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ChIP-seq Library Preparation and NGS Data Analysis Using the Galaxy Platform (ChIP-seq 라이브러리 제작 및 Galaxy 플랫폼을 이용한 NGS 데이터 분석)

  • Kang, Yujin;Kang, Jin;Kim, Yea Woon;Kim, AeRi
    • Journal of Life Science
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    • v.31 no.4
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    • pp.410-417
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    • 2021
  • Next-generation sequencing (NGS) is a high-throughput technique for sequencing large numbers of DNA fragments that are prepared from a genome. This sequencing technique has been used to elucidate whole genome sequences of living organisms and to analyze complementary DNA (cDNA) or chromatin immunoprecipitated DNA (ChIPed DNA) at the genome level. After NGS, the use of proper tools is important for processing and analyzing data with reasonable parameters. However, handling large-scale sequencing data and programing for data analysis can be difficult. The Galaxy platform, a public web service system, provides many different tools for NGS data analysis, and it allows researchers to analyze their data on a web browser with no deep knowledge about bioinformatics and/or programing. In this study, we explain the procedure for preparing chromatin immunoprecipitation-sequencing (ChIP-seq) libraries and steps for analyzing ChIP-seq data using the Galaxy platform. The data analysis steps include the NGS data upload to Galaxy, quality check of the NGS data, premapping processes, read mapping, the post-mapping process, peak-calling and visualization by window view, heatmaps, average profile, and correlation analysis. Analysis of our histone H3K4me1 ChIP-seq data in K562 cells shows that it correlates with public data. Thus, NGS data analysis using the Galaxy platform can provide an easy approach to bioinformatics.

Effects of Lactic Acid Bacteria Inoculants on Fermentation of Low Moisture Fresh Rice Straw Silage at Different Storage Periods

  • Kuppusamy, Palaniselvam;Soundharrajan, Ilavenil;Park, Hyung Soo;Kim, Ji Hea;Kim, Won Ho;Jung, Jeong Sung;Choi, Ki Choon
    • Journal of The Korean Society of Grassland and Forage Science
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    • v.39 no.3
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    • pp.165-170
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    • 2019
  • The purpose of this study was to analyze the effectiveness of different storage periods of lactic acid bacteria (LAB)-fermented low moisture fresh rice straw silage. The low moisture fresh rice straw sample was inculcated with LAB and stored for different storage periods such as 45, 90, and 365 days, respectively. The low moisture fresh rice straw (LMFRS) silage inoculated with LAB exhibited reduction in pH throughout the fermentation as compared with the control (P<0.05). The lactic acid content was increased at the late fermentation period (90 and 365 days, respectively) in LAB inoculated LMFRS silage as compared with the control (P<0.05). In contrast, the acetic acid and butyric acid concentrations were slightly reduced in the LAB inoculated LMFRS silage sample at 90 and 365 days fermentation, respectively. Meanwhile, the non-inoculated LMFRS silage showed higher amounts of acetic acid and butyric acid at an extended fermentation with low bacterial population as compared with the LAB inoculated LMFRS silage. However, lactic acid concentration was slightly high in the non-inoculated LMFRS silage at early 45 days fermentation. Additionally, the nutrient profile such as crude protein (CP), acid detergent fibre (ADF), neutral detergent fibre (NDF), and total digestibility nutrients (TDN) were not significantly different in control and LAB inculcated samples during all fermentation. Though, the microbial population was greater in the LAB inoculated LMFRS silage as compared with the control. However, the massive population was noted in the LAB inoculated LMFRS silage during all fermentation. It indicates that the inoculated LAB is the main reason for increasing fermentation quality in the sample through pH reduction by organic acids production. Overall results suggest that the LAB inoculums are the effective strain that could be a suitable for LMFRS silage fermentation at prolonged days.

Interplay between the Gut Microbiome and Metabolism in Ulcerative Colitis Mice Treated with the Dietary Ingredient Phloretin

  • Ren, Jie;Li, Puze;Yan, Dong;Li, Min;Qi, Jinsong;Wang, Mingyong;Zhong, Genshen;Wu, Minna
    • Journal of Microbiology and Biotechnology
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    • v.31 no.10
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    • pp.1409-1419
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    • 2021
  • A growing number of healthy dietary ingredients in fruits and vegetables have been shown to exhibit diverse biological activities. Phloretin, a dihydrochalcone flavonoid that is abundant in apples and pears, has anti-inflammatory effects on ulcerative colitis (UC) mice. The gut microbiota and metabolism are closely related to each other due to the existence of the food-gut axis in the human colon. To investigate the interplay of faecal metabolites and the microbiota in UC mice after phloretin treatment, phloretin (60 mg/kg) was administered by gavage to ameliorate dextran sulfate sodium (DSS)-induced UC in mice. Gut microbes and faecal metabolite profiles were detected by high-throughput sequencing and liquid chromatography mass spectrometry (LC-MS) analysis, respectively. The correlations between gut microbes and their metabolites were evaluated by Spearman correlation coefficients. The results indicated that phloretin reshaped the disturbed faecal metabolite profile in UC mice and improved the metabolic pathways by balancing the composition of faecal metabolites such as norepinephrine, mesalazine, tyrosine, 5-acetyl-2,4-dimethyloxazole, and 6-acetyl-2,3-dihydro-2-(hydroxymethyl)-4(1H)-pyridinone. Correlation analysis identified the relations between the gut microbes and their metabolites. Proteus was negatively related to many faecal metabolites, such as norepinephrine, L-tyrosine, laccarin, dopamine glucuronide, and 5-acetyl-2,4-dimethyloxazole. The abundance of unidentified Bacteriodales_S24-7_group was positively related to ecgonine, 15-KETE and 6-acetyl-2,3-dihydro-2-(hydroxymethyl)-4(1H)-pyridinone. The abundance of Christensenellaceae_R-7_group was negatively related to the levels of 15-KETE and netilmicin. Stenotrophomonas and 15-KETE were negatively related, while Intestinimonas and alanyl-serine were positively related. In conclusion, phloretin treatment had positive impacts on faecal metabolites in UC mice, and the changes in faecal metabolites were closely related to the gut microbiota.

Efficacy of combination of endo-xylanase and xylan-debranching enzymes in improving cereal bran utilization in piglet diet

  • Wang, Weiwei;Zheng, Dawen;Zhang, Zhenzhen;Ye, Hui;Cao, Qingyun;Zhang, Changming;Dong, Zemin;Feng, Dingyuan;Zuo, Jianjun
    • Animal Bioscience
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    • v.35 no.11
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    • pp.1733-1743
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    • 2022
  • Objective: This study was aimed to explore the efficacy of combination of endo-xylanase (Xyn) and xylan-debranching enzymes (arabinofuranosidase, Afd and feruloyl esterase, FE) in improving utilization of bran in piglet diet. Methods: In vitro experiments were firstly conducted to examine the enzymological properties of Xyn, Afd, and FE, concurrent with their effect on degradation of arabinoxylan (Abx) in bran. In vivo experiment was then implemented by allocating two hundred and seventy 35-d-old postweaning piglets into 3 groups (6 replicates/group), which received bran-containing diet supplemented with Xyn (1,600 U/kg) or its combination with Afd (0.8 U/kg) and FE (4 U/kg) or without enzyme. Results: Both Xyn, Afd, and FE are relatively stable against the changes in temperature and pH value. Combining Xyn with Afd and FE had a superiority (p<0.05) over Xyn alone and its combination with Afd or FE in promoting (p<0.05) degradation of Abx in different brans. Combined treatment with Xyn, Afd, and FE was more beneficial than Xyn alone to induce increasing trends (p<0.10) of average daily gain, final body weight and feed efficiency of piglets fed bran-containing diet. Moreover, combination of Xyn, Afd, and FE showed advantages (p<0.05) over Xyn alone in causing reductions (p<0.05) in diarrhea rate and cecal pH value, concurrent with increases (p<0.05) in cecal and colonic acetic acid and total volatile fatty acid concentrations, as well as cecal butyric acid concentration of piglets fed bran-containing diet. Conclusion: Combining Xyn with Afd and FE was more beneficial than Xyn alone in promoting degradation of Abx in bran, along with growth performance and intestinal volatile fatty acid profile of piglets received bran-containing diet. Thereby, combination of Xyn, Afd, and FE had a superior efficacy relative to Xyn alone in improving application of cereal bran in piglet diet.

Genome-wide identification, organization, and expression profiles of the chicken fibroblast growth factor genes in public databases and Vietnamese indigenous Ri chickens against highly pathogenic avian influenza H5N1 virus infection

  • Anh Duc Truong;Ha Thi Thanh Tran;Nhu Thi Chu;Huyen Thi Nguyen;Thi Hao Vu;Yeojin Hong;Ki-Duk Song;Hoang Vu Dang;Yeong Ho Hong
    • Animal Bioscience
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    • v.36 no.4
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    • pp.570-583
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    • 2023
  • Objective: Fibroblast growth factors (FGFs) play critical roles in embryo development, and immune responses to infectious diseases. In this study, to investigate the roles of FGFs, we performed genome-wide identification, expression, and functional analyses of FGF family members in chickens. Methods: Chicken FGFs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the FGFs genes in different chicken tissues were obtained from the genome-wide RNA-seq. Results: A total of 20 FGF genes were identified in the chicken genome, which were classified into seven distinct groups (A-F) in the phylogenetic tree. Gene structure analysis revealed that members of the same clade had the same or similar exon-intron structure. Chromosome mapping suggested that FGF genes were widely dispersed across the chicken genome and were located on chromosomes 1, 4-6, 9-10, 13, 15, 28, and Z. In addition, the interactions among FGF proteins and between FGFs and mitogen-activated protein kinase (MAPK) proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. Kyoto encyclopedia of genes and genomes pathway analysis showed that FGF gene interacts with MAPK genes and are involved in stimulating signaling pathway and regulating immune responses. Furthermore, this study identified 15 differentially expressed genes (DEG) in 21 different growth stages during early chicken embryo development. RNA-sequencing data identified the DEG of FGFs on 1- and 3-days post infection in two indigenous Ri chicken lines infected with the highly pathogenic avian influenza virus H5N1 (HPAIV). Finally, all the genes examined through quantitative real-time polymerase chain reaction and RNA-Seq analyses showed similar responses to HPAIV infection in indigenous Ri chicken lines (R2 = 0.92-0.95, p<0.01). Conclusion: This study provides significant insights into the potential functions of FGFs in chickens, including the regulation of MAPK signaling pathways and the immune response of chickens to HPAIV infections.

Performance, blood and antioxidant status in dual-purpose laying hens supplemented with aqueous extract of Christ's thorn jujube (Ziziphus spina-christi L.) leaves as phytogenic agent in subtropical conditions

  • Khaled H. El-Kholy;Hasan Tag El-Din;Found A. Tawfeek;Vincenzo Tufarelli;Caterina Losacco;Rashed A. Alhotan;Manal E. Shafi;Mohamed A. Korish;Youssef A. Attia;Sara H. M. Hassab
    • Animal Bioscience
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    • v.37 no.5
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    • pp.896-907
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    • 2024
  • Objective: The potential of aqueous extract of Christ's thorn jujube (Ziziphus spina-christi) leaves (SLAE) to reduce the negative impacts of heat stress on production performance and physiological traits was investigated in dual-purpose layers under subtropical farming. Methods: A total of 200, 25-week-old laying hens (Inshas strain) were randomly assigned to four dietary treatments including SLAE at 0, 2.5, 5.0, and 7.5 mL/kg, respectively. The average temperature-humidity index value was 26.69 during the experimental period. The SLAE contained saponin (0.045%), total flavonoid content of 17.9 mg of quercetin equivalent/100 g and overall antioxidant capacity concentration of 17.9 mg of ascorbic acid equivalent/100 g. Results: The maximum final body weight (BW), BW gain, egg weight, number, and mass occurred at the level of SLAE7.5 inclusion. The egg quality was significantly higher in SLAE groups than in control, and overall, SLAE7.5 had the most favorable influence at 28 and 32 weeks. Liver and kidney function, as well as lipids profile, improved significantly by SLAE inclusion; the lowest concentrations of these parameters were in SLAE7.5 hens. Treatment with SLAE7.5 increased total antioxidant capacity and endogenous antioxidant enzymes compared to control, whereas no effect on superoxide dismutase was noticed. Conclusion: The addition of SLAE at 7.5 mL/kg diet improved egg laying performance and quality, metabolic profiles, and antioxidant status during hyperthermia conditions.

Characteristics and classification of paddy soils on the Gimje-Mangyeong plains (김제만경평야(金堤萬頃平野)의 답토양특성(沓土壤特性)과 그 분류(分類)에 관(關)한 연구(硏究))

  • Shin, Yong Hwa
    • Korean Journal of Soil Science and Fertilizer
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    • v.5 no.2
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    • pp.1-38
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    • 1972
  • This study, designed to establish a classification system of paddy soils and suitability groups on productivity and management of paddy land based on soil characteristics, has been made for the paddy soils on the Gimje-Mangyeong plains. The morphological, physical and chemical properties of the 15 paddy soil series found on these plains are briefly as follows: Ten soil series (Baeggu, Bongnam, Buyong, Gimje, Gongdeog, Honam, Jeonbug, Jisan, Mangyeong and Suam) have a B horizon (cambic B), two soil series (Geugrag and Hwadong) have a Bt horizon (argillic B), and three soil series (Gwanghwal, Hwagye and Sindab) have no B or Bt horizons. Uniquely, both the Bongnam and Gongdeog series contain a muck layer in the lower part of subsoil. Four soil series (Baeggu, Gongdeog, Gwanghwal and Sindab) generally are bluish gray and dark gray, and eight soil series (Bongnam, Buyong, Gimje, Honam, Jeonbug, Jisan, Mangyeong and Suam) are either gray or grayish brown. Three soil series (Geugrag, Hwadong and Hwagye), however, are partially gleyed in the surface and subsurface, but have a yellowish brown to brown subsoil or substrata. Seven soil series (Bongnam, Buyong, Geugrag, Gimje, Gongdeog, Honam and Hwadong) are of fine clayey texture, three soil series (Baeggu, Jeonbug and Jisan) belong to fine loamy and fine silty, three soil series (Gwanghwal, Mangyeong and Suam) to coarse loamy and coarse silty, and two soil series (Hwagye and Sindab) to sandy and sandy skeletal texture classes. The carbon content of the surface soil ranges from 0.29 to 2.18 percent, mostly 1.0 to 2.0 percent. The total nitrogen content of the surface soil ranges from 0.03 to 0.25 percent, showing a tendency to decrease irregularly with depth. The C/N ratio in the surface soil ranges from 4.6 to 15.5, dominantly from 8 to 10. The C/N ratio in the subsoil and substrata, however, has a wide range from 3.0 to 20.25. The soil reaction ranges from 4.5 to 8.0. All soil series except the Gwanghwal and Mangyeong series belong to the acid reaction class. The cation exchange cpacity in the surface soil ranges from 5 to 13 milliequivalents per 100 grams of soil, and in all the subsoil and substrata except those of a sandy texture, from 10 to 20 milliequivalents per 100 grams of soil. The base saturation of the soil series except Baeggu and Gongdeog is more than 60 percent. The active iron content of the surface soil ranges from 0.45 to 1.81 ppm, easily-reduceable manganese from 15 to 148 ppm, and available silica from 36 to 366 ppm. The iron and manganese are generally accumulated in a similar position (10 to 70cm. depth), and silica occurs in the same horizon with that of iron and manganese, or in the deeper horizons in the soil profile. The properties of each soil series extending from the sea shore towards the continental plains change with distance and they are related with distance (x) as follows: y(surface soil, clay content) = $$-0.2491x^2+6.0388x-1.1251$$ y(subsoil or subsurface soil, clay content) = $$-0.31646x^2+7.84818x-2.50008$$ y(surface soil, organic carbon content) = $$-0.0089x^2+0.2192x+0.1366$$ y(subsoil or subsurface soil, pH) = $$-0.0178x^2-0.04534x+8.3531$$ Soil profile development, soil color, depositional and organic layers, soil texture and soil reaction etc. are thought to be the major items that should be considered in a paddy soil classification. It was found that most of the soils belonging to the moderately well, somewhat poorly and poorly drained fine and medium textured soils and moderately deep fine textured soils over coarse materials, produce higher paddy yields in excess of 3,750 kg/ha. and most of the soils belonging to the coarse textured soils, well drained fine textured soils, moderately deep medium textured soils over coarse materials and saline soils, produce yields less than 3,750kg/ha. Soil texture of the profile, available soil depth, salinity and gleying of the surface and subsurface soils etc. seem to be the major factors determining rice yields, and these factors are considered when establishing suitability groups for paddy land. The great group, group, subgroup, family and series are proposed for the classification categories of paddy soils. The soil series is the basic category of the classification. The argillic horizon (Bt horizon) and cambic horizon (B horizon) are proposed as two diagnostic horizons of great group level for the determination of the morphological properties of soils in the classification. The specific soil characteristics considered in the group and subgroup levels are soil color of the profile (bluish gray, gray or yellowish brown), salinity (salic), depositonal (fluvic) and muck layers (mucky), and gleying of surface and subsurface soils (gleyic). The family levels are classified on the basis of soil reaction, soil texture and gravel content of the profile. The definitions are given on each classification category, diagnostic horizons and specific soil characteristics respectively. The soils on these plains are classified in eight subgroups and examined under the existing classification system. Further, the suitability group, can be divided into two major categories, suitability class and subclass. The soils within a suitability class are similar in potential productivity and limitation on use and management. Class 1 through 4 are distinguished from each other by combination of soil characteristics. Subclasses are divided from classes that have the same kind of dominant limitations such as slope(e), wettness(w), sandy(s), gravels(g), salinity(t) and non-gleying of the surface and subsurface soils(n). The above suitability classes and subclasses are examined, and the definitions are given. Seven subclasses are found on these plains for paddy soils. The classification and suitability group of 15 paddy soil series on the Gimje-Mangyeong plains may now be tabulated as follows.

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Alterations of Binding Capacities of Dopamine Receptors After Treatment with Haloperidol and Sulpiride in Rat Brain (Haloperidol 및 Sulpiride 투여후 백서 뇌내 Dopamine 수용체 결합력의 변화)

  • Hahn, Kyu-Hee;Ahn, Yun-Young
    • Korean Journal of Biological Psychiatry
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    • v.2 no.1
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    • pp.63-69
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    • 1995
  • The effects of chronic treatment with haloperidol and sulpiride on the binding capacities of dopamine(DA) receptor were examined in rat striatum and olfactory tubercle. Additionally, the stereotypy scores were assessed after apomorphine administration. Rats were treated with haloperidol(0.5mg/kg/day) or sulpiride(40mg/kg/day) for four weeks. Apomorphine(0.5mg/kg) was injected after three-day washout from neuroleptics, and stereotypy scores were assessed. Haloperidol group showed high scores of stereotyped behavior in comparison with control and sulpiride groups. With control group, sulpiride group displayed similar stereotyped behaviors. Saturation analysis of the binding of [$^3H$]spiperone to striatal membranes showed that the Bmax of haloperidol and sulpiride groups increased significantly in comparison with that of control group. The $K_D$ decreased significantly after sulpiride treatment in striatum. Although sulpiride produces the same proliferation of DA receptor, the low stereotypy scores of sulpiride group indirectly suggest that sulpiride acts differently from haloperidol in brain DA system. The Bmax increased remarkably following both treatment with haloperidol and sulpiride in olfactory tubercle. Also, the increase in $K_D$ was significant after treatment with haloperidol and sulpiride in olfactory tubercle. Moreover, the $K_D$ of control group in olfactory tubercle was more than twice the $K_D$ of control group in striatum. The $K_D$ was 86.2 in striatum and 37.5 pM in olfactory tubercle. The present finding indicates that sulpiride also induces the proliferation of DA receptor in olfactory tubercle and may interact with some DA receptor subtype with high affinity profile. The different affinities of the control groups of striatum and olfactory tubercle suggest that striatal DA receptor subtypes labeled by [$^3H$]spiperone could differ from those of olfactory tubercle.

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Variation of Inflow Density Currents with Different Flood Magnitude in Daecheong Reservoir (홍수 규모별 대청호에 유입하는 하천 밀도류의 특성 변화)

  • Yoon, Sung-Wan;Chung, Se-Woong;Choi, Jung-Kyu
    • Journal of Korea Water Resources Association
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    • v.41 no.12
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    • pp.1219-1230
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    • 2008
  • Stream inflows induced by flood runoffs have a higher density than the ambient reservoir water because of a lower water temperature and elevated suspended sediment(SS) concentration. As the propagation of density currents that formed by density difference between inflow and ambient water affects reservoir water quality and ecosystem, an understanding of reservoir density current is essential for an optimization of filed monitoring, analysis and forecast of SS and nutrient transport, and their proper management and control. This study was aimed to quantify the characteristics of inflow density current including plunge depth($d_p$) and distance($X_p$), separation depth($d_s$), interflow thickness($h_i$), arrival time to dam($t_a$), reduction ratio(${\beta}$) of SS contained stream inflow for different flood magnitude in Daecheong Reservoir with a validated two-dimensional(2D) numerical model. 10 different flood scenarios corresponding to inflow densimetric Froude number($Fr_i$) range from 0.920 to 9.205 were set up based on the hydrograph obtained from June 13 to July 3, 2004. A fully developed stratification condition was assumed as an initial water temperature profile. Higher $Fr_i$(inertia-to-buoyancy ratio) resulted in a greater $d_p,\;X_p,\;d_s,\;h_i$, and faster propagation of interflow, while the effect of reservoir geometry on these characteristics was significant. The Hebbert equation that estimates $d_p$ assuming steady-state flow condition with triangular cross section substantially over-estimated the $d_p$ because it does not consider the spatial variation of reservoir geometry and water surface changes during flood events. The ${\beta}$ values between inflow and dam sites were decreased as $Fr_i$ increased, but reversed after $Fr_i$>9.0 because of turbulent mixing effect. The results provides a practical and effective prediction measures for reservoir operators to first capture the behavior of turbidity inflow.

Effects of NaCl Concentration on Physicochemical Properties of Pork Emulsion (NaCl 첨가량에 따른 돈육 유화물의 이화학적 특성)

  • Park, Sin-Young;Kim, Hack-Youn
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.45 no.4
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    • pp.551-556
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    • 2016
  • This study was conducted to investigate the effects of NaCl concentration on the physicochemical properties of pork emulsion. Pork emulsion was produced containing 0% (control), 0.3%, 0.6%, 0.9%, 1.2%, and 1.5% NaCl. Proximate composition of pork emulsion containing 1.5% NaCl showed the highest moisture content (P<0.05). The ash contents of pork emulsion increased with an increase in NaCl, and protein contents decreased with increasing NaCl concentration. The pH levels of uncooked pork emulsion containing 0.9%, 1.2%, and 1.5% NaCl were lower than those of other treatments (P<0.05), and the pH level of cooked pork emulsion containing NaCl was lower than that of the control (P<0.05). The CIE $L^*$ value of the uncooked pork emulsion samples containing NaCl was higher than that of the control (P<0.05), whereas CIE $a^*$ and CIE $b^*$ values of samples with NaCl were lower than the control (P<0.05). CIE $L^*$ and CIE $b^*$ values of cooked pork emulsion decreased with an increase in NaCl level, and CIE $a^*$ value increased with increasing NaCl concentration (P<0.05). Viscosity of the pork emulsion increased with an increase in NaCl. Texture profile analysis of pork emulsion containing NaCl showed no significant difference in springiness or cohesiveness (P>0.05). Pork emulsion containing 1.5% NaCl showed the highest hardness, gumminess, and chewiness (P<0.05). These results suggest that pork emulsion containing 0.9% and 1.2% NaCl can be used as a low-salt meat product.