Article
Virology
Maik Wolfram-Schauerte, Nadiia Pozhydaieva, Madita Viering, Timo Glatter, Katharina Hoefer
Summary: This study used transcriptomics and proteomics to investigate the temporal patterns of transcription and protein synthesis during T4 phage infection of E. coli. The research revealed the degradation of E. coli transcripts and the stability of the host proteome during infection. Additionally, the correlation between phage transcriptome and proteome provided insights into post-transcriptional and translational regulation mechanisms.
Article
Immunology
Julia Lopez-Perez, Jennifer Otero, Miquel Sanchez-Osuna, Ivan Erill, Pilar Cortes, Montserrat Llagostera
Summary: This study investigates the emergence of Salmonella strains with reduced susceptibility to a cocktail of three phages in different scenarios. The results show that the mechanisms of resistance vary in different environments, but they do not significantly impair the success of Salmonella biocontrol and oral phage therapy.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Anne Kupczok, Zachary M. Bailey, Dominik Refardt, Carolin C. Wendling
Summary: Lambdoid phages are related temperate phages that can infect gut bacteria. These phages have a mosaic genome structure and evolve by transferring genomic regions. The study identified groups of genes that are frequently co-transferred and observed that they tend to be near each other on the genome. These co-transferred genes are involved in related functions and play an important role in the evolution of the modular structure of these genomes.
MICROBIAL GENOMICS
(2022)
Review
Cell Biology
Rachel L. Cohn, Nathan S. Gasek, George A. Kuchel, Ming Xu
Summary: Senescent cells play a significant role in aging and disease, and targeting them could slow down the aging process. The commonly used marker p16 has led to important discoveries, but new markers and investigating heterogeneity are crucial. Advanced technologies like single-cell RNA-seq can help uncover new markers and the urgent need to investigate senescence heterogeneity.
TRENDS IN CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Nicholas E. Phillips, Alice Hugues, Jake Yeung, Eric Durandau, Damien Nicolas, Felix Naef
Summary: Research on single-cell mRNA dynamics of core clock genes in mouse fibroblasts using single-molecule fluorescence technology revealed significant variability between cells. A probabilistic model was developed to account for transcriptional bursting, circadian time, and cell-to-cell heterogeneity, with clock time contributing only a small fraction to mRNA number variability between cells.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemical Research Methods
Nabil Ibtehaz, Ishtiaque Ahmed, Md Sabbir Ahmed, M. Sohel Rahman, Rajeev K. Azad, Md Shamsuzzoha Bayzid
Summary: Genomic Islands (GIs) are clusters of genes mobilized through horizontal gene transfer, playing a key role in bacterial evolution. SSG-LUGIA is an automated and unsupervised approach for identifying GIs and horizontally transferred genes, achieving superior performance in comparison to existing methods with a better precision-recall trade-off. Its nondependency on the functional annotation of genomes makes it suitable for analyzing newly sequenced genomes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Cuifen Gan, Rongrong Wu, Yeshen Luo, Jianhua Song, Dizhou Luo, Bei Li, Yonggang Yang, Meiying Xu
Summary: In this study, FeRM were visualized using a sensitive and selective fluorescent chemodosimeter, allowing for evaluation of their activity even at the single-cell level. When combined with a single-cell sorter, this method proved effective in isolating FeRM from samples containing multiple species, providing a powerful tool to uncover the in situ or ex situ role of FeRM and their interactions.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Viacheslav N. Kachalov, Huyen Nguyen, Suraj Balakrishna, Luisa Salazar-Vizcaya, Rami Sommerstein, Stefan P. Kuster, Anthony Hauser, Pia Abel zur Wiesch, Eili Klein, Roger D. Kouyos
Summary: This study developed a transmission model that explained the variability in ESBL and CRK prevalence across European countries, with inpatient antibiotic consumption and nosocomial transmission rates identified as the strongest drivers of resistance. The findings underscore the importance of improving infection control and antibiotic stewardship in hospitals to prevent antibiotic resistance in gram-negative bacteria even at a national or regional level.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Cell Biology
Li Yang, Xin Wang, Jia-Xi Zheng, Zi-Ran Xu, Lin-Chen Li, Yu-Long Xiong, Bi-Chen Zhou, Jie Gao, Cheng-Ran Xu
Summary: In this study, the process of hepatocyte development in mice was investigated using single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA sequencing (snRNA-seq). Three maturation stages of post-natal hepatocytes were defined, each with specific metabolic functions and distinct proliferation rates. Hepatic zonation gradually formed during hepatocyte maturation, with hepatocytes or their nuclei exhibiting preferences in distribution and asynchrony in maturation based on ploidy. Furthermore, critical transcription factors related to maturation and zonation were identified through gene regulatory network analysis and in vivo genetic manipulation.
DEVELOPMENTAL CELL
(2023)
Article
Oncology
Yingcheng Wu, Shuaixi Yang, Jiaqiang Ma, Zechuan Chen, Guohe Song, Dongning Rao, Yifei Cheng, Siyuan Huang, Yifei Liu, Shan Jiang, Jinxia Liu, Xiaowu Huang, Xiaoying Wang, Shuangjian Qiu, Jianmin Xu, Ruibin Xi, Fan Bai, Jian Zhou, Jia Fan, Xiaoming Zhang, Qiang Gao
Summary: This study presents a single-cell and spatial atlas of colorectal liver metastasis, revealing highly metabolically activated MRCP+ CCL18(+) M2-like macrophages at the metastatic sites. Effective neoadjuvant chemotherapy can slow down this metabolic activation, raising the possibility of targeting metabolic pathways in metastasis.
Article
Microbiology
Joao Pedro Rueda Furlan, Eliana Guedes Stehling
Summary: This study conducted a genomic analysis of Pluralibacter gergoviae, a member of the Enterobacteriaceae family, and found a highly diverse population. While P. gergoviae strains were found in humans and the environment, only human and environmental strains exhibited multidrug-resistant profiles. Additionally, numerous antimicrobial resistance genes were identified, including those encoding mobile colistin resistance. The findings indicate that P. gergoviae is emerging as a new multidrug-resistant species, necessitating continuous epidemiological genomic surveillance.
Article
Biochemistry & Molecular Biology
Ting-Wei Liao, Lin Huang, Timothy J. Wilson, Laura R. Ganser, David M. J. Lilley, Taekjip Ha
Summary: Riboswitches are regulatory elements in bacterial mRNAs that control gene expression through ligand-induced conformational changes. Single-molecule FRET was used to study the conformational landscape of the SAM/SAH riboswitch and how ligand-induced conformational changes affect translation regulation. We found that riboswitch folding is heterogeneous and addition of ligand shifts the landscape towards the ligand-bound conformation. We also investigated ribosome binding site accessibility and found that co-transcriptional folding reduces ligand affinity through slower equilibration.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Physical
Yayang Xu, Shiqiang Yu, Fengxia Tong, Zeyan Wang, Peng Wang, Yuanyuan Liu, Hefeng Cheng, Yuchen Fan, Wei Wei, Ying Dai, Zhaoke Zheng, Baibiao Huang
Summary: The coupling of W18O49 and Au in W18O49-Au heterostructures enhanced the light absorption and carrier separation ability of this dual-plasmonic system, leading to highly enhanced performance for nitrophenol hydrogenation. The rate constant of W18O49-Au reached 0.2044 min(-1), which was 12 and 102 times higher than that of Au and W18O49, respectively. The hot electron injection process from W18O49 to Au, demonstrated by single-particle photoluminescence (PL) spectroscopy, was found to be beneficial for boosting the catalytic performance.
CATALYSIS SCIENCE & TECHNOLOGY
(2023)
Review
Gastroenterology & Hepatology
Tatiana Borodovich, Andrey N. Shkoporov, R. Paul Ross, Colin Hill
Summary: Horizontal gene transfer (HGT) plays a significant role in human health and disease, particularly in the spread of antibiotic resistance genes and pathogenic factors. The abundance of bacteriophages in the human gut suggests that phage transduction could be an important mode of HGT in the gut microbiome. This review provides an in-depth understanding of phage-mediated HGT mechanisms, detection methods, and potential implications for the human gut microbiome.
GASTROENTEROLOGY REPORT
(2022)
Article
Biochemical Research Methods
Lei Sun, Gongming Wang, Zhihua Zhang
Summary: Single-cell RNA sequencing (scRNA-seq) is a powerful technology for studying gene expression at the single-cell level. However, the evaluation of computational methods used in scRNA-seq analysis is challenging. In this study, we propose a simulation tool called Simulation of Cellular Heterogeneity (SimCH) that can accurately simulate scRNA-seq data and be used to benchmark computational methods. We demonstrate the utility of SimCH in evaluating various computational methods and conducting power evaluation of cell clustering methods.
BRIEFINGS IN BIOINFORMATICS
(2023)
