Duncan, William Cummins, Breschine Gedeon, Tomáš
Published in
Frontiers in Applied Mathematics and Statistics
This study addresses a problem of correspondence between dynamics of a parameterized system and the structure of interactions within that system. The structure of interactions is captured by a signed network. A network dynamics is parameterized by collections of multi-level monotone Boolean functions (MBFs), which are organized in a parameter graph...
Rakibova, Yulduz Dunham, Drew Seed, Kim Freddolino, Lydia
UNLABELLED: Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control an...
Akhtar, Nosheen Shahzad, Asim Ilyas, Noshin Bostan, Nageen Jameel, Muhammad Azhar Mukhtar, Shahid Qin, Mingzhou Li, Hao Yang Alhewairini, Saleh S.
Published in
Nanotechnology Reviews
Cold stress has an immediate impact on plant structure and function. A large number of free radicals cause oxidative stress in plants. Cold stress causes altered membrane permeability, lipid peroxidation, and DNA damage. It denatures enzymes and disrupts plant metabolism. Different methods are being investigated for acclimatizing plants subjected t...
Wang, Yimei Tu, Mei-Juan Yu, Ai-Ming
Published in
Frontiers in Pharmacology
ATP-binding cassette (ABC) transporters are transmembrane proteins expressed commonly in metabolic and excretory organs to control xenobiotic or endobiotic disposition and maintain their homeostasis. Changes in ABC transporter expression may directly affect the pharmacokinetics of relevant drugs involving absorption, distribution, metabolism, and e...
Yu, Xinghua Teng, Tingkai Duan, Zhuowen Wang, Jinwen
Published in
Journal of Virology
Virus-encoded miRNAs have been extensively studied for their pivotal roles in finetuning viral infections. Baculoviruses, highly pathogenic in insects, remain underexplored concerning their encoded miRNAs. Previous reports outlined three AcMNPV-encoded miRNAs, AcMNPV-miR-1, -miR-3, and -miR-4. This study delves into the functions of another AcMNPV-...
Yu, Xinghua Teng, Tingkai Duan, Zhuowen Wang, Jinwen
Published in
Journal of Virology
Virus-encoded miRNAs have been extensively studied for their pivotal roles in finetuning viral infections. Baculoviruses, highly pathogenic in insects, remain underexplored concerning their encoded miRNAs. Previous reports outlined three AcMNPV-encoded miRNAs, AcMNPV-miR-1, -miR-3, and -miR-4. This study delves into the functions of another AcMNPV-...
Yang, Yuening Lu, Yanming Wang, Yan Wen, Xianghui Qi, Changhai Piao, Weilan Jin, Hua
Published in
Frontiers in Cell and Developmental Biology
Various methods have been developed so far for detecting N 6-methyladenosine (m6A). The total m6A level or the m6A status at individual positions on mRNA can be detected and quantified through some sequencing-independent biochemical methods, such as LC/MS, SCARLET, SELECT, and m6A-ELISA. However, the m6A-detection techniques relying on high-through...
Valton, Anne-Laure Mair, Barbara Khokhar, Eraj Usaj, Matej Moffat, Jason Dekker, Job
SUMMARY Cohesin-mediated loop extrusion folds interphase chromosomes at the ten to hundreds kilobases scale. This process produces structural features such as loops and topologically associating domains. We identify three types of cis -elements that define the chromatin folding landscape generated by loop extrusion. First, CTCF sites form boundarie...
Rakibova, Yulduz Dunham, Drew T. Seed, Kimberley D. Freddolino, Lydia
Published in
mSphere
New strains of the bacterial pathogen Vibrio cholerae, bearing novel horizontally acquired elements (HAEs), frequently emerge. HAEs provide beneficial traits to the bacterium, such as antibiotic resistance and defense against invading bacteriophages. Xenogeneic silencers are proteins that help bacteria harness new HAEs and silence those HAEs until ...
Shi, Shuqun Hamann, Catherine A. Lee, Joanne C. Brunger, Jonathan M.
Published in
Frontiers in Bioengineering and Biotechnology
Uncovering the stimulus-response histories that give rise to cell fates and behaviors is an area of great interest in developmental biology, tissue engineering, and regenerative medicine. A comprehensive accounting of cell experiences that lead to the development of organs and tissues can help us to understand developmental anomalies that may under...
