Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss
    Lewis, William H. ; Lind, Anders E. ; Sendra, Kacper M. ; Onsbring, Henning ; Williams, Tom A. ; Esteban, Genoveva F. ; Hirt, Robert P. ; Ettema, Thijs J.G. ; Embley, T.M. - \ 2020
    Molecular Biology and Evolution 37 (2020)2. - ISSN 0737-4038 - p. 524 - 539.
    anaerobic metabolism - evolution - genomics - hydrogenosomes - microbial eukaryotes - mitochondria

    Hydrogenosomes are H2-producing mitochondrial homologs found in some anaerobic microbial eukaryotes that provide a rare intracellular niche for H2-utilizing endosymbiotic archaea. Among ciliates, anaerobic and aerobic lineages are interspersed, demonstrating that the switch to an anaerobic lifestyle with hydrogenosomes has occurred repeatedly and independently. To investigate the molecular details of this transition, we generated genomic and transcriptomic data sets from anaerobic ciliates representing three distinct lineages. Our data demonstrate that hydrogenosomes have evolved from ancestral mitochondria in each case and reveal different degrees of independent mitochondrial genome and proteome reductive evolution, including the first example of complete mitochondrial genome loss in ciliates. Intriguingly, the FeFe-hydrogenase used for generating H2 has a unique domain structure among eukaryotes and appears to have been present, potentially through a single lateral gene transfer from an unknown donor, in the common aerobic ancestor of all three lineages. The early acquisition and retention of FeFe-hydrogenase helps to explain the facility whereby mitochondrial function can be so radically modified within this diverse and ecologically important group of microbial eukaryotes.

    Investigating microbial associations from sequencing survey data with co-correspondence analysis
    Alric, Benjamin ; Braak, Cajo J.F. ter; Desdevises, Yves ; Lebredonchel, Hugo ; Dray, Stéphane - \ 2020
    Molecular Ecology Resources 20 (2020)2. - ISSN 1755-098X - p. 468 - 480.
    co-correspondence analysis - co-occurrence network - Mamiellophyceae - microbial eukaryotes - next-generation sequencing - Prasinovirus

    Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next-generation sequencing (NGS) techniques with refined statistical analysis (e.g., network analysis, multivariate analysis) to characterize the structures of microbial communities. However, most of these approaches consider a single table of sequencing data measured for several samples. Technological advances now make it possible to collect NGS data on different taxonomic groups simultaneously for the same samples, allowing us to analyse a pair of tables. Here, an analytical framework based on co-correspondence analysis (CoCA) is proposed to study the distributions, assemblages and interactions between two microbial communities. We show the ability of this approach to highlight the relationships between two microbial communities, using two data sets exhibiting various types of interactions. CoCA identified strong association patterns between autotrophic and heterotrophic microbial eukaryote assemblages, on the one hand, and between microalgae and viruses, on the other. We demonstrate also how CoCA can be used, complementary to network analysis, to reorder co-occurrence networks and thus investigate the presence of patterns in ecological networks.

    RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration
    Onsbring, Henning ; Jamy, Mahwash ; Ettema, Thijs J.G. - \ 2018
    Current Biology 28 (2018)8. - ISSN 0960-9822 - p. 1281 - 1288.e3.
    cell damage repair - cell regeneration - ciliate - microbial eukaryotes - protist - RNA-seq - single-cell transcriptomics - Stentor

    While ciliates of the genus Stentor are known for their ability to regenerate when their cells are damaged or even fragmented, the physical and molecular mechanisms underlying this process are poorly understood. To identify genes involved in the regenerative capability of Stentor cells, RNA sequencing of individual Stentor polymorphus cell fragments was performed. After splitting a cell over the anterior-posterior axis, the posterior fragment has to regenerate the oral apparatus, while the anterior part needs to regenerate the hold fast. Altogether, differential expression analysis of both posterior and anterior S. polymorphus cell fragments for four different post-split time points revealed over 10,000 upregulated genes throughout the regeneration process. Among these, genes involved in cell signaling, microtubule-based movement, and cell cycle regulation seemed to be particularly important during cellular regeneration. We identified roughly nine times as many upregulated genes in regenerating S. polymorphus posterior fragments as compared to anterior fragments, indicating that regeneration of the anterior oral apparatus is a complex process that involves many genes. Our analyses identified several expanded groups of genes, such as dual-specific tyrosine-(Y)-phosphorylation-regulated kinases and MORN domain-containing proteins that seemingly act as key regulators of cellular regeneration. In agreement with earlier morphological and cell biological studies [1, 2], our differential expression analyses indicate that cellular regeneration and vegetative division share many similarities. Onsbring et al. sequence transcriptomes of individual bisections of regenerating cells of the giant heterotrichous ciliate Stentor polymorphus. Their differential expression analysis reveals that protein phosporylation, microtubule-based processes, and genes involved in the cell cycle are important for cellular regeneration.

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