Browsing Bergen Open Research Archive by Author "Johnston, Iain"
Now showing items 1-20 of 21
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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 ... -
Comparing Structure and Dynamics of Transition Graphs by the Symmetric Difference Metric Over an Edge-Filtration
Pascual, Belen Garcia; Salbu, Lars Moberg; Renz, Jessica; Giannakis, Konstantinos; Johnston, Iain (Journal article; Peer reviewed, 2024)Transition graphs or transition diagrams, describing the rates and probabilities with which a system changes between discrete states, are common throughout the sciences. In many cases, parameterisations of transition graphs ... -
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-CT: Inference and prediction for accumulation pathways with flexible data and model structures
Aga, Olav Nicolay Larsson; Brun, Morten; Dauda, Kazeem Adesina; Diaz-Uriarte, Ramon; Giannakis, Konstantinos; Johnston, Iain (Journal article; Peer reviewed, 2024-09-04)Accumulation processes, where many potentially coupled features are acquired over time, occur throughout the sciences from evolutionary biology to disease progression, and particularly in the study of cancer progression. ... -
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 ...