The pepper virome: natural co-infection of diverse viruses and their quasispecies.

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.

Integrated analyses using RNA-Seq data reveal viral genomes, single nucleotide variations, the phylogenetic relationship, and recombination for Apple stem grooving virus.

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.

The complete genomic sequence of a tentative new polerovirus identified in barley in South Korea.

The complete nucleotide sequence of a new barley polerovirus, tentatively named barley virus G (BVG), which was isolated in Gimje, South Korea, has been determined using an RNA sequencing technique combined with polymerase chain reaction methods. The viral genomic RNA of BVG is 5,620 nucleotides long and contains six typical open reading frames commonly observed in other poleroviruses. Sequence comparisons revealed that BVG is most closely related to maize yellow dwarf virus-RMV, with the highest amino acid identities being less than 90 % for all of the corresponding proteins. These results suggested that BVG is a member of a new species in the genus Polerovirus.

Mangosenone F, A Furanoxanthone from Garciana mangostana, Induces Reactive Oxygen Species-Mediated Apoptosis in Lung Cancer Cells and Decreases Xenograft Tumor Growth.

Mangosenone F (MSF), a natural xanthone, was isolated form Carcinia mangotana, and a few studies have reported its glycosidase inhibitor effect. In this study we investigated the anti lung cancer effect of MSF both in vitro and in vivo. MSF inhibited cancer cell cytotoxicity and induced and induced apoptosis via reactive oxygen species (ROS) generation in NCI-H460. MSF treatment also showed in pronounced release of apoptogenic cytochrome c from the mitochondria to the cytosol, downregulation of Bcl-2 and Bcl-xL, and upregulation of Bax, suggesting that caspase-mediated pathways were involved in MSF-induced apoptosis. ROS activation of the mitogen-activated protein kinase signaling pathway was shown to play a predominant role in the apoptosis mechanism of MSF. Compared with cisplatin treatment, MSF treatment showed significantly increased inhibition of the growth of NCI-H460 cells xenografted in nude mice. Together, these results indicate the potential of MSF as a candidate natural anticancer drug by promoting ROS production.

A correlation between tocopherol content and antioxidant activity in seeds and germinating seeds of soybean cultivars.

BACKGROUND: Tocopherols are crucial lipid-soluble antioxidants and essential nutrients. There is increasing interest in the biofortification of crops with vitamin E for reducing micronutrient malnutrition. However, relatively little is known about the development of soybean cultivars with high levels of tocopherol through combined breeding. RESULT: Tocopherol contents of seeds and germinating seeds of 28 Korean soybean cultivars were analyzed and evaluated for health-promoting activities. Total tocopherol concentrations ranged from 203.9 to 503.1 µg g⁻¹ in seeds and from 20.1 to 230.1 µg g⁻¹ in germinating seeds. The traditional landraces of HaNagari (HN, 503.1 µg g⁻¹), Orialtae (OL, 486.6 µg g⁻¹), SuMoktae (SM, 476.5 µg g⁻¹) and SoRitae (SR, 475.5 µg g⁻¹) showed high levels of tocopherol content. The contents of the four isomers of tocopherol in seeds and germinating seeds were correlated with lipid peroxidation. The γ- and δ-tocopherol contents in seeds were related to 1,1-diphenyl-2-picrylhydrazyl free radical scavenging activity (0.434; P < 0.01 and 0.373; P < 0.05). CONCLUSION: Total tocopherol content was higher in soybean landraces as compared with modern cultivars developed by cross-breeding. These results suggest that soybean breeding is necessary to increase tocopherol levels.

Variation block-based genomics method for crop plants.

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 short-read 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.

Timing and Pattern of Anthocyanin Accumulation during Grain Filling in Purple Waxy Corn (Zea mays L.) Suggest Optimal Harvest Dates.

Purple-corn kernels contain anthocyanins, a group of antioxidants proposed to be beneficial to human health. This study investigated the concentrations of anthocyanins and amino acids and the composition of fatty acids in the kernels of purple waxy corn (Zea mays L.) "Heukjinjuchal" during grain filling to determine when the grain nutritional value is at its highest. During grain filling, anthocyanin contents increased as the kernel color darkened. Among the anthocyanins measured, cyanidin-3-ß-O-glucoside reached the highest contents, 57.0-409.1 mg kg-1 fresh weight in raw kernels and 1027.6 mg kg-1 in dry seeds. Pelargonidin-3-ß-O-glucoside and malvidin-3-ß-O-glucoside became detectable at 21 days after silking; they occurred in the second- and third-highest amounts, respectively, among anthocyanins in the purple-corn cultivars tested. The anthocyanin accumulation pattern was strongly associated with physicochemical properties and partly associated with amino acid content. Anthocyanin contents increased in a stepwise rather than linear fashion. This study showed that kernels undergo dramatic changes that affect the nutritional value of fresh corn.

Germinated soy germ extract ameliorates obesity through beige fat activation.

Obesity is a worldwide public health concern requiring safe and effective strategies. Recent studies suggest that bioactive compounds from soybeans have beneficial effects on weight loss and reducing fat accumulation. However, despite the biochemical and nutritional changes during germination, the biological effects of germinated soy germ have not been fully investigated. In this article, germinated soy germ extract (GSGE) was evaluated as a potential treatment option for obesity using 3T3-L1 pre-adipocyte and high-fat diet (HFD)-induced obese mice. In vitro studies demonstrated that GSGE suppressed the differentiation of 3T3-L1 cells into mature adipocytes, along with reductions in lipid accumulation and lipid droplet formation. In vivo studies also showed that a daily dose of 1 mg kg-1 of GSGE reduced weight gain, adipocyte area, serum triglyceride, and LDL-cholesterol in HFD-fed mice. The GSGE treatment promoted browning, which was associated with increased UCP1 expression in vitro and in vivo. In addition, GSGE treatment induced beige fat activation by upregulation of lipolysis and beta-oxidation. Furthermore, gene and protein expression levels of endocannabinoid system-related factors such as NAPE-PLD, FAAH, DAGL-α, and CB2 were altered along with browning and beige fat activation by GSGE. The present study indicates that GSGE effectively inhibits lipid accumulation and promotes beige fat transition and activation. Therefore, we suggest that GSGE treatment could be a promising strategy for the prevention of obesity by promoting weight loss, reducing fat accumulation, and improving obesity-related metabolic disorders.

Characterization of Soybean Germinated Embryo Extract as an Estrogen Receptor Subtype-Selective and Tissue-Specific Modulator.

Phytoestrogens possess beneficial effects in the management of menopausal symptoms with few side effects. Soybeans are major natural sources of isoflavones, with high estrogen receptor (ER)-ß selectivity. The objective of this study therefore was to develop a solvent-mediated extraction method for soybean germinated embryos (SGEs) and to investigate the biological activities of the extract. Ethanolic extraction yielded the SGE extract (SGEE), which had a unique composition of biologically active aglycones and soyasaponins. SGEE showed a proliferative effect in MCF7 cells and ERß-selective transcriptional activities in human embryonic kidney cells. In addition, oral administration of SGEE to ovariectomized rats resulted in the induction of ERß and estrogen-responsive genes in the uterus and a decrease in tail skin temperature and uterus weight. Our data suggest that germination and ethanolic extraction are effective measures for producing isoflavone-rich food supplements, which may be useful as alternative menopausal hormone therapy.

Acute and Subacute Toxicity Evaluation of Corn Silk Extract.

Many studies have reported therapeutic efficacy of corn silk extract. However, research on its toxicity and safe dose range is limited. Thus, the objective of this study was to determine the acute and subacute toxicity of corn silk extract in ICR mice. To determine acute toxicity, corn silk extract containing high levels of maysin was orally administered to mice at a dose of 0 or 2,000 mg/kg. Clinical symptoms, mortality, and body weight changes were recorded for 14 days. To determine subacute toxicity, corn silk extract was orally administered to mice over a 4-week period, and then body weight, water and food consumption, and organ weight were determined. In addition, urine and serum analyses were performed. In the acute toxicity study, no death or abnormal symptoms was observed in all treatment groups during the study period. Body weights did not show any significant change compared to those of the control group. Lethal dose of corn silk extract was estimated to be more than 2,000 mg/kg. In the 4-week subacute toxicity study, there was no corn silk extract related toxic effect on body weight, water intake, food consumption, urine parameters, clinical chemistry, or organ weight. Histopathological examination showed no abnormality related to the administration of corn silk extract at 500 mg/kg. The maximum non-toxic dose of corn silk extract containing high levels of maysin was found to be more than 500 mg/kg.

Changes in the functional components and radical scavenging activity of maize under various roasting conditions.

The phenolic compounds and radical scavenging activity of ethanolic extracts from maize at various roasting conditions were evaluated in this research. The free sugar contents in roasted maize significantly decreased with higher roasting temperature and longer roasting time. The total polyphenol and total flavonoid contents in roasted maize significantly increased with higher roasting temperature and longer roasting time. The predominant phenolic acid in the roasted maize was homogentisic acid. The contents of homogentisic acid and myricetin in roasted maize significantly increased with higher roasting temperature and longer roasting time. The DPPH and ABTS radical scavenging activities of roasted maize significantly increased with higher roasting temperature and longer roasting time. DPPH and ABTS radical scavenging activities were positively correlated with phenolic compounds. The activities of these components increased following heat treatments because of the low molecularization effects of the heating process, which resulted in active, low-molecular-weight components that were readily extracted.

Germinated soy germ with increased soyasaponin Ab improves BMP-2-induced bone formation and protects against in vivo bone loss in osteoporosis.

Osteoporosis is frequently induced following menopause, and bone fractures result in serious problems including skeletal deformity, pain, and increased mortality. Therefore, safe and effective therapeutic agents are needed for osteoporosis. This study aimed to clarify the bone protecting effects of germinated soy germ extracts (GSGE) and their mode of action. GSGE increased expression of alkaline phosphatase (ALP) and osteocalcin (OCL) by stimulating the expression of runt-related transcription factor 2 (Runx2) and osterix (Osx) through activation of Smad signaling molecules. Furthermore, germination of soy germ increased levels of nutritional components, especially soyasaponin Ab. The anabolic activity of soyasaponin Ab in GSGE was also evaluated. GSGE and soyasaponin Ab significantly protected against ovariectomy (OVX)-induced bone loss and improved bone-specific alkaline phosphatase (BALP) level in mouse serum. These in vitro and in vivo study results demonstrated that GSGE and soyasaponin Ab have potential as therapeutic candidate agents for bone protection in postmenopausal osteoporosis.

Comparison of isoflavone concentrations in soybean (Glycine max (L.) Merrill) sprouts grown under two different light conditions.

We determined and compared the composition and content of isoflavones in the cotyledon, hypocotyl, and root of 17 soybean sprout varieties grown under dark and light conditions. The total average isoflavone concentrations in 17 soybean sprout varieties were 2167 microg g(-1) (green sprout) and 2538 microg g(-1) (yellow sprout) in cotyledons, 1169 microg g(-1) (green sprout) and 1132 microg g(-1) (yellow sprout) in hypocotyls, and 2399 microg g(-1) (green sprout) and 2852 microg g(-1) (yellow sprout) in roots. There were no significant differences in total isoflavone concentrations between the green and yellow sprouts. However, significant differences in total isoflavone amounts were observed among the three organs, with roots exhibiting the highest total isoflavone concentrations followed by cotyledons and hypocotyls. Total daidzin concentrations of green (775 microg g(-1)) and yellow (897 microg g(-1)) sprouts increased to more than 4 times that in seeds (187 microg g(-1)). Yellow sprouts contained the highest (1122 microg g(-1)) total genistin concentrations, and green (155 microg g(-1)) and yellow (155 microg g(-1)) sprouts had more total glycitin concentrations than seeds. In cotyledons of green and yellow sprouts, genistin, daidzen, and glycitin constituted more than 67%, more than 28%, and less than 4% of the total isoflavone contents, respectively. In hypocotyls, total daidzin represented more than 45% of the total isoflavones, and total glycitin was higher than in cotyledons and roots. Malonylglycoside concentrations were highest in cotyledons, whereas glycoside concentrations were highest in hypocotyls and roots. The high accumulation of isoflavones in roots is consistent with isoflavones serving as signal molecules in the induction of microbial genes involved in soybean (Glycine max) nodulation.

Anti-inflammatory effect of Ulmus davidiana Planch (Ulmaceae) on collagen-induced inflammation in rats.

Ulmus davidiana Planch (Ulmaceae) extract (UD) has long been known to have anti-inflammatory and anticancer activities. UD has been also known to have protective effects on damaged tissue, inflammation and bone among other functions. Effects of UD on inflammatory and immune responses and its mechanisms in collagen-induced inflammation (CII) rat were studied. Hind paw volumes of rats were measured by volume meter; lymphocyte proliferation, interleukin (IL)-1, IL-2, tumor necrosis factor (TNF)-α level was determined by 3-(4,5-2dimethylthiazal-2yl)2,5-diphenyltetrazoliumbromide assay. Antibodies to collagen type II (BC-II) were determined by enzyme-linked immunosorbent assay. There was a marked secondary inflammatory response in CII model, which accompanied with the decrease of body weight and the weight of immune organs simultaneously. The administration of UD (20, 80, 150mg/kg, intragastrically×10 days) inhibited the inflammatory response and restored body weight and the weight of immune organs of CII rats. Lymphocyte proliferation and IL-2 production of CII rats increases, together with IL-1 and TNF-α in peritoneal macrophages and synoviocytes. The administration of UD (20, 80, 150mg/kg, 10 days) reduced above changes significantly. UD had no effect on the concentration of antibodies to BC-II. From the results, it was concluded that UD possesses anti-inflammatory and immunoregulatory activities and has a therapeutic effect on CII rats.

Corn silk maysin ameliorates obesity in vitro and in vivo via suppression of lipogenesis, differentiation, and function of adipocytes.

Present study was aimed to investigate the potential anti-obesity effects of maysin, a major flavonoid of corn silk, in vitro and in vivo using 3T3-L1 preadipocyte cells and C57BL/6 mice. Maysin decreased the levels of intracellular lipid droplets and triglycerides (TG), and down-regulated the protein expression levels of C/EBP-ß, C/EBP-α, PPAR-γ, and aP2 in 3T3-L1 preadipocyte cells, suggesting that maysin inhibits lipid accumulation and adipocyte differentiation. In addition, maysin was shown to induce the apoptotic cell death in 3T3-L1 preadipocyte cells via activation of caspase cascades and mitochondrial dysfunction, which may ultimately lead to reduction of adipose tissue mass. Furthermore, oral administration of maysin (25mg/kg body weight) decreased weight gain and epididymal fat weight in high-fat diet (HFD)-fed C57BL/6 mice. Administration of maysin also reduced serum levels of TG, total-cholesterol, LDL-cholesterol, and glucose. Taken collectively, these results suggest for the first time that the purified maysin exerts an anti-obesity effect in vitro and in vivo. These observations may support the applicability of maysin as a potent functional ingredient in health-beneficial foods or as a therapeutic agent to prevent or treat obesity.

Corn silk extract improves benign prostatic hyperplasia in experimental rat model.

BACKGROUND/OBJECTIVES: This study was conducted to investigate the effect of a corn silk extract on improving benign prostatic hyperplasia (BPH). MATERIALS/METHODS: The experimental animals, 6-week-old male Wistar rats, were divided into sham-operated control (Sham) and experimental groups. The experimental group, which underwent orchiectomy and received subcutaneous injection of 10 mg/kg of testosterone propionate to induce BPH, was divided into a Testo Only group that received only testosterone, a Testo+Fina group that received testosterone and 5 mg/kg finasteride, a Testo+CSE10 group that received testosterone and 10 mg/kg of corn silk extract, and a Testo+CSE100 group that received testosterone and 100 mg/kg of corn silk extract. Prostate weight and concentrations of dihydrotestosterone (DHT), 5α-reductase 2 (5α-R2), and prostate specific antigen (PSA) in serum or prostate tissue were determined. The mRNA expressions of 5α-R2 and proliferating cell nuclear antigen (PCNA) in prostate tissue were also measured. RESULTS: Compared to the Sham group, prostate weight was significantly higher in the Testo Only group and decreased significantly in the Testo+Fina, Testo+CSE10, and Testo+CSE100 groups (P < 0.05), results that were consistent with those for serum DHT concentrations. The concentrations of 5α-R2 in serum and prostate as well as the mRNA expression of 5α-R2 in prostate were significantly lower in the Testo+Fina, Testo+CSE10, and Testo+CSE100 groups than that in the Testo Only group (P < 0.05). Similarly, the concentrations of PSA in serum and prostate were significantly lower in the Testo+Fina, Testo+CSE10, and Testo+CSE100 groups (P < 0.05) than in the Testo Only group. The mRNA expression of PCNA in prostate dose-independently decreased in the Testo+CSE-treated groups (P < 0.05). CONCLUSIONS: BPH was induced through injection of testosterone, and corn silk extract treatment improved BPH symptoms by inhibiting the mRNA expression of 5α-R2 and decreasing the amount of 5α-R2, DHT, and PSA in serum and prostate tissue.

De novo Genome Assembly and Single Nucleotide Variations for Soybean Mosaic Virus Using Soybean Seed Transcriptome Data.

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.

Evaluation of soyasaponin, isoflavone, protein, lipid, and free sugar accumulation in developing soybean seeds.

A combination of analytical techniques was used to examine and quantify seed compositional components such as protein, lipid, free sugars, isoflavones, and soyasaponins during soybean development and maturation in two Korean soybean cultivars. Protein accumulation was rapid during reproductive stages, while lipid content was only relatively moderately increased. The major carbohydrate saccarides sucrose and stachyose constantly increased during the reproductive stage. Previously published results suggest that the free sugar and lipid content reached their maximal concentrations at a relatively early stage of seed development and remain constant in comparison to other chemical components. The malonylglucosides were the predominant isoflavone form followed by the glucosides, acetyl glucosides, and aglycone forms. As soybean seed matures, total soyasaponin concentration was constantly decreased until the R8 stage. Soyasaponin beta(g) was the major soyasaponin in DDMP-conjugated group B soyasaponins, followed by the non-DDMP counterpart soyasaponin I and soyasaponin A1. The ratio of total isoflavone to total soyasaponin in the developing soybean increased from 0.06 to 1.31. Protein, lipid, and free sugar contents in the developing soybean seeds showed significant positive correlations with conjugated isoflavones and total isoflavone concentration, while the lipid contents showed a negative correlation with the isoflavone aglycone. Protein, lipid, and free sugar contents showed a negative correlation with total group A and B soyasaponins and total soyasaponins; however, only the soyasaponin A content was significantly negatively correlated with free sugar content. Total soyasaponin content was negatively correlated with isoflavone content (r = -0.828 at p < 0.01).

Classification of 31 Korean Wheat (Triticum aestivum L.) Cultivars Based on the Chemical Compositions.

Whole grain wheat flour (WGWF) is the entire grain (bran, endosperm, and germ) milled to make flour. The WGWF of 31 Korean wheat (Triticum aestivum L.) cultivars were analyzed for the chemical compositions, and classified into groups by hierarchical cluster analysis (HCL). The average composition values showed a substantial variation among wheat varieties due to different wheat varieties. Wheat cv. Shinmichal1 (waxy wheat) had the highest ash, lipid, and total dietary fiber contents of 1.76, 3.14, and 15.49 g/100 g, respectively. Using HCL efficiently classified wheat cultivars into 7 clusters. Namhae, Sukang, Gobun, and Joeun contained higher protein values (12.88%) and dietary fiber (13.74 %). Regarding multi-trait crop breeding, the variation in chemical compositions found between the clusters might be attributed to wheat genotypes, which was an important factor in accumulating those chemicals in wheat grains. Thus, once wheat cultivars with agronomic characteristics were identified, those properties might be included in the breeding process to develop a new variety of wheat with the trait.

De novo transcriptome assembly of Sorghum bicolor variety Taejin.

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.