NADH Dehydrogenase Subunit Research Articles

Polymorphism of Russian Populations of Rhopalosiphum padi L. Based on DNA Markers

Using the next-generation sequencing (NGS) technology, the nucleotide polymorphism in a fragment of the ND4 gene encoding NADH dehydrogenase subunit 4 was studied in 14 samples from three populations of the bird cherry-oat aphid (Rhopalosiphum padi L.) and the range of nucleotide polymorphism was determined. The insects were collected in 2021 and 2022 in the North-West of Russia (in the vicinity of St. Petersburg) and in the northern Caucasus (Krasnodar Territory and Dagestan). Mitochondrial DNA haplotypes were identified, which have 97.95–99.80% sequence identity with the reference GenBank accession number KT447631.1. The level of intraspecific polymorphism of a 438 bp ND4 gene fragment in Rh. padi varied from 0.2 to 4.3%. In the two-year experiments, 33 polymorphic sites (17 transitions and 16 transversions) were found in the ND4 sequences, which made it possible to identify 30 mitochondrial DNA haplotypes. The Rh. padi populations collected simultaneously on different host plants or at different times on bird cherry (spring) and cereals (summer) differed in the proportion of the main haplotype, as well as in the composition of unique minor haplotypes. Analysis of the ratio of mitochondrial DNA haplotypes suggests the important role of the host plant genotype in the formation of the structure of Rh. padi populations.

Abstract 4132149: Elevated Levels of Plasma Mitochondrial DNA Damage-Associated Molecular Patterns (DAMPS) in Humans and Dogs with Heart Failure and Reduced Ejection Fraction

Background: Heart failure (HF) with reduced ejection fraction (HFrEF) is associated with increased inflammatory response that contributes to progressive worsening of the HF state. Potential endogenous triggers of this process include damage-associated molecular patterns (DAMPs). DAMPs originate from within cells following tissue stress or injury and activate pattern recognition receptors of the immune system, triggering an inflammatory response. Mitochondria are the major cell organelles that release DAMPs into the circulation. Chronic HF is associated with multi-organ mitochondrial dysfunction and cell injury and death. Purpose: The present study sought to quantify differences in mitochondrial DNA (mtDNA) DAMPs in the setting of HFrEF in humans and dogs compared to normal humans and dogs. Methods: Plasma samples were obtained from 9 HFrEF patients with left ventricular ejection fraction (LVEF) ≤35% and 9 age-matched healthy subjects, and from 6 dogs with coronary microembolization-induced HF (LVEF ≤35%) and 6 normal dogs. DNA fragments were isolated from 1 ml of plasma using a commercially available kit. Quantitative PCR and specifically designed primers were used to measure the amount of DNA in plasma from COX1 (cytochrome c oxidase subunit 1), ND1 (NADH dehydrogenase subunit 1) and ND6 (NADH dehydrogenase subunit 6) using an Applied Biosystems 7500 Fast-PCR unit. The relative abundances of plasma mtDNA DAMPs were expressed as threshold cycles (C T ). Results: Compared to normal human subjects, mtDNA DAMPs levels of COX1 , ND1 and ND6 in plasma of HFrEF patients was 4-fold, 9-fold and 8-fold greater, respectively. Similarly, compared to normal dogs, mtDNA DAMPs levels of COX1 , ND1 and ND6 in plasma of HFrEF dogs was increased 48-fold, 12-fold and 4-fold, respectively. Conclusions: These findings indicate a marked increase of mtDNA DAMPs in plasma of humans and dogs with HFrEF. The increase of mtDNA DAMPs is consistent with the elevated systemic inflammatory state of HFrEF. The results underscore mitochondrial abnormalities as integral players in the progressive worsening of HFrEF.

Comparative Mitogenomics Provides Valuable Insights for the Phylogeny and New DNA Barcodes of Ganoderma.

Ganoderma is the most important genus in the family Ganodermataceae; many species have attracted much attention and widely cultivated because of their medicinal values, but so far, not a sequenced mitogenome derived from dikaryon strains has been explicitly recorded. Herein, four novel mitogenomes of commonly cultivated Ganoderma (G. leucocontextum H4, G. lucidum G6, G. sinense MZ96 and G. tsugae SS) were de novo assembled and given detail functional annotations. Collinearity analysis revealed that the four mitogenomes shared 82.93-92.02% similarity with their corresponding reference mitogenomes at the nucleotide level. A total of 15 core protein-coding genes (PCGs), along with rrnL and rrnS (mtLSU and mtSSU) were chosen as potential candidates for constructing their individual phylogenetic trees. These trees were compared with those derived from the concatenated sequences of 15 core PCGs. And finally, we found that the atp9 and nad4L were the most reliable markers for the phylogenetic analysis of Ganoderma and chosen as standard sequences to generate new DNA barcodes. This finding was further verified by comparing it against almost all available Ganoderma mitogenomes in the NCBI, with Trametes versicolor (Polyporaceae) and Rigidoporus microporus (Meripilaceae) as two outgroups. A total of 52 mitogenomes from three families were highly conserved, with identical gene lengths for atp9 (222 bp) and nad4L (267 bp). These genes were capable of distinguish distinctly different various species, which are grouped into separate clades within the phylogenetic trees. The closest related clades (I and II), including at least 30 samples of the three classical taxonomic species (G. lingzhi, G. sichuanense and G. lucidum), differed in only one SNP. The single base mutation rate increased with the evolutionary divergence of the phylogenetic clades, from two to three SNPs in earlier clades (e.g., clade IV containing G. leucocontextum) to five to six SNPs in later clades (e.g., clade X containing G. sinense). Despite these variations between species, the atp9 and nad4L genes of Ganoderma mitogenomes consistently encoded the same ATP synthase F0 subunit c (73 aa) and NADH dehydrogenase subunit 4L (88 aa). These two genes have been identified as reliable markers of new DNA barcodes, offering valuable insights and contributing significantly to understanding the evolutionary relationships and phylogeny of the Ganoderma genus and even the Ganodermataceae family.

Contrasting the role of historic factors in phylogeograpic patterns in the native Johnny darter (Etheostoma nigrum) and invasive round goby (Neogobius melanostomus) in lower michigan.

Round goby (Neogobius melanostomus) is an invasive fish present in all five Great Lakes and is becoming increasingly common in their tributaries. Johnny darter (Etheostoma nigrum) is a native species that often coexists with N. melanostomus. In this work, historic factors are addressed as a source of genomic variation in study populations of these species. To do this, patterns of variation in the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) were characterized for both species throughout Lower Michigan. Populations of N. melanostomus and E. nigrum were sampled from 17 localities representing both eastern and western basins of Lower Michigan to test the hypothesis that populations differ between the eastern and western basins of the Great Lakes. Neogobius melanostomus populations were largely homogenous with no significant differences detected among populations or between the eastern and western basins. Additionally, N. melanostomus exhibited no evidence of overarching historical genetic structure, consistent with the recent invasion and rapid expansion of this species. Etheostoma nigrum exhibited significant differentiation among local populations; however, similarity among mtDNA haplotypes indicated that differences among populations are recent, suggesting that local forces are a more important factor in shaping patterns of variation than historical factors. Contrary to predictions, there were no significant differences detected between the eastern and western basins of the Great Lakes; however, construction of a neighbor-joining tree with F ST estimates revealed clustering of populations by basin with some anomalies. These anomalies may be the result of recent stream capture events facilitating gene flow between the two basins.

Electroacupuncture Slows Experimental Myopia Progression by Improving Retinal Mitochondrial Function: A Study Based on Single-Cell RNA Sequencing.

This study aimed to establish a complete atlas of retinal cells in lens-induced myopia (LIM) and electroacupuncture (EA) intervention by single-cell RNA sequencing (scRNA-seq) and to explore the potential mechanism of EA in improving experimental myopia progression in guinea pigs. scRNA-seq is used to assess changes in individual cellular gene levels in the retina of LIM- and EA-treated guinea pigs. In addition, the role of EA in slowing myopia progression by improving retinal mitochondrial function is further investigated. scRNA-seq identified ten cell clusters in the retina of LIM and EA guinea pigs and mitochondrial respiratory chain-related genes in Cones and Muller-glia cells-Cytochrome oxidase subunit III (COX3), NADH dehydrogenase subunit 4 (ND4), and NADH dehydrogenase subunit 2 (ND2) are closely related to lens-induced myopia. A comprehensive atlas in the retina of LIM and EA guinea pigs at a single-cell level is established, and the positive role of EA in improving retinal mitochondrial function to slow the experimental myopia progression in guinea pigs is revealed.

The seventh species of the newt genus Tylototriton in Thailand: a new species (Urodela, Salamandridae) from Tak Province, northwestern Thailand.

A new species of the crocodile newt genus Tylototriton from Doi Soi Malai located at Mae Tuen Wildlife Sanctuary, Tak Province, northwestern Thailand is described based on molecular and morphological evidence, and named as Tylototritonsoimalai sp. nov. The new species is the seventh recorded species of the genus Tylototriton reported in Thailand. It differs morphologically from its congeners by a combination of the following morphological characteristics: head longer than wide; snout blunt or truncate; sagittal ridge on head narrow, short and distinct; dorsolateral bony ridges on head pronounced and rough; parotoids distinct; vertebral ridge prominent, wide and not segmented; 14-16 distinct, rounded and isolated rib nodules but posterior nodules connected; tips of fore- and hind limbs overlapping when adpressed along the body. The body background color is black, while the color markings are orange. Molecular analysis indicated that Tylototritonsoimalai sp. nov. is a distinct lineage and sister to T.uyenoi with a 4.1% genetic sequence divergence based on the mitochondrial NADH dehydrogenase subunit 2 gene. The new species is currently restricted to the hill evergreen forests of Doi Soi Malai. The implementation of a strategic plan is recommended to protect both the species and its habitat from anthropogenic activities.

Phylogeographic structure of Italian Formica pratensis (Retzius 1783) populations in the framework of the species Eurasian range

AbstractThe phylogeography and demographical history of Italian Formica pratensis populations were examined and compared with the Eurasian-wide dataset available for this species and the other red wood ant species Formica lugubris. Forty-eight workers belonging to eight populations from both Alps and Apennines were analysed sequencing a 1.5-kilobase mitochondrial DNA fragment, including the cytochrome b gene and part of the NADH dehydrogenase subunit 6 gene. A total of 127 sequences were screened, scoring 53 different haplotypes amongst all specimens, with five new haplotypes discovered in the Italian populations. All the Italian haplotypes clustered in a monophyletic clade, underlining a clear phylogeographical separation of this group from the other Eurasian groups and suggesting a glacial separate forest refugia and different post-glacial colonisation patterns. The haplotypes from the Alps and the Apennines showed a high genetic proximity, pointing out an ancient (Pleistocene) wide distribution of this species across all these areas and common ancestral lineages. No shared haplotypes were scored between Northern and Central Apennine populations, but the low inter-population genetic distance indicated similar post-glacial selective processes acting on these groups. The diversity we recorded may be influenced by the actual fragmentation of F. pratensis populations across its entire Eurasian range, and by the limited geographical origin and sample dimension of the dataset analysed. Future studies with a more extensive sampling in the Alps and Eastern Europe are needed to confirm our result.

Whole genome sequence analysis of population structure and insecticide resistance markers in Anopheles melas from the Bijagós Archipelago, Guinea-Bissau

BackgroundAnopheles melas is an understudied malaria vector with a potential role in malaria transmission on the Bijagós Archipelago of Guinea-Bissau. This study presents the first whole-genome sequencing and population genetic analysis for this species from the Bijagós. To our knowledge, this also represents the largest population genetic analysis using WGS data from non-pooled An. melas mosquitoes.MethodsWGS was conducted for 30 individual An. melas collected during the peak malaria transmission season in 2019 from six different islands on the Bijagós Archipelago. Bioinformatics tools were used to investigate the population structure and prevalence of insecticide resistance markers in this mosquito population.ResultsInsecticide resistance mutations associated with pyrethroid resistance in Anopheles gambiae s.s. from the Bijagós were absent in the An. melas population, and no signatures of selective sweeps were identified in insecticide resistance-associated genes. Analysis of structural variants identified a large duplication encompassing the cytochrome-P450 gene cyp9k1. Phylogenetic analysis using publicly available mitochondrial genomes indicated that An. melas from the Bijagós split into two phylogenetic groups because of differentiation on the mitochondrial genome attributed to the cytochrome C oxidase subunits COX I and COX II and the NADH dehydrogenase subunits 1, 4, 4L and 5.ConclusionsThis study identified an absence of insecticide-resistant SNPs common to An. gambiae in the An. melas population, but did identify structural variation over insecticide resistance-associated genes. Furthermore, this study presents novel insights into the population structure of this malaria vector using WGS analysis. Additional studies are required to further understand the role of this vector in malaria transmission.Graphical abstract

A new species of karst-dwelling bent-toed gecko of the Cyrtodactylusintermedius group (Squamata, Gekkonidae) from eastern Thailand and the phylogenetic placement of C.intermedius.

A new karst-dwelling bent-toed gecko of the Cyrtodactylusintermedius group is described from Khlong Hat District, Sa Kaeo Province, eastern Thailand, based on an integrative taxonomic analysis of genetic data and morphological characteristics. Phylogenetic analyses using the mitochondrial NADH dehydrogenase subunit 2 (ND2) gene revealed that topotypes of C.intermedius were sister to a clade containing C.kulenensis from Cambodia, an unnamed lineage from Sakaerat Biosphere Reserve in Nakhon Ratchasima Province, Thailand, and the Khlong Hat lineage described here as Cyrtodactyluskhlonghatensis sp. nov. Multivariate analyses of morphometric and meristic characters showed that C.khlonghatensis sp. nov. is morphologically distinct from all other species in the group by having the combination of SVL 76.5-82.8 mm in adult males and 88.5 mm in an adult female; eight supralabial and nine infralabial scales; 30-32 paravertebral tubercles; 20 or 21 longitudinal rows of dorsal tubercles; 43 or 44 ventral scales; seven or eight expanded subdigital lamellae on the 4th toe; 12 unmodified subdigital lamellae on the 4th toe; 19 or 20 total subdigital lamellae on the 4th toe; 31 or 32 total number of enlarged femoral scales; enlarged femoral and precloacal scales continuous; 6-8 pore-bearing precloacal scales in males; three or four rows of enlarged post-precloacal scales; 1-3 postcloacal tubercles; proximal femoral scales less than one-half the size of distal femoral scales; absence of interdigital pocketing between digits of forefeet and hindfeet; and posterior border of the nuchal loop rounded. Uncorrected pairwise genetic divergences (p-distances) between the new species and other species of the intermedius group ranged from 4.73-22.55%. The discovery of this new species exclusively in isolated karst formations from the Thai-Cambodia border suggests that there may be further undiscovered Cyrtodactylus in unexplored karst landscapes along the border of eastern Thailand and western Cambodia.

Decreased in Mitochondrial Complex I Subunit NDUFS2 Is Critical for Oocyte Quality During Postovulatory Aging in Pigs.

The levels of nicotinamide adenine dinucleotide (NADH) dehydrogenase [ubiquinone] iron-sulfur protein 2 (NDUFS2, a subunit of NADH dehydrogenase) decrease in aged tissues, and these reductions may be partly associated with age-related conditions such as Parkinson's disease. Aging leads to many mitochondrial defects, such as biogenesis disruption, dysfunction, defects in the mitochondrial membrane potential, and production of reactive oxygen species, that may be highly related to NDUFS2 expression. The relationship between NDUFS2 and postovulatory oocyte aging in pigs remains unknown. In this study, we investigated changes in NDUFS2 expression during postovulatory aging (POA). Furthermore, NDUFS2 was knocked down via dsRNA microinjection at the MII stage to evaluate the effects on mitochondrial-related processes during POA. The mRNA expression of NDUFS2 decreased significantly after 48-h aging compared with that in fresh oocytes. NDUFS2 knockdown (KD) significantly impaired the maintenance of oocyte morphology and blastocyst development of embryos after POA. The levels of PGC1α (mitochondrial biogenesis-related proteins) decreased significantly after NDUFS2 KD, while the level of GSNOR, a protein denitrosylase, was reduced by NDUFS2 KD after 48 h of aging. These data suggest that NDUFS2 is vital for maintaining the oocyte quality during POA in pigs.

Study of the population genetic structure of Opisthorchis-like eggs in northern Thailand using mitochondrial genes.

Opisthorchis-like eggs are a public health problem in northern and northeastern Thailand. However, the genetic epidemiology and structure of these parasites in northern Thailand are unknown. Thus, this study investigated their population genetic structure using cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) nucleotide sequences. A study was conducted in the hill tribe regions of Chiang Mai Province, northern Thailand. Internal transcribed spacer 2 polymerase chain reaction and restriction fragment length polymorphism were used to distinguish 205 positive feces samples for Opisthorchis-like eggs. The results showed that the prevalence of O. viverrini and Haplorchis taichui was 10.5% and 38.2%, respectively, and the co-infection rate was 37.2%. To determine the genetic structure of O. viverrini and H. taichui using cox1 and nad1 genes, genetic analysis was performed using 30 randomly chosen fecal samples for Opisthorchis-like eggs. Pairwise FST analysis indicated that O. viverrini and H. taichui displayed nonsignificant genetic differentiation within Chiang Mai Province and between interpopulations from different geographic areas. Moreover, within the intrapopulation in Chiang Mai Province,cox1 presented higher gene flow than nad1 in O. viverrini, while nad1 demonstrated higher gene flow than cox1 in H. taichui. The neutrality tests based on Fu's Fs indicated population expansion and selective sweep from bottleneck or hitchhiking in O. viverrini and H. taichui populations, supported by haplotype network patterns. Phylogenetic tree analysis based on cox1 and nad1 revealed the monophyly of O. viverrini and H. taichui and genetic relationships with other isolates collected from Thailand, Lao People's Democratic Republic (PDR), and Vietnam. This study investigated the molecular discrimination and genetic structure of Opisthorchis-like eggs in northern Thailand. The genetic information derived from this study could be associated with the background, molecular epidemiology, and disease severity of these parasites.

A new species of the newt genus Hypselotriton (Amphibia, Urodela, Salamandridae) from Jiangxi Province, southeastern China.

A new newt species, Hypselotritonhuanggangensis sp. nov., is described based on nine specimens collected from Huanggangshan Mountains, Yanshan County, Jiangxi, China. Morphologically, the new species is characterized by the combination of nine external characters: (1) obvious black patches with clear boundaries on the whole body; (2) ground color of the dorsal body tan; (3) ground color of venter bright orange; (4) skin rough; (5) vertebral ridge weak; (6) fingers and toes overlapping when forelimb and hindlimb adpressed towards each other along body; (7) postocular orange spot absent; (8) small white warty glands around the eye; (9) two discontinuous longitudinal lines formed by white warty glands from neck to lateral parts of tail. Molecularly, the new species forms an independent clade with strong support in the phylogenetic trees of the genus based on the mitochondrial locus of NADH dehydrogenase subunit 2 (ND2) gene fragments. The new species distinctly differs from H.fudingensis by differences in its body measurements, vertebral ridge, dorsal black patches, and ventral black patches. Furthermore, the new species and H.fudingensis are geographically isolated by a series of high mountain ranges, including the Wuyishan and Jiufengshan Mountains. The number of Hypselotriton species is now 11.

Integrating Genetic and Cytogenetic Data: A Diversity Study of Astyanax and Psalidodon (Characidae) Species from the Paraná River Basin.

Astyanax is one of the most specious fish groups in the Neotropical region, with many cryptic species, which represents a challenge for correct identification through traditional taxonomic methods. Psalidodon is a recently resurrected genus group of species previously belonging to Astyanax, specifically those with extensive chromosomal variation of the A. scabripinnis and fasciatus complexes. In the present study, the mitochondrial genes cytochrome c oxidase subunit 1 (COI), mitochondrial ATP synthase 6 and 8 (ATPase 6/8), and NADH dehydrogenase subunit 2 (ND2) were used in conjunction with chromosomal data to characterize molecularly and cytogenetically populations of Astyanax and Psalidodon from rivers and streams of the Ivaí River Basin (Paraná Basin). The results demonstrated the effectiveness of the integrative use of molecular and cytogenetic techniques, with the confirmation of at least three species for the sampled sites: A. lacustris, P. paranae, and P. fasciatus, which showed inter- and intrapopulation karyotype variations. In addition, extensive haplotypic variation can be observed for these species within the Ivaí River Basin and throughout the Paraná River Basin. The data demonstrate a hidden diversity among the species analyzed, enrich the ichthyofaunistic knowledge of small rivers and streams, and contribute to future conservation projects in these areas.

Gene expression analyses of the ovaries in black tiger shrimp (Penaeus monodon) for reproductive trait using reference genome

The black tiger shrimp (Penaeus monodon) is widely cultured in Vietnam and worldwide. Broodstock source for post-larval production still relies on the wild shrimps due to their higher reproductive quality in comparison with the domesticated broodstock. The aims of the current study were to analyse differential gene expression in the ovaries of black tiger shrimp between the stages of reproductive maturation using the reference genome-based approaches and to compare the results generated by these approaches. cDNAs of the ovarian samples were sequenced using the Illumina platform. Genome-guided assembly (GGA) was employed to generate 71,678 contigs with an N50 length of 1,587 bp. For gene expression analysis, the newly built-transcriptome-based approach identified a total number of 288 differentially expressed genes (DEGs) when the samples between the non-mature and mature stages were compared. The gene expression analysis using the reference mapping approach resulted in only 49 DEGs. The analyses indicated that many genes involved in the reproductive maturation were up-regulated, including vitellogenin, NADH dehydrogenase subunit 2, and anti-lipopolysaccharide factor-like. Different results of gene expression from both approaches are discussed.

Prevalence, molecular characterisation and phylogenetic analyses of hydatid cysts and cysticercus tenuicollis isolates and first report of E. canadensis (G6/G7) in wild boars in Bingol province, Türkiye

Wild boars can directly or indirectly transmit numerous zoonotic helminths to humans in rural communities as they serve as reservoir hosts. This study was conducted to determine the occurrence and molecular characterisation of cystic metacestode forms of helminth parasites in wild boar and to identify haplotypes. To this end, 23 wild boar carcasses shot by hunters during the 2023 hunting season were necropsied and all internal organs were examined. Cysticercus tenuicollis (n = 07) and hydatid cyst (n = 10) isolates were obtained from the examined boars. Species identification of Cysticercus and hydatid cyst isolates was performed by amplification of partial fragments of the cox1 gene. According to BLAST search, all sequences of C. tenuicollis isolates were identified as Taenia hydatigena. Out of the hydatid cyst isolates, seven were classified as Echinococcus granulosus sensu stricto (G1/G3) and one sample was identified as Echinococcus canadensis (G6/G7). All isolates of E. granulosus s.s. (G1/G3) were re-amplified with the NADH dehydrogenase subunit 5 (nad5) in order to distinguish between G1 and G3 genotypes. Based on the sequence analysis, it was found that five of the E. granulosus s.s. isolates were classified as G1, while two were classified as G3. Based on the results of this study, it can be concluded that the G1 genotype is the most prevalent genetic variant among wild boar populations in Bingol province, Türkiye. In this study, a total of five novel haplotypes were identified. A previously unidentified haplotype was revealed through the haplotype analysis of E. canadensis (G6/G7). All isolates in the haplotype network of T. hydatigena were shown to exhibit distinct and geographically specific haplotypes. According to the findings of the study, wild boars include a substantial amount of genetic variety in E. granulosus s.s. And T. hydatigena.

An Exploratory Case-Control Study for Mitochondrial DNA G10398A in Bipolar I Disorder Patients with a Family History of Affective Disorders.

The mitochondrial DNA (mtDNA) G10398A polymorphism has been associated with bipolar disorder (BD). It leads to an amino acid substitution within NADH dehydrogenase subunit, thereby altering the mitochondrial complex I function. This exploratory case-control study assesses the association of mtDNA G10398A with the risk of BD and its relationship to clinical variables in Indian patients. Cases met the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition diagnosis of BD-I in remission and had a family history of BD or recurrent unipolar disorder in biological relatives. The healthy controls (HC) had no known illness and were screened negative for Family Interview for Genetic Studies. Participants were assessed using Clinical Pro forma, NIMH-Life Chart Method and Alda lithium response scale. The mtDNA G10398A was assessed with real-time polymerase chain reaction using TaqMan assay. A total of 82 participants were recruited across cases and controls, with 42 patients (50% with maternal history) and 40 healthy individuals with similar demographic profiles. The mean age of onset was 25.16 (standard deviation [SD] 7.6) years, with illness for 11.59 years (SD: 7.18). Allele A was found in 50% of cases compared to 32.5% HC (odds ratio = 2.08; 95% confidence interval [CI]: 0.85-5.09). Findings remain non-significant for patients with maternal mood disorders (allele A: 38.9%; 21/42). Cases with allele G had significantly higher body mass index (BMI) (P = 0.008) than those with allele A. The study adds information on mtDNA 10398A amongst Indian patient samples and healthy individuals. No significant group difference was found with respect to mtDNA G10398A. The positive association of allele G with higher BMI has potential clinical relevance that can be further investigated in larger samples.

Population Structure of Aetobatus narinari (Myliobatiformes) Caught by the Artisanal Fishery in Northeast Brazil

In Brazil, the Whitespotted Eagle Ray Aetobatus narinari is considered data-deficient due to the scarcity of basic information on its biology, ecology, and vulnerability to capture. Despite this, the species is caught by artisanal fishing along most of the coast, especially in the northeast of Brazil. This study analyzed mitochondrial DNA data in specimens of A. narinari caught by artisanal fishing in the northeast coast of Brazil to understand their population structure. For this, 42 individuals were sequenced at three mitochondrial genes: cytochrome oxidase 1 (COI), cytochrome b (Cytb), and NADH dehydrogenase subunit 4 (ND4). Concatenated COI-Cytb-ND4 sequences yielded 14 haplotypes, with moderate haplotype diversity (h = 0.646), low nucleotide diversity (π = 0.00087), and low fixation index ΦST values, indicating no population structure. Our results suggest that there is only one population of A. narinari in the study area. Genetic studies can contribute to improving management plans in these areas, avoiding the overexploitation of this and other species.

The absence of canonical respiratory complex I subunits in male-type mitogenomes of three Donax species

Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.

Implication of homoplasy in hypervariable region (HVR) of mitochondrial DNA in a population of marbled flounder Pseudopleuronectes yokohamae: consideration for conducting population genetic analyses using the HVR

The hypervariable region (HVR) in the control region of the mitochondrial DNA has frequently been used for population genetics and phylogeographic studies because of its highly variable nature. Although the HVR is beneficial for evaluating recent evolutionary history, including population demography, recent studies have implied the incidence of homoplasy in this region. To assess the accuracy of relying solely on the HVR for population genetics studies, molecular evolutionary analysis of the HVR, NADH-dehydrogenase subunit 2 (ND2), and cytochrome b genes were performed using 120 individuals of marbled flounder Pseudopleuronectes yokohamae. The HVR exhibited the highest genetic variability among the three regions, with sites showing high site-specific substitution rates. Considering the reticulate haplotype network structure and evolutionary linkages between regions, homoplastic mutations were indicated in the HVR in addition to ND2, underestimating genetic diversity. We found that homoplasy was less likely to affect coalescent-based demographic inferences in the population; however, there is still a potential risk of misinterpretation of population demography when solely using the HVR owing to its hypervariable nature. Collectively, we suggest analyzing other regions in addition to the HVR in fish population genetic research to improve accuracy and eliminate biases caused by homoplasy.

The use of real-time polymerase chain reaction for detection of raw rat meat (Rattus norvegicus) with species-specific primer for halal authentication

Rat meat (RM) can be obtained freely from farmers and can be used as a potential adulterant in meat-based food products. The presence of RM in any food products is prohibited by the Muslim community and is considered non-halal meat. Therefore, an analytical method capable of analysing RM specifically is very urgent. In this study, a real -time polymerase chain reaction using a species-specific primer targeting NADH dehydrogenase subunit 6 (ND6) is applied to analyze RM. DNA extraction was carried out using FavorPrepTM Tissue Genomic DNA Extraction Mini Kit, and the extracted DNA was subjected to purity index using NANO-Quant SPARK TECAN. The annealing temperature (Ta) used for PCR analysis was optimized to get the best Ta capable of providing the optimum amplification reaction. Furthermore, some performance characteristics were evaluated for Real-Time PCR, including sensitivity, efficiency and repeatability. The results exhibited that the designed primer is specific to rat DNA extracted toward other DNAs from meats typically used in food products. For quantitative evaluation, the limit of detection found was 0.39 ng with an efficiency of amplification (E) of 94.4% with a coefficient of determination (R2 ) of 0.986 for the relationship between log concentrations of DNA and cycle threshold (Ct) values. The repeatability assay was acceptable with an RSD value ≤ 25%. The developed method was reliable, provided high sensitivity for the analysis of RM. Therefore, this method is suitable to be used as a standard method for halal authentication analysis.