Displaying publications 1 - 20 of 38 in total

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  1. Ho CL, Tan YC, Yeoh KA, Ghazali AK, Yee WY, Hoh CC
    BMC Genomics, 2016;17:66.
    PMID: 26781612 DOI: 10.1186/s12864-016-2368-0
    Basal stem rot (BSR) is a fungal disease in oil palm (Elaeis guineensis Jacq.) which is caused by hemibiotrophic white rot fungi belonging to the Ganoderma genus. Molecular responses of oil palm to these pathogens are not well known although this information is crucial to strategize effective measures to eradicate BSR. In order to elucidate the molecular interactions between oil palm and G. boninense and its biocontrol fungus Trichoderma harzianum, we compared the root transcriptomes of untreated oil palm seedlings with those inoculated with G. boninense and T. harzianum, respectively.
  2. Tan KK, Tan YC, Chang LY, Lee KW, Nore SS, Yee WY, et al.
    BMC Genomics, 2015;16:93.
    PMID: 25888205 DOI: 10.1186/s12864-015-1294-x
    Brucellosis is an important zoonotic disease that affects both humans and animals. We sequenced the full genome and characterised the genetic diversity of two Brucella melitensis isolates from Malaysia and the Philippines. In addition, we performed a comparative whole-genome single nucleotide polymorphism (SNP) analysis of B. melitensis strains collected from around the world, to investigate the potential origin and the history of the global spread of B. melitensis.
  3. Mohan A, Munusamy C, Tan YC, Muthuvelu S, Hashim R, Chien SL, et al.
    BMC Infect Dis, 2019 Apr 18;19(1):330.
    PMID: 30999894 DOI: 10.1186/s12879-019-3963-x
    BACKGROUND: Invasive Salmonella infections result in significant morbidity and mortality in developing countries. In Asia, typhoid and paratyphoid fever are reported to be the major invasive Salmonella infections, while invasive non-typhoidal Salmonella (iNTS) infections are believed to be uncommon. Data from Sarawak, in Malaysian Borneo, are limited.

    METHODS: A retrospective study identifying all children aged

  4. Cheong WH, Tan YC, Yap SJ, Ng KP
    Bioinformatics, 2015 Nov 15;31(22):3685-7.
    PMID: 26227146 DOI: 10.1093/bioinformatics/btv433
    : We present ClicO Free Service, an online web-service based on Circos, which provides a user-friendly, interactive web-based interface with configurable features to generate Circos circular plots.
  5. Chai CY, Maran S, Thew HY, Tan YC, Rahman NMANA, Cheng WH, et al.
    Biology (Basel), 2022 Nov 02;11(11).
    PMID: 36358305 DOI: 10.3390/biology11111604
    The Harvey rat sarcoma (HRAS) proto-oncogene belongs to the RAS family and is one of the pathogenic genes that cause cancer. Deleterious nsSNPs might have adverse consequences at the protein level. This study aimed to investigate deleterious nsSNPs in the HRAS gene in predicting structural alterations associated with mutants that disrupt normal protein-protein interactions. Functional and structural analysis was employed in analyzing the HRAS nsSNPs. Putative post-translational modification sites and the changes in protein-protein interactions, which included a variety of signal cascades, were also investigated. Five different bioinformatics tools predicted 33 nsSNPs as "pathogenic" or "harmful". Stability analysis predicted rs1554885139, rs770492627, rs1589792804, rs730880460, rs104894227, rs104894227, and rs121917759 as unstable. Protein-protein interaction analysis revealed that HRAS has a hub connecting three clusters consisting of 11 proteins, and changes in HRAS might cause signal cascades to dissociate. Furthermore, Kaplan-Meier bioinformatics analyses indicated that the HRAS gene deregulation affected the overall survival rate of patients with breast cancer, leading to prognostic significance. Thus, based on these analyses, our study suggests that the reported nsSNPs of HRAS may serve as potential targets for different proteomic studies, diagnoses, and therapeutic interventions focusing on cancer.
  6. Kuan CS, Ng KP, Yew SM, Umar Meleh H, Seow HF, How KN, et al.
    Braz J Microbiol, 2023 Sep;54(3):1351-1372.
    PMID: 37351789 DOI: 10.1007/s42770-023-01032-z
    Neoscytalidium dimidiatum and Bipolaris species are fungal plant pathogens that have been reported to cause human diseases. Recently, we have isolated numerous N. dimidiatum and Bipolaris species from the skin scrapings and nails of different patients. In this work, we have sequenced the genome of one strain of N. dimidiatum. The sequenced genome was compared to that of a previously reported Bipolaris papendorfii genome for a better understanding of their complex lifestyle and broad host-range pathogenicity. Both N. dimidiatum UM 880 (~ 43 Mb) and B. papendorfii UM 226 (~ 33 Mb) genomes include 11,015-12,320 putative coding DNA sequences, of which 0.51-2.49% are predicted transposable elements. Analysis of secondary metabolism gene clusters revealed several genes involved in melanin biosynthesis and iron uptake. The arsenal of CAZymes related to plants pathogenicity is comparable between the species, including genes involved in hemicellulose and pectin decomposition. Several important gene encoding keratinolytic peptidases were identified in N. dimidiatum and B. papendorfii, reflecting their potential pathogenic role in causing skin and nail infections. In this study, additional information on the metabolic features of these two species, such as nutritional profiling, pH tolerance, and osmotolerant, are revealed. The genomic characterization of N. dimidiatum and B. papendorfii provides the basis for the future functional studies to gain further insights as to what makes these fungi persist in plants and why they are pathogenic to humans.
  7. Tan YC, Mustangin M, Rosli N, Wan Ahmad Kammal WSE, Md Isa N, Low TY, et al.
    Cryobiology, 2024 Mar;114:104843.
    PMID: 38158171 DOI: 10.1016/j.cryobiol.2023.104843
    Coolant-assisted liquid nitrogen (LN) flash freezing of frozen tissues has been widely adopted to preserve tissue morphology for histopathological annotations in mass spectrometry-based spatial proteomics techniques. However, existing coolants pose health risks upon inhalation and are expensive. To overcome this challenge, we present our pilot study by introducing the EtOH-LN workflow, which demonstrates the feasibility of using 95 % ethanol as a safer and easily accessible alternative to existing coolants for LN-based cryoembedding of frozen tissues. Our study reveals that both the EtOH-LN and LN-only cryoembedding workflows exhibit significantly reduced freezing artifacts compared to cryoembedding in cryostat (p 
  8. Ejyj J, Ang WJ, Wh WH, Tan YC
    Cureus, 2018 Jun 19;10(6):e2835.
    PMID: 30131928 DOI: 10.7759/cureus.2835
    Traumatic optic neuropathy (TON) is a rare devastating complication of traumatic head injury and is an ophthalmic emergency. Herein, we report a rare case of a 46-year-old gentleman who experienced severe blurring of vision, binocular diplopia, and pain over his left eye following a fall from a tree about three meters in height. Examinations revealed the visual acuity was 6/60 with a marked relative afferent pupillary defect and generalized ophthalmoplegia over his left eye. Emergency computed tomography (CT) brain and orbit showed a left frontotemporoparietal extradural hemorrhage, comminuted frontotemporoparietal and greater wing of sphenoid fracture with a bony spur impinging the lateral rectus and indirectly on the optic nerve. A diagnosis of left frontotemporoparietal bone fracture with traumatic optic neuropathy was made. An emergency left craniotomy, elevation of depressed skull fracture, and evacuation of clot was done. Postoperatively, his visual acuity showed marked improvement with visual acuity of 6/6 and all optic nerve functions were normal.
  9. Asghar A, Tan YC, Shahid M, Yow YY, Lahiri C
    Front Microbiol, 2021;12:653562.
    PMID: 34276590 DOI: 10.3389/fmicb.2021.653562
    With a continuous threat of antimicrobial resistance on human health worldwide, efforts for new alternatives are ongoing for the management of bacterial infectious diseases. Natural products of land and sea, being conceived to be having fewer side effects, pose themselves as a welcome relief. In this respect, we have taken a scaffolded approach to unearthing the almost unexplored chemical constituents of Malaysian red seaweed, Gracilaria edulis. Essentially, a preliminary evaluation of the ethyl acetate and acetone solvent extracts, among a series of six such, revealed potential antibacterial activity against six MDR species namely, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella enterica, methicillin-resistant Staphylococcus aureus (MRSA), Streptococcus pyogenes, and Bacillus subtilis. Detailed analyses of the inlying chemical constituents, through LC-MS and GC-MS chromatographic separation, revealed a library of metabolic compounds. These were led for further virtual screening against selected key role playing proteins in the virulence of the aforesaid bacteria. To this end, detailed predictive pharmacological analyses added up to reinforce Eplerenone as a natural alternative from the plethora of plausible bioactives. Our work adds the ongoing effort to re-discover and repurpose biochemical compounds to combat the antimicrobial resistance offered by the Gram-positive and the -negative bacterial species.
  10. Wong YC, Abd El Ghany M, Naeem R, Lee KW, Tan YC, Pain A, et al.
    Front Microbiol, 2016;7:1288.
    PMID: 27597847 DOI: 10.3389/fmicb.2016.01288
    Burkholderia cenocepacia infection often leads to fatal cepacia syndrome in cystic fibrosis patients. However, antibiotic therapy rarely results in complete eradication of the pathogen due to its intrinsic resistance to many clinically available antibiotics. Recent attention has turned to the identification of essential genes as the proteins encoded by these genes may serve as potential targets for development of novel antimicrobials. In this study, we utilized TraDIS (Transposon Directed Insertion-site Sequencing) as a genome-wide screening tool to facilitate the identification of B. cenocepacia genes essential for its growth and viability. A transposon mutant pool consisting of approximately 500,000 mutants was successfully constructed, with more than 400,000 unique transposon insertion sites identified by computational analysis of TraDIS datasets. The saturated library allowed for the identification of 383 genes that were predicted to be essential in B. cenocepacia. We extended the application of TraDIS to identify conditionally essential genes required for in vitro growth and revealed an additional repertoire of 439 genes to be crucial for B. cenocepacia growth under nutrient-depleted conditions. The library of B. cenocepacia mutants can subsequently be subjected to various biologically related conditions to facilitate the discovery of genes involved in niche adaptation as well as pathogenicity and virulence.
  11. Jabeen S, Yap HY, Abdullah FFJ, Zakaria Z, Isa NM, Tan YC, et al.
    Genes (Basel), 2019 01 25;10(2).
    PMID: 30691021 DOI: 10.3390/genes10020081
    Although more than 100 genome sequences of Pasteurella multocida are available, comprehensive and complete genome sequence analysis is limited. This study describes the analysis of complete genome sequence and pathogenomics of P. multocida strain PMTB2.1. The genome of PMTB2.1 has 2176 genes with more than 40 coding sequences associated with iron regulation and 140 virulence genes including the complete tad locus. The tad locus includes several previously uncharacterized genes such as flp2, rcpC and tadV genes. A transposable phage resembling to Mu phages was identified in P. multocida that has not been identified in any other serotype yet. The multi-locus sequence typing analysis assigned the PMTB2.1 genome sequence as type ST101, while the comparative genome analysis showed that PMTB2.1 is closely related to other P. multocida strains with the genomic distance of less than 0.13. The expression profiling of iron regulating-genes of PMTB2.1 was characterized under iron-limited environment. Results showed significant changes in the expression profiles of iron-regulating genes (p < 0.05) whereas the highest expression of fecE gene (281 fold) at 30 min suggests utilization of the outer-membrane proteins system in iron acquisition at an early stage of growth. This study showed the phylogenomic relatedness of P. multocida and improved annotation of important genes and functional characterization of iron-regulating genes of importance to the bacterial growth.
  12. Chan CL, Yew SM, Na SL, Tan YC, Lee KW, Yee WY, et al.
    Genome Announc, 2014;2(2).
    PMID: 24744321 DOI: 10.1128/genomeA.00074-14
    Ochroconis constricta is a soilborne dematiaceous fungus that has never been reported to be associated with human infection. Here we report the first draft genome sequence of strain UM 578, isolated from human skin scraping. The genomic information revealed will contribute to a better understanding of this species.
  13. Jabeen S, Yong YH, Abdullah FJF, Zakaria Z, Mat Isa N, Tan YC, et al.
    Genome Announc, 2017 Nov 02;5(44).
    PMID: 29097462 DOI: 10.1128/genomeA.01190-17
    Pasteurella multocida causes pneumonic pasteurellosis and hemorrhagic septicemia (HS) in large ruminants. In this study, we determined the complete genome sequence of P. multocida strain PMTB2.1 capsular serotype A isolated from buffaloes that died of septicemia.
  14. Mohan A, Manan K, Tan LS, Tan YC, Chin ST, Ahmad R, et al.
    Int J Infect Dis, 2020 Sep;98:59-66.
    PMID: 32535300 DOI: 10.1016/j.ijid.2020.06.025
    OBJECTIVES: Melioidosis is associated with extremely high case fatality ratios. The aim of this study was to determine whether detection of abdominal visceral abscesses can facilitate diagnosis of melioidosis in children.

    METHODS: We conducted a retrospective analysis of all children who had liver and/or spleen abscesses on abdominal ultrasonography admitted to Bintulu Hospital in Sarawak, Malaysia, from January 2014 until December 2018.

    RESULTS: Fifty-three children had liver and/or spleen abscesses. Spleen abscesses were present in 48 (91%) cases; liver abscesses in 15 (28%). Melioidosis was confirmed by culture in 9 (17%) children; small occult splenic abscesses were present in all cases. In 78% of these cases, the lesions were detected before any positive culture (or serology) results were available. Four (8%) children had bacteriologically-confirmed tuberculosis. Two (4%) had Staphylococcus aureus infection. Of the remaining 38 (72%) culture-negative cases, 36 (95%) had clinical and imaging characteristics similar to that of children with culture-confirmed melioidosis and improved with empirical melioidosis antibiotic therapy.

    CONCLUSIONS: A large number of children in Bintulu Hospital in Sarawak, Malaysia, were found to have spleen abscesses. Melioidosis was the most common etiology identified in these children. Abdominal ultrasonography is extremely useful in facilitating the diagnosis of pediatric melioidosis.

  15. Tan IKP, Foong CP, Tan HT, Lim H, Zain NA, Tan YC, et al.
    J Biotechnol, 2020 Apr 10;313:18-28.
    PMID: 32171790 DOI: 10.1016/j.jbiotec.2020.03.006
    The polyhydroxyalkanoate (PHA) producing capability of four bacterial strains isolated from Antarctica was reported in a previous study. This study analyzed the PHA synthase genes and the PHA-associated gene clusters from the two antarctic Pseudomonas isolates (UMAB-08 and UMAB-40) and the two antarctic Janthinobacterium isolates (UMAB-56 and UMAB-60) through whole-genome sequence analysis. The Pseudomonas isolates were found to carry PHA synthase genes which fall into two different PHA gene clusters, namely Class I and Class II, which are involved in the biosynthesis of short-chain-length-PHA (SCL-PHA) and medium-chain-length-PHA (MCL-PHA), respectively. On the other hand, the Janthinobacterium isolates carry a Class I and an uncharacterized putative PHA synthase genes. No other gene involved in PHA synthesis was detected in close proximity to the uncharacterized putative PHA synthase gene in the Janthinobacterium isolates, therefore it falls into a separate clade from the ordinary Class I, II, III and IV clades of PHA synthase (PhaC) phylogenetic tree. Multiple sequence alignment showed that the uncharacterized putative PHA synthase gene contains all the highly conserved amino acid residues and the proposed catalytic triad of PHA synthase. PHA biosynthesis and in vitro PhaC enzymatic assay results showed that this uncharacterized putative PHA synthase from Janthinobacterium sp. UMAB-60 is funtional. This report adds new knowledge to the PHA synthase database as we describe scarce information of PHA synthase genes and PHA-associated gene clusters from the antarctic bacterial isolates (extreme and geographically isolated environment) and comparing with those from non-antarctic PHA-producing bacteria.
  16. Tan KK, Tan YC, Chang LY, Lee KW, Nor'e SS, Yee WY, et al.
    J Infect Dev Ctries, 2017 Jun 01;11(5):420-425.
    PMID: 30943180 DOI: 10.3855/jidc.7598
    INTRODUCTION: Currently available tests have limitations for the identification of Brucella species and strains, and their genetic lineage. The genome sequence of the rpoB gene encoding the β-subunit of DNA-dependent RNA polymerase was investigated for its use in genotyping Brucella melitensis.

    METHODOLOGY: Complete rpoB gene sequences of globally distributed Brucella melitensis strains were analyzed. Single nucleotides polymorphisms (SNPs) of the rpoB gene sequences were identified and used to type Brucella melitensis strains.

    RESULTS: Six DNA polymorphisms were identified, of which two (nucleotides 3201 and 558) were novel. Analysis of the geographical distribution of the strains revealed a spatial clustering pattern with rpoB type 1 representing European and American strains, rpoB type 2 representing European, African, and Asian strains, rpoB type 3 representing Mediterranean strains, and rpoB type 4 representing African (C3201T) and European (C3201T/T558A) strains.

    CONCLUSIONS: We report the discovery of two novel SNPs of rpoB gene that can serve as useful markers for epidemiology and geographical tracking of B. melitensis.

  17. Abdullah MZ, Awang MS, Tan YC, Abdullah JM
    J Neurol Surg A Cent Eur Neurosurg, 2014 Mar;75(2):155-7.
    PMID: 23636911 DOI: 10.1055/s-0032-1330954
    The study assesses the capability and accuracy of a robotic arm to perform burr holes.
  18. Idris Z, Tan YC, Kandasamy R, Ghani RI, Abdullah JM
    J Neurol Surg A Cent Eur Neurosurg, 2017 Mar;78(2):210-215.
    PMID: 26968147 DOI: 10.1055/s-0035-1571161
    Symptomatic intracranial arachnoid cysts are commonly treated using neuroendoscopy. Cysts located within the posterior fossa may present a greater surgical challenge to the neurosurgeon due to the numerous vital neurovascular structures located within this confined space. Adding neuronavigation during endoscopy helps a neurosurgeon to visualize and utilize both anterior and posterior corridors safely to access and manage these lesions. We present three symptomatic posterior fossa arachnoid cysts that were treated successfully using minimally invasive neuronavigation-guided endoscopic neurosurgery utilizing the anterior transfrontal transaqueductal, anterior transfrontal transtrigonal, and posterior suboccipital infratentorial supracerebellar approaches.
  19. Tan YC, Yeoh KA, Wong MY, Ho CL
    J Plant Physiol, 2013 Nov 01;170(16):1455-60.
    PMID: 23769496 DOI: 10.1016/j.jplph.2013.05.009
    Basal stem rot (BSR) is a major disease of oil palm caused by a pathogenic fungus, Ganoderma boninense. However, the interaction between the host plant and its pathogen is not well characterized. To better understand the response of oil palm to G. boninense, transcript profiles of eleven putative defence-related genes from oil palm were measured by quantitative reverse-transcription (qRT)-PCR in the roots of oil palms treated with G. boninense from 3 to 12 weeks post infection (wpi). These transcripts encode putative Bowman-Birk serine protease inhibitors (EgBBI1 and 2), defensin (EgDFS), dehydrin (EgDHN), early methionine-labeled polypeptides (EgEMLP1 and 2), glycine-rich RNA binding protein (EgGRRBP), isoflavone reductase (EgIFR), metallothionein-like protein (EgMT), pathogenesis-related-1 protein (EgPRP), and type 2 ribosome-inactivating protein (EgT2RIP). The transcript abundance of EgBBI2 increased in G. boninense-treated roots at 3 and 6wpi compared to those of controls; while the transcript abundance of EgBBI1, EgDFS, EgEMLP1, EgMT, and EgT2RIP increased in G. boninense-treated roots at 6 or 12wpi. Meanwhile, the gene expression of EgDHN was up-regulated at all three time points in G. boninense-treated roots. The expression profiles of the eleven transcripts were also studied in leaf samples upon inoculation of G. boninense and Trichoderma harzianum to identify potential biomarkers for early detection of BSR. Two candidate genes (EgEMLP1 and EgMT) that have different profiles in G. boninense-treated leaves compared to those infected by T. harzianum may have the potential to be developed as biomarkers for early detection of G. boninense infection.
  20. Ibraheem ZO, Satar M, Abdullah NA, Rathore H, Tan YC, Uldin F, et al.
    Pak J Pharm Sci, 2014 Jan;27(1):1-9.
    PMID: 24374430
    Recently, it is suggested to use POLE (palm oil leaf extract) as a nutraceutical health product in food industry due to its newly discovered content of polyphenols and antioxidant vitamins. In the experiment, the antioxidant and anti-lipid-peroxidation activities of the extract were confirmed using; DPPH (1-diphenyl-2-picryl-hydrazil) radical scavenging activity, ferric ion induced lipid peroxidation inhibition, reducing power and hydrogen peroxide scavenging activity assays. The cardio-protective activity was studied in vivo using a model of metabolic syndrome induced by high fat diet. Lipid profile, obesity indices, renal tubular handling of water and electrolytes, blood pressure and arterial stiffness were measured at the end of the treatment period. Sprague Dawley rats weighing 150-200 g were divided into six groups, viz; group C; was treated as a negative control and fed with standard rodents chow, group H; was treated as a positive control and fed with an experimental diet enriched with saturated free fatty acids for 8 weeks, groups HP0.5, HP1 and HP2 which were fed with 0.5,1 and 2 g/kg (body weight) /day of POLE orally during the last 24 days of the high fat diet feeding period and group P; fed with highest dose of POLE. Results revealed that POLE possesses a cardio-protective effect which is ascribed to its content of polyphenols.
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