• 전기전자학회논문지
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• 제27권1호
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• pp.116-121
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• 2023

본 논문에서는 딥러닝 예측 결과 정보를 적용하는 복합 미생물 배양기를 위한 딥러닝 구조를 개발한다. 제안하는 복합 미생물 배양기는 수집한 복합 미생물 데이터에 대해 복합 미생물 데이터 전처리, 복합 미생물 데이터 구조 변환, 딥러닝 네트워크 설계, 설계한 딥러닝 네트워크 학습, 시제품에 적용되는 GUI 개발 등으로 구성된다. 복합 미생물 데이터 전처리에서는 미생물 배양에 필요한 당밀, 영양제, 식물엑기스, 소금 등의 양에 대해 원-핫 인코딩을 실시하며, 배양된 결과로 측정된 pH 농도와 미생물의 셀 수에 대해 최대-최소 정규화 방법을 사용하여 데이터를 전처리한다. 복합 미생물 데이터 구조 변환에서는 전처리된 데이터를 물 온도와 미생물의 셀 수를 연결하여 그래프 구조로 변환 후, 인접 행렬과 속성 정보로 나타내어 딥러닝 네트워크의 입력 데이터로 사용한다. 딥러닝 네트워크 설계에서는 그래프 구조에 특화된 그래프 합성곱 네트워크를 설계하여 복합 미생물 데이터를 학습시킨다. 설계한 딥러닝 네트워크는 Cosine 손실함수를 사용하여 학습 시에 발생하는 오차를 최소화하는 방향으로 학습을 진행한다. 시제품에 적용되는 GUI 개발은 사용자가 선택하는 물 온도에 따라 목표하는 pH 농도(3.8 이하) 복합 미생물의 셀 수(10⁸ 이상)를 배양시키기 적합한 순으로 나타낸다. 제안된 미생물 배양기의 성능을 평가하기 위하여 공인시험기관에서 실험한 결과는, pH 농도의 경우 평균 3.7로, 복합 미생물의 셀 수는 1.7 × 10⁸으로 측정되었다. 따라서, 본 논문에서 제안한 딥러닝 예측 결과 정보를 적용하는 복합 미생물 배양기를 위한 딥러닝 구조의 효용성이 입증되었다.

• 문화기술의 융합
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• 제10권3호
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• pp.873-878
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• 2024

우리는 Loperamide로 유도한 변비 Sprague-Dawley 랫드 모델에서 프락토올리고당 및 과채류복합 추출물을 2 주간 경구 투여 한 후 랫 분변의 그룹 기간별로 수집 한 후 장내 마크로바이옴 변화 경향을 분석하였다. 프락토올리고당 및 과채복합추출물(FVCE)에 대한 미생물 군집 분석을 16S rDNA 클로닝 및 pyrosequencing을 통해 수행하여 표준화 및 체계화를 위한 기초 데이터를 얻었다. 과채복합추출물(FVCE) 제조 공정은 원핵생물 군집에 대한 미생물 분석을 통해 문 수준에서 미생물 verrucomicrobiota의 약간의 차이가 우세한 것으로 나타났다. 속 수준에서는 prevotella와 muribaculaceae가 종 수준에서 더 많은 차이를 보였다. 이러한 결과는 사용된 미생물 군집이 생산되는 과일 및 채소 복합 추출물(FVCE)의 품질에 영향을 미친다는 것을 시사한다고 할 수 있다. 따라서, 일관된 품질의 과일 및 채소 복합 추출물(FVCE)을 생산하기 위해서는 안정적인 미생물 군집이 유지되어야 한다.

• Biotechnology and Bioprocess Engineering:BBE
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• 제10권5호
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• pp.385-399
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• 2005

The phenotypic response of a cell results from a well orchestrated web of complex interactions which propagate from the genetic architecture through the metabolic flux network. To rationally design cell factories which carry out specific functional objectives by controlling this hierarchical system is a challenge. Transcriptome analysis, the most mature high-throughput measurement technology, has been readily applied In strain improvement programs in an attempt to Identify genes involved in expressing a given phenotype. Unfortunately, while differentially expressed genes may provide targets for metabolic engineering, phenotypic responses are often not directly linked to transcriptional patterns, This limits the application of genome-wide transcriptional analysis for the design of cell factories. However, improved tools for integrating transcriptional data with other high-throughput measurements and known biological interactions are emerging. These tools hold significant promise for providing the framework to comprehensively dissect the regulatory mechanisms that identify the cellular control mechanisms and lead to more effective strategies to rewire the cellular control elements for metabolic engineering.

• 식물병연구
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• 제24권4호
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• pp.313-320
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• 2018

벼 붉은곰팡이병에 대한 품종별 반응과 기상조건에 따른 감염영향을 알아보기 위하여 장려품종 재배포장의 기상자료와 수확한 벼의 이병립율과 Fusarium 균을 동정하였다. 출수개화 전인 7월 하순부터 등숙기인 9월말까지의 평균기온이 수확후 산물벼의 이병립율에 크게 영향을 주었으며, 평균기온이 비슷한 2010년과 2013년에는 같은 기간의 누적강우량, 누적 강우일수, 2일 이상 강우지속횟수와 관련이 있었다. 2010년과 2013년에 수확한 벼에서 Fusarium 균의 종복합체별 분리비율은 FGSC에 대해 각각 57%과 45%, FIESC에 대해 35%과 50%, FFSC에 대해 8%과 5%이었다. FGSC와 FFSC의 분포비율은 2010년이 2013년에 비해 높았다. Fusarium 균의 자연감염에 대한 품종반응은 26개 장려품종 중 미향 품종만이 FGSC 자연감염에 대한 저항성을 보였으며, 남평, 하이아미, 영호진미 품종은 총 Fusarium 병원균의 자연감염에 대하여 전반적인 저항성을 보였다. 그 밖의 대부분의 장려품종은 저항성 또는 감수성으로 구분할 수 없었다. 본 연구결과는 Fusarium 균 자연감염에 대한 저항성과 감수성을 판단하는 기초자료로서 의의가 있다.

• 유통과학연구
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• 제19권4호
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• pp.53-60
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• 2021

Purpose: This study focuses on exploring ways to improve the distribution method of shrimp farming so that it is eco-friendly and increases the distribution of shrimp. Research design, data and methodology: The experimental device installed in a biofloc shrimp culture in one area tested 10 times. Complex odor, concentration of H2S, water quality improvement effected by decomposition of organic substances, and degree of microbial activation measured. The data of the experimental results verified using the T-test technique, and the p value was determined based on the significance probability of 0.05. Results: This experimental device was effective in reducing odor and hydrogen sulfide in shrimp farms. With the improvement of water quality, dissolved oxygen increased due to the microbubble and cavitation action of air ejector and ultrasonic waves. In addition, the cultured microorganisms in the cultured water treated by the experimental device were remarkably proliferated compared to the raw water. Conclusions: The biofloc distribution method has a significant effect on improving water quality and reducing odor substances and will become a new eco-friendly and efficient distribution method for shrimp farming in the future.

• Asian-Australasian Journal of Animal Sciences
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• 제14권6호
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• pp.880-884
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• 2001

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

• 한국환경보건학회지
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• 제35권6호
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• pp.517-525
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• 2009

The water quality of Lake Shihwa had been rapidly deteriorating since 1994 due to wastewater input from the watersheds, limited water circulation and the lack of a wastewater treatment policy. In 2000, the government decided to open the tidal embankment and make a comprehensive management plan to improve the water quality, especially inflowing stream water around Shihwa and Banwol industrial complex. However, the water quality and microbial community have not as yet been fully evaluated. The purpose of this study is to investigate the influent water quality around the industrial area based on chemical and biological analysis, and collected surface water sample from the Siheung Stream, up-stream to down-stream through the industrial complex, Samples were collected in July 2009. The results show that the downstream site near the industrial complex had higher concentrations of heavy metals (Cu, Mn, Fe, Mg, and Zn) and organic matter than upstream sites. A combination of DGGE (Denaturing Gradient Gel Electrophoresis) gels, lists of K-WQI (Korean Water Quality Index), cluster analysis, MDS (Multi-Dimensional Scaling) and PCA (Principal Component Analysis) has demonstrated clear clustering between Siheung stream 3 and 4 and with a high similarity and detected metal reducing bacteria (Shewanella spp.) and biodegrading bacteria (Acinetobacter spp.). These results suggest that use of both chemical and microbiological marker would be useful to fully evaluate the water quality.

• International Journal of Oral Biology
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• 제45권3호
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• pp.77-83
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• 2020

In the oral cavity, complex microbial community is shaped by various host and environmental factors. Extensive literature describing the oral microbiome in the context of oral health and disease is available. Advances in DNA sequencing technologies and data analysis have drastically improved the analysis of the oral microbiome. For microbiome study, bacterial 16S ribosomal RNA gene amplification and sequencing is often employed owing to the cost-effective and fast nature of the method. In this review, practical considerations for performing a microbiome study, including experimental design, molecular analysis technology, and general data analysis, will be discussed.

• Journal of Microbiology and Biotechnology
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• 제26권12호
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• pp.2141-2147
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• 2016

As one of the most complex human-associated microbial habitats, the oral cavity harbors hundreds of bacteria. Halitosis is a prevalent oral condition that is typically caused by bacteria. The aim of this study was to analyze the microbial communities and predict functional profiles in supragingival plaque from healthy individuals and those with halitosis. Ten preschool children were enrolled in this study; five with halitosis and five without. Supragingival plaque was isolated from each participant and 16S rRNA gene pyrosequencing was used to identify the microbes present. Samples were primarily composed of Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes, Fusobacteria, and Candidate phylum TM7. The ${\alpha}$ and ${\beta}$ diversity indices did not differ between healthy and halitosis subjects. Fifteen operational taxonomic units (OTUs) were identified with significantly different relative abundances between healthy and halitosis plaques, and included the phylotypes of Prevotella sp., Leptotrichia sp., Actinomyces sp., Porphyromonas sp., Selenomonas sp., Selenomonas noxia, and Capnocytophaga ochracea. We suggest that these OTUs are candidate halitosis-associated pathogens. Functional profiles were predicted using PICRUSt, and nine level-3 KEGG Orthology groups were significantly different. Hub modules of co-occurrence networks implied that microbes in halitosis dental plaque were more highly conserved than microbes of healthy individuals' plaque. Collectively, our data provide a background for the oral microbiota associated with halitosis from supragingival plaque, and help explain the etiology of halitosis.

• Molecules and Cells
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• 제41권4호
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• pp.331-341
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• 2018

L-pipecolic acid is a non-protein amino acid commonly found in plants, animals, and microorganisms. It is a well-known precursor to numerous microbial secondary metabolites and pharmaceuticals, including anticancer agents, immunosuppressants, and several antibiotics. Lysine cyclodeaminase (LCD) catalyzes ${\beta}$-deamination of L-lysine into L-pipecolic acid using ${\beta}$-nicotinamide adenine dinucleotide as a cofactor. Expression of a human homolog of LCD, ${\mu}$-crystallin, is elevated in prostate cancer patients. To understand the structural features and catalytic mechanisms of LCD, we determined the crystal structures of Streptomyces pristinaespiralis LCD (SpLCD) in (i) a binary complex with $NAD^+$, (ii) a ternary complex with $NAD^+$ and L-pipecolic acid, (iii) a ternary complex with $NAD^+$ and L-proline, and (iv) a ternary complex with $NAD^+$ and L-2,4-diamino butyric acid. The overall structure of SpLCD was similar to that of ornithine cyclodeaminase from Pseudomonas putida. In addition, SpLCD recognized L-lysine, L-ornithine, and L-2,4-diamino butyric acid despite differences in the active site, including differences in hydrogen bonding by Asp236, which corresponds with Asp228 from Pseudomonas putida ornithine cyclodeaminase. The substrate binding pocket of SpLCD allowed substrates smaller than lysine to bind, thus enabling binding to ornithine and L-2,4-diamino butyric acid. Our structural and biochemical data facilitate a detailed understanding of substrate and product recognition, thus providing evidence for a reaction mechanism for SpLCD. The proposed mechanism is unusual in that $NAD^+$ is initially converted into NADH and then reverted back into $NAD^+$ at a late stage of the reaction.