Machine-learning prediction of a novel diagnostic model using mitochondria-related genes for patients with bladder cancer.

Bladder cancer (BC) is the ninth most-common cancer worldwide and it is associated with high morbidity and mortality. Mitochondrial Dysfunction is involved in the progression of BC. This study aimed to developed a novel diagnostic model based on mitochondria-related genes (MRGs) for BC patients using Machine Learning. In this study, we analyzed GSE13507 datasets and identified 752 DE-MRGs in BC specimens. Functional enrichment analysis uncovered the significant roles of 752 DE-MRGs in key processes such as cellular and organ development, as well as gene regulation. The analysis revealed the crucial functions of these genes in transcriptional regulation and protein-DNA interactions. Then, we performed LASSO and SVM-RFE, and identified four critical diagnostic genes including GLRX2, NMT1, OXSM and TRAF3IP3. Based on the above four genes, we developed a novel diagnostic model whose diagnostic value was confirmed in GSE13507, GSE3167 and GSE37816 datasets. Moreover, we reported the expressing pattern of GLRX2, NMT1, OXSM and TRAF3IP3 in BC samples. Immune cell infiltration analysis revealed that the four genes were associated with several immune cells. Finally, we performed RT-PCR and confirmed NMT1 was highly expressed in BC cells. Functional experiments revealed that knockdown of NMT1 suppressed the proliferation of BC cells. Overall, we have formulated a diagnostic potential that offered a comprehensive framework for delving into the underlying mechanisms of BC. Before proceeding with clinical implementation, it is essential to undertake further investigative efforts to validate its diagnostic effectiveness in BC patients.

ADNP dysregulates methylation and mitochondrial gene expression in the cerebellum of a Helsmoortel-Van der Aa syndrome autopsy case.

BACKGROUND: Helsmoortel-Van der Aa syndrome is a neurodevelopmental disorder in which patients present with autism, intellectual disability, and frequent extra-neurological features such as feeding and gastrointestinal problems, visual impairments, and cardiac abnormalities. All patients exhibit heterozygous de novo nonsense or frameshift stop mutations in the Activity-Dependent Neuroprotective Protein (ADNP) gene, accounting for a prevalence of 0.2% of all autism cases worldwide. ADNP fulfills an essential chromatin remodeling function during brain development. In this study, we investigated the cerebellum of a died 6-year-old male patient with the c.1676dupA/p.His559Glnfs*3 ADNP mutation. RESULTS: The clinical presentation of the patient was representative of the Helsmoortel-Van der Aa syndrome. During his lifespan, he underwent two liver transplantations after which the child died because of multiple organ failure. An autopsy was performed, and various tissue samples were taken for further analysis. We performed a molecular characterization of the cerebellum, a brain region involved in motor coordination, known for its highest ADNP expression and compared it to an age-matched control subject. Importantly, epigenome-wide analysis of the ADNP cerebellum identified CpG methylation differences and expression of multiple pathways causing neurodevelopmental delay. Interestingly, transcription factor motif enrichment analysis of differentially methylated genes showed that the ADNP binding motif was the most significantly enriched. RNA sequencing of the autopsy brain further identified downregulation of the WNT signaling pathway and autophagy defects as possible causes of neurodevelopmental delay. Ultimately, label-free quantification mass spectrometry identified differentially expressed proteins involved in mitochondrial stress and sirtuin signaling pathways amongst others. Protein-protein interaction analysis further revealed a network including chromatin remodelers (ADNP, SMARCC2, HDAC2 and YY1), autophagy-related proteins (LAMP1, BECN1 and LC3) as well as a key histone deacetylating enzyme SIRT1, involved in mitochondrial energy metabolism. The protein interaction of ADNP with SIRT1 was further biochemically validated through the microtubule-end binding proteins EB1/EB3 by direct co-immunoprecipitation in mouse cerebellum, suggesting important mito-epigenetic crosstalk between chromatin remodeling and mitochondrial energy metabolism linked to autophagy stress responses. This is further supported by mitochondrial activity assays and stainings in patient-derived fibroblasts which suggest mitochondrial dysfunctions in the ADNP deficient human brain. CONCLUSION: This study forms the baseline clinical and molecular characterization of an ADNP autopsy cerebellum, providing novel insights in the disease mechanisms of the Helsmoortel-Van der Aa syndrome. By combining multi-omic and biochemical approaches, we identified a novel SIRT1-EB1/EB3-ADNP protein complex which may contribute to autophagic flux alterations and impaired mitochondrial metabolism in the Helsmoortel-Van der Aa syndrome and holds promise as a new therapeutic target.

The complete mitochondrial genome of Leucoptera coffeella (Lepidoptera: Lyonetiidae) and phylogenetic relationships within the Yponomeutoidea superfamily.

The coffee leaf miner (Leucoptera coffeella) is one of the major pests of coffee crops in the neotropical regions, and causes major economic losses. Few molecular data are available to identify this pest and advances in the knowledge of the genome of L. coffeella will contribute to improving pest identification and also clarify taxonomy of this microlepidoptera. L. coffeella DNA was extracted and sequenced using PacBio HiFi technology. Here we report the complete L. coffeella circular mitochondrial genome (16,407 bp) assembled using Aladin software. We found a total of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs) and an A + T rich-region and a D-loop. The L. coffeella mitochondrial gene organization is highly conserved with similarities to lepidopteran mitochondrial gene rearrangements (trnM-trnI-trnQ). We concatenated the 13 PCG to construct a phylogenetic tree and inferred the relationship between L. coffeella and other lepidopteran species. L. coffeella is found in the Lyonetiidae clade together with L. malifoliella and Lyonetia clerkella, both leaf miners. Interestingly, this clade is assigned in the Yponomeutoidea superfamily together with Gracillariidae, and both superfamilies displayed species with leaf-mining feeding habits.

A Two-Genome Portrayal of Mitochondrial Disorders: A Review with Clinical Presentations.

Disorders of mitochondrial function are responsible for many inherited neuromuscular and metabolic diseases. Their combination of high mortality, multi-systemic involvement, and economic burden cause devastating effects on patients and their families. Molecular diagnostic tools are becoming increasingly important in providing earlier diagnoses and guiding more precise therapeutic treatments for patients suffering from mitochondrial disorders. This review addresses fundamental molecular concepts relating to the pathogenesis of mitochondrial dysfunction and disorders. A series of short cases highlights the various clinical presentations, inheritance patterns, and pathogenic mutations in nuclear and mitochondrial genes that cause mitochondrial diseases. Graphical and tabular representations of the results are presented to guide the understanding of the important concepts related to mitochondrial molecular genetics and pathology. Emerging technology is incorporating preimplantation genetic testing for mtDNA disorders, while mitochondrial replacement shows promise in significantly decreasing the transfer of diseased mitochondrial DNA (mtDNA) to embryos. Medical professionals must maintain an in-depth understanding of the gene mutations and molecular mechanisms underlying mitochondrial disorders. Continued diagnostic advances and comprehensive management of patients with mitochondrial disorders are essential to achieve robust clinical impacts from comprehensive genomic testing. This is especially true when supported by non-genetic tests such as biochemical analysis, histochemical stains, and imaging studies. Such a multi-pronged investigation should improve the management of mitochondrial disorders by providing accurate and timely diagnoses to reduce disease burden and improve the lives of patients and their families.

Insights into the mitochondrial cytochrome oxidase I (mt-COI) gene and wing morphometrics of Anopheles baimaii (Diptera: Culicidae) in malaria-endemic islands of Thailand.

Anopheles baimaii (Diptera: Culicidae) significantly contributes to the transmission of parasites causing malaria in Southeast Asia and South Asia. This study examined the morphological (wing shape) and molecular (mitochondrial gene) variations of An. baimaii in four of Thailand's border islands, and also investigated the presence of Plasmodium parasites in these mosquitoes. No Plasmodium infections were detected in the samples. Significant differences in wing shape were observed in most island populations (p < 0.05). A single-linkage tree, constructed using Mahalanobis distances, clustered the populations into two groups based on geographical locations. Genetic variation in An. baimaii was also analyzed through cytochrome c oxidase subunit I (COI) gene sequences. This analysis identified 22 segregating sites and a low nucleotide diversity of 0.004. Furthermore, 18 distinct haplotypes were identified, indicating a high haplotype diversity of 0.825. Neutrality tests for the overall population revealed a significantly negative Fu's Fs value (-5.029), indicating a population expansion. In contrast, Tajima's D yielded a negative value (-1.028) that did not reach statistical significance. The mismatch distribution analysis exhibited a bimodal pattern, and the raggedness index was 0.068, showing no significant discrepancy (p = 0.485) between observed and expected distributions. Pairwise genetic differentiation assessments demonstrated significant differences between all populations (p < 0.05). These findings provide valuable insights into the COI gene and wing morphometric variations in An. baimaii across Thailand's islands, offering critical information for understanding the adaptations of this malaria vector and guiding future comprehensive research.

Illuminating the immunological landscape: mitochondrial gene defects in pancreatic cancer through a multiomics lens.

This comprehensive review delves into the complex interplay between mitochondrial gene defects and pancreatic cancer pathogenesis through a multiomics approach. By amalgamating data from genomic, transcriptomic, proteomic, and metabolomic studies, we dissected the mechanisms by which mitochondrial genetic variations dictate cancer progression. Emphasis has been placed on the roles of these genes in altering cellular metabolic processes, signal transduction pathways, and immune system interactions. We further explored how these findings could refine therapeutic interventions, with a particular focus on precision medicine applications. This analysis not only fills pivotal knowledge gaps about mitochondrial anomalies in pancreatic cancer but also paves the way for future investigations into personalized therapy options. This finding underscores the crucial nexus between mitochondrial genetics and oncological immunology, opening new avenues for targeted cancer treatment strategies.

Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea).

BACKGROUND: Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acariformes; they are strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to the limited number of available morphological characters-some of them are homoplastic. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving the higher-level phylogenetic relationships. RESULTS: Here, we sequenced and compared the complete mt genomes of 153 eriophyoid mite species, which showed 54 patterns of rearranged mt gene orders relative to that of the hypothetical ancestor of arthropods. The shared derived mt gene clusters support the monophyly of eriophyoid mites (Eriophyoidea) as a whole and the monophylies of six clades within Eriophyoidea. These monophyletic groups and their relationships were largely supported in the phylogenetic trees inferred from mt genome sequences as well. Our molecular dating results showed that Eriophyoidea originated in the Triassic and diversified in the Cretaceous, coinciding with the diversification of angiosperms. CONCLUSIONS: This study reveals multiple molecular synapomorphies (i.e. shared derived mt gene clusters) at different levels (i.e. family, subfamily or tribe level) from the complete mt genomes of 153 eriophyoid mite species. We demonstrated the use of derived mt gene clusters in unveiling the higher-level phylogeny of eriophyoid mites, and underlines the origin of these mites and their co-diversification with angiosperms.

A peek into the population genetics of white teatfish (Holothuria fuscogilva) of Kenya's south coast.

BACKGROUND: The white teatfish, Holothuria fuscogilva, is widely distributed in coastal areas, including waters around coral reefs and seagrasses in the Indo-Pacific. In Kenya, the species is distributed in shallow reefs with higher landings reported from the Vanga-Shimoni-Gazi seascape on the Kenyan south coast. Despite its high exploitation for export and its vulnerable and endangered statuses under IUCN and CITES respectively, Kenya's H. fuscogilva populations and how they may have been impacted by the fishing pressure have not been studied. METHODS: We estimated the genetic diversity and structure of H. fuscogilva population conveniently sampled from three sites in Kenyan south coast using the mitochondrial cytochrome oxidase subunit I (COI) gene sequences. We recorded 30 haplotypes with 43 polymorphic sites across the population. Furthermore, we estimated an overall high haplotype diversity and low nucleotide diversity of estimates of h = 0.970 ± 0.013 and π = 0.010 ± 0.001 respectively. CONCLUSIONS: These preliminary findings suggest several population outcomes, among them a fit population, which require confirming with more comprehensive study to inform strategies for the sustainable exploitation and management of the species.

Comparative Analysis and Phylogenetic Study of Dawkinsia filamentosa and Pethia nigrofasciata Mitochondrial Genomes.

Smiliogastrinae are recognized for their high nutritional and ornamental value. In this study, we employed high-throughput sequencing technology to acquire the complete mitochondrial genome sequences of Dawkinsia filamentosa and Pethia nigrofasciata. The gene composition and arrangement order in these species were similar to those of typical vertebrates, comprising 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 non-coding region. The mitochondrial genomes of D. filamentosa and P. nigrofasciata measure 16,598 and 16,948 bp, respectively. Both D. filamentosa and P. nigrofasciata exhibit a significant preference for AT bases and an anti-G bias. Notably, the AT and GC skew values of the ND6 gene fluctuated markedly, suggesting that the selection and mutation pressures on this gene may differ from those affecting other genes. Phylogenetic analysis, based on the complete mitochondrial genomes of 23 Cyprinidae fishes, revealed that D. filamentosa is closely related to the sister group comprising Dawkinsia denisonii and Sahyadria chalakkudiensis. Similarly, P. nigrofasciata forms a sister group with Pethia ticto and Pethia stoliczkana.

Comparative mitogenomics of Brachiopods reveals conservatism in articulate species and unusualness in inarticulate species.

BACKGROUND: Brachiopods are a phylum of marine invertebrates with over 10,000 fossil species. Today, there are fewer than 500 extant species assigned to the class Articulata or Inarticulata and for which knowledge of evolutionary genetics and genomics is still poor. Until now, complete mitogenome sequences of two inarticulate species and four articulate species were available. METHODS AND RESULTS: The complete mitogenome of the inarticulate brachiopod species Lingula reevii (20,778 bp) was obtained by using next generation sequencing. It contains 12 protein-coding genes (the annotation of atp8 is unsure), two ribosomal RNA genes, 26 transfer RNA genes, and one supernumerary ORF that is also conserved in the inarticulate species Lingula anatina. It is hypothesized that this ORF could represent a Lingula-specific mtORFan gene (without obvious homology to other genes). Comparative mitogenomics indicate the mitochondrial gene order of L. reevii is unique among brachiopods, and that compared to articulate species, inarticulate species exhibit massive mitogenome rearrangements, deviant ATP8 protein sequences and supernumerary ORFs, possibly representing species- or lineage-specific mtORFan genes. CONCLUSION: The results of this study enrich genetics knowledge of extant brachiopods, which may eventually help to test hypotheses about their decline.

Prognosis prediction and risk stratification of breast cancer patients based on a mitochondria-related gene signature.

As the malignancy with the highest global incidence, breast cancer represents a significant threat to women's health. Recent advances have shed light on the importance of mitochondrial function in cancer, particularly in metabolic reprogramming within tumors. Recognizing this, we developed a novel risk signature based on mitochondrial-related genes to improve prognosis prediction and risk stratification in breast cancer patients. In this study, transcriptome data and clinical features of breast cancer samples were extracted from two sources: the TCGA, serving as the training set, and the METABRIC, used as the independent validation set. We developed the signature using LASSO-Cox regression and assessed its prognostic efficacy via ROC curves. Furthermore, the signature was integrated with clinical features to create a Nomogram model, whose accuracy was validated through clinical calibration curves and decision curve analysis. To further elucidate prognostic variations between high and low-risk groups, we conducted functional enrichment and immune infiltration analyses. Additionally, the study encompassed a comparison of mutation landscapes and drug sensitivity, providing a comprehensive understanding of the differing characteristics in these groups. Conclusively, we established a risk signature comprising 8 mitochondrial-related genes-ACSL1, ALDH2, MTHFD2, MRPL13, TP53AIP1, SLC1A1, ME3, and BCL2A1. This signature was identified as an independent risk predictor for breast cancer patient survival, exhibiting a significant high hazard ratio (HR = 3.028, 95%CI 2.038-4.499, P < 0.001). Patients in the low-risk group showed a more favorable prognosis, with enhanced immune infiltration, distinct mutation landscapes, and greater sensitivity to anti-tumor drugs. In contrast, the high-risk group exhibited an adverse trend in these aspects. This risk signature represents a novel and effective prognostic indicator, suggesting valuable insights for patient stratification in breast cancer.

Phylogenetic relationships and genetic differentiation of two Salamandrella species as revealed via COI gene from Northeastern China.

Due to traditional classification methods' limitations, some cryptic species remain undiscovered. To better explore the existence of the Schrenck salamander (Salamandrella tridactyla, a cryptic species of Siberian salamander S. keyserlingii) in China, we conducted a molecular phylogenetic analysis to confirm the taxonomic relationship among Salamandrella species and investigate genetic variation. We used complete sequences of the mitochondrial COI gene from 65 specimens collected across a wide range in Northeastern China. Thirty-five haplotypes were obtained from six populations. They showed medium-high haplotype diversity (Hd) and low nucleotide polymorphism (π). The phylogenetic tree and haplotype network analysis revealed that populations from Greater Khingan Ridge (Huma: HM) and Lesser Khingan Ridge (Tieli: TL) belong to S. keyserlingii, while populations from Changbai Mountain (Shangzhi-zhuziying: SZ, Shangzhi-cuijia: SC, Hailin: HL, and Baishan: BS) belong to S. tridactyla. This indicates the monophyly of Salamandrella and each of the two species. There was a substantial level of genetic differentiation between different species and within populations of the same species. This differentiation was significantly related to geographical distance. At last, the mismatch distribution and neutrality analyses indicated that the TL populations have undergone expansion of history. The study supplements the distributional range of Schrenck salamander. And it provides a theoretical basis for species conservation of Salamandrella species.

Variants in Human ATP Synthase Mitochondrial Genes: Biochemical Dysfunctions, Associated Diseases, and Therapies.

Mitochondrial ATP synthase (Complex V) catalyzes the last step of oxidative phosphorylation and provides most of the energy (ATP) required by human cells. The mitochondrial genes MT-ATP6 and MT-ATP8 encode two subunits of the multi-subunit Complex V. Since the discovery of the first MT-ATP6 variant in the year 1990 as the cause of Neuropathy, Ataxia, and Retinitis Pigmentosa (NARP) syndrome, a large and continuously increasing number of inborn variants in the MT-ATP6 and MT-ATP8 genes have been identified as pathogenic. Variants in these genes correlate with various clinical phenotypes, which include several neurodegenerative and multisystemic disorders. In the present review, we report the pathogenic variants in mitochondrial ATP synthase genes and highlight the molecular mechanisms underlying ATP synthase deficiency that promote biochemical dysfunctions. We discuss the possible structural changes induced by the most common variants found in patients by considering the recent cryo-electron microscopy structure of human ATP synthase. Finally, we provide the state-of-the-art of all therapeutic proposals reported in the literature, including drug interventions targeting mitochondrial dysfunctions, allotopic gene expression- and nuclease-based strategies, and discuss their potential translation into clinical trials.

Discovery of Encyclometra bungara (Digenea: Encyclometridae) in a new host (Enhydris enhydris) from Thailand and Cambodia through morphological and molecular identification.

The genus Encyclometra is one of the two genera in family Encyclometridae, known for parasitising the oesophagus, stomach and intestine of snakes. Among Encyclometra, the species present are: Encyclometra colubrimurorum, Encyclometra japonica, Encyclometra asymmetrica and Encyclometra bungara. Species discrimination within Encyclometra has predominantly relied on morphological differences, such as the length of the caeca and the position of the testes. Morphological overlaps exist among these species making species discrimination challenging. Additionally, the use of molecular information has been limited for Encyclometra. To determine the Encyclometra species infecting Enhydris enhydris from Thailand and Cambodia, morphological and molecular identification was conducted. Morphological characters and measurements were obtained from 30 Encyclometra adults, and they were compared with previous studies of other Encyclometra species. Novel sequences of E. bungara were generated using the nuclear 18S and 28S ribosomal RNA genes, and the mitochondrial cytochrome c oxidase subunit 1 gene. Our results revealed that the specimens could be morphologically identified as E. bungara, with support from molecular information obtained from the phylogenies of the 3 genetic markers employed. Molecular analysis showed that the Encyclometra specimens were distinct from E. colubrimurorum and E. japonica. Through morphological and molecular identification of the Encyclometra specimens found in E. enhydris from Thailand and Cambodia, we describe and provide a record of E. bungara in a new host and new locality. Additionally, novel molecular sequences were generated, revealing the phylogenetic position of E. bungara within the superfamily Gorgoderoidea.

Maternal mitochondrial function affects paternal mitochondrial inheritance in Drosophila.

The maternal inheritance of mitochondria is a widely accepted paradigm, and mechanisms that prevent paternal mitochondria transmission to offspring during spermatogenesis and postfertilization have been described. Although certain species do retain paternal mitochondria, the factors affecting paternal mitochondria inheritance in these cases are unclear. More importantly, the evolutionary benefit of retaining paternal mitochondria and their ultimate fate are unknown. Here we show that transplanted exogenous paternal D. yakuba mitochondria can be transmitted to offspring when maternal mitochondria are dysfunctional in D. melanogaster. Furthermore, we show that the preserved paternal mitochondria are functional, and can be stably inherited, such that the proportion of paternal mitochondria increases gradually in subsequent generations. Our work has important implications that paternal mitochondria inheritance should not be overlooked as a genetic phenomenon in evolution, especially when paternal mitochondria are of significant differences from the maternal mitochondria or the maternal mitochondria are functionally abnormal. Our results improve the understanding of mitochondrial inheritance and provide a new model system for its study.

Multifaceted roles of t6A biogenesis in efficiency and fidelity of mitochondrial gene expression.

N 6-Threonylcarbamoyladenosine at A37 (t6A37) of ANN-decoding transfer RNAs (tRNAs) is a universal modification whose functions have been well documented in bacteria and lower eukaryotes; however, its role in organellar translation is not completely understood. In this study, we deleted the mitochondrial t6A37-modifying enzyme OSGEPL1 in HEK293T cells. OSGEPL1 is dispensable for cell viability. t6A37 hypomodification selectively stimulated N1-methyladenosine at A9 (m1A9) and N2-methylguanosine at G10 (m2G10) modifications and caused a substantial reduction in the aminoacylation of mitochondrial tRNAThr and tRNALys, resulting in impaired translation efficiency. Multiple types of amino acid misincorporation due to the misreading of near-cognate codons by t6A37-unmodified tRNAs were detected, indicating a triggered translational infidelity. Accordingly, the alterations in mitochondrial structure, function, and the activated mitochondrial unfolded protein response were observed. Mitochondrial function was efficiently restored by wild-type, but not by tRNA-binding-defective OSGEPL1. Lastly, in Osgepl1 deletion mice, disruption to mitochondrial translation was evident but resulted in no observable deficiency under physiological conditions in heart, which displays the highest Osgepl1 expression. Taken together, our data delineate the multifaceted roles of mitochondrial t6A37 modification in translation efficiency and quality control in mitochondria.

Unexpected diversity and co-occurrence of phytotelmic frogs (Guibemantis) around Andasibe, one of the most intensively surveyed amphibian hotspots of Madagascar, and descriptions of three new species.

The area around the Malagasy village of Andasibe, which includes Analamazaotra-Mantadia National Park as well as other protected areas, is characterized by very species-rich and well-studied communities of animals and plants, but new species are still regularly discovered. Three species of phytotelmic frogs of the subgenus Pandanusicola in the genus Guibemantis are known from this area, G. flavobrunneus, G. liber, and G. pulcher. Further Pandanusicola frogs from this area have been provisionally assigned to G. bicalcaratus or G. albolineatus, pending detailed taxonomic review. During preliminary exploration of the ecology of these specialized frogs that live and reproduce in the leaf axils of Pandanus screw pines, we noticed the syntopic presence of two differently colored and differently sized Pandanusicola in Andasibe that could not be unambiguously assigned to any known species. A genetic screening revealed that these correspond to yet two further species in the area. Based on our data, seven species of Pandanusicola occur in Andasibe and nearby forests: (1) G. liber, the only non-phytotelmic species of the subgenus in the region; (2) G. flavobrunneus which is the largest species and characterized by a diagnostic yellowish brown dorsal pattern; (3) G. pulcher, characterized by translucent-green color with purplish brown spotting not observed in any other species in the area; (4) G. methueni, a brownish species usually lacking contrasted dorsolateral bands that differs from the other species in the area by emitting a characteristic trill-like advertisement call series (rather than clicks or chirps) and according to our data is widespread along Madagascars east coast; as well as three new species: (5) G. ambakoana sp. nov., a brownish species, typically with contrasted incomplete light dorsolateral bands and with single click-like advertisement calls; (6) G. vakoa sp. nov., a species that is equally brownish but lacks contrasted light dorsolateral bands and that has single click-like advertisement calls of very short duration; and (7) G. rianasoa sp. nov., a species that is smaller sized and has less distinct femoral glands than all the others, and emits a short series of soft chirp-like advertisement calls. All these species are genetically highly distinct, with >5% uncorrected pairwise distances in the mitochondrial 16S rRNA gene, and lack of haplotype sharing in two nuclear-encoded genes. The co-occurrence of seven Pandanusicola frogs in a relatively small geographic area is unprecedented in Madagascar and calls for in-depth studies of a possible differentiation in habitat use and life history.

Increased dosage of DYRK1A leads to congenital heart defects in a mouse model of Down syndrome.

Down syndrome (DS) is caused by trisomy of human chromosome 21 (Hsa21). DS is a gene dosage disorder that results in multiple phenotypes including congenital heart defects. This clinically important cardiac pathology is the result of a third copy of one or more of the approximately 230 genes on Hsa21, but the identity of the causative dosage-sensitive genes and hence mechanisms underlying this cardiac pathology remain unclear. Here, we show that hearts from human fetuses with DS and embryonic hearts from the Dp1Tyb mouse model of DS show reduced expression of mitochondrial respiration genes and cell proliferation genes. Using systematic genetic mapping, we determined that three copies of the dual-specificity tyrosine phosphorylation-regulated kinase 1A (Dyrk1a) gene, encoding a serine/threonine protein kinase, are associated with congenital heart disease pathology. In embryos from Dp1Tyb mice, reducing Dyrk1a gene copy number from three to two reversed defects in cellular proliferation and mitochondrial respiration in cardiomyocytes and rescued heart septation defects. Increased dosage of DYRK1A protein resulted in impairment of mitochondrial function and congenital heart disease pathology in mice with DS, suggesting that DYRK1A may be a useful therapeutic target for treating this common human condition.

Phylogenetic relationship of Prohemistomum vivax to other trematodes based on the internal transcribed spacer region and mitochondrial genes.

Prohemistomum vivax is a zoonotic small cyathocotylid trematode that inhabits the intestines of fish-eating birds and mammals. Here, we amplified the internal transcribed spacer (ITS) sequence and six mitochondrial protein-coding genes (PCGs) from P. vivax. The ITS region was 1389 base pairs long and had a partial 18S ribosomal RNA gene, a full ITS1, 5.8S rRNA, and ITS2 sequence, and a partial 28S rRNA gene. The ITS region of P. vivax showed a minimum pairwise distance (0.3-0.6%) from the ITS sequences of Cyathocotylidae sp. 1 and 2 metacercariae from Clarias gariepinus. This result suggests that these metacercariae belong to P. vivax metacercariae. We first amplified mitochondrial genes from P. vivax, including cytochrome c oxidase subunit III (cox3) partial sequence; tRNA-His, cytochrome b (cytb), and NADH dehydrogenase subunit 4L (nad4L) complete sequences; and NADH dehydrogenase subunit 4 (nad4), cytochrome c oxidase I (cox1), and NADH dehydrogenase subunit 5 (nad5) partial sequences. P. vivax was most closely related to Cyathocotyle prussica (NC_039780) and Holostephanus sp. (OP082179), with cox1, cox3, and cytb genes conserved among the three trematodes. The ML phylogenetic tree of ITS sequences supports the order Diplostomida, divided into two main clades (the superfamily Diplostomoidea and Schistosomatoidea). The phylogeny of concatenated amino acid sequences of P. vivax six PCGs revealed that diplostomoids and Clinostomum sp. evolved in a clade with Plagiorchiida members, away from Schistosoma species. These results may yield ribosomal and mitochondrial genetic markers for molecular epidemiological investigations of cyathocotylid intestinal flukes.

Limits of mitochondrial genes in delimiting species within a Carbula species complex (Hemiptera: Pentatomidae).

Molecular data has become a powerful tool for species delimitation, particularly among those that present limited morphological differences; while the mitochondrial genome, with its moderate length, low cost of sequencing and fast lineage sorting, has emerged as a practical data set. Due to the limited morphological differences among the closely related species of Carbula Stål 1865, the species boundaries between Carbula abbreviata (Motschulsky, 1866), Carbula humerigera (Uhler, 1860), and Carbula putoni (Jakovlev, 1876) have remained particularly unclear. In this study, we applied two phylogenetic reconstruction methods to two data sets (mitogenome and COI) to assess the phylogeny of Carbula distributed in Asia, and five species delimitation methods to determine the boundaries between East Asian Carbula species. Our phylogenetic analyses showed Carbula to be paraphyletic; the seven known species distributed within East Asia to form a single monophyletic group, and within this, C. abbreviata, C. humerigera, C. putoni and middle-type to comprise a C. humerigera species complex. Our results show that mitogenome data alone, while effective in the differentiation of more distantly related Carbula species, is not sufficient to accurately delimit the species within this newly described complex.