MyMedR

In vitro vascular effects produced by crude aqueous extract of green marine algae, Cladophora patentiramea (Mont.) Kützing, in aorta from normotensive rats

Lim YL, Mok SL

Med Princ Pract, 2010;19(4):260-8.

PMID: 20516701 DOI: 10.1159/000312711

To investigate the antihypertensive activity of aqueous extracts obtained from Malaysian coastal seaweeds and to determine the pharmacological mechanisms of the extracts on rat aorta in vitro.

Fulltext Complete Genome Sequence of Pseudomonas aeruginosa Strain YL84, a Quorum-Sensing Strain Isolated from Compost

Chan KG, Yin WF, Lim YL

Genome Announc, 2014;2(2).

PMID: 24699957 DOI: 10.1128/genomeA.00246-14

Here, we report the complete genome sequence of Pseudomonas aeruginosa strain YL84, which was isolated from compost. This strain was found to be a chitinase-producing quorum-sensing bacterium.

Fulltext De Novo Assembly of the Quorum-Sensing Pandoraea sp. Strain RB-44 Complete Genome Sequence Using PacBio Single-Molecule Real-Time Sequencing Technology

Ee R, Lim YL, Yin WF, Chan KG

Genome Announc, 2014;2(2).

PMID: 24699956 DOI: 10.1128/genomeA.00245-14

We report the first complete genome sequence of Pandoraea sp. strain RB-44, which was found to possess quorum-sensing properties. To the best of our knowledge, this is the first documentation of both a complete genome sequence and quorum-sensing properties of a Pandoraea species.

Fulltext Quorum sensing activity of Aeromonas caviae strain YL12, a bacterium isolated from compost

Lim YL, Ee R, Yin WF, Chan KG

Sensors (Basel), 2014 Apr 22;14(4):7026-40.

PMID: 24759107 DOI: 10.3390/s140407026

Quorum sensing is a well-studied cell-to-cell communication method that involves a cell-density dependent regulation of genes expression mediated by signalling molecules. In this study, a bacterium isolated from a plant material compost pile was found to possess quorum sensing activity based on bioassay screening. Isolate YL12 was identified using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and molecular typing using rpoD gene which identified the isolate as Aeromonas caviae. High resolution tandem mass spectrometry was subsequently employed to identify the N-acyl homoserine lactone profile of Aeromonas caviae YL12 and confirmed that this isolate produced two short chain N-acyl homoserine lactones, namely C4-HSL and C6, and the production was observed to be cell density-dependent. Using the thin layer chromatography (TLC) bioassay, both AHLs were found to activate C. violaceum CV026, whereas only C6-HSL was revealed to induce bioluminescence expression of E. coli [pSB401]. The data presented in this study will be the leading steps in understanding the role of quorum sensing in Aeromonas caviae strain YL12.

Fulltext Quorum sensing activity in Pandoraea pnomenusa RB38

Ee R, Lim YL, Kin LX, Yin WF, Chan KG

Sensors (Basel), 2014;14(6):10177-86.

PMID: 24919016 DOI: 10.3390/s140610177

Strain RB38 was recovered from a former dumping area in Malaysia. MALDI-TOF mass spectrometry and genomic analysis identified strain RB-38 as Pandoraea pnomenusa. Various biosensors confirmed its quorum sensing properties. High resolution triple quadrupole liquid chromatography-mass spectrometry analysis was subsequently used to characterize the N-acyl homoserine lactone production profile of P. pnomenusa strain RB38, which validated that this isolate produced N-octanoyl homoserine lactone as a quorum sensing molecule. This is the first report of the production of N-octanoyl homoserine lactone by P. pnomenusa strain RB38.

Fulltext Complete Genome Sequence and Methylome Analysis of Aeromonas hydrophila Strain YL17, Isolated from a Compost Pile

Lim YL, Roberts RJ, Ee R, Yin WF, Chan KG

Genome Announc, 2016 Mar 03;4(2).

PMID: 26941143 DOI: 10.1128/genomeA.00060-16

In this report, we announce the complete genome sequence of Aeromonas hydrophila strain YL17. Single-molecule real-time (SMRT) DNA sequencing was used to generate the complete genome sequence and the genome-wide DNA methylation profile of this environmental isolate. A total of five unique DNA methyltransferase recognition motifs were reported here.

Fulltext Insights on Quorum-Quenching Properties of Lysinibacillus fusiformis Strain RB21, a Malaysian Municipal Solid-Waste Landfill Soil Isolate, via Complete Genome Sequence Analysis

Yong D, Ee R, Lim YL, Chang CY, Yin WF, Chan KG

Genome Announc, 2015;3(3).

PMID: 25953192 DOI: 10.1128/genomeA.00409-15

Lysinibacillus fusiformis strain RB21 is a quorum-quenching bacterium that is able to degrade quorum-sensing signaling molecules. Here, we present the first complete genome sequence of L. fusiformis strain RB21. The finished genome is 4.8 Mbp in size, and the quorum-quenching gene was identified.

Ethnic differences in acute myocardial infarction in Singapore

Mak KH, Chia KS, Kark JD, Chua T, Tan C, Foong BH, et al.

Eur Heart J, 2003 Jan;24(2):151-60.

PMID: 12573272

AIMS: We compare the myocardial infarction (MI) event and mortality rates among Chinese, Malay and Indian residents of Singapore.

METHODS: Residents, aged 20 to 64 years, with an MI event were identified from hospital discharge listings, postmortem reports, and the Registry of Births and Deaths. All pathology laboratories flagged patients with elevated creatine phosphokinase (CPK) levels. Modified MONICA (multinational monitoring of trends and determinants in cardiovascular disease) criteria were used for determining MI events.

RESULTS: From 1991 to 1999, 12 481 MI events were identified. Chinese patients were older and less likely to have typical symptoms or previous MI. Malays had the highest peak CPK level. Among all three ethnic groups, MI event and age-adjusted case-fatality rates declined. Compared with Chinese, MI event rates were >2-fold and >3-fold higher, and age-standardized coronary mortality rates were 2.4 and 3.0 higher times for Malays and Indians, respectively. Malays have the highest 3.1-year case-fatality, with an adjusted hazard ratio of 1.26 (95% confidence interval, 1.14 to 1.38) compared with Chinese.

CONCLUSION: We found strong ethnic differences in MI event, case-fatality and coronary mortality rates among the three ethnic groups in Singapore. While Indians have the greatest MI event rates, Malays have the highest case-fatality.

Fulltext In silico Analysis Reveals Distribution of Quorum Sensing Genes and Consistent Presence of LuxR Solos in the Pandoraea Species

Chua KO, See-Too WS, Ee R, Lim YL, Yin WF, Chan KG

Front Microbiol, 2019;10:1758.

PMID: 31447806 DOI: 10.3389/fmicb.2019.01758

The most common quorum sensing (QS) system in Gram-negative bacteria consists of signaling molecules called N-acyl-homoserine lactones (AHLs), which are synthesized by an enzyme AHL synthase (LuxI) and detected by a transcriptional regulator (LuxR) that are usually located in close proximity. However, many recent studies have also evidenced the presence of LuxR solos that are LuxR-related proteins in Proteobacteria that are devoid of a cognate LuxI AHL synthase. Pandoraea species are opportunistic pathogens frequently isolated from sputum specimens of cystic fibrosis (CF) patients. We have previously shown that P. pnomenusa strains possess QS activity. In this study, we examined the presence of QS activity in all type strains of Pandoraea species and acquired their complete genome sequences for holistic bioinformatics analyses of QS-related genes. Only four out of nine type strains (P. pnomenusa, P. sputorum, P. oxalativorans, and P. vervacti) showed QS activity, and C8-HSL was the only AHL detected. A total of 10 canonical luxIs with adjacent luxRs were predicted by bioinformatics from the complete genomes of aforementioned species and publicly available Pandoraea genomes. No orphan luxI was identified in any of the genomes. However, genes for two LuxR solos (LuxR2 and LuxR3 solos) were identified in all Pandoraea genomes (except two draft genomes with one LuxR solo gene), and P. thiooxydans was the only species that harbored no QS-related activity and genes. Except the canonical LuxR genes, LuxIs and LuxR solos of Pandoraea species were distantly related to the other well-characterized QS genes based on phylogenetic clustering. LuxR2 and LuxR3 solos might represent two novel evolutionary branches of LuxR system as they were found exclusively only in the genus. As a few luxR solos were located in close proximity with prophage sequence regions in the genomes, we thus postulated that these luxR solos could be transmitted into genus Pandoraea by transduction process mediated by bacteriophage. The bioinformatics approach developed in this study forms the basis for further characterization of closely related species. Overall, our findings improve the current understanding of QS in Pandoraea species, which is a potential pharmacological target in battling Pandoraea infections in CF patients.

Complete genome sequence of oxalate-degrading bacterium Pandoraea vervacti DSM 23571(T)

Ee R, Yong D, Lim YL, Yin WF, Chan KG

J Biotechnol, 2015 Jun 20;204:5-6.

PMID: 25848988 DOI: 10.1016/j.jbiotec.2015.03.020

Pandoraea vervacti DSM 23571(T) is an oxalate metabolizing bacterium isolated from an uncultivated field soil in Mugla, Turkey. Here, we present the first complete genome sequence of P. vervacti DSM 23571(T). A complete pathway for degradation of oxalate was revealed from the genome analysis. These data are important to path new opportunities for genetic engineering in the field of biotechnology.

Complete genome of Pseudomonas sp. strain L10.10, a psychrotolerant biofertilizer that could promote plant growth

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

J Biotechnol, 2016 Mar 20;222:84-5.

PMID: 26876481 DOI: 10.1016/j.jbiotec.2016.02.017

Pseudomonas sp. strain L10.10 (=DSM 101070) is a psychrotolerant bacterium which was isolated from Lagoon Island, Antarctica. Analysis of its complete genome sequence indicates its possible role as a plant-growth promoting bacterium, including nitrogen-fixing ability and indole acetic acid (IAA)-producing trait, with additional suggestion of plant disease prevention attributes via hydrogen cyanide production.

Complete genome of Planococcus rifietoensis M8(T), a halotolerant and potentially plant growth promoting bacterium

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

J Biotechnol, 2016 Mar 10;221:114-5.

PMID: 26808870 DOI: 10.1016/j.jbiotec.2016.01.026

Planococcus rifietoensis M8(T) (=DSM 15069(T)=ATCC BAA-790(T)) is a halotolerant bacterium with potential plant growth promoting properties isolated from an algal mat collected from a sulfurous spring in Campania (Italy). This paper presents the first complete genome of P. rifietoensis M8(T). Genes coding for various potentially plant growth promoting properties were identified within its genome.

Complete genome of Pandoraea pnomenusa RB-38, an oxalotrophic bacterium isolated from municipal solid waste landfill site

Lim YL, Ee R, Yong D, Tee KK, Yin WF, Chan KG

J Biotechnol, 2015 Nov 20;214:83-4.

PMID: 26393955 DOI: 10.1016/j.jbiotec.2015.09.018

Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens.

Complete genome sequence of Serratia fonticola DSM 4576 T, a potential plant growth promoting bacterium

Lim YL, Yong D, Ee R, Krishnan T, Tee KK, Yin WF, et al.

J Biotechnol, 2015 Nov 20;214:43-4.

PMID: 26376471 DOI: 10.1016/j.jbiotec.2015.09.005

Here, we present the first complete genome sequence of Serratia fonticola DSM 4576(T), a potential plant growth promoting (PGP) bacterium which confers solubilization of inorganic phosphate, indole-3-acetic acid production, hydrogen cyanideproduction, siderophore production and assimilation of ammonia through the glutamate synthase (GS/GOGAT) pathway. This genome sequence is valuable for functional genomics and ecological studies which are related to PGP and biocontrol activities.

Complete genome sequence of Serratia multitudinisentens RB-25(T), a novel chitinolytic bacterium

Lim YL, Yong D, Ee R, Tee KK, Yin WF, Chan KG

J Biotechnol, 2015 Aug 10;207:32-3.

PMID: 25975625 DOI: 10.1016/j.jbiotec.2015.04.027

Serratia multitudinisentens RB-25(T) (=DSM 28811(T) =LMG 28304(T)) is a newly proposed type strain in the genus of Serratia isolated from a municipal landfill site. Here, we present the complete genome of S. multitudinisentens RB-25(T) which contains a complete chitinase operon and other chitin and N-acetylglucosamine utilisation enzymes. To our knowledge, this is the first report of the complete genome sequence of this novel isolate and its chitinase gene discovery.

Fulltext Novel Methyltransferase Recognition Motif Identified in Chania multitudinisentens RB-25(T) gen. nov., sp. nov

Ee R, Lim YL, Yin WF, See-Too WS, Roberts RJ, Chan KG

Front Microbiol, 2016;7:1362.

PMID: 27630623 DOI: 10.3389/fmicb.2016.01362

Fulltext Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses

Yaakop AS, Chan KG, Ee R, Lim YL, Lee SK, Manan FA, et al.

Sci Rep, 2016 09 19;6:33660.

PMID: 27641516 DOI: 10.1038/srep33660

Jeotgalibacillus malaysiensis, a moderate halophilic bacterium isolated from a pelagic area, can endure higher concentrations of sodium chloride (NaCl) than other Jeotgalibacillus type strains. In this study, we therefore chose to sequence and assemble the entire J. malaysiensis genome. This is the first report to provide a detailed analysis of the genomic features of J. malaysiensis, and to perform genetic comparisons between this microorganism and other halophiles. J. malaysiensis encodes a native megaplasmid (pJeoMA), which is greater than 600 kilobases in size, that is absent from other sequenced species of Jeotgalibacillus. Subsequently, RNA-Seq-based transcriptome analysis was utilised to examine adaptations of J. malaysiensis to osmotic stress. Specifically, the eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) and KEGG (Kyoto Encyclopaedia of Genes and Genomes) databases were used to elucidate the overall effects of osmotic stress on the organism. Generally, saline stress significantly affected carbohydrate, energy, and amino acid metabolism, as well as fatty acid biosynthesis. Our findings also indicate that J. malaysiensis adopted a combination of approaches, including the uptake or synthesis of osmoprotectants, for surviving salt stress. Among these, proline synthesis appeared to be the preferred method for withstanding prolonged osmotic stress in J. malaysiensis.

Fulltext AidP, a novel N-Acyl homoserine lactonase gene from Antarctic Planococcus sp

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

Sci Rep, 2017 02 22;7:42968.

PMID: 28225085 DOI: 10.1038/srep42968

Planococcus is a Gram-positive halotolerant bacterial genus in the phylum Firmicutes, commonly found in various habitats in Antarctica. Quorum quenching (QQ) is the disruption of bacterial cell-to-cell communication (known as quorum sensing), which has previously been described in mesophilic bacteria. This study demonstrated the QQ activity of a psychrotolerant strain, Planococcus versutus strain L10.15T, isolated from a soil sample obtained near an elephant seal wallow in Antarctica. Whole genome analysis of this bacterial strain revealed the presence of an N-acyl homoserine lactonase, an enzyme that hydrolyzes the ester bond of the homoserine lactone of N-acyl homoserine lactone (AHLs). Heterologous gene expression in E. coli confirmed its functions for hydrolysis of AHLs, and the gene was designated as aidP (autoinducer degrading gene from Planococcus sp.). The low temperature activity of this enzyme suggested that it is a novel and uncharacterized class of AHL lactonase. This study is the first report on QQ activity of bacteria isolated from the polar regions.

Fulltext Quorum sensing activity of Serratia fonticola strain RB-25 isolated from an ex-landfill site

Ee R, Lim YL, Tee KK, Yin WF, Chan KG

Sensors (Basel), 2014 Mar 12;14(3):5136-46.

PMID: 24625739 DOI: 10.3390/s140305136

Quorum sensing is a unique bacterial communication system which permits bacteria to synchronize their behaviour in accordance with the population density. The operation of this communication network involves the use of diffusible autoinducer molecules, termed N-acylhomoserine lactones (AHLs). Serratia spp. are well known for their use of quorum sensing to regulate the expression of various genes. In this study, we aimed to characterized the AHL production of a bacterium designated as strain RB-25 isolated from a former domestic waste landfill site. It was identified as Serratia fonticola using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry analysis and this was confirmed by 16S ribosomal DNA sequencing. High resolution triple quadrupole liquid chromatography-mass spectrometry analysis of S. fonticola strain RB-25 spent culture supernatant indicated the existence of three AHLs namely: N-butyryl-L-homoserine lactone (C4-HSL), N-hexanoyl-L-homoserine lactone (C6-HSL) and N-(3-oxohexanoyl) homoserine-lactone (3-oxo-C6 HSL). This is the first report of the production of these AHLs in S. fonticola.

On the feasibility of self-mixing interferometer sensing for detection of the surface electrocardiographic signal using a customized electro-optic phase modulator

Bakar AA, Lim YL, Wilson SJ, Fuentes M, Bertling K, Taimre T, et al.

Physiol Meas, 2013 Feb;34(2):281-9.

PMID: 23363933 DOI: 10.1088/0967-3334/34/2/281

Optical sensing offers an attractive option for detection of surface biopotentials in human subjects where electromagnetically noisy environments exist or safety requirements dictate a high degree of galvanic isolation. Such circumstances may be found in modern magnetic resonance imaging systems for example. The low signal amplitude and high source impedance of typical biopotentials have made optical transduction an uncommon sensing approach. We propose a solution consisting of an electro-optic phase modulator as a transducer, coupled to a vertical-cavity surface-emitting laser and the self-mixing signal detected via a photodiode. This configuration is physically evaluated with respect to synthesized surface electrocardiographic (EKG) signals of varying amplitudes and using differing optical feedback regimes. Optically detected EKG signals using strong optical feedback show the feasibility of this approach and indicate directions for optimization of the electro-optic transducer for improved signal-to-noise ratios. This may provide a new means of biopotential detection suited for environments characterized by harsh electromagnetic interference.

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