Displaying publications 21 - 40 of 69 in total

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  1. Tan JB, Lim YY
    Food Chem, 2015 Apr 1;172:814-22.
    PMID: 25442625 DOI: 10.1016/j.foodchem.2014.09.141
    Natural product research is an active branch of science, driven by the increased value placed on individual health and well-being. Many naturally-occurring phytochemicals in plants, fruits and vegetables have been reported to exhibit antioxidant and antibacterial activity; often touted as being beneficial for human health. In vitro screening is a common practice in many research laboratories as a means of rapidly assessing these properties. However, the methods used by many are not necessarily optimal; a result of poor standardization, redundant assays and/or outdated methodology. This review primarily aims to give a better understanding in the selection of in vitro assays, with emphasis placed on some common assays such as the total phenolic content assay, free radical scavenging activity, disc-diffusion and broth microdilution. This includes a discussion on the reasons for choosing a particular assay, its strengths and weaknesses, ways to improve the accuracy of results and alternative assays.
  2. Chen AH, Bleything W, Lim YY
    Optometry, 2011 May;82(5):267-73.
    PMID: 21524597 DOI: 10.1016/j.optm.2011.02.004
    Vision affects daily activities, but of particular importance is the impact upon the learning process. Many studies have been conducted to establish the relationship between vision problems and academic performance. The results are varied, however, and suggest additional research is needed with particular care given to study design.
  3. Tan JB, Lim YY
    BMC Res Notes, 2015;8:468.
    PMID: 26395256 DOI: 10.1186/s13104-015-1414-3
    For generations, the rhizomes of Drynaria ferns have been used as traditional medicine in Asia. Despite this, the bioactivities of Drynaria rhizomes and leaves have rarely been studied scientifically.
  4. Ship CP, Zainudin A, Lim YY
    J Colloid Interface Sci, 1999 Sep 1;217(1):211-213.
    PMID: 10441432
    The rate of hydrolysis of p-nitrophenyldiphenylphosphate in the presence of micellized [Cu(C(12)tmed)(L)](+) where C(12)tmed is N,N,N'-trimethyl-N'-dodecylethylenediamine and L is the anion part of the amino acid has been investigated. It was found that the observed maximum rate obtained under the excess surfactant over the substrate condition depends very much on the ability of the amino acid ligand to form a mixed-chelate complex with the [Cu(C(12)tmed)](2+) moiety. In general, a chelating ligand with better coordination ability gives a slower rate because of the reduction in the supply of Cu-OH nucleophile in the micelle. Copyright 1999 Academic Press.
  5. Oh HKF, Siow LF, Lim YY
    J Food Biochem, 2019 07;43(7):e12856.
    PMID: 31353691 DOI: 10.1111/jfbc.12856
    Different drying methods and blanching were investigated as to their effects on antioxidant and oxidase activities of Thunbergia laurifolia leaves. Results showed that oven-drying had the highest degradation of total phenolic content (TPC) and antioxidant activity at >85%, while freeze-drying had the lowest at <20%. However, inactivation of oxidase enzymes by blanching at 100°C resulted in a lesser decrease in TPC for oven-drying at 50 and 100°C (51% and 65%, respectively), indicating the importance of inactivating the oxidase enzymes for lower degradation of phenolics on drying. The high-performance liquid chromatography analysis showed that its major antioxidant, rosmarinic acid, degraded tremendously in the presence of oxidase enzymes, but only degraded slightly upon inactivation of oxidase enzymes. Hence, this work showed that by controlling the enzymatic activity, the preservation of phenolics with specific bioactivity in herbal tea leaves can be achieved. PRACTICAL APPLICATIONS: Thunbergia laurifolia leaves have been frequently consumed in the form of a tea or pill due to its medicinal properties. Processing of fresh herbal plant leaves by drying is required to preserve antioxidant phenolic compounds and quality of the plant leaves. Although the drying effects on the antioxidant properties have been studied, the factors that cause the change in properties have not been investigated in-depth. Controlling the factors that affect the phenolic content can help to preserve the beneficial antioxidants when processing the leaves by drying. The result of this study will be of relevance and beneficial to the herbal tea industry.
  6. Chew YL, Khor MA, Lim YY
    Heliyon, 2021 Mar;7(3):e06553.
    PMID: 33855234 DOI: 10.1016/j.heliyon.2021.e06553
    Stability indicating assay describes a technique which is used to analyse the stability of drug substance or active pharmaceutical ingredient (API) in bulk drug and pharmaceutical products. Stability indicating assay must be properly validated as per ICH guidelines. The important components in a stability indicating assay include sensitivity, specificity, accuracy, reliability, reproducibility and robustness. A validated assay is able to measure the concentration changes of drug substance/API with time and make reliable estimation of the quantity of the degradation impurities. The drug substance is separated and resolved from the impurities. Pros and cons of HPLC, GC, HPTLC, CE and SFC were discussed and reviewed. Stability indicating assay may consist of the combination of chromatographic separation and spectroscopic detection techniques. Hyphenated system could demonstrate parallel quantitative and qualitative analysis of drug substances and impurities. Examples are HPLC-DAD, HPLC-FL, GC-MS, LC-MS and LC-NMR. The analytes in the samples are separated in the chromatography while the impurities are chemically characterised by the spectroscopy in the system. In this review, various chromatographic methods which had been employed as stability indicating assays for drug substance and pharmaceutical formulation were systematically reviewed, and the application of hyphenated techniques in impurities characterisation and identification were also discussed with supporting literatures.
  7. Tan KE, Lim YY
    FEBS J, 2021 08;288(15):4488-4502.
    PMID: 33236482 DOI: 10.1111/febs.15639
    Circular RNAs (circRNAs) are a recently discovered class of noncoding RNAs found in many species across the eukaryotic kingdom. These intriguing RNA species are formed through a unique mechanism that is known as back splicing in which the 5' and 3' termini are covalently joined. Recent research has revealed that viruses also encode a repertoire of circRNAs. Some of these viral circRNAs are abundantly expressed and are reported to play a role in disease pathogenesis. A growing number of studies also indicate that host circRNAs are involved in immune responses against virus infections with either an antiviral or proviral role. In this review, we briefly introduce circRNA, its biogenesis, and mechanism of action. We go on to summarize the latest research on the expression, regulation, and functions of viral and host-encoded circRNAs during the host-virus interaction, with the aim of highlighting the potential of viral and host circRNAs as a suitable target for diagnostic biomarker development and therapeutic treatment of viral-associated diseases. We conclude by discussing the current limitations in knowledge and significance of elucidating the roles of circRNAs in host-virus interactions, as well as future directions for this emerging field.
  8. Yew PN, Lee WL, Lim YY
    Pharmacognosy Res, 2017 Oct-Dec;9(4):366-371.
    PMID: 29263630 DOI: 10.4103/pr.pr_145_16
    Background: Porcupine dates are phytobezoar stones that are used in Traditional Chinese Medicine (TCM) treatments against cancer, postsurgical recovery, dengue fever, etc. The medicinal values have not been scientifically investigated due to the availability and high pricing of the dates.

    Objectives: This paper represents the first report on the phytochemical content, in vitro antioxidant and intracellular reactive oxygen species (ROS)/reactive nitrogen species (RNS) scavenging properties of the extracts of three porcupine dates: grassy date (GD), black date (BD), and powdery date (PD).

    Materials and Methods: Dried samples were extracted with methanol and lyophilized. Samples were screened for phytochemical constituents, in vitro antioxidant assays based on total phenolic content (TPC), free radical scavenging, and ferric reducing power (FRP) as well as intracellular ROS and RNS scavenging properties.

    Results: Phytochemical screening and total tannins assay revealed that tannins, cardiac glycosides, and terpenoids were found in all porcupine dates with tannins forming the major portion of the TPC. In comparison to GD, BD and PD were found to contain significantly high TPC, radical scavenging activity, and FRP. At 200 μg/ml, BD and PD remarkably scavenged 2, 2-azobis (2-amidinopropane) dihydrochloride-induced ROS in RAW264.7 cells and significantly reduced nitric oxide in lipopolysaccharide-stimulated cells.

    Conclusion: Overall, BD and PD exhibited promising in vitro antioxidant as well as intracellular ROS/RNS scavenging properties.

    SUMMARY: Tannins, cardiac glycoside, and terpenoids were found in all three types of porcupine dates with tannins being the major compoundsAntioxidant contents and properties of three dates were in the order black date (BD) > powdery date (PD) > grassy dateBD and PD extracts showed significant intracellular reactive oxygen species and reactive nitrogen species scavenging properties. Abbreviations Used: TCM: Traditional Chinese Medicine, BD: Black date, GD: Grassy date, PD: Powdery date, TPC: Total phenolic content, FRS: Free radical scavenging, FRP: Ferric reducing power, NO: Nitric oxide, ROS: Reactive oxygen species, RNS: Reactive nitrogen species, GAE: Gallic acid equivalent, AAE: Ascorbic acid equivalent, PVPP: Polyvinylpolypyrrolidone, DCFH-DA: Dichloro-dihydro-fluorescein diacetate, AAPH: 2, 2-azobis (2-amidinopropane) dihydrochloride, LPS: Lipopolysaccharide.
  9. Choong YS, Lee YV, Soong JX, Law CT, Lim YY
    Adv Exp Med Biol, 2017;1053:221-243.
    PMID: 29549642 DOI: 10.1007/978-3-319-72077-7_11
    The use of monoclonal antibody as the next generation protein therapeutics with remarkable success has surged the development of antibody engineering to design molecules for optimizing affinity, better efficacy, greater safety and therapeutic function. Therefore, computational methods have become increasingly important to generate hypotheses, interpret and guide experimental works. In this chapter, we discussed the overall antibody design by computational approches.
  10. Ealam Selvan M, Lim KS, Teo CH, Lim YY
    J Vis Exp, 2022 Oct 21.
    PMID: 36342167 DOI: 10.3791/64565
    Circular RNAs (circRNAs) are a class of non-coding RNAs that are formed via back-splicing. These circRNAs are predominantly studied for their roles as regulators of various biological processes. Notably, emerging evidence demonstrates that host circRNAs can be differentially expressed (DE) upon infection with pathogens (e.g., influenza and coronaviruses), suggesting a role for circRNAs in regulating host innate immune responses. However, investigations on the role of circRNAs during pathogenic infections are limited by the knowledge and skills required to carry out the necessary bioinformatic analysis to identify DE circRNAs from RNA sequencing (RNA-seq) data. Bioinformatics prediction and identification of circRNAs is crucial before any verification, and functional studies using costly and time-consuming wet-lab techniques. To solve this issue, a step-by-step protocol of in silico prediction and characterization of circRNAs using RNA-seq data is provided in this manuscript. The protocol can be divided into four steps: 1) Prediction and quantification of DE circRNAs via the CIRIquant pipeline; 2) Annotation via circBase and characterization of DE circRNAs; 3) CircRNA-miRNA interaction prediction through Circr pipeline; 4) functional enrichment analysis of circRNA parental genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). This pipeline will be useful in driving future in vitro and in vivo research to further unravel the role of circRNAs in host-pathogen interactions.
  11. Tan KE, Ng WL, Marinov GK, Yu KH, Tan LP, Liau ES, et al.
    Sci Rep, 2021 Jul 13;11(1):14392.
    PMID: 34257379 DOI: 10.1038/s41598-021-93781-w
    Epstein-Barr virus (EBV) has been recently found to generate novel circular RNAs (circRNAs) through backsplicing. However, comprehensive catalogs of EBV circRNAs in other cell lines and their functional characterization are still lacking. In this study, we have identified a list of putative EBV circRNAs in GM12878, an EBV-transformed lymphoblastoid cell line, with a significant majority encoded from the EBV latent genes. A novel EBV circRNA derived from the exon 5 of LMP-2 gene which exhibited highest prevalence, was further validated using RNase R assay and Sanger sequencing. This circRNA, which we term circLMP-2_e5, can be universally detected in a panel of EBV-positive cell lines modelling different latency programs. It ranges from lower expression in nasopharyngeal carcinoma (NPC) cells to higher expression in B cells, and is localized to both the cytoplasm and the nucleus. We provide evidence that circLMP-2_e5 is expressed concomitantly with its cognate linear LMP-2 RNA upon EBV lytic reactivation, and may be produced as a result of exon skipping, with its circularization possibly occurring without the involvement of cis elements in the short flanking introns. Furthermore, we show that circLMP-2_e5 is not involved in regulating cell proliferation, host innate immune response, its linear parental transcripts, or EBV lytic reactivation. Taken together, our study expands the current repertoire of putative EBV circRNAs, broadens our understanding of the biology of EBV circRNAs, and lays the foundation for further investigation of their function in the EBV life cycle and disease development.
  12. Tan KE, Ng WL, Ea CK, Lim YY
    Bio Protoc, 2023 Sep 05;13(17):e4798.
    PMID: 37849784 DOI: 10.21769/BioProtoc.4798
    Circular RNA (circRNA) is an intriguing class of non-coding RNA that exists as a continuous closed loop. With the improvements in high throughput sequencing, biochemical analysis, and bioinformatic algorithms, studies on circRNA expression became abundant in recent years. However, functional studies of circRNA are still limited. Subcellular localization of circRNA may provide some clues in elucidating its biological functions by performing subcellular fractionation assay. Notably, circRNAs that are predominantly found in the cytoplasm are more likely to be involved in post-transcriptional gene regulation, e.g., acting as micoRNA sponge, whereas nuclear-retained circRNAs are predicted to play a role in transcriptional regulation. Subcellular fractionation could help researchers to narrow down and prioritize downstream experiments. The majority of the currently available protocols describe the steps for subcellular fractionation followed by western blot analysis for protein molecules. Here, we present a protocol for the subcellular fractionation of cells to detect circRNA via RT-qPCR with divergent primers. Moreover, detailed steps for the generation of specific circRNAs-enriched cDNA included in this protocol will enhance the amplification and detection of low-abundance circRNAs. This will be useful for researchers studying low-abundance circRNAs. Key features This protocol builds upon the method developed by Gagnon et al. (2014) and extends its application to circRNA study. Protocol for amplification of low levels of circRNA expression. Analysis takes into consideration the ratio of cytoplasmic RNA concentration to nuclear RNA concentration.
  13. Yule CM, Lim YY, Lim TY
    Carbon Balance Manag, 2018 Feb 07;13(1):3.
    PMID: 29417248 DOI: 10.1186/s13021-018-0092-6
    BACKGROUND: Tropical peat swamp forests (TPSF) are globally significant carbon stores, sequestering carbon mainly as phenolic polymers and phenolic compounds (particularly as lignin and its derivatives) in peat layers, in plants, and in the acidic blackwaters. Previous studies show that TPSF plants have particularly high levels of phenolic compounds which inhibit the decomposition of organic matter and thus promote peat accumulation. The studies of phenolic compounds are thus crucial to further understand how TPSF function with respect to carbon sequestration. Here we present a study of cycling of phenolic compounds in five forests in Borneo differing in flooding and acidity, leaching of phenolic compounds from senescent Macaranga pruinosa leaves, and absorption of phenolics by M. pruinosa seedlings.

    RESULTS: The results of the study show that total phenolic content (TPC) in soil and leaves of three species of Macaranga were highest in TPSF followed by freshwater swamp forest and flooded limestone forest, then dry land sites. Highest TPC values were associated with acidity (in TPSF) and waterlogging (in flooded forests). Moreover, phenolic compounds are rapidly leached from fallen senescent leaves, and could be reabsorbed by tree roots and converted into more complex phenolics within the leaves.

    CONCLUSIONS: Extreme conditions-waterlogging and acidity-may facilitate uptake and synthesis of protective phenolic compounds which are essential for impeded decomposition of organic matter in TPSF. Conversely, the ongoing drainage and degradation of TPSF, particularly for conversion to oil palm plantations, reverses the conditions necessary for peat accretion and carbon sequestration.

  14. Rahumatullah A, Balachandra D, Noordin R, Baharudeen Z, Lim YY, Choong YS, et al.
    Sci Rep, 2021 01 28;11(1):2502.
    PMID: 33510342 DOI: 10.1038/s41598-021-82125-3
    Antibodies have different chemical properties capable of targeting a diverse nature of antigens. Traditionally, immune antibody libraries are perceived to be disease-specific with a skewed repertoire. The complexity during the generation of a combinatorial antibody library allows for a skewed but diverse repertoire to be generated. Strongyloides stercoralis is a parasite that causes strongyloidiasis, a potentially life-threatening disease with a complex diagnosis that impedes effective control and treatment of the disease. This study describes the isolation of monoclonal antibodies against S. stercoralis NIE recombinant protein using an immune antibody phage display library derived from lymphatic filaria-infected individuals. The isolated antibody clones showed both lambda and kappa light chains gene usage, with diverse amino acid distributions. Structural analysis showed that electropositivity and the interface area could determine the binding affinity of the clones with NIE. The successful identification of S. stercoralis antibodies from the filarial immune library highlights the breadth of antibody gene diversification in an immune antibody library that can be applied for closely related infections.
  15. Lim CC, Chan SK, Lim YY, Ishikawa Y, Choong YS, Nagaoka Y, et al.
    Mol Immunol, 2021 07;135:191-203.
    PMID: 33930714 DOI: 10.1016/j.molimm.2021.04.016
    The murine double minute 2 (MDM2) protein is a major negative regulator of the tumour suppressor protein p53. Under normal conditions, MDM2 constantly binds to p53 transactivation domain and/or ubiquinates p53 via its role as E3 ubiquitin ligase to promote p53 degradation as well as nuclear export to maintain p53 levels in cells. Meanwhile, amplification of MDM2 and appearance of MDM2 spliced variants occur in many tumours and normal tissues making it a prognostic indicator for human cancers. The mutation or deletion of p53 protein in half of human cancers inactivates its tumour suppressor activity. However, cancers with wild type p53 have its function effectively inhibited through direct interaction with MDM2 oncoprotein. Here, we described the construction of a MDM2 spliced variant (rMDM215kDa) consisting of SWIB/MDM2 domain and its central region for antibody generation. Biopanning with a human naïve scFv library generated four scFv clones specific to rMDM215kDa. Additionally, the selected scFv clones were able to bind to the recombinant full length MDM2 (rMDM2-FL). Computational prediction showed that the selected scFv clones potentially bind to exon 7-8 of MDM2 while leaving the MDM2/SWIB domain free for p53 interaction. The developed antibodies exhibit good specificity can be further investigated for downstream biomedical and research applications.
  16. Ida J, Chan SK, Glökler J, Lim YY, Choong YS, Lim TS
    Molecules, 2019 Mar 19;24(6).
    PMID: 30893817 DOI: 10.3390/molecules24061079
    G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.
  17. Lim YY, Lim KH
    J Colloid Interface Sci, 1997 Dec 01;196(1):116-9.
    PMID: 9441659
    Micellar properties of binary mixed surfactants of a surface active mixed copper(II) chelate, [Cu(C12-tmed)(acac)Cl] (where C12-tmed is N,N,N'-trimethyl-N'-dodecylethylenediamine) with three common surfactants, viz. sodium dodecyl sulfate (SDS), cetyltrimethylammonium bromide (CTAB), and octaethylene glycol monododecyl ether (C12E8), were investigated by surface tensiometry, ESR, and UV-visible absorption techniques. The surface tension data were treated with Rubingh's method for mixed micelle formation and Rosen's method for mixed monolayer formation at the aqueous solution/air interface. It was found that in the mixed micelle there is strong attractive interaction between cationic copper surfactant and anonic dodecyl sulfate while there is almost ideal mixing between copper surfactant and CTAB and C12E8. From the ESR and UV-visible studies, a mixed block-type arrangement of head groups is proposed. Copyright 1997 Academic Press. Copyright 1997Academic Press
  18. Lim YY, Liew LP
    J Colloid Interface Sci, 2002 Nov 15;255(2):425-7.
    PMID: 12505092
    The rate of autooxidation of 3,5-di-tert-butylcatechol (3,5-DTBC) in the presence of micelles formed from mixing equal concentrations of [Cu(C(12)-tmed)Br(2)] (where C(12)-tmed is N,N,N'-trimethyl-N'-dodecylethylenediamine) and several amino acids has been investigated. It was found that the rate in air-saturated solution is very much dependent on pH, which affects the availability of copper(II) coordination site for the catechol and the degree of micellization. At a given pH, the rates in [Cu(C(12)-tmed)Br(2)] micellar media are greatly enhanced in the presence sodium halide.
  19. Piyarathna IE, Lim YY, Edla M, Thabet AM, Ucgul M, Lemckert C
    Sensors (Basel), 2023 Jan 26;23(3).
    PMID: 36772411 DOI: 10.3390/s23031372
    In recent years, harvesting energy from ubiquitous ultralow-frequency vibration sources, such as biomechanical motions using piezoelectric materials to power wearable devices and wireless sensors (e.g., personalized assistive tools for monitoring human locomotion and physiological signals), has drawn considerable interest from the renewable energy research community. Conventional linear piezoelectric energy harvesters (PEHs) generally consist of a cantilever beam with a piezoelectric patch and a proof mass, and they are often inefficient in such practical applications due to their narrow operating bandwidth and low voltage generation. Multimodal harvesters with multiple resonances appear to be a viable solution, but most of the previously proposed designs are unsuitable for ultralow-frequency vibration. This study investigated a novel multimode design, which included a bent branched beam harvester (BBBH) to enhance PEHs' bandwidth output voltage and output power for ultralow-frequency applications. The study was conducted using finite element method (FEM) analysis to optimize the geometrical design of the BBBH on the basis of the targeted frequency spectrum of human motion. The selected design was then experimentally studied using a mechanical shaker and human motion as excitation sources. The performance was also compared to the previously proposed V-shaped bent beam harvester (VBH) and conventional cantilever beam harvester (CBH) designs. The results prove that the proposed BBBH could harness considerably higher output voltages and power with lower idle time. Its operating bandwidth was also remarkably widened as it achieved three close resonances in the ultralow-frequency range. It was concluded that the proposed BBBH outperformed the conventional counterparts when used to harvest energy from ultralow-frequency sources, such as human motion.
  20. Tan JB, Lim YY, Lee SM
    J Food Sci Technol, 2015 Apr;52(4):2394-400.
    PMID: 25829624 DOI: 10.1007/s13197-013-1236-z
    The decoction and infusion of Rhoeo spathacea (Swartz) Stearn leaves have been recognized as a functional food particularly in South America, but has not yet gained international popularity as a beverage. The primary aim of this study was to establish the viability of R. spathacea aqueous leaf extracts as a beverage, in terms of its antioxidant activity and antibacterial activity. The antioxidant contents of aqueous and methanol leaf extracts were evaluated by the total phenolic content (TPC) and total flavonoid content (TFC) assays. The antioxidant activities measured were DPPH radical scavenging activity (FRS), ferric reducing power (FRP) and ferrous ion chelating (FIC) activity. The aqueous leaf extracts in the forms of decoction and infusion, were found to have comparable TPC and antioxidant activity with other herbal teas previously reported by our research group. Both decoction and infusion also exhibited antibacterial activity against six species of Gram positive and four species of Gram negative bacteria, notably methicillin-resistant Staphylococcus aureus and Neisseria gonorrhoeae. A total of four different known phenolic compounds were identified by HPLC and MS, three of which have not been previously reported to be found in this plant. Both the decoction and infusion of the leaves R. spathacea have potential to be popularized into a common beverage.
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