• Journal of Microbiology and Biotechnology
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• v.23 no.4
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• pp.459-466
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• 2013

The lactic acid bacterium Streptococcus thermophilus is widely used as a starter culture for the production of dairy products. Whole-genome sequencing is expected to utilize the genetic basis behind the metabolic functioning of lactic acid bacterium (LAB), for development of their use in biotechnological and probiotic applications. We sequenced the whole genome of Streptococcus thermophilus MTCC 5461, the strain isolated from a curd source, by 454 GS-FLX titanium and Ion Torrent PGM. We performed comparative genome analysis using the local BLAST and RDP for 16S rDNA comparison and by the RAST server for functional comparison against the published genome sequence of Streptococcus thermophilus CNRZ 1066. The whole genome size of S. thermophilus MTCC 5461 is of 1.73Mb size with a GC content of 39.3%. Streptococcal virulence-related genes are either inactivated or absent in the strain. The genome possesses coding sequences for features important for a probiotic organism such as adhesion, acid tolerance, bacteriocin production, and lactose utilization, which was found to be conserved among the strains MTCC 5461 and CNRZ 1066. Biochemical analysis revealed the utilization of 17 sugars by the bacterium, where the presence of genes encoding enzymes involved in metabolism for 16 of these 17 sugars were confirmed in the genome. This study supports the facts that the strain MTCC 5461 is nonpathogenic and harbors essential features that can be exploited for its probiotic potential.

• The Plant Pathology Journal
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• v.31 no.4
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• pp.379-387
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• 2015

Melon necrotic spot virus (MNSV) was recently identified on watermelon (Citrullus vulgaris) in Korea, displaying as large necrotic spots and vein necrosis on the leaves and stems. The average occurrence of MNSV on watermelon was found to be 30-65% in Hapcheon and Andong City, respectively. Four isolates of the virus (MNSV-HW, MNSV-AW, MNSV-YW, and MNSV-SW) obtained from watermelon plants in different areas were non-pathogenic on ten general indicator plants, including Chenopodium quinoa, while they infected systemically six varieties of Cucurbitaceae. The virus particles purified by 10-40% sucrose density gradient centrifugation had a typical ultraviolet spectrum, with a minimum at 245 nm and a maximum at 260 nm. The morphology of the virus was spherical with a diameter of 28-30 nm. Virus particles were observed scattered throughout the cytoplasm of watermelon cells, but no crystals were detected. An ELISA was conducted using antiserum against MNSV-HW; the optimum concentrations of IgG and conjugated IgG for the assay were $1{\mu}l/ml$ and a 1:8,000-1:10,000 dilutions, respectively. Antiserum against MNSV-HW could capture specifically both MNSV-MN from melon and MNSV-HW from watermelon by IC/RT-PCR, and they were effectively detected with the same specific primer to produce product of 1,172 bp. The dsRNA of MNSV-HW had the same profile (4.5, 1.8, and 1.6 kb) as that of MNSV-MN from melon. The nucleotide sequence of the coat protein of MNSV-HW gave a different phylogenetic tree, having 17.2% difference in nucleotide sequence compared with MNSV isolates from melon.

• Korean journal of food and cookery science
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• v.29 no.1
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• pp.29-36
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• 2013

The present study was conducted to supply more scientific information for standardization of preparation method of Gyungdan and to determine the standard for manufacturing procedure adapted with mechanically impacting technology (MIT) for mass production. The optimum preparation condition for non-waxy Gyungdan adapted with MIT was 35% of water, 0.5% of wheat flour (w/w of soaked rice), and mechanically impacting for 10 min at 450 rpm. In the present study, standardization of manufacturing procedure for merchandizing of Gyungdan was established with width, weight, and height. Average of Gyungdan adapted with MIT at 90 rpm (stuffing speed) and 46.58 Herz (cutting speed) is 18.3 g of weight, 28.4 mm of height, and 32.4 mm of width. Hardness, as a main parameter of texture profile, of Gyungdan was maintained lower than 100 g up to 3 days at the storage of $20^{\circ}C$ and up to 70 days at the storage of $-20^{\circ}C$. And, it was performed to develop rice cake as meal-replacement adapted with MIT and sub-ingredients such as strawberry, pumpkin, and mugwort. Gyungdan prepared under controlling manufacturing condition of MIT was supplemented with 0-1.6% of sub-ingredients, respectively. In sensory tests, the best substitute ratios of strawberry, pumpkin, and mugwort were 1.6%, 0.8%, and 1.6%, respectively. With the results above, not-harden Gyungdan supplemented with sub-ingredients and various stuffs can be expected to application for wheat-substitute meal-replacement.

• Korean Journal of Soil Science and Fertilizer
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• v.48 no.6
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• pp.593-601
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• 2015

The NDVI (Normalized difference vegetation index) is used as indicators of crop growth situation in remote sensing. To measure or validate the NDVI, reliable NDVI sensors have been needed. We tested new fixed-field NDVI sensor, "SRS (Spectral Reflectance Sensor)" developed by Decagon Devices, during Kimchi cabbage growing season at the cultivation area located in Gochang, Gangneung and Taebaek in Korea from 2014 to 2015. The diurnal variation of NDVI measured by SRS (SRS NDVI) showed a slight ${\cap}$-profile shape and was affected by water on the sensor surface. This means that SRS NDVI around noontime is resonable, except rainy day. Comparisons were made between the SRS NDVI and NDVI of used widely mobile sensor (Cropcircle NDVI). The comparisons indicate that SRS NDVI are close to Cropcircle NDVI (R=0.99). SRS NDVI time series displayed change of the plant height and leaf width of Kimchi cabbage. An obvious exponential relationship is found between SRS NDVI and the plant height ($R^2{\geq}0.92$) and leaf width ($R^2{\geq}0.92$) of Kimchi cabbage. Thus, SRS NDVI will be used as indicator of crop growth situation and a very powerful tool for evaluation of remote sensing NDVI estimates and associated corrections.

• Korean Journal of Soil Science and Fertilizer
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• v.48 no.4
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• pp.246-254
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• 2015

This study explored the effect of rainfall pattern and soil characteristics on water management in rice paddy fields, using a soil water balance model, BUDGET. In two sites with different soil textural group, coarse loamy soil (Gangseo series) and fine soil (Hwadong series), respectively, we have monitored daily decrease of water depth, percolation rate, and groundwater table. The observed evapotranspiration (ET) was obtained from differences between water depth decrease and percolation rate. The root mean square difference values between observed and BUDGET-estimated ET ranged between 10% and 20% of the average observed ET. This is comparable to the measurement uncertainty, suggesting that the BUDGET model can provide reliable ET estimation for rice fields. In BUDGET model of this study, irrigation requirement was determined as minimum water need for maintaining water-saturated soil surface, assuming 100 mm of bund height and no lateral loss of water. The model results showed different water balance and irrigation requirement with the different soil profile and indicated that minimum percolation rate by plow pan could determine the irrigation requirement of rice paddy field. For the condition of different rainfall distribution, the results presented different irrigation period and amounts, representing the importance of securing water for irrigation against different rainfall pattern.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.38-48
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• 2019

Objective: In this study, the transcriptome profile of cow experiencing miscarriage during peri-implantation was investigated. Methods: Total transcriptomes were checked by RNA sequencing, and the analyzed by bioinformatics methods, the differentially expressed genes (DEGs) were analysed with hierarchical clustering and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Results: The results suggested that serum progesterone levels were significantly decreased in cows that miscarried as compared to the pregnant cows at 18, 21, 33, 39, and 51 days after artificial insemination. The RNA sequencing results suggested that 32, 176, 5, 10, and 2 DEGs were identified in the pregnant cows and miscarried cows at 18, 21, 33, 39, and 51 d after artificial insemination. And 15, 101, 1, 2, and 2 DEGs were upregulated, and 17, 74, 4, and 8 DEGs were downregulated in the cows in the pregnant and miscarriage groups, respectively at 18, 21, 33, and 39, but no gene was downregulated at 51 d after artificial insemination. These DEGs were distributed to 13, 20, 3, 6, and 20 pathways, and some pathway essential for pregnancy, such as cell adhesion molecules, tumor necrosis factor signaling pathway and PI3K-Akt signaling pathway. Conclusion: This analysis has identified several genes and related pathways crucial for pregnancy and miscarriage in cows, as well as these genes supply molecular markers to predict the miscarriage in cows.

• Food Science of Animal Resources
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• v.41 no.2
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• pp.312-323
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• 2021

The purpose of this study was to use 1H nuclear magnetic resonance (1H NMR) to quantify taste-active and bioactive compounds in chicken breasts and thighs from Korean native chicken (KNC) [newly developed KNCs (KNC-A, -C, and -D) and commercial KNC-H] and white-semi broiler (WSB) used in Samgye. Further, each breed was differentiated using multivariate analyses, including a machine learning algorithm designed to use metabolic information from each type of chicken obtained using 1H-13C heteronuclear single quantum coherence (2D NMR). Breast meat from KNC-D chickens were superior to those of conventional KNC-H and WSB chickens in terms of both taste-active and bioactive compounds. In the multivariate analysis, meat portions (breast and thigh) and chicken breeds (KNCs and WSB) could be clearly distinguished based on the outcomes of the principal component analysis and partial least square-discriminant analysis (R2=0.945; Q2=0.901). Based on this, we determined the receiver operating characteristic (ROC) curve for each of these components. AUC analysis identified 10 features which could be consistently applied to distinguish between all KNCs and WSB chickens in both breast (0.988) and thigh (1.000) meat without error. Here, both 1H NMR and 2D NMR could successfully quantify various target metabolites which could be used to distinguish between different chicken breeds based on their metabolic profile.

• Animal Bioscience
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• v.35 no.8
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• pp.1162-1173
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• 2022

Objective: This study aimed to investigate the fermentation profiles, bacterial community and predicted metabolic characteristics of Sudangrass (Sorghum sudanense Stapf.) during ensiling. Methods: First-cutting Sudangrass was harvested at the vegetative stage and ensiled in laboratory-scale silos (1 L capacity). Triplicate silos were sampled after 1, 3, 7, 15, 30, and 60 days of ensiling, respectively. The bacterial communities on day 3 and 60 were assessed through high-throughput sequencing technology, and 16S rRNA-gene predicted functional profiles were analyzed according to the Kyoto encyclopedia of genes and genomes using Tax4Fun. Results: The Sudangrass silages showed good fermentation quality, indicated by higher lactic acid contents, and lower pH, butyric acid and ammonia nitrogen contents. The dominant genus Lactococcus on day 3 was replaced by Lactobacillus on day 60. The metabolism of amino acid, energy, cofactors and vitamins was restricted, and metabolism of nucleotide and carbohydrate was promoted after ensiling. The 1-phosphofructokinase and pyruvate kinase of bacterial community seemed to play important roles in stimulating the lactic acid fermentation, and the promotion of arginine deiminase could help lactic acid bacteria to tolerate the acidic environment. Conclusion: High-throughput sequencing technology combined with 16S rRNA gene-predicted functional analyses revealed the differences during the early and late stages of Sudangrass ensiling not only for distinct bacterial community but also for specific functional metabolites. The results could provide a comprehensive insight into bacterial community and metabolic characteristics to further improve the silage quality.

• Food Science of Animal Resources
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• v.43 no.5
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• pp.840-858
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• 2023

This study was designed to compare the quality changes in mackerel fillets stored under different conditions by using hyperspectral imaging (HSI) techniques. Fillets packaged in vacuum were stored for six days under five different conditions: refrigerated at 4℃ (R group); iced at 5±3℃ (I group); kept at an ambient of 17±2℃ (A group); frozen at -18℃ for 24 h and thawed in a refrigerator at 4℃ for 5 h on the sampling day (FTR group); FTR thawed in tap water instead of thawing in a refrigerator (FTW group). The FTR group had the lowest total bacterial count, drip loss, 2-thiobarbituric acid reactive substances, volatile basic nitrogen, and texture profile analysis values among groups during the entire storage period (p<0.05). Scanning electron microscopy revealed that the FTR group had less damage, while the other groups had shrunken muscle tissues. HIS integrated with the partial least squares model yielded reliable and efficient results, with high R²_cv values, for several quality parameters of the mackerel fillets. Overall, the FTR group, involving freezing and thawing in a refrigerator, appears to be the most favorable option for maintaining the quality of mackerel fillets, which could be practically implemented in the industry. HSI is a suitable and effective technique for determining the quality of mackerel fillets stored under different conditions.

• Animal Bioscience
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• v.35 no.9
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• pp.1367-1378
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• 2022

Objective: The present study was conducted to examine the gas production, fermentation characteristics, nutrient degradation, and methanogenic community composition of a rumen fluid culture with Broussonetia papyrifera (B. papyrifera) subjected to ensiling or steam explosion (SE) pretreatment. Methods: Fresh B. papyrifera was collected and pretreated by ensiling or SE, which was then fermented with ruminal fluids as ensiled B. papyrifera group, steam-exploded B. papyrifera group, and untreated B. papyrifera group. The gas and methane production, fermentation characteristics, nutrient degradation, and methanogenic community were determined during the fermentation. Results: Cumulative methane production was significantly improved with SE pretreatment compared with ensiled or untreated biomass accompanied with more volatile fatty acids production. After 72 h incubation, SE and ensiling pretreatments decreased the acid detergent fiber contents by 39.4% and 22.9%, and neutral detergent fiber contents by 10.6% and 47.2%, respectively. Changes of methanogenic diversity and abundance of methanogenic archaea corresponded to the variations in fermentation pattern and methane production. Conclusion: Compared with ensiling pretreatment, SE can be a promising technique for the efficient utilization of B. papyrifera, which would contribute to sustainable livestock production systems.