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  1. Article ; Online: Correction for Ghazali et al., "Transitioning from Soil to Host: Comparative Transcriptome Analysis Reveals the

    Ghazali, Ahmad-Kamal / Firdaus-Raih, Mohd / Uthaya Kumar, Asqwin / Lee, Wei-Kang / Hoh, Chee-Choong / Nathan, Sheila

    Microbiology spectrum

    2024  Volume 12, Issue 4, Page(s) e0052224

    Language English
    Publishing date 2024-03-08
    Publishing country United States
    Document type Journal Article ; Published Erratum
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.00522-24
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Gene introduction approaches in chloroplast transformation and its applications.

    Kumar, Asqwin Uthaya / Ling, Anna Pick Kiong

    Journal, genetic engineering & biotechnology

    2021  Volume 19, Issue 1, Page(s) 148

    Abstract: Background: Chloroplast is a type of plastid that is believed to be originated from ancestral cyanobacteria. Chloroplast besides being a major component for photosynthesis, also takes part in another major plant metabolism, making it one of the major ... ...

    Abstract Background: Chloroplast is a type of plastid that is believed to be originated from ancestral cyanobacteria. Chloroplast besides being a major component for photosynthesis, also takes part in another major plant metabolism, making it one of the major components of plants.
    Main body: Chloroplast transformation is an alternative and better genetic engineering approach compared to the nuclear transformation that has been widely applied in plant genetic engineering. Chloroplast transformation has exhibited various positive effects as compared to nuclear transformation. This is a more preferred technique by researchers. To carry out chloroplast transformation, the vector design must be performed, and a selectable marker needs to be incorporated before the chloroplast could uptake the construct. The common way of introducing a gene into the host, which is the chloroplast, involves the biolistic, PEG-mediated, carbon nanotubes carriers, UV-laser microbeam, and Agrobacterium-mediated transformation approaches. Apart from discussing the processes involved in introducing the gene into the chloroplast, this review also focuses on the various applications brought about by chloroplast transformation, particularly in the field of agriculture and environmental science.
    Conclusion: Chloroplast transformation has shown a lot of advantages and proven to be a better alternative compared to nuclear genome transformation. Further studies must be conducted to uncover new knowledge regarding chloroplast transformation as well as to discover its additional applications in the fields of biotechnology.
    Language English
    Publishing date 2021-10-06
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2637420-1
    ISSN 2090-5920 ; 1687-157X ; 2090-5920
    ISSN (online) 2090-5920
    ISSN 1687-157X ; 2090-5920
    DOI 10.1186/s43141-021-00255-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Transitioning from Soil to Host: Comparative Transcriptome Analysis Reveals the Burkholderia pseudomallei Response to Different Niches.

    Ghazali, Ahmad-Kamal / Firdaus-Raih, Mohd / Uthaya Kumar, Asqwin / Lee, Wei-Kang / Hoh, Chee-Choong / Nathan, Sheila

    Microbiology spectrum

    2023  , Page(s) e0383522

    Abstract: Burkholderia pseudomallei, a soil and water saprophyte, is responsible for the tropical human disease melioidosis. A hundred years since its discovery, there is still much to learn about B. pseudomallei proteins that are essential for the bacterium's ... ...

    Abstract Burkholderia pseudomallei, a soil and water saprophyte, is responsible for the tropical human disease melioidosis. A hundred years since its discovery, there is still much to learn about B. pseudomallei proteins that are essential for the bacterium's survival in and interaction with the infected host, as well as their roles within the bacterium's natural soil habitat. To address this gap, bacteria grown under conditions mimicking the soil environment were subjected to transcriptome sequencing (RNA-seq) analysis. A dual RNA-seq approach was used on total RNA from spleens isolated from a B. pseudomallei mouse infection model at 5 days postinfection. Under these conditions, a total of 1,434 bacterial genes were induced, with 959 induced in the soil environment and 475 induced in bacteria residing within the host. Genes encoding metabolism and transporter proteins were induced when the bacteria were present in soil, while virulence factors, metabolism, and bacterial defense mechanisms were upregulated during active infection of mice. On the other hand, capsular polysaccharide and quorum-sensing pathways were inhibited during infection. In addition to virulence factors, reactive oxygen species, heat shock proteins, siderophores, and secondary metabolites were also induced to assist bacterial adaptation and survival in the host. Overall, this study provides crucial insights into the transcriptome-level adaptations which facilitate infection by soil-dwelling B. pseudomallei. Targeting novel therapeutics toward B. pseudomallei proteins required for adaptation provides an alternative treatment strategy given its intrinsic antimicrobial resistance and the absence of a vaccine.
    Language English
    Publishing date 2023-03-01
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2807133-5
    ISSN 2165-0497 ; 2165-0497
    ISSN (online) 2165-0497
    ISSN 2165-0497
    DOI 10.1128/spectrum.03835-22
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Bioinformatics approaches and applications in plant biotechnology.

    Tan, Yung Cheng / Kumar, Asqwin Uthaya / Wong, Ying Pei / Ling, Anna Pick Kiong

    Journal, genetic engineering & biotechnology

    2022  Volume 20, Issue 1, Page(s) 106

    Abstract: Background: In recent years, major advance in molecular biology and genomic technologies have led to an exponential growth in biological information. As the deluge of genomic information, there is a parallel growth in the demands of tools in the storage ...

    Abstract Background: In recent years, major advance in molecular biology and genomic technologies have led to an exponential growth in biological information. As the deluge of genomic information, there is a parallel growth in the demands of tools in the storage and management of data, and the development of software for analysis, visualization, modelling, and prediction of large data set.
    Main body: Particularly in plant biotechnology, the amount of information has multiplied exponentially with a large number of databases available from many individual plant species. Efficient bioinformatics tools and methodologies are also developed to allow rapid genome sequence and the study of plant genome in the 'omics' approach. This review focuses on the various bioinformatic applications in plant biotechnology, and their advantages in improving the outcome in agriculture. The challenges or limitations faced in plant biotechnology in the aspect of bioinformatics approach that explained the low progression in plant genomics than in animal genomics are also reviewed and assessed.
    Conclusion: There is a critical need for effective bioinformatic tools, which are able to provide longer reads with unbiased coverage in order to overcome the complexity of the plant's genome. The advancement in bioinformatics is not only beneficial to the field of plant biotechnology and agriculture sectors, but will also contribute enormously to the future of humanity.
    Language English
    Publishing date 2022-07-15
    Publishing country Netherlands
    Document type Journal Article ; Review
    ZDB-ID 2637420-1
    ISSN 2090-5920 ; 1687-157X ; 2090-5920
    ISSN (online) 2090-5920
    ISSN 1687-157X ; 2090-5920
    DOI 10.1186/s43141-022-00394-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Current updates and research on plant-based vaccines for coronavirus disease 2019.

    Uthaya Kumar, Asqwin / Kadiresen, Kirthikah / Gan, Wen Cong / Ling, Anna Pick Kiong

    Clinical and experimental vaccine research

    2021  Volume 10, Issue 1, Page(s) 13–23

    Abstract: The primary outbreak of severe acute respiratory syndrome coronavirus 2, causing pneumonia-like symptoms in patients named coronavirus disease 2019 (COVID-19) had evolved into a global pandemic. COVID-19 has surpassed Middle East respiratory syndrome and ...

    Abstract The primary outbreak of severe acute respiratory syndrome coronavirus 2, causing pneumonia-like symptoms in patients named coronavirus disease 2019 (COVID-19) had evolved into a global pandemic. COVID-19 has surpassed Middle East respiratory syndrome and severe acute respiratory syndrome in terms of rate and scale causing more than one million deaths. Development of an effective vaccine to fight against the spread of COVID-19 is the main goal of many countries around the world and plant-based vaccines are one of the available methods in vaccine developments. Plant-based vaccine has gained its reputation among researchers for its known effective manufacturing process and cost effectiveness. Many companies around the world are participating in the race to develop an effective vaccine by using the plant system. This review discusses different approaches used as well as highlights the challenges faced by various companies and research groups in developing the plant-based COVID-19 vaccine.
    Language English
    Publishing date 2021-01-31
    Publishing country Korea (South)
    Document type Journal Article ; Review
    ZDB-ID 2684652-4
    ISSN 2287-366X ; 2287-3651
    ISSN (online) 2287-366X
    ISSN 2287-3651
    DOI 10.7774/cevr.2021.10.1.13
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Identification of B-Cell Epitopes for Eliciting Neutralizing Antibodies against the SARS-CoV-2 Spike Protein through Bioinformatics and Monoclonal Antibody Targeting

    Hui Xuan Lim / Malihe Masomian / Kanwal Khalid / Asqwin Uthaya Kumar / Paul A. MacAry / Chit Laa Poh

    International Journal of Molecular Sciences, Vol 23, Iss 4341, p

    2022  Volume 4341

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global public health crisis. Effective COVID-19 vaccines developed by Pfizer-BioNTech, Moderna, and Astra Zeneca have made significant impacts in controlling the COVID-19 burden, ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global public health crisis. Effective COVID-19 vaccines developed by Pfizer-BioNTech, Moderna, and Astra Zeneca have made significant impacts in controlling the COVID-19 burden, especially in reducing the transmission of SARS-CoV-2 and hospitalization incidences. In view of the emergence of new SARS-CoV-2 variants, vaccines developed against the Wuhan strain were less effective against the variants. Neutralizing antibodies produced by B cells are a critical component of adaptive immunity, particularly in neutralizing viruses by blocking virus attachment and entry into cells. Therefore, the identification of protective linear B-cell epitopes can guide epitope-based peptide designs. This study reviews the identification of SARS-CoV-2 B-cell epitopes within the spike, membrane and nucleocapsid proteins that can be incorporated as potent B-cell epitopes into peptide vaccine constructs. The bioinformatic approach offers a new in silico strategy for the mapping and identification of potential B-cell epitopes and, upon in vivo validation, would be useful for the rapid development of effective multi-epitope-based vaccines. Potent B-cell epitopes were identified from the analysis of three-dimensional structures of monoclonal antibodies in a complex with SARS-CoV-2 from literature mining. This review provides significant insights into the elicitation of potential neutralizing antibodies by potent B-cell epitopes, which could advance the development of multi-epitope peptide vaccines against SARS-CoV-2.
    Keywords B-cell epitope ; vaccine ; SARS-CoV-2 ; spike protein ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Subject code 570
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Identification of B-Cell Epitopes for Eliciting Neutralizing Antibodies against the SARS-CoV-2 Spike Protein through Bioinformatics and Monoclonal Antibody Targeting.

    Lim, Hui Xuan / Masomian, Malihe / Khalid, Kanwal / Kumar, Asqwin Uthaya / MacAry, Paul A / Poh, Chit Laa

    International journal of molecular sciences

    2022  Volume 23, Issue 8

    Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global public health crisis. Effective COVID-19 vaccines developed by Pfizer-BioNTech, Moderna, and Astra Zeneca have made significant impacts in controlling the COVID-19 burden, ... ...

    Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global public health crisis. Effective COVID-19 vaccines developed by Pfizer-BioNTech, Moderna, and Astra Zeneca have made significant impacts in controlling the COVID-19 burden, especially in reducing the transmission of SARS-CoV-2 and hospitalization incidences. In view of the emergence of new SARS-CoV-2 variants, vaccines developed against the Wuhan strain were less effective against the variants. Neutralizing antibodies produced by B cells are a critical component of adaptive immunity, particularly in neutralizing viruses by blocking virus attachment and entry into cells. Therefore, the identification of protective linear B-cell epitopes can guide epitope-based peptide designs. This study reviews the identification of SARS-CoV-2 B-cell epitopes within the spike, membrane and nucleocapsid proteins that can be incorporated as potent B-cell epitopes into peptide vaccine constructs. The bioinformatic approach offers a new in silico strategy for the mapping and identification of potential B-cell epitopes and, upon in vivo validation, would be useful for the rapid development of effective multi-epitope-based vaccines. Potent B-cell epitopes were identified from the analysis of three-dimensional structures of monoclonal antibodies in a complex with SARS-CoV-2 from literature mining. This review provides significant insights into the elicitation of potential neutralizing antibodies by potent B-cell epitopes, which could advance the development of multi-epitope peptide vaccines against SARS-CoV-2.
    MeSH term(s) Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19/prevention & control ; COVID-19 Vaccines ; Computational Biology ; Epitopes, B-Lymphocyte ; Humans ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Vaccines, Subunit
    Chemical Substances Antibodies, Monoclonal ; Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 Vaccines ; Epitopes, B-Lymphocyte ; Spike Glycoprotein, Coronavirus ; Vaccines, Subunit ; spike protein, SARS-CoV-2
    Language English
    Publishing date 2022-04-14
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23084341
    Database MEDical Literature Analysis and Retrieval System OnLINE

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