Comparative analysis of metabolite profiling and free radical scavenging activity in phenotypic variants of OsCOP1 colored rice mutant seed.

Interest in colored rice has been increasing due to its health benefits. This study examined the metabolite profiling of CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) mutated rice seed (yel-mutant). The wild-type (WT) and the yel-mutant having yellow (y)- and purple (p)-pericarp variants from Chucheong (cc) and Samkwang (sk) cultivars were investigated for differences in bioactive metabolite profiles and free radical scavenging activity. The total fatty acid content decreased by >50% in the yel-mutant against the WT, while no significant difference was observed between yellow- and purple-pericarp variants (p < 0.05). The yel-mutant of both cultivars showed significantly higher flavone contents than their WT (non-detected). Most of the metabolites examined were highly produced in the yel-cc-p and the yel-sk-y than in the other phenotypic variants studied. This study provides further useful information for colored rice breeding by revealing the detailed biofunctional metabolic profile under COP1 mutation in colored rice.

Crosstalk between RNA silencing and RNA quality control in plants.

RNAs are pivotal molecules acting as messengers of genetic information and regulatory molecules for cellular development and survival. From birth to death, RNAs face constant cellular decision for the precise control of cellular function and activity. Most eukaryotic cells employ conserved machineries for RNA decay including RNA silencing and RNA quality control (RQC). In plants, RQC monitors endogenous RNAs and degrades aberrant and dysfunctional species, whereas RNA silencing promotes RNA degradation to repress the expression of selected endogenous RNAs or exogenous RNA derived from transgenes and virus. Interestingly, emerging evidences have indicated that RQC and RNA silencing interact with each by sharing target RNAs and regulatory components. Such interaction should be tightly organized for proper cellular survival. However, it is still elusive that how each machinery specifically recognizes target RNAs. In this review, we summarize recent advances on RNA silencing and RQC pathway and discuss potential mechanisms underlying the interaction between the two machineries. [BMB Reports 2023; 56(6): 321-325].

Geographical origin discrimination of Agaricus bisporus produced by the complete medium: A pilot study in South Korea.

The complete medium used for mushroom cultivation is important for reliable crop production. We aimed to identify how the origin of Agaricus bisporus grown in Korea was affected by complete media produced in different geographical regions using stable isotope ratios (SIRs). We found that the SIR features of A. bisporus significantly depended on the complete media origin used; in particular, it appeared the high δ34S in the Chinese complete medium, low δ34S in the Dutch complete medium, and high δ15N in the Korean complete medium (P < 0.05). The support vector machine method appeared better geo-origin classification of A. bisporus by the complete media compared to a linear discriminant analysis. A large-scale study should be conducted to establish a reliable origin identification model for A. bisporus grown in complete media to improve the global mushroom marketplace.

Improved accuracy of geographical origin identification of shiitake grown in sawdust medium: A compound-specific isotope model-based pilot study.

In countries like South Korea and the USA, origin labeling of shiitake grown using imported Chinese-inoculated medium is an issue. Therefore, we evaluated the use of compound-specific isotope analysis (CSIA) for the accurate identification of the geographical origin of shiitake (Korean, Chinese-inoculated medium, and Chinese); Chinese-inoculated medium shiitake were cultivated in Korea using inoculated sawdust medium from China. The CSIA-discriminant model showed an overall accuracy of 100% in the geographical classification of the original set and 96.4% for the cross-validated set. Glutamate and aspartate δ15N values were the most important variables for differentiating shiitake based on their origins. Compared to that observed upon using the bulk stable isotope analysis, the CSIA model was associated with significantly improved predictability of origin identification. Our findings elucidate the importance of isotope signatures in developing a reliable origin labeling method for shiitake cultured on the sawdust medium for the global market.

Long-term isotopic model study for ecofriendly rice (Oryza sativa L.) authentication: Updating a case study in South Korea.

To overcome the lack of consumer trust in ecofriendly products due to low reliability of ecofriendly certification and decreasing areas certified for growing ecofriendly agricultural products, alternative approaches for reliable certification are required. Isotopic-chemometric analysis has potential for determining organic authenticity, but previous studies have struggled to differentiate the authenticities of different rice types. The present study examined 5-year variations in δ13C and δ15N in ecofriendly and conventional rice sold at retail markets in South Korea, while assessing the feasibility of discriminant models for authentication of organic rice. Supporting vector machine analysis showed 4.4-14.6% better overall predictability of rice types than discriminant analysis and was effective in discriminating organic or conventional rice from pesticide-free rice, potentially enabling high-throughput screening to authenticate organic rice at marketplaces. Our findings provide reliable information for authenticating ecofriendly rice, with a potential to improve consumer safety and thus the confidence in organic products.

An origin identification model for labeling of shiitake (Lentinula edodes).

With the increasing globalization of the food trade across countries and continents, reliable identification of the geographical origin of products is critical. In this study, we describe the limitations of the current origin labeling system for non-soil-based agricultural products and suggest alternative strategies for the identification of the geographical origin of such products. An origin identification model based on stable isotope ratio analysis combined with discriminant analysis is used to evaluate the similarities and dissimilarities between domestic and foreign shiitake mushrooms, including Chinese inoculated sawdust blocks and Chinese origin. The results show a classification sensitivity of 92.0%, classification specificity of 91.5%, and overall accuracy of 93.5%. In particular, δ15N was the most important isotope marker for the identification of the origin of shiitake mushrooms. Hence, the current origin labeling system for mushroom species has to be revised to establish fair trade and avoid improper origin labeling in the global shiitake market.

Regional Characterization Study of Fatty Acids and Tocopherol in Organic Milk as a Tool for Potential Geographical Identification.

Reliable geographical identification can protect producers of excellent agroproducts, and also provide reliable purchasing information to satisfy consumers. Therefore, this study aimed to evaluate the regional and monthly variation in fatty acid (FA) and tocopherol (TOC) in organic milk (OM) and develop a geographical discriminant model of OM in Korea. In this study, OM had α-TOC and showed a regional or monthly difference of 3-5%. Moreover, C16:0, C18:1 n9 cis + trans, C18:0, and C14:0 were the predominant FAs in OM, and OM mostly had higher ∑UFA, including nutritionally desirable FAs; but lower ∑SFA among four regions or in April and August (p < 0.001). The model prepared using stepwise discriminant analysis showed a classification accuracy of 100% for original and cross-validated sample sets. Our results have characterized regional and monthly nutritional variations of OM, thereby potentially suggesting the applicability of a reliable Korean geographical identification labeling system using nutrient compositional analysis of OM.

Assessment of Mineral and Phenolic Profiles and Their Association with the Antioxidant, Cytotoxic Effect, and Antimicrobial Potential of Lycium chinense Miller.

This study aimed at investigating the Lycium chinense Miller leaf extract mineral and phenolic compound profiles as well as antioxidant and antimicrobial potential. We determined the leaf extract mineral composition, identified its major mineral components, and quantified secondary metabolites. We also measured the leaf extract antioxidant potential and found that it varies in a concentration-dependent manner. We observed a significant and higher positive correlation between DPPH and ABTS assays compared with the total phenolic and flavonoid content. Furthermore, our assay results positively correlated with several observed acids, indicating their strong association with the L. chinense antioxidant potential. Our cytotoxic assay revealed weak toxicity at higher tested concentrations. Our MIC assay showed that the 80% methanol extract effectively inhibited the growth of Escherichia coli Castellani and Chalmers (ATCC35150). The 625-ppm leaf extract completely suppressed the growth of Staphylococcus aureus Rosenbach (ATCC13150), Bacillus cereus (ATCC 14579), and Helicobacter pylori (ATCC43504). These results allow us to understand the indigenous medicinal value of L. chinense. Our study suggests that the L. chinense leaf extract phenolic compounds possess a good antioxidant activity against free radicals and are effective antimicrobial agents. Finally, the presence and high level of diverse minerals suggest the potential of L. chinense for nutraceutical and functional food applications.

Glycosyltransferase-Like RSE1 Negatively Regulates Leaf Senescence Through Salicylic Acid Signaling in Arabidopsis.

Leaf senescence is a developmental process designed for nutrient recycling and relocation to maximize growth competence and reproductive capacity of plants. Thus, plants integrate developmental and environmental signals to precisely control senescence. To genetically dissect the complex regulatory mechanism underlying leaf senescence, we identified an early leaf senescence mutant, rse1. RSE1 encodes a putative glycosyltransferase. Loss-of-function mutations in RSE1 resulted in precocious leaf yellowing and up-regulation of senescence marker genes, indicating enhanced leaf senescence. Transcriptome analysis revealed that salicylic acid (SA) and defense signaling cascades were up-regulated in rse1 prior to the onset of leaf senescence. We found that SA accumulation was significantly increased in rse1. The rse1 phenotypes are dependent on SA-INDUCTION DEFICIENT 2 (SID2), supporting a role of SA in accelerated leaf senescence in rse1. Furthermore, RSE1 protein was localized to the cell wall, implying a possible link between the cell wall and RSE1 function. Together, we show that RSE1 negatively modulates leaf senescence through an SID2-dependent SA signaling pathway.

Regulation of stomatal development by stomatal lineage miRNAs.

Stomata in the plant epidermis play a critical role in growth and survival by controlling gas exchange, transpiration, and immunity to pathogens. Plants modulate stomatal cell fate and patterning through key transcriptional factors and signaling pathways. MicroRNAs (miRNAs) are known to contribute to developmental plasticity in multicellular organisms; however, no miRNAs appear to target the known regulators of stomatal development. It remains unclear as to whether miRNAs are involved in stomatal development. Here, we report highly dynamic, developmentally stage-specific miRNA expression profiles from stomatal lineage cells. We demonstrate that stomatal lineage miRNAs positively and negatively regulate stomatal formation and patterning to avoid clustered stomata. Target prediction of stomatal lineage miRNAs implicates potential cellular processes in stomatal development. We show that miR399-mediated PHO2 regulation, involved in phosphate homeostasis, contributes to the control of stomatal development. Our study demonstrates that miRNAs constitute a critical component in the regulatory mechanisms controlling stomatal development.

Comparison of survival outcomes according of patients with metastatic gastric cancer receiving trastuzumab with systemic chemotherapy.

Purpose: Currently, trastuzumab plus chemotherapy is the standard first-line therapy for human epidermal growth factor receptor 2 (HER2)-positive advanced or metastatic gastric cancer (mGC) or esophagogastric junction cancer. However, it is not clear whether the prognosis of HER2-positive mGC treated with trastuzumab plus chemotherapy is better than that of HER2-negative mGC treated with chemotherapy as the first-line therapy. Methods: We performed a retrospective study comparing the prognosis of mGC according to first-line treatment with trastuzumab plus chemotherapy or chemotherapy only, at the Korea Cancer Center Hospital from 2011 to 2018. The Kaplan-Meier method and Cox proportional hazards model were used for univariate and multivariate survival analyses. Results: The median overall survival of trastuzumab group was 26.1 months and that of chemotherapy group was 14.8 months (P=0.047). Trastuzumab group had a longer median progression-free survival than chemotherapy group (23.4 vs. 9.2 months, P=0.026). By univariate analysis, sex, age, World Health Organization (WHO) histology, HER2 status, primary tumor site, extent of disease, number of lesions, number of metastatic, measurability of disease, prior gastrectomy, and chemotherapy group are statistically significant. Using multivariate analysis, number of lesions, number of metastatic, prior gastrectomy, and trastuzumab group (hazard ratio, 0.594; 95% confidence interval, 0.384-0.921; P=0.020) were found to be independent prognostic factors of overall survival. Conclusion: The result suggests prognosis of HER2-positive mGC treated by trastuzumab plus chemotherapy could be better than that of HER2-negative mGC treated by chemotherapy only. Well-designed prospective cohort studies are needed to confirm the results of this study. HER2 testing should be performed routinely in all patients newly diagnosed with mGC.

Proteasome subunit RPT2a promotes PTGS through repressing RNA quality control in Arabidopsis.

RNA quality control (RQC) and post-transcriptional gene silencing (PTGS) target and degrade aberrant endogenous RNAs and foreign RNAs, contributing to homeostasis of cellular RNAs. In plants, RQC and PTGS compete for foreign and selected endogenous RNAs; however, little is known about the mechanism interconnecting the two pathways. Using a reporter system designed for monitoring PTGS, we revealed that the 26S proteasome subunit RPT2a enhances transgene PTGS by promoting the accumulation of transgene-derived short interfering RNAs without affecting their biogenesis. RPT2a physically associated with a subset of RQC components and downregulated the protein level. Overexpression of the RQC components interfered with transgene silencing, and impairment of the RQC machinery reinforced transgene PTGS attenuated by rpt2a. Overall, we demonstrate that the 26S proteasome subunit RPT2a promotes PTGS by repressing the RQC machinery to control foreign RNAs.

The Spectrum of Hepatic Involvement in Patients With Telomere Disease.

Loss-of-function mutations in genes that encode for components of the telomere repair complex cause accelerated telomere shortening. Hepatic involvement has been recognized as a cause of morbidity in telomere diseases, but very few studies have characterized the nature and extent of liver involvement in affected patients. We report the prevalence and characteristics of liver involvement in a large cohort of patients with telomere disease evaluated serially at the National Institutes of Health. One hundred twenty-one patients with known or suspected telomere disease were screened; 40 patients with liver involvement were included in the current study. Median follow-up was 2.4 years. Data were collected regarding their demographic information, laboratory analysis, imaging, and histopathology. Forty patients (40% of the cohort) with a median age of 42 years were found to have liver involvement. Liver enzyme elevation was cholestatic in pattern; 8 (21%) had drug-related enzyme elevations. The most common imaging finding was increased hepatic echogenicity on ultrasound in 39% (9) of patients, followed by hepatomegaly in 26% (6). Biopsies were infrequent because of risk associated with thrombocytopenia, but in 6 patients, there were varying findings: nodular regenerative hyperplasia, steatohepatitis, hemosiderosis, cholestasis, and cirrhosis with hepatic steatosis. Almost half the cohort had pulmonary diffusion abnormalities, and 25% died during the follow-up period. Conclusion: In patients with telomere disease, hepatic involvement is common and can present in diverse ways, including elevated liver enzymes as well as histopathologic and imaging abnormalities. Liver disease has important implications for morbidity and mortality in patients with telomere disease.

Contrast-Enhanced Ultrasound for Early Prediction of Response of Breast Cancer to Neoadjuvant Chemotherapy.

PURPOSE: To evaluate the time-intensity curve (TIC) parameters on contrast-enhanced ultrasound (CEUS) for early prediction of the response of breast cancer to neoadjuvant chemotherapy (NAC). MATERIALS AND METHODS: This prospective study included 41 patients with breast cancer. CEUS was performed before and after the first cycle of NAC. TIC parameters were analyzed for different regions of interest (ROIs). ROI 1 targeted the hotspot area of greatest enhancement, ROI 2 delineated the area of hyperenhancement, ROI 3 included the entire tumor on grayscale ultrasound, and ROI 4 encircled the normal parenchyma. The TIC perfusion values for ROI 1, 2, and 3 were divided by the ROI 4 value. RESULTS: 11 (26.8 %) of the 41 patients showed a good response (Miller-Payne score 4 or 5) and 30 (73.2 %) showed a minor response (Miller-Payne score 1, 2, or 3). There were significant differences in the wash-out area under the curve, the wash-in and wash-out areas under the curve on ROI 1/4 after the first cycle of NAC, pre-NAC mean transit time local (mTTl) on ROI 2/4, and pre-NAC mTTl on ROI 3/4 between good and minor responders (area under the receiver-operating characteristic curve > 0.70, p < 0.05). CONCLUSION: Some TIC parameters obtained by CEUS may allow prediction of the response of breast cancer to NAC at a very early time point.

Composition Characterization of Fatty Acid Zinc Salts by Chromatographic and NMR Spectroscopic Analyses on Their Fatty Acid Methyl Esters.

To implement EU REACH- (Registration, Evaluation, and Authorization of Chemicals-) like chemical legislations in various countries of which the purpose is human and environment safety, the first step is substance identification followed by the hazard and risk assessments. Although both structural and composition identifications are required, the latter can more importantly result in the essential data to fill out the required substance information such as purity and concentrations of constituents, as well as impurities. With fatty acid zinc salts (FAZSs) as an exemplary industrial chemical of which chromatographic and nuclear magnetic resonance (NMR) analyses were impossible due to their insolubility in water and any organic solvents, the composition characterization was tried by preparing their fatty acid methyl esters (FAMEs) using the conc. HCl/methanol/toluene method. This acid-catalyzed methyl esterification was optimized with zinc stearate as a surrogate substance. Gas chromatography-mass spectrometry (GC-MS) and NMR analyses on methyl-esterified products revealed that the optimum conditions were at 90°C for 10 min or 45°C for 30 min with two equivalent HCl as well as at 45°C for 10 min with five equivalent HCl. Almost all zinc stearates were converted into the corresponding fatty acids with 97-99% conversion rates. Free fatty acids (FFAs) were detected in extracted ion chromatograms of pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS) in the methyl-esterified products with incomplete conversions of 73∼79%. The optimized conc. HCl/methanol/toluene method of direct one-step reaction from FAZSs was compared with the two-step NaOH saponification/BF3-methanol method after acidic hydrolysis of FAZSs. The mechanism of fatty acid zinc salts into free fatty acids and fatty acid methyl esters was suggested with the evidence of the formation of Zn(OH)2.

Prognostic impact of skeletal muscle volume derived from cross-sectional computed tomography images in breast cancer.

PURPOSE: This study aimed to determine whether the prognosis of breast cancer is affected by muscle or fat volume as measured from computed tomography (CT) images. METHODS: We identified 1460 patients with chest CT who were diagnosed as having breast cancer at the National Cancer Center, Korea, between January 2001 and December 2009. Using CT images of 10-mm slices, we measured the cross-sectional areas of skeletal muscle and adipose tissue at the 3rd lumbar vertebrae, and derived their volumes. The skeletal muscle volume, fat volume, and muscle-to-fat ratio were evaluated for association with overall survival (OS) and recurrence-free survival (RFS). RESULTS: The median skeletal muscle and fat volumes among the patients were 93.3 cc (range 39.6-236.9) and 420.1 cc (range 19.5-1392.3), respectively. Patients with higher muscle volume had better prognosis than those with lower muscle volume [hazard ratio (HR) 0.56, 95% confidence interval (CI) 0.34-0.92, P = 0.022 for OS; HR 0.72, 95% CI 0.52-0.99, P = 0.046 for RFS]. However, body mass index (BMI) and fat volume were not associated with prognosis. In addition, muscle volume was a significant prognosticator for OS, regardless of BMI (HR 0.55, 95% CI 0.32-0.93, P = 0.034 in BMI < 25.0; HR 0.44, 95% CI 0.21-0.91, P = 0.026 in BMI ≥ 25.0). Among older patients (≥ 50), those with higher muscle volume showed better OS and RFS (HR 0.44, 95% CI 0.23-0.85, P = 0.015; HR 0.55, 95% CI 0.34-0.90, P = 0.017, respectively). CONCLUSION: This study demonstrated that breast cancer patients with higher skeletal muscle volume showed more favorable prognosis.

Beyond the genetic code in leaf senescence.

Leaf senescence is not only genetically programmed but also induced by exogenous stress to ensure completion of the plant life cycle, successful reproduction and environmental adaptability. Genetic reprogramming is a major aspect of leaf senescence, and the senescence signaling that follows is controlled by a complex regulatory network. Recent studies suggest that the activity of transcription factors together with epigenetic mechanisms ensures the robustness of this network, with the latter including chromatin remodeling, DNA modification, and RNA-mediated control of transcription factors and other senescence-associated genes. In this review, we provide an overview of the relevant epigenetic mechanisms and summarize recent findings of epigenetic regulators of plant leaf senescence involved in DNA methylation and histone modification along with the functions of small RNAs in this process.

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status.

DNA methylation is associated with gene silencing in eukaryotic organisms. Although pathways controlling the establishment, maintenance and removal of DNA methylation are known, relatively little is understood about how DNA methylation influences gene expression. Here we identified a METHYL-CpG-BINDING DOMAIN 7 (MBD7) complex in Arabidopsis thaliana that suppresses the transcriptional silencing of two LUCIFERASE (LUC) reporters via a mechanism that is largely downstream of DNA methylation. Although mutations in components of the MBD7 complex resulted in modest increases in DNA methylation concomitant with decreased LUC expression, we found that these hyper-methylation and gene expression phenotypes can be genetically uncoupled. This finding, along with genome-wide profiling experiments showing minimal changes in DNA methylation upon disruption of the MBD7 complex, places the MBD7 complex amongst a small number of factors acting downstream of DNA methylation. This complex, however, is unique as it functions to suppress, rather than enforce, DNA methylation-mediated gene silencing.

POWERDRESS and HDA9 interact and promote histone H3 deacetylation at specific genomic sites in Arabidopsis.

Histone acetylation is a major epigenetic control mechanism that is tightly linked to the promotion of gene expression. Histone acetylation levels are balanced through the opposing activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). Arabidopsis HDAC genes (AtHDACs) compose a large gene family, and distinct phenotypes among AtHDAC mutants reflect the functional specificity of individual AtHDACs However, the mechanisms underlying this functional diversity are largely unknown. Here, we show that POWERDRESS (PWR), a SANT (SWI3/DAD2/N-CoR/TFIII-B) domain protein, interacts with HDA9 and promotes histone H3 deacetylation, possibly by facilitating HDA9 function at target regions. The developmental phenotypes of pwr and hda9 mutants were highly similar. Three lysine residues (K9, K14, and K27) of H3 retained hyperacetylation status in both pwr and hda9 mutants. Genome-wide H3K9 and H3K14 acetylation profiling revealed elevated acetylation at largely overlapping sets of target genes in the two mutants. Highly similar gene-expression profiles in the two mutants correlated with the histone H3 acetylation status in the pwr and hda9 mutants. In addition, PWR and HDA9 modulated flowering time by repressing AGAMOUS-LIKE 19 expression through histone H3 deacetylation in the same genetic pathway. Finally, PWR was shown to physically interact with HDA9, and its SANT2 domain, which is homologous to that of subunits in animal HDAC complexes, showed specific binding affinity to acetylated histone H3. We therefore propose that PWR acts as a subunit in a complex with HDA9 to result in lysine deacetylation of histone H3 at specific genomic targets.

Histogram analysis of apparent diffusion coefficients after neoadjuvant chemotherapy in breast cancer.

PURPOSE: To evaluate the changes in the apparent diffusion coefficient (ADC) histogram during neoadjuvant chemotherapy (NAC) for breast cancer, and to compare the observed changes in pathologically verified responders and non-responders. MATERIALS AND METHODS: Sixty-two patients received NAC followed by surgery. Responders were defined by a tumor cell reduction of at least 30 % using the Miller-Payne grading system. All the patients underwent 3T magnetic resonance with diffusion-weighted imaging (b values of 0 and 750 s/mm2) before the NAC and after the completion of two cycles of NAC. RESULTS: Mean, minimum, 10th, 25th, 50th, and 75th percentile of ADCs significantly increased after NAC and maximum ADC significantly decreased. Skewness became less positive and kurtosis decreased. A tendential, although not statistically significant, higher increase in mean, minimum, 10th, 25th, 50th, 75th, and 90th percentiles of ADCs was observed in responders in comparison with non-responders. CONCLUSION: ADC histogram analysis quantitatively demonstrates the alterations during the treatment course.