• Genomics & Informatics
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• 제17권3호
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• pp.31.1-31.7
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• 2019

We sought the novel concept, transcript capacity (TC) and analyzed TC. Our approach to estimate TC was through an in silico method. TC refers to the capacity that a transcript exerts in a cell as enzyme or protein function after translation. We used the genome-wide association study (GWAS) beta effect and transcription level in RNA-sequencing to estimate TC. The trait was body fat percent and the transcript reads were obtained from the human protein atlas. The assumption was that the GWAS beta effect is the gene's effect and TC was related to the corresponding gene effect and transcript reads. Further, we surveyed gene ontology (GO) in the highest TC and the lowest TC genes. The most frequent GOs with the highest TC were neuronal-related and cell projection organization related. The most frequent GOs with the lowest TC were wound-healing related and embryo development related. We expect that our analysis contributes to estimating TC in the diverse species and playing a benevolent role to the new bioinformatic analysis.

• 환경생물
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• 제36권2호
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• pp.131-139
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• 2018

기후 변화로 인한 수온의 상승은 어류 서식지에 영향을 미친다. 수온의 변화는 어류 생리 거의 모든 부분에 영향을 미치는 것으로 알려져 있다. 기후 변화에 따른 수온의 상승은 산소 용해도의 감소 및 산소 운반 헤모글로빈의 결합 능력의 감소로 인해 저산소증을 초래할 수 있다. 본 연구는 대서양 연어(Salmo salar) 치어 성장의 최적수온($15^{\circ}C$)보다 고수온($20^{\circ}C$)에 사육 시, 대서양 연어 치어의 건강상태를 평가하기 위해 수행되었다. 평가 방법은 NGS RNAseq 분석방법을 이용하여 생체지표유전자를 개발하고, RT-qPCR 분석을 이용하여 생체지표유전자의 발현양상을 조사하는 것이다. 개발한 생체지표유전자로는 interferon alpha-inducible protein 27-like protein 2A transcript variant X3, protein L-Myc-1b-like, placenta growth factor-like transcript variant X1, fibroblast growth factor receptor-like 1 transcript variant X1, transferrin, intelectin, thioredoxin-like, c-type lectin lectoxin-Thr1-like, ladderlectin-like 및 calponin-1 등이다. 선택된 생체지표 유전자는 NGS RNAseq 분석을 통해 수온변화에 민감하게 발현한 유전자들이며, RT-qPCR 분석을 통한 이들 유전자의 발현 양상은 NGS RNAseq 분석을 통한 발현 양상과 매우 유사하게 나타났다.

• Journal of Animal Science and Technology
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• 제55권4호
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• pp.249-255
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• 2013

Intercellular interactions are important for the proper development and regulation of tissue function. This is especially necessary in the epididymis, a part of male reproductive tract where sperm become mature and acquire their fertilizing capacity. The caput region of the epididymis consists of several types of cells, including principal, basal, and apical cells. Direct intercellular communication is thus required to precisely regulate the functions of the caput epididymis. In this regard, connexin (Cx) is a molecule that forms channels, which allow the direct exchange of small molecules between cells, enabling intercellular communication. In this study, the expression of Cx isoforms in the caput epididymis at different postnatal ages was determined by using quantitative real-time polymerase chain reaction analysis. Nine of 13 Cx isoforms were detected. The transcript levels of Cx30.3, 31, 31.1, 32, and 40 were highest at 45 days of age, while the expression of Cx43 and 45 gradually decreased with age. A substantial fluctuation of Cx26 expression was detected, with significant decreases before and during puberty, followed by a transient increase at adult-hood and rapid decreases at an old age. A significant increase in Cx37 transcript was observed at 25 days of age, followed by gradual decreases at adult and old ages. These results indicate the significant differential expression of various Cx isoforms in the caput epididymis during postnatal development. It further suggests that the functional regulation and developmental maturation of the caput epididymis are highly related to the postnatal age-related differential expression of Cx isoforms.

• Journal of Microbiology and Biotechnology
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• 제23권5호
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• pp.587-601
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• 2013

During the last few decades, it has become evident that the compatibility of the yeast biochemical environment with the ability to process and translate the RNA transcript, along with its capacity to modify a translated protein, are relevant requirements for selecting this host cell for protein expression in several pharmaceutical and clinical applications. In particular, Pichia pastoris is used as an industrial host for recombinant protein and metabolite production, showing a powerful capacity to meet required biomolecular target production levels in high-throughput assays for functional genomics and drug screening. In addition, there is a great advantage to using P. pastoris for protein secretion, even at high molecular weights, since the recovery and purification steps are simplified owing to relatively low levels of endogenous proteins in the extracellular medium. Clearly, no single microexpression system can provide all of the desired properties for human protein production. Moreover, chemical and physical bioprocess parameters, including culture medium formulation, temperature, pH, agitation, aeration rates, induction, and feeding strategies, can highly influence product yield and quality. In order to benefit from the currently available wide range of biosynthesis strategies using P. pastoris, this mini review focuses on the developments and technological fermentation achievements, providing both a comparative and an overall integration analysis. The main aim is to highlight the relevance and versatility of the P. pastoris biosystem to the design of more cost-effective microfactories to meet the increasing demands for recombinant membrane proteins and clinical antibodies for several therapeutic applications.

• 식물병연구
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• 제17권3호
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• pp.302-310
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• 2011

Elsinoe fawcettii는 현재 감귤 산업의 경제 가치를 떨어뜨리며, 감귤 더뎅이병을 일으키는 원인중 하나로 일반적으로 살균제를 이용하여 방제가 이루어지고 있다. 하지만 안전한 농산물에 대한 관심이 증대되면서 생물학적인 방제에 대한 연구가 많이 요구되고 있다. 이에 미생물 방제에 대한 연구로서 제주에서 분리한 식물근권세균 215개 중 Elsinoe fawcettii에 의해 발병되는 감귤 더뎅이병균의 항균 효과와 병원균 발병 억제효과가 나타나는지 조사하였다. 그 중 in vitro 실험에서 더뎅이병균에 저지원을 형성하며 항균 효과를 나타내는 근권세균은 THJ 609-3, MRL 408-3, TRH 423-3이었다. 또한 이들 식물근권세균을 선처리하고 병원균을 접종한 결과 감귤 더뎅이병 억제효과가 있었다. 근권세균에 의한 병억제 기작을 알아보기 위해 형광현미경을 이용하여 조사한 결과 선발된 식물근권 세균이 병원균의 포자수를 감소시켰으며 병원균 발아율도 접종 1일 후에 감소되었다. 식물근권세균 rDNA의 Internal Transcript Spaces(ITS)을 분석을 통해 동정한 결과 THJ 609-3은 Pseudomonas pudia로 동정되었으며, MRL 408-3과 TRH 423-3은 Burkholderia gladioli로 동정되었다. 본 연구는 생물적 방제로 감귤 더뎅이병균을 방제할 수 있는 친환경적 미생물제제로 유용하게 이용할 수 있는 가치가 있다고 생각된다.

• Journal of Microbiology and Biotechnology
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• 제23권12호
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• pp.1673-1682
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• 2013

Citrobacter sp. is a cause of significant opportunistic nosocomial infection and is frequently found in human and animal feces, soil, and sewage water, and even in industrial waste or putrefaction. Biofilm formation is an important virulence trait of Citrobacter sp. pathogens but the process and characteristics of this formation are unclear. Therefore, we employed in vitro assays to study the nutritional and environmental parameters that might influence biofilm formation of C. werkmanii BF-6 using 96-well microtiter plates. In addition, we detected the relative transcript levels of biofilm formation genes by RT-PCR. Our results indicated that the capacity of C. werkmanii BF-6 to form biofilms was affected by culture temperature, media, time, pH, and the osmotic agents glucose, sucrose, NaCl, and KCl. Confocal laser scanning microscopy results illustrated that the structure of biofilms and extracellular polysaccharide was influenced by 100 mM NaCl or 100 mM KCl. In addition, nine biofilm formation genes (bsmA, bssR, bssS, csgD, csgE, csgF, mrkA, mrkB, and mrkE) were found to contribute to planktonic and biofilm growth. Our data suggest that biofilm formation by C. werkmanii BF-6 is affected by nutritional and environmental factors, which could pave the way to the prevention and elimination of biofilm formation using proper strategies.

• Journal of Microbiology and Biotechnology
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• 제26권6호
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• pp.1018-1025
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• 2016

Probiotics are considered as the best effective alternatives to antibiotics. The aim of this study was to characterize the probiotic potential of lactobacilli for use in swine farming by using in vitro evaluation methods. A total of 106 lactic acid bacterial isolates, originating from porcine feces, were first screened for the capacity to survive stresses considered important for putative probiotic strains. Sixteen isolates showed notable acid and bile resistance, antibacterial activity, and adherence to intestinal porcine epithelial cells (IPEC-1). One isolate, LR1, identified as Lactobacillus reuteri, was selected for extensive study of its probiotic and functional properties in IPEC-1 cell models. L. reuteri LR1 exhibited good adhesion to IPEC-1 cells and could inhibit the adhesion of enterotoxigenic Escherichia coli (ETEC) to IPEC-1 cells. L. reuteri LR1 could also modulate transcript and protein expression of cytokines involved in inflammation in IPEC-1 cells; the Lactobacillus strain inhibited the ETEC-induced expression of proinflammatory transcripts (IL-6 and TNF-α) and protein (IL-6), and increased the level of anti-inflammatory cytokine (IL-10). Measurement of the permeation of FD-4 showed that L. reuteri LR1 could maintain barrier integrity in monolayer IPEC-1 cells exposed to ETEC. Immunolocalization experiments showed L. reuteri LR1 could also prevent ETEC-induced tight junction ZO-1 disruption. Together, these results indicate that L. reuteri LR1 exhibits desirable probiotic properties and could be a potential probiotic for use in swine production.