Article
Microbiology
Rebecca S. Clarke, Kam Pou Ha, Andrew M. Edwards
Summary: Antibiotics inhibit bacterial growth and lead to cell death, while certain antibiotics can also induce the production of reactive oxygen species that damage bacterial DNA and promote drug resistance. Different classes of antibiotics were found to dose-dependently induce the SOS response in Staphylococcus aureus, indicating DNA damage, with the RexAB helicase/nuclease complex playing a key role in this process. This study confirms that several classes of antibiotics cause DNA damage in S. aureus and highlights the importance of RexAB in triggering the mutagenic SOS response and promoting bacterial survival.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2021)
Article
Biochemistry & Molecular Biology
Mu-Rong Chao, Mark D. Evans, Chiung-Wen Hu, Yunhee Ji, Peter Moller, Pavel Rossner, Marcus S. Cooke
Summary: Research on oxidative damage to DNA has implications for understanding the pathogenesis of various diseases, with increasing interest in the effects of damage to RNA and nucleotide pools. LCMS/MS and comet assays are important methods for assessing oxidative stress, but have limitations in sample requirements and application scope. Urine is an ideal matrix for studying nucleic acid-derived biomarkers of oxidative stress, with progress being made in validating measurements, particularly through DNA adductomics approaches that offer insights into the role of oxidatively damaged nucleic acids in disease.
Article
Biochemistry & Molecular Biology
Feifei Zhao, Sara Whiting, Sarah Lambourne, R. John Aitken, Ying-pu Sun
Summary: The study demonstrates that melatonin can protect human sperm from heat-induced oxidative stress by suppressing sperm mitochondrial ROS generation, increasing mitochondrial membrane potential, reducing lipid peroxidation product 4-HNE formation, and decreasing sperm DNA damage and apoptosis. This suggests melatonin as a potential treatment option for male infertility caused by heat-induced oxidative stress.
FREE RADICAL BIOLOGY AND MEDICINE
(2021)
Article
Medicine, Research & Experimental
Yujie Zhang, Chunyang Ding, Wenkang Zhu, Xinyu Li, Techang Chen, Qingxi Liu, Sa Zhou, Tong-Cun Zhang, Wenjian Ma
Summary: This study reveals that bulky DNA damage inducing chemotherapeutic cancer drugs can stimulate persistent endogenous reactive oxygen species (ROS) production, which correlates with DNA double-strand breaks (DSBs) formation. The knockdown of key player BRCA1 in homologous recombination (HR) pathway enhances ROS accumulation, while inhibiting nonhomologous end-joining (NHEJ) repair pathway and restoring HR can partially suppress ROS levels. Knockdown of DNA repair regulator PP2A can also reduce ROS production.
Article
Oncology
Silvia Codenotti, Francesco Marampon, Luca Triggiani, Marco Lorenzo Bonu, Stefano Maria Magrini, Paola Ceccaroli, Michele Guescini, Stefano Gastaldello, Vincenzo Tombolini, Pietro Luigi Poliani, Michela Asperti, Maura Poli, Eugenio Monti, Alessandro Fanzani
Summary: The study investigated the role of Caveolin-1 (Cav-1) in radiation response in rhabdomyosarcoma (RMS), suggesting that Cav-1 may play a vital role in promoting radioresistance through mechanisms involving cell cycle regulation, apoptosis, oxidative stress and DNA repair pathways. The findings reveal that Cav-1, in conjunction with catalase, Src-kinase, and Akt pathways, may form a network of essential mechanisms that allow irradiated RMS cells to evade cell death induced by radiation.
Article
Environmental Sciences
Sonalin Rath, Surajit Das
Summary: Bacteria thriving in the mangrove ecosystem play a significant role in elemental cycles, but their performance is influenced by climate change and environmental stressors. This study investigates the genotoxic effect of such stressors on mangrove bacteria and their adaptation strategies. The results show cellular injuries and DNA damage in response to stressors, with different bacterial strains exhibiting varying levels of tolerance and adaptive mechanisms.
ENVIRONMENTAL POLLUTION
(2023)
Article
Cell Biology
Anna Brzostek, Przemyslaw Plocinski, Alina Minias, Aneta Ciszewska, Filip Gasior, Jakub Pawelczyk, Bozena Dziadek, Marcin Slomka, Jaroslaw Dziadek
Summary: This study identified elements of RecA-independent responses to DNA damage in pathogenic intracellular mycobacteria through global transcriptional profiling, revealing the differences between different response pathways.
Review
Biochemistry & Molecular Biology
Haiqi Fu, Yongqing Yang
Summary: Soil salinization inhibits plant growth and seriously restricts food security and agricultural development. Excessive salt can cause ionic stress, osmotic stress, and ultimately oxidative stress in plants. Plants exclude excess salt from their cells to help maintain ionic homeostasis and stimulate phytohormone signaling pathways, thereby balancing growth and stress tolerance to enhance their survival. Continuous innovations in scientific research techniques have allowed great strides in understanding how plants actively resist salt stress. Here, we briefly summarize recent achievements in elucidating ionic homeostasis, osmotic stress regulation, oxidative stress regulation, and plant hormonal responses under salt stress. Such achievements lay the foundation for a comprehensive understanding of plant salt-tolerance mechanisms.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Dandan Sun, Shimei Chen, Shenping Li, Ning Wang, Shuchang Zhang, Li Xu, Shaopin Zhu, Huiming Li, Qing Gu, Xun Xu, Fang Wei
Summary: The accumulation of DNA damage induced by oxidative stress is a crucial pathogenic factor of endothelial loss in diabetic vascular complications. It is still unclear whether aberrant glucose metabolism leads to defective DNA repair and accounts for hyperglycemia-induced endothelial oxidative stress injury. Our study showed that Foxo1 knockdown alleviated diabetes-associated retinal DNA damage and vascular dysfunction by promoting DNA repair mediated by the MRN-ATM pathway and restoring glycolysis capacity. Our findings suggest that defective glycolysis-dependent DNA repair could be a novel therapeutic target for diabetic vascular complications.
Article
Biochemistry & Molecular Biology
Merle M. Nicolai, Ann-Kathrin Weishaupt, Jessica Baesler, Vanessa Brinkmann, Anna Wellenberg, Nicola Winkelbeiner, Anna Gremme, Michael Aschner, Gerhard Fritz, Tanja Schwerdtle, Julia Bornhorst
Summary: Although manganese is an essential trace element, overexposure can lead to toxicity and neurological dysfunction. This study investigated the mode of action of manganese toxicity on genomic integrity, focusing on DNA damage and repair mechanisms using Caenorhabditis elegans as a model organism. The results suggest that excessive manganese exposure can decrease genomic integrity and activate base excision repair.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Porntipha Vitheejongjaroen, Anongnard Kasorn, Narathip Puttarat, Fabien Loison, Malai Taweechotipatr
Summary: The results of this study suggest that B. animalis MSMC83 has a beneficial role in alleviating oxidative stress in rats by increasing the expression of antioxidant enzymes and reducing pro-inflammatory cytokines. It also restores microbiota diversity after D-galactose injection.
Article
Cell Biology
Wei Zhao, Zhongjie Liu, Jiaming Luo, Changqing Ma, Luying Lai, Zhengyuan Xia, Shiyuan Xu
Summary: The study indicates that PARP-1 plays a key role in repairing oxidative DNA damage induced by bupivacaine, with interactions with XPD protein contributing to DNA integrity maintenance.
Article
Biochemistry & Molecular Biology
Philipp Palombo, Alexander Buerkle, Maria Moreno-Villanueva
Summary: In vitro mechanistic research often overlooks the potential influence of cell culture media and supplements, leading to the potential oversight of interactions between compounds and medium ingredients. Isoproterenol, a synthetic catecholamine commonly used in biomedical research, has different stability in different cell culture media. The differences in effective levels of isoproterenol and the formation of oxidation products may explain the discrepancies observed in its genotoxicity and cytotoxicity.
CHEMICO-BIOLOGICAL INTERACTIONS
(2022)
Review
Cell Biology
Yueying Yang, Man Zhu, Jing Liang, Hui Wang, Dejuan Sun, Hua Li, Lixia Chen
Summary: As a member of the sirtuins family, SIRT6 plays a crucial role in regulating various biological processes and maintaining organism homeostasis. This review focuses on the structural basis of SIRT6 enzyme activity, its mechanism of maintaining organism homeostasis in different phenotypes, and the regulation of SIRT6 expression and downstream substrates. Protein interaction is explored as a perspective to understand the regulatory mechanism of SIRT6 in different phenotypes.
JOURNAL OF CELLULAR PHYSIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Elle E. M. Scheijen, Sven Hendrix, David M. Wilson
Summary: Oxidative stress plays a crucial role in spinal cord injury (SCI), causing damage to proteins, nucleic acids, lipids, cytoskeleton, and organelles. Oxidative DNA damage is likely a major contributor to the pathogenesis of SCI, although the evidence supporting this hypothesis is limited. Improved analysis methods are needed to uncover the role of DNA damage and repair in SCI.
Article
Microbiology
Kristian Jensen, Kosai Al-Nakeeb, Anna Koza, Ahmad A. Zeidan
Summary: The genome of Bifidobacterium animalis subsp. lactis BB-12 was sequenced using Oxford Nanopore Technologies and Illumina sequencing platforms. A hybrid genome assembly approach was used to construct an updated complete genome sequence for BB-12 with 1,944,152 bp, a G+C content of 60.5%, and 1,615 genes.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Biotechnology & Applied Microbiology
Marie Schopping, Tammi Vesth, Kristian Jensen, Carl Johan Franzen, Ahmad A. Zeidan
Summary: This study compiled a list of stress response genes in bifidobacteria and evaluated their prevalence among different strains. The study found that the regulation of stress response differs among phylogenetic groups, and genes associated with oxidative stress have low sequence similarity across species. In addition, the oxygen tolerance and regulation of stress-associated gene transcription vary among different species and strains of bifidobacteria.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Martin H. Rau, Paula Gaspar, Maiken Lund Jensen, Asger Geppel, Ana Rute Neves, Ahmad A. Zeidan
Summary: This study provides insights into the metabolism of Streptococcus thermophilus through the construction of a genome-scale metabolic model and transcriptome analysis. The study revealed an imbalance in amino acid supply and demand that limits bacterial growth and identified the mechanism of secretion product profile. It also strengthens the hypothesis of protocooperative interaction between S. thermophilus and Lactobacillus delbrueckii subsp. bulgaricus.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Andreas Ulmer, Florian Erdemann, Susanne Mueller, Maren Loesch, Sandy Wildt, Maiken Lund Jensen, Paula Gaspar, Ahmad A. Zeidan, Ralf Takors
Summary: A mechanistic understanding of microorganisms in starter cultures is crucial for improving fermented milk products like yogurt. This study developed a synthetic medium for culturing microorganisms under defined conditions and used flow cytometry to measure their biomass. The study analyzed amino acid concentrations in the mono-cultures and co-cultures of L. bulgaricus and different strains of S. thermophilus, revealing that amino acid release rates in co-cultures were not equal to the sum of release rates in mono-cultures. Data-driven and pH-dependent models were developed to compare this release behavior. The study also identified specific amino acids, such as histidine, isoleucine, and arginine, that were affected by co-culture conditions. These findings contribute to the understanding of inter-species interactions and the targeted improvement of yogurt qualities.
Article
Biotechnology & Applied Microbiology
Svenja Battling, Tobias Engel, Elena Herweg, Paul-Joachim Niehoff, Matthias Pesch, Theresa Scholand, Marie Schoepping, Nina Sonntag, Jochen Buechs
Summary: The study optimized the production process of 5-keto-d-fructose, successfully increasing both the titre and productivity through different feeding strategies, and demonstrated the scale-up of the process to a 150 L pressurized fermenter.
MICROBIAL CELL FACTORIES
(2022)
Article
Biotechnology & Applied Microbiology
Marie Schopping, Anisha Goel, Kristian Jensen, Ricardo Almeida Faria, Carl Johan Franzen, Ahmad A. A. Zeidan
Summary: Probiotics are important microorganisms in industry and clinical applications. The viability and stability of probiotic microorganisms are crucial for their health-promoting effects. Some bifidobacteria strains have high robustness and stability, while others are difficult to produce due to their sensitivity to stressors.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2023)
Review
Microbiology
Signe T. Karlsen, Martin H. Rau, Benjamin J. Sanchez, Kristian Jensen, Ahmad A. Zeidan
Summary: When selecting microbial strains for fermented food production, it is important to consider various microbial phenotypes that affect product characteristics. With advances in sequencing technologies, genome sequences can now be obtained faster and cheaper, making genome-based characterization more relevant. By predicting microbial phenotypes from genome sequences, it is possible to quickly screen large strain collections and identify candidates with desirable traits. This review discusses knowledge- and data-driven computational methods for phenotype prediction in the context of the fermented food industry.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Microbiology
Sofia Markakiou, Ana Rute Neves, Ahmad A. Zeidan, Paula Gaspar
Summary: Lactococcus lactis and Streptococcus thermophilus are important lactic acid bacteria used globally in dairy fermentations. They are being explored as hosts for heterologous protein production. The tetracycline-inducible expression system was implemented in both bacteria and optimization of the repression level was found to be necessary for efficient induction.
MICROBIOLOGY SPECTRUM
(2023)