Mitochondrial Region Research Articles

Targeting the ‘DNA methylation mark’: Analysis of early epigenetic-alterations in children chronically exposed to arsenic

Chronic exposure to arsenic causes adverse health effects in children. Aberrant epigenetic modifications including altered DNA methylation pattern are one of the major steps towards malignant transformation of cells. Our group has previously identified significant alteration in DNA methylation mark in arsenic exposed adults, affecting major biological pathways. Till date, no information is available exploring the altered DNA methylation mark in telomere regulation and altered mitochondrial functionality in association with DNA damage in arsenic-exposed children. Our study aims in identifying signature epigenetic pattern associated with telomere lengthening, mitochondrial functionality and DNA damage repair in children with special emphasis on DNA methylation. Biological samples (blood and urine) and drinking water were collected from the children aged between 5 and 16 years of arsenic exposed areas (N = 52) of Murshidabad district and unexposed areas (N = 50) of East Midnapur districts, West Bengal, India. Methylation-specific PCR was performed to analyse subtelomeric methylation status and promoter methylation status of target genes. Results revealed altered DNA methylation profile in the exposed children compared to unexposed. Promoter hypermethylation was observed in MLH1 and MSH2 (p < 0.05 and p < 0.001) indicating inefficiency in DNA damage repair. Hypomethylation in mitochondrial D-loop (p < 0.05) and TFAM promoter region (p < 0.05) along with increased mitochondrial DNA copy number among exposed children was also observed. Significant increase in telomere length and region specific subtelomeric hypermethylation (XpYp, p < 0.05) was found. Analysis of S-Adenosyl Methionine (SAM) and 8-oxoDG level revealed significant depletion of SAM (p < 0.001) and elevated oxidative DNA damage (p < 0.001) respectively in arsenic toxicity. Our study identified key methylation patterns in arsenic-exposed children which may act as an early predictive biomarker in the near future. Further in-depth studies involving large sample size and transcriptomic analysis are required for understanding the mechanistic details.

Molecular Identification of Three Species of Leaf Miners from the Order Diptera on Brassicaceae Crops in Basra Governorate

The leafminer (Order: Diptera) is an insect that can be found throughout the Middle East and many other parts of the world. It feeds on a range of plants. It was discovered on several Brassicaceae family leaves in Iraq. In this study, the leafminer samples were collected from the Agricultural Experimental Station – the University of Basrah campus. These samples were microscopically analysed and morphologically characterized to distinguish leafminer genera. Our results revealed that the Agromyzidae family included two species Liriomyza sativae, and Chromatomyia horticola. While the Drosophilidae family involved Scaptomyza flava. These three genera belong to the 420 bases pair. For both intra- and interspecific variation, the mitochondrial region’s COX area has been thoroughly investigated. The results of all these studies combine to create a sizable collection of sequencing data for the Agromyzidae and Drosophilidae families.

A CircRNA-miRNA-mRNA Network for Exploring Doxorubicin- and Myocet-Induced Cardiotoxicity in a Translational Porcine Model.

Despite the widespread use of doxorubicin (DOX) as a chemotherapeutic agent, its severe cumulative cardiotoxicity represents a significant limitation. While the liposomal encapsulation of doxorubicin (Myocet, MYO) reduces cardiotoxicity, it is crucial to understand the molecular background of doxorubicin-induced cardiotoxicity. Here, we examined circular RNA expression in a translational model of pigs treated with either DOX or MYO and its potential impact on the global gene expression pattern in the myocardium. This study furthers our knowledge about the regulatory network of circRNA/miRNA/mRNA and its interaction with chemotherapeutics. Domestic pigs were treated with three cycles of anthracycline drugs (DOX, n = 5; MYO, n = 5) to induce cardiotoxicity. Untreated animals served as controls (control, n = 3). We applied a bulk mRNA-seq approach and the CIRIquant algorithm to identify circRNAs. The most differentially regulated circRNAs were validated under cell culture conditions, following forecasting of the circRNA-miRNA-mRNA network. We identified eight novel significantly regulated circRNAs from exonic and mitochondrial regions in the porcine myocardium. The forecasted circRNA-miRNA-mRNA network suggested candidate circRNAs that sponge miR-17, miR-15b, miR-130b, the let-7 family, and miR125, together with their mRNA targets. The identified circRNA-miRNA-mRNA network provides an updated, coherent view of the mechanisms involved in anthracycline-induced cardiotoxicity.

An assessment of South African small mammal barcode sequence libraries: Implications for future carnivore diet analyses by DNA

AbstractDNA metabarcoding requires reference libraries that link DNA sequences to species. Mitochondrial gene regions cytochrome c oxidase I (COI), 12S ribosomal RNA (12S rRNA), 16S ribosomal RNA (16S rRNA), cytochrome b (cyt b) and the hypervariable control region (D‐loop) are routinely used in studies that measure genetic diversity in animal species. This study aimed to review the state of DNA reference libraries for small South African mammals as small mammals constitute a large portion of small and medium carnivore diet. Analyses of DNA records revealed that of 193 small mammal species in South Africa, only 141 have DNA sequences available for one or more of the mitochondrial genes examined. Cyt b had the highest species coverage, with 59.1% of South African species represented in the reference libraries. COI only has 33.7%, 12S rRNA has 23.8%, D‐loop has 17.6%, and 16S rRNA has the lowest species coverage of 15%. This study supports the use of multiple gene regions when performing scat metabarcoding, particularly when wanting to determine the small mammal component of the diet. Additionally, it emphasises the need to build comprehensive DNA reference libraries linking sequences to taxonomically identified species.

Mitochondrial Diversity and Phylogenetic Relationship of Eight Native Bulgarian Sheep Breeds

The geographical, geomorphological, and climatic characteristics of Bulgaria are particularly favorable for animal breeding and, above all, for pastoral farming and sheep breeding. These conditions created prerequisites for the creation of about 30 unique local breeds of sheep. In this study we investigated the genetic diversity of eight of the most popular Bulgarian native breeds, based on the sequence analysis of a part of the mitochondrial D-loop region. An almost entire mitochondrial DNA (mtDNA) D-loop region (1180 bp) was amplified and sequenced. The obtained results showed the presence of a large number of haplotypes – 225, belonging to two main haplogroups. The majority of samples showed a high prevalence of the European haplogroup B (95.2%) while the remaining individuals were assigned to haplogroup A (4.8%). None of the other reported mitochondrial haplogroups were observed. The number of polymorphic sites, nucleotide and haplotype diversity was high (240, 0.01237, and 0.9968, respectively), which is evidence for multiple maternal origins in all populations. The Tajima D-test value in all the study populations was −1.905 (p &lt; 0.05), indicating that the abundance of rare alleles was most likely due to population expansion after a recent bottleneck. The Median joining network showed that almost all haplotypes belonging to haplogroup B formed a star-like network, which revealed a weak genetic differentiation and a large gene flow between the Bulgarian native breeds.

Fine-scale phylogeography of the Japanese Genji firefly

Abstract The Japanese Archipelago consists of four major islands and numerous small islands. The Goto Islands are located near Kyushu, a major island in the Japanese Archipelago. We have previously reported that the population of the Japanese Genji firefly, Nipponoluciola cruciata, inhabiting the Goto Islands displays a unique flashing pattern that is used for pre-mating communication between males and females, indicating the possibility of genetic isolation of the Goto Islands population from neighbouring N. cruciata populations. In this study, we aimed to elucidate the gene flow between the Goto Islands N. cruciata population and its neighbouring island populations by molecular phylogenetic analyses based on the mitochondrial DNA regions of cytochrome c oxidase subunit II and ND5, also coupled to genome-wide analysis of nuclear DNA single nucleotide polymorphisms. Our results suggested that the Goto Islands N. cruciata population is genetically isolated from other populations of this species. Nuclear DNA-based population analyses indicated gene flow between the populations inhabiting the Kyushu and Iki Islands, situated at a distance approximately equal to that between the Goto and Kyushu Islands. Therefore, the genetic isolation of the Goto Islands N. cruciata population is largely affected by flashing pattern behaviour, underlining an ongoing speciation process.

Choice of primer pairs and PCR polymerase affect the detection of fish eDNA

Efficient biomonitoring is essential for fish protection and management. Environmental DNA (eDNA) has become a promising tool for fish surveys, and its accuracy and robustness are closely related to the primer pairs and DNA polymerases, especially for different environmental samples. However, there is still a lack of sufficient efforts to assess the effects of both two factors on fish biomonitoring. Here, we selected ten primer pairs in the mitochondrial 12S rRNA gene region and three commercial DNA polymerases and analyzed their effects on fish eDNA monitoring in surface water and sediment samples of Dianchi Lake. We found that primer pairs and DNA polymerases significantly affected fish biomonitoring in surface water and sediments of Dianchi Lake. First, there were significant variations in annotated fish eDNA sequences in different groups of primer pairs and DNA polymerases, the percentage of fish sequences amplified by the groups related to primers Riaz-12S and 12S-V5 was more than 90% of the total sequences. Second, the composition of different classification levels of fish taxa varied considerably across groups of primer pairs and DNA polymerases, and the groups related to primers Riaz-12S (i.e., Taq Master‒Riaz-12S, Rapid Taq‒Riaz-12S) and 12S-V5 (i.e., Taq Master‒12S-V5, Rapid Taq‒12S-V5) identified more taxa than other groups. Third, primer pairs had greater impacts on the structure of fish communities than DNA polymerases, and the interactions between two factors had more significant effects than any single one. This study highlights that primer pairs and DNA polymerases play critical roles in fish biomonitoring, and this work aimed to provide methodological guidance for assisting the design of the fish eDNA survey scheme.

Dolphins from a prehistoric midden imply long-term philopatry of delphinids around Tokyo Bay

Abstract Cetaceans of the family Delphinidae are widely distributed throughout the global ocean, and it has been suggested that females exhibit philopatry. However, the duration of time that a maternal group of these highly mobile creatures spends inhabiting a particular region remains unknown. The objective of this study is to examine the genetic diversity of delphinids in the past and to shed light on the above question. In this study, we amplified and sequenced the mitochondrial DNA D-loop region from the skeletal remains of delphinids that were excavated from the Shomyoji Midden, a site situated on the western coast of Tokyo Bay and dating to 5000–3000 years before the present. We acquired prehistoric D-loop sequences of seven bottlenose dolphins, six Pacific white-sided dolphins, and a false killer whale. Notably, one or more haplotypes from the prehistoric individuals were detected in the geographically proximate modern conspecific populations across all three species. Whilst the genetic diversity of prehistoric and modern Pacific white-sided dolphin populations appears to be comparable, the modern bottlenose dolphin population demonstrates significantly lower genetic diversity when compared to its prehistoric counterpart in the vicinity of Tokyo Bay. The maternal groups of these species are speculated to have persisted in the same habitat for at least 4000 years.

Genomic analysis of wolves from Pakistan clarifies boundaries among three divergent wolf lineages.

Among the three main divergent lineages of gray wolf (Canis lupus), the Holarctic lineage is the most widespread and best studied, particularly in North America and Europe. Less is known about Tibetan (also called Himalayan) and Indian wolf lineages in southern Asia, especially in areas surrounding Pakistan where all three lineages are thought to meet. Given the endangered status of the Indian wolf in neighboring India and unclear southwestern boundary of the Tibetan wolf range, we conducted mitochondrial and genome-wide sequencing of wolves from Pakistan and Kyrgyzstan. Sequences of the mitochondrial D-loop region of 81 wolves from Pakistan indicated contact zones between Holarctic and Indian lineages across the northern and western mountains of Pakistan. Reduced-representation genome sequencing of eight wolves indicated an east-to-west cline of Indian to Holarctic ancestry, consistent with a contact zone between these two lineages in Pakistan. The western boundary of the Tibetan lineage corresponded to the Ladakh region of India's Himalayas with a narrow zone of admixture spanning this boundary from the Karakoram Mountains of northern Pakistan into Ladakh, India. Our results highlight the conservation significance of Pakistan's wolf populations, especially the remaining populations in Sindh and Southern Punjab that represent the highly endangered Indian lineage.

Genetic diversity and maternal origin of Vietnamese indigenous chicken breeds inferred from complete sequences of mitochondrial DNA D-loop region

Genetic diversity and maternal origin of Vietnamese indigenous chicken breeds inferred from complete sequences of mitochondrial DNA D-loop region

On the conservation of white-clawed crayfish in the Iberian Peninsula: Unraveling its genetic diversity and structure, and origin.

European crayfish species are a clear example of the drastic decline that freshwater species are experiencing. In particular, the native species of the Iberian Peninsula, the white clawed-crayfish (WCC) Austropotamobius pallipes, is listed as "endangered" by the IUCN and included in Annex II of the EU Habitat Directive and requires especially attention. Currently, implemented conservation management strategies require a better understanding of the genetic diversity and phylogeographic patterns, as well as of its evolutionary history. For this purpose, we have generated the largest datasets of two informative ribosomal mitochondrial DNA regions, i.e., cytochrome oxidase subunit I and 16S, from selected populations of the WCC covering its geographical distribution. These datasets allowed us to analyze in detail the (i) genetic diversity and structure of WCC populations, and (ii) divergence times for Iberian populations by testing three evolutionary scenarios with different mtDNA substitution rates (low, intermediate, and high rates). The results indicate high levels of haplotype diversity and a complex geographical structure for WCC in the Iberian Peninsula. The diversity found includes new unique haplotypes from the Iberian Peninsula and reveals that most of the WCC genetic variability is concentrated in the northern and central-eastern regions. Despite the fact that molecular dating analyses provided divergence times that were not statistically supported, the proposed scenarios were congruent with previous studies, which related the origin of these populations with paleogeographic events during the Pleistocene, which suggests an Iberian origin for these WCC. All results generated in this study, indicate that the alternative hypothesis of an introduced origin of the Iberian WCC is highly improbable. The result of this study, therefore, has allowed us to better understand of the genetic diversity, structure patterns, and evolutionary history of the WCC in the Iberian Peninsula, which is crucial for the management and conservation needs of this endangered species.

New species of the genus Trichosetodes Ulmer, 1915 (Trichoptera, Leptoceridae) from Ratanakiri province, Cambodia, based on morphological and molecular data.

Three new species of Trichosetodes, namely T.carmelaesp. nov., T.katiengensissp. nov. and T.ratanakiriensissp. nov. are described and illustrated by male specimens. The male genitalia of T.carmelaesp. nov. can be distinguished from the other 16 species of the genus found in Southeast Asia by the shape of the phallicata. The phallicata of T.carmelaesp. nov. bears a tuft of long hairs in the middle of the dorsal edge. Trichosetodeskatiengensissp. nov. can be distinguished from the other species in Southeast Asia by the shape of the phallicata which is divided into dorsal and ventral branches in lateral view, and T.ratanakiriensissp. nov. by the characters of the left inferior appendage and the shape of segment IX. The posterior end of the left inferior appendage of T.ratanakiriensissp. nov. is not forked and the ventral and lateral views of the posteroventral lobes of segment IX are rounded. Illustrations of male genitalia of Trichosetodeskampongspeuensis Malicky & Kong, 2020 are provided for comparison. The molecular diversity of new Trichosetodes species was analyzed using the mitochondrial large subunit ribosomal rRNA gene region (16S rRNA). In terms of their genetic divergence, T.ratanakiriensissp. nov. and T.kampongspeuensis exhibited remarkable proximity, with only a 1.4% distance. On the contrary, T.carmelaesp. nov. displayed genetic disparity exceeding 6.3% when compared to both T.ratanakiriensissp. nov. and T.kampongspeuensis.

Aphanomyces astaci in Mexico: A new haplotype from dwarf crayfish Cambarellus montezumae

The crayfish plague is an emerging infectious disease caused by the pathogen Aphanomyces astaci (Oomycota), which is responsible for the decimation of Eurasian freshwater crayfish. This pathogen can coexist with the North American crayfish. These are chronic carriers of the disease as consequence of an immune response that can contain the growth of the pathogen without killing it. The origin of A. astaci locates in the southeastern United States and coincides with the origin of the family Cambaridae. This diverse family of decapods is distributed in North America from southern Canada to Honduras. However, only the native crayfish species from Canada and the USA have been examined for the presence of A. astaci. In this study, we describe for the first time the presence of A. astaci in Mexico in a population of the native species Cambarellus montezumae. By analyzing the small (rrnS) and large (rrnL) mitochondrial ribosomal regions, we showed the presence of two haplotypes of A. astaci within the same population (d1-haplotype and, a novel haplotype that was named, mex1-haplotype). The finding of A. astaci in Mexico confirms the occurrence of this pathogen within the range of the family Cambaridae. The individuals of C. montezumae appear to be chronic carriers of A. astaci, indicated by the lack of documented crayfish plague outbreaks in this population, similar to the pattern observed in other North American species. Thus, the results are of special concern to susceptible species of southern regions of America, i.e., Parastacidae. Therefore, this work emphasizes the need to better understand the distribution and genetic diversity of A. astaci within the distribution range of the natural carriers, i.e., North American species, especially the unexplored area of the family Cambaridae.

Wing pattern diversity in Eunica butterflies (Nymphalidae: Biblidinae): phylogenetic analysis implies decoupled adaptive trends in dorsal sexual dimorphism and ventral eyespot evolution.

Butterfly eyespots are wing patterns reminiscent of vertebrate eyes, formed by concentric rings of contrastingly coloured scales. Eyespots are usually located close to the wing margin and often regarded as the single most conspicuous pattern element of butterfly wing colour displays. Recent efforts to understand the processes involved in the formation of eyespots have been driven mainly by evo-devo approaches focused on model species. However, patterns of change implied by phylogenetic relationships can also inform hypotheses about the underlying developmental mechanisms associated with the formation or disappearance of eyespots, and the limits of phenotypic diversity occurring in nature. Here we present a combined evidence phylogenetic hypothesis for the genus Eunica, a prominent member of diverse Neotropical butterfly communities, that features notable variation among species in eyespot patterns on the ventral hind wing surface. The data matrix consists of one mitochondrial gene region (COI), four nuclear gene regions (GAPDH, RPS5, EF1a and Wingless) and 68 morphological characters. A combined cladistic analysis with all the characters concatenated produced a single most parsimonious tree that, although fully resolved, includes many nodes with modest branch support. The phylogenetic hypothesis presented corroborates a previously proposed morphological trend leading to the loss of eyespots, together with an increase in the size of the conserved eyespots, relative to outgroup taxa. Furthermore, wing colour pattern dimorphism and the presence of androconia suggest that the most remarkable instances of sexual dimorphism are present in the species of Eunica with the most derived eyespot patterns, and are in most cases accompanied by autapomorphic combinations of scent scales and "hair pencils". We discuss natural and sexual selection as potential adaptive explanations for dorsal and ventral wing patterns.

Raman microscopy reveals how cell inflammation activates glucose and lipid metabolism

Metabolism of endothelial cells (ECs) depends on the availability of the energy substrates. Since the endothelium is the first line of defence against inflammation in the cardiovascular system and its dysfunction can lead to the development of cardiovascular diseases, it is important to understand how glucose metabolism changes during inflammation. In this work, glucose uptake was studied in human microvascular endothelial cells (HMEC-1) in high glucose (HG), and additionally in an inflammatory state, using Raman imaging. HG state was induced by incubation of ECs with a deuterated glucose analogue, while the EC inflammation was caused by TNF-α pre-treatment. Spontaneous and stimulated Raman scattering spectroscopy provided comprehensive information on biochemical changes, including lipids and the extent of unsaturation induced by excess glucose in ECs., induced by excess glucose in ECs. In this work, we indicated spectroscopic markers of metabolic changes in ECs as a strong increase in the ratio of the intensity of lipids / (proteins + lipids) bands and an increase in the level of lipid unsaturation and mitochondrial changes. Inflamed ECs treated with HG, revealed enhanced glucose uptake, and intensified lipid production i.a. of unsaturated lipids. Additionally, increased cytochrome c signal in the mitochondrial region indicated higher mitochondrial activity and biogenesis. Raman spectroscopy is a powerful method for determining the metabolic markers of ED which will better inform understanding of disease onset, development, and treatment.

First detection of the potato cyst nematode, Globodera rostochiensis, infecting potato in the central region of Colombia.

Potato cyst nematodes (PCNs; Globodera spp.) cause significant losses in worldwide cultivated potato (Solanum tuberosum) crops. In Colombia, PCN was first reported in 1970 (Baeza 1972), although this report lacked a comprehensive species description and diagnosis. After that, G. pallida has been the only PCN species reported affecting potatoes in the main producing regions of Colombia (Evans et al. 1975; Nieto et al. 1983; Vallejo et al. 2021). However, in the survey conducted by Vallejo et al. (2021), a single sample from Chocontá, Cundinamarca in the central region of the country (N 5,22396046668291, W -73,6571338400244) showed molecular characters similar to G. rostochiensis. As correct identification is essential for effective pest management, the location was re-sampled in September 2022. From the soil samples collected, PCN cysts and second-stage juveniles (J2s) were retrieved from soil using Fenwick and centrifugation methods, respectively. Morphometric characters of cysts (n = 53) were consistent with G. rostochiensis, with a length without neck (L) ranging from 451 to 614 μm (X̅ = 546.9 ± 20.3 μm), width (W) from 424 to 658 μm (X̅ = 546.9 ± 25.5 μm) and L/W ratio was 1.00 ± 0.02. Distance from anus to vulva varied from 41 to 109 μm (X̅ =75.67 ± 13.8 μm), Granek's ratio from 2.3 to 5.5 μm (X̅ = 3.89 ± 0.7 μm), and the number of cuticular ridges between the vulva and the anus were 14 to 20 (X̅ = 16.19 ± 1.7). The second-stage juvenile (n = 90) length ranged from 394 to 547 μm (X̅ = 495.62 ± 31.0 μm), the stylet length varied from 18 to 24 μm (X̅ = 21.21 ± 0.9 μm) with rounded knobs. The length of the hyaline tail ranged from 20 - 31 μm (X̅ = 24.09 ± 1.92) and the true tail from 31- 56 μm (X̅ = 48.30 ± 5.71 μm). Molecular analyses confirmed morphological identification. DNA was extracted from cysts and J2s. PCR was performed for the 28S rDNA D2-D3 segment using primers D2A and D3B (Subbotin et al. 2006), and for the mitochondrial COI gene region using primers JB3 and JB5 (Derycke et al. 2005). BLAST analyses of target 28S rDNA D2-D3 sequences (OP293373-OP293380) showed 100% identity of the 658 bp to other sequences on Genbank, including isolates from Turkey, United Kingdom, and Iran (MK311329.1, MG994942.1, KU297659.1, and KU297658.1). Similarly, the target COI region sequences (OP297993-OP298001) were 100% identical to the 407 bp of G. rostochiensis POT01 isolate from Germany, and 99.75% identical to voucher NRM67 from Indonesia, and isolate CD2200 from USA (MF773722.1, MT240262.1, and MN095979.1). Phylogenetic analysis of both gene regions strongly supported G. rostochiensis, with the Colombian sequences clustering with MH399815.1, and KU297654.1 isolates for the COI and 28S regions, respectively (Fig. 1S). In addition, a pathogenicity test was conducted in the greenhouse. For this, ten cysts were inoculated to potato plants of Criolla variety grown in 5 pots of 15 cm diameter with sterile soil and sand (1:1). Noninoculated plants served as controls (three replicates each). After three months, 54 ± 23 cysts/100 g of soil were isolated from inoculated plants (Fig. 2S), resulting in a reproduction factor (R=Pf/Pi) of 4.54 ± 0.86, while no yellow females or cysts were observed on the control plants. To our knowledge, this is the first report of G. rostochiensis in Colombia. This is an important pest that causes serious yield losses of potatoes and is a quarantine nematode in many countries (EPPO 2017). Further studies are necessary to prevent the spread of this PCN species in the main producing potato regions of Colombia.

Distribution and habitat preference of polar cod (Boreogadus saida) in the Bering and Chukchi Seas inferred from species-specific detection of environmental DNA

Ongoing warming and sea-ice reductions in the Arctic can seriously impact cold-water species, such as polar cod (Boreogadus saida), necessitating biomonitoring to reveal the ecological consequences. Recent methodological advancements in environmental DNA (eDNA) techniques have increased our ability to conduct ecological monitoring at various locations, including the Arctic. This study aimed to provide an overview of the distribution of polar cod across the Bering and Chukchi Seas by employing species-specific detection of eDNA. First, we successfully developed novel species-specific qPCR assay targeting the mitochondrial D-loop region, which exclusively amplifies eDNA derived from polar cod. Subsequently, polar cod eDNA was detected using the assay from the samples that we collected latitudinally across the study area during the open-water season. Polar cod eDNA was primarily detected in the surface water from the central Chukchi Sea shelf and the northernmost observation line (75°N), which was located on the shelf slope, off the Point Barrow, and in the marginal ice zone. In contrast, only trace amounts of eDNA were detected in the Bering Sea. This pattern corresponded well with the distribution of water masses classified based on environmental conditions. The detection of eDNA in surface water was clearly limited to cold (-1 to 5°C) and low salinity (25–32) water, whereas it was detected in a higher salinity range (32–34) in the middle and bottom layers. These findings are consistent with current knowledge about the distribution and habitat of the polar cod, suggesting that eDNA can be regarded as a reliable tool to replace or supplement conventional methods. Incorporating eDNA techniques into large-scale oceanographic surveys can improve the spatial and temporal resolution of fish species detection with a reasonable sampling effort and will facilitate the continuous monitoring of Arctic ecosystems.

Exploring Genetic Markers: Mitochondrial DNA and Genomic Screening for Biodiversity and Production Traits in Donkeys.

Donkeys (Equus asinus) play a pivotal role as essential livestock in arid and semi-arid regions, serving various purposes such as transportation, agriculture, and milk production. Despite their significance, donkey breeding has often been overlooked in comparison to other livestock species, resulting in limited genetic improvement programs. Preserving donkey genetic resources within each country necessitates the establishment of breed conservation programs, focusing on managing genetic diversity among populations. In recent years, significant strides have been made in sequencing and analyzing complete mitochondrial DNA (mtDNA) molecules in donkeys. Notably, numerous studies have honed in on the mitochondrial D-loop region, renowned for its remarkable variability and higher substitution rate within the mtDNA genome, rendering it an effective genetic marker for assessing genetic diversity in donkeys. Furthermore, genetic markers at the RNA/DNA level have emerged as indispensable tools for enhancing production and reproduction traits in donkeys. Traditional animal breeding approaches based solely on phenotypic traits, such as milk yields, weight, and height, are influenced by both genetic and environmental factors. To overcome these challenges, genetic markers, such as polymorphisms, InDel, or entire gene sequences associated with desirable traits in animals, have achieved widespread usage in animal breeding practices. These markers have proven increasingly valuable for facilitating the selection of productive and reproductive traits in donkeys. This comprehensive review examines the cutting-edge research on mitochondrial DNA as a tool for assessing donkey biodiversity. Additionally, it highlights the role of genetic markers at the DNA/RNA level, enabling the informed selection of optimal production and reproductive traits in donkeys, thereby driving advancements in donkey genetic conservation and breeding programs.

Insights on the Evolutionary History and Genetic Patterns of Octopus vulgaris Cuvier, 1797 in the Northeastern Atlantic Using Mitochondrial DNA.

Octopus vulgaris is one of the most harvested octopus species in the world. In the Iberian Peninsula, there are several small-scale fisheries that have a long-term tradition of harvesting octopus. The Asturias fleet (in Northern Spain) has an internationally recognized MSC label for its exploitation. Of concern, genetic assessments of exploited stocks are currently scarce, which could prevent the implementation of adequate managing strategies. We use two mitochondrial regions (cytochrome oxidase subunit 1 and control region) to analyze the genetic status and evolutionary events that conditioned octopus populations' characteristics in the Northeastern Atlantic. A total of 90 individuals were sampled from three different localities in the Iberian Peninsula as well as a location in Macaronesia. Temporal genetic analyses on Asturias and Algarve populations were also performed. Results indicated the absence of fine spatial genetic structuring but showed the Canary Islands (in Macaronesia) as the most distinct population. Our analyses detected two distinct clades, already described in the literature, but, for the first time, we confirmed the presence of the α-southern haplogroup in the Northern Iberian Peninsula. This result indicates a more continuous cline for the distribution of these two haplogroups than previously reported. Temporal changes in the distribution of both haplogroups in contact zones were also detected.

Mitochondrial displacement loop region single nucleotide polymorphisms and mitochondrial DNA copy number associated with risk of ankylosing spondylitis.

The pathogenesis of ankylosing spondylitis (AS) seems to be associated with genetics, the environment, heredity, and oxidative stress. Single nucleotide polymorphisms (SNPs) in the displacement loop (D-loop) region of mitochondrial DNA (mtDNA) and mtDNA copy number were investigated for their correlation with AS patients. This study included 83 AS patients and 100 healthy controls from the Second Hospital of Hebei Medical University. DNAs were extracted from blood samples for polymerase chain reaction analysis and quantitative real-time polymerase chain reaction analysis. Plasma reactive oxygen species (ROS) levels were measured by fluorescent probe technology. The distribution frequencies of the minor alleles of nucleotides 16304C (p = .037), 16311C (p = .027), and 152C (p = .034) were remarkably higher in AS patients than in healthy controls, which indicated that the16304C, 16311C, and 152C alleles were correlated with an increased risk of AS. Simultaneously, mtDNA copy number was statistically higher in patients with AS compared with controls (1.450 ± 0.876 versus 0.835 ± 0.626, p < .001). We also observed an increased ROS generation in AS patients compared with controls (27 066.169 ± 18 364.819 versus 14 758.330 ± 5854.946, p < .001) subsequently. In addition, the AS susceptible SNP 16311C is associated with high ROS levels (35 065.177 ± 26 999.934 vs. 25 005.818 ± 14 999.495, p = .043). Our study demonstrated that SNPs in the mtDNA D-loop could be AS risk biomarkers with the potential to promote oxidative stress levels; mtDNA copy number-induced mitochondrial dysfunction may also be involved in AS pathogenesis.