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Shade Avoidance and the Regulation of Leaf Inclination in Rice
Shin, Juhee,Park, Phun Bum Korean Society of Photoscience 2014 Rapid communication in photoscience Vol.3 No.3
The shade avoidance syndrome is a morphological and physiological response when plants are exposed to shade. Recent work in Arabidopsis had begun to define the molecular components of the shade avoidance syndrome in dicotyledonous model plant. However, little is known about the shade avoidance response networks in agriculturally important monocotyledon crops such as rice. Here, we found that the degree of bending at the lamina joint is inversely proportional to the R:FR ratio. To elucidate which phytochrome is involved in this response, we did lamina joint inclination assay with the rice phytochrome-deficient mutants (osphyA, osphyB, and osphyC) and the wild type plants. Whereas the osphyA and osphyC knockout mutants bent at the lamina joint in the far-red rich condition as the wild type plants, the osphyB knockout mutants no longer bent at the lamina joint in the far-red rich condition. These results suggest that PHYB acts as a sole photoreceptor in the lamina joint inclination response in rice.
Shin, Seung Gu,Han, Gyuseong,Lee, Joonyeob,Shin, Juhee,Hwang, Seokhwan Elsevier 2019 Journal of environmental management Vol.248 No.-
<P><B>Abstract</B></P> <P>This study aimed to identify significant factors shaping the microbial populations in biogas plants treating food waste (FW). Twenty full-scale anaerobic acidogenic/methanogenic bioreactors, located at 11 FW treatment facilities, were compared to find patterns in their microbial community structures and potential interactions with the process parameters. Temperature, hydraulic retention time, and organic loading rate were design parameters that systematically influenced the microbial communities. The latter two clearly separated the acidogenic and methanogenic bioreactors. <I>Lactobacillus</I> was the dominant (69.7 ± 19.8%) bacteria in the acidogenic reactors, while hydrogen-utilizing methanogens, such as <I>Methanoculleus</I> (65.1 ± 33.5%), were the dominant archaea in most methanogenic digesters. <I>Defluiviitoga</I> was the dominant (82.7 ± 1.4%) bacteria in the thermophilic digesters, but was also the most abundant (33.1–33.6%) bacteria in dry mesophilic digesters. The two bioreactor categories had lower bacterial diversities, and also higher propionate concentrations (>5 g/L in 4 out of 5 cases), which may impose potential risks for the management of such digesters. The current ‘snapshot’ of the microbial communities suggests several bacterial and archaeal taxa as potential indicators of bioreactor categories and/or process variables.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Twenty full-scale acidogenic/methanogenic reactors treating solely FW were compared. </LI> <LI> <I>Lactobacillus</I> was dominant in the acidogenic bioreactors. </LI> <LI> <I>Defluiviitoga</I> was the most abundant bacteria in thermophilic or dry digesters. </LI> <LI> <I>Hydrogen</I>-utilizing methanogens including <I>Methanoculleus</I> (65.1%) were dominant. </LI> </UL> </P>
DNA 추출법에 따른 혐기소화조 미생물 군집 분석 결과 비교
신주희(Juhee Shin),김영백(Youngback Kim),신승구(Seung Gu Shin) 대한환경공학회 2021 대한환경공학회지 Vol.43 No.1
목적: DNA 추출 방법에 따른 혐기소화조 시료의 미생물 군집 분석 결과를 비교한다. 방법: 실규모 중온 혐기소화조 시료를 동일 볼륨으로 소분하였다. DNA 추출법으로는 국내에서 많이 사용하는 제품 중 미국 MP Biomedicals사의 FastDNA spin kit for soil, 한국 GeneAll사의 Exgene stool DNA mini kit, 그리고 한국 Bioneer사의 AccuPrep genomic DNA extraction kit의 세 종류를 사용하였다. 박테리아의 경우 V3-4, 고세균의 경우 V4-5 region에 해당하는 16S rDNA amplicon을 제작한 뒤, 일루미나 iSeq 100 장비로 염기 서열을 분석하였다. 미생물 군집 분석을 위해서 quality filter를 거친 유효한 read만을 얻은 뒤, OTU clustering을 하여 RDP classifier를 이용해 계통 분석(taxonomic assignment)하였다. 결과 및 토의 : Weighted UniFrac distance로 군집 결과를 시각화한 결과, 박테리아와 고세균 모두 사용한 세 가지 kit에 따라 군집 구조 차이를 보였으며, 특정 군집들은 DNA 추출 방법에 따라 존재 비율의 차이가 크게 나타났다. 예를 들어, soil kit은 Proteobacteria 문에 대한 추출 효율이 다른 추출법에 비해 낮고, Thermotogae에 대해서는 높은 것으로 나타났으며, stool kit은 이와 반대의 경향성을 보였다. 고세균의 경우, genus 중 Methanomethylovorans와 Methanosarcina가 DNA 추출법의 영향을 특히 많이 받는 것으로 나타났다. 결론: 미생물 군집 결과는 DNA 추출 방법에 영향을 받았다. 동일 선상의 실험에서 미생물 군집을 비교하려면 반드시 동일한 DNA 추출 방법을 사용해야 한다는 것을 확인하였다. Objectives : This study was performed to compare three commercial kits for the extraction of genomic DNA from anaerobic digestate for subsequent iSeq 100 sequencing and microbial community analysis. Methods : A full-scale mesophilic biogas plant was sampled, and made into aliquots of identical volumes to extract DNA using three commercial kits: FastDNA spin kit for soil (MP Biomedicals, USA), Exgene stool DNA mini (GeneAll, South Korea) and AccuPrep genomic DNA extraction kit (Bioneer, South Korea). To analyze the microbial communities in the purified DNA, 16S rDNA amplicon sequencing (V3-4 region for bacteria and V4-5 region for archaea) was performed on the Illumina iSeq 100 platform. Quality filtered sequence reads were OTU-clustered for taxonomic assignment conducted using the RDP classifier on-line. Results and Discussion : The microbial community structure visualized on the NMDS plot using the weighted UniFrac distance revealed that both bacteria and archaeal communities have phylogenetic differences depending on the DNA extraction kit used. In addition, the abundance of certain microbial populations was significantly different among the DNA extraction methods. For example, Proteobacteria was the least abundant using the soil kit, while this phylum was the most abundant when the stool kit was used. However, in the case of Thermotogae, this tendency was vice versa. The abundance of archaeal genera Methanomethylovorans and Methanosarcina was also affected by DNA extraction methods. Conclusions : The microbial populations analyzed by 16S based sequencing were affected by DNA extraction methods. To compare microbial community changes in the identical set of research, one DNA extraction method should be chosen and used consistently for the whole experiment.