Displaying publications 1 - 20 of 69 in total

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  1. 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.

  2. Yu KH, Shi CH, Wang B, Chow SH, Chung GT, Lung RW, et al.
    Genome Res, 2021 Dec;31(12):2340-2353.
    PMID: 34663689 DOI: 10.1101/gr.275348.121
    Circular RNAs (circRNAs) are abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with different types of biomolecules. Alternative splicing can create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels from RNA sequencing data. We confirm the effectiveness and computational efficiency of psirc using both simulated and actual experimental data. Applying psirc on transcriptome profiles from nasopharyngeal carcinoma and normal nasopharynx samples, we discover and validate circRNA isoforms differentially expressed between the two groups. Compared with the assumed circular isoforms derived from linear transcript annotations, some of the alternatively spliced circular isoforms have 100 times higher expression and contain substantially fewer microRNA response elements, showing the importance of quantifying full-length circRNA isoforms.
  3. 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.
  4. Yeo KS, Tan MC, Wong WY, Loh SW, Lam YL, Tan CL, et al.
    Sci Rep, 2016 Sep 27;6:34125.
    PMID: 27671354 DOI: 10.1038/srep34125
    TNF-induced signaling mediates pleiotropic biological consequences including inflammation, immunity, cell proliferation and apoptosis. Misregulation of TNF signaling has been attributed as a major cause of chronic inflammatory diseases and cancer. Jumonji domain-containing protein 8 (JMJD8) belongs to the JmjC family. However, only part of the family members has been described as hydroxylase enzymes that function as histone demethylases. Here, we report that JMJD8 positively regulates TNF-induced NF-κB signaling. Silencing the expression of JMJD8 using RNA interference (RNAi) greatly suppresses TNF-induced expression of several NF-κB-dependent genes. Furthermore, knockdown of JMJD8 expression reduces RIP ubiquitination, IKK kinase activity, delays IκBα degradation and subsequently blocks nuclear translocation of p65. In addition, JMJD8 deficiency enhances TNF-induced apoptosis. Taken together, these findings indicate that JMJD8 functions as a positive regulator of TNF-induced NF-κB signaling.
  5. Yeo KS, Tan MC, Lim YY, Ea CK
    Sci Rep, 2017 11 13;7(1):15407.
    PMID: 29133832 DOI: 10.1038/s41598-017-15676-z
    Jumonji C (JmjC) domain-containing proteins have been shown to regulate cellular processes by hydroxylating or demethylating histone and non-histone targets. JMJD8 belongs to the JmjC domain-only family that was recently shown to be involved in angiogenesis and TNF-induced NF-κB signaling. Here, we employed bioinformatic analysis and immunofluorescence microscopy to examine the physiological properties of JMJD8. We demonstrated that JMJD8 localizes to the lumen of endoplasmic reticulum and that JMJD8 forms dimers or oligomers in vivo. Furthermore, we identified potential JMJD8-interacting proteins that are known to regulate protein complex assembly and protein folding. Taken together, this work demonstrates that JMJD8 is the first JmjC domain-containing protein found in the lumen of the endoplasmic reticulum that may function in protein complex assembly and protein folding.
  6. Wong SK, Lim YY, Ling SK, Chiang Chan EW
    Pharmacogn Mag, 2014 Apr;10(Suppl 2):S232-9.
    PMID: 24991097 DOI: 10.4103/0973-1296.133238
    Our earlier study on the antiproliferative (APF) activity of leaf extracts of ten Apocynaceae species showed that leaves of Vallaris glabra possessed strong and broad-spectrum properties.
  7. Wong SK, Lim YY, Ling SK, Chan EW
    Pharmacognosy Res, 2014 Jan;6(1):67-72.
    PMID: 24497746 DOI: 10.4103/0974-8490.122921
    Three compounds isolated from the methanol (MeOH) leaf extract of Vallaris glabra (Apocynaceae) were those of caffeoylquinic acids (CQAs). This prompted a quantitative analysis of their contents in leaves of V. glabra in comparison with those of five other Apocynaceae species (Alstonia angustiloba, Dyera costulata, Kopsia fruticosa, Nerium oleander, and Plumeria obtusa), including flowers of Lonicera japonica (Japanese honeysuckle), the commercial source of chlorogenic acid (CGA).
  8. Wong SK, Lim YY, Abdullah NR, Nordin FJ
    Pharmacognosy Res, 2011 Apr;3(2):100-6.
    PMID: 21772753 DOI: 10.4103/0974-8490.81957
    The anticancer properties of Apocynaceae species are well known in barks and roots but less so in leaves.
  9. Wong SK, Lim YY, Abdullah NR, Nordin FJ
    PMID: 21232161 DOI: 10.1186/1472-6882-11-3
    Studies have shown that the barks and roots of some Apocynaceae species have anticancer and antimalarial properties. In this study, leaf extracts of five selected species of Apocynaceae used in traditional medicine (Alstonia angustiloba, Calotropis gigantea, Dyera costulata, Kopsia fruticosa and Vallaris glabra) were assessed for antiproliferative (APF) and antiplasmodial (APM) activities, and analysed for total alkaloid content (TAC), total phenolic content (TPC) and radical-scavenging activity (RSA). As V. glabra leaf extracts showed wide spectrum APF and APM activities, they were further screened for saponins, tannins, cardenolides and terpenoids.
  10. Wang Y, Lim YY, He Z, Wong WT, Lai WF
    PMID: 33559482 DOI: 10.1080/10408398.2021.1882381
    The last decide has witnessed a growing research interest in the role of dietary phytochemicals in influencing the gut microbiota. On the other hand, recent evidence reveals that dietary phytochemicals exhibit properties of preventing and tackling symptoms of Alzheimer's disease, which is a neurodegenerative disease that has also been linked with the status of the gut microbiota over the last decade. Till now, little serious discussions, however, have been made to link recent understanding of Alzheimer's disease, dietary phytochemicals and the gut microbiota together and to review the roles played by phytochemicals in gut dysbiosis induced pathologies of Alzheimer's disease. Deciphering these connections can provide insights into the development and future use of dietary phytochemicals as anti-Alzheimer drug candidates. This review aims at presenting latest evidence in the modulating role of phytochemicals in the gut microbiota and its relevance to Alzheimer's disease and summarizing the mechanisms behind the modulative activities. Limitations of current research in this field and potential directions will also be discussed for future research on dietary phytochemicals as anti-Alzheimer agents.
  11. Vidana Gamage GC, Lim YY, Choo WS
    J Food Sci Technol, 2022 Mar;59(3):831-845.
    PMID: 35185195 DOI: 10.1007/s13197-021-05054-z
    Anthocyanins are considered as the largest group of water-soluble pigments found in the vacuole of plant cells, displaying range of colors from pink, orange, red, purple and blue. They belong to flavonoids, a polyphenolic subgroup. Application of anthocyanins in food systems as natural food colourants is limited due to the lack of stability under different environmental conditions such as light, pH, heat etc. Anthocyanins esterified with one or more acid groups are referred as acylated anthocyanins. Based on the presence or absence of acyl group, anthocyanins are categorized as acylated and nonacylated anthocyanins. Acylated anthocyanins are further classified as mono, di, tri, tetra acylated anthocyanins according to the number of acyl groups present in the anthocyanin. This review classifies common anthocyanin sources into non-acylated, mono-, di-, tri- and tetra-acylated anthocyanins based on the major anthocyanins present in these sources. The relative stabilities of these anthocyanins with respect to thermal, pH and photo stress in beverage systems are specifically discussed. Common anthocyanin sources such as elderberry, blackberry, and blackcurrant mainly contain nonacylated anthocyanins. Red radish, purple corn, black carrot also mainly contain mono acylated anthocyanins. Red cabbage and purple sweet potato have both mono and diacylated anthocyanins. Poly acylated anthocyanins show relatively higher stability compared with nonacylated and monoacylated anthocyanins. Several techniques such as addition of sweeteners, co-pigmentation and acylation techniques could enhance the stability of nonacylated anthocyanins. Flowers are main sources of polyacylated anthocyanins having higher stability, yet they have not been commercially exploited for their anthocyanins.
  12. Vidana Gamage GC, Lim YY, Choo WS
    Front Plant Sci, 2021;12:792303.
    PMID: 34975979 DOI: 10.3389/fpls.2021.792303
    Clitoria ternatea plant is commonly grown as an ornamental plant and possesses great medicinal value. Its flower is edible and also known as blue pea or butterfly pea flower. The unique feature of anthocyanins present in blue pea flowers is the high abundance of polyacylated anthocyanins known as ternatins. Ternatins are polyacylated derivatives of delphinidin 3,3',5'-triglucoside. This review covers the biosynthesis, extraction, stability, antioxidant activity, and applications of anthocyanins from Clitoria ternatea flower. Hot water extraction of dried or fresh petals of blue pea flower could be employed successfully to extract anthocyanins from blue pea flower for food application. Blue pea flower anthocyanins showed good thermal and storage stability, but less photostability. Blue pea flower anthocyanins also showed an intense blue colour in acidic pH between pH 3.2 to pH 5.2. Blue pea flower anthocyanin extracts demonstrate significant in vitro and cellular antioxidant activities. Blue pea flower anthocyanins could be used as a blue food colourant in acidic and neutral foods. The incorporation of blue pea flower anthocyanins in food increased the functional properties of food such as antioxidant and antimicrobial properties. Blue pea flower anthocyanins have also been used in intelligent packaging. A comparison of blue pea flower anthocyanins with two other natural blue colouring agents used in the food industry, spirulina or phycocyanin and genipin-derived pigments is also covered. Anthocyanins from blue pea flowers are promising natural blue food colouring agent.
  13. Tong KL, Tan KE, Lim YY, Tien XY, Wong PF
    Mol Cell Biochem, 2022 Dec;477(12):2703-2733.
    PMID: 35604519 DOI: 10.1007/s11010-022-04455-8
    Atherosclerosis is the major cause of coronary artery disease (CAD) which includes unstable angina, myocardial infarction, and heart failure. The onset of atherogenesis, a process of atherosclerotic lesion formation in the intima of arteries, is driven by lipid accumulation, a vicious cycle of reactive oxygen species (ROS)-induced oxidative stress and inflammatory reactions leading to endothelial cell (EC) dysfunction, vascular smooth muscle cell (VSMC) activation, and foam cell formation which further fuel plaque formation and destabilization. In recent years, there is a surge in the number of publications reporting the involvement of circular RNAs (circRNAs) in the pathogenesis of cardiovascular diseases, cancers, and metabolic syndromes. These studies have advanced our understanding on the biological functions of circRNAs. One of the most common mechanism of action of circRNAs reported is the sponging of microRNAs (miRNAs) by binding to the miRNAs response element (MRE), thereby indirectly increases the transcription of their target messenger RNAs (mRNAs). Individual networks of circRNA-miRNA-mRNA associated with atherogenesis have been extensively reported, however, there is a need to connect these findings for a complete overview. This review aims to provide an update on atherogenesis-related circRNAs and analyze the circRNA-miRNA-mRNA interactions in atherogenesis. The atherogenic mechanisms and clinical relevance of each atherogenesis-related circRNA were systematically discussed for better understanding of the knowledge gap in this area.
  14. Ten LC, Chin YM, Tai MC, Chin EF, Lim YY, Suthandiram S, et al.
    Sci Rep, 2017 01 31;7:41400.
    PMID: 28139690 DOI: 10.1038/srep41400
    Large consortia efforts and genome-wide association studies (GWASs) have linked a number of genetic variants within the 6p21 chromosomal region to non-Hodgkin lymphoma (NHL). Complementing these efforts, we genotyped previously reported SNPs in the human leukocyte antigen (HLA) class I (rs6457327) and class II (rs9271100, rs2647012 and rs10484561) regions in a total of 1,145 subjects (567 NHL cases and 578 healthy controls) from two major ethnic groups in Malaysia, the Malays and the Chinese. We identified a NHL-associated (PNHL_add = 0.0008; ORNHL_add = 0.54; 95% CI = 0.37-0.77) and B-cell associated (PBcell_add = 0.0007; ORBcell_add = 0.51; 95% CI = 0.35-0.76) SNP rs2647012 in the Malaysian Malays. In silico cis-eQTL analysis of rs2647012 suggests potential regulatory function of nearby HLA class II molecules. Minor allele rs2647012-T is linked to higher expression of HLA-DQB1, rendering a protective effect to NHL risk. Our findings suggest that the HLA class II region plays an important role in NHL etiology.
  15. Tan MC, Wong WY, Ng WL, Yeo KS, Mohidin TB, Lim YY, et al.
    PLoS One, 2017;12(1):e0170352.
    PMID: 28114392 DOI: 10.1371/journal.pone.0170352
    Influenza virus is estimated to cause 3-5 million severe complications and about 250-500 thousand deaths per year. Different kinds of anti-influenza virus drugs have been developed. However, the emergence of drug resistant strains has presented a big challenge for efficient antiviral therapy. Indole derivatives have been shown to exhibit both antiviral and anti-inflammatory activities. In this study, we adopted a cell-based system to screen for potential anti-IAV agents. Four indole derivatives (named 525A, 526A, 527A and 528A) were subjected to the antiviral screening, of which 526A was selected for further investigation. We reported that pre-treating cells with 526A protects cells from IAV infection. Furthermore, 526A inhibits IAV replication by inhibiting the expression of IAV genes. Interestingly, 526A suppresses the activation of IRF3 and STAT1 in host cells and thus represses the production of type I interferon response and cytokines in IAV-infected cells. Importantly, 526A also partially blocks the activation of RIG-I pathway. Taken together, these results suggest that 526A may be a potential anti-influenza A virus agent.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
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