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Transcript mining using fuzzy rough set theory in Oryza sativa grown under N-limited condition
David-Torrejos Yokimiko C.,Redillas Mark Christian Felipe R.,Maniquiz-Redillas Marla C.,Ubando Aristotle T.,Africa Aaron Don M.,Culaba Alvin,Kim Ju-Kon 한국식물생명공학회 2023 Plant biotechnology reports Vol.17 No.5
In rice cultivation, crop yield and productivity rely on the efficient supply of nitrogen. Mismanagement of nitrogen, such as insufficient and oversupply, lowers the plant vigor and stability. Using next-generation sequencing, transcriptome mining can discover nitrogen-responsive genes, regulators, and markers that can be used to improve the nitrogen use efficiency in rice plants. Here, we present an extension of the RNA Sequencing pipeline to generate a list of candidate genes that have the potential for molecular-based sensor development in Oryza sativa for nitrogen monitoring. The RNA Sequencing data used in this study represents 4714 genes from O. sativa seedlings that showed a dynamic response toward nitrogen availability. To generate a pool of candidate genes, we designed an algorithm for a two-step screening process that evaluates the expression of each gene across different sampling points using fuzzy logic. On the first screening, the genes were clustered based on their expression pattern, wherein a total of 135 genes from leaf tissues were found to exhibit an antagonistic response to nitrogen starvation and adaptation. These were further evaluated for the second screening where 27 genes showed at least 72% change in expression. Most of the genes were found associated with the plant’s response to stress, biotic and abiotic stimulus, transport, protein modification, and metabolic processes. This set of genes will serve as the target transcripts for nitrogen sensor development.
Yokimiko David,Mary Grace Baylon,Sudheer D. V. N. Pamidimarri,Kei-Anne Baritugo,채철기,김유진,김태완,김민식,나정걸,박시재 한국생물공학회 2017 Biotechnology and Bioprocess Engineering Vol.22 No.2
Coal is one of the major sources of energy, fuel, and other related chemicals. The processes to utilize coal for energy, fuel and other chemicals such as coal combustion, liquefaction, carbonization, and gasification pose a great threat to the environment by emitting toxic particles and CO2 to the atmosphere. Thus, biological beneficiation of coal can be a good strategy to utilize coal with environmental sustainability. Here, we report the screening of microorganisms able to degrade or depolymerize coal. These host strains are potential candidates for the development of biological treatment process of coal. A total of 45 microbial strains were isolated from sludge enriched with coal and were identified based on 16S rRNA sequencing. Four strains of three genera, Cupriavidus sp., Pseudomonas sp., and Alcaligenes sp., were further characterized for their abilities to degrade coal. The degree of coal degradation was analyzed by measuring the increase in absorbance at 450 nm by UV spectroscopy. These microorganisms were also able to increase the pH of the culture media as a response to the acidic nature of coal. Laccase-like activity was also found in these strains when tested for RBBR dye degradation. Since biological degradation of coal through the use of microorganisms is a good alternative to chemical combustion of coal, microbial strains isolated in this study can be potential biological catalysts for coal conversion into valuable chemicals.
Ravikumar, Sambandam,David, Yokimiko,Park, Si Jae,Choi, Jong-il Humana Press 2018 Applied biochemistry and biotechnology Vol.186 No.2
<P>In this study, we constructed amino acid biosensors that can be used as a high-throughput system to screen microorganisms that produce glutamate. The biosensors are based on two-component regulatory systems (TCRSs) combined with green fluorescent protein (GFP) as a reporter. A chimeric DegS/EnvZ (DegSZ) TCRS was constructed by fusing the N-terminal domain of the sensor kinase DegS from Planococcus sp. PAMC21323 with the catalytic domain of the osmosensor EnvZ from Escherichia coli to control expression of gfp in response to glutamate. gfp was controlled by the ompC promoter through the activated response regulator OmpR-P. The chimeric TCRS-based biosensors showed a 4-fold increase in the fluorescent signal after adding glutamate. A linear correlation was observed between fluorescence intensity and exogenously added glutamate concentration. The chimeric TCRS-based biosensor was used to determine glutamate concentration at the single-cell level by fluorescence-activated cell sorting. Therefore, this biosensor can be used to isolate novel gene products and optimize pathways involved in amino acid production.</P>
미니총설 : 바이오플라스틱 생산 미생물 플랫폼 제작을 위한 대사공학 전략 개발
박시재 ( Si Jae Park ),요키미코데이비드 ( Yokimiko David ),메리그레이스베일런 ( Mary Grace Baylon ),홍순호 ( Soon Ho Hong ),오영훈 ( Young Hoon Oh ),양정은 ( Jung Eun Yang ),최소영 ( So Young Choi ),이승환 ( Seung Hwan Lee ),이상엽 ( Sang 한국공업화학회 2014 공업화학 Vol.25 No.2
환경오염, 기후변화, 고갈되어가는 화석원료에 대한 문제를 해결하기 위해 재생가능한 자원으로부터 케미칼 및 고분자 등의 산업자원을 생산하는 친환경 공정개발에 많은 연구가 진행되고 있다. 최근에 재생가능한 바이오매스로부터 다양한 케미칼 및 고분자 등을 생산하는 바이오리파이너리 공정이 많은 관심을 받고 있으며, 석유화학기반산업을 보완 혹은 대체할 가능성이 매우 높은 친환경공정으로 생각되고 있다. 본 총설에서는 바이오리파이너리 공정에 핵심적인 촉매로 사용되고 있는 재조합 미생물의 개발의 최근 동향을 바이오나일론, 바이오폴리에스터의 생산을 위하여 개발되고 있는 재조합 미생물의 대사공학전략을 중심으로 살펴보고자 한다. As the concerns about environmental problems, climate change and limited fossil resources increase, bio-based production of chemicals and polymers from renewable resources gains much attention as one of the promising solutions to deal with these problems. To solve these problems, much effort has been devoted to the development of sustainable process using renewable resources. Recently, many chemicals and polymers have been synthesized by biorefinery process and these bio-based chemicals and plastics have been suggested as strong candidates to substitute petroleum-based products. In this review, we discuss current advances on the development of metabolically engineered microorganisms for the efficient production of bio-based chemicals and polymers.
조서영,손유정,박세영,손진아,유지인,BARITUGOKEIANNE,Yokimiko David,강경희,김호용,최종일,이미나,김희택,주정찬,박시재 한국화학공학회 2021 Korean Journal of Chemical Engineering Vol.38 No.7
Sugarcane molasses was examined for the production of poly(3-hydroxybutyrate) [P(3HB)] and poly(3- hydroxybutyrate-co-lactate) [P(3HB-co-LA)] in recombinant Ralstonia eutropha strains expressing Mannheimia succiniciproducens sacC gene encoding -fructofuranosidase, which can hydrolyze sucrose into glucose and fructose in the culture medium. When crude sugarcane molasses was added to the culture medium to support 20 g/L of sucrose in flask cultivation, the growth of R. eutropha NCIMB11599 expressing the sacC gene was significantly inhibited, which resulted in OD600 of 1.2 with P(3HB) content of 0.1wt%. The inhibition of cell growth due to the usage of the crude sugarcane molasses was relieved by pretreatment of sugarcane molasses with activated charcoal. Sugarcane molasses pretreated with activated charcoal could support the growth of R. eutropha NCIMB11599 expressing the sacC gene to OD600 of 87.2 with P(3HB) content of 82.5 wt% in batch fermentation when it was added to culture medium to support 20 g/L of sucrose. Also, R. eutropha 437-540 expressing Escherichia coli ldhA gene encoding lactate dehydrogenase along with the sacC gene produced P(3HB-co-6.2mol%LA) with 29.1 wt% polymer content from sugarcane molasses in batch fermentation.