Article
Biochemical Research Methods
Daniel Ruediger, Lars Pelz, Marc D. Hein, Sascha Y. Kupke, Udo Reichl
Summary: Cell culture-derived defective interfering particles (DIPs) have shown potential as antiviral agents as they can inhibit the production of standard virus (STV) during influenza A virus (IAV) infection. High concentrations of DIPs can completely shut down STV propagation, and a mathematical model developed in this study can accurately predict optimal dosing ratios for DIPs to suppress STV infections. This research provides insight into the interplay between STVs and DIPs during co-infection, which can be important for vaccine manufacturing and therapeutic DIP production.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Olga A. Nikolaitchik, Saiful Islam, Jonathan P. Kitzrow, Alice Duchon, Zetao Cheng, Yang Liu, Jonathan M. O. Rawson, Wei Shao, Maria Nikolaitchik, Mary F. Kearney, Frank Maldarelli, Karin Musier-Forsyth, Vinay K. Pathak, Wei-Shau Hu, Malcolm Martin
Summary: HIV-1 uses host RNA polymerase II (Pol II) to transcribe its genome and employs multiple transcription start sites (TSS). Selection of TSS is regulated by specific sequences near the TATA box and R. Mutants expressing specific RNA transcripts with different numbers of guanosines at the 5'-end exhibit replication defects compared to the wild-type. These findings highlight the importance of TSS selection for HIV-1 replication fitness and genome integrity during reverse transcription.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Jack P. K. Bravo, Kira Bartnik, Luca Venditti, Julia Acker, Emma H. Gail, Alice Colyer, Chen Davidovich, Don C. Lamb, Roman Tuma, Antonio N. Calabrese, Alexander Borodavka
Summary: It was found that NSP2 autoregulates its chaperone activity through its C-terminal region, promoting RNA-RNA interactions. Additionally, structural proteomics data revealed that the CTR does not directly interact with RNA, but accelerates RNA release from NSP2.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
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
Verena Hurst, Kiran Challa, Felix Jonas, Romain Forey, Ragna Sack, Jan Seebacher, Christoph D. Schmid, Naama Barkai, Kenji Shimada, Susan M. Gasser, Jerome Poli
Summary: In budding yeast, the Mec1 kinase plays a crucial role in evicting RNAPII and RNAPIII to facilitate replication fork progression. The non-phosphorylatable mec1-S1991A mutant hinders replication fork progression and compromises survival on hydroxyurea. Disrupting chromatin-bound RNAPII can alleviate the lethality in mec1-S1991A mutants.
Article
Microbiology
Megan R. Edwards, Olivia A. Vogel, Hiroyuki Mori, Robert A. Davey, Christopher F. Basler
Summary: This study investigates the role of VP30 in Marburg virus transcription. It demonstrates that VP30 is essential for the transcription reinitiation at the GP gene start site, resulting in the loss of expression of GP and downstream genes when VP30 is absent. The study also identifies a region at the GP gene start site and a zinc binding motif in VP30 as critical factors for transcription reinitiation. These findings enhance our understanding of Marburg virus gene expression regulation.
Review
Virology
Guido Papa, Alexander Borodavka, Ulrich Desselberger
Summary: Viroplasms are membraneless structures assembled in rotavirus-infected cells intricately involved in viral replication, driven by non-structural proteins NSP2 and NSP5 through liquid-liquid phase separation, facilitating molecular interactions and equimolar packaging of RNA transcripts. Future research should focus on the complex molecular composition of viroplasms to support distinct stages of virion assembly throughout the replication cycle.
Article
Biochemistry & Molecular Biology
Congcong Cao, Aolin Li, Chaojie Xu, Baorui Wu, Jun Liu, Yuchen Liu
Summary: The CRISPR/dCasRx-SINEB2 technology has been developed to target translation of mRNAs using lncRNA functional elements. It has shown effective and adaptable results in increasing the expression of various proteins with minimal off-target effects. Additionally, it can prevent cancer cell proliferation and migration by targeting mRNA translation of antitumor proteins. This study provides an innovative protein enhancement method with multiple applications in biopharmaceutical production and cancer research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Daniel J. Emerson, Peiyao A. Zhao, Ashley L. Cook, R. Jordan Barnett, Kyle N. Klein, Dalila Saulebekova, Chunmin Ge, Linda Zhou, Zoltan Simandi, Miriam K. Minsk, Katelyn R. Titus, Weitao Wang, Wanfeng Gong, Di Zhang, Liyan Yang, Sergey V. Venev, Johan H. Gibcus, Hongbo Yang, Takayo Sasaki, Masato T. Kanemaki, Feng Yue, Job Dekker, Chun-Long Chen, David M. Gilbert, Jennifer E. Phillips-Cremins
Summary: This article reveals the determinants of replication origin positioning in the human genome. The study found that topologically associating domains and loops play crucial roles in the localization of replication initiation zones. By disrupting cohesin-mediated loop extrusion, the positioning of replication origins can be altered. These findings contribute to a better understanding of the mechanism of DNA replication.
Review
Virology
Rui-Zhu Shi, Yuan-Qing Pan, Li Xing
Summary: RNA helicase A (RHA) is a DExH-box helicase that unwinds double-stranded RNA and plays a crucial role in RNA metabolism, especially in the replication of RNA viruses.
Article
Biochemistry & Molecular Biology
Mahamaya Biswal, Stephen Diggs, Duo Xu, Nelli Khudaverdyan, Jiuwei Lu, Jian Fang, Gregor Blaha, Rong Hai, Jikui Song
Summary: The replication of the coronavirus genome is regulated by a complex of non-structural proteins, with NSP7 and NSP8 playing key roles. The crystal structure of the NSP7-NSP8 complex reveals a heterotetrameric form, and mutations in interface I and II affect the stability and activity of the complex. This study provides insights into the dynamic assembly of NSP7 and NSP8 in regulating viral genome replication, with implications for antiviral drug development.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Hyeonji Lee, Seong-Yeob You, Dong Wook Han, Hyeonwoo La, Chanhyeok Park, Seonho Yoo, Kiye Kang, Min-Hee Kang, Youngsok Choi, Kwonho Hong
Summary: The study reveals that R-loop dynamics are associated with the regulation of zygotic genome activation (ZGA) in mice, especially in the minor ZGA stage. R-loop formation and level changes may modulate gene transcription and DNA replication.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Vanessa Meier-Stephenson, Maulik D. Badmalia, Tyler Mrozowich, Keith C. K. Lau, Sarah K. Schultz, Darren L. Gemmill, Carla Osiowy, Guido van Marle, Carla S. Coffin, Trushar R. Patel
Summary: A unique G-quadruplex structure in the pre-core promoter region of the HBV genome has been discovered in this study, which may lead to the identification of novel anti-HBV cccDNA targets and enhance the understanding of the HBV pre-core region.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Oncology
Jessica Marinello, Andrea Arleo, Marco Russo, Maria Delcuratolo, Francesca Ciccarelli, Yves Pommier, Giovanni Capranico
Summary: This study used molecular, genetic, and bioinformatic approaches to investigate the mechanism of micronuclei formation induced by TOP1 poisons in different cancer cells. The results revealed an immune signaling mechanism activated by TOP1 poisons, which is often impaired in human small-cell lung cancer tumors.
BRITISH JOURNAL OF CANCER
(2022)
Article
Virology
Reimar Johne, Simon H. Tausch, Rainer G. Ulrich, Katja Schilling-Loeffler
Summary: Rotaviruses are responsible for diarrhea in humans and animals. A new strain, RVK, was identified in common shrews in Germany and was found to be a separate species with low sequence identity to other rotavirus reference strains. Phylogenetic analysis showed that RVK and RVC formed a common branch within the RVA-like phylogenetic clade. Comparison of nucleotide sequences of other RVK strains from common shrews in Germany indicated high sequence variability within the putative species. RVK represents a novel rotavirus species closely related to RVC.
Article
Virology
Nayeli Aguilar-Hernandez, Lena Meyer, Susana Lopez, Rebecca M. DuBois, Carlos F. Arias
Summary: In this study, the researchers identified PDIA4 as a binding partner for HAstV-1 and -8 spikes, with the PDI inhibitor 16F16 strongly inhibiting infection by HAstV serotypes 1 and 8. It was also shown that RNA interference of PDIA4 expression selectively blocked HAstV-8 infectivity. These findings suggest that PDIA4 is essential for the uncoating of the viral genome during the cell entry process of HAstV-1 and -8.
Article
Multidisciplinary Sciences
Blanca Taboada, Patricia Moran, Angelica Serrano-Vazquez, Pavel Isa, Liliana Rojas-Velazquez, Horacio Perez-Juarez, Susana Lopez, Javier Torres, Cecilia Ximenez, Carlos F. Arias
Summary: This study determined the diversity and dynamics of the gut virome of infants during the first year of life, revealing a rich variety of viruses and their continuous presence throughout infancy.
Article
Virology
Lena Ricemeyer, Nayeli Aguilar-Hernandez, Tomas Lopez, Rafaela Espinosa, Sarah Lanning, Santanu Mukherjee, Carolina Cuellar, Susana Lopez, Carlos F. Arias, Rebecca M. DuBois
Summary: Human astrovirus is a major cause of viral gastroenteritis worldwide, and this study provides a basis for developing an effective vaccine to prevent and treat human astrovirus infection by understanding how antibodies block the virus at the molecular level.
JOURNAL OF VIROLOGY
(2022)
Article
Virology
Jing-Hsiung James Ou, Richard J. Kuhn, Susana Lopez, Charles M. Rice
JOURNAL OF VIROLOGY
(2022)
Article
Virology
Jose L. Martinez, Catherine Eichwald, Elisabeth M. Schraner, Susana Lopez, Carlos F. Arias
Summary: Lipid metabolism is crucial for rotavirus replication, not only in viroplasm assembly but also in maintaining infectious virus production and membrane synthesis.
Article
Virology
Catalina Aguilera-Flores, Tomas Lopez, Fernando Zamudio, Carlos Sandoval-Jaime, Edmundo Perez, Susana Lopez, Rebecca DuBois, Carlos F. Arias
Summary: Human astrovirus VA1, associated with neurological disease in immunocompromised patients, can replicate in cell culture without trypsin. The capsid precursor protein of astrovirus VA1 undergoes intracellular cleavage to form mature infectious particles, composed of two polypeptides, VP33 and VP38. These studies provide insight into astrovirus VA1 cell entry and replication.
JOURNAL OF VIROLOGY
(2022)
Article
Virology
Carlos Baez-Navarro, Ivan R. Quevedo, Susana Lopez, Carlos F. Arias, Pavel Isa
Summary: Astroviruses are a significant cause of diarrhea, especially in vulnerable populations like children. Recent research has found these viruses in organs outside the intestines, leading to unexpected clinical diseases. This study discovered that human astrovirus strain Yuc8 is associated with extracellular vesicles, potentially during or after their release from cells. This association increases the infectivity of the virus and protects it from neutralization by antibodies, indicating that extracellular vesicles could be a novel pathway for astrovirus dissemination.
JOURNAL OF VIROLOGY
(2022)
Article
Virology
Joaquin Moreno-Contreras, Liliana Sanchez-Tacuba, Carlos F. Arias, Susana Lopez
Summary: Rotaviruses have a genome composed of 11 segments of double-stranded RNA. A study found that there were similar proportions of capped and noncapped viral RNAs in rotavirus-infected cells and viral particles.
JOURNAL OF VIROLOGY
(2022)
Article
Veterinary Sciences
Pavel Isa, Luis Felipe Paulin, Jesus Hernandez, Maricela Montalvo-Corral, Susana Lopez, Carlos F. Arias
Summary: Genetic characterization of field samples from Mexican wetlands revealed the genomics and virus circulation of influenza A viruses, highlighting the importance of further studies in this region.
VETERINARIA MEXICO
(2022)
Article
Virology
Matthew Ykema, Kai Ye, Meng Xun, Justin Harper, Miguel A. A. Betancourt-Solis, Carlos F. F. Arias, James A. A. McNew, Yizhi Jane Tao
Summary: The human astrovirus (HAstV) is a common cause of gastroenteritis, and its cell entry mechanism and membrane penetration activity have been investigated in this study. It was found that the capsid protein of HAstV has a trypsin-dependent lipid disruption activity, essential for virus infectivity. This discovery provides valuable insights into HAstV pathogenesis and offers a potential target for therapeutics.
JOURNAL OF VIROLOGY
(2023)
Article
Infectious Diseases
Adriana Becerra, Pavel Isa, Ana Lorena Gutierrez-Escolano, Federico Raul Velazquez, Javier Torres, Carlos Federico Arias, Teresa Estrada-Garcia
Summary: Diarrhoeal illness is a major cause of morbidity/mortality in children from less-developed regions. This study investigated the gut microbiome of children with diarrhoea, focusing on the virome. The results showed inter-individual viral species composition in the stools of diarrhoeal children, with bacteriophages being the most abundant group. Children under 2 years of age had significantly higher viral richness compared to older children, primarily due to bacteriophages and diarrheagenic-viral species. Stool samples preserved at -70 degrees C can be successfully used for microbiome studies.
JOURNAL OF INFECTION IN DEVELOPING COUNTRIES
(2023)
Article
Microbiology
Xaira Rivera-Gutierrez, Patricia Moran, Blanca Taboada, Angelica Serrano-Vazquez, Pavel Isa, Liliana Rojas-Velazquez, Horacio Perez-Juarez, Susana Lopez, Javier Torres, Cecilia Ximenez, Carlos F. Arias
Summary: A metagenomic study in a semirural community in Mexico revealed a high prevalence of norovirus and sapovirus in infants' fecal samples, with no symptomatic cases observed. The study highlights the importance of metagenomic analysis in understanding the diversity and prevalence of gastrointestinal viruses in early life.
MICROBIOLOGY SPECTRUM
(2022)