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  1. Article ; Online: Predicting potential SARS-CoV-2 spillover and spillback in animals.

    Tan, Zi Hian / Yong, Kian Yan / Shu, Jian-Jun

    Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi

    2024  Volume 57, Issue 2, Page(s) 225–237

    Abstract: Background: The COVID-19 pandemic is spreading rapidly around the world, causing countries to impose lockdowns and efforts to develop vaccines on a global scale. However, human-to-animal and animal-to-human transmission cannot be ignored, as severe ... ...

    Abstract Background: The COVID-19 pandemic is spreading rapidly around the world, causing countries to impose lockdowns and efforts to develop vaccines on a global scale. However, human-to-animal and animal-to-human transmission cannot be ignored, as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can spread rapidly in farmed and wild animals. This could create a worrying cycle of SARS-CoV-2 spillover from humans to animals and spillback of new strains back into humans, rendering vaccines ineffective.
    Method: This study provides a key indicator of animals that may be potential susceptible hosts for SARS-CoV-2 and coronavirus infections by analysing the phylogenetic distance between host angiotensin-converting enzyme 2 and the coronavirus spike protein. Crucially, our analysis identifies animals that are at elevated risk from a spillover and spillback incident.
    Results: One group of animals has been identified as potentially susceptible to SARS-CoV-2 by harbouring a parasitic coronavirus spike protein similar to the SARS-CoV-2 spike protein. These animals may serve as amplification hosts in spillover events from zoonotic reservoirs. This group consists of a mixture of animals infected internally and naturally: minks, dogs, cats, tigers. Additionally, no internal or natural infections have been found in masked palm civet.
    Conclusion: Tracing interspecies transmission in multi-host environments based solely on in vitro and in vivo examinations of animal susceptibility or serology is a time-consuming task. This approach allows rapid identification of high-risk animals to prioritize research and assessment of the risk of zoonotic disease transmission in the environment. It is a tool to rapidly identify zoonotic species that may cause outbreaks or participate in expansion cycles of coexistence with their hosts. This prevents the spread of coronavirus infections between species, preventing spillover and spillback incidents from occurring.
    MeSH term(s) Animals ; Humans ; Dogs ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/metabolism ; COVID-19/epidemiology ; Phylogeny ; Pandemics/prevention & control ; Communicable Disease Control ; Vaccines
    Chemical Substances spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Vaccines
    Language English
    Publishing date 2024-01-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 1497590-7
    ISSN 1995-9133 ; 1684-1182 ; 0253-2662
    ISSN (online) 1995-9133
    ISSN 1684-1182 ; 0253-2662
    DOI 10.1016/j.jmii.2024.01.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Programmable Biomolecule-Mediated Processors.

    Shu, Jian-Jun / Tan, Zi Hian / Wang, Qi-Wen / Yong, Kian-Yan

    Journal of the American Chemical Society

    2023  Volume 145, Issue 46, Page(s) 25033–25042

    Abstract: Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to tackle ... ...

    Abstract Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to tackle computational problems. It is of great significance to investigate the various issues of programmable biomolecule-mediated processors that are capable of automatically processing, storing, and displaying information. This Perspective provides several conceptual designs of programmable biomolecule-mediated processors and provides some insights into potential future research directions for programmable biomolecule-mediated processors.
    Language English
    Publishing date 2023-10-21
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 3155-0
    ISSN 1520-5126 ; 0002-7863
    ISSN (online) 1520-5126
    ISSN 0002-7863
    DOI 10.1021/jacs.3c04142
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Evolution of Viral Pathogens Follows a Linear Order.

    Tan, Zi Hian / Yong, Kian Yan / Shu, Jian-Jun

    Microbiology spectrum

    2022  Volume 10, Issue 1, Page(s) e0165521

    Abstract: Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are possible, as shown ... ...

    Abstract Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are possible, as shown by the current coronavirus disease 2019 (COVID-19) outbreak. Therefore, it is necessary to better understand the evolution of coronaviruses as well as viruses in general. This study reports a comparative analysis of the amino acid usage within several key viral families and genera that are prone to triggering outbreaks, including coronavirus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], SARS-CoV, MERS-CoV, human coronavirus-HKU1 [HCoV-HKU1], HCoV-OC43, HCoV-NL63, and HCoV-229E), influenza A (H1N1 and H3N2), flavivirus (dengue virus serotypes 1 to 4 and Zika) and ebolavirus (Zaire, Sudan, and Bundibugyo ebolavirus). Our analysis reveals that the distribution of amino acid usage in the viral genome is constrained to follow a linear order, and the distribution remains closely related to the viral species within the family or genus. This constraint can be adapted to predict viral mutations and future variants of concern. By studying previous SARS and MERS outbreaks, we have adapted this naturally occurring pattern to determine that although pangolin plays a role in the outbreak of COVID-19, it may not be the sole agent as an intermediate animal. In addition to this study, our findings contribute to the understanding of viral mutations for subsequent development of vaccines and toward developing a model to determine the source of the outbreak.
    MeSH term(s) Codon ; Coronavirus/classification ; Coronavirus/genetics ; Ebolavirus/genetics ; Evolution, Molecular ; Flavivirus/genetics ; Genome, Viral ; Humans ; Influenza A Virus, H1N1 Subtype/genetics ; Influenza A Virus, H3N2 Subtype/genetics ; Linear Models ; Mutation ; SARS-CoV-2/genetics ; Virus Diseases/virology
    Chemical Substances Codon
    Language English
    Publishing date 2022-02-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.01655-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Book ; Online: Programmable biomolecule-mediated processors

    Shu, Jian-Jun / Tan, Zi Hian / Wang, Qi-Wen / Yong, Kian-Yan

    2024  

    Abstract: Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to tackle ... ...

    Abstract Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to tackle computational problems. It is of great significance to investigate the various issues of programmable biomolecule-mediated processors that are capable of automatically processing, storing, and displaying information. This Perspective provides several conceptual designs of programmable biomolecule-mediated processors and provides some insights into potential future research directions for programmable biomolecule-mediated processors.
    Keywords Computer Science - Emerging Technologies ; Quantitative Biology - Biomolecules
    Publishing date 2024-01-28
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Book ; Online: Evolution of viral pathogens follows a linear order

    Tan, Zi Hian / Yong, Kian Yan / Shu, Jian-Jun

    2022  

    Abstract: Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are possible, as shown ... ...

    Abstract Although lessons have been learned from previous severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) outbreaks, the rapid evolution of the viruses means that future outbreaks of a much larger scale are possible, as shown by the current coronavirus disease 2019 (COVID-19) outbreak. Therefore, it is necessary to better understand the evolution of coronaviruses as well as viruses in general. This study reports a comparative analysis of the amino acid usage within several key viral families and genera that are prone to triggering outbreaks, including coronavirus (SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-HKU1, HCoV-OC43, HCoV-NL63, HCoV-229E), influenza A (H1N1, H3N2), flavivirus (dengue virus serotypes 1-4, Zika) and ebolavirus (Zaire, Sudan, Bundibugyo ebolavirus). Our analysis reveals that the distribution of amino acid usage in the viral genome is constrained to follow a linear order, and the distribution remains closely related to the viral species within the family or genus. This constraint can be adapted to predict viral mutations and future variants of concern. By studying previous SARS and MERS outbreaks, we have adapted this naturally occurring pattern to determine that although pangolin plays a role in the outbreak of COVID-19, it may not be the sole agent as an intermediate animal. In addition to this study, our findings contribute to the understanding of viral mutations for subsequent development of vaccines and toward developing a model to determine the source of the outbreak.
    Keywords Quantitative Biology - Populations and Evolution
    Subject code 572
    Publishing date 2022-05-11
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Fourier-based classification of protein secondary structures.

    Shu, Jian-Jun / Yong, Kian Yan

    Biochemical and biophysical research communications

    2017  Volume 485, Issue 4, Page(s) 731–735

    Abstract: The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify ... ...

    Abstract The correct prediction of protein secondary structures is one of the key issues in predicting the correct protein folded shape, which is used for determining gene function. Existing methods make use of amino acids properties as indices to classify protein secondary structures, but are faced with a significant number of misclassifications. The paper presents a technique for the classification of protein secondary structures based on protein "signal-plotting" and the use of the Fourier technique for digital signal processing. New indices are proposed to classify protein secondary structures by analyzing hydrophobicity profiles. The approach is simple and straightforward. Results show that the more types of protein secondary structures can be classified by means of these newly-proposed indices.
    MeSH term(s) Algorithms ; Amino Acid Sequence ; Amino Acids/chemistry ; Animals ; Cattle ; Databases, Protein ; Fourier Analysis ; Humans ; Hydrophobic and Hydrophilic Interactions ; Myoglobin/chemistry ; Myoglobin/classification ; Phospholipases A2/chemistry ; Phospholipases A2/classification ; Protein Structure, Secondary ; Proteins/chemistry ; Proteins/classification ; Sequence Analysis, Protein
    Chemical Substances Amino Acids ; Myoglobin ; Proteins ; Phospholipases A2 (EC 3.1.1.4)
    Language English
    Publishing date 2017-02-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 205723-2
    ISSN 1090-2104 ; 0006-291X ; 0006-291X
    ISSN (online) 1090-2104 ; 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2017.02.117
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Programmable DNA-Mediated Multitasking Processor

    Shu, Jian-Jun / Wang Qi-Wen / Yong Kian-Yan / Shao Fangwei / Lee Kee Jin

    Journal of physical chemistry. 2015 Apr. 30, v. 119, no. 17

    2015  

    Abstract: Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing ... ...

    Abstract Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing substrates to tackle the computational problems. The massive parallelism of DNA hybridization exhibits transcendent potential to improve multitasking capabilities and yield a tremendous speed-up over the conventional electronic processors with stepwise signal cascade. As an example of multitasking capability, we present an in vitro programmable DNA-mediated optimal route planning processor as a functional unit embedded in contemporary navigation systems. The novel programmable DNA-mediated processor has several advantages over the existing silicon-mediated methods, such as conducting massive data storage and simultaneous processing via much fewer materials than conventional silicon devices.
    Keywords DNA ; bioinformatics ; databases ; nucleic acid hybridization ; physical chemistry ; silicon
    Language English
    Dates of publication 2015-0430
    Size p. 5639-5644.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021%2Facs.jpcb.5b02165
    Database NAL-Catalogue (AGRICOLA)

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  8. Article ; Online: DNA-based computing of strategic assignment problems.

    Shu, Jian-Jun / Wang, Qi-Wen / Yong, Kian-Yan

    Physical review letters

    2011  Volume 106, Issue 18, Page(s) 188702

    Abstract: DNA-based computing is a novel technique to tackle computationally difficult problems, in which computing time grows exponentially corresponding to problematic size. A strategic assignment problem is a typical nondeterministic polynomial problem, which ... ...

    Abstract DNA-based computing is a novel technique to tackle computationally difficult problems, in which computing time grows exponentially corresponding to problematic size. A strategic assignment problem is a typical nondeterministic polynomial problem, which is often associated with strategy applications. In this Letter, a new approach dealing with strategic assignment problems is proposed based on manipulating DNA strands, which is believed to be better than the conventional silicon-based computing in solving the same problem.
    MeSH term(s) Computer Simulation ; Computers, Molecular ; DNA/chemistry ; DNA/genetics ; Molecular Biology/methods ; Task Performance and Analysis
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2011-05-06
    Publishing country United States
    Document type Journal Article
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.106.188702
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Programmable DNA-Mediated Multitasking Processor.

    Shu, Jian-Jun / Wang, Qi-Wen / Yong, Kian-Yan / Shao, Fangwei / Lee, Kee Jin

    The journal of physical chemistry. B

    2015  Volume 119, Issue 17, Page(s) 5639–5644

    Abstract: Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing ... ...

    Abstract Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing substrates to tackle the computational problems. The massive parallelism of DNA hybridization exhibits transcendent potential to improve multitasking capabilities and yield a tremendous speed-up over the conventional electronic processors with stepwise signal cascade. As an example of multitasking capability, we present an in vitro programmable DNA-mediated optimal route planning processor as a functional unit embedded in contemporary navigation systems. The novel programmable DNA-mediated processor has several advantages over the existing silicon-mediated methods, such as conducting massive data storage and simultaneous processing via much fewer materials than conventional silicon devices.
    MeSH term(s) Base Sequence ; Computers, Molecular ; DNA/chemistry ; DNA/genetics ; Nucleic Acid Hybridization ; Polymerase Chain Reaction
    Chemical Substances DNA (9007-49-2)
    Language English
    Publishing date 2015-04-30
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.5b02165
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Book ; Online: Programmable DNA-mediated multitasking processor

    Shu, Jian-Jun / Wang, Qi-Wen / Yong, Kian-Yan / Shao, Fangwei / Lee, Kee Jin

    2015  

    Abstract: Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing ... ...

    Abstract Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and processing substrates to tackle the computational problems. The massive parallelism of DNA hybridization exhibits transcendent potential to improve multitasking capabilities and yield a tremendous speed-up over the conventional electronic processors with stepwise signal cascade. As an example of multitasking capability, we present an in vitro programmable DNA-mediated optimal route planning processor as a functional unit embedded in contemporary navigation systems. The novel programmable DNA-mediated processor has several advantages over the existing silicon-mediated methods, such as conducting massive data storage and simultaneous processing via much fewer materials than conventional silicon devices.
    Keywords Physics - Biological Physics
    Subject code 612
    Publishing date 2015-08-14
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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