• 제목/요약/키워드: Artificial RNA

검색결과 104건 처리시간 0.024초

Characterization of Vaginal Microbiota Associated with Pregnancy Outcomes of Artificial Insemination in Dairy Cows

  • Chen, Shi-Yi;Deng, Feilong;Zhang, Ming;Jia, Xianbo;Lai, Song-Jia
    • Journal of Microbiology and Biotechnology
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    • 제30권6호
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    • pp.804-810
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    • 2020
  • The profitability of the dairy and beef industries is largely affected by the actually achieved reproductive efficiency. Although a large proportion of cows worldwide are bred by artificial insemination (AI) services, many potential factors affecting the outcome of pregnancy by AI remain to be addressed. In the present study, we investigated the vaginal microbiota by high-throughput sequencing of 16S rRNA gene and analyzed their association with differential pregnancy outcomes (i.e., pregnant vs. nonpregnant) of multiple AI services in dairy cows. Sequencing of the V3-V4 region totally produced 512,046 high-quality sequences that were computationally clustered into 2,584 operational taxonomic units (OTUs). All OTUs were taxonomically assigned to 10 bacterial phyla. There were statistically significant differences among the three AI service times (T1, T2 and T3) with respect to the Shannon index and number of observed OTUs (p < 0.05). Bray-Curtis distance-based PCoA analysis also revealed that T2 group could be significantly distinguished from T1 and T3. However, no significant difference between the pregnant and nonpregnant cows was found in confidence regarding both alpha diversity and beta diversity. These results could help us better understand the possible influence of vaginal microbial community on pregnancy outcomes of AI service in cows.

Streptomyces BAC Cloning of a Large-Sized Biosynthetic Gene Cluster of NPP B1, a Potential SARS-CoV-2 RdRp Inhibitor

  • Park, Ji-Hee;Park, Heung-Soon;Nah, Hee-Ju;Kang, Seung-Hoon;Choi, Si-Sun;Kim, Eung-Soo
    • Journal of Microbiology and Biotechnology
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    • 제32권7호
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    • pp.911-917
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    • 2022
  • As valuable antibiotics, microbial natural products have been in use for decades in various fields. Among them are polyene compounds including nystatin, amphotericin, and nystatin-like Pseudonocardia polyenes (NPPs). Polyene macrolides are known to possess various biological effects, such as antifungal and antiviral activities. NPP A1, which is produced by Pseudonocardia autotrophica, contains a unique disaccharide moiety in the tetraene macrolide backbone. NPP B1, with a heptane structure and improved antifungal activity, was then developed via genetic manipulation of the NPP A1 biosynthetic gene cluster (BGC). Here, we generated a Streptomyces artificial chromosomal DNA library to isolate a large-sized NPP B1 BGC. The NPP B1 BGC was successfully isolated from P. autotrophica chromosome through the construction and screening of a bacterial artificial chromosome (BAC) library, even though the isolated 140-kb BAC clone (named pNPPB1s) lacked approximately 8 kb of the right-end portion of the NPP B1 BGC. The additional introduction of the pNPPB1s as well as co-expression of the 32-kb portion including the missing 8 kb led to a 7.3-fold increase in the production level of NPP B1 in P. autotrophica. The qRT-PCR confirmed that the transcription level of NPP B1 BGC was significantly increased in the P. autotrophica strain containing two copies of the NPP B1 BGCs. Interestingly, the NPP B1 exhibited a previously unidentified SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibition activity in vitro. These results suggest that the Streptomyces BAC cloning of a large-sized, natural product BGC is a valuable approach for titer improvement and biological activity screening of natural products in actinomycetes.

육미지황탕합사백산(六味地黃湯合瀉白散)과 상백피(桑白皮)가 인간 기관지상피세포의 IL-6, IL-8, GM-CSF mRNA level에 미치는 영향 (The Inhibitory Effects of Yukmijihwang-tang-Hap-Sabaek-san and Root Cortex of Morus alba L. on the IL-6, IL-8 and GM-CSF mRNA Levels in Human Epithelial Cells)

  • 황우석;허태석;정희재;정승기;이형구;주창엽
    • 대한한방내과학회지
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    • 제22권3호
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    • pp.415-422
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    • 2001
  • Objectives: We aimed to identify the dose-dependent inhibitory effects of Yukmijihwang-tang-Hap-Sabaek-san(YMHSB) and Root cortex of Morus alba L.(RCM) on the mRNA expression of Interieukin(IL)-6, IL-S, granulocyte macrophage colony stimulating factor(GM-CSF) involved in the asthma model. Methods: In this study BEAS-2B cell lines, human epithelial cells, were used. These cells were stimulated by tumor necrosis $factor(TNF)-{\alpha},\;IL-1{\beta}$ and histamine for artificial inflammatory expression. ${\beta}-actin$ messenger RNA(mRNA) was used for the internal standard. After each 24 hours of the YMHSB and RCM treatment, total cellular RNAs were collected by treating RNA zol directly on the living cells. Then the transcriptional activities of IL-6, 8 and GM-CSF were measured by RT-PCR with electrophoresis. Results: In the YMHSB study, the mRNA expression of GM-CSF and IL-8 is significantly inhibited compared to that of control group. But the mRNA expression of IL-6 is not significantly inhibited. In the RCM study, the mRNA expression of GM-CSF and IL-S is significantly inhibited compared to that of control group. But the mRNA expression of IL-6 is not significantly inhibited. Conclusions: This study shows that YMHSB and RCM have dose-dependent inhibitory effects on the mRNA expression of IL-S and GMCSF in human epithelial cells. So these herbal medicines may inhibit the inflammatory process of asthma. Advanced studies are required to investigate the mechanisms of inhibition by herbal medicine in the asthma model.

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Establishment of the large-scale longitudinal multi-omics dataset in COVID-19 patients: data profile and biospecimen

  • Jo, Hye-Yeong;Kim, Sang Cheol;Ahn, Do-hwan;Lee, Siyoung;Chang, Se-Hyun;Jung, So-Young;Kim, Young-Jin;Kim, Eugene;Kim, Jung-Eun;Kim, Yeon-Sook;Park, Woong-Yang;Cho, Nam-Hyuk;Park, Donghyun;Lee, Ju-Hee;Park, Hyun-Young
    • BMB Reports
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    • 제55권9호
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    • pp.465-471
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    • 2022
  • Understanding and monitoring virus-mediated infections has gained importance since the global outbreak of the coronavirus disease 2019 (COVID-19) pandemic. Studies of high-throughput omics-based immune profiling of COVID-19 patients can help manage the current pandemic and future virus-mediated pandemics. Although COVID-19 is being studied since past 2 years, detailed mechanisms of the initial induction of dynamic immune responses or the molecular mechanisms that characterize disease progression remains unclear. This study involved comprehensively collected biospecimens and longitudinal multi-omics data of 300 COVID-19 patients and 120 healthy controls, including whole genome sequencing (WGS), single-cell RNA sequencing combined with T cell receptor (TCR) and B cell receptor (BCR) sequencing (scRNA(+scTCR/BCR)-seq), bulk BCR and TCR sequencing (bulk TCR/BCR-seq), and cytokine profiling. Clinical data were also collected from hospitalized COVID-19 patients, and HLA typing, laboratory characteristics, and COVID-19 viral genome sequencing were performed during the initial diagnosis. The entire set of biospecimens and multi-omics data generated in this project can be accessed by researchers from the National Biobank of Korea with prior approval. This distribution of large-scale multi-omics data of COVID-19 patients can facilitate the understanding of biological crosstalk involved in COVID-19 infection and contribute to the development of potential methodologies for its diagnosis and treatment.

Catalytic Activity of DNA-Pt Complex

  • Matsuoka, Yuki;Kojima, Toshinori;Higuchi, Akon
    • 한국고분자학회:학술대회논문집
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    • 한국고분자학회 2006년도 IUPAC International Symposium on Advanced Polymers for Emerging Technologies
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    • pp.253-253
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    • 2006
  • DNA has not been played the role as a biocatalyst in evolutionary history, although RNA and protein function as a biocatalyst. DNA double helix structure is believed to be impossible to form intricate active enzymatic sites. In addition, the chemical stability of DNA prevents the ability from self-modifying reactions. However, recent development of DNA engineering enables to create artificial enzymatic ability of DNA (deoxyribozyme) such as RNA cleavage and DNA modification. We investigated optimal conditions for enzymatic activity of DNA-Pt complex, and compared it with that of horse radish peroxidase. We report here that base sequence of DNA, pH and temperature affect the enzymatic activity of DNA-Pt complex.

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Isolation and Identification of Lactic Acid Bacteria Isolated from a Traditional Jeotgal Product in Korea

  • Cho, Gyu-Sung;Do, Hyung-Ki
    • Ocean Science Journal
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    • 제41권2호
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    • pp.113-119
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    • 2006
  • Seventeen lactic acid bacterial strains (LAB) were isolated using MRS agar medium from Jeotgal, a Korean fermented food, purchased at the Jukdo market of Pohang. To identify the strains isolated, they were tested by examining their cell morphologies, gram-staining, catalase activity, arginine hydrolase activity, D-L lactate form and carbohydrate fermentation. According to the phenotypic characteristics, three strains were tentatively identified as Lactobacillus spp., ten were Enterococcus spp. (or Streptococcus spp., or Pediococcus spp.) and the rest were Leuconostoc spp. (or Weissella spp.). Five strains among 17 were chosen by preliminary bacteriocin activity test. Four bacterial strains which inhibited both indicator microorganisms were identified by 16S rRNA sequencing. The results are as follows; Leuconostoc mesenteroides (HK 4), Leuconostoc mesenteroides (HK 5), Leuconostoc mesenteroides(HK 11), Streptococcus salivarius(HK 8). In order to check LAB which are showing a high survival rate in gut, we investigated three strains inhibiting both indicator microorganisms in artificial gastric acid and bile juice -all except HK8. The three strains mentioned above grew in extreme low acid conditions.

Non-invasive evaluation of embryo quality for the selection of transferable embryos in human in vitro fertilization-embryo transfer

  • Jihyun Kim;Jaewang Lee;Jin Hyun Jun
    • Clinical and Experimental Reproductive Medicine
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    • 제49권4호
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    • pp.225-238
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    • 2022
  • The ultimate goal of human assisted reproductive technology is to achieve a healthy pregnancy and birth, ideally from the selection and transfer of a single competent embryo. Recently, techniques for efficiently evaluating the state and quality of preimplantation embryos using time-lapse imaging systems have been applied. Artificial intelligence programs based on deep learning technology and big data analysis of time-lapse monitoring system during in vitro culture of preimplantation embryos have also been rapidly developed. In addition, several molecular markers of the secretome have been successfully analyzed in spent embryo culture media, which could easily be obtained during in vitro embryo culture. It is also possible to analyze small amounts of cell-free nucleic acids, mitochondrial nucleic acids, miRNA, and long non-coding RNA derived from embryos using real-time polymerase chain reaction (PCR) or digital PCR, as well as next-generation sequencing. Various efforts are being made to use non-invasive evaluation of embryo quality (NiEEQ) to select the embryo with the best developmental competence. However, each NiEEQ method has some limitations that should be evaluated case by case. Therefore, an integrated analysis strategy fusing several NiEEQ methods should be urgently developed and confirmed by proper clinical trials.

Antiviral Treatment Reveals a Cooperative Pathogenicity of Baculovirus and Iflavirus in Spodoptera exigua, a Lepidopteran Insect

  • Roy, Miltan Chandra;Ahmed, Shabbir;Mollah, Md. Mahi Imam;Kim, Yonggyun
    • Journal of Microbiology and Biotechnology
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    • 제31권4호
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    • pp.529-539
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    • 2021
  • The beet armyworm, Spodoptera exigua, is a serious insect pest infesting various vegetable crops. Two infectious insect viruses, baculovirus and iflavirus, are known to induce epizootics in S. exigua populations. Indeed, some laboratory colonies have appeared to be covertly infected by these viruses. Diagnostic PCR tests detected two different viruses: Spodoptera exigua multiple nucleopolyhedrosis virus (SeMNPV) and iflaviruses (SeIfV1 and SeIfV2). Viral extract from dead larvae of S. exigua could infect Sf9 cells and produce occlusion bodies (OBs). Feeding OBs to asymptomatic larvae of S. exigua caused significant viral disease. Interestingly, both SeIfV1 and SeIfV2 increased their titers at late larval stages. Sterilization of laid eggs with 1% sodium hypochloride significantly reduced SeMNPV titers and increased larval survival rate. Double-stranded RNA (dsRNA) specific to SeIfV1 or SeIfV2 significantly reduced viral titers and increased larval survival rate. To continuously feed dsRNA, a recombinant Escherichia coli HT115 expressing SeIfV1-dsRNA was constructed with an L4440 expression vector. Adding this recombinant E. coli to the artificial diet significantly reduced the SeIfV1 titer and increased larval survival. These results indicate that laboratory colony collapse of S. exigua is induced by multiple viral infections. In addition, either suppression of SeMNPV or SeIfV infection significantly increased larval survival, suggesting a cooperative pathogenicity between baculovirus and iflavirus against S. exigua.

사백산(瀉白散)과 사백산가사삼(瀉白散加沙蔘)이 인간 기관지상피세포의 IL-6, IL-8 및 GM-CSF 발현에 미치는 영향 (The Inhibitory Effects of Sabaek-san and Sabaeksan plus Sasam on the IL-6, IL-8 and GM-CSF mRNA Levels in Human Epithelial Cells)

  • 정희재;정승기;이형구;정광진
    • 대한한방내과학회지
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    • 제23권1호
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    • pp.15-23
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    • 2002
  • Objective : We aimed to identify the dose-dependent inhibitory effects of Sabaek-san(瀉白散) and Sabaeksan plus Sasam(Adenophorae Radix) 瀉白散加沙蔘) on the mRNA expressions of Interleukin(IL)-6, IL-8 and granulocyte macrophage colony stimulating factor(GM-CSF) involved in the asthma model. Materials and Methods : Through this study, BEAS-2B cell lines, human epithelial cells were used. These cells were stimulated by tumor necrosis factor(TNF)-${\alpha}$, IL-1${\beta}$ and histamine for artificial inflammatory expression. ${\beta}$-action messenger RNA(mRNA) was used for standards. After each 24hours of Sabaeksan and Sabaeksan plus Sasam treatment, total cellular RNAs were collected by treating RNA zol directly on living cells, Then the transcriptional activities of IL-6, 8 and GM-CSF were measured by RT-PCR with electrophoresis, Results : The mRNA expressions of IL-6 are significantly inhibited compared to those of controlled group at 40 and 100ug/ml of Sabaeksan extract and $100{\mu}g/ml$ of Sabaeksan plus Sasam extract (p<0.05). The mRNA expressions of IL-8 are significantly inhibited compared to that of controlled group at 2.40 and 100 ug/ml of Sabaeksan extract and $40.100{\mu}g/ml$ of Sabaeksan plus Sasam extract(p<0.05) THe mRNA expressions of GM-CSF are significantly inhibited compared to those of the controlled group at $100{\mu}g/ml$ of Sabaeksan extract adn $40.100{\mu}g/ml$ of Sabaeksan plus Sasam extract.(p<0.05) Conclusions : This study shows that Sabaeksan and Sabaeksan plus Sasam have dose-dependent inhibitory effects on the mRNA expressions of IL-6, IL-8 and GM-CSF in human epithelial cells. Therefore, these types of herb medicine may inhibit the inflammatory process of asthma. Advanced studies are required to investigate the mechanisms of inhibition by herb medicine in the asthma model.

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Culture Conditions for Mycelial Growth and Anti-Cancer Properties of Termitomyces

  • Suphachai Tharavecharak;Corina N. D'Alessandro-Gabazza;Masaaki Toda;Taro Yasuma;Taku Tsuyama;Ichiro Kamei;Esteban C. Gabazza
    • Mycobiology
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    • 제51권2호
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    • pp.94-108
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    • 2023
  • Termitomyces sp. that grow in symbiosis with fungus-farming Termites have medicinal properties. However, they are rare in nature, and their artificial culture is challenging. The expression of AXL receptor tyrosine kinase and immune checkpoint molecules favor the growth of cancer cells. The study evaluated the optimal conditions for the artificial culture of Termitomyces and their inhibitory activity on AXL and immune checkpoint molecules in lung adenocarcinoma and melanoma cell lines. The culture of 45 strains of Termitomyces was compared. Five strains with marked growth rates were selected. Four of the selected strains form a single cluster by sequence analysis. The mycelium of 4 selected strains produces more fungal mass in potato dextrose broth than in a mixed media. The bark was the most appropriate solid substrate for Termitomyces mycelia culture. The mycelium of all five selected strains showed a higher growth rate under normal CO2 conditions. The culture broth, methanol, and ethyl acetate of one selected strain (T-120) inhibited the mRNA relative expression of AXL receptor tyrosine kinase and immune checkpoint molecules in cancer cell lines. Overall, these results suggest the potential usefulness of Termitomyces extracts as a coadjuvant therapy in malignant diseases.