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.

beta-Glucan enhanced apoptosis in human colon cancer cells SNU-C4.

The apoptotic effect of bacteria-derived beta-glucan was investigated in human colon cancer cells SNU-C4 using terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick end labeling (TUNEL) assay, reverse transcription-polymerase chain reaction (RT-PCR) expressions of Bcl-2, Bax, and Caspase-3 genes, and assay of caspase-3 enzyme activity. beta-Glucan of 10, 50, and 100 microg/mL decreased cell viability in a dose-dependent manner with typical apoptotic characteristics, such as morphological changes of chromatin condensation and apoptotic body formation from TUNEL assay. In addition, beta-glucan (100 microg/mL) decreased the expression of Bcl-2 by 0.6 times, whereas the expression of Bax and Caspase-3 were increased by 3.1 and 2.3 times, respectively, compared to untreated control group. Furthermore, the caspase-3 activity in the beta-glucan-treated group was significantly increased compared to those in control group (P < 0.05). Bacterial derived beta-glucan could be used as an effective compound inducing apoptosis in human colon cancer.

Immunostimulatory effects of oriental plum (Prunus salicina Lindl.).

The fruit of the plum tree (Prunus salicina Lindl.) has been used as a traditional medicinal food in humans to enhance immunity against infectious agents and to treat cancers. However, limited information exists on the mechanisms responsible for its immune enhancing properties. In this study, the immunostimulatory effects of a methanol extract of plum fruit following methanol evaporation and dissolving in PBS were assessed by in vitro lymphocyte proliferation, tumor cell cytotoxicity, and nitric oxide (NO) production. The crude methanol extract stimulated spleen lymphocyte proliferation and NO production by cultured macrophages, and inhibited the viability of tumor cells, significantly greater than media controls. Sequential gel filtration chromatographic separation of the extract on Sephadex G-25 and Sephacryl S-200 gel filtration columns resulted in a more purified preparation that retained the ability to induce lymphoproliferation, tumor killing, and NO production. These results suggest that Prunus salicina contains immunostimulatory components that potentially may be useful in human and veterinary medicine.

A fluorometric assay to determine antioxidant activity of both hydrophilic and lipophilic components in plant foods.

This study aimed to develop a fluorometric method to determine total antioxidant activity of plant foods. The antioxidant activities in plant foods were determined after extracting (1) hydrophilic components with acidified methanol (methanol:glacial acetate acid:water=50:3.7:46.3), (2) lipophilic components with methanol followed by tetrahydrofuran (THF), or (3) both hydrophilic and lipophilic components using sequential extraction of acidified methanol and THF together. Both the hydrophilic assay [using the hydrophilic radical initiator 2,2'-azobis-(2-amidinopropane)dihydrochloride (10 mmol/L) and hydrophilic probe 2,7-dichlorodihydrofluorescein (DCFH)] and the lipophilic assay [using the lipophilic radical initiator [2,2'-azobis (4-methoxiy-2,4-dimethylvaleronitrile), 2 mmol/L], and the lipophilic probe 4,4-difluoro-5-(4-phenyl-1,3-butadienyl)-4-bora-3a,4a-diaza-s-indacene-3-undecanoic acid (C11-BODIPY 581/591) (BODIPY: 2 micromol/L)] were used to measure antioxidant activity. The inhibition of BODIPY oxidation was significantly increased (P<.01) when both the hydrophilic and lipophilic components were extracted using acidified methanol and organic solvent as compared to those extracted by organic solvent alone. In addition, the rate of DCFH oxidation was significantly delayed (P<.05) when both components coexisted compared to DCFH oxidation of the hydrophilic component alone. The combination of lipophilic and hydrophilic components in these plant foods showed significantly greater antioxidant activity than that of either hydrophilic or lipophilic component alone. Thus, both hydrophilic and lipophilic components in plant foods and their interactions should be considered when determining their antioxidant activity.

Immunomodulatory properties of dietary plum on coccidiosis.

The current study was conducted to evaluate the effect of dietary supplementation with a lyophilized powder made from plums (P) on host protective immune responses against avian coccidiosis, the most economically important parasitic disease of poultry. One-day-old White Leghorn chickens were fed from the time of hatch with a standard diet either without P (control and P 0 groups) or supplemented with P at 0.5% (P 0.5) or 1.0% (P 1.0) of the diet. Animals in the P 0, P 0.5, and P 1.0 groups were orally challenged with 5000 sporulated oocysts of Eimeria acervulina at day 12 post-hatch, while control animals were uninfected. Dietary supplementation of P increased body weight gain, reduced fecal oocyst shedding, and increased the levels of mRNAs for interferon-gamma and interleukin-15 in the P 1.0 group at 10 days post-infection compared with the P 0 group. Furthermore, chickens fed either the P 0.5 or P 1.0 diets exhibited significantly greater spleen cell proliferation compared with the non-plum P 0 group. These results indicate that plum possesses immune enhancing properties, and that feeding chickens a plum-supplemented diet augments protective immunity against coccidiosis.

In vitro treatment of chicken peripheral blood lymphocytes, macrophages, and tumor cells with extracts of Korean medicinal plants.

A variety of different medicinal plants have traditionally been used in Asian cultures as medicinal plants to enhance immunity and treat cancers. However, limited information exists on the underlying mechanisms responsible for these immune enhancing properties. The current investigation was conducted to examine the effects of methanol extracts of 3 Korean indigenous plants (dandelion root, mustard leaf, and safflower leaf) on various in vitro parameters of innate immunity (peripheral blood lymphocyte proliferation, nitric oxide production by macrophages, and free radical scavenging activity) and tumor cell growth. All plant extracts inhibited tumor cell growth and exerted antioxidant effects compared with vehicle controls. In addition, safflower leaf extract stimulated lymphocyte proliferation and mustard leaf induced nitric oxide production. These results demonstrate, for the first time, that traditional Korean medicinal plant extracts are effective in enhancing innate immunity and suppressing tumor cell growth.

Effect of a Pholiota adiposa Extract on Fat Mass in Hyperlipidemic Mice.

The purpose of this study was to investigate the effect of a Pholiota adiposa extract on fat mass in hyperlipidemic mice fed on a high-fat diet. The water extracts from P. adiposa (ASI 24018) were not affected in the total triglyceride contents and epididymal fat mass in mice fed on a high-fat diet, but the retroperitoneal fat mass decreased significantly. This result suggests that the P. adiposa extract may be a potential candidate for use as a functional food that can act as a prophylactic against hyperlipidemia. However, the P. adiposa extract showed no effect in the total triglyceride contents and epididymal fat mass.