An improved Raphanus sativus cv. WK10039 genome localizes centromeres, uncovers variation of DNA methylation and resolves arrangement of the ancestral Brassica genome blocks in radish chromosomes.

KEY MESSAGE: This study presents an improved genome of Raphanus sativus cv. WK10039 uncovering centromeres and differentially methylated regions of radish chromosomes. Comprehensive genome comparison of radish and diploid Brassica species of U's triangle reveals that R. sativus arose from the Brassica B genome lineage and is a sibling species of B. nigra. Radish (Raphanus sativus L.) is a key root vegetable crop closely related to the Brassica crop species of the family Brassicaceae. We reported a draft genome of R. sativus cv. WK10039 (Rs1.0), which had 54.6 Mb gaps. To study the radish genome and explore previously unknown regions, we generated an improved genome assembly (Rs2.0) by long-read sequencing and high-resolution genome-wide mapping of chromatin interactions. Rs2.0 was 434.9 Mb in size with 0.27 Mb gaps, and the N50 scaffold length was 37.3 Mb (40-fold larger assembly compared to Rs1.0). Approximately 38% of Rs2.0 was comprised of repetitive sequences, and 52,768 protein-coding genes and 4845 non-protein-coding genes were predicted and annotated. The improved contiguity and coverage of Rs2.0, along with the detection of highly methylated regions, enabled localization of centromeres where R. sativus-specific centromere-associated repeats, full-length OTA and CRM LTR-Gypsy retrotransposons, hAT-Ac, CMC-EnSpm and Helitron DNA transposons, and sequences highly homologous to B. nigra centromere-specific CENH3-associated CL sequences were enriched. Whole-genome bisulfite sequencing combined with mRNA sequencing identified differential epigenetic marks in the radish genome related to tissue development. Synteny comparison and genomic distance analysis of radish and three diploid Brassica species of U's triangle suggested that the radish genome arose from the Brassica B genome lineage through unique rearrangement of the triplicated ancestral Brassica genome after splitting of the Brassica A/C and B genomes.

Atraric Acid Exhibits Anti-Inflammatory Effect in Lipopolysaccharide-Stimulated RAW264.7 Cells and Mouse Models.

Lichens, composite organisms resulting from the symbiotic association between the fungi and algae, produce a variety of secondary metabolites that exhibit pharmacological activities. This study aimed to investigate the anti-inflammatory activities of the secondary metabolite atraric acid produced by Heterodermia hypoleuca. The results confirmed that atraric acid could regulate induced pro-inflammatory cytokine, nitric oxide, prostaglandin E2, induced nitric oxide synthase and cyclooxygenase-2 enzyme expression in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Meanwhile, atraric acid downregulated the expression of phosphorylated IκB, extracellular signal-regulated kinases (ERK) and nuclear factor kappa B (NFκB) signaling pathway to exhibit anti-inflammatory effects in LPS-stimulated RAW264.7 cells. Based on these results, the anti-inflammatory effect of atraric acid during LPS-induced endotoxin shock in a mouse model was confirmed. In the atraric acid treated-group, cytokine production was decreased in the peritoneum and serum, and each organ damaged by LPS-stimulation was recovered. These results indicate that atraric acid has an anti-inflammatory effect, which may be the underlying molecular mechanism involved in the inactivation of the ERK/NFκB signaling pathway, demonstrating its potential therapeutic value for treating inflammatory diseases.

Role of Th2 cytokines on the onset of asthma induced by meta-xylene in mice.

meta-Xylene (m-xylene) is one of three isomers of xylene, which is widely used as a solvent and detergent in various industries and medical technology. Exposure to volatile organic compounds, such as m-xylene, causes pulmonary inflammation and airway inflammation, thereby contributing to the onset of asthma. Exposure to m-xylene increases acute wheezing and intensity of asthma symptom. However, the mechanism of the onset of asthma by m-xylene has not been studied yet. C57BL/6 mice were sensitized and challenged by m-xylene at 100 or 300 mg/kg. The mice were then sacrificed after the last challenge. Exposure to m-xylene increased the total number of inflammatory cells and the production of interleukin (IL)-4, IL-5, IL-13, and immunoglobulin E related to the Th2 immune response. In contrast, the production of interferon-γ related to the Th1 immune response was decreased. In addition, the airway resistance increased according to the airway hyper-responsiveness measurements. Finally, a histological analysis revealed infiltration of inflammatory cells, mucus production, and lung fibrosis. These results suggest that m-xylene is a potential risk factor for asthma and the onset of asthma is caused by TH2 cytokines.

Increased Accumulation of Ginsenosides in Panax ginseng Sprouts Cultivated with Kelp Fermentates.

Currently, new agri-tech has been developed and adapted for the cultivation of crops using smart farming technologies, e.g., plant factories and hydroponics. Kelp (Laminaria japonica), which has a high industrial value, was considered as an alternative to chemicals for its eco-friendly and sustainably wide use in crop cultivation. In this study, a fermented kelp (FK) was developed for use in hydroponics. The FK contained various free and protein-bound amino acid compositions produced by fermenting the kelp with Saccharomyces cerevisiae. Supplementing FK as an aeroponic medium when cultivating ginseng sprouts (GSs) elevated the total phenolic and flavonoid contents. Additionally, seven ginsenosides (Rg1, Re, Rb1, Rc, Rg2, Rb2, and Rd) in GSs cultivated with FK in a smart-farm system were identified and quantified by a high-performance liquid chromatography-evaporative light scattering detector/mass spectrometry analysis. Administering FK significantly increased the ginsenosides in the GSs compared to the control group, which was cultivated with tap water. These results indicate the FK administration contributed to the increased accumulation of ginsenosides in the GSs. Overall, this study suggests that FK, which contains abundant nutrients for plant growth, can be used as a novel nutrient solution to enhance the ginsenoside content in GSs during hydroponic cultivation.

Effect of structural variation in the promoter region of RsMYB1.1 on the skin color of radish taproot.

Accumulation of anthocyanins in the taproot of radish is an agronomic trait beneficial for human health. Several genetic loci are related to a red skin or flesh color of radish, however, the functional divergence of candidate genes between non-red and red radishes has not been investigated. Here, we report that a novel genetic locus on the R2 chromosome, where RsMYB1.1 is located, is associated with the red color of the skin of radish taproot. A genome-wide association study (GWAS) of 66 non-red-skinned (nR) and 34 red-skinned (R) radish accessions identified three nonsynonymous single nucleotide polymorphisms (SNPs) in the third exon of RsMYB1.1. Although the genotypes of SNP loci differed between the nR and R radishes, no functional difference in the RsMYB1.1 proteins of nR and R radishes in their physical interaction with RsTT8 was detected by yeast-two hybrid assay or in anthocyanin accumulation in tobacco and radish leaves coexpressing RsMYB1.1 and RsTT8. By contrast, insertion- or deletion-based GWAS revealed that one large AT-rich low-complexity sequence of 1.3-2 kb was inserted in the promoter region of RsMYB1.1 in the nR radishes (RsMYB1.1nR), whereas the R radishes had no such insertion; this represents a presence/absence variation (PAV). This insertion sequence (RsIS) was radish specific and distributed among the nine chromosomes of Raphanus genomes. Despite the extremely low transcription level of RsMYB1.1nR in the nR radishes, the inactive RsMYB1.1nR promoter could be functionally restored by deletion of the RsIS. The results of a transient expression assay using radish root sections suggested that the RsIS negatively regulates the expression of RsMYB1.1nR, resulting in the downregulation of anthocyanin biosynthesis genes, including RsCHS, RsDFR, and RsANS, in the nR radishes. This work provides the first evidence of the involvement of PAV in an agronomic trait of radish.

Changes in Functionality of Tenebrio molitor Larvae Fermented by Cordyceps militaris Mycelia.

The Food and Agriculture Organization (FAO) has been estimating the potential of insects as human food since 2010, and for this reason, Tenebrio molitor larvae, also called mealworms, have been explored as an alternative protein source for various foods. In this study, in order to increase nutrient contents and improve preference as an alternative protein source, we fermented the T. molitor larvae by Cordyceps militaris mycelia. T. molitor larvae were prepared at optimal conditions for fermentation and fermented with C. militaris mycelia, and we analyzed T. molitor larvae change in functionality with proximate composition, ß-glucan, cordycepin, adenosine, and free amino acids content. T. molitor larvae fermented by C. militaris mycelia showed higher total protein, total fiber, and ß-glucan content than the unfermented larvae. In addition, the highest cordycepin content (13.75 mg/g) was observed in shaded dried T. molitor larvae fermented by C. militaris mycelia. Additionally, the isolated cordycepin from fermented T. molitor larvae showed similar cytotoxicity as standard cordycepin when treated with PC-9 cells. Therefore, we report that the optimized methods of T. molitor larvae fermented by C. militaris mycelia increase total protein, total fiber, ß-glucan and produce the amount of cordycepin content, which can be contributed to healthy food and increase T. molitor larvae utilization.

Choice of graft material in relation to maxillary sinus width in internal sinus floor augmentation.

PURPOSE: When grafts with solely osteoinductive or osteoconductive effects are used in the maxillary sinus, the medial wall of the sinus membrane should be reflected to receive the vascular supply and the osteoconductive effect. Because the internal sinus floor augmentation is a blind technique, it is impossible to directly verify whether the medial sinus wall is reflected in the operation. The purpose of this study is to describe the modality of choice among the grafting materials and techniques in relation to the width of the maxillary sinus through preoperative planning and measuring in computed tomography (CT) images. PATIENTS AND METHODS: In a total of 57 patients, 100 implants were placed by 3 different sinus floor augmentation techniques. Postoperative cone-beam CT (CBCT) scans were performed and the arrival distance of grafts from lateral wall to medial wall at the apical end level of the implant in the maxillary sinus was measured. RESULTS: Buccolingual arrival distances of grafts were measured to be a mean of 12.1 mm +/- 2.0 in postoperative CT images. In 23 of 77 cases (29.9%) in which distances were greater than 12.1 mm, the grafts made contact with the medial wall. However, in 22 of 23 cases (95.7%) in which distances were less than 12.1 mm, the grafts made complete contact with the medial wall. CONCLUSIONS: The buccolingual width of the maxillary sinus should be measured at the apical end level of the implant that will be placed in preoperative CT. In the internal sinus floor augmentation, grafting materials with solely osteoconductive potential are to be used for narrow sinuses. For large sinuses, autogenous bone with osteogenic potential should be used; alternatively, the reflection of the medial wall by the lateral window technique is recommended.

Measurement of mandibular lingula location using cone-beam computed tomography and internal oblique ridge-guided inferior alveolar nerve block.

OBJECTIVES: Inferior alveolar nerve block (IANB) is the most frequently used treatment for mandibular molars. Successful IANB requires insertion of the dental needle near the mandibular foramen. In this study, we aimed to analyze the anatomic location of the mandibular lingula and evaluate the effects of internal oblique ridge (IOR)-guided IANB. MATERIALS AND METHODS: The location of the mandibular lingula was measured using cone-beam computed tomography images of the mandibles obtained from 125 patients. We measured the distances from the occlusal plane to the lingula and from the IOR to the lingula in 250 mandibular rami. Based on the mean of these distances, alternative anesthesia was carried out on 300 patients, and the success rate of the technique was evaluated. RESULTS: The mean vertical distance was 8.85±2.59 mm, and the mean horizontal distance was 14.68±1.44 mm. The vertical (P<0.001) and the horizontal (P<0.05) distances showed significant differences between the sex groups. The success rate of the IOR-guided technique was 97.3%. CONCLUSION: IANB-based location of mandibular lingula showed a high success rate. From this study, we concluded that analysis of the anatomic locations for mandibular lingula and IOR-guided IANB are useful for restorative and surgical dental procedures of the mandibular molars.

Verification of the Functional Antioxidant Activity and Antimelanogenic Properties of Extracts of Poria cocos Mycelium Fermented with Freeze-Dried Plum Powder.

Here we examine the effects of extracts of Poria cocos mycelium fermented with freeze-dried plum powder (PPE) on the α-melanocyte stimulating hormone (α-MSH)-stimulated melanogenesis in cultured murine B16 melanoma cells (B16 cells), relative to the effects of Prunus extract. We found that an extract of Prunus fermentation showed significant inhibition of melanogenesis and tyrosinase activity with no effect on cell proliferation and was more active compared to Prunus extract alone. Furthermore, we confirmed that medium containing 3% Prunus was the optimal culture substrate for fermentation with Poria cocos. These results provide evidence that Prunus fermentation extract affects skin whiting in murine B16 melanoma cells (B16 cells). Prunus contains rutin, oxalic acid, succinic acid, and fumaric acid, which help in digestion and fatigue recovery. The rutin of Prunus mume is reported to have antioxidant and anti-inflammatory effects. Also, Prunus extract has a tyrosinase inhibitory activity for skin whiting through its antioxidant activity. Therefore, we believe the Prunus extract for Poria cocos fermentation can be provided as a potential mediator to induce skin whiting.

Draft genome sequence of wild Prunus yedoensis reveals massive inter-specific hybridization between sympatric flowering cherries.

BACKGROUND: Hybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ornamental characteristics were acquired both naturally and through artificially hybridizing species with heterozygous genomes. Therefore, the genome of hybrid flowering Prunus presents important challenges both in plant genomics and evolutionary biology. RESULTS: We use long reads to sequence and analyze the highly heterozygous genome of wild Prunus yedoensis. The genome assembly covers > 93% of the gene space; annotation identified 41,294 protein-coding genes. Comparative analysis of the genome with 16 accessions of six related taxa shows that 41% of the genes were assigned into the maternal or paternal state. This indicates that wild P. yedoensis is an F1 hybrid originating from a cross between maternal P. pendula f. ascendens and paternal P. jamasakura, and it can be clearly distinguished from its confusing taxon, Yoshino cherry. A focused analysis of the S-locus haplotypes of closely related taxa distributed in a sympatric natural habitat suggests that reduced restriction of inter-specific hybridization due to strong gametophytic self-incompatibility is likely to promote complex hybridization of wild Prunus species and the development of a hybrid swarm. CONCLUSIONS: We report the draft genome assembly of a natural hybrid Prunus species using long-read sequencing and sequence phasing. Based on a comprehensive comparative genome analysis with related taxa, it appears that cross-species hybridization in sympatric habitats is an ongoing process that facilitates the diversification of flowering Prunus.