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Postmenopausal obesity is becoming a serious global health concern. Soyasaponin Ab (SA) inhibits adipocyte differentiation; however, the preventive and therapeutic potential of SA in postmenopausal obesity has not been clearly established. Here, we investigated the anti-obesity effects of SA in postmenopausal obesity in vitro and in vivo. SA inhibited adipocytic differentiation of 3T3-L1 cells and reduced lipid accumulation and lipid droplet formation. Moreover, SA significantly decreased weight gain, adipocyte area, serum metabolic profiles in OVX mice. SA also inhibited the lipid metabolism-related factors but increased the thermoregulatory factors in both in vitro and in vivo. SA treatment further increased energy expenditure through beige fat activation. Overall, we found that SA effectively accelerated energy consumption by stimulating beige fat activation, even under estrogen-deficient conditions. Thus, SA treatment may be a promising strategy for the prevention of postmenopausal obesity by promoting weight loss, reducing fat accumulation, and improving obesity-related metabolic disorders.

Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.

Abstract Background The co-infection of diverse viruses in a host plant is common; however, little is known about viral populations and their quasispecies in the host. Results Here, we report the first pepper viromes that were co-infected by different types of viral genomes. The pepper viromes are dominated by geminivirus DNA-A followed by a novel carlavirus referred to as Pepper virus A. The two pepper cultivars share similar viral populations and replications. However, the quasispecies for double-stranded RNA virus and two satellite DNAs were heterogeneous and homogenous in susceptible and resistant cultivars, respectively, indicating the quasispecies of an individual virus depends on the host. Conclusions Taken together, we provide the first evidence that the host plant resistant to viruses has an unrevealed antiviral system, affecting viral quasispecies, not replication.

The changes in phenolic and antioxidant capacities of seedlings of various barley cultivars through four different harvest times were investigated. Ten phenolics were characterised as hydroxycinnamic acid, orientin, isoorientin, and isovitexin derivatives using UPLC-PDA-ESI/MS and NMR. In particular, lutonarin (2) and saponarin (3) were the predominant constituents (71–75%) with significant differences in cultivars and harvest times. The highest average total phenolic content was found as 2671.8 mg/100 g on 23 days after the sowing, whereas the lowest was 1400.8 mg/100 g on 56 days. The radical scavenging abilities also exhibited considerable differences in 80% of methanol extracts (40 µg/mL), depending upon the phenolic contents. Interestingly, isoorientin (5) and orientin (6) possessed potent antioxidant effects with IC50 values of 20.7 ± 1.1 and 27.5 ± 7.3 µM (DPPH) and 5.7 ± 0.3 and 8.2 ± 0.3 µM (ABTS), respectively. These results may be contributed to enhancing the value of barley as a functional food ingredient and dietary supplement.

Sorghum (Sorghum bicolor), also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers.

The adzuki bean (Vigna angularis), a member of the family Fabaceae, is widely grown in Asia, from East Asia to the Himalayas. The adzuki bean is known as an ingredient that adds sweetness to diverse desserts made in Eastern Asian countries. Libraries prepared from two V. angularis varieties referred to as Taejin Black and Taejin Red were paired-end sequenced using the Illumina HiSeq 2000 system. The raw data in this study can be available in NCBI SRA database with accession numbers of SRR3406660 and SRR3406553. After de novo transcriptome assembly using Trinity, we obtained 324,219 and 280,056 transcripts from Taejin Black and Taejin Red, respectively. We predicted a total of 238,321 proteins and 179,519 proteins for Taejin Black and Taejin Red, respectively, by the TransDecoder program. We carried out BLASTP on the predicted proteins against the Swiss-Prot protein sequence database to predict the putative functions of identified proteins. Taken together, we provide transcriptomes of two adzuki bean varieties by RNA-Seq, which might be usefully applied to generate molecular markers.

Foxtail millet (Setaria italica) belonging to the family Poaceae is an important millet that is widely cultivated in East Asia. Of the cultivated millets, the foxtail millet has the longest history and is one of the main food crops in South India and China. Moreover, foxtail millet is a model plant system for biofuel generation utilizing the C4 photosynthetic pathway. In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676 GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins. Taken together, this study provides transcriptome data for the foxtail millet variety Taejin by RNA-Seq.

Background: Next-generation sequencing (NGS) provides many possibilities for plant virology research. In this study, we performed integrated analyses using plant transcriptome data for plant virus identification using Apple stem grooving virus (ASGV) as an exemplar virus. We used 15 publicly available transcriptome libraries from three different studies, two mRNA-Seq studies and a small RNA-Seq study. Results: We de novo assembled nearly complete genomes of ASGV isolates Fuji and Cuiguan from apple and pear transcriptomes, respectively, and identified single nucleotide variations (SNVs) of ASGV within the transcriptomes. We demonstrated the application of NGS raw data to confirm viral infections in the plant transcriptomes. In addition, we compared the usability of two de novo assemblers, Trinity and Velvet, for virus identification and genome assembly. A phylogenetic tree revealed that ASGV and Citrus tatter leaf virus (CTLV) are the same virus, which was divided into two clades. Recombination analyses identified six recombination events from 21 viral genomes. Conclusions: Taken together, our in silico analyses using NGS data provide a successful application of plant transcriptomes to reveal extensive information associated with viral genome assembly, SNVs, phylogenetic relationships, and genetic recombination. [ABSTRACT FROM AUTHOR]

Aims Neuroprotective effects of maysin, which is a flavone glycoside that was isolated from the corn silk (CS, Zea mays L.) of a Korean hybrid corn Kwangpyeongok, against oxidative stress (H2O2)-induced apoptotic cell death of human neuroblastoma SK-N-MC cells were investigated. Main methods Maysin cytotoxicity was determined by measuring cell viability using MTT and lactate dehydrogenase (LDH) assays. Intracellular reactive oxygen species (ROS) were measured using a 2,7-dichlorofluorescein diacetate (DCF-DA) assay. Apoptotic cell death was monitored by annexin V-FITC/PI double staining and by a TUNEL assay. Antioxidant enzyme mRNA levels were determined by real-time PCR. The cleavage of poly (ADP-ribose) polymerase (PARP) was measured by western blotting. Key findings Maysin pretreatment reduced the cytotoxic effect of H2O2 on SK-N-MC cells, as shown by the increase in cell viability and by reduced LDH release. Maysin pretreatment also dose-dependently reduced the intracellular ROS level and inhibited PARP cleavage. In addition, DNA damage and H2O2-induced apoptotic cell death were significantly attenuated by maysin pretreatment. Moreover, maysin pretreatment (5-50 μg/ml) for 2 h significantly and dose-dependently increased the mRNA levels of antioxidant enzymes (CAT, GPx-1, SOD-1, SOD-2 and HO-1) in H2O2 (200 μM)-insulted cells. Significance These results suggest that CS maysin has neuroprotective effects against oxidative stress (H2O2)-induced apoptotic death of human brain SK-N-MC cells through its antioxidative action. This report is the first regarding neuroprotective health benefits of corn silk maysin by its anti-apoptotic action and by triggering the expression of intracellular antioxidant enzyme systems in SK-N-MC cells. [ABSTRACT FROM AUTHOR]

Background In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits. Results We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the shortread DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. Conclusions We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding. [ABSTRACT FROM AUTHOR]

Abstract  The phenolic content and the antioxidant capacity of ethanolic extract of rice grains were examined using three different rice (Oryza sativa L. var. japonica) varieties, Jakwangchalbyeo (red pericarp glutinous rice), Hwasunchalbyeo (white pericarp glutinous rice), and Ilpumbyeo (white pericarp non-glutinous rice). Quantitative high performance liquid chromatography (HPLC) analyses showed that Jakwangchalbyeo contains the highest amount of total phenolic substances. Radical scavenging activities measured by the 1,1-diphenyl-2-picryl hydrazyl (DPPH) assay were 87.5% (Jakwangchalbyeo), 45.0% (Hwasunchalbyeo), and 50.0% (Ilpumbyeo). The results suggest a positive correlation between the phenolic content and the antioxidation capacity. Antioxidant activity in the ethanolic extract of rice grain was further assessed with 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) cell viability assay and fluorescence-activated cell sorting (FACS) analysis of H4IIE cells treated with hydrogen peroxide (H2O2). Hwasunchalbyeo and Ilpumbyeo extracts showed no significant effects on H2O2-induced oxidative stress. Jakwangchalbyeo extract increased cell viability by up to 82% and 74% after 5- and 24-h treatments at 100 μg/mL, respectively. Consistent with the results of DPPH and MTT assays, dichlorofluorescein (DCF) fluorescence was further reduced when H2O2 was applied with Jakwangchalbyeo extract. In conclusion, red pericarp Jakwangchalbyeo grain extracts exerted significantly higher inhibitory effects on H2O2-induced oxidative stress in H4IIE cells than did other white pericarp rice grain extracts. [ABSTRACT FROM AUTHOR]

A chemical, MNU-induced hulless barley mutant line designated as 'Mutant 98 (M98)' was developed from a Korean hulless waxy barley cultivar, 'Chalssalbori'. The objective of the study was to determine the genetic basis of 'M98' and the possibility of using 'M98' as breeding parent to improve lysine level. Compared to 'Chalssalbori', 'M98' had large embryo and higher lysine content in both the embryo and endosperm. Significantly different lysine content in 'M98' and the other high-lysine barley mutant stocks was observed for two years. However, the genotype by year interaction was not significant. 'M98' was higher than the other high-lysine barley mutant stocks in the percentage of lysine of total amino acid composition (0.75%). The trait of shrunken endosperm of 'M98', which was typical in the high-lysine mutants, was inherited by a single recessive gene. Based on seed morphology and lysine content of F1 seeds, 'M98' had a genetically different gene from the other high-lysine mutants for shrunken endosperm. Segregation of F2 for plump/shrunken endosperm did not fit the expected ratio of Mendelian inheritance except for only one cross combination (GSHO1784 (lys1)/M98). The amino acid analysis of F5 and F6 progenies from the cross between 'M98' and 'Chalssalbori' revealed that the attempt to increase the range of lysine content of plump lines did not go beyond the limit of the average high-lysine barley germplasm. [ABSTRACT FROM AUTHOR]

We studied on improvement method of rutin content using mulberry leaf powder. Mulberry leaves were collected and then hot-air dried and powdered for experiment. As a result, we have developed a pre-treatment method that extracts mulberry leaf powder with water or fermented alcohol with reflux extractor and then increases the rutin content by improving the process. Citric acid (0.1 ~ 1%) and 1000 ml fermented alcohol (50 ~ 95%) or water (10 ~ 50 times) was extracted with 100 g of mulberry leaf powder using a reflux extraction device (80~90°C, 1 hour, twice). The extracts were collected, filtered and concentrated. For the recrystallization, the concentrate was dissolved by adding distilled water and allowed to stand at a low temperature. Then, the supernatant was discarded by centrifugation, and only the residue was lyophilized to prepare a final powder. As a result, regardless of the concentration of citric acid added, the content of rutin was higher in 90% fermented alcohol extract. Whereas, in the case of extracting with water, citric acid 0.5% was added to water 25 times as much as the weight of mulberry leaf powder, and 2274.4 (mg / 100g) of rutin content was highest in the case of refluxing twice at 80 ° C for 1 hour. The powder with increased rutin content is expected to be applicable to various foods as a food additive. In addition, it can contribute to the improvement of the farm income by promoting consumption of mulberry leaf while satisfying the consumers' desire for functional food intake. [ABSTRACT FROM AUTHOR]