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Rule-based knowledge aggregation for large-scale protein sequence analysis of influenza A viruses

Olivo Miotto, Tin Tan, Vladimir Brusic
2008 BMC Bioinformatics  
Conclusion: To overcome the quality issues inherent in public databases, automated knowledge aggregation with embedded intelligence is needed for large-scale analyses.  ...  We applied this approach to more than 90,000 influenza A records, to annotate sequences with protein name, virus subtype, isolate, host, geographic origin, and year of isolation.  ...  Acknowledgements The authors thank A. T  ... 
doi:10.1186/1471-2105-9-s1-s7 pmid:18315860 pmcid:PMC2259408 fatcat:4kuzd5yranbf3fkkro6m6g65by

Evolutionarily Conserved Protein Sequences of Influenza A Viruses, Avian and Human, as Vaccine Targets

A. T. Heiny, Olivo Miotto, Kellathur N. Srinivasan, Asif M. Khan, G. L. Zhang, Vladimir Brusic, Tin Wee Tan, J. Thomas August, Berend Snel
2007 PLoS ONE  
Methodologies for large-scale analysis of the evolutionary variability of the influenza A virus proteins recorded in public databases were developed and used to elucidate the amino acid sequence diversity  ...  This is a necessary first step in the design and analysis of a polyepitope, pan-influenza A vaccine.  ...  Nordstrom August for help with the illustrations and valuable suggestions.  ... 
doi:10.1371/journal.pone.0001190 pmid:18030326 pmcid:PMC2065905 fatcat:2kbl5wgn5bddranhenhlfbjnhi

Complete-Proteome Mapping of Human Influenza A Adaptive Mutations: Implications for Human Transmissibility of Zoonotic Strains

Olivo Miotto, A. T. Heiny, Randy Albrecht, Adolfo García-Sastre, Tin Wee Tan, J. Thomas August, Vladimir Brusic, Art F. Y. Poon
2010 PLoS ONE  
We performed a large-scale comparative analysis of proteins from avian and human strains, to produce a catalogue of mutations associated with H2H transmissibility, and to detect their presence in avian  ...  Methodology/Principal Findings: We constructed a dataset of influenza A protein sequences from 92,343 public database records.  ...  Khan for helpful discussions and suggestions. Author Contributions  ... 
doi:10.1371/journal.pone.0009025 pmid:20140252 pmcid:PMC2815782 fatcat:bwhr6n25ujgadoydf2dmzyyo5u

Application perspectives of localization microscopy in virology

C. Cremer, R. Kaufmann, M. Gunkel, F. Polanski, P. Müller, R. Dierkes, S. Degenhard, C. Wege, M. Hausmann, U. Birk
2014 Histochemistry and Cell Biology  
To gain a better understanding of cell entry mechanisms during influenza a virus infection, SPDM was used  ...  On the basis of the experimental evidence so far obtained, we finally discuss additional application perspectives of localization microscopy approaches for the fast detection and identification of viruses  ...  For support in some of the localization microscopy measurements we thank Qiao Wang and Sebastian Pres, and for critical reading of the manuscript Prof.  ... 
doi:10.1007/s00418-014-1203-4 pmid:24614971 fatcat:llu2bkpe5ba43hqvtxcg6wljvi

Physiochemical Constraints in Influenza A Hemagglutinin

Pei-Chun Chang, Jiunn-I Shieh, Jing-Doo Wang, Kuei-Jen Lee, Chung-Hung Li, Hsiang-Chuan Liu
2008 2008 Fourth International Conference on Natural Computation  
Influenza A viruses are negative-strand RNA viruses. The gene of hemagglutinin (HA) protein in the virus genome is the major molecule that determining the range of hosts.  ...  Fuzzy measure and Choquet integral were used to estimate the combining effect of different physicochemical properties for single residue in HA protein that related to infective events.  ...  Introduction Influenza A viruses are negative-strand RNA viruses that infect a wide variety of animals in the nature.  ... 
doi:10.1109/icnc.2008.712 dblp:conf/icnc/ChangSWLLL08 fatcat:pdtzpb6rxjbqvgygej46mw5szi

Moving H5N1 studies into the era of systems biology

Laurence Josset, Jennifer Tisoncik-Go, Michael G. Katze
2013 Virus Research  
The dynamics of H5N1 influenza virus pathogenesis are multifaceted and can be seen as an emergent property that cannot be comprehended without looking at the system as a whole.  ...  This review provides a roadmap for what needs to be done in the future and what computational strategies should be used to build a global model of H5N1 pathogenesis.  ...  We also thank Patrick Lane of ScEYEnce Studios for his illustration (Figure 2 ), and Ilhem Messaoudi and, Balaji Manicassamy for contributing images to the illustration.  ... 
doi:10.1016/j.virusres.2013.02.011 pmid:23499671 pmcid:PMC3834220 fatcat:dzmpbx4hnzd35mjqarlsv2xh3u

Critical Assessment of Purification and Analytical Technologies for Enveloped Viral Vector and Vaccine Processing and Their Current Limitations in Resolving Co-Expressed Extracellular Vesicles

Aline Minh, Amine A. Kamen
2021 Vaccines  
EVs share similar sizes, biophysical characteristics and even biogenesis pathways with enveloped viruses, which are currently used as key ingredients in a number of viral vectors and licensed vaccine products  ...  Within a context of well-established viral vector and vaccine safety profiles, this review provides insights on the likely presence of EVs in the final formulation of enveloped virus products and discusses  ...  Large scale technologies used in the field of viral vectors and vaccines for the purification of enveloped viruses are the main focus of this review.  ... 
doi:10.3390/vaccines9080823 pmid:34451948 pmcid:PMC8402407 fatcat:5r6wcfccajbnvleqw46aoevysy

Synthetic viruses: a new opportunity to understand and prevent viral disease

Eckard Wimmer, Steffen Mueller, Terrence M Tumpey, Jeffery K Taubenberger
2009 Nature Biotechnology  
Rapid progress in DNA synthesis and sequencing is spearheading the deliberate, large-scale genetic alteration of organisms.  ...  and is largely a matter of available resources.  ...  Burgin for information provided. The work described here was supported partially by US National Institutes of Health (NIH) grants AI075219  ... 
doi:10.1038/nbt.1593 pmid:20010599 pmcid:PMC2819212 fatcat:ia5kdgkavrhujpqn6cpggbwnuu

Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis

Olivo Miotto, AT Heiny, Tin Tan, J Thomas August, Vladimir Brusic
2008 BMC Bioinformatics  
This paper describes a novel method for identifying amino acid sites that distinguish specific sets of protein sequences, by comparative analysis of matched alignments.  ...  The method presented was applied to an analysis of influenza A PB2 protein sequences, with the objective of identifying the components of adaptation to human-to-human transmission, and reconstructing the  ...  Collecting annotations is currently a significant obstacle for large-scale analysis, largely due to the uneven quality of annotations in large public databases.  ... 
doi:10.1186/1471-2105-9-s1-s18 pmid:18315849 pmcid:PMC2259419 fatcat:cvvp2vos4feyhj3fd5p5jyrw6q

Structure-based design of stabilized recombinant influenza neuraminidase tetramers [article]

Daniel Ellis, Julia Lederhofer, Oliver J Acton, Yaroslav Tsybovsky, Sally Kephart, Christina Yap, Rebecca A Gillespie, Adrian Creanga, Tyler Stephens, Deleah Pettie, Michael Murphy, Andrew J Borst (+6 others)
2021 bioRxiv   pre-print
Influenza virus neuraminidase (NA) is a major antiviral drug target and has recently reemerged as a key target of antibody-mediated protective immunity.  ...  Our findings provide a deeper understanding of NA structure, stability, and antigenicity, as well as a roadmap towards structure-based discovery of NA-directed therapeutics and vaccines.  ...  (Right) Phylogenetic tree of NA of influenza A and B viruses. Scale bar, 0.1 amino acid substitutions per site. (B) Construct diagram for recombinant NA proteins used in this work.  ... 
doi:10.1101/2021.05.17.444468 fatcat:v5bkbzpbabf4tkh5dhbenxjm6i

Synthetic biology for bioengineering virus-like particle vaccines

Hayley K. Charlton Hume, João Vidigal, Manuel J. T. Carrondo, Anton P. J. Middelberg, António Roldão, Linda H. L. Lua
2018 Biotechnology and Bioengineering  
Current and developing technologies for the identification of novel target-specific antigens and their usefulness for rational engineering of VLP functions (e.g., presentation of structurally diverse antigens  ...  Expansively, a plethora of studies now confirms that VLPs can be designed to safely present heterologous antigens from a variety of pathogens unrelated to the chosen carrier VLPs.  ...  More recently, a universal label-free analytical tool for influenza VLPs quantification based on biolayer interferometry technology applied on an octet platform was developed ogies hold promise for large-scale  ... 
doi:10.1002/bit.26890 pmid:30597533 pmcid:PMC7161758 fatcat:5krtu3dxzvaonmmgq34n65jnte

Bioaerosols and Corona Virus Diffusion, Transmission, Carriers, Viral Size, Surfaces Properties and other Factor Involved

Luisetto M, Nili BA, Khaled Edbey, Mashori GR, Ahmed Yesvi Rafa, Oleg Yurevich Latishev
2021 INTERNATIONAL JOURNAL OF MEDICINE AND HEALTHCARE REPORTS  
The proteins are highly basic, with isoelectric points (pI) of 10.3 to 10.7. A three domain structure for the protein has been proposed based on early sequence comparisons of MHV strains.  ...  "To our knowledge, the oldest study on the sampling of airborne -viruses was performed with a laboratory setup using a chamber and an artificially produced aerosol of influenza-virus " [1] .  ...  Interests No Ethical Consideration This work is produced under all international ethical rules, that can be applied.  ... 
doi:10.51521/ijmhr.2021.1108 fatcat:gid7xxtyyvhidhybu53imwn5ni

Contribution of antibody production against neuraminidase to the protection afforded by influenza vaccines

Glendie Marcelin, Matthew R. Sandbulte, Richard J. Webby
2012 Reviews in Medical Virology  
HA proteins of type A influenza viruses have been classified into 16 subtypes based on serological cross-reactivity.  ...  Carrying out NA drift analysis on a scale similar to what takes place semi-annually for HA antigenic drift would be an imposing task considering that even the newer, microplate-formatted NI assays are  ...  Table 1 Methods for analysis of NA-specific antibodies Listed in this table are methods currently in use for serological evaluation of NA-specific antibodies, and practical considerations associated  ... 
doi:10.1002/rmv.1713 pmid:22438243 pmcid:PMC3389592 fatcat:3syjpligbvgfdmjmslnydcz56i

Intrinsically disordered proteins of viruses: Involvement in the mechanism of cell regulation and pathogenesis [chapter]

Pushpendra Mani Mishra, Navneet Chandra Verma, Chethana Rao, Vladimir N. Uversky, Chayan Kanti Nandi
2020 Progress in Molecular Biology and Translational Science  
The current book chapter summarizes the aforementioned details and suggests the novel opportunities for further research of IDPs senses in viruses.  ...  The exploration of these dancing proteins in viruses has just started and crucial details such as correlation of rapid evolution, high rate of mutation and accumulation of disordered contents in viral  ...  Acknowledgments The authors acknowledge the funding support from the Council of Scientific and Industrial Research (CSIR), India. The file no. for the same is 09/1058(0013)/2019-EMR-I.  ... 
doi:10.1016/bs.pmbts.2020.03.001 pmid:32828463 pmcid:PMC7129803 fatcat:fzdkvurysffojcdp3ht425xdjy

Biodiagnostics in an era of global pandemics—From biosensing materials to data management

Yoav Y. Broza, Hossam Haick
2021 View  
As a result, different approaches for fast diagnostic and screening are made and yet to find the ideal way.  ...  The review discusses how integration of sensing devices with big data analysis, artificial Intelligence or machine learning, and clinical decision support system, could improve the accuracy of the recorded  ...  The knowledge base contains the rules and associations of compiled data that most often take the form of IF-THEN rules.  ... 
doi:10.1002/viw.20200164 pmid:34766159 pmcid:PMC8441813 fatcat:l6b4h6zxybbbdant22yumd3npa
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