Article
Biochemistry & Molecular Biology
Jian Xie, Daniel DiMaio
Summary: Historically, genetic analysis of mammalian cells involved isolating randomly arising mutant cell lines to identify the mutant gene responsible for altered properties. Recent advancements in somatic cell genetics have introduced functional genomics screens which systematically perturb the expression of every protein-coding gene to determine the resulting phenotype. A novel functional genomics screening strategy has been outlined where libraries of artificial transmembrane proteins, called traptamers, are expressed to select rare cells with desired phenotypes that can help dissect complex biological processes. By using this new strategy, insights into the process of how human papillomaviruses enter cells have been gained.
Article
Biochemistry & Molecular Biology
Wenli Bai, Melissa L. Wells, Wi S. Lai, Stephanie N. Hicks, Adam B. Burkholder, Lalith Perera, Alan R. Kimmel, Perry J. Blackshear
Summary: Post-transcriptional processes mediated by mRNA-binding proteins are critical control points in gene expression. Dictyostelium discoideum may regulate expression of functionally related proteins through a single RNA-binding protein, TtpA, forming an "RNA regulon".
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Lauriane Velot, Frederic Lessard, Felix-Antoine Berube-Simard, Christophe Tav, Bertrand Neveu, Valentine Teyssier, Imene Boudaoud, Ugo Dionne, Noemie Lavoie, Steve Bilodeau, Frederic Pouliot, Nicolas Bisson
Summary: Prostate cancer is a frequently diagnosed cancer in men, driven by the androgen receptor (AR) which is activated by androgens. By utilizing proximity labeling proteomics, researchers identified an expanded AR signaling network with newly discovered AR-associated proteins involved in key biological processes like DNA metabolism and RNA processing.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Biotechnology & Applied Microbiology
Hyunjun Ko, Minsik Kang, Mi-Jin Kim, Jiyeon Yi, Jin Kang, Jung-Hoon Bae, Jung-Hoon Sohn, Bong Hyun Sung
Summary: A novel fusion tag CBM66 was developed for improving soluble protein expression in E. coli, showing better performance compared to commercial tags. This tag maintains protein bioactivity and facilitates the easy production of high-value proteins.
MICROBIAL CELL FACTORIES
(2021)
Article
Chemistry, Medicinal
Christoph Oehlknecht, Sonja Katz, Christina Kroess, Bernhard Sprenger, Petra Engele, Rainer Schneider, Chris Oostenbrink
Summary: The article introduces an efficient method for calculating protein binding free energies by combining the one-step perturbation and the third-power fitting approach. Experimental in silico saturation mutagenesis confirms the method's high accuracy in predicting relative free energies of amino acid mutations.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Plant Sciences
Ava N. Medberry, Ashish Srivastava, Alfredo Diaz-Lara, Maher Al Rwahnih, Dan E. V. Villamor, Ioannis E. Tzanetakis
Summary: Strawberry (Fragaria x ananassa) is a global important berry crop that is constantly threatened by viruses. A novel virus called strawberry virus 3 (StrV-3) was discovered, which does not show significant similarity with known rhabdoviruses, suggesting the establishment of a new genus. A triplex reverse-transcription PCR test was developed for detecting the virus in the National Clonal Germplasm Repository Fragaria collection. A CRISPR-Cas-based protocol was also developed for detecting the virus in candidate G1 plants. The potential of the strawberry aphid (Chaetosiphon fragaefolii) as a vector of the virus was evaluated, but with no success. This work enhances our knowledge of the Rhabdoviridae family and aids in the goal of releasing virus-free plant materials.
Article
Chemistry, Multidisciplinary
Precious Jolugbo, Thomas Willott, Wei-Hsiang Lin, Thomas Maisey, Dermott O'Callaghan, Mark A. Green, David G. Jayne, M. Ibrahim Khot
Summary: We developed a CEA-conjugated polymer nanoparticle probe for targeting CEA-expressing CRC cells in vitro. Its efficacy was evaluated in 2D and 3D cultures of LS174T, LoVo, and HT29 CRC cell lines. CPN510-CEA-Af demonstrated higher fluorescent signal intensity than unconjugated particles, indicating its potential as a probe for image-guided colorectal cancer surgery.
Article
Cell Biology
Dongyun Yang, Tobias D. Strobel, Julia Bulkescher, Claudia Tessmer, Ilse Hofmann, Felix Hoppe-Seyler, Karin Hoppe-Seyler
Summary: The FAM57A gene has an important regulatory role in cervical cancer cells, with its protein expression being influenced by cell density, hypoxia, and inhibition of HPV gene expression. Inhibition of FAM57A leads to significant suppression of proliferation and migration in cervical cancer cells.
Article
Biochemistry & Molecular Biology
Xiaoyu Sun, Gregory M. Alushin
Summary: This article discusses the importance of the actin cytoskeleton and explains how actin filaments can function as molecular force sensors. It introduces two classes of proteins that interpret forces applied to actin filaments, speculating that these proteins are suitable for coordinating cytoskeletal force-feedback and mechanical signaling.
Article
Gastroenterology & Hepatology
Komal Ramani, Aaron E. Robinson, Joshua Berlind, Wei Fan, Aushinie Abeynayake, Aleksandra Binek, Lucia Barbier-Torres, Mazen Noureddin, Nicholas N. Nissen, Zehra Yildirim, Ebru Erbay, Jose M. Mato, Jennifer E. Van Eyk, Shelly C. Lu
Summary: Our study identified a SAMe-sensitive mechanism of LARP1 phosphorylation that may be involved in the progression from NASH to HCC.
Article
Microbiology
Catherine A. Klancher, George Minasov, Ram Podicheti, Douglas B. Rusch, Triana N. Dalia, Karla J. F. Satchell, Matthew B. Neiditch, Ankur B. Dalia
Summary: The text highlights the significance of sequence-specific DNA-binding domains in all domains of life and presents a novel cryptic variant of these domains discovered in a bacterial protein. The study reveals a new structural domain that contributes to understanding cellular functions and gene expression regulation.
Article
Biochemistry & Molecular Biology
Xuanwei Mei, Guanchen Liu, Jingjing Shen, Guangning Chen, Yuying Zhang, Changhu Xue, Yaoguang Chang
Summary: A new carbohydrate-binding module (CBM) called Fun174A-CBM was discovered, which displayed specific binding capacity to sulfated fucan. Fun174A-CBM belongs to a novel CBM family and shares no significant sequence similarity with any identified CBMs. This discovery would be beneficial for the investigations of sulfated fucan-binding proteins.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Multidisciplinary Sciences
Liya Hu, Wilhelm Salmen, Rong Chen, Yi Zhou, Frederick Neill, James E. Crowe, Robert L. Atmar, Mary K. Estes, B. V. Venkataram Prasad
Summary: This study reveals the structure and features of human norovirus GII.4 virus-like particles using X-ray crystallography and cryo-EM. It uncovers the adaptability and stability of the capsid protein VP1, as well as its potential antigen presentation mechanism, providing valuable insights for vaccine development.
NATURE COMMUNICATIONS
(2022)
Review
Microbiology
Mansi Srivastava, Dwight Hall, Okiemute Beatrice Omoru, Hunter Mathias Gill, Sarah Smith, Sarath Chandra Janga
Summary: The emergence and rapid evolution of SARS-CoV-2 has created a global health crisis, with mutations impacting the development of therapeutics and vaccines. Understanding the interaction between host cellular components and the virus is crucial, as studying viral evolution and mutational patterns can help in combating therapeutic and vaccine evasion mechanisms.
Article
Plant Sciences
Xiang Zhou, Zheng Wang, Guangchao Cui, Zimeng Du, Yunlong Qian, Shumei Yang, Minghui Liu, Jixing Guo
Summary: In this study, the cDNA sequence of TrufOBP4 from T. rufivena is cloned and analyzed. The results show that TrufOBP4 has high binding abilities with the host plant volatiles and may play a crucial role in the integrated management of T. rufivena.
Article
Biochemistry & Molecular Biology
Simon C. Baker, Andrew S. Mason, Raphael G. Slip, Katie T. Skinner, Andrew Macdonald, Omar Masood, Reuben S. Harris, Tim R. Fenton, Manikandan Periyasamy, Simak Ali, Jennifer Southgate
Summary: Limited understanding of bladder cancer aetiopathology hampers progress in reducing incidence. This study provides missing mechanistic evidence linking reactivated BKPyV-infection to bladder cancer risk.
Article
Biology
Eleni-Anna Loundras, James Streetley, Morgan R. Herod, Rebecca Thompson, Mark Harris, David Bhella, Nicola J. Stonehouse
Summary: Replication of positive-sense RNA viruses occurs within intracellular membrane-associated compartments. The molecular interactions and dynamics within these structures are limited. This study focuses on the role of RNA-dependent RNA polymerase in replication and proposes models for its importance in this process.
COMMUNICATIONS BIOLOGY
(2022)
Article
Microbiology
Muhammad Ashir Zia, Samuel J. Dobson, David J. Rowlands, Nicola J. Stonehouse, Muhammad Salahuddin Shah, Mudasser Habib
Summary: Foot-and-mouth disease is a highly contagious viral disease that causes significant economic losses in the livestock industry. This study developed a low-cost diagnostic ELISA method that can effectively differentiate between infected and vaccinated animals, which is crucial for monitoring the effectiveness of disease control programs.
JOURNAL OF MEDICAL MICROBIOLOGY
(2022)
Article
Virology
James T. Kelly, Jessica Swanson, Joseph Newman, Elisabetta Groppelli, Nicola J. Stonehouse, Tobias J. Tuthill
Summary: pH plays a critical role in AiV uncoating and membrane interactions, and low pH conditions enhance genome exposure and membrane permeability.
JOURNAL OF VIROLOGY
(2022)
Article
Microbiology
Natalie J. Kingston, Keith Grehan, Joseph S. Snowden, Mona Shegdar, Helen Fox, Andrew J. Macadam, David J. Rowlands, Nicola J. Stonehouse
Summary: EVA71 is a medically important virus commonly associated with hand, foot, and mouth disease. Vaccination is crucial for controlling outbreaks, but the antigenic characterization of vaccine candidates is challenging due to limited tools to characterize different forms of the virus. This study developed a tool to specifically detect the native conformation of EVA71, aiding in characterizing the antigenic state of the virus.
Article
Biotechnology & Applied Microbiology
Natalie J. Kingston, Mona Shegdar, Joseph S. Snowden, Helen Fox, Elisabetta Groppelli, Andrew Macadam, David J. Rowlands, Nicola J. Stonehouse
Summary: This study selected an antigenically stable EVA71 virus population through successive heating and passage, and characterized the antigenic conversion of both virions and empty capsids. Mutations were identified across the capsid, including key sites associated with particle expansion, in the heated passaged virus. The findings suggest that the mutant sequence may serve as a valuable resource for investigating the importance of antigenic conformation in EVA71 vaccines.
JOURNAL OF GENERAL VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Morgan R. R. Herod, Joseph C. C. Ward, Andrew Tuplin, Mark Harris, Nicola J. J. Stonehouse, Christopher J. J. McCormick
Summary: Genome replication of positive strand RNA viruses requires the production of a complementary negative strand RNA, but evidence of structural RNA elements in the negative strand is limited. This study found that different viruses have different capacities for the folding of the negative strand RNA, which may explain the limited observation.
Article
Microbiology
Lee Sherry, Jessica J. Swanson, Keith Grehan, Huijun Xu, Mai Uchida, Ian M. Jones, Nicola J. Stonehouse, David J. Rowlands
Summary: The production of virus-like particles (VLPs) without viral genome has great potential for vaccine development. By using specific peptide sequences to terminate translation, natural antigenic VLPs can be produced without potential cytotoxicity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Pharmacology & Pharmacy
Oliver Prosser, Nicola J. Stonehouse, Andrew Tuplin
Summary: Based on previous analysis of the 5' region of the CHIKV genome, a panel of locked nucleic acid oligonucleotides was designed to target structured RNA replication elements. These targeted elements were shown to significantly inhibit CHIKV genome replication and production of infectious virus. This study reveals potential novel antiviral targets in the CHIKV lifecycle.
ANTIVIRAL RESEARCH
(2023)
Article
Virology
Danielle M. M. Pierce, Connor Hayward, David J. J. Rowlands, Nicola J. J. Stonehouse, Morgan R. R. Herod
Summary: FMDV is the causative agent of FMD, a significant disease in farmed animals that can result in major economic losses. The replication of this virus involves a highly coordinated processing of nonstructural proteins within membrane-associated compartments. Mutations at the 3B(3)-3C boundary increase the rate of proteolysis and affect the production of enzymatic nonstructural proteins.
JOURNAL OF VIROLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Samuel J. Dobson, Joseph C. Ward, Morgan R. Herod, David J. Rowlands, Nicola J. Stonehouse
Summary: This article describes a method using 5-ethynyl uridine to label replicating RNA, which is then purified by linking the modified base to a biotin tag using click chemistry. The selected RNA can be amplified by strand-specific quantitative PCR to investigate the effects of mutations on the synthesis of negative-sense and positive-strand RNAs.
JOURNAL OF GENERAL VIROLOGY
(2023)
Article
Virology
Yigen Li, Molly R. Patterson, Ethan L. Morgan, Christopher W. Wasson, Emma L. Ryder, Diego Barba-Moreno, James A. Scarth, Miao Wang, Andrew Macdonald
Summary: This study found that CREB1 plays an oncogenic role in HPV-positive cervical cancer and is closely related to HPV oncogenes. Inhibition of CREB1 activity can suppress cell proliferation, epithelial-mesenchymal transition, and cell migration.
JOURNAL OF MEDICAL VIROLOGY
(2023)
Article
Microbiology
Danielle M. Pierce, Frazer J. T. Buchanan, Fraser L. Macrae, Jake T. Mills, Abigail Cox, Khadijah M. Abualsaoud, Joseph C. Ward, Robert A. S. Ariens, Mark Harris, Nicola J. Stonehouse, Morgan R. Herod
Summary: The genome of hepatitis E virus does not encode a viral protease, and instead relies on the host cellular protease thrombin for polyprotein processing, which is essential for viral replication. This finding challenges the previously held belief that positive-strand RNA viruses possess an auto-proteolytic activity and suggests a model where HEV has evolved to use host proteases for replication.
Article
Virology
Jake T. Mills, Susanna C. Minogue, Joseph S. Snowden, Wynter K. C. Arden, David J. Rowlands, Nicola J. Stonehouse, Christiane E. Wobus, Morgan R. Herod
Summary: Viruses rely on receptor interactions to infect host cells. This study demonstrates how a single amino acid variation in the major capsid protein of murine norovirus can affect viral infectivity and cellular attachment. Understanding these interactions is critical for understanding viral evolution and dissemination.
JOURNAL OF VIROLOGY
(2023)