scholarly journals New Insights Into Mitochondrial DNA Reconstruction and Variant Detection in Ancient Samples

2021 ◽  
Vol 12 ◽  
Author(s):  
Maria Angela Diroma ◽  
Alessandra Modi ◽  
Martina Lari ◽  
Luca Sineo ◽  
David Caramelli ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Iron Age ◽  
Comprehensive Evaluation ◽  
Nuclear Genome ◽  
Sequencing Technologies ◽  
Almost All ◽  
Mtdna Variants ◽  
First Time ◽  
Adna Analysis ◽  
Ancient Remains

Ancient DNA (aDNA) studies are frequently focused on the analysis of the mitochondrial DNA (mtDNA), which is much more abundant than the nuclear genome, hence can be better retrieved from ancient remains. However, postmortem DNA damage and contamination make the data analysis difficult because of DNA fragmentation and nucleotide alterations. In this regard, the assessment of the heteroplasmic fraction in ancient mtDNA has always been considered an unachievable goal due to the complexity in distinguishing true endogenous variants from artifacts. We implemented and applied a computational pipeline for mtDNA analysis to a dataset of 30 ancient human samples from an Iron Age necropolis in Polizzello (Sicily, Italy). The pipeline includes several modules from well-established tools for aDNA analysis and a recently released variant caller, which was specifically conceived for mtDNA, applied for the first time to aDNA data. Through a fine-tuned filtering on variant allele sequencing features, we were able to accurately reconstruct nearly complete (>88%) mtDNA genome for almost all the analyzed samples (27 out of 30), depending on the degree of preservation and the sequencing throughput, and to get a reliable set of variants allowing haplogroup prediction. Additionally, we provide guidelines to deal with possible artifact sources, including nuclear mitochondrial sequence (NumtS) contamination, an often-neglected issue in ancient mtDNA surveys. Potential heteroplasmy levels were also estimated, although most variants were likely homoplasmic, and validated by data simulations, proving that new sequencing technologies and software are sensitive enough to detect partially mutated sites in ancient genomes and discriminate true variants from artifacts. A thorough functional annotation of detected and filtered mtDNA variants was also performed for a comprehensive evaluation of these ancient samples.

Male identification, generic classification and sexual dimorphism of Micronychus pardus (Kazantsev, 2018) comb. nov. (Coleoptera: Lycidae: Calochrominae)

Zootaxa ◽  
2019 ◽  
Vol 4657 (1) ◽  
pp. 177-182 ◽  
Author(s):  
MICHAL MOTYKA
Keyword(s):  
Mitochondrial Dna ◽  
Sexual Dimorphism ◽  
Species Identification ◽  
Dna Sequences ◽  
Morphological Characters ◽  
Molecular Data ◽  
Large Specimen ◽  
Molecular Analyses ◽  
Almost All ◽  
First Time

Almost all net-winged beetles are members of Müllerian complexes and their similarity due to phenotypic coevolution sometimes complicates species identification and generic placement. Therefore, large specimen series, detailed exhaustive examination of morphological characters and molecular data are needed to clarify the taxonomic placement. Using mitochondrial DNA sequences, I investigated the sexual dimorphism and generic placement of the recently described species Calochromus pardus Kazantsev, 2018. I found that the species does not belong in Calochromus Guérin-Méneville, 1833 and all morphological characters and molecular analyses point to its placement in Micronychus Motschulsky, 1861. Therefore, Micronychus pardus (Kazantsev, 2018), comb. nov. is proposed. Additionally, the male is described here for the first time showing the sexual dimorphism in the species. Unlike the females, the males do not superficially resemble members of Xylobanus Waterhouse, 1879 with bright coloured elytral costae and black background, but mimics the sympatrically occurring yellow and black lycids in the genus Cautires Waterhouse, 1879. 

scholarly journals Intracellular quality control of mitochondrial DNA: evidence and limitations

2019 ◽  
Vol 375 (1790) ◽  
pp. 20190176 ◽  
Author(s):  
Dmitry A. Knorre
Keyword(s):  
Quality Control ◽  
Mitochondrial Dna ◽  
Atp Synthase ◽  
Transmembrane Potential ◽  
Nuclear Genome ◽  
Mitochondrial Transmembrane Potential ◽  
Control Mechanisms ◽  
Mitochondrial Genotype ◽  
Mitochondrial Heterogeneity ◽  
Mtdna Variants

Eukaryotic cells can harbour mitochondria with markedly different transmembrane potentials. Intracellular mitochondrial quality-control mechanisms (e.g. mitophagy) rely on this intracellular variation to distinguish functional and damaged (depolarized) mitochondria. Given that intracellular mitochondrial DNA (mtDNA) genetic variation can induce mitochondrial heterogeneity, mitophagy could remove deleterious mtDNA variants in cells. However, the reliance of mitophagy on the mitochondrial transmembrane potential suggests that mtDNAs with deleterious mutations in ATP synthase can evade the control. This evasion is possible because inhibition of ATP synthase can increase the mitochondrial transmembrane potential. Moreover, the linkage of the mtDNA genotype to individual mitochondrial performance is expected to be weak owing to intracellular mitochondrial intercomplementation. Nonetheless, I reason that intracellular mtDNA quality control is possible and crucial at the zygote stage of the life cycle. Indeed, species with biparental mtDNA inheritance or frequent ‘leakage’ of paternal mtDNA can be vulnerable to invasion of selfish mtDNAs at the stage of gamete fusion. Here, I critically review recent findings on intracellular mtDNA quality control by mitophagy and discuss other mechanisms by which the nuclear genome can affect the competition of mtDNA variants in the cell. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.

Development of a mito-CRISPR system for generating mitochondrial DNA-deleted strain in Saccharomyces cerevisiae

2020 ◽  
Vol 85 (4) ◽  
pp. 895-901
Author(s):  
Takamitsu Amai ◽  
Tomoka Tsuji ◽  
Mitsuyoshi Ueda ◽  
Kouichi Kuroda
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mitochondrial Dna ◽  
Ethidium Bromide ◽  
Nuclear Genome ◽  
Target Sequence ◽  
Guide Rna ◽  
Crispr System ◽  
Mitochondrial Target ◽  
Gene Treatment ◽  
Mtdna Deletion

ABSTRACT Mitochondrial dysfunction can occur in a variety of ways, most often due to the deletion or mutation of mitochondrial DNA (mtDNA). The easy generation of yeasts with mtDNA deletion is attractive for analyzing the functions of the mtDNA gene. Treatment of yeasts with ethidium bromide is a well-known method for generating ρ° cells with complete deletion of mtDNA from Saccharomyces cerevisiae. However, the mutagenic effects of ethidium bromide on the nuclear genome cannot be excluded. In this study, we developed a “mito-CRISPR system” that specifically generates ρ° cells of yeasts. This system enabled the specific cleavage of mtDNA by introducing Cas9 fused with the mitochondrial target sequence at the N-terminus and guide RNA into mitochondria, resulting in the specific generation of ρ° cells in yeasts. The mito-CRISPR system provides a concise technology for deleting mtDNA in yeasts.

scholarly journals Deciphering the effects of kosmotrope and chaotrope salts during aqueous two phase extraction (ATPE) of polyphenolic compounds and glycoalkaloids from the leaves of a nutraceutical plant, Solanum retroflexum, with the aid of UPLC-QTOF-MS

2021 ◽  
Vol 64 (1) ◽  
Author(s):  
Tebogo Mokgehle ◽  
Ntakadzeni Madala ◽  
Wilson Gitari ◽  
Nikita Tavengwa
Keyword(s):  
Polar Compounds ◽  
Ultra Performance Liquid Chromatography ◽  
Polyphenolic Compounds ◽  
Phase Extraction ◽  
Two Phase ◽  
Solanum Retroflexum ◽  
Chaotropic Salts ◽  
Almost All ◽  
First Time ◽  
Aqueous Two Phase Extraction

AbstractSolanum plants (Solanaceae) are renowned source of nutraceuticals and have widely been explored for their phytochemical constituents. This work investigated the effects of kosmotropic and chaotropic salts on the number of phytochemicals extracted from the leaves of a nutraceutical plant, Solanum retroflexum, and analyzed on the ultra-performance liquid chromatography hyphenated to a quadrupole time of flight mass spectrometer (UPLC-QTOF-MS) detector. Here, a total of 20 different compounds were putatively characterized. The majority of the identified compounds were polyphenols and glycoalkaloids. Another compound, caffeoyl malate was identified for the first time in this plant. Glycoalkaloids such as solanelagnin, solamargine, solasonine, β-solanine (I) and β-solanine (II) were found to be extracted by almost all the salts used herein. Kosmotrope salts, overall, were more efficient in extracting polar compounds with 4 more polyphenolic compounds extracted compared to the chaotropes. Chaotropes were generally more selective for the extraction of less polar compounds (glycoalkaloids) with 3 more extracted than the kosmotropes. The chaotrope and the kosmotrope that extracted the most metabolites were NaCl and Na2SO4, respectively, with 12 metabolites extracted for each salt. This work demonstrated that a comprehensive metabolome of S. retroflexum, more than what was previously reported on the same plant, can be achieved by application of kosmotropes and chaotropes as extractants with the aid of the Aqueous Two Phase Extraction approach. The best-performing salts, Na2SO4 or NaCl, could potentially be applied on a commercial scale, to meet the ever-growing demand of the studied metabolites. The Aqueous Two Phase Extraction technique was found to be efficient in simultaneous extraction of multiple metabolites which can be applied in metabolomics.

scholarly journals Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 481 ◽  
Author(s):  
Chen ◽  
Lin ◽  
Xie ◽  
Zhong ◽  
Zhang ◽  
...  
Keyword(s):  
Insecticide Resistance ◽  
Single Molecule ◽  
Functional Categories ◽  
Genetic Studies ◽  
Sequencing Technologies ◽  
Clusters Of Orthologous Groups ◽  
Long Read ◽  
Main Gene ◽  
First Time ◽  
Main Factor

The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of B. odoriphaga was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in B. odoriphaga.

scholarly journals Mitochondrial DNA Methylation and Human Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4594
Author(s):  
Andrea Stoccoro ◽  
Fabio Coppedè
Keyword(s):  
Dna Methylation ◽  
Mitochondrial Dna ◽  
Mitochondrial Genome ◽  
Nuclear Dna ◽  
Epigenetic Modification ◽  
Nuclear Genome ◽  
Epigenetic Modifications ◽  
Human Diseases ◽  
Loop Region ◽  
D Loop

Epigenetic modifications of the nuclear genome, including DNA methylation, histone modifications and non-coding RNA post-transcriptional regulation, are increasingly being involved in the pathogenesis of several human diseases. Recent evidence suggests that also epigenetic modifications of the mitochondrial genome could contribute to the etiology of human diseases. In particular, altered methylation and hydroxymethylation levels of mitochondrial DNA (mtDNA) have been found in animal models and in human tissues from patients affected by cancer, obesity, diabetes and cardiovascular and neurodegenerative diseases. Moreover, environmental factors, as well as nuclear DNA genetic variants, have been found to impair mtDNA methylation patterns. Some authors failed to find DNA methylation marks in the mitochondrial genome, suggesting that it is unlikely that this epigenetic modification plays any role in the control of the mitochondrial function. On the other hand, several other studies successfully identified the presence of mtDNA methylation, particularly in the mitochondrial displacement loop (D-loop) region, relating it to changes in both mtDNA gene transcription and mitochondrial replication. Overall, investigations performed until now suggest that methylation and hydroxymethylation marks are present in the mtDNA genome, albeit at lower levels compared to those detectable in nuclear DNA, potentially contributing to the mitochondria impairment underlying several human diseases.

scholarly journals Comparison on the Nutrient Plunder Capacity of Orychophragmus violaceus and Brassica napus L. Based on Electrophysiological Information

Horticulturae ◽  
2021 ◽  
Vol 7 (8) ◽  
pp. 206
Author(s):  
Cheng Zhang ◽  
Yue Su ◽  
Yanyou Wu ◽  
Haitao Li ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Orychophragmus Violaceus ◽  
Nutrient Metabolism ◽  
Brassica Napus L ◽  
Adaptive Mechanisms ◽  
Capacitive Reactance ◽  
Time Determination ◽  
Almost All ◽  
First Time

The nutrient metabolism, growth and development of plants are strongly affected by its nutrient plunder, and plants have different adaptive mechanisms to low-nutrient environments. The electrophysiological activities involve almost all life processes of plants. In this study, the active transport flow of nutrient (NAF) and nutrient plunder capacity (NPC) of plants were defined based on leaf intrinsic impedance (IZ), capacitive reactance (IXc), inductive reactance (IXL) and capacitance (IC) to evaluate the nutrient plunder capacity of plants for the first time. The results indicate that Orychophragmus violaceus had higher (p < 0.01) NPC and IC and lower (p < 0.01) IR, IXc, IXL and IZ as compared to Brassica napus L., which supports a superior ion affinity and that it could be better adapted to low-nutrient environments. UAF and NPC of plants exhibited good correlations with crude protein, crude ash and water content, and precisely revealed the plunder capacity and adaptive strategies of plants to nutrients. The present work highlights that O. violaceus had superior NPC and ion affinity compared with B. napus, and provided a novel, rapid, reliable method based on the plant’s electrophysiological information for real-time determination of the nutrient plunder capacity of plants.

The champions' mitochondria: is it genetically determined? A review on mitochondrial DNA and elite athletic performance

2011 ◽  
Vol 43 (13) ◽  
pp. 789-798 ◽  
Author(s):  
Nir Eynon ◽  
María Morán ◽  
Ruth Birk ◽  
Alejandro Lucia
Keyword(s):  
Mitochondrial Dna ◽  
Endurance Exercise ◽  
Current Knowledge ◽  
Geographic Origin ◽  
Aerobic Performance ◽  
East African ◽  
Athletic Status ◽  
The Status ◽  
Genetically Determined ◽  
Mtdna Variants

Aerobic ATP generation by the mitochondrial respiratory oxidative phosphorylation system (OXPHOS) is a vital metabolic process for endurance exercise. Notably, mitochondrial DNA (mtDNA) codifies 13 of the 83 polypeptides implied in the respiratory chain. As such, there is a strong rationale for identifying an association between mtDNA variants and “aerobic” (endurance) exercise phenotypes. The aim of this review is to summarize current knowledge on the association between mtDNA, nuclear genes involved in mitochondriogenesis, and elite endurance athletic status. Several studies in nonathletic people have demonstrated an association between certain mtDNA lineages and aerobic performance, characterized by maximal oxygen uptake (V̇o2max). Whether mtDNA haplogroups are also associated with the status of being an elite endurance athlete is more controversial, with differences between studies arising from the different ethnic backgrounds of the athletic cohorts (Caucasian of mixed geographic origin, Asiatic, or East African).

A New Sahidic Fragment of the Gospel of Luke from the Michigan Collection

2014 ◽  
Vol 56 (2) ◽  
pp. 198-204
Author(s):  
Brice C. Jones
Keyword(s):  
Gospel Of Luke ◽  
Almost All ◽  
First Time

AbstractThis article publishes for the first time the extant remains of a Sahidic Coptic manuscript containing portions of Luke 17-19. Almost all of the special Lukan pericope concerning Jesus and Zacchaeus is preserved (19:1-10), as well as most of the parable of the Dishonest Judge (18:1-8). The edition includes a transcription, translation, palaeographical analysis, critical apparatus, as well as images of the fragment.

European Mail Armour

2021 ◽  
Author(s):  
Martijn A. Wijnhoven
Keyword(s):  
Early Modern ◽  
Middle Ages ◽  
Iron Age ◽  
Early Modern Period ◽  
Vital Role ◽  
Military Technology ◽  
Roman Army ◽  
Solid Foundation ◽  
First Time

Mail armour (commonly mislabelled 'chainmail') was used for more than two millennia on the battlefield. After its invention in the Iron Age, mail rapidly spread all over Europe and beyond. The Roman army, keen on new military technology, soon adopted mail armour and used it successfully for centuries. Its history did not stop there and mail played a vital role in warfare during the Middle Ages up to the Early Modern Period. Given its long history, one would think mail is a well-documented material, but that is not the case. For the first time, this books lays a solid foundation for the understanding of mail armour and its context through time. It applies a long-term multi-dimensional approach to extract a wealth of as yet untapped information from archaeological, iconographic and written sources. This is complemented with technical insights on the mail maker’s chaîne opératoire.

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