92 results on '"Zoller, Stefan"'
Search Results
52. Signatures of local adaptation in candidate genes of oaks (Quercusspp.) with respect to present and future climatic conditions
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Rellstab, Christian, primary, Zoller, Stefan, additional, Walthert, Lorenz, additional, Lesur, Isabelle, additional, Pluess, Andrea R., additional, Graf, René, additional, Bodénès, Catherine, additional, Sperisen, Christoph, additional, Kremer, Antoine, additional, and Gugerli, Felix, additional
- Published
- 2016
- Full Text
- View/download PDF
53. Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing
- Author
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Stockenhuber, Reinhold, Zoller, Stefan, Shimizu-Inatsugi, Rie, Gugerli, Felix, Shimizu, Kentaro K, Widmer, Alex, Fischer, Martin C, and University of Zurich
- Subjects
Cell Nucleus ,Genetic Markers ,1000 Multidisciplinary ,Sequence Analysis, RNA ,Gene Expression Profiling ,Science ,Computational Biology ,1100 General Agricultural and Biological Sciences ,UFSP13-7 Evolution in Action: From Genomes to Ecosystems ,10127 Institute of Evolutionary Biology and Environmental Studies ,10126 Department of Plant and Microbial Biology ,Genetic Loci ,1300 General Biochemistry, Genetics and Molecular Biology ,Brassicaceae ,570 Life sciences ,biology ,590 Animals (Zoology) ,Medicine ,U7 Systems Biology / Functional Genomics ,Phylogeny ,Research Article ,Plant Proteins - Abstract
The lack of DNA sequence information for most non-model organisms impairs the design of primers that are universally applicable for the study of molecular polymorphisms in nuclear markers. Next-generation sequencing (NGS) techniques nowadays provide a powerful approach to overcome this limitation. We present a flexible and inexpensive method to identify large numbers of nuclear primer pairs that amplify in most Brassicaceae species. We first obtained and mapped NGS transcriptome sequencing reads from two of the distantly related Brassicaceae species, Cardamine hirsuta and Arabis alpina, onto the Arabidopsis thaliana reference genome, and then identified short conserved sequence motifs among the three species bioinformatically. From these, primer pairs to amplify coding regions (nuclear protein coding loci, NPCL) and exon-primed intron-crossing sequences (EPIC) were developed. We identified 2,334 universally applicable primer pairs, targeting 1,164 genes, which provide a large pool of markers as readily usable genomic resource that will help addressing novel questions in the Brassicaceae family. Testing a subset of the newly designed nuclear primer pairs revealed that a great majority yielded a single amplicon in all of the 30 investigated Brassicaceae taxa. Sequence analysis and phylogenetic reconstruction with a subset of these markers on different levels of phylogenetic divergence in the mustard family were compared with previous studies. The results corroborate the usefulness of the newly developed primer pairs, e.g., for phylogenetic analyses or population genetic studies. Thus, our method provides a cost-effective approach for designing nuclear loci across a broad range of taxa and is compatible with current NGS technologies., PLoS ONE, 10 (6), ISSN:1932-6203
- Published
- 2015
54. Approaches for parametrization of Markovian models of molecular evolution for protein-coding sequences
- Author
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Zoller, Stefan, Buhmann, Joachim M., and Gonnet, Gastón H.
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PROTEIN SEQUENCE ANALYSIS + PEPTIDE SEQUENCE ANALYSIS ,STOCHASTISCHE MODELLE + STOCHASTISCHE SIMULATION (WAHRSCHEINLICHKEITSRECHNUNG) ,MOLECULAR EVOLUTION (BIOLOGICAL EVOLUTION) ,ddc:570 ,MOLEKULARE EVOLUTION (BIOLOGISCHE EVOLUTION) ,STOCHASTIC MODELS + STOCHASTIC SIMULATION (PROBABILITY THEORY) ,PROTEIN-SEQUENZANALYSE + PEPTID-SEQUENZANALYSE ,Life sciences - Published
- 2015
55. Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species
- Author
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Rellstab, Christian, Zoller, Stefan, Tedder, Andrew, Gugerli, Felix, Fischer, Martin C, and University of Zurich
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1000 Multidisciplinary ,Genotype ,lcsh:R ,lcsh:Medicine ,Genetic Variation ,High-Throughput Nucleotide Sequencing ,1100 General Agricultural and Biological Sciences ,Polymorphism, Single Nucleotide ,10127 Institute of Evolutionary Biology and Environmental Studies ,Gene Frequency ,1300 General Biochemistry, Genetics and Molecular Biology ,Brassicaceae ,570 Life sciences ,biology ,590 Animals (Zoology) ,lcsh:Q ,lcsh:Science ,Research Article - Abstract
Sequencing of pooled samples (Pool-Seq) using next-generation sequencing technologies has become increasingly popular, because it represents a rapid and cost-effective method to determine allele frequencies for single nucleotide polymorphisms (SNPs) in population pools. Validation of allele frequencies determined by Pool-Seq has been attempted using an individual genotyping approach, but these studies tend to use samples from existing model organism databases or DNA stores, and do not validate a realistic setup for sampling natural populations. Here we used pyrosequencing to validate allele frequencies determined by Pool-Seq in three natural populations of Arabidopsis halleri (Brassicaceae). The allele frequency estimates of the pooled population samples (consisting of 20 individual plant DNA samples) were determined after mapping Illumina reads to (i) the publicly available, high-quality reference genome of a closely related species (Arabidopsis thaliana) and (ii) our own de novo draft genome assembly of A. halleri. We then pyrosequenced nine selected SNPs using the same individuals from each population, resulting in a total of 540 samples. Our results show a highly significant and accurate relationship between pooled and individually determined allele frequencies, irrespective of the reference genome used. Allele frequencies differed on average by less than 4%. There was no tendency that either the Pool-Seq or the individual-based approach resulted in higher or lower estimates of allele frequencies. Moreover, the rather high coverage in the mapping to the two reference genomes, ranging from 55 to 284x, had no significant effect on the accuracy of the Pool-Seq. A resampling analysis showed that only very low coverage values (below 10-20x) would substantially reduce the precision of the method. We therefore conclude that a pooled re-sequencing approach is well suited for analyses of genetic variation in natural populations. ISSN:1932-6203
- Published
- 2013
56. Improved recovery of ancient DNA from subfossil wood – application to the world's oldest Late Glacial pine forest.
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Lendvay, Bertalan, Hartmann, Martin, Brodbeck, Sabine, Nievergelt, Daniel, Reinig, Frederick, Zoller, Stefan, Parducci, Laura, Gugerli, Felix, Büntgen, Ulf, and Sperisen, Christoph
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TREE populations ,PLANT genetics ,SAPWOOD ,PINE ,CYTOSINE ,THYMINE - Abstract
Summary: Ancient DNA from historical and subfossil wood has a great potential to provide new insights into the history of tree populations. However, its extraction and analysis have not become routine, mainly because contamination of the wood with modern plant material can complicate the verification of genetic information. Here, we used sapwood tissue from 22 subfossil pines that were growing
c . 13 000 yr bp in Zurich, Switzerland. We developed and evaluated protocols to eliminate surface contamination, and we tested ancient DNA authenticity based on plastid DNA metabarcoding and the assessment of post‐mortem DNA damage. A novel approach using laser irradiation coupled with bleaching and surface removal was most efficient in eliminating contaminating DNA. DNA metabarcoding confirmed which ancient DNA samples repeatedly amplified pine DNA and were free of exogenous plant taxa. Pine DNA sequences of these samples showed a high degree of cytosine to thymine mismatches, typical of post‐mortem damage. Stringent decontamination of wood surfaces combined with DNA metabarcoding and assessment of post‐mortem DNA damage allowed us to authenticate ancient DNA retrieved from the oldest Late Glacial pine forest. These techniques can be applied to any subfossil wood and are likely to improve the accessibility of relict wood for genome‐scale ancient DNA studies. [ABSTRACT FROM AUTHOR]- Published
- 2018
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57. Walking the thin line… ten years later: the dilemma of above- versus below-ground features to support phylogenies in the <italic>Russulaceae</italic> (Basidiomycota).
- Author
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Buyck, Bart, Zoller, Stefan, and Hofstetter, Valerie
- Abstract
For the very first time, morpho-anatomical features of both fruiting bodies as well as below-ground structures have been confronted with a newly produced multigene phylogeny of root symbiotic basidiomycetes using one of the most speciose genera of ectomycorrhizal fungi (
Russula , Russulales) as an example. In this first of two papers, the authors focus more specifically on below-ground structures. Our five-gene phylogeny divides the genus in five main clades, here interpreted as representing seven subgenera, all significantly supported. Although more conserved than features of fruiting bodies, the anatomy of ectomycorrhiza does not allow for an unambiguous characterization of the main clades resolved by phylogenetic analysis, but the anatomy of ectomycorrhiza performs better to naturally classify the species of this genus. Features of fruiting bodies remain much more adequate for the delimitation of terminal clades and are irreplaceable for morphological species identification. Tropical taxa mostly nest in ancient lineages, but are also present in some terminal clades of otherwise temperate species groups. The shift from plectenchymatic to pseudoparenchymatic ECM outer mantle structures happened most likely already in the paleotropics, and is here hypothesized to have facilitated a major diversification of the genus with new hosts in the northern hemisphere. Available data as well as our own observations on below ground structures of severalLactifluus species suggests that this genus shares withRussula the absence of lactifers in ECM mantles and rhizomorphs, contrary to species ofLactarius where lactifers are always present. First observations on rhizomorphs of species inMultifurca confirm the presence of vessel-like and ladder-like hyphae, also found in the other agarioid genera of this family, while distinct lactifers are only present in the lactarioid, but not in russuloid members of this genus. [ABSTRACT FROM AUTHOR]- Published
- 2018
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58. Circulating FABP4 Is a Prognostic Biomarker in Patients With Acute Coronary Syndrome but Not in Asymptomatic Individuals
- Author
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Reiser, Hans, primary, Klingenberg, Roland, additional, Hof, Danielle, additional, Cooksley-Decasper, Seraina, additional, Fuchs, Nina, additional, Akhmedov, Alexander, additional, Zoller, Stefan, additional, Marques-Vidal, Pedro, additional, Marti Soler, Helena, additional, Heg, Dik, additional, Landmesser, Ulf, additional, Rodondi, Nicolas, additional, Mach, Francois, additional, Windecker, Stephan, additional, Vollenweider, Peter, additional, Matter, Christian M., additional, Lüscher, Thomas F., additional, von Eckardstein, Arnold, additional, and Gawinecka, Joanna, additional
- Published
- 2015
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59. TRAL: tandem repeat annotation library
- Author
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Schaper, Elke, primary, Korsunsky, Alexander, additional, Pečerska, Jūlija, additional, Messina, Antonio, additional, Murri, Riccardo, additional, Stockinger, Heinz, additional, Zoller, Stefan, additional, Xenarios, Ioannis, additional, and Anisimova, Maria, additional
- Published
- 2015
- Full Text
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60. Maximum-Likelihood Tree Estimation Using Codon Substitution Models with Multiple Partitions
- Author
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Zoller, Stefan, primary, Boskova, Veronika, additional, and Anisimova, Maria, additional
- Published
- 2015
- Full Text
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61. New semi-empirical codon substitution models based on principal component analysis of mammalian sequences
- Author
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Zoller, Stefan
- Subjects
MATHEMATICAL MODELING AND SIMULATION IN BIOCHEMISTRY AND MOLECULAR BIOLOGY ,MOLECULAR EVOLUTION (BIOLOGICAL EVOLUTION) ,MODELLRECHNUNG UND SIMULATION IN BIOCHEMIE UND MOLEKULARBIOLOGIE ,MOLEKULARE EVOLUTION (BIOLOGISCHE EVOLUTION) ,Life sciences - Published
- 2010
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62. Genetic Evidence for Reproductive Isolation Among Sympatric Epichloë Endophytes as Inferred from Newly Developed Microsatellite Markers
- Author
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Schirrmann, Melanie K., primary, Zoller, Stefan, additional, Fior, Simone, additional, and Leuchtmann, Adrian, additional
- Published
- 2014
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63. Detection and genetic characterisation of a novel mycovirus in Hymenoscyphus fraxineus, the causal agent of ash dieback
- Author
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Schoebel, Corine N., primary, Zoller, Stefan, additional, and Rigling, Daniel, additional
- Published
- 2014
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64. Signatures of local adaptation in candidate genes of oaks ( Quercus spp.) with respect to present and future climatic conditions.
- Author
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Rellstab, Christian, Zoller, Stefan, Walthert, Lorenz, Lesur, Isabelle, Pluess, Andrea R., Graf, René, Bodénès, Catherine, Sperisen, Christoph, Kremer, Antoine, and Gugerli, Felix
- Subjects
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GENES , *WHITE oak , *TREES & climate , *FOREST genetics , *TREE populations - Abstract
Testing how populations are locally adapted and predicting their response to their future environment is of key importance in view of climate change. Landscape genomics is a powerful approach to investigate genes and environmental factors involved in local adaptation. In a pooled amplicon sequencing approach of 94 genes in 71 populations, we tested whether >3500 single nucleotide polymorphisms ( SNPs) in the three most common oak species in Switzerland ( Quercus petraea, Q. pubescens, Q. robur) show an association with abiotic factors related to local topography, historical climate and soil characteristics. In the analysis including all species, the most frequently associated environmental factors were those best describing the habitats of the species. In the species-specific analyses, the most important environmental factors and associated SNPs greatly differed among species. However, we identified one SNP and seven genes that were associated with the same environmental factor across all species. We finally used regressions of allele frequencies of the most strongly associated SNPs along environmental gradients to predict the risk of nonadaptedness ( RONA), which represents the average change in allele frequency at climate-associated loci theoretically required to match future climatic conditions. RONA is considerable for some populations and species (up to 48% in single populations) and strongly differs among species. Given the long generation time of oaks, some of the required allele frequency changes might not be realistic to achieve based on standing genetic variation. Hence, future adaptedness requires gene flow or planting of individuals carrying beneficial alleles from habitats currently matching future climatic conditions. [ABSTRACT FROM AUTHOR]
- Published
- 2016
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65. Distinct evolutionary strategies in the GGPPS family from plants
- Author
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Coman, Diana, primary, Altenhoff, Adrian, additional, Zoller, Stefan, additional, Gruissem, Wilhelm, additional, and Vranová, Eva, additional
- Published
- 2014
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66. Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps
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Fischer, Martin C., primary, Rellstab, Christian, additional, Tedder, Andrew, additional, Zoller, Stefan, additional, Gugerli, Felix, additional, Shimizu, Kentaro K., additional, Holderegger, Rolf, additional, and Widmer, Alex, additional
- Published
- 2013
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67. Die Landschaft als Wahrnehmungsproblem
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Tanner, Karl Martin and Zoller, Stefan
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- 1997
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68. Rust fungi on Annonaceae II: the genusDasysporaBerk. & M.A. Curtis
- Author
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Beenken, Ludwig, primary, Zoller, Stefan, additional, and Berndt, Reinhard, additional
- Published
- 2012
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69. A Genomic Approach to Examine the Complex Evolution of Laurasiatherian Mammals
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Hallström, Björn M., primary, Schneider, Adrian, additional, Zoller, Stefan, additional, and Janke, Axel, additional
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- 2011
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70. Hepatocyte-specific deletion of the antiapoptotic protein myeloid cell leukemia-1 triggers proliferation and hepatocarcinogenesis in mice
- Author
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Weber, Achim, primary, Boger, Regina, additional, Vick, Binje, additional, Urbanik, Toni, additional, Haybaeck, Johannes, additional, Zoller, Stefan, additional, Teufel, Andreas, additional, Krammer, Peter H., additional, Opferman, Joseph T., additional, Galle, Peter R., additional, Schuchmann, Marcus, additional, Heikenwalder, Mathias, additional, and Schulze-Bergkamen, Henning, additional
- Published
- 2009
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71. Systematics of the genusChaetosphaeriaand its allied genera: morphological and phylogenetic diversity in north temperate and neotropical taxa
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Fernández, Fernando A., primary, Miller, Andrew N., additional, Huhndorf, Sabine M., additional, Lutzoni, François M., additional, and Zoller, Stefan, additional
- Published
- 2006
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72. Effects of Angiotensin II on Rat Pancreatic Stellate Cells
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Reinehr, Roland, primary, Zoller, Stefan, additional, Klonowski-Stumpe, Hanne, additional, Kordes, Claus, additional, and Häussinger, Dieter, additional
- Published
- 2004
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73. New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve thePeltigera caninaspecies complex
- Author
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Miadlikowska, Jolanta, primary, Lutzoni, François, additional, Goward, Trevor, additional, Zoller, Stefan, additional, and Posada, David, additional
- Published
- 2003
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74. Pcr Primers for the Amplification of Mitochondrial Small Subunit Ribosomal DNA of Lichen-forming Ascomycetes
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Zoller, Stefan, primary, Scheidegger, Christoph, additional, and Sperisen, Christoph, additional
- Published
- 1999
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75. 'Dare more security'
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Zoller, Stefan
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Europe -- Military aspects ,Europe -- Safety and security measures ,Military strategy -- Evaluation ,Aerospace and defense industries ,Military and naval science - Abstract
The European security strategy 'A secure Europe in a better world' should be the guiding principle for all nations, even though it is a tough task based on the complex modern conditions.
- Published
- 2007
76. The trans-Atlantic link
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Zoller, Stefan, Stevens, Robert J., Guarguaglini, Pier Francesco, and Ranque, Denis
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Defense contracts -- Negotiation, mediation and arbitration ,Defense industry -- Negotiation, mediation and arbitration ,Government contract ,Defense industry ,Aerospace and defense industries ,History ,Military and naval science ,North Atlantic Treaty Organization -- Military policy - Abstract
Leading defense contractors express need for trans-Atlantic ties as the best way as owing to increasing military demands the industry faces the challenge of providing complex, compact solutions at lower prices while still making profits. They emphasize that cooperation is the best option, as the consolidation, the defense technological revolution and the impact of globalization have transformed the industry to such an extent, making it difficult to operate alone in an antiquated, unrealistic business model.
- Published
- 2006
77. Mitochondrial genome evolution in species belonging to the Phialocephala fortinii s.l. - Acephala applanata species complex.
- Author
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Du�, Angelo, Bruggmann, R�my, Zoller, Stefan, Bernt, Matthias, and Gr�nig, Christoph R.
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BIOLOGICAL evolution ,PHYLOGENY ,OXIDATIVE phosphorylation ,BIVALVES ,MITOCHONDRIA - Abstract
Background: Mitochondrial (mt) markers are successfully applied in evolutionary biology and systematics because mt genomes often evolve faster than the nuclear genomes. In addition, they allow robust phylogenetic analysis based on conserved proteins of the oxidative phosphorylation system. In the present study we sequenced and annotated the complete mt genome of P. subalpina, a member of the Phialocephala fortinii s.l.--Acephala applanata species complex (PAC). PAC belongs to the Helotiales, which is one of the most diverse groups of ascomycetes including more than 2,000 species. The gene order was compared to deduce the mt genome evolution in the Pezizomycotina. Genetic variation in coding and intergenic regions of the mtDNA was studied for PAC to assess the usefulness of mt DNA for species diagnosis. Results: The mt genome of P. subalpina is 43,742 bp long and codes for 14 mt genes associated with the oxidative phosphorylation. In addition, a GIY-YIG endonuclease, the ribosomal protein S3 (Rps3) and a putative N-acetyl-transferase were recognized. A complete set of tRNA genes as well as the large and small rRNA genes but no introns were found. All protein-coding genes were confirmed by EST sequences. The gene order in P. subalpina deviated from the gene order in Sclerotinia sclerotiorum, the only other helotialean species with a fully sequenced and annotated mt genome. Gene order analysis within Pezizomycotina suggests that the evolution of gene orders is mostly driven by transpositions. Furthermore, sequence diversity in coding and non-coding mtDNA regions in seven additional PAC species was pronounced and allowed for unequivocal species diagnosis in PAC. Conclusions: The combination of non-interrupted ORFs and EST sequences resulted in a high quality annotation of the mt genome of P. subalpina, which can be used as a reference for the annotation of other mt genomes in the Helotiales. In addition, our analyses show that mtDNA loci will be the marker of choice for future analysis of PAC communities. [ABSTRACT FROM AUTHOR]
- Published
- 2012
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78. Hepatocyte-specific deletion of the antiapoptotic protein myeloid cell leukemia-1 triggers proliferation and hepatocarcinogenesis in mice.
- Author
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Weber, Achim, Boger, Regina, Vick, Binje, Urbanik, Toni, Haybaeck, Johannes, Zoller, Stefan, Teufel, Andreas, Krammer, Peter H., Opferman, Joseph T., Galle, Peter R., Schuchmann, Marcus, Heikenwalder, Mathias, and Schulze-Bergkamen, Henning
- Published
- 2010
- Full Text
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79. Slow algae, fast fungi: exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa
- Author
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Zoller, Stefan and Lutzoni, François
- Subjects
- *
PLANT genetics , *FUNGAL diseases of plants , *COCCOMYCES , *SYMBIOSIS - Abstract
Omphalina basidiolichens are obligate mutualistic associations of a fungus of the genus Omphalina (the exhabitant) and a unicellular green alga of the genus Coccomyxa (the inhabitant). It has been suggested that symbiotic inhabitants have a lower rate of genetic change compared to exhabitants because the latter are more exposed to abiotic environmental variation and competition from other organisms. In order to test this hypothesis we compared substitution rates in the nuclear ribosomal internal transcribed spacer region (ITS1, 5.8S, ITS2) among fungal species with rates among their respective algal symbionts. To ensure valid comparisons, only taxon pairs (12) with a common evolutionary history were used. On average, substitution rates in the ITS1 portion of Omphalina pairs were 27.5 times higher than rates in the corresponding pairs of Coccomyxa since divergence from their respective ancestor at the base of the Omphalina/Coccomyxa lineage. Substitution rates in the 5.8S and the ITS2 portions were 2.4 and 18.0 times higher, respectively. The highest rate difference (43.0) was found in the ITS1 region. These are, to our knowledge, the highest differences of substitution rates reported for symbiotic organisms. We conclude that the Omphalina model system conforms to the proposed hypothesis of lower substitution rates in the inhabitant, but that the mode of transmission of the inhabitant (vertical versus horizontal) could be a prevailing factor in the regulation of unequal rates of nucleotide substitution between co-evolving symbionts. Our phylogenetic study of Coccomyxa revealed three main lineages within this genus, corresponding to free-living Coccomyxa, individuals isolated from basidiolichens Omphalina and Coccomyxa isolated from ascolichens belonging to the Peltigerales. [Copyright &y& Elsevier]
- Published
- 2003
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80. Rust fungi on Annonaceae II: the genus DasysporaBerk. & M.A. Curtis
- Author
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Beenken, Ludwig, Zoller, Stefan, and Berndt, Reinhard
- Abstract
Dasyspora gregaria, the single species of the allegedly monotypic rust genus Dasyspora(Basidiomycota, Pucciniales), was investigated by light microscopy and DNA sequencing (ITS1–5.8S–ITS2 region, partial LSU and SSU of the nuclear rDNA, mt cytochrome oxidase subunit 3). Both methods indicated that D. gregariais not a single species but can be split in 11 distinct taxa, each of which appear confined to a single Xylopiaspecies (Annonaceae) host. Herein nine of these are described as new. Both the phylogenetic analyses and morphology show that the species are grouped into two main clades designated Dasyspora gregariaand D. winteri. The first comprises D. gregaria, the type species of the genus, which is restricted to X. cayennensis,two new species on X. aromatica, D. segregariafrom northern South America and D. echinatafrom Brazil. The second clade is formed by D. winteri, recombined from Puccinia winterion X. sericea,and the new species D. amazonicaon X. amazonica, D. emarginataeon X. emarginata, D. frutescentison X. frutescens, D. ferrugineaeon X. frutescensvar. ferruginea, D. guianensison X. benthamii, D. mesoamericanaon X. frutescens, and D. nitidaeon X. nitida. Dasyspora frutescentisand D. mesoamericanawere not clearly distinguishable by their morphology and host associations but differed from another in their sequences and geographic distributions. They are considered cryptic species. An identification key and the distributions are given for all recognized species. Along with molecular data we discuss the systematic position of Dasysporain the Pucciniales.
- Published
- 2012
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81. Systematics of the genus Chaetosphaeriaand its allied genera: morphological and phylogenetic diversity in north temperate and neotropical taxa
- Author
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Fernández, Fernando A., Miller, Andrew N., Huhndorf, Sabine M., Lutzoni, François M., and Zoller, Stefan
- Abstract
Chaetosphaeriais a common saprobic pyrenomycete genus with simple, homogeneous teleomorphs and complex, diverse anamorphs. As currently circumscribed in the literature, the genus encompasses 30 species distributed in four ‘natural groups’, and includes morphological entities in 11 anamorphic genera. Species frequently have been defined primarily based on characters of the anamorphs resulting in species with almost indistinguishable teleomorphs. This study aimed to assess the value and significance of morphological characters in resolving phylogenetic relationships in Chaetosphaeriaand its allied genera. Phylogenetic relationships of 42 taxa, representing 29 species distributed in Chaetosphaeriaand five related genera, were estimated with partial sequences of the nuclear LSU rDNA and β-tubulin genes. Sequences were analyzed with maximum parsimony, maximum likelihood and Bayesian methods. Phylogenetic analyses of these two genes combined revealed two major lineages. The Chaetosphaerialineage includes 21 species possessing both typical and new sexual and asexual morphologies. The lineage contains a strongly supported monophyletic clade of 13 species and eight paraphyletic taxa; the latter includes C. innumera, the type species of the genus. The second major lineage includes groupings concordant with the morphological circumscriptions of the genera Melanochaeta, Melanopsammella, Striatosphaeria, Zignoëllaand the new genus Tainosphaeria.
- Published
- 2006
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82. New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera caninaspecies complex
- Author
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Miadlikowska, Jolanta, Lutzoni, François, Goward, Trevor, Zoller, Stefan, and Posada, David
- Abstract
The Peltigera caninaspecies complex consists of foliose lichenized bitunicate ascohymenial discomycetes forming section Peltigerawithin the genus Peltigera(Lecanoromycetes, lichen-forming Ascomycetes). To test the circumscription of highly polymorphic species and to resolve relationships among putative members of the P. caninacomplex, part of the nuclear ribosomal DNA large subunit (LSU rDNA) and the entire internal-transcribed spacer (ITS rDNA) were sequenced for 84 individuals representing 33 putative Peltigerataxa. Seventeen of the 25 taxa from the P. caninacomplex are well established and widely accepted. The remaining eight taxa have been proposed recently but are undescribed. A hypervariable region in ITS1 (ITS1-HR, sites 111–237 in our alignment) showed remarkable variation in length, especially in the P. caninacomplex, ranging from 8 to 126 bp, and contained several microsatellites. We describe here an alignment-free method to code such large gap-rich hypervariable regions for phylogenetic analyses. Variation among ITS1-HR sequences greatly contributed to species delimitation and species identification and can be a major asset to future population studies for specific species within section Peltigera. Sequences of ITS1-HR alone were sufficient to identify all existing species of Peltigerafrom the P. caninaspecies complex and related sections Retifoveataeand Horizontalesincluded in this study. However, only when INAASE (for short ambiguously aligned regions) and ITS1-HR coded characters were added to the combined analysis of nonambiguous LSU and ITS sites was it possible to reach the level of phylogenetic resolution and support necessary to disentangle the P. caninacomplex. We report here complete concordance between phylogenetically based and morphologically based species delimitation for 15 of the 17 species from the P. caninacomplex (P. canina, P. cinnamomea, P. degenii, P. evansiana, P. frigida, P. kristinssonii, P. laciniata, P. lambinonii, P. lepidophora, P. membranacea, P. monticola, P. ponojensis, P. praetextata, P. rufescensand P. ulcerata). Four of the eight newly proposed but undescribed taxa most likely represent new species (P. “fuscopraetextata”, P. “neocanina”, P. “neorufescens” and P. “scotteri”) within the P. caninacomplex. We found that morphologically and chemically distinct P. didactylas. str. and P. didactylavar. extenuataform two non-sister monophyletic entities, therefore the latter taxon should be recognized at the species level (P. extenuata). The North American and European populations of the morphologically uniform P. degeniimight represent two sibling species because they were found to be genetically distinct and monophyletic. Two major monophyletic groups within the P. caninacomplex (CICADE = CInnamomea + CAnina + DEgenii group and PORUDI = POnojensis + RUfescens + DIdactyla group) seem to be correlated with different humidity preferences. Although some authors previously have suggested interspecies recombination within the P. caninacomplex, we did not find statistically significant evidence for this phenomenon based on LSU and ITS sequences.
- Published
- 2004
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83. Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)
- Author
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Rogivue, Aude, Choudhury, Rimjhim R., Zoller, Stefan, Joost, Stéphane, Felber, François, Kasser, Michel, Parisod, Christian, and Gugerli, Felix
- Subjects
Arabis alpina ,Genescale ,Vaud Prealps ,Linkage disequilibrium ,Single‐nucleotide polymorphisms ,food and beverages ,Genome‐wide diversity ,Transposable elements - Abstract
Advances in high‐throughput sequencing have promoted the collection of reference genomes and genome‐wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single‐nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural populations to genotype SNPs as well as polymorphic long terminal repeat retrotransposons (polymorphic TEs; i.e. presence/absence of TE insertions at specific loci). We identified 291,396 SNPs and 20,548 polymorphic TEs, comparing their contributions to genomic diversity and divergence across populations. Few SNPs were shared among populations and overall showed high population‐specific variation, whereas most polymorphic TEs segregated among populations. The genomic context of these two classes of variants further highlighted candidate adaptive loci having a putative impact on functional genes. In particular, 4.96% of the SNPs were identified as non‐synonymous or affecting start/stop codons. In contrast, 43% of the polymorphic TEs were present next to Arabis genes enriched in functional categories related to the regulation of reproduction and responses to biotic as well as abiotic stresses. This unprecedented dataset, mapping variation gained from SNPs and complementary polymorphic TEs within and among populations, will serve as a rich resource for addressing microevolutionary processes shaping genome variation.
84. Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species
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Rellstab, Christian, Zoller, Stefan, Tedder, Andrew, Gugerli, Felix, and Fischer, Martin C.
- Subjects
15. Life on land - Abstract
Sequencing of pooled samples (Pool-Seq) using next-generation sequencing technologies has become increasingly popular, because it represents a rapid and cost-effective method to determine allele frequencies for single nucleotide polymorphisms (SNPs) in population pools. Validation of allele frequencies determined by Pool-Seq has been attempted using an individual genotyping approach, but these studies tend to use samples from existing model organism databases or DNA stores, and do not validate a realistic setup for sampling natural populations. Here we used pyrosequencing to validate allele frequencies determined by Pool-Seq in three natural populations of Arabidopsis halleri (Brassicaceae). The allele frequency estimates of the pooled population samples (consisting of 20 individual plant DNA samples) were determined after mapping Illumina reads to (i) the publicly available, high-quality reference genome of a closely related species (Arabidopsis thaliana) and (ii) our own de novo draft genome assembly of A. halleri. We then pyrosequenced nine selected SNPs using the same individuals from each population, resulting in a total of 540 samples. Our results show a highly significant and accurate relationship between pooled and individually determined allele frequencies, irrespective of the reference genome used. Allele frequencies differed on average by less than 4%. There was no tendency that either the Pool-Seq or the individual-based approach resulted in higher or lower estimates of allele frequencies. Moreover, the rather high coverage in the mapping to the two reference genomes, ranging from 55 to 284x, had no significant effect on the accuracy of the Pool-Seq. A resampling analysis showed that only very low coverage values (below 10-20x) would substantially reduce the precision of the method. We therefore conclude that a pooled re-sequencing approach is well suited for analyses of genetic variation in natural populations., PLoS ONE, 8 (11), ISSN:1932-6203
85. A de novo chromosome‐level genome assembly of Coregonus sp. 'Balchen' : one representative of the Swiss Alpine whitefish radiation
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De-Kayne, Rishi, Zoller, Stefan, and Feulner, Philine G. D.
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570 Life sciences ,biology ,14. Life underwater - Abstract
Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life-history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild-caught Coregonus sp. “Balchen” from Lake Thun to ~90x coverage. PacBio reads were assembled independently using three different assemblers, Falcon, Canu and wtdbg2 and subsequently scaffolded with additional Hi-C data. All three assemblies were highly contiguous, had strong synteny to a previously published Coregonus linkage map, and when mapping additional short-read data to each of the assemblies, coverage was fairly even across most chromosome-scale scaffolds. Here, we present the first de novo genome assembly for the Salmonid subfamily Coregoninae. The final 2.2 Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb, and was 93.3% complete for BUSCOs. The assembly consisted of ~52% TEs and contained 44,525 genes.
86. Circulating FABP4 Is a Prognostic Biomarker in Patients With Acute Coronary Syndrome but Not in Asymptomatic Individuals
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Vollenweider, Peter, Cooksley-Decasper, Seraina, Klingenberg, Roland, Mach, Francois, Heg, Dik, Rodondi, Nicolas, Zoller, Stefan, Matter, Christian M, Von Eckardstein, Arnold, Reiser, Hans, Akhmedov, Alexander, Fuchs, Nina, Lüscher, Thomas F, Windecker, Stephan, Landmesser, Ulf, Gawinecka, Joanna, Marti Soler, Helena, Hof, Danielle, and Marques-Vidal, Pedro
- Subjects
2. Zero hunger ,610 Medicine & health ,360 Social problems & social services ,3. Good health - Abstract
OBJECTIVE Blood-borne biomarkers reflecting atherosclerotic plaque burden have great potential to improve clinical management of atherosclerotic coronary artery disease and acute coronary syndrome (ACS). APPROACH AND RESULTS Using data integration from gene expression profiling of coronary thrombi versus peripheral blood mononuclear cells and proteomic analysis of atherosclerotic plaque-derived secretomes versus healthy tissue secretomes, we identified fatty acid-binding protein 4 (FABP4) as a biomarker candidate for coronary artery disease. Its diagnostic and prognostic performance was validated in 3 different clinical settings: (1) in a cross-sectional cohort of patients with stable coronary artery disease, ACS, and healthy individuals (n=820), (2) in a nested case-control cohort of patients with ACS with 30-day follow-up (n=200), and (3) in a population-based nested case-control cohort of asymptomatic individuals with 5-year follow-up (n=414). Circulating FABP4 was marginally higher in patients with ST-segment-elevation myocardial infarction (24.9 ng/mL) compared with controls (23.4 ng/mL; P=0.01). However, elevated FABP4 was associated with adverse secondary cerebrovascular or cardiovascular events during 30-day follow-up after index ACS, independent of age, sex, renal function, and body mass index (odds ratio, 1.7; 95% confidence interval, 1.1-2.5; P=0.02). Circulating FABP4 predicted adverse events with similar prognostic performance as the GRACE in-hospital risk score or N-terminal pro-brain natriuretic peptide. Finally, no significant difference between baseline FABP4 was found in asymptomatic individuals with or without coronary events during 5-year follow-up. CONCLUSIONS Circulating FABP4 may prove useful as a prognostic biomarker in risk stratification of patients with ACS.
87. Distinct evolutionary strategies in the GGPPS family from plants
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Coman, Diana, Altenhoff, Adrian, Zoller, Stefan, Gruissem, Wilhelm, and Vranová, Eva
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GGPPS ,Paralogs ,fungi ,Subfunctionalization ,food and beverages ,15. Life on land ,Isoprenoids ,Specialized metabolism - Abstract
Multiple geranylgeranyl diphosphate synthases (GGPPS) for biosynthesis of geranylgeranyl diphosphate (GGPP) exist in plants. GGPP is produced in the isoprenoid pathway and is a central precursor for various primary and specialized plant metabolites. Therefore, its biosynthesis is an essential regulatory point in the isoprenoid pathway. We selected 119 GGPPSs from 48 species representing all major plant lineages, based on stringent homology criteria. After the diversification of land plants, the number of GGPPS paralogs per species increases. Already in the moss Physcomitrella patens, GGPPS appears to be encoded by multiple paralogous genes. In gymnosperms, neofunctionalization of GGPPS may have enabled optimized biosynthesis of primary and specialized metabolites. Notably, lineage-specific expansion of GGPPS occurred in land plants. As a representative species we focused here on Arabidopsis thaliana, which retained the highest number of GGPPS paralogs (twelve) among the 48 species we considered in this study. Our results show that the A. thaliana GGPPS gene family is an example of evolution involving neo- and subfunctionalization as well as pseudogenization. We propose subfunctionalization as one of the main mechanisms allowing the maintenance of multiple GGPPS paralogs in A. thaliana genome. Accordingly, the changes in the expression patterns of the GGPPS paralogs occurring after gene duplication led to developmental and/or condition specific functional evolution., Frontiers in Plant Science, 5, ISSN:1664-462X
88. Cysteine-rich angiogenic inducer 61 (Cyr61): a novel soluble biomarker of acute myocardial injury improves risk stratification after acute coronary syndromes
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Klingenberg, Roland, Aghlmandi, Soheila, Liebetrau, Christoph, Räber, Lorenz, Gencer, Baris, Nanchen, David, Carballo, David, Akhmedov, Alexander, Montecucco, Fabrizio, Zoller, Stefan, Brokopp, Chad, Heg, Dik, Jüni, Peter, Marti Soler, Helena, Marques-Vidal, Pedro-Manuel, Vollenweider, Peter, Dörr, Oliver, Rodondi, Nicolas, Mach, François, Windecker, Stephan, Landmesser, Ulf, Von Eckardstein, Arnold, Hamm, Christian W, Matter, Christian M, and Lüscher, Thomas F
- Subjects
cardiovascular diseases ,610 Medicine & health ,360 Social problems & social services ,3. Good health - Abstract
Aims We aimed to identify a novel biomarker involved in the early events leading to an acute coronary syndrome (ACS) and evaluate its role in diagnosis and risk stratification. Methods and results Biomarker identification was based on gene expression profiling. In coronary thrombi of ACS patients, cysteine-rich angiogenic inducer 61 (Cyr61, CCN1) gene transcripts were highly up-regulated compared with peripheral mononuclear cells. In a murine ischaemia-reperfusion model (I/R), myocardial Cyr61 expression was markedly increased compared with the controls. Cyr61 levels were determined in human serum using an enzyme-linked immunosorbent assay. Cohorts of ACS (n = 2168) referred for coronary angiography, stable coronary artery disease (CAD) (n = 53), and hypertrophic obstructive cardiomyopathy (HOCM) patients (n = 15) served to identify and evaluate the diagnostic and prognostic performance of the biomarker. Cyr61 was markedly elevated in ST-elevation myocardial infarction patients compared with non-ST-elevation myocardial infarction/unstable angina or stable CAD patients, irrespective of whether coronary thrombi were present. Cyr61 was rapidly released after occlusion of a septal branch in HOCM patients undergoing transcoronary ablation of septal hypertrophy. Cyr61 improved risk stratification for all-cause mortality when added to the reference GRACE risk score at 30 days (C-statistic 0.88 to 0.89, P = 0.001) and 1 year (C-statistic 0.77 to 0.80, P
89. A de novo chromosome-level genome assembly of Coregonus sp. 'Balchen': One representative of the Swiss Alpine whitefish radiation
- Author
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De-Kayne, Rishi, Zoller, Stefan, and Feulner, Philine G.D.
- Subjects
Coregonus ,Genome assembly ,Whitefish ,Alpine whitefish ,14. Life underwater ,Salmonidae - Abstract
Salmonids are of particular interest to evolutionary biologists due to their incredible diversity of life‐history strategies and the speed at which many salmonid species have diversified. In Switzerland alone, over 30 species of Alpine whitefish from the subfamily Coregoninae have evolved since the last glacial maximum, with species exhibiting a diverse range of morphological and behavioural phenotypes. This, combined with the whole genome duplication which occurred in the ancestor of all salmonids, makes the Alpine whitefish radiation a particularly interesting system in which to study the genetic basis of adaptation and speciation and the impacts of ploidy changes and subsequent rediploidization on genome evolution. Although well‐curated genome assemblies exist for many species within Salmonidae, genomic resources for the subfamily Coregoninae are lacking. To assemble a whitefish reference genome, we carried out PacBio sequencing from one wild‐caught Coregonus sp. “Balchen ” from Lake Thun to ~90× coverage. PacBio reads were assembled independently using three different assemblers, falcon , canu and wtdbg2 and subsequently scaffolded with additional Hi‐C data. All three assemblies were highly contiguous, had strong synteny to a previously published Coregonus linkage map, and when mapping additional short‐read data to each of the assemblies, coverage was fairly even across most chromosome‐scale scaffolds. Here, we present the first de novo genome assembly for the Salmonid subfamily Coregoninae. The final 2.2‐Gb wtdbg2 assembly included 40 scaffolds, an N50 of 51.9 Mb and was 93.3% complete for BUSCOs. The assembly consisted of ~52% transposable elements and contained 44,525 genes., Molecular Ecology Resources, 20 (4), ISSN:1755-098X, ISSN:1471-8278, ISSN:1755-0998, ISSN:1471-8286
90. Depletion of FOXP3+ regulatory T cells promotes hypercholesterolemia and atherosclerosis.
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Klingenberg, Roland, Gerdes, Norbert, Badeau, Robert M., Gisterå, Anton, Strodthoff, Daniela, Ketelhuth, Daniel F. J., Lundberg, Anna M., Rudling, Mats, Nilsson, Stefan K., Olivecrona, Gunilla, Zoller, Stefan, Lohmann, Christine, Lüscher, Thomas F., Jauhiainen, Matti, Sparwasser, Tim, and Hansson, Göran K.
- Subjects
- *
HYPERCHOLESTEREMIA , *T cells , *ATHEROSCLEROSIS , *DIPHTHERIA toxin , *LIPOPROTEINS , *GENE expression , *LIPASES , *PHENOTYPES - Abstract
Atherosclerosis is a chronic inflammatory disease promoted by hyperlipidemia. Several studies support FOXP3-positive regulatory T cells (Tregs) as inhibitors of atherosclerosis; however, the mechanism underlying this protection remains elusive. To define the role of FOXP3-expressing Tregs in atherosclerosis, we used the DEREG mouse, which expresses the diphtheria toxin (DT) receptor under control of the Treg-specific Foxp3 promoter, allowing for specific ablation of FOXP3+ Tregs. Lethally irradiated, atherosclerosis-prone, low-den-sity lipoprotein receptor-deficient (Ldlr-/-) mice received DEREG bone marrow and were injected with DT to eliminate FOXP3+ Tregs. Depletion of Tregs caused a 2.1-fold increase in atherosclerosis without a concomi-tant increase in vascular inflammation. These mice also exhibited a 1.7-fold increase in plasma cholesterol and an atherogenic lipoprotein profile with increased levels of VLDL. Clearance of VLDL and chylomicron rem-nants was hampered, leading to accumulation of cholesterol-rich particles in the circulation. Functional and protein analyses complemented by gene expression array identified reduced protein expression of sortilin-1 in liver and increased plasma enzyme activity of lipoprotein lipase, hepatic lipase, and phospholipid transfer protein as mediators of the altered lipid phenotype. These results demonstrate that FOXP3+ Tregs inhibit atherosclerosis by modulating lipoprotein metabolism. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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- View/download PDF
91. Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism.
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Zajac N, Zoller S, Seppälä K, Moi D, Dessimoz C, Jokela J, Hartikainen H, and Glover N
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- Animals, Gene Ontology, Genome, Genome Size, Genomics, Phylogeny, Snails parasitology, Trematoda classification, Adaptation, Physiological genetics, Gene Duplication, Parasites, Trematoda genetics
- Abstract
Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trematode Atriophallophorus winterbourni and its comparative genomic analysis to other major parasitic trematodes. First, we reconstructed the species phylogeny, and dated the split of A. winterbourni from the Opisthorchiata suborder to approximately 237.4 Ma (±120.4 Myr). We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to parasitism. To do this, we used hierarchical orthologous groups to reconstruct three ancestral genomes on the phylogeny leading to A. winterbourni and performed a GO (Gene Ontology) enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subsequent genomic changes. Out of the 11,499 genes in the A. winterbourni genome, as much as 24% have arisen through duplication events since the speciation of A. winterbourni from the Opisthorchiata, and as much as 31.9% appear to be novel, that is, newly acquired. We found 13 gene families in A. winterbourni to have had more than ten genes arising through these recent duplications; all of which have functions potentially relating to host behavioral manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. We identified several families with genes evolving under positive selection. Our results provide a valuable resource for future studies on the genomic basis of adaptation to parasitism and point to specific candidate genes putatively involved in antagonistic host-parasite adaptation., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2021
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92. Accounting for Programmed Ribosomal Frameshifting in the Computation of Codon Usage Bias Indices.
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Garcia V, Zoller S, and Anisimova M
- Subjects
- Algorithms, Saccharomyces cerevisiae genetics, Selection, Genetic, Codon, Frameshifting, Ribosomal, Models, Genetic, Protein Biosynthesis genetics, RNA, Messenger genetics
- Abstract
Experimental evidence shows that synonymous mutations can have important consequences on genetic fitness. Many organisms display codon usage bias (CUB), where synonymous codons that are translated into the same amino acid appear with distinct frequency. Within genomes, CUB is thought to arise from selection for translational efficiency and accuracy, termed the translational efficiency hypothesis (TEH). Indeed, CUB indices correlate with protein expression levels, which is widely interpreted as evidence for translational selection. However, these tests neglect -1 programmed ribosomal frameshifting (-1 PRF), an important translational disruption effect found across all organisms of the tree of life. Genes that contain -1 PRF signals should cost more to express than genes without. Thus, CUB indices that do not consider -1 PRF may overestimate genes' true adaptation to translational efficiency and accuracy constraints. Here, we first investigate whether -1 PRF signals do indeed carry such translational cost. We then propose two corrections for CUB indices for genes containing -1 PRF signals. We retest the TEH in Saccharomyces cerevisiae under these corrections. We find that the correlation between corrected CUB index and protein expression remains intact for most levels of uniform -1 PRF efficiencies, and tends to increase when these efficiencies decline with protein expression. We conclude that the TEH is strengthened and that -1 PRF events constitute a promising and useful tool to examine the relationships between CUB and selection for translation efficiency and accuracy., (Copyright © 2018 Garcia et al.)
- Published
- 2018
- Full Text
- View/download PDF
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