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Fulltext The possible culprit of obesity in malaysia – pisang goreng

Tan Jia Yi

Borneo Journal of Medical Sciences, 2020;14(3):65-66.
MyJurnal

Obesity has become a global health issue, not to mention Malaysia, which topped over the list of countries in Asia. On World Health Day in 2019, the World Health Organization (WHO) announced that 64% of the male population and 65% of the female population in Malaysia are either obese or overweight1. The ringing of alarm is tremendously loud in the silence. Depending on each of us, this can be an issue that we laugh over or a kind but severe urge for us to take a step backwards, observe, and self-reflect.
Fulltext Taiwan’s response to COVID -19: a success story

Tan, Jia Yi, Teoh, Xie Jing

Borneo Journal of Medical Sciences, 2021;15(2):75-77.
MyJurnal

Since the COVID-19 pandemic, Taiwan reported a total of 776 cases of COVID-19 (Dong et al., 2020) in comparison with its neighbouring countries, Japan and the Philippines which reported 210,769 and 465,724 cases of COVID-19 respectively, until 24 December 2020. Looking at the curve of the COVID-19 pandemic among various countries, Taiwan had indeed distinguished herself and stood out considering her well-contained COVID-19 infection despite it being a widespread infection in other countries.
Fulltext Quorum sensing activity of Hafnia alvei isolated from packed food

Tan JY, Yin WF, Chan KG

Sensors (Basel), 2014 Apr 14;14(4):6788-96.
PMID: 24736131 DOI: 10.3390/s140406788

Quorum sensing (QS) is a mechanism adopted by bacteria to regulate expression of genes according to population density. N-acylhomoserine lactones (AHLs) are a type of QS signalling molecules commonly found in Gram-negative bacteria which have been reported to play a role in microbial spoilage of foods and pathogenesis. In this study, we isolated an AHL-producing Hafnia alvei strain (FB1) from spherical fish pastes. Analysis via high resolution triple quadrupole liquid chromatography/mass spectrometry (LC/MS) on extracts from the spent supernatant of H. alvei FB1 revealed the existence of two short chain AHLs: N-(3-oxohexanoyl) homoserine lactone (3-oxo-C6-HSL) and N-(3-oxo- octanoyl) homoserine lactone (3-oxo-C8-HSL). To our knowledge, this is the first report of the production of AHLs, especially 3-oxo-C8-HSL, by H. alvei.
Fulltext Gene clusters of Hafnia alvei strain FB1 important in survival and pathogenesis: a draft genome perspective

Tan JY, Yin WF, Chan KG

Gut Pathog, 2014;6:29.
PMID: 25075225 DOI: 10.1186/1757-4749-6-29

Hafnia alvei is an opportunistic pathogen involved in various types of nosocomical infections. The species has been found to inhabit food and mammalian guts. However, its status as an enteropathogen, and whether the food-inhabiting strains could be a source of gastrointestinal infection remains obscure. In this report we present a draft genome of H. alvei strain FB1 isolated from fish paste meatball, a food popular among Malaysian and Chinese populations. The data was generated on the Illumina MiSeq platform.
Fulltext Genetic polymorphisms of human platelet antigens-1 to -6, and -15 in the Malaysian population

Tan JY, Lian LH, Nadarajan VS

Blood Transfus, 2012 Jul;10(3):368-76.
PMID: 22682339 DOI: 10.2450/2012.0095-11

Human platelet antigens (HPA) are determinant in several platelet-specific alloimmune disorders, such as neonatal alloimmune thrombocytopenia, post-transfusion purpura and platelet transfusion refractoriness. The distribution of HPA systems in the Malaysian population is not known. Defining the patterns of HPA systems provides a basis for risk assessment and management of the above complications.
Fulltext Complete Genome Sequence of Pluralibacter gergoviae FB2, an N-Acyl Homoserine Lactone-Degrading Strain Isolated from Packed Fish Paste

Chan KG, Tee KK, Yin WF, Tan JY

Genome Announc, 2014;2(6).
PMID: 25502672 DOI: 10.1128/genomeA.01276-14

Pluralibacter gergoviae FB2, a bacterial strain isolated from packed food, has been found to exhibit quorum-quenching properties. Hence, we report the first, complete genome of P. gergoviae sequenced using the Pacific Biosciences single-molecule, real-time (SMRT) platform.
Fulltext Complete Genome Sequence of Cedecea neteri Strain SSMD04, a Bacterium Isolated from Pickled Mackerel Sashimi

Chan KG, Tan KH, Yin WF, Tan JY

Genome Announc, 2014;2(6).
PMID: 25523782 DOI: 10.1128/genomeA.01339-14

We report here the complete genome sequence of C. neteri SSMD04, a strain isolated from pickled mackerel sashimi, sequenced by third-generation sequencing technology. To the best of our knowledge, this is the first documentation that reports the complete genome of Cedecea neteri.
Fulltext Genome analysis of quorum sensing Cedecea neteri SSMD04 leads to identification of its novel signaling synthase (cneI), cognate receptor (cneR) and an orphan receptor

Tan KH, Tan JY, Yin WF, Chan KG

PeerJ, 2015;3:e1216.
PMID: 26355540 DOI: 10.7717/peerj.1216

Cedecea neteri is a very rare human pathogen. We have isolated a strain of C. neteri SSMD04 from pickled mackerel sashimi identified using molecular and phenotypics approaches. Using the biosensor Chromobacterium violaceum CV026, we have demonstrated the presence of short chain N-acyl-homoserine lactone (AHL) type quorum sensing (QS) activity in C. neteri SSMD04. Triple quadrupole LC/MS analysis revealed that C. neteri SSMD04 produced short chain N-butyryl-homoserine lactone (C4-HSL). With the available genome information of C. neteri SSMD04, we went on to analyse and identified a pair of luxI/R homologues in this genome that share the highest similarity with croI/R homologues from Citrobacter rodentium. The AHL synthase, which we named cneI(636 bp), was found in the genome sequences of C. neteri SSMD04. At a distance of 8bp from cneI is a sequence encoding a hypothetical protein, potentially the cognate receptor, a luxR homologue which we named it as cneR. Analysis of this protein amino acid sequence reveals two signature domains, the autoinducer-binding domain and the C-terminal effector which is typical characteristic of luxR. In addition, we found that this genome harboured an orphan luxR that is most closely related to easR in Enterobacter asburiae. To our knowledge, this is the first report on the AHL production activity in C. neteri, and the discovery of its luxI/R homologues, the orphan receptor and its whole genome sequence.
Virus Propagation and Cell-Based Colorimetric Quantification

Tan JY, Wong JE, Zainal N, AbuBakar S, Tan KK

J Vis Exp, 2023 Apr 07.
PMID: 37092849 DOI: 10.3791/64578

Zika virus (ZIKV) is a mosquito-borne virus belonging to the genus Flavivirus. ZIKV infection has been associated with congenital brain abnormalities and potentially Guillain-Barré syndrome in adults. Research on ZIKV to understand the disease mechanisms is important to facilitate vaccine and treatment development. The method of quantifying viruses is crucial and fundamental in the field of virology. The focus forming assay (FFA) is a virus quantification assay that detects the viral antigen with antibodies and identifies the infection foci of cells using the peroxidase immunostaining technique. The current study describes the virus propagation and quantification protocol using both 24-well and 96-well (high throughput) formats. Compared with other similar studies, this protocol has further described foci size optimization, which can serve as a guide to expand the use of this assay for other viruses. Firstly, ZIKV propagation is performed in Vero cells for 3 days. The culture supernatant containing ZIKV is harvested and quantitated using the FFA. Briefly, the virus culture is inoculated onto Vero cells and incubated for 2-3 days. Foci formation is then determined after optimized staining processes, including cell fixation, permeabilization, blocking, antibody binding, and incubation with peroxidase substrate. The stained virus foci are visualized using a stereo microscope (manual counting in 24-well format) or software analyzer (automated counting in 96-well format). The FFA provides reproducible, relatively fast results (3-4 days) and is suitable to be used for different viruses, including non-plaque-forming viruses. Subsequently, this protocol is useful for the study of ZIKV infection and could be used to detect other clinically important viruses.
Fulltext Cloning and Characterization of the Autoinducer Synthase Gene from Lipid-Degrading Bacterium Cedecea neteri

Tan KH, How KY, Tan JY, Yin WF, Chan KG

Front Microbiol, 2017;8:72.
PMID: 28197135 DOI: 10.3389/fmicb.2017.00072

The process of intercellular communication among bacteria, termed quorum sensing (QS), is mediated by small diffusible molecules known as the autoinducers. QS allows the population to react to the change of cell density in unison, in processes such as biofilm formation, plasmid conjugation, virulence, motility and root nodulation. In Gram-negative proteobacteria, N-acyl homoserine lactone (AHL) is the common "language" to coordinate gene expression. This signaling molecule is usually synthesized by LuxI-type proteins. We have previously discovered that a rare bacterium, Cedecea neteri, exhibits AHL-type QS activity. With information generated from genome sequencing, we have identified the luxIR gene pair responsible for AHL-type QS and named it cneIR. In this study, we have cloned and expressed the 636 bp luxI homolog in an Escherichia coli host for further characterization. Our findings show that E. coli harboring cneI produced the same AHL profile as the wild type C. neteri, with the synthesis of AHL known as N-butyryl-homoserine lactone. This 25 kDa LuxI homolog shares high similarity with other AHL synthases from closely related species. This work is the first documentation of molecular cloning and characterization of luxI homolog from C. neteri.
Risk of infection and vascular complications with cardiac implantable electronic device implantation in patients with a history of mastectomy

Yeo YH, San BJ, Tan JY, Jaiyesimi I, Mehta N

Heart Rhythm, 2024 Apr 06.
PMID: 38588994 DOI: 10.1016/j.hrthm.2024.04.007
De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650(T), a potential plant growth promoting bacterium

See-Too WS, Tan JY, Ee R, Lim YL, Convey P, Pearce DA, et al.

Mar Genomics, 2016 Apr 22.
PMID: 27117861 DOI: 10.1016/j.margen.2016.04.007

Planococcus kocurii ATCC 43650(T) is a halotolerant and psychrotolerant bacterium isolated from the skin of a North sea cod. Here, we present the first complete genome and annotation of P. kocurii ATCC 43650(T), identifying its potential as a plant growth promoting bacterium and its capability in the biosynthesis of butanol.
Oecophyllibacter saccharovorans gen. nov. sp. nov., a bacterial symbiont of the weaver ant Oecophylla smaragdina

Chua KO, See-Too WS, Tan JY, Song SL, Yong HS, Yin WF, et al.

J Microbiol, 2020 Dec;58(12):988-997.
PMID: 33095388 DOI: 10.1007/s12275-020-0325-8

In this study, bacterial strains Ha5T, Ta1, and Jb2 were isolated from different colonies of weaver ant Oecophylla smaragdina. They were identified as bacterial symbionts of the ant belonging to family Acetobacteraceae and were distinguished as different strains based on distinctive random-amplified polymorphic DNA (RAPD) fingerprints. Cells of these bacterial strains were Gram-negative, rod-shaped, aerobic, non-motile, catalase-positive and oxidase-negative. They were able to grow at 15-37°C (optimum, 28-30°C) and in the presence of 0-1.5% (w/v) NaCl (optimum 0%). Their predominant cellular fatty acids were C18:1ω7c, C16:0, C19:0ω8c cyclo, C14:0, and C16:0 2-OH. Strains Ha5T, Ta1, and Jb2 shared highest 16S rRNA gene sequence similarity (94.56-94.63%) with Neokomagataea tanensis NBRC106556T of family Acetobacteraceae. Both 16S rRNA gene sequence-based phylogenetic analysis and core gene-based phylogenomic analysis placed them in a distinct lineage in family Acetobacteraceae. These bacterial strains shared higher than species level thresholds in multiple overall genome-relatedness indices which indicated that they belonged to the same species. In addition, they did not belong to any of the current taxa of Acetobacteraceae as they had low pairwise average nucleotide identity (< 71%), in silico DNA-DNA hybridization (< 38%) and average amino acid identity (< 67%) values with all the type members of the family. Based on these results, bacterial strains Ha5T, Ta1, and Jb2 represent a novel species of a novel genus in family Acetobacteaceae, for which we propose the name Oecophyllibacter saccharovorans gen. nov. sp. nov., and strain Ha5T as the type strain.
Current attempts to implement microRNA-based diagnostics and therapy in cardiovascular and metabolic disease: a promising future

Thanikachalam PV, Ramamurthy S, Wong ZW, Koo BJ, Wong JY, Abdullah MF, et al.

Drug Discov Today, 2018 Mar;23(3):460-480.
PMID: 29107764 DOI: 10.1016/j.drudis.2017.10.020

MicroRNAs (miRNAs) are small, noncoding RNAs regulating gene expression at the post-translational level. miRNA-based therapeutic agents are important because of the functionality of miRNAs in regulating lipid and glucose metabolism and their role in the pathogenesis of metabolic disorders such as diabetes and obesity, where dysregulation leads to disease; they are also important in angiogenesis. miRNAs additionally serve as biomarkers in the diagnosis, prognosis and risk assessment of disease and in monitoring the response to treatment. Here, we provide a brief overview of progress in miRNA-based therapeutics in the preclinical and clinical setting and highlight the novel outcomes and opportunities in the diagnosis and treatment of metabolic conditions. In addition, we present the role of miRNAs in stem cell therapy which could have great potential in regenerative medicine.
Planococcus versutus sp. nov., isolated from soil

See-Too WS, Ee R, Madhaiyan M, Kwon SW, Tan JY, Lim YL, et al.

Int J Syst Evol Microbiol, 2017 Apr;67(4):944-950.
PMID: 27959786 DOI: 10.1099/ijsem.0.001721

A taxonomic study was performed on a novel Gram-stain-positive, coccus-shaped, orange-pigmented motile bacterium, designated as strain L10.15T. The organism was isolated from a soil sample collected in Lagoon Island (close to Adelaide Island, western Antarctic Peninsula) using a quorum-quenching enrichment medium. Growth occurred at 4-30 °C, pH 6-11 and at moderately high salinity (0-15 %, w/v, NaCl), with optimal growth at 26 °C, at pH 7-8 and with 6 % (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain L10.15T belonged to the genus Planococcus and was closely related to Planococcus halocryophilus Or1T (99.3 % similarity), Planococcus donghaensis JH1T (99.0 %), Planococcus antarcticus DSM 14505T (98.3 %), Planococcus plakortidis AS/ASP6 (II)T (97.6 %), Planococcus maritimus TF-9T (97.5 %), Planococcus salinarum ISL-6T (97.5 %) and Planococcus kocurii NCIMB 629T (97.5 %). However, the average nucleotide identity-MUMmer analysis showed low genomic relatedness values of 71.1-81.7 % to the type strains of these closely related species of the genus Planococcus. The principal fatty acids were anteiso-C15 : 0, C16 : 1ω7c and anteiso-C17 : 0, and the major menaquinones of strain L10.15T were MK-5 (48 %), MK-6 (6 %) and MK-7 (44 %). Polar lipid analysis revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and aminophospholipid. The DNA G+C content was 39.4 mol%. The phenotypic and genotypic data indicate that strain L10.15T represents a novel species of the genus Planococcus, for which the name Planococcus versutus sp. nov. is proposed. The type strain is L10.15T (=DSM 101994T=KACC 18918T).
Fulltext Emergence of B.1.524(G) SARS-CoV-2 in Malaysia during the third COVID-19 epidemic wave

Tan KK, Tan JY, Wong JE, Teoh BT, Tiong V, Abd-Jamil J, et al.

Sci Rep, 2021 11 11;11(1):22105.
PMID: 34764315 DOI: 10.1038/s41598-021-01223-4

The COVID-19 pandemic first emerged in Malaysia in Jan 2020. As of 12th Sept 2021, 1,979,698 COVID-19 cases that occurred over three major epidemic waves were confirmed. The virus contributing to the three epidemic waves has not been well-studied. We sequenced the genome of 22 SARS-CoV-2 strains detected in Malaysia during the second and the ongoing third wave of the COVID-19 epidemic. Detailed phylogenetic and genetic variation analyses of the SARS-CoV-2 isolate genomes were performed using these newly determined sequences and all other available sequences. Results from the analyses suggested multiple independent introductions of SARS-CoV-2 into Malaysia. A new B.1.524(G) lineage with S-D614G mutation was detected in Sabah, East Malaysia and Selangor, Peninsular Malaysia on 7th October 2020 and 14th October 2020, respectively. This new B.1.524(G) group was not the direct descendant of any of the previously detected lineages. The new B.1.524(G) carried a set of genetic variations, including A701V (position variant frequency = 0.0007) in Spike protein and a novel G114T mutation at the 5'UTR. The biological importance of the specific mutations remained unknown. The sequential appearance of the mutations, however, suggests that the spread of the new B.1.524(G) lineages likely begun in Sabah and then spread to Selangor. The findings presented here support the importance of SARS-CoV-2 full genome sequencing as a tool to establish an epidemiological link between cases or clusters of COVID-19 worldwide.
A Cross-Sectional Evaluation of Complementary and Alternative Medicine Use in a Non-urban Malaysian Population

Teow YEE, Ng SC, Azmi AHM, Hamzah MR, Kaur J, Mathiarasu DS, et al.

J Community Health, 2021 06;46(3):515-521.
PMID: 32710232 DOI: 10.1007/s10900-020-00891-z

Complementary and alternative medicine (CAM) therapies have been an integral part of Malaysia culture for many centuries. In recent years influences from other parts of the world have gained a foot-hold in Malaysian popular culture. We investigated the engagement with CAM in a non-urban, Malaysian population. We investigated the association of CAM use with cultural influence, perceived health status, gender and age. We recruited 700 adult participants to this study across three sites in central Malaysia. We found massage, Vitamin supplements, Herbal medicine and traditional Chinese medicine to be the most popular CAM modalities with participation at 67.7%, 55.7%, 55.5% and 26.3% respectively. CAM use was equally high at 67% among those people who claimed a predominantly Malay or Chinese cultural influence. The use of vitamins and participation in yoga were at higher prevalence among female participants compared to males. There was no gender difference for other CAM modalities. There were differences between age groups for most CAM modalities, and those over 50 years tended to be the highest frequency users for most modalities. There is a high rate of CAM use in non-urban Malaysia with younger people being more engaged with less traditional modalities such as aromatherapy, yoga and music therapy.
Fulltext SARS-CoV-2 genomic surveillance in Malaysia: displacement of B.1.617.2 with AY lineages as the dominant Delta variants and the introduction of Omicron during the fourth epidemic wave

Azami NAM, Perera D, Thayan R, AbuBakar S, Sam IC, Salleh MZ, et al.

Int J Infect Dis, 2022 Dec;125:216-226.
PMID: 36336246 DOI: 10.1016/j.ijid.2022.10.044

OBJECTIVES: This study reported SARS-CoV-2 whole genome sequencing results from June 2021 to January 2022 from seven genome sequencing centers in Malaysia as part of the national surveillance program.
METHODS: COVID-19 samples that tested positive by reverse transcription polymerase chain reaction and with cycle threshold values <30 were obtained throughout Malaysia. Sequencing of SARS-CoV-2 complete genomes was performed using Illumina, Oxford Nanopore, or Ion Torrent platforms. A total of 6163 SARS-CoV-2 complete genome sequences were generated over the surveillance period. All sequences were submitted to the Global Initiative on Sharing All Influenza Data database.
RESULTS: From June 2021 to January 2022, Malaysia experienced the fourth wave of COVID-19 dominated by the Delta variant of concern, including the original B.1.617.2 lineage and descendant AY lineages. The B.1.617.2 lineage was identified as the early dominant circulating strain throughout the country but over time, was displaced by AY.59 and AY.79 lineages in Peninsular (west) Malaysia, and the AY.23 lineage in east Malaysia. In December 2021, pilgrims returning from Saudi Arabia facilitated the introduction and spread of the BA.1 lineage (Omicron variant of concern) in the country.
CONCLUSION: The changing trends of circulating SARS-CoV-2 lineages were identified, with differences observed between west and east Malaysia. This initiative highlighted the importance of leveraging research expertise in the country to facilitate pandemic response and preparedness.

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