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Review
Insights into the immune responses of SARS-CoV-2 in relation to COVID-19 vaccines
Heedo Park , Mee Sook Park , Jong Hyeon Seok , Jaehwan You , Jineui Kim , Jeonghun Kim , Man-Seong Park
J. Microbiol. 2022;60(3):308-320.   Published online March 2, 2022
DOI: https://doi.org/10.1007/s12275-022-1598-x
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AbstractAbstract
The three types of approved coronavirus disease 2019 (COVID- 19) vaccines that have been emergency-use listed (EUL) by the World Health Organization are mRNA vaccines, adenovirus- vectored vaccines, and inactivated vaccines. Canonical vaccine developments usually take years or decades to be completed to commercialization; however, the EUL vaccines being used in the current situation comprise several COVID- 19 vaccine candidates applied in studies and clinical settings across the world. The extraordinary circumstances of the COVID-19 pandemic have necessitated the emergency authorization of these EUL vaccines, which have been rapidly developed. Although the benefits of the EUL vaccines outweigh their adverse effects, there have been reports of rare but fatal cases directly associated with COVID-19 vaccinations. Thus, a reassessment of the immunological rationale underlying EUL vaccines in relation to COVID-19 caused by SARSCOV- 2 virus infection is now required. In this review, we discuss the manifestations of COVID-19, immunologically projected effects of EUL vaccines, reported immune responses, informed issues related to COVID-19 vaccination, and the potential strategies for future vaccine use against antigenic variants.

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  • Single intranasal immunization with attenuated Wuhan-like SARS-CoV-2 provides highly effective cross-protection against Delta and Omicron variants of concern
    Evgeny B. Faizuloev, Anastasiia V. Gracheva, Ekaterina R. Korchevaya, Yulia I. Ammour, Daria I. Smirnova, Darya M. Khokhlova, Andrey O. Drokov, Andrey A. Pankratov, Galina V. Trunova, Varvara A. Khokhlova, Maria S. Vorontsova, Irina A. Leneva, Oksana A. S
    Journal of microbiology, epidemiology and immunobiology.2024; 101(1): 36.     CrossRef
  • Real-time infectious disease endurance indicator system for scientific decisions using machine learning and rapid data processing
    Shivendra Dubey, Dinesh Kumar Verma, Mahesh Kumar
    PeerJ Computer Science.2024; 10: e2062.     CrossRef
  • A systematic review and meta-analysis of the seroconversion rates and adverse effects of COVID-19 mRNA vaccine and COVID-19 viral vector vaccine in kidney transplant recipient patients
    Sikai Chen, Wenxin Wei, Fengyu Huang, Jing Wang, Xingyu Li, Zhixin Geng, Feng Gao, Taiwei Dong, Peifeng Wei, Xinbo Yang, Feng Miao
    Human Vaccines & Immunotherapeutics.2023;[Epub]     CrossRef
  • Extracellular Vesicle-Based SARS-CoV-2 Vaccine
    Yasunari Matsuzaka, Ryu Yashiro
    Vaccines.2023; 11(3): 539.     CrossRef
  • Immunity after COVID-19 Recovery and Vaccination: Similarities and Differences
    Dorota Kamińska, Dominika Dęborska-Materkowska, Katarzyna Kościelska-Kasprzak, Oktawia Mazanowska, Agata Remiorz, Paweł Poznański, Magdalena Durlik, Magdalena Krajewska
    Vaccines.2022; 10(7): 1068.     CrossRef
  • Two years of COVID-19 pandemic: where are we now?
    Jinjong Myoung
    Journal of Microbiology.2022; 60(3): 235.     CrossRef
Journal Article
Effects of digested Cheonggukjang on human microbiota assessed by in vitro fecal fermentation
Vineet Singh , Nakwon Hwang , Gwangpyo Ko , Unno Tatsuya
J. Microbiol. 2021;59(2):217-227.   Published online February 1, 2021
DOI: https://doi.org/10.1007/s12275-021-0525-x
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  • 13 Web of Science
  • 13 Crossref
AbstractAbstract
In vitro fecal fermentation is an assay that uses fecal microbes to ferment foods, the results of which can be used to evaluate the potential of prebiotic candidates. To date, there have been various protocols used for in vitro fecal fermentation- based assessments of food substances. In this study, we investigated how personal gut microbiota differences and external factors affect the results of in vitro fecal fermentation assays. We used Cheonggukjang (CGJ), a Korean traditional fermented soybean soup that is acknowledged as healthy functional diet. CGJ was digested in vitro using acids and enzymes, and then fermented with human feces anaerobically. After fecal fermentation, the microbiota was analyzed using MiSeq, and the amount of short chain fatty acids (SCFAs) were measured using GC-MS. Our results suggest that CGJ was effectively metabolized by fecal bacteria to produce SCFAs, and this process resulted in an increase in the abundance of Coprococcus, Ruminococcus, and Bifidobacterium and a reduction in the growth of Sutterella, an opportunistic pathogen. The metabolic activities predicted from the microbiota shifts indicated enhanced metabolism linked to methionine biosynthesis and depleted chondroitin sulfate degradation. Moreover, the amount of SCFAs and microbiota shifts varied depending on personal microbiota differences. Our findings also suggest that in vitro fecal fermentation of CGJ for longer durations may partially affect certain fecal microbes. Overall, the study discusses the usability of in vitro gastrointestinal digestion and fecal fermentation (GIDFF) to imitate the effects of diet-induced microbiome modulation and its impact on the host.

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  • Significance of Soy-Based Fermented Food and Their Bioactive Compounds Against Obesity, Diabetes, and Cardiovascular Diseases
    Sushmita Dwivedi, Vineet Singh, Kritika Sharma, Amani Sliti, Mamta Baunthiyal, Jae-Ho Shin
    Plant Foods for Human Nutrition.2024; 79(1): 1.     CrossRef
  • Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health
    Ramya Balasubramanian, Elizabeth Schneider, Eoin Gunnigle, Paul D. Cotter, John F. Cryan
    Neuroscience & Biobehavioral Reviews.2024; 158: 105562.     CrossRef
  • The nutrition and therapeutic potential of millets: an updated narrative review
    Jinu Jacob, Veda Krishnan, Chris Antony, Masimukka Bhavyasri, C. Aruna, Kiran Mishra, Thirunavukkarasu Nepolean, Chellapilla Tara Satyavathi, Kurella B. R. S. Visarada
    Frontiers in Nutrition.2024;[Epub]     CrossRef
  • Effects of OsomeFood Clean Label plant-based meals on the gut microbiome
    Dwiyanto Jacky, Chia Bibi, Look Melvin Chee Meng, Fong Jason, Tan Gwendoline, Lim Jeremy, Chong Chun Wie
    BMC Microbiology.2023;[Epub]     CrossRef
  • Fermented soybean foods and diabetes
    Yoshitaka Hashimoto, Masahide Hamaguchi, Michiaki Fukui
    Journal of Diabetes Investigation.2023; 14(12): 1329.     CrossRef
  • Early response of the gut microbiome and serum metabolites to Cheonggukjang intake in healthy Korean subjects
    Eun-Ji Song, Min Jung Kim, Chang Hwa Jung, Won-Hyong Chung, Young-Do Nam, Mi Young Lim
    Journal of Functional Foods.2023; 101: 105420.     CrossRef
  • Role, relevance, and possibilities of in vitro fermentation models in human dietary, and gut‐microbial studies
    Vineet Singh, HyunWoo Son, GyuDae Lee, Sunwoo Lee, Tatsuya Unno, Jae‐Ho Shin
    Biotechnology and Bioengineering.2022; 119(11): 3044.     CrossRef
  • Evaluation of Prebiotics through an In Vitro Gastrointestinal Digestion and Fecal Fermentation Experiment: Further Idea on the Implementation of Machine Learning Technique
    Hokyung Song, Dabin Jeon, Tatsuya Unno
    Foods.2022; 11(16): 2490.     CrossRef
  • Anti-diabetic prospects of dietary bio-actives of millets and the significance of the gut microbiota: A case of finger millet
    Vineet Singh, GyuDae Lee, HyunWoo Son, Sliti Amani, Mamta Baunthiyal, Jae-Ho Shin
    Frontiers in Nutrition.2022;[Epub]     CrossRef
  • Current Perspectives on the Physiological Activities of Fermented Soybean-Derived Cheonggukjang
    Il-Sup Kim, Cher-Won Hwang, Woong-Suk Yang, Cheorl-Ho Kim
    International Journal of Molecular Sciences.2021; 22(11): 5746.     CrossRef
  • Alleviation of Neuronal Cell Death and Memory Deficit with Chungkookjang Made with Bacillus amyloliquefaciens and Bacillus subtilis Potentially through Promoting Gut–Brain Axis in Artery-Occluded Gerbils
    Ting Zhang, Myeong-Seon Ryu, Xuangao Wu, Hee-Jong Yang, Su Ji Jeong, Ji-Won Seo, Do-Yeon Jeong, Sunmin Park
    Foods.2021; 10(11): 2697.     CrossRef
  • The final fate of food: On the establishment of in vitro colon models
    Saartje Hernalsteens, Song Huang, Hai Hua Cong, Xiao Dong Chen
    Food Research International.2021; 150: 110743.     CrossRef
  • In Vitro Simulation of Human Colonic Fermentation: A Practical Approach towards Models’ Design and Analytical Tools
    Elena Veintimilla-Gozalbo, Andrea Asensio-Grau, Joaquim Calvo-Lerma, Ana Heredia, Ana Andrés
    Applied Sciences.2021; 11(17): 8135.     CrossRef
Review
Functional interplay between the oxidative stress response and DNA damage checkpoint signaling for genome maintenance in aerobic organisms
Ji Eun Choi , Woo-Hyun Chung
J. Microbiol. 2020;58(2):81-91.   Published online December 23, 2019
DOI: https://doi.org/10.1007/s12275-020-9520-x
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AbstractAbstract
The DNA damage checkpoint signaling pathway is a highly conserved surveillance mechanism that ensures genome integrity by sequential activation of protein kinase cascades. In mammals, the main pathway is orchestrated by two central sensor kinases, ATM and ATR, that are activated in response to DNA damage and DNA replication stress. Patients lacking functional ATM or ATR suffer from ataxia-telangiectasia (A-T) or Seckel syndrome, respectively, with pleiotropic degenerative phenotypes. In addition to DNA strand breaks, ATM and ATR also respond to oxidative DNA damage and reactive oxygen species (ROS), suggesting an unconventional function as regulators of intracellular redox status. Here, we summarize the multiple roles of ATM and ATR, and of their orthologs in Saccharomyces cerevisiae, Tel1 and Mec1, in DNA damage checkpoint signaling and the oxidative stress response, and discuss emerging ideas regarding the possible mechanisms underlying the elaborate crosstalk between those pathways. This review may provide new insights into the integrated cellular strategies responsible for maintaining genome stability in eukaryotes with a focus on the yeast model organism.

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  • DSB-induced oxidative stress: Uncovering crosstalk between DNA damage response and cellular metabolism
    Xinyu Li, Caini Yang, Hengyu Wu, Hongran Chen, Xing Gao, Sa Zhou, Tong-Cun Zhang, Wenjian Ma
    DNA Repair.2024; 141: 103730.     CrossRef
  • Effects of Stress on Biological Characteristics and Metabolism of Periodontal Ligament Stem Cells of Deciduous Teeth
    Zhengyang Li, Jinyi Li, Shanshan Dai, Xuelong Su, Meiyue Ren, Shuyang He, Qingyu Guo, Fei Liu
    International Dental Journal.2024;[Epub]     CrossRef
  • Signification and Application of Mutator and Antimutator Phenotype-Induced Genetic Variations in Evolutionary Adaptation and Cancer Therapeutics
    Woo-Hyun Chung
    Journal of Microbiology.2023; 61(12): 1013.     CrossRef
  • Metabolic Stress and Mitochondrial Dysfunction in Ataxia-Telangiectasia
    Goutham Narayanan Subramanian, Abrey Jie Yeo, Magtouf Hnaidi Gatei, David John Coman, Martin Francis Lavin
    Antioxidants.2022; 11(4): 653.     CrossRef
  • The Rad9–Rad1–Hus1 DNA Repair Clamp is Found in Microsporidia
    Anne Caroline Mascarenhas dos Santos, Alexander Thomas Julian, Jean-François Pombert, Emmanuelle Lerat
    Genome Biology and Evolution.2022;[Epub]     CrossRef
  • Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM)
    Elias A. Tannous, Peter M. Burgers
    Critical Reviews in Biochemistry and Molecular Biology.2021; 56(5): 441.     CrossRef
  • DNA damage checkpoint and repair: From the budding yeast Saccharomyces cerevisiae to the pathogenic fungus Candida albicans
    Shuangyan Yao, Yuting Feng, Yan Zhang, Jinrong Feng
    Computational and Structural Biotechnology Journal.2021; 19: 6343.     CrossRef
  • Acute Toxicity and DNA Instability Induced by Exposure to Low Doses of Triclosan and Phthalate DEHP, and Their Combinations, in vitro
    Nathalia de Assis Aguilar Duarte, Lindiane Eloisa de Lima, Flora Troina Maraslis, Michael Kundi, Emilene Arusievicz Nunes, Gustavo Rafael Mazzaron Barcelos
    Frontiers in Genetics.2021;[Epub]     CrossRef
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    Mingzhe Li, Baoan Ning, Tianhui Wang
    Journal of Physiology and Biochemistry.2021; 77(2): 215.     CrossRef
Journal Article
Hydrogen sulfide inhibits the growth of Escherichia coli through oxidative damage
Liu-Hui Fu , Zeng-Zheng Wei , Kang-Di Hu , Lan-Ying Hu , Yan-Hong Li , Xiao-Yan Chen , Zhuo Han , Gai-Fang Yao , Hua Zhang
J. Microbiol. 2018;56(4):238-245.   Published online February 28, 2018
DOI: https://doi.org/10.1007/s12275-018-7537-1
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AbstractAbstract
Many studies have shown that hydrogen sulfide (H2S) is both detrimental and beneficial to animals and plants, whereas its effect on bacteria is not fully understood. Here, we report that H2S, released by sodium hydrosulfide (NaHS), significantly inhibits the growth of Escherichia coli in a dose-dependent manner. Further studies have shown that H2S treatment stimulates the production of reactive oxygen species (ROS) and decreases glutathione (GSH) levels in E. coli, resulting in lipid peroxidation and DNA damage. H2S also inhibits the antioxidative enzyme activities of superoxide dismutase (SOD), catalase (CAT) and glutathione reductase (GR) and induces the response of the SoxRS and OxyR regulons in E. coli. Moreover, pretreatment with the antioxidant ascorbic acid (AsA) could effectively prevent H2S-induced toxicity in E. coli. Taken together, our results indicate that H2S exhibits an antibacterial effect on E. coli through oxidative damage and suggest a possible application for H2S in water and food processing.

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    Akihiro Kaidow, Noriko Ishii, Shingo Suzuki, Takashi Shiina, Hirokazu Kasahara
    International Journal of Molecular Sciences.2022; 23(21): 12786.     CrossRef
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    Noah Hitchcock, David J. Kelly, Andrew Hitchcock, Aidan J. Taylor
    Biomolecules.2022; 13(1): 86.     CrossRef
  • Transcriptomic analysis of chloride tolerance in Leptospirillum ferriphilum DSM 14647 adapted to NaCl
    Javier Rivera-Araya, Thomas Heine, Renato Chávez, Michael Schlömann, Gloria Levicán, Benjamin J. Koestler
    PLOS ONE.2022; 17(4): e0267316.     CrossRef
  • Acute stress of the typical disinfectant glutaraldehyde-didecyldimethylammonium bromide (GD) on sludge microecology in livestock wastewater treatment plants: Effect and its mechanisms
    Yuxin Li, Jiayin Ling, Jinghao Xue, Junwei Huang, Xiao Zhou, Fei Wang, Waner Hou, Jianbin Zhao, Yanbin Xu
    Water Research.2022; 227: 119342.     CrossRef
  • Sulfide Treatment Alters Antioxidant Response and Related Genes Expressions in Rice Field Eel (Monopterus albus)
    Liqiao Zhong, Fan Yao, He Zhang, Huaxiao Xie, Huijun Ru, Nian Wei, Zhaohui Ni, Zhong Li, Yunfeng Li
    Water.2022; 14(20): 3230.     CrossRef
  • Development of Polycaprolactone–Zeolite Nanoporous Composite Films for Topical Therapeutic Release of Different Gasotransmitters
    Rosana V. Pinto, Sílvia Carvalho, Fernando Antunes, João Pires, Moisés L. Pinto
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  • Near-infrared laser-controlled nitric oxide-releasing gold nanostar/hollow polydopamine Janus nanoparticles for synergistic elimination of methicillin-resistant Staphylococcus aureus and wound healing
    Zhuoying Liang, Wenkang Liu, Ziqiang Wang, Peilian Zheng, Wei Liu, Jianfu Zhao, Yunlong Zhong, Yan Zhang, Jing Lin, Wei Xue, Siming Yu
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  • Cysteine supplementation enhanced inhibitor tolerance of Zymomonas mobilis for economic lignocellulosic bioethanol production
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Review
Minireview] Microbial radiation-resistance mechanisms
Kwang-Woo Jung , Sangyong Lim , Yong-Sun Bahn
J. Microbiol. 2017;55(7):499-507.   Published online June 30, 2017
DOI: https://doi.org/10.1007/s12275-017-7242-5
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AbstractAbstract
Organisms living in extreme environments have evolved a wide range of survival strategies by changing biochemical and physiological features depending on their biological niches. Interestingly, organisms exhibiting high radiation resistance have been discovered in the three domains of life (Bacteria, Archaea, and Eukarya), even though a naturally radiationintensive environment has not been found. To counteract the deleterious effects caused by radiation exposure, radiation- resistant organisms employ a series of defensive systems, such as changes in intracellular cation concentration, excellent DNA repair systems, and efficient enzymatic and non-enzymatic antioxidant systems. Here, we overview past and recent findings about radiation-resistance mechanisms in the three domains of life for potential usage of such radiationresistant microbes in the biotechnology industry.

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Research Support, Non-U.S. Gov't
Role of RNA Polymerase II Carboxy Terminal Domain Phosphorylation in DNA Damage Response
Su-Jin Jeong , Hye-Jin Kim , Yong-Jin Yang , Ja-Hwan Seol , Bo-Young Jung , Jeong-Whan Han , Hyang-Woo Lee , Eun-Jung Cho
J. Microbiol. 2005;43(6):516-522.
DOI: https://doi.org/2296 [pii]
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AbstractAbstract
The phosphorylation of C-terminal domain (CTD) of Rpb1p, the largest subunit of RNA polymerase II plays an important role in transcription and the coupling of various cellular events to transcription. In this study, its role in DNA damage response is closely examined in Saccharomyces cerevisiae, focusing specifically on several transcription factors that mediate or respond to the phosphorylation of the CTD. CTDK-1, the pol II CTD kinase, FCP1, the CTD phosphatase, ESS1, the CTD phosphorylation dependent cis-trans isomerase, and RSP5, the phosphorylation dependent pol II ubiquitinating enzyme, were chosen for the study. We determined that the CTD phosphorylation of CTD, which occurred predominantly at serine 2 within a heptapeptide repeat, was enhanced in response to a variety of sources of DNA damage. This modification was shown to be mediated by CTDK-1. Although mutations in ESS1 or FCP1 caused cells to become quite sensitive to DNA damage, the characteristic pattern of CTD phosphorylation remained unaltered, thereby implying that ESS1 and FCP1 play roles downstream of CTD phosphorylation in response to DNA damage. Our data suggest that the location or extent of CTD phosphorylation might be altered in response to DNA damage, and that the modified CTD, ESS1, and FCP1 all contribute to cellular survival in such conditions.

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