• Microbiology and Biotechnology Letters
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• v.47 no.1
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• pp.25-33
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• 2019

Lactobacillus rhamnosus BFE5264, isolated from a Maasai fermented milk product ("kule naoto"), was previously shown to exhibit bile acid resistance, cholesterol assimilation, and adhesion to HT29-MTX cells in vitro. In this study, we re-annotated and analyzed the previously reported complete genome sequence of strain BFE5264. The genome consists of a circular chromosome of 3,086,152 bp and a putative plasmid, which is the largest one identified among L. rhamnosus strains. Among the 2,883 predicted protein-coding genes, those with carbohydrate-related functions were the most abundant. Genome analysis of strain BFE5264 revealed two consecutive CRISPR regions and no known virulence factors or antimicrobial resistance genes. In addition, previously known highly variable regions in the genomes of L. rhamnosus strains were also evident in strain BFE5264. Pairwise comparison with the most studied probiotic strain L. rhamnosus GG revealed strain BFE5264-specific deletions, probably due to insertion sequence-mediated recombination. The latter was associated with loss of the spaCBA pilin gene cluster and exopolysaccharide biosynthetic genes. Comparative genomic analysis of the sequences from all available L. rhamnosus strains revealed that they were clustered into two groups, being within the same species boundary based on the average nucleotide identities. Strain BFE5264 had a sister group relationship with the group that contained strain GG, but neither ANI-based hierarchical clustering nor core-gene-based phylogenetic tree construction showed a clear distinctive pattern associated with the isolation source, implying that the genotype alone cannot account for their ecological niches. These results provide insights into the probiotic mechanisms of strain BFE5264 at the genomic level.

• Journal of Microbiology and Biotechnology
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• v.32 no.5
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• pp.575-581
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• 2022

A Gram-stain-negative, white-coloured, and rod-shaped bacterium, strain DR4-4^T, was isolated from Daechung Reservoir, Republic of Korea, during Microcystis bloom. Strain DR4-4^T was most closely related to Caenimonas terrae SGM1-15^T and Caenimonas koreensis EMB320^T with 98.1% 16S rRNA gene sequence similarities. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain DR4-4^T and closely related type strains were below 79.46% and 22.30%, respectively. The genomic DNA G+C content was 67.5%. The major cellular fatty acids (≥10% of the total) were identified as C_16:0, cyclo C_17:0, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c), and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). Strain DR4-4^T possessed phosphatidylethanolamine, diphosphatidylglycerol, and phosphatidylglycerol as the main polar lipids and Q-8 as the respiratory quinone. The polyamine profile was composed of putrescine, cadaverine, and spermidine. The results of polyphasic characterization indicated that the isolated strain DR4-4^T represents a novel species within the genus Caenimonas, for which the name Caenimonas aquaedulcis sp. nov. is proposed. The type strain is DR4-4^T (=KCTC 82470^T =JCM 34453^T).

• Journal of Microbiology and Biotechnology
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• v.32 no.7
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• pp.855-861
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• 2022

A white-pigmented, non-motile, gram-negative, and rod-shaped bacterium, designated CYS-02^T, was isolated from soil sampled at Suwon, Gyeonggi-do, Republic of Korea. Cells were strictly aerobic, grew optimally at 20-28℃ and hydrolyzed Tween 40. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain CYS-02^T formed a lineage within the family Comamonadaceae and clustered as members of the genus Variovorax. The closest members were Variovorax guangxiensis DSM 27352^T (98.6% sequence similarity), Variovorax paradoxus NBRC 15149^T (98.5%), and Variovorax gossypii JM-310^T (98.3%). The principal respiratory quinone was Q-8 and the major polar lipids contain phosphatidylethanolamine (PE), phosphatidylethanolamine (PG), and diphosphatidylglycerol (DPG). The predominant cellular fatty acids were C_16:0, summed feature 3 (C_16:1ω7c and/or C_16:1ω6c) and summed feature 8 (C_18:1ω7c and/or C_18:1ω6c). The DNA GC content was 67.7 mol%. The ANI and dDDH values between strain CYS-02T and the closest members in the genus Variovorax were ≤ 79.0 and 22.4%, respectively, and the AAI and POCP values between CYS-02^T and the other related species in the family Comamonadaceae were > 70% and > 50%, respectively. The genome of strain CYS-02^T showed a putative terpene biosynthetic cluster responsible for antioxidant activity which was supported by DPPH radical scavenging activity test. Based on genomic, phenotypic and chemotaxonomic analyses, strain CYS-02^T was classified into a novel species in the genus Variovorax, for which the name Variovorax terrae sp. nov., has been proposed. The type strain is CYS-02^T (= KACC 22656^T = NBRC 00115645^T).

• Animal Bioscience
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• v.36 no.2
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• pp.209-217
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• 2023

Objective: The conservation of Bali bulls, the Indonesian native breed of cattle, is crucial for cattle breeding in Indonesia. To guarantee the spread of Bali bulls through artificial insemination the quality of the frozen semen must be high. To this end, adding an extender material to semen that increases spermatozoa's survival during cryopreservation is important. Green tea extract (GTE) can be used as cryoprotectant because its high antioxidant activity can help avoid reactive oxygen species formation. Methods: Semen of five Bali bulls from the National Artificial Insemination Center at Singosari, Indonesia was collected routinely twice a week. First, fresh semen inspection was performed to determine the feasibility of using Bali bulls as animal samples. The extender used in this study was Tris-based egg yolk. The samples were divided into four treatments: T0, no GTE added to the extender; T1, 0.05 mg GTE plus 100 mL extender; T2, 0.10 mg GTE plus 100 mL extender; and T3, 0.15 mg GTE plus 100 mL extender. The semen freezing process was conducted according to standard procedures and sperm quality parameters, i.e., sperm motility, viability, abnormalities, and membrane integrity observed pre-freezing and post-thawing. Results: There were significant differences in total motility, progressive motility, viability, and integrity membrane of Bali bull sperm at both pre-freezing and post-thawing after adding GTE into the extender. In contrast, there were no differences in abnormalities among treatments. Conclusion: Adding GTE at a 0.15 mg into 100 mL Tris-based egg yolk extender can improve the quality of cryopreserved Bali bull sperm.

• International Journal of Computer Science & Network Security
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• v.23 no.4
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• pp.139-145
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• 2023

These days, protecting location privacy has become essential and really challenging, especially protecting it from smart applications and services that rely on Location-Based Services (LBS). As the technology and the services that are based on it are developed, the capability and the experience of the attackers are increased. Therefore, the traditional protection ways cannot be enough and are unable to fully ensure and preserve privacy. Previously, a hybrid approach to privacy has been introduced. It used an obfuscation technique, called Double-Obfuscation Approach (DOA), to improve the privacy level. However, this approach has some weaknesses. The most important ones are the fog nodes that have been overloaded due to the number of communications. It is also unable to prevent the Tracking and Identification attacks in the Mix-Zone technique. For these reasons, this paper introduces a developed and enhanced approach, called Multi-Obfuscation Approach (MOA that mainly depends on the communication between neighboring fog nodes to overcome the drawbacks of the previous approach. As a result, this will increase the resistance to new kinds of attacks and enhance processing. Meanwhile, this approach will increase the level of the users' privacy and their locations protection. To do so, a big enough memory is needed on the users' sides, which already is available these days on their devices. The simulation and the comparison prove that the new approach (MOA) exceeds the DOA in many Standards for privacy protection approaches.

• Journal of Microbiology and Biotechnology
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• v.33 no.6
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• pp.753-759
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• 2023

The genus Paenibacillus contains a variety of biologically active compounds that have potential applications in a range of fields, including medicine, agriculture, and livestock, playing an important role in the health and economy of society. Our study focused on the bacterium SS4^T (KCTC 43402^T = GDMCC 1.3498^T), which was characterized using a polyphasic taxonomic approach. This strain was analyzed using antiSMASH, BAGEL4, and PRISM to predict the secondary metabolites. Lassopeptide clusters were found using all three analysis methods, with the possibility of secretion. Additionally, PRISM found three biosynthetic gene clusters (BGC) and predicted the structure of the product. Genome analysis indicated that glucoamylase is present in SS4^T. 16S rRNA sequence analysis showed that strain SS4^T most closely resembled Paenibacillus marchantiophytorum DSM 29850^T (98.22%), Paenibacillus nebraskensis JJ-59^T (98.19%), and Paenibacillus aceris KCTC 13870^T (98.08%). Analysis of the 16S rRNA gene sequences and Type Strain Genome Server (TYGS) analysis revealed that SS4^T belongs to the genus Paenibacillus based on the results of the phylogenetic analysis. As a result of the matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) results, SS4^T was determined to belong to the genus Paenibacillus. Comparing P. marchantiophytorum DSM 29850^T with average nucleotide identity (ANI 78.97%) and digital DNA-DNA hybridization (dDDH 23%) revealed values that were all less than the threshold for bacterial species differentiation. The results of this study suggest that strain SS4^T can be classified as a Paenibacillus andongensis species and is a novel member of the genus Paenibacillus.

• Animal Bioscience
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• v.37 no.3
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• pp.536-546
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• 2024

Objective: This experiment was conducted to investigate the effect of grain-based pecking blocks on productivity and welfare status at two commercial broiler welfare-certified farms. Methods: Production and welfare indicators were assessed at two farms (designated Farm A and B). Both farms had two windowless houses with forced tunnel-type ventilation and housed broilers at stocking densities of approximately 16.7 birds/m² (Farm A) and 16.8 birds/m² (Farm B). Each house was divided into two or three equal sections and was provided with or without pecking blocks. Grain-based pecking blocks, measuring 25 × 25 × 25 cm, were given to broilers in both farms at 1 block per 1,000 birds. Various parameters including productivity (body weight and flock uniformity), corticosterone levels (in fecal droppings and feathers), footpad dermatitis, hock burn, feather dirtiness, gait score, litter quality, body surface temperature, and volatile fatty acids in fecal samples were assessed at 26 days of age, whereas litter quality was analyzed at 13 and 26 days of age. Results: There were no significant effects of providing pecking blocks on productivity (body weight and uniformity), fecal and feather corticosterone, welfare indicators (i.e., footpad dermatitis, hock burn, feather cleanliness, and gait score), and litter quality (i.e., moisture, nitrogen, and pH). No differences in body surface temperature between the control and enrichment treatments were noted in Farm B, but body surface temperatures of the head (p = 0.029) and legs (p = 0.011) in the enrichment vs. control group were elevated in Farm A. Butyrate concentration in the enrichment vs control group was higher in Farm B (p = 0.023), but this effect was not detected in Farm A. Conclusion: It is concluded that grain-based pecking blocks did not affect performance and welfare indicators. Further studies are warranted to elucidate the potential impact of grain-based pecking blocks on gut health indicators.

• Journal of Practical Agriculture & Fisheries Research
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• v.6 no.1
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• pp.102-115
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• 2004

Main objectives of this study were to increase digestibilities of indigestible ingredients in spent mushroom composts (SMC) consisted of sawdust mainly as well as to fortify conversion of inorganic Se present in SMC to organic Se via fermentable microbial actions. Experimental feeds were designed to contain the increasing level of selenium (0.06ppm, 0.54ppm, 1.26ppm and 1.86ppm) in combination with SMCs of Se-enriched and non-Se mushrooms. Feeds were also fermented using commercial microbial feed additives (Sambae, Ltd., Korea) comprised Saccharomyces, Bacillus, Aspergillus, Streptococcus and Actinomycetes before feeding trial for Hanwoo (Korean native cattle). Those were fermented for 0, 12, 24, and 48 hrs. Initial pH was linearly increased as Se concentration increases or the proportion of SMC of Se-enriched mushroom increased (p<0.0001). pH values of fermented feeds (0.54ppm, 1.26ppm and 1.86ppm) containing SMC of Se-enriched mushroom were not different since 12 hrs of fermentation time and their pH was significantly lowered compared to control group. The increasing level of Se concentration in fermented feeds showed significant differences in organic and inorganic Se contents and proportion of organic Se among treatments. As a SMC proportion of Se-enriched mushrooms in the fermented feed was increased, organic Se proportion was significantly decreased (p<0.0001). The control treatment (0.06ppm) comprising the non-Se SMC only was estimated of the organic Se to be 100% and the treatment groups containing the increasing level of Se were estimated of organic Se to be approximately 70%.

• Journal of Practical Agriculture & Fisheries Research
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• v.6 no.1
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• pp.116-135
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• 2004

This study was conducted to investigate effects of spent composts of Se-enriched mushrooms as the dietary Se source on muscular Se deposition and plasma glutathione peroxidase (GSH-Px) activity in the finishing Hanwoo steer. Twenty Hanwoo steers were used in the experiment and they were divided into four groups in a randomized complete block design with five replicates. Treatments were four levels (0.1, 0.3, 0.6 and 0.9ppm as fed basis) of dietary Se from the combination with spent composts of Se-enriched mushrooms and/or Se non-enriched mushrooms, in which each treatment was formulated with corn and corn gluten meal and so forth. Treatment diets were fed to Hanwoo steers for 90 days until the slaughter. Dry matter intakes had no significant differences among treatments and there were no significant differences for performances such as total BW gain and ADG among treatments. The Se concentration in blood was linearly increased with increasing dietary selenium levels and reached a plateau level after 8 weeks (p<0.001). Plasma GSH-Px activities had the similar trends to blood Se concentrations by showing that the increased dietary Se level significantly increased plasma GSH-Px activities of both total and Se-dependent (p<0.001). Muscle Se contents of Se-supplemented groups were linearly increased by 1.35 ~ 1.68 folds compared with the control group (0.1ppm; 0.273㎍/dry g) and especially those of the hind legs for 0.9ppm treatment showed the highest Se content as shown 0.457㎍ per dry gram (p<0.01) corresponding to approximately 70% increase of the control group. Se retention rate in the muscle of dietary Se originated from spent composts of Se-enriched mushrooms was estimated of maximum approximately 30% and dietary Se content showed the significant correlation with plasma GSH-Px activities and muscle Se contents (p<0.01). Accordingly, Se present in spent composts of Se-enriched mushroom as the dietary Se source not only had great bioavailabilities showing higher blood Se concentration and plasma GSH-Px activities, but also increased Se deposition in the muscle for Hanwoo beef cattle.

• Radiation Oncology Journal
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• v.31 no.2
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• pp.97-103
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• 2013

Purpose: To investigate the patterns of locoregional recurrence of pathologic T3N0 (pT3N0) lower rectal cancer omitting postoperative radiotherapy (RT) and explore the potential of modification of a RT field. Materials and Methods: From Jan 2003 to Nov 2011, 35 patients omitting preoperative or postoperative RT for pT3N0 lower rectal cancer were included. We defined the lower rectal cancer as the tumor with the inferior margin located below the virtual line-a convergent level between rectal wall and levator ani muscle. All patients had radiologic examinations for recurrence evaluation during the follow-up duration. Results: The median follow-up duration was 66.4 months (range, 1.4 to 126.1 months). Eight (22.9%) of the 35 patients had recurrence. Three (8.6%) was local recurrence (LR) only, 3 (8.6%) was distant metastasis (DM) only, and 2 (5.7%) was LR with DM. All LR were located at primary tumor sites. The overall survival rate, LR-free survival rate, and DM-free survival rate at 5 years was 79.8%, 83%, and 87%, respectively. All LR developed from tumors over 5 cm. However, there was no statistical significance (p = 0.065). There was no other risk factor for LR. Conclusion: Even though the patients included in this study had pathologically favorable pT3N0 rectal cancer, LR developed in 14.3% of patients. Most of the LR was located at primary tumor sites prior to surgery. Based on these findings, it might seem reasonable to consider postoperative RT with a smaller radiation field to the primary tumor site rather than the conventional whole pelvic irradiation.