A Study of Small Intestinal Epigenomic Changes Induced by Royal Jelly.

This study explores the impact of royal jelly (RJ) on small intestinal epigenomic changes. RJ, produced by honeybees, is known for its effects on metabolic diseases. The hypothesis is that RJ induces epigenomic modifications in small intestinal epithelial cells, affecting gene expression and contributing to metabolic health. Male db/m and db/db mice were used to examine RJ's effects through mRNA sequencing and CUT&Tag methods. This study focused on histone modifications and gene expression changes, with statistical significance set at p < 0.05. RJ administration improved insulin sensitivity and lipid metabolism without affecting body weight. GO and KEGG pathway analyses showed significant enrichment in metabolic processes, cellular components, and molecular functions. RJ altered histone modifications, increasing H3K27me3 and decreasing H3K23Ac in genes associated with the G2M checkpoint. These genes, including Smc2, Mcm3, Ccnd1, Rasal2, Mcm6, and Mad2l1, are linked to cancer progression and metabolic regulation. RJ induces beneficial epigenomic changes in small intestinal epithelial cells, improving metabolic health and reducing cancer-associated gene expression. These findings highlight RJ's potential as a therapeutic agent for metabolic disorders. Further research is needed to fully understand the mechanisms behind these effects and their implications for human health.

Cost-efficient PCR based DNA barcoding of marine invertebrate specimens with NovaSeq amplicon sequencing.

BACKGROUND: The marine environment harbors high biodiversity; however, it is poorly understood. Nucleotide sequence data of all marine organisms should be accumulated before natural and/or anthropogenic environmental changes jeopardize the marine environment. In this study, we report a cost-effective and easy DNA barcoding method. This method can be readily adopted without using library preparation kits. It includes multiplex PCR of short targets, indexing PCR, and outsourcing to a sequencing service using the NovaSeq system. METHODS AND RESULTS: We targeted four mitochondrial genes [cytochrome c oxidase subunit I (COI), COIII, 16S rRNA (16S), and 12S rRNA (12S)] and three nuclear genes [18S rRNA (18S), 28S rRNA (28S), internal transcribed spacer 2 (ITS2)] in 95 marine invertebrate specimens, which were primarily annelids. The primers, including adapters and indices for NovaSeq sequencing, were newly designed. Two PCR runs were conducted. The 1st PCR amplified specific loci with universal primers and the 2nd added sequencing adapters and indices to the 1st PCR products. The gene sequences obtained from the FASTQ files were subjected to BLAST search and phylogenetic analyses. One run using 95 specimens yielded sequences averaging 2816 bp per specimen for a total length of six loci. Nuclear genes were more successfully assembled compared with mitochondrial genes. A weak but significantly negative correlation was observed between the average length of each locus and success rate of the assembly. Some of the sequences were almost identical to the sequences obtained from specimens collected far from Japan, indicating the presence of potentially invasive species identified for the first time. CONCLUSIONS: We obtained gene sequences efficiently using next-generation sequencing rather than Sanger sequencing. Although this method requires further optimization to increase the success rate for some loci, it is used as a first step to select specimens for further analyses by determining the specific loci of the targets.

A multi-omics approach to overeating and inactivity-induced muscle atrophy in db/db mice.

BACKGROUND: Overeating and inactivity are associated with type 2 diabetes. This study aimed to investigate its pathological basis using integrated omics and db/db/mice, a model representing this condition. METHODS: The study involved housing 8-week-old db/m and db/db mice for 8 weeks. Various analyses were conducted, including gene expression in skeletal muscle and small intestine using next-generation sequencing; cytokine arrays of serum; assessment of metabolites in skeletal muscle, stool, and serum; and analysis of the gut microbiota. Histone modifications in small intestinal epithelial cells were profiled using CUT&Tag. RESULTS: Compared with db/m mice, db/db mice had 22.4% lower grip strength and approximately five times the visceral fat weight (P < 0.0001). Serum cytokine arrays showed a 2.8-fold relative concentration of VEGF-A in db/db mice (P < 0.0001) and lower concentrations of several other cytokines. mRNA sequencing revealed downregulation of Myh expression in skeletal muscle, upregulation of lipid and glucose transporters, and downregulation of amino acid transporters in the small intestine of db/db/mice. The concentrations of saturated fatty acids in skeletal muscle were significantly higher, and the levels of essential amino acids were lower in db/db mice. Analysis of the gut microbiota, 16S rRNA sequencing, revealed lower levels of the phylum Bacteroidetes (59.7% vs. 44.9%) and higher levels of the phylum Firmicutes (20.9% vs. 31.4%) in db/db mice (P = 0.003). The integrated signal of histone modifications of lipid and glucose transporters was higher, while the integrated signal of histone modifications of amino acid transporters was lower in the db/db mice. CONCLUSIONS: The multi-omics approach provided insights into the epigenomic alterations in the small intestine, suggesting their involvement in the pathogenesis of inactivity-induced muscle atrophy in obese mice.

Mechanical Properties of Twisted Cellulose Nanofiber-Reinforced Silk Yarns.

Silk has recently attracted considerable interest owing to its versatile properties as a natural fiber, especially in the medical sector. However, the mechanical properties of silk limit its potential applications. In our earlier work, the mechanical performance of silk filaments was enhanced owing to the insertion of cellulose nanofibers (CNFs). Nevertheless, silk filaments must be assembled and twisted to form a continuous yarn. In this study, the mechanical properties of CNF-reinforced silk yarns were evaluated to determine the optimal yarn structure. The evolution of the Young's modulus, ultimate tensile strength, toughness, and elongation at break was assessed as a function of the twist level in comparison with regular silk. The results demonstrated that the most favorable compromise of the mechanical properties was obtained at 1000 twists per meter.

Protocol of efficacy of bifidobacteria intake on gastrointestinal symptoms in symptomatic type 2 diabetes mellitus patients in abdominis: An open-label, randomized controlled trial (Binary STAR study).

BACKGROUND: This randomized, parallel-group study aims to investigate the effects of the probiotic Bifidobacterium bifidum G9-1 (BBG9-1) on the symptoms of diarrhea or constipation in patients with type 2 diabetes mellitus (T2DM). METHODS: This study will examine 100 patients with T2DM who suffering from symptoms of diarrhea or constipation. Eligible patients will be randomly assigned 1:1 to two groups (group A, BBG9-1 group; group B, control group), after the baseline examination. Patients assigned to group A will receive probiotic BBG9-1 oral administration along with their current treatment for 12 weeks, and patients assigned to group B will continue the current treatment for 12 weeks without probiotic BBG9-1 oral administration. Subsequently, examinations similar to the baseline examinations will be performed. The primary endpoint will be a change in the Gastrointestinal Symptom Rating Scale (GSRS) total score from baseline to week 12. Secondary endpoints will include the following: change and percent change in parameters such as GSRS subdomain scores, fecal properties/Bristol stool form scale, defecation frequency, biomarkers, gut microbiota, and macronutrients and factors that affect GSRS total score or constipation/diarrhea subdomain scores from baseline to week 12. DISCUSSION: The results of this study will clarify the utility of probiotic BBG9-1 in the treatment of diarrhea or constipation in patients with T2DM. TRIAL REGISTRATION: jRCTs051220127.

Buried treasure in a public repository: Mining mitochondrial genes of 32 annelid species from sequence reads deposited in the Sequence Read Archive (SRA).

Background: The mitochondrial genomes (mitogenomes) of metazoans generally include the same set of protein-coding genes, which ensures the homology of mitochondrial genes between species. The mitochondrial genes are often used as reference data for species identification based on genetic data (DNA barcoding). The need for such reference data has been increasing due to the application of environmental DNA (eDNA) analysis for environmental assessments. Recently, the number of publicly available sequence reads obtained with next-generation sequencing (NGS) has been increasing in the public database (the NCBI Sequence Read Archive, SRA). Such freely available NGS reads would be promising sources for assembling mitochondrial protein-coding genes (mPCGs) of organisms whose mitochondrial genes are not available in GenBank. The present study aimed to assemble annelid mPCGs from raw data deposited in the SRA. Methods: The recent progress in the classification of Annelida was briefly introduced. In the present study, the mPCGs of 32 annelid species of 19 families in clitellates and allies in Sedentaria (echiurans and polychaetes) were newly assembled from the reads deposited in the SRA. Assembly was performed with a recently published pipeline mitoRNA, which includes cycles of Bowtie2 mapping and Trinity assembly. Assembled mPCGs were deposited in GenBank as Third Party Data (TPA) data. A phylogenetic tree was reconstructed with maximum likelihood (ML) analysis, together with other mPCGs deposited in GenBank. Results and Discussion: mPCG assembly was largely successful except for Travisia forbesii; only four genes were detected from the assembled contigs of the species probably due to the reads targeting its parasite. Most genes were largely successfully obtained, whereas atp8, nad2, and nad4l were only successful in 22-24 species. The high nucleotide substitution rates of these genes might be relevant to the failure in the assembly although nad6, which showed a similarly high substitution rate, was successfully assembled. Although the phylogenetic positions of several lineages were not resolved in the present study, the phylogenetic relationships of some polychaetes and leeches that were not inferred by transcriptomes were well resolved probably due to a more dense taxon sampling than previous phylogenetic analyses based on transcriptomes. Although NGS data are generally better sources for resolving phylogenetic relationships of both higher and lower classifications, there are ensuring needs for specific loci of the mitochondrial genes for analyses that do not require high resolutions, such as DNA barcoding, eDNA, and phylogenetic analysis among lower taxa. Assembly from publicly available NGS reads would help design specific primers for the mitochondrial gene sequences of species, whose mitochondrial genes are hard to amplify by Sanger sequencing using universal primers.

Host-Shift Speciation Proceeded with Gene Flow in Algae Covering Shells.

AbstractHost shifts represent the advancement of a novel niche and often lead to speciation in symbionts. However, its mechanisms are not well understood. Here, we focused on the alga Pseudocladophora conchopheria growing on the shells of intertidal snails. Previous surveys have shown that the alga has host specificity-only attaching to the shell of Lunella correensis-but we discovered that the alga attaches to the shells of multiple sympatric snails. A genome-wide single-nucleotide polymorphism analysis (MIG-seq) was performed to determine whether host-associated speciation occurred in the algae. As a result, there was no gene flow or limited gene flow among the algae from different hosts, and some algae were genetically differentiated among hosts. In addition, the demographic estimate revealed that speciation with gene flow occurred between the algae from different hosts. Therefore, these results support the idea that host-shift speciation gradually proceeded with gene flow in the algae, providing insight into the early evolution of host shifts.

Populations of the Intertidal Crab Macrophthalmus banzai are Not Grouped by Latitude: Taiwan Population is Genetically Closer to the Populations in the Japanese Mainland Than the Ryukyu Islands.

Macrophthalmus banzai is an intertidal crab species of Macrophthalmidae inhabiting muddy tidal flats in the northwestern Pacific. A previous study on the population genetic structure of Japanese M. banzai based on the mitochondrial COI gene sequences revealed the presence of two genetically distinguished groups, i.e., the northern group (Honshu, Shikoku, and Kyushu Islands) and the southern group (the Ryukyu Islands). In the present study, we newly determined the COI gene sequences of M. banzai collected from Taiwan and conducted population genetic analyses of these sequences together with Japanese sequences obtained from GenBank to reveal the genetic relationship of this species between Japan and Taiwan. The SAMOVA and pairwise ΦST analysis showed that the Taiwan population is more closely related to the northern group than the southern group. This indicates that the populations of M. banzai are not genetically differentiated by latitude but probably by the pathway of the Kuroshio Current, resulting in the isolation of the population in the Ryukyu Islands. Such a pattern is consistent with the population genetic structure of the fiddler crab Tubuca arcuata shown by a previous study, whereas the pattern differs from those of other intertidal invertebrates. The difference in the larval durations may have influenced the difference in population genetic structures among species. The present study provides a further case of the genetic structure of intertidal species that are not simply regulated by geographic distances.

Molecular and Morphological Assessment of Juvenile and Adult Forms in the Giant Worm Eunice Cf. Aphroditois (Annelida: Eunicidae) and Its Phylogenetic Position in the Family.

Eunice aphroditois (Pallas, 1788) is a large polychaete worm (up to 3 m in length) and the type species of the genus. In Japan, a similar but potentially different species, Eunice cf. aphroditois, is distributed mainly in the rocky shores of the temperate and warm Pacific coasts. Juveniles and adults were suggested to be distinguished by their body color. The juvenile form was previously regarded as distinct species, Eunice flavopicta Izuka, 1912 and Eunice ovalifera Fauvel, 1936, although they are now considered synonymous with E. aphroditois. In this study, we revisited the validity of the present taxonomy based on morphological observations including SEM and microCT, and three molecular markers (cytochrome c oxidase subunit I [COI], 16S rRNA, and histone H3 genes) and investigated the phylogenetic position of E. cf. aphroditois in the family Eunicidae using the combined dataset of three genes (COI + 16S rRNA + 18S rRNA). The adult and juvenile forms were different in body size, color, the distribution of the branchiae and subacicular hooks, and maxillae shape, but not in other characteristics. One individual showed an intermediate body color between the two forms. The adult and juvenile forms shared major haplotypes and the maximum K2P genetic distance of COI was 1.7%, which can be considered within intraspecific variation. In the phylogenetic tree based on the combined gene dataset, E. cf. aphroditois was closely related to Eunice roussaei Quatrefages, 1866 and Eunice cf. violaceomaculata Ehlers, 1887, which are large species from the Mediterranean Sea and the Caribbean Sea, respectively.

First report of the mitogenome of the invasive reef-building polychaete Ficopomatus enigmaticus (Annelida: Serpulidae) and a cryptic lineage from the Japanese Archipelago.

BACKGROUND: The mitochondrial genomes (mitogenomes) of the family Serpulidae are characterized by a high nucleotide sequence divergence and a significant number of gene order rearrangements compared with other families within the phylum Annelida. However, only two of 50 genera of serpulids have mitogenomes already sequenced. In this study, we report the first sequencing and assembly of the complete mitogenome of Ficopomatus, thus providing further knowledge on mitochondrial gene sequences of Serpulidae. METHODS AND RESULTS: A mitogenome of the invasive reef-building polychaete Ficopomatus enigmaticus was amplified by long PCR and sequenced using the Illumina MiSeq System. It comprised 15,853 bp and consisted of 12 protein-coding genes (atp8 was not found), 23 tRNA, and two rRNA genes. The AT and GC skew values were infrequent when compared to annelid mitogenomes but similar to other serpulids sequenced to date (i.e., Spirobranchus and Hydroides). The mitochondrial gene order of F. enigmaticus was highly rearranged compared to other serpulids. To amplify 16S rRNA gene sequences, we developed a 16S rRNA primer set by modifying the universal primer set 16SarL/16SbrH. We detected the 16S rRNA sequence of F. enigmaticus deposited in GenBank erroneously characterized as of serpulid origin. We reported for the first time the presence of two lineages of F. enigmaticus in Japan, which have already been identified in California, Australia, and the Mediterranean. CONCLUSIONS: The first mitochondrial genome of F. enigmaticus showed a unique gene order rearrangement, corroborating the remarkable diversity in the previously reported mitogenomes of other serpulid species. The presence of the two lineages of F. enigmaticus identified for the first time in Japan represents another case of cryptic invasion. The first 16S rRNA gene sequences of F. enigmaticus obtained in the present study can be used as reference sequences in future DNA metabarcoding studies.

A new family of anti-perovskite oxyhydrides with tetrahedral GaO4 polyanions.

New solid compounds A3-xGaO4H1-y (A = Sr, Ba; x ∼0.15, y ∼0.3), which are the first oxyhydrides containing gallium ions, have been synthesized by high-pressure synthesis. Powder X-ray and neutron diffraction experiments revealed that the series adopts an anti-perovskite structure consisting of hydride-anion-centered HA6 octahedra with tetrahedral GaO4 polyanions, wherein the A- and H-sites show partial defect. Formation energy calculations from the raw materials support that stoichiometric Ba3GaO4H is thermodynamically stable with a wide band gap. Annealing the A = Ba powder under flowing Ar and O2 gas suggests topochemical H- desorption and O2-/H- exchange reactions, respectively.

Effects of Royal Jelly on Gut Dysbiosis and NAFLD in db/db Mice.

Royal jelly (RJ) is a naturally occurring substance synthesized by honeybees and has various health benefits. Herein, we focused on the medium-chain fatty acids (MCFAs) unique to RJ and evaluated their therapeutic efficacy in treating non-alcoholic fatty liver disease (NAFLD). We examined db/m mice that were exclusively fed a normal diet, db/db mice exclusively fed a normal diet, and db/db mice fed varying RJ quantities (0.2, 1, and 5%). RJ improved NAFLD activity scores and decreased gene expression related to fatty acid metabolism, fibrosis, and inflammation in the liver. RJ regulated innate immunity-related inflammatory responses in the small intestine and decreased the expression of genes associated with inflammation and nutrient absorption transporters. RJ increased the number of operational taxonomic units, the abundance of Bacteroides, and seven taxa, including bacteria that produce short-chain fatty acids. RJ increased the concentrations of RJ-related MCFAs (10-hidroxy-2-decenoic acid, 10-hydroxydecanoic acid, 2-decenedioic acid, and sebacic acid) in the serum and liver. These RJ-related MCFAs decreased saturated fatty acid deposition in HepG2 cells and decreased the gene expression associated with fibrosis and fatty acid metabolism. RJ and RJ-related MCFAs improved dysbiosis and regulated the expression of inflammation-, fibrosis-, and nutrient absorption transporter-related genes, thereby preventing NAFLD.

Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes.

Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.

Association between uric acid levels and incidence of type 2 diabetes: Population-based Panasonic cohort study 11.

AIMS: This cohort study intended to assess the association between serum uric acid levels and incidence of type 2 diabetes in a Japanese population. METHODS: Individuals who participated a medical health checkup program carried out by Panasonic Corporation from 2008 to 2018 were included in this study. A total of 122,123 participants (92,718 men and 29,405 women) were included. During the research period, 6,386 participants developed type 2 diabetes. RESULTS: Multivariate analysis showed that, in men, serum uric acid levels were not significantly associated with incident type 2 diabetes after adjusting for diabetes risk factors. However, in women, the risk of type 2 diabetes incidence was higher in the group with uric acid levels 5.1-6.0 mg/dL (hazard ratio, 2.01 [95 % confidence interval: 1.26-3.42]) or > 6.1 mg/dL (hazard ratio, 1.85 [95 % confidence interval: 1.11-3.22]) than in the group with uric acid levels ≤ 3 mg/dL. Furthermore, in women, the area under the receiver operating characteristic curve and optimized cut-off values of uric acid for the incidence of type 2 diabetes at 10 years were 0.720 and 4.8 mg/dL, respectively. CONCLUSIONS: Serum uric acid levels were associated with incident type 2 diabetes in Japanese women but not in Japanese men.

Impact of Na Concentration on the Phase Transition Behavior and H- Conductivities in the Ba-Li-Na-H-O Oxyhydride System.

K2 NiF4 -type Ba-Li oxyhydride (BLHO) transitions to a so-called hydride superionic conductor, exhibiting a high and essentially temperature-independent hydride ion (H- ) conductivity over 0.01 S cm-1 through the disordering of H- vacancies above 300 °C. In this study, a Ba-Li-Na-H-O oxyhydride system synthesized in which lithium is partially substituted with sodium in BLHO and investigated the effects of Na content on the phase transition behavior and the conductivity. Structural refinements and differential scanning calorimetry experiments confirmed a lowering trend in the phase transition temperatures and decreasing enthalpy changes for the transition with increasing Na content. Substitution of not <40% of Li with Na lowered the degree of ordered vacancies at the H- sites at room temperature and improved conductivities by more than two orders of magnitude in the low-temperature region (T < 300 °C) before the phase transition. These findings clearly show that introducing Na into the lattice effectively stabilizes the high-conductive phase of BLHO.

Dyslipidemia and 10-year diabetes incidence in Japanese people: Population-based Panasonic cohort study 9.

Low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and LDL/HDL ratio have been associated with new-onset diabetes; however, their cut-off levels have not been determined. We clarified the association between dyslipidemia and the incidence of diabetes. People who underwent a health checkup under a program conducted by Panasonic Corporation from 2008 to 2018 were included. In total, 87,570 participants were included, of whom 5,110 developed type 2 diabetes. Cox regression analyses and time-dependent receiver operating characteristic (ROC) curves were used to evaluate the association between LDL cholesterol, HDL cholesterol, or LDL/HDL ratio and incident diabetes and to identify the cut-off values for incident diabetes. Multivariate analysis showed that LDL cholesterol, HDL cholesterol, and LDL/HDL ratio were significantly associated with the risk of incident type 2 diabetes. Further, the area under the ROC curve and optimized cut-off values for LDL cholesterol, HDL cholesterol, and LDL/HDL ratio for incident type 2 diabetes at 10 years were 0.613 and 124 mg/dl, 0.640 and 54 mg/dl, and 0.662 and 2.4 mg/dl, respectively. The LDL/HDL ratio with a cut-off value of 2.4 was a better predictor of incident diabetes within 10 years than LDL and HDL cholesterol.

Impact of Eating Speed on Muscle Mass in Older Patients With Type 2 Diabetes: A Prospective Study of KAMOGAWA-DM Cohort.

Background and Aims: Maintenance of muscle mass is important for sarcopenia prevention. However, the effect of eating speed, especially fast, normal, or slow speed, on muscle mass changes remains unclear. Therefore, the purpose of this prospective study was to investigate the effect of eating speed on muscle mass changes in patients with type 2 diabetes (T2DM). Methods: This study included 284 patients with T2DM. Based on a self-reported questionnaire, participants were classified into three groups: fast-, normal-, and slow-speed eating. Muscle mass was assessed using a multifrequency impedance body composition analyzer, and skeletal muscle mass (SMI) decrease (kg/m2/year) was defined as [baseline SMI (kg/m2)-follow-up SMI (kg/m2)] ÷ follow-up duration (year). The rate of SMI decrease (%) was defined as [SMI decrease (kg/m2/year) ÷ baseline SMI (kg/m2)] × 100. Results: The proportions of patients with fast-, normal-, and slow-speed eating were, respectively, 50.5%, 42.9%, and 6.6% among those aged <65 years and 40.4%, 38.3%, and 21.3% among those aged ≥65 years. In patients aged ≥65 years, the rate of SMI decrease in the normal (0.85 [95% confidence interval, CI: -0.66 to 2.35]) and slow (0.93 [95% CI -0.61 to 2.46]) speed eating groups was higher than that in the fast speed eating group (-1.08 [95% CI -2.52 to 0.36]). On the contrary, there was no difference in the rate of SMI decrease among the groups in patients aged <65 years. Compared with slow speed eating, the adjusted odds ratios of incident muscle loss [defined as rate of SMI decrease (%) ≥0.5%] due to fast- and normal-speed eating were 0.42 (95% CI 0.18 to 0.98) and 0.82 (95% CI 0.36 to 2.03), respectively. Conclusion: Slow-speed eating is associated with a higher risk of muscle mass loss in older patients with T2DM.

Sequential Pressure-Induced B1-B2 Transitions in the Anion-Ordered Oxyhydride Ba2YHO3.

We present a detailed experimental and computational investigation of the influence of pressure on the mixed-anion oxyhydride phase Ba2YHO3, which has recently been shown to support hydride conductivity. The unique feature of this layered perovskite is that the oxide and hydride anions are segregated into distinct regions of the unit cell, in contrast to the disordered arrangement in closely related Ba2ScHO3. Density functional theory (DFT) calculations reveal that the application of pressure drives two sequential B1-B2 transitions in the interlayer regions from rock salt to CsCl-type ordering, one in the hydride-rich layer at approximately 10 GPa and another in the oxide-rich layer at 35-40 GPa. To verify the theoretical predictions, we experimentally observe the structural transition at 10 GPa using high-pressure X-ray diffraction (XRD), but the details of the structure cannot be solved due to peak broadening of the XRD patterns. We use DFT to explore the structural impact of pressure on the atomic scale and show how the pressure-dependent properties can be understood in terms of simple electrostatic engineering.

First mitochondrial genomes of Capitellidae and Opheliidae (Annelida) and their phylogenetic placement.

The complete mitochondrial genomes of Notomastus sp. (15,776 bp) (Annelida: Capitellidae) and Armandia sp. (18,538 bp) (Annelida: Opheliidae) were assembled for the first time. A group II intron (303 bp) was found in cox1 of Notomastus sp. A phylogenetic analysis revealed that Notomastus sp. and Armandia sp. were monophyletic, and this clade was clustered with echiurans, although the possibility of the effect of long-branch attraction should be considered.

Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species.

Mitogenomes are useful for inferring phylogenetic relationships between organisms. Although the mitogenomes of Annelida, one of the most morphologically and ecologically diverse metazoan groups have been well sequenced, those of several families remain unexamined. This study determined the first mitogenome from the family Travisiidae (Travisia sanrikuensis), analyzed its mitogenomic features, and reconstructed a phylogeny of Sedentaria. The monophyly of the Terebellida + Arenicolida + Travisiidae clade is supported by molecular phylogenetic analysis. The placement of Travisiidae is unclear because of the lack of mitogenomes from closely related lineages. An unexpected intron appeared within the cox1 gene of T. sanrikuensis and in the same positions of five undescribed Travisia spp. Although the introns are shorter (790-1386 bp) than other group II introns, they can be considered degenerate group II introns due to type II intron maturase open reading frames, found in two of the examined species, and motifs characteristic of group II introns. This is likely the first known case in metazoans where mitochondrial group II introns obtained by a common ancestor are conserved in several descendants. Insufficient evolutionary time for intron loss in Travisiidae, or undetermined mechanisms may have helped maintain the degenerate introns.