Base-excision repair deficiency alone or combined with increased oxidative stress does not increase mtDNA point mutations in mice

…, NA Bonekamp, A Mourier, MA Isokallio… - Nucleic Acids …, 2018 - academic.oup.com
Mitochondrial DNA (mtDNA) mutations become more prevalent with age and are postulated
to contribute to the ageing process. Point mutations of mtDNA have been suggested to …

Mitochondrial stress response triggered by defects in protein synthesis quality control

…, E Jokitalo, TA Nyman, MA Isokallio… - Life science …, 2019 - life-science-alliance.org
Mitochondria have a compartmentalized gene expression system dedicated to the synthesis
of membrane proteins essential for oxidative phosphorylation. Responsive quality control …

[PDF][PDF] Genotype imputation workflow v3. 0 V. 2

K Pärn, MA Isokallio, J Nuñez-Fontarnau, A Palotie… - 2019 - protocols.io
1 The actual imputation protocol begins at step 2. All consecutive steps (commands given in'cmd
COMMAND'sections) must be run to ensure high-quality results. For a'quick and dirty'…

High-throughput detection of mtDNA mutations leading to tRNA processing errors

MA Isokallio, JB Stewart - Mitochondrial Gene Expression: Methods and …, 2021 - Springer
Some mutations in the tRNA genes of mitochondrial DNA (mtDNA) have been demonstrated
to affect the processing of the mitochondrial transcriptome in human patients with …

[HTML][HTML] Isolation of high-quality, highly enriched mitochondrial DNA from mouse tissues

MA Isokallio, JB Stewart - 2018 - protocols.io
One remarkable issue in mitochondrial DNA sequencing and variant detection is heavy nuclear
DNA contamination persistent throughout the commonly used mitochondria enrichment …

[HTML][HTML] Transcriptomic Analysis of (Group I) Clostridium botulinum ATCC 3502 Cold Shock Response

E Dahlsten, M Isokallio, P Somervuo, M Lindström… - PloS one, 2014 - journals.plos.org
Profound understanding of the mechanisms foodborne pathogenic bacteria utilize in
adaptation to the environmental stress they encounter during food processing and storage is of …

The two-component system CBO2306/CBO2307 is important for cold adaptation of Clostridium botulinum ATCC 3502

Y Derman, M Isokallio, M Lindström… - International journal of food …, 2013 - Elsevier
Clostridium botulinum is a notorious foodborne pathogen. Its ability to adapt to and grow at
low temperatures is of interest for food safety. Two-component systems (TCSs) have been …

[HTML][HTML] Low-frequency variant calling from high-quality mtDNA sequencing data

MA Isokallio, J Stewart - 2018 - protocols.io
High-quality, highly enriched mitochondrial DNA (mtDNA) sample enables detection of
extremely low-frequency mtDNA variants. When mtDNA is carefully enriched, fragmented in the …

The source and fate of mitochondrial DNA mutations using high-sensitivity next-generation sequencing technologies

M Isokallio - 2017 - kups.ub.uni-koeln.de
Pathogenic mutations in mitochondrial DNA (mtDNA) are known to cause numerous inherited
diseases. However, the lack of methods to transgenically manipulate the mtDNA limits the …

[HTML][HTML] Genotyping chip data lift-over to reference genome build GRCh38/hg38

K Pärn, JN Fontarnau, MA Isokallio, T Sipilä… - 2019 - protocols.io
For a'quick and dirty'lift-over you can jump straight to Step 2 and only run that. For high-
quality and veri ed results we strongly recommend running at least through Steps 1-4 and …