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The inference of body fluids and tissues is critical in reconstructing crime scenes and inferring criminal behaviors. Nevertheless, present methods are incompatible with conventional DNA genotyping, and additional testing might result in excessive consumption of forensic scene materials. This study aims to investigate the feasibility of distinguishing common body fluids/tissues through the difference in mitochondrial DNA copy number (mtDNAcn). Four types of body fluids/tissues were analyzed in this study - hair, saliva, semen, and skeletal muscle. MtDNAcn was estimated by dividing the read counts of mitochondrial DNA to that of nuclear DNA (RRmt/nu). Results indicated that there were significant differences in RRmt/nu between different body fluids/tissues. Specifically, hair samples exhibited the highest RRmt/nu (log10RRmt/nu: 4.3 ± 0.28), while semen samples showed the lowest RRmt/nu (log10RRmt/nu: -0.1 ± 0.28). RRmt/nu values for DNA samples without extraction were notably higher (approximately 2.9 times) than those obtained after extraction. However, no significant difference in RRmt/nu was observed between various age and gender groups. Hierarchical clustering and Kmeans clustering analyses showed that body fluids/tissues of the same type clustered closely to each other and could be inferred with high accuracy. In conclusion, this study demonstrated that the simultaneous detection of nuclear and mitochondrial DNA made it possible to perform conventional DNA analyses and body fluid/tissue inference at the same time, thus killing two birds with one stone. Furthermore, mtDNAcn has the potential to serve as a novel and promising biomarker for the identification of body fluids/tissues. [ABSTRACT FROM AUTHOR]

Objective: Identify the genotype and clinical characteristics of mitochondrial epilepsy caused by nDNA mutations in Chinese children and explore the treatment and prognosis of the condition. Study design: This is a retrospective cohort study conducted at a single center, including patients diagnosed with an established nDNA mutation-associated primary mitochondrial disease between October 2012 and March 2023 who also met the practical clinical definition of epilepsy published by the ILAE in 2014. Results: Of the 58 patients identified, 74.1% had an onset before the age of 1 year and 63.8% had seizures as their initial symptom. Developmental and epileptic encephalopathy (DEE) (31%) are the most common phenotypes. The most frequently observed MRI abnormalities include abnormal signal asymmetry in the bilateral basal ganglia and/or brainstem (34.7%), as well as brain atrophy, myelin sheath dysplasia, and corpus callosum dysplasia (32.7%). Of the 40 patients followed, seizure treatment was effective in 18 of the cases, while it was ineffective in 22. The mitochondrial DNA depletion syndrome (MDS) was found to be more difficult to control seizures than other phenotypes (P < 0.05). Additionally, the MDS was associated with a significantly higher mortality rate compared to alternative phenotypes (P < 0.05). Conclusions: The onset of mitochondrial epilepsy due to nDNA mutations is early and seizures are the most common initial symptom. DEE is the most common phenotype. Characteristic MRI abnormalities in the brain may be helpful in the diagnosis of primary mitochondrial disease. People with MDS typically face challenges in seizure control and have a poor prognosis. [ABSTRACT FROM AUTHOR]

DNA damage is one of the most important effects induced by chemical agents. We report a comparative analysis of DNA fragmentation on three different cell lines using terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay, generally applied to detect apoptosis. Our approach combines cytogenetic techniques and investigation in detached cellular structures, recovered from the culture medium with the aim to compare the DNA fragmentation of three different cell line even beyond the cells adherent to substrate. Consequently, we detect any fragmentation points on single chromosomes, whole nuclei and other cellular structures. Cells were exposed to resveratrol (RSV) and doxorubicin (Doxo), in single and combined treatments. Control and treated astrocytes showed DNA damage in condensed nuclei and detached structures. Caco-2 cells showed fragmented DNA only after Doxo-treatment, while controls showed fragmented chromosomes, indicating DNA damage in replicating cells. MDA-MB-231 cells showed nuclear condensation and DNA fragmentation above all after RSV-treatment and related to detached structures. This model proved to perform a grading of genomic instability (GI). Astrocytes show a hybrid level of GI. Caco-2 cells showed fragmented metaphase chromosomes, proving that the DNA damage was transmitted to the daughter cells probably due to an absence of DNA repair mechanisms. Instead, MDA–MB-231 cells showed few or no fragmented metaphase, suggesting a probable activation of DNA repair mechanisms. By applying this alternative approach of TUNEL test, we obtained data that can more specifically characterize DNA fragmentation for a suitable application in various fields. [ABSTRACT FROM AUTHOR]

Mitochondria serve as the cellular powerhouse, and their distinct DNA makes them a prospective target for gene editing to treat genetic disorders. However, the impact of genome editing on mitochondrial DNA (mtDNA) stability remains a mystery. Our study reveals previously unknown risks of genome editing that both nuclear and mitochondrial editing cause discernible transfer of mitochondrial DNA segments into the nuclear genome in various cell types including human cell lines, primary T cells, and mouse embryos. Furthermore, drug-induced mitochondrial stresses and mtDNA breaks exacerbate this transfer of mtDNA into the nuclear genome. Notably, we observe that mitochondrial editors, including mitoTALEN and recently developed base editor DdCBE, can also enhance crosstalk between mtDNA and the nuclear genome. Moreover, we provide a practical solution by co-expressing TREX1 or TREX2 exonucleases during DdCBE editing. These findings imply genome instability of mitochondria during induced DNA breaks and explain the origins of mitochondrial-nuclear DNA segments. Emerging genome editing tools have been reported to possess threats to genome stability, while their impact on mitochondrial DNA (mtDNA) remains unknown. Here, authors report that genome editing of both nuclear and mitochondrial genome triggers transfer of mtDNA fragments into the nuclear genome. [ABSTRACT FROM AUTHOR]

As one of the most vital organelles within biological cells, mitochondria hold an irreplaceable status and play crucial roles in various diseases. Research and therapies targeting mitochondria have achieved significant progress in numerous conditions. Throughout an organism's lifespan, mitochondrial dynamics persist continuously, and due to their inherent characteristics and various external factors, mitochondria are highly susceptible to damage. This susceptibility is particularly evident during aging, where the decline in biological function is closely intertwined with mitochondrial dysfunction. Despite being an ancient and enigmatic organelle, much remains unknown about mitochondria. Here, we will explore the past and present knowledge of mitochondria, providing a comprehensive review of their intrinsic properties and interactions with nuclear DNA, as well as the challenges and impacts they face during the aging process. [ABSTRACT FROM AUTHOR]

GLABRA2 (GL2), a class IV homeodomain leucine-zipper (HD-Zip IV) transcription factor from Arabidopsis, is a developmental regulator of specialized cell types in the epidermis. GL2 contains a monopartite nuclear localization sequence (NLS) that is conserved in most HD-Zip IV members across the plants. We demonstrate that NLS mutations affect nuclear transport and result in a loss-of-function phenotypes. NLS fusions to enhanced yellow fluorescent protein (EYFP) show that it is sufficient for nuclear localization in roots and trichomes. Despite partial overlap of the NLS with the homeodomain, genetic dissection indicates that nuclear localization and DNA binding are separable functions. Affinity purification of GL2 from plants followed by MS-based proteomics identified importin α (IMPα) isoforms as potential GL2 interactors. NLS structural prediction and molecular docking studies with IMPα-3 revealed major interacting residues. Cytosolic yeast two-hybrid assays and co-immunoprecipitation experiments with recombinant proteins verified NLS-dependent interactions between GL2 and several IMPα isoforms. IMPα triple mutants (impα-1,2,3) exhibit abnormal trichome formation and defects in GL2 nuclear localization in trichomes, consistent with tissue-specific and redundant functions of IMPα isoforms. Taken together, our findings provide mechanistic evidence for IMPα-dependent nuclear localization of GL2 in Arabidopsis, a process that is critical for cell type differentiation of the epidermis. [ABSTRACT FROM AUTHOR]

The species of Ramaria are coralloid-fungi with intricately branched and vividly coloured basidiomata. There are many studies on the genus Ramaria in China, but molecular phylogenetic analysis is rarely employed. In this study, we performed a multigene phylogenetic analysis to identify Ramaria species in Shanxi Province of northern China. Phylogenetic analyses based on four loci, the internal transcribed spacer region of nuclear ribosomal DNA (ITS), the nuclear large subunit ribosomal DNA (nrLSU), ATPase subunit 6 (atp6), and mitochondrial small subunit ribosomal DNA (mtSSU), revealed 13 Ramaria species from our collections. Combined with morphological examinations, 12 of them were identified as new species, plus a new report to China. The thirteen species were described and illustrated in this paper. [ABSTRACT FROM AUTHOR]

Ovarian cancer is a prevalent gynecologic malignancy with the second-highest mortality rate among gynecologic malignancies. Platinum-based chemotherapy is the first-line treatment for ovarian cancer; however, a majority of patients with ovarian cancer experience relapse and develop platinum resistance following initial treatment. Despite extensive research on the mechanisms of platinum resistance at the nuclear level, the issue of platinum resistance in ovarian cancer remains largely unresolved. It is noteworthy that mitochondrial DNA (mtDNA) exhibits higher affinity for platinum compared to nuclear DNA (nDNA). Mutations in mtDNA can modulate tumor chemosensitivity through various mechanisms, including DNA damage responses, shifts in energy metabolism, maintenance of Reactive Oxygen Species (ROS) homeostasis, and alterations in mitochondrial dynamics. Concurrently, retrograde signals produced by mtDNA mutations and their subsequent cascades establish communication with the nucleus, leading to the reorganization of the nuclear transcriptome and governing the transcription of genes and signaling pathways associated with chemoresistance. Furthermore, mitochondrial translocation among cells emerges as a crucial factor influencing the effectiveness of chemotherapy in ovarian cancer. This review aims to explore the role and mechanism of mitochondria in platinum resistance, with a specific focus on mtDNA mutations and the resulting metabolic reprogramming, ROS regulation, changes in mitochondrial dynamics, mitochondria-nucleus communication, and mitochondrial transfer. Highlights: Directly targeting mitochondria is one of the main mechanisms by which platinum induces apoptosis in tumor cells. mtDNA mutations occur frequently in ovarian cancer and significantly contribute to platinum resistance. The metabolic heterogeneity induced by mtDNA mutations can directly drive platinum resistance in ovarian cancer cells. Targeting mitochondria could be a novel approach for platinum-resistant ovarian cancer. [ABSTRACT FROM AUTHOR]

The Andean uplift and the concomitant aridification drove the rapid diversification of several plant lineages that were able to colonize warmer and drier habitats at low elevations and wetter and colder habitats at high elevations. These transitions may be facilitated by shifts in plant strategies to cope with drought and cold, which in turn can trigger episodes of accelerated species diversification. Here, we used four nuclear DNA markers to infer phylogenetic relationships of 80 Adesmia species of annuals, perennial herbs, shrubs and small shrubs that occur in Chile and Argentina. We reconstructed ancestral states for area, climatic niche and growth form to explore how Andean uplift and aridification promoted Adesmia diversification. We also performed logistic and linear regression analyses between different components of growth form (life span, woodiness and plant height) and climate. Finally, we estimated speciation rates across the phylogeny. Our results suggest that the ancestor of Chilean Adesmia was a perennial herb that probably originated in the high Andes of northern and central Chile. The low elevations of Central Chile were colonized in the late Miocene, whereas the high latitudes of Patagonia and the hyperarid coastal Atacama Desert were colonized repeatedly since Pliocene by lineages with different growth forms. Multiple and bidirectional transitions between annual and perennial habits and between herbaceous and woody habits were detected. These shifts were not correlated with climate, suggesting that the different growth forms are alternative and successful strategies to survive unfavorable seasons of both desert and high Andes. Net diversification analysis indicated a constant rate of diversification, suggesting that the high species diversity of Adesmia that occur in Chile is due to a uniform speciation process rather than to accelerated episodes of speciation. [ABSTRACT FROM AUTHOR]

Background: The family Lauraceae is subdivided into six main lineages: Caryodaphnopsideae, Cassytheae, Cryptocaryeae, Hypodaphnideae, Laureae, and Neocinnamomeae. However, phylogenetic relationships among these lineages have been debatable due to incongruence between trees constructed using nuclear ribosomal DNA (nrDNA) sequences and chloroplast (cp) genomes. As with cp DNA, the mitochondrial (mt) DNA of most flowering plants is maternally inherited, so the phylogenetic relationships recovered with mt genomes are expected to be consistent with that from cp genomes, rather than nrDNA sequences. Results: The mitogenome of Machilus yunnanensis, with a length of 735,392 bp, has a very different genome size and gene linear order from previously published magnoliid mitogenomes. Phylogenomic reconstructions based on 41 mt genes from 92 Lauraceae mitogenomes resulted in highly supported relationships: sisterhood of the Laureae and a group containing Neocinnamomeae and Caryodaphnopsideae, with Cassytheae being the next sister group, followed by Cryptocaryeae. However, we found significant incongruence among the mitochondrial, chloroplast, and nuclear phylogenies, especially for the species within the Caryodaphnopsideae and Neocinnamomeae lineages. Time-calibrated phylogenetic analyses showed that the split between Caryodaphnopsideae and Neocinnamomeae dated to the later Eocene, around 38.5 Ma, Laureae originated in the Late Cretaceous, around 84.9 Ma, Cassytheae originated in the mid-Cretaceous around 102 Ma, and Cryptocaryeae originated in the Early Cretaceous around 116 Ma. From the Late Cretaceous to the Paleocene, net diversification rates significantly increased across extant clades of major lineages, and both speciation rates and net diversification rates continued steady growth towards the present. Conclusions: The topology obtained here for the first time shows that mt genes can be used to support relationships among lineages of Lauraceae. Our results highlight that both Caryodaphnopsideae and Neocinnamomeae lineages are younger than previously thought, likely first diversifying in the Eocene, and species in the other extant lineages of Lauraceae dates in a long-time span from the Early Cretaceous to the Eocene, and the climate of a period of about 90 million years was relatively warm, while the extant species of Lauraceae then continuously diversified with global cooling from the Eocene to the present day. [ABSTRACT FROM AUTHOR]

The acquisition of mitochondria was imperative for initiating eukaryogenesis and thus is a characteristic feature of eukaryotic cells. 1,2 The parasitic protist Trypanosoma brucei contains a singular mitochondrion with a unique mitochondrial genome, termed the kinetoplast DNA (kDNA). 3 Replication of the kDNA occurs during the G 1 phase of the cell cycle, prior to the start of nuclear DNA replication. 4 Although numerous proteins have been functionally characterized and identified as vital components of kDNA replication and division, the molecular mechanisms governing this highly precise process remain largely unknown. 5,6 One division-related and morphologically characteristic structure that remains most enigmatic is the "nabelschnur," an undefined, filament-resembling structure observed by electron microscopy between segregating daughter kDNA networks. 7,8,9 To date, only one protein, TbLAP1, an M17 family leucyl aminopeptidase metalloprotease, is known to localize to the nabelschnur. 9 While screening proteins from the T. brucei MitoTag project, 10 we identified a previously uncharacterized protein with an mNeonGreen signal localizing to the kDNA as well as forming a point of connection between dividing kDNAs. Here, we demonstrate that this kDNA-associated protein, named TbNAB70, indeed localizes to the nabelschnur and plays an essential role in the segregation of newly replicated kDNAs and subsequent cytokinesis in T. brucei. [Display omitted] • TbNAB70 localizes to both the kDNA and the nabelschnur in Trypanosoma brucei • TbNAB70 is identified to be vital for the segregation, but not replication, of kDNA • TbNAB70 depletion results in a near-complete arrest of cytokinesis • TbNAB70 evolutionary emergence occurred after the development of the kDNA network Cadena et al. identify TbNAB70 as localizing to the "nabelschnur," an enigmatic structure observed between dividing kDNA networks in Trypanosoma brucei. TbNAB70 is shown to be essential for the segregation of kDNA and basal bodies, while the loss of TbNAB70 results in the arrest of cytokinesis, highlighting its critical role in cellular division processes. [ABSTRACT FROM AUTHOR]

Mitochondrial function relies on the coordinated expression of mitochondrial and nuclear genes, exhibiting remarkable resilience despite high mitochondrial mutation rates. The nuclear compensation mechanism suggests deleterious mitochondrial alleles drive compensatory nuclear mutations to preserve mito-nuclear compatibility. However, prevalence and factors conditioning this phenomenon remain debated due to its conflicting evidence. Here, we investigate how mito-nuclear incompatibilities impact substitutions in a model for species radiation. Mating success depends on genetic compatibility (nuclear DNA) and spatial proximity. Populations evolve from partially compatible mito-nuclear states, simulating mitochondrial DNA (mtDNA) introgression. Mutations do not confer advantages nor disadvantages, but individual fecundity declines with increasing incompatibilities, selecting for mito-nuclear coordination. We find that selection for mito-nuclear compatibility affects each genome differently based on their initial state. In compatible gene pairs, selection reduces substitutions in both genomes, while in incompatible nuclear genes, it consistently promotes compensation, facilitated by more mismatches. Interestingly, high mitochondrial mutation rates can reduce nuclear compensation by increasing mtDNA rectification, while substitutions in initially compatible nuclear gene are boosted. Finally, the presence of incompatibilities accelerates species radiation, but equilibrium richness is not directly correlated to substitution rates, revealing the complex dynamics triggered by mitochondrial introgression and mito-nuclear coevolution. Our study provides a perspective on nuclear compensation and the role of mito-nuclear incompatibilities in speciation by exploring extreme scenarios and identifying trends that empirical data alone cannot reveal. We emphasize the challenges in detecting these dynamics and propose analyzing specific genomic signatures could shed light on this evolutionary process. [ABSTRACT FROM AUTHOR]

Finalization of eukaryotic nuclear DNA replication relies on DNA ligase 1 (LIG1) to seal DNA nicks generated during Okazaki Fragment Maturation (OFM). Using a mutational reporter in Saccharomyces cerevisiae, we previously showed that mutation of the high-fidelity magnesium binding site of LIG1Cdc9 strongly increases the rate of single-base insertions. Here we show that this rate is increased across the nuclear genome, that it is synergistically increased by concomitant loss of DNA mismatch repair (MMR), and that the additions occur in highly specific sequence contexts. These discoveries are all consistent with incorporation of an extra base into the nascent lagging DNA strand that can be corrected by MMR following mutagenic ligation by the Cdc9-EEAA variant. There is a strong preference for insertion of either dGTP or dTTP into 3–5 base pair mononucleotide sequences with stringent flanking nucleotide requirements. The results reveal unique LIG1Cdc9-dependent mutational motifs where high fidelity DNA ligation of a subset of OFs is critical for preventing mutagenesis across the genome. DNA ligase 1 finalizes nuclear DNA replication by accurately sealing nicks generated during Okazaki Fragment Maturation. Here, Williams et al employ a low fidelity DNA ligase 1 variant to study mutation rates and specificity across the yeast genome [ABSTRACT FROM AUTHOR]

Background: The mortality rate of COVID-19 patients with critical symptoms is reported to be 40.5%. Early identification of patients with poor progression in the critical cohort is essential to timely clinical intervention and reduction of mortality. Although older age, chronic diseases, have been recognized as risk factors for COVID-19 mortality, we still lack an accurate prediction method for every patient. This study aimed to delve into the cell-free DNA fragmentomics of critically ill patients, and develop new promising biomarkers for identifying the patients with high mortality risk. Methods: We utilized whole genome sequencing on the plasma cell-free DNA (cfDNA) from 33 COVID-19 patients with critical symptoms, whose outcomes were classified as survival (n = 16) and death (n = 17). Mitochondrial DNA (mtDNA) abundance and fragmentomic properties of cfDNA, including size profiles, ends motif and promoter coverages were interrogated and compared between survival and death groups. Results: Significantly decreased abundance (~ 76% reduction) and dramatically shorter fragment size of cell-free mtDNA were observed in deceased patients. Likewise, the deceased patients exhibited distinct end-motif patterns of cfDNA with an enhanced preference for "CC" started motifs, which are related to the activity of nuclease DNASE1L3. Several dysregulated genes involved in the COVID-19 progression-related pathways were further inferred from promoter coverages. These informative cfDNA features enabled a high PPV of 83.3% in predicting deceased patients in the critical cohort. Conclusion: The dysregulated biological processes observed in COVID-19 patients with fatal outcomes may contribute to abnormal release and modifications of plasma cfDNA. Our findings provided the feasibility of plasma cfDNA as a promising biomarker in the prognosis prediction in critically ill COVID-19 patients in clinical practice. [ABSTRACT FROM AUTHOR]

New Guinea is the largest tropical island in the world and hosts immense endemic biodiversity. However, our understanding of how the gradual emergence of the terrestrial ecosystems of the island over the last 40 Myr has generated this biological richness is hampered by poorly documented species diversity and distributions. Here, we address both these issues through an integrative taxonomy and biogeographical approach using Hylophorbus , a New Guinea-endemic genus of frogs with 12 recognized species. We delimited candidate species by integrating mitochondrial DNA, nuclear DNA, and bioacoustics, then investigated their evolutionary history. Our results suggest that the current taxonomy of the genus misses true species diversity by ≥3.5-fold. Nevertheless, most candidate species (27) remain unconfirmed because of missing data, whereas five were identified unambiguously as undescribed (we describe three of these formally). Time-calibrated phylogenetic analyses suggest that Hylophorbus diversification began ~9 Mya in the northern or eastern portion of New Guinea. It would appear that lineages dispersed to new terrestrial habitats in the west, notably uplifted by the central range orogeny, until eventually reaching the Bird's Head during the Mio-Pliocene (7–5 Mya). Conversely, a past barrier appears to have prevented north–south dispersal. These data suggest that new habitat availability has primarily driven the diversification of Hylophorbus. [ABSTRACT FROM AUTHOR]

Arctic regions of northeastern Asia represent areas of secondary contact of the glacial phylogenetic lineages of charrs belonging to the genus Salvelinus (Salmoniformes: Salmonidae). However, the post‐glacial dispersion of charr across Arctic regions is poorly understood, as knowledge of populations from Chukotka and its neighbouring areas remains limited. Specifically, there is no clear understanding of which charr species inhabit significant regions of Chukotka from the sea coasts to the Kolyma drainage. In this study, we explored the affiliation of lacustrine charrs from the Chukotka area with (1) the Arctic lineage of Taranetz' charr (Salvelinus taranetzi); (2) the Bering lineage of Northern Dolly Varden (Salvelinus malma malma) and (3) the Siberia and Atlantic lineages of Arctic charr (Salvelinus alpinus). We analysed sequence variation of the mitochondrial DNA control region (mtDNA CR; 960 base pairs) and genotyped seven microsatellite loci of nuclear DNA from charr collected at 13 sampling sites. We found different consequences of secondary contact: (1) complete fixation of introgressed mtDNA (mitochondrial capture) and (2) preservation of several mtDNA lineages with the absence of contemporary gene flow between resident populations. Combining the distribution patterns, phylogenetic network topology and knowledge of the glaciation history of the region, we propose two zones of secondary contact of the glacial lineages in Chukotka–Kolima‐Chukotka River system and Paleo‐Amguema River–from where charrs with introgressed genomes spread throughout this range. However, in some cases, the process of foreign mtDNA capture likely occurs in a more localised manner. [ABSTRACT FROM AUTHOR]

Sand cats, Felis margarita, range from northern Africa and the Arabian Peninsula to Central Asia. Their apparently discontinuous distribution is recognized as comprising four subspecies. Recent genetic research found little differentiation between subspecies except for the North African form. In this study, 90 skins and 88 skulls were analyzed from the four subspecies. A discriminant function analysis of the scores, ranging from 1 to 4, of four pelage characteristics revealed differentiation between putative subspecies, except between Turkmenian and Pakistani sand cats. Northern African and Arabian sand cats tend to be spotted and striped, while Turkmenian and Pakistani sand cats are less spotted and have a dorsal crest of fur. Nonmetric multidimensional scaling (NMDS) models generated from 21 skull measurements revealed an overlap in morphospace between all subspecies, except for larger Turkmenian sand cats; northern African sand cats were smallest. Therefore, both pelage characteristics and skull morphometrics support up to three subspecies. However, considering recent genetic research, it is likely that two subspecies should be recognized, F. m. margarita from northern Africa and F. m. thinobia from the Arabian Peninsula, and Southwest and Central Asia. Widening of the dataset and nuclear DNA evidence are required to increase our understanding of geographical variation in this little studied species. [ABSTRACT FROM AUTHOR]

Autosomal dominant polycystic kidney disease (ADPKD) is a predominant genetic disease, which is caused by mutations in PKD genes and is associated with DNA damage in cystic cells. The intrinsic stimulator of interferon genes (STING) pathway is crucial for recognizing damaged DNA in the cytosol, triggering the expression of inflammatory cytokines to activate defense mechanisms. However, the precise roles and mechanisms of STING in ADPKD remain elusive. In this study, we show that Pkd1 mutant mouse kidneys show upregulation of STING, which is stimulated by the DNAs of nuclear and mitochondrial origin. The activation of STING promotes cyst growth through increasing (1) the activation of NF-κB in Pkd1 mutant cells and (2) the recruitment of macrophages in the interstitial and peri-cystic regions in Pkd1 mutant mouse kidneys via NF-κB mediating the upregulation of TNF-α and MCP-1. Targeting STING with its specific inhibitor C-176 delays cyst growth in an early-stage aggressive Pkd1 conditional knockout mouse model and a milder long-lasting Pkd1 mutant mouse model. Targeting STING normalizes mitochondrial structure and function, decreases the formation of micronuclei, induces Pkd1 mutant renal epithelial cell death via p53 signaling, and decreases renal fibrosis in Pkd1 mutant mouse kidneys. These results support that STING is a novel therapeutic target for ADPKD treatment. [ABSTRACT FROM AUTHOR]

Simple Summary: Four families (Cydnidae, Parastrachiidae, Thaumastellidae, and Thyreocoridae) in the superfamily Pentatomoidea are morphologically defined by a similar body outline and the presence of a series of stout setae on the distal margin of the coxae. These structures, called coxal combs, are thought to protect the coxal–trochanteral articulation from damage caused by soil and sand particles and have not been observed in other true bugs (Hemiptera: Heteroptera). Therefore, they have been consistently considered a synapomorphy for these four families. However, their independent origin in these families has been suggested by nuclear ribosomal DNA sequence analysis (28S rDNA and 18S rDNA). This study investigated whether the analysis of mitochondrial 16S ribosomal DNA sequences would confirm these results. In addition, we examined whether any group of species possessing the coxal combs could be considered a well-supported independent monophylum. Coxal combs, found only in members of the 'cydnoid' complex (comprising four families: Cydnidae, Parastrachiidae, Thaumastellidae, and Thyreocoridae) within the superfamily Pentatomoidea, have long been regarded as a character confirming their close evolutionary relationship. However, many studies have demonstrated that these four families are phylogenetically distant. Others have been treated as subfamilies of the broadly defined Cydnidae, with the coxal combs as the only character linking them. This is the first study on the origin of coxal combs in species of all families and subfamilies that represent the broadly conceived Cydnidae (69 species in 39 genera). Moreover, this study presents the first 16S rDNA gene sequences providing a basis for such analyses. The analyses included DNA sequences of 62 species in 34 genera of Cydnidae sensu stricto, three species in two genera of Thyreocoridae, two species in two genera of Parastrachiidae, and two species in one genus of Thaumastellidae. The sequence analysis in the family Cydnidae covered 35 species representing 19 genera of the subfamily Cydninae, 16 species in eight genera of the subfamily Sehirinae, five species in two genera of Amnestinae, three species in three genera of Garsauriinae, two species in one genus of Cephalocteinae, and one species of Amaurocorinae. The results of our study demonstrate the independent origin of coxal combs in taxa of the 'cydnoid' complex within the superfamily Pentatomoidea. They confirm the polyphyly not only of the entire 'cydnoid' complex but also of the family Cydnidae itself. [ABSTRACT FROM AUTHOR]

Jambu plants (Acmella oleracea) exhibiting necrotic angular leaf spots were collected in Belém—Pará, Brazil. Suspected to be a disease caused by nematodes, the jambu leaves were processed and the presence of nematodes from Aphelenchoides genus was observed using a light microscope. These nematodes were reared on Fusarium sp. and subsequently morphologically and molecularly characterized to species level. Aphelenchoides sp. associated with jambu exhibited morphological and morphometric characteristics similar to those within the A. besseyi complex (A. besseyi sensu stricto, A. oryzae and A. pseudobesseyi). Still, these characteristics were insufficient to confirm the identity of this population. However, the Bayesian inference analysis, utilizing the expansion segment of the large subunit (D2-D3 LSU) of nuclear ribosomal DNA, yielded results with a high posterior probability, indicating that the Aphelenchoides sp. associated with jambu belongs to the A. pseudobesseyi species. Under controlled conditions, the reproduction of the nematode in the leaf tissues (RF > 1) was observed, resulting in disease symptoms. The highest reproductive rate of A. pseudobesseyi (RF = 2.6) was observed from inoculation with 100 nematodes per leaf (500 nematodes per plant). Based on Seinhorst analysis, the tolerance limit in jambu plants infected with A. pseudobesseyi was 250 nematodes. It is concluded that A. pseudobesseyi is the etiological agent of the jambu angular leaf spot. For future evaluation of jambu resistance on A. pseudobesseyi, an inoculate maximum of 100 nematodes per leaf is recommended. [ABSTRACT FROM AUTHOR]

The Doradidae fishes constitute one of the most diverse groups of Neotropical freshwater environments. Acanthodoradinae is the oldest lineage and the sister group to all other thorny catfishes, and it includes only the genus Acanthodoras. The diversity of Acanthodoras remains underestimated, and the use of complementary approaches, including genetic studies, is an important step to better characterize this diversity and the relationships among the species within the genus. Therefore, we conducted a comprehensive analysis using conventional cytogenetic techniques and physical mapping of three multigene families (18S and 5S ribosomal DNA [rDNA], U2 small nuclear DNA [snDNA]) and four microsatellite motifs, namely (AC)n, (AT)n, (GA)n, and (GATA)n, in two sympatric species from the Negro River: Acanthodoras cataphractus and Acanthodoras cf. polygrammus. We found significant differences in constitutive heterochromatin (CH) content, distribution of the microsatellite (AT)n, and the number of 5S rDNA and U2 snDNA sites. These differences may result from chromosome rearrangements and repetitive DNA dispersal mechanisms. Furthermore, the characterization of the diploid number (2n) of these Acanthodoras species enables us to propose 2n = 58 chromosomes as the plesiomorphic 2n state in Doradidae based on ancestral state reconstruction. Acanthodoradinae is the oldest lineage of the thorny catfishes, and knowledge about its cytogenetic patterns is crucial for disentangling the karyotype evolution of the whole group. Thus, this study contributes to the understanding of the mechanisms behind chromosome diversification of Doradidae and highlights the importance of Acanthodoradinae in the evolutionary history of thorny catfishes. [ABSTRACT FROM AUTHOR]

During the second third of last century, the Orinoco Crocodile (Crocodylus intermedius) underwent a hunting process driven by the demand from the North American, European, and Japanese leather industry, resulting in a sharp decline of its populations. Currently, only two known remaining populations of this Critically Endangered species persist in the Colombian Orinoquía: in the Guayabero-Duda-Lozada and the Cravo Norte-Ele-Lipa River Systems. The latter has been the only population subject of study, including recent surveys and local conservation initiatives such as egg and hatchling ranching. Despite suggestions for population recovery based on the observed increase in clutches in the area, information regarding its genetic status has been pending assessment. This research aims to provide a genetic characterization of this remaining population and to evaluate the diversity recovered during a period of the egg ranching initiative. For this purpose, we utilized variable molecular markers, specifically 17 microsatellite loci, nuclear DNA. Despite revealing intermediate levels of genetic diversity, we identified an effective population size of 11.5–17, well below the minimum values proposed for short-term subsistence. While no evidence of inbreeding was found, it is acknowledged as a potential risk based on the population's history. Additionally, we detected a historical bottleneck possibly influenced by arid periods affecting the region since the Pleistocene. While the evaluated population presents a unique opportunity for C. intermedius conservation, it also exposes a high risk of entering the extinction vortex. The primary action to be taken is to support the egg and hatchling ranching program, which successfully recovered most of the genetic diversity present in the population. [ABSTRACT FROM AUTHOR]

The Salix genus of the Salicaceae family has advantages such as rapid initial growth, a high germination rate, and asexual reproduction; therefore, it is used as a short-rotation energy crop for biomass production. The National Institute of Forest Science created new interspecific hybrid cultivars with superior biomass production by artificially interbreeding Salix caprea L. and Salix gracilistyla Miq. Identifying these hybrids during the seedling stage is challenging because their separate reproductive and vegetative growth stages necessitate prolonged observation of their morphological characteristics. Consequently, a reliable identification method is required to overcome these limitations. This study aimed to develop nuclear DNA markers to distinguish between S. caprea, S. gracilistyla, and their interspecific hybrids. An evaluation of 35 nuclear simple-sequence repeat (nSSR) markers in the Salix genus revealed two markers that distinguish these parent species and their hybrids. A sequence analysis confirmed the presence of insertion-deletion (InDel) regions within the nSSR markers that differed between S. caprea and S. gracilistyla. To effectively identify hybrids, a primer set comprising the InDel region, which exhibited only interspecies differences and no intraspecies differences, was developed. The results of this study will facilitate the genetic resource management of interspecific hybrids between S. caprea and S. gracilistyla, thus allowing for early identification and improved management of hybrids. [ABSTRACT FROM AUTHOR]

Phoebe and Machilus trees, whose wood is known as Nanmu in China, face endangerment owing to long-term manmade destruction and climate change. Therefore, effective and accurate forensic tools to identify Nanmu species are required. This study developed a method for DNA identification of woods from six commonly traded Phoebe and Machilus species. DNA was efficiently extracted from oil cell-rich wood tissues, DNA barcodes were screened, species were compared, and a Nanmu DNA database was constructed. Comparison and analysis involved 26 sets of plastid genomes of Phoebe and Machilus. The five highest variable regions (Pi>0.009; psbA-trnH, psbJ, psbJ-petA, rpl32-trnL, and ycf1) were identified, and three nuclear regions (ITS, LEAFY, and RPB2) were compared. Among single DNA fragments, the nuclear DNA region LEAFY proved optimal for identifying Nanmu species, while psbA-trnH+psbJ+ycf1 was the optimal plastid combination locus. Compared with distance-based (TaxonDNA) and machine-learning analyses, the tree-based method had a lower success rate for species identification. Four labelled Nanmu samples were selected to validate the method and clustered with P. zhennan and P. sheareri data based on the LEAFY region and plastid combination locus. These findings will contribute to the conservation, classification, architecture maintenance, and trade monitoring of Nanmu natural resources. [ABSTRACT FROM AUTHOR]

The nucleus is a key cell mechanosensor of the local microenvironment. Nondestructive nuclear mechanosensation responses in confinement involve the build-up of the nuclear lamina, nuclear pore complex stretching-dependent exchange of nuclear–cytoplasmic constituents, and nuclear pressurization. Destructive nuclear mechanoresponses include the nuclear depletion of DNA repair factors and nuclear influx of TREX1 exonuclease, which promote DNA damage, as well as the cytoplasmic access of double-strand (ds)DNA, which can trigger a cyclic GMP-AMP synthase pathway/stimulator of interferon genes (cGAS/STING) response. Ion channels are among the first molecules to sense and respond to different physical stimuli, including confinement, by regulating intracellular ionic concentrations and water fluxes, thereby altering cell motility. The crosstalk between nuclear mechanotransduction and ion channel-mediated signaling enables efficient cell migration through confining spaces. Cell surface and intracellular mechanosensors enable cells to perceive different geometric, topographical, and physical cues. Mechanosensitive ion channels (MICs) localized at the cell surface and on the nuclear envelope (NE) are among the first to sense and transduce these signals. Beyond compartmentalizing the genome of the cell and its transcription, the nucleus also serves as a mechanical gauge of different physical and topographical features of the tissue microenvironment. In this review, we delve into the intricate mechanisms by which the nucleus and different ion channels regulate cell migration in confinement. We review evidence suggesting an interplay between macromolecular nuclear–cytoplasmic transport (NCT) and ionic transport across the cell membrane during confined migration. We also discuss the roles of the nucleus and ion channel-mediated mechanosensation, whether acting independently or in tandem, in orchestrating migratory mechanoresponses. Understanding nuclear and ion channel sensing, and their crosstalk, is critical to advancing our knowledge of cell migration in health and disease. [ABSTRACT FROM AUTHOR]

Pine wilt disease (PWD), which poses a significant risk to pine plantations across the globe, is caused by the pathogenic agent Bursaphelenchus xylophilus, also referred to as the pine wood nematode (PWN). A droplet digital PCR (ddPCR) assay was developed for the quick identification of the PWN in order to improve detection sensitivity. The research findings indicate that the ddPCR assay demonstrated significantly higher analysis sensitivity and detection sensitivity in comparison to traditional quantitative PCR (qPCR). However, it had a more limited dynamic range. High specificity was shown by both the ddPCR and qPCR techniques in the diagnosis of the PWN. Assessments of reproducibility revealed that ddPCR had lower coefficients of variation at every template concentration. Inhibition tests showed that ddPCR was less susceptible to inhibitors. There was a strong linear association between standard template measurements obtained using ddPCR and qPCR (Pearson correlation = 0.9317; p < 0.001). Likewise, there was strong agreement (Pearson correlation = 0.9348; p < 0.001) between ddPCR and qPCR measurements in the evaluation of pine wood samples. Additionally, wood samples from symptomatic (100% versus 86.67%) and asymptomatic (31.43% versus 2.9%) pine trees were diagnosed with greater detection rates using ddPCR. This study's conclusions highlight the advantages of the ddPCR assay over qPCR for the quantitative detection of the PWN. This method has a lot of potential for ecological research on PWD and use in quarantines. [ABSTRACT FROM AUTHOR]

True morels (Morchella spp.) are highly valuable and medicinal mushrooms. Saprophytic morels have been cultivated, especially in China and some Western countries, over the last few decades. Türkiye has a rich potential in terms of wild morel diversity, with nearly 40 Morchella species in its genetic pool, though only 22 of these have been identified molecularly. It has high economic value worldwide, and Türkiye exports morels worth approximately 2 million $ annually. There is also significant interest in morel mushroom cultivation in Türkiye. In this study, 40 Morchella strains were collected and isolated from different regions of Türkiye and analyzed based on the Internal Transcribed Spacer (ITS) of the nuclear ribosomal DNA (rDNA) region. A phylogenetic dendrogram was drawn. The isolates of M. importuna, M. exima, M. exuberans, M. dunali, M. tridentina, M. crassipes, and M. esculenta were identified based on the ITS rDNA region. However, the identification of isolates 849-Kg027 and 966-Kg142 could not be determined clearly, and the isolates of M. vulgarius and M. spongiola were not distinct based on the ITS analysis. The macro-morphological features of the mycelia were investigated. Mycelia colors ranged from off-white to pale gray in the juvenile stage, orange to pale brown during early pigmentation, and pale brown to dark brown in the senescence stage. M. crassipes, M. exuberans, and 966-Kg142 formed lighter-colored mycelia, whereas M. dunali and M. vulgarius exhibited the darkest mycelial pigments. Sclerotia formation was compact, pale yellow to yellow, and abundant. In conclusion, molecular identification of Turkish morel cultures was performed, and cultural characteristics along with morphological differences were examined. The cultures have been deposited for further study in the Mushroom Gene Bank at the Atatürk Central Horticultural Research Institute. [ABSTRACT FROM AUTHOR]

The genus Didymocarpus Wall. is a core group of the subfamily Didymocarpoideae in Gesneriaceae with a complex taxonomic history. It has long been controversial to delimit Didymocarpus and its allies. We conducted phylogenetic reconstructions with high‐density sampling of Didymocarpus and related genera by using four nuclear ribosomal DNAs (external transcribed spacer [ETS], internal transcribed spacer [ITS], 18S, 26S) and five chloroplast DNAs (atpB‐rbcL, rpl16, rps16, trnH‐psbA, and trnL‐F). The results indicated that neither Didymocarpus nor Allocheilos are monophyletic. Based on molecular phylogenetic and morphological analyses, we delimitated the range of the Didymocarpus sensu stricto (s. str.) with two‐section division, and established a new genus Palmatiboea for species originally placed in Didymocarpus. This genus is remarkably distinguished from Didymocarpus s. str. not only in molecular phylogeny and morphology but also in its specific geographic distribution, in that it is found only in Southeast China. In addition, we proposed a new monotypic genus Hequnia for Allocheilos guangxiensis that is completely isolated in phylogeny, consistent with a range of remarkably distinctive morphological characteristics. Our results clarify the systematics of Didymocarpus and the delimitation between it and related genera with establishment of two new genera. [ABSTRACT FROM AUTHOR]

Volvox sect. Volvox is a group of green algae with unique morphological features (thick cytoplasmic bridges between somatic cells and spiny zygote walls) and a worldwide distribution. Despite research interest in the diversity of organisms in ancient lakes, Volvox sect. Volvox from ancient lakes worldwide has not been identified to the species level. Here, we established clonal cultures of two species of this group originating from Lake Biwa, an ancient lake in Japan, and performed identification based on morphological and molecular data. One was identified as Volvox kirkiorum based on the nuclear ribosomal DNA internal spacer region (ITS) sequence, bisexual (monoicous or monoecious) spheroids, and zygote morphology. The other showed genetic separation from related species based on the secondary structure of the ITS and results of phylogenetic analysis of a combined data set from the nuclear actin gene, ITS, and two plastid genes (large subunit of RuBisCO and photosystem II CP43 apoprotein gene); it represented a new phylogenetic lineage within Volvox sect. Volvox, suggesting possible endemism in Lake Biwa. This species produced bisexual spheroids with different zygote morphology and zygote number from other species with bisexual spheroids in Volvox sect. Volvox. Therefore, Volvox biwakoensis Nozaki et H. Yamaguchi sp. nov. is described herein. This is the first endemic species of the genus Volvox described from an ancient lake. [ABSTRACT FROM AUTHOR]

In recent years, breeding initiatives have been made to reduce the fecundity of invasive plants leading to sterile cultivars. The wildtype form of heavenly bamboo (Nandina domestica Thunb. (Berberidaceae) and seven cultivars were evaluated for landscape performance, fruit production and seed viability at three sites in Florida located in southwest, northcentral, and north Florida. For heavenly bamboo cultivars in north Florida, 'Emerald Sea', 'Greray' (Sunray®), 'Lemon-Lime', 'Murasaki' (Flirt™), 'SEIKA' (Obsession™), and 'Twilight' performed well throughout much of the study with average visual quality ratings between 3.54 and 4.60 (scale of 1 to 5). In northcentral Florida heavenly bamboo cultivars are 'Emerald Sea', 'Greray', 'Lemon-Lime', 'Murasaki', 'SEIKA', and 'Twilight' performed well throughout much of the study with average quality ratings between 4.49 and 4.94. In southwest Florida, 'Emerald Sea', 'Greray', 'Lemon-Lime', 'Murasaki', and 'SEIKA' performed well with average quality ratings between 3.40 and 4.83. At all three sites, 'Emerald Sea' and the wildtype were similar in size, having the greatest growth indices compared to medium-sized cultivars ('Greray', 'Lemon-Lime', 'Twilight' and 'SEIKA') and dwarf-sized cultivars ('Chime' and 'Murasaki'). For three consecutive fall-winter seasons of the study, 'Chime', 'Greray', and 'Lemon-Lime' heavenly bamboo did not fruit at any of the study sites. Among the three sites, 'Murasaki' had 97.7% to 99.9% fruit reduction, 'SEIKA' had 97.7% to 100% fruit reduction, and 'Twilight' had 95.9% to 100% fruit reduction compared to the wildtype at respective sites. Seeds collected from low fruiting cultivars ('Murasaki', 'SEIKA', and 'Twilight') had 33.3% to 66.7% viability, as determined by tetrazolium tests. In comparison, 'Emerald Sea' produced as much, if not more, fruit as the wildtype, especially in northern Florida, with seed viability ranging from 6.7% to 29.0% among sites. Nuclear DNA content of cultivars were comparable to the wildtype, suggesting they are diploids. These findings identified four low to no fruiting heavenly bamboo cultivars recommended for landscape use ('Lemon-Lime', 'SEIKA', 'Murasaki', and 'Greray'). [ABSTRACT FROM AUTHOR]

ABSTRACT Although the frequency of ancient hybridization across the Tree of Life is greater than previously thought, little work has been devoted to uncovering the extent, timeline, and geographic and ecological context of ancient hybridization. Using an expansive new dataset of nuclear and chloroplast DNA sequences, we conducted a multifaceted phylogenomic investigation to identify ancient reticulation in the early evolution of oaks (Quercus). We document extensive nuclear gene tree and cytonuclear discordance among major lineages of Quercus and relatives in Quercoideae. Our analyses recovered clear signatures of gene flow against a backdrop of rampant incomplete lineage sorting, with gene flow most prevalent among major lineages of Quercus and relatives in Quercoideae during their initial radiation, dated to the Early‐Middle Eocene. Ancestral reconstructions including fossils suggest ancestors of Castanea + Castanopsis, Lithocarpus, and the Old World oak clade probably co‐occurred in North America and Eurasia, while the ancestors of Chrysolepis, Notholithocarpus, and the New World oak clade co‐occurred in North America, offering ample opportunity for hybridization in each region. Our study shows that hybridization—perhaps in the form of ancient syngameons like those seen today—has been a common and important process throughout the evolutionary history of oaks and their relatives. Concomitantly, this study provides a methodological framework for detecting ancient hybridization in other groups. [ABSTRACT FROM AUTHOR]

Introduction: Modern understanding of the concept of genetic diversity must include the study of both nuclear and organellar DNA, which differ greatly in terms of their structure, organization, gene content and distribution. This study comprises an analysis of the genetic diversity of the smut fungus Sporisorium reilianum f. sp. zeae from a mitochondrial perspective. Methods: Whole-genome sequencing data was generated from biological samples of S. reilianum collected from different geographical regions. Multiple sequence alignment and gene synteny analysis were performed to further characterize genetic diversity in the context of mitogenomic polymorphisms. Results: Mitochondria of strains collected in China contained unique sequences. The largest unique sequence stretch encompassed a portion of cox1, a mitochondrial gene encoding one of the subunits that make up complex IV of the mitochondrial electron transport chain. This unique sequence had high percent identity to the mitogenome of the related species Sporisorium scitamineum and Ustilago bromivora. Discussion: The results of this study hint at potential horizontal gene transfer or mitochondrial genome recombination events during the evolutionary history of basidiomycetes. Additionally, the distinct polymorphic region detected in the Chinese mitogenome provides the ideal foundation to develop a diagnostic method to discern between mitotypes and enhance knowledge on the genetic diversity of this organism. [ABSTRACT FROM AUTHOR]

Background: The integration of nuclear mitochondrial DNA (mtDNA) into the mammalian genomes is an ongoing, yet rare evolutionary process that produces nuclear sequences of mitochondrial origin (NUMT). In this study, we identified and analysed NUMT inserted into the pig (Sus scrofa) genome and in the genomes of a few other Suinae species. First, we constructed a comparative distribution map of NUMT in the Sscrofa11.1 reference genome and in 22 other assembled S. scrofa genomes (from Asian and European pig breeds and populations), as well as the assembled genomes of the Visayan warty pig (Sus cebifrons) and warthog (Phacochoerus africanus). We then analysed a total of 485 whole genome sequencing datasets, from different breeds, populations, or Sus species, to discover polymorphic NUMT (inserted/deleted in the pig genome). The insertion age was inferred based on the presence or absence of orthologous NUMT in the genomes of different species, taking into account their evolutionary divergence. Additionally, the age of the NUMT was calculated based on sequence degradation compared to the authentic mtDNA sequence. We also validated a selected set of representative NUMT via PCR amplification. Results: We have constructed an atlas of 418 NUMT regions, 70 of which were not present in any assembled genomes. We identified ancient NUMT regions (older than 55 million years ago, Mya) and NUMT that appeared at different time points along the Suinae evolutionary lineage. We identified very recent polymorphic NUMT (private to S. scrofa, with < 1 Mya), and more ancient polymorphic NUMT (3.5–10 Mya) present in various Sus species. These latest polymorphic NUMT regions, which segregate in European and Asian pig breeds and populations, are likely the results of interspecies admixture within the Sus genus. Conclusions: This study provided a first comprehensive analysis of NUMT present in the Sus scrofa genome, comparing them to NUMT found in other species within the order Cetartiodactyla. The NUMT-based evolutionary window that we reconstructed from NUMT integration ages could be useful to better understand the micro-evolutionary events that shaped the modern pig genome and enriched the genetic diversity of this species. [ABSTRACT FROM AUTHOR]

Background: Cascade testing can offer improved surveillance and timely introduction of clinical management for the at-risk biological relatives. Data on cascade testing and costs in mitochondrial diseases are lacking. To address this gap, we performed a cross-sectional retrospective study to provide a framework for cascade testing in mitochondrial diseases, to estimate the eligibility versus real-time uptake of cascade testing and to evaluate the cost of the genetic diagnosis of index cases and the cost of predictive cascade testing. Methods: Data was collected through retrospective chart review. The variant inheritance pattern guided the identification of eligible first-degree relatives: (i) Males with mitochondrial DNA (mtDNA) single nucleotide variants (SNVs) – siblings and mothers. (ii) Females with mtDNA SNVs – siblings, mothers and offspring. (iii) Autosomal Dominant (AD) nuclear DNA (nDNA) variants – siblings, offspring and both parents. (iv) Autosomal Recessive (AR) nDNA variants – siblings. Results: We recruited 99 participants from the Adult Mitochondrial Disease Clinic in Sydney. The uptake of cascade testing was 55.2% in the mtDNA group, 55.8% in the AD nDNA group and 0% in AR nDNA group. Of the relatives in mtDNA group who underwent cascade testing, 65.4% were symptomatic, 20.5% were oligosymptomatic and 14.1% were asymptomatic. The mean cost of cascade testing for eligible first-degree relatives (mtDNA group: $694.7; AD nDNA group: $899.1) was lower than the corresponding index case (mtDNA group: $4578.4; AD nDNA group: $5715.1) (p < 0.001). Conclusion: The demand for cascade testing in mitochondrial diseases varies according to the genotype and inheritance pattern. The real-time uptake of cascade testing can be influenced by multiple factors. Early diagnosis of at-risk biological relatives of index cases through cascade testing, confirms the diagnosis in those who are symptomatic and facilitates implementation of surveillance strategies and clinical care at an early stage of the disease. [ABSTRACT FROM AUTHOR]

The integration of nanoparticles into plant cryopreservation protocols holds great promise for improving the survival rates and recovery potential of explants. This study aimed to verify the effect of nanoparticles on the ex-vitro performance of cryopreservation-derived plants. Lamprocapnos spectabilis (L.) Fukuhara (bleeding heart) 'Gold Heart' and 'Valentine' cultivars were used as the plant material. The encapsulation-vitrification cryopreservation protocol of shoot tips included the preculture, encapsulation, dehydration, storage in liquid nitrogen, rewarming, and recovery steps. Gold (AuNPs), silver (AgNPs), or zinc oxide (ZnONPs) nanoparticles were added at varying concentrations, either into the preculture medium or the protective bead matrix during encapsulation. After the in vitro recovery, the plants were transferred to the glasshouse and subjected to detailed biometrical, biochemical and cytogenetic analyses. Nanoparticles had no evident effect on the acclimatization efficiency (80–100% survival) and leaf number in L. spectabilis 'Gold Heart'. Nonetheless, shoots developed from alginate beads supplemented with 5 ppm AuNPs were twice as long as the control, while the leaves of plants grown on the preculture medium with ZnONPs contained significantly more chlorophyll and had higher Leaf Soil-Plant Analysis Development (SPAD) values. Moreover, several NPs treatments stimulated the development of leaves, including their surface area, length, and perimeter. Higher ZnONPs levels enhanced also the replication process, resulting in higher nuclear DNA content. As for L. spectabilis 'Valentine', alginate augmentation with 5 ppm AgNPs or 5 ppm ZnONPs stimulated the elongation of shoots. There was also a tendency suggesting a positive influence of 5 ppm AgNPs in the alginate bead matrix on foliar growth. The effect of nanoparticles on the content of flavonoids, anthocyanins, and stress markers in the plants varied depending on the treatment and cultivar, but also on the organ studied (leaf or stem). Overall, L. spectabilis 'Gold Heart' was more stress-tolerant and genetically stable than 'Valentine' judging by the activity of Photosystem II (PSII) and flow cytometric analyses, respectively. The complex effects of nanoparticles on survival, biometric parameters, physiological responses, and cytogenetic events underscore the intricate interplay between nanoparticles and plant systems. Nonetheless, our research confirmed the positive effect of nanoparticles on the ex-vitro growth and development of L. spectabilis plants after cryostorage. [ABSTRACT FROM AUTHOR]

Due to its nutritional value and health benefits, the date palm (Phoenix dactylifera L.) is an essential dietary food crop throughout Middle Eastern and African countries. Consumers are concerned about the possible microbial contamination of dates, especially since most dates arriving in local markets are unprocessed. The absence of processing increases the possibility of microbial contamination, which raises the probability of microbial contamination. This study aims to analyze and evaluate the variability of fungal and bacterial microbiota identified in the most popular date palm fruits in Saudi Arabia. The study assessed ten date variety fruits from the most popular date palm varieties for consumption in Saudi Arabia and analyzed the microbial count. Morphological and molecular characterization and comparison of nuclear ribosomal DNA internal transcribed spacer (ITS) sequences identified 78 fungi, including 36 distinct species across 15 fungal genera. Alternaria, Fusarium, Curvilaria, Aspergillus, and Penicillium were the most frequent genera among the ten fruit cultivars studied, according to ITS-rDNA sequence analysis. Furthermore, 36 bacterial isolates were obtained from ten date varieties studied, each with a unique colony morphology. These isolates were identified based on sequence alignment and comparison of their 16S rDNA internal spacer regions to those available in public databases. The results showed that the bacterial isolates included 15 species from five bacterial genera. The results suggested that Bacillus, Stenotrophomonas, and Brucella were the prevailing genera among the ten tested fruit varieties. Some bacterial genera, such as Brucella, Achromobacter, and Stenotrophomonas, are well-known potential human pathogens. Chaetomium globosum was also recognized as air pollution causing adverse health effects such as allergies and as the causal agent of human fungal infections among the tested date varieties; the Rashodiah type exhibited the highest fungal contamination, whereas the Sagai variety displayed the lowest fungal contamination. Conversely, the Sukkari, Barhi, and Mejdool varieties were the most contaminated with bacteria among the ten tested varieties, while the Khalas variety showed the least bacterial contamination. To the best of the authors' knowledge, this study provides the initial comprehensive account of the molecular and morphological identification of all fungal and bacterial genera associated with date palm (P. dactylifera) fruits. [ABSTRACT FROM AUTHOR]

In this work, we describe a new species of the genus Oreonectes, Oreonectes yuedongensis sp. nov., collected from the Lianhua Mountains in eastern Guangdong, China. Phylogenetic trees constructed based on the mitochondrial cytochrome b (Cyt b) gene showed that this new species represents an independent evolutionary lineage, with uncorrected genetic distances (Kimura 2‐parameter model) from congeners ranging from 5.1% to 8.3%. In addition, nuclear DNA analysis indicated O. yuedongensis as an independent lineage separate from its closely related species. Morphologically, the new species can be distinguished from other six species in the genus Oreonectes by a combination of serial characters. The description of this new species suggests that it is necessary to reassess the biodiversity of Oreonectes platycephalus as a complex, especially in the middle reaches of the Pearl River near the border between Guangdong and Guangxi. Morphological and genetic evidence supports O. yenlingi as a synonym of O. platycephalus. [ABSTRACT FROM AUTHOR]

High-throughput sequencing technologies have increasingly led to discovery of disease-causing genetic variants, primarily in postnatal multi-cell DNA samples. However, applying these technologies to preimplantation genetic testing (PGT) in nuclear or mitochondrial DNA from single or few-cells biopsied from in vitro fertilised (IVF) embryos is challenging. PGT aims to select IVF embryos without genetic abnormalities. Although genotyping-by-sequencing (GBS)-based haplotyping methods enabled PGT for monogenic disorders (PGT-M), structural rearrangements (PGT-SR), and aneuploidies (PGT-A), they are labour intensive, only partially cover the genome and are troublesome for difficult loci and consanguineous couples. Here, we devise a simple, scalable and universal whole genome sequencing haplarithmisis-based approach enabling all forms of PGT in a single assay. In a comparison to state-of-the-art GBS-based PGT for nuclear DNA, shallow sequencing-based PGT, and PCR-based PGT for mitochondrial DNA, our approach alleviates technical limitations by decreasing whole genome amplification artifacts by 68.4%, increasing breadth of coverage by at least 4-fold, and reducing wet-lab turn-around-time by ~2.5-fold. Importantly, this method enables trio-based PGT-A for aneuploidy origin, an approach we coin PGT-AO, detects translocation breakpoints, and nuclear and mitochondrial single nucleotide variants and indels in base-resolution. This work demonstrates a novel preimplantation genetic testing (PGT) method that detects aberrations in both the nuclear and mitochondrial genomes of IVF embryos. The technology traces the origin of chromosomal aberrations to before or after fertilisation. [ABSTRACT FROM AUTHOR]

Mitochondria, essential components of eukaryotic cells, play a central role in generating cellular energy, regulating metabolism, and facilitating cellular interactions. A distinguishing characteristic of mitochondria is their unique circular double-stranded DNA, known as mitochondrial DNA (mtDNA), essential for energy synthesis and overall mitochondrial function. MtDNA depletion is a notable decrease in mtDNA levels and is affected by a combination of genetic and environmental elements. Genetic contributors include inherited mutations, nuclear DNA changes that impact mitochondrial activity, and mutations within the D-loop region of mtDNA. Environmental factors encompass exposure to specific medications, oxidative stress, and insufficient nutrient consumption. Prostate cancer, a primary contributor to male cancer fatalities, has been associated with anomalies in mtDNA structure and function. The involvement of mitochondria in prostate cancer is intricate, influencing energy metabolism, the stability of the genome, and the emergence of aggressive, androgen-independent cancer variants. Notably, mtDNA depletion is implicated in the shift from androgen-sensitive to androgen-resistant prostate cancer, emphasizing its crucial role in disease advancement. Additionally, mtDNA depletion correlates with the development of a cancer stem cell-like phenotype, marked by increased tumor aggressiveness and heightened resistance to therapeutic agents. Research indicates that changes in mtDNA quantity are linked to the progression and prognosis of prostate cancer. Elevated levels of POLRMT, a nuclear enzyme essential for mtDNA synthesis, have been associated with prostate cancer proliferation, while diminished mtDNA levels are linked to increased invasiveness and a shift towards a mesenchymal cell state. In summary, grasping the intricate relationship between mtDNA depletion and prostate cancer is essential for formulating targeted treatment approaches and enhancing patient outcomes. This review article emphasizes the critical role of mtDNA in the advancement of prostate cancer and underscores its potential as a therapeutic focal point in addressing this widespread cancer. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

The contemporary diversity and distribution of species are shaped by their evolutionary and ecological history. This can be deciphered with the help of phylogenetic and demographic analysis methods, ideally combining and supplementing information from mitochondrial and nuclear genomes. In this study, we investigated the demographic history of Eurasian perch (Perca fluviatilis), a highly adaptable teleost with a distribution range across Eurasia. We combined whole‐genome resequencing data with available genomic resources to analyse the phylogeny, phylogeography, and demographic history of P. fluviatilis populations from Europe and Siberia. We identified five highly diverged evolutionary mtDNA lineages, three of which show a strong signal of admixture in the Baltic Sea region. The estimated mean divergence time between these lineages ranged from 0.24 to 1.42 million years. Based on nuclear genomes, two distinct demographic trajectories were observed in European and Siberian samples reflecting contrasting demographic histories ca. 30,000–100,000 years before the present. A comparison of mtDNA and nuclear DNA evolutionary trees and AMOVA revealed concordances, as well as incongruences, between the two types of data, most likely reflecting recent postglacial colonization and hybridization events. Overall, our findings demonstrate the power and usefulness of genome‐wide information for delineating historical processes that have shaped the genome of P. fluviatilis. We also highlight the added value of data‐mining existing transcriptomic resources to complement novel sequence data, helping to shed light on putative glacial refugia and postglacial recolonization routes. [ABSTRACT FROM AUTHOR]

Ten populations of Caucasian juniper J. communis var. oblonga were analyzed using seven microsatellite nSSR loci to draw conclusions about migration routes and genetic relationships with populations in the northern part of their range. These new data were combined with data previously obtained from the main Eurasian range. The results of nSSR analysis confirm the data on the cpDNA structure of J. communis var. oblonga about the existence of a deep divergence between the populations of the eastern part of the Greater Caucasus and the populations of the main range, which is likely due to the long-term isolation of juniper in this part of the Caucasus. At the same time, the results indicate the existence of a juniper gene flow from the main range toward the Western Caucasus, which was more intense with seeds. The migration routes of birds established during interglacial periods contributed to the dispersal of seeds over long distances and contacts of juniper from the main part of its range with juniper in the western part of the Caucasus, which was reflected in the structure of nuclear DNA. [ABSTRACT FROM AUTHOR]

This study presents the first record of T. lindbergi from the southwestern Atlantic Ocean, based on specimens collected from the smalleye croaker Nebris microps Cuvier (Sciaenidae), off the coast of Maranhão Island, State of Maranhão, Brazil. Our approach included a morphological analysis complemented by DNA sequencing (28S, ITS2 rDNA, and cox1 mtDNA). Our phylogenetic analysis revealed the affinity of T. lindbergi to its congener T. laticaudi Parukhin, 1969, a digenean parasite commonly found in hydrophiine snakes inhabiting the Pacific Ocean. The interspecific divergence between T. lindbergi and T. laticaudi measures 3.80% for 28S, 7.49–7.64% for ITS2, and 16.29–16.70% for cox1. Our findings expand the documented geographic range of T. lindbergi into the southwestern Atlantic Ocean, report a novel host record, and increase the number of hemiurids known from Brazil to 30 species. Additionally, this study represents the initial documentation of a marine digenean fish within the North Brazil Shelf. [ABSTRACT FROM AUTHOR]

Mitochondria play a crucial role in maintaining the energy status and redox homeostasis of eukaryotic cells. They are responsible for the metabolic efficiency of cells, providing both ATP and intermediate metabolic products. They also regulate cell survival and death under stress conditions by controlling the cell response or activating the apoptosis process. This functional diversity of mitochondria indicates their great importance for cellular metabolism. Hence, dysfunctions of these structures are increasingly recognized as an element of the etiology of many human diseases and, therefore, an extremely promising therapeutic target. Mitochondrial dysfunctions can be caused by mutations in both nuclear and mitochondrial DNA, as well as by stress factors or replication errors. Progress in knowledge about the biology of mitochondria, as well as the consequences for the efficiency of the entire organism resulting from the dysfunction of these structures, is achieved through the use of model organisms. They are an invaluable tool for analyzing complex cellular processes, leading to a better understanding of diseases caused by mitochondrial dysfunction. In this work, we review the most commonly used model organisms, discussing both their advantages and limitations in modeling fundamental mitochondrial processes or mitochondrial diseases. [ABSTRACT FROM AUTHOR]

Discordance between mitochondrial and nuclear DNA is common among animals and can be the result of a number of evolutionary processes, including incomplete lineage sorting and introgression. Particularly relevant in contact zones, mitonuclear discordance is expected because the mitochondrial genome is haploid and primarily uniparentally inherited, whereas nuclear loci are evolving at slower rates. In addition, when closely related taxa come together in hybrid zones, the distribution of diagnostic phenotypic characters and their concordance with the mitochondrial or nuclear lineages can also inform on historical and ongoing dynamics within hybrid zones. Overall, genetic and phenotypic discordances provide evidence for evolutionary divergence and processes that maintain boundaries among sister species or lineages. In this study, we characterized patterns of genetic and phenotypic variation in a contact zone between Cycloramphus dubius and Cycloramphus boraceiensis, two sister species of frogs endemic to the Atlantic Coastal Forest of Brazil. We examined genomic‐scale nuclear diversification across 19 populations, encompassing the two parental forms and a contact zone between them. We compared the distribution of genomic DNA variability with that of a mitochondrial locus (16S) and two morphological traits (dorsal tubercles and body size). Our results reveal multiple divergent lineages with ongoing admixture. We detected discordance in patterns of introgression across the three data types. Cycloramphus dubius males are significantly larger than C. boraceiensis males, and we posit that competition among males in the hybrid zone, coupled with mate choice by females, may be one mechanism leading to patterns of introgression observed between the species. [ABSTRACT FROM AUTHOR]

In this study, we report a novel platinum–doxorubicin conjugate that demonstrates superior therapeutic indices to cisplatin, doxorubicin, or their combination, which are commonly used in cancer treatment. This new molecular structure (1) was formed by conjugating an amphiphilic Pt(IV) prodrug of cisplatin with doxorubicin. Due to its amphiphilic nature, the Pt(IV)–doxorubicin conjugate effectively penetrates cell membranes, delivering both cisplatin and doxorubicin payloads intracellularly. The intracellular accumulation of these payloads was assessed using graphite furnace atomic absorption spectrometry and fluorescence imaging. Since the therapeutic effects of cisplatin and doxorubicin stem from their ability to target nuclear DNA, we hypothesized that the amphiphilic Pt(IV)–doxorubicin conjugate (1) would effectively induce nuclear DNA damage toward killing cancer cells. To test this hypothesis, we used flow the cytometric analysis of phosphorylated H2AX (γH2AX), a biomarker of nuclear DNA damage. The Pt(IV)–doxorubicin conjugate (1) markedly induced γH2AX in treated MDA-MB-231 breast cancer cells, showing higher levels than cells treated with either cisplatin or doxorubicin alone. Furthermore, MTT cell viability assays revealed that the enhanced DNA-damaging capability of complex 1 resulted in superior cytotoxicity and selectivity against human cancer cells compared to cisplatin, doxorubicin, or their combination. Overall, the development of this amphiphilic Pt(IV)–doxorubicin conjugate represents a new form of combination therapy with improved therapeutic efficacy. [ABSTRACT FROM AUTHOR]

Besleria , a genus of perennial herbs, shrubs, or small trees growing in the understorey of rainforests, is one of the largest genera of neotropical Gesneriaceae, with over 165 species. Despite the ecological importance and ubiquity of Besleria in rainforest ecosystems, taxonomic and evolutionary studies of Besleria are limited. Here, we generated a phylogenetic analysis of Besleria using four nuclear and chloroplast DNA regions (ITS, mat K, rps 16, and trn L- trn F) covering more than 50% of the recognized species, along with two secondary calibration points to infer divergence times. Our results support the monophyly of Besleria and allowed us to revise the infrageneric classification and biogeographical history of the genus. We identified five major clades that do not correspond to sections or subsections in previous classifications. These clades are well circumscribed geographically but remain difficult to characterize using previously hypothesized morphological characters. Biogeographical reconstructions indicate an origin in the northern Andes during the Middle Miocene (ca. 15 Mya). The current distribution patterns of this plant group have been significantly shaped by geological and climatic events, particularly Andean uplift and the formation of the Panama Isthmus. [ABSTRACT FROM AUTHOR]

The practice of hybridization is carried out globally in fish farms. Here, we present the first record of the parasitic fauna of hybrids among genus Colossoma and Piaractus in natural environments. We identified a total of 48 hybrids, nine F1 hybrids (nuclear DNA from both species present in the cross) and 38 advanced hybrids (nuclear DNA from one species), both from crosses between Piaractus brachypomus and Piaractus mesopotamicus, and one F1 "tambacu" corresponding to cross between Colossoma macropomum and Piaractus mesopotamicus. This is the first record of Anacanthorus penilabiatus, Anacanthorus toledoensis, Mymarothecium viatorum, Mymarothecium ianwhittington, Haementeria sp., Dadaytrema oxycephala, Rondonia rondoni, and Echinorhynchus gomesi parasitizing hybrids collected in a natural environment. With this, we expand knowledge about the diversity of fish and parasites in the upper Paraná River and warn about the risk that fish escapes can cause in the basin. [ABSTRACT FROM AUTHOR]

Aim: Various species distributed in the Alps have their disjunct occurrences in the Carpathians. Fossil evidence for some woodland snails of Alpine distribution suggests that they colonized the Carpathians during the Holocene forest optimum or later. Here, we focus on disjunct Carpathian populations of the rock‐dwelling alpine snail Pyramidula saxatilis. As it occupies very stable habitats, that is, high‐elevation limestone rocks, one can assume its potential survival in Carpathian refugia over the glacial period(s). For comparison, the more widespread and warm‐climate P. pusilla is analysed. Location: Europe. Taxon: Pyramidula saxatilis and P. pusilla. Methods: We analysed the genetic diversity of P. saxatilis and P. pusilla populations across their entire ranges using mitochondrial DNA and nuclear DNA markers. Seven fossil mollusc successions from the area where P. saxatilis occurs in the Carpathians were analysed and dated using the radiocarbon method. Habitat suitability models of both species were calculated for selected time periods since the Last Glacial Maximum. Results: All Carpathian P. saxatilis populations were genetically homogeneous and similar to those from the Eastern Alps. In P. pusilla, we found a genetically distinct lineage in the southern Western Carpathians. Both species were found in three fossil profiles since the Middle Holocene, and in one already in the Late Glacial. Habitat suitability models suggested the fluctuations of suitable conditions in the Carpathians driven by summer precipitation, especially for P. saxatilis. Main Conclusions: Our results suggest that the Carpathian populations of P. saxatilis represent a post‐LGM colonization from the Eastern Alps triggered by climatic changes, mainly by the increase in summer precipitation during the Late Glacial interstadials and Middle Holocene. The evidence for P. pusilla is similar, but also suggests rare long‐term survival in the Carpathian microrefugia. The palaeoecological evidence indicates a possible threat to high‐elevation species from future fluctuations in precipitation regimes. [ABSTRACT FROM AUTHOR]

Long interspersed nuclear element-1 (LINE-1) methylation serves as an indicator of global DNA methylation. This study explored the correlation between LINE-1 methylation and chronic kidney disease (CKD). We also evaluated whether LINE-1 methylation could modify the association between CKD and metal exposure. A total of 213 patients with clinically defined CKD, without hemodialysis and 416 age and sex matched controls were recruited. Levels of LINE-1 methylation, total urinary arsenic, blood lead, blood cadmium, and plasma selenium were assessed. The results reveal a positive association between LINE-1 methylation and CKD, with an odds ratio (OR) of 5.30 (95% confidence interval: 2.81 to 9.99). Total urinary arsenic and blood cadmium concentrations were positively related with LINE-1 methylation. This study was the first to observe that low plasma selenium, high blood cadmium, and high blood lead levels significantly and additively interact with increased LINE-1 methylation to increase the OR of CKD. Additionally, high LINE-1 methylation interacted multiplicatively with low plasma selenium to increase the OR of CKD (p < 0.001). This study highlighted the significant association between LINE-1 hypermethylation and CKD. Furthermore, the results demonstrate that LINE-1 methylation can interact with high blood cadmium or low plasma selenium to affect CKD risk. [ABSTRACT FROM AUTHOR]