Changes in the Mitochondria-Related Nuclear Gene Expression Profile during Human Oocyte Maturation by the IVM Technique

To address which mitochondria-related nuclear differentially expressed genes (DEGs) and related pathways are altered during human oocyte maturation, single-cell analysis was performed in three oocyte states: in vivo matured (M-IVO), in vitro matured (M-IVT), and failed to mature in vitro (IM-IVT). There were 691 DEGs and 16 mitochondria-related DEGs in the comparison of M-IVT vs. IM-IVT oocytes, and 2281 DEGs and 160 mitochondria-related DEGs in the comparison of M-IVT vs. M-IVO oocytes, respectively. The GO and KEGG analyses showed that most of them were involved in pathways such as oxidative phosphorylation, pyruvate metabolism, peroxisome, and amino acid metabolism, i.e., valine, leucine, isoleucine, glycine, serine, and threonine metabolism or degradation. During the progress of oocyte maturation, the metabolic pathway, which derives the main source of ATP, shifted from glucose metabolism to pyruvate and fatty acid oxidation in order to maintain a low level of damaging reactive oxygen species (ROS) production. Although the immature oocytes could be cultured to a mature stage by an in vitro technique (IVM), there were still some differences in mitochondria-related regulations, which showed that the mitochondria were regulated by nuclear genes to compensate for their developmental needs. Meanwhile, the results indicated that the current IVM culture medium should be optimized to compensate for the special need for further development according to this disclosure, as it was a latent strategy to improve the effectiveness of the IVM procedure.

Identification and Fine Mapping of the Recessive Gene BK-5, Which Affects Cell Wall Biosynthesis and Plant Brittleness in Maize

The cellulose of the plant cell wall indirectly affects the cell shape and straw stiffness of the plant. Here, the novel brittleness mutant brittle stalk-5 (bk-5) of the maize inbred line RP125 was characterized. We found that the mutant displayed brittleness of the stalk and even the whole plant, and that the brittleness phenotype existed during the whole growth period from germination to senescence. The compressive strength was reduced, the cell wall was thinner, and the cellulose content was decreased compared to that of the wild type. Genetic analysis and map-based cloning indicated that bk-5 was controlled by a single recessive nuclear gene and that it was located in a 90.2-Kb region on chromosome 3 that covers three open reading frames (ORFs). Sequence analysis revealed a single non-synonymous missense mutation, T-to-A, in the last exon of Zm00001d043477 (B73: version 4, named BK-5) that caused the 951th amino acid to go from leucine to histidine. BK-5 encodes a cellulose synthase catalytic subunit (CesA), which is involved with cellulose synthesis. We found that BK-5 was constitutively expressed in all tissues of the germinating stage and silking stage, and highly expressed in the leaf, auricula, and root of the silking stage and the 2-cm root and bud of the germinating stage. We found that BK-5 mainly localized to the Golgi apparatus, suggesting that the protein might move to the plasma membrane with the aid of Golgi in maize. According to RNA-seq data, bk-5 had more downregulated genes than upregulated genes, and many of the downregulated genes were enzymes and transcription factors related to cellulose, hemicellulose, and lignin biosynthesis of the secondary cell wall. The other differentially expressed genes were related to metabolic and cellular processes, and were significantly enriched in hormone signal transduction, starch and sucrose metabolism, and the plant–pathogen interaction pathway. Taken together, we propose that the mutation of gene BK-5 causes the brittle stalk phenotype and provides important insights into the regulatory mechanism of cellulose biosynthesis and cell wall development in maize.

Increased resolution in the face of conflict: phylogenomics of the Neotropical bellflowers (Campanulaceae: Lobelioideae), a rapid plant radiation

Background and Aims- The centropogonid clade (Lobelioideae: Campanulaceae) is an Andean-centered rapid radiation characterized by repeated convergent evolution of morphological traits, including fruit type and pollination syndromes. While previous studies have resolved relationships of lineages with fleshy fruits into subclades, relationships among capsular species remain unresolved. This lack of resolution has impeded reclassification of non-monophyletic genera, whose current taxonomy relies heavily on traits that have undergone convergent evolution. Methods- Targeted sequence capture using a probeset recently developed for the centropogonid clade was used to obtain phylogenomic data from DNA extracted from both silica-dried and herbarium leaf tissue. These data were used to infer relationships among species using concatenated and partitioned species tree methods, and to quantify gene tree discordance. Key Results- While silica-dried leaf tissue resulted in more and longer sequence data, the inclusion of herbarium samples improved phylogenetic reconstruction. Relationships among baccate lineages are similar previous studies, though differ within and among capsular lineages. We improve phylogenetic resolution of Siphocampylus, which forms ten groups of closely related species which we informally name. Two subclades of Siphocampylus and two individual species are rogue taxa whose placement differs widely across analyses. Gene tree discordance (including cytonuclear discordance) is rampant. Conclusions- The first phylogenomic study of the centropogonid clade considerably improves our understanding of relationships in this rapid radiation. Differences across analyses and the possibility of additional lineage discoveries still hamper a solid and stable reclassification. Rapid morphological innovation corresponds with a high degree of phylogenomic complexity, including cytonuclear discordance, nuclear gene tree conflict, and well-supported differences between analyses based on different nuclear loci. Taken together, these results point to a potential role of hemiplasy underlying repeated convergent evolution. This hallmark of rapid radiations is likely present in many other species-rich Andean plant radiations.

New record of bioluminescence in Odontosyllis cf. australiensis (Annelida: Syllidae: Eusyllinae) in Japan

Bioluminescence is widespread in the marine environment. The bioluminescence of some species of the fireworm Odontosyllis (Annelida: Syllidae: Eusyllinae) has been well studied, although the presence or absence of bioluminescence in most species of this genus is yet to be revealed. The bioluminescent worms were observed after sunset around the new moon day in July and October 2020 and in July to October 2021 in Nagasaki Prefecture, Japan. Molecular phylogenetic analysis based on two mitochondrial and one nuclear gene sequence showed that the worms were closely related to Odontosyllis australiensis, but the partial 16S rRNA gene sequences differed by 2% between those of the Japanese and Australian material. Because only epitokes, i.e. morphologically modified sexually mature worms, were collected, further studies on morphological characters of atokes would be required in the future. We therefore tentatively refer to them as Odontosyllis cf. australiensis. Molecular phylogenetic analysis also showed that known bioluminescent Odontosyllis species belong to various lineages.

Case Report: Whole Exome Sequencing Identifies Compound Heterozygous Variants in TSFM Gene Causing Juvenile Hypertrophic Cardiomyopathy

We report a case of hypertrophic cardiomyopathy and lactic acidosis in a 3-year-old female. Cardiac and skeletal muscles biopsies exhibited mitochondrial hyperplasia with decreased complex IV activity. Whole exome sequencing identified compound heterozygous variants, p.Arg333Trp and p.Val119Leu, in TSFM, a nuclear gene that encodes a mitochondrial translation elongation factor, resulting in impaired oxidative phosphorylation and juvenile hypertrophic cardiomyopathy.

Mitochondrial Retinopathies

The retina is an exquisite target for defects of oxidative phosphorylation (OXPHOS) associated with mitochondrial impairment. Retinal involvement occurs in two ways, retinal dystrophy (retinitis pigmentosa) and subacute or chronic optic atrophy, which are the most common clinical entities. Both can present as isolated or virtually exclusive conditions, or as part of more complex, frequently multisystem syndromes. In most cases, mutations of mtDNA have been found in association with mitochondrial retinopathy. The main genetic abnormalities of mtDNA include mutations associated with neurogenic muscle weakness, ataxia and retinitis pigmentosa (NARP) sometimes with earlier onset and increased severity (maternally inherited Leigh syndrome, MILS), single large-scale deletions determining Kearns–Sayre syndrome (KSS, of which retinal dystrophy is a cardinal symptom), and mutations, particularly in mtDNA-encoded ND genes, associated with Leber hereditary optic neuropathy (LHON). However, mutations in nuclear genes can also cause mitochondrial retinopathy, including autosomal recessive phenocopies of LHON, and slowly progressive optic atrophy caused by dominant or, more rarely, recessive, mutations in the fusion/mitochondrial shaping protein OPA1, encoded by a nuclear gene on chromosome 3q29.

A Foliar Pigment-Based Bioassay for Interrogating Chloroplast Signalling Reveals that Chlorophyll Biosynthesis Requires Carotenoid Isomerisation.

Background: Plastid-derived metabolites can signal control over nuclear gene expression, chloroplast biogenesis, and chlorophyll biosynthesis. Norflurazon (NFZ) inhibition of carotenoid biosynthesis in seedlings can elicit a protoporphyrin retrograde signal that controls chlorophyll and chloroplast biogenesis. Recent evidence reveals that plastid development can be regulated by carotenoid cleavage products called apocarotenoids. The key steps in carotenoid biosynthesis and catabolism that generate apocarotenoid signalling metabolites in foliar tissues remains to be elucidated. Here, we established an Arabidopsis foliar pigment-based bioassay using detached rosettes to differentiate plastid signalling processes in young expanding leaves containing dividing cells with active chloroplast biogenesis, from fully expanded leaves containing mature chloroplasts. Results: We demonstrate that environmental (extended darkness and cold exposure) as well as chemical (norflurazon; NFZ) inhibition of carotenoid biosynthesis can reduce chlorophyll levels in young, but not older leaves following a 24 h of rosette treatment. Mutants that disrupted xanthophyll accumulation, phytohormone biosynthesis (abscisic acid and strigolactone), or enzymatic carotenoid cleavage, did not alter chlorophyll levels in young or old leaves. Perturbations in acyclic cis-carotene biosynthesis revealed that disruption of CAROTENOID ISOMERASE (CRTISO), but not ZETA-CAROTENE ISOMERASE (Z-ISO) activity, reduced chlorophyll levels in young but not older leaves of plants growing under a long photoperiod. NFZ-induced inhibition of PHYTOENE DESATURASE (PDS) activity triggered phytoene accumulation more so in younger relative to older leaves from both WT and the crtiso mutant, indicating a continued substrate supply from the methylerythritol 4-phosphate (MEP) pathway for carotenogenesis. NFZ treatment of WT and crtiso mutant rosettes reveal similar, additive, and opposite effects on individual pigment accumulation.Conclusion: The Arabidopsis foliar pigment-based bioassay was used to differentiate signalling events elicited by environmental, chemical, genetic, and combinations thereof, that control chlorophyll biosynthesis. Genetic perturbations that impaired xanthophyll biosynthesis and/or carotenoid catabolism did not affect chlorophyll biosynthesis. The lack of CAROTENOID ISOMERISATION generated a signal that rate-limited chlorophyll accumulation, but not phytoene biosynthesis in young Arabidopsis leaves exposed to a long photoperiod. Findings generated using this new foliar pigment bioassay implicate that carotenoid isomerisation and NFZ elicit different signalling pathways to control chlorophyll homeostasis in young emerging leaves.

Reconstruction of intrageneric relationships within the Indo-West Pacific littoral crab genus Metopograpsus (Decapoda, Brachyura, Grapsidae): an alternative speciation order according to a 28S rDNA molecular phylogeny

The genus Metopograpsus H. Milne Edwards, 1853 is widespread throughout the Indo-West Pacific and currently consists of seven species that can only be separated by minor morphological differences. Therefore, it represents a good example for the usefulness of genetic analyses for identification and classification. In order to obtain phylogenetic information at both lower and higher evolutionary levels, it is best to use a combination of mitochondrial and nuclear molecular markers. Here we present for the first time a molecular phylogeny based on a relative long fragment of the 28S rRNA nuclear gene for the genus Metopograpsus, after application of newly developed primers. Our data suggest an alternative intrageneric speciation order, with M. thukuhar and M. cannicci holding a basal position and a monophyletic grouping of M. frontalis, M. oceanicus and M. quadridentatus, which differs from prior phylogenetic reconstructions. Previously recognized intraspecific phylogeographic patterns in M. latifrons and M. quadridentatus could not be confirmed, due to limited variability of this conserved nuclear gene and due to an incomplete geographic coverage of the corresponding species. In contrast, the previously indicated phylogenetic subdivision within the formerly widespread species M. thukuhar, which led to the recent description of M. cannicci, is here supported.

Four new species of troglomorphic Coecobrya Yosii, 1956 (Collembola, Entomobryidae) from Thailand based on morphological and molecular evidence, with an updated key of Thai troglomorphic species

Four new species of troglomorphic Coecobrya Yosii, 1956 are described from caves located in the central and northeastern regions of Thailand. Coecobrya whittenisp. nov. and C. troglobiasp. nov. are from Khon Kaen province, C. ellisisp. nov. is from Phetchabun province and C. phitsanulokensissp. nov. is from Phitsanulok province. They all exhibit remarkable troglobitic characters i.e. elongated antennae, legs and furca, slender claw complex and large body size. Coecobrya whittenisp. nov. is similar to C. troglobiasp. nov. and they were found a distance of only 3.4 km from each other. However, they are mainly different in the number of An mac on dorsal head and number of chaetae of Th. II. Likewise, C. ellisisp. nov. is similar to C. phitsanulokensissp. nov.. However, they differ in the number of An mac on the dorsal head, the number of central mac on Abd. II, central mac on Abd. IV, lateral mac on Abd. IV and the number of inner teeth of the claw. Moreover, C. ellisisp. nov. has orange pigment dots on the body, a unique character, considering that all other troglomorphic Coecobrya species in Thailand are devoid of pigmentation. The results of the molecular approach based on two partial mitochondrial markers (COI and 16S rDNA) and a nuclear gene fragment (28S rDNA) supported the results of morphological species discrimination in separating the four nominal populations as valid species. An updated dichotomous key of Thai troglomorphic Coecobrya species is also given.

A new and very spiny lizard (Gymnophthalmidae: Echinosaura) from the Andes in northwestern Ecuador

We describe a new species of Neotropical spiny-lizard of the genus Echinosaura from the Imbabura and Carchi Provinces on the western slopes of the Andes in northwestern Ecuador. The new species mostly resembles E. horrida. However, it can be distinguished from all congeners by having keeled enlarged dorsal scales forming a paired vertebral row, two paravertebral series of short oblique rows of projecting scales, and a pair of spine-like scales on temporal and nuchal regions. We also provide a detailed description of the osteology of the skull and pectoral girdle of the new species and present a phylogenetic hypothesis for Echinosaura based on three mitochondrial genes (12S, 16S, ND4) and one nuclear gene (c-mos).