Article
Multidisciplinary Sciences
Qing Cheng, Xiao Zhang, Lin S. Chen, Jin Liu
Summary: Mendelian randomization uses genetic variation to study the causal effect of exposure on outcome, but results can be biased by confounders, such as horizontal pleiotropy. Here, the authors present MR-CUE, a method to determine causal effects by accounting for correlated and uncorrelated horizontal pleiotropic effects.
NATURE COMMUNICATIONS
(2022)
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
Environmental Sciences
Xiang Xiao, Xiao-Lin Ma, Xue Han, Li-Jun Wu, Chang Liu, Han-Qing Yu
Summary: This study found that TiO2 photoexcitation has a synergistic promotion effect on phage infection, but excessive UV irradiation may result in a decrease in transductant formation. ROS produced by moderate TiO2 photoexcitation facilitate the phage infection process.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Review
Infectious Diseases
Claudia Michaelis, Elisabeth Grohmann
Summary: Bacteria form biofilms to resist antibiotic treatment, and environmental biofilms are hotspots for the spread of antibiotic resistance genes. This review summarizes the latest research on biofilms and the techniques used to visualize horizontal gene transfer mechanisms in biofilms.
Article
Agronomy
Yi Kan, Hong-Xuan Lin
Summary: Rice, as a vital food crop vulnerable to heat stress, responds to high temperatures through various mechanisms at cell-component and functional levels, including membrane, endoplasmic reticulum, chloroplasts, mitochondria, denatured protein elimination, ROS scavenging, stabilization of DNA and RNA, translation, and metabolic flux changes. Breeding thermotolerant rice species without yield penalties through natural alleles mining and transgenic editing should be the future focus.
Article
Thermodynamics
Kun-Ru Wang, Jian Chen, Rui Zhao, Wen -Long Cheng
Summary: This study experimentally investigates the impact of transverse vibration on heat transfer characteristics of S-CO 2 in a 1200 mm tube. The results demonstrate that vibration significantly enhances the heat transfer of S-CO 2. The heat transfer enhancement efficiency (HTE) tends to rise with the increase of vibration amplitude, frequency, mass flux, or pressure, and the HTE of the upper vertex is better than the lower vertex. Within the tested range, the highest average HTE is 10.2%. The local HTE in the pseudo critical region is much more noteworthy than in other regions. Finally, a heat transfer correlation is proposed based on the experimental findings, with 95.6% of the data error within ±15%.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2023)
Review
Agronomy
Lu Yang, Na Li, Yang Liu, Pengfei Miao, Ji Liu, Zhi Wang
Summary: Waterlogging is a significant threat to global crop growth and production, caused by extreme weather conditions. It hinders plant growth and development by limiting oxygen and light availability. To cope with waterlogging stress, plants regulate their morphological structure, photosynthesis, respiration, energy metabolism, and plant hormone biosynthesis/signal transduction. This review examines the molecular mechanisms and key genes involved in crop survival under waterlogging conditions and highlights the importance of stress memory and cross-stress mechanisms in plant response to abiotic stress. The study of these interactions provides insights for improving crop resistance to waterlogging through genetic breeding.
Review
Plant Sciences
Xiaofeng Liu, Jiacai Chen, Xiaolan Zhang
Summary: Cucumber is an important vegetable crop with significant economic value, and its shoot architecture plays a crucial role in crop management and yield. Unlike most plant species, cucumber undergoes both vegetative and reproductive growth simultaneously, a unique feature of the Cucurbitaceae family. Despite advances in understanding shoot architecture in other crops, mechanisms controlling cucumber's architecture are still limited.
HORTICULTURE RESEARCH
(2021)
Article
Multidisciplinary Sciences
Alicia Broto, Erika Gaspari, Samuel Miravet-Verde, Vitor A. P. Martins dos Santos, Mark Isalan
Summary: This study provides a robust genetic toolkit for Mycoplasma, demonstrating the application of gene circuit engineering to control and limit the growth of Mycoplasma. The synthetic gene circuits developed were found to be stable and robust in the long-term, laying the foundation for developing viable biosafety systems using a synthetic Mycoplasma chassis.
NATURE COMMUNICATIONS
(2022)
Review
Biology
Matthieu Haudiquet, Jorge Moura de Sousa, Marie Touchon, Eduardo P. C. Rocha
Summary: Horizontal gene transfer (HGT) is a driving force in microbial adaptation, but it is controlled by mobile genetic elements (MGEs) whose interests may not align with those of their hosts. The interactions between cells and MGEs, as well as between MGEs themselves, result in complex evolutionary processes that affect gene flow and microbial adaptation.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Multidisciplinary Sciences
Kulkarni Madhurima, Bodhisatwa Nandi, Sneha Munshi, Athi N. Naganathan, Ashok Sekhar
Summary: The structure of a thermally accessible excited state in equilibrium with the native ensemble of a bacterial transcriptional regulator CytR has been determined using multinuclear CEST NMR. Evidence from double resonance CEST experiments suggests that the excited state, which resembles the DNA-bound form of CytR, recognizes DNA through a folding-before-binding conformational selection pathway. The disorder-to-order regulatory switch in DNA recognition by natively disordered CytR operates through a dynamical variant of the lock-and-key mechanism.
Article
Biochemistry & Molecular Biology
Seonggyun Han, Yirang Na, Insong Koh, Kwangsik Nho, Younghee Lee
Summary: The study utilized a splicing-guided aggregation method to investigate the functional impact of multiple low-frequency TREM2 variants on alternative splicing in Alzheimer's disease, revealing an exon skipping event in the second exon of TREM2 in individuals with a low-frequency variant causing loss of function for a splicing regulatory element. Genes differentially expressed between AD patients with high vs. low skipping of the second exon were significantly enriched in immune-related pathways. This method provides new insights into the regulation of alternative splicing of TREM2 by low-frequency variants and could aid in exploring potential molecular mechanisms of disease-related variants.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Jiahua Deng, Qiang Cui
Summary: This study investigates the impact of electronic polarization on the stability and properties of buried charged residues in proteins using advanced polarizable CHARMM force field and free energy simulations. The results demonstrate the essential role of electronic polarization in the stability, hydration, dynamics, and function of buried charges. The study suggests that explicit consideration of electronic polarization is crucial for mechanistic and engineering studies involving buried charged residues in proteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Evolutionary Biology
Tuane L. Carvalho, Juliana Cordeiro, Jeferson Vizentin-Bugoni, Pedro M. Fonseca, Elgion L. S. Loreto, Lizandra J. Robe
Summary: Understanding the mechanisms that shape genomes and their interfaces is crucial for biological evolution. Transposable elements (TEs) play a significant role in genome evolution by providing sites for nonallelic recombination. In this study, the patterns and processes of TE-driven genome evolution related to niche diversification in flower-breeding Drosophila were investigated. The results showed that ecological traits and abiotic niche overlap influence TE content and horizontal transposon transfers (HTTs).
GENOME BIOLOGY AND EVOLUTION
(2023)
Article
Infectious Diseases
James B. Doub
Summary: Bacteriophage therapy shows promise in treating multidrug-resistant infections and chronic biofilm infections, but there is limited knowledge on how best to utilize these agents in vivo, resulting in a wide range of treatment protocols. Clinicians need to be aware of the differences between bacteriophages and antibiotics, as well as the potential risks associated with horizontal transfer of genetic material and contamination with other contaminants. Regulatory agencies are beginning to recommend evaluation of these issues, highlighting the importance of testing for and mitigating adverse effects in bacteriophage therapy.
INFECTION AND DRUG RESISTANCE
(2021)
Article
Virology
James E. Cherwa, Joshua Tyson, Gregory J. Bedwell, Dewey Brooke, Ashton G. Edwards, Terje Dokland, Peter E. Prevelige, Bentley A. Fane
JOURNAL OF VIROLOGY
(2017)
Article
Biochemistry & Molecular Biology
Sandeep C. Chaudhary, Maria Kuzynski, Massimo Bottini, Elia Beniash, Terje Dokland, Callie G. Mobley, Manisha C. Yadav, Anne Poliard, Odile Kellermann, Jose Luis Millan, Dobrawa Napierala
Article
Biology
Nuria Carpena, Keith A. Manning, Terje Dokland, Alberto Marina, Jose R. Penades
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2016)
Article
Biochemistry & Molecular Biology
Rosanne L. L. Hill, Jiri Vlach, Laura K. Parker, Gail E. Christie, Jamil S. Saad, Terje Dokland
JOURNAL OF MOLECULAR BIOLOGY
(2017)
Article
Biology
Altaira D. Dearborn, Erin A. Wall, James L. Kizziah, Laura Klenow, Laura K. Parker, Keith A. Manning, Michael S. Spilman, John M. Spear, Gail E. Christie, Terje Dokland
Article
Biochemistry & Molecular Biology
Kenneth P. Hough, Jennifer L. Trevor, John G. Strenkowski, Yong Wang, Balu K. Chacko, Sultan Tousif, Diptiman Chanda, Chad Steele, Veena B. Antony, Terje Dokland, Xiaosen Ouyang, Jianhua Zhang, Steven R. Duncan, Victor J. Thannickal, Victor M. Darley-Usmar, Jessy S. Deshane
Article
Biochemistry & Molecular Biology
Erin A. Wall, J. Harry Caufield, Charles E. Lyons, Keith A. Manning, Terje Dokland, Gail E. Christie
MOLECULAR MICROBIOLOGY
(2015)
Review
Virology
Terje Dokland
Article
Microbiology
James L. Kizziah, Keith A. Manning, Altaira D. Dearborn, Terje Dokland
Article
Virology
Keith A. Manning, Terje Dokland
Article
Virology
James L. Kizziah, Cynthia M. Rodenburg, Terje Dokland
Article
Multidisciplinary Sciences
Uday Tak, Terje Dokland, Michael Niederweis
Summary: The tuberculosis necrotizing toxin (TNT) is secreted by Mycobacterium tuberculosis to kill host cells, with proteins EsxE and EsxF forming membrane-spanning hetero-oligomeric pores that are essential for TNT secretion.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
N'Toia C. Hawkins, James L. Kizziah, Jose R. Penades, Terje Dokland
Summary: Phage-inducible chromosomal islands (PICIs) are mobile genetic elements that hijack helper bacteriophages' replication and assembly machinery. Staphylococcus aureus pathogenicity islands (SaPIs), such as SaPIbov5, redirect the assembly pathway of their helper phages by introducing a capsid protein homolog, Ccm. Cryo-electron microscopy studies show that Ccm occupies the pentameric capsomers in SaPIbov5 procapsids, preventing the formation of the cylindrical midsection seen in typical phage procapsids.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
N'Toia C. Hawkins, James L. Kizziah, Asma Hatoum-Aslan, Terje Dokland
Summary: In this study, the structure of the complete virion of the Staphylococcus epidermidis-infecting phage Andhra was determined using high-resolution cryo-electron microscopy. The findings provide insights into critical features for virion assembly, host recognition, and penetration.
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)