Browsing by Subject "mitochondrial DNA"

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  • Pratas, Diogo; Toppinen, Mari; Pyöriä, Lari; Hedman, Klaus; Sajantila, Antti; Perdomo, Maria F. (2020)
    Background: Advances in sequencing technologies have enabled the characterization of multiple microbial and host genomes, opening new frontiers of knowledge while kindling novel applications and research perspectives. Among these is the investigation of the viral communities residing in the human body and their impact on health and disease. To this end, the study of samples from multiple tissues is critical, yet, the complexity of such analysis calls for a dedicated pipeline. We provide an automatic and efficient pipeline for identification, assembly, and analysis of viral genomes that combines the DNA sequence data from multiple organs. TRACESPipe relies on cooperation among 3 modalities: compression-based prediction, sequence alignment, and de novo assembly. The pipeline is ultra-fast and provides, additionally, secure transmission and storage of sensitive data. Findings: TRACESPipe performed outstandingly when tested on synthetic and ex vivo datasets, identifying and reconstructing all the viral genomes, including those with high levels of single-nucleotide polymorphisms. It also detected minimal levels of genomic variation between different organs. Conclusions: TRACESPipe's unique ability to simultaneously process and analyze samples from different sources enables the evaluation of within-host variability. This opens up the possibility to investigate viral tissue tropism, evolution, fitness, and disease associations. Moreover, additional features such as DNA damage estimation and mitochondrial DNA reconstruction and analysis, as well as exogenous-source controls, expand the utility of this pipeline to other fields such as forensics and ancient DNA studies. TRACESPipe is released under GPLv3 and is available for free download at https://github.com/viromelab/tracespipe.
  • Roed, Knut H; Kvie, Kjersti S; Bardsen, Bård-J; Laaksonen, Sauli; Lohi, Hannes; Kumpula, Jouko; Aronsson, Kjell-Å; Ahman, Birgitta; Vage, Jørn; Holand, Oystein (2021)
    We have analyzed DNA microsatellites and the mitochondrial control region in reindeer from 31 different husbandry areas in Norway, Sweden, and Finland in order to better understand the processes that underlie the genetic variability of the Nordic domestic herds. The distinct differentiation found in the nuclear markers but less so in the mitochondrial marker gives evidence of an origin from a common ancestral population which later evolved into the two main gene pools characterizing the nuclear genomes of domestic reindeer in Finland and most of Sweden and Norway. Analyses of temporal trends in effective population size give evidence of a rapid increase in number of reindeer before the population growth associated with the pastoral transition. This implies that the ancestry of contemporary domestic reindeer lay among a rapidly growing wild population possibly located in the boreal areas of eastern Fennoscandia or European Russia. The evolution of reindeer husbandry in Finland, perhaps with input from European Russia, which later spread to northern Norway could explain the shared genomic pattern observed in these areas today. The structured selection of productive female-centered herds may explain the genetic structure in other parts of Norway and in Sweden. The further substructuring of the Swedish/ Norwegian gene pool appears to follow the traditional language borders with the South Sami language dominating the southern and the Central Sami language in the more northern genetic subclusters. This suggests that traditional knowledge, cultural identities, and herd migrations have contributed to shape the genetic structure seen today. Ecological gradients are more pronounced within as compared to between the genetic clusters, giving further evidence that historical and social-cultural processes are important drivers for the genetic differentiations found in domestic reindeer across the Nordic countries.
  • Kvist, Laura; Honka, Johanna; Salazar, Daniela; Kirkinen, Tuija; Hemmann, Karin (2022)
    We used historical DNA samples to examine the history of a native horse breed, the Finnhorse. Samples were collected from private collections, museums, schools and excavations, representing the times prior to, during, and after the foundation of the breed; from the end of the 19th century and throughout the 20th century. We sequenced a fragment of mitochondrial DNA from these historical samples to study the history and evolution of maternal lineages of horses back to the early days of the breed, compared the mitochondrial DNA sequence diversity of different historical periods and modern day Finnhorses, estimated the effective population sizes, and searched for both temporal and geographic population genetic structure. We observed high maternal haplotype and nucleotide diversity at the time during the foundation of the breed, and a decrease in both measures during 1931-1970. In addition, we observed losses of some haplotypes present in the early stages of the breed. There was only slight evidence of geographical or temporal population structure. This study is, to our knowledge, the first to use such temporal sampling to reveal the history of a specific animal breed.
  • Plis, Kamila; Niedzialkowska, Magdalena; Borowik, Tomasz; Lang, Johannes; Heddergott, Mike; Tiainen, Juha; Bunevich, Aleksey; Sprem, Nikica; Paule, Ladislav; Danilkin, Aleksey; Kholodova, Marina; Zvychaynaya, Elena; Kashinina, Nadezhda; Pokorny, Bostjan; Flajsman, Katarina; Paulauskas, Algimantas; Djan, Mihajla; Ristic, Zoran; Novak, Lubos; Kusza, Szilvia; Miller, Christine; Tsaparis, Dimitris; Stoyanov, Stoyan; Shkvyria, Maryna; Suchentrunk, Franz; Kutal, Miroslav; Lavadinovic, Vukan; Snjegota, Dragana; Krapal, Ana-Maria; Danila, Gabriel; Veeroja, Rauno; Dulko, Elzbieta; Jedrzejewska, Bogumila (2022)
    To provide the most comprehensive picture of species phylogeny and phylogeography of European roe deer (Capreolus capreolus), we analyzed mtDNA control region (610 bp) of 1469 samples of roe deer from Central and Eastern Europe and included into the analyses additional 1541 mtDNA sequences from GenBank from other regions of the continent. We detected two mtDNA lineages of the species: European and Siberian (an introgression of C. pygargus mtDNA into C. capreolus). The Siberian lineage was most frequent in the eastern part of the continent and declined toward Central Europe. The European lineage contained three clades (Central, Eastern, and Western) composed of several haplogroups, many of which were separated in space. The Western clade appeared to have a discontinuous range from Portugal to Russia. Most of the haplogroups in the Central and the Eastern clades were under expansion during the Weichselian glacial period before the Last Glacial Maximum (LGM), while the expansion time of the Western clade overlapped with the Eemian interglacial. The high genetic diversity of extant roe deer is the result of their survival during the LGM probably in a large, contiguous range spanning from the Iberian Peninsula to the Caucasus Mts and in two northern refugia.
  • Chaudhry, Shafqat Rasul; Hafez, Ahmad; Rezai Jahromi, Behnam; Kinfe, Thomas Mehari; Lamprecht, Alf; Niemelä, Mika; Muhammad, Sajjad (2018)
    Aneurysmal subarachnoid hemorrhage (aSAH) represents only a small portion of all strokes, but accounts for almost half of the deaths caused by stroke worldwide. Neurosurgical clipping and endovascular coiling can successfully obliterate the bleeding aneurysms, but ensuing complications such as cerebral vasospasm, acute and chronic hydrocephalus, seizures, cortical spreading depression, delayed ischemic neurological deficits, and delayed cerebral ischemia lead to poor clinical outcomes. The mechanisms leading to these complications are complex and poorly understood. Early brain injury resulting from transient global ischemia can release molecules that may be critical to initiate and sustain inflammatory response. Hence, the events during early brain injury can influence the occurrence of delayed brain injury. Since the damage associated molecular pattern molecules (DAMPs) might be the initiators of inflammation in the pathophysiology of aSAH, so the aim of this review is to highlight their role in the context of aSAH from diagnostic, prognostic, therapeutic, and drug therapy monitoring perspectives. DAMPs represent a diverse and a heterogenous group of molecules derived from different compartments of cells upon injury. Here, we have reviewed the most important DAMPs molecules including high mobility group box-1 (HMGB1), S100B, hemoglobin and its derivatives, extracellular matrix components, IL-1α, IL-33, and mitochondrial DNA in the context of aSAH and their role in post-aSAH complications and clinical outcome after aSAH.
  • Fukuoh, Atsushi; Cannino, Giuseppe; Gerards, Mike; Buckley, Suzanne; Kazancioglu, Selena; Scialo, Filippo; Lihavainen, Eero; Ribeiro, Andre; Dufour, Eric; Jacobs, Howard T. (2014)
  • Richter, Uwe; McFarland, Robert; Taylor, Robert W.; Pickett, Sarah J. (2021)
    Mitochondrial diseases are clinically and genetically heterogeneous disorders, caused by pathogenic variants in either the nuclear or mitochondrial genome. This heterogeneity is particularly striking for disease caused by variants in mitochondrial DNA-encoded tRNA (mt-tRNA) genes, posing challenges for both the treatment of patients and understanding the molecular pathology. In this review, we consider disease caused by the two most common pathogenic mt-tRNA variants: m.3243A>G (within MT-TL1, encoding mt-tRNA(Leu(UUR))) and m.8344A>G (within MT-TK, encoding mt-tRNA(Lys)), which together account for the vast majority of all mt-tRNA-related disease. We compare and contrast the clinical disease they are associated with, as well as their molecular pathologies, and consider what is known about the likely molecular mechanisms of disease. Finally, we discuss the role of mitochondrial-nuclear crosstalk in the manifestation of mt-tRNA-associated disease and how research in this area not only has the potential to uncover molecular mechanisms responsible for the vast clinical heterogeneity associated with these variants but also pave the way to develop treatment options for these devastating diseases.
  • Översti, Sanni; Palo, Jukka U. (2022)
    Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from C-14-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age.