Article
Biochemistry & Molecular Biology
Anna A. Mikkelsen, Feng Gao, Elizabeth Carino, Sayanta Bera, Anne E. Simon
Summary: Plus-strand RNA viruses often use -1 programmed ribosomal frameshifting to maximize their coding capacity. This study discovered six tertiary interactions associated with the FSE of citrus yellow vein associated virus, which covers three-quarters of the genomic RNA. Two long-distance interactions connect sequences on opposite sides of the critical FSE central stem, destabilizing the FSE and potentially allowing ribosome progression through a disrupted upstream FSE.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Jamie Richards, Joel G. Belasco
Summary: In many bacteria, RNase E controls the lifespan of most mRNAs by degrading RNAs with a 5' monophosphate and cleaving them linearly from the 5' terminus. Obstacles encountered along the scanning path of this enzyme, such as bound proteins or ribosomes or base pairing, determine its rate of cleavage at distal sites. We found that the protection provided by these obstacles depends on the size and persistence of the structural discontinuities they create, rather than their molecular composition. Incrementally larger discontinuities have a proportionally greater impact on mRNA stability, suggesting that the effect of obstacles on scanning is not binary.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Physical
Jing-Jie Su, Xing-liang Xu, Ting-Ting Sun, Yu Shen, Yan Wang
Summary: By using a helix-based transition rate model and master equation, the study investigated the refolding and cotranscriptional folding processes of RNA pseudoknots, revealing differences in final states and intermediates between refolding and cotranscriptional folding. These findings provide insights into the cotranscription folding of hTR pseudoknot with different rates.
CHEMICAL PHYSICS LETTERS
(2021)
Article
Microbiology
Fuxiao Liu, Di Zhao, Ning Wang, Ziwei Li, Yaqin Dong, Shuang Liu, Feng Zhang, Jin Cui, Hailan Meng, Bo Ni, Rong Wei, Hu Shan
Summary: This study reveals the viral abilities to tolerate mutations in the predicted kissing-loop forming motif (KLFM) or pseudoknot-forming motifs (PFMs). The results show that the putative kissing-loop structure is unnecessary for Senecavirus A (SVA) replication, while the deformation of the pseudoknot structure has a lethal effect on SVA propagation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Xia Zhou, Zhihua Du, Xiaolan Huang
Summary: Researchers have proposed a computational method to identify a certain kind of long-range intra-molecular RNA-RNA interactions involving loop nucleotides of a hairpin loop. Using this method, they discovered a potential long-range intra-molecular RNA-RNA interaction within HIV-1 genomic mRNA. The interaction is mediated by a kissing loop structure between two stem-loops of the previously reported secondary structure of the entire HIV-1 genome.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Physics, Multidisciplinary
Vinayak Shantaram Bhat, Sho Watanabe, Florian Kronast, Korbinian Baumgaertl, Dirk Grundler
Summary: The study finds that artificial ferromagnetic quasicrystals with aperiodicity and unconventional rotational symmetries exhibit unusual physical and functional properties. By conducting spin-wave spectroscopy and X-ray photoemission electron microscopy, it is revealed that exchange-coupled quasicrystals show non-stochastic switching and collective phenomena, while both exchange and dipolarly coupled quasicrystals display magnonic excitations with narrow linewidths. These findings have practical implications for reconfigurable functionalities in spintronics and magnonics.
COMMUNICATIONS PHYSICS
(2023)
Article
Endocrinology & Metabolism
Hongjiao Gao, Yujue Li, Xiang Chen
Summary: There is a regulatory loop between glucocorticoid receptor alpha and peroxisome proliferator-activated receptor alpha, which affects energy and lipid metabolism and has anti-inflammatory effects.
REVIEWS IN ENDOCRINE & METABOLIC DISORDERS
(2022)
Review
Biochemistry & Molecular Biology
Benita Wiatrak, Janusz Piasny, Amadeusz Kuzniarski, Kazimierz Gasiorowski
Summary: As the elderly population increases globally, there is a growing concern about neurodegenerative diseases like Alzheimer's disease. The understanding of the pathomechanism and effective treatment for this disease still remains a challenge.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Coline Arnould, Vincent Rocher, Anne-Laure Finoux, Thomas Clouaire, Kevin Li, Felix Zhou, Pierre Caron, Philippe. E. Mangeot, Emiliano P. Ricci, Raphael Mourad, James E. Haber, Daan Noordermeer, Gaelle Legube
Summary: The repair of DNA double-strand breaks is essential for maintaining genome integrity. This study demonstrates the functional role of topologically associating domains in establishing gamma H2AX-53BP1 chromatin domains, involving cohesin-mediated loop extrusion on both sides of the DSB.
Article
Multidisciplinary Sciences
Qiaoqiao Zhang, Kai Deng, Mengyou Liu, Shengye Yang, Wei Xu, Tong Feng, Minwen Jie, Zhiming Liu, Xiao Sheng, Haiyang Chen, Hao Jiang
Summary: This study explores the role of phase separation in intracellular compartment formation and reveals that BuGZ and m(6)A regulators may play critical roles in ISC-dependent gut regeneration and aging.
NATURE COMMUNICATIONS
(2023)
Article
Gastroenterology & Hepatology
Mei Yang, J. Andrew McClure, Kerollos N. Wanis, Kelly N. Vogt, Julie Ann M. Van Koughnett, Michael C. Ott, Christopher M. Vinden
Summary: There is significant morbidity and mortality associated with the formation and closure of defunctioning loop ileostomies, with approximately 1 in 8 patients requiring a permanent ostomy.
DISEASES OF THE COLON & RECTUM
(2022)
Article
Automation & Control Systems
Ai-Guo Wu, Yu Wang, Ying Zhang
Summary: This article introduces a parametric predictor and a predictor-based feedback controller to predict the future state of a discrete-time linear system and attenuate disturbance signals. The proposed predictor has a good disturbance attenuation capacity within a certain parameter range and can eliminate estimation errors.
IEEE TRANSACTIONS ON CYBERNETICS
(2022)
Article
Multidisciplinary Sciences
Baocheng Liu, Yao He, Yaqiang Wang, He Song, Z. Hong Zhou, Juli Feigon
Summary: This study reveals the structure of human telomerase and its interaction with TPP1. The binding of TPP1 to TERT activates telomerase activity. Additionally, the study found that elements in TERT and TER involved in template and telomeric DNA handling are structurally similar to those in Tetrahymena telomerase, providing unique insights into the mechanism of telomerase activity.
Article
Multidisciplinary Sciences
Yu Sun, Laura Abriola, Rachel O. Niederer, Savannah F. Pedersen, Mia M. Alfajaroe, Valter Silva Monteiro, Craig B. Wilen, Ya-Chi Ho, Wendy Gilbert, Yulia Surovtseva, Brett D. Lindenbach, Junjie U. Guo
Summary: The study found that merafloxacin can inhibit -1 PRF activity of SARS-CoV-2 and is similarly effective on other betacoronaviruses.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Automation & Control Systems
Xiaojun Yang, Lunjia Liao, Qin Yang, Bo Sun, Jianxiang Xi
Summary: This paper addresses limited-energy output formation design and analysis problems for multiagent systems with intermittent interactions. It proposes a new dynamic output feedback formation control protocol with limited energy supply and sufficient conditions for leaderless limited-energy output formation. The paper also extends main conclusions for leaderless multiagent systems into leader-follower ones and provides numerical simulations to demonstrate theoretical results.
JOURNAL OF THE FRANKLIN INSTITUTE-ENGINEERING AND APPLIED MATHEMATICS
(2021)
Article
Biochemistry & Molecular Biology
Weina Ke, Enping Hong, Renata F. Saito, Maria Cristina Rangel, Jian Wang, Mathias Viard, Melina Richardson, Emil F. Khisamutdinov, Martin Panigaj, Nikolay Dokholyan, Roger Chammas, Marina A. Dobrovolskaia, Kirill A. Afonin
NUCLEIC ACIDS RESEARCH
(2019)
Article
Nanoscience & Nanotechnology
Ridhima Juneja, Zachary Lyles, Hemapriyadarshini Vadarevu, Kirill A. Afonin, Juan L. Vivero-Escoto
ACS APPLIED MATERIALS & INTERFACES
(2019)
Article
Biochemistry & Molecular Biology
Enping Hong, Justin R. Halman, Ankit Shah, Edward Cedrone, Nguyen Truong, Kirill A. Afonin, Marina A. Dobrovolskaia
Review
Chemistry, Multidisciplinary
Morgan Chandler, Kirill A. Afonin
Review
Chemistry, Multidisciplinary
Ryan C. Oliver, Lewis A. Rolband, Alanna M. Hutchinson-Lundy, Kirill A. Afonin, Joanna K. Krueger
Article
Chemistry, Multidisciplinary
Liam E. Yourston, Alexander Y. Lushnikov, Oleg A. Shevchenko, Kirill A. Afonin, Alexey Krasnoslobodtsev
Editorial Material
Chemistry, Multidisciplinary
Justin R. Halman, Kirill A. Afonin
Review
Chemistry, Multidisciplinary
Martin Panigaj, M. Brittany Johnson, Weina Ke, Jessica McMillan, Ekaterina A. Goncharova, Morgan Chandler, Kirill A. Afonin
Article
Nanoscience & Nanotechnology
Justin R. Halman, Ki-Taek Kim, So-Jung Gwak, Richard Pace, M. Brittany Johnson, Morgan R. Chandler, Lauren Rackley, Mathias Viard, Ian Marriott, Jeoung Soo Lee, Kirill A. Afonin
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE
(2020)
Review
Biochemical Research Methods
Morgan Chandler, Morgan Brittany Johnson, Martin Panigaj, Kirill A. Afonin
CURRENT OPINION IN BIOTECHNOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Yelixza I. Avila, Morgan Chandler, Edward Cedrone, Hannah S. Newton, Melina Richardson, Jie Xu, Jeffrey D. Clogston, Neill J. Liptrott, Kirill A. Afonin, Marina A. Dobrovolskaia
Summary: Recent insights have shown that variations in the shape, size, and composition of nucleic acid nanoparticles (NANPs) can lead to distinct patterns in their immunostimulatory properties. The choice of delivery platform can impact the immune response of nanoparticles, with differences in cytokine induction seen between dendrimers and lipid-based platforms.
Review
Biochemistry & Molecular Biology
Dominika Bila, Yasmine Radwan, Marina A. Dobrovolskaia, Martin Panigaj, Kirill A. Afonin
Summary: Nucleic acid nanoparticles (NANPs) have advantages for diverse diagnostic and therapeutic approaches, but their immune recognition is a key area of investigation for potential clinical application. Interactions with the immune system are crucial for understanding the unique properties of NANPs and their potential use in vaccines and immunotherapy.
Article
Biochemistry & Molecular Biology
Lewis Rolband, Liam Yourston, Morgan Chandler, Damian Beasock, Leyla Danai, Seraphim Kozlov, Nolan Marshall, Oleg Shevchenko, Alexey Krasnoslobodtsev, Kirill A. Afonin
Summary: This study combines atomically precise metal nanoclusters with nucleic acid nanotechnology to create DNA-templated silver nanoclusters with reproducible fluorescent properties and antibacterial activity. Additionally, the use of cytosine-rich single-stranded DNA oligonucleotides improves stability, modulates antibacterial properties, and enhances the quality of observed fluorescent signals of the silver nanoclusters. The research characterizes the sequence-specific fluorescence and composition of four representative DNA-AgNCs, compares their antibacterial effectiveness at different pH levels, and evaluates cytotoxicity to various mammalian cell lines.
Article
Biochemistry & Molecular Biology
Hannah S. Newton, Yasmine Radwan, Jie Xu, Jeffrey D. Clogston, Marina A. Dobrovolskaia, Kirill A. Afonin
Summary: Nucleic acid nanoparticles (NANPs) require a carrier for intracellular delivery to immune cells, and the carrier's impact on NANP immunostimulation can be monitored through cytokine production. Recent studies have shown that changes in the delivery platform can alter NANPs' immunorecognition and cytokine production. This study used flow cytometry and measured cytokine induction to investigate the impact of compositional variations in commercially available lipofectamine carriers on the immunostimulatory properties of NANPs with different architectural characteristics.
Editorial Material
Biochemistry & Molecular Biology
Marina A. A. Dobrovolskaia, Kirill A. A. Afonin