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Sökning: WFRF:(Sicheritz Ponten Thomas)

  • Resultat 11-18 av 18
  • Föregående 1[2]
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  • Sinding, Mikkel-Holger S., et al. (författare)
  • Population genomics of grey wolves and wolf-like canids in North America
  • 2018
  • Ingår i: PLOS Genetics. - 1553-7390 .- 1553-7404. ; 14:11
  • Tidskriftsartikel (refereegranskat)abstract
    • North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified "Polar wolf" population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.
  • Alsmark, Cecilia, et al. (författare)
  • Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes
  • 2013
  • Ingår i: Genome Biology. - 1465-6906 .- 1474-760X. ; 14:2, s. R19-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of prokaryotes. A number of independent investigations focusing on specific genes, individual genomes, or specific functional categories from various eukaryotes have indicated that lateral gene transfer does indeed affect eukaryotic genomes. However, the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution. Results: We used a phylogenomic approach to systematically investigate lateral gene transfer affecting the proteomes of thirteen, mainly parasitic, microbial eukaryotes, representing four of the six eukaryotic super-groups. All of the genomes investigated have been significantly affected by prokaryote-to-eukaryote lateral gene transfers, dramatically affecting the enzymes of core pathways, particularly amino acid and sugar metabolism, but also providing new genes of potential adaptive significance in the life of parasites. A broad range of prokaryotic donors is involved in such transfers, but there is clear and significant enrichment for bacterial groups that share the same habitats, including the human microbiota, as the parasites investigated. Conclusions: Our data show that ecology and lifestyle strongly influence gene origins and opportunities for gene transfer and reveal that, although the outlines of the core eukaryotic metabolism are conserved among lineages, the genes making up those pathways can have very different origins in different eukaryotes. Thus, from the perspective of the effects of lateral gene transfer on individual gene ancestries in different lineages, eukaryotic metabolism appears to be chimeric.
  • Alsmark, U. Cecilia, et al. (författare)
  • Horizontal gene transfer in eukaryotic parasites : a case study of Entamoeba histolytica and Trichomonas vaginalis
  • 2009
  • Ingår i: Horizontal Gene Transfer. - : Humana Press. - 9781603278522 - 9781603278539 ; , s. 489-500
  • Bokkapitel (övrigt vetenskapligt)abstract
    • Over the past few years it has become apparent that horizontal gene transfer (HGT) has played an important role in the evolution of pathogenic prokaryotes. What is less clear is the exact role that HGT has played in shaping the metabolism of eukaryotic organisms. The main problems are the reliable inference of HGT on a genomic scale as well as the functional assignment of genes in these poorly studied organisms. We have screened the completed genomes of the protists Entamoeba histolytica and Trichomonas vaginalis for cases of HGT from prokaryotes. Using a fast primary screen followed by a conservative phylogenetic approach, we found 68 and 153 recent cases of HGT in the respective organisms. The majority of transferred genes that fall into functional categories code for enzymes involved in metabolism. We found a broad range of prokaryotic lineages represented among the donors, but organisms that share similar environmental niches with E. histolytica and T. vaginalis, such as the gut and the vaginal mucosa, dominate.
  • Jensen, Lars Juhl, et al. (författare)
  • Analysis of two large functionally uncharacterized regions in theMethanopyrus kandleri AV19 genome
  • 2003
  • Ingår i: BMC Genomics. - 1471-2164 .- 1471-2164. ; 4, s. 12-
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: For most sequenced prokaryotic genomes, about a third of the protein coding genes annotated are "orphan proteins", that is, they lack homology to known proteins. These hypothetical genes are typically short and randomly scattered throughout the genome. This trend is seen for most of the bacterial and archaeal genomes published to date. RESULTS: In contrast we have found that a large fraction of the genes coding for such orphan proteins in the Methanopyrus kandleri AV19 genome occur within two large regions. These genes have no known homologs except from other M. kandleri genes. However, analysis of their lengths, codon usage, and Ribosomal Binding Site (RBS) sequences shows that they are most likely true protein coding genes and not random open reading frames.CONCLUSIONS: Although these regions can be considered as candidates for massive lateral gene transfer, our bioinformatics analysis suggests that this is not the case. We predict many of the organism specific proteins to be transmembrane and belong to protein families that are non-randomly distributed between the regions. Consistent with this, we suggest that the two regions are most likely unrelated, and that they may be integrated plasmids.
  • Knudsen, Steen, et al. (författare)
  • GenePublisher : automated analysis of DNA microarray data
  • 2003
  • Ingår i: Nucleic Acids Research. - 0305-1048 .- 1362-4962. ; 31:13, s. 3471-3476
  • Tidskriftsartikel (refereegranskat)abstract
    • GenePublisher, a system for automatic analysis of data from DNA microarray experiments, has been implemented with a web interface at http://www.cbs.dtu.dk/services/GenePublisher. Raw data are uploaded to the server together with a specification of the data. The server performs normalization, statistical analysis and visualization of the data. The results are run against databases of signal transduction pathways, metabolic pathways and promoter sequences in order to extract more information. The results of the entire analysis are summarized in report form and returned to the user.
  • Rasmussen, Simon, et al. (författare)
  • Early Divergent Strains of Yersinia pestis in Eurasia 5,000 Years Ago
  • 2015
  • Ingår i: Cell. - : Elsevier. - 0092-8674. ; 163:3, s. 571-582
  • Tidskriftsartikel (refereegranskat)abstract
    • The bacteria Yersinia pestis is the etiological agent of plague and has caused human pandemics with millions of deaths in historic times. How and when it originated remains contentious. Here, we report the oldest direct evidence of Yersinia pestis identified by ancient DNA in human teeth from Asia and Europe dating from 2,800 to 5,000 years ago. By sequencing the genomes, we find that these ancient plague strains are basal to all known Yersinia pestis. We find the origins of the Yersinia pestis lineage to be at least two times older than previous estimates. We also identify a temporal sequence of genetic changes that lead to increased virulence and the emergence of the bubonic plague. Our results show that plague infection was endemic in the human populations of Eurasia at least 3,000 years before any historical recordings of pandemics.
  • Sicheritz-Pontén, Thomas (författare)
  • Bioinformatic tools for the analysis of microbial genomes
  • 2000
  • Doktorsavhandling (övrigt vetenskapligt)abstract
    • High throughput genome sequencing projects are producing an enormous amount of rawdata which has to be converted into biological knowledge. The newly established field ofbioinformatics is concerned with the continuous development of novel methods and toolsfor the comparative analysis of DNA sequences and genomic data.The primary task of bioinformatics in genome sequencing projects is to identify andfunctionally classify all proteins putatively encoded by the genome. Due to the amountof data, first time analyses in large-scale projects have to be rudimentary and fast. We have sequenced Rickettsia prowazekii, an α-proteobacterium and the cauative agent of epidemic typhus in humans. For the analysis of the R. prowazekii genome we have developed CapDB, a sequence analysis and management system for automatic functional gene annotations and graphical display of the genome together with the biological information.Analysis of the 1.111.523 bp R. prowazekii genome revealed 834 complete open read-ing frames of which 523 could be linked to a biological function. In addition, 12 putativepseudogenes and an unusually high proportion of non-coding DNA (24%) were identified.Phylogenetic analyses indicate that R. prowazekii is more closely related to mitochondriathan other microbes studied thus far.With the availability of complete genomes, new ways of comparing organisms haveemerged., To study genomic structures, we have developed tools and methods for geneorder based comparisons (GRS) and complete genome alignments (GOBLIN). We de-fine the complete set of phylogenetic trees derived from the proteome of an organism asthe "phylome" and present software for automatic, large-scale reconstructions of phylo-genetic relationships - thus setting the stage for phylogenomic comparisons of microbialgenomes which are likely to reveal a rich web of evolutionary connections.
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  • Resultat 11-18 av 18
  • Föregående 1[2]
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