Detection of the Cochlodinium polykrikoides On the Site using Real-Time PCR Method

Cochlodinium polykrikoides is one of the most harmful microalgae causing algal blooms. It is responsible for impacting to aquaculture and economics. For managing algal blooms, It is necessary that improving rapid detection method on the site. In the present study, C. polykrikoides was detected on the site by real-time PCR method during September 2019 algal blooms of the Korean southern costal. LSU gene was selected as a target for C. polykrikoide, and standard curves were produced for quantitative cell number analysis. At 2nd and 4th September, which is first research, Yeosu, especially station G2, G17 and G20, was detect the algal bloom. It spread to southeastern water, including Namhae and Tongyeong. Next research period, at 11th and 12th, C. polykrikoides bloomed in Tongyeong, which is station R1, R2, R3, R5. Between first and second research period, there was a typhoon, LINGLING. It may be considered that typhoon put C. polykrikoides into the costal. In addition, Detection C. polykrikoides method was applied on the site. The results correspond with performing experiments in vitro and it could contribute to the rapid monitoring of C. polykrikoides in the field.2

Dynamics of Host-Driven Viral Community and Auxiliary Metabolic Genes by latitudinal gradient

Auxiliary metabolic genes (AMGs) encoded by viruses are pivotal in modulating host metabolism and driving microbial biogeochemical cycles across diverse ecosystems. AMGs play a crucial role in processes such as nutrient cycling, carbon fixation, and energy flow, making them key components in regulating ecosystem functions. Bacteriophages often carry AMGs, empowering them to boost their host's metabolism or enhance virus fitness. Understanding the factors influencing AMG analysis within viral communities is essential for elucidating the complex interactions between viruses, hosts, and their environments. To explore the ecological diversity and metabolic functions of viral communities, we analyzed AMGs across latitudinal gradients, focusing on the Arctic (Svalbard, Norway), Temperate (Tongyeong, South Korea), and Tropical (Chuuk, Micronesia) regions using metagenomic analysis. Our findings revealed that bacteriophage communities in the Temperate and Tropical regions exhibited similar AMG analysis, particularly associated with photosynthetic electron transport and productivity. In contrast, viral communities in the Arctic region displayed distinct AMG analysis, focusing on genes involved in the biosynthesis of unsaturated fatty acids, a crucial process for cold adaptation. These differences likely reflect the selective pressures imposed by varying environmental conditions, such as temperature and light availability. This study reveals the adaptive roles of viruses in modulating host metabolism through distinct AMG analysis across different ecosystems. It emphasizes the importance of AMGs in microbial biogeochemical processes and sets the stage for future research on their global distribution and ecological significance.2

Rapid Detection of Cochlodinium polykrikoides by Sandwich Hybridization Integrated with Invertase Assay

Rapid and accurate identification of marine microalgae causing harmful algal blooms (HABs) is a very important tool for predicting and managing HABs. We previously developed a nuclease protection assay sandwich hybridization (NPA-SH) method for the in situ detection of blooming microalgae Cochlodinium polykrikoides. In this study, we improved the applicability of the NPA-SH method for the detection of C. polykrikoides by simplifying the reaction step. For this purpose, invertase (INV) was conjugated to signal probe instead of using fluorescence, and sucrose was used as a reactant to induce a color reaction. The INV-signal probe conjugation was confirmed by SDS-PAGE and epifluoromicroscopy, and the amounts of the appropriate probe and sucrose, and the treatment time for optimizing the reaction were determined. As a result, the developed INV-SH reduced the treatment time in the field compared with NPA-SH, and it was possible to use a relatively small volume and low-priced personal glucose meter as well as an absorbance meter. INV-SH is the first C. polykrikoides species identification technology to which INV has been applied and could be an improved field technique.2

Ecological interaction between bacteriophages and bacteria community during the early white night and mid-summer in Sub-arctic Kongsfjorden bay of Svalbard (Norway)

Marine viruses including viruses and phages infect various marine organisms. However, little is known about the diversity of marine viruses and their relationships with their hosts in marine environments. This study investigated the co-occurrence between marine DNA bacteriophages (phages) and the bacteria community in the sub-Arctic area using metagenomics tools in the Kongsfjorden Bay of Svalbard (Norway) in April and June 2018. Among all identified marine viruses, 48-81% were phages involving the families Myoviridae, Siphoviridae, and Podoviridae (in Caudoviriales) as the common groups (order levels). In addition, Puniceispirillum phage HMO-2011 was the most dominant at 7.61% in April, and Puniceispirillum phage HMO-2011 and Pelagibacter phage HTVC008M was the most dominant at 3.32% and 3.28%, respectively, in June. In the bacteria community, Gammaproteobacteria was 58% of the prevalent group (class level) and Eionea flava (14.3%) and Pseudomonas sabulinigri (12.2%) (Gammaproteobacteria) were the most predominant taxa in April, but Alphaproteobacteria showed an absolute predominance of 87%, and Sulfitobacter profundi and Loktanella acticola (Alphaproteobacteria) were the most predominant taxa at 51.5% and 32.4%, respectively, in June. In species- specific relationship between bacteria and phages, Puniceispirillum phage HMO-2011 and Synechococcus phage S-SSM7 was stronger correlated with Eionea flava (r=0.764, p<0.01) and Sulfitobacter profundi (r=0.842, p<0.01), respectively. This relationship between phages and bacteria community may be caused by changes in response to environmental changes, such as increases in water temperature and light intensity. Taken together, these findings are particularly relevant considering the anticipated impact of phages-induced bacterial control mechanisms on the Sub-Arctic Kongsfjorden ecosystem.2

Method for detecting nervous necrosis virus, and primer-probe set, composition and kit for the same

본 발명은 신경 괴사 바이러스 검출 방법, 및 이를 위한 프라이머-프로브 세트, 조성물 및 키트에 관한 것 으로, 구체적으로 a) 시료로부터 RNA를 분리하는 단계 b) 상기 분리된 RNA를 주형으로 하여 cDNA를 합성 하는 단계 c) 상기 합성된 cDNA를 주형으로 하고, 서열번호 1의 서열로 이루어지는 정방향 프라이머 서 열번호 2의 서열로 이루어지는 역방향 프라이머 및 서열번호 3의 서열 중 35번 염기가 비염기 형태로 치 환된 서열로 이루어지는 프로브 를 사용하여 엔도뉴클레아제의 존재 하에서 재조합효소 중합효소 증폭을 수행하는 단계 및 d) 상기 재조합효소 중합효소 증폭으로 생성된 증폭산물 중 상기 역방향 프라이머 및 상기 프로브의 5‘ 부위가 포함된 증폭산물을 검출하는 단계 를 포함하는 신경 괴사 바이러스 검출 방법, 및 상기 프라이머 및 프로브를 포함하는 프라이머-프로브 세트, 조성물 및 키트에 관한 것이다. 본 발명에 따르면 재조합효소 중합효소 증폭법을 사용하여 간단하고 신속하며 높은 정확도로 신경 괴사 바 이러스를 검출할 수 있다. 특히, 본 발명의 검출 방법, 프라이머-프로브 세트, 조성물, 키트는 측면흐름분 석법에 적용할 수 있어 검출의 편의성을 더욱 높일 수 있다. 이에 따라 본 발명의 검출 방법, 프라이머-프 로브 세트, 조성물 및 키트는 해양 어류의 신경 괴사 바이러스 감염을 조기에 발견하고, 이의 확산을 방지 하는데 크게 기여할 수 있을 것으로 기대된다

Prediction of Stress Distribution and Fatigue Life of Needle Roller Bearing for an Automobile Engine Rocker Arm

A needle roller bearing is an essential machine element for the precise operation of an automobile engine rocker arm. The fuel efficiency, noise, durability, and power of the engines can be improved by mounting the needle roller bearing on the rocker arm. In particular, as the driving performance and power of automobiles improve, it is necessary to design and manufacture needle roller bearings to prevent accidents caused by issues such as bearing failure from fatigue, wear, and fracture, even under extreme operating conditions. In this study, an automobile engine rocker arm was modeled, and the load acting on the needle roller bearing was calculated using a multi-body dynamic simulation (MBDS). In addition, the static safety factor and dynamic life were evaluated according to ISO 76 and ISO/TS 16281 using the calculated load and bearing parameters. Furthermore, the effects of the bearing roller profile on the bearing contact stress distribution were analyzed, and an optimal roller profile was chosen. Finally, the safety of the bearing roller was quantitatively evaluated by comparing the loads acting on each roller with the roller capacity.N

Cochlodinium polykrikoides적조 발생 시 Core-bacteria의 다양성

Cochlodinium polykrikoides 적조 발생에 따른 박테리아 군집의 변화양상 및 적조발생으로 인한 C. polykikroides-phycoshphere의 core 박테리아의 다양성을 파악하기 위하여 2019년 9월 2일과 4일 격일에 걸쳐서 거제, 통영 그리고 여수(약 90 km x 20 km)해역에서 110개의 시료를 채집하였다. 분석항목은 기본 이화학적 특성, 식물플랑크톤 종조성 그리고 16S rDNA metabarcoding을 통한 박테리아 군집을 분석하였다. 이화학적 환경요인 및 식물플랑크톤 종 조성 결과를 바탕으로 non-metric multidimensional scaling (nMDS) 분석 결과, 85%의 유사도로 3개의 그룹으로 구분되었다. 그룹 I은 C. polykrikoides 적조 발생이 일어난 (평균 개체수: 1,560 cells mL-1) 정점들로 주로 구성되었고, 그룹 II와 그룹 III는 상대적으로 C. polykrikoides의 개체수가 적은 해역의 시료를 포함하며 각각 평균 68과 57 cells mL-1로 나타났다. 1% 이상의 출현비율을 차지한 박테리아는 총 89 operational taxonomic units (OTUs)였고 그룹 I에서는 40 OTUs이고 다른 그룹과 중복되는 않는 고유 OTUs는 6개로 나타났다. 그룹 II와 그룹 III는 각각 61개와 60개의 OTUs가 출현하였고 고유 OTUs는 각각 18과 17이었다. 그리고 89 OTUs는 Gammaproteobacteria (36 OTUs), Flavobacteriia (24), Alphaproteobacteria (18) 및 Acidimicrobiia (3) 등에 포함되었다. 그룹 I의 박테리아 군집은 Gammaproteobacteria와 Alphaproteobacteria의 비중이 증가한 반면 Flavobacteriia와 Acidimicrobiia는 감소했다. 이와 반대로 그룹 II와 그룹 III에서 Gammaproteobacteria와 Alphaproteobacteria의 비중이 감소하고 Flavobacteriia와 Acidimicrobiia는 증가했다. Pearson correlation 분석 결과, C. polykrikoides와 일부 박테리아 OTUs (#012, #015, #023, #024, #029, #033 및 #059)간 음의 상관관계를 보였고 OTUs #003 및 #030과 양의 상관관계를 보였다. 이 중 특히 OTUs #030 (Gammaproteobacteria; Francisella persica)은 C. polykrikoides와의 상관계수가 0.95 (p<0.001)로 나타났을 뿐만 아니라 DO, pH, DIN, DIP, DOC 그리고 Chl-a 값과 양의 상관관계를 보였다. 본 연구결과에서 C. polykrikoides 적조 발생은 특이 박테리아 종들과의 관계가 있으며 Gammaproteobacteria와 Alphaproteobacteria의 높은 비중을 보였다. 특히, C. polykikroides적조 발생과 OTU #30은 상호 증식에 positive effect를 나타낸 반면, 일부 Flavobacteriia 및 Acidimicrobiia 상호 성장을 저해하는 것으로 판단된다.2

Optimization of capture system for RNA virus analysis in marine environments

Marine RNA viruses have primarily been studied in terms of their pathogenicity, as they infect a wide range of hosts. However, their diversity and ecological roles remain largely unexplored. In particular, they are generally smaller than DNA viruses, making them more challenging to capture, and their inherent instability leads to rapid degradation. Therefore, optimizing an efficient RNA virus capture system is crucial. This study conducted a total of 121 experiments with seawater volumes ranging from 60 L to 300 L to evaluate the capture efficiency of RNA viruses using three concentration methods: membrane filtration, filter tubes, and ultracentrifugation. The optimal method for capturing marine RNA viruses involved filtering 100 L of seawater through a 0.2 μm membrane, followed by an initial concentration using a 30 kDa tangential flow filtration system, and a final concentration step via ultracentrifugation. This approach demonstrated high reproducibility. Our results present an effective method for capturing and analyzing RNA viruses in marine environments, providing a valuable tool for investigating their diversity and ecological roles.2

Effect of Environmental Changes on DNA Viral Community Diversity and Composition in Korean Coastal Waters

Recent advances in metavirome technologies have provided new insights into viral diversity and function. Research on viral metagenomes has uncovered numerous putative viral genomes previously unidentified in various environments. Most marine metavirome studies have primarily focused on open ocean ecosystems, whereas viral community structures in coastal environments remain comparatively underexplored. Here, we performed a comprehensive metavirome analysis using quarterly surface water samples collected in coastal waters of South Korea, 2021, yielding 307 gigabytes of sequencing data. Overall, 7,510 DNA viral contigs were obtained, with 89.7% being bacteriophages and 7% being nucleocytoplasmic large DNA viruses (NCLDVs). Taxonomic profiling identified 2,115 bacteriophages taxa and 116 NCLDVs taxa. Pelagibacter phage HTVC008M of bacteriophage and Micromonas sp. RCC1109 virus MpV1 of NCLDVs exhibited the highest relative abundance. Bacteriophage diversity was approximately twice that of NCLDVs, with the diversity being larger in summer and smaller in winter, likely due to seasonal salinity changes. These findings enhance our understanding of DNA viral community diversity and provide insights into temporal and spatial environmental changes in viral community composition.2