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Trends in Biotechnology Dec 2020Microfluidics has proven to be a powerful tool for probing biology at the single-cell level. However, it is only in the past 5 years that single-cell microfluidics has... (Review)
Review
Microfluidics has proven to be a powerful tool for probing biology at the single-cell level. However, it is only in the past 5 years that single-cell microfluidics has been used in the field of virology. An array of strategies based on microwells, microvalves, and droplets is now available for tracking viral infection dynamics, identifying cell subpopulations with particular phenotypes, as well as high-throughput screening. The insights into the virus-host interactions gained at the single-cell level are unprecedented and usually inaccessible by population-based experiments. Therefore, single-cell microfluidics, which opens new avenues for mechanism elucidation and development of antiviral therapeutics, would be a valuable tool for the study of viral pathogenesis.
Topics: High-Throughput Screening Assays; Microfluidics; Single-Cell Analysis; Virology
PubMed: 32430227
DOI: 10.1016/j.tibtech.2020.04.010 -
Nature Immunology Jul 2019
Topics: Allergy and Immunology; Animals; Famous Persons; History, 20th Century; Humans; Mice; Virology
PubMed: 31182808
DOI: 10.1038/s41590-019-0428-8 -
Cellular Microbiology Aug 2019
Topics: Animals; Argentina; France; History, 20th Century; History, 21st Century; Humans; Insecta; Molecular Biology; Virology
PubMed: 31112322
DOI: 10.1111/cmi.13061 -
BMC Microbiology Jun 2021Phages are one of the key components in the structure, dynamics, and interactions of microbial communities in different bins. It has a clear impact on human health and... (Review)
Review
Phages are one of the key components in the structure, dynamics, and interactions of microbial communities in different bins. It has a clear impact on human health and the food industry. Bacteriophage characterization using in vitro approaches are time/cost consuming and laborious tasks. On the other hand, with the advent of new high-throughput sequencing technology, the development of a powerful computational framework to characterize the newly identified bacteriophages is inevitable for future research. Machine learning includes powerful techniques that enable the analysis of complex datasets for knowledge discovery and pattern recognition. In this study, we have conducted a comprehensive review of machine learning methods application using different types of features were applied in various aspects of bacteriophage research including, automated curation, identification, classification, host species recognition, virion protein identification, and life cycle prediction. Moreover, potential limitations and advantages of the developed frameworks were discussed.
Topics: Bacteriophages; Machine Learning; Virology
PubMed: 34174831
DOI: 10.1186/s12866-021-02256-5 -
PLoS Pathogens Feb 2018
Topics: Animals; Biomedical Research; Computational Biology; Europe; Humans; Professional Role; Virology; Workforce
PubMed: 29420617
DOI: 10.1371/journal.ppat.1006771 -
Chemical Reviews Feb 2020Uncovering the mechanisms of virus infection and assembly is crucial for preventing the spread of viruses and treating viral disease. The technique of single-virus... (Review)
Review
Uncovering the mechanisms of virus infection and assembly is crucial for preventing the spread of viruses and treating viral disease. The technique of single-virus tracking (SVT), also known as single-virus tracing, allows one to follow individual viruses at different parts of their life cycle and thereby provides dynamic insights into fundamental processes of viruses occurring in live cells. SVT is typically based on fluorescence imaging and reveals insights into previously unreported infection mechanisms. In this review article, we provide the readers a broad overview of the SVT technique. We first summarize recent advances in SVT, from the choice of fluorescent labels and labeling strategies to imaging implementation and analytical methodologies. We then describe representative applications in detail to elucidate how SVT serves as a valuable tool in virological research. Finally, we present our perspectives regarding the future possibilities and challenges of SVT.
Topics: Animals; Humans; Virology; Virus Diseases; Virus Physiological Phenomena
PubMed: 31951121
DOI: 10.1021/acs.chemrev.9b00692 -
Journal of Virology Oct 2016With the enormous sizes viral populations reach, many variants are at too low a frequency to be detected by conventional next-generation sequencing (NGS) methods.... (Review)
Review
With the enormous sizes viral populations reach, many variants are at too low a frequency to be detected by conventional next-generation sequencing (NGS) methods. Circular sequencing (CirSeq) is a method by which the error rate of next-generation sequencing is decreased so that even low-frequency viral variants can be accurately detected. The ability to visualize almost the entire genetic makeup of a viral swarm has implications for epidemiology, viral evolution, and vaccine design. Here we discuss experimental planning, analysis, and recent insights using CirSeq.
Topics: High-Throughput Nucleotide Sequencing; Metagenomics; Virology; Viruses
PubMed: 27440878
DOI: 10.1128/JVI.00804-14 -
Proteomics Jun 2015
Topics: Host-Pathogen Interactions; Humans; Proteome; Proteomics; Viral Proteins; Virology
PubMed: 26082410
DOI: 10.1002/pmic.201570103 -
Viruses Nov 2015Different animal models have been proposed to investigate the mechanisms of Human T-lymphotropic Virus (HTLV)-induced pathogenesis: rats, transgenic and NOD-SCID/γcnull... (Review)
Review
Different animal models have been proposed to investigate the mechanisms of Human T-lymphotropic Virus (HTLV)-induced pathogenesis: rats, transgenic and NOD-SCID/γcnull (NOG) mice, rabbits, squirrel monkeys, baboons and macaques. These systems indeed provide useful information but have intrinsic limitations such as lack of disease relevance, species specificity or inadequate immune response. Another strategy based on a comparative virology approach is to characterize a related pathogen and to speculate on possible shared mechanisms. In this perspective, bovine leukemia virus (BLV), another member of the deltaretrovirus genus, is evolutionary related to HTLV-1. BLV induces lymphoproliferative disorders in ruminants providing useful information on the mechanisms of viral persistence, genetic determinants of pathogenesis and potential novel therapies.
Topics: Animals; Biomedical Research; Disease Models, Animal; Host-Pathogen Interactions; Human T-lymphotropic virus 1; Humans; Leukemia Virus, Bovine; Virology
PubMed: 26610551
DOI: 10.3390/v7112929 -
Cold Spring Harbor Perspectives in... Jun 2021Early studies of transmissible tumors in chickens provided evidence that viruses such as avian leukosis virus (ALV) and Rous sarcoma virus (RSV) can cause cancer in... (Review)
Review
Early studies of transmissible tumors in chickens provided evidence that viruses such as avian leukosis virus (ALV) and Rous sarcoma virus (RSV) can cause cancer in these animals. Doubts about the relevance to human tumors and failures to replicate some early work meant the field of tumor virology followed a bumpy course. Nevertheless, viruses that can cause cancers in rodents and humans were ultimately identified, and several Nobel prizes were awarded for work in this area. In this excerpt from his forthcoming book on the history of cancer research, Joe Lipsick looks back at the early history of tumor virus research, from some of the early false starts and debates, to discovery of reverse transcriptase, and identification of human papilloma virus (HPV) as the major cause of cervical cancer.
Topics: Animals; History, 20th Century; Humans; Neoplasms; Oncogenic Viruses; Proviruses; Virology
PubMed: 34074674
DOI: 10.1101/cshperspect.a035774