Korea Research Institute of Bioscience and Biotechnology
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Induction of glucoraphasatin biosynthesis genes by MYB29 in radish ( Raphanus sativus L.) roots
No full textGlucoraphasatin (GRH) is a specific aliphatic glucosinolate (GSL) that is only abundant in radish (Raphanus sativus L.). The gene expression regulating GRH biosynthesis in radish is still poorly understood. We employed a total of 59 radish accessions to analyze GSL profiles and showed that GRH was specific and predominant among the aliphatic GSLs in radish roots. We selected five accessions roots with high, moderate and low GSL biosynthesis, respectively, to conduct a comparative transcriptome analysis and the qRT-PCR of the biosynthesis genes for aliphatic GSLs. In this study, among all the accessions tested, roots with the accession RA157-74 had a high GRH content and showed a significant expression of the aliphatic GSL biosynthesis genes. We defined the genes involved in the GRH biosynthesis process and found that they were regulated by a transcription factor (RSG00789) at the MYB29 locus in radish roots. We found 13 aliphatic GSL biosynthesis genes regulated by the RSG00789 gene in the GRH biosynthesis pathway.
A preliminary study on bacterial composition in the subgingival plaque of woman with periodontitis during pregnancy and menopause
No full textAim: The aim of the present study was to explore the bacterial composition in subgingival plaque of females with periodontitis during pregnancy and menopause stages using 16S ribosomal RNA (rRNA) gene pyrosequencing approach.
Methodology: Subgingival plaque was collected from four woman volunteers (healthy, periodontitis, periodontitis at pregnancy and periodontitis at menopause). The microbial community composition was analyzed by 454/Roche GS FLX chemistry pyrosequencing approach using the variable (V1-V3) region of the 16S rRNA gene. Pyrosequencing reads were sorted to get the clean reads that were annotated against the EzBioCloud data base for taxonomic classification. Operational Taxonomic Units (OTUs) were assigned and shared, and subsequently identified using CLCOMMUNITY software.
Results: Pyrosequencing yielded 13,939 sequences comprising of 13 phyla, 124 genera, and 372 species. The predominant microbial phyla in subgingival plaque of all woman volunteers included Firmicutes, Actinobacteria, Fusobacteria, Bacteroidetes, and Proteobacteria. In the healthy volunteer, Streptococcus (52.4%) formed the predominant genus while in woman with periodontitis Streptococcus (24.6%) and Fusobacterium (11.7%) predominated. In the periodontitis volunteer with pregnancy, the predominant genus included Streptococcus (25.8%) and Fusobacterium (22.4%), whereas volunteer with menopause, the gingivitis was associated with genus Alloprevotella (19.5%), Leptotrichia (14.3%), Fusobacterium (12.3%), and Porphyromonas (12.0%).
Interpretation: This study proves on preliminary basis that the subgingival microbiome of woman with periodontitis at pregnancy or menopause tend to differ from that of healthy woman, and these species included certain periodontal pathogens such as Fusobacterium nucleatum and Porphyromonas gingivalis.
Two base pair deletion in IL2 receptor γ gene in NOD/SCID mice induces a highly severe immunodeficiency
No full textGenome editing has recently emerged as a powerful tool for generating mutant mice. Small deletions of nucleotides in the target genes are frequently found in CRISPR/Cas9 mediated mutant mice. However, there are very few reports analyzing the phenotypes in small deleted mutant mice generated by CRISPR/Cas9. In this study, we generated a mutant by microinjecting sgRNAs targeting the IL2 receptor γ gene and Cas9 protein, into the cytoplasm of IVF-derived NOD.CB17/Prkdcscid/JKrb (NOD/SCID) mice embryos, and further investigated whether a 2 bp deletion of the IL2 receptor γ gene affects severe deficiency of immune cells as seen in NOD/LtSz-scid IL2 receptor γ-/- (NSG) mice. Our results show that the thymus weight of mutant mice is significantly less than that of NOD/SCID mice, whereas the spleen weight was marginally less. T and B cells in the mutant mice were severely deficient, and NK cells were almost absent. In addition, tumor growth was exceedingly increased in the mutant mice transplanted with HepG2, Raji and A549 cells, but not in nude and NOD/SCID mice. These results suggest that the NOD/SCID mice with deletion of 2 bp in the IL2 receptor γ gene shows same phenotype as NSG mice. Taken together, our data indicates that small deletions by genome editing is sufficient to generate null mutant mice.
A new nano-platform of erythromycin combined with Ag nano-particle ZnO nano-structure against methicillin-resistant Staphylococcus aureus
No full textNano-particles have been combined with antibiotics in recent studies to overcome multidrug-resistant bacteria. Here, we synthesized a nano-material in which Ag nano-particles were assembled with a ZnO nano-structure to form an Ag-ZnO (AZO) nano-composite at low temperature. This material was combined with erythromycin (Ery), an antibiotic effective towards gram-positive bacteria, using three different approaches (AZO + Ery (AZE) [centrifuged (AZE1), used separately after 1-h gap (AZE2), without centrifugation (AZE3)]) to prepare a nano-antibiotic against clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA). X-ray diffraction analysis and transmission electron microscopy confirmed the presence of Ag nano-particles and ZnO nano-structure. The elemental and chemical state of the elements present in the AZO nano-composite were assessed by X-ray photoelectron spectroscopy. The antibacterial activity of AZE samples against both Escherichia coli and S. aureus strains including MRSA was evaluated in antibacterial and morphological analyses. The AZE3 sample showed greater antibacterial activity than the other samples and was comparable to erythromycin. AZE3 was ~20-fold less prone to developing bacterial resistance following multiple exposures to bacteria compared to erythromycin alone. The AZE3 nano-composite showed good biocompatibility with 293 human embryonic kidney cells. Our newly synthesized nano-platform antibiotics may be useful against multidrug-resistant gram-positive bacteria.
Complete genome sequence of Spirosoma sp. strain KCTC 42546, isolated from a reservoir in South Korea
No full textThis study reports on the complete genome sequence of Spirosoma sp. strain KCTC 42546, isolated from fresh water in a reservoir in South Korea. The genome contained genes for various glycosyl hydrolases, which are associated with degrading sugars and DNA-repairing enzymes.
Isolation and characterization of the insect growth regulatory substances from actinomycetes
No full textInsect growth regulators (IGRs) are attractive alternatives to chemical insecticides. Since it has been reported that secondary metabolites from actinomycetes show insecticidal activities against various insect pests, actinomycetes could be a potential source of novel IGR compounds. In the present study, insect juvenile hormone antagonists (JHANs) were identified from actinomycetes and their insect growth regulatory and insecticidal activities were investigated. A total of 363 actinomycetes were screened for their insect growth regulatory and insecticidal activities against Aedes albopictus and Plutella xylostella. Among them, Streptomyces sp. AN120537 showed the highest JHAN and insecticidal activities. Five antimycins were isolated as active compounds by assay-guided fractionation and showed high JHAN activities. These antimycins also exhibited significant insecticidal activities against A. albopictus, P. xylostella, F. occidentalis, and T. urticae. Moreover, dead larvae treated with these antimycins displayed morphological deformities that are similar to those of JH-based IGR-treated insects. This is the first report demonstrating that the insecticidal activities of antimycins resulted from their possible JHAN activity. Based on our results, it is expected that novel JHAN compounds potentially derived from actinomycetes could be efficiently applied as IGR insecticides with a broad insecticidal spectrum.
Molecular detection of Enterocytozoon hepatopenaei and Vibrio parahaemolyticus-associated acute hepatopancreatic necrosis disease in Southeast Asian Penaeus vannamei shrimp imported into Korea
No full textSixty batches of white leg shrimp (Penaeus vannamei, 40？50 shrimp per batch) imported from multiple countries, including Vietnam, Indonesia, Malaysia, and Peru were collected from fishery markets in South Korea. Five shrimp were randomly selected from each batch, the hepatopancreases of shrimp were collected, and samples from each batch were pooled and analyzed via PCR. Examination by qPCR indicated that the shrimp were infected by two emerging pathogens, Enterocytozoon hepatopenaei (EHP) and Vibrio parahaemolyticus carrying pirA and pirB toxins, which are associated with acute hepatopancreatic necrosis disease (VpAHPND). Specifically, EHP was detected in the shrimp imported from Vietnam and Indonesia (17/60 samples, 28%) and VpAHPND was detected in the shrimp imported from Vietnam (1/60, 2%). One sample highly infected with EHP (Ct = 20.86 ± 1.47, corresponding to the copy number of 8.5 × 105？5.2 × 106) was also infected with VpAHPND (Ct = 29.36 ± 0.25, corresponding to the copy number of 2.5 × 103？3.4 × 103). These results indicate that EHP and VpAHPND, which are not currently listed as quarantine-required shrimp pathogens in Korea, can be introduced to Korea through shrimp importing activities and may pose a potential threat to Korean shrimp culture industry. Greater awareness regarding importing of diseased shrimps, and subsequent enforcement of quarantine policies relating to these pathogens are required to ensure that South Korea remains EHP- and VpAHPND-free.
Cathepsin K inhibition-induced mitochondrial ROS enhances sensitivity of cancer cells to anti-cancer drugs through USP27x-mediated Bim protein stabilization
No full textCathepsin K (Cat K) is expressed in cancer cells, but the effect of Cat K on apoptosis is still elusive. Here, we showed that inhibition of Cat K sensitized the human carcinoma cells to anti-cancer drug through up-regulation of Bim. Inhibition of Cat K increased USP27x expression, and knock down of USP27x markedly blocked Cat K-induced up-regulation of Bim expression. Furthermore, inhibition of Cat K induced proteasome-dependent degradation of regulatory associated protein of mammalian target of rapamycin (Raptor). Down-regulation of Raptor expression increased mitochondrial ROS production, and mitochondria specific superoxide scavengers prevented USP27x-mediated stabilization of Bim by inhibition of Cat K. Moreover, combined treatment with Cat K inhibitor (odanacatib) and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) reduced tumor growth and induced cell death in a xenograft model. Our results demonstrate that Cat K inhibition enhances anti-cancer drug sensitivity through USP27x-mediated the up-regulation of Bim via the down-regulation of Raptor.
ChimerDB 4.0: an updated and expanded database of fusion genes
No full textFusion genes represent an important class of biomarkers and therapeutic targets in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data (ChimerSeq) and text mining of publications (ChimerPub) with extensive manual annotations (ChimerKB). In this update, we present all three modules substantially enhanced by incorporating the recent flood of deep sequencing data and related publications. ChimerSeq now covers all 10 565 patients in the TCGA project, with compilation of computational results from two reliable programs of STAR-Fusion and FusionScan with several public resources. In sum, ChimerSeq includes 65 945 fusion candidates, 21 106 of which were predicted by multiple programs (ChimerSeq-Plus). ChimerPub has been upgraded by applying a deep learning method for text mining followed by extensive manual curation, which yielded 1257 fusion genes including 777 cases with experimental supports (ChimerPub-Plus). ChimerKB includes 1597 fusion genes with publication support, experimental evidences and breakpoint information. Importantly, we implemented several new features to aid estimation of functional significance, including the fusion structure viewer with domain information, gene expression plot of fusion positive versus negative patients and a STRING network viewer. The user interface also was greatly enhanced by applying responsive web design. ChimerDB 4.0 is available at http://www.kobic.re.kr/chimerdb/.
Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.
No full textPeppers (Capsicum annuum L.), belonging to the Solanaceae family, are one of the most economically important crops globally. Like other crops, peppers are threatened by diverse environmental conditions due to different pathogens and abiotic stresses. High-quality reference genomes with massive datasets of transcriptomes from various conditions can provide clues to preferred agronomic traits for breeding. However, few global gene expression profiling datasets have been published to examine the environmental stress-resistant mechanisms in peppers. In this study, we report the RNA-seq analyses of peppers treated with heat, cold, salinity, and osmotic stress at six different time points. RNA-seq libraries from 78 RNA samples containing three biological replicates per time point for each of the abiotic stresses and a mock control were constructed. A total of 204.68？Gb of transcriptome data were verified by differentially expressed genes and gene ontology enrichment analysis. Analyses of the transcriptome data in this study will provide useful information for basic studies of various stimuli to facilitate the development of stress-resistant pepper cultivars.