Transcriptomic and metabolic analyses revealed the modulatory effect of vernalization on glucosinolate metabolism in radish (Raphanus sativus L.).

Vernalization is the process by which long-term cold like winter triggers transition to flowering in plants. Many biennial and perennial plants including Brassicaceae family plants require vernalization for floral transition. Not only floral transition, but dynamic physiological and metabolic changes might also take place during vernalization. However, vernalization-mediated metabolic change is merely investigated so far. One of secondary metabolites found in Brassiceceae family plants is glucosinolates (GSLs). GSLs provides defense against pathogens and herbivores attack in plants and also exhibits inhibitory activity against human cancer cell. Profiles of GSLs are highly modulated by different environmental stresses in Brassciaceae family plants. To grasp the effect of vernalization on GSLs metabolic dynamics in radish (Raphanus sativus L.), we performed transcriptomic and metabolic analysis during vernalization in radish. Through transcriptome analysis, we found many GSLs metabolic genes were significantly down-regulated by vernalization in radish plants. Ultra-High Performance Liquid Chromatography analysis also revealed that GSLs compounds were substantially reduced in vernalized radish samples compared to non-vernalized radish samples. Furthermore, we found that repressive histone modification (i.e. H3K27me3) is involved in the modulation of GSLs metabolism via epigenetic suppression of Glucoraphasatin Synthase 1 (GRS1) during vernalization in radish. This study revealed that GSLs metabolism is modulated by vernalization, suggestive of a newly identified target of vernalization in radish.

Tissue-specific distribution of primary and secondary metabolites of Baemoochae (×Brassicoraphanus) and its changes as a function of developmental stages.

The distribution and changes in the primary and secondary metabolite profiles of Baemoochae, an inter-generic hybrid of Chinese cabbage and radish, during the plant's developmental stages were investigated. Metabolites were analyzed using gas chromatography-mass spectrometry (GC-MS) and ultra-high-performance liquid chromatography-electrospray ionization-quadrupole time-of-flight (UHPLC-ESI-qTOF MS). Free sugar, organic acid, and amino acid composition depended on the tissue type and developmental stage of Baemoochae. For example, glucose and alanine levels were higher in mature leaves than in young leaves; citric acid content in mature roots was lower than that in young roots. Several glucosinolates were identified for the first time in Baemoochae. Glucoraphasatin was predominant in both leaves and roots, regardless of plant maturity. Total glucosinolate content was significantly higher in roots than in leaves and in mature than in young plants. The roots of mature Baemoochae could be used as a rich source of glucosinolates, with several potential health-promoting effects.

Correction to: Differential expression of major genes involved in the biosynthesis of aliphatic glucosinolates in intergeneric Baemoochae (Brassicaceae) and its parents during development.

Due to an unfortunate turn of events, an incorrect note was provided in the original publication as it should have read.

Differential expression of major genes involved in the biosynthesis of aliphatic glucosinolates in intergeneric Baemoochae (Brassicaceae) and its parents during development.

KEY MESSAGE: Thus study found the temporal and spatial relationship between production of aliphatic glucosinolate compounds and the expression profile of glucosinolate-related genes during growth and development in radish, Chinese cabbage, and their intergeneric hybrid baemoochae plants. Glucosinolates (GSLs) are one of major bioactive compounds in Brassicaceae plants. GSLs play a role in defense against microbes as well as chemo-preventative activity against cancer, which draw attentions from plant scientists. We investigated the temporal relationship between production of aliphatic Glucosinolate (GSLs) compounds and the expression profile of GSL related genes during growth and development in radish, Chinese cabbage, and their intergeneric hybrid, baemoochae. Over the complete life cycle, Glucoraphasatin (GRH) and glucoraphanin (GRE) predominated in radish, whereas gluconapin (GNP), glucobrassicanapin (GBN), and glucoraphanin (GRA) abounded in Chinese cabbage. Baemoochae contained intermediate levels of all GSLs studied, indicating inheritance from both radish and Chinese cabbage. Expression patterns of BCAT4, CYP79F1, CYP83A1, UGT74B1, GRS1, FMOgs-ox1, and AOP2 genes showed a correlation to their corresponding encoded proteins in radish, Chinese cabbage, and baemoochae. Interestingly, there is a sharp change in gene expression pattern involved in side chain modification, particularly GRS1, FMOgs-ox1, and AOP2, among these plants during the vegetative and reproductive stage. For instance, the GRS1 was strongly expressed during leaf development, while both of FMOgs-ox1 and AOP2 was manifested high in floral tissues. Furthermore, expression of GRS1 gene which is responsible for GRH production was predominantly expressed in leaf tissues of radish and baemoochae, whereas it was only slightly detected in Chinese cabbage root tissue, explaining why radish has an abundance of GRH compared to other Brassica plants. Altogether, our comprehensive and comparative data proved that aliphatic GSLs biosynthesis is dynamically and precisely regulated in a tissue- and development-dependent manner in Brassicaceae family members.

The mechanism of deterioration of the glucosinolate-myrosynase system in radish roots during cold storage after harvest.

The hydrolysis of glucosinolates (GSLs) by myrosinase yields varieties of degradation products including isothiocyanates (ITCs). This process is controlled by the glucosinolate-myrosinase (G-M) system. The major ITCs in radish roots are raphasatin and sulforaphene (SFE), and the levels of these compounds decrease during storage after harvest. We investigated the G-M system to understand the mechanism behind the decrease in the ITCs in radish roots. Six varieties of radish roots were stored for 8weeks at 0-1.5°C. The concentrations of GSLs (glucoraphasatin and glucoraphenin) were maintained at harvest levels without significant changes during the storage period. However, SFE concentration and myrosinase activity remarkably decreased for 8weeks. Pearson correlation analysis between ITCs, GSLs, and myrosinase activity showed that a decrease of SFE during storage had a positive correlation with a decrease in myrosinase activity, which resulted from a decrease of ascorbic acid but also a decrease of myrosinase activity-related gene expressions.

Sulforaphene promotes Bax/Bcl2, MAPK-dependent human gastric cancer AGS cells apoptosis and inhibits migration via EGFR, p-ERK1/2 down-regulation.

Gastric cancer migration and invasion considered as main causes of this cancer-related death around the world. Sulforaphene (4-isothiocyanato-4R-(methylsulfinyl)-1-butene), a structural analog of sulforaphane, has been found to exhibit anticancer potential against different cancers. Our aim was to investigate whether dietary isothiocyanate sulforaphene (SFE) can promote human gastric cancer (AGS) cells apoptosis and inhibit migration. Cells were treated with various concentrations of SFE and cell viability, morphology, intracellular ROS, migration and different signaling protein expressions were investigated. The results indicate that SFE decreases AGS cell viability and induces apoptosis in a dose-dependent manner. Intracellular ROS generation, dose- and time-dependent Bax/Bcl2 alteration and signaling proteins like cytochrome c, Casp-3, Casp-8 and PARP-1 higher expression demonstrated the SFE-induced apoptotic pathway in AGS cells. Again, SFE induced apoptosis also accompanied by the phosphorylation of mitogen-activated protein kinases (MAPKs) like JNK and P-38. Moreover, dose-dependent EGFR, p-ERK1/2 down-regulation and cell migration inhibition at non-toxic concentration confirms SFE activity in AGS cell migration inhibition. Thus, this study demonstrated effective chemotherapeutic potential of SFE by inducing apoptisis as well as inhibiting migration and their preliminary mechanism for human gastric cancer management.

Antioxidant activity of the methanolic extract of the newly generated vegetable, baemuchae (xBrassicoraphanus).

We investigated the radical scavenging activity and protective effects of the methanol extract (ME) and ferulic acid (FA) from baemuchae (xBrassicoraphanus) against oxidative stress in vitro and on a cellular system using LLC-PK1 renal epithelial cells. In vitro, ME and FA showed dose-dependent radical scavenging activity against 1,1-diphenyl-2-picrylhydrazyl and hydroxyl radicals. LLC-PK1 cells displayed decreased viability in response to nitric oxide-induced oxidative stress. However, ME and FA significantly increased LLC-PK1 cell viability in a dose-dependent manner. Based on HPLC/UV analysis, the FA content was higher in the shoot of baemuchae than in the root. The results of the present study suggest that baemuchae may be a promising source of antioxidants against oxidative stress induced by free radicals.

Developing stable progenies of ×Brassicoraphanus, an intergeneric allopolyploid between Brassica rapa and Raphanus sativus, through induced mutation using microspore culture.

Induced mutations were used to improve the low seed fertility of an intergeneric allopolyploid, 'Baemoochae,' ×Brassicoraphanus, synthesized following hybridization between Brassica rapa and Raphanus sativus. The mutagen N-methyl-N-nitroso-urethane (NMU) was added to microspore cultures. Four lines of nine in the Mi(2) generation showed very high fertility under controlled pollination. The progeny lines (Mi(3)) confirmed this result under open pollination, and excellent uniformity was observed in plants grown in the field, as well as in their AFLP profile. On attaining high fertility and uniformity, one of the lines was released to farmers as a new leafy vegetable crop. The original nine lines shared very similar AFLP banding patterns, without any large differences between the high and low seed fertility lines. Thus, mutation induction accelerated genetic stabilization of a newly synthesized allopolyploid, ×Brassicoraphanus.

Detection of sexually transmitted infection and human papillomavirus in negative cytology by multiplex-PCR.

BACKGROUND: The aim of this study was to determine the prevalence of human papillomavirus (HPV) and 15 species that cause sexually transmitted infections (STIs) in negative cytology. In addition, we compared the diagnostic performance of multiplex polymerase chain reaction (PCR) with widely available techniques used to detect HPV. METHODS: We recruited 235 women of reproductive age who had negative cytology findings in a liquid-based cervical smear. STIs were identified by multiplex PCR, and HPV genotypes by multiplex PCR, hybrid capture 2, and DNA microaray; discordant results were analyzed by direct sequencing. RESULTS: Approximately 96.6% of patients with negative cytology results were positive for pathogens that cause STIs. The pathogens most frequently detected were Gardnerella vaginalis, Ureaplasma urealyticum. The incidence of HPV in negative cytology was 23.3%. Low-risk HPV infection was significantly correlated with Chalmaydia trachomatis, and high-risk HPV infection was significantly correlated with Group ß streptococcus. The analytical sensitivities of the multiplex PCR and DNA microarray were higher than 80%, and the analytical specificity was nearly 100% for all tests. CONCLUSIONS: Multiplex PCR yielded results that most of patients with negative cytology were positive for pathogens that cause STIs, and were more similar to that of DNA microarray, than that of hybrid capture 2 in terms of analytical sensitivity and prediction value of HPV infection.

Dual priming oligonucleotide-based multiplex PCR analysis for detection of BRAFV600E mutation in FNAB samples of thyroid nodules in BRAFV600E mutation-prevalent area.

BACKGROUND: To evaluate the diagnostic value of dual priming oligonucleotide (DPO)-based multiplex polymerase chain reaction (PCR) for the detection of BRAF(V600E) mutations in ultrasound-guided fine-needle aspiration biopsy (US-FNAB) of thyroid nodules. METHODS: Our institutional review board approved this retrospective study, and informed consent was not required from patients. The 130 patients underwent US-FNAB to evaluate BRAF status in thyroid nodules. In FNAB washouts, DPO-based multiplex PCR, direct DNA sequencing, and PCR-restriction fragment length polymorphism (RFLP) were used to detect BRAF(V600E). The diagnostic performance of these methods was calculated. We compared cytologic results by BRAF status. RESULTS: Diagnostic accuracy and sensitivity were highest when screening with DPO-based multiplex PCR. BRAF(V600E) positivity was a useful marker at thyroid nodules with "suspicious for papillary thyroid carcinoma" or "inadequate" cytological result. CONCLUSIONS: DPO-based multiplex PCR may be an alternative to direct DNA sequencing because of its high sensitivity, high accuracy, and simplicity. BRAF(V600E) may be a useful additional diagnostic marker in BRAF(V600E)-prevalent areas.

Overexpression of the downward leaf curling (DLC) gene from melon changes leaf morphology by controlling cell size and shape in Arabidopsis leaves.

A plant-specific gene was cloned from melon fruit. This gene was named downward leaf curling (CmDLC) based on the phenotype of transgenic Arabidopsis plants overexpressing the gene. This expression level of this gene was especially upregulated during melon fruit enlargement. Overexpression of CmDLC in Arabidopsis resulted in dwarfism and narrow, epinastically curled leaves. These phenotypes were found to be caused by a reduction in cell number and cell size on the adaxial and abaxial sides of the epidermis, with a greater reduction on the abaxial side of the leaves. These phenotypic characteristics, combined with the more wavy morphology of epidermal cells in overexpression lines, indicate that CmDLC overexpression affects cell elongation and cell morphology. To investigate intracellular protein localization, a CmDLC-GFP fusion protein was made and expressed in onion epidermal cells. This protein was observed to be preferentially localized close to the cell membrane. Thus, we report here a new plant-specific gene that is localized to the cell membrane and that controls leaf cell number, size and morphology.

Detection of a novel CBFB/MYH11 variant fusion transcript (K-type) showing partial insertion of exon 6 of CBFB gene using two commercially available multiplex RT-PCR kits.

We report on a 20-year-old man with acute myeloid leukemia (AML) showing a distinct novel CBFB/MYH11 variant fusion transcript. Initial results of bone marrow, chromosome, and flow cytometric analyses were not in accordance with the diagnosis of acute myelomonocytic leukemia with eosinophilia (AML-M4Eo) or AML with a CBFB/MYH11 rearrangement. However, results from 2 commercially available multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) tests repeatedly showed an unusual PCR product from his bone marrow specimen. Not only does this case show a partial insertion of exon 6 of the CBFB (ENSG00000067955) gene, but it also involves novel breakpoints within both exon 6 of the CBFB gene and exon 28 (previously exon 7) of the MYH11 (ENSG00000133392) gene, which is regarded as a previously non-reported, new type (K-type) of CBFB/MYH11 fusion transcript. In addition, our study result was in agreement with the recent report of Schnittger et al. that rare fusion transcripts of CBFB/MYH11 are correlated with an atypical cytomorphology and other aberrant characteristics. Therefore, multiplex RT-PCR and sequence analysis of these atypical products should be performed to diagnose atypical AML with CBFB/MYH11 rearrangement, to predict prognosis of these patients as well as to elucidate the molecular mechanism.

Acute promyelocytic leukemia with insertion of PML exon 7a and partial deletion of exon 3 of RARA: a novel variant transcript related to aggressive course and not detected with real-time polymerase chain reaction analysis.

We report the case of a 38-year-old man with acute promyelocytic leukemia (APL) showing a distinct breakpoint cluster region 2 (bcr2) variant transcript. Findings from bone marrow, cytogenetic, fluorescence in situ hybridization, and qualitative reverse transcriptase-polymerase chain reaction (RT-PCR) analyses were consistent with the diagnosis of APL. Although PCR products of size 841 bp and 984 bp were amplified from bone marrow specimen, the quantitative PCR (RQ-PCR) findings were negative. Given the discrepancy in PCR results, sequencing of PCR products was performed to determine the detailed composition of these fusion transcripts. By cloning and sequencing, we discovered that these two bands were isoforms, in which one exon (exon 5, 144 bp) of the PML gene was spliced out of the smaller products (minor PCR products); one sequence (G) insertion and one base substitution (T-->C) of PML exon 4 generate a stop codon in the smaller fusion transcript. In addition, a search of the Ensembl database revealed that these variant PML/RARA fusion transcripts were composed of exon 7a insertion of the PML gene and partial deletion (46 bp) of exon 3 of the RARA gene, in addition to inserted sequences of intron 7 of PML and genomic sequence ATCT of unknown origin at the fusion junction site. Although the biological significance of most atypical transcripts remains unclear, sequence analysis of these atypical products should be performed, to reveal the composition of such a fusion transcript and elucidate the molecular mechanism.

Acute promyelocytic leukemia in early pregnancy with translocation t(15;17) and variant PML/RARA fusion transcripts.

A 32-year-old pregnant woman in the 13th gestational week was brought to Severance Hospital with gum bleeding and easy bruising. Initial laboratory results revealed anemia and thrombocytopenia. In a peripheral blood smear, 81% of leukocytes were large, abnormal promyelocytes. Bone marrow aspiration showed a hypercellular marrow with packed leukemic promyelocytes, and chromosome study revealed a karyotype of 46,XX,t(15;17)(q22;q21)[10]/46,XX[10]. In addition, variant fusion transcripts of PML/RARA were detected in the marrow specimen. The patient was diagnosed with acute promyelocytic leukemia (APL) and was treated with all-trans retinoic acid (ATRA) and idarubicin. One month from the patient's initial diagnosis a follow-up bone marrow examination was performed, revealing complete remission (CR). We know of no previous reports of APL during pregnancy associated with variant PML/RARA fusion transcripts. Here, we describe a novel case of APL in a pregnant woman with a t(15;17) translocation and variant fusion transcripts.

Direct detection of lamivudine-resistant hepatitis B virus mutants by a multiplex PCR using dual-priming oligonucleotide primers.

Mutations in the YMDD motif of the hepatitis B virus (HBV) polymerase gene increase lamivudine resistance of HBV, highlighting the clinical importance of accurate and sensitive detection of HBV mutants. Using dual-priming oligonucleotide primer technology, an assay that can detect mutations at codons 180 (L528M) and 204 (YVDD, YIDD, and YSDD) by a single-step multiplex PCR was developed. This Seeplex Lami-DR assay was sufficiently sensitive to detect 10(3)HBV/ml and was able to detect minor mutants comprising as little as 2% of the viral population. Mutants were detected in 57 of 65 serum samples (88%) from patients with chronic hepatitis B who had been treated with lamivudine (median, 32 months; range, 1-83 months). The agreement with direct sequencing was only 38.5% (25/65). Discrepancies between these methods resulted from detection of additional mutants by the Seeplex Lami-DR assay, as confirmed by a novel verification analysis. This assay is not only highly accurate and sensitive, but is also simple and cost-effective, requiring no expensive probes, laborious sequencing procedures, or digestion with restriction enzymes. Accordingly, the Seeplex HBV Lami-DR assay should be considered as a first-line, cost-effective tool for detecting viral mutations in patients with chronic hepatitis B receiving lamivudine therapy.

Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene.

Successful PCR starts with proper priming between an oligonucleotide primer and the template DNA. However, the inevitable risk of mismatched priming cannot be avoided in the currently used primer system, even though considerable time and effort are devoted to primer design and optimization of reaction conditions. Here, we report a novel dual priming oligonucleotide (DPO) which contains two separate priming regions joined by a polydeoxyinosine linker. The linker assumes a bubble-like structure which itself is not involved in priming, but rather delineates the boundary between the two parts of the primer. This structure results in two primer segments with distinct annealing properties: a longer 5'-segment that initiates stable priming, and a short 3'-segment that determines target-specific extension. This DPO-based system is a fundamental tool for blocking extension of non-specifically primed templates, and thereby generates consistently high PCR specificity even under less than optimal PCR conditions. The strength and utility of the DPO system are demonstrated here using multiplex PCR and SNP genotyping PCR.