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Transcriptomics expression analysis to unveil the molecular mechanisms underlying the cocoa polyphenol treatment in diet-induced obesity rats

Ali F, Ismail A, Esa NM, Pei CP

Genomics, 2015 Jan;105(1):23-30.
PMID: 25451742 DOI: 10.1016/j.ygeno.2014.11.002

Cocoa polyphenol (CP), due to their biological actions, may be supplementary treatments for adipose tissue-fat gain. However, the molecular mechanism of CPs is still ambiguous. This study investigated the hypothesis that CP treatment modulates expressing of lipid metabolism genes in mesenteric white adipose tissue (MES-WAT). Sprague-Dawley (SD) rats were fed a low-fat (LF) or high-fat (HF) diet for 12 weeks. Thereafter, HFD rats (n = 10/group) were treated at a dose of 600 mg/kg bw/day CPs (HFD + CPs) for 4 weeks. DNA microarray analysis resulted in 753 genes of the 13,008 genes expressed. Bioinformatics tools showed CP treatment significantly decreased gene expression levels for lipogenic enzymes, while increased the mRNA levels responsible for lipolysis enzymes. CP administration differentially regulates gene expression involved in lipid metabolism in MES-WAT. These data unveil a new insight into the molecular mechanisms underlying the pharmacological effect of CPs on obesity biomarkers in obese rats.
Gender effect on in vitro lymphocyte subset levels of healthy individuals

Abdullah M, Chai PS, Chong MY, Tohit ER, Ramasamy R, Pei CP, et al.

Cell Immunol, 2012;272(2):214-9.
PMID: 22078320 DOI: 10.1016/j.cellimm.2011.10.009

Differences in gender immune response have resulted in differences in immune protection and susceptibility to inflammatory diseases. Cultured peripheral blood mononuclear cells (PBMC) are widely used in immunomodulation studies, yet the influence of gender is usually not considered. We examined the effect of in vitro culture and phytohaemagglutinin (PHA) stimulation on PBMC lymphocyte subsets using flowcytometry. Full blood counts of whole blood showed higher levels of lymphocyte in male subjects. Lymphocyte subsets enumeration revealed higher NK cell counts in males and higher B cells in females. Cultured PBMC resulted in significant increases in B and total T cell percentages among females and NK cells among males. PHA stimulated significantly increased percentages of NK and total T cells in males and total activated T cells (CD69+) in females. Our results showed significant gender differences in lymphocyte subsets in cultured conditions. This may affect experimental outcome.
Improved method for the isolation of RNA from bacteria refractory to disruption, including S. aureus producing biofilm

Atshan SS, Shamsudin MN, Lung LT, Ling KH, Sekawi Z, Pei CP, et al.

Gene, 2012 Feb 25;494(2):219-24.
PMID: 22222139 DOI: 10.1016/j.gene.2011.12.010

The development of fast, reliable and inexpensive phenol protocol is described for the isolation of RNA from bacterial biofilm producers. The method was tested on Staphylococcus aureus (S. aureus) and other biofilm-producing gram-negative microorganisms and provided the highest integrity of RNA recovery in comparison to other methods reported here. In parallel experiments, bacterial lysis with Qiagen, NucleoSpin RNAII, InnuREP RNA Mini, Trizol and MasterPure RNA extraction Kits using standard protocols consistently gave low RNA yields with an absence of integrity. The boiling method presented here yielded high concentration of RNA that was free from 16S and 23S rRNA, contained 5S RNA. Higher yields due to improved biofilm bacterial cell lysis were achieved with an added hot phenol incubation step without the need for a bead mill or the enzyme. This method when used in conjunction with the Qiagen RNeasy Mini kit, RNA isolation was a success with greater integrity and contained undegraded 16S and 23S rRNA and did not require further purification. Contaminating DNA was a problem with the RNA processing samples; we used quantitative real-time PCR (RT-qPCR) to measure the recovery of RNA from bacterial biofilm cells using the method described here.
Effects of cocoa extract on glucometabolism, oxidative stress, and antioxidant enzymes in obese-diabetic (Ob-db) rats

Jalil AM, Ismail A, Pei CP, Hamid M, Kamaruddin SH

J Agric Food Chem, 2008 Sep 10;56(17):7877-84.
PMID: 18702467 DOI: 10.1021/jf8015915

In this present study, we investigated the effects of cocoa extract containing polyphenols and methylxanthines prepared from cocoa powder on the biochemical parameters of obese-diabetic (Ob-db) rats. Obese-diabetic (Ob-db) rats were developed using a high-fat diet (49% fat, 32% carbohydrate, and 19% protein from total energy, kcal) for 3 months, followed by a low dose (35 mg/kg body weight) streptozotocin (STZ) injection. Cocoa extract (600 mg/kg body weight/day) was given to the rats for 4 weeks. The results indicated that there were no significant differences in fasting plasma glucose and insulin level after 4 weeks of cocoa extract administration. Oral glucose tolerance test revealed that cocoa supplementation in Ob-db rats significantly (p < 0.05) reduced plasma glucose at 60 and 90 min compared to unsupplemented Ob-db rats. Plasma free fatty acid and oxidative stress biomarker (8-isoprostane) were significantly (p < 0.05) reduced after cocoa supplementation. Superoxide dismutase activity was enhanced in Ob-db compared to that in nonsupplemented rats. However, no change was observed in catalase activity. The results showed that cocoa supplementation had an effect on postprandial glucose control but not for long term (4 weeks). Moreover, cocoa supplementation could reduce circulating plasma free fatty acid and 8-isoprostane and may enhance the antioxidant defense system.
Comparative Assessment of a Self-sampling Device and Gynecologist Sampling for Cytology and HPV DNA Detection in a Rural and Low Resource Setting: Malaysian Experience

Latiff LA, Ibrahim Z, Pei CP, Rahman SA, Akhtari-Zavare M

Asian Pac J Cancer Prev, 2015;16(18):8495-501.
PMID: 26745108

PURPOSE: This study was conducted to assess the agreement and differences between cervical self-sampling with a Kato device (KSSD) and gynecologist sampling for Pap cytology and human papillomavirus DNA (HPV DNA) detection.
MATERIALS AND METHODS: Women underwent self-sampling followed by gynecologist sampling during screening at two primary health clinics. Pap cytology of cervical specimens was evaluated for specimen adequacy, presence of endocervical cells or transformation zone cells and cytological interpretation for cells abnormalities. Cervical specimens were also extracted and tested for HPV DNA detection. Positive HPV smears underwent gene sequencing and HPV genotyping by referring to the online NCBI gene bank. Results were compared between samplings by Kappa agreement and McNemar test.
RESULTS: For Pap specimen adequacy, KSSD showed 100% agreement with gynecologist sampling but had only 32.3% agreement for presence of endocervical cells. Both sampling showed 100% agreement with only 1 case detected HSIL favouring CIN2 for cytology result. HPV DNA detection showed 86.2%agreement (K=0.64, 95% CI 0.524-0.756, p=0.001) between samplings. KSSD and gynaecologist sampling identified high risk HPV in 17.3% and 23.9% respectively (p= 0.014).
CONCLUSION: The self-sampling using Kato device can serve as a tool in Pap cytology and HPV DNA detection in low resource settings in Malaysia. Self-sampling devices such as KSSD can be used as an alternative technique to gynaecologist sampling for cervical cancer screening among rural populations in Malaysia.
Comparative Study of the Effects of Fluconazole and Voriconazole on Candida glabrata, Candida parapsilosis and Candida rugosa Biofilms

Madhavan P, Jamal F, Pei CP, Othman F, Karunanidhi A, Ng KP

Mycopathologia, 2018 Jun;183(3):499-511.
PMID: 29380188 DOI: 10.1007/s11046-018-0243-z

Infections by non-albicans Candida species are a life-threatening condition, and formation of biofilms can lead to treatment failure in a clinical setting. This study was aimed to demonstrate the in vitro antibiofilm activity of fluconazole (FLU) and voriconazole (VOR) against C. glabrata, C. parapsilosis and C. rugosa with diverse antifungal susceptibilities to FLU and VOR. The antibiofilm activities of FLU and VOR in the form of suspension as well as pre-coatings were assessed by XTT [2,3-bis-(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide] reduction assay. Morphological and intracellular changes exerted by the antifungal drugs on Candida cells were examined by scanning electron microscope (SEM) and transmission electron microscope (TEM). The results of the antibiofilm activities showed that FLU drug suspension was capable of killing C. parapsilosis and C. rugosa at minimum inhibitory concentrations (MICs) of 4× MIC FLU and 256× MIC FLU, respectively. While VOR MICs ranging from 2× to 32× were capable of killing the biofilms of all Candida spp tested. The antibiofilm activities of pre-coated FLU were able to kill the biofilms at ¼× MIC FLU and ½× MIC FLU for C. parapsilosis and C. rugosa strains, respectively. While pre-coated VOR was able to kill the biofilms, all three Candida sp at ½× MIC VOR. SEM and TEM examinations showed that FLU and VOR treatments exerted significant impact on Candida cell with various degrees of morphological changes. In conclusion, a fourfold reduction in MIC50 of FLU and VOR towards ATCC strains of C. glabrata, C. rugosa and C. rugosa clinical strain was observed in this study.
Fulltext A review of studies examining the association between genetic biomarkers (short tandem repeats and single-nucleotide polymorphisms) and risk of prostate cancer: the need for valid predictive biomarkers

Albujja MH, Vasudevan R, Alghamdi S, Pei CP, Bin Mohd Ghani KA, Ranneh Y, et al.

Prostate Int, 2020 Dec;8(4):135-145.
PMID: 33425790 DOI: 10.1016/j.prnil.2019.11.003

Prostate cancer (PCa) is a challenging polygenic disease because the genes that cause PCa remain largely elusive and are affected by several causal factors. Consequently, research continuously strives to identify a genetic marker which could be used as an indicator to predict the most vulnerable (i.e., predisposed) segments of the population to the disease or for the gene which may be directly responsible for PCa. To enhance the genetic etiology of PCa, this research sought to discover the key studies conducted in this field using data from the main journal publication search engines, as it was hoped that this could shed light on the main research findings from these studies, which in turn could assist in determining these genes or markers. From the research highlighted, the studies primarily used two kinds of markers: short tandem repeats or single-nucleotide polymorphisms. These markers were found to be quite prevalent in all the chromosomes within the research carried out. It also became apparent that the studies differed in both quantity and quality, as well as being conducted in a variety of societies. Links were also determined between the degree and strength of the relationship between these markers and the occurrence of the disease. From the studies identified, most recommended a larger and more diverse survey for the parameters which had not been studied before, as well as an increase in the size of the community (i.e., the population) being studied. This is an indication that work in this field is far from complete, and thus, current research remains committed toward finding genetic markers that can be used clinically for the diagnosis and screening of patients with PCa.
Fulltext Comparative characterisation of genotypically different clones of MRSA in the production of biofilms

Atshan SS, Shamsudin MN, Lung LT, Sekawi Z, Ghaznavi-Rad E, Pei CP

J Biomed Biotechnol, 2012;2012:417247.
PMID: 22529705 DOI: 10.1155/2012/417247

The ability to adhere and produce biofilms is characteristic of enhanced virulence among isolates of methicillin-resistant Staphylococcus aureus (MRSA). The aim of the study is to find out whether these characteristics are consistently similar among isolates variations of MRSA. The study used 30 various isolates of MRSA belong to 13 spa types and 5 MLST types and determined the aggregation, the adherence, and the production of biofilms and slime for each isolate. The methods used to evaluate these characteristics were a modified Congo red agar assay (MCRA), a microtiter plate assay (MPA), high-magnification light microscopy, scanning electron microscopy (SEM), and PCR. The study found that isolates belonging to similar Spa, SCCmec, and ST types have similar abilities to produce biofilms; however, their ability to produce slime on CRA was found to be different. Moreover, isolates that have different Spa types showed high variation in their ability to produce biofilms. The results of light microscope revealed the isolates that produced strong and weak biofilms and formed similar aggregation on the glass surfaces. SEM results showed that all 30 MRSA isolates that were tested were 100% positive for biofilm formation, although to varying degrees. Further testing using PCR confirmed that 100% of the 30 isolates tested were positive for the presence of the icaADBC, fnbA, eno, ebps, clfA, and clfB genes. The prevalence of fib, cna, fnbB, and bbp in MRSA clones was 90, 93.33, 53.33, and 10%, respectively. This study indicate that differences in biofilm production capacities are caused by the differences in surface protein A (Spa) type and are not due to differences in MLST and SCCmec types.
Identification and validation of novel breed-specific biomarker for the purpose of village chicken authentication using genomics approaches

Nematbakhsh S, Pei CP, Nordin N, Selamat J, Idris LH, Razis AFA

Poult Sci, 2024 Jul 31;103(11):104128.
PMID: 39180779 DOI: 10.1016/j.psj.2024.104128

Local village chicken, or "Ayam kampung" as it's known in Malaysia, is considered a premium chicken breed with a higher price than other chicken breeds. As a result of their comparable appearances and sizes, colored broiler chickens are often sold as village chickens, which is a form of food fraud that can result in a 3- to 4-fold rise in profit. Therefore, developing a breed-specific authentication method is crucial for preventing food fraud in the poultry industry. This study aims to investigate the genetic diversity of village chickens from other commercial chicken breed populations available in the market (broiler [Cobb], colored broiler [Hubbard], and layer [DeKalb]) to identify breed-specific DNA fragments as biomarkers for village chicken authentication. The Whole-genome sequencing and mutation calling of 12 chickens (3 chickens/breed) led to the identification of a total of 73,454,654 single nucleotide polymorphisms (SNP) and 8,762,338 insertion and deletions (InDel) variants, with more variants detected in the village chicken population (6,346,704 SNPs; 752,408 InDels) compared to commercial breeds. Therefore, this study revealed that village chickens were more genetically variable compared to other breeds in Malaysia. Furthermore, the breed-specific genomic region located on chromosome 1 (1:84,405,652) harboring SNP (C-T) with high discrimination power was discovered and validated which can be considered as a novel breed-specific biomarker to develop a method for accurate authentication of village chickens in Malaysia. This authentication method offers potentialw applications in the chicken industry and food safety.
Fulltext Analysis of Gln223Agr polymorphism of Leptin Receptor Gene in type II diabetic mellitus subjects among Malaysians

Etemad A, Ramachandran V, Pishva SR, Heidari F, Aziz AF, Yusof AK, et al.

Int J Mol Sci, 2013;14(9):19230-44.
PMID: 24051404 DOI: 10.3390/ijms140919230

Leptin is known as the adipose peptide hormone. It plays an important role in the regulation of body fat and inhibits food intake by its action. Moreover, it is believed that leptin level deductions might be the cause of obesity and may play an important role in the development of Type 2 Diabetes Mellitus (T2DM), as well as in cardiovascular diseases (CVD). The Leptin Receptor (LEPR) gene and its polymorphisms have not been extensively studied in relation to the T2DM and its complications in various populations. In this study, we have determined the association of Gln223Agr loci of LEPR gene in three ethnic groups of Malaysia, namely: Malays, Chinese and Indians. A total of 284 T2DM subjects and 281 healthy individuals were recruited based on International Diabetes Federation (IDF) criteria. Genomic DNA was extracted from the buccal specimens of the subjects. The commercial polymerase chain reaction (PCR) method was carried out by proper restriction enzyme MSP I to both amplify and digest the Gln223Agr polymorphism. The p-value among the three studied races was 0.057, 0.011 and 0.095, respectively. The values such as age, WHR, FPG, HbA1C, LDL, HDL, Chol and Family History were significantly different among the subjects with Gln223Agr polymorphism of LEPR (p < 0.05).
Fulltext Bioinformatics analysis of rhinovirus capsid proteins VP1-4 sequences for cross-serotype vaccine development

Alshrari AS, Hudu SA, Asdaq SMB, Ali AM, Kin CV, Omar AR, et al.

J Infect Public Health, 2021 Nov;14(11):1603-1611.
PMID: 34624714 DOI: 10.1016/j.jiph.2021.09.001

BACKGROUND: Rhinoviruses (RV) are associated with the development and exacerbations of asthma and chronic obstructive pulmonary disease. They've also been linked to more severe diseases like pneumonia, acute bronchiolitis, croup, and otitis media. Because of the hypervariable sequences in the same serotypes, no effective vaccine against rhinoviruses has been developed to date. With the availability of new full-length genome sequences for all RV-A and RV-B serotyped strains, this study used bioinformatics to find a suitable RV strain with the highest similarity matrices to the other strains.
METHODS: The full genomic sequences of all known different RV-A and -B prototypes were downloaded from the National Centre for Biotechnology Information (NCBI) and divided into minor low-density lipoprotein receptor (LDLR) and major intercellular adhesion molecule groups (ICAM). The sequences were edited using Biological Sequence Alignment Editor, v 7.2.0 (BioEdit software) to study each capsid protein (VP1, VP2, VP3, and VP4) and analyzed using the EMBL-EBI ClustalW server and the more current Clustal Omega tool for the calculation of the identities and similarities.
RESULTS: We analyzed and predicted immunogenic motifs from capsid proteins that are conserved across distinct RV serotypes using a bioinformatics technique. The amino acid sequences of VP3 were found to be the most varied, while VP4 was the most conserved protein among all RV-A and RV-B strains. Among all strains studied, RV-74 demonstrated the highest degree of homology to other strains and could be a potential genetic source for recombinant protein production. Nine highly conserved regions with a minimum length of 9-mers were identified, which could serve as potential immune targets against rhinoviruses.
CONCLUSION: Therefore, bioinformatics analysis conducted in the current study has paved the way for the selection of immunogenic targets. Bioinformatically, the ideal strain's capsid protein is suggested to contain the most common RVs immunogenic sites.
Fulltext Prevalence of adhesion and regulation of biofilm-related genes in different clones of Staphylococcus aureus

Atshan SS, Nor Shamsudin M, Sekawi Z, Lung LT, Hamat RA, Karunanidhi A, et al.

J Biomed Biotechnol, 2012;2012:976972.
PMID: 22701309 DOI: 10.1155/2012/976972

Clinical information about genotypically different clones of biofilm-producing Staphylococcus aureus is largely unknown. We examined whether different clones of methicillin-sensitive and methicillin-resistant S. aureus (MSSA and MRSA) differ with respect to staphylococcal microbial surface components recognizing adhesive matrix molecules (MSCRAMMs) in biofilm formation. The study used 60 different types of spa and determined the phenotypes, the prevalence of the 13 MSCRAMM, and biofilm genes for each clone. The current investigation was carried out using a modified Congo red agar (MCRA), a microtiter plate assay (MPA), polymerase chain reaction (PCR), and reverse transcriptase polymerase chain reaction (RT-PCR). Clones belonging to the same spa type were found to have similar properties in adheringto the polystyrene microtiter plate surface. However, their ability to produce slime on MCRA medium was different. PCR experiments showed that 60 clones of MSSA and MRSA were positive for 5 genes (out of 9 MSCRAMM genes). icaADBC genes were found to be present in all the 60 clones tested indicating a high prevalence, and these genes were equally distributed among the clones associated with MSSA and those with MRSA. The prevalence of other MSCRAMM genes among MSSA and MRSA clones was found to be variable. MRSA and MSSA gene expression (MSCRAMM and icaADBC) was confirmed by RT-PCR.

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