Sofia Annis
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View article: Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive
Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive Open
The resilience of the mitochondrial genome (mtDNA) to a high mutational pressure depends, in part, on negative purifying selection in the germline. A paradigm in the field has been that such selection, at least in part, takes place in prim…
View article: A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand
A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand Open
The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since …
View article: Systems-level regulation of microRNA networks by miR-130/301 promotes pulmonary hypertension
Systems-level regulation of microRNA networks by miR-130/301 promotes pulmonary hypertension Open
The authors recently became aware that in Figure 3D, lung images from a 10% O 2 -exposed mouse were inadvertently presented in the row labeled as lung images from a 10% O 2 + SU5416-exposed mouse.The authors reviewed the original data and …
View article: Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors
Mitochondrial Pseudogenes Suggest Repeated Inter-Species Hybridization among Direct Human Ancestors Open
The hypothesis that the evolution of humans involves hybridization between diverged species has been actively debated in recent years. We present the following novel evidence in support of this hypothesis: the analysis of nuclear pseudogen…
View article: 3GOLD: optimized Levenshtein distance for clustering third-generation sequencing data
3GOLD: optimized Levenshtein distance for clustering third-generation sequencing data Open
Background Third-generation sequencing offers some advantages over next-generation sequencing predecessors, but with the caveat of harboring a much higher error rate. Clustering-related sequences is an essential task in modern biology. To …
View article: Nuclear DNA-encoded fragments of mitochondrial DNA (mtDNA) confound analysis of selection of mtDNA mutations in human primordial germ cells
Nuclear DNA-encoded fragments of mitochondrial DNA (mtDNA) confound analysis of selection of mtDNA mutations in human primordial germ cells Open
The resilience of the mitochondrial genome to a high mutational pressure depends, in part, on purifying selection against detrimental mutations in the germline. It is crucial to understand the mechanisms of this process. Recently, Floros e…
View article: 3GOLD: Optimized Levenshtein distance for clustering third-generation sequencing data
3GOLD: Optimized Levenshtein distance for clustering third-generation sequencing data Open
Background:Third-generation sequencing offers some advantages over next-generation sequencing predecessors, but with the caveat of harboring a much higher error rate. Clustering-related sequences is an essential task in modern biology. To …
View article: LUCS: a high-resolution nucleic acid sequencing tool for accurate long-read analysis of individual DNA molecules
LUCS: a high-resolution nucleic acid sequencing tool for accurate long-read analysis of individual DNA molecules Open
Nucleic acid sequence analyses are fundamental to all aspects of biological research, spanning aging, mitochondrial DNA (mtDNA) and cancer, as well as microbial and viral evolution. Over the past several years, significant improvements in …
View article: High-resolution sequencing of mitochondrial DNA
High-resolution sequencing of mitochondrial DNA Open
Mitochondria, heralded as the powerhouses of the cell, contain small, highly-conserved genomes. This mitochondrial DNA (mtDNA) is abundant in most eukaryotic cells, reflecting its crucial role in providing protein subunits that are necessa…
View article: Quasi-Mendelian paternal inheritance of mitochondrial DNA: A notorious artifact, or anticipated behavior?
Quasi-Mendelian paternal inheritance of mitochondrial DNA: A notorious artifact, or anticipated behavior? Open
A recent report (1) presents the long-awaited confirmation of paternal inheritance of mtDNA in humans (2). Surprisingly, paternal transmission of mtDNA (1) follows a bimodal pattern: About half of the offspring show fairly uniform paternal…
View article: Quasi-Mendelian Paternal Inheritance of mitochondrial DNA: A notorious artifact, or anticipated mtDNA behavior?
Quasi-Mendelian Paternal Inheritance of mitochondrial DNA: A notorious artifact, or anticipated mtDNA behavior? Open
A recent report by Luo et al (2018) in PNAS (DOI:10.1073/pnas.1810946115) presented evidence of biparental inheritance of mitochondrial DNA. The pattern of inheritance, however, resembled that of a nuclear gene. The authors explained this …
View article: Impact of exercise on oocyte quality in the POLG mitochondrial DNA mutator mouse
Impact of exercise on oocyte quality in the POLG mitochondrial DNA mutator mouse Open
The mtDNA ‘mutator’ mouse, also called the ‘POLG’ mouse, is a well-characterized model frequently used for studies of progeroid aging. Harboring a mutation in the proofreading domain of the mitochondrial polymerase, polymerase-γ ( Polg ), …
View article: Nuclear pseudogenes of mtDNA (NUMTS) suggest repeated distant inter-species hybridization among direct human ancestors
Nuclear pseudogenes of mtDNA (NUMTS) suggest repeated distant inter-species hybridization among direct human ancestors Open
Introduction : Increasingly, the emergence and evolution of our species is being tied to genetic exchange between divergent lineages within ~1Ma (e.g., Neanderthals, Denisovans). However, little is known about genetic exchange during earli…
View article: Human evolution: Gradual or Punctuated? Accelerated integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A Hypothesis.
Human evolution: Gradual or Punctuated? Accelerated integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A Hypothesis. Open
The question: human evolution- gradual process or a rapid discontinuous change? Whether human origin was a gradual process or a result of rapid change has been a focus of intense debate. Of particular interest is the climate change ~2.9-2.…
View article: Human evolution: Gradual or Punctuated? Accelerated integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A Hypothesis.
Human evolution: Gradual or Punctuated? Accelerated integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A Hypothesis. Open
The question: human evolution- gradual process or a rapid discontinuous change? Whether human origin was a gradual process or a result of rapid change has been a focus of intense debate. Of particular interest is the climate change ~2.9-2.…
View article: Nuclear pseudogenes of mtDNA (NUMTS) suggest repeated distant inter-species hybridization among direct human ancestors
Nuclear pseudogenes of mtDNA (NUMTS) suggest repeated distant inter-species hybridization among direct human ancestors Open
Introduction : Increasingly, the emergence and evolution of our species is being tied to genetic exchange between divergent lineages within ~1Ma (e.g., Neanderthals, Denisovans). However, little is known about genetic exchange during earli…
View article: Human evolution: Gradual or Punctuated? Accelerated integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A Hypothesis.
Human evolution: Gradual or Punctuated? Accelerated integration of mtDNA pseudogenes into the nuclear genome coincides with speciation of the human genus. A Hypothesis. Open
The question: human evolution- gradual process or a rapid discontinuous change? Whether human origin was a gradual process or a result of rapid change has been a focus of intense debate. Of particular interest is the climate change ~2.9-2.…
View article: Genetic and hypoxic alterations of the microRNA-210-ISCU1/2 axis promote iron-sulfur deficiency and pulmonary hypertension.
Genetic and hypoxic alterations of the microRNA-210-ISCU1/2 axis promote iron-sulfur deficiency and pulmonary hypertension. Open
Iron-sulfur (Fe-S) clusters are essential for mitochondrial metabolism, but their regulation in pulmonary hypertension (PH) remains enigmatic. We demonstrate that alterations of the miR-210-ISCU1/2 axis cause Fe-S deficiencies in vivo and …
View article: Genetic and hypoxic alterations of the micro <scp>RNA</scp> ‐210‐ <scp>ISCU</scp> 1/2 axis promote iron–sulfur deficiency and pulmonary hypertension
Genetic and hypoxic alterations of the micro <span>RNA</span> ‐210‐ <span>ISCU</span> 1/2 axis promote iron–sulfur deficiency and pulmonary hypertension Open
Iron–sulfur (Fe‐S) clusters are essential for mitochondrial metabolism, but their regulation in pulmonary hypertension (PH) remains enigmatic. We demonstrate that alterations of the miR‐210‐ISCU1/2 axis cause Fe‐S deficiencies in vivo and …