The complete mitochondrial genome of a ground beetle Synuchus nitidus (Carabidae: Harpalinae: Sphodrini) from South Korea.

The ground beetle Synuchus nitidus (Motschulsky, 1861) (Carabidae: Harpalinae: Sphodrini) is one of the most common species in the forests of South Korea, which has the potential to be utilized as an environmental indicator. Here, we characterized the complete mitochondrial genome (mitogenome) of S. nitidus, which is the first in the harpaline tribe Sphodrini. Its genome is 16,392 bp in length and composed of 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and an A + T rich region. In addition, we reconstructed a maximum likelihood tree to elucidate the phylogenetic position of Sphodrini among the seven harpaline tribes using nucleotide sequences of the 13 PCGs. The ML tree supported a monophyletic clade of the subfamily Harpalinae and showed a close relationship between Sphodrini and Lebinii with a low bootstrap value. The complete mitogenome of S. nitidus could be helpful for molecular species identification and exploring phylogenetic relationships among carabids.

M(II) effect on encapsulation of guests into a series of M3L2 chiral cages: enantio-recognition.

Self-assembly of M(ClO4)2 (M2+ = Ni2+, Cu2+, and Zn2+) with (1S,1'S,1''S,2R,2'R,2''R)-(benzenetricarbonyltris(azanediyl))tris(2,3-dihydro-1H-indene-2,1-diyl) trinicotinate (s,r-L) and the corresponding enantiomer (r,s-L) as a pair of chiral tridentate donors gives rise to the chiral cage pairs [M3(s,r- and r,s-L)2](ClO4)6. For the two pairs of [(Me2CO)(H2O)@M3(r,-s and s,r-L)2](ClO4)6 (M2+ = Ni2+ and Zn2+), the inner cavity is occupied by both an acetone and a single water molecule, whereas for the copper(II) pair of [Me2CO@Cu3(r,s- and s,r-L)2](ClO4)6 under the same conditions, the cavity is filled by only one acetone molecule. Thus, the encapsulation of guest molecules into the cages during self-assembly shows significant metal(II) ion effects. These chiral cages are effective for the enantio-recognition of chiral (S)-2-butanol and (R)-2-butanol via the shifts of the electrochemical oxidation potentials obtained by the linear sweep voltammetry (LSV) technique, density functional theory (DFT) calculations, and the chiral 2-butanol adsorption in the single-crystal-to-single-crystal (SCSC) mode.

LC3B drives transcription-associated homologous recombination via direct interaction with R-loops.

Exploring the connection between ubiquitin-like modifiers (ULMs) and the DNA damage response (DDR), we employed several advanced DNA damage and repair assay techniques and identified a crucial role for LC3B. Notably, its RNA recognition motif (RRM) plays a pivotal role in the context of transcription-associated homologous recombination (HR) repair (TA-HRR), a particular subset of HRR pathways. Surprisingly, independent of autophagy flux, LC3B interacts directly with R-loops at DNA lesions within transcriptionally active sites via its RRM, promoting TA-HRR. Using native RNA immunoprecipitation (nRIP) coupled with high-throughput sequencing (nRIP-seq), we discovered that LC3B also directly interacts with the 3'UTR AU-rich elements (AREs) of BRCA1 via its RRM, influencing its stability. This suggests that LC3B regulates TA-HRR both proximal to and distal from DNA lesions. Data from our LC3B depletion experiments showed that LC3B knockdown disrupts end-resection for TA-HRR, redirecting it towards the non-homologous end joining (NHEJ) pathway and leading to chromosomal instability, as evidenced by alterations in sister chromatid exchange (SCE) and interchromosomal fusion (ICF). Thus, our findings unveil autophagy-independent functions of LC3B in DNA damage and repair pathways, highlighting its importance. This could reshape our understanding of TA-HRR and the interaction between autophagy and DDR.

The population genetic structure and phylogeographic dispersal of Nodularia breviconcha in the Korean Peninsula based on COI and 16S rRNA genes.

A freshwater mussel, Nodularia breviconcha (Mollusca: Bivalvia: Unionida) is endemic to Korean Peninsula. It has recently been taxonomically reexamined and elevated from a subspecies of N. douglasiae to an independent species. But population genetic studies for the species have rarely been conducted. To explore the population genetic structure of N. breviconcha, the nucleotide sequences of cytochrome oxidase subunit I(COI) and 16S rRNA genes from 135 N. breviconcha individuals, including 52 from this study and 83 from Choi et al. (2020). We found 23 COI and 11 16S rRNA genes haplotypes. Phylogeny, TCS network, Principal coordinates analysis, and spatial analysis of molecular variance performed with COI gene indicated that there are exist three different genetic lineages in the N. breviconcha populations: West lineage, Southwest lineage, and Southeast lineage. According to the time calibrated phylogeny, they are likely to be diverged during the late Miocene (8-6 Ma). Geographical distribution patterns of the three genetic lineages may be related to the formation of Taebaek and Sobaek-Noryeong mountain ranges in the Korean Peninsula occurred during the Miocene (30-10 Ma). The present results of this study will be helpful not only for the conservation, but also for the exploration of the population genetic structure of endemic freshwater mussels in the Korean Peninsula.

Transcriptome profiling for developmental stages Protaetia brevitarsis seulensis with focus on wing development and metamorphosis.

A white-spotted flower chafer Protaetia brevitarsis seulensis widely distributed in Asian countries is traditionally used in oriental medicine. This study explored gene expression abundance with respect to wing development and metamorphosis in P. b. seulensis based on the large-scale RNA-seq data. The transcriptome assembly consists of 23,551 high-quality transcripts which are approximately 96.7% covered. We found 265 wing development genes, 19 metamorphosis genes, and 1,314 candidates. Of the 1,598 genes, 1,594 are included exclusively in cluster 4 with similar gene co-expression patterns. The network centrality analyses showed that wing development- and metamorphosis-related genes have a high degree of betweenness centrality and are expressed most highly in eggs, moderately in pupa and adults, and lowest in larva. This study provides some meaningful clues for elucidating the genetic modulation mechanism of wing development and metamorphosis in P. b. seulensis.

Drug_SNSMiner: standard pharmacovigilance pipeline for detection of adverse drug reaction using SNS data.

As society continues to age, it is becoming increasingly important to monitor drug use in the elderly. Social media data have been used for monitoring adverse drug reactions. The aim of this study was to determine whether social network studies (SNS) are useful sources of drug side effects information. We propose a method for utilizing SNS data to plot the known side effects of geriatric drugs in a dosing map. We developed a lexicon of drug terms associated with side effects and mapped patterns from social media data. We confirmed that well-known side effects may be obtained by utilizing SNS data. Based on these results, we propose a pharmacovigilance pipeline that can be extended to unknown side effects. We propose the standard analysis pipeline Drug_SNSMiner for monitoring side effects using SNS data and evaluated it as a drug prescription platform for the elderly. We confirmed that side effects may be monitored from the consumer's perspective based on SNS data using only drug information. SNS data were deemed good sources of information to determine ADRs and obtain other complementary data. We established that these learning data are invaluable for AI requiring the acquisition of ADR posts on efficacious drugs.

Possible species discrimination of a blotched nerite Nerita albicilla with their distribution pattern and demographic history in the Indo-Pacific.

The blotched nerite Nerita albicilla (Linnaeus 1758) is distributed in intertidal areas of the Indo-Pacific. In South Korea, it has been found only in the southernmost region of Jeju Island so far. Owing to its limited distribution, it can be a promising intertidal species helpful for monitoring global climate change effects in the Korean Peninsula. We performed population genetic analyses based on 393 COI haplotypes from 697 N. albicilla, including 167 from this study and 530 from public databases. The results showed that there are two distinct genetic lineages in N. albicilla: PAIO (Palearctic, Australasia, Indo-Malay, and Oceania) and Afrotropic lineages. DNA barcoding gap analyses indicated that the two lineages could be differentiated into two different species: N. albicilla (PAIO) and N. originalis sp. nov. (Afrotropic) (3.96%). Additionally, it was revealed that their divergence time was ca. 5.96 Ma and dramatic diversification of COI haplotypes occurred during the late Pliocene and Pleistocene. The results of MDA, BSP, and neutrality test implied recent population size expansion, which was estimated to be ca. 250 Ka. Finally, we discussed whether the observation of N. originalis sp. nov. in South Korea is due to the northward migration through ocean currents caused by global warming or due to artificial activity through marine transportation.

Generation of multilineage liver organoids with luminal vasculature and bile ducts from human pluripotent stem cells via modulation of Notch signaling.

BACKGROUND: The generation of liver organoids recapitulating parenchymal and non-parenchymal cell interplay is essential for the precise in vitro modeling of liver diseases. Although different types of multilineage liver organoids (mLOs) have been generated from human pluripotent stem cells (hPSCs), the assembly and concurrent differentiation of multiple cell types in individual mLOs remain a major challenge. Particularly, most studies focused on the vascularization of mLOs in host tissue after transplantation in vivo. However, relatively little information is available on the in vitro formation of luminal vasculature in mLOs themselves. METHODS: The mLOs with luminal blood vessels and bile ducts were generated by assembling hepatic endoderm, hepatic stellate cell-like cells (HscLCs), and endothelial cells derived entirely from hPSCs using 96-well ultra-low attachment plates. We analyzed the effect of HscLC incorporation and Notch signaling modulation on the formation of both bile ducts and vasculature in mLOs using immunofluorescence staining, qRT-PCR, ELISA, and live-perfusion imaging. The potential use of the mLOs in fibrosis modeling was evaluated by histological and gene expression analyses after treatment with pro-fibrotic cytokines. RESULTS: We found that hPSC-derived HscLCs are crucial for generating functional microvasculature in mLOs. HscLC incorporation and subsequent vascularization substantially reduced apoptotic cell death and promoted the survival and growth of mLOs with microvessels. In particular, precise modulation of Notch signaling during a specific time window in organoid differentiation was critical for generating both bile ducts and vasculature. Live-cell imaging, a series of confocal scans, and electron microscopy demonstrated that blood vessels were well distributed inside mLOs and had perfusable lumens in vitro. In addition, exposure of mLOs to pro-fibrotic cytokines induced early fibrosis-associated events, including upregulation of genes associated with fibrotic induction and endothelial cell activation (i.e., collagen I, α-SMA, and ICAM) together with destruction of tissue architecture and organoid shrinkage. CONCLUSION: Our results demonstrate that mLOs can reproduce parenchymal and non-parenchymal cell interactions and suggest that their application can advance the precise modeling of liver diseases in vitro.

Associations between digital media use and lack of physical exercise among middle-school adolescents in Korea.

OBJECTIVES: The reported effects of digital media overuse on physical activity among adolescents are inconsistent. This study examined the association between hours of digital media use and lack of moderate-intensity physical exercise (mPE) according to the type of digital media. METHODS: This study included 1,837 middle school students from the iCURE (Internet user Cohort for Unbiased Recognition of gaming disorder in Early Adolescence) study conducted in Korea. Hours spent using digital media were measured by self-reported daily usage time for Internet games, messengers, social media, and watching game streaming on weekdays. Lack of mPE was defined as performing a minimum of 30 minutes at a time less than twice weekly. Multivariable logistic regression analysis stratified by sex was performed. RESULTS: Among male students, the group with the highest hours of using either Internet games or watching game streaming was more likely to lack mPE than each non-user group. In contrast, among male students, the group using either messengers or social media had a higher rate of mPE compared to each non-user group. Female students showed no association between hours spent using Internet games, messengers, social media, or watching game streaming and a lack of mPE. CONCLUSIONS: Among male middle school students in Korea, the excessive use of Internet games or watching game streaming was associated with a lack of mPE. Thus, guidelines should be established regarding adolescent use of internet games and watching game streaming.

In Vitro Generation of Luminal Vasculature in Liver Organoids: From Basic Vascular Biology to Vascularized Hepatic Organoids.

Liver organoids have gained much attention in recent years for their potential applications to liver disease modeling and pharmacologic drug screening. Liver organoids produced in vitro reflect some aspects of the in vivo physiological and pathological conditions of the liver. However, the generation of liver organoids with perfusable luminal vasculature remains a major challenge, hindering precise and effective modeling of liver diseases. Furthermore, vascularization is required for large organoids or assembloids to closely mimic the complexity of tissue architecture without cell death in the core region. A few studies have successfully generated liver organoids with endothelial cell networks, but most of these vascular networks produced luminal structures after being transplanted into tissues of host animals. Therefore, formation of luminal vasculature is an unmet need to overcome the limitation of liver organoids as an in vitro model investigating different acute and chronic liver diseases. Here, we provide an overview of the unique features of hepatic vasculature under pathophysiological conditions and summarize the biochemical and biophysical cues that drive vasculogenesis and angiogenesis in vitro. We also highlight recent progress in generating vascularized liver organoids in vitro and discuss potential strategies that may enable the generation of perfusable luminal vasculature in liver organoids.

Generation of cytochrome P450 enzyme-polymorphic human induced pluripotent stem cell lines with CYP2D6*10/CYP3A5*3C and CYP2D6*10/CYP2C19*2.

Cytochrome P450 (CYP) reaction phenotyping has become crucial for predicting drug reactions and side effects. Single nucleotide polymorphisms (SNPs) in CYP genes alter drug metabolism capacity and cause unexpected drug-related reactions. Here, we established two human induced pluripotent stem cell (hiPSC) lines with pharmacologically important SNPs in CYP2D6 in conjunction with CYP2C19 or CYP3A5 genes. These hiPSC lines can serve as valuable resources for expanding our understanding of the relationships between genotypes and drug reactions.

The first case report of thorn-induced Alternaria alternata infection of the hand in an immunocompetent host.

BACKGROUND: Fungal infection secondary to a penetrating plant thorn injury in upper extremities is infrequently reported especially in immunocompetent hosts. Alternaria is a dematicaceous hyphomycete, commonly found in decay and plant pathogens, and Alternaria alternata has been regarded as the most frequent species among more than 400 s of its species. This case is the first report of thorn-induced Alternaria alternata infection of the hand in an immunocompetent host. CASE PRESENTATION: A 47-year-old male patient was admitted to our institution with persistent pain and swelling of the right hand even after a prior surgical removal of a previous thorn injury. Upon impression of abscess, chronic extensor tenosynovitis, and septic arthritis at the 3rd metacarpophalangeal joint based on advanced imaging, the patient underwent surgical incision and drainage. Intraoperative culture, biopsy, and gene molecular sequencing results revealed fungal infection with Alternaria alternata. Postoperatively, the patient was treated with oral itraconazole (200 mg q 12 h) for nine consecutive months. CONCLUSIONS: We report the first case of chronic extensor tenosynovitis and septic arthritis of the hand with Alternaria alternata after a thorn injury in an immunocompetent host. Despite rare incidences of fungal extensor tenosynovitis and septic arthritis, the current case strongly suggests a careful examination of social history and surgical debridement along with a prolonged use of appropriate anti-fungal agents in thorn injuries.

Therapeutic correction of hemophilia A using 2D endothelial cells and multicellular 3D organoids derived from CRISPR/Cas9-engineered patient iPSCs.

The bleeding disorder hemophilia A (HA) is caused by a single-gene (F8) defect and its clinical symptom can be substantially improved by a small increase in the plasma coagulation factor VIII (FVIII) level. In this study, we used F8-defective human induced pluripotent stem cells from an HA patient (F8d-HA hiPSCs) and F8-corrected (F8c) HA hiPSCs produced by CRISPR/Cas9 genome engineering of F8d-HA hiPSCs. We obtained a highly enriched population of CD157+ cells from CRISPR/Cas9-edited F8c-HA hiPSCs. These cells exhibited multiple cellular and functional phenotypes of endothelial cells (ECs) with significant levels of FVIII activity, which was not observed in F8d-HA hiPSC-ECs. After transplantation, the engineered F8c-HA hiPSC-ECs dramatically changed bleeding episodes in HA animals and restored plasma FVIII activity. Notably, grafting a high dose of ECs substantially reduced the bleeding time during multiple consecutive bleeding challenges in HA mice, demonstrating a robust hemostatic effect (90% survival). Furthermore, the engrafted ECs survived more than 3 months in HA mice and reversed bleeding phenotypes against lethal wounding challenges. We also produced F8c-HA hiPSC-derived 3D liver organoids by assembling three different cell types in microwell devices and confirmed its therapeutic effect in HA animals. Our data demonstrate that the combination of genome-engineering and iPSC technologies represents a novel modality that allows autologous cell-mediated gene therapy for treating HA.

Secretome of Stem Cells: Roles of Extracellular Vesicles in Diseases, Stemness, Differentiation, and Reprogramming.

Increasing evidence suggests that stem cells or stem cell-derived cells may contribute to tissue repair, not only by replacing lost tissue but also by delivering complex sets of secretory molecules, called secretomes, into host injured tissues. In recent years, extracellular vesicles (EVs) have gained much attention for their diverse and important roles in a wide range of pathophysiological processes. EVs are released from most types of cells and mediates cell-cell communication by activating receptors on target cells or by being taken up by recipient cells. EVs, including microvesicles and exosomes, encapsulate and carry proteins, nucleic acids, and lipids in the lumen and on the cell surface. Thus, EV-mediated intercellular communication has been extensively studied across various biological processes. While a number of investigations has been conducted in different tissues and body fluids, the field lacks a systematic review on stem cell-derived EVs, especially regarding their roles in stemness and differentiation. Here, we provide an overview of the pathophysiological roles of EVs and summarize recent findings focusing on EVs released from various types of stem cells. We also highlight emerging evidence for the potential implication of EVs in self-renewal, differentiation, and reprograming and discuss the benefits and limitations in translational approaches.

Liolophura species discrimination with geographical distribution patterns and their divergence and expansion history on the northwestern Pacific coast.

The chiton Liolophura japonica (Lischke 1873) is distributed in intertidal areas of the northwestern Pacific. Using COI and 16S rRNA, we found three genetic lineages, suggesting separation into three different species. Population genetic analyses, the two distinct COI barcoding gaps albeit one barcoding gap in the 16S rRNA, and phylogenetic relationships with a congeneric species supported this finding. We described L. koreana, sp. nov. over ca. 33°24' N (JJ), and L. sinensis, sp. nov. around ca. 27°02'-28°00' N (ZJ). We confirmed that these can be morphologically distinguished by lateral and dorsal black spots on the tegmentum and the shape of spicules on the perinotum. We also discuss species divergence during the Plio-Pleistocene, demographic expansions following the last interglacial age in the Pleistocene, and augmentation of COI haplotype diversity during the Pleistocene. Our study sheds light on the potential for COI in examining marine invertebrate species discrimination and distribution in the northwestern Pacific.

Comparative evaluation of three different formulas for predicting the parturition date of German Shepherds following somatic cell nuclear transfer.

Several studies have reported methods to estimate the parturition date of dogs using ultrasonographic measurements. However, these prediction models were mainly determined using ultrasonographic measurements of naturally pregnant small- and medium-sized dogs, and no such studies have been performed using dogs carrying cloned fetuses produced via somatic cell nuclear transfer. The present study evaluated the abilities of three reference formulas (Luvoni and Grioni, Milani et al., and Groppetti et al.), all of which were developed using data from naturally occurring pregnancies, to accurately predict the parturition date in surrogates carrying cloned German Shepherd (GS) fetuses. All three formulas were based on the use of inner chorionic cavity diameter (ICC) measurements, obtained via ultrasonography. For evaluation, a total of 54 ICC measurements were collected from 14 pregnant bitches carrying cloned GS fetuses. We found that the clinical accuracy of the breed-specific Groppetti et al. formula was highest among those of the three formulas tested, with 87% and 100% of the estimated parturition dates (calculated based on the ICC measurements) being within 1 and 2 days, respectively, of the actual delivery date. By contrast, the Luvoni and Grioni formula showed relatively low accuracy, and the Milani et al. formula showed higher accuracy than that reported previously for natural pregnancies.

Validation of the Korean Version of the Psychosis Screener to Identify Patients With Psychosis.

OBJECTIVE: This study aimed to validate the Korean version of a short screening tool for psychosis as the first stage in finding undiagnosed psychosis in the community. METHODS: The sample contained 126 consecutive psychiatric outpatients in National Medical Center, Seoul, Korea, between July 20 and July 22, 2020. The Psychosis Screener (PS) comprises 7 items covering psychotic symptoms. The presence of each psychotic symptom was determined by a trained mental health professional and coded "yes" or "no." Two psychiatrists reviewed the medical records independently and extracted the ICD-10-based diagnoses. Any differences between the two clinicians were resolved by consensus, and the agreed diagnosis was used as a gold standard in the study. RESULTS: Among 126 psychiatric outpatients who were enrolled in a consecutive manner during the study period, the proportion of psychosis was 15.1%. The PS showed 78.9% sensitivity and 72.0% specificity when the optimal cut-off was 2, indicating that a score of 2 or more on the screener identified a likely case of psychosis. The area under the curve for the PS was 0.78 (95% CI: 0.67-0.87). CONCLUSION: The Korean version of the PS has an ability to discriminate between those who meet the diagnostic criteria for psychosis and those who do not in a high-prevalence group.

Characterization of metapopulation of Ellobium chinense through Pleistocene expansions and four covariate COI guanine-hotspots linked to G-quadruplex conformation.

The land snail Ellobium chinense (L. Pfeiffer, 1855) (Eupulmonata, Ellobiida, Ellobiidae), which inhabits the salt marshes along the coastal areas of northwestern Pacific, is an endangered species on the IUCN Red List. Over recent decades, the population size of E. chinense has consistently decreased due to environmental interference caused by natural disasters and human activities. Here, we provide the first assessment of the genetic diversity and population genetic structures of northwestern Pacific E. chinense. The results analyzed with COI and microsatellites revealed that E. chinense population exhibit metapopulation characteristics, retaining under the influence of the Kuroshio warm currents through expansion of the Late-Middle and Late Pleistocene. We also found four phylogenetic groups, regardless of geographical distributions, which were easily distinguishable by four unidirectional and stepwise adenine-to-guanine transitions in COI (sites 207-282-354-420: A-A-A-A, A-A-G-A, G-A-G-A, and G-G-G-G). Additionally, the four COI hotspots were robustly connected with a high degree of covariance between them. We discuss the role of these covariate guanines which link to form four consecutive G-quadruplexes, and their possible beneficial effects under positive selection pressure.

The mitochondrial genome of a giant water bug Lethocerus deyrollei (Hemiptera: Belostomatidae) from South Korea.

A giant water bug Lethocerus deyrollei (Hemiptera: Belostomatidae) is a large, predatory, and nocturnal hemipteran insect, which has been considered threatened and thus enrolled as an endangered species in South Korea and Japan. Here, we characterized the complete mitochondrial genome of L. deyrollei, which has a circular form with 19,295 bp in length, which is the longest when compared to those of the 111 hemipteran species reported so far. Its longest genome size is due to the extremely extended CR (4686 bp), which is much longer than those of China and Japan. It consisted of a total of 37 genes (13 PCGs, 22 tRNA genes, and two rRNA genes) and one control region (CR). The genome composition and gene order were identical to those previously reported from the same species of China and Japan with over 99.7% sequence similarities except for CR and trnI. The nucleotide composition was highly A + T biased, accounting for 71% of the whole mitochondrial genome, as in other species of Nepoidea. Based on the aa sequences of 13 PCGs, we reconstructed a maximum likelihood tree, which indicated that the three mitochondrial genomes of L. deyrollei from South Korea, China, and Japan are grouped, and also Lethocerus, Belostomatidae, Nepoidea, Nepomorpha, Heteroptra are strong monophyletic groups, respectively.

The complete mitochondrial genome of the two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae) from South Korea.

The complete mitochondrial genome of a two-spotted cricket Gryllus bimaculatus (Orthoptera: Gryllidae) from South Korea is determined and characterized in this study. The circular genome is 16,075 bp long, which consists of 13 protein-coding genes (PCGs), 2 ribosomal RNA genes, 22 transfer RNA genes, and an A + T-rich region. It has a base composition of A (40.35%), G (9.09%), C (16.80%), and T (33.76%). The gene order is identical to the ancestral gene arrangement pattern generally shown in arthropods, with the exception of an inversion of trnN-trnS1-trnE into trnE-trnS1-trnN. The maximum likelihood (ML) tree supports that G. bimaculatus is a distinct member of the monophyletic family Gryllidae.