Search

Aggressive chemicals intended for cleaning pools or unclogging drains contain high concentrations of dangerous compounds, leading to their nefarious use in dissolving human remains in some criminal cases. The use of these readily accessible household cleaners to destroy human remains and hide evidence of a crime presents a considerable challenge for human identification. However, research on the success of recovering DNA from such remains is limited. Therefore, we investigated the effects of submerging partial human remains (including whole heads, forearms, and hands) in five different household products: bleach, Rid‐X® septic treatment, lye drain opener, sulfuric acid drain opener, and muriatic acid (hydrochloric acid) pool cleaner. We evaluated the impact of each chemical, focusing on visual changes, DNA recovery, and the potential for successful human identification through traditional STR or mitochondrial DNA analyses. Exposure to all chemicals altered the appearance of the remains, but DNA recovery was still possible across various time periods, up to 28 days. Human remains exposed to bleach, Rid‐X®, and lye produced full STR profiles after 4 weeks. Sulfuric acid shortened this time to 3 weeks, while hydrochloric acid, the most damaging chemical, limited full STR profile recovery to just the first 3 days of exposure. This study demonstrates that although differences in the rate of damage occur depending on the amount of tissue introduced, volume of chemical used, and the specific chemical of choice, DNA‐based human identification of remains treated with everyday household cleaners is likely, particularly if bone fragments are recovered. [ABSTRACT FROM AUTHOR]

The taxonomic status of the Neotropical bat genus Trachops is reevaluated through an integrated study that incorporates morphological, morphometric, and molecular data across its extensive geographic range. Our research, which included previously unexamined geographical regions, revealed substantial insights into the diversity within Trachops. Genetic and morphological results support elevation of T. cirrhosus ehrhardti , distributed within the Atlantic Forest of Brazil, to species status due to differences in southeastern Brazil specimens. Conversely, our analysis found insufficient evidence to maintain the subspecific distinction of T. c. coffini , which lacks diagnosable morphological characters and is not genetically distinct from T. c. cirrhosus across its distribution range. Additionally, our findings challenge a prior notion of latitudinal differentiation in body size in T. cirrhosus , because specimens from western South America and northeastern South America exhibit similar sizes to those from Central America. These results underscore the importance of revising the taxonomic framework for this bat genus—contributing to a more precise understanding of its evolutionary relationships—and further enhancing conservation efforts considering potential threats to the newly recognized species in the imperiled Atlantic Forest of Brazil. [ABSTRACT FROM AUTHOR]

Simple Summary: Mitochondria are important organelles in the human body, and they act as a source of chemical energy for different cellular processes. Multiple copies of mitochondria are normally detected in cells, and their copy number has also been reported to be aberrated in cancers, including liver cancer. Target-panel sequencing is frequently used in oncology studies, but the optimal pooling ratio of nuclear and mitochondrial probes has remained elusive. Therefore, it is necessary to determine the physiological mitochondrial DNA copy number in non-liver cancer subjects, which can serve as a useful reference for deciding the desirable ratio of nuclear and mitochondrial probes for a less biased target enrichment of nuclear and mitochondrial genomes and hence their even representation. In addition, it can also be used as a physiological basis that can distinguish normal physiological variations from the pathological conditions in liver cancer. Mitochondria generate energy to support cells. They are important organelles that engage in key biological pathways. The dysfunction of mitochondria can be linked to hepatocarcinogenesis, which has been actively explored in recent years. To investigate the mitochondrial dysfunction caused by genetic variations, target-panel sequencing is a flexible and promising strategy. However, the copy number of mitochondria generally exceeds nuclear DNA, which raises a concern that uneven target enrichment of mitochondrial DNA (mtDNA) and nuclear DNA (ncDNA) in target-panel sequencing would lead to an undesirably biased representation of them. To resolve this issue, we evaluated the optimal pooling of mtDNA probes and ncDNA probes by a series of dilutions of mtDNA probes in both genomic DNA (gDNA) and cell-free DNA (cfDNA) samples. The evaluation was based on read count, average sequencing depth and coverage of targeted regions. We determined that an mtDNA:ncDNA probe ratio of around 1:10 would offer a good balance of sequencing performance and cost effectiveness. Moreover, we estimated the median physiological mtDNA:ncDNA copy ratio as 38.1 and 2.9 in cfDNA and gDNA samples of non-liver cancer subjects, respectively, whereas they were 20.0 and 2.1 in the liver cancer patients. Taken together, this study revealed the appropriate pooling strategy of mtDNA probes and ncDNA probes in target-panel sequencing and suggested the normal range of physiological variation of the mtDNA:ncDNA copy ratio in non-liver cancer individuals. This can serve as a useful reference for future target-panel sequencing investigations of the mitochondrial genome in liver cancer. [ABSTRACT FROM AUTHOR]

The use of pesticide use has been linked to the higher production of reactive oxygen species, resulting in oxidative stress, which in turn can cause genomic instability. A marker for instability is the copy number variation of the mitochondrial genome (mtDNAcn), which has been found to be altered in diverse human diseases, including tumors. This research aimed to examine the variation of mtDNAcn in individuals occupationally exposed to pesticides. Real-time PCR assays were conducted on 154 individuals (78 exposed and 76 non-exposed). Pesticide-exposed ndividuals exhibited a significant reduction in mtDNAcn (1.11 ± 0.37mtDNAcn/genome) compared to non-exposed individuals (1.30 ± 0.33mtDNAcn/genome; p = 0.001). The multivariate analysis indicated that individuals who reported using haloxyfop and copper sulfate demonstrated an increase (β = 0.200, p = 0.053) and a decrease (β=-0.2, p = 0.021), respectively, in mtDNAcn. In conclusion, our findings suggest that chronic exposure to pesticides results in changes in mtDNAcn. [ABSTRACT FROM AUTHOR]

Liquid biopsy (LB) represents an advanced, minimally invasive approach that elevates the precision of oncological decision-making by identifying tumor DNA in bodily fluids. However, despite numerous endorsements from international specialty societies and working groups, implementation of LB into routine care is lagging behind due to conceptual and methodological uncertainties. This concise mini review aims to help catalyzing the translation of LB into routine care by exploring key considerations for incorporating circulating tumor DNA (ctDNA) analysis into clinical practice. Addressing eight pertinent questions from the perspective of a molecular oncology laboratory, this review synthesizes insights from the European Society for Medical Oncology (ESMO) recommendations and incorporates the latest findings from relevant literature, offering a comprehensive guide to the implementation of ctDNA assays. [ABSTRACT FROM AUTHOR]

Background: Recent studies show testosterone (T) deficiency worsens cognitive impairment in Alzheimer's disease (AD) patients. Mitochondrial dysfunction, as an early event of AD, is becoming critical hallmark of AD pathogenesis. However, currently, whether T deficiency exacerbates mitochondrial dysfunction of men with AD remains unclear. Objective: The purpose of this study is to explore the effects of T deficiency on mitochondrial dysfunction of male AD mouse models and its potential mechanisms. Methods: Alzheimer's disease animal model with T deficiency was performed by castration to 3-month-old male APP/PS1 mice. Hippocampal mitochondrial function of mice was analyzed by spectrophotometry and flow cytometry. The gene expression levels related to mitochondrial biogenesis and mitochondrial dynamics were determined through quantitative real-time PCR (qPCR) and western blot analysis. SH-SY5Y cells treated with flutamide, T and/or H2O2 were processed for analyzing the potential mechanisms of T on mitochondrial dysfunction. Results: Testosterone deficiency significantly aggravated the cognitive deficits and hippocampal pathologic damage of male APP/PS1 mice. These effects were consistent with exacerbated mitochondrial dysfunction by gonadectomy to male APP/PS1 mice, reflected by further increase in oxidative damage and decrease in mitochondrial membrane potential, complex IV activity and ATP levels. More importantly, T deficiency induced the exacerbation of compromised mitochondrial homeostasis in male APP/PS1 mice by exerting detrimental effects on mitochondrial biogenesis and mitochondrial dynamics at mRNA and protein level, leading to more defective mitochondria accumulated in the hippocampus. In vitro studies using SH-SY5Y cells validated T's protective effects on the H2O2-induced mitochondrial dysfunction, mitochondrial biogenesis impairment, and mitochondrial dynamics imbalance. Administering androgen receptor (AR) antagonist flutamide weakened the beneficial effects of T pretreatment on H2O2-treated SH-SY5Y cells, demonstrating a critical role of classical AR pathway in maintaining mitochondrial function. Conclusion: Testosterone deficiency exacerbates hippocampal mitochondrial dysfunction of male APP/PS1 mice by accumulating more defective mitochondria. Thus, appropriate T levels in the early stage of AD might be beneficial in delaying AD pathology by improving mitochondrial biogenesis and mitochondrial dynamics. [ABSTRACT FROM AUTHOR]

Spirometra infections in companion animals and wildlife in Japan have been diagnosed based on the morphology of the adult worms and eggs, and the etiological agent has been mainly ascribed to Spirometra erinaceieuropaei. However, recent studies have revealed that two other species, Spirometra mansoni and Spirometra asiana, coexist in Japan. Spirometra asiana is a new species recently discovered in Japan. Although morphological discrimination between these two species is difficult, molecular identification is useful. Therefore, to understand which species commonly parasitizes companion animals and wildlife in Japan, a preliminary study was performed based on mitochondrial DNA analysis. Eleven adult worms examined were identified as S. mansoni, suggesting that S. mansoni infects companion animals and wildlife commonly than S. asiana in Japan. [ABSTRACT FROM AUTHOR]

Aging is the major risk factor in most of the leading causes of mortality worldwide, yet its fundamental causes mostly remain unclear. One of the clear hallmarks of aging is mitochondrial dysfunction. Mitochondria are best known for their roles in cellular energy generation, but they are also critical biosynthetic and signaling organelles. They also undergo multiple changes with organismal age, including increased genetic errors in their independent, circular genome. A key group of studies looking at mice with increased mtDNA mutations showed that premature aging phenotypes correlated with increased deletions but not point mutations. This generated an interest in mitochondrial deletions as a potential fundamental cause of aging. However, subsequent studies in different models have yielded diverse results. This review summarizes the research on mitochondrial deletions in various organisms to understand their possible roles in causing aging while identifying the key complications in quantifying deletions across all models. [ABSTRACT FROM AUTHOR]

Context.--Evidence of T-cell clonality is often critical in supporting the diagnosis of a T-cell lymphoma. Objectives.--To retrospectively explore the significance of copy number losses at the 14q11.2 T-cell receptor a locus in relation to the presence of a T-cell neoplasm and proportion of T cells by targeted next-generation sequencing. Design.--Targeted next-generation sequencing data from 139 tissue biopsies, including T-cell lymphomas, B-cell lymphomas, classic Hodgkin lymphomas, nonhematopoietic malignancies, and normal samples, were reviewed for copy number losses involving the T-cell receptor a gene segments at chr14q11.2. Results.--We found that biallelic or homozygous deletion of 14q11.2 was found in most (28 of 33, 84.8%) T-cell lymphomas. The magnitude of 14q11.2 loss showed a statistically significant correlation with the proportion of T cells in lymphoma tissue samples. Copy number losses could also be detected in other lymphomas with high numbers of T cells (8 of 32, 25% of B-cell lymphomas, 4 of 4 classical Hodgkin lymphomas), though biallelic/homozygous deletion of 14q11.2 was not significantly observed outside of T-cell lymphomas. Most nonhematopoietic neoplasms and normal tissues (59 of 64, 92.2%) showed no significant copy number losses involving the T-cell receptor a locus at chr14q11.2. Conclusions.--Analysis of copy number losses at the T-cell receptor a locus chr14q11.2 with targeted next-generation sequencing can potentially be used to estimate the proportion of T cells and detect T-cell neoplasms. [ABSTRACT FROM AUTHOR]

Introduction: Alzheimer’s disease remains the most common neurodegenerative disorder, depicted mainly by memory loss and the presence in the brain of senile plaques and neurofibrillary tangles. This disease is related to several cellular alterations like the loss of synapses, neuronal death, disruption of lipid homeostasis, mitochondrial fragmentation, or raised oxidative stress. Notably, changes in the autophagic pathway have turned out to be a key factor in the early development of the disease. The aim of this research is to determine the impact of the APOE allele ε4 and G206D-PSEN1 on the underlying mechanisms of Alzheimer’s disease. Methods: Fibroblasts from Alzheimer’s patients with APOE 3/4 + G206D-PSEN1 mutation and homozygous APOE ε4 were used to study the effects of APOE polymorphism and PSEN1 mutation on the autophagy pathway, mitochondrial network fragmentation, superoxide anion levels, lysosome clustering, and p62/SQSTM1 levels. Results: We observed that the APOE allele ε4 in homozygosis induces mitochondrial network fragmentation that correlates with an increased colocalization with p62/SQSTM1, probably due to an inefficient autophagy. Moreover, G206D-PSEN1 mutation causes an impairment of the integrity of mitochondrial networks, triggering high superoxide anion levels and thus making APOE 3/4 + PSEN1 fibroblasts more vulnerable to cell death induced by oxidative stress. Of note, PSEN1 mutation induces accumulation and clustering of lysosomes that, along with an increase of global p62/SQSTM1, could compromise lysosomal function and, ultimately, its degradation. Conclusion: The findings suggest that all these modifications could eventually contribute to the neuronal degeneration that underlies the pathogenesis of Alzheimer’s disease. Further research in this area may help to develop targeted therapies for the treatment of Alzheimer’s disease. [ABSTRACT FROM AUTHOR]

Background: Type 2 diabetes (T2D), one of the most common metabolic diseases, is the result of insulin resistance or impaired insulin secretion due to mitochondrial dysfunction. Mitochondrial DNA (mtDNA) polymorphisms play an important role in the physiological and pathological characteristics of T2D. However, their mechanism is poorly understood. Methods: To directly identify candidate mtDNA variants associated with T2D at the genome-wide level, we constructed forty libraries from ten patients with T2D and thirty control individuals for deep sequencing. We characterized their mtDNA atlas, analysed their single nucleotide polymorphisms (MtSNPs) and screened potential mtDNA mutation sites associated with T2D. Results: We found ten mtDNA polymorphisms at nucleotides 489 T > C, 3105AC > A, 3107 N > C, 8701A > G, 9540 T > C, 10398A > G, 10400C > T, 10873 T > C, 12705C > T and 14783 T > C that showed a significant difference between patients and control subjects. Conclusion: Therefore, our results characterize the mtDNA atlas of patients with T2D and further demonstrate that mtDNA variants participate in the pathophysiology of T2D and other diseases. In addition, mtDNA variants may be candidate molecular biomarkers of T2D and may be valuable for early diagnosis of T2D in the future. [ABSTRACT FROM AUTHOR]

In order to explore the effect of treadmill exercise on mitochondrial DNA damage and myocardial telomerase activity in aging model rats based on the classical apoptosis signaling pathway, a total of 36 clean-grade male SD rats are selected. After modeling, the rats are randomly divided into groups, namely, control and 3 times/w and 6 times/w exercise rats, with 12 rats in each group. After the rats of each group are modeled, the myocardial tissue and cells are collected, the apoptosis of myocardial cells is detected by TUNEL method, and the protein expressions of Bax and Bcl-2 in myocardial tissue are detected by western blotting. The mtDNA content of the control rats is the highest, which is significantly higher than that of the exercise group (P < 0.05); the expression of mtDNA content in the heart of the rats exercising 3 times/w is significantly higher than that of the rats exercising 6 times/w (P < 0.05); cardiomyocyte apoptosis AI value, Bcl-2, and Bax expressions of the control rats is the highest and significantly higher than those in the exercise group (P < 0.05); Bcl-2/Bax in the control rats is the lowest and is significantly lower than that in the exercise group (P < 0.05). The AI value, Bcl-2, and Bax expression of myocardial cell apoptosis in 3 times/w exercise rats are significantly higher than those in 6 times/w exercise rats (P < 0.05); Bcl-2/Bax of 3 times/w exercise rats is significantly lower than that in 6 times/w exercise rats (P < 0.05); by observing the rats that completed treadmill exercise, Akt2 protein of 3 times/w exercise rats and 6 times/w exercise rats is observed and analyzed. Compared with the control rats, the expressions of the two proteins are increased in 3 times/w exercise rats and 6 times/w exercise rats, and the upregulation in 6 times/w exercise rats is significantly increased and higher than that in 3 times/w exercise rats (P < 0.05). For aging rats, treadmill exercise can reduce the body Bcl-2 and Bax values, improve the mitochondrial DNA damage and myocardial cell telomerase activity in aging model rats, and slow down the aging process. [ABSTRACT FROM AUTHOR]

A new short - horned lizard species of the genus Acanthosaura from southern Thailand, is described herein. The species was previously recognised as Acanthosaura crucigera and has been reported to present a wide distribution across mainland south-east Asia. The combination of modern morphological studies of Acanthosaura meridiona sp. nov. allows its separation from closely related species A. crucigera, on the basis of presenting more nuchal scales, more scales between diastema, more scales bordering rostral scales and more midline ventral scales. Mitochondrial DNA analysis also indicated a sister relationship between A. meridiona sp. nov. and A. crucigera with a 100 % probability according to Bayesian and maximum - likelihood analyses. The pairwise distance between A. meridiona sp. nov. and A. crucigera ranges from 9.9 - 11.1 %, while the distance between A. meridiona populations ranges from 0 - 0.9 %. This new discovery contributes to the redescription of the distribution of A. crucigera under Kra Isthmus and its replacement by A. meridiona sp. nov. [ABSTRACT FROM AUTHOR]

Dirofilariasis is a vector-borne disease that is present worldwide. This report describes a giant subconjunctival granuloma which mimics scleritis, caused by D. immitis. A 60-year-old man was referred with the complaints of irritation, redness, and swelling at the medial part of the right eye. He was living in Izmir province located in western Turkey. Slit-lamp examination showed a firm, immobile mass measuring 13.0 × 5.0 × 5.0 mm with yellowish creamy color. The mass was completely removed surgically under local anesthesia mainly for diagnosis. Histopathology revealed typical morphological features of a filarioid nematode in favor of Dirofilaria as characterized by the external smooth cuticular surface, cuticular layer, muscle layer, and intestinal tubule. Molecular study was performed using DNA isolated from paraffin-embedded tissue sections of the worm. PCR amplification and then DNA sequence analysis of cytochrome c oxidase subunit 1 (cox1) gene fragment confirmed that the worm was D. immitis. It is suggested that this may represent the first human case of D. immitis occurring in subconjunctival granuloma in Turkey. Although rare, D. immitis caused by ocular dirofilariasis in humans should be considered. [ABSTRACT FROM AUTHOR]

Spirometra infections in companion animals and wildlife in Japan have been diagnosed based on the morphology of the adult worms and eggs, and the etiological agent has been mainly ascribed to Spirometra erinaceieuropaei. However, recent studies have revealed that two other species, Spirometra mansoni and Spirometra asiana, coexist in Japan. Spirometra asiana is a new species recently discovered in Japan. Although morphological discrimination between these two species is difficult, molecular identification is useful. Therefore, to understand which species commonly parasitizes companion animals and wildlife in Japan, a preliminary study was performed based on mitochondrial DNA analysis. Eleven adult worms examined were identified as S. mansoni, suggesting that S. mansoni infects companion animals and wildlife commonly than S. asiana in Japan.

Hares from Iran can be divided into three morphological groups, with Lepus europaeus inhabiting the western parts of Iran. Hares from lowland areas along the southeastern corner of the Caspian Sea are morphologically similar to both L. tolai and L. tibetanus, but diagnosis is complicated by a lack of taxonomic agreement. Mitochondrial DNA suggests L. tibetanus rather than L. tolai, although comparative material is not incontestable. The third group, in more xeric habitats of eastern Iran, shows a mixture of traits characteristic of both the west Iranian L. europaeus and the Golestan population, the southeast Caspian Sea. Mitochondrial and nuclear loci reveal conflicting patterns, where hares from eastern Iran cluster with L. europaeus based on mtDNA, but with the Golestan population based on nuclear transferrin, suggesting a mixed ancestry. Ecological niche modeling indicates that the preferred habitat of the Golestan population is more restricted than that of the other two groups. Pure L. europaeus occur in areas of high seasonality, low temperature, and high precipitation, whereas the population in eastern Iran inhabits areas characterized by high contrast in daily temperatures and the highest isothermality in eastern Iran. Parts of the range of this population are also indicated to correspond to the fundamental niche of L. europaeus, yet both parental forms appear to be absent from this area occupied by individuals of apparent mixed ancestry. This suggests that the population of mixed ancestry may have selective advantages over the parental forms, and that the absence of the latter from this area may be due to competitive exclusion. As the population of mixed ancestry thus appears to be self-sustaining, incipient speciation of a stabilized hybrid may be implied. [ABSTRACT FROM AUTHOR]

Summary: Bacterial symbioses play important roles in shaping diverse biological processes in nematodes, and serve as targets in nematode biocontrol strategies. Focusing on the Xiphinema americanum species complex, we expanded upon recent research investigating patterns of coevolution between Xiphinema spp. and Xiphinematobacter spp., utilising two symbiont genetic markers of varying evolutionary rates. Phylogenetic analysis of nematode mitochondrial DNA (mtDNA) revealed five strongly supported major clades. Analysis of slow-evolving 16S rDNA in bacterial symbionts resulted in a phylogenetic topology composed of four major clades that grouped taxa highly congruent with the nematode mtDNA topology. A faster evolving protein-coding symbiont gene (nad) provided more phylogenetic resolution with seven well-supported clades, also congruent with the nematode mtDNA tree topology. Our results reinforce recent studies suggesting extensive coevolution between Xiphinema spp. and their vertically transmitted endosymbionts Xiphinematobacter spp. and illustrate the advantages of including genetic markers of varying evolutionary rates in coevolutionary and phylogenetic studies. [ABSTRACT FROM AUTHOR]

• mtDNA revealed three major lineages with high genetic divergence among them: 6–10%. • nuDNA indicated L. ferreirai as the closest bisexual species to the complex. • First hybridization in late Miocene-Pliocene and second in Pliocene-Pleistocene. • L. percarinatum cross with males of the new bisexual species, occasionally. • L. percarinatum 2n experienced a wide demographic expansion. In vertebrates, true parthenogenesis is found only in squamate reptiles and (mostly) originates via interspecific hybridization after secondary contact. In many cases, parthenogenesis is followed by an increase of ploidy, resulting in triploid lineages. Phylogenetic analyses derived from nuclear and maternally inherited markers can help to clarify the mechanisms of origin and the potential parental species involved. In the Amazon region, parthenogenetic lizards of the Loxopholis percarinatum complex are widely distributed, comprising both diploid and triploid clones. Recently, putative males of L. percarinatum were reported, suggesting the existence of bisexual populations based on morphological data. Here, we used mitochondrial and nuclear data to investigate the origin of parthenogenesis in Loxopholis. Mitochondrial DNA analysis revealed three major lineages: unisexual/2n, unisexual/3n and bisexual, the last of which comprised two sub-lineages placed as the sister taxon to the unisexual/3n lineage. Genetic divergence among the lineages was ∼10% but was lower between the unisexual/3n and bisexual lineages (∼6%). Both mtDNA and nuDNA indicated that individuals from the bisexual lineages might belong to a new species. Nuclear DNA evidence indicates that crossings occasionally occur between unisexual 2n and males from the new bisexual species. Phylogenetic analysis of nuDNA showed L. ferreirai as the closest described bisexual species to the complex. Our results revealed an ancient origin of parthenogenesis in the L. percarinatum complex, in contrast to most young (Pleistocene) parthenogenetic lizards described thus far. Two hybridization events seem to have been involved: the first event occurred in late Miocene, between the ancestral lineage ("A") of the new bisexual species (as a maternal species) and the ancestral lineage of L. ferreirai , as a paternal species of L. percarinatum 2n; and the second event occurred in Pliocene-Pleistocene, in a backcross between L. percarinatum 2n and a male from the common ancestor ("B") of the new bisexual species giving rise to the lineage of L. percarinatum 3n. With these results, we showed that L. percarinatum complex also includes, at least, one undescribed bisexual species in addition to the two known parthenogenetic lineages (2n and 3n). Finally, we present evidence that diploid individuals of L. percarinatum experienced an event of wide demographic expansion over the past million years under an allele surfing model. [ABSTRACT FROM AUTHOR]

The leaf miner Coptodisca lucifluella and the carpophagous Rhagoletis completa, of American origin, are two non‐native walnut (Juglans spp.) pests in Italy. For the Friuli Venezia Giulia region (FVG) (N‐E Italy), C. lucifluella is not yet listed, while R. completa has been present for over 25 years. During 2015, samples of leaves and fruits were collected from 219 single old common walnut trees (Juglans regia) placed at different altitudes (0–1,073 m a.s.l.) in FVG to detect the distribution and abundance of both pests. Samples of leaf miner larvae and their parasitoids were subjected to mitochondrial DNA analysis for identification. C. lucifluella has been found in 55 out of 219 sites. The species has been identified by typical leaf symptoms and by its DNA barcode. This is the first report of the species for FVG. The leaf miner distribution was negatively correlated with altitude. The species has not been observed at sites over 600 m a.s.l. Larvae were parasitized by native parasitoids identified as belonging to the genus Chrysocharis by morphological features and by DNA barcode. R. completa has been found in 89 out of 165 sites on walnut trees with fruits. The infestation level was very high in lowland localities. At sites over 700 m a.s.l., no infestation was found. Both species are widespread in the region, and their occurrence is significantly affected by altitude. Data suggest that walnut trees could be cultivated in some mountain areas without the need to control R. completa with insecticides. [ABSTRACT FROM AUTHOR]

The Luangwa Valley in eastern Zambia is a transverse offshoot of the Great Rift Valley system. This region appears to have an isolating effect as evidenced by suspected endemic subspecies, such as the Cookson’s wildebeest and Thornicroft’s giraffe. Recent mitochondrial DNA studies demonstrated that African lions in Zambia consist of two highly diverse eastern and western sub-populations. Herein, we report nuclear and mitochondrial DNA results from 409 lions that support this population substructure across Zambia but proposes only partial isolation of the Luangwa Valley with more movement between the populations than previously thought. Population assignment analysis identifies two populations with little evidence of admixture assigning lions to either the eastern or western sub-populations. A high occurrence of private alleles and clear evidence for a Wahlund effect further justify the presence of a highly structured population. But, while mitochondrial DNA analysis still shows little to no matrilineal gene flow (FST = 0.53) between sub-populations, microsatellite analysis suggests there is gene flow (FST = 0.04) with low but significant isolation-by-distance and an average of 6 migrants per generation. Evidence of isolation-by-distance is also found in factorial correspondence analysis with the Lower Zambezi National Park and eastern corridor clusters overlapping isolated clusters of the Luangwa Valley and western sub-population. From this evidence, the Luangwa Valley appears separated from the western sub-population with some dispersal through the southern regions of the eastern sub-population. Both the eastern and western sub-populations have high heterozygosity (0.68 and 0.69, respectively) and genetic diversity (0.47 and 0.50, respectively) values, indicative of genetically healthy populations. [ABSTRACT FROM AUTHOR]

Recent molecular studies have indicated that phylogeographical history of Japanese biota is likely shaped by geohistory along with biological events, such as distribution shifts, isolation, and divergence of populations. However, the genetic structure and phylogeographical history of terrestrial Annelida species, including leech species, are poorly understood. Therefore, we aimed to understand the genetic structure and phylogeographical history across the natural range of Haemadipsa japonica, a sanguivorous land leech species endemic to Japan, by using nine polymorphic nuclear microsatellites (nSSR) and cytochrome oxidase subunit one (COI) sequences of mitochondrial DNA (mtDNA). Analyses using nSSR revealed that H. japonica exhibited a stronger regional genetic differentiation among populations (G'ST = 0.77) than other animal species, probably because of the low mobility of land leech. Analyses using mtDNA indicated that H. japonica exhibited two distinct lineages (A and B), which were estimated to have diverged in the middle Pleistocene and probably because of range fragmentation resulting from climatic change and glacial and interglacial cycles. Lineage A was widely distributed across Japan, and lineage B was found in southwestern Japan. Analyses using nSSR revealed that lineage A was roughly divided into two population groups (i.e., northeastern and southwestern Japan); these analyses also revealed a gradual decrease in genetic diversity with increasing latitude in lineage A and a strong genetic drift in populations of northeastern Japan. Combined with the largely unresolved shallow polytomies from the mtDNA phylogeny, these results implied that lineage A may have undergone a rapid northward migration, probably during the Holocene. Then, the regional genetic structure with local unique gene pools may have been formed within each lineage because of the low mobility of this leech species. [ABSTRACT FROM AUTHOR]

Discordance between entities revealed by nuclear versus mitochondrial genes is a common phenomenon in evolutionary and taxonomic studies. However, little attention has been paid to analysis of how such discordant entities correspond to traditional species detected through investigation of their morphology, ecology, and distribution. Here, we used one mitochondrial (COI, DNA barcode fragment) and four nuclear (CAD, Ca‐ATPase, arginine kinase, wg) genes to analyze the genetic structure of the taxonomically well‐studied butterfly genus Brenthis (Lepidoptera, Nymphalidae). Analysis of COI revealed multiple diverged allopatric and sympatric mitochondrial lineages within the known Brenthis species hinting at possible presence of unrecognized cryptic species. However, these multiple‐species hypotheses were not supported by further studies of nuclear genes and phenotypic traits. The discovered mitochondrial lineages did not correspond to the clusters revealed by nuclear genes. Simultaneously, we found a complete congruence between (a) traditional species boundaries, (b) clusters recognized by nuclear genes, and (c) clusters identified via cladistic analysis of phenotypic traits (genitalia and wing pattern characters, ecological preferences, and chromosome numbers). We conclude that in case of the genus Brenthis, nuclear genes rather than mtDNA barcodes reveal real species boundaries. Additionally, we suggest to support each DNA barcode‐based taxonomic conclusion by analysis of phased alleles of nuclear genes, avoiding widely used practice of nuclear and mitochondrial genes concatenation without any examination of interaction of these different types of data. Discordance between entities revealed by nuclear versus mitochondrial genes is a common phenomenon, but little attention has been paid to analysis of how such discordant entities correspond to traditional species. In the butterfly genus Brenthis, analysis of mitochondrial DNA barcodes (COI) revealed several diverged lineages which were supported neither by nuclear genes nor by cladistics analysis of phenotypic traits. In case of the genus Brenthis, nuclear genes rather than mtDNA barcodes reveal real species boundaries. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Mitochondrial and nuclear genetic data indicate strong phylogeographic structure. • Results consistent with biogeographic barriers at the Nullarbor Plain and Murray River. • Molecular clock analyses suggest diversification occurred in the Plio-Pleistocene. • Analyses indicate presence of one or more refugia associated with each of the three main populations. Abstract Palaeoclimatic events and biogeographical processes since the mid-Tertiary have played an important role in shaping the evolution and distribution of Australian fauna. However, their impacts on fauna in southern and arid zone regions of Australia are not well understood. Here we investigate the phylogeography of an Australian scincid lizard, Tiliqua rugosa , across southern Australia using mitochondrial DNA (mtDNA) and 11 nuclear DNA markers (nuDNA), including nine anonymous nuclear loci. Phylogenetic analyses revealed three major mtDNA lineages within T. rugosa , geographically localised north and south of the Murray River in southern Australia, and west of the Nullarbor Plain. Molecular variance and population analyses of both mtDNA and nuDNA haplotypes revealed significant variation among the three populations, although potential introgression of nuDNA markers was also detected for the Northern and Southern population. Coalescent times for major mtDNA lineages coincide with an aridification phase, which commenced after the early Pliocene and increased in intensity during the Late Pliocene-Pleistocene. Species distribution modelling and a phylogeographic diffusion model suggest that the range of T. rugosa may have contracted during the Last Glacial Maximum and the locations of optimal habitat appear to coincide with the geographic origin of several distinct mtDNA lineages. Overall, our analyses suggest that Plio-Pleistocene climatic changes and biogeographic barriers associated with the Nullarbor Plain and Murray River have played a key role in shaping the present-day distribution of genetic diversity in T. rugosa and many additional ground-dwelling animals distributed across southern Australia. [ABSTRACT FROM AUTHOR]

There are two morphotypes of Penaeus semisulcatus described hitherto in the Persian Gulf, namely the banded and non-banded antennae morphotypes. In this study, we used morphometric measurements and two mitochondrial genes (16S rRNA and cytochrome oxidase subunit I—COI) to assess relationships between the two morphotypes of P. semisulcatus. Out of 25 morphological characters examined, 10 characters were found significantly different between the two morphotypes when tested against separate sexes or both sexes combined. Results from the 16S rRNA and COI sequence analysis of two morphotypes of P. semisulcatus morphotype showed up to 6% and 17% sequence divergence, respectively. The 16S rDNA and COI sequences of the non-banding morphotype were not only very different to those of the banding morphotype but was also very different to all other Penaeus species (i.e., P. monodon, P. merguiensis, and P. indicus) included in the study. Both parsimony and Neighbor-Joining trees based on 16S rDNA and COI sequences provide similar tree topology that clearly separated the two morphotypes into two distinct groups. Based on these findings, we propose the two morphotypes of P. semisulcatus to be relegated as two sympatric species. [ABSTRACT FROM AUTHOR]

This paper presents an exploratory analysis of the mitochondrial DNA (mtDNA) of 32 species in the subphylum Vertebrata, divided in 7 taxonomic classes. Multiple stochastic parameters, such as the Hurst and detrended fluctuation analysis (DFA) exponents, Shannon entropy, and Chargaff ratio are computed for each DNA sequence. The biological interpretation of these parameters leads to defining a triplet of novel indices. These new functions incorporate the long-range correlations, the probability of occurrence of nucleic bases, and the ratio of pyrimidines-to-purines. Results suggest that relevant regions in mtDNA can be located using the proposed indices. Furthermore, early results from clustering algorithms indicate that the indices introduced might be useful in phylogenetic studies. [ABSTRACT FROM AUTHOR]

The molecular phylogeny of extant genets (Carnivora, Viverridae, Genetta) was generated using all species with the exception of the Ethiopian genet Genetta abyssinica. Herein, we provide the first molecular phylogenetic assessment of G. abyssinica using molecular sequence data from multiple mitochondrial genes generated from a recent record of this species from the Forêt du Day (the Day Forest) in Djibouti. This record represents the first verified museum specimen of G. abyssinica collected in over 60 years and the first specimen with a specific locality for the country of Djibouti. Multiple phylogenetic analyses revealed conflicting results as to the exact relationship of G. abyssinica to other Genetta species, providing statistical support for a sister relationship to all other extant genets for only a subset of mitochondrial analyses. Despite the inclusion of this species for the first time, phylogenetic relationships among Genetta species remain unclear, with limited nodal support for many species. In addition to providing an alternative hypothesis of the phylogenetic relationships among extant genets, this recent record provides the first complete skeleton of this species to our knowledge and helps to shed light on the distribution and habitat use of this understudied African small carnivore. [ABSTRACT FROM AUTHOR]

Highlights • A superior method for recovery of DNA from ammunition was identified. • MPS of mtDNA recovered from different metallic surfaces was evaluated. • Noise (error) in the MPS mtDNA data was analyzed. • Alignment statistics for the MPS mtDNA data were assessed. • The impact of DNA damage lesions was assessed. Abstract Recovery of suitable amounts of quality DNA from copper and brass surfaces, like those encountered in ammunition, has been a challenge for the forensic community. The ability of copper ions to rapidly facilitate oxidative damage leading to fragmentation of DNA significantly reduces the pool of templates for PCR amplification. We compared two methods for recovering mitochondrial (mt) DNA from the surface of unfired copper projectiles, brass casings, and aluminum casings, and found that using a cotton swab moistened with 0.5M EDTA was the favored approach, especially when the metallic surface was etched. Degradation was significantly higher for DNA samples recovered from copper and brass surfaces, when compared to aluminum. Massively parallel sequencing (MPS) of the control region, using the PowerSeq™ CRM Nested System kit and the Illumina MiSeq instrument, produced full haplotypes for aluminum samples regardless of the method used to deposit or collect DNA, while less than 60% of the copper and brass samples produced partial or full profile information. Touch DNA collected from copper and brass samples produced higher rates of partial or full MPS profile information (∼88-96%), while collection with 0.5M EDTA produced better results than when collection was performed with water; average of ∼70% versus ∼47%. While MPS data was not impacted by noise in the sequencing process, a higher than expected rate of noise was observed, potentially due to an increase in low-level damage lesions. Noise patterns were strikingly different when compared to control data, suggesting that noisy sites may be predictable when testing samples with high levels of oxidative damage. Library preparation was a poor predictor of MPS data quality, as a large percentage of reads did not align with the reference genome. This may impact the number of samples that can be run when a deep-coverage MPS approach is being considered for analysis of mtDNA heteroplasmy. Overall, when applying an MPS approach to the analysis of mtDNA recovered from ammunition, results are expected from touch DNA, will be limited for copper and brass components when the DNA is exposed to an aqueous environment, and DNA degradation will be accelerated when DNA comes in contact with copper or brass surfaces. Practitioners should consider collecting DNA from metallic surfaces with 0.5M EDTA, as this will maximize yield and mitigate degradation. The results of this study directly impact MPS analysis of minor mtDNA sequence variants from metallic surfaces, and are particularly relevant to forensic investigations. [ABSTRACT FROM AUTHOR]

Highlights • Densely packed mtDNA & TFAM complexes (including other gene expression proteins) form ∼100 nm nucleoids within the mitochondrial matrix. • Putative nucleoid division concomitant to mtDNA replication is yet to be observed in detail. • mtDNA transcription may proceed in larger nucleoids, i.e. with unwinded mtDNA with still attached polycistronic RNA. • Nucleoids are located in cristae-free regions and spatially coordinated with RNA granules and mt ribosomes. • Nucleoids may be attached to the inner mitochondrial membrane in fission sites, hence fragments contain always one nucleoid. • Upon mild fission of the mitochondrial network, all nucleoids (typically ∼10 per 10 μm mitochondrial tubule) do cluster in resulting spheroidal fragments. Abstract The mitochondrion owns an autonomous genome. Double-stranded circular mitochondrial DNA (mtDNA) is organized in complexes with a packing/stabilizing transcription factor TFAM, having multiple roles, and proteins of gene expression machinery in structures called nucleoids. From hundreds to thousands nucleoids exist distributed in the matrix of mitochondrial reticulum network. A single mtDNA molecule contained within the single nucleoid is a currently preferred but questioned model. Nevertheless, mtDNA replication should lead transiently to its doubling within a nucleoid. However, nucleoid division has not yet been documented in detail. A 3D superresolution microscopy is required to resolve nucleoid biology occurring in ∼100 nm space, having an advantage over electron microscopy tomography in resolving the particular protein components. We discuss stochastic vs. stimulated emission depletion microscopy yielding wide vs. narrow nucleoid size distribution, respectively. Nucleoid clustering into spheroids fragmented from the continuous mitochondrial network, likewise possible nucleoid attachment to the inner membrane is reviewed. [ABSTRACT FROM AUTHOR]

Highlights • 1,25D 3 increases mtDNA content and attenuates BPA-induced mtDNA deletion. • 1,25D 3 inhibits BPA-induced decrease in COXI expression and 17β-estradiol secretion. • 1,25D 3 increases mitochondrial biogenesis-related proteins by PI3K-Akt signalling. • 1,25D 3 increases ATP production and cellular oxygen consumption rate. Abstract Bisphenol A (BPA), an endocrine-disrupting chemical, is capable of producing reproductive toxicity. BPA results in mitochondrial DNA (mtDNA) deletion and mitochondrial dysfunction; however, the effect of BPA on the mitochondria of ovarian granulosa cells is not clear. Further, 1,25-dihydroxyvitamin D 3 (1,25D 3) may play a role in reproduction, because its receptor, VDR, contributes to the inhibition of oxidative stress and predominantly exists in the nuclei of granulosa cells. Hence, the role of 1,25D 3 in BPA-mediated effects on mitochondrial function was examined in this study. Primary rat granulosa cells treated with BPA, 1,25D 3 , or both were subjected to molecular/biochemical assays to measure cell survival, mtDNA content, mtDNA deletion, superoxide dismutase activity, levels of proteins related to mitochondrial biogenesis, and mitochondrial function. We found that cell viability was dose-dependently reduced and reactive oxygen species (ROS) levels were increased by BPA treatment. BPA administration elevated Mn-superoxide dismutase (MnSOD) expression but negatively regulated total SOD activity. 1,25D 3 treatment alone increased 17β-estradiol secretion, ATP production, and cellular oxygen consumption. In cells treated with both agents, 1,25D 3 enhanced BPA-induced MnSOD protein upregulation and blocked the BPA-mediated decline in total SOD activity. Furthermore, 1,25D 3 attenuated BPA-mediated mtDNA deletion but showed no effect on BPA-induced increases in mtDNA content. Although BPA had no influence on the levels of peroxisome proliferator-activated receptor-γ coactivator-1 α, nuclear respiratory factor-1, mitochondrial transcription factor A, or cytochrome c oxidase subunit IV, 1,25D 3 plus BPA markedly increased mitochondrial biogenesis-related protein expression via the PI3K-Akt pathway. Moreover, BPA-mediated negative regulation of cytochrome c oxidase subunit I levels and 17β-estradiol secretion was attenuated by 1,25D 3 pre-treatment. Our results suggest that 1,25D 3 attenuates BPA-induced decreases in 17β-estradiol and that treatment with 1,25D 3 plus BPA regulates granulosa cell mitochondria by elevating mitochondrial biogenesis-related protein levels. [ABSTRACT FROM AUTHOR]

Recently, mitochondria have been shown to have a vital role in the innate immune response to viral infection. In response, viruses such as adenovirus, have developed mechanisms to alter mitochondrial function through direct or indirect interaction with the mitochondria. The interaction of human recombinant adenoviral vectors directly with human mitochondria has not previously been shown. We demonstrate that human recombinant adenoviral vectors co-localize to mitochondria. We show that the adenoviral vectors are present within the membranes of the mitochondria and that they cause ultrastructural changes to the cristae. Further, we show that the adenoviral genome is also present in intact mitochondria. We have posited that the interaction between the adenovirus and the mitochondria may act to inhibit mitochondrial function. We have also posited that the transport of the adenoviral genome to the mitochondria may allow the future use of this vector as a tool for gene therapy of mitochondrial diseases. [ABSTRACT FROM AUTHOR]

Mitochondrial DNA copy number (mtDNA-CN), a measure of the number of mitochondrial genomes per cell. A cell contains two copies of genomic DNA compared to a single copy of DNA per chromosome. The quantitative real-time PCR (qPCR) is the gold standard method for measuring mtDNA-CN, the quantification after DNA extraction it is an important step, the quantitation of DNA plays a central role inmedical and forensic DNA analysis, which provides the information about the amount of DNA present in unknown samples. In this study the quantitative results showed that the higher value 74941 and the lower value 190. A multiplex quantitative PCR assay developed to amplify target sequences of different length, which allows for the assessment of DNA degradation in samples of forensic interest. The quantification of DNA by qPCR relies on the detection of amplified product (amplicon) at each cycle of the PCR. [ABSTRACT FROM AUTHOR]

Surveys of the freshwater crabs of two islands in the Gulf of Guinea, Central Africa, allowed a revision of the taxonomy of two little-known island endemic species, based for the first time on adult males: Potamonautes margaritarius (A. Milne-Edwards, 1869) from São Tomé, and of P. principe Cumberlidge, Clark and Baillie, 2002, from Príncipe (Brachyura; Potamonautidae). A new species of Potamonautes from southern São Tomé (Potamonautes saotome sp. nov.) is also described that is genetically distinct and has a clearly separate geographic distribution from P. margaritarius from northern São Tomé. The new species from southern São Tomé can be recognized by a suite of characters of the carapace, thoracic sternum, and gonopods. The taxonomy of P. margaritarius (A. Milne-Edwards, 1869) is stabilized by selecting a neotype from northern São Tomé. Potamonautes principe from Príncipe is the most distinct of the three taxa, with a more swollen carapace that has smooth anterolateral margins, and a shorter, straighter male first gonopod. All three taxa are morphologically distinct species that have also been clearly distinguished as evolutionarily separate lineages by mtDNA analysis and haplotyping in an earlier study. Previous phylogenetic evidence supports two separate island colonization events at different times in the past from different ancestral populations, one to São Tomé and another to Príncipe that resulted in the establishment of the endemic freshwater crab faunas of these two islands. [ABSTRACT FROM AUTHOR]

Highlights • A new mtDNA sequence query algorithm results is presented for the EMPOP database. • Updated nomenclature conventions for the instable regions are presented. • Neighbours can be queried by phylogenetic costs. • A total of 28 block indels containing between 2 and 264 basepairs were defined. • The effect of length variant regions for matches and neighbours was evaluated. Abstract Mitochondrial DNA (mtDNA) variation is being reported relative to the corrected version of the first sequenced human mitochondrial genome. A review of the existing literature across disciplines that employ mtDNA demonstrates that insertions and deletions are not reported in a standardized way. This may lead to false exclusions of identical sequences, unidentified matches in missing persons mtDNA databases, biased mtDNA database frequency estimates and overestimation of the genetic evidence. Seven years ago we introduced alignment-free database search software (SAM) and implemented it into the mtDNA database EMPOP (https://empop.online) to produce reliable and conservative frequency estimates that are required in the forensic context. However, ambiguity remained in how laboratories have been reporting mitotypes, as often more than one single alignment of a given mtDNA sequence was feasible. In order to overcome this limitation we here describe a concept and provide software for producing stable, harmonized phylogenetic alignment of mtDNA sequences for database searches. The new software SAM 2 will be made available via EMPOP and provide the user with the already established conservative frequency estimates. In addition, SAM 2 offers the rCRS-coded haplotype of a given mtDNA sequence following the established and widely accepted phylogenetic alignment. This provides the user with feedback on how mitotypes are stored in EMPOP and how they should be reported in order to harmonize nomenclature. Finally, this approach does not only permit reliable mtDNA nomenclature in forensics but invites related disciplines to take advantage of a standardized way of reporting mtDNA variation, thus closing the ranks between different genetic fields and supporting dialogue and collaboration between mtDNA scholars from various disciplines. [ABSTRACT FROM AUTHOR]

Sevan trout, Salmo ischchan, dwelling in the mountain Lake Sevan (Caucasus) is a unique species complex. Four sympatric forms of Sevan trout were divergent in both their phenotypes and ecologies. Three forms were lacustrine spawners but were unique in their spawning times and the type of substrate. The fish community of Lake Sevan was strongly impacted by human activity in twentieth century. Two forms of Sevan trout went extinct in the 1980s and the other two forms are at the brink of extinction. The present study demonstrated that archived/historical scales of extinct forms stored at room temperature for up to 44 years are a suitable source of DNA for high-throughput sequencing and for the reconstruction of mitochondrial genomes. In addition, we obtained the mitochondrial genomes of the extant forms for comparison to the extinct forms and reconstruction of a mitogenomic phylogeny of all forms of Sevan trout. The mitogenome gene arrangement was identical in all individuals studied with structure similar to other Salmo spp. The nucleotide sequence divergence between sympatric forms was shallow (P-distance = 0.0003-0.0012). A phylogenetic tree based on mitogenomes confirmed sister position of Sevan trout to the Caspian trout, Salmo trutta caspius (P-distance = 0.0049). [ABSTRACT FROM AUTHOR]

Abstract Background Mitochondria are sensitive to air pollutants due to their lack of repair capacity. Changes in mitochondrial DNA copy number (mtDNAcn) or content is a proxy of mitochondrial damage and has been associated with recent exposure to traffic-derived air pollutants, nitrogen dioxide (NO 2) and black carbon (BC). Inhaled BC can be phagocytosed by airway macrophages (AMs), and its amount in AM reflects personal exposure to traffic-related air pollution. Objectives The present study investigated the relation between the internal marker AM BC and ambient NO 2 concentration and examined the associations of mtDNAcn with NO 2 and AM BC. Methods A panel of 20 healthy retired participants (10 couples) living in Belgium underwent repeated assessments of health and air pollution exposure at 11 time points over one year. We increased exposure contrast temporarily by moving participants for 10 days to Milan, Italy (high exposure) and to Vindeln, Sweden (low exposure). Personal exposure to NO 2 was measured during 5 consecutive days prior to each assessment time point. The amount of BC was assessed by image analysis in AMs retrieved from induced sputum collected at 7 time points. Blood mtDNAcn was determined by qPCR at each time point. Associations between AM BC and NO 2 , and of mtDNAcn with NO 2 and AM BC were estimated using linear mixed effect models adjusted for covariates and potential confounders. Results Mean concentrations of 5-day average NO 2 were higher in Milan (64 μg/m3) and lower in Vindeln (4 μg/m3) than Belgium (26 μg/m3). Each 10 μg/m3 increment in NO 2 exposure during the last 5 days was associated with 0.07 μm2 (95% CI: 0.001 to 0.012) increase in median area of AM BC. A 10 μg/m3 increase in NO 2 was associated with 3.9% (95% CI: 2.2 to 5.5%) decrease in mtDNAcn. Consistently, each 1 μm2 increment in median area of AM BC was associated with 24.8% (95% CI: 6.8 to 39.3%) decrease in mtDNAcn. Conclusion In this quasi-experimental setting involving moving persons to places with high and low ambient air pollution, we found changes in AM BC according to ambient air pollution levels measured during the previous 5 days. Both higher ambient NO 2 and the internal lung BC load, paralleled mitochondrial compromises as exemplified by lower mtDNA content. Highlights • Personal exposure to air pollution was assessed by external and internal markers. • Repeated measures over 1-year and changing places to contrast exposures • Carbon load in airway macrophages was associated with ambient NO 2 over a 5-day period. • Decreased blood mitochondrial DNA content in response to higher airway carbon load [ABSTRACT FROM AUTHOR]

A freshwater sculpin, Coitus nozawae Snyder, 1911, endemic to Japan, inhabits Hokkaido and northeastern Honshu Island. Previous mitochondrial DNA analyses have shown that the species includes three distinct phylogenetic groups that diverged in the early Pleistocene, that is, the "Hokkaido Group", "Northern Tohoku Group," and "Yamagata Group." To date, comprehensive population genetic analyses have not been performed, except for the Hokkaido Group. In this study, to elucidate the phylogeographical patterns of the C. nozawae Yamagata Group and obtain basic information for the conservation of the group, we conducted population genetic analyses based on mitochondrial and nuclear microsatellite markers using individual samples collected from five localities in Yamagata. For both DNA markers, each population had only the endemic haplotype, and genetic diversity was extremely low in all populations (haplotype diversity [/;] = 0.000; observed heterozygosity [H0] = 0.000-0.300), particularly in the Ohtaru population (both h and H„ = 0.000). The degree of genetic differentiation was extremely high among populations (ΦST, = 1.000 for the mitochondrial marker; FST = 0.532-0.931 for the microsatellite marker), and genetic clusters in an assignment test were completely concordant with grouping based on sampling localities. These results suggest that gene flow is completely lacking among habitats and each population has been isolated for a long evolutionary time. According to these results, each population should be separately managed as evolutionarily significant units. [ABSTRACT FROM AUTHOR]

Abstract: Piracatinga (Callophysius macropterus) are a type of bottom feeder catfish encountered in the Amazon River and its tributaries. We report two cases in which human remains were first located based on a characteristic circular distortion of the surface of the river that the Piracatinga make while they feed. Human skin samples of one of the victims recovered from the Piracatinga digestive tract were subjected to mitochondrial DNA analysis that allowed identification of the body of Case 1; the family recognized body parts of Case 2. Importantly, the location of human body parts and their identification based on DNA analysis enabled the respective families to obtain a death certificate expeditiously in the absence of identifiable remains—a process that normally requires 5 years under current Brazilian law, and in the absence of closure, imposes severe emotional stress on the family of the deceased. [ABSTRACT FROM AUTHOR]

Nucleotide sequences of the mtDNA control region were studied in 64 Daurian ground squirrels of the Spermophilus dauricus dauricus subspecies from 20 localities from the territory of Mongolia and Transbaikalia of the Russian Federation. A large number of slightly different haplotypes were detected. It was found that genetic polymorphism is not associated with geographical variability. It seems that the Kherlen River is not an ecological and geographical barrier for Daurian ground squirrels, while an exchange between Mongolian and Chinese populations probably occurs within the southwest end of the Greater Khingan Range. By comparative analysis of a number of molecular genetic markers, it was found that the mitochondrial genome numbered KR534854 (GenBank NCBI) belongs not to S. dauricus, but to one of the members of the Sciurus genus. [ABSTRACT FROM AUTHOR]

Abstract: Vesicomyid clams of the subfamily Pliocardinae are among the dominant chemosymbiotic bivalves found in sulfide‐rich deep‐sea habitats. Plastic morphologies and present molecular data could not resolve taxonomic uncertainties. The complete mitochondrial (mt) genomes will provide more data for comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group, and help to clarify generic classifications. In this study, we analyze the features and evolutionary dynamics of mt genomes from three Archivesica species (Archivesica sp., Ar. gigas and Ar. pacifica) pertaining to subfamily Pliocardinae. Sequence coverage is nearly complete for the three newly sequenced mt genomes, with only the control region and some tRNA genes missing. Gene content, base composition, and codon usage are highly conserved in these pliocardiin species. Comparative analysis revealed the vesicomyid have a relatively lower ratio of Ka/Ks, and all 13 protein‐coding genes (PGCs) are under strong purifying selection with a ratio of Ka/Ks far lower than one. Minimal changes in gene arrangement among vesicomyid species are due to the translocation trnaG in Isorropodon fossajaponicum. Additional tRNA genes were detected between trnaG and nad2 in Abyssogena mariana (trnaL3), Ab. phaseoliformis (trnaS3), and Phreagena okutanii (trnaM2), and display high similarity to other pliocardiin sequences at the same location. Single base insertion in multiple sites of this location could result in new tRNA genes, suggesting a possible tRNA arising from nongeneic sequence. Phylogenetic analysis based on 12 PCGs (excluding atp8) supports the monophyly of Pliocardiinae. These nearly complete mitogenomes provide relevant data for further comparative studies on molecular phylogeny and systematics of this taxonomically uncertain group of chemosymbiotic bivalves. [ABSTRACT FROM AUTHOR]

Mitochondrial structural and functional integrity is maintained through the coordination of several processes (e.g., biogenesis, dynamics, mitophagy), collectively referred to as mitochondrial quality control (MQC). Dysfunctional MQC and inflammation are hallmarks of aging and are involved in the pathogenesis of muscle wasting disorders, including sarcopenia and cachexia. One of the consequences of failing MQC is the release of mitochondria-derived damage-associated molecular patterns (DAMPs). By virtue of their bacterial ancestry, these molecules can trigger an inflammatory response by interacting with receptors similar to those involved in pathogen-associated responses. Mitochondria-derived DAMPs, especially cell-free mitochondrial DNA, have recently been associated with conditions characterized by chronic inflammation, such as aging and degenerative diseases. Yet, their actual implication in the aging process and muscle wasting disorders is at an early stage of investigation. Here, we review the contribution of mitochondria-derived DAMPs to age-related systemic inflammation. We also provide arguments in support of the exploitation of such signaling pathways for the management of muscle wasting conditions. [ABSTRACT FROM AUTHOR]

The gecko genus Phyllopezus is distributed mainly along South America’s “Dry Diagonal” (Caatinga, Cerrado, and Chaco). The genus has been the subject of recent taxonomic analyses and includes four described species and seven candidate species referred to here as Phyllopezus pollicaris sensu lato. In Paraguay, Phyllopezus is known from the Chaco and Cerrado where it is abundant, and also from a small isolated population from a rocky hill formation named “Cordillera de Los Altos” (Los Altos mountain range). Here we analyzed genetic samples from across its range, including new samples from Paraguay, using DNA barcoding analysis of the mitochondrial 16S gene and phylogenetic analyses using both Bayesian and Maximum Likelihood methods. We found genetic and morphological differences among geckos from the Los Altos mountain range and the remaining Phyllopezus populations. Using both molecular and morphological evidence we describe a new Phyllopezus species, sister to P. przewalskii. Genetic differentiation among described and putative Phyllopezus species is greater than their morphological differences, which likely accounts for these cryptic taxa remaining undescribed for so long. [ABSTRACT FROM AUTHOR]

Summary: Mammalian phosphatidic acid phosphatases, also called lipins, show high amino acid sequence identity to Saccharomyces cerevisiae Pah1p and catalyze the dephosphorylation of phosphatidic acid (PA) to diacylglycerol. Both the substrate and product of the reaction are key precursors for the synthesis of phospholipids and triacylglycerol (TAG). We now show that expression of the Trypanosoma brucei lipin homolog TbLpn is essential for parasite survival in culture. Inducible down‐regulation of TbLpn in T. brucei procyclic forms increased cellular PA content, decreased the numbers of lipid droplets, reduced TAG steady‐state levels and inhibited in vivo [3H]TAG formation after labeling trypanosomes with [3H]glycerol. In addition, fluorescence and transmission electron microscopy revealed that depletion of TbLpn caused major alterations in mitochondrial morphology and function, i.e., the appearance of distorted mitochondrial matrix, and reduced ATP production via oxidative phosphorylation. Effects of lipin depletion on mitochondrial integrity have previously not been reported. N‐ and C‐terminally tagged forms of TbLpn were localized in the cytosol. [ABSTRACT FROM AUTHOR]

Abstract: Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates and cultural hitchhiking (linkage of genetic variation to culturally‐transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal. One such species is the sperm whale, which shows very limited phylogeographic structure and low mtDNA diversity despite a worldwide distribution and large population. Here, we use analyses of 175 globally distributed mitogenomes and three nuclear genomes to evaluate hypotheses of a population bottleneck/expansion vs. a selective sweep due to cultural hitchhiking or selection on mtDNA as the mechanism contributing to low worldwide mitochondrial diversity in sperm whales. In contrast to mtDNA control region (CR) data, mitogenome haplotypes are largely ocean‐specific, with only one of 80 shared between the Atlantic and Pacific. Demographic analyses of nuclear genomes suggest low mtDNA diversity is consistent with a global reduction in population size that ended approximately 125,000 years ago, correlated with the Eemian interglacial. Phylogeographic analysis suggests that extant sperm whales descend from maternal lineages endemic to the Pacific during the period of reduced abundance and have subsequently colonized the Atlantic several times. Results highlight the apparent impact of past climate change, and suggest selection and hitchhiking are not the sole processes responsible for low mtDNA diversity in this highly social species. [ABSTRACT FROM AUTHOR]

Abstract: Aim: Phylogeographic studies on a number of Western Palaearctic taxa imply that the southern Caspian Sea region served as a refugium during the Last Glacial Maximum (LGM). Nevertheless, the LGM biogeography of the terrestrial and freshwater organisms in this region is poorly understood. By studying phylogeography of a species of freshwater crab, we unravel the location of probable local refugia and colonization patterns across this topographically complex landscape. Location: Southern Caspian Sea region. Taxon: The freshwater crab Potamon ibericum. Methods: We inferred the demographic history of Potamon ibericum using 163 mtDNA Cox1 sequences from 16 localities. For a subset of specimens, we amplified mtDNA 16S and four nuclear markers (28S, Histone3, Enolase, NaK) to confirm the phylogeographic structure. We tested Pleistocene expansion–contraction dynamics, using species distribution modelling (SDM) and assessed morphological variability by geometric–morphometric methods. Results: Mitochondrial markers revealed the existence of three parapatrically distributed lineages in the western, central and eastern parts of the region. The more conserved nuclear markers did not reflect this. The SDM revealed the fundamental niche expansion of P. ibericum along the southern Caspian Sea during the LGM, agreeing with results from the Cox1 data of demographic expansions. Despite strong morphological resemblance, geometric–morphometrics elucidated clinal carapace shape variation. Main Conclusions: Considering the Caspian Sea level fluctuations during the late Pleistocene, we hypothesize a scenario of demographic contraction during interglacial/warmer conditions, due to the Caspian Sea transgression and latitudinal range shift within the narrow distribution of the species between the southern Caspian Sea and northern slopes of the Alborz Mountains. During the glacial periods, the sea regressed and moist and warm conditions, characterizing glacial refugia, became prevalent in the region and caused isolated populations to expand. Our study confirms the deep transverse phylogeographic break, previously identified for Darevskia lizards in the region, and adds support to the presence of several LGM refugia in the southern Caspian Sea region. [ABSTRACT FROM AUTHOR]

Abstract: In the Ryukyu Archipelago, Japan, Goniurosaurus geckos are currently divided into six allopatric taxa among nearby islands. Recent studies suggested the occurrence of large genetic divergence within a single island and the possible non‐monophyly of a few taxa, but their species delimitation is not well resolved. We investigated the taxonomic relationships between the possibly geographically overlapped, highly diverged entities as well as other island populations via dense sampling. Our mitochondrial and nuclear DNA analyses showed that the two genetic groups were distributed in parapatry within Okinawajima Island and that they were hybridizing in narrow area around the contact zone. Geohistorical evidence suggests that the restricted gene flow has been caused by some intrinsic isolation mechanisms. Thus, we conclude that the two lineages represent full species. Mitochondrial analysis also showed that the genetic differences among other island populations were comparable to those between these species, thereby suggesting the presence of seven full species, including one unnamed taxon. We also discuss the possible cause of this divergence and why it has occurred at such a fine geographic scale. [ABSTRACT FROM AUTHOR]

In this study, we report a novel perpective of metabolic consequences for the m.8993T>G variant using fibroblasts from a proband with clinical symptoms compatible with Maternally Inherited Leigh Syndrome (MILS). Definitive diagnosis was corroborated by mitochondrial DNA testing for the pathogenic variant m.8993T>G in MT-ATP6 subunit by Sanger sequencing. The long-range PCR followed by massively parallel sequencing method detected the near homoplasmic m.8993T>G variant at 83% in the proband's fibroblasts and at 0.4% in the mother's fibroblasts. Our results are compatible with very low levels of germline heteroplasmy or an apparent de novo mutation. Our mitochondrial morphometric analysis reveals severe defects in mitochondrial cristae structure in the proband's fibroblasts. Our live-cell mitochondrial respiratory analyses show impaired oxidative phosphorylation with decreased spare respiratory capacity in response to energy stress in the proband's fibroblasts. We detected a diminished glycolysis with a lessened glycolytic capacity and reserve, revealing a stunted ability to switch to glycolysis upon full inhibition of OXPHOS activities. This dysregulated energy reprogramming results in a defective interplay between OXPHOS and glycolysis during an energy crisis. Our study sheds light on the potential pathophysiologic mechanism leading to chronic energy crisis in this MILS patient harboring the m.8993T>G variant. [ABSTRACT FROM AUTHOR]

Investigating how recombination might modify gene order during the evolution has become a routine part of mitochondrial genome analysis. A new method of genomic maps analysis based on formal logic is described. The purpose of this method is to 1) use mitochondrial gene order of current taxa as datasets 2) calculate rearrangements between all mitochondrial gene orders and 3) reconstruct phylogenetic relationships according to these calculated rearrangements within a tree under the assumption of maximum parsimony. Unlike existing methods mainly based on the probabilistic approach, the main strength of this new approach is that it calculates all the exact tree solutions with completeness and provides logical consequences as highly robust results. Moreover, this method infers all possible hypothetical ancestors and reconstructs character states for all internal nodes of the trees. We started by testing our method using the deuterostomes as a study case. Then, with sponges as an outgroup, we investigated the evolutionary history of mitochondrial genomes of 47 bilaterian phyla and emphasised the peculiar case of chaetognaths. This pilot work showed that the use of formal logic in a hypothetico-deductive background such as phylogeny (where experimental testing of hypotheses is impossible) is very promising to explore mitochondrial gene order in deuterostomes and should be applied to many other bilaterian clades. [ABSTRACT FROM AUTHOR]

Given the paucity of archaeogenetic data available for medieval European populations in comparison to other historical periods, the genetic landscape of this age appears as a puzzle of dispersed, small, known pieces. In particular, Southeastern Europe has been scarcely investigated to date. In this paper, we report the study of mitochondrial DNA in 10th century AD human samples from Capidava necropolis, located in Dobruja (Southeastern Romania, Southeastern Europe). This geographical region is particularly interesting because of the extensive population flux following diverse migration routes, and the complex interactions between distinct population groups during the medieval period. We successfully amplified and typed the mitochondrial control region of 10 individuals. For five of them, we also reconstructed the complete mitochondrial genomes using hybridization-based DNA capture combined with Next Generation Sequencing. We have portrayed the genetic structure of the Capidava medieval population, represented by 10 individuals displaying 8 haplotypes (U5a1c2a, V1a, R0a2’3, H1, U3a, N9a9, H5e1a1, and H13a1a3). Remarkable for this site is the presence of both Central Asiatic (N9a) and common European mtDNA haplotypes, establishing Capidava as a point of convergence between East and West. The distribution of mtDNA lineages in the necropolis highlighted the existence of two groups of two individuals with close maternal relationships as they share the same haplotypes. We also sketch, using comparative statistical and population genetic analyses, the genetic relationships between the investigated dataset and other medieval and modern Eurasian populations. [ABSTRACT FROM AUTHOR]

Abstract: The taxonomy of French ninespined sticklebacks (Pungitius spp.) has long been controversial. To clarify the taxonomy in this group, we use mitochondrial (COI) and nuclear (RNF213) sequence markers, as well as morphological data. In France, both genetic markers discriminate three evolutionary lineages. Morphological analysis on fresh and type specimens supports the different lineages and the existence of three species in France. Pungitius pungitius, occurring in the North of France and Rhone basin, is characterized by specimens longer than 35 mm SL, by a flat head with a straight or slightly concave snout, typically 9–10 dorsal spines, 10–11 dorsal soft rays, 9–10 anal soft rays, 0–12 scutes on the caudal peduncle with a keel reaching the last anal‐fin ray, longer pelvic fin, post‐dorsal and caudal peduncle lengths, and a slim caudal peduncle (caudal peduncle depth/length 11.8%–21.9%). Pungitius laevis, occurring in France, in the English Channel basins and Loire drainage, differs from the other species by a head rounded with concave snout in specimens longer than 35 mm SL, accentuating the impression of fleshy lips, 0–4 scutes on the caudal peduncle and a higher caudal peduncle depth/length ratio (15.7%–34.5%). Finally, Pungitius vulgaris, endemic to the Vienne River and rivers of south‐western France as far north as the Garonne estuary, is differentiated by a rounded head with a straight or slightly convex snout, the absence of scutes on the caudal peduncle and by having 11 pectoral‐fin rays. Our data confirm the existence of a hybridization zone in the North of France between P. pungitius and P. laevis. As a result, Pungitius lotharingus is invalid, as it was described based on hybrid specimens. A lectotype for P. laevis was designated because the syntypes included hybrids. This revision provides new perspectives for evolutionary biology studies and will have consequences for Pungitius conservation in France. [ABSTRACT FROM AUTHOR]