Displaying publications 1 - 20 of 67 in total

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  1. Agbolade O, Nazri A, Yaakob R, Ghani AA, Cheah YK
    BMC Bioinformatics, 2019 Dec 02;20(1):619.
    PMID: 31791234 DOI: 10.1186/s12859-019-3153-2
    BACKGROUND: Expression in H-sapiens plays a remarkable role when it comes to social communication. The identification of this expression by human beings is relatively easy and accurate. However, achieving the same result in 3D by machine remains a challenge in computer vision. This is due to the current challenges facing facial data acquisition in 3D; such as lack of homology and complex mathematical analysis for facial point digitization. This study proposes facial expression recognition in human with the application of Multi-points Warping for 3D facial landmark by building a template mesh as a reference object. This template mesh is thereby applied to each of the target mesh on Stirling/ESRC and Bosphorus datasets. The semi-landmarks are allowed to slide along tangents to the curves and surfaces until the bending energy between a template and a target form is minimal and localization error is assessed using Procrustes ANOVA. By using Principal Component Analysis (PCA) for feature selection, classification is done using Linear Discriminant Analysis (LDA).

    RESULT: The localization error is validated on the two datasets with superior performance over the state-of-the-art methods and variation in the expression is visualized using Principal Components (PCs). The deformations show various expression regions in the faces. The results indicate that Sad expression has the lowest recognition accuracy on both datasets. The classifier achieved a recognition accuracy of 99.58 and 99.32% on Stirling/ESRC and Bosphorus, respectively.

    CONCLUSION: The results demonstrate that the method is robust and in agreement with the state-of-the-art results.

  2. Ishak DH, Ooi KK, Ang KP, Akim AM, Cheah YK, Nordin N, et al.
    J Inorg Biochem, 2014 Jan;130:38-51.
    PMID: 24176918 DOI: 10.1016/j.jinorgbio.2013.09.018
    The compound with R=CH2CH3 in Bi(S2CNR2)3 (1) is highly cytotoxic against a range of human carcinoma, whereas that with R=CH2CH2OH (2) is considerably less so. Both 1 and 2 induce apoptosis in HepG2 cells with some evidence for necrosis induced by 2. Based on DNA fragmentation, caspase activities and human apoptosis PCR-array analysis, both the extrinsic and intrinsic pathways of apoptosis have been shown to occur. While both compounds activate mitochondrial and FAS apoptotic pathways, compound 1 was also found to induce another death receptor-dependent pathway by induction of CD40, CD40L and TNF-R1 (p55). Further, 1 highly expressed DAPK1, a tumour suppressor, with concomitant down-regulation of XIAP and NF-κB. Cell cycle arrest at the S and G2/M phases correlates with the inhibition of the growth of HepG2 cells. The cell invasion rate of 2 is 10-fold higher than that of 1, a finding correlated with the down-regulation of survivin and XIAP expression by 1. Compounds 1 and 2 interact with DNA through different binding motifs with 1 interacting with AT- or TA-specific sites followed by inhibition of restriction enzyme digestion; 2 did not interfere with any of the studied restriction enzymes.
  3. Nazri A, Agbolade O, Yaakob R, Ghani AA, Cheah YK
    BMC Bioinformatics, 2020 May 24;21(1):208.
    PMID: 32448182 DOI: 10.1186/s12859-020-3497-7
    BACKGROUND: Landmark-based approaches of two- or three-dimensional coordinates are the most widely used in geometric morphometrics (GM). As human face hosts the organs that act as the central interface for identification, more landmarks are needed to characterize biological shape variation. Because the use of few anatomical landmarks may not be sufficient for variability of some biological patterns and form, sliding semi-landmarks are required to quantify complex shape.

    RESULTS: This study investigates the effect of iterations in sliding semi-landmarks and their results on the predictive ability in GM analyses of soft-tissue in 3D human face. Principal Component Analysis (PCA) is used for feature selection and the gender are predicted using Linear Discriminant Analysis (LDA) to test the effect of each relaxation state. The results show that the classification accuracy is affected by the number of iterations but not in progressive pattern. Also, there is stability at 12 relaxation state with highest accuracy of 96.43% and an unchanging decline after the 12 relaxation state.

    CONCLUSIONS: The results indicate that there is a particular number of iteration or cycle where the sliding becomes optimally relaxed. This means the higher the number of iterations is not necessarily the higher the accuracy.

  4. Nur Syazwani Jarkasi, Zamberi Sekawi, Cheah, Yoke Kqueen, Zulkefley Othman
    MyJurnal
    Torque Teno Virus (TTV) is a human-infected virus that is present ubiquitously in nature. Globally, it infects up to 95% of the healthy individuals without any clinical manifestations. The widely used laboratory diagnosis of TTV infection is Polymerase chain reaction (PCR). Nevertheless, several other methods have been developed. The rapid growth of TTV variants over time has posed a challenge in estimating the global TTV infection as none of the PCR protocol has the ability to detect the entire spectrum of TTV variants. Multiple TTV epidemiological studies have been conducted among Asian population, whereas other continents showed a limited number of studies. The horizontal and vertical transmission of TTV among humans population, as well as interspecies transmission are potentially related to the global widespread of TTV infection.
  5. Tham CL, Liew CY, Lam KW, Mohamad AS, Kim MK, Cheah YK, et al.
    Eur J Pharmacol, 2010 Feb 25;628(1-3):247-54.
    PMID: 19958764 DOI: 10.1016/j.ejphar.2009.11.053
    Curcumin is a highly pleiotropic molecule with significant regulatory effects upon inflammation and inflammatory related diseases. However curcumin has one major important limitation in which it has poor bioavailability. Design of synthetic structural derivatives of curcumin is but one approach that has been used to overcome its poor bioavailability while retaining, or further enhancing, its drug-like effects. We have synthesized a series of curcumin analogues and describe the effects of 2,6-bis-4-(hydroxyl-3-methoxy-benzylidine)-cyclohexanone or BHMC upon nitric oxide and cytokine synthesis in cellular models of inflammation. BHMC showed a significant dose-response inhibitory action upon the synthesis of NO and we have shown that this effect was due to suppression of both iNOS gene and enzyme expression without any effects upon scavenging of nitrite. We also demonstrated that BHMC has a very minimal effect upon iNOS activity with no effect at all upon the secretion of PGE(2) but has a strong inhibitory effect upon MCP-1 and IL-10 secretion and gene expression. Secretion and gene expression of TNF-alpha and IL-6 were moderately inhibited whereas IL-8 and IL-1beta were not altered. We conclude that BHMC selectively inhibits the synthesis of several inflammatory mediators. BHMC should be considered a promising drug lead for preclinical and further pharmacological studies.
  6. Liew CY, Tham CL, Lam KW, Mohamad AS, Kim MK, Cheah YK, et al.
    Immunopharmacol Immunotoxicol, 2010 Sep;32(3):495-506.
    PMID: 20109039 DOI: 10.3109/08923970903575708
    HMP [3-(2-hydroxyphenyl)-1-(5-methyl-furan-2-y-l) propenone] was evaluated for its ability to inhibit the synthesis of major proinflammatory mediators and cytokines in interferon-gamma (IFN-gamma)- and lipopolysaccharide (LPS)-induced RAW 264.7 cells and phorbol myristate acetate (PMA)-differentiated/LPS-induced U937 cells. HMP suppressed the production of nitric oxide (NO) with significant inhibitory effects at doses as low as 0.78 microM (P < 0.05). Prostaglandin E2 (PGE2) secretion was also inhibited at doses of 12.5 microM and above (P < 0.01). The secretion of both TNF-alpha and IL-6 were only inhibited at the highest dose used (25 microM; P < 0.001). IL-1beta secretion was also inhibited from 12.5 microM onwards (P < 0.01). This inhibition was demonstrated to be caused by down-regulation of inducible enzymes, inducible nitric oxide synthase (iNOS), and cyclooxygenase-2 (COX-2), without direct effect upon iNOS or COX-2 enzyme activity. HMP only inhibited iNOS (P < 0.001) and IL-1beta (P < 0.05) gene expression at the highest tested concentration. HMP did not affect the secretion of chemokines IL-8 and monocyte chemotactic protein-1 (MCP-1) and the anti-inflammatory cytokine IL-10. The most striking effect of HMP was its NO inhibitory activity and therefore we conclude that HMP is a selective inhibitor of iNOS.
  7. Tan WL, Subha ST, Mohtarrudin N, Cheah YK
    Mol Biol Rep, 2023 Jun;50(6):5395-5405.
    PMID: 37074612 DOI: 10.1007/s11033-023-08421-5
    The self-renew ability of cancer stem cells (CSCs) continues to challenge our determination for accomplishing cancer therapy breakthrough. Ineffectiveness of current cancer therapies to eradicate CSCs has contributed to chemoresistance and tumor recurrence. Yet, the discoveries of highly effective therapies have not been thoroughly developed. Further insights into cancer metabolomics and gene-regulated mechanisms of mitochondria in CSCs can expedite the development of novel anticancer drugs. In cancer cells, the metabolism is reprogrammed from oxidative phosphorylation (OXPHOS) to glycolysis. This alteration allows the cancer cell to receive continuous energy supplies and avoid apoptosis. The pyruvate obtained from glycolysis produces acetyl-coenzyme A (Acetyl-CoA) via oxidative decarboxylation and enters the tricarboxylic acid cycle for adenosine triphosphate generation. Mitochondrial calcium ion (Ca2+) uptake is responsible for mitochondrial physiology regulation, and reduced uptake of Ca2+  inhibits apoptosis and enhances cell survival in cancer. There have been many discoveries of mitochondria-associated microRNAs (miRNAs) stimulating the metabolic alterations in mitochondria via gene regulation which promote cancer cell survival. These miRNAs are also found in CSCs where they regulate genes and activate different mechanisms to destroy the mitochondria and enhance CSCs survival. By targeting the miRNAs that induced mitochondrial destruction, the mitochondrial functions can be restored; thus, it triggers CSCs apoptosis and completely eliminates the CSCs. In general, this review article aims to address the associations between miRNAs with mitochondrial activities in cancer cells and cancer stem cells that support cancer cell survival and self-renewal.
  8. Aziz MNM, Rahim NFC, Hussin Y, Yeap SK, Masarudin MJ, Mohamad NE, et al.
    Pharmaceuticals (Basel), 2021 Jun 03;14(6).
    PMID: 34204873 DOI: 10.3390/ph14060532
    Osteosarcoma (OS) is a life-threatening malignant bone tumor associated with poor prognosis among children. The survival rate of the patient is still arguably low even with intensive treatment provided, plus with the inherent side effects from the chemotherapy, which gives more unfavorable outcomes. Hence, the search for potent anti-osteosarcoma agent with promising safety profile is still on going. Natural occurring substance like curcumin has gained a lot of attention due to its splendid safety profile as well as it pharmacological advantages such as anti-metastasis and anti-angiogenesis. However, natural curcumin was widely known for its poor cellular uptake, which undermines all potential that it possesses. This prompted the development of synthetically synthesized curcuminoid analog, known as (Z)-3-hydroxy-1-(2-hydroxyphenyl)-3-phenylprop-2- en-1-one (DK1). In this present study, in vitro scratch assay, transwell migration/invasion assay, HUVEC tube formation assay, and ex vivo rat aortic ring assays were performed in order to investigate the anti-metastatic and anti-angiogenic potential of DK1. For further comprehension of DK1 mechanism on human osteosarcoma cell lines, microarray gene expression analysis, quantitative polymerase chain reaction (qPCR), and proteome profiler were adopted, providing valuable forecast from the expression of important genes and proteins related to metastasis and angiogenesis. Based on the data gathered from the bioassays, DK1 was able to inhibit the metastasis and angiogenesis of human osteosarcoma cell lines by significantly reducing the cell motility, number of migrated and invaded cells as well as the tube formation and micro-vessels sprouting. Additionally, DK1 also has significantly regulated several cancer pathways involved in OS proliferation, metastasis, and angiogenesis such as PI3K/Akt and NF-κB in both U-2 OS and MG-63. Regulation of PI3K/Akt caused up-regulation of genes related to metastasis inhibition, namely, PTEN, FOXO, PLK3, and GADD45A. Meanwhile, NF-κB pathway was regulated by mitigating the expression of NF-κB activator such as IKBKB and IKBKE in MG-63, whilst up-regulating the expression of NF-κB inhibitors such as NFKBIA and NFKBIE in U-2 OS. Finally, DK1 also has successfully hindered the metastatic and angiogenic capability of OS cell lines by down-regulating the expression of pro-metastatic genes and proteins like MMP3, COL11A1, FGF1, Endoglin, uPA, and IGFBP2 in U-2 OS. Whilst for MG-63, the significantly down-regulated oncogenes were Serpin E1, AKT2, VEGF, uPA, PD-ECGF, and Endoglin. These results suggest that curcumin analog DK1 may serve as a potential new anti-osteosarcoma agent due to its anti-metastatic and anti-angiogenic attributes.
  9. Wan KF, Radu S, Cheah YK, Benjamin PG, Ling CM, Hon SF, et al.
    PMID: 15115139
    Enteropathogenic Escherichia coli (EPEC) is a leading cause of diarrhea among infants in developing countries. A total of 38 EPEC isolates, obtained from diarrhea patients of Hospital Miri, Sarawak, were investigated through plasmid profile, antibiotic resistance and randomly amplified polymorphic DNA (RAPD) analysis. From the 8 types of antibiotics used, all isolates were 100% resistant to furoxime, cephalothin and sulphamethoxazole and showed high multiple antibiotic resistant (MAR) indexes, ranging from 0.5 to 1.0. In plasmid profiling, 22 isolates (58%) showed the presence of one or more plasmids in the range 1.0 to 30.9 mDa. The dendrogram obtained from the results of the RAPD-PCR discriminated the isolates into 30 single isolates and 3 clusters at the level of 40% similarity. The EPEC isolates were highly diverse, as shown by their differing plasmid profiles, antibiotic resistance patterns and RAPD profiles.
  10. Chu WC, Aziz AF, Nordin AJ, Cheah YK
    Clin Appl Thromb Hemost, 2016 Sep;22(6):581-8.
    PMID: 25667236 DOI: 10.1177/1076029615571628
    Genetic variants of cholesteryl ester transfer protein (CETP) and endothelial nitric oxide synthase (eNOS) influence high-density lipoprotein cholesterol (HDL-C) metabolism and nitric oxide (NO) synthesis, respectively, and might increase the risk of coronary artery disease (CAD). This study is to investigate the relationship between genetic polymorphisms and the risk of CAD and to evaluate their potential interactions. A total of 237 patients with CAD and 101 controls were genotyped. The association of the polymorphism with the risk of CAD varied among the ethnic groups. Moreover, the concomitant presence of both CETP B1 and eNOS 4a alleles significantly increased the risk of CAD in the Malay group (OR = 33.8, P < .001) and the Indian group (OR = 10.9, P = .031) but not in the Chinese group. This study has identified a novel ethnic-specific gene-gene interaction and suggested that the combination of CETP B1 allele and eNOS 4a allele significantly increases the risk of CAD in Malays and Indians.
  11. Mohamed Ikhtifar Rafi, Cheah, Yoke Kqueen
    MyJurnal
    Bacterial endophytes are found on all types of plants and is a potential source of bioactive compounds which can be utilized to fight against multi-resistant pathogens and could be further develop into new leads for antibiotic development. However, the research done on the bacterial endophytes is relatively new and has potential to grow as it is theorized that each plant has one or more bacterial endophytes inhabiting them. This review aims to review the studies that have been done previously and give new insights on the latest trends in this field of research.
  12. Lee LH, Cheah YK, Sidik SM, Xie QY, Tang YL, Lin HP, et al.
    Int J Syst Evol Microbiol, 2013 Jan;63(Pt 1):241-248.
    PMID: 22389286 DOI: 10.1099/ijs.0.038232-0
    Three novel actinobacteria, strains 39(T), 40 and 41, were isolated from soil collected from Barrientos Island in the Antarctic. The taxonomic status of these strains was determined using a polyphasic approach. Comparison of 16S rRNA gene sequences revealed that strain 39(T) represented a novel lineage within the family Dermacoccaceae and was most closely related to members of the genera Demetria (96.9 % 16S rRNA gene sequence similarity), Branchiibius (95.7 %), Dermacoccus (94.4-95.3 %), Calidifontibacter (94.6 %), Luteipulveratus (94.3 %), Yimella (94.2 %) and Kytococcus (93.1 %). Cells were irregular cocci and short rods. The peptidoglycan type was A4α with an L-Lys-L-Ser-D-Asp interpeptide bridge. The cell-wall sugars were galactose and glucose. The major menaquinone was MK-8(H(4)). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphoglycolipid, two glycolipids and one unknown phospholipid. The acyl type of the cell-wall polysaccharide was N-acetyl. The major cellular fatty acids were anteiso-C(17 : 0) (41.97 %), anteiso-C(17 : 1)ω9c (32.16 %) and iso-C(16 : 0) (7.68 %). The DNA G+C content of strain 39(T) was 68.4 mol%. On the basis of phylogenetic and phenotypic differences from other genera of the family Dermacoccaceae, a novel genus and species, Barrientosiimonas humi gen. nov., sp. nov., is proposed; the type strain of the type species is 39(T) (=CGMCC 4.6864(T) = DSM 24617(T)).
  13. Ng SW, Selvarajah GT, Cheah YK, Mustaffa Kamal F, Omar AR
    Pathogens, 2020 May 25;9(5).
    PMID: 32466289 DOI: 10.3390/pathogens9050412
    Feline infectious peritonitis (FIP) is a fatal feline immune-mediated disease caused by feline infectious peritonitis virus (FIPV). Little is known about the biological pathways associated in FIP pathogenesis. This is the first study aiming to determine the phenotypic characteristics on the cellular level in relation to specific metabolic pathways of importance to FIP pathogenesis.

    METHODS: The internalization of type II FIPV WSU 79-1146 in Crandell-Rees Feline Kidney (CrFK) cells was visualized using a fluorescence microscope, and optimization prior to phenotype microarray (PM) study was performed. Then, four types of Biolog Phenotype MicroArray™ plates (PM-M1 to PM-M4) precoated with different carbon and nitrogen sources were used to determine the metabolic profiles in FIPV-infected cells.

    RESULTS: The utilization of palatinose was significantly low in FIPV-infected cells; however, there were significant increases in utilizing melibionic acid, L-glutamine, L-glutamic acid and alanyl-glutamine (Ala-Gln) compared to non-infected cells.

    CONCLUSION: This study has provided the first insights into the metabolic profiling of a feline coronavirus infection in vitro using PMs and deduced that glutamine metabolism is one of the essential metabolic pathways for FIPV infection and replication. Further studies are necessary to develop strategies to target the glutamine metabolic pathway in FIPV infection.

  14. Sahabi K, Selvarajah GT, Abdullah R, Cheah YK, Tan GC
    J Vet Sci, 2018 Mar 31;19(2):162-171.
    PMID: 28927253 DOI: 10.4142/jvs.2018.19.2.162
    MicroRNAs (miRNAs) have important roles in all biological pathways in multicellular organisms. Over 1,400 human miRNAs have been identified, and many are conserved among vertebrates and invertebrates. Regulation of miRNA is the most common mode of post-transcriptional gene regulation. The miRNAs that are involved in the initiation and progression of cancers are termed oncomiRs and several of them have been identified in canine and human cancers. Similarly, several miRNAs have been reported to be down-regulated in cancers of the two species. In this review, current information on the expression and roles of miRNAs in oncogenesis and progression of human and canine cancers, as well the roles miRNAs have in cancer stem cell biology, are highlighted. The potential for the use of miRNAs as therapeutic targets in personalized cancer therapy in domestic dogs and their possible application in human cancer counterparts are also discussed.
  15. Ching XJ, Najimudin N, Cheah YK, Wong CMVL
    Data Brief, 2022 Feb;40:107764.
    PMID: 35024395 DOI: 10.1016/j.dib.2021.107764
    Parageobacillus caldoxylosilyticus, or previously identified as Geobacillus caldoxylosilyticus, is a thermophilic Gram-positive bacterium which can easily withstand growth temperatures ranging from 40 °C to 70 °C. Here, we present the first complete genome sequence of Parageobacillus caldoxylosilyticus ER4B which was isolated from an empty oil palm fruit bunch compost in Malaysia. Whole genome sequencing was performed using the PacBio RSII platform. The genome size of strain ER4B was around 3.9Mbp, with GC content of 44.31%. The genome consists of two contigs, in which the larger contig (3,909,276bp) represents the chromosome, while the smaller one (54,250bp) represents the plasmid. A total of 4,164 genes were successfully predicted, including 3,972 protein coding sequences, 26 rRNAs, 91 tRNAs, 74 miscRNA, and 1 tmRNA. The genome sequence data of strain ER4B reported here may contribute to the current molecular information of the species. It may also facilitate the discovery of molecular traits related to thermal stress, thus, expanding our understanding in the acclimation or adaptation towards extreme temperature in bacteria.
  16. Aziz MNM, Hussin Y, Che Rahim NF, Nordin N, Mohamad NE, Yeap SK, et al.
    Molecules, 2018 Jan 05;23(1).
    PMID: 29303982 DOI: 10.3390/molecules23010075
    Osteosarcoma is one of the primary malignant bone tumors that confer low survival rates for patients even with intensive regime treatments. Therefore, discovery of novel anti-osteosarcoma drugs derived from natural products that are not harmful to the normal cells remains crucial. Curcumin is one of the natural substances that have been extensively studied due to its anti-cancer properties and is pharmacologically safe considering its ubiquitous consumption for centuries. However, curcumin suffers from a poor circulating bioavailability, which has led to the development of a chemically synthesized curcuminoid analog, namely (Z)-3-hydroxy-1-(2-hydroxyphenyl)-3-phenylprop-2-en-1-one (DK1). In this study, the cytotoxic effects of the curcumin analog DK1 was investigated in both U-2OS and MG-63 osteosarcoma cell lines using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and cell death was microscopically examined via acridine orange/propidium iodide (AO/PI) double staining. Flow cytometer analysis including Annexin V/Fluorescein isothiocyanate (FITC), cell cycle analysis and JC-1 were adapted to determine the mode of cell death. Subsequently in order to determine the mechanism of cell death, quantitative polymerase chain reaction (qPCR) and proteome profiling was carried out to measure the expression of several apoptotic-related genes and proteins. Results indicated that DK1 induced U-2 OS and MG-63 morphological changes and substantially reduced cell numbers through induction of apoptosis. Several apoptotic genes and proteins were steadily expressed after treatment with DK1; including caspase 3, caspase 9, and BAX, which indicated that apoptosis occurred through a mitochondria-dependent signaling pathway. In conclusion, DK1 could be considered as a potential candidate for an anti-osteosarcoma drug in the near future, contingent upon its ability to induce apoptosis in osteosarcoma cell lines.
  17. Shi Yeen TN, Pathmanathan R, Shiran MS, Ahmad Zaid FA, Cheah YK
    J Biomed Sci, 2013 Apr 16;20:22.
    PMID: 23590575 DOI: 10.1186/1423-0127-20-22
    BACKGROUND: Somatic mutations of the epidermal growth factor receptor (EGFR) are reportedly associated with various responses in non-small cell lung cancer (NSCLC) patients receiving the anti-EGFR agents. Detection of the mutation therefore plays an important role in therapeutic decision making. The aim of this study was to detect EGFR mutations in formalin fixed paraffin embedded (FFPE) samples using both Scorpion ARMS and high resolution melt (HRM) assay, and to compare the sensitivity of these methods.

    RESULTS: All of the mutations were found in adenocarcinoma, except one that was in squamous cell carcinoma. The mutation rate was 45.7% (221/484). Complex mutations were also observed, wherein 8 tumours carried 2 mutations and 1 tumour carried 3 mutations.

    CONCLUSIONS: Both methods detected EGFR mutations in FFPE samples. HRM assays gave more EGFR positive results compared to Scorpion ARMS.

  18. Foo JB, Saiful Yazan L, Tor YS, Wibowo A, Ismail N, Armania N, et al.
    J Ethnopharmacol, 2016 Jul 1;187:195-204.
    PMID: 27131434 DOI: 10.1016/j.jep.2016.04.048
    Dillenia suffruticosa is traditionally used for treatment of cancerous growth including breast cancer in Malaysia.
  19. Mohd Asrore Mohd Shaufi, Chin, Chin Sieo, Abdul Rahman Omar, Yin, Wan Ho, Cheah, Yoke-Kqueen, Chun, Wie Chong, et al.
    MyJurnal
    Repetitive sequence-based PCR (rep-PCR) is a distinctive typing approach that is used to
    differentiate between bacterial strains. This method is also useful for studying bacterial diversity
    from different sources. In this study, four rep-PCR which are enterobacterial repetitive intergenic
    consensus PCR (ERIC-PCR), BOX-PCR, repetitive extragenic palindromic PCR (REP-PCR)
    and polytrinucleotide (GTG)5-PCR were evaluated for differentiation of eighteen Escherichia
    coli isolates to correct source based on part of intestine and age. These isolates were recovered
    earlier from ileal and caecal mucosal contents of chickens at different age. The purpose of this
    study was to investigate the efficacy of four rep-PCR methods and composite of rep-PCR
    patterns to differentiate E. coli isolates to original sources of part of intestines and age based on
    the D index (discriminatory power determined based on Simpson’s index of diversity calculated
    at similarity coefficient of 90%). The (GTG)5-PCR had the highest D index (0.9804) for part of
    intestine and age factors. The similar D index was observed in the composite of rep-PCR
    patterns. The lowest D index was observed in ERIC- and BOX-PCR at 0.9020 and 0.8039 for
    part of intestine and age factors, respectively. (GTG)5-PCR was also the most discriminative rep-
    PCR observed due to its ability to cluster 14I 3E and 14I 2X isolates, and 14C 1E and 14C 3E
    isolates correctly in part of intestine and age factors. It was concluded that (GTG)5-PCR is a
    promising tool for discriminating E. coli isolates extracted from chicken intestines.
  20. Lee CM, Sieo CC, Cheah YK, Abdullah N, Ho YW
    J Sci Food Agric, 2012 Feb;92(3):660-6.
    PMID: 21919004 DOI: 10.1002/jsfa.4627
    Four repetitive element sequence-based polymerase chain reaction (rep-PCR) methods, namely repetitive extragenic palindromic PCR (REP-PCR), enterobacterial repetitive intergenic consensus PCR (ERIC-PCR), polytrinucleotide (GTG)₅ -PCR and BOX-PCR, were evaluated for the molecular differentiation of 12 probiotic Lactobacillus strains previously isolated from the gastrointestinal tract of chickens and used as a multistrain probiotic. This study represents the first analysis of the comparative efficacy of these four rep-PCR methods and their combination (composite rep-PCR) in the molecular typing of Lactobacillus strains based on a discriminatory index (D).
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