Article
Multidisciplinary Sciences
Chien- Yang, Zikun Zhu, Jeffrey J. Jones, Brett Lomenick, Tsui-Fen Chou, Shu-Ou Shan
Summary: This study investigated the impact of PDF inhibition on bacterial physiology through the analyses of transcriptome and proteome in Escherichia coli. The results showed that loss of PDF activity rapidly induces cellular stress responses, especially those associated with protein misfolding and membrane defects, and leads to a global down-regulation of metabolic pathways. Furthermore, the study revealed that PDF inhibition causes rapid membrane hyperpolarization and impaired membrane integrity, indicating that formyl group retention on nascent proteins is the most immediate and primary consequence of plasma membrane disruption.
Article
Multidisciplinary Sciences
Chun-Ying Wang, Martin Lempp, Niklas Farke, Stefano Donati, Timo Glatter, Hannes Link
Summary: The study explores how to alleviate the growth burden on E. coli strains caused by synthetic pathways, highlighting the role of misregulated Cra transcription factor in impairing growth during glycerol production. Engineering Cra-binding sites in promoters maintains metabolic balance in the synthetic pathway, demonstrating a successful solution to the growth burden issue.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Kaleb Abram, Zulema Udaondo, Carissa Bleker, Visanu Wanchai, Trudy M. Wassenaar, Michael S. Robeson, David W. Ussery
Summary: In this study, over 100,000 publicly available Escherichia coli and Shigella genome sequences were analyzed using Mash-based analysis to identify 14 unique phylogroups. The results revealed that most of the sequenced E. coli genomes belong to four distinct phylogroups.
COMMUNICATIONS BIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Haotian Deng, Bo Xue, Mingyue Wang, Yuqi Tong, Chang Tan, Meizhi Wan, Yanwen Kong, Xianjun Meng, Jinyan Zhu
Summary: In this study, the antibacterial mechanism of Aronia melanocarpa anthocyanins (AMAs) against Escherichia coli was explored at the protein level using a quantitative proteomics method. The results showed that AMAs can affect various protein pathways in E. coli, leading to morphological changes and cell death. These findings are important for understanding the molecular mechanism of plant-derived antimicrobial agents.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Acoustics
Jiao Li, Donghong Liu, Tian Ding
Summary: The study investigated the gene regulation at the transcription level in Escherichia coli O157:H7 after ultrasonic stimulation, revealing significant differential expressions of 1217 genes, including up-regulated and down-regulated genes related to crucial biomolecular processes. The most enriched pathways were analyzed in carbohydrate metabolism, energy metabolism, membrane transport, signal transduction, transcription, and translation categories. Additionally, the study found that the citrate cycle genes were down-regulated, affecting carbohydrate decomposition and energy production under ultrasonic stress.
ULTRASONICS SONOCHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Swati Dubey, Puja Majumder, Aravind Penmatsa, Abhijit A. Sardesai
Summary: The study elucidated the membrane topology and export mechanism of LysO protein, suggesting that Thl may be exported in antiport with H+ while Lys may be a low-affinity export substrate. This finding provides insight into how LysO mediates Lys/Thl export and affords protection from Thl toxicity in Escherichia coli.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Delia Tomoiaga, Jaclyn Bubnell, Liam Herndon, Paul Feinstein
Summary: Griffith proposed the concept of DNA transfer between bacteria in 1928. Researchers have demonstrated that E. coli can accept multiple plasmids simultaneously, resulting in widespread aclonality during colony development. Tracking clonally related bacteria allows for mosaic analysis of gene function. Additionally, it was discovered that clonally related bacterium rods self-organize fractally and can remain linked during colony growth, presenting a potential target for controlling microbiota growth.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Steven Russum, Katie Jing Kay Lam, Nicholas Alan Wong, Vasu Iddamsetty, Kevin J. Hendargo, Jianing Wang, Aditi Dubey, Yichi Zhang, Arturo Medrano-Soto, Milton H. Saier
Summary: The Asgard superphylum of archaea, especially the Loki phylum, is closely related to eukaryotes and heavily relies on proton motive force for substrate transport, mainly organic molecules such as lipid precursors, amino acids, and sugars. The majority of identified transporters are more similar to prokaryotic transporters, supporting the mixotrophic and anaerobic nature of Asgard organisms while clarifying their metabolic potential and relation to eukaryotes.
Article
Microbiology
Jiayuan Zhang, Hai Yang, Lei Zhang, Zhihua Lv, Mingming Yu, Sherwin K. B. Sy, Yuanchao Zhan
Summary: The combination of aztreonam and clavulanate has a synergistic killing effect on Escherichia coli carrying NDM, inhibiting cell wall synthesis and disrupting multiple metabolic pathways. This study provides a theoretical basis for the combined use of aztreonam and clavulanate in treating multidrug-resistant E. coli infections.
Article
Multidisciplinary Sciences
Francois Bertaux, Sebastian Sosa-Carrillo, Viktoriia Gross, Achille Fraisse, Chetan Aditya, Mariela Furstenheim, Gregory Batt
Summary: Small-scale, low-cost bioreactors are gaining popularity in quantitative systems and synthetic biology. In this study, the authors present ReacSight, a strategy that enhances bioreactor arrays by connecting them with sensitive measurement devices using low-cost pipetting robots. They demonstrate the capabilities of ReacSight in yeast, including real-time optogenetic control of gene expression, exploration of nutrient scarcity effects on fitness and cellular stress, and dynamic control of a two-strain consortium's composition.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Siriluck Ponsuksili, Eduard Murani, Frieder Hadlich, Muhammad Arsalan Iqbal, Beate Fuchs, Christina E. E. Galuska, Alvaro Perdomo-Sabogal, Fabio Sarais, Nares Trakooljul, Henry Reyer, Michael Oster, Klaus Wimmers
Summary: The liver undergoes metabolic changes in intrauterine growth restriction (IUGR). The study found that lipid metabolic pathways, especially sphingolipids and phospholipids, were altered in the liver tissue of IUGR fetuses. Differentially expressed miRNAs, such as miR-34a, and their mRNA targets were also identified. Sex-specific adaptations in the metabolic system were observed, particularly in males.
Article
Multidisciplinary Sciences
Jeongjoon Choi, Matias Schmukler, Eduardo A. Groisman
Summary: Horizontal gene transfer drives bacterial evolution, and H-NS proteolysis is a mechanism essential for derepressing foreign genes and colonization of mammalian hosts.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Shailab Shrestha, Najwa Taib, Simonetta Gribaldo, Aimee Shen
Summary: The pathogen Clostridioides difficile lacks canonical cell division factors and utilizes a bifunctional enzyme for peptidoglycan synthesis during cell division. This unique divisome may serve as a potential target for therapeutic interventions.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Lirong Hu, Abdul Sammad, Congcong Zhang, Luiz F. Brito, Qing Xu, Yachun Wang
Summary: This study evaluated the changes in milk yield, physiological indicators, blood biochemical parameters, and alternative splicing patterns in lactating Holstein cows under heat stress conditions. The results showed that heat stress negatively impacted various biological processes of Holstein cows. Additionally, heat stress increased the occurrence of alternative splicing events, with genes involved in mRNA splicing, immune, and metabolic processes being enriched. Two candidate genes associated with heat stress responses in dairy cows were identified.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Microbiology
Melanie R. Silvis, Manohary Rajendram, Handuo Shi, Hendrik Osadnik, Andrew N. Gray, Spencer Cesar, Jason M. Peters, Cameron C. Hearne, Parth Kumar, Horia Todor, Kerwyn Casey Huang, Carol A. Gross
Summary: CRISPR interference (CRISPRi) has been used to study the role of genes in cellular homeostasis, allowing targeted depletion of essential genes. This study built and characterized an arrayed library of CRISPRi strains targeting essential genes of E. coli, enabling targeted depletion studies and high-throughput antibiotic target identification.
Article
Biotechnology & Applied Microbiology
Chinwe U. Chukwudi, Liam Good
JOURNAL OF ANTIBIOTICS
(2019)
Article
Veterinary Sciences
Rekaz A. Ibrahim, Tillie L. Cryer, Shawkat Q. Lafi, Ehab-Abu Basha, Liam Good, Yaser H. Tarazi
BMC VETERINARY RESEARCH
(2019)
Article
Nutrition & Dietetics
A. M. Madden, S. Baines, S. Bothwell, E. Chen, S. Goh, L. Jerome, C. Sommariva-Nagle, M. Szychta
JOURNAL OF HUMAN NUTRITION AND DIETETICS
(2019)
Article
Multidisciplinary Sciences
Chinwe Uzoma Chukwudi, Liam Good
Review
Public, Environmental & Occupational Health
Bugwesa Z. Katale, Gerald Misinzo, Stephen E. Mshana, Harriet Chiyangi, Susana Campino, Taane G. Clark, Liam Good, Mark M. Rweyemamu, Mecky Matee
ANTIMICROBIAL RESISTANCE AND INFECTION CONTROL
(2020)
Article
Pharmacology & Pharmacy
Alexandru Chivu, Kantaraja Chindera, Graca Mendes, Angela An, Brian Davidson, Liam Good, Wenhui Song
Summary: This study demonstrates the efficient intracellular delivery of pDNA and ODNs using PHMB as a nano-vector, with comparable or even higher gene expression levels than PEI analogues in various cell lines. The well-established safety profile of PHMB makes it a promising candidate for further research and potential clinical applications.
EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS
(2021)
Article
Microbiology
Valwynne Faulkner, Adrienne Adele Cox, Shan Goh, Annelies van Bohemen, Amanda J. Gibson, Oliver Liebster, Brendan W. Wren, Sam Willcocks, Sharon L. Kendall
Summary: CRISPRi-based gene silencing can be as impactful as gene deletion for studying non-essential genes, and can be applied to other non-essential antimicrobial resistance genes. Designing sgRNAs targeting transcription initiation or early elongation stages has the most impact on rifampicin susceptibility.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Marion Schuller, Rachel E. Butler, Antonio Ariza, Callum Tromans-Coia, Gytis Jankevicius, Tim D. W. Claridge, Sharon L. Kendall, Shan Goh, Graham R. Stewart, Ivan Ahel
Summary: ADP-ribosyltransferases use NAD(+) to catalyze substrate ADP-ribosylation and regulate cellular pathways or contribute to bacterial pathogenicity. Recent studies have suggested nucleic acids as targets of reversible ADP-ribosylation. This research provides evidence of specific ADP-ribosylation of DNA in cells through the DarT-DarG system in bacteria, including global pathogens. The study reveals the structure and mechanism of the DarT enzyme, showing its evolution into specific DNA-modifying enzymes and its role in regulating growth through DNA ADP-ribosylation.
Article
Immunology
Shan Goh, Jeannine Kolakowski, Angela Holder, Mark Pfuhl, Daniel Ngugi, Keith Ballingall, Kata Tombacz, Dirk Werling
Summary: The study aimed to develop an affordable and easy-to-administer subunit vaccine for East Coast Fever (ECF) using yeast as an expression platform. Results showed that recombinant yeast expressing T. parva antigens could induce immune responses and specific antibodies in mice, suggesting a promising vaccination platform for sub-Saharan Africa. Further evaluation of antigen-specific cellular immune responses, especially cytotoxic CD8(+) T cell immunity in cattle, will contribute to the development of a yeast-based vaccine for ECF.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Winnie Ntow-Boahene, David Cook, Liam Good
Summary: Advancements in medicine leading to rising global populations have increased the number of patients susceptible to fungal infections, impacting plant pathogens on preharvested crops and stored food. Current antifungal strategies face limitations, leading to the exploration of antimicrobial polymers as an alternative strategy that can be combined with other antimicrobial compounds for synergistic effects. Antifungal polymers and nanocomposites show promising antifungal effects and reduced toxicity compared to traditional small molecule antifungal drugs.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Editorial Material
Microbiology
Shan Goh, Peter Mullany, Thomas V. Riley
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Oluwawemimo Adebowale, Liam Good
BIOLOGY METHODS & PROTOCOLS
(2020)
Article
Veterinary Sciences
Pamela Martinez-Orellana, Marta Baxarias, Liam Good, Laia Solano-Gallego
VETERINARY SCIENCES
(2020)
Article
Multidisciplinary Sciences
Oluwawemimo O. Adebowale, Shan Goh, Liam Good