Article
Virology
Mariya Kolchenko, Anastasiya Kapytina, Nazym Kerimbek, Alexandr Pozharskiy, Gulnaz Nizamdinova, Marina Khusnitdinova, Aisha Taskuzhina, Dilyara Gritsenko
Summary: This study sequenced the genomic RNA2 of cultivated and wild raspberry in Kazakhstan and compared them with European isolates to investigate their genetic diversity and phylogenetic relationships, as well as predict their protein structure. The results revealed a new clade among the investigated isolates and differences in protein structure between alpha- and beta-structures.
Article
Agriculture, Multidisciplinary
Kadriye Caglayan, Kivilcim Ordek, Mona Gazel, Eminur Elci, Vahid Roumi, Janja Lamovsek, Irena Mavric Plesko
Summary: Raspberry bushy dwarf virus (RBDV), also known as Idaeovirus rubi, is widely present in raspberry and blackberry orchards in Turkey. A study monitored the distribution and incidence of RBDV in Turkey from 2015 to 2019 using DAS-ELISA and RT-PCR tests. The results showed low nucleotide diversity among Turkish isolates and significant variation among blackberry isolates. The study emphasizes the importance of regular monitoring and choosing appropriate detection and management strategies.
ANNALS OF APPLIED BIOLOGY
(2023)
Article
Plant Sciences
Kadriye Caglayan, Mona Gazel, Vahid Roumi, Janja Lamovsek, Aljosa Beber, Irena Mavric Plesko
Summary: This study detected the presence of Raspberry bushy dwarf virus (RBDV) in cherry samples collected from Bursa, Turkey. The nearly full genome sequences of RBDV RNA2 from two cherry trees were determined, showing high similarity to the sequences from other RBDV isolates. Phylogenetic analyses revealed host-dependent differentiation and no geographical differentiation.
JOURNAL OF PLANT PATHOLOGY
(2023)
Article
Multidisciplinary Sciences
Carl J. Schiltz, Jennifer R. Wilson, Christopher J. Hosford, Myfanwy C. Adams, Stephanie E. Preising, Stacy L. DeBlasio, Hannah J. MacLeod, Joyce Van Eck, Michelle L. Heck, Joshua S. Chappie
Summary: This study presents the structures of plant polerovirus (RTD)-R-N proteins, which can inhibit insect transmission and act as a bioinsecticide. Poleroviruses, enamoviruses, and luteoviruses are RNA viruses that cause economically important diseases in crops and are transmitted by aphids. The study provides a blueprint for controlling related viruses.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Dulanjani Wijayasekara, Akhtar Ali
Summary: This study used Illumina sequencing to sequence 19 MDMV isolates collected from Oklahoma and Missouri, revealing the genetic diversity and evolutionary relationship among the isolates. Negative selection was observed in all genes based on site-specific selection analysis. Analysis of FST indicated no gene flow between the two main phylogenetic clusters of MDMV isolates in the USA, with the highest genetic distance and nucleotide diversity observed in the P1 gene coding region.
SCIENTIFIC REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Jianting Zhang, Ranjith Kumar Kankala, Jingyao Ma, Yihao Zhou, Shi-Bin Wang, Ai-Zheng Chen
Summary: Utilizing the hollow tobacco mosaic virus coat protein as a restrictive template, well-organized one-dimensional inorganic nanostructures were successfully fabricated with high yields, including gold nanoparticles and silver sulfide quantum dots. Different types of functional nanoparticles were encapsulated and assembled into ordered 1D nanochains through TMV-assisted self-assembly approach, showing potential for the fabrication of highly complex hybrid-metal nanostructures.
Article
Plant Sciences
Shuzhen Hu, Yueyan Yin, Buyang Chen, Qi Lin, Yanzhen Tian, Xijiao Song, Jiejun Peng, Hongying Zheng, Shaofei Rao, Guanwei Wu, Xiaohan Mo, Fei Yan, Jianping Chen, Yuwen Lu
Summary: Research has shown that potato virus X utilizes the apoplast in a one-way manner, dominated by the coat protein, releasing viral particles that are not associated with exosomes and showing infectivity when transferred to healthy leaves.
MOLECULAR PLANT PATHOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Narjes Sheibani, Seyed Shahriar Arab, Mohammad Kamalvand
Summary: The coat protein of Tobacco Mosaic Virus plays a crucial role in protecting the virus RNA. The interaction between the virus coat protein and host plant proteins leads to infection and mosaic patterns on crops, affecting plant growth and function. By studying mutants of the coat protein through molecular dynamics simulation, this study confirms their role in coat protein-mediated resistance against TMV infection.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Physics, Fluids & Plasmas
Inbal Mizrahi, Robijn Bruinsma, Joseph Rudnick
Summary: This article discusses the self-assembly of single-stranded RNA viruses and the selection of viral genome molecules in the cytoplasm, and introduces a simple mathematical model to address this question.
Article
Biochemistry & Molecular Biology
Jennifer M. Podgorski, Krista Freeman, Sophia Gosselin, Alexis Huet, James F. Conway, Mary Bird, John Grecco, Shreya Patel, Deborah Jacobs-Sera, Graham Hatfull, Johann Peter Gogarten, Janne Ravantti, Simon J. White
Summary: Many double-stranded DNA viruses, including tailed bacteriophages and herpesviruses, use the HK97-fold in their major capsid protein. The evolution of capsid structural stability within the actinobacteriophages has been investigated using cryo-EM structure determination, structural comparisons, phylogenetic analyses, and AlphaFold predictions. The actinobacteriophage major capsid proteins can be classified into 15 groups based on their HK97-fold.
Article
Biochemical Research Methods
Inbal Mizrahi, Robijn Bruinsma, Joseph Rudnick
Summary: The paper presents a statistical-mechanics model for the kinetic selection of viral RNA molecules during the nucleation stage of small RNA virus assembly. The effects of RNA secondary structure and folding geometry of packaging signals on assembly activation energy barrier are encoded by a pair of characteristics. Kinetic selection is found to be optimal under conditions of supersaturation and when the concentration ratio of capsid protein and viral RNA concentrations equals the stoichiometric ratio of assembled viral particles. A form of order-disorder transition occurs as a function of the activation energy barrier, erasing kinetic selectivity through entropic effects associated with the number of assembly pathways.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Plant Sciences
Qing Liu, Guofang Lan, Yajun Zhu, Kai Chen, Congcong Shen, Xiuqin Zhao, Fan Zhang, Jianlong Xu, Zhikang Li
Summary: This study evaluated RBSDV resistance in a global collection of 1,953 rice accessions and identified several genomic regions associated with resistance, including two previously reported regions and three novel ones. The findings may enhance the breeding of RBSDV-resistant rice varieties.
Article
Plant Sciences
Hoseong Choi, Yeonhwa Jo, Hyunjung Chung, Soo Yeon Choi, Sang-Min Kim, Jin-Sung Hong, Bong Choon Lee, Won Kyong Cho
Summary: This study analyzed 83 coat protein (CP) sequences of Soybean mosaic virus (SMV) obtained from different provinces in Korea, revealing the genetic diversity, evolution, and divergence patterns of SMV CP sequences. The study found that plant species had a greater impact on genetic diversity than geographical origin or location.
Article
Plant Sciences
Francisco Mosquera-Yuqui, Francisco J. Flores, Eduardo A. Moncayo, Brighitte A. Garzon-Proano, Miguel A. Mendez, Fiama E. Guevara, Diego F. Quito-Avila, William Viera, Juan F. Cornejo-Franco, Andres R. Izquierdo, Carlos Noceda
Summary: This study investigated the distribution and epidemiological patterns of Babaco mosaic virus (BabMV) in babaco and chamburo, and modeled its three-dimensional structure based on the coat protein (CP) gene. The evolution rate of BabMV was estimated and the most recent common ancestor was traced back to around 1958.80. The CP exhibited higher flexibility compared to other proteins of BabMV, and the reconstructed viral distribution has implications for control approaches of BabMV.
Article
Zoology
Sana Khalid, Muhammad Zia-ur-Rehman, Usman Hameed, Shabnum Shaheen, Muhammad Naveed Shahid, Khajista Jabeen, Farah Khan, Muhammad Saleem Haider
Summary: This study confirms that whiteflies cannot acquire and transmit CpCDV and MCV from infected tobacco and tomato plants. However, they are able to successfully transmit CLCuKoV-Bu from symptomatic tomato leaves to healthy ones.
PAKISTAN JOURNAL OF ZOOLOGY
(2022)