Review
Immunology
Nikolai Nikitin, Yuri Vasiliev, Angelina Kovalenko, Ekaterina Ryabchevskaya, Olga Kondakova, Ekaterina Evtushenko, Olga Karpova
Summary: Plant viruses have potential as vaccine components and adjuvants in cancer immunotherapy.
Article
Virology
Qi Wu, Jizong Li, Wei Wang, Jinzhu Zhou, Dandan Wang, Baochao Fan, Xuehan Zhang, Dongbo Sun, Ga Gong, Sizhu Suolang, Bin Li
Summary: The study identified multiple viruses in calf diarrhea samples and suggested a potential for the emergence of new serotype/genotype in bovine astrovirus. Additionally, six amino acid mutation sites were found in the S gene of bovine coronavirus, mainly in the S1 subunit region.
Review
Plant Sciences
Rahul B. Nitnavare, Joorie Bhattacharya, Satnam Singh, Amardeep Kour, Malcolm J. Hawkesford, Naveen Arora
Summary: RNA interference is a method of gene silencing that has potential applications in pest management in various insect classes. Different insect classes exhibit varying levels of response to RNAi, with coleopterans showing the highest efficiency, hemipterans being relatively inefficient, and lepidopterans showing the least response. Various methods have been developed to safely deliver dsRNA into insect biological systems.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Infectious Diseases
Filippo Marzoli, Mario Forzan, Laura Bortolotti, Maria Irene Pacini, Maria Shantal Rodriguez-Flores, Antonio Felicioli, Maurizio Mazzei
Summary: The study identified multiple viral types in both Asian hornets and honeybees, suggesting efficient transmission of viruses from bees to wasps and highlighting the environment as an important source of infection.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
Article
Virology
Martha Malapi-Wight, Bishwo Adhikari, Jing Zhou, Leticia Hendrickson, Clarissa J. Maroon-Lango, Clint McFarland, Joseph A. Foster, Oscar P. Hurtado-Gonzales
Summary: Global germplasm trade has raised concerns about the spread of plant pathogens and pests, with a focus on viral pathogens that are difficult to control. High-throughput sequencing plays a crucial role in quarantine programs for sugarcane viruses, requiring increased sequencing depth for accurate detection.
Review
Plant Sciences
Jill C. Preston
Summary: The development of plant model organisms is traditionally analyzed using resource-heavy, tailored applications that are not easily transferable to non-model taxa. Next-generation sequencing (NGS) is increasingly becoming a powerful tool in evolutionary developmental biology (evo-devo) studies. Plant biologists are utilizing natural diversity for crop improvement, enhancing ecosystem functioning, and better understanding plant responses to climate change.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Review
Microbiology
Muhammad Shafiq Shahid, Muhammad Naeem Sattar, Zafar Iqbal, Amir Raza, Abdullah M. Al-Sadi
Summary: In recent years, next-generation sequencing (NGS) and CRISPR-Cas technologies have revolutionized plant virology. NGS allows for rapid sequencing and deciphering of viral metagenomes, while CRISPR-Cas enables the development of effective virus resistance approaches.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Muhammad Furqan Ashraf, Dan Hou, Quaid Hussain, Muhammad Imran, Jialong Pei, Mohsin Ali, Aamar Shehzad, Muhammad Anwar, Ali Noman, Muhammad Waseem, Xinchun Lin
Summary: Crop production is a major challenge in providing food for the projected 10 billion individuals in 2050. Utilizing genomics and metabolomics strategies can help enhance crop yield and generate stress-tolerant plants. Next-generation sequencing innovation has laid the foundation for understanding genetic potential and improving crops. The application of NGS and metabolomics can improve crop suitability and nutritional value.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Agronomy
Antonino F. Catara, Moshe Bar-Joseph, Grazia Licciardello
Summary: This review discusses the importance of citrus production in the Mediterranean area in both cultural and economic terms, emphasizing the need for proper phytosanitary management in order to ensure the viability of the industry. The focus is on exotic and emerging dangerous citrus viruses that have not yet been reported in the region, as well as the potential contribution of old and new technologies for better control measures and the production of pathogen-tested citrus trees and rootstocks.
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Microbiology
Ilayda Akacin, Seymanur Ersoy, Osman Doluca, Mine Gungormusler
Summary: This review provides a comprehensive overview of recent literature on the utilization of TGS and NGS technologies in microbial metagenomics research. It discusses the advantages and limitations of these technologies and presents real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.
MICROBIOLOGICAL RESEARCH
(2022)
Review
Microbiology
David M. Morens, Jeffery K. Taubenberger, Anthony S. Fauci
Summary: Viruses that replicate in the human respiratory mucosa cause significant mortality and morbidity and have not been effectively controlled by vaccines. This review examines challenges in developing effective mucosal respiratory vaccines and discusses possible approaches for next-generation vaccines, considering variables such as vaccine antigen configuration, dose and adjuvantation, route and timing of vaccination, vaccine boosting, adjunctive therapies, and public health vaccination policies.
CELL HOST & MICROBE
(2023)
Review
Microbiology
Kai Sun, Yi Liu, Xin Zhou, Chuanlin Yin, Pengjun Zhang, Qianqian Yang, Lingfeng Mao, Xuping Shentu, Xiaoping Yu
Summary: Plant viruses pose a threat to crop yield and quality, making efficient and accurate pathogen diagnostics crucial for crop disease management. Recent advancements in sequencing technology, particularly metagenomics sequencing and Oxford Nanopore Technologies, have greatly improved virus diagnostics research in plants.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Ecology
Zi-Wen Yang, Yu Men, Jing Zhang, Zhi-Hui Liu, Jiu-Yang Luo, Yan-Hui Wang, Wen-Jun Li, Qiang Xie
Summary: The study found that air dried preservation method had poor effects on insect microbiome samples, while RNAlater was not suitable for longer field works. CTAB and ethanol were recommended as more effective and cost-efficient preservatives. Additionally, NGS sequencing of the V4 region of the 16S rRNA gene had lower resolution compared to TGS sequencing, potentially leading to misestimations of microbial community compositions.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Biochemical Research Methods
Atif Khurshid Wani, Chirag Chopra, Daljeet Singh Dhanjal, Nahid Akhtar, Himanshu Singh, Poorvi Bhau, Anjuvan Singh, Varun Sharma, Rafael Silvio Bonilha Pinheiro, Juliana Heloisa Pine Americo-Pinheiro, Reena Singh
Summary: Zoonotic viral infections pose significant threats to global public health. Understanding the origins and dynamics of these infections is crucial for prevention and management of future outbreaks. Metagenomics is a powerful tool for studying the diversity of viral populations and potential zoonotic events.
JOURNAL OF VIROLOGICAL METHODS
(2024)
Article
Biochemical Research Methods
Michel V. F. Sucupira, Ana P. C. Argondizzo, Mariana Miguez, Anna E. de Araujo, Leila B. R. Silva, Marcelle B. Mello, Christiane F. S. Marques, Danielle Brito Cunha, Renata C. Bastos, Vanessa S. de Paula, Luciane A. Amado Leon
Summary: This study focuses on improving the purification, solubility, and protein expression levels of recombinant VP1-2A, a hepatitis A virus (HAV) structural protein with immunogenic activity. The results show that the modified approach successfully produces biologically active HAV VP1-2A, which can be used as a diagnostic tool for HAV infection.
JOURNAL OF VIROLOGICAL METHODS
(2024)
Article
Biochemical Research Methods
Arun K. Dhar, Roberto Cruz-Flores, Hung N. Mai, Janet Warg
Summary: A sensitive and robust TaqMan PCR method for detecting IHHNV in three commercially important shrimp species was developed and compared with other published methods. Multiple primer/probe sets, including qIH-Fw/qIH-Rv and 3144F/3232R, are recommended for the detection of IHHNV. These findings are valuable for large-scale screening of shrimp using a TaqMan real-time PCR assay.
JOURNAL OF VIROLOGICAL METHODS
(2024)
Article
Biochemical Research Methods
Kemal Mehinagic, Matthias Liniger, Maksym Samoilenko, Nick Soltermann, Markus Gerber, Nicolas Ruggli
Summary: A plasmid-based reporter assay has been developed for sensitive detection and titration of infectious African swine fever virus (ASFV). This novel method allows accurate measurement of ASFV titers and is applicable to ASFV of different genotypes, virulence, and sources.
JOURNAL OF VIROLOGICAL METHODS
(2024)
Article
Biochemical Research Methods
Jan Van Slambrouck, Charlotte Schoenaers, Lies Laenen, Xin Jin, Kurt Beuselinck, Ann Verdonck, Joost Wauters, Geert Molenberghs, Bart M. Vanaudenaerde, Robin Vos, Peter Mombaerts, Katrien Lagrou, Laurens J. Ceulemans
Summary: The ability to detect SARS-CoV-2 RNA or antigen in BAL fluid samples using point-of-care tests (POCTs) can reduce the risk of developing severe COVID-19 after lung transplantation.
JOURNAL OF VIROLOGICAL METHODS
(2024)