Article
Virology
Sho Miyamoto, Yukiko Muramoto, Keiko Shindo, Yoko Fujita-Fujiharu, Takeshi Morikawa, Ryoma Tamura, Jamie L. Gilmore, Masahiro Nakano, Takeshi Noda
Summary: This study provides evidence that the packaging signals between HA vRNA and PB2 vRNA are important for the selective genome packaging of the influenza A virus. Understanding the packaging mechanism of the influenza virus genome is crucial for developing strategies to combat influenza.
JOURNAL OF VIROLOGY
(2022)
Article
Virology
Qingxia Gao, Cha Yang, Caiyue Ren, Shishuo Zhang, Xiaochen Gao, Meilin Jin, Huanchun Chen, Wenjun Ma, Hongbo Zhou
Summary: The study reveals that eEF1D negatively regulates IAV replication by inhibiting the nuclear import of RNP subunits, uncovering a novel role of eEF1D in IAV replication and providing new insights into the mechanisms of nuclear import of vRNP proteins.
JOURNAL OF VIROLOGY
(2021)
Article
Microbiology
Fadi G. Alnaji, William K. Reiser, Joel Rivera-Cardona, Aartjan J. W. te Velthuis, Christopher B. Brooke
Summary: Deletion-containing viral genomes (DelVGs) are commonly produced during influenza A virus infection, influenced by specific molecular mechanisms such as direct sequence repeats and base enrichment. DelVGs face a significant bottleneck during genome packaging, with larger DelVGs showing signs of enrichment in packaged virions, suggesting size as an important determinant of packaging efficiency.
Article
Virology
Justine Girard, Celia Jakob, Lina Kathrin Toews, Jonas Fuchs, Anne Pohlmann, Kati Franzke, Larissa Kolesnikova, Csaba Jeney, Martin Beer, Patrick Bron, Martin Schwemmle, Hardin Bolte
Summary: This study reveals the phenomenon of vRNA loss and replacement by host RNA caused by mutations in the influenza virus. The disruption of two packaging signals in a model H7N7 influenza A virus leads to a mixture of virions with different vRNA content, including empty virions, virions with one to four vRNAs, and virions with octameric complexes composed of vRNA duplicates. These results suggest that the assembly of complete octameric complexes proceeds through a series of defined vRNA sub-complexes and that virions can bud without incorporating complete octameric complexes.
JOURNAL OF VIROLOGY
(2023)
Article
Biochemistry & Molecular Biology
Young Hyun Park, Seung Je Woo, Kelly Chungu, Su Bin Lee, Ji Hyeon Shim, Hong Jo Lee, Iktae Kim, Deivendran Rengaraj, Chang-Seon Song, Jeong-Yong Suh, Jeong Mook Lim, Jae Yong Han
Summary: The study found that the 27 residues of human ANP32A play a crucial role in AIV vPol activity, while ANP32C cannot support this activity. Asp149 and Asp152 are involved in supporting vPol activity, and mutations in these residues decreases the interaction between ANP32A and vPol.
Article
Biochemistry & Molecular Biology
Hanjun Zhao, Chuyuan Zhang, Hoiyan Lam, Xinjie Meng, Zheng Peng, Man Lung Yeung, Jasper Fuk-Woo Chan, Kelvin Kai-Wang To, Kwok-Yung Yuen
Summary: It has been found that the specially designed SARS-CoV-2 and influenza defective interfering genes (DIGs) can significantly inhibit the replication of corresponding viruses. Through the gene delivery vector TAT2-P1&LAH4, DIGs can be effectively delivered in the lungs to inhibit the replication of SARS-CoV-2 variants and influenza virus.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Virology
Periyasamy Vijayakumar, Ashwin Ashok Raut, Santhalembi Chingtham, Harshad Murugkar, Diwakar D. Kulkarni, Richa Sood, Vijendra Pal Singh, Anamika Mishra
Summary: Proteomic analysis of chicken lung infected with HPAI H5N1 virus identified signaling pathways and proteins associated with disease pathogenesis, including Toll-like receptors, RLRs, NLRs, and JAK-STAT signaling. Activation of these pathways may lead to cytokine storm effect and severity of HPAI H5N1 infection in chickens.
ARCHIVES OF VIROLOGY
(2022)
Review
Virology
Andrea Modrego, Diego Carlero, Rocio Arranz, Jaime Martin-Benito
Summary: Single-stranded RNA viruses (ssRNAv) pose a major threat to human health due to their biological diversity and adaptability to different hosts. Understanding the mechanisms of viral proliferation is crucial to address the challenges they bring. Ribonucleoproteins (RNPs), which carry out viral transcription and replication, play a key role in these processes. Cryogenic electron microscopy (cryoEM) has revolutionized the study of RNP and nucleocapsid structures in lipid-enveloped ssRNAv, providing valuable insights into their organization and functional implications.
Article
Microbiology
Ekaterina Stepanova, Elena Krutikova, Pei-Fong Wong, Victoria Matyushenko, Ekaterina Bazhenova, Irina Isakova-Sivak, Larisa Rudenko
Summary: This study developed an experimental chimeric influenza vaccine that efficiently induced immune responses against both influenza A and B viruses, providing comprehensive protection. However, further optimization may be needed due to mismatch of T-cell epitopes.
Article
Virology
Klaudia Chrzastek, Karen Segovia, Mia Torchetti, Mary Lee Killian, Mary Pantin-Jackwood, Darrell R. Kapczynski
Summary: The study found that H7N9 avian influenza viruses could readily spread between avian species in the southeastern United States, with domestic duck-origin H7N9 low pathogenic virus replicating and transmitting in chickens, showing possible virus adaptation in the new host. Mutations were observed in viruses from both chickens and clinical samples from the outbreak, contributing to the virus spread and evolution in the region.
Article
Medicine, Research & Experimental
Rute M. Pinto, Samantha Lycett, Eleanor Gaunt, Paul Digard
Summary: Influenza A virus encodes a core proteome of 10 major polypeptides, with accessory proteins expressed at lower levels through noncanonical transcriptional and translational events. The expression and activity of these accessory proteins vary between virus strains and can affect virulence and transmission in vivo, despite often being nonessential for virus replication in cell culture.
COLD SPRING HARBOR PERSPECTIVES IN MEDICINE
(2021)
Article
Multidisciplinary Sciences
Aakash Basu, Dmitriy G. Bobrovnikov, Zan Qureshi, Tunc Kayikcioglu, Thuy T. M. Ngo, Anand Ranjan, Sebastian Eustermann, Basilio Cieza, Michael T. Morgan, Miroslav Hejna, H. Tomas Rube, Karl-Peter Hopfner, Cynthia Wolberger, Jun S. Song, Taekjip Ha
Summary: Mechanical deformations of DNA, such as bending, are common and have been implicated in various cellular functions. A high-throughput assay called 'loop-seq' was developed to measure DNA looping propensity and intrinsic cyclizabilities of DNA fragments across different genomic regions. The study found regions of low bendability in nucleosome-depleted regions, which affects nucleosome sliding and gene transcription. Overall, the study shows that local DNA mechanics have broad functional implications on chromatin organization and transcription.
Article
Multidisciplinary Sciences
Yanbo Wang, John Mallon, Haobo Wang, Digvijay Singh, Myung Hyun Jo, Boyang Hua, Scott Bailey, Taekjip Ha
Summary: The research discovered that the HNH domain of CRISPR-Cas9 exhibits high flexibility post-DNA cleavage, exposing a 3' flap after cleavage of the non-target strand, potentially interacting with the DNA repair machinery. These findings reveal the regulatory role of DNA cleavage activity on Cas9 conformation and suggest potential applications in biotechnology.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biophysics
Tapas Paul, Taekjip Ha, Sua Myong
Summary: This study presents strategies for regenerating PEG surfaces for multiple rounds of experiments, including washing out bound proteins, reannealing double-stranded DNA, and stripping off NeutrAvidin to regenerate the biotin-PEG layer. These methods enhance the efficiency of single-molecule experiments.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Myung Hyun Jo, Byoung Choul Kim, Keewon Sung, Reynold A. Panettieri, Steven S. An, Jian Liu, Taekjip Ha
Summary: The study found that cell shortening and focal adhesion disassembly occurred after an increase in intracellular calcium levels induced by histamine. A mathematical model predicted that stabilizing focal adhesions hinders cell shortening, while focal adhesion disruption is preceded by strengthening due to actomyosin-activated tension.
Article
Multidisciplinary Sciences
Nilmani Singh, Adriana Reyes-Ordonez, Michael A. Compagnone, Jesus F. Moreno Castillo, Benjamin J. Leslie, Taekjip Ha, Jie Chen
Summary: This study explores the specific interactions of human PH domain-containing proteins with PIPs and reveals unexpected lipid-binding specificity among these proteins. By analyzing the structural requirements and functional relevance of PIP binding, as well as using a prediction algorithm, the researchers demonstrate widespread PIP binding among human PH domains.
NATURE COMMUNICATIONS
(2021)
Review
Biochemistry & Molecular Biology
Taekjip Ha, Christian Kaiser, Sua Myong, Bin Wu, Jie Xiao
Summary: Due to their unique abilities to manipulate, label, and image individual molecules, single-molecule techniques provide unprecedented access to elementary biological processes.
Article
Multidisciplinary Sciences
Li Dai, Digvijay Singh, Suoang Lu, Vishal Kottadiel, Reza Vafabakhsh, Marthandan Mahalingam, Yann R. Chemla, Taekjip Ha, Venigalla B. Rao
Summary: The study revealed that the active bacteriophage T4 DNA packaging motor is a pentamer and is able to tolerate inactive subunits. However, motors with inactive subunits showed decreased DNA engagements, higher failure rates in encapsidation, reduced packaging velocity, and increased pausing. This suggests that strict coordination among motor subunits is not crucial for the function of packaging motors.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Hossein Moghimianavval, Chintan Patel, Sonisilpa Mohapatra, Sung-Won Hwang, Tunc Kayikcioglu, Yashar Bashirzadeh, Allen P. Liu, Taekjip Ha
Summary: InterSpy is introduced as a synthetic biology tool for engineering membrane-membrane interfaces. It allows tracking and reconstitution of functional fluorescent protein between apposing synthetic or cell membranes, demonstrating the potential for designing non-native cellular communication pathways and creating synthetic tissues. The technology is tested using a mammalian cell-free expression system and shows promising results.
Article
Biology
Claudia C. Carcamo, Matthew F. Poyton, Anand Ranjan, Giho Park, Robert K. Louder, Xinyu A. Feng, Jee Min Kim, Thuc Dzu, Carl Wu, Taekjip Ha
Summary: This study characterizes the 1D scanning properties of SWR1, a chromatin remodeler, and reveals the impacts of various factors on its scanning process. By directly observing SWR1 diffusion on DNA, the study demonstrates that ATP and a DNA-binding subunit play important roles in the overall diffusive behavior of the complex. The findings provide valuable insights into the role of SWR1 in chromatin remodeling.
Article
Cell Biology
Roger S. Zou, Alberto Marin-Gonzalez, Yang Liu, Hans B. Liu, Leo Shen, Rachel K. Dveirin, Jay X. J. Luo, Reza Kalhor, Taekjip Ha
Summary: Here, we propose an approach that combines CRISPR system with high-throughput sequencing to target hundreds of epigenetically diverse endogenous genomic sites simultaneously, measuring Cas9 dynamics and cellular responses. The use of multi-target guide RNAs (mgRNAs) enables massive multiplexing of CRISPR, providing insights into Cas9 binding, cleavage, and cellular response to DNA damage.
NATURE CELL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Momcilo Gavrilov, Joshua Y. C. Yang, Roger S. Zou, Wen Ma, Chun-Ying Lee, Sonisilpa Mohapatra, Jimin Kang, Ting-Wei Liao, Sua Myong, Taekjip Ha
Summary: Polymerase Chain Reaction (PCR) is a crucial method in molecular diagnostics and life sciences. This study introduces a new method, SHARP (SSB-Helicase Assisted Rapid PCR), which uses an engineered helicase and single-stranded DNA binding protein (SSB) to replace the heating step of PCR. The new method allows the isothermal amplification of DNA fragments up to 6000 base pairs.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Ikenna C. Okafor, Taekjip Ha
Summary: CRISPR Cas9 is an RNA-guided endonuclease that is a part of bacterial adaptive immune system. By developing a single molecule FRET assay, the study investigated the conformational changes of sgRNA and the binding of Cas9 to sgRNA, providing insights into the assembly dynamics of Cas9 RNA ribonucleoprotein complex. This research could contribute to the rational design of sgRNAs and improve the editing outcomes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Aakash Basu, Dmitriy G. Bobrovnikov, Basilio Cieza, Juan Pablo Arcon, Zan Qureshi, Modesto Orozco, Taekjip Ha
Summary: In this study, we comprehensively characterized the mechanical code of DNA using high-throughput experimental methods and developed a physical model to describe the sequence and methylation dependence of DNA deformation. Our measurements and model validations demonstrated that sequence and epigenetic modifications can encode regulatory information in diverse contexts.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Yanbo Wang, W. Taylor Cottle, Haobo Wang, Momcilo Gavrilov, Roger S. Zou, Minh-Tam Pham, Srinivasan Yegnasubramanian, Scott Bailey, Taekjip Ha
Summary: We describe a method called sgGOLDFISH for direct visualization of point mutations in situ, which can differentiate wild-type and mutant sequences with single-nucleotide sensitivity. This method has potential applications in studying genetic diseases and nuclear biology.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Aman Y. Husbands, Antje Feller, Vasudha Aggarwal, Courtney E. Dresden, Ashton S. Holub, Taekjip Ha, Marja C. P. Timmermans
Summary: The START domain of the HD-ZIPIII transcription factors plays a crucial role in promoting homodimerization and increasing transcriptional potency, while also binding to phospholipids. This discovery resolves a long-standing mystery in plant development and highlights the regulatory potential of this evolutionary module.