• Title/Summary/Keyword: DNA-index

Search Result 317, Processing Time 0.023 seconds

Effects of Bacillus subtilis KN-42 on Growth Performance, Diarrhea and Faecal Bacterial Flora of Weaned Piglets

  • Hu, Yuanliang;Dun, Yaohao;Li, Shenao;Zhao, Shumiao;Peng, Nan;Liang, Yunxiang
    • Asian-Australasian Journal of Animal Sciences
    • /
    • v.27 no.8
    • /
    • pp.1131-1140
    • /
    • 2014
  • This research focused on the effects of different doses of Bacillus subtilis KN-42 on the growth performance, diarrhea incidence, faecal bacterial flora, and the relative number of Lactobacillus and Escherichia coli in faeces of weaned piglets to determine whether the strain can serve as a candidate antimicrobial growth promoter. A total of 360 piglets (initial body weight $7.14{\pm}0.63$ kg) weaned at $26{\pm}2$ days of age were randomly allotted to 5 treatment groups (4 pens per treatment with 18 pigs per pen) for a 28-day trial. Dietary treatments were basal diet without any antimicrobial (negative control; NC), basal diet supplemented with 120 mg/kg feed of neomycin sulfate (positive control; PC) and basal diet supplemented with $2{\times}10^9$ (L), $4{\times}10^9$ (M) and $20{\times}10^9$ (H) CFU/kg feed of B. subtilis KN-42. During the overall period, average daily gain and feed efficiency of piglets were higher in groups PC, M, and H than those in group NC (p<0.05), and all probiotics and antibiotics groups had a lower diarrhea index than group NC (p<0.05). The 16S rDNA gene-based methods were used to analyze faecal bacterial flora on day 28 of experiment. The result of denaturing gradient gel electrophoresis analysis showed that supplementation of B. subtilis KN-42 to the diet changed the bacterial communities, with a higher bacterial diversity and band number in group M than in the other four groups. Real-time polymerase chain reaction analysis showed that the relative number of Lactobacillus were higher in groups PC and H than in group NC (p<0.05), and the supplemented B. subtilis KN-42 to the diet also reduced the relative number of E. coli (p<0.05). These results suggest that dietary addition of B. subtilis KN-42 can improve the growth performance and gastrointestinal health of piglets.

Molecular Genetic Identification of Yeast Strains Isolated from Egyptian Soils for Solubilization of Inorganic Phosphates and Growth Promotion of Corn Plants

  • Hesham, Abd El-Latif;Mohamed, Hashem M.
    • Journal of Microbiology and Biotechnology
    • /
    • v.21 no.1
    • /
    • pp.55-61
    • /
    • 2011
  • Forty yeast strains isolated from soils taken from different locations in Egypt were tested for their P-solubilizing activities on the basis of analyzing the clear zone around colonies growing on a tricalcium phosphate medium after incubation for 5 days at $25^{\circ}C$, denoted as the solubilization index (SI). Nine isolates that exhibited P-solubilization potential with an SI ranging from 1.19 to 2.76 were genetically characterized as five yeasts belonging to the genus Saccharomyces cerevisiae and four non-Saccharomyces, based on a PCR analysis of the ITS1-26S region amplied by SC1/SC2 species-specific primers. The highest P-solubilization efficiency was demonstrated by isolate PSY- 4, which was identified as Saccharomyces cerevisiae by a sequence analysis of the variable D1/D2 domain of the 26S rDNA. The effects of single and mixed inoculations with yeast PSY-4 and Bacillus polymyxa on the P-uptake and growth of corn were tested in a greenhouse experiment using different levels of a phosphorus chemical fertilizer (50, 100, and 200 kg/ha super phosphate 15.5% $P_2O_5$). The results showed that inoculating the corn with yeast PSY-4 or B. polymyxa caused significant increases in the shoot and root dry weights and P-uptake in the shoots and roots. The P-fertilization level also had a significant influence on the shoot and root dry weights and P-uptake in the shoots and roots when increasing the P-level from 50 up to 200 kg/ha. Dual inoculation with yeast strain PSY-4 and B. polymyxa at a P-fertilization level of 200 kg/ha gave higher values for the shoot and root dry weights and P-uptake in the shoots and roots, yet these increases were nonsignificant when compared with dual inoculation with yeast strain PSY-4 and B. polymyxa at a P-fertilization level of 100 kg/ha. The best increases were obtained from dual inoculation with yeast strain PSY-4 and B. polymyxa at a P-fertilization level of 100 kg/ha, which induced the following percentage increases in the shoot and root dry weights, and P-uptake in the shoots and roots; 16.22%, 46.92%, 10.09%, and 31.07%, respectively, when compared with the uninoculated control (fertilized with 100 kg/ha).

The Effect of Isoflavone Supplement on Plasma Lipids & Antioxidant Status in Hypercholesterolemic Postmenopausal Women (고지혈증인 폐경 후 여성에서 이소플라본 보충이 혈청 지질 농도 및 항산화능에 미치는 영향)

  • Lee, Jong-Ho;Kim, Eun-Mi;Chae, Ji-Sook;Jang, Yang-Soo;Lee, Jin-Hee;Lee, Geun
    • Journal of Nutrition and Health
    • /
    • v.36 no.6
    • /
    • pp.603-612
    • /
    • 2003
  • Postmenopausal women are at an increased risk of developing coronary artery disease. This is due to primarily dyslipidemia accompanying the loss of estrogen secretion. Soy isoflavones are known to have weak estrogenic effects. The purpose of this study is to investigate whether isoflavone supplement improves the risk of cardiovascular disease in hypercholesterolemic postmenopausal women. Subjects consisted of 39 Korean postmenopausal women with hypercholesterolemia (total cholesterol $\geq$ 200 mg/㎗ or LDL cholesterol $\geq$ 130 mg/㎗). Subjects were divided into 2 groups; placebo group (PG), isoflavone supplement group (IG). During 12 weeks, subjects were given placebo and 80mg isoflavone daily. Anthropometric measurement, blood sample analysis and dietary intake measurement were taken at baseline and after 12 weeks. After 12 weeks, systolic blood pressure was decreased significantly (p < 0.01) and plasma HDL cholesterol level was increased significantly (p < 0.05) in IG. But there were no significant changes in plasma total cholesterol, LDL cholesterol and triglyceride levels after isoflavone supplementation. There was a negative correlation between initial plasma HDL cholesterol level and the extent of plasma HDL cholesterol reduction in IG (r=-0.572, p=0.012). Atherogenic index (AI), total-/LDL- cholesterol ratio and LDL/HDL cholesterol ratio were improved significantly after isoflavone supplementation. In subjects whose initial plasma LDL cholesterol level were above 160 mg/㎗, plasma malondialdehyde (MDA) level were decreased and total antioxidant status (TAS) were increased significantly after isoflavone supplement (p < 0.05). However there were no significant changes in flow-mediated dilator (FMD), the marker of endothelium-dependent vasodilation and nitroglycerine-mediated dilator (NMD), the marker of endothelium-independent vasodilation and the extent of DNA damage after isoflavone supplement. In conclusion, these results indicate that isoflavone supplement may decrease the risk of cardiovascular disease via improving blood pressure, HDL cholesterol level and AI in hypercholesterolemic postmenopausal women. Futhermore, in case of subjects with elevated LDL cholesterol level, isoflavone supplementation may have more antiatherogenic effects via improving antioxidant status.

A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Carcass Traits in Hanwoo Populations

  • Lee, Y.-M.;Han, C.-M.;Li, Yi;Lee, J.-J.;Kim, L.H.;Kim, J.-H.;Kim, D.-I.;Lee, S.-S.;Park, B.-L.;Shin, H.-D.;Kim, K.-S.;Kim, N.-S.;Kim, Jong-Joo
    • Asian-Australasian Journal of Animal Sciences
    • /
    • v.23 no.4
    • /
    • pp.417-424
    • /
    • 2010
  • The purpose of this study was to detect significant SNPs for carcass quality traits using DNA chips of high SNP density in Hanwoo populations. Carcass data of two hundred and eighty nine steers sired by 30 Korean proven sires were collected from two regions; the Hanwoo Improvement Center of National Agricultural Cooperative Federation in Seosan, Chungnam province and the commercial farms in Gyeongbuk province. The steers in Seosan were born between spring and fall of 2006 and those in Gyeonbuk between falls of 2004 and 2005. The former steers were slaughtered at approximately 24 months, while the latter steers were fed six months longer before slaughter. Among the 55,074 SNPs in the Illumina bovine 50K chip, a total of 32,756 available SNPs were selected for whole genome association study. After adjusting for the effects of sire, region and slaughter age, phenotypes were regressed on each SNP using a simple linear regression model. For the significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were selected using a stepwise regression procedure, and inclusion and exclusion of each SNP out of the model was determined at the p<0.001 level. A total of 118 SNPs were detected; 15, 20, 22, 28, 20, and 13 SNPs for final weight before slaughter, carcass weight, backfat thickness, weight index, longissimus dorsi muscle area, and marbling score, respectively. Among the significant SNPs, the best set of 44 SNPs was determined by stepwise regression procedures with 7, 9, 6, 9, 7, and 6 SNPs for the respective traits. Each set of SNPs per trait explained 20-40% of phenotypic variance. The number of detected SNPs per trait was not great in whole genome association tests, suggesting additional phenotype and genotype data are required to get more power to detect the trait-related SNPs with high accuracy for estimation of the SNP effect. These SNP markers could be applied to commercial Hanwoo populations via marker-assisted selection to verify the SNP effects and to improve genetic potentials in successive generations of the Hanwoo populations.

Comparative Analysis of Endophytic Bacterial Communities in the Roots of Rice Grown under Long-term Fertilization Practice using Pyrosequencing Method (파이로시퀀싱을 이용한 비료 장기 연용지의 벼 뿌리 내생세균의 군집 분석)

  • Kim, Byung-Yong;Ahn, Jae-Hyung;Song, Jaekyeong;Kim, Myung-Sook;Weon, Hang-Yeon
    • Korean Journal of Soil Science and Fertilizer
    • /
    • v.45 no.6
    • /
    • pp.1100-1107
    • /
    • 2012
  • Bacterial endophytes may be important factors in plant growth and ecologically relevant functions in rice. Using pyrosequencing technology, we analyzed the composition of endophytic bacterial communities that colonized the roots of rice cultivated in long-term fertilized (APK) and non-fertilized (NF) paddy soils. A total of 1,900 reads were obtained from 2 samples. All sequences were classified into 177 OTUs (APK sample) or 72 OTUs (NF sample) at a 97% similarity cut-off. Twenty-two OTUs were shared between the 2 samples, and these were also the most dominant OTUs in both samples. Proteobacteria was the most dominant phylum with 90.2%, followed by Actinobacteria (7.1%) and Bacteroidetes (1.1%). Furthermore, Pseudomonas was the most abundant genus in both samples. We observed clear differences in the structure of the endophytic bacterial community structure between the 2 samples. Notably, the distributions of Alphaproteobacteria and Gammaproteobacteria were markedly different. The diversity index of the APK sample was higher than that of the NF sample. These findings showed that the endophytic bacterial community of rice roots was affected by the presence of fertilizers in the rice field soil.

Fungal Biodiversity in Cardamom Protected Forests and Seima Biodiversity Conservation Area of Cambodia

  • Kim, Nam Kyu;Lee, Jin Heung;Jo, Jong Won;Bunthoeun, Roth;Ngeth, Chea;Lee, Jong Kyu
    • Journal of Forest and Environmental Science
    • /
    • v.32 no.2
    • /
    • pp.158-163
    • /
    • 2016
  • Mushroom surveys and collections were conducted in the western and eastern forest areas in Cambodia, and then fungal biodiversity was analyzed by identifying mushrooms. One thousand and three hundreds eighty three specimens were identified by morphological and genetical characteristics, and were classified into 238 species, 160 genera, 52 families, 15 orders, and 3 phylums. The collected mushrooms were immersed in 70% ethyl alcohol for DNA extraction, and the rest of them were dried in the portable mushroom dryer for 12 hrs. Among these mushrooms, the genera Mycena (8.7%), Ganoderma (5.6%), Microporus (5.3%), Marasmius (4.2%), Marasmiellus (3.0%), Phellinus (2.5%), Trametes (2.5%), Hygrocybe (1.9%) and Pycnoporus (1.5%) were dominant. In the western Cambodia, 1,061 specimens were collected from Koh Kong forests, while 263 specimens were collected from the eastern Cambodia, Seima and Mondulkiri forests. Elevations of surveyed sites were ranged from 0 to 750 m above sea level. The number of species observed in the elevation of 251-500 m was the highest as compared to the other ranges of elevation. Daldinia concentrica, Microporus vernicipes, Microporus xanthopus, Pycnoporus coccineus, Stereum hirsutum, and Stereum ostrea were commonly distributed in all ranges of elevation, while the distribution of Ceratomyxa fruticulosa, Panus fulvus, Schizophyllum, Trametes versicolor, and Tyromyces chioneus were limited under 500 m. One hundred and forty one species including Amauroderma sp., Bjerkandera adusta, Trichaptum abietinum, and Tyromyces chioneus were collected only in Cardamom, while 20 species including Auricularia auricula-judae, Coriolopsis sanguinaria, Rigidoporus microporus, and Xylaria polymorpha were collected only in Seima. Ganoderma sp., Mycena sp., Marasmius sp., Microporus xanthopus, Phellinus sp., and Russula sp. were dominant species in both the western and eastern Cambodia. Species diversity indices in the eastern and western survey sites were 1.83 and 1.77, respectively, while evenness indices were 0.92 and 0.90. The species similarity index between two survey sites was 0.42.

Apolipoprotein A5 3'-UTR variants and cardiometabolic traits in Koreans: results from the Korean genome and epidemiology study and the Korea National Health and Nutrition Examination Survey

  • Kim, Oh Yoen;Moon, Jiyoung;Jo, Garam;Kwak, So-Young;Kim, Ji Young;Shin, Min-Jeong
    • Nutrition Research and Practice
    • /
    • v.12 no.1
    • /
    • pp.61-68
    • /
    • 2018
  • BACKGROUND/OBJECTIVES: This study aimed to test the association between APOA5 3'-UTR variants (rs662799) and cardiometabolic traits in Koreans. SUBJECTS/METHODS: For this study, epidemiological data, Apolipoprotein A5 (APOA5) genotype information, and lymphoblastoid cell line (LCL) biospecimens from a subset of the Ansung-Ansan cohort within the Korean Genome and Epidemiology study (KoGES-ASAS; n = 7,704) as well as epidemiological data along with genomic DNA biospecimens of participants from a subset of the Korea National Health and Nutrition Examination Survey (KNHANES 2011-12; n = 2,235) were obtained. APOA5 mRNA expression was also measured. RESULTS: APOA5 rs662799 genotype distributions in both the KoGES-ASAS and KNHANES groups were 50.6% for TT, 41.3% for TC, and 8.1% for CC, which are similar to those in previous reports. In both groups, minor C allele carriers, particularly subjects with CC homozygosity, had lower high-density lipoprotein (HDL) cholesterol and higher triglyceride levels than TT homozygotes. Linear regression analysis showed that the minor C allele significantly contributed to reduction of circulating HDL cholesterol levels [${\beta}=-2.048$, P < 0.001; ${\beta}=-2.199$, P < 0.001] as well as elevation of circulating triglyceride levels [${\beta}=0.053$, P < 0.001; ${\beta}=0.066$, P < 0.001] in both the KoGES-ASAS and KNHANES groups. In addition, higher expression levels of APOA5 in LCLs of 64 healthy individuals were negatively associated with body mass index (r = -0.277, P = 0.027) and circulating triglyceride level (r = -0.340, P = 0.006) but not significantly correlated with circulating HDL cholesterol level. On the other hand, we observed no significant difference in the mRNA level of APOA5 according to APOA5 rs662799 polymorphisms. CONCLUSIONS: The C allele of APOA5 rs662799 was found to be significantly associated with cardiometabolic traits in a large Korean population from the KoGES-ASAS and KNHANES. The effect of this genotype may be associated with post-transcriptional regulation, which deserves further experimental confirmation.

Endophytic Fungal Diversity Associated with the Roots of Coastal Sand-dune Plants in the Sindu-ri Coastal Sand Dune, Korea (신두리 해안사구에 자생하는 사구식물 내생진균의 다양성 분석)

  • You, Young-Hyun;Seo, Yeonggyo;Yoon, Hyeokjun;Kim, Hyun;Kim, Ye-Eun;Khalmuratova, Irina;Rim, Soon-Ok;Kim, Changmu;Kim, Jong-Guk
    • Microbiology and Biotechnology Letters
    • /
    • v.41 no.3
    • /
    • pp.300-310
    • /
    • 2013
  • The coastal sand-dune plants of eight species; Argusia sibirica, Calystegia soldanella, Elymus mollis, Lithospermum zollingeri, Raphanus sativus, Salsola collina, Zoysia macrostachya, and Zoysia sinica were collected from the Shindu-ri coastal sand dune. Ninety-eight endophytic fungal strains were isolated from the roots of these plants, analyzed, and identified by sequences in their internal transcribed spacers (ITS) at the ITS1, 5.8S, and ITS2 regions. The diversity of endophytic fungi isolated from coastal sand-dune plants was confirmed with various diversity indices. The fungal strains belonged to thirteen orders: Capnodiales (3.09%), Eurotiales (70.10%), Glomerellales (1.03%), Helotiales (3.09%), Hypocreales (9.28%), Mortierellales (2.06%), Onygenales (1.03%), Ophiostomatales (1.03%), Pleosporales (1.03%), Polyporales (1.03%), Russulales (1.03%), Saccharomycetales (2.06%), and Xylariales (1.03%). Of the endophytic fungal strains collected, Penicillium (59.18% in Eurotiales) and Fusarium (5.10% in Hypocreales) were the most abundant in coastal sand-dune plants. The endophytic fungal strains isolated from C. soldanella were more diverse compared to strains from the other coastal sand-dune plants.

Integrative Study on PPARGC1A: Hypothalamic Expression of Ppargc1a in ob/ob Mice and Association between PPARGC1A and Obesity in Korean Population

  • Hong, Mee-Suk;Kim, Hye-Kyung;Shin, Dong-Hoon;Song, Dae-Kyu;Ban, Ju Yeon;Kim, Bum Shik;Chung, Joo-Ho
    • Molecular & Cellular Toxicology
    • /
    • v.4 no.4
    • /
    • pp.318-322
    • /
    • 2008
  • Obesity is an increasing worldwide health problem that is strongly related to the imbalance of food intake and energy metabolism. It was well-known that several substances in the hypothalamus regulate food intake and energy metabolism. We planned an integrative study to elucidate the mechanism of the development of obesity. Firstly, to find candidate genes with the marvelous effect, the different expression in the hypothalamus between ob/ob and 48-h fasting mice was investigated by using DNA microarray technology. As a result, we found 3 genes [peroxisome proliferator activated receptor, gamma, coactivator 1 alpha (Ppargc1a), calmodulin 1 (Calm1), and complexin 2 (Cplx2)] showing the different hypothalamic expression between ob/ob and 48-h fasting mice. Secondly, a genetic approach on PPARGC1A gene was performed, because PPARGC1A acts as a transcriptional coactivator and a metabolic regulator. Two hundred forty three obese female patients with body mass index (BMI)${\geq}$25 and 285 control female subjects with BMI 18 to<23 were recruited according to the Classification of Korean Society for the Study of Obesity. Among the coding single nucleotide polymorphisms (cSNPs) of PPARGC1A, 2 missense SNPs (rs8192678, Gly482Ser; rs3736265, Thr612Met) and 1 synonymous SNP (rs3755863, Thr528Thr) were selected, and analyzed by PCR-RFLP and pyrosequencing. For the analysis of genetic data, chi-square ($X^2$) test and EH program were used. The rs8192678 was significantly associated with obese women (P<0.0006; odds ratio, 1.5327; 95% confidence interval, 1.2006-1.9568). Haplotypes also showed significant association with obese women ($X^2$=33.28, P<0.0008). These results suggest that PPARGC1A might be related to the development of obesity.

Antioxidative and Anti-diabetic Activity of C3GHi, Novel Black Rice Breed (Cyanidine-3-glucoside (C3G) 색소의 함유량이 증대된 쌀 신품종(C3GHi)의 항산화 및 항당뇨 활성)

  • Kim, Hwa-Young;Kim, Joong-Hark;Lee, Sung-Ae;Ryu, Su-Noh;Han, Sang-Jun;Hong, Seong-Gil
    • KOREAN JOURNAL OF CROP SCIENCE
    • /
    • v.55 no.1
    • /
    • pp.38-46
    • /
    • 2010
  • C3GHi, a novel black rice variety developed by conventional breeding has more high contents of cyanidine-3-glucoside (C3G) and a more strong antioxidant than normal black rice. In this study, we investigate the antioxidative potential and anti-diabetic activity of C3GHi and extract of it for the purpose of development of functional materials or replacement meal for diabetic patients. Using in vitro antioxidative activity assay system such as DPPH radical quenching assay, superoxide anion radical scavenging assay, inhibition of lipid peroxidation and DNA breakage assay, C3GHi extract was observed to have more high antioxidative activity than normal black rice breed. The glycemic index of a freeze dried powder of C3GHi brown rice showed $43.7\pm18.8$, which belonged to low GI food (GI of 55 or less). Using in vivo diabetic model such as db/db mice model and streptozotocininduced diabetic model, C3GHi rice extract decrease blood glucose level and inhibit oxidative stress in blood. From the results, we think that the C3GHi varieties have a potential for the functional materials or ingredient of meal replacement for diabetic patients.