• Journal of Microbiology and Biotechnology
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• 제33권7호
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• pp.909-914
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• 2023

While searching for the bacteria which are responsible for degradation of pesticide in soybean field soil, a novel bacterial strain, designated 5-5^T, was isolated. The cells of the strain were Gram-staining-positive, aerobic and non-motile rods. Growth occurred at 10-42℃ (optimum, 30℃), pH 5.5-9.0 (optimum, pH 7.0-7.5), and 0-2% (w/v) NaCl (optimum, 1%). The predominant fatty acids were C_15:0 anteiso, C_17:0 anteiso, and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The predominant menaquinone was MK-9 (H₂). Diphosphatidylglycerol, glycolipids, phosphatidylinositol, and phosphatidylglycerol were the major polar lipids. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain 5-5^T is a member of the genus Sinomonas and its closest relative is Sinomonas humi MUSC 117^T, sharing a genetic similarity of 98.4%. The draft genome of strain 5-5^T was 4,727,205 bp long with an N50 contig of 4,464,284 bp. Genomic DNA G+C content of strain 5-5^T was68.0 mol%. The average nucleotide identity (ANI) values between strain 5-5^T and its closest strains S. humi MUSC 117^T and S. susongensis A31^T were 87.0, and 84.3 % respectively. In silico DNA-DNA hybridization values between strain 5-5^T and its closest strains S. humi MUSC 117^T and S. susongensis A31^T were 32.5% and 27.9% respectively. Based on the ANI and in silico DNA-DNA hybridization analyses, the 5-5^T strain was considered as novel species belonging to the genus Sinomonas. On the basis of the results from phenotypic, genotypic and chemotaxonomic analyses, strain 5-5^T represents a novel speciesof the genus Sinomonas, for which the name Sinomonas terrae sp. nov. is proposed. The type strain is 5-5^T (=KCTC 49650^T =NBRC 115790^T).

• Journal of Microbiology and Biotechnology
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• 제30권4호
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• pp.526-532
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• 2020

A bacterial strain, designated B301^T and isolated from raw chicken meat obtained from a local market in Korea, was characterized and identified using a polyphasic taxonomic approach. Cells were gram-negative, non-motile, obligate-aerobic coccobacilli that were catalase-positive and oxidase-negative. The optimum growth conditions were 30℃, pH 7.0, and 0% NaCl in tryptic soy broth. Colonies were round, convex, smooth, and cream-colored on tryptic soy agar. Strain B301^T has a genome size of 3,102,684 bp, with 2,840 protein-coding genes and 102 RNA genes. The 16S rRNA gene analysis revealed that strain B301^T belongs to the genus Acinetobacter and shares highest sequence similarity (97.12%) with A. celticus ANC 4603^T and A. sichuanensis WCHAc060041^T. The average nucleotide identity and digital DNA-DNA hybridization values for closely related species were below the cutoff values for species delineation (95-96% and 70%, respectively). The DNA G+C content of strain B301^T was 37.0%. The major respiratory quinone was Q-9, and the cellular fatty acids were primarily summed feature 3 (C_16:1 ω6c/C_16:1 ω7c), C_16:0, and C_18:1 ω9c. The major polar lipids were phosphatidylethanolamine, diphosphatidyl-glycerol, phosphatidylglycerol, and phosphatidyl-serine. The antimicrobial resistance profile of strain B301^T revealed the absence of antibiotic-resistance genes. Susceptibility to a wide range of antimicrobials, including imipenem, minocycline, ampicillin, and tetracycline, was also observed. The results of the phenotypic, chemotaxonomic, and phylogenetic analyses indicate that strain B301^T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter pullorum sp. nov. is proposed. The type strain is B301^T (=KACC 21653^T = JCM 33942^T).

• Investigative Magnetic Resonance Imaging
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• 제24권3호
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• pp.123-131
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• 2020

Purpose: Joint label fusion (JLF) is a popular multi-atlas-based segmentation algorithm, which compensates for dependent errors that may exist between atlases. However, in order to get good segmentation results, it is very important to set the several free parameters of the algorithm to optimal values. In this study, we first investigate the feasibility of a JLF algorithm for prostate segmentation in MR images, and then suggest the optimal set of parameters for the automatic prostate segmentation by validating the results of each parameter combination. Materials and Methods: We acquired T2-weighted prostate MR images from 20 normal heathy volunteers and did a series of cross validations for every set of parameters of JLF. In each case, the atlases were rigidly registered for the target image. Then, we calculated their voting weights for label fusion from each combination of JLF's parameters (r_pxy, r_pz, r_sxy, r_sz, β). We evaluated the segmentation performances by five validation metrics of the Prostate MR Image Segmentation challenge. Results: As the number of voxels participating in the voting weight calculation and the number of referenced atlases is increased, the overall segmentation performance is gradually improved. The JLF algorithm showed the best results for dice similarity coefficient, 0.8495 ± 0.0392; relative volume difference, 15.2353 ± 17.2350; absolute relative volume difference, 18.8710 ± 13.1546; 95% Hausdorff distance, 7.2366 ± 1.8502; and average boundary distance, 2.2107 ± 0.4972; in parameters of r_pxy = 10, r_pz = 1, r_sxy = 3, r_sz = 1, and β = 3. Conclusion: The evaluated results showed the feasibility of the JLF algorithm for automatic segmentation of prostate MRI. This empirical analysis of segmentation results by label fusion allows for the appropriate setting of parameters.

• 한국항공우주학회지
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• 제48권5호
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• pp.323-334
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• 2020

경계층 천이는 극초음속 비행체의 열공력 성능에 직접적인 영향을 미치기 때문에, 성능 해석과 설계를 위해 천이지점의 정확한 예측 능력이 필수적으로 요구된다. 본 연구에서는 극초음속 경계층 천이 예측을 위한 γ-Re_θt 모델을 개선하고 검증하였다. 천이 시작 위치 결정에 영향을 주는 간헐도 수송방정식 생성항의 계수를 압축성 경계층 상사해를 기반으로 마하수와 벽면온도, 자유류 정체온도 등에 대한 함수 형태로 구성하고 적용하였다. 기본 모델의 Re_θc와 F_length 상관관계식에 마하수에 따른 천이 시작 운동량두께 레이놀즈수와 천이구간의 길이 변화를 반영할 수 있도록 마하수에 대한 관계식을 추가로 결정하여 적용하였다. 실용적인 사용을 고려하여 제안 모델을 상용 CFD 코드에 적용하였으며, 검증을 위해 모델을 사용하여 극초음속 평판과 원뿔 경계층 해석을 수행하였다. 실험 결과와의 비교를 통해 마하수와 단위 레이놀즈수 변화에 대한 개선된 예측성능을 확인하였다.

• 한국수산과학회지
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• 제55권5호
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• pp.612-624
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• 2022

A novel Gram-positive, motile, non-spore forming aerobic marine bacterium, designated 107-1^T was isolated from tidal mud collected in Gyehwa-do, South Korea. Cells of strain 107-1^T were short rod or coccoid, oxidase negative, catalase positive and grew at 10-40℃ (with optimum growth at 25-30℃). It utilized menaquinones MK-7 and 8 as its respiratory quinones and its major fatty acids were anteiso-C_15:0 (37.9%), iso-C_16:0 (14.9%), and iso-C_14:0 (10.8%). Phylogenetic analysis based on 16S rRNA gene sequences revealed a distinct clade containing strain 107-1^T and close species Planococcus ruber CW1^T(98.52% sequence similarity), P. faecalis KCTC 33580^T(97.67%), P. kocurii ATCC 43650T(97.48%), P. donghaensis DSM 22276T(97.47%), and P. halocryophilus DSM 24743T(97.37%). Strain 107-1^T contains one circular chromosome (3,513,248bp in length) with G+C content of 44.6 mol%. Estimated ranges for genome to genome distance, average nucleotide identity, and average amino acid identity comparing strain 107-1^T with close taxa were 20.3-34.8%, 77.9-86.9%, and 73.6-92.8%, respectively. Based on polyphasic analysis, strain 107-1^T represents a novel species belonging to the genus Planococcus.

• 한국농림기상학회지
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• 제25권3호
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• pp.129-141
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• 2023

작물 모형은 작물의 유전적 특성을 나타내는 품종모수를 요구하며, 품종모수는 작물의 개별 품종별로 추정되어야 한다. 품종모수의 추정에는 고품질의 많은 생육 자료가 요구되지만, 자료의 생산에 상당한 비용이 필요하다. 비교적 낮은 품질의 가용성이 높은 자료를 활용하는 대신, 대량의 랜덤 모수를 생성하고 이를 평가하여 품종모수를 추정할 수 있다. 본 연구에서는 SIMPLE 작물 모델의 불확도를 최소화하기 위해 품종모수 추정 방식을 비교하고, 두 앙상블 방식과 대한 비교를 하였다. 모수 추정을 위한 Metropolis-Hastings (MH) 알고리즘에 대한 목적함수로 로그 가능도(log-likelihood: LL)와 generic composite similarity measure (GCSM)를 사용하였다. 또한 품종모수의 평균값을 사용한 예측(E_pm)과 개별 모수들로부터 얻어진 추정값의 평균값(E_em)의 일치도를 분석하여 앙상블 방식에 따른 불확도 변화를 파악하였다. 국내에서 재배되는 사료용 벼 품종인 조우 벼와 영우 벼를 대상으로 품종모수를 추정하였다. 2013년, 2014년, 2016년에 대한 수원, 전주, 나주, 익산에 위치한 실험포장에서 얻은 수량 관측 자료를 사용하였다. 또한 2016년부터 2018년까지 수원에서 보고된 별도의 수량 관측 자료를 사용하였다. 목적함수에 따라 추정된 품종모수의 분포에 차이가 있었다. LL을 통해 얻은 품종모수는 GCSM으로 얻은 품종모수보다 좁은 범위에 분포하였다. 두 가지 앙상블 접근법은 통계적으로 유의한 차이가 나타나지 않음을 확인하였다. GCSM의 상대적으로 높은 불확도는 수용확률을 조정하여 낮출 수 있다고 사료되고, E_pm의 결과는 기존과 다른 앙상블 방식을 통해 적은 연산을 통해 불확도를 낮출 수 있음을 보인다.

• Journal of Microbiology and Biotechnology
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• 제33권10호
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• pp.1292-1298
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• 2023

PAMB 00755^T, a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20℃, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755^T was most closely related to Sphingomonas chungangi MAH-6^T (97.7%) and Sphingomonas polyaromaticivorans B2-7^T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9-81.3%), average amino acid identity (73.3-75.9%), and digital DNA-DNA hybridization (73.3-75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755^T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C_18:1ω7c and/or C_18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755^T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755^T as the type strain (= KCTC 92781^T = GDMCC 1.3779^T).

• 산업경영시스템학회지
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• 제28권1호
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• pp.121-128
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• 2005

This paper proposes the heuristic approach for the generalized GT(Group Technology) problem to consider the restrictions which are given the number of cell, maximum number of machines and minimum number of machines. This approach is classified into two stages. In the first stage, we use the similarity coefficient method which is proposed and calculate the similarity values about each pair of all machines and align these values in descending order. If two machines which is selected is possible to link the each other on the edge of machine cell and they don't have zero similarity value, then we assign the machines to the machine cell. In the second stage, it is the course to form part families using proposed grouping efficacy. Finally, machine-part incidence matrix is realigned to block diagonal structure. The results of using the proposed approach are compared to the Modified p-median model.

• Journal of Microbiology and Biotechnology
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• 제30권6호
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• pp.937-945
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• 2020

N-acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) plays a major role in development of biofilms, which contribute to rise in infections and biofouling in water-related industries. Interference in QS, called quorum quenching (QQ), has recieved a lot of attention in recent years. Rhodococcus spp. are known to have prominent quorum quenching activity and in previous reports it was suggested that this genus possesses multiple QQ enzymes, but only one gene, qsdA, which encodes an AHL-lactonase belonging to phosphotriesterase family, has been identified. Therefore, we conducted a whole genome sequencing and analysis of Rhodococcus sp. BH4 isolated from a wastewater treatment plant. The sequencing revealed another gene encoding a QQ enzyme (named jydB) that exhibited a high AHL degrading activity. This QQ enzyme had a 46% amino acid sequence similarity with the AHL-lactonase (AidH) of Ochrobactrum sp. T63. HPLC analysis and AHL restoration experiments by acidification revealed that the jydB gene encodes an AHL-lactonase which shares the known characteristics of the α/β hydrolase family. Purified recombinant JydB demonstrated a high hydrolytic activity against various AHLs. Kinetic analysis of JydB revealed a high catalytic efficiency (k_cat/K_M) against C4-HSL and 3-oxo-C6 HSL, ranging from 1.88 x 10⁶ to 1.45 x 10⁶ M^-1 s^-1, with distinctly low K_M values (0.16-0.24 mM). This study affirms that the AHL degrading activity and biofilm inhibition ability of Rhodococcus sp. BH4 may be due to the presence of multiple quorum quenching enzymes, including two types of AHL-lactonases, in addition to AHL-acylase and oxidoreductase, for which the genes have yet to be described.

• Journal of Microbiology and Biotechnology
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• 제33권8호
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• pp.1023-1029
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• 2023

Biosurfactants reduce surface and interfacial tension due to their amphiphilic properties and are an eco-friendly alternative for chemical surfactants. In this study, a new yeast strain JAF-11 that produces a biosurfactant was selected using drop collapse method, and the properties of the extracts were investigated. The nucleotide sequences of the strain were compared with closely related strains and identified based on the D1/D2 domain of the large subunit ribosomal DNA (LSU) and internal transcribed spacer (ITS) regions. Neodothiora populina CPC 39399^T, the closest species with strain JAF-11, showed a sequence similarity of 97.75% for LSU and 94.27% for ITS, respectively. The result suggests that the strain JAF-11 represents a distinct species that cannot be assigned to any existing genus or species in the family Dothideaceae. Strain JAF-11 produced a biosurfactant reducing the surface tension of water from 72 mN/m to 34.5 mN/m on the sixth day of culture and the result of measuring the critical micelle concentration (CMC) by extracting the crude biosurfactant was found to be 24 mg/l. The molecular weight 502 of the purified biosurfactant was confirmed by measuring the fast atom bombardment mass spectrum. The chemical structure was analyzed by measuring ¹H nuclear magnetic resonance (NMR), ¹³C NMR, and two-dimensional NMRs of the compound. The molecular formula was C₂₆H₄₆O₉, and it was composed of one octanoyl group and two hexanoyl groups to myo-inositol moiety. The new biosurfactant is the first report of a compound produced by a new yeast strain, JAF-11.