Article
Biochemistry & Molecular Biology
Viktoriya O. Samarskaya, Nadezhda Spechenkova, Irina Ilina, Tatiana P. Suprunova, Natalia O. Kalinina, Andrew J. Love, Michael E. Taliansky
Summary: The external application of dsRNA has emerged as a non-transgenic approach for crop protection. However, it has been found that externally administered dsRNA generates a non-canonical pool of sRNAs, which have different characteristics from the naturally occurring RNAi mechanism. These findings have significant implications for the application of dsRNA in crop protection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Virology
Matthew Ykema, Yizhi J. Tao
Summary: Astroviruses are non-enveloped RNA viruses that cause inflammatory diseases in hosts, with a unique ability to infect host cells using proteases and spike proteins. The capsid undergoes significant structural changes during maturation and interacts with host membranes, playing important roles in the virus life cycle. Understanding the capsid structure and maturation process can lead to new vaccines, therapies, and engineering applications.
Article
Virology
Marlonni Maurastoni, Tathiana Sa F. Antunes, Emanuel F. M. Abreu, Simone G. Ribeiro, Angela Mehta, Marcio M. Sanches, Wagner Fontes, Elliot W. Kitajima, Fabiano T. Cruz, Alexandre M. C. Santos, Jose A. Ventura, Ana C. M. M. Gomes, F. Murilo Zerbini, Patricia Sosa-Acosta, Fabio C. S. Nogueira, Silas P. Rodrigues, Francisco J. L. Aragao, Anna E. Whitfield, Patricia M. B. Fernandes
Summary: Papaya sticky disease is caused by papaya meleira virus (PMeV) and papaya meleira virus 2 (PMeV2). Two major proteins were identified in the purified virus. A potential interaction between the viral proteins and the 50S ribosomal protein L17 (AtRPL17) was discovered, suggesting the importance of virus-host interactions in the disease.
Article
Biochemistry & Molecular Biology
Dwaipayan Chaudhuri, Satyabrata Majumder, Joyeeta Datta, Kalyan Giri
Summary: This study focuses on utilizing conventional nanobodies for Dengue virus, which can potentially serve as therapeutics and diagnostic tools due to their high specificity and delivery capabilities.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Fisheries
Yesseinia I. Anglero-Rodriguez, Chinmay V. Tikhe, Seokyoung Kang, George Dimopoulos
Summary: This study demonstrates the role of dsRNA in activating immune responses in mosquitoes, reducing dengue virus infection, and potentially inducing immune responses through the Toll pathway.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2021)
Article
Virology
Wattana Weerachatyanukul, Pauline Kiatmetha, Ponlawoot Raksat, Supawich Boonkua, Orawan Thongsum, Pitchanee Jariyapong, Charoonroj Chotwiwatthanakun, Puey Ounjai, Zoltan Metlagel
Summary: This study aimed to encapsulate large-sized double-stranded DNA (dsDNA) into a small-sized virus-like particle and compare the changes in capsid structure between dsDNA-filled and empty particles. The results showed that the dsDNA-filled particles were slightly bigger and had a thicker capsid structure compared to the empty particles. The shape of the capsid exterior also changed, particularly at the five-fold axes. The ability to encapsulate dsDNA opens up opportunities for gene delivery and targeting susceptible cells to combat viral infections in shrimp.
Article
Chemistry, Physical
Chung Bin Park, Bong June Sung
Summary: The shape of a viral capsid affects the equilibrium DNA conformation inside. DNA ejection kinetics are influenced by the jammed conformation of DNA inside the capsid, which is determined by the capsid shape. In simulations, the ejection rate is faster from a spherical capsid compared to cubic or cuboid capsids due to the easier collective rotational relaxation of the polymer chain inside the spherical capsid, while threading motion dominates in cubic and cuboid capsids.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Xiangxiang Wang, Zhiyong Yue, Feifei Xu, Sufang Wang, Xin Hu, Junbiao Dai, Guanghou Zhao
Summary: By swapping the 25S rRNA genes of Saccharomyces cerevisiae with non-S. cerevisiae homologs, species-specific rRNA variations were shown to cause pre-rRNA processing defects, particularly severe growth defects when substituted by Candida albicans rRNA. The defects were primarily attributed to variations in expansion segment 7L (ES7(L)).
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Devlina Chakravarty, Shwetha Sreenivasan, Liskin Swint-Kruse, Lauren L. Porter
Summary: Although homologous protein sequences are expected to adopt similar structures, this study found that a family of bacterial response regulator proteins exhibited divergent structures in their homologous DNA-binding subunits. This structural transformation was facilitated by amino acid substitutions and likely expanded DNA-binding specificity. The approach used in this study provides a methodology to identify secondary structure switching in other protein families.
NATURE COMMUNICATIONS
(2023)
Review
Virology
Sari Maentynen, Meri M. Salomaa, Minna M. Poranen
Summary: Half a century after the discovery of Pseudomonas phage phi6, more dsRNA phages have been identified, indicating their prevalent existence in nature. Most dsRNA phages infect Pseudomonas strains and utilize bacterial receptors for cell entry. Despite high sequence diversity, a common set of genes can typically be found in dsRNA phage genomes, suggesting shared evolutionary trajectories.
Article
Multidisciplinary Sciences
Ekaterina Selivanovitch, Benjamin LaFrance, Trevor Douglas
Summary: The study investigates the size and charge limitations of molecules entering virus-like particles, finding that negatively charged substrates diffuse across more readily compared to neutral ones. The research provides important insights into molecular transport across physical barriers.
NATURE COMMUNICATIONS
(2021)
Article
Cell Biology
Huixin Gao, Yuxia Lin, Changbai Huang, Xiaobo Li, Michael S. Diamond, Chao Liu, Rong Zhang, Ping Zhang
Summary: We performed a whole-genome CRISPR/Cas9 screen in A549 cells and identified potential regulators involved in cell death triggered by double-stranded RNA. Among the candidate genes, we found that the RNA-binding gene ELAV like protein 1 (HuR) plays a crucial role in apoptosis. We further showed that HuR regulates apoptosis by suppressing the translation of the antiapoptotic gene BCL2.
JOURNAL OF CELL SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Mathilde Briday, Francois Halle, Lauriane Lecoq, Sylvie Radix, Juliette Martin, Roland Montserret, Marie Dujardin, Marie-Laure Fogeron, Michael Nassal, Beat H. Meier, Thierry Lomberget, Anja Bockmann
Summary: Hepatitis B virus (HBV) is a significant human pathogen and its capsid-forming core protein (Cp) plays a key role in envelopment. Recent studies have found that Triton X-100, a detergent used in Cp purification, strongly binds to the hydrophobic pocket of Cp. The aromatic moiety is crucial for binding, while the aliphatic chain affects binding affinity. Moreover, the hydrophilic tail shows high tolerance to changes in length and type.
Article
Biochemistry & Molecular Biology
Declan L. Turner, Rachel M. Templin, Adele A. Barugahare, Brendan E. Russ, Stephen J. Turner, Georg Ramm, Rommel A. Mathias
Summary: UL34 is a viral protein expressed with leaky late kinetics and primarily located in the nucleus during infection. Deletion of UL34 from the HCMV genome did not stop viral spread, but significantly reduced the production of infectious virions by over 100-fold, indicating that UL34 is an augmenting gene in HCMV infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Microbiology
Zhaobin Zhou, Yinqian Xie, Chunyan Wu, Yuchen Nan
Summary: Hepatitis E virus (HEV) is a zoonotic pathogen responsible for acute hepatitis outbreaks globally. The HEV-ORF2 protein, in addition to forming the viral capsid, plays multiple roles in viral replication and pathogenesis, making it a potential target for vaccine development and treatment of HEV infection.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Computer Science, Interdisciplinary Applications
J. Bernard Heymann
Summary: This study aims to assess and improve the quality of cryoEM reconstructions by calculating the spectral SNR (SSNR) and radiation damage. Through alignment and calculation of several test cases of movie frames, it was found that alignment compensated for global movement, the effect on SSNR was negligible, and the subset SSNR confirmed residual movement. The progressive SSNR reflected radiation damage and signal accumulation decrease. The results contribute to the assessment of micrograph quality and progression of radiation damage.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Article
Health Care Sciences & Services
Jitka Polechova, Kory D. Johnson, Pavel Payne, Alex Crozier, Mathias Beiglboeck, Pavel Plevka, Eva Schernhammer
Summary: This paper discusses the advantages of antigen tests compared to PCR tests and summarizes evidence from the literature and Austrian schools. Antigen tests can identify the disease during its infectious phase, while PCR tests can diagnose COVID-19 before the infectious phase. Large-scale antigen testing in Austrian schools showed low false-positive rates and a reduction in the effective reproduction number in the tested cohort.
JOURNAL OF CLINICAL EPIDEMIOLOGY
(2022)
Article
Immunology
Valerie Lorin, Ignacio Fernandez, Guillemette Masse-Ranson, Melanie Bouvin-Pley, Luis M. Molinos-Albert, Cyril Planchais, Thierry Hieu, Gerard Pehau-Arnaudet, Dominik Hrebik, Giulia Girelli-Zubani, Oriane Fiquet, Florence Guivel-Benhassine, Rogier W. Sanders, Bruce D. Walker, Olivier Schwartz, Johannes F. Scheid, Jordan D. Dimitrov, Pavel Plevka, Martine Braibant, Michael S. Seaman, Francois Bontems, James P. Di Santo, Felix A. Rey, Hugo Mouquet
Summary: Decrypting the B cell ontogeny of HIV-1 broadly neutralizing antibodies is crucial for vaccine design. This study found that multiple B cell lineages in HIV-1 viremic controllers can develop antibodies targeting a unique site of vulnerability on the virus, primarily composed of specific sugar residues. These antibodies exhibit high neutralizing capacity and delay viral rebound in animal models.
JOURNAL OF EXPERIMENTAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Eva Konkolova, Katerina Krejcova, Ludek Eyer, Jan Hodek, Michala Zgarbova, Andrea Fortova, Michael Jirasek, Filip Teply, Paul E. Reyes-Gutierrez, Daniel Ruzek, Jan Weber, Evzen Boura
Summary: Positive-sense single-stranded RNA (+RNA) viruses are important pathogens that pose a significant threat to modern societies, as evidenced by the ongoing COVID-19 pandemic. This study presents a compound called PR673, which is a helquat-like compound that can inhibit the replication of SARS-CoV-2 and tick-borne encephalitis virus in cell culture. Using in vitro polymerase assays, the researchers demonstrate that PR673 inhibits RNA synthesis by viral RNA-dependent RNA polymerases (RdRps). This study suggests the feasibility of developing broad-spectrum non-nucleoside inhibitors of RdRps.
Article
Biochemistry & Molecular Biology
Anna Simonova, Veronika Romanska, Barbora Benoni, Karel Skubnik, Lenka Smerdova, Michaela Prochazkova, Kristina Spustova, Ondrej Moravcik, Lenka Gahurova, Jan Paces, Pavel Plevka, Hana Cahova
Summary: The Picornavirales include viruses that infect vertebrates, insects, and plants, and their RNA particles contain various methylated nucleosides, primarily in tRNA molecules, which are present in the form of 3' and 5' fragments and are selectively packaged.
Article
Virology
Tibor Fuzik, Jana Moravcova, Sergei Kalynych, Pavel Plevka
Summary: Globally distributed enterovirus 70 (EV70) causes local outbreaks of acute hemorrhagic conjunctivitis. The structure of EV70, a human pathogen causing severe eye disease, has been determined using cryo-electron microscopy. The antiviral compounds WIN51711 and pleconaril target the partially collapsed hydrophobic pocket in the EV70 virion, preventing virus infection by stabilizing EV70 particles. This knowledge enables the development of therapeutics against EV70.
JOURNAL OF VIROLOGY
(2022)
Article
Virology
Michaela Prochazkova, Tibor Fuzik, Danyil Grybchuk, Vyacheslav Yurchenko, Pavel Plevka
Summary: This study presents the structure of Leishmania RNA virus 1 (LRV1), revealing that its capsid is built from dimers and exhibits icosahedral symmetry. Additionally, the location of the RNA polymerase within the viral particle varies.
Article
Multidisciplinary Sciences
Marta Siborova, Tibor Fuzik, Michaela Prochazkova, Jiri Novacek, Martin Benesik, Anders S. Nilsson, Pavel Plevka
Summary: The authors demonstrate that E. coli phage SU10 undergoes conformational changes in nozzle proteins and tail fibers after cell binding, forming a nozzle that allows the delivery of phage DNA into bacterial cytoplasm.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Dominik Hrebik, Maria Gondova, Lucie Valentova, Tibor Fuzik, Antonin Pridal, Jiri Novacek, Pavel Plevka
Summary: This article introduces a method of coating cryo-EM grids with negatively charged polyelectrolytes to reduce macromolecular aggregation and improve their distribution. This method not only enables the successful determination of high-resolution structures on conventional grids, but also reduces the negative effects of macromolecules contacting the grid support and blotting paper.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Biology
Danyil Grybchuk, Michaela Prochazkova, Tibor Fuzik, Aleksandras Konovalovas, Saulius Serva, Vyacheslav Yurchenko, Pavel Plevka
Summary: This study determined the structure and assembly mechanism of the L-BC virus using cryo-electron microscopy. The L-BC capsid has an icosahedral symmetry and the capsid proteins are stabilized by domain swapping. Additionally, some L-BC virus particles were found to be open and lacked one decamer of capsid proteins.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biology
Carina R. Buettner, Radovan Spurny, Tibor Fuezik, Pavel Plevka
Summary: CV-A6 has become the primary causative agent of hand, foot, and mouth disease worldwide. Unlike other enteroviruses, CV-A6 uses altered particles to infect cells. The structure of CV-A6 virion is similar to other enteroviruses and plays a crucial role in infection.
COMMUNICATIONS BIOLOGY
(2022)
Review
Ophthalmology
J. Bernard Heymann, Camasamudram Vijayasarathy, Robert N. Fariss, Paul A. Sieving
Summary: Retinoschisin (RS1) is crucial for maintaining retinal integrity, but mutations in RS1 cause X-linked retinoschisis (XLRS) and vision loss. The formation of cysts and schisis in the retina disrupts synaptic transmission. Gene augmentation therapy using AAV vectors is being evaluated as a potential treatment for XLRS. Understanding the secretion and molecular function of RS1 is essential for improving therapeutic strategies.
PROGRESS IN RETINAL AND EYE RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
J. Bernard Heymann
Summary: In cryoEM, it is essential to consider the Ewald sphere/focus gradient and its implications for high resolution and handedness information recovery. Different approaches have been proposed, but the correct one remains uncertain. The traditional projection approximation breaks down at high acceleration voltages, but correct reconstruction along the Ewald spheres can avoid its limitations and reach resolutions to the Nyquist frequency.
JOURNAL OF STRUCTURAL BIOLOGY-X
(2023)
Article
Cell Biology
Andrea Eisenreichova, Martin Klima, Midhun Mohan Anila, Alena Koukalova, Jana Humpolickova, Bartosz Rozycki, Evzen Boura
Summary: ORPs are lipid-transport proteins that play a role in transferring lipids between intracellular membranes. In this study, the crystal structure of the ORP8 lipid transport domain (ORD8) was solved, revealing a β-barrel fold. The structure of ORD8 and its lipid-binding site were analyzed using computer simulations and comparative experiments. The findings provide insights into the structure and lipid transport mechanisms of ORD8, as well as potential targets for inhibitor design.
Article
Biology
J. Bernard Heymann
Summary: Bsoft is a software package developed for processing electron micrographs. It has over 150 programs for manipulating and understanding images. The primary aim is to provide powerful capabilities for processing large numbers of images.
