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  1. Fulltext Lipoprotein-induced cell growth and hemocyanin biosynthesis in rhogocytes
    Sairi F, Gomes VG, Dehghani F, Valtchev P
    Cell Tissue Res, 2022 May;388(2):359-371.
    PMID: 35088179 DOI: 10.1007/s00441-022-03577-1
    Rhogocyte is a unique molluscan cell that synthesises a supramolecular respiratory protein known as hemocyanin. Its ability to synthesise the protein has eluded the scientists despite hemocyanin's importance as a carrier protein and complex molecule with anti-viral activity. Although a hypothetical model of hemocyanin release from the rhogocytes lacunae was proposed based on colloid-osmotic pressure mechanism, lack of in vitro studies limits further validation of this model. In this study, we aim to investigate the impact of cell culture conditions and nature of hemocyanin biosynthesis of rhogocyte cells dissociated from Haliotis laevigata mantle tissue. Population of cells with different hemocyanin expression levels was profiled using flow cytometry, while hemocyanin concentrations in the media were elucidated by ELISA assay. We demonstrated that addition of lipoprotein supplement into the media resulted in a burst secretion of hemocyanin into the culture media. Over 7 days of culture, the population of cells tagged with hemocyanin antibody increased steadily while hemocyanin release in the media decreased significantly. Variation of culture medium, temperature, growth supplement type and concentration also impacted the cell growth and hemocyanin biosynthesis. These results indicated the possibility of an active process triggered by the addition of supplement to synthesise the protein at the highest amount during the first hour. The current study provides a glimpse of the hemocyanin biosynthesis by rhogocyte that may be significant to understand the cell ability to synthesise supramolecular protein and secretion through lacunae.
  2. Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database
    Al-Khdhairawi A, Sanuri D, Akbar R, Lam SD, Sugumar S, Ibrahim N, et al.
    Comput Biol Chem, 2023 Feb;102:107800.
    PMID: 36516617 DOI: 10.1016/j.compbiolchem.2022.107800
    Antimicrobial peptides (AMPs) are short peptides with a broad spectrum of antimicrobial activity. They play a key role in the host innate immunity of many organisms. The growing threat of microorganisms resistant to antimicrobial agents and the lack of new commercially available antibiotics have made in silico discovery of AMPs increasingly important. Machine learning (ML) has improved the speed and efficiency of AMP discovery while reducing the cost of experimental approaches. Despite various ML platforms developed, there is still a lack of integrative use of ML platforms for AMP discovery from publicly available protein databases. Therefore, our study aims to screen potential AMPs with antibiofilm properties from databases using ML platforms, followed by protein-peptide molecular docking analysis and molecular dynamics (MD) simulations. A total of 5850 peptides classified as non-AMP were screened from UniProtKB and analyzed using various online ML platforms (e.g., CAMPr3, DBAASP, dPABBs, Hemopred, and ToxinPred). Eight potential AMP peptides against Klebsiella pneumoniae with antibiofilm, non-toxic and non-hemolytic properties were then docked to MrkH, a transcriptional regulator of type 3 fimbriae involved in biofilm formation. Five of eight peptides bound more strongly than the native MrkH ligand when analyzed using HADDOCK and HPEPDOCK. Following the docking studies, our MD simulated that a Neuropeptide B (Peptide 3) bind strongly to the MrkH active sites. The discovery of putative AMPs that exceed the binding energies of the native ligand underscores the utility of the combined ML and molecular simulation strategies for discovering novel AMPs with antibiofilm properties.
  3. Fulltext Characterization of putative pathogenic Shewanella algae isolated from ballast water
    Ibrahim NNN, Nasir NM, Sahrani FK, Ahmad A, Sairi F
    Vet World, 2021 Mar;14(3):678-688.
    PMID: 33935414 DOI: 10.14202/vetworld.2021.678-688
    BACKGROUND AND AIM: Shewanella algae is ubiquitous in marine-associated environments and has been increasingly recognized as a significant human pathogen that can cause serious infections mainly associated with exposure to seawater and ingestion of raw seafood. This study aimed to isolate and characterize S. algae from ballast water of ships berthed at Port Klang, Malaysia.

    MATERIALS AND METHODS: Ballast water was sampled from nine ships docked at Port Klang, Malaysia. The isolates were identified and characterized based on biochemical and enzymatic properties, 16S rRNA and gyrB sequencing, biofilm formation capability, and antibiotic susceptibility.

    RESULTS: A total of four S. algae isolates were isolated from four ballast water samples tentatively name Sa-BW1, Sa-BW2, Sa-BW7, and Sa-BW8. All isolates showed positive reaction for cytochrome oxidase, catalase, high tolerance to NaCl (6% and 8%), ability to grow at 42°C, and on Salmonella-Shigella agar. The strains also exhibited b-hemolytic activity on sheep blood and human blood agar, positive reaction for lipase, protease, DNase and gelatinase, strong biofilm adherence capabilities and multiple antibiotic resistances against ampicillin, carbenicillin, cephalothin, colistin, novobiocin, oxacillin, penicillin, rifampicin, and tobramycin which suggested their potential pathogenicity.

    CONCLUSION: This study demonstrated the occurrence of putative pathogen S. algae in ballast water of ships docked at Malaysian port.

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