Article
Engineering, Environmental
Yuta Hatano, Manna Wang, Zhongyu Guo, Chihiro Yoshimura
Summary: Ultraviolet (UV) disinfection is effective in bacterial disinfection without yielding by-products. However, there is a lack of knowledge about the relation of water quality to bacterial regrowth after UV disinfection. This study aimed to investigate the effect of dissolved organic matter (DOM) property on the regrowth process of Escherichia coli (E. coli) under dark and light conditions. The results showed that DOM weakened visible light disinfection after UV disinfection while promoting bacterial dark repair and photoreactivation. The study emphasized the importance of considering DOM property in UV disinfection.
JOURNAL OF WATER PROCESS ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Marie-Pierre Duviau, Fan Chen, Anthony Emile, Muriel Cocaign-Bousquet, Laurence Girbal, Sebastien Nouaille
Summary: mRNA plays a crucial role in the interplay of transcription, translation and mRNA degradation. This study investigates the impact of translation on mRNA stability and concentration by manipulating translation initiation and elongation. The results show that a decrease in translation initiation efficiency leads to mRNA destabilization and uniform reduction in mRNA concentration throughout the molecule. Premature termination of translation elongation results in localized decrease in mRNA concentration downstream of the stop codon, due to the decoupling of transcription and translation. These findings highlight the interconnectedness of translation, mRNA degradation and transcription in maintaining gene expression quality control.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Macarena Toll-Riera, Miriam Olombrada, Francesc Castro-Giner, Andreas Wagner
Summary: Climate change can cause extreme heat waves exceeding the upper thermal limit of organisms. A study on Antarctic bacteria found that they can rapidly adapt to higher temperatures through genomic changes that mitigate protein misfolding. However, there is a physiological limit beyond which populations cannot survive.
Article
Multidisciplinary Sciences
Joivier Vichi, Emmanuel Salazar, Veronica Jimenez Jacinto, Leticia Olvera Rodriguez, Ricardo Grande, Edgar Dantan-Gonzalez, Enrique Morett, Armando Hernandez-Mendoza
Summary: The study investigated the transcriptome expression of Escherichia coli and Schizosaccharomyces pombe under different carbon sources, showing that genes associated with cell proliferation were predominant in aerobic glycolysis, while genes related to flagellar assembly and membrane proteins were differentially expressed in glycerol/acetate condition.
Article
Green & Sustainable Science & Technology
Paola Duque-Sarango, Leonardo Romero-Martinez, Veronica Pinos-Velez, Esteban Sanchez-Cordero, Esteban Samaniego
Summary: In countries with water scarcity, wastewater from treatment plants is being recycled. To ensure quality, tertiary disinfection treatments are required. This study evaluates the efficacy of an ultraviolet (UV) system in inactivating fecal bacteria in urban wastewater effluents and the post-treatment influence of environmental illumination. The results show that a UV dose of approximately 12 mJ cm(-2) is needed to achieve a 3 log-reduction of Escherichia coli, but there is a risk of reactivation if the treated organisms are stored in an illuminated environment.
Article
Agricultural Engineering
Ning An, Chong Xie, Shubin Zhou, Jia Wang, Xinxiao Sun, Yajun Yan, Xiaolin Shen, Qipeng Yuan
Summary: In this study, a novel growth-coupled strategy for the efficient production of (i-arbutin using engineered Escherichia coli and glycerol was developed. By coupling E4P formation with cell growth, high levels of (i-arbutin were achieved, with the highest production ever reported through microbial fermentation. This study has significant implications for large-scale production of (i-arbutin and other important aromatic compounds.
BIORESOURCE TECHNOLOGY
(2023)
Article
Biochemical Research Methods
Axel von Kamp, Steffen Klamt
Summary: In this study, a method is presented to modify the stoichiometry of the biomass reaction in order to make the flux balance analysis problem feasible and improve the accuracy of the model. Realistic flux measurements of E.coli are used to demonstrate the value of this approach, highlighting the overestimation of growth-associated maintenance (GAM) demand of ATP in recent genome-scale models.
Editorial Material
Biochemistry & Molecular Biology
Anthony Burnetti, William C. Ratcliff
Summary: In a new paper published in PLOS Biology, Dudin and colleagues have successfully evolved simple multicellularity in Sphaeroforma arctica, a unicellular relative of animals. This research establishes a new pathway for studying the evolution of multicellularity in this important but understudied group of organisms.
Article
Microbiology
Jacob Hogins, Ethan Fan, Zheyar Seyan, Sam Kusin, Alana L. Christie, Philippe E. Zimmern, Larry Reitzer
Summary: Urinary tract infections (UTIs) are common in women, especially postmenopausal women, and can be difficult to treat. Escherichia coli is the main cause, but its virulence mechanisms and host-pathogen interactions are complex and varied. Bacterial growth in urine shows significant individual variations.
MICROBIOLOGY SPECTRUM
(2022)
Article
Biochemical Research Methods
Mauricio Alexander de Moura Ferreira, Wendel Batista da Silveira, Zoran Nikoloski
Summary: This study explores the allocation of proteins in cellular pathways and proposes a method, called PARROT, to predict enzyme allocation based on the minimization of differences between growth conditions. The results suggest that minimizing protein allocation adjustments is a key principle in microorganisms under alternative growth conditions.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Maxwell Neal, Deepan Thiruppathy, Karsten Zengler
Summary: This study developed a genome-scale metabolic model of B. fragilis strain 638R, providing a basis for understanding its relationship with human diet and metabolic products.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Bhishem Thakur, Kanika Arora, Archit Gupta, Purnananda Guptasarma
Summary: Researchers investigated whether the nucleoid-associated histone-like protein (HU) could act as a glue in biofilms, finding evidence through various experiments to support this hypothesis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Physics, Multidisciplinary
Luyi Qiu, John W. Hutchinson, Ariel Amir
Summary: This study investigates the instability of pressurized tubes and finds that internal pressure significantly affects the onset of the instability, while the bending stiffness of the cell wall has almost no influence. This research suggests a new method to infer turgor pressure in rod-shaped bacteria through bending experiments.
PHYSICAL REVIEW LETTERS
(2022)
Article
Biochemical Research Methods
Deyu Yang, Ziming Yu, Mengxin Zheng, Wei Yang, Zhangcai Liu, Jianhua Zhou, Lu Huang
Summary: Microfluidic platforms are used for drug screening due to their advantages of lower reagent consumption, higher throughput, and automation. However, screening complex antibiotic combinations in a high-throughput and systematic manner is still challenging. To address this issue, an artificial intelligence-accelerated high-throughput combinatorial drug evaluation system (AI-HTCDES) is proposed. This system allows high-throughput production of antibiotic combinations and automated analysis of bacterial growth. It provides useful guidance for clinical use of antibiotic combination therapy and offers a promising tool for combinatorial screenings of other medicines.
Article
Biochemical Research Methods
Zahra Razaghi-Moghadam, Zoran Nikoloski
Summary: Existing computational approaches often neglect the impact of gene expression regulation on metabolic engineering strategies. This study finds that the association of genes with multiple reactions may render engineering strategies infeasible at the flux level, and proposes a constraint-based approach called GeneReg to facilitate the design of feasible strategies at the gene level.
Article
Oncology
Bohan Dong, Guangli Dai, Lei Xu, Damin Shi
MOLECULAR MEDICINE REPORTS
(2017)
Article
Biochemistry & Molecular Biology
Lei Xu, Bin Wen, Wengui Shao, Pengcheng Yao, Wei Zheng, Zhiqiang Zhou, Yao Zhang, Guoping Zhu
Article
Biochemistry & Molecular Biology
Lei Xu, Lu Sun, Guoyu Guan, Qianwu Huang, Jun Lv, Liang Yan, Liefeng Ling, Yao Zhang
NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS
(2019)
Article
Pathology
Liang Yan, Yizonheng Zhang, Kai Li, Mengze Wang, Jiaping Li, Zhilin Qi, Juan Wu, Zhen Wang, Liefeng Ling, Haijun Liu, Yaohua Wu, Xinyu Lu, Lei Xu, Yiping Zhu, Yao Zhang
PATHOLOGY RESEARCH AND PRACTICE
(2020)
Article
Pharmacology & Pharmacy
Qianwu Huang, Jun Lv, Ting Dong, Haijun Liu, Lei Xu, Mingcai Wu
Article
Chemistry, Organic
Liang Yan, Xu Wu, Yizongheng Zhang, Mathan Sankaran, Lei Xu, Liefeng Ling, Yi Wang, Yuxin Jiang, Jinzhu Ma, Lingyu Kong
JOURNAL OF HETEROCYCLIC CHEMISTRY
(2020)
Article
Cell Biology
Qi Dong, Chenkang Zhou, Haodong Ren, Zhijian Zhang, Feng Cheng, Zhenkai Xiong, Chuantao Chen, Jianke Yang, Jiguang Gao, Yao Zhang, Lei Xu, Jian Fang, Yuxiang Cao, Huijun Wei, Zhihao Wu
CELL COMMUNICATION AND SIGNALING
(2020)
Article
Cell Biology
Xiaopeng Shen, Feng Xu, Meng Li, Shen Wu, Jingyi Zhang, Ao Wang, Lei Xu, Yu Liu, Guoping Zhu
CELL DEATH & DISEASE
(2020)
Article
Biochemistry & Molecular Biology
Lei Xu, Simeng Chen, Bin Wen, Hao Shi, Changbiao Chi, Chenxi Liu, Kangyu Wang, Xianglin Tao, Ming Wang, Jun Lv, Liang Yan, Liefeng Ling, Guoping Zhu
Summary: UV irradiation leads to the formation of CPDs and 6-4 photoproducts in DNA, which can be repaired by CPD photolyases and 6-4 photolyases. A novel class of short photolyase-like proteins, identified through phylogenetic analyses, have high similarity to CPD photolyases and may be the ancestors of the cryptochrome/photolyase family.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Changqing Tian, Bin Wen, Mingjie Bian, Mingming Jin, Peng Wang, Lei Xu, Guoping Zhu
Summary: The study successfully constructed a chimeric monomeric isocitrate dehydrogenase, demonstrating the potential of dimeric IDHs to evolve into monomeric ones. The evolution of the IDH family was also discussed in the research.
Article
Biochemistry & Molecular Biology
Simeng Chen, Chenxi Liu, Chenchen Zhou, Zhihui Wei, Yuting Li, Lei Xiong, Liang Yan, Jun Lv, Liang Shen, Lei Xu
Summary: A new photolyase, SePhrB, has been characterized in Synechococcus elongatus, demonstrating its ability to repair 6-4 photoproducts in DNA. SePhrB contains an antenna chromophore called 8-HDF and can be photoreduced without external electron donors. These findings suggest a greater diversity of FeS-BCPs than previously thought and warrant further investigation.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Bin Wen, Lei Xu, Yawei Tang, Zhen Jiang, Mengting Ge, Li Liu, Guoping Zhu
Summary: In this study, the researchers discovered that a specific residue at site 377 in photolyase proteins can fine-tune the stability of the HQ cofactor, thereby affecting the photorepair activity of these enzymes. This finding might shed light on the evolutionary transition from photolyases to cryptochromes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Lei Xu, Bin Wen, Yuan Wang, Changqing Tian, Mingcai Wu, Guoping Zhu
Article
Medicine, Research & Experimental
Jun Lv, Can Qun Lv, Bo-Liang Wang, Ping Mei, Lei Xu
MEDICAL SCIENCE MONITOR BASIC RESEARCH
(2016)
Article
Biochemistry & Molecular Biology
Girgis Obaid, Menitte Eroy, Jie Zhao, Shazia Bano, Mari Mino-Kenudson, Tayyaba Hasan
Summary: The presence of desmoplasia in pancreatic ductal adenocarcinoma (PDAC) is associated with poor treatment outcomes and reduced drug delivery. By analyzing collagen subtypes in PDAC tumors following different treatment regimens, immunofluorescence profiling can predict long-term survival and tumor growth inhibition. This information can aid in personalized treatment and improve patient survival.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
(2024)
Article
Biochemistry & Molecular Biology
Fatemeh Malekpour, Rashin Bahrami, Mahshid Hodjat, Neda Hakimiha, Behnam Bolhari, Aidin Sooratgar, Soheil Niavarzi
Summary: This study investigated the effect of photobiomodulation (PBM) therapy using an 808 nm diode laser on cellular modulation mechanisms in regenerative endodontic procedures (REPs). The results showed that PBM treatment significantly increased cell viability and migration, and enhanced the release of TGF-131 from dentin.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
(2024)
Article
Biochemistry & Molecular Biology
Pranathi Tata, Ramakrishnan Ganesan, Jayati Ray Dutta
Summary: Thin film coatings with potent antibacterial properties are widely used in medical devices, frequently touched surfaces, and food packaging. However, achieving antibacterial performance under both light and dark conditions remains a challenge. In this study, we successfully prepared AgBr-coated ZnO nanorod thin film architecture using a unique surfactant-mediated solution-phase spin-coating approach. The resulting structures showed dual functionality as antimicrobial agents and photosensitizers, effectively enhancing the visible-light photodisinfection efficacy of ZnO nanorods. The concentration of the surfactant-based precursor solution could be modulated to control the AgBr content. Additionally, components like urea and lactic acid were found to enhance the photocatalytic efficiency of the structures.
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY
(2024)