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Direct recovery of malate dehydrogenase from highly turbid yeast cell homogenate using dye-ligand affinity chromatography in stirred fluidized bed

Chen KH, Lee SY, Show PL, Hong SC, Chang YK

J Chromatogr B Analyt Technol Biomed Life Sci, 2018 Nov 15;1100-1101:65-75.
PMID: 30292951 DOI: 10.1016/j.jchromb.2018.09.039

Dye-ligand affinity chromatography in a stirred fluidized bed has been developed for the rapid recovery of malate dehydrogenase (MDH) from highly turbid baker's yeast cell homogenate in a single step. The most suitable dye, namely Reactive Orange 4, in its optimal immobilized concentration of 8.78 mg/mL was immobilized onto high-density STREAMLINE matrix. To further examine optimal adsorption and elution conditions, the enzyme recovery operation was carried out using unclarified cell homogenates in stirred fluidized bed system. Aiming to develop a non-specific eluent, namely NaCl, to effectively elute the MDH adsorbed, direct recovery of MDH from highly turbid cell homogenate (50% w/v) in a stirred fluidized bed adsorption system was performed. The proposed system successfully achieved a recovery yield of 73.6% and a purification factor of 73.5 in a single step by using 0.6 M NaCl as an eluent at a high liquid velocity of 200 cm/h.
Fulltext An Ultrasensitive Voltammetric Genosensor for the Detection of Bacteria Vibrio cholerae in Vegetable and Environmental Water Samples

Futra D, Tan LL, Lee SY, Lertanantawong B, Heng LY

Biosensors (Basel), 2023 Jun 04;13(6).
PMID: 37366981 DOI: 10.3390/bios13060616

In view of the presence of pathogenic Vibrio cholerae (V. cholerae) bacteria in environmental waters, including drinking water, which may pose a potential health risk to humans, an ultrasensitive electrochemical DNA biosensor for rapid detection of V. cholerae DNA in the environmental sample was developed. Silica nanospheres were functionalized with 3-aminopropyltriethoxysilane (APTS) for effective immobilization of the capture probe, and gold nanoparticles were used for acceleration of electron transfer to the electrode surface. The aminated capture probe was immobilized onto the Si-Au nanocomposite-modified carbon screen printed electrode (Si-Au-SPE) via an imine covalent bond with glutaraldehyde (GA), which served as the bifunctional cross-linking agent. The targeted DNA sequence of V. cholerae was monitored via a sandwich DNA hybridization strategy with a pair of DNA probes, which included the capture probe and reporter probe that flanked the complementary DNA (cDNA), and evaluated by differential pulse voltammetry (DPV) in the presence of an anthraquninone redox label. Under optimum sandwich hybridization conditions, the voltammetric genosensor could detect the targeted V. cholerae gene from 1.0 × 10-17-1.0 × 10-7 M cDNA with a limit of detection (LOD) of 1.25 × 10-18 M (i.e., 1.1513 × 10-13 µg/µL) and long-term stability of the DNA biosensor up to 55 days. The electrochemical DNA biosensor was capable of giving a reproducible DPV signal with a relative standard deviation (RSD) of <5.0% (n = 5). Satisfactory recoveries of V. cholerae cDNA concentration from different bacterial strains, river water, and cabbage samples were obtained between 96.5% and 101.6% with the proposed DNA sandwich biosensing procedure. The V. cholerae DNA concentrations determined by the sandwich-type electrochemical genosensor in the environmental samples were correlated to the number of bacterial colonies obtained from standard microbiological procedures (bacterial colony count reference method).
Fulltext 1H NMR-Based Metabolomics Approach Revealing Metabolite Variation of Black Turmeric (Curcuma caesia) Extracts and Correlation with Its Antioxidant and α-Glucosidase Inhibitory Activities

Ain Ibrahim NN, Kamal N, Mediani A, Sajak AAB, Lee SY, Shaari K, et al.

Food Technol Biotechnol, 2023 Mar;61(1):107-117.
PMID: 37200789 DOI: 10.17113/ftb.61.01.23.7711

RESEARCH BACKGROUND: Curcuma species (Zingiberaceae) are well known medicinal herbs in India and Southeast Asia. Despite various findings reporting their beneficial biological activities, very little information has been recorded on the Curcuma caesia. Thus, this study aims to determine the phenolic content, antioxidant and α-glucosidase inhibitory activity of both rhizome and leaves of C. caesia.
EXPERIMENTAL APPROACH: Rhizome and leaves of C. caesia were dried with oven (OD) and freeze (FD)-drying methods, and extracted with different Φ(ethanol,water)=100:0, 80:20, 50:50 and 0:100. The bioactivities of C. caesia extracts were evaluated using in vitro tests; total phenolic content (TPC), antioxidant (DPPH and FRAP) and α-glucosidase inhibitory activity. Proton nuclear magnetic resonance (1H NMR)-based metabolomics approach was employed to differentiate the most active extracts based on their metabolite profiles and correlation with bioactivities.
RESULTS AND CONCLUSIONS: The FD rhizome extracted with Φ(ethanol,water)=100:0 was observed to have potent TPC expressed as gallic acid equivalents, FRAP expressed as Trolox equivalents and α-glucosidase inhibitory activity with values of (45.4±2.1) mg/g extract, (147.7±8.3) mg/g extract and (265.5±38.6) µg/mL (IC50), respectively. Meanwhile, for DPPH scavenging activity, the Φ(ethanol,water)=80:20 and 100:0 extracts of FD rhizome showed the highest activity with no significant difference between them. Hence, the FD rhizome extracts were selected for further metabolomics analysis. Principal component analysis (PCA) showed clear discrimination among the different extracts. Partial least square (PLS) analysis showed positive correlations of the metabolites, including xanthorrhizol derivative, 1-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)-(6E)-6-heptene-3,4-dione, valine, luteolin, zedoardiol, β-turmerone, selina-4(15),7(11)-dien-8-one, zedoalactone B and germacrone, with the antioxidant and α-glucosidase inhibition activities, whereas curdione and 1-(4-hydroxy-3,5-dimethoxyphenyl)-7-(4-hydroxy-3-methoxyphenyl)-(lE,6E)-1,6-heptadiene3,4-dione were correlated with α-glucosidase inhibitory activity.
NOVELTY AND SCIENTIFIC CONTRIBUTION: C. caesia rhizome and leaf extracts contained phenolic compounds and had varies antioxidant and α-glucosidase inhibitory capacities. These findings strongly suggest that the rhizomes of C. caesia are an invaluable natural source of active ingredients for applications in pharmaceutical and food industries.
Fulltext Diversity and Characterization of Endophytic Fungi Isolated From the Tropical Mangrove Species, Rhizophora mucronata, and Identification of Potential Antagonists Against the Soil-Borne Fungus, Fusarium solani

Hamzah TNT, Lee SY, Hidayat A, Terhem R, Faridah-Hanum I, Mohamed R

Front Microbiol, 2018;9:1707.
PMID: 30090097 DOI: 10.3389/fmicb.2018.01707

Rhizophora mucronata is an important ecosystem entity of the Malaysian mangrove forest. Since the species grows in a harsh environment, any organism that is isolated from this species would be of huge interest due to its potential in having novel bioactive compounds. In the present work, we isolated, identified and characterized, a total of 78 fungal isolates harboring inside the leaf tissues of R. mucronata. Molecular identification using the nuclear ribosomal DNA internal transcribe spacer (ITS) sequences returned with high similarity matches to known sequences in the GenBank. Maximum likelihood analysis revealed the phylogenetic relationship of all isolates from this study. Most of the dominating fungal endophytes were from the genera Pestalotiopsis, followed by Alternaria and Cladosporium. Six isolates representing the genera Alternaria, Fusarium, Nigrospora, Pestalotiopsis, Phoma, and Xylaria, were further screened for their antagonism activities. Dual culture test assay revealed their inhibition percentages against the phytopathogenic fungus Fusarium solani between 45-66%, and 0.8-23% when using non-volatile test assay. Of the six isolates, only Fusarium lateritium and Xylaria sp. showed antibacterial activities against the pathogenic bacteria, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus, with the Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal Concentration (MBC) ranging from 0.5 to 2 mg/mL. The DPPH radical scavenging assay recorded a high level of antioxidant activity in Xylaria sp., 3-fold above that of F. lateritium. We demonstrate for the first time, two members belonging to the endophytic fungal community in the tropical mangrove species that have potential use as antagonists and antibacterial agents for future biotechnological applications.
Fulltext Metabolite Characterization and Correlations with Antioxidant and Wound Healing Properties of Oil Palm (Elaeis guineensis Jacq.) Leaflets via 1H-NMR-Based Metabolomics Approach

Che Zain MS, Lee SY, Nasir NM, Fakurazi S, Shaari K

Molecules, 2020 Nov 30;25(23).
PMID: 33265992 DOI: 10.3390/molecules25235636

Oil palm (Elaeis guineensis Jacq.) leaflets (OPLs) are one of the major agricultural by-products generated from the massive cultivation of Malaysian palm oil. This biomass is also reported to be of potential value based on its health-improving effects. By employing proton nuclear magnetic resonance (1H-NMR) spectroscopy combined with multivariate data analysis (MVDA), the metabolite profile of OPLs was characterized and correlated with their antioxidant and wound healing properties. Principal component analysis (PCA) classified four varieties of extracts, prepared using solvents ranging from polar to medium polarity, into three distinct clusters. Cumulatively, six flavonoids, eight organic acids, four carbohydrates, and an amine were identified from the solvent extracts. The more polar extracts, such as, the ethyl acetate-methanol, absolute methanol, and methanol-water, were richer in phytochemicals. Based on partial least square (PLS) analysis, the constituents in these extracts, such as (+)-catechin, (-)-epicatechin, orientin, isoorientin, vitexin, and isovitexin, were strongly correlated with the measured antioxidant activities, comprising ferric reducing antioxidant power (FRAP), 2,2-diphenyl-1-picrylhydrazyl (DPPH), and nitric oxide (NO) free radical scavenging activities, as well as with cell proliferation and migration activities. This study has provided crucial evidence on the importance of these natural antioxidant compounds on the wound healing properties of OPL.
Fulltext DNA Barcoding of the Endangered Aquilaria (Thymelaeaceae) and Its Application in Species Authentication of Agarwood Products Traded in the Market

Lee SY, Ng WL, Mahat MN, Nazre M, Mohamed R

PLoS One, 2016;11(4):e0154631.
PMID: 27128309 DOI: 10.1371/journal.pone.0154631

The identification of Aquilaria species from their resinous non-wood product, the agarwood, is challenging as conventional techniques alone are unable to ascertain the species origin. Aquilaria is a highly protected species due to the excessive exploitation of its precious agarwood. Here, we applied the DNA barcoding technique to generate barcode sequences for Aquilaria species and later applied the barcodes to identify the source species of agarwood found in the market. We developed a reference DNA barcode library using eight candidate barcode loci (matK, rbcL, rpoB, rpoC1, psbA-trnH, trnL-trnF, ITS, and ITS2) amplified from 24 leaf accessions of seven Aquilaria species obtained from living trees. Our results indicated that all single barcodes can be easily amplified and sequenced with the selected primers. The combination of trnL-trnF+ITS and trnL-trnF+ITS2 yielded the greatest species resolution using the least number of loci combination, while matK+trnL-trnF+ITS showed potential in detecting the geographical origins of Aquilaria species. We propose trnL-trnF+ITS2 as the best candidate barcode for Aquilaria as ITS2 has a shorter sequence length compared to ITS, which eases PCR amplification especially when using degraded DNA samples such as those extracted from processed agarwood products. A blind test conducted on eight agarwood samples in different forms using the proposed barcode combination proved successful in their identification up to the species level. Such potential of DNA barcoding in identifying the source species of agarwood will contribute to the international timber trade control, by providing an effective method for species identification and product authentication.
Fulltext Genome Size, Molecular Phylogeny, and Evolutionary History of the Tribe Aquilarieae (Thymelaeaceae), the Natural Source of Agarwood

Farah AH, Lee SY, Gao Z, Yao TL, Madon M, Mohamed R

Front Plant Sci, 2018;9:712.
PMID: 29896211 DOI: 10.3389/fpls.2018.00712

The tribe Aquilarieae of the family Thymelaeaceae consists of two genera, Aquilaria and Gyrinops, with a total of 30 species, distributed from northeast India, through southeast Asia and the south of China, to Papua New Guinea. They are an important botanical resource for fragrant agarwood, a prized product derived from injured or infected stems of these species. The aim of this study was to estimate the genome size of selected Aquilaria species and comprehend the evolutionary history of Aquilarieae speciation through molecular phylogeny. Five non-coding chloroplast DNA regions and a nuclear region were sequenced from 12 Aquilaria and three Gyrinops species. Phylogenetic trees constructed using combined chloroplast DNA sequences revealed relationships of the studied 15 members in Aquilarieae, while nuclear ribosomal DNA internal transcribed spacer (ITS) sequences showed a paraphyletic relationship between Aquilaria species from Indochina and Malesian. We exposed, for the first time, the estimated divergence time for Aquilarieae speciation, which was speculated to happen during the Miocene Epoch. The ancestral split and biogeographic pattern of studied species were discussed. Results showed no large variation in the 2C-values for the five Aquilaria species (1.35-2.23 pg). Further investigation into the genome size may provide additional information regarding ancestral traits and its evolution history.
Detection of high-risk HPV 16 genotypes in cervical cancers using isothermal DNA amplification with electrochemical genosensor

Nakowong P, Chatchawal P, Chaibun T, Boonapatcharoen N, Promptmas C, Buajeeb W, et al.

Talanta, 2024 Mar 01;269:125495.
PMID: 38043336 DOI: 10.1016/j.talanta.2023.125495

Cervical cancer emerges as the third most prevalent types of malignancy among women on a global scale. Cervical cancer is significantly associated with the persistent infection of human papillomavirus (HPV) type 16. The process of diagnosing is crucial in order to prevent the progression of a condition into a malignant state. The early detection of cervical cancer through initial stage screening is of the utmost significance in both the prevention and effective management of this disease. The present detection methodology is dependent on quantitative polymerase chain reaction (qPCR), which necessitates the use of a costly heat cycler instrument. In this study, we report the development of an electrochemical DNA biosensor integrated with an isothermal recombinase polymerase amplification (RPA) reaction for the detection and identification of the high-risk HPV-16 genotype. The electrochemical biosensor exhibited a high degree of specificity and sensitivity, as evidenced by its limit of detection (LOD) of 0.23 copies/μL of HPV-16 DNA. The validity of this electrochemical platform was confirmed through the analysis of 40 cervical tissues samples, and the findings were consistent with those obtained through polymerase chain reaction (PCR) testing. Our straightforward electrochemical detection technology and quick turnaround time at 75 min make the assay suitable for point-of-care testing in low-resource settings.
Highly divergent regions in the complete plastome sequences of Aquilaria are suitable for DNA barcoding applications including identifying species origin of agarwood products

Hishamuddin MS, Lee SY, Syazwan SA, Ramlee SI, Lamasudin DU, Mohamed R

3 Biotech, 2023 Mar;13(3):78.
PMID: 36761338 DOI: 10.1007/s13205-023-03479-1

Members of Aquilaria Lam. (Thymelaeaceae) are evergreen trees that are widely distributed in the Indomalesia region. Aquilaria is highly prized for its unique scented resin, agarwood, which is often the subject of unlawful trade activities. Survival of the tree is heavily threatened by destructive harvesting and agarwood poaching, leading to its protection under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Unfortunately, an efficient species identification method, which is crucial to aid in the conservation efforts of Aquilaria is lacking. Here, we described our search for a suitable specific DNA barcode for Aquilaria species using eight complete plastome sequences. We identified five highly variable regions (HVR) (matK-rps16, ndhF-rpl32, psbJ-petA, trnD, and trnT-trnL) in the plastomes. These regions were further analyzed using the neighbor-joining (NJ) method to assess their ability at discriminating the eight species. Coupled with in silico primer design, two potential barcoding regions, psbJ-petA and trnT-trnL, were identified. Their strengths in species delimitation were evaluated individually and in combination, via DNA barcoding analysis. Our findings showed that the combined dataset, psbJ-petA + trnT-trnL, effectively resolved members of the genus Aquilaria by clustering all species into their respective clades. In addition, we demonstrated that the newly proposed DNA barcode was capable at identifying the species of origin of six commercial agarwood samples that were included as unknown samples. Such achievement offers a new technical advancement, useful in the combat against illicit agarwood trades and in assisting the conservation of these valuable species in natural populations.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03479-1.
Fulltext In Vitro Wound Healing Potential of Flavonoid C-Glycosides from Oil Palm (Elaeis guineensis Jacq.) Leaves on 3T3 Fibroblast Cells

Che Zain MS, Lee SY, Sarian MN, Fakurazi S, Shaari K

Antioxidants (Basel), 2020 Apr 17;9(4).
PMID: 32316665 DOI: 10.3390/antiox9040326

Oil palm (Elaeis guineensis Jacq.) leaves (OPL) are widely available at zero cost in Southeast Asia countries, especially in Malaysia and Indonesia due to large scale oil palm plantations. OPLs contain a large amount of flavonoids in particular flavonoid C-glycosides, which are known to possess useful biological properties including antioxidant and wound healing properties. The present study aimed at evaluating the wound healing efficacy of OPL in various solvent extracts and flavonoid enriched fractions and to determine the contribution of flavonoid C-glycosides (orientin, isoorientin, vitexin and isovitexin) using in-vitro scratch assay on 3T3 fibroblast cells. Solvent crude extracts with different polarity were screened and the most active extract was subjected to acid hydrolysis. The crude and acid hydrolysed extracts were further enriched using macroporous resins, XAD7HP. UHPLC-UV/PDA and LC-MS/MS analysis were applied for identification and confirmation of flavonoid C-glycosides. The wound healing properties comprised of cell viability, cell proliferation and cell migration were studied. Allantoin was used as a positive control to compare the efficacy among the tested samples. The results revealed all OPL crude extracts, flavonoid enriched fractions and flavonoid C-glycosides were non-toxic at concentrations below 25 µg/mL and showed better cell proliferation and migration activities at low concentrations than higher concentrations.. This study also demonstrated orientin, isoorientin, vitexin and isovitexin presented in OPL extracts and flavonoid enriched fractions stimulated proliferation and migration of 3T3 fibroblast cells. Hence, these findings may pose potential therapeutic bioactive agents for wound healing by enhancing fibroblast proliferation and migration.
Fulltext Optimization of protein extraction from Chlorella Vulgaris via novel sugaring-out assisted liquid biphasic electric flotation system

Koyande AK, Chew KW, Lim JW, Lee SY, Lam MK, Show PL

Eng Life Sci, 2019 Dec;19(12):968-977.
PMID: 32624986 DOI: 10.1002/elsc.201900068

Microalgae biomass has been consumed as animal feed, fish feed and in human diet due to its high nutritional value. In this experiment, microalgae specie of Chlorella Vulgaris FSP-E was utilized for protein extraction via simple sugaring-out assisted liquid biphasic electric flotation system. The external electric force provided to the two-phase system assists in disruption of rigid microalgae cell wall and releases the contents of microalgae cell. This experiment manipulates various parameters to optimize the set-up. The liquid biphasic electric flotation set-up is compared with a control liquid biphasic flotation experiment without the electric field supply. The optimized separation efficiency of the liquid biphasic electric flotation system was 73.999 ± 0.739% and protein recovery of 69.665 ± 0.862% compared with liquid biphasic flotation, the separation efficiency was 61.584 ± 0.360% and protein recovery was 48.779 ± 0.480%. The separation efficiency and protein recovery for 5 × time scaled-up system was observed at 52.871 ± 1.236% and 73.294 ± 0.701%. The integration of simultaneous cell-disruption and protein extraction ensures high yield of protein from microalgae. This integrated method for protein extraction from microalgae demonstrated its potential and further research can lead this technology to commercialization.
Fulltext Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships

Hishamuddin MS, Lee SY, Ng WL, Ramlee SI, Lamasudin DU, Mohamed R

Sci Rep, 2020 Aug 03;10(1):13034.
PMID: 32747724 DOI: 10.1038/s41598-020-70030-0

Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.
Machine Learning-Assisted Real-Time Polymerase Chain Reaction and High-Resolution Melt Analysis for SARS-CoV-2 Variant Identification

Promja S, Puenpa J, Achakulvisut T, Poovorawan Y, Lee SY, Athamanolap P, et al.

Anal Chem, 2023 Jan 12.
PMID: 36633573 DOI: 10.1021/acs.analchem.2c05112

Since the declaration of COVID-19 as a pandemic in early 2020, multiple variants of the severe acute respiratory syndrome-related coronavirus (SARS-CoV-2) have been detected. The emergence of multiple variants has raised concerns due to their impact on public health. Therefore, it is crucial to distinguish between different viral variants. Here, we developed a machine learning web-based application for SARS-CoV-2 variant identification via duplex real-time polymerase chain reaction (PCR) coupled with high-resolution melt (qPCR-HRM) analysis. As a proof-of-concept, we investigated the platform's ability to identify the Alpha, Delta, and wild-type strains using two sets of primers. The duplex qPCR-HRM could identify the two variants reliably in as low as 100 copies/μL. Finally, the platform was validated with 167 nasopharyngeal swab samples, which gave a sensitivity of 95.2%. This work demonstrates the potential for use as automated, cost-effective, and large-scale viral variant surveillance.
Fulltext The complete chloroplast genome sequence and phylogenetic analysis of Strobilanthes dalzielii (W.W.Sm.) Benoist 1935 (Acanthaceae)

Zeng N, Gao W, Chen Z, Chong JY, Lee SY, Xu G

Mitochondrial DNA B Resour, 2024;9(4):465-469.
PMID: 38591052 DOI: 10.1080/23802359.2024.2316069

Strobilanthes dalzielii of Acanthaceae is an herb species with potentially extensive applications for its pharmaceutical and ornamental values. Due to taxonomic complications and limited genetic information, the structural characteristics, and phylogenetic relationships of the S. dalzielii chloroplast genome were assembled and characterized here for the first time. The complete chloroplast genome of S. dalzielii was 144,580 bp in length. The genome is quadripartite in structure and consists of a large single-copy region (92,137 bp) and a small single-copy region (17,669 bp), which are separated by a pair of inverted repeats (each 17,387 bp). A total of 125 genes were annotated, including 80 protein-coding, 37 transfer RNA, and eight ribosomal RNA genes. The overall GC content was 36.4%. Phylogenetic analysis based on the complete chloroplast genome sequence of 21 taxa within the tribe Ruellieae of Acanthaceae using the maximum likelihood and Bayesian inference methods revealed that Strobilanthes diverged after Ruellia; S. dalzielii is closely related to S. tonkinensis. The genomic data obtained from this study will serve as valuable information to the species delimitation and genetic classification of Strobilanthes.
The complete chloroplast genome of Pandanus amaryllifolius Roxb. ex Lindl. (Pandanaceae) and its phylogenetic relationship

Chin JH, Wong XJ, Chong TF, Muangkot P, Heng AT, Tanee T, et al.

Mitochondrial DNA B Resour, 2024;9(4):541-545.
PMID: 38665928 DOI: 10.1080/23802359.2024.2345773

Pandanus amaryllifolius of Pandanaceae, a plant native to Southeast Asia, has been domesticated for its health benefits and aromatic leaves. It is also used for phytoremediation and soil rehabilitation. However, genetic studies of this species are limited. This study aims to expand its genomic information by assembling and characterizing the complete chloroplast genome of P. amaryllifolius. The chloroplast genome, which was 157,839 bp long, contains a total of 133 genes, including 87 protein-coding (CDS), 38 tRNA, and eight rRNA genes. The overall G/C content was 37.7%. A phylogenetic analysis using 79 shared unique CDS revealed a monophyletic relationship in Pandanales. Based on the limited sampling size, Pandanus amaryllifolius was the first to diverge in Pandanaceae. The genomic data will be useful for future phylogenetic and evolutionary studies of Pandanaceae.
Genetic and immunologic relationships between vaccine and field strains for vaccine selection of type A foot-and-mouth disease virus circulating in East Asia

Lee SY, Park ME, Kim RH, Ko MK, Lee KN, Kim SM, et al.

Vaccine, 2015 Jan 29;33(5):664-9.
PMID: 25528521 DOI: 10.1016/j.vaccine.2014.12.007

Of the seven known serotypes of foot-and-mouth disease virus (FMDV), type A has the most diverse variations. Genetic variations also occur frequently at VP1, VP2, VP3, and VP4 because these proteins constitute the viral capsid. The structural proteins of FMDV, which are closely related to immunologic correlations, are the most easily analyzed because they have highly accessible information. In this study we analyzed the type A vaccine viruses by alignment of available sequences in order to find appropriate vaccine strains. The matching rate of ASIA topotype-specific sites (20 amino acids) located on the viral surface, which are mainly VP1 and VP2, was highly related to immunologic reactivity. Among the available vaccines analyzed in this study, we suggest that A Malaysia 97 could be used as a vaccine virus as it has the highest genetic similarity and immunologic aspects to field strains originating in East Asia.
Supermacroporous poly(vinyl alcohol)-carboxylmethyl chitosan-poly(ethylene glycol) scaffold: an in vitro and in vivo pre-assessments for cartilage tissue engineering

Lee SY, Wee AS, Lim CK, Abbas AA, Selvaratnam L, Merican AM, et al.

J Mater Sci Mater Med, 2013 Jun;24(6):1561-70.
PMID: 23512151 DOI: 10.1007/s10856-013-4907-4

This study aims to pre-assess the in vitro and in vivo biocompatibility of poly(vinyl alcohol)-carboxylmethyl-chitosan-poly(ethylene glycol) (PCP) scaffold. PCP was lyophilised to create supermacroporous structures. 3-(4, 5-dimethyl-thiazol-2yl)-2, 5-diphenyltetrazolium bromide (MTT) assay and immunohistochemistry (IHC) were used to evaluate the effectiveness of PCP scaffolds for chondrocytes attachment and proliferation. The ultrastructural was assessed using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Extracellular matrix (ECM) formation was evaluated using collagen type-II staining, glycosaminoglycan (GAG) and collagen assays. Histological analysis was conducted on 3-week implanted Sprague-Dawley rats. The MTT, IHC, SEM and TEM analyses confirm that PCP scaffolds promoted cell attachment and proliferation in vitro. The chondrocyte-PCP constructs secreted GAG and collagen type-II, both increased significantly from day-14 to day-28 (P
Analysis of lolB gene sequence and its use in the development of a PCR assay for the detection of Vibrio cholerae

Lalitha P, Siti Suraiya MN, Lim KL, Lee SY, Nur Haslindawaty AR, Chan YY, et al.

J Microbiol Methods, 2008 Sep;75(1):142-4.
PMID: 18579241 DOI: 10.1016/j.mimet.2008.05.001

A PCR assay has been developed based on a lolB (hemM) gene, which was found to be highly conserved among the Vibrio cholerae species but non-conserved among the other enteric bacteria. The lolB PCR detected all O1, O139 and non-O1/non-O139 serogroup and biotypes of V. cholerae. The analytical specificity of this assay was 100% while the analytical sensitivity was 10 pg/microL and 10(3) CFU/mL at DNA and bacterial level respectively. The diagnostic sensitivity and specificity was 98.5% and 100% respectively.
Fulltext COVID-19 in the elderly: A Malaysian perspective

Mustaffa N, Lee SY, Mohd Nawi SN, Che Rahim MJ, Chee YC, Muhd Besari A, et al.

J Glob Health, 2020 Dec;10(2):020370.
PMID: 33214887 DOI: 10.7189/jogh.10.020370
Identification of germline alterations in breast cancer predisposition genes among Malaysian breast cancer patients using panel testing

Ng PS, Wen WX, Fadlullah MZ, Yoon SY, Lee SY, Thong MK, et al.

Clin Genet, 2016 10;90(4):315-23.
PMID: 26757417 DOI: 10.1111/cge.12735

Although an association between protein-truncating variants and breast cancer risk has been established for 11 genes, only alterations in BRCA1, BRCA2, TP53 and PALB2 have been reported in Asian populations. Given that the age of onset of breast cancer is lower in Asians, it is estimated that inherited predisposition to breast cancer may be more significant. To determine the potential utility of panel testing, we investigated the prevalence of germline alterations in 11 established and 4 likely breast cancer genes in a cross-sectional hospital-based cohort of 108 moderate to high-risk breast cancer patients using targeted next generation sequencing. Twenty patients (19%) were identified to carry deleterious mutations, of whom 13 (12%) were in the BRCA1 or BRCA2, 6 (6%) were in five other known breast cancer predisposition genes and 1 patient had a mutation in both BRCA2 and BARD1. Our study shows that BRCA1 and BRCA2 account for the majority of genetic predisposition to breast cancer in our cohort of Asian women. Although mutations in other known breast cancer genes are found, the functional significance and breast cancer risk have not yet been determined, thus limiting the clinical utility of panel testing in Asian populations.

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