Displaying publications 1 - 20 of 28 in total

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  1. Proteomics of edible mushrooms: A mini-review
    Al-Obaidi JR
    Electrophoresis, 2016 05;37(10):1257-63.
    PMID: 26891916 DOI: 10.1002/elps.201600031
    Mushrooms are considered an important food for their traditionally famous nutritional and medicinal values, although much information about their potential at the molecular level is unfortunately unknown. Edible mushrooms include fungi that are either collected wild or cultivated. Many important species are difficult to cultivate but attempts have been made with varying degrees of success, with the results showing unsatisfactory economical cultivation methods. Recently, proteomic analysis has been developed as a powerful tool to study the protein content of fungi, particularly basidiomycetes. This mini-review article highlights the contribution of proteomics platforms to the study of edible mushrooms, focusing on the molecular mechanisms involved in developmental stages. This includes extracellular and cytoplasmic effector proteins that have potential or are involved in the synthesis of anticancer, antidiabetic, antioxidant, and antibiotic, in blood pressure control, in the supply of vitamins and minerals, and in other responses to environmental changes. The contribution of different proteomics techniques including classical and more advanced techniques is also highlighted.
  2. Mycopharmaceuticals and Nutraceuticals: Promising Agents to Improve Human Well-Being and Life Quality
    Al-Obaidi JR, Jambari NN, Ahmad-Kamil EI
    J Fungi (Basel), 2021 Jun 24;7(7).
    PMID: 34202552 DOI: 10.3390/jof7070503
    Fungi, especially edible mushrooms, are considered as high-quality food with nutritive and functional values. They are of considerable interest and have been used in the synthesis of nutraceutical supplements due to their medicinal properties and economic significance. Specific fungal groups, including predominantly filamentous endophytic fungi from Ascomycete phylum and several Basidiomycetes, produce secondary metabolites (SMs) with bioactive properties that are involved in the antimicrobial and antioxidant activities. These beneficial fungi, while high in protein and important fat contents, are also a great source of several minerals and vitamins, in particular B vitamins that play important roles in carbohydrate and fat metabolism and the maintenance of the nervous system. This review article will summarize and discuss the abilities of fungi to produce antioxidant, anticancer, antiobesity, and antidiabetic molecules while also reviewing the evidence from the last decade on the importance of research in fungi related products with direct and indirect impact on human health.
  3. Comparative Proteomic Analysis on Fruit Ripening Processes in Two Varieties of Tropical Mango (Mangifera indica)
    Chin CF, Teoh EY, Chee MJY, Al-Obaidi JR, Rahmad N, Lawson T
    Protein J, 2019 12;38(6):704-715.
    PMID: 31552579 DOI: 10.1007/s10930-019-09868-x
    Mango (Mangifera indica L.) is an economically important fruit. However, the marketability of mango is affected by the perishable nature and short shelf-life of the fruit. Therefore, a better understanding of the mango ripening process is of great importance towards extending its postharvest shelf life. Proteomics is a powerful tool that can be used to elucidate the complex ripening process at the cellular and molecular levels. This study utilized 2-dimensional gel electrophoresis (2D-GE) coupled with MALDI-TOF/TOF to identify differentially abundant proteins during the ripening process of the two varieties of tropical mango, Mangifera indica cv. 'Chokanan' and Mangifera indica cv 'Golden Phoenix'. The comparative analysis between the ripe and unripe stages of mango fruit mesocarp revealed that the differentially abundant proteins identified could be grouped into the three categories namely, ethylene synthesis and aromatic volatiles, cell wall degradation and stress-response proteins. There was an additional category for differential proteins identified from the 'Chokanan' variety namely, energy and carbohydrate metabolism. However, of all the differential proteins identified, only methionine gamma-lyase was found in both 'Chokanan' and 'Golden Phoenix' varieties. Six differential proteins were selected from each variety for validation by analysing their respective transcript expression using reverse transcription-quantitative PCR (RT-qPCR). The results revealed that two genes namely, glutathione S-transferase (GST) and alpha-1,4 glucan phosphorylase (AGP) were found to express in concordant with protein abundant. The findings will provide an insight into the fruit ripening process of different varieties of mango fruits, which is important for postharvest management.
  4. Comparison of Different Protein Extraction Methods for Gel-Based Proteomic Analysis of Ganoderma spp
    Al-Obaidi JR, Saidi NB, Usuldin SR, Hussin SN, Yusoff NM, Idris AS
    Protein J, 2016 Apr;35(2):100-6.
    PMID: 27016942 DOI: 10.1007/s10930-016-9656-z
    Ganoderma species are a group of fungi that have the ability to degrade lignin polymers and cause severe diseases such as stem and root rot and can infect economically important plants and perennial crops such as oil palm, especially in tropical countries such as Malaysia. Unfortunately, very little is known about the complex interplay between oil palm and Ganoderma in the pathogenesis of the diseases. Proteomic technologies are simple yet powerful tools in comparing protein profile and have been widely used to study plant-fungus interaction. A critical step to perform a good proteome research is to establish a method that gives the best quality and a wide coverage of total proteins. Despite the availability of various protein extraction protocols from pathogenic fungi in the literature, no single extraction method was found suitable for all types of pathogenic fungi. To develop an optimized protein extraction protocol for 2-DE gel analysis of Ganoderma spp., three previously reported protein extraction protocols were compared: trichloroacetic acid, sucrose and phenol/ammonium acetate in methanol. The third method was found to give the most reproducible gels and highest protein concentration. Using the later method, a total of 10 protein spots (5 from each species) were successfully identified. Hence, the results from this study propose phenol/ammonium acetate in methanol as the most effective protein extraction method for 2-DE proteomic studies of Ganoderma spp.
  5. Proteomics of Sago Palm Towards Identifying Contributory Proteins in Stress-Tolerant Cultivar
    Hussain H, Mustafa Kamal M, Al-Obaidi JR, Hamdin NE, Ngaini Z, Mohd-Yusuf Y
    Protein J, 2020 02;39(1):62-72.
    PMID: 31863255 DOI: 10.1007/s10930-019-09878-9
    Metroxylon sagu Rottb. or locally known as sago palm is a tropical starch crop grown for starch production in commercial plantations in Malaysia, especially in Sarawak, East Malaysia. This plant species accumulate the highest amount of edible starch compared to other starch-producing crops. However, the non-trunking phenomenon has been observed to be one of the major issues restricting the yield of sago palm starch. In this study, proteomics approach was utilised to discover differences between trunking and non-trunking proteomes in sago palm leaf tissues. Total protein from 16 years old trunking and non-trunking sago palm leaves from deep peat area were extracted with PEG fractionation extraction method and subjected to two-dimensional gel electrophoresis (2D PAGE). Differential protein spots were subjected to MALDI-ToF/ToF MS/MS. Proteomic analysis has identified 34 differentially expressed proteins between trunking and non-trunking sago samples. From these protein spots, all 19 proteins representing different enzymes and proteins have significantly increased in abundance in non-trunking sago plant when subjected to mass spectrometry. The identified proteins mostly function in metabolic pathways including photosynthesis, tricarboxylic acid cycle, glycolysis, carbon utilization and oxidative stress. The current study indicated that the several proteins identified through differentially expressed proteome contributed to physical differences in trunking and non-trunking sago palm.
  6. Cytotoxic and cell cycle arrest induction of pentacyclic triterpenoides separated from Lantana camara leaves against MCF-7 cell line in vitro
    Shamsee ZR, Al-Saffar AZ, Al-Shanon AF, Al-Obaidi JR
    Mol Biol Rep, 2019 Feb;46(1):381-390.
    PMID: 30426385 DOI: 10.1007/s11033-018-4482-3
    Lantana camara is an important medicinal plant that contains many active compounds, including pentacyclic triterpenoids, with numerous biological activities. The present study was conducted to evaluate the anti-oxidant, anti-tumour, and cell cycle arrest properties of chemical compounds extracted from L. camara leaves. Four compounds were identified after subjecting the plant methanolic extract to LC-MS/MS analysis: lantadene A, lantadene B, icterogenin, and lantadene C. Potential antioxidant activity was examined using 2, 2-diphenyl-1-picrylhydrazyl and compared with vitamin C as a control. Lantadene A and B were confirmed to possess the highest scavenging activity, while icterogenin and lantadene C exhibited a lesser antioxidant effect. All extracted compounds exerted a dose-dependent reduction in MCF-7 cell viability; however, lantadene B showed the highest anti-cancer activity, with an IC50 of 112.2 μg mL-1, and was therefore used in subsequent experiments. The results also confirmed the significant release of caspase 9 in a dose-dependent pattern following treatment of MCF-7 cells with a range of lantadene B concentrations. Lantadene B was found to induce MCF-7 cell cycle arrest in G1, blocking the G1/S transition with a maximum significant (p ≤ 0.01) cell count of 80.35% at 25 µg mL-1. No significant changes were observed in S phase, but a decrease in the MCF-7 population was exhibited in G2/M phase.
  7. Protein profile of MCF-7 breast cancer cell line treated with lectin delivered by CaCO3NPs revealed changes in molecular chaperones, cytoskeleton, and membrane-associated proteins
    Mahmood RI, Abbass AK, Razali N, Al-Saffar AZ, Al-Obaidi JR
    Int J Biol Macromol, 2021 Aug 01;184:636-647.
    PMID: 34174302 DOI: 10.1016/j.ijbiomac.2021.06.144
    The second most predominant cancer in the world and the first among women is breast cancer. We aimed to study the protein abundance profiles induced by lectin purified from the Agaricus bisporus mushroom (ABL) and conjugated with CaCO3NPs in the MCF-7 breast cancer cell line. Two-dimensional electrophoresis (2-DE) and orbitrap mass spectrometry techniques were used to reveal the protein abundance pattern induced by lectin. Flow cytometric analysis showed the accumulation of ABL-CaCO3NPs treated cells in the G1 phase than the positive control. Thirteen proteins were found different in their abundance in breast cancer cells after 24 h exposure to lectin conjugated with CaCO3NPs. Most of the identified proteins were showing a low abundance in ABL-CaCO3NPs treated cells in comparison to the positive and negative controls, including V-set and immunoglobulin domain, serum albumin, actin cytoplasmic 1, triosephosphate isomerase, tropomyosin alpha-4 chain, and endoplasmic reticulum chaperone BiP. Hornerin, tropomyosin alpha-1 chain, annexin A2, and protein disulfide-isomerase were up-regulated in comparison to the positive. Bioinformatic analyses revealed the regulation changes of these proteins mainly affected the pathways of 'Bcl-2-associated athanogene 2 signalling pathway', 'Unfolded protein response', 'Caveolar-mediated endocytosis signalling', 'Clathrin-mediated endocytosis signalling', 'Calcium signalling' and 'Sucrose degradation V', which are associated with breast cancer. We concluded that lectin altered the abundance in molecular chaperones/heat shock proteins, cytoskeletal, and metabolic proteins. Additionally, lectin induced a low abundance of MCF-7 cancer cell proteins in comparison to the positive and negative controls, including; V-set and immunoglobulin domain, serum albumin, actin cytoplasmic 1, triosephosphate isomerase, tropomyosin alpha-4 chain, and endoplasmic reticulum chaperone BiP.
  8. Fulltext Methicillin-Resistant Staphylococcus aureus Biofilms and Their Influence on Bacterial Adhesion and Cohesion
    Dakheel KH, Abdul Rahim R, Neela VK, Al-Obaidi JR, Hun TG, Yusoff K
    Biomed Res Int, 2016;2016:4708425.
    PMID: 28078291 DOI: 10.1155/2016/4708425
    Twenty-five methicillin-resistant Staphylococcus aureus (MRSA) isolates were characterized by staphylococcal protein A gene typing and the ability to form biofilms. The presence of exopolysaccharides, proteins, and extracellular DNA and RNA in biofilms was assessed by a dispersal assay. In addition, cell adhesion to surfaces and cell cohesion were evaluated using the packed-bead method and mechanical disruption, respectively. The predominant genotype was spa type t127 (22 out of 25 isolates); the majority of isolates were categorized as moderate biofilm producers. Twelve isolates displayed PIA-independent biofilm formation, while the remaining 13 isolates were PIA-dependent. Both groups showed strong dispersal in response to RNase and DNase digestion followed by proteinase K treatment. PIA-dependent biofilms showed variable dispersal after sodium metaperiodate treatment, whereas PIA-independent biofilms showed enhanced biofilm formation. There was no correlation between the extent of biofilm formation or biofilm components and the adhesion or cohesion abilities of the bacteria, but the efficiency of adherence to glass beads increased after biofilm depletion. In conclusion, nucleic acids and proteins formed the main components of the MRSA clone t127 biofilm matrix, and there seems to be an association between adhesion and cohesion in the biofilms tested.
  9. Proteomic and metabolomic study of wax apple (Syzygium samarangense) fruit during ripening process
    Jamil NAM, Rahmad N, Rosli NHM, Al-Obaidi JR
    Electrophoresis, 2018 12;39(23):2954-2964.
    PMID: 30074628 DOI: 10.1002/elps.201800185
    Wax apple is one of the underutilized fruits that is considered a good source of fibers, vitamins, minerals as well as antioxidants. In this study, a comparative analysis of the developments of wax fruit ripening at the proteomic and metabolomic level was reported. 2D electrophoresis coupled with MALDI-TOF/TOF was used to compare the proteome profile from three developmental stages named immature, young, and mature fruits. In general, the protein expression profile and the identified proteins function were discussed for their potential roles in fruit physiological development and ripening processes. The metabolomic investigation was also performed on the same samples using quadrupole LC-MS (LC-QTOF/MS). Roles of some of the differentially expressed proteins and metabolites are discussed in relation to wax apple ripening during the development. This is the first study investigating the changes in the proteins and metabolites in wax apple at different developmental stages. The information obtained from this research will be helpful in developing biomarkers for breeders and help the plant researchers to avoid wax apple cultivation problems such as fruit cracking.
  10. Comparative nutritional and mycochemical contents, biological activities and LC/MS screening of tuber from new recipe cultivation technique with wild type tuber of tiger's milk mushroom of species Lignosus rhinocerus
    Jamil NAM, Rashid NMN, Hamid MHA, Rahmad N, Al-Obaidi JR
    World J Microbiol Biotechnol, 2017 Dec 04;34(1):1.
    PMID: 29204733 DOI: 10.1007/s11274-017-2385-4
    Tiger's milk mushroom is known for its valuable medicinal properties, especially the tuber part. However, wild tuber is very hard to obtain as it grows underground. This study first aimed to cultivate tiger's milk mushroom tuber through a cultivation technique, and second to compare nutritional and mycochemical contents, antioxidant and cytotoxic activities and compound screening of the cultivated tuber with the wild tuber. Results showed an increase in carbohydrate content by 45.81% and protein content by 123.68% in the cultivated tuber while fat content reduced by 13.04%. Cultivated tuber also showed an increase of up to 64.21% for total flavonoid-like compounds and 62.51% of total β-D-glucan compared to the wild tuber. The antioxidant activity of cultivated tuber and wild tuber was 760 and 840 µg mL-1, respectively. The cytotoxic activity of boiled water extract of cultivated tuber against a human lung cancer cell line (A549) was 65.50 ± 2.12 µg mL-1 and against a human breast cancer cell line (MCF7) was 19.35 ± 0.11 µg mL-1. β-D-glucan extract from the purification of boiled water extract of cultivated tuber showed cytotoxic activity at 57.78 ± 2.29 µg mL-1 against A549 and 33.50 ± 1.41 µg mL-1 against MCF7. However, the β-glucan extract from wild tuber did not show a cytotoxic effect against either the A549 or MCF7 cell lines. Also, neither of the extracts from cultivated tuber and wild tuber showed an effect against a normal cell line (MRC5). Compound profiling through by liquid chromatography mass spectrometry (LC/MS) showed the appearance of new compounds in the cultivated tuber. In conclusion, our cultivated tuber of tiger's milk mushroom using a new recipe cultivation technique showed improved nutrient and bioactive compound contents, and antioxidant and cytotoxic activities compared to the wild tuber. Further investigations are required to obtain a better quality of cultivated tuber.
  11. Antiproliferative and cell cycle arrest potentials of 3-O-acetyl-11-keto-β-boswellic acid against MCF-7 cells in vitro
    Ahmed SA, Al-Shanon AF, Al-Saffar AZ, Tawang A, Al-Obaidi JR
    J Genet Eng Biotechnol, 2023 Jul 02;21(1):75.
    PMID: 37393563 DOI: 10.1186/s43141-023-00529-2
    INTRODUCTION: Cancer is a major issue in medical science with increasing death cases every year worldwide. Therefore, searching for alternatives and nonorthodox methods of treatments with high efficiency, selectivity and less toxicity is the main goal in fighting cancer. Acetyl-11-keto-β-boswellic acid (AKBA), is a derivative pentacyclic triterpenoid that exhibited various biological activities with potential anti-tumoral agents. In this research, AKBA was utilized to examine the potential cytotoxic activity against MCF-7 cells in vitro and monitor the cellular and morphological changes with a prospective impact on apoptosis induction.

    METHODS: The cytotoxic activity of AKBA was measured by 3(4,5dimethylthiazole- 2-yl)-2,5 diphyneltetrazolium bromide (MTT) assay. A dose-dependent inhibition in MCF-7 cell viability was detected. The clonogenicity of MCF-7 cells was significantly suppressed by AKBA increment in comparison with untreated cells.

    RESULT: Morphologically, exposure of MCF-7 cells to high AKBA concentrations caused changes in cell nuclear morphology which was indicated by increasing in nuclear size and cell permeability intensity. The mitochondrial membrane potential (ΔΨm) was reduced by increasing AKBA concentration with a significant release of cytochrome c. Acridine orange/ethidium bromide dual staining experiment confirmed that MCF-7 cells treated with AKBA (IC50 concentration) displayed a late stage of apoptosis indicated by intense and bright reddish colour.

    CONCLUSION: A significant increase in reactive oxygen species formation was observed. Caspase 8 and caspase 9 activities were estimated and AKBA activated the production of caspase 8 and caspase 9 in a dose-dependent pattern. Finally, the cell phase distribution analysis was conducted, and flow cytometric analysis showed that AKBA at 200 μg mL-1 significantly arrest MCF-7 cells at the G1 phase and triggered apoptosis.

  12. Fulltext Determination of the Use of Lactobacillus plantarum and Propionibacterium freudenreichii Application on Fermentation Profile and Chemical Composition of Corn Silage
    Abdul Rahman N, Abd Halim MR, Mahawi N, Hasnudin H, Al-Obaidi JR, Abdullah N
    Biomed Res Int, 2017;2017:2038062.
    PMID: 28503566 DOI: 10.1155/2017/2038062
    Corn was inoculated with Lactobacillus plantarum and Propionibacterium freudenreichii subsp. shermanii either independently or as a mixture at ensiling, in order to determine the effect of bacterial additives on corn silage quality. Grain corn was harvested at 32-37% of dry matter and ensiled in a 4 L laboratory silo. Forage was treated as follows: bacterial types: B0 (without bacteria-control), B1 (L. plantarum), B2 (P. freudenreichii subsp. shermanii), and B3 (combination of L. plantarum and P. freudenreichii subsp. shermanii). Each 2 kg of chopped forage was treated with 10 mL of bacterial culture and allowed to ferment for 27 days. The first experiment determined the most suitable wavelength for detection of bacteria (490 nm and 419 nm for B1 and B2, resp.) and the preferable inoculation size (1 × 105 cfu/g). The second experiment analysed the effect of B1 and B2 applied singly or as a mixture on the fermentation characteristics and quality of corn silage. L. plantarum alone increased crude protein (CP) and reduced pH rapidly. In a mixture with P. freudenreichii, the final pH was the lowest compared to other treatments. As a mixture, inclusion of bacteria resulted in silage with lower digestibility than control. Corn silage treated with L. plantarum or P. freudenreichii either alone or mixed together produced desirable silage properties; however, this was not significantly better than untreated silage.
  13. Fulltext A review on plant importance, biotechnological aspects, and cultivation challenges of jojoba plant
    Al-Obaidi JR, Halabi MF, AlKhalifah NS, Asanar S, Al-Soqeer AA, Attia MF
    Biol Res, 2017 Aug 24;50(1):25.
    PMID: 28838321 DOI: 10.1186/s40659-017-0131-x
    Jojoba is considered a promising oil crop and is cultivated for diverse purposes in many countries. The jojoba seed produces unique high-quality oil with a wide range of applications such as medical and industrial-related products. The plant also has potential value in combatting desertification and land degradation in dry and semi-dry areas. Although the plant is known for its high-temperature and high-salinity tolerance growth ability, issues such as its male-biased ratio, relatively late flowering and seed production time hamper the cultivation of this plant. The development of efficient biotechnological platforms for better cultivation and an improved production cycle is a necessity for farmers cultivating the plant. In the last 20 years, many efforts have been made for in vitro cultivation of jojoba by applying different molecular biology techniques. However, there is a lot of work to be done in order to reach satisfactory results that help to overcome cultivation problems. This review presents a historical overview, the medical and industrial importance of the jojoba plant, agronomy aspects and nutrient requirements for the plant's cultivation, and the role of recent biotechnology and molecular biology findings in jojoba research.
  14. How plants respond to heavy metal contamination: a narrative review of proteomic studies and phytoremediation applications
    Al-Obaidi JR, Jamaludin AA, Rahman NA, Ahmad-Kamil EI
    Planta, 2024 Mar 29;259(5):103.
    PMID: 38551683 DOI: 10.1007/s00425-024-04378-2
    Heavy metal pollution caused by human activities is a serious threat to the environment and human health. Plants have evolved sophisticated defence systems to deal with heavy metal stress, with proteins and enzymes serving as critical intercepting agents for heavy metal toxicity reduction. Proteomics continues to be effective in identifying markers associated with stress response and metabolic processes. This review explores the complex interactions between heavy metal pollution and plant physiology, with an emphasis on proteomic and biotechnological perspectives. Over the last century, accelerated industrialization, agriculture activities, energy production, and urbanization have established a constant need for natural resources, resulting in environmental degradation. The widespread buildup of heavy metals in ecosystems as a result of human activity is especially concerning. Although some heavy metals are required by organisms in trace amounts, high concentrations pose serious risks to the ecosystem and human health. As immobile organisms, plants are directly exposed to heavy metal contamination, prompting the development of robust defence mechanisms. Proteomics has been used to understand how plants react to heavy metal stress. The development of proteomic techniques offers promising opportunities to improve plant tolerance to toxicity from heavy metals. Additionally, there is substantial scope for phytoremediation, a sustainable method that uses plants to extract, sequester, or eliminate contaminants in the context of changes in protein expression and total protein behaviour. Changes in proteins and enzymatic activities have been highlighted to illuminate the complex effects of heavy metal pollution on plant metabolism, and how proteomic research has revealed the plant's ability to mitigate heavy metal toxicity by intercepting vital nutrients, organic substances, and/or microorganisms.
  15. Fulltext Identification of proteins of altered abundance in oil palm infected with Ganoderma boninense
    Al-Obaidi JR, Mohd-Yusuf Y, Razali N, Jayapalan JJ, Tey CC, Md-Noh N, et al.
    Int J Mol Sci, 2014;15(3):5175-92.
    PMID: 24663087 DOI: 10.3390/ijms15035175
    Basal stem rot is a common disease that affects oil palm, causing loss of yield and finally killing the trees. The disease, caused by fungus Ganoderma boninense, devastates thousands of hectares of oil palm plantings in Southeast Asia every year. In the present study, root proteins of healthy oil palm seedlings, and those infected with G. boninense, were analyzed by 2-dimensional gel electrophoresis (2-DE). When the 2-DE profiles were analyzed for proteins, which exhibit consistent significant change of abundance upon infection with G. boninense, 21 passed our screening criteria. Subsequent analyses by mass spectrometry and database search identified caffeoyl-CoA O-methyltransferase, caffeic acid O-methyltransferase, enolase, fructokinase, cysteine synthase, malate dehydrogenase, and ATP synthase as among proteins of which abundances were markedly altered.
  16. Fulltext Genomic analyses of two novel biofilm-degrading methicillin-resistant Staphylococcus aureus phages
    Dakheel KH, Rahim RA, Neela VK, Al-Obaidi JR, Hun TG, Isa MNM, et al.
    BMC Microbiol, 2019 05 28;19(1):114.
    PMID: 31138130 DOI: 10.1186/s12866-019-1484-9
    BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) biofilm producers represent an important etiological agent of many chronic human infections. Antibiotics and host immune responses are largely ineffective against bacteria within biofilms. Alternative actions and novel antimicrobials should be considered. In this context, the use of phages to destroy MRSA biofilms presents an innovative alternative mechanism.

    RESULTS: Twenty-five MRSA biofilm producers were used as substrates to isolate MRSA-specific phages. Despite the difficulties in obtaining an isolate of this phage, two phages (UPMK_1 and UPMK_2) were isolated. Both phages varied in their ability to produce halos around their plaques, host infectivity, one-step growth curves, and electron microscopy features. Furthermore, both phages demonstrated antagonistic infectivity on planktonic cultures. This was validated in an in vitro static biofilm assay (in microtiter-plates), followed by the visualization of the biofilm architecture in situ via confocal laser scanning microscopy before and after phage infection, and further supported by phages genome analysis. The UPMK_1 genome comprised 152,788 bp coding for 155 putative open reading frames (ORFs), and its genome characteristics were between the Myoviridae and Siphoviridae family, though the morphological features confined it more to the Siphoviridae family. The UPMK_2 has 40,955 bp with 62 putative ORFs; morphologically, it presented the features of the Podoviridae though its genome did not show similarity with any of the S. aureus in the Podoviridae family. Both phages possess lytic enzymes that were associated with a high ability to degrade biofilms as shown in the microtiter plate and CLSM analyses.

    CONCLUSIONS: The present work addressed the possibility of using phages as potential biocontrol agents for biofilm-producing MRSA.

  17. Proteomic analysis revealed the biofilm-degradation abilities of the bacteriophage UPMK_1 and UPMK_2 against Methicillin-resistant Staphylococcus aureus
    Dakheel KH, Abdul Rahim R, Al-Obaidi JR, Neela VK, Hun TG, Mat Isa MN, et al.
    Biotechnol Lett, 2022 Feb 05.
    PMID: 35122191 DOI: 10.1007/s10529-022-03229-y
    OBJECTIVE: The degradation activity of two bacteriophages UPMK_1 and UPMK_2 against methicillin-resistant Staphylococcus aureus phages were examined using gel zymography.

    METHODS: The analysis was done using BLASTP to detect peptides catalytic domains. Many peptides that are related to several phage proteins were revealed.

    RESULTS: UPMK_1 and UPMK_2 custom sequence database were used for peptide identification. The biofilm-degrading proteins in the bacteriophage UPMK_2 revealed the same lytic activity towards polysaccharide intercellular adhesin-dependent and independent of Methicillin-resistant Staphylococcus aureus (MRSA) biofilm producers in comparison to UPMK_1, which had lytic activity restricted solely to its host.

    CONCLUSION: Both bacteriophage enzymes were involved in MRSA biofilm degradation during phage infection and they have promising enzybiotics properties against MRSA biofilm formation.

  18. Fulltext Convalescent-plasma-transfusion intelligent framework for rescuing COVID-19 patients across centralised/decentralised telemedicine hospitals based on AHP-group TOPSIS and matching component
    Mohammed TJ, Albahri AS, Zaidan AA, Albahri OS, Al-Obaidi JR, Zaidan BB, et al.
    Appl Intell (Dordr), 2021;51(5):2956-2987.
    PMID: 34764579 DOI: 10.1007/s10489-020-02169-2
    As coronavirus disease 2019 (COVID-19) spreads across the world, the transfusion of efficient convalescent plasma (CP) to the most critical patients can be the primary approach to preventing the virus spread and treating the disease, and this strategy is considered as an intelligent computing concern. In providing an automated intelligent computing solution to select the appropriate CP for the most critical patients with COVID-19, two challenges aspects are bound to be faced: (1) distributed hospital management aspects (including scalability and management issues for prioritising COVID-19 patients and donors simultaneously), and (2) technical aspects (including the lack of COVID-19 dataset availability of patients and donors and an accurate matching process amongst them considering all blood types). Based on previous reports, no study has provided a solution for CP-transfusion-rescue intelligent framework during this pandemic that has addressed said challenges and issues. This study aimed to propose a novel CP-transfusion intelligent framework for rescuing COVID-19 patients across centralised/decentralised telemedicine hospitals based on the matching component process to provide an efficient CP from eligible donors to the most critical patients using multicriteria decision-making (MCDM) methods. A dataset, including COVID-19 patients/donors that have met the important criteria in the virology field, must be augmented to improve the developed framework. Four consecutive phases conclude the methodology. In the first phase, a new COVID-19 dataset is generated on the basis of medical-reference ranges by specialised experts in the virology field. The simulation data are classified into 80 patients and 80 donors on the basis of the five biomarker criteria with four blood types (i.e., A, B, AB, and O) and produced for COVID-19 case study. In the second phase, the identification scenario of patient/donor distributions across four centralised/decentralised telemedicine hospitals is identified 'as a proof of concept'. In the third phase, three stages are conducted to develop a CP-transfusion-rescue framework. In the first stage, two decision matrices are adopted and developed on the basis of the five 'serological/protein biomarker' criteria for the prioritisation of patient/donor lists. In the second stage, MCDM techniques are analysed to adopt individual and group decision making based on integrated AHP-TOPSIS as suitable methods. In the third stage, the intelligent matching components amongst patients/donors are developed on the basis of four distinct rules. In the final phase, the guideline of the objective validation steps is reported. The intelligent framework implies the benefits and strength weights of biomarker criteria to the priority configuration results and can obtain efficient CPs for the most critical patients. The execution of matching components possesses the scalability and balancing presentation within centralised/decentralised hospitals. The objective validation results indicate that the ranking is valid.
  19. Enhancing orthodontic treatment control with fish scale-derived hydroxyapatite nanoparticles: Insights from an animal model study
    Mohammed-Salih HS, Ghazi A, Mahmood RI, Al-Qazzaz HH, Supian FL, Al-Obaidi JR, et al.
    Saudi Dent J, 2024 Aug;36(8):1128-1134.
    PMID: 39176163 DOI: 10.1016/j.sdentj.2024.06.007
    OBJECTIVES: This study investigates the impact of injected fish-scale-derived hydroxyapatite nanoparticles (FsHA-NPs) on orthodontic tooth movement (OTM) and the width of the periodontal ligament (PDL) space.

    MATERIALS AND METHODS: Twenty-six Wistar rats underwent mesial orthodontic traction with a force of 50 g for 21 days. Following the application of the orthodontic appliance, the rats were randomly divided into two groups: a control group, which received a 0.3 µg saline injection, and the experimental FsHA group, which received 100 mg/0.3 ml of FsHA-NPs after thorough characterisation. Injections were administered immediately after appliance application and repeated at 7 and 14 days. Statistical analysis was conducted with a significance level of P ≤ 0.05.

    RESULT: The experimental group exhibited a significant reduction in OTM at 7-, 14-, and 21-day post-force application. Additionally, a reduction in PDL width was observed in the mesiocervical and disto-apical regions of the mesial and distal roots of the first molar.

    CONCLUSION: FsHA-NPs derived from biowaste fish scales exhibit promising potential as biomaterials for enhancing control over OTM. This study underscores the viability, accessibility, and safety of FsHA-NPs as a locally injectable material for orthodontic applications.

  20. Fulltext Rescuing emergency cases of COVID-19 patients: An intelligent real-time MSC transfusion framework based on multicriteria decision-making methods
    Alsalem MA, Albahri OS, Zaidan AA, Al-Obaidi JR, Alnoor A, Alamoodi AH, et al.
    Appl Intell (Dordr), 2022;52(9):9676-9700.
    PMID: 35035091 DOI: 10.1007/s10489-021-02813-5
    Mesenchymal stem cells (MSCs) have shown promising ability to treat critical cases of coronavirus disease 2019 (COVID-19) by regenerating lung cells and reducing immune system overreaction. However, two main challenges need to be addressed first before MSCs can be efficiently transfused to the most critical cases of COVID-19. First is the selection of suitable MSC sources that can meet the standards of stem cell criteria. Second is differentiating COVID-19 patients into different emergency levels automatically and prioritising them in each emergency level. This study presents an efficient real-time MSC transfusion framework based on multicriteria decision-making(MCDM) methods. In the methodology, the testing phase represents the ability to adhere to plastic surfaces, the upregulation and downregulation of specific surface protein markers and finally the ability to differentiate into different kinds of cells. In the development phase, firstly, two scenarios of an augmented dataset based on the medical perspective are generated to produce 80 patients with different emergency levels. Secondly, an automated triage algorithm based on a formal medical guideline is proposed for real-time monitoring of COVID-19 patients with different emergency levels (i.e. mild, moderate, severe and critical) considering the improvement and deterioration procedures from one level to another. Thirdly, a unique decision matrix for each triage level (except mild) is constructed on the basis of the intersection between the evaluation criteria of each emergency level and list of COVID-19 patients. Thereafter, MCDM methods (i.e. analytic hierarchy process [AHP] and vlsekriterijumska optimizcija i kaompromisno resenje [VIKOR]) are integrated to assign subjective weights for the evaluation criteria within each triage level and then prioritise the COVID-19 patients on the basis of individual and group decision-making(GDM) contexts. Results show that: (1) in both scenarios, the proposed algorithm effectively classified the patients into four emergency levels, including mild, moderate, severe and critical, taking into consideration the improvement and deterioration cases. (2) On the basis of experts' perspectives, clear differences in most individual prioritisations for patients with different emergency levels in both scenarios were found. (3) In both scenarios, COVID-19 patients were prioritised identically between the internal and external group VIKOR. During the evaluation, the statistical objective method indicated that the patient prioritisations underwent systematic ranking. Moreover, comparison analysis with previous work proved the efficiency of the proposed framework. Thus, the real-time MSC transfusion for COVID-19 patients can follow the order achieved in the group VIKOR results.
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