• Avoiding misleading estimates using mtDNA heteroplasmy statistics to study bottleneck size and selection 

      Giannakis, Konstantinos; Broz, Amanda K.; Sloan, Daniel B.; Johnston, Iain (Journal article; Peer reviewed, 2023)
      Mitochondrial DNA heteroplasmy samples can shed light on vital developmental and genetic processes shaping mitochondrial DNA populations. The sample means and sample variance of a set of heteroplasmy observations are ...
    • Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck 

      Edwards, David; Røyrvik, Ellen Christine; Chustecki, Joanne; Giannakis, Konstantinos; Glastad, Robert Clay; Radzvilavicius, Arunas; Johnston, Iain (Journal article; Peer reviewed, 2021)
      Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic “bottleneck” ...
    • Cell identity and nucleo-mitochondrial genetic context modulate OXPHOS performance and determine somatic heteroplasmy dynamics 

      Lechuga-Vieco, Ana Victoria; Latorre-Pellicer, Ana; Johnston, Iain; Prota, Gennaro; Gileadi, Uzi; Justo-Méndez, Raquel; Acín-Pérez, Rebeca; Martínez-De-Mena, Raquel; Fernández-Toro, Jose María; Jimenez-Blasco, Daniel; Mora, Alfonso; Nicolás-Ávila, Jose A.; Santiago, Demetrio J.; Priori, Silvia G.; Bolaños, Juan Pedro; Sabio, Guadalupe; Criado, Luis Miguel; Ruíz-Cabello, Jesús; Cerundolo, Vincenzo; Jones, Nick S.; Enríquez, Jose Antonio (Journal article; Peer reviewed, 2020)
      Heteroplasmy, multiple variants of mitochondrial DNA (mtDNA) in the same cytoplasm, may be naturally generated by mutations but is counteracted by a genetic mtDNA bottleneck during oocyte development. Engineered heteroplasmic ...
    • Cellular and environmental dynamics influence species-specific extents of organelle gene retention 

      Garcia Pascual, Belen; Nordbotten, Jan Martin; Johnston, Iain (Journal article; Peer reviewed, 2023)
      Mitochondria and plastids rely on many nuclear-encoded genes, but retain small subsets of the genes they need to function in their own organelle DNA (oDNA). Different species retain different numbers of oDNA genes, and the ...
    • Data science approaches provide a roadmap to understanding the role of abscisic acid in defence 

      Stevens, Katie; Johnston, Iain; Luna, Estrella (Journal article; Peer reviewed, 2023)
      Abscisic acid (ABA) is a plant hormone well known to regulate abiotic stress responses. ABA is also recognised for its role in biotic defence, but there is currently a lack of consensus on whether it plays a positive or ...
    • Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations 

      Hoitzing, Hanne; Gammage, Payam; van Haute, Lindsey; Minczuk, Michal; Johnston, Iain; Jones, Nick (Peer reviewed; Journal article, 2019-06-26)
      The dynamics of the cellular proportion of mutant mtDNA molecules is crucial for mitochondrial diseases. Cellular populations of mitochondria are under homeostatic control, but the details of the control mechanisms involved ...
    • Evolutionary inference across eukaryotes identifies universal features shaping organelle gene retention 

      Giannakis, Konstantinos; Arrowsmith, Samuel J.; Richards, Luke; Gasparini, Sara; Chustecki, Joanna M.; Røyrvik, Ellen Christine; Johnston, Iain (Journal article; Peer reviewed, 2022)
      Mitochondria and plastids power complex life. Why some genes and not others are retained in their organelle DNA (oDNA) genomes remains a debated question. Here, we attempt to identify the properties of genes and associated ...
    • HyperTraPS: Inferring probabilistic patterns of trait acquisition in evolutionary and disease progression pathways 

      Greenbury, Sam; Barahona, Mauricio; Johnston, Iain (Peer reviewed; Journal article, 2020)
      The explosion of data throughout the biomedical sciences provides unprecedented opportunities to learn about the dynamics of evolution and disease progression, but harnessing these large and diverse datasets remains ...
    • Interdisciplinary and Transferable Concepts in Bioinformatics Education: Observations and Approaches From a UK MSc Course 

      Johnston, Iain; Slater, Mark; Cazier, Jean-Baptiste (Journal article; Peer reviewed, 2022-02-24)
      Bioinformatics is a highly interdisciplinary subject, with substantial and growing influence in health, environmental science and society, and is utilised by scientists from many diverse academic backgrounds. Education in ...
    • Intracellular Energy Variability Modulates Cellular Decision-Making Capacity 

      Kerr, Ryan; Jabbari, Sara; Johnston, Iain (Journal article; Peer reviewed, 2019)
      Cells generate phenotypic diversity both during development and in response to stressful and changing environments, aiding survival. Functionally vital cell fate decisions from a range of phenotypic choices are made by ...
    • Metabolic role of the hepatic valine/3-hydroxyisobutyrate (3-HIB) pathway in fatty liver disease 

      Bjune, Mona Synnøve; Dyer, Laurence; Laupsa-Borge, Johnny; Sommersten, Cathrine Horn; McCann, Adrian; Glastad, Robert Clay; Johnston, Iain; Kern, Matthias; Blüher, Matthias; Mellgren, Gunnar; Dankel, Simon N (Journal article; Peer reviewed, 2023)
      Background: The valine (branched-chain amino acid) metabolite 3-hydroxyisobutyrate (3-HIB), produced by 3-Hydroxyisobutyryl-CoA Hydrolase (HIBCH), is associated with insulin resistance and type 2 diabetes, but implicated ...
    • Mitochondrial network structure controls cell-to-cell mtDNA variability generated by cell divisions 

      Glastad, Robert Clay; Johnston, Iain (Journal article; Peer reviewed, 2023)
      Mitochondria are highly dynamic organelles, containing vital populations of mitochondrial DNA (mtDNA) distributed throughout the cell. Mitochondria form diverse physical structures in different cells, from cell-wide ...
    • MtDNA sequence features associated with 'selfish genomes' predict tissue-specific segregation and reversion 

      Røyrvik, Ellen Christine; Johnston, Iain (Journal article; Peer reviewed, 2020)
      Mitochondrial DNA (mtDNA) encodes cellular machinery vital for cell and organism survival. Mutations, genetic manipulation, and gene therapies may produce cells where different types of mtDNA coexist in admixed populations. ...
    • Organelle bottlenecks facilitate evolvability by traversing heteroplasmic fitness valleys 

      Radzvilavicius, Arunas; Johnston, Iain (Journal article; Peer reviewed, 2022)
      Bioenergetic organelles—mitochondria and plastids—retain their own genomes (mtDNA and ptDNA), and these organelle DNA (oDNA) molecules are vital for eukaryotic life. Like all genomes, oDNA must be able to evolve to suit ...
    • S100A4 mRNA-protein relationship uncovered by measurement noise reduction 

      Athanasiou, Angelos-Theodoros; Nussbaumer, T; Kummer, Stefan; Hofer, Martin; Johnston, Iain; Staltner, Moritz; Allmer, Daniela M.; Scott, Milcah C.; Vogl, Claus; Fenger, Joelle M.; Modiano, Jaime F.; Walter, Ingrid; Steinborn, Ralf (Journal article; Peer reviewed, 2020)
      Intrinsic biological fluctuation and/or measurement error can obscure the association of gene expression patterns between RNA and protein levels. Appropriate normalization of reverse-transcription quantitative PCR (RT-qPCR) ...
    • Sorting of mitochondrial and plastid heteroplasmy in Arabidopsis is extremely rapid and depends on MSH1 activity 

      Broz, Amanda K.; Keene, Alexandra; Gyorfy, Matheus Fernandes; Hodous, Mychaela; Johnston, Iain; Sloan, Daniel B. (Journal article; Peer reviewed, 2022)
      The fate of new mitochondrial and plastid mutations depends on their ability to persist and spread among the numerous organellar genome copies within a cell (heteroplasmy). The extent to which heteroplasmies are transmitted ...
    • Stochastic organelle genome segregation through Arabidopsis development and reproduction 

      Broz, Amanda K.; Sloan, Daniel B.; Johnston, Iain (Journal article; Peer reviewed, 2024)
      Organelle DNA (oDNA) in mitochondria and plastids is vital for plant (and eukaryotic) life. Selection against damaged oDNA is mediated in part by segregation – sorting different oDNA types into different cells in the ...
    • Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution 

      Johnston, Iain; Dingle, Kamaludin; Greenbury, Sam; Camargo, Chico Q.; Doye, Jonathan P K; Ahnert, Sebastian E.; Louis, Ard A. (Journal article; Peer reviewed, 2022)
      Engineers routinely design systems to be modular and symmetric in order to increase robustness to perturbations and to facilitate alterations at a later date. Biological structures also frequently exhibit modularity and ...
    • What is quantitative plant biology? 

      Autran, Daphné; Bassel, George W.; Chae, Eunyoung; Ezer, Daphne; Ferjani, Ali; Fleck, Christian; Hamant, Olivier; Hartmann, Félix P.; Jiao, Yuling; Johnston, Iain; Kwiatkowska, Dorota; Lim, Boon L.; Mahönen, Ari Pekka; Morris, Richard J.; Mulder, Bela M.; Nakayama, Naomi; Sozzani, Ross; Strader, Lucia C.; Ten Tusscher, Kirsten; Ueda, Minako; Wolf, Sebastian (Journal article; Peer reviewed, 2021)
      Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new ...