MyMedR

Fulltext Complete genome of Arthrobacter alpinus strain R3.8, bioremediation potential unraveled with genomic analysis

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

Stand Genomic Sci, 2017;12:52.

PMID: 28904741 DOI: 10.1186/s40793-017-0264-0

Arthrobacter alpinus R3.8 is a psychrotolerant bacterial strain isolated from a soil sample obtained at Rothera Point, Adelaide Island, close to the Antarctic Peninsula. Strain R3.8 was sequenced in order to help discover potential cold active enzymes with biotechnological applications. Genome analysis identified various cold adaptation genes including some coding for anti-freeze proteins and cold-shock proteins, genes involved in bioremediation of xenobiotic compounds including naphthalene, and genes with chitinolytic and N-acetylglucosamine utilization properties and also plant-growth-influencing properties. In this genome report, we present a complete genome sequence of A. alpinus strain R3.8 and its annotation data, which will facilitate exploitation of potential novel cold-active enzymes.

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 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 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.

Fulltext Exploring molecular variation in Schistosoma japonicum in China

Young ND, Chan KG, Korhonen PK, Min Chong T, Ee R, Mohandas N, et al.

Sci Rep, 2015;5:17345.

PMID: 26621075 DOI: 10.1038/srep17345

Schistosomiasis is a neglected tropical disease that affects more than 200 million people worldwide. The main disease-causing agents, Schistosoma japonicum, S. mansoni and S. haematobium, are blood flukes that have complex life cycles involving a snail intermediate host. In Asia, S. japonicum causes hepatointestinal disease (schistosomiasis japonica) and is challenging to control due to a broad distribution of its snail hosts and range of animal reservoir hosts. In China, extensive efforts have been underway to control this parasite, but genetic variability in S. japonicum populations could represent an obstacle to eliminating schistosomiasis japonica. Although a draft genome sequence is available for S. japonicum, there has been no previous study of molecular variation in this parasite on a genome-wide scale. In this study, we conducted the first deep genomic exploration of seven S. japonicum populations from mainland China, constructed phylogenies using mitochondrial and nuclear genomic data sets, and established considerable variation between some of the populations in genes inferred to be linked to key cellular processes and/or pathogen-host interactions. Based on the findings from this study, we propose that verifying intraspecific conservation in vaccine or drug target candidates is an important first step toward developing effective vaccines and chemotherapies against schistosomiasis.

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 Female tilapia, Oreochromis sp. mobilised energy differently for growth and reproduction according to living environment

Razali RS, Rahmah S, Shirly-Lim YL, Ghaffar MA, Mazelan S, Jalilah M, et al.

Sci Rep, 2024 Feb 05;14(1):2903.

PMID: 38316820 DOI: 10.1038/s41598-024-52864-0

This study was conducted to investigate the energy mobilisation preference and ionoregulation pattern of female tilapia, Oreochromis sp. living in different environments. Three different treatments of tilapia as physiology compromising model were compared; tilapia cultured in recirculating aquaculture system (RAS as Treatment I-RAS), tilapia cultured in open water cage (Treatment II-Cage) and tilapia transferred from cage and cultured in RAS (Treatment III-Compensation). Results revealed that tilapia from Treatment I and III mobilised lipid to support gonadogenesis, whilst Treatment II tilapia mobilised glycogen as primary energy for daily exercise activity and reserved protein for growth. The gills and kidney Na+/K+ ATPase (NKA) activities remained relatively stable to maintain homeostasis with a stable Na+ and K+ levels. As a remark, this study revealed that tilapia strategized their energy mobilisation preference in accessing glycogen as an easy energy to support exercise metabolism and protein somatogenesis in cage culture condition, while tilapia cultured in RAS mobilised lipid for gonadagenesis purposes.

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.

Fulltext Complete genome sequencing of Pandoraea pnomenusa RB38 and Molecular Characterization of Its N-acyl homoserine lactone synthase gene ppnI

Lim YL, Ee R, How KY, Lee SK, Yong D, Tee KK, et al.

PeerJ, 2015;3:e1225.

PMID: 26336650 DOI: 10.7717/peerj.1225

In this study, we sequenced the genome of Pandoraea pnomenusa RB38 using Pacific Biosciences RSII (PacBio) Single Molecule Real Time (SMRT) sequencing technology. A pair of cognate luxI/R homologs was identified where the luxI homolog, ppnI, was found adjacent to a luxR homolog, ppnR1. An additional orphan luxR homolog, ppnR2, was also discovered. Multiple sequence alignment and phylogenetic analysis revealed that ppnI is an N-acyl homoserine lactone (AHL) synthase gene that is distinct from those of the nearest phylogenetic neighbor viz. Burkholderia spp. High resolution tandem mass spectrometry (LC-MS/MS) analysis showed that Escherichia coli BL21 harboring ppnI produced a similar AHL profile (N-octanoylhomoserine lactone, C8-HSL) as P. pnomenusa RB38, the wild-type donor strain, confirming that PpnI directed the synthesis of AHL in P. pnomenusa RB38. To our knowledge, this is the first documentation of the luxI/R homologs of the genus Pandoraea.

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.

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.

Development and validation of patient diabetes knowledge questionnaire (PDKQ)

Lim PC, Rajah R, Lim YL, Kam JLH, Wong TY, Krishnanmurthi V, et al.

J Pharm Policy Pract, 2023 Oct 19;16(1):121.

PMID: 37858279 DOI: 10.1186/s40545-023-00631-3

BACKGROUND: Evaluation of diabetes knowledge plays a pivotal role in identifying and addressing patients' knowledge gaps. The implementation of a standardized diabetes knowledge assessment tool is important to ensure consistent scoring and facilitating the development of effective and standardized education programs.

AIM: To develop and validate a patient diabetes knowledge questionnaire (PDKQ) to assess knowledge of diabetes mellitus patients.

METHODS: The development of the PDKQ questionnaire involved three phases: item development, content validation, and reliability testing. In the item development phase, the initial draft of the PDKQ, comprising a multiple-choice answer questionnaire was developed. The content validation phase comprised two stages. Firstly, ten experts participated in the expert validation process, followed by face validation involving six patients. In the final phase, test-retest analysis was performed among diabetes mellitus patients to assess reliability.

RESULTS: The first draft of PDKQ consisted of 11 patient characteristics items and 37 items of multiple choices questions. During the expert validation, three items were eliminated due to low clarity, and an additional six items were removed as they were deemed irrelevant or unimportant. During the face validation, three patients' characteristic items and eight multiple-choice questions were excluded due to a content validity index of less than 0.83. In the test-retest phase, 36 subjects responded to 8 items pertaining to patients' characteristics and 20 multiple-choice questions. The test-retest analysis yielded an intraclass correlation coefficient of 0.88, indicating good reliability.

CONCLUSION: The 20-item PDKQ is a reliable and robust tool in assessing the knowledge of diabetes mellitus patients in Malaysia. Its implementation allows standardized assessment of diabetic patients' knowledge levels, enabling targeted interventions to empower patients and optimize diabetes care practices.

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 sequence of Pandoraea oxalativorans DSM 23570(T), an oxalate metabolizing soil bacterium

Chan KG, Yong D, Ee R, Lim YL, Yu CY, Tee KK, et al.

J Biotechnol, 2016 Feb 10;219:124-5.

PMID: 26742625 DOI: 10.1016/j.jbiotec.2015.12.037

Pandoraea oxalativorans DSM 23570(T) is an oxalate-degrading bacterium that was originally isolated from soil litter near to oxalate-producing plant of the genus Oxalis. Here, we report the first complete genome of P. oxalativorans DSM 23570(T) which would allow its potential biotechnological applications to be unravelled.

Complete genome sequence of Pandoraea thiooxydans DSM 25325(T), a thiosulfate-oxidizing bacterium

Yong D, Ee R, Lim YL, Yu CY, Ang GY, How KY, et al.

J Biotechnol, 2016 Jan 10;217:51-2.

PMID: 26603120 DOI: 10.1016/j.jbiotec.2015.11.009

Pandoraea thiooxydans DSM 25325(T) is a thiosulfate-oxidizing bacterium isolated from rhizosphere soils of a sesame plant. Here, we present the first complete genome of P. thiooxydans DSM 25325(T). Several genes involved in thiosulfate oxidation and biodegradation of aromatic compounds were identified.

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.

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