both species. Our results show that, although H. erato and H. melpomene co-occur, mimic each other, and exhibit parallel shifts in color pattern, they experienced very different modes of diversification and geographic histories. Our results suggest that H. erato originated on the western side of South America whereas H. melpomene originated in the east. H. erato underwent rapid diversification and expansion with continued gene-flow following diversification, resulting in widely dispersed sister taxa. In contrast, H. melpomene underwent a slower pace of diversification with lower levels of gene flow, producing a stepwise directional expansion from west to east. Our results also suggest that each of the three main wing pattern phenotypes originated and/or was lost multiple times in each species. The rayed pattern is likely to be the ancestral phenotype in H. erato whereas postman or red patch is likely to be ancestral in H. melpomene. Finally, H. cydno and H. himera are monophyletic entities clearly nested within H. melpomene and H. erato, rather than being their respective sister species. Estimates of mtDNA divergence suggest a minimum age of 2.8 and 2.1 My for H. erato and H. melpomene, respectively, placing their origins in the late Pliocene. PMID:20368448

  11. [Characteristics of pupil function in patients with dissociated vertical divergence].

    PubMed

    Wermund, T K; Schmidt, C; Wilhelm, H

    2012-11-01

    Dissociated vertical divergence (DVD) is frequently associated with the infantile strabismus syndrome. There are different theories on the pathomechanism of this disorder, but none of them is generally accepted. Some authors believe that the slow upward movement of the covered eye is due to a different illumination of both retinae and consequently an unequal activity of the oculomotor nerve's nuclei. In one hypothesis a predominance of crossing pupillary tract fibres from the pretectal area to motor and parasympathetic nuclei of the oculomotor nerve was supposed. The consequence of this abnormal pathway in the midbrain would be a pronounced contraction anisocoria in patients with DVD. In contraction anisocoria the directly illuminated pupil contracts more strongly than the contralateral pupil without any efferent defect. In a small study we compared direct and indirect pupillary light reflexes in 11 DVD patients and 10 normal subjects. We found no significant differences of contraction anisocoria between the two groups. The results do not support the hypothesis of a different pupillary tract pathway in the midbrain of patients with DVD. PMID:23172621

  12. Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax.

    PubMed

    Li, Kexin; Hong, Wei; Jiao, Hengwu; Wang, Guo-Dong; Rodriguez, Karl A; Buffenstein, Rochelle; Zhao, Yang; Nevo, Eviatar; Zhao, Huabin

    2015-09-22

    Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2-0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be an

  13. On the divergence of gradient expansions for kinetic energy functionals in the potential functional theory

    NASA Astrophysics Data System (ADS)

    Sergeev, Alexey; Jovanovic, Raka; Kais, Sabre; Alharbi, Fahhad H.

    2016-07-01

    We consider the density of a fermionic system as a functional of the potential, in one-dimensional case, where it is approximated by the Thomas–Fermi term plus semiclassical corrections through the gradient expansion. We compare this asymptotic series with the exact answer for the case of the harmonic oscillator and the Morse potential. It is found that the leading (Thomas–Fermi) term is in agreement with the exact density, but the subdominant term does not agree in terms of the asymptotic behavior because of the presence of oscillations in the exact density, but their absence in the gradient expansion. However, after regularization of the density by convolution with a Gaussian, the agreement can be established even in the subdominant term. Moreover, it is found that the expansion is always divergent, and its terms grow proportionally to the factorial function of the order, similar to the well-known divergence of perturbation series in field theory and the quantum anharmonic oscillator. Padé–Hermite approximants allow summation of the series, and one of the branches of the approximants agrees with the density.

  14. Divergent functions through alternative splicing: the Drosophila CRMP gene in pyrimidine metabolism, brain, and behavior.

    PubMed

    Morris, Deanna H; Dubnau, Josh; Park, Jae H; Rawls, John M

    2012-08-01

    DHP and CRMP proteins comprise a family of structurally similar proteins that perform divergent functions, DHP in pyrimidine catabolism in most organisms and CRMP in neuronal dynamics in animals. In vertebrates, one DHP and five CRMP proteins are products of six genes; however, Drosophila melanogaster has a single CRMP gene that encodes one DHP and one CRMP protein through tissue-specific, alternative splicing of a pair of paralogous exons. The proteins derived from the fly gene are identical over 90% of their lengths, suggesting that unique, novel functions of these proteins derive from the segment corresponding to the paralogous exons. Functional homologies of the Drosophila and mammalian CRMP proteins are revealed by several types of evidence. Loss-of-function CRMP mutation modifies both Ras and Rac misexpression phenotypes during fly eye development in a manner that is consistent with the roles of CRMP in Ras and Rac signaling pathways in mammalian neurons. In both mice and flies, CRMP mutation impairs learning and memory. CRMP mutant flies are defective in circadian activity rhythm. Thus, DHP and CRMP proteins are derived by different processes in flies (tissue-specific, alternative splicing of paralogous exons of a single gene) and vertebrates (tissue-specific expression of different genes), indicating that diverse genetic mechanisms have mediated the evolution of this protein family in animals. PMID:22649077

  15. Functional Promiscuity of Two Divergent Paralogs of Type III Plant Polyketide Synthases.

    PubMed

    Pandith, Shahzad A; Dhar, Niha; Rana, Satiander; Bhat, Wajid Waheed; Kushwaha, Manoj; Gupta, Ajai P; Shah, Manzoor A; Vishwakarma, Ram; Lattoo, Surrinder K

    2016-08-01

    Plants effectively defend themselves against biotic and abiotic stresses by synthesizing diverse secondary metabolites, including health-protective flavonoids. These display incredible chemical diversity and ubiquitous occurrence and confer impeccable biological and agricultural applications. Chalcone synthase (CHS), a type III plant polyketide synthase, is critical for flavonoid biosynthesis. It catalyzes acyl-coenzyme A thioesters to synthesize naringenin chalcone through a polyketidic intermediate. The functional divergence among the evolutionarily generated members of a gene family is pivotal in driving the chemical diversity. Against this backdrop, this study was aimed to functionally characterize members of the CHS gene family from Rheum emodi, an endangered and endemic high-altitude medicinal herb of northwestern Himalayas. Two full-length cDNAs (1,179 bp each), ReCHS1 and ReCHS2, encoding unique paralogs were isolated and characterized. Heterologous expression and purification in Escherichia coli, bottom-up proteomic characterization, high-performance liquid chromatography-electrospray ionization-tandem mass spectrometry analysis, and enzyme kinetic studies using five different substrates confirmed their catalytic potential. Phylogenetic analysis revealed the existence of higher synonymous mutations in the intronless divergents of ReCHS. ReCHS2 displayed significant enzymatic efficiency (Vmax/Km) with different substrates. There were significant spatial and altitudinal variations in messenger RNA transcript levels of ReCHSs correlating positively with metabolite accumulation. Furthermore, the elicitations in the form of methyl jasmonate, salicylic acid, ultraviolet B light, and wounding, chosen on the basis of identified cis-regulatory promoter elements, presented considerable differences in the transcript profiles of ReCHSs. Taken together, our results demonstrate differential propensities of CHS paralogs in terms of the accumulation of flavonoids and

  16. Functionally conserved enhancers with divergent sequences in distant vertebrates

    SciTech Connect

    Yang, Song; Oksenberg, Nir; Takayama, Sachiko; Heo, Seok -Jin; Poliakov, Alexander; Ahituv, Nadav; Dubchak, Inna; Boffelli, Dario

    2015-10-30

    To examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. In conclusion, our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species.

  17. Role of Positive Selection in Functional Divergence of Mammalian Neuronal Apoptosis Inhibitor Proteins during Evolution

    PubMed Central

    Kong, Fanzhi; Su, Zhaoliang; Zhou, Chenglin; Sun, Caixia; Liu, Yanfang; Zheng, Dong; Yuan, Hongyan; Yin, Jingping; Fang, Jie; Wang, Shengjun; Xu, Huaxi

    2011-01-01

    Neuronal apoptosis inhibitor proteins (NAIPs) are members of Nod-like receptor (NLR) protein family. Recent research demostrated that some NAIP genes were strongly associated with both innate immunity and many inflammatory diseases in humans. However, no similar phenomena have been reported in other mammals. Furthermore, some NAIP genes have undergone pseudogenization or have been lost during the evolution of some higher mammals. We therefore aimed to determine if functional divergence had occurred, and if natural selection had played an important role in the evolution of these genes. The results showed that NAIP genes have undergone pseudogenization and functional divergence, driven by positive selection. Positive selection has also influenced NAIP protein structure, resulting in further functional divergence. PMID:22131819

  18. Intraspecific Polymorphism, Interspecific Divergence, and the Origins of Function-Altering Mutations in Deer Mouse Hemoglobin

    PubMed Central

    Natarajan, Chandrasekhar; Hoffmann, Federico G.; Lanier, Hayley C.; Wolf, Cole J.; Cheviron, Zachary A.; Spangler, Matthew L.; Weber, Roy E.; Fago, Angela; Storz, Jay F.

    2015-01-01

    Major challenges for illuminating the genetic basis of phenotypic evolution are to identify causative mutations, to quantify their functional effects, to trace their origins as new or preexisting variants, and to assess the manner in which segregating variation is transduced into species differences. Here, we report an experimental analysis of genetic variation in hemoglobin (Hb) function within and among species of Peromyscus mice that are native to different elevations. A multilocus survey of sequence variation in the duplicated HBA and HBB genes in Peromyscus maniculatus revealed that function-altering amino acid variants are widely shared among geographically disparate populations from different elevations, and numerous amino acid polymorphisms are also shared with closely related species. Variation in Hb-O2 affinity within and among populations of P. maniculatus is attributable to numerous amino acid mutations that have individually small effects. One especially surprising feature of the Hb polymorphism in P. maniculatus is that an appreciable fraction of functional standing variation in the two transcriptionally active HBA paralogs is attributable to recurrent gene conversion from a tandemly linked HBA pseudogene. Moreover, transpecific polymorphism in the duplicated HBA genes is not solely attributable to incomplete lineage sorting or introgressive hybridization; instead, it is mainly attributable to recurrent interparalog gene conversion that has occurred independently in different species. Partly as a result of concerted evolution between tandemly duplicated globin genes, the same amino acid changes that contribute to variation in Hb function within P. maniculatus also contribute to divergence in Hb function among different species of Peromyscus. In the case of function-altering Hb mutations in Peromyscus, there is no qualitative or quantitative distinction between segregating variants within species and fixed differences between species. PMID:25556236

  19. Functional divergence of gene duplicates through ectopic recombination

    PubMed Central

    Christiaens, Joaquin F; Van Mulders, Sebastiaan E; Duitama, Jorge; Brown, Chris A; Ghequire, Maarten G; De Meester, Luc; Michiels, Jan; Wenseleers, Tom; Voordeckers, Karin; Verstrepen, Kevin J

    2012-01-01

    Gene duplication stimulates evolutionary innovation as the resulting paralogs acquire mutations that lead to sub- or neofunctionalization. A comprehensive in silico analysis of paralogs in Saccharomyces cerevisiae reveals that duplicates of cell-surface and subtelomeric genes also undergo ectopic recombination, which leads to new chimaeric alleles. Mimicking such intergenic recombination events in the FLO (flocculation) family of cell-surface genes shows that chimaeric FLO alleles confer different adhesion phenotypes than the parental genes. Our results indicate that intergenic recombination between paralogs can generate a large set of new alleles, thereby providing the raw material for evolutionary adaptation and innovation. PMID:23070367

  20. Phylogeny of Galactolipid Synthase Homologs Together with their Enzymatic Analyses Revealed a Possible Origin and Divergence Time for Photosynthetic Membrane Biogenesis

    PubMed Central

    Yuzawa, Yuichi; Nishihara, Hidenori; Haraguchi, Tsuyoshi; Masuda, Shinji; Shimojima, Mie; Shimoyama, Atsushi; Yuasa, Hideya; Okada, Norihiro; Ohta, Hiroyuki

    2012-01-01

    The photosynthetic membranes of cyanobacteria and chloroplasts of higher plants have remarkably similar lipid compositions. In particular, thylakoid membranes of both cyanobacteria and chloroplasts are composed of galactolipids, of which monogalactosyldiacylglycerol (MGDG) is the most abundant, although MGDG biosynthetic pathways are different in these organisms. Comprehensive phylogenetic analysis revealed that MGDG synthase (MGD) homologs of filamentous anoxygenic phototrophs Chloroflexi have a close relationship with MGDs of Viridiplantae (green algae and land plants). Furthermore, analyses for the sugar specificity and anomeric configuration of the sugar head groups revealed that one of the MGD homologs exhibited a true MGDG synthetic activity. We therefore presumed that higher plant MGDs are derived from this ancestral type of MGD genes, and genes involved in membrane biogenesis and photosystems have been already functionally associated at least at the time of Chloroflexi divergence. As MGD gene duplication is an important event during plastid evolution, we also estimated the divergence time of type A and B MGDs. Our analysis indicated that these genes diverged ∼323 million years ago, when Spermatophyta (seed plants) were appearing. Galactolipid synthesis is required to produce photosynthetic membranes; based on MGD gene sequences and activities, we have proposed a novel evolutionary model that has increased our understanding of photosynthesis evolution. PMID:22210603

  1. The APOBEC Protein Family: United by Structure, Divergent in Function.

    PubMed

    Salter, Jason D; Bennett, Ryan P; Smith, Harold C

    2016-07-01

    The APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like) family of proteins have diverse and important functions in human health and disease. These proteins have an intrinsic ability to bind to both RNA and single-stranded (ss) DNA. Both function and tissue-specific expression varies widely for each APOBEC protein. We are beginning to understand that the activity of APOBEC proteins is regulated through genetic alterations, changes in their transcription and mRNA processing, and through their interactions with other macromolecules in the cell. Loss of cellular control of APOBEC activities leads to DNA hypermutation and promiscuous RNA editing associated with the development of cancer or viral drug resistance, underscoring the importance of understanding how APOBEC proteins are regulated. PMID:27283515

  2. Convergent and Divergent Functional Connectivity Patterns in Schizophrenia and Depression

    PubMed Central

    Zeng, Ling-Li; Ma, Qiongmin; Hu, Dewen

    2013-01-01

    Major depression and schizophrenia are two of the most serious psychiatric disorders and share similar behavioral symptoms. Whether these similar behavioral symptoms underlie any convergent psychiatric pathological mechanisms is not yet clear. To address this issue, this study sought to investigate the whole-brain resting-state functional magnetic resonance imaging (MRI) of major depression and schizophrenia by using multivariate pattern analysis. Thirty-two schizophrenic patients, 19 major depressive disorder patients and 38 healthy controls underwent resting-state functional MRI scanning. A support vector machine in conjunction with intrinsic discriminant analysis was used to solve the multi-classification problem, resulting in a correct classification rate of 80.9% via leave-one-out cross-validation. The depression and schizophrenia groups both showed altered functional connections associated with the medial prefrontal cortex, anterior cingulate cortex, thalamus, hippocampus, and cerebellum. However, the prefrontal cortex, amygdala, and temporal poles were found to be affected differently by major depression and schizophrenia. Our preliminary study suggests that altered connections within or across the default mode network and the cerebellum may account for the common behavioral symptoms between major depression and schizophrenia. In addition, connections associated with the prefrontal cortex and the affective network showed promise as biomarkers for discriminating between the two disorders. PMID:23844175

  3. Convergent and divergent functional connectivity patterns in schizophrenia and depression.

    PubMed

    Yu, Yang; Shen, Hui; Zeng, Ling-Li; Ma, Qiongmin; Hu, Dewen

    2013-01-01

    Major depression and schizophrenia are two of the most serious psychiatric disorders and share similar behavioral symptoms. Whether these similar behavioral symptoms underlie any convergent psychiatric pathological mechanisms is not yet clear. To address this issue, this study sought to investigate the whole-brain resting-state functional magnetic resonance imaging (MRI) of major depression and schizophrenia by using multivariate pattern analysis. Thirty-two schizophrenic patients, 19 major depressive disorder patients and 38 healthy controls underwent resting-state functional MRI scanning. A support vector machine in conjunction with intrinsic discriminant analysis was used to solve the multi-classification problem, resulting in a correct classification rate of 80.9% via leave-one-out cross-validation. The depression and schizophrenia groups both showed altered functional connections associated with the medial prefrontal cortex, anterior cingulate cortex, thalamus, hippocampus, and cerebellum. However, the prefrontal cortex, amygdala, and temporal poles were found to be affected differently by major depression and schizophrenia. Our preliminary study suggests that altered connections within or across the default mode network and the cerebellum may account for the common behavioral symptoms between major depression and schizophrenia. In addition, connections associated with the prefrontal cortex and the affective network showed promise as biomarkers for discriminating between the two disorders. PMID:23844175

  4. Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species

    PubMed Central

    Barik, Suvakanta; Kumar, Ashutosh; Sarkar Das, Shabari; Yadav, Sandeep; Gautam, Vibhav; Singh, Archita; Singh, Sharmila; Sarkar, Ananda K.

    2015-01-01

    microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20–21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the “miRBase”, 27 have been annotated to be processed from the 3′ end, and have diverged distinctively from the other miR167s produced from 5′ end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3′ end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species. PMID:26459056

  5. Adaptive phylogeography: functional divergence between haemoglobins derived from different glacial refugia in the bank vole

    PubMed Central

    Kotlík, Petr; Marková, Silvia; Vojtek, Libor; Stratil, Antonín; Šlechta, Vlastimil; Hyršl, Pavel; Searle, Jeremy B.

    2014-01-01

    Over the years, researchers have used presumptively neutral molecular variation to infer the origins of current species' distributions in northern latitudes (especially Europe). However, several reported examples of genic and chromosomal replacements suggest that end-glacial colonizations of particular northern areas may have involved genetic input from different source populations at different times, coupled with competition and selection. We investigate the functional consequences of differences between two bank vole (Clethrionomys glareolus) haemoglobins deriving from different glacial refugia, one of which partially replaced the other in Britain during end-glacial climate warming. This allows us to examine their adaptive divergence and hence a possible role of selection in the replacement. We determine the amino acid substitution Ser52Cys in the major expressed β-globin gene as the allelic difference. We use structural modelling to reveal that the protein environment renders the 52Cys thiol a highly reactive functional group and we show its reactivity in vitro. We demonstrate that possessing the reactive thiol in haemoglobin increases the resistance of bank vole erythrocytes to oxidative stress. Our study thus provides striking evidence for physiological differences between products of genic variants that spread at the expense of one another during colonization of an area from different glacial refugia. PMID:24827438

  6. Conservation patterns in different functional sequence categoriesof divergent Drosophila species

    SciTech Connect

    Papatsenko, Dmitri; Kislyuk, Andrey; Levine, Michael; Dubchak, Inna

    2005-10-01

    We have explored the distributions of fully conservedungapped blocks in genome-wide pairwise alignments of recently completedspecies of Drosophila: D.yakuba, D.ananassae, D.pseudoobscura, D.virilisand D.mojavensis. Based on these distributions we have found that nearlyevery functional sequence category possesses its own distinctiveconservation pattern, sometimes independent of the overall sequenceconservation level. In the coding and regulatory regions, the ungappedblocks were longer than in introns, UTRs and non-functional sequences. Atthe same time, the blocks in the coding regions carried 3N+2 signaturecharacteristic to synonymic substitutions in the 3rd codon positions.Larger block sizes in transcription regulatory regions can be explainedby the presence of conserved arrays of binding sites for transcriptionfactors. We also have shown that the longest ungapped blocks, or'ultraconserved' sequences, are associated with specific gene groups,including those encoding ion channels and components of the cytoskeleton.We discussed how restrained conservation patterns may help in mappingfunctional sequence categories and improving genomeannotation.

  7. Comparison of morphological and genetic analyses reveals cryptic divergence and morphological plasticity in Stylophora (Cnidaria, Scleractinia)

    NASA Astrophysics Data System (ADS)

    Stefani, Fabrizio; Benzoni, F.; Yang, S.-Y.; Pichon, M.; Galli, P.; Chen, C. A.

    2011-12-01

    A combined morphological and genetic study of the coral genus Stylophora investigated species boundaries in the Gulf of Aden, Yemen. Two mitochondrial regions, including the hypervariable IGS9 spacer and the control region, and a fragment of rDNA were used for phylogenetic analysis. Results were compared by multivariate analysis on the basis of branch morphology and corallite morphometry. Two species were clearly discriminated by both approaches. The first species was characterised by small corallites and a low morphological variability and was ascribed to a new geographical record of Stylophora madagascarensis on the basis of its phylogenetic distinction and its morphological similarity to the type material. The second species was characterised by larger corallite size and greater morphological variability and was ascribed to Stylophora pistillata. The analysis was extended to the intrageneric level for other S. pistillata populations from the Red Sea and the Pacific Ocean. Strong internal divergence was evident in the genus Sty lophora. S. pistillata populations were split into two highly divergent Red Sea/Gulf of Aden and western Pacific lineages with significant morphological overlap, which suggests they represent two distinct cryptic species. The combined use of morphological and molecular approaches, so far proved to be a powerful tool for the re-delineation of species boundaries in corals, provided novel evidence of cryptic divergence in this group of marine metazoans.

  8. Functionalities of expressed messenger RNAs revealed from mutant phenotypes.

    PubMed

    Liao, Ben-Yang; Weng, Meng-Pin

    2016-07-01

    Total messenger RNAs mRNAs that are produced from a given gene under a certain set of conditions include both functional and nonfunctional transcripts. The high prevalence of nonfunctional mRNAs that have been detected in cells has raised questions regarding the functional implications of mRNA expression patterns and divergences. Phenotypes that result from the mutagenesis of protein-coding genes have provided the most straightforward descriptions of gene functions, and such data obtained from model organisms have facilitated investigations of the functionalities of expressed mRNAs. Mutant phenotype data from mouse tissues have revealed various attributes of functional mRNAs, including tissue-specificity, strength of expression, and evolutionary conservation. In addition, the role that mRNA expression evolution plays in driving morphological evolution has been revealed from studies designed to exploit morphological and physiological phenotypes of mouse mutants. Investigations into yeast essential genes (defined by an absence of colony growth after gene deletion) have further described gene regulatory strategies that reduce protein expression noise by mediating the rates of transcription and translation. In addition to the functional significance of expressed mRNAs as described in the abovementioned findings, the functionalities of other type of RNAs (i.e., noncoding RNAs) remain to be characterized with systematic mutations and phenotyping of the DNA regions that encode these RNA molecules. WIREs RNA 2016, 7:416-427. doi: 10.1002/wrna.1329 For further resources related to this article, please visit the WIREs website. PMID:26748449

  9. Genomic characterization of emergent pseudorabies virus in China reveals marked sequence divergence: Evidence for the existence of two major genotypes.

    PubMed

    Ye, Chao; Zhang, Qing-Zhan; Tian, Zhi-Jun; Zheng, Hao; Zhao, Kuan; Liu, Fei; Guo, Jin-Chao; Tong, Wu; Jiang, Cheng-Gang; Wang, Shu-Jie; Shi, Mang; Chang, Xiao-Bo; Jiang, Yi-Feng; Peng, Jin-Mei; Zhou, Yan-Jun; Tang, Yan-Dong; Sun, Ming-Xia; Cai, Xue-Hui; An, Tong-Qing; Tong, Guang-Zhi

    2015-09-01

    Recently pseudorabies outbreaks have occurred in many vaccinated farms in China. To identify genetic characteristics of pseudorabies virus (PRV) strains, we obtained the genomic sequences of PRV strains HeN1 and JS, which were compared to 4 PRV genomes and 729 partial gene sequences. PRV strains isolated in China showed marked sequence divergence compared to European and American strains. Phylogenetic analysis revealed that for the first time PRV can be divided into 2 distinct clusters, with Chinese strains being genotype II and PRVs isolated from other countries being genotype I. Restriction fragment length polymorphism analysis confirmed differences between HeN1 and Bartha strains, as did the presence of unique insertion/deletion polymorphisms and microsatellites. This divergence between the two genotypes may have been generated from long-term, independent evolution, which could also explain the low efficacy of the Bartha vaccine in protecting pigs infected with genotype II PRV. PMID:25965793

  10. Molecular Evolution and Functional Divergence of Soluble Starch Synthase Genes in Cassava (Manihot Esculenta Crantz)

    PubMed Central

    Yang, Zefeng; Wang, Yifan; Xu, Shuhui; Xu, Chenwu; Yan, Changjie

    2013-01-01

    Soluble starch synthases (SSs) are major enzymes involved in starch biosynthesis in plants. Cassava starch has many remarkable characteristics, which should be influenced by the evolution of SS genes in this starchy root crop. In this work, we performed a comprehensive phylogenetic and evolutionary analysis of the soluble starch synthases in cassava. Genome-wide identification showed that there are 9 genes encoding soluble starch synthases in cassava. All of the soluble starch synthases encoded by these genes contain both Glyco_transf_5 and Glycos_transf_1 domains, and a correlation analysis showed evidence of coevolution between these 2 domains in cassava SS genes. The SS genes in land plants can be divided into 6 subfamilies that were formed before the origin of seed plants, and species-specific expansion has contributed to the evolution of this family in cassava. A functional divergence analysis for this family provided statistical evidence for shifted evolutionary rates between the subfamilies of land plant soluble starch synthases. Although the main selective pressure acting on land plant SS genes was purifying selection, our results also revealed that point mutation with positive selection contributed to the evolution of 2 SS genes in cassava. The remarkable cassava starch characteristics might be the result of both the duplication and adaptive selection of SS genes. PMID:23888108

  11. Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis.

    PubMed

    Pimkin, Maxim; Kossenkov, Andrew V; Mishra, Tejaswini; Morrissey, Christapher S; Wu, Weisheng; Keller, Cheryl A; Blobel, Gerd A; Lee, Dongwon; Beer, Michael A; Hardison, Ross C; Weiss, Mitchell J

    2014-12-01

    Combinatorial actions of relatively few transcription factors control hematopoietic differentiation. To investigate this process in erythro-megakaryopoiesis, we correlated the genome-wide chromatin occupancy signatures of four master hematopoietic transcription factors (GATA1, GATA2, TAL1, and FLI1) and three diagnostic histone modification marks with the gene expression changes that occur during development of primary cultured megakaryocytes (MEG) and primary erythroblasts (ERY) from murine fetal liver hematopoietic stem/progenitor cells. We identified a robust, genome-wide mechanism of MEG-specific lineage priming by a previously described stem/progenitor cell-expressed transcription factor heptad (GATA2, LYL1, TAL1, FLI1, ERG, RUNX1, LMO2) binding to MEG-associated cis-regulatory modules (CRMs) in multipotential progenitors. This is followed by genome-wide GATA factor switching that mediates further induction of MEG-specific genes following lineage commitment. Interaction between GATA and ETS factors appears to be a key determinant of these processes. In contrast, ERY-specific lineage priming is biased toward GATA2-independent mechanisms. In addition to its role in MEG lineage priming, GATA2 plays an extensive role in late megakaryopoiesis as a transcriptional repressor at loci defined by a specific DNA signature. Our findings reveal important new insights into how ERY and MEG lineages arise from a common bipotential progenitor via overlapping and divergent functions of shared hematopoietic transcription factors. PMID:25319996

  12. In Silico Characterization of Functional Divergence of Two Cathelicidin Variants in Indian Sheep

    PubMed Central

    Dhaliwal, Kamaljeet K; Arora, Jaspreet S; Mukhopadhyay, Chandra S; Dubey, Prem P

    2015-01-01

    The present work focuses on the in silico characterization of functional divergence of two ovine cathelicidin coding sequence (cds) variants (ie, Cath1 and Cath2) of Indian sheep. Overlapping partial cds of both the cathelicidin variants were cloned in pJet1.2/blunt vector and sequenced. Evolutionary analysis of the Cath2 and Cath1 indicated that the mammalian cathelicidins clustered separately from avian fowlicidins. The avian fowlicidins, which are very different from mammalian cathelicidins (Caths), clearly displayed signatures of purifying selection. The pairwise sequence alignments of translated amino acid sequences of these two sheep cathelicidins showed gaps in the antimicrobial domain of Cath1 variant; however, the amino terminal cathelin regions of both the Caths were conserved. Amino acid sequence analysis of full-length cathelicidins available at public database revealed that Cath1, Cath2, and Cath7 of different ruminant species (including our Cath1 and Cath2 variants) formed individual clads, suggesting that these types have evolved to target specific types of microbes. In silico analysis of Cath1 and Cath2 peptide sequences indicated that the C-terminal antimicrobial peptide domain of Cath2 is more immunogenic than that of the ovine Cath1 due to its higher positive antigenic index, making Cath1 a promising antigen for production of monoclonal antibodies. PMID:26380546

  13. Acid stress mediated adaptive divergence in ion channel function during embryogenesis in Rana arvalis

    PubMed Central

    Shu, Longfei; Laurila, Anssi; Räsänen, Katja

    2015-01-01

    Ion channels and pumps are responsible for ion flux in cells, and are key mechanisms mediating cellular function. Many environmental stressors, such as salinity and acidification, are known to severely disrupt ionic balance of organisms thereby challenging fitness of natural populations. Although ion channels can have several vital functions during early life-stages (e.g. embryogenesis), it is currently not known i) how developing embryos maintain proper intracellular conditions when exposed to environmental stress and ii) to what extent environmental stress can drive intra-specific divergence in ion channels. Here we studied the moor frog, Rana arvalis, from three divergent populations to investigate the role of different ion channels and pumps for embryonic survival under acid stress (pH 4 vs 7.5) and whether populations adapted to contrasting acidities differ in the relative role of different ion channel/pumps. We found that ion channels that mediate Ca2+ influx are essential for embryonic survival under acidic pH, and, intriguingly, that populations differ in calcium channel function. Our results suggest that adaptive divergence in embryonic acid stress tolerance of amphibians may in part be mediated by Ca2+ balance. We suggest that ion flux may mediate adaptive divergence of natural populations at early life-stages in the face of environmental stress. PMID:26381453

  14. High-dimensional variance partitioning reveals the modular genetic basis of adaptive divergence in gene expression during reproductive character displacement.

    PubMed

    McGraw, Elizabeth A; Ye, Yixin H; Foley, Brad; Chenoweth, Stephen F; Higgie, Megan; Hine, Emma; Blows, Mark W

    2011-11-01

    Although adaptive change is usually associated with complex changes in phenotype, few genetic investigations have been conducted on adaptations that involve sets of high-dimensional traits. Microarrays have supplied high-dimensional descriptions of gene expression, and phenotypic change resulting from adaptation often results in large-scale changes in gene expression. We demonstrate how genetic analysis of large-scale changes in gene expression generated during adaptation can be accomplished by determining high-dimensional variance partitioning within classical genetic experimental designs. A microarray experiment conducted on a panel of recombinant inbred lines (RILs) generated from two populations of Drosophila serrata that have diverged in response to natural selection, revealed genetic divergence in 10.6% of 3762 gene products examined. Over 97% of the genetic divergence in transcript abundance was explained by only 12 genetic modules. The two most important modules, explaining 50% of the genetic variance in transcript abundance, were genetically correlated with the morphological traits that are known to be under selection. The expression of three candidate genes from these two important genetic modules was assessed in an independent experiment using qRT-PCR on 430 individuals from the panel of RILs, and confirmed the genetic association between transcript abundance and morphological traits under selection. PMID:22023580

  15. Recurrent Tandem Gene Duplication Gave Rise to Functionally Divergent Genes in Drosophila

    PubMed Central

    Chen, Ying; Long, Manyuan

    2008-01-01

    Tandem gene duplication is one of the major gene duplication mechanisms in eukaryotes, as illustrated by the prevalence of gene family clusters. Tandem duplicated paralogs usually share the same regulatory element, and as a consequence, they are likely to perform similar biological functions. Here, we provide an example of a newly evolved tandem duplicate acquiring novel functions, which were driven by positive selection. CG32708, CG32706, and CG6999 are 3 clustered genes residing in the X chromosome of Drosophila melanogaster. CG6999 and CG32708 have been examined for their molecular population genetic properties (Thornton and Long 2005). We further investigated the evolutionary forces acting on these genes with greater sample sizes and a broader approach that incorporate between-species divergence, using more variety of statistical methods. We explored the possible functional implications by characterizing the tissue-specific and developmental expression patterns of these genes. Sequence comparison of species within D. melanogaster subgroup reveals that this 3-gene cluster was created by 2 rounds of tandem gene duplication in the last 5 Myr. Based on phylogenetic analysis, CG32708 is clearly the parental copy that is shared by all species. CG32706 appears to have originated in the ancestor of Drosophila simulans and D. melanogaster about 5 Mya, and CG6999 is the newest duplicate that is unique to D. melanogaster. All 3 genes have different expression profiles, and CG6999 has in addition acquired a novel transcript. Biased polymorphism frequency spectrum, linkage disequilibrium, nucleotide substitution, and McDonald–Kreitman analyses suggested that the evolution of CG6999 and CG32706 were driven by positive Darwinian selection. PMID:18408233

  16. DNA barcoding reveals species level divergence between populations of the microhylid frog genus Arcovomer (Anura: Microhylidae) in the Atlantic Rainforest of southeastern Brazil.

    PubMed

    Jennings, W Bryan; Wogel, Henrique; Bilate, Marcos; Salles, Rodrigo de O L; Buckup, Paulo A

    2016-09-01

    The microhylid frogs belonging to the genus Arcovomer have been reported from lowland Atlantic Rainforest in the Brazilian states of Espírito Santo, Rio de Janeiro, and São Paulo. Here, we use DNA barcoding to assess levels of genetic divergence between apparently isolated populations in Espírito Santo and Rio de Janeiro. Our mtDNA data consisting of cytochrome oxidase subunit I (COI) nucleotide sequences reveals 13.2% uncorrected and 30.4% TIM2 + I + Γ corrected genetic divergences between these two populations. This level of divergence exceeds the suggested 10% uncorrected divergence threshold for elevating amphibian populations to candidate species using this marker, which implies that the Espírito Santo population is a species distinct from Arcovomer passarellii. Calibration of our model-corrected sequence divergence estimates suggests that the time of population divergence falls between 12 and 29 million years ago. PMID:26016873

  17. Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation

    PubMed Central

    Zhang, Xian; Feng, Xue; Tao, Jiemeng; Ma, Liyuan; Xiao, Yunhua; Liang, Yili; Liu, Xueduan; Yin, Huaqun

    2016-01-01

    Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains. PMID:27548157

  18. Comparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation.

    PubMed

    Zhang, Xian; Feng, Xue; Tao, Jiemeng; Ma, Liyuan; Xiao, Yunhua; Liang, Yili; Liu, Xueduan; Yin, Huaqun

    2016-01-01

    Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains. PMID:27548157

  19. Phylogenetic analyses reveal deeply divergent species lineages in the genus Sphaerobolus (Phallales: Basidiomycota).

    PubMed

    Geml, József; Davis, Donald D; Geiser, David M

    2005-05-01

    Phylogenetic analyses of 27 artillery fungus (Sphaerobolus sp.) isolates were conducted to identify species boundaries in the genus Sphaerobolus. Multiple gene genealogies inferred from maximum likelihood, Bayesian, and maximum-parsimony analyses of sequence data from individual loci (mtSSU, ITS, EF 1-alpha, and LSU) and a combined dataset (mtSSU, ITS, and EF 1-alpha) concordantly indicate the existence of three deeply divergent lineages in the genus Sphaerobolus, each representing a phylogenetic species. These three phylogenetic species correspond to two known species: Sphaerobolus iowensis and Sphaerobolus stellatus, and a newly discovered species. Suprageneric phylogenetic analyses of the mtSSU and LSU datasets containing representatives of related genera of the gomphoid-phalloid clade of Homobasidiomycetes suggested that the undescribed taxon likely is more closely related to S. stellatus than to S. iowensis. PMID:15804406

  20. Ultrastructure of stomatal development in early-divergent angiosperms reveals contrasting patterning and pre-patterning

    PubMed Central

    Rudall, Paula J.; Knowles, Emma V. W.

    2013-01-01

    Background and Aims Angiosperm stomata consistently possess a pair of guard cells, but differ between taxa in the patterning and developmental origin of neighbour cells. Developmental studies of phylogenetically pivotal taxa are essential as comparative yardsticks for understanding the evolution of stomatal development. Methods We present a novel ultrastructural study of developing stomata in leaves of Amborella (Amborellales), Nymphaea and Cabomba (Nymphaeales), and Austrobaileya and Schisandra (Austrobaileyales), representing the three earliest-divergent lineages of extant angiosperms (the ANITA-grade). Key Results Alternative developmental pathways occur in early-divergent angiosperms, resulting partly from differences in pre-patterning and partly from the presence or absence of highly polarized (asymmetric) mitoses in the stomatal cell lineage. Amplifying divisions are absent from ANITA-grade taxa, indicating that ostensible similarities with the stomatal patterning of Arabidopsis are superficial. In Amborella, ‘squared’ pre-patterning occurs in intercostal regions, with groups of four protodermal cells typically arranged in a rectangle; most guard-mother cells are formed by asymmetric division of a precursor cell (the mesoperigenous condition) and are typically triangular or trapezoidal. In contrast, water-lily stomata are always perigenous (lacking asymmetric divisions). Austrobaileya has occasional ‘giant’ stomata. Conclusions Similar mature stomatal phenotypes can result from contrasting morphogenetic factors, although the results suggest that paracytic stomata are invariably the product of at least one asymmetric division. Loss of asymmetric divisions in stomatal development could be a significant factor in land plant evolution, with implications for the diversity of key structural and physiological pathways. PMID:23969762

  1. Enantioselective and Regiodivergent Functionalization of N-Allylcarbamates by Mechanistically Divergent Multicatalysis.

    PubMed

    Richmond, Edward; Khan, Ismat Ullah; Moran, Joseph

    2016-08-22

    A pair of mechanistically divergent multicatalytic reaction sequences has been developed consisting of nickel-catalyzed isomerization of N-allylcarbamates and subsequent phosphoric-acid-catalyzed enantioselective functionalization of the resulting intermediates. By appropriate selection of reaction partners, in situ generated imines and ene-carbamates are mechanistically partitioned to yield opposing functionalized products. Formal α-functionalization to give protected α-arylamines is achieved upon enantioselective Friedel-Crafts reaction with arene nucleophiles, whereas formal β-functionalization is achieved upon reaction with diarylimine electrophiles in an enantioselective Povarov-[4+2] cycloaddition. PMID:27461524

  2. Multiple functionally divergent and conserved copies of alpha tubulin in bdelloid rotifers

    PubMed Central

    2012-01-01

    Background Bdelloid rotifers are microscopic animals that have apparently survived without sex for millions of years and are able to survive desiccation at all life stages through a process called anhydrobiosis. Both of these characteristics are believed to have played a role in shaping several unusual features of bdelloid genomes discovered in recent years. Studies into the impact of asexuality and anhydrobiosis on bdelloid genomes have focused on understanding gene copy number. Here we investigate copy number and sequence divergence in alpha tubulin. Alpha tubulin is conserved and normally present in low copy numbers in animals, but multiplication of alpha tubulin copies has occurred in animals adapted to extreme environments, such as cold-adapted Antarctic fish. Using cloning and sequencing we compared alpha tubulin copy variation in four species of bdelloid rotifers and four species of monogonont rotifers, which are facultatively sexual and cannot survive desiccation as adults. Results were verified using transcriptome data from one bdelloid species, Adineta ricciae. Results In common with the typical pattern for animals, monogonont rotifers contain either one or two copies of alpha tubulin, but bdelloid species contain between 11 and 13 different copies, distributed across five classes. Approximately half of the copies form a highly conserved group that vary by only 1.1% amino acid pairwise divergence with each other and with the monogonont copies. The other copies have divergent amino acid sequences that evolved significantly faster between classes than within them, relative to synonymous changes, and vary in predicted biochemical properties. Copies of each class were expressed under the laboratory conditions used to construct the transcriptome. Conclusions Our findings are consistent with recent evidence that bdelloids are degenerate tetraploids and that functional divergence of ancestral copies of genes has occurred, but show how further duplication events

  3. Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds.

    PubMed

    Singh, Rajinder; Ong-Abdullah, Meilina; Low, Eng-Ti Leslie; Manaf, Mohamad Arif Abdul; Rosli, Rozana; Nookiah, Rajanaidu; Ooi, Leslie Cheng-Li; Ooi, Siew-Eng; Chan, Kuang-Lim; Halim, Mohd Amin; Azizi, Norazah; Nagappan, Jayanthi; Bacher, Blaire; Lakey, Nathan; Smith, Steven W; He, Dong; Hogan, Michael; Budiman, Muhammad A; Lee, Ernest K; DeSalle, Rob; Kudrna, David; Goicoechea, Jose Luis; Wing, Rod A; Wilson, Richard K; Fulton, Robert S; Ordway, Jared M; Martienssen, Robert A; Sambanthamurthi, Ravigadevi

    2013-08-15

    Oil palm is the most productive oil-bearing crop. Although it is planted on only 5% of the total world vegetable oil acreage, palm oil accounts for 33% of vegetable oil and 45% of edible oil worldwide, but increased cultivation competes with dwindling rainforest reserves. We report the 1.8-gigabase (Gb) genome sequence of the African oil palm Elaeis guineensis, the predominant source of worldwide oil production. A total of 1.535 Gb of assembled sequence and transcriptome data from 30 tissue types were used to predict at least 34,802 genes, including oil biosynthesis genes and homologues of WRINKLED1 (WRI1), and other transcriptional regulators, which are highly expressed in the kernel. We also report the draft sequence of the South American oil palm Elaeis oleifera, which has the same number of chromosomes (2n = 32) and produces fertile interspecific hybrids with E. guineensis but seems to have diverged in the New World. Segmental duplications of chromosome arms define the palaeotetraploid origin of palm trees. The oil palm sequence enables the discovery of genes for important traits as well as somaclonal epigenetic alterations that restrict the use of clones in commercial plantings, and should therefore help to achieve sustainability for biofuels and edible oils, reducing the rainforest footprint of this tropical plantation crop. PMID:23883927

  4. Molecular Properties and Functional Divergence of the Dehydroascorbate Reductase Gene Family in Lower and Higher Plants

    PubMed Central

    Zhang, Yuan-Jie; Wang, Wei; Yang, Hai-Ling; Li, Yue; Kang, Xiang-Yang; Wang, Xiao-Ru; Yang, Zhi-Ling

    2015-01-01

    Dehydroascorbate reductase (DHAR), which reduces oxidized ascorbate, is important for maintaining an appropriate ascorbate redox state in plant cells. To date, genome-wide molecular characterization of DHARs has only been conducted in bryophytes (Physcomitrella patens) and eudicots (e.g. Arabidopsis thaliana). In this study, to gain a general understanding of the molecular properties and functional divergence of the DHARs in land plants, we further conducted a comprehensive analysis of DHARs from the lycophyte Selaginella moellendorffii, gymnosperm Picea abies and monocot Zea mays. DHARs were present as a small gene family in all of the land plants we examined, with gene numbers ranging from two to four. All the plants contained cytosolic and chloroplastic DHARs, indicating dehydroascorbate (DHA) can be directly reduced in the cytoplasm and chloroplast by DHARs in all the plants. A novel vacuolar DHAR was found in Z. mays, indicating DHA may also be reduced in the vacuole by DHARs in Z. mays. The DHARs within each species showed extensive functional divergence in their gene structures, subcellular localizations, and enzymatic characteristics. This study provides new insights into the molecular characteristics and functional divergence of DHARs in land plants. PMID:26684301

  5. Divergence in male cricket song and female preference functions in three allopatric sister species.

    PubMed

    Hennig, Ralf Matthias; Blankers, Thomas; Gray, David A

    2016-05-01

    Multivariate female preference functions for male sexual signals have rarely been investigated, especially in a comparative context among sister species. Here we examined male signal and female preference co-variation in three closely related, but allopatric species of Gryllus crickets and quantified male song traits as well as female preferences. We show that males differ conspicuously in either one of two relatively static song traits, carrier frequency or pulse rate; female preference functions for these traits also differed, and would in combination enhance species discrimination. In contrast, the relatively dynamic song traits, chirp rate and chirp duty cycle, show minimal divergence among species and relatively greater conservation of female preference functions. Notably, among species we demonstrate similar mechanistic rules for the integration of pulse and chirp time scales, despite divergence in pulse rate preferences. As these are allopatric taxa, selection for species recognition per se is unlikely. More likely sexual selection combined with conserved properties of preference filters enabled divergent coevolution of male song and female preferences. PMID:27026021

  6. Molecular Properties and Functional Divergence of the Dehydroascorbate Reductase Gene Family in Lower and Higher Plants.

    PubMed

    Zhang, Yuan-Jie; Wang, Wei; Yang, Hai-Ling; Li, Yue; Kang, Xiang-Yang; Wang, Xiao-Ru; Yang, Zhi-Ling

    2015-01-01

    Dehydroascorbate reductase (DHAR), which reduces oxidized ascorbate, is important for maintaining an appropriate ascorbate redox state in plant cells. To date, genome-wide molecular characterization of DHARs has only been conducted in bryophytes (Physcomitrella patens) and eudicots (e.g. Arabidopsis thaliana). In this study, to gain a general understanding of the molecular properties and functional divergence of the DHARs in land plants, we further conducted a comprehensive analysis of DHARs from the lycophyte Selaginella moellendorffii, gymnosperm Picea abies and monocot Zea mays. DHARs were present as a small gene family in all of the land plants we examined, with gene numbers ranging from two to four. All the plants contained cytosolic and chloroplastic DHARs, indicating dehydroascorbate (DHA) can be directly reduced in the cytoplasm and chloroplast by DHARs in all the plants. A novel vacuolar DHAR was found in Z. mays, indicating DHA may also be reduced in the vacuole by DHARs in Z. mays. The DHARs within each species showed extensive functional divergence in their gene structures, subcellular localizations, and enzymatic characteristics. This study provides new insights into the molecular characteristics and functional divergence of DHARs in land plants. PMID:26684301

  7. Mitogenomics of 'Old World Acraea' butterflies reveals a highly divergent 'Bematistes'.

    PubMed

    Timmermans, M J T N; Lees, D C; Thompson, M J; Sáfián, Sz; Brattström, O

    2016-04-01

    Afrotropical Acraeini butterflies provide a fascinating potential model system to contrast with the Neotropical Heliconiini, yet their phylogeny remains largely unexplored by molecular methods and their generic level nomenclature is still contentious. To test the potential of mitogenomes in a simultaneous analysis of the radiation, we sequenced the full mitochondrial genomes of 19 African species. Analyses show the potential of mitogenomic phylogeny reconstruction in this group. Inferred relationships are largely congruent with a previous multilocus study. We confirm a monophyletic Telchinia to include the Asiatic Pareba with a complicated paraphylum, traditional (sub)genus Acraea, toward the base. The results suggest that several proposed subgenera and some species groups within Telchinia are not monophyletic, while two other (sub)genera could possibly be combined. Telchinia was recovered without strong support as sister to the potentially interesting system of distasteful model butterflies known as Bematistes, a name that is suppressed in some treatments. Surprisingly, we find that this taxon has remarkably divergent mitogenomes and unexpected synapomorphic tRNA rearrangements. These gene order changes, combined with evidence for deviating dN/dS ratios and evidence for episodal diversifying selection, suggest that the ancestral Bematistes mitogenome has had a turbulent past. Our study adds genetic support for treating this clade as a distinct genus, while the alternative option, adopted by some authors, of Acraea being equivalent to Acraeini merely promotes redundancy. We pave the way for more detailed mitogenomic and multi-locus molecular analyses which can determine how many genera are needed (possibly at least six) to divide Acraeini into monophyletic groups that also facilitate communication about their biology. PMID:26724404

  8. Phylogenomic Analysis Reveals Deep Divergence and Recombination in an Economically Important Grapevine Virus

    PubMed Central

    Maree, Hans J.; Pirie, Michael D.; Oosthuizen, Kristin; Bester, Rachelle; Rees, D. Jasper G.; Burger, Johan T.

    2015-01-01

    The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombination in one whole genome sequence and further evidence for recombination in two more, including GH24. We inferred phylogenetic trees and networks and estimated the ages of common ancestors of GLRaV-3 clades by means of relaxed clock models calibrated with asynchronous sampling dates. Our results generally confirm previously identified variant groups as well as two new groups (VII and VIII). Higher order groups were defined as supergroups designated A to D. Supergroup A includes variant groups I-V and supergroup B group VI and its related unclassified isolates. Supergroups C and D are less well known, including the newly identified groups VII (including isolate GH24) and VIII respectively. The inferred node ages suggest that the origins of the major groups of GLRaV-3, including isolate GH24, may have occurred prior to worldwide cultivation of grapevines, whilst the current diversity represents closely related isolates that diverged from common ancestors within the last century. PMID:25992606

  9. Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences

    PubMed Central

    Nguyen Ba, Alex N.; Strome, Bob; Hua, Jun Jie; Desmond, Jonathan; Gagnon-Arsenault, Isabelle; Weiss, Eric L.; Landry, Christian R.; Moses, Alan M.

    2014-01-01

    Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization. Consistent with functional divergence after gene duplication, recent studies have shown accelerated evolution in retained paralogs. However, little is known in general about the impact of this accelerated evolution on the molecular functions of retained paralogs. For example, do new functions typically involve changes in enzymatic activities, or changes in protein regulation? Here we study the evolution of posttranslational regulation by examining the evolution of important regulatory sequences (short linear motifs) in retained duplicates created by the whole-genome duplication in budding yeast. To do so, we identified short linear motifs whose evolutionary constraint has relaxed after gene duplication with a likelihood-ratio test that can account for heterogeneity in the evolutionary process by using a non-central chi-squared null distribution. We find that short linear motifs are more likely to show changes in evolutionary constraints in retained duplicates compared to single-copy genes. We examine changes in constraints on known regulatory sequences and show that for the Rck1/Rck2, Fkh1/Fkh2, Ace2/Swi5 paralogs, they are associated with previously characterized differences in posttranslational regulation. Finally, we experimentally confirm our prediction that for the Ace2/Swi5 paralogs, Cbk1 regulated localization was lost along the lineage leading to SWI5 after gene duplication. Our analysis suggests that changes in posttranslational regulation mediated by short regulatory motifs systematically contribute to functional divergence after gene duplication. PMID:25474245

  10. Comparative Genetic Analysis of Mycobacterium ulcerans and Mycobacterium marinum Reveals Evidence of Recent Divergence

    PubMed Central

    Stinear, Timothy P.; Jenkin, Grant A.; Johnson, Paul D. R.; Davies, John K.

    2000-01-01

    Previous studies of the 16S rRNA genes from Mycobacterium ulcerans and Mycobacterium marinum have suggested a very close genetic relationship between these species (99.6% identity). However, these organisms are phenotypically distinct and cause diseases with very different pathologies. To investigate this apparent paradox, we compared 3,306 nucleotides from the partial sequences of eight housekeeping and structural genes derived from 18 M. ulcerans strains and 22 M. marinum strains. This analysis confirmed the close genetic relationship inferred from the 16S rRNA data, with nucleotide sequence identity ranging from 98.1 to 99.7%. The multilocus sequence analysis also confirmed previous genotype studies of M. ulcerans that have identified distinct genotypes within a geographical region. Single isolates of both M. ulcerans and M. marinum that were shown by the sequence analysis to be the most closely related were then selected for further study. One- and two-dimensional pulsed-field gel electrophoresis was employed to compare the architecture and size of the genome from each species. Genome sizes of approximately 4.4 and 4.6 Mb were obtained for M. ulcerans and M. marinum, respectively. Significant macrorestriction fragment polymorphism was observed between the species. However, hybridization analysis of DNA cleaved with more frequently cutting enzymes identified significant preservation of the flanking sequence at seven of the eight loci sequenced. The exception was the 16S rRNA locus. Two high-copy-number insertion sequences, IS2404 and IS2606, have recently been reported in M. ulcerans, and significantly, these elements are not present in M. marinum. Hybridization of the AseI restriction fragments from M. ulcerans with IS2404 and IS2606 indicated widespread genome distribution for both of these repeated sequences. Taken together, these data strongly suggest that M. ulcerans has recently diverged from M. marinum by the acquisition and concomitant loss of DNA in a

  11. LncRNA profiling of human lymphoid progenitors reveals transcriptional divergence of B and T lineages

    PubMed Central

    Casero, David; Sandoval, Salemiz; Seet, Christopher S.; Scholes, Jessica; Zhu, Yuhua; Ha, Vi Luan; Luong, Annie; Parekh, Chintan; Crooks, Gay M.

    2015-01-01

    To elucidate the transcriptional landscape that regulates human lymphoid commitment during postnatal life, we used RNA sequencing to assemble the long non-coding transcriptome across human bone marrow and thymic progenitors spanning the earliest stages of B and T lymphoid specification. Over 3000 novel long non-coding RNA genes (lncRNAs) were revealed through the analysis of these rare populations. Lymphoid commitment was characterized by lncRNA expression patterns that were highly stage-specific and more lineage-specific than protein coding patterns. Protein-coding genes co-expressed with neighboring lncRNA genes were enriched for ontologies related to lymphoid differentiation. The exquisite cell-type specificity of global lncRNA expression patterns independently revealed new developmental relationships between the earliest progenitors in the human bone marrow and thymus. PMID:26502406

  12. Individual differences in children's innovative problem-solving are not predicted by divergent thinking or executive functions.

    PubMed

    Beck, Sarah R; Williams, Clare; Cutting, Nicola; Apperly, Ian A; Chappell, Jackie

    2016-03-19

    Recent studies of children's tool innovation have revealed that there is variation in children's success in middle-childhood. In two individual differences studies, we sought to identify personal characteristics that might predict success on an innovation task. In Study 1, we found that although measures of divergent thinking were related to each other they did not predict innovation success. In Study 2, we measured executive functioning including: inhibition, working memory, attentional flexibility and ill-structured problem-solving. None of these measures predicted innovation, but, innovation was predicted by children's performance on a receptive vocabulary scale that may function as a proxy for general intelligence. We did not find evidence that children's innovation was predicted by specific personal characteristics. PMID:26926280

  13. Individual differences in children's innovative problem-solving are not predicted by divergent thinking or executive functions

    PubMed Central

    2016-01-01

    Recent studies of children's tool innovation have revealed that there is variation in children's success in middle-childhood. In two individual differences studies, we sought to identify personal characteristics that might predict success on an innovation task. In Study 1, we found that although measures of divergent thinking were related to each other they did not predict innovation success. In Study 2, we measured executive functioning including: inhibition, working memory, attentional flexibility and ill-structured problem-solving. None of these measures predicted innovation, but, innovation was predicted by children's performance on a receptive vocabulary scale that may function as a proxy for general intelligence. We did not find evidence that children's innovation was predicted by specific personal characteristics. PMID:26926280

  14. Open chromatin reveals the functional maize genome

    PubMed Central

    Rodgers-Melnick, Eli; Vera, Daniel L.; Bass, Hank W.

    2016-01-01

    Cellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots, focusing biased gene conversion at their flanks. Although MNase HS regions map to less than 1% of the genome, they consistently explain a remarkably large amount (∼40%) of heritable phenotypic variance in diverse complex traits. MNase HS regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome. These results imply that less than 3% of the maize genome (coding and MNase HS regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome. PMID:27185945

  15. Open chromatin reveals the functional maize genome.

    PubMed

    Rodgers-Melnick, Eli; Vera, Daniel L; Bass, Hank W; Buckler, Edward S

    2016-05-31

    Cellular processes mediated through nuclear DNA must contend with chromatin. Chromatin structural assays can efficiently integrate information across diverse regulatory elements, revealing the functional noncoding genome. In this study, we use a differential nuclease sensitivity assay based on micrococcal nuclease (MNase) digestion to discover open chromatin regions in the maize genome. We find that maize MNase-hypersensitive (MNase HS) regions localize around active genes and within recombination hotspots, focusing biased gene conversion at their flanks. Although MNase HS regions map to less than 1% of the genome, they consistently explain a remarkably large amount (∼40%) of heritable phenotypic variance in diverse complex traits. MNase HS regions are therefore on par with coding sequences as annotations that demarcate the functional parts of the maize genome. These results imply that less than 3% of the maize genome (coding and MNase HS regions) may give rise to the overwhelming majority of phenotypic variation, greatly narrowing the scope of the functional genome. PMID:27185945

  16. Defining natural species of bacteria: clear-cut genomic boundaries revealed by a turning point in nucleotide sequence divergence

    PubMed Central

    2013-01-01

    Background Bacteria are currently classified into arbitrary species, but whether they actually exist as discrete natural species was unclear. To reveal genomic features that may unambiguously group bacteria into discrete genetic clusters, we carried out systematic genomic comparisons among representative bacteria. Results We found that bacteria of Salmonella formed tight phylogenetic clusters separated by various genetic distances: whereas over 90% of the approximately four thousand shared genes had completely identical sequences among strains of the same lineage, the percentages dropped sharply to below 50% across the lineages, demonstrating the existence of clear-cut genetic boundaries by a steep turning point in nucleotide sequence divergence. Recombination assays supported the genetic boundary hypothesis, suggesting that genetic barriers had been formed between bacteria of even very closely related lineages. We found similar situations in bacteria of Yersinia and Staphylococcus. Conclusions Bacteria are genetically isolated into discrete clusters equivalent to natural species. PMID:23865772

  17. Training your brain to be more creative: brain functional and structural changes induced by divergent thinking training.

    PubMed

    Sun, Jiangzhou; Chen, Qunlin; Zhang, Qinglin; Li, Yadan; Li, Haijiang; Wei, Dongtao; Yang, Wenjing; Qiu, Jiang

    2016-10-01

    Creativity is commonly defined as the ability to produce something both novel and useful. Stimulating creativity has great significance for both individual success and social improvement. Although increasing creative capacity has been confirmed to be possible and effective at the behavioral level, few longitudinal studies have examined the extent to which the brain function and structure underlying creativity are plastic. A cognitive stimulation (20 sessions) method was used in the present study to train subjects and to explore the neuroplasticity induced by training. The behavioral results revealed that both the originality and the fluency of divergent thinking were significantly improved by training. Furthermore, functional changes induced by training were observed in the dorsal anterior cingulate cortex (dACC), dorsal lateral prefrontal cortex (DLPFC), and posterior brain regions. Moreover, the gray matter volume (GMV) was significantly increased in the dACC after divergent thinking training. These results suggest that the enhancement of creativity may rely not only on the posterior brain regions that are related to the fundamental cognitive processes of creativity (e.g., semantic processing, generating novel associations), but also on areas that are involved in top-down cognitive control, such as the dACC and DLPFC. Hum Brain Mapp 37:3375-3387, 2016. © 2016 Wiley Periodicals, Inc. PMID:27159407

  18. A Dense Linkage Map for Chinook salmon (Oncorhynchus tshawytscha) Reveals Variable Chromosomal Divergence After an Ancestral Whole Genome Duplication Event

    PubMed Central

    Brieuc, Marine S. O.; Waters, Charles D.; Seeb, James E.; Naish, Kerry A.

    2014-01-01

    Comparisons between the genomes of salmon species reveal that they underwent extensive chromosomal rearrangements following whole genome duplication that occurred in their lineage 58−63 million years ago. Extant salmonids are diploid, but occasional pairing between homeologous chromosomes exists in males. The consequences of re-diploidization can be characterized by mapping the position of duplicated loci in such species. Linkage maps are also a valuable tool for genome-wide applications such as genome-wide association studies, quantitative trait loci mapping or genome scans. Here, we investigated chromosomal evolution in Chinook salmon (Oncorhynchus tshawytscha) after genome duplication by mapping 7146 restriction-site associated DNA loci in gynogenetic haploid, gynogenetic diploid, and diploid crosses. In the process, we developed a reference database of restriction-site associated DNA loci for Chinook salmon comprising 48528 non-duplicated loci and 6409 known duplicated loci, which will facilitate locus identification and data sharing. We created a very dense linkage map anchored to all 34 chromosomes for the species, and all arms were identified through centromere mapping. The map positions of 799 duplicated loci revealed that homeologous pairs have diverged at different rates following whole genome duplication, and that degree of differentiation along arms was variable. Many of the homeologous pairs with high numbers of duplicated markers appear conserved with other salmon species, suggesting that retention of conserved homeologous pairing in some arms preceded species divergence. As chromosome arms are highly conserved across species, the major resources developed for Chinook salmon in this study are also relevant for other related species. PMID:24381192

  19. Genome-wide analysis of the AP2/ERF family in Musa species reveals divergence and neofunctionalisation during evolution

    PubMed Central

    Lakhwani, Deepika; Pandey, Ashutosh; Dhar, Yogeshwar Vikram; Bag, Sumit Kumar; Trivedi, Prabodh Kumar; Asif, Mehar Hasan

    2016-01-01

    AP2/ERF domain containing transcription factor super family is one of the important regulators in the plant kingdom. The involvement of AP2/ERF family members has been elucidated in various processes associated with plant growth, development as well as in response to hormones, biotic and abiotic stresses. In this study, we carried out genome-wide analysis to identify members of AP2/ERF family in Musa acuminata (A genome) and Musa balbisiana (B genome) and changes leading to neofunctionalisation of genes. Analysis identified 265 and 318 AP2/ERF encoding genes in M. acuminata and M. balbisiana respectively which were further classified into ERF, DREB, AP2, RAV and Soloist groups. Comparative analysis indicated that AP2/ERF family has undergone duplication, loss and divergence during evolution and speciation of the Musa A and B genomes. We identified nine genes which are up-regulated during fruit ripening and might be components of the regulatory machinery operating during ethylene-dependent ripening in banana. Tissue-specific expression analysis of the genes suggests that different regulatory mechanisms might be involved in peel and pulp ripening process through recruiting specific ERFs in these tissues. Analysis also suggests that MaRAV-6 and MaERF026 have structurally diverged from their M. balbisiana counterparts and have attained new functions during ripening. PMID:26733055

  20. Divergent whole-genome methylation maps of human and chimpanzee brains reveal epigenetic basis of human regulatory evolution.

    PubMed

    Zeng, Jia; Konopka, Genevieve; Hunt, Brendan G; Preuss, Todd M; Geschwind, Dan; Yi, Soojin V

    2012-09-01

    DNA methylation is a pervasive epigenetic DNA modification that strongly affects chromatin regulation and gene expression. To date, it remains largely unknown how patterns of DNA methylation differ between closely related species and whether such differences contribute to species-specific phenotypes. To investigate these questions, we generated nucleotide-resolution whole-genome methylation maps of the prefrontal cortex of multiple humans and chimpanzees. Levels and patterns of DNA methylation vary across individuals within species according to the age and the sex of the individuals. We also found extensive species-level divergence in patterns of DNA methylation and that hundreds of genes exhibit significantly lower levels of promoter methylation in the human brain than in the chimpanzee brain. Furthermore, we investigated the functional consequences of methylation differences in humans and chimpanzees by integrating data on gene expression generated with next-generation sequencing methods, and we found a strong relationship between differential methylation and gene expression. Finally, we found that differentially methylated genes are strikingly enriched with loci associated with neurological disorders, psychological disorders, and cancers. Our results demonstrate that differential DNA methylation might be an important molecular mechanism driving gene-expression divergence between human and chimpanzee brains and might potentially contribute to the evolution of disease vulnerabilities. Thus, comparative studies of humans and chimpanzees stand to identify key epigenomic modifications underlying the evolution of human-specific traits. PMID:22922032

  1. The Complete Sequence of the Acacia ligulata Chloroplast Genome Reveals a Highly Divergent clpP1 Gene

    PubMed Central

    Williams, Anna V.; Boykin, Laura M.; Howell, Katharine A.; Nevill, Paul G.; Small, Ian

    2015-01-01

    Legumes are a highly diverse angiosperm family that include many agriculturally important species. To date, 21 complete chloroplast genomes have been sequenced from legume crops confined to the Papilionoideae subfamily. Here we report the first chloroplast genome from the Mimosoideae, Acacia ligulata, and compare it to the previously sequenced legume genomes. The A. ligulata chloroplast genome is 158,724 bp in size, comprising inverted repeats of 25,925 bp and single-copy regions of 88,576 bp and 18,298 bp. Acacia ligulata lacks the inversion present in many of the Papilionoideae, but is not otherwise significantly different in terms of gene and repeat content. The key feature is its highly divergent clpP1 gene, normally considered essential in chloroplast genomes. In A. ligulata, although transcribed and spliced, it probably encodes a catalytically inactive protein. This study provides a significant resource for further genetic research into Acacia and the Mimosoideae. The divergent clpP1 gene suggests that Acacia will provide an interesting source of information on the evolution and functional diversity of the chloroplast Clp protease complex. PMID:25955637

  2. Genome-wide analysis of the AP2/ERF family in Musa species reveals divergence and neofunctionalisation during evolution.

    PubMed

    Lakhwani, Deepika; Pandey, Ashutosh; Dhar, Yogeshwar Vikram; Bag, Sumit Kumar; Trivedi, Prabodh Kumar; Asif, Mehar Hasan

    2016-01-01

    AP2/ERF domain containing transcription factor super family is one of the important regulators in the plant kingdom. The involvement of AP2/ERF family members has been elucidated in various processes associated with plant growth, development as well as in response to hormones, biotic and abiotic stresses. In this study, we carried out genome-wide analysis to identify members of AP2/ERF family in Musa acuminata (A genome) and Musa balbisiana (B genome) and changes leading to neofunctionalisation of genes. Analysis identified 265 and 318 AP2/ERF encoding genes in M. acuminata and M. balbisiana respectively which were further classified into ERF, DREB, AP2, RAV and Soloist groups. Comparative analysis indicated that AP2/ERF family has undergone duplication, loss and divergence during evolution and speciation of the Musa A and B genomes. We identified nine genes which are up-regulated during fruit ripening and might be components of the regulatory machinery operating during ethylene-dependent ripening in banana. Tissue-specific expression analysis of the genes suggests that different regulatory mechanisms might be involved in peel and pulp ripening process through recruiting specific ERFs in these tissues. Analysis also suggests that MaRAV-6 and MaERF026 have structurally diverged from their M. balbisiana counterparts and have attained new functions during ripening. PMID:26733055

  3. Comparative Evolutionary Histories of Kisspeptins and Kisspeptin Receptors in Vertebrates Reveal Both Parallel and Divergent Features

    PubMed Central

    Pasquier, Jérémy; Lafont, Anne-Gaëlle; Tostivint, Hervé; Vaudry, Hubert; Rousseau, Karine; Dufour, Sylvie

    2012-01-01

    During the past decade, the kisspeptin system has been identified in various vertebrates, leading to the discovery of multiple genes encoding both peptides (Kiss) and receptors (Kissr). The investigation of recently published genomes from species of phylogenetic interest, such as a chondrichthyan, the elephant shark, an early sarcopterygian, the coelacanth, a non-teleost actinopterygian, the spotted gar, and an early teleost, the European eel, allowed us to get new insights into the molecular diversity and evolution of both Kiss and Kissr families. We identified four Kissr in the spotted gar and coelacanth genomes, providing the first evidence of four Kissr genes in vertebrates. We also found three Kiss in the coelacanth and elephant shark genomes revealing two new species, in addition to Xenopus, presenting three Kiss genes. Considering the increasing diversity of kisspeptin system, phylogenetic, and synteny analyses enabled us to clarify both Kiss and Kissr classifications. We also could trace back the evolution of both gene families from the early steps of vertebrate history. Four Kissr and four Kiss paralogs may have arisen via the two whole genome duplication rounds (1R and 2R) in early vertebrates. This would have been followed by multiple independent Kiss and Kissr gene losses in the sarcopterygian and actinopterygian lineages. In particular, no impact of the teleost-specific 3R could be recorded on the numbers of teleost Kissr or Kiss paralogs. The origin of their diversity via 1R and 2R, as well as the subsequent occurrence of multiple gene losses, represent common features of the evolutionary histories of Kiss and Kissr families in vertebrates. In contrast, comparisons also revealed un-matching numbers of Kiss and Kissr genes in some species, as well as a large variability of Kiss/Kissr couples according to species. These discrepancies support independent features of the Kiss and Kissr evolutionary histories across vertebrate radiation. PMID:23272003

  4. Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence

    PubMed Central

    2010-01-01

    Background The Ralstonia solanacearum species complex includes thousands of strains pathogenic to an unusually wide range of plant species. These globally dispersed and heterogeneous strains cause bacterial wilt diseases, which have major socio-economic impacts. Pathogenicity is an ancestral trait in R. solanacearum and strains with high genetic variation can be subdivided into four phylotypes, correlating to isolates from Asia (phylotype I), the Americas (phylotype IIA and IIB), Africa (phylotype III) and Indonesia (phylotype IV). Comparison of genome sequences strains representative of this phylogenetic diversity can help determine which traits allow this bacterium to be such a pathogen of so many different plant species and how the bacteria survive in many different habitats. Results The genomes of three tomato bacterial wilt pathogens, CFBP2957 (phy. IIA), CMR15 (phy. III) and PSI07 (phy. IV) were sequenced and manually annotated. These genomes were compared with those of three previously sequenced R. solanacearum strains: GMI1000 (tomato, phy. I), IPO1609 (potato, phy. IIB), and Molk2 (banana, phy. IIB). The major genomic features (size, G+C content, number of genes) were conserved across all of the six sequenced strains. Despite relatively high genetic distances (calculated from average nucleotide identity) and many genomic rearrangements, more than 60% of the genes of the megaplasmid and 70% of those on the chromosome are syntenic. The three new genomic sequences revealed the presence of several previously unknown traits, probably acquired by horizontal transfers, within the genomes of R. solanacearum, including a type IV secretion system, a rhi-type anti-mitotic toxin and two small plasmids. Genes involved in virulence appear to be evolving at a faster rate than the genome as a whole. Conclusions Comparative analysis of genome sequences and gene content confirmed the differentiation of R. solanacearum species complex strains into four phylotypes. Genetic

  5. Heterologous expression of mammalian Plk1 in Drosophila reveals divergence from Polo during late mitosis

    SciTech Connect

    Pearson, John . E-mail: jrobpea@upo.es; Godinho, Susana A.; Tavares, Alvaro; Glover, David M.

    2006-04-01

    Drosophila Polo kinase is the founder member of a conserved kinase family required for multiple stages of mitosis. We assessed the ability of mouse Polo-like kinase 1 (Plk1) to perform the multiple mitotic functions of Polo kinase, by expressing a Plk1-GFP fusion in Drosophila. Consistent with the previously reported localization of Polo kinase, Plk1-GFP was strongly localized to centrosomes and recruited to the centromeric regions of condensing chromosomes during early mitosis. However, in contrast to a functional Polo-GFP fusion, Plk1-GFP failed to localize to the central spindle midzone in both syncytial embryo mitosis and the conventional mitoses of cellularized embryos and S2 cells. Moreover, unlike endogenous Polo kinase and Polo-GFP, Plk1-GFP failed to associate with the contractile ring. Expression of Plk1-GFP enhanced the lethality of hypomorphic polo mutants and disrupted the organization of the actinomyosin cytoskeleton in a dominant-negative manner. Taken together, our results suggest that endogenous Polo kinase has specific roles in regulating actinomyosin rearrangements during Drosophila mitoses that its mammalian counterpart, Plk1, cannot fulfill. Consistent with this hypothesis, we observed defects in the cortical recruitment of myosin and myosin regulatory light chain in Polo deficient cells.

  6. The structure of tryptophanyl-tRNA synthetase from Giardia lamblia reveals divergence from eukaryotic homologs

    PubMed Central

    Arakaki, Tracy L; Carter, Megan; Napuli, Alberto J; Verlinde, Christophe L M J; Fan, Erkang; Zucker, Frank; Buckner, Frederick S; Van Voorhis, Wesley C; Hol, Wim G J; Merritt, Ethan A

    2010-01-01

    The 2.1 Å crystal structure of tryptophanyl-tRNA synthetase (TrpRS) from the diplomonad Giardia lamblia reveals that the N-terminus of this class I aminoacyl-tRNA synthetase forms a 16-residue α-helix. This helix replaces a β-hairpin that is required by human TrpRS for normal activity and has been inferred to play a similar role in all eukaryotic TrpRS. The primary sequences of TrpRS homologs from several basal eukaryotes including Giardia lack a set of three residues observed to stabilize interactions with this β-hairpin in the human TrpRS. Thus the present structure suggests that the activation reaction mechanism of TrpRS from the basal eukaryote G. lamblia differs from that of higher eukaryotes. Furthermore, the protein as observed in the crystal forms an (α2)2 homotetramer. The canonical dimer interface observed in all previous structures of tryptophanyl-tRNA synthetases is maintained, but in addition each N-terminal α-helix reciprocally interlocks with the equivalent helix from a second dimer to form a dimer of dimers. Although we have no evidence for tetramer formation in vivo, modeling indicates that the crystallographically observed tetrameric structure would be compatible with the tRNA binding mode used by dimeric TrpRS and TyrRS. PMID:20438846

  7. First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns.

    PubMed

    Knapp, Michael; Rohland, Nadin; Weinstock, Jacobo; Baryshnikov, Gennady; Sher, Andrei; Nagel, Doris; Rabeder, Gernot; Pinhasi, Ron; Schmidt, Heiko A; Hofreiter, Michael

    2009-03-01

    Until recently, cave bears were believed to have only inhabited Europe. However, recent morphological evidence suggests that cave bears' geographic range extended as far east as Transbaikalia, Eastern Siberia. These Asian cave bears were morphologically distinct from European cave bears. However, how they related to European lineages remains unclear, stressing the need to assess the phylogenetic and phylogeographic relationship between Asian cave bears and their European relatives. In this work, we address this issue using a 227 base-pair fragment of the mitochondrial control region obtained from nine fossil bone samples from eight sites from the Urals, Caucasus, Altai Mountains, Ukraine and Yana River region in Eastern Siberia. Results of the phylogenetic analyses indicate that (i) the cave bear from the Yana River is most closely related to cave bears from the Caucasus region; (ii) the Caucasus/Yana group of bears is genetically very distinct from both European cave bears and brown bears, suggesting that these bears could represent an independent species; and (iii) the Western European cave bear lineage reached at least temporarily to the Altai Mountains, 7000 km east of their known centre of distribution. These results suggest that the diversity of cave bears was greater than previously believed, and that they could survive in a much wider range of ecological conditions than previously assumed. They also agree with recent studies on other extinct and extant species, such as wolves, hyenas and steppe bison, which have also revealed higher genetic and ecological diversity in Pleistocene populations than previously known. PMID:19226321

  8. Oligocene primates from China reveal divergence between African and Asian primate evolution.

    PubMed

    Ni, Xijun; Li, Qiang; Li, Lüzhou; Beard, K Christopher

    2016-05-01

    Profound environmental and faunal changes are associated with climatic deterioration during the Eocene-Oligocene transition (EOT) roughly 34 million years ago. Reconstructing how Asian primates responded to the EOT has been hindered by a sparse record of Oligocene primates on that continent. Here, we report the discovery of a diverse primate fauna from the early Oligocene of southern China. In marked contrast to Afro-Arabian Oligocene primate faunas, this Asian fauna is dominated by strepsirhines. There appears to be a strong break between Paleogene and Neogene Asian anthropoid assemblages. Asian and Afro-Arabian primate faunas responded differently to EOT climatic deterioration, indicating that the EOT functioned as a critical evolutionary filter constraining the subsequent course of primate evolution across the Old World. PMID:27151861

  9. Predicting functional divergence in protein evolution by site-specific rate shifts

    NASA Technical Reports Server (NTRS)

    Gaucher, Eric A.; Gu, Xun; Miyamoto, Michael M.; Benner, Steven A.

    2002-01-01

    Most modern tools that analyze protein evolution allow individual sites to mutate at constant rates over the history of the protein family. However, Walter Fitch observed in the 1970s that, if a protein changes its function, the mutability of individual sites might also change. This observation is captured in the "non-homogeneous gamma model", which extracts functional information from gene families by examining the different rates at which individual sites evolve. This model has recently been coupled with structural and molecular biology to identify sites that are likely to be involved in changing function within the gene family. Applying this to multiple gene families highlights the widespread divergence of functional behavior among proteins to generate paralogs and orthologs.

  10. Diverging drought resistance of Scots pine provenances revealed by infrared thermography and mortality

    NASA Astrophysics Data System (ADS)

    Seidel, Hannes; Schunk, Christian; Matiu, Michael; Menzel, Annette

    2016-04-01

    Climate warming and more frequent and severe drought events will alter the adaptedness and fitness of tree species. Especially, Scots pine forests have been affected above average by die-off events during the last decades. Assisted migration of adapted provenances might help alleviating impacts by recent climate change and successfully regenerating forests. However, the identification of suitable provenances based on established ecophysiological methods is time consuming, sometimes invasive, and data on provenance-specific mortality are lacking. We studied the performance, stress and survival of potted Scots pine seedlings from 12 European provenances grown in a greenhouse experiment with multiple drought and warming treatments. In this paper, we will present results of drought stress impacts monitored with four different thermal indices derived from infrared thermography imaging as well as an ample mortality study. Percent soil water deficit (PSWD) was shown to be the main driver of drought stress response in all thermal indices. In spite of wet and dry reference surfaces, however, fluctuating environmental conditions, mainly in terms of air temperature and humidity, altered the measured stress response. In linear mixed-effects models, besides PSWD and meteorological covariates, the factors provenance and provenance - PSWD interactions were included. The explanatory power of the models (R2) ranged between 0.51 to 0.83 and thus, provenance-specific responses to strong and moderate drought and subsequent recovery were revealed. However, obvious differences in the response magnitude of provenances to drought were difficult to explicitly link to general features such Mediterranean - continental type or climate at the provenances' origin. We conclude that seedlings' drought resistance may be linked to summer precipitation and their experienced stress levels are a.o. dependent on their above ground dimensions under given water supply. In respect to mortality, previous

  11. Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence

    PubMed Central

    Blekhman, Ran; Perry, George H.; Shahbaz, Sevini; Fiehn, Oliver; Clark, Andrew G.; Gilad, Yoav

    2014-01-01

    Human diets differ from those of non-human primates. Among few obvious differences, humans consume more meat than most non-human primates and regularly cook their food. It is hypothesized that a dietary shift during human evolution has been accompanied by molecular adaptations in metabolic pathways. Consistent with this notion, comparative studies of gene expression levels in primates have found that the regulation of genes with metabolic functions tend to evolve rapidly in the human lineage. The metabolic consequences of these regulatory differences, however, remained unknown. To address this gap, we performed a comparative study using a combination of gene expression and metabolomic profiling in livers from humans, chimpanzees, and rhesus macaques. We show that dietary differences between species have a strong effect on metabolic concentrations. In addition, we found that differences in metabolic concentration across species are correlated with inter-species differences in the expression of the corresponding enzymes, which control the same metabolic reaction. We identified a number of metabolic compounds with lineage-specific profiles, including examples of human-species metabolic differences that may be directly related to dietary differences. PMID:25069065

  12. Virome Analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks Reveals Novel Highly Divergent Vertebrate and Invertebrate Viruses

    PubMed Central

    Williams, Simon Hedley; Sameroff, Stephen; Sanchez Leon, Maria; Jain, Komal; Lipkin, W. Ian

    2014-01-01

    ABSTRACT A wide range of bacterial pathogens have been identified in ticks, yet the diversity of viruses in ticks is largely unexplored. In the United States, Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis are among the principal tick species associated with pathogen transmission. We used high-throughput sequencing to characterize the viromes of these tick species and identified the presence of Powassan virus and eight novel viruses. These included the most divergent nairovirus described to date, two new clades of tick-borne phleboviruses, a mononegavirus, and viruses with similarity to plant and insect viruses. Our analysis revealed that ticks are reservoirs for a wide range of viruses and suggests that discovery and characterization of tick-borne viruses will have implications for viral taxonomy and may provide insight into tick-transmitted diseases. IMPORTANCE Ticks are implicated as vectors of a wide array of human and animal pathogens. To better understand the extent of tick-borne diseases, it is crucial to uncover the full range of microbial agents associated with ticks. Our current knowledge of the diversity of tick-associated viruses is limited, in part due to the lack of investigation of tick viromes. In this study, we examined the viromes of three tick species from the United States. We found that ticks are hosts to highly divergent viruses across several taxa, including ones previously associated with human disease. Our data underscore the diversity of tick-associated viruses and provide the foundation for further studies into viral etiology of tick-borne diseases. PMID:25056893

  13. Highly Divergent Integration Profile of Adeno-Associated Virus Serotype 5 Revealed by High-Throughput Sequencing

    PubMed Central

    Janovitz, Tyler; Oliveira, Thiago; Sadelain, Michel

    2014-01-01

    ABSTRACT Adeno-associated virus serotype 5 (AAV-5) is a human parvovirus that infects a high percentage of the population. It is the most divergent AAV, the DNA sequence cleaved by the viral endonuclease is distinct from all other described serotypes and, uniquely, AAV-5 does not cross-complement the replication of other serotypes. In contrast to the well-characterized integration of AAV-2, no published studies have investigated the genomic integration of AAV-5. In this study, we analyzed more than 660,000 AAV-5 integration junctions using high-throughput integrant capture sequencing of infected human cells. The integration activity of AAV-5 was 99.7% distinct from AAV-2 and favored intronic sequences. Genome-wide integration was highly correlated with viral replication protein binding and endonuclease sites, and a 39-bp consensus integration motif was revealed that included these features. Algorithmic scanning identified 126 AAV-5 hot spots, the largest of which encompassed 3.3% of all integration events. The unique aspects of AAV-5 integration may provide novel tools for biotechnology and gene therapy. IMPORTANCE Viral integration into the host genome is an important aspect of virus host cell biology. Genomic integration studies of the small single-stranded AAVs have largely focused on site preferential integration of AAV-2, which depends on the viral replication protein (Rep). We have now established the first genome wide integration profile of the highly divergent AAV-5 serotype. Using integrant capture sequencing, more than 600,000 AAV-5 integration junctions in human cells were analyzed. AAV-5 integration hot spots were 99.7% distinct from AAV-2. Integration favored intronic sequences, occurred on all chromosomes, and integration hot spot distribution was correlated with human genomic GAGC repeats and transcriptional activity. These features support expansion of AAV-5 based vectors for gene transfer considerations. PMID:24335317

  14. Functional divergence and convergence between the transcript network and gene network in lung adenocarcinoma

    PubMed Central

    Hsu, Min-Kung; Pan, Chia-Lin; Chen, Feng-Chi

    2016-01-01

    Introduction Alternative RNA splicing is a critical regulatory mechanism during tumorigenesis. However, previous oncological studies mainly focused on the splicing of individual genes. Whether and how transcript isoforms are coordinated to affect cellular functions remain underexplored. Also of great interest is how the splicing regulome cooperates with the transcription regulome to facilitate tumorigenesis. The answers to these questions are of fundamental importance to cancer biology. Results Here, we report a comparative study between the transcript-based network (TN) and the gene-based network (GN) derived from the transcriptomes of paired tumor–normal tissues from 77 lung adenocarcinoma patients. We demonstrate that the two networks differ significantly from each other in terms of patient clustering and the number and functions of network modules. Interestingly, the majority (89.5%) of multi-transcript genes have their transcript isoforms distributed in at least two TN modules, suggesting regulatory and functional divergences between transcript isoforms. Furthermore, TN and GN modules share onlŷ50%–60% of their biological functions. TN thus appears to constitute a regulatory layer separate from GN. Nevertheless, our results indicate that functional convergence and divergence both occur between TN and GN, implying complex interactions between the two regulatory layers. Finally, we report that the expression profiles of module members in both TN and GN shift dramatically yet concordantly during tumorigenesis. The mechanisms underlying this coordinated shifting remain unclear yet are worth further explorations. Conclusion We show that in lung adenocarcinoma, transcript isoforms per se are coordinately regulated to conduct biological functions not conveyed by the network of genes. However, the two networks may interact closely with each other by sharing the same or related biological functions. Unraveling the effects and mechanisms of such interactions will

  15. Positive Selection and Functional Divergence of R2R3-MYB Paralogous Genes Expressed in Inflorescence Buds of Scutellaria Species (Labiatae)

    PubMed Central

    Huang, Bing-Hong; Pang, Erli; Chen, Yi-Wen; Cao, Huifen; Ruan, Yu; Liao, Pei-Chun

    2015-01-01

    Anthocyanin is the main pigment forming floral diversity. Several transcription factors that regulate the expression of anthocyanin biosynthetic genes belong to the R2R3-MYB family. Here we examined the transcriptomes of inflorescence buds of Scutellaria species (skullcaps), identified the expression R2R3-MYBs, and detected the genetic signatures of positive selection for adaptive divergence across the rapidly evolving skullcaps. In the inflorescence buds, seven R2R3-MYBs were identified. MYB11 and MYB16 were detected to be positively selected. The signature of positive selection on MYB genes indicated that species diversification could be affected by transcriptional regulation, rather than at the translational level. When comparing among the background lineages of Arabidopsis, tomato, rice, and Amborella, heterogeneous evolutionary rates were detected among MYB paralogs, especially between MYB13 and MYB19. Significantly different evolutionary rates were also evidenced by type-I functional divergence between MYB13 and MYB19, and the accelerated evolutionary rates in MYB19, implied the acquisition of novel functions. Another paralogous pair, MYB2/7 and MYB11, revealed significant radical amino acid changes, indicating divergence in the regulation of different anthocyanin-biosynthetic enzymes. Our findings not only showed that Scutellaria R2R3-MYBs are functionally divergent and positively selected, but also indicated the adaptive relevance of regulatory genes in floral diversification. PMID:25782156

  16. Positive selection and functional divergence of R2R3-MYB paralogous genes expressed in inflorescence buds of Scutellaria species (Labiatae).

    PubMed

    Huang, Bing-Hong; Pang, Erli; Chen, Yi-Wen; Cao, Huifen; Ruan, Yu; Liao, Pei-Chun

    2015-01-01

    Anthocyanin is the main pigment forming floral diversity. Several transcription factors that regulate the expression of anthocyanin biosynthetic genes belong to the R2R3-MYB family. Here we examined the transcriptomes of inflorescence buds of Scutellaria species (skullcaps), identified the expression R2R3-MYBs, and detected the genetic signatures of positive selection for adaptive divergence across the rapidly evolving skullcaps. In the inflorescence buds, seven R2R3-MYBs were identified. MYB11 and MYB16 were detected to be positively selected. The signature of positive selection on MYB genes indicated that species diversification could be affected by transcriptional regulation, rather than at the translational level. When comparing among the background lineages of Arabidopsis, tomato, rice, and Amborella, heterogeneous evolutionary rates were detected among MYB paralogs, especially between MYB13 and MYB19. Significantly different evolutionary rates were also evidenced by type-I functional divergence between MYB13 and MYB19, and the accelerated evolutionary rates in MYB19, implied the acquisition of novel functions. Another paralogous pair, MYB2/7 and MYB11, revealed significant radical amino acid changes, indicating divergence in the regulation of different anthocyanin-biosynthetic enzymes. Our findings not only showed that Scutellaria R2R3-MYBs are functionally divergent and positively selected, but also indicated the adaptive relevance of regulatory genes in floral diversification. PMID:25782156

  17. Innate-like functions of natural killer T cell subsets result from highly divergent gene programs.

    PubMed

    Engel, Isaac; Seumois, Grégory; Chavez, Lukas; Samaniego-Castruita, Daniela; White, Brandie; Chawla, Ashu; Mock, Dennis; Vijayanand, Pandurangan; Kronenberg, Mitchell

    2016-06-01

    Natural killer T cells (NKT cells) have stimulatory or inhibitory effects on the immune response that can be attributed in part to the existence of functional subsets of NKT cells. These subsets have been characterized only on the basis of the differential expression of a few transcription factors and cell-surface molecules. Here we have analyzed purified populations of thymic NKT cell subsets at both the transcriptomic level and epigenomic level and by single-cell RNA sequencing. Our data indicated that despite their similar antigen specificity, the functional NKT cell subsets were highly divergent populations with many gene-expression and epigenetic differences. Therefore, the thymus 'imprints' distinct gene programs on subsets of innate-like NKT cells that probably impart differences in proliferative capacity, homing, and effector functions. PMID:27089380

  18. Divergent brain functional network alterations in dementia with Lewy bodies and Alzheimer's disease

    PubMed Central

    Peraza, Luis R.; Taylor, John-Paul; Kaiser, Marcus

    2015-01-01

    The clinical phenotype of dementia with Lewy bodies (DLB) is different from Alzheimer's disease (AD), suggesting a divergence between these diseases in terms of brain network organization. To fully understand this, we studied functional networks from resting-state functional magnetic resonance imaging in cognitively matched DLB and AD patients. The DLB group demonstrated a generalized lower synchronization compared with the AD and healthy controls, and this was more severe for edges connecting distant brain regions. Global network measures were significantly different between DLB and AD. For instance, AD showed lower small-worldness than healthy controls, while DLB showed higher small-worldness (AD < controls < DLB), and this was also the case for global efficiency (DLB > controls > AD) and clustering coefficient (DLB < controls < AD). Differences were also found for nodal measures at brain regions associated with each disease. Finally, we found significant associations between network performance measures and global cognitive impairment and severity of cognitive fluctuations in DLB. These results show network divergences between DLB and AD which appear to reflect their neuropathological differences. PMID:26115566

  19. Functional convergence and divergence of mating-type genes fulfilling in Cordyceps militaris.

    PubMed

    Lu, Yuzhen; Xia, Yongliang; Luo, Feifei; Dong, Caihong; Wang, Chengshu

    2016-03-01

    Fungal sexual lives are considerably diversified in terms of the types of mating systems and mating-control gene functions. Sexual fruiting bodies of the ascomycete fungus Cordyceps militaris have been widely consumed as edible and medicinal mushrooms, whereas the regulation of fruiting-body development and sex in this fungus remain elusive. Herein, we performed the comprehensive functional analyses of mating-type (MAT) genes in C. militaris. Interspecies functional convergence was evident that MAT1-1 and MAT1-2-1 null mutants were sterile and lost the ability to produce stromata in outcrosses with the opposite mating-type partner. In contrast to other fungal species, functional divergence of MAT1-1-1 and MAT1-1-2 was also observed that ΔMAT1-1-1 produced barren stromata in outcrosses, whereas ΔMAT1-1-2 generated fruiting bodies morphologically similar to that of the parental strain but with sterile perithecia. The homothallic-like transformants MAT1-2::MAT1-1-1 (haploidic MAT1-2 isolate transformed with the MAT1-1-1 gene) produced sterile stromata, whereas the MAT1-1::MAT1-2-1 (haploidic MAT1-1 isolate transformed with the MAT1-2-1 gene) mutant was determined to be completely fruitless. The findings relating to the fully fertile gene-complementation mutants suggest that the genomic location is not essential for the MAT genes to fulfill their functions in C. militaris. Comparison of the production of bioactive constituents cordycepin and adenosine provides experimental support that the fungal sexual cycle is an energy consuming process. The results of the present study enrich our knowledge of both convergent and divergent controls of fungal sex. PMID:26812121

  20. Comparative Genomic Hybridizations Reveal Genetic Regions within the Mycobacterium avium Complex That Are Divergent from Mycobacterium avium subsp. paratuberculosis Isolates†

    PubMed Central

    Paustian, Michael L.; Kapur, Vivek; Bannantine, John P.

    2005-01-01

    Mycobacterium avium subsp. paratuberculosis is genetically similar to other members of the Mycobacterium avium complex (MAC), some of which are nonpathogenic and widespread in the environment. We have utilized an M. avium subsp. paratuberculosis whole-genome microarray representing over 95% of the predicted coding sequences to examine the genetic conservation among 10 M. avium subsp. paratuberculosis isolates, two isolates each of Mycobacterium avium subsp. silvaticum and Mycobacterium avium subsp. avium, and a single isolate each of both Mycobacterium intracellulare and Mycobacterium smegmatis. Genomic DNA from each isolate was competitively hybridized with DNA from M. avium subsp. paratuberculosis K10, and open reading frames (ORFs) were classified as present, divergent, or intermediate. None of the M. avium subsp. paratuberculosis isolates had ORFs classified as divergent. The two M. avium subsp. avium isolates had 210 and 135 divergent ORFs, while the two M. avium subsp. silvaticum isolates examined had 77 and 103 divergent ORFs. Similarly, 130 divergent ORFs were identified in M. intracellulare. A set of 97 ORFs were classified as divergent or intermediate in all of the nonparatuberculosis MAC isolates tested. Many of these ORFs are clustered together on the genome in regions with relatively low average GC content compared with the entire genome and contain mobile genetic elements. One of these regions of sequence divergence contained genes homologous to a mammalian cell entry (mce) operon. Our results indicate that closely related MAC mycobacteria can be distinguished from M. avium subsp. paratuberculosis by multiple clusters of divergent ORFs. PMID:15774884

  1. Functional divergence outlines the evolution of novel protein function in NifH/BchL protein family.

    PubMed

    Thakur, Subarna; Bothra, Asim K; Sen, Arnab

    2013-11-01

    Biological nitrogen fixation is accomplished by prokaryotes through the catalytic action of complex metalloenzyme, nitrogenase. Nitrogenase is a two-protein component system comprising MoFe protein (NifD and K) and Fe protein (NifH). NifH shares structural and mechanistic similarities as well as evolutionary relationships with light-independent protochlorophyllide reductase (BchL), a photosynthesis-related metalloenzyme belonging to the same protein family. We performed a comprehensive bioinformatics analysis of the NifH/BchL family in order to elucidate the intrinsic functional diversity and the underlying evolutionary mechanism among the members. To analyse functional divergence in the NifH/ BchL family, we have conducted pair-wise estimation in altered evolutionary rates between the member proteins. We identified a number of vital amino acid sites which contribute to predicted functional diversity. We have also made use of the maximum likelihood tests for detection of positive selection at the amino acid level followed by the structure-based phylogenetic approach to draw conclusion on the ancient lineage and novel characterization of the NifH/BchL protein family. Our investigation provides ample support to the fact that NifH protein and BchL share robust structural similarities and have probably deviated from a common ancestor followed by divergence in functional properties possibly due to gene duplication. PMID:24287653

  2. Transcriptome profiling reveals divergent expression shifts in brown and white adipose tissue from long-lived GHRKO mice

    PubMed Central

    Zhi, Xu; Rohde, Kyle; List, Edward O.; Berryman, Darlene E.; Kopchick, John J.; Gesing, Adam; Fang, Yimin; Masternak, Michal M.

    2015-01-01

    Mice lacking the growth hormone receptor (GHRKO) exhibit improved lifespan and healthspan due to loss of growth hormone signaling. Both the distribution and activity of brown and white adipose tissue (BAT and WAT) are altered in GHRKO mice, but the contribution of each tissue to age-related phenotypes has remained unclear. We therefore used whole-genome microarrays to evaluate transcriptional differences in BAT and WAT depots between GHRKO and normal littermates at six months of age. Our findings reveal a unique BAT transcriptome as well as distinctive responses of BAT to Ghr ablation. BAT from GHRKO mice exhibited elevated expression of genes associated with mitochondria and metabolism, along with reduced expression of genes expressed by monocyte-derived cells (dendritic cells [DC] and macrophages). Largely the opposite was observed in WAT, with increased expression of DC-expressed genes and reduced expression of genes associated with metabolism, cellular respiration and the mitochondrial inner envelope. These findings demonstrate divergent response patterns of BAT and WAT to loss of GH signaling in GHRKO mice. These patterns suggest both BAT and WAT contribute in different ways to phenotypes in GHRKO mice, with Ghr ablation blunting inflammation in BAT as well as cellular metabolism and mitochondrial biogenesis in WAT. PMID:26436954

  3. Transcriptome profiling reveals divergent expression shifts in brown and white adipose tissue from long-lived GHRKO mice.

    PubMed

    Stout, Michael B; Swindell, William R; Zhi, Xu; Rohde, Kyle; List, Edward O; Berryman, Darlene E; Kopchick, John J; Gesing, Adam; Fang, Yimin; Masternak, Michal M

    2015-09-29

    Mice lacking the growth hormone receptor (GHRKO) exhibit improved lifespan and healthspan due to loss of growth hormone signaling. Both the distribution and activity of brown and white adipose tissue (BAT and WAT) are altered in GHRKO mice, but the contribution of each tissue to age-related phenotypes has remained unclear. We therefore used whole-genome microarrays to evaluate transcriptional differences in BAT and WAT depots between GHRKO and normal littermates at six months of age. Our findings reveal a unique BAT transcriptome as well as distinctive responses of BAT to Ghr ablation. BAT from GHRKO mice exhibited elevated expression of genes associated with mitochondria and metabolism, along with reduced expression of genes expressed by monocyte-derived cells (dendritic cells [DC] and macrophages). Largely the opposite was observed in WAT, with increased expression of DC-expressed genes and reduced expression of genes associated with metabolism, cellular respiration and the mitochondrial inner envelope. These findings demonstrate divergent response patterns of BAT and WAT to loss of GH signaling in GHRKO mice. These patterns suggest both BAT and WAT contribute in different ways to phenotypes in GHRKO mice, with Ghr ablation blunting inflammation in BAT as well as cellular metabolism and mitochondrial biogenesis in WAT. PMID:26436954

  4. Efficient projection and backprojection scheme for spherically symmetric basis functions in divergent beam geometry

    SciTech Connect

    Ziegler, Andy; Koehler, Thomas; Nielsen, Tim; Proksa, Roland

    2006-12-15

    In cone-beam transmission tomography the measurements are performed with a divergent beam of x-rays. The reconstruction with iterative methods is an approach that offers the possibility to reconstruct the corresponding images directly from these measurements. Another approach based on spherically symmetric basis functions (blobs) has been reported with results demonstrating a better image quality for iterative reconstruction algorithms. When combining the two approaches (i.e., using blobs in iterative cone-beam reconstruction of divergent rays) the problem of blob sampling without introducing aliasing must be addressed. One solution to this problem is to select a blob size large enough to ensure a sufficient sampling, but this prevents a high resolution reconstruction, which is not desired. Another solution is a heuristic low-pass filtering, which removes this aliasing, but neglects the different contributions of blobs to the absorption depending on the spatial position in the volume and, therefore, cannot achieve the best image quality. This article presents a model of sampling the blobs which is motivated by the beam geometry. It can be used for high resolution reconstruction and can be implemented efficiently.

  5. Direct comparison of mice null for liver or intestinal fatty acid-binding proteins reveals highly divergent phenotypic responses to high fat feeding.

    PubMed

    Gajda, Angela M; Zhou, Yin Xiu; Agellon, Luis B; Fried, Susan K; Kodukula, Sarala; Fortson, Walter; Patel, Khamoshi; Storch, Judith

    2013-10-18

    The enterocyte expresses two fatty acid-binding proteins (FABP), intestinal FABP (IFABP; FABP2) and liver FABP (LFABP; FABP1). LFABP is also expressed in liver. Despite ligand transport and binding differences, it has remained uncertain whether these intestinally coexpressed proteins, which both bind long chain fatty acids (FA), are functionally distinct. Here, we directly compared IFABP(-/-) and LFABP(-/-) mice fed high fat diets containing long chain saturated or unsaturated fatty acids, reasoning that providing an abundance of dietary lipid would reveal unique functional properties. The results showed that mucosal lipid metabolism was indeed differentially modified, with significant decreases in FA incorporation into triacylglycerol (TG) relative to phospholipid (PL) in IFABP(-/-) mice, whereas LFABP(-/-) mice had reduced monoacylglycerol incorporation in TG relative to PL, as well as reduced FA oxidation. Interestingly, striking differences were found in whole body energy homeostasis; LFABP(-/-) mice fed high fat diets became obese relative to WT, whereas IFABP(-/-) mice displayed an opposite, lean phenotype. Fuel utilization followed adiposity, with LFABP(-/-) mice preferentially utilizing lipids, and IFABP(-/-) mice preferentially metabolizing carbohydrate for energy production. Changes in body weight and fat may arise, in part, from altered food intake; mucosal levels of the endocannabinoids 2-arachidonoylglycerol and arachidonoylethanolamine were elevated in LFABP(-/-), perhaps contributing to increased energy intake. This direct comparison provides evidence that LFABP and IFABP have distinct roles in intestinal lipid metabolism; differential intracellular functions in intestine and in liver, for LFABP(-/-) mice, result in divergent downstream effects at the systemic level. PMID:23990461

  6. Reevaluation of a classic phylogeographic barrier: new techniques reveal the influence of microgeographic climate variation on population divergence

    PubMed Central

    Soto-Centeno, J Angel; Barrow, Lisa N; Allen, Julie M; Reed, David L

    2013-01-01

    We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis-based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow in Southeastern United States (Alabama, Florida, and Georgia). Our DNA sequence dataset confirmed and strongly supported two distinct lineages within G. pinetis occurring east and west of the ARD. Divergence date estimates showed that eastern and western lineages diverged about 1.37 Ma (1.9 Ma–830 ka). Predicted distributions from ENMs were consistent with molecular data and defined each population east and west of the ARD with little overlap. Niche identity and background similarity tests were statistically significant suggesting that ENMs from eastern and western lineages are not identical or more similar than expected based on random localities drawn from the environmental background. ENMs also support the hypothesis that the ARD represents a ribbon of unsuitable climate between more suitable areas where these populations are distributed. The estimated age of divergence between eastern and western lineages of G. pinetis suggests that the divergence was driven by climatic conditions during Pleistocene glacial–interglacial cycles. The ARD at the contact zone of eastern and western lineages of G. pinetis forms a significant barrier promoting microgeographic isolation that helps maintain ecological and genetic divergence. PMID:23789071

  7. Reevaluation of a classic phylogeographic barrier: new techniques reveal the influence of microgeographic climate variation on population divergence.

    PubMed

    Soto-Centeno, J Angel; Barrow, Lisa N; Allen, Julie M; Reed, David L

    2013-06-01

    We evaluated the mtDNA divergence and relationships within Geomys pinetis to assess the status of formerly recognized Geomys taxa. Additionally, we integrated new hypothesis-based tests in ecological niche models (ENM) to provide greater insight into causes for divergence and potential barriers to gene flow in Southeastern United States (Alabama, Florida, and Georgia). Our DNA sequence dataset confirmed and strongly supported two distinct lineages within G. pinetis occurring east and west of the ARD. Divergence date estimates showed that eastern and western lineages diverged about 1.37 Ma (1.9 Ma-830 ka). Predicted distributions from ENMs were consistent with molecular data and defined each population east and west of the ARD with little overlap. Niche identity and background similarity tests were statistically significant suggesting that ENMs from eastern and western lineages are not identical or more similar than expected based on random localities drawn from the environmental background. ENMs also support the hypothesis that the ARD represents a ribbon of unsuitable climate between more suitable areas where these populations are distributed. The estimated age of divergence between eastern and western lineages of G. pinetis suggests that the divergence was driven by climatic conditions during Pleistocene glacial-interglacial cycles. The ARD at the contact zone of eastern and western lineages of G. pinetis forms a significant barrier promoting microgeographic isolation that helps maintain ecological and genetic divergence. PMID:23789071

  8. Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis

    PubMed Central

    2012-01-01

    Background Following gene duplication, retained paralogs undergo functional divergence, which is reflected in changes in DNA sequence and expression patterns. The extent of divergence is influenced by several factors, including protein function. We examine whether an epigenetic modification, trimethylation of histone H3 at lysine 27 (H3K27me3), could be a factor in the evolution of expression patterns after gene duplication. Whereas in animals this repressive mark for transcription is deposited on long regions of DNA, in plants its localization is gene-specific. Because of this and a well-annotated recent whole-genome duplication, Arabidopsis thaliana is uniquely suited for studying the potential association of H3K27me3 with the evolutionary fate of genes. Results Paralogous pairs with H3K27me3 show the highest coding sequence divergence, which can be explained by their low expression levels. Interestingly, they also show the highest similarity in expression patterns and upstream regulatory regions, while paralogous pairs where only one gene is an H3K27me3 target show the highest divergence in expression patterns and upstream regulatory sequence. These trends in divergence of expression and upstream regions are especially pronounced for transcription factors. Conclusions After duplication, a histone modification can be associated with a particular fate of paralogs: H3K27me3 is linked to lower expression divergence yet higher coding sequence divergence. Our results show that H3K27me3 constrains expression divergence after duplication. Moreover, its association with higher conservation of upstream regions provides a potential mechanism for the conserved H3K27me3 targeting of the paralogs. PMID:23034476

  9. Comparative microanatomy of the orbicularis oris muscle between chimpanzees and humans: evolutionary divergence of lip function

    PubMed Central

    Rogers, Carolyn R; Mooney, Mark P; Smith, Timothy D; Weinberg, Seth M; Waller, Bridget M; Parr, Lisa A; Docherty, Beth A; Bonar, Christopher J; Reinholt, Lauren E; Deleyiannis, Frederic W-B; Siegel, Michael I; Marazita, Mary L; Burrows, Anne M

    2009-01-01

    The orbicularis oris muscle plays a role in the production of primate facial expressions and vocalizations, nutrient intake, and in some non-human primates it is used as a prehensile, manipulative tool. As the chimpanzee (Pan troglodytes) is the closest living relative of humans, a comparison of the orbicularis oris muscle between these species may increase our understanding of the morphological specializations related to the differing functional demands of their lips and the factors responsible for their divergent evolution. To this end, this study compares the microanatomy of the mid-line upper fibers of the orbicularis oris muscle between chimpanzees and humans. A mid-line portion of the orbicularis oris muscle was harvested from the upper lips of three chimpanzee and five human cadavers. The sampled blocks included the area between the lateral borders of the nasal alar cartilages in both species. Each sample was processed for paraffin histology, sectioned and stained with a variety of protocols. Sections were examined for fiber direction and relative thickness of muscle layers. Ratios of cross-sectional connective tissue area vs. cross-sectional muscle tissue area, muscle fiber diameter and relative dermal thickness were calculated for each species. In both species, a clear pars marginalis layer was recognized, contrary to previous reports that only humans possess this layer. In chimpanzees, the relative fiber diameter and relative amount of muscle tissue (i.e. based on ratio of connective tissue area : muscle tissue area) were significantly (P < 0.05) greater than in humans. In contrast, measurements of relative dermal thickness showed that humans have a greater average dermal thickness of the upper lip than chimpanzees. Taken together, these results suggest that both human and chimpanzee orbicularis oris muscle upper fibers meet the specific functional demands associated with their divergent vocal and facial display repertoires, the development of human

  10. Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition

    PubMed Central

    Yooseph, Shibu; Ininbergs, Karolina; Goll, Johannes; Asplund-Samuelsson, Johannes; McCrow, John P.; Celepli, Narin; Allen, Lisa Zeigler; Ekman, Martin; Lucas, Andrew J.; Hagström, Åke; Thiagarajan, Mathangi; Brindefalk, Björn; Richter, Alexander R.; Andersson, Anders F.; Tenney, Aaron; Lundin, Daniel; Tovchigrechko, Andrey; Nylander, Johan A. A.; Brami, Daniel; Badger, Jonathan H.; Allen, Andrew E.; Rusch, Douglas B.; Hoffman, Jeff; Norrby, Erling; Friedman, Robert; Pinhassi, Jarone; Venter, J. Craig; Bergman, Birgitta

    2014-01-01

    Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity. PMID:24586863

  11. Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

    PubMed

    Dupont, Chris L; Larsson, John; Yooseph, Shibu; Ininbergs, Karolina; Goll, Johannes; Asplund-Samuelsson, Johannes; McCrow, John P; Celepli, Narin; Allen, Lisa Zeigler; Ekman, Martin; Lucas, Andrew J; Hagström, Åke; Thiagarajan, Mathangi; Brindefalk, Björn; Richter, Alexander R; Andersson, Anders F; Tenney, Aaron; Lundin, Daniel; Tovchigrechko, Andrey; Nylander, Johan A A; Brami, Daniel; Badger, Jonathan H; Allen, Andrew E; Rusch, Douglas B; Hoffman, Jeff; Norrby, Erling; Friedman, Robert; Pinhassi, Jarone; Venter, J Craig; Bergman, Birgitta

    2014-01-01

    Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity. PMID:24586863

  12. Phylogeography of Australia's king brown snake (Pseudechis australis) reveals Pliocene divergence and Pleistocene dispersal of a top predator.

    PubMed

    Kuch, Ulrich; Keogh, J Scott; Weigel, John; Smith, Laurie A; Mebs, Dietrich

    2005-03-01

    King brown snakes or mulga snakes (Pseudechis australis) are the largest and among the most dangerous and wide-ranging venomous snakes in Australia and New Guinea. They occur in diverse habitats, are important predators, and exhibit considerable morphological variation. We infer the relationships and historical biogeography of P. australis based on phylogenetic analysis of 1,249 base pairs from the mitochondrial cytochrome b, NADH dehydrogenase subunit 4 and three adjacent tRNA genes using Bayesian, maximum-likelihood, and maximum-parsimony methods. All methods reveal deep phylogenetic structure with four strongly supported clades comprising snakes from New Guinea (I), localities all over Australia (II), the Kimberleys of Western Australia (III), and north-central Australia (IV), suggesting a much more ancient radiation than previously believed. This conclusion is robust to different molecular clock estimations indicating divergence in Pliocene or Late Miocene, after landbridge dispersal to New Guinea had occurred. While members of clades I, III and IV are medium-sized, slender snakes, those of clade II attain large sizes and a robust build, rendering them top predators in their ecosystems. Genetic differentiation within clade II is low and haplotype distribution largely incongruent with geography or colour morphs, suggesting Pleistocene dispersal and recent ecomorph evolution. Significant haplotype diversity exists in clades III and IV, implying that clade IV comprises two species. Members of clade II are broadly sympatric with members of both northern Australian clades. Thus, our data support the recognition of at least five species from within P. australis (auct.) under various criteria. We discuss biogeographical, ecological and medical implications of our findings. PMID:15688185

  13. Phylogeography of Australia's king brown snake (Pseudechis australis) reveals Pliocene divergence and Pleistocene dispersal of a top predator

    NASA Astrophysics Data System (ADS)

    Kuch, Ulrich; Keogh, J. Scott; Weigel, John; Smith, Laurie A.; Mebs, Dietrich

    2005-03-01

    King brown snakes or mulga snakes (Pseudechis australis) are the largest and among the most dangerous and wide-ranging venomous snakes in Australia and New Guinea. They occur in diverse habitats, are important predators, and exhibit considerable morphological variation. We infer the relationships and historical biogeography of P. australis based on phylogenetic analysis of 1,249 base pairs from the mitochondrial cytochrome b, NADH dehydrogenase subunit 4 and three adjacent tRNA genes using Bayesian, maximum-likelihood, and maximum-parsimony methods. All methods reveal deep phylogenetic structure with four strongly supported clades comprising snakes from New Guinea (I), localities all over Australia (II), the Kimberleys of Western Australia (III), and north-central Australia (IV), suggesting a much more ancient radiation than previously believed. This conclusion is robust to different molecular clock estimations indicating divergence in Pliocene or Late Miocene, after landbridge dispersal to New Guinea had occurred. While members of clades I, III and IV are medium-sized, slender snakes, those of clade II attain large sizes and a robust build, rendering them top predators in their ecosystems. Genetic differentiation within clade II is low and haplotype distribution largely incongruent with geography or colour morphs, suggesting Pleistocene dispersal and recent ecomorph evolution. Significant haplotype diversity exists in clades III and IV, implying that clade IV comprises two species. Members of clade II are broadly sympatric with members of both northern Australian clades. Thus, our data support the recognition of at least five species from within P. australis (auct.) under various criteria. We discuss biogeographical, ecological and medical implications of our findings.

  14. Functional and population genomic divergence within and between two species of killifish adapted to different osmotic niches.

    PubMed

    Kozak, Genevieve M; Brennan, Reid S; Berdan, Emma L; Fuller, Rebecca C; Whitehead, Andrew

    2014-01-01

    Adaptation to salinity affects species distributions, promotes speciation, and guides many evolutionary patterns in fishes. To uncover the basis of a complex trait like osmoregulation, genome-level analyses are sensible. We combine population genomic scans with genome expression profiling to discover candidate genes and pathways associated with divergence between osmotic environments. We compared transcriptome sequence divergence between multiple freshwater and saltwater populations of the rainwater killifish, Lucania parva. We also compared sequence divergence between L. parva and its sister species, Lucania goodei, a freshwater specialist. We found highly differentiated single nucleotide polymorphisms (SNPs) between freshwater and saltwater L. parva populations in cell junction and ion transport genes, including V-type H(+) ATPase. Between species, we found divergence in reproduction and osmotic stress genes. Genes that were differentially expressed between species during osmotic acclimation included genes involved in ion transport and cell volume regulation. Gene sets that were divergent in coding sequence and divergent in expression did not overlap, although they did converge in function. Like many studies using genomic scans, our approach may miss some loci that contribute to adaptation but have complicated patterns of allelic variation. Our study suggests that gene expression and coding sequence may evolve independently as populations adapt to a complex physiological challenge. PMID:24134703

  15. A Trans-Amazonian Screening of mtDNA Reveals Deep Intraspecific Divergence in Forest Birds and Suggests a Vast Underestimation of Species Diversity

    PubMed Central

    Milá, Borja; Tavares, Erika S.; Muñoz Saldaña, Alberto; Karubian, Jordan; Smith, Thomas B.; Baker, Allan J.

    2012-01-01

    The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%), yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%), with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In-depth phylogeographic surveys

  16. A trans-Amazonian screening of mtDNA reveals deep intraspecific divergence in forest birds and suggests a vast underestimation of species diversity.

    PubMed

    Milá, Borja; Tavares, Erika S; Muñoz Saldaña, Alberto; Karubian, Jordan; Smith, Thomas B; Baker, Allan J

    2012-01-01

    The Amazonian avifauna remains severely understudied relative to that of the temperate zone, and its species richness is thought to be underestimated by current taxonomy. Recent molecular systematic studies using mtDNA sequence reveal that traditionally accepted species-level taxa often conceal genetically divergent subspecific lineages found to represent new species upon close taxonomic scrutiny, suggesting that intraspecific mtDNA variation could be useful in species discovery. Surveys of mtDNA variation in Holarctic species have revealed patterns of variation that are largely congruent with species boundaries. However, little information exists on intraspecific divergence in most Amazonian species. Here we screen intraspecific mtDNA genetic variation in 41 Amazonian forest understory species belonging to 36 genera and 17 families in 6 orders, using 758 individual samples from Ecuador and French Guiana. For 13 of these species, we also analyzed trans-Andean populations from the Ecuadorian Chocó. A consistent pattern of deep intraspecific divergence among trans-Amazonian haplogroups was found for 33 of the 41 taxa, and genetic differentiation and genetic diversity among them was highly variable, suggesting a complex range of evolutionary histories. Mean sequence divergence within families was the same as that found in North American birds (13%), yet mean intraspecific divergence in Neotropical species was an order of magnitude larger (2.13% vs. 0.23%), with mean distance between intraspecific lineages reaching 3.56%. We found no clear relationship between genetic distances and differentiation in plumage color. Our results identify numerous genetically and phenotypically divergent lineages which may result in new species-level designations upon closer taxonomic scrutiny and thorough sampling, although lineages in the tropical region could be older than those in the temperate zone without necessarily representing separate species. In-depth phylogeographic surveys

  17. Differential Selection within the Drosophila Retinal Determination Network and Evidence for Functional Divergence between Paralog Pairs

    PubMed Central

    Datta, Rhea R.; Cruickshank, Tami; Kumar, Justin P.

    2011-01-01

    The retinal determination (RD) network in Drosophila comprises fourteen known nuclear proteins that include DNA binding proteins, transcriptional co-activators, kinases and phosphatases. The composition of the network varies considerably throughout the animal kingdom, with the network in several basal insects having fewer members and with vertebrates having potentially significantly higher numbers of retinal determination genes. One important contributing factor for the variation in gene number within the network is gene duplication. For example, ten members of the RD network in Drosophila are derived from duplication events. Here we present an analysis of the coding regions of the five pairs of duplicate genes from within the retinal determination network of several different Drosophila species. We demonstrate that there is differential selection across the coding regions of all RD genes. Additionally, some of the most significant differences in ratios of non-silent to silent site substitutions (dN/dS) between paralog pairs are found within regions that have no ascribed function. Previous structure/function analyses of several duplicate genes have identified areas within one gene that contain novel activities when compared to its paralog. The evolutionary analysis presented here identifies these same areas in the paralogs as being under high levels of relaxed selection. We suggest that sequence divergence between paralogs and selection signatures can be used as a reasonable predictor of functional changes in rapidly evolving motifs. PMID:21210943

  18. Functional and Structural Divergence of an Unusual LTR Retrotransposon Family in Plants

    PubMed Central

    Iwata, Aiko; Gill, Navdeep; Jackson, Scott A.

    2012-01-01

    Retrotransposons with long terminal repeats (LTRs) more than 3 kb are not frequent in most eukaryotic genomes. Rice LTR retrotransposon, Retrosat2, has LTRs greater than 3.2 kb and two open reading frames (ORF): ORF1 encodes enzymes for retrotransposition whereas no function can be assigned to ORF0 as it is not found in any other organism. A variety of experimental and in silico approaches were used to determine the origin of Retrosat2 and putative function of ORF0. Our data show that not only is Retrosat2 highly abundant in the Oryza genus, it may yet be active in rice. Homologs of Retrosat2 were identified in maize, sorghum, Arabidopsis and other plant genomes suggesting that the Retrosat2 family is of ancient origin. Several putatively cis-acting elements, some multicopy, that regulate retrotransposon replication or responsiveness to environmental factors were found in the LTRs of Retrosat2. Unlike the ORF1, the ORF0 sequences from Retrosat2 and homologs are divergent at the sequence level, 3D-structures and predicted biological functions. In contrast to other retrotransposon families, Retrosat2 and its homologs are dispersed throughout genomes and not concentrated in the specific chromosomal regions, such as centromeres. The genomic distribution of Retrosat2 homologs varies across species which likely reflects the differing evolutionary trajectories of this retrotransposon family across diverse species. PMID:23119066

  19. Divergent immune responses to house dust mite lead to distinct structural-functional phenotypes.

    PubMed

    Johnson, Jill R; Swirski, Filip K; Gajewska, Beata U; Wiley, Ryan E; Fattouh, Ramzi; Pacitto, Stephanie R; Wong, Jonathan K; Stämpfli, Martin R; Jordana, Manel

    2007-09-01

    Asthma is a chronic airway inflammatory disease that encompasses three cardinal processes: T helper (Th) cell type 2 (Th2)-polarized inflammation, bronchial hyperreactivity, and airway wall remodeling. However, the link between the immune-inflammatory phenotype and the structural-functional phenotype remains to be fully defined. The objective of these studies was to evaluate the relationship between the immunologic nature of chronic airway inflammation and the development of abnormal airway structure and function in a mouse model of chronic asthma. Using IL-4-competent and IL-4-deficient mice, we created divergent immune-inflammatory responses to chronic aeroallergen challenge. Immune-inflammatory, structural, and physiological parameters of chronic allergic airway disease were evaluated in both strains of mice. Although both strains developed airway inflammation, the profiles of the immune-inflammatory responses were markedly different: IL-4-competent mice elicited a Th2-polarized response and IL-4-deficient mice developed a Th1-polarized response. Importantly, this chronic Th1-polarized immune response was not associated with airway remodeling or bronchial hyperresponsiveness. Transient reconstitution of IL-4 in IL-4-deficient mice via an airway gene transfer approach led to partial Th2 repolarization and increased bronchial hyperresponsiveness, along with full reconstitution of airway remodeling. These data show that distinct structural-functional phenotypes associated with chronic airway inflammation are strictly dependent on the nature of the immune-inflammatory response. PMID:17586699

  20. Molecular Evolution and Functional Divergence of the Cytochrome P450 3 (CYP3) Family in Actinopterygii (Ray-Finned Fish)

    PubMed Central

    Yan, Jun; Cai, Zhonghua

    2010-01-01

    Background The cytochrome P450 (CYP) superfamily is a multifunctional hemethiolate enzyme that is widely distributed from Bacteria to Eukarya. The CYP3 family contains mainly the four subfamilies CYP3A, CYP3B, CYP3C and CYP3D in vertebrates; however, only the Actinopterygii (ray-finned fish) have all four subfamilies and detailed understanding of the evolutionary relationship of Actinopterygii CYP3 family members would be valuable. Methods and Findings Phylogenetic relationships were constructed to trace the evolutionary history of the Actinopterygii CYP3 family genes. Selection analysis, relative rate tests and functional divergence analysis were combined to interpret the relationship of the site-specific evolution and functional divergence in the Actinopterygii CYP3 family. The results showed that the four CYP3 subfamilies in Actinopterygii might be formed by gene duplication. The first gene duplication event was responsible for divergence of the CYP3B/C clusters from ancient CYP3 before the origin of the Actinopterygii, which corresponded to the fish-specific whole genome duplication (WGD). Tandem repeat duplication in each of the homologue clusters produced stable CYP3B, CYP3C, CYP3A and CYP3D subfamilies. Acceleration of asymmetric evolutionary rates and purifying selection together were the main force for the production of new subfamilies and functional divergence in the new subset after gene duplication, whereas positive selection was detected only in the retained CYP3A subfamily. Furthermore, nearly half of the functional divergence sites appear to be related to substrate recognition, which suggests that site-specific evolution is closely related with functional divergence in the Actinopterygii CYP3 family. Conclusions The split of fish-specific CYP3 subfamilies was related to the fish-specific WGD, and site-specific acceleration of asymmetric evolutionary rates and purifying selection was the main force for the origin of the new subfamilies and functional

  1. pRb Inactivation in Mammary Cells Reveals Common Mechanisms for Tumor Initiation and Progression in Divergent Epithelia

    PubMed Central

    2004-01-01

    Retinoblastoma 1 (pRb) and the related pocket proteins, retinoblastoma-like 1 (p107) and retinoblastoma-like 2 (p130) (pRbf, collectively), play a pivotal role in regulating eukaryotic cell cycle progression, apoptosis, and terminal differentiation. While aberrations in the pRb-signaling pathway are common in human cancers, the consequence of pRbf loss in the mammary gland has not been directly assayed in vivo. We reported previously that inactivating these critical cell cycle regulators in divergent cell types, either brain epithelium or astrocytes, abrogates the cell cycle restriction point, leading to increased cell proliferation and apoptosis, and predisposing to cancer. Here we report that mouse mammary epithelium is similar in its requirements for pRbf function; Rbf inactivation by T121, a fragment of SV40 T antigen that binds to and inactivates pRbf proteins, increases proliferation and apoptosis. Mammary adenocarcinomas form within 16 mo. Most apoptosis is regulated by p53, which has no impact on proliferation, and heterozygosity for a p53 null allele significantly shortens tumor latency. Most tumors in p53 heterozygous mice undergo loss of the wild-type p53 allele. We show that the mechanism of p53 loss of heterozygosity is not simply the consequence of Chromosome 11 aneuploidy and further that chromosomal instability subsequent to p53 loss is minimal. The mechanisms for pRb and p53 tumor suppression in the epithelia of two distinct tissues, mammary gland and brain, are indistinguishable. Further, this study has produced a highly penetrant breast cancer model based on aberrations commonly observed in the human disease. PMID:14966529

  2. Genomic and Metabolic Profiling of Nonulosonic Acids in Vibrionaceae Reveal Biochemical Phenotypes of Allelic Divergence in Vibrio vulnificus ▿

    PubMed Central

    Lewis, Amanda L.; Lubin, Jean-Bernard; Argade, Shilpa; Naidu, Natasha; Choudhury, Biswa; Boyd, E. Fidelma

    2011-01-01

    Nonulosonic acids (NulOs) encompass a large group of structurally diverse nine-carbon backbone α-keto sugars widely distributed among the three domains of life. Mammals express a specialized version of NulOs called sialic acids, which are displayed in prominent terminal positions of cell surface and secreted glycoconjugates. Within bacteria, the ability to synthesize NulOs has been demonstrated in a number of human pathogens and is phylogenetically widespread. Here we examine the distribution, diversity, evolution, and function of NulO biosynthesis pathways in members of the family Vibrionaceae. Among 27 species of Vibrionaceae examined at the genomic level, 12 species contained nab gene clusters. We document examples of duplication, divergence, horizontal transfer, and recombination of nab gene clusters in different Vibrionaceae lineages. Biochemical analyses, including mass spectrometry, confirmed that many species do, in fact, produce di-N-acetylated NulOs. A library of clinical and environmental isolates of Vibrio vulnificus served as a model for further investigation of nab allele genotypes and levels of NulO expression. The data show that lineage I isolates produce about 20-fold higher levels of NulOs than lineage II isolates. Moreover, nab gene alleles found in a subset of V. vulnificus clinical isolates express 40-fold higher levels of NulOs than nab alleles associated with environmental isolates. Taken together, the data implicate the family Vibrionaceae as a “hot spot” of NulO evolution and suggest that these molecules may have diverse roles in environmental persistence and/or animal virulence. PMID:21724895

  3. Divergent functional profiles of acidic and basic phospholipases A2 in the venom of the snake Porthidium lansbergii lansbergii.

    PubMed

    Jiménez-Charris, Eliécer; Montealegre-Sánchez, Leonel; Solano-Redondo, Luis; Castro-Herrera, Fernando; Fierro-Pérez, Leonardo; Lomonte, Bruno

    2016-09-01

    The Lansberg's hognose pitviper, Porthidium lansbergii lansbergii, inhabits northern Colombia. A recent proteomic characterization of its venom (J. Proteomics [2015] 114, 287-299) revealed the presence of phospholipases A2 (PLA2) accounting for 16.2% of its proteins. The two most abundant PLA2s were biochemically and functionally characterized. Pllans-I is a basic, dimeric enzyme with a monomer mass of 14,136 Da, while Pllans-II is an acidic, monomeric enzyme of 13,901 Da. Both have Asp49 in their partial amino acid sequences and, accordingly, are catalytically active upon natural or synthetic substrates. Nevertheless, these two enzymes differ markedly in their bioactivities. Pllans-I induces myonecrosis, edema, and is lethal by intracerebro-ventricular injection in mice, as well as cytolytic and anticoagulant in vitro. In contrast, Pllans-II is devoid of these effects, except for the induction of a moderate edema. In spite of lacking myotoxicity, Pllans-II enhances the muscle damaging action of Pllans-I in vivo. Altogether, results further illustrate the divergent functional profiles of basic and acidic PLA2s in viperid venoms, and suggest that Pllans-I plays a myotoxic role in envenomings by P. l. lansbergii, whereas Pllans-II, apparently devoid of toxicity, enhances muscle damage caused by Pllans-I. PMID:27381371

  4. Experimental demonstration of using divergence cost-function in SPGD algorithm for coherent beam combining with tip/tilt control.

    PubMed

    Geng, Chao; Luo, Wen; Tan, Yi; Liu, Hongmei; Mu, Jinbo; Li, Xinyang

    2013-10-21

    A novel approach of tip/tilt control by using divergence cost function in stochastic parallel gradient descent (SPGD) algorithm for coherent beam combining (CBC) is proposed and demonstrated experimentally in a seven-channel 2-W fiber amplifier array with both phase-locking and tip/tilt control, for the first time to our best knowledge. Compared with the conventional power-in-the-bucket (PIB) cost function for SPGD optimization, the tip/tilt control using divergence cost function ensures wider correction range, automatic switching control of program, and freedom of camera's intensity-saturation. Homemade piezoelectric-ring phase-modulator (PZT PM) and adaptive fiber-optics collimator (AFOC) are developed to correct piston- and tip/tilt-type aberrations, respectively. The PIB cost function is employed for phase-locking via maximization of SPGD optimization, while the divergence cost function is used for tip/tilt control via minimization. An average of 432-μrad of divergence metrics in open loop has decreased to 89-μrad when tip/tilt control implemented. In CBC, the power in the full width at half maximum (FWHM) of the main lobe increases by 32 times, and the phase residual error is less than λ/15. PMID:24150347

  5. Neural convergence and divergence in the mammalian cerebral cortex: from experimental neuroanatomy to functional neuroimaging

    PubMed Central

    Man, Kingson; Kaplan, Jonas; Damasio, Hanna; Damasio, Antonio

    2013-01-01

    A development essential for understanding the neural basis of complex behavior and cognition is the description, during the last quarter of the twentieth century, of detailed patterns of neuronal circuitry in the mammalian cerebral cortex. This effort established that sensory pathways exhibit successive levels of convergence, from the early sensory cortices to sensory-specific association cortices and to multisensory association cortices, culminating in maximally integrative regions; and that this convergence is reciprocated by successive levels of divergence, from the maximally integrative areas all the way back to the early sensory cortices. This article first provides a brief historical review of these neuroanatomical findings, which were relevant to the study of brain and mind-behavior relationships using a variety of approaches and to the proposal of heuristic anatomo-functional frameworks. In a second part, the article reviews new evidence that has accumulated from studies of functional neuroimaging, employing both univariate and multivariate analyses, as well as electrophysiology, in humans and other mammals, that the integration of information across the auditory, visual, and somatosensory-motor modalities proceeds in a content-rich manner. Behaviorally and cognitively relevant information is extracted from and conserved across the different modalities, both in higher-order association cortices and in early sensory cortices. Such stimulus-specific information is plausibly relayed along the neuroanatomical pathways alluded to above. The evidence reviewed here suggests the need for further in-depth exploration of the intricate connectivity of the mammalian cerebral cortex in experimental neuroanatomical studies. PMID:23840023

  6. Duplicated CFTR isoforms in eels diverged in regulatory structures and osmoregulatory functions.

    PubMed

    Wong, Marty Kwok-Shing; Pipil, Supriya; Kato, Akira; Takei, Yoshio

    2016-09-01

    Two cystic fibrosis transmembrane conductance regulator (CFTR) isoforms, CFTRa and CFTRb, were cloned in Japanese eel and their structures and functions were studied in different osmoregulatory tissues in freshwater (FW) and seawater (SW) eels. Molecular phylogenetic results suggested that the CFTR duplication in eels occurred independently of the duplication event in salmonid. CFTRa was expressed in the intestine and kidney and downregulated in both tissues in SW eels, while CFTRb was specifically expressed in the gill and greatly upregulated in SW eels. Structurally, the CFTR isoforms are similar in most functional domains except the regulatory R domain, where the R domain of CFTRa is similar to that of human CFTR but the R domain of CFTRb is unique in having high intrinsic negative charges and fewer phosphorylation sites, suggesting divergence of isoforms in terms of gating properties and hormonal regulation. Immunohistochemical results showed that CFTR was localized on the apical regions of SW ionocytes, suggesting a Cl(-) secretory role as in other teleosts. In intestine and kidney, however, immunoreactive CFTR was mostly found in the cytosolic vesicles in FW eels, indicating that Cl(-) channel activity could be low at basal conditions, but could be rapidly increased by membrane insertion of the stored channels. Guanylin (GN), a known hormone that increases CFTR activity in mammalian intestine, failed to redistribute CFTR and to affect its expression in eel intestine. The results suggested that GN-independent CFTR regulation is present in eel intestine and kidney. PMID:27322796

  7. Massive expansion and functional divergence of innate immune genes in a protostome

    PubMed Central

    Zhang, Linlin; Li, Li; Guo, Ximing; Litman, Gary W.; Dishaw, Larry J.; Zhang, Guofan

    2015-01-01

    The molecules that mediate innate immunity are encoded by relatively few genes and exhibit broad specificity. Detailed annotation of the Pacific oyster (Crassostrea gigas) genome, a protostome invertebrate, reveals large-scale duplication and divergence of multigene families encoding molecules that effect innate immunity. Transcriptome analyses indicate dynamic and orchestrated specific expression of numerous innate immune genes in response to experimental challenge with pathogens, including bacteria, and a pathogenic virus. Variable expression of individual members of the multigene families encoding these genes also occurs during different types of abiotic stress (environmentally-equivalent conditions of temperature, salinity and desiccation). Multiple families of immune genes are responsive in concert to certain biotic and abiotic challenges. Individual members of expanded families of immune genes are differentially expressed under both biotic challenge and abiotic stress conditions. Members of the same families of innate immune molecules also are transcribed in developmental stage- and tissue-specific manners. An integrated, highly complex innate immune system that exhibits remarkable discriminatory properties and responses to different pathogens as well as environmental stress has arisen through the adaptive recruitment of tandem duplicated genes. The co-adaptive evolution of stress and innate immune responses appears to have an ancient origin in phylogeny. PMID:25732911

  8. Comparative studies of Munc18c and Munc18-1 reveal conserved and divergent mechanisms of Sec1/Munc18 proteins

    PubMed Central

    Yu, Haijia; Rathore, Shailendra S.; Lopez, Jamie A.; Davis, Eric M.; James, David E.; Martin, Jennifer L.; Shen, Jingshi

    2013-01-01

    Sec1/Munc18 (SM) family proteins are essential for every vesicle fusion pathway. The best-characterized SM protein is the synaptic factor Munc18-1, but it remains unclear whether its functions represent conserved mechanisms of SM proteins or specialized activities in neurotransmitter release. To address this question, we dissected Munc18c, a functionally distinct SM protein involved in nonsynaptic exocytic pathways. We discovered that Munc18c binds to the trans-SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) complex and strongly accelerates the fusion rate. Further analysis suggests that Munc18c recognizes both vesicle-rooted SNARE and target membrane-associated SNAREs, and promotes trans-SNARE zippering at the postdocking stage of the fusion reaction. The stimulation of fusion by Munc18c is specific to its cognate SNARE isoforms. Because Munc18-1 regulates fusion in a similar manner, we conclude that one conserved function of SM proteins is to bind their cognate trans-SNARE complexes and accelerate fusion kinetics. Munc18c also binds syntaxin-4 monomer but does not block target membrane-associated SNARE assembly, in agreement with our observation that six- to eightfold increases in Munc18c expression do not inhibit insulin-stimulated glucose uptake in adipocytes. Thus, the inhibitory “closed” syntaxin binding mode demonstrated for Munc18-1 is not conserved in Munc18c. Unexpectedly, we found that Munc18c recognizes the N-terminal region of the vesicle-rooted SNARE, whereas Munc18-1 requires the C-terminal sequences, suggesting that the architecture of the SNARE/SM complex likely differs across fusion pathways. Together, these comparative studies of two distinct SM proteins reveal conserved as well as divergent mechanisms of SM family proteins in intracellular vesicle fusion. PMID:23918365

  9. Direct Comparison of Mice Null for Liver or Intestinal Fatty Acid-binding Proteins Reveals Highly Divergent Phenotypic Responses to High Fat Feeding*

    PubMed Central

    Gajda, Angela M.; Zhou, Yin Xiu; Agellon, Luis B.; Fried, Susan K.; Kodukula, Sarala; Fortson, Walter; Patel, Khamoshi; Storch, Judith

    2013-01-01

    The enterocyte expresses two fatty acid-binding proteins (FABP), intestinal FABP (IFABP; FABP2) and liver FABP (LFABP; FABP1). LFABP is also expressed in liver. Despite ligand transport and binding differences, it has remained uncertain whether these intestinally coexpressed proteins, which both bind long chain fatty acids (FA), are functionally distinct. Here, we directly compared IFABP−/− and LFABP−/− mice fed high fat diets containing long chain saturated or unsaturated fatty acids, reasoning that providing an abundance of dietary lipid would reveal unique functional properties. The results showed that mucosal lipid metabolism was indeed differentially modified, with significant decreases in FA incorporation into triacylglycerol (TG) relative to phospholipid (PL) in IFABP−/− mice, whereas LFABP−/− mice had reduced monoacylglycerol incorporation in TG relative to PL, as well as reduced FA oxidation. Interestingly, striking differences were found in whole body energy homeostasis; LFABP−/− mice fed high fat diets became obese relative to WT, whereas IFABP−/− mice displayed an opposite, lean phenotype. Fuel utilization followed adiposity, with LFABP−/− mice preferentially utilizing lipids, and IFABP−/− mice preferentially metabolizing carbohydrate for energy production. Changes in body weight and fat may arise, in part, from altered food intake; mucosal levels of the endocannabinoids 2-arachidonoylglycerol and arachidonoylethanolamine were elevated in LFABP−/−, perhaps contributing to increased energy intake. This direct comparison provides evidence that LFABP and IFABP have distinct roles in intestinal lipid metabolism; differential intracellular functions in intestine and in liver, for LFABP−/− mice, result in divergent downstream effects at the systemic level. PMID:23990461

  10. Recent Duplication and Functional Divergence in Parasitic Nematode Levamisole-Sensitive Acetylcholine Receptors

    PubMed Central

    Duguet, Thomas B.; Charvet, Claude L.; Forrester, Sean G.; Wever, Claudia M.; Dent, Joseph A.; Neveu, Cedric; Beech, Robin N.

    2016-01-01

    Helminth parasites rely on fast-synaptic transmission in their neuromusculature to experience the outside world and respond to it. Acetylcholine plays a pivotal role in this and its receptors are targeted by a wide variety of both natural and synthetic compounds used in human health and for the control of parasitic disease. The model, Caenorhabditis elegans is characterized by a large number of acetylcholine receptor subunit genes, a feature shared across the nematodes. This dynamic family is characterized by both gene duplication and loss between species. The pentameric levamisole-sensitive acetylcholine receptor has been characterized from C. elegans, comprised of five different subunits. More recently, cognate receptors have been reconstituted from multiple parasitic nematodes that are found to vary in subunit composition. In order to understand the implications of receptor composition change and the origins of potentially novel drug targets, we investigated a specific example of subunit duplication based on analysis of genome data for 25 species from the 50 helminth genome initiative. We found multiple independent duplications of the unc-29, acetylcholine receptor subunit, where codon substitution rate analysis identified positive, directional selection acting on amino acid positions associated with subunit assembly. Characterization of four gene copies from a model parasitic nematode, Haemonchus contortus, demonstrated that each copy has acquired unique functional characteristics based on phenotype rescue of transgenic C. elegans and electrophysiology of receptors reconstituted in Xenopus oocytes. We found evidence that a specific incompatibility has evolved for two subunits co-expressed in muscle. We demonstrated that functional divergence of acetylcholine receptors, driven by directional selection, can occur more rapidly than previously thought and may be mediated by alteration of receptor assembly. This phenomenon is common among the clade V parasitic

  11. Recent Duplication and Functional Divergence in Parasitic Nematode Levamisole-Sensitive Acetylcholine Receptors.

    PubMed

    Duguet, Thomas B; Charvet, Claude L; Forrester, Sean G; Wever, Claudia M; Dent, Joseph A; Neveu, Cedric; Beech, Robin N

    2016-07-01

    Helminth parasites rely on fast-synaptic transmission in their neuromusculature to experience the outside world and respond to it. Acetylcholine plays a pivotal role in this and its receptors are targeted by a wide variety of both natural and synthetic compounds used in human health and for the control of parasitic disease. The model, Caenorhabditis elegans is characterized by a large number of acetylcholine receptor subunit genes, a feature shared across the nematodes. This dynamic family is characterized by both gene duplication and loss between species. The pentameric levamisole-sensitive acetylcholine receptor has been characterized from C. elegans, comprised of five different subunits. More recently, cognate receptors have been reconstituted from multiple parasitic nematodes that are found to vary in subunit composition. In order to understand the implications of receptor composition change and the origins of potentially novel drug targets, we investigated a specific example of subunit duplication based on analysis of genome data for 25 species from the 50 helminth genome initiative. We found multiple independent duplications of the unc-29, acetylcholine receptor subunit, where codon substitution rate analysis identified positive, directional selection acting on amino acid positions associated with subunit assembly. Characterization of four gene copies from a model parasitic nematode, Haemonchus contortus, demonstrated that each copy has acquired unique functional characteristics based on phenotype rescue of transgenic C. elegans and electrophysiology of receptors reconstituted in Xenopus oocytes. We found evidence that a specific incompatibility has evolved for two subunits co-expressed in muscle. We demonstrated that functional divergence of acetylcholine receptors, driven by directional selection, can occur more rapidly than previously thought and may be mediated by alteration of receptor assembly. This phenomenon is common among the clade V parasitic

  12. Functional Divergence in the Role of N-Linked Glycosylation in Smoothened Signaling

    PubMed Central

    Marada, Suresh; Navarro, Gemma; Truong, Ashley; Stewart, Daniel P.; Arensdorf, Angela M.; Nachtergaele, Sigrid; Angelats, Edgar; Opferman, Joseph T.; Rohatgi, Rajat; McCormick, Peter J.; Ogden, Stacey K.

    2015-01-01

    The G protein-coupled receptor (GPCR) Smoothened (Smo) is the requisite signal transducer of the evolutionarily conserved Hedgehog (Hh) pathway. Although aspects of Smo signaling are conserved from Drosophila to vertebrates, significant differences have evolved. These include changes in its active sub-cellular localization, and the ability of vertebrate Smo to induce distinct G protein-dependent and independent signals in response to ligand. Whereas the canonical Smo signal to Gli transcriptional effectors occurs in a G protein-independent manner, its non-canonical signal employs Gαi. Whether vertebrate Smo can selectively bias its signal between these routes is not yet known. N-linked glycosylation is a post-translational modification that can influence GPCR trafficking, ligand responsiveness and signal output. Smo proteins in Drosophila and vertebrate systems harbor N-linked glycans, but their role in Smo signaling has not been established. Herein, we present a comprehensive analysis of Drosophila and murine Smo glycosylation that supports a functional divergence in the contribution of N-linked glycans to signaling. Of the seven predicted glycan acceptor sites in Drosophila Smo, one is essential. Loss of N-glycosylation at this site disrupted Smo trafficking and attenuated its signaling capability. In stark contrast, we found that all four predicted N-glycosylation sites on murine Smo were dispensable for proper trafficking, agonist binding and canonical signal induction. However, the under-glycosylated protein was compromised in its ability to induce a non-canonical signal through Gαi, providing for the first time evidence that Smo can bias its signal and that a post-translational modification can impact this process. As such, we postulate a profound shift in N-glycan function from affecting Smo ER exit in flies to influencing its signal output in mice. PMID:26291458

  13. Molecular Evolution and Functional Divergence of Trace Amine–Associated Receptors

    PubMed Central

    Eyun, Seong-il; Moriyama, Hideaki; Hoffmann, Federico G.; Moriyama, Etsuko N.

    2016-01-01

    Trace amine-associated receptors (TAARs) are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes) were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey. We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian-specific) in addition to previously known nine subfamilies. Many species-specific TAAR gene duplications and losses contributed to a large variation of TAAR gene numbers among mammals, ranging from 0 in dolphin to 26 in flying fox. TAARs are classified into two groups based on binding preferences for primary or tertiary amines as well as their sequence similarities. Primary amine-detecting TAARs (TAAR1-4) have emerged earlier, generally have single-copy orthologs (very few duplication or loss), and have evolved under strong functional constraints. In contrast, tertiary amine-detecting TAARs (TAAR5-9) have emerged more recently and the majority of them experienced higher rates of gene duplications. Protein members that belong to the tertiary amine-detecting TAAR group also showed the patterns of positive selection especially in the area surrounding the ligand-binding pocket, which could have affected ligand-binding activities and specificities. Expansions of the tertiary amine-detecting TAAR gene family may have played important roles in terrestrial adaptations of therian mammals. Molecular evolution of the TAAR gene family appears to be governed by a complex, species-specific, interplay between environmental and evolutionary factors. PMID:26963722

  14. Molecular Evolution and Functional Divergence of Trace Amine-Associated Receptors.

    PubMed

    Eyun, Seong-Il; Moriyama, Hideaki; Hoffmann, Federico G; Moriyama, Etsuko N

    2016-01-01

    Trace amine-associated receptors (TAARs) are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes) were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey. We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian-specific) in addition to previously known nine subfamilies. Many species-specific TAAR gene duplications and losses contributed to a large variation of TAAR gene numbers among mammals, ranging from 0 in dolphin to 26 in flying fox. TAARs are classified into two groups based on binding preferences for primary or tertiary amines as well as their sequence similarities. Primary amine-detecting TAARs (TAAR1-4) have emerged earlier, generally have single-copy orthologs (very few duplication or loss), and have evolved under strong functional constraints. In contrast, tertiary amine-detecting TAARs (TAAR5-9) have emerged more recently and the majority of them experienced higher rates of gene duplications. Protein members that belong to the tertiary amine-detecting TAAR group also showed the patterns of positive selection especially in the area surrounding the ligand-binding pocket, which could have affected ligand-binding activities and specificities. Expansions of the tertiary amine-detecting TAAR gene family may have played important roles in terrestrial adaptations of therian mammals. Molecular evolution of the TAAR gene family appears to be governed by a complex, species-specific, interplay between environmental and evolutionary factors. PMID:26963722

  15. POLYMICROBIAL SEPSIS INDUCES DIVERGENT EFFECTS ON SPLENIC AND PERITONEAL DENDRITIC CELL FUNCTION IN MICE

    PubMed Central

    Ding, Yanli; Chung, Chun-Shiang; Newton, Sarah; Chen, Yaping; Carlton, Stacey; Albina, Jorge E.; Ayala, Alfred

    2008-01-01

    Dendritic cells (DCs) are professional antigen-presenting cells that act as sentinels in the cell-mediated response against invading pathogens associated with septic challenge. The purpose of the present study was to determine whether there is a loss of dendritic cells and/or changes in function of these cells in septic mice. Here we report that the number of DCs, in both spleen and peritoneum, decreased over 24 h postsepsis [cecal ligation and puncture (CLP)] when compared with sham. The most dramatic change was seen in the peritoneal cavity. This decrease appeared to be caused mainly by the depletion of immature DCs rather than mature DCs. This change was LPS independent and minimally affected by FasL; however, overexpression of human Bcl-2 gene provides protection of the septic peritoneal DCs. Moreover, although the level of IL-12 release decreased significantly in splenic DCs obtained from CLP mice, IL-12 secretion was markedly elevated by peritoneal DCs as well as in both plasma and peritoneal fluid at 24 h post-CLP. In peritoneal cells, the expression of CD40, CD80, and CD86 was unchanged, but their respective ligands CD40L, CD28, and CD152 all increased in mice 24 h after CLP, although no such change was observed in splenocytes. Regardless of the presence or absence of antigen, peritoneal DCs from CLP mice showed higher capacity to stimulate T-cell proliferation than those cells from the sham control. However, splenic DCs from CLP mice only showed augmented capacity to induce antigen-dependent stimulation of T-cell proliferation. Together, these data indicate that sepsis produces divergent functional changes in splenic and peritoneal DC populations. PMID:15257086

  16. Functional divergence of FimX in PilZ binding and type IV pilus regulation.

    PubMed

    Qi, Yaning; Xu, Linghui; Dong, Xueming; Yau, Yin Hoe; Ho, Chun Loong; Koh, Siew Lee; Shochat, Susana Geifman; Chou, Shan-Ho; Tang, Kai; Liang, Zhao-Xun

    2012-11-01

    Type IV pili (T4P) are polar surface structures that play important roles in bacterial motility, biofilm formation, and pathogenicity. The protein FimX and its orthologs are known to mediate T4P formation in the human pathogen Pseudomonas aeruginosa and some other bacterial species. It was reported recently that FimX(XAC2398) from Xanthomonas axonopodis pv. citri interacts with PilZ(XAC1133) directly through the nonenzymatic EAL domain of FimX(XAC2398). Here we present experimental data to reveal that the strong interaction between FimX(XAC2398) and PilZ(XAC1133) is not conserved in P. aeruginosa and likely other Pseudomonas species. In vitro and in vivo binding experiments showed that the interaction between FimX and PilZ in P. aeruginosa is below the measurable limit. Surface plasmon resonance assays further confirmed that the interaction between the P. aeruginosa proteins is at least more than 3 orders of magnitude weaker than that between the X. axonopodis pv. citri pair. The N-terminal lobe region of FimX(XAC2398) was identified as the binding surface for PilZ(XAC1133) by amide hydrogen-deuterium exchange and site-directed mutagenesis studies. Lack of several key residues in the N-terminal lobe region of the EAL domain of FimX is likely to account for the greatly reduced binding affinity between FimX and PilZ in P. aeruginosa. All together, the results suggest that the interaction between PilZ and FimX in Xanthomonas species is not conserved in P. aeruginosa due to the evolutionary divergence among the FimX orthologs. The precise roles of FimX and PilZ in bacterial motility and T4P biogenesis are likely to vary among bacterial species. PMID:22942245

  17. Molecular evolution accompanying functional divergence of duplicated genes along the plant starch biosynthesis pathway

    PubMed Central

    2014-01-01

    Background Starch is the main source of carbon storage in the Archaeplastida. The starch biosynthesis pathway (sbp) emerged from cytosolic glycogen metabolism shortly after plastid endosymbiosis and was redirected to the plastid stroma during the green lineage divergence. The SBP is a complex network of genes, most of which are members of large multigene families. While some gene duplications occurred in the Archaeplastida ancestor, most were generated during the sbp redirection process, and the remaining few paralogs were generated through compartmentalization or tissue specialization during the evolution of the land plants. In the present study, we tested models of duplicated gene evolution in order to understand the evolutionary forces that have led to the development of SBP in angiosperms. We combined phylogenetic analyses and tests on the rates of evolution along branches emerging from major duplication events in six gene families encoding sbp enzymes. Results We found evidence of positive selection along branches following cytosolic or plastidial specialization in two starch phosphorylases and identified numerous residues that exhibited changes in volume, polarity or charge. Starch synthases, branching and debranching enzymes functional specializations were also accompanied by accelerated evolution. However, none of the sites targeted by selection corresponded to known functional domains, catalytic or regulatory. Interestingly, among the 13 duplications tested, 7 exhibited evidence of positive selection in both branches emerging from the duplication, 2 in only one branch, and 4 in none of the branches. Conclusions The majority of duplications were followed by accelerated evolution targeting specific residues along both branches. This pattern was consistent with the optimization of the two sub-functions originally fulfilled by the ancestral gene before duplication. Our results thereby provide strong support to the so-called “Escape from Adaptive Conflict

  18. Functional Divergence of APETALA1 and FRUITFULL is due to Changes in both Regulation and Coding Sequence.

    PubMed

    McCarthy, Elizabeth W; Mohamed, Abeer; Litt, Amy

    2015-01-01

    Gene duplications are prevalent in plants, and functional divergence subsequent to duplication may be linked with the occurrence of novel phenotypes in plant evolution. Here, we examine the functional divergence of Arabidopsis thaliana APETALA1 (AP1) and FRUITFULL (FUL), which arose via a duplication correlated with the origin of the core eudicots. Both AP1 and FUL play a role in floral meristem identity, but AP1 is required for the formation of sepals and petals whereas FUL is involved in cauline leaf and fruit development. AP1 and FUL are expressed in mutually exclusive domains but also differ in sequence, with unique conserved motifs in the C-terminal domains of the proteins that suggest functional differentiation. To determine whether the functional divergence of AP1 and FUL is due to changes in regulation or changes in coding sequence, we performed promoter swap experiments, in which FUL was expressed in the AP1 domain in the ap1 mutant and vice versa. Our results show that FUL can partially substitute for AP1, and AP1 can partially substitute for FUL; thus, the functional divergence between AP1 and FUL is due to changes in both regulation and coding sequence. We also mutated AP1 and FUL conserved motifs to determine if they are required for protein function and tested the ability of these mutated proteins to interact in yeast with known partners. We found that these motifs appear to play at best a minor role in protein function and dimerization capability, despite being strongly conserved. Our results suggest that the functional differentiation of these two paralogous key transcriptional regulators involves both differences in regulation and in sequence; however, sequence changes in the form of unique conserved motifs do not explain the differences observed. PMID:26697035

  19. Functional Divergence of APETALA1 and FRUITFULL is due to Changes in both Regulation and Coding Sequence

    PubMed Central

    McCarthy, Elizabeth W.; Mohamed, Abeer; Litt, Amy

    2015-01-01

    Gene duplications are prevalent in plants, and functional divergence subsequent to duplication may be linked with the occurrence of novel phenotypes in plant evolution. Here, we examine the functional divergence of Arabidopsis thaliana APETALA1 (AP1) and FRUITFULL (FUL), which arose via a duplication correlated with the origin of the core eudicots. Both AP1 and FUL play a role in floral meristem identity, but AP1 is required for the formation of sepals and petals whereas FUL is involved in cauline leaf and fruit development. AP1 and FUL are expressed in mutually exclusive domains but also differ in sequence, with unique conserved motifs in the C-terminal domains of the proteins that suggest functional differentiation. To determine whether the functional divergence of AP1 and FUL is due to changes in regulation or changes in coding sequence, we performed promoter swap experiments, in which FUL was expressed in the AP1 domain in the ap1 mutant and vice versa. Our results show that FUL can partially substitute for AP1, and AP1 can partially substitute for FUL; thus, the functional divergence between AP1 and FUL is due to changes in both regulation and coding sequence. We also mutated AP1 and FUL conserved motifs to determine if they are required for protein function and tested the ability of these mutated proteins to interact in yeast with known partners. We found that these motifs appear to play at best a minor role in protein function and dimerization capability, despite being strongly conserved. Our results suggest that the functional differentiation of these two paralogous key transcriptional regulators involves both differences in regulation and in sequence; however, sequence changes in the form of unique conserved motifs do not explain the differences observed. PMID:26697035

  20. Revealing neuronal function through microelectrode array recordings

    PubMed Central

    Obien, Marie Engelene J.; Deligkaris, Kosmas; Bullmann, Torsten; Bakkum, Douglas J.; Frey, Urs

    2015-01-01

    Microelectrode arrays and microprobes have been widely utilized to measure neuronal activity, both in vitro and in vivo. The key advantage is the capability to record and stimulate neurons at multiple sites simultaneously. However, unlike the single-cell or single-channel resolution of intracellular recording, microelectrodes detect signals from all possible sources around every sensor. Here, we review the current understanding of microelectrode signals and the techniques for analyzing them. We introduce the ongoing advancements in microelectrode technology, with focus on achieving higher resolution and quality of recordings by means of monolithic integration with on-chip circuitry. We show how recent advanced microelectrode array measurement methods facilitate the understanding of single neurons as well as network function. PMID:25610364

  1. Revealing remodeler function: Varied and unique

    NASA Astrophysics Data System (ADS)

    Eastlund, Allen

    Chromatin remodelers perform a necessary and required function for the successful expression of our genetic code. By modifying, shifting, or ejecting nucleosomes from the chromatin structure they allow access to the underlying DNA to the rest of the cell's machinery. This research has focused on two major remodeler motors from major families of chromatin remodelers: the trimeric motor domain of RSC and the motor domain of the ISWI family, ISWI. Using primarily stopped-flow spectrofluorometry, I have categorized the time-dependent motions of these motor domains along their preferred substrate, double-stranded DNA. Combined with collected ATP utilization data, I present the subsequent analysis and associated conclusions that stem from the underlying assumptions and models. Interestingly, there is little in common between the investigated proteins aside from their favored medium. While RSC exhibits modest translocation characteristics and highly effective motion with the ability for large molecular forces, ISWI is not only structurally different but highly inefficient in its motion leading to difficulties in determining its specific translocation mechanics. While chromatin remodeling is a ubiquitous facet of eukaryotic life, there remains much to be understood about their general mechanisms.

  2. Sequence divergence and diversity suggests ongoing functional diversification of vertebrate NAD metabolism.

    PubMed

    Gossmann, Toni I; Ziegler, Mathias

    2014-11-01

    NAD is not only an important cofactor in redox reactions but has also received attention in recent years because of its physiological importance in metabolic regulation, DNA repair and signaling. In contrast to the redox reactions, these regulatory processes involve degradation of NAD and therefore necessitate a constant replenishment of its cellular pool. NAD biosynthetic enzymes are common to almost all species in all clades, but the number of NAD degrading enzymes varies substantially across taxa. In particular, vertebrates, including humans, have a manifold of NAD degrading enzymes which require a high turnover of NAD. As there is currently a lack of a systematic study of how natural selection has shaped enzymes involved in NAD metabolism we conducted a comprehensive evolutionary analysis based on intraspecific variation and interspecific divergence. We compare NAD biosynthetic and degrading enzymes in four eukaryotic model species and subsequently focus on human NAD metabolic enzymes and their orthologs in other vertebrates. We find that the majority of enzymes involved in NAD metabolism are subject to varying levels of purifying selection. While NAD biosynthetic enzymes appear to experience a rather high level of evolutionary constraint, there is evidence for positive selection among enzymes mediating NAD-dependent signaling. This is particularly evident for members of the PARP family, a diverse protein family involved in DNA damage repair and programmed cell death. Based on haplotype information and substitution rate analysis we pinpoint sites that are potential targets of positive selection. We also link our findings to a three dimensional structure, which suggests that positive selection occurs in domains responsible for DNA binding and polymerization rather than the NAD catalytic domain. Taken together, our results indicate that vertebrate NAD metabolism is still undergoing functional diversification. PMID:25084685

  3. A cryptic species of Aphis gossypii (Hemiptera: Aphididae) complex revealed by genetic divergence and different host plant association.

    PubMed

    Lee, Y; Lee, W; Lee, S; Kim, H

    2015-02-01

    Three cryptic species, Aphis gossypii, Aphis glycines, and Aphis rhamnicola sp. nov., are recognized as sharing buckthorn plant, Rhamnus spp. as primary hosts. These aphid species have morphological similarities; however, there are significant genetic differences between the three cryptic species. Based on the high level of genetic divergence and the different secondary host association, we described a new species, Aphis rhamnicola sp. nov., for apterous and alate vivipara, fundatrix, ovipara, and gynopara, including diagnostic key for the host sharing species in the genus Aphis. PMID:25413997

  4. Genome-wide identification and evolution of ATP-binding cassette transporters in the ciliate Tetrahymena thermophila: A case of functional divergence in a multigene family

    PubMed Central

    2010-01-01

    Background In eukaryotes, ABC transporters that utilize the energy of ATP hydrolysis to expel cellular substrates into the environment are responsible for most of the efflux from cells. Many members of the superfamily of ABC transporters have been linked with resistance to multiple drugs or toxins. Owing to their medical and toxicological importance, members of the ABC superfamily have been studied in several model organisms and warrant examination in newly sequenced genomes. Results A total of 165 ABC transporter genes, constituting a highly expanded superfamily relative to its size in other eukaryotes, were identified in the macronuclear genome of the ciliate Tetrahymena thermophila. Based on ortholog comparisons, phylogenetic topologies and intron characterizations, each highly expanded ABC transporter family of T. thermophila was classified into several distinct groups, and hypotheses about their evolutionary relationships are presented. A comprehensive microarray analysis revealed divergent expression patterns among the members of the ABC transporter superfamily during different states of physiology and development. Many of the relatively recently formed duplicate pairs within individual ABC transporter families exhibit significantly different expression patterns. Further analysis showed that multiple mechanisms have led to functional divergence that is responsible for the preservation of duplicated genes. Conclusion Gene duplications have resulted in an extensive expansion of the superfamily of ABC transporters in the Tetrahymena genome, making it the largest example of its kind reported in any organism to date. Multiple independent duplications and subsequent divergence contributed to the formation of different families of ABC transporter genes. Many of the members within a gene family exhibit different expression patterns. The combination of gene duplication followed by both sequence divergence and acquisition of new patterns of expression likely plays a

  5. Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing

    PubMed Central

    Liu, Hong-Wei; Wu, Jun-Lan; Li, Zheng-Guo; Zhang, Liang; Jian, Jian-Bo; Li, Ye-Yun; Tai, Yu-Ling; Zhang, Jing; Zhang, Zheng-Zhu; Jiang, Chang-Jun; Xia, Tao; Wan, Xiao-Chun

    2016-01-01

    Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants. PMID:26962860

  6. Gene-based polymorphisms reveal limited genomic divergence in a species with a heritable life-history dimorphism.

    PubMed

    Zakas, Christina; Rockman, Matthew V

    2015-01-01

    Understanding the genetic basis of life-history traits is a long-standing goal of evolutionary biology. Many closely related species have contrasting life-history strategies, suggesting that the switches in early development that lead to divergent life-histories evolve quickly and frequently. Life-history changes that originate in early development have profound downstream effects on a species' morphology, ecology, genetic diversity, and even speciation rate. How do such transitions in development mode occur, and what is the underlying genetic architecture? To begin to address these questions, we investigated genetic variation in an emerging model in developmental evolution, the polychaete Streblospio benedicti, which has two contrasting and highly heritable offspring types. We compare transcript-based SNP genotypes of individuals of the two development modes to determine the extent of genomic differentiation between them. We find that there is extensive allele sharing across the two types, and minimal fixed differences. We use the site frequency spectrum to fit demographic models to our data and determine that there is recent gene flow between developmental morphs. Our data suggest that the evolution of a genetic developmental dimorphism is not associated with longstanding genetic isolation or genomically extensive divergence. Rather, differences at developmentally important loci, or modest allele-frequency differences at many loci, may be responsible for the drastic life-history differences. PMID:26174100

  7. Refugial isolation and divergence in the Narrowheaded Gartersnake species complex (Thamnophis rufipunctatus) as revealed by multilocus DNA sequence data

    USGS Publications Warehouse

    Wood, Dustin A.; Vandergast, A.G.; Espinal, A. Lemos; Fisher, R.N.; Holycross, A.T.

    2011-01-01

    Glacial–interglacial cycles of the Pleistocene are hypothesized as one of the foremost contributors to biological diversification. This is especially true for cold-adapted montane species, where range shifts have had a pronounced effect on population-level divergence. Gartersnakes of the Thamnophis rufipunctatus species complex are restricted to cold headwater streams in the highlands of the Sierra Madre Occidental and southwestern USA. We used coalescent and multilocus phylogenetic approaches to test whether genetic diversification of this montane-restricted species complex is consistent with two prevailing models of range fluctuation for species affected by Pleistocene climate changes. Our concatenated nuDNA and multilocus species analyses recovered evidence for the persistence of multiple lineages that are restricted geographically, despite a mtDNA signature consistent with either more recent connectivity (and introgression) or recent expansion (and incomplete lineage sorting). Divergence times estimated using a relaxed molecular clock and fossil calibrations fall within the Late Pleistocene, and zero gene flow scenarios among current geographically isolated lineages could not be rejected. These results suggest that increased climate shifts in the Late Pleistocene have driven diversification and current range retraction patterns and that the differences between markers reflect the stochasticity of gene lineages (i.e. ancestral polymorphism) rather than gene flow and introgression. These results have important implications for the conservation of T. rufipunctatus (sensu novo), which is restricted to two drainage systems in the southwestern US and has undergone a recent and dramatic decline.

  8. The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

    PubMed Central

    Merchant, Sabeeha S.; Prochnik, Simon E.; Vallon, Olivier; Harris, Elizabeth H.; Karpowicz, Steven J.; Witman, George B.; Terry, Astrid; Salamov, Asaf; Fritz-Laylin, Lillian K.; Maréchal-Drouard, Laurence; Marshall, Wallace F.; Qu, Liang-Hu; Nelson, David R.; Sanderfoot, Anton A.; Spalding, Martin H.; Kapitonov, Vladimir V.; Ren, Qinghu; Ferris, Patrick; Lindquist, Erika; Shapiro, Harris; Lucas, Susan M.; Grimwood, Jane; Schmutz, Jeremy; Cardol, Pierre; Cerutti, Heriberto; Chanfreau, Guillaume; Chen, Chun-Long; Cognat, Valérie; Croft, Martin T.; Dent, Rachel; Dutcher, Susan; Fernández, Emilio; Ferris, Patrick; Fukuzawa, Hideya; González-Ballester, David; González-Halphen, Diego; Hallmann, Armin; Hanikenne, Marc; Hippler, Michael; Inwood, William; Jabbari, Kamel; Kalanon, Ming; Kuras, Richard; Lefebvre, Paul A.; Lemaire, Stéphane D.; Lobanov, Alexey V.; Lohr, Martin; Manuell, Andrea; Meier, Iris; Mets, Laurens; Mittag, Maria; Mittelmeier, Telsa; Moroney, James V.; Moseley, Jeffrey; Napoli, Carolyn; Nedelcu, Aurora M.; Niyogi, Krishna; Novoselov, Sergey V.; Paulsen, Ian T.; Pazour, Greg; Purton, Saul; Ral, Jean-Philippe; Riaño-Pachón, Diego Mauricio; Riekhof, Wayne; Rymarquis, Linda; Schroda, Michael; Stern, David; Umen, James; Willows, Robert; Wilson, Nedra; Zimmer, Sara Lana; Allmer, Jens; Balk, Janneke; Bisova, Katerina; Chen, Chong-Jian; Elias, Marek; Gendler, Karla; Hauser, Charles; Lamb, Mary Rose; Ledford, Heidi; Long, Joanne C.; Minagawa, Jun; Page, M. Dudley; Pan, Junmin; Pootakham, Wirulda; Roje, Sanja; Rose, Annkatrin; Stahlberg, Eric; Terauchi, Aimee M.; Yang, Pinfen; Ball, Steven; Bowler, Chris; Dieckmann, Carol L.; Gladyshev, Vadim N.; Green, Pamela; Jorgensen, Richard; Mayfield, Stephen; Mueller-Roeber, Bernd; Rajamani, Sathish; Sayre, Richard T.; Brokstein, Peter; Dubchak, Inna; Goodstein, David; Hornick, Leila; Huang, Y. Wayne; Jhaveri, Jinal; Luo, Yigong; Martínez, Diego; Ngau, Wing Chi Abby; Otillar, Bobby; Poliakov, Alexander; Porter, Aaron; Szajkowski, Lukasz; Werner, Gregory; Zhou, Kemin; Grigoriev, Igor V.; Rokhsar, Daniel S.; Grossman, Arthur R.

    2010-01-01

    Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the ∼120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella. PMID:17932292

  9. The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

    SciTech Connect

    Merchant, Sabeeha S

    2007-04-09

    Chlamydomonas reinhardtii is a unicellular green alga whose lineage diverged from land plants over 1 billion years ago. It is a model system for studying chloroplast-based photosynthesis, as well as the structure, assembly, and function of eukaryotic flagella (cilia), which were inherited from the common ancestor of plants and animals, but lost in land plants. We sequenced the 120-megabase nuclear genome of Chlamydomonas and performed comparative phylogenomic analyses, identifying genes encoding uncharacterized proteins that are likely associated with the function and biogenesis of chloroplasts or eukaryotic flagella. Analyses of the Chlamydomonas genome advance our understanding of the ancestral eukaryotic cell, reveal previously unknown genes associated with photosynthetic and flagellar functions, and establish links between ciliopathy and the composition and function of flagella.

  10. Extensive homology of chicken macrochromosomes in the karyotypes of Trachemys scripta elegans and Crocodylus niloticus revealed by chromosome painting despite long divergence times.

    PubMed

    Kasai, F; O'Brien, P C M; Martin, S; Ferguson-Smith, M A

    2012-01-01

    We report extensive chromosome homology revealed by chromosome painting between chicken (Gallus gallus domesticus, GGA, 2n = 78) macrochromosomes (representing 70% of the chicken genome) and the chromosomes of a turtle, the red-eared slider (Trachemys scripta elegans, TSC, 2n = 50), and the Nile crocodile (Crocodylus niloticus, CNI, 2n = 32). Our data show that GGA1-8 arms seem to be conserved in the arms of TSC chromosomes, GGA1-2 arms are separated and homologous to CNI1p, 3q, 4q and 5q. In addition to GGAZ homologues in our previous study, large-scale GGA autosome syntenies have been conserved in turtle and crocodile despite hundreds of millions of years divergence time. Based on phylogenetic hypotheses that crocodiles diverged after the divergence of birds and turtles, our results in CNI suggest that GGA1-2 and TSC1-2 represent the ancestral state and that chromosome fissions followed by fusions have been the mechanisms responsible for the reduction of chromosome number in crocodiles. PMID:22572532

  11. Functional divergence of HBHA from Mycobacterium tuberculosis and its evolutionary relationship with TadA from Rhodococcus opacus.

    PubMed

    Lanfranconi, Mariana P; Alvarez, Héctor M

    2016-08-01

    Rhodococcus opacus PD630 and Rhodococcus jostii RHA1 are oleaginous bacteria able to synthesize and accumulate triacylglycerols (TAG) in lipid bodies (LB). Highly relevant to the structure of LB is a protein homologous to heparin-binding hemagglutinin (HBHA) (called TadA in rhodococci), which is a virulence factor found in Mycobacterium tuberculosis. HBHA is an adhesin involved in binding to non-phagocytic cells and extrapulmonary dissemination. We observed a conserved synteny of three genes encoding a transcriptional regulator (TR), the HBHA protein and a membrane protein (MP) between TAG-accumulating actinobacteria belonging to Rhodococcus, Mycobacterium, Nocardia and Dietzia genera, among others. A 354 bp-intergenic spacing containing a SigF-binding site was found between hbha and the TR genes in M. tuberculosis, which was absent in genomes of other investigated actinobacteria. Analyses of available "omic" information revealed that TadA and TR were co-induced in rhodococci under TAG-accumulating conditions; whereas in M. tuberculosis and Mycobacterium smegmatis, HBHA and TR were regulated independently under stress conditions occurring during infection. We also found differences in protein lengths, domain content and distribution between HBHA and TadA proteins from mycobacteria and rhodococci, which may explain their different roles in cells. Based on the combination of results obtained in model actinobacteria, we hypothesize that HBHA and TadA proteins originated from a common ancestor, but later suffered a process of functional divergence during evolution. Thus, rhodococcal TadA probably has maintained its original role; whereas HBHA may have evolved as a virulence factor in pathogenic mycobacteria. PMID:27287527

  12. SPATULA and ALCATRAZ, are partially redundant, functionally diverging bHLH genes required for Arabidopsis gynoecium and fruit development.

    PubMed

    Groszmann, Michael; Paicu, Teodora; Alvarez, John P; Swain, Steve M; Smyth, David R

    2011-12-01

    The Arabidopsis gynoecium is a complex organ that facilitates fertilization, later developing into a dehiscent silique that protects seeds until their dispersal. Identifying genes important for development is often hampered by functional redundancy. We report unequal redundancy between two closely related genes, SPATULA (SPT) and ALCATRAZ (ALC), revealing previously unknown developmental roles for each. SPT is known to support septum, style and stigma development in the flower, whereas ALC is involved in dehiscence zone development in the fruit. ALC diverged from a SPT-like ancestor following gene duplication coinciding with the At-β polyploidy event. Here we show that ALC is also involved in early gynoecium development, and SPT in later valve margin generation in the silique. Evidence includes the increased severity of early gynoecium disruption, and of later valve margin defects, in spt-alc double mutants. In addition, a repressive version of SPT (35S:SPT-SRDX) disrupts both structures. Consistent with redundancy, ALC and SPT expression patterns overlap in these tissues, and the ALC promoter carries two atypical E-box elements identical to one in SPT required for valve margin expression. Further, SPT can heterodimerize with ALC, and 35S:SPT can fully complement dehiscence defects in alc mutants, although 35S:ALC can only partly complement spt gynoecium disruptions, perhaps associated with its sequence simplification. Interactions with FRUITFULL and SHATTERPROOF genes differ somewhat between SPT and ALC, reflecting their different specializations. These two genes are apparently undergoing subfunctionalization, with SPT essential for earlier carpel margin tissues, and ALC specializing in later dehiscence zone development. PMID:21801252

  13. Two deeply divergent mitochondrial clades in the wild mouse Mus macedonicus reveal multiple glacial refuges south of Caucasus.

    PubMed

    Orth, A; Auffray, J-C; Bonhomme, F

    2002-11-01

    A survey of 77 individuals covering the range of Mus macedonicus from Georgia in the East to Greece and Bulgaria in the West and Israel in the South has shown the existence of two deeply divergent mitochondrial clades. The southern clade was until now undetected and characterises mice from Israel. Nuclear genes also show some amount of regional differentiation tending to separate the southern M. macedonicus from the northern ones. These results point towards the fact that the eastern Mediterranean short-tailed mouse, which was seen as a fairly homogeneous monotypic species, has in fact a more complex phylogeographic history than has been suspected, and that it warrants the existence of two subspecies. The reasons for this non-uniformity probably ought to be looked for in the history of faunal movements linked to glacial periods, underlining the possible existence of at least two refugia south of the Caucasus. PMID:12399993

  14. Cloning of quantitative trait genes from rice reveals conservation and divergence of photoperiod flowering pathways in Arabidopsis and rice

    PubMed Central

    Matsubara, Kazuki; Hori, Kiyosumi; Ogiso-Tanaka, Eri; Yano, Masahiro

    2014-01-01

    Flowering time in rice (Oryza sativa L.) is determined primarily by daylength (photoperiod), and natural variation in flowering time is due to quantitative trait loci involved in photoperiodic flowering. To date, genetic analysis of natural variants in rice flowering time has resulted in the positional cloning of at least 12 quantitative trait genes (QTGs), including our recently cloned QTGs, Hd17, and Hd16. The QTGs have been assigned to specific photoperiodic flowering pathways. Among them, 9 have homologs in the Arabidopsis genome, whereas it was evident that there are differences in the pathways between rice and Arabidopsis, such that the rice Ghd7–Ehd1–Hd3a/RFT1 pathway modulated by Hd16 is not present in Arabidopsis. In this review, we describe QTGs underlying natural variation in rice flowering time. Additionally, we discuss the implications of the variation in adaptive divergence and its importance in rice breeding. PMID:24860584

  15. Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages.

    PubMed

    Gilbert, Maarten J; Miller, William G; Yee, Emma; Zomer, Aldert L; van der Graaf-van Bloois, Linda; Fitzgerald, Collette; Forbes, Ken J; Méric, Guillaume; Sheppard, Samuel K; Wagenaar, Jaap A; Duim, Birgitta

    2016-01-01

    Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C fetus was performed. The genomes of C fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C fetus subspecies, but a clear distinction between mammal- and reptile-associated C fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C fetus subsp. testudinum strains. Within C fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C fetus Overall, this study shows that reptile-associated C fetus subsp. testudinum is genetically divergent from mammal-associated C fetus subspecies. PMID:27333878

  16. Comparative Genomics of Campylobacter fetus from Reptiles and Mammals Reveals Divergent Evolution in Host-Associated Lineages

    PubMed Central

    Gilbert, Maarten J.; Miller, William G.; Yee, Emma; Zomer, Aldert L.; van der Graaf-van Bloois, Linda; Fitzgerald, Collette; Forbes, Ken J.; Méric, Guillaume; Sheppard, Samuel K.; Wagenaar, Jaap A.; Duim, Birgitta

    2016-01-01

    Campylobacter fetus currently comprises three recognized subspecies, which display distinct host association. Campylobacter fetus subsp. fetus and C. fetus subsp. venerealis are both associated with endothermic mammals, primarily ruminants, whereas C. fetus subsp. testudinum is primarily associated with ectothermic reptiles. Both C. fetus subsp. testudinum and C. fetus subsp. fetus have been associated with severe infections, often with a systemic component, in immunocompromised humans. To study the genetic factors associated with the distinct host dichotomy in C. fetus, whole-genome sequencing and comparison of mammal- and reptile-associated C. fetus was performed. The genomes of C. fetus subsp. testudinum isolated from either reptiles or humans were compared with elucidate the genetic factors associated with pathogenicity in humans. Genomic comparisons showed conservation of gene content and organization among C. fetus subspecies, but a clear distinction between mammal- and reptile-associated C. fetus was observed. Several genomic regions appeared to be subspecies specific, including a putative tricarballylate catabolism pathway, exclusively present in C. fetus subsp. testudinum strains. Within C. fetus subsp. testudinum, sapA, sapB, and sapAB type strains were observed. The recombinant locus iamABC (mlaFED) was exclusively associated with invasive C. fetus subsp. testudinum strains isolated from humans. A phylogenetic reconstruction was consistent with divergent evolution in host-associated strains and the existence of a barrier to lateral gene transfer between mammal- and reptile-associated C. fetus. Overall, this study shows that reptile-associated C. fetus subsp. testudinum is genetically divergent from mammal-associated C. fetus subspecies. PMID:27333878

  17. Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co-distributed species.

    PubMed

    McGovern, Tamara M; Keever, Carson C; Saski, Christopher A; Hart, Michael W; Marko, Peter B

    2010-11-01

    Coalescent samplers are computational time machines for inferring the historical demographic genetic processes that have given rise to observable patterns of spatial genetic variation among contemporary populations. We have used traditional characterizations of population structure and coalescent-based inferences about demographic processes to reconstruct the population histories of two co-distributed marine species, the frilled dog whelk, Nucella lamellosa, and the bat star, Patiria miniata. Analyses of population structure were consistent with previous work in both species except that additional samples of N. lamellosa showed a larger regional genetic break on Vancouver Island (VI) rather than between the southern Alexander Archipelago as in P. miniata. Our understanding of the causes, rather than just the patterns, of spatial genetic variation was dramatically improved by coalescent analyses that emphasized variation in population divergence times. Overall, gene flow was greater in bat stars (planktonic development) than snails (benthic development) but spatially homogeneous within species. In both species, these large phylogeographic breaks corresponded to relatively ancient divergence times between populations rather than regionally restricted gene flow. Although only N. lamellosa shows a large break on VI, population separation times on VI are congruent between species, suggesting a similar response to late Pleistocene ice sheet expansion. The absence of a phylogeographic break in P. miniata on VI can be attributed to greater gene flow and larger effective population size in this species. Such insights put the relative significance of gene flow into a more comprehensive historical biogeographic context and have important implications for conservation and landscape genetic studies that emphasize the role of contemporary gene flow and connectivity in shaping patterns of population differentiation. PMID:21040048

  18. High genetic divergence in miniature breeds of Japanese native chickens compared to Red Junglefowl, as revealed by microsatellite analysis.

    PubMed

    Tadano, R; Nishibori, M; Imamura, Y; Matsuzaki, M; Kinoshita, K; Mizutani, M; Namikawa, T; Tsudzuki, M

    2008-02-01

    A wide diversity of domesticated chicken breeds exist due to artificial selection on the basis of human interests. Miniature variants (bantams) are eminently illustrative of the large changes from ancestral junglefowls. In this report, the genetic characterization of seven Japanese miniature chicken breeds and varieties, together with institute-kept Red Junglefowl, was conducted by means of typing 40 microsatellites located on 21 autosomes. We drew focus to genetic differentiation between the miniature chicken breeds and Red Junglefowl in particular. A total of 305 alleles were identified: 27 of these alleles (8.9%) were unique to the Red Junglefowl with high frequencies (>20%). Significantly high genetic differences (F(ST)) were obtained between Red Junglefowl and all other breeds with a range of 0.3901-0.5128. Individual clustering (constructed from combinations of the proportion of shared alleles and the neighbour-joining method) indicated high genetic divergence among breeds including Red Junglefowl. There were also individual assignments on the basis of the Bayesian and distance-based approaches. The microsatellite differences in the miniature chicken breeds compared to the presumed wild ancestor reflected the phenotypic diversity among them, indicating that each of these miniature chicken breeds is a unique gene pool. PMID:18254737

  19. AFLP Genome Scanning Reveals Divergent Selection in Natural Populations of Liriodendron chinense (Magnoliaceae) along a Latitudinal Transect.

    PubMed

    Yang, Ai-Hong; Wei, Na; Fritsch, Peter W; Yao, Xiao-Hong

    2016-01-01

    Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci) provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined Amplified Fragment Length Polymorphism (AFLP) genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae) along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Both frequency-based (Dfdist and BayeScan) and correlation-based (MLM) methods were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity toward the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation, and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies. PMID:27303414

  20. AFLP Genome Scanning Reveals Divergent Selection in Natural Populations of Liriodendron chinense (Magnoliaceae) along a Latitudinal Transect

    PubMed Central

    Yang, Ai-Hong; Wei, Na; Fritsch, Peter W.; Yao, Xiao-Hong

    2016-01-01

    Understanding adaptive genetic variation and its relation to environmental factors are important for understanding how plants adapt to climate change and for managing genetic resources. Genome scans for the loci exhibiting either notably high or low levels of population differentiation (outlier loci) provide one means of identifying genomic regions possibly associated with convergent or divergent selection. In this study, we combined Amplified Fragment Length Polymorphism (AFLP) genome scan and environmental association analysis to test for signals of natural selection in natural populations of Liriodendron chinense (Chinese Tulip Tree; Magnoliaceae) along a latitudinal transect. We genotyped 276 individuals from 11 populations of L. chinense using 987 AFLP markers. Both frequency-based (Dfdist and BayeScan) and correlation-based (MLM) methods were applied to detect outlier loci. Our analyses recovered both neutral and potentially adaptive genetic differentiation among populations of L. chinense. We found moderate genetic diversity within populations and high genetic differentiation among populations with reduced genetic diversity toward the periphery of the species ranges. Nine AFLP marker loci showed evidence of being outliers for population differentiation for both detection methods. Of these, six were strongly associated with at least one climate factor. Temperature, precipitation, and radiation were found to be three important factors influencing local adaptation of L. chinense. The outlier AFLP loci are likely not the target of natural selection, but the neighboring genes of these loci might be involved in local adaptation. Hence, these candidates should be validated by further studies. PMID:27303414

  1. Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts

    PubMed Central

    Bass, David; Moureau, Gregory; Tang, Shuoya; McAlister, Erica; Culverwell, C. Lorna; Glücksman, Edvard; Wang, Hui; Brown, T. David K.; Gould, Ernest A.; Harbach, Ralph E.; de Lamballerie, Xavier; Firth, Andrew E.

    2013-01-01

    We investigated whether small RNA (sRNA) sequenced from field-collected mosquitoes and chironomids (Diptera) can be used as a proxy signature of viral prevalence within a range of species and viral groups, using sRNAs sequenced from wild-caught specimens, to inform total RNA deep sequencing of samples of particular interest. Using this strategy, we sequenced from adult Anopheles maculipennis s.l. mosquitoes the apparently nearly complete genome of one previously undescribed virus related to chronic bee paralysis virus, and, from a pool of Ochlerotatus caspius and Oc. detritus mosquitoes, a nearly complete entomobirnavirus genome. We also reconstructed long sequences (1503-6557 nt) related to at least nine other viruses. Crucially, several of the sequences detected were reconstructed from host organisms highly divergent from those in which related viruses have been previously isolated or discovered. It is clear that viral transmission and maintenance cycles in nature are likely to be significantly more complex and taxonomically diverse than previously expected. PMID:24260463

  2. Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories.

    PubMed

    Statham, Mark J; Murdoch, James; Janecka, Jan; Aubry, Keith B; Edwards, Ceiridwen J; Soulsbury, Carl D; Berry, Oliver; Wang, Zhenghuan; Harrison, David; Pearch, Malcolm; Tomsett, Louise; Chupasko, Judith; Sacks, Benjamin N

    2014-10-01

    Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization time frame suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y-chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long-term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva. PMID:25212210

  3. Phylogenetic Analysis, Lineage-Specific Expansion and Functional Divergence of seed dormancy 4-Like Genes in Plants

    PubMed Central

    Subburaj, Saminathan; Cao, Shuanghe; Xia, Xianchun; He, Zhonghu

    2016-01-01

    The rice gene seed dormancy 4 (OsSdr4) functions in seed dormancy and is a major factor associated with pre-harvest sprouting (PHS). Although previous studies of this protein family were reported for rice and other species, knowledge of the evolution of genes homologous to OsSdr4 in plants remains inadequate. Fifty four Sdr4-like (hereafter designated Sdr4L) genes were identified in nine plant lineages including 36 species. Phylogenetic analysis placed these genes in eight subfamilies (I-VIII). Genes from the same lineage clustered together, supported by analysis of conserved motifs and exon-intron patterns. Segmental duplications were present in both dicot and monocot clusters, while tandemly duplicated genes occurred only in monocot clusters indicating that both tandem and segmental duplications contributed to expansion of the grass I and II subfamilies. Estimation of the approximate ages of the duplication events indicated that ancestral Sdr4 genes evolved from a common angiosperm ancestor, about 160 million years ago (MYA). Moreover, diversification of Sdr4L genes in mono and dicot plants was mainly associated with genome-wide duplication and speciation events. Functional divergence was observed in all subfamily pairs, except IV/VIIIa. Further analysis indicated that functional constraints between subfamily pairs I/II, I/VIIIb, II/VI, II/VIIIb, II/IV, and VI/VIIIb were statistically significant. Site and branch-site model analyses of positive selection suggested that these genes were under strong adaptive selection pressure. Critical amino acids detected for both functional divergence and positive selection were mostly located in the loops, pointing to functional importance of these regions in this protein family. In addition, differential expression studies by transcriptome atlas of 11 Sdr4L genes showed that the duplicated genes may have undergone divergence in expression between plant species. Our findings showed that Sdr4L genes are functionally divergent

  4. Highly diverged homologs of Saccharomyces cerevisiae mitochondrial mRNA-specific translational activators have orthologous functions in other budding yeasts.

    PubMed Central

    Costanzo, M C; Bonnefoy, N; Williams, E H; Clark-Walker, G D; Fox, T D

    2000-01-01

    Translation of mitochondrially coded mRNAs in Saccharomyces cerevisiae depends on membrane-bound mRNA-specific activator proteins, whose targets lie in the mRNA 5'-untranslated leaders (5'-UTLs). In at least some cases, the activators function to localize translation of hydrophobic proteins on the inner membrane and are rate limiting for gene expression. We searched unsuccessfully in divergent budding yeasts for orthologs of the COX2- and COX3-specific translational activator genes, PET111, PET54, PET122, and PET494, by direct complementation. However, by screening for complementation of mutations in genes adjacent to the PET genes in S. cerevisiae, we obtained chromosomal segments containing highly diverged homologs of PET111 and PET122 from Saccharomyces kluyveri and of PET111 from Kluyveromyces lactis. All three of these genes failed to function in S. cerevisiae. We also found that the 5'-UTLs of the COX2 and COX3 mRNAs of S. kluyveri and K. lactis have little similarity to each other or to those of S. cerevisiae. To determine whether the PET111 and PET122 homologs carry out orthologous functions, we deleted them from the S. kluyveri genome and deleted PET111 from the K. lactis genome. The pet111 mutations in both species prevented COX2 translation, and the S. kluyveri pet122 mutation prevented COX3 translation. Thus, while the sequences of these translational activator proteins and their 5'-UTL targets are highly diverged, their mRNA-specific functions are orthologous. PMID:10757749

  5. Divergent roles of BECN1 in LC3 lipidation and autophagosomal function.

    PubMed

    He, Ruina; Peng, Jingyu; Yuan, Pengfei; Xu, Fang; Wei, Wensheng

    2015-01-01

    BECN1/Beclin 1 is regarded as a critical component in the class III phosphatidylinositol 3-kinase (PtdIns3K) complex to trigger autophagy in mammalian cells. Despite its significant role in a number of cellular and physiological processes, the exact function of BECN1 in autophagy remains controversial. Here we created a BECN1 knockout human cell line using the TALEN technique. Surprisingly, the complete loss of BECN1 had little effect on LC3 (MAP1LC3B/LC3B) lipidation, and LC3B puncta resembling autophagosomes by fluorescence microscopy were still evident albeit significantly smaller than those in the wild-type cells. Electron microscopy (EM) analysis revealed that BECN1 deficiency led to malformed autophagosome-like structures containing multiple layers of membranes under amino acid starvation. We further confirmed that the PtdIns3K complex activity and autophagy flux were disrupted in BECN1(-/-) cells. Our results demonstrate the essential role of BECN1 in the functional formation of autophagosomes, but not in LC3B lipidation. PMID:25955014

  6. Floral development of Hydrocera and Impatiens reveals evolutionary trends in the most early diverged lineages of the Balsaminaceae

    PubMed Central

    Janssens, Steven B.; Smets, Erik F.; Vrijdaghs, Alexander

    2012-01-01

    Background and Aims Balsaminaceae consist of two genera, the monospecific Hydrocera and its species-rich sister Impatiens. Although both genera are seemingly rather similar in overall appearance, they differ in ecology, distribution range, habitat preference and morphology. Because morphological support for the current molecular phylogenetic hypothesis of Impatiens is low, a developmental study is necessary in order to obtain better insights into the evolutionary history of the family. Therefore, the floral development of H. triflora and I. omeiana was investigated, representing the most early-diverged lineage of Impatiens, and the observations were compared with the literature. Methods Flowers at all developmental stages were examined using scanning electron microscopy and light microscopy. Key results In Hydrocera, two whorls of five free perianth primordia develop into a less zygomorphic perianth compared with its sister genus. The androecial cap originates from five individual stamen primordia. Post-genital fusion of the upper parts of the filaments result in a filament ring below the anthers. The anthers fuse forming connivent anther-like units. The gynoecium of Hydrocera is pentamerous; it is largely synascidiate in early development. Only then is a symplicate zone formed resulting in style and stigmas. In I. omeiana, the perianth is formed as in Hydrocera. Five individual stamen primordia develop into five stamens, of which the upper part of the filaments converge with each other. The gynoecium of I. omeiana is tetramerous; it appears annular in early development. Conclusions Comparison of the present results with developmental data from the literature confirms the perianth morphocline hypothesis in which a congenital fusion of the parts of the perianth results in a shift from pentasepalous to trisepalous flowers. In addition, the development of the androecial cap and the gynoecium follows several distinct ontogenetic sequences within the family. PMID

  7. DNA Barcoding of Gypsy Moths From China (Lepidoptera: Erebidae) Reveals New Haplotypes and Divergence Patterns Within Gypsy Moth Subspecies.

    PubMed

    Chen, Fang; Luo, Youqing; Keena, Melody A; Wu, Ying; Wu, Peng; Shi, Juan

    2016-02-01

    The gypsy moth from Asia (two subspecies) is considered a greater threat to North America than European gypsy moth, because of a broader host range and females being capable of flight. Variation within and among gypsy moths from China (nine locations), one of the native countries of Asian gypsy moth, were compared using DNA barcode sequences (658 bp of mtDNA cytochrome c oxidase subunit 1 [COI] sequence), together with two restriction site mtDNA markers (NlaIII and BamHI in COI), which is the standard system used to distinguish European gypsy moths from Asian gypsy moths. Relatedness of these populations to gypsy moths from seven other world areas was also examined. The restriction site markers showed that two Chinese populations had both Asian and European haplotypes. DNA barcode sequence divergence between the Asian populations and the European populations was three times greater than the variation within each group. Using Bayesian and parsimonious network analyses, nine previously unknown barcode haplotypes were documented from China and a single haplotype was found to be shared by 55% of the Chinese and some Far Eastern Russian and Japanese individuals. Some gypsy moths from two Chinese populations showed genetic affinity with mtDNA haplotypes from Siberia, Russia, suggesting there could be a cryptic new subspecies in Lymantria dispar (L.) or human-aided movement of moths between these two locations at an earlier point in time. The previously unknown haplotype patterns may complicate efforts to identify Asian gypsy moth introductions and require changes in monitoring and exclusion programs. PMID:26371156

  8. Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals

    PubMed Central

    Daugherty, Matthew D; Schaller, Aaron M; Geballe, Adam P; Malik, Harmit S

    2016-01-01

    IFIT (interferon-induced with tetratricopeptide repeats) proteins are critical mediators of mammalian innate antiviral immunity. Mouse IFIT1 selectively inhibits viruses that lack 2'O-methylation of their mRNA 5' caps. Surprisingly, human IFIT1 does not share this antiviral specificity. Here, we resolve this discrepancy by demonstrating that human and mouse IFIT1 have evolved distinct functions using a combination of evolutionary, genetic and virological analyses. First, we show that human IFIT1 and mouse IFIT1 (renamed IFIT1B) are not orthologs, but are paralogs that diverged >100 mya. Second, using a yeast genetic assay, we show that IFIT1 and IFIT1B proteins differ in their ability to be suppressed by a cap 2'O-methyltransferase. Finally, we demonstrate that IFIT1 and IFIT1B have divergent antiviral specificities, including the discovery that only IFIT1 proteins inhibit a virus encoding a cap 2'O-methyltransferase. These functional data, combined with widespread turnover of mammalian IFIT genes, reveal dramatic species-specific differences in IFIT-mediated antiviral repertoires. DOI: http://dx.doi.org/10.7554/eLife.14228.001 PMID:27240734

  9. Evolution-guided functional analyses reveal diverse antiviral specificities encoded by IFIT1 genes in mammals.

    PubMed

    Daugherty, Matthew D; Schaller, Aaron M; Geballe, Adam P; Malik, Harmit S

    2016-01-01

    IFIT (interferon-induced with tetratricopeptide repeats) proteins are critical mediators of mammalian innate antiviral immunity. Mouse IFIT1 selectively inhibits viruses that lack 2'O-methylation of their mRNA 5' caps. Surprisingly, human IFIT1 does not share this antiviral specificity. Here, we resolve this discrepancy by demonstrating that human and mouse IFIT1 have evolved distinct functions using a combination of evolutionary, genetic and virological analyses. First, we show that human IFIT1 and mouse IFIT1 (renamed IFIT1B) are not orthologs, but are paralogs that diverged >100 mya. Second, using a yeast genetic assay, we show that IFIT1 and IFIT1B proteins differ in their ability to be suppressed by a cap 2'O-methyltransferase. Finally, we demonstrate that IFIT1 and IFIT1B have divergent antiviral specificities, including the discovery that only IFIT1 proteins inhibit a virus encoding a cap 2'O-methyltransferase. These functional data, combined with widespread turnover of mammalian IFIT genes, reveal dramatic species-specific differences in IFIT-mediated antiviral repertoires. PMID:27240734

  10. Snake venomics of Micrurus alleni and Micrurus mosquitensis from the Caribbean region of Costa Rica reveals two divergent compositional patterns in New World elapids.

    PubMed

    Fernández, Julián; Vargas-Vargas, Nancy; Pla, Davinia; Sasa, Mahmood; Rey-Suárez, Paola; Sanz, Libia; Gutiérrez, José María; Calvete, Juan J; Lomonte, Bruno

    2015-12-01

    Protein composition, toxicity, and neutralization of the venoms of Micrurus alleni and Micrurus mosquitensis, two sympatric monadal coral snakes found in humid environments of the Caribbean region of Costa Rica, were studied. Proteomic profiling revealed that these venoms display highly divergent compositions: the former dominated by three-finger toxins (3FTx) and the latter by phospholipases A2 (PLA2). Protein family abundances correlated with enzymatic and toxic characteristics of the venoms. Selective inhibition experiments showed that PLA2s play only a marginal role in the lethal effect of M. alleni venom, but have a major role in M. mosquitensis venom. Proteomic data gathered from other Micrurus species evidenced that the two divergent venom phenotypes are recurrent, and may constitute a general trend across New World elapids. Further, M. mosquitensis, but not M. alleni, venom contains PLA2-like/Kunitz-type inhibitor complex(es) that resemble the ASIC1a/2-activating MitTx heterodimeric toxin isolated from Micrurus tener venom. The evolutionary origin and adaptive relevance of the puzzling phenotypic variability of Micrurus venoms remain to be understood. An antivenom against the PLA2-predominant Micrurus nigrocinctus venom strongly cross-recognized and neutralized M. mosquitensis venom, but only weakly M. alleni venom. PMID:26325292

  11. Linkage Maps of the dwarf and Normal Lake Whitefish (Coregonus clupeaformis) Species Complex and Their Hybrids Reveal the Genetic Architecture of Population Divergence

    PubMed Central

    Rogers, S. M.; Isabel, N.; Bernatchez, L.

    2007-01-01

    Elucidating the genetic architecture of population divergence may reveal the evolution of reproductive barriers and the genomic regions implicated in the process. We assembled genetic linkage maps for the dwarf and Normal lake whitefish species complex and their hybrids. A total of 877 AFLP loci and 30 microsatellites were positioned. The homology of mapped loci between families supported the existence of 34 linkage groups (of 40n expected) exhibiting 83% colinearity among linked loci between these two families. Classes of AFLP markers were not randomly distributed among linkage groups. Both AFLP and microsatellites exhibited deviations from Mendelian expectations, with 30.4% exhibiting significant segregation distortion across 28 linkage groups of the four linkage maps in both families (P < 0.00001). Eight loci distributed over seven homologous linkage groups were significantly distorted in both families and the level of distortion, when comparing homologous loci of the same phase between families, was correlated (Spearman R = 0.378, P = 0.0021). These results suggest that substantial divergence incurred during allopatric glacial separation and subsequent sympatric ecological specialization has resulted in several genomic regions that are no longer complementary between dwarf and Normal populations issued from different evolutionary glacial lineages. PMID:17110497

  12. Conserved and Diverged Functions of the Calcineurin-Activated Prz1 Transcription Factor in Fission Yeast.

    PubMed

    Chatfield-Reed, Kate; Vachon, Lianne; Kwon, Eun-Joo Gina; Chua, Gordon

    2016-04-01

    Gene regulation in response to intracellular calcium is mediated by the calcineurin-activated transcription factor Prz1 in the fission yeastSchizosaccharomyces pombe Genome-wide studies of theCrz1and CrzA fungal orthologs have uncovered numerous target genes involved in conserved and species-specific cellular processes. In contrast, very few target genes of Prz1 have been published. This article identifies an extensive list of genes using transcriptome and ChIP-chip analyses under inducing conditions of Prz1, including CaCl2and tunicamycin treatment, as well as a∆pmr1genetic background. We identified 165 upregulated putative target genes of Prz1 in which the majority contained a calcium-dependent response element in their promoters, similar to that of theSaccharomyces cerevisiaeorthologCrz1 These genes were functionally enriched forCrz1-conserved processes such as cell-wall biosynthesis. Overexpression ofprz1(+)increased resistance to the cell-wall degradation enzyme zymolyase, likely from upregulation of theO-mannosyltransferase encoding geneomh1(+) Loss ofomh1(+)abrogates this phenotype. We uncovered a novel inhibitory role in flocculation for Prz1. Loss ofprz1(+)resulted in constitutive flocculation and upregulation of genes encoding the flocculins Gsf2 and Pfl3, as well as the transcription factor Cbf12. The constitutive flocculation of the∆prz1strain was abrogated by the loss ofgsf2(+)orcbf12(+) This study reveals that Prz1 functions as a positive and negative transcriptional regulator of genes involved in cell-wall biosynthesis and flocculation, respectively. Moreover, comparison of target genes betweenCrz1/CrzA and Prz1 indicate some conservation in DNA-binding specificity, but also substantial rewiring of the calcineurin-mediated transcriptional regulatory network. PMID:26896331

  13. Conserved and Diverged Functions of the Calcineurin-Activated Prz1 Transcription Factor in Fission Yeast

    PubMed Central

    Chatfield-Reed, Kate; Vachon, Lianne; Kwon, Eun-Joo Gina; Chua, Gordon

    2016-01-01

    Gene regulation in response to intracellular calcium is mediated by the calcineurin-activated transcription factor Prz1 in the fission yeast Schizosaccharomyces pombe. Genome-wide studies of the Crz1 and CrzA fungal orthologs have uncovered numerous target genes involved in conserved and species-specific cellular processes. In contrast, very few target genes of Prz1 have been published. This article identifies an extensive list of genes using transcriptome and ChIP-chip analyses under inducing conditions of Prz1, including CaCl2 and tunicamycin treatment, as well as a ∆pmr1 genetic background. We identified 165 upregulated putative target genes of Prz1 in which the majority contained a calcium-dependent response element in their promoters, similar to that of the Saccharomyces cerevisiae ortholog Crz1. These genes were functionally enriched for Crz1-conserved processes such as cell-wall biosynthesis. Overexpression of prz1+ increased resistance to the cell-wall degradation enzyme zymolyase, likely from upregulation of the O-mannosyltransferase encoding gene omh1+. Loss of omh1+ abrogates this phenotype. We uncovered a novel inhibitory role in flocculation for Prz1. Loss of prz1+ resulted in constitutive flocculation and upregulation of genes encoding the flocculins Gsf2 and Pfl3, as well as the transcription factor Cbf12. The constitutive flocculation of the ∆prz1 strain was abrogated by the loss of gsf2+ or cbf12+. This study reveals that Prz1 functions as a positive and negative transcriptional regulator of genes involved in cell-wall biosynthesis and flocculation, respectively. Moreover, comparison of target genes between Crz1/CrzA and Prz1 indicate some conservation in DNA-binding specificity, but also substantial rewiring of the calcineurin-mediated transcriptional regulatory network. PMID:26896331

  14. Functional divergence of BAK1 genes from Brassica rapa in regulating plant architecture.

    PubMed

    Zhang, S; Li, C; Li, Q; Wang, Q N; Huang, S H; Zhang, Y F; Wang, X F

    2015-01-01

    BAK1 is a co-receptor of BRI1 in early signaling pathways mediated by brassinosteroids (BRs) and is thought to play a major role in plant growth and development. As the role of BAK1 has not yet been fully elucidated then further research is required to explore its potential for use in genetic modification to improve crops. In this study, three BAK1 genes from the amphidiploid species Brassica rapa were isolated and their kinase functions were predicted following DNA sequence analysis. A bioinformatic analysis revealed that two genes, BrBAK1-1 and BrBAK1-8, shared a conserved kinase domain and 5 tandem leucine-rich repeats (LRRs) that are characteristic of a BAK1 receptor for BR perception, whereas the third gene, BrBAK1-3, was deficient for a signal peptide, but had 4 leucine zippers and 3 leucine-rich repeats (LRRs) in an extracellular domain. All three BrBAK1 kinases localized on the cellular membrane. Ectopic expression of each BrBAK1 gene in BR-insensitive (bri1-5 mutant) Arabidopsis plants indicated that BrBAK1-1 and BrBAK1-8 were functional homologues of AtBAK1 based on the rescue of growth in the bri1-5 mutant. Overexpression of BrBAK1-3 caused a severe dwarf phenotype resembling the phenotype of null BRI1 alleles. The results here suggest there are significant differences among the three BrBAK1 kinases for their effects on plant architecture. This conclusion has important implications for genetic modification of B. rapa. PMID:26600518

  15. The effects of a single night of sleep deprivation on fluency and prefrontal cortex function during divergent thinking

    PubMed Central

    Vartanian, Oshin; Bouak, Fethi; Caldwell, J. L.; Cheung, Bob; Cupchik, Gerald; Jobidon, Marie-Eve; Lam, Quan; Nakashima, Ann; Paul, Michel; Peng, Henry; Silvia, Paul J.; Smith, Ingrid

    2014-01-01

    The dorsal and ventral aspects of the prefrontal cortex (PFC) are the two regions most consistently recruited in divergent thinking tasks. Given that frontal tasks have been shown to be vulnerable to sleep loss, we explored the impact of a single night of sleep deprivation on fluency (i.e., number of generated responses) and PFC function during divergent thinking. Participants underwent functional magnetic resonance imaging scanning twice while engaged in the Alternate Uses Task (AUT) – once following a single night of sleep deprivation and once following a night of normal sleep. They also wore wrist activity monitors, which enabled us to quantify daily sleep and model cognitive effectiveness. The intervention was effective, producing greater levels of fatigue and sleepiness. Modeled cognitive effectiveness and fluency were impaired following sleep deprivation, and sleep deprivation was associated with greater activation in the left inferior frontal gyrus (IFG) during AUT. The results suggest that an intervention known to temporarily compromise frontal function can impair fluency, and that this effect is instantiated in the form of an increased hemodynamic response in the left IFG. PMID:24795594

  16. Comparative developmental analysis of Drosophila and Tribolium reveals conserved and diverged roles of abrupt in insect wing evolution.

    PubMed

    Ravisankar, Padmapriyadarshini; Lai, Yi-Ting; Sambrani, Nagraj; Tomoyasu, Yoshinori

    2016-01-15

    Morphological innovation is a fundamental process in evolution, yet its molecular basis is still elusive. Acquisition of elytra, highly modified beetle forewings, is an important innovation that has driven the successful radiation of beetles. Our RNAi screening for candidate genes has identified abrupt (ab) as a potential key player in elytron evolution. In this study, we performed a series of RNA interference (RNAi) experiments in both Tribolium and Drosophila to understand the contributions of ab to the evolution of beetle elytra. We found that (i) ab is essential for proper wing vein patterning both in Tribolium and Drosophila, (ii) ab has gained a novel function in determining the unique elytron shape in the beetle lineage, (iii) unlike Hippo and Insulin, other shape determining pathways, the shape determining function of ab is specific to the elytron and not required in the hindwing, (iv) ab has a previously undescribed role in the Notch signal-associated wing formation processes, which appears to be conserved between beetles and flies. These data suggest that ab has gained a new function during elytron evolution in beetles without compromising the conserved wing-related functions. Gaining a new function without losing evolutionarily conserved functions may be a key theme in the evolution of morphologically novel structures. PMID:26687509

  17. Conserved and divergent functions of RcrRPQ in Streptococcus gordonii and S. mutans

    PubMed Central

    Shields, Robert C.; Burne, Robert A.

    2015-01-01

    In the dental caries pathogen Streptococcus mutans, an MarR-like transcriptional regulator (RcrR), two ABC efflux pumps (RcrPQ) and two effector peptides encoded in the rcrRPQ operon provide molecular connections between stress tolerance, (p)ppGpp metabolism and genetic competence. Here, we examined the role of RcrRPQ in the oral commensal S. gordonii. Unlike in S. mutans, introduction of polar or non-polar rcrR mutations into S. gordonii elicited no significant changes in transformation efficiency. However, S. gordonii rcrR mutants were markedly impaired in their ability to grow in the presence of hydrogen peroxide, paraquat, low pH or elevated temperature. Sensitivity to paraquat could also be conferred by mutation of cysteine residues that are present in the RcrR protein of S. gordonii, but not in S. mutans RcrR. Thus, stress tolerance is a conserved function of RcrRPQ in a commensal and pathogenic streptococcus, but the study reveals additional differences in regulation of genetic competence development between S. mutans and S. gordonii. PMID:26229070

  18. Conserved and divergent functions of RcrRPQ in Streptococcus gordonii and S. mutans.

    PubMed

    Shields, Robert C; Burne, Robert A

    2015-08-01

    In the dental caries pathogen Streptococcus mutans, an MarR-like transcriptional regulator (RcrR), two ABC efflux pumps (RcrPQ) and two effector peptides encoded in the rcrRPQ operon provide molecular connections between stress tolerance, (p)ppGpp metabolism and genetic competence. Here, we examined the role of RcrRPQ in the oral commensal S. gordonii. Unlike in S. mutans, introduction of polar or non-polar rcrR mutations into S. gordonii elicited no significant changes in transformation efficiency. However, S. gordonii rcrR mutants were markedly impaired in their ability to grow in the presence of hydrogen peroxide, paraquat, low pH or elevated temperature. Sensitivity to paraquat could also be conferred by mutation of cysteine residues that are present in the RcrR protein of S. gordonii, but not in S. mutans RcrR. Thus, stress tolerance is a conserved function of RcrRPQ in a commensal and pathogenic streptococcus, but the study reveals additional differences in regulation of genetic competence development between S. mutans and S. gordonii. PMID:26229070

  19. Functional Divergence of Diterpene Syntheses in the Medicinal Plant Salvia miltiorrhiza1[OPEN

    PubMed Central

    Cui, Guanghong; Duan, Lixin; Jin, Baolong; Qian, Jun; Xue, Zheyong; Shen, Guoan; Snyder, John Hugh; Song, Jingyuan; Chen, Shilin; Huang, Luqi; Peters, Reuben J.; Qi, Xiaoquan

    2015-01-01

    The medicinal plant Salvia miltiorrhiza produces various tanshinone diterpenoids that have pharmacological activities such as vasorelaxation against ischemia reperfusion injury and antiarrhythmic effects. Their biosynthesis is initiated from the general diterpenoid precursor (E,E,E)-geranylgeranyl diphosphate by sequential reactions catalyzed by copalyl diphosphate synthase (CPS) and kaurene synthase-like cyclases. Here, we report characterization of these enzymatic families from S. miltiorrhiza, which has led to the identification of unique pathways, including roles for separate CPSs in tanshinone production in roots versus aerial tissues (SmCPS1 and SmCPS2, respectively) as well as the unique production of ent-13-epi-manoyl oxide by SmCPS4 and S. miltiorrhiza kaurene synthase-like2 in floral sepals. The conserved SmCPS5 is involved in gibberellin plant hormone biosynthesis. Down-regulation of SmCPS1 by RNA interference resulted in substantial reduction of tanshinones, and metabolomics analysis revealed 21 potential intermediates, indicating a complex network for tanshinone metabolism defined by certain key biosynthetic steps. Notably, the correlation between conservation pattern and stereochemical product outcome of the CPSs observed here suggests a degree of correlation that, especially when combined with the identity of certain key residues, may be predictive. Accordingly, this study provides molecular insights into the evolutionary diversification of functional diterpenoids in plants. PMID:26077765

  20. Comparative Genomics Including the Early-Diverging Smut Fungus Ceraceosorus bombacis Reveals Signatures of Parallel Evolution within Plant and Animal Pathogens of Fungi and Oomycetes

    PubMed Central

    Sharma, Rahul; Xia, Xiaojuan; Riess, Kai; Bauer, Robert; Thines, Marco

    2015-01-01

    Ceraceosorus bombacis is an early-diverging lineage of smut fungi and a pathogen of cotton trees (Bombax ceiba). To study the evolutionary genomics of smut fungi in comparison with other fungal and oomycete pathogens, the genome of C. bombacis was sequenced and comparative genomic analyses were performed. The genome of 26.09 Mb encodes for 8,024 proteins, of which 576 are putative-secreted effector proteins (PSEPs). Orthology analysis revealed 30 ortholog PSEPs among six Ustilaginomycotina genomes, the largest groups of which are lytic enzymes, such as aspartic peptidase and glycoside hydrolase. Positive selection analyses revealed the highest percentage of positively selected PSEPs in C. bombacis compared with other Ustilaginomycotina genomes. Metabolic pathway analyses revealed the absence of genes encoding for nitrite and nitrate reductase in the genome of the human skin pathogen Malassezia globosa, but these enzymes are present in the sequenced plant pathogens in smut fungi. Interestingly, these genes are also absent in cultivable oomycete animal pathogens, while nitrate reductase has been lost in cultivable oomycete plant pathogens. Similar patterns were also observed for obligate biotrophic and hemi-biotrophic fungal and oomycete pathogens. Furthermore, it was found that both fungal and oomycete animal pathogen genomes are lacking cutinases and pectinesterases. Overall, these findings highlight the parallel evolution of certain genomic traits, revealing potential common evolutionary trajectories among fungal and oomycete pathogens, shaping the pathogen genomes according to their lifestyle. PMID:26314305

  1. Comparative Genomics Including the Early-Diverging Smut Fungus Ceraceosorus bombacis Reveals Signatures of Parallel Evolution within Plant and Animal Pathogens of Fungi and Oomycetes.

    PubMed

    Sharma, Rahul; Xia, Xiaojuan; Riess, Kai; Bauer, Robert; Thines, Marco

    2015-09-01

    Ceraceosorus bombacis is an early-diverging lineage of smut fungi and a pathogen of cotton trees (Bombax ceiba). To study the evolutionary genomics of smut fungi in comparison with other fungal and oomycete pathogens, the genome of C. bombacis was sequenced and comparative genomic analyses were performed. The genome of 26.09 Mb encodes for 8,024 proteins, of which 576 are putative-secreted effector proteins (PSEPs). Orthology analysis revealed 30 ortholog PSEPs among six Ustilaginomycotina genomes, the largest groups of which are lytic enzymes, such as aspartic peptidase and glycoside hydrolase. Positive selection analyses revealed the highest percentage of positively selected PSEPs in C. bombacis compared with other Ustilaginomycotina genomes. Metabolic pathway analyses revealed the absence of genes encoding for nitrite and nitrate reductase in the genome of the human skin pathogen Malassezia globosa, but these enzymes are present in the sequenced plant pathogens in smut fungi. Interestingly, these genes are also absent in cultivable oomycete animal pathogens, while nitrate reductase has been lost in cultivable oomycete plant pathogens. Similar patterns were also observed for obligate biotrophic and hemi-biotrophic fungal and oomycete pathogens. Furthermore, it was found that both fungal and oomycete animal pathogen genomes are lacking cutinases and pectinesterases. Overall, these findings highlight the parallel evolution of certain genomic traits, revealing potential common evolutionary trajectories among fungal and oomycete pathogens, shaping the pathogen genomes according to their lifestyle. PMID:26314305

  2. Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions

    PubMed Central

    Pezer, Željka; Harr, Bettina; Teschke, Meike; Babiker, Hiba; Tautz, Diethard

    2015-01-01

    Copy number variation represents a major source of genetic divergence, yet the evolutionary dynamics of genic copy number variation in natural populations during differentiation and adaptation remain unclear. We applied a read depth approach to genome resequencing data to detect copy number variants (CNVs) ≥1 kb in wild-caught mice belonging to four populations of Mus musculus domesticus. We complemented the bioinformatics analyses with experimental validation using droplet digital PCR. The specific focus of our analysis is CNVs that include complete genes, as these CNVs could be expected to contribute most directly to evolutionary divergence. In total, 1863 transcription units appear to be completely encompassed within CNVs in at least one individual when compared to the reference assembly. Further, 179 of these CNVs show population-specific copy number differences, and 325 are subject to complete deletion in multiple individuals. Among the most copy-number variable genes are three highly conserved genes that encode the splicing factor CWC22, the spindle protein SFI1, and the Holliday junction recognition protein HJURP. These genes exhibit population-specific expansion patterns that suggest involvement in local adaptations. We found that genes that overlap with large segmental duplications are generally more copy-number variable. These genes encode proteins that are relevant for environmental and behavioral interactions, such as vomeronasal and olfactory receptors, as well as major urinary proteins and several proteins of unknown function. The overall analysis shows that genic CNVs contribute more to population differentiation in mice than in humans and may promote and speed up population divergence. PMID:26149421

  3. Expansion and Functional Divergence of Jumonji C-Containing Histone Demethylases: Significance of Duplications in Ancestral Angiosperms and Vertebrates.

    PubMed

    Qian, Shengzhan; Wang, Yingxiang; Ma, Hong; Zhang, Liangsheng

    2015-08-01

    Histone modifications, such as methylation and demethylation, are crucial mechanisms altering chromatin structure and gene expression. Recent biochemical and molecular studies have uncovered a group of histone demethylases called Jumonji C (JmjC) domain proteins. However, their evolutionary history and patterns have not been examined systematically. Here, we report extensive analyses of eukaryotic JmjC genes and define 14 subfamilies, including the Lysine-Specific Demethylase3 (KDM3), KDM5, JMJD6, Putative-Lysine-Specific Demethylase11 (PKDM11), and PKDM13 subfamilies, shared by plants, animals, and fungi. Other subfamilies are detected in plants and animals but not in fungi (PKDM12) or in animals and fungi but not in plants (KDM2 and KDM4). PKDM7, PKDM8, and PKDM9 are plant-specific groups, whereas Jumonji, AT-Rich Interactive Domain2, KDM6, and PKDM10 are animal specific. In addition to known domains, most subfamilies have characteristic conserved amino acid motifs. Whole-genome duplication (WGD) was likely an important mechanism for JmjC duplications, with four pairs from an angiosperm-wide WGD and others from subsequent WGDs. Vertebrates also experienced JmjC duplications associated with the vertebrate ancestral WGDs, with additional mammalian paralogs from tandem duplication and possible transposition. The sequences of paralogs have diverged in both known functional domains and other regions, showing evidence of selection pressure. The increases of JmjC copy number and the divergences in sequence and expression might have contributed to the divergent functions of JmjC genes, allowing the angiosperms and vertebrates to adapt to a great number of ecological niches and contributing to their evolutionary successes. PMID:26059336

  4. Three Homologous Genes Encoding sn-Glycerol-3-Phosphate Acyltransferase 4 Exhibit Different Expression Patterns and Functional Divergence in Brassica napus1[C][W][OA

    PubMed Central

    Chen, Xue; Truksa, Martin; Snyder, Crystal L.; El-Mezawy, Aliaa; Shah, Saleh; Weselake, Randall J.

    2011-01-01

    Brassica napus is an allotetraploid (AACC) formed from the fusion of two diploid progenitors, Brassica rapa (AA) and Brassica oleracea (CC). Polyploidy and genome-wide rearrangement during the evolution process have resulted in genes that are present as multiple homologs in the B. napus genome. In this study, three B. napus homologous genes encoding endoplasmic reticulum-bound sn-glycerol-3-phosphate acyltransferase 4 (GPAT4) were identified and characterized. Although the three GPAT4 homologs share a high sequence similarity, they exhibit different expression patterns and altered epigenetic features. Heterologous expression in yeast further revealed that the three BnGPAT4 homologs encoded functional GPAT enzymes but with different levels of polypeptide accumulation. Complementation of the Arabidopsis (Arabidopsis thaliana) gpat4 gpat8 double mutant line with individual BnGPAT4 homologs suggested their physiological roles in cuticle formation. Analysis of gpat4 RNA interference lines of B. napus revealed that the BnGPAT4 deficiency resulted in reduced cutin content and altered stomatal structures in leaves. Our results revealed that the BnGPAT4 homologs have evolved into functionally divergent forms and play important roles in cutin synthesis and stomatal development. PMID:21173024

  5. Flower development of Phalaenopsis orchid involves functionally divergent SEPALLATA-like genes

    PubMed Central

    Pan, Zhao-Jun; Chen, You-Yi; Du, Jian-Syun; Chen, Yun-Yu; Chung, Mei-Chu; Tsai, Wen-Chieh; Wang, Chun-Neng; Chen, Hong-Hwa

    2014-01-01

    The Phalaenopsis orchid produces complex flowers that are commercially valuable, which has promoted the study of its flower development. E-class MADS-box genes, SEPALLATA (SEP), combined with B-, C- and D-class MADS-box genes, are involved in various aspects of plant development, such as floral meristem determination, organ identity, fruit maturation, seed formation and plant architecture. Four SEP-like genes were cloned from Phalaenopsis orchid, and the duplicated PeSEPs were grouped into PeSEP1/3 and PeSEP2/4. All PeSEPs were expressed in all floral organs. PeSEP2 expression was detectable in vegetative tissues. The study of protein–protein interactions suggested that PeSEPs may form higher order complexes with the B-, C-, D-class and AGAMOUS LIKE6-related MADS-box proteins to determine floral organ identity. The tepal became a leaf-like organ when PeSEP3 was silenced by virus-induced silencing, with alterations in epidermis identity and contents of anthocyanin and chlorophyll. Silencing of PeSEP2 had minor effects on the floral phenotype. Silencing of the E-class genes PeSEP2 and PeSEP3 resulted in the downregulation of B-class PeMADS2-6 genes, which indicates an association of PeSEP functions and B-class gene expression. These findings reveal the important roles of PeSEP in Phalaenopsis floral organ formation throughout the developmental process by the formation of various multiple protein complexes. PMID:24571782

  6. Flower development of Phalaenopsis orchid involves functionally divergent SEPALLATA-like genes.

    PubMed

    Pan, Zhao-Jun; Chen, You-Yi; Du, Jian-Syun; Chen, Yun-Yu; Chung, Mei-Chu; Tsai, Wen-Chieh; Wang, Chun-Neng; Chen, Hong-Hwa

    2014-05-01

    The Phalaenopsis orchid produces complex flowers that are commercially valuable, which has promoted the study of its flower development. E-class MADS-box genes, SEPALLATA (SEP), combined with B-, C- and D-class MADS-box genes, are involved in various aspects of plant development, such as floral meristem determination, organ identity, fruit maturation, seed formation and plant architecture. Four SEP-like genes were cloned from Phalaenopsis orchid, and the duplicated PeSEPs were grouped into PeSEP1/3 and PeSEP2/4. All PeSEPs were expressed in all floral organs. PeSEP2 expression was detectable in vegetative tissues. The study of protein-protein interactions suggested that PeSEPs may form higher order complexes with the B-, C-, D-class and AGAMOUS LIKE6-related MADS-box proteins to determine floral organ identity. The tepal became a leaf-like organ when PeSEP3 was silenced by virus-induced silencing, with alterations in epidermis identity and contents of anthocyanin and chlorophyll. Silencing of PeSEP2 had minor effects on the floral phenotype. Silencing of the E-class genes PeSEP2 and PeSEP3 resulted in the downregulation of B-class PeMADS2-6 genes, which indicates an association of PeSEP functions and B-class gene expression. These findings reveal the important roles of PeSEP in Phalaenopsis floral organ formation throughout the developmental process by the formation of various multiple protein complexes. PMID:24571782

  7. Two functionally divergent UDP-Gal nucleotide sugar transporters participate in phosphoglycan synthesis in Leishmania major.

    PubMed

    Capul, Althea A; Barron, Tamara; Dobson, Deborah E; Turco, Salvatore J; Beverley, Stephen M

    2007-05-11

    In the protozoan parasite Leishmania, abundant surface and secreted molecules, such as lipophosphoglycan (LPG) and proteophosphoglycans (PPGs), contain extensive galactose in the form of phosphoglycans (PGs) based on (Gal-Man-PO(4)) repeating units. PGs are synthesized in the parasite Golgi apparatus and require transport of cytoplasmic nucleotide sugar precursors to the Golgi lumen by nucleotide sugar transporters (NSTs). GDP-Man transport is mediated by the LPG2 gene product, and here we focused on transporters for UDP-Gal. Data base mining revealed 12 candidate NST genes in the L. major genome, including LPG2 as well as a candidate endoplasmic reticulum UDP-glucose transporter (HUT1L) and several pseudogenes. Gene knock-out studies established that two genes (LPG5A and LPG5B) encoded UDP-Gal NSTs. Although the single lpg5A(-) and lpg5B(-) mutants produced PGs, an lpg5A(-)/5B(-) double mutant was completely deficient. PG synthesis was restored in the lpg5A(-)/5B(-) mutant by heterologous expression of the human UDP-Gal transporter, and heterologous expression of LPG5A and LPG5B rescued the glycosylation defects of the mammalian Lec8 mutant, which is deficient in UDP-Gal uptake. Interestingly, the LPG5A and LPG5B functions overlap but are not equivalent, since the lpg5A(-) mutant showed a partial defect in LPG but not PPG phosphoglycosylation, whereas the lpg5B(-) mutant showed a partial defect in PPG but not LPG phosphoglycosylation. Identification of these key NSTs in Leishmania will facilitate the dissection of glycoconjugate synthesis and its role(s) in the parasite life cycle and further our understanding of NSTs generally. PMID:17347153

  8. Deep divergence and apparent sex-biased dispersal revealed by a Y-linked marker in rainbow trout

    PubMed Central

    Brunelli, Joseph P.; Steele, Craig A.; Thorgaard, Gary H.

    2010-01-01

    Y-chromosome and mitochondrial DNA markers can reveal phylogenetic patterns by allowing tracking of male and female lineages, respectively. We used sequence data from a recently discovered Y-linked marker and a mitochondrial marker to examine phylogeographic structure in the widespread and economically important rainbow trout (Oncorhynchus mykiss). Two distinct geographic groupings that generally correspond to coastal and inland subspecies were evident within the Y marker network while the mtDNA haplotype network showed little geographic structure. Our results suggest that male-specific behavior has prevented widespread admixture of Y haplotypes and that gene flow between the coastal and inland subspecies has largely occurred through females. This new Y marker may also aid conservation efforts by genetically identifying inland populations that have not hybridized with widely stocked coastal-derived hatchery fish. PMID:20546904

  9. Genetic divergence in wild population of endangered yellowtail catfish Pangasius pangasius (Hamilton-Buchanan, 1822) revealed by mtDNA.

    PubMed

    Mohindra, Vindhya; Singh, Rajeev K; Kumar, Rajesh; Sah, R S; Lal, Kuldeep K

    2015-04-01

    Pangasius pangasius, an endangered freshwater fish species, is an important component of capture fishery from Indian rivers. Samples collected through commercial catches from three riverine populations were analyzed with cytb (307 bp) and ATPase6&8 (842 bp) regions for population variation and differentiation. The sequences of the both the mitochondrial regions revealed high haplotype and low nucleotide diversity. Shallow genetic diversity based on ATPase6&8 was observed, however its haplotypes network clearly indicated two distinct mitochondrial lineages. Mismatch distribution suggested population bottlenecks followed by expansion in Mahanadi population. The present study indicated the ATPase6&8 to be a potential mitochondrial marker for studying the population sub-structuring in the wild population of P. pangasius. PMID:24409876

  10. Key herbivores reveal limited functional redundancy on inshore coral reefs

    NASA Astrophysics Data System (ADS)

    Johansson, C. L.; van de Leemput, I. A.; Depczynski, M.; Hoey, A. S.; Bellwood, D. R.

    2013-12-01

    Marine ecosystems are facing increasing exposure to a range of stressors and declines in critical ecological functions. The likelihood of further loss of functions and resilience is dependent, in part, on the extent of functional redundancy (i.e. the capacity of one species to functionally compensate for the loss of another species) within critical functional groups. We used multiple metrics; species richness, generic richness, abundance and reserve capacity (i.e. the relative number of individuals available to fulfil the function if the numerically dominant species is lost), as indicators to assess the potential functional redundancy of four functional groups of herbivorous fishes (browsers, excavators, grazers and scrapers) in two of the worlds' most intact coral reef ecosystems: the Great Barrier Reef (GBR) and Ningaloo Reef in Western Australia. We found marked variations in potential redundancy among habitats within each reef system and functional groups. Despite negligible fishing of herbivorous fishes, coastal habitats in both reef systems had lower functional redundancy compared to offshore locations for all herbivorous fishes collectively and the four functional groups independently. This pattern was consistent in all four indicators of redundancy. The potential vulnerability of these coastal habitats is highlighted by recent shifts from coral to macroalgal dominance on several coastal reefs of the GBR. Our approach provides a simple yet revealing evaluation of potential functional redundancy. Moreover, it highlights the spatial variation in potential vulnerability and resilience of reef systems.

  11. Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens

    PubMed Central

    Xu, Jun; Saunders, Charles W.; Hu, Ping; Grant, Raymond A.; Boekhout, Teun; Kuramae, Eiko E.; Kronstad, James W.; DeAngelis, Yvonne M.; Reeder, Nancy L.; Johnstone, Kevin R.; Leland, Meredith; Fieno, Angela M.; Begley, William M.; Sun, Yiping; Lacey, Martin P.; Chaudhary, Tanuja; Keough, Thomas; Chu, Lien; Sears, Russell; Yuan, Bo; Dawson, Thomas L.

    2007-01-01

    Fungi in the genus Malassezia are ubiquitous skin residents of humans and other warm-blooded animals. Malassezia are involved in disorders including dandruff and seborrheic dermatitis, which together affect >50% of humans. Despite the importance of Malassezia in common skin diseases, remarkably little is known at the molecular level. We describe the genome, secretory proteome, and expression of selected genes of Malassezia globosa. Further, we report a comparative survey of the genome and secretory proteome of Malassezia restricta, a close relative implicated in similar skin disorders. Adaptation to the skin environment and associated pathogenicity may be due to unique metabolic limitations and capabilities. For example, the lipid dependence of M. globosa can be explained by the apparent absence of a fatty acid synthase gene. The inability to synthesize fatty acids may be complemented by the presence of multiple secreted lipases to aid in harvesting host lipids. In addition, an abundance of genes encoding secreted hydrolases (e.g., lipases, phospholipases, aspartyl proteases, and acid sphingomyelinases) was found in the M. globosa genome. In contrast, the phylogenetically closely related plant pathogen Ustilago maydis encodes a different arsenal of extracellular hydrolases with more copies of glycosyl hydrolase genes. M. globosa shares a similar arsenal of extracellular hydrolases with the phylogenetically distant human pathogen, Candida albicans, which occupies a similar niche, indicating the importance of host-specific adaptation. The M. globosa genome sequence also revealed the presence of mating-type genes, providing an indication that Malassezia may be capable of sex. PMID:18000048

  12. epg-1 functions in autophagy-regulated processes and may encode a highly divergent Atg13 homolog in C. elegans.

    PubMed

    Tian, E; Wang, Fuxin; Han, Jinghua; Zhang, Hong

    2009-07-01

    Autophagy is an evolutionarily conserved intracellular catabolic system for degradation of long-lived proteins or damaged organelles. In this study, we have identified and characterized a new gene, epg-1, that plays a role in the autophagy pathway in C. elegans. Loss of function of epg-1 causes defects in various autophagy-regulated processes, including degradation of aggregate-prone proteins and optimal survival of animals during starvation. epg-1 encodes a novel protein that shows limited sequence similarity to the yeast autophagy protein Atg13. epg-1 displays a similar expression pattern to, and directly interacts with, the C. elegans Atg1 homolog UNC-51, suggesting that epg-1 encodes a divergent functional homolog of Atg13 in C. elegans. PMID:19377305

  13. Revealing quantum correlation by negativity of the Wigner function

    NASA Astrophysics Data System (ADS)

    Taghiabadi, Razieh; Akhtarshenas, Seyed Javad; Sarbishaei, Mohsen

    2016-05-01

    We analyze two two-mode continuous variable separable states with the same marginal states. We adopt the definition of classicality in the form of well-defined positive Wigner function describing the state and find that although the states possess positive local Wigner functions, they exhibit negative Wigner functions for the global states. Using the negativity of Wigner function as an indicator of nonclassicality, we show that despite these states possess different negativities of the Wigner function, they do not reveal this difference as phase space nonclassicalities such as negativity of the Mandel Q parameter or quadrature squeezing. We then concentrate on quantum correlation of these states and show that quantum discord and local quantum uncertainty, as two well-defined measures of quantum correlation, manifest the difference between negativity of the Wigner functions. The non-Gaussianity of these states is also examined and show that the difference in behavior of their non-Gaussianity is the same as the difference between negativity of their Wigner functions. We also investigate the influence of correlation rank criterion and find that when the states can be produced locally from classical states, the Wigner functions cannot reveal their quantum correlations.

  14. Expression divergence of the AGL6 MADS domain transcription factor lineage after a core eudicot duplication suggests functional diversification

    PubMed Central

    2010-01-01

    Background Because of their known role as transcriptional regulators of key plant developmental processes, the diversification of MADS-box gene function is thought to be a major driving force in the developmental evolution of plants. Yet the function of some MADS-box gene subfamilies has remained elusive thus far. One such lineage, AGL6, has now been functionally characterized in three angiosperm species, but a phylogenetic framework for comparison of AGL6 gene function is currently missing. Results Based on phylogenetic analyses of newly isolated and EST-based sequences, we describe the duplication history of the AGL6 subfamily in angiosperms. Our analyses provide support for four ancient duplications in the evolution of the AGL6 lineage: one at the base of core eudicots resulting in euAGL6 and AGL6-like gene clades, one during basal angiosperm diversification and two in monocot evolution. To investigate whether the spatial domains in which AGL6 genes function have diverged after duplication, we use quantitative Real Time PCR. We show that the core eudicot AGL6-like clade acquired expression in vegetative tissues, while its paralog euAGL6 remains predominantly confined to reproductive tissues. Conclusions These and previous data lead us to propose that the AGL6 lineage in core eudicots, in addition to functions related to the expression in reproductive structures, may have acquired a function in developmental transitions of vegetative shoots. PMID:20633275

  15. Evolutionary and functional divergence between the cystic fibrosis transmembrane conductance regulator and related ATP-binding cassette transporters

    PubMed Central

    King Jordan, I.; Kota, Karthik C.; Cui, Guiying; Thompson, Christopher H.; McCarty, Nael A.

    2008-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) is a member of the ATP-binding cassette (ABC) transporter superfamily, an ancient family of proteins found in all phyla. In nearly all cases, ABC proteins are transporters that couple the hydrolysis of ATP to the transmembrane movement of substrate via an alternating access mechanism. In contrast, CFTR is best known for its activity as an ATP-dependent chloride channel. We asked why CFTR, which shares the domain architecture of ABC proteins that function as transporters, exhibits functional divergence. We compared CFTR protein sequences to those of other ABC transporters, which identified the ABCC4 proteins as the closest mammalian paralogs, and used statistical analysis of the CFTR-ABCC4 multiple sequence alignment to identify the specific domains and residues most likely to be involved in the evolutionary transition from transporter to channel activity. Among the residues identified as being involved in CFTR functional divergence, by virtue of being both CFTR-specific and conserved among all CFTR orthologs, was R352 in the sixth transmembrane helix (TM6). Patch-clamp experiments show that R352 interacts with D993 in TM9 to stabilize the open-channel state; D993 is absolutely conserved between CFTRs and ABCC4s. These data suggest that CFTR channel activity evolved, at least in part, by converting the conformational changes associated with binding and hydrolysis of ATP, as are found in true ABC Transporters, into an open permeation pathway by means of intraprotein interactions that stabilize the open state. This analysis sets the stage for understanding the evolutionary and functional relationships that make CFTR a unique ABC transporter protein. PMID:19020075

  16. Evolutionary and functional divergence between the cystic fibrosis transmembrane conductance regulator and related ATP-binding cassette transporters.

    PubMed

    Jordan, I King; Kota, Karthik C; Cui, Guiying; Thompson, Christopher H; McCarty, Nael A

    2008-12-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) is a member of the ATP-binding cassette (ABC) transporter superfamily, an ancient family of proteins found in all phyla. In nearly all cases, ABC proteins are transporters that couple the hydrolysis of ATP to the transmembrane movement of substrate via an alternating access mechanism. In contrast, CFTR is best known for its activity as an ATP-dependent chloride channel. We asked why CFTR, which shares the domain architecture of ABC proteins that function as transporters, exhibits functional divergence. We compared CFTR protein sequences to those of other ABC transporters, which identified the ABCC4 proteins as the closest mammalian paralogs, and used statistical analysis of the CFTR-ABCC4 multiple sequence alignment to identify the specific domains and residues most likely to be involved in the evolutionary transition from transporter to channel activity. Among the residues identified as being involved in CFTR functional divergence, by virtue of being both CFTR-specific and conserved among all CFTR orthologs, was R352 in the sixth transmembrane helix (TM6). Patch-clamp experiments show that R352 interacts with D993 in TM9 to stabilize the open-channel state; D993 is absolutely conserved between CFTRs and ABCC4s. These data suggest that CFTR channel activity evolved, at least in part, by converting the conformational changes associated with binding and hydrolysis of ATP, as are found in true ABC Transporters, into an open permeation pathway by means of intraprotein interactions that stabilize the open state. This analysis sets the stage for understanding the evolutionary and functional relationships that make CFTR a unique ABC transporter protein. PMID:19020075

  17. An Integrated Bioinformatics Analysis Reveals Divergent Evolutionary Pattern of Oil Biosynthesis in High- and Low-Oil Plants

    PubMed Central

    Zhang, Li; Wang, Shi-Bo; Li, Qi-Gang; Song, Jian; Hao, Yu-Qi; Zhou, Ling; Zheng, Huan-Quan; Dunwell, Jim M.; Zhang, Yuan-Ming

    2016-01-01

    Seed oils provide a renewable source of food, biofuel and industrial raw materials that is important for humans. Although many genes and pathways for acyl-lipid metabolism have been identified, little is known about whether there is a specific mechanism for high-oil content in high-oil plants. Based on the distinct differences in seed oil content between four high-oil dicots (20~50%) and three low-oil grasses (<3%), comparative genome, transcriptome and differential expression analyses were used to investigate this mechanism. Among 4,051 dicot-specific soybean genes identified from 252,443 genes in the seven species, 54 genes were shown to directly participate in acyl-lipid metabolism, and 93 genes were found to be associated with acyl-lipid metabolism. Among the 93 dicot-specific genes, 42 and 27 genes, including CBM20-like SBDs and GPT2, participate in carbohydrate degradation and transport, respectively. 40 genes highly up-regulated during seed oil rapid accumulation period are mainly involved in initial fatty acid synthesis, triacylglyceride assembly and oil-body formation, for example, ACCase, PP, DGAT1, PDAT1, OLEs and STEROs, which were also found to be differentially expressed between high- and low-oil soybean accessions. Phylogenetic analysis revealed distinct differences of oleosin in patterns of gene duplication and loss between high-oil dicots and low-oil grasses. In addition, seed-specific GmGRF5, ABI5 and GmTZF4 were predicted to be candidate regulators in seed oil accumulation. This study facilitates future research on lipid biosynthesis and potential genetic improvement of seed oil content. PMID:27159078

  18. Divergence and Functional Degradation of a Sex Chromosome-like Supergene.

    PubMed

    Tuttle, Elaina M; Bergland, Alan O; Korody, Marisa L; Brewer, Michael S; Newhouse, Daniel J; Minx, Patrick; Stager, Maria; Betuel, Adam; Cheviron, Zachary A; Warren, Wesley C; Gonser, Rusty A; Balakrishnan, Christopher N

    2016-02-01

    A major challenge in biology is to understand the genetic basis of adaptation. One compelling idea is that groups of tightly linked genes (i.e., "supergenes" [1, 2]) facilitate adaptation in suites of traits that determine fitness. Despite their likely importance, little is known about how alternate supergene alleles arise and become differentiated, nor their ultimate fate within species. Herein we address these questions by investigating the evolutionary history of a supergene in white-throated sparrows, Zonotrichia albicollis. This species comprises two morphs, tan and white, that differ in pigmentation and components of social behavior [3-5]. Morph is determined by alternative alleles at a balanced >100-Mb inversion-based supergene, providing a unique system for studying gene-behavior relationships. Using over two decades of field data, we document near-perfect disassortative mating among morphs, as well as the fitness consequences of rare assortative mating. We use de novo whole-genome sequencing coupled with population- and phylogenomic data to show that alternate supergene alleles are highly divergent at over 1,000 genes and that these alleles originated prior to the split of Z. albicollis from its sister species and may be polymorphic in Z. albicollis due to a past hybridization event. We provide evidence that the "white" allele may be degrading, similar to neo-Y/W sex chromosomes. We further show that the "tan" allele has surprisingly low levels of genetic diversity yet does not show several canonical signatures of recurrent positive selection. We discuss these results in the context of the origin, molecular evolution, and possible fate of this remarkable polymorphism. PMID:26804558

  19. Insight Into Genomic Changes Accompanying Divergence: Genetic Linkage Maps and Synteny of Lucania goodei and L. parva Reveal a Robertsonian Fusion

    PubMed Central

    Berdan, Emma L.; Kozak, Genevieve M.; Ming, Ray; Rayburn, A. Lane; Kiehart, Ryan; Fuller, Rebecca C.

    2014-01-01

    Linkage maps are important tools in evolutionary genetics and in studies of speciation. We performed a karyotyping study and constructed high-density linkage maps for two closely related killifish species, Lucania parva and L. goodei, that differ in salinity tolerance and still hybridize in their contact zone in Florida. Using SNPs from orthologous EST contigs, we compared synteny between the two species to determine how genomic architecture has shifted with divergence. Karyotyping revealed that L. goodei possesses 24 acrocentric chromosomes (1N) whereas L. parva possesses 23 chromosomes (1N), one of which is a large metacentric chromosome. Likewise, high-density single-nucleotide polymorphism−based linkage maps indicated 24 linkage groups for L. goodei and 23 linkage groups for L. parva. Synteny mapping revealed two linkage groups in L. goodei that were highly syntenic with the largest linkage group in L. parva. Together, this evidence points to the largest linkage group in L. parva being the result of a chromosomal fusion. We further compared synteny between Lucania with the genome of a more distant teleost relative medaka (Oryzias latipes) and found good conservation of synteny at the chromosomal level. Each Lucania LG had a single best match with each medaka chromosome. These results provide the groundwork for future studies on the genetic architecture of reproductive isolation and salinity tolerance in Lucania and other Fundulidae. PMID:24898707

  20. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition.

    PubMed

    Joardar, Vinita; Lindeberg, Magdalen; Jackson, Robert W; Selengut, Jeremy; Dodson, Robert; Brinkac, Lauren M; Daugherty, Sean C; Deboy, Robert; Durkin, A Scott; Giglio, Michelle Gwinn; Madupu, Ramana; Nelson, William C; Rosovitz, M J; Sullivan, Steven; Crabtree, Jonathan; Creasy, Todd; Davidsen, Tanja; Haft, Dan H; Zafar, Nikhat; Zhou, Liwei; Halpin, Rebecca; Holley, Tara; Khouri, Hoda; Feldblyum, Tamara; White, Owen; Fraser, Claire M; Chatterjee, Arun K; Cartinhour, Sam; Schneider, David J; Mansfield, John; Collmer, Alan; Buell, C Robin

    2005-09-01

    Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific. PMID:16159782

  1. Functional Divergence in Teleost Cardiac Troponin Paralogs Guides Variation in the Interaction of TnI Switch Region with TnC.

    PubMed

    Genge, Christine E; Stevens, Charles M; Davidson, William S; Singh, Gurpreet; Peter Tieleman, D; Tibbits, Glen F

    2016-01-01

    Gene duplication results in extra copies of genes that must coevolve with their interacting partners in multimeric protein complexes. The cardiac troponin (Tn) complex, containing TnC, TnI, and TnT, forms a distinct functional unit critical for the regulation of cardiac muscle contraction. In teleost fish, the function of the Tn complex is modified by the consequences of differential expression of paralogs in response to environmental thermal challenges. In this article, we focus on the interaction between TnI and TnC, coded for by genes that have independent evolutionary origins, but the co-operation of their protein products has necessitated coevolution. In this study, we characterize functional divergence of TnC and TnI paralogs, specifically the interrelated roles of regulatory subfunctionalization and structural subfunctionalization. We determined that differential paralog transcript expression in response to temperature acclimation results in three combinations of TnC and TnI in the zebrafish heart: TnC1a/TnI1.1, TnC1b/TnI1.1, and TnC1a/TnI1.5. Phylogenetic analysis of these highly conserved proteins identified functionally divergent residues in TnI and TnC. The structural and functional effect of these Tn combinations was modeled with molecular dynamics simulation to link divergent sites to changes in interaction strength. Functional divergence in TnI and TnC were not limited to the residues involved with TnC/TnI switch interaction, which emphasizes the complex nature of Tn function. Patterns in domain-specific divergent selection and interaction energies suggest that substitutions in the TnI switch region are crucial to modifying TnI/TnC function to maintain cardiac contraction with temperature changes. This integrative approach introduces Tn as a model of functional divergence that guides the coevolution of interacting proteins. PMID:26979795

  2. Functional Divergence in Teleost Cardiac Troponin Paralogs Guides Variation in the Interaction of TnI Switch Region with TnC

    PubMed Central

    Genge, Christine E.; Stevens, Charles M.; Davidson, William S.; Singh, Gurpreet; Peter Tieleman, D.; Tibbits, Glen F.

    2016-01-01

    Gene duplication results in extra copies of genes that must coevolve with their interacting partners in multimeric protein complexes. The cardiac troponin (Tn) complex, containing TnC, TnI, and TnT, forms a distinct functional unit critical for the regulation of cardiac muscle contraction. In teleost fish, the function of the Tn complex is modified by the consequences of differential expression of paralogs in response to environmental thermal challenges. In this article, we focus on the interaction between TnI and TnC, coded for by genes that have independent evolutionary origins, but the co-operation of their protein products has necessitated coevolution. In this study, we characterize functional divergence of TnC and TnI paralogs, specifically the interrelated roles of regulatory subfunctionalization and structural subfunctionalization. We determined that differential paralog transcript expression in response to temperature acclimation results in three combinations of TnC and TnI in the zebrafish heart: TnC1a/TnI1.1, TnC1b/TnI1.1, and TnC1a/TnI1.5. Phylogenetic analysis of these highly conserved proteins identified functionally divergent residues in TnI and TnC. The structural and functional effect of these Tn combinations was modeled with molecular dynamics simulation to link divergent sites to changes in interaction strength. Functional divergence in TnI and TnC were not limited to the residues involved with TnC/TnI switch interaction, which emphasizes the complex nature of Tn function. Patterns in domain-specific divergent selection and interaction energies suggest that substitutions in the TnI switch region are crucial to modifying TnI/TnC function to maintain cardiac contraction with temperature changes. This integrative approach introduces Tn as a model of functional divergence that guides the coevolution of interacting proteins. PMID:26979795

  3. A divergent route to core- and peripherally functionalized diazacoronenes that act as colorimetric and fluorescence proton sensors

    DOE PAGESBeta

    He, Bo; Dai, Jing; Zherebetskyy, Danylo; Chen, Teresa L.; Zhang, Benjamin A.; Teat, Simon J.; Zhang, Qichun; Wang, Linwang; Liu, Yi

    2015-03-31

    Combining core annulation and peripheral group modification, we have demonstrated a divergent synthesis of a family of highly functionalized coronene derivatives from a readily accessible dichlorodiazaperylene intermediate. Various reactions, such as aromatic nucleophilic substitution, Kumada coupling and Suzuki coupling proceed effectively on α-positions of the pyridine sites, giving rise to alkoxy, thioalkyl, alkyl or aryl substituted polycyclic aromatic hydrocarbons. In addition to peripheral group modulation, the aromatic core structures can be altered by annulation with thiophene or benzene ring systems. Corresponding single crystal X-ray diffraction and optical studies indicate that the heteroatom linkages not only impact the solid state packing,more » but also significantly influence the optoelectronic properties. Moreover, these azacoronene derivatives display significant acid-induced spectroscopic changes, suggesting their great potential as colorimetric and fluorescence proton sensors.« less

  4. A divergent route to core- and peripherally functionalized diazacoronenes that act as colorimetric and fluorescence proton sensors

    SciTech Connect

    He, Bo; Dai, Jing; Zherebetskyy, Danylo; Chen, Teresa L.; Zhang, Benjamin A.; Teat, Simon J.; Zhang, Qichun; Wang, Linwang; Liu, Yi

    2015-03-31

    Combining core annulation and peripheral group modification, we have demonstrated a divergent synthesis of a family of highly functionalized coronene derivatives from a readily accessible dichlorodiazaperylene intermediate. Various reactions, such as aromatic nucleophilic substitution, Kumada coupling and Suzuki coupling proceed effectively on α-positions of the pyridine sites, giving rise to alkoxy, thioalkyl, alkyl or aryl substituted polycyclic aromatic hydrocarbons. In addition to peripheral group modulation, the aromatic core structures can be altered by annulation with thiophene or benzene ring systems. Corresponding single crystal X-ray diffraction and optical studies indicate that the heteroatom linkages not only impact the solid state packing, but also significantly influence the optoelectronic properties. Moreover, these azacoronene derivatives display significant acid-induced spectroscopic changes, suggesting their great potential as colorimetric and fluorescence proton sensors.

  5. Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly.

    PubMed

    Nie, Yong; Zhao, Jie-Yu; Tang, Yue-Qin; Guo, Peng; Yang, Yunfeng; Wu, Xiao-Lei; Zhao, Fangqing

    2016-01-01

    Oil reservoirs exhibit extreme environmental conditions such as high salinity and high temperature. Insights into microbial community assemblages in oil reservoirs and their functional potentials are important for understanding biogeochemical cycles in the subterranean biosphere. In this study, we performed shotgun metagenomic sequencing of crude oil samples from two geographically distant oil reservoirs in China, and compared them with all the 948 available environmental metagenomes deposited in IMG database (until October 2013). Although the dominant bacteria and the proportion of hydrogenotrophic and acetoclastic methanogens were different among oil metagenomes, compared with the metagenomes from other environments, all the oil metagenomes contained higher abundances of genes involved in methanogenic hydrocarbon degradation and stress response systems. In addition, a "shape-sorting" manner was proposed for the assembly of microbial communities in oil reservoirs, with the oil reservoir acting as a function sorter to select microbes with special functions from its endemic pool of microorganisms. At the functional level, we found that environmental metagenomes were generally clustered according to their isolation environments but not their geographical locations, suggesting selective processes to be involved in the assembly of microbial communities based on functional gene composition. PMID:27570522

  6. Regressive evolution of the arthropod tritocerebral segment linked to functional divergence of the Hox gene labial

    PubMed Central

    Pechmann, Matthias; Schwager, Evelyn E.; Turetzek, Natascha; Prpic, Nikola-Michael

    2015-01-01

    The intercalary segment is a limbless version of the tritocerebral segment and is present in the head of all insects, whereas other extant arthropods have retained limbs on their tritocerebral segment (e.g. the pedipalp limbs in spiders). The evolutionary origin of limb loss on the intercalary segment has puzzled zoologists for over a century. Here we show that an intercalary segment-like phenotype can be created in spiders by interfering with the function of the Hox gene labial. This links the origin of the intercalary segment to a functional change in labial. We show that in the spider Parasteatoda tepidariorum the labial gene has two functions: one function in head tissue maintenance that is conserved between spiders and insects, and a second function in pedipalp limb promotion and specification, which is only present in spiders. These results imply that labial was originally crucial for limb formation on the tritocerebral segment, but that it has lost this particular subfunction in the insect ancestor, resulting in limb loss on the intercalary segment. Such loss of a subfunction is a way to avoid adverse pleiotropic effects normally associated with mutations in developmental genes, and may thus be a common mechanism to accelerate regressive evolution. PMID:26311666

  7. Species Divergence vs. Functional Convergence Characterizes Crude Oil Microbial Community Assembly

    PubMed Central

    Nie, Yong; Zhao, Jie-Yu; Tang, Yue-Qin; Guo, Peng; Yang, Yunfeng; Wu, Xiao-Lei; Zhao, Fangqing

    2016-01-01

    Oil reservoirs exhibit extreme environmental conditions such as high salinity and high temperature. Insights into microbial community assemblages in oil reservoirs and their functional potentials are important for understanding biogeochemical cycles in the subterranean biosphere. In this study, we performed shotgun metagenomic sequencing of crude oil samples from two geographically distant oil reservoirs in China, and compared them with all the 948 available environmental metagenomes deposited in IMG database (until October 2013). Although the dominant bacteria and the proportion of hydrogenotrophic and acetoclastic methanogens were different among oil metagenomes, compared with the metagenomes from other environments, all the oil metagenomes contained higher abundances of genes involved in methanogenic hydrocarbon degradation and stress response systems. In addition, a “shape-sorting” manner was proposed for the assembly of microbial communities in oil reservoirs, with the oil reservoir acting as a function sorter to select microbes with special functions from its endemic pool of microorganisms. At the functional level, we found that environmental metagenomes were generally clustered according to their isolation environments but not their geographical locations, suggesting selective processes to be involved in the assembly of microbial communities based on functional gene composition. PMID:27570522

  8. A comparative analysis of liver transcriptome suggests divergent liver function among human, mouse and rat.

    PubMed

    Yu, Yao; Ping, Jie; Chen, Hui; Jiao, Longxian; Zheng, Siyuan; Han, Ze-Guang; Hao, Pei; Huang, Jian

    2010-11-01

    The human liver plays a vital role in meeting the body's metabolic needs and maintaining homeostasis. To address the molecular mechanisms of liver function, we integrated multiple gene expression datasets from microarray, MPSS, SAGE and EST platforms to generate a transcriptome atlas of the normal human liver. Our results show that 17396 genes are expressed in the human liver. 238 genes were identified as liver enrichment genes, involved in the functions of immune response and metabolic processes, from the MPSS and EST datasets. A comparative analysis of liver transcriptomes was performed in humans, mice and rats with microarray datasets shows that the expression profile of homologous genes remains significantly different between mouse/rat and human, suggesting a functional variance and regulation bias of genes expressed in the livers. The integrated liver transcriptome data should provide a valuable resource for the in-depth understanding of human liver biology and liver disease. PMID:20800674

  9. Synthetic protein interactions reveal a functional map of the cell

    PubMed Central

    Berry, Lisa K; Ólafsson, Guðjón; Ledesma-Fernández, Elena; Thorpe, Peter H

    2016-01-01

    To understand the function of eukaryotic cells, it is critical to understand the role of protein-protein interactions and protein localization. Currently, we do not know the importance of global protein localization nor do we understand to what extent the cell is permissive for new protein associations – a key requirement for the evolution of new protein functions. To answer this question, we fused every protein in the yeast Saccharomyces cerevisiae with a partner from each of the major cellular compartments and quantitatively assessed the effects upon growth. This analysis reveals that cells have a remarkable and unanticipated tolerance for forced protein associations, even if these associations lead to a proportion of the protein moving compartments within the cell. Furthermore, the interactions that do perturb growth provide a functional map of spatial protein regulation, identifying key regulatory complexes for the normal homeostasis of eukaryotic cells. DOI: http://dx.doi.org/10.7554/eLife.13053.001 PMID:27098839

  10. Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

    PubMed Central

    Manning, Viola A.; Pandelova, Iovanna; Dhillon, Braham; Wilhelm, Larry J.; Goodwin, Stephen B.; Berlin, Aaron M.; Figueroa, Melania; Freitag, Michael; Hane, James K.; Henrissat, Bernard; Holman, Wade H.; Kodira, Chinnappa D.; Martin, Joel; Oliver, Richard P.; Robbertse, Barbara; Schackwitz, Wendy; Schwartz, David C.; Spatafora, Joseph W.; Turgeon, B. Gillian; Yandava, Chandri; Young, Sarah; Zhou, Shiguo; Zeng, Qiandong; Grigoriev, Igor V.; Ma, Li-Jun; Ciuffetti, Lynda M.

    2013-01-01

    Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes. PMID:23316438

  11. Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

    SciTech Connect

    Manning, Viola A.; Pandelova, Iovanna; Dhillon, Braham; Wilhelm, Larry J.; Goodwin, Stephen B.; Berlin, Aaron M.; Figueroa, Melania; Freitag, Michael; Hane, James K.; Henrissat, Bernard; Holman, Wade H.; Kodira, Chinnappa D.; Martin, Joel; Oliver, Richard P.; Robbertse, Barbara; Schackwitz, Wendy; Schwartz, David C.; Spatafora, Joseph W.; Turgeon, B. Gillian; Yandava, Chandri; Young, Sarah; Zhou, Shiguo; Zeng, Qiandong; Grigoriev, Igor V.; Ma, Li-Jun; Ciuffetti, Lynda M.

    2012-08-16

    Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins (HST), which are recognized by their host in a genotype-specific manner. To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. A pathogenic isolate that produces two known HSTs was used to assemble a reference nuclear genome of approximately 40 Mb composed of 11 chromosomes that encode 12,141 predicted genes. Comparison of the reference genome with those of a pathogenic isolate that produces a third HST, and a nonpathogenic isolate, showed the nonpathogen genome to be more diverged than those of the two pathogens. Examination of gene-coding regions has provided candidate pathogen-specific proteins and revealed gene families that may play a role in a necrotrophic lifestyle. Analysis of transposable elements suggests that their presence in the genome of pathogenic isolates contributes to the creation of novel genes, effector diversification, possible horizontal gene transfer events, identified copy number variation, and the first example of transduplication by DNA transposable elements in fungi. Overall, comparative analysis of these genomes provides evidence that pathogenicity in this species arose through an influx of transposable elements, which created a genetically flexible landscape that can easily respond to environmental changes.

  12. Active Fragments from Pro- and Antiapoptotic BCL-2 Proteins Have Distinct Membrane Behavior Reflecting Their Functional Divergence

    PubMed Central

    Guillemin, Yannis; Lopez, Jonathan; Gimenez, Diana; Fuertes, Gustavo; Valero, Juan Garcia; Blum, Loïc; Gonzalo, Philippe; Salgado, Jesùs; Girard-Egrot, Agnès; Aouacheria, Abdel

    2010-01-01

    Background The BCL-2 family of proteins includes pro- and antiapoptotic members acting by controlling the permeabilization of mitochondria. Although the association of these proteins with the outer mitochondrial membrane is crucial for their function, little is known about the characteristics of this interaction. Methodology/Principal Findings Here, we followed a reductionist approach to clarify to what extent membrane-active regions of homologous BCL-2 family proteins contribute to their functional divergence. Using isolated mitochondria as well as model lipid Langmuir monolayers coupled with Brewster Angle Microscopy, we explored systematically and comparatively the membrane activity and membrane-peptide interactions of fragments derived from the central helical hairpin of BAX, BCL-xL and BID. The results show a connection between the differing abilities of the assayed peptide fragments to contact, insert, destabilize and porate membranes and the activity of their cognate proteins in programmed cell death. Conclusion/Significance BCL-2 family-derived pore-forming helices thus represent structurally analogous, but functionally dissimilar membrane domains. PMID:20140092

  13. Structural and Functional Divergence of Gonadotropin-Inhibitory Hormone from Jawless Fish to Mammals

    PubMed Central

    Ogawa, Satoshi; Parhar, Ishwar S.

    2014-01-01

    Gonadotropin-inhibitory hormone (GnIH) was discovered as a novel hypothalamic peptide that inhibits gonadotropin release in the quail. The presence of GnIH-homologous peptides and its receptors (GnIHRs) have been demonstrated in various vertebrate species including teleosts, suggesting that the GnIH-GnIHR family is evolutionarily conserved. In avian and mammalian brain, GnIH neurons are localized in the hypothalamic nuclei and their neural projections are widely distributed. GnIH acts on the pituitary and gonadotropin-releasing hormone neurons to inhibit reproductive functions by decreasing gonadotropin release and synthesis. In addition, GnIH-GnIHR signaling is regulated by various factors, such as environmental cues and stress. However, the function of fish GnIH orthologs remains inconclusive because the physiological properties of fish GnIH peptides are debatable. This review summarizes the current research progress in GnIH-GnIHR signaling and their physiological functions in vertebrates with special emphasis on non-mammalian vertebrate species. PMID:25386165

  14. The effect of functional compensation among duplicate genes can constrain their evolutionary divergence.

    PubMed

    Bozorgmehr, Joseph Esfandiar Hannon

    2012-01-01

    Gene duplicates have the inherent property of initially being functionally redundant. This means that they can compensate for the effect of deleterious variation occurring at one or more sister sites. Here, I present data bearing on evolutionary theory that illustrates the manner in which any functional adaptation in duplicate genes is markedly constrained because of the compensatory utility provided by a sustained genetic redundancy. Specifically, a two-locus epistatic model of paralogous genes was simulated to investigate the degree of purifying selection imposed, and whether this would serve to impede any possible biochemical innovation. Three population sizes were considered to see if, as expected, there was a significant difference in any selection for robustness. Interestingly, physical linkage between tandem duplicates was actually found to increase the probability of any neofunctionalization and the efficacy of selection, contrary to what is expected in the case of singleton genes. The results indicate that an evolutionary trade-off often exists between any functional change under either positive or relaxed selection and the need to compensate for failures due to degenerative mutations, thereby guaranteeing the reliability of protein production. PMID:22546821

  15. The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes

    PubMed Central

    Pombert, Jean-François; Lemieux, Claude; Turmel, Monique

    2006-01-01

    Background The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA) sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of Pseudendoclonium (Ulvophyceae), in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR) featuring an inverted rRNA operon and a small single-copy (SSC) region containing 14 genes normally found in the large single-copy (LSC) region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of Oltmannsiellopsis viridis, a representative of a distinct, early diverging lineage. Results The 151,933 bp IR-containing genome of Oltmannsiellopsis differs considerably from Pseudendoclonium and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. Oltmannsiellopsis cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in Pseudendoclonium cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in Pseudendoclonium cpDNA. Surprisingly, the overall gene organization of Oltmannsiellopsis cp

  16. Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region from Phaseolus vulgaris[W][OA

    PubMed Central

    Lin, Jer-Young; Stupar, Robert M.; Hans, Christian; Hyten, David L.; Jackson, Scott A.

    2010-01-01

    Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ~1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ~13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in Gm8) and a nearly twofold increase in the deletion of long terminal repeat (LTR) retrotransposons via solo LTR formation. Functional analyses of Gm15 and Gm8 revealed decreases in gene expression and synonymous substitution rates for Gm15, for instance, a 38% increase in transcript levels from Gm8 relative to Gm15. Transcriptional divergence of homoeologs was found based on expression patterns among seven tissues and developmental stages. Our results indicate asymmetric evolution between homoeologous regions of soybean as evidenced by structural changes and expression variances of homoeologous genes. PMID:20729383

  17. Functional complementation of anthocyanin sequestration in the vacuole by widely divergent glutathione S-transferases.

    PubMed Central

    Alfenito, M R; Souer, E; Goodman, C D; Buell, R; Mol, J; Koes, R; Walbot, V

    1998-01-01

    Glutathione S-transferases (GSTs) traditionally have been studied in plants and other organisms for their ability to detoxify chemically diverse herbicides and other toxic organic compounds. Anthocyanins are among the few endogenous substrates of plant GSTs that have been identified. The Bronze2 (Bz2) gene encodes a type III GST and performs the last genetically defined step of the maize anthocyanin pigment pathway. This step is the conjugation of glutathione to cyanidin 3-glucoside (C3G). Glutathionated C3G is transported to the vacuole via a tonoplast Mg-ATP-requiring glutathione pump (GS-X pump). Genetically, the comparable step in the petunia anthocyanin pathway is controlled by the Anthocyanin9 (An9) gene. An9 was cloned by transposon tagging and found to encode a type I plant GST. Bz2 and An9 have evolved independently from distinct types of GSTs, but each is regulated by the conserved transcriptional activators of the anthocyanin pathway. Here, a phylogenetic analysis is presented, with special consideration given to the origin of these genes and their relaxed substrate requirements. In particle bombardment tests, An9 and Bz2 functionally complement both mutants. Among several other GSTs tested, only soybean GmGST26A (previously called GmHsp26A and GH2/4) and maize GSTIII were found to confer vacuolar sequestration of anthocyanin. Previously, these genes had not been associated with the anthocyanin pathway. Requirements for An9 and Bz2 gene function were investigated by sequencing functional and nonfunctional germinal revertants of an9-T3529, bz2::Ds, and bz2::Mu1. PMID:9668133

  18. Functional morphology of the tetra fish Astyanax lacustris differs between divergent habitats in the Pantanal wetlands.

    PubMed

    Costa-Pereira, R; Araújo, M S; Paiva, F; Tavares, L E R

    2016-08-01

    This study investigated whether the body morphology of the tetra fish Astyanax lacustris (previously Astyanax asuncionensis) varied between populations inhabiting one lagoon (a lentic, shallow environment, with great habitat complexity created by aquatic macrophytes) and an adjacent river (a deeper, lotic environment where aquatic macrophytes are scarce) in a seasonally flooded wetland, despite population mixing during the wet season. Morphological differences matched a priori predictions of the theory relating functional body morphology and swimming performance in fishes between lagoon and river habitats. Observed morphological variation could have resulted from adaptive habitat choice by tetras, predation by piscivores and adaptive phenotypic plasticity during development. PMID:27238590

  19. Regulatory circuit rewiring and functional divergence of the duplicate admp genes in dorsoventral axial patterning.

    PubMed

    Chang, Yi-Cheng; Pai, Chih-Yu; Chen, Yi-Chih; Ting, Hsiu-Chi; Martinez, Pedro; Telford, Maximilian J; Yu, Jr-Kai; Su, Yi-Hsien

    2016-02-01

    The spatially opposed expression of Antidorsalizing morphogenetic protein (Admp) and BMP signals controls dorsoventral (DV) polarity across Bilateria and hence represents an ancient regulatory circuit. Here, we show that in addition to the conserved admp1 that constitutes the ancient circuit, a second admp gene (admp2) is present in Ambulacraria (Echinodermata+Hemichordata) and two marine worms belonging to Xenoturbellida and Acoelomorpha. The phylogenetic distribution implies that the two admp genes were duplicated in the Bilaterian common ancestor and admp2 was subsequently lost in chordates and protostomes. We show that the ambulacrarian admp1 and admp2 are under opposite transcriptional control by BMP signals and knockdown of Admps in sea urchins impaired their DV polarity. Over-expression of either Admps reinforced BMP signaling but resulted in different phenotypes in the sea urchin embryo. Our study provides an excellent example of signaling circuit rewiring and protein functional changes after gene duplications. PMID:26719126

  20. Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling.

    PubMed

    Kumar, Indrajit; Swaminathan, Kankshita; Hudson, Karen; Hudson, Matthew E

    2016-07-01

    Two maize phytochrome-interacting factor (PIF) basic helix-loop-helix (bHLH) family members, ZmPIF3.1 and ZmPIF3.2, were identified, cloned and expressed in vitro to investigate light-signaling interactions. A phylogenetic analysis of sequences of the maize bHLH transcription factor gene family revealed the extent of the PIF family, and a total of seven predicted PIF-encoding genes were identified from genes encoding bHLH family VIIa/b proteins in the maize genome. To investigate the role of maize PIFs in phytochrome signaling, full-length cDNAs for phytochromes PhyA2, PhyB1, PhyB2 and PhyC1 from maize were cloned and expressed in vitro as chromophorylated holophytochromes. We showed that ZmPIF3.1 and ZmPIF3.2 interact specifically with the Pfr form of maize holophytochrome B1 (ZmphyB1), showing no detectable affinity for the Pr form. Maize holophytochrome B2 (ZmphyB2) showed no detectable binding affinity for PIFs in either Pr or Pfr forms, but phyB Pfr from Arabidopsis interacted with ZmPIF3.1 similarly to ZmphyB1 Pfr. We conclude that subfunctionalization at the protein-protein interaction level has altered the role of phyB2 relative to that of phyB1 in maize. Since the phyB2 mutant shows photomorphogenic defects, we conclude that maize phyB2 is an active photoreceptor, without the binding of PIF3 seen in other phyB family proteins. PMID:27262126

  1. Structural and Functional Divergence of Growth Hormone-Releasing Hormone Receptors in Early Sarcopterygians: Lungfish and Xenopus

    PubMed Central

    Tam, Janice K. V.; Chow, Billy K. C.; Lee, Leo T. O.

    2013-01-01

    The evolutionary trajectories of growth hormone-releasing hormone (GHRH) receptor remain enigmatic since the discovery of physiologically functional GHRH-GHRH receptor (GHRHR) in non-mammalian vertebrates in 2007. Interestingly, subsequent studies have described the identification of a GHRHR2 in chicken in addition to the GHRHR and the closely related paralogous receptor, PACAP-related peptide (PRP) receptor (PRPR). In this article, we provide information, for the first time, on the GHRHR in sarcopterygian fish and amphibians by the cloning and characterization of GHRHRs from lungfish (P. dolloi) and X. laevis. Sequence alignment and phylogenetic analyses demonstrated structural resemblance of lungfish GHRHR to their mammalian orthologs, while the X. laevis GHRHR showed the highest homology to GHRHR2 in zebrafish and chicken. Functionally, lungfish GHRHR displayed high affinity towards GHRH in triggering intracellular cAMP and calcium accumulation, while X. laevis GHRHR2 was able to react with both endogenous GHRH and PRP. Tissue distribution analyses showed that both lungfish GHRHR and X. laevis GHRHR2 had the highest expression in brain, and interestingly, X. laevis GHRHR2 also had high abundance in the reproductive organs. These findings, together with previous reports, suggest that early in the Sarcopterygii lineage, GHRHR and PRPR have already established diverged and specific affinities towards their cognate ligands. GHRHR2, which has only been found in xenopus, zebrafish and chicken hitherto, accommodates both GHRH and PRP. PMID:23308232

  2. Structural and functional divergence of growth hormone-releasing hormone receptors in early sarcopterygians: lungfish and Xenopus.

    PubMed

    Tam, Janice K V; Chow, Billy K C; Lee, Leo T O

    2013-01-01

    The evolutionary trajectories of growth hormone-releasing hormone (GHRH) receptor remain enigmatic since the discovery of physiologically functional GHRH-GHRH receptor (GHRHR) in non-mammalian vertebrates in 2007. Interestingly, subsequent studies have described the identification of a GHRHR(2) in chicken in addition to the GHRHR and the closely related paralogous receptor, PACAP-related peptide (PRP) receptor (PRPR). In this article, we provide information, for the first time, on the GHRHR in sarcopterygian fish and amphibians by the cloning and characterization of GHRHRs from lungfish (P. dolloi) and X. laevis. Sequence alignment and phylogenetic analyses demonstrated structural resemblance of lungfish GHRHR to their mammalian orthologs, while the X. laevis GHRHR showed the highest homology to GHRHR(2) in zebrafish and chicken. Functionally, lungfish GHRHR displayed high affinity towards GHRH in triggering intracellular cAMP and calcium accumulation, while X. laevis GHRHR(2) was able to react with both endogenous GHRH and PRP. Tissue distribution analyses showed that both lungfish GHRHR and X. laevis GHRHR(2) had the highest expression in brain, and interestingly, X. laevis(GHRHR2) also had high abundance in the reproductive organs. These findings, together with previous reports, suggest that early in the Sarcopterygii lineage, GHRHR and PRPR have already established diverged and specific affinities towards their cognate ligands. GHRHR(2), which has only been found in xenopus, zebrafish and chicken hitherto, accommodates both GHRH and PRP. PMID:23308232

  3. Functional Divergence in Shrimp Anti-Lipopolysaccharide Factors (ALFs): From Recognition of Cell Wall Components to Antimicrobial Activity

    PubMed Central

    Rosa, Rafael Diego; Vergnes, Agnès; de Lorgeril, Julien; Goncalves, Priscila; Perazzolo, Luciane Maria; Sauné, Laure; Romestand, Bernard; Fievet, Julie; Gueguen, Yannick; Bachère, Evelyne; Destoumieux-Garzón, Delphine

    2013-01-01

    Antilipopolysaccharide factors (ALFs) have been described as highly cationic polypeptides with a broad spectrum of potent antimicrobial activities. In addition, ALFs have been shown to recognize LPS, a major component of the Gram-negative bacteria cell wall, through conserved amino acid residues exposed in the four-stranded β-sheet of their three dimensional structure. In penaeid shrimp, ALFs form a diverse family of antimicrobial peptides composed by three main variants, classified as ALF Groups A to C. Here, we identified a novel group of ALFs in shrimp (Group D ALFs), which corresponds to anionic polypeptides in which many residues of the LPS binding site are lacking. Both Group B (cationic) and Group D (anionic) shrimp ALFs were produced in a heterologous expression system. Group D ALFs were found to have impaired LPS-binding activities and only limited antimicrobial activity compared to Group B ALFs. Interestingly, all four ALF groups were shown to be simultaneously expressed in an individual shrimp and to follow different patterns of gene expression in response to a microbial infection. Group B was by far the more expressed of the ALF genes. From our results, nucleotide sequence variations in shrimp ALFs result in functional divergence, with significant differences in LPS-binding and antimicrobial activities. To our knowledge, this is the first functional characterization of the sequence diversity found in the ALF family. PMID:23861837

  4. Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination1[W][OPEN

    PubMed Central

    Sekhon, Rajandeep S.; Hirsch, Candice N.; Childs, Kevin L.; Breitzman, Matthew W.; Kell, Paul; Duvick, Susan; Spalding, Edgar P.; Buell, C. Robin; de Leon, Natalia; Kaeppler, Shawn M.

    2014-01-01

    Seed size is a component of grain yield and an important trait in crop domestication. To understand the mechanisms governing seed size in maize (Zea mays), we examined transcriptional and developmental changes during seed development in populations divergently selected for large and small seed size from Krug, a yellow dent maize cultivar. After 30 cycles of selection, seeds of the large seed population (KLS30) have a 4.7-fold greater weight and a 2.6-fold larger size compared with the small seed population (KSS30). Patterns of seed weight accumulation from the time of pollination through 30 d of grain filling showed an earlier onset, slower rate, and earlier termination of grain filling in KSS30 relative to KLS30. This was further supported by transcriptome patterns in seeds from the populations and derived inbreds. Although the onset of key genes was earlier in small seeds, similar maximum transcription levels were observed in large seeds at later stages, suggesting that functionally weaker alleles, rather than transcript abundance, may be the basis of the slow rate of seed filling in KSS30. Gene coexpression networks identified several known genes controlling cellularization and proliferation as well as novel genes that will be useful candidates for biotechnological approaches aimed at altering seed size in maize and other cereals. PMID:24710068

  5. Two subclasses of odorant-binding proteins in Spodoptera exigua display structural conservation and functional divergence.

    PubMed

    Liu, N-Y; Yang, F; Yang, K; He, P; Niu, X-H; Xu, W; Anderson, A; Dong, S-L

    2015-04-01

    Although many studies on lepidopteran pheromone-binding proteins (PBPs)/ general odorant-binding proteins (GOBPs) have been reported, the functional differentiation within and between the two odorant-binding protein (OBP) subclasses is still elusive. Here we conducted a comparative study on three SexiPBPs and two SexiGOBPs in Spodoptera exigua. Results showed that all five SexiPBP/GOBP genes have the same intron numbers and conserved exon/intron splice sites. Reverse transcription PCR results showed that these five SexiPBP/GOBPs were primarily expressed in antennae of both sexes and some were also detected in other tissues. Further, quantitative real-time PCR showed that five SexiPBP/GOBPs had different sex-biased expression patterns, with PBP1 being highly male-biased (5.96-fold difference) and PBP3 slightly female-biased (2.43-fold difference), while PBP2 and two GOBPs were approximately sex-equivalent (the absolute value<1.90-fold difference). Binding assays showed that all three SexiPBPs could bind all six sex pheromone components, but SexiPBP1 had much higher affinities [dissociation constant (Ki ) <1.10 μM] than did the other two SexiPBPs (Ki  >1.20 μM). Very intriguingly, SexiGOBP2 displayed even stronger binding to five sex pheromone components (Ki  <0.40 μM) than SexiPBP1. In contrast, SexiGOBP1 only exhibited weak binding to three alcohol-pheromone components. Similar results were obtained for tested pheromone analogues. In addition, each of SexiPBP/GOBPs selectively bound some plant odorants with considerable affinities (Ki  <10.0 μM). Taken together, of the three SexiPBPs, SexiPBP1 may play the most important role in female sex pheromone reception, and additionally all three SexiPBPs can detect some plant odorants, while SexiGOBP2 may be involved in the detection of female sex pheromones in addition to plant odorants. The results strongly suggest functional differentiation within and between the two OBP sub-classes. PMID:25345813

  6. Divergent regulation of functionally distinct γ-tubulin complexes during differentiation.

    PubMed

    Muroyama, Andrew; Seldin, Lindsey; Lechler, Terry

    2016-06-20

    Differentiation induces the formation of noncentrosomal microtubule arrays in diverse tissues. The formation of these arrays requires loss of microtubule-organizing activity (MTOC) at the centrosome, but the mechanisms regulating this transition remain largely unexplored. Here, we use the robust loss of centrosomal MTOC activity in the epidermis to identify two pools of γ-tubulin that are biochemically and functionally distinct and differentially regulated. Nucleation-competent CDK5RAP2-γ-tubulin complexes were maintained at centrosomes upon initial epidermal differentiation. In contrast, Nedd1-γ-tubulin complexes did not promote nucleation but were required for anchoring of microtubules, a previously uncharacterized activity for this complex. Cell cycle exit specifically triggered loss of Nedd1-γ-tubulin complexes, providing a mechanistic link connecting MTOC activity and differentiation. Collectively, our studies demonstrate that distinct γ-tubulin complexes regulate different microtubule behaviors at the centrosome and show that differential regulation of these complexes drives loss of centrosomal MTOC activity. PMID:27298324

  7. Functional Divergence of Hsp90 Genetic Interactions in Biofilm and Planktonic Cellular States

    PubMed Central

    Cowen, Leah E.

    2015-01-01

    Candida albicans is among the most prevalent opportunistic fungal pathogens. Its capacity to cause life-threatening bloodstream infections is associated with the ability to form biofilms, which are intrinsically drug resistant reservoirs for dispersal. A key regulator of biofilm drug resistance and dispersal is the molecular chaperone Hsp90, which stabilizes many signal transducers. We previously identified 226 C. albicans Hsp90 genetic interactors under planktonic conditions, of which 56 are involved in transcriptional regulation. Six of these transcriptional regulators have previously been implicated in biofilm formation, suggesting that Hsp90 genetic interactions identified in planktonic conditions may have functional significance in biofilms. Here, we explored the relationship between Hsp90 and five of these transcription factor genetic interactors: BCR1, MIG1, TEC1, TUP1, and UPC2. We deleted each transcription factor gene in an Hsp90 conditional expression strain, and assessed biofilm formation and morphogenesis. Strikingly, depletion of Hsp90 conferred no additional biofilm defect in the mutants. An interaction was observed in which deletion of BCR1 enhanced filamentation upon reduction of Hsp90 levels. Further, although Hsp90 modulates expression of TEC1, TUP1, and UPC2 in planktonic conditions, it has no impact in biofilms. Lastly, we probed for physical interactions between Hsp90 and Tup1, whose WD40 domain suggests that it might interact with Hsp90 directly. Hsp90 and Tup1 formed a stable complex, independent of temperature or developmental state. Our results illuminate a physical interaction between Hsp90 and a key transcriptional regulator of filamentation and biofilm formation, and suggest that Hsp90 has distinct genetic interactions in planktonic and biofilm cellular states. PMID:26367740

  8. In actio optophysiological analyses reveal functional diversification of dopaminergic neurons in the nematode C. elegans.

    PubMed

    Tanimoto, Yuki; Zheng, Ying Grace; Fei, Xianfeng; Fujie, Yukako; Hashimoto, Koichi; Kimura, Koutarou D

    2016-01-01

    Many neuronal groups such as dopamine-releasing (dopaminergic) neurons are functionally divergent, although the details of such divergence are not well understood. Dopamine in the nematode Caenorhabditis elegans modulates various neural functions and is released from four left-right pairs of neurons. The terminal identities of these dopaminergic neurons are regulated by the same genetic program, and previous studies have suggested that they are functionally redundant. In this study, however, we show functional divergence within the dopaminergic neurons of C. elegans. Because dopaminergic neurons of the animals were supposedly activated by mechanical stimulus upon entry into a lawn of their food bacteria, we developed a novel integrated microscope system that can auto-track a freely-moving (in actio) C. elegans to individually monitor and stimulate the neuronal activities of multiple neurons. We found that only head-dorsal pair of dopaminergic neurons (CEPD), but not head-ventral or posterior pairs, were preferentially activated upon food entry. In addition, the optogenetic activation of CEPD neurons alone exhibited effects similar to those observed upon food entry. Thus, our results demonstrated functional divergence in the genetically similar dopaminergic neurons, which may provide a new entry point toward understanding functional diversity of neurons beyond genetic terminal identification. PMID:27193056

  9. In actio optophysiological analyses reveal functional diversification of dopaminergic neurons in the nematode C. elegans

    PubMed Central

    Tanimoto, Yuki; Zheng, Ying Grace; Fei, Xianfeng; Fujie, Yukako; Hashimoto, Koichi; Kimura, Koutarou D.

    2016-01-01

    Many neuronal groups such as dopamine-releasing (dopaminergic) neurons are functionally divergent, although the details of such divergence are not well understood. Dopamine in the nematode Caenorhabditis elegans modulates various neural functions and is released from four left-right pairs of neurons. The terminal identities of these dopaminergic neurons are regulated by the same genetic program, and previous studies have suggested that they are functionally redundant. In this study, however, we show functional divergence within the dopaminergic neurons of C. elegans. Because dopaminergic neurons of the animals were supposedly activated by mechanical stimulus upon entry into a lawn of their food bacteria, we developed a novel integrated microscope system that can auto-track a freely-moving (in actio) C. elegans to individually monitor and stimulate the neuronal activities of multiple neurons. We found that only head-dorsal pair of dopaminergic neurons (CEPD), but not head-ventral or posterior pairs, were preferentially activated upon food entry. In addition, the optogenetic activation of CEPD neurons alone exhibited effects similar to those observed upon food entry. Thus, our results demonstrated functional divergence in the genetically similar dopaminergic neurons, which may provide a new entry point toward understanding functional diversity of neurons beyond genetic terminal identification. PMID:27193056

  10. In actio optophysiological analyses reveal functional diversification of dopaminergic neurons in the nematode C. elegans

    NASA Astrophysics Data System (ADS)

    Tanimoto, Yuki; Zheng, Ying Grace; Fei, Xianfeng; Fujie, Yukako; Hashimoto, Koichi; Kimura, Koutarou D.

    2016-05-01

    Many neuronal groups such as dopamine-releasing (dopaminergic) neurons are functionally divergent, although the details of such divergence are not well understood. Dopamine in the nematode Caenorhabditis elegans modulates various neural functions and is released from four left-right pairs of neurons. The terminal identities of these dopaminergic neurons are regulated by the same genetic program, and previous studies have suggested that they are functionally redundant. In this study, however, we show functional divergence within the dopaminergic neurons of C. elegans. Because dopaminergic neurons of the animals were supposedly activated by mechanical stimulus upon entry into a lawn of their food bacteria, we developed a novel integrated microscope system that can auto-track a freely-moving (in actio) C. elegans to individually monitor and stimulate the neuronal activities of multiple neurons. We found that only head-dorsal pair of dopaminergic neurons (CEPD), but not head-ventral or posterior pairs, were preferentially activated upon food entry. In addition, the optogenetic activation of CEPD neurons alone exhibited effects similar to those observed upon food entry. Thus, our results demonstrated functional divergence in the genetically similar dopaminergic neurons, which may provide a new entry point toward understanding functional diversity of neurons beyond genetic terminal identification.

  11. Reveal genes functionally associated with ACADS by a network study.

    PubMed

    Chen, Yulong; Su, Zhiguang

    2015-09-15

    Establishing a systematic network is aimed at finding essential human gene-gene/gene-disease pathway by means of network inter-connecting patterns and functional annotation analysis. In the present study, we have analyzed functional gene interactions of short-chain acyl-coenzyme A dehydrogenase gene (ACADS). ACADS plays a vital role in free fatty acid β-oxidation and regulates energy homeostasis. Modules of highly inter-connected genes in disease-specific ACADS network are derived by integrating gene function and protein interaction data. Among the 8 genes in ACADS web retrieved from both STRING and GeneMANIA, ACADS is effectively conjoined with 4 genes including HAHDA, HADHB, ECHS1 and ACAT1. The functional analysis is done via ontological briefing and candidate disease identification. We observed that the highly efficient-interlinked genes connected with ACADS are HAHDA, HADHB, ECHS1 and ACAT1. Interestingly, the ontological aspect of genes in the ACADS network reveals that ACADS, HAHDA and HADHB play equally vital roles in fatty acid metabolism. The gene ACAT1 together with ACADS indulges in ketone metabolism. Our computational gene web analysis also predicts potential candidate disease recognition, thus indicating the involvement of ACADS, HAHDA, HADHB, ECHS1 and ACAT1 not only with lipid metabolism but also with infant death syndrome, skeletal myopathy, acute hepatic encephalopathy, Reye-like syndrome, episodic ketosis, and metabolic acidosis. The current study presents a comprehensible layout of ACADS network, its functional strategies and candidate disease approach associated with ACADS network. PMID:26045367

  12. Divergent RNA transcription

    PubMed Central

    Naughton, Catherine; Corless, Samuel; Gilbert, Nick

    2013-01-01

    New approaches using biotinylated-psoralen as a probe for investigating DNA structure have revealed new insights into the relationship between DNA supercoiling, transcription and chromatin compaction. We explore a hypothesis that divergent RNA transcription generates negative supercoiling at promoters facilitating initiation complex formation and subsequent promoter clearance. PMID:23863199

  13. Chloroplast division in higher plants requires members of two functionally divergent gene families with homology to bacterial ftsZ.

    PubMed Central

    Osteryoung, K W; Stokes, K D; Rutherford, S M; Percival, A L; Lee, W Y

    1998-01-01

    The division of plastids is critical for viability in photosynthetic eukaryotes, but the mechanisms associated with this process are still poorly understood. We previously identified a nuclear gene from Arabidopsis encoding a chloroplast-localized homolog of the bacterial cell division protein FtsZ, an essential cytoskeletal component of the prokaryotic cell division apparatus. Here, we report the identification of a second nuclear-encoded FtsZ-type protein from Arabidopsis that does not contain a chloroplast targeting sequence or other obvious sorting signals and is not imported into isolated chloroplasts, which strongly suggests that it is localized in the cytosol. We further demonstrate using antisense technology that inhibiting expression of either Arabidopsis FtsZ gene (AtFtsZ1-1 or AtFtsZ2-1) in transgenic plants reduces the number of chloroplasts in mature leaf cells from 100 to one, indicating that both genes are essential for division of higher plant chloroplasts but that each plays a distinct role in the process. Analysis of currently available plant FtsZ sequences further suggests that two functionally divergent FtsZ gene families encoding differentially localized products participate in chloroplast division. Our results provide evidence that both chloroplastic and cytosolic forms of FtsZ are involved in chloroplast division in higher plants and imply that important differences exist between chloroplasts and prokaryotes with regard to the roles played by FtsZ proteins in the division process. PMID:9836740

  14. Proteomic profiling reveals insights into Triticeae stigma development and function.

    PubMed

    Nazemof, Nazila; Couroux, Philippe; Rampitsch, Christof; Xing, Tim; Robert, Laurian S

    2014-11-01

    To our knowledge, this study represents the first high-throughput characterization of a stigma proteome in the Triticeae. A total of 2184 triticale mature stigma proteins were identified using three different gel-based approaches combined with mass spectrometry. The great majority of these proteins are described in a Triticeae stigma for the first time. These results revealed many proteins likely to play important roles in stigma development and pollen-stigma interactions, as well as protection against biotic and abiotic stresses. Quantitative comparison of the triticale stigma transcriptome and proteome showed poor correlation, highlighting the importance of having both types of analysis. This work makes a significant contribution towards the elucidation of the Triticeae stigma proteome and provides novel insights into its role in stigma development and function. PMID:25170101

  15. Proteomic profiling reveals insights into Triticeae stigma development and function

    PubMed Central

    Nazemof, Nazila; Couroux, Philippe; Rampitsch, Christof; Xing, Tim; Robert, Laurian S.

    2014-01-01

    To our knowledge, this study represents the first high-throughput characterization of a stigma proteome in the Triticeae. A total of 2184 triticale mature stigma proteins were identified using three different gel-based approaches combined with mass spectrometry. The great majority of these proteins are described in a Triticeae stigma for the first time. These results revealed many proteins likely to play important roles in stigma development and pollen–stigma interactions, as well as protection against biotic and abiotic stresses. Quantitative comparison of the triticale stigma transcriptome and proteome showed poor correlation, highlighting the importance of having both types of analysis. This work makes a significant contribution towards the elucidation of the Triticeae stigma proteome and provides novel insights into its role in stigma development and function. PMID:25170101

  16. Genome-Wide Analysis Reveals Diverged Patterns of Codon Bias, Gene Expression, and Rates of Sequence Evolution in Picea Gene Families

    PubMed Central

    De La Torre, Amanda R.; Lin, Yao-Cheng; Van de Peer, Yves; Ingvarsson, Pär K.

    2015-01-01

    The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms. PMID:25747252

  17. Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition

    PubMed Central

    2013-01-01

    Background In pigs, adipose tissue is one of the principal organs involved in the regulation of lipid metabolism. It is particularly involved in the overall fatty acid synthesis with consequences in other lipid-target organs such as muscles and the liver. With this in mind, we have used massive, parallel high-throughput sequencing technologies to characterize the porcine adipose tissue transcriptome architecture in six Iberian x Landrace crossbred pigs showing extreme phenotypes for intramuscular fatty acid composition (three per group). Results High-throughput RNA sequencing was used to generate a whole characterization of adipose tissue (backfat) transcriptome. A total of 4,130 putative unannotated protein-coding sequences were identified in the 20% of reads which mapped in intergenic regions. Furthermore, 36% of the unmapped reads were represented by interspersed repeats, SINEs being the most abundant elements. Differential expression analyses identified 396 candidate genes among divergent animals for intramuscular fatty acid composition. Sixty-two percent of these genes (247/396) presented higher expression in the group of pigs with higher content of intramuscular SFA and MUFA, while the remaining 149 showed higher expression in the group with higher content of PUFA. Pathway analysis related these genes to biological functions and canonical pathways controlling lipid and fatty acid metabolisms. In concordance with the phenotypic classification of animals, the major metabolic pathway differentially modulated between groups was de novo lipogenesis, the group with more PUFA being the one that showed lower expression of lipogenic genes. Conclusions These results will help in the identification of genetic variants at loci that affect fatty acid composition traits. The implications of these results range from the improvement of porcine meat quality traits to the application of the pig as an animal model of human metabolic diseases. PMID:24289474

  18. Functional similarity and molecular divergence of a novel reproductive transcriptome in two male-pregnant Syngnathus pipefish species

    PubMed Central

    Small, Clayton M; Harlin-Cognato, April D; Jones, Adam G

    2013-01-01

    Evolutionary studies have revealed that reproductive proteins in animals and plants often evolve more rapidly than the genome-wide average. The causes of this pattern, which may include relaxed purifying selection, sexual selection, sexual conflict, pathogen resistance, reinforcement, or gene duplication, remain elusive. Investigative expansions to additional taxa and reproductive tissues have the potential to shed new light on this unresolved problem. Here, we embark on such an expansion, in a comparison of the brood-pouch transcriptome between two male-pregnant species of the pipefish genus Syngnathus. Male brooding tissues in syngnathid fishes represent a novel, nonurogenital reproductive trait, heretofore mostly uncharacterized from a molecular perspective. We leveraged next-generation sequencing (Roche 454 pyrosequencing) to compare transcript abundance in the male brooding tissues of pregnant with nonpregnant samples from Gulf (S. scovelli) and dusky (S. floridae) pipefish. A core set of protein-coding genes, including multiple members of astacin metalloprotease and c-type lectin gene families, is consistent between species in both the direction and magnitude of expression bias. As predicted, coding DNA sequence analysis of these putative “male pregnancy proteins” suggests rapid evolution relative to nondifferentially expressed genes and reflects signatures of adaptation similar in magnitude to those reported from Drosophila male accessory gland proteins. Although the precise drivers of male pregnancy protein divergence remain unknown, we argue that the male pregnancy transcriptome in syngnathid fishes, a clade diverse with respect to brooding morphology and mating system, represents a unique and promising object of study for understanding the perplexing evolutionary nature of reproductive molecules. PMID:24324861

  19. Toll-Like Receptors and Dectin-1, a C-Type Lectin Receptor, Trigger Divergent Functions in CNS Macrophages

    PubMed Central

    Wang, Yan; Guan, Zhen; Beckwith, Kyle A.; Braun, Kaitlyn J.; Wei, Ping; McTigue, Dana M.

    2015-01-01

    Spinal cord injury (SCI) activates macrophages, endowing them with both reparative and pathological functions. The mechanisms responsible for these divergent functions are unknown but are likely controlled through stochastic activation of different macrophage receptor subtypes. Various danger-associated molecular patterns released from dying cells in the injured spinal cord likely activate distinct subtypes of macrophage pattern recognition receptors, including bacterial toll-like receptors (TLRs) and fungal C-type lectin receptors (e.g., dectin-1). To determine the in vivo consequences of activating these receptors, ligands specific for TLR2 or dectin-1 were microinjected, alone or in combination, into intact spinal cord. Both ligands elicit a florid macrophage reaction; however, only dectin-1 activation causes macrophage-mediated demyelination and axonal injury. Coactivating TLR2 reduced the injurious effects of dectin-1 activation. When injected into traumatically injured spinal cord, TLR2 agonists enhance the endogenous macrophage reaction while conferring neuroprotection. Indeed, dieback of axons was reduced, leading to smaller lesion volumes at the peak of the macrophage response. Moreover, the density of NG2+ cells expressing vimentin increased in and near lesions that were enriched with TLR2-activated macrophages. In dectin-1-null mutant (knock-out) mice, dieback of corticospinal tract axons also is reduced after SCI. Collectively, these data support the hypothesis that the ability of macrophages to create an axon growth-permissive microenvironment or cause neurotoxicity is receptor dependent and it may be possible to exploit this functional dichotomy to enhance CNS repair. SIGNIFICANCE STATEMENT There is a growing appreciation that macrophages exert diverse functions in the injured and diseased CNS. Indeed, both macrophage-mediated repair and macrophage-mediated injury occur, and often these effector functions are elicited simultaneously. Understanding the

  20. Uncovering Divergence of Rice Exon Junction Complex Core Heterodimer Gene Duplication Reveals Their Essential Role in Growth, Development, and Reproduction1[W

    PubMed Central

    Gong, Pichang; He, Chaoying

    2014-01-01

    The exon junction complex (EJC) plays important developmental roles in animals; however, its role in plants is not well known. Here, we show various aspects of the divergence of each duplicated MAGO NASHI (MAGO) and Y14 gene pair in rice (Oryza sativa) encoding the putative EJC core subunits that form the obligate MAGO-Y14 heterodimers. OsMAGO1, OsMAGO2, and OsY14a were constitutively expressed in all tissues, while OsY14b was predominantly expressed in embryonic tissues. OsMAGO2 and OsY14b were more sensitive to different stresses than OsMAGO1 and OsY14a, and their encoded protein pair shared 93.8% and 46.9% sequence identity, respectively. Single MAGO down-regulation in rice did not lead to any phenotypic variation; however, double gene knockdowns generated short rice plants with abnormal flowers, and the stamens of these flowers showed inhibited degradation and absorption of both endothecium and tapetum, suggesting that OsMAGO1 and OsMAGO2 were functionally redundant. OsY14a knockdowns phenocopied OsMAGO1OsMAGO2 mutants, while down-regulation of OsY14b failed to induce plantlets, suggesting the functional specialization of OsY14b in embryogenesis. OsMAGO1OsMAGO2OsY14a triple down-regulation enhanced the phenotypes of OsMAGO1OsMAGO2 and OsY14a down-regulated mutants, indicating that they exert developmental roles in the MAGO-Y14 heterodimerization mode. Modified gene expression was noted in the altered developmental pathways in these knockdowns, and the transcript splicing of UNDEVELOPED TAPETUM1 (OsUDT1), a key regulator in stamen development, was uniquely abnormal. Concomitantly, MAGO and Y14 selectively bound to the OsUDT1 premessenger RNA, suggesting that rice EJC subunits regulate splicing. Our work provides novel insights into the function of the EJC locus in growth, development, and reproduction in angiosperms and suggests a role for these genes in the adaptive evolution of cereals. PMID:24820023

  1. Knock-out models reveal new aquaporin functions.

    PubMed

    Verkman, Alan S

    2009-01-01

    Knockout mice have been informative in the discovery of unexpected biological functions of aquaporins. Knockout mice have confirmed the predicted roles of aquaporins in transepithelial fluid transport, as in the urinary concentrating mechanism and glandular fluid secretion. A less obvious, though predictable role of aquaporins is in tissue swelling under stress, as in the brain in stroke, tumor and infection. Phenotype analysis of aquaporin knockout mice has revealed several unexpected cellular roles of aquaporins whose mechanisms are being elucidated. Aquaporins facilitate cell migration, as seen in aquaporin-dependent tumor angiogenesis and tumor metastasis, by a mechanism that may involve facilitated water transport in lamellipodia of migrating cells. The ' aquaglyceroporins', aquaporins that transport both glycerol and water, regulate glycerol content in epidermis, fat and other tissues, and lead to a multiplicity of interesting consequences of gene disruption including dry skin, resistance to skin carcinogenesis, impaired cell proliferation and altered fat metabolism. An even more surprising role of a mammalian aquaporin is in neural signal transduction in the central nervous system. The many roles of aquaporins might be exploited for clinical benefit by modulation of aquaporin expression/function - as diuretics, and in the treatment of brain swelling, glaucoma, epilepsy, obesity and cancer. PMID:19096787

  2. Proteomics Analysis Reveals Overlapping Functions of Clustered Protocadherins*

    PubMed Central

    Han, Meng-Hsuan; Lin, Chengyi; Meng, Shuxia; Wang, Xiaozhong

    2010-01-01

    The three tandem-arrayed protocadherin (Pcdh) gene clusters, namely Pcdh-α, Pcdh-β, and Pcdh-γ, play important roles in the development of the vertebrate central nervous system. To gain insight into the molecular action of PCDHs, we performed a systematic proteomics analysis of PCDH-γ-associated protein complexes. We identified a list of 154 non-redundant proteins in the PCDH-γ complexes. This list includes nearly 30 members of clustered Pcdh-α, -β, and -γ families as core components of the complexes and additionally over 120 putative PCDH-associated proteins. We validated a selected subset of PCDH-γ-associated proteins using specific antibodies. Analysis of the identities of PCDH-associated proteins showed that the majority of them overlap with the proteomic profile of postsynaptic density preparations. Further analysis of membrane protein complexes revealed that several validated PCDH-γ-associated proteins exhibit reduced levels in Pcdh-γ-deficient brain tissues. Therefore, PCDH-γs are required for the integrity of the complexes. However, the size of the overall complexes and the abundance of many other proteins remained unchanged, raising a possibility that PCDH-αs and PCDH-βs might compensate for PCDH-γ function in complex formation. As a test of this idea, RNA interference knockdown of both PCDH-αs and PCDH-γs showed that PCDHs have redundant functions in regulating neuronal survival in the chicken spinal cord. Taken together, our data provide evidence that clustered PCDHs coexist in large protein complexes and have overlapping functions during vertebrate neural development. PMID:19843561

  3. Nucleotide substitutions revealing specific functions of Polycomb group genes.

    PubMed

    Bajusz, Izabella; Sipos, László; Pirity, Melinda K

    2015-04-01

    POLYCOMB group (PCG) proteins belong to the family of epigenetic regulators of genes playing important roles in differentiation and development. Mutants of PcG genes were isolated first in the fruit fly, Drosophila melanogaster, resulting in spectacular segmental transformations due to the ectopic expression of homeotic genes. Homologs of Drosophila PcG genes were also identified in plants and in vertebrates and subsequent experiments revealed the general role of PCG proteins in the maintenance of the repressed state of chromatin through cell divisions. The past decades of gene targeting experiments have allowed us to make significant strides towards understanding how the network of PCG proteins influences multiple aspects of cellular fate determination during development. Being involved in the transmission of specific expression profiles of different cell lineages, PCG proteins were found to control wide spectra of unrelated epigenetic processes in vertebrates, such as stem cell plasticity and renewal, genomic imprinting and inactivation of X-chromosome. PCG proteins also affect regulation of metabolic genes being important for switching programs between pluripotency and differentiation. Insight into the precise roles of PCG proteins in normal physiological processes has emerged from studies employing cell culture-based systems and genetically modified animals. Here we summarize the findings obtained from PcG mutant fruit flies and mice generated to date with a focus on PRC1 and PRC2 members altered by nucleotide substitutions resulting in specific alleles. We also include a compilation of lessons learned from these models about the in vivo functions of this complex protein family. With multiple knockout lines, sophisticated approaches to study the consequences of peculiar missense point mutations, and insights from complementary gain-of-function systems in hand, we are now in a unique position to significantly advance our understanding of the molecular basis of

  4. Revealing the Functions of the Transketolase Enzyme Isoforms in Rhodopseudomonas palustris Using a Systems Biology Approach

    PubMed Central

    Hu, Chia-Wei; Chang, Ya-Ling; Chen, Shiang Jiuun; Kuo-Huang, Ling-Long; Liao, James C.; Huang, Hsuan-Cheng; Juan, Hsueh-Fen

    2011-01-01

    Background Rhodopseudomonas palustris (R. palustris) is a purple non-sulfur anoxygenic phototrophic bacterium that belongs to the class of proteobacteria. It is capable of absorbing atmospheric carbon dioxide and converting it to biomass via the process of photosynthesis and the Calvin–Benson–Bassham (CBB) cycle. Transketolase is a key enzyme involved in the CBB cycle. Here, we reveal the functions of transketolase isoforms I and II in R. palustris using a systems biology approach. Methodology/Principal Findings By measuring growth ability, we found that transketolase could enhance the autotrophic growth and biomass production of R. palustris. Microarray and real-time quantitative PCR revealed that transketolase isoforms I and II were involved in different carbon metabolic pathways. In addition, immunogold staining demonstrated that the two transketolase isoforms had different spatial localizations: transketolase I was primarily associated with the intracytoplasmic membrane (ICM) but transketolase II was mostly distributed in the cytoplasm. Comparative proteomic analysis and network construction of transketolase over-expression and negative control (NC) strains revealed that protein folding, transcriptional regulation, amino acid transport and CBB cycle-associated carbon metabolism were enriched in the transketolase I over-expressed strain. In contrast, ATP synthesis, carbohydrate transport, glycolysis-associated carbon metabolism and CBB cycle-associated carbon metabolism were enriched in the transketolase II over-expressed strain. Furthermore, ATP synthesis assays showed a significant increase in ATP synthesis in the transketolase II over-expressed strain. A PEPCK activity assay showed that PEPCK activity was higher in transketolase over-expressed strains than in the negative control strain. Conclusions/Significance Taken together, our results indicate that the two isoforms of transketolase in R. palustris could affect photoautotrophic growth through both

  5. Functional Genomics Reveals Linkers Critical for Influenza Virus Polymerase

    PubMed Central

    Wang, Lulan; Wu, Aiping; Wang, Yao E.; Quanquin, Natalie; Li, Chunfeng; Wang, Jingfeng; Chen, Hsiang-Wen; Liu, Suyang; Liu, Ping; Zhang, Hong; Qin, F. Xiao-Feng

    2015-01-01

    ABSTRACT Influenza virus mRNA synthesis by the RNA-dependent RNA polymerase involves binding and cleavage of capped cellular mRNA by the PB2 and PA subunits, respectively, and extension of viral mRNA by PB1. However, the mechanism for such a dynamic process is unclear. Using high-throughput mutagenesis and sequencing analysis, we have not only generated a comprehensive functional map for the microdomains of individual subunits but also have revealed the PA linker to be critical for polymerase activity. This PA linker binds to PB1 and also forms ionic interactions with the PA C-terminal channel. Nearly all mutants with five-amino-acid insertions in the linker were nonviable. Our model further suggests that the PA linker plays an important role in the conformational changes that occur between stages that favor capped mRNA binding and cleavage and those associated with viral mRNA synthesis. IMPORTANCE The RNA-dependent RNA polymerase of influenza virus consists of the PB1, PB2, and PA subunits. By combining genome-wide mutagenesis analysis with the recently discovered crystal structure of the influenza polymerase heterotrimer, we generated a comprehensive functional map of the entire influenza polymerase complex. We identified the microdomains of individual subunits, including the catalytic domains, the interaction interfaces between subunits, and nine linkers interconnecting different domains. Interestingly, we found that mutants with five-amino-acid insertions in individual linkers were nonviable, suggesting the critical roles these linkers play in coordinating spatial relationships between the subunits. We further identified an extended PA linker that binds to PB1 and also forms ionic interactions with the PA C-terminal channel. PMID:26719244

  6. Divergent expression patterns of miR164 and CUP-SHAPED COTYLEDON genes in palms and other monocots: implication for the evolution of meristem function in angiosperms.

    PubMed

    Adam, Hélène; Marguerettaz, Mélanie; Qadri, Rashad; Adroher, Bernard; Richaud, Frédérique; Collin, Myriam; Thuillet, Anne-Céline; Vigouroux, Yves; Laufs, Patrick; Tregear, James W; Jouannic, Stefan

    2011-04-01

    In order to understand how the morphology of plant species has diversified over time, it is necessary to decipher how the underlying developmental programs have evolved. The regulatory network controlling shoot meristem activity is likely to have played an important role in morphological diversification and useful insights can be gained by comparing monocots and eudicots. These two distinct monophyletic groups of angiosperms diverged 130 Ma and are characterized by important differences in their morphology. Several studies of eudicot species have revealed a conserved role for NAM and CUC3 genes in meristem functioning and pattern formation through the definition of morphogenetic boundaries during development. In this study, we show that NAM- and CUC3-related genes are conserved in palms and grasses, their diversification having predated the radiation of monocots and eudicots. Moreover, the NAM-miR164 posttranscriptional regulatory module is also conserved in palm species. However, in contrast to the CUC3-related genes, which share a similar expression pattern between the two angiosperm groups, the expression domain of the NAM-miR164 module differs between monocot and eudicot species. In our studies of spatial expression patterns, we compared existing eudicot data with novel results from our work using two palm species (date palm and oil palm) and two members of the Poaceae (rice and millet). In addition to contrasting results obtained at the gene expression level, major differences were also observed between eudicot and monocot NAM-related genes in the occurrence of putative cis-regulatory elements in their promoter sequences. Overall, our results suggest that although NAM- and CUC3-related proteins are functionally equivalent between monocots and eudicots, evolutionary radiation has resulted in heterotopy through alterations in the expression domain of the NAM-miR164 regulatory module. PMID:21135149

  7. Overexpression of Three TaEXPA1 Homoeologous Genes with Distinct Expression Divergence in Hexaploid Wheat Exhibit Functional Retention in Arabidopsis

    PubMed Central

    Xing, Jiewen; Chen, Yanhong; Han, Zongfu; Yao, Yingyin; Peng, Huiru; Ni, Zhongfu; Sun, Qixin

    2013-01-01

    Common wheat is a hexaploid species with most of the genes present as triplicate homoeologs. Expression divergences of homoeologs are frequently observed in wheat as well as in other polyploid plants. However, little is known about functional variances among homologous genes arising from polyploidy. Expansins play diverse roles in plant developmental processes related to the action of cell wall loosening. Expression of the three TaEXPA1 homoeologs varied dynamically at different stages and organs, and epigenetic modifications contribute to the expression divergence of three TaEXPA1 homoeologs during wheat development. Nevertheless, their functions remain to be clarified. We found that over expression of TaEXPA1-A, -B and -D produced similar morphological changes in transgenic Arabidopsis plants, including increased germination and growth rate during seedling and adult stages, indicating that the proteins encoded by these three wheat TaEXPA1 homoeologs have similar (or conserved) functions in Arabidopsis. Collectively, our present study provided an example of a set of homoeologous genes expression divergence in different developmental stages and organs in hexaploid wheat but functional retention in transgenic Arabidopsis plants. PMID:23696842

  8. Functional divergence within class B MADS-box genes TfGLO and TfDEF in Torenia fournieri Lind

    PubMed Central

    Sasaki, Katsutomo; Aida, Ryutaro; Yamaguchi, Hiroyasu; Shikata, Masahito; Niki, Tomoya; Nishijima, Takaaki

    2010-01-01

    Homeotic class B genes GLOBOSA (GLO)/PISTILLATA (PI) and DEFICIENS (DEF)/APETALA3 (AP3) are involved in the development of petals and stamens in Arabidopsis. However, functions of these genes in the development of floral organs in torenia are less well known. Here, we demonstrate the unique floral phenotypes of transgenic torenia formed due to the modification of class B genes, TfGLO and TfDEF. TfGLO-overexpressing plants showed purple-stained sepals that accumulated anthocyanins in a manner similar to that of petals. TfGLO-suppressed plants showed serrated petals and TfDEF-suppressed plants showed partially decolorized petals. In TfGLO-overexpressing plants, cell shapes on the surfaces of sepals were altered to petal-like cell shapes. Furthermore, TfGLO- and TfDEF-suppressed plants partially had sepal-like cells on the surfaces of their petals. We isolated putative class B gene-regulated genes and examined their expression in transgenic plants. Three xyloglucan endo-1,4-beta-d-glucanase genes were up-regulated in TfGLO- and TfDEF-overexpressing plants and down-regulated in TfGLO- and TfDEF-suppressed plants. In addition, 10 anthocyanin biosynthesis-related genes, including anthocyanin synthase and chalcone isomerase, were up-regulated in TfGLO-overexpressing plants and down-regulated in TfGLO-suppressed plants. The expression patterns of these 10 genes in TfDEF transgenic plants were diverse and classified into several groups. HPLC analysis indicated that sepals of TfGLO-overexpressing plants accumulate the same type of anthocyanins and flavones as wild-type plants. The difference in phenotypes and expression patterns of the 10 anthocyanin biosynthesis-related genes between TfGLO and TfDEF transgenic plants indicated that TfGLO and TfDEF have partial functional divergence, while they basically work synergistically in torenia. Electronic supplementary material The online version of this article (doi:10.1007/s00438-010-0574-z) contains supplementary material, which

  9. Phylogenetic and transcriptomic analysis of chemosensory receptors in a pair of divergent ant species reveals sex-specific signatures of odor coding.

    PubMed

    Zhou, Xiaofan; Slone, Jesse D; Rokas, Antonis; Berger, Shelley L; Liebig, Jürgen; Ray, Anandasankar; Reinberg, Danny; Zwiebel, Laurence J

    2012-01-01

    Ants are a highly successful family of insects that thrive in a variety of habitats across the world. Perhaps their best-known features are complex social organization and strict division of labor, separating reproduction from the day-to-day maintenance and care of the colony, as well as strict discrimination against foreign individuals. Since these social characteristics in ants are thought to be mediated by semiochemicals, a thorough analysis of these signals, and the receptors that detect them, is critical in revealing mechanisms that lead to stereotypic behaviors. To address these questions, we have defined and characterized the major chemoreceptor families in a pair of behaviorally and evolutionarily distinct ant species, Camponotus floridanus and Harpegnathos saltator. Through comprehensive re-annotation, we show that these ant species harbor some of the largest yet known repertoires of odorant receptors (Ors) among insects, as well as a more modest number of gustatory receptors (Grs) and variant ionotropic glutamate receptors (Irs). Our phylogenetic analyses further demonstrate remarkably rapid gains and losses of ant Ors, while Grs and Irs have also experienced birth-and-death evolution to different degrees. In addition, comparisons of antennal transcriptomes between sexes identify many chemoreceptors that are differentially expressed between males and females and between species. We have also revealed an agonist for a worker-enriched OR from C. floridanus, representing the first case of a heterologously characterized ant tuning Or. Collectively, our analysis reveals a large number of ant chemoreceptors exhibiting patterns of differential expression and evolution consistent with sex/species-specific functions. These differentially expressed genes are likely associated with sex-based differences, as well as the radically different social lifestyles observed between C. floridanus and H. saltator, and thus are targets for further functional characterization

  10. Divergent Realities and Perceived Inequalities: Adolescents', Mothers', and Observers' Perceptions of Family Interactions and Adolescent Psychological Functioning.

    ERIC Educational Resources Information Center

    Welsh, Deborah P.; Galliher, Renee V.; Powers, Sally I.

    1998-01-01

    Used two approaches to examine mothers', adolescents', and observers' discrepancies in perceptions of family interaction in rural, working-class families. Results using the divergent-realities approach support a developmental lifespan perspective positing that developmental tasks influence perception. Results using perceived-inequalities approach…

  11. Mitochondrial Analysis of the Most Basal Canid Reveals Deep Divergence between Eastern and Western North American Gray Foxes (Urocyon spp.) and Ancient Roots in Pleistocene California

    PubMed Central

    Goddard, Natalie S.; Statham, Mark J.; Sacks, Benjamin N.

    2015-01-01

    Pleistocene aridification in central North America caused many temperate forest-associated vertebrates to split into eastern and western lineages. Such divisions can be cryptic when Holocene expansions have closed the gaps between once-disjunct ranges or when local morphological variation obscures deeper regional divergences. We investigated such cryptic divergence in the gray fox (Urocyon cinereoargenteus), the most basal extant canid in the world. We also investigated the phylogeography of this species and its diminutive relative, the island fox (U. littoralis), in California. The California Floristic Province was a significant source of Pleistocene diversification for a wide range of taxa and, we hypothesized, for the gray fox as well. Alternatively, gray foxes in California potentially reflected a recent Holocene expansion from further south. We sequenced mitochondrial DNA from 169 gray foxes from the southeastern and southwestern United States and 11 island foxes from three of the Channel Islands. We estimated a 1.3% sequence divergence in the cytochrome b gene between eastern and western foxes and used coalescent simulations to date the divergence to approximately 500,000 years before present (YBP), which is comparable to that between recognized sister species within the Canidae. Gray fox samples collected from throughout California exhibited high haplotype diversity, phylogeographic structure, and genetic signatures of a late-Holocene population decline. Bayesian skyline analysis also indicated an earlier population increase dating to the early Wisconsin glaciation (~70,000 YBP) and a root height extending back to the previous interglacial (~100,000 YBP). Together these findings support California’s role as a long-term Pleistocene refugium for western Urocyon. Lastly, based both on our results and re-interpretation of those of another study, we conclude that island foxes of the Channel Islands trace their origins to at least 3 distinct female founders from

  12. Functional analysis and regulation of the divergent spuABCDEFGH-spuI operons for polyamine uptake and utilization in Pseudomonas aeruginosa PAO1.

    PubMed

    Lu, Chung-Dar; Itoh, Yoshifumi; Nakada, Yuji; Jiang, Ying

    2002-07-01

    A multiple-gene locus for polyamine uptake and utilization was discovered in Pseudomonas aeruginosa PAO1. This locus contained nine genes designated spuABCDEFGHI (spu for spermidine and putrescine utilization). The physiological functions of the spu genes in utilization of two polyamines (putrescine and spermidine) were analyzed by using Tn5 transposon-mediated spu knockout mutants. Growth and uptake experiments support that the spuDEFGH genes specify components of a major ABC-type transport system for spermidine uptake, and enzymatic measurements indicated that spuC encodes putrescine aminotransferase with pyruvate as the amino group receptor. Although spuA and spuB mutants showed an apparent defect in spermidine utilization, the biochemical functions of the gene products have yet to be elucidated. Assays of lacZ fusions demonstrated the presence of agmatine-, putrescine-, and spermidine-inducible promoters for the spuABCDEFGH operon and the divergently transcribed spuI gene of unknown function. Since the observed induction effect of agmatine was abolished in an aguA mutant where conversion of agmatine into putrescine was blocked, putrescine or spermidine, but not agmatine, serves as the inducer molecule of the spuA-spuI divergent promoters. S1 nuclease mappings confirmed further the induction effects of the polyamines on transcription of the divergent promoters and localized the transcription initiation sites. Gel retardation assays with extracts from the cells grown on putrescine or spermidine demonstrated the presence of a polyamine-responsive regulatory protein interacting with the divergent promoter region. Finally, the absence of the putrescine-inducible spuA expression and putrescine aminotransferase (spuC) formation in the cbrB mutant indicated that the spu operons are regulated by the global CbrAB two-component system perhaps via the putative polyamine-responsive transcriptional activator. PMID:12081945

  13. Genome-Wide Identification, Evolution and Functional Divergence of MYB Transcription Factors in Chinese White Pear (Pyrus bretschneideri).

    PubMed

    Li, Xiaolong; Xue, Cheng; Li, Jiaming; Qiao, Xin; Li, Leiting; Yu, Li'ang; Huang, Yuhua; Wu, Jun

    2016-04-01

    The MYB superfamily is large and functionally diverse in plants. To date, MYB family genes have not yet been identified in Chinese white pear (Pyrus bretschneideri), and their functions remain unclear. In this study, we identified 231 genes as candidate MYB genes and divided them into four subfamilies. The R2R3-MYB (PbrMYB) family shared an R2R3 domain with 104 amino acid residues, including five conserved tryptophan residues. The Pbr MYB family was divided into 37 functional subgroups including 33 subgroups which contained both MYB genes of Rosaceae plants and AtMYB genes, and four subgroups which included only Rosaceae MYB genes or AtMYB genes. PbrMYB genes with similar functions clustered into the same subgroup, indicating functional conservation. We also found that whole-genome duplication (WGD) and dispersed duplications played critical roles in the expansion of the MYB family. The 87 Pbr MYB duplicated gene pairs dated back to the two WGD events. Purifying selection was the primary force driving Pbr MYB gene evolution. The 15 gene pairs presented 1-7 codon sites under positive selection. A total of 147 expressed genes were identified from RNA-sequencing data of fruit, and six Pbr MYB members in subgroup C1 were identified as important candidate genes in the regulation of lignin synthesis by quantitative real-time PCR analysis. Further correlation analysis revealed that six PbrMYBs were significantly correlated with five structural gene families (F5H, HCT, CCR, POD and C3'H) in the lignin pathway. The phylogenetic, evolution and expression analyses of the MYB gene family in Chinese white pear establish a solid foundation for future comprehensive functional analysis of Pbr MYB genes. PMID:26872835

  14. The Bilingual Brain as Revealed by Functional Neuroimaging.

    ERIC Educational Resources Information Center

    Abutalebi, Jubin; Cappa, Stefano F.; Perani, Daniela

    2001-01-01

    Functional neuroimaging of bilinguals and monolinguals used in conjunction with experimental cognitive tasks has been successful in establishing functional specialization as a principle of brain organization in humans. Consistent results show that attained proficiency and possibly language exposure are more important than age of acquisition as a…

  15. Functional organization of the fusiform gyrus revealed with connectivity profiles.

    PubMed

    Zhang, Wen; Wang, Jiaojian; Fan, Lingzhong; Zhang, Yuanchao; Fox, Peter T; Eickhoff, Simon B; Yu, Chunshui; Jiang, Tianzi

    2016-08-01

    Within the object recognition-related ventral visual stream, the human fusiform gyrus (FG), which topographically connects the striate cortex to the inferior temporal lobe, plays a pivotal role in high-level visual/cognitive functions. However, though there are many previous investigations of distinct functional modules within the FG, the functional organization of the whole FG in its full functional heterogeneity has not yet been established. In the current study, a replicable functional organization of the FG based on distinct anatomical connectivity patterns was identified. The FG was parcellated into medial (FGm), lateral (FGl), and anterior (FGa) regions using diffusion tensor imaging. We validated the reasonability of such an organizational scheme from the perspective of resting-state whole brain functional connectivity patterns and the involvement of functional subnetworks. We found corroborating support for these three distinct modules, and suggest that the FGm serves as a transition region that combines multiple stimuli, the FGl is responsible for categorical recognition, and the FGa is involved in semantic understanding. These findings support two organizational functional transitions of the ventral temporal gyrus, a posterior/anterior direction of visual/semantic processing, and a media/lateral direction of high-level visual processing. Our results may facilitate a more detailed study of the human FG in the future. Hum Brain Mapp 37:3003-3016, 2016. © 2016 Wiley Periodicals, Inc. PMID:27132874

  16. Distinct hippocampal functional networks revealed by tractography-based parcellation.

    PubMed

    Adnan, Areeba; Barnett, Alexander; Moayedi, Massieh; McCormick, Cornelia; Cohn, Melanie; McAndrews, Mary Pat

    2016-07-01

    Recent research suggests the anterior and posterior hippocampus form part of two distinct functional neural networks. Here we investigate the structural underpinnings of this functional connectivity difference using diffusion-weighted imaging-based parcellation. Using this technique, we substantiated that the hippocampus can be parcellated into distinct anterior and posterior segments. These structurally defined segments did indeed show different patterns of resting state functional connectivity, in that the anterior segment showed greater connectivity with temporal and orbitofrontal cortex, whereas the posterior segment was more highly connected to medial and lateral parietal cortex. Furthermore, we showed that the posterior hippocampal connectivity to memory processing regions, including the dorsolateral prefrontal cortex, parahippocampal, inferior temporal and fusiform gyri and the precuneus, predicted interindividual relational memory performance. These findings provide important support for the integration of structural and functional connectivity in understanding the brain networks underlying episodic memory. PMID:26206251

  17. Attentional networks reveal executive function deficits in posttraumatic stress disorder.

    PubMed

    Leskin, Lorraine P; White, Patricia M

    2007-05-01

    Executive function was assessed with the Trail Making Test (Army Individual Test Battery; M. D. Lezak, 1983), the Comprehensive Trail Making Test (C. Reynolds, 2002), and a neurocognitive measure of executive control (Attentional Network Task [ANT]; J. I. Fan, B. D. McCandliss, T. Somer, A. Raz, & M. I. Posner, 2002) in 19 undergraduates with posttraumatic stress disorder (PTSD; Posttraumatic Stress Disorder Symptom Scale-Self-Report version; E. B. Foa, D. S. Riggs, C. V. Dancu, & B. O. Rothbaum, 1993), 15 high trauma participants without PTSD, and 18 low trauma control participants. Although groups did not differ on any trail making task or on the ANT measures of alerting or orienting, PTSD participants were significantly more impaired on the ANT executive network index than were high or low trauma control participants, even when level of depressive symptoms was covaried. Previous animal research identified a relationship between dopamine and the ANT measure of executive function. Elevated PTSD symptom severity and levels of hyperarousal, reexperiencing, and avoidance-numbing were associated significantly with executive function deficits indexed by the ANT. These results indicate a potentially subtle but specific deficit in executive function and a possible relationship between PTSD symptoms and irregularities in dopamine function. PMID:17484590

  18. Molecular phylogeny of the subfamily Amphistichinae (Teleostei: Embiotocidae) reveals parallel divergent evolution of red pigmentation in two rapidly evolving lineages of sand-dwelling surfperch.

    PubMed

    Westphal, M F; Morey, S R; Uyeda, J C; Morgan, T J

    2011-08-01

    Pigment evolution was reconstructed in the subfamily Amphistichinae, a six-species clade of the surfperches, family Embiotocidae. Assignment was confirmed for all species within the subfamily, but low levels of differentiation were found among species within the subfamily, suggesting a recent radiation. The new phylogeny differs from previous hypotheses by the placement of the spotfin surfperch Hyperprosopon anale at the base of the subfamily, while still preserving the calico surfperch Amphistichus koelzi and the redtailed surfperch Amphistichus rhodoterus as sister species. Phenotypically, A. rhodoterus, A. koelzi and the silver surfperch Hyperprosopon ellipticum express high levels of red pigmentation. The barred surfperch, Amphistichus argenteus and the walleye surfperch Hyperprosopon argenteum express little to no red pigment, while basal H. anale expresses an intermediate amount of red pigment. Red pigmentation is proposed to have experienced parallel divergent evolution in each genus within the subfamily. PMID:21781095

  19. Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns.

    PubMed

    Shao, Zhu-Qing; Xue, Jia-Yu; Wu, Ping; Zhang, Yan-Mei; Wu, Yue; Hang, Yue-Yu; Wang, Bin; Chen, Jian-Qun

    2016-04-01

    Nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes make up the largest plant disease resistance gene family (R genes), with hundreds of copies occurring in individual angiosperm genomes. However, the expansion history of NBS-LRR genes during angiosperm evolution is largely unknown. By identifying more than 6,000 NBS-LRR genes in 22 representative angiosperms and reconstructing their phylogenies, we present a potential framework of NBS-LRR gene evolution in the angiosperm. Three anciently diverged NBS-LRR classes (TNLs, CNLs, and RNLs) were distinguished with unique exon-intron structures and DNA motif sequences. A total of seven ancient TNL, 14 CNL, and two RNL lineages were discovered in the ancestral angiosperm, from which all current NBS-LRR gene repertoires were evolved. A pattern of gradual expansion during the first 100 million years of evolution of the angiosperm clade was observed for CNLs. TNL numbers remained stable during this period but were eventually deleted in three divergent angiosperm lineages. We inferred that an intense expansion of both TNL and CNL genes started from the Cretaceous-Paleogene boundary. Because dramatic environmental changes and an explosion in fungal diversity occurred during this period, the observed expansions of R genes probably reflect convergent adaptive responses of various angiosperm families. An ancient whole-genome duplication event that occurred in an angiosperm ancestor resulted in two RNL lineages, which were conservatively evolved and acted as scaffold proteins for defense signal transduction. Overall, the reconstructed framework of angiosperm NBS-LRR gene evolution in this study may serve as a fundamental reference for better understanding angiosperm NBS-LRR genes. PMID:26839128

  20. Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax).

    PubMed

    Calduch-Giner, Josep A; Sitjà-Bobadilla, Ariadna; Pérez-Sánchez, Jaume

    2016-01-01

    High-quality sequencing reads from the intestine of European sea bass were assembled, annotated by similarity against protein reference databases and combined with nucleotide sequences from public and private databases. After redundancy filtering, 24,906 non-redundant annotated sequences encoding 15,367 different gene descriptions were obtained. These annotated sequences were used to design a custom, high-density oligo-microarray (8 × 15 K) for the transcriptomic profiling of anterior (AI), middle (MI), and posterior (PI) intestinal segments. Similar molecular signatures were found for AI and MI segments, which were combined in a single group (AI-MI) whereas the PI outstood separately, with more than 1900 differentially expressed genes with a fold-change cutoff of 2. Functional analysis revealed that molecular and cellular functions related to feed digestion and nutrient absorption and transport were over-represented in AI-MI segments. By contrast, the initiation and establishment of immune defense mechanisms became especially relevant in PI, although the microarray expression profiling validated by qPCR indicated that these functional changes are gradual from anterior to posterior intestinal segments. This functional divergence occurred in association with spatial transcriptional changes in nutrient transporters and the mucosal chemosensing system via G protein-coupled receptors. These findings contribute to identify key indicators of gut functions and to compare different fish feeding strategies and immune defense mechanisms acquired along the evolution of teleosts. PMID:27610085

  1. Gene Expression Profiling Reveals Functional Specialization along the Intestinal Tract of a Carnivorous Teleostean Fish (Dicentrarchus labrax)

    PubMed Central

    Calduch-Giner, Josep A.; Sitjà-Bobadilla, Ariadna; Pérez-Sánchez, Jaume

    2016-01-01

    High-quality sequencing reads from the intestine of European sea bass were assembled, annotated by similarity against protein reference databases and combined with nucleotide sequences from public and private databases. After redundancy filtering, 24,906 non-redundant annotated sequences encoding 15,367 different gene descriptions were obtained. These annotated sequences were used to design a custom, high-density oligo-microarray (8 × 15 K) for the transcriptomic profiling of anterior (AI), middle (MI), and posterior (PI) intestinal segments. Similar molecular signatures were found for AI and MI segments, which were combined in a single group (AI-MI) whereas the PI outstood separately, with more than 1900 differentially expressed genes with a fold-change cutoff of 2. Functional analysis revealed that molecular and cellular functions related to feed digestion and nutrient absorption and transport were over-represented in AI-MI segments. By contrast, the initiation and establishment of immune defense mechanisms became especially relevant in PI, although the microarray expression profiling validated by qPCR indicated that these functional changes are gradual from anterior to posterior intestinal segments. This functional divergence occurred in association with spatial transcriptional changes in nutrient transporters and the mucosal chemosensing system via G protein-coupled receptors. These findings contribute to identify key indicators of gut functions and to compare different fish feeding strategies and immune defense mechanisms acquired along the evolution of teleosts. PMID:27610085

  2. Genome-Wide Association and Functional Follow-Up Reveals New Loci for Kidney Function

    PubMed Central

    Fuchsberger, Christian; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Taliun, Daniel; Li, Man; Gao, Xiaoyi; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C.; O'Seaghdha, Conall M.; Glazer, Nicole; Isaacs, Aaron; Liu, Ching-Ti; Smith, Albert V.; O'Connell, Jeffrey R.; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Johnson, Andrew D.; Gierman, Hinco J.; Feitosa, Mary; Hwang, Shih-Jen; Atkinson, Elizabeth J.; Lohman, Kurt; Cornelis, Marilyn C.; Johansson, Åsa; Tönjes, Anke; Dehghan, Abbas; Chouraki, Vincent; Holliday, Elizabeth G.; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y.; Murgia, Federico; Trompet, Stella; Imboden, Medea; Kollerits, Barbara; Pistis, Giorgio; Harris, Tamara B.; Launer, Lenore J.; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D.; Boerwinkle, Eric; Schmidt, Helena; Cavalieri, Margherita; Rao, Madhumathi; Hu, Frank B.; Demirkan, Ayse; Oostra, Ben A.; de Andrade, Mariza; Turner, Stephen T.; Ding, Jingzhong; Andrews, Jeanette S.; Freedman, Barry I.; Koenig, Wolfgang; Illig, Thomas; Döring, Angela; Wichmann, H.-Erich; Kolcic, Ivana; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E.; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H.; Wright, Alan F.; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Endlich, Karlhans; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K.; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G.; Rivadeneira, Fernando; Aulchenko, Yurii S.; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Ketkar, Shamika; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Giulianini, Franco; Krämer, Bernhard K.; Portas, Laura; Ford, Ian; Buckley, Brendan M.; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Metzger, Marie; Mitchell, Paul; Ciullo, Marina; Kim, Stuart K.; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J. Wouter; Probst-Hensch, Nicole M.; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R.; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; Siscovick, David S.; van Duijn, Cornelia M.; Borecki, Ingrid; Kardia, Sharon L. R.; Liu, Yongmei; Curhan, Gary C.; Rudan, Igor; Gyllensten, Ulf; Wilson, James F.; Franke, Andre; Pramstaller, Peter P.; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline C. M.; Hayward, Caroline; Ridker, Paul; Parsa, Afshin; Bochud, Murielle; Heid, Iris M.; Goessling, Wolfram; Chasman, Daniel I.; Kao, W. H. Linda; Fox, Caroline S.

    2012-01-01

    Chronic kidney disease (CKD) is an important public health problem with a genetic component. We performed genome-wide association studies in up to 130,600 European ancestry participants overall, and stratified for key CKD risk factors. We uncovered 6 new loci in association with estimated glomerular filtration rate (eGFR), the primary clinical measure of CKD, in or near MPPED2, DDX1, SLC47A1, CDK12, CASP9, and INO80. Morpholino knockdown of mpped2 and casp9 in zebrafish embryos revealed podocyte and tubular abnormalities with altered dextran clearance, suggesting a role for these genes in renal function. By providing new insights into genes that regulate renal function, these results could further our understanding of the pathogenesis of CKD. PMID:22479191

  3. Integrating phosphorylation network with transcriptional network reveals novel functional relationships.

    PubMed

    Wang, Lin; Hou, Lin; Qian, Minping; Deng, Minghua

    2012-01-01

    Phosphorylation and transcriptional regulation events are critical for cells to transmit and respond to signals. In spite of its importance, systems-level strategies that couple these two networks have yet to be presented. Here we introduce a novel approach that integrates the physical and functional aspects of phosphorylation network together with the transcription network in S.cerevisiae, and demonstrate that different network motifs are involved in these networks, which should be considered in interpreting and integrating large scale datasets. Based on this understanding, we introduce a HeRS score (hetero-regulatory similarity score) to systematically characterize the functional relevance of kinase/phosphatase involvement with transcription factor, and present an algorithm that predicts hetero-regulatory modules. When extended to signaling network, this approach confirmed the structure and cross talk of MAPK pathways, inferred a novel functional transcription factor Sok2 in high osmolarity glycerol pathway, and explained the mechanism of reduced mating efficiency upon Fus3 deletion. This strategy is applicable to other organisms as large-scale datasets become available, providing a means to identify the functional relationships between kinases/phosphatases and transcription factors. PMID:22432002

  4. Unsuspected functional disparity in Devonian fishes revealed by tooth morphometrics?

    NASA Astrophysics Data System (ADS)

    Gauchey, Samuel; Girard, Catherine; Adnet, Sylvain; Renaud, Sabrina

    2014-09-01

    The shape of features involved in key biological functions, such as teeth in nutrition, can provide insights into ecological processes even in ancient time, by linking the occupation of the morphological space (disparity) to the occupation of the ecological space. Investigating disparity in radiating groups may provide insights into the ecological diversification underlying evolution of morphological diversity. Actinopterygian fishes initiated their radiation in the Devonian, a period characterized by the diversification of marine ecosystem. Although a former morpho-functional analysis of jaw shape concluded to conservative and poorly diversified morphologies in this early part of their history, fish tooth disparity evidenced here an unsuspected diversity of possible functional significance in the pivotal period of the Late Devonian (Famennian). All teeth being caniniforms, some were stocky and robust, in agreement with expectations for active generalist predators. More surprisingly, elongated teeth also occurred at the beginning of Famennian. Their needle-like shape challenges morpho-functional interpretations by making them fragile in response to bending or torsion. The occurrence of both types of fish teeth during the beginning of the Famennian points to a discrete but real increase in disparity, thus testifying a first burst of feeding specialization despite overall conservative jaw morphology. The disappearance of these needle-like teeth in the Late Famennian might have been related to a relay in dental diversity with abundant co-occurring groups, namely conodonts and chondrichthyans (sharks).

  5. Unsuspected functional disparity in Devonian fishes revealed by tooth morphometrics?

    NASA Astrophysics Data System (ADS)

    Gauchey, Samuel; Girard, Catherine; Adnet, Sylvain; Renaud, Sabrina

    2014-07-01

    The shape of features involved in key biological functions, such as teeth in nutrition, can provide insights into ecological processes even in ancient time, by linking the occupation of the morphological space (disparity) to the occupation of the ecological space. Investigating disparity in radiating groups may provide insights into the ecological diversification underlying evolution of morphological diversity. Actinopterygian fishes initiated their radiation in the Devonian, a period characterized by the diversification of marine ecosystem. Although a former morpho-functional analysis of jaw shape concluded to conservative and poorly diversified morphologies in this early part of their history, fish tooth disparity evidenced here an unsuspected diversity of possible functional significance in the pivotal period of the Late Devonian (Famennian). All teeth being caniniforms, some were stocky and robust, in agreement with expectations for active generalist predators. More surprisingly, elongated teeth also occurred at the beginning of Famennian. Their needle-like shape challenges morpho-functional interpretations by making them fragile in response to bending or torsion. The occurrence of both types of fish teeth during the beginning of the Famennian points to a discrete but real increase in disparity, thus testifying a first burst of feeding specialization despite overall conservative jaw morphology. The disappearance of these needle-like teeth in the Late Famennian might have been related to a relay in dental diversity with abundant co-occurring groups, namely conodonts and chondrichthyans (sharks).

  6. Unsuspected functional disparity in Devonian fishes revealed by tooth morphometrics?

    PubMed

    Gauchey, Samuel; Girard, Catherine; Adnet, Sylvain; Renaud, Sabrina

    2014-09-01

    The shape of features involved in key biological functions, such as teeth in nutrition, can provide insights into ecological processes even in ancient time, by linking the occupation of the morphological space (disparity) to the occupation of the ecological space. Investigating disparity in radiating groups may provide insights into the ecological diversification underlying evolution of morphological diversity. Actinopterygian fishes initiated their radiation in the Devonian, a period characterized by the diversification of marine ecosystem. Although a former morpho-functional analysis of jaw shape concluded to conservative and poorly diversified morphologies in this early part of their history, fish tooth disparity evidenced here an unsuspected diversity of possible functional significance in the pivotal period of the Late Devonian (Famennian). All teeth being caniniforms, some were stocky and robust, in agreement with expectations for active generalist predators. More surprisingly, elongated teeth also occurred at the beginning of Famennian. Their needle-like shape challenges morpho-functional interpretations by making them fragile in response to bending or torsion. The occurrence of both types of fish teeth during the beginning of the Famennian points to a discrete but real increase in disparity, thus testifying a first burst of feeding specialization despite overall conservative jaw morphology. The disappearance of these needle-like teeth in the Late Famennian might have been related to a relay in dental diversity with abundant co-occurring groups, namely conodonts and chondrichthyans (sharks). PMID:25078254

  7. Revealing the density of encoded functions in a viral RNA

    PubMed Central

    Patel, Nikesh; Dykeman, Eric C.; Coutts, Robert H. A.; Lomonossoff, George P.; Rowlands, David J.; Phillips, Simon E. V.; Ranson, Neil; Twarock, Reidun; Tuma, Roman; Stockley, Peter G.

    2015-01-01

    We present direct experimental evidence that assembly of a single-stranded RNA virus occurs via a packaging signal-mediated mechanism. We show that the sequences of coat protein recognition motifs within multiple, dispersed, putative RNA packaging signals, as well as their relative spacing within a genomic fragment, act collectively to influence the fidelity and yield of capsid self-assembly in vitro. These experiments confirm that the selective advantages for viral yield and encapsidation specificity, predicted from previous modeling of packaging signal-mediated assembly, are found in Nature. Regions of the genome that act as packaging signals also function in translational and transcriptional enhancement, as well as directly coding for the coat protein, highlighting the density of encoded functions within the viral RNA. Assembly and gene expression are therefore direct molecular competitors for different functional folds of the same RNA sequence. The strongest packaging signal in the test fragment, encodes a region of the coat protein that undergoes a conformational change upon contact with packaging signals. A similar phenomenon occurs in other RNA viruses for which packaging signals are known. These contacts hint at an even deeper density of encoded functions in viral RNA, which if confirmed, would have profound consequences for the evolution of this class of pathogens. PMID:25646435

  8. The brain's functional network architecture reveals human motives.

    PubMed

    Hein, Grit; Morishima, Yosuke; Leiberg, Susanne; Sul, Sunhae; Fehr, Ernst

    2016-03-01

    Goal-directed human behaviors are driven by motives. Motives are, however, purely mental constructs that are not directly observable. Here, we show that the brain's functional network architecture captures information that predicts different motives behind the same altruistic act with high accuracy. In contrast, mere activity in these regions contains no information about motives. Empathy-based altruism is primarily characterized by a positive connectivity from the anterior cingulate cortex (ACC) to the anterior insula (AI), whereas reciprocity-based altruism additionally invokes strong positive connectivity from the AI to the ACC and even stronger positive connectivity from the AI to the ventral striatum. Moreover, predominantly selfish individuals show distinct functional architectures compared to altruists, and they only increase altruistic behavior in response to empathy inductions, but not reciprocity inductions. PMID:26941317

  9. Yeast studies reveal moonlighting functions of the ancient actin cytoskeleton.

    PubMed

    Sattlegger, Evelyn; Chernova, Tatiana A; Gogoi, Neeku M; Pillai, Indu V; Chernoff, Yury O; Munn, Alan L

    2014-08-01

    Classic functions of the actin cytoskeleton include control of cell size and shape and the internal organization of cells. These functions are manifest in cellular processes of fundamental importance throughout biology such as the generation of cell polarity, cell migration, cell adhesion, and cell division. However, studies in the unicellular model eukaryote Saccharomyces cerevisiae (Baker's yeast) are giving insights into other functions in which the actin cytoskeleton plays a critical role. These include endocytosis, control of protein translation, and determination of protein 3-dimensional shape (especially conversion of normal cellular proteins into prions). Here, we present a concise overview of these new "moonlighting" roles for the actin cytoskeleton and how some of these roles might lie at the heart of important molecular switches. This is an exciting time for researchers interested in the actin cytoskeleton. We show here how studies of actin are leading us into many new and exciting realms at the interface of genetics, biochemistry, and cell biology. While many of the pioneering studies have been conducted using yeast, the conservation of the actin cytoskeleton and its component proteins throughout eukaryotes suggests that these new roles for the actin cytoskeleton may not be restricted to yeast cells but rather may reflect new roles for the actin cytoskeleton of all eukaryotes. PMID:25138357

  10. Yeast studies reveal moonlighting functions of the ancient actin cytoskeleton

    PubMed Central

    Sattlegger, Evelyn; Chernova, Tatiana A.; Gogoi, Neeku M.; Pillai, Indu V.; Chernoff, Yury O.; Munn, Alan L.

    2014-01-01

    Classic functions of the actin cytoskeleton include control of cell size and shape and the internal organisation of cells. These functions are manifest in cellular processes of fundamental importance throughout biology such as the generation of cell polarity, cell migration, cell adhesion and cell division. However, studies in the unicellular model eukaryote Saccharomyces cerevisiae (Baker's yeast) are giving insights into other functions in which the actin cytoskeleton plays a critical role. These include endocytosis, control of protein translation and determination of protein 3-dimensional shape (especially conversion of normal cellular proteins into prions). Here we present a concise overview of these new "moonlighting" roles for the actin cytoskeleton and how some of these roles might lie at the heart of important molecular switches. This is an exciting time for researchers interested in the actin cytoskeleton. We show here how studies of actin are leading us into many new and exciting realms at the interface of genetics, biochemistry and cell biology. While many of the pioneering studies have been conducted using yeast, the conservation of the actin cytoskeleton and its component proteins throughout eukaryotes suggests that these new roles for the actin cytoskeleton may not be restricted to yeast cells but rather may reflect new roles for the actin cytoskeleton of all eukaryotes. PMID:25138357

  11. Expansion and Functional Divergence of Jumonji C-Containing Histone Demethylases: Significance of Duplications in Ancestral Angiosperms and Vertebrates1[OPEN

    PubMed Central

    Qian, Shengzhan; Wang, Yingxiang; Ma, Hong; Zhang, Liangsheng

    2015-01-01

    Histone modifications, such as methylation and demethylation, are crucial mechanisms altering chromatin structure and gene expression. Recent biochemical and molecular studies have uncovered a group of histone demethylases called Jumonji C (JmjC) domain proteins. However, their evolutionary history and patterns have not been examined systematically. Here, we report extensive analyses of eukaryotic JmjC genes and define 14 subfamilies, including the Lysine-Specific Demethylase3 (KDM3), KDM5, JMJD6, Putative-Lysine-Specific Demethylase11 (PKDM11), and PKDM13 subfamilies, shared by plants, animals, and fungi. Other subfamilies are detected in plants and animals but not in fungi (PKDM12) or in animals and fungi but not in plants (KDM2 and KDM4). PKDM7, PKDM8, and PKDM9 are plant-specific groups, whereas Jumonji, AT-Rich Interactive Domain2, KDM6, and PKDM10 are animal specific. In addition to known domains, most subfamilies have characteristic conserved amino acid motifs. Whole-genome duplication (WGD) was likely an important mechanism for JmjC duplications, with four pairs from an angiosperm-wide WGD and others from subsequent WGDs. Vertebrates also experienced JmjC duplications associated with the vertebrate ancestral WGDs, with additional mammalian paralogs from tandem duplication and possible transposition. The sequences of paralogs have diverged in both known functional domains and other regions, showing evidence of selection pressure. The increases of JmjC copy number and the divergences in sequence and expression might have contributed to the divergent functions of JmjC genes, allowing the angiosperms and vertebrates to adapt to a great number of ecological niches and contributing to their evolutionary successes. PMID:26059336

  12. Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana1[OPEN

    PubMed Central

    Lehti-Shiu, Melissa D.; Uygun, Sahra; Moghe, Gaurav D.; Panchy, Nicholas; Fang, Liang; Hufnagel, David E.; Jasicki, Hannah L.; Feig, Michael; Shiu, Shin-Han

    2015-01-01

    Functional divergence between duplicate transcription factors (TFs) has been linked to critical events in the evolution of land plants and can result from changes in patterns of expression, binding site divergence, and/or interactions with other proteins. Although plant TFs tend to be retained post polyploidization, many are lost within tens to hundreds of million years. Thus, it can be hypothesized that some TFs in plant genomes are in the process of becoming pseudogenes. Here, we use a pair of salt tolerance-conferring transcription factors, DWARF AND DELAYED FLOWERING1 (DDF1) and DDF2, that duplicated through paleopolyploidy 50 to 65 million years ago, as examples to illustrate potential mechanisms leading to duplicate retention and loss. We found that the expression patterns of Arabidopsis thaliana (At)DDF1 and AtDDF2 have diverged in a highly asymmetric manner, and AtDDF2 has lost most inferred ancestral stress responses. Consistent with promoter disablement, the AtDDF2 promoter has fewer predicted cis-elements and a methylated repetitive element. Through comparisons of AtDDF1, AtDDF2, and their Arabidopsis lyrata orthologs, we identified significant differences in binding affinities and binding site preference. In particular, an AtDDF2-specific substitution within the DNA-binding domain significantly reduces binding affinity. Cross-species analyses indicate that both AtDDF1 and AtDDF2 are under selective constraint, but among A. thaliana accessions, AtDDF2 has a higher level of nonsynonymous nucleotide diversity compared with AtDDF1. This may be the result of selection in different environments or may point toward the possibility of ongoing functional decay despite retention for millions of years after gene duplication. PMID:26103993

  13. Remote Synchronization Reveals Network Symmetries and Functional Modules

    NASA Astrophysics Data System (ADS)

    Nicosia, Vincenzo; Valencia, Miguel; Chavez, Mario; Díaz-Guilera, Albert; Latora, Vito

    2013-04-01

    We study a Kuramoto model in which the oscillators are associated with the nodes of a complex network and the interactions include a phase frustration, thus preventing full synchronization. The system organizes into a regime of remote synchronization where pairs of nodes with the same network symmetry are fully synchronized, despite their distance on the graph. We provide analytical arguments to explain this result, and we show how the frustration parameter affects the distribution of phases. An application to brain networks suggests that anatomical symmetry plays a role in neural synchronization by determining correlated functional modules across distant locations.

  14. Statistical universals reveal the structures and functions of human music

    PubMed Central

    Savage, Patrick E.; Brown, Steven; Sakai, Emi; Currie, Thomas E.

    2015-01-01

    Music has been called “the universal language of mankind.” Although contemporary theories of music evolution often invoke various musical universals, the existence of such universals has been disputed for decades and has never been empirically demonstrated. Here we combine a music-classification scheme with statistical analyses, including phylogenetic comparative methods, to examine a well-sampled global set of 304 music recordings. Our analyses reveal no absolute universals but strong support for many statistical universals that are consistent across all nine geographic regions sampled. These universals include 18 musical features that are common individually as well as a network of 10 features that are commonly associated with one another. They span not only features related to pitch and rhythm that are often cited as putative universals but also rarely cited domains including performance style and social context. These cross-cultural structural regularities of human music may relate to roles in facilitating group coordination and cohesion, as exemplified by the universal tendency to sing, play percussion instruments, and dance to simple, repetitive music in groups. Our findings highlight the need for scientists studying music evolution to expand the range of musical cultures and musical features under consideration. The statistical universals we identified represent important candidates for future investigation. PMID:26124105

  15. Statistical universals reveal the structures and functions of human music.

    PubMed

    Savage, Patrick E; Brown, Steven; Sakai, Emi; Currie, Thomas E

    2015-07-21

    Music has been called "the universal language of mankind." Although contemporary theories of music evolution often invoke various musical universals, the existence of such universals has been disputed for decades and has never been empirically demonstrated. Here we combine a music-classification scheme with statistical analyses, including phylogenetic comparative methods, to examine a well-sampled global set of 304 music recordings. Our analyses reveal no absolute universals but strong support for many statistical universals that are consistent across all nine geographic regions sampled. These universals include 18 musical features that are common individually as well as a network of 10 features that are commonly associated with one another. They span not only features related to pitch and rhythm that are often cited as putative universals but also rarely cited domains including performance style and social context. These cross-cultural structural regularities of human music may relate to roles in facilitating group coordination and cohesion, as exemplified by the universal tendency to sing, play percussion instruments, and dance to simple, repetitive music in groups. Our findings highlight the need for scientists studying music evolution to expand the range of musical cultures and musical features under consideration. The statistical universals we identified represent important candidates for future investigation. PMID:26124105

  16. Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-α-induced apoptosis in vivo

    PubMed Central

    Simmons, Alan J; Banerjee, Amrita; McKinley, Eliot T; Scurrah, Cherie' R; Herring, Charles A; Gewin, Leslie S; Masuzaki, Ryota; Karp, Seth J; Franklin, Jeffrey L; Gerdes, Michael J; Irish, Jonathan M; Coffey, Robert J; Lau, Ken S

    2015-01-01

    Understanding heterogeneous cellular behaviors in a complex tissue requires the evaluation of signaling networks at single-cell resolution. However, probing signaling in epithelial tissues using cytometry-based single-cell analysis has been confounded by the necessity of single-cell dissociation, where disrupting cell-to-cell connections inherently perturbs native cell signaling states. Here, we demonstrate a novel strategy (Disaggregation for Intracellular Signaling in Single Epithelial Cells from Tissue—DISSECT) that preserves native signaling for Cytometry Time-of-Flight (CyTOF) and fluorescent flow cytometry applications. A 21-plex CyTOF analysis encompassing core signaling and cell-identity markers was performed on the small intestinal epithelium after systemic tumor necrosis factor-alpha (TNF-α) stimulation. Unsupervised and supervised analyses robustly selected signaling features that identify a unique subset of epithelial cells that are sensitized to TNF-α-induced apoptosis in the seemingly homogeneous enterocyte population. Specifically, p-ERK and apoptosis are divergently regulated in neighboring enterocytes within the epithelium, suggesting a mechanism of contact-dependent survival. Our novel single-cell approach can broadly be applied, using both CyTOF and multi-parameter flow cytometry, for investigating normal and diseased cell states in a wide range of epithelial tissues. PMID:26519361

  17. Cytometry-based single-cell analysis of intact epithelial signaling reveals MAPK activation divergent from TNF-α-induced apoptosis in vivo.

    PubMed

    Simmons, Alan J; Banerjee, Amrita; McKinley, Eliot T; Scurrah, Cherie' R; Herring, Charles A; Gewin, Leslie S; Masuzaki, Ryota; Karp, Seth J; Franklin, Jeffrey L; Gerdes, Michael J; Irish, Jonathan M; Coffey, Robert J; Lau, Ken S

    2015-10-01

    Understanding heterogeneous cellular behaviors in a complex tissue requires the evaluation of signaling networks at single-cell resolution. However, probing signaling in epithelial tissues using cytometry-based single-cell analysis has been confounded by the necessity of single-cell dissociation, where disrupting cell-to-cell connections inherently perturbs native cell signaling states. Here, we demonstrate a novel strategy (Disaggregation for Intracellular Signaling in Single Epithelial Cells from Tissue-DISSECT) that preserves native signaling for Cytometry Time-of-Flight (CyTOF) and fluorescent flow cytometry applications. A 21-plex CyTOF analysis encompassing core signaling and cell-identity markers was performed on the small intestinal epithelium after systemic tumor necrosis factor-alpha (TNF-α) stimulation. Unsupervised and supervised analyses robustly selected signaling features that identify a unique subset of epithelial cells that are sensitized to TNF-α-induced apoptosis in the seemingly homogeneous enterocyte population. Specifically, p-ERK and apoptosis are divergently regulated in neighboring enterocytes within the epithelium, suggesting a mechanism of contact-dependent survival. Our novel single-cell approach can broadly be applied, using both CyTOF and multi-parameter flow cytometry, for investigating normal and diseased cell states in a wide range of epithelial tissues. PMID:26519361

  18. Genetic Divergence and Heritability of 42 Coloured Upland Rice Genotypes (Oryzasativa) as Revealed by Microsatellites Marker and Agro-Morphological Traits

    PubMed Central

    Ahmad, Faiz; Hanafi, Mohamed Musa; Hakim, Md Abdul; Rafii, Mohd Y.; Arolu, Ibrahim Wasiu; Akmar Abdullah, Siti Nor

    2015-01-01

    Coloured rice genotypes have greater nutritious value and consumer demand for these varieties is now greater than ever. The documentation of these genotypes is important for the improvement of the rice plant. In this study, 42 coloured rice genotypes were selected for determination of their genetic divergence using 25 simple sequence repeat (SSR) primers and 15 agro-morphological traits. Twenty-one out of the 25 SSR primers showed distinct, reproducible polymorphism. A dendrogram constructed using the SSR primers clustered the 42 coloured rice genotypes into 7 groups. Further, principle component analysis showed 75.28% of total variations were explained by the first—three components. All agro-morphological traits showed significant difference at the (p≤0.05) and (p≤0.01) levels. From the dendrogram constructed using the agro-morphological traits, all the genotypes were clustered into four distinct groups. Pearson’s correlation coefficient showed that among the 15 agro-morphological traits, the yield contributing factor had positive correlation with the number of tillers, number of panicles, and panicle length. The heritability of the 15 traits ranged from 17.68 to 99.69%. Yield per plant and harvest index showed the highest value for both heritability and genetic advance. The information on the molecular and agro-morphological traits can be used in rice breeding programmes to improve nutritional value and produce higher yields. PMID:26393807

  19. Biochemical analysis of encapsulated and non-encapsulated species of Trichinella (Nematoda, Trichinellidae) from cold- and warm-blooded animals reveals a high genetic divergence in the genus.

    PubMed

    La Rosa, Giuseppe; Marucci, Gianluca; Pozio, Edoardo

    2003-12-01

    Multilocus enzyme electrophoresis was used to analyse genetic variation in the genus Trichinella. Twenty-eight isolates belonging to eight species and six genotypes were analysed for 12 enzyme systems, producing 19 different phenotypes. According to Jaccard's similarity index, the isolates clustered into two main groups, specifically, encapsulated species/genotypes and non-encapsulated species/genotypes. Furthermore, the non-encapsulated species clustered into two other groups: the species infecting mammals and birds ( Trichinella pseudospiralis) and those infecting mammals and reptiles ( Trichinella papuaeand Trichinella zimbabwensis). The encapsulated species/genotypes, which only infect mammals, clustered into four main groups: the cosmopolitan species Trichinella spiralis, the species/genotypes of the temperate regions ( Trichinella britovi, Trichinella murrelli, Trichinella T8, and Trichinella T9), the species/genotype of the arctic region ( Trichinella nativa and Trichinella T6), and the equatorial species Trichinella nelsoni. These results are consistent with biological, epidemiological, and molecular data, which show a high genetic divergence in this genus. PMID:14557876

  20. Divergent evolutionary mechanisms of co-located Tak/Lrk and Glu-D3 loci revealed by comparative analysis of grass genomes.

    PubMed

    Wang, Zi-Ning; Banik, Mitali; Cloutier, Sylvie

    2013-04-01

    Seed storage and disease resistance proteins are major traits of wheat. The study of their gene organization and evolution has some implications in breeding. In this study, we characterized the hexaploid wheat D-genome BAC clone TaBAC703A9 that contains a low molecular weight glutenin locus (Glu-D3) and a resistance gene analogue cluster. With a gene density of one gene per 4.8 kb, the cluster contains four resistance gene analogues, namely Tak703-1, Lrr703, Tak703, and Lrk703. This structural cluster unit was conserved across nine grass genomes, but divergent evolutionary mechanisms have been involved in shaping the Tak/Lrk loci in the different species. Gene duplication was the major force for the Tak/Lrk evolution in oats, maize, barley, wheat, sorghum, and Brachypodium, while tandem duplication drove the expansion of this locus in japonica rice. Despite the close proximity of the Glu-D3 and the Tak/Lrk loci in wheat, the evolutionary mechanisms that drove their amplification differ. The Glu-D3 region had a lower gene density, and its amplification was driven by retroelements. PMID:23706072

  1. Functional metagenomic screen reveals new and diverse microbial rhodopsins

    PubMed Central

    Pushkarev, Alina; Béjà, Oded

    2016-01-01

    Ion-translocating retinylidene rhodopsins are widely distributed among marine and freshwater microbes. The translocation is light-driven, contributing to the production of biochemical energy in diverse microbes. Until today, most microbial rhodopsins had been detected using bioinformatics based on homology to other rhodopsins. In the past decade, there has been increased interest in microbial rhodopsins in the field of optogenetics since microbial rhodopsins were found to be most useful in vertebrate neuronal systems. Here we report on a functional metagenomic assay for detecting microbial rhodopsins. Using an array of narrow pH electrodes and light-emitting diode illumination, we were able to screen a metagenomic fosmid library to detect diverse marine proteorhodopsins and an actinorhodopsin based solely on proton-pumping activity. Our assay therefore provides a rather simple phenotypic means to enrich our understanding of microbial rhodopsins without any prior knowledge of the genomic content of the environmental entities screened. PMID:26894445

  2. Functional metagenomic screen reveals new and diverse microbial rhodopsins.

    PubMed

    Pushkarev, Alina; Béjà, Oded

    2016-09-01

    Ion-translocating retinylidene rhodopsins are widely distributed among marine and freshwater microbes. The translocation is light-driven, contributing to the production of biochemical energy in diverse microbes. Until today, most microbial rhodopsins had been detected using bioinformatics based on homology to other rhodopsins. In the past decade, there has been increased interest in microbial rhodopsins in the field of optogenetics since microbial rhodopsins were found to be most useful in vertebrate neuronal systems. Here we report on a functional metagenomic assay for detecting microbial rhodopsins. Using an array of narrow pH electrodes and light-emitting diode illumination, we were able to screen a metagenomic fosmid library to detect diverse marine proteorhodopsins and an actinorhodopsin based solely on proton-pumping activity. Our assay therefore provides a rather simple phenotypic means to enrich our understanding of microbial rhodopsins without any prior knowledge of the genomic content of the environmental entities screened. PMID:26894445

  3. Scalable Semisupervised Functional Neurocartography Reveals Canonical Neurons in Behavioral Networks.

    PubMed

    Frady, E Paxon; Kapoor, Ashish; Horvitz, Eric; Kristan, William B

    2016-08-01

    Large-scale data collection efforts to map the brain are underway at multiple spatial and temporal scales, but all face fundamental problems posed by high-dimensional data and intersubject variability. Even seemingly simple problems, such as identifying a neuron/brain region across animals/subjects, become exponentially more difficult in high dimensions, such as recognizing dozens of neurons/brain regions simultaneously. We present a framework and tools for functional neurocartography-the large-scale mapping of neural activity during behavioral states. Using a voltage-sensitive dye (VSD), we imaged the multifunctional responses of hundreds of leech neurons during several behaviors to identify and functionally map homologous neurons. We extracted simple features from each of these behaviors and combined them with anatomical features to create a rich medium-dimensional feature space. This enabled us to use machine learning techniques and visualizations to characterize and account for intersubject variability, piece together a canonical atlas of neural activity, and identify two behavioral networks. We identified 39 neurons (18 pairs, 3 unpaired) as part of a canonical swim network and 17 neurons (8 pairs, 1 unpaired) involved in a partially overlapping preparatory network. All neurons in the preparatory network rapidly depolarized at the onsets of each behavior, suggesting that it is part of a dedicated rapid-response network. This network is likely mediated by the S cell, and we referenced VSD recordings to an activity atlas to identify multiple cells of interest simultaneously in real time for further experiments. We targeted and electrophysiologically verified several neurons in the swim network and further showed that the S cell is presynaptic to multiple neurons in the preparatory network. This study illustrates the basic framework to map neural activity in high dimensions with large-scale recordings and how to extract the rich information necessary to perform

  4. Dolphin whistles: a functional misnomer revealed by heliox breathing.

    PubMed

    Madsen, P T; Jensen, F H; Carder, D; Ridgway, S

    2012-04-23

    Delphinids produce tonal whistles shaped by vocal learning for acoustic communication. Unlike terrestrial mammals, delphinid sound production is driven by pressurized air within a complex nasal system. It is unclear how fundamental whistle contours can be maintained across a large range of hydrostatic pressures and air sac volumes. Two opposing hypotheses propose that tonal sounds arise either from tissue vibrations or through actual whistle production from vortices stabilized by resonating nasal air volumes. Here, we use a trained bottlenose dolphin whistling in air and in heliox to test these hypotheses. The fundamental frequency contours of stereotyped whistles were unaffected by the higher sound speed in heliox. Therefore, the term whistle is a functional misnomer as dolphins actually do not whistle, but form the fundamental frequency contour of their tonal calls by pneumatically induced tissue vibrations analogous to the operation of vocal folds in terrestrial mammals and the syrinx in birds. This form of tonal sound production by nasal tissue vibrations has probably evolved in delphinids to enable impedance matching to the water, and to maintain tonal signature contours across changes in hydrostatic pressures, air density and relative nasal air volumes during dives. PMID:21900314

  5. Revealing humans' sensorimotor functions with electrical cortical stimulation.

    PubMed

    Desmurget, Michel; Sirigu, Angela

    2015-09-19

    Direct electrical stimulation (DES) of the human brain has been used by neurosurgeons for almost a century. Although this procedure serves only clinical purposes, it generates data that have a great scientific interest. Had DES not been employed, our comprehension of the organization of the sensorimotor systems involved in movement execution, language production, the emergence of action intentionality or the subjective feeling of movement awareness would have been greatly undermined. This does not mean, of course, that DES is a gold standard devoid of limitations and that other approaches are not of primary importance, including electrophysiology, modelling, neuroimaging or psychophysics in patients and healthy subjects. Rather, this indicates that the contribution of DES cannot be restricted, in humans, to the ubiquitous concepts of homunculus and somatotopy. DES is a fundamental tool in our attempt to understand the human brain because it represents a unique method for mapping sensorimotor pathways and interfering with the functioning of localized neural populations during the performance of well-defined behavioural tasks. PMID:26240422

  6. Selection on soil microbiomes reveals reproducible impacts on plant function.

    PubMed

    Panke-Buisse, Kevin; Poole, Angela C; Goodrich, Julia K; Ley, Ruth E; Kao-Kniffin, Jenny

    2015-04-01

    Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. Here, we report a high level of reproducibility of soil microbiomes in altering plant flowering time and soil functions when partnered within and between plant hosts. We used a multi-generation experimental system using Arabidopsis thaliana Col to select for soil microbiomes inducing earlier or later flowering times of their hosts. We then inoculated the selected microbiomes from the tenth generation of plantings into the soils of three additional A. thaliana genotypes (Ler, Be, RLD) and a related crucifer (Brassica rapa). With the exception of Ler, all other plant hosts showed a shift in flowering time corresponding with the inoculation of early- or late-flowering microbiomes. Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment. Plant hosts grown with the late-flowering-associated microbiomes showed consequent increases in inflorescence biomass for three A. thaliana genotypes and an increase in total biomass for B. rapa. The increase in biomass was correlated with two- to five-fold enhancement of microbial extracellular enzyme activities associated with nitrogen mineralization in soils. The reproducibility of the flowering phenotype across plant hosts suggests that microbiomes can be selected to modify plant traits and coordinate changes in soil resource pools. PMID:25350154

  7. Broadly-Reactive Neutralizing and Non-neutralizing Antibodies Directed against the H7 Influenza Virus Hemagglutinin Reveal Divergent Mechanisms of Protection

    PubMed Central

    Albrecht, Randy A.; Margine, Irina; Hirsh, Ariana; Bahl, Justin; Krammer, Florian

    2016-01-01

    In the early spring of 2013, Chinese health authorities reported several cases of H7N9 influenza virus infections in humans. Since then the virus has established itself at the human-animal interface in Eastern China and continues to cause several hundred infections annually. In order to characterize the antibody response to the H7N9 virus we generated several mouse monoclonal antibodies against the hemagglutinin of the A/Shanghai/1/13 (H7N9) virus. Of particular note are two monoclonal antibodies, 1B2 and 1H5, that show broad reactivity to divergent H7 hemagglutinins. Monoclonal antibody 1B2 binds to viruses of the Eurasian and North American H7 lineages and monoclonal antibody 1H5 reacts broadly to virus isolates of the Eurasian lineage. Interestingly, 1B2 shows broad hemagglutination inhibiting and neutralizing activity, while 1H5 fails to inhibit hemagglutination and demonstrates no neutralizing activity in vitro. However, both monoclonal antibodies were highly protective in an in vivo passive transfer challenge model in mice, even at low doses. Experiments using mutant antibodies that lack the ability for Fc/Fc-receptor and Fc/complement interactions suggest that the protection provided by mAb 1H5 is, at least in part, mediated by the Fc-fragment of the mAb. These findings highlight that a protective response to a pathogen may not only be due to neutralizing antibodies, but can also be the result of highly efficacious non-neutralizing antibodies not readily detected by classical in vitro neutralization or hemagglutination inhibition assays. This is of interest because H7 influenza virus vaccines induce only low hemagglutination inhibiting antibody titers while eliciting robust antibody titers as measured by ELISA. Our data suggest that these binding but non-neutralizing antibodies contribute to protection in vivo. PMID:27081859

  8. Genetic and morphological divergences in the cosmopolitan deep-sea amphipod Eurythenes gryllus reveal a diverse abyss and a bipolar species.

    PubMed

    Havermans, Charlotte; Sonet, Gontran; d'Udekem d'Acoz, Cédric; Nagy, Zoltán T; Martin, Patrick; Brix, Saskia; Riehl, Torben; Agrawal, Shobhit; Held, Christoph

    2013-01-01

    Eurythenes gryllus is one of the most widespread amphipod species, occurring in every ocean with a depth range covering the bathyal, abyssal and hadal zones. Previous studies, however, indicated the existence of several genetically and morphologically divergent lineages, questioning the assumption of its cosmopolitan and eurybathic distribution. For the first time, its genetic diversity was explored at the global scale (Arctic, Atlantic, Pacific and Southern oceans) by analyzing nuclear (28S rDNA) and mitochondrial (COI, 16S rDNA) sequence data using various species delimitation methods in a phylogeographic context. Nine putative species-level clades were identified within E. gryllus. A clear distinction was observed between samples collected at bathyal versus abyssal depths, with a genetic break occurring around 3,000 m. Two bathyal and two abyssal lineages showed a widespread distribution, while five other abyssal lineages each seemed to be restricted to a single ocean basin. The observed higher diversity in the abyss compared to the bathyal zone stands in contrast to the depth-differentiation hypothesis. Our results indicate that, despite the more uniform environment of the abyss and its presumed lack of obvious isolating barriers, abyssal populations might be more likely to show population differentiation and undergo speciation events than previously assumed. Potential factors influencing species' origins and distributions, such as hydrostatic pressure, are discussed. In addition, morphological findings coincided with the molecular clades. Of all specimens available for examination, those of the bipolar bathyal clade seemed the most similar to the 'true' E. gryllus. We present the first molecular evidence for a bipolar distribution in a macro-benthic deep-sea organism. PMID:24086322

  9. Genetic and Morphological Divergences in the Cosmopolitan Deep-Sea Amphipod Eurythenes gryllus Reveal a Diverse Abyss and a Bipolar Species

    PubMed Central

    Havermans, Charlotte; Sonet, Gontran; d’Udekem d’Acoz, Cédric; Nagy, Zoltán T.; Martin, Patrick; Brix, Saskia; Riehl, Torben; Agrawal, Shobhit; Held, Christoph

    2013-01-01

    Eurythenes gryllus is one of the most widespread amphipod species, occurring in every ocean with a depth range covering the bathyal, abyssal and hadal zones. Previous studies, however, indicated the existence of several genetically and morphologically divergent lineages, questioning the assumption of its cosmopolitan and eurybathic distribution. For the first time, its genetic diversity was explored at the global scale (Arctic, Atlantic, Pacific and Southern oceans) by analyzing nuclear (28S rDNA) and mitochondrial (COI, 16S rDNA) sequence data using various species delimitation methods in a phylogeographic context. Nine putative species-level clades were identified within E. gryllus. A clear distinction was observed between samples collected at bathyal versus abyssal depths, with a genetic break occurring around 3,000 m. Two bathyal and two abyssal lineages showed a widespread distribution, while five other abyssal lineages each seemed to be restricted to a single ocean basin. The observed higher diversity in the abyss compared to the bathyal zone stands in contrast to the depth-differentiation hypothesis. Our results indicate that, despite the more uniform environment of the abyss and its presumed lack of obvious isolating barriers, abyssal populations might be more likely to show population differentiation and undergo speciation events than previously assumed. Potential factors influencing species’ origins and distributions, such as hydrostatic pressure, are discussed. In addition, morphological findings coincided with the molecular clades. Of all specimens available for examination, those of the bipolar bathyal clade seemed the most similar to the ‘true’ E. gryllus. We present the first molecular evidence for a bipolar distribution in a macro-benthic deep-sea organism. PMID:24086322

  10. Phylogenetic Comparison of F-Box (FBX) Gene Superfamily within the Plant Kingdom Reveals Divergent Evolutionary Histories Indicative of Genomic Drift

    PubMed Central

    Hua, Zhihua; Zou, Cheng; Shiu, Shin-Han; Vierstra, Richard D.

    2011-01-01

    The emergence of multigene families has been hypothesized as a major contributor to the evolution of complex traits and speciation. To help understand how such multigene families arose and diverged during plant evolution, we examined the phylogenetic relationships of F-Box (FBX) genes, one of the largest and most polymorphic superfamilies known in the plant kingdom. FBX proteins comprise the target recognition subunit of SCF-type ubiquitin-protein ligases, where they individually recruit specific substrates for ubiquitylation. Through the extensive analysis of 10,811 FBX loci from 18 plant species, ranging from the alga Chlamydomonas reinhardtii to numerous monocots and eudicots, we discovered strikingly diverse evolutionary histories. The number of FBX loci varies widely and appears independent of the growth habit and life cycle of land plants, with a little as 198 predicted for Carica papaya to as many as 1350 predicted for Arabidopsis lyrata. This number differs substantially even among closely related species, with evidence for extensive gains/losses. Despite this extraordinary inter-species variation, one subset of FBX genes was conserved among most species examined. Together with evidence of strong purifying selection and expression, the ligases synthesized from these conserved loci likely direct essential ubiquitylation events. Another subset was much more lineage specific, showed more relaxed purifying selection, and was enriched in loci with little or no evidence of expression, suggesting that they either control more limited, species-specific processes or arose from genomic drift and thus may provide reservoirs for evolutionary innovation. Numerous FBX loci were also predicted to be pseudogenes with their numbers tightly correlated with the total number of FBX genes in each species. Taken together, it appears that the FBX superfamily has independently undergone substantial birth/death in many plant lineages, with its size and rapid evolution potentially

  11. Divergence and long-distance overseas dispersals of island populations of the Ryukyu five-lined skink, Plestiodon marginatus (Scincidae: Squamata), in the Ryukyu Archipelago, Japan, as revealed by mitochondrial DNA phylogeography.

    PubMed

    Kurita, Kazuki; Hikida, Tsutomu

    2014-04-01

    We assessed the historical biogeography of the Ryukyu five-lined skink, Plestiodon marginatus, and related species (P. stimpsonii and P. elegans). Our specific aims were to reveal the origin, tim- ing, and route of the colonization to three volcanic islands in the northern Tokara Group of the northern Ryukyus: Kuchinoshima, Nakanoshima, and Suwanosejima. We conducted phylogenetic analyses and divergence time estimation using a partial sequence of the mitochondrial cytochrome b gene for P. marginatus collected from across its whole range (the northern and central Ryukyus), and for P. stimpsonii (from the Yaeyama Group of the southern Ryukyus) and P. elegans (from Taiwan). Our results suggest three major clades (A, B, and C). Clades A and B consist of P. marginatus, excluding the Kuchinoshima population, and Clade C consisted of the Kuchinoshima population, P. stimpsonii, and P. elegans. These clades are estimated to have diverged during the Late Miocene to the Late Pliocene. Among the three examined northern Tokara populations, the Kuchinoshima population was shown to be a sister group of P. stimpsonii. The two other populations from Nakanoshima and Suwanosejima Islands were closely related to P. marginatus from the northern part of the Okinawa Group and that from Kodakarajima Island in the southern Tokara Group, respectively. These populations are estimated to have diverged from their respective related spe cies in various ages of the Early to Late Pleistocene, suggesting that they colonized the islands by independent overseas dispersals of approximately 50-850 km via the Kuroshio Current. Taxonomic implications for P. marginatus are also discussed. PMID:24694220

  12. Natural gas leak location with K-L divergence-based adaptive selection of Ensemble Local Mean Decomposition components and high-order ambiguity function

    NASA Astrophysics Data System (ADS)

    Sun, Jiedi; Xiao, Qiyang; Wen, Jiangtao; Zhang, Ying

    2015-07-01

    In this study, a time-delay estimation method based on Ensemble Local Mean Decomposition (ELMD) method and high-order ambiguity function (HAF) is proposed for locating natural gas pipeline leaks. The leakage signals were decomposed using ELMD, and numerous production functions (PFs) were obtained. An adaptive selection method based on Kullback-Leibler (K-L) divergence was proposed to process these PF components and choose the characteristic PFs that contain most of the leakage information. The HAF was employed to analyze the instantaneous parameters of the characteristic PFs and calculate the difference in arrival time of characteristic frequencies. From the time difference and the signal propagation speed, the natural gas pipeline leakage location can be determined. The experiment results show that the proposed method can locate leaks with higher accuracy than cross-correlation method.

  13. Long non-coding RNA profiling of human lymphoid progenitor cells reveals transcriptional divergence of B cell and T cell lineages.

    PubMed

    Casero, David; Sandoval, Salemiz; Seet, Christopher S; Scholes, Jessica; Zhu, Yuhua; Ha, Vi Luan; Luong, Annie; Parekh, Chintan; Crooks, Gay M

    2015-12-01

    To elucidate the transcriptional 'landscape' that regulates human lymphoid commitment during postnatal life, we used RNA sequencing to assemble the long non-coding transcriptome across human bone marrow and thymic progenitor cells spanning the earliest stages of B lymphoid and T lymphoid specification. Over 3,000 genes encoding previously unknown long non-coding RNAs (lncRNAs) were revealed through the analysis of these rare populations. Lymphoid commitment was characterized by lncRNA expression patterns that were highly stage specific and were more lineage specific than those of protein-coding genes. Protein-coding genes co-expressed with neighboring lncRNA genes showed enrichment for ontologies related to lymphoid differentiation. The exquisite cell-type specificity of global lncRNA expression patterns independently revealed new developmental relationships among the earliest progenitor cells in the human bone marrow and thymus. PMID:26502406

  14. Analysis of TIR- and non-TIR-NBS-LRR disease resistance gene analogous in pepper: characterization, genetic variation, functional divergence and expression patterns

    PubMed Central

    2012-01-01

    Background Pepper (Capsicum annuum L.) is one of the most important vegetable crops worldwide. However, its yield and fruit quality can be severely threatened by several pathogens. The plant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) gene family is the largest class of known disease resistance genes (R genes) effective against such pathogens. Therefore, the isolation and identification of such R gene homologues from pepper will provide a critical foundation for improving disease resistance breeding programs. Results A total of 78 R gene analogues (CaRGAs) were identified in pepper by degenerate PCR amplification and database mining. Phylogenetic tree analysis of the deduced amino acid sequences for 51 of these CaRGAs with typically conserved motifs ( P-loop, kinase-2 and GLPL) along with some known R genes from Arabidopsis and tomato grouped these CaRGAs into the non-Toll interleukin-1 receptor (TIR)-NBS-LRR (CaRGAs I to IV) and TIR-NBS-LRR (CaRGAs V to VII) subfamilies. The presence of consensus motifs (i.e. P-loop, kinase-2 and hydrophobic domain) is typical of the non-TIR- and TIR-NBS-LRR gene subfamilies. This finding further supports the view that both subfamilies are widely distributed in dicot species. Functional divergence analysis provided strong statistical evidence of altered selective constraints during protein evolution between the two subfamilies. Thirteen critical amino acid sites involved in this divergence were also identified using DIVERGE version 2 software. Analyses of non-synonymous and synonymous substitutions per site showed that purifying selection can play a critical role in the evolutionary processes of non-TIR- and TIR-NBS-LRR RGAs in pepper. In addition, four specificity-determining positions were predicted to be responsible for functional specificity. qRT-PCR analysis showed that both salicylic and abscisic acids induce the expression of CaRGA genes, suggesting that they may primarily be involved in defence responses by

  15. Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes

    PubMed Central

    2013-01-01

    Background Elongation factor-1α (EF-1α) and elongation factor-like (EFL) proteins are functionally homologous to one another, and are core components of the eukaryotic translation machinery. The patchy distribution of the two elongation factor types across global eukaryotic phylogeny is suggestive of a ‘differential loss’ hypothesis that assumes that EF-1α and EFL were present in the most recent common ancestor of eukaryotes followed by independent differential losses of one of the two factors in the descendant lineages. To date, however, just one diatom and one fungus have been found to have both EF-1α and EFL (dual-EF-containing species). Results In this study, we characterized 35 new EF-1α/EFL sequences from phylogenetically diverse eukaryotes. In so doing we identified 11 previously unreported dual-EF-containing species from diverse eukaryote groups including the Stramenopiles, Apusomonadida, Goniomonadida, and Fungi. Phylogenetic analyses suggested vertical inheritance of both genes in each of the dual-EF lineages. In the dual-EF-containing species we identified, the EF-1α genes appeared to be highly divergent in sequence and suppressed at the transcriptional level compared to the co-occurring EFL genes. Conclusions According to the known EF-1α/EFL distribution, the differential loss process should have occurred independently in diverse eukaryotic lineages, and more dual-EF-containing species remain unidentified. We predict that dual-EF-containing species retain the divergent EF-1α homologues only for a sub-set of the original functions. As the dual-EF-containing species are distantly related to each other, we propose that independent re-modelling of EF-1α function took place in multiple branches in the tree of eukaryotes. PMID:23800323

  16. Ancient Duplications Have Led to Functional Divergence of Vitellogenin-Like Genes Potentially Involved in Inflammation and Oxidative Stress in Honey Bees

    PubMed Central

    Salmela, Heli; Stark, Taina; Stucki, Dimitri; Fuchs, Siiri; Freitak, Dalial; Dey, Alivia; Kent, Clement F.; Zayed, Amro; Dhaygude, Kishor; Hokkanen, Heikki; Sundström, Liselotte

    2016-01-01

    Protection against inflammation and oxidative stress is key in slowing down aging processes. The honey bee (Apis mellifera) shows flexible aging patterns linked to the social role of individual bees. One molecular factor associated with honey bee aging regulation is vitellogenin, a lipoglycophosphoprotein with anti-inflammatory and antioxidant properties. Recently, we identified three genes in Hymenopteran genomes arisen from ancient insect vitellogenin duplications, named vg-like-A, -B, and -C. The function of these vitellogenin homologs is unclear. We hypothesize that some of them might share gene- and protein-level similarities and a longevity-supporting role with vitellogenin. Here, we show how the structure and modifications of the vg-like genes and proteins have diverged from vitellogenin. Furthermore, all three vg-like genes show signs of positive selection, but the spatial location of the selected protein sites differ from those found in vitellogenin. We show that all these genes are expressed in both long-lived winter worker bees and in summer nurse bees with intermediate life expectancy, yet only vg-like-A shows elevated expression in winter bees as found in vitellogenin. Finally, we show that vg-like-A responds more strongly than vitellogenin to inflammatory and oxidative conditions in summer nurse bees, and that also vg-like-B responds to oxidative stress. We associate vg-like-A and, to lesser extent, vg-like-B to the antiaging roles of vitellogenin, but that vg-like-C probably is involved in some other function. Our analysis indicates that an ancient duplication event facilitated the adaptive and functional divergence of vitellogenin and its paralogs in the honey bee. PMID:26961250

  17. Ancient Duplications Have Led to Functional Divergence of Vitellogenin-Like Genes Potentially Involved in Inflammation and Oxidative Stress in Honey Bees.

    PubMed

    Salmela, Heli; Stark, Taina; Stucki, Dimitri; Fuchs, Siiri; Freitak, Dalial; Dey, Alivia; Kent, Clement F; Zayed, Amro; Dhaygude, Kishor; Hokkanen, Heikki; Sundström, Liselotte

    2016-03-01

    Protection against inflammation and oxidative stress is key in slowing down aging processes. The honey bee (Apis mellifera) shows flexible aging patterns linked to the social role of individual bees. One molecular factor associated with honey bee aging regulation is vitellogenin, a lipoglycophosphoprotein with anti-inflammatory and antioxidant properties. Recently, we identified three genes in Hymenopteran genomes arisen from ancient insect vitellogenin duplications, named vg-like-A, -B, and -C. The function of these vitellogenin homologs is unclear. We hypothesize that some of them might share gene- and protein-level similarities and a longevity-supporting role with vitellogenin. Here, we show how the structure and modifications of the vg-like genes and proteins have diverged from vitellogenin. Furthermore, all three vg-like genes show signs of positive selection, but the spatial location of the selected protein sites differ from those found in vitellogenin. We show that all these genes are expressed in both long-lived winter worker bees and in summer nurse bees with intermediate life expectancy, yet only vg-like-A shows elevated expression in winter bees as found in vitellogenin. Finally, we show that vg-like-A responds more strongly than vitellogenin to inflammatory and oxidative conditions in summer nurse bees, and that also vg-like-B responds to oxidative stress. We associate vg-like-A and, to lesser extent, vg-like-B to the antiaging roles of vitellogenin, but that vg-like-C probably is involved in some other function. Our analysis indicates that an ancient duplication event facilitated the adaptive and functional divergence of vitellogenin and its paralogs in the honey bee. PMID:26961250

  18. Genomic Analysis of Xanthomonas oryzae Isolates from Rice Grown in the United States Reveals Substantial Divergence from Known X. oryzae Pathovars ▿ †

    PubMed Central

    Triplett, L. R.; Hamilton, J. P.; Buell, C. R.; Tisserat, N. A.; Verdier, V.; Zink, F.; Leach, J. E.

    2011-01-01

    The species Xanthomonas oryzae is comprised of two designated pathovars, both of which cause economically significant diseases of rice in Asia and Africa. Although X. oryzae is not considered endemic in the United States, an X. oryzae-like bacterium was isolated from U.S. rice and southern cutgrass in the late 1980s. The U.S. strains were weakly pathogenic and genetically distinct from characterized X. oryzae pathovars. In the current study, a draft genome sequence from two U.S. Xanthomonas strains revealed that the U.S. strains form a novel clade within the X. oryzae species, distinct from all strains known to cause significant yield loss. Comparative genome analysis revealed several putative gene clusters specific to the U.S. strains and supported previous reports that the U.S. strains lack transcriptional activator-like (TAL) effectors. In addition to phylogenetic and comparative analyses, the genome sequence was used for designing robust U.S. strain-specific primers, demonstrating the usefulness of a draft genome sequence in the rapid development of diagnostic tools. PMID:21515727

  19. Molecular Cloning and Functional Characterization of Xenopus tropicalis Frog Transient Receptor Potential Vanilloid 1 Reveal Its Functional Evolution for Heat, Acid, and Capsaicin Sensitivities in Terrestrial Vertebrates*

    PubMed Central

    Ohkita, Masashi; Saito, Shigeru; Imagawa, Toshiaki; Takahashi, Kenji; Tominaga, Makoto; Ohta, Toshio

    2012-01-01

    The functional difference of thermosensitive transient receptor potential (TRP) channels in the evolutionary context has attracted attention, but thus far little information is available on the TRP vanilloid 1 (TRPV1) function of amphibians, which diverged earliest from terrestrial vertebrate lineages. In this study we cloned Xenopus tropicalis frog TRPV1 (xtTRPV1), and functional characterization was performed using HeLa cells heterologously expressing xtTRPV1 (xtTRPV1-HeLa) and dorsal root ganglion neurons isolated from X. tropicalis (xtDRG neurons) by measuring changes in the intracellular calcium concentration ([Ca2+]i). The channel activity was also observed in xtTRPV1-expressing Xenopus oocytes. Furthermore, we tested capsaicin- and heat-induced nocifensive behaviors of the frog X. tropicalis in vivo. At the amino acid level, xtTRPV1 displays ∼60% sequence identity to other terrestrial vertebrate TRPV1 orthologues. Capsaicin induced [Ca2+]i increases in xtTRPV1-HeLa and xtDRG neurons and evoked nocifensive behavior in X. tropicalis. However, its sensitivity was extremely low compared with mammalian orthologues. Low extracellular pH and heat activated xtTRPV1-HeLa and xtDRG neurons. Heat also evoked nocifensive behavior. In oocytes expressing xtTRPV1, inward currents were elicited by heat and low extracellular pH. Mutagenesis analysis revealed that two amino acids (tyrosine 523 and alanine 561) were responsible for the low sensitivity to capsaicin. Taken together, our results indicate that xtTRPV1 functions as a polymodal receptor similar to its mammalian orthologues. The present study demonstrates that TRPV1 functions as a heat- and acid-sensitive channel in the ancestor of terrestrial vertebrates. Because it is possible to examine vanilloid and heat sensitivities in vitro and in vivo, X. tropicalis could be the ideal experimental lower vertebrate animal for the study of TRPV1 function. PMID:22130664

  20. The divergent impact of COMT Val158Met on executive function in children with and without attention-deficit/hyperactivity disorder.

    PubMed

    Jin, J; Liu, L; Gao, Q; Chan, R C K; Li, H; Chen, Y; Wang, Y; Qian, Q

    2016-02-01

    Children with attention-deficit/hyperactivity disorder (ADHD) usually display deficits in executive function (EF), which are primarily mediated by prefrontal cortex (PFC). The functional polymorphism of catechol-O-methyltransferase (COMT), Val158Met (rs4680), leads to observed polymorphic differences in the degradation of dopamine within PFC. This study aimed to explore the effect of rs4680 on EF using case-control design. In addition, considering the dynamic development of EF, we also attempted to investigate whether this genetic influence changes during development or not. A total of 597 ADHD children and 154 unaffected controls were recruited. The EF was evaluated using Rey-Osterrieth complex figure test (RCFT), trail making test (TMT) and Stroop color and word test for working memory, shifting and inhibition. Association between genotype and EF was analyzed using analysis of covariance (ancova). The results showed significant interaction effect of genotype and ADHD diagnosis on RCFT performance (P < 0.001). However, the associated genotypes between ADHD and controls were divergent. In ADHD, the Met carriers performed better than the Val homozygotes on detail immediate [(10.38 ± 6.90) vs. (9.33 ± 6.92), P = 0.007] and detail delay [(9.96 ± 6.86) vs. (8.86 ± 6.89), P = 0.004], while Val homozygotes showed better performance compared with Met carrier controls [for detail immediate (14.55 ± 6.18) vs. (11.10 ± 6.45), P<0.001; for detail delay (14.31 ± 5.96) vs. (11.31 ± 6.96), P = 0.001]. We did not find significant interaction between genetic variant and development. COMT Val158Met (rs4680) may have divergent effect on working memory in ADHD children compared with healthy controls. PMID:26560848

  1. An Evaluation of the Divergent Physics Laboratory

    ERIC Educational Resources Information Center

    Lerch, Robert D.

    1973-01-01

    The study was conducted to evaluate divergent physics laboratories in accomplishing objectives of Commission on College Physics. A questionnaire was used to collect data from students. Analysis revealed students in divergent laboratories had more opportunity to choose or design their own experiments and develop a model for data interpretation. (PS)

  2. Possible divergences in Tsallis' thermostatistics

    NASA Astrophysics Data System (ADS)

    Plastino, A.; Rocca, M. C.

    2013-12-01

    Lutsko and Boon have shown via elegant theoretical reasoning (EPL, 95 (2011) 20006), that Tsallis' thermostatistics is affected by divergence problems. We explicitly verify such fact in trying to compute the nonextensive q-partition function for the harmonic oscillator in more than two dimensions. One can see that it indeed diverges. The appeal to the so-called q-Laplace transform, where the q-exponential function plays the role of the ordinary exponential, is seen to overcome the serious problem envisaged by Lutsko and Boon.

  3. Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases

    PubMed Central

    Pulicherla, Nagesh; Pogorzala, Leah A.; Xu, Zhili; O’Farrell, Heather C.; Musayev, Faik N.; Scarsdale, J. Neel; Sia, Elaine A.; Culver, Gloria M.; Rife, Jason P.

    2009-01-01

    The enzymes of the KsgA/Dim1 family are universally distributed throughout all phylogeny; however, structural and functional differences are known to exist. The well-characterized function of these enzymes is to dimethylate two adjacent adenosines of the small ribosomal subunit in the normal course of ribosome maturation and the structures of KsgA from Escherichia coli and Dim1 from Homo sapiens and Plasmodium falciparum have been determined. To this point no examples of archaeal structures have been reported. Here we report the structure of Dim1 from the thermophilic archaeon Methanocaldococcus jannaschii. While it shares obvious similarities with the bacterial and eukaryotic orthologs, notable structural differences exist among the three members, particularly in the C-terminal domain. Previous work showed that eukaryotic and archaeal Dim1 were able to robustly complement for KsgA in E. coli. Here we repeated similar experiments to test for complementarity of archaeal Dim1 and bacterial KsgA in Saccharomyces cerevisiae. However, neither the bacterial nor the archaeal ortholog could complement for the eukaryotic Dim1. This might be related to the secondary, non-methyltransferase function that Dim1 is known to play in eukaryotic ribosomal maturation. To further delineate regions of the eukaryotic Dim1 critical to its function, we created and tested KsgA/Dim1 chimeras. Of the chimeras, only one constructed with the N-terminal domain from eukaryotic Dim1 and the C-terminal domain from archaeal Dim1 was able to complement, suggesting that eukaryotic-specific Dim1 function resides in the N-terminal domain also, where few structural differences are observed between members of the KsgA/Dim1 family. Future work is required to identify those determinants directly responsible for Dim1 function in ribosome biogenesis. Finally, we have conclusively established that none of the methyl groups are critically important to growth in yeast under standard conditions at a variety of

  4. Sequencing of transcriptomes from two Miscanthus species reveals functional specificity in rhizomes, and clarifies evolutionary relationships

    PubMed Central

    2014-01-01

    Background Miscanthus is a promising biomass crop for temperate regions. Despite the increasing interest in this plant, limited sequence information has constrained research into its biology, physiology, and breeding. The whole genome transcriptomes of M. sinensis and M. sacchariflorus presented in this study may provide good resources to understand functional compositions of two important Miscanthus genomes and their evolutionary relationships. Results For M. sinensis, a total of 457,891 and 512,950 expressed sequence tags (ESTs) were produced from leaf and rhizome tissues, respectively, which were assembled into 12,166 contigs and 89,648 singletons for leaf, and 13,170 contigs and 112,138 singletons for rhizome. For M. sacchariflorus, a total of 288,806 and 267,952 ESTs from leaf and rhizome tissues, respectively, were assembled into 8,732 contigs and 66,881 singletons for leaf, and 8,104 contigs and 63,212 singletons for rhizome. Based on the distributions of synonymous nucleotide substitution (Ks), sorghum and Miscanthus diverged about 6.2 million years ago (MYA), Saccharum and Miscanthus diverged 4.6 MYA, and M. sinensis and M. sacchariflorus diverged 1.5 MYA. The pairwise alignment of predicted protein sequences from sorghum-Miscanthus and two Miscanthus species found a total of 43,770 and 35,818 nsSNPs, respectively. The impacts of striking mutations found by nsSNPs were much lower between sorghum and Miscanthus than those between the two Miscanthus species, perhaps as a consequence of the much higher level of gene duplication in Miscanthus and resulting ability to buffer essential functions against disturbance. Conclusions The ESTs generated in the present study represent a significant addition to Miscanthus functional genomics resources, permitting us to discover some candidate genes associated with enhanced biomass production. Ks distributions based on orthologous ESTs may serve as a guideline for future research into the evolution of Miscanthus species

  5. Atypical cortical language organization in epilepsy patients: evidence for divergent hemispheric dominance for receptive and expressive language function.

    PubMed

    Eliashiv, Dawn S; Kurelowech, Lacey; Quint, Patti; Chung, Jeffrey M; Otis, Shirley M; Gage, Nicole M

    2014-06-01

    The central goal of presurgical language mapping is to identify brain regions that subserve cortical language function to minimize postsurgical language deficits. Presurgical language mapping in patients with epilepsy presents a key challenge because of the atypical pattern of hemispheric language dominance found in this population, with higher incidences of bilateral and right-biased language dominance than typical. In this prospective study, we combine magnetoencephalography with a panel of tasks designed to separately assess receptive and expressive function to provide a sensitive measure of language function in 15 candidates for resective surgery. We report the following: 4 of 15 patients (27%) showed left hemisphere dominance across all tasks, 4 of 15 patients (27%) showed right hemisphere dominance across all tasks, and 7 of 15 (46%) showed discordant language dominance, with right-dominant receptive and left-dominant expressive language. All patients with discordant language dominance showed this right-receptive and left-expressive pattern. Results provide further evidence supporting the importance of using a panel of tasks to assess separable aspects of language function. The clinical relevance of the findings is discussed, especially about current clinical operative measures for assessing language dominance, which use single hemisphere procedure (intracarotid amobarbital procedure and awake intraoperative stimulation) for determining language laterality. PMID:24887603

  6. Phylogenomic network and comparative genomics reveal a diverged member of the ΦKZ-related group, marine vibrio phage ΦJM-2012.

    PubMed

    Jang, Ho Bin; Fagutao, Fernand F; Nho, Seong Won; Park, Seong Bin; Cha, In Seok; Yu, Jong Earn; Lee, Jung Seok; Im, Se Pyeong; Aoki, Takashi; Jung, Tae Sung

    2013-12-01

    Bacteriophages are the largest reservoir of genetic diversity. Here we describe the novel phage ΦJM-2012. This natural isolate from marine Vibrio cyclitrophicus possesses very few gene contents relevant to other well-studied marine Vibrio phages. To better understand its evolutionary history, we built a mathematical model of pairwise relationships among 1,221 phage genomes, in which the genomes (nodes) are linked by edges representing the normalized number of shared orthologous protein families. This weighted network revealed that ΦJM-2012 was connected to only five members of the Pseudomonas ΦKZ-like phage family in an isolated network, strongly indicating that it belongs to this phage group. However, comparative genomic analyses highlighted an almost complete loss of colinearity with the ΦKZ-related genomes and little conservation of gene order, probably reflecting the action of distinct evolutionary forces on the genome of ΦJM-2012. In this phage, typical conserved core genes, including six RNA polymerase genes, were frequently displaced and the hyperplastic regions were rich in both unique genes and predicted unidirectional promoters with highly correlated orientations. Further, analysis of the ΦJM-2012 genome showed that segments of the conserved N-terminal parts of ΦKZ tail fiber paralogs exhibited evidence of combinatorial assortment, having switched transcriptional orientation, and there was recruitment and/or structural changes among phage endolysins and tail spike protein. Thus, this naturally occurring phage appears to have branched from a common ancestor of the ΦKZ-related groups, showing a distinct genomic architecture and unique genes that most likely reflect adaptation to its chosen host and environment. PMID:24067958

  7. Duplicate gene divergence by changes in microRNA binding sites in Arabidopsis and Brassica.

    PubMed

    Wang, Sishuo; Adams, Keith L

    2015-03-01

    Gene duplication provides large numbers of new genes that can lead to the evolution of new functions. Duplicated genes can diverge by changes in sequences, expression patterns, and functions. MicroRNAs play an important role in the regulation of gene expression in many eukaryotes. After duplication, two paralogs may diverge in their microRNA binding sites, which might impact their expression and function. Little is known about conservation and divergence of microRNA binding sites in duplicated genes in plants. We analyzed microRNA binding sites in duplicated genes in Arabidopsis thaliana and Brassica rapa. We found that duplicates are more often targeted by microRNAs than singletons. The vast majority of duplicated genes in A. thaliana with microRNA binding sites show divergence in those sites between paralogs. Analysis of microRNA binding sites in genes derived from the ancient whole-genome triplication in B. rapa also revealed extensive divergence. Paralog pairs with divergent microRNA binding sites show more divergence in expression patterns compared with paralog pairs with the same microRNA binding sites in Arabidopsis. Close to half of the cases of binding site divergence are caused by microRNAs that are specific to the Arabidopsis genus, indicating evolutionarily recent gain of binding sites after target gene duplication. We also show rapid evolution of microRNA binding sites in a jacalin gene family. Our analyses reveal a dynamic process of changes in microRNA binding sites after gene duplication in Arabidopsis and highlight the role of microRNA regulation in the divergence and contrasting evolutionary fates of duplicated genes. PMID:25644246

  8. The twin-arginine translocation pathway in α-proteobacteria is functionally preserved irrespective of genomic and regulatory divergence.

    PubMed

    Nuñez, Pablo A; Soria, Marcelo; Farber, Marisa D

    2012-01-01

    The twin-arginine translocation (Tat) pathway exports fully folded proteins out of the cytoplasm of Gram-negative and Gram-positive bacteria. Although much progress has been made in unraveling the molecular mechanism and biochemical characterization of the Tat system, little is known concerning its functionality and biological role to confer adaptive skills, symbiosis or pathogenesis in the α-proteobacteria class. A comparative genomic analysis in the α-proteobacteria class confirmed the presence of tatA, tatB, and tatC genes in almost all genomes, but significant variations in gene synteny and rearrangements were found in the order Rickettsiales with respect to the typically described operon organization. Transcription of tat genes was confirmed for Anaplasma marginale str. St. Maries and Brucella abortus 2308, two α-proteobacteria with full and partial intracellular lifestyles, respectively. The tat genes of A. marginale are scattered throughout the genome, in contrast to the more generalized operon organization. Particularly, tatA showed an approximately 20-fold increase in mRNA levels relative to tatB and tatC. We showed Tat functionality in B. abortus 2308 for the first time, and confirmed conservation of functionality in A. marginale. We present the first experimental description of the Tat system in the Anaplasmataceae and Brucellaceae families. In particular, in A. marginale Tat functionality is conserved despite operon splitting as a consequence of genome rearrangements. Further studies will be required to understand how the proper stoichiometry of the Tat protein complex and its biological role are achieved. In addition, the predicted substrates might be the evidence of role of the Tat translocation system in the transition process from a free-living to a parasitic lifestyle in these α-proteobacteria. PMID:22438962

  9. The Twin-Arginine Translocation Pathway in α-Proteobacteria Is Functionally Preserved Irrespective of Genomic and Regulatory Divergence

    PubMed Central

    Nuñez, Pablo A.; Soria, Marcelo; Farber, Marisa D.

    2012-01-01

    The twin-arginine translocation (Tat) pathway exports fully folded proteins out of the cytoplasm of Gram-negative and Gram-positive bacteria. Although much progress has been made in unraveling the molecular mechanism and biochemical characterization of the Tat system, little is known concerning its functionality and biological role to confer adaptive skills, symbiosis or pathogenesis in the α-proteobacteria class. A comparative genomic analysis in the α-proteobacteria class confirmed the presence of tatA, tatB, and tatC genes in almost all genomes, but significant variations in gene synteny and rearrangements were found in the order Rickettsiales with respect to the typically described operon organization. Transcription of tat genes was confirmed for Anaplasma marginale str. St. Maries and Brucella abortus 2308, two α-proteobacteria with full and partial intracellular lifestyles, respectively. The tat genes of A. marginale are scattered throughout the genome, in contrast to the more generalized operon organization. Particularly, tatA showed an approximately 20-fold increase in mRNA levels relative to tatB and tatC. We showed Tat functionality in B. abortus 2308 for the first time, and confirmed conservation of functionality in A. marginale. We present the first experimental description of the Tat system in the Anaplasmataceae and Brucellaceae families. In particular, in A. marginale Tat functionality is conserved despite operon splitting as a consequence of genome rearrangements. Further studies will be required to understand how the proper stoichiometry of the Tat protein complex and its biological role are achieved. In addition, the predicted substrates might be the evidence of role of the Tat translocation system in the transition process from a free-living to a parasitic lifestyle in these α-proteobacteria. PMID:22438962

  10. All the better to see you with: eyes and claws reveal the evolution of divergent ecological roles in giant pterygotid eurypterids.

    PubMed

    McCoy, Victoria E; Lamsdell, James C; Poschmann, Markus; Anderson, Ross P; Briggs, Derek E G

    2015-08-01

    Pterygotid eurypterids have traditionally been interpreted as active, high-level, visual predators; however, recent studies of the visual system and cheliceral morphology of the pterygotid Acutiramus contradict this interpretation. Here, we report similar analyses of the pterygotids Erettopterus, Jaekelopterus and Pterygotus, and the pterygotid sister taxon Slimonia. Representative species of all these genera have more acute vision than A. cummingsi. The visual systems of Jaekelopterus rhenaniae and Pterygotus anglicus are comparable to that of modern predatory arthropods. All species of Jaekelopterus and Pterygotus have robust crushing chelicerae, morphologically distinct from the weaker slicing chelicerae of Acutiramus. Vision in Erettopterus osiliensis and Slimonia acuminata is more acute than in Acutiramus cummingsi, but not to the same degree as in modern active predators, and the morphology of the chelicerae in these genera suggests a grasping function. The pterygotids evolved with a shift in ecology from generalized feeder to specialized predator. Pterygotid eurypterids share a characteristic morphology but, although some were top predators, their ecology differs radically between genera. PMID:26289442

  11. Organelle proteomics reveals cargo maturation mechanisms associated with Golgi-like encystation vesicles in the early-diverged protozoan Giardia lamblia.

    PubMed

    Stefanic, Sasa; Palm, Daniel; Svärd, Staffan G; Hehl, Adrian B

    2006-03-17

    During encystation Giardia trophozoites secrete a fibrillar extracellular matrix of glycans and cyst wall proteins on the cell surface. The cyst wall material is accumulated in encystation-specific vesicles (ESVs), specialized Golgi-like compartments generated de novo, after export from the endoplasmic reticulum (ER) and before secretion. These large post-ER vesicles neither have the morphological characteristics of Golgi cisternae nor sorting functions, but may represent an evolutionary early form of the Golgi-like maturation compartment. Because little is known about the genesis and maturation of ESVs, we used a limited proteomics approach to discover novel proteins that are specific for developing ESVs or associated peripherally with these organelles. Unexpectedly, we identified cytoplasmic and luminal factors of the ER quality control system on two-dimensional electrophoresis gels, i.e. several proteasome subunits and HSP70-BiP. We show that BiP is exported to ESVs and retrieved via its C-terminal KDEL signal from ESVs. In contrast, cytoplasmic proteasome complexes undergo a developmentally regulated re-localization to ESVs during encystation. This suggests that maturation of bulk exported cyst wall material in the Golgi-like ESVs involves both continuous activity of ER-associated quality control mechanisms and retrograde Golgi to ER transport. PMID:16407213

  12. A unique midgut-associated bacterial community hosted by the cave beetle Cansiliella servadeii (Coleoptera: Leptodirini) reveals parallel phylogenetic divergences from universal gut-specific ancestors

    PubMed Central

    2013-01-01

    Background Cansiliella servadeii (Coleoptera) is an endemic troglobite living in deep carbonate caves in North-Eastern Italy. The beetle constantly moves and browses in its preferred habitat (consisting in flowing water and moonmilk, a soft speleothem colonized by microorganisms) self-preens to convey material from elytra, legs, and antennae towards the mouth. We investigated its inner and outer microbiota using microscopy and DNA-based approaches. Results Abundant microbial cell masses were observed on the external appendages. Cansiliella’s midgut is fully colonized by live microbes and culture-independent analyses yielded nearly 30 different 16S phylotypes that have no overlap with the community composition of the moonmilk. Many of the lineages, dominated by Gram positive groups, share very low similarity to database sequences. However for most cases, notwithstanding their very limited relatedness with existing records, phylotypes could be assigned to bacterial clades that had been retrieved from insect or other animals’ digestive traits. Conclusions Results suggest a history of remote separation from a common ancestor that harboured a set of gut-specific bacteria whose functions are supposedly critical for host physiology. The phylogenetic and coevolutionary implications of the parallel occurrences of these prokaryotic guilds appear to apply throughout a broad spectrum of animal diversity. Their persistence and conservation underlies a possibly critical role of precise bacterial assemblages in animal-bacteria interactions. PMID:23758657

  13. Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses

    PubMed Central

    Kapeli, Katannya; Pratt, Gabriel A.; Vu, Anthony Q.; Hutt, Kasey R.; Martinez, Fernando J.; Sundararaman, Balaji; Batra, Ranjan; Freese, Peter; Lambert, Nicole J.; Huelga, Stephanie C.; Chun, Seung J.; Liang, Tiffany Y.; Chang, Jeremy; Donohue, John P.; Shiue, Lily; Zhang, Jiayu; Zhu, Haining; Cambi, Franca; Kasarskis, Edward; Hoon, Shawn; Ares Jr., Manuel; Burge, Christopher B.; Ravits, John; Rigo, Frank; Yeo, Gene W.

    2016-01-01

    The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs enriched for GGUA motifs in adult mouse brains. TAF15 and FUS exhibit similar binding patterns in introns, are enriched in 3′ untranslated regions and alter genes distinct from TDP-43. However, unlike FUS and TDP-43, TAF15 has a minimal role in alternative splicing. In human neural progenitors, TAF15 and FUS affect turnover of their RNA targets. In human stem cell-derived motor neurons, the RNA profile associated with concomitant loss of both TAF15 and FUS resembles that observed in the presence of the ALS-associated mutation FUS R521G, but contrasts with late-stage sporadic ALS patients. Taken together, our findings reveal convergent and divergent roles for FUS, TAF15 and TDP-43 in RNA metabolism. PMID:27378374

  14. Saccharomyces cerevisiae Bat1 and Bat2 Aminotransferases Have Functionally Diverged from the Ancestral-Like Kluyveromyces lactis Orthologous Enzyme

    PubMed Central

    Colón, Maritrini; Hernández, Fabiola; López, Karla; Quezada, Héctor; González, James; López, Geovani; Aranda, Cristina; González, Alicia

    2011-01-01

    Background Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. Principal Findings Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs). This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1), while catabolic substrates are accumulated in the cytosol (Bat2). Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. Conclusions Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the biosynthetic and catabolic

  15. Divergent composition but similar function of soil food webs of individual plants: plant species and community effects.

    PubMed

    Bezemer, T M; Fountain, M T; Barea, J M; Christensen, S; Dekker, S C; Duyts, H; van Hal, R; Harvey, J A; Hedlund, K; Maraun, M; Mikola, J; Mladenov, A G; Robin, C; de Ruiter, P C; Scheu, S; Setälä, H; Smilauer, P; van der Putten, W H

    2010-10-01

    Soils are extremely rich in biodiversity, and soil organisms play pivotal roles in supporting terrestrial life, but the role that individual plants and plant communities play in influencing the diversity and functioning of soil food webs remains highly debated. Plants, as primary producers and providers of resources to the soil food web, are of vital importance for the composition, structure, and functioning of soil communities. However, whether natural soil food webs that are completely open to immigration and emigration differ underneath individual plants remains unknown. In a biodiversity restoration experiment we first compared the soil nematode communities of 228 individual plants belonging to eight herbaceous species. We included grass, leguminous, and non-leguminous species. Each individual plant grew intermingled with other species, but all plant species had a different nematode community. Moreover, nematode communities were more similar when plant individuals were growing in the same as compared to different plant communities, and these effects were most apparent for the groups of bacterivorous, carnivorous, and omnivorous nematodes. Subsequently, we analyzed the composition, structure, and functioning of the complete soil food webs of 58 individual plants, belonging to two of the plant species, Lotus corniculatus (Fabaceae) and Plantago lanceolata (Plantaginaceae). We isolated and identified more than 150 taxa/groups of soil organisms. The soil community composition and structure of the entire food webs were influenced both by the species identity of the plant individual and the surrounding plant community. Unexpectedly, plant identity had the strongest effects on decomposing soil organisms, widely believed to be generalist feeders. In contrast, quantitative food web modeling showed that the composition of the plant community influenced nitrogen mineralization under individual plants, but that plant species identity did not affect nitrogen or carbon

  16. Conserved function of medaka pink-eyed dilution in melanin synthesis and its divergent transcriptional regulation in gonads among vertebrates.

    PubMed

    Fukamachi, Shoji; Asakawa, Shuichi; Wakamatsu, Yuko; Shimizu, Nobuyoshi; Mitani, Hiroshi; Shima, Akihiro

    2004-11-01

    Medaka is emerging as a model organism for the study of vertebrate development and genetics, and its effectiveness in forward genetics should prove equal to that of zebrafish. Here, we identify by positional cloning a gene responsible for the medaka i-3 albino mutant. i-3 larvae have weakly tyrosinase-positive cells but lack strongly positive and dendritic cells, suggesting loss of fully differentiated melanophores. The region surrounding the i-3 locus is syntenic to human 19p13, but a BAC clone covering the i-3 locus contained orthologs located at 15q11-13, including OCA2 (P). Medaka P consists of 842 amino acids and shares approximately 65% identity with mammalian P proteins. The i-3 mutation is a four-base deletion in exon 13, which causes a frameshift and truncation of the protein. We detected medaka P transcripts in melanin-producing eyeballs and (putative) skin melanophores on embryos and an alternatively spliced form in the non-melanin-producing ovary or oocytes. The mouse p is similarly expressed in gonads, but not alternatively spliced. This is the first isolation of nonmammalian P, the functional mechanism of action of which has not yet been elucidated, even in mammals. Further investigation of the functions of P proteins and the regulation of their expression will provide new insight into body color determination and gene evolution. PMID:15579703

  17. Nup2 requires a highly divergent partner, NupA, to fulfill functions at nuclear pore complexes and the mitotic chromatin region

    PubMed Central

    Markossian, Sarine; Suresh, Subbulakshmi; Osmani, Aysha H.; Osmani, Stephen A.

    2015-01-01

    Chromatin and nuclear pore complexes (NPCs) undergo dramatic changes during mitosis, which in vertebrates and Aspergillus nidulans involves movement of Nup2 from NPCs to the chromatin region to fulfill unknown functions. This transition is shown to require the Cdk1 mitotic kinase and be promoted prematurely by ectopic expression of the NIMA kinase. Nup2 localizes with a copurifying partner termed NupA, a highly divergent yet essential NPC protein. NupA and Nup2 locate throughout the chromatin region during prophase but during anaphase move to surround segregating DNA. NupA function is shown to involve targeting Nup2 to its interphase and mitotic locations. Deletion of either Nup2 or NupA causes identical mitotic defects that initiate a spindle assembly checkpoint (SAC)–dependent mitotic delay and also cause defects in karyokinesis. These mitotic problems are not caused by overall defects in mitotic NPC disassembly–reassembly or general nuclear import. However, without Nup2 or NupA, although the SAC protein Mad1 locates to its mitotic locations, it fails to locate to NPCs normally in G1 after mitosis. Collectively the study provides new insight into the roles of Nup2 and NupA during mitosis and in a surveillance mechanism that regulates nucleokinesis when mitotic defects occur after SAC fulfillment. PMID:25540430

  18. Divergent responses of functional gene expression to various nutrient conditions during microcystin-LR biodegradation by Novosphingobium sp. THN1 strain.

    PubMed

    Li, Jieming; Peng, Liujing; Li, Ji; Qiao, Yuhui

    2014-03-01

    To better understand the mechanisms for microcystin-LR (MCLR) biodegradation, the linkage between MCLR-biodegradation kinetics and functional gene expression dynamics was originally investigated with Novosphingobium sp. THN1 as inoculum under various nutrient conditions. Along biodegradation, mlrA gene expression, coupled with mlrD, presented similar trend but was regulated differentially among different conditions. Good positive correlation was observed between MCLR degraded and induction ratios of functional genes until 42h at respective condition. Compared to those under nutrient-free condition, the stimulated or decelerated biodegradation with dipotassium phosphate (DP) or ammonium chloride (AC) (both at 100mg L(-1)) was related to higher or lower up-regulation in mlr gene expression, suggesting that divergent mlr gene expression was one of the reasons for different effects of DP or AC on degradation. However, stimulated degradation with sodium nitrate (100mg L(-1)) might involve other mechanisms where mlr expression was not the decisive prerequisite to govern MCLR-biodegradation. PMID:24530889

  19. Guises and disguises of quadratic divergences

    SciTech Connect

    Cherchiglia, A.L.; Vieira, A.R.; Hiller, Brigitte; Baêta Scarpelli, A.P.; Sampaio, Marcos

    2014-12-15

    In this contribution, we present a new perspective on the control of quadratic divergences in quantum field theory, in general, and in the Higgs naturalness problem, in particular. Our discussion is essentially based on an approach where UV divergences are parameterized, after being reduced to basic divergent integrals (BDI) in one internal momentum, as functions of a cutoff and a renormalization group scale λ. We illustrate our proposal with well-known examples, such as the gluon vacuum self energy of QCD and the Higgs decay in two photons within this approach. We also discuss frameworks in effective low-energy QCD models, where quadratic divergences are indeed fundamental.

  20. Determining the Effect of Natural Selection on Linked Neutral Divergence across Species

    PubMed Central

    Phung, Tanya N.; Lohmueller, Kirk E.

    2016-01-01

    A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only

  1. Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.

    PubMed

    Phung, Tanya N; Huber, Christian D; Lohmueller, Kirk E

    2016-08-01

    A major goal in evolutionary biology is to understand how natural selection has shaped patterns of genetic variation across genomes. Studies in a variety of species have shown that neutral genetic diversity (intra-species differences) has been reduced at sites linked to those under direct selection. However, the effect of linked selection on neutral sequence divergence (inter-species differences) remains ambiguous. While empirical studies have reported correlations between divergence and recombination, which is interpreted as evidence for natural selection reducing linked neutral divergence, theory argues otherwise, especially for species that have diverged long ago. Here we address these outstanding issues by examining whether natural selection can affect divergence between both closely and distantly related species. We show that neutral divergence between closely related species (e.g. human-primate) is negatively correlated with functional content and positively correlated with human recombination rate. We also find that neutral divergence between distantly related species (e.g. human-rodent) is negatively correlated with functional content and positively correlated with estimates of background selection from primates. These patterns persist after accounting for the confounding factors of hypermutable CpG sites, GC content, and biased gene conversion. Coalescent models indicate that even when the contribution of ancestral polymorphism to divergence is small, background selection in the ancestral population can still explain a large proportion of the variance in divergence across the genome, generating the observed correlations. Our findings reveal that, contrary to previous intuition, natural selection can indirectly affect linked neutral divergence between both closely and distantly related species. Though we cannot formally exclude the possibility that the direct effects of purifying selection drive some of these patterns, such a scenario would be possible only

  2. Divergence-based vector quantization.

    PubMed

    Villmann, Thomas; Haase, Sven

    2011-05-01

    Supervised and unsupervised vector quantization methods for classification and clustering traditionally use dissimilarities, frequently taken as Euclidean distances. In this article, we investigate the applicability of divergences instead, focusing on online learning. We deduce the mathematical fundamentals for its utilization in gradient-based online vector quantization algorithms. It bears on the generalized derivatives of the divergences known as Fréchet derivatives in functional analysis, which reduces in finite-dimensional problems to partial derivatives in a natural way. We demonstrate the application of this methodology for widely applied supervised and unsupervised online vector quantization schemes, including self-organizing maps, neural gas, and learning vector quantization. Additionally, principles for hyperparameter optimization and relevance learning for parameterized divergences in the case of supervised vector quantization are given to achieve improved classification accuracy. PMID:21299418

  3. Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality

    PubMed Central

    Wu, Nicholas C.; Olson, C. Anders; Du, Yushen; Le, Shuai; Tran, Kevin; Remenyi, Roland; Gong, Danyang; Al-Mawsawi, Laith Q.; Qi, Hangfei; Wu, Ting-Ting; Sun, Ren

    2015-01-01

    Viruses often encode proteins with multiple functions due to their compact genomes. Existing approaches to identify functional residues largely rely on sequence conservation analysis. Inferring functional residues from sequence conservation can produce false positives, in which the conserved residues are functionally silent, or false negatives, where functional residues are not identified since they are species-specific and therefore non-conserved. Furthermore, the tedious process of constructing and analyzing individual mutations limits the number of residues that can be examined in a single study. Here, we developed a systematic approach to identify the functional residues of a viral protein by coupling experimental fitness profiling with protein stability prediction using the influenza virus polymerase PA subunit as the target protein. We identified a significant number of functional residues that were influenza type-specific and were evolutionarily non-conserved among different influenza types. Our results indicate that type-specific functional residues are prevalent and may not otherwise be identified by sequence conservation analysis alone. More importantly, this technique can be adapted to any viral (and potentially non-viral) protein where structural information is available. PMID:26132554

  4. Preschool executive functions, single-parent status, and school quality predict diverging trajectories of classroom inattention in elementary school.

    PubMed

    Sasser, Tyler R; Beekman, Charles R; Bierman, Karen L

    2015-08-01

    A sample of 356 children recruited from Head Start (58% European American, 25% African American, and 17% Hispanic; 54% girls; M age = 4.59 years) were followed longitudinally from prekindergarten through fifth grade. Latent profile analyses of teacher-rated inattention from kindergarten through third grade identified four developmental trajectories: stable low (53% of the sample), stable high (11.3%), rising over time (16.4%), and declining over time (19.3%). Children with stable low inattention had the best academic outcomes in fifth grade, and children exhibiting stable high inattention had the worst, with the others in between. Self-regulation difficulties in preschool (poor executive function skills and elevated opposition-aggression) differentiated children with rising versus stable low inattention. Elementary schools characterized by higher achievement differentiated children with declining versus stable high inattention. Boys and children from single-parent families were more likely to remain high or rise in inattention, whereas girls and children from dual-parent families were more likely to remain low or decline in inattention. PMID:25200465

  5. Preschool Executive Functions, Single-Parent Status, and School Quality Predict Diverging Trajectories of Classroom Inattention in Elementary School

    PubMed Central

    Sasser, Tyler R.; Beekman, Charles R.; Bierman, Karen L.

    2016-01-01

    A sample of 356 children recruited from Head Start (58% European American, 25% African American, and 17% Hispanic; 54% girls; Mage ¼ 4.59 years) were followed longitudinally from prekindergarten through fifth grade. Latent profile analyses of teacher-rated inattention from kindergarten through third grade identified four developmental trajectories: stable low (53% of the sample), stable high (11.3%), rising over time (16.4%), and declining over time (19.3%). Children with stable low inattention had the best academic outcomes in fifth grade, and children exhibiting stable high inattention had the worst, with the others in between. Self-regulation difficulties in preschool (poor executive function skills and elevated opposition–aggression) differentiated children with rising versus stable low inattention. Elementary schools characterized by higher achievement differentiated children with declining versus stable high inattention. Boys and children from single-parent families were more likely to remain high or rise in inattention, whereas girls and children from dual-parent families were more likely to remain low or decline in inattention. PMID:25200465

  6. Functional Divergence in the Genus Oenococcus as Predicted by Genome Sequencing of the Newly-Described Species, Oenococcus kitaharae

    PubMed Central

    Borneman, Anthony R.; McCarthy, Jane M.; Chambers, Paul J.; Bartowsky, Eveline J.

    2012-01-01

    Oenococcus kitaharae is only the second member of the genus Oenococcus to be identified and is the closest relative of the industrially important wine bacterium Oenococcus oeni. To provide insight into this new species, the genome of the type strain of O. kitaharae, DSM 17330, was sequenced. Comparison of the sequenced genomes of both species show that the genome of O. kitaharae DSM 17330 contains many genes with predicted functions in cellular defence (bacteriocins, antimicrobials, restriction-modification systems and a CRISPR locus) which are lacking in O. oeni. The two genomes also appear to differentially encode several metabolic pathways associated with amino acid biosynthesis and carbohydrate utilization and which have direct phenotypic consequences. This would indicate that the two species have evolved different survival techniques to suit their particular environmental niches. O. oeni has adapted to survive in the harsh, but predictable, environment of wine that provides very few competitive species. However O. kitaharae appears to have adapted to a growth environment in which biological competition provides a significant selective pressure by accumulating biological defence molecules, such as bacteriocins and restriction-modification systems, throughout its genome. PMID:22235313

  7. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations.

    PubMed

    Raamsdonk, L M; Teusink, B; Broadhurst, D; Zhang, N; Hayes, A; Walsh, M C; Berden, J A; Brindle, K M; Kell, D B; Rowland, J J; Westerhoff, H V; van Dam, K; Oliver, S G

    2001-01-01

    A large proportion of the 6,000 genes present in the genome of Saccharomyces cerevisiae, and of those sequenced in other organisms, encode proteins of unknown function. Many of these genes are "silent, " that is, they show no overt phenotype, in terms of growth rate or other fluxes, when they are deleted from the genome. We demonstrate how the intracellular concentrations of metabolites can reveal phenotypes for proteins active in metabolic regulation. Quantification of the change of several metabolite concentrations relative to the concentration change of one selected metabolite can reveal the site of action, in the metabolic network, of a silent gene. In the same way, comprehensive analyses of metabolite concentrations in mutants, providing "metabolic snapshots," can reveal functions when snapshots from strains deleted for unstudied genes are compared to those deleted for known genes. This approach to functional analysis, using comparative metabolomics, we call FANCY-an abbreviation for functional analysis by co-responses in yeast. PMID:11135551

  8. TOMATO AGAMOUS1 and ARLEQUIN/TOMATO AGAMOUS-LIKE1 MADS-box genes have redundant and divergent functions required for tomato reproductive development.

    PubMed

    Gimenez, Estela; Castañeda, Laura; Pineda, Benito; Pan, Irvin L; Moreno, Vicente; Angosto, Trinidad; Lozano, Rafael

    2016-07-01

    Within the tomato MADS-box gene family, TOMATO AGAMOUS1 (TAG1) and ARLEQUIN/TOMATO AGAMOUS LIKE1 (hereafter referred to as TAGL1) are, respectively, members of the euAG and PLE lineages of the AGAMOUS clade. They perform crucial functions specifying stamen and carpel development in the flower and controlling late fruit development. To gain insight into the roles of TAG1 and TAGL1 genes and to better understand their functional redundancy and diversification, we characterized single and double RNAi silencing lines of these genes and analyzed expression profiles of regulatory genes involved in reproductive development. Double RNAi lines did show cell abnormalities in stamens and carpels and produced extremely small fruit-like organs displaying some sepaloid features. Expression analyses indicated that TAG1 and TAGL1 act together to repress fourth whorl sepal development, most likely through the MACROCALYX gene. Results also proved that TAG1 and TAGL1 have diversified their functions in fruit development: while TAG1 controls placenta and seed formation, TAGL1 participates in cuticle development and lignin biosynthesis inhibition. It is noteworthy that both TAG1 and double RNAi plants lacked seed development due to abnormalities in pollen formation. This seedless phenotype was not associated with changes in the expression of B-class stamen identity genes Tomato MADS-box 6 and Tomato PISTILLATA observed in silencing lines, suggesting that other regulatory factors should participate in pollen formation. Taken together, results here reported support the idea that both redundant and divergent functions of TAG1 and TAGL1 genes are needed to control tomato reproductive development. PMID:27125648

  9. Power divergences in overlapping Wilson lines

    NASA Astrophysics Data System (ADS)

    Berwein, Matthias

    2016-01-01

    We discuss the divergence structure of Wilson line operators with partially overlapping segments on the basis of the cyclic Wilson loop as an explicit example. The generalized exponentiation theorem is used to show the exponentiation and factorization of power divergences for certain linear combinations of associated loop functions.

  10. Functional Divergence of the Nuclear Receptor NR2C1 as a Modulator of Pluripotentiality During Hominid Evolution.

    PubMed

    Baker, Jennifer L; Dunn, Katherine A; Mingrone, Joseph; Wood, Bernard A; Karpinski, Beverly A; Sherwood, Chet C; Wildman, Derek E; Maynard, Thomas M; Bielawski, Joseph P

    2016-06-01

    Genes encoding nuclear receptors (NRs) are attractive as candidates for investigating the evolution of gene regulation because they (1) have a direct effect on gene expression and (2) modulate many cellular processes that underlie development. We employed a three-phase investigation linking NR molecular evolution among primates with direct experimental assessment of NR function. Phase 1 was an analysis of NR domain evolution and the results were used to guide the design of phase 2, a codon-model-based survey for alterations of natural selection within the hominids. By using a series of reliability and robustness analyses we selected a single gene, NR2C1, as the best candidate for experimental assessment. We carried out assays to determine whether changes between the ancestral and extant NR2C1s could have impacted stem cell pluripotency (phase 3). We evaluated human, chimpanzee, and ancestral NR2C1 for transcriptional modulation of Oct4 and Nanog (key regulators of pluripotency and cell lineage commitment), promoter activity for Pepck (a proxy for differentiation in numerous cell types), and average size of embryological stem cell colonies (a proxy for the self-renewal capacity of pluripotent cells). Results supported the signal for alteration of natural selection identified in phase 2. We suggest that adaptive evolution of gene regulation has impacted several aspects of pluripotentiality within primates. Our study illustrates that the combination of targeted evolutionary surveys and experimental analysis is an effective strategy for investigating the evolution of gene regulation with respect to developmental phenotypes. PMID:27075724

  11. Ewes With Divergent Cortisol Responses to ACTH Exhibit Functional Differences in the Hypothalamo-Pituitary-Adrenal (HPA) Axis.

    PubMed

    Hewagalamulage, Sakda D; Clarke, Iain J; Rao, Alexandra; Henry, Belinda A

    2016-09-01

    Within any population, the cortisol response to ACTH covers a considerable range. High responders (HRs) exhibit a greater cortisol secretory response to stress or ACTH, compared with individuals classified as low cortisol responders (LRs). We administered ACTH (0.2 μg/kg, iv) to 160 female sheep and selected subpopulations of animals as LR and HR. In the present study, we aimed to characterize the hypothalamo-pituitary-adrenal axis in HR and LR and to identify factors that underlie the differing cortisol responses to ACTH. Hypothalami, pituitaries, and adrenals were collected from nonstressed HR and LR ewes. Expression of genes for CRH, arginine vasopressin (AVP), oxytocin, glucocorticoid receptor, and mineralocorticoid receptor were measured by in situ hybridization in the paraventricular nucleus of the hypothalamus, and proopiomelanocortin (POMC) gene expression was measured in the anterior pituitary. Expression of CRH, AVP, and POMC was higher in HR, with no differences in either glucocorticoid receptor or mineralocorticoid receptor expression. Oxytocin expression was greater in LR. In the adrenal gland, real-time PCR analysis indicated that expression of the ACTH receptor and a range of steroidogenic enzymes was similar in HR and LR. Adrenal weights, the cortex to medulla ratio and adrenal cortisol content were also similar in LR and HR. In conclusion, LR and HR display innate differences in the steady-state expression of CRH, AVP, oxytocin, and POMC, indicating that selection for cortisol responsiveness identifies distinct subpopulations that exhibit innate differences in the gene expression/function of hypothalamo-pituitary-adrenal axis markers. PMID:27414744

  12. Structural and functional characterization of two genetically related meucin peptides highlights evolutionary divergence and convergence in antimicrobial peptides.

    PubMed

    Gao, Bin; Sherman, Patrick; Luo, Lan; Bowie, John; Zhu, Shunyi

    2009-04-01

    organization, three-dimensional structure, and biological function suggests that meucins are two evolutionarily related AMPs and likely originated from a common ancestor by gene duplication. Our work presented here also provides new insights into an evolutionary link among AMPs from invertebrates and vertebrates and clues for evolutionary convergence between AMPs and virus fusion domains. PMID:19088182

  13. Function and regulation of TRPP2 ion channel revealed by a gain-of-function mutant.

    PubMed

    Arif Pavel, Mahmud; Lv, Caixia; Ng, Courtney; Yang, Lei; Kashyap, Parul; Lam, Clarissa; Valentino, Victoria; Fung, Helen Y; Campbell, Thomas; Møller, Simon Geir; Zenisek, David; Holtzman, Nathalia G; Yu, Yong

    2016-04-26

    Mutations in polycystin-1 and transient receptor potential polycystin 2 (TRPP2) account for almost all clinically identified cases of autosomal dominant polycystic kidney disease (ADPKD), one of the most common human genetic diseases. TRPP2 functions as a cation channel in its homomeric complex and in the TRPP2/polycystin-1 receptor/ion channel complex. The activation mechanism of TRPP2 is unknown, which significantly limits the study of its function and regulation. Here, we generated a constitutively active gain-of-function (GOF) mutant of TRPP2 by applying a mutagenesis scan on the S4-S5 linker and the S5 transmembrane domain, and studied functional properties of the GOF TRPP2 channel. We found that extracellular divalent ions, including Ca(2+), inhibit the permeation of monovalent ions by directly blocking the TRPP2 channel pore. We also found that D643, a negatively charged amino acid in the pore, is crucial for channel permeability. By introducing single-point ADPKD pathogenic mutations into the GOF TRPP2, we showed that different mutations could have completely different effects on channel activity. The in vivo function of the GOF TRPP2 was investigated in zebrafish embryos. The results indicate that, compared with wild type (WT), GOF TRPP2 more efficiently rescued morphological abnormalities, including curly tail and cyst formation in the pronephric kidney, caused by down-regulation of endogenous TRPP2 expression. Thus, we established a GOF TRPP2 channel that can serve as a powerful tool for studying the function and regulation of TRPP2. The GOF channel may also have potential application for developing new therapeutic strategies for ADPKD. PMID:27071085

  14. BcMF26a and BcMF26b Are Duplicated Polygalacturonase Genes with Divergent Expression Patterns and Functions in Pollen Development and Pollen Tube Formation in Brassica campestris

    PubMed Central

    Lyu, Meiling; Yu, Youjian; Jiang, Jingjing; Song, Limin; Liang, Ying; Ma, Zhiming; Xiong, Xingpeng; Cao, Jiashu

    2015-01-01

    Polygalacturonase (PG) is one of the cell wall hydrolytic enzymes involving in pectin degradation. A comparison of two highly conserved duplicated PG genes, namely, Brassica campestris Male Fertility 26a (BcMF26a) and BcMF26b, revealed the different features of their expression patterns and functions. We found that these two genes were orthologous genes of At4g33440, and they originated from a chromosomal segmental duplication. Although structurally similar, their regulatory and intron sequences largely diverged. QRT-PCR analysis showed that the expression level of BcMF26b was higher than that of BcMF26a in almost all the tested organs and tissues in Brassica campestris. Promoter activity analysis showed that, at reproductive development stages, BcMF26b promoter was active in tapetum, pollen grains, and pistils, whereas BcMF26a promoter was only active in pistils. In the subcellular localization experiment, BcMF26a and BcMF26b proteins could be localized to the cell wall. When the two genes were co-inhibited, pollen intine was formed abnormally and pollen tubes could not grow or stretch. Moreover, the knockout mutants of At4g33440 delayed the growth of pollen tubes. Therefore, BcMF26a/b can participate in the construction of pollen wall by modulating intine information and BcMF26b may play a major role in co-inhibiting transformed plants. PMID:26153985

  15. BcMF26a and BcMF26b Are Duplicated Polygalacturonase Genes with Divergent Expression Patterns and Functions in Pollen Development and Pollen Tube Formation in Brassica campestris.

    PubMed

    Lyu, Meiling; Yu, Youjian; Jiang, Jingjing; Song, Limin; Liang, Ying; Ma, Zhiming; Xiong, Xingpeng; Cao, Jiashu

    2015-01-01

    Polygalacturonase (PG) is one of the cell wall hydrolytic enzymes involving in pectin degradation. A comparison of two highly conserved duplicated PG genes, namely, Brassica campestris Male Fertility 26a (BcMF26a) and BcMF26b, revealed the different features of their expression patterns and functions. We found that these two genes were orthologous genes of At4g33440, and they originated from a chromosomal segmental duplication. Although structurally similar, their regulatory and intron sequences largely diverged. QRT-PCR analysis showed that the expression level of BcMF26b was higher than that of BcMF26a in almost all the tested organs and tissues in Brassica campestris. Promoter activity analysis showed that, at reproductive development stages, BcMF26b promoter was active in tapetum, pollen grains, and pistils, whereas BcMF26a promoter was only active in pistils. In the subcellular localization experiment, BcMF26a and BcMF26b proteins could be localized to the cell wall. When the two genes were co-inhibited, pollen intine was formed abnormally and pollen tubes could not grow or stretch. Moreover, the knockout mutants of At4g33440 delayed the growth of pollen tubes. Therefore, BcMF26a/b can participate in the construction of pollen wall by modulating intine information and BcMF26b may play a major role in co-inhibiting transformed plants. PMID:26153985

  16. Quantum skew divergence

    SciTech Connect

    Audenaert, Koenraad M. R.

    2014-11-15

    In this paper, we study the quantum generalisation of the skew divergence, which is a dissimilarity measure between distributions introduced by Lee in the context of natural language processing. We provide an in-depth study of the quantum skew divergence, including its relation to other state distinguishability measures. Finally, we present a number of important applications: new continuity inequalities for the quantum Jensen-Shannon divergence and the Holevo information, and a new and short proof of Bravyi's Small Incremental Mixing conjecture.

  17. Dynamic functional connectivity reveals altered variability in functional connectivity among patients with major depressive disorder.

    PubMed

    Demirtaş, Murat; Tornador, Cristian; Falcón, Carles; López-Solà, Marina; Hernández-Ribas, Rosa; Pujol, Jesús; Menchón, José M; Ritter, Petra; Cardoner, Narcis; Soriano-Mas, Carles; Deco, Gustavo

    2016-08-01

    Resting-state fMRI (RS-fMRI) has become a useful tool to investigate the connectivity structure of mental health disorders. In the case of major depressive disorder (MDD), recent studies regarding the RS-fMRI have found abnormal connectivity in several regions of the brain, particularly in the default mode network (DMN). Thus, the relevance of the DMN to self-referential thoughts and ruminations has made the use of the resting-state approach particularly important for MDD. The majority of such research has relied on the grand averaged functional connectivity measures based on the temporal correlations between the BOLD time series of various brain regions. We, in our study, investigated the variations in the functional connectivity over time at global and local level using RS-fMRI BOLD time series of 27 MDD patients and 27 healthy control subjects. We found that global synchronization and temporal stability were significantly increased in the MDD patients. Furthermore, the participants with MDD showed significantly increased overall average (static) functional connectivity (sFC) but decreased variability of functional connectivity (vFC) within specific networks. Static FC increased to predominance among the regions pertaining to the default mode network (DMN), while the decreased variability of FC was observed in the connections between the DMN and the frontoparietal network. Hum Brain Mapp 37:2918-2930, 2016. © 2016 Wiley Periodicals, Inc. PMID:27120982

  18. CNL Disease Resistance Genes in Soybean and Their Evolutionary Divergence

    PubMed Central

    Nepal, Madhav P; Benson, Benjamin V

    2015-01-01

    Disease resistance genes (R-genes) encode proteins involved in detecting pathogen attack and activating downstream defense molecules. Recent availability of soybean genome sequences makes it possible to examine the diversity of gene families including disease-resistant genes. The objectives of this study were to identify coiled-coil NBS-LRR (= CNL) R-genes in soybean, infer their evolutionary relationships, and assess structural as well as functional divergence of the R-genes. Profile hidden Markov models were used for sequence identification and model-based maximum likelihood was used for phylogenetic analysis, and variation in chromosomal positioning, gene clustering, and functional divergence were assessed. We identified 188 soybean CNL genes nested into four clades consistent to their orthologs in Arabidopsis. Gene clustering analysis revealed the presence of 41 gene clusters located on 13 different chromosomes. Analyses of the Ks-values and chromosomal positioning suggest duplication events occurring at varying timescales, and an extrapericentromeric positioning may have facilitated their rapid evolution. Each of the four CNL clades exhibited distinct patterns of gene expression. Phylogenetic analysis further supported the extrapericentromeric positioning effect on the divergence and retention of the CNL genes. The results are important for understanding the diversity and divergence of CNL genes in soybean, which would have implication in soybean crop improvement in future. PMID:25922568

  19. MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors

    PubMed Central

    Firacative, Carolina; Roe, Chandler C.; Malik, Richard; Ferreira-Paim, Kennio; Escandón, Patricia; Sykes, Jane E.; Castañón-Olivares, Laura Rocío; Contreras-Peres, Cudberto; Samayoa, Blanca; Sorrell, Tania C.; Castañeda, Elizabeth; Lockhart, Shawn R.; Engelthaler, David M.; Meyer, Wieland

    2016-01-01

    The emerging pathogen Cryptococcus gattii causes life-threatening disease in immunocompetent and immunocompromised hosts. Of the four major molecular types (VGI-VGIV), the molecular type VGIII has recently emerged as cause of disease in otherwise healthy individuals, prompting a need to investigate its population genetic structure to understand if there are potential genotype-dependent characteristics in its epidemiology, environmental niche(s), host range and clinical features of disease. Multilocus sequence typing (MLST) of 122 clinical, environmental and veterinary C. gattii VGIII isolates from Australia, Colombia, Guatemala, Mexico, New Zealand, Paraguay, USA and Venezuela, and whole genome sequencing (WGS) of 60 isolates representing all established MLST types identified four divergent sub-populations. The majority of the isolates belong to two main clades, corresponding either to serotype B or C, indicating an ongoing species evolution. Both major clades included clinical, environmental and veterinary isolates. The C. gattii VGIII population was genetically highly diverse, with minor differences between countries, isolation source, serotype and mating type. Little to no recombination was found between the two major groups, serotype B and C, at the whole and mitochondrial genome level. C. gattii VGIII is widespread in the Americas, with sporadic cases occurring elsewhere, WGS revealed Mexico and USA as a likely origin of the serotype B VGIII population and Colombia as a possible origin of the serotype C VGIII population. Serotype B isolates are more virulent than serotype C isolates in a murine model of infection, causing predominantly pulmonary cryptococcosis. No specific link between genotype and virulence was observed. Antifungal susceptibility testing against six antifungal drugs revealed that serotype B isolates are more susceptible to azoles than serotype C isolates, highlighting the importance of strain typing to guide effective treatment to improve the

  20. MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors.

    PubMed

    Firacative, Carolina; Roe, Chandler C; Malik, Richard; Ferreira-Paim, Kennio; Escandón, Patricia; Sykes, Jane E; Castañón-Olivares, Laura Rocío; Contreras-Peres, Cudberto; Samayoa, Blanca; Sorrell, Tania C; Castañeda, Elizabeth; Lockhart, Shawn R; Engelthaler, David M; Meyer, Wieland

    2016-08-01

    The emerging pathogen Cryptococcus gattii causes life-threatening disease in immunocompetent and immunocompromised hosts. Of the four major molecular types (VGI-VGIV), the molecular type VGIII has recently emerged as cause of disease in otherwise healthy individuals, prompting a need to investigate its population genetic structure to understand if there are potential genotype-dependent characteristics in its epidemiology, environmental niche(s), host range and clinical features of disease. Multilocus sequence typing (MLST) of 122 clinical, environmental and veterinary C. gattii VGIII isolates from Australia, Colombia, Guatemala, Mexico, New Zealand, Paraguay, USA and Venezuela, and whole genome sequencing (WGS) of 60 isolates representing all established MLST types identified four divergent sub-populations. The majority of the isolates belong to two main clades, corresponding either to serotype B or C, indicating an ongoing species evolution. Both major clades included clinical, environmental and veterinary isolates. The C. gattii VGIII population was genetically highly diverse, with minor differences between countries, isolation source, serotype and mating type. Little to no recombination was found between the two major groups, serotype B and C, at the whole and mitochondrial genome level. C. gattii VGIII is widespread in the Americas, with sporadic cases occurring elsewhere, WGS revealed Mexico and USA as a likely origin of the serotype B VGIII population and Colombia as a possible origin of the serotype C VGIII population. Serotype B isolates are more virulent than serotype C isolates in a murine model of infection, causing predominantly pulmonary cryptococcosis. No specific link between genotype and virulence was observed. Antifungal susceptibility testing against six antifungal drugs revealed that serotype B isolates are more susceptible to azoles than serotype C isolates, highlighting the importance of strain typing to guide effective treatment to improve the

  1. Functional Analysis of GLRX5 Mutants Reveals Distinct Functionalities of GLRX5 Protein.

    PubMed

    Liu, Gang; Wang, Yongwei; Anderson, Gregory J; Camaschella, Clara; Chang, Yanzhong; Nie, Guangjun

    2016-01-01

    Glutaredoxin 5 (GLRX5) is a 156 amino acid mitochondrial protein that plays an essential role in mitochondrial iron-sulfur cluster transfer. Mutations in this protein were reported to result in sideroblastic anemia and variant nonketotic hyperglycinemia in human. Recently, we have characterized a Chinese congenital sideroblastic anemia patient who has two compound heterozygous missense mutations (c. 301 A>C and c. 443 T>C) in his GLRX5 gene. Herein, we developed a GLRX5 knockout K562 cell line and studied the biochemical functions of the identified pathogenic mutations and other conserved amino acids with predicted essential functions. We observed that the K101Q mutation (due to c. 301 A>C mutation) may prevent the binding of [Fe-S] to GLRX5 protein, while L148S (due to c. 443 T>C mutation) may interfere with [Fe-S] transfer from GLRX5 to iron regulatory protein 1 (IRP1), mitochondrial aconitase (m-aconitase) and ferrochelatase. We also demonstrated that L148S is functionally complementary to the K51del mutant with respect to Fe/S-ferrochelatase, Fe/S-IRP1, Fe/S-succinate dehydrogenase, and Fe/S-m-aconitase biosynthesis and lipoylation of pyruvate dehydrogenase complex and α-ketoglutarate dehydrogenase complex. Furthermore, we demonstrated that the mutations of highly conserved amino acid residues in GLRX5 protein can have different effects on downstream Fe/S proteins. Collectively, our current work demonstrates that GLRX5 protein is multifunctional in [Fe-S] protein synthesis and maturation and defects of the different amino acids of the protein will lead to distinct effects on downstream Fe/S biosynthesis. PMID:26100117

  2. Structural Divergence of the Group I Intron Binding Surface in Fungal Mitochondrial Tyrosyl-tRNA Synthetases That Function in RNA Splicing.

    PubMed

    Lamech, Lilian T; Saoji, Maithili; Paukstelis, Paul J; Lambowitz, Alan M

    2016-05-27

    The mitochondrial tyrosyl-tRNA synthetases (mtTyrRSs) of Pezizomycotina fungi, a subphylum that includes many pathogenic species, are bifunctional proteins that both charge mitochondrial tRNA(Tyr) and act as splicing cofactors for autocatalytic group I introns. Previous studies showed that one of these proteins, Neurospora crassa CYT-18, binds group I introns by using both its N-terminal catalytic and C-terminal anticodon binding domains and that the catalytic domain uses a newly evolved group I intron binding surface that includes an N-terminal extension and two small insertions (insertions 1 and 2) with distinctive features not found in non-splicing mtTyrRSs. To explore how this RNA binding surface diverged to accommodate different group I introns in other Pezizomycotina fungi, we determined x-ray crystal structures of C-terminally truncated Aspergillus nidulans and Coccidioides posadasii mtTyrRSs. Comparisons with previous N. crassa CYT-18 structures and a structural model of the Aspergillus fumigatus mtTyrRS showed that the overall topology of the group I intron binding surface is conserved but with variations in key intron binding regions, particularly the Pezizomycotina-specific insertions. These insertions, which arose by expansion of flexible termini or internal loops, show greater variation in structure and amino acids potentially involved in group I intron binding than do neighboring protein core regions, which also function in intron binding but may be more constrained to preserve mtTyrRS activity. Our results suggest a structural basis for the intron specificity of different Pezizomycotina mtTyrRSs, highlight flexible terminal and loop regions as major sites for enzyme diversification, and identify targets for therapeutic intervention by disrupting an essential RNA-protein interaction in pathogenic fungi. PMID:27036943

  3. MHD simple waves and the divergence wave

    SciTech Connect

    Webb, G. M.; Pogorelov, N. V.; Zank, G. P.

    2010-03-25

    In this paper we investigate magnetohydrodynamic (MHD) simple divergence waves in MHD, for models in which nablacentre dotBnot =0. These models are related to the eight wave Riemann solvers in numerical MHD, in which the eighth wave is the divergence wave associated with nablacentre dotBnot =0. For simple wave solutions, all physical variables (the gas density, pressure, fluid velocity, entropy, and magnetic field induction in the MHD case) depend on a single phase function phi. We consider the form of the MHD equations used by both Powell et al. and Janhunen. It is shown that the Janhunen version of the equations possesses fully nonlinear, exact simple wave solutions for the divergence wave, but no physically meaningful simple divergence wave solution exists for the Powell et al. system. We suggest that the 1D simple, divergence wave solution for the Janhunen system, may be useful for the testing and validation of numerical MHD codes.

  4. Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

    PubMed Central

    Bocian-Ostrzycka, Katarzyna M.; Łasica, Anna M.; Dunin-Horkawicz, Stanisław; Grzeszczuk, Magdalena J.; Drabik, Karolina; Dobosz, Aneta M.; Godlewska, Renata; Nowak, Elżbieta; Collet, Jean-Francois; Jagusztyn-Krynicka, Elżbieta K.

    2015-01-01

    Helicobacter pylori does not encode the classical DsbA/DsbB oxidoreductases that are crucial for oxidative folding of extracytoplasmic proteins. Instead, this microorganism encodes an untypical two proteins playing a role in disulfide bond formation – periplasmic HP0231, which structure resembles that of EcDsbC/DsbG, and its redox partner, a membrane protein HpDsbI (HP0595) with a β-propeller structure. The aim of presented work was to assess relations between HP0231 structure and function. We showed that HP0231 is most closely related evolutionarily to the catalytic domain of DsbG, even though it possesses a catalytic motif typical for canonical DsbA proteins. Similarly, the highly diverged N-terminal dimerization domain is homologous to the dimerization domain of DsbG. To better understand the functioning of this atypical oxidoreductase, we examined its activity using in vivo and in vitro experiments. We found that HP0231 exhibits oxidizing and chaperone activities but no isomerizing activity, even though H. pylori does not contain a classical DsbC. We also show that HP0231 is not involved in the introduction of disulfide bonds into HcpC (Helicobacter cysteine-rich protein C), a protein involved in the modulation of the H. pylori interaction with its host. Additionally, we also constructed a truncated version of HP0231 lacking the dimerization domain, denoted HP0231m, and showed that it acts in Escherichia coli cells in a DsbB-dependent manner. In contrast, HP0231m and classical monomeric EcDsbA (E. coli DsbA protein) were both unable to complement the lack of HP0231 in H. pylori cells, though they exist in oxidized forms. HP0231m is inactive in the insulin reduction assay and possesses high chaperone activity, in contrast to EcDsbA. In conclusion, HP0231 combines oxidative functions characteristic of DsbA proteins and chaperone activity characteristic of DsbC/DsbG, and it lacks isomerization activity. PMID:26500620

  5. Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment

    NASA Astrophysics Data System (ADS)

    Chao, Yuanqing; Ma, Liping; Yang, Ying; Ju, Feng; Zhang, Xu-Xiang; Wu, Wei-Min; Zhang, Tong

    2013-12-01

    The metagenomic approach was applied to characterize variations of microbial structure and functions in raw (RW) and treated water (TW) in a drinking water treatment plant (DWTP) at Pearl River Delta, China. Microbial structure was significantly influenced by the treatment processes, shifting from Gammaproteobacteria and Betaproteobacteria in RW to Alphaproteobacteria in TW. Further functional analysis indicated the basic metabolic functions of microorganisms in TW did not vary considerably. However, protective functions, i.e. glutathione synthesis genes in `oxidative stress' and `detoxification' subsystems, significantly increased, revealing the surviving bacteria may have higher chlorine resistance. Similar results were also found in glutathione metabolism pathway, which identified the major reaction for glutathione synthesis and supported more genes for glutathione metabolism existed in TW. This metagenomic study largely enhanced our knowledge about the influences of treatment processes, especially chlorination, on bacterial community structure and protective functions (e.g. glutathione metabolism) in ecosystems of DWTPs.

  6. Dynamic functional network connectivity reveals unique and overlapping profiles of insula subdivisions.

    PubMed

    Nomi, Jason S; Farrant, Kristafor; Damaraju, Eswar; Rachakonda, Srinivas; Calhoun, Vince D; Uddin, Lucina Q

    2016-05-01

    The human insular cortex consists of functionally diverse subdivisions that engage during tasks ranging from interoception to cognitive control. The multiplicity of functions subserved by insular subdivisions calls for a nuanced investigation of their functional connectivity profiles. Four insula subdivisions (dorsal anterior, dAI; ventral, VI; posterior, PI; middle, MI) derived using a data-driven approach were subjected to static- and dynamic functional network connectivity (s-FNC and d-FNC) analyses. Static-FNC analyses replicated previous work demonstrating a cognition-emotion-interoception division of the insula, where the dAI is functionally connected to frontal areas, the VI to limbic areas, and the PI and MI to sensorimotor areas. Dynamic-FNC analyses consisted of k-means clustering of sliding windows to identify variable insula connectivity states. The d-FNC analysis revealed that the most frequently occurring dynamic state mirrored the cognition-emotion-interoception division observed from the s-FNC analysis, with less frequently occurring states showing overlapping and unique subdivision connectivity profiles. In two of the states, all subdivisions exhibited largely overlapping profiles, consisting of subcortical, sensory, motor, and frontal connections. Two other states showed the dAI exhibited a unique connectivity profile compared with other insula subdivisions. Additionally, the dAI exhibited the most variable functional connections across the s-FNC and d-FNC analyses, and was the only subdivision to exhibit dynamic functional connections with regions of the default mode network. These results highlight how a d-FNC approach can capture functional dynamics masked by s-FNC approaches, and reveal dynamic functional connections enabling the functional flexibility of the insula across time. Hum Brain Mapp 37:1770-1787, 2016. © 2016 Wiley Periodicals, Inc. PMID:26880689

  7. Systems-Based Analyses of Brain Regions Functionally Impacted in Parkinson's Disease Reveals Underlying Causal Mechanisms

    PubMed Central

    Emig-Agius, Dorothea; Bessarabova, Marina; Ivliev, Alexander E.; Schüle, Birgit; Alexander, Jeff; Wallace, William; Halliday, Glenda M.; Langston, J. William; Braxton, Scott; Yednock, Ted; Shaler, Thomas; Johnston, Jennifer A.

    2014-01-01

    Detailed analysis of disease-affected tissue provides insight into molecular mechanisms contributing to pathogenesis. Substantia nigra, striatum, and cortex are functionally connected with increasing degrees of alpha-synuclein pathology in Parkinson's disease. We undertook functional and causal pathway analysis of gene expression and proteomic alterations in these three regions, and the data revealed pathways that correlated with disease progression. In addition, microarray and RNAseq experiments revealed previously unidentified causal changes related to oligodendrocyte function and synaptic vesicle release, and these and other changes were reflected across all brain regions. Importantly, subsets of these changes were replicated in Parkinson's disease blood; suggesting peripheral tissue may provide important avenues for understanding and measuring disease status and progression. Proteomic assessment revealed alterations in mitochondria and vesicular transport proteins that preceded gene expression changes indicating defects in translation and/or protein turnover. Our combined approach of proteomics, RNAseq and microarray analyses provides a comprehensive view of the molecular changes that accompany functional loss and alpha-synuclein pathology in Parkinson's disease, and may be instrumental to understand, diagnose and follow Parkinson's disease progression. PMID:25170892

  8. Functional Redundancy Patterns Reveal Non-Random Assembly Rules in a Species-Rich Marine Assemblage

    PubMed Central

    Guillemot, Nicolas; Kulbicki, Michel; Chabanet, Pascale; Vigliola, Laurent

    2011-01-01

    The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species. PMID:22039543

  9. Genetic Interaction Maps in Escherichia coli Reveal Functional Crosstalk among Cell Envelope Biogenesis Pathways

    PubMed Central

    Vlasblom, James; Gagarinova, Alla; Phanse, Sadhna; Graham, Chris; Yousif, Fouad; Ding, Huiming; Xiong, Xuejian; Nazarians-Armavil, Anaies; Alamgir, Md; Ali, Mehrab; Pogoutse, Oxana; Pe'er, Asaf; Arnold, Roland; Michaut, Magali; Parkinson, John; Golshani, Ashkan; Whitfield, Chris; Wodak, Shoshana J.; Moreno-Hagelsieb, Gabriel; Greenblatt, Jack F.; Emili, Andrew

    2011-01-01

    As the interface between a microbe and its environment, the bacterial cell envelope has broad biological and clinical significance. While numerous biosynthesis genes and pathways have been identified and studied in isolation, how these intersect functionally to ensure envelope integrity during adaptive responses to environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens to generate quantitative functional association maps encompassing virtually the entire cell envelope biosynthetic machinery of Escherichia coli under both auxotrophic (rich medium) and prototrophic (minimal medium) culture conditions. The differential patterns of genetic interactions detected among >235,000 digenic mutant combinations tested reveal unexpected condition-specific functional crosstalk and genetic backup mechanisms that ensure stress-resistant envelope assembly and maintenance. These networks also provide insights into the global systems connectivity and dynamic functional reorganization of a universal bacterial structure that is both broadly conserved among eubacteria (including pathogens) and an important target. PMID:22125496

  10. Modelling NifH2 protein of Clostridium pasteurianum reveals clues about its physiological function.

    PubMed

    Kasap, Murat

    2006-11-01

    Clostridium pasteurianum is an anaerobic free-living nitrogen fixer. As a unique feature, the organism contains five extra nifH-like genes in addition to nifH1. Detailed analysis with respect to the structure and function of the nifH-like gene products is missing due to the lack of information about the presence of their translation products in the cell. Recent work indicates that the nifH2 gene is transcribed and translated into a polypeptide of expected size in nitrogen-fixing cells of C. pasteurianum and is regulated both at the transcriptional and translational levels. However, the current data do not reveal the physiological function of the NifH2 protein. In this study, we have used computer tools and the NifH1 of C. pasteurianum as the template to predict a possible tertiary structure and assign a putative function for NifH2 protein. A comparison of the structures of the NifH1 and modelled NifH2 revealed similarities in the polypeptide conformations for both monomers. Analysis of the properties of nucleotide binding, dimer interacting and cluster containing regions did not reveal major differences between NifH1 and modelled NifH2, although minor differences were observed. Rigid docking results revealed the possibility of formation of a NifH1-NifH2 heterodimer as well as formation of a NifH2 homodimer. We, therefore, propose that NifH2 can form a dimer with NifH1, albeit less efficiently and may function as a regulatory Fe-protein. PMID:16495101

  11. Primate molecular divergence dates.

    PubMed

    Steiper, Michael E; Young, Nathan M

    2006-11-01

    With genomic data, alignments can be assembled that greatly increase the number of informative sites for analysis of molecular divergence dates. Here, we present an estimate of the molecular divergence dates for all of the major primate groups. These date estimates are based on a Bayesian analysis of approximately 59.8 kbp of genomic data from 13 primates and 6 mammalian outgroups, using a range of paleontologically supported calibration estimates. Results support a Cretaceous last common ancestor of extant primates (approximately 77 mya), an Eocene divergence between platyrrhine and catarrhine primates (approximately 43 mya), an Oligocene origin of apes and Old World monkeys (approximately 31 mya), and an early Miocene (approximately 18 mya) divergence of Asian and African great apes. These dates are examined in the context of other molecular clock studies. PMID:16815047

  12. Using Common Spatial Distributions of Atoms to Relate Functionally Divergent Influenza Virus N10 and N11 Protein Structures to Functionally Characterized Neuraminidase Structures, Toxin Cell Entry Domains, and Non-Influenza Virus Cell Entry Domains

    PubMed Central

    Weininger, Arthur; Weininger, Susan

    2015-01-01

    The ability to identify the functional correlates of structural and sequence variation in proteins is a critical capability. We related structures of influenza A N10 and N11 proteins that have no established function to structures of proteins with known function by identifying spatially conserved atoms. We identified atoms with common distributed spatial occupancy in PDB structures of N10 protein, N11 protein, an influenza A neuraminidase, an influenza B neuraminidase, and a bacterial neuraminidase. By superposing these spatially conserved atoms, we aligned the structures and associated molecules. We report spatially and sequence invariant residues in the aligned structures. Spatially invariant residues in the N6 and influenza B neuraminidase active sites were found in previously unidentified spatially equivalent sites in the N10 and N11 proteins. We found the corresponding secondary and tertiary structures of the aligned proteins to be largely identical despite significant sequence divergence. We found structural precedent in known non-neuraminidase structures for residues exhibiting structural and sequence divergence in the aligned structures. In N10 protein, we identified staphylococcal enterotoxin I-like domains. In N11 protein, we identified hepatitis E E2S-like domains, SARS spike protein-like domains, and toxin components shared by alpha-bungarotoxin, staphylococcal enterotoxin I, anthrax lethal factor, clostridium botulinum neurotoxin, and clostridium tetanus toxin. The presence of active site components common to the N6, influenza B, and S. pneumoniae neuraminidases in the N10 and N11 proteins, combined with the absence of apparent neuraminidase function, suggests that the role of neuraminidases in H17N10 and H18N11 emerging influenza A viruses may have changed. The presentation of E2S-like, SARS spike protein-like, or toxin-like domains by the N10 and N11 proteins in these emerging viruses may indicate that H17N10 and H18N11 sialidase-facilitated cell

  13. Using common spatial distributions of atoms to relate functionally divergent influenza virus N10 and N11 protein structures to functionally characterized neuraminidase structures, toxin cell entry domains, and non-influenza virus cell entry domains.

    PubMed

    Weininger, Arthur; Weininger, Susan

    2015-01-01

    The ability to identify the functional correlates of structural and sequence variation in proteins is a critical capability. We related structures of influenza A N10 and N11 proteins that have no established function to structures of proteins with known function by identifying spatially conserved atoms. We identified atoms with common distributed spatial occupancy in PDB structures of N10 protein, N11 protein, an influenza A neuraminidase, an influenza B neuraminidase, and a bacterial neuraminidase. By superposing these spatially conserved atoms, we aligned the structures and associated molecules. We report spatially and sequence invariant residues in the aligned structures. Spatially invariant residues in the N6 and influenza B neuraminidase active sites were found in previously unidentified spatially equivalent sites in the N10 and N11 proteins. We found the corresponding secondary and tertiary structures of the aligned proteins to be largely identical despite significant sequence divergence. We found structural precedent in known non-neuraminidase structures for residues exhibiting structural and sequence divergence in the aligned structures. In N10 protein, we identified staphylococcal enterotoxin I-like domains. In N11 protein, we identified hepatitis E E2S-like domains, SARS spike protein-like domains, and toxin components shared by alpha-bungarotoxin, staphylococcal enterotoxin I, anthrax lethal factor, clostridium botulinum neurotoxin, and clostridium tetanus toxin. The presence of active site components common to the N6, influenza B, and S. pneumoniae neuraminidases in the N10 and N11 proteins, combined with the absence of apparent neuraminidase function, suggests that the role of neuraminidases in H17N10 and H18N11 emerging influenza A viruses may have changed. The presentation of E2S-like, SARS spike protein-like, or toxin-like domains by the N10 and N11 proteins in these emerging viruses may indicate that H17N10 and H18N11 sialidase-facilitated cell

  14. Dynamic changes in network synchrony reveal resting-state functional networks

    NASA Astrophysics Data System (ADS)

    Vuksanović, Vesna; Hövel, Philipp

    2015-02-01

    Experimental functional magnetic resonance imaging studies have shown that spontaneous brain activity, i.e., in the absence of any external input, exhibit complex spatial and temporal patterns of co-activity between segregated brain regions. These so-called large-scale resting-state functional connectivity networks represent dynamically organized neural assemblies interacting with each other in a complex way. It has been suggested that looking at the dynamical properties of complex patterns of brain functional co-activity may reveal neural mechanisms underlying the dynamic changes in functional interactions. Here, we examine how global network dynamics is shaped by different network configurations, derived from realistic brain functional interactions. We focus on two main dynamics measures: synchrony and variations in synchrony. Neural activity and the inferred hemodynamic response of the network nodes are simulated using a system of 90 FitzHugh-Nagumo neural models subject to system noise and time-delayed interactions. These models are embedded into the topology of the complex brain functional interactions, whose architecture is additionally reduced to its main structural pathways. In the simulated functional networks, patterns of correlated regional activity clearly arise from dynamical properties that maximize synchrony and variations in synchrony. Our results on the fast changes of the level of the network synchrony also show how flexible changes in the large-scale network dynamics could be.

  15. Expression Divergence of Duplicate Genes in the Protein Kinase Superfamily in Pacific Oyster.

    PubMed

    Gao, Dahai; Ko, Dennis C; Tian, Xinmin; Yang, Guang; Wang, Liuyang

    2015-01-01

    Gene duplication has been proposed to serve as the engine of evolutionary innovation. It is well recognized that eukaryotic genomes contain a large number of duplicated genes that evolve new functions or expression patterns. However, in mollusks, the evolutionary mechanisms underlying the divergence and the functional maintenance of duplicate genes remain little understood. In the present study, we performed a comprehensive analysis of duplicate genes in the protein kinase superfamily using whole genome and transcriptome data for the Pacific oyster. A total of 64 duplicated gene pairs were identified based on a phylogenetic approach and the reciprocal best BLAST method. By analyzing gene expression from RNA-seq data from 69 different developmental and stimuli-induced conditions (nine tissues, 38 developmental stages, eight dry treatments, seven heat treatments, and seven salty treatments), we found that expression patterns were significantly correlated for a number of duplicate gene pairs, suggesting the conservation of regulatory mechanisms following divergence. Our analysis also identified a subset of duplicate gene pairs with very high expression divergence, indicating that these gene pairs may have been subjected to transcriptional subfunctionalization or neofunctionalization after the initial duplication events. Further analysis revealed a significant correlation between expression and sequence divergence (as revealed by synonymous or nonsynonymous substitution rates) under certain conditions. Taken together, these results provide evidence for duplicate gene sequence and expression divergence in the Pacific oyster, accompanying its adaptation to harsh environments. Our results provide new insights into the evolution of duplicate genes and their expression levels in the Pacific oyster. PMID:26417197

  16. Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

    PubMed

    Ferreira, Ari J S; Siam, Rania; Setubal, João C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A C; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B; El-Dorry, Hamza

    2014-01-01

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. PMID:24921648

  17. Core Microbial Functional Activities in Ocean Environments Revealed by Global Metagenomic Profiling Analyses

    PubMed Central

    Ferreira, Ari J. S.; Siam, Rania; Setubal, João C.; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S.; Dawe, Adam S.; Ghazy, Mohamed A.; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M.; Lehvaslaiho, Heikki; Ramadan, Eman; Antunes, André; Stingl, Ulrich; Archer, John A. C.; Jankovic, Boris R.; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

    2014-01-01

    Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light. PMID:24921648

  18. Divergence of Biochemical Function in the HAD Superfamily: D-Glycero-D-manno-heptose 1,7-bisphosphate Phosphatase, GmhB

    PubMed Central

    Wang, Liangbing; Huang, Hua; Nguyen, Henry; Allen, Karen N.; Mariano, Patrick S.; Dunaway-Mariano, Debra

    2010-01-01

    D-Glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB) is a member of the histidinol-phosphate phosphatase (HisB) subfamily of the Haloalkanoic Acid Dehalogenase (HAD) enzyme superfamily. GmhB supports two divergent biochemical pathways in bacteria: the D-glycero-D-manno-heptose-1α-GDP pathway (in S-layer glycoprotein biosynthesis) and the L-glycero-D-manno-heptose-1β-ADP pathway (in lipid A biosynthesis). Herein, we report the comparative analysis of substrate recognition in selected GmhB orthologs. The substrate specificity of the L-glycero-D-manno-heptose-1β-ADP pathway GmhB from Escherichia coli K-12 was evaluated using hexose- and heptose-bisphosphates, histinol-phosphate and common organophosphate metabolites. Only D-glycero-D-manno-heptose-1β,7-bisphosphate (kcat/Km = 7 × 106 M−1 s−1) and D-glycero-D-manno-heptose-1α,7-bisphosphate (kcat/Km = 7 × 104 M−1 s−1) displayed physiologically significant substrate activity. 31P-NMR analysis demonstrated that E. coli GmhB selectively removes the C(7)phosphate. Steady-state kinetic inhibition studies showed that D-glycero-D-manno-heptose-1β-phosphate (Kis = 60 μM, Kii = 150 μM) and histidinol-phosphate (Kis= 1 mM and Kii = 6 mM) while not hydrolyzed, do in fact bind to E. coli GmhB, which leads to the conclusion that nonproductive binding contributes to substrate discrimination. High catalytic efficiency and a narrow substrate range are characteristic of a well-evolved metabolic enzyme and, as such, E. coli GmhB is set apart from most HAD phosphatases (which are typically inefficient and promiscuous). The specialization of the biochemical function of GmhB was examined by measuring the kinetic constants for hydrolysis of the α- and β-anomers of D-glycero-D-manno-heptose-1β,7-bisphosphate catalyzed by the GmhB orthologs of the L-glycero-D-manno heptose 1β-ADP pathways operative in Bordetella bronchiseptica and Mesorhizobium loti and by the GmhB of the D-glycero-D-manno-heptose-1

  19. An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.

    PubMed

    Jin, Jinpu; He, Kun; Tang, Xing; Li, Zhe; Lv, Le; Zhao, Yi; Luo, Jingchu; Gao, Ge

    2015-07-01

    Transcription factors (TFs) play key roles in both development and stress responses. By integrating into and rewiring original systems, novel TFs contribute significantly to the evolution of transcriptional regulatory networks. Here, we report a high-confidence transcriptional regulatory map covering 388 TFs from 47 families in Arabidopsis. Systematic analysis of this map revealed the architectural heterogeneity of developmental and stress response subnetworks and identified three types of novel network motifs that are absent from unicellular organisms and essential for multicellular development. Moreover, TFs of novel families that emerged during plant landing present higher binding specificities and are preferentially wired into developmental processes and these novel network motifs. Further unveiled connection between the binding specificity and wiring preference of TFs explains the wiring preferences of novel-family TFs. These results reveal distinct functional and evolutionary features of novel TFs, suggesting a plausible mechanism for their contribution to the evolution of multicellular organisms. PMID:25750178

  20. Bubble Divergences from Twisted Cohomology

    NASA Astrophysics Data System (ADS)

    Bonzom, Valentin; Smerlak, Matteo

    2012-06-01

    We consider a class of lattice topological field theories, among which are the weak-coupling limit of 2d Yang-Mills theory and 3d Riemannian quantum gravity, whose dynamical variables are flat discrete connections with compact structure group on a cell 2-complex. In these models, it is known that the path integral measure is ill-defined because of a phenomenon known as `bubble divergences'. In this paper, we extend recent results of the authors to the cases where these divergences cannot be understood in terms of cellular cohomology. We introduce in its place the relevant twisted cohomology, and use it to compute the divergence degree of the partition function. We also relate its dominant part to the Reidemeister torsion of the complex, thereby generalizing previous results of Barrett and Naish-Guzman. The main limitation to our approach is the presence of singularities in the representation variety of the fundamental group of the complex; we illustrate this issue in the well-known case of two-dimensional manifolds.

  1. Maps on Quantum States Preserving Bregman and Jensen Divergences

    NASA Astrophysics Data System (ADS)

    Virosztek, Dániel

    2016-09-01

    We describe the structure of the bijective transformations on the set of density operators which preserve the Bregman f-divergence for an arbitrary differentiable strictly convex function f. Furthermore, we determine the preservers of the Jensen f-divergence in the case when the generating function f belongs to a recently introduced function class called Matrix Entropy Class.

  2. Structural and functional analysis of amphioxus HIFα reveals ancient features of the HIFα family.

    PubMed

    Gao, Shan; Lu, Ling; Bai, Yan; Zhang, Peng; Song, Weibo; Duan, Cunming

    2014-04-01

    Hypoxia-inducible factors (HIFs) are master regulators of the transcriptional response to hypoxia. To gain insight into the structural and functional evolution of the HIF family, we characterized the HIFα gene from amphioxus, an invertebrate chordate, and identified several alternatively spliced HIFα isoforms. Whereas HIFα Ia, the full-length isoform, contained a complete oxygen-dependent degradation (ODD) domain, the isoforms Ib, Ic, and Id had 1 or 2 deletions in the ODD domain. When tagged with GFP and tested in mammalian cells, the amphioxus HIFα Ia protein level increased in response to hypoxia or CoCl2 treatment, whereas HIFα Ib, Ic, and Id showed reduced or no hypoxia regulation. Deletion of the ODD sequence in HIFα Ia up-regulated the HIFα Ia levels under normoxia. Gene expression analysis revealed HIFα Ic to be the predominant isoform in embryos and larvae, whereas isoform Ia was the most abundant form in the adult stage. The expression levels of Ib and Id were very low. Hypoxia treatment of adults had no effect on the mRNA levels of these HIFα isoforms. Functional analyses in mammalian cells showed all 4 HIFα isoforms capable of entering the nucleus and activating hypoxia response element-dependent reporter gene expression. The functional nuclear location signal (NLS) mapped to 3 clusters of basic residues. (775)KKARL functioned as the primary NLS, but (737)KRK and (754)KK also contributed to the nuclear localization. All amphioxus HIFα isoforms had 2 functional transactivation domains (TADs). Its C-terminal transactivation (C-TAD) shared high sequence identity with the human HIF-1α and HIF-2α C-TAD. This domain contained a conserved asparagine, and its mutation resulted in an increase in transcriptional activity. These findings reveal many ancient features of the HIFα family and provide novel insights into the evolution of the HIFα family. PMID:24174425

  3. Divergence and Convergence in Enzyme Evolution*

    PubMed Central

    Galperin, Michael Y.; Koonin, Eugene V.

    2012-01-01

    Comparative analysis of the sequences of enzymes encoded in a variety of prokaryotic and eukaryotic genomes reveals convergence and divergence at several levels. Functional convergence can be inferred when structurally distinct and hence non-homologous enzymes show the ability to catalyze the same biochemical reaction. In contrast, as a result of functional diversification, many structurally similar enzyme molecules act on substantially distinct substrates and catalyze diverse biochemical reactions. Here, we present updates on the ATP-grasp, alkaline phosphatase, cupin, HD hydrolase, and N-terminal nucleophile (Ntn) hydrolase enzyme superfamilies and discuss the patterns of sequence and structural conservation and diversity within these superfamilies. Typically, enzymes within a superfamily possess common sequence motifs and key active site residues, as well as (predicted) reaction mechanisms. These observations suggest that the strained conformation (the entatic state) of the active site, which is responsible for the substrate binding and formation of the transition complex, tends to be conserved within enzyme superfamilies. The subsequent fate of the transition complex is not necessarily conserved and depends on the details of the structures of the enzyme and the substrate. This variability of reaction outcomes limits the ability of sequence analysis to predict the exact enzymatic activities of newly sequenced gene products. Nevertheless, sequence-based (super)family assignments and generic functional predictions, even if imprecise, provide valuable leads for experimental studies and remain the best approach to the functional annotation of uncharacterized proteins from new genomes. PMID:22069324

  4. Genome-wide search for eliminylating domains reveals novel function for BLES03-like proteins.

    PubMed

    Khater, Shradha; Mohanty, Debasisa

    2014-08-01

    Bacterial phosphothreonine lyases catalyze a novel posttranslational modification involving formation of dehydrobutyrine/dehyroalanine by β elimination of the phosphate group of phosphothreonine or phosphoserine residues in their substrate proteins. Though there is experimental evidence for presence of dehydro amino acids in human proteins, no eukaryotic homologs of these lyases have been identified as of today. A comprehensive genome-wide search for identifying phosphothreonine lyase homologs in eukaryotes was carried out. Our fold-based search revealed structural and catalytic site similarity between bacterial phosphothreonine lyases and BLES03 (basophilic leukemia-expressed protein 03), a human protein with unknown function. Ligand induced conformational changes similar to bacterial phosphothreonine lyases, and movement of crucial arginines in the loop region to the catalytic pocket upon binding of phosphothreonine-containing peptides was seen during docking and molecular dynamics studies. Genome-wide search for BLES03 homologs using sensitive profile-based methods revealed their presence not only in eukaryotic classes such as chordata and fungi but also in bacterial and archaebacterial classes. The synteny of these archaebacterial BLES03-like proteins was remarkably similar to that of type IV lantibiotic synthetases which harbor LanL-like phosphothreonine lyase domains. Hence, context-based analysis reinforced our earlier sequence/structure-based prediction of phosphothreonine lyase catalytic function for BLES03. Our in silico analysis has revealed that BLES03-like proteins with previously unknown function are novel eukaryotic phosphothreonine lyases involved in biosynthesis of dehydro amino acids, whereas their bacterial and archaebacterial counterparts might be involved in biosynthesis of natural products similar to lantibiotics. PMID:25062915

  5. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession

    NASA Astrophysics Data System (ADS)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-01

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth’s biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  6. Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves.

    PubMed

    Schweizer, Rena M; Robinson, Jacqueline; Harrigan, Ryan; Silva, Pedro; Galverni, Marco; Musiani, Marco; Green, Richard E; Novembre, John; Wayne, Robert K

    2016-01-01

    In an era of ever-increasing amounts of whole-genome sequence data for individuals and populations, the utility of traditional single nucleotide polymorphisms (SNPs) array-based genome scans is uncertain. We previously performed a SNP array-based genome scan to identify candidate genes under selection in six distinct grey wolf (Canis lupus) ecotypes. Using this information, we designed a targeted capture array for 1040 genes, including all exons and flanking regions, as well as 5000 1-kb nongenic neutral regions, and resequenced these regions in 107 wolves. Selection tests revealed striking patterns of variation within candidate genes relative to noncandidate regions and identified potentially functional variants related to local adaptation. We found 27% and 47% of candidate genes from the previous SNP array study had functional changes that were outliers in sweed and bayenv analyses, respectively. This result verifies the use of genomewide SNP surveys to tag genes that contain functional variants between populations. We highlight nonsynonymous variants in APOB, LIPG and USH2A that occur in functional domains of these proteins, and that demonstrate high correlation with precipitation seasonality and vegetation. We find Arctic and High Arctic wolf ecotypes have higher numbers of genes under selection, which highlight their conservation value and heightened threat due to climate change. This study demonstrates that combining genomewide genotyping arrays with large-scale resequencing and environmental data provides a powerful approach to discern candidate functional variants in natural populations. PMID:26562361

  7. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession

    PubMed Central

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-01-01

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth’s biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession. PMID:25943705

  8. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

    PubMed

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-01-01

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession. PMID:25943705

  9. Genome-wide survey and expression analysis of the bHLH-PAS genes in the amphioxus Branchiostoma floridae reveal both conserved and diverged expression patterns between cephalochordates and vertebrates

    PubMed Central

    2014-01-01

    Background The bHLH-PAS transcription factors are found in both protostomes and deuterostomes. They are involved in many developmental and physiological processes, including regional differentiation of the central nervous system, tube-formation, hypoxia signaling, aromatic hydrocarbon sensing, and circadian rhythm regulation. To understand the evolution of these genes in chordates, we analyzed the bHLH-PAS genes of the basal chordate amphioxus (Branchiostoma floridae). Results From the amphioxus draft genome database, we identified ten bHLH-PAS genes, nine of which could be assigned to known orthologous families. The tenth bHLH-PAS gene could not be assigned confidently to any known bHLH family; however, phylogenetic analysis clustered this gene with arthropod Met family genes and two spiralian bHLH-PAS-containing sequences, suggesting that they may share the same ancestry. We examined temporal and spatial expression patterns of these bHLH-PAS genes in developing amphioxus embryos. We found that BfArnt, BfNcoa, BfSim, and BfHifα were expressed in the central nervous system in patterns similar to those of their vertebrate homologs, suggesting that their functions may be conserved. By contrast, the amphioxus BfAhr and BfNpas4 had expression patterns distinct from those in vertebrates. These results imply that there were changes in gene regulation after the divergence of cephalochordates and vertebrates. Conclusions We have identified ten bHLH-PAS genes from the amphioxus genome and determined the embryonic expression profiles for these genes. In addition to the nine currently recognized bHLH-PAS families, our survey suggests that the BfbHLHPAS-orphan gene along with arthropod Met genes and the newly identified spiralian bHLH-PAS-containing sequences represent an ancient group of genes that were lost in the vertebrate lineage. In a comparison with the expression patterns of the vertebrate bHLH-PAS paralogs, which are the result of whole-genome duplication, we found

  10. Functional splicing network reveals extensive regulatory potential of the core spliceosomal machinery.

    PubMed

    Papasaikas, Panagiotis; Tejedor, J Ramón; Vigevani, Luisa; Valcárcel, Juan

    2015-01-01

    Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the effect of knocking down the components of the splicing machinery on alternative splicing events relevant for cell proliferation and apoptosis and used this information to reconstruct a network of functional interactions. The network accurately captures known physical and functional associations and identifies new ones, revealing remarkable regulatory potential of core spliceosomal components, related to the order and duration of their recruitment during spliceosome assembly. In contrast with standard models of regulation at early steps of splice site recognition, factors involved in catalytic activation of the spliceosome display regulatory properties. The network also sheds light on the antagonism between hnRNP C and U2AF, and on targets of antitumor drugs, and can be widely used to identify mechanisms of splicing regulation. PMID:25482510

  11. Novel aspects of COP9 signalosome functions revealed through analysis of hypomorphic csn mutants

    PubMed Central

    Parker, Jane E

    2009-01-01

    The COP9 signalosome (CSN) is a conserved eukaryotic protein complex implicated in the regulation of cullin-RING type E3 ubiquitin ligases by cleaving the small peptide RUB/Nedd8 from cullins. However, detailed analysis of CSN physiological functions in Arabidopsis has been hampered by the early seedling-lethality of csn null mutants. We and others have now identified a number of viable hypomorphic csn mutants which start to reveal novel CSN-dependent activities in adult Arabidopsis plants.1 Here, we present a detailed comparative analysis of the csn5a-1 and csn2-5 mutants as a mean to improve understanding of CSN functions in plant cells. Our observations point to CSN-independent activities of CSN5 and suggest a role of the CSN in cytoskeleton assembly/organization. PMID:19847120

  12. Conditional Epistatic Interaction Maps Reveal Global Functional Rewiring of Genome Integrity Pathways in Escherichia coli.

    PubMed

    Kumar, Ashwani; Beloglazova, Natalia; Bundalovic-Torma, Cedoljub; Phanse, Sadhna; Deineko, Viktor; Gagarinova, Alla; Musso, Gabriel; Vlasblom, James; Lemak, Sofia; Hooshyar, Mohsen; Minic, Zoran; Wagih, Omar; Mosca, Roberto; Aloy, Patrick; Golshani, Ashkan; Parkinson, John; Emili, Andrew; Yakunin, Alexander F; Babu, Mohan

    2016-01-26

    As antibiotic resistance is increasingly becoming a public health concern, an improved understanding of the bacterial DNA damage response (DDR), which is commonly targeted by antibiotics, could be of tremendous therapeutic value. Although the genetic components of the bacterial DDR have been studied extensively in isolation, how the underlying biological pathways interact functionally remains unclear. Here, we address this by performing systematic, unbiased, quantitative synthetic genetic interaction (GI) screens and uncover widespread changes in the GI network of the entire genomic integrity apparatus of Escherichia coli under standard and DNA-damaging growth conditions. The GI patterns of untreated cultures implicated two previously uncharacterized proteins (YhbQ and YqgF) as nucleases, whereas reorganization of the GI network after DNA damage revealed DDR roles for both annotated and uncharacterized genes. Analyses of pan-bacterial conservation patterns suggest that DDR mechanisms and functional relationships are near universal, highlighting a modular and highly adaptive genomic stress response. PMID:26774489

  13. Single-cell analysis reveals functionally distinct classes within the planarian stem cell compartment

    PubMed Central

    van Wolfswinkel, Josien C.; Wagner, Daniel E.; Reddien, Peter W.

    2014-01-01

    Planarians are flatworms capable of regenerating any missing body region. This capacity is mediated by neoblasts, a proliferative cell population that contains pluripotent stem cells. Although population-based studies have revealed many neoblast characteristics, whether functionally distinct classes exist within this population is unclear. Here, we used high-dimensional single-cell transcriptional profiling from over a thousand individual neoblasts to directly compare gene expression fingerprints during homeostasis and regeneration. We identified two prominent neoblast classes that we named ζ (zeta) and σ (sigma). Zeta-neoblasts encompass specified cells that give rise to an abundant postmitotic lineage including epidermal cells, and are not required for regeneration. By contrast, sigma-neoblasts proliferate in response to injury, possess broad lineage capacity, and can give rise to zeta-neoblasts. These findings present a new view of planarian neoblasts, in which the population is comprised of two major and functionally distinct cellular compartments. PMID:25017721

  14. Genetic Variability and Divergence in Grayling, THYMALLUS ARCTICUS

    PubMed Central

    Lynch, J. C.; Vyse, E. R.

    1979-01-01

    In North America there are two disjunct forms of grayling, Montana and arctic, which have been separated for approximately 75,000 to 100,000 years. Electrophoretic analysis of thirty-six protein loci in these forms has revealed: (1) levels of gene duplication comparable to other salmonids, (2) a level of heterozygosity similar to other salmonids, (3) a fast and a slow evolving set of proteins, and (4) no obvious relationship between genetic variability and enzyme function. The genetic divergence between these populations may warrant subspecific designations for these two forms. PMID:499766

  15. Protease proteomics: revealing protease in vivo functions using systems biology approaches.

    PubMed

    Doucet, Alain; Overall, Christopher M

    2008-10-01

    Proteases irreversibly modify proteins by cleaving their amide bonds and are implicated in virtually every important biological process such as immunity, development and tissue repair. Accordingly, it is easy to see that deregulated proteolysis is a pathognomic feature of many diseases. Most of the current information available on proteases was acquired using in vitro methods, which reveals molecular structure, enzyme kinetics and active-site specificity. However, considerably less is known about the relevant biological functions and combined roles of proteases in moulding the proteome. Although models using genetically modified animals are powerful, they are slow to develop, they can be difficult to interpret, and while useful, they remain only models of human disease. Therefore, to understand how proteases accomplish their tasks in organisms and how they participate in pathology, we need to elucidate the protease degradome-the repertoire of proteases expressed by a cell, a tissue or an organism at a particular time-their expression level, activation state, their biological substrates, also known as the substrate degradome-the repertoire of substrates for each protease-and the effect of the activity of each protease on the pathways of the system under study. Achieving this goal is challenging because several proteases might cleave the same protein, and proteases also form pathways and interact to form the protease web [Overall, C.M., Kleifeld, O., 2006. Tumour microenvironment - opinion: validating matrix metalloproteinases as drug targets and anti-targets for cancer therapy. Nat. Rev. Cancer 6 (3), 227-239]. Hence, the net proteolytic potential of the degradome at a particular time on a substrate and pathway must also be understood. Proteomics offers one of the few routes to the understanding of proteolysis in complex in vivo systems and especially in man where genetic manipulations are impossible. The aim of this chapter is to review methods and tools that allow

  16. Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function.

    PubMed

    Arda, H Efsun; Li, Lingyu; Tsai, Jennifer; Torre, Eduardo A; Rosli, Yenny; Peiris, Heshan; Spitale, Robert C; Dai, Chunhua; Gu, Xueying; Qu, Kun; Wang, Pei; Wang, Jing; Grompe, Markus; Scharfmann, Raphael; Snyder, Michael S; Bottino, Rita; Powers, Alvin C; Chang, Howard Y; Kim, Seung K

    2016-05-10

    Intensive efforts are focused on identifying regulators of human pancreatic islet cell growth and maturation to accelerate development of therapies for diabetes. After birth, islet cell growth and function are dynamically regulated; however, establishing these age-dependent changes in humans has been challenging. Here, we describe a multimodal strategy for isolating pancreatic endocrine and exocrine cells from children and adults to identify age-dependent gene expression and chromatin changes on a genomic scale. These profiles revealed distinct proliferative and functional states of islet α cells or β cells and histone modifications underlying age-dependent gene expression changes. Expression of SIX2 and SIX3, transcription factors without prior known functions in the pancreas and linked to fasting hyperglycemia risk, increased with age specifically in human islet β cells. SIX2 and SIX3 were sufficient to enhance insulin content or secretion in immature β cells. Our work provides a unique resource to study human-specific regulators of islet cell maturation and function. PMID:27133132

  17. Separable roles of UFO during floral development revealed by conditional restoration of gene function.

    PubMed

    Laufs, Patrick; Coen, Enrico; Kronenberger, Jocelyne; Traas, Jan; Doonan, John

    2003-02-01

    The UNUSUAL FLORAL ORGANS (UFO) gene is required for several aspects of floral development in Arabidopsis including specification of organ identity in the second and third whorls and the proper pattern of primordium initiation in the inner three whorls. UFO is expressed in a dynamic pattern during the early phases of flower development. Here we dissect the role of UFO by ubiquitously expressing it in ufo loss-of-function flowers at different developmental stages and for various durations using an ethanol-inducible expression system. The previously known functions of UFO could be separated and related to its expression at specific stages of development. We show that a 24- to 48-hour period of UFO expression from floral stage 2, before any floral organs are visible, is sufficient to restore normal petal and stamen development. The earliest requirement for UFO is during stage 2, when the endogenous UFO gene is transiently expressed in the centre of the wild-type flower and is required to specify the initiation patterns of petal, stamen and carpel primordia. Petal and stamen identity is determined during stages 2 or 3, when UFO is normally expressed in the presumptive second and third whorl. Although endogenous UFO expression is absent from the stamen whorl from stage 4 onwards, stamen identity can be restored by UFO activation up to stage 6. We also observed floral phenotypes not observed in loss-of-function or constitutive gain-of-function backgrounds, revealing additional roles of UFO in outgrowth of petal primordia. PMID:12506008

  18. Validation of Skeletal Muscle cis-Regulatory Module Predictions Reveals Nucleotide Composition Bias in Functional Enhancers

    PubMed Central

    Kwon, Andrew T.; Chou, Alice Yi; Arenillas, David J.; Wasserman, Wyeth W.

    2011-01-01

    We performed a genome-wide scan for muscle-specific cis-regulatory modules (CRMs) using three computational prediction programs. Based on the predictions, 339 candidate CRMs were tested in cell culture with NIH3T3 fibroblasts and C2C12 myoblasts for capacity to direct selective reporter gene expression to differentiated C2C12 myotubes. A subset of 19 CRMs validated as functional in the assay. The rate of predictive success reveals striking limitations of computational regulatory sequence analysis methods for CRM discovery. Motif-based methods performed no better than predictions based only on sequence conservation. Analysis of the properties of the functional sequences relative to inactive sequences identifies nucleotide sequence composition can be an important characteristic to incorporate in future methods for improved predictive specificity. Muscle-related TFBSs predicted within the functional sequences display greater sequence conservation than non-TFBS flanking regions. Comparison with recent MyoD and histone modification ChIP-Seq data supports the validity of the functional regions. PMID:22144875

  19. High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase.

    PubMed

    Gajula, Kiran S; Huwe, Peter J; Mo, Charlie Y; Crawford, Daniel J; Stivers, James T; Radhakrishnan, Ravi; Kohli, Rahul M

    2014-09-01

    Antibody maturation is a critical immune process governed by the enzyme activation-induced deaminase (AID), a member of the AID/APOBEC DNA deaminase family. AID/APOBEC deaminases preferentially target cytosine within distinct preferred sequence motifs in DNA, with specificity largely conferred by a small 9-11 residue protein loop that differs among family members. Here, we aimed to determine the key functional characteristics of this protein loop in AID and to thereby inform our understanding of the mode of DNA engagement. To this end, we developed a methodology (Sat-Sel-Seq) that couples saturation mutagenesis at each position across the targeting loop, with iterative functional selection and next-generation sequencing. This high-throughput mutational analysis revealed dominant characteristics for residues within the loop and additionally yielded enzymatic variants that enhance deaminase activity. To rationalize these functional requirements, we performed molecular dynamics simulations that suggest that AID and its hyperactive variants can engage DNA in multiple specific modes. These findings align with AID's competing requirements for specificity and flexibility to efficiently drive antibody maturation. Beyond insights into the AID-DNA interface, our Sat-Sel-Seq approach also serves to further expand the repertoire of techniques for deep positional scanning and may find general utility for high-throughput analysis of protein function. PMID:25064858

  20. High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase

    PubMed Central

    Gajula, Kiran S.; Huwe, Peter J.; Mo, Charlie Y.; Crawford, Daniel J.; Stivers, James T.; Radhakrishnan, Ravi; Kohli, Rahul M.

    2014-01-01

    Antibody maturation is a critical immune process governed by the enzyme activation-induced deaminase (AID), a member of the AID/APOBEC DNA deaminase family. AID/APOBEC deaminases preferentially target cytosine within distinct preferred sequence motifs in DNA, with specificity largely conferred by a small 9–11 residue protein loop that differs among family members. Here, we aimed to determine the key functional characteristics of this protein loop in AID and to thereby inform our understanding of the mode of DNA engagement. To this end, we developed a methodology (Sat-Sel-Seq) that couples saturation mutagenesis at each position across the targeting loop, with iterative functional selection and next-generation sequencing. This high-throughput mutational analysis revealed dominant characteristics for residues within the loop and additionally yielded enzymatic variants that enhance deaminase activity. To rationalize these functional requirements, we performed molecular dynamics simulations that suggest that AID and its hyperactive variants can engage DNA in multiple specific modes. These findings align with AID's competing requirements for specificity and flexibility to efficiently drive antibody maturation. Beyond insights into the AID-DNA interface, our Sat-Sel-Seq approach also serves to further expand the repertoire of techniques for deep positional scanning and may find general utility for high-throughput analysis of protein function. PMID:25064858

  1. Predicting invasive species impacts: a community module functional response approach reveals context dependencies.

    PubMed

    Paterson, Rachel A; Dick, Jaimie T A; Pritchard, Daniel W; Ennis, Marilyn; Hatcher, Melanie J; Dunn, Alison M

    2015-03-01

    Predatory functional responses play integral roles in predator-prey dynamics, and their assessment promises greater understanding and prediction of the predatory impacts of invasive species. Other interspecific interactions, however, such as parasitism and higher-order predation, have the potential to modify predator-prey interactions and thus the predictive capability of the comparative functional response approach. We used a four-species community module (higher-order predator; focal native or invasive predators; parasites of focal predators; native prey) to compare the predatory functional responses of native Gammarus duebeni celticus and invasive Gammarus pulex amphipods towards three invertebrate prey species (Asellus aquaticus, Simulium spp., Baetis rhodani), thus, quantifying the context dependencies of parasitism and a higher-order fish predator on these functional responses. Our functional response experiments demonstrated that the invasive amphipod had a higher predatory impact (lower handling time) on two of three prey species, which reflects patterns of impact observed in the field. The community module also revealed that parasitism had context-dependent influences, for one prey species, with the potential to further reduce the predatory impact of the invasive amphipod or increase the predatory impact of the native amphipod in the presence of a higher-order fish predator. Partial consumption of prey was similar for both predators and occurred increasingly in the order A. aquaticus, Simulium spp. and B. rhodani. This was associated with increasing prey densities, but showed no context dependencies with parasitism or higher-order fish predator. This study supports the applicability of comparative functional responses as a tool to predict and assess invasive species impacts incorporating multiple context dependencies. PMID:25265905

  2. Predicting invasive species impacts: a community module functional response approach reveals context dependencies

    PubMed Central

    Paterson, Rachel A; Dick, Jaimie T A; Pritchard, Daniel W; Ennis, Marilyn; Hatcher, Melanie J; Dunn, Alison M

    2015-01-01

    Summary Predatory functional responses play integral roles in predator–prey dynamics, and their assessment promises greater understanding and prediction of the predatory impacts of invasive species. Other interspecific interactions, however, such as parasitism and higher-order predation, have the potential to modify predator–prey interactions and thus the predictive capability of the comparative functional response approach. We used a four-species community module (higher-order predator; focal native or invasive predators; parasites of focal predators; native prey) to compare the predatory functional responses of native Gammarus duebeni celticus and invasive Gammarus pulex amphipods towards three invertebrate prey species (Asellus aquaticus, Simulium spp., Baetis rhodani), thus, quantifying the context dependencies of parasitism and a higher-order fish predator on these functional responses. Our functional response experiments demonstrated that the invasive amphipod had a higher predatory impact (lower handling time) on two of three prey species, which reflects patterns of impact observed in the field. The community module also revealed that parasitism had context-dependent influences, for one prey species, with the potential to further reduce the predatory impact of the invasive amphipod or increase the predatory impact of the native amphipod in the presence of a higher-order fish predator. Partial consumption of prey was similar for both predators and occurred increasingly in the order A. aquaticus, Simulium spp. and B. rhodani. This was associated with increasing prey densities, but showed no context dependencies with parasitism or higher-order fish predator. This study supports the applicability of comparative functional responses as a tool to predict and assess invasive species impacts incorporating multiple context dependencies. PMID:25265905

  3. Dissociable Temporo-Parietal Memory Networks Revealed by Functional Connectivity during Episodic Retrieval

    PubMed Central

    Hirose, Satoshi; Kimura, Hiroko M.; Jimura, Koji; Kunimatsu, Akira; Abe, Osamu; Ohtomo, Kuni; Miyashita, Yasushi; Konishi, Seiki

    2013-01-01

    Episodic memory retrieval most often recruits multiple separate processes that are thought to involve different temporal regions. Previous studies suggest dissociable regions in the left lateral parietal cortex that are associated with the retrieval processes. Moreover, studies using resting-state functional connectivity (RSFC) have provided evidence for the temporo-parietal memory networks that may support the retrieval processes. In this functional MRI study, we tested functional significance of the memory networks by examining functional connectivity of brain activity during episodic retrieval in the temporal and parietal regions of the memory networks. Recency judgments, judgments of the temporal order of past events, can be achieved by at least two retrieval processes, relational and item-based. Neuroimaging results revealed several temporal and parietal activations associated with relational/item-based recency judgments. Significant RSFC was observed between one parahippocampal region and one left lateral parietal region associated with relational recency judgments, and between four lateral temporal regions and another left lateral parietal region associated with item-based recency judgments. Functional connectivity during task was found to be significant between the parahippocampal region and the parietal region in the RSFC network associated with relational recency judgments. However, out of the four tempo-parietal RSFC networks associated with item-based recency judgments, only one of them (between the left posterior lateral temporal region and the left lateral parietal region) showed significant functional connectivity during task. These results highlight the contrasting roles of the parahippocampal and the lateral temporal regions in recency judgments, and suggest that only a part of the tempo-parietal RSFC networks are recruited to support particular retrieval processes. PMID:24009657

  4. Parallels and Divergences?

    ERIC Educational Resources Information Center

    Spray, Martin

    1985-01-01

    Discusses the varying philosophical viewpoints and program orientations associated with the conservation movement, assessing the implications of these divergences on the objectives and instructional methods of environmental education. Also identifies and explains the range of differences existing in environmental education programs. (ML)

  5. Converging or Diverging Lens?

    ERIC Educational Resources Information Center

    Branca, Mario

    2013-01-01

    Why does a lens magnify? Why does it shrink objects? Why does this happen? The activities that we propose here are useful in helping us to understand how lenses work, and they show that the same lens can have different magnification capabilities. A converging lens can also act as a diverging lens. (Contains 4 figures.)

  6. Measuring Divergent Abilities.

    ERIC Educational Resources Information Center

    Sefer, Jasmina

    The validity and reliability of the Yugoslavian (Beograd) version of the Hungarian adaptation of the Torrance Divergent Capacities Test (HAT-DAT) were tested, with a view toward improving the methodology of scoring the creative abilities test and determining standards for Yugoslavia. The test, based on the work of J. P. Guilford (1977), examines…

  7. GDNF Overexpression from the Native Locus Reveals its Role in the Nigrostriatal Dopaminergic System Function.

    PubMed

    Kumar, Anmol; Kopra, Jaakko; Varendi, Kärt; Porokuokka, Lauriina L; Panhelainen, Anne; Kuure, Satu; Marshall, Pepin; Karalija, Nina; Härma, Mari-Anne; Vilenius, Carolina; Lilleväli, Kersti; Tekko, Triin; Mijatovic, Jelena; Pulkkinen, Nita; Jakobson, Madis; Jakobson, Maili; Ola, Roxana; Palm, Erik; Lindahl, Maria; Strömberg, Ingrid; Võikar, Vootele; Piepponen, T Petteri; Saarma, Mart; Andressoo, Jaan-Olle

    2015-12-01

    Degeneration of nigrostriatal dopaminergic system is the principal lesion in Parkinson's disease. Because glial cell line-derived neurotrophic factor (GDNF) promotes survival of dopamine neurons in vitro and in vivo, intracranial delivery of GDNF has been attempted for Parkinson's disease treatment but with variable success. For improving GDNF-based therapies, knowledge on physiological role of endogenous GDNF at the sites of its expression is important. However, due to limitations of existing genetic model systems, such knowledge is scarce. Here, we report that prevention of transcription of Gdnf 3'UTR in Gdnf endogenous locus yields GDNF hypermorphic mice with increased, but spatially unchanged GDNF expression, enabling analysis of postnatal GDNF function. We found that increased level of GDNF in the central nervous system increases the number of adult dopamine neurons in the substantia nigra pars compacta and the number of dopaminergic terminals in the dorsal striatum. At the functional level, GDNF levels increased striatal tissue dopamine levels and augmented striatal dopamine release and re-uptake. In a proteasome inhibitor lactacystin-induced model of Parkinson's disease GDNF hypermorphic mice were protected from the reduction in striatal dopamine and failure of dopaminergic system function. Importantly, adverse phenotypic effects associated with spatially unregulated GDNF applications were not observed. Enhanced GDNF levels up-regulated striatal dopamine transporter activity by at least five fold resulting in enhanced susceptibility to 6-OHDA, a toxin transported into dopamine neurons by DAT. Further, we report how GDNF levels regulate kidney development and identify microRNAs miR-9, miR-96, miR-133, and miR-146a as negative regulators of GDNF expression via interaction with Gdnf 3'UTR in vitro. Our results reveal the role of GDNF in nigrostriatal dopamine system postnatal development and adult function, and highlight the importance of correct spatial

  8. Diurnal Changes in Mitochondrial Function Reveal Daily Optimization of Light and Dark Respiratory Metabolism in Arabidopsis*

    PubMed Central

    Lee, Chun Pong; Eubel, Holger; Millar, A. Harvey

    2010-01-01

    Biomass production by plants is often negatively correlated with respiratory rate, but the value of this rate changes dramatically during diurnal cycles, and hence, biomass is the cumulative result of complex environment-dependent metabolic processes. Mitochondria in photosynthetic plant tissues undertake substantially different metabolic roles during light and dark periods that are dictated by substrate availability and the functional capacity of mitochondria defined by their protein composition. We surveyed the heterogeneity of the mitochondrial proteome and its function during a typical night and day cycle in Arabidopsis shoots. This used a staged, quantitative analysis of the proteome across 10 time points covering 24 h of the life of 3-week-old Arabidopsis shoots grown under 12-h dark and 12-h light conditions. Detailed analysis of enzyme capacities and substrate-dependent respiratory processes of isolated mitochondria were also undertaken during the same time course. Together these data reveal a range of dynamic changes in mitochondrial capacity and uncover day- and night-enhanced protein components. Clear diurnal changes were evident in mitochondrial capacities to drive the TCA cycle and to undertake functions associated with nitrogen and sulfur metabolism, redox poise, and mitochondrial antioxidant defense. These data quantify the nature and nuances of a daily rhythm in Arabidopsis mitochondrial respiratory capacity. PMID:20601493

  9. Edge reconstruction in armchair phosphorene nanoribbons revealed by discontinuous Galerkin density functional theory.

    PubMed

    Hu, Wei; Lin, Lin; Yang, Chao

    2015-12-21

    With the help of our recently developed massively parallel DGDFT (Discontinuous Galerkin Density Functional Theory) methodology, we perform large-scale Kohn-Sham density functional theory calculations on phosphorene nanoribbons with armchair edges (ACPNRs) containing a few thousands to ten thousand atoms. The use of DGDFT allows us to systematically achieve a conventional plane wave basis set type of accuracy, but with a much smaller number (about 15) of adaptive local basis (ALB) functions per atom for this system. The relatively small number of degrees of freedom required to represent the Kohn-Sham Hamiltonian, together with the use of the pole expansion the selected inversion (PEXSI) technique that circumvents the need to diagonalize the Hamiltonian, results in a highly efficient and scalable computational scheme for analyzing the electronic structures of ACPNRs as well as their dynamics. The total wall clock time for calculating the electronic structures of large-scale ACPNRs containing 1080-10,800 atoms is only 10-25 s per self-consistent field (SCF) iteration, with accuracy fully comparable to that obtained from conventional planewave DFT calculations. For the ACPNR system, we observe that the DGDFT methodology can scale to 5000-50,000 processors. We use DGDFT based ab initio molecular dynamics (AIMD) calculations to study the thermodynamic stability of ACPNRs. Our calculations reveal that a 2 × 1 edge reconstruction appears in ACPNRs at room temperature. PMID:25698178

  10. Gas7-Deficient Mouse Reveals Roles in Motor Function and Muscle Fiber Composition during Aging

    PubMed Central

    Huang, Bo-Tsang; Chang, Pu-Yuan; Su, Ching-Hua; Chao, Chuck C.-K.; Lin-Chao, Sue

    2012-01-01

    Background Growth arrest-specific gene 7 (Gas7) has previously been shown to be involved in neurite outgrowth in vitro; however, its actual role has yet to be determined. To investigate the physiological function of Gas7 in vivo, here we generated a Gas7-deficient mouse strain with a labile Gas7 mutant protein whose functions are similar to wild-type Gas7. Methodology/Principal Findings Our data show that aged Gas7-deficient mice have motor activity defects due to decreases in the number of spinal motor neurons and in muscle strength, of which the latter may be caused by changes in muscle fiber composition as shown in the soleus. In cross sections of the soleus of Gas7-deficient mice, gross morphological features and levels of myosin heavy chain I (MHC I) and MHC II markers revealed significantly fewer fast fibers. In addition, we found that nerve terminal sprouting, which may be associated with slow and fast muscle fiber composition, was considerably reduced at neuromuscular junctions (NMJ) during aging. Conclusions/Significance These findings indicate that Gas7 is involved in motor neuron function associated with muscle strength maintenance. PMID:22662195

  11. Hearing Without Listening: Functional Connectivity Reveals the Engagement of Multiple Nonauditory Networks During Basic Sound Processing

    PubMed Central

    Melcher, Jennifer R.

    2011-01-01

    Abstract The present functional magnetic resonance imaging (fMRI) study presents data challenging the traditional view that sound is processed almost exclusively in the classical auditory pathway unless imbued with behavioral significance. In a first experiment, subjects were presented with broadband noise in on/off fashion as they performed an unrelated visual task. A conventional analysis assuming predictable sound-evoked responses demonstrated a typical activation pattern that was confined to classical auditory centers. In contrast, spatial independent component analysis (sICA) disclosed multiple networks of acoustically responsive brain centers. One network comprised classical auditory centers, but four others included nominally “nonauditory” areas: cingulo-insular cortex, mediotemporal limbic lobe, basal ganglia, and posterior orbitofrontal cortex, respectively. Functional connectivity analyses confirmed the sICA results by demonstrating coordinated activity between the involved brain structures. In a second experiment, fMRI data obtained from unstimulated (i.e., resting) subjects revealed largely similar networks. Together, these two experiments suggest the existence of a coordinated system of multiple acoustically responsive intrinsic brain networks, comprising classical auditory centers but also other brain areas. Our results suggest that nonauditory centers play a role in sound processing at a very basic level, even when the sound is not intertwined with behaviors requiring the well-known functionality of these regions. PMID:22433051

  12. Conditional Degradation of Plasmodium Calcineurin Reveals Functions in Parasite Colonization of both Host and Vector

    PubMed Central

    Philip, Nisha; Waters, Andrew P.

    2015-01-01

    Summary Functional analysis of essential genes in the malarial parasite, Plasmodium, is hindered by lack of efficient strategies for conditional protein regulation. We report the development of a rapid, specific, and inducible chemical-genetic tool in the rodent malaria parasite, P. berghei, in which endogenous proteins engineered to contain the auxin-inducible degron (AID) are selectively degraded upon adding auxin. Application of AID to the calcium-regulated protein phosphatase, calcineurin, revealed functions in host and vector stages of parasite development. Whereas depletion of calcineurin in late-stage schizonts demonstrated its critical role in erythrocyte attachment and invasion in vivo, stage-specific depletion uncovered roles in gamete development, fertilization, and ookinete-to-oocyst and sporozoite-to-liver stage transitions. Furthermore, AID technology facilitated concurrent generation and phenotyping of transgenic lines, allowing multiple lines to be assessed simultaneously with significant reductions in animal use. This study highlights the broad applicability of AID for functional analysis of proteins across the Plasmodium life cycle. PMID:26118994

  13. Information Filtering Using Kullback-Leibler Divergence

    NASA Astrophysics Data System (ADS)

    Yanagimoto, Hidekazu; Omatu, Sigeru

    In this paper we describe an information filtering system using the Kullback-Leibler divergence. To cope with information flood, many information filtering systems have been proposed up to now. Since almost all information filtering systems are developed with techniques of information retrieval, machine learning, and pattern recognition, they often use a linear function as the discriminant function. To classify information in the field of document classification more precisely, the systems have been reported which use a non-linear function as the discriminant function. The proposed method is to use the Kullback-Leibler divergence as the discriminat function which denotes to user's interest in the information filtering system. To identify the optimal discriminat function with documents which a user evaluates, we decide the optimal function using the genetic algorithm. We compare the present method with the other one using a linear discriminant function and confirm the effectiveness of the proposed method.

  14. Structural and Functional Studies of the Rap1 C-Terminus Reveal Novel Separation-of-Function Mutants

    SciTech Connect

    Feeser, Elizabeth A.; Wolberger, Cynthia

    2010-02-19

    The yeast Rap1 protein plays an important role in transcriptional silencing and in telomere length homeostasis. Rap1 mediates silencing at the HM loci and at telomeres by recruiting the Sir3 and Sir4 proteins to chromatin via a Rap1 C-terminal domain, which also recruits the telomere length regulators, Rif1 and Rif2. We report the 1.85 {angstrom} resolution crystal structure of the Rap1 C-terminus, which adopts an all-helical fold with no structural homologues. The structure was used to engineer surface mutations in Rap1, and the effects of these mutations on silencing and telomere length regulation were assayed in vivo. Our surprising finding was that there is no overlap between mutations affecting mating-type and telomeric silencing, suggesting that Rap1 plays distinct roles in silencing at the silent mating-type loci and telomeres. We also found novel Rap1 phenotypes and new separation-of-function mutants, which provide new tools for studying Rap1 function. Yeast two-hybrid studies were used to determine how specific mutations affect recruitment of Sir3, Rif1, and Rif2. A comparison of the yeast two-hybrid and functional data reveals patterns of protein interactions that correlate with each Rap1 phenotype. We find that Sir3 interactions are important for telomeric silencing, but not mating type silencing, and that Rif1 and Rif2 interactions are important in different subsets of telomeric length mutants. Our results show that the role of Rap1 in silencing differs between the HM loci and the telomeres and offer insight into the interplay between HM silencing, telomeric silencing, and telomere length regulation. These findings suggest a model in which competition and multiple recruitment events modulate silencing and telomere length regulation.

  15. Investigating properties of a family of quantum Rényi divergences

    NASA Astrophysics Data System (ADS)

    Lin, Simon M.; Tomamichel, Marco

    2015-04-01

    Audenaert and Datta recently introduced a two-parameter family of relative Rényi entropies, known as the --relative Rényi entropies. The definition of the --relative Rényi entropy unifies all previously proposed definitions of the quantum Rényi divergence of order under a common framework. Here, we will prove that the --relative Rényi entropies are a proper generalization of the quantum relative entropy by computing the limit of the - divergence as approaches one and is an arbitrary function of . We also show that certain operationally relevant families of Rényi divergences are differentiable at . Finally, our analysis reveals that the derivative at evaluates to half the relative entropy variance, a quantity that has attained operational significance in second-order quantum hypothesis testing and channel coding for finite block lengths.

  16. Fitness Assays Reveal Incomplete Functional Redundancy of the HoxA1 and HoxB1 Paralogs of Mice.

    PubMed

    Ruff, James S; Saffarini, Raed B; Ramoz, Leda L; Morrison, Linda C; Baker, Shambralyn; Laverty, Sean M; Tvrdik, Petr; Potts, Wayne K

    2015-10-01

    Gene targeting techniques have led to the phenotypic characterization of numerous genes; however, many genes show minimal to no phenotypic consequences when disrupted, despite many having highly conserved sequences. The standard explanation for these findings is functional redundancy. A competing hypothesis is that these genes have important ecological functions in natural environments that are not needed under laboratory settings. Here we discriminate between these hypotheses by competing mice (Mus musculus) whose Hoxb1 gene has been replaced by Hoxa1, its highly conserved paralog, against matched wild-type controls in seminatural enclosures. This Hoxb1(A1) swap was reported as a genetic manipulation resulting in no discernible embryonic or physiological phenotype under standard laboratory tests. We observed a transient decline in first litter size for Hoxb1(A1) homozygous mice in breeding cages, but their fitness was consistently and more dramatically reduced when competing against controls within seminatural populations. Specifically, males homozygous for the Hoxb1(A1) swap acquired 10.6% fewer territories and the frequency of the Hoxb1(A1) allele decreased from 0.500 in population founders to 0.419 in their offspring. The decrease in Hoxb1(A1) frequency corresponded with a deficiency of both Hoxb1(A1) homozygous and heterozygous offspring. These data suggest that Hoxb1 and Hoxa1 are more phenotypically divergent than previously reported and support that sub- and/or neofunctionalization has occurred in these paralogous genes leading to a divergence of gene function and incomplete redundancy. Furthermore, this study highlights the importance of obtaining fitness measures of mutants in ecologically relevant conditions to better understand gene function and evolution. PMID:26447130

  17. Transcriptome analyses reveal molecular mechanisms underlying functional recovery after spinal cord injury

    PubMed Central

    Duan, Hongmei; Ge, Weihong; Zhang, Aifeng; Xi, Yue; Chen, Zhihua; Luo, Dandan; Cheng, Yin; Fan, Kevin S.; Horvath, Steve; Sofroniew, Michael V.; Cheng, Liming; Yang, Zhaoyang; Sun, Yi E.; Li, Xiaoguang

    2015-01-01

    Spinal cord injury (SCI) is considered incurable because axonal regeneration in the central nervous system (CNS) is extremely challenging, due to harsh CNS injury environment and weak intrinsic regeneration capability of CNS neurons. We discovered that neurotrophin-3 (NT3)-loaded chitosan provided an excellent microenvironment to facilitate nerve growth, new neurogenesis, and functional recovery of completely transected spinal cord in rats. To acquire mechanistic insight, we conducted a series of comprehensive transcriptome analyses of spinal cord segments at the lesion site, as well as regions immediately rostral and caudal to the lesion, over a period of 90 days after SCI. Using weighted gene coexpression network analysis (WGCNA), we established gene modules/programs corresponding to various pathological events at different times after SCI. These objective measures of gene module expression also revealed that enhanced new neurogenesis and angiogenesis, and reduced inflammatory responses were keys to conferring the effect of NT3-chitosan on regeneration. PMID:26460053

  18. Real-time Redox Measurements during Endoplasmic Reticulum Stress Reveal Interlinked Protein Folding Functions

    PubMed Central

    Merksamer, Philip I.; Trusina, Ala; Papa, Feroz R.

    2008-01-01

    SUMMARY Disruption of protein folding in the endoplasmic reticulum (ER) causes unfolded proteins to accumulate, triggering the unfolded protein response (UPR). UPR outputs in turn decrease ER unfolded proteins to close a negative feedback loop. However, because it is infeasible to directly measure the concentration of unfolded proteins in vivo, cells are generically described as experiencing “ER stress” whenever the UPR is active. Because ER redox potential is optimized for oxidative protein folding, we reasoned that measureable redox changes should accompany unfolded protein accumulation. To test this concept, we employed fluorescent protein reporters to dynamically measure ER redox status and UPR activity in single cells. Using these tools, we show that diverse stressors, both experimental and physiological, compromise ER protein oxidation when UPR-imposed homeostatic control is lost. Using genetic analysis we uncovered redox heterogeneities in isogenic cell populations, and revealed functional interlinks between ER protein folding, modification, and quality control systems. PMID:19026441

  19. Structure of Prokaryotic Polyamine Deacetylase Reveals Evolutionary Functional Relationships with Eukaryotic Histone Deacetylases

    SciTech Connect

    P Lombardi; H Angell; D Whittington; E Flynn; K Rajashankar; D Christianson

    2011-12-31

    Polyamines are a ubiquitous class of polycationic small molecules that can influence gene expression by binding to nucleic acids. Reversible polyamine acetylation regulates nucleic acid binding and is required for normal cell cycle progression and proliferation. Here, we report the structures of Mycoplana ramosa acetylpolyamine amidohydrolase (APAH) complexed with a transition state analogue and a hydroxamate inhibitor and an inactive mutant complexed with two acetylpolyamine substrates. The structure of APAH is the first of a histone deacetylase-like oligomer and reveals that an 18-residue insert in the L2 loop promotes dimerization and the formation of an 18 {angstrom} long 'L'-shaped active site tunnel at the dimer interface, accessible only to narrow and flexible substrates. The importance of dimerization for polyamine deacetylase function leads to the suggestion that a comparable dimeric or double-domain histone deacetylase could catalyze polyamine deacetylation reactions in eukaryotes.

  20. Transcriptome analyses reveal molecular mechanisms underlying functional recovery after spinal cord injury.

    PubMed

    Duan, Hongmei; Ge, Weihong; Zhang, Aifeng; Xi, Yue; Chen, Zhihua; Luo, Dandan; Cheng, Yin; Fan, Kevin S; Horvath, Steve; Sofroniew, Michael V; Cheng, Liming; Yang, Zhaoyang; Sun, Yi E; Li, Xiaoguang

    2015-10-27

    Spinal cord injury (SCI) is considered incurable because axonal regeneration in the central nervous system (CNS) is extremely challenging, due to harsh CNS injury environment and weak intrinsic regeneration capability of CNS neurons. We discovered that neurotrophin-3 (NT3)-loaded chitosan provided an excellent microenvironment to facilitate nerve growth, new neurogenesis, and functional recovery of completely transected spinal cord in rats. To acquire mechanistic insight, we conducted a series of comprehensive transcriptome analyses of spinal cord segments at the lesion site, as well as regions immediately rostral and caudal to the lesion, over a period of 90 days after SCI. Using weighted gene coexpression network analysis (WGCNA), we established gene modules/programs corresponding to various pathological events at different times after SCI. These objective measures of gene module expression also revealed that enhanced new neurogenesis and angiogenesis, and reduced inflammatory responses were keys to conferring the effect of NT3-chitosan on regeneration. PMID:26460053

  1. Lipidomic profiling reveals protective function of fatty acid oxidation in cocaine-induced hepatotoxicity[S

    PubMed Central

    Shi, Xiaolei; Yao, Dan; Gosnell, Blake A.; Chen, Chi

    2012-01-01

    During cocaine-induced hepatotoxicity, lipid accumulation occurs prior to necrotic cell death in the liver. However, the exact influences of cocaine on the homeostasis of lipid metabolism remain largely unknown. In this study, the progression of subacute hepatotoxicity, including centrilobular necrosis in the liver and elevation of transaminase activity in serum, was observed in a three-day cocaine treatment, accompanying the disruption of triacylglycerol (TAG) turnover. Serum TAG level increased on day 1 of cocaine treatment but remained unchanged afterwards. In contrast, hepatic TAG level was elevated continuously during three days of cocaine treatment and was better correlated with the development of hepatotoxicity. Lipidomic analyses of serum and liver samples revealed time-dependent separation of the control and cocaine-treated mice in multivariate models, which was due to the accumulation of long-chain acylcarnitines together with the disturbances of many bioactive phospholipid species in the cocaine-treated mice. An in vitro function assay confirmed the progressive inhibition of mitochondrial fatty acid oxidation after the cocaine treatment. Cotreatment of fenofibrate significantly increased the expression of peroxisome proliferator-activated receptor α (PPARα)-targeted genes and the mitochondrial fatty acid oxidation activity in the cocaine-treated mice, resulting in the inhibition of cocaine-induced acylcarnitine accumulation and other hepatotoxic effects. Overall, the results from this lipidomics-guided study revealed that the inhibition of fatty acid oxidation plays an important role in cocaine-induced liver injury. PMID:22904346

  2. Functional genomic analysis reveals overlapping and distinct features of chronologically long-lived yeast populations.

    PubMed

    Wierman, Margaret B; Matecic, Mirela; Valsakumar, Veena; Li, Mingguang; Smith, Daniel L; Bekiranov, Stefan; Smith, Jeffrey S

    2015-03-01

    Yeast chronological lifespan (CLS) is extended by multiple genetic and environmental manipulations, including caloric restriction (CR). Understanding the common changes in molecular pathways induced by such manipulations could potentially reveal conserved longevity mechanisms. We therefore performed gene expression profiling on several long-lived yeast populations, including anade4∆mutant defective in de novo purine (AMP) biosynthesis, and a calorie restricted WT strain. CLS was also extended by isonicotinamide (INAM) or expired media derived from CR cultures. Comparisons between these diverse long-lived conditions revealed a common set of differentially regulated genes, several of which were potential longevity biomarkers. There was also enrichment for genes that function in CLS regulation, including a long-lived adenosine kinase mutant (ado1∆) that links CLS regulation to the methyl cycle and AMP. Genes co-regulated between the CR and ade4∆ conditions were dominated by GO terms related to metabolism of alternative carbon sources, consistent with chronological longevity requiring efficient acetate/acetic acid utilization. Alternatively, treating cells with isonicotinamide (INAM) or the expired CR media resulted in GO terms predominantly related to cell wall remodeling, consistent with improved stress resistance and protection against external insults like acetic acid. Acetic acid therefore has both beneficial and detrimental effects on CLS. PMID:25769345

  3. Targeted mutagenesis of zebrafish antithrombin III triggers disseminated intravascular coagulation and thrombosis, revealing insight into function

    PubMed Central

    Liu, Yang; Kretz, Colin A.; Maeder, Morgan L.; Richter, Catherine E.; Tsao, Philip; Vo, Andy H.; Huarng, Michael C.; Rode, Thomas; Hu, Zhilian; Mehra, Rohit; Olson, Steven T.; Joung, J. Keith

    2014-01-01

    Pathologic blood clotting is a leading cause of morbidity and mortality in the developed world, underlying deep vein thrombosis, myocardial infarction, and stroke. Genetic predisposition to thrombosis is still poorly understood, and we hypothesize that there are many additional risk alleles and modifying factors remaining to be discovered. Mammalian models have contributed to our understanding of thrombosis, but are low throughput and costly. We have turned to the zebrafish, a tool for high-throughput genetic analysis. Using zinc finger nucleases, we show that disruption of the zebrafish antithrombin III (at3) locus results in spontaneous venous thrombosis in larvae. Although homozygous mutants survive into early adulthood, they eventually succumb to massive intracardiac thrombosis. Characterization of null fish revealed disseminated intravascular coagulation in larvae secondary to unopposed thrombin activity and fibrinogen consumption, which could be rescued by both human and zebrafish at3 complementary DNAs. Mutation of the human AT3-reactive center loop abolished the ability to rescue, but the heparin-binding site was dispensable. These results demonstrate overall conservation of AT3 function in zebrafish, but reveal developmental variances in the ability to tolerate excessive clot formation. The accessibility of early zebrafish development will provide unique methods for dissection of the underlying mechanisms of thrombosis. PMID:24782510

  4. Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

    PubMed Central

    Inskeep, William P.; Rusch, Douglas B.; Jay, Zackary J.; Herrgard, Markus J.; Kozubal, Mark A.; Richardson, Toby H.; Macur, Richard E.; Hamamura, Natsuko; Jennings, Ryan deM.; Fouke, Bruce W.; Reysenbach, Anna-Louise; Roberto, Frank; Young, Mark; Schwartz, Ariel; Boyd, Eric S.; Badger, Jonathan H.; Mathur, Eric J.; Ortmann, Alice C.; Bateson, Mary; Geesey, Gill; Frazier, Marvin

    2010-01-01

    The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14–15,000 Sanger reads per site) was obtained for five high-temperature (>65°C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport

  5. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function

    SciTech Connect

    Frank Roberto

    2010-03-01

    The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host numerous deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site) was obtained for five high-temperature (> 65 oC) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved O2 and ferrous Fe. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is

  6. Functional characterization of chicken TLR5 reveals species-specific recognition of flagellin.

    PubMed

    Keestra, A Marijke; de Zoete, Marcel R; van Aubel, Rémon A M H; van Putten, Jos P M

    2008-03-01

    Mammalian Toll-like receptor 5 (TLR5) senses flagellin of several bacterial species and activates the innate immune system. The avian TLR repertoire exhibits considerable functional diversity compared to mammalian TLRs and evidence of a functional TLR5 in the avian species is lacking. In the present study we cloned and successfully expressed chicken TLR5 (chTLR5) in HeLa cells, as indicated by laser confocal microscopy. Infection of chTLR5 transfected cells with Salmonella enterica serovar Enteritidis activated NF-kappaB in a dose- and flagellin-dependent fashion. Similar NF-kappaB activation was observed with recombinant bacterial flagellin. Targeted mutagenesis of the proline residue at position 737 in the chTLR5-TIR domain was detrimental to chTLR5 function, confirming that the observed effects were conferred via chTLR5 and the MyD88 signaling pathway. Comparison of human, mouse and chicken TLR5 activation by flagellin of S. enterica serovar Typhimurium revealed that chTLR5 consistently yielded stronger responses than human but not mouse TLR5. This species-specific reactivity was not observed with flagellin of serovar Enteritidis. The species-specific TLR5 response was nullified after targeted mutagenesis of a single amino acid (Q89A) in serovar Typhimurium flagellin, while L415A and N100A substitutions had no effect. These results show that chickens express a functional TLR5 albeit with different flagellin sensing qualities compared to human TLR5. The finding that single amino acid substitutions in bacterial flagellin can alter the species-specific TLR5 response may influence the host range and susceptibility of infection. PMID:17964652

  7. Multivoxel patterns reveal functionally differentiated networks underlying auditory feedback processing of speech.

    PubMed

    Zheng, Zane Z; Vicente-Grabovetsky, Alejandro; MacDonald, Ewen N; Munhall, Kevin G; Cusack, Rhodri; Johnsrude, Ingrid S

    2013-03-01

    The everyday act of speaking involves the complex processes of speech motor control. An important component of control is monitoring, detection, and processing of errors when auditory feedback does not correspond to the intended motor gesture. Here we show, using fMRI and converging operations within a multivoxel pattern analysis framework, that this sensorimotor process is supported by functionally differentiated brain networks. During scanning, a real-time speech-tracking system was used to deliver two acoustically different types of distorted auditory feedback or unaltered feedback while human participants were vocalizing monosyllabic words, and to present the same auditory stimuli while participants were passively listening. Whole-brain analysis of neural-pattern similarity revealed three functional networks that were differentially sensitive to distorted auditory feedback during vocalization, compared with during passive listening. One network of regions appears to encode an "error signal" regardless of acoustic features of the error: this network, including right angular gyrus, right supplementary motor area, and bilateral cerebellum, yielded consistent neural patterns across acoustically different, distorted feedback types, only during articulation (not during passive listening). In contrast, a frontotemporal network appears sensitive to the speech features of auditory stimuli during passive listening; this preference for speech features was diminished when the same stimuli were presented as auditory concomitants of vocalization. A third network, showing a distinct functional pattern from the other two, appears to capture aspects of both neural response profiles. Together, our findings suggest that auditory feedback processing during speech motor control may rely on multiple, interactive, functionally differentiated neural systems. PMID:23467350

  8. Metagenomes from high-temperature chemotrophic systems reveal geochemical controls on microbial community structure and function.

    PubMed

    Inskeep, William P; Rusch, Douglas B; Jay, Zackary J; Herrgard, Markus J; Kozubal, Mark A; Richardson, Toby H; Macur, Richard E; Hamamura, Natsuko; Jennings, Ryan deM; Fouke, Bruce W; Reysenbach, Anna-Louise; Roberto, Frank; Young, Mark; Schwartz, Ariel; Boyd, Eric S; Badger, Jonathan H; Mathur, Eric J; Ortmann, Alice C; Bateson, Mary; Geesey, Gill; Frazier, Marvin

    2010-01-01

    The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure and function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site) was obtained for five high-temperature (>65 degrees C) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H2-oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron

  9. Divergence Boundary Conditions for Vector Helmholtz Equations with Divergence Constraints

    NASA Technical Reports Server (NTRS)

    Kangro, Urve; Nicolaides, Roy

    1997-01-01

    The idea of replacing a divergence constraint by a divergence boundary condition is investigated. The connections between the formulations are considered in detail. It is shown that the most common methods of using divergence boundary conditions do not always work properly. Necessary and sufficient conditions for the equivalence of the formulations are given.

  10. Comparative RNAi Screens in C. elegans and C. briggsae Reveal the Impact of Developmental System Drift on Gene Function

    PubMed Central

    Verster, Adrian J.; Ramani, Arun K.; McKay, Sheldon J.; Fraser, Andrew G.

    2014-01-01

    Although two related species may have extremely similar phenotypes, the genetic networks underpinning this conserved biology may have diverged substantially since they last shared a common ancestor. This is termed Developmental System Drift (DSD) and reflects the plasticity of genetic networks. One consequence of DSD is that some orthologous genes will have evolved different in vivo functions in two such phenotypically similar, related species and will therefore have different loss of function phenotypes. Here we report an RNAi screen in C. elegans and C. briggsae to identify such cases. We screened 1333 genes in both species and identified 91 orthologues that have different RNAi phenotypes. Intriguingly, we find that recently evolved genes of unknown function have the fastest evolving in vivo functions and, in several cases, we identify the molecular events driving these changes. We thus find that DSD has a major impact on the evolution of gene function and we anticipate that the C. briggsae RNAi library reported here will drive future studies on comparative functional genomics screens in these nematodes. PMID:24516395

  11. Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases

    PubMed Central

    Riley, B.E.; Lougheed, J.C.; Callaway, K.; Velasquez, M.; Brecht, E.; Nguyen, L.; Shaler, T.; Walker, D.; Yang, Y.; Regnstrom, K.; Diep, L.; Zhang, Z.; Chiou, S.; Bova, M.; Artis, D.R.; Yao, N.; Baker, J.; Yednock, T.; Johnston, J.A.

    2013-01-01

    Parkin is a RING-between-RING E3 ligase that functions in the covalent attachment of ubiquitin to specific substrates, and mutations in Parkin are linked to Parkinson’s disease, cancer and mycobacterial infection. The RING-between-RING family of E3 ligases are suggested to function with a canonical RING domain and a catalytic cysteine residue usually restricted to HECT E3 ligases, thus termed ‘RING/HECT hybrid’ enzymes. Here we present the 1.58 Å structure of Parkin-R0RBR, revealing the fold architecture for the four RING domains, and several unpredicted interfaces. Examination of the Parkin active site suggests a catalytic network consisting of C431 and H433. In cells, mutation of C431 eliminates Parkin-catalysed degradation of mitochondria, and capture of an ubiquitin oxyester confirms C431 as Parkin’s cellular active site. Our data confirm that Parkin is a RING/HECT hybrid, and provide the first crystal structure of an RING-between-RING E3 ligase at atomic resolution, providing insight into this disease-related protein. PMID:23770887

  12. Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins.

    PubMed

    Desdouits, Nathan; Nilges, Michael; Blondel, Arnaud

    2015-02-01

    Protein conformation has been recognized as the key feature determining biological function, as it determines the position of the essential groups specifically interacting with substrates. Hence, the shape of the cavities or grooves at the protein surface appears to drive those functions. However, only a few studies describe the geometrical evolution of protein cavities during molecular dynamics simulations (MD), usually with a crude representation. To unveil the dynamics of cavity geometry evolution, we developed an approach combining cavity detection and Principal Component Analysis (PCA). This approach was applied to four systems subjected to MD (lysozyme, sperm whale myoglobin, Dengue envelope protein and EF-CaM complex). PCA on cavities allows us to perform efficient analysis and classification of the geometry diversity explored by a cavity. Additionally, it reveals correlations between the evolutions of the cavities and structures, and can even suggest how to modify the protein conformation to induce a given cavity geometry. It also helps to perform fast and consensual clustering of conformations according to cavity geometry. Finally, using this approach, we show that both carbon monoxide (CO) location and transfer among the different xenon sites of myoglobin are correlated with few cavity evolution modes of high amplitude. This correlation illustrates the link between ligand diffusion and the dynamic network of internal cavities. PMID:25424655

  13. Genetic Manipulations Reveal Dynamic Cell and Gene Functions: Cre-ating a New View of Myogenesis

    PubMed Central

    Hutcheson, David A.; Kardon, Gabrielle

    2010-01-01

    Development of multicellular organisms is temporally and spatially complex. The Cre/loxP and Flp/FRT systems for genetic manipulation in mammals now enable researchers to explicitly examine in vivo the temporal and spatial role of cells and genes during development via cell lineage and ablation studies and conditional gene inactivation and activation. Recently we have used these methods to genetically dissect the role of Pax3+ and Pax7+ progenitor populations and the function of β-catenin, an important regulator of myogenesis, in vertebrate limb myogenesis. Our lineage and ablation studies of Pax3+ and Pax7+ progenitors revealed surprising insights into myogenesis not apparent from Pax3 and Pax7 expression and functional studies. In addition, conditional inactivation and activation of β-catenin in different progenitor populations and their progeny demonstrated that β-catenin plays several cell-autonomous roles in myogenesis. Our studies highlight the hierarchical (i.e. genes versus cells), temporal, and spatial complexity of development and demonstrate that manipulations of both cells and genes will be required to obtain a full understanding of the development of multicellular organisms. PMID:19844163

  14. Comparative materials differences revealed in engineered bone as a function of cell-specific differentiation

    NASA Astrophysics Data System (ADS)

    Gentleman, Eileen; Swain, Robin J.; Evans, Nicholas D.; Boonrungsiman, Suwimon; Jell, Gavin; Ball, Michael D.; Shean, Tamaryn A. V.; Oyen, Michelle L.; Porter, Alexandra; Stevens, Molly M.

    2009-09-01

    An important aim of regenerative medicine is to restore tissue function with implantable, laboratory-grown constructs that contain tissue-specific cells that replicate the function of their counterparts in the healthy native tissue. It remains unclear, however, whether cells used in bone regeneration applications produce a material that mimics the structural and compositional complexity of native bone. By applying multivariate analysis techniques to micro-Raman spectra of mineralized nodules formed in vitro, we reveal cell-source-dependent differences in interactions between multiple bone-like mineral environments. Although osteoblasts and adult stem cells exhibited bone-specific biological activities and created a material with many of the hallmarks of native bone, the `bone nodules' formed from embryonic stem cells were an order of magnitude less stiff, and lacked the distinctive nanolevel architecture and complex biomolecular and mineral composition noted in the native tissue. Understanding the biological mechanisms of bone formation in vitro that contribute to cell-source-specific materials differences may facilitate the development of clinically successful engineered bone.

  15. Deletion of CFTR Translation Start Site Reveals Functional Isoforms of the Protein in CF Patients

    PubMed Central

    Ramalho, Anabela S.; Lewandowska, Marzena A.; Farinha, Carlos M.; Mendes, Filipa; Gonçalves, Juan; Barreto, Celeste; Harris, Ann; Amaral, Margarida D.

    2009-01-01

    Background/Aims: Mutations in the CFTR gene cause Cystic Fibrosis (CF) the most common life-threatening autosomal recessive disease affecting Caucasians. We identified a CFTR mutation (c.120del23) abolishing the normal translation initiation codon, which occurs in two Portuguese CF patients. This study aims at functionally characterizing the effect of this novel mutation. Methods: RNA and protein techniques were applied to both native tissues from CF patients and recombinant cells expressing CFTR constructs to determine whether c.120del23 allows CFTR protein production through usage of alternative internal codons, and to characterize the putative truncated CFTR form(s). Results: Our data show that two shorter forms of CFTR protein are produced when the initiation translation codon is deleted indicating usage of internal initiation codons. The N-truncated CFTR generated by this mutation has decreased stability, very low processing efficiency, and drastically reduced function. Analysis of mutants of four methionine codons downstream to M1 (M82, M150, M152, M156) revealed that each of the codons M150/M152/M156 (exon 4) can mediate CFTR alternative translation. Conclusions: The CFTR N-terminus has an important role in avoiding CFTR turnover and in rendering effective its plasma membrane traffic. These data correlate well with the severe clinical phenotype of CF patients bearing the c.120del23 mutation. PMID:19910674

  16. Metagenomics Reveals Microbial Community Composition And Function With Depth In Arctic Permafrost Cores

    NASA Astrophysics Data System (ADS)

    Jansson, J.; Tas, N.; Wu, Y.; Ulrich, C.; Kneafsey, T. J.; Torn, M. S.; Hubbard, S. S.; Chakraborty, R.; Graham, D. E.; Wullschleger, S. D.

    2013-12-01

    The Arctic is one of the most climatically sensitive regions on Earth and current surveys show that permafrost degradation is widespread in arctic soils. Biogeochemical feedbacks of permafrost thaw are expected to be dominated by the release of currently stored carbon back into the atmosphere as CO2 and CH4. Understanding the dynamics of C release from permafrost requires assessment of microbial functions from different soil compartments. To this end, as part of the Next Generation Ecosystem Experiment in the Arctic, we collected two replicate permafrost cores (1m and 3m deep) from a transitional polygon near Barrow, AK. At this location, permafrost starts from 0.5m in depth and is characterized by variable ice content and higher pH than surface soils. Prior to sectioning, the cores were CT-scanned to determine the physical heterogeneity throughout the cores. In addition to detailed geochemical characterization, we used Illumina MiSeq technology to sequence 16SrRNA genes throughout the depths of the cores at 1 cm intervals. Selected depths were also chosen for metagenome sequencing of total DNA (including phylogenetic and functional genes) using the Illumina HiSeq platform. The 16S rRNA gene sequence data revealed that the microbial community composition and diversity changed dramatically with depth. The microbial diversity decreased sharply below the first few centimeters of the permafrost and then gradually increased in deeper layers. Based on the metagenome sequence data, the permafrost microbial communities were found to contain members with a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. The surface active layers had more representatives of Verrucomicrobia (potential methane oxidizers) whereas the deep permafrost layers were dominated by several different species of Actinobacteria. The latter are known to have a diverse metabolic capability and are able to adapt to stress by entering a dormant yet

  17. Revealing the Functional Neuroanatomy of Intrinsic Alertness Using fMRI: Methodological Peculiarities

    PubMed Central

    Clemens, Benjamin; Zvyagintsev, Mikhail; Sack, Alexander; Heinecke, Armin; Willmes, Klaus; Sturm, Walter

    2011-01-01

    Clinical observations and neuroimaging data revealed a right-hemisphere fronto-parietal-thalamic-brainstem network for intrinsic alertness, and additional left fronto-parietal activity during phasic alertness. The primary objective of this fMRI study was to map the functional neuroanatomy of intrinsic alertness as precisely as possible in healthy participants, using a novel assessment paradigm already employed in clinical settings. Both the paradigm and the experimental design were optimized to specifically assess intrinsic alertness, while at the same time controlling for sensory-motor processing. The present results suggest that the processing of intrinsic alertness is accompanied by increased activity within the brainstem, thalamus, anterior cingulate gyrus, right insula, and right parietal cortex. Additionally, we found increased activation in the left hemisphere around the middle frontal gyrus (BA 9), the insula, the supplementary motor area, and the cerebellum. Our results further suggest that rather minute aspects of the experimental design may induce aspects of phasic alertness, which in turn might lead to additional brain activation in left-frontal areas not normally involved in intrinsic alertness. Accordingly, left BA 9 activation may be related to co-activation of the phasic alertness network due to the switch between rest and task conditions functioning as an external warning cue triggering the phasic alertness network. Furthermore, activation of the intrinsic alertness network during fixation blocks due to enhanced expectancy shortly before the switch to the task block might, when subtracted from the task block, lead to diminished activation in the typical right hemisphere intrinsic alertness network. Thus, we cautiously suggest that – as a methodological artifact – left frontal activations might show up due to phasic alertness involvement and intrinsic alertness activations might be weakened due to contrasting with fixation blocks, when assessing

  18. Genetic Analysis Reveals Different Functions for the Products of the Thyroid Hormone Receptor α Locus

    PubMed Central

    Gauthier, Karine; Plateroti, Michelina; Harvey, Clare B.; Williams, Graham R.; Weiss, Roy E.; Refetoff, Samuel; Willott, James F.; Sundin, Victoria; Roux, Jean-Paul; Malaval, Luc; Hara, Masahiro; Samarut, Jacques; Chassande, Olivier

    2001-01-01

    Thyroid hormone receptors are encoded by the TRα (NR1A1) and TRβ (NR1A2) loci. These genes are transcribed into multiple variants whose functions are unclear. Analysis by gene inactivation in mice has provided new insights into the functional complexity of these products. Different strategies designed to modify the TRα locus have led to strikingly different phenotypes. In order to analyze the molecular basis for these alterations, we generated mice devoid of all known isoforms produced from the TRα locus (TRα0/0). These mice are viable and exhibit reduced linear growth, bone maturation delay, moderate hypothermia, and reduced thickness of the intestinal mucosa. Compounding TRα0 and TRβ− mutations produces viable TRα0/0β−/− mice, which display a more severe linear growth reduction and a more profound hypothermia as well as impaired hearing. A striking phenotypic difference is observed between TRα0/0 and the previously described TRα−/− mice, which retain truncated TRΔα isoforms arising from a newly described promoter in intron 7. The lethality and severe impairment of the intestinal maturation in TRα−/− mice are rescued in TRα0/0 animals. We demonstrate that the TRΔα protein isoforms, which are natural products of the TRα locus, are the key determinants of these phenotypical differences. These data reveal the functional importance of the non-T3-binding variants encoded by the TRα locus in vertebrate postnatal development and homeostasis. PMID:11416150

  19. Antigenic and Mutational Analyses of Herpes Simplex Virus Glycoprotein B Reveal Four Functional Regions▿

    PubMed Central

    Bender, Florent C.; Samanta, Minu; Heldwein, Ekaterina E.; de Leon, Manuel Ponce; Bilman, Elina; Lou, Huan; Whitbeck, J. Charles; Eisenberg, Roselyn J.; Cohen, Gary H.

    2007-01-01

    Glycoprotein B (gB), along with gD, gH, and gL, is essential for herpes simplex virus (HSV) entry. Th